Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold330
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: 1763736
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 14
Found at i:1308422 original size:10 final size:10
Alignment explanation
Indices: 1308407--1308433 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1308397 ATCCCTTGTT
1308407 GCTACAACAA
1 GCTACAACAA
1308417 GCTACAACAA
1 GCTACAACAA
1308427 GCTACAA
1 GCTACAA
1308434 ATGCCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.30, G:0.11, T:0.11
Consensus pattern (10 bp):
GCTACAACAA
Found at i:1308686 original size:20 final size:19
Alignment explanation
Indices: 1308661--1308735 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
1308651 TTTTTACCCA
1308661 AATGTATCGATACATTTTT
1 AATGTATCGATACATTTTT
* *
1308680 CAATGTATCGATACATGTATG
1 -AATGTATCGATACAT-TTTT
*
1308701 AATGTATCGATGCATTCTTT
1 AATGTATCGATACATT-TTT
1308721 AATGTATCGATACAT
1 AATGTATCGATACAT
1308736 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (19 bp):
AATGTATCGATACATTTTT
Found at i:1313719 original size:20 final size:20
Alignment explanation
Indices: 1313693--1313810 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
1313683 TAGATGTACT
1313693 GATACATTTTTCAATGTATC
1 GATACATTTTTCAATGTATC
* * * * * *
1313713 GAAACATGTATGAATGAATT
1 GATACATTTTTCAATGTATC
*
1313733 GATACATTCTTCAATGTATC
1 GATACATTTTTCAATGTATC
1313753 GATACATTCTGTCTTTTTACCTAGATGTATC
1 GATACA-------TTTTT--C-A-ATGTATC
1313784 GATACATTTTTCAATGTATC
1 GATACATTTTTCAATGTATC
1313804 GATACAT
1 GATACAT
1313811 CTCGTTAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
20 47 0.64
21 1 0.01
22 1 0.01
24 5 0.07
27 4 0.05
29 1 0.01
30 1 0.01
31 13 0.18
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
GATACATTTTTCAATGTATC
Found at i:1315989 original size:27 final size:27
Alignment explanation
Indices: 1315959--1316023 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
1315949 ATTCATCGGG
*
1315959 GATACTCTAACCCCATTCCTCCGATGA
1 GATACTCCAACCCCATTCCTCCGATGA
*
1315986 GATACTCCAACCCCATTCCTCCGATGG
1 GATACTCCAACCCCATTCCTCCGATGA
1316013 GATACTCCAAC
1 GATACTCCAAC
1316024 TCCGCTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.23
Consensus pattern (27 bp):
GATACTCCAACCCCATTCCTCCGATGA
Found at i:1325536 original size:49 final size:49
Alignment explanation
Indices: 1325318--1326161 Score: 862
Period size: 49 Copynumber: 17.7 Consensus size: 49
1325308 GTGAAAAAGA
* * * * *
1325318 TGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA--AG---AAGG
* * * * *
1325372 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA---AGAAGG
1325425 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* *
1325468 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
** *
1325517 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAACG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* *** * *
1325566 TGCCAATGTGCTGATTCAAGGCCAGCGCCATTGGACTTAAAGATGACAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA--A-GAAGG
* *
1325618 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA-AGAAGG
* *
1325667 TGCCAATATGCAGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* * * * *
1325710 TGCCAATGTGCTGATTCAAGGCCAGTTACATTGGACTTAAAGATGAAAAATG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GAAGAAGG
*
1325762 TGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT-----A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* * *
1325805 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
1325854 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* * *
1325897 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
*
1325946 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* * *
1325989 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
*
1326038 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* * *
1326081 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
* *
1326130 TGCCAATATGCTGATTTAAGGCCAGCGATATT
1 TGCCAATATGCTGATTCAAGGCCAGCTATATT
1326162 TGGCTTAGAA
Statistics
Matches: 665, Mismatches: 80, Indels: 94
0.79 0.10 0.11
Matches are distributed among these distances:
43 229 0.34
44 2 0.00
45 2 0.00
46 1 0.00
47 2 0.00
48 1 0.00
49 277 0.42
50 1 0.00
51 1 0.00
52 109 0.16
53 4 0.01
55 34 0.05
56 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGG
Found at i:1325551 original size:92 final size:87
Alignment explanation
Indices: 1325420--1326161 Score: 802
Period size: 92 Copynumber: 7.9 Consensus size: 87
1325410 TAAAGATGGA
* *
1325420 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAGGTGCCAATGTGCTGATT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGTGCCAATATGCTGATT
* *
1325484 CAAGGCCAGCTACATTGGACTT
66 CAAGGCCAGCGATATTGGACTT
* *
1325506 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAACGTGCCA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT-AA----AAGGTGCCA
* **
1325571 ATGTGCTGATTCAAGGCCAGCGCCATTGGACTT
55 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1325604 AAAGATGACAAAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
1 -AA-A-G-----G-TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT----A-AAAGGTG
*
1325669 CCAATATGCAGATTCAAGGCCAGCGATATTGGACTT
52 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1325705 AAAGATGCCAATGTGCTGATTCAAGGCCAGTTACATTGGACTTAAAGATGAAAAATGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAA-A-G------GTGCCAATA
* *
1325770 TGCTAATTCAAGGCCAGCTATATTGGACTT
58 TGCTGATTCAAGGCCAGCGATATTGGACTT
*
1325800 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT--A-A--AAGGTGCCAATATGC
*
1325865 TGATTCAAGGCCAGCTATATTGGACTT
61 TGATTCAAGGCCAGCGATATTGGACTT
1325892 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--A-GGTGCCAATATGC
1325957 TGATTCAAGGCCAGCGATATTGGACTT
61 TGATTCAAGGCCAGCGATATTGGACTT
1325984 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--A-GGTGCCAATATGC
1326049 TGATTCAAGGCCAGCGATATTGGACTT
61 TGATTCAAGGCCAGCGATATTGGACTT
*
1326076 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT--A-A--AAGGTGCCAATATGC
*
1326141 TGATTTAAGGCCAGCGATATT
61 TGATTCAAGGCCAGCGATATT
1326162 TGGCTTAGAA
Statistics
Matches: 586, Mismatches: 27, Indels: 75
0.85 0.04 0.11
Matches are distributed among these distances:
87 2 0.00
88 2 0.00
89 3 0.01
90 1 0.00
91 4 0.01
92 361 0.62
93 4 0.01
94 5 0.01
95 80 0.14
97 1 0.00
98 42 0.07
99 2 0.00
100 4 0.01
101 73 0.12
104 1 0.00
105 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (87 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTT
Found at i:1325896 original size:22 final size:22
Alignment explanation
Indices: 1325871--1325938 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
1325861 ATGCTGATTC
1325871 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
1325893 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
1325914 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
1325936 AAG
1 AAG
1325939 ATGATGGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:1326304 original size:33 final size:32
Alignment explanation
Indices: 1326168--1326359 Score: 307
Period size: 32 Copynumber: 6.0 Consensus size: 32
1326158 TATTTGGCTT
1326168 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1326199 AGAGAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AGA-AGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1326232 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1326264 AG-GGGGTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
* *
1326296 AGAAGGGTTTCCACCTACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1326329 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1326360 TGAAAAGGAG
Statistics
Matches: 149, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
31 29 0.19
32 61 0.41
33 59 0.40
ACGTcount: A:0.15, C:0.18, G:0.38, T:0.30
Consensus pattern (32 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
Found at i:1326407 original size:27 final size:27
Alignment explanation
Indices: 1326375--1326428 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1326365 AGGAGAAAGA
*
1326375 TGCCACAGAGTTGTAGACTTAAAAGGG
1 TGCCACAGAATTGTAGACTTAAAAGGG
*
1326402 TGCCACAGAATTGTGGACTTAAAAGGG
1 TGCCACAGAATTGTAGACTTAAAAGGG
1326429 AAAAAGAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (27 bp):
TGCCACAGAATTGTAGACTTAAAAGGG
Found at i:1326490 original size:67 final size:61
Alignment explanation
Indices: 1326362--1326495 Score: 153
Period size: 67 Copynumber: 2.1 Consensus size: 61
1326352 TGGGCTTTTG
* *
1326362 AAAA-GGAGAAAGATGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAATTGTGGACTT
1 AAAAGGGAAAAAGATGCCACAGAGTTGTAGACTTAAAAGGATGCCACAGAATTGTGGACTT
* * * *
1326422 AAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACAGGAGTTGTGGGC
1 AAAAGGGAAAAAGA-TGCCACAGAGTTGTAGAC-TT-AAAAG--GATGCCACA-GAATTGTGGAC
1326487 TT
60 TT
1326489 AAAAGGG
1 AAAAGGG
1326496 TGCCACGGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
60 4 0.07
61 8 0.13
62 16 0.26
63 2 0.03
64 5 0.08
66 8 0.13
67 18 0.30
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.19
Consensus pattern (61 bp):
AAAAGGGAAAAAGATGCCACAGAGTTGTAGACTTAAAAGGATGCCACAGAATTGTGGACTT
Found at i:1326566 original size:30 final size:30
Alignment explanation
Indices: 1326431--1326665 Score: 159
Period size: 31 Copynumber: 7.9 Consensus size: 30
1326421 TAAAAGGGAA
* *
1326431 AAAGAG-TGCCACAGAGTTGTGGGCTTTGA
1 AAAGAGATGCCACTGAGTTGTGGGCTTTGG
* *
1326460 AAAGAAGATGCCACAGGAGTTGTGGGC-TT-A
1 AAAG-AGATGCCAC-TGAGTTGTGGGCTTTGG
* * * *
1326490 AAAG-GGTGCCACGGAGTCGTGGACTTTGAAG
1 AAAGAGATGCCACTGAGTTGTGGGCTTTG--G
* * * *
1326521 AAA-AAATGTCACTGAGTCGTGGACTTTGG
1 AAAGAGATGCCACTGAGTTGTGGGCTTTGG
*
1326550 AAAGAGATGCCACTGAGTTGTGGGC-TT-A
1 AAAGAGATGCCACTGAGTTGTGGGCTTTGG
* *
1326578 AAAG-GGTGCCACAGAGTTGTGGGCTTTGAG
1 AAAGAGATGCCACTGAGTTGTGGGCTTTG-G
*
1326608 ACAA-A-ATGCCACTGAGTTGTGGGCATT-G
1 A-AAGAGATGCCACTGAGTTGTGGGCTTTGG
* *
1326636 AGAAGAGATTGCCACTGAGTCGTGGACTTT
1 A-AAGAGA-TGCCACTGAGTTGTGGGCTTT
1326666 AAGAAGGTAT
Statistics
Matches: 165, Mismatches: 24, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
27 28 0.17
28 19 0.12
29 11 0.07
30 45 0.27
31 51 0.31
32 11 0.07
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (30 bp):
AAAGAGATGCCACTGAGTTGTGGGCTTTGG
Found at i:1326587 original size:88 final size:88
Alignment explanation
Indices: 1326372--1326660 Score: 330
Period size: 88 Copynumber: 3.2 Consensus size: 88
1326362 AAAAGGAGAA
* * * * **
1326372 AGATGCCACAGAGTTGTAGACTTAAAAGGGTGCCACAGAATTGTGGACTTAAAAGGGAAAAAGAG
1 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAA--GAAAAA-A-
* *
1326437 TGCCACAGAGTTGTGGGCTTTGAAAAG
62 TGCCACTGAGTTGTGGGCTTTGGAAAG
* * *
1326464 AAGATGCCACAGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTCGTGGACTTTGAAGAAAAAATG
1 -AGATGCCAC-TGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAATG
* * *
1326529 TCACTGAGTCGTGGACTTTGGAAAG
64 CCACTGAGTTGTGGGCTTTGGAAAG
* *
1326554 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGGCTTTG-AGACAAAATGCC
1 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAATGCC
*
1326618 ACTGAGTTGTGGGCATT-GAGAAG
66 ACTGAGTTGTGGGCTTTGGA-AAG
*
1326641 AGATTGCCACTGAGTCGTGG
1 AGA-TGCCACTGAGTTGTGG
1326661 ACTTTAAGAA
Statistics
Matches: 170, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
86 2 0.01
87 30 0.18
88 54 0.32
89 9 0.05
90 22 0.13
91 1 0.01
92 6 0.04
93 9 0.05
94 37 0.22
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (88 bp):
AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAATGCC
ACTGAGTTGTGGGCTTTGGAAAG
Found at i:1327664 original size:17 final size:17
Alignment explanation
Indices: 1327624--1327677 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
1327614 TCTTCTTCTT
1327624 CTTTTTT-TTTTGTTT-
1 CTTTTTTGTTTTGTTTC
*
1327639 C-TTCTT-TTTT-TTTC
1 CTTTTTTGTTTTGTTTC
1327653 CTTTTTTGTTTTGTTTC
1 CTTTTTTGTTTTGTTTC
*
1327670 TTTTTTTG
1 CTTTTTTG
1327678 GAAAAGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 3 0.09
14 9 0.28
15 5 0.16
16 4 0.12
17 11 0.34
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (17 bp):
CTTTTTTGTTTTGTTTC
Found at i:1327676 original size:25 final size:25
Alignment explanation
Indices: 1327613--1327663 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1327603 GGTTTTTCCC
*
1327613 TTCTTCTTCTTCTTTT--TTTTTTGT
1 TTCTTCTT-TTTTTTTCCTTTTTTGT
1327637 TTCTTCTTTTTTTTTCCTTTTTTGT
1 TTCTTCTTTTTTTTTCCTTTTTTGT
1327662 TT
1 TT
1327664 TGTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 8 0.33
25 10 0.42
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTCTTTTTTTTTCCTTTTTTGT
Found at i:1327939 original size:10 final size:10
Alignment explanation
Indices: 1327915--1327982 Score: 95
Period size: 10 Copynumber: 6.8 Consensus size: 10
1327905 CCTTTGCACC
*
1327915 TTTTTTCTGT
1 TTTTTTTTGT
1327925 GTTTTTTTTG-
1 -TTTTTTTTGT
1327935 -TTTTTTTGT
1 TTTTTTTTGT
1327944 TTTTTTTTGT
1 TTTTTTTTGT
1327954 TTTTTTTGTGT
1 TTTTTTT-TGT
1327965 TTTTTTTTGT
1 TTTTTTTTGT
1327975 TTTTTTTT
1 TTTTTTTT
1327983 CATCACTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
8 8 0.15
10 27 0.51
11 18 0.34
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:1327941 original size:21 final size:20
Alignment explanation
Indices: 1327915--1327981 Score: 102
Period size: 19 Copynumber: 3.4 Consensus size: 20
1327905 CCTTTGCACC
*
1327915 TTTTTTCTGTGTTTTTTTTG
1 TTTTTTTTGTGTTTTTTTTG
1327935 -TTTTTTTGT-TTTTTTTTG
1 TTTTTTTTGTGTTTTTTTTG
1327953 TTTTTTTTGTGTTTTTTTTTG
1 TTTTTTTTGTG-TTTTTTTTG
1327974 TTTTTTTT
1 TTTTTTTT
1327982 TCATCACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 9 0.21
19 17 0.40
21 17 0.40
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (20 bp):
TTTTTTTTGTGTTTTTTTTG
Found at i:1327995 original size:1 final size:1
Alignment explanation
Indices: 1327926--1327982 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
1327916 TTTTTCTGTG
* * * * * *
1327926 TTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTGTGTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1327983 CATCACTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:1334938 original size:52 final size:52
Alignment explanation
Indices: 1334853--1334977 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1334843 ATATGAAAAG
* *
1334853 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
*
1334905 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
*
1334957 TTGCCTACATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1334978 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
Found at i:1334990 original size:52 final size:51
Alignment explanation
Indices: 1334853--1334997 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1334843 ATATGAAAAG
*
1334853 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAT
* *
1334905 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAT
* *
1334957 TTGCCTACATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1334998 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAAT
Found at i:1335004 original size:13 final size:13
Alignment explanation
Indices: 1334986--1335010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1334976 CAAAGATCAG
1334986 TGTATCGATACAA
1 TGTATCGATACAA
1334999 TGTATCGATACA
1 TGTATCGATACA
1335011 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1335092 original size:32 final size:33
Alignment explanation
Indices: 1335051--1335116 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1335041 AGTAGCTTAA
1335051 ATTGTATCGATACAAAAC-TTATGTATCAATAC
1 ATTGTATCGATACAAAACTTTATGTATCAATAC
* *
1335083 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCAATAC
1335116 A
1 A
1335117 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCAATAC
Found at i:1340021 original size:1 final size:1
Alignment explanation
Indices: 1340017--1340097 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
1340007 CCAAAAATAC
** * * * * * * * *
1340017 AAAAAAAACCAAAAAAACAAAAAAAAACAAAAAAACAAAAAAACAAAAAAAACAAACAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1340082 AAACAAACAAAAAAAA
1 AAAAAAAAAAAAAAAA
1340098 GGTCCAGATG
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1340021 original size:8 final size:8
Alignment explanation
Indices: 1340008--1340097 Score: 92
Period size: 8 Copynumber: 10.6 Consensus size: 8
1339998 TCCTTCGTAC
*
1340008 CAAAAATA
1 CAAAAAAA
1340016 CAAAAAAAA
1 C-AAAAAAA
1340025 CCAAAAAAA
1 -CAAAAAAA
1340034 CAAAAAAAAA
1 C--AAAAAAA
1340044 CAAAAAAA
1 CAAAAAAA
1340052 CAAAAAAA
1 CAAAAAAA
1340060 CAAAAAAAA
1 C-AAAAAAA
*
1340069 CAAACAAA
1 CAAAAAAA
*
1340077 CAAACAAA
1 CAAAAAAA
1340085 CAAACAAAA
1 CAAA-AAAA
1340094 -AAAA
1 CAAAA
1340098 GGTCCAGATG
Statistics
Matches: 73, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
7 1 0.01
8 39 0.53
9 24 0.33
10 9 0.12
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.01
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1340029 original size:18 final size:18
Alignment explanation
Indices: 1340006--1340097 Score: 114
Period size: 18 Copynumber: 5.1 Consensus size: 18
1339996 CGTCCTTCGT
*
1340006 ACCAAAAATACAAAAAAA
1 ACCAAAAAAACAAAAAAA
1340024 ACCAAAAAAACAAAAAAA
1 ACCAAAAAAACAAAAAAA
*
1340042 AACAAAAAAAC-AAAAAA
1 ACCAAAAAAACAAAAAAA
*
1340059 ACAAAAAAAACAAACAAACA
1 ACCAAAAAAACAAA-AAA-A
* *
1340079 AACAAACAAACAAAAAAA
1 ACCAAAAAAACAAAAAAA
1340097 A
1 A
1340098 GGTCCAGATG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
17 15 0.23
18 31 0.48
19 6 0.09
20 12 0.19
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.01
Consensus pattern (18 bp):
ACCAAAAAAACAAAAAAA
Found at i:1340038 original size:25 final size:24
Alignment explanation
Indices: 1340009--1340094 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 24
1339999 CCTTCGTACC
*
1340009 AAAAATACAAAAAAAACCAAAAAAACAA
1 AAAAAAAC-AAAAAAA-C-AAAAAAC-A
1340037 AAAAAAACAAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAAC-AAAAAACA
*
1340062 AAAAAAACAAACAAACAAACAAACA
1 AAAAAAACAAAAAAACAAA-AAACA
1340087 AACAAAAA
1 AA-AAAAA
1340095 AAAGGTCCAG
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.06
25 23 0.43
26 14 0.26
27 7 0.13
28 7 0.13
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (24 bp):
AAAAAAACAAAAAAACAAAAAACA
Found at i:1340051 original size:29 final size:27
Alignment explanation
Indices: 1340009--1340097 Score: 110
Period size: 29 Copynumber: 3.2 Consensus size: 27
1339999 CCTTCGTACC
*
1340009 AAAAATACAAAAAAAACCAAAAAAACAA
1 AAAAAAACAAAAAAAA-CAAAAAAACAA
1340037 AAAAAAAC-AAAAAAACAAAAAAAC-A
1 AAAAAAACAAAAAAAACAAAAAAACAA
*
1340062 AAAAAAACAAACAAACAAACAAACAAACAA
1 AAAAAAAC-AA-AAA-AAACAAAAAAACAA
1340092 AAAAAA
1 AAAAAA
1340098 GGTCCAGATG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 9 0.17
26 9 0.17
27 8 0.15
28 10 0.19
29 11 0.20
30 7 0.13
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (27 bp):
AAAAAAACAAAAAAAACAAAAAAACAA
Found at i:1341382 original size:28 final size:28
Alignment explanation
Indices: 1341345--1341762 Score: 399
Period size: 28 Copynumber: 14.5 Consensus size: 28
1341335 TGTTCATCTC
*
1341345 TTCAAAGCCCACAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1341373 TTCAATGCCCATAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1341401 TTCAATGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * **
1341429 TTCAAAGCCCACAAGTCGGTGGTAACTATT
1 TTCAAAGCCCACAAGTCAGTGG-CA-TCCT
* *
1341459 TTTAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1341487 TTCAAAAGACCACAAGTTAGTGGCACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
1341516 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1341544 TTCAAAGCCCACAAGTCAGTGACATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
1341574 TTCAAAGCCCACACAAATCAGTGGCA-CTCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATC-CT
* *
1341604 TCCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1341632 CTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1341660 TTCAAAGCCTACAAGTCAGTGGTACCCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
**
1341689 TT-AAAGCCCATGAGTCAGTGGCATCCCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
1341718 TTTAAAGCCCACAAAAGTCAGTGGCAACTCTT
1 TTCAAAGCCCAC--AAGTCAGTGGC-A-TCCT
1341750 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1341763 TAAGTTAGTG
Statistics
Matches: 327, Mismatches: 46, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
28 197 0.60
29 41 0.13
30 49 0.15
31 2 0.01
32 36 0.11
33 1 0.00
34 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1341549 original size:115 final size:113
Alignment explanation
Indices: 1341348--1341760 Score: 445
Period size: 116 Copynumber: 3.6 Consensus size: 113
1341338 TCATCTCTTC
* * * * * * *
1341348 AAAGCCCACAGGTCAGTGGCATCCTTTCAATGCCCATAAGTTAGTGGCATCTTTTCAATGCCCAT
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCAT
* * **
1341413 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGTAACTATTTTT
66 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTAAC-CCTTTT
*
1341462 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
* * ** *
1341527 CAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACATACCCTTTC
65 TAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTA-ACCCTTTT
* * * *
1341577 AAAGCCCACACAAATCAGTGGCA-CTCTTCCAAAGCCCACAAGTCAGTGGCACCCTCTCAAAGCC
1 AAAG-CC-CACAAGTCAGTGGCATCT-TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
* *
1341641 CATAAGTCAGTGGCACCCTTTCAAAGCCTACAAGTCAGTGGT-ACCCCTTT
63 CATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTAACCCTTTT
** * *
1341691 AAAGCCCATGAGTCAGTGGCATCCCCTTTT-AAAGCCCACAAAAGTCAGTGGCAACTCTTTTCAA
1 AAAGCCCACAAGTCAGTGGCAT---CTTTTCAAAGCCCAC--AAGTTAGTGGC-AC-CCTTTCAA
1341755 AGCCCA
59 AGCCCA
1341761 CATAAGTTAG
Statistics
Matches: 251, Mismatches: 35, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
112 12 0.05
113 2 0.01
114 45 0.18
115 74 0.29
116 87 0.35
117 19 0.08
118 12 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (113 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCAT
AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTAACCCTTTT
Found at i:1341718 original size:144 final size:143
Alignment explanation
Indices: 1341346--1341762 Score: 484
Period size: 144 Copynumber: 2.9 Consensus size: 143
1341336 GTTCATCTCT
* * * * * * *
1341346 TCAAAGCCCACAGGTCAGTGGCATCCTTTCAATGCCCATAAGTTAGTGGCATCTTTTCAATGCCC
1 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
* * * * *
1341411 ATAAGTCAGTGGCAT-CCTTTCAAAG-CC-CACAAGTCGGTGGTAACTATTTTTAAAGCCCACAA
66 ATAAGTCAGTGGCATCCCTTTCAAAGCCCACACAAATCAGTGG-CACT-CTTTCAAAGCCCACAA
* * *
1341473 GTCAGTGGCATCTTT
129 GTCAGTGGCACCCTC
* *
1341488 TCAAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
1 TC-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
* * *
1341553 CACAAGTCAGTGACATACCCTTTCAAAGCCCACACAAATCAGTGGCACTCTTCCAAAGCCCACAA
65 CATAAGTCAGTGGCAT-CCCTTTCAAAGCCCACACAAATCAGTGGCACTCTTTCAAAGCCCACAA
1341618 GTCAGTGGCACCCTC
129 GTCAGTGGCACCCTC
* * * *
1341633 TCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCTACAAGTCAGTGGTACCCCTTT-AAAGCC
1 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCCTTTCAAAGCC
* *
1341697 CATGAGTCAGTGGCATCCCCTTTTAAAGCCCACA-AAAGTCAGTGGCAACTCTTTTCAAAGCCCA
65 CATAAGTCAGTGGCAT-CCCTTTCAAAGCCCACACAAA-TCAGTGGC-ACTC-TTTCAAAGCCCA
1341761 CA
126 CA
1341763 TAAGTTAGTG
Statistics
Matches: 234, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
142 2 0.01
143 70 0.30
144 86 0.37
145 47 0.20
146 18 0.08
147 11 0.05
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (143 bp):
TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
ATAAGTCAGTGGCATCCCTTTCAAAGCCCACACAAATCAGTGGCACTCTTTCAAAGCCCACAAGT
CAGTGGCACCCTC
Found at i:1342718 original size:20 final size:20
Alignment explanation
Indices: 1342693--1342889 Score: 106
Period size: 20 Copynumber: 8.8 Consensus size: 20
1342683 TTTTTACCCA
1342693 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
1342713 AATGTATCGATACATTCTGTCTTTCTACCC
1 AATGTATCGATACA-----T-TTT-T---C
1342743 AGATGTATCGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * *
1342764 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
1342784 AATGTATCGATACTTCTGTCTTTTTACCC
1 AATGTATCGATA---C---ATTTTT---C
*
1342813 AAATGTATCGATACATTCTTC
1 -AATGTATCGATACATTTTTC
* * *
1342834 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
1342854 AATGTATCGATACGTTCTTC
1 AATGTATCGATACATTTTTC
*
1342874 AATGTATCGTTACATT
1 AATGTATCGATACATT
1342890 CTGTCTTTTT
Statistics
Matches: 136, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
20 87 0.64
21 3 0.02
23 1 0.01
24 5 0.04
25 4 0.03
26 7 0.05
27 2 0.01
30 14 0.10
31 13 0.10
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1342826 original size:70 final size:71
Alignment explanation
Indices: 1342693--1342871 Score: 288
Period size: 70 Copynumber: 2.5 Consensus size: 71
1342683 TTTTTACCCA
* * * *
1342693 AATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTCTACCCAGATGTATCGATACA
1 AATGTATCGATACATGTATGAATGTATCGATACATTCTGTCTTTCTACCCAAATGTATCGATACA
*
1342758 TTTTTC
66 TTCTTC
*
1342764 AATGTATCGATACATGTATGAATGTATCGATAC-TTCTGTCTTTTTACCCAAATGTATCGATACA
1 AATGTATCGATACATGTATGAATGTATCGATACATTCTGTCTTTCTACCCAAATGTATCGATACA
1342828 TTCTTC
66 TTCTTC
*
1342834 AATGTATCGATACATGTATGAATGTATCGATACGTTCT
1 AATGTATCGATACATGTATGAATGTATCGATACATTCT
1342872 TCAATGTATC
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
70 67 0.66
71 34 0.34
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (71 bp):
AATGTATCGATACATGTATGAATGTATCGATACATTCTGTCTTTCTACCCAAATGTATCGATACA
TTCTTC
Found at i:1346273 original size:36 final size:35
Alignment explanation
Indices: 1346192--1346288 Score: 132
Period size: 36 Copynumber: 2.9 Consensus size: 35
1346182 CTTACAGCAT
*
1346192 TATCTTTT-GAAGGCTAAGATAGAA---C-CTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCTCCC
*
1346222 TATCTTTTCACAGGCTAAGATAGAACCTCTCTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCTCCC
1346257 TATCTCTTTCAAAGGCTAAGATAGAACCTCTC
1 TATCT-TTTCAAAGGCTAAGATAGAACCTCTC
1346289 AATCACTTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
30 8 0.14
31 14 0.24
34 1 0.02
35 10 0.17
36 25 0.43
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (35 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTCTCCC
Found at i:1347373 original size:13 final size:13
Alignment explanation
Indices: 1347355--1347380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1347345 CTCACCCAGA
1347355 TGTATCGATACAT
1 TGTATCGATACAT
1347368 TGTATCGATACAT
1 TGTATCGATACAT
1347381 GTTCATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1347414 original size:20 final size:19
Alignment explanation
Indices: 1347364--1347420 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1347354 ATGTATCGAT
*
1347364 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
1347383 TCATTATATCGATACATGG
1 ACATTGTATCGATACATGG
1347402 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1347421 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1347493 original size:20 final size:20
Alignment explanation
Indices: 1347449--1347502 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1347439 CTACCACTAT
*
1347449 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGATACA
*
1347469 ATGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
*
1347489 TTGTATTGATACAT
1 TTGTATCGATACAT
1347503 TGCTTATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:1353799 original size:21 final size:22
Alignment explanation
Indices: 1353770--1353810 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1353760 AAACCCTAAC
*
1353770 AATCTTTCTTCAAAATTCTTCA
1 AATCTTTCTACAAAATTCTTCA
*
1353792 AATC-TTCTACAAATTTCTT
1 AATCTTTCTACAAAATTCTT
1353811 GTTTTTCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (22 bp):
AATCTTTCTACAAAATTCTTCA
Found at i:1355606 original size:21 final size:21
Alignment explanation
Indices: 1355570--1355642 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 21
1355560 TTGACAAAGC
*
1355570 GGGAGAAATGTTTTGATCAAGG
1 GGGAGAAAT-TTTTGATTAAGG
**
1355592 GGGAGAAATTTTTGATTAAAA
1 GGGAGAAATTTTTGATTAAGG
*
1355613 GGGAGAAATTCTTTAATTAAGG
1 GGGAGAAATT-TTTGATTAAGG
1355635 GGGAGAAA
1 GGGAGAAA
1355643 AACGAAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
21 19 0.43
22 25 0.57
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (21 bp):
GGGAGAAATTTTTGATTAAGG
Found at i:1356190 original size:20 final size:19
Alignment explanation
Indices: 1356167--1356259 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 19
1356157 CTCACCCAGA
*
1356167 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
1356187 TGTATCGGTACATGTTCAT
1 TGTATCGATACATGTTCAT
*
1356206 TGTATCGATACATAG-ACAAT
1 TGTATCGATACAT-GTTC-AT
* **
1356226 TGTATTGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1356246 TGTATCGATACATG
1 TGTATCGATACATG
1356260 AGATTGGCAG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 46 0.73
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1356326 original size:13 final size:13
Alignment explanation
Indices: 1356310--1356334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1356300 ATGGTACAAC
1356310 GTATCGATACATT
1 GTATCGATACATT
1356323 GTATCGATACAT
1 GTATCGATACAT
1356335 GATGAATTGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1358168 original size:13 final size:13
Alignment explanation
Indices: 1358150--1358176 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1358140 TACAATGAAC
1358150 ATGTATCGATACA
1 ATGTATCGATACA
1358163 ATGTATCGATACA
1 ATGTATCGATACA
1358176 A
1 A
1358177 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1358192 original size:33 final size:32
Alignment explanation
Indices: 1358133--1358195 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
1358123 AATTGTCCAA
*
1358133 GTATCGATACAATGAACATGTATCGATACAAT
1 GTATCGATACAAAGAACATGTATCGATACAAT
1358165 GTATCGATACAAAGCATA-ATGTATCGATACA
1 GTATCGATACAAAG-A-ACATGTATCGATACA
1358196 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (32 bp):
GTATCGATACAAAGAACATGTATCGATACAAT
Found at i:1359397 original size:22 final size:21
Alignment explanation
Indices: 1359362--1359411 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1359352 TTTGTTGATG
*
1359362 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1359382 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1359403 AATTTGAAG
1 ATTTTGAAG
1359412 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1359408 original size:21 final size:22
Alignment explanation
Indices: 1359369--1359411 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1359359 ATGATTTTGA
* *
1359369 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1359391 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1359412 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1365740 original size:13 final size:13
Alignment explanation
Indices: 1365700--1365748 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1365690 CCGTTTGAAG
1365700 CAATGTATCGATA
1 CAATGTATCGATA
1365713 CAA--T-TC-AT-
1 CAATGTATCGATA
1365721 C-ATGTATCGATA
1 CAATGTATCGATA
1365733 CAATGTATCGATA
1 CAATGTATCGATA
1365746 CAA
1 CAA
1365749 AGCATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 17 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1365742 original size:33 final size:33
Alignment explanation
Indices: 1365700--1365767 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1365690 CCGTTTGAAG
** *
1365700 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAAAGCATAATGTATCGATA
1365733 CAATGTATCGATACAAAGCATAATGTATCGATA
1 CAATGTATCGATACAAAGCATAATGTATCGATA
1365766 CA
1 CA
1365768 TCTGGGTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (33 bp):
CAATGTATCGATACAAAGCATAATGTATCGATA
Found at i:1366294 original size:22 final size:20
Alignment explanation
Indices: 1366254--1366297 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
1366244 GATACAAAGA
*
1366254 ATTATTTTTACTTGCAAAAC
1 ATTATTTTTACTTGAAAAAC
1366274 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA--CTTGAAAAAC
1366296 AT
1 AT
1366298 CTATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTATTTTTACTTGAAAAAC
Found at i:1367181 original size:22 final size:21
Alignment explanation
Indices: 1367137--1367182 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1367127 AAGGGAAATT
* *
1367137 AAAAATAAGCATTCATGAATA
1 AAAAATAAGCATTAAGGAATA
*
1367158 AAAAATAGAGCATTAAGGAGTA
1 AAAAATA-AGCATTAAGGAATA
1367180 AAA
1 AAA
1367183 TTTTCATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAATAAGCATTAAGGAATA
Found at i:1369171 original size:22 final size:21
Alignment explanation
Indices: 1369123--1369172 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1369113 ATGCAAATTT
1369123 TTATTTTTATTAGTTAACTCA
1 TTATTTTTATTAGTTAACTCA
* *
1369144 TCATTTTTATT-TTGTAACTCA
1 TTATTTTTATTAGT-TAACTCA
1369165 CTTATTTT
1 -TTATTTT
1369173 CTTTTCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.71
22 6 0.25
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTTTTATTAGTTAACTCA
Found at i:1369183 original size:21 final size:21
Alignment explanation
Indices: 1369159--1369199 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1369149 TTTATTTTGT
*
1369159 AACTCACTTATTTTCTTTTCC
1 AACTCACTTACTTTCTTTTCC
*
1369180 AACTCATTTACTTTCTTTTC
1 AACTCACTTACTTTCTTTTC
1369200 AAGAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (21 bp):
AACTCACTTACTTTCTTTTCC
Found at i:1370235 original size:32 final size:34
Alignment explanation
Indices: 1370187--1370276 Score: 116
Period size: 36 Copynumber: 2.7 Consensus size: 34
1370177 CTTACAACAT
1370187 TATC-TTTCAAGGCTAAGATAGAAAC-CTC-C-C
1 TATCTTTTCAAGGCTAAGATAGAAACTCTCTCTC
*
1370217 TATCTTTTCACAGGCTAAGATAGAACCTCTCTCTC
1 TATCTTTTCA-AGGCTAAGATAGAAACTCTCTCTC
1370252 TATCTTTTTCAAAGGCTAAGATAGA
1 TATC-TTTTC-AAGGCTAAGATAGA
1370277 CCCTTTCAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
30 4 0.08
31 5 0.10
32 15 0.29
33 3 0.06
34 1 0.02
35 5 0.10
36 18 0.35
37 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (34 bp):
TATCTTTTCAAGGCTAAGATAGAAACTCTCTCTC
Found at i:1370738 original size:20 final size:20
Alignment explanation
Indices: 1370713--1370763 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1370703 ATTGGGCTTA
1370713 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
* *
1370733 ATGTATCTATACAATTCATC
1 ATGTATCGATACAATTCACC
*
1370753 ATGTATTGATA
1 ATGTATCGATA
1370764 AAATGTATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1374396 original size:20 final size:22
Alignment explanation
Indices: 1374348--1374399 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1374338 ATTTAATTCA
*
1374348 TCATTTTCTTCTTGCAACTCATT
1 TCATTTTC-TCTTCCAACTCATT
1374371 TC-TTTTCT-TTCCAACTCA-T
1 TCATTTTCTCTTCCAACTCATT
1374390 TCATTTTCTC
1 TCATTTTCTC
1374400 CTCTAGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 1 0.04
22 5 0.19
23 2 0.08
ACGTcount: A:0.15, C:0.29, G:0.02, T:0.54
Consensus pattern (22 bp):
TCATTTTCTCTTCCAACTCATT
Found at i:1376297 original size:19 final size:20
Alignment explanation
Indices: 1376260--1376297 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1376250 TCTCGTAGCT
1376260 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1376280 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
1376298 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1376438 original size:19 final size:20
Alignment explanation
Indices: 1376394--1376447 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1376384 CTGCCAGTTT
**
1376394 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1376414 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1376433 CATGTATCGATACAA
1 CATGTATCGATACAA
1376448 CGTATCGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1376454 original size:13 final size:13
Alignment explanation
Indices: 1376436--1376460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1376426 CAATGAACAT
1376436 GTATCGATACAAC
1 GTATCGATACAAC
1376449 GTATCGATACAA
1 GTATCGATACAA
1376461 GGCATAATGT
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:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:1378777 original size:19 final size:19
Alignment explanation
Indices: 1378753--1378799 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1378743 TTTGTTGATA
1378753 ATTTTGAAGAAAATGAAGT
1 ATTTTGAAGAAAATGAAGT
1378772 ATTTTGAAGAAAATGAAGT
1 ATTTTGAAGAAAATGAAGT
1378791 ATTTTGAAG
1 ATTTTGAAG
1378800 TGAAAACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (19 bp):
ATTTTGAAGAAAATGAAGT
Found at i:1378961 original size:13 final size:13
Alignment explanation
Indices: 1378943--1378969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1378933 ATAGTAACCC
1378943 ATGTATCGATACA
1 ATGTATCGATACA
1378956 ATGTATCGATACA
1 ATGTATCGATACA
1378969 A
1 A
1378970 GAAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1385047 original size:19 final size:20
Alignment explanation
Indices: 1385010--1385047 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1385000 TCCCGTAGCT
1385010 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1385030 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
1385048 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1385224 original size:19 final size:20
Alignment explanation
Indices: 1385180--1385230 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1385170 CTGCCAGTTT
* **
1385180 CATGTATCGATATAATTGTC
1 CATGTATCGATAGAATTGAA
1385200 CATGTATCGATAGAA-TGAA
1 CATGTATCGATAGAATTGAA
1385219 CATGTATCGATA
1 CATGTATCGATA
1385231 CAAAGCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
CATGTATCGATAGAATTGAA
Found at i:1386010 original size:31 final size:30
Alignment explanation
Indices: 1385959--1386054 Score: 102
Period size: 36 Copynumber: 3.0 Consensus size: 30
1385949 CCTTCCAACA
* *
1385959 CTATCTTTTGAAGGCTAAGATAGAACCTCC
1 CTATCTTTTCAAAGCTAAGATAGAACCTCC
*
1385989 CTATCTTTTCACAAGCTAAGATAAAACCTCTCTCC
1 CTATCTTTTCA-AAGCTAAGATAGAA---C-CTCC
1386024 CTATCTTTTTCAAAGGCTAAGATAGAACCTC
1 CTATC-TTTTCAAA-GCTAAGATAGAACCTC
1386055 TCAATCATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
30 10 0.18
31 12 0.22
32 3 0.05
33 1 0.02
34 1 0.02
35 11 0.20
36 17 0.31
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (30 bp):
CTATCTTTTCAAAGCTAAGATAGAACCTCC
Found at i:1386031 original size:35 final size:36
Alignment explanation
Indices: 1385985--1386056 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
1385975 AAGATAGAAC
1385985 CTCCCTATC-TTTTCACAA-GCTAAGATAAAACCTCT
1 CTCCCTATCTTTTTCA-AAGGCTAAGATAAAACCTCT
*
1386020 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
1386056 C
1 C
1386057 AATCATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 11 0.32
36 23 0.68
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
Found at i:1386067 original size:31 final size:31
Alignment explanation
Indices: 1385959--1386067 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
1385949 CCTTCCAACA
* *
1385959 CTATCTTTT-GAAGGCTAAGATAGAACCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCT
*
1385989 CTATCTTTTCACAA-GCTAAGATAAAACCTCTCT
1 CTATCTTTTCA-AAGGCTAAGATAGAA-C-CTCT
1386022 CCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 --CTATC-TTTTCAAAGGCTAAGATAGAACCTCT
* *
1386056 CAATCATTTCAA
1 CTATCTTTTCAA
1386068 GAATATACCC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
30 9 0.14
31 17 0.26
32 7 0.11
33 3 0.05
34 4 0.06
35 8 0.12
36 17 0.26
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (31 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:1388305 original size:52 final size:52
Alignment explanation
Indices: 1388249--1388370 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 52
1388239 GAATACTAAT
*
1388249 ATGCTAATTCAAGGCCAGTGACATTGGACTTAAAAACTAA-AAAAATGCCAAC
1 ATGCTAATTCAAGGCCAATGACATTGGACTTAAAAA-TAATAAAAATGCCAAC
* * * ** * *
1388301 ATGCTGATTCTAGGCCAATGACATTGGGCTTATGAATAATAAAGATGCCAAT
1 ATGCTAATTCAAGGCCAATGACATTGGACTTAAAAATAATAAAAATGCCAAC
*
1388353 ATACTAATTCAAGGCCAA
1 ATGCTAATTCAAGGCCAA
1388371 CGATATCAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 3 0.05
52 55 0.95
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (52 bp):
ATGCTAATTCAAGGCCAATGACATTGGACTTAAAAATAATAAAAATGCCAAC
Found at i:1388437 original size:53 final size:51
Alignment explanation
Indices: 1388341--1388477 Score: 143
Period size: 53 Copynumber: 2.6 Consensus size: 51
1388331 TATGAATAAT
* * * * *
1388341 AAAGATGCCAATATACTAATTCAAGGCCAACGATATCAAACTTAA-AGATGA
1 AAAGGTGCCAATATGCTTATTCAAGGCCAGCGATATCAAACTTAAGA-AAGA
***
1388392 CAAAGGTGACCAATATGCTTATTCAAGGCCAGCGATATTTGACTTAAGAAAGA
1 -AAAGGTG-CCAATATGCTTATTCAAGGCCAGCGATATCAAACTTAAGAAAGA
*
1388445 AAAGGTGCCAATGTG-TTGATTCAAGGCCAGCGA
1 AAAGGTGCCAATATGCTT-ATTCAAGGCCAGCGA
1388478 CATTGGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.03
51 22 0.30
52 13 0.18
53 35 0.48
54 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTTATTCAAGGCCAGCGATATCAAACTTAAGAAAGA
Found at i:1388475 original size:51 final size:51
Alignment explanation
Indices: 1388393--1388494 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
1388383 TAAAGATGAC
* *
1388393 AAAGGTGACCAATATGCTTATTCAAGGCCAGCGATATTTGACTTAAGAAAGA
1 AAAGGTGACCAATATGCTTATTCAAGGCCAGCGACATTGGA-TTAAGAAAGA
* *
1388445 AAAGGTG-CCAATGTG-TTGATTCAAGGCCAGCGACATTGGATTTAGAAAGA
1 AAAGGTGACCAATATGCTT-ATTCAAGGCCAGCGACATTGGATTAAGAAAGA
1388495 GATGGTTTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
50 11 0.24
51 27 0.60
52 7 0.16
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (51 bp):
AAAGGTGACCAATATGCTTATTCAAGGCCAGCGACATTGGATTAAGAAAGA
Found at i:1388663 original size:31 final size:31
Alignment explanation
Indices: 1388564--1390023 Score: 850
Period size: 31 Copynumber: 46.5 Consensus size: 31
1388554 GATGCAAGCG
*
1388564 ACTTGTGTGGGCTTTTGAGAGGGTTGCCACTA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
* ** * *
1388596 GCTCATGTGGGCTTTTGAATGGGTTGCCACTG
1 ACTTGTGTGGGCTTTAGAA-GGGTTGCCACTA
* *
1388628 ACTTGTGTGGGCTCTAGAAGGGGTGCCACTA
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* * *
1388659 ACTTGTGTGGGCTTTAGAAGGAGGTTACC-TTCG
1 ACTTGTGTGGGCTTTAGAA-G-GGTTGCCACT-A
* * **
1388692 ATTTTTGTGGGCTTTAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* **** *
1388723 ACTTGTATGGGCTTTGGAGAAGGGTT-ATTGTCG
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACT-A
* * * * *
1388756 ACTAGTGTGGGCATTAGAAGGAGGTTACC-TTCG
1 ACTTGTGTGGGCTTTAGAA-G-GGTTGCCACT-A
* * **
1388789 ATTTTTGTGGGCTTTAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* * ** * *
1388820 ACTTATATGGGCTTTGGAGAAGGGTTATC-GTCG
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACT-A
* *
1388853 ACTTGTGTGGGCTTTAGAAGGCTTGCCACTG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* **
1388884 ACTTGTGTGGGCTTCAGAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTT--TAGAAGGGTTGCCACTA
* * * * *
1388917 ACTTGTGTGGGCCTTGAGAAAGGATGCCATTG
1 ACTTGTGTGGG-CTTTAGAAGGGTTGCCACTA
* * *
1388949 ACTTGTGTAGG-TTT----TGG--ACCAGC--
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCA-CTA
* * *
1388972 -C-TGTGTGGGTTTTAAAGA-GGTTGCCATTA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
* * * **
1389001 GCTTGTGTGGGCTTTGGAGAA-GGTTGTCGCCG
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
* ** * *
1389033 ACCTGTGTGGGCTTTAGAGAAAGTTTCCACCA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
* *
1389065 ACTTGTGTGAGCTTTA-AAGGGGTTGCCACCA
1 ACTTGTGTGGGCTTTAGAA-GGGTTGCCACTA
* *
1389096 GCTTGTGTGGGCTTTGGAGAA-GGTTGCCACTG
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
* * *
1389128 ACTTGTGTAGGCTTTAGAGGGGTTGCCA-TCG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACT-A
* **
1389159 ACTTGTTTGGGCTTTAAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* * **
1389191 AGTTGTGTGGGCTTTTAGAAGGGTTTCCACCG
1 ACTTGTGTGGGC-TTTAGAAGGGTTGCCACTA
* * **
1389223 ATTTGTGTAGGGC-TTAGAAGAGTTGCCACCG
1 ACTTGTGT-GGGCTTTAGAAGGGTTGCCACTA
* * * **
1389254 ACTTCTGTGGGCTTTAAAAAGAGTTGCCACCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
*
1389286 ACTTGTGTGGGTTTTAGAGAAGGGTTGCCACTA
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
*
1389319 ACTTGTGTGTG-TTTAAGAAGGGTTGCCACTA
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
** * *
1389350 ACTTGTACGTGCTTTAGAGAAGGGTTGCCACTG
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
* *
1389383 ACTTGTGTGGGCTTT--AAGAGTTGCCACCA
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* * * *
1389412 ACTTGTGTGGGCTATGAGAAGGGTTTCTACCA
1 ACTTGTGTGGGCT-TTAGAAGGGTTGCCACTA
*
1389444 ACTTGTGTGGGCTTTGAGAAGGGTTGCCA-TCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACT-A
* **
1389476 ACTTGCGTGGGCTTTGAGAAGGG-TGCCACCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* *
1389507 ACTTATGTGGGCTTTAGAGAGGG-TGCCAGTA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
* * * *
1389538 CCTTGTGTAGGCTTTAGAGGGGTTGCCACCA
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* * *
1389569 GCTTGTGTGGGCTTTGGAGAA-GGTTTCCACCA
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
* * * *
1389601 GCTTGTGTGGGCTTTGGGAAAGGTTGCCACTG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* * * *
1389633 ACTTGTGTAGGCTTTAGAGGGGTTGCCATTG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* **
1389664 ACTTGCGTGGGCTTTGAGAAGGG-TGCCACCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
*
1389695 ACTTATGTGGGCTTTAGAGAGGG-TGCCACTA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
* * *
1389726 ACTTGTGTAGGCTTTAGAGGGGTTGCCACCA
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
* * *
1389757 GCTTGTGTGGGCTTTGGAGAA-GGTTTCCACCA
1 ACTTGTGTGGGCTTT--AGAAGGGTTGCCACTA
* * * * * *
1389789 GCTTTTGTGGGCTTTGGGAAAGGTTGCTACTG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* * *
1389821 ACTTGTGTAGGCTTTAGAGGGGTTGCCA-TCG
1 ACTTGTGTGGGCTTTAGAAGGGTTGCCACT-A
1389852 ACTTGTGTGGGCTTTAAGAAGGGTTGCCACTA
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* * * *
1389884 ATTTTTGTGGGCTTTGAGAA-GATTTCCACTA
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
**
1389915 ACTTGTGTGGGCTTTGAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACTA
* *
1389947 AGTTGTGTGGGCTTTGAGAAGGG-TGCCA-TCG
1 ACTTGTGTGGGCTTT-AGAAGGGTTGCCACT-A
* *
1389978 ACTTATGTGGGCTTTAGAGAGGG-TGCCACCA
1 ACTTGTGTGGGCTTTAGA-AGGGTTGCCACTA
1390009 ACTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
1390024 GAAAAGAAAA
Statistics
Matches: 1138, Mismatches: 215, Indels: 151
0.76 0.14 0.10
Matches are distributed among these distances:
21 7 0.01
22 4 0.00
24 3 0.00
26 4 0.00
28 3 0.00
29 24 0.02
30 32 0.03
31 455 0.40
32 420 0.37
33 181 0.16
34 5 0.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTAGAAGGGTTGCCACTA
Found at i:1388703 original size:33 final size:32
Alignment explanation
Indices: 1388601--1388928 Score: 181
Period size: 33 Copynumber: 10.2 Consensus size: 32
1388591 CACTAGCTCA
* * * *
1388601 TGTGGGCTTTTGAATGGGTTGCC-ACTGACTTG
1 TGTGGGCTTTAGAAGGGGTTACCTTC-GACTTG
* * * *
1388633 TGTGGGCTCTAGAAGGGG-TGCC-ACTAACTTG
1 TGTGGGCTTTAGAAGGGGTTACCTTC-GACTTG
* *
1388664 TGTGGGCTTTAGAAGGAGGTTACCTTCGATTTT
1 TGTGGGCTTTAGAAGG-GGTTACCTTCGACTTG
* **
1388697 TGTGGGCTTTAGAA-GGGTTGCCACCGACTTG
1 TGTGGGCTTTAGAAGGGGTTACCTTCGACTTG
* * *
1388728 TATGGGCTTTGGAGAA-GGGTTA-TTGTCGACTAG
1 TGTGGGCTTT--AGAAGGGGTTACCT-TCGACTTG
* * *
1388761 TGTGGGCATTAGAAGGAGGTTACCTTCGATTTT
1 TGTGGGCTTTAGAAGG-GGTTACCTTCGACTTG
* ** *
1388794 TGTGGGCTTTAGAA-GGGTTGCCACCGACTTA
1 TGTGGGCTTTAGAAGGGGTTACCTTCGACTTG
* * *
1388825 TATGGGCTTTGGAGAA-GGGTTATCGTCGACTTG
1 TGTGGGCTTT--AGAAGGGGTTACCTTCGACTTG
* * *
1388858 TGTGGGCTTTAGAA-GGCTTGCC-ACTGACTTG
1 TGTGGGCTTTAGAAGGGGTTACCTTC-GACTTG
* * * **
1388889 TGTGGGCTTCAGAGAAGGGTTGCCACCGACTTG
1 TGTGGGCTTTAGA-AGGGGTTACCTTCGACTTG
1388922 TGTGGGC
1 TGTGGGC
1388929 CTTGAGAAAG
Statistics
Matches: 234, Mismatches: 47, Indels: 29
0.75 0.15 0.09
Matches are distributed among these distances:
30 1 0.00
31 98 0.42
32 21 0.09
33 111 0.47
34 3 0.01
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTAGAAGGGGTTACCTTCGACTTG
Found at i:1388715 original size:95 final size:93
Alignment explanation
Indices: 1388563--1390023 Score: 1051
Period size: 95 Copynumber: 15.5 Consensus size: 93
1388553 AGATGCAAGC
* * ** * *
1388563 GACTTGTGTGGGCTTTTG-AGAGGGTTGCCACTAGCTCATGTGGGCTTTTGAATGGGTTGCCACT
1 GACTTGTGTGGGCTTTAGAAGA-GGTTGCCACGA-CTTGTGTGGGCTTTAGAA-GGGTTGCCACC
* *
1388627 GACTTGTGTGGGCTCT-AGAAGGGGTGCCACT
63 GACTTGTGTGGGCTTTGAGAA-GGTTGCCACT
* * * * *
1388658 AACTTGTGTGGGCTTTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCG
1 GACTTGTGTGGGCTTTAGAA-GAGGTTGCC-ACGACTTGTGTGGGCTTTAGAAGGGTTGCCACCG
* ****
1388723 ACTTGTATGGGCTTTGGAGAAGGGTT-ATTGT
64 ACTTGTGTGGGCTTT-GAGAA-GGTTGCCACT
* * * * * *
1388754 CGACTAGTGTGGGCATTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACC
1 -GACTTGTGTGGGCTTTAGAA-GAGGTTGCC-ACGACTTGTGTGGGCTTTAGAAGGGTTGCCACC
* * ** *
1388819 GACTTATATGGGCTTTGGAGAAGGGTTATC-GT
63 GACTTGTGTGGGCTTT-GAGAA-GGTTGCCACT
* *
1388851 CGACTTGTGTGGGCTTTAGAAG-GCTTGCCACTGACTTGTGTGGGCTTCAGAGAAGGGTTGCCAC
1 -GACTTGTGTGGGCTTTAGAAGAGGTTGCCAC-GACTTGTGTGGGCTT--TAGAAGGGTTGCCAC
* * *
1388915 CGACTTGTGTGGGCCTTGAGAAAGGATGCCATT
62 CGACTTGTGTGGGCTTTGAG-AAGGTTGCCACT
* * * * **
1388948 GACTTGTGTAGG-TTTTG--GA-----CCA-G-CCTGTGTGGGTTTTA-AAGAGGTTGCCA-TTA
1 GACTTGTGTGGGCTTTAGAAGAGGTTGCCACGACTTGTGTGGGCTTTAGAAG-GGTTGCCACCGA
* * *
1389001 GCTTGTGTGGGCTTTGGAGAAGGTTGTCGCC
65 -CTTGTGTGGGCTTT-GAGAAGGTTGCCACT
* * * * *
1389032 GACCTGTGTGGGCTTTAG-AGAAAGTTTCCACCAACTTGTGTGAGCTTTA-AAGGGGTTGCCACC
1 GACTTGTGTGGGCTTTAGAAG-AGGTTGCCA-CGACTTGTGTGGGCTTTAGAA-GGGTTGCCACC
1389095 -AGCTTGTGTGGGCTTTGGAGAAGGTTGCCACT
63 GA-CTTGTGTGGGCTTT-GAGAAGGTTGCCACT
* * *
1389127 GACTTGTGTAGGCTTTAG-AGGGGTTGCCATCGACTTGTTTGGGCTTTAAGAAGGGTTGCCACCG
1 GACTTGTGTGGGCTTTAGAAGAGGTTGCCA-CGACTTGTGTGGGCTTT-AGAAGGGTTGCCACCG
* * * *
1389191 AGTTGTGTGGGCTTTTAGAAGGGTTTCCACC
64 ACTTGTGTGGGCTTTGAGAA-GGTTGCCACT
* * * *
1389222 GATTTGTGTAGGGC-TTAGAAGA-GTTGCCACCGACTTCTGTGGGCTTTAAAAAGAGTTGCCACC
1 GACTTGTGT-GGGCTTTAGAAGAGGTTGCCA-CGACTTGTGTGGGCTTT-AGAAGGGTTGCCACC
*
1389285 GACTTGTGTGGGTTTTAGAGAAGGGTTGCCACT
63 GACTTGTGTGGGCTTT-GAGAA-GGTTGCCACT
* * * ** *
1389318 AACTTGTGTGTG-TTTAAGAAG-GGTTGCCACTAACTTGTACGTGCTTTAGAGAAGGGTTGCCAC
1 GACTTGTGTGGGCTTT-AGAAGAGGTTGCCAC-GACTTGTGTGGGCTTT--AGAAGGGTTGCCAC
* * *
1389381 TGACTTGTGTGGGCTTTAAG-A-GTTGCCACC
62 CGACTTGTGTGGGCTTTGAGAAGGTTGCCACT
* * * * * *
1389411 AACTTGTGTGGGCTATGAGAAG-GGTTTCTACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCATC
1 GACTTGTGTGGGCT-TTAGAAGAGGTTGCCA-CGACTTGTGTGGGCTTT-AGAAGGGTTGCCACC
* * *
1389475 GACTTGCGTGGGCTTTGAGAAGGGTGCCACC
63 GACTTGTGTGGGCTTTGAGAAGGTTGCCACT
* * * *
1389506 GACTTATGTGGGCTTTAG-AGAGGGTGCCA-GTACCTTGTGTAGGCTTTAGAGGGGTTGCCACC-
1 GACTTGTGTGGGCTTTAGAAGAGGTTGCCACG-A-CTTGTGTGGGCTTTAGAAGGGTTGCCACCG
*
1389568 AGCTTGTGTGGGCTTTGGAGAAGGTTTCCAC-
64 A-CTTGTGTGGGCTTT-GAGAAGGTTGCCACT
* * * * **
1389599 CAGCTTGTGTGGGCTTTGGGAA-AGGTTGCCACTGACTTGTGTAGGCTTTAGAGGGGTTGCCATT
1 GA-CTTGTGTGGGCTTT-AGAAGAGGTTGCCAC-GACTTGTGTGGGCTTTAGAAGGGTTGCCACC
* * *
1389663 GACTTGCGTGGGCTTTGAGAAGGGTGCCACC
63 GACTTGTGTGGGCTTTGAGAAGGTTGCCACT
* * * * *
1389694 GACTTATGTGGGCTTTAG-AGAGGGTGCCACTAACTTGTGTAGGCTTTAGAGGGGTTGCCACC-A
1 GACTTGTGTGGGCTTTAGAAGAGGTTGCCAC-GACTTGTGTGGGCTTTAGAAGGGTTGCCACCGA
*
1389757 GCTTGTGTGGGCTTTGGAGAAGGTTTCCAC-
65 -CTTGTGTGGGCTTT-GAGAAGGTTGCCACT
* * * * * * *
1389787 CAGCTTTTGTGGGCTTTGGGAA-AGGTTGCTACTGACTTGTGTAGGCTTTAGAGGGGTTGCCATC
1 GA-CTTGTGTGGGCTTT-AGAAGAGGTTGCCAC-GACTTGTGTGGGCTTTAGAAGGGTTGCCACC
*
1389851 GACTTGTGTGGGCTTTAAGAAGGGTTGCCACT
63 GACTTGTGTGGGCTTTGAGAA-GGTTGCCACT
* * * * *
1389883 AATTTTTGTGGGCTTTGAGAAGA--TTTCCACTAACTTGTGTGGGCTTTGAGAAGGGTTGCCACC
1 GACTTGTGTGGGCTTT-AGAAGAGGTTGCCAC-GACTTGTGTGGGCTTT-AGAAGGGTTGCCACC
* *
1389946 GAGTTGTGTGGGCTTTGAGAAGGGTGCCA-T
63 GACTTGTGTGGGCTTTGAGAAGGTTGCCACT
* * *
1389976 CGACTTATGTGGGCTTTAG-AGAGGGTGCCACCAACTTGTGTGGGCTTT
1 -GACTTGTGTGGGCTTTAGAAGAGGTTGCCA-CGACTTGTGTGGGCTTT
1390024 GAAAAGAAAA
Statistics
Matches: 1120, Mismatches: 173, Indels: 147
0.78 0.12 0.10
Matches are distributed among these distances:
83 4 0.00
84 39 0.03
85 7 0.01
86 12 0.01
87 2 0.00
89 3 0.00
92 9 0.01
93 137 0.12
94 211 0.19
95 415 0.37
96 102 0.09
97 179 0.16
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (93 bp):
GACTTGTGTGGGCTTTAGAAGAGGTTGCCACGACTTGTGTGGGCTTTAGAAGGGTTGCCACCGAC
TTGTGTGGGCTTTGAGAAGGTTGCCACT
Found at i:1388765 original size:64 final size:64
Alignment explanation
Indices: 1388627--1388776 Score: 162
Period size: 64 Copynumber: 2.3 Consensus size: 64
1388617 GGTTGCCACT
* * *
1388627 GACTTGTGTGGGCTCTAGAAGGGGTGCCACTAACTTGTGTGGGCTTTAGAAGGAGGTTACCTTC
1 GACTTGTGTGGGCTTTAGAAGGGGTGCCACCAACTTGTATGGGCTTTAGAAGGAGGTTACCTTC
* * * * *
1388691 GATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTGGAGAA-G-GGTTA-TTG
1 GACTTGTGTGGGCTTTAGAAGGGGTGCCACCAACTTGTATGGGCTTT--AGAAGGAGGTTACCT-
1388753 TC
63 TC
* *
1388755 GACTAGTGTGGGCATTAGAAGG
1 GACTTGTGTGGGCTTTAGAAGG
1388777 AGGTTACCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 65 0.92
65 1 0.01
66 4 0.06
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.31
Consensus pattern (64 bp):
GACTTGTGTGGGCTTTAGAAGGGGTGCCACCAACTTGTATGGGCTTTAGAAGGAGGTTACCTTC
Found at i:1388776 original size:97 final size:97
Alignment explanation
Indices: 1388663--1388873 Score: 386
Period size: 97 Copynumber: 2.2 Consensus size: 97
1388653 CCACTAACTT
*
1388663 GTGTGGGCTTTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTG
1 GTGTGGGCTTTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTA
*
1388728 TATGGGCTTTGGAGAAGGGTTATTGTCGACTA
66 TATGGGCTTTGGAGAAGGGTTATCGTCGACTA
*
1388760 GTGTGGGCATTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTA
1 GTGTGGGCTTTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTA
*
1388825 TATGGGCTTTGGAGAAGGGTTATCGTCGACTT
66 TATGGGCTTTGGAGAAGGGTTATCGTCGACTA
1388857 GTGTGGGCTTTAGAAGG
1 GTGTGGGCTTTAGAAGG
1388874 CTTGCCACTG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 109 1.00
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.33
Consensus pattern (97 bp):
GTGTGGGCTTTAGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCACCGACTTA
TATGGGCTTTGGAGAAGGGTTATCGTCGACTA
Found at i:1388822 original size:64 final size:63
Alignment explanation
Indices: 1388754--1390025 Score: 219
Period size: 63 Copynumber: 20.3 Consensus size: 63
1388744 GGGTTATTGT
* * * *
1388754 CGACTAGTGTGGGCATT-AGAAGGAGGTTACCTTCGATTTTTGTGGGCTTTAGAAGGGTTGCCAC
1 CGACTAGTGTGGGCATTGAGAA-G-GGTTACCGTCGACTTGTGTGGGCTTTAGAAGGCTTGCCAC
* * *
1388818 CGACTTA-TATGGGCTTTGGAGAAGGGTTATCGTCGACTTGTGTGGGCTTTAGAAGGCTTGCCAC
1 CGAC-TAGTGTGGGCATT-GAGAAGGGTTACCGTCGACTTGTGTGGGCTTTAGAAGGCTTGCCAC
* * * ** * *
1388882 TGACTTGTGTGGGC-TTCAGAGAAGGGTTGCCACCGACTTGTGTGGGCCTTGAGAAAGG-ATGCC
1 CGACTAGTGTGGGCATT--GAGAAGGGTTACCGTCGACTTGTGTGGG-CTTTAG-AAGGCTTGCC
*
1388945 AT
62 AC
* * * ** * *
1388947 TGACTTGTGTAGG--TT----TTGG--ACCAG-C--C-TGTGTGGGTTTTA-AAGAGGTTGCCA-
1 CGACTAGTGTGGGCATTGAGAAGGGTTACC-GTCGACTTGTGTGGGCTTTAGAAG-GCTTGCCAC
** * * ** * * * *
1388998 TTAGCTTGTGTGGGCTTTGGAGAA-GGTTGTCGCCGACCTGTGTGGGCTTTAGAGAAAG-TTTCC
1 CGA-CTAGTGTGGGCATT-GAGAAGGGTTACCGTCGACTTGTGTGGGCTTT--AGAAGGCTTGCC
1389061 AC
62 AC
* * * * * * *
1389063 CAACTTGTGTGAGC-TTTA-AAGGGGTTGCC-ACCAGCTTGTGTGGGCTTTGGAGAAGG-TTGCC
1 CGACTAGTGTGGGCATTGAGAA-GGGTTACCGTCGA-CTTGTGTGGGCTTT--AGAAGGCTTGCC
1389124 AC
62 AC
* * * * * * * * *
1389126 TGACTTGTGTAGGC-TTTAGAGGGGTTGCCATCGACTTGTTTGGGCTTTAAGAAGGGTTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTT-AGAAGGCTTGCCAC
* * * * * ** *
1389189 CGAGTTGTGTGGGCTTTTAGAAGGGTTTCCACCGATTTGTGTAGGGC-TTAGAAGAG-TTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGT-GGGCTTTAGAAG-GCTTGCCAC
** * * * * * ** * *
1389252 CGACTTCTGTGGGCTTTAAAAAGAGTTGCCACCGACTTGTGTGGGTTTTAGAGAAGGGTTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTT--AGAAGGCTTGCCAC
** * * * * * * * ** * *
1389317 TAACTTGTGTGTG-TTTAAGAAGGGTTGCC-ACTAACTTGTACGTGCTTTAGAGAAGGGTTGCCA
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTC-GACTTGTGTGGGCTTT--AGAAGGCTTGCCA
1389380 C
63 C
* * * * * ** * * * * *
1389381 TGACTTGTGTGGGC-TT--TAAGAGTTGCCACCAACTTGTGTGGGCTATGAGAAGGGTTTCTAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCT-TTAGAAGGCTTGCCAC
* * * * * * *
1389442 CAACTTGTGTGGGCTTTGAGAAGGGTTGCCATCGACTTGCGTGGGCTTTGAGAAGG-GTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTT-AGAAGGCTTGCCAC
* * * * *
1389505 CGACTTA-TGTGGGC-TTTAGAGAGGG-TGCCAGT--ACCTTGTGTAGGCTTTAGAGGGGTTGCC
1 CGAC-TAGTGTGGGCATTGAGA-AGGGTTACC-GTCGA-CTTGTGTGGGCTTTAGAAGGCTTGCC
1389565 AC
62 AC
* * * * * *
1389567 C-AGCTTGTGTGGGCTTTGGAGAA-GGTTTCC-ACCAGCTTGTGTGGGCTTTGGGAAAGG-TTGC
1 CGA-CTAGTGTGGGCATT-GAGAAGGGTTACCGTCGA-CTTGTGTGGGCTTT-AG-AAGGCTTGC
1389628 CAC
61 CAC
* * * * * * * * * *
1389631 TGACTTGTGTAGGC-TTTAGAGGGGTTGCCATTGACTTGCGTGGGCTTTGAGAAGG-GTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTT-AGAAGGCTTGCCAC
* * * * * * *
1389693 CGACTTA-TGTGGGC-TTTAGAGAGGG-TGCC-ACTAACTTGTGTAGGCTTTAGAGGGGTTGCCA
1 CGAC-TAGTGTGGGCATTGAGA-AGGGTTACCGTC-GACTTGTGTGGGCTTTAGAAGGCTTGCCA
1389754 C
63 C
* * * * * * *
1389755 C-AGCTTGTGTGGGCTTTGGAGAA-GGTTTCC-ACCAGCTTTTGTGGGCTTTGGGAAAGG-TTGC
1 CGA-CTAGTGTGGGCATT-GAGAAGGGTTACCGTCGA-CTTGTGTGGGCTTT-AG-AAGGCTTGC
*
1389816 TAC
61 CAC
* * * * * * * *
1389819 TGACTTGTGTAGGC-TTTAGAGGGGTTGCCATCGACTTGTGTGGGCTTTAAGAAGGGTTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTT-AGAAGGCTTGCCAC
** * ** * * * * * *
1389882 TAATTTTTGTGGGCTTTGAGAA-GATTTCC-ACTAACTTGTGTGGGCTTTGAGAAGGGTTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTC-GACTTGTGTGGGCTTT-AGAAGGCTTGCCAC
* * * * * * *
1389945 CGAGTTGTGTGGGCTTTGAGAAGGG-TGCCATCGACTTATGTGGGCTTTAGAGAGG-GTGCCAC
1 CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTTAGA-AGGCTTGCCAC
* * *
1390007 CAACTTGTGTGGGCTTTGA
1 CGACTAGTGTGGGCATTGA
1390026 AAAGAAAAAA
Statistics
Matches: 936, Mismatches: 185, Indels: 176
0.72 0.14 0.14
Matches are distributed among these distances:
50 3 0.00
51 3 0.00
52 17 0.02
53 8 0.01
54 3 0.00
56 3 0.00
58 4 0.00
59 1 0.00
60 2 0.00
61 41 0.04
62 170 0.18
63 349 0.37
64 261 0.28
65 61 0.07
66 10 0.01
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.31
Consensus pattern (63 bp):
CGACTAGTGTGGGCATTGAGAAGGGTTACCGTCGACTTGTGTGGGCTTTAGAAGGCTTGCCAC
Found at i:1389089 original size:63 final size:63
Alignment explanation
Indices: 1389030--1390023 Score: 627
Period size: 63 Copynumber: 15.8 Consensus size: 63
1389020 AAGGTTGTCG
* * * *
1389030 CCGACCTGTGTGGGCTTTAGAGAAAGTTTCCACCAACTTGTGTGAGCTTTAAAGGGGTTGCCA
1 CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGAGCTTTAAAGGGGTTGCCA
* * *
1389093 CC-AGCTTGTGTGGGCTTTGGAGAAGGTTGCCACTGACTTGTGT-AGGCTTTAGAGGGGTTGCCA
1 CCGA-CTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGA-GCTTTAAAGGGGTTGCCA
* * * * *
1389156 TCGACTTGTTTGGGCTTTA-AGAAGGGTTGCCACCGAGTTGTGTGGGCTTTTAGAA-GGGTTTCC
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGC-TTTA-AAGGGGTTGCC
1389219 A
63 A
* * * * *
1389220 CCGATTTGTGTAGGGC-TT--AGAAGAGTTGCCACCGACTTCTGTGGGCTTTAAAAAGAGTTGCC
1 CCGACTTGTGT-GGGCTTTAGAGAAG-GTTGCCACCGACTTGTGTGAGCTTT-AAAGGGGTTGCC
1389282 A
63 A
* ** * *
1389283 CCGACTTGTGTGGGTTTTAGAGAAGGGTTGCCACTAACTTGTGTGTG-TTTAAGAAGGGTTGCCA
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGCTTTAA-AGGGGTTGCCA
** ** * * * *
1389347 CTAACTTGTACGTGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTT-AA-GAGTTGCCA
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGCTTTAAAGGGGTTGCCA
* * * * * *
1389409 CCAACTTGTGTGGGCTAT-GAGAAGGGTTTCTACCAACTTGTGTGGGCTTTGAGAA-GGGTTGCC
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGCTTT-A-AAGGGGTTGCC
1389472 A
63 A
* * * * * *
1389473 TCGACTTGCGTGGGCTTT-GAGAAGGGTGCCACCGACTTATGTGGGCTTTAGAGAGGG-TGCCA
1 CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGAGCTTTAAAG-GGGTTGCCA
* * * ** * *
1389535 --GTACCTTGTGTAGGCTTTAGAG-GGGTTGCCACC-AGCTTGTGTGGGCTTTGGAGAAGGTTTC
1 CCG-A-CTTGTGTGGGCTTTAGAGAAGGTTGCCACCGA-CTTGTGTGAGCTTTAAAG-GGGTTGC
1389596 CA
62 CA
* * *
1389598 CC-AGCTTGTGTGGGCTTT-GGGAAAGGTTGCCACTGACTTGTGT-AGGCTTTAGAGGGGTTGCC
1 CCGA-CTTGTGTGGGCTTTAGAG-AAGGTTGCCACCGACTTGTGTGA-GCTTTAAAGGGGTTGCC
1389660 A
63 A
** * * * * *
1389661 TTGACTTGCGTGGGCTTT-GAGAAGGGTGCCACCGACTTATGTGGGCTTTAGAGAGGG-TGCCA
1 CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGAGCTTTAAAG-GGGTTGCCA
** * * * ** * *
1389723 CTAACTTGTGTAGGCTTTAGAG-GGGTTGCCACC-AGCTTGTGTGGGCTTTGGAGAAGGTTTCCA
1 CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGA-CTTGTGTGAGCTTTAAAG-GGGTTGCCA
* * * * *
1389786 CC-AGCTTTTGTGGGCTTT-GGGAAAGGTTGCTACTGACTTGTGT-AGGCTTTAGAGGGGTTGCC
1 CCGA-CTTGTGTGGGCTTTAGAG-AAGGTTGCCACCGACTTGTGTGA-GCTTTAAAGGGGTTGCC
1389848 A
63 A
* ** * * * * *
1389849 TCGACTTGTGTGGGCTTTA-AGAAGGGTTGCCACTAATTTTTGTGGGCTTTGAGAA--GATTTCC
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGCTTT-A-AAGGGGTTGCC
1389911 A
63 A
** * *
1389912 CTAACTTGTGTGGGCTTT-GAGAAGGGTTGCCACCGAGTTGTGTGGGCTTTGAGAA-GGG-TGCC
1 CCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGAGCTTT-A-AAGGGGTTGCC
1389974 A
63 A
* * * * *
1389975 TCGACTTATGTGGGCTTTAGAG-AGGGTGCCACCAACTTGTGTGGGCTTT
1 CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGAGCTTT
1390024 GAAAAGAAAA
Statistics
Matches: 747, Mismatches: 131, Indels: 107
0.76 0.13 0.11
Matches are distributed among these distances:
60 1 0.00
61 32 0.04
62 186 0.25
63 336 0.45
64 159 0.21
65 32 0.04
66 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (63 bp):
CCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGAGCTTTAAAGGGGTTGCCA
Found at i:1389197 original size:126 final size:124
Alignment explanation
Indices: 1388989--1390023 Score: 795
Period size: 126 Copynumber: 8.2 Consensus size: 124
1388979 GGTTTTAAAG
* * * *
1388989 AGGTTGCCA-TTAGCTTGTGTGGGCTTTGGAGAAGGTTGTCGC-CGACCTGTGTGGGCTTTAGAG
1 AGGTTGCCACTGA-CTTGTGTGGGCTTTAGAG-GGGTTG-C-CACGACTTGTGTGGGCTTT-GAG
* * * *
1389052 AA-AGTTTCCACCAACTTGTGTGAGCTTTAAAGGGGTTGCCACC-AGCTTGTGTGGGCTTTGGAG
61 AAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGGGGTTGCCACCGA-CTTGTGTGGGCTTT-GAG
1389115 A
124 A
* * *
1389116 AGGTTGCCACTGACTTGTGTAGGCTTTAGAGGGGTTGCCATCGACTTGTTTGGGCTTTAAGAAGG
1 AGGTTGCCACTGACTTGTGTGGGCTTTAGAGGGGTTGCCA-CGACTTGTGTGGGCTTTGAGAAGG
* * *
1389181 GTTGCCACCGAGTTGTGTGGGCTTTTAGAA-GGGTTTCCACCGATTTGTGTAGGGC-TT-AGA
65 GTTGCCACCGACTTGTGTGGGC-TTTA-AAGGGGTTGCCACCGACTTGTGT-GGGCTTTGAGA
* * * * * *
1389241 AGAGTTGCCACCGACTTCTGTGGGCTTTAAAAAGAGTTGCCACCGACTTGTGTGGGTTTTAGAGA
1 AG-GTTGCCACTGACTTGTGTGGGCTTT-AGAGGGGTTGCCA-CGACTTGTGTGGGCTTT-GAGA
** * * ** ** *
1389306 AGGGTTGCCACTAACTTGTGTGTG-TTTAAGAAGGGTTGCCACTAACTTGTACGTGCTTTAGAGA
62 AGGGTTGCCACCGACTTGTGTGGGCTTTAA-AGGGGTTGCCACCGACTTGTGTGGGCTTT-GAGA
* * *
1389370 AGGGTTGCCACTGACTTGTGTGGGCTTTA-A-GAGTTGCCACCAACTTGTGTGGGCTATGAGAAG
1 A-GGTTGCCACTGACTTGTGTGGGCTTTAGAGGGGTTGCCA-CGACTTGTGTGGGCTTTGAGAAG
* * * * *
1389433 GGTTTCTACCAACTTGTGTGGGCTTTGAGAA-GGGTTGCCATCGACTTGCGTGGGCTTTGAGA
64 GGTTGCCACCGACTTGTGTGGGCTTT-A-AAGGGGTTGCCACCGACTTGTGTGGGCTTTGAGA
* * * * *
1389495 AGGGTGCCACCGACTTATGTGGGCTTTAGAGAGGG-TGCCA-GTACCTTGTGTAGGCTTT-AGAG
1 AGGTTGCCACTGACTTGTGTGGGCTTTAGAG-GGGTTGCCACG-A-CTTGTGTGGGCTTTGAGAA
** * * *
1389557 GGGTTGCCACC-AGCTTGTGTGGGCTTTGGAGAAGGTTTCCACC-AGCTTGTGTGGGCTTTGGGA
63 GGGTTGCCACCGA-CTTGTGTGGGCTTTAAAG-GGGTTGCCACCGA-CTTGTGTGGGCTTTGAG-
1389620 A
124 A
* * *
1389621 AGGTTGCCACTGACTTGTGTAGGCTTTAGAGGGGTTGCCATTGACTTGCGTGGGCTTTGAGAAGG
1 AGGTTGCCACTGACTTGTGTGGGCTTTAGAGGGGTTGCCA-CGACTTGTGTGGGCTTTGAGAAGG
* * ** *
1389686 G-TGCCACCGACTTATGTGGGCTTTAGAGAGGG-TGCCACTAACTTGTGTAGGCTTT-AGA
65 GTTGCCACCGACTTGTGTGGGCTTTAAAG-GGGTTGCCACCGACTTGTGTGGGCTTTGAGA
* * * * * * * *
1389744 GGGGTTGCCAC-CAGCTTGTGTGGGCTTTGGAGAAGGTTTCCACCAGCTTTTGTGGGCTTTGGGA
1 -AGGTTGCCACTGA-CTTGTGTGGGCTTTAGAG-GGGTTGCCACGA-CTTGTGTGGGCTTTGAGA
* * * * * * *
1389808 AAGGTTGCTACTGACTTGTGTAGGCTTTAGAGGGGTTGCCATCGACTTGTGTGGGCTTTAAGA
62 AGGGTTGCCACCGACTTGTGTGGGCTTTAAAGGGGTTGCCACCGACTTGTGTGGGCTTTGAGA
* * * * * * *
1389871 AGGGTTGCCACTAATTTTTGTGGGCTTT-GAGAAGATTTCCACTAACTTGTGTGGGCTTTGAGAA
1 A-GGTTGCCACTGACTTGTGTGGGCTTTAGAG-GGGTTGCCAC-GACTTGTGTGGGCTTTGAGAA
* * *
1389935 GGGTTGCCACCGAGTTGTGTGGGCTTTGAGAA-GGG-TGCCATCGACTTATGTGGGCTTT-AGA
63 GGGTTGCCACCGACTTGTGTGGGCTTT-A-AAGGGGTTGCCACCGACTTGTGTGGGCTTTGAGA
* **
1389996 GAGGGTGCCACCAACTTGTGTGGGCTTT
1 -AGGTTGCCACTGACTTGTGTGGGCTTT
1390024 GAAAAGAAAA
Statistics
Matches: 738, Mismatches: 121, Indels: 100
0.77 0.13 0.10
Matches are distributed among these distances:
123 3 0.00
124 54 0.07
125 165 0.22
126 321 0.43
127 130 0.18
128 37 0.05
129 27 0.04
130 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (124 bp):
AGGTTGCCACTGACTTGTGTGGGCTTTAGAGGGGTTGCCACGACTTGTGTGGGCTTTGAGAAGGG
TTGCCACCGACTTGTGTGGGCTTTAAAGGGGTTGCCACCGACTTGTGTGGGCTTTGAGA
Found at i:1390065 original size:45 final size:45
Alignment explanation
Indices: 1389997--1390115 Score: 222
Period size: 45 Copynumber: 2.7 Consensus size: 45
1389987 GGCTTTAGAG
1389997 AGGG-TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGAA
1 AGGGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGAA
1390041 AGGGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGAA
1 AGGGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGAA
*
1390086 AGGGATGCCACCAACTTGTGTGAGCTTTGA
1 AGGGATGCCACCAACTTGTGTGGGCTTTGA
1390116 GAAGGGTTGC
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
44 4 0.05
45 69 0.95
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (45 bp):
AGGGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGAA
Found at i:1390127 original size:32 final size:32
Alignment explanation
Indices: 1390084--1390152 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1390074 GAAAAAAAAG
1390084 AAAGGGATGCCACCAACTTGTGTGAGCTTTGA
1 AAAGGGATGCCACCAACTTGTGTGAGCTTTGA
* * *** *
1390116 GAAGGGTTGCCACTGGCTTGTGTGGGCTTTGA
1 AAAGGGATGCCACCAACTTGTGTGAGCTTTGA
1390148 AAAGG
1 AAAGG
1390153 TTACTTTACT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (32 bp):
AAAGGGATGCCACCAACTTGTGTGAGCTTTGA
Found at i:1400632 original size:20 final size:20
Alignment explanation
Indices: 1400607--1400684 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
1400597 GTAAAAAGAC
*
1400607 AGAATGTATCGATACCTTGA
1 AGAATGTATCGATACATTGA
* *
1400627 AGAATGTATCAATACATTCA
1 AGAATGTATCGATACATTGA
* *
1400647 TA-CATATATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1400667 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
1400685 TGGGTAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1400736 original size:65 final size:68
Alignment explanation
Indices: 1400627--1400829 Score: 234
Period size: 65 Copynumber: 3.0 Consensus size: 68
1400617 GATACCTTGA
* * * *
1400627 AGAATGTATCAATACATTCATACATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAA
1 AGAATGTATCGATACATTCATAC--A-ATCGATACATTGAAAAATATATCGATACATCTAGGTAA
1400692 AAAGAC
63 AAAGAC
1400698 AGAATGTATCGATACATTCATAC-A-CG-TACATTGAAAAATATATCGATACATCTAGGTAAAAA
1 AGAATGTATCGATACATTCATACAATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAA
1400760 GAC
66 GAC
* *** * *
1400763 AAAATGTATCGATACATGT-ATGATGTCTCGATACATTGAAAAATTTATCGATACATCTAGGTGA
1 AGAATGTATCGATACAT-TCAT-A-CAATCGATACATTGAAAAATATATCGATACATCTAGGTAA
1400827 AAA
63 AAA
1400830 TGTGACTTTT
Statistics
Matches: 117, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
65 54 0.46
66 4 0.03
67 1 0.01
69 2 0.02
70 34 0.29
71 22 0.19
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (68 bp):
AGAATGTATCGATACATTCATACAATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAA
GAC
Found at i:1400773 original size:31 final size:31
Alignment explanation
Indices: 1400667--1400779 Score: 111
Period size: 31 Copynumber: 3.5 Consensus size: 31
1400657 GATACATTGA
* *
1400667 AAAATGTATCGATACATTTGGGTAAAAAGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
* * * **
1400698 AGAATGTATCGATACATTCATACACGTACATTGA-
1 AAAATGTATCGATACA-TC-T--AGGTAAAAAGAC
*
1400732 AAAATATATCGATACATCTAGGTAAAAAGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
1400763 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
1400780 GTATGATGTC
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
30 7 0.11
31 31 0.49
32 2 0.03
33 3 0.05
34 14 0.22
35 6 0.10
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (31 bp):
AAAATGTATCGATACATCTAGGTAAAAAGAC
Found at i:1401792 original size:40 final size:40
Alignment explanation
Indices: 1401716--1401834 Score: 157
Period size: 40 Copynumber: 3.0 Consensus size: 40
1401706 AAGGCAAAAT
* * * *
1401716 CGATAAGTCAACGAGTTAAAGAGGTTAACGAGGATGAAAC
1 CGATAAGTCAACAAGTTAAAGAGGTTGACCAAGATGAAAC
* * *
1401756 CGATAAGTCAACAAATTGAAGATGTTGACCAAGATGAAAC
1 CGATAAGTCAACAAGTTAAAGAGGTTGACCAAGATGAAAC
* *
1401796 CGACAAGTCAACAAGTTAAAGAGGTTGGCCAAGATGAAA
1 CGATAAGTCAACAAGTTAAAGAGGTTGACCAAGATGAAA
1401835 TTAACAAGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (40 bp):
CGATAAGTCAACAAGTTAAAGAGGTTGACCAAGATGAAAC
Found at i:1401972 original size:105 final size:105
Alignment explanation
Indices: 1401779--1402374 Score: 474
Period size: 105 Copynumber: 5.7 Consensus size: 105
1401769 AATTGAAGAT
* * * ** * * * *
1401779 GTTGACCAAGATGAAA-CCGACAAGTCAACAAGTTAAAGAGGTTGGCCAAGATGAAATTAACAAG
1 GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAGA-CAAAATCACAAG
* * * * * * *
1401843 TTAAAAAAGAGTGACTCGAGTAAAACCCAAGTCAGAATAAG
65 TCAACAAAGAGTGAATAGGGTAAAACCTAAGTCAAAATAAG
* * * * * * *
1401884 ATTGGCCATGGTGAAATCT-ATAAGTTAACAAGTTAAAGAGATTGATCG-GTACGAAATCGATAA
1 GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAG-ACAAAATC-ACAA
* * *
1401947 GTCAACAAATAGTGAATAGGGTAAAACTTAAGTTAAAATAAG
64 GTCAACAAAGAGTGAATAGGGTAAAACCTAAGTCAAAATAAG
* * * * * *
1401989 GTTGATCAAGG-CAAAACTGATAAGTCAAAAAGTTAAAAAGGTTGATTGAGACAAAATCAGCAAG
1 GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAGACAAAATCA-CAAG
* * * * * *
1402053 TCTACAAAGAGTGATTAAGGTAAAACTTAAGTTAAAATAGG
65 TCAACAAAGAGTGAATAGGGTAAAACCTAAGTCAAAATAAG
* * *
1402094 GTTGACCAAGATGAAAT-TGATAAGTCAACGAGTTAAAGAGGTTGACCGAGACAAAATCAACAAG
1 GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAGACAAAATC-ACAAG
* *
1402158 TCAACAAAGAGTGAATAGGGTAAAATCTAAGCCAAAATAAG
65 TCAACAAAGAGTGAATAGGGTAAAACCTAAGTCAAAATAAG
* ** * * * * * * **
1402199 GTTGACCAGGGTGAAA-CCAATAAGTTAACAAGTTAAAAAGGCTAACCAAGATGAAATCGACAAG
1 GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAGACAAAATC-ACAAG
* *
1402263 TCAACAAAGAAT-AACTAGGGTAAAACCTAAGTCAAAATAGG
65 TCAACAAAGAGTGAA-TAGGGTAAAACCTAAGTCAAAATAAG
* * * * * *
1402304 GTTGA-CTAGCGTGAAA-CTAATAAGTCAACAAGTT-AAGAATGTTGATCGAAACGAAACCAACA
1 GTTGACCAAG-GTGAAATCTGATAAGTCAACAAGTTAAAG-AGGTTGATCGAGACAAAATC-ACA
1402366 AGTCAACAA
63 AGTCAACAA
1402375 GTTAAGGAGG
Statistics
Matches: 387, Mismatches: 92, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
104 16 0.04
105 365 0.94
106 6 0.02
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (105 bp):
GTTGACCAAGGTGAAATCTGATAAGTCAACAAGTTAAAGAGGTTGATCGAGACAAAATCACAAGT
CAACAAAGAGTGAATAGGGTAAAACCTAAGTCAAAATAAG
Found at i:1402360 original size:40 final size:40
Alignment explanation
Indices: 1402316--1402411 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
1402306 TGACTAGCGT
* *
1402316 GAAACTAATAAGTCAACAAGTTAAGAATGTTGATCGAAAC
1 GAAACTAACAAGTCAACAAGTTAAGAAGGTTGATCGAAAC
* * *
1402356 GAAACCAACAAGTCAACAAGTTAAGGAGGTTGATCGAGAC
1 GAAACTAACAAGTCAACAAGTTAAGAAGGTTGATCGAAAC
*
1402396 GAAACTGACAAGTCAA
1 GAAACTAACAAGTCAA
1402412 TAAAGAGTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.18
Consensus pattern (40 bp):
GAAACTAACAAGTCAACAAGTTAAGAAGGTTGATCGAAAC
Found at i:1402361 original size:145 final size:144
Alignment explanation
Indices: 1402211--1402524 Score: 353
Period size: 145 Copynumber: 2.2 Consensus size: 144
1402201 TGACCAGGGT
*
1402211 GAAACCAATAAGTTAACAAGTTAAAAAGGCTAACCAAGATGAAA-TCGACAAGTCAACAAAGAAT
1 GAAACCAATAAGTTAACAAGTTAAAAAGGCTAACCAAGACGAAACT-GACAAGTCAACAAAGAAT
* * * *
1402275 AACTAGGGTAAAACCTAAGTCAAAATAGGGTTGACTAGCGTGAAA-CTAATAAGTCAACAAGTTA
65 AACTAGGGTAAAACCCAAGTCAAAATAGGGTCGACTAGAGCGAAATC-AATAAGTCAACAAGTTA
1402339 AGAATGTTGATCGAAAC
129 AGAA-GTTGATCGAAAC
* * ** * * * * * * *
1402356 GAAACCAACAAGTCAACAAGTTAAGGAGGTTGATCGAGACGAAACTGACAAGTCAATAAAGAGTG
1 GAAACCAATAAGTTAACAAGTTAAAAAGGCTAACCAAGACGAAACTGACAAGTCAACAAAGAATA
** * *
1402421 ACTAGGGTAAAACCCCTGTCAAAATAGGGTCGACTAGAGCGAAATCGATAAGTTAACAAGTTAAG
66 ACTAGGGTAAAACCCAAGTCAAAATAGGGTCGACTAGAGCGAAATCAATAAGTCAACAAGTTAAG
** *
1402486 AAGTTGATCGGGAT
131 AAGTTGATCGAAAC
***
1402500 GAAACTGCTAAGTTAACAAGTTAAA
1 GAAACCAATAAGTTAACAAGTTAAA
1402525 GATGTTTACA
Statistics
Matches: 138, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
144 28 0.20
145 108 0.78
146 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (144 bp):
GAAACCAATAAGTTAACAAGTTAAAAAGGCTAACCAAGACGAAACTGACAAGTCAACAAAGAATA
ACTAGGGTAAAACCCAAGTCAAAATAGGGTCGACTAGAGCGAAATCAATAAGTCAACAAGTTAAG
AAGTTGATCGAAAC
Found at i:1402598 original size:40 final size:40
Alignment explanation
Indices: 1402541--1402825 Score: 270
Period size: 40 Copynumber: 7.1 Consensus size: 40
1402531 TACAAGGACA
* * *
1402541 AAACTGACAAGCTAACAAAAAGTAAAGGTTGGCCAAGATG
1 AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
* * * *
1402581 AAA-TCGATAAGCCAAC-AAAAGTAAAAGTTGACTGGGATG
1 AAACT-GACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
*
1402620 AAACTGACAAGCCATCTATAAAGAGTAAAGGTTGACCGAGATG
1 AAACTGACAAGCCAAC-A-AAA-AGTAAAGGTTGACCGAGATG
* * * **
1402663 AAACTGATAAGCCAACAAAGATTAAAGGTTGATTGAGATG
1 AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
* * * * *
1402703 AAACTGACAAGTCAATAAAGAGTAAAGGTTCACCGGGATG
1 AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
* * *
1402743 AAACTGACAAGCCAACAAAGAGTAAAGGTTGGCCAAGATG
1 AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
* * * * * *
1402783 AAACTAATAAGCCAAC-AAAGGTAAAAGTTGACCCAGACG
1 AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
1402822 AAAC
1 AAAC
1402826 CAACAAGCTA
Statistics
Matches: 199, Mismatches: 40, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
39 52 0.26
40 110 0.55
41 2 0.01
42 4 0.02
43 31 0.16
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (40 bp):
AAACTGACAAGCCAACAAAAAGTAAAGGTTGACCGAGATG
Found at i:1402744 original size:80 final size:80
Alignment explanation
Indices: 1402541--1402825 Score: 299
Period size: 80 Copynumber: 3.5 Consensus size: 80
1402531 TACAAGGACA
* * * *
1402541 AAACTGACAAG-CTAACAAAAAGTAAAGGTTGGCCAAGATGAAA-TCGATAAGCCAACAAA-AGT
1 AAACTGACAAGTC-AATAAAGAGTAAAGGTTGACCGAGATGAAACT-GATAAGCCAACAAAGAGT
* *
1402603 AAAAGTTGACTGGGATG
64 AAAGGTTGACTGAGATG
* *
1402620 AAACTGACAAGCCATCTATAAAGAGTAAAGGTTGACCGAGATGAAACTGATAAGCCAACAAAGAT
1 AAACTGACAAG---TCAATAAAGAGTAAAGGTTGACCGAGATGAAACTGATAAGCCAACAAAGAG
*
1402685 TAAAGGTTGATTGAGATG
63 TAAAGGTTGACTGAGATG
* * *
1402703 AAACTGACAAGTCAATAAAGAGTAAAGGTTCACCGGGATGAAACTGACAAGCCAACAAAGAGTAA
1 AAACTGACAAGTCAATAAAGAGTAAAGGTTGACCGAGATGAAACTGATAAGCCAACAAAGAGTAA
* **
1402768 AGGTTGGCCAAGATG
66 AGGTTGACTGAGATG
* * * * * * *
1402783 AAACTAATAAGCCAACAAAG-GTAAAAGTTGACCCAGACGAAAC
1 AAACTGACAAGTCAATAAAGAGTAAAGGTTGACCGAGATGAAAC
1402826 CAACAAGCTA
Statistics
Matches: 173, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
79 29 0.17
80 76 0.44
82 39 0.23
83 29 0.17
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (80 bp):
AAACTGACAAGTCAATAAAGAGTAAAGGTTGACCGAGATGAAACTGATAAGCCAACAAAGAGTAA
AGGTTGACTGAGATG
Found at i:1403445 original size:76 final size:76
Alignment explanation
Indices: 1403354--1403930 Score: 474
Period size: 76 Copynumber: 7.7 Consensus size: 76
1403344 AACACAATAA
* ** * * * * * * * *
1403354 GGAATATATGGTTTCTAAAATTTTTATTAACATCTAAAATAAACTAATAATAGGCTGAAGGAAAG
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
1403419 GAACATGATAG
66 GAACATGATAG
* * * * *
1403430 GGAATATGTGATTTCTAAAATTTTCATCAATAGCCGAAACAAACTGATAATAGGCTAAAGGAAAA
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
* *
1403495 TAACATAATAG
66 GAACATGATAG
* * * *** * * *
1403506 AGAATATGTGGTTTCTAAAATCTCCATCAACAGTTGAAACAAATTGATAACAAGCTAAAAGAAAG
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
1403571 GAACA-GAATAG
66 GAACATG-ATAG
* * * * * *
1403582 GGAATATGTGGTTTCCAAAATTTCCATTATTAGCCAAAACAAAATGATGACAAGCTAAAGGAAAG
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
*
1403647 GAACATAATAG
66 GAACATGATAG
* ** ** * * *
1403658 GGAATATGTGGTTTCTAAAATTTCCATCAACA-ATAGAAGTAAACTAATAA-TGGCCTGAA-GAA
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCA-AAACAAACTGATAACAGG-CTAAAGGAA
* *
1403720 GAAGAACATGATGG
64 -AGGAACATGATAG
* * * * * * * * *
1403734 GGAATATGTGATTTTTACAATTTCAATTAATAGTC-AAACAAACTGACAACA-ACTTGAA--AAA
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGC-TAAAGGAAA
1403795 --AACATGAT-G
65 GGAACATGATAG
* * **
1403804 GGAATATGTAGTTTCTAAAATTTCCATCAATAGCCAAAATAATGTGATAACAGGCTAAAGGAAAG
1 GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
*
1403869 GAACATGATGG
66 GAACATGATAG
* * *
1403880 GGAATATGTGGTTTCTACAATTTCCCATCAACAGCCAAAATAAACTGATAA
1 GGAATATGTGGTTTCTAAAATTT-CCATCAATAGCCAAAACAAACTGATAA
1403931 AAGTGATGAT
Statistics
Matches: 395, Mismatches: 90, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
70 29 0.07
71 23 0.06
72 1 0.00
73 4 0.01
74 3 0.01
75 27 0.07
76 284 0.72
77 24 0.06
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (76 bp):
GGAATATGTGGTTTCTAAAATTTCCATCAATAGCCAAAACAAACTGATAACAGGCTAAAGGAAAG
GAACATGATAG
Found at i:1404066 original size:23 final size:24
Alignment explanation
Indices: 1404035--1404080 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1404025 GACTTAAGGG
*
1404035 AAACCAAAATT-TATAAAATGACA
1 AAACCAAAATTCTACAAAATGACA
*
1404058 AAACTAAAATTCTACAAAATGAC
1 AAACCAAAATTCTACAAAATGAC
1404081 TTGGGTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.22
Consensus pattern (24 bp):
AAACCAAAATTCTACAAAATGACA
Found at i:1409073 original size:13 final size:13
Alignment explanation
Indices: 1409055--1409080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1409045 TACACCAAGT
1409055 ATGTATCGATACA
1 ATGTATCGATACA
1409068 ATGTATCGATACA
1 ATGTATCGATACA
1409081 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1411333 original size:21 final size:21
Alignment explanation
Indices: 1411300--1411349 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1411290 TTGCAAGTTG
*
1411300 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1411322 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1411343 AAATAAA
1 AAATAAA
1411350 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1415273 original size:13 final size:13
Alignment explanation
Indices: 1415255--1415293 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1415245 ACATTTTTCC
1415255 TTGTATCGATACA
1 TTGTATCGATACA
1415268 TTGTATCGATACA
1 TTGTATCGATACA
*
1415281 TTGCATCGATACA
1 TTGTATCGATACA
1415294 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1415457 original size:20 final size:20
Alignment explanation
Indices: 1415419--1415458 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1415409 TTTTGCGAAA
1415419 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
1415440 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
1415459 ACCAGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:1417861 original size:13 final size:13
Alignment explanation
Indices: 1417843--1417868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1417833 TACAACAAGT
1417843 ATGTATCGATACA
1 ATGTATCGATACA
1417856 ATGTATCGATACA
1 ATGTATCGATACA
1417869 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1419063 original size:20 final size:19
Alignment explanation
Indices: 1419038--1419112 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
1419028 TTTTACCCAG
1419038 ATGTATCGATACATCTTTCA
1 ATGTATCGATACAT-TTTCA
* ***
1419058 ATGTATCGATTCATGTAAAA
1 ATGTATCGATACAT-TTTCA
1419078 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
* *
1419098 CTATATCGATACATT
1 ATGTATCGATACATT
1419113 CTATCTTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:1422463 original size:52 final size:52
Alignment explanation
Indices: 1422319--1422441 Score: 219
Period size: 52 Copynumber: 2.4 Consensus size: 52
1422309 ATATGAAAAG
1422319 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
* * *
1422371 TTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1422423 TTGCCTGCATGTATCGATA
1 TTGCCTGCATGTATCGATA
1422442 GAAGGAATAG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1422556 original size:13 final size:13
Alignment explanation
Indices: 1422538--1422562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1422528 ACAAAACTTA
1422538 TGTATCGATACAT
1 TGTATCGATACAT
1422551 TGTATCGATACA
1 TGTATCGATACA
1422563 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1422562 original size:32 final size:33
Alignment explanation
Indices: 1422517--1422582 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1422507 AGTAGCTTAA
1422517 ATTGGATCGATACAAAAC-TTATGTATCGATAC
1 ATTGGATCGATACAAAACTTTATGTATCGATAC
* *
1422549 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGGATCGATACAAAACTTTATGTATCGATAC
1422582 A
1 A
1422583 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
ATTGGATCGATACAAAACTTTATGTATCGATAC
Found at i:1423306 original size:67 final size:68
Alignment explanation
Indices: 1423184--1423310 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
1423174 ATTGGGTTTT
* * *
1423184 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTAAAGATGAAGGTG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACTAGCAATATTGGACTTAAAGATGAAGGTG
1423249 AGA
66 AGA
* * * *
1423252 AAAG-TGATAAAGATGCCAATATGTTGATTCACGACTAGCGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACTAGCAATATTGGACTTAAAGATGA
1423311 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGACTAGCAATATTGGACTTAAAGATGAAGGTG
AGA
Found at i:1423590 original size:141 final size:141
Alignment explanation
Indices: 1423323--1423687 Score: 555
Period size: 141 Copynumber: 2.6 Consensus size: 141
1423313 AAAAGGATGT
* * * *
1423323 CAATGTGCTAATTCAAGACCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
1423388 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
63 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1423453 AAAGAAGAAGGTGC
128 AAAGAAGAAGGTGC
*
1423467 CAATATGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* *
1423532 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGATTTAAA
66 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
*
1423597 GATGAAGGTGC
131 GAAGAAGGTGC
* *
1423608 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
1423667 GGCCAGCTACATTGGA-TTAAA
66 GGCCAGCTATATTGGACTTAAA
1423688 AGATGAAGGT
Statistics
Matches: 209, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
134 5 0.02
135 37 0.18
137 1 0.00
141 129 0.62
143 1 0.00
144 36 0.17
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (141 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
GAAGAAGGTGC
Found at i:1423690 original size:92 final size:91
Alignment explanation
Indices: 1423367--1423740 Score: 508
Period size: 92 Copynumber: 4.1 Consensus size: 91
1423357 TAAAGATGGA
* *
1423367 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGA-TTAAAGATGAAGGTGCCAATATGC
*
1423426 TGATTCAAGGCCAGCTACATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
*
1423453 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGAAGGTGCCA
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATT-GGATTAAAGATGAAGGTGCCA
1423518 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
59 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1423551 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGA-TTAAAGATGAAGGTGCCAATATGC
1423616 TGATTCAAGGCCAGCTATATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* * *
1423643 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTAAAAGATGAAGGTGCTAATATGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGATT-AAAGATGAAGGTGCCAATATGC
* *
1423708 TGATTCAAGGCCAGCGATATTGGGCTT
65 TGATTCAAGGCCAGCTATATTGGACTT
1423735 AGAAGG
1 A-AAGG
1423741 GTTGCCACTG
Statistics
Matches: 260, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
91 5 0.02
92 207 0.80
93 7 0.03
96 1 0.00
98 40 0.15
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (91 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGATTAAAGATGAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTT
Found at i:1423730 original size:49 final size:49
Alignment explanation
Indices: 1423323--1423722 Score: 487
Period size: 49 Copynumber: 8.5 Consensus size: 49
1423313 AAAAGGATGT
* * * *
1423323 CAATGTGCTAATTCAAGACCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
1423375 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1423418 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1423467 CAATATGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1423516 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1423559 CAATGTGTTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1423608 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1423651 CAATGTGCTGATTCAAGGCCAGCTACATTGGA-TTAAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGC
* *
1423700 TAATATGTTGATTCAAGGCCAGC
1 CAATATGCTGATTCAAGGCCAGC
1423723 GATATTGGGC
Statistics
Matches: 304, Mismatches: 25, Indels: 41
0.82 0.07 0.11
Matches are distributed among these distances:
42 2 0.01
43 115 0.38
45 2 0.01
47 3 0.01
48 1 0.00
49 151 0.50
52 30 0.10
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1423809 original size:32 final size:33
Alignment explanation
Indices: 1423749--1423890 Score: 207
Period size: 32 Copynumber: 4.4 Consensus size: 33
1423739 GGGTTGCCAC
*
1423749 TGTGTGGGCTTTAGAGAATGGTTGCCACCAACT
1 TGTGTGGGCTTTAGAGAAGGGTTGCCACCAACT
* *
1423782 TGTGTGTGCTTTAGAG-AGGGTTGCCACCGACT
1 TGTGTGGGCTTTAGAGAAGGGTTGCCACCAACT
*
1423814 TGTGTGGGCTTT-GAGAAGGCTTGCCACCAACT
1 TGTGTGGGCTTTAGAGAAGGGTTGCCACCAACT
* **
1423846 TGTGTGGGCTTTAGAAAAGGGTTGCCACTGACT
1 TGTGTGGGCTTTAGAGAAGGGTTGCCACCAACT
1423879 TGTGTGGGCTTT
1 TGTGTGGGCTTT
1423891 TGAAAAGGAG
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 3 0.03
32 51 0.53
33 43 0.44
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.32
Consensus pattern (33 bp):
TGTGTGGGCTTTAGAGAAGGGTTGCCACCAACT
Found at i:1423983 original size:34 final size:34
Alignment explanation
Indices: 1423881--1424153 Score: 227
Period size: 34 Copynumber: 8.3 Consensus size: 34
1423871 CACTGACTTG
* *
1423881 TGTGGGCTTTTGAAAAGGAGAAAGATGCCACGGAGT
1 TGTGGGC-TTT-AAAAGGAAAAAGGTGCCACGGAGT
* *
1423917 TGTAGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGT
*
1423952 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
* *
1423986 TGTGGAC-TTAAAA-G-----GGTGCCACGAAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
* *
1424013 TGTGGGCTTTAAAAAGGAAAAAGAATGCCACAGAGT
1 TGTGGGCTTT-AAAAGGAAAAAG-GTGCCACGGAGT
* ** *
1424049 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACAAAAT
1 TGTGGGCTTTAAAAGGAAAAAG-GTGCCACGGAGT
*
1424083 TGTGGGCTTT------AAAAAGGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
* *
1424111 TGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
1424144 TGTGGGCTTT
1 TGTGGGCTTT
1424154 GAAGAAAAAA
Statistics
Matches: 194, Mismatches: 23, Indels: 42
0.75 0.09 0.16
Matches are distributed among these distances:
27 20 0.10
28 18 0.09
29 10 0.05
30 1 0.01
32 1 0.01
33 32 0.16
34 57 0.29
35 28 0.14
36 27 0.14
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
Found at i:1424006 original size:27 final size:28
Alignment explanation
Indices: 1423968--1424029 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
1423958 CTTTAAAAAG
*
1423968 AAAAAGGTGCCACGGAGTTGTGGAC-TT
1 AAAAAGGTGCCACGAAGTTGTGGACTTT
* *
1423995 AAAAGGGTGCCACGAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGAAGTTGTGGACTTT
1424023 AAAAAGG
1 AAAAAGG
1424030 AAAAAGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (28 bp):
AAAAAGGTGCCACGAAGTTGTGGACTTT
Found at i:1424034 original size:97 final size:98
Alignment explanation
Indices: 1423901--1424153 Score: 311
Period size: 97 Copynumber: 2.6 Consensus size: 98
1423891 TGAAAAGGAG
* * * *
1423901 AAAGATGCCACGGAGTTGTAGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGGTGCCACGAAGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
** *
1423966 AGAAAAAG-GTGCCACGGAGTTGTGGAC-TTAA
66 AGAAAAAGAGTGCCACAAAATTGTGGACTTTAA
* * * * *
1423997 AAGGGTGCCACGAAGTTGTGGGCTTTAAAAAGGAAAAAGAATGCCACAGAGTTGTGGGC-TTAGA
1 AAAGGTGCCACGAAGTTGTGGAC-TTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* *
1424061 AGGAAAAAGAGTGCCACAAAATTGTGGGCTTTAA
65 AAGAAAAAGAGTGCCACAAAATTGTGGACTTTAA
*
1424095 AAAGGTGCCAC-AGAGTTGTGGACTT-AAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTT
1 AAAGGTGCCACGA-AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1424154 GAAGAAAAAA
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
95 17 0.13
96 43 0.32
97 50 0.38
98 23 0.17
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.21
Consensus pattern (98 bp):
AAAGGTGCCACGAAGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAAAAGAGTGCCACAAAATTGTGGACTTTAA
Found at i:1424105 original size:28 final size:28
Alignment explanation
Indices: 1424064--1424123 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1424054 GCTTAGAAGG
*
1424064 AAAAAGAGTGCCACAAAATTGTGGGCTTT
1 AAAAAGAGTGCCACAAAATTGTGGAC-TT
* *
1424093 AAAAAG-GTGCCACAGAGTTGTGGACTT
1 AAAAAGAGTGCCACAAAATTGTGGACTT
1424120 AAAA
1 AAAA
1424124 GGAACAAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 16 0.57
29 6 0.21
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (28 bp):
AAAAAGAGTGCCACAAAATTGTGGACTT
Found at i:1424114 original size:62 final size:61
Alignment explanation
Indices: 1424038--1424153 Score: 169
Period size: 62 Copynumber: 1.9 Consensus size: 61
1424028 GGAAAAAGAA
* *
1424038 TGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAAAATTGTGGGCTTTAAAAAGG
1 TGCCACAGAGTTGTGGACTTAAAAGGAAAAAG-GTGCCACAAAATTGTGGGCTTTAAAAAGG
* ** *
1424100 TGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
1 TGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAAAATTGTGGGCTTT
1424154 GAAGAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 19 0.40
62 29 0.60
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (61 bp):
TGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAAAATTGTGGGCTTTAAAAAGG
Found at i:1424153 original size:131 final size:126
Alignment explanation
Indices: 1423881--1424125 Score: 323
Period size: 131 Copynumber: 1.9 Consensus size: 126
1423871 CACTGACTTG
* * *
1423881 TGTGGGCTTTTGAAAAGGAGAAAGATGCCACGGAGTTGTAGACTTAAAAGGGAAAAAGAGTGCCA
1 TGTGGGC-TTTAAAAAGGAAAAAGATGCCACAGAGTTGTAGACTTAAAAGGGAAAAAGAGTGCCA
** * *
1423946 CGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAA
65 CAAAATTGTGGGCTTT----A-AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGAA
1424011 GT
125 GT
* * *
1424013 TGTGGGCTTTAAAAAGGAAAAAGAATGCCACAGAGTTGTGGGCTTAGAA-GGAAAAAGAGTGCCA
1 TGTGGGCTTTAAAAAGGAAAAAG-ATGCCACAGAGTTGTAGACTTAAAAGGGAAAAAGAGTGCCA
1424077 CAAAATTGTGGGCTTT-AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
65 CAAAATTGTGGGCTTTAAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
1424126 AACAAGGTGC
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
125 32 0.31
131 42 0.41
132 28 0.27
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.21
Consensus pattern (126 bp):
TGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTAGACTTAAAAGGGAAAAAGAGTGCCAC
AAAATTGTGGGCTTTAAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGAAGT
Found at i:1424196 original size:30 final size:29
Alignment explanation
Indices: 1424133--1424282 Score: 156
Period size: 31 Copynumber: 4.9 Consensus size: 29
1424123 AGGAACAAGG
* * *
1424133 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AG-AAAAA
*
1424164 TGCCACTGAGTCTTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGA-AAAA
1424194 TGCCACTGAGTCGTGGACTTTGAGGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTGA-GAAAA--A
*
1424226 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAA-A-AA
* * *
1424257 TACCATTGAGTCGTGGGCTTTGAGAA
1 TGCCACTGAGTCGTGGACTTTGAGAA
1424283 GAGATTTGAA
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.01
30 31 0.30
31 46 0.44
32 25 0.24
33 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (29 bp):
TGCCACTGAGTCGTGGACTTTGAGAAAAA
Found at i:1424243 original size:62 final size:61
Alignment explanation
Indices: 1424133--1424250 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
1424123 AGGAACAAGG
* * *
1424133 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAATGCCACTGAGTCTTGGACTTTGAGACAAAA
1 TGCCACGGAGTCGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGACAAAA
* * *
1424194 TGCCACTGAGTCGTGGACTTTGAGGAAAAGGATGCCACTGAGTCGTGGACTTTGAGA
1 TGCCACGGAGTCGTGGACTTTGAAGAAAA-AATGCCACTGAGTCGTGGACTTTGAGA
1424251 AGAGATTACC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 25 0.50
62 25 0.50
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25
Consensus pattern (61 bp):
TGCCACGGAGTCGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1424267 original size:93 final size:94
Alignment explanation
Indices: 1424100--1424281 Score: 208
Period size: 93 Copynumber: 1.9 Consensus size: 94
1424090 TTTAAAAAGG
* * *
1424100 TGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAAT
1 TGCCACAGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTGAAGAAAAAAT
* *
1424165 GCCACTGAGTCTTGGACTTTGAGACAAAA
66 ACCACTGAGTCGTGGACTTTGAGACAAAA
* ** * *
1424194 TGCCACTGAGTCGTGGACTT-TGAGGAA-AAGGATGCCACTGAGTCGTGGACTTTG-AGAAGAGA
1 TGCCACAGAGTCGTGGACTTAAAAGGAACAAGG-TGCCACGGAGTCGTGGACTTTGAAGAA-AAA
* * *
1424256 TTACCATTGAGTCGTGGGCTTTGAGA
64 ATACCACTGAGTCGTGGACTTTGAGA
1424282 AGAGATTTGA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
92 8 0.11
93 47 0.64
94 18 0.25
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (94 bp):
TGCCACAGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTGAAGAAAAAAT
ACCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1425276 original size:29 final size:28
Alignment explanation
Indices: 1425231--1425295 Score: 100
Period size: 26 Copynumber: 2.4 Consensus size: 28
1425221 TTTTCCCTTC
1425231 TTCTTCTTTTTTTT-TTTTTT-TTTTGT
1 TTCTTCTTTTTTTTCTTTTTTGTTTTGT
1425257 TTCTTCTTTTTTTTCCTTTTTTGTTTTGT
1 TTCTTCTTTTTTTT-CTTTTTTGTTTTGT
1425286 TTCTT-TTTTT
1 TTCTTCTTTTT
1425296 GGAAAAGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.39
28 11 0.31
29 11 0.31
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.85
Consensus pattern (28 bp):
TTCTTCTTTTTTTTCTTTTTTGTTTTGT
Found at i:1425283 original size:17 final size:17
Alignment explanation
Indices: 1425239--1425296 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1425229 TCTTCTTCTT
* **
1425239 TTTTTTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTCC
* *
1425256 TTTCTTCTTTTTTTTCC
1 TTTTTTGTTTTTTTTCC
* *
1425273 TTTTTTGTTTTGTTTCT
1 TTTTTTGTTTTTTTTCC
1425290 TTTTTTG
1 TTTTTTG
1425297 GAAAAGAACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTCC
Found at i:1425294 original size:24 final size:24
Alignment explanation
Indices: 1425234--1425282 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1425224 TCCCTTCTTC
**
1425234 TTCTT-TTTTTTTTTTTTTTTTGT
1 TTCTTCTTTTTTTTCCTTTTTTGT
1425257 TTCTTCTTTTTTTTCCTTTTTTGT
1 TTCTTCTTTTTTTTCCTTTTTTGT
1425281 TT
1 TT
1425283 TGTTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (24 bp):
TTCTTCTTTTTTTTCCTTTTTTGT
Found at i:1432507 original size:52 final size:52
Alignment explanation
Indices: 1432422--1432543 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
1432412 ATATGAAAAG
*
1432422 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1432474 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1432526 TTACCTGCATGTATCGAT
1 TTGCCTGCATGTATCGAT
1432544 TCAAAATCAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1432660 original size:32 final size:33
Alignment explanation
Indices: 1432619--1432684 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1432609 AATAGCTTAA
*
1432619 ATTGTATCGATACAAAAC-TTATGTATCTATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1432651 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1432684 A
1 A
1432685 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1435154 original size:51 final size:52
Alignment explanation
Indices: 1435098--1435213 Score: 121
Period size: 52 Copynumber: 2.2 Consensus size: 52
1435088 ACAATTGGGC
* *
1435098 TGGAGTATCCCCGATTATG-GAAAATCGATG-TTCT-GAAAATAAAATCGGGGT
1 TGGAGTATCCCCGATTATGAAAAAATCGATGCTT-TAG-AAATAAAACCGGGGT
* * * * **
1435149 TGGAGTGTCCTCAATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGT
1 TGGAGTATCCCCGATTATGAAAAAATCGATGCTTTAGAAATAAAACCGGGGT
1435201 TGGAGTATCCCCG
1 TGGAGTATCCCCG
1435214 TAAAAATAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
51 15 0.29
52 33 0.65
53 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (52 bp):
TGGAGTATCCCCGATTATGAAAAAATCGATGCTTTAGAAATAAAACCGGGGT
Found at i:1435304 original size:51 final size:51
Alignment explanation
Indices: 1435226--1435342 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
1435216 AAAATAATAG
* * *
1435226 GGTTGGAGTATCCCTGATTATAGAAAATCGGTGTTTTAAAAATAAAATC-A
1 GGTTGAAGTATCCCCGATTATAGAAAATCGGTATTTTAAAAATAAAATCGA
* * *
1435276 GAGTTGAAGTATCCCCGATTGT-GAAAAATTGGTATTTTAGAAATAAAATCGA
1 G-GTTGAAGTATCCCCGATTATAG-AAAATCGGTATTTTAAAAATAAAATCGA
1435328 GGTT-AGAGTATCCCC
1 GGTTGA-AGTATCCCC
1435343 TCAGAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 3 0.05
51 52 0.91
52 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (51 bp):
GGTTGAAGTATCCCCGATTATAGAAAATCGGTATTTTAAAAATAAAATCGA
Found at i:1435356 original size:28 final size:28
Alignment explanation
Indices: 1435325--1435396 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
1435315 GAAATAAAAT
1435325 CGAGGTTAGAGTATCCCCTCA-GAAATAA
1 CGAGGTTAGAGTATCCCC-CATGAAATAA
* * * **
1435353 CGAGATTGGAGTATCCCCGATGTCATAA
1 CGAGGTTAGAGTATCCCCCATGAAATAA
*
1435381 CGGGGTTAGAGTATCC
1 CGAGGTTAGAGTATCC
1435397 TTAATTGTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (28 bp):
CGAGGTTAGAGTATCCCCCATGAAATAA
Found at i:1444565 original size:13 final size:13
Alignment explanation
Indices: 1444547--1444572 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1444537 TACACAAAGT
1444547 ATGTATCGATACA
1 ATGTATCGATACA
1444560 ATGTATCGATACA
1 ATGTATCGATACA
1444573 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1444570 original size:32 final size:33
Alignment explanation
Indices: 1444529--1444592 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1444519 TAGCCAAACT
**
1444529 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1444561 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1444593 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1446797 original size:84 final size:84
Alignment explanation
Indices: 1446624--1446784 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 84
1446614 ACTCAAAGAA
* * * *
1446624 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
1446689 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
1446708 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
1446771 AA-AAGAAATGAGTT
64 AATAAGAAA-GAGTT
1446785 GCAAGTGGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 56 0.85
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Done.