Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 13 of 33
Found at i:1937509 original size:41 final size:41
Alignment explanation
Indices: 1937452--1937545 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1937442 CTGCCAAGAA
1937452 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1937493 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1937534 ATGTATCGATAC
1 ATGTATCGATAC
1937546 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1942446 original size:18 final size:18
Alignment explanation
Indices: 1942413--1942461 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1942403 ATCGCGCAAC
*
1942413 TCGATGATCCTGAGCACA
1 TCGATGATCCTAAGCACA
* *
1942431 TCGATGATCTTAAGCACC
1 TCGATGATCCTAAGCACA
* *
1942449 CCGATGCTCCTAA
1 TCGATGATCCTAA
1942462 AGGCCATGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (18 bp):
TCGATGATCCTAAGCACA
Found at i:1943033 original size:15 final size:15
Alignment explanation
Indices: 1943013--1943046 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1943003 ATCTTGAAAT
1943013 ATATTG-ATATGTTGG
1 ATATTGAATATGTT-G
1943028 ATATTGAATATGTTG
1 ATATTGAATATGTTG
1943043 ATAT
1 ATAT
1943047 ATTAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (15 bp):
ATATTGAATATGTTG
Found at i:1943037 original size:24 final size:23
Alignment explanation
Indices: 1942979--1943046 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
1942969 ATATGCTTAC
* * * *
1942979 GATATTGAGTTTATTAACATGTT
1 GATATTGAATATATTGATATGTT
*
1943002 GATCTTGAAATATATTGATATGTT
1 GATATTG-AATATATTGATATGTT
*
1943026 GGATATTGAATATGTTGATAT
1 -GATATTGAATATATTGATAT
1943047 ATTAGTATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 6 0.17
24 24 0.67
25 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (23 bp):
GATATTGAATATATTGATATGTT
Found at i:1944322 original size:24 final size:24
Alignment explanation
Indices: 1944281--1944338 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1944271 AAGATTCTAT
**
1944281 CTTAACCTTGTTGCAAGGTTATAC
1 CTTAACCTCATTGCAAGGTTATAC
* *
1944305 CTTAACCTCATTGTAAGGTTTTAC
1 CTTAACCTCATTGCAAGGTTATAC
*
1944329 TTTAACCTCA
1 CTTAACCTCA
1944339 AAGGTAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (24 bp):
CTTAACCTCATTGCAAGGTTATAC
Found at i:1946609 original size:19 final size:19
Alignment explanation
Indices: 1946551--1946609 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1946541 TATTATTCAA
*
1946551 AATTAAATTAATAATAA-TT
1 AATTAAATTTA-AATAATTT
**
1946570 AATTTAAATTTAAATTTTTT
1 AA-TTAAATTTAAATAATTT
1946590 AATTAAATTTAAATAATTT
1 AATTAAATTTAAATAATTT
1946609 A
1 A
1946610 TAGATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAATTTAAATAATTT
Found at i:1946632 original size:3 final size:3
Alignment explanation
Indices: 1946620--1946668 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1946610 TAGATATAAA
*
1946620 TAT T-T TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1946666 TAT
1 TAT
1946669 ACTCTTAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1947091 original size:11 final size:11
Alignment explanation
Indices: 1947046--1947114 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1947036 TATGGACGTG
1947046 TATA-TATATT
1 TATATTATATT
*
1947056 TATATTAGATT
1 TATATTATATT
**
1947067 GGTA-TA-ATT
1 TATATTATATT
1947076 T-TATTATATT
1 TATATTATATT
*
1947086 TATATTAATTTT
1 TATATT-ATATT
*
1947098 TATATTATAAT
1 TATATTATATT
1947109 TATATT
1 TATATT
1947115 TAAAATATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
8 2 0.04
9 5 0.11
10 10 0.21
11 20 0.43
12 10 0.21
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TATATTATATT
Found at i:1947110 original size:18 final size:19
Alignment explanation
Indices: 1947079--1947115 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1947069 TATAATTTTA
1947079 TTATATTTATATTA-ATTT
1 TTATATTTATATTATATTT
1947097 TTATA-TTATAATTATATTT
1 TTATATTTAT-ATTATATTT
1947116 AAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTTATATTATATTT
Found at i:1947886 original size:20 final size:20
Alignment explanation
Indices: 1947863--1947904 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1947853 TGTATTTTAT
*
1947863 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATATAAA
1947883 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAA
1947903 AT
1 AT
1947905 TTTGATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:1947982 original size:24 final size:25
Alignment explanation
Indices: 1947950--1947997 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1947940 AATATATTTG
*
1947950 TATTGTGTT-CATTTTATTTTTTTA
1 TATTATGTTACATTTTATTTTTTTA
*
1947974 TATTATGTTATATTTTATTTTTTT
1 TATTATGTTACATTTTATTTTTTT
1947998 TTTACATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (25 bp):
TATTATGTTACATTTTATTTTTTTA
Found at i:1949028 original size:2 final size:2
Alignment explanation
Indices: 1949016--1949044 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1949006 TGCCAATGAG
1949016 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1949045 GTTATCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1952170 original size:2 final size:2
Alignment explanation
Indices: 1952165--1952194 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1952155 TAATATATGC
*
1952165 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1952195 CTATCACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1953109 original size:22 final size:22
Alignment explanation
Indices: 1953070--1953120 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1953060 CCATAAATAT
* *
1953070 TATATTTATATATATTTTATAA
1 TATAATTATATATATTTTAAAA
1953092 TATAATTATAT-TATTTTTAAAA
1 TATAATTATATATA-TTTTAAAA
*
1953114 TCTAATT
1 TATAATT
1953121 TTGATATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATTATATATATTTTAAAA
Found at i:1954620 original size:183 final size:183
Alignment explanation
Indices: 1954312--1954677 Score: 687
Period size: 183 Copynumber: 2.0 Consensus size: 183
1954302 AATATTATTG
1954312 CACACACCAAATAAAATTGATATTAAATTTGAAATTTATATTTGATGAAATAAAAATATACAAGC
1 CACACACCAAATAAAATTGATATTAAATTTGAAATTTATATTTGATGAAATAAAAATATACAAGC
* *
1954377 ATTATACATTATCAATACACTACTATATCCATGAATTTGTTAAAATAAAACAAAAATAAATTATA
66 ATTATACATTATCAATACACTACAATATCCATGAATTTCTTAAAATAAAACAAAAATAAATTATA
*
1954442 AAATTTATCCCCTTTTTATGCATAATATACACATCATATAATTTATTGATAAT
131 AAATTTATCCCCTTTTTATGCATAATATACACATCATATAATTCATTGATAAT
*
1954495 CACACACCGAATAAAATTGATATTAAATTTGAAATTTATATTTGATGAAATAAAAATATACAAGC
1 CACACACCAAATAAAATTGATATTAAATTTGAAATTTATATTTGATGAAATAAAAATATACAAGC
*
1954560 ATTATACATTATCAATACATTACAATATCCATGAATTTCTTAAAATAAAACAAAAATAAATTATA
66 ATTATACATTATCAATACACTACAATATCCATGAATTTCTTAAAATAAAACAAAAATAAATTATA
1954625 AAATTTATCCCCTTTTTATGCATAATATACACATCATATAATTCATTGATAAT
131 AAATTTATCCCCTTTTTATGCATAATATACACATCATATAATTCATTGATAAT
1954678 ATATAATTTA
Statistics
Matches: 178, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 178 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (183 bp):
CACACACCAAATAAAATTGATATTAAATTTGAAATTTATATTTGATGAAATAAAAATATACAAGC
ATTATACATTATCAATACACTACAATATCCATGAATTTCTTAAAATAAAACAAAAATAAATTATA
AAATTTATCCCCTTTTTATGCATAATATACACATCATATAATTCATTGATAAT
Found at i:1955820 original size:30 final size:30
Alignment explanation
Indices: 1955730--1955880 Score: 93
Period size: 30 Copynumber: 5.1 Consensus size: 30
1955720 AGTCTAAAAG
* * *
1955730 AATTTTTAAATTTT-ATCATTACACTTATATA
1 AATTTTTAATTTTTAAT--TTATACTTAAATA
* *
1955761 AATTTTTACATTTTT-ATTTGT--TAAAATA
1 AATTTTTA-ATTTTTAATTTATACTTAAATA
1955789 AATTTTTAATTTTTAATTTATACTTAAATA
1 AATTTTTAATTTTTAATTTATACTTAAATA
* *
1955819 AATCATTT-ATTTTCAATTTATA-TTAAATTA
1 AAT-TTTTAATTTTTAATTTATACTTAAA-TA
* * * * *
1955849 TACTCTTAAATTTTAATTTACAC--AAATA
1 AATTTTTAATTTTTAATTTATACTTAAATA
1955877 AATT
1 AATT
1955881 AATTTTTTTA
Statistics
Matches: 94, Mismatches: 18, Indels: 19
0.72 0.14 0.15
Matches are distributed among these distances:
27 6 0.06
28 22 0.23
29 10 0.11
30 38 0.40
31 11 0.12
32 7 0.07
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (30 bp):
AATTTTTAATTTTTAATTTATACTTAAATA
Found at i:1955979 original size:25 final size:25
Alignment explanation
Indices: 1955933--1955983 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
1955923 ATAAAAATTT
1955933 ATTTAAATACAATAAAATTTTAAAA
1 ATTTAAATACAATAAAATTTTAAAA
1955958 ATTTAAA-A-AATAAAATAATTTAAAA
1 ATTTAAATACAATAAAAT--TTTAAAA
1955983 A
1 A
1955984 CTTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 15 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATTTAAATACAATAAAATTTTAAAA
Found at i:1957831 original size:13 final size:13
Alignment explanation
Indices: 1957813--1957839 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1957803 AATCTTCCAC
1957813 ATCACATATGTTA
1 ATCACATATGTTA
1957826 ATCACATATGTTA
1 ATCACATATGTTA
1957839 A
1 A
1957840 CTAAGCTATT
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ATCACATATGTTA
Found at i:1959674 original size:29 final size:31
Alignment explanation
Indices: 1959610--1959674 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1959600 TTTGAAATAA
1959610 AGACTTGTTTAGATACAAATCAAAAATTTAT
1 AGACTTGTTTAGATACAAATCAAAAATTTAT
* *
1959641 -GACTTGTTTGGATA-AAAT-AAAAGTTTAT
1 AGACTTGTTTAGATACAAATCAAAAATTTAT
1959669 AGACTT
1 AGACTT
1959675 ATCTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.29
29 9 0.29
30 13 0.42
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (31 bp):
AGACTTGTTTAGATACAAATCAAAAATTTAT
Found at i:1961193 original size:2 final size:2
Alignment explanation
Indices: 1961186--1961217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1961176 AATATCAACA
1961186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1961218 TTCATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1969891 original size:16 final size:17
Alignment explanation
Indices: 1969855--1969897 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1969845 GTCATATGTA
*
1969855 ATTATATTTATATTCAT
1 ATTATTTTTATATTCAT
*
1969872 ATTATTTTTTTATT-AT
1 ATTATTTTTATATTCAT
1969888 ATTATTTTTA
1 ATTATTTTTA
1969898 AAATATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTTTATATTCAT
Found at i:1969992 original size:28 final size:29
Alignment explanation
Indices: 1969960--1970030 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1969950 TTTTAATGCA
1969960 TTATATTGTGTCGTA-ATTAT-ATTATTTT
1 TTATATTGTGTC-TATATTATAATTATTTT
* * *
1969988 TTATATTATAT-TATATTTTAATTATTTT
1 TTATATTGTGTCTATATTATAATTATTTT
1970016 TTATATTGTGTCTAT
1 TTATATTGTGTCTAT
1970031 GTTGTGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.06
27 4 0.11
28 26 0.74
29 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (29 bp):
TTATATTGTGTCTATATTATAATTATTTT
Found at i:1969997 original size:17 final size:16
Alignment explanation
Indices: 1969973--1970012 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
1969963 TATTGTGTCG
*
1969973 TAATTATATTATTTTT
1 TAATTATATTATATTT
1969989 TATATTATATTATATTT
1 TA-ATTATATTATATTT
1970006 TAATTAT
1 TAATTAT
1970013 TTTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTATATTATATTT
Found at i:1971193 original size:22 final size:22
Alignment explanation
Indices: 1971168--1971209 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1971158 GTTTCATAAA
1971168 CCTTCTTTTCATTTTTCACATG
1 CCTTCTTTTCATTTTTCACATG
1971190 CCTTCTTTTCATTTTTCACA
1 CCTTCTTTTCATTTTTCACA
1971210 CATACATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (22 bp):
CCTTCTTTTCATTTTTCACATG
Found at i:1971219 original size:24 final size:22
Alignment explanation
Indices: 1971170--1971219 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1971160 TTCATAAACC
* *
1971170 TTCTTTTCATTTTTCACATGCC
1 TTCTTTTCATTTTTCACATACA
1971192 TTCTTTTCATTTTTCACACATACA
1 TTCTTTTCATTTTT--CACATACA
1971216 TTCT
1 TTCT
1971220 CACATCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
24 10 0.42
ACGTcount: A:0.18, C:0.26, G:0.02, T:0.54
Consensus pattern (22 bp):
TTCTTTTCATTTTTCACATACA
Found at i:1971738 original size:23 final size:21
Alignment explanation
Indices: 1971707--1971778 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
1971697 CTACAATTTA
*
1971707 TATCAATATAAATAGTAAATATG
1 TATCGATATAAATAGT-AA-ATG
1971730 TATCGATATAAATAGTAAATG
1 TATCGATATAAATAGTAAATG
* * *
1971751 TATCGATACATA-AGTGAATG
1 TATCGATATAAATAGTAAATG
1971771 TATCGATA
1 TATCGATA
1971779 CATGCCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 15 0.33
21 13 0.29
22 2 0.04
23 15 0.33
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
TATCGATATAAATAGTAAATG
Found at i:1971972 original size:20 final size:20
Alignment explanation
Indices: 1971921--1971972 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1971911 TTTTGACTTA
1971921 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
* *
1971941 AATATATCGATACATTTTTC
1 AATGTATCGATACATTCTTC
*
1971961 AATGTATAGATA
1 AATGTATCGATA
1971973 GATACATGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1976352 original size:58 final size:57
Alignment explanation
Indices: 1976287--1976650 Score: 256
Period size: 58 Copynumber: 6.3 Consensus size: 57
1976277 AATTACATGA
1976287 AAAATGACCTAAATGATCTTAACATACAT-AAATTTGCATAAAAGTCTTTAGATTATAG
1 AAAATGACCTAAATGA-CTTAACATACATGAAA-TTGCATAAAAGTCTTTAGATTATAG
* *
1976345 AAAATGACCTAAATGACTTTAACATATATGAAATTGCATAAAAGT-TTCT-GAATTATAA
1 AAAATGACCTAAATGAC-TTAACATACATGAAATTGCATAAAAGTCTT-TAG-ATTATAG
** * ** * * * *
1976403 AAAATGATTTAAATAAACCCAACATACATGAAGTTGTATAAAAGTCTTTAGATCATAA
1 AAAATGACCTAAAT-GACTTAACATACATGAAATTGCATAAAAGTCTTTAGATTATAG
* * * * ** ** * * *
1976461 AAAAAGACTTAAATGACCTCAATATTTATGAAATCACATTAAAGT-TTCAGATCT-TGG
1 AAAATGACCTAAATGA-CTTAACATACATGAAATTGCATAAAAGTCTTTAGAT-TATAG
* * ** * *
1976518 AAAATGACCTAAATGACTTCAAGC-TACTTGAAATTGCATCAAAGTCCCTAGATCATGG
1 AAAATGACCTAAATGACTT-AA-CATACATGAAATTGCATAAAAGTCTTTAGATTATAG
* * * * * * *
1976576 AAAATTACTTGAATGA-TATAAACATACATGAAACTGCATAAAAGTCCTTAGAATATGG
1 AAAATGACCTAAATGACT-T-AACATACATGAAATTGCATAAAAGTCTTTAGATTATAG
1976634 AAAATGACCTAAATGAC
1 AAAATGACCTAAATGAC
1976651 ATAAAAAATG
Statistics
Matches: 236, Mismatches: 54, Indels: 31
0.74 0.17 0.10
Matches are distributed among these distances:
56 2 0.01
57 45 0.19
58 181 0.77
59 8 0.03
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (57 bp):
AAAATGACCTAAATGACTTAACATACATGAAATTGCATAAAAGTCTTTAGATTATAG
Found at i:1976655 original size:58 final size:57
Alignment explanation
Indices: 1976287--1976786 Score: 222
Period size: 58 Copynumber: 8.6 Consensus size: 57
1976277 AATTACATGA
* *
1976287 AAAATGACCTAAATGATC-TTAACATACAT-AAATTTGCATAAAAGTCTTTAGATTATAG
1 AAAATGACCTAAATGA-CATAAACATACATGAAA-TTGCATAAAAGTC-TTAGATCATAG
* * * * * *
1976345 AAAATGACCTAAATGACTTTAACATATATGAAATTGCATAAAAGT-TTCTGAATTATAA
1 AAAATGACCTAAATGACATAAACATACATGAAATTGCATAAAAGTCTT-AG-ATCATAG
** * ** * * *
1976403 AAAATGATTTAAAT-AAACCCAACATACATGAAGTTGTATAAAAGTCTTTAGATCATAA
1 AAAATGACCTAAATGACA-TAAACATACATGAAATTGCATAAAAGTC-TTAGATCATAG
* * * * * ** ** * * *
1976461 AAAAAGACTTAAATGACCTCAATATTTATGAAATCACATTAAAGT-TTCAGATCTTGG
1 AAAATGACCTAAATGACATAAACATACATGAAATTGCATAAAAGTCTT-AGATCATAG
* * * * * *
1976518 AAAATGACCTAAATGACTTCAAGC-TACTTGAAATTGCATCAAAGTCCCTAGATCATGG
1 AAAATGACCTAAATGACAT-AAACATACATGAAATTGCATAAAAGT-CTTAGATCATAG
* * * * * *
1976576 AAAATTACTTGAATGATATAAACATACATGAAACTGCATAAAAGTCCTTAGAAT-ATGG
1 AAAATGACCTAAATGACATAAACATACATGAAATTGCATAAAAGT-CTTAG-ATCATAG
* * *
1976634 AAAATGACCTAAATGACATAAAAAATGCATAAAAAGTT--ATAAAA-TCTCTA-AGTCATAG
1 AAAATGACCTAAATGACAT-AAACATACAT-GAAA-TTGCATAAAAGTCT-TAGA-TCATAG
* * * *
1976692 AAAATGA-CTAGAATAACATAAAAACT-CATGAAATAT-CATAAACATTCCTA-AGTCATAG
1 AAAATGACCTA-AATGACATAAACA-TACATGAAAT-TGCATAAA-AGTCTTAGA-TCATAG
* * *
1976750 AAAAT-AACTAAAATTACATAAAAATACATGAGAATTG
1 AAAATGACCT-AAATGACATAAACATACATGA-AATTG
1976787 TAAAATAGCC
Statistics
Matches: 344, Mismatches: 67, Indels: 61
0.73 0.14 0.13
Matches are distributed among these distances:
55 1 0.00
56 9 0.03
57 64 0.19
58 236 0.69
59 28 0.08
60 5 0.01
61 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.28
Consensus pattern (57 bp):
AAAATGACCTAAATGACATAAACATACATGAAATTGCATAAAAGTCTTAGATCATAG
Found at i:1977849 original size:21 final size:20
Alignment explanation
Indices: 1977778--1977848 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1977768 CCCCCATTTC
*
1977778 TATCGATACACATG-AAAATG
1 TATCGATACACATGTGAAA-G
*
1977798 TATCGATACACAT-TGCAATG
1 TATCGATACACATGTG-AAAG
*
1977818 TATTGATACATCATGTGAAAG
1 TATCGATACA-CATGTGAAAG
1977839 TATCGATACA
1 TATCGATACA
1977849 TTTTATTGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 23 0.55
21 17 0.40
22 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
TATCGATACACATGTGAAAG
Found at i:1980895 original size:52 final size:52
Alignment explanation
Indices: 1980782--1980959 Score: 207
Period size: 52 Copynumber: 3.4 Consensus size: 52
1980772 GAAATAACGA
* * * *
1980782 GGTTGGAGTATCCTCGATTGTAAA-AAAAATTGGTGTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGA-T-TAAAGGAAAATTAGTG-TTTTAAAAATAAAATCGG
* * *
1980836 AGCTGGAGTATCCTCGATTAAAGGAAAATTAGTGTTTTAAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTAAAAATAAAATCGG
** **
1980888 GGTTGGAGTATCCCCGATT-GTGGAAATATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAA-ATTAGTGTTTTAAAAATAAAATCGG
1980940 GGTTGGAGTATCCCCGATTA
1 GGTTGGAGTATCCCCGATTA
1980960 TGAGACATCA
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
51 5 0.05
52 79 0.72
53 10 0.09
54 15 0.14
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTAAAAATAAAATCGG
Found at i:1980998 original size:51 final size:52
Alignment explanation
Indices: 1980825--1981005 Score: 158
Period size: 52 Copynumber: 3.5 Consensus size: 52
1980815 TGTTTTTGAA
* * * * * * *
1980825 AATAAAATCGGAGCTGGAGTATCCTCGATTAAAGGAAA-ATTAGTGTTTTAA-A
1 AATAAAAGCGGGGTTGGAGTATCCCCGATT-ATGGAAATAATAGTG-TTTAAGC
* * * *
1980877 AATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAATATTAGTGTTTTAGC
1 AATAAAAGCGGGGTTGGAGTATCCCCGATTATGGAAATAATAGTGTTTAAGC
* *
1980929 AATAAAATCGGGGTTGGAGTATCCCCGATTATGAGACATCAATA-T-TTTAAG-
1 AATAAAAGCGGGGTTGGAGTATCCCCGATTATG-GAAAT-AATAGTGTTTAAGC
1980980 AAT-AAAGCAGGGGTTGGAGTATCCCC
1 AATAAAAGC-GGGGTTGGAGTATCCCC
1981006 TCGGAAATAA
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
50 4 0.04
51 29 0.26
52 71 0.63
53 5 0.04
54 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (52 bp):
AATAAAAGCGGGGTTGGAGTATCCCCGATTATGGAAATAATAGTGTTTAAGC
Found at i:1981085 original size:53 final size:51
Alignment explanation
Indices: 1981020--1981142 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
1981010 AAATAACGGG
* *
1981020 GTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAG-AAAATTAGTG--TTTTGAAAATAAAATCGAA
*
1981073 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCGAA
* * *
1981124 GATGGAATATTCCCGATTG
1 GTTGGAGTATCCCCGATTG
1981143 CGGAGAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 32 0.52
53 29 0.47
54 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCGAA
Found at i:1983515 original size:20 final size:20
Alignment explanation
Indices: 1983488--1983542 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1983478 TAAAATTTCC
*
1983488 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1983508 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1983528 AAATGTATCGATACA
1 AAATGTATCGATACA
1983543 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1983602 original size:13 final size:13
Alignment explanation
Indices: 1983584--1983639 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 13
1983574 ATAATACTTA
1983584 TGTATCGATACAT
1 TGTATCGATACAT
1983597 TGTATCGATACAAACTT
1 TGTATCGATAC--A--T
1983614 ATGTATCGATACAT
1 -TGTATCGATACAT
1983628 TGTATCGATACA
1 TGTATCGATACA
1983640 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1983617 original size:31 final size:31
Alignment explanation
Indices: 1983565--1983658 Score: 161
Period size: 32 Copynumber: 3.0 Consensus size: 31
1983555 TAGCTAATTA
*
1983565 TGTATCGATATAATACTTATGTATCGATACAT
1 TGTATCGATACAA-ACTTATGTATCGATACAT
1983597 TGTATCGATACAAACTTATGTATCGATACAT
1 TGTATCGATACAAACTTATGTATCGATACAT
1983628 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATAC-AAACTTATGTATCGATACA
1983659 AATTTTTGAC
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 29 0.48
32 31 0.52
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
TGTATCGATACAAACTTATGTATCGATACAT
Found at i:1983706 original size:21 final size:21
Alignment explanation
Indices: 1983680--1983819 Score: 237
Period size: 21 Copynumber: 6.7 Consensus size: 21
1983670 GTTGGGACTC
* *
1983680 TGTATCGATACATT-TATAGAA
1 TGTATCGATACATTCCACA-AA
1983701 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
*
1983722 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCCACAAA
1983743 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
1983764 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
1983785 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
1983806 TGTATCGATACATT
1 TGTATCGATACATT
1983820 TGAAATTTTT
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
21 112 0.98
22 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATTCCACAAA
Found at i:1986005 original size:2 final size:2
Alignment explanation
Indices: 1985998--1986034 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1985988 TTACTCCGTA
1985998 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1986035 ACTTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1990449 original size:16 final size:16
Alignment explanation
Indices: 1990427--1990481 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1990417 ATATATATAT
*
1990427 ATTTTCTATCTTCCCA
1 ATTTTCTATCTTTCCA
*
1990443 CTTTTCT-TCTCTTCCA
1 ATTTTCTATCT-TTCCA
*
1990459 ATTTTCCATCTTTCCA
1 ATTTTCTATCTTTCCA
1990475 ATTTTCT
1 ATTTTCT
1990482 TTCCATCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 3 0.09
16 26 0.81
17 3 0.09
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTCTATCTTTCCA
Found at i:1995316 original size:37 final size:37
Alignment explanation
Indices: 1995273--1995354 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
1995263 TATAAAAATT
1995273 AATTATTTTTAA-AATAAAATAAAAAT-ATTTTTTATAA
1 AATTATTTTTAATAATAAAA-AAAAATAATTTTTT-TAA
* * *
1995310 AATTA-TTTAAATAATAAAAAATATTAATTTTTTTAA
1 AATTATTTTTAATAATAAAAAAAAATAATTTTTTTAA
1995346 AA-TATTTTT
1 AATTATTTTT
1995355 TTACGAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.05
36 17 0.45
37 19 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
AATTATTTTTAATAATAAAAAAAAATAATTTTTTTAA
Found at i:1997308 original size:37 final size:38
Alignment explanation
Indices: 1997267--1997363 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 38
1997257 TATTTCAAAG
1997267 TTAATATATAATTGAATTAAAAGTAACTCTAA-AAT-AT
1 TTAATATATAATTGAATTAAAAGTAACT-TAATAATAAT
* *
1997304 TTAATATATATTTGAATTAGAATGTAACTTAATAATAAT
1 TTAATATATAATTGAATTA-AAAGTAACTTAATAATAAT
*
1997343 TTAATTTAATAA-T-AATTAAAA
1 TTAATAT-ATAATTGAATTAAAA
1997364 ATAGTTTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 23 0.45
38 16 0.31
39 9 0.18
40 3 0.06
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (38 bp):
TTAATATATAATTGAATTAAAAGTAACTTAATAATAAT
Found at i:1998338 original size:21 final size:22
Alignment explanation
Indices: 1998312--1998352 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1998302 ATGGAAGGAG
*
1998312 GAAAAGAAGAAG-AAGGAATAA
1 GAAAAGAAAAAGCAAGGAATAA
1998333 GAAAAGAAAAAGCAAGGAAT
1 GAAAAGAAAAAGCAAGGAAT
1998353 TTTTATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.66, C:0.02, G:0.27, T:0.05
Consensus pattern (22 bp):
GAAAAGAAAAAGCAAGGAATAA
Found at i:2007294 original size:2 final size:2
Alignment explanation
Indices: 2007287--2007320 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2007277 AATTTACAAT
*
2007287 TA TA TA TA -A AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2007321 CAATAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2008461 original size:21 final size:21
Alignment explanation
Indices: 2008437--2008477 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2008427 AAATATTAAA
2008437 ATATATTAT-ATTAATATTTTT
1 ATATATTATAATTAA-ATTTTT
*
2008458 ATATTTTATAATTAAATTTT
1 ATATATTATAATTAAATTTT
2008478 AAAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTATAATTAAATTTTT
Found at i:2008941 original size:14 final size:14
Alignment explanation
Indices: 2008906--2008952 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 14
2008896 TTTCTATTAC
2008906 TTTATTAATAATCATT
1 TTTA-TAATAAT-ATT
2008922 TATTATAATAATATT
1 T-TTATAATAATATT
2008937 TTTAT-A-AATATT
1 TTTATAATAATATT
2008949 TTTA
1 TTTA
2008953 GTTAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.33
13 1 0.03
14 4 0.13
15 4 0.13
16 8 0.27
17 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAATAATATT
Found at i:2009374 original size:25 final size:25
Alignment explanation
Indices: 2009345--2009398 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2009335 AAGTTTTAAC
*
2009345 ATATTTTT-CCATATAAAATAATTAT
1 ATATTTTTACCAAATAAAA-AATTAT
*
2009370 ATATTTTTACTAAATAAAAAATTAT
1 ATATTTTTACCAAATAAAAAATTAT
2009395 -TATT
1 ATATT
2009399 AAATAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 14 0.54
26 8 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATTTTTACCAAATAAAAAATTAT
Found at i:2010907 original size:17 final size:16
Alignment explanation
Indices: 2010887--2010923 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2010877 AAATTGATAT
2010887 ATTTTGTTATTTAAATA
1 ATTTT-TTATTTAAATA
2010904 A--TTTTATTTAAATA
1 ATTTTTTATTTAAATA
2010918 ATTTTT
1 ATTTTT
2010924 ATTATTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.67
15 2 0.11
16 3 0.17
17 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTTTATTTAAATA
Found at i:2010926 original size:15 final size:14
Alignment explanation
Indices: 2010893--2010922 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2010883 ATATATTTTG
2010893 TTATTTAAATAATT
1 TTATTTAAATAATT
2010907 TTATTTAAATAATT
1 TTATTTAAATAATT
2010921 TT
1 TT
2010923 TATTATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTAAATAATT
Found at i:2017849 original size:26 final size:27
Alignment explanation
Indices: 2017820--2017873 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2017810 TTTTAAAATC
*
2017820 AAATATGAATTTATTTA-ATTTATTTA
1 AAATATAAATTTATTTATATTTATTTA
*
2017846 AAATTTAAATTTATTTATTATTTATTTA
1 AAATATAAATTTATTTA-TATTTATTTA
2017874 CTATTTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
AAATATAAATTTATTTATATTTATTTA
Found at i:2017868 original size:17 final size:17
Alignment explanation
Indices: 2017830--2017869 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2017820 AAATATGAAT
2017830 TTATTT-AATTTATTTA
1 TTATTTAAATTTATTTA
**
2017846 AAATTTAAATTTATTTA
1 TTATTTAAATTTATTTA
2017863 TTATTTA
1 TTATTTA
2017870 TTTACTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTAAATTTATTTA
Found at i:2022143 original size:22 final size:23
Alignment explanation
Indices: 2022112--2022160 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2022102 TTTTTTCCTT
2022112 TGCTATTTGCTGCTTTTC-TTTGC
1 TGCTATTTGCTG-TTTTCGTTTGC
2022135 TGCTA-TTGCTGTTTTCGTTTGC
1 TGCTATTTGCTGTTTTCGTTTGC
2022157 TGCT
1 TGCT
2022161 GATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.04, C:0.20, G:0.20, T:0.55
Consensus pattern (23 bp):
TGCTATTTGCTGTTTTCGTTTGC
Found at i:2022169 original size:2 final size:2
Alignment explanation
Indices: 2022162--2022199 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2022152 TTTGCTGCTG
2022162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2022200 TTACTGCTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2022372 original size:30 final size:29
Alignment explanation
Indices: 2022334--2022437 Score: 123
Period size: 30 Copynumber: 3.8 Consensus size: 29
2022324 AGCTACTATT
2022334 CGTGCTTGTTGGAGCTGCTGTTGTTGTTGC
1 CGTGCTTGTTGGAGCTGCTGTTGTTGTT-C
*
2022364 CATGCTTGTTGGA---GC---TGTTGTT-
1 CGTGCTTGTTGGAGCTGCTGTTGTTGTTC
*
2022386 CGTGCTTGTTGGAGCTGCTGTTGTTGCTAC
1 CGTGCTTGTTGGAGCTGCTGTTGTTG-TTC
2022416 CGTGCTTGTTGGAGCTGCTGTT
1 CGTGCTTGTTGGAGCTGCTGTT
2022438 CGTGCTTGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
22 12 0.19
24 7 0.11
25 2 0.03
27 2 0.03
28 5 0.08
29 1 0.02
30 34 0.54
ACGTcount: A:0.06, C:0.17, G:0.35, T:0.42
Consensus pattern (29 bp):
CGTGCTTGTTGGAGCTGCTGTTGTTGTTC
Found at i:2022374 original size:52 final size:52
Alignment explanation
Indices: 2022300--2022446 Score: 240
Period size: 52 Copynumber: 2.8 Consensus size: 52
2022290 CCTCTTTTGT
* *
2022300 TGTTGTTGCTGCCGTGCTTGTTGGAGCTACTATTCGTGCTTGTTGGAGCTGC
1 TGTTGTTGCTGCCGTGCTTGTTGGAGCTGCTGTTCGTGCTTGTTGGAGCTGC
* * *
2022352 TGTTGTTGTTGCCATGCTTGTTGGAGCTGTTGTTCGTGCTTGTTGGAGCTGC
1 TGTTGTTGCTGCCGTGCTTGTTGGAGCTGCTGTTCGTGCTTGTTGGAGCTGC
*
2022404 TGTTGTTGCTACCGTGCTTGTTGGAGCTGCTGTTCGTGCTTGT
1 TGTTGTTGCTGCCGTGCTTGTTGGAGCTGCTGTTCGTGCTTGT
2022447 CGATTGCTGG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.43
Consensus pattern (52 bp):
TGTTGTTGCTGCCGTGCTTGTTGGAGCTGCTGTTCGTGCTTGTTGGAGCTGC
Found at i:2022413 original size:22 final size:22
Alignment explanation
Indices: 2022366--2022407 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2022356 GTTGTTGCCA
*
2022366 TGCTTGTTGGAGCTGTTGTTCG
1 TGCTTGTTGGAGCTGCTGTTCG
2022388 TGCTTGTTGGAGCTGCTGTT
1 TGCTTGTTGGAGCTGCTGTT
2022408 GTTGCTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.14, G:0.36, T:0.45
Consensus pattern (22 bp):
TGCTTGTTGGAGCTGCTGTTCG
Found at i:2022997 original size:14 final size:14
Alignment explanation
Indices: 2022978--2023033 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2022968 TTTTTTTTAA
2022978 TTTTATTATTTGAT
1 TTTTATTATTTGAT
*
2022992 TTTTATTATTTTTTATT
1 TTTTATTA--TTTGA-T
2023009 TTTTAATT-TTTGAT
1 TTTT-ATTATTTGAT
2023023 TTTTACTTATT
1 TTTTA-TTATT
2023034 GTTATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
13 1 0.03
14 15 0.44
15 6 0.18
16 4 0.12
17 5 0.15
18 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTATTATTTGAT
Found at i:2023005 original size:24 final size:23
Alignment explanation
Indices: 2022965--2023009 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2022955 ATGCATTTCA
*
2022965 TGATTTTTTTTAATTTTATTATT
1 TGATTTTTATTAATTTTATTATT
2022988 TGATTTTTATT-ATTTT-TTATT
1 TGATTTTTATTAATTTTATTATT
2023009 T
1 T
2023010 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TGATTTTTATTAATTTTATTATT
Found at i:2023013 original size:31 final size:32
Alignment explanation
Indices: 2022978--2023043 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
2022968 TTTTTTTTAA
2022978 TTTT-ATTATTTGATTTTTA-TTATTTTTTATT
1 TTTTAATT-TTTGATTTTTACTTATTTTTTATT
*
2023009 TTTTAATTTTTGATTTTTACTTATTGTTATATT
1 TTTTAATTTTTGATTTTTACTTATT-TTTTATT
2023042 TT
1 TT
2023044 ATATCGAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 15 0.48
32 8 0.26
33 8 0.26
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.74
Consensus pattern (32 bp):
TTTTAATTTTTGATTTTTACTTATTTTTTATT
Found at i:2024723 original size:9 final size:9
Alignment explanation
Indices: 2024709--2024759 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
2024699 CAAATGATAC
2024709 TAAATAAAT
1 TAAATAAAT
2024718 TAAATAAA-
1 TAAATAAAT
* *
2024726 TAAAT-TAC
1 TAAATAAAT
*
2024734 CAAATAAAT
1 TAAATAAAT
2024743 TAAATAAAT
1 TAAATAAAT
*
2024752 TACATAAA
1 TAAATAAA
2024760 ATTCAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 1 0.03
8 9 0.26
9 24 0.71
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAATAAAT
Found at i:2025096 original size:14 final size:14
Alignment explanation
Indices: 2025070--2025118 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 14
2025060 TTAAATTTGG
2025070 ATAATATTAAATATA
1 ATAATA-TAAATATA
*
2025085 ATTATATAAATATA
1 ATAATATAAATATA
2025099 A-AATATAAA-AT-
1 ATAATATAAATATA
2025110 ATAATATAA
1 ATAATATAA
2025119 TACAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
13 7 0.23
14 9 0.29
15 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATATAAATATA
Found at i:2025102 original size:7 final size:7
Alignment explanation
Indices: 2025072--2025223 Score: 53
Period size: 7 Copynumber: 20.4 Consensus size: 7
2025062 AAATTTGGAT
*
2025072 AATATTA
1 AATATAA
2025079 AATAT-A
1 AATATAA
*
2025085 ATTATATA
1 AATATA-A
2025093 AATATAA
1 AATATAA
2025100 AATATAA
1 AATATAA
2025107 AATATAA
1 AATATAA
*
2025114 TATAATACA
1 AAT-ATA-A
2025123 AA-AT-A
1 AATATAA
2025128 AATA-AA
1 AATATAA
*
2025134 AATTTTAA
1 AA-TATAA
*
2025142 AATTTATAT
1 AA--TATAA
2025151 AATATAA
1 AATATAA
*
2025158 ATTATAA
1 AATATAA
*
2025165 ATTTATAA
1 A-ATATAA
*
2025173 CATTTGATATA
1 -A-AT-ATA-A
2025184 AATATAA
1 AATATAA
*
2025191 AATATTTTA
1 AATA--TAA
2025200 AATAT-A
1 AATATAA
*
2025206 ATTATAA
1 AATATAA
2025213 AATAATAA
1 AAT-ATAA
2025221 AAT
1 AAT
2025224 TATACATAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 33
0.71 0.08 0.20
Matches are distributed among these distances:
5 3 0.03
6 14 0.12
7 45 0.39
8 29 0.25
9 19 0.17
10 4 0.03
11 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (7 bp):
AATATAA
Found at i:2025159 original size:23 final size:22
Alignment explanation
Indices: 2025128--2025171 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2025118 ATACAAAATA
*
2025128 AATAAAAATTTTAAAATTTATAT
1 AATAAAAATTAT-AAATTTATAT
*
2025151 AATATAAATTATAAATTTATA
1 AATAAAAATTATAAATTTATA
2025172 ACATTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAAAATTATAAATTTATAT
Found at i:2025162 original size:14 final size:14
Alignment explanation
Indices: 2025078--2025227 Score: 67
Period size: 14 Copynumber: 10.0 Consensus size: 14
2025068 GGATAATATT
2025078 AAATAT-AATTATA
1 AAATATAAATTATA
*
2025091 TAAATATAAAATATA
1 -AAATATAAATTATA
*
2025106 AAATATAATATAATA
1 AAATATAA-ATTATA
2025121 CAAA-ATAAA-TA-A
1 -AAATATAAATTATA
*
2025133 AAATTTTAAAATTTATA
1 AAA-TAT-AAA-TTATA
*
2025150 TAATATAAATTATA
1 AAATATAAATTATA
*
2025164 AATTTATAACATTTGATA
1 AA-ATATAA-A-TT-ATA
* *
2025182 TAAATATAAAATATTTT
1 -AAATAT-AAAT-TATA
2025199 AAATAT-AATTATA
1 AAATATAAATTATA
2025212 AAATAATAAAATTATA
1 AAAT-AT-AAATTATA
2025228 CATAAATCAT
Statistics
Matches: 103, Mismatches: 14, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
11 3 0.03
12 1 0.01
13 8 0.08
14 29 0.28
15 22 0.21
16 21 0.20
17 7 0.07
18 8 0.08
19 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (14 bp):
AAATATAAATTATA
Found at i:2025227 original size:22 final size:22
Alignment explanation
Indices: 2025088--2025223 Score: 61
Period size: 22 Copynumber: 6.1 Consensus size: 22
2025078 AAATATAATT
2025088 ATATAAATAT-AAA-ATATAAA
1 ATATAAATATAAAATATATAAA
*
2025108 ATAT-AATATAATACA-AAAT-AA
1 ATATAAATATAA-A-ATATATAAA
* * * *
2025129 ATAAAAATTTTAAAATTTATATA
1 ATATAAA-TATAAAATATATAAA
*
2025152 ATATAAAT-TATAAATTTATAACA
1 ATATAAATATA-AAATATATAA-A
* *
2025175 TTTGATATAAATATAAAATATTTTAA
1 ----ATATAAATATAAAATATATAAA
*
2025201 ATATAATTATAAAATA-ATAAA
1 ATATAAATATAAAATATATAAA
2025222 AT
1 AT
2025224 TATACATAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
19 5 0.06
20 5 0.06
21 14 0.16
22 34 0.39
23 12 0.14
26 1 0.01
27 15 0.17
28 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (22 bp):
ATATAAATATAAAATATATAAA
Found at i:2026778 original size:23 final size:23
Alignment explanation
Indices: 2026752--2026821 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
2026742 TGACTTTATA
*
2026752 GATTAACATTAGTGGGTTTTTAG
1 GATTAACATTTGTGGGTTTTTAG
2026775 GATTAACATTTGTGGGTTTTTAG
1 GATTAACATTTGTGGGTTTTTAG
2026798 GATTAACATTTGTGGGTTTTTAG
1 GATTAACATTTGTGGGTTTTTAG
2026821 G
1 G
2026822 TTTTTCGTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.04, G:0.27, T:0.46
Consensus pattern (23 bp):
GATTAACATTTGTGGGTTTTTAG
Found at i:2033260 original size:19 final size:18
Alignment explanation
Indices: 2033227--2033266 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
2033217 GTATGATTAT
2033227 AATATAATAAAATATATA
1 AATATAATAAAATATATA
2033245 AATATAATATAAATATATA
1 AATATAATA-AAATATATA
2033264 AAT
1 AAT
2033267 TATTAAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:2033941 original size:153 final size:151
Alignment explanation
Indices: 2033645--2033952 Score: 347
Period size: 153 Copynumber: 2.0 Consensus size: 151
2033635 ACTATATATC
* * * *
2033645 AATTGGAGTAGTAATAACTAATTTCAATTAAGACGCATAGATGTTTATTTAATTGAACTACTTAA
1 AATTGGAGTAGTAACAACTAATTCCAATTAAGACGCATAGATGTATATTAAATTGAACTACTTAA
* * * * *
2033710 ACAAATAATGATCAATTTCAGTTAGAATTAATGTAACAATATCTACAAATTCATCAATTAAATTA
66 ACAAACAATGACCAATTTCAATTAGAATTAATGTAACAAAATATACAAATTCATCAATTAAATTA
* * *
2033775 TTATTAACTAATTTAAAGTAT
131 CTATTAACCAATTTAAACTAT
*
2033796 AATTGGAGTAGTAACAACTAATTCCAATTAAGACTAGTGCA-AG-TGTATATTAAATTGGACTA-
1 AATTGGAGTAGTAACAACTAATTCCAATTAAGAC----GCATAGATGTATATTAAATTGAACTAC
* *
2033858 TTGGAACAACCAATGACCAATCTT-AATTAGAATTAATGTAACAAAATATACAAATTCA-CTAAT
62 TT-AAACAAACAATGACCAAT-TTCAATTAGAATTAATGTAACAAAATATACAAATTCATC-AAT
** * *
2033921 TGGATTACTATTCACCAATTTTAACTAT
124 TAAATTACTATTAACCAATTTAAACTAT
2033949 AATT
1 AATT
2033953 AGTATAATTA
Statistics
Matches: 131, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
151 32 0.24
152 3 0.02
153 89 0.68
154 4 0.03
155 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (151 bp):
AATTGGAGTAGTAACAACTAATTCCAATTAAGACGCATAGATGTATATTAAATTGAACTACTTAA
ACAAACAATGACCAATTTCAATTAGAATTAATGTAACAAAATATACAAATTCATCAATTAAATTA
CTATTAACCAATTTAAACTAT
Found at i:2036443 original size:2 final size:2
Alignment explanation
Indices: 2036438--2036466 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2036428 TTTTTCCACT
2036438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2036467 CACTTTATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2044859 original size:2 final size:2
Alignment explanation
Indices: 2044852--2044878 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2044842 ATGACTTGCT
2044852 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2044879 TGTTAGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2048778 original size:22 final size:21
Alignment explanation
Indices: 2048753--2048799 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
2048743 TTTAAATGAT
2048753 TTTTAAATTTTAATATTTATAA
1 TTTTAAATTTTAATA-TTATAA
** *
2048775 TTTTTTATTTTTATATTATAA
1 TTTTAAATTTTAATATTATAA
2048796 TTTT
1 TTTT
2048800 TATTGTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAAATTTTAATATTATAA
Found at i:2048800 original size:22 final size:22
Alignment explanation
Indices: 2048759--2048800 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2048749 TGATTTTTAA
2048759 ATTTTAATATTTATAATTTTTT
1 ATTTTAATATTTATAATTTTTT
*
2048781 ATTTTTATA-TTATAATTTTT
1 ATTTTAATATTTATAATTTTT
2048801 ATTGTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTAATATTTATAATTTTTT
Found at i:2049367 original size:2 final size:2
Alignment explanation
Indices: 2049325--2049355 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2049315 TTTATCATTT
2049325 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2049356 GAGTGGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2051829 original size:2 final size:2
Alignment explanation
Indices: 2051822--2051854 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2051812 AATCTCAAAG
*
2051822 AT AT AT AT AT AT AT AT AT -T AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2051855 GCAACTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2051845 original size:15 final size:15
Alignment explanation
Indices: 2051825--2051854 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2051815 CTCAAAGATA
2051825 TATATATATATATAT
1 TATATATATATATAT
*
2051840 TATATATTTATATAT
1 TATATATATATATAT
2051855 GCAACTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:2052292 original size:17 final size:18
Alignment explanation
Indices: 2052270--2052307 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2052260 GCTCTTGTAT
2052270 TTTATG-AAAATTTTTAA
1 TTTATGTAAAATTTTTAA
* *
2052287 TTTATGTAATATTTTTTA
1 TTTATGTAAAATTTTTAA
2052305 TTT
1 TTT
2052308 TTAAAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTATGTAAAATTTTTAA
Found at i:2052332 original size:25 final size:25
Alignment explanation
Indices: 2052278--2052332 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
2052268 ATTTTATGAA
** *
2052278 AATTTTTAATTTATGTAATATTTTT
1 AATTTTTAAAATATGTAATATATTT
*
2052303 TATTTTTAAAATATGTAA-ATAATTT
1 AATTTTTAAAATATGTAATAT-ATTT
2052328 AATTT
1 AATTT
2052333 ATTATTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AATTTTTAAAATATGTAATATATTT
Found at i:2053970 original size:2 final size:2
Alignment explanation
Indices: 2053963--2053998 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2053953 AAATGAACTC
2053963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2053999 TAAAGCAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2055541 original size:2 final size:2
Alignment explanation
Indices: 2055534--2055567 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2055524 ATGTATAACA
2055534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2055568 TTCCCCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2057236 original size:15 final size:15
Alignment explanation
Indices: 2057200--2057240 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2057190 TAATAATATT
2057200 ATAATA-TTAA-ACA
1 ATAATATTTAATACA
*
2057213 ATATTTATTTAATACA
1 ATA-ATATTTAATACA
2057229 ATAATATTTAAT
1 ATAATATTTAAT
2057241 TTATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.13
14 2 0.09
15 12 0.52
16 6 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATATTTAATACA
Found at i:2057250 original size:19 final size:19
Alignment explanation
Indices: 2057186--2057251 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
2057176 TCAAATTTAG
*
2057186 TATTTAATAATATTATAA--
1 TATTAAATAATATT-TAATT
*
2057204 TATTAAACAATATTT-ATT
1 TATTAAATAATATTTAATT
*
2057222 TAATACAATAATATTTAATT
1 TATTA-AATAATATTTAATT
2057242 TATTAAATAA
1 TATTAAATAA
2057252 CAGTACTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.03
17 1 0.03
18 16 0.41
19 14 0.36
20 7 0.18
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTAAATAATATTTAATT
Found at i:2057369 original size:13 final size:13
Alignment explanation
Indices: 2057351--2057376 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2057341 ACAAATTTAA
2057351 ATAAAATTATATT
1 ATAAAATTATATT
2057364 ATAAAATTATATT
1 ATAAAATTATATT
2057377 TTTATGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAATTATATT
Found at i:2057683 original size:21 final size:20
Alignment explanation
Indices: 2057656--2057698 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
2057646 TTGCCTTCCA
*
2057656 AAAAAAATTAAGACATAAAACG
1 AAAAAAA-TAAAACA-AAAACG
2057678 AAAAAAATAAAACAAAAACG
1 AAAAAAATAAAACAAAAACG
2057698 A
1 A
2057699 TACCAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAAAATAAAACAAAAACG
Found at i:2058152 original size:3 final size:3
Alignment explanation
Indices: 2058146--2058183 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2058136 TTTTTTTATA
2058146 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2058184 GCAGCTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2058520 original size:2 final size:2
Alignment explanation
Indices: 2058513--2058542 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2058503 GGGTGTGCCC
2058513 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
2058543 GTTATATTTC
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:2059405 original size:10 final size:10
Alignment explanation
Indices: 2059392--2059439 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
2059382 TTAAAAAATT
2059392 ATAAATTAAA
1 ATAAATTAAA
2059402 ATAAAACTTAAA
1 AT-AAA-TTAAA
* *
2059414 TTAAATTATA
1 ATAAATTAAA
2059424 ATAAATTAAA
1 ATAAATTAAA
2059434 A-AAATT
1 ATAAATT
2059440 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.16
10 15 0.47
11 6 0.19
12 6 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:2059879 original size:7 final size:7
Alignment explanation
Indices: 2059867--2059939 Score: 50
Period size: 7 Copynumber: 10.9 Consensus size: 7
2059857 AAAATTTAGA
2059867 TAAAATT
1 TAAAATT
2059874 TAAAATT
1 TAAAATT
2059881 TAAAATT
1 TAAAATT
2059888 T--AATT
1 TAAAATT
2059893 T-AAATT
1 TAAAATT
2059899 TAATTAAGTT
1 TAA--AA-TT
*
2059909 T-TAATT
1 TAAAATT
*
2059915 TTAAATT
1 TAAAATT
*
2059922 TTAAATT
1 TAAAATT
2059929 T--AATT
1 TAAAATT
2059934 TAAAAT
1 TAAAAT
2059940 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
5 10 0.18
6 8 0.14
7 33 0.59
9 2 0.04
10 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (7 bp):
TAAAATT
Found at i:2059898 original size:36 final size:36
Alignment explanation
Indices: 2059858--2059936 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
2059848 AAATTATAAA
2059858 AAATTTAGATAAAATTTAAAATTTAAAATTT-AATTT
1 AAATTTA-ATAAAATTTAAAATTTAAAATTTAAATTT
* * * * *
2059894 AAATTTAATTAAGTTTTAATTTTAAATTTTAAATTT
1 AAATTTAATAAAATTTAAAATTTAAAATTTAAATTT
2059930 -AATTTAA
1 AAATTTAA
2059937 AATAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (36 bp):
AAATTTAATAAAATTTAAAATTTAAAATTTAAATTT
Found at i:2059900 original size:6 final size:6
Alignment explanation
Indices: 2059869--2059951 Score: 57
Period size: 6 Copynumber: 13.8 Consensus size: 6
2059859 AATTTAGATA
* *
2059869 AAATTT AAAATTT AAAATTT -AATTT AAATTT -AA-TT AAGTTTT AATTTT
1 AAATTT -AAATTT -AAATTT AAATTT AAATTT AAATTT AA-ATTT AAATTT
* * *
2059917 AAATTTT AAATTT -AATTT AAAATA AAAATT AAATT
1 AAA-TTT AAATTT AAATTT AAATTT AAATTT AAATT
2059952 ATTTAAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.03
5 13 0.20
6 26 0.41
7 23 0.36
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:2059942 original size:23 final size:23
Alignment explanation
Indices: 2059916--2059988 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
2059906 GTTTTAATTT
2059916 TAAATTTTAAATTTAATTTAAAA
1 TAAATTTTAAATTTAATTTAAAA
**
2059939 TAAAAATTAAA-TT-ATTT-AAA
1 TAAATTTTAAATTTAATTTAAAA
* *
2059959 TAAACTTGTT-TATTTAA-TAAAAA
1 TAAA-TT-TTAAATTTAATTTAAAA
2059982 TAAATTT
1 TAAATTT
2059989 AATTCTCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 7 0.18
21 6 0.15
22 9 0.23
23 17 0.44
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
TAAATTTTAAATTTAATTTAAAA
Found at i:2060042 original size:20 final size:21
Alignment explanation
Indices: 2060005--2060046 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2059995 CATTAACAAC
*
2060005 TTTAAAATAGAATATTTTTAA
1 TTTAAAATAAAATATTTTTAA
*
2060026 TTTAAATTAAAAT-TTTTTAA
1 TTTAAAATAAAATATTTTTAA
2060046 T
1 T
2060047 AATAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAAAATAAAATATTTTTAA
Found at i:2060200 original size:30 final size:30
Alignment explanation
Indices: 2060141--2060202 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2060131 AATTCAAAAC
* *
2060141 TTAAATTATTTAAATTTAATTTGATAATAA
1 TTAAATTATTTAAATTAAACTTGATAATAA
2060171 TTAAATTACTTTTAAATTAAACTT-A-AATAA
1 TTAAATTA--TTTAAATTAAACTTGATAATAA
2060201 TT
1 TT
2060203 TACTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 15 0.54
31 1 0.04
32 12 0.43
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAAATTATTTAAATTAAACTTGATAATAA
Found at i:2061460 original size:3 final size:3
Alignment explanation
Indices: 2061452--2061484 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2061442 ATCATAGCTC
2061452 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2061485 GTGAAGGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2061829 original size:2 final size:2
Alignment explanation
Indices: 2061822--2061857 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2061812 ACCAATTTAA
2061822 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2061858 GCGTGTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2062368 original size:21 final size:23
Alignment explanation
Indices: 2062344--2062391 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
2062334 TTTTTAAATT
*
2062344 TTTTAT-CTTTGTTGGTTTT-GG
1 TTTTATGCTTTGTGGGTTTTGGG
*
2062365 TTTT-TGTTTTGTGGGTTTTGGG
1 TTTTATGCTTTGTGGGTTTTGGG
2062387 TTTTA
1 TTTTA
2062392 ATTATGGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.05
21 15 0.68
22 6 0.27
ACGTcount: A:0.04, C:0.02, G:0.27, T:0.67
Consensus pattern (23 bp):
TTTTATGCTTTGTGGGTTTTGGG
Found at i:2064933 original size:18 final size:18
Alignment explanation
Indices: 2064912--2064946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2064902 GTTCTTTCAA
*
2064912 AGCAAGCAAATCTTTTAG
1 AGCAAACAAATCTTTTAG
*
2064930 AGCAAACAAGTCTTTTA
1 AGCAAACAAATCTTTTA
2064947 AAACATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (18 bp):
AGCAAACAAATCTTTTAG
Found at i:2069893 original size:16 final size:14
Alignment explanation
Indices: 2069851--2069977 Score: 66
Period size: 14 Copynumber: 8.6 Consensus size: 14
2069841 ATGAATATAA
2069851 TATTAAATA-AAATT
1 TATTAAATATAAA-T
*
2069865 TATAAAATATAAAT
1 TATTAAATATAAAT
2069879 TATTAATATATTAAAATT
1 TATTAA-ATA-T-AAA-T
2069897 TATATAAATATAAAT
1 TAT-TAAATATAAAT
2069912 TATTTTAAATAT-AAT
1 TA--TTAAATATAAAT
*
2069927 TA-TAATATAATAAAA
1 TATTAA-AT-ATAAAT
*
2069942 TATATAAAT-TTAA-
1 TAT-TAAATATAAAT
*
2069955 TATAAATATATAAAT
1 TATTAA-ATATAAAT
*
2069970 TATCAAAT
1 TATTAAAT
2069978 TTACGCTTAA
Statistics
Matches: 90, Mismatches: 7, Indels: 32
0.70 0.05 0.25
Matches are distributed among these distances:
12 5 0.06
13 7 0.08
14 24 0.27
15 23 0.26
16 13 0.14
17 8 0.09
18 7 0.08
19 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTAAATATAAAT
Found at i:2069907 original size:18 final size:18
Alignment explanation
Indices: 2069858--2069907 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2069848 TAATATTAAA
2069858 TAAAATTTATA-AAATA-
1 TAAAATTTATATAAATAT
2069874 T-AAA-TTAT-TAATATAT
1 TAAAATTTATATAA-ATAT
2069890 TAAAATTTATATAAATAT
1 TAAAATTTATATAAATAT
2069908 AAATTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 2 0.07
17 3 0.11
18 8 0.29
19 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTATATAAATAT
Found at i:2069935 original size:33 final size:32
Alignment explanation
Indices: 2069851--2069936 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
2069841 ATGAATATAA
2069851 TATTAAATAAAATTTATA-AAATATAAATTAT
1 TATTAAATAAAATTTATATAAATATAAATTAT
* *
2069882 TAATATATTAAAATTTATATAAATATAAATTAT
1 TATTA-AATAAAATTTATATAAATATAAATTAT
*
2069915 T-TTAAATATAATTATAATATAA
1 TATTAAATAAAATT-T-ATATAA
2069937 TAAAATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
31 11 0.24
32 15 0.33
33 20 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TATTAAATAAAATTTATATAAATATAAATTAT
Found at i:2070682 original size:18 final size:19
Alignment explanation
Indices: 2070659--2070704 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2070649 ACATCAATTT
2070659 AATTAAAAAATA-ATAAAA
1 AATTAAAAAATATATAAAA
2070677 AATTAAAAAATATTATAAAA
1 AATTAAAAAATA-TATAAAA
*
2070697 ATTTAAAA
1 AATTAAAA
2070705 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATTAAAAAATATATAAAA
Found at i:2070823 original size:3 final size:3
Alignment explanation
Indices: 2070815--2070848 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2070805 ATAATTAGTT
2070815 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2070849 ATAAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2071030 original size:2 final size:2
Alignment explanation
Indices: 2071025--2071054 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2071015 TAAAAATTAC
2071025 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
2071055 TTCATCCGGA
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:2071123 original size:3 final size:3
Alignment explanation
Indices: 2071110--2071161 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
2071100 CCAAAAAATA
* *
2071110 AAT AGT AAT AAT AAT AAT AGT 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
2071158 AAT A
1 AAT A
2071162 GTAGCGCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2077552 original size:16 final size:16
Alignment explanation
Indices: 2077531--2077564 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2077521 ATTTTGACAC
2077531 AATACTAAAAATACAG
1 AATACTAAAAATACAG
2077547 AATACTAAAAATACAG
1 AATACTAAAAATACAG
2077563 AA
1 AA
2077565 CCCTTCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AATACTAAAAATACAG
Found at i:2078246 original size:32 final size:32
Alignment explanation
Indices: 2078205--2078271 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
2078195 ATTGAAGGGT
2078205 TGATTGAGGCGTCCGTTGAATTTCACCTTATC
1 TGATTGAGGCGTCCGTTGAATTTCACCTTATC
*
2078237 TGATTGAGGCTTCCGTTGAATTTCACCTTATC
1 TGATTGAGGCGTCCGTTGAATTTCACCTTATC
2078269 TGA
1 TGA
2078272 GGTGGAACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (32 bp):
TGATTGAGGCGTCCGTTGAATTTCACCTTATC
Found at i:2078900 original size:21 final size:20
Alignment explanation
Indices: 2078851--2078901 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2078841 GTAACCAAAA
*
2078851 TAATTATATTTTTTTATAAT
1 TAATTAAATTTTTTTATAAT
* *
2078871 CAATGAAATTTTAATTT-TAAT
1 TAATTAAATTTT--TTTATAAT
2078892 TAATTAAATT
1 TAATTAAATT
2078902 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 9 0.38
21 12 0.50
22 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TAATTAAATTTTTTTATAAT
Found at i:2083530 original size:14 final size:15
Alignment explanation
Indices: 2083501--2083540 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2083491 AAATATTTTA
*
2083501 AATATAATTATAATAT
1 AATATAAATAT-ATAT
2083517 AATA-AAATATATAT
1 AATATAAATATATAT
2083531 AATATAAATA
1 AATATAAATA
2083541 CATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATATATAT
Found at i:2085857 original size:29 final size:27
Alignment explanation
Indices: 2085825--2085895 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 27
2085815 TTTTATTATT
*
2085825 TTTTAGTTGTTTTTAAATTAGTTATATCA
1 TTTTAGTTATTTTTAAATTAGTTA-AT-A
* * *
2085854 TTTTATTTATGTTTAAATTATTTAATA
1 TTTTAGTTATTTTTAAATTAGTTAATA
* *
2085881 ATTTAGTTTTTTTTA
1 TTTTAGTTATTTTTA
2085896 TATTTTATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 12 0.35
28 2 0.06
29 20 0.59
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63
Consensus pattern (27 bp):
TTTTAGTTATTTTTAAATTAGTTAATA
Found at i:2086649 original size:2 final size:2
Alignment explanation
Indices: 2086642--2086670 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2086632 AATCATTGAA
2086642 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
2086671 AATTCGAAAT
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:2093172 original size:13 final size:13
Alignment explanation
Indices: 2093154--2093180 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2093144 AAAAAGTTAC
2093154 ATATGTTAATTTA
1 ATATGTTAATTTA
2093167 ATATGTTAATTTA
1 ATATGTTAATTTA
2093180 A
1 A
2093181 ATATTATATA
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATATGTTAATTTA
Found at i:2099691 original size:20 final size:20
Alignment explanation
Indices: 2099666--2099703 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2099656 TCTCTATTTA
2099666 AATTATTGATTATAAATAAT
1 AATTATTGATTATAAATAAT
**
2099686 AATTATTTTTTATAAATA
1 AATTATTGATTATAAATA
2099704 TTAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTATTGATTATAAATAAT
Found at i:2100343 original size:20 final size:20
Alignment explanation
Indices: 2100298--2100344 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2100288 TTATACACAC
* *
2100298 ATATACATACATATATATAT
1 ATATATATACATATATAAAT
*
2100318 ATATATATACATTTATAAAT
1 ATATATATACATATATAAAT
2100338 ATATATA
1 ATATATA
2100345 ATCGTCCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATACATATATAAAT
Found at i:2102814 original size:36 final size:36
Alignment explanation
Indices: 2102773--2102863 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 36
2102763 GAATCGATTT
* *
2102773 AATTAATTTTTAATAAT-TAAAAAATATTTTTATATA
1 AATTAAATTATAA-AATATAAAAAATATTTTTATATA
* *
2102809 AATTAAATTATAAAATATATAAAATTTTTTTAT-TA
1 AATTAAATTATAAAATATAAAAAATATTTTTATATA
* *
2102844 ATTATAAATAAT-AAATATAA
1 AAT-TAAATTATAAAATATAA
2102864 GTGAGTCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
35 14 0.30
36 32 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AATTAAATTATAAAATATAAAAAATATTTTTATATA
Found at i:2102860 original size:35 final size:36
Alignment explanation
Indices: 2102793--2102862 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2102783 TAATAATTAA
*
2102793 AAAATATTTTTATATAAATTAAATTATAAAATATAT
1 AAAATATTTTTATATAAATTAAATAATAAAATATAT
* *
2102829 AAAATTTTTTTAT-TAATTATAAATAAT-AAATATA
1 AAAATATTTTTATATAAAT-TAAATAATAAAATATA
2102863 AGTGAGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AAAATATTTTTATATAAATTAAATAATAAAATATAT
Found at i:2102907 original size:14 final size:16
Alignment explanation
Indices: 2102882--2102913 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2102872 AGCAAGATCA
2102882 AAAATGAACTTAA-TT
1 AAAATGAACTTAACTT
2102897 AAAAT-AACTTAACTT
1 AAAATGAACTTAACTT
2102912 AA
1 AA
2102914 CTTGATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATGAACTTAACTT
Found at i:2103352 original size:16 final size:16
Alignment explanation
Indices: 2103333--2103364 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2103323 AATTATCTTT
2103333 AATTACTATTAAATTA
1 AATTACTATTAAATTA
*
2103349 AATTATTATTAAATTA
1 AATTACTATTAAATTA
2103365 TACTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTACTATTAAATTA
Found at i:2105574 original size:2 final size:2
Alignment explanation
Indices: 2105569--2105605 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2105559 ACACACACAC
2105569 AT AT AT AT 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
2105606 AAATCACCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2105750 original size:15 final size:15
Alignment explanation
Indices: 2105732--2105764 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2105722 TTTAATTAGT
2105732 TTTTTTTTTACAAAA
1 TTTTTTTTTACAAAA
*
2105747 TTTTTTTTTATAAAA
1 TTTTTTTTTACAAAA
2105762 TTT
1 TTT
2105765 ATAAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTACAAAA
Found at i:2109469 original size:28 final size:29
Alignment explanation
Indices: 2109421--2109482 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
2109411 TTTATTTAAT
2109421 ATAAAAAATTTTAATCATTAAAT-ATATA
1 ATAAAAAATTTTAATCATTAAATAATATA
*
2109449 TTAAAAAATTATT-AT-ACTTAAATAATATA
1 ATAAAAAATT-TTAATCA-TTAAATAATATA
2109478 ATAAA
1 ATAAA
2109483 GATATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 1 0.03
28 17 0.59
29 11 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAAAAATTTTAATCATTAAATAATATA
Found at i:2115496 original size:17 final size:17
Alignment explanation
Indices: 2115474--2115507 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2115464 TTTTTTAATT
*
2115474 AATAAAAGATTATATTA
1 AATAAAAGATAATATTA
*
2115491 AATAAAATATAATATTA
1 AATAAAAGATAATATTA
2115508 TTATAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AATAAAAGATAATATTA
Found at i:2115499 original size:22 final size:22
Alignment explanation
Indices: 2115474--2115522 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2115464 TTTTTTAATT
2115474 AATAAAAGATTA-TATTAAATAA
1 AATAAAAGATTATTA-TAAATAA
* * *
2115496 AATATAATATTATTATAAATAT
1 AATAAAAGATTATTATAAATAA
2115518 AATAA
1 AATAA
2115523 TAGTTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATAAAAGATTATTATAAATAA
Done.