Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008100.1 Hibiscus syriacus cultivar Beakdansim tig00110630_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: 1372717
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 7
Found at i:173969 original size:26 final size:27
Alignment explanation
Indices: 173818--174006 Score: 96
Period size: 28 Copynumber: 7.1 Consensus size: 27
173808 TAGTTTATAC
* * *
173818 ATATATAGTT-TATATACATAGTTTAT
1 ATATATAGTTATATAAATATAATTTAT
* * *
173844 ATGTATAGTTCACATAAACATAATTTAT
1 ATATATAGTT-ATATAAATATAATTTAT
*
173872 ATATATAGCTTATAATAATTATATAGTTTAT
1 ATATATAG-TTAT-ATAA--ATATAATTTAT
* *
173903 A-ATATA--AATATAATTTATAATTT-T
1 ATATATAGTTATATAA-ATATAATTTAT
*
173927 ATATA-ATGTTGACATAAATATAATTTAT
1 ATATATA-GTT-ATATAAATATAATTTAT
173955 ATATATAGTT-TAT--A-ATAA-TTAT
1 ATATATAGTTATATAAATATAATTTAT
* * *
173977 ATAGTTTA-TAATATAAATATAGTTTAT
1 ATA-TATAGTTATATAAATATAATTTAT
174004 ATA
1 ATA
174007 ATTTATATTA
Statistics
Matches: 126, Mismatches: 18, Indels: 37
0.70 0.10 0.20
Matches are distributed among these distances:
22 8 0.06
23 10 0.08
24 4 0.03
25 12 0.10
26 18 0.14
27 17 0.13
28 35 0.28
29 7 0.06
30 5 0.04
31 10 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (27 bp):
ATATATAGTTATATAAATATAATTTAT
Found at i:173970 original size:47 final size:49
Alignment explanation
Indices: 173905--174006 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 49
173895 TAGTTTATAA
* * *
173905 TATAAATATAATTTATAAT-TTTATATAATGT-TGACATAAATATAATT
1 TATATATATAATTTATAATAATTATATAATGTATAACATAAATATAATT
* * * * *
173952 TATATATATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTT
1 TATATATATAATTTATAATAATTATATAATGTATAACATAAATATAATT
174001 TATATA
1 TATATA
174007 ATTTATATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
47 17 0.38
48 9 0.20
49 19 0.42
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (49 bp):
TATATATATAATTTATAATAATTATATAATGTATAACATAAATATAATT
Found at i:174024 original size:20 final size:20
Alignment explanation
Indices: 173944--174026 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
173934 GTTGACATAA
173944 ATATAATTT-ATATATATAGT
1 ATATAATTTAAT-TATATAGT
*
173964 TTATAA--TAATTATATAGT
1 ATATAATTTAATTATATAGT
* *
173982 TTATAATATAA--ATATAGTTT
1 ATATAATTTAATTATATAG--T
174002 ATATAATTTATATTATATA-T
1 ATATAATTTA-ATTATATAGT
174022 ATATA
1 ATATA
174027 TTATATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
18 21 0.40
19 2 0.04
20 23 0.44
21 1 0.02
23 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATATAATTTAATTATATAGT
Found at i:175384 original size:38 final size:36
Alignment explanation
Indices: 175269--175617 Score: 243
Period size: 38 Copynumber: 9.5 Consensus size: 36
175259 ATATATACAT
* *
175269 ATTTTGAAACTACGTATATAATATATAGTTTTTAATA-
1 ATTTTGAAAATA--TATATAATATATAGTTTTTAAAAC
* * **
175306 GTTTTTAAAAT-TATATAATATATAGTTTAAAAAAAAC
1 ATTTTGAAAATATATATAATATATAGTTT--TTAAAAC
*
175343 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAATATATATAATATATAGTTTTTAAAA-C
175381 ATTTTGAAAACT-TATATATATATATAGTTTTTGAAAAC
1 ATTTTGAAAA-TATATATA-ATATATAGTTTTT-AAAAC
* *
175419 ATTTTTGAAAACATATAT-AT-TATAGTTTTGAAAAC
1 A-TTTTGAAAATATATATAATATATAGTTTTTAAAAC
* *
175454 ATTTTGAAAACATTTATATATTATATAGTTTTTAAAAC
1 ATTTTG-AAA-ATATATATAATATATAGTTTTTAAAAC
* * * *
175492 GTTTTTGGAAAATTTATATAATCT-T-TTTTTTGAAAAC
1 -ATTTT-GAAAATATATATAATATATAGTTTTT-AAAAC
* * *
175529 ATGTTGAAAA-ATTCATATATTATATAG-TTTAAAAAC
1 ATTTTGAAAATA-T-ATATAATATATAGTTTTTAAAAC
* * *
175565 ATTTTG-AAATTTATATATTATAT-GTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTT-AAAAC
* *
175600 ATTTATGTATATATATAT
1 ATTT-TGAAAATATATAT
175618 TATTTATTAT
Statistics
Matches: 250, Mismatches: 35, Indels: 54
0.74 0.10 0.16
Matches are distributed among these distances:
33 1 0.00
34 36 0.14
35 27 0.11
36 45 0.18
37 48 0.19
38 51 0.20
39 41 0.16
40 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
Found at i:175460 original size:11 final size:11
Alignment explanation
Indices: 175444--175468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
175434 TATATTATAG
175444 TTTTGAAAACA
1 TTTTGAAAACA
175455 TTTTGAAAACA
1 TTTTGAAAACA
175466 TTT
1 TTT
175469 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:175547 original size:74 final size:71
Alignment explanation
Indices: 175312--175603 Score: 263
Period size: 74 Copynumber: 4.0 Consensus size: 71
175302 AATAGTTTTT
* ** * *
175312 AAAATTATATAATATATAGTTTAAAAAAAACATTTTAGAAAATATATATAATATATAATTTTT-A
1 AAAATTATATATTATATAGTTT--TTAAAAC-TTTTTGAAAATTTATATAAT-TAT-ATTTTTGA
175376 AAATCATTTTGA
61 AAA-CATTTTGA
* ** *
175388 AAACTTATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATAT-ATTATAGTTTTGAAA
1 AAAATTATATAT-TATATAGTTTTT-AAAAC-TTTTTGAAAATTTATATAATTATATTTTTGAAA
175452 ACATTTTGA
63 ACATTTTGA
*
175461 AAACATTTATATATTATATAGTTTTTAAAACGTTTTTGGAAAATTTATATAATCT-TTTTTTTGA
1 AAA-A-TTATATATTATATAGTTTTTAAAAC-TTTTT-GAAAATTTATATAAT-TATATTTTTGA
*
175525 AAACATGTTGA
61 AAACATTTTGA
* *
175536 AAAATTCATATATTATATAG-TTTAAAAACATTTTG-AAATTTATAT-ATTATATGTTTTTGAAA
1 AAAATT-ATATATTATATAGTTTTTAAAACTTTTTGAAAATTTATATAATTATA--TTTTTGAAA
*
175598 ATATTT
63 ACATTT
175604 ATGTATATAT
Statistics
Matches: 185, Mismatches: 19, Indels: 29
0.79 0.08 0.12
Matches are distributed among these distances:
68 1 0.01
69 3 0.02
70 10 0.05
71 14 0.08
72 4 0.02
73 36 0.19
74 43 0.23
75 32 0.17
76 32 0.17
77 10 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (71 bp):
AAAATTATATATTATATAGTTTTTAAAACTTTTTGAAAATTTATATAATTATATTTTTGAAAACA
TTTTGA
Found at i:175610 original size:24 final size:24
Alignment explanation
Indices: 175566--175611 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
175556 TTTAAAAACA
*
175566 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
175590 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
175612 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:176838 original size:16 final size:18
Alignment explanation
Indices: 176807--176839 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
176797 TGATCATAAG
176807 TTTTATCTTTATCTTTTT
1 TTTTATCTTTATCTTTTT
176825 TTTTAT-TTTA-CTTTT
1 TTTTATCTTTATCTTTT
176840 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATCTTTATCTTTTT
Found at i:178690 original size:19 final size:19
Alignment explanation
Indices: 178656--178700 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
178646 ATTTAGACAT
178656 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
178674 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
178693 TTTGCATT
1 TTTGCATT
178701 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:182267 original size:84 final size:82
Alignment explanation
Indices: 182049--182705 Score: 542
Period size: 81 Copynumber: 8.0 Consensus size: 82
182039 TGCAGCTTAG
* * *
182049 CTCAAGGCCAGAAGGGCTATCTG-CCACCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTGACCA--AAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGG
* * * *
182112 CACATCATTTGCAGTATAG
64 CACAACATTTACAGCATAA
* * * * * * * * * *
182131 CTTAAGTCGAGAAGAGCTATCTG-CCAAAGACCCTTAAGTTCAATTACACTCAGCTTCAAGGGCA
1 CTCAAGGCTAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGGCA
*
182195 TAACATTTACAGCATAA
66 CAACATTTACAGCATAA
*
182212 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTG--ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGG
* * ** *
182276 CACATCATTTGCAATATAG
64 CACAACATTTACAGCATAA
* * * * * * * * * *
182295 CTTAAGTCGAGAAGAGCTATCTG-CCAAAGACCCTTAAGTTCAATTACACTCAGCTTCAAGGGCA
1 CTCAAGGCTAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGGCA
*
182359 TAACATTTACAGCATAA
66 CAACATTTACAGCATAA
* *
182376 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTG--ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGG
* * * *
182440 CACATCATTTGCAGTATAG
64 CACAACATTTACAGCATAA
* * * * * * *
182459 CTTAA-GTTGAGAAGAGTTATCTG-CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGC
1 CTCAAGGCT-AGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGGC
*
182522 ATAACATTTACAGCATAA
65 ACAACATTTACAGCATAA
* *
182540 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GG
1 CTCAAGGCTAGAAGGGTTATCTG--ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGG
* ** * *
182604 CACATCATTTGTAGAATAG
64 CACAACATTTACAGCATAA
* * * * *** * * * *
182623 CTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTTGATTACGCTCAGCTTCGAGGGCG
1 CTCAAGGCTAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGGCA
* *
182687 CATCATTTGCAGCATAA
66 CAACATTTACAGCATAA
182704 CT
1 CT
182706 GCTATCTGCC
Statistics
Matches: 449, Mismatches: 111, Indels: 31
0.76 0.19 0.05
Matches are distributed among these distances:
80 115 0.26
81 119 0.27
82 26 0.06
83 100 0.22
84 89 0.20
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (82 bp):
CTCAAGGCTAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGGCA
CAACATTTACAGCATAA
Found at i:182319 original size:164 final size:164
Alignment explanation
Indices: 182049--182705 Score: 1057
Period size: 164 Copynumber: 4.0 Consensus size: 164
182039 TGCAGCTTAG
* * ** *
182049 CTCAAGGCCAGAAGGGCTATCTGCCA-CCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* *
182113 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCAATTAC
66 ACATCATTTGCAATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCAATTAC
182178 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
*
182212 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
182277 ACATCATTTGCAATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCAATTAC
66 ACATCATTTGCAATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCAATTAC
182342 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
182376 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * *
182441 ACATCATTTGCAGTATAGCTTAAGTTGAGAAGAGTTATCTGCCAAAGACCCTCGAGTTCGATTAC
66 ACATCATTTGCAATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCAATTAC
182506 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
182540 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * **
182605 ACATCATTTGTAGA-ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTA
66 ACATCATTTGCA-ATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCAATTA
* * ** * *
182669 CGCTCAGCTTCGAGGGCGCATCATTTGCAGCATAA
130 CACTCAGCTTCAAGGGCATAACATTTACAGCATAA
182704 CT
1 CT
182706 GCTATCTGCC
Statistics
Matches: 465, Mismatches: 27, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
163 22 0.05
164 443 0.95
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAATATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCAATTAC
ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
Found at i:182747 original size:68 final size:68
Alignment explanation
Indices: 182638--182773 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 68
182628 GTCGAGAAGG
* * * * * * *
182638 GCTATCTGCCAAAGACCCCCGAGTTTGATTACGCTCAGCTTCGAGGGCGCATCATTTGCAGCATA
1 GCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATA
182703 ACT
66 ACT
** *
182706 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATA
1 GCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATA
182771 ACT
66 ACT
182774 CAAGGCTAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (68 bp):
GCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATA
ACT
Found at i:182882 original size:232 final size:232
Alignment explanation
Indices: 182476--182937 Score: 897
Period size: 232 Copynumber: 2.0 Consensus size: 232
182466 TGAGAAGAGT
*
182476 TATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
1 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
182541 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
66 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
*
182606 CATCATTTGTAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACG
131 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACG
182671 CTCAGCTTCGAGGGCGCATCATTTGCAGCATAACTGC
196 CTCAGCTTCGAGGGCGCATCATTTGCAGCATAACTGC
*
182708 TATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
1 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
182773 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
66 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
182838 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACG
131 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACG
182903 CTCAGCTTCGAGGGCGCATCATTTGCAGCATAACT
196 CTCAGCTTCGAGGGCGCATCATTTGCAGCATAACT
182938 TAAGTCAAGA
Statistics
Matches: 227, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 227 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (232 bp):
TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACG
CTCAGCTTCGAGGGCGCATCATTTGCAGCATAACTGC
Found at i:183022 original size:165 final size:164
Alignment explanation
Indices: 182706--183116 Score: 561
Period size: 165 Copynumber: 2.5 Consensus size: 164
182696 CAGCATAACT
*** * *
182706 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATA
1 GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAACATTTACAGCATA
* ** * *
182771 ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
66 ACTCAAGGCAAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
182836 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
131 CACATCATTTGCAGAATAGCTTAAGTCAAGAAGG
* * * * *
182870 GCTATCTGCCAAAGACCCCCGAGTTTGATTACGCTCAGCTTCGAGGGCGCATCATTTGCAGCATA
1 GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAACATTTACAGCATA
* *
182935 ACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
66 ACTCAAGGCAAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* *
183000 GCATATCATTTGCAGCATAGCTTAAGTCAAGAAGG
130 GCACATCATTTGCAGAATAGCTTAAGTCAAGAAGG
* * * * * *
183035 GCTATCTGCCAAAGACTCCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAACATA
1 GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAACATTTACAGCATA
* *
183100 GCTCATGGCAAGAAGGG
66 ACTCAAGGCAAGAAGGG
183117 CTATTTGTCA
Statistics
Matches: 213, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
164 76 0.36
165 137 0.64
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
GCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAACATTTACAGCATA
ACTCAAGGCAAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAGAATAGCTTAAGTCAAGAAGG
Found at i:183046 original size:84 final size:83
Alignment explanation
Indices: 182714--183043 Score: 344
Period size: 84 Copynumber: 4.0 Consensus size: 83
182704 CTGCTATCTG
* * * * * * * *
182714 CCAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAG
1 CCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAG
* * * **
182778 GCTAGAAGGGTTATCTGTTA
64 TCAAGAAGGGCTATCTGCAA
* * * *
182798 GCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
182863 GAGAAGGGCTATCTG---
66 AAGAAGGGCTATCTGCAA
** * * * * *
182878 CCAAAGACCCCCGAGTTTGATTACGCTCAGCTTCGAGGGCGCATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
182943 CAAGAAGGGTTATCTGCCAA
65 CAAGAAGGGCTATCTG-CAA
* *
182963 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
183028 AAGAAGGGCTATCTGC
66 AAGAAGGGCTATCTGC
183044 CAAAGACTCC
Statistics
Matches: 203, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
80 25 0.12
81 42 0.21
83 40 0.20
84 69 0.34
85 27 0.13
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
AAGAAGGGCTATCTGCAA
Found at i:183116 original size:81 final size:79
Alignment explanation
Indices: 182706--183120 Score: 380
Period size: 81 Copynumber: 5.1 Consensus size: 79
182696 CAGCATAACT
** * * *
182706 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATA
1 GCTATCTGCCAAAGACCC-CGAGTTCGATTACGCTCAGCTTCAA-GGCATATCATTTGCAGCATA
* * * *
182771 ACTCAAGGCTAGAAGG
64 GCTTAAGTCAAGAAGG
* * ** * * * *
182787 GTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAA
1 GCTATCTG---CCAAAGACC-CCGAGTTCGATTACGCTCAGCTTCAAGGCATATCATTTGCAGCA
*
182852 TAGCTTAAGTCGAGAAGG
62 TAGCTTAAGTCAAGAAGG
* * **
182870 GCTATCTGCCAAAGACCCCCGAGTTTGATTACGCTCAGCTTCGAGGGCGCATCATTTGCAGCATA
1 GCTATCTGCCAAAGA-CCCCGAGTTCGATTACGCTCAGCTTC-AAGGCATATCATTTGCAGCATA
*
182935 ACTTAAGTCAAGAAGG
64 GCTTAAGTCAAGAAGG
* * * *
182951 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGC
1 GCTATCTG----CCAAAGACC-CCGAGTTCGATTACGCTCAGCTTCAAGGCATATCATTTGCAGC
183016 ATAGCTTAAGTCAAGAAGG
61 ATAGCTTAAGTCAAGAAGG
* * * * *
183035 GCTATCTGCCAAAGACTCCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAACATA
1 GCTATCTGCCAAAGAC-CCCGAGTTCGATTACGCTCAGCTTCAAGG-CATATCATTTGCAGCATA
* * *
183100 GCTCATGGCAAGAAGG
64 GCTTAAGTCAAGAAGG
183116 GCTAT
1 GCTAT
183121 TTGTCAATAA
Statistics
Matches: 273, Mismatches: 48, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
80 55 0.20
81 84 0.31
83 35 0.13
84 72 0.26
85 27 0.10
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (79 bp):
GCTATCTGCCAAAGACCCCGAGTTCGATTACGCTCAGCTTCAAGGCATATCATTTGCAGCATAGC
TTAAGTCAAGAAGG
Found at i:183820 original size:38 final size:36
Alignment explanation
Indices: 183702--184054 Score: 231
Period size: 37 Copynumber: 9.5 Consensus size: 36
183692 ATATATACAT
* *
183702 ATTTTGAAACTACGTATATAATATATAGTTTTTAATA-
1 ATTTTGAAAATA--TATATAATATATAGTTTTTAAAAC
* * *
183739 GTTTTTAAAAT-TATATAATATATAGTTTTAAAAAAAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTT-----TAAAAC
*
183779 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAATATATATAATATATAGTTTTTAAAA-C
183817 ATTTTGAAAACT-TATATATATATATAGTTTTTGAAAAC
1 ATTTTGAAAA-TATATATA-ATATATAGTTTTT-AAAAC
* *
183855 ATTTTTGAAAACATATAT-AT-TATAGTTTTGAAAAC
1 A-TTTTGAAAATATATATAATATATAGTTTTTAAAAC
* *
183890 ATTTTGAAAACATTTATATATTATATAGTTTTTAAAAC
1 ATTTTG-AAA-ATATATATAATATATAGTTTTTAAAAC
* * * **
183928 GTTTTTGGAAAATTTATATAATCT-TTTTTTTTGAAAAC
1 -ATTTT-GAAAATATATATAATATATAGTTTTT-AAAAC
* * *
183966 ATGTTGAAAA-ATTCATATATTATATAG-TTTAAAAAC
1 ATTTTGAAAATA-T-ATATAATATATAGTTTTTAAAAC
* * *
184002 ATTTTG-AAATTTATATATTATAT-GTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTT-AAAAC
* *
184037 ATTTATGTATATATATAT
1 ATTT-TGAAAATATATAT
184055 TATTTATTAT
Statistics
Matches: 252, Mismatches: 35, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
33 1 0.00
34 37 0.15
35 21 0.08
36 33 0.13
37 53 0.21
38 52 0.21
39 28 0.11
40 5 0.02
41 5 0.02
42 17 0.07
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
Found at i:183896 original size:11 final size:11
Alignment explanation
Indices: 183880--183904 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
183870 TATATTATAG
183880 TTTTGAAAACA
1 TTTTGAAAACA
183891 TTTTGAAAACA
1 TTTTGAAAACA
183902 TTT
1 TTT
183905 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:183908 original size:36 final size:36
Alignment explanation
Indices: 183774--184040 Score: 217
Period size: 38 Copynumber: 7.2 Consensus size: 36
183764 TTTTAAAAAA
* * *
183774 AAAACATTTT-AGAAAATATATATAATATATAATTTTT
1 AAAACATTTTGA-AAAATTTATAT-ATATATAGTTTTG
*
183811 AAAATCATTTTGAAAACTTATATATATATATAGTTTTTG
1 AAAA-CATTTTGAAAAATT-TATATATATATAG-TTTTG
183850 AAAACATTTTTGAAAACA--TATATAT-TATAGTTTTG
1 AAAACA-TTTTGAAAA-ATTTATATATATATAGTTTTG
*
183885 AAAACATTTTGAAAACATTTATATATTATATAGTTTTT
1 AAAACATTTTGAAAA-ATTTATATA-TATATAGTTTTG
* * * * **
183923 AAAACGTTTTTGGAAAATTTATATAATCTTTTTTTTTG
1 AAAAC-ATTTTGAAAAATTTATAT-ATATATAGTTTTG
* * *
183961 AAAACATGTTGAAAAATTCATATATTATATAG-TTTA
1 AAAACATTTTGAAAAATTTATATA-TATATAGTTTTG
183997 AAAACATTTTG--AAATTTATATAT-TATATGTTTTTG
1 AAAACATTTTGAAAAATTTATATATATATA-G-TTTTG
*
184032 AAAATATTT
1 AAAACATTT
184041 ATGTATATAT
Statistics
Matches: 188, Mismatches: 26, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
32 4 0.02
33 2 0.01
34 21 0.11
35 22 0.12
36 25 0.13
37 29 0.15
38 53 0.28
39 32 0.17
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
AAAACATTTTGAAAAATTTATATATATATAGTTTTG
Found at i:183959 original size:111 final size:111
Alignment explanation
Indices: 183773--184040 Score: 288
Period size: 112 Copynumber: 2.4 Consensus size: 111
183763 GTTTTAAAAA
* * *
183773 AAAAACATTTT-AGAAAATATATATAATATATAATTTTTAAAATCATTTTGAAAACTTATATATA
1 AAAAACATTTTGA-AAAATTTATATATTATATAGTTTTTAAAATCATTTTGAAAACTTATATATA
*
183837 TATATAGTTTTTGAAAACATTTTTGAAAACA-T-ATATATTATAGT-TTT
65 TATATAGTTTTTGAAAACA-TGTTGAAAA-ATTCATATATTATA-TATTT
* * *
183884 GAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAA-CGTTTTTGGAAAATTTATATA
1 AAAAACATTTTGAAAA-ATTTATATATTATATAGTTTTTAAAATC-ATTTT-GAAAACTTATATA
* **
183948 -ATCT-TTTTTTTTGAAAACATGTTGAAAAATTCATATATTATATAGTTT
63 TATATATAGTTTTTGAAAACATGTTGAAAAATTCATATATTATATA-TTT
183996 AAAAACATTTTG--AAATTTATATATTATAT-GTTTTTGAAAAT-ATTT
1 AAAAACATTTTGAAAAATTTATATATTATATAGTTTTT-AAAATCATTT
184041 ATGTATATAT
Statistics
Matches: 135, Mismatches: 12, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
108 9 0.07
109 20 0.15
110 12 0.09
111 37 0.27
112 45 0.33
113 12 0.09
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (111 bp):
AAAAACATTTTGAAAAATTTATATATTATATAGTTTTTAAAATCATTTTGAAAACTTATATATAT
ATATAGTTTTTGAAAACATGTTGAAAAATTCATATATTATATATTT
Found at i:184047 original size:24 final size:24
Alignment explanation
Indices: 184003--184048 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
183993 TTTAAAAACA
*
184003 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
184027 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
184049 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:185272 original size:16 final size:18
Alignment explanation
Indices: 185241--185273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
185231 TGATCATAAG
185241 TTTTATCTTTATCTTTTT
1 TTTTATCTTTATCTTTTT
185259 TTTTAT-TTTA-CTTTT
1 TTTTATCTTTATCTTTT
185274 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATCTTTATCTTTTT
Found at i:194106 original size:23 final size:24
Alignment explanation
Indices: 194071--194120 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
194061 TAGGATGCAC
*
194071 TTTTAATAGAT-AATTTATTTTTGT
1 TTTTAATAGATAAATTTA-TCTTGT
*
194095 TTTTTATA-ATAAATTTATCTTGT
1 TTTTAATAGATAAATTTATCTTGT
194118 TTT
1 TTT
194121 AAAGTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTTAATAGATAAATTTATCTTGT
Found at i:194872 original size:3 final size:3
Alignment explanation
Indices: 194864--194897 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
194854 ACTTTAGCCG
*
194864 TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
194898 CCAAGTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:197757 original size:63 final size:64
Alignment explanation
Indices: 197636--197759 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
197626 GTGTGGAGGA
*
197636 ATCCAATTTAAACACTTTCTCTAACTGTATATATATATATTCATATTTTCTTTGCATTGTAGGG
1 ATCCAATTTAAACACTTTCTCTAACTATATATATATATATTCATATTTTCTTTGCATTGTAGGG
** *
197700 ATCCAATTTAAGTACTTTCTCTAACTATATA-ATATATATAT-ATATTTTGTTTGCATTGTA
1 ATCCAATTTAAACACTTTCTCTAACTATATATATATATAT-TCATATTTTCTTTGCATTGTA
197760 ATATTATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
63 26 0.47
64 29 0.53
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (64 bp):
ATCCAATTTAAACACTTTCTCTAACTATATATATATATATTCATATTTTCTTTGCATTGTAGGG
Found at i:198775 original size:18 final size:18
Alignment explanation
Indices: 198749--198783 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
198739 ATCAGCCGTT
198749 GACCATTGATTGTTGACC
1 GACCATTGATTGTTGACC
*
198767 GACCGTTGATTGTTGAC
1 GACCATTGATTGTTGAC
198784 TGTTGACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (18 bp):
GACCATTGATTGTTGACC
Found at i:199804 original size:3 final size:3
Alignment explanation
Indices: 199798--199901 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
199788 TTTTTATCCA
*
199798 TAT TAT TAT TAT TAA 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
** * *
199846 TCC TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
199894 TAT TAT TA
1 TAT TAT TA
199902 AATATATTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:199941 original size:20 final size:19
Alignment explanation
Indices: 199900--199956 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
199890 CTATTATTAT
* *
199900 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
199919 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
199939 TAAATA-A-TAAAAA-AAA
1 TAAATATATTAAAAACAAA
199955 TA
1 TA
199957 TAATTACAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 1 0.03
19 6 0.18
20 16 0.47
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:201302 original size:19 final size:19
Alignment explanation
Indices: 201264--201299 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
201254 AAATTTAGTC
201264 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
201283 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
201300 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:202107 original size:18 final size:18
Alignment explanation
Indices: 202060--202108 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
202050 CTTTTCAAAG
202060 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
202077 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
202094 TGTTTTATTTTATTT
1 T-TTTTATTTTATTT
202109 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:202130 original size:13 final size:15
Alignment explanation
Indices: 202099--202135 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
202089 TTATATGTTT
202099 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
202114 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
202127 TA-TTTATTT
1 TATTTTATTT
202136 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:213150 original size:18 final size:17
Alignment explanation
Indices: 213112--213156 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
213102 CTATTTCAAG
*
213112 TTCAATTTA-TTTGAGA
1 TTCAATTTATTTTGAAA
213128 TTCAATTTATTTTGGAAA
1 TTCAATTTATTTT-GAAA
213146 TTCAATTTATT
1 TTCAATTTATT
213157 CTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:214515 original size:84 final size:84
Alignment explanation
Indices: 213906--214508 Score: 1091
Period size: 84 Copynumber: 7.2 Consensus size: 84
213896 ATATCTTAGT
213906 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
213971 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
213990 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214055 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
214074 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214139 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
* *
214158 CCAATCATTGAATTTGGAAGATGAATTTGCTGAATAGTATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214223 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
* *
214242 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTCGAAGAGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214307 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
* *
214326 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTCGAAGAGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214391 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
214410 CCAATCATTGAATTTGGAAGATAAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
214475 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
214494 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
214509 AAAAGATGAA
Statistics
Matches: 505, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
83 4 0.01
84 496 0.98
85 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:215818 original size:114 final size:113
Alignment explanation
Indices: 215203--215989 Score: 1243
Period size: 113 Copynumber: 7.0 Consensus size: 113
215193 CAAAGATTCA
* * *
215203 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
215268 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
* * * **
215316 AATCCATCATTTGGTGGACCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
215381 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
* * **
215429 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
215494 AGGAAGGAGAAGTTCATAATTAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
**
215542 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
215607 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
* ** *
215655 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTCCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
215720 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-AACCTTTTATATG
* ** *
215769 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTCCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
215834 AGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-AACCTTTTATATG
* *
215883 AATCCATCATTTAATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
215948 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
215990 GGCATAATTC
Statistics
Matches: 643, Mismatches: 30, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
112 5 0.01
113 420 0.65
114 218 0.34
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
Found at i:216315 original size:3 final size:3
Alignment explanation
Indices: 216309--216394 Score: 154
Period size: 3 Copynumber: 28.7 Consensus size: 3
216299 TTTTTATCCA
*
216309 TAT TAT TAT TAT TAA 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
*
216357 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
216395 AATATATTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:216434 original size:20 final size:19
Alignment explanation
Indices: 216393--216437 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
216383 CTATTATTAT
* *
216393 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
216412 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
216432 TAAATA
1 TAAATA
216438 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:217782 original size:18 final size:17
Alignment explanation
Indices: 217761--217794 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
217751 AAATTTAGTC
217761 ATTTATTTTATATGTTTA
1 ATTTATTTTAT-TGTTTA
217779 ATTTATTTTATTGTTT
1 ATTTATTTTATTGTTT
217795 TTAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
ATTTATTTTATTGTTTA
Found at i:218639 original size:2 final size:2
Alignment explanation
Indices: 218634--218663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
218624 CGATTTTTTG
218634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218664 TTATTTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228578 original size:36 final size:36
Alignment explanation
Indices: 228524--228592 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
228514 CTTAAATATA
* * *
228524 TAAATTCCTAATCTTAAATTTAAT-AGGTGAGAATGT
1 TAAATCCCTAACCCTAAATTTAATGA-GTGAGAATGT
228560 TAAATCCCTAACCCTAAATTTAATGAGTGAGAA
1 TAAATCCCTAACCCTAAATTTAATGAGTGAGAA
228593 AATTTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (36 bp):
TAAATCCCTAACCCTAAATTTAATGAGTGAGAATGT
Found at i:237067 original size:13 final size:13
Alignment explanation
Indices: 237049--237108 Score: 57
Period size: 13 Copynumber: 4.3 Consensus size: 13
237039 CGTTGCTACA
237049 TTATATAATATAT
1 TTATATAATATAT
*
237062 TTATATTATAAATTAT
1 TTATA-TA-ATA-TAT
*
237078 ATTATATAATATGT
1 -TTATATAATATAT
*
237092 TCATATAATATAT
1 TTATATAATATAT
237105 TTAT
1 TTAT
237109 TTACATCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
13 19 0.51
14 4 0.11
15 4 0.11
16 5 0.14
17 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (13 bp):
TTATATAATATAT
Found at i:238344 original size:2 final size:2
Alignment explanation
Indices: 238337--238376 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
238327 GTATTATTAA
238337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238377 TATTATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250533 original size:99 final size:101
Alignment explanation
Indices: 250361--250660 Score: 408
Period size: 99 Copynumber: 2.9 Consensus size: 101
250351 GGCTTCCCAG
* * ** *
250361 TTTCAGAGCCAAGTTCAACTTCACAATAAAGGATATTGAACTCAAGACAACACAAGCTCAACTTC
1 TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
* *
250426 ACGACGAAGGGGCGGCTGATTGTCAACAAACAA-C-
66 ACGGCGAAGGGGCGGCTGACTGTCAACAAACAACCA
*
250460 TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTC
1 TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
*
250525 ACGGCGAAGAGGCGGCTGACTGTCAACAAACAATTCCCCAA
66 ACGGCGAAGGGGCGGCTGACTGTCAACAAACAA----CC-A
* * *
250566 ATTCAGA-TCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTT
1 TTTCAGAGT-CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTT
*
250630 CACGGCGAAGGGGCGGTTGACTGTCAACAAA
65 CACGGCGAAGGGGCGGCTGACTGTCAACAAA
250661 TAATTTTCCA
Statistics
Matches: 178, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
99 89 0.50
104 1 0.01
105 1 0.01
106 87 0.49
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (101 bp):
TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
ACGGCGAAGGGGCGGCTGACTGTCAACAAACAACCA
Found at i:250706 original size:106 final size:104
Alignment explanation
Indices: 250357--250695 Score: 454
Period size: 106 Copynumber: 3.3 Consensus size: 104
250347 AAGGGGCTTC
* ** *
250357 CCAGTTTCAGAGCCAAGTTCAACTTCACAATAAAGGATATTGAACTCAAGACAACACAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAA
* *
250422 CTTCACGACGAAGGGGCGGCTGATTGTCAACAAACAA--
66 CTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATT
* *
250459 -C--TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAA
*
250521 CTTCACGGCGAAGAGGCGGCTGACTGTCAACAAACAATT
66 CTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATT
** * * *
250560 CCCCAAATTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTC
1 --CCAGTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTC
* *
250625 AACTTCACGGCGAAGGGGCGGTTGACTGTCAACAAATAATTTT
64 AACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA--TT
*
250668 CCAGTTCCAGAGCCAATTTCAACTTCAC
1 CCAGTTTCAGAGCCAATTTCAACTTCAC
250696 GGCGGAGGAT
Statistics
Matches: 206, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
99 89 0.43
101 1 0.00
104 1 0.00
106 113 0.55
108 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (104 bp):
CCAGTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAA
CTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATT
Found at i:252775 original size:19 final size:20
Alignment explanation
Indices: 252742--252779 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
252732 TTTCTTTTGT
*
252742 TTTTTTGTTTTTTTTATGTA
1 TTTTTTGTTTGTTTTATGTA
252762 TTTTTT-TTTGTTTTATGT
1 TTTTTTGTTTGTTTTATGT
252780 TTTCATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.82
Consensus pattern (20 bp):
TTTTTTGTTTGTTTTATGTA
Found at i:253452 original size:26 final size:27
Alignment explanation
Indices: 253396--253459 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
253386 AGAAACGGAT
* *
253396 TTATAAAATTTTAAAATATAAAATAAC
1 TTATAAAATTTTAAAATAAAAAATAAA
*
253423 TTATAAAATTTT-AAGTAAAAAATAAA
1 TTATAAAATTTTAAAATAAAAAATAAA
253449 TTATAAAATTT
1 TTATAAAATTT
253460 GAAAGGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 22 0.65
27 12 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TTATAAAATTTTAAAATAAAAAATAAA
Found at i:260095 original size:57 final size:57
Alignment explanation
Indices: 260025--260142 Score: 191
Period size: 57 Copynumber: 2.1 Consensus size: 57
260015 AAATTTATCC
*
260025 ATAATATTTTCAGTACATCATTTTAATAGTATATTACAATATATAACATAAATTATA
1 ATAATATTTTCAGTACATCATTTTAATAATATATTACAATATATAACATAAATTATA
** **
260082 ATAATATTTTCAGTACATCATTTTAATAATATATTATGATATATAACATACGTTATA
1 ATAATATTTTCAGTACATCATTTTAATAATATATTACAATATATAACATAAATTATA
260139 ATAA
1 ATAA
260143 GAATTAATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (57 bp):
ATAATATTTTCAGTACATCATTTTAATAATATATTACAATATATAACATAAATTATA
Found at i:260110 original size:25 final size:25
Alignment explanation
Indices: 260025--260113 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 25
260015 AAATTTATCC
260025 ATAATATTTTCAGTACATCATTTTA
1 ATAATATTTTCAGTACATCATTTTA
* * * *
260050 ATAGTATATTACAATATATAACATAAATTATA
1 ATAATAT-TTTCAGTACAT--CAT---TT-TA
260082 ATAATATTTTCAGTACATCATTTTA
1 ATAATATTTTCAGTACATCATTTTA
260107 ATAATAT
1 ATAATAT
260114 ATTATGATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 15 0.31
26 10 0.20
28 3 0.06
29 3 0.06
31 10 0.20
32 8 0.16
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (25 bp):
ATAATATTTTCAGTACATCATTTTA
Found at i:263684 original size:21 final size:22
Alignment explanation
Indices: 263640--263686 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
263630 TAATTTGGGA
*
263640 GCCCGATTACAAAGGCACGCAG
1 GCCCGATTACAAAGGCACACAG
*
263662 GCCCGATTAC-AAGGCACATAG
1 GCCCGATTACAAAGGCACACAG
263683 GCCC
1 GCCC
263687 AATTCAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.11
Consensus pattern (22 bp):
GCCCGATTACAAAGGCACACAG
Found at i:264560 original size:25 final size:25
Alignment explanation
Indices: 264531--264580 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
264521 AGGTTTATTA
264531 TTATATA-TATAATATATAATT-TAAT
1 TTATATAGT-TAATAT-TAATTATAAT
264556 TTATATAGTTAATATTAATTATAAT
1 TTATATAGTTAATATTAATTATAAT
264581 AATAGGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 17 0.74
26 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTATATAGTTAATATTAATTATAAT
Found at i:271621 original size:20 final size:20
Alignment explanation
Indices: 271598--271642 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
271588 GGGTCATTAA
*
271598 TAAATCCTCCAGGTAATTTT
1 TAAATCCTCCAGGTAATTTG
* **
271618 TAAAGCCTTTAGGTAATTTG
1 TAAATCCTCCAGGTAATTTG
271638 TAAAT
1 TAAAT
271643 TCTTTGTGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
TAAATCCTCCAGGTAATTTG
Found at i:272387 original size:12 final size:11
Alignment explanation
Indices: 272348--272389 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
272338 CCGAGTGATG
272348 ATTATTATAAT
1 ATTATTATAAT
*
272359 ATATATAATAAT
1 AT-TATTATAAT
272371 A-TATTATAAAT
1 ATTATTAT-AAT
272382 ATTATTAT
1 ATTATTAT
272390 TTATAAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.19
11 6 0.23
12 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTATTATAAT
Found at i:272489 original size:21 final size:22
Alignment explanation
Indices: 272449--272491 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
272439 TTGGGAGCCC
*
272449 GATTACAAAGGCACGCAGGCCT
1 GATTACAAAGGCACACAGGCCT
*
272471 GATTAC-AAGGCACATAGGCCT
1 GATTACAAAGGCACACAGGCCT
272492 AATTCAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (22 bp):
GATTACAAAGGCACACAGGCCT
Found at i:274883 original size:42 final size:42
Alignment explanation
Indices: 274812--274955 Score: 225
Period size: 42 Copynumber: 3.4 Consensus size: 42
274802 TCCCACACTT
*
274812 TAGGATTATTAACCGAATCATTAGGTGAATCATTGGAATTTCCAA
1 TAGGATTATT-A--GAAGCATTAGGTGAATCATTGGAATTTCCAA
* *
274857 TAGGATTATTAGAAGTATTAGGTGAATCATTGAAATTTCCAA
1 TAGGATTATTAGAAGCATTAGGTGAATCATTGGAATTTCCAA
274899 TAGGATTATTAGAAGCATTAGGTGAATCATTGGAATTTCCAA
1 TAGGATTATTAGAAGCATTAGGTGAATCATTGGAATTTCCAA
*
274941 TCGGATTATTAGAAG
1 TAGGATTATTAGAAG
274956 GTTTAACCAG
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 82 0.88
44 1 0.01
45 10 0.11
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (42 bp):
TAGGATTATTAGAAGCATTAGGTGAATCATTGGAATTTCCAA
Found at i:276456 original size:65 final size:65
Alignment explanation
Indices: 276382--276538 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
276372 ACACCCTATT
* *
276382 TCGAATGCATTTTGTGTACCGATGTACAAACCATGCATCGATGCACTCATGA-TTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCATGACTCTT-TTGAAAC
276446 A
65 A
* ** * *
276447 TCGAATGCATTTTATGTATTGATGCACAAGCCATGCATCGATGCACTCCTGACTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCATGACTCTTTTGAAACA
* * * *
276512 TTGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
276539 CCCAAGTGTA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 74 0.96
66 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCATGACTCTTTTGAAACA
Found at i:276548 original size:19 final size:19
Alignment explanation
Indices: 276524--276595 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
276514 GAATGTAATT
276524 AGTGTACCGATGCACCCCA
1 AGTGTACCGATGCACCCCA
276543 AGTGTACCGATGCACCCCA
1 AGTGTACCGATGCACCCCA
276562 AGTGTACCGATGCACCCCA
1 AGTGTACCGATGCACCCCA
276581 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
276596 TAGGTCTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (19 bp):
AGTGTACCGATGCACCCCA
Found at i:278853 original size:2 final size:2
Alignment explanation
Indices: 278846--278886 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
278836 AAATCAAATG
*
278846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
278887 AGGAAAGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:280286 original size:20 final size:20
Alignment explanation
Indices: 280242--280461 Score: 166
Period size: 20 Copynumber: 10.8 Consensus size: 20
280232 AATGACCAAC
*
280242 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
280261 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
280281 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
280301 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
280321 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
280342 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
280363 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
280384 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
280405 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
280427 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
280445 AAAATCGCAATGCGATT
1 AAAATCGCAACGCGATT
280462 CTTGGGTAAA
Statistics
Matches: 162, Mismatches: 24, Indels: 29
0.75 0.11 0.13
Matches are distributed among these distances:
18 4 0.02
19 15 0.09
20 99 0.61
21 14 0.09
22 30 0.19
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:280369 original size:42 final size:42
Alignment explanation
Indices: 280318--280460 Score: 227
Period size: 42 Copynumber: 3.5 Consensus size: 42
280308 CAACGGTCAA
*
280318 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
280360 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
280402 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
280442 AAGAAAATCGCAATGCGAT
1 AAGAAAATCGCAACGCGAT
280461 TCTTGGGTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 37 0.41
42 54 0.59
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:280435 original size:40 final size:40
Alignment explanation
Indices: 280242--280462 Score: 218
Period size: 40 Copynumber: 5.5 Consensus size: 40
280232 AATGACCAAC
* * *
280242 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAG
* **** *
280281 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
*
280321 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* *
280363 AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
280405 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
280445 AAAATCGCAATGCGATTC
1 AAAATCGCAACGCGATTC
280463 TTGGGTAAAT
Statistics
Matches: 153, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
38 1 0.01
39 16 0.10
40 67 0.44
41 5 0.03
42 62 0.41
43 1 0.01
44 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:280571 original size:6 final size:6
Alignment explanation
Indices: 280560--280644 Score: 170
Period size: 6 Copynumber: 14.2 Consensus size: 6
280550 GACACGTATT
280560 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
280608 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
280645 GACGAGACGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:281133 original size:6 final size:6
Alignment explanation
Indices: 281124--281208 Score: 170
Period size: 6 Copynumber: 14.2 Consensus size: 6
281114 CGCCGCCGTC
281124 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
281172 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
281209 AATACGTGTC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:281327 original size:20 final size:20
Alignment explanation
Indices: 281304--281656 Score: 340
Period size: 20 Copynumber: 17.6 Consensus size: 20
281294 TTCTTCGACA
*
281304 CGTTGTGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
281324 CGTTGCGA--TTCTTGGAATCG
1 CGTTGCGATTTTCTT--AATCG
281344 CGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
281364 CGTTGCGA--TTCTTGGAATCG
1 CGTTGCGATTTTCTT--AATCG
*
281384 TGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
*
281404 CATTGCGA--TTCTTGGAATCG
1 CGTTGCGATTTTCTT--AATCG
281424 CGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
*
281444 CATTGCGA--TTCTTGGAATCG
1 CGTTGCGATTTTCTT--AATCG
281464 CGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
*
281484 CGTTGCGATTTTCTGAATCG
1 CGTTGCGATTTTCTTAATCG
281504 CGTTGCGA--TTCTTGGAATCG
1 CGTTGCGATTTTCTT--AATCG
281524 CGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
***
281544 CGTTGCGATTCTTGGAAGATCG
1 CGTTGCGATT-TTCTTA-ATCG
*
281566 CGTTGCGATTTTCTT--TTG
1 CGTTGCGATTTTCTTAATCG
* *
281584 ACCGTTGCGATTTTCTT-TTCAA
1 --CGTTGCGATTTTCTTAATC-G
*
281606 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTTAATCG
*
281626 CGTTGCGA-TTT-TTATTTCG
1 CGTTGCGATTTTCTTA-ATCG
281645 CGTTGCGATTTT
1 CGTTGCGATTTT
281657 GTTGGTCATT
Statistics
Matches: 281, Mismatches: 23, Indels: 58
0.78 0.06 0.16
Matches are distributed among these distances:
18 28 0.10
19 14 0.05
20 192 0.68
21 8 0.03
22 39 0.14
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTCTTAATCG
Found at i:281348 original size:40 final size:40
Alignment explanation
Indices: 281304--281654 Score: 375
Period size: 40 Copynumber: 8.8 Consensus size: 40
281294 TTCTTCGACA
*
281304 CGTTGTGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
281344 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
* *
281384 TGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
*
281424 CGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
*
281464 CGTTGCGATTTTCTTAATCGCGTTGCGATT-TTCTGAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTT-GGAATCG
281504 CGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTT--AATCG
1 CGTTGCGATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCG
*** *
281544 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTTTG-A-C-
1 CGTTGCGATT-TTCTTA-ATCGCGTTGCGA--TTC-TTGGAATCG
* * **
281586 CGTTGCGATTTTCTT-TTCAACGTTGCGATT-TTCTAAATCG
1 CGTTGCGATTTTCTTAATC-GCGTTGCGATTCTT-GGAATCG
*
281626 CGTTGCGA-TTT-TTATTTCGCGTTGCGATT
1 CGTTGCGATTTTCTTA-ATCGCGTTGCGATT
281655 TTGTTGGTCA
Statistics
Matches: 275, Mismatches: 16, Indels: 41
0.83 0.05 0.12
Matches are distributed among these distances:
36 2 0.01
37 1 0.00
38 10 0.04
39 18 0.07
40 204 0.74
41 3 0.01
42 29 0.11
43 7 0.03
44 1 0.00
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (40 bp):
CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCG
Found at i:281368 original size:60 final size:60
Alignment explanation
Indices: 281304--281656 Score: 379
Period size: 60 Copynumber: 5.9 Consensus size: 60
281294 TTCTTCGACA
*
281304 CGTTGTGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
* *
281364 CGTTGCGA--TTCTTGGAATCGTGTTGCGATTTTCTT--AATCGCATTGCGA--TTCTTGGAATC
1 CGTTGCGATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTT--AATC
281423 G
60 G
*
281424 CGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
*
281484 CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
*** * *
281544 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTTTG-A-C-CGTTGCGATTTTCTT-TTCA
1 CGTTGCGATT-TTCTTA-ATCGCGTTGCGA--TTC-TTGGAATCGCGTTGCGATTTTCTTAATC-
*
281605 A
60 G
* * *
281606 CGTTGCGATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCGATTTT
281657 GTTGGTCATT
Statistics
Matches: 253, Mismatches: 18, Indels: 45
0.80 0.06 0.14
Matches are distributed among these distances:
56 2 0.01
58 18 0.07
59 12 0.05
60 152 0.60
61 9 0.04
62 52 0.21
63 1 0.00
64 4 0.02
65 3 0.01
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (60 bp):
CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCG
Found at i:292001 original size:13 final size:12
Alignment explanation
Indices: 291942--292008 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
291932 ATCGATAGAT
291942 TTTATTTTTTTA
1 TTTATTTTTTTA
* *
291954 -TTATATTTGTA
1 TTTATTTTTTTA
* *
291965 TTTAGTTGTTTA
1 TTTATTTTTTTA
*
291977 TTGGACTTTTTTTA
1 TT-TA-TTTTTTTA
291991 TTGTATTTTTTTA
1 TT-TATTTTTTTA
292004 TTTAT
1 TTTAT
292009 CATTTAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
11 9 0.21
12 12 0.29
13 11 0.26
14 10 0.24
ACGTcount: A:0.18, C:0.01, G:0.09, T:0.72
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:292076 original size:21 final size:22
Alignment explanation
Indices: 292052--292105 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
292042 TTAAAATTTG
*
292052 TTTTGTTTATTT-TTTTGGAT-T
1 TTTTGTTTATTTATTTT-GATAA
*
292073 TTTTGTTAATTTATTTTGATAA
1 TTTTGTTTATTTATTTTGATAA
292095 TTTTGTTTATT
1 TTTTGTTTATT
292106 ACCATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTGTTTATTTATTTTGATAA
Found at i:292084 original size:34 final size:34
Alignment explanation
Indices: 292023--292101 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
292013 TAATAATTAC
*
292023 TTTATTTTGTTGGATTTTTTTAAAATTTGTTTTG
1 TTTATTTTGTTGGATTTTTTTAAAATTTATTTTG
* *
292057 TTTATTTTTTTGGATTTTTTGT-TAATTTATTTTG
1 TTTATTTTGTTGGATTTTTT-TAAAATTTATTTTG
* *
292091 ATAATTTTGTT
1 TTTATTTTGTT
292102 TATTACCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 37 0.97
35 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.70
Consensus pattern (34 bp):
TTTATTTTGTTGGATTTTTTTAAAATTTATTTTG
Found at i:316479 original size:125 final size:125
Alignment explanation
Indices: 316257--316631 Score: 705
Period size: 125 Copynumber: 3.0 Consensus size: 125
316247 AAATTTTTAA
*
316257 ATAGATGATCATCAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
1 ATAGATGATCATTAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
* *
316322 TAATAGTGAACTACAATATCACAGTCTCATTAAAGCATTAAAAAGTTTTACGTACGATAT
66 TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGATAT
316382 ATAGATGATCATTAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
1 ATAGATGATCATTAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
*
316447 TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGACAT
66 TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGATAT
*
316507 ATAGATGATCATTAATAACATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
1 ATAGATGATCATTAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
316572 TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGATAT
66 TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGATAT
316632 TTTATCTAAA
Statistics
Matches: 244, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 244 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (125 bp):
ATAGATGATCATTAATAATATGACTATATACTTAATTCAATGTGATTATTTAAAAATACATAAAT
TAATAGTGAACTACAATATCACAATCTCATTAAAGCATTAAAAAGTTTTACGTATGATAT
Found at i:320664 original size:36 final size:36
Alignment explanation
Indices: 320624--320696 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
320614 TGTCTAAATC
* *
320624 TAATCTTAAATATGGTCCATTACATCTAATTATCAT
1 TAATCTCAAATATGATCCATTACATCTAATTATCAT
* **
320660 TAATCTCAAATATGATCCCTTTTATCTAATTATCAT
1 TAATCTCAAATATGATCCATTACATCTAATTATCAT
320696 T
1 T
320697 TCCAAGGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (36 bp):
TAATCTCAAATATGATCCATTACATCTAATTATCAT
Found at i:326946 original size:36 final size:36
Alignment explanation
Indices: 326863--326976 Score: 169
Period size: 35 Copynumber: 3.2 Consensus size: 36
326853 CAACTTTAAA
*
326863 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTG
326899 -AAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTG
* * *
326934 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAATGGTTTTT-AAAGTTTGGTAAATGTTTCTTTG
326970 AAAAATG
1 AAAAATG
326977 ATAATGGGAT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 34 0.48
36 20 0.28
37 17 0.24
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (36 bp):
AAAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTG
Found at i:331425 original size:36 final size:35
Alignment explanation
Indices: 331317--331423 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 35
331307 CAACTTTGAA
331317 AAAATAG-TTTCAAAG-TTGGTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
331350 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
331385 AAAATAGTTTTTCAAAGTTTGGTAAATGTTT-GTTG
1 AAAATAG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
331420 AAAA
1 AAAA
331424 ATGATAATGG
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
33 6 0.09
34 8 0.12
35 31 0.46
36 23 0.34
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.43
Consensus pattern (35 bp):
AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:333682 original size:224 final size:227
Alignment explanation
Indices: 333274--333726 Score: 885
Period size: 224 Copynumber: 2.0 Consensus size: 227
333264 ATCCTGGTTT
333274 ATATTCCTGCATGATAAAAATATTAAATAGTTATTTTTTATTTATTTATAACTGTTAATTTTCTT
1 ATATTCCTGCATGATAAAAATATTAAATAGTTATTTTTTATTTATTTATAACTGTTAATTTTCTT
333339 ATTTCAATGTTAGAATAAAGATTAAATAAACCTCTAGGAAAGTTTTTGGATTAAAAAATCAAAGC
66 ATTTCAATGTTAGAATAAAGATTAAATAAACCTCTAGGAAAGTTTTTGGATTAAAAAATCAAAGC
333404 AATTATTATTTTTTTTAAAAACCTTAGCAGACAATTCCAGGAATCTGAGAAATTGATATTTAAAT
131 AATTATTATTTTTTTTAAAAACCTTAGCAGACAATTCCAGGAATCTGAGAAATTGATATTTAAAT
333469 GAAGTAATGCAGCCATAATCGGAAATAATTAA
196 GAAGTAATGCAGCCATAATCGGAAATAATTAA
333501 ATATTCCTGCATGAT-AAAATATTAAATAGTTATTTTTTATTTATTTATAACTGTTAATTTTCTT
1 ATATTCCTGCATGATAAAAATATTAAATAGTTATTTTTTATTTATTTATAACTGTTAATTTTCTT
333565 ATTTCAATGTTAGAATAAAGATT-AATAAACCTCTAGGAAAG-TTTTGGATTAAAAAATCAAAGC
66 ATTTCAATGTTAGAATAAAGATTAAATAAACCTCTAGGAAAGTTTTTGGATTAAAAAATCAAAGC
333628 AATTATTATTTTTTTTAAAAACCTTAGCAGACAATTCCAGGAATCTGAGAAATTGATATTTAAAT
131 AATTATTATTTTTTTTAAAAACCTTAGCAGACAATTCCAGGAATCTGAGAAATTGATATTTAAAT
333693 GAAGTAATGCAGCCATAATCGGAAATAATTAA
196 GAAGTAATGCAGCCATAATCGGAAATAATTAA
333725 AT
1 AT
333727 TATATTTTAG
Statistics
Matches: 226, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
224 121 0.54
225 18 0.08
226 72 0.32
227 15 0.07
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (227 bp):
ATATTCCTGCATGATAAAAATATTAAATAGTTATTTTTTATTTATTTATAACTGTTAATTTTCTT
ATTTCAATGTTAGAATAAAGATTAAATAAACCTCTAGGAAAGTTTTTGGATTAAAAAATCAAAGC
AATTATTATTTTTTTTAAAAACCTTAGCAGACAATTCCAGGAATCTGAGAAATTGATATTTAAAT
GAAGTAATGCAGCCATAATCGGAAATAATTAA
Found at i:338963 original size:198 final size:198
Alignment explanation
Indices: 338569--339163 Score: 842
Period size: 198 Copynumber: 3.0 Consensus size: 198
338559 ATAAAATCAG
* *
338569 TATATTTATACCG-GTAACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
1 TATATTTCTACCGAGT-ACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTT
* *
338633 TGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
65 TGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATT-GGCATTCATTC
* * * *
338696 AGGGAAAAAAGTATCAACACAAACTTAAAACGTGTCGATACATTATGTAAACCTATTTTCTCATA
128 -TGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATA
338761 AAACCGA
192 AAACCGA
* * * *
338768 TATATTTCTATCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTGGAT-TTTTT
1 TATATTTCTACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTT
* * *
338832 GGGATAGATACTTTTAATAAATGTATCGACACTTTATGTGTGTACCTCATTGGACATTCATTCTG
66 GGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTGG-CATTCATTCTG
338897 GAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA
130 GAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA
338962 CCGA
195 CCGA
* *
338966 TATATTTCTACCGAGTACATTGTAAATTTACCTACTACATTATAATTATCGGTTTCGATATTTTT
1 TATATTTCTACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTT
* * *
339031 GGGATCGA-ACTTTTAATAAGTGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTTTG
66 GGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTC-ATTGGCATTCATTCTG
* *** * *
339095 GACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTAGACCTATTCTCTCATAA
130 GA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAGACCTATTTTCTCATAA
339159 AACCG
193 AACCG
339164 GTGTAACACC
Statistics
Matches: 357, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
197 3 0.01
198 190 0.53
199 162 0.45
200 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
TATATTTCTACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTT
GGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGCATTCATTCTGG
AAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
CGA
Found at i:339958 original size:18 final size:18
Alignment explanation
Indices: 339935--339991 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
339925 GGTCACAACA
339935 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
339953 CGACCCGACCCGTTTACC
1 CGACCCGACCCGTTGACC
339971 CGACCCGTTA-CCGTTGACC
1 CGACCCG--ACCCGTTGACC
339990 CG
1 CG
339992 TTGACCGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 24 0.69
19 10 0.29
20 1 0.03
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:339971 original size:13 final size:13
Alignment explanation
Indices: 339955--339979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339945 CGTTGACCCG
339955 ACCCGACCCGTTT
1 ACCCGACCCGTTT
339968 ACCCGACCCGTT
1 ACCCGACCCGTT
339980 ACCGTTGACC
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:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:339991 original size:14 final size:15
Alignment explanation
Indices: 339972--340012 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
339962 CCGTTTACCC
339972 GACCCGTT-ACCGTT
1 GACCCGTTGACCGTT
339986 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
340001 GA-CCGTTGACCG
1 GACCCGTTGACCG
340013 GAGTTGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:340001 original size:7 final size:7
Alignment explanation
Indices: 339975--340012 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
339965 TTTACCCGAC
339975 CCGTT-A
1 CCGTTGA
339981 CCGTTGA
1 CCGTTGA
339988 CCCGTTGA
1 -CCGTTGA
339996 CCGTTGA
1 CCGTTGA
340003 CCGTTGA
1 CCGTTGA
340010 CCG
1 CCG
340013 GAGTTGACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:341332 original size:18 final size:18
Alignment explanation
Indices: 341306--341341 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
341296 TTCGAAGGAC
*
341306 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
341324 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
341342 CAGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:342401 original size:24 final size:24
Alignment explanation
Indices: 342374--342468 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
342364 ATTTCCAACT
** *
342374 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
342398 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
342422 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
342446 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
342469 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:342412 original size:12 final size:12
Alignment explanation
Indices: 342397--342466 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
342387 GATAAATGAC
342397 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
342409 CTGATTTCTGAT
1 CTGAATTCTGTT
*
342421 CTGGATTCTGTT
1 CTGAATTCTGTT
342433 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
342445 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
342457 TTGATTTCTG
1 CTGAATTCTG
342467 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:342412 original size:48 final size:48
Alignment explanation
Indices: 342360--342464 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
342350 TAATATTTTA
342360 TCTGATTTCCAA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCCAATC-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
** * ** **
342408 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCAATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
342456 TTTGATTTC
1 TCTGATTTC
342465 TGATATCTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 47 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCAATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:342465 original size:48 final size:48
Alignment explanation
Indices: 342377--342468 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
342367 TCCAACTTGA
342377 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
** ** *
342425 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGAT
342469 ATCTTCGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:344587 original size:18 final size:18
Alignment explanation
Indices: 344564--344602 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
344554 ACTGGTCACA
*
344564 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
344582 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
344600 ACC
1 ACC
344603 GTTGACCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.51, G:0.18, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:344615 original size:15 final size:15
Alignment explanation
Indices: 344591--344624 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
344581 GACCCGACCC
344591 GACCCATTGACCGTT
1 GACCCATTGACCGTT
*
344606 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
344621 GACC
1 GACC
344625 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:346736 original size:106 final size:105
Alignment explanation
Indices: 346491--346700 Score: 345
Period size: 106 Copynumber: 2.0 Consensus size: 105
346481 ATGGATTTTT
* *
346491 AACCAC-AATCAAGTACGTCAGCATTTCATGGTATAGTTGAAACATGGAAATAAAATAAAGACCA
1 AACCACAAATCAAGTACGTAAGAATTT-ATGGTATAGTTGAAACATGGAAATAAAATAAAGACCA
346555 TTAGAATATTTGTTTGTCTCCTTAAGATCTATTCAGTGATG
65 TTAGAATATTTGTTTGTCTCCTTAAGATCTATTCAGTGATG
* *
346596 AACCACAAATCAAGTACGTCAGCATTTCATGGTATAGTTGAAACATGGAAATAAAAT-AA-ACCA
1 AACCACAAATCAAGTACGTAAGAATTT-ATGGTATAGTTGAAACATGGAAATAAAATAAAGACCA
346659 TTAGAATATTTGTTTGTCTCCTTAAGATCTATTCAGTGATG
65 TTAGAATATTTGTTTGTCTCCTTAAGATCTATTCAGTGATG
346700 A
1 A
346701 CTCAGATGAT
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
104 46 0.44
105 8 0.08
106 50 0.48
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (105 bp):
AACCACAAATCAAGTACGTAAGAATTTATGGTATAGTTGAAACATGGAAATAAAATAAAGACCAT
TAGAATATTTGTTTGTCTCCTTAAGATCTATTCAGTGATG
Found at i:347141 original size:12 final size:12
Alignment explanation
Indices: 347126--347194 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
347116 GATAAATGAC
347126 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
347138 CTG-ATTTTGAT
1 CTGAATTCTGTT
*
347149 CTGGATTCTGTT
1 CTGAATTCTGTT
347161 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
347173 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
347185 TTGATTTCTG
1 CTGAATTCTG
347195 ATATCTTCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
11 11 0.23
12 35 0.73
13 2 0.04
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:347160 original size:47 final size:48
Alignment explanation
Indices: 347106--347196 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
347096 TCCAACTTGA
347106 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTT-TGATCTGG
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
** ** *
347153 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGAT
347197 ATCTTCGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 34 0.89
48 4 0.11
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:347194 original size:24 final size:24
Alignment explanation
Indices: 347103--347196 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
347093 ATTTCCAACT
*** *
347103 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATTTCTGATC
347127 TGAATTCTGTTCTGATTT-TGATC
1 TGAATTCTGTTCTGATTTCTGATC
* * *
347150 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATC
*
347174 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
347197 ATCTTCGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.34
24 39 0.66
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:349216 original size:15 final size:15
Alignment explanation
Indices: 349198--349231 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
349188 GACCCGACCC
*
349198 GACCCGTTTACCGTT
1 GACCCGTTGACCGTT
349213 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
349228 GACC
1 GACC
349232 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:350546 original size:18 final size:18
Alignment explanation
Indices: 350520--350555 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
350510 TCGAAAGGAC
*
350520 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
350538 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
350556 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:351725 original size:24 final size:24
Alignment explanation
Indices: 351698--351792 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
351688 ATTTCCGACT
** *
351698 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
351722 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
351746 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
351770 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
351793 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:351736 original size:12 final size:12
Alignment explanation
Indices: 351721--351790 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
351711 GATAAATGAC
351721 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
351733 CTGATTTCTGAT
1 CTGAATTCTGTT
*
351745 CTGGATTCTGTT
1 CTGAATTCTGTT
351757 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
351769 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
351781 TTGATTTCTG
1 CTGAATTCTG
351791 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:351789 original size:48 final size:48
Alignment explanation
Indices: 351684--351792 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
351674 AAATATTTTA
* *
351684 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATAAATGACCTGAATTCTGT
** **
351732 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
*
351780 TTTGATTTCTGAT
1 TCTGATTTCTGAT
351793 ATCTTCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:352938 original size:2 final size:2
Alignment explanation
Indices: 352933--352965 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
352923 ATATTGTAAT
352933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
352966 TTTATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353354 original size:20 final size:20
Alignment explanation
Indices: 353329--353375 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
353319 TGTATATAAG
353329 TTACATTGTAAATTTACCTA
1 TTACATTGTAAATTTACCTA
353349 TTACATTGTAAATTTACCTA
1 TTACATTGTAAATTTACCTA
353369 TTACATT
1 TTACATT
353376 ATAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (20 bp):
TTACATTGTAAATTTACCTA
Found at i:353524 original size:31 final size:31
Alignment explanation
Indices: 353487--353579 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 31
353477 TAAAAAATAA
353487 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TTATAATAATTTTATTATTAAT
* * *
353518 AAAATATAACTATCATAATTTT-TTATTTAT
1 AAAATATAATTATAATAATTTTATTATTAAT
* * *
353548 AAAATTATAGTTATAAT-ATTTTAATAATAAT
1 AAAA-TATAATTATAATAATTTTATTATTAAT
353579 A
1 A
353580 TTTACATAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.04
30 24 0.48
31 24 0.48
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
AAAATATAATTATAATAATTTTATTATTAAT
Found at i:353536 original size:33 final size:28
Alignment explanation
Indices: 353487--353570 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 28
353477 TAAAAAATAA
*
353487 AAAATATAATTTATAATAATTTTATTTTAAT
1 AAAATATAATTCATAAT-ATTTTA-TTT-AT
*
353518 AAAATATAACTATCATAATTTTTTATTTAT
1 AAAATATAA-T-TCATAATATTTTATTTAT
*
353548 AAAATTATAGTT-ATAATATTTTA
1 AAAA-TATAATTCATAATATTTTA
353571 ATAATAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 10 0.22
29 1 0.02
30 7 0.15
31 16 0.35
32 6 0.13
33 6 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (28 bp):
AAAATATAATTCATAATATTTTATTTAT
Found at i:353602 original size:14 final size:15
Alignment explanation
Indices: 353560--353604 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
353550 AATTATAGTT
*
353560 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
353574 ATAATATTTACATAA
1 ATAATATTTAAATAA
353589 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
353603 AT
1 AT
353605 TATTCTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:353664 original size:24 final size:24
Alignment explanation
Indices: 353613--353664 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
353603 ATTATTCTAA
353613 TATT-TTAAAAATAATATTATTAT
1 TATTGTTAAAAATAATATTATTAT
*
353636 T-TTGTTAATAAATAATATTGTT-T
1 TATTGTTAA-AAATAATATTATTAT
353659 TATTGT
1 TATTGT
353665 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTGTTAAAAATAATATTATTAT
Found at i:353946 original size:21 final size:23
Alignment explanation
Indices: 353919--353968 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
353909 ACCTATTTTA
*
353919 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
353942 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
353965 TTAT
1 TTAT
353969 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:354049 original size:87 final size:87
Alignment explanation
Indices: 353903--354220 Score: 546
Period size: 87 Copynumber: 3.7 Consensus size: 87
353893 ACAAATTAAA
* *
353903 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTA
353968 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
* * * *
353990 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTGTATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTA
*
354055 TTGTGCTTGATAATGTTTTCAG
66 TTGTGCTTGATAATGTTTCCAG
*
354077 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTA
354142 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
* *
354164 TAATTAACCTATTTTATTATATAAGCGCTACAAATTACATTATATAAGTGCTACCTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGCTACCTA
354221 TTACATCATA
Statistics
Matches: 219, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 219 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGCTTGATAATGTTTCCAG
Found at i:354142 original size:23 final size:23
Alignment explanation
Indices: 354092--354136 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
354082 AACCTATTTT
*
354092 ATTATATAAGCGCTACATATTAC
1 ATTATATAAGCGCTACATAATAC
* *
354115 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACATAATA
354137 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACATAATAC
Found at i:354209 original size:23 final size:23
Alignment explanation
Indices: 354179--354231 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
354169 AACCTATTTT
354179 ATTATATAAGCGCTACAAATTAC
1 ATTATATAAGCGCTACAAATTAC
* **
354202 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACAAATTAC
*
354225 ATCATAT
1 ATTATAT
354232 TTTTACCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACAAATTAC
Found at i:358870 original size:23 final size:22
Alignment explanation
Indices: 358825--358884 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 22
358815 AAATACTTTA
358825 AAAATAATTATTTTTTGAAATATT
1 AAAAT-ATT-TTTTTTGAAATATT
358849 AAAATGATTTTTATTT-AAATATT
1 AAAAT-ATTTTT-TTTGAAATATT
358872 AGAAATATTTTTT
1 A-AAATATTTTTT
358885 AACATTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 17 0.52
24 15 0.45
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
AAAATATTTTTTTTGAAATATT
Found at i:362378 original size:51 final size:50
Alignment explanation
Indices: 362322--362442 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 50
362312 GTAAAGCGTG
* * * ** *
362322 CCCCTGCATCGCGTTATATGATGATTTGGCGCCACGTGGGGTATAGTGCGC
1 CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGT-GGGTATAGCGCGC
* * * *
362373 CCCCTGTACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTATAGCGTGG
1 CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGC
*
362423 CCCCTGCAGCGCGCTATACG
1 CCCCTGCACCGCGCTATACG
362443 TCACGTAGGG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 28 0.48
51 30 0.52
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (50 bp):
CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGC
Found at i:362436 original size:50 final size:51
Alignment explanation
Indices: 362316--362442 Score: 141
Period size: 50 Copynumber: 2.5 Consensus size: 51
362306 TTAGTAGTAA
* * * **
362316 AGCGT-GCCCCTGCATCGCGTTATATGATGATTTGGCGCCACGTGGGGTAT
1 AGCGTGGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* * * * *
362366 AGTGCGCCCCCTGTACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGTGGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
*
362416 AGCGTGGCCCCTGCAGCGCGCTATACG
1 AGCGTGGCCCCTGCACCGCGCTATACG
362443 TCACGTAGGG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
50 31 0.51
51 30 0.49
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (51 bp):
AGCGTGGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:369050 original size:23 final size:26
Alignment explanation
Indices: 369013--369081 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
369003 TTCTCTTGTG
369013 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
369037 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
369062 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
369082 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:369063 original size:12 final size:12
Alignment explanation
Indices: 369046--369081 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
369036 TATCATGTTC
369046 TCATATCACATG
1 TCATATCACATG
*
369058 TCATATCACATA
1 TCATATCACATG
369070 TCATATCACATG
1 TCATATCACATG
369082 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:369477 original size:64 final size:63
Alignment explanation
Indices: 369389--369609 Score: 169
Period size: 64 Copynumber: 3.4 Consensus size: 63
369379 TAATGAAGGT
* * * * * * **
369389 ATGCATCGATACACTACTGATGCATCGGTGTATAAAAGGTATTCGATGTATT-ATTATTGTTGGG
1 ATGCATCGATGCACTCCT-ATGCATCGATGCACAAAAGGCATTCGATGT-TTCATTATTAATGGG
* **
369453 ATGCATCGATGCACTCCCTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACT-CCTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGG
* ** ** * * **
369517 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCAATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACT-CCTATGCATCGATGCACAAAAGGCATTCGATG-TTTCATTATTAATGGG
*
369580 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACT-CCTATGCATCGAT
369610 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 4 0.03
64 120 0.91
65 8 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGG
Found at i:379064 original size:2 final size:2
Alignment explanation
Indices: 379057--379083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
379047 TCGCTCTATT
379057 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
379084 TTCAATCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:380820 original size:20 final size:20
Alignment explanation
Indices: 380782--380821 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
380772 CATTCAAGAT
*
380782 GGTATCGATACATTTCTTAA
1 GGTATCGATACATTCCTTAA
* *
380802 GGTATCGGTACCTTCCTTAA
1 GGTATCGATACATTCCTTAA
380822 TTTTACTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (20 bp):
GGTATCGATACATTCCTTAA
Found at i:382896 original size:3 final size:3
Alignment explanation
Indices: 382888--382953 Score: 80
Period size: 3 Copynumber: 22.3 Consensus size: 3
382878 TTTATATTTA
* * * *
382888 TAT TAT TAT TAT AAT TAT AAT TAT TAT AAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
382936 TAT TAT TAA TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
382954 TAATATTACA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:382897 original size:12 final size:12
Alignment explanation
Indices: 382874--382961 Score: 52
Period size: 12 Copynumber: 7.8 Consensus size: 12
382864 TCATTTTTAT
382874 TTTAT-TTA-TA
1 TTTATATTATTA
382884 TTTATATTATTA
1 TTTATATTATTA
382896 -TTATA--ATTA
1 TTTATATTATTA
382905 --TA-ATTATTA
1 TTTATATTATTA
382914 TAATTATAATTATTA
1 T--TTAT-ATTATTA
382929 -TTATTATTATTA
1 TTTA-TATTATTA
*
382941 TTAATA-TATTA
1 TTTATATTATTA
382952 TTTAATATTA
1 TTT-ATATTA
382962 CAAGCCCAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
7 1 0.02
8 2 0.03
9 8 0.13
10 5 0.08
11 15 0.24
12 17 0.27
13 7 0.11
15 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:383440 original size:15 final size:15
Alignment explanation
Indices: 383430--383461 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
383420 AAAGAAACAT
383430 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
383445 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
383460 AA
1 AA
383462 CTTACTGTCA
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:384512 original size:109 final size:107
Alignment explanation
Indices: 384327--384550 Score: 249
Period size: 109 Copynumber: 2.1 Consensus size: 107
384317 ATATATATAT
* * *
384327 AATAATTAATAATTAATTTTTTTTAAAATAAATTATTTTAATATTTATTTTCAATATCGAAGAAA
1 AATATTTAATAATTAA-TTTTTTTAAAATAAATTAATTTAATATTTATTTTCAATATCAAAGAAA
* * * *
384392 AGGACAGTCTTAATACAACTGGATGTCCTATTCTGGTATTTTA
65 AGGACAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTA
*
384435 AA-ATTTAATAATTAA-TTTTTTAAAATATTATTTAATTTAA-ATTAATATTTATCAATATCAAA
1 AATATTTAATAATTAATTTTTTTAAAATA--AATTAATTTAATATT--TATTT-TCAATATCAAA
* * * *
384497 GAAAA-GAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTTA
61 GAAAAGGA-CAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTA
384544 AATATTT
1 AATATTT
384551 TTTATAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
105 12 0.12
106 3 0.03
107 21 0.22
108 9 0.09
109 48 0.49
110 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (107 bp):
AATATTTAATAATTAATTTTTTTAAAATAAATTAATTTAATATTTATTTTCAATATCAAAGAAAA
GGACAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTA
Found at i:395684 original size:11 final size:11
Alignment explanation
Indices: 395665--395725 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 11
395655 ATTATGCTTG
*
395665 AAGAAAAAAAA
1 AAGAGAAAAAA
395676 AAGAGAAAAAA
1 AAGAGAAAAAA
*
395687 AACAG--AAAA
1 AAGAGAAAAAA
*
395696 AA-TG-AAAAA
1 AAGAGAAAAAA
*
395705 AAGAAAAAAAA
1 AAGAGAAAAAA
395716 AAG-GAAAAAA
1 AAGAGAAAAAA
395726 GAAAAGGGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 1 0.02
9 12 0.29
10 6 0.15
11 22 0.54
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (11 bp):
AAGAGAAAAAA
Found at i:395703 original size:7 final size:7
Alignment explanation
Indices: 395668--395730 Score: 53
Period size: 7 Copynumber: 9.3 Consensus size: 7
395658 ATGCTTGAAG
395668 AAAA-AA
1 AAAAGAA
*
395674 AAAAGAG
1 AAAAGAA
395681 AAAA-AA
1 AAAAGAA
*
395687 AACAGAA
1 AAAAGAA
395694 AAAATGAA
1 AAAA-GAA
395702 AAAA-AGA
1 AAAAGA-A
395709 AAAA-AA
1 AAAAGAA
*
395715 AAAGGAA
1 AAAAGAA
395722 AAAAGAA
1 AAAAGAA
395729 AA
1 AA
395731 GGGGGGGGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 13 0.28
7 26 0.57
8 7 0.15
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:395711 original size:27 final size:28
Alignment explanation
Indices: 395668--395730 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
395658 ATGCTTGAAG
*
395668 AAAA-AAAAAAGAGAAAAAAAACA-GAA
1 AAAAGAAAAAAGAGAAAAAAAAAAGGAA
395694 AAAATGAAAAAA-AGAAAAAAAAAAGGAA
1 AAAA-GAAAAAAGAGAAAAAAAAAAGGAA
395722 AAAAGAAAA
1 AAAAGAAAA
395731 GGGGGGGGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 4 0.12
27 16 0.48
28 13 0.39
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (28 bp):
AAAAGAAAAAAGAGAAAAAAAAAAGGAA
Found at i:396962 original size:83 final size:83
Alignment explanation
Indices: 396860--397308 Score: 799
Period size: 83 Copynumber: 5.4 Consensus size: 83
396850 ATCCCAGTCT
*
396860 AATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
396925 ATCTGGTTTGGTAGAACC
66 ATCTGGTTTGGCAGAACC
* * * *
396943 AATAATTGAATTTGGAAGATGAATCTACTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
397008 ATCTGGTTTGGCATAACC
66 ATCTGGTTTGGCAGAACC
397026 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
397091 ATCTGGTTTGGCAGAACC
66 ATCTGGTTTGGCAGAACC
*
397109 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
397174 ATCTGGTTTGGCAGAACC
66 ATCTGGTTTGGCAGAACC
* *
397192 AATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
397257 ATCTGGTTTGGCAGAACC
66 ATCTGGTTTGGCAGAACC
*
397275 AATCATTGAATTTGGAAGATGAATTTGCTCATAG
1 AATCATTGAATTTGGAAGATGAATGTGCTCATAG
397309 TAGAAATAAG
Statistics
Matches: 349, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 349 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGGTTTGGCAGAACC
Found at i:398298 original size:113 final size:113
Alignment explanation
Indices: 398111--399005 Score: 1547
Period size: 113 Copynumber: 7.9 Consensus size: 113
398101 TCAATAGTGT
*
398111 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
398176 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
* *
398224 CAATTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAATTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
*
398289 TTTGTTCAACCTTTTGATCAAATCGATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
*
398337 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
398402 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
*
398450 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
398515 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
398563 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
398628 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
*
398676 CAGTCCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * * *
398741 TTTATTCAACCTTTTGATCAAATCCATCACTTGATAGATTATCTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
* *
398789 CAGTTCGAGTTCATAATGAGAAGAACTTATCTGAAGAAATAGATGAAGAAGTTCATAATGAGAAG
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG-AA-GGATGAAGAAGTTCATAATGAGAAG
* * * * * *
398854 AATTTGTTCAACCTTCTGCTCAAATCTATCACTTGATAGATTATCTTTTC
64 AATTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
* *
398904 CAGTTCGAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * * *
398969 TTTGTTCAGCTTTTTGCTCAAATCCATTACTTGATGG
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGG
399006 GTCAGTTTTT
Statistics
Matches: 749, Mismatches: 31, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
113 641 0.86
114 4 0.01
115 104 0.14
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (113 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
Done.