Multiple sequence alignment - TraesCS6A01G372900

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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 TraesCS6A01G372900 chr6A 100.000 2633 0 0 1 2633 596514941 596517573 0.000000e+00 4863.0
1 TraesCS6A01G372900 chr6A 81.564 537 82 8 379 914 615947999 615948519 6.730000e-116 427.0
2 TraesCS6A01G372900 chr6A 85.537 242 28 2 974 1215 615640350 615640584 2.020000e-61 246.0
3 TraesCS6A01G372900 chr6A 95.238 42 2 0 1276 1317 615640626 615640667 1.690000e-07 67.6
4 TraesCS6A01G372900 chr6D 95.349 645 18 3 321 965 450859240 450859872 0.000000e+00 1014.0
5 TraesCS6A01G372900 chr6D 90.323 465 27 10 2170 2633 450888513 450888960 6.270000e-166 593.0
6 TraesCS6A01G372900 chr6D 96.564 291 9 1 1638 1928 450861579 450861868 5.100000e-132 481.0
7 TraesCS6A01G372900 chr6D 90.031 321 20 6 12 324 450858764 450859080 3.160000e-109 405.0
8 TraesCS6A01G372900 chr6D 98.165 218 4 0 1422 1639 450861325 450861542 5.320000e-102 381.0
9 TraesCS6A01G372900 chr6D 95.434 219 5 2 1126 1343 450861115 450861329 6.980000e-91 344.0
10 TraesCS6A01G372900 chr6D 80.370 433 70 7 526 957 471177217 471176799 5.470000e-82 315.0
11 TraesCS6A01G372900 chr6D 94.624 186 6 1 1158 1343 450861068 450860887 4.290000e-73 285.0
12 TraesCS6A01G372900 chr6D 93.082 159 7 1 974 1132 450860005 450860159 2.040000e-56 230.0
13 TraesCS6A01G372900 chr6D 96.364 110 4 0 1957 2066 450861959 450862068 5.790000e-42 182.0
14 TraesCS6A01G372900 chr6D 92.473 93 3 1 2062 2150 450888273 450888365 2.130000e-26 130.0
15 TraesCS6A01G372900 chr6B 82.540 756 105 17 204 957 719910398 719909668 7.950000e-180 640.0
16 TraesCS6A01G372900 chr6B 81.915 376 53 7 974 1347 719904151 719903789 1.180000e-78 303.0
17 TraesCS6A01G372900 chr1A 100.000 87 0 0 1339 1425 557095274 557095188 7.540000e-36 161.0
18 TraesCS6A01G372900 chr4A 97.826 92 2 0 1340 1431 163914568 163914477 2.710000e-35 159.0
19 TraesCS6A01G372900 chr4A 98.864 88 1 0 1339 1426 621812561 621812474 9.760000e-35 158.0
20 TraesCS6A01G372900 chr2D 97.778 90 2 0 1337 1426 548274245 548274156 3.510000e-34 156.0
21 TraesCS6A01G372900 chr1D 97.778 90 2 0 1338 1427 356580327 356580416 3.510000e-34 156.0
22 TraesCS6A01G372900 chr7D 96.739 92 3 0 1337 1428 581296356 581296265 1.260000e-33 154.0
23 TraesCS6A01G372900 chr5A 96.739 92 3 0 1340 1431 580273581 580273672 1.260000e-33 154.0
24 TraesCS6A01G372900 chr2A 97.753 89 2 0 1339 1427 88278123 88278035 1.260000e-33 154.0
25 TraesCS6A01G372900 chr1B 94.059 101 4 2 1324 1424 37590659 37590757 4.540000e-33 152.0


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 TraesCS6A01G372900 chr6A 596514941 596517573 2632 False 4863.000000 4863 100.000000 1 2633 1 chr6A.!!$F1 2632
1 TraesCS6A01G372900 chr6A 615947999 615948519 520 False 427.000000 427 81.564000 379 914 1 chr6A.!!$F2 535
2 TraesCS6A01G372900 chr6D 450858764 450862068 3304 False 433.857143 1014 94.998429 12 2066 7 chr6D.!!$F1 2054
3 TraesCS6A01G372900 chr6D 450888273 450888960 687 False 361.500000 593 91.398000 2062 2633 2 chr6D.!!$F2 571
4 TraesCS6A01G372900 chr6B 719909668 719910398 730 True 640.000000 640 82.540000 204 957 1 chr6B.!!$R2 753

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
972 1145 0.17668 CCCCTGTCACATTCTCTCGG 59.823 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 4106 0.037877 AGCTTCTCTGCATGCCAAGT 59.962 50.0 16.68 1.16 34.99 3.16 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
35 36 2.159612 CGATCTGCACCTGTCACATTTG 60.160 50.000 0.00 0.00 0.00 2.32
72 73 9.388506 GAATACTCATAGGGATACATTTCCATG 57.611 37.037 0.00 0.00 37.53 3.66
95 96 2.648059 CAAGTATCTTCTTGCCCTGGG 58.352 52.381 8.86 8.86 38.35 4.45
116 121 3.063588 GGCACTGTTAGCTTATTCCGAAC 59.936 47.826 0.00 0.00 0.00 3.95
118 123 4.332819 GCACTGTTAGCTTATTCCGAACAT 59.667 41.667 0.00 0.00 30.16 2.71
127 132 2.990066 ATTCCGAACATGAGAGGACC 57.010 50.000 0.00 0.00 31.69 4.46
145 150 3.057806 GGACCACCACTGAAATTTAACCG 60.058 47.826 0.00 0.00 35.97 4.44
154 159 8.581578 ACCACTGAAATTTAACCGTATCAAAAT 58.418 29.630 0.00 0.00 0.00 1.82
157 162 8.921670 ACTGAAATTTAACCGTATCAAAATTGC 58.078 29.630 0.00 0.00 33.16 3.56
178 183 3.440522 GCCGCTTTTAGAGTTCCTTTGAT 59.559 43.478 0.00 0.00 0.00 2.57
179 184 4.082733 GCCGCTTTTAGAGTTCCTTTGATT 60.083 41.667 0.00 0.00 0.00 2.57
185 190 9.133627 GCTTTTAGAGTTCCTTTGATTTTCATC 57.866 33.333 0.00 0.00 0.00 2.92
190 195 6.436532 AGAGTTCCTTTGATTTTCATCAGCAT 59.563 34.615 0.00 0.00 40.66 3.79
200 205 8.102800 TGATTTTCATCAGCATACATGGATAC 57.897 34.615 0.00 0.00 34.22 2.24
319 327 7.899973 ACCTGCAAAACATCATTTTCTTATCT 58.100 30.769 0.00 0.00 0.00 1.98
354 526 9.277783 CTAATTAACATGCTACTTATGCCTCTT 57.722 33.333 0.00 0.00 0.00 2.85
356 528 9.799106 AATTAACATGCTACTTATGCCTCTTAT 57.201 29.630 0.00 0.00 0.00 1.73
397 570 4.823989 ACTGTTTTTCTACTGCTTGCAGAT 59.176 37.500 26.71 14.26 0.00 2.90
398 571 5.997746 ACTGTTTTTCTACTGCTTGCAGATA 59.002 36.000 26.71 14.58 0.00 1.98
479 652 3.966543 CCCCCTGCTTGTTCCGGT 61.967 66.667 0.00 0.00 0.00 5.28
727 900 4.381612 CCGTGAGCTACTCAAATGTAAGGA 60.382 45.833 0.00 0.00 42.46 3.36
775 948 1.649664 CTTCACTGCCAGATTCCTCG 58.350 55.000 0.00 0.00 0.00 4.63
794 967 4.833380 CCTCGAGAAACCCTGGAGAATATA 59.167 45.833 15.71 0.00 46.77 0.86
870 1043 1.849219 GCATCGTCGATGTCTTCACTC 59.151 52.381 30.29 12.03 41.60 3.51
871 1044 2.478709 GCATCGTCGATGTCTTCACTCT 60.479 50.000 30.29 0.00 41.60 3.24
872 1045 3.763902 CATCGTCGATGTCTTCACTCTT 58.236 45.455 24.11 0.00 35.54 2.85
873 1046 3.473093 TCGTCGATGTCTTCACTCTTC 57.527 47.619 4.21 0.00 0.00 2.87
874 1047 2.812011 TCGTCGATGTCTTCACTCTTCA 59.188 45.455 4.21 0.00 0.00 3.02
875 1048 2.911723 CGTCGATGTCTTCACTCTTCAC 59.088 50.000 0.00 0.00 0.00 3.18
876 1049 3.365465 CGTCGATGTCTTCACTCTTCACT 60.365 47.826 0.00 0.00 0.00 3.41
965 1138 1.985159 TCTAACAGCCCCTGTCACATT 59.015 47.619 0.00 0.00 44.62 2.71
966 1139 2.027192 TCTAACAGCCCCTGTCACATTC 60.027 50.000 0.00 0.00 44.62 2.67
967 1140 0.773644 AACAGCCCCTGTCACATTCT 59.226 50.000 0.00 0.00 44.62 2.40
969 1142 0.617413 CAGCCCCTGTCACATTCTCT 59.383 55.000 0.00 0.00 0.00 3.10
970 1143 0.908198 AGCCCCTGTCACATTCTCTC 59.092 55.000 0.00 0.00 0.00 3.20
971 1144 0.460987 GCCCCTGTCACATTCTCTCG 60.461 60.000 0.00 0.00 0.00 4.04
972 1145 0.176680 CCCCTGTCACATTCTCTCGG 59.823 60.000 0.00 0.00 0.00 4.63
976 1273 2.167281 CCTGTCACATTCTCTCGGATGT 59.833 50.000 0.00 0.00 0.00 3.06
981 1278 3.511540 TCACATTCTCTCGGATGTTCAGT 59.488 43.478 0.00 0.00 0.00 3.41
1023 1320 0.106708 GTGGTTCCACTCTGTGCAGA 59.893 55.000 13.97 1.69 34.42 4.26
1043 1340 1.995626 GGCCCCTCAGCTTGGTCTA 60.996 63.158 0.00 0.00 0.00 2.59
1044 1341 1.222113 GCCCCTCAGCTTGGTCTAC 59.778 63.158 2.26 0.00 0.00 2.59
1045 1342 1.553690 GCCCCTCAGCTTGGTCTACA 61.554 60.000 2.26 0.00 0.00 2.74
1046 1343 1.207791 CCCCTCAGCTTGGTCTACAT 58.792 55.000 2.26 0.00 0.00 2.29
1053 1350 2.338577 GCTTGGTCTACATGCAGGAT 57.661 50.000 4.84 0.00 46.36 3.24
1071 1368 5.050490 CAGGATATAACAACCGACAAGGAG 58.950 45.833 0.00 0.00 45.00 3.69
1083 1380 1.971357 GACAAGGAGGACTGGAGTCAA 59.029 52.381 8.99 0.00 46.47 3.18
1116 1413 2.124320 ACAGCGCTGGTGGTTTGT 60.124 55.556 38.27 15.48 35.13 2.83
1150 2410 6.096423 GCTTATCGTTTTTATTCCCTTCCCTT 59.904 38.462 0.00 0.00 0.00 3.95
1224 2484 0.465097 AGAAGCTGGATGATTGGGCG 60.465 55.000 0.00 0.00 0.00 6.13
1273 2533 1.503542 CCACTTTCGTGCATGAGCC 59.496 57.895 8.93 0.00 39.86 4.70
1274 2534 1.503542 CACTTTCGTGCATGAGCCC 59.496 57.895 8.93 0.00 41.13 5.19
1275 2535 2.034879 ACTTTCGTGCATGAGCCCG 61.035 57.895 8.93 0.00 43.21 6.13
1276 2536 3.386867 CTTTCGTGCATGAGCCCGC 62.387 63.158 8.93 0.00 41.55 6.13
1344 2604 3.750828 GCTCTCAGCCTTGTACTCC 57.249 57.895 0.00 0.00 34.48 3.85
1345 2605 0.176910 GCTCTCAGCCTTGTACTCCC 59.823 60.000 0.00 0.00 34.48 4.30
1346 2606 1.859302 CTCTCAGCCTTGTACTCCCT 58.141 55.000 0.00 0.00 0.00 4.20
1347 2607 1.754226 CTCTCAGCCTTGTACTCCCTC 59.246 57.143 0.00 0.00 0.00 4.30
1348 2608 1.359474 TCTCAGCCTTGTACTCCCTCT 59.641 52.381 0.00 0.00 0.00 3.69
1349 2609 1.480137 CTCAGCCTTGTACTCCCTCTG 59.520 57.143 0.00 0.00 0.00 3.35
1350 2610 1.203187 TCAGCCTTGTACTCCCTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
1351 2611 2.042569 TCAGCCTTGTACTCCCTCTGTA 59.957 50.000 0.00 0.00 0.00 2.74
1352 2612 2.832129 CAGCCTTGTACTCCCTCTGTAA 59.168 50.000 0.00 0.00 0.00 2.41
1353 2613 3.260884 CAGCCTTGTACTCCCTCTGTAAA 59.739 47.826 0.00 0.00 0.00 2.01
1354 2614 3.261137 AGCCTTGTACTCCCTCTGTAAAC 59.739 47.826 0.00 0.00 0.00 2.01
1355 2615 3.261137 GCCTTGTACTCCCTCTGTAAACT 59.739 47.826 0.00 0.00 0.00 2.66
1356 2616 4.465305 GCCTTGTACTCCCTCTGTAAACTA 59.535 45.833 0.00 0.00 0.00 2.24
1357 2617 5.046807 GCCTTGTACTCCCTCTGTAAACTAA 60.047 44.000 0.00 0.00 0.00 2.24
1358 2618 6.351966 GCCTTGTACTCCCTCTGTAAACTAAT 60.352 42.308 0.00 0.00 0.00 1.73
1359 2619 7.147776 GCCTTGTACTCCCTCTGTAAACTAATA 60.148 40.741 0.00 0.00 0.00 0.98
1360 2620 8.925338 CCTTGTACTCCCTCTGTAAACTAATAT 58.075 37.037 0.00 0.00 0.00 1.28
1366 2626 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
1368 2628 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
1401 2661 9.654663 AACTAAAATAGTGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 39.39 2.85
1415 2675 9.669353 TCTAAACGCTCTTATAATAGTTTACGG 57.331 33.333 0.42 0.45 34.29 4.02
1416 2676 9.669353 CTAAACGCTCTTATAATAGTTTACGGA 57.331 33.333 0.42 0.00 34.29 4.69
1417 2677 8.571461 AAACGCTCTTATAATAGTTTACGGAG 57.429 34.615 0.42 0.00 31.14 4.63
1418 2678 6.675987 ACGCTCTTATAATAGTTTACGGAGG 58.324 40.000 0.42 0.00 0.00 4.30
1419 2679 6.091437 CGCTCTTATAATAGTTTACGGAGGG 58.909 44.000 0.42 0.00 0.00 4.30
1420 2680 6.072286 CGCTCTTATAATAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 32.14 4.20
1421 2681 7.314393 GCTCTTATAATAGTTTACGGAGGGAG 58.686 42.308 0.42 0.00 0.00 4.30
1422 2682 7.039853 GCTCTTATAATAGTTTACGGAGGGAGT 60.040 40.741 0.42 0.00 0.00 3.85
1423 2683 9.512588 CTCTTATAATAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1424 2684 9.289782 TCTTATAATAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1425 2685 9.294614 CTTATAATAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
1439 2699 0.038526 AGTACTTTCCACGGACTGCG 60.039 55.000 0.00 0.00 0.00 5.18
1728 3026 9.613428 CAGTTAATTATTACCCAAGTCTCATGA 57.387 33.333 0.00 0.00 0.00 3.07
1739 3037 2.983229 AGTCTCATGATGTTGGTCTGC 58.017 47.619 0.00 0.00 0.00 4.26
1740 3038 2.012673 GTCTCATGATGTTGGTCTGCC 58.987 52.381 0.00 0.00 0.00 4.85
1742 3040 0.612744 TCATGATGTTGGTCTGCCGA 59.387 50.000 0.00 0.00 37.67 5.54
1869 3167 5.029014 GCTACTGTCGTGTATACTCACTTG 58.971 45.833 4.17 3.29 36.33 3.16
1928 3226 3.681897 CAGCTTCTTATCGTTTCAGTGCT 59.318 43.478 0.00 0.00 0.00 4.40
1929 3227 4.153117 CAGCTTCTTATCGTTTCAGTGCTT 59.847 41.667 0.00 0.00 0.00 3.91
1930 3228 4.390297 AGCTTCTTATCGTTTCAGTGCTTC 59.610 41.667 0.00 0.00 0.00 3.86
1932 3230 4.168922 TCTTATCGTTTCAGTGCTTCGA 57.831 40.909 6.01 6.01 35.14 3.71
1933 3231 4.744570 TCTTATCGTTTCAGTGCTTCGAT 58.255 39.130 15.86 15.86 42.45 3.59
1934 3232 5.886992 TCTTATCGTTTCAGTGCTTCGATA 58.113 37.500 14.46 14.46 40.72 2.92
1935 3233 5.971792 TCTTATCGTTTCAGTGCTTCGATAG 59.028 40.000 16.36 12.96 41.88 2.08
1937 3235 3.499048 TCGTTTCAGTGCTTCGATAGTC 58.501 45.455 0.00 0.00 37.40 2.59
1940 3238 1.746470 TCAGTGCTTCGATAGTCCGA 58.254 50.000 0.00 0.00 36.70 4.55
1942 3240 2.159421 TCAGTGCTTCGATAGTCCGAAC 60.159 50.000 0.00 0.00 42.74 3.95
1943 3241 1.816835 AGTGCTTCGATAGTCCGAACA 59.183 47.619 0.00 0.00 42.74 3.18
1944 3242 2.427453 AGTGCTTCGATAGTCCGAACAT 59.573 45.455 0.00 0.00 42.74 2.71
1945 3243 2.535984 GTGCTTCGATAGTCCGAACATG 59.464 50.000 0.00 0.00 42.74 3.21
1946 3244 1.523095 GCTTCGATAGTCCGAACATGC 59.477 52.381 0.00 0.00 42.74 4.06
1949 3247 1.754803 TCGATAGTCCGAACATGCCTT 59.245 47.619 0.00 0.00 35.42 4.35
1950 3248 2.953648 TCGATAGTCCGAACATGCCTTA 59.046 45.455 0.00 0.00 35.42 2.69
1952 3250 3.675225 CGATAGTCCGAACATGCCTTATG 59.325 47.826 0.00 0.00 42.68 1.90
1953 3251 4.558697 CGATAGTCCGAACATGCCTTATGA 60.559 45.833 0.00 0.00 39.21 2.15
1954 3252 3.845781 AGTCCGAACATGCCTTATGAT 57.154 42.857 0.00 0.00 39.21 2.45
2007 3367 6.151312 GCTCCGATAGTTCATATTAGTCCTGA 59.849 42.308 0.00 0.00 0.00 3.86
2055 3415 2.203280 TTGAGGCCCGTGTTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
2089 3449 4.444081 CTCGGACGAGGAGGGGGT 62.444 72.222 13.59 0.00 38.51 4.95
2114 3478 1.393603 CGTGCTCAGAGGAGATACCA 58.606 55.000 0.00 0.00 44.26 3.25
2168 3546 2.493278 GGTGATGTGGAAATCTTGGTGG 59.507 50.000 0.00 0.00 0.00 4.61
2225 3717 4.539293 ACTAGTAGTTGAGGAGTGGTAGGA 59.461 45.833 0.00 0.00 0.00 2.94
2294 3786 2.107366 TGGTCAATCTGGTATGCGAGA 58.893 47.619 0.00 0.00 34.04 4.04
2333 3825 5.369404 TGGTGATGAATATCAGAGCCCTTTA 59.631 40.000 0.00 0.00 43.66 1.85
2335 3827 6.597280 GGTGATGAATATCAGAGCCCTTTATC 59.403 42.308 0.00 0.00 43.66 1.75
2388 3880 2.225068 TCTCGATTTCATTCGGGAGC 57.775 50.000 0.00 0.00 43.38 4.70
2416 3908 1.954382 TGCGAGACAGACTAGTTGTGT 59.046 47.619 10.71 10.71 0.00 3.72
2417 3909 2.361119 TGCGAGACAGACTAGTTGTGTT 59.639 45.455 13.23 5.17 0.00 3.32
2418 3910 2.726760 GCGAGACAGACTAGTTGTGTTG 59.273 50.000 13.23 13.41 0.00 3.33
2419 3911 2.726760 CGAGACAGACTAGTTGTGTTGC 59.273 50.000 13.23 8.13 0.00 4.17
2420 3912 3.717707 GAGACAGACTAGTTGTGTTGCA 58.282 45.455 13.23 0.00 0.00 4.08
2421 3913 4.119862 GAGACAGACTAGTTGTGTTGCAA 58.880 43.478 13.23 0.00 34.16 4.08
2444 3936 1.992557 TGCAAGGGACCTAAGTGGATT 59.007 47.619 0.00 0.00 39.71 3.01
2472 3964 4.619160 CGCCTCCGAATATCATGAAGATCA 60.619 45.833 0.00 0.00 35.86 2.92
2490 3982 4.637534 AGATCAATGTTGACGCAGCTTTAT 59.362 37.500 0.00 0.00 40.49 1.40
2495 3987 3.637432 TGTTGACGCAGCTTTATTTTGG 58.363 40.909 0.00 0.00 0.00 3.28
2522 4014 3.056754 GCCAATAAGGGGGCGGTCT 62.057 63.158 0.00 0.00 40.93 3.85
2551 4044 0.107945 CAGAACTGCTACAGGGGAGC 60.108 60.000 0.00 0.00 40.53 4.70
2553 4046 1.605058 GAACTGCTACAGGGGAGCGA 61.605 60.000 0.00 0.00 43.19 4.93
2554 4047 1.889530 AACTGCTACAGGGGAGCGAC 61.890 60.000 0.00 0.00 43.19 5.19
2563 4056 2.732619 GGGGAGCGACTACTTGGGG 61.733 68.421 0.00 0.00 0.00 4.96
2568 4061 0.034896 AGCGACTACTTGGGGTGTTG 59.965 55.000 0.00 0.00 0.00 3.33
2587 4080 5.355910 GTGTTGGTCTGTAACTTTTGAAGGA 59.644 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.949142 CAGATCGATCATCTCTGCAGG 58.051 52.381 26.47 4.77 40.20 4.85
4 5 2.296752 AGGTGCAGATCGATCATCTCTG 59.703 50.000 26.47 17.10 40.20 3.35
5 6 2.296752 CAGGTGCAGATCGATCATCTCT 59.703 50.000 26.47 13.74 40.20 3.10
6 7 2.035704 ACAGGTGCAGATCGATCATCTC 59.964 50.000 26.47 16.53 40.20 2.75
7 8 2.035704 GACAGGTGCAGATCGATCATCT 59.964 50.000 26.47 10.19 43.33 2.90
8 9 2.223900 TGACAGGTGCAGATCGATCATC 60.224 50.000 26.47 17.12 0.00 2.92
9 10 1.758862 TGACAGGTGCAGATCGATCAT 59.241 47.619 26.47 9.59 0.00 2.45
10 11 1.134995 GTGACAGGTGCAGATCGATCA 60.135 52.381 26.47 4.61 0.00 2.92
11 12 1.134995 TGTGACAGGTGCAGATCGATC 60.135 52.381 17.91 17.91 0.00 3.69
12 13 0.897621 TGTGACAGGTGCAGATCGAT 59.102 50.000 0.00 0.00 0.00 3.59
13 14 0.897621 ATGTGACAGGTGCAGATCGA 59.102 50.000 0.00 0.00 0.00 3.59
14 15 1.730501 AATGTGACAGGTGCAGATCG 58.269 50.000 0.00 0.00 0.00 3.69
15 16 2.415090 GCAAATGTGACAGGTGCAGATC 60.415 50.000 15.78 0.00 35.28 2.75
16 17 1.542915 GCAAATGTGACAGGTGCAGAT 59.457 47.619 15.78 0.00 35.28 2.90
35 36 7.727181 TCCCTATGAGTATTCTTTCTGTAAGC 58.273 38.462 0.00 0.00 33.66 3.09
90 91 2.717639 ATAAGCTAACAGTGCCCAGG 57.282 50.000 0.00 0.00 0.00 4.45
91 92 2.945668 GGAATAAGCTAACAGTGCCCAG 59.054 50.000 0.00 0.00 0.00 4.45
92 93 2.679639 CGGAATAAGCTAACAGTGCCCA 60.680 50.000 0.00 0.00 0.00 5.36
93 94 1.940613 CGGAATAAGCTAACAGTGCCC 59.059 52.381 0.00 0.00 0.00 5.36
94 95 2.901249 TCGGAATAAGCTAACAGTGCC 58.099 47.619 0.00 0.00 0.00 5.01
95 96 3.682858 TGTTCGGAATAAGCTAACAGTGC 59.317 43.478 0.00 0.00 0.00 4.40
96 97 5.580691 TCATGTTCGGAATAAGCTAACAGTG 59.419 40.000 2.74 0.00 33.90 3.66
97 98 5.730550 TCATGTTCGGAATAAGCTAACAGT 58.269 37.500 2.74 0.00 33.90 3.55
100 105 5.463724 CCTCTCATGTTCGGAATAAGCTAAC 59.536 44.000 0.00 0.00 0.00 2.34
116 121 1.269958 TCAGTGGTGGTCCTCTCATG 58.730 55.000 0.00 0.00 35.65 3.07
118 123 1.801242 TTTCAGTGGTGGTCCTCTCA 58.199 50.000 0.00 0.00 35.65 3.27
127 132 6.489127 TGATACGGTTAAATTTCAGTGGTG 57.511 37.500 0.00 0.00 0.00 4.17
145 150 6.322491 ACTCTAAAAGCGGCAATTTTGATAC 58.678 36.000 1.45 0.00 32.38 2.24
154 159 2.561478 AGGAACTCTAAAAGCGGCAA 57.439 45.000 1.45 0.00 0.00 4.52
157 162 5.629079 AATCAAAGGAACTCTAAAAGCGG 57.371 39.130 0.00 0.00 38.49 5.52
178 183 5.469760 CGGTATCCATGTATGCTGATGAAAA 59.530 40.000 0.00 0.00 0.00 2.29
179 184 4.996758 CGGTATCCATGTATGCTGATGAAA 59.003 41.667 0.00 0.00 0.00 2.69
185 190 7.549134 ACAAATATACGGTATCCATGTATGCTG 59.451 37.037 3.47 0.00 31.63 4.41
190 195 7.541916 TGGACAAATATACGGTATCCATGTA 57.458 36.000 3.47 0.00 29.85 2.29
200 205 5.215252 AGAGTGGATGGACAAATATACGG 57.785 43.478 0.00 0.00 0.00 4.02
230 238 4.320608 ACAAACTTGTTATTGCACCAGG 57.679 40.909 0.00 0.00 38.47 4.45
328 500 8.839310 AGAGGCATAAGTAGCATGTTAATTAG 57.161 34.615 13.58 8.10 0.00 1.73
417 590 2.046988 GCTGGGGTTTTGCATGGC 60.047 61.111 0.00 0.00 0.00 4.40
533 706 1.795768 TGTCTCGAAAAGAGCGCAAT 58.204 45.000 11.47 0.00 46.44 3.56
537 710 3.181526 CCAAGAATGTCTCGAAAAGAGCG 60.182 47.826 0.00 0.00 46.44 5.03
727 900 1.774254 TCGGGTTGGCAGGATCAATAT 59.226 47.619 0.00 0.00 0.00 1.28
775 948 8.753497 ACATTTTATATTCTCCAGGGTTTCTC 57.247 34.615 0.00 0.00 0.00 2.87
794 967 5.163195 ACCATAGGAAGAGCCGATACATTTT 60.163 40.000 0.00 0.00 43.43 1.82
873 1046 1.597742 CTGAAACCTCCACACCAGTG 58.402 55.000 0.00 0.00 45.47 3.66
874 1047 0.179018 GCTGAAACCTCCACACCAGT 60.179 55.000 0.00 0.00 0.00 4.00
875 1048 0.109342 AGCTGAAACCTCCACACCAG 59.891 55.000 0.00 0.00 0.00 4.00
876 1049 0.108585 GAGCTGAAACCTCCACACCA 59.891 55.000 0.00 0.00 0.00 4.17
965 1138 4.464244 AGAATGAACTGAACATCCGAGAGA 59.536 41.667 0.00 0.00 0.00 3.10
966 1139 4.753233 AGAATGAACTGAACATCCGAGAG 58.247 43.478 0.00 0.00 0.00 3.20
967 1140 4.464244 AGAGAATGAACTGAACATCCGAGA 59.536 41.667 0.00 0.00 0.00 4.04
969 1142 4.675408 CGAGAGAATGAACTGAACATCCGA 60.675 45.833 0.00 0.00 0.00 4.55
970 1143 3.549471 CGAGAGAATGAACTGAACATCCG 59.451 47.826 0.00 0.00 0.00 4.18
971 1144 3.868077 CCGAGAGAATGAACTGAACATCC 59.132 47.826 0.00 0.00 0.00 3.51
972 1145 4.748892 TCCGAGAGAATGAACTGAACATC 58.251 43.478 0.00 0.00 0.00 3.06
976 1273 3.679917 GCCATCCGAGAGAATGAACTGAA 60.680 47.826 0.00 0.00 0.00 3.02
981 1278 3.208594 CATTGCCATCCGAGAGAATGAA 58.791 45.455 0.00 0.00 0.00 2.57
1023 1320 2.943265 ACCAAGCTGAGGGGCCAT 60.943 61.111 4.39 0.00 0.00 4.40
1043 1340 4.127171 GTCGGTTGTTATATCCTGCATGT 58.873 43.478 0.00 0.00 0.00 3.21
1044 1341 4.126437 TGTCGGTTGTTATATCCTGCATG 58.874 43.478 0.00 0.00 0.00 4.06
1045 1342 4.415881 TGTCGGTTGTTATATCCTGCAT 57.584 40.909 0.00 0.00 0.00 3.96
1046 1343 3.897141 TGTCGGTTGTTATATCCTGCA 57.103 42.857 0.00 0.00 0.00 4.41
1053 1350 4.081862 CAGTCCTCCTTGTCGGTTGTTATA 60.082 45.833 0.00 0.00 0.00 0.98
1071 1368 2.028930 ACGATGTTCTTGACTCCAGTCC 60.029 50.000 4.25 0.00 44.15 3.85
1083 1380 3.375642 CGCTGTCATATCACGATGTTCT 58.624 45.455 0.00 0.00 0.00 3.01
1116 1413 6.751514 ATAAAAACGATAAGCATGTCACCA 57.248 33.333 0.00 0.00 0.00 4.17
1150 2410 2.442272 GAGGCGGTAGAGCTCCCA 60.442 66.667 10.93 0.00 37.29 4.37
1192 2452 2.413142 GCTTCTCCATGGGCAGCAC 61.413 63.158 19.95 0.00 0.00 4.40
1224 2484 3.081554 TCTGCCCCCAGAAAGAGC 58.918 61.111 0.00 0.00 44.79 4.09
1273 2533 3.457263 CCCCATTTTTCCGGGCGG 61.457 66.667 0.00 0.00 41.57 6.13
1274 2534 2.361865 TCCCCATTTTTCCGGGCG 60.362 61.111 0.00 0.00 41.57 6.13
1275 2535 2.058001 CCTCCCCATTTTTCCGGGC 61.058 63.158 0.00 0.00 41.57 6.13
1276 2536 1.381191 CCCTCCCCATTTTTCCGGG 60.381 63.158 0.00 0.00 42.67 5.73
1317 2577 3.133014 GCTGAGAGCCATAGCCGA 58.867 61.111 0.00 0.00 41.25 5.54
1375 2635 9.654663 AAGAGCGTTTAGATCACTATTTTAGTT 57.345 29.630 0.00 0.00 37.82 2.24
1389 2649 9.669353 CCGTAAACTATTATAAGAGCGTTTAGA 57.331 33.333 7.03 0.00 30.36 2.10
1390 2650 9.669353 TCCGTAAACTATTATAAGAGCGTTTAG 57.331 33.333 7.03 0.00 30.36 1.85
1391 2651 9.669353 CTCCGTAAACTATTATAAGAGCGTTTA 57.331 33.333 7.03 4.27 0.00 2.01
1392 2652 7.650903 CCTCCGTAAACTATTATAAGAGCGTTT 59.349 37.037 7.03 5.14 0.00 3.60
1393 2653 7.144000 CCTCCGTAAACTATTATAAGAGCGTT 58.856 38.462 7.03 4.77 0.00 4.84
1394 2654 6.294397 CCCTCCGTAAACTATTATAAGAGCGT 60.294 42.308 7.03 0.00 0.00 5.07
1395 2655 6.072286 TCCCTCCGTAAACTATTATAAGAGCG 60.072 42.308 7.03 2.96 0.00 5.03
1396 2656 7.039853 ACTCCCTCCGTAAACTATTATAAGAGC 60.040 40.741 7.03 0.00 0.00 4.09
1397 2657 8.406730 ACTCCCTCCGTAAACTATTATAAGAG 57.593 38.462 5.56 5.56 0.00 2.85
1398 2658 9.289782 GTACTCCCTCCGTAAACTATTATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1399 2659 9.294614 AGTACTCCCTCCGTAAACTATTATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1400 2660 9.646522 AAGTACTCCCTCCGTAAACTATTATAA 57.353 33.333 0.00 0.00 0.00 0.98
1401 2661 9.646522 AAAGTACTCCCTCCGTAAACTATTATA 57.353 33.333 0.00 0.00 0.00 0.98
1402 2662 8.544687 AAAGTACTCCCTCCGTAAACTATTAT 57.455 34.615 0.00 0.00 0.00 1.28
1403 2663 7.068716 GGAAAGTACTCCCTCCGTAAACTATTA 59.931 40.741 0.00 0.00 0.00 0.98
1404 2664 6.127225 GGAAAGTACTCCCTCCGTAAACTATT 60.127 42.308 0.00 0.00 0.00 1.73
1405 2665 5.362143 GGAAAGTACTCCCTCCGTAAACTAT 59.638 44.000 0.00 0.00 0.00 2.12
1406 2666 4.706962 GGAAAGTACTCCCTCCGTAAACTA 59.293 45.833 0.00 0.00 0.00 2.24
1407 2667 3.513119 GGAAAGTACTCCCTCCGTAAACT 59.487 47.826 0.00 0.00 0.00 2.66
1408 2668 3.259123 TGGAAAGTACTCCCTCCGTAAAC 59.741 47.826 13.46 0.00 34.22 2.01
1409 2669 3.259123 GTGGAAAGTACTCCCTCCGTAAA 59.741 47.826 13.46 0.00 34.22 2.01
1410 2670 2.827921 GTGGAAAGTACTCCCTCCGTAA 59.172 50.000 13.46 0.00 34.22 3.18
1411 2671 2.450476 GTGGAAAGTACTCCCTCCGTA 58.550 52.381 13.46 0.00 34.22 4.02
1412 2672 1.264295 GTGGAAAGTACTCCCTCCGT 58.736 55.000 13.46 0.00 34.22 4.69
1413 2673 0.172803 CGTGGAAAGTACTCCCTCCG 59.827 60.000 13.46 11.66 34.22 4.63
1414 2674 0.535797 CCGTGGAAAGTACTCCCTCC 59.464 60.000 13.46 11.91 34.22 4.30
1415 2675 1.204231 GTCCGTGGAAAGTACTCCCTC 59.796 57.143 13.46 9.82 34.22 4.30
1416 2676 1.203149 AGTCCGTGGAAAGTACTCCCT 60.203 52.381 13.46 0.00 34.22 4.20
1417 2677 1.067071 CAGTCCGTGGAAAGTACTCCC 60.067 57.143 0.00 1.23 34.22 4.30
1418 2678 1.672145 GCAGTCCGTGGAAAGTACTCC 60.672 57.143 0.00 0.00 35.88 3.85
1419 2679 1.711206 GCAGTCCGTGGAAAGTACTC 58.289 55.000 0.00 0.00 0.00 2.59
1420 2680 0.038526 CGCAGTCCGTGGAAAGTACT 60.039 55.000 0.00 0.00 0.00 2.73
1421 2681 2.442084 CGCAGTCCGTGGAAAGTAC 58.558 57.895 0.00 0.00 0.00 2.73
1422 2682 4.979204 CGCAGTCCGTGGAAAGTA 57.021 55.556 0.00 0.00 0.00 2.24
1439 2699 2.060980 ACAGGATCCGGCTCCTCAC 61.061 63.158 24.12 0.00 44.04 3.51
1564 2824 0.971447 AGAGCTAACTCCACGGGGTC 60.971 60.000 2.12 0.00 44.65 4.46
1573 2833 1.134848 CCAGAGTGGCAGAGCTAACTC 60.135 57.143 13.67 13.67 43.82 3.01
1595 2855 3.247006 AGTAGAACATGCTTGGGTACG 57.753 47.619 4.44 0.00 0.00 3.67
1739 3037 3.886505 AGAGAGAGCATAGGTAAAGTCGG 59.113 47.826 0.00 0.00 0.00 4.79
1740 3038 4.336993 ACAGAGAGAGCATAGGTAAAGTCG 59.663 45.833 0.00 0.00 0.00 4.18
1742 3040 6.613153 AAACAGAGAGAGCATAGGTAAAGT 57.387 37.500 0.00 0.00 0.00 2.66
1795 3093 8.418662 CCTGTGCCAACTATATAAAGTACAGTA 58.581 37.037 13.26 0.00 33.43 2.74
1797 3095 6.706270 CCCTGTGCCAACTATATAAAGTACAG 59.294 42.308 0.00 0.00 34.37 2.74
1798 3096 6.408776 CCCCTGTGCCAACTATATAAAGTACA 60.409 42.308 0.00 0.00 0.00 2.90
1828 3126 1.338973 AGCATGCAAATTGATAGGGCG 59.661 47.619 21.98 0.00 0.00 6.13
1840 3138 2.734276 TACACGACAGTAGCATGCAA 57.266 45.000 21.98 0.00 0.00 4.08
1869 3167 7.615403 TCAGAACCATGTCCTGAATATATAGC 58.385 38.462 6.50 0.00 34.38 2.97
1928 3226 1.754803 AGGCATGTTCGGACTATCGAA 59.245 47.619 0.00 0.00 45.34 3.71
1929 3227 1.399714 AGGCATGTTCGGACTATCGA 58.600 50.000 0.00 0.00 37.38 3.59
1930 3228 2.225068 AAGGCATGTTCGGACTATCG 57.775 50.000 0.00 0.00 0.00 2.92
1932 3230 4.955811 TCATAAGGCATGTTCGGACTAT 57.044 40.909 0.00 0.00 35.96 2.12
1933 3231 4.955811 ATCATAAGGCATGTTCGGACTA 57.044 40.909 0.00 0.00 35.96 2.59
1934 3232 3.845781 ATCATAAGGCATGTTCGGACT 57.154 42.857 0.00 0.00 35.96 3.85
1935 3233 7.667043 TTATAATCATAAGGCATGTTCGGAC 57.333 36.000 0.00 0.00 35.96 4.79
1937 3235 8.567948 ACTTTTATAATCATAAGGCATGTTCGG 58.432 33.333 0.00 0.00 35.96 4.30
2007 3367 1.131126 CTGCCGCAATCGAAGTGAAAT 59.869 47.619 3.77 0.00 38.10 2.17
2038 3398 2.203280 CCACAACACGGGCCTCAA 60.203 61.111 0.84 0.00 0.00 3.02
2047 3407 3.670377 GAAGGCCGGCCACAACAC 61.670 66.667 45.13 24.55 38.92 3.32
2089 3449 4.020617 CCTCTGAGCACGGGCCAA 62.021 66.667 5.73 0.00 42.56 4.52
2114 3478 3.149648 GAGCCGCCATTGCCCATT 61.150 61.111 0.00 0.00 0.00 3.16
2152 3530 3.304911 TGAACCACCAAGATTTCCACA 57.695 42.857 0.00 0.00 0.00 4.17
2155 3533 3.996363 GCAAATGAACCACCAAGATTTCC 59.004 43.478 0.00 0.00 0.00 3.13
2168 3546 1.464608 TCGCTACAGCTGCAAATGAAC 59.535 47.619 15.27 0.00 39.32 3.18
2191 3683 7.870027 TCCTCAACTACTAGTAGGAGTACATT 58.130 38.462 29.05 12.90 37.49 2.71
2199 3691 4.857679 ACCACTCCTCAACTACTAGTAGG 58.142 47.826 29.05 16.85 37.49 3.18
2200 3692 6.056884 CCTACCACTCCTCAACTACTAGTAG 58.943 48.000 25.30 25.30 39.04 2.57
2201 3693 5.728253 TCCTACCACTCCTCAACTACTAGTA 59.272 44.000 1.89 1.89 0.00 1.82
2202 3694 4.539293 TCCTACCACTCCTCAACTACTAGT 59.461 45.833 0.00 0.00 0.00 2.57
2203 3695 4.883006 GTCCTACCACTCCTCAACTACTAG 59.117 50.000 0.00 0.00 0.00 2.57
2204 3696 4.624843 CGTCCTACCACTCCTCAACTACTA 60.625 50.000 0.00 0.00 0.00 1.82
2205 3697 3.699413 GTCCTACCACTCCTCAACTACT 58.301 50.000 0.00 0.00 0.00 2.57
2206 3698 2.422832 CGTCCTACCACTCCTCAACTAC 59.577 54.545 0.00 0.00 0.00 2.73
2207 3699 2.619849 CCGTCCTACCACTCCTCAACTA 60.620 54.545 0.00 0.00 0.00 2.24
2219 3711 2.509422 GATTGGCCCCGTCCTACC 59.491 66.667 0.00 0.00 0.00 3.18
2225 3717 2.432300 CGACTAGGATTGGCCCCGT 61.432 63.158 0.00 0.00 37.37 5.28
2279 3771 1.399714 TCCGTCTCGCATACCAGATT 58.600 50.000 0.00 0.00 0.00 2.40
2282 3774 1.560923 CTTTCCGTCTCGCATACCAG 58.439 55.000 0.00 0.00 0.00 4.00
2294 3786 3.810310 TCACCAAAAATTGCTTTCCGT 57.190 38.095 0.00 0.00 0.00 4.69
2364 3856 3.384789 TCCCGAATGAAATCGAGATCACT 59.615 43.478 5.18 0.00 45.48 3.41
2388 3880 1.000283 AGTCTGTCTCGCAGGTTTCTG 60.000 52.381 0.00 0.00 45.08 3.02
2418 3910 1.541588 CTTAGGTCCCTTGCAAGTTGC 59.458 52.381 24.35 21.17 45.29 4.17
2419 3911 2.554032 CACTTAGGTCCCTTGCAAGTTG 59.446 50.000 24.35 15.17 0.00 3.16
2420 3912 2.489073 CCACTTAGGTCCCTTGCAAGTT 60.489 50.000 24.35 7.62 0.00 2.66
2421 3913 1.073923 CCACTTAGGTCCCTTGCAAGT 59.926 52.381 24.35 8.64 0.00 3.16
2422 3914 1.351017 TCCACTTAGGTCCCTTGCAAG 59.649 52.381 19.93 19.93 39.02 4.01
2432 3924 1.449601 CGGCGCAATCCACTTAGGT 60.450 57.895 10.83 0.00 39.02 3.08
2444 3936 3.858868 GATATTCGGAGGCGGCGCA 62.859 63.158 34.36 12.58 0.00 6.09
2456 3948 7.533222 GCGTCAACATTGATCTTCATGATATTC 59.467 37.037 0.00 0.00 39.73 1.75
2472 3964 4.685628 CCAAAATAAAGCTGCGTCAACATT 59.314 37.500 0.00 0.00 0.00 2.71
2495 3987 1.338020 CCCCTTATTGGCTGATTTCGC 59.662 52.381 0.00 0.00 0.00 4.70
2506 3998 1.227556 CGAGACCGCCCCCTTATTG 60.228 63.158 0.00 0.00 0.00 1.90
2551 4044 0.395312 ACCAACACCCCAAGTAGTCG 59.605 55.000 0.00 0.00 0.00 4.18
2553 4046 1.420138 CAGACCAACACCCCAAGTAGT 59.580 52.381 0.00 0.00 0.00 2.73
2554 4047 1.420138 ACAGACCAACACCCCAAGTAG 59.580 52.381 0.00 0.00 0.00 2.57
2563 4056 5.355910 TCCTTCAAAAGTTACAGACCAACAC 59.644 40.000 0.00 0.00 0.00 3.32
2568 4061 5.123936 ACAGTCCTTCAAAAGTTACAGACC 58.876 41.667 0.00 0.00 0.00 3.85
2587 4080 1.556911 AGAATTGCTGGATCGGACAGT 59.443 47.619 0.00 0.00 38.22 3.55
2613 4106 0.037877 AGCTTCTCTGCATGCCAAGT 59.962 50.000 16.68 1.16 34.99 3.16


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

AutoCloner maintained by Alex Coulton.