Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 12 of 33
Found at i:1585604 original size:18 final size:18
Alignment explanation
Indices: 1585581--1585637 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
1585571 ATAATTGTAG
1585581 ATATAATATGAAAATATA
1 ATATAATATGAAAATATA
*
1585599 ATATAA-ATACAAAATATTTA
1 ATATAATAT-GAAAATA--TA
1585619 ATA-AATATGAAAAGTATA
1 ATATAATATGAAAA-TATA
1585637 A
1 A
1585638 CAAATGTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 2 0.06
18 15 0.47
19 6 0.19
20 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATAATATGAAAATATA
Found at i:1586927 original size:19 final size:19
Alignment explanation
Indices: 1586905--1587004 Score: 73
Period size: 19 Copynumber: 5.1 Consensus size: 19
1586895 ATAATTTGTG
1586905 TTTTTATATTATATTTATA
1 TTTTTATATTATATTTATA
1586924 TTTTTTATATATTATAATTTAT-
1 --TTTT-TATATTAT-ATTTATA
* *
1586946 TTTATACATTATATATTTATA
1 TTTTTATA-T-TATATTTATA
* *
1586967 TATTTATATAATATTTATA
1 TTTTTATATTATATTTATA
1586986 TTATTT-T-TTATATTT-TA
1 TT-TTTATATTATATTTATA
1587003 TT
1 TT
1587005 ATATCTTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.06
18 7 0.11
19 14 0.22
20 14 0.22
21 12 0.18
22 8 0.12
23 6 0.09
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATATTATATTTATA
Found at i:1586936 original size:17 final size:17
Alignment explanation
Indices: 1586914--1587022 Score: 62
Period size: 19 Copynumber: 6.0 Consensus size: 17
1586904 GTTTTTATAT
1586914 TATATTTATATTTTTTA
1 TATATTTATATTTTTTA
1586931 TATA-TTATAATTTATTT-
1 TATATTTAT-ATTT-TTTA
* *
1586948 TATACATTATA-TATTTA
1 TATA-TTTATATTTTTTA
*
1586965 TATATTTATATAATATTTA
1 TATATTTATAT--TTTTTA
* *
1586984 TATTATTTTTTATATTTTA
1 TA-TA-TTTATATTTTTTA
1587003 TTATATCTTATATTATTTTA
1 -TATAT-TTATATT-TTTTA
1587023 AGAAAGCTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 23
0.71 0.07 0.23
Matches are distributed among these distances:
16 12 0.17
17 17 0.24
18 5 0.07
19 23 0.32
20 9 0.12
21 6 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTATATTTTTTA
Found at i:1587016 original size:12 final size:10
Alignment explanation
Indices: 1586908--1587022 Score: 52
Period size: 10 Copynumber: 12.0 Consensus size: 10
1586898 ATTTGTGTTT
*
1586908 TTATATTATA
1 TTATATTTTA
1586918 TTTATATTTT-
1 -TTATATTTTA
1586928 TTATA---TA
1 TTATATTTTA
*
1586935 TTATAATTTA
1 TTATATTTTA
* **
1586945 TTTTA-TACA
1 TTATATTTTA
1586954 TTATATATTTA
1 TTATAT-TTTA
1586965 -TATATTTATA
1 TTATATTT-TA
*
1586975 TAATA-TTTA
1 TTATATTTTA
1586984 -TATTATTTT-
1 TTA-TATTTTA
1586993 TTATATTTTA
1 TTATATTTTA
*
1587003 TTATATCTTA
1 TTATATTTTA
1587013 -TATTATTTTA
1 TTA-TATTTTA
1587023 AGAAAGCTGA
Statistics
Matches: 80, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
6 1 0.01
7 5 0.06
8 1 0.01
9 25 0.31
10 35 0.44
11 13 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATATTTTA
Found at i:1587084 original size:4 final size:4
Alignment explanation
Indices: 1587075--1587101 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1587065 TGTTCCCAAA
1587075 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1587102 GTGATGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1587531 original size:21 final size:21
Alignment explanation
Indices: 1587507--1587546 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1587497 ATAATAATAA
*
1587507 TAATAATAATAGAATTTAATT
1 TAATAATAAGAGAATTTAATT
*
1587528 TAATAATTAGAGAATTTAA
1 TAATAATAAGAGAATTTAA
1587547 GGTTAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAATAATAAGAGAATTTAATT
Found at i:1587534 original size:3 final size:3
Alignment explanation
Indices: 1587481--1587517 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1587471 ATCATTTAGG
1587481 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1587518 GAATTTAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1587612 original size:5 final size:5
Alignment explanation
Indices: 1587602--1587633 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1587592 TACATATATA
1587602 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
1587634 GTTATAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1588884 original size:18 final size:21
Alignment explanation
Indices: 1588845--1588885 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1588835 AAACTGTGAT
1588845 ATAAATATAATATAAATATTA
1 ATAAATATAATATAAATATTA
1588866 ATAAAT-TAATA-AAAT-TTA
1 ATAAATATAATATAAATATTA
1588884 AT
1 AT
1588886 TTTATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 5 0.25
21 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAATATAATATAAATATTA
Found at i:1588906 original size:19 final size:18
Alignment explanation
Indices: 1588884--1588927 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
1588874 ATAAAATTTA
*
1588884 ATTTTATTAATATATTAAT
1 ATTTTATAAATATA-TAAT
1588903 ATTTATATAAATATATAAT
1 ATTT-TATAAATATATAAT
1588922 ATTTTA
1 ATTTTA
1588928 AATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTATAAATATATAAT
Found at i:1588921 original size:27 final size:30
Alignment explanation
Indices: 1588891--1588946 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
1588881 TTAATTTTAT
1588891 TAATATATT-AATAT-TTAT-ATAAATATA
1 TAATATATTAAATATATTATAATAAATATA
*
1588918 TAATATTTTAAATATAATTATAATAAATA
1 TAATATATTAAATAT-ATTATAATAAATA
1588947 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 5 0.21
30 4 0.17
31 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATATATTAAATATATTATAATAAATATA
Found at i:1588927 original size:20 final size:20
Alignment explanation
Indices: 1588884--1588942 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1588874 ATAAAATTTA
1588884 ATTTTAT-T-AATATATTAAT
1 ATTTTATATAAATATA-TAAT
1588903 A-TTTATATAAATATATAAT
1 ATTTTATATAAATATATAAT
*
1588922 ATTTTAAATATAAT-TATAAT
1 ATTTTATATA-AATATATAAT
1588942 A
1 A
1588943 AATAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 20 0.57
21 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTATATAAATATATAAT
Found at i:1588957 original size:22 final size:22
Alignment explanation
Indices: 1588927--1588970 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1588917 ATAATATTTT
1588927 AAATATAAT-TATAATAAATAAAA
1 AAATATAATAT-TAA-AAATAAAA
1588950 AAAT-TAATATTAAAAATAAAA
1 AAATATAATATTAAAAATAAAA
1588971 GATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATATAATATTAAAAATAAAA
Found at i:1588978 original size:14 final size:15
Alignment explanation
Indices: 1588960--1588993 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1588950 AAATTAATAT
1588960 TAAAAAT-AAAAG-A
1 TAAAAATAAAAAGAA
1588973 TAAAAATAAAAAGAA
1 TAAAAATAAAAAGAA
1588988 TAAAAA
1 TAAAAA
1588994 AATTTCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (15 bp):
TAAAAATAAAAAGAA
Found at i:1589372 original size:31 final size:30
Alignment explanation
Indices: 1589308--1589369 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1589298 TATTTATGAT
*
1589308 ATATTTTTATTTATTAAAATTATATTTAAA
1 ATATTTTTATTTATTAAAATTATATATAAA
*
1589338 ATATTATTTATTTATTTAAATTTAATATATAA
1 ATATT-TTTATTTA-TTAAAATT-ATATATAA
1589370 TATAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 5 0.19
31 8 0.30
32 7 0.26
33 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATTTTTATTTATTAAAATTATATATAAA
Found at i:1595503 original size:2 final size:2
Alignment explanation
Indices: 1595498--1595529 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1595488 CGCGCTCGCG
1595498 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1595530 AATACACATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1595536 original size:12 final size:12
Alignment explanation
Indices: 1595498--1595543 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1595488 CGCGCTCGCG
*
1595498 CACACACACACA
1 CACACACAAACA
*
1595510 CACACACACACA
1 CACACACAAACA
*
1595522 CACACACAAATA
1 CACACACAAACA
*
1595534 CACATACAAA
1 CACACACAAA
1595544 GGTACCCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.54, C:0.41, G:0.00, T:0.04
Consensus pattern (12 bp):
CACACACAAACA
Found at i:1598433 original size:7 final size:8
Alignment explanation
Indices: 1598416--1598440 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1598406 GAATTCCCTG
1598416 AAATAAAA
1 AAATAAAA
1598424 AAATAAAA
1 AAATAAAA
1598432 AAATAAAA
1 AAATAAAA
1598440 A
1 A
1598441 TTTAGTGCCA
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):
AAATAAAA
Found at i:1599160 original size:8 final size:7
Alignment explanation
Indices: 1599139--1599171 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1599129 TAATGATTGA
1599139 TTCTTTT
1 TTCTTTT
1599146 TTCTTTT
1 TTCTTTT
1599153 TTCTTTT
1 TTCTTTT
1599160 TT-TTTT
1 TTCTTTT
*
1599166 GTCTTT
1 TTCTTT
1599172 GAATCTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (7 bp):
TTCTTTT
Found at i:1599165 original size:13 final size:14
Alignment explanation
Indices: 1599139--1599171 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1599129 TAATGATTGA
1599139 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
1599153 TTCTTTTTT-TTTT
1 TTCTTTTTTCTTTT
*
1599166 GTCTTT
1 TTCTTT
1599172 GAATCTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:1599489 original size:35 final size:35
Alignment explanation
Indices: 1599443--1599514 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1599433 AAAAGAAGAA
1599443 AAGAAAAAGGATAACAATACTATGGAATTGTGGTC
1 AAGAAAAAGGATAACAATACTATGGAATTGTGGTC
1599478 AAGAAAAAGGATAACAATACTATGGAATTGTGGTC
1 AAGAAAAAGGATAACAATACTATGGAATTGTGGTC
1599513 AA
1 AA
1599515 ATAAAACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (35 bp):
AAGAAAAAGGATAACAATACTATGGAATTGTGGTC
Found at i:1599700 original size:47 final size:47
Alignment explanation
Indices: 1599631--1599820 Score: 371
Period size: 47 Copynumber: 4.0 Consensus size: 47
1599621 TATTTCATCC
*
1599631 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCCAAAAACT
1 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1599678 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1599725 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1599772 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1 TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
1599819 TA
1 TA
1599821 CACTGTTGTT
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 142 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (47 bp):
TAATCCCAAAAGACTAAGACAAAGTCCTATTACAATCTCAAAAAACT
Found at i:1604797 original size:106 final size:107
Alignment explanation
Indices: 1604611--1604814 Score: 383
Period size: 106 Copynumber: 1.9 Consensus size: 107
1604601 TTTCGAAATA
* *
1604611 GAAATAGGTAATTTCTAGCCTTCTTCCTTTTATTTTTTTTCCTTGTTAGTTTTAATAGAGATATT
1 GAAATAGGTAATTTCTAGCCTTCTTCCTTTTATTTTTTTTCCTTGCTACTTTTAATAGAGATATT
1604676 TAGAATAAATGTTCCAAATCTTTAAGCAATCATTTCAAGATT
66 TAGAATAAATGTTCCAAATCTTTAAGCAATCATTTCAAGATT
1604718 GAAATAGGTAATTTCTAGCCTTCTTCCTTTTA-TTTTTTTCCTTGCTACTTTTAATAGAGATATT
1 GAAATAGGTAATTTCTAGCCTTCTTCCTTTTATTTTTTTTCCTTGCTACTTTTAATAGAGATATT
1604782 TAGAATAAATGTTCCAAATCTTTAAGCAATCAT
66 TAGAATAAATGTTCCAAATCTTTAAGCAATCAT
1604815 GCAGAATCAG
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
106 63 0.66
107 32 0.34
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (107 bp):
GAAATAGGTAATTTCTAGCCTTCTTCCTTTTATTTTTTTTCCTTGCTACTTTTAATAGAGATATT
TAGAATAAATGTTCCAAATCTTTAAGCAATCATTTCAAGATT
Found at i:1605895 original size:2 final size:2
Alignment explanation
Indices: 1605888--1605925 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1605878 AGATTAGAAG
1605888 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
1605926 TCTAATTAAA
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:1618261 original size:23 final size:26
Alignment explanation
Indices: 1618212--1618261 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1618202 TATCAAACAT
*
1618212 ATAAATATTTTATATTAATATCATTAA
1 ATAAATATTTGATATTAATAT-ATTAA
1618239 ATAAATA-TTGATA-TAATAT-TTAA
1 ATAAATATTTGATATTAATATATTAA
1618262 TATTTAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
25 6 0.27
26 5 0.23
27 7 0.32
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATAAATATTTGATATTAATATATTAA
Found at i:1618849 original size:23 final size:24
Alignment explanation
Indices: 1618818--1618868 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1618808 GAAAAACATG
1618818 TAATGAAAATGAT-ATATA-AAAAA
1 TAATGAAAAT-ATAATATATAAAAA
* *
1618841 TAATTAAAATATAATATATCAAAA
1 TAATGAAAATATAATATATAAAAA
1618865 TAAT
1 TAAT
1618869 AATACTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 14 0.58
24 8 0.33
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (24 bp):
TAATGAAAATATAATATATAAAAA
Found at i:1618919 original size:16 final size:16
Alignment explanation
Indices: 1618877--1618951 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 16
1618867 ATAATACTGT
*
1618877 TATAATATAAATTATTGA
1 TATAATATAAA--ATTTA
1618895 TAT-AT-TAAAATTTA
1 TATAATATAAAATTTA
1618909 TATAATAT-AAA-TTA
1 TATAATATAAAATTTA
*
1618923 TATGGAT-TAAAATTTA
1 TAT-AATATAAAATTTA
1618939 TATAATAATAAAA
1 TATAAT-ATAAAA
1618952 ATAAATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
14 14 0.30
15 12 0.26
16 11 0.23
17 7 0.15
18 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
TATAATATAAAATTTA
Found at i:1618932 original size:30 final size:32
Alignment explanation
Indices: 1618877--1618950 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 32
1618867 ATAATACTGT
*
1618877 TATAATATAAATTATTGATATATTAAAATTTA
1 TATAATATAAATTATTGATAGATTAAAATTTA
*
1618909 TATAATATAAATTA-T-ATGGATTAAAATTTA
1 TATAATATAAATTATTGATAGATTAAAATTTA
1618939 TATAATAATAAA
1 TATAAT-ATAAA
1618951 AATAAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 19 0.49
31 6 0.15
32 14 0.36
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (32 bp):
TATAATATAAATTATTGATAGATTAAAATTTA
Found at i:1619519 original size:19 final size:21
Alignment explanation
Indices: 1619481--1619527 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1619471 AAAATATGAT
1619481 ATATAAAATACTACTAATATA
1 ATATAAAATACTACTAATATA
*
1619502 ATAT-AAATA-TATTAATAT-
1 ATATAAAATACTACTAATATA
1619520 AT-TAAAAT
1 ATATAAAAT
1619528 TTATATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 6 0.25
19 8 0.33
20 5 0.21
21 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAATACTACTAATATA
Found at i:1619631 original size:29 final size:28
Alignment explanation
Indices: 1619574--1619632 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
1619564 ATAAATATAT
* * *
1619574 AAAATATTAAATATTATTATGATATATA
1 AAAATATTAAATATGATTACGATACATA
1619602 AAAATATATAAATATGA-TACGAATACATA
1 AAAATAT-TAAATATGATTACG-ATACATA
1619631 AA
1 AA
1619633 TTATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATATTAAATATGATTACGATACATA
Found at i:1620074 original size:12 final size:13
Alignment explanation
Indices: 1620048--1620072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1620038 TAATAGAGAG
1620048 AAAAAATTATTTT
1 AAAAAATTATTTT
1620061 AAAAAATTATTT
1 AAAAAATTATTT
1620073 AATTTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAAATTATTTT
Found at i:1620100 original size:18 final size:18
Alignment explanation
Indices: 1620056--1620090 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1620046 AGAAAAAATT
1620056 ATTTTAAAAAATTATTTA
1 ATTTTAAAAAATTATTTA
*
1620074 ATTTTAAAATATTATTT
1 ATTTTAAAAAATTATTT
1620091 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAAAAAATTATTTA
Found at i:1620101 original size:19 final size:17
Alignment explanation
Indices: 1620058--1620102 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1620048 AAAAAATTAT
1620058 TTTAAAAAATTATTTAA
1 TTTAAAAAATTATTTAA
* *
1620075 TTTTAAAATATTATTTTTA
1 -TTTAAAAAATTA-TTTAA
1620094 TTTAAAAAA
1 TTTAAAAAA
1620103 AGTATGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAAAATTATTTAA
Found at i:1620813 original size:6 final size:6
Alignment explanation
Indices: 1620802--1620848 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
1620792 TGTTTATAAT
* *
1620802 AATATA AATATA AATATA AATATA AATA-A ATAGATA AGTATA AATAT
1 AATATA AATATA AATATA AATATA AATATA A-ATATA AATATA AATAT
1620849 TTATTTAGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 2 0.06
6 31 0.89
7 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:1622027 original size:41 final size:42
Alignment explanation
Indices: 1621912--1622037 Score: 109
Period size: 41 Copynumber: 3.0 Consensus size: 42
1621902 TCGTAAATTC
* *
1621912 AATATATCAAAATTTATATAAATATAATATT-TTAAATAAAT-
1 AATATATCAAAATTTACATAAATATAA-ATTATTAAATATATA
* * * * * *
1621953 ATTATGTAAAAAATAACATAAATATGTAA--ATTAAATATATA
1 AATATATCAAAATTTACATAAATAT-AAATTATTAAATATATA
1621994 AATATATCAAAATTTACATAAA-ATAAATTATTAACATAATATA
1 AATATATCAAAATTTACATAAATATAAATTATTAA-AT-ATATA
1622037 A
1 A
1622038 GTTATATAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.03
40 11 0.17
41 42 0.66
42 3 0.05
43 6 0.09
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (42 bp):
AATATATCAAAATTTACATAAATATAAATTATTAAATATATA
Found at i:1622032 original size:18 final size:19
Alignment explanation
Indices: 1622009--1622061 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
1621999 ATCAAAATTT
1622009 ACATAAAATAAATTAT-TA
1 ACATAAAATAAATTATATA
* *
1622027 ACATAATATAAGTTATATA
1 ACATAAAATAAATTATATA
1622046 A-ATATATAATAAATTA
1 ACATA-A-AATAAATTA
1622062 AATATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 17 0.61
19 4 0.14
20 7 0.25
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
ACATAAAATAAATTATATA
Found at i:1622080 original size:17 final size:17
Alignment explanation
Indices: 1622009--1622086 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
1621999 ATCAAAATTT
1622009 ACATAAA-ATAAATTATTA
1 ACATAAATAT-AATTA-TA
1622027 ACAT-AATATAAGTTAT-
1 ACATAAATATAA-TTATA
*
1622043 --ATAAATAT-ATAATA
1 ACATAAATATAATTATA
1622057 A-ATTAAATATAATTATA
1 ACA-TAAATATAATTATA
*
1622074 ACATAAAAATAAT
1 ACATAAATATAAT
1622087 AAAAATCAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 6 0.12
16 7 0.14
17 20 0.41
18 10 0.20
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (17 bp):
ACATAAATATAATTATA
Found at i:1622843 original size:3 final size:3
Alignment explanation
Indices: 1622835--1622863 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1622825 TTTTGAAATC
1622835 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1622864 TGAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1622977 original size:19 final size:19
Alignment explanation
Indices: 1622945--1622981 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1622935 TATTATTTTT
1622945 TAATGTATTAAAACTATTA
1 TAATGTATTAAAACTATTA
1622964 TAATG-ATTATAAACTATT
1 TAATGTATTA-AAACTATT
1622982 GCATTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TAATGTATTAAAACTATTA
Found at i:1623169 original size:2 final size:2
Alignment explanation
Indices: 1623162--1623194 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1623152 TCCCAATTAA
1623162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1623195 TTTGTGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1626207 original size:16 final size:17
Alignment explanation
Indices: 1626182--1626223 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1626172 ATAAATAATA
*
1626182 TAAATATTATATT-ATT
1 TAAATTTTATATTGATT
1626198 TAAATTTTATATTGATT
1 TAAATTTTATATTGATT
*
1626215 TATATTTTA
1 TAAATTTTA
1626224 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAAATTTTATATTGATT
Found at i:1627113 original size:19 final size:17
Alignment explanation
Indices: 1627079--1627138 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 17
1627069 AATTTAGATA
*
1627079 TTTATTATT--ATTAAT
1 TTTATTATTCGATAAAT
1627094 TTTATTATTCGTAATAAAT
1 TTTATTATTCG--ATAAAT
* *
1627113 TTTAATATGCGATAAAT
1 TTTATTATTCGATAAAT
*
1627130 GTTATTATT
1 TTTATTATT
1627139 TAATTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.26
17 12 0.34
19 14 0.40
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (17 bp):
TTTATTATTCGATAAAT
Found at i:1628514 original size:21 final size:21
Alignment explanation
Indices: 1628468--1628533 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1628458 TAATTATTTT
* * *
1628468 ATAA-AAATAAAATAAAATAA
1 ATAATAAATTAAATGAATTAA
*
1628488 AAAATAAATTAAAT-AATTATA
1 ATAATAAATTAAATGAATTA-A
* *
1628509 ATAATAATTTAATTGAATTAA
1 ATAATAAATTAAATGAATTAA
1628530 ATAA
1 ATAA
1628534 AATATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 7 0.19
21 25 0.68
22 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAAATTAAATGAATTAA
Found at i:1628683 original size:16 final size:16
Alignment explanation
Indices: 1628651--1628722 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 16
1628641 AAATTTTATA
1628651 AAAT-TTTAATAAA-T
1 AAATATTTAATAAATT
1628665 AAATATTTAATAAATT
1 AAATATTTAATAAATT
* *
1628681 AAATAATT-ATATTATT
1 AAATATTTAATA-AATT
1628697 ATAATATATATAATAAATT
1 A-AATAT-T-TAATAAATT
1628716 AAATATT
1 AAATATT
1628723 ATATTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.09
15 12 0.26
16 12 0.26
17 5 0.11
18 6 0.13
19 5 0.11
20 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTTAATAAATT
Found at i:1628711 original size:35 final size:33
Alignment explanation
Indices: 1628663--1628728 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 33
1628653 ATTTTAATAA
*
1628663 ATAAATATTTAATAAATTAAATAATTATATTATT
1 ATAAATATATAATAAATTAAAT-ATTATATTATT
1628697 ATAATATATATAATAAATTAAATATTATATTA
1 ATAA-ATATATAATAAATTAAATATTATATTA
1628729 ATTTTATCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAAATATATAATAAATTAAATATTATATTATT
Found at i:1633215 original size:23 final size:23
Alignment explanation
Indices: 1633189--1633238 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1633179 CAAAGTAAAG
*
1633189 TAAATTTAGAAATTTTAA-AAATA
1 TAAATGTAGAAA-TTTAATAAATA
* *
1633212 TAAATGTATATATTTAATAAATA
1 TAAATGTAGAAATTTAATAAATA
1633235 TAAA
1 TAAA
1633239 AAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATGTAGAAATTTAATAAATA
Found at i:1633244 original size:22 final size:22
Alignment explanation
Indices: 1633202--1633245 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1633192 ATTTAGAAAT
**
1633202 TTTAAAAATATAAATGTATATA
1 TTTAAAAATATAAATAAATATA
1633224 TTTAATAAATATAAA-AAATATA
1 TTTAA-AAATATAAATAAATATA
1633246 ATAAATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTAAAAATATAAATAAATATA
Found at i:1633265 original size:18 final size:17
Alignment explanation
Indices: 1633211--1633279 Score: 68
Period size: 18 Copynumber: 4.0 Consensus size: 17
1633201 TTTTAAAAAT
*
1633211 ATAAATGTATATATTTA
1 ATAAATATATATATTTA
* * *
1633228 ATAAATATAAAAAATATA
1 ATAAATAT-ATATATTTA
1633246 ATAAATATGATATATTTA
1 ATAAATAT-ATATATTTA
*
1633264 ATATATAT-TATATTTA
1 ATAAATATATATATTTA
1633280 TGTTTAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.19
17 7 0.17
18 27 0.64
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATAAATATATATATTTA
Found at i:1633267 original size:9 final size:9
Alignment explanation
Indices: 1633255--1633310 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
1633245 AATAAATATG
1633255 ATATATTTA
1 ATATATTTA
1633264 ATATATATTA
1 ATATAT-TTA
*
1633274 TATTTATGTTTA
1 -A--TATATTTA
1633286 ATAT-TTTA
1 ATATATTTA
1633294 ATATATTTA
1 ATATATTTA
1633303 ATA-ATTTA
1 ATATATTTA
1633311 TATTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 13 0.32
9 16 0.39
10 3 0.07
11 2 0.05
12 3 0.07
13 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
ATATATTTA
Found at i:1633317 original size:17 final size:17
Alignment explanation
Indices: 1633258--1633318 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 17
1633248 AAATATGATA
1633258 TATTTAATATATATTATATT
1 TATTTAATA-AT-TTATA-T
*
1633278 TATGTTTAATATTTTA-AT
1 TA--TTTAATAATTTATAT
1633296 ATATTTAATAATTTATAT
1 -TATTTAATAATTTATAT
1633314 TATTT
1 TATTT
1633319 TTATATTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
17 16 0.46
18 3 0.09
19 3 0.09
20 5 0.14
21 1 0.03
22 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTAATAATTTATAT
Found at i:1636096 original size:28 final size:28
Alignment explanation
Indices: 1636073--1636130 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1636063 TATAATAATG
1636073 ACCTTTGGACATTGATCTTCTAATTGGA
1 ACCTTTGGACATTGATCTTCTAATTGGA
* *
1636101 ACCTTTGGACATTGCTCTTCTAAGTGGA
1 ACCTTTGGACATTGATCTTCTAATTGGA
1636129 AC
1 AC
1636131 TTAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (28 bp):
ACCTTTGGACATTGATCTTCTAATTGGA
Found at i:1636613 original size:2 final size:2
Alignment explanation
Indices: 1636606--1636636 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1636596 GCTTGAAATT
1636606 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
1636637 TAAAAATATT
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:1637462 original size:2 final size:2
Alignment explanation
Indices: 1637446--1637482 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1637436 TATGTGCTTC
* *
1637446 TA TA TA CA TA CA 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 T
1637483 GTTCATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1641026 original size:33 final size:34
Alignment explanation
Indices: 1640956--1641028 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 34
1640946 CAAGTATTTG
* **
1640956 AAGCTAAATAACATTGAACAGACACTTCTTTTTA
1 AAGCTAAATAACATTGAAAAGACACTTCTTTCCA
* * *
1640990 AAGCTAAATGACTTTGAAAAGATAC-TCTTTCCA
1 AAGCTAAATAACATTGAAAAGACACTTCTTTCCA
1641023 AAGCTA
1 AAGCTA
1641029 CTCCGATGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (34 bp):
AAGCTAAATAACATTGAAAAGACACTTCTTTCCA
Found at i:1645085 original size:21 final size:19
Alignment explanation
Indices: 1645052--1645090 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1645042 TTTTATTTAA
*
1645052 TTTTTTATTTTATAATTTTG
1 TTTTTTATATTAT-ATTTTG
1645072 TTTTGTTATATTATATTTT
1 TTTT-TTATATTATATTTT
1645091 CATTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTATATTATATTTTG
Found at i:1645331 original size:17 final size:16
Alignment explanation
Indices: 1645301--1645332 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1645291 ACTCATCAAC
1645301 AAAAAATTAATTTTTT
1 AAAAAATTAATTTTTT
*
1645317 AAAAAATTAGTTTTTT
1 AAAAAATTAATTTTTT
1645333 CTTTTCAAAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AAAAAATTAATTTTTT
Found at i:1645447 original size:9 final size:8
Alignment explanation
Indices: 1645436--1645461 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1645426 TTTAATTTTA
1645436 AAAATATT
1 AAAATATT
1645444 AAAATATT
1 AAAATATT
1645452 AAAATATT
1 AAAATATT
1645460 AA
1 AA
1645462 TATACAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:1645913 original size:22 final size:22
Alignment explanation
Indices: 1645871--1645920 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1645861 TAATTTACAG
1645871 AATTAAAAAATTTTAAATTATT
1 AATTAAAAAATTTTAAATTATT
* *
1645893 ATTTAAAAATATTTT-ATTTATT
1 AATTAAAAA-ATTTTAAATTATT
1645915 AATTAA
1 AATTAA
1645921 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAAAAATTTTAAATTATT
Found at i:1645964 original size:12 final size:12
Alignment explanation
Indices: 1645947--1645971 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1645937 AAATTAATTT
1645947 AAAATATTTTAA
1 AAAATATTTTAA
1645959 AAAATATTTTAA
1 AAAATATTTTAA
1645971 A
1 A
1645972 TTTAATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:1646484 original size:26 final size:25
Alignment explanation
Indices: 1646422--1646484 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 25
1646412 GTTGTAATTG
1646422 TTTATAAATTAAATTATTTATTTACA
1 TTTA-AAATTAAATTATTTATTTACA
* *
1646448 -TTAAATTTTAAATATAGTTT-TTTATA
1 TTTAAA-ATTAAAT-TA-TTTATTTACA
1646474 TTTAAAATTAA
1 TTTAAAATTAA
1646485 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
24 2 0.07
25 9 0.30
26 11 0.37
27 8 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTAAAATTAAATTATTTATTTACA
Found at i:1647836 original size:2 final size:2
Alignment explanation
Indices: 1647829--1647857 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1647819 CAGAAACAAA
1647829 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
1647858 GAAAGAGAGA
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:1648787 original size:2 final size:2
Alignment explanation
Indices: 1648780--1648834 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1648770 TTAAAGCATT
* *
1648780 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1648822 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1648835 GGGGTTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1648962 original size:34 final size:34
Alignment explanation
Indices: 1648906--1649123 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
1648896 AGTGTATTAT
*
1648906 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * *
1648939 TTATTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
1648973 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
1649007 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
1649041 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
1649075 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
1649109 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
1649124 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 143 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:1649081 original size:102 final size:101
Alignment explanation
Indices: 1648906--1649123 Score: 355
Period size: 102 Copynumber: 2.1 Consensus size: 101
1648896 AGTGTATTAT
** * * *
1648906 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1648971 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1649007 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
1649072 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1649109 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
1649124 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:1649490 original size:19 final size:19
Alignment explanation
Indices: 1649430--1649490 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
1649420 GTTGTCGAGG
**
1649430 TACTATTCACGTATATAGT
1 TACTATTCACGTATACGGT
1649449 TACTATTCACGTATACGAG-
1 TACTATTCACGTATACG-GT
*
1649468 TACTATTCAAGTATACGGT
1 TACTATTCACGTATACGGT
1649487 TACT
1 TACT
1649491 GTACACGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 35 0.95
20 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (19 bp):
TACTATTCACGTATACGGT
Found at i:1653613 original size:34 final size:34
Alignment explanation
Indices: 1653556--1653774 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
1653546 AAGTGGGAGA
*
1653556 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1653589 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1653623 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1653657 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1653691 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1653725 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1653759 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1653775 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1653696 original size:102 final size:101
Alignment explanation
Indices: 1653556--1653774 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
1653546 AAGTGGGAGA
** * * *
1653556 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1653621 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1653657 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1653722 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1653759 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1653775 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1654354 original size:12 final size:12
Alignment explanation
Indices: 1654339--1654373 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1654329 TGATAATTTT
1654339 AAATATAATAAA
1 AAATATAATAAA
*
1654351 AAATATAAT-AT
1 AAATATAATAAA
1654362 AAATATAATAAA
1 AAATATAATAAA
1654374 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:1654358 original size:9 final size:10
Alignment explanation
Indices: 1654339--1654389 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
1654329 TGATAATTTT
1654339 AAATATAATAAA
1 AAATATAAT--A
1654351 AAATATAATA
1 AAATATAATA
1654361 TAAATATAAT-
1 -AAATATAATA
*
1654371 AAATTTAATA
1 AAATATAATA
*
1654381 AAAAATAAT
1 AAATATAAT
1654390 TTTAAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 9 0.26
12 9 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATAATA
Found at i:1654374 original size:20 final size:19
Alignment explanation
Indices: 1654345--1654389 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1654335 TTTTAAATAT
*
1654345 AATAAAAAATATAATATAAA
1 AATAATAAATATAATA-AAA
* *
1654365 TATAATAAATTTAATAAAA
1 AATAATAAATATAATAAAA
1654384 AATAAT
1 AATAAT
1654390 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAAATATAATAAAA
Found at i:1654961 original size:114 final size:118
Alignment explanation
Indices: 1654830--1655051 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 118
1654820 AGCTTTTAAG
* *
1654830 TAAGTGAATCCTTCATCAGTGGCGAGAAAAAATTGTAACCCTTTTGTATGCAAAA-A-TA-GTAT
1 TAAGTGAATCCTTCATCAGTGGCGAGAAAAAATTGTAACCCTCTTGTATGCAAAATAGTATATAT
*
1654892 TAAA-TTTTTGAAGTCACGGGGTGTCGCTGTCATTTGGTTTTTGCTTTTTGAT
66 TAAATTTTTTGAAGTCACGGGGTGTCGCTCTCATTTGGTTTTTGCTTTTTGAT
*
1654944 TAAGTGAATCCTTCATCAGTGGCGAGAAAATATTGTAACCCTCTTGTATGCAAAATAGTATTATA
1 TAAGTGAATCCTTCATCAGTGGCGAGAAAAAATTGTAACCCTCTTGTATGCAAAATAGTA-TATA
*
1655009 TTAAATTTTTTTGAAGTCATGGGGTGTCGCTCTCATTTGGTTT
65 TTAAA-TTTTTTGAAGTCACGGGGTGTCGCTCTCATTTGGTTT
1655052 AAAAGTTTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
114 53 0.55
115 1 0.01
116 2 0.02
118 7 0.07
120 34 0.35
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (118 bp):
TAAGTGAATCCTTCATCAGTGGCGAGAAAAAATTGTAACCCTCTTGTATGCAAAATAGTATATAT
TAAATTTTTTGAAGTCACGGGGTGTCGCTCTCATTTGGTTTTTGCTTTTTGAT
Found at i:1655388 original size:3 final size:3
Alignment explanation
Indices: 1655380--1655405 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1655370 TGCATTGCTG
1655380 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1655406 GCAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1659941 original size:25 final size:24
Alignment explanation
Indices: 1659899--1659952 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1659889 ATAATTTAAA
* *
1659899 ATTTATTTAATAATTTATTATTATT
1 ATTT-TTTAATAAATTATTATAATT
1659924 ATTTTTTAATTAAATTATTATAATT
1 ATTTTTTAA-TAAATTATTATAATT
1659949 -TTTT
1 ATTTT
1659953 ATTCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTTAATAAATTATTATAATT
Found at i:1659962 original size:22 final size:22
Alignment explanation
Indices: 1659909--1659962 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1659899 ATTTATTTAA
*
1659909 TAATT-TATTATTATTATTTTT
1 TAATTATATTATTATAATTTTT
*
1659930 TAATTAAATTATTATAATTTTT
1 TAATTATATTATTATAATTTTT
1659952 T-ATTCATATTA
1 TAATT-ATATTA
1659963 CATTGTTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTATATTATTATAATTTTT
Found at i:1662016 original size:31 final size:30
Alignment explanation
Indices: 1661949--1662046 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
1661939 TATACTGAAA
1661949 ATTTATTTAAATATAAATTAAAAGTTAAAT
1 ATTTATTTAAATATAAATTAAAAGTTAAAT
* **
1661979 ATTTATTTAAATAT-AATTCAAAATTTTACGT
1 ATTTATTTAAATATAAATT-AAAA-GTTAAAT
* ** *
1662010 ATTTATTTGAATATGATTTTAAAA-TTAAAG
1 ATTTATTTAAATAT-AAATTAAAAGTTAAAT
1662040 ATTTATT
1 ATTTATT
1662047 GATTTTACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
29 4 0.07
30 28 0.51
31 17 0.31
32 4 0.07
33 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (30 bp):
ATTTATTTAAATATAAATTAAAAGTTAAAT
Found at i:1662397 original size:24 final size:25
Alignment explanation
Indices: 1662340--1662412 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
1662330 TGTTACTGAA
*
1662340 TTAAAT-AAATTTTTATTATTTAAT
1 TTAAATAAAAATTTTATTATTTAAT
* *
1662364 TTATAA-AAAAATTTTGTT-TTTATT
1 TTA-AATAAAAATTTTATTATTTAAT
1662388 TTAAATAAAAGATTTCT-TTATTTAA
1 TTAAATAAAA-ATTT-TATTATTTAA
1662413 CGATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
23 2 0.05
24 15 0.38
25 17 0.44
26 5 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (25 bp):
TTAAATAAAAATTTTATTATTTAAT
Found at i:1662453 original size:30 final size:30
Alignment explanation
Indices: 1662419--1662490 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
1662409 TTAACGATTT
1662419 ATTTAAGTATAAATTAAAAATTAAGTATTC
1 ATTTAAGTATAAATTAAAAATTAAGTATTC
* * *
1662449 ATTTAAGTATAATTTAAAATTTAAGTATTT
1 ATTTAAGTATAAATTAAAAATTAAGTATTC
1662479 ATTTGAA-TATAA
1 ATTT-AAGTATAA
1662491 TTTTAAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTAAGTATAAATTAAAAATTAAGTATTC
Found at i:1662593 original size:465 final size:453
Alignment explanation
Indices: 1661873--1662789 Score: 1301
Period size: 465 Copynumber: 2.0 Consensus size: 453
1661863 TTTATTATTT
* **
1661873 TTAAATAAGTTTTTATTATTTAATTTATAATCAATTTATGTTTTTATTTTAAATAAAAGATTGTT
1 TTAAATAAATTTTTATTATTTAATTTATAAAAAATTTATGTTTTTATTTTAAATAAAAGATTGTT
* *
1661938 TTATACTGAAAATTTATTTAAATATAAATTAAAAGTTAAATATTTATTTAAATATAATTCAAAAT
66 TTATA-TGAAAATTTATTTAAATATAAATTAAAAATTAAATATTCATTTAAATATAATTCAAAAT
* * *
1662003 TTTACGTATTTATTTGAATATGATTTTAAAATTAAAGATTTATTGATTTTACGATAAAATAAAAG
130 TTTAAGTATTTATTTGAATATAATTTTAAAATTAAAGATTTATTGA-TTTACAATAAAATAAAAG
* *
1662068 TATAGATATTTATTTAAATAAAATAATAAAATTTAAGAGTTTTTTTAAAAATTATTTTTAACCAA
194 TATAGATATCTATTTAAATAAAATAATAAAATTTAAAAGTTTTTTTAAAAATTATTTTTAACCAA
1662133 TTTTTTCCTTAA-TTTTATAATAATACTAAGTAATCTGGATGCCCTGATACTAAATTTTATTAGA
259 -TTTTTCCTTAATTTTTATAATAATACTAAGTAATCTGGATGCCCTGATACTAAATTTTATTAGA
* *
1662197 TTTCATAATTTTAATGCAAAAAATTTAATAGATCTATCATATTTGTACTCAAGATTTTAATATAA
323 TTTCATAATTTTAAGGCAAAAAATTAAATAG----A-C--A----T--TCAAGATTTTAATATAA
* *
1662262 TTAATATTTTTATAATATTTATATTTT-AATAAATAAAATACAAAGATGAATAATCATATTTAAA
375 TTAATATTTTTATAATATTTATATTTTAAAAAAATAAAATACAAAGAAGAATAATCATATTTAAA
1662326 TCTCTGTTACTGAA
440 TCTCTGTTACTGAA
1662340 TTAAATAAATTTTTATTATTTAATTTATAAAAAAATTT-TGTTTTTATTTTAAATAAAAGATT-T
1 TTAAATAAATTTTTATTATTTAATTTAT-AAAAAATTTATGTTTTTATTTTAAATAAAAGATTGT
* * * * * *
1662403 CTTTAT-TTAACGATTTATTTAAGTATAAATTAAAAATTAAGTATTCATTTAAGTATAATTTAAA
65 -TTTATATGAA-AATTTATTTAAATATAAATTAAAAATTAAATATTCATTTAAATATAATTCAAA
*
1662467 A-TTTAAGTATTTATTTGAATATAATTTTAAGATTAAAGATTTATTTG-TTTACAATAAAATAAA
128 ATTTTAAGTATTTATTTGAATATAATTTTAAAATTAAAGATTTA-TTGATTTACAATAAAATAAA
* **
1662530 AGTATAGATATCTATTTAAATAAAATGATAAAATTTAAAAGCTTTTATTT-TTAATTATTTTTAA
192 AGTATAGATATCTATTTAAATAAAATAATAAAATTTAAAAG-TTTT-TTTAAAAATTATTTTTAA
* * * *
1662594 CCAATTTTTCCTTAATTTTTATAATAATATTAAGTAATCTTGATGCCTTGATACTGAATTTTATT
255 CCAATTTTTCCTTAATTTTTATAATAATACTAAGTAATCTGGATGCCCTGATACTAAATTTTATT
*
1662659 AGATTTCATAATTTTAAGGTAAAAAATTAAATAGACATTCAAGATTTTAATATAATTAATATTTT
320 AGATTTCATAATTTTAAGGCAAAAAATTAAATAGACATTCAAGATTTTAATATAATTAATATTTT
* *
1662724 TATAATATTTATATTTTAAAAAAATAAAATACGAAGAAGAATAATTATATTTAAATCTCTGTTAC
385 TATAATATTTATATTTTAAAAAAATAAAATACAAAGAAGAATAATCATATTTAAATCTCTGTTAC
1662789 T
450 T
1662790 CTCTGCCCTT
Statistics
Matches: 411, Mismatches: 31, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
452 44 0.11
453 44 0.11
454 1 0.00
458 1 0.00
460 1 0.00
461 1 0.00
464 64 0.16
465 138 0.34
466 54 0.13
467 56 0.14
468 7 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (453 bp):
TTAAATAAATTTTTATTATTTAATTTATAAAAAATTTATGTTTTTATTTTAAATAAAAGATTGTT
TTATATGAAAATTTATTTAAATATAAATTAAAAATTAAATATTCATTTAAATATAATTCAAAATT
TTAAGTATTTATTTGAATATAATTTTAAAATTAAAGATTTATTGATTTACAATAAAATAAAAGTA
TAGATATCTATTTAAATAAAATAATAAAATTTAAAAGTTTTTTTAAAAATTATTTTTAACCAATT
TTTCCTTAATTTTTATAATAATACTAAGTAATCTGGATGCCCTGATACTAAATTTTATTAGATTT
CATAATTTTAAGGCAAAAAATTAAATAGACATTCAAGATTTTAATATAATTAATATTTTTATAAT
ATTTATATTTTAAAAAAATAAAATACAAAGAAGAATAATCATATTTAAATCTCTGTTACTGAA
Found at i:1667077 original size:18 final size:18
Alignment explanation
Indices: 1667047--1667097 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
1667037 ATTTAGAAAT
*
1667047 AATTTAT-TAAAATTTTA
1 AATTTATATAAAATTATA
1667064 AATTTATATAAAATTATA
1 AATTTATATAAAATTATA
**
1667082 AAAATATATAAAATTA
1 AATTTATATAAAATTA
1667098 ATTAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 7 0.23
18 23 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTATATAAAATTATA
Found at i:1667078 original size:28 final size:27
Alignment explanation
Indices: 1667033--1667086 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1667023 AATTATAAAA
*
1667033 TTAAATTTAGAAATAATTTATTAAAATT
1 TTAAATTTAGAAATAA-TTATAAAAATT
*
1667061 TTAAATTTATATAA-AATTATAAAAAT
1 TTAAATTTAGA-AATAATTATAAAAAT
1667087 ATATAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 12 0.52
29 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TTAAATTTAGAAATAATTATAAAAATT
Found at i:1670040 original size:11 final size:11
Alignment explanation
Indices: 1670012--1670064 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
1670002 AAATTTATTG
*
1670012 ATATTATTTTT
1 ATATTATTTAT
1670023 A-ATTATTTAT
1 ATATTATTTAT
*
1670033 ATATTATTAAT
1 ATATTATTTAT
*
1670044 ATATTATATAT
1 ATATTATTTAT
*
1670055 AAATTATTTA
1 ATATTATTTA
1670065 AAAATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTATTTAT
Found at i:1670249 original size:26 final size:26
Alignment explanation
Indices: 1670207--1670264 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1670197 ATTTAATATA
* *
1670207 TTAATATAATTTTTTAAAATATTATT
1 TTAATATAATTTATTAAAAAATTATT
*
1670233 TTAAT-TAATATTATTAAAAAATTA-A
1 TTAATATAAT-TTATTAAAAAATTATT
1670258 TTAATAT
1 TTAATAT
1670265 TTTTTATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATATAATTTATTAAAAAATTATT
Found at i:1670671 original size:21 final size:21
Alignment explanation
Indices: 1670645--1670687 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1670635 CGTTTAATAT
1670645 AATATTAAAATTTTAATTTTA
1 AATATTAAAATTTTAATTTTA
1670666 AATATTAAAATTTTAATTTTA
1 AATATTAAAATTTTAATTTTA
1670687 A
1 A
1670688 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTAAAATTTTAATTTTA
Found at i:1670679 original size:15 final size:16
Alignment explanation
Indices: 1670658--1670701 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
1670648 ATTAAAATTT
1670658 TAATTTTAAATATTAA
1 TAATTTTAAATATTAA
*
1670674 -AATTTT-AATTTTAA
1 TAATTTTAAATATTAA
1670688 TAATTTTAAATATT
1 TAATTTTAAATATT
1670702 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 12 0.50
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTTAAATATTAA
Found at i:1671205 original size:24 final size:21
Alignment explanation
Indices: 1671176--1671227 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 21
1671166 AAATTTAATT
1671176 TAAATATAATAAAAATAAATTATA
1 TAAATATAAT--AAA-AAATTATA
1671200 TAAATAT-ATAAAAAATTATA
1 TAAATATAATAAAAAATTATA
1671220 T-AATATAA
1 TAAATATAA
1671228 ATTATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.19
20 10 0.37
21 3 0.11
23 2 0.07
24 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATAATAAAAAATTATA
Found at i:1674373 original size:20 final size:21
Alignment explanation
Indices: 1674318--1674381 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 21
1674308 GTTTATTTGA
*
1674318 TTTTTCAAAATTAATTTTTAATTT
1 TTTTTCATAATT-ATTTTT-A-TT
*
1674342 TTTTATCTTAATTATTTTTA-T
1 TTTT-TCATAATTATTTTTATT
*
1674363 TTTTTCATAATTATATTTA
1 TTTTTCATAATTATTTTTA
1674382 AAAATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 13 0.37
21 5 0.14
23 1 0.03
24 10 0.29
25 6 0.17
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTCATAATTATTTTTATT
Found at i:1674458 original size:4 final size:4
Alignment explanation
Indices: 1674449--1674477 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1674439 TATTTTTAAA
1674449 TATT TATT TATT TATT TATT T-TT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
1674478 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1674485 original size:8 final size:8
Alignment explanation
Indices: 1674474--1674514 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1674464 TTATTTTTTA
1674474 TTTAAAAT
1 TTTAAAAT
1674482 TTT-AAAT
1 TTTAAAAT
*
1674489 ATT-AAAT
1 TTTAAAAT
1674496 ATTTAAAAT
1 -TTTAAAAT
1674505 TTTAAAAT
1 TTTAAAAT
1674513 TT
1 TT
1674515 ATATTTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 10 0.34
8 15 0.52
9 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1676138 original size:2 final size:2
Alignment explanation
Indices: 1676131--1676169 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1676121 CAAAGGCTAA
*
1676131 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1676170 TGCATGACAT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1682749 original size:2 final size:2
Alignment explanation
Indices: 1682742--1682775 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1682732 CAAACATAAC
*
1682742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1682776 GTCCCACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1684122 original size:25 final size:24
Alignment explanation
Indices: 1684082--1684144 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
1684072 TTTTATAATT
* *
1684082 ACAAAATAT--AAGTATAATATGAA
1 ACAAAATATAAAAATATAACAT-AA
1684105 A-AAAATAATAAAAATATAACATAA
1 ACAAAAT-ATAAAAATATAACATAA
*
1684129 ACATAATATAAAAATA
1 ACAAAATATAAAAATA
1684145 AAAATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 12 0.36
25 13 0.39
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (24 bp):
ACAAAATATAAAAATATAACATAA
Found at i:1684438 original size:19 final size:20
Alignment explanation
Indices: 1684390--1684444 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
1684380 TTTTATATTA
*
1684390 AATAATATTTATTTAATTTAT
1 AATAAAATTT-TTTAATTTAT
1684411 AAGTAAAATTTTTTAATTT-T
1 AA-TAAAATTTTTTAATTTAT
1684431 AATAAAATTTTTTA
1 AATAAAATTTTTTA
1684445 TTAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.38
20 3 0.09
21 10 0.31
22 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATAAAATTTTTTAATTTAT
Found at i:1684477 original size:57 final size:59
Alignment explanation
Indices: 1684368--1684506 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 59
1684358 TTTTAAATTA
* * * * * *
1684368 TTATTATAAATATTTTATATTAAATAATATTTATTTAATTTATAAGTAAAATTTTTTAAT
1 TTATAATAAA-ATTTTTTATTAAATAATATTTATCTAATTGATAAGTAAAATTATTAAAT
* *
1684428 TT-TAATAAAATTTTTTATTAAAT-ATATTTATCTGA-TGATAATTAAAAATTATTAAAT
1 TTATAATAAAATTTTTTATTAAATAATATTTATCTAATTGATAAGT-AAAATTATTAAAT
*
1684485 TTAATAATAAATTATTTTTATT
1 TT-ATAATAAAAT-TTTTTATT
1684507 TTTATAAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
56 6 0.09
57 23 0.35
58 13 0.20
59 14 0.21
60 10 0.15
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (59 bp):
TTATAATAAAATTTTTTATTAAATAATATTTATCTAATTGATAAGTAAAATTATTAAAT
Found at i:1684497 original size:58 final size:59
Alignment explanation
Indices: 1684372--1684502 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 59
1684362 AAATTATTAT
* * * * *
1684372 TATAAATATTTTATATTAAATAATATTTATTTAATTTATAAGTAAAATTTTTTAATTTTAA
1 TATAAAT-TTTT-TATTAAATAATATTTATCTAATTGATAAGTAAAAATTATTAAATTTAA
* *
1684433 TA-AAATTTTTTATTAAAT-ATATTTATCTGA-TGATAATTAAAAATTATTAAATTTAA
1 TATAAATTTTTTATTAAATAATATTTATCTAATTGATAAGTAAAAATTATTAAATTTAA
1684489 TAATAAATTATTTT
1 T-ATAAATT-TTTT
1684503 TATTTTTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
56 22 0.37
57 11 0.18
58 13 0.22
59 8 0.13
60 4 0.07
61 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (59 bp):
TATAAATTTTTTATTAAATAATATTTATCTAATTGATAAGTAAAAATTATTAAATTTAA
Found at i:1684669 original size:25 final size:26
Alignment explanation
Indices: 1684626--1684675 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1684616 GATTAAAAAT
*
1684626 AATAAATTTATATATTTAA-ATATTG
1 AATAAATTTATACATTTAAGATATTG
1684651 AATAAATTT-TACATGTTAAGATATT
1 AATAAATTTATACAT-TTAAGATATT
1684676 TATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (26 bp):
AATAAATTTATACATTTAAGATATTG
Found at i:1689669 original size:2 final size:2
Alignment explanation
Indices: 1689662--1689707 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1689652 TGCATTACAA
*
1689662 AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
1689704 AT AT
1 AT AT
1689708 GTATTAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1690294 original size:32 final size:33
Alignment explanation
Indices: 1690219--1690295 Score: 79
Period size: 33 Copynumber: 2.3 Consensus size: 33
1690209 CTTTATTTCA
* *
1690219 ATTATTAAAATATAAATTATTGATAATTTTAATT
1 ATTA-TAAAATATAAATTATTGAAAAATTTAATT
*
1690253 ATTAAAAAATATAAATT-TT-AAAAATTT-ATT
1 ATTATAAAATATAAATTATTGAAAAATTTAATT
1690283 ATATGATAAAATA
1 AT-T-ATAAAATA
1690296 CCAAAAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
30 5 0.14
31 7 0.19
32 9 0.24
33 12 0.32
34 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (33 bp):
ATTATAAAATATAAATTATTGAAAAATTTAATT
Found at i:1698172 original size:41 final size:41
Alignment explanation
Indices: 1698121--1698200 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
1698111 CACATGCGAA
*
1698121 GCAATCGTACATCATGCTTATCATCAATCATTTGTCAAGTG
1 GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAGTG
* * *
1698162 GCAATGGTACATGACGCTTATTATCAATCATTTGTCAAG
1 GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAG
1698201 ATGGTACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (41 bp):
GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAGTG
Found at i:1701393 original size:126 final size:131
Alignment explanation
Indices: 1701198--1701457 Score: 467
Period size: 126 Copynumber: 2.0 Consensus size: 131
1701188 TGAGCATGGG
1701198 AAAGTTTCTTAAATTACTCCTATATAATATATATATATATATATGCATATATTGTATTTTAGCAT
1 AAAGTTTCTTAAATTACTCC-ATATAATATATATATATATATATGCATATATTGTATTTTAGCAT
1701263 CTGCGAAGCAGCGATTAAGT-AAGTAAAATTTGATT-AAAAAAATCTTATATTTACATTGTATTG
65 CTGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTG
1701326 AA
130 AA
1701328 AAAGTTTCTTAAATTACTCC-TAT-ATA-ATATATATATATATGCATATATTGTATTTTAGCATC
1 AAAGTTTCTTAAATTACTCCATATAATATATATATATATATATGCATATATTGTATTTTAGCATC
*
1701390 TGCGAAGCAGTGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
66 TGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
1701455 A
131 A
1701456 AA
1 AA
1701458 TATCTTTTGG
Statistics
Matches: 127, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
126 54 0.43
127 18 0.14
128 35 0.28
130 20 0.16
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (131 bp):
AAAGTTTCTTAAATTACTCCATATAATATATATATATATATATGCATATATTGTATTTTAGCATC
TGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
A
Found at i:1702005 original size:2 final size:2
Alignment explanation
Indices: 1701930--1701989 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
1701920 TTGAAGTTAT
1701930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1701970 TA -A TT TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1701990 TTAATTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
1 5 0.10
2 46 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1703352 original size:21 final size:21
Alignment explanation
Indices: 1703313--1703352 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1703303 ATTAATAATA
**
1703313 TAAACATAAAATTTTAACACG
1 TAAACATAAAATTAAAACACG
1703334 TAAACATAAAATTAAAACA
1 TAAACATAAAATTAAAACA
1703353 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAACATAAAATTAAAACACG
Found at i:1705194 original size:15 final size:15
Alignment explanation
Indices: 1705174--1705205 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1705164 AACTTCCAAT
1705174 AGGTGAACGCGCGAA
1 AGGTGAACGCGCGAA
1705189 AGGTGAACGCGCGAA
1 AGGTGAACGCGCGAA
1705204 AG
1 AG
1705206 CTATTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.41, T:0.06
Consensus pattern (15 bp):
AGGTGAACGCGCGAA
Found at i:1705822 original size:3 final size:3
Alignment explanation
Indices: 1705814--1705863 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1705804 ATTCATTTCT
1705814 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1705862 TT
1 TT
1705864 TGCTTTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1710564 original size:16 final size:16
Alignment explanation
Indices: 1710545--1710608 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
1710535 ATCAGAATTA
1710545 TATTTA-AAATATTTTT
1 TATTTATAAAT-TTTTT
*
1710561 TATTTATAAATTTTTAA
1 TATTTATAAATTTTT-T
1710578 TATGTTAATAAATTTTATT
1 TAT-TT-ATAAATTTT-TT
1710597 TA--TATAAATTTT
1 TATTTATAAATTTT
1710609 AAAATAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 9 0.22
16 11 0.27
17 7 0.17
18 2 0.05
19 11 0.27
20 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTATAAATTTTTT
Found at i:1710620 original size:33 final size:33
Alignment explanation
Indices: 1710558--1710644 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
1710548 TTAAAATATT
* * **
1710558 TTTTATTTATA-AATTTTTAATATGTTAATAAA
1 TTTTATTTATATAAATTTTAAAATAATAATAAA
*
1710590 TTTTATTTATATAAATTTTAAAATAATAATATA
1 TTTTATTTATATAAATTTTAAAATAATAATAAA
*
1710623 -TTTATATTATATTATATTTTAA
1 TTTTAT-TTATA-TAAATTTTAA
1710645 TCATCTTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 16 0.35
33 21 0.46
34 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TTTTATTTATATAAATTTTAAAATAATAATAAA
Found at i:1713993 original size:2 final size:2
Alignment explanation
Indices: 1713986--1714027 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1713976 AAATCAATTG
1713986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1714028 GCACACACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1720666 original size:14 final size:13
Alignment explanation
Indices: 1720624--1720666 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1720614 TAAAATAAAT
*
1720624 TATTTTAATAATA
1 TATTTTAATATTA
1720637 TAATTTTAATATTTA
1 T-ATTTTAATA-TTA
1720652 TATTTTGAATATTA
1 TATTTT-AATATTA
1720666 T
1 T
1720667 TAAACATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 18 0.69
15 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TATTTTAATATTA
Found at i:1720713 original size:57 final size:52
Alignment explanation
Indices: 1720612--1720718 Score: 117
Period size: 57 Copynumber: 2.0 Consensus size: 52
1720602 AGTGTAAAAA
* * *
1720612 ATTAAAATAAATTATTTTAATAATATAATTTTAATATTTATATTTTGAATATT
1 ATTAAAATAAATTATTTTAATAATACAATTATAACATTTATATTTT-AATATT
*
1720665 ATTAAACATAAATATATATTCTAATAATACAA-TATAACATTATTTATTTTAATA
1 ATTAAA-ATAAAT-TAT-TT-TAATAATACAATTATAACATT-TATATTTTAATA
1720719 GCACATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
53 6 0.13
54 6 0.13
55 3 0.07
56 13 0.29
57 17 0.38
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (52 bp):
ATTAAAATAAATTATTTTAATAATACAATTATAACATTTATATTTTAATATT
Found at i:1720769 original size:17 final size:17
Alignment explanation
Indices: 1720736--1720787 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
1720726 ATTAATAAAA
*
1720736 TTAATAAAATTTATTATT
1 TTAATAAAATATATTA-T
1720754 TTAATAAAA-ATATTAT
1 TTAATAAAATATATTAT
1720770 TTAATAAAATAATATTAT
1 TTAATAAAAT-ATATTAT
1720788 CATTTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 16 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATAAAATATATTAT
Found at i:1720812 original size:21 final size:22
Alignment explanation
Indices: 1720769--1720812 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1720759 AAAAATATTA
*
1720769 TTTAATAAAATAATATTATCAT
1 TTTAATAAAATAATATTAACAT
* *
1720791 TTTAATAATA-AATTTTAACAT
1 TTTAATAAAATAATATTAACAT
1720812 T
1 T
1720813 ATCAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAATAAAATAATATTAACAT
Found at i:1720958 original size:21 final size:23
Alignment explanation
Indices: 1720932--1720975 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1720922 TAGTAAATTT
1720932 TTTTAATA-TA-AAATATTAATA
1 TTTTAATAGTAGAAATATTAATA
1720953 TTTTAATAGTAGAAATATTAATA
1 TTTTAATAGTAGAAATATTAATA
1720976 AAAATATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTTAATAGTAGAAATATTAATA
Found at i:1720958 original size:37 final size:39
Alignment explanation
Indices: 1720876--1720963 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 39
1720866 TTCATATGAC
* * **
1720876 TATTGTAATAATAAATTTATATTAATATTAAGTTATAAA
1 TATTTTAATAGTAAATTTATATTAATATTAAAATATAAA
* *
1720915 TA-TTTAATAGTAAATTT-TTTTAATA-TAAAATATTAA
1 TATTTTAATAGTAAATTTATATTAATATTAAAATATAAA
1720951 TATTTTAATAGTA
1 TATTTTAATAGTA
1720964 GAAATATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
36 10 0.24
37 17 0.40
38 13 0.31
39 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (39 bp):
TATTTTAATAGTAAATTTATATTAATATTAAAATATAAA
Found at i:1721095 original size:13 final size:14
Alignment explanation
Indices: 1721077--1721111 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1721067 CAATAATATT
1721077 TTATTATT-AAATA
1 TTATTATTCAAATA
1721090 TTATTATTCAAATA
1 TTATTATTCAAATA
*
1721104 TTACTATT
1 TTATTATT
1721112 TGAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTATTCAAATA
Found at i:1721160 original size:170 final size:171
Alignment explanation
Indices: 1720984--1721327 Score: 507
Period size: 170 Copynumber: 2.0 Consensus size: 171
1720974 TAAAAATATC
1720984 ATTTTAAATTATTCATTATA-TTTTAAAATATTTATATAATAAATGTTTTAATAATA-AATAATA
1 ATTTT-AA-TATTCATTATATTTTTAAAATATTTATATAATAAATGTTTTAATAATATAATAATA
* * * *
1721047 TTATTTTAAGTGTTTAATA-TCAATAATATTTTATTATTAAATATTATTATTCAAATATTACTAT
64 TTATATTAAGTATTTAATACTC-ATAATATTTTATTATTAAAAATTATTATTCAAATATTACCAT
* *
1721111 TTGAATATTAAAAATTAATAGTTTAATAATAAATAG-TTTTAAT
128 TTGAATATTAAAAATTAATAGTTTAACAATAAAGAGTTTTTAAT
* * * * * *
1721154 ATTTTAATATTTATTATATTTTTAAAATATTTGTCTAATTAATGTTTTAATAATATTATAGTATT
1 ATTTTAATATTCATTATATTTTTAAAATATTTATATAATAAATGTTTTAATAATATAATAATATT
1721219 ATATTAAGTATTTAATACTCATAATATTTTATTATTAAAAATTATTATTCAAATATTACCATTTG
66 ATATTAAGTATTTAATACTCATAATATTTTATTATTAAAAATTATTATTCAAATATTACCATTTG
* *
1721284 AATATTAAAAGTTAATAGTTTAACGATAAAGAGTTTTTAAT
131 AATATTAAAAATTAATAGTTTAACAATAAAGAGTTTTTAAT
1721325 ATT
1 ATT
1721328 AAAAATTGTA
Statistics
Matches: 156, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
168 10 0.06
169 35 0.22
170 99 0.63
171 12 0.08
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (171 bp):
ATTTTAATATTCATTATATTTTTAAAATATTTATATAATAAATGTTTTAATAATATAATAATATT
ATATTAAGTATTTAATACTCATAATATTTTATTATTAAAAATTATTATTCAAATATTACCATTTG
AATATTAAAAATTAATAGTTTAACAATAAAGAGTTTTTAAT
Found at i:1722297 original size:20 final size:20
Alignment explanation
Indices: 1722274--1722312 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1722264 ATTTAGTAAC
*
1722274 TTTAAAGATTATTTTTTAAT
1 TTTAAAAATTATTTTTTAAT
*
1722294 TTTAAAAATTGTTTTTTAA
1 TTTAAAAATTATTTTTTAA
1722313 GATATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTAAAAATTATTTTTTAAT
Found at i:1722874 original size:2 final size:2
Alignment explanation
Indices: 1722867--1722894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1722857 CTCAATTGGA
1722867 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
1722895 GTGTGTTATA
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:1723944 original size:34 final size:34
Alignment explanation
Indices: 1723877--1724092 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
1723867 GAGAAAAAGA
* * *
1723877 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1723910 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1723944 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1723977 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1724011 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1724045 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1724079 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1724093 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1724058 original size:68 final size:67
Alignment explanation
Indices: 1723877--1724094 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1723867 GAGAAAAAGA
* * * * *
1723877 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1723942 AT
66 AT
* * * *
1723944 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1724009 AT
66 AT
* * *
1724011 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
1724076 CAT
65 CAT
1724079 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1724095 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:1728572 original size:34 final size:34
Alignment explanation
Indices: 1728503--1728720 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
1728493 AAGTGGGAGA
* * *
1728503 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1728536 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1728570 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1728603 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1728637 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1728671 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1728705 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1728721 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1728686 original size:68 final size:67
Alignment explanation
Indices: 1728503--1728722 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1728493 AAGTGGGAGA
* * * * *
1728503 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1728568 CC
66 CC
* * * *
1728570 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1728635 CC
66 CC
* * *
1728637 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1728702 GCC
65 GCC
1728705 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1728723 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Done.