Multiple sequence alignment - TraesCS2B01G152700

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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 TraesCS2B01G152700 chr2B 100.000 6310 0 0 1 6310 119635054 119628745 0.000000e+00 11653.0
1 TraesCS2B01G152700 chr2B 88.340 1235 106 24 1259 2473 456699990 456698774 0.000000e+00 1448.0
2 TraesCS2B01G152700 chr2B 88.097 1235 109 24 1259 2473 693044171 693042955 0.000000e+00 1432.0
3 TraesCS2B01G152700 chr2B 87.692 1235 114 23 1259 2473 123135742 123136958 0.000000e+00 1404.0
4 TraesCS2B01G152700 chr2B 83.680 913 84 33 1259 2154 14600497 14599633 0.000000e+00 800.0
5 TraesCS2B01G152700 chr2B 90.547 402 27 6 424 823 120533459 120533067 7.250000e-144 521.0
6 TraesCS2B01G152700 chr2B 87.855 387 29 10 900 1271 120182314 120181931 7.510000e-119 438.0
7 TraesCS2B01G152700 chr2B 87.958 382 28 10 1 379 120185210 120184844 9.710000e-118 435.0
8 TraesCS2B01G152700 chr2B 82.000 500 47 18 802 1271 120532573 120532087 9.920000e-103 385.0
9 TraesCS2B01G152700 chr2B 84.300 293 18 19 1 278 120533757 120533478 1.740000e-65 261.0
10 TraesCS2B01G152700 chr2B 84.360 211 18 9 666 874 120182509 120182312 6.460000e-45 193.0
11 TraesCS2B01G152700 chr2A 92.674 5160 230 76 852 5904 78560221 78565339 0.000000e+00 7299.0
12 TraesCS2B01G152700 chr2A 90.581 499 37 6 1984 2473 465363706 465363209 0.000000e+00 652.0
13 TraesCS2B01G152700 chr2A 85.739 568 48 20 17 552 78559408 78559974 2.550000e-158 569.0
14 TraesCS2B01G152700 chr2A 84.615 286 11 18 5944 6213 78565410 78565678 2.920000e-63 254.0
15 TraesCS2B01G152700 chr2A 84.397 141 18 3 3822 3962 777734432 777734296 1.100000e-27 135.0
16 TraesCS2B01G152700 chr2D 92.940 4235 176 51 1 4174 77384531 77380359 0.000000e+00 6050.0
17 TraesCS2B01G152700 chr2D 87.293 1873 123 60 4477 6268 77380167 77378329 0.000000e+00 2034.0
18 TraesCS2B01G152700 chr2D 82.105 475 37 25 21 478 77458406 77457963 4.650000e-96 363.0
19 TraesCS2B01G152700 chr2D 84.568 324 26 11 967 1269 78009152 78008832 3.700000e-77 300.0
20 TraesCS2B01G152700 chr2D 82.927 287 25 14 693 973 78010266 78009998 2.940000e-58 237.0
21 TraesCS2B01G152700 chr2D 86.294 197 18 6 194 386 102715198 102715007 8.290000e-49 206.0
22 TraesCS2B01G152700 chr2D 93.913 115 7 0 1074 1188 77449968 77449854 2.340000e-39 174.0
23 TraesCS2B01G152700 chr2D 96.907 97 3 0 1 97 77400634 77400538 5.060000e-36 163.0
24 TraesCS2B01G152700 chr2D 91.071 112 9 1 311 422 78010967 78010857 3.940000e-32 150.0
25 TraesCS2B01G152700 chr2D 96.226 53 2 0 1219 1271 77449852 77449800 3.130000e-13 87.9
26 TraesCS2B01G152700 chr2D 96.000 50 2 0 449 498 78010540 78010491 1.460000e-11 82.4
27 TraesCS2B01G152700 chr4D 90.114 1224 95 17 1259 2473 456261532 456260326 0.000000e+00 1567.0
28 TraesCS2B01G152700 chr7B 88.269 1236 105 25 1259 2473 25067212 25068428 0.000000e+00 1443.0
29 TraesCS2B01G152700 chr1B 87.692 1235 113 23 1259 2473 345335044 345336259 0.000000e+00 1402.0
30 TraesCS2B01G152700 chr1D 87.243 486 40 11 1261 1742 163479377 163479844 9.310000e-148 534.0
31 TraesCS2B01G152700 chr5A 83.688 141 19 3 3822 3962 48877891 48878027 5.130000e-26 130.0
32 TraesCS2B01G152700 chr4A 82.979 141 18 4 3822 3962 562399200 562399066 8.590000e-24 122.0
33 TraesCS2B01G152700 chr4B 76.966 178 38 3 3501 3677 172775223 172775398 1.450000e-16 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G152700 chr2B 119628745 119635054 6309 True 11653.000000 11653 100.000000 1 6310 1 chr2B.!!$R2 6309
1 TraesCS2B01G152700 chr2B 456698774 456699990 1216 True 1448.000000 1448 88.340000 1259 2473 1 chr2B.!!$R3 1214
2 TraesCS2B01G152700 chr2B 693042955 693044171 1216 True 1432.000000 1432 88.097000 1259 2473 1 chr2B.!!$R4 1214
3 TraesCS2B01G152700 chr2B 123135742 123136958 1216 False 1404.000000 1404 87.692000 1259 2473 1 chr2B.!!$F1 1214
4 TraesCS2B01G152700 chr2B 14599633 14600497 864 True 800.000000 800 83.680000 1259 2154 1 chr2B.!!$R1 895
5 TraesCS2B01G152700 chr2B 120532087 120533757 1670 True 389.000000 521 85.615667 1 1271 3 chr2B.!!$R6 1270
6 TraesCS2B01G152700 chr2B 120181931 120185210 3279 True 355.333333 438 86.724333 1 1271 3 chr2B.!!$R5 1270
7 TraesCS2B01G152700 chr2A 78559408 78565678 6270 False 2707.333333 7299 87.676000 17 6213 3 chr2A.!!$F1 6196
8 TraesCS2B01G152700 chr2D 77378329 77384531 6202 True 4042.000000 6050 90.116500 1 6268 2 chr2D.!!$R4 6267
9 TraesCS2B01G152700 chr4D 456260326 456261532 1206 True 1567.000000 1567 90.114000 1259 2473 1 chr4D.!!$R1 1214
10 TraesCS2B01G152700 chr7B 25067212 25068428 1216 False 1443.000000 1443 88.269000 1259 2473 1 chr7B.!!$F1 1214
11 TraesCS2B01G152700 chr1B 345335044 345336259 1215 False 1402.000000 1402 87.692000 1259 2473 1 chr1B.!!$F1 1214

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
140 162 0.106719 CTTCCCACCACACACAACCT 60.107 55.000 0.00 0.00 0.00 3.50 F
583 2702 0.167470 CAAGACCTGTCTGCAATGCG 59.833 55.000 0.00 0.00 40.36 4.73 F
844 3516 0.182775 ACAAAGCGGAAAGACACCCT 59.817 50.000 0.00 0.00 0.00 4.34 F
845 3517 1.318576 CAAAGCGGAAAGACACCCTT 58.681 50.000 0.00 0.00 36.47 3.95 F
1568 4327 1.611261 CGGGGACACCTACAAGGGA 60.611 63.158 0.00 0.00 40.58 4.20 F
2959 5774 0.329596 ATCTTCCTTCTGGTGCCACC 59.670 55.000 7.01 7.01 39.22 4.61 F
3048 5863 2.224257 TGCTGCTGACTACATGTTGTCA 60.224 45.455 31.65 31.65 41.58 3.58 F
4659 7501 2.028748 ACGGTTTTATGTGCTACTCCGT 60.029 45.455 0.00 0.00 43.87 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 4327 0.842030 TGAGGTTCATGGACCAGGCT 60.842 55.000 25.54 3.89 42.35 4.58 R
1867 4633 0.957395 CTTCTGCTGGACAATGCCGT 60.957 55.000 0.00 0.00 0.00 5.68 R
2135 4913 1.552792 TCCACAATGTCGCAGGTGATA 59.447 47.619 12.55 0.00 33.16 2.15 R
2534 5330 2.478539 GCATGATTCGAAGCAAACCCTC 60.479 50.000 21.22 2.00 0.00 4.30 R
3365 6188 0.097674 CCTTCTTCTGATTTGCGCCG 59.902 55.000 4.18 0.00 0.00 6.46 R
4148 6977 0.108377 TGCATTCCACTACGACGCAT 60.108 50.000 0.00 0.00 0.00 4.73 R
4823 7674 0.403655 TTGCAGGCATACTTGTCCCA 59.596 50.000 0.00 0.00 0.00 4.37 R
5619 8504 0.539051 AGGCATCACTACCAGTCTGC 59.461 55.000 0.00 3.05 34.74 4.26 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
123 134 2.975536 GCACCATGCCATGCACTT 59.024 55.556 0.00 0.00 43.04 3.16
129 151 1.683365 ATGCCATGCACTTCCCACC 60.683 57.895 0.00 0.00 43.04 4.61
130 152 2.283101 GCCATGCACTTCCCACCA 60.283 61.111 0.00 0.00 0.00 4.17
131 153 2.639327 GCCATGCACTTCCCACCAC 61.639 63.158 0.00 0.00 0.00 4.16
132 154 1.228521 CCATGCACTTCCCACCACA 60.229 57.895 0.00 0.00 0.00 4.17
133 155 1.526575 CCATGCACTTCCCACCACAC 61.527 60.000 0.00 0.00 0.00 3.82
134 156 0.822944 CATGCACTTCCCACCACACA 60.823 55.000 0.00 0.00 0.00 3.72
135 157 0.823356 ATGCACTTCCCACCACACAC 60.823 55.000 0.00 0.00 0.00 3.82
136 158 1.453015 GCACTTCCCACCACACACA 60.453 57.895 0.00 0.00 0.00 3.72
140 162 0.106719 CTTCCCACCACACACAACCT 60.107 55.000 0.00 0.00 0.00 3.50
193 216 8.807118 TGTCAAGTAAACTGACATTCTCTCTAT 58.193 33.333 1.63 0.00 37.61 1.98
270 297 2.509336 GCCACGTCGTCATGGGAG 60.509 66.667 0.00 0.00 36.41 4.30
273 300 0.744874 CCACGTCGTCATGGGAGTAT 59.255 55.000 0.00 0.00 31.83 2.12
322 352 1.691976 TGGCTTACTACTGTGCAGTGT 59.308 47.619 14.44 12.11 42.52 3.55
344 378 6.365518 GTGTAAACCTAGGAGAAAGAAAGACG 59.634 42.308 17.98 0.00 0.00 4.18
537 2656 1.599518 CAAGCACCCGCACTAACCA 60.600 57.895 0.00 0.00 42.27 3.67
583 2702 0.167470 CAAGACCTGTCTGCAATGCG 59.833 55.000 0.00 0.00 40.36 4.73
596 2715 4.823442 TCTGCAATGCGAGGATTAAATCAT 59.177 37.500 0.00 0.00 0.00 2.45
842 3514 2.863401 AAACAAAGCGGAAAGACACC 57.137 45.000 0.00 0.00 0.00 4.16
844 3516 0.182775 ACAAAGCGGAAAGACACCCT 59.817 50.000 0.00 0.00 0.00 4.34
845 3517 1.318576 CAAAGCGGAAAGACACCCTT 58.681 50.000 0.00 0.00 36.47 3.95
963 3678 2.618053 CGTGTGTCTCCATTAACTCCC 58.382 52.381 0.00 0.00 0.00 4.30
1308 4051 4.735132 ACGATGCCGACCACCACG 62.735 66.667 0.00 0.00 39.50 4.94
1408 4161 1.833787 GCCGGGAAGTACCTGTGGAA 61.834 60.000 2.18 0.00 43.20 3.53
1568 4327 1.611261 CGGGGACACCTACAAGGGA 60.611 63.158 0.00 0.00 40.58 4.20
1859 4625 2.496817 GGCTTCTGGACGCGAGAT 59.503 61.111 15.93 0.00 0.00 2.75
1867 4633 4.467084 GACGCGAGATGGCCCCAA 62.467 66.667 15.93 0.00 0.00 4.12
2439 5231 3.481453 TGGTTGTGGAATTCGATCAACA 58.519 40.909 25.32 11.23 39.71 3.33
2465 5257 6.295039 AGAAATTTGCATTTGCTTTCAGTG 57.705 33.333 14.38 0.00 42.66 3.66
2480 5272 2.083774 TCAGTGCCTTTGCCGATTTAG 58.916 47.619 0.00 0.00 36.33 1.85
2487 5279 3.191791 GCCTTTGCCGATTTAGTTACCAA 59.808 43.478 0.00 0.00 0.00 3.67
2534 5330 4.223032 ACCCTGTCAGTGGTGAATTAGTAG 59.777 45.833 11.06 0.00 33.27 2.57
2564 5360 4.273235 TGCTTCGAATCATGCAATCGTTAT 59.727 37.500 7.29 0.00 37.79 1.89
2565 5361 5.207768 GCTTCGAATCATGCAATCGTTATT 58.792 37.500 0.00 0.00 37.79 1.40
2566 5362 6.018343 TGCTTCGAATCATGCAATCGTTATTA 60.018 34.615 7.29 0.00 37.79 0.98
2616 5412 1.778334 TCCGATTTCGATACATGGCG 58.222 50.000 0.67 0.00 43.02 5.69
2955 5770 4.142609 TGATGTATCTTCCTTCTGGTGC 57.857 45.455 0.00 0.00 34.23 5.01
2959 5774 0.329596 ATCTTCCTTCTGGTGCCACC 59.670 55.000 7.01 7.01 39.22 4.61
2991 5806 2.964464 ACATGCCATTTGTTCTGAACCA 59.036 40.909 17.26 4.09 0.00 3.67
2994 5809 3.791245 TGCCATTTGTTCTGAACCAAAC 58.209 40.909 17.26 7.90 0.00 2.93
3048 5863 2.224257 TGCTGCTGACTACATGTTGTCA 60.224 45.455 31.65 31.65 41.58 3.58
3144 5959 4.036567 TGACCGGTACATGATAAAGACG 57.963 45.455 7.34 0.00 0.00 4.18
3201 6017 2.429250 GTTCCCTCTGTCTCTAGGCTTC 59.571 54.545 0.00 0.00 0.00 3.86
3311 6134 2.760634 ACTACAATCATGTCCGTGCA 57.239 45.000 0.00 0.00 41.05 4.57
3365 6188 4.392138 GGTCTACATTGTGTCAAGTTAGCC 59.608 45.833 0.00 0.00 0.00 3.93
3483 6312 6.873076 TCATTATGGCCAATGTTCAAAACTTC 59.127 34.615 10.96 0.00 37.23 3.01
3583 6412 5.784177 TCTATCCATAGGCGTTTTGATCTC 58.216 41.667 0.00 0.00 0.00 2.75
3667 6496 8.160106 ACAACTCTGAAAGACCTTGATCTAAAT 58.840 33.333 0.00 0.00 38.67 1.40
3918 6747 6.747414 TTAGGCATAATGGAGAGAAGCTTA 57.253 37.500 0.00 0.00 0.00 3.09
3938 6767 3.593442 ATGACTGAAGGTTGGTTGGAA 57.407 42.857 0.00 0.00 0.00 3.53
3945 6774 2.721425 AGGTTGGTTGGAAAACTCGA 57.279 45.000 0.00 0.00 32.01 4.04
3951 6780 3.349022 TGGTTGGAAAACTCGAAACACT 58.651 40.909 0.00 0.00 32.01 3.55
4012 6841 8.850007 TTATACCTTACAATGTGCACTGTTTA 57.150 30.769 19.41 6.07 0.00 2.01
4026 6855 4.209080 GCACTGTTTAATTGAAGGTTGCAC 59.791 41.667 0.00 0.00 0.00 4.57
4027 6856 5.591099 CACTGTTTAATTGAAGGTTGCACT 58.409 37.500 0.00 0.00 0.00 4.40
4044 6873 3.752747 TGCACTGACAATGATACCAACAG 59.247 43.478 0.00 0.00 0.00 3.16
4045 6874 3.753272 GCACTGACAATGATACCAACAGT 59.247 43.478 0.00 0.00 37.56 3.55
4124 6953 8.504005 CAAATGGGTAAGCTAGATATTTTACCG 58.496 37.037 0.00 0.00 43.74 4.02
4148 6977 6.517697 CGCCCTTATCTGTTATACCATGTACA 60.518 42.308 0.00 0.00 0.00 2.90
4150 6979 7.334421 GCCCTTATCTGTTATACCATGTACATG 59.666 40.741 26.02 26.02 38.51 3.21
4221 7050 6.966534 ATCTCTTTGTTTGATCCTTGTGTT 57.033 33.333 0.00 0.00 0.00 3.32
4295 7124 3.017048 TCGAGCCATTTTTCATGGGAT 57.983 42.857 3.07 0.00 39.53 3.85
4385 7214 8.673626 TCTTTCTTAAGCAGCATTTTAATTCG 57.326 30.769 0.00 0.00 0.00 3.34
4397 7226 6.742718 AGCATTTTAATTCGAATGAGAACACG 59.257 34.615 12.25 0.05 35.74 4.49
4405 7234 2.337644 CGAATGAGAACACGTCGTGTAC 59.662 50.000 29.79 22.41 46.79 2.90
4449 7278 7.921786 TGATAAGTCAACTGGTCCTTTAATG 57.078 36.000 0.00 0.00 0.00 1.90
4547 7376 8.786898 TCTTCTGTGACCTATTCAATTTCAAAG 58.213 33.333 0.00 0.00 35.39 2.77
4653 7495 6.874664 TGTCTTTGATACGGTTTTATGTGCTA 59.125 34.615 0.00 0.00 0.00 3.49
4654 7496 7.148540 TGTCTTTGATACGGTTTTATGTGCTAC 60.149 37.037 0.00 0.00 0.00 3.58
4655 7497 7.064253 GTCTTTGATACGGTTTTATGTGCTACT 59.936 37.037 0.00 0.00 0.00 2.57
4656 7498 6.897259 TTGATACGGTTTTATGTGCTACTC 57.103 37.500 0.00 0.00 0.00 2.59
4657 7499 5.353938 TGATACGGTTTTATGTGCTACTCC 58.646 41.667 0.00 0.00 0.00 3.85
4658 7500 2.613691 ACGGTTTTATGTGCTACTCCG 58.386 47.619 0.00 0.00 41.95 4.63
4659 7501 2.028748 ACGGTTTTATGTGCTACTCCGT 60.029 45.455 0.00 0.00 43.87 4.69
4660 7502 3.193267 ACGGTTTTATGTGCTACTCCGTA 59.807 43.478 4.13 0.00 46.15 4.02
4693 7541 6.260271 GCTGAACAGTAGGTTGTAAATATCCC 59.740 42.308 3.77 0.00 40.63 3.85
4701 7549 8.174757 AGTAGGTTGTAAATATCCCCAAAACTT 58.825 33.333 0.00 0.00 0.00 2.66
4949 7800 9.429359 CTGTATTTTGGGATCATAGACATACTC 57.571 37.037 0.00 0.00 0.00 2.59
4988 7839 1.755179 AAAGGCTTGAGCATGCGTAT 58.245 45.000 13.01 0.00 44.36 3.06
5042 7893 1.133976 GCAGTGGATCCAAGGCAGTAT 60.134 52.381 26.08 2.13 0.00 2.12
5045 7896 2.173569 AGTGGATCCAAGGCAGTATTCC 59.826 50.000 18.20 0.00 0.00 3.01
5190 8044 2.345991 GCACAGCGAAGTGGGGTA 59.654 61.111 9.29 0.00 39.87 3.69
5191 8045 1.078426 GCACAGCGAAGTGGGGTAT 60.078 57.895 9.29 0.00 39.87 2.73
5216 8082 3.367025 CCGTCGATTTTCAGTACAAGGAC 59.633 47.826 0.00 0.00 0.00 3.85
5226 8093 0.677842 GTACAAGGACGGGTGAGTGT 59.322 55.000 0.00 0.00 0.00 3.55
5236 8103 1.227943 GGTGAGTGTGGCTTCAGCA 60.228 57.895 0.30 0.00 44.36 4.41
5299 8171 5.275788 CGGCTCTCGCGTAAATATAAATAGC 60.276 44.000 5.77 0.00 36.88 2.97
5392 8264 8.547967 TGGAGATGTTAACTTAGTGATTCAAC 57.452 34.615 7.22 0.00 0.00 3.18
5548 8431 3.727726 CTTGTCGACATACATGCCCATA 58.272 45.455 20.80 0.00 0.00 2.74
5571 8454 3.659183 AGGGACATCCTTGGATTTCTG 57.341 47.619 13.49 2.00 45.47 3.02
5572 8455 2.922283 AGGGACATCCTTGGATTTCTGT 59.078 45.455 13.49 4.89 45.47 3.41
5573 8456 3.054065 AGGGACATCCTTGGATTTCTGTC 60.054 47.826 13.49 12.16 45.47 3.51
5574 8457 3.054065 GGGACATCCTTGGATTTCTGTCT 60.054 47.826 16.11 0.00 34.77 3.41
5575 8458 4.195416 GGACATCCTTGGATTTCTGTCTC 58.805 47.826 16.11 7.16 34.77 3.36
5577 8460 3.588842 ACATCCTTGGATTTCTGTCTCCA 59.411 43.478 0.00 0.00 39.78 3.86
5580 8463 3.588842 TCCTTGGATTTCTGTCTCCACAT 59.411 43.478 0.00 0.00 41.20 3.21
5596 8481 7.148000 TGTCTCCACATTTGTACATTGTTTTCA 60.148 33.333 8.76 3.74 0.00 2.69
5611 8496 0.469144 TTTCAGTTTGGGACCTGGCC 60.469 55.000 0.00 0.00 0.00 5.36
5673 8563 3.359033 CTTTTCCTGGGCTGAATGATCA 58.641 45.455 0.00 0.00 0.00 2.92
5682 8572 2.034305 GGCTGAATGATCATGTCTTGGC 59.966 50.000 9.46 12.99 34.37 4.52
5904 8804 3.560481 GCCATGAGAGTGACAGATTCATG 59.440 47.826 12.66 12.66 42.84 3.07
5905 8805 4.767478 CCATGAGAGTGACAGATTCATGT 58.233 43.478 16.00 0.00 42.07 3.21
5906 8806 5.183969 CCATGAGAGTGACAGATTCATGTT 58.816 41.667 16.00 0.00 42.07 2.71
5907 8807 5.646793 CCATGAGAGTGACAGATTCATGTTT 59.353 40.000 16.00 0.00 42.07 2.83
5910 8810 8.724229 CATGAGAGTGACAGATTCATGTTTTAA 58.276 33.333 11.88 0.00 39.96 1.52
5912 8812 7.173218 TGAGAGTGACAGATTCATGTTTTAACC 59.827 37.037 0.00 0.00 36.32 2.85
5914 8814 7.173907 AGAGTGACAGATTCATGTTTTAACCTG 59.826 37.037 0.00 0.00 36.32 4.00
5915 8815 5.858581 GTGACAGATTCATGTTTTAACCTGC 59.141 40.000 0.00 0.00 36.32 4.85
5916 8816 5.534278 TGACAGATTCATGTTTTAACCTGCA 59.466 36.000 0.00 0.00 32.25 4.41
5917 8817 6.017400 ACAGATTCATGTTTTAACCTGCAG 57.983 37.500 6.78 6.78 0.00 4.41
5919 8819 6.714810 ACAGATTCATGTTTTAACCTGCAGTA 59.285 34.615 13.81 0.00 0.00 2.74
5922 8822 8.100791 AGATTCATGTTTTAACCTGCAGTAGTA 58.899 33.333 13.81 0.00 0.00 1.82
5923 8823 7.667043 TTCATGTTTTAACCTGCAGTAGTAG 57.333 36.000 13.81 0.00 0.00 2.57
5924 8824 5.642063 TCATGTTTTAACCTGCAGTAGTAGC 59.358 40.000 13.81 0.00 0.00 3.58
5925 8825 4.963373 TGTTTTAACCTGCAGTAGTAGCA 58.037 39.130 13.81 0.59 40.19 3.49
5932 8832 2.879002 TGCAGTAGTAGCAGATGAGC 57.121 50.000 0.00 0.00 37.02 4.26
5933 8833 2.102578 TGCAGTAGTAGCAGATGAGCA 58.897 47.619 0.00 0.00 37.02 4.26
5935 8835 3.058450 GCAGTAGTAGCAGATGAGCATG 58.942 50.000 0.00 0.00 36.85 4.06
5936 8836 3.492309 GCAGTAGTAGCAGATGAGCATGT 60.492 47.826 0.00 0.00 36.85 3.21
5938 8838 5.459768 CAGTAGTAGCAGATGAGCATGTAG 58.540 45.833 0.00 0.00 36.85 2.74
5966 8897 5.546621 ACTAGAAGGAACTGCAACAGTAA 57.453 39.130 0.00 0.00 44.62 2.24
5967 8898 6.115448 ACTAGAAGGAACTGCAACAGTAAT 57.885 37.500 0.00 0.00 44.62 1.89
5968 8899 7.241042 ACTAGAAGGAACTGCAACAGTAATA 57.759 36.000 0.00 0.00 44.62 0.98
5969 8900 7.852263 ACTAGAAGGAACTGCAACAGTAATAT 58.148 34.615 0.00 0.00 44.62 1.28
5970 8901 7.982354 ACTAGAAGGAACTGCAACAGTAATATC 59.018 37.037 0.00 0.00 44.62 1.63
5971 8902 6.951971 AGAAGGAACTGCAACAGTAATATCT 58.048 36.000 0.00 1.30 44.62 1.98
5972 8903 6.820656 AGAAGGAACTGCAACAGTAATATCTG 59.179 38.462 0.00 0.00 44.62 2.90
5973 8904 6.299805 AGGAACTGCAACAGTAATATCTGA 57.700 37.500 0.00 0.00 44.62 3.27
5974 8905 6.893583 AGGAACTGCAACAGTAATATCTGAT 58.106 36.000 0.00 0.00 44.62 2.90
5977 8912 7.254590 GGAACTGCAACAGTAATATCTGATCAC 60.255 40.741 0.00 0.00 44.62 3.06
5986 8921 8.144478 ACAGTAATATCTGATCACCACATGTAC 58.856 37.037 0.00 0.00 38.63 2.90
6131 9066 2.009774 GTTTGATACGCATGTCTGCCT 58.990 47.619 0.00 0.00 46.07 4.75
6132 9067 1.655484 TTGATACGCATGTCTGCCTG 58.345 50.000 0.00 0.00 46.07 4.85
6133 9068 0.811219 TGATACGCATGTCTGCCTGC 60.811 55.000 0.00 0.00 46.07 4.85
6134 9069 1.502163 GATACGCATGTCTGCCTGCC 61.502 60.000 0.00 0.00 46.07 4.85
6135 9070 1.976132 ATACGCATGTCTGCCTGCCT 61.976 55.000 0.00 0.00 46.07 4.75
6136 9071 2.857575 TACGCATGTCTGCCTGCCTG 62.858 60.000 0.00 0.00 46.07 4.85
6137 9072 2.045634 GCATGTCTGCCTGCCTGA 60.046 61.111 0.00 0.00 42.88 3.86
6138 9073 2.404995 GCATGTCTGCCTGCCTGAC 61.405 63.158 0.00 5.72 42.88 3.51
6149 9084 1.575576 CTGCCTGACTGACTGCTTGC 61.576 60.000 0.00 0.00 0.00 4.01
6223 9175 0.752743 TTTCACCTTGTGCTGCTGCT 60.753 50.000 17.00 0.00 40.48 4.24
6224 9176 1.449726 TTCACCTTGTGCTGCTGCTG 61.450 55.000 17.00 0.77 40.48 4.41
6225 9177 3.292936 ACCTTGTGCTGCTGCTGC 61.293 61.111 22.51 22.51 40.48 5.25
6233 9185 4.415332 CTGCTGCTGCGCCTTTGG 62.415 66.667 4.18 0.00 43.34 3.28
6240 9192 2.032528 TGCGCCTTTGGTCTGGAG 59.967 61.111 4.18 0.00 0.00 3.86
6241 9193 3.435186 GCGCCTTTGGTCTGGAGC 61.435 66.667 0.00 0.00 41.45 4.70
6242 9194 2.747855 CGCCTTTGGTCTGGAGCC 60.748 66.667 0.00 0.00 0.00 4.70
6258 9210 1.869767 GAGCCTAGCAATGATTGGACG 59.130 52.381 7.35 0.00 0.00 4.79
6268 9220 3.713826 ATGATTGGACGGTGTTAGGTT 57.286 42.857 0.00 0.00 0.00 3.50
6269 9221 4.829872 ATGATTGGACGGTGTTAGGTTA 57.170 40.909 0.00 0.00 0.00 2.85
6270 9222 4.196626 TGATTGGACGGTGTTAGGTTAG 57.803 45.455 0.00 0.00 0.00 2.34
6271 9223 3.055675 TGATTGGACGGTGTTAGGTTAGG 60.056 47.826 0.00 0.00 0.00 2.69
6272 9224 0.609662 TGGACGGTGTTAGGTTAGGC 59.390 55.000 0.00 0.00 0.00 3.93
6273 9225 0.107993 GGACGGTGTTAGGTTAGGCC 60.108 60.000 0.00 0.00 37.58 5.19
6274 9226 0.107993 GACGGTGTTAGGTTAGGCCC 60.108 60.000 0.00 0.00 38.26 5.80
6275 9227 1.153509 CGGTGTTAGGTTAGGCCCG 60.154 63.158 0.00 0.00 38.26 6.13
6276 9228 1.222661 GGTGTTAGGTTAGGCCCGG 59.777 63.158 0.00 0.00 38.26 5.73
6277 9229 1.450848 GTGTTAGGTTAGGCCCGGC 60.451 63.158 0.00 0.00 38.26 6.13
6278 9230 2.202974 GTTAGGTTAGGCCCGGCG 60.203 66.667 0.00 0.00 38.26 6.46
6279 9231 2.684655 TTAGGTTAGGCCCGGCGT 60.685 61.111 10.00 10.00 38.26 5.68
6280 9232 2.292559 TTAGGTTAGGCCCGGCGTT 61.293 57.895 10.44 0.00 38.26 4.84
6281 9233 2.524951 TTAGGTTAGGCCCGGCGTTG 62.525 60.000 10.44 0.00 38.26 4.10
6282 9234 4.397832 GGTTAGGCCCGGCGTTGA 62.398 66.667 10.44 0.00 0.00 3.18
6283 9235 2.358984 GTTAGGCCCGGCGTTGAA 60.359 61.111 10.44 0.00 0.00 2.69
6284 9236 2.046700 TTAGGCCCGGCGTTGAAG 60.047 61.111 10.44 0.00 0.00 3.02
6285 9237 4.770874 TAGGCCCGGCGTTGAAGC 62.771 66.667 10.44 0.02 0.00 3.86
6288 9240 3.670377 GCCCGGCGTTGAAGCTTT 61.670 61.111 6.01 0.00 37.29 3.51
6289 9241 2.255252 CCCGGCGTTGAAGCTTTG 59.745 61.111 6.01 0.00 37.29 2.77
6290 9242 2.551912 CCCGGCGTTGAAGCTTTGT 61.552 57.895 6.01 0.00 37.29 2.83
6291 9243 1.358759 CCGGCGTTGAAGCTTTGTT 59.641 52.632 6.01 0.00 37.29 2.83
6292 9244 0.934436 CCGGCGTTGAAGCTTTGTTG 60.934 55.000 6.01 0.00 37.29 3.33
6293 9245 1.539776 CGGCGTTGAAGCTTTGTTGC 61.540 55.000 0.00 3.19 37.29 4.17
6294 9246 1.215014 GGCGTTGAAGCTTTGTTGCC 61.215 55.000 15.06 15.06 37.29 4.52
6295 9247 1.539776 GCGTTGAAGCTTTGTTGCCG 61.540 55.000 0.00 0.00 0.00 5.69
6296 9248 1.539776 CGTTGAAGCTTTGTTGCCGC 61.540 55.000 0.00 0.00 0.00 6.53
6297 9249 1.067250 TTGAAGCTTTGTTGCCGCC 59.933 52.632 0.00 0.00 0.00 6.13
6298 9250 2.049156 GAAGCTTTGTTGCCGCCC 60.049 61.111 0.00 0.00 0.00 6.13
6299 9251 2.837291 AAGCTTTGTTGCCGCCCA 60.837 55.556 0.00 0.00 0.00 5.36
6300 9252 2.158561 GAAGCTTTGTTGCCGCCCAT 62.159 55.000 0.00 0.00 0.00 4.00
6301 9253 0.897863 AAGCTTTGTTGCCGCCCATA 60.898 50.000 0.00 0.00 0.00 2.74
6302 9254 1.153842 GCTTTGTTGCCGCCCATAC 60.154 57.895 0.00 0.00 0.00 2.39
6303 9255 1.136565 CTTTGTTGCCGCCCATACG 59.863 57.895 0.00 0.00 0.00 3.06
6304 9256 2.865669 CTTTGTTGCCGCCCATACGC 62.866 60.000 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 133 0.106918 GAGGTTGTGTGTGGTGGGAA 60.107 55.000 0.00 0.00 0.00 3.97
123 134 1.275421 TGAGGTTGTGTGTGGTGGGA 61.275 55.000 0.00 0.00 0.00 4.37
129 151 1.330521 CTCCGTTTGAGGTTGTGTGTG 59.669 52.381 0.00 0.00 37.45 3.82
130 152 1.663695 CTCCGTTTGAGGTTGTGTGT 58.336 50.000 0.00 0.00 37.45 3.72
140 162 0.603707 CTCTTGCAGCCTCCGTTTGA 60.604 55.000 0.00 0.00 0.00 2.69
212 235 8.873830 ACACGAATCAGTTTGATAGATTACTTG 58.126 33.333 0.00 0.00 35.76 3.16
214 237 8.873830 CAACACGAATCAGTTTGATAGATTACT 58.126 33.333 0.00 0.00 35.76 2.24
215 238 7.636359 GCAACACGAATCAGTTTGATAGATTAC 59.364 37.037 0.00 0.00 35.76 1.89
219 242 4.994217 TGCAACACGAATCAGTTTGATAGA 59.006 37.500 0.00 0.00 35.76 1.98
220 243 5.082059 GTGCAACACGAATCAGTTTGATAG 58.918 41.667 0.00 0.00 34.07 2.08
221 244 4.754618 AGTGCAACACGAATCAGTTTGATA 59.245 37.500 0.00 0.00 41.43 2.15
270 297 4.430007 TCAGCAGGAAACATACGACATAC 58.570 43.478 0.00 0.00 0.00 2.39
273 300 3.056179 TCATCAGCAGGAAACATACGACA 60.056 43.478 0.00 0.00 0.00 4.35
322 352 6.071503 CCTCGTCTTTCTTTCTCCTAGGTTTA 60.072 42.308 9.08 0.00 0.00 2.01
344 378 1.694133 CCCATGAGCCTCCTGTCCTC 61.694 65.000 0.00 0.00 0.00 3.71
537 2656 2.624364 GGTTATTGTGGTGGTTTTCGGT 59.376 45.455 0.00 0.00 0.00 4.69
583 2702 3.823304 GCCCTGGTGATGATTTAATCCTC 59.177 47.826 2.22 3.07 0.00 3.71
684 2836 6.592798 TGGTTCTTGTCTGTTTTACTTACG 57.407 37.500 0.00 0.00 0.00 3.18
687 2839 7.123547 TGGATTTGGTTCTTGTCTGTTTTACTT 59.876 33.333 0.00 0.00 0.00 2.24
689 2841 6.801575 TGGATTTGGTTCTTGTCTGTTTTAC 58.198 36.000 0.00 0.00 0.00 2.01
719 2872 4.457949 GGCCTCCGTTCTTCATTCTAAAAA 59.542 41.667 0.00 0.00 0.00 1.94
730 2883 1.079127 CGTGATGGCCTCCGTTCTT 60.079 57.895 3.32 0.00 0.00 2.52
842 3514 1.852626 ACAGGGGAGGTGGGAAAGG 60.853 63.158 0.00 0.00 0.00 3.11
844 3516 0.402861 AAGACAGGGGAGGTGGGAAA 60.403 55.000 0.00 0.00 0.00 3.13
845 3517 0.840722 GAAGACAGGGGAGGTGGGAA 60.841 60.000 0.00 0.00 0.00 3.97
846 3518 1.229529 GAAGACAGGGGAGGTGGGA 60.230 63.158 0.00 0.00 0.00 4.37
850 3522 0.193574 TGGAAGAAGACAGGGGAGGT 59.806 55.000 0.00 0.00 0.00 3.85
896 3590 0.890683 AAGAAATGCGCTTTGGGAGG 59.109 50.000 9.73 0.00 0.00 4.30
963 3678 2.280186 GAGGCGGGTAATGGCGAG 60.280 66.667 0.00 0.00 36.92 5.03
1308 4051 2.467826 CGACGTACTCCTCCGGACC 61.468 68.421 0.00 0.00 0.00 4.46
1312 4055 2.708255 GCTCGACGTACTCCTCCG 59.292 66.667 0.00 0.00 0.00 4.63
1408 4161 1.945354 CTCGTACATGCACCCGTCCT 61.945 60.000 0.00 0.00 0.00 3.85
1568 4327 0.842030 TGAGGTTCATGGACCAGGCT 60.842 55.000 25.54 3.89 42.35 4.58
1867 4633 0.957395 CTTCTGCTGGACAATGCCGT 60.957 55.000 0.00 0.00 0.00 5.68
1945 4723 1.745489 GGCAATTCCCTCGCGAACT 60.745 57.895 11.33 0.00 0.00 3.01
2135 4913 1.552792 TCCACAATGTCGCAGGTGATA 59.447 47.619 12.55 0.00 33.16 2.15
2439 5231 5.613329 TGAAAGCAAATGCAAATTTCTCCT 58.387 33.333 8.28 0.00 45.16 3.69
2465 5257 2.750712 TGGTAACTAAATCGGCAAAGGC 59.249 45.455 0.00 0.00 36.93 4.35
2480 5272 7.514721 TGTATCCCCTAATTCAGATTGGTAAC 58.485 38.462 0.00 0.00 0.00 2.50
2487 5279 9.047947 GGTAATACTGTATCCCCTAATTCAGAT 57.952 37.037 0.00 0.00 30.92 2.90
2534 5330 2.478539 GCATGATTCGAAGCAAACCCTC 60.479 50.000 21.22 2.00 0.00 4.30
2564 5360 7.610580 ACCCACAATTCTTTTCATTTCCTAA 57.389 32.000 0.00 0.00 0.00 2.69
2565 5361 7.610580 AACCCACAATTCTTTTCATTTCCTA 57.389 32.000 0.00 0.00 0.00 2.94
2566 5362 6.499106 AACCCACAATTCTTTTCATTTCCT 57.501 33.333 0.00 0.00 0.00 3.36
2616 5412 5.249420 AGAATCCACAAAGTAGAAGCCTTC 58.751 41.667 0.00 0.00 0.00 3.46
2628 5426 6.264970 TGTCATGTTGATTGAGAATCCACAAA 59.735 34.615 7.16 0.00 43.86 2.83
2955 5770 1.202371 GCATGTTGATCAGCATGGTGG 60.202 52.381 37.64 22.35 46.04 4.61
3048 5863 1.882989 GAGCCTCGCTTCCACAGAGT 61.883 60.000 0.00 0.00 39.88 3.24
3144 5959 7.446001 AACCTTCACTTCTGATTTCTTCATC 57.554 36.000 0.00 0.00 32.72 2.92
3249 6072 5.591643 AGCATCTGTAACGTTAACAAGTG 57.408 39.130 10.11 11.75 0.00 3.16
3311 6134 7.496346 TTTGGTCACTAGAGTATCCTCAAAT 57.504 36.000 0.00 0.00 40.40 2.32
3365 6188 0.097674 CCTTCTTCTGATTTGCGCCG 59.902 55.000 4.18 0.00 0.00 6.46
3483 6312 1.981256 ACAGCAAACAGTTAGGGTGG 58.019 50.000 16.89 4.54 33.33 4.61
3583 6412 1.301677 GGCCAAGAGACGAGCCTTTG 61.302 60.000 0.00 0.00 42.34 2.77
3918 6747 3.593442 TTCCAACCAACCTTCAGTCAT 57.407 42.857 0.00 0.00 0.00 3.06
3938 6767 5.227152 AGTTTGCAAAAGTGTTTCGAGTTT 58.773 33.333 14.67 0.00 0.00 2.66
3945 6774 8.770438 TCTTTGATAAGTTTGCAAAAGTGTTT 57.230 26.923 14.67 6.43 31.87 2.83
3951 6780 9.376075 TGATTGTTCTTTGATAAGTTTGCAAAA 57.624 25.926 14.67 0.00 31.87 2.44
4012 6841 4.341806 TCATTGTCAGTGCAACCTTCAATT 59.658 37.500 0.00 0.00 37.80 2.32
4026 6855 7.239166 GATACACTGTTGGTATCATTGTCAG 57.761 40.000 11.37 0.00 44.11 3.51
4045 6874 3.734463 TGAAAGCCGAAGTGTTGATACA 58.266 40.909 0.00 0.00 0.00 2.29
4124 6953 6.765403 TGTACATGGTATAACAGATAAGGGC 58.235 40.000 0.00 0.00 0.00 5.19
4148 6977 0.108377 TGCATTCCACTACGACGCAT 60.108 50.000 0.00 0.00 0.00 4.73
4150 6979 1.006832 ATTGCATTCCACTACGACGC 58.993 50.000 0.00 0.00 0.00 5.19
4204 7033 6.983307 CCAATTACAACACAAGGATCAAACAA 59.017 34.615 0.00 0.00 0.00 2.83
4221 7050 7.440505 TGAAGCCTACCTAATACCAATTACA 57.559 36.000 0.00 0.00 0.00 2.41
4268 7097 4.015872 TGAAAAATGGCTCGAACCTAGT 57.984 40.909 6.39 0.00 0.00 2.57
4295 7124 4.042311 TCCGGCATATATAAGCAAAGGGAA 59.958 41.667 11.74 0.00 0.00 3.97
4385 7214 2.337644 CGTACACGACGTGTTCTCATTC 59.662 50.000 35.71 16.81 45.08 2.67
4397 7226 0.595567 TTGCTCACCACGTACACGAC 60.596 55.000 9.04 0.00 43.02 4.34
4405 7234 3.044986 CAAGTTTTGATTGCTCACCACG 58.955 45.455 0.00 0.00 0.00 4.94
4429 7258 8.934023 TTTATCATTAAAGGACCAGTTGACTT 57.066 30.769 0.00 0.00 0.00 3.01
4654 7496 4.142359 ACTGTTCAGCTAGTTGATACGGAG 60.142 45.833 23.93 15.56 0.00 4.63
4655 7497 3.762288 ACTGTTCAGCTAGTTGATACGGA 59.238 43.478 23.93 5.98 0.00 4.69
4656 7498 4.111375 ACTGTTCAGCTAGTTGATACGG 57.889 45.455 10.32 16.24 0.00 4.02
4657 7499 5.163642 ACCTACTGTTCAGCTAGTTGATACG 60.164 44.000 10.32 9.77 0.00 3.06
4658 7500 6.210287 ACCTACTGTTCAGCTAGTTGATAC 57.790 41.667 10.32 11.33 0.00 2.24
4659 7501 6.210784 ACAACCTACTGTTCAGCTAGTTGATA 59.789 38.462 23.25 2.40 34.00 2.15
4660 7502 5.012148 ACAACCTACTGTTCAGCTAGTTGAT 59.988 40.000 23.25 0.00 34.00 2.57
4693 7541 6.202762 GCCCTGTCTTCAAATTTAAGTTTTGG 59.797 38.462 11.05 0.00 35.31 3.28
4701 7549 6.121776 TCTGTAGCCCTGTCTTCAAATTTA 57.878 37.500 0.00 0.00 0.00 1.40
4708 7556 4.762251 ACAAAAATCTGTAGCCCTGTCTTC 59.238 41.667 0.00 0.00 0.00 2.87
4806 7657 7.287696 ACTTGTCCCAAGTTTGATTTTAGACAT 59.712 33.333 3.85 0.00 32.30 3.06
4823 7674 0.403655 TTGCAGGCATACTTGTCCCA 59.596 50.000 0.00 0.00 0.00 4.37
4949 7800 6.270815 CCTTTTGCTGATGTCATAATCTTGG 58.729 40.000 0.00 0.00 0.00 3.61
4982 7833 5.745294 GTCGTACTGGAAAGATTTATACGCA 59.255 40.000 0.00 0.00 35.20 5.24
4988 7839 3.763360 TCGGGTCGTACTGGAAAGATTTA 59.237 43.478 0.00 0.00 0.00 1.40
5042 7893 8.801882 ATATGAAATCCTTAAAACGTCTGGAA 57.198 30.769 0.00 0.00 0.00 3.53
5205 8070 0.966920 ACTCACCCGTCCTTGTACTG 59.033 55.000 0.00 0.00 0.00 2.74
5206 8071 0.966920 CACTCACCCGTCCTTGTACT 59.033 55.000 0.00 0.00 0.00 2.73
5216 8082 1.669115 CTGAAGCCACACTCACCCG 60.669 63.158 0.00 0.00 0.00 5.28
5312 8184 9.984590 TGAGCCCTATGTATTGTATGTATAGTA 57.015 33.333 0.00 0.00 0.00 1.82
5313 8185 8.750298 GTGAGCCCTATGTATTGTATGTATAGT 58.250 37.037 0.00 0.00 0.00 2.12
5314 8186 8.972127 AGTGAGCCCTATGTATTGTATGTATAG 58.028 37.037 0.00 0.00 0.00 1.31
5315 8187 8.749354 CAGTGAGCCCTATGTATTGTATGTATA 58.251 37.037 0.00 0.00 0.00 1.47
5392 8264 6.940298 TGGTTACAACTCTCCCATCTTTTAAG 59.060 38.462 0.00 0.00 0.00 1.85
5396 8269 4.993705 TGGTTACAACTCTCCCATCTTT 57.006 40.909 0.00 0.00 0.00 2.52
5402 8275 1.439679 CGCTTGGTTACAACTCTCCC 58.560 55.000 0.00 0.00 32.14 4.30
5559 8442 3.423539 TGTGGAGACAGAAATCCAAGG 57.576 47.619 0.00 0.00 46.87 3.61
5571 8454 7.199766 TGAAAACAATGTACAAATGTGGAGAC 58.800 34.615 15.83 8.67 0.00 3.36
5572 8455 7.068103 ACTGAAAACAATGTACAAATGTGGAGA 59.932 33.333 15.83 3.87 0.00 3.71
5573 8456 7.202526 ACTGAAAACAATGTACAAATGTGGAG 58.797 34.615 15.83 11.95 0.00 3.86
5574 8457 7.106439 ACTGAAAACAATGTACAAATGTGGA 57.894 32.000 15.83 3.33 0.00 4.02
5575 8458 7.769272 AACTGAAAACAATGTACAAATGTGG 57.231 32.000 15.83 8.56 0.00 4.17
5577 8460 7.279758 CCCAAACTGAAAACAATGTACAAATGT 59.720 33.333 10.86 10.86 0.00 2.71
5580 8463 6.814146 GTCCCAAACTGAAAACAATGTACAAA 59.186 34.615 0.00 0.00 0.00 2.83
5596 8481 1.153756 CAAGGCCAGGTCCCAAACT 59.846 57.895 5.01 0.00 0.00 2.66
5611 8496 1.271054 ACTACCAGTCTGCCTTGCAAG 60.271 52.381 19.93 19.93 38.41 4.01
5619 8504 0.539051 AGGCATCACTACCAGTCTGC 59.461 55.000 0.00 3.05 34.74 4.26
5621 8506 2.106566 CTGAGGCATCACTACCAGTCT 58.893 52.381 0.00 0.00 0.00 3.24
5622 8507 1.827969 ACTGAGGCATCACTACCAGTC 59.172 52.381 0.00 0.00 29.93 3.51
5623 8508 1.944177 ACTGAGGCATCACTACCAGT 58.056 50.000 0.00 0.00 0.00 4.00
5624 8509 3.340814 AAACTGAGGCATCACTACCAG 57.659 47.619 0.00 0.00 0.00 4.00
5625 8510 3.181445 ACAAAACTGAGGCATCACTACCA 60.181 43.478 0.00 0.00 0.00 3.25
5626 8511 3.412386 ACAAAACTGAGGCATCACTACC 58.588 45.455 0.00 0.00 0.00 3.18
5682 8572 3.630892 TCATTGGGATTTGGCAAATGG 57.369 42.857 28.78 11.37 0.00 3.16
5693 8583 2.364324 GTGCAGCATCATTCATTGGGAT 59.636 45.455 0.00 0.00 0.00 3.85
5781 8681 1.690633 ATCACAGGCTGACCCCGAT 60.691 57.895 23.66 11.25 36.11 4.18
5914 8814 2.879002 TGCTCATCTGCTACTACTGC 57.121 50.000 0.00 0.00 0.00 4.40
5915 8815 4.319139 ACATGCTCATCTGCTACTACTG 57.681 45.455 0.00 0.00 0.00 2.74
5916 8816 4.022416 GCTACATGCTCATCTGCTACTACT 60.022 45.833 0.00 0.00 38.95 2.57
5917 8817 4.233789 GCTACATGCTCATCTGCTACTAC 58.766 47.826 0.00 0.00 38.95 2.73
5919 8819 3.383620 GCTACATGCTCATCTGCTACT 57.616 47.619 0.00 0.00 38.95 2.57
5931 8831 5.776173 TCCTTCTAGTTCTAGCTACATGC 57.224 43.478 0.00 0.00 43.29 4.06
5932 8832 7.199766 CAGTTCCTTCTAGTTCTAGCTACATG 58.800 42.308 0.00 0.00 0.00 3.21
5933 8833 6.183360 GCAGTTCCTTCTAGTTCTAGCTACAT 60.183 42.308 0.00 0.00 0.00 2.29
5935 8835 5.125739 TGCAGTTCCTTCTAGTTCTAGCTAC 59.874 44.000 0.00 0.00 0.00 3.58
5936 8836 5.262009 TGCAGTTCCTTCTAGTTCTAGCTA 58.738 41.667 0.00 0.00 0.00 3.32
5938 8838 4.457834 TGCAGTTCCTTCTAGTTCTAGC 57.542 45.455 2.31 0.00 0.00 3.42
5942 8842 4.381411 ACTGTTGCAGTTCCTTCTAGTTC 58.619 43.478 0.00 0.00 42.59 3.01
5966 8897 4.907269 TGGGTACATGTGGTGATCAGATAT 59.093 41.667 9.11 0.00 0.00 1.63
5967 8898 4.294347 TGGGTACATGTGGTGATCAGATA 58.706 43.478 9.11 0.00 0.00 1.98
5968 8899 3.114606 TGGGTACATGTGGTGATCAGAT 58.885 45.455 9.11 0.00 0.00 2.90
5969 8900 2.545810 TGGGTACATGTGGTGATCAGA 58.454 47.619 9.11 0.00 0.00 3.27
5970 8901 3.118298 TGATGGGTACATGTGGTGATCAG 60.118 47.826 9.11 0.00 37.47 2.90
5971 8902 2.843113 TGATGGGTACATGTGGTGATCA 59.157 45.455 9.11 8.29 37.47 2.92
5972 8903 3.558931 TGATGGGTACATGTGGTGATC 57.441 47.619 9.11 5.79 37.47 2.92
5973 8904 4.166725 AGATTGATGGGTACATGTGGTGAT 59.833 41.667 9.11 0.00 37.47 3.06
5974 8905 3.523157 AGATTGATGGGTACATGTGGTGA 59.477 43.478 9.11 0.00 37.47 4.02
5977 8912 6.772233 TGATTTAGATTGATGGGTACATGTGG 59.228 38.462 9.11 0.00 37.47 4.17
5986 8921 4.940046 CCGGATCTGATTTAGATTGATGGG 59.060 45.833 2.08 0.00 46.12 4.00
6082 9017 3.082698 TCATCAGCACAAAACAACAGC 57.917 42.857 0.00 0.00 0.00 4.40
6083 9018 5.749588 TCATTTCATCAGCACAAAACAACAG 59.250 36.000 0.00 0.00 0.00 3.16
6084 9019 5.658468 TCATTTCATCAGCACAAAACAACA 58.342 33.333 0.00 0.00 0.00 3.33
6131 9066 1.598962 GCAAGCAGTCAGTCAGGCA 60.599 57.895 0.00 0.00 0.00 4.75
6132 9067 2.331132 GGCAAGCAGTCAGTCAGGC 61.331 63.158 0.00 0.00 0.00 4.85
6133 9068 1.673665 GGGCAAGCAGTCAGTCAGG 60.674 63.158 0.00 0.00 0.00 3.86
6134 9069 2.031516 CGGGCAAGCAGTCAGTCAG 61.032 63.158 0.00 0.00 0.00 3.51
6135 9070 2.031012 CGGGCAAGCAGTCAGTCA 59.969 61.111 0.00 0.00 0.00 3.41
6136 9071 3.426568 GCGGGCAAGCAGTCAGTC 61.427 66.667 0.00 0.00 37.05 3.51
6137 9072 4.254709 TGCGGGCAAGCAGTCAGT 62.255 61.111 2.71 0.00 42.92 3.41
6149 9084 3.423154 GCGACTGAAAGGTGCGGG 61.423 66.667 0.00 0.00 39.30 6.13
6223 9175 2.032528 CTCCAGACCAAAGGCGCA 59.967 61.111 10.83 0.00 0.00 6.09
6224 9176 3.435186 GCTCCAGACCAAAGGCGC 61.435 66.667 0.00 0.00 0.00 6.53
6225 9177 1.899437 TAGGCTCCAGACCAAAGGCG 61.899 60.000 0.00 0.00 40.27 5.52
6233 9185 2.877168 CAATCATTGCTAGGCTCCAGAC 59.123 50.000 0.00 0.00 0.00 3.51
6240 9192 0.947244 CCGTCCAATCATTGCTAGGC 59.053 55.000 0.00 0.00 0.00 3.93
6241 9193 1.942657 CACCGTCCAATCATTGCTAGG 59.057 52.381 0.00 0.00 0.00 3.02
6242 9194 2.632377 ACACCGTCCAATCATTGCTAG 58.368 47.619 0.00 0.00 0.00 3.42
6258 9210 1.222661 CCGGGCCTAACCTAACACC 59.777 63.158 0.84 0.00 39.10 4.16
6268 9220 4.770874 GCTTCAACGCCGGGCCTA 62.771 66.667 14.55 0.00 0.00 3.93
6271 9223 3.670377 AAAGCTTCAACGCCGGGC 61.670 61.111 9.54 9.54 0.00 6.13
6272 9224 2.070654 AACAAAGCTTCAACGCCGGG 62.071 55.000 2.18 0.00 0.00 5.73
6273 9225 0.934436 CAACAAAGCTTCAACGCCGG 60.934 55.000 0.00 0.00 0.00 6.13
6274 9226 1.539776 GCAACAAAGCTTCAACGCCG 61.540 55.000 0.00 0.00 0.00 6.46
6275 9227 1.215014 GGCAACAAAGCTTCAACGCC 61.215 55.000 12.45 12.45 34.17 5.68
6276 9228 1.539776 CGGCAACAAAGCTTCAACGC 61.540 55.000 0.00 0.49 34.17 4.84
6277 9229 1.539776 GCGGCAACAAAGCTTCAACG 61.540 55.000 0.00 0.49 34.17 4.10
6278 9230 1.215014 GGCGGCAACAAAGCTTCAAC 61.215 55.000 3.07 0.00 34.17 3.18
6279 9231 1.067250 GGCGGCAACAAAGCTTCAA 59.933 52.632 3.07 0.00 34.17 2.69
6280 9232 2.727544 GGCGGCAACAAAGCTTCA 59.272 55.556 3.07 0.00 34.17 3.02
6281 9233 2.049156 GGGCGGCAACAAAGCTTC 60.049 61.111 12.47 0.00 34.17 3.86
6282 9234 0.897863 TATGGGCGGCAACAAAGCTT 60.898 50.000 12.47 0.00 34.17 3.74
6283 9235 1.304052 TATGGGCGGCAACAAAGCT 60.304 52.632 12.47 0.00 34.17 3.74
6284 9236 1.153842 GTATGGGCGGCAACAAAGC 60.154 57.895 12.47 0.00 0.00 3.51
6285 9237 1.136565 CGTATGGGCGGCAACAAAG 59.863 57.895 12.47 0.00 0.00 2.77
6286 9238 2.983930 GCGTATGGGCGGCAACAAA 61.984 57.895 12.47 0.00 0.00 2.83
6287 9239 3.436055 GCGTATGGGCGGCAACAA 61.436 61.111 12.47 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.