Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 11 of 15
Found at i:1717628 original size:22 final size:22
Alignment explanation
Indices: 1717601--1717645 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1717591 AAATATTAAA
1717601 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAAT-TTT
1717623 ATATATTTTTATAATTAATTTT
1 ATATATTTTTATAATTAATTTT
1717645 A
1 A
1717646 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATATTTTTATAATTAATTTT
Found at i:1717782 original size:14 final size:14
Alignment explanation
Indices: 1717747--1717785 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1717737 AGTTTAGTTT
*
1717747 TATATATATATATA
1 TATATATGTATATA
*
1717761 TATATATGTATATG
1 TATATATGTATATA
*
1717775 TATGTATGTAT
1 TATATATGTAT
1717786 GTGCACGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:1717891 original size:3 final size:3
Alignment explanation
Indices: 1717885--1717937 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
1717875 TTGGGTTATT
* * * * *
1717885 ATC ATC ATC ATC ATC ATC ATC ATC AAC ATT ATC ATT ATC ATT ATC ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1717933 ATC AT
1 ATC AT
1717938 TTTCATTTTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:1717938 original size:6 final size:6
Alignment explanation
Indices: 1717882--1717955 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
1717872 TATTTGGGTT
* * * * *
1717882 ATTATC ATCATC ATCATC ATCATC ATCAAC ATTATC ATTATC ATTATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
* *
1717930 ATTATC ATTTTC ATTTTC ATTATC AT
1 ATTATC ATTATC ATTATC ATTATC AT
1717956 CATTATTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTATC
Found at i:1717963 original size:18 final size:17
Alignment explanation
Indices: 1717911--1717963 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
1717901 TCATCATCAA
* *
1717911 CATTATCATTATCATTAT
1 CATTATCA-TATTATTTT
*
1717929 CATTATCATTTTCATTTT
1 CATTATCATATT-ATTTT
1717947 CATTATCATCATTATTT
1 CATTATCAT-ATTATTT
1717964 ATTTTAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (17 bp):
CATTATCATATTATTTT
Found at i:1718278 original size:29 final size:30
Alignment explanation
Indices: 1718245--1718323 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
1718235 ACATTCAATT
* * *
1718245 TTTTTAATTTTTTATTTATATTCAAATAAA
1 TTTTTAATTTTTAATTTATACTCAAACAAA
* * *
1718275 -TTTTAATATTTAATTTGTGCTCAAACAAA
1 TTTTTAATTTTTAATTTATACTCAAACAAA
1718304 TTTTTAATTTTTAATTTATA
1 TTTTTAATTTTTAATTTATA
1718324 ATTTTTTTCA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTTTAATTTTTAATTTATACTCAAACAAA
Found at i:1720030 original size:36 final size:36
Alignment explanation
Indices: 1719990--1720062 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1719980 TTCTTTTTCC
1719990 TTTTCCCCATTTAGTCCAACAAATATTTTTAATGTA
1 TTTTCCCCATTTAGTCCAACAAATATTTTTAATGTA
1720026 TTTTCCCCATTTAGTCCAACAAATATTTTTAATGTA
1 TTTTCCCCATTTAGTCCAACAAATATTTTTAATGTA
1720062 T
1 T
1720063 CCCAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTCCCCATTTAGTCCAACAAATATTTTTAATGTA
Found at i:1720371 original size:16 final size:16
Alignment explanation
Indices: 1720329--1720360 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1720319 TAAAATAACT
*
1720329 AATCAAATTAATTTAA
1 AATCAAAATAATTTAA
1720345 AATCAAAATAATTTAA
1 AATCAAAATAATTTAA
1720361 TTCATAAATA
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:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCAAAATAATTTAA
Found at i:1723833 original size:18 final size:17
Alignment explanation
Indices: 1723796--1723852 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1723786 TTTATTAAAT
* **
1723796 TATTATATAATTTTAAA
1 TATTATATTATTTTTTA
1723813 TATTTATATTATTTTTTA
1 TA-TTATATTATTTTTTA
* *
1723831 TATCATATTATATTTTA
1 TATTATATTATTTTTTA
1723848 -ATTAT
1 TATTAT
1723853 TTTTTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
18 14 0.42
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATATTATTTTTTA
Found at i:1725422 original size:2 final size:2
Alignment explanation
Indices: 1725415--1725455 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1725405 ATGGGGTTGA
* *
1725415 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1725456 GTTATTGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1725737 original size:24 final size:24
Alignment explanation
Indices: 1725710--1725756 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1725700 TACATATTTA
1725710 ATTTTTTAATTTAT-TAAATAATAT
1 ATTTTTT-ATTTATATAAATAATAT
*
1725734 ATTTTTTATTTTTATAAATAATA
1 ATTTTTTATTTATATAAATAATA
1725757 AATTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTTATTTATATAAATAATAT
Found at i:1725738 original size:22 final size:24
Alignment explanation
Indices: 1725712--1725756 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1725702 CATATTTAAT
1725712 TTTTTAATTTAT-TAAATAATATA
1 TTTTTAATTTATATAAATAATATA
* *
1725735 TTTTTTATTTTTATAAATAATA
1 TTTTTAATTTATATAAATAATA
1725757 AATTAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTAATTTATATAAATAATATA
Found at i:1736483 original size:7 final size:7
Alignment explanation
Indices: 1736471--1736495 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1736461 TATATTTATT
1736471 TTAAAAA
1 TTAAAAA
1736478 TTAAAAA
1 TTAAAAA
1736485 TTAAAAA
1 TTAAAAA
1736492 TTAA
1 TTAA
1736496 TATTATATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TTAAAAA
Found at i:1736987 original size:10 final size:10
Alignment explanation
Indices: 1736972--1737025 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
1736962 TTATTTGTCT
*
1736972 TATATACACA
1 TATATACATA
*
1736982 TATATATATA
1 TATATACATA
*
1736992 TATATATATA
1 TATATACATA
*
1737002 TATATACACA
1 TATATACATA
**
1737012 CGTATACATA
1 TATATACATA
1737022 TATA
1 TATA
1737026 CCCTACTAGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (10 bp):
TATATACATA
Found at i:1737025 original size:2 final size:2
Alignment explanation
Indices: 1736981--1737007 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1736971 TTATATACAC
1736981 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 A
1737008 CACACGTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1737145 original size:23 final size:25
Alignment explanation
Indices: 1737100--1737145 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1737090 TATAAAAAAT
* *
1737100 AAAAATATTATATGATTATAATATA
1 AAAAATAATATATAATTATAATATA
1737125 AAAAATAATATA-AATT-TAATA
1 AAAAATAATATATAATTATAATA
1737146 CAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 3 0.16
25 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAAATAATATATAATTATAATATA
Found at i:1737310 original size:22 final size:25
Alignment explanation
Indices: 1737271--1737330 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 25
1737261 TTTTAATTAT
1737271 TATTCAAATA-TAATTATAAAAAT-A
1 TATT-AAATATTAATTATAAAAATAA
1737295 TA-TAAATATTAA-TATAAAAATAA
1 TATTAAATATTAATTATAAAAATAA
1737318 TATTATAATATTA
1 TATTA-AATATTA
1737331 TAATATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 14 0.44
23 7 0.22
24 4 0.12
25 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TATTAAATATTAATTATAAAAATAA
Found at i:1738133 original size:13 final size:14
Alignment explanation
Indices: 1738098--1738127 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1738088 AGAAATGGTC
1738098 CAAATTTTTTTTTT
1 CAAATTTTTTTTTT
1738112 CAGAATTTTTTTTTT
1 CA-AATTTTTTTTTT
1738127 C
1 C
1738128 CATTTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 2 0.13
15 13 0.87
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (14 bp):
CAAATTTTTTTTTT
Found at i:1739121 original size:19 final size:19
Alignment explanation
Indices: 1739099--1739136 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1739089 TTTAAAATTT
* *
1739099 TTTTAAATATATAAAAATA
1 TTTTAAAAAAATAAAAATA
1739118 TTTTAAAAAAATAAAAATA
1 TTTTAAAAAAATAAAAATA
1739137 ATCATATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTTAAAAAAATAAAAATA
Found at i:1740962 original size:6 final size:6
Alignment explanation
Indices: 1740951--1740976 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1740941 ATTATCTGGA
1740951 ATTTTG ATTTTG ATTTTG ATTTTG AT
1 ATTTTG ATTTTG ATTTTG ATTTTG AT
1740977 GTTTCTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:1741536 original size:16 final size:16
Alignment explanation
Indices: 1741511--1741550 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1741501 TCTCGTTAAA
*
1741511 TTTTAATATTTTATTT
1 TTTTAATATTTTAATT
*
1741527 TTTTATTATTTTAATT
1 TTTTAATATTTTAATT
1741543 TTTTAATA
1 TTTTAATA
1741551 GCTTACAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAATATTTTAATT
Found at i:1743687 original size:14 final size:14
Alignment explanation
Indices: 1743665--1743694 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1743655 GGTCACATAG
1743665 TAAGGTTGTCGACA
1 TAAGGTTGTCGACA
*
1743679 TAAGTTTGTCGACA
1 TAAGGTTGTCGACA
1743693 TA
1 TA
1743695 CGTCTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (14 bp):
TAAGGTTGTCGACA
Found at i:1744254 original size:2 final size:2
Alignment explanation
Indices: 1744247--1744271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1744237 ATTTATATTT
1744247 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1744272 TGGAATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1746059 original size:83 final size:83
Alignment explanation
Indices: 1745920--1746087 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
1745910 TGACCCCTGC
* * * *
1745920 TCTCGAAAATACACTCTTCCAAGTCCAGACTACTCTCGGATCAACCATGACACTGACACTTTATC
1 TCTCGAAAACACACTCTTCCAAGTCCAAACTACTCTCGGAACAACCATGACACTGACACTGTATC
*
1745985 CCACCAATTCCAAACTAT
66 CCACCAATGCCAAACTAT
1746003 TCTCGAAAACACACTCTTCCAAGTCCAAACTACTCTCGGAACAACCATGACACTGACACTGTATC
1 TCTCGAAAACACACTCTTCCAAGTCCAAACTACTCTCGGAACAACCATGACACTGACACTGTATC
1746068 CCACCAATGCCAAACTAT
66 CCACCAATGCCAAACTAT
1746086 TC
1 TC
1746088 GCGGACTGTG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.23
Consensus pattern (83 bp):
TCTCGAAAACACACTCTTCCAAGTCCAAACTACTCTCGGAACAACCATGACACTGACACTGTATC
CCACCAATGCCAAACTAT
Found at i:1752293 original size:16 final size:15
Alignment explanation
Indices: 1752259--1752305 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1752249 AAAAGAGATG
*
1752259 TAAATATTAATAT-T
1 TAAATATTAATTTAT
*
1752273 TAAATTTTATATTTAT
1 TAAATATTA-ATTTAT
1752289 TAAATATTAATTTAT
1 TAAATATTAATTTAT
1752304 TA
1 TA
1752306 TATAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.29
15 11 0.39
16 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTAATTTAT
Found at i:1753304 original size:17 final size:17
Alignment explanation
Indices: 1753282--1753314 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1753272 CATACATTAT
1753282 ATATAA-ATTAATTATAA
1 ATATAATATT-ATTATAA
1753299 ATATAATATTATTATA
1 ATATAATATTATTATA
1753315 TATTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATTATTATAA
Found at i:1755153 original size:15 final size:14
Alignment explanation
Indices: 1755129--1755158 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1755119 TCAATCATAT
1755129 AAAAAAATAAAATA
1 AAAAAAATAAAATA
1755143 AAAATAAATAAAATA
1 AAAA-AAATAAAATA
1755158 A
1 A
1755159 TTATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAATAAAATA
Found at i:1755914 original size:25 final size:27
Alignment explanation
Indices: 1755886--1755972 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 27
1755876 GTATAATACG
1755886 AATATAATATAAAA-AT-AATAATTTA
1 AATATAATATAAAATATAAATAATTTA
1755911 AATATAATATAAAATTATAAATAATTTA
1 AATATAATATAAAA-TATAAATAATTTA
* * *
1755939 AA-AT-TTATATAATATAAATTA-TT-
1 AATATAATATAAAATATAAATAATTTA
1755962 AATAT-ATATAA
1 AATATAATATAA
1755973 TTTTATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
23 2 0.04
24 8 0.15
25 22 0.42
26 6 0.11
27 4 0.08
28 11 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATAATATAAAATATAAATAATTTA
Found at i:1755934 original size:17 final size:17
Alignment explanation
Indices: 1755914--1755972 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1755904 TAATTTAAAT
1755914 ATAATATAAAATTATAA
1 ATAATATAAAATTATAA
* *
1755931 ATAATTTAAAATT-TAT
1 ATAATATAAAATTATAA
*
1755947 ATAATAT-AAATTATTA
1 ATAATATAAAATTATAA
1755963 ATATATATAA
1 ATA-ATATAA
1755973 TTTTATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 5 0.15
16 12 0.35
17 16 0.47
18 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATAAAATTATAA
Found at i:1756910 original size:26 final size:26
Alignment explanation
Indices: 1756881--1756933 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1756871 TCATTAGATT
* *
1756881 TTATTAATAAT-ATATTTTTAAAATTA
1 TTATAAATAATAATATTTAT-AAATTA
1756907 TTATAAATAATAATATTTATAAATTA
1 TTATAAATAATAATATTTATAAATTA
1756933 T
1 T
1756934 AAATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTATAAATAATAATATTTATAAATTA
Found at i:1756946 original size:23 final size:23
Alignment explanation
Indices: 1756906--1756951 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1756896 TTTTAAAATT
*
1756906 ATTATAAATAATAATATTTATAA
1 ATTATAAATAATAATATTAATAA
1756929 ATTATAAATAA-AATTATTAATAA
1 ATTATAAATAATAA-TATTAATAA
1756952 CATTTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTATAAATAATAATATTAATAA
Found at i:1757043 original size:15 final size:15
Alignment explanation
Indices: 1757018--1757052 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1757008 TTTTTTATTA
1757018 TTTTATTA-TTTTAT
1 TTTTATTATTTTTAT
1757032 TTTTAGTTATTTTTAT
1 TTTTA-TTATTTTTAT
1757048 TTTTA
1 TTTTA
1757053 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 3 0.16
16 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:1757462 original size:2 final size:2
Alignment explanation
Indices: 1757455--1757481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1757445 TAGTTATGTT
1757455 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
1757482 GACAATTTCA
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:1757662 original size:38 final size:36
Alignment explanation
Indices: 1757609--1757686 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
1757599 TATTTTTTAT
*
1757609 TAAAAAAATAAAAATT-TAATTTTT-TTCCTATAAATAA
1 TAAAAAAATAAAAATTAAAATTTTTATT--TATAAAT-A
*
1757646 TAAAAAAATATCAAATTAAAATTTTTATTTATAAATA
1 TAAAAAAATA-AAAATTAAAATTTTTATTTATAAATA
1757683 TAAA
1 TAAA
1757687 TTCAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
37 15 0.42
38 12 0.33
39 7 0.19
40 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (36 bp):
TAAAAAAATAAAAATTAAAATTTTTATTTATAAATA
Found at i:1757752 original size:15 final size:14
Alignment explanation
Indices: 1757733--1757771 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1757723 ATAATTTAAT
1757733 TATTATTTTTATAA
1 TATTATTTTTATAA
*
1757747 TAATTATTTTAAT-A
1 T-ATTATTTTTATAA
1757761 TATTATTTTTA
1 TATTATTTTTA
1757772 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 3 0.14
15 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTTTTATAA
Found at i:1757783 original size:28 final size:27
Alignment explanation
Indices: 1757716--1757784 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
1757706 CAAATACTAA
1757716 TTAAAA-AATAA-TTTAATTATTATTT
1 TTAAAATAATAATTTTAATTATTATTT
* *
1757741 TTATAATAATTATTTTAATATATTATTT
1 TTAAAATAATAATTTTAAT-TATTATTT
1757769 TTAAAAATAA-AATTTT
1 TT-AAAATAATAATTTT
1757785 TTAAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
26 4 0.11
27 6 0.17
28 15 0.42
29 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAAATAATAATTTTAATTATTATTT
Found at i:1764237 original size:97 final size:99
Alignment explanation
Indices: 1764064--1764258 Score: 279
Period size: 97 Copynumber: 2.0 Consensus size: 99
1764054 TGCTTTCCTT
* *
1764064 GTGCCAATAATAGGGCCTATGCTTTGACAGGTCTTTCTCATCCACAAACAACTTATTGACCACCA
1 GTGCCAATAATAGGGCCTATGCTTTGACAGGCCTTTCCCATCCACAAACAACTTATTGACCACCA
* *
1764129 CAAAGTGGATCCCCTTAGGTTAAGTGATTTGTTG
66 CAAAGTGGATCCCCTTAGATTAAATGATTTGTTG
** * *
1764163 GTGCC-ATAATAGGGCCTATGC-TTGACAGGCCTTTCCCATTTACTAAA-AATTTATTGACGACC
1 GTGCCAATAATAGGGCCTATGCTTTGACAGGCCTTTCCCATCCAC-AAACAACTTATTGACCACC
*
1764225 ACAAAGTGGATCCCCTTCGATTAAATGATTTGTT
65 ACAAAGTGGATCCCCTTAGATTAAATGATTTGTT
1764259 CATAACCTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 62 0.72
98 19 0.22
99 5 0.06
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (99 bp):
GTGCCAATAATAGGGCCTATGCTTTGACAGGCCTTTCCCATCCACAAACAACTTATTGACCACCA
CAAAGTGGATCCCCTTAGATTAAATGATTTGTTG
Found at i:1772983 original size:34 final size:35
Alignment explanation
Indices: 1772906--1772985 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
1772896 GTAAGTTTTA
**
1772906 AATATAAAT-TTTTTAATTTAAATTATTATTTAAT
1 AATATAAATATTTTTAATTTAAATTATTATGAAAT
*
1772940 AATAAAAATATTTTT-ATTTAAATTAATTATGAAAT
1 AATATAAATATTTTTAATTTAAATT-ATTATGAAAT
1772975 -ATATAAATATT
1 AATATAAATATT
1772986 AATATAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 27 0.68
35 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (35 bp):
AATATAAATATTTTTAATTTAAATTATTATGAAAT
Found at i:1774088 original size:45 final size:46
Alignment explanation
Indices: 1774016--1774110 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 46
1774006 ACAATTAATA
*
1774016 ATTTATTCTTTAAAAAACAGAACTTCC-ATTACAAAAGAAGAAAAT
1 ATTTATTCTTTAAAAAACAGAACTTCCTATTACAAAAGAAAAAAAT
***
1774061 ATTTATTCTTTAAAAAACAGTGTTTCCATTATTACAAAAGAAAAAAAT
1 ATTTATTCTTTAAAAAACAGAACTTCC--TATTACAAAAGAAAAAAAT
1774109 AT
1 AT
1774111 CATGTAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 24 0.56
48 19 0.44
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (46 bp):
ATTTATTCTTTAAAAAACAGAACTTCCTATTACAAAAGAAAAAAAT
Found at i:1774567 original size:3 final size:3
Alignment explanation
Indices: 1774561--1774597 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1774551 CATATTAAAA
* *
1774561 CAG CAG CAG TAG CAG CAG CAG CAG AAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1774598 TGGTCCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.30, G:0.32, T:0.03
Consensus pattern (3 bp):
CAG
Found at i:1774579 original size:15 final size:15
Alignment explanation
Indices: 1774561--1774597 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1774551 CATATTAAAA
*
1774561 CAGCAGCAGTAGCAG
1 CAGCAGCAGAAGCAG
1774576 CAGCAGCAGAAGCAG
1 CAGCAGCAGAAGCAG
1774591 CAGCAGC
1 CAGCAGC
1774598 TGGTCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.32, T:0.03
Consensus pattern (15 bp):
CAGCAGCAGAAGCAG
Found at i:1781481 original size:23 final size:23
Alignment explanation
Indices: 1781443--1781502 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1781433 TATTATTATT
*
1781443 TTTAATAAAATT-AAAATAA-TA
1 TTTAATAAAATTAAAAAAAATTA
*
1781464 TTTAATTAAATTAAAAAAAATTA
1 TTTAATAAAATTAAAAAAAATTA
*
1781487 TATTAA-CAAATTAAAA
1 T-TTAATAAAATTAAAA
1781503 TATTAACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 11 0.33
22 6 0.18
23 12 0.36
24 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAATAAAATTAAAAAAAATTA
Found at i:1781507 original size:21 final size:21
Alignment explanation
Indices: 1781439--1781507 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1781429 TTATTATTAT
*
1781439 TATT-TTTAATAAAATTAAAA
1 TATTATTTAATCAAATTAAAA
* *
1781459 TAATATTTAATTAAATTAAAAAA
1 TATTATTTAATCAAATT--AAAA
*
1781482 AATTATATTAA-CAAATTAAAA
1 TATTAT-TTAATCAAATTAAAA
1781503 TATTA
1 TATTA
1781508 ACTAATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 3 0.08
21 19 0.49
23 13 0.33
24 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTATTTAATCAAATTAAAA
Found at i:1781557 original size:15 final size:15
Alignment explanation
Indices: 1781520--1781557 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1781510 TAATATATTT
1781520 TATAAAAATAAAAAA
1 TATAAAAATAAAAAA
* *
1781535 TTTTAAAATAAAAAA
1 TATAAAAATAAAAAA
1781550 TATAAAAA
1 TATAAAAA
1781558 AATTATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
TATAAAAATAAAAAA
Found at i:1781647 original size:130 final size:128
Alignment explanation
Indices: 1781362--1781657 Score: 361
Period size: 130 Copynumber: 2.3 Consensus size: 128
1781352 CTATATTTCT
* *
1781362 ATTACCAAATTAAAATAATTAATTAGT-T-TTTTT-AAAATAAAAAAATTTAAATAAAAATAATA
1 ATTAACAAATTAAAAT-ATTAATTAATATATTTTTAAAAATAAAAAAATTTAAATAAAAATAATA
*** * * *
1781424 ACAGTTTATTATTATTATTTTTAATAAAATTAAAATAATATTTAATTAAATTAAAAAAAATTAT
65 ACAGAAAATTATTATAATTTTTAATAAAATAAAAATAATATTTAATTAAATTAAAAAAAATTAC
* *
1781488 ATTAACAAATTAAAATATTAACTAATATATTTTATAAAAATAAAAAATTTTAAAATAAAAA-ATA
1 ATTAACAAATTAAAATATTAATTAATATATTTT-TAAAAATAAAAAAATTT-AAATAAAAATA-A
* **
1781552 TAA-A-AAAATTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTTAAAAAATTT
63 TAACAGAAAATTATTATAATTTTTAATAAAAT-AAAAATAATATTTAATTAA-ATTAAAAAAAAT
1781615 TAC
126 TAC
* *
1781618 ATTAACAAATTAAAATATTAATTATTATATTTTTTAAAAT
1 ATTAACAAATTAAAATATTAATTAATATATTTTTAAAAAT
1781658 TTTAAATTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
125 8 0.05
126 16 0.11
127 4 0.03
128 23 0.16
129 40 0.27
130 55 0.38
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (128 bp):
ATTAACAAATTAAAATATTAATTAATATATTTTTAAAAATAAAAAAATTTAAATAAAAATAATAA
CAGAAAATTATTATAATTTTTAATAAAATAAAAATAATATTTAATTAAATTAAAAAAAATTAC
Found at i:1781975 original size:24 final size:23
Alignment explanation
Indices: 1781941--1782021 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
1781931 TAAATAAAAA
* *
1781941 TTTTTTCATTTGAATAATGATAAT
1 TTTTTTAATTTG-TTAATGATAAT
* *
1781965 TTTTTTAATTTCTTAAAT-ATTAT
1 TTTTTTAATTTGTT-AATGATAAT
*
1781988 TTTTTTAATTTGTTATTG-TAAAT
1 TTTTTTAATTTGTTAATGAT-AAT
1782011 TTTTTTAATTT
1 TTTTTTAATTT
1782022 AATTAAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 3 0.06
23 31 0.66
24 13 0.28
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTTTTAATTTGTTAATGATAAT
Found at i:1781989 original size:23 final size:23
Alignment explanation
Indices: 1781963--1782037 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
1781953 AATAATGATA
*
1781963 ATTTTTTTAATTTCTTAAATATT
1 ATTTTTTTAATTTATTAAATATT
* * * *
1781986 ATTTTTTTAATTTGTT-ATTGTAA
1 ATTTTTTTAATTTATTAAATAT-T
1782009 ATTTTTTTAATTTAATTAAATATT
1 ATTTTTTTAATTT-ATTAAATATT
1782033 ATTTT
1 ATTTT
1782038 ATTTTATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.07
23 28 0.68
24 7 0.17
25 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (23 bp):
ATTTTTTTAATTTATTAAATATT
Found at i:1781992 original size:46 final size:46
Alignment explanation
Indices: 1781940--1782037 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 46
1781930 TTAAATAAAA
* *
1781940 ATTTTTTCATTTGAATAATG-ATAATTTTTTTAATTT-CTTAAATATT
1 ATTTTTTAATTTG-ATAATGTA-AATTTTTTTAATTTAATTAAATATT
* *
1781986 ATTTTTTTAATTTGTTATTGTAAATTTTTTTAATTTAATTAAATATT
1 A-TTTTTTAATTTGATAATGTAAATTTTTTTAATTTAATTAAATATT
1782033 ATTTT
1 ATTTT
1782038 ATTTTATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 23 0.51
47 22 0.49
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (46 bp):
ATTTTTTAATTTGATAATGTAAATTTTTTTAATTTAATTAAATATT
Found at i:1781992 original size:47 final size:47
Alignment explanation
Indices: 1781927--1782037 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
1781917 TATATATAAA
** * *
1781927 TAATTAAATAAAAATTTTTTCATTTGAATAATG-ATAATTTTTTTAATT
1 TAATTAAATATTATTTTTTTAATTTG-ATAATGTA-AATTTTTTTAATT
* * *
1781975 T-CTTAAATATTATTTTTTTAATTTGTTATTGTAAATTTTTTTAATT
1 TAATTAAATATTATTTTTTTAATTTGATAATGTAAATTTTTTTAATT
1782021 TAATTAAATATTATTTT
1 TAATTAAATATTATTTT
1782038 ATTTTATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
46 18 0.34
47 34 0.64
48 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (47 bp):
TAATTAAATATTATTTTTTTAATTTGATAATGTAAATTTTTTTAATT
Found at i:1791473 original size:12 final size:12
Alignment explanation
Indices: 1791456--1791485 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1791446 AATAAAGGAC
1791456 AAAAGAGGTCCA
1 AAAAGAGGTCCA
1791468 AAAAGAGGTCCA
1 AAAAGAGGTCCA
*
1791480 AGAAGA
1 AAAAGA
1791486 AAACAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.27, T:0.07
Consensus pattern (12 bp):
AAAAGAGGTCCA
Found at i:1794941 original size:1 final size:1
Alignment explanation
Indices: 1794935--1794961 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1794925 TAAAGAATGG
1794935 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1794962 GAGGTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1796968 original size:3 final size:3
Alignment explanation
Indices: 1796962--1796987 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1796952 CTGCGACAAG
1796962 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1796988 CAATGAAGAA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1797310 original size:2 final size:2
Alignment explanation
Indices: 1797305--1797343 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1797295 CAACCAAAAA
*
1797305 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1797344 ATTGTGGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1797480 original size:14 final size:14
Alignment explanation
Indices: 1797442--1797480 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1797432 GCAACCGCTA
*
1797442 TTTTTTATTTTCCT
1 TTTTTTTTTTTCCT
*
1797456 TTTCTTTTTTTCCT
1 TTTTTTTTTTTCCT
1797470 TTTTTTTTTTT
1 TTTTTTTTTTT
1797481 TAAGATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTCCT
Found at i:1797631 original size:21 final size:22
Alignment explanation
Indices: 1797591--1797651 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
1797581 TTTTTTTTTT
*
1797591 AATTATTTTATATATAATAAAA
1 AATTATATTATATATAATAAAA
*
1797613 AATTATATTTATATGATAATTTAAA
1 AATTATA-TTATAT-ATAA-TAAAA
*
1797638 AA-TATATAATATAT
1 AATTATATTATATAT
1797652 GCGTATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 8 0.24
23 11 0.33
24 8 0.24
25 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTATATTATATATAATAAAA
Found at i:1797717 original size:23 final size:23
Alignment explanation
Indices: 1797674--1797717 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1797664 TGTAAATATA
* *
1797674 ATATATATTATTTAATTATTTTT
1 ATATATATTATTAAATAATTTTT
1797697 ATATAATATTA-TAAATAATTT
1 ATAT-ATATTATTAAATAATTT
1797718 AAATTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATATATTATTAAATAATTTTT
Found at i:1797822 original size:20 final size:20
Alignment explanation
Indices: 1797785--1797822 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1797775 TTAGTTTGAG
*
1797785 ATATTTTTATTAATTTTAAA
1 ATATTTTTATAAATTTTAAA
1797805 ATATTTTT-TAAATATTTA
1 ATATTTTTATAAAT-TTTA
1797823 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTTTATAAATTTTAAA
Found at i:1802822 original size:13 final size:14
Alignment explanation
Indices: 1802798--1802826 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1802788 ATTTTTAATA
1802798 TAAAATTTAAATTT
1 TAAAATTTAAATTT
1802812 TAAAA-TTAAATTT
1 TAAAATTTAAATTT
1802825 TA
1 TA
1802827 TCAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATTTAAATTT
Found at i:1803077 original size:10 final size:10
Alignment explanation
Indices: 1803059--1803087 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1803049 TTAAATATAT
1803059 AAAAA-ATTA
1 AAAAATATTA
1803068 AAAAATATTA
1 AAAAATATTA
1803078 AAAAATATTA
1 AAAAATATTA
1803088 TATATCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATATTA
Found at i:1806370 original size:23 final size:23
Alignment explanation
Indices: 1806329--1806391 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1806319 TATTTTTAAT
*
1806329 ATTTTAATAATTTTATTATATAA
1 ATTTTAATAATATTATTATATAA
*
1806352 ATTTTAATAAATATT-TTATATTA
1 ATTTTAAT-AATATTATTATATAA
* *
1806375 TTTTTATTTAATATTAT
1 ATTTTA-ATAATATTAT
1806392 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 26 0.79
24 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTAATAATATTATTATATAA
Found at i:1806708 original size:14 final size:15
Alignment explanation
Indices: 1806678--1806715 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1806668 CTTAAAATTT
*
1806678 ATTAATTATATTATA
1 ATTATTTATATTATA
*
1806693 ATTTTTTATA-TATA
1 ATTATTTATATTATA
1806707 ATTATTTAT
1 ATTATTTAT
1806716 TCTTGATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTTATATTATA
Found at i:1807670 original size:8 final size:8
Alignment explanation
Indices: 1807659--1807683 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1807649 CCCAAAACAC
1807659 AAAAATAA
1 AAAAATAA
1807667 AAAAATAA
1 AAAAATAA
1807675 AAAAATAA
1 AAAAATAA
1807683 A
1 A
1807684 GCTGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:1808593 original size:3 final size:3
Alignment explanation
Indices: 1808585--1808610 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1808575 TACAACCAAA
1808585 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1808611 AGAAAAAAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1809650 original size:28 final size:27
Alignment explanation
Indices: 1809616--1809669 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1809606 CTATAATTCA
1809616 AATCAATTGTTTAATTTTCTCAA-ATTTT
1 AATCAATT-TTT-ATTTTCTCAATATTTT
*
1809644 AATCAATTTTTATTTTTTCAATATTT
1 AATCAATTTTTATTTTCTCAATATTT
1809670 CTTTCCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 7 0.29
28 8 0.33
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.57
Consensus pattern (27 bp):
AATCAATTTTTATTTTCTCAATATTTT
Found at i:1809878 original size:2 final size:2
Alignment explanation
Indices: 1809855--1809901 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1809845 TTTTATTTAC
* * *
1809855 AT AT GT AT AC AT AT AA AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809896 AT AT AT
1 AT AT AT
1809902 TTGCATGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1811142 original size:27 final size:27
Alignment explanation
Indices: 1811112--1811199 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
1811102 GCTGGAAACT
* *
1811112 CAAAAGCTTTTCGCCTAGCTTTGAGTC
1 CAAAAGCTTTTCCCCAAGCTTTGAGTC
*
1811139 CAAAAGCTTTTCCCCAAGCCTTGAGTC
1 CAAAAGCTTTTCCCCAAGCTTTGAGTC
*
1811166 CAAAAGCTTTTCCCCAAGCTCTGAGTC
1 CAAAAGCTTTTCCCCAAGCTTTGAGTC
1811193 CAAAAGC
1 CAAAAGC
1811200 CTGCAGCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (27 bp):
CAAAAGCTTTTCCCCAAGCTTTGAGTC
Found at i:1813266 original size:2 final size:2
Alignment explanation
Indices: 1813261--1813290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1813251 TTTTTTCTTT
1813261 TA TA TA 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
1813291 CACACTTTTA
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):
TA
Found at i:1815339 original size:18 final size:18
Alignment explanation
Indices: 1815318--1815362 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1815308 TTGATTTAGT
1815318 TTAAATTATTATTTTACA
1 TTAAATTATTATTTTACA
*
1815336 TTAAATTACTATTTTACA
1 TTAAATTATTATTTTACA
1815354 TTAAATTAT
1 TTAAATTAT
1815363 GTTTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTATTATTTTACA
Found at i:1816034 original size:17 final size:19
Alignment explanation
Indices: 1816012--1816048 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1816002 TTTTTACATT
1816012 TAAATATT-TAT-TAAATA
1 TAAATATTATATATAAATA
1816029 TAAATATTATATATAAATA
1 TAAATATTATATATAAATA
1816048 T
1 T
1816049 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATTATATATAAATA
Found at i:1816042 original size:13 final size:13
Alignment explanation
Indices: 1816020--1816052 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1816010 TTTAAATATT
1816020 TATTAAATATAAA
1 TATTAAATATAAA
*
1816033 TATTATATATAAA
1 TATTAAATATAAA
1816046 TATTAAA
1 TATTAAA
1816053 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:1816529 original size:2 final size:2
Alignment explanation
Indices: 1816522--1816551 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1816512 TAACAATTAT
1816522 TA TA TA 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
1816552 AAATAAAATA
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):
TA
Found at i:1817045 original size:36 final size:30
Alignment explanation
Indices: 1816962--1817030 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
1816952 AAAATAAAAT
*
1816962 ACTTTTGCTGATGTTATTCTCTTTCATTTC
1 ACTTTTGCTGATGTTTTTCTCTTTCATTTC
1816992 ACTTTTGCTGATGTTTTTCTCTTTCATTTC
1 ACTTTTGCTGATGTTTTTCTCTTTCATTTC
1817022 ACTTTTGCT
1 ACTTTTGCT
1817031 TTGTTGGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.58
Consensus pattern (30 bp):
ACTTTTGCTGATGTTTTTCTCTTTCATTTC
Found at i:1817453 original size:18 final size:18
Alignment explanation
Indices: 1817421--1817464 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1817411 GAGATTCAAA
*
1817421 TTTTAATATATTTAATCTT
1 TTTTATTATATTTAAT-TT
1817440 TTTTATTATA-TTAATTT
1 TTTTATTATATTTAATTT
1817457 TTTT-TTAT
1 TTTTATTAT
1817465 TTTTTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 5 0.21
19 9 0.38
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATATTTAATTT
Found at i:1818589 original size:13 final size:13
Alignment explanation
Indices: 1818563--1818595 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1818553 AAATAAATTA
1818563 TTAAT-TATTAAT
1 TTAATCTATTAAT
*
1818575 TTAATCTATTGAT
1 TTAATCTATTAAT
1818588 TTAATCTA
1 TTAATCTA
1818596 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (13 bp):
TTAATCTATTAAT
Found at i:1819056 original size:32 final size:33
Alignment explanation
Indices: 1818996--1819073 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 33
1818986 TTAGTTTAAA
* *
1818996 ATTTAAAACTATTTTATCCAATTTTTT-AAAAAT
1 ATTT-AAATTATTCTATCCAATTTTTTAAAAAAT
*
1819029 ATTTAAATTATTCTATCTAATTTTTTAAAAAAT
1 ATTTAAATTATTCTATCCAATTTTTTAAAAAAT
1819062 ATTTAATATTAT
1 ATTTAA-ATTAT
1819074 AATTTAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 19 0.47
33 16 0.40
34 5 0.12
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.51
Consensus pattern (33 bp):
ATTTAAATTATTCTATCCAATTTTTTAAAAAAT
Found at i:1823497 original size:2 final size:2
Alignment explanation
Indices: 1823490--1823520 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1823480 TGATCCGAAC
1823490 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 A
1823521 ATTTAAGTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1824434 original size:2 final size:2
Alignment explanation
Indices: 1824429--1824472 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1824419 AAATAAAAAA
*
1824429 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1824471 AT
1 AT
1824473 GAAAAATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826348 original size:2 final size:2
Alignment explanation
Indices: 1826341--1826368 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1826331 TTTAGAAAGG
1826341 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1826369 ACCATTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1828045 original size:67 final size:67
Alignment explanation
Indices: 1827937--1828068 Score: 176
Period size: 67 Copynumber: 2.0 Consensus size: 67
1827927 ATTGTTTCAG
* * * * * *
1827937 CTCTTTATTTTCTTTAATATTCGTGTCCAATCAATACATATCCTAACATAGATACAAGGACATGA
1 CTCTTCATTTTCTTTAATATTCATATCCAACCAACACATATCCTAACATAGATACAAAGACATGA
1828002 CC
66 CC
* *
1828004 CTCTTCATTTTCTTTAATA-TCTATATTCAACCAACACATATCCTAACATAGATATAAAGACATG
1 CTCTTCATTTTCTTTAATATTC-ATATCCAACCAACACATATCCTAACATAGATACAAAGACATG
1828068 A
65 A
1828069 TCTTTTTAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 2 0.04
67 54 0.96
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (67 bp):
CTCTTCATTTTCTTTAATATTCATATCCAACCAACACATATCCTAACATAGATACAAAGACATGA
CC
Found at i:1832310 original size:19 final size:19
Alignment explanation
Indices: 1832285--1832327 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1832275 ATAACCCAAG
*
1832285 AAAACAAATACTCAAAGTT
1 AAAACAAAAACTCAAAGTT
* *
1832304 TAAACAAAAATTCAAAGTT
1 AAAACAAAAACTCAAAGTT
1832323 AAAAC
1 AAAAC
1832328 CACAATATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAACAAAAACTCAAAGTT
Found at i:1836522 original size:19 final size:20
Alignment explanation
Indices: 1836487--1836524 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1836477 AATTTTTTAA
*
1836487 ATTTTTATTTTTATAATTAG
1 ATTTTTACTTTTATAATTAG
1836507 ATTTTTACTTTT-TAATTA
1 ATTTTTACTTTTATAATTA
1836525 TCTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTTACTTTTATAATTAG
Found at i:1838012 original size:29 final size:31
Alignment explanation
Indices: 1837980--1838045 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1837970 TGATAATTTT
* *
1837980 TTTTAAAAGCTTATAAAT-AGT-AAATATAAT
1 TTTTAAAAG-TTATAAATAAATAAAATATAAC
*
1838010 TTTTAAAAGTTATGAATAAATAAAATATAAC
1 TTTTAAAAGTTATAAATAAATAAAATATAAC
1838041 TTTTA
1 TTTTA
1838046 TAAAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
30 11 0.35
31 13 0.42
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (31 bp):
TTTTAAAAGTTATAAATAAATAAAATATAAC
Found at i:1838015 original size:30 final size:32
Alignment explanation
Indices: 1837979--1838057 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 32
1837969 GTGATAATTT
*
1837979 TTTTTAAAAGCTTATAAAT-AGT-AAATATAA-
1 TTTTTAAAAG-TTATAAATAAATAAAATATAAC
*
1838009 TTTTTAAAAGTTATGAATAAATAAAATATAAC
1 TTTTTAAAAGTTATAAATAAATAAAATATAAC
*
1838041 TTTTATAAAAATTATAA
1 TTTT-TAAAAGTTATAA
1838058 TGAAAATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.17
30 12 0.29
31 8 0.20
32 4 0.10
33 10 0.24
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (32 bp):
TTTTTAAAAGTTATAAATAAATAAAATATAAC
Found at i:1838029 original size:33 final size:33
Alignment explanation
Indices: 1837992--1838055 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
1837982 TTAAAAGCTT
*
1837992 ATAAATAGTAAATATAA-TTTT-TAAAAGTTATGA
1 ATAAATA--AAATATAACTTTTATAAAAATTATGA
1838025 ATAAATAAAATATAACTTTTATAAAAATTAT
1 ATAAATAAAATATAACTTTTATAAAAATTAT
1838056 AATGAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
32 4 0.14
33 16 0.57
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (33 bp):
ATAAATAAAATATAACTTTTATAAAAATTATGA
Found at i:1838719 original size:72 final size:72
Alignment explanation
Indices: 1838639--1838805 Score: 325
Period size: 72 Copynumber: 2.3 Consensus size: 72
1838629 ATTTATTATC
*
1838639 GATAAAATTATTAGTATTATGTATTTATAAATCAATCATATATCATTAAGTAACAAATATATTTA
1 GATAAAATTATTAGTATTAAGTATTTATAAATCAATCATATATCATTAAGTAACAAATATATTTA
1838704 AATTGTA
66 AATTGTA
1838711 GATAAAATTATTAGTATTAAGTATTTATAAATCAATCATATATCATTAAGTAACAAATATATTTA
1 GATAAAATTATTAGTATTAAGTATTTATAAATCAATCATATATCATTAAGTAACAAATATATTTA
1838776 AATTGTA
66 AATTGTA
1838783 GATAAAATTATTAGTATTAAGTA
1 GATAAAATTATTAGTATTAAGTA
1838806 ATTGTAGGGT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (72 bp):
GATAAAATTATTAGTATTAAGTATTTATAAATCAATCATATATCATTAAGTAACAAATATATTTA
AATTGTA
Found at i:1839382 original size:16 final size:18
Alignment explanation
Indices: 1839363--1839396 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1839353 TTAAATATCC
1839363 TTAA-TATA-ATATATAT
1 TTAATTATATATATATAT
1839379 TTAATTATATATATATAT
1 TTAATTATATATATATAT
1839397 ATATATGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTATATATATATAT
Found at i:1841043 original size:2 final size:2
Alignment explanation
Indices: 1841036--1841069 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1841026 GGCAAAAGTA
1841036 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
1841070 GAACTCCAAT
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:1844159 original size:40 final size:43
Alignment explanation
Indices: 1844077--1844171 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
1844067 TTTTGAGCTT
1844077 AAAAGTGCTACTTCTTAATTATCCCCAAAAAAAATAAATTAATA
1 AAAAGTGCTACTTCTTAATTAT-CCCAAAAAAAATAAATTAATA
*
1844121 AAAAG-GCTACTTTTTAATTAT-CCAAAAAAAA-AAATTAAT-
1 AAAAGTGCTACTTCTTAATTATCCCAAAAAAAATAAATTAATA
*
1844160 AAAAGTGTTACT
1 AAAAGTGCTACT
1844172 GTCGAAAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
39 5 0.10
40 13 0.27
41 10 0.21
43 15 0.31
44 5 0.10
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (43 bp):
AAAAGTGCTACTTCTTAATTATCCCAAAAAAAATAAATTAATA
Found at i:1844641 original size:19 final size:19
Alignment explanation
Indices: 1844617--1844660 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1844607 CTAAAAGCCC
* *
1844617 TTAATTTAATTTATTTTAT
1 TTAATTTAATTAAGTTTAT
*
1844636 TTAATTTAATTAAGTTTGT
1 TTAATTTAATTAAGTTTAT
1844655 TTAATT
1 TTAATT
1844661 AGTGACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTAATTTAATTAAGTTTAT
Found at i:1844828 original size:3 final size:3
Alignment explanation
Indices: 1844820--1844849 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1844810 AAATTTCTTA
1844820 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1844850 GAGAAGCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1845142 original size:2 final size:2
Alignment explanation
Indices: 1845135--1845160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1845125 GTATTAGGTA
1845135 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
1845161 TATTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1847057 original size:24 final size:24
Alignment explanation
Indices: 1847030--1847079 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1847020 ACCTAACTCT
* *
1847030 TAAACAAATCTAACTAAT-TATATA
1 TAAAAAAAT-TAAATAATATATATA
*
1847054 TAAAAAAATTAAATTATATATATA
1 TAAAAAAATTAAATAATATATATA
1847078 TA
1 TA
1847080 TATATGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAAAATTAAATAATATATATA
Found at i:1847093 original size:8 final size:8
Alignment explanation
Indices: 1847070--1847104 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1847060 AATTAAATTA
*
1847070 TATATATA
1 TATATATG
1847078 TATATATG
1 TATATATG
1847086 TATATATG
1 TATATATG
*
1847094 TATGTATG
1 TATATATG
1847102 TAT
1 TAT
1847105 GTATTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:1847105 original size:12 final size:12
Alignment explanation
Indices: 1847074--1847108 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1847064 AAATTATATA
*
1847074 TATATATATATG
1 TATATATGTATG
1847086 TATATATGTATG
1 TATATATGTATG
*
1847098 TATGTATGTAT
1 TATATATGTAT
1847109 TGATTGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (12 bp):
TATATATGTATG
Found at i:1847495 original size:35 final size:35
Alignment explanation
Indices: 1847455--1847522 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1847445 TGAAAATGTG
* *
1847455 ATGTATCCATTTGTTACAAACTAATTAAAATAATT
1 ATGTATCCATTTATTACAAACTAACTAAAATAATT
* *
1847490 ATGTATCTATTTATTATAAACTAACTAAAATAA
1 ATGTATCCATTTATTACAAACTAACTAAAATAA
1847523 CACTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (35 bp):
ATGTATCCATTTATTACAAACTAACTAAAATAATT
Found at i:1848222 original size:71 final size:71
Alignment explanation
Indices: 1848100--1848243 Score: 189
Period size: 71 Copynumber: 2.0 Consensus size: 71
1848090 GAAATTGGCC
* * * * *
1848100 AAGTTGTCAGGATCAAACCCTAATTTTATGAAAATTCATTTTCGAAGAGAACTTAATGAATCATT
1 AAGTTGTCAAGATCAAACCCTAATTTTACGAAAATTCATTTTCGAAAAGAACTGAAGGAATCATT
*
1848165 TAGATT
66 TAAATT
* * * **
1848171 AAGTTGTCAATATCAAATCCTAATTTTACGAAAATTGATTTTTTAAAAGAACTGAAGGAATCATT
1 AAGTTGTCAAGATCAAACCCTAATTTTACGAAAATTCATTTTCGAAAAGAACTGAAGGAATCATT
1848236 TAAATT
66 TAAATT
1848242 AA
1 AA
1848244 ATTTTAATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (71 bp):
AAGTTGTCAAGATCAAACCCTAATTTTACGAAAATTCATTTTCGAAAAGAACTGAAGGAATCATT
TAAATT
Found at i:1849031 original size:2 final size:2
Alignment explanation
Indices: 1849024--1849083 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
1849014 ATATTAATCC
* * * * *
1849024 AT AT AT AT AT AT AC AT AC AT AT AT AT AC AC AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1849066 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1849084 GAAGAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1849045 original size:16 final size:16
Alignment explanation
Indices: 1849026--1849083 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
1849016 ATTAATCCAT
1849026 ATATATATATACATAC
1 ATATATATATACATAC
*
1849042 ATATATATACACATAC
1 ATATATATATACATAC
* *
1849058 ATATATATATATATAT
1 ATATATATATACATAC
1849074 ATATATATAT
1 ATATATATAT
1849084 GAAGAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATATATACATAC
Found at i:1849368 original size:3 final size:3
Alignment explanation
Indices: 1849360--1849396 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1849350 ACATCTATGC
1849360 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1849397 TCATATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1851227 original size:2 final size:2
Alignment explanation
Indices: 1851220--1851260 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1851210 ATGCTTATTT
1851220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1851261 CTATCTCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1853392 original size:163 final size:164
Alignment explanation
Indices: 1853210--1853624 Score: 439
Period size: 171 Copynumber: 2.5 Consensus size: 164
1853200 TGTTAGGTCG
* * * * *
1853210 GTAAGACTTTTAGTTTTAATAATCAAAATTCAATTTCCGATCATTTCAAATACCCAAAAATGATG
1 GTAAGACTTTTAGTTTTAATAATCGAAATTTAATTTCCGATAATTT-AAATA-CAAAAAAAG-TG
* *
1853275 TCAAATATT-GTTACCT-A-TAGCAGACTGTGGATGATTTC-AATGATCTCAT-AAAGAATGTGT
63 TCAAATATTAG-TACCTAATTAGCAGACTGTGAATGATTTCTAATGATCTCATGAAAGAAAGTGT
*
1853335 CAAATATGCCAACAACCGTATGATTTATTGGTAAAATA
127 CAAATATGCCAACAACCATATGATTTATTGGTAAAATA
* *** *
1853373 GTAAGACTTTTAATTTTAATAATCGAAATTTAATTTTTAATAATTTAAATATAAAAAAAGTGTCA
1 GTAAGACTTTTAGTTTTAATAATCGAAATTTAATTTCCGATAATTTAAATACAAAAAAAGTGTCA
* * * *
1853438 AATATTAGTATCTAAAGATTTTGTAGCCGACTGTGAATGATTTCTAATGATCTCATGTATGAAAG
66 AATATTAGTACCT--A-A---T-TAGCAGACTGTGAATGATTTCTAATGATCTCATGAAAGAAAG
* *
1853503 TGTCAAATATGCCAACAGCCATATGATTTGTTGGTAAAATA
124 TGTCAAATATGCCAACAACCATATGATTTATTGGTAAAATA
* * * *
1853544 GTAAGATTTTTAGTTCTAATAATCGAAATTTAATCTCCGATAATTTTAAATATC-GAAAAAGTGA
1 GTAAGACTTTTAGTTTTAATAATCGAAATTTAATTTCCGATAA-TTTAAATA-CAAAAAAAGTG-
*
1853608 T-AAATATTATTACCTAA
63 TCAAATATTAGTACCTAA
1853625 AGATTTTTAG
Statistics
Matches: 207, Mismatches: 30, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
160 15 0.07
161 7 0.03
162 5 0.02
163 39 0.19
164 1 0.00
169 20 0.10
170 12 0.06
171 79 0.38
172 28 0.14
173 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (164 bp):
GTAAGACTTTTAGTTTTAATAATCGAAATTTAATTTCCGATAATTTAAATACAAAAAAAGTGTCA
AATATTAGTACCTAATTAGCAGACTGTGAATGATTTCTAATGATCTCATGAAAGAAAGTGTCAAA
TATGCCAACAACCATATGATTTATTGGTAAAATA
Found at i:1853530 original size:171 final size:169
Alignment explanation
Indices: 1853292--1853647 Score: 482
Period size: 171 Copynumber: 2.1 Consensus size: 169
1853282 TTGTTACCTA
* * *
1853292 TAGCAGACTGTGGATGATTTCAATGATCTCATAAAGAATGTGTCAAATATGCCAACAACCGTATG
1 TAGCAGACTGTGAATGATTTCAATGATCTCATAAAGAAAGTGTCAAATATGCCAACAACCATATG
* * **
1853357 ATTTATTGGTAAAATAGTAAGACTTTTAATTTTAATAATCGAAATTTAATTTTTAATAA-TTTAA
66 ATTTATTGGTAAAATAGTAAGACTTTTAATTCTAATAATCGAAATTTAATCTCCAATAATTTTAA
*
1853421 ATATAAAAAAAGTG-TCAAATATTAGTATCTAAAGATTTT
131 ATATAAAAAAAGTGAT-AAATATTAGTACCTAAAGATTTT
* * * *
1853460 GTAGCCGACTGTGAATGATTTCTAATGATCTCATGTATGAAAGTGTCAAATATGCCAACAGCCAT
1 -TAGCAGACTGTGAATGATTTC-AATGATCTCAT-AAAGAAAGTGTCAAATATGCCAACAACCAT
* * * *
1853525 ATGATTTGTTGGTAAAATAGTAAGATTTTTAGTTCTAATAATCGAAATTTAATCTCCGATAATTT
63 ATGATTTATTGGTAAAATAGTAAGACTTTTAATTCTAATAATCGAAATTTAATCTCCAATAATTT
** *
1853590 TAAATATCGAAAAAGTGATAAATATTATTACCTAAAGATTTT
128 TAAATATAAAAAAAGTGATAAATATTAGTACCTAAAGATTTT
*
1853632 TAGCAGACTATGAATG
1 TAGCAGACTGTGAATG
1853648 GGGATTCCAT
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
169 19 0.12
170 11 0.07
171 93 0.57
172 38 0.23
173 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (169 bp):
TAGCAGACTGTGAATGATTTCAATGATCTCATAAAGAAAGTGTCAAATATGCCAACAACCATATG
ATTTATTGGTAAAATAGTAAGACTTTTAATTCTAATAATCGAAATTTAATCTCCAATAATTTTAA
ATATAAAAAAAGTGATAAATATTAGTACCTAAAGATTTT
Found at i:1857174 original size:10 final size:10
Alignment explanation
Indices: 1857147--1857177 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1857137 GACCTCATAC
1857147 AAAAAAAA-A
1 AAAAAAAACA
1857156 AAAAAAAACA
1 AAAAAAAACA
1857166 AAAAAAAACA
1 AAAAAAAACA
1857176 AA
1 AA
1857178 TTTTCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1858668 original size:26 final size:25
Alignment explanation
Indices: 1858639--1858764 Score: 66
Period size: 26 Copynumber: 5.1 Consensus size: 25
1858629 AATAAAAATA
1858639 AATTAATTATAATATAAATATATTAT
1 AATTAA-TATAATATAAATATATTAT
* *
1858665 AATT-ATATATTGTAAA-AT-TTAT
1 AATTAATATAATATAAATATATTAT
* * * *
1858687 ATAGTAA-A-AATAATTAATATATCAA
1 A-ATTAATATAAT-ATAAATATATTAT
* *
1858712 AATTTATATAATATAAA-ATATTTTT
1 AATTAATATAATATAAATATA-TTAT
** *
1858737 AAAAAATTATAATATAAATATAATAT
1 AATTAA-TATAATATAAATATATTAT
1858763 AA
1 AA
1858765 ATACATAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
22 7 0.10
23 8 0.11
24 18 0.25
25 13 0.18
26 22 0.31
27 3 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTAATATAATATAAATATATTAT
Found at i:1858671 original size:22 final size:20
Alignment explanation
Indices: 1858626--1858663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1858616 AATATGATTA
1858626 TATAATAAAAATAAATTAAT
1 TATAATAAAAATAAATTAAT
* *
1858646 TATAATATAAATATATTA
1 TATAATAAAAATAAATTA
1858664 TAATTATATA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAATAAAAATAAATTAAT
Found at i:1858747 original size:60 final size:58
Alignment explanation
Indices: 1858622--1858760 Score: 129
Period size: 60 Copynumber: 2.3 Consensus size: 58
1858612 ATCAAATATG
* * *
1858622 ATTATATAATAAAAATAAATTAATTATAATATAAATATATTATAATTATATATTGTAAAA
1 ATTATAT-ATAAAAAT-AATTAATTATAAAATAAATATAATATAATAATATATTGTAAAA
* ** *
1858682 TTTATATAGTAAAAATAATTAATATATCAAAATTTATATAATATAA-AATAT-TTTTAAAAA
1 ATTATATA-TAAAAATAATTAAT-TAT-AAAATAAATATAATATAATAATATATTGT-AAAA
*
1858742 ATTATAATATAAATATAAT
1 ATTAT-ATATAAAAATAAT
1858761 ATAAATACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
59 11 0.17
60 37 0.57
61 17 0.26
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (58 bp):
ATTATATATAAAAATAATTAATTATAAAATAAATATAATATAATAATATATTGTAAAA
Found at i:1859552 original size:7 final size:7
Alignment explanation
Indices: 1859540--1859580 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
1859530 TTTGCCCATT
1859540 CAGCAGG
1 CAGCAGG
1859547 CAGCAGG
1 CAGCAGG
1859554 CAGCAGG
1 CAGCAGG
1859561 CAGCAGG
1 CAGCAGG
1859568 CAGCAGG
1 CAGCAGG
1859575 CAGCAG
1 CAGCAG
1859581 ACATCAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.41, T:0.00
Consensus pattern (7 bp):
CAGCAGG
Found at i:1863721 original size:2 final size:2
Alignment explanation
Indices: 1863714--1863738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1863704 ATAGCTTTAT
1863714 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1863739 TGAAAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1864892 original size:21 final size:21
Alignment explanation
Indices: 1864868--1864916 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1864858 TTCAATCACA
* *
1864868 TTCTTCTTCTCCTTCTTTGTT
1 TTCTTCTTCTCATTCTTTGTC
*
1864889 TTCTTCTTCTTATTCTTTGTC
1 TTCTTCTTCTCATTCTTTGTC
1864910 TTCTTCT
1 TTCTTCT
1864917 CCGACGTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (21 bp):
TTCTTCTTCTCATTCTTTGTC
Found at i:1865576 original size:20 final size:20
Alignment explanation
Indices: 1865543--1865584 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1865533 ATTTTTTATT
1865543 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
*
1865563 TAAATATTAA-TATAAAATTA
1 TAAAT-TTAATTATAAAAATA
1865583 TA
1 TA
1865585 TTTAATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:1865600 original size:22 final size:22
Alignment explanation
Indices: 1865575--1865621 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1865565 AATATTAATA
* *
1865575 TAAAATTAT-ATTTAATAACTTT
1 TAAAATAATAATTTAA-AAATTT
1865597 T-AAATAATAATTTAAAAATTT
1 TAAAATAATAATTTAAAAATTT
1865618 TAAA
1 TAAA
1865622 TTAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATAATAATTTAAAAATTT
Found at i:1865647 original size:10 final size:11
Alignment explanation
Indices: 1865595--1865661 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
1865585 TTTAATAACT
1865595 TTTAAATAATAA
1 TTTAAATAA-AA
*
1865607 TTT-AA-AAAT
1 TTTAAATAAAA
*
1865616 TTTAAATTAAA
1 TTTAAATAAAA
*
1865627 -TTAAATTAAA
1 TTTAAATAAAA
1865637 TTTAAA-AAAA
1 TTTAAATAAAA
1865647 TTTTAAA-AAAA
1 -TTTAAATAAAA
1865658 TTTA
1 TTTA
1865662 TTTGATAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 4 0.09
10 21 0.45
11 19 0.40
12 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTTAAATAAAA
Found at i:1883492 original size:2 final size:2
Alignment explanation
Indices: 1883485--1883520 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1883475 TGCAGTCACC
1883485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1883521 ATCCTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1883881 original size:2 final size:2
Alignment explanation
Indices: 1883874--1883901 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1883864 GCAGATGATA
1883874 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
1883902 GTTTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1887716 original size:15 final size:16
Alignment explanation
Indices: 1887696--1887725 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1887686 AATATTTTAA
1887696 TAAAATTAAA-AAAAT
1 TAAAATTAAATAAAAT
1887711 TAAAATTAAATAAAA
1 TAAAATTAAATAAAA
1887726 ATATTTTTAT
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATTAAATAAAAT
Found at i:1887997 original size:26 final size:25
Alignment explanation
Indices: 1887968--1888023 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1887958 ATTATTATTT
1887968 TTAATAAATTTAATTATATTTAAATA
1 TTAATAAATTTAATT-TATTTAAATA
* * * *
1887994 TTAATTATTTTAATTTATTTTAATT
1 TTAATAAATTTAATTTATTTAAATA
1888019 TTAAT
1 TTAAT
1888024 TTAAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATAAATTTAATTTATTTAAATA
Found at i:1888003 original size:36 final size:37
Alignment explanation
Indices: 1887961--1888030 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
1887951 GTATTACATT
1887961 ATTATTTTTAA-TAAATTTAATTAT-ATTTAAATATTA
1 ATTA-TTTTAATTAAATTTAATTATAATTTAAATATTA
* * *
1887997 ATTATTTTAATTTATTTTAATTTTAATTTAAATA
1 ATTATTTTAATTAAATTTAATTATAATTTAAATA
1888031 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 14 0.48
37 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
ATTATTTTAATTAAATTTAATTATAATTTAAATATTA
Found at i:1888005 original size:16 final size:16
Alignment explanation
Indices: 1887972--1888072 Score: 66
Period size: 16 Copynumber: 6.1 Consensus size: 16
1887962 TTATTTTTAA
1887972 TAAATTTAATTATATT
1 TAAATTTAATTATATT
1887988 TAAATATTAATTAT-TT
1 TAAAT-TTAATTATATT
*
1888004 T-AATTT-ATTTTAATT
1 TAAATTTAATTAT-ATT
* *
1888019 TTAATTTAAATAATATT
1 TAAATTT-AATTATATT
*
1888036 AAAATTTTAAATTAATTATT
1 TAAA-TTT-AATT-A-TATT
*
1888056 TAAATTCAA-TATATT
1 TAAATTTAATTATATT
1888071 TA
1 TA
1888073 TATAGATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
13 4 0.06
14 2 0.03
15 12 0.18
16 14 0.21
17 14 0.21
18 12 0.18
19 3 0.04
20 7 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAATTTAATTATATT
Found at i:1888012 original size:25 final size:26
Alignment explanation
Indices: 1887976--1888024 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1887966 TTTTAATAAA
1887976 TTTAATTATATTTAAATATTAATTAT
1 TTTAATTATATTTAAATATTAATTAT
* *
1888002 TTTAATT-TATTTTAATTTTAATT
1 TTTAATTATATTTAAATATTAATT
1888025 TAAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTAATTATATTTAAATATTAATTAT
Found at i:1888057 original size:13 final size:15
Alignment explanation
Indices: 1888041--1888072 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1888031 ATATTAAAAT
1888041 TTTAAATT-AAT-TA
1 TTTAAATTCAATATA
1888054 TTTAAATTCAATATA
1 TTTAAATTCAATATA
1888069 TTTA
1 TTTA
1888073 TATAGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAATTCAATATA
Done.