Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 14 of 100
Found at i:3751295 original size:33 final size:33
Alignment explanation
Indices: 3751258--3751322 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
3751248 AATTTAAATT
*
3751258 AAAATCAATTTAAATTATAATGAAATTTCTTTA
1 AAAATCAATTTAAATTATAATGAAATTCCTTTA
3751291 AAAATCAATTTAAATTATAATGAAATTCCTTT
1 AAAATCAATTTAAATTATAATGAAATTCCTTT
3751323 CTTATGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (33 bp):
AAAATCAATTTAAATTATAATGAAATTCCTTTA
Found at i:3755320 original size:14 final size:14
Alignment explanation
Indices: 3755301--3755328 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3755291 TTCGAAAATT
3755301 GTAAGTCATATATA
1 GTAAGTCATATATA
3755315 GTAAGTCATATATA
1 GTAAGTCATATATA
3755329 CGTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
GTAAGTCATATATA
Found at i:3759470 original size:3 final size:3
Alignment explanation
Indices: 3759464--3759515 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
3759454 TGATAATGCT
* * *
3759464 GAA GAA GGA GGA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3759511 GAA GA
1 GAA GA
3759516 TCAATGCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3762061 original size:12 final size:11
Alignment explanation
Indices: 3762031--3762061 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3762021 AGTTTTCTTG
3762031 CATTGTCCATA
1 CATTGTCCATA
3762042 CATTGTCCATA
1 CATTGTCCATA
3762053 CATTTGTCC
1 CA-TTGTCC
3762062 CAAGCTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.39
Consensus pattern (11 bp):
CATTGTCCATA
Found at i:3767273 original size:5 final size:5
Alignment explanation
Indices: 3767263--3767288 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3767253 GTAGCTTTAA
3767263 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
3767289 CTTTAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:3770532 original size:99 final size:99
Alignment explanation
Indices: 3770341--3770634 Score: 386
Period size: 99 Copynumber: 3.0 Consensus size: 99
3770331 CTCGAACGAA
* *
3770341 CCTATGTTTGTTTTGAATTTT-GCCGTTCGATCTGCTCTGATCTTGAATAATACTA-TT-TTTTA
1 CCTATGTTTGTTTTGAATTTTGGCCGTTGGATCTGCTCTGATCTTGAATAATACTATTTATTTTT
3770403 ATTTCAAATTAAATTGATGATTATGGAAATTGAT
66 ATTTCAAATTAAATTGATGATTATGGAAATTGAT
* * *
3770437 CCTATGTTTGTTTTAAATTTTGGCGGTTGGATCTGCTCTGATCTTGAATAACACTATTTATTTTT
1 CCTATGTTTGTTTTGAATTTTGGCCGTTGGATCTGCTCTGATCTTGAATAATACTATTTATTTTT
* * *
3770502 ATTTCAAATTAAATTGGTGATTTTGGAAATTTAT
66 ATTTCAAATTAAATTGATGATTATGGAAATTGAT
* *
3770536 CCTA----TGTTTTGAATTTTGGCCGTTGGATCTGCTCCGGTCTTGAATAATACTATTTATTTTA
1 CCTATGTTTGTTTTGAATTTTGGCCGTTGGATCTGCTCTGATCTTGAATAATACTATTTA---T-
* * *
3770597 TTTTTTTTCAAATTAAAATGATGATTATGTAAATTGAT
62 TTTTATTTCAAATTAAATTGATGATTATGGAAATTGAT
3770635 ATGTGGGTTT
Statistics
Matches: 172, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
95 47 0.27
96 20 0.12
97 31 0.18
98 3 0.02
99 71 0.41
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (99 bp):
CCTATGTTTGTTTTGAATTTTGGCCGTTGGATCTGCTCTGATCTTGAATAATACTATTTATTTTT
ATTTCAAATTAAATTGATGATTATGGAAATTGAT
Found at i:3779371 original size:25 final size:24
Alignment explanation
Indices: 3779334--3779400 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
3779324 GTGAAATTAA
* **
3779334 AAAAAAAAATATTATAATTGTGATT
1 AAAAAAATATATTATAATTACGA-T
*
3779359 AAAAAAATTTATTATAATTACGAT
1 AAAAAAATATATTATAATTACGAT
* *
3779383 AAAAAAATAAATTTTAAT
1 AAAAAAATATATTATAAT
3779401 AAAAAATTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAAAAATATATTATAATTACGAT
Found at i:3779400 original size:24 final size:25
Alignment explanation
Indices: 3779329--3779400 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
3779319 TTATAGTGAA
* **
3779329 ATTAAAAAAAAAAATATTATAATTGTG
1 ATTAAAAAAATAAAT-TT-TAATTACG
** *
3779356 ATTAAAAAAATTTATTATAATTACG
1 ATTAAAAAAATAAATTTTAATTACG
3779381 A-TAAAAAAATAAATTTTAAT
1 ATTAAAAAAATAAATTTTAAT
3779401 AAAAAATTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
24 16 0.44
25 7 0.19
26 1 0.03
27 12 0.33
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (25 bp):
ATTAAAAAAATAAATTTTAATTACG
Found at i:3791547 original size:8 final size:8
Alignment explanation
Indices: 3791534--3791566 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
3791524 GTTACTTAGC
3791534 AAATATAT
1 AAATATAT
3791542 AAATATAT
1 AAATATAT
3791550 AAATATAT
1 AAATATAT
3791558 AAATATAT
1 AAATATAT
3791566 A
1 A
3791567 TCGTTTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATAT
Found at i:3793271 original size:12 final size:12
Alignment explanation
Indices: 3793256--3793283 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3793246 TAACACATTT
3793256 CTTTGCTTTTTC
1 CTTTGCTTTTTC
3793268 CTTTGCTTTTTC
1 CTTTGCTTTTTC
3793280 CTTT
1 CTTT
3793284 CTAGTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (12 bp):
CTTTGCTTTTTC
Found at i:3793688 original size:2 final size:2
Alignment explanation
Indices: 3793681--3793716 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3793671 TTCTTACCAA
*
3793681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3793717 CTTCCAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3797042 original size:2 final size:2
Alignment explanation
Indices: 3797037--3797084 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3797027 ATGTGTGTAC
* * *
3797037 AT AT AT AT AT AT AT AT GT AT GT AT AT CT 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 AT
3797079 AT AT AT
1 AT AT AT
3797085 CTTTTTCGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3797071 original size:24 final size:24
Alignment explanation
Indices: 3797025--3797076 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3797015 AAACATATTC
*
3797025 ATATGTGTGTACATATATATATAT
1 ATATGTATGTACATATATATATAT
* *
3797049 ATATGTATGTATATCTATATATAT
1 ATATGTATGTACATATATATATAT
3797073 ATAT
1 ATAT
3797077 ATATATATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATATGTATGTACATATATATATAT
Found at i:3800520 original size:2 final size:2
Alignment explanation
Indices: 3800515--3800540 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3800505 AAAAAAAAAA
3800515 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
3800541 GAAAGCCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3807016 original size:12 final size:12
Alignment explanation
Indices: 3806996--3807065 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
3806986 ACTATTTTTT
3806996 AAATATAAATATA
1 AAAT-TAAATATA
3807009 AAATT-AA-ATA
1 AAATTAAATATA
3807019 AAA-TATAA-A-A
1 AAATTA-AATATA
3807029 AAATATAAATATA
1 AAAT-TAAATATA
3807042 AAATTAAATA-A
1 AAATTAAATATA
*
3807053 ATAATAAAATATA
1 A-AATTAAATATA
3807066 TTATATATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
9 1 0.02
10 10 0.21
11 9 0.19
12 18 0.38
13 10 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTAAATATA
Found at i:3807021 original size:10 final size:11
Alignment explanation
Indices: 3806996--3807053 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
3806986 ACTATTTTTT
3806996 AAATATAAATA
1 AAATATAAATA
3807007 TAAA-ATTAAATA
1 -AAATA-TAAATA
3807019 AAATATAAA-A
1 AAATATAAATA
3807029 AAATATAAATA
1 AAATATAAATA
3807040 TAAA-ATTAAATA
1 -AAATA-TAAATA
3807052 AA
1 AA
3807054 TAATAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.24
11 12 0.29
12 19 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATATAAATA
Found at i:3807024 original size:17 final size:18
Alignment explanation
Indices: 3806994--3807051 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
3806984 ATACTATTTT
3806994 TTAAATATAAATATAAAA
1 TTAAATATAAATATAAAA
3807012 TTAAATA-AAATATAAAA
1 TTAAATATAAATATAAAA
3807029 --AAATATAAATATAAAA
1 TTAAATATAAATATAAAA
3807045 TTAAATA
1 TTAAATA
3807052 AATAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.14
16 10 0.27
17 10 0.27
18 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATATAAATATAAAA
Found at i:3807061 original size:17 final size:16
Alignment explanation
Indices: 3807000--3807062 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 16
3806990 TTTTTTAAAT
3807000 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
*
3807016 ATAAAATATAAAA-AAA
1 AT-AAATATAAAATTAA
3807032 TATAAATATAAAATTAA
1 -ATAAATATAAAATTAA
3807049 ATAAATAATAAAAT
1 ATAAAT-ATAAAAT
3807063 ATATTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 20 0.49
17 21 0.51
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:3807074 original size:33 final size:33
Alignment explanation
Indices: 3806996--3807061 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3806986 ACTATTTTTT
3806996 AAATATAAATATAAAATTAAATAAAATATAAAA
1 AAATATAAATATAAAATTAAATAAAATATAAAA
3807029 AAATATAAATATAAAATTAAAT-AAATAATAAAA
1 AAATATAAATATAAAATTAAATAAAAT-ATAAAA
3807062 TATATTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 4 0.12
33 28 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (33 bp):
AAATATAAATATAAAATTAAATAAAATATAAAA
Found at i:3807843 original size:12 final size:11
Alignment explanation
Indices: 3807818--3807854 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3807808 TATTCTTTCA
3807818 TTTTT-CTCTT
1 TTTTTGCTCTT
3807828 TTTTTGAC-CTT
1 TTTTTG-CTCTT
3807839 TTTTTGCTCTT
1 TTTTTGCTCTT
3807850 TTTTT
1 TTTTT
3807855 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.25
11 17 0.71
12 1 0.04
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTGCTCTT
Found at i:3812232 original size:10 final size:10
Alignment explanation
Indices: 3812205--3812242 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3812195 AATTTATCAT
*
3812205 TTTAATAAAA
1 TTTATTAAAA
3812215 -TT-TTAAAA
1 TTTATTAAAA
3812223 TTTATTAAAA
1 TTTATTAAAA
3812233 TTTATTAAAA
1 TTTATTAAAA
3812243 AAATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 5 0.20
9 4 0.16
10 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTATTAAAA
Found at i:3813254 original size:21 final size:20
Alignment explanation
Indices: 3813230--3813276 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
3813220 AAATATTAAT
*
3813230 AATAAAATTTAAAGTAACAAA
1 AATAAAATTTAAAATAA-AAA
* *
3813251 AATAATATTTAAAATAAATA
1 AATAAAATTTAAAATAAAAA
3813271 AATAAA
1 AATAAA
3813277 TTTTTTTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAAAATTTAAAATAAAAA
Found at i:3814298 original size:24 final size:21
Alignment explanation
Indices: 3814269--3814317 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3814259 TTTTTTGTAT
* *
3814269 TATTATTATATTTAATAATA-A
1 TATTATTAT-CTTATTAATATA
3814290 TATTATTATCTTATTAATATA
1 TATTATTATCTTATTAATATA
3814311 TATTATT
1 TATTATT
3814318 TAATAGCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATTATCTTATTAATATA
Found at i:3825580 original size:3 final size:3
Alignment explanation
Indices: 3825572--3825597 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3825562 ATTATGTACG
3825572 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3825598 TATTTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3831859 original size:2 final size:2
Alignment explanation
Indices: 3831852--3831910 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
3831842 GTTATCTAAC
* * * *
3831852 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AA AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3831894 AT AT GT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT A
3831911 CATAAACATA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3831869 original size:12 final size:12
Alignment explanation
Indices: 3831852--3831909 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
3831842 GTTATCTAAC
*
3831852 ATATATATATAT
1 ATATATATATGT
3831864 ATATATATATGT
1 ATATATATATGT
*
3831876 ATATATAAATGT
1 ATATATATATGT
*
3831888 ATATGTATATGT
1 ATATATATATGT
*
3831900 ATATACATAT
1 ATATATATAT
3831910 ACATAAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (12 bp):
ATATATATATGT
Found at i:3831879 original size:24 final size:24
Alignment explanation
Indices: 3831852--3831924 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
3831842 GTTATCTAAC
3831852 ATATATATATATATATATATATGT
1 ATATATATATATATATATATATGT
* * *
3831876 ATATATAAATGTATATGTATATGT
1 ATATATATATATATATATATATGT
* * * *
3831900 ATATACATATACATAAACATATGT
1 ATATATATATATATATATATATGT
3831924 A
1 A
3831925 CCTTTAGTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (24 bp):
ATATATATATATATATATATATGT
Found at i:3835922 original size:25 final size:25
Alignment explanation
Indices: 3835870--3835922 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3835860 TTAGATTATT
* *
3835870 TATAAAATATTAAAATTTATATTGA
1 TATAAAATATTAAAATATATATTAA
*
3835895 TATAAAATA-TAAAATATATTTTTAA
1 TATAAAATATTAAAATATA-TATTAA
3835920 TAT
1 TAT
3835923 TATTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TATAAAATATTAAAATATATATTAA
Found at i:3835933 original size:32 final size:35
Alignment explanation
Indices: 3835897--3835960 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
3835887 TATATTGATA
3835897 TAAAA-TATAAAATATA-T-TTTTAATATTATTAT
1 TAAAATTATAAAATATATTATTTTAATATTATTAT
* *
3835929 TAAAATTTTAAATTATATTATTTTAATATTAT
1 TAAAATTATAAAATATATTATTTTAATATTAT
3835961 ATTCATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 9 0.33
34 1 0.04
35 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TAAAATTATAAAATATATTATTTTAATATTATTAT
Found at i:3835959 original size:16 final size:17
Alignment explanation
Indices: 3835914--3835963 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
3835904 TAAAATATAT
3835914 TTTTAATATTATTATTAAAA
1 TTTTAATATTA-TATT--AA
3835934 TTTTAA-ATTATATT-A
1 TTTTAATATTATATTAA
3835949 TTTTAATATTATATT
1 TTTTAATATTATATT
3835964 CATATTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
18 4 0.14
19 4 0.14
20 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATATTATATTAA
Found at i:3836209 original size:28 final size:26
Alignment explanation
Indices: 3836176--3836242 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 26
3836166 TATATGAATA
* * *
3836176 AAAATTATATTTTATATTTTTTATCTAT
1 AAAATTATAATATATAATTTTTA--TAT
3836204 AAAATTATAATATATAATTTTTATAT
1 AAAATTATAATATATAATTTTTATAT
3836230 AAAA-TATAATATA
1 AAAATTATAATATA
3836243 AATATAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.25
26 7 0.19
28 20 0.56
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AAAATTATAATATATAATTTTTATAT
Found at i:3836245 original size:11 final size:12
Alignment explanation
Indices: 3836201--3836252 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
3836191 ATTTTTTATC
3836201 TATAAAATTATAA
1 TATAAAA-TATAA
* * *
3836214 TATATAATTTTTA
1 TATA-AAATATAA
3836227 TATAAAATATAA
1 TATAAAATATAA
3836239 TAT-AAATATAA
1 TATAAAATATAA
3836250 TAT
1 TAT
3836253 TTTATAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
11 11 0.34
12 8 0.25
13 11 0.34
14 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:3839010 original size:16 final size:16
Alignment explanation
Indices: 3838989--3839021 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3838979 ATCGGTTCGA
3838989 TTAAATTTATTGATTT
1 TTAAATTTATTGATTT
3839005 TTAAATTTATTGATTT
1 TTAAATTTATTGATTT
3839021 T
1 T
3839022 ATTTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TTAAATTTATTGATTT
Found at i:3839043 original size:13 final size:13
Alignment explanation
Indices: 3839020--3839059 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3839010 TTTATTGATT
3839020 TTATTTT-ATATA
1 TTATTTTAATATA
3839032 TTATTTTAATATA
1 TTATTTTAATATA
**
3839045 AAATTTTAATATA
1 TTATTTTAATATA
3839058 TT
1 TT
3839060 TAAGTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTTTAATATA
Found at i:3841057 original size:13 final size:14
Alignment explanation
Indices: 3841041--3841069 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3841031 ACTTTATTTT
3841041 TTATA-TTTTAAAA
1 TTATATTTTTAAAA
3841054 TTATATTTTTAAAA
1 TTATATTTTTAAAA
3841068 TT
1 TT
3841070 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATTTTTAAAA
Found at i:3841070 original size:22 final size:23
Alignment explanation
Indices: 3841009--3841071 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
3840999 AAATTATATT
* *
3841009 TTATATTTTTGAACATTTAAAAAC
1 TTATATTTTT-AAAATTTTAAAAC
* *
3841033 TT-TATTTTTTATATTTTAAAA-
1 TTATATTTTTAAAATTTTAAAAC
3841054 TTATATTTTTAAAATTTT
1 TTATATTTTTAAAATTTT
3841072 TTATTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 22 0.67
23 7 0.21
24 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATATTTTTAAAATTTTAAAAC
Found at i:3842517 original size:12 final size:13
Alignment explanation
Indices: 3842496--3842525 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3842486 GCAAATTCCT
3842496 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
3842509 AAAAA-AAAAAAG
1 AAAAAGAAAAAAG
3842521 AAAAA
1 AAAAA
3842526 CATCTCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:3847601 original size:15 final size:15
Alignment explanation
Indices: 3847581--3847610 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3847571 ATTCCATATA
3847581 GAATAAATTATGTTT
1 GAATAAATTATGTTT
3847596 GAATAAATTATGTTT
1 GAATAAATTATGTTT
3847611 AGGTATGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
GAATAAATTATGTTT
Found at i:3856008 original size:21 final size:21
Alignment explanation
Indices: 3855982--3856073 Score: 166
Period size: 21 Copynumber: 4.4 Consensus size: 21
3855972 ATACATTATG
3855982 TTACAGCTTACAACTAACTAC
1 TTACAGCTTACAACTAACTAC
*
3856003 TTACAGCTTGCAACTAACTAC
1 TTACAGCTTACAACTAACTAC
*
3856024 TTACAGCTTGCAACTAACTAC
1 TTACAGCTTACAACTAACTAC
3856045 TTACAGCTTACAACTAACTAC
1 TTACAGCTTACAACTAACTAC
3856066 TTACAGCT
1 TTACAGCT
3856074 CAAAAGATGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.29
Consensus pattern (21 bp):
TTACAGCTTACAACTAACTAC
Found at i:3861914 original size:28 final size:28
Alignment explanation
Indices: 3861874--3861954 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
3861864 TTTGGTTAAG
3861874 AATGATTGTTTGAAATCTTATAAGTGCA
1 AATGATTGTTTGAAATCTTATAAGTGCA
* * * *
3861902 AATGATTGTTTG-AATTTTACAAGGGTA
1 AATGATTGTTTGAAATCTTATAAGTGCA
** *
3861929 AAAAATTGGTTGAAATCTTATAAGTG
1 AATGATTGTTTGAAATCTTATAAGTG
3861955 ATGATTTTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (28 bp):
AATGATTGTTTGAAATCTTATAAGTGCA
Found at i:3866243 original size:21 final size:21
Alignment explanation
Indices: 3866204--3866243 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3866194 AAAAATATTT
* **
3866204 AATAAAATGTCAATGAAAAAA
1 AATAAAATGTAAACCAAAAAA
3866225 AATAAAATGTAAACCAAAA
1 AATAAAATGTAAACCAAAA
3866244 TTTATTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.17
Consensus pattern (21 bp):
AATAAAATGTAAACCAAAAAA
Found at i:3867015 original size:33 final size:33
Alignment explanation
Indices: 3866956--3867025 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3866946 TATTATTTGT
* * *
3866956 AGCATTGTGAAAAAGGGGAGATTTTAGCCGTAA
1 AGCATTGTGAAAAAGAGAAGACTTTAGCCGTAA
**
3866989 AGCATTGTGAAAAAGAGAAGACTTTAGTTGTAA
1 AGCATTGTGAAAAAGAGAAGACTTTAGCCGTAA
3867022 AGCA
1 AGCA
3867026 ACTAAGCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (33 bp):
AGCATTGTGAAAAAGAGAAGACTTTAGCCGTAA
Found at i:3876508 original size:19 final size:21
Alignment explanation
Indices: 3876484--3876524 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
3876474 TAAAATCTTA
*
3876484 TCGGATTTTATT-TG-ATTTT
1 TCGGATATTATTATGAATTTT
3876503 TCGGATATTATTATGAATTTT
1 TCGGATATTATTATGAATTTT
3876524 T
1 T
3876525 TCAATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.59
Consensus pattern (21 bp):
TCGGATATTATTATGAATTTT
Found at i:3876653 original size:21 final size:23
Alignment explanation
Indices: 3876615--3876664 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
3876605 GTTGGTTTCA
*
3876615 AAATTTTTATATTATTTTAATAT
1 AAATTTTTATATTATTTTAAAAT
3876638 AAATTTTTA-A-TATTTTAAAAT
1 AAATTTTTATATTATTTTAAAAT
3876659 AAATTT
1 AAATTT
3876665 GATATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 16 0.62
22 1 0.04
23 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTTTATATTATTTTAAAAT
Found at i:3876717 original size:18 final size:17
Alignment explanation
Indices: 3876689--3876722 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3876679 ATTTTATTTT
3876689 ATTAAAAAATATATAAA
1 ATTAAAAAATATATAAA
3876706 ATTAATAAAATATATAA
1 ATTAA-AAAATATATAA
3876723 TTTGATTCAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAAAAATATATAAA
Found at i:3883593 original size:23 final size:23
Alignment explanation
Indices: 3883545--3883593 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3883535 TTATTTTAAG
* **
3883545 AAAAAGAAAAAGAGAACAAATTT
1 AAAAAAAAAAAGAGAACAAAGAT
3883568 AAAAAAAAAAAG-GTAACAAAGAT
1 AAAAAAAAAAAGAG-AACAAAGAT
3883591 AAA
1 AAA
3883594 GAACTATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAAAAAAAAGAGAACAAAGAT
Found at i:3886212 original size:19 final size:19
Alignment explanation
Indices: 3886171--3886215 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3886161 TTTAATTGAT
*
3886171 AATAAAAATTTTTAAATAT
1 AATAAAAATTTTTAAATAA
*
3886190 AATAAAATATTTTT-CATAA
1 AATAAAA-ATTTTTAAATAA
3886209 AATAAAA
1 AATAAAA
3886216 GAAAAGAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAAAATTTTTAAATAA
Found at i:3900022 original size:18 final size:17
Alignment explanation
Indices: 3899977--3900025 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
3899967 TGACAAAGTC
3899977 AAAGAAGAAAGACAAAACG
1 AAAG-AGAAA-ACAAAACG
*
3899996 AAAGA-AAAACACAAACT
1 AAAGAGAAAACA-AAACG
3900013 AAAGAGAAAACAA
1 AAAGAGAAAACAA
3900026 GAAACAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.11
17 13 0.48
18 7 0.26
19 4 0.15
ACGTcount: A:0.71, C:0.12, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAGAGAAAACAAAACG
Found at i:3900030 original size:19 final size:17
Alignment explanation
Indices: 3899981--3900024 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3899971 AAAGTCAAAG
*
3899981 AAGAAAGACA-AAACGA
1 AAGAAAAACACAAACGA
*
3899997 AAGAAAAACACAAACTA
1 AAGAAAAACACAAACGA
3900014 AAGAGAAAACA
1 AAGA-AAAACA
3900025 AGAAACAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 9 0.38
18 6 0.25
ACGTcount: A:0.70, C:0.14, G:0.14, T:0.02
Consensus pattern (17 bp):
AAGAAAAACACAAACGA
Found at i:3912649 original size:30 final size:30
Alignment explanation
Indices: 3912613--3912671 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3912603 CAAGCACATT
*
3912613 GGTTTTAAGTTCATGTTGAGAAGAAATAAA
1 GGTTTTAAGTTCATATTGAGAAGAAATAAA
3912643 GGTTTTAAGTTCATATTGAGAAGAAATAA
1 GGTTTTAAGTTCATATTGAGAAGAAATAA
3912672 TTCCAGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
GGTTTTAAGTTCATATTGAGAAGAAATAAA
Found at i:3919570 original size:6 final size:6
Alignment explanation
Indices: 3919559--3919591 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3919549 GCAAAGGATT
*
3919559 ATTGAC ATTGAC ATTGAC ATTGAT ATTGAC ATT
1 ATTGAC ATTGAC ATTGAC ATTGAC ATTGAC ATT
3919592 CAGAGCACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (6 bp):
ATTGAC
Found at i:3921868 original size:17 final size:15
Alignment explanation
Indices: 3921824--3921879 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 15
3921814 TTTTTACATA
3921824 TTAT-TTATTATTTT
1 TTATGTTATTATTTT
*
3921838 TGTATGTTACTATTTT
1 T-TATGTTATTATTTT
*
3921854 TTATGGATTATTATTAT
1 TTAT-G-TTATTATTTT
3921871 TTAT-TTATT
1 TTATGTTATT
3921880 TTCATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.17
15 6 0.17
16 11 0.31
17 12 0.34
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (15 bp):
TTATGTTATTATTTT
Found at i:3921968 original size:21 final size:21
Alignment explanation
Indices: 3921910--3921968 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
3921900 AACATTGTTA
*
3921910 ATATATTACCA-TTTTTTCTT
1 ATATATTATCATTTTTTTCTT
* *
3921930 ATATGTTAT-AGTTATTTTCTT
1 ATATATTATCA-TTTTTTTCTT
*
3921951 ATGTATTATCATTTTTTT
1 ATATATTATCATTTTTTT
3921969 AATATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.03
20 7 0.23
21 21 0.70
22 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (21 bp):
ATATATTATCATTTTTTTCTT
Found at i:3922001 original size:15 final size:16
Alignment explanation
Indices: 3921954--3922001 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3921944 TTTTCTTATG
3921954 TATTATCATTTTTTTAA
1 TATTATCA-TTTTTTAA
*
3921971 TATTTTATCACTTTTT-A
1 TA--TTATCATTTTTTAA
3921988 TATTATCATTTTTT
1 TATTATCATTTTTT
3922002 GTAAATTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 11 0.41
17 5 0.19
18 5 0.19
19 6 0.22
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATCATTTTTTAA
Found at i:3922333 original size:27 final size:26
Alignment explanation
Indices: 3922298--3922358 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
3922288 ATATATAATG
*
3922298 ATATTATTTAATCTAATCTTATTCATA
1 ATATTATTTAATCTAATCCTA-TCATA
* * *
3922325 ATATTATTTTATTTTATCCTATCATA
1 ATATTATTTAATCTAATCCTATCATA
3922351 ATATTATT
1 ATATTATT
3922359 CTTTAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATTATTTAATCTAATCCTATCATA
Found at i:3929215 original size:14 final size:15
Alignment explanation
Indices: 3929181--3929214 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
3929171 ATTAAATTTT
3929181 AAAAAATACAAAATC
1 AAAAAATACAAAATC
3929196 AAAAAAT-CAAAA-C
1 AAAAAATACAAAATC
3929209 AAAAAA
1 AAAAAA
3929215 AAAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAATACAAAATC
Found at i:3933891 original size:38 final size:38
Alignment explanation
Indices: 3933849--3933925 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
3933839 GGTTGACCAC
3933849 CCTGCCTACCTCCCTTGAAAG-GCTTGGCGTGGATCGAA
1 CCTGCCTACCTCCCTT-AAAGAGCTTGGCGTGGATCGAA
* * *
3933887 CCTGCCTATCTCCCTTAAGGAGCTTGGTGTGGATCGAA
1 CCTGCCTACCTCCCTTAAAGAGCTTGGCGTGGATCGAA
3933925 C
1 C
3933926 GGTTTAGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (38 bp):
CCTGCCTACCTCCCTTAAAGAGCTTGGCGTGGATCGAA
Found at i:3934675 original size:35 final size:35
Alignment explanation
Indices: 3934617--3934684 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3934607 GCAAAAGTTC
*
3934617 GATTCTCTTCAGTATTGCATATAGTAATGTTCTAA
1 GATTCTCTCCAGTATTGCATATAGTAATGTTCTAA
* * *
3934652 GATTCTCTCCAGTTTTGCGTATAGTAATTTTCT
1 GATTCTCTCCAGTATTGCATATAGTAATGTTCT
3934685 TTGTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.46
Consensus pattern (35 bp):
GATTCTCTCCAGTATTGCATATAGTAATGTTCTAA
Found at i:3942204 original size:2 final size:2
Alignment explanation
Indices: 3942197--3942221 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3942187 CGGTCCAGGT
3942197 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3942222 AGAAACTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3944865 original size:15 final size:15
Alignment explanation
Indices: 3944845--3944875 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3944835 GATCAGCCTC
3944845 ATCCAGTACCAAATA
1 ATCCAGTACCAAATA
3944860 ATCCAGTACCAAATA
1 ATCCAGTACCAAATA
3944875 A
1 A
3944876 GTTGCTCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.06, T:0.19
Consensus pattern (15 bp):
ATCCAGTACCAAATA
Found at i:3955968 original size:2 final size:2
Alignment explanation
Indices: 3955961--3955989 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3955951 ATGTACATAC
3955961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3955990 CACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3965445 original size:7 final size:7
Alignment explanation
Indices: 3965433--3965458 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3965423 AGGAAATCAG
3965433 GTGGATA
1 GTGGATA
3965440 GTGGATA
1 GTGGATA
3965447 GTGGATA
1 GTGGATA
3965454 GTGGA
1 GTGGA
3965459 AAGCACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.46, T:0.27
Consensus pattern (7 bp):
GTGGATA
Found at i:3965916 original size:2 final size:2
Alignment explanation
Indices: 3965904--3965939 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3965894 CAATCGCCAA
3965904 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3965940 ATTTCAGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3966929 original size:34 final size:34
Alignment explanation
Indices: 3966865--3966930 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
3966855 TTGATAATCT
* *
3966865 ATTTTCAAAAAATATATTAATTTTTTGAAAATAG
1 ATTTTCAAAAAATATATTAATTATTCGAAAATAG
3966899 ATTTT-AAAAAATATAATATAA-TATTCGAAAAT
1 ATTTTCAAAAAATAT-AT-TAATTATTCGAAAAT
3966931 TTATTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.32
34 16 0.57
35 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (34 bp):
ATTTTCAAAAAATATATTAATTATTCGAAAATAG
Found at i:3966937 original size:34 final size:34
Alignment explanation
Indices: 3966864--3966955 Score: 82
Period size: 35 Copynumber: 2.7 Consensus size: 34
3966854 TTTGATAATC
* *
3966864 TATTTTCAAAAAATAT-AT-TAATTTTTTGAAAATA
1 TATTTT-AAAAAATATAATATAA-TATTCGAAAATA
* *
3966898 GATTTTAAAAAATATAATATAATATTCGAAAATT
1 TATTTTAAAAAATATAATATAATATTCGAAAATA
*
3966932 TATTTTTGAAAAATATGAA-ATAAT
1 TA-TTTTAAAAAATAT-AATATAAT
3966956 TTTTGAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 9 0.19
34 17 0.35
35 20 0.42
36 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.42
Consensus pattern (34 bp):
TATTTTAAAAAATATAATATAATATTCGAAAATA
Found at i:3970566 original size:10 final size:10
Alignment explanation
Indices: 3970551--3970595 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
3970541 CAGATGCTAT
3970551 AAAAATCATA
1 AAAAATCATA
3970561 AAAAATCATA
1 AAAAATCATA
3970571 AAAAATCA-A
1 AAAAATCATA
3970580 AAGAATATC-TA
1 AA-AA-ATCATA
3970591 AAAAA
1 AAAAA
3970596 AAATTGTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.12
10 22 0.69
11 6 0.19
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (10 bp):
AAAAATCATA
Found at i:3986156 original size:23 final size:25
Alignment explanation
Indices: 3986120--3986165 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
3986110 TGTGCATCTG
*
3986120 GTTTTTGTTTCTATATT-ACCTTCA
1 GTTTTTGTTCCTATATTCACCTTCA
*
3986144 GTTTTT-TTCCTATCTTCACCTT
1 GTTTTTGTTCCTATATTCACCTT
3986166 AGGAAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.59
Consensus pattern (25 bp):
GTTTTTGTTCCTATATTCACCTTCA
Found at i:3999016 original size:23 final size:24
Alignment explanation
Indices: 3998960--3999007 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3998950 TTGAAAAAAA
*
3998960 AATAAAATTTTGATATATATTTTT
1 AATAAAATATTGATATATATTTTT
3998984 AATAAAATATTGATA-ATATTTTT
1 AATAAAATATTGATATATATTTTT
3999007 A
1 A
3999008 TTGTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AATAAAATATTGATATATATTTTT
Found at i:3999133 original size:14 final size:12
Alignment explanation
Indices: 3999105--3999145 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
3999095 TCGTTTTAAA
3999105 TTTATTAAAATT
1 TTTATTAAAATT
3999117 TTTATTAAATTATT
1 TTTATTAAA--ATT
*
3999131 TTTAATAAAATT
1 TTTATTAAAATT
3999143 TTT
1 TTT
3999146 TCATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATTAAAATT
Found at i:4007016 original size:3 final size:3
Alignment explanation
Indices: 4007008--4007032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4006998 ACTCTGAGCT
4007008 TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC T
4007033 CTCCTCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:4007764 original size:12 final size:12
Alignment explanation
Indices: 4007734--4007770 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4007724 AGAAACAATA
*
4007734 AGGAGGAAGGAG
1 AGGAAGAAGGAG
4007746 A-GAAGAAGGAG
1 AGGAAGAAGGAG
4007757 AGGAAGAAGGAG
1 AGGAAGAAGGAG
4007769 AG
1 AG
4007771 AGGCGATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AGGAAGAAGGAG
Found at i:4008573 original size:2 final size:2
Alignment explanation
Indices: 4008560--4008591 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4008550 AGCTTCTTAC
*
4008560 AT AT AT AC 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
4008592 CAAAGAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4014727 original size:18 final size:20
Alignment explanation
Indices: 4014700--4014754 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
4014690 TTATATTCGA
*
4014700 ATAATTATAATTATTTAT-T
1 ATAAATATAATTATTTATGT
*
4014719 ATATA-ATAATTATTTATGT
1 ATAAATATAATTATTTATGT
*
4014738 TTAAATATAATTATTTA
1 ATAAATATAATTATTTA
4014755 AAATATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 12 0.40
19 7 0.23
20 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATAAATATAATTATTTATGT
Found at i:4016001 original size:31 final size:30
Alignment explanation
Indices: 4015925--4016001 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
4015915 GTCGCTACAC
4015925 TTCTCATGGAT-ATTTC-AATCCTTTACGT
1 TTCTCATGGATAATTTCTAATCCTTTACGT
* * *
4015953 TTGTTATGGATACTTTCTAATCCTTTACGCT
1 TTCTCATGGATAATTTCTAATCCTTTACG-T
*
4015984 TTCTCGTGGATAATTTCT
1 TTCTCATGGATAATTTCT
4016002 TGTTGAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 9 0.23
29 4 0.10
30 11 0.28
31 15 0.38
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48
Consensus pattern (30 bp):
TTCTCATGGATAATTTCTAATCCTTTACGT
Found at i:4023015 original size:24 final size:24
Alignment explanation
Indices: 4022975--4023020 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4022965 TTAATATATT
*
4022975 TAAAATTAAAATTAAAATTTTTTA
1 TAAAATTAAAATTAAAAATTTTTA
*
4022999 TAAAA-TAAAGTTCAAAAATTTT
1 TAAAATTAAAATT-AAAAATTTT
4023021 AATGTCAAAA
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:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAATTAAAATTAAAAATTTTTA
Found at i:4023071 original size:22 final size:22
Alignment explanation
Indices: 4023038--4023084 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
4023028 AAAGGTAAAA
* *
4023038 AAAATTATAAAAT-ATAATTTT
1 AAAATTACAAAATAAAAATTTT
4023059 AAAATATACAAAATAAAAATTTT
1 AAAAT-TACAAAATAAAAATTTT
4023082 AAA
1 AAA
4023085 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 7 0.32
23 10 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTACAAAATAAAAATTTT
Found at i:4026427 original size:2 final size:2
Alignment explanation
Indices: 4026420--4026504 Score: 126
Period size: 2 Copynumber: 45.0 Consensus size: 2
4026410 ATGTCTCTTG
4026420 AT AT AT AT AT AT AT A- AT AT AT AT AT A- AT AT A- 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 AT
*
4026459 AT A- AT AT AT AT AT AT AT AT AT AA AT AT A- 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 AT
4026499 AT AT AT
1 AT AT AT
4026505 CTGTTTGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
1 5 0.07
2 71 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4026457 original size:27 final size:26
Alignment explanation
Indices: 4026420--4026504 Score: 138
Period size: 25 Copynumber: 3.3 Consensus size: 26
4026410 ATGTCTCTTG
4026420 ATATATATATATATAATATATATATA
1 ATATATATATATATAATATATATATA
4026446 ATATAATATATATATAATATATATAT-
1 ATAT-ATATATATATAATATATATATA
*
4026472 ATATATATAAATATAATATATATAT-
1 ATATATATATATATAATATATATATA
4026497 ATATATAT
1 ATATATAT
4026505 CTGTTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
25 28 0.49
26 8 0.14
27 21 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATATATATATAATATATATATA
Found at i:4028020 original size:2 final size:2
Alignment explanation
Indices: 4028013--4028037 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4028003 ATTTACAGCT
4028013 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 T
4028038 TTTATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4042949 original size:13 final size:13
Alignment explanation
Indices: 4042931--4042957 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4042921 TGAGGGGGAG
4042931 TGTTAATTGGTGT
1 TGTTAATTGGTGT
4042944 TGTTAATTGGTGT
1 TGTTAATTGGTGT
4042957 T
1 T
4042958 ATTCCACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (13 bp):
TGTTAATTGGTGT
Found at i:4059276 original size:35 final size:37
Alignment explanation
Indices: 4059237--4059312 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
4059227 TTCACATACG
4059237 TTTTTGAAAAT-AA-ATATTTAAAAAAATTATAAACC
1 TTTTTGAAAATGAATATATTTAAAAAAATTATAAACC
* * * * *
4059272 TTTTTTAAAATGAATTTTTTTCAAAAAATTATAAATC
1 TTTTTGAAAATGAATATATTTAAAAAAATTATAAACC
4059309 TTTT
1 TTTT
4059313 GAGAAAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 10 0.29
36 2 0.06
37 22 0.65
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATGAATATATTTAAAAAAATTATAAACC
Found at i:4060801 original size:36 final size:37
Alignment explanation
Indices: 4060730--4060803 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
4060720 TTTTAGACCT
4060730 CACAAATTGCAGCGATGAAGGCACGCACCGGATCAAG
1 CACAAATTGCAGCGATGAAGGCACGCACCGGATCAAG
*
4060767 CACAAATTGCAGCGATGAA-GCATGCACCGGATCAAG
1 CACAAATTGCAGCGATGAAGGCACGCACCGGATCAAG
4060803 C
1 C
4060804 TAGTGGCAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.47
37 19 0.53
ACGTcount: A:0.35, C:0.27, G:0.26, T:0.12
Consensus pattern (37 bp):
CACAAATTGCAGCGATGAAGGCACGCACCGGATCAAG
Found at i:4062419 original size:12 final size:11
Alignment explanation
Indices: 4062386--4062423 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
4062376 TTTTGAATCC
4062386 TATATTATATA
1 TATATTATATA
4062397 -ATATTATATA
1 TATATTATATA
4062407 TATA-TATATA
1 TATATTATATA
4062417 TAT-TTAT
1 TATATTAT
4062424 TCAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTATATA
Found at i:4078401 original size:13 final size:13
Alignment explanation
Indices: 4078383--4078407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4078373 ATTTTTCTAT
4078383 TTTTTTTATTTTA
1 TTTTTTTATTTTA
4078396 TTTTTTTATTTT
1 TTTTTTTATTTT
4078408 TTATTAACAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:4078402 original size:15 final size:15
Alignment explanation
Indices: 4078372--4078412 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4078362 CTCAACTACC
4078372 TATTTTTCTATTTTTT
1 TATTTTT-TATTTTTT
*
4078388 T-TATTTTATTTTTT
1 TATTTTTTATTTTTT
4078402 TATTTTTTATT
1 TATTTTTTATT
4078413 AACAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 9 0.41
15 12 0.55
16 1 0.05
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (15 bp):
TATTTTTTATTTTTT
Found at i:4078541 original size:3 final size:3
Alignment explanation
Indices: 4078533--4078563 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4078523 ACTCGATATA
4078533 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4078564 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4078749 original size:40 final size:42
Alignment explanation
Indices: 4078617--4078755 Score: 185
Period size: 41 Copynumber: 3.3 Consensus size: 42
4078607 GCTTAACGAC
* * *
4078617 TTTAAAAAATAAATTAAGCTCCTCTAAATAGAGGCACCACAACT
1 TTTAAAAAATAAA--ATGCTCCTCTAAATAGAAGCATCACAACT
*
4078661 TTTGAAAAAT-AAATGCTCCTCTAAATAGAAGCATCACAAC-
1 TTTAAAAAATAAAATGCTCCTCTAAATAGAAGCATCACAACT
* *
4078701 TTTGAAAAATAAAATGCTCCTCTAAACAGAAGCATCACAA-T
1 TTTAAAAAATAAAATGCTCCTCTAAATAGAAGCATCACAACT
4078742 TTTAAAAAATAAAA
1 TTTAAAAAATAAAA
4078756 AACTCATTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
40 10 0.11
41 66 0.76
43 2 0.02
44 9 0.10
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (42 bp):
TTTAAAAAATAAAATGCTCCTCTAAATAGAAGCATCACAACT
Found at i:4079292 original size:46 final size:45
Alignment explanation
Indices: 4079238--4079342 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
4079228 GAAACTGTCT
* *
4079238 TAAAGATTCTCATGTAAAAATATCTTAAAGATTCTT-ATTTAAGAC
1 TAAAGATTCTCATGTAAAAAGATCTTAAAAATT-TTCATTTAAGAC
* * *
4079283 TCAAAGATTCTCATTTGAAAAGGTCTTAAAAATTTTCATTTAAGAC
1 T-AAAGATTCTCATGTAAAAAGATCTTAAAAATTTTCATTTAAGAC
*
4079329 TAAAAACTTCTCAT
1 TAAAGA-TTCTCAT
4079343 TTAAGATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
45 7 0.14
46 44 0.86
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (45 bp):
TAAAGATTCTCATGTAAAAAGATCTTAAAAATTTTCATTTAAGAC
Found at i:4079376 original size:67 final size:67
Alignment explanation
Indices: 4079269--4079411 Score: 178
Period size: 67 Copynumber: 2.1 Consensus size: 67
4079259 ATCTTAAAGA
* * * * *
4079269 TTCTTATTTAAGACTCAAAGATTCTCATTTGAAAAGGTCTTAAAAATTTTCATTTAAGACTAAAA
1 TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAAGGTCTTAAAAATTCTCATTTAAGACTAAAA
4079334 AC
66 AC
* * * * *
4079336 TTCTCATTTAAGATTAAAAAATTCTCTTTTAAAAATGTCTTAAAGATTCTCATTTAAGACTTAAA
1 TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAAGGTCTTAAAAATTCTCATTTAAGACTAAAA
**
4079401 GG
66 AC
4079403 TTCTCATTT
1 TTCTCATTT
4079412 GAAAATATCT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (67 bp):
TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAAGGTCTTAAAAATTCTCATTTAAGACTAAAA
AC
Found at i:4079386 original size:46 final size:46
Alignment explanation
Indices: 4079336--4079589 Score: 312
Period size: 46 Copynumber: 5.5 Consensus size: 46
4079326 GACTAAAAAC
* * ** * *
4079336 TTCTCATTTAAGATTAAAAAATTCTCTTTTAAAAATGTCTTAAAGA
1 TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
* *
4079382 TTCTCATTTAAGACTTAAAGGTTCTCATTTGAAAATATCTTAAAGA
1 TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
* *
4079428 TTTTCATTTAAGACTCAAAGGTTCTC-TTTGAAAAGGTCTTAAAGA
1 TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
* * *
4079473 TTCTCATTTAAGACTCAAAAGTTTTCATTTGAAAACGTCTTAAAGA
1 TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
* ** * * *
4079519 TTTTTTTTTAAGACTCAAAGGTTCTTATTTGAAAATATCTTAAAAA
1 TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
* *
4079565 TTCTCATTTAAAAATCAAAGGTTCT
1 TTCTCATTTAAGACTCAAAGGTTCT
4079590 TAAAAATGTC
Statistics
Matches: 178, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
45 40 0.22
46 138 0.78
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (46 bp):
TTCTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGA
Found at i:4079482 original size:91 final size:91
Alignment explanation
Indices: 4079339--4079589 Score: 322
Period size: 91 Copynumber: 2.7 Consensus size: 91
4079329 TAAAAACTTC
* * ** * *
4079339 TCATTTAAGATTAAAAAATTCTCTTTTAAAAATGTCTTAAAGATTCTCATTTAAGACTTAAAGGT
1 TCATTTAAGACTCAAAGGTTCTC-TTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGGT
*
4079404 TCTCATTTGAAAATATCTTAAAGATTT
65 TCTCATTTGAAAACATCTTAAAGATTT
* *
4079431 TCATTTAAGACTCAAAGGTTCTCTTTGAAAAGGTCTTAAAGATTCTCATTTAAGACTCAAAAGTT
1 TCATTTAAGACTCAAAGGTTCTCTTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGGTT
* *
4079496 TTCATTTGAAAACGTCTTAAAGATTT
66 CTCATTTGAAAACATCTTAAAGATTT
** * * * * *
4079522 TTTTTTAAGACTCAAAGGTTCTTATTTGAAAATATCTTAAAAATTCTCATTTAAAAATCAAAGGT
1 TCATTTAAGACTCAAAGGTTC-TCTTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGGT
4079587 TCT
65 TCT
4079590 TAAAAATGTC
Statistics
Matches: 137, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
91 80 0.58
92 57 0.42
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (91 bp):
TCATTTAAGACTCAAAGGTTCTCTTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGGTT
CTCATTTGAAAACATCTTAAAGATTT
Found at i:4079501 original size:21 final size:22
Alignment explanation
Indices: 4079264--4079502 Score: 100
Period size: 21 Copynumber: 10.6 Consensus size: 22
4079254 AAAATATCTT
*
4079264 AAAGATTCTTATTTAAGACTC-
1 AAAGATTCTCATTTAAGACTCA
* *
4079285 AAAGATTCTCATTTGAAAAGGTCTTA
1 AAAGATTCTCATTT---AA-GACTCA
*
4079311 AAA-ATTTTCATTTAAGACT-A
1 AAAGATTCTCATTTAAGACTCA
*
4079331 AAA-ACTTCTCATTTAAGA-TTA
1 AAAGA-TTCTCATTTAAGACTCA
* * * * *
4079352 AAAAATTCTCTTTTAAAAATGTCTT
1 AAAGATTCTCATTT-AAGA-CTC-A
*
4079377 AAAGATTCTCATTTAAGACT-T
1 AAAGATTCTCATTTAAGACTCA
* * * *
4079398 AAAGGTTCTCATTTGAAAATATCTT
1 AAAGATTCTCATTT-AAGA-CTC-A
*
4079423 AAAGATTTTCATTTAAGACTC-
1 AAAGATTCTCATTTAAGACTCA
* * * *
4079444 AAAGGTTCTC-TTTGAAAAGGTCTT
1 AAAGATTCTCATTT-AAGA-CTC-A
4079468 AAAGATTCTCATTTAAGACTCA
1 AAAGATTCTCATTTAAGACTCA
*
4079490 AAAG-TTTTCATTT
1 AAAGATTCTCATTT
4079503 GAAAACGTCT
Statistics
Matches: 167, Mismatches: 30, Indels: 42
0.70 0.13 0.18
Matches are distributed among these distances:
20 9 0.05
21 73 0.44
22 15 0.09
23 6 0.04
24 21 0.13
25 40 0.24
26 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (22 bp):
AAAGATTCTCATTTAAGACTCA
Found at i:4079539 original size:137 final size:137
Alignment explanation
Indices: 4079336--4079589 Score: 364
Period size: 137 Copynumber: 1.9 Consensus size: 137
4079326 GACTAAAAAC
* * * *
4079336 TTCTCATTTAAGATTAAAAAATTCTCTTTTAAAAATGTCTTAAAGATTCTCATTTAAGACTTAAA
1 TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAGACTCAAA
* * * *
4079401 GGTTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTCAAAGGTTCTCTTTGAAAAGGTC
66 GGTTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAAAATCAAAGGTTCTCTTTGAAAAGGTC
4079466 TTAAAGA
131 TTAAAGA
* * * * * **
4079473 TTCTCATTTAAGACTCAAAAGTTTTCATTTGAAAACGTCTTAAAGATTTTTTTTTAAGACTCAAA
1 TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAGACTCAAA
*
4079538 GGTTCTTATTTGAAAATATCTTAAAAATTCTCATTTAAAAATCAAAGGTTCT
66 GGTTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAAAATCAAAGGTTCT
4079590 TAAAAATGTC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 101 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (137 bp):
TTCTCATTTAAGACTAAAAAATTCTCATTTAAAAACGTCTTAAAGATTCTCATTTAAGACTCAAA
GGTTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAAAATCAAAGGTTCTCTTTGAAAAGGTC
TTAAAGA
Found at i:4081030 original size:23 final size:23
Alignment explanation
Indices: 4081004--4081047 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
4080994 TTGGAACAGG
4081004 TTTCATCAAC-TGATCATCATTAT
1 TTTCATC-ACTTGATCATCATTAT
4081027 TTTCATCACTTGATCATCATT
1 TTTCATCACTTGATCATCATT
4081048 CATAGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTCATCACTTGATCATCATTAT
Found at i:4081226 original size:71 final size:71
Alignment explanation
Indices: 4081140--4081322 Score: 260
Period size: 71 Copynumber: 2.6 Consensus size: 71
4081130 TGTACTAGAA
* * * *
4081140 ATTTTAGTATCAATTTCATCCATTGACCCATATTATTTTCACCATAATTCACAAGCTTTTCAGTA
1 ATTTTAGAATAAATTTTATCCATTGACCCATATTATTTTCACCATAATTCACAAGCTTCTCAGTA
*
4081205 TTAGCC
66 TCAGCC
* * *
4081211 ATTTTAGAATAAATTTTATCCATTGACCCATATTATTTTCACCATAATTTATAGGCTTCTCAGTA
1 ATTTTAGAATAAATTTTATCCATTGACCCATATTATTTTCACCATAATTCACAAGCTTCTCAGTA
4081276 TCAGCC
66 TCAGCC
* *
4081282 ATTTTAGAATAAATTTTATCC-TCTGATCCATATTATGTTCA
1 ATTTTAGAATAAATTTTATCCAT-TGACCCATATTATTTTCA
4081323 TCACTTGATC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
70 1 0.01
71 100 0.99
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.42
Consensus pattern (71 bp):
ATTTTAGAATAAATTTTATCCATTGACCCATATTATTTTCACCATAATTCACAAGCTTCTCAGTA
TCAGCC
Found at i:4081950 original size:23 final size:24
Alignment explanation
Indices: 4081923--4081980 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
4081913 TCAATATGAG
4081923 TTTTTCT-TTTCTCTCA-TTTTCAT
1 TTTTTCTATTT-TCTCATTTTTCAT
* *
4081946 TTTTTCTATTTTTTCATTTTTTAT
1 TTTTTCTATTTTCTCATTTTTCAT
4081970 TTTTT-TATTTT
1 TTTTTCTATTTT
4081981 TATTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 17 0.55
24 14 0.45
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTCTATTTTCTCATTTTTCAT
Found at i:4081957 original size:8 final size:7
Alignment explanation
Indices: 4081946--4081992 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
4081936 TCATTTTCAT
4081946 TTTTTCTA
1 TTTTT-TA
4081954 TTTTTTCA
1 TTTTTT-A
4081962 TTTTTTA
1 TTTTTTA
4081969 TTTTTT-
1 TTTTTTA
4081975 TATTTTTA
1 T-TTTTTA
4081983 TTTTATTA
1 TTTT-TTA
4081991 TT
1 TT
4081993 GATATCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.03
7 16 0.46
8 18 0.51
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:4081959 original size:17 final size:16
Alignment explanation
Indices: 4081939--4081981 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
4081929 TTTTCTCTCA
4081939 TTTTCATTTTTTCTATT
1 TTTTCATTTTTT-TATT
4081956 TTTTCA-TTTTTTATT
1 TTTTCATTTTTTTATT
*
4081971 TTTTTATTTTT
1 TTTTCATTTTT
4081982 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCATTTTTTTATT
Found at i:4081980 original size:14 final size:14
Alignment explanation
Indices: 4081947--4081992 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
4081937 CATTTTCATT
*
4081947 TTTTCTATTTTTTCA
1 TTTT-TATTTTTTTA
4081962 TTTTTTATTTTTTTA
1 -TTTTTATTTTTTTA
*
4081977 TTTTTATTTTATTA
1 TTTTTATTTTTTTA
4081991 TT
1 TT
4081993 GATATCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
15 9 0.32
16 4 0.14
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:4086515 original size:14 final size:13
Alignment explanation
Indices: 4086496--4086534 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4086486 TTTAATTCCA
4086496 TTTTTTTATTTTT
1 TTTTTTTATTTTT
*
4086509 TTCTTTTTATTCTT
1 TT-TTTTTATTTTT
*
4086523 TTTTTTTGTTTT
1 TTTTTTTATTTT
4086535 GAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.05, C:0.05, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTTTTATTTTT
Found at i:4087128 original size:19 final size:19
Alignment explanation
Indices: 4087083--4087128 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
4087073 ATTTTCTTTG
4087083 AATTT-CAACTTTAAACAC
1 AATTTCCAACTTTAAACAC
*
4087101 AA-CTCCAACTTTATAA-AC
1 AATTTCCAACTTTA-AACAC
4087119 AATTTCCAAC
1 AATTTCCAAC
4087129 AATTTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 8 0.35
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTTCCAACTTTAAACAC
Found at i:4091168 original size:33 final size:33
Alignment explanation
Indices: 4091126--4091189 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
4091116 ATATATATAC
*
4091126 ATATATATATATATATACACACTTTATAAGTGT
1 ATATATATATATATATACACACTATATAAGTGT
* *
4091159 ATATATATATATATATGCACTCTATATAAGT
1 ATATATATATATATATACACACTATATAAGT
4091190 AGCATATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (33 bp):
ATATATATATATATATACACACTATATAAGTGT
Found at i:4091186 original size:2 final size:2
Alignment explanation
Indices: 4091112--4091174 Score: 56
Period size: 2 Copynumber: 31.0 Consensus size: 2
4091102 TGCTTATAAA
* * * *
4091112 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC AC ACT TT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
4091154 AGT GT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT
4091175 GCACTCTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4103270 original size:12 final size:12
Alignment explanation
Indices: 4103253--4103278 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4103243 TTTGTTTCTA
4103253 TGAATTATGGGT
1 TGAATTATGGGT
4103265 TGAATTATGGGT
1 TGAATTATGGGT
4103277 TG
1 TG
4103279 TAACAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (12 bp):
TGAATTATGGGT
Found at i:4107702 original size:3 final size:3
Alignment explanation
Indices: 4107690--4107719 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4107680 TTTTTCATTT
*
4107690 TCA TCG TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
4107720 ACACTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:4113015 original size:2 final size:2
Alignment explanation
Indices: 4113008--4113041 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4112998 AAGTAGAGGC
*
4113008 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4113042 GTGGTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4115772 original size:24 final size:23
Alignment explanation
Indices: 4115741--4115789 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
4115731 GATAAATTTG
*
4115741 ATATATATGATTATAAT-AATAAA
1 ATATATAT-AATATAATAAATAAA
*
4115764 ATATAATATAATATTATAAATAAA
1 ATAT-ATATAATATAATAAATAAA
4115788 AT
1 AT
4115790 TTATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATATATAATATAATAAATAAA
Found at i:4116840 original size:21 final size:21
Alignment explanation
Indices: 4116798--4116840 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4116788 AAAAAAATAA
* **
4116798 TCGATTACTTTATAGGTGAAG
1 TCGACTACTTTATAGGAAAAG
*
4116819 TCGACTACTTTATATGAAAAG
1 TCGACTACTTTATAGGAAAAG
4116840 T
1 T
4116841 TACAATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGACTACTTTATAGGAAAAG
Found at i:4117899 original size:2 final size:2
Alignment explanation
Indices: 4117892--4117921 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4117882 GAACACGTAA
4117892 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
4117922 TAGTGGGGCT
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:4118463 original size:12 final size:13
Alignment explanation
Indices: 4118440--4118468 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4118430 ATCATCGTTT
4118440 AATTATAATTTAA
1 AATTATAATTTAA
4118453 AATTA-AATTTAA
1 AATTATAATTTAA
4118465 AATT
1 AATT
4118469 TAACTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATAATTTAA
Found at i:4138993 original size:5 final size:5
Alignment explanation
Indices: 4138980--4139012 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4138970 ACATTGGATT
*
4138980 TATTA TATTG TATTA -ATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
4139013 TATGGATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:4140561 original size:23 final size:22
Alignment explanation
Indices: 4140508--4140564 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
4140498 ATGAATTTTG
* *
4140508 ATATAATATAATTTATATTATAT
1 ATATAATAT-ATTTAAAATATAT
*
4140531 ATATTAATATATTTAAAATATGT
1 ATA-TAATATATTTAAAATATAT
4140554 AATATAATATA
1 -ATATAATATA
4140565 AATATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATAATATATTTAAAATATAT
Found at i:4140731 original size:11 final size:11
Alignment explanation
Indices: 4140717--4140742 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4140707 TTTTATATTA
4140717 ATAATATAAAT
1 ATAATATAAAT
4140728 ATAATATAAAT
1 ATAATATAAAT
4140739 ATAA
1 ATAA
4140743 ATATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:4140757 original size:17 final size:17
Alignment explanation
Indices: 4140719--4140767 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
4140709 TTATATTAAT
* *
4140719 AATATAAATATAATATA
1 AATATAAATATTATTTA
4140736 AATATAAATATTATTTA
1 AATATAAATATTATTTA
* *
4140753 TATAT-ATTATTATTT
1 AATATAAATATTATTT
4140768 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATAAATATTATTTA
Found at i:4140864 original size:11 final size:11
Alignment explanation
Indices: 4140850--4140875 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4140840 TAAAATTAAA
4140850 AAATATATATT
1 AAATATATATT
4140861 AAATATATATT
1 AAATATATATT
4140872 AAAT
1 AAAT
4140876 GAGTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATATATATT
Found at i:4140996 original size:19 final size:20
Alignment explanation
Indices: 4140974--4141045 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
4140964 TTATTTTTTA
* *
4140974 ATTATATTCT-TATATTCAT
1 ATTATATTATATATAATCAT
4140993 ATTA-ATTATATATAATCAT
1 ATTATATTATATATAATCAT
4141012 A-TATATT-TATATTAATCAT
1 ATTATATTATATA-TAATCAT
*
4141031 GTT-TATTCATATATA
1 ATTATATT-ATATATA
4141046 TTTATGTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.23
19 27 0.61
20 3 0.07
21 4 0.09
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (20 bp):
ATTATATTATATATAATCAT
Found at i:4141023 original size:29 final size:29
Alignment explanation
Indices: 4140984--4141050 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
4140974 ATTATATTCT
* *
4140984 TATATTCATATTAATTATATATAATCATA
1 TATATTTATATTAATCATATATAATCATA
* * *
4141013 TATATTTATATTAATCATGTTTATTCATA
1 TATATTTATATTAATCATATATAATCATA
4141042 TATATTTAT
1 TATATTTAT
4141051 GTTATATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
TATATTTATATTAATCATATATAATCATA
Found at i:4141025 original size:25 final size:25
Alignment explanation
Indices: 4140997--4141085 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 25
4140987 ATTCATATTA
* *
4140997 ATTATATATAATCATATATATTTAT
1 ATTATATTTATTCATATATATTTAT
4141022 ATTAATCATGTTTATTCATATATATTTAT
1 ATT-AT-A--TTTATTCATATATATTTAT
* * *
4141051 GTTATATTTATTCGTATTTATTTAT
1 ATTATATTTATTCATATATATTTAT
*
4141076 ATCATATTTA
1 ATTATATTTA
4141086 AATAAATAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 28 0.53
26 2 0.04
27 2 0.04
28 2 0.04
29 19 0.36
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTATATTTATTCATATATATTTAT
Found at i:4141047 original size:10 final size:10
Alignment explanation
Indices: 4140976--4141047 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
4140966 ATTTTTTAAT
4140976 TATATTC-T-
1 TATATTCATA
4140984 TATATTCATA
1 TATATTCATA
4140994 T-TAATT-ATA
1 TAT-ATTCATA
*
4141003 TATAATCATA
1 TATATTCATA
*
4141013 TATATTTATA
1 TATATTCATA
* *
4141023 T-TAATCATG
1 TATATTCATA
*
4141032 TTTATTCATA
1 TATATTCATA
4141042 TATATT
1 TATATT
4141048 TATGTTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
8 7 0.14
9 14 0.29
10 28 0.57
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (10 bp):
TATATTCATA
Found at i:4147733 original size:18 final size:19
Alignment explanation
Indices: 4147707--4147744 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4147697 TTTCATGGTT
*
4147707 TTAAATAG-AATATAAAAA
1 TTAAATAGAAAGATAAAAA
*
4147725 TTAATTAGAAAGATAAAAA
1 TTAAATAGAAAGATAAAAA
4147744 T
1 T
4147745 GATTTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (19 bp):
TTAAATAGAAAGATAAAAA
Done.