Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 116 of 172
Found at i:38646633 original size:20 final size:20
Alignment explanation
Indices: 38646608--38646647 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38646598 CTATATTTAC
38646608 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
38646628 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
38646648 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:38646646 original size:18 final size:18
Alignment explanation
Indices: 38646602--38646647 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
38646592 GAAAAGCTAT
*
38646602 ATTTACATATATTAATAA
1 ATTTATATATATTAATAA
38646620 ATTTATATATATATTAATAA
1 A-TT-TATATATATTAATAA
38646640 ATTTATAT
1 ATTTATAT
38646648 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATATATATTAATAA
Found at i:38649011 original size:6 final size:6
Alignment explanation
Indices: 38648997--38649052 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
38648987 GATGAGTGAG
* * *
38648997 GGGGAA GGAGAA GGAGAA GGGGAA GGGGAA GGGGAA GGGGAA GGAGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
38649045 GGGGAA GG
1 GGGGAA GG
38649053 AGCTTCATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:38649020 original size:18 final size:18
Alignment explanation
Indices: 38648997--38649052 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
38648987 GATGAGTGAG
*
38648997 GGGGAAGGAGAAGGAGAA
1 GGGGAAGGAGAAGGGGAA
*
38649015 GGGGAAGGGGAAGGGGAA
1 GGGGAAGGAGAAGGGGAA
38649033 GGGGAAGGAGAAGGGGAA
1 GGGGAAGGAGAAGGGGAA
38649051 GG
1 GG
38649053 AGCTTCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (18 bp):
GGGGAAGGAGAAGGGGAA
Found at i:38652242 original size:14 final size:14
Alignment explanation
Indices: 38652223--38652262 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
38652213 GAAAAGGTTG
38652223 AAAAGCTTTT-CTGC
1 AAAAGCTTTTAC-GC
38652237 AAAAGCTTTTACGC
1 AAAAGCTTTTACGC
38652251 AAAAGCTTTTAC
1 AAAAGCTTTTAC
38652263 CCCTAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 24 0.96
15 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (14 bp):
AAAAGCTTTTACGC
Found at i:38657195 original size:6 final size:7
Alignment explanation
Indices: 38657177--38657202 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38657167 TCTACTATTT
38657177 TAAAAAA
1 TAAAAAA
38657184 TAAAAAA
1 TAAAAAA
38657191 TAAAAAA
1 TAAAAAA
38657198 TAAAA
1 TAAAA
38657203 TATCTAATAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:38658933 original size:29 final size:30
Alignment explanation
Indices: 38658894--38658951 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
38658884 AATTGGTCTC
38658894 TTCTTTTTGAGAA-ACTCTGTAATTATTCT
1 TTCTTTTTGAGAAGACTCTGTAATTATTCT
*
38658923 TTCTTTTTGAGAAGGTCTCTGTAATTATT
1 TTCTTTTTGAGAA-GACTCTGTAATTATT
38658952 ATAGTGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (30 bp):
TTCTTTTTGAGAAGACTCTGTAATTATTCT
Found at i:38667769 original size:23 final size:26
Alignment explanation
Indices: 38667729--38667776 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
38667719 AGTTTTTATA
38667729 TTTTTATTTTTAAGAATTT-AGTCTT
1 TTTTTATTTTTAAGAATTTAAGTCTT
38667754 TTTTTA-TTTTAA-AATTTAAGTCT
1 TTTTTATTTTTAAGAATTTAAGTCT
38667777 AATTGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTTTATTTTTAAGAATTTAAGTCTT
Found at i:38677297 original size:52 final size:53
Alignment explanation
Indices: 38677241--38677378 Score: 163
Period size: 52 Copynumber: 2.6 Consensus size: 53
38677231 CATGTGCTTT
* *
38677241 CGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGAT-ACGTG-TTCC
1 CGTATAAGACCATAACTGGGCTATGGCATCGGTGCAATGTGATAACATGATT-C
* ** *
38677293 CGTATAAGACCATAACTGGGCTATGACATCGGTGTTATGTGATAATATGATTC
1 CGTATAAGACCATAACTGGGCTATGGCATCGGTGCAATGTGATAACATGATTC
* * * *
38677346 TGTATAAGACTATATCTGGGATATGGCATCGGT
1 CGTATAAGACCATAACTGGGCTATGGCATCGGT
38677379 ATGATATGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
52 39 0.53
53 32 0.44
54 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (53 bp):
CGTATAAGACCATAACTGGGCTATGGCATCGGTGCAATGTGATAACATGATTC
Found at i:38681529 original size:18 final size:17
Alignment explanation
Indices: 38681478--38681542 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
38681468 GGCACGTAAC
38681478 ATATATAAATTTTTAAA
1 ATATATAAATTTTTAAA
38681495 AT-TA-AAATTTTTAAAA
1 ATATATAAATTTTT-AAA
*
38681511 ATATATAAATTAATTAAA
1 ATATATAAATT-TTTAAA
38681529 A-AGTATAAATTTTT
1 ATA-TATAAATTTTT
38681543 TCCACATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 8 0.20
16 7 0.17
17 7 0.17
18 17 0.41
19 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATAAATTTTTAAA
Found at i:38681848 original size:3 final size:3
Alignment explanation
Indices: 38681840--38681876 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
38681830 ACATATTAAC
*
38681840 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38681877 TAAAGAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:38687392 original size:70 final size:70
Alignment explanation
Indices: 38687240--38687484 Score: 232
Period size: 71 Copynumber: 3.6 Consensus size: 70
38687230 AGATGGAATC
* * *
38687240 ATCATTTACACTGATCTTAGGACTTTTATCTCATTTTATCAGAA-T-T--T-T-GAACAAACAAG
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
38687299 ATGGG
66 ATGGG
* * ** * *
38687304 GTCATTTATACCAATTTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGACCAAACAAA
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
*
38687369 ATGGT
66 ATGGG
* * * * * ***
38687374 TTCATTTACACTGATTTTAGGACTTCTATCTCATCTTTTTCGGAGTTCTAGTCTAGATCAAGTTA
1 ATCATTTACACTGATCTTAGGACTTCTATCTCAT-TTTATCGGAATTCTAGTCTAGAACAAACAA
38687439 AATGGG
65 AATGGG
* ** * *
38687445 ATCATTTTCGTTGGTCTTAGGACTTCTATCTCATCTTATC
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATC
38687485 AGCTGTATGG
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
64 37 0.26
65 1 0.01
66 1 0.01
68 1 0.01
69 1 0.01
70 47 0.32
71 57 0.39
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (70 bp):
ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
ATGGG
Found at i:38692892 original size:20 final size:20
Alignment explanation
Indices: 38692867--38692908 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
38692857 GAACAATTAG
38692867 ATATTACAACCCAAGAATCA
1 ATATTACAACCCAAGAATCA
38692887 ATATTACAACCCAAGAATCA
1 ATATTACAACCCAAGAATCA
38692907 AT
1 AT
38692909 TATGAGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (20 bp):
ATATTACAACCCAAGAATCA
Found at i:38699653 original size:14 final size:14
Alignment explanation
Indices: 38699634--38699661 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38699624 GCATGTACAT
38699634 AAGTGTTAATATAA
1 AAGTGTTAATATAA
38699648 AAGTGTTAATATAA
1 AAGTGTTAATATAA
38699662 GAGACTTTAG
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:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
AAGTGTTAATATAA
Found at i:38703164 original size:157 final size:157
Alignment explanation
Indices: 38702874--38703191 Score: 629
Period size: 157 Copynumber: 2.0 Consensus size: 157
38702864 TTTGGCGAAT
38702874 ATTT-TGAGTTATGCCATTGTTGAAAGCTTGTGATTTTTTTTGTTTGATGATGAAATATGAAAGA
1 ATTTGTGAGTTATGCCATTGTTGAAAGCTTGTGATTTTTTTTGTTTGATGATGAAATATGAAAGA
38702938 TATGTTTAGGGTTAGCATATTTTGTATTGGAGTTTTTGACGATTTTGAGTAATTAGGACTAAATT
66 TATGTTTAGGGTTAGCATATTTTGTATTGGAGTTTTTGACGATTTTGAGTAATTAGGACTAAATT
38703003 GTAAAAATAATAACTTGATGGACTAAA
131 GTAAAAATAATAACTTGATGGACTAAA
38703030 ATTTGTGAGTTATGCCATTGTTGAAAGCTTGTGATTTTTTTTGTTTGATGATGAAATATGAAAGA
1 ATTTGTGAGTTATGCCATTGTTGAAAGCTTGTGATTTTTTTTGTTTGATGATGAAATATGAAAGA
38703095 TATGTTTAGGGTTAGCATATTTTGTATTGGAGTTTTTGACGATTTTGAGTAATTAGGACTAAATT
66 TATGTTTAGGGTTAGCATATTTTGTATTGGAGTTTTTGACGATTTTGAGTAATTAGGACTAAATT
38703160 GTAAAAATAATAACTTGATGGACTAAA
131 GTAAAAATAATAACTTGATGGACTAAA
38703187 ATTTG
1 ATTTG
38703192 AAATAAATAA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 4 0.02
157 157 0.98
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.42
Consensus pattern (157 bp):
ATTTGTGAGTTATGCCATTGTTGAAAGCTTGTGATTTTTTTTGTTTGATGATGAAATATGAAAGA
TATGTTTAGGGTTAGCATATTTTGTATTGGAGTTTTTGACGATTTTGAGTAATTAGGACTAAATT
GTAAAAATAATAACTTGATGGACTAAA
Found at i:38705500 original size:16 final size:16
Alignment explanation
Indices: 38705479--38705510 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38705469 TAGAGACAAG
38705479 TTGGATATGCTATTTA
1 TTGGATATGCTATTTA
38705495 TTGGATATGCTATTTA
1 TTGGATATGCTATTTA
38705511 GACTTAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
TTGGATATGCTATTTA
Found at i:38708306 original size:42 final size:42
Alignment explanation
Indices: 38708244--38708401 Score: 138
Period size: 42 Copynumber: 3.6 Consensus size: 42
38708234 TAAGTGATTT
*
38708244 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGTCC
1 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
* * *
38708286 CGTATAAGACCATGTTTGGGATATGGCATCAGCATCGATATGA-GACTT
1 CGTATAAGACCATGTCTGGGACATGGCAT-----T-GATATGAGGAC-C
* * * * * *
38708334 CGTATAAGACCATATTTGGGATATGACATCGATATGCGGACC
1 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
* *
38708376 CATGTAAGACCATGTCTGGGACATGG
1 CGTATAAGACCATGTCTGGGACATGG
38708402 ATTTGGCACT
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
42 53 0.57
43 3 0.03
47 3 0.03
48 34 0.37
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (42 bp):
CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
Found at i:38708311 original size:90 final size:90
Alignment explanation
Indices: 38708103--38708401 Score: 244
Period size: 90 Copynumber: 3.2 Consensus size: 90
38708093 AGATCCTGTG
* * * * *
38708103 TAAGACCATGTCTGGGACATGGCATCAGCATCCGAGATGAGAGC--CAGTGTAAGACCACATCTG
1 TAAGACCATGTCTGGGATATGGCATCAGCAT-CGATAAGAGA-CTTC-GTATAAGACCATATCTG
* * * *
38708166 GGATATGGCATCAGTACCAATATGTGATCCCGTA
63 GGACAT-G-A-CA-T--CGATATGAGGTCCCGTA
* * * * * * *
38708200 TAAGACCATATCAGGGATATGGCTTC-GACATCGTTAAGTGATTTCGTATAAGACCATGTCTGGG
1 TAAGACCATGTCTGGGATATGGCATCAG-CATCGATAAGAGACTTCGTATAAGACCATATCTGGG
* *
38708264 ACATGGCATTGATATGAGGTCCCGTA
65 ACATGACATCGATATGAGGTCCCGTA
* * *
38708290 TAAGACCATGTTTGGGATATGGCATCAGCATCGATATGAGACTTCGTATAAGACCATATTTGGGA
1 TAAGACCATGTCTGGGATATGGCATCAGCATCGATAAGAGACTTCGTATAAGACCATATCTGGGA
* * * * *
38708355 TATGACATCGATATGCGGACCCATG
66 CATGACATCGATATGAGGTCCCGTA
*
38708380 TAAGACCATGTCTGGGACATGG
1 TAAGACCATGTCTGGGATATGG
38708402 ATTTGGCACT
Statistics
Matches: 161, Mismatches: 37, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
90 104 0.65
91 1 0.01
92 1 0.01
93 2 0.01
95 1 0.01
96 26 0.16
97 26 0.16
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (90 bp):
TAAGACCATGTCTGGGATATGGCATCAGCATCGATAAGAGACTTCGTATAAGACCATATCTGGGA
CATGACATCGATATGAGGTCCCGTA
Found at i:38708345 original size:48 final size:48
Alignment explanation
Indices: 38708090--38708363 Score: 183
Period size: 48 Copynumber: 5.8 Consensus size: 48
38708080 ACCATGGTTA
* * * *
38708090 ATGAGA-TCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
1 ATGAGACTCC-GTATAAGACCATATCTGGGATATGGCATCAGCAT-CGAT
* * * * * *
38708139 ATGAGAGC-CAGTGTAAGACCACATCTGGGATATGGCATCAGTACCAAT
1 ATGAGA-CTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * * *
38708187 ATGTGA-TCCCGTATAAGACCATATCAGGGATATGGCTTC-GACATCGTT
1 ATGAGACT-CCGTATAAGACCATATCTGGGATATGGCATCAG-CATCGAT
* * * * * *
38708235 AAGTGATTTCGTATAAGACCATGTCTGGGACATGGCAT-----T-GAT
1 ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * *
38708277 ATGAG-GTCCCGTATAAGACCATGTTTGGGATATGGCATCAGCATCGAT
1 ATGAGACT-CCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * *
38708325 ATGAGACTTCGTATAAGACCATATTTGGGATATGACATC
1 ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATC
38708364 GATATGCGGA
Statistics
Matches: 176, Mismatches: 35, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.01
42 32 0.18
43 1 0.01
47 2 0.01
48 102 0.58
49 37 0.21
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (48 bp):
ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
Found at i:38711175 original size:10 final size:10
Alignment explanation
Indices: 38711142--38711175 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38711132 GAATTAGATC
38711142 AAAATTACTA
1 AAAATTACTA
*
38711152 AAAA-TAATA
1 AAAATTACTA
38711161 AAAATTACTA
1 AAAATTACTA
38711171 AAAAT
1 AAAAT
38711176 AACTTCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTACTA
Found at i:38712717 original size:20 final size:20
Alignment explanation
Indices: 38712648--38712717 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
38712638 TGTACAAAAA
* *
38712648 GCATACTTGGCACACGAAGT
1 GCATTCTTGGCACATGAAGT
* * * *
38712668 ACATTCCTAGCATAT-AAGT
1 GCATTCTTGGCACATGAAGT
38712687 GCATATC-TGGCACATGAAGT
1 GCAT-TCTTGGCACATGAAGT
38712707 GCATTCTTGGC
1 GCATTCTTGGC
38712718 GCATAAATGC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (20 bp):
GCATTCTTGGCACATGAAGT
Found at i:38715128 original size:36 final size:36
Alignment explanation
Indices: 38715088--38715158 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
38715078 GCTCGAGAAG
38715088 AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
1 AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
38715124 AGCTAATATATCAATATTTAAAGGAACAAATTTTT
1 AGCTAATATATCAATATTTAAAGGAACAAATTTTT
38715159 TTATAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (36 bp):
AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
Found at i:38716470 original size:43 final size:44
Alignment explanation
Indices: 38716387--38716472 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
38716377 CTATGTATAT
* * * *
38716387 ATTAATATGGTTAAATCATATGAGATGGTAAACCAGAAGTTTAC
1 ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTAC
*
38716431 ATTAGTATCGTTAAATCATATG-CATAGTAAACCAAAAGTTTA
1 ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTA
38716473 TTAGTCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 17 0.46
44 20 0.54
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (44 bp):
ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTAC
Found at i:38720340 original size:23 final size:23
Alignment explanation
Indices: 38720308--38720359 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
38720298 GGACTCACCA
*
38720308 CAGCTTATTGGAGCTTACCGATT
1 CAGCTCATTGGAGCTTACCGATT
*
38720331 CAGCTCATTGGAGCTTACTGATT
1 CAGCTCATTGGAGCTTACCGATT
38720354 CAGCTC
1 CAGCTC
38720360 GAAAAAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (23 bp):
CAGCTCATTGGAGCTTACCGATT
Found at i:38720422 original size:24 final size:24
Alignment explanation
Indices: 38720329--38720431 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
38720319 AGCTTACCGA
* * *
38720329 TTCAGCTCATTGGAGCTTACTG-A
1 TTCAGCTCAATAGAGCTTACTGTT
*
38720352 TTCAGCTCGAA-AAAGCTTACTG--
1 TTCAGCTC-AATAGAGCTTACTGTT
38720374 TTCAGCTCAATAGAGCTTA-TCGTT
1 TTCAGCTCAATAGAGCTTACT-GTT
*
38720398 TTCAACTCAATAGAGCTTACTGTT
1 TTCAGCTCAATAGAGCTTACTGTT
38720422 TATCAGCTCA
1 T-TCAGCTCA
38720432 GGAGGAGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.04
22 16 0.24
23 17 0.25
24 23 0.34
25 8 0.12
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (24 bp):
TTCAGCTCAATAGAGCTTACTGTT
Found at i:38720664 original size:20 final size:20
Alignment explanation
Indices: 38720636--38720715 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
38720626 ATATTGTATT
*
38720636 AATGCATGAATTACTGTTGA
1 AATGAATGAATTACTGTTGA
38720656 AATGAATGAATTACTGTTGA
1 AATGAATGAATTACTGTTGA
* * * *
38720676 TATGGATGAGTTACTGCTGA
1 AATGAATGAATTACTGTTGA
*
38720696 AATGAATGAATTACAGTTGA
1 AATGAATGAATTACTGTTGA
38720716 TACGGATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (20 bp):
AATGAATGAATTACTGTTGA
Found at i:38720701 original size:40 final size:40
Alignment explanation
Indices: 38720641--38720731 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
38720631 GTATTAATGC
* * *
38720641 ATGAATTACTGTTGAAATGAATGAATTACTGTTGATATGG
1 ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
*
38720681 ATGAGTTACTGCTGAAATGAATGAATTACAGTTGATACGG
1 ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
*
38720721 ATAAATTACTG
1 ATGAATTACTG
38720732 TTATTACTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (40 bp):
ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
Found at i:38720744 original size:40 final size:39
Alignment explanation
Indices: 38720697--38720799 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 39
38720687 TACTGCTGAA
*
38720697 ATGAATGAATTACAGTTGATACGGATAAATTACT-GTTATT
1 ATGAATGAATTACAGTT-ATACGGATAAACTACTAGTTA-T
* * *
38720737 ACT-AATGAGTTACTGGTTATACGGATGAACTACTAGTTAT
1 A-TGAATGAATTAC-AGTTATACGGATAAACTACTAGTTAT
*
38720777 ATGAATGAATTAGAGTTTATACG
1 ATGAATGAATTACAG-TTATACG
38720800 AATAGAAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.04
40 41 0.80
41 8 0.16
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (39 bp):
ATGAATGAATTACAGTTATACGGATAAACTACTAGTTAT
Found at i:38720784 original size:20 final size:20
Alignment explanation
Indices: 38720699--38720785 Score: 52
Period size: 20 Copynumber: 4.3 Consensus size: 20
38720689 CTGCTGAAAT
*
38720699 GAATGAATTAC-AGTTGATAC
1 GAATGAACTACTAGTT-ATAC
* * *
38720719 GGATAAATTACT-GTTATTAC
1 GAATGAACTACTAGTTA-TAC
* ** *
38720739 TAATGAGTTACTGGTTATAC
1 GAATGAACTACTAGTTATAC
* *
38720759 GGATGAACTACTAGTTATAT
1 GAATGAACTACTAGTTATAC
38720779 GAATGAA
1 GAATGAA
38720786 TTAGAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
19 1 0.02
20 46 0.90
21 4 0.08
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (20 bp):
GAATGAACTACTAGTTATAC
Found at i:38722518 original size:20 final size:21
Alignment explanation
Indices: 38722487--38722527 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
38722477 AGAGGGGAAG
38722487 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
38722508 GAAAG-AAGAAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
38722528 TTGAAGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:38724441 original size:46 final size:46
Alignment explanation
Indices: 38724382--38724509 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
38724372 TTGAATGAAA
*
38724382 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA-GAAAATG
*
38724428 TGTAAGTCCATGGTTGAAAGATACCATGGCAACATGATAGAAAATG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATG
* ** * * *
38724474 AGTAAGACCACAGTTGAAAGACACTATGGCATCATG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACATG
38724510 TTAAAGATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 71 0.99
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (46 bp):
TGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATG
Found at i:38724790 original size:16 final size:17
Alignment explanation
Indices: 38724769--38724800 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38724759 ATGATGGAGC
38724769 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
38724785 ATGAAATGATTGATAT
1 ATGAAATGATTGATAT
38724801 GTACTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:38727128 original size:42 final size:42
Alignment explanation
Indices: 38727016--38727150 Score: 116
Period size: 42 Copynumber: 3.2 Consensus size: 42
38727006 CTGAAGGCTG
* * * * *
38727016 AACAGAAGCTC-ATGAGAGCTAAACAAAAACCCGTAAGGGTTG
1 AACAGAAGCTCAAT-AGAGCTGAACAGAAACCCATAAGAGTTA
* * *
38727058 AAC-GAAAG-TC-GTAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AACAG-AAGCTCAAT-AGAGCTGAACAGAAACCCATAAGAGTTA
* * *
38727099 AATAGAAGCTCAATAGAGCTGAACAGAAACTCATATGAGTTA
1 AACAGAAGCTCAATAGAGCTGAACAGAAACCCATAAGAGTTA
38727141 AACAGAAGCT
1 AACAGAAGCT
38727151 TATGAGATCT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
41 32 0.43
42 42 0.56
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCAATAGAGCTGAACAGAAACCCATAAGAGTTA
Found at i:38728068 original size:57 final size:57
Alignment explanation
Indices: 38727980--38728097 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 57
38727970 ATGAAGCTAA
* *
38727980 AATATGAAATCCGGAATTAAGAGCTTTTCAATGGTGTTTTTGGA-AAAAAATTTGGAG
1 AATATGAAATCCGGAATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAA-TCGGAG
38728037 AATATGAAATCC-GACATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
1 AATATGAAATCCGGA-ATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
38728094 AATA
1 AATA
38728098 AATGGTCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
56 2 0.04
57 49 0.86
58 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (57 bp):
AATATGAAATCCGGAATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
Found at i:38736041 original size:68 final size:63
Alignment explanation
Indices: 38735894--38736041 Score: 156
Period size: 63 Copynumber: 2.3 Consensus size: 63
38735884 ATATAATTCG
* *
38735894 GCTCTCTTGTACACATGGTGAACACTCAGTACCACCCATGTGACCTAACCAATTTATCTCGTA
1 GCTCTCTTGTACACATGGTGAACACTCAGTACCACCCATGCGACCTAACCAATATATCTCGTA
* * * *
38735957 GCTCTCTTGT-CTACATGGTGTACACAT-AGTATCACCCATGCGACCTAGCTACATCATAATGTC
1 GCTCTCTTGTAC-ACATGGTGAACAC-TCAGTACCACCCATGCGACCTAAC--CA--AT-ATATC
*
38736020 TTGTA
59 TCGTA
38736025 GCTCTCTTGTACACATG
1 GCTCTCTTGTACACATG
38736042 ATGTGCACTC
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 41 0.59
64 1 0.01
65 2 0.03
67 2 0.03
68 22 0.31
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (63 bp):
GCTCTCTTGTACACATGGTGAACACTCAGTACCACCCATGCGACCTAACCAATATATCTCGTA
Found at i:38736779 original size:30 final size:30
Alignment explanation
Indices: 38736745--38736805 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
38736735 TCCTTAACTC
38736745 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
38736775 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
38736805 A
1 A
38736806 TGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:38739035 original size:23 final size:22
Alignment explanation
Indices: 38738990--38739033 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38738980 ATGTTATTGT
*
38738990 TTGTTAAATTTTAATTATAAAA
1 TTGTTAAATATTAATTATAAAA
38739012 TTGTATAAATATTAA-TATAAAA
1 TTGT-TAAATATTAATTATAAAA
38739034 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TTGTTAAATATTAATTATAAAA
Found at i:38744250 original size:6 final size:6
Alignment explanation
Indices: 38744236--38744284 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
38744226 ACCGTGCCCG
* *
38744236 ACATAT ACATGT ACATAT ACATAT ACATAT ACATAT ACATAT ACGTAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
38744284 A
1 A
38744285 TAACACTCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:38744879 original size:16 final size:16
Alignment explanation
Indices: 38744858--38744890 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38744848 TCAACAATTC
38744858 GAAGAAAAAAAAAGAA
1 GAAGAAAAAAAAAGAA
*
38744874 GAAGAAGAAAAAAGAA
1 GAAGAAAAAAAAAGAA
38744890 G
1 G
38744891 CTTATGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
GAAGAAAAAAAAAGAA
Found at i:38744998 original size:13 final size:13
Alignment explanation
Indices: 38744971--38745008 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
38744961 GTCGTAGGTA
*
38744971 AATTCATTTTCTGT
1 AATT-ATTTTTTGT
38744985 AATTATTTTTTGT
1 AATTATTTTTTGT
38744998 AATTATTTTTT
1 AATTATTTTTT
38745009 AAAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (13 bp):
AATTATTTTTTGT
Found at i:38747133 original size:21 final size:21
Alignment explanation
Indices: 38747107--38747147 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38747097 TTTACCCTAG
38747107 TTTTAATTTCAATGTAATTCA
1 TTTTAATTTCAATGTAATTCA
*
38747128 TTTTAATTTCAATGTGATTC
1 TTTTAATTTCAATGTAATTC
38747148 GAAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTAATTTCAATGTAATTCA
Found at i:38748708 original size:56 final size:55
Alignment explanation
Indices: 38748593--38748733 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 55
38748583 TCAGGAATTG
* * * *
38748593 AAAAAAAAATTTGGGTGCTGGGTCATTGATGGCCAGCACCCTTGTAATAGATTTAA
1 AAAAAAAAATTT-GGTGCTGGGACACTGATAGCCAGCACCCTTGTAACAGATTTAA
* *
38748649 AAAAAAAAATTTGGTGCTGGGACACTGATAGCC-GACACCTTTGTACCAGATTT--
1 AAAAAAAAATTTGGTGCTGGGACACTGATAGCCAG-CACCCTTGTAACAGATTTAA
**
38748702 TTAAAAAAATTCTAAGGTGCTGGGACACTGAT
1 AAAAAAAAATT-T--GGTGCTGGGACACTGAT
38748734 GGTCAGGACC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
53 9 0.12
54 2 0.03
55 33 0.45
56 29 0.40
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (55 bp):
AAAAAAAAATTTGGTGCTGGGACACTGATAGCCAGCACCCTTGTAACAGATTTAA
Found at i:38749630 original size:3 final size:3
Alignment explanation
Indices: 38749622--38749647 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38749612 AGTAAAAATA
38749622 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
38749648 AGCTATAAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:38749796 original size:32 final size:30
Alignment explanation
Indices: 38749756--38749818 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
38749746 TACATTTGTA
38749756 TTATTTTATGTA-TAATTAGTGAAAAGATATT
1 TTATTTTAT-TATTAATTAGT-AAAAGATATT
*
38749787 TTATATTTATTATTAATTAGTAAAATATATT
1 TTAT-TTTATTATTAATTAGTAAAAGATATT
38749818 T
1 T
38749819 ATTAGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TTATTTTATTATTAATTAGTAAAAGATATT
Found at i:38750946 original size:18 final size:18
Alignment explanation
Indices: 38750915--38750958 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38750905 TGAATATGTG
38750915 AATTGAAAATTGATTGAA
1 AATTGAAAATTGATTGAA
38750933 AATTGGAAAA-TGATTG--
1 AATT-GAAAATTGATTGAA
38750949 AATTGAAAAT
1 AATTGAAAAT
38750959 GTGAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
18 10 0.42
19 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
AATTGAAAATTGATTGAA
Found at i:38752510 original size:90 final size:89
Alignment explanation
Indices: 38752291--38752524 Score: 269
Period size: 90 Copynumber: 2.6 Consensus size: 89
38752281 GGTGTTACAC
* * *
38752291 AAAATGTTCGTATTA-TTTTGTAT-TCGTAAAT-CAATTGTAGTCAGTATTATTTTTTGGTCAAA
1 AAAATGTTCGTATTATTTTTGTATCT-GTAAATAAAATT-TAGTC-GTATTATTTGTCGGTCAAA
* *
38752353 TTTTATATTTTCGTATATCAGTTTTGT
63 TTTTATATTTTCGTATATCAATTTTCT
* * * * * *
38752380 AAAATATTTGTGTTATTTTTGGATCTGTAAA-AATATTTTAGAACGTATTATTTGTCGGTCAAAT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAA-AATTTAG-TCGTATTATTTGTCGGTCAAAT
*
38752444 TTTATATTTTTGTATATCAATTTTCT
64 TTTATATTTTCGTATATCAATTTTCT
*
38752470 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAGTTGGTATTATTTGT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAG-TCGTATTATTTGT
38752525 TTATTGAATT
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
89 12 0.10
90 100 0.84
91 7 0.06
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.51
Consensus pattern (89 bp):
AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAGTCGTATTATTTGTCGGTCAAATTT
TATATTTTCGTATATCAATTTTCT
Found at i:38752588 original size:16 final size:17
Alignment explanation
Indices: 38752563--38752596 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38752553 GAATGCTTGT
38752563 ATTTTCTTATATATGTA
1 ATTTTCTTATATATGTA
*
38752580 ATTTT-TTATATCTGTA
1 ATTTTCTTATATATGTA
38752596 A
1 A
38752597 ATAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTTCTTATATATGTA
Found at i:38755670 original size:16 final size:16
Alignment explanation
Indices: 38755649--38755683 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
38755639 TTAATTATGA
38755649 ATATTAATATTCATGG
1 ATATTAATATTCATGG
*
38755665 ATATTACTATTCATGG
1 ATATTAATATTCATGG
38755681 ATA
1 ATA
38755684 GATGAGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (16 bp):
ATATTAATATTCATGG
Found at i:38767765 original size:31 final size:29
Alignment explanation
Indices: 38767721--38767785 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
38767711 TGTTTTGTTA
*
38767721 TGGTACTTATATTTTTATAAAATATAAAATG
1 TGGTACATATA-TTTTA-AAAATATAAAATG
* **
38767752 TGGTACATGTATTTTAAAAATATTTAATG
1 TGGTACATATATTTTAAAAATATAAAATG
38767781 TGGTA
1 TGGTA
38767786 TCTAAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 5 0.17
31 9 0.30
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (29 bp):
TGGTACATATATTTTAAAAATATAAAATG
Found at i:38768122 original size:21 final size:21
Alignment explanation
Indices: 38768079--38768120 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
38768069 CCATCTAAAA
38768079 TAATAATTTTAATTGATTTTT
1 TAATAATTTTAATTGATTTTT
38768100 TAATAATTATT-ATT-ATTTTT
1 TAATAATT-TTAATTGATTTTT
38768120 T
1 T
38768121 TATCAACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TAATAATTTTAATTGATTTTT
Found at i:38769805 original size:26 final size:28
Alignment explanation
Indices: 38769744--38769806 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
38769734 AATATATATA
*
38769744 TTTATATATTTATAATTTTTTTAATAAT
1 TTTATATATTTATAATTTTATTAATAAT
* * *
38769772 TTTCTATATTTCTTA-TTTATTAA-AAT
1 TTTATATATTTATAATTTTATTAATAAT
38769798 TTTATATAT
1 TTTATATAT
38769807 AATCATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 11 0.37
27 7 0.23
28 12 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTATATATTTATAATTTTATTAATAAT
Found at i:38772472 original size:26 final size:28
Alignment explanation
Indices: 38772411--38772473 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
38772401 AATATATATA
*
38772411 TTTATATATTTATAATTTTTTTAATAAT
1 TTTATATATTTATAATTTTATTAATAAT
* * *
38772439 TTTCTATATTTCTTA-TTTATTAA-AAT
1 TTTATATATTTATAATTTTATTAATAAT
38772465 TTTATATAT
1 TTTATATAT
38772474 AGTCATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 11 0.37
27 7 0.23
28 12 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTATATATTTATAATTTTATTAATAAT
Found at i:38776141 original size:20 final size:20
Alignment explanation
Indices: 38776118--38776157 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38776108 TATTCAAACT
* *
38776118 ATATTACTTGAATAGTTATA
1 ATATTACATGAATAATTATA
*
38776138 ATATTAGATGAATAATTATA
1 ATATTACATGAATAATTATA
38776158 TGTCTTTTTT
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:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:38778828 original size:11 final size:11
Alignment explanation
Indices: 38778812--38778839 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
38778802 TGACTTTAGA
38778812 GTATGTATTTT
1 GTATGTATTTT
38778823 GTATGTATTTT
1 GTATGTATTTT
38778834 GTATGT
1 GTATGT
38778840 TAGACTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (11 bp):
GTATGTATTTT
Found at i:38779024 original size:15 final size:16
Alignment explanation
Indices: 38779004--38779033 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38778994 CAATATTGCC
38779004 TTGTTTTGGT-TAAAG
1 TTGTTTTGGTATAAAG
38779019 TTGTTTTGGTATAAA
1 TTGTTTTGGTATAAA
38779034 TGATGTGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (16 bp):
TTGTTTTGGTATAAAG
Found at i:38782567 original size:18 final size:18
Alignment explanation
Indices: 38782530--38782581 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
38782520 AAAAGTCTAG
*
38782530 AAAAATACAAATAAACAA
1 AAAAATAAAAATAAACAA
38782548 AAAAATAAAAATAAGA-AA
1 AAAAATAAAAATAA-ACAA
*
38782566 AAATATAAAAAATAAA
1 AAAAAT-AAAAATAAA
38782582 TGGATTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAATAAACAA
Found at i:38784240 original size:21 final size:22
Alignment explanation
Indices: 38784218--38784329 Score: 126
Period size: 21 Copynumber: 5.1 Consensus size: 22
38784208 AAACTTATAT
*
38784218 TAATAAATGAATAA-AA-AATAT
1 TAATAAAT-AATAATAATAATAA
*
38784239 TAATATATTAATAAATAAATGAATAA
1 TAATA-AATAAT-AAT-AAT-AATAA
38784265 TAAT-AATAATAATAATAATAA
1 TAATAAATAATAATAATAATAA
38784286 TAAT-AATAATAATAATAATAA
1 TAATAAATAATAATAATAATAA
38784307 TAAT-AATAATAATAATAATAA
1 TAATAAATAATAATAATAATAA
38784328 TA
1 TA
38784330 GAAGAAATGT
Statistics
Matches: 82, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
21 57 0.70
22 7 0.09
23 3 0.04
24 7 0.09
26 8 0.10
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAAATAATAATAATAATAA
Found at i:38784268 original size:3 final size:3
Alignment explanation
Indices: 38784260--38784329 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
38784250 TAAATAAATG
38784260 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38784308 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
38784330 GAAGAAATGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38786425 original size:42 final size:43
Alignment explanation
Indices: 38786319--38786435 Score: 166
Period size: 43 Copynumber: 2.7 Consensus size: 43
38786309 TACCAGTGCT
* *
38786319 ATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCA
1 ATATCCCAGATATGGTCTTACATGTAATCTCATATCAATGCCA
* *
38786362 ATAGCCCAGCTATGGTCTTACATG-AAGTCTCATATCAATGCC-
1 ATATCCCAGATATGGTCTTACATGTAA-TCTCATATCAATGCCA
*
38786404 ATATCCCAGATATAGTCTTACATGTAATCTCA
1 ATATCCCAGATATGGTCTTACATGTAATCTCA
38786436 GTAACCCTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 28 0.43
43 37 0.57
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (43 bp):
ATATCCCAGATATGGTCTTACATGTAATCTCATATCAATGCCA
Found at i:38789597 original size:139 final size:139
Alignment explanation
Indices: 38789347--38789624 Score: 556
Period size: 139 Copynumber: 2.0 Consensus size: 139
38789337 TGTATGAGCT
38789347 TGAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAGGTTGTTTTGCGAGAA
1 TGAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAGGTTGTTTTGCGAGAA
38789412 AACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACCGAAATGTCTCATCTCTTAAAATCCCTAC
66 AACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACCGAAATGTCTCATCTCTTAAAATCCCTAC
38789477 CTTTAGTCA
131 CTTTAGTCA
38789486 TGAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAGGTTGTTTTGCGAGAA
1 TGAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAGGTTGTTTTGCGAGAA
38789551 AACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACCGAAATGTCTCATCTCTTAAAATCCCTAC
66 AACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACCGAAATGTCTCATCTCTTAAAATCCCTAC
38789616 CTTTAGTCA
131 CTTTAGTCA
38789625 AGCCCCATTA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 139 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (139 bp):
TGAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAGGTTGTTTTGCGAGAA
AACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACCGAAATGTCTCATCTCTTAAAATCCCTAC
CTTTAGTCA
Found at i:38790790 original size:7 final size:7
Alignment explanation
Indices: 38790757--38790788 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38790747 ACATTTCTAA
38790757 TCATCCC
1 TCATCCC
38790764 TCATCCC
1 TCATCCC
38790771 TCATCCC
1 TCATCCC
*
38790778 TCATTCC
1 TCATCCC
38790785 TCAT
1 TCAT
38790789 TCATTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (7 bp):
TCATCCC
Found at i:38796706 original size:29 final size:29
Alignment explanation
Indices: 38796664--38796734 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
38796654 GTTCTTCAAC
*
38796664 ATAGTTTGATTTGATTGTTAATTGGTGTG
1 ATAGTTTGATTTGATTGTTAATTGGTGCG
38796693 ATAGTTTGATTTGATTGTTAATTGGTGCG
1 ATAGTTTGATTTGATTGTTAATTGGTGCG
38796722 A-A--TTGATTTGATT
1 ATAGTTTGATTTGATT
38796735 AAATCATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 11 0.27
28 1 0.02
29 29 0.71
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (29 bp):
ATAGTTTGATTTGATTGTTAATTGGTGCG
Found at i:38797059 original size:125 final size:127
Alignment explanation
Indices: 38796905--38797203 Score: 338
Period size: 125 Copynumber: 2.4 Consensus size: 127
38796895 GCCACACGGC
* * * * *
38796905 TGTGTGT-CAGGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACATACGCTAGAAACACGAGCA
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
* **
38796969 TGTGTCTAGGCATG-CAACTCA-T-TGTTTGTGAATTAGGGTCACACGG-GCTAAAGACATGGG
66 TGTGTCCAGGC-TGACAACTCACTAT-TTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
* * ** * **
38797029 TGTGTGTCCAGGCTGTGTAATTCACTGTTTGTGAATTAGGGTCAGACGGGCAAGAGACACGAATG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
* * *
38797094 TGTGTCCAGGCTGTATAACTCACTATTTTTTGAATTAGGGTCACACGGAGCTAAAGACCCCGG
66 TGTGTCCAGGCTG-ACAACTCACTATTTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
* * * *
38797157 CGTGTGTCTAGGCTGTGTAACTCACTATTTATGAATTAGGGTCACAC
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACAC
38797204 GATCCAGAGA
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
124 9 0.06
125 55 0.38
126 6 0.04
127 22 0.15
128 53 0.37
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (127 bp):
TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
TGTGTCCAGGCTGACAACTCACTATTTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
Found at i:38797066 original size:63 final size:63
Alignment explanation
Indices: 38796905--38797204 Score: 304
Period size: 63 Copynumber: 4.8 Consensus size: 63
38796895 GCCACACGGC
* * ***
38796905 TGTGTGT-CAGGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACATACGCTAGAA-ACACGAG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTA-AAGACACGAG
** * * * * * *
38796967 CATGTGTCTAGGC-ATGCAACTCATTGTTTGTGAATTAGGGTCACACGGGCTAAAGACATGGG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAAAGACACGAG
* * *
38797029 TGTGTGTCCAGGCTGTGTAATTCACTGTTTGTGAATTAGGGTCAGACGGGC-AAGAGACACGAA
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAA-AGACACGAG
* * * *
38797092 TGTGTGTCCAGGCTGTATAACTCACTATTTTTTGAATTAGGGTCACACGGAGCTAAAGACCCCG-
1 TGTGTGTCCAGGCTGTGTAACTCACT-GTTTGTGAATTAGGGTCACACGG-GCTAAAGA-CACGA
38797156 G
63 G
* * * *
38797157 CGTGTGTCTAGGCTGTGTAACTCACTATTTATGAATTAGGGTCACACG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACG
38797205 ATCCAGAGAC
Statistics
Matches: 195, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
61 2 0.01
62 54 0.28
63 66 0.34
64 40 0.21
65 28 0.14
66 5 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (63 bp):
TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAAAGACACGAG
Found at i:38799109 original size:22 final size:23
Alignment explanation
Indices: 38799071--38799116 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
38799061 TAATTAGAGA
*
38799071 AATATGATTTTATTGA-TATTTT
1 AATAAGATTTTATTGATTATTTT
38799093 AATAAGATATTTA-TGATTATTTT
1 AATAAGAT-TTTATTGATTATTTT
38799116 A
1 A
38799117 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (23 bp):
AATAAGATTTTATTGATTATTTT
Found at i:38803623 original size:16 final size:16
Alignment explanation
Indices: 38803602--38803632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38803592 TTTGCTATTA
*
38803602 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
38803618 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
38803633 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:38805120 original size:24 final size:24
Alignment explanation
Indices: 38805092--38805137 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38805082 CAGTGGTGCC
38805092 GGCGGTTGCGTCA-CAATGGTTGGT
1 GGCGGTTG-GTCATCAATGGTTGGT
*
38805116 GGCGGTTGGTCATCAGTGGTTG
1 GGCGGTTGGTCATCAATGGTTG
38805138 AGTAGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.15, G:0.43, T:0.30
Consensus pattern (24 bp):
GGCGGTTGGTCATCAATGGTTGGT
Found at i:38807263 original size:19 final size:19
Alignment explanation
Indices: 38807239--38807288 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
38807229 ATTCTAACCT
38807239 TGTCTCATAAAAATTCAAA
1 TGTCTCATAAAAATTCAAA
38807258 TGTCTCATAAAAATTCAAA
1 TGTCTCATAAAAATTCAAA
*
38807277 TATCTCATAAAA
1 TGTCTCATAAAA
38807289 TGAAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (19 bp):
TGTCTCATAAAAATTCAAA
Found at i:38809120 original size:26 final size:26
Alignment explanation
Indices: 38809087--38809139 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
38809077 AAAAATTACA
38809087 TTTTTGCCCCTAAACTTTGTCATATT
1 TTTTTGCCCCTAAACTTTGTCATATT
38809113 TTTTTGCCCCTAAACTTTGTCATATT
1 TTTTTGCCCCTAAACTTTGTCATATT
38809139 T
1 T
38809140 ACACTTTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTTTGCCCCTAAACTTTGTCATATT
Found at i:38814280 original size:42 final size:42
Alignment explanation
Indices: 38814220--38814300 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
38814210 GTGCAGGTTT
* *
38814220 CACACGGCCAAGATACACACCTATGT-TCTAGGCCATGTGTTA
1 CACACGGCCAAGACACACACCTATGTCTCT-GCCCATGTGTTA
**
38814262 CACACGGCTGAGACACACACCTATGTCTCTGCCCATGTG
1 CACACGGCCAAGACACACACCTATGTCTCTGCCCATGTG
38814301 CTTAATTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (42 bp):
CACACGGCCAAGACACACACCTATGTCTCTGCCCATGTGTTA
Found at i:38817751 original size:16 final size:16
Alignment explanation
Indices: 38817727--38817759 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38817717 TTTTATATAT
*
38817727 TAAATTATTATATTAA
1 TAAAATATTATATTAA
38817743 TAAAATATTATATTAA
1 TAAAATATTATATTAA
38817759 T
1 T
38817760 TAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:38817959 original size:5 final size:5
Alignment explanation
Indices: 38817949--38817980 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
38817939 TTATTAATTA
38817949 AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
38817981 AGTAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:38818497 original size:44 final size:44
Alignment explanation
Indices: 38818447--38818535 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
38818437 TGTTTAGGGA
* *
38818447 TACTTCGACCTT-GAGTCGATGAGGCA-CTATGAGTGTCGTACTGT
1 TACTTCGA-CTTCAAGTCGATAAGGCACCT-TGAGTGTCGTACTGT
*
38818491 TACTTCGACTTCAAGTCGATAAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
38818535 T
1 T
38818536 GCTATTACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 3 0.08
44 35 0.88
45 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (44 bp):
TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
Found at i:38821864 original size:22 final size:22
Alignment explanation
Indices: 38821825--38821866 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
38821815 ATATTGTGTA
*
38821825 ACATATCATAACACATCTCATG
1 ACATATCATAACAAATCTCATG
* *
38821847 ACATATCTTAGCAAATCTCA
1 ACATATCATAACAAATCTCA
38821867 AATCATATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (22 bp):
ACATATCATAACAAATCTCATG
Found at i:38823134 original size:206 final size:206
Alignment explanation
Indices: 38822775--38823181 Score: 672
Period size: 206 Copynumber: 2.0 Consensus size: 206
38822765 AAACTTGGCA
*
38822775 TCCTGAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
1 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
* * * *
38822840 GGCTATTTTGGGGTGGTTTCATGACCTTCCCGACGGCCACACGGGCGTGTGCTGAGGCACACGAC
66 GGCTATTTTGGGGTGGTGTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
* *
38822905 TGTGTGGATTTGGGGATTAGGGTTT-TGAGCCAAATTTGGTGCAACACGACTGTGTGACCGATTG
131 TGTGTGGATTTGGGGATTAGGGTTTCAG-GCCAAATTTGGTGCAACACGACCGTGTGACCGATTG
38822969 GGGGATTAGGCT
195 GGGGATTAGGCT
*
38822981 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTGGTTTGGG
1 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
* * * *
38823046 GGCTATTTTGGGGTGGTGTCGTGACCTCCCCTACTGCCACACGGGCATGTGCTAAGGCACACGGC
66 GGCTATTTTGGGGTGGTGTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
* *
38823111 TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAATACGACCGTGTGATCGATTGG
131 TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAACACGACCGTGTGACCGATTGG
38823176 GGGATT
196 GGGATT
38823182 TTGTCATTTC
Statistics
Matches: 186, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
206 185 0.99
207 1 0.01
ACGTcount: A:0.16, C:0.17, G:0.37, T:0.30
Consensus pattern (206 bp):
TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
GGCTATTTTGGGGTGGTGTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAACACGACCGTGTGACCGATTGG
GGGATTAGGCT
Found at i:38826349 original size:16 final size:15
Alignment explanation
Indices: 38826331--38826404 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 15
38826321 TCTCATTTTA
*
38826331 ATTATTCTTTTTATT
1 ATTATTATTTTTATT
38826346 AATTATTTATTTTTATT
1 -ATTA-TTATTTTTATT
*
38826363 GTTATAATATTTTTATT
1 ATTAT--TATTTTTATT
*
38826380 ATTCTTATTTTTA-T
1 ATTATTATTTTTATT
38826394 -TTATTATTTTT
1 ATTATTATTTTT
38826405 CTTTTCTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
15 9 0.18
16 7 0.14
17 23 0.46
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (15 bp):
ATTATTATTTTTATT
Found at i:38829579 original size:8 final size:8
Alignment explanation
Indices: 38829567--38829606 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
38829557 CAAGAGCACC
*
38829567 AAAAGAAC
1 AAAAGAAA
38829575 AAAAGAAA
1 AAAAGAAA
38829583 ACAAAGAAA
1 A-AAAGAAA
*
38829592 GAAAGAAA
1 AAAAGAAA
38829600 AAAAGAA
1 AAAAGAA
38829607 TAGGAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:38829590 original size:17 final size:17
Alignment explanation
Indices: 38829576--38829621 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
38829566 CAAAAGAACA
38829576 AAAGAAAACAAAGAAAG
1 AAAGAAAACAAAGAAAG
38829593 AAAGAAAA-AAAGAATAG
1 AAAGAAAACAAAGAA-AG
*
38829610 GAAGAAAACAAA
1 AAAGAAAACAAA
38829622 ACAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 17 0.65
18 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAGAAAACAAAGAAAG
Found at i:38831503 original size:17 final size:18
Alignment explanation
Indices: 38831461--38831503 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
38831451 TAAATAAATC
38831461 TAAA-TAAAACTCTTAAG
1 TAAACTAAAACTCTTAAG
* *
38831478 TATACTAAAACTC-TAAT
1 TAAACTAAAACTCTTAAG
38831495 TAAACTAAA
1 TAAACTAAA
38831504 CAAGAAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAACTAAAACTCTTAAG
Found at i:38832240 original size:13 final size:14
Alignment explanation
Indices: 38832217--38832245 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38832207 TAACCATAAA
38832217 TTTAGCCTTTTATG
1 TTTAGCCTTTTATG
38832231 TTTA-CCTTTTATG
1 TTTAGCCTTTTATG
38832244 TT
1 TT
38832246 ATATTGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (14 bp):
TTTAGCCTTTTATG
Found at i:38833649 original size:26 final size:28
Alignment explanation
Indices: 38833620--38833676 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
38833610 TCAGTAACTT
*
38833620 AAATAAAAATTTTTA-AAT-AATTGACC
1 AAATAAAAATTTTTATAATCAAGTGACC
** *
38833646 AAATTTAACTTTTTATAATCAAGTGACC
1 AAATAAAAATTTTTATAATCAAGTGACC
38833674 AAA
1 AAA
38833677 ACGAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 12 0.48
27 3 0.12
28 10 0.40
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (28 bp):
AAATAAAAATTTTTATAATCAAGTGACC
Found at i:38845103 original size:135 final size:138
Alignment explanation
Indices: 38844820--38845233 Score: 640
Period size: 135 Copynumber: 3.0 Consensus size: 138
38844810 AGTGGGAGGC
*
38844820 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCGGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* *
38844885 TGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCG
66 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
38844950 GTTTTTCT
131 GTTTTTCT
* * *
38844958 TCTGGATCATATTGTCTACT-TCCGACGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCC
1 TCTGGATCATATTGTCTA-TATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCC
* ** *
38845022 TCAAGTTTGAAGCAGAAAAATCGGATCCTCCAT-C-T-TTT-TTGGCCCAATTCCTCGTCTTTTC
65 TCGAGTTTGAAGCAGACGAATCAGATCCTCC-TCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTC
*
38845083 CTGTTTTTCT
129 CAGTTTTTCT
*
38845093 TCTGGATCATATTGTCTATGTCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* * *
38845158 CGAGTTTGAAGCATACGAATCAGATCCTCCTCCGTCTTTCTTTGCCCAATTCCTTGTCTTTTCCA
66 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
38845223 GTTTTTCT
131 GTTTTTCT
38845231 TCT
1 TCT
38845234 CTAGTTGCTT
Statistics
Matches: 248, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
134 2 0.01
135 118 0.48
136 4 0.02
137 4 0.02
138 118 0.48
139 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (138 bp):
TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
GTTTTTCT
Found at i:38849434 original size:73 final size:73
Alignment explanation
Indices: 38849315--38849518 Score: 239
Period size: 73 Copynumber: 2.7 Consensus size: 73
38849305 GTCATGAGAG
* * * *
38849315 TGTTCACCAAATAAGTTCATAAAAAATGACAATTTTAAATAAATTAAAAGTATACATTAATCAAA
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGTATACATTAACCAAA
38849380 TTCAATTA
66 TTCAATTA
* * *
38849388 TGTTCACCGAATAAGTTTAAAAAAAATAACAATTTAAAATAAATTAAAGCCATTAAATATATACA
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATT------A--AAA-GTATACA
38849453 TTAACCAAATTCAATTA
57 TTAACCAAATTCAATTA
* *
38849470 TGTTCACCAAATAAG-TTCATAAAAATGACAATTTAAAATAAATTAAAAG
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAG
38849519 CAATTAAATA
Statistics
Matches: 110, Mismatches: 12, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
73 43 0.39
75 1 0.01
79 1 0.01
81 29 0.26
82 36 0.33
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (73 bp):
TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGTATACATTAACCAAA
TTCAATTA
Found at i:38849444 original size:82 final size:82
Alignment explanation
Indices: 38849356--38849548 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 82
38849346 ATTTTAAATA
* *
38849356 AATTAAA-AGTATACATTAATCAAATTCAATTATGTTCACCGAATAAGTTTAAAAAAAATAACAA
1 AATTAAATA-TATACATTAACCAAATTCAATTATGTTCACCAAATAAG-TTAAAAAAAATAACAA
38849420 TTTAAAATAAATT-AAAGC
64 TTTAAAATAAATTAAAAGC
* * * *
38849438 CATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTCATAAAAATGACAATT
1 AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTAAAAAAAATAACAATT
38849503 TAAAATAAATTAAAAGC
66 TAAAATAAATTAAAAGC
*
38849520 AATTAAATATATACATTAACCGAATTCAA
1 AATTAAATATATACATTAACCAAATTCAA
38849549 ATTGCCGCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 26 0.26
82 74 0.73
83 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (82 bp):
AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTAAAAAAAATAACAATT
TAAAATAAATTAAAAGC
Found at i:38852257 original size:20 final size:20
Alignment explanation
Indices: 38852232--38852285 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
38852222 AAGTTAAGTA
*
38852232 TTTATATTAAATTAATATAT
1 TTTATATTAAATTAAGATAT
*
38852252 TTTATAATAAATTTAAGATAT
1 TTTATATTAAA-TTAAGATAT
38852273 TTTATATTTAAAT
1 TTTATA-TTAAAT
38852286 ATATTCTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTATATTAAATTAAGATAT
Found at i:38852272 original size:21 final size:20
Alignment explanation
Indices: 38852219--38852278 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
38852209 TTGTAGATTA
*
38852219 AATAAGTTAAG-TA-TTTAT
1 AATAAATTAAGATATTTTAT
* *
38852237 ATTAAATTAATATATTTTAT
1 AATAAATTAAGATATTTTAT
38852257 AATAAATTTAAGATATTTTAT
1 AATAAA-TTAAGATATTTTAT
38852278 A
1 A
38852279 TTTAAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 10 0.29
21 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
AATAAATTAAGATATTTTAT
Found at i:38852331 original size:18 final size:20
Alignment explanation
Indices: 38852308--38852346 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38852298 ATTAATAGTT
*
38852308 TATA-TTATA-ATTTTTTTA
1 TATATTTATATATTATTTTA
38852326 TATATTTATATATTATTTTA
1 TATATTTATATATTATTTTA
38852346 T
1 T
38852347 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTTATATATTATTTTA
Found at i:38855525 original size:43 final size:43
Alignment explanation
Indices: 38855444--38855525 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
38855434 AAGTCGTACA
**
38855444 ATGCCAACGTCCCAGACGTGGTCTTACATGTAGTCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
38855487 ATGCC-ACAGTCCCAGACAG-GGTCTTAC-TCGTAAACACAT
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAT-GTAAACACAT
38855526 CTCGGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 3 0.09
43 30 0.88
44 1 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:38855583 original size:30 final size:30
Alignment explanation
Indices: 38855549--38855608 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
38855539 ATCGATGCCA
38855549 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
38855579 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
38855609 CTATGTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (30 bp):
TGGTCTTACTCGCACACATATATCAGAATC
Found at i:38861670 original size:29 final size:30
Alignment explanation
Indices: 38861632--38861746 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
38861622 TAAAAAATAA
* *
38861632 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
38861662 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
38861691 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
38861721 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
38861747 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:38861698 original size:30 final size:30
Alignment explanation
Indices: 38861632--38861747 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
38861622 TAAAAAATAA
* *
38861632 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
38861662 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
38861691 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
38861721 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
38861748 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:38861753 original size:29 final size:29
Alignment explanation
Indices: 38861629--38861760 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
38861619 TTTTAAAAAA
* *
38861629 TAAAAATTGCATTTTGACCCCTAAACTTT-
1 TAAAAATTTCATTTT-AACCCTAAACTTTC
*** *
38861658 TCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
38861688 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
38861718 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
38861747 TAAAAATTACATTT
1 TAAAAATTTCATTT
38861761 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:38861754 original size:59 final size:59
Alignment explanation
Indices: 38861629--38861754 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
38861619 TTTTAAAAAA
* * *
38861629 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
** * * *
38861688 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTC
38861747 TAAAAATT
1 TAAAAATT
38861755 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 36 0.65
60 15 0.27
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
Found at i:38862315 original size:14 final size:14
Alignment explanation
Indices: 38862282--38862322 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
38862272 AAAAAGCAGC
38862282 AAAAA-AAGAAG-A
1 AAAAAGAAGAAGAA
* *
38862294 AGAAAGAAGTAGAA
1 AAAAAGAAGAAGAA
38862308 AAAAAGAAGAAGAA
1 AAAAAGAAGAAGAA
38862322 A
1 A
38862323 GAAGCAGCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 14 0.61
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (14 bp):
AAAAAGAAGAAGAA
Found at i:38862960 original size:17 final size:17
Alignment explanation
Indices: 38862917--38862964 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
38862907 AGAAAAAAAT
38862917 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
38862936 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
38862952 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
38862965 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:38863067 original size:16 final size:16
Alignment explanation
Indices: 38863019--38863067 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
38863009 TTTCTTTCTA
*
38863019 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
38863035 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
38863052 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
38863068 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:38863114 original size:15 final size:14
Alignment explanation
Indices: 38863096--38863132 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
38863086 CTCGTGTTTC
38863096 AAAAAAATAAAAATA
1 AAAAAAATAAAAA-A
38863111 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
38863125 AATAAAAA
1 AA-AAAAA
38863133 AAATTCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAA
Found at i:38863116 original size:9 final size:9
Alignment explanation
Indices: 38863104--38863136 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
38863094 TCAAAAAAAT
38863104 AAAAATAAA
1 AAAAATAAA
38863113 AAAAATAAA
1 AAAAATAAA
38863122 AAAAATAAA
1 AAAAATAAA
38863131 AAAAAT
1 AAAAAT
38863137 TCTCGTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:38863251 original size:17 final size:18
Alignment explanation
Indices: 38863200--38863627 Score: 221
Period size: 18 Copynumber: 25.0 Consensus size: 18
38863190 AAATTTAGTG
38863200 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
38863218 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
38863236 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
38863252 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
38863269 TTTTCGTGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
38863287 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
38863305 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
38863322 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
38863340 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
38863356 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
38863374 TTCTCGCG-TTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
38863390 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
38863408 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
38863422 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
38863437 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
38863451 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
38863468 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
38863485 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
38863502 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
38863521 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
38863539 ATTTCGTTTTTTTCTAAAAA
1 TTTTCG-TGTTTTC-AAAAA
*
38863559 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
38863576 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
38863592 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
38863610 TTCTCGTATTTTTAAAAA
1 TTTTCGTGTTTTCAAAAA
38863628 AAAAACTTTC
Statistics
Matches: 316, Mismatches: 60, Indels: 68
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 3 0.01
16 46 0.15
17 110 0.35
18 112 0.35
19 16 0.05
20 11 0.03
21 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:38863330 original size:35 final size:35
Alignment explanation
Indices: 38863200--38863627 Score: 177
Period size: 34 Copynumber: 12.5 Consensus size: 35
38863190 AAATTTAGTG
*
38863200 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* * * *
38863235 ATCT-GTGTTTTCAAAAATTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
**
38863269 TTTTCGTGTTTAAAAAAATT-TACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAATTCT-CGTGTTTTCA-AAA
*
38863305 TTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
** * ** *
38863339 ACTCCAGTG-TTTCAAAGTTTC-CATGTTTTCAAAAA
1 TTTTC-GTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
* * * *
38863374 TTCTCGCG-TTTAAAAAAAT-TCGTG-TTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
** * **
38863406 TATTCTCG-CATTTC---AATT-T-TTGTTTTTTAAA
1 T-TT-TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* * *
38863437 ---TCGTG-TTTCAAAAAATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* * *
38863468 TTTTCGTG-TTTCTAAAATT-TCCCTGTTTTAAAAA
1 TTTTCGTGTTTTCAAAAATTCT-CGTGTTTTCAAAA
** * * *
38863502 TTCCCGTG-TTTCAAAAAAAATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTTC--AAAAATTCTCGTGTTTTCA-AAA
* * *
38863539 ATTTCGTTTTTTTCTAAAAATTTTCGTG-TTTCTAAAA
1 TTTTCG-TGTTTTC-AAAAATTCTCGTGTTTTC-AAAA
*
38863576 TTTTCGTG-TTT-ACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
* * *
38863610 TTCTCGTATTTTTAAAAA
1 TTTTCGTGTTTTCAAAAA
38863628 AAAAACTTTC
Statistics
Matches: 293, Mismatches: 67, Indels: 65
0.69 0.16 0.15
Matches are distributed among these distances:
26 7 0.02
29 3 0.01
30 3 0.01
31 19 0.06
32 5 0.02
33 21 0.07
34 106 0.36
35 59 0.20
36 35 0.12
37 18 0.06
38 13 0.04
39 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (35 bp):
TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
Found at i:38863339 original size:53 final size:51
Alignment explanation
Indices: 38863200--38863616 Score: 225
Period size: 51 Copynumber: 8.1 Consensus size: 51
38863190 AAATTTAGTG
38863200 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
* * * ** * *
38863252 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCT--GTGTTTTCAAAAA
* * * *
38863305 TTTTCGTGTTTCACAAATTCTCGTGTTTTCAAAAACTCCAGTG-TTTC-AAAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA-T-CTGTGTTTTCAAAAA
* * * * **
38863356 TTTCCATGTTTTCAAAAATTCTCGCGTTTAAAAAAAT-TCGTG-TTTCAAAATA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAATCT-GTGTTTTCAAAA-A
* ** **
38863408 TTCTCGCATTTC---AATTTT--TGTTTT-TTAAATC-GTG-TTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
* * * * **
38863451 ATGTCGTGTTTTAAAAATTTTCGTG-TTTCTAAAATTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTC-AAAA-ATCTGTGTTTTCAAAAA
** * * * * *
38863502 TTCCCGTGTTTCAAAAAAAATGTCGTGTTTTAAGAAAATTTCGTTTTTTTCTAAAAA
1 TTTTCGTGTTTC--AAAAATTTTCGTGTTTTCA-AAAATCT-G-TGTTTTC-AAAAA
* * *
38863559 TTTTCGTGTTTCTAAAATTTTCGTGTTTAC-AAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCT-GTGTTTTCAAAAA
*
38863610 TTCTCGT
1 TTTTCGT
38863617 ATTTTTAAAA
Statistics
Matches: 270, Mismatches: 68, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
43 8 0.03
44 11 0.04
45 4 0.01
46 10 0.04
47 3 0.01
48 7 0.03
49 2 0.01
50 9 0.03
51 69 0.26
52 44 0.16
53 63 0.23
54 7 0.03
55 18 0.07
57 15 0.06
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (51 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
Found at i:38863468 original size:16 final size:17
Alignment explanation
Indices: 38863437--38863627 Score: 117
Period size: 17 Copynumber: 10.9 Consensus size: 17
38863427 GTTTTTTAAA
* *
38863437 TCGTGTTTCAAAAAATG
1 TCGTGTTTCTAAAAATT
38863454 TCGTGTTT-TAAAAATTT
1 TCGTGTTTCTAAAAA-TT
38863471 TCGTGTTTCT-AAAATT
1 TCGTGTTTCTAAAAATT
*
38863487 TCCCTGTTT-TAAAAATT
1 T-CGTGTTTCTAAAAATT
* * *
38863504 CCCGTGTTTCAAAAAAAATG
1 -TCGTGTTTC--TAAAAATT
38863524 TCGTGTTT-TAAGAAAATT
1 TCGTGTTTCT-A-AAAATT
*
38863542 TCGTTTTTTTCTAAAAATTT
1 TCG--TGTTTCTAAAAA-TT
*
38863562 TCGTGTTTCTAAAATTT
1 TCGTGTTTCTAAAAATT
*
38863579 TCGTG-TT-TACAAATT
1 TCGTGTTTCTAAAAATT
38863594 CTCGTGTTT-TCAAAAATT
1 -TCGTGTTTCT-AAAAATT
* *
38863612 CTCGTATTTTTAAAAA
1 -TCGTGTTTCTAAAAA
38863628 AAAAACTTTC
Statistics
Matches: 139, Mismatches: 17, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.04
16 16 0.12
17 50 0.36
18 38 0.27
19 12 0.09
20 16 0.12
21 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCTAAAAATT
Found at i:38875562 original size:76 final size:76
Alignment explanation
Indices: 38875447--38875962 Score: 978
Period size: 76 Copynumber: 6.8 Consensus size: 76
38875437 TTAATTTCTG
38875447 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875512 AATTTCTGTTA
66 AATTTCTGTTA
*
38875523 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875588 AATTTCTGTTA
66 AATTTCTGTTA
38875599 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875664 AATTTCTGTTA
66 AATTTCTGTTA
38875675 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875740 AATTTCTGTTA
66 AATTTCTGTTA
38875751 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875816 AATTTCTGTTA
66 AATTTCTGTTA
38875827 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
38875892 AATTTCTGTTA
66 AATTTCTGTTA
* * * * *
38875903 TTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA
1 TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
38875963 TTTTTAGTTT
Statistics
Matches: 433, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 433 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (76 bp):
TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTGTTA
Found at i:38876128 original size:122 final size:123
Alignment explanation
Indices: 38875903--38876136 Score: 292
Period size: 122 Copynumber: 1.9 Consensus size: 123
38875893 ATTTCTGTTA
* ** *
38875903 TTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
* ***** ** *
38875968 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG
66 AATTTATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTG
** *
38876026 TTTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGATGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
*
38876090 AAATTTA-AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
66 -AATTTATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCT
38876137 CGGGGCACGC
Statistics
Matches: 93, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
122 82 0.88
123 11 0.12
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (123 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT
AATTTATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTG
Found at i:38876165 original size:191 final size:192
Alignment explanation
Indices: 38875909--38876260 Score: 670
Period size: 191 Copynumber: 1.8 Consensus size: 192
38875899 GTTATTTTTC
38875909 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
38875974 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
*
38876038 AACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGATGTATTTTTAAATTTAAAA
131 AACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGATGTATTTTTAAATTTAAAA
38876100 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
38876165 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
**
38876230 AACTCATATTGCAAGAGGTGAGTTGAGCCTC
131 AACTCATATTGCAAGAAATGAGTTGAGCCTC
38876261 GGCTCACATG
Statistics
Matches: 157, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
191 123 0.78
192 34 0.22
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (192 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
AACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGATGTATTTTTAAATTTAAAA
Found at i:38876301 original size:17 final size:18
Alignment explanation
Indices: 38876279--38876313 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38876269 TGCTGAGGTA
*
38876279 TTTTCAATTTATG-TTTT
1 TTTTCAATCTATGCTTTT
38876296 TTTTCAATCTATGCTTTT
1 TTTTCAATCTATGCTTTT
38876314 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTCAATCTATGCTTTT
Found at i:38876477 original size:85 final size:87
Alignment explanation
Indices: 38876218--38876477 Score: 280
Period size: 92 Copynumber: 2.9 Consensus size: 87
38876208 TAATTTTTGT
*
38876218 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGC-CACATGCTGAGGTATTT
* *
38876282 TCAATTTATGTTTTTTTTCAA-TCTATGC
64 TCAA---ATGCTGTTTTT-AATTCTA-GC
* * *
38876310 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGGCAC--GCTGAGGTATTTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGCCACATGCTGAGGTATTTT
* * *
38876373 CAATTTCTGCTTTACTAATTCTA-C
65 CAAATGCTG-TTT-TTAATTCTAGC
* * *
38876397 TTTTC-AAATCAACTCATATTGCAAGAGGTGAATTGAGTCTCAAGCCACATGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGCCACATGCTGAGGTATTTTC
38876461 AAATGCTGTTTTTAATT
66 AAATGCTGTTTTTAATT
38876478 TTTGTTTTTT
Statistics
Matches: 144, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
85 43 0.30
86 3 0.02
87 27 0.19
88 5 0.03
89 5 0.03
90 16 0.11
92 44 0.31
93 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGCCACATGCTGAGGTATTTTC
AAATGCTGTTTTTAATTCTAGC
Found at i:38877885 original size:55 final size:55
Alignment explanation
Indices: 38877820--38877929 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
38877810 GAGTTCACCA
38877820 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
* *
38877875 ACACCCTTTTACAATAATCCTATAGCAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
38877930 GTAATCCAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (55 bp):
ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
Found at i:38883930 original size:14 final size:14
Alignment explanation
Indices: 38883911--38883938 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38883901 TATACCTCTA
38883911 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
38883925 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
38883939 CATTAATATA
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:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTAATTGCTTAAC
Found at i:38887501 original size:24 final size:24
Alignment explanation
Indices: 38887463--38887515 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
38887453 ATTTCTAGAT
* *
38887463 ATTTTT-AAACTTTTAGAAAGCTCA
1 ATTTTTAAAAATTTAAGAAA-CTCA
*
38887487 ATTTTTAAAAATTTAAGAAACTTA
1 ATTTTTAAAAATTTAAGAAACTCA
38887511 ATTTT
1 ATTTT
38887516 GAAAGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTTTAAAAATTTAAGAAACTCA
Found at i:38889639 original size:6 final size:7
Alignment explanation
Indices: 38889619--38889643 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38889609 TAAAATCACA
38889619 TTATTTT
1 TTATTTT
38889626 TTATTTT
1 TTATTTT
38889633 TTATTTT
1 TTATTTT
38889640 TTAT
1 TTAT
38889644 ATAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTATTTT
Found at i:38889651 original size:14 final size:14
Alignment explanation
Indices: 38889620--38889671 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
38889610 AAAATCACAT
**
38889620 TATTTTTTATTTTT
1 TATTTTTTATTTAA
*
38889634 TATTTTTTATATAA
1 TATTTTTTATTTAA
38889648 TATTATTTTTAGTTTAA
1 TA-T-TTTTTA-TTTAA
38889665 TATTTTT
1 TATTTTT
38889672 ATTAAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 13 0.42
15 5 0.16
16 7 0.23
17 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTTAA
Found at i:38890724 original size:22 final size:23
Alignment explanation
Indices: 38890696--38890744 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
38890686 AATATAAATT
*
38890696 AAAATAAAT-TGAATAAAACATA
1 AAAATAAATCTGAAAAAAACATA
* *
38890718 AAAATAAATCTTAAAAAAATATA
1 AAAATAAATCTGAAAAAAACATA
38890741 AAAA
1 AAAA
38890745 GTTTAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAATCTGAAAAAAACATA
Found at i:38900614 original size:21 final size:21
Alignment explanation
Indices: 38900590--38900629 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38900580 GATTATATTT
*
38900590 ATATATTTTAAATATTATAAA
1 ATATATTTAAAATATTATAAA
38900611 ATATATTTAAAATATTATA
1 ATATATTTAAAATATTATA
38900630 GATCTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATTTAAAATATTATAAA
Found at i:38904824 original size:20 final size:20
Alignment explanation
Indices: 38904759--38904826 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
38904749 CCACATTTAC
*
38904759 TAAATTTTATTTTTTATTTGT
1 TAAATTTT-CTTTTTATTTGT
* * *
38904780 TTAATTTCCTTTTTCTTT-T
1 TAAATTTTCTTTTTATTTGT
38904799 TAAATTTTCTTTATT-TTTGT
1 TAAATTTTCTTT-TTATTTGT
*
38904819 TGAATTTT
1 TAAATTTT
38904827 TTTCACCACA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 14 0.37
20 18 0.47
21 6 0.16
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (20 bp):
TAAATTTTCTTTTTATTTGT
Found at i:38906274 original size:4 final size:4
Alignment explanation
Indices: 38906265--38906295 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
38906255 ATGTACACCA
38906265 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
38906296 ACTCATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:38909436 original size:21 final size:21
Alignment explanation
Indices: 38909407--38909446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38909397 TGACTACAAA
*
38909407 TCAGATTTTTGCTCCTGATTT
1 TCAGATTTTTCCTCCTGATTT
*
38909428 TCAGTTTTTTCCTCCTGAT
1 TCAGATTTTTCCTCCTGAT
38909447 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.53
Consensus pattern (21 bp):
TCAGATTTTTCCTCCTGATTT
Found at i:38913571 original size:39 final size:39
Alignment explanation
Indices: 38913528--38913607 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
38913518 TGTAATTGTA
38913528 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
** *
38913567 AATCAATGAGCTGTTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
38913606 AA
1 AA
38913608 CTTAGAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
Found at i:38913683 original size:94 final size:94
Alignment explanation
Indices: 38913574--38913759 Score: 282
Period size: 94 Copynumber: 2.0 Consensus size: 94
38913564 ACTAATCAAT
* * * * *
38913574 GAGCTGTTTGGAGTTGCGATTGTAAATCAACTAACTTAGAAGAAATTGTTCATGATCGTAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
*
38913639 ATGAACTTAGGTTATGATCGTAAATCAGC
66 ATGAACTCAGGTTATGATCGTAAATCAGC
* * *
38913668 GAGCTATTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAATAAATTGTTCATGATTATAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
*
38913733 ATGAACTCAGGTTGTGATCGTAAATCA
66 ATGAACTCAGGTTATGATCGTAAATCA
38913760 ATGAGCCTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (94 bp):
GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
ATGAACTCAGGTTATGATCGTAAATCAGC
Found at i:38913853 original size:130 final size:130
Alignment explanation
Indices: 38913653--38913990 Score: 435
Period size: 130 Copynumber: 2.6 Consensus size: 130
38913643 ACTTAGGTTA
* * * * * *
38913653 TGATCGTAAATCAGCGAGCTATTTGGAGTTGA-GATCGTAAATCAGCTAACTCAGAATAAATTGT
1 TGATCATAAATCAACGAGTTGTTTGGAGTT-ACAATCGTAAATCAGCTAACTCAGAAGAAATTGT
* * *
38913717 TCATGATTATAAATCAATGAACTCAGGTTGTGATCGTAAATCAATGAGCCTTAATAATATCAACC
65 TCATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACC
38913782 G
130 G
** * * * *
38913783 TGATTGTAAATCAATGAGTTGTTTGGAGTTACAATTGTAAATCAGCTAACTAAAAAGAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* * * *
38913848 CATGATTGTAAATCAATGAACTTAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAGCTG
66 CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
* * * *
38913913 TGATCATAAATCAGCGAGTTGTTTGGAGTTGCGATCGTAAATCAACTAACTCAGAAGAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* *
38913978 TATGATCATAAAT
66 CATGATTATAAAT
38913991 TAGTGAGCCT
Statistics
Matches: 177, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
129 1 0.01
130 176 0.99
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (130 bp):
TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
Done.