Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008418.1 Hibiscus syriacus cultivar Beakdansim tig00111198_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 855397
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:197318 original size:57 final size:58
Alignment explanation
Indices: 197149--197320 Score: 224
Period size: 57 Copynumber: 3.0 Consensus size: 58
197139 CATAACCATA
* * * * *
197149 CAACCCCGTCACGAACATTAAGGCCCTGAGCACAAAGCCA-AGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
* * * *
197206 CAACCCCGTCACGAATAGTAAGGCTCTCAGCACAAAGCT-GAGAAACTTGCAAGTATT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
* *
197263 CAGCCCCGTCACGAACACTAAGGCTCTCAGCGCAAAG-TAGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
197320 C
1 C
197321 TTCCTCTAAC
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
56 1 0.01
57 98 0.99
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (58 bp):
CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
Found at i:197397 original size:24 final size:24
Alignment explanation
Indices: 197369--197417 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
197359 ATAAATGGAT
*
197369 ATGTCAAAAATCAAAACATAATTC
1 ATGTCAAAAATCAAAACAGAATTC
** *
197393 ATGTCAAGTATCATAACAGAATTC
1 ATGTCAAAAATCAAAACAGAATTC
197417 A
1 A
197418 AATAAGAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (24 bp):
ATGTCAAAAATCAAAACAGAATTC
Found at i:201798 original size:56 final size:57
Alignment explanation
Indices: 201733--201900 Score: 239
Period size: 56 Copynumber: 3.0 Consensus size: 57
201723 CATAACCATA
* * * *
201733 CAACCCCGTCACGAACAGTAAGGCCCTTAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
* * *
201790 CAA-CCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
* * *
201846 CAACCCCGTCACGAATAGTAAGGCTCTCAGTGCAAAGTCGAGGAACCTGCAAGTA
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTA
201901 TTCTTCCTCC
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
56 49 0.50
57 49 0.50
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
Found at i:201882 original size:57 final size:57
Alignment explanation
Indices: 201733--201903 Score: 238
Period size: 57 Copynumber: 3.0 Consensus size: 57
201723 CATAACCATA
* * * ** *
201733 CAACCCCGTCACGAACAGTAAGGCCCTTAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTGCAAGTATT
*
201790 CAA-CCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTGCAAGTATT
* *
201846 CAACCCCGTCACGAATAGTAAGGCTCTCAGTGCAAAG-TCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCT-GAGGAACCTGCAAGTATT
201903 C
1 C
201904 TTCCTCCAAC
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
56 50 0.49
57 52 0.51
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTGCAAGTATT
Found at i:202012 original size:24 final size:25
Alignment explanation
Indices: 201954--202014 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 25
201944 AAACAGATAT
*
201954 ATCAA-AAATCAAAACATAATTCAA
1 ATCAAGAAATCAAAACAGAATTCAA
* * *
201978 GTCAAG-TATCATAACAGAATTCAA
1 ATCAAGAAATCAAAACAGAATTCAA
202002 AT-AAGAAATCAAA
1 ATCAAGAAATCAAA
202015 TAAAATATTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.21
Consensus pattern (25 bp):
ATCAAGAAATCAAAACAGAATTCAA
Found at i:214281 original size:6 final size:6
Alignment explanation
Indices: 214265--214307 Score: 77
Period size: 6 Copynumber: 7.0 Consensus size: 6
214255 TTTGCGTGAC
214265 TTTTGGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG
1 TTTT-GG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG
214308 GGTTAATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 32 0.89
7 4 0.11
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (6 bp):
TTTTGG
Found at i:219725 original size:20 final size:20
Alignment explanation
Indices: 219688--219726 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
219678 AGATTGAGTG
* * *
219688 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
219708 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
219727 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:219947 original size:20 final size:21
Alignment explanation
Indices: 219901--219961 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
219891 TTCCCCTGTG
219901 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
219924 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
219944 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
219962 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:226854 original size:27 final size:27
Alignment explanation
Indices: 226812--227048 Score: 93
Period size: 27 Copynumber: 8.6 Consensus size: 27
226802 TTAGATTGAA
226812 GCACAGAGGTGCTCAGTCATAGTTGACT
1 GCACAGAGGTGCTCAGTCAT-GTTGACT
* *
226840 GCACAGAGGTG-TCAGTCCTCGATTGA-A
1 GCACAGAGGTGCTCAGTCAT-G-TTGACT
* *
226867 GCACAGAGGTGCTCAATCATCTT-AGCT
1 GCACAGAGGTGCTCAGTCATGTTGA-CT
* * *
226894 ACACAGAGGTG-TCAGCTC-TCGGCTGA-A
1 GCACAGAGGTGCTCAG-TCAT--GTTGACT
* *
226921 GCACAGAGGTGCTCAGTCATTTTTTTTAACT
1 GCACAGAGGTGCTCAGTCA----TGTTGACT
*
226952 GCACAGAGGTG-TCAGTTC-TCGATTGA-A
1 GCACAGAGGTGCTCAG-TCAT-G-TTGACT
* * *
226979 GCACAGAGGTGCTCAATCACTTTTGGCT
1 GCACAGAGGTGCTCAGTCA-TGTTGACT
* *
227007 ACACAGAGGTG-TCAGCTC-TCGATTGA-A
1 GCACAGAGGTGCTCAG-TCAT-G-TTGACT
227034 GCACAGAGGTGCTCA
1 GCACAGAGGTGCTCA
227049 ATCGTTAATT
Statistics
Matches: 153, Mismatches: 30, Indels: 52
0.65 0.13 0.22
Matches are distributed among these distances:
25 1 0.01
26 8 0.05
27 72 0.47
28 50 0.33
29 2 0.01
30 6 0.04
31 13 0.08
32 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (27 bp):
GCACAGAGGTGCTCAGTCATGTTGACT
Found at i:226875 original size:55 final size:55
Alignment explanation
Indices: 226751--227051 Score: 322
Period size: 55 Copynumber: 5.5 Consensus size: 55
226741 CTTGATCTTA
* ** * * * * * *
226751 GATTGTAGCACAGAGGTGCTCAATCA--TTCCAATGCACAGAGGTGCCAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTGACTACACAGAGGTGTCAG-CTCTC
* ** *
226805 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGACTGCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTGACTACACAGAGGTGTCAGCT-CTC
* *
226860 GATTGAAGCACAGAGGTGCTCAATCATCTTAG-CTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTGACTACACAGAGGTGTCAGCTCTC
** * * * *
226914 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTGACTACACAGAGGTGTCAGCTCTC
* *
226972 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTGACTACACAGAGGTGTCAGCTCTC
227027 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
227052 GTTAATTCTA
Statistics
Matches: 209, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
54 67 0.32
55 79 0.38
56 17 0.08
57 3 0.01
58 43 0.21
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTGACTACACAGAGGTGTCAGCTCTC
Found at i:233799 original size:29 final size:29
Alignment explanation
Indices: 233728--233793 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
233718 TCCTTCCTCA
233728 TTGCCATTTTTCTCTCTTGTTTATTGGTG
1 TTGCCATTTTTCTCTCTTGTTTATTGGTG
233757 TTGCCATTTTTCTCTCTTGTTTATTGGTG
1 TTGCCATTTTTCTCTCTTGTTTATTGGTG
233786 TTGCCATT
1 TTGCCATT
233794 GATCTCCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.08, C:0.18, G:0.17, T:0.58
Consensus pattern (29 bp):
TTGCCATTTTTCTCTCTTGTTTATTGGTG
Found at i:236708 original size:15 final size:15
Alignment explanation
Indices: 236690--236719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
236680 TAATAGAACA
236690 TTTAATTTCATATTT
1 TTTAATTTCATATTT
*
236705 TTTATTTTCATATTT
1 TTTAATTTCATATTT
236720 GAAAAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTCATATTT
Found at i:239838 original size:33 final size:33
Alignment explanation
Indices: 239796--239895 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
239786 AGTTTACAAT
* *
239796 AATTGAAATACTTAAATACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
239829 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
239862 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
239895 A
1 A
239896 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:239915 original size:21 final size:21
Alignment explanation
Indices: 239890--239931 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
239880 CTTCCAAGTT
239890 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
239911 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
239932 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:242307 original size:13 final size:13
Alignment explanation
Indices: 242289--242313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242279 TTTTTTCCCA
242289 AACCGGTTAAAAT
1 AACCGGTTAAAAT
242302 AACCGGTTAAAA
1 AACCGGTTAAAA
242314 AAATCCGATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:246094 original size:24 final size:24
Alignment explanation
Indices: 246067--246160 Score: 152
Period size: 24 Copynumber: 3.9 Consensus size: 24
246057 TCTACATAGA
* *
246067 ATTTTGAATTAAGTAATTCAATGC
1 ATTTCGAATTAAGCAATTCAATGC
246091 ATTTCGAATTAAGCAATTCAATGC
1 ATTTCGAATTAAGCAATTCAATGC
246115 ATTTCGAATTAAGCAATTCAATGC
1 ATTTCGAATTAAGCAATTCAATGC
* *
246139 ATTTTGAATTAAGGAATTCAAT
1 ATTTCGAATTAAGCAATTCAAT
246161 CTATCCAGCA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (24 bp):
ATTTCGAATTAAGCAATTCAATGC
Found at i:246675 original size:41 final size:41
Alignment explanation
Indices: 246630--247003 Score: 299
Period size: 41 Copynumber: 9.1 Consensus size: 41
246620 AAGCATGAAC
* ** * *
246630 TAATTCACAATTCAATTCAGTTTTATTATAGCAACATGCAA
1 TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
* * * ** *
246671 TAATTCACCATTCGACTCAATTGGATCATGGCAACATGAAA
1 TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
* *
246712 TAATTCACAATTCGATTCAATTCAATCATGGAAACATGCAA
1 TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
* * *
246753 TAATTCAGAATTCAACTT-AATTCAATCAAGACAACATGCAA
1 TAATTCACAATTCAA-TTCAATTCAATCATGGCAACATGCAA
* * *
246794 TAGTTCACCATTCGATTCAATTCAATCAT-GCAACATGCAA
1 TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
** * *
246834 TAATTCACAATTCAACTT-AATTTGATCATGGCAGCATGCAG
1 TAATTCACAATTCAA-TTCAATTCAATCATGGCAACATGCAA
* * ** * * *
246875 TAATCCATAATTCAATTCAATTCGGTCATGGAAATATGCAT
1 TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
* ** * * *
246916 TTATTCACAAACCAATTCAATT-AGATCATGGTAACATGTAT
1 TAATTCACAATTCAATTCAATTCA-ATCATGGCAACATGCAA
* * * * *
246957 TAATTCATAA-TCTAATTCAATTTAAATCAAGGCAACAAGTAA
1 TAATTCACAATTC-AATTCAA-TTCAATCATGGCAACATGCAA
246999 TAATT
1 TAATT
247004 AATTTACCAA
Statistics
Matches: 266, Mismatches: 58, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
40 36 0.14
41 207 0.78
42 22 0.08
43 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (41 bp):
TAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAA
Found at i:246923 original size:122 final size:122
Alignment explanation
Indices: 246661--246897 Score: 309
Period size: 122 Copynumber: 1.9 Consensus size: 122
246651 TTTATTATAG
** *
246661 CAACATGCAATAATTCACCATTCGACTCAATTGGATCATGGCAACATGAAATAATTCACAATTCG
1 CAACATGCAAT-ATTCACCATTCGACTCAATTCAATCATGGCAACATGAAATAATTCACAATTCA
*
246726 ATTCAATTCAATCATGGAAACATGCAATAATTCAGAATTCAACTTAATTCAATCAAGA
65 ATTCAATTCAATCATGGAAACATGCAATAATCCAGAATTCAACTTAATTCAATCAAGA
* *
246784 CAACATGCAATAGTTCACCATTCGATTCAATTCAATCAT-GCAACATGCAATAATTCACAATTCA
1 CAACATGCAATA-TTCACCATTCGACTCAATTCAATCATGGCAACATGAAATAATTCACAATTCA
** * * * *
246848 ACTT-AATTTGATCATGGCAGCATGCAGTAATCCATAATTCAA-TTCAATTC
65 A-TTCAATTCAATCATGGAAACATGCAATAATCCAGAATTCAACTT-AATTC
246898 GGTCATGGAA
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
121 2 0.02
122 61 0.62
123 36 0.36
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (122 bp):
CAACATGCAATATTCACCATTCGACTCAATTCAATCATGGCAACATGAAATAATTCACAATTCAA
TTCAATTCAATCATGGAAACATGCAATAATCCAGAATTCAACTTAATTCAATCAAGA
Found at i:246978 original size:163 final size:163
Alignment explanation
Indices: 246630--246930 Score: 368
Period size: 163 Copynumber: 1.8 Consensus size: 163
246620 AAGCATGAAC
* ** * * *
246630 TAATTCACAATTCAATTCAGTTTTATTATAGCAACATGCAATAATTCACCATTCGACTCAATTGG
1 TAATTCACAATTCAATTCAATTCAATCAT-GCAACATGCAATAATTCACAATTCAACTCAATTGG
* *
246695 ATCATGGCAACATGAAATAATTCACAATTCGATTCAATTCAATCATGGAAACATGCAATAATTCA
65 ATCATGGCAACATGAAATAATCCACAATTCAATTCAATTCAATCATGGAAACATGCAATAATTCA
* **
246760 GAATTCAACTTAATTCAATCAAGACAACATGCAA
130 CAAACCAACTTAATTCAATCAAGACAACATGCAA
* * * * *
246794 TAGTTCACCATTCGATTCAATTCAATCATGCAACATGCAATAATTCACAATTCAACTTAATTTGA
1 TAATTCACAATTCAATTCAATTCAATCATGCAACATGCAATAATTCACAATTCAACTCAATTGGA
* * * * ** * * *
246859 TCATGGCAGCATGCAGTAATCCATAATTCAATTCAATTCGGTCATGGAAATATGCATTTATTCAC
66 TCATGGCAACATGAAATAATCCACAATTCAATTCAATTCAATCATGGAAACATGCAATAATTCAC
246924 AAACCAA
131 AAACCAA
246931 TTCAATTAGA
Statistics
Matches: 112, Mismatches: 25, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
163 90 0.80
164 22 0.20
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (163 bp):
TAATTCACAATTCAATTCAATTCAATCATGCAACATGCAATAATTCACAATTCAACTCAATTGGA
TCATGGCAACATGAAATAATCCACAATTCAATTCAATTCAATCATGGAAACATGCAATAATTCAC
AAACCAACTTAATTCAATCAAGACAACATGCAA
Found at i:259613 original size:20 final size:20
Alignment explanation
Indices: 259559--259613 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
259549 GACATGACAC
* * *
259559 TTAATTACTTTT-TTAGTTT
1 TTAATTAATTTTATTAATAT
259578 TTAAATT-ATTTATATTAATAT
1 TT-AATTAATTT-TATTAATAT
259599 TTAATTAATTTTATT
1 TTAATTAATTTTATT
259614 CAATTAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.17
20 13 0.45
21 11 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAATTAATTTTATTAATAT
Found at i:260435 original size:79 final size:79
Alignment explanation
Indices: 260304--260453 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 79
260294 GTTTGTGTCT
* * *
260304 TAGAGAGCACTCCTTTTGGGGGTTTAAATTTTGTTTTGTTTCTAATAAGGTGGGACATGTGTCAC
1 TAGAGAGCACTCCTTTTGGAGGTTTAAACTTTGTTTTGTTTCTAATAAGGTGGAACATGTGTCAC
260369 CAACTTATTAGTCA
66 CAACTTATTAGTCA
260383 TAGAGAGCACTTCC-TTTGGAGGTTTAAACTTTGTTTTGTTTCTAATAAGGTGGAACATGTGTCA
1 TAGAGAGCAC-TCCTTTTGGAGGTTTAAACTTTGTTTTGTTTCTAATAAGGTGGAACATGTGTCA
260447 CCAACTT
65 CCAACTT
260454 CTCGAAGCCC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
79 64 0.96
80 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.39
Consensus pattern (79 bp):
TAGAGAGCACTCCTTTTGGAGGTTTAAACTTTGTTTTGTTTCTAATAAGGTGGAACATGTGTCAC
CAACTTATTAGTCA
Found at i:267851 original size:115 final size:115
Alignment explanation
Indices: 267648--267864 Score: 344
Period size: 115 Copynumber: 1.9 Consensus size: 115
267638 GATAATCCAA
* *
267648 GGTGGGTATCGATACTAGGATTTTAATTGTAATTCTAATAGCCAAATTGGTATCGGTACTCATAG
1 GGTGGGTATCGATACTAGGATTTCAATTGTAATTCCAATAGCCAAATTGGTATCGGTACTCATAG
* * *
267713 GAGTATCAATACCCATGATTGTGAGTATCGATACTCTATTGATACTCTAG
66 GAGTATCAATACCCATAACTGTGAGTATCAATACTCTATTGATACTCTAG
* * *
267763 GGTGGGTATCGATACTAGGATTTCAATTGTGATTCCAATAGCCAAATTGGTATTGGTACTCATGG
1 GGTGGGTATCGATACTAGGATTTCAATTGTAATTCCAATAGCCAAATTGGTATCGGTACTCATAG
* *
267828 GAGTATCGATACTCATAACTGTGAGTATCAATACTCT
66 GAGTATCAATACCCATAACTGTGAGTATCAATACTCT
267865 GGGATGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 92 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (115 bp):
GGTGGGTATCGATACTAGGATTTCAATTGTAATTCCAATAGCCAAATTGGTATCGGTACTCATAG
GAGTATCAATACCCATAACTGTGAGTATCAATACTCTATTGATACTCTAG
Found at i:268402 original size:48 final size:48
Alignment explanation
Indices: 268346--268440 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
268336 CAAGACCATG
* *
268346 ATATATATATGATTGCATACTTACACCTGTGTTATTTAATACTTGTTT
1 ATATATATATGATGGCATACTTACACATGTGTTATTTAATACTTGTTT
* *
268394 ATATATATATGATGGCATACTTATACATGTGTTGTTTAATACTTGTT
1 ATATATATATGATGGCATACTTACACATGTGTTATTTAATACTTGTT
268441 ATGCCTCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (48 bp):
ATATATATATGATGGCATACTTACACATGTGTTATTTAATACTTGTTT
Found at i:268779 original size:13 final size:13
Alignment explanation
Indices: 268761--268788 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
268751 GGGATCTCCC
268761 TGTTATTTTATTA
1 TGTTATTTTATTA
268774 TGTTATTTTATTA
1 TGTTATTTTATTA
268787 TG
1 TG
268789 CTAATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (13 bp):
TGTTATTTTATTA
Found at i:268969 original size:13 final size:12
Alignment explanation
Indices: 268951--269016 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 12
268941 ATTATTATTA
268951 TTATGGACATAGT
1 TTATGGACA-AGT
268964 TTATGGACAAGATT
1 TTATGGACAAG--T
*
268978 GTTATGGACAATCT
1 -TTATGGACAA-GT
*
268992 TATATGGATATAGT
1 T-TATGGACA-AGT
269006 TTATGGACAAG
1 TTATGGACAAG
269017 ATTGTTATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
12 4 0.09
13 17 0.40
14 11 0.26
15 11 0.26
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (12 bp):
TTATGGACAAGT
Found at i:274728 original size:27 final size:28
Alignment explanation
Indices: 274672--274729 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
274662 GCATTGCATA
* **
274672 ATTTGCAGTCCCATTTTTTCATTTTCAT
1 ATTTGCAGTCACATTTTTTCATTTAAAT
274700 ATTTGCA-TCACATTTATTT-ATTTAAAT
1 ATTTGCAGTCACATTT-TTTCATTTAAAT
274727 ATT
1 ATT
274730 ATTTCATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTGCAGTCACATTTTTTCATTTAAAT
Found at i:277092 original size:16 final size:16
Alignment explanation
Indices: 277073--277122 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
277063 AAGAAAAAAG
277073 AAGGAAAAAAAGAGAA
1 AAGGAAAAAAAGAGAA
*
277089 AAGGAAAAAATGA-AA
1 AAGGAAAAAAAGAGAA
*
277104 AATGAAAAAAAGATGAA
1 AAGGAAAAAAAGA-GAA
277121 AA
1 AA
277123 AAAGGGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.45
16 12 0.41
17 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (16 bp):
AAGGAAAAAAAGAGAA
Found at i:280346 original size:123 final size:123
Alignment explanation
Indices: 280177--280662 Score: 462
Period size: 124 Copynumber: 3.8 Consensus size: 123
280167 AATCAAATAT
* * *
280177 TGGATTTCAACTTCACGACAAAGGATATCCAATTCTAGGCTCAACTTCACGACGAA-GGGTCATC
1 TGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGTCATC
*
280241 CACGATTTTAACTTCACGATGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
66 CACGATTTTAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
* *
280299 TGGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAC-AGCGAAGGGGCTT
1 T-GGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGA-CGAAGGGG--T
** * * * * *
280363 CCCAGTTTTATTCAGAGCTAATTTCAACTTCACGGCGAAGGACATTG-GACTCGAAACAGCAACA
62 --CA--TCCA--C-GA--T--TTT-AACTTCACGACGAAGGATATCGTG--TC-CACCAGCAAC-
* * **
280427 ATGCAACCCT---
111 ATTCATCTTTAGA
*
280437 TGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATC
1 TGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGTCATC
* * *
280502 CACGATTTCAACTTCACGACGAATGATATCGTGTTCACCAGCAACATTCATCTTTAGA
66 CACGATTTTAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
* * *
280560 TTGGATTTTAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGATGAAGGGGCCAT
1 -TGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGTCAT
* * * * * * *
280625 TCATGATATCAACTTCACGGCAAAAGATATCGTGTCCA
65 CCACGATTTTAACTTCACGACGAAGGATATCGTGTCCA
280663 TCAACCTCAT
Statistics
Matches: 295, Mismatches: 42, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
120 6 0.02
121 8 0.03
122 3 0.01
123 67 0.23
124 99 0.34
126 2 0.01
128 4 0.01
129 1 0.00
130 2 0.01
131 2 0.01
132 1 0.00
133 4 0.01
135 1 0.00
137 59 0.20
138 20 0.07
139 2 0.01
140 8 0.03
141 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (123 bp):
TGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGTCATC
CACGATTTTAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
Found at i:280621 original size:261 final size:258
Alignment explanation
Indices: 280107--280610 Score: 762
Period size: 261 Copynumber: 1.9 Consensus size: 258
280097 AACAACTTTT
*
280107 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGCAATACAATCA
1 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGACATTGAACTCAAAGCAATACAATCA
* * * *
280172 AATATTGGATTTCAACTTCACGACAAAGGATATCCAATTCTAGGCTCAACTTCACGACGAAGGGT
66 AACATTGGATTTCAACTTCACAACAAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGC
* *
280237 CATCCACGATTTTAACTTCACGATGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATGG
131 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATGG
280302 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCC
196 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCC
* * *
280365 CAGTTTTATTCAGAG-CTAATTTCAACTTCACGGCGAAGGACATTGGACTCGAAA-CAGCA-ACA
1 CAGTTTCATTCAGAGTC-AATTTCAACTTCACAGCGAAGGACATTGAACTC-AAAGCA--ATACA
* * *
280427 ATGCAACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGA
62 AT-CAAACATTGGATTTCAACTTCACAACAAAGGATATCCAATTCGAGGCTCAACTTCACGACGA
* *
280492 AGGGGCCATCCACGATTTCAACTTCACGACGAATGATATCGTGTTCACCAGCAACATTCATCTTT
126 A-GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTT
* * * *
280557 AGATTGGATTTTAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCAC
190 AGATGGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAC
280611 GATGAAGGGG
Statistics
Matches: 221, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
257 1 0.00
258 46 0.21
259 8 0.04
260 58 0.26
261 108 0.49
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (258 bp):
CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGACATTGAACTCAAAGCAATACAATCA
AACATTGGATTTCAACTTCACAACAAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGC
CATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATGG
GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCC
Found at i:280799 original size:40 final size:40
Alignment explanation
Indices: 280744--280882 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 40
280734 TGGCCAGACG
280744 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
* ** * * *
280784 TCCTCATCACGAAGGAGCAACATCATTC-TTAGATAGCCAGAAG
1 TCCTCATCACGAAGGAACAATGTCATCCACT-GAT---CAGAAC
** * *
280827 TCCTCATCAAAAAGGAACAATGTCATCCACCGATCAAAAC
1 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
* *
280867 TCGTCATCACGTAGGA
1 TCCTCATCACGAAGGA
280883 GATAAGTCAT
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
39 1 0.01
40 43 0.58
43 30 0.41
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (40 bp):
TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
Found at i:280875 original size:83 final size:83
Alignment explanation
Indices: 280731--280932 Score: 282
Period size: 83 Copynumber: 2.4 Consensus size: 83
280721 ATATCATTAA
* * * *
280731 AGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCACGA
1 AGATAGCCAGAAGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACGA
280796 AGGAGCA-ACA-TCATTCTT
66 AGGAG-ATA-AGTCATTCTT
** * *
280814 AGATAGCCAGAAGTCCTCATCAAAAAGGAACAATGTCATCCACCGATCAAAACTCGTCATCACGT
1 AGATAGCCAGAAGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACGA
280879 AGGAGATAAGTCATTCTT
66 AGGAGATAAGTCATTCTT
* *
280897 AGATAGCCAGATGTCCTCATCACGAAGGAACCATGT
1 AGATAGCCAGAAGTCCTCATCACGAAGGAACAATGT
280933 TATCTCAAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
82 2 0.02
83 103 0.98
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (83 bp):
AGATAGCCAGAAGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACGA
AGGAGATAAGTCATTCTT
Found at i:281163 original size:3 final size:3
Alignment explanation
Indices: 281155--281225 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
281145 GAGACTATCA
281155 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
281203 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
281226 CAAAATAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:283267 original size:15 final size:15
Alignment explanation
Indices: 283247--283276 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
283237 AAGTCAAAGA
283247 TAACTCCTGAGAATC
1 TAACTCCTGAGAATC
*
283262 TAACTCTTGAGAATC
1 TAACTCCTGAGAATC
283277 CAAATGACTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (15 bp):
TAACTCCTGAGAATC
Found at i:284949 original size:16 final size:15
Alignment explanation
Indices: 284928--284980 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
284918 AAAGGGCAAA
284928 AACAAAAAAGAAAAG
1 AACAAAAAAGAAAAG
284943 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAAGAA-AAG
*
284959 AAAAAAAAAG-AAAG
1 AACAAAAAAGAAAAG
284973 AACAAAAA
1 AACAAAAA
284981 TCAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 8 0.24
15 9 0.27
16 12 0.36
17 2 0.06
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAAG
Found at i:284972 original size:19 final size:20
Alignment explanation
Indices: 284950--284991 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
284940 AAGAAGCAAA
*
284950 AAAGAAGAAAAA-AAAAAAG
1 AAAGAACAAAAATAAAAAAG
*
284969 AAAGAACAAAAATCAAAAAG
1 AAAGAACAAAAATAAAAAAG
284989 AAA
1 AAA
284992 AAGGGACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAGAACAAAAATAAAAAAG
Found at i:284979 original size:12 final size:12
Alignment explanation
Indices: 284925--284994 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
284915 CAAAAAGGGC
*
284925 AAAAACAAAAAA
1 AAAAAGAAAAAA
*
284937 GAAAAGAAGCAAAA
1 AAAAAGAA--AAAA
*
284951 AAGAAGAAAAAA
1 AAAAAGAAAAAA
284963 AAAAAGAAAGAACA
1 AAAAAGAAA-AA-A
** *
284977 AAAATCAAAAAG
1 AAAAAGAAAAAA
284989 AAAAAG
1 AAAAAG
284995 GGACAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
12 22 0.50
13 4 0.09
14 18 0.41
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:284986 original size:26 final size:25
Alignment explanation
Indices: 284924--284994 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
284914 ACAAAAAGGG
*
284924 CAAAAACAAAAAAGAAAAGAAGCAA
1 CAAAAACAAAAAAAAAAAGAAGCAA
* *
284949 AAAAGAAGAAAAAAAAAAAGAAAG-AA
1 CAAA-AACAAAAAAAAAAAG-AAGCAA
*
284975 CAAAAATCAAAAAGAAAAAG
1 CAAAAA-CAAAAAAAAAAAG
284995 GGACAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 5 0.14
26 29 0.78
27 3 0.08
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (25 bp):
CAAAAACAAAAAAAAAAAGAAGCAA
Found at i:286959 original size:211 final size:212
Alignment explanation
Indices: 286590--287122 Score: 899
Period size: 211 Copynumber: 2.5 Consensus size: 212
286580 ATATCGTGCC
*
286590 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
286655 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
**
286720 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
286785 ACAACGAA-GATATTGG
196 ACAACAAAGGATATTGG
* * *
286801 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
286866 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGATAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
286931 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
286996 ACAACAAAGGATATTGG
196 ACAACAAAGGATATTGG
* *
287013 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGCACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * *
287078 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTAGACTC
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
287123 GGAACAATGC
Statistics
Matches: 301, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
211 194 0.64
212 107 0.36
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (212 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAACAAAGGATATTGG
Found at i:287123 original size:106 final size:105
Alignment explanation
Indices: 286557--287122 Score: 821
Period size: 106 Copynumber: 5.3 Consensus size: 105
286547 TGGCTATCCG
* * * * *
286557 CAATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACG
1 CAATTTCAACTTCAC-ACGAAGGATAT--TG-GACTCCAGACAACACAAGTTCAACTTCACGACG
* *
286622 AAGGGA-CGACTGGTTGTCAACAAACAACTTCCCAAATTCAGAGC
62 AAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
*
286666 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
* **
286731 GGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGC
65 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
286772 CAATTTCAACTTCACAACGAA-GATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
*
286836 GGACCACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
65 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* *
286877 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
286942 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
65 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* * *
286983 CAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
* * * *
287048 GCACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGC
65 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* *
287089 CAATTTCAACTTCACGACGGAGGATATTAGACTC
1 CAATTTCAACTTCAC-ACGAAGGATATTGGACTC
287123 GGAACAATGC
Statistics
Matches: 421, Mismatches: 30, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
104 1 0.00
105 98 0.23
106 292 0.69
107 6 0.01
108 1 0.00
109 23 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAATTTCAACTTCACACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
Found at i:287961 original size:37 final size:37
Alignment explanation
Indices: 287872--287967 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
287862 CTTTTTGTCC
*
287872 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* * *
287909 TGCTAGGATTCAAACTCCTAAAAATAGGATATAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** *
287946 TACTATTATTTAAACTCCTAAA
1 TACTAGGATTCAAACTCCTAAA
287968 GATATGATCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:288703 original size:22 final size:22
Alignment explanation
Indices: 288668--288722 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
288658 CTATTTAGTA
*
288668 TTTTATTA-TATTATACATACAT
1 TTTTATTATTTTTATACATA-AT
* *
288690 TTTTA-TATTTTTATATATATT
1 TTTTATTATTTTTATACATAAT
288711 TTTTATTATTTT
1 TTTTATTATTTT
288723 ATTTATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTTTATACATAAT
Found at i:288715 original size:21 final size:21
Alignment explanation
Indices: 288689--288756 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
288679 TATACATACA
288689 TTTTTATATTTTTATATATAT
1 TTTTTATATTTTTATATATAT
*
288710 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTT-TATATA-TAT
* *
288734 TTATT-TATTTTCAT-TATAT
1 TTTTTATATTTTTATATATAT
288753 TTTT
1 TTTT
288757 AGTTTCTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.15
20 2 0.05
21 7 0.18
22 12 0.31
23 5 0.13
24 7 0.18
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATATTTTTATATATAT
Found at i:288752 original size:43 final size:43
Alignment explanation
Indices: 288668--288756 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
288658 CTATTTAGTA
*
288668 TTTTATTATATTATACATACATTTTTATATTTTTATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
* **
288711 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATT
288754 TTT
1 TTT
288757 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 26 0.65
44 12 0.30
45 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
Found at i:288757 original size:21 final size:21
Alignment explanation
Indices: 288615--288757 Score: 59
Period size: 22 Copynumber: 6.6 Consensus size: 21
288605 TTTAGTTAAT
* *
288615 ATTATATGTATATTTATTTTTC
1 ATTATATTTTTATTTA-TTTTC
288637 ATT-TATTTATTA-TTATTATTAC
1 ATTATATTT-TTATTTATT-TT-C
*
288659 TATT-TAGTATTTTATTATATTATAC
1 -ATTATA-T-TTTTATT-TATT-TTC
* *
288684 A-TACATTTTTA--TATTTTT
1 ATTATATTTTTATTTATTTTC
288702 ATATATATTTTT-TATTATTTT-
1 AT-TATATTTTTAT-TTATTTTC
*
288723 ATTTATACTATTTATTTATTTTC
1 A-TTATA-TTTTTATTTATTTTC
288746 ATTATATTTTTA
1 ATTATATTTTTA
288758 GTTTCTTTGC
Statistics
Matches: 94, Mismatches: 9, Indels: 37
0.67 0.06 0.26
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 10 0.11
21 19 0.20
22 34 0.36
23 9 0.10
24 6 0.06
25 4 0.04
26 6 0.06
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (21 bp):
ATTATATTTTTATTTATTTTC
Found at i:289573 original size:41 final size:41
Alignment explanation
Indices: 289516--289599 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
289506 TATTTATTAT
289516 GGTTTGGTTCTACATAGCTATGCAAGGATAAAGGTTTACAA
1 GGTTTGGTTCTACATAGCTATGCAAGGATAAAGGTTTACAA
*
289557 GGTTTGGTTCTACATAGCTATGCAAGGATATAGGTTTACAA
1 GGTTTGGTTCTACATAGCTATGCAAGGATAAAGGTTTACAA
289598 GG
1 GG
289600 AACATGAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (41 bp):
GGTTTGGTTCTACATAGCTATGCAAGGATAAAGGTTTACAA
Found at i:290637 original size:43 final size:43
Alignment explanation
Indices: 290561--290660 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
290551 GCCATTTTTT
* * *
290561 ATGCCCAAACGAACGAACAAATATCTATGAATACTTTGTAAAC
1 ATGCCCAAATGAATGAACAAATATCTATAAATACTTTGTAAAC
* *
290604 ATTCTCAAATGAATGAACAAATATCTATAAATACTTTGTAAAC
1 ATGCCCAAATGAATGAACAAATATCTATAAATACTTTGTAAAC
290647 ATGCCCAAATGAAT
1 ATGCCCAAATGAAT
290661 TTATTTGCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (43 bp):
ATGCCCAAATGAATGAACAAATATCTATAAATACTTTGTAAAC
Found at i:298545 original size:14 final size:14
Alignment explanation
Indices: 298528--298577 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
298518 TGACCCGACT
*
298528 GAGTCAACTCGTCT
1 GAGTCAACTCGTCC
* *
298542 GAGTCAAATCATCC
1 GAGTCAACTCGTCC
298556 GAGTCAACTCGTCC
1 GAGTCAACTCGTCC
298570 GAGTCAAC
1 GAGTCAAC
298578 CTGTTGACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (14 bp):
GAGTCAACTCGTCC
Found at i:302574 original size:17 final size:17
Alignment explanation
Indices: 302552--302588 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
302542 TATAATTATA
302552 GAAATGTATTTAAAGTG
1 GAAATGTATTTAAAGTG
302569 GAAATGTATTTAAAGTG
1 GAAATGTATTTAAAGTG
302586 GAA
1 GAA
302589 TCAAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.32
Consensus pattern (17 bp):
GAAATGTATTTAAAGTG
Found at i:302971 original size:22 final size:21
Alignment explanation
Indices: 302919--302971 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
302909 CGATTCAACC
*
302919 TAAATTTTTTTTATTTTTTAT
1 TAAATTTTTTTGATTTTTTAT
*
302940 TAAATATTTTTGATATTTTTAT
1 TAAATTTTTTTGAT-TTTTTAT
*
302962 TTAATTTTTT
1 TAAATTTTTT
302972 AAATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TAAATTTTTTTGATTTTTTAT
Found at i:304503 original size:16 final size:16
Alignment explanation
Indices: 304484--304534 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
304474 TTAAATTTTA
304484 AAAATATTTATAAAAT
1 AAAATATTTATAAAAT
304500 AAAATATATT-TAAAAT
1 AAAATAT-TTATAAAAT
304516 AAAA-A---ATAAAAT
1 AAAATATTTATAAAAT
304528 AAAATAT
1 AAAATAT
304535 ATATTTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
15 1 0.03
16 17 0.55
17 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATTTATAAAAT
Found at i:304510 original size:18 final size:15
Alignment explanation
Indices: 304482--304536 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 15
304472 ATTTAAATTT
304482 TAAAAATATTTATAAAA
1 TAAAAATA-TT-TAAAA
304499 TAAAATATATTTAAAA
1 TAAAA-ATATTTAAAA
304515 TAAAAA-A--TAAAA
1 TAAAAATATTTAAAA
304527 TAAAATATAT
1 TAAAA-ATAT
304537 ATTTTGTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 10 0.29
13 1 0.03
14 2 0.06
15 1 0.03
16 10 0.29
17 7 0.21
18 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAAATATTTAAAA
Found at i:305307 original size:14 final size:14
Alignment explanation
Indices: 305256--305340 Score: 80
Period size: 14 Copynumber: 6.0 Consensus size: 14
305246 TGACCCGATC
* *
305256 GAGTCAACTCAGACC
1 GAGTCAACTC-GTCT
305271 GAGTCAACTCGTCT
1 GAGTCAACTCGTCT
* * *
305285 AAGTTAACTCATCT
1 GAGTCAACTCGTCT
*
305299 GAGTCAACTTGTCT
1 GAGTCAACTCGTCT
* * *
305313 GAGTTAAATCGTCA
1 GAGTCAACTCGTCT
305327 GAGTCAACTCGTCT
1 GAGTCAACTCGTCT
305341 AAGTTAAATC
Statistics
Matches: 54, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
14 44 0.81
15 10 0.19
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (14 bp):
GAGTCAACTCGTCT
Found at i:305351 original size:28 final size:28
Alignment explanation
Indices: 305271--305353 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
305261 AACTCAGACC
* * *
305271 GAGTCAACTCGTCTAAGTTAACTCATCT
1 GAGTCAACTCGTCTAAGTTAAATCGTCA
* *
305299 GAGTCAACTTGTCTGAGTTAAATCGTCA
1 GAGTCAACTCGTCTAAGTTAAATCGTCA
305327 GAGTCAACTCGTCTAAGTTAAATCGTC
1 GAGTCAACTCGTCTAAGTTAAATCGTC
305354 CTAGTTAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (28 bp):
GAGTCAACTCGTCTAAGTTAAATCGTCA
Found at i:305352 original size:14 final size:14
Alignment explanation
Indices: 305276--305362 Score: 70
Period size: 14 Copynumber: 6.2 Consensus size: 14
305266 AGACCGAGTC
305276 AACTCGTCTAAGTT
1 AACTCGTCTAAGTT
* * *
305290 AACTCATCTGAGTC
1 AACTCGTCTAAGTT
* *
305304 AACTTGTCTGAGTT
1 AACTCGTCTAAGTT
* *
305318 AAATCGTC-AGAGTC
1 AACTCGTCTA-AGTT
305332 AACTCGTCTAAGTT
1 AACTCGTCTAAGTT
*
305346 AAATCGTCCT-AGTT
1 AACTCGT-CTAAGTT
305360 AAC
1 AAC
305363 CCTTTAACTT
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
14 53 0.95
15 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (14 bp):
AACTCGTCTAAGTT
Found at i:309646 original size:23 final size:23
Alignment explanation
Indices: 309620--309688 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
309610 CACCACAGCT
*
309620 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
309643 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
309666 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
309689 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:309877 original size:103 final size:103
Alignment explanation
Indices: 309704--309921 Score: 355
Period size: 103 Copynumber: 2.1 Consensus size: 103
309694 TAATGTCCAT
* * * *
309704 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
309769 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * * *
309807 AATGACCACATATCATTCCTTACGAATCATATACATATGCCAAGAATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
*
309872 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
309910 AAGGACCACATA
1 AAGGACCACATA
309922 GACCCTCAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:314696 original size:23 final size:23
Alignment explanation
Indices: 314665--314733 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
314655 CACCACAGCT
* *
314665 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
314688 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
314711 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
314734 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:314920 original size:103 final size:103
Alignment explanation
Indices: 314749--314966 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
314739 TAATGTCCAT
* *
314749 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
314814 GACTTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
314852 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
314917 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
314955 AAGGACCACATA
1 AAGGACCACATA
314967 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:320954 original size:30 final size:31
Alignment explanation
Indices: 320889--320974 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
320879 TAGGATTTGA
*
320889 GGCCCCGAGATCTTTCTTGGGTAGCCCCTGT
1 GGCCCCGAGATCATTCTTGGGTAGCCCCTGT
*
320920 GGCCCCGAGATCATTCTTGGGTAGGCCC-GT
1 GGCCCCGAGATCATTCTTGGGTAGCCCCTGT
* *
320950 GGCCCCGAGTAACCTTCTTGGGTAG
1 GGCCCCGAG-ATCATTCTTGGGTAG
320975 ACTTTCAGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 11 0.22
31 39 0.78
ACGTcount: A:0.13, C:0.30, G:0.31, T:0.26
Consensus pattern (31 bp):
GGCCCCGAGATCATTCTTGGGTAGCCCCTGT
Found at i:321754 original size:24 final size:25
Alignment explanation
Indices: 321725--321771 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
321715 TATTTAAACT
321725 AAGCTAAGAATAA-AAT-ATATATTG
1 AAGCTAAG-ATAAGAATAATATATTG
321749 AAGCTAAGATAAGAATAATATAT
1 AAGCTAAGATAAGAATAATATAT
321772 ATATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (25 bp):
AAGCTAAGATAAGAATAATATATTG
Found at i:321755 original size:29 final size:29
Alignment explanation
Indices: 321711--321775 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
321701 CTATGGGGGT
* *
321711 TATATATTTAAACTAAGCTAAGAATAAAA
1 TATATATTGAAACTAAGATAAGAATAAAA
* *
321740 TATATATTGAAGCTAAGATAAGAATAATA
1 TATATATTGAAACTAAGATAAGAATAAAA
321769 TATATAT
1 TATATAT
321776 ATTTAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (29 bp):
TATATATTGAAACTAAGATAAGAATAAAA
Found at i:321807 original size:21 final size:23
Alignment explanation
Indices: 321783--321826 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
321773 TATATTTAAA
321783 TTAAA-AA-ATAATAATAAAATC
1 TTAAATAAGATAATAATAAAATC
*
321804 TTAAATTAAGTTAATAATAAAAT
1 TTAAA-TAAGATAATAATAAAAT
321827 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
TTAAATAAGATAATAATAAAATC
Found at i:322631 original size:21 final size:21
Alignment explanation
Indices: 322602--322644 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
322592 TGATTCTATA
322602 TTTTAATTTAATATAAT-TTAT
1 TTTTAATTT-ATATAATGTTAT
* *
322623 TTTTTATTTTTATAATGTTAT
1 TTTTAATTTATATAATGTTAT
322644 T
1 T
322645 AATGTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAATTTATATAATGTTAT
Found at i:326324 original size:135 final size:131
Alignment explanation
Indices: 326112--326359 Score: 354
Period size: 132 Copynumber: 1.9 Consensus size: 131
326102 TTTAGGAGAT
*
326112 TACAATAGTTTGAATAAACCGAGTTGTTAACTTCTAATAGGACTTTTTTGCTAAAGATAAAATTC
1 TACAATAGTTTAAATAAACCGAGTTGTTAACTTCTAATAGGACTTTTTTGCTAAAGATAAAATTC
* * *
326177 TATCTAGAGATAGAGATTACAAAGATTCCTAAGGCTTATC-TTTCTTATCGTGATAGACTCCTAA
66 TATCTAGAGATAGAG--TACAAAGACTCCTAAGACTTAACATTTCTTATCGTGATAGACTCCTAA
326241 ACA
129 ACA
* * * * *
326244 TACAATAGTTTAAATAAACTGAGTTGTTGACTTGTAATAGGATAATTTTTTTGCTAAATATAAAA
1 TACAATAGTTTAAATAAACCGAGTTGTTAACTTCTAATAGG---ACTTTTTTGCTAAAGATAAAA
*
326309 TTCTATCTAGAGATAGAGTACAAAGGCTCCTAAGACTTAACATTTCTTATC
63 TTCTATCTAGAGATAGAGTACAAAGACTCCTAAGACTTAACATTTCTTATC
326360 ATAAGACTAA
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
132 37 0.36
133 19 0.19
134 9 0.09
135 37 0.36
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (131 bp):
TACAATAGTTTAAATAAACCGAGTTGTTAACTTCTAATAGGACTTTTTTGCTAAAGATAAAATTC
TATCTAGAGATAGAGTACAAAGACTCCTAAGACTTAACATTTCTTATCGTGATAGACTCCTAAAC
A
Found at i:332558 original size:44 final size:44
Alignment explanation
Indices: 332495--332584 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
332485 CAACATTTGG
332495 TAGGCTCAGTTATAAGATAAAATTGCATTTCATTTGAATAATCT
1 TAGGCTCAGTTATAAGATAAAATTGCATTTCATTTGAATAATCT
332539 TAGGCTCAGTTATAAGATAAAATTGCATTTCATTTGAATAATCT
1 TAGGCTCAGTTATAAGATAAAATTGCATTTCATTTGAATAATCT
332583 TA
1 TA
332585 CTTAACCCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (44 bp):
TAGGCTCAGTTATAAGATAAAATTGCATTTCATTTGAATAATCT
Found at i:347945 original size:7 final size:7
Alignment explanation
Indices: 347933--348018 Score: 50
Period size: 7 Copynumber: 11.9 Consensus size: 7
347923 GCTTGAAGAT
347933 GAAAAAA
1 GAAAAAA
347940 GAAAAAAAA
1 G--AAAAAA
*
347949 TGAAAAAT
1 -GAAAAAA
*
347957 GAAAAAT
1 GAAAAAA
347964 GAAAAAA
1 GAAAAAA
347971 TGAAAAAA
1 -GAAAAAA
347979 TGAAAAAA
1 -GAAAAAA
**
347987 -ATGAAA
1 GAAAAAA
*
347993 -AAAAAT
1 GAAAAAA
347999 GAAAAAA
1 GAAAAAA
*
348006 AAAAAAA
1 GAAAAAA
*
348013 CAAAAA
1 GAAAAA
348019 CAAATAAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
6 7 0.11
7 30 0.47
8 20 0.31
9 6 0.09
10 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.10, T:0.08
Consensus pattern (7 bp):
GAAAAAA
Found at i:347947 original size:8 final size:8
Alignment explanation
Indices: 347934--348012 Score: 56
Period size: 8 Copynumber: 9.6 Consensus size: 8
347924 CTTGAAGATG
347934 AAAAAAGA
1 AAAAAAGA
347942 AAAAAA-A
1 AAAAAAGA
*
347949 TGAAAAATG-
1 --AAAAAAGA
*
347958 AAAAATGA
1 AAAAAAGA
*
347966 AAAAATGA
1 AAAAAAGA
*
347974 AAAAATGA
1 AAAAAAGA
347982 AAAAAATGAA
1 AAAAAA-G-A
347992 AAAAAATGA
1 AAAAAA-GA
348001 AAAAAA-A
1 AAAAAAGA
348008 AAAAA
1 AAAAA
348013 CAAAAACAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
7 14 0.22
8 27 0.43
9 13 0.21
10 9 0.14
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (8 bp):
AAAAAAGA
Found at i:347953 original size:17 final size:17
Alignment explanation
Indices: 347931--348012 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
347921 TTGCTTGAAG
347931 ATGAAAAAAGAAAAAAA
1 ATGAAAAAAGAAAAAAA
*
347948 ATGAAAAATG---AAAA
1 ATGAAAAAAGAAAAAAA
347962 ATGAAAAAATG--AAAAA
1 ATGAAAAAA-GAAAAAAA
347978 ATGAAAAAAATGAAAAAAA
1 ATG-AAAAAA-GAAAAAAA
347997 ATGAAAAAA-AAAAAAA
1 ATGAAAAAAGAAAAAAA
348013 CAAAAACAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 14 0.24
17 17 0.29
18 6 0.10
19 8 0.14
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (17 bp):
ATGAAAAAAGAAAAAAA
Found at i:348003 original size:6 final size:7
Alignment explanation
Indices: 347944--347985 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
347934 AAAAAAGAAA
347944 AAAAATG
1 AAAAATG
347951 AAAAATG
1 AAAAATG
347958 AAAAATG
1 AAAAATG
347965 AAAAAATG
1 -AAAAATG
347973 AAAAAATG
1 -AAAAATG
347981 AAAAA
1 AAAAA
347986 AATGAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 19 0.56
8 15 0.44
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:349349 original size:53 final size:53
Alignment explanation
Indices: 349210--349724 Score: 865
Period size: 53 Copynumber: 9.7 Consensus size: 53
349200 GCAACAGAAG
* *
349210 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCATAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
349261 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
349315 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
349368 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
349421 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
349475 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
349528 ATTGTTCGAGTTCTTATTCCCTGAAGAAAAAGAGAGCGGACCCATAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
349582 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
349635 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
349689 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGAGC
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC
349725 AGACACGATT
Statistics
Matches: 439, Mismatches: 17, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
51 13 0.03
52 18 0.04
53 226 0.51
54 182 0.41
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:349446 original size:107 final size:107
Alignment explanation
Indices: 349210--349724 Score: 887
Period size: 107 Copynumber: 4.8 Consensus size: 107
349200 GCAACAGAAG
* * *
349210 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAG-G-GTGGACCCATAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
349272 TCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAAT
66 TC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
349315 ATTGTTTGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
349379 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
349421 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
349486 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
349528 ATTGTTCGAGTTCTTATTCCCTGAAGAAAAAGAGAGCGGACCCATAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
349593 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
349635 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
349700 TCTACTCCCTGAAGAAATAGGGAGC
66 TCTACTCCCTGAAGAAATAGAGAGC
349725 AGACACGATT
Statistics
Matches: 393, Mismatches: 13, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
105 30 0.08
106 48 0.12
107 315 0.80
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (107 bp):
ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:354010 original size:14 final size:14
Alignment explanation
Indices: 353991--354027 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
353981 TACGCAACGT
353991 CCGCAATCGCGACA
1 CCGCAATCGCGACA
*
354005 CCGCAATTGCGACA
1 CCGCAATCGCGACA
354019 CCGCAATCG
1 CCGCAATCG
354028 TATCCGCGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.41, G:0.22, T:0.11
Consensus pattern (14 bp):
CCGCAATCGCGACA
Found at i:356043 original size:18 final size:19
Alignment explanation
Indices: 356017--356054 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
356007 CACAATTAAT
356017 ATTTAATTAT-TAAAAATA
1 ATTTAATTATATAAAAATA
* *
356035 ATTTTATTATATGAAAATA
1 ATTTAATTATATAAAAATA
356054 A
1 A
356055 AAAAAAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTAATTATATAAAAATA
Found at i:356850 original size:22 final size:22
Alignment explanation
Indices: 356808--356850 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
356798 CCCCCGCCGC
*
356808 TTCTCTTTCTCTTTCTCTCATT
1 TTCTCTTTCTCTTTATCTCATT
*
356830 TTCTCATTTCT-TTTATTTCAT
1 TTCTC-TTTCTCTTTATCTCAT
356851 CAACCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (22 bp):
TTCTCTTTCTCTTTATCTCATT
Found at i:357671 original size:3 final size:3
Alignment explanation
Indices: 357651--357687 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
357641 TAATTTTAAA
357651 TAT TAT T-T TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
357688 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:359797 original size:26 final size:27
Alignment explanation
Indices: 359745--359802 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
359735 TAATTATTTC
*
359745 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
359773 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
359799 TTTT
1 TTTT
359803 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:363108 original size:15 final size:15
Alignment explanation
Indices: 363088--363119 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
363078 GATCAATACC
363088 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
363103 TTTTGCATACATTCA
1 TTTTGCATACATGCA
363118 TT
1 TT
363120 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:363685 original size:26 final size:27
Alignment explanation
Indices: 363649--363711 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
363639 GAAAATAGGG
*
363649 GATTTTAATGCTGAGCATCTAAT-CCA
1 GATTTGAATGCTGAGCATCTAATCCCA
363675 GATTTGAATGCTGAGCATCTAATCCCA
1 GATTTGAATGCTGAGCATCTAATCCCA
363702 GATTTGAATG
1 GATTTGAATG
363712 AGAAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (27 bp):
GATTTGAATGCTGAGCATCTAATCCCA
Found at i:370771 original size:11 final size:11
Alignment explanation
Indices: 370755--370835 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
370745 GCTTGAAGAA
*
370755 AAAAAATGATG
1 AAAAAATAATG
* *
370766 AAAAAAAAGAAG
1 AAAAAATA-ATG
370778 AAAAAATAATG
1 AAAAAATAATG
370789 AAAAAATAATG
1 AAAAAATAATG
370800 AAGAAAA-AAT-
1 AA-AAAATAATG
*
370810 AATAAA-AAT-
1 AAAAAATAATG
370819 AAAATAA-AATG
1 AAAA-AATAATG
370830 AAAAAA
1 AAAAAA
370836 ATGAGTGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
9 9 0.15
10 9 0.15
11 28 0.47
12 13 0.22
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.14
Consensus pattern (11 bp):
AAAAAATAATG
Found at i:370777 original size:25 final size:25
Alignment explanation
Indices: 370750--370821 Score: 91
Period size: 23 Copynumber: 3.1 Consensus size: 25
370740 ATTATGCTTG
*
370750 AAGAA-AAAAAATGATG-AAAAA-A
1 AAGAAGAAAAAATAATGAAAAAATA
370772 AAGAAGAAAAAATAATGAAAAAATA
1 AAGAAGAAAAAATAATGAAAAAATA
*
370797 ATGAAGAAAAAATAAT--AAAAATA
1 AAGAAGAAAAAATAATGAAAAAATA
370820 AA
1 AA
370822 ATAAAATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 5 0.11
23 18 0.41
24 5 0.11
25 16 0.36
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.12
Consensus pattern (25 bp):
AAGAAGAAAAAATAATGAAAAAATA
Found at i:370807 original size:14 final size:14
Alignment explanation
Indices: 370748--370825 Score: 80
Period size: 13 Copynumber: 6.0 Consensus size: 14
370738 TTATTATGCT
370748 TGAAGAAAAAA-AA
1 TGAAGAAAAAATAA
*
370761 TGATGAAAAAA-AA
1 TGAAGAAAAAATAA
370774 -GAAGAAAAAATAA
1 TGAAGAAAAAATAA
370787 T---GAAAAAATAA
1 TGAAGAAAAAATAA
370798 TGAAGAAAAAATAA
1 TGAAGAAAAAATAA
*
370812 T-AAAAATAAAATAA
1 TGAAGAA-AAAATAA
370826 AATGAAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
11 11 0.20
12 9 0.16
13 18 0.32
14 18 0.32
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (14 bp):
TGAAGAAAAAATAA
Found at i:371222 original size:18 final size:18
Alignment explanation
Indices: 371199--371233 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
371189 CAAGTTTATC
371199 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
371217 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
371234 GTTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:372628 original size:124 final size:124
Alignment explanation
Indices: 372408--374242 Score: 3115
Period size: 124 Copynumber: 15.0 Consensus size: 124
372398 CATTCGATGG
*
372408 ATCAACTTTTCCAGAAAAAGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
372473 AATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
*
372532 ATCAACTTTTCTAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
372597 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAA-GAGAT-GA-C-GC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
372652 ATCAACTTTTCTAGAAAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
372717 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
** *
372776 ATCAACTTTTTTAGAAAAAGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
372841 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
372900 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAAAACTCATCTGAAAAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
372965 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
*
373024 ATCAACTTTTCCATAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTCCA-GAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
373089 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
373149 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
373214 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
373273 ATCAACTTTTCCAGAAAAAGTTCATAATAAGACGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
373338 AATGAGAAGAGCTTGTTC-ACC-TTTGCATAACTCTATCACAGAA-GAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
373394 ATCAACTTTTCCAGAAAAA-ATCATAATAAGAAGAACTTATCTG-AGAA-G--GAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
373454 AATGAGAAGATCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
373513 ATCAACTTTT-TAG--AAAGTTTATAATAAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
373572 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
*
373631 ATCAAACTTTTCCAGAAAAAGTTCATAATAAGAAAAACTCATCTGAA-AAGGAAGAAGAAGTTCA
1 ATC-AACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
373695 TAATGAG-AGAGCTTGTTC-ACCTTTTGCATAACTCTATCACAGAAGGAG-TAGATCAGC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* *
373752 ATCAACTTATCCATAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTCCA-GAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
373817 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
373877 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
373942 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
*
374001 ATCAACTTTTCCAAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
374066 AATGAGAAAAGTTTGTTCAACCTTTTGCCTGACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
* * **
374125 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTTTCTGAAGAA-GAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
374189 AATGAGAAGAACTTGTTCAACCTTTTGTATGA-TCTATCACAGAAGGAGATAGAT
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGAT
374243 TAGCATCGAG
Statistics
Matches: 1628, Mismatches: 61, Indels: 46
0.94 0.04 0.03
Matches are distributed among these distances:
116 31 0.02
117 24 0.01
118 102 0.06
119 33 0.02
120 142 0.09
121 82 0.05
122 131 0.08
123 73 0.04
124 869 0.53
125 141 0.09
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (124 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
Found at i:373941 original size:728 final size:739
Alignment explanation
Indices: 372408--374242 Score: 3279
Period size: 728 Copynumber: 2.5 Consensus size: 739
372398 CATTCGATGG
*
372408 ATCAACTTTTCCAGAAAAAGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
372473 AATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
*
372538 TTTTCTAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
131 TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
372603 AAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGAGAT-GA-C-GCATCAACTTTTCTA
196 AAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGAGATAGATCAGCATCAACTTTTCCA
*
372665 GAAAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCT
261 GAAAAA-TTCATAATAAGAAGAACTTATCTGAAGAA-G-AGAAGAAGTTCATAATGAGAAGAACT
372730 TGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTTTAGAAAAA
323 TGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTTTAG-AAAA
372795 GTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
387 GTTTATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
372860 ACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAAAAAGTTCAT
451 ACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAAAAAGTTCAT
372925 AATAAGAAAAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
516 AATAAGAAAAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
*
372990 TGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCATAAAAAAGTTCATAATAA
581 TGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTATCCATAAAAAAGTTCATAATAA
373055 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT
646 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT
373120 AACTCTATCACAGAAGGAGATAGATCAGC
711 AACTCTATCACAGAAGGAGATAGATCAGC
373149 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
373214 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
* *
373279 TTTTCCAGAAAAAGTTCATAATAAGACGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAG
131 TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
373344 AAGAGCTTGTTC-ACC-TTTGCATAACTCTATCACAGAAGAGATAGATCAGCATCAACTTTTCCA
196 AAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGAGATAGATCAGCATCAACTTTTCCA
* *
373407 GAAAAAATCATAATAAGAAGAACTTATCTG-AGAAG-GAAGAAGTTCATAATGAGAAGATCTTGT
261 GAAAAATTCATAATAAGAAGAACTTATCTGAAGAAGAGAAGAAGTTCATAATGAGAAGAACTTGT
373470 TCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC-TTTTTAG-AAAGTTT
326 TCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTTTAGAAAAGTTT
373533 ATAATAAGAAGAACTCATCTGAAGAA-G-GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
391 ATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
373596 TTGCATAACTCTATCACAGAAGGAGATAGATCAGCATCAAACTTTTCCAGAAAAAGTTCATAATA
456 TTGCATAACTCTATCACAGAAGGAGATAGATCAGCATC-AACTTTTCCAGAAAAAGTTCATAATA
373661 AGAAAAACTCATCTG-AAAAGGAAGAAGAAGTTCATAATGAG-AGAGCTTGTTC-ACCTTTTGCA
520 AGAAAAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCA
*
373723 TAACTCTATCACAGAAGGAG-TAGATCAGCATCAACTTATCCATAAAAAAGTTCATAATAAGAAG
585 TAACTCTATCACAGAAGGAGATAGATCAACATCAACTTATCCATAAAAAAGTTCATAATAAGAAG
373787 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAACT
650 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAACT
373852 CTATCACAGAAGGAGATAGATCAGC
715 CTATCACAGAAGGAGATAGATCAGC
373877 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
373942 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
*
374007 TTTTCCAAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
131 TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * * *
374072 AAAAGTTTGTTCAACCTTTTGCCTGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCC
196 AAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAA-GAGATAGATCAGCATCAACTTTTCC
* * *
374137 AGAGAAAGTTCATAATGAGAAGAACTTTTCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACT
260 AGA-AAAATTCATAATAAGAAGAACTTATCTGAAGAAG-AGAAGAAGTTCATAATGAGAAGAACT
* *
374202 TGTTCAACCTTTTGTATGA-TCTATCACAGAAGGAGATAGAT
323 TGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGAT
374243 TAGCATCGAG
Statistics
Matches: 1058, Mismatches: 25, Indels: 29
0.95 0.02 0.03
Matches are distributed among these distances:
728 334 0.32
729 33 0.03
730 31 0.03
731 127 0.12
732 65 0.06
733 6 0.01
734 55 0.05
735 41 0.04
736 7 0.01
737 76 0.07
739 28 0.03
740 9 0.01
741 226 0.21
742 20 0.02
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (739 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAAC
TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGAGATAGATCAGCATCAACTTTTCCA
GAAAAATTCATAATAAGAAGAACTTATCTGAAGAAGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTTTAGAAAAGTTT
ATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
TTGCATAACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAAAAAGTTCATAATAA
GAAAAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT
AACTCTATCACAGAAGGAGATAGATCAACATCAACTTATCCATAAAAAAGTTCATAATAAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTC
TATCACAGAAGGAGATAGATCAGC
Found at i:374206 original size:20 final size:20
Alignment explanation
Indices: 374144--374207 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
374134 TCCAGAGAAA
374144 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
***
374164 -TTC-TGAA-GAAGAAGAAGAA
1 GTTCAT-AATG-AGAAGAACTT
374183 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
374203 GTTCA
1 GTTCA
374208 ACCTTTTGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 17 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:374262 original size:58 final size:58
Alignment explanation
Indices: 374192--374482 Score: 198
Period size: 59 Copynumber: 4.9 Consensus size: 58
374182 AGTTCATAAT
* *
374192 GAGAAGAACTTGTTCAACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATC
1 GAGAAGAGCTTGTTCAACCTTTTGCATGATCTATCACAGAAGGAGATAGATTAGCATC
* * * *
374250 GAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATATATCAACCTAAACTT
1 GAGAAGAGCTTGTTCAACCTTTTGCATGA-TCTATCACAGAAGGAGATAGAT-TAGC---A-TC
**** *** ** * * * * **
374314 TTCCAGAGAAAGTTC-A--TAATGAGAAGAACTCATCTGA-AGAAGAAGA-AGAAGTTCATAAT-
1 GAGAAGAGCTTGTTCAACCTTTTG-CATGATCT-ATC--ACAGAAGGAGATAG-A-TT-AGCATC
* *
374373 GAGAAGAACTTGTTCAACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATC
1 GAGAAGAGCTTGTTCAACCTTTTGCATGATCTATCACAGAAGGAGATAGATTAGCATC
*
374431 AAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGAT
1 GAGAAGAGCTTGTTCAACCTTTTGCATGA-TCTATCACAGAAGGAGATAGAT
374483 CAACATCAAC
Statistics
Matches: 171, Mismatches: 42, Indels: 39
0.68 0.17 0.15
Matches are distributed among these distances:
57 3 0.02
58 56 0.33
59 59 0.35
60 9 0.05
61 11 0.06
62 10 0.06
63 11 0.06
64 12 0.07
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (58 bp):
GAGAAGAGCTTGTTCAACCTTTTGCATGATCTATCACAGAAGGAGATAGATTAGCATC
Found at i:374601 original size:122 final size:122
Alignment explanation
Indices: 374432--374656 Score: 337
Period size: 122 Copynumber: 1.8 Consensus size: 122
374422 ATTAGCATCA
*
374432 AGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAAC-TTT
1 AGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
*
374496 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATG
66 T-CAGA-AAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATG
* * *
374555 AGAAGAACTTGTTCAACCTTTTGTATGA-TCTATCACAGAAGGAGATAGATTAGCATCAACATTT
1 AGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
** * *
374619 TCAGAAGTGTTTATAATGATAAGAACTCATCTAAAGAA
66 TCAGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAA
374657 TAAGGAGCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
121 28 0.30
122 34 0.37
123 30 0.33
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (122 bp):
AGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTT
TCAGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATG
Found at i:374612 original size:181 final size:181
Alignment explanation
Indices: 374078--374613 Score: 1009
Period size: 181 Copynumber: 3.0 Consensus size: 181
374068 TGAGAAAAGT
*
374078 TTGTTCAACCTTTTGCCTGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
1 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
**
374143 AGTTCATAATGAGAAGAACTTTTCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
374208 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCGAGAAGAGC
131 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAAGAAGAGC
* * *
374259 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATATATCAACCTAAACTTTTCCAGAGAA
1 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
374324 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
374389 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAAGAAGAGC
131 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAAGAAGAGC
374440 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
1 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
374505 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
374570 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAA
131 ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAA
374614 CATTTTCAGA
Statistics
Matches: 345, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 345 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (181 bp):
TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATCAAGAAGAGC
Found at i:374928 original size:3 final size:3
Alignment explanation
Indices: 374922--374958 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
374912 TTTTTTTAAA
374922 TAT TAT T-T TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
374959 AATTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:375912 original size:22 final size:23
Alignment explanation
Indices: 375868--375915 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
375858 ATTATTAGTT
375868 TTTATTATATAGTTTTCATTTAA
1 TTTATTATATAGTTTTCATTTAA
*
375891 TTTATT-T-TAGTTGTTGATTTAA
1 TTTATTATATAGTT-TTCATTTAA
375913 TTT
1 TTT
375916 TATATGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (23 bp):
TTTATTATATAGTTTTCATTTAA
Found at i:375917 original size:23 final size:24
Alignment explanation
Indices: 375867--375918 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
375857 AATTATTAGT
375867 TTTTATTATATAGTTTTCATTTAA
1 TTTTATTATATAGTTTTCATTTAA
*
375891 -TTTATT-T-TAGTTGTTGATTTAA
1 TTTTATTATATAGTT-TTCATTTAA
375913 TTTTAT
1 TTTTAT
375919 ATGTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 11 0.44
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (24 bp):
TTTTATTATATAGTTTTCATTTAA
Found at i:376683 original size:14 final size:15
Alignment explanation
Indices: 376666--376694 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
376656 AGTAATATAT
376666 AAATAATAAT-AAAA
1 AAATAATAATGAAAA
376680 AAATAATAATGAAAA
1 AAATAATAATGAAAA
376695 TTATCCAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAATAATGAAAA
Found at i:378472 original size:24 final size:24
Alignment explanation
Indices: 378445--378510 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
378435 AAACAGGAGA
378445 AAAAAGTTTGATGAAAAAATT-ATG
1 AAAAA-TTTGATGAAAAAATTAATG
* *
378469 AAAATATTTTATGAAAGAATTAATG
1 AAAA-ATTTGATGAAAAAATTAATG
378494 AAAGAATTT--TGAAAAAA
1 AAA-AATTTGATGAAAAAA
378511 AATGTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.19
24 17 0.47
25 11 0.31
26 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (24 bp):
AAAAATTTGATGAAAAAATTAATG
Found at i:383648 original size:23 final size:24
Alignment explanation
Indices: 383604--383648 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
383594 ACGTTTATTT
* *
383604 AAAAATGAAATAAGATACATATAA
1 AAAAATGAAATAAGAAAAATATAA
*
383628 AAAAAT-AAATAATAAAAATAT
1 AAAAATGAAATAAGAAAAATAT
383649 TCAAAATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAAATGAAATAAGAAAAATATAA
Found at i:385106 original size:72 final size:74
Alignment explanation
Indices: 384966--385111 Score: 201
Period size: 72 Copynumber: 2.0 Consensus size: 74
384956 TTATAATTAA
* * *
384966 AAAAACATGAAAAATGAGAAGGTTGCAAAGTATCGATACTTTTCAAAAGGTATTGATACTTTCGA
1 AAAAACATGAAAAATGAGAAGGTTACAAAGTATCGATACTTTTCAAAAGGTATCGATACTTTCAA
385031 ATTT-AAAG
66 ATTTGAAAG
* *
385039 AAAAACATGAAAAATG-GAAGGTTACAAAGTAT-GAATACTTTTTCAAAA-GTATCGATGCTTTT
1 AAAAACATGAAAAATGAGAAGGTTACAAAGTATCG-ATAC-TTTTCAAAAGGTATCGATACTTTC
385101 AAATTTGAAAG
64 AAATTTGAAAG
385112 TTAAAATATC
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
71 1 0.02
72 35 0.54
73 29 0.45
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (74 bp):
AAAAACATGAAAAATGAGAAGGTTACAAAGTATCGATACTTTTCAAAAGGTATCGATACTTTCAA
ATTTGAAAG
Found at i:385190 original size:29 final size:29
Alignment explanation
Indices: 385158--385218 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
385148 AGTATGGACA
* * *
385158 TTTTTTCAT-AAATATCGATACTTTTGAAT
1 TTTTTTAATAAAATATCAATA-TTTTAAAT
385187 TTTTTTAATAAAATATCAATATTTTAAAT
1 TTTTTTAATAAAATATCAATATTTTAAAT
385216 TTT
1 TTT
385219 GATCTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTTTAATAAAATATCAATATTTTAAAT
Found at i:385440 original size:82 final size:76
Alignment explanation
Indices: 385283--385474 Score: 194
Period size: 82 Copynumber: 2.4 Consensus size: 76
385273 TTTTTTCGGT
*
385283 GCAACCTATTTTATTAATAAAAATATTAACA-TAAAATATCACAACTCATTTCATAGTGAACCAT
1 GCAACCTATTTTATTAA-AAAAATATTAACATTAAAATATCACAACTCATTTCATAGCGAACCAT
* *
385347 GACATTTTTGGG
65 AACATTCTTGGG
* *
385359 CGCAACCTATTTTATTAAAAAAATATTAACATTAAATTA-CAGATCGTAACAT-ATTTTCTTAGC
1 -GCAACCTATTTTATTAAAAAAATATTAACATTAAAATATC--A-C--AAC-TCA-TTTCATAGC
*
385422 GAACCATAATATTCTTGGG
58 GAACCATAACATTCTTGGG
*
385441 G-AGACCTATTTTATTACTAAAAATATTAACATTA
1 GCA-ACCTATTTTATTA-AAAAAATATTAACATTA
385475 CAGGTTAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
76 14 0.14
77 23 0.23
78 1 0.01
79 1 0.01
80 1 0.01
81 18 0.18
82 40 0.41
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (76 bp):
GCAACCTATTTTATTAAAAAAATATTAACATTAAAATATCACAACTCATTTCATAGCGAACCATA
ACATTCTTGGG
Found at i:396759 original size:270 final size:271
Alignment explanation
Indices: 396278--396795 Score: 966
Period size: 270 Copynumber: 1.9 Consensus size: 271
396268 TTGACCTTAG
* *
396278 GGTTATGAATATAAGGGTGTAGATCATTATAATAGTGTAAGAATCGTTGATTGTTCATTATTAAG
1 GGTTATGAATATAAGGGTGTAGATCATTATAATAGCGTAAAAATCGTTGATTGTTCATTATTAAG
396343 TTAAAGGTCAACTCTAAAGAGACAGTTGGTAGTAGATTCATCCATCTGGGAGTGTTTCATGAGGG
66 TTAAAGGTCAACTCTAAAGAGACAGTTGGTAGTAGATTCATCCATCTGGGAGTGTTTCATGAGGG
* *
396408 ATCATTTAAGTGAATGTTCAAGGATAAGATTAAGATTACGAGATCATGTTTCCATATCAAGAGTT
131 ATCATTTAAGTGAATATTCAAGGATAAGACTAAGATTACGAGATCATGTTTCCATATCAAGAGTT
396473 GATGGTTCGTGTGACAAGCTCAATA-AGCCTCAACAATCCTAAATTTGGAGTTAGAAATGTATAT
196 GATGGTTCGTGTGACAAGCTCAATAGAGCCTCAACAATCCTAAATTTGGAGTTAGAAATGTATAT
396537 CTCCAAGATTT
261 CTCCAAGATTT
*
396548 GGTTATGAATATAAGGGTGTAGATCATTATAATAGCGTAAAAATCGTTGATTGTTCGTTATTAAG
1 GGTTATGAATATAAGGGTGTAGATCATTATAATAGCGTAAAAATCGTTGATTGTTCATTATTAAG
*
396613 TTAAAGGTCAACTCTAAAGAGACATTTGGTAGTAGATTCATCCATCTGGGAGTGTTTCATGAGGG
66 TTAAAGGTCAACTCTAAAGAGACAGTTGGTAGTAGATTCATCCATCTGGGAGTGTTTCATGAGGG
*
396678 ATCATTTAAGTGAATATTCAAGGATAAGACTAAGATTACGAGATCATGTTTCCATATTAAGAGTT
131 ATCATTTAAGTGAATATTCAAGGATAAGACTAAGATTACGAGATCATGTTTCCATATCAAGAGTT
396743 GATGGTTCGTGTGACAAGCTCAATAGAGCCTCAACAATCCTAAATTTGGAGTT
196 GATGGTTCGTGTGACAAGCTCAATAGAGCCTCAACAATCCTAAATTTGGAGTT
396796 GCTTGTGTTG
Statistics
Matches: 240, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
270 213 0.89
271 27 0.11
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (271 bp):
GGTTATGAATATAAGGGTGTAGATCATTATAATAGCGTAAAAATCGTTGATTGTTCATTATTAAG
TTAAAGGTCAACTCTAAAGAGACAGTTGGTAGTAGATTCATCCATCTGGGAGTGTTTCATGAGGG
ATCATTTAAGTGAATATTCAAGGATAAGACTAAGATTACGAGATCATGTTTCCATATCAAGAGTT
GATGGTTCGTGTGACAAGCTCAATAGAGCCTCAACAATCCTAAATTTGGAGTTAGAAATGTATAT
CTCCAAGATTT
Found at i:398556 original size:19 final size:20
Alignment explanation
Indices: 398518--398557 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
398508 TTTTATGGGT
398518 TGTAGTATCAATATTATTCA
1 TGTAGTATCAATATTATTCA
398538 TGTAGTAT-AGATA-TATTCA
1 TGTAGTATCA-ATATTATTCA
398557 T
1 T
398558 ATTATGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (20 bp):
TGTAGTATCAATATTATTCA
Found at i:409392 original size:45 final size:45
Alignment explanation
Indices: 409343--409761 Score: 502
Period size: 45 Copynumber: 9.3 Consensus size: 45
409333 AGGATGCCAA
* *
409343 AGTTGAAAGGCATATGGGTGCATTATCAACAGAAAAGTATACTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * *
409388 AGTTGAAATGCATATGGGTGCATTATCAACATAAACGTATGCTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
* *
409433 AGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATACTATG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTA-G
* * * *
409479 -GTTGAGATGTATATGGGTACATTATCAACATAAAAGTATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
* *
409523 AGTTGAAATGCATATGGGTGCATTATCAACAAAAAAGTATACTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * *
409568 AGTTAAAAAGCATAAGGGTACATTATCAACAGAAAAGTATGCTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
*
409613 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTA-G
* * * * * * *
409659 -GTTGAGATGTATATGAGTAAATTATCAATATAAAAGTATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * **
409703 AATTGAAATGCATATGGGTGCATTATGAACAGAAAAG-ATGTTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
*
409747 AGTTTAAAATGCATA
1 AG-TTGAAATGCATA
409762 ATGATGTATT
Statistics
Matches: 323, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
44 5 0.02
45 316 0.98
46 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.29
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAG
Found at i:415857 original size:22 final size:20
Alignment explanation
Indices: 415826--415881 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
415816 ATAATGGTAG
*
415826 GGGGTATCGATACTATAGTA
1 GGGGTATCGATACTATAATA
*
415846 GGGTAGTATCGATACCATAATA
1 GGG--GTATCGATACTATAATA
415868 GGGGTATCGATACT
1 GGGGTATCGATACT
415882 GAAGGGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 13 0.42
22 18 0.58
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
GGGGTATCGATACTATAATA
Found at i:416750 original size:45 final size:45
Alignment explanation
Indices: 416295--416730 Score: 579
Period size: 45 Copynumber: 9.7 Consensus size: 45
416285 ATAAAAGAAT
*** * * * *
416295 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTAA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTAGAGTTGA
416340 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
* *
416385 AATGCATATGGGTGCATTATCAATAGAAAAATATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
* * *
416430 AATGTATATGGGTACATTATCAACAGAAAAATATACTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTA-GAGTTGA
* * * * *
416475 GATGTATATGGGTACATTATCAACATAAAAGTATACTAGAGCTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
*
416520 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGATGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
*
416565 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
* * * *
416610 AATGTATATGGGTACATTATCAACAGAAAAGTATAATATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
* * * * *
416655 GATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
*
416700 AATGCATATGGGTGCATTATCAATAGAAAAG
1 AATGCATATGGGTGCATTATCAACAGAAAAG
416731 ATGTTAGAGT
Statistics
Matches: 352, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
44 2 0.01
45 349 0.99
46 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
Found at i:424683 original size:21 final size:19
Alignment explanation
Indices: 424655--424700 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
424645 TCATTGAATC
424655 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
424675 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
424694 ACTTAGT
1 A-TTAGT
424701 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:445198 original size:29 final size:28
Alignment explanation
Indices: 445165--445257 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
445155 AAAAAATCGG
445165 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTC-GTTAATAATTTTCAAA
*
445194 TTAATTTGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTC-GTTAATAATTTTCAAA
* * *
445223 TTAATTCGTTTCGATTAATAGTTTCCAAA
1 TTAATTCGGTTCG-TTAATAATTTTCAAA
*
445252 TAAATT
1 TTAATT
445258 TTGGTTCGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 1 0.02
29 55 0.98
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (28 bp):
TTAATTCGGTTCGTTAATAATTTTCAAA
Found at i:445826 original size:28 final size:28
Alignment explanation
Indices: 445777--445844 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
445767 AACGATGCGA
*
445777 TGGTCTGATTGAATAAATAAAAAATT-GG
1 TGGTCTGATTGAA-CAATAAAAAATTCGG
*
445805 TGGTCTGATTGAGACAA-AAAAAGTTCGG
1 TGGTCTGATTGA-ACAATAAAAAATTCGG
*
445833 TGGTCAGATTGA
1 TGGTCTGATTGA
445845 TTATTGAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.20
28 27 0.77
29 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.29
Consensus pattern (28 bp):
TGGTCTGATTGAACAATAAAAAATTCGG
Found at i:446124 original size:16 final size:16
Alignment explanation
Indices: 446103--446133 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
446093 TAGTAATTGA
446103 ACATTATAATAGCTCT
1 ACATTATAATAGCTCT
446119 ACATTATAATAGCTC
1 ACATTATAATAGCTC
446134 CACAAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
ACATTATAATAGCTCT
Found at i:447050 original size:30 final size:29
Alignment explanation
Indices: 447016--447075 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
447006 AAATGGTTTT
* *
447016 AGTTTAGTGACCAAATTATAAGATTTTGAA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAA
*
447046 AGTTTGGTGACCAAAGTATAAACTTTGAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAA
447075 A
1 A
447076 ACTTCAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (29 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAA
Found at i:449379 original size:21 final size:21
Alignment explanation
Indices: 449353--449404 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
449343 GTTCTGCAGG
*
449353 TCCTTCAGGACACAGATGACA
1 TCCTTCAGGACACAGACGACA
* * * *
449374 TCCTTCGGGACATATACGAGA
1 TCCTTCAGGACACAGACGACA
449395 TCCTTCAGGA
1 TCCTTCAGGA
449405 TAATTTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (21 bp):
TCCTTCAGGACACAGACGACA
Found at i:449526 original size:30 final size:30
Alignment explanation
Indices: 449492--449554 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
449482 CCTTGAGTTC
* *
449492 TCAGTAATGTACATGGGCTTATAAAAGATA
1 TCAGTAATGTACATGAGATTATAAAAGATA
*
449522 TCAGTACTGTACATGAGATTATAAAAGATA
1 TCAGTAATGTACATGAGATTATAAAAGATA
449552 TCA
1 TCA
449555 AAAGTATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (30 bp):
TCAGTAATGTACATGAGATTATAAAAGATA
Found at i:449801 original size:18 final size:18
Alignment explanation
Indices: 449778--449841 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
449768 ATGTATTACA
*
449778 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
** **
449796 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
449814 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
*
449832 GGATAATGAT
1 TGATAATGAT
449842 GGCATATGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:452351 original size:9 final size:9
Alignment explanation
Indices: 452337--452398 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
452327 CATAAGAACT
452337 AAAAAGAAG
1 AAAAAGAAG
452346 AAAAAGAAG
1 AAAAAGAAG
452355 AAGAAA-AAGG
1 AA-AAAGAA-G
*
452365 AAAAA-AAT
1 AAAAAGAAG
452373 AAAAAGAAG
1 AAAAAGAAG
*
452382 AAGAAGAAG
1 AAAAAGAAG
*
452391 AAGAAGAA
1 AAAAAGAA
452399 AATAGAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.11
9 36 0.77
10 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:452355 original size:3 final size:3
Alignment explanation
Indices: 452340--452398 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
452330 AAGAACTAAA
* * * * *
452340 AAG AAG AAA AAG AAG AAG AAA AAGG AA- AAA AAT AAA AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG
452385 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
452399 AATAGAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:452447 original size:6 final size:6
Alignment explanation
Indices: 452343--452447 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
452333 AACTAAAAAG
* * * * *
452343 AAGAAA AAGAAG AAGAAA AAGGAAAAA AATAAA AAGAAG AAGAAG AAGAAG
1 AAGAAA AAGAAA AAGAAA AA-G--AAA AAGAAA AAGAAA AAGAAA AAGAAA
*
452394 AAGAAA ATAGAAA ACAGAAAA AATGAAA AA-AATA AAAAAA AATG-AA
1 AAGAAA A-AGAAA A-AG-AAA AA-GAAA AAGAA-A AAGAAA AA-GAAA
452440 AAGAAA AA
1 AAGAAA AA
452448 AATTAGAGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
5 3 0.04
6 51 0.63
7 17 0.21
8 5 0.06
9 5 0.06
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:453711 original size:30 final size:30
Alignment explanation
Indices: 453677--453751 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
453667 AAATGGATTT
*
453677 AGTTTAGTGACCAAATTATAAGA-TTTCAAA
1 AGTTTAGTGACCAAAGTATAA-ACTTTCAAA
* *
453707 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTCAAA
*
453737 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
453752 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTCAAA
Found at i:456026 original size:30 final size:30
Alignment explanation
Indices: 455992--456054 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
455982 CCTTGAGTTC
*
455992 TCAGTAATGTAC-ATGGGCTTATAAAAGATA
1 TCAGTAATGT-CTATGGGATTATAAAAGATA
*
456022 TCAGTATTGTCTATGGGATTATAAAAGATA
1 TCAGTAATGTCTATGGGATTATAAAAGATA
456052 TCA
1 TCA
456055 AAAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (30 bp):
TCAGTAATGTCTATGGGATTATAAAAGATA
Found at i:457043 original size:23 final size:23
Alignment explanation
Indices: 457013--457060 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
457003 TGGTGGTTGG
*
457013 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
457036 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
457059 TT
1 TT
457061 CGGTTCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:463948 original size:19 final size:20
Alignment explanation
Indices: 463908--463950 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
463898 TTTAGTTTTT
*
463908 CTTTTCTCTTTCATCCTTAA
1 CTTTTCTATTTCATCCTTAA
*
463928 CTTTTCTATTTCAT-TTTAA
1 CTTTTCTATTTCATCCTTAA
463947 CTTT
1 CTTT
463951 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTTTCTATTTCATCCTTAA
Found at i:467155 original size:9 final size:9
Alignment explanation
Indices: 467141--467166 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
467131 TTTATTACTT
467141 TTTTATTTA
1 TTTTATTTA
467150 TTTTATTTA
1 TTTTATTTA
467159 TTTTATTT
1 TTTTATTT
467167 GAGGGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTTA
Found at i:468948 original size:29 final size:29
Alignment explanation
Indices: 468906--468966 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
468896 ATGATTTCAT
468906 TGAAAAGTTCTACTGTGACTTTCATACTA
1 TGAAAAGTTCTACTGTGACTTTCATACTA
468935 TGAAAAGTTCTACTGTGACTTTCATACTA
1 TGAAAAGTTCTACTGTGACTTTCATACTA
468964 TGA
1 TGA
468967 TTTTTAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (29 bp):
TGAAAAGTTCTACTGTGACTTTCATACTA
Found at i:470727 original size:3 final size:3
Alignment explanation
Indices: 470713--470744 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
470703 TTGAAAAATT
*
470713 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
470745 TGAAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Done.