Multiple sequence alignment - TraesCS7B01G191500

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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 TraesCS7B01G191500 chr7B 100.000 5561 0 0 1 5561 329357089 329362649 0.000000e+00 10270
1 TraesCS7B01G191500 chr7D 96.224 3734 77 22 1859 5561 186412221 186415921 0.000000e+00 6056
2 TraesCS7B01G191500 chr7D 89.260 1527 102 28 355 1853 186410548 186412040 0.000000e+00 1855
3 TraesCS7B01G191500 chr7D 80.315 254 43 6 4808 5057 618063735 618063485 9.510000e-43 185
4 TraesCS7B01G191500 chr7D 92.241 116 8 1 1879 1994 550233539 550233653 4.460000e-36 163
5 TraesCS7B01G191500 chr7A 96.851 3207 59 19 2044 5226 198669689 198666501 0.000000e+00 5325
6 TraesCS7B01G191500 chr7A 89.551 890 63 25 578 1459 198671325 198670458 0.000000e+00 1101
7 TraesCS7B01G191500 chr7A 97.313 335 8 1 5227 5561 198666216 198665883 8.080000e-158 568
8 TraesCS7B01G191500 chr7A 92.879 323 11 1 1546 1856 198670462 198670140 5.080000e-125 459
9 TraesCS7B01G191500 chr7A 85.442 419 58 3 1 417 198672060 198671643 3.080000e-117 433
10 TraesCS7B01G191500 chr7A 96.257 187 7 0 1857 2043 198669985 198669799 1.950000e-79 307
11 TraesCS7B01G191500 chr1D 88.629 299 29 4 4728 5024 194677638 194677343 5.300000e-95 359
12 TraesCS7B01G191500 chr3B 83.810 315 46 5 4743 5057 204753262 204752953 1.520000e-75 294
13 TraesCS7B01G191500 chr3B 95.327 107 5 0 1881 1987 505264572 505264678 2.660000e-38 171
14 TraesCS7B01G191500 chr3B 94.444 108 6 0 1881 1988 211111462 211111355 3.450000e-37 167
15 TraesCS7B01G191500 chr1B 83.946 299 32 7 4728 5024 271104483 271104767 7.100000e-69 272
16 TraesCS7B01G191500 chr1B 76.970 330 64 10 4734 5057 626160413 626160090 1.590000e-40 178
17 TraesCS7B01G191500 chr1B 76.923 234 49 4 4825 5055 207523251 207523482 1.630000e-25 128
18 TraesCS7B01G191500 chr1A 87.565 193 21 2 4834 5024 242793676 242793485 2.610000e-53 220
19 TraesCS7B01G191500 chr5B 93.966 116 7 0 1879 1994 364132774 364132659 5.730000e-40 176
20 TraesCS7B01G191500 chr2D 94.643 112 6 0 1876 1987 473292194 473292305 2.060000e-39 174
21 TraesCS7B01G191500 chr6A 95.327 107 5 0 1881 1987 222555005 222554899 2.660000e-38 171
22 TraesCS7B01G191500 chr5D 91.379 116 10 0 1879 1994 315929084 315928969 5.770000e-35 159


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 TraesCS7B01G191500 chr7B 329357089 329362649 5560 False 10270.0 10270 100.000000 1 5561 1 chr7B.!!$F1 5560
1 TraesCS7B01G191500 chr7D 186410548 186415921 5373 False 3955.5 6056 92.742000 355 5561 2 chr7D.!!$F2 5206
2 TraesCS7B01G191500 chr7A 198665883 198672060 6177 True 1365.5 5325 93.048833 1 5561 6 chr7A.!!$R1 5560

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
208 210 0.241213 CTCTCCAGCGACGTCTGAAA 59.759 55.0 14.7 7.24 36.19 2.69 F
1397 1610 0.250858 TGTGTGCCTCCATTCCTGTG 60.251 55.0 0.0 0.00 0.00 3.66 F
2744 3260 0.167251 CGCAACACGTAATTCCCCAC 59.833 55.0 0.0 0.00 36.87 4.61 F
3239 3755 0.249911 GGACCGTGTGCTCTCAAAGT 60.250 55.0 0.0 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1712 0.457851 CAACCCCAACAAACGCTTGA 59.542 50.0 5.39 0.00 36.33 3.02 R
3061 3577 0.928505 AATCCCCATGCATGTGAGGA 59.071 50.0 24.44 24.44 0.00 3.71 R
3974 4492 0.612453 AACAGACGGAGGAGAGGGTC 60.612 60.0 0.00 0.00 0.00 4.46 R
5034 5576 0.109272 GTTGGAAAAAGCGCTAGGCC 60.109 55.0 12.05 11.06 45.17 5.19 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.286170 GTCCTTAAAACTTAAGAAGATTGACCT 57.714 33.333 10.09 0.00 0.00 3.85
32 33 9.284968 TCCTTAAAACTTAAGAAGATTGACCTG 57.715 33.333 10.09 0.00 0.00 4.00
43 44 8.635765 AAGAAGATTGACCTGCAACTTATTAA 57.364 30.769 0.00 0.00 39.78 1.40
49 50 5.815581 TGACCTGCAACTTATTAATGACCT 58.184 37.500 0.00 0.00 0.00 3.85
50 51 5.880332 TGACCTGCAACTTATTAATGACCTC 59.120 40.000 0.00 0.00 0.00 3.85
51 52 4.876107 ACCTGCAACTTATTAATGACCTCG 59.124 41.667 0.00 0.00 0.00 4.63
56 58 5.465724 GCAACTTATTAATGACCTCGTAGGG 59.534 44.000 0.00 0.00 40.58 3.53
60 62 7.627311 ACTTATTAATGACCTCGTAGGGTTTT 58.373 34.615 0.00 3.81 40.58 2.43
73 75 2.727544 GTTTTTCTGCTGGCGCCA 59.272 55.556 30.59 30.59 34.43 5.69
74 76 1.290009 GTTTTTCTGCTGGCGCCAT 59.710 52.632 32.87 0.00 34.43 4.40
114 116 5.238583 GGCTTGCTGTTGTATATAGTAGGG 58.761 45.833 0.00 0.00 0.00 3.53
138 140 8.541234 GGGTTAGGATTATATCTAGTTTGGAGG 58.459 40.741 0.00 0.00 0.00 4.30
155 157 4.603946 GCTATCCACGGGGCGTCC 62.604 72.222 0.00 0.00 38.32 4.79
206 208 2.691771 GCTCTCCAGCGACGTCTGA 61.692 63.158 14.70 4.06 35.39 3.27
208 210 0.241213 CTCTCCAGCGACGTCTGAAA 59.759 55.000 14.70 7.24 36.19 2.69
215 217 1.860078 CGACGTCTGAAAGTTGCCC 59.140 57.895 14.70 0.00 33.76 5.36
218 220 2.954611 GTCTGAAAGTTGCCCGCC 59.045 61.111 0.00 0.00 33.76 6.13
237 239 1.219393 CCCTCTTCCGGTTGCTCTC 59.781 63.158 0.00 0.00 0.00 3.20
242 244 0.745845 CTTCCGGTTGCTCTCCATGG 60.746 60.000 4.97 4.97 0.00 3.66
269 271 2.115291 GGCTGCCAAAGGACGATCC 61.115 63.158 15.17 0.00 36.58 3.36
271 273 1.815421 CTGCCAAAGGACGATCCGG 60.815 63.158 0.00 0.00 42.75 5.14
282 284 0.811915 ACGATCCGGTGTTCTCTGAG 59.188 55.000 0.00 0.00 0.00 3.35
285 287 2.619177 CGATCCGGTGTTCTCTGAGTAT 59.381 50.000 0.00 0.00 0.00 2.12
307 309 0.322456 TTGGTGAAAGGCTGGATCGG 60.322 55.000 0.00 0.00 0.00 4.18
309 311 1.299976 GTGAAAGGCTGGATCGGGT 59.700 57.895 0.00 0.00 0.00 5.28
315 317 4.301027 GCTGGATCGGGTAGCCGG 62.301 72.222 31.34 16.82 43.46 6.13
332 334 2.585153 GGGGCCTCGTTCCTCTTC 59.415 66.667 0.84 0.00 0.00 2.87
335 337 0.973496 GGGCCTCGTTCCTCTTCTCT 60.973 60.000 0.84 0.00 0.00 3.10
336 338 0.899019 GGCCTCGTTCCTCTTCTCTT 59.101 55.000 0.00 0.00 0.00 2.85
345 347 4.074970 GTTCCTCTTCTCTTTTGCCATCA 58.925 43.478 0.00 0.00 0.00 3.07
346 348 3.679389 TCCTCTTCTCTTTTGCCATCAC 58.321 45.455 0.00 0.00 0.00 3.06
352 354 1.734465 CTCTTTTGCCATCACGAGGAC 59.266 52.381 0.00 0.00 0.00 3.85
353 355 1.071542 TCTTTTGCCATCACGAGGACA 59.928 47.619 0.00 0.00 0.00 4.02
367 369 0.419459 AGGACAGAAGGGATGGAGGT 59.581 55.000 0.00 0.00 0.00 3.85
380 382 1.228245 GGAGGTGGCAAAGCTGTGA 60.228 57.895 8.49 0.00 36.52 3.58
409 411 2.047179 GGGTCTGGAGTTCCACGC 60.047 66.667 0.00 0.00 42.01 5.34
418 423 0.667792 GAGTTCCACGCGAAGAAGCT 60.668 55.000 15.93 13.95 34.40 3.74
420 425 0.944311 GTTCCACGCGAAGAAGCTGA 60.944 55.000 15.93 0.00 34.40 4.26
437 446 4.135306 AGCTGACATGTTCATCATCATCC 58.865 43.478 0.00 0.00 34.09 3.51
446 455 3.625252 TCATCATCATCCTCTCCCTCA 57.375 47.619 0.00 0.00 0.00 3.86
483 492 5.976458 TGAGGCAAATCTTTTGTCTTTGTT 58.024 33.333 8.35 0.00 34.05 2.83
486 495 8.037758 TGAGGCAAATCTTTTGTCTTTGTTTAA 58.962 29.630 8.35 0.00 34.05 1.52
487 496 8.424274 AGGCAAATCTTTTGTCTTTGTTTAAG 57.576 30.769 1.42 0.00 28.58 1.85
505 516 7.802738 TGTTTAAGAAAATGTGGATCTACACG 58.197 34.615 14.74 0.00 44.21 4.49
572 591 2.684881 CACCATTGATCCCTTCCTTTCG 59.315 50.000 0.00 0.00 0.00 3.46
600 797 1.152984 CACTCACACCTGCCCACAA 60.153 57.895 0.00 0.00 0.00 3.33
605 802 1.453745 ACACCTGCCCACAACACAG 60.454 57.895 0.00 0.00 0.00 3.66
609 806 4.912395 TGCCCACAACACAGCCCC 62.912 66.667 0.00 0.00 0.00 5.80
613 810 2.518349 CACAACACAGCCCCGGTT 60.518 61.111 0.00 0.00 0.00 4.44
614 811 2.203294 ACAACACAGCCCCGGTTC 60.203 61.111 0.00 0.00 0.00 3.62
615 812 2.203280 CAACACAGCCCCGGTTCA 60.203 61.111 0.00 0.00 0.00 3.18
618 815 1.178534 AACACAGCCCCGGTTCATTG 61.179 55.000 0.00 0.00 0.00 2.82
623 823 2.676121 CCCCGGTTCATTGCAGCA 60.676 61.111 0.00 0.00 0.00 4.41
656 856 3.000819 ATCGCCCAACGGTCTCCA 61.001 61.111 0.00 0.00 43.89 3.86
716 917 3.556306 ACACCTCCACACCCACCG 61.556 66.667 0.00 0.00 0.00 4.94
728 929 4.499633 CCACCGCCGGGGCTTTAT 62.500 66.667 14.15 0.00 40.62 1.40
739 940 1.602377 GGGGCTTTATCCGTCATTTCG 59.398 52.381 0.00 0.00 0.00 3.46
741 942 1.940613 GGCTTTATCCGTCATTTCGCT 59.059 47.619 0.00 0.00 0.00 4.93
796 999 1.485294 TACCCCGCAGAAAGGCAGAA 61.485 55.000 0.00 0.00 0.00 3.02
797 1000 2.042831 CCCCGCAGAAAGGCAGAAG 61.043 63.158 0.00 0.00 0.00 2.85
798 1001 2.694760 CCCGCAGAAAGGCAGAAGC 61.695 63.158 0.00 0.00 41.10 3.86
799 1002 1.673665 CCGCAGAAAGGCAGAAGCT 60.674 57.895 0.00 0.00 41.70 3.74
803 1006 1.885790 GCAGAAAGGCAGAAGCTCCTT 60.886 52.381 0.00 0.00 44.07 3.36
805 1008 1.004161 AGAAAGGCAGAAGCTCCTTCC 59.996 52.381 4.98 0.00 41.54 3.46
806 1009 1.004161 GAAAGGCAGAAGCTCCTTCCT 59.996 52.381 4.98 0.00 41.54 3.36
807 1010 0.617935 AAGGCAGAAGCTCCTTCCTC 59.382 55.000 0.00 0.00 40.98 3.71
988 1195 2.031163 GATTCGGGGCTCATCCGG 59.969 66.667 0.00 0.00 46.78 5.14
1045 1252 2.460275 CCCGATTCGATTGTGCGCA 61.460 57.895 5.66 5.66 0.00 6.09
1070 1277 1.154073 GTCTCGCGCGGTTCTAAGT 60.154 57.895 31.69 0.00 0.00 2.24
1092 1299 1.664306 GATTCGGTAGCGGTAGGGG 59.336 63.158 15.23 0.00 0.00 4.79
1299 1508 0.395311 ATGTTCCTCCGCGGTAGAGA 60.395 55.000 27.15 14.66 32.86 3.10
1397 1610 0.250858 TGTGTGCCTCCATTCCTGTG 60.251 55.000 0.00 0.00 0.00 3.66
1421 1634 2.080693 GCGTTACCATGTTCACATCCA 58.919 47.619 0.00 0.00 33.61 3.41
1430 1643 2.781923 TGTTCACATCCACCATCTGTG 58.218 47.619 0.00 0.00 45.01 3.66
1442 1655 1.069022 CCATCTGTGGCGTTCTTTGTG 60.069 52.381 0.00 0.00 39.01 3.33
1443 1656 1.069022 CATCTGTGGCGTTCTTTGTGG 60.069 52.381 0.00 0.00 0.00 4.17
1450 1667 2.903547 CGTTCTTTGTGGTGCCCCG 61.904 63.158 0.00 0.00 0.00 5.73
1472 1689 4.437390 CGCTTTGGGTTATGAATCTGTGAC 60.437 45.833 0.00 0.00 0.00 3.67
1478 1695 5.665360 TGGGTTATGAATCTGTGACCTATCA 59.335 40.000 0.00 0.00 0.00 2.15
1482 1699 3.785486 TGAATCTGTGACCTATCAAGCG 58.215 45.455 0.00 0.00 36.31 4.68
1488 1705 3.472652 TGTGACCTATCAAGCGTTTGTT 58.527 40.909 11.93 6.35 36.31 2.83
1489 1706 3.249799 TGTGACCTATCAAGCGTTTGTTG 59.750 43.478 11.93 3.76 36.31 3.33
1490 1707 3.496884 GTGACCTATCAAGCGTTTGTTGA 59.503 43.478 11.93 3.29 36.31 3.18
1491 1708 3.496884 TGACCTATCAAGCGTTTGTTGAC 59.503 43.478 11.93 1.82 36.76 3.18
1492 1709 2.812011 ACCTATCAAGCGTTTGTTGACC 59.188 45.455 11.93 0.00 36.76 4.02
1493 1710 3.074412 CCTATCAAGCGTTTGTTGACCT 58.926 45.455 11.93 0.00 36.76 3.85
1494 1711 4.250464 CCTATCAAGCGTTTGTTGACCTA 58.750 43.478 11.93 0.00 36.76 3.08
1495 1712 4.876107 CCTATCAAGCGTTTGTTGACCTAT 59.124 41.667 11.93 0.00 36.76 2.57
1496 1713 4.946784 ATCAAGCGTTTGTTGACCTATC 57.053 40.909 11.93 0.00 36.76 2.08
1497 1714 3.734463 TCAAGCGTTTGTTGACCTATCA 58.266 40.909 11.93 0.00 35.73 2.15
1498 1715 4.130857 TCAAGCGTTTGTTGACCTATCAA 58.869 39.130 11.93 0.00 36.46 2.57
1499 1716 4.213270 TCAAGCGTTTGTTGACCTATCAAG 59.787 41.667 11.93 0.00 45.58 3.02
1500 1717 2.484264 AGCGTTTGTTGACCTATCAAGC 59.516 45.455 0.00 0.00 45.58 4.01
1501 1718 2.724839 GCGTTTGTTGACCTATCAAGCG 60.725 50.000 8.47 8.47 45.58 4.68
1502 1719 2.478894 CGTTTGTTGACCTATCAAGCGT 59.521 45.455 0.00 0.00 45.58 5.07
1503 1720 3.059188 CGTTTGTTGACCTATCAAGCGTT 60.059 43.478 0.00 0.00 45.58 4.84
1504 1721 4.553938 CGTTTGTTGACCTATCAAGCGTTT 60.554 41.667 0.00 0.00 45.58 3.60
1505 1722 4.481930 TTGTTGACCTATCAAGCGTTTG 57.518 40.909 5.53 5.53 45.58 2.93
1506 1723 3.472652 TGTTGACCTATCAAGCGTTTGT 58.527 40.909 11.93 2.51 45.58 2.83
1507 1724 3.880490 TGTTGACCTATCAAGCGTTTGTT 59.120 39.130 11.93 6.35 45.58 2.83
1517 1734 1.227118 GCGTTTGTTGGGGTTGGTG 60.227 57.895 0.00 0.00 0.00 4.17
1530 1747 4.724798 TGGGGTTGGTGCTTAGTATATCTT 59.275 41.667 0.00 0.00 0.00 2.40
1531 1748 5.163237 TGGGGTTGGTGCTTAGTATATCTTC 60.163 44.000 0.00 0.00 0.00 2.87
1535 1752 7.226918 GGGTTGGTGCTTAGTATATCTTCTTTC 59.773 40.741 0.00 0.00 0.00 2.62
1837 2066 3.314080 TGGGTTTGCGACTAAAAGTTCAG 59.686 43.478 0.00 0.00 0.00 3.02
1853 2082 8.685838 AAAAGTTCAGTTAACCTTGCTGTATA 57.314 30.769 0.88 0.00 39.03 1.47
1915 2319 5.483811 TCCATATTAGTTGTCGCTGAAACA 58.516 37.500 0.00 0.00 0.00 2.83
2054 2567 9.917129 TTCTTCACGAACTACATTCTTATTACA 57.083 29.630 0.00 0.00 34.88 2.41
2135 2648 6.165659 AGCAAATACTTACTGCTGTTAACG 57.834 37.500 0.09 0.00 44.56 3.18
2583 3099 6.127814 CCAGACTTCACAATGCATATCTTGTT 60.128 38.462 0.00 0.00 33.45 2.83
2744 3260 0.167251 CGCAACACGTAATTCCCCAC 59.833 55.000 0.00 0.00 36.87 4.61
2930 3446 3.526899 TGGAGGAATGAGGTCCAACTTA 58.473 45.455 0.00 0.00 40.48 2.24
3239 3755 0.249911 GGACCGTGTGCTCTCAAAGT 60.250 55.000 0.00 0.00 0.00 2.66
3250 3766 2.611473 GCTCTCAAAGTCTACTGCTGCA 60.611 50.000 0.88 0.88 0.00 4.41
3518 4034 1.531602 GGTCTTGTGCCCCAGCTTT 60.532 57.895 0.00 0.00 40.80 3.51
3602 4118 7.946655 TGAATGAGCCGTATCAATTTACTAG 57.053 36.000 0.00 0.00 31.76 2.57
3617 4133 9.733556 TCAATTTACTAGAAATGGCACTTCTAA 57.266 29.630 17.91 6.93 35.50 2.10
3926 4444 3.095163 AGGCCAGCTCCATCCCAG 61.095 66.667 5.01 0.00 0.00 4.45
3944 4462 0.535102 AGCGCTGTTGGCAGTAACTT 60.535 50.000 10.39 0.00 44.32 2.66
3974 4492 5.597806 TCGGAACACTGGTAGCTAATAATG 58.402 41.667 0.00 0.00 0.00 1.90
4068 4586 8.996651 TTGTGTCCTCTCTAGTATTATCATCA 57.003 34.615 0.00 0.00 0.00 3.07
4069 4587 8.628630 TGTGTCCTCTCTAGTATTATCATCAG 57.371 38.462 0.00 0.00 0.00 2.90
4070 4588 8.221251 TGTGTCCTCTCTAGTATTATCATCAGT 58.779 37.037 0.00 0.00 0.00 3.41
4071 4589 9.073475 GTGTCCTCTCTAGTATTATCATCAGTT 57.927 37.037 0.00 0.00 0.00 3.16
4191 4709 6.815641 TGTTATGTTCAAGTTTGCATGTGTTT 59.184 30.769 0.00 0.00 0.00 2.83
4236 4754 7.496529 TTCTTGCCGATTATTTTCCTAGATG 57.503 36.000 0.00 0.00 0.00 2.90
4393 4911 1.739371 GCCGCTTGGAAGAAGTCGTAT 60.739 52.381 0.00 0.00 33.02 3.06
4570 5091 1.635487 TGCATCTTTAGGGACCTGCTT 59.365 47.619 0.00 0.00 0.00 3.91
4759 5301 0.525761 GCGCTAGGCAATGACCAAAA 59.474 50.000 0.00 0.00 42.87 2.44
4847 5389 2.879826 TCATGTCATACTGCACTGACG 58.120 47.619 12.27 0.00 43.74 4.35
5034 5576 2.191128 AGGTCAACTGCCTTGCTTAG 57.809 50.000 0.00 0.00 31.04 2.18
5139 5681 1.718361 CGAACTTGTGCAATCACGACG 60.718 52.381 0.00 0.00 46.01 5.12
5149 5691 1.464608 CAATCACGACGCCTGACATTT 59.535 47.619 0.00 0.00 0.00 2.32
5288 6114 3.585862 TGAGATTTCGCTGTCTACCAAC 58.414 45.455 0.00 0.00 0.00 3.77
5360 6186 5.990120 ACTGCTGCTTTATCTCCAATTTT 57.010 34.783 0.00 0.00 0.00 1.82
5361 6187 6.350629 ACTGCTGCTTTATCTCCAATTTTT 57.649 33.333 0.00 0.00 0.00 1.94
5534 6360 0.811616 GCCTGGATGACCTTGTAGCG 60.812 60.000 0.00 0.00 37.04 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.023706 GCAGGTCAATCTTCTTAAGTTTTAAGG 58.976 37.037 1.63 0.00 0.00 2.69
12 13 6.547510 AGTTGCAGGTCAATCTTCTTAAGTTT 59.452 34.615 1.63 0.00 36.99 2.66
22 23 7.067494 GGTCATTAATAAGTTGCAGGTCAATCT 59.933 37.037 0.00 0.00 36.99 2.40
31 32 6.046593 CCTACGAGGTCATTAATAAGTTGCA 58.953 40.000 0.00 0.00 0.00 4.08
32 33 5.465724 CCCTACGAGGTCATTAATAAGTTGC 59.534 44.000 0.00 0.00 31.93 4.17
43 44 3.868754 GCAGAAAAACCCTACGAGGTCAT 60.869 47.826 0.00 0.00 40.05 3.06
49 50 1.880646 GCCAGCAGAAAAACCCTACGA 60.881 52.381 0.00 0.00 0.00 3.43
50 51 0.521735 GCCAGCAGAAAAACCCTACG 59.478 55.000 0.00 0.00 0.00 3.51
51 52 0.521735 CGCCAGCAGAAAAACCCTAC 59.478 55.000 0.00 0.00 0.00 3.18
60 62 2.747460 GTGATGGCGCCAGCAGAA 60.747 61.111 44.91 23.72 43.29 3.02
73 75 1.689273 GCCGACCTCCTAATCAGTGAT 59.311 52.381 0.00 0.00 0.00 3.06
74 76 1.112113 GCCGACCTCCTAATCAGTGA 58.888 55.000 0.00 0.00 0.00 3.41
114 116 8.817876 AGCCTCCAAACTAGATATAATCCTAAC 58.182 37.037 0.00 0.00 0.00 2.34
134 136 3.942439 GCCCCGTGGATAGCCTCC 61.942 72.222 0.00 0.00 45.19 4.30
138 140 4.603946 GGACGCCCCGTGGATAGC 62.604 72.222 0.00 0.00 41.37 2.97
165 167 3.950794 AAATGAAGCTCCGCCGCGA 62.951 57.895 15.93 0.00 34.40 5.87
167 169 2.405191 GAAATGAAGCTCCGCCGC 59.595 61.111 0.00 0.00 0.00 6.53
170 172 1.345176 CGTCGAAATGAAGCTCCGC 59.655 57.895 0.00 0.00 0.00 5.54
171 173 1.345176 GCGTCGAAATGAAGCTCCG 59.655 57.895 0.00 0.00 46.89 4.63
198 200 1.860078 CGGGCAACTTTCAGACGTC 59.140 57.895 7.70 7.70 0.00 4.34
206 208 4.678743 GAGGGGGCGGGCAACTTT 62.679 66.667 3.27 0.00 0.00 2.66
215 217 4.778143 CAACCGGAAGAGGGGGCG 62.778 72.222 9.46 0.00 35.02 6.13
218 220 2.245438 GAGAGCAACCGGAAGAGGGG 62.245 65.000 9.46 0.00 35.02 4.79
263 265 0.811915 CTCAGAGAACACCGGATCGT 59.188 55.000 9.46 0.00 0.00 3.73
264 266 0.811915 ACTCAGAGAACACCGGATCG 59.188 55.000 9.46 0.00 0.00 3.69
269 271 2.926200 CAAGCATACTCAGAGAACACCG 59.074 50.000 3.79 0.00 0.00 4.94
271 273 3.681897 CACCAAGCATACTCAGAGAACAC 59.318 47.826 3.79 0.00 0.00 3.32
282 284 1.474077 CCAGCCTTTCACCAAGCATAC 59.526 52.381 0.00 0.00 0.00 2.39
285 287 0.112995 ATCCAGCCTTTCACCAAGCA 59.887 50.000 0.00 0.00 0.00 3.91
315 317 1.962321 GAGAAGAGGAACGAGGCCCC 61.962 65.000 0.00 0.00 0.00 5.80
317 319 0.899019 AAGAGAAGAGGAACGAGGCC 59.101 55.000 0.00 0.00 0.00 5.19
323 325 4.074970 TGATGGCAAAAGAGAAGAGGAAC 58.925 43.478 0.00 0.00 0.00 3.62
329 331 2.417933 CCTCGTGATGGCAAAAGAGAAG 59.582 50.000 14.89 0.41 0.00 2.85
332 334 1.734465 GTCCTCGTGATGGCAAAAGAG 59.266 52.381 8.76 8.76 0.00 2.85
335 337 1.071542 TCTGTCCTCGTGATGGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
336 338 0.684535 TCTGTCCTCGTGATGGCAAA 59.315 50.000 0.00 0.00 0.00 3.68
345 347 0.041238 TCCATCCCTTCTGTCCTCGT 59.959 55.000 0.00 0.00 0.00 4.18
346 348 0.749649 CTCCATCCCTTCTGTCCTCG 59.250 60.000 0.00 0.00 0.00 4.63
352 354 1.225704 GCCACCTCCATCCCTTCTG 59.774 63.158 0.00 0.00 0.00 3.02
353 355 0.846427 TTGCCACCTCCATCCCTTCT 60.846 55.000 0.00 0.00 0.00 2.85
367 369 1.383456 GGTGTGTCACAGCTTTGCCA 61.383 55.000 24.51 0.00 42.83 4.92
409 411 3.681417 TGATGAACATGTCAGCTTCTTCG 59.319 43.478 0.00 0.00 43.39 3.79
418 423 5.454329 GGAGAGGATGATGATGAACATGTCA 60.454 44.000 0.00 0.00 39.56 3.58
420 425 4.202440 GGGAGAGGATGATGATGAACATGT 60.202 45.833 0.00 0.00 39.56 3.21
480 489 7.658167 TCGTGTAGATCCACATTTTCTTAAACA 59.342 33.333 0.00 0.00 34.98 2.83
483 492 7.383687 AGTCGTGTAGATCCACATTTTCTTAA 58.616 34.615 0.00 0.00 34.98 1.85
486 495 5.407407 AGTCGTGTAGATCCACATTTTCT 57.593 39.130 0.00 0.00 34.98 2.52
487 496 4.265556 CGAGTCGTGTAGATCCACATTTTC 59.734 45.833 3.82 0.00 34.98 2.29
549 568 4.625324 CGAAAGGAAGGGATCAATGGTGTA 60.625 45.833 0.00 0.00 0.00 2.90
560 579 2.150719 TGGGCACGAAAGGAAGGGA 61.151 57.895 0.00 0.00 0.00 4.20
572 591 1.598130 GTGTGAGTGGAGTGGGCAC 60.598 63.158 0.00 0.00 0.00 5.01
600 797 1.603455 CAATGAACCGGGGCTGTGT 60.603 57.895 6.32 0.00 0.00 3.72
605 802 4.133796 GCTGCAATGAACCGGGGC 62.134 66.667 6.32 0.00 0.00 5.80
609 806 1.074319 GCACATGCTGCAATGAACCG 61.074 55.000 18.26 0.96 46.29 4.44
645 845 3.411351 CCGCGTTGGAGACCGTTG 61.411 66.667 4.92 0.00 42.00 4.10
647 847 4.353437 GACCGCGTTGGAGACCGT 62.353 66.667 4.92 0.00 42.00 4.83
656 856 3.732892 CATTTGGCCGACCGCGTT 61.733 61.111 4.92 0.00 39.70 4.84
667 868 2.495866 GGCATGGGCGTCATTTGG 59.504 61.111 0.00 0.00 42.47 3.28
697 898 2.594592 GTGGGTGTGGAGGTGTGC 60.595 66.667 0.00 0.00 0.00 4.57
724 925 1.591158 GCGAGCGAAATGACGGATAAA 59.409 47.619 0.00 0.00 0.00 1.40
726 927 0.596600 GGCGAGCGAAATGACGGATA 60.597 55.000 0.00 0.00 0.00 2.59
728 929 2.508439 GGCGAGCGAAATGACGGA 60.508 61.111 0.00 0.00 0.00 4.69
739 940 1.366854 CCTAAAAACGGGAGGCGAGC 61.367 60.000 0.00 0.00 0.00 5.03
741 942 0.686224 TTCCTAAAAACGGGAGGCGA 59.314 50.000 0.00 0.00 0.00 5.54
776 977 1.745489 CTGCCTTTCTGCGGGGTAC 60.745 63.158 0.00 0.00 33.86 3.34
796 999 0.776080 TTTTGGGGGAGGAAGGAGCT 60.776 55.000 0.00 0.00 0.00 4.09
797 1000 0.114364 TTTTTGGGGGAGGAAGGAGC 59.886 55.000 0.00 0.00 0.00 4.70
839 1042 3.444805 GTCTGTCTCGCCCTCGCT 61.445 66.667 0.00 0.00 35.26 4.93
843 1046 1.228583 TGTCTGTCTGTCTCGCCCT 60.229 57.895 0.00 0.00 0.00 5.19
845 1048 1.214062 CCTGTCTGTCTGTCTCGCC 59.786 63.158 0.00 0.00 0.00 5.54
994 1201 2.184020 CTCTTGGTGGACATGGCCGA 62.184 60.000 14.43 2.07 0.00 5.54
1022 1229 1.967319 CACAATCGAATCGGGGGAAT 58.033 50.000 1.76 0.00 0.00 3.01
1070 1277 2.067091 CTACCGCTACCGAATCCGCA 62.067 60.000 0.00 0.00 36.29 5.69
1127 1334 3.009115 GGCTCAGTGGCACCCCTA 61.009 66.667 15.27 0.00 41.37 3.53
1137 1345 0.549950 CAATCCATCCAGGGCTCAGT 59.450 55.000 0.00 0.00 38.24 3.41
1220 1429 1.021390 CATGTTGTCACCTCCGGCTC 61.021 60.000 0.00 0.00 0.00 4.70
1233 1442 2.096466 TCTAAGCACGAAACGCATGTTG 60.096 45.455 0.00 0.00 38.62 3.33
1234 1443 2.139917 TCTAAGCACGAAACGCATGTT 58.860 42.857 0.00 0.00 40.98 2.71
1299 1508 0.899717 TTACTTACTCCCGTGGGCGT 60.900 55.000 5.77 5.77 37.04 5.68
1397 1610 1.604755 TGTGAACATGGTAACGCAACC 59.395 47.619 0.00 0.00 40.19 3.77
1430 1643 2.335011 GGCACCACAAAGAACGCC 59.665 61.111 0.00 0.00 0.00 5.68
1450 1667 4.142381 GGTCACAGATTCATAACCCAAAGC 60.142 45.833 0.00 0.00 0.00 3.51
1472 1689 3.074412 AGGTCAACAAACGCTTGATAGG 58.926 45.455 5.39 0.00 36.33 2.57
1478 1695 3.058224 GCTTGATAGGTCAACAAACGCTT 60.058 43.478 0.00 0.00 39.36 4.68
1482 1699 4.483476 AACGCTTGATAGGTCAACAAAC 57.517 40.909 0.00 0.00 39.36 2.93
1488 1705 2.811431 CCAACAAACGCTTGATAGGTCA 59.189 45.455 5.39 0.00 36.33 4.02
1489 1706 2.161609 CCCAACAAACGCTTGATAGGTC 59.838 50.000 5.39 0.00 36.33 3.85
1490 1707 2.159382 CCCAACAAACGCTTGATAGGT 58.841 47.619 5.39 0.00 36.33 3.08
1491 1708 1.472480 CCCCAACAAACGCTTGATAGG 59.528 52.381 5.39 3.94 36.33 2.57
1492 1709 2.159382 ACCCCAACAAACGCTTGATAG 58.841 47.619 5.39 0.00 36.33 2.08
1493 1710 2.279935 ACCCCAACAAACGCTTGATA 57.720 45.000 5.39 0.00 36.33 2.15
1494 1711 1.068434 CAACCCCAACAAACGCTTGAT 59.932 47.619 5.39 0.00 36.33 2.57
1495 1712 0.457851 CAACCCCAACAAACGCTTGA 59.542 50.000 5.39 0.00 36.33 3.02
1496 1713 0.529555 CCAACCCCAACAAACGCTTG 60.530 55.000 0.00 0.00 38.61 4.01
1497 1714 0.973496 ACCAACCCCAACAAACGCTT 60.973 50.000 0.00 0.00 0.00 4.68
1498 1715 1.380650 ACCAACCCCAACAAACGCT 60.381 52.632 0.00 0.00 0.00 5.07
1499 1716 1.227118 CACCAACCCCAACAAACGC 60.227 57.895 0.00 0.00 0.00 4.84
1500 1717 1.227118 GCACCAACCCCAACAAACG 60.227 57.895 0.00 0.00 0.00 3.60
1501 1718 0.539518 AAGCACCAACCCCAACAAAC 59.460 50.000 0.00 0.00 0.00 2.93
1502 1719 2.035632 CTAAGCACCAACCCCAACAAA 58.964 47.619 0.00 0.00 0.00 2.83
1503 1720 1.063567 ACTAAGCACCAACCCCAACAA 60.064 47.619 0.00 0.00 0.00 2.83
1504 1721 0.553819 ACTAAGCACCAACCCCAACA 59.446 50.000 0.00 0.00 0.00 3.33
1505 1722 2.572209 TACTAAGCACCAACCCCAAC 57.428 50.000 0.00 0.00 0.00 3.77
1506 1723 4.724798 AGATATACTAAGCACCAACCCCAA 59.275 41.667 0.00 0.00 0.00 4.12
1507 1724 4.303794 AGATATACTAAGCACCAACCCCA 58.696 43.478 0.00 0.00 0.00 4.96
1517 1734 7.921745 AGACAACGGAAAGAAGATATACTAAGC 59.078 37.037 0.00 0.00 0.00 3.09
1530 1747 0.834612 ACCCACAGACAACGGAAAGA 59.165 50.000 0.00 0.00 0.00 2.52
1531 1748 0.944386 CACCCACAGACAACGGAAAG 59.056 55.000 0.00 0.00 0.00 2.62
1535 1752 1.891919 CCACACCCACAGACAACGG 60.892 63.158 0.00 0.00 0.00 4.44
1786 2015 8.986477 AAAATGATTTGTTAAATCCTCGGAAG 57.014 30.769 10.72 0.00 45.23 3.46
1828 2057 5.914898 ACAGCAAGGTTAACTGAACTTTT 57.085 34.783 5.42 0.00 35.29 2.27
1837 2066 9.392259 AGTTCCTTAATATACAGCAAGGTTAAC 57.608 33.333 0.00 0.00 38.92 2.01
1853 2082 6.980416 ATCGCTCTACCTAAGTTCCTTAAT 57.020 37.500 0.00 0.00 0.00 1.40
1915 2319 6.918569 GCACTGACATACGTCTAGATACATTT 59.081 38.462 0.00 0.00 43.06 2.32
2583 3099 5.804639 ACAAGCATCATAGTAAGGAACACA 58.195 37.500 0.00 0.00 0.00 3.72
2744 3260 4.776322 TGATGGTGGCGGGCGAAG 62.776 66.667 0.00 0.00 0.00 3.79
2930 3446 3.724478 TCCCATCCTCTGATACACTGTT 58.276 45.455 0.00 0.00 0.00 3.16
3061 3577 0.928505 AATCCCCATGCATGTGAGGA 59.071 50.000 24.44 24.44 0.00 3.71
3239 3755 3.769739 TTTCCTTTCTGCAGCAGTAGA 57.230 42.857 22.10 11.51 34.50 2.59
3622 4138 5.774690 AGGAAATAAGAACATGTGAGGCAAA 59.225 36.000 0.00 0.00 0.00 3.68
3944 4462 3.998341 GCTACCAGTGTTCCGAATAAACA 59.002 43.478 0.00 0.00 34.37 2.83
3974 4492 0.612453 AACAGACGGAGGAGAGGGTC 60.612 60.000 0.00 0.00 0.00 4.46
4067 4585 4.820897 TGAGGAGTGCATAACTGTAACTG 58.179 43.478 0.00 0.00 40.07 3.16
4068 4586 4.528596 ACTGAGGAGTGCATAACTGTAACT 59.471 41.667 0.00 0.00 40.07 2.24
4069 4587 4.822026 ACTGAGGAGTGCATAACTGTAAC 58.178 43.478 0.00 0.00 40.07 2.50
4070 4588 5.483685 AACTGAGGAGTGCATAACTGTAA 57.516 39.130 0.00 0.00 40.07 2.41
4071 4589 5.105473 GGTAACTGAGGAGTGCATAACTGTA 60.105 44.000 0.00 0.00 40.07 2.74
4072 4590 4.322801 GGTAACTGAGGAGTGCATAACTGT 60.323 45.833 0.00 0.00 40.07 3.55
4236 4754 7.029563 CCACAGTTTCTACAATAAATGAAGCC 58.970 38.462 0.00 0.00 0.00 4.35
4247 4765 8.729756 CAACAATCATATCCACAGTTTCTACAA 58.270 33.333 0.00 0.00 0.00 2.41
4393 4911 4.002316 TCATCACAATCAAGATGTCGCAA 58.998 39.130 0.00 0.00 41.74 4.85
4847 5389 1.482182 GGAAGATGGCCAATTTGGTCC 59.518 52.381 17.16 17.17 42.76 4.46
5034 5576 0.109272 GTTGGAAAAAGCGCTAGGCC 60.109 55.000 12.05 11.06 45.17 5.19
5139 5681 4.003648 AGTGCTGTTAGTAAATGTCAGGC 58.996 43.478 0.00 0.00 0.00 4.85
5149 5691 3.912496 ATGGATGCAGTGCTGTTAGTA 57.088 42.857 17.60 0.00 0.00 1.82
5187 5729 8.843885 AGAGTAGTTTGGTAGGAATAAAACAC 57.156 34.615 0.00 0.00 35.46 3.32
5197 5739 9.503399 AACTGATTAAAAGAGTAGTTTGGTAGG 57.497 33.333 0.00 0.00 0.00 3.18
5229 6055 4.100653 TGGATGCAAATTTTCCAGTTCACA 59.899 37.500 6.06 0.00 34.65 3.58
5288 6114 6.479990 TGATGTCTTCGGAATACTGCAAATAG 59.520 38.462 7.62 0.00 0.00 1.73
5360 6186 1.737363 GCGACAAAGCAACCACCAAAA 60.737 47.619 0.00 0.00 37.05 2.44
5361 6187 0.179124 GCGACAAAGCAACCACCAAA 60.179 50.000 0.00 0.00 37.05 3.28
5515 6341 0.811616 CGCTACAAGGTCATCCAGGC 60.812 60.000 0.00 0.00 35.89 4.85
5534 6360 4.458989 TCCATTGTTTCACTGGTCAATAGC 59.541 41.667 6.14 0.00 35.94 2.97


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

AutoCloner maintained by Alex Coulton.