Multiple sequence alignment - TraesCS5D01G217600

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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 TraesCS5D01G217600 chr5D 100.000 5685 0 0 670 6354 326461458 326455774 0.000000e+00 10499.0
1 TraesCS5D01G217600 chr5D 100.000 447 0 0 1 447 326462127 326461681 0.000000e+00 826.0
2 TraesCS5D01G217600 chr5D 97.368 38 1 0 5933 5970 410289312 410289275 1.480000e-06 65.8
3 TraesCS5D01G217600 chr5A 95.621 5252 140 37 700 5905 429980758 429985965 0.000000e+00 8342.0
4 TraesCS5D01G217600 chr5A 87.500 448 49 5 1 445 429968339 429968782 1.580000e-140 510.0
5 TraesCS5D01G217600 chr5A 92.025 163 11 2 4448 4608 320214244 320214406 1.780000e-55 228.0
6 TraesCS5D01G217600 chr5B 95.697 3765 110 32 712 4449 379002477 378998738 0.000000e+00 6008.0
7 TraesCS5D01G217600 chr5B 91.245 1325 77 20 4606 5923 378998739 378997447 0.000000e+00 1768.0
8 TraesCS5D01G217600 chr5B 85.938 448 39 3 1 446 379002994 379002569 2.090000e-124 457.0
9 TraesCS5D01G217600 chr5B 83.377 385 59 1 5967 6351 378997281 378996902 1.010000e-92 351.0
10 TraesCS5D01G217600 chr5B 92.121 165 11 2 4449 4611 407219553 407219389 1.380000e-56 231.0
11 TraesCS5D01G217600 chr5B 91.837 98 8 0 4216 4313 166379086 166379183 3.090000e-28 137.0
12 TraesCS5D01G217600 chr5B 95.122 41 2 0 5933 5973 492143778 492143738 1.480000e-06 65.8
13 TraesCS5D01G217600 chr6D 87.000 2123 189 41 2147 4222 411193395 411191313 0.000000e+00 2311.0
14 TraesCS5D01G217600 chr6D 79.772 791 92 39 1254 2029 411194286 411193549 4.390000e-141 512.0
15 TraesCS5D01G217600 chr6D 86.830 448 46 7 4567 5013 411191185 411190750 7.400000e-134 488.0
16 TraesCS5D01G217600 chr6D 77.151 674 92 30 5114 5754 411190459 411189815 1.020000e-87 335.0
17 TraesCS5D01G217600 chr6A 88.272 1134 101 18 2190 3297 555934072 555932945 0.000000e+00 1328.0
18 TraesCS5D01G217600 chr6A 90.461 933 75 10 3281 4204 555932934 555932007 0.000000e+00 1218.0
19 TraesCS5D01G217600 chr6A 80.000 1050 127 44 1001 2024 555935083 555934091 0.000000e+00 699.0
20 TraesCS5D01G217600 chr6A 91.209 364 30 2 4650 5013 555931959 555931598 1.590000e-135 494.0
21 TraesCS5D01G217600 chr6A 77.143 665 100 26 5114 5754 555931300 555930664 7.890000e-89 339.0
22 TraesCS5D01G217600 chr6B 87.223 1174 110 26 2145 3297 617982994 617981840 0.000000e+00 1301.0
23 TraesCS5D01G217600 chr6B 90.285 947 77 12 3279 4217 617981828 617980889 0.000000e+00 1225.0
24 TraesCS5D01G217600 chr6B 79.963 1073 116 35 1001 2029 617984179 617983162 0.000000e+00 699.0
25 TraesCS5D01G217600 chr6B 88.664 494 31 13 4606 5089 617980753 617980275 4.270000e-161 579.0
26 TraesCS5D01G217600 chr6B 79.356 683 86 32 5126 5755 617980025 617979345 4.550000e-116 429.0
27 TraesCS5D01G217600 chr3D 92.683 164 10 2 4446 4607 375693992 375693829 1.060000e-57 235.0
28 TraesCS5D01G217600 chr3D 91.124 169 13 2 4442 4608 187836302 187836470 1.780000e-55 228.0
29 TraesCS5D01G217600 chrUn 93.125 160 8 3 4448 4604 409687564 409687723 1.380000e-56 231.0
30 TraesCS5D01G217600 chrUn 92.784 97 7 0 4216 4312 15904017 15903921 2.390000e-29 141.0
31 TraesCS5D01G217600 chr7D 92.593 162 9 3 4448 4607 619400834 619400674 4.950000e-56 230.0
32 TraesCS5D01G217600 chr7D 91.000 100 9 0 4216 4315 580850179 580850080 1.110000e-27 135.0
33 TraesCS5D01G217600 chr3B 93.038 158 10 1 4448 4604 529407790 529407947 4.950000e-56 230.0
34 TraesCS5D01G217600 chr4D 90.643 171 14 2 4439 4607 64390641 64390471 6.410000e-55 226.0
35 TraesCS5D01G217600 chr7B 88.430 121 12 2 4216 4334 162120908 162120788 1.850000e-30 145.0
36 TraesCS5D01G217600 chr4B 90.476 105 9 1 4216 4319 511163805 511163701 3.090000e-28 137.0
37 TraesCS5D01G217600 chr4B 94.737 38 2 0 2052 2089 390663580 390663617 6.880000e-05 60.2
38 TraesCS5D01G217600 chr3A 90.385 104 10 0 4216 4319 470095682 470095785 3.090000e-28 137.0
39 TraesCS5D01G217600 chr2D 91.753 97 8 0 4216 4312 74149732 74149828 1.110000e-27 135.0
40 TraesCS5D01G217600 chr7A 84.146 82 11 1 223 304 19549035 19549114 1.900000e-10 78.7
41 TraesCS5D01G217600 chr2A 87.719 57 7 0 251 307 701777333 701777277 4.110000e-07 67.6
42 TraesCS5D01G217600 chr2A 97.368 38 1 0 5933 5970 57972456 57972419 1.480000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G217600 chr5D 326455774 326462127 6353 True 5662.5 10499 100.00000 1 6354 2 chr5D.!!$R2 6353
1 TraesCS5D01G217600 chr5A 429980758 429985965 5207 False 8342.0 8342 95.62100 700 5905 1 chr5A.!!$F3 5205
2 TraesCS5D01G217600 chr5B 378996902 379002994 6092 True 2146.0 6008 89.06425 1 6351 4 chr5B.!!$R3 6350
3 TraesCS5D01G217600 chr6D 411189815 411194286 4471 True 911.5 2311 82.68825 1254 5754 4 chr6D.!!$R1 4500
4 TraesCS5D01G217600 chr6A 555930664 555935083 4419 True 815.6 1328 85.41700 1001 5754 5 chr6A.!!$R1 4753
5 TraesCS5D01G217600 chr6B 617979345 617984179 4834 True 846.6 1301 85.09820 1001 5755 5 chr6B.!!$R1 4754

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
957 977 0.033991 TCTCTCCTCCCAGAACCTCG 60.034 60.000 0.00 0.00 0.00 4.63 F
1645 1705 0.036765 TGTCGGGCAGTTGTATGACC 60.037 55.000 0.00 0.00 45.82 4.02 F
2023 2388 1.202915 ACTGGATTGTGTCATGGCACA 60.203 47.619 28.62 28.62 46.30 4.57 F
2865 3258 4.973168 ACTTCTAATCTGCAAGGTGTTCA 58.027 39.130 0.00 0.00 0.00 3.18 F
3500 3968 0.179113 CCCTGCCACAACAACACAAC 60.179 55.000 0.00 0.00 0.00 3.32 F
5090 5880 1.029681 AGTGCGAGGAAAACCAAACC 58.970 50.000 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2390 0.035056 ACAACTATCTGTGCCCTGCC 60.035 55.000 0.00 0.0 0.00 4.85 R
3209 3615 0.908910 TGGTGTTGGCGACCTATCAT 59.091 50.000 1.61 0.0 34.26 2.45 R
3487 3955 2.281517 TCGGGTAGTTGTGTTGTTGTG 58.718 47.619 0.00 0.0 0.00 3.33 R
4637 5193 0.398381 AGGAGAGGAGAGGTGGCATC 60.398 60.000 0.00 0.0 0.00 3.91 R
5099 5890 0.036765 TTTCTCGTGTCCAATCGGGG 60.037 55.000 0.00 0.0 37.22 5.73 R
6324 7600 0.035739 TCGTTACTCTTTGGGCCACC 59.964 55.000 5.23 0.0 37.24 4.61 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
31 32 4.617520 TCGCCAGCGCAACAAGGA 62.618 61.111 11.47 0.00 39.59 3.36
35 36 2.281761 CAGCGCAACAAGGAGGGT 60.282 61.111 11.47 0.00 0.00 4.34
58 59 1.641123 GCCGGGGTGTTGTAATGTCG 61.641 60.000 2.18 0.00 0.00 4.35
64 65 3.078837 GGGTGTTGTAATGTCGACCAAT 58.921 45.455 14.12 0.00 0.00 3.16
65 66 3.126343 GGGTGTTGTAATGTCGACCAATC 59.874 47.826 14.12 7.32 0.00 2.67
80 81 1.471119 CAATCAATGCCCTCACTGCT 58.529 50.000 0.00 0.00 0.00 4.24
88 89 2.360852 CCTCACTGCTGCAAGGGG 60.361 66.667 10.39 8.39 0.00 4.79
94 95 3.797507 CTGCTGCAAGGGGGTGTGT 62.798 63.158 3.02 0.00 0.00 3.72
110 111 2.029666 GTGAGCCGCAGACACTGT 59.970 61.111 0.00 0.00 33.43 3.55
119 120 1.794003 CAGACACTGTCGCGAGTCG 60.794 63.158 10.24 8.54 37.67 4.18
140 141 0.815734 ATGTGCTGCCATGAAGCTTC 59.184 50.000 19.89 19.89 41.42 3.86
142 143 1.003476 TGCTGCCATGAAGCTTCGA 60.003 52.632 21.11 11.01 41.42 3.71
150 151 0.254178 ATGAAGCTTCGACAGGCCAT 59.746 50.000 21.11 4.67 0.00 4.40
151 152 0.674581 TGAAGCTTCGACAGGCCATG 60.675 55.000 21.11 2.64 0.00 3.66
160 161 1.808531 GACAGGCCATGTTGCTGCAA 61.809 55.000 11.69 11.69 44.17 4.08
170 171 1.269883 TGTTGCTGCAATGGAGCTTTG 60.270 47.619 26.10 0.00 37.35 2.77
203 204 2.079158 GAGCTGCAATGAAGCACTACA 58.921 47.619 16.64 0.00 43.37 2.74
207 208 1.098050 GCAATGAAGCACTACAGGGG 58.902 55.000 0.00 0.00 0.00 4.79
222 223 0.398318 AGGGGTGTTGAAGCTCAGTC 59.602 55.000 0.00 0.00 0.00 3.51
239 240 0.725784 GTCGTGGTTGCAATGAAGCG 60.726 55.000 0.59 4.05 37.31 4.68
242 243 2.504681 GGTTGCAATGAAGCGCCG 60.505 61.111 2.29 0.00 37.31 6.46
243 244 3.174573 GTTGCAATGAAGCGCCGC 61.175 61.111 2.29 0.00 37.31 6.53
244 245 3.364441 TTGCAATGAAGCGCCGCT 61.364 55.556 5.39 5.39 42.56 5.52
282 284 0.664166 CACCGTGGTTGCAATGAAGC 60.664 55.000 0.59 0.00 0.00 3.86
283 285 1.442520 CCGTGGTTGCAATGAAGCG 60.443 57.895 0.59 3.76 37.31 4.68
284 286 1.282570 CGTGGTTGCAATGAAGCGT 59.717 52.632 0.59 0.00 37.31 5.07
285 287 0.725784 CGTGGTTGCAATGAAGCGTC 60.726 55.000 0.59 0.00 37.31 5.19
286 288 0.725784 GTGGTTGCAATGAAGCGTCG 60.726 55.000 0.59 0.00 37.31 5.12
287 289 1.797537 GGTTGCAATGAAGCGTCGC 60.798 57.895 9.80 9.80 37.31 5.19
288 290 1.797537 GTTGCAATGAAGCGTCGCC 60.798 57.895 14.86 0.00 37.31 5.54
289 291 3.307505 TTGCAATGAAGCGTCGCCG 62.308 57.895 14.86 0.00 37.31 6.46
290 292 3.487202 GCAATGAAGCGTCGCCGA 61.487 61.111 14.86 0.00 35.63 5.54
291 293 3.022401 GCAATGAAGCGTCGCCGAA 62.022 57.895 14.86 0.00 35.63 4.30
292 294 1.059369 CAATGAAGCGTCGCCGAAG 59.941 57.895 14.86 0.00 35.63 3.79
293 295 2.740714 AATGAAGCGTCGCCGAAGC 61.741 57.895 17.25 17.25 37.32 3.86
295 297 3.843240 GAAGCGTCGCCGAAGCTG 61.843 66.667 27.11 0.31 45.60 4.24
299 301 3.490759 CGTCGCCGAAGCTGCAAT 61.491 61.111 1.02 0.00 36.60 3.56
300 302 2.099062 GTCGCCGAAGCTGCAATG 59.901 61.111 1.02 0.00 36.60 2.82
301 303 2.047370 TCGCCGAAGCTGCAATGA 60.047 55.556 1.02 0.00 36.60 2.57
302 304 1.670730 TCGCCGAAGCTGCAATGAA 60.671 52.632 1.02 0.00 36.60 2.57
303 305 1.226211 CGCCGAAGCTGCAATGAAG 60.226 57.895 1.02 0.00 36.60 3.02
318 320 0.601046 TGAAGAGCCTCGTTGCACTG 60.601 55.000 0.00 0.00 32.32 3.66
410 412 2.355756 ACAATATCAACGATGGTGCTGC 59.644 45.455 0.00 0.00 0.00 5.25
425 428 1.596934 CTGCCTGGTACATCACGGT 59.403 57.895 0.00 0.00 38.20 4.83
430 433 0.320374 CTGGTACATCACGGTGGTGT 59.680 55.000 28.07 28.07 45.01 4.16
438 441 2.048222 ACGGTGGTGTGAGCGATG 60.048 61.111 0.00 0.00 40.07 3.84
446 449 2.887568 GTGAGCGATGGGAGTGCG 60.888 66.667 0.00 0.00 0.00 5.34
687 690 3.751767 TTGGAAGTGCAAGCAGGAT 57.248 47.368 0.00 0.00 0.00 3.24
688 691 1.999648 TTGGAAGTGCAAGCAGGATT 58.000 45.000 0.00 0.00 0.00 3.01
689 692 1.250328 TGGAAGTGCAAGCAGGATTG 58.750 50.000 0.00 0.00 0.00 2.67
690 693 1.251251 GGAAGTGCAAGCAGGATTGT 58.749 50.000 0.00 0.00 32.56 2.71
691 694 1.200948 GGAAGTGCAAGCAGGATTGTC 59.799 52.381 0.00 0.00 32.56 3.18
692 695 1.881973 GAAGTGCAAGCAGGATTGTCA 59.118 47.619 0.00 0.00 32.56 3.58
693 696 1.531423 AGTGCAAGCAGGATTGTCAG 58.469 50.000 0.00 0.00 32.56 3.51
694 697 1.072806 AGTGCAAGCAGGATTGTCAGA 59.927 47.619 0.00 0.00 32.56 3.27
695 698 1.467734 GTGCAAGCAGGATTGTCAGAG 59.532 52.381 0.00 0.00 32.56 3.35
696 699 1.093159 GCAAGCAGGATTGTCAGAGG 58.907 55.000 0.00 0.00 32.56 3.69
697 700 1.093159 CAAGCAGGATTGTCAGAGGC 58.907 55.000 0.00 0.00 0.00 4.70
698 701 0.034670 AAGCAGGATTGTCAGAGGCC 60.035 55.000 0.00 0.00 0.00 5.19
729 732 1.418334 AGAGGATCGAAGGGTCATGG 58.582 55.000 0.00 0.00 42.67 3.66
821 826 1.856259 TGCAGAGACTCCCTAGGATCT 59.144 52.381 11.48 10.11 0.00 2.75
822 827 3.056832 TGCAGAGACTCCCTAGGATCTA 58.943 50.000 11.48 0.00 0.00 1.98
957 977 0.033991 TCTCTCCTCCCAGAACCTCG 60.034 60.000 0.00 0.00 0.00 4.63
958 978 0.323908 CTCTCCTCCCAGAACCTCGT 60.324 60.000 0.00 0.00 0.00 4.18
959 979 0.323542 TCTCCTCCCAGAACCTCGTC 60.324 60.000 0.00 0.00 0.00 4.20
960 980 0.323908 CTCCTCCCAGAACCTCGTCT 60.324 60.000 0.00 0.00 0.00 4.18
1095 1115 4.761058 TCCCGCTCCTTCGCCTCT 62.761 66.667 0.00 0.00 0.00 3.69
1213 1242 4.214327 CTCCCGAGCCTCGCTTCC 62.214 72.222 9.01 0.00 39.88 3.46
1387 1437 1.210155 GCGCGCTCAAGGTGATTTT 59.790 52.632 26.67 0.00 0.00 1.82
1416 1466 3.879295 CTCTATGTGTGGCATTTAGGTGG 59.121 47.826 0.00 0.00 38.94 4.61
1645 1705 0.036765 TGTCGGGCAGTTGTATGACC 60.037 55.000 0.00 0.00 45.82 4.02
1699 1759 2.100584 CTGCCGTATCTGCTCTTCTTCT 59.899 50.000 0.00 0.00 0.00 2.85
2023 2388 1.202915 ACTGGATTGTGTCATGGCACA 60.203 47.619 28.62 28.62 46.30 4.57
2857 3250 7.476540 TGTTAGAGGTACTTCTAATCTGCAA 57.523 36.000 25.02 5.56 41.55 4.08
2865 3258 4.973168 ACTTCTAATCTGCAAGGTGTTCA 58.027 39.130 0.00 0.00 0.00 3.18
3500 3968 0.179113 CCCTGCCACAACAACACAAC 60.179 55.000 0.00 0.00 0.00 3.32
3590 4058 1.168407 TCTGGTGTCTTTGCTGCAGC 61.168 55.000 31.89 31.89 42.50 5.25
4001 4476 4.323257 CCACCAGATAGAAGGTAACCGTTT 60.323 45.833 0.00 0.00 36.07 3.60
4044 4519 9.072375 TGTGGTGTTAACTTGATTGATATTTGA 57.928 29.630 7.22 0.00 0.00 2.69
4097 4575 6.128363 CCCTTTTAACAAGGAAGCTACTTACG 60.128 42.308 14.42 0.00 39.81 3.18
4207 4685 3.378427 GGTACTAAGCCAAAGCCATTGAG 59.622 47.826 1.58 0.00 41.85 3.02
4457 5013 2.168496 TCTTGTCTTGTACTCCCTCCG 58.832 52.381 0.00 0.00 0.00 4.63
4529 5085 7.011389 CGGAGCAAAATGAATGAATCTACACTA 59.989 37.037 0.00 0.00 0.00 2.74
4620 5176 4.161377 GGAGGGAATATCTGCTATCTCCAC 59.839 50.000 0.00 0.00 39.30 4.02
4786 5342 6.127507 TGTTTTCATGATTATTGCGATCCCAA 60.128 34.615 0.00 0.00 0.00 4.12
4992 5548 8.789762 TGAATGATTCCTTTATGTGCATCTATG 58.210 33.333 2.26 0.00 0.00 2.23
5005 5561 7.160547 TGTGCATCTATGTGTTGAATTGATT 57.839 32.000 0.00 0.00 0.00 2.57
5008 5564 7.972277 GTGCATCTATGTGTTGAATTGATTTCT 59.028 33.333 0.00 0.00 35.23 2.52
5089 5879 2.357952 AGAAGTGCGAGGAAAACCAAAC 59.642 45.455 0.00 0.00 0.00 2.93
5090 5880 1.029681 AGTGCGAGGAAAACCAAACC 58.970 50.000 0.00 0.00 0.00 3.27
5099 5890 3.826729 AGGAAAACCAAACCATAGCAGAC 59.173 43.478 0.00 0.00 0.00 3.51
5102 5893 0.331616 ACCAAACCATAGCAGACCCC 59.668 55.000 0.00 0.00 0.00 4.95
5124 6165 3.250040 CGATTGGACACGAGAAACCTTTT 59.750 43.478 0.00 0.00 0.00 2.27
5135 6176 8.936864 ACACGAGAAACCTTTTCTTTATCTATG 58.063 33.333 2.79 0.00 0.00 2.23
5314 6362 5.227908 TGATCTTTACAGGTCGACTTCAAC 58.772 41.667 16.46 0.00 31.91 3.18
5355 6408 2.436646 CCGCTTGGGGCTGTAGTG 60.437 66.667 0.00 0.00 39.13 2.74
5356 6409 2.662596 CGCTTGGGGCTGTAGTGA 59.337 61.111 0.00 0.00 39.13 3.41
5357 6410 1.448540 CGCTTGGGGCTGTAGTGAG 60.449 63.158 0.00 0.00 39.13 3.51
5358 6411 1.746991 GCTTGGGGCTGTAGTGAGC 60.747 63.158 0.00 0.00 38.34 4.26
5359 6412 1.986413 CTTGGGGCTGTAGTGAGCT 59.014 57.895 0.00 0.00 39.11 4.09
5360 6413 0.326264 CTTGGGGCTGTAGTGAGCTT 59.674 55.000 0.00 0.00 39.11 3.74
5361 6414 0.771127 TTGGGGCTGTAGTGAGCTTT 59.229 50.000 0.00 0.00 39.11 3.51
5362 6415 0.771127 TGGGGCTGTAGTGAGCTTTT 59.229 50.000 0.00 0.00 39.11 2.27
5363 6416 1.144913 TGGGGCTGTAGTGAGCTTTTT 59.855 47.619 0.00 0.00 39.11 1.94
5392 6445 8.553459 AATGTAGTGAGGTTGATAGAACTTTG 57.447 34.615 0.00 0.00 0.00 2.77
5409 6499 3.276857 CTTTGTCTGGATGTCTGGATGG 58.723 50.000 0.00 0.00 0.00 3.51
5488 6583 3.009473 AGGGAGTGCAGAAATACACACAT 59.991 43.478 0.00 0.00 39.30 3.21
5489 6584 3.127548 GGGAGTGCAGAAATACACACATG 59.872 47.826 0.00 0.00 39.30 3.21
5490 6585 3.753272 GGAGTGCAGAAATACACACATGT 59.247 43.478 0.00 0.00 43.30 3.21
5504 6611 5.793817 ACACACATGTTGTAGCTCTGAATA 58.206 37.500 10.65 0.00 35.67 1.75
5512 6619 7.076842 TGTTGTAGCTCTGAATAGCAATTTC 57.923 36.000 0.00 0.00 45.30 2.17
5531 6638 2.606108 TCGAGGTGTTCATGTTCGATG 58.394 47.619 0.00 0.00 35.60 3.84
5615 6743 2.703409 CTCCACGCAAGCGCATAC 59.297 61.111 15.09 0.00 44.19 2.39
5628 6756 0.526954 CGCATACCCTACACACGGTC 60.527 60.000 0.00 0.00 33.36 4.79
5707 6835 0.109132 CATTTTGAAGCCCGTCCTGC 60.109 55.000 0.00 0.00 0.00 4.85
5747 6875 6.924060 GGCCAACTGTGTAGACTAATATACAG 59.076 42.308 0.00 8.52 45.34 2.74
5844 6998 0.263765 ATGGGCTCCTGGCATGATTT 59.736 50.000 0.00 0.00 44.01 2.17
5872 7026 4.652131 TTTGGCGCCCACGGTGAT 62.652 61.111 26.77 0.00 40.57 3.06
5881 7035 1.448540 CCACGGTGATCCAGACTGC 60.449 63.158 10.28 0.00 0.00 4.40
5885 7039 2.581354 GTGATCCAGACTGCCGCT 59.419 61.111 0.00 0.00 0.00 5.52
5911 7065 2.859165 TTGATGTTGTGGAGGAGGAC 57.141 50.000 0.00 0.00 0.00 3.85
5914 7068 1.625818 GATGTTGTGGAGGAGGACTGT 59.374 52.381 0.00 0.00 0.00 3.55
5920 7074 2.378886 TGTGGAGGAGGACTGTTAGAGA 59.621 50.000 0.00 0.00 0.00 3.10
5923 7077 2.024751 GGAGGAGGACTGTTAGAGAGGT 60.025 54.545 0.00 0.00 0.00 3.85
5924 7078 3.020984 GAGGAGGACTGTTAGAGAGGTG 58.979 54.545 0.00 0.00 0.00 4.00
5925 7079 2.380590 AGGAGGACTGTTAGAGAGGTGT 59.619 50.000 0.00 0.00 0.00 4.16
5926 7080 3.592427 AGGAGGACTGTTAGAGAGGTGTA 59.408 47.826 0.00 0.00 0.00 2.90
5928 7082 4.333690 GAGGACTGTTAGAGAGGTGTACA 58.666 47.826 0.00 0.00 0.00 2.90
5929 7083 4.737578 AGGACTGTTAGAGAGGTGTACAA 58.262 43.478 0.00 0.00 0.00 2.41
5931 7085 5.186021 AGGACTGTTAGAGAGGTGTACAATG 59.814 44.000 0.00 0.00 0.00 2.82
5934 7088 5.775701 ACTGTTAGAGAGGTGTACAATGAGT 59.224 40.000 0.00 0.00 0.00 3.41
5935 7089 6.946583 ACTGTTAGAGAGGTGTACAATGAGTA 59.053 38.462 0.00 0.00 0.00 2.59
5950 7104 6.920817 ACAATGAGTACAATGAGTTCTACGA 58.079 36.000 0.00 0.00 32.00 3.43
5951 7105 6.807230 ACAATGAGTACAATGAGTTCTACGAC 59.193 38.462 0.00 0.00 32.00 4.34
5952 7106 6.761099 ATGAGTACAATGAGTTCTACGACT 57.239 37.500 0.00 0.00 0.00 4.18
5954 7108 6.609533 TGAGTACAATGAGTTCTACGACTTC 58.390 40.000 0.00 0.00 0.00 3.01
5957 7111 5.470047 ACAATGAGTTCTACGACTTCCTT 57.530 39.130 0.00 0.00 0.00 3.36
5958 7112 5.230942 ACAATGAGTTCTACGACTTCCTTG 58.769 41.667 0.00 0.00 0.00 3.61
5959 7113 5.010719 ACAATGAGTTCTACGACTTCCTTGA 59.989 40.000 0.00 0.00 0.00 3.02
5960 7114 4.500603 TGAGTTCTACGACTTCCTTGAC 57.499 45.455 0.00 0.00 0.00 3.18
5961 7115 3.887110 TGAGTTCTACGACTTCCTTGACA 59.113 43.478 0.00 0.00 0.00 3.58
5962 7116 4.340097 TGAGTTCTACGACTTCCTTGACAA 59.660 41.667 0.00 0.00 0.00 3.18
5963 7117 5.163488 TGAGTTCTACGACTTCCTTGACAAA 60.163 40.000 0.00 0.00 0.00 2.83
5964 7118 5.855045 AGTTCTACGACTTCCTTGACAAAT 58.145 37.500 0.00 0.00 0.00 2.32
5965 7119 5.696724 AGTTCTACGACTTCCTTGACAAATG 59.303 40.000 0.00 0.00 0.00 2.32
5970 7246 3.753272 CGACTTCCTTGACAAATGGATGT 59.247 43.478 12.27 12.27 39.78 3.06
5998 7274 2.216898 GTAGCCACTCCTTGATCATGC 58.783 52.381 0.00 0.00 0.00 4.06
6001 7277 0.549950 CCACTCCTTGATCATGCCCT 59.450 55.000 0.00 0.00 0.00 5.19
6006 7282 3.782523 ACTCCTTGATCATGCCCTAAAGA 59.217 43.478 0.00 0.00 0.00 2.52
6012 7288 6.774656 CCTTGATCATGCCCTAAAGACTAATT 59.225 38.462 0.00 0.00 0.00 1.40
6013 7289 7.255381 CCTTGATCATGCCCTAAAGACTAATTG 60.255 40.741 0.00 0.00 0.00 2.32
6014 7290 6.662755 TGATCATGCCCTAAAGACTAATTGT 58.337 36.000 0.00 0.00 0.00 2.71
6016 7292 5.815581 TCATGCCCTAAAGACTAATTGTGT 58.184 37.500 0.00 0.00 0.00 3.72
6017 7293 6.953101 TCATGCCCTAAAGACTAATTGTGTA 58.047 36.000 0.00 0.00 0.00 2.90
6018 7294 6.821665 TCATGCCCTAAAGACTAATTGTGTAC 59.178 38.462 0.00 0.00 0.00 2.90
6020 7296 5.013287 TGCCCTAAAGACTAATTGTGTACCA 59.987 40.000 0.00 0.00 0.00 3.25
6021 7297 5.941647 GCCCTAAAGACTAATTGTGTACCAA 59.058 40.000 0.00 0.00 37.49 3.67
6022 7298 6.128090 GCCCTAAAGACTAATTGTGTACCAAC 60.128 42.308 0.00 0.00 35.44 3.77
6023 7299 6.938030 CCCTAAAGACTAATTGTGTACCAACA 59.062 38.462 0.00 0.00 35.44 3.33
6043 7319 3.201266 ACACTTGTAGGAAAGGTGGTCAA 59.799 43.478 0.00 0.00 0.00 3.18
6044 7320 4.204012 CACTTGTAGGAAAGGTGGTCAAA 58.796 43.478 0.00 0.00 0.00 2.69
6056 7332 7.363007 GGAAAGGTGGTCAAAGGATTCTTTATC 60.363 40.741 0.00 0.00 40.92 1.75
6063 7339 4.394920 TCAAAGGATTCTTTATCGCGCTTT 59.605 37.500 5.56 0.00 40.92 3.51
6073 7349 0.687354 ATCGCGCTTTCATAGGGGAT 59.313 50.000 5.56 0.00 37.30 3.85
6076 7352 2.069273 CGCGCTTTCATAGGGGATAAG 58.931 52.381 5.56 0.00 37.30 1.73
6077 7353 2.427506 GCGCTTTCATAGGGGATAAGG 58.572 52.381 0.00 0.00 37.30 2.69
6114 7390 1.969589 ACGTTTGGCCAACCGATCC 60.970 57.895 37.67 12.37 39.70 3.36
6116 7392 3.059386 TTTGGCCAACCGATCCGC 61.059 61.111 20.35 0.00 39.70 5.54
6117 7393 3.561120 TTTGGCCAACCGATCCGCT 62.561 57.895 20.35 0.00 39.70 5.52
6123 7399 1.811266 CAACCGATCCGCTGTCCAG 60.811 63.158 0.00 0.00 0.00 3.86
6129 7405 0.755686 GATCCGCTGTCCAGATCCTT 59.244 55.000 0.00 0.00 32.03 3.36
6162 7438 6.017109 TGGCAGGATAAGCGAAGAATTTAATC 60.017 38.462 0.00 0.00 0.00 1.75
6163 7439 6.374578 GCAGGATAAGCGAAGAATTTAATCC 58.625 40.000 0.00 0.00 0.00 3.01
6164 7440 6.593978 CAGGATAAGCGAAGAATTTAATCCG 58.406 40.000 0.00 0.00 0.00 4.18
6171 7447 4.694339 CGAAGAATTTAATCCGGAGAGGT 58.306 43.478 11.34 0.00 41.99 3.85
6173 7449 5.429130 GAAGAATTTAATCCGGAGAGGTGT 58.571 41.667 11.34 0.00 41.99 4.16
6174 7450 5.024785 AGAATTTAATCCGGAGAGGTGTC 57.975 43.478 11.34 3.50 41.99 3.67
6182 7458 1.831652 CGGAGAGGTGTCCAAGCCTT 61.832 60.000 0.00 0.00 36.23 4.35
6184 7460 0.980423 GAGAGGTGTCCAAGCCTTCT 59.020 55.000 0.00 0.00 34.81 2.85
6191 7467 1.418637 TGTCCAAGCCTTCTAAACCGT 59.581 47.619 0.00 0.00 0.00 4.83
6197 7473 0.796927 GCCTTCTAAACCGTGTGCTC 59.203 55.000 0.00 0.00 0.00 4.26
6201 7477 2.093306 TCTAAACCGTGTGCTCCATG 57.907 50.000 0.00 0.00 0.00 3.66
6205 7481 4.802051 CCGTGTGCTCCATGGGGG 62.802 72.222 15.13 7.52 45.20 5.40
6218 7494 1.863155 ATGGGGGAACGAATGGTGCT 61.863 55.000 0.00 0.00 0.00 4.40
6229 7505 1.895131 GAATGGTGCTGTGGAATTGGT 59.105 47.619 0.00 0.00 0.00 3.67
6233 7509 1.541588 GGTGCTGTGGAATTGGTCTTC 59.458 52.381 0.00 0.00 0.00 2.87
6241 7517 1.475213 GGAATTGGTCTTCCTAGGCGG 60.475 57.143 2.96 0.00 41.32 6.13
6263 7539 1.689273 AGCCGATGAGTAGGAACCATC 59.311 52.381 0.00 0.00 33.47 3.51
6266 7542 1.681793 CGATGAGTAGGAACCATCGGT 59.318 52.381 14.03 0.00 44.36 4.69
6267 7543 2.882761 CGATGAGTAGGAACCATCGGTA 59.117 50.000 14.03 0.00 44.36 4.02
6269 7545 2.662866 TGAGTAGGAACCATCGGTAGG 58.337 52.381 0.00 0.00 33.12 3.18
6287 7563 0.598065 GGGTGCTTCCACACAATGTC 59.402 55.000 0.00 0.00 44.90 3.06
6293 7569 2.290641 GCTTCCACACAATGTCGTCTTT 59.709 45.455 0.00 0.00 0.00 2.52
6295 7571 2.217750 TCCACACAATGTCGTCTTTGG 58.782 47.619 11.68 4.91 34.41 3.28
6296 7572 1.946768 CCACACAATGTCGTCTTTGGT 59.053 47.619 11.68 5.39 34.41 3.67
6297 7573 2.286950 CCACACAATGTCGTCTTTGGTG 60.287 50.000 11.68 13.88 34.41 4.17
6335 7611 1.247567 CTACACAAGGTGGCCCAAAG 58.752 55.000 0.00 0.00 37.94 2.77
6347 7623 3.078837 TGGCCCAAAGAGTAACGAATTC 58.921 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
9 10 3.482783 GTTGCGCTGGCGAGTCTC 61.483 66.667 19.31 0.98 44.10 3.36
19 20 2.281761 CACCCTCCTTGTTGCGCT 60.282 61.111 9.73 0.00 0.00 5.92
20 21 4.043200 GCACCCTCCTTGTTGCGC 62.043 66.667 0.00 0.00 0.00 6.09
42 43 1.270947 TGGTCGACATTACAACACCCC 60.271 52.381 18.91 0.00 0.00 4.95
58 59 1.747355 CAGTGAGGGCATTGATTGGTC 59.253 52.381 0.00 0.00 33.97 4.02
64 65 1.676635 GCAGCAGTGAGGGCATTGA 60.677 57.895 0.00 0.00 33.97 2.57
65 66 1.529152 TTGCAGCAGTGAGGGCATTG 61.529 55.000 0.00 0.00 35.98 2.82
80 81 2.515398 CTCACACACCCCCTTGCA 59.485 61.111 0.00 0.00 0.00 4.08
88 89 3.044305 GTCTGCGGCTCACACACC 61.044 66.667 0.00 0.00 0.00 4.16
94 95 2.340078 GACAGTGTCTGCGGCTCA 59.660 61.111 16.26 0.00 34.37 4.26
103 104 3.166630 GCGACTCGCGACAGTGTC 61.167 66.667 13.56 13.56 44.55 3.67
134 135 0.250901 AACATGGCCTGTCGAAGCTT 60.251 50.000 3.32 0.00 36.98 3.74
140 141 2.872557 CAGCAACATGGCCTGTCG 59.127 61.111 3.32 0.00 36.98 4.35
142 143 1.189524 ATTGCAGCAACATGGCCTGT 61.190 50.000 10.85 2.75 40.84 4.00
150 151 1.042229 AAAGCTCCATTGCAGCAACA 58.958 45.000 10.85 0.00 39.56 3.33
151 152 1.425412 CAAAGCTCCATTGCAGCAAC 58.575 50.000 10.85 0.00 39.56 4.17
203 204 0.398318 GACTGAGCTTCAACACCCCT 59.602 55.000 0.00 0.00 0.00 4.79
207 208 0.861837 CCACGACTGAGCTTCAACAC 59.138 55.000 0.00 0.00 0.00 3.32
222 223 2.082366 GCGCTTCATTGCAACCACG 61.082 57.895 0.00 2.91 0.00 4.94
239 240 2.803155 TTCATGGACCACTCAGCGGC 62.803 60.000 0.00 0.00 0.00 6.53
242 243 0.035630 AGCTTCATGGACCACTCAGC 60.036 55.000 11.20 11.20 0.00 4.26
243 244 1.406614 GGAGCTTCATGGACCACTCAG 60.407 57.143 0.00 0.00 0.00 3.35
244 245 0.615331 GGAGCTTCATGGACCACTCA 59.385 55.000 0.00 0.00 0.00 3.41
254 256 0.606401 CAACCACGGTGGAGCTTCAT 60.606 55.000 32.72 6.26 40.96 2.57
286 288 0.098376 CTCTTCATTGCAGCTTCGGC 59.902 55.000 0.00 0.00 42.17 5.54
287 289 0.098376 GCTCTTCATTGCAGCTTCGG 59.902 55.000 0.00 0.00 0.00 4.30
288 290 0.098376 GGCTCTTCATTGCAGCTTCG 59.902 55.000 0.00 0.00 33.38 3.79
289 291 1.401199 GAGGCTCTTCATTGCAGCTTC 59.599 52.381 7.40 0.00 32.81 3.86
290 292 1.461559 GAGGCTCTTCATTGCAGCTT 58.538 50.000 7.40 0.00 33.38 3.74
291 293 0.743701 CGAGGCTCTTCATTGCAGCT 60.744 55.000 13.50 0.00 33.38 4.24
292 294 1.023513 ACGAGGCTCTTCATTGCAGC 61.024 55.000 13.50 0.00 0.00 5.25
293 295 1.129998 CAACGAGGCTCTTCATTGCAG 59.870 52.381 13.50 0.00 0.00 4.41
294 296 1.159285 CAACGAGGCTCTTCATTGCA 58.841 50.000 13.50 0.00 0.00 4.08
295 297 0.179179 GCAACGAGGCTCTTCATTGC 60.179 55.000 19.64 19.64 36.07 3.56
296 298 1.135859 GTGCAACGAGGCTCTTCATTG 60.136 52.381 13.50 12.08 34.04 2.82
297 299 1.160137 GTGCAACGAGGCTCTTCATT 58.840 50.000 13.50 0.00 34.04 2.57
298 300 0.322975 AGTGCAACGAGGCTCTTCAT 59.677 50.000 13.50 0.00 45.86 2.57
299 301 0.601046 CAGTGCAACGAGGCTCTTCA 60.601 55.000 13.50 2.07 45.86 3.02
300 302 1.905922 GCAGTGCAACGAGGCTCTTC 61.906 60.000 11.09 0.00 45.86 2.87
301 303 1.963338 GCAGTGCAACGAGGCTCTT 60.963 57.895 11.09 0.00 45.86 2.85
302 304 2.358003 GCAGTGCAACGAGGCTCT 60.358 61.111 11.09 0.00 45.86 4.09
303 305 2.253758 TTGCAGTGCAACGAGGCTC 61.254 57.895 26.36 3.87 43.99 4.70
318 320 3.423154 CTCCGCCGGTGAAGTTGC 61.423 66.667 18.79 0.00 0.00 4.17
370 372 2.954611 TCGTCACCGACAGAGCTG 59.045 61.111 0.00 0.00 38.40 4.24
386 388 5.615544 GCAGCACCATCGTTGATATTGTATC 60.616 44.000 0.00 0.00 0.00 2.24
393 395 0.541392 AGGCAGCACCATCGTTGATA 59.459 50.000 0.00 0.00 43.14 2.15
410 412 0.391130 CACCACCGTGATGTACCAGG 60.391 60.000 0.00 0.00 43.14 4.45
425 428 1.913262 ACTCCCATCGCTCACACCA 60.913 57.895 0.00 0.00 0.00 4.17
669 672 1.614903 CAATCCTGCTTGCACTTCCAA 59.385 47.619 0.00 0.00 0.00 3.53
670 673 1.250328 CAATCCTGCTTGCACTTCCA 58.750 50.000 0.00 0.00 0.00 3.53
671 674 1.200948 GACAATCCTGCTTGCACTTCC 59.799 52.381 0.00 0.00 0.00 3.46
672 675 1.881973 TGACAATCCTGCTTGCACTTC 59.118 47.619 0.00 0.00 0.00 3.01
673 676 1.884579 CTGACAATCCTGCTTGCACTT 59.115 47.619 0.00 0.00 0.00 3.16
674 677 1.072806 TCTGACAATCCTGCTTGCACT 59.927 47.619 0.00 0.00 0.00 4.40
675 678 1.467734 CTCTGACAATCCTGCTTGCAC 59.532 52.381 0.00 0.00 0.00 4.57
676 679 1.612462 CCTCTGACAATCCTGCTTGCA 60.612 52.381 0.00 0.00 0.00 4.08
677 680 1.093159 CCTCTGACAATCCTGCTTGC 58.907 55.000 0.00 0.00 0.00 4.01
678 681 1.093159 GCCTCTGACAATCCTGCTTG 58.907 55.000 0.00 0.00 0.00 4.01
679 682 0.034670 GGCCTCTGACAATCCTGCTT 60.035 55.000 0.00 0.00 0.00 3.91
680 683 1.606531 GGCCTCTGACAATCCTGCT 59.393 57.895 0.00 0.00 0.00 4.24
681 684 1.817099 CGGCCTCTGACAATCCTGC 60.817 63.158 0.00 0.00 0.00 4.85
682 685 0.250234 TTCGGCCTCTGACAATCCTG 59.750 55.000 0.00 0.00 0.00 3.86
683 686 0.539051 CTTCGGCCTCTGACAATCCT 59.461 55.000 0.00 0.00 0.00 3.24
684 687 1.092345 GCTTCGGCCTCTGACAATCC 61.092 60.000 0.00 0.00 34.32 3.01
685 688 0.391661 TGCTTCGGCCTCTGACAATC 60.392 55.000 0.00 0.00 40.91 2.67
686 689 0.392193 CTGCTTCGGCCTCTGACAAT 60.392 55.000 0.00 0.00 40.91 2.71
687 690 1.004560 CTGCTTCGGCCTCTGACAA 60.005 57.895 0.00 0.00 40.91 3.18
688 691 1.881903 CTCTGCTTCGGCCTCTGACA 61.882 60.000 0.00 0.00 40.91 3.58
689 692 1.153667 CTCTGCTTCGGCCTCTGAC 60.154 63.158 0.00 0.00 40.91 3.51
690 693 2.354401 CCTCTGCTTCGGCCTCTGA 61.354 63.158 0.00 0.00 40.91 3.27
691 694 1.892819 TTCCTCTGCTTCGGCCTCTG 61.893 60.000 0.00 0.00 40.91 3.35
692 695 1.610673 TTCCTCTGCTTCGGCCTCT 60.611 57.895 0.00 0.00 40.91 3.69
693 696 1.153469 CTTCCTCTGCTTCGGCCTC 60.153 63.158 0.00 0.00 40.91 4.70
694 697 1.610673 TCTTCCTCTGCTTCGGCCT 60.611 57.895 0.00 0.00 40.91 5.19
695 698 1.153469 CTCTTCCTCTGCTTCGGCC 60.153 63.158 0.00 0.00 40.91 6.13
696 699 1.153469 CCTCTTCCTCTGCTTCGGC 60.153 63.158 0.00 0.00 42.19 5.54
697 700 1.068434 GATCCTCTTCCTCTGCTTCGG 59.932 57.143 0.00 0.00 0.00 4.30
698 701 1.268999 CGATCCTCTTCCTCTGCTTCG 60.269 57.143 0.00 0.00 0.00 3.79
821 826 2.142756 TGATGGGGAATGAATGGCCTA 58.857 47.619 3.32 0.00 0.00 3.93
822 827 0.935942 TGATGGGGAATGAATGGCCT 59.064 50.000 3.32 0.00 0.00 5.19
957 977 2.776913 CGGCGAGGAGGAGGAAGAC 61.777 68.421 0.00 0.00 0.00 3.01
958 978 2.440430 CGGCGAGGAGGAGGAAGA 60.440 66.667 0.00 0.00 0.00 2.87
959 979 4.214327 GCGGCGAGGAGGAGGAAG 62.214 72.222 12.98 0.00 0.00 3.46
1119 1139 1.546029 CTCTTGATGACGTCCTCCACA 59.454 52.381 14.12 3.29 0.00 4.17
1213 1242 3.787001 GGAACTCGGGGCAGGGAG 61.787 72.222 0.00 0.00 36.36 4.30
1387 1437 1.007118 TGCCACACATAGAGAGAGGGA 59.993 52.381 0.00 0.00 0.00 4.20
1416 1466 2.370281 TTCACTCCAATCGAGCAGAC 57.630 50.000 0.00 0.00 43.01 3.51
1632 1692 2.744202 CTGAACTGGGTCATACAACTGC 59.256 50.000 0.00 0.00 0.00 4.40
1633 1693 3.748048 CACTGAACTGGGTCATACAACTG 59.252 47.826 0.00 0.00 0.00 3.16
1636 1696 3.135712 ACACACTGAACTGGGTCATACAA 59.864 43.478 0.00 0.00 0.00 2.41
1645 1705 6.429692 TCCAATACAAATACACACTGAACTGG 59.570 38.462 0.00 0.00 0.00 4.00
1699 1759 1.202114 GCAAATTGAGAACATCGCCCA 59.798 47.619 0.00 0.00 0.00 5.36
2023 2388 0.921896 AACTATCTGTGCCCTGCCAT 59.078 50.000 0.00 0.00 0.00 4.40
2024 2389 0.035152 CAACTATCTGTGCCCTGCCA 60.035 55.000 0.00 0.00 0.00 4.92
2025 2390 0.035056 ACAACTATCTGTGCCCTGCC 60.035 55.000 0.00 0.00 0.00 4.85
2026 2391 1.826385 AACAACTATCTGTGCCCTGC 58.174 50.000 0.00 0.00 0.00 4.85
2027 2392 4.517285 ACATAACAACTATCTGTGCCCTG 58.483 43.478 0.00 0.00 0.00 4.45
2028 2393 4.844349 ACATAACAACTATCTGTGCCCT 57.156 40.909 0.00 0.00 0.00 5.19
2029 2394 5.424757 TGTACATAACAACTATCTGTGCCC 58.575 41.667 0.00 0.00 34.29 5.36
2101 2466 3.260888 TCAAACGGGATGGGGGCA 61.261 61.111 0.00 0.00 0.00 5.36
2102 2467 2.440247 CTCAAACGGGATGGGGGC 60.440 66.667 0.00 0.00 0.00 5.80
2283 2658 3.334691 GCTGGCACTTATTGACACTGTA 58.665 45.455 0.00 0.00 38.87 2.74
2345 2724 7.413330 ATTTCCTGGAAAAACAGCGAAGCAA 62.413 40.000 24.44 0.00 45.95 3.91
3124 3528 9.057089 ACTACAAACAGGTATGAGAAAAGAAAG 57.943 33.333 0.00 0.00 0.00 2.62
3209 3615 0.908910 TGGTGTTGGCGACCTATCAT 59.091 50.000 1.61 0.00 34.26 2.45
3487 3955 2.281517 TCGGGTAGTTGTGTTGTTGTG 58.718 47.619 0.00 0.00 0.00 3.33
3500 3968 6.039941 ACTTTCTCAAGATAGTCATCGGGTAG 59.960 42.308 0.00 0.00 32.16 3.18
3590 4058 9.050601 CCTCAAATTATAAACTCTCTGGCTAAG 57.949 37.037 0.00 0.00 0.00 2.18
4001 4476 4.278170 CACCACATAGGCAAGAAACAAGAA 59.722 41.667 0.00 0.00 43.14 2.52
4044 4519 7.329588 TGTGTGTGACATCTACGATAAGTAT 57.670 36.000 0.00 0.00 34.34 2.12
4097 4575 7.565323 AATAAGACCTGAAATCAGAAGCATC 57.435 36.000 11.94 2.26 46.59 3.91
4585 5141 2.678471 TTCCCTCCGTTCCGAAATAC 57.322 50.000 0.00 0.00 0.00 1.89
4593 5149 4.464597 AGATAGCAGATATTCCCTCCGTTC 59.535 45.833 0.00 0.00 0.00 3.95
4620 5176 8.099537 AGGTGGCATCATTAAATCTCTATGTAG 58.900 37.037 0.00 0.00 0.00 2.74
4637 5193 0.398381 AGGAGAGGAGAGGTGGCATC 60.398 60.000 0.00 0.00 0.00 3.91
5026 5816 0.868406 CAAGGACTGCGAAGGTGTTC 59.132 55.000 0.00 0.00 0.00 3.18
5089 5879 0.250467 CCAATCGGGGTCTGCTATGG 60.250 60.000 0.00 0.00 0.00 2.74
5090 5880 0.758734 TCCAATCGGGGTCTGCTATG 59.241 55.000 0.00 0.00 37.22 2.23
5099 5890 0.036765 TTTCTCGTGTCCAATCGGGG 60.037 55.000 0.00 0.00 37.22 5.73
5102 5893 2.080286 AGGTTTCTCGTGTCCAATCG 57.920 50.000 0.00 0.00 0.00 3.34
5124 6165 8.821686 TTTCTTTGCAATCCCATAGATAAAGA 57.178 30.769 0.00 0.00 36.19 2.52
5135 6176 3.256558 GCACAGATTTCTTTGCAATCCC 58.743 45.455 12.58 0.00 45.99 3.85
5314 6362 1.523258 CGGGCTGCTCTTGATCAGG 60.523 63.158 0.00 0.00 0.00 3.86
5366 6419 9.653287 CAAAGTTCTATCAACCTCACTACATTA 57.347 33.333 0.00 0.00 0.00 1.90
5367 6420 8.157476 ACAAAGTTCTATCAACCTCACTACATT 58.843 33.333 0.00 0.00 0.00 2.71
5368 6421 7.680730 ACAAAGTTCTATCAACCTCACTACAT 58.319 34.615 0.00 0.00 0.00 2.29
5369 6422 7.015292 AGACAAAGTTCTATCAACCTCACTACA 59.985 37.037 0.00 0.00 0.00 2.74
5378 6431 6.876257 AGACATCCAGACAAAGTTCTATCAAC 59.124 38.462 0.00 0.00 0.00 3.18
5392 6445 1.500474 TCCCATCCAGACATCCAGAC 58.500 55.000 0.00 0.00 0.00 3.51
5409 6499 8.410912 GGTATAACCACAAATAAACATCCTTCC 58.589 37.037 0.00 0.00 38.42 3.46
5445 6538 6.014070 TCCCTCTGTTAAATGCACAAGTACTA 60.014 38.462 0.00 0.00 0.00 1.82
5488 6583 6.183360 CGAAATTGCTATTCAGAGCTACAACA 60.183 38.462 0.00 0.00 43.27 3.33
5489 6584 6.036083 TCGAAATTGCTATTCAGAGCTACAAC 59.964 38.462 0.00 0.00 43.27 3.32
5490 6585 6.106003 TCGAAATTGCTATTCAGAGCTACAA 58.894 36.000 0.00 0.00 43.27 2.41
5504 6611 3.149196 ACATGAACACCTCGAAATTGCT 58.851 40.909 0.00 0.00 0.00 3.91
5512 6619 1.061131 GCATCGAACATGAACACCTCG 59.939 52.381 0.00 0.00 0.00 4.63
5531 6638 3.956744 AGAAATGGAAGACCCTACTTGC 58.043 45.455 0.00 0.00 38.40 4.01
5615 6743 0.033781 TTTTCCGACCGTGTGTAGGG 59.966 55.000 0.00 0.00 39.98 3.53
5628 6756 4.021981 AGCCCTTGATTCTTTTCTTTTCCG 60.022 41.667 0.00 0.00 0.00 4.30
5679 6807 2.094026 GGGCTTCAAAATGACATGGGAC 60.094 50.000 0.00 0.00 0.00 4.46
5707 6835 0.322997 TGGCCGTGGTTGGAAATAGG 60.323 55.000 0.00 0.00 0.00 2.57
5763 6891 3.708563 TCTTTTGCCTCCGTTTCAAAG 57.291 42.857 0.00 0.00 32.22 2.77
5872 7026 2.032528 CCAAAGCGGCAGTCTGGA 59.967 61.111 1.45 0.00 0.00 3.86
5881 7035 2.539274 CACAACATCAAAACCAAAGCGG 59.461 45.455 0.00 0.00 42.50 5.52
5885 7039 4.026744 TCCTCCACAACATCAAAACCAAA 58.973 39.130 0.00 0.00 0.00 3.28
5911 7065 6.274157 ACTCATTGTACACCTCTCTAACAG 57.726 41.667 0.00 0.00 0.00 3.16
5925 7079 7.966753 GTCGTAGAACTCATTGTACTCATTGTA 59.033 37.037 0.00 0.00 39.69 2.41
5926 7080 6.807230 GTCGTAGAACTCATTGTACTCATTGT 59.193 38.462 0.00 0.00 39.69 2.71
5928 7082 7.159322 AGTCGTAGAACTCATTGTACTCATT 57.841 36.000 0.00 0.00 39.69 2.57
5929 7083 6.761099 AGTCGTAGAACTCATTGTACTCAT 57.239 37.500 0.00 0.00 39.69 2.90
5931 7085 6.028987 GGAAGTCGTAGAACTCATTGTACTC 58.971 44.000 0.00 0.00 39.69 2.59
5934 7088 6.208007 TCAAGGAAGTCGTAGAACTCATTGTA 59.792 38.462 0.00 0.00 39.69 2.41
5935 7089 5.010719 TCAAGGAAGTCGTAGAACTCATTGT 59.989 40.000 0.00 0.00 39.69 2.71
5936 7090 5.346281 GTCAAGGAAGTCGTAGAACTCATTG 59.654 44.000 0.00 0.00 39.69 2.82
5939 7093 3.887110 TGTCAAGGAAGTCGTAGAACTCA 59.113 43.478 0.00 0.00 39.69 3.41
5940 7094 4.500603 TGTCAAGGAAGTCGTAGAACTC 57.499 45.455 0.00 0.00 39.69 3.01
5941 7095 4.931661 TTGTCAAGGAAGTCGTAGAACT 57.068 40.909 0.00 0.00 39.69 3.01
5942 7096 5.107065 CCATTTGTCAAGGAAGTCGTAGAAC 60.107 44.000 0.00 0.00 39.69 3.01
5943 7097 4.994852 CCATTTGTCAAGGAAGTCGTAGAA 59.005 41.667 0.00 0.00 39.69 2.10
5944 7098 4.282449 TCCATTTGTCAAGGAAGTCGTAGA 59.718 41.667 0.00 0.00 0.00 2.59
5945 7099 4.566004 TCCATTTGTCAAGGAAGTCGTAG 58.434 43.478 0.00 0.00 0.00 3.51
5946 7100 4.610605 TCCATTTGTCAAGGAAGTCGTA 57.389 40.909 0.00 0.00 0.00 3.43
5947 7101 3.485463 TCCATTTGTCAAGGAAGTCGT 57.515 42.857 0.00 0.00 0.00 4.34
5948 7102 3.753272 ACATCCATTTGTCAAGGAAGTCG 59.247 43.478 0.00 0.00 34.62 4.18
5949 7103 5.006386 AGACATCCATTTGTCAAGGAAGTC 58.994 41.667 16.04 16.04 46.81 3.01
5950 7104 4.990526 AGACATCCATTTGTCAAGGAAGT 58.009 39.130 7.28 2.35 46.81 3.01
5951 7105 6.656693 ACTTAGACATCCATTTGTCAAGGAAG 59.343 38.462 7.28 7.02 46.81 3.46
5952 7106 6.542821 ACTTAGACATCCATTTGTCAAGGAA 58.457 36.000 7.28 0.00 46.81 3.36
5954 7108 6.207417 ACAACTTAGACATCCATTTGTCAAGG 59.793 38.462 7.28 0.00 46.81 3.61
5957 7111 6.371548 GCTACAACTTAGACATCCATTTGTCA 59.628 38.462 7.28 0.00 46.81 3.58
5958 7112 6.183360 GGCTACAACTTAGACATCCATTTGTC 60.183 42.308 0.00 0.00 45.15 3.18
5959 7113 5.648092 GGCTACAACTTAGACATCCATTTGT 59.352 40.000 0.00 0.00 0.00 2.83
5960 7114 5.647658 TGGCTACAACTTAGACATCCATTTG 59.352 40.000 0.00 0.00 0.00 2.32
5961 7115 5.648092 GTGGCTACAACTTAGACATCCATTT 59.352 40.000 0.00 0.00 34.70 2.32
5962 7116 5.045578 AGTGGCTACAACTTAGACATCCATT 60.046 40.000 2.02 0.00 34.70 3.16
5963 7117 4.471386 AGTGGCTACAACTTAGACATCCAT 59.529 41.667 2.02 0.00 34.70 3.41
5964 7118 3.838317 AGTGGCTACAACTTAGACATCCA 59.162 43.478 2.02 0.00 34.70 3.41
5965 7119 4.434520 GAGTGGCTACAACTTAGACATCC 58.565 47.826 2.02 0.00 34.70 3.51
5970 7246 4.157246 TCAAGGAGTGGCTACAACTTAGA 58.843 43.478 2.02 4.47 0.00 2.10
5977 7253 2.420547 GCATGATCAAGGAGTGGCTACA 60.421 50.000 0.00 0.00 0.00 2.74
5998 7274 6.938030 TGTTGGTACACAATTAGTCTTTAGGG 59.062 38.462 0.00 0.00 41.95 3.53
6014 7290 4.164604 ACCTTTCCTACAAGTGTTGGTACA 59.835 41.667 10.98 0.00 40.89 2.90
6016 7292 4.445162 CCACCTTTCCTACAAGTGTTGGTA 60.445 45.833 10.98 0.15 40.89 3.25
6017 7293 3.551846 CACCTTTCCTACAAGTGTTGGT 58.448 45.455 10.98 0.00 40.89 3.67
6018 7294 2.884639 CCACCTTTCCTACAAGTGTTGG 59.115 50.000 5.66 5.66 41.33 3.77
6020 7296 3.201266 TGACCACCTTTCCTACAAGTGTT 59.799 43.478 0.00 0.00 0.00 3.32
6021 7297 2.775384 TGACCACCTTTCCTACAAGTGT 59.225 45.455 0.00 0.00 0.00 3.55
6022 7298 3.485463 TGACCACCTTTCCTACAAGTG 57.515 47.619 0.00 0.00 0.00 3.16
6023 7299 4.461198 CTTTGACCACCTTTCCTACAAGT 58.539 43.478 0.00 0.00 0.00 3.16
6024 7300 3.821033 CCTTTGACCACCTTTCCTACAAG 59.179 47.826 0.00 0.00 0.00 3.16
6025 7301 3.460340 TCCTTTGACCACCTTTCCTACAA 59.540 43.478 0.00 0.00 0.00 2.41
6026 7302 3.050089 TCCTTTGACCACCTTTCCTACA 58.950 45.455 0.00 0.00 0.00 2.74
6027 7303 3.782656 TCCTTTGACCACCTTTCCTAC 57.217 47.619 0.00 0.00 0.00 3.18
6028 7304 4.601857 AGAATCCTTTGACCACCTTTCCTA 59.398 41.667 0.00 0.00 0.00 2.94
6029 7305 3.399305 AGAATCCTTTGACCACCTTTCCT 59.601 43.478 0.00 0.00 0.00 3.36
6030 7306 3.767711 AGAATCCTTTGACCACCTTTCC 58.232 45.455 0.00 0.00 0.00 3.13
6031 7307 5.791336 AAAGAATCCTTTGACCACCTTTC 57.209 39.130 0.00 0.00 40.83 2.62
6043 7319 3.938963 TGAAAGCGCGATAAAGAATCCTT 59.061 39.130 12.10 0.00 0.00 3.36
6044 7320 3.531538 TGAAAGCGCGATAAAGAATCCT 58.468 40.909 12.10 0.00 0.00 3.24
6056 7332 2.069273 CTTATCCCCTATGAAAGCGCG 58.931 52.381 0.00 0.00 0.00 6.86
6063 7339 2.782922 TGTTGCCCTTATCCCCTATGA 58.217 47.619 0.00 0.00 0.00 2.15
6073 7349 3.513515 GGATGGTCAAATTGTTGCCCTTA 59.486 43.478 0.00 0.00 33.72 2.69
6076 7352 1.622811 TGGATGGTCAAATTGTTGCCC 59.377 47.619 0.00 0.00 33.14 5.36
6077 7353 2.687370 GTGGATGGTCAAATTGTTGCC 58.313 47.619 0.00 0.00 34.50 4.52
6129 7405 4.265893 TCGCTTATCCTGCCATACAAAAA 58.734 39.130 0.00 0.00 0.00 1.94
6135 7411 4.623932 ATTCTTCGCTTATCCTGCCATA 57.376 40.909 0.00 0.00 0.00 2.74
6140 7416 6.347725 CCGGATTAAATTCTTCGCTTATCCTG 60.348 42.308 0.00 0.00 0.00 3.86
6142 7418 5.699458 TCCGGATTAAATTCTTCGCTTATCC 59.301 40.000 0.00 0.00 0.00 2.59
6144 7420 6.522054 TCTCCGGATTAAATTCTTCGCTTAT 58.478 36.000 3.57 0.00 0.00 1.73
6145 7421 5.909477 TCTCCGGATTAAATTCTTCGCTTA 58.091 37.500 3.57 0.00 0.00 3.09
6162 7438 2.266055 GCTTGGACACCTCTCCGG 59.734 66.667 0.00 0.00 39.35 5.14
6163 7439 1.831652 AAGGCTTGGACACCTCTCCG 61.832 60.000 0.00 0.00 34.31 4.63
6164 7440 0.035915 GAAGGCTTGGACACCTCTCC 60.036 60.000 3.46 0.00 34.31 3.71
6171 7447 1.418637 ACGGTTTAGAAGGCTTGGACA 59.581 47.619 3.46 0.00 0.00 4.02
6173 7449 1.418637 ACACGGTTTAGAAGGCTTGGA 59.581 47.619 3.46 0.00 0.00 3.53
6174 7450 1.535462 CACACGGTTTAGAAGGCTTGG 59.465 52.381 3.46 0.00 0.00 3.61
6182 7458 1.338674 CCATGGAGCACACGGTTTAGA 60.339 52.381 5.56 0.00 0.00 2.10
6184 7460 0.322098 CCCATGGAGCACACGGTTTA 60.322 55.000 15.22 0.00 0.00 2.01
6191 7467 2.763215 GTTCCCCCATGGAGCACA 59.237 61.111 15.22 0.00 46.24 4.57
6197 7473 1.037030 CACCATTCGTTCCCCCATGG 61.037 60.000 4.14 4.14 41.85 3.66
6201 7477 2.046285 CAGCACCATTCGTTCCCCC 61.046 63.158 0.00 0.00 0.00 5.40
6204 7480 0.605319 TCCACAGCACCATTCGTTCC 60.605 55.000 0.00 0.00 0.00 3.62
6205 7481 1.234821 TTCCACAGCACCATTCGTTC 58.765 50.000 0.00 0.00 0.00 3.95
6241 7517 1.480954 TGGTTCCTACTCATCGGCTTC 59.519 52.381 0.00 0.00 0.00 3.86
6248 7524 3.231818 CCTACCGATGGTTCCTACTCAT 58.768 50.000 0.00 0.00 37.09 2.90
6249 7525 2.662866 CCTACCGATGGTTCCTACTCA 58.337 52.381 0.00 0.00 37.09 3.41
6256 7532 0.252197 AAGCACCCTACCGATGGTTC 59.748 55.000 0.00 0.00 37.09 3.62
6258 7534 1.623542 GGAAGCACCCTACCGATGGT 61.624 60.000 0.00 0.00 40.16 3.55
6263 7539 1.375523 GTGTGGAAGCACCCTACCG 60.376 63.158 0.00 0.00 38.00 4.02
6266 7542 1.423541 ACATTGTGTGGAAGCACCCTA 59.576 47.619 0.00 0.00 38.52 3.53
6267 7543 0.185901 ACATTGTGTGGAAGCACCCT 59.814 50.000 0.00 0.00 38.52 4.34
6269 7545 0.238289 CGACATTGTGTGGAAGCACC 59.762 55.000 0.00 0.00 38.52 5.01
6287 7563 2.217750 TCAATGTGGACACCAAAGACG 58.782 47.619 0.00 0.00 34.18 4.18
6293 7569 0.250858 CCAGCTCAATGTGGACACCA 60.251 55.000 0.00 0.00 35.67 4.17
6295 7571 1.808945 CTTCCAGCTCAATGTGGACAC 59.191 52.381 0.00 0.00 42.75 3.67
6296 7572 1.883638 GCTTCCAGCTCAATGTGGACA 60.884 52.381 0.00 0.00 42.75 4.02
6297 7573 0.807496 GCTTCCAGCTCAATGTGGAC 59.193 55.000 0.00 0.00 42.75 4.02
6324 7600 0.035739 TCGTTACTCTTTGGGCCACC 59.964 55.000 5.23 0.00 37.24 4.61


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

AutoCloner maintained by Alex Coulton.