Multiple sequence alignment - TraesCS1A01G051300

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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 TraesCS1A01G051300 chr1A 100.000 4640 0 0 981 5620 32890600 32895239 0.000000e+00 8569.0
1 TraesCS1A01G051300 chr1A 100.000 744 0 0 1 744 32889620 32890363 0.000000e+00 1375.0
2 TraesCS1A01G051300 chr1A 84.436 257 38 2 3739 3994 32893106 32893361 9.350000e-63 252.0
3 TraesCS1A01G051300 chr1A 84.436 257 38 2 3487 3742 32893358 32893613 9.350000e-63 252.0
4 TraesCS1A01G051300 chr1B 91.883 4497 238 50 1170 5589 52898385 52902831 0.000000e+00 6165.0
5 TraesCS1A01G051300 chr1B 80.026 761 75 33 14 744 52897513 52898226 5.060000e-135 492.0
6 TraesCS1A01G051300 chr1B 86.256 422 58 0 3477 3898 52900776 52901197 5.130000e-125 459.0
7 TraesCS1A01G051300 chr1B 83.529 340 56 0 3655 3994 52900702 52901041 9.090000e-83 318.0
8 TraesCS1A01G051300 chr1B 89.815 108 9 2 69 174 52781495 52781602 2.730000e-28 137.0
9 TraesCS1A01G051300 chr1B 96.296 54 2 0 981 1034 52898247 52898300 7.760000e-14 89.8
10 TraesCS1A01G051300 chr1D 92.177 4244 190 33 1439 5598 34617928 34622113 0.000000e+00 5867.0
11 TraesCS1A01G051300 chr1D 78.139 892 145 24 1587 2453 474503663 474502797 6.450000e-144 521.0
12 TraesCS1A01G051300 chr1D 87.298 433 55 0 3478 3910 34620078 34620510 3.910000e-136 496.0
13 TraesCS1A01G051300 chr1D 86.506 415 50 4 3571 3982 34620003 34620414 8.590000e-123 451.0
14 TraesCS1A01G051300 chr1D 90.811 185 12 2 1 184 34616438 34616618 5.630000e-60 243.0
15 TraesCS1A01G051300 chr1D 84.211 133 11 7 983 1112 34617511 34617636 2.750000e-23 121.0
16 TraesCS1A01G051300 chr1D 80.952 105 15 4 1263 1363 34617766 34617869 1.680000e-10 78.7
17 TraesCS1A01G051300 chr2D 79.286 700 105 23 1777 2453 626409958 626409276 2.390000e-123 453.0
18 TraesCS1A01G051300 chr2A 80.392 357 46 15 1968 2310 756118772 756118426 3.360000e-62 250.0
19 TraesCS1A01G051300 chr2A 80.308 325 45 11 2138 2453 756068711 756068397 1.580000e-55 228.0
20 TraesCS1A01G051300 chr2A 80.000 325 46 11 2138 2453 756042614 756042300 7.330000e-54 222.0
21 TraesCS1A01G051300 chrUn 80.247 324 45 11 2138 2452 180874491 180874178 5.670000e-55 226.0
22 TraesCS1A01G051300 chrUn 79.692 325 47 11 2138 2453 180905231 180904917 3.410000e-52 217.0


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 TraesCS1A01G051300 chr1A 32889620 32895239 5619 False 2612.00 8569 92.2180 1 5620 4 chr1A.!!$F1 5619
1 TraesCS1A01G051300 chr1B 52897513 52902831 5318 False 1504.76 6165 87.5980 14 5589 5 chr1B.!!$F2 5575
2 TraesCS1A01G051300 chr1D 34616438 34622113 5675 False 1209.45 5867 86.9925 1 5598 6 chr1D.!!$F1 5597
3 TraesCS1A01G051300 chr1D 474502797 474503663 866 True 521.00 521 78.1390 1587 2453 1 chr1D.!!$R1 866
4 TraesCS1A01G051300 chr2D 626409276 626409958 682 True 453.00 453 79.2860 1777 2453 1 chr2D.!!$R1 676

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
285 300 0.256177 CTTTCTACCTCCCCCAAGGC 59.744 60.0 0.00 0.0 40.34 4.35 F
1027 1186 0.179089 CTCCTCCAGATCAAGGTGCG 60.179 60.0 8.23 0.0 34.12 5.34 F
1385 1575 0.038166 TTTCCTCTTCCAATGGCGCT 59.962 50.0 7.64 0.0 0.00 5.92 F
3164 3418 0.039708 GCAAAGCAGAGGAAGCACAC 60.040 55.0 0.00 0.0 0.00 3.82 F
3933 4187 0.463474 GGGCCTTCAAGAGCAGCTAG 60.463 60.0 0.84 0.0 0.00 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1096 1255 0.179059 CAACCAACCAGCCCAAAACC 60.179 55.0 0.00 0.0 0.00 3.27 R
2303 2556 0.681564 TGAACCTCTCGAGCTCCTCC 60.682 60.0 7.81 0.0 0.00 4.30 R
3316 3570 0.463474 GCTCACCTCAGCCTCCAATC 60.463 60.0 0.00 0.0 32.76 2.67 R
4272 4526 0.462047 GAGTTCCCATTGGCGACGAT 60.462 55.0 0.00 0.0 33.50 3.73 R
4883 5155 1.103803 TTACAAGCAAACGGCCACAA 58.896 45.0 2.24 0.0 46.50 3.33 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
57 58 1.448540 CGTGAAGGGGTAGCTGCTG 60.449 63.158 13.43 0.00 0.00 4.41
98 100 0.584876 AACGGCGACAAAAGCAGTAC 59.415 50.000 16.62 0.00 41.81 2.73
146 148 3.179265 CGGCGTCATGGTCACGAC 61.179 66.667 9.39 5.46 42.20 4.34
151 153 2.566997 GTCATGGTCACGACGATCG 58.433 57.895 14.88 14.88 46.93 3.69
201 203 3.084786 ACATGGAAGGAAAAGTAGCAGC 58.915 45.455 0.00 0.00 0.00 5.25
202 204 2.949177 TGGAAGGAAAAGTAGCAGCA 57.051 45.000 0.00 0.00 0.00 4.41
204 206 3.347216 TGGAAGGAAAAGTAGCAGCATC 58.653 45.455 0.00 0.00 0.00 3.91
205 207 3.244875 TGGAAGGAAAAGTAGCAGCATCA 60.245 43.478 0.00 0.00 0.00 3.07
206 208 3.758554 GGAAGGAAAAGTAGCAGCATCAA 59.241 43.478 0.00 0.00 0.00 2.57
244 248 4.856607 GGAAGGACGGCGAGCGAG 62.857 72.222 16.62 0.00 0.00 5.03
281 296 1.358152 CACACTTTCTACCTCCCCCA 58.642 55.000 0.00 0.00 0.00 4.96
282 297 1.702957 CACACTTTCTACCTCCCCCAA 59.297 52.381 0.00 0.00 0.00 4.12
283 298 1.985895 ACACTTTCTACCTCCCCCAAG 59.014 52.381 0.00 0.00 0.00 3.61
284 299 1.282157 CACTTTCTACCTCCCCCAAGG 59.718 57.143 0.00 0.00 42.55 3.61
285 300 0.256177 CTTTCTACCTCCCCCAAGGC 59.744 60.000 0.00 0.00 40.34 4.35
286 301 1.212250 TTTCTACCTCCCCCAAGGCC 61.212 60.000 0.00 0.00 40.34 5.19
287 302 3.097162 CTACCTCCCCCAAGGCCC 61.097 72.222 0.00 0.00 40.34 5.80
298 313 1.543944 CCAAGGCCCCAACCAATCAC 61.544 60.000 0.00 0.00 0.00 3.06
299 314 1.229177 AAGGCCCCAACCAATCACC 60.229 57.895 0.00 0.00 0.00 4.02
300 315 2.683572 GGCCCCAACCAATCACCC 60.684 66.667 0.00 0.00 0.00 4.61
301 316 2.119391 GCCCCAACCAATCACCCA 59.881 61.111 0.00 0.00 0.00 4.51
302 317 1.306056 GCCCCAACCAATCACCCAT 60.306 57.895 0.00 0.00 0.00 4.00
303 318 1.329913 GCCCCAACCAATCACCCATC 61.330 60.000 0.00 0.00 0.00 3.51
311 336 2.244695 CCAATCACCCATCCATCCATG 58.755 52.381 0.00 0.00 0.00 3.66
446 492 2.283966 AGTGTGACCTCCCTCCCG 60.284 66.667 0.00 0.00 0.00 5.14
486 532 3.601685 CACCAACCGGCCACCAAC 61.602 66.667 0.00 0.00 34.57 3.77
493 539 2.760159 CCGGCCACCAACAATAGCG 61.760 63.158 2.24 0.00 0.00 4.26
512 566 8.487970 CAATAGCGTCACCAGTAGTAATATTTG 58.512 37.037 0.00 0.00 0.00 2.32
548 602 2.498077 GCATCTGCTCTTTTCCCCC 58.502 57.895 0.00 0.00 38.21 5.40
591 649 1.950630 GGTGTGCGCTTTGCCTTTG 60.951 57.895 9.73 0.00 45.60 2.77
672 744 3.637273 GACGCCCCCACTTCCACT 61.637 66.667 0.00 0.00 0.00 4.00
673 745 3.175710 ACGCCCCCACTTCCACTT 61.176 61.111 0.00 0.00 0.00 3.16
674 746 2.359975 CGCCCCCACTTCCACTTC 60.360 66.667 0.00 0.00 0.00 3.01
675 747 2.035783 GCCCCCACTTCCACTTCC 59.964 66.667 0.00 0.00 0.00 3.46
697 769 4.016706 CACCCCCGTCGCTTCCTT 62.017 66.667 0.00 0.00 0.00 3.36
698 770 3.703127 ACCCCCGTCGCTTCCTTC 61.703 66.667 0.00 0.00 0.00 3.46
699 771 4.468689 CCCCCGTCGCTTCCTTCC 62.469 72.222 0.00 0.00 0.00 3.46
700 772 3.391382 CCCCGTCGCTTCCTTCCT 61.391 66.667 0.00 0.00 0.00 3.36
728 800 1.557371 CCCCTCCTTCTTCTTCACCTC 59.443 57.143 0.00 0.00 0.00 3.85
1027 1186 0.179089 CTCCTCCAGATCAAGGTGCG 60.179 60.000 8.23 0.00 34.12 5.34
1040 1199 3.462678 GTGCGTCCTCCCCTCCTC 61.463 72.222 0.00 0.00 0.00 3.71
1043 1202 2.123640 CGTCCTCCCCTCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1065 1224 1.827344 CCCCTCCTTTTCTGCCATTTC 59.173 52.381 0.00 0.00 0.00 2.17
1077 1236 1.798735 CCATTTCTGTCTGGCTGCG 59.201 57.895 0.00 0.00 0.00 5.18
1084 1243 1.909141 CTGTCTGGCTGCGCTTCTTG 61.909 60.000 9.73 0.00 0.00 3.02
1088 1247 2.256461 GGCTGCGCTTCTTGGTTG 59.744 61.111 9.73 0.00 0.00 3.77
1089 1248 2.256461 GCTGCGCTTCTTGGTTGG 59.744 61.111 9.73 0.00 0.00 3.77
1092 1251 1.799258 CTGCGCTTCTTGGTTGGCTT 61.799 55.000 9.73 0.00 0.00 4.35
1095 1254 1.770957 CGCTTCTTGGTTGGCTTTTC 58.229 50.000 0.00 0.00 0.00 2.29
1096 1255 1.770957 GCTTCTTGGTTGGCTTTTCG 58.229 50.000 0.00 0.00 0.00 3.46
1097 1256 1.602920 GCTTCTTGGTTGGCTTTTCGG 60.603 52.381 0.00 0.00 0.00 4.30
1098 1257 1.681264 CTTCTTGGTTGGCTTTTCGGT 59.319 47.619 0.00 0.00 0.00 4.69
1099 1258 1.770294 TCTTGGTTGGCTTTTCGGTT 58.230 45.000 0.00 0.00 0.00 4.44
1100 1259 2.104170 TCTTGGTTGGCTTTTCGGTTT 58.896 42.857 0.00 0.00 0.00 3.27
1101 1260 2.498078 TCTTGGTTGGCTTTTCGGTTTT 59.502 40.909 0.00 0.00 0.00 2.43
1102 1261 2.301577 TGGTTGGCTTTTCGGTTTTG 57.698 45.000 0.00 0.00 0.00 2.44
1103 1262 1.134670 TGGTTGGCTTTTCGGTTTTGG 60.135 47.619 0.00 0.00 0.00 3.28
1104 1263 1.577468 GTTGGCTTTTCGGTTTTGGG 58.423 50.000 0.00 0.00 0.00 4.12
1106 1265 1.045911 TGGCTTTTCGGTTTTGGGCT 61.046 50.000 0.00 0.00 0.00 5.19
1108 1267 0.599991 GCTTTTCGGTTTTGGGCTGG 60.600 55.000 0.00 0.00 0.00 4.85
1110 1269 1.138069 CTTTTCGGTTTTGGGCTGGTT 59.862 47.619 0.00 0.00 0.00 3.67
1122 1281 1.441311 GCTGGTTGGTTGGTTGGTG 59.559 57.895 0.00 0.00 0.00 4.17
1136 1295 2.769095 GGTTGGTGCTATCCTCTTCTCT 59.231 50.000 0.00 0.00 0.00 3.10
1137 1296 3.198853 GGTTGGTGCTATCCTCTTCTCTT 59.801 47.826 0.00 0.00 0.00 2.85
1139 1298 3.987745 TGGTGCTATCCTCTTCTCTTCT 58.012 45.455 0.00 0.00 0.00 2.85
1141 1300 4.215109 GGTGCTATCCTCTTCTCTTCTCT 58.785 47.826 0.00 0.00 0.00 3.10
1150 1309 4.772100 CCTCTTCTCTTCTCTATCCATCCC 59.228 50.000 0.00 0.00 0.00 3.85
1197 1356 4.933064 CGGATCTCGCCGCCACTC 62.933 72.222 0.00 0.00 45.38 3.51
1299 1481 4.767255 CCTGCCTCTGCCGTCACC 62.767 72.222 0.00 0.00 36.33 4.02
1300 1482 4.007644 CTGCCTCTGCCGTCACCA 62.008 66.667 0.00 0.00 36.33 4.17
1333 1515 2.917933 TGATCCACTTAATTCCGCCTG 58.082 47.619 0.00 0.00 0.00 4.85
1339 1521 1.287425 CTTAATTCCGCCTGTCCGTC 58.713 55.000 0.00 0.00 0.00 4.79
1341 1523 0.174845 TAATTCCGCCTGTCCGTCTG 59.825 55.000 0.00 0.00 0.00 3.51
1342 1524 2.521958 AATTCCGCCTGTCCGTCTGG 62.522 60.000 0.00 0.00 38.06 3.86
1376 1558 6.419484 TTTTTCCTCCATTTTTCCTCTTCC 57.581 37.500 0.00 0.00 0.00 3.46
1378 1560 4.740154 TCCTCCATTTTTCCTCTTCCAA 57.260 40.909 0.00 0.00 0.00 3.53
1379 1561 5.275263 TCCTCCATTTTTCCTCTTCCAAT 57.725 39.130 0.00 0.00 0.00 3.16
1385 1575 0.038166 TTTCCTCTTCCAATGGCGCT 59.962 50.000 7.64 0.00 0.00 5.92
1386 1576 0.392998 TTCCTCTTCCAATGGCGCTC 60.393 55.000 7.64 0.00 0.00 5.03
1387 1577 1.821332 CCTCTTCCAATGGCGCTCC 60.821 63.158 7.64 0.00 0.00 4.70
1388 1578 1.821332 CTCTTCCAATGGCGCTCCC 60.821 63.158 7.64 0.00 0.00 4.30
1412 1602 1.338389 GCCATGGCTGATTTTGCTTGT 60.338 47.619 29.98 0.00 38.26 3.16
1418 1608 3.386078 TGGCTGATTTTGCTTGTGGTTTA 59.614 39.130 0.00 0.00 0.00 2.01
1421 1611 5.469760 GGCTGATTTTGCTTGTGGTTTATTT 59.530 36.000 0.00 0.00 0.00 1.40
1422 1612 6.648725 GGCTGATTTTGCTTGTGGTTTATTTA 59.351 34.615 0.00 0.00 0.00 1.40
1425 1615 8.027440 TGATTTTGCTTGTGGTTTATTTATGC 57.973 30.769 0.00 0.00 0.00 3.14
1426 1616 6.459257 TTTTGCTTGTGGTTTATTTATGCG 57.541 33.333 0.00 0.00 0.00 4.73
1427 1617 3.506810 TGCTTGTGGTTTATTTATGCGC 58.493 40.909 0.00 0.00 0.00 6.09
1428 1618 3.192422 TGCTTGTGGTTTATTTATGCGCT 59.808 39.130 9.73 0.00 0.00 5.92
1429 1619 3.791353 GCTTGTGGTTTATTTATGCGCTC 59.209 43.478 9.73 0.00 0.00 5.03
1432 1622 2.610374 GTGGTTTATTTATGCGCTCGGA 59.390 45.455 9.73 0.00 0.00 4.55
1433 1623 3.250040 GTGGTTTATTTATGCGCTCGGAT 59.750 43.478 9.73 1.40 0.00 4.18
1434 1624 3.880490 TGGTTTATTTATGCGCTCGGATT 59.120 39.130 9.73 0.00 0.00 3.01
1435 1625 4.024387 TGGTTTATTTATGCGCTCGGATTC 60.024 41.667 9.73 0.00 0.00 2.52
1448 1638 0.734889 CGGATTCGCTCCTGCATTTT 59.265 50.000 0.00 0.00 42.47 1.82
1480 1670 1.073763 TGGTGGATGTGGAAGAGGTTG 59.926 52.381 0.00 0.00 0.00 3.77
1503 1693 1.560860 GCTCTAATCGATGGCGGTGC 61.561 60.000 0.00 0.00 38.28 5.01
1901 2124 1.896660 GCTGTCGGCAGGGTGAAAA 60.897 57.895 20.36 0.00 42.78 2.29
1910 2133 0.240945 CAGGGTGAAAATGACGTGCC 59.759 55.000 0.00 0.00 0.00 5.01
1944 2169 1.059835 GACTTGCGAATTCTCTGCGAC 59.940 52.381 3.52 0.00 0.00 5.19
2228 2475 0.681564 ACGAGTCGCAGAAGAGGGAT 60.682 55.000 13.59 0.00 39.69 3.85
2249 2496 2.664081 GGAGTGGCAGAGGGAGGTG 61.664 68.421 0.00 0.00 0.00 4.00
2303 2556 4.602259 ACGCTGGTCACCACCACG 62.602 66.667 0.00 0.00 46.63 4.94
2468 2722 4.410099 TGAAAGGATTGCTTGATTCCAGT 58.590 39.130 0.00 0.00 31.65 4.00
2488 2742 1.433879 CGGCGGTTGAGGAGAGTAG 59.566 63.158 0.00 0.00 0.00 2.57
2520 2774 4.293662 AGGGAGGAGTTTGTGAAGAATC 57.706 45.455 0.00 0.00 0.00 2.52
2528 2782 5.942826 GGAGTTTGTGAAGAATCTGGAATCT 59.057 40.000 0.00 0.00 0.00 2.40
2619 2873 3.764237 AACTGACCGAGGAGCTTAAAA 57.236 42.857 0.00 0.00 0.00 1.52
2646 2900 1.514553 GCTGATGCAAAGAAGGCCC 59.485 57.895 0.00 0.00 39.41 5.80
2709 2963 3.119352 GGCTGGATCACTTGAAATGGAAC 60.119 47.826 0.00 0.00 0.00 3.62
2756 3010 2.552743 GGCCAAAAGCGATACCCTTATC 59.447 50.000 0.00 0.00 45.17 1.75
2762 3016 2.958818 AGCGATACCCTTATCTCCACA 58.041 47.619 0.00 0.00 33.07 4.17
2792 3046 5.251700 AGAATTGGACAAGACCCTGTCTATT 59.748 40.000 0.00 4.63 42.59 1.73
2844 3098 3.793465 GCTGAAAGGAAAGACAACAGCAC 60.793 47.826 0.00 0.00 45.33 4.40
2895 3149 2.672961 AATCAACGAATCCAGCGAGA 57.327 45.000 0.00 0.00 0.00 4.04
3038 3292 6.528537 AATGCAAATATTGTAAGCCTGACA 57.471 33.333 0.00 0.00 0.00 3.58
3056 3310 4.573900 TGACAGAGGAGAAAATCAAGCTC 58.426 43.478 0.00 0.00 0.00 4.09
3062 3316 7.833183 ACAGAGGAGAAAATCAAGCTCATTAAT 59.167 33.333 0.00 0.00 0.00 1.40
3098 3352 3.551635 AGGGACAGAGAGGAGAAAGAA 57.448 47.619 0.00 0.00 0.00 2.52
3103 3357 5.221742 GGGACAGAGAGGAGAAAGAAAGAAA 60.222 44.000 0.00 0.00 0.00 2.52
3105 3359 6.463755 GGACAGAGAGGAGAAAGAAAGAAAGT 60.464 42.308 0.00 0.00 0.00 2.66
3110 3364 6.894682 AGAGGAGAAAGAAAGAAAGTCAGTT 58.105 36.000 0.00 0.00 0.00 3.16
3164 3418 0.039708 GCAAAGCAGAGGAAGCACAC 60.040 55.000 0.00 0.00 0.00 3.82
3308 3562 7.681939 TGACATCACTTGTTTAAGGAATACC 57.318 36.000 0.00 0.00 39.18 2.73
3316 3570 4.497300 TGTTTAAGGAATACCGTCGGAAG 58.503 43.478 20.51 0.00 41.83 3.46
3380 3634 4.382470 GCTAAGGAGCTTGAGATTGTCAGA 60.382 45.833 0.00 0.00 45.98 3.27
3382 3636 4.405116 AGGAGCTTGAGATTGTCAGATC 57.595 45.455 0.00 0.00 36.21 2.75
3503 3757 7.706179 GTCAATGAGGAGAAAGAGATACTTCAG 59.294 40.741 0.00 0.00 37.93 3.02
3563 3817 1.200760 ACAGGGCTGTGCAGGATGTA 61.201 55.000 1.11 0.00 43.11 2.29
3569 3823 1.098050 CTGTGCAGGATGTAAAGGCC 58.902 55.000 0.00 0.00 39.31 5.19
3665 3919 3.262151 AGGTAAAGGCTGAGAAAGAGGAC 59.738 47.826 0.00 0.00 0.00 3.85
3673 3927 3.333804 CTGAGAAAGAGGACCTTCAAGC 58.666 50.000 0.00 0.00 33.02 4.01
3719 3973 1.068264 GTTGCTGAAGCTAACAAGGCC 60.068 52.381 0.00 0.00 42.66 5.19
3722 3976 1.200948 GCTGAAGCTAACAAGGCCTTG 59.799 52.381 38.30 38.30 41.09 3.61
3728 3982 1.457346 CTAACAAGGCCTTGCAGGAG 58.543 55.000 39.52 27.20 44.03 3.69
3780 4034 2.419673 CAGCTAATGCACACGGAATCAA 59.580 45.455 0.00 0.00 42.74 2.57
3803 4057 1.882623 GTTGCTGAAGCTAACAAGGCT 59.117 47.619 3.61 0.00 42.66 4.58
3804 4058 1.527034 TGCTGAAGCTAACAAGGCTG 58.473 50.000 3.61 0.00 42.66 4.85
3827 4081 2.290323 GCAGGAGGTAAAGGCTGAGAAA 60.290 50.000 0.00 0.00 0.00 2.52
3830 4084 4.080638 CAGGAGGTAAAGGCTGAGAAAGAT 60.081 45.833 0.00 0.00 0.00 2.40
3843 4097 6.339730 GCTGAGAAAGATGATCTTCAAGAGA 58.660 40.000 8.32 0.00 35.27 3.10
3860 4114 4.506886 AGAGAAGTTCTTGTACACGGAG 57.493 45.455 6.88 0.00 29.61 4.63
3865 4119 2.059541 GTTCTTGTACACGGAGTCAGC 58.940 52.381 0.00 0.00 41.61 4.26
3866 4120 1.324383 TCTTGTACACGGAGTCAGCA 58.676 50.000 0.00 0.00 41.61 4.41
3884 4138 2.926165 GCAGTTGCTGAAGCTAACAAG 58.074 47.619 15.25 10.44 42.66 3.16
3899 4153 1.729586 ACAAGGCTGTTCAGGAGGTA 58.270 50.000 1.97 0.00 28.57 3.08
3912 4166 3.261897 TCAGGAGGTAAAGGCTGAGAAAG 59.738 47.826 0.00 0.00 0.00 2.62
3933 4187 0.463474 GGGCCTTCAAGAGCAGCTAG 60.463 60.000 0.84 0.00 0.00 3.42
3950 4204 1.596260 CTAGCACACATGGAATCAGCG 59.404 52.381 0.00 0.00 0.00 5.18
4016 4270 4.520492 AGTTTGCAACTGAAGGATAGGTTG 59.480 41.667 0.00 0.00 41.01 3.77
4061 4315 2.168728 GAGCTTAACCCAGGAGAACGAT 59.831 50.000 0.00 0.00 0.00 3.73
4071 4325 3.369892 CCAGGAGAACGATGAATTCAGGT 60.370 47.826 14.54 11.26 0.00 4.00
4082 4336 0.678048 AATTCAGGTTGCGAGAGGCC 60.678 55.000 0.00 0.00 42.61 5.19
4109 4363 5.178996 CGCCATGAAGAAGATAGAGGAATTG 59.821 44.000 0.00 0.00 0.00 2.32
4116 4370 6.558488 AGAAGATAGAGGAATTGTCTGCTT 57.442 37.500 0.00 0.00 0.00 3.91
4169 4423 3.360867 TGAGGAGGAAGAGAAGCTAGTG 58.639 50.000 0.00 0.00 0.00 2.74
4184 4438 2.500098 GCTAGTGGTTGTGGATGAGGTA 59.500 50.000 0.00 0.00 0.00 3.08
4232 4486 3.072944 GACAGCTGCAGAAACTGAAGAT 58.927 45.455 20.43 1.37 39.42 2.40
4235 4489 3.061831 CAGCTGCAGAAACTGAAGATACG 59.938 47.826 20.43 0.00 39.42 3.06
4272 4526 2.270352 AAAACCGAGCATGGAACTCA 57.730 45.000 0.69 0.00 33.58 3.41
4286 4540 0.744414 AACTCATCGTCGCCAATGGG 60.744 55.000 0.00 0.00 37.18 4.00
4312 4566 1.234615 AACGGCGACATGAACCAAGG 61.235 55.000 16.62 0.00 0.00 3.61
4547 4807 1.090625 TGTCCCCGACAACAACAACG 61.091 55.000 0.00 0.00 39.78 4.10
4770 5035 0.163146 GTCGACGCCTGTACTTTTGC 59.837 55.000 0.00 0.00 0.00 3.68
4799 5064 2.287608 GCAGTAGCTTTGTGGGTGTTTC 60.288 50.000 0.00 0.00 37.91 2.78
4811 5076 4.714308 TGTGGGTGTTTCCATTTTTCTCTT 59.286 37.500 0.00 0.00 39.26 2.85
4812 5077 5.188751 TGTGGGTGTTTCCATTTTTCTCTTT 59.811 36.000 0.00 0.00 39.26 2.52
4813 5078 5.753438 GTGGGTGTTTCCATTTTTCTCTTTC 59.247 40.000 0.00 0.00 39.26 2.62
4814 5079 5.660864 TGGGTGTTTCCATTTTTCTCTTTCT 59.339 36.000 0.00 0.00 38.11 2.52
4815 5080 6.156083 TGGGTGTTTCCATTTTTCTCTTTCTT 59.844 34.615 0.00 0.00 38.11 2.52
4816 5081 7.047891 GGGTGTTTCCATTTTTCTCTTTCTTT 58.952 34.615 0.00 0.00 38.11 2.52
4817 5082 7.552687 GGGTGTTTCCATTTTTCTCTTTCTTTT 59.447 33.333 0.00 0.00 38.11 2.27
4883 5155 7.545965 GCTGTGGCTATTATTATCTACACGATT 59.454 37.037 0.00 0.00 32.93 3.34
4911 5183 2.811431 CGTTTGCTTGTAACCAGATGGA 59.189 45.455 5.72 0.00 38.94 3.41
4912 5184 3.120199 CGTTTGCTTGTAACCAGATGGAG 60.120 47.826 5.72 0.00 38.94 3.86
4913 5185 4.072131 GTTTGCTTGTAACCAGATGGAGA 58.928 43.478 5.72 0.00 38.94 3.71
4914 5186 3.616956 TGCTTGTAACCAGATGGAGAG 57.383 47.619 5.72 0.00 38.94 3.20
4915 5187 2.284190 GCTTGTAACCAGATGGAGAGC 58.716 52.381 5.72 3.83 38.94 4.09
4918 5190 0.470341 GTAACCAGATGGAGAGCCCC 59.530 60.000 5.72 0.00 38.94 5.80
4919 5191 0.343372 TAACCAGATGGAGAGCCCCT 59.657 55.000 5.72 0.00 38.94 4.79
4920 5192 0.343372 AACCAGATGGAGAGCCCCTA 59.657 55.000 5.72 0.00 38.94 3.53
4921 5193 0.399233 ACCAGATGGAGAGCCCCTAC 60.399 60.000 5.72 0.00 38.94 3.18
4922 5194 0.105246 CCAGATGGAGAGCCCCTACT 60.105 60.000 0.00 0.00 37.39 2.57
4923 5195 1.148027 CCAGATGGAGAGCCCCTACTA 59.852 57.143 0.00 0.00 37.39 1.82
4924 5196 2.426414 CCAGATGGAGAGCCCCTACTAA 60.426 54.545 0.00 0.00 37.39 2.24
4925 5197 3.515562 CAGATGGAGAGCCCCTACTAAT 58.484 50.000 0.00 0.00 0.00 1.73
4950 5222 5.940470 CCTCCTGATTAAAAACTGTGTAGCT 59.060 40.000 0.00 0.00 0.00 3.32
4983 5256 5.548181 AGCTGATGTCACTCATATCATGT 57.452 39.130 0.00 0.00 36.83 3.21
4984 5257 5.298347 AGCTGATGTCACTCATATCATGTG 58.702 41.667 0.00 0.00 36.83 3.21
4985 5258 5.070047 AGCTGATGTCACTCATATCATGTGA 59.930 40.000 0.00 0.00 36.83 3.58
4986 5259 5.932883 GCTGATGTCACTCATATCATGTGAT 59.067 40.000 0.68 0.68 41.78 3.06
4987 5260 6.128526 GCTGATGTCACTCATATCATGTGATG 60.129 42.308 5.78 0.00 41.78 3.07
4988 5261 5.699458 TGATGTCACTCATATCATGTGATGC 59.301 40.000 5.78 0.00 41.78 3.91
4989 5262 5.026038 TGTCACTCATATCATGTGATGCA 57.974 39.130 5.78 0.00 41.78 3.96
4990 5263 4.812626 TGTCACTCATATCATGTGATGCAC 59.187 41.667 5.78 0.00 41.78 4.57
4991 5264 4.212847 GTCACTCATATCATGTGATGCACC 59.787 45.833 5.78 0.00 41.78 5.01
4992 5265 4.102054 TCACTCATATCATGTGATGCACCT 59.898 41.667 5.78 0.00 36.03 4.00
5005 5278 6.515832 TGTGATGCACCTCTACTATAATGTG 58.484 40.000 0.00 0.00 32.73 3.21
5013 5286 7.543868 GCACCTCTACTATAATGTGATGTGATC 59.456 40.741 0.00 0.00 0.00 2.92
5020 5293 8.828688 ACTATAATGTGATGTGATCTGATGTG 57.171 34.615 0.00 0.00 0.00 3.21
5021 5294 8.645110 ACTATAATGTGATGTGATCTGATGTGA 58.355 33.333 0.00 0.00 0.00 3.58
5092 5365 4.321156 GCTTGTTGGCATGATCTGTTGTTA 60.321 41.667 0.00 0.00 0.00 2.41
5499 5829 5.594317 GGCTGGGTGTAAAGTATCAAATGAT 59.406 40.000 1.01 1.01 38.51 2.45
5541 5871 6.757897 TGCTTCCCAGTGTTTCTATTATTG 57.242 37.500 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.324108 TACCCCTTCACGGTGGGC 61.324 66.667 8.50 0.00 43.54 5.36
146 148 3.554692 GTGCGCTTGGGACGATCG 61.555 66.667 14.88 14.88 0.00 3.69
198 200 2.095059 GGTAAAGTGCAGGTTGATGCTG 60.095 50.000 0.00 0.00 46.63 4.41
201 203 2.749621 GAGGGTAAAGTGCAGGTTGATG 59.250 50.000 0.00 0.00 0.00 3.07
202 204 2.644798 AGAGGGTAAAGTGCAGGTTGAT 59.355 45.455 0.00 0.00 0.00 2.57
204 206 2.568623 AGAGGGTAAAGTGCAGGTTG 57.431 50.000 0.00 0.00 0.00 3.77
205 207 2.305052 GGTAGAGGGTAAAGTGCAGGTT 59.695 50.000 0.00 0.00 0.00 3.50
206 208 1.907255 GGTAGAGGGTAAAGTGCAGGT 59.093 52.381 0.00 0.00 0.00 4.00
249 253 2.359230 GTGTGGCAGGAGTGGAGC 60.359 66.667 0.00 0.00 0.00 4.70
281 296 1.229177 GGTGATTGGTTGGGGCCTT 60.229 57.895 0.84 0.00 0.00 4.35
282 297 2.445155 GGTGATTGGTTGGGGCCT 59.555 61.111 0.84 0.00 0.00 5.19
283 298 2.683572 GGGTGATTGGTTGGGGCC 60.684 66.667 0.00 0.00 0.00 5.80
284 299 1.306056 ATGGGTGATTGGTTGGGGC 60.306 57.895 0.00 0.00 0.00 5.80
285 300 0.687427 GGATGGGTGATTGGTTGGGG 60.687 60.000 0.00 0.00 0.00 4.96
286 301 0.040942 TGGATGGGTGATTGGTTGGG 59.959 55.000 0.00 0.00 0.00 4.12
287 302 2.034124 GATGGATGGGTGATTGGTTGG 58.966 52.381 0.00 0.00 0.00 3.77
359 394 3.181967 CACCGCGCCTCTTTCTCG 61.182 66.667 0.00 0.00 0.00 4.04
413 453 2.317609 ACTGCTAACGCTGCCAACG 61.318 57.895 0.00 0.00 38.51 4.10
422 462 0.389948 GGGAGGTCACACTGCTAACG 60.390 60.000 0.00 0.00 0.00 3.18
448 494 3.724494 GCTAATCAGCGTCCCTGC 58.276 61.111 0.00 0.00 41.50 4.85
482 528 1.808411 ACTGGTGACGCTATTGTTGG 58.192 50.000 0.00 0.00 0.00 3.77
486 532 8.487970 CAAATATTACTACTGGTGACGCTATTG 58.512 37.037 0.00 0.00 0.00 1.90
493 539 7.812648 TGCAAACAAATATTACTACTGGTGAC 58.187 34.615 0.00 0.00 0.00 3.67
512 566 5.149054 GATGCTACACTACATCTGCAAAC 57.851 43.478 0.00 0.00 39.66 2.93
546 600 0.614812 CCAAAGGCAAAGAATGGGGG 59.385 55.000 0.00 0.00 0.00 5.40
547 601 0.614812 CCCAAAGGCAAAGAATGGGG 59.385 55.000 1.08 0.00 45.72 4.96
567 622 1.300080 CAAAGCGCACACCCCAAAG 60.300 57.895 11.47 0.00 0.00 2.77
568 623 2.811101 CAAAGCGCACACCCCAAA 59.189 55.556 11.47 0.00 0.00 3.28
569 624 3.910490 GCAAAGCGCACACCCCAA 61.910 61.111 11.47 0.00 41.79 4.12
670 742 2.933834 CGGGGGTGAAGGGGAAGT 60.934 66.667 0.00 0.00 0.00 3.01
671 743 2.933834 ACGGGGGTGAAGGGGAAG 60.934 66.667 0.00 0.00 0.00 3.46
672 744 2.931649 GACGGGGGTGAAGGGGAA 60.932 66.667 0.00 0.00 0.00 3.97
1027 1186 2.284151 GGAGGAGGAGGGGAGGAC 59.716 72.222 0.00 0.00 0.00 3.85
1077 1236 1.602920 CCGAAAAGCCAACCAAGAAGC 60.603 52.381 0.00 0.00 0.00 3.86
1084 1243 1.577468 CCAAAACCGAAAAGCCAACC 58.423 50.000 0.00 0.00 0.00 3.77
1088 1247 0.599991 CAGCCCAAAACCGAAAAGCC 60.600 55.000 0.00 0.00 0.00 4.35
1089 1248 0.599991 CCAGCCCAAAACCGAAAAGC 60.600 55.000 0.00 0.00 0.00 3.51
1092 1251 0.461961 CAACCAGCCCAAAACCGAAA 59.538 50.000 0.00 0.00 0.00 3.46
1095 1254 1.681486 AACCAACCAGCCCAAAACCG 61.681 55.000 0.00 0.00 0.00 4.44
1096 1255 0.179059 CAACCAACCAGCCCAAAACC 60.179 55.000 0.00 0.00 0.00 3.27
1097 1256 0.179059 CCAACCAACCAGCCCAAAAC 60.179 55.000 0.00 0.00 0.00 2.43
1098 1257 0.618968 ACCAACCAACCAGCCCAAAA 60.619 50.000 0.00 0.00 0.00 2.44
1099 1258 0.618968 AACCAACCAACCAGCCCAAA 60.619 50.000 0.00 0.00 0.00 3.28
1100 1259 1.002274 AACCAACCAACCAGCCCAA 59.998 52.632 0.00 0.00 0.00 4.12
1101 1260 1.760086 CAACCAACCAACCAGCCCA 60.760 57.895 0.00 0.00 0.00 5.36
1102 1261 2.506957 CCAACCAACCAACCAGCCC 61.507 63.158 0.00 0.00 0.00 5.19
1103 1262 1.760480 ACCAACCAACCAACCAGCC 60.760 57.895 0.00 0.00 0.00 4.85
1104 1263 1.441311 CACCAACCAACCAACCAGC 59.559 57.895 0.00 0.00 0.00 4.85
1106 1265 0.259065 TAGCACCAACCAACCAACCA 59.741 50.000 0.00 0.00 0.00 3.67
1108 1267 1.544246 GGATAGCACCAACCAACCAAC 59.456 52.381 0.00 0.00 0.00 3.77
1110 1269 1.004277 GAGGATAGCACCAACCAACCA 59.996 52.381 0.00 0.00 0.00 3.67
1122 1281 6.245408 TGGATAGAGAAGAGAAGAGGATAGC 58.755 44.000 0.00 0.00 0.00 2.97
1136 1295 1.185618 CCGCGGGGATGGATAGAGAA 61.186 60.000 20.10 0.00 34.06 2.87
1137 1296 1.606601 CCGCGGGGATGGATAGAGA 60.607 63.158 20.10 0.00 34.06 3.10
1181 1340 4.593864 GGAGTGGCGGCGAGATCC 62.594 72.222 12.98 8.17 0.00 3.36
1282 1464 4.767255 GGTGACGGCAGAGGCAGG 62.767 72.222 0.00 0.00 43.71 4.85
1294 1476 1.876156 CAAGAAGCAGTTCCTGGTGAC 59.124 52.381 0.00 0.00 41.59 3.67
1299 1481 2.746362 GTGGATCAAGAAGCAGTTCCTG 59.254 50.000 0.00 0.00 32.48 3.86
1300 1482 2.641815 AGTGGATCAAGAAGCAGTTCCT 59.358 45.455 0.00 0.00 32.48 3.36
1333 1515 0.389948 ATCGAAACTGCCAGACGGAC 60.390 55.000 0.00 0.00 0.00 4.79
1359 1541 4.382362 GCCATTGGAAGAGGAAAAATGGAG 60.382 45.833 15.14 0.00 46.74 3.86
1360 1542 3.515104 GCCATTGGAAGAGGAAAAATGGA 59.485 43.478 15.14 0.00 46.74 3.41
1362 1544 3.514645 CGCCATTGGAAGAGGAAAAATG 58.485 45.455 6.95 0.00 0.00 2.32
1363 1545 2.094026 GCGCCATTGGAAGAGGAAAAAT 60.094 45.455 6.95 0.00 0.00 1.82
1369 1551 1.821332 GGAGCGCCATTGGAAGAGG 60.821 63.158 6.95 0.00 0.00 3.69
1372 1554 2.045045 TGGGAGCGCCATTGGAAG 60.045 61.111 9.31 0.19 35.15 3.46
1373 1555 2.045045 CTGGGAGCGCCATTGGAA 60.045 61.111 9.31 0.00 35.15 3.53
1374 1556 3.008517 TCTGGGAGCGCCATTGGA 61.009 61.111 9.31 0.00 35.15 3.53
1376 1558 3.207669 GCTCTGGGAGCGCCATTG 61.208 66.667 9.31 0.00 45.85 2.82
1392 1582 1.338389 ACAAGCAAAATCAGCCATGGC 60.338 47.619 30.12 30.12 42.33 4.40
1395 1585 1.972795 ACCACAAGCAAAATCAGCCAT 59.027 42.857 0.00 0.00 0.00 4.40
1396 1586 1.412079 ACCACAAGCAAAATCAGCCA 58.588 45.000 0.00 0.00 0.00 4.75
1399 1589 8.170553 GCATAAATAAACCACAAGCAAAATCAG 58.829 33.333 0.00 0.00 0.00 2.90
1408 1598 4.028383 CGAGCGCATAAATAAACCACAAG 58.972 43.478 11.47 0.00 0.00 3.16
1412 1602 2.907634 TCCGAGCGCATAAATAAACCA 58.092 42.857 11.47 0.00 0.00 3.67
1432 1622 3.727419 GCAAAATGCAGGAGCGAAT 57.273 47.368 0.00 0.00 44.26 3.34
1458 1648 0.393537 CCTCTTCCACATCCACCAGC 60.394 60.000 0.00 0.00 0.00 4.85
1480 1670 1.423395 CGCCATCGATTAGAGCTTCC 58.577 55.000 0.00 0.00 38.10 3.46
1503 1693 1.129998 CCAGATCTGCAAACAAGAGCG 59.870 52.381 17.76 0.00 0.00 5.03
1514 1705 0.883814 CTCATTCGGCCCAGATCTGC 60.884 60.000 17.76 6.86 0.00 4.26
1861 2082 4.785341 GCGTAAAGTTTGTGGTGAAGTGAG 60.785 45.833 0.00 0.00 0.00 3.51
1870 2091 1.070175 CCGACAGCGTAAAGTTTGTGG 60.070 52.381 0.00 0.00 35.23 4.17
1901 2124 3.055719 CCGGCAAAGGCACGTCAT 61.056 61.111 0.00 0.00 43.71 3.06
1910 2133 2.061028 GCAAGTCAATTTCCGGCAAAG 58.939 47.619 0.00 0.00 0.00 2.77
2228 2475 1.305633 CTCCCTCTGCCACTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
2249 2496 4.687215 TGGCTGCGCACACTCTCC 62.687 66.667 5.66 1.38 0.00 3.71
2303 2556 0.681564 TGAACCTCTCGAGCTCCTCC 60.682 60.000 7.81 0.00 0.00 4.30
2468 2722 4.069232 CTCTCCTCAACCGCCGCA 62.069 66.667 0.00 0.00 0.00 5.69
2488 2742 1.071857 ACTCCTCCCTTTCACGGTTTC 59.928 52.381 0.00 0.00 0.00 2.78
2619 2873 1.338973 CTTTGCATCAGCCAACTGTGT 59.661 47.619 0.00 0.00 44.77 3.72
2646 2900 2.028294 ACTGCTGATGGACTTCTGACTG 60.028 50.000 0.00 0.00 0.00 3.51
2709 2963 1.478654 GGAGAGAGTAGCCTCCTCCAG 60.479 61.905 15.92 0.00 45.32 3.86
2756 3010 4.645535 TGTCCAATTCTTCTTCTGTGGAG 58.354 43.478 0.00 0.00 35.88 3.86
2762 3016 4.352298 AGGGTCTTGTCCAATTCTTCTTCT 59.648 41.667 0.00 0.00 0.00 2.85
2792 3046 6.881065 CCATTTCAGATTCTCTGTCCTGTAAA 59.119 38.462 4.21 0.00 44.58 2.01
2844 3098 1.547372 CCTTGCCACCTCAATTTCCAG 59.453 52.381 0.00 0.00 0.00 3.86
2895 3149 2.948720 GCTGAGAGGCGTCCAGGTT 61.949 63.158 19.60 0.00 0.00 3.50
3038 3292 8.051535 TCATTAATGAGCTTGATTTTCTCCTCT 58.948 33.333 14.23 0.00 32.11 3.69
3056 3310 7.446319 TCCCTAGCATCATTCAACTCATTAATG 59.554 37.037 9.29 9.29 32.96 1.90
3062 3316 3.519107 TGTCCCTAGCATCATTCAACTCA 59.481 43.478 0.00 0.00 0.00 3.41
3098 3352 5.306678 AGTGAGATCCTCAACTGACTTTCTT 59.693 40.000 0.00 0.00 42.46 2.52
3103 3357 2.233431 GCAGTGAGATCCTCAACTGACT 59.767 50.000 20.24 0.00 42.46 3.41
3105 3359 2.233186 CAGCAGTGAGATCCTCAACTGA 59.767 50.000 20.24 0.00 42.46 3.41
3110 3364 1.253593 ACGCAGCAGTGAGATCCTCA 61.254 55.000 0.00 0.00 38.25 3.86
3164 3418 7.758980 TCATCTTCTTTCTTCAGAAATCTCTCG 59.241 37.037 2.45 0.00 42.44 4.04
3308 3562 0.807667 CAGCCTCCAATCTTCCGACG 60.808 60.000 0.00 0.00 0.00 5.12
3316 3570 0.463474 GCTCACCTCAGCCTCCAATC 60.463 60.000 0.00 0.00 32.76 2.67
3380 3634 1.347707 TCCTCCGACTGCTTGTTTGAT 59.652 47.619 0.00 0.00 0.00 2.57
3382 3636 1.532868 CTTCCTCCGACTGCTTGTTTG 59.467 52.381 0.00 0.00 0.00 2.93
3503 3757 4.785511 TTCTGTGTACAGTAGCTTCTCC 57.214 45.455 11.44 0.00 44.12 3.71
3563 3817 0.325272 GACCCTCTTTCTCGGCCTTT 59.675 55.000 0.00 0.00 0.00 3.11
3569 3823 2.165437 CTCCTGAAGACCCTCTTTCTCG 59.835 54.545 0.00 0.00 36.73 4.04
3601 3855 2.490217 CGACCGCTGATTCCGAGT 59.510 61.111 0.00 0.00 0.00 4.18
3638 3892 0.905357 TCTCAGCCTTTACCTCCTGC 59.095 55.000 0.00 0.00 0.00 4.85
3665 3919 0.248377 GCATTAGCTGCGCTTGAAGG 60.248 55.000 9.73 0.39 41.97 3.46
3719 3973 1.003580 TCAGCCTTTACCTCCTGCAAG 59.996 52.381 0.00 0.00 0.00 4.01
3722 3976 0.905357 TCTCAGCCTTTACCTCCTGC 59.095 55.000 0.00 0.00 0.00 4.85
3728 3982 2.188817 TCCTCCTTCTCAGCCTTTACC 58.811 52.381 0.00 0.00 0.00 2.85
3780 4034 1.873591 CTTGTTAGCTTCAGCAACCGT 59.126 47.619 0.75 0.00 45.16 4.83
3803 4057 0.036732 CAGCCTTTACCTCCTGCACA 59.963 55.000 0.00 0.00 0.00 4.57
3804 4058 0.324943 TCAGCCTTTACCTCCTGCAC 59.675 55.000 0.00 0.00 0.00 4.57
3843 4097 3.799232 GCTGACTCCGTGTACAAGAACTT 60.799 47.826 10.61 0.00 0.00 2.66
3846 4100 1.684450 TGCTGACTCCGTGTACAAGAA 59.316 47.619 10.61 0.00 0.00 2.52
3849 4103 1.037493 ACTGCTGACTCCGTGTACAA 58.963 50.000 0.00 0.00 0.00 2.41
3852 4106 0.319555 GCAACTGCTGACTCCGTGTA 60.320 55.000 0.00 0.00 38.21 2.90
3865 4119 2.351157 GCCTTGTTAGCTTCAGCAACTG 60.351 50.000 0.75 0.00 45.16 3.16
3866 4120 1.882623 GCCTTGTTAGCTTCAGCAACT 59.117 47.619 0.75 0.00 45.16 3.16
3884 4138 1.950954 GCCTTTACCTCCTGAACAGCC 60.951 57.143 0.00 0.00 0.00 4.85
3899 4153 0.038890 GGCCCTCTTTCTCAGCCTTT 59.961 55.000 0.00 0.00 40.57 3.11
3912 4166 1.748500 GCTGCTCTTGAAGGCCCTC 60.749 63.158 0.00 0.00 0.00 4.30
3933 4187 1.308069 ACCGCTGATTCCATGTGTGC 61.308 55.000 0.00 0.00 0.00 4.57
3935 4189 1.167851 CAACCGCTGATTCCATGTGT 58.832 50.000 0.00 0.00 0.00 3.72
3950 4204 1.068264 GCCTTGTTAGCTTCAGCAACC 60.068 52.381 0.75 0.00 45.16 3.77
4016 4270 3.788163 GCAATGCGTTCTCTTTATCAAGC 59.212 43.478 0.00 0.00 0.00 4.01
4061 4315 1.945819 GCCTCTCGCAACCTGAATTCA 60.946 52.381 8.12 8.12 37.47 2.57
4082 4336 3.304257 CTCTATCTTCTTCATGGCGTCG 58.696 50.000 0.00 0.00 0.00 5.12
4109 4363 2.047679 CTTCAGCAAGCAAAGCAGAC 57.952 50.000 0.00 0.00 0.00 3.51
4169 4423 2.038557 ACTGTGTACCTCATCCACAACC 59.961 50.000 0.00 0.00 38.52 3.77
4184 4438 1.490693 CTTCACGCGCTGAACTGTGT 61.491 55.000 16.54 0.00 33.65 3.72
4232 4486 2.873094 TGTCACTCTCTCCTTCCGTA 57.127 50.000 0.00 0.00 0.00 4.02
4272 4526 0.462047 GAGTTCCCATTGGCGACGAT 60.462 55.000 0.00 0.00 33.50 3.73
4286 4540 0.669318 TCATGTCGCCGTTGGAGTTC 60.669 55.000 0.00 0.00 0.00 3.01
4295 4549 2.398554 CCCTTGGTTCATGTCGCCG 61.399 63.158 0.00 0.00 0.00 6.46
4312 4566 1.149148 GCTGTCGTGTTTCTCTTCCC 58.851 55.000 0.00 0.00 0.00 3.97
4340 4594 1.035139 CACCTTTTGCTTCCTGCTGT 58.965 50.000 0.00 0.00 43.37 4.40
4371 4625 2.987149 CAACTTTGTCGCTCTCGTGTAT 59.013 45.455 0.00 0.00 36.96 2.29
4547 4807 3.850010 GCTTGTTCTTCTTCTGCGGTTTC 60.850 47.826 0.00 0.00 0.00 2.78
4688 4948 6.141462 GCTGTCATCAAACAAGAAGAAGAAG 58.859 40.000 0.00 0.00 0.00 2.85
4689 4949 5.589855 TGCTGTCATCAAACAAGAAGAAGAA 59.410 36.000 0.00 0.00 0.00 2.52
4770 5035 1.806542 ACAAAGCTACTGCAATCACCG 59.193 47.619 0.00 0.00 42.74 4.94
4864 5136 8.656849 GGCCACAAATCGTGTAGATAATAATAG 58.343 37.037 0.00 0.00 44.78 1.73
4883 5155 1.103803 TTACAAGCAAACGGCCACAA 58.896 45.000 2.24 0.00 46.50 3.33
4911 5183 2.157289 AGGAGGATTAGTAGGGGCTCT 58.843 52.381 0.00 0.00 0.00 4.09
4912 5184 2.158295 TCAGGAGGATTAGTAGGGGCTC 60.158 54.545 0.00 0.00 0.00 4.70
4913 5185 1.866943 TCAGGAGGATTAGTAGGGGCT 59.133 52.381 0.00 0.00 0.00 5.19
4914 5186 2.400467 TCAGGAGGATTAGTAGGGGC 57.600 55.000 0.00 0.00 0.00 5.80
4915 5187 7.388638 TTTTAATCAGGAGGATTAGTAGGGG 57.611 40.000 0.00 0.00 46.34 4.79
4918 5190 9.892130 ACAGTTTTTAATCAGGAGGATTAGTAG 57.108 33.333 0.00 0.00 46.34 2.57
4919 5191 9.667107 CACAGTTTTTAATCAGGAGGATTAGTA 57.333 33.333 0.00 0.00 46.34 1.82
4920 5192 8.164070 ACACAGTTTTTAATCAGGAGGATTAGT 58.836 33.333 0.00 0.00 46.34 2.24
4921 5193 8.567285 ACACAGTTTTTAATCAGGAGGATTAG 57.433 34.615 0.00 0.00 46.34 1.73
4922 5194 9.667107 CTACACAGTTTTTAATCAGGAGGATTA 57.333 33.333 0.00 0.00 44.38 1.75
4924 5196 6.599638 GCTACACAGTTTTTAATCAGGAGGAT 59.400 38.462 0.00 0.00 38.05 3.24
4925 5197 5.938125 GCTACACAGTTTTTAATCAGGAGGA 59.062 40.000 0.00 0.00 0.00 3.71
4950 5222 2.239402 TGACATCAGCTTGCCATAAGGA 59.761 45.455 0.00 0.00 36.89 3.36
4983 5256 6.976934 TCACATTATAGTAGAGGTGCATCA 57.023 37.500 0.00 0.00 0.00 3.07
4984 5257 7.330454 CACATCACATTATAGTAGAGGTGCATC 59.670 40.741 0.00 0.00 34.84 3.91
4985 5258 7.015584 TCACATCACATTATAGTAGAGGTGCAT 59.984 37.037 0.00 0.00 39.86 3.96
4986 5259 6.323739 TCACATCACATTATAGTAGAGGTGCA 59.676 38.462 0.00 0.00 39.86 4.57
4987 5260 6.749139 TCACATCACATTATAGTAGAGGTGC 58.251 40.000 0.00 0.00 39.86 5.01
4988 5261 8.801299 AGATCACATCACATTATAGTAGAGGTG 58.199 37.037 0.00 0.00 40.97 4.00
4989 5262 8.801299 CAGATCACATCACATTATAGTAGAGGT 58.199 37.037 0.00 0.00 0.00 3.85
4990 5263 9.018582 TCAGATCACATCACATTATAGTAGAGG 57.981 37.037 0.00 0.00 0.00 3.69
5005 5278 6.051074 TGGTAACATCACATCAGATCACATC 58.949 40.000 0.00 0.00 46.17 3.06
5020 5293 4.638865 GGTTTATCACCCACTGGTAACATC 59.361 45.833 0.00 0.00 45.57 3.06
5021 5294 4.595986 GGTTTATCACCCACTGGTAACAT 58.404 43.478 0.00 0.00 45.57 2.71
5092 5365 5.762218 GCCAACAGACATGATTAGAATAGCT 59.238 40.000 0.00 0.00 0.00 3.32
5245 5551 8.341903 CCCAAAAAGCAAGTAAATAAAAAGGTG 58.658 33.333 0.00 0.00 0.00 4.00
5248 5554 8.888716 ACACCCAAAAAGCAAGTAAATAAAAAG 58.111 29.630 0.00 0.00 0.00 2.27
5249 5555 8.669243 CACACCCAAAAAGCAAGTAAATAAAAA 58.331 29.630 0.00 0.00 0.00 1.94
5250 5556 7.281100 CCACACCCAAAAAGCAAGTAAATAAAA 59.719 33.333 0.00 0.00 0.00 1.52
5365 5671 7.440505 TTTTAGCTGTACCACCTCCAATATA 57.559 36.000 0.00 0.00 0.00 0.86
5366 5672 5.968676 TTTAGCTGTACCACCTCCAATAT 57.031 39.130 0.00 0.00 0.00 1.28
5367 5673 5.765576 TTTTAGCTGTACCACCTCCAATA 57.234 39.130 0.00 0.00 0.00 1.90
5368 5674 4.650972 TTTTAGCTGTACCACCTCCAAT 57.349 40.909 0.00 0.00 0.00 3.16
5499 5829 2.352651 GCAAATGAATGCTGCTCTCGTA 59.647 45.455 0.00 0.00 43.06 3.43
5501 5831 1.823828 GCAAATGAATGCTGCTCTCG 58.176 50.000 0.00 0.00 43.06 4.04


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

AutoCloner maintained by Alex Coulton.