Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold30
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: 2650045
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.30
Warning! 144233 characters in sequence are not A, C, G, or T
File 10 of 17
Found at i:1561708 original size:107 final size:104
Alignment explanation
Indices: 1561365--1562108 Score: 771
Period size: 107 Copynumber: 7.3 Consensus size: 104
1561355 TTGGGAAGGA
* *
1561365 AAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1561429 AAAGG-AAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
66 AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
*
1561469 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
1561532 GAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGG
65 -AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
* **
1561575 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
1561640 AAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
65 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * *
1561679 AAGAAGGTTGCCACGGAGTTGTGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGAC
1 AAAAAGG-TGCCACGGAG-T-TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1561743 -TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
62 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * * * * *
1561786 AAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGAC
1 AAAAAGG-TGCCACGGA-GT-TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1561850 -TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
62 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
1561893 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGC-TT-
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* *
1561954 AAACG-----G-GTGCCACGGAGTTGTGGAC-TTAAAGATG
66 AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
* * * *
1561988 AAAAAAGTGCCACAGAATTGTGGGCTTTAAAA--G-----G-GTGCCACGGAGTTGTGGAC-TTA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* *
1562044 AAAGGAACAAG-GTGCCACGGAGTTATGGGCTTT-AAAG
66 AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
** * * *
1562081 AAAAAAATGCCACTGAGTCGTGGACTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT
1562109 GAGACAAAAT
Statistics
Matches: 570, Mismatches: 41, Indels: 69
0.84 0.06 0.10
Matches are distributed among these distances:
89 21 0.04
90 4 0.01
93 29 0.05
94 21 0.04
95 52 0.09
96 2 0.00
100 1 0.00
101 3 0.01
102 25 0.04
103 2 0.00
104 68 0.12
105 80 0.14
106 36 0.06
107 161 0.28
108 65 0.11
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (104 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:1561967 original size:61 final size:61
Alignment explanation
Indices: 1561832--1562079 Score: 318
Period size: 61 Copynumber: 3.9 Consensus size: 61
1561822 GGGAGAAAGA
1561832 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAG----
*
1561897 AAG
60 -GG
* * *
1561900 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
1561961 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
1562023 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
1562080 GAAAAAAATG
Statistics
Matches: 161, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
60 5 0.03
61 70 0.43
62 31 0.19
66 6 0.04
67 19 0.12
68 24 0.15
69 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:1561970 original size:27 final size:26
Alignment explanation
Indices: 1561932--1562045 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 26
1561922 AAAAGAAAAA
*
1561932 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAA-G
1561959 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* * *
1561985 ATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
1562021 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
1562046 AGGAACAAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
26 4 0.06
27 26 0.37
28 17 0.24
34 17 0.24
35 2 0.03
36 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (26 bp):
GGTGCCACGGAGTTGTGGACTTAAAG
Found at i:1562028 original size:28 final size:27
Alignment explanation
Indices: 1561994--1562048 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1561984 GATGAAAAAA
*
1561994 GTGCCACAGAATTGTGGGCTTTAAAAGG
1 GTGCCACAGAATTGTGGAC-TTAAAAGG
* *
1562022 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAATTGTGGACTTAAAAGG
1562049 AACAAGGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAATTGTGGACTTAAAAGG
Found at i:1562092 original size:32 final size:33
Alignment explanation
Indices: 1562023--1562107 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 33
1562013 TTTAAAAGGG
* * **
1562023 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTATGGACTTAAAAGGAAAAAAA
* *
1562056 TGCCACGGAGTTATGGGCTTTAAA-GAAAAAAA
1 TGCCACGGAGTTATGGACTTAAAAGGAAAAAAA
* **
1562088 TGCCACTGAGTCGTGGACTT
1 TGCCACGGAGTTATGGACTT
1562108 TGAGACAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 21 0.50
33 21 0.50
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.22
Consensus pattern (33 bp):
TGCCACGGAGTTATGGACTTAAAAGGAAAAAAA
Found at i:1562122 original size:95 final size:93
Alignment explanation
Indices: 1561825--1562142 Score: 292
Period size: 95 Copynumber: 3.3 Consensus size: 93
1561815 TTAGGAAGGG
* *
1561825 AGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AGAAAAATGCCACGGAGTTGTGGACTTAAAA-GGAACAAG-GTGCCACGGAGTTGTGGGCTTT-A
* *
1561890 AAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
63 AAGAAAAAAATGCCACAGAGTTGTGGGCTTT
* * *
1561921 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT---A--AAC-GGGTGCCACGGAGTTGTGGAC-
1 ----AGAAAAA--TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCT
*
1561979 TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
60 TTAAAGA--AAAAAA-TGCCACAGAGTTGTGGGCTTT
** *
1562016 A-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA
1 AGAAA-AATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * *
1562080 GAAAAAAATGCCACTGAGTCGTGGACTTT
65 GAAAAAAATGCCACAGAGTTGTGGGCTTT
* *
1562109 GAGACAAAATGCCACTGAGTCGTGGACTTTAAAA
1 -AGA-AAAATGCCACGGAGTTGTGGAC-TTAAAA
1562143 AGGTATTTGA
Statistics
Matches: 179, Mismatches: 22, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
89 19 0.11
90 3 0.02
91 1 0.01
92 6 0.03
93 19 0.11
94 33 0.18
95 55 0.31
96 17 0.09
99 1 0.01
100 6 0.03
102 19 0.11
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (93 bp):
AGAAAAATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAG
AAAAAAATGCCACAGAGTTGTGGGCTTT
Found at i:1563119 original size:1 final size:1
Alignment explanation
Indices: 1563080--1563106 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1563070 TGAAAAGGGG
1563080 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1563107 GCATCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1566419 original size:1 final size:1
Alignment explanation
Indices: 1566413--1566441 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1566403 CCTTAAGAGC
1566413 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1566442 GGTGACCGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1570427 original size:52 final size:52
Alignment explanation
Indices: 1570357--1570477 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
1570347 GAAAATTTAT
1570357 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATGA-TGTATCGATACATCTGGGCAAATTTGC
*
1570409 CTGCATGTATCGATACATTTTATGATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATGATGTATCGATACATCTGGGCAAATTTGC
1570461 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1570478 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 66 0.99
53 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATGATGTATCGATACATCTGGGCAAATTTGC
Found at i:1570490 original size:52 final size:51
Alignment explanation
Indices: 1570357--1570497 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
1570347 GAAAATTTAT
1570357 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1570409 CTGCATGTATCGATACATT-TTATGATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTAATA-G-TGTATCGATACATCTGGGCAAATTTGC
*
1570461 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1570498 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
50 2 0.02
51 3 0.04
52 73 0.90
53 2 0.02
54 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1570504 original size:13 final size:13
Alignment explanation
Indices: 1570486--1570510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1570476 CAAAGATCAG
1570486 TGTATCGATACAA
1 TGTATCGATACAA
1570499 TGTATCGATACA
1 TGTATCGATACA
1570511 TGTGAGTAAT
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:1570593 original size:13 final size:13
Alignment explanation
Indices: 1570575--1570599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1570565 CAAAAAAATA
1570575 TGTATCGATACAT
1 TGTATCGATACAT
1570588 TGTATCGATACA
1 TGTATCGATACA
1570600 ACATTTTATG
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:1570595 original size:33 final size:33
Alignment explanation
Indices: 1570553--1570619 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1570543 AGTAGCTTAA
1570553 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1570586 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1570619 A
1 A
1570620 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1570974 original size:13 final size:13
Alignment explanation
Indices: 1570956--1570983 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1570946 CATTATTCAA
1570956 TGTATCGATACAT
1 TGTATCGATACAT
1570969 TGTATCGATACAT
1 TGTATCGATACAT
1570982 TG
1 TG
1570984 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1570978 original size:33 final size:33
Alignment explanation
Indices: 1570936--1571001 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1570926 GCCAAGGAAA
1570936 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
1570969 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
1571002 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:1583539 original size:21 final size:20
Alignment explanation
Indices: 1583510--1583552 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1583500 GACTAGTGTG
* *
1583510 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1583531 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1583551 GG
1 GG
1583553 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1584002 original size:13 final size:13
Alignment explanation
Indices: 1583986--1584021 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1583976 AATCCCCCTA
1583986 TATCGATACAGTG
1 TATCGATACAGTG
*
1583999 TATCGATACATTG
1 TATCGATACAGTG
1584012 TATCGATACA
1 TATCGATACA
1584022 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:1586264 original size:13 final size:13
Alignment explanation
Indices: 1586246--1586271 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1586236 CAATTTTTTG
1586246 TGTATCGATACAT
1 TGTATCGATACAT
1586259 TGTATCGATACAT
1 TGTATCGATACAT
1586272 ACTTGCTGTA
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:1588832 original size:13 final size:13
Alignment explanation
Indices: 1588814--1588852 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1588804 ATAATCACCC
1588814 TGTATCGATACAA
1 TGTATCGATACAA
1588827 TGTATCGATACAA
1 TGTATCGATACAA
* *
1588840 TATATCCATACAA
1 TGTATCGATACAA
1588853 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1590943 original size:15 final size:15
Alignment explanation
Indices: 1590923--1590953 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1590913 ATTTCGTTTG
*
1590923 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1590938 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1590953 G
1 G
1590954 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1591181 original size:21 final size:21
Alignment explanation
Indices: 1591152--1591196 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1591142 CAAATTTCAT
*
1591152 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1591172 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1591194 TTT
1 TTT
1591197 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1593432 original size:13 final size:13
Alignment explanation
Indices: 1593414--1593439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1593404 CAATTTTTTG
1593414 TGTATCGATACAT
1 TGTATCGATACAT
1593427 TGTATCGATACAT
1 TGTATCGATACAT
1593440 ACTTGCTGTA
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:1597979 original size:13 final size:13
Alignment explanation
Indices: 1597961--1597986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1597951 CAACTTTATG
1597961 TGTATCGATACAT
1 TGTATCGATACAT
1597974 TGTATCGATACAT
1 TGTATCGATACAT
1597987 ACTTTGTGTA
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:1598000 original size:32 final size:33
Alignment explanation
Indices: 1597941--1598004 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1597931 TACAGGCCAA
1597941 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
1597974 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
1598005 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:1603988 original size:37 final size:37
Alignment explanation
Indices: 1603938--1604022 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
1603928 TGCCACAATC
* *
1603938 ATGCATTTGTGACATTCATAACATTTTATTTTGCATG
1 ATGCATTTGTGACATTCACAACATTTCATTTTGCATG
1603975 ATGCATTTGTGACATTCACAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCACAACATTTCATTTTGCATG
1604012 ATGCATTTGTG
1 ATGCATTTGTG
1604023 CTTCATCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCACAACATTTCATTTTGCATG
Found at i:1604408 original size:29 final size:28
Alignment explanation
Indices: 1604372--1604725 Score: 369
Period size: 29 Copynumber: 12.4 Consensus size: 28
1604362 CCTCACCTTC
* *
1604372 CAAAGCCCACAAGTTAGTGGCGCCCTTTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* * *
1604401 CAAAGCCCATAAGTCAATGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
1604429 CAAAAGCCCACAAGTCTGTGGCAACC--TT
1 C-AAAGCCCACAAGTCAGTGGC-ACCTTTT
*
1604457 CAGAAGCCCATAAGTCAGTGGCACCTTTTT
1 CA-AAGCCCACAAGTCAGTGGCACC-TTTT
1604487 CAAAGCCCACAAGTCAGTGGCACTCTTTT
1 CAAAGCCCACAAGTCAGTGGCAC-CTTTT
*
1604516 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
1604544 CAAAAGCTCACAAGTCAGTGGCACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
* *
1604573 CAAAGCCCACAAGTTAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
* * *
1604601 CAAAAGCCCATAAGTTAGTGGCACCTCTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
*
1604630 CAAAGCCCATAAGTCAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* * *
1604657 CAGAAGCCCACAAGTCGGGGGCACCCCTTT
1 CA-AAGCCCACAAGTCAGTGGCA-CCTTTT
* *
1604687 CGAAGCCCACAAGTTAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
1604714 CAAAAGCCCACA
1 C-AAAGCCCACA
1604726 CAAGTTGGTG
Statistics
Matches: 279, Mismatches: 30, Indels: 33
0.82 0.09 0.10
Matches are distributed among these distances:
27 12 0.04
28 103 0.37
29 153 0.55
30 11 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCACCTTTT
Found at i:1604479 original size:57 final size:57
Alignment explanation
Indices: 1604373--1604725 Score: 355
Period size: 57 Copynumber: 6.2 Consensus size: 57
1604363 CTCACCTTCC
** * *
1604373 AAAGCCCACAAGT-TAGTGGCGCCCTTTTCAAAGCCCATAAGTCAATGGCATCTTTTCA
1 AAAGCCCACAAGTCT-GTGGCAACC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
1604431 AAAGCCCACAAGTCTGTGGCAACC-TTCAGAAGCCCATAAGTCAGTGGCACCTTTTTC-
1 AAAGCCCACAAGTCTGTGGCAACCTTTCA-AAGCCCACAAGTCAGTGGCATC-TTTTCA
*
1604488 AAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCTGTGGCAAC-C-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
* * *
1604546 AAAGCTCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCTGTGGCAACC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * *
1604603 AAAGCCCATAAGT-TAGTGGC-ACCTCTTCAAAGCCCATAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCT-GTGGCAACCT-TTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * * * * * *
1604659 GAAGCCCACAAGTCGGGGGCACCCCTTTCGAAGCCCACAAGTTAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCTGTGGCA-ACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
1604716 AAAGCCCACA
1 AAAGCCCACA
1604726 CAAGTTGGTG
Statistics
Matches: 258, Mismatches: 25, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
56 26 0.10
57 158 0.61
58 69 0.27
59 5 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (57 bp):
AAAGCCCACAAGTCTGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
Found at i:1604521 original size:86 final size:84
Alignment explanation
Indices: 1604366--1604725 Score: 406
Period size: 86 Copynumber: 4.2 Consensus size: 84
1604356 GACATTCCTC
* * * *
1604366 ACCTTCCAAAGCCCACAAGTTAGTGGCGCCCTTTTCAAAGCCCATAAGTCAATGGCATCTTTTCA
1 ACCTT-CAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
1604431 AAAGCCCACAAGTCT-GTGGCA
64 AAAGCCCACAAGT-TAGTGGCA
*
1604452 ACCTTCAGAAGCCCATAAGTCAGTGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 ACCTTCA-AAGCCCACAAGTCAGTGGCACC-TTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTC
*
1604517 -AAAGCCCACAAGTCAGTGGCA
63 AAAAGCCCACAAGTTAGTGGCA
* * * *
1604538 TCTTTTCAAAAGCTCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCA
1 AC-CTTC-AAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCA
*
1604603 AAAGCCCATAAGTTAGTGGCA
64 AAAGCCCACAAGTTAGTGGCA
* * * * * *
1604624 CCTCTTCAAAGCCCATAAGTCAGTGGCAACC--TTCAGAAGCCCACAAGTCGGGGGCACCCCTTT
1 AC-CTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTCA-AAGCCCACAAGTCAGTGGCA-TCTTTT
*
1604687 C-GAAGCCCACAAGTTAGTGGCA
62 CAAAAGCCCACAAGTTAGTGGCA
1604709 ACCTTCAAAAGCCCACA
1 ACCTTC-AAAGCCCACA
1604726 CAAGTTGGTG
Statistics
Matches: 237, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
84 8 0.03
85 75 0.32
86 123 0.52
87 30 0.13
88 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (84 bp):
ACCTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAA
AGCCCACAAGTTAGTGGCA
Found at i:1604579 original size:115 final size:113
Alignment explanation
Indices: 1604372--1604742 Score: 430
Period size: 115 Copynumber: 3.2 Consensus size: 113
1604362 CCTCACCTTC
* *
1604372 CAAAGCCCACAAGTTAGTGGCGCCCTTTTCAAAGCCCATAAGTCAATGGCATCTTTTCAAAAGCC
1 CAAAGCCCACAAGTTAGTGGC-ACCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAAGCC
* * *
1604437 CACAAGTCTGTGGCAACC-TTCAGAAGCCCATAAGTCAGTGGCACCTTTTT
65 CACAAGTCAGTGGC-ACCTTTCA-AAGCCCACAAGTTAGTGGCACCTTTTT
* * *
1604487 CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCT
1 CAAAGCCCACAAGTTAGTGGCAC-CTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAAGCC
*
1604552 CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATC-TTTT
65 CACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTTAGTGGCACCTTTTT
* * * * *
1604601 CAAAAGCCCATAAGTTAGTGGCACCTCTTCAAAGCCCATAAGTCAGTGGCAAC-CTTCAGAAGCC
1 C-AAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAAGCC
* * *
1604665 CACAAGTCGGGGGCACCCCTTTCGAAGCCCACAAGTTAGTGGCAACC---TT
65 CACAAGTCAGTGGCA--CCTTTCAAAGCCCACAAGTTAGTGGC-ACCTTTTT
*
1604714 CAAAAGCCCACACAAGTTGGTGGCACCTT
1 C-AAAG-CC-CACAAGTTAGTGGCACCTT
1604743 CATTTTTAAG
Statistics
Matches: 223, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
113 29 0.13
114 60 0.27
115 130 0.58
116 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (113 bp):
CAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAAGCCC
ACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTT
Found at i:1604868 original size:49 final size:49
Alignment explanation
Indices: 1604734--1605306 Score: 407
Period size: 52 Copynumber: 11.2 Consensus size: 49
1604724 CACAAGTTGG
* * * *
1604734 TGGCACCTTCATTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * *
1604783 TGGCGCCTTTGTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATTAGGACAT
1 TGGCACC--T-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* *
1604835 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* *
1604884 TGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACAT
1 TGGCACC--T-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * *
1604936 TGGCACCTTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATTAGCACAT
1 TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * * *
1604985 TGGCACCTTCATCTTTAAGCCCAATATTGCTGACCTTAAATCAGCATAT
1 TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
** *
1605034 TGGTGTCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTAGCACAT
1 TGG-CAC-CT-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAA-T----C---AGCACAT
* * * ** * * *
1605094 TAGCACCTTCACCTTTAACTCCAAAATCAC-AGCCTTGAATCAGCATAT
1 TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * ** *
1605142 TGGGATCTGTAACAT-TTCTAAACCCAATGTCGTTGGCCTTGAATCAGCACAT
1 TGGCACCT-T--CATCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * * *
1605194 TGGCATTCTTCTCATCTTCAAGTCTAATGTCGTTGACCGTGAATCAGCACAT
1 TGGCA--CCT-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * * *
1605246 TGACATTCTTTACATCTTTAAG-CCTAATATCACTGGTCC-TGAATCAGTATAT
1 TGGCA--CCTT-CATCTTTAAGTCC-AATGTCGCTGG-CCTTGAATCAGCACAT
1605298 TGGCACCTT
1 TGGCACCTT
1605307 TATCACTATT
Statistics
Matches: 411, Mismatches: 85, Indels: 55
0.75 0.15 0.10
Matches are distributed among these distances:
48 11 0.03
49 130 0.32
50 8 0.02
51 17 0.04
52 201 0.49
53 5 0.01
54 2 0.00
55 1 0.00
56 8 0.02
57 18 0.04
58 1 0.00
59 1 0.00
60 8 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
Found at i:1604909 original size:101 final size:101
Alignment explanation
Indices: 1604734--1605082 Score: 443
Period size: 101 Copynumber: 3.5 Consensus size: 101
1604724 CACAAGTTGG
* * *
1604734 TGGCACCTTCATTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACC
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
* *
1604799 TTTAAGTCCAATGTTGCTGGCCTTGAATTAGGACAT
66 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
1604835 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
**
1604900 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACAT
66 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
* * * * * *
1604936 TGGCACCTTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATTAGCACATTGGCACC--T-TCATC
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
* * * * *
1604998 TTTAAGCCCAATATTGCTGACCTTAAATCAGCATAT
66 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
** * * *
1605034 TGGTGTCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCA
1 TGG-CAC-CT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
1605083 CATTAGCACA
Statistics
Matches: 220, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
98 37 0.17
99 2 0.01
100 1 0.00
101 180 0.82
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (101 bp):
TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
Found at i:1605027 original size:150 final size:152
Alignment explanation
Indices: 1604742--1605091 Score: 542
Period size: 150 Copynumber: 2.3 Consensus size: 152
1604732 GGTGGCACCT
* * * * *
1604742 TCATTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCACCTTTAAGTC
* * *
1604807 CAATGTTGCTGGCCTTGAATTAGGACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTT
65 CAATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGCCCAATATCGCTGACCTT
*
1604872 GAATCAGCATATTGGCGCCTTTG
130 AAATCAGCATATTGGCGCCTTTG
*
1604895 TCATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACC-T-TCACCTTTAAGTCC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCACCTTTAAGTCC
*
1604958 AATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGCCCAATATTGCTGACCTTA
66 AATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGCCCAATATCGCTGACCTTA
* *
1605023 AATCAGCATATTGGTGTCTTTG
131 AATCAGCATATTGGCGCCTTTG
* *
1605045 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTAGCAC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1605092 ATTAGCACCT
Statistics
Matches: 181, Mismatches: 16, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
150 138 0.76
151 1 0.01
153 42 0.23
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (152 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCACCTTTAAGTCC
AATGTTGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGCCCAATATCGCTGACCTTA
AATCAGCATATTGGCGCCTTTG
Found at i:1605083 original size:101 final size:100
Alignment explanation
Indices: 1604734--1605306 Score: 429
Period size: 101 Copynumber: 5.6 Consensus size: 100
1604724 CACAAGTTGG
* * * * *
1604734 TGGCACCTTCATTTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACC
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATC
* *
1604799 TTTAAGTCCAATGTTGCTGGCCTTGAATTAGGACAT
65 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
* *
1604835 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATC
**
1604900 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACAT
65 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
* * * *
1604936 TGGCACCTTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATTAGCACATTGGCACC-T-TCATCT
1 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCT
* * * * *
1604999 TTAAGCCCAATATTGCTGACCTTAAATCAGCATAT
66 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
** * * * * *
1605034 TGGTGTCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTAGCACATTAGCA
1 TGG-CAC-CT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-G--
* * ** ** * *
1605099 CCTTCACCTTTAACTCCAAAATCAC-AGCCTTGAATCAGCATAT
60 ---TCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
* * ** * * * *
1605142 TGGGATCTGTAACAT-TTCTAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCT
1 TGGCACCT-T--CATCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTTGT
* * * * * *
1605206 CATCTTCAAGTCTAATGTCGTTGACCGTGAATCAGCACAT
61 CATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
* * * * *
1605246 TGACATTCTTTACATCTTTAAG-CCTAATATCACTGGTCC-TGAATCAGTATATTGGCACCTT
1 TGGCA--CCTT-CATCTTTAAGTCC-AATATCGCTGG-CCTTGAATCAGCACATTGGCACCTT
1605307 TATCACTATT
Statistics
Matches: 381, Mismatches: 70, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
98 37 0.10
99 2 0.01
100 1 0.00
101 188 0.49
102 1 0.00
103 19 0.05
104 48 0.13
105 5 0.01
106 4 0.01
107 3 0.01
108 55 0.14
109 18 0.05
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (100 bp):
TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCT
TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACAT
Found at i:1605976 original size:20 final size:20
Alignment explanation
Indices: 1605951--1606005 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1605941 TCGCCAAGGA
1605951 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
1605971 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
1605991 TTTGTATCGATACAT
1 AATGTATCGATACAT
1606006 CTGGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:1614853 original size:52 final size:52
Alignment explanation
Indices: 1614705--1614833 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1614695 CGAAATATGA
1614705 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
1614757 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATTTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1614809 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1614834 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1614860 original size:13 final size:13
Alignment explanation
Indices: 1614842--1614866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1614832 CAAAGATCAG
1614842 TGTATCGATACAA
1 TGTATCGATACAA
1614855 TGTATCGATACA
1 TGTATCGATACA
1614867 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:1615875 original size:102 final size:102
Alignment explanation
Indices: 1615745--1616002 Score: 489
Period size: 102 Copynumber: 2.5 Consensus size: 102
1615735 CTTAGGAATG
1615745 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGACAAAG
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGACAAAG
*
1615810 GCACCAATATGCCGATTCAAGGCCAGCGATATTGGAC
66 GCACCAATATGCCAATTCAAGGCCAGCGATATTGGAC
*
1615847 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGACAAAG
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGACAAAG
*
1615912 GCACCAATATGCTAATTCAAGGCCAGCGATATTGGAC
66 GCACCAATATGCCAATTCAAGGCCAGCGATATTGGAC
1615949 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
1616003 GAAGAATGCC
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 152 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.22
Consensus pattern (102 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGACAAAG
GCACCAATATGCCAATTCAAGGCCAGCGATATTGGAC
Found at i:1615885 original size:49 final size:49
Alignment explanation
Indices: 1615745--1616146 Score: 365
Period size: 49 Copynumber: 8.1 Consensus size: 49
1615735 CTTAGGAATG
*
1615745 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
1615794 TTAAAAGGTGACAAAGGC-ACCAATATGCCGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATG---AA-GCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1615847 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
1615896 TTAAAAGGTGACAAAGGC-ACCAATATGCTAATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATG---AA-GCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
*
1615949 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *** **
1615998 TTAAAGAAGAA--TGCCAATGTGTTGATTCAAGGCCAATAACATTTGGGTT
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACA-TT-GGAC
* * * * * * *
1616047 TTAAAGATGATGGTGCTAATATGCTAATTCAAGACCAGCGATATTGGAC
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
1616096 TT-AA-A-G--G-TGTCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1616139 TTAGAAGA
1 TTA-AAGA
1616147 AGATGCCACC
Statistics
Matches: 287, Mismatches: 47, Indels: 41
0.77 0.13 0.11
Matches are distributed among these distances:
43 33 0.11
44 1 0.00
45 2 0.01
46 2 0.01
47 27 0.09
48 7 0.02
49 95 0.33
50 14 0.05
51 21 0.07
52 12 0.04
53 70 0.24
54 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (49 bp):
TTAAAGATGAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:1616137 original size:141 final size:143
Alignment explanation
Indices: 1615813--1616154 Score: 404
Period size: 141 Copynumber: 2.3 Consensus size: 143
1615803 GACAAAGGCA
* * *
1615813 CCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGCTGCCAATGTGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAA--TGCCAATGTGCTGATTCA
* * * *
1615878 AGGCCAGCGACATTGGACTTAAAAGGTGACAAAGGCACCAATATGCTAATTCAAGGCCAGCGATA
64 AGGCCAACAACATTGGACTTAAAAGATG--AAAGGCACCAATATGCTAATTCAAGACCAGCGATA
1615943 TTGGACTTAAAGATGAAGGTG
127 TTGGACTT--A-A-GAAGGTG
* *
1615964 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGTTGATTCAAG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAATGCCAATGTGCTGATTCAAG
* ** * * ** *
1616029 GCCAATAACATTTGGGTTTTAAAGATG-ATGGTGCTAATATGCTAATTCAAGACCAGCGATATTG
66 GCCAACAACA-TTGGACTTAAAAGATGAAAGGCACCAATATGCTAATTCAAGACCAGCGATATTG
1616093 GACTT-A-AAGGTG
130 GACTTAAGAAGGTG
*
1616105 TCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGAAG-ATGCCA
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGAAGAATGCCA
1616155 CCAACTTTTG
Statistics
Matches: 170, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
141 47 0.28
142 6 0.04
143 1 0.01
147 37 0.22
149 26 0.15
150 12 0.07
151 41 0.24
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (143 bp):
CCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAGAATGCCAATGTGCTGATTCAAG
GCCAACAACATTGGACTTAAAAGATGAAAGGCACCAATATGCTAATTCAAGACCAGCGATATTGG
ACTTAAGAAGGTG
Found at i:1616251 original size:58 final size:55
Alignment explanation
Indices: 1616162--1616470 Score: 305
Period size: 58 Copynumber: 5.3 Consensus size: 55
1616152 CCACCAACTT
** * * *
1616162 TTGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGAC
1 TTGTGGGC-TTTG-AAGGG-TGCCACTGACTTGTGGGCTTTAGAAGGATGCCACTGAC
* *
1616219 TTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGAC
1 TTGTGGGCTTT-G--AAGGGTGCCACTGACTTGTGGGCTTTAG-AAGGATGCCACTGAC
* * * *
1616278 TTGTGGGCTTTTGAAGGATCCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGAT
1 TTGTGGGC-TTTGAAGGGTGCCACTGACTTGTGGGCTTT---AGAAGGATGCCACTGAC
* * *
1616337 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGAT
1 TTGTGGGCTTTGAAGGGTGCCACTGACTTGTGGGCTTT---AGAAGGATGCCACTGAC
* * *
1616395 TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGAC
1 TTGTGGGCTTTGAAGGGTGCCACTGACTTGTGGGCTTT-AGAAGGATGCCACTGAC
*
1616451 TTGTAGGCTTTTGAAGGGTG
1 TTGTGGGC-TTTGAAGGGTG
1616471 AGGTAATATC
Statistics
Matches: 223, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
56 24 0.11
57 45 0.20
58 108 0.48
59 42 0.19
60 4 0.02
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.31
Consensus pattern (55 bp):
TTGTGGGCTTTGAAGGGTGCCACTGACTTGTGGGCTTTAGAAGGATGCCACTGAC
Found at i:1616308 original size:87 final size:86
Alignment explanation
Indices: 1616189--1616467 Score: 368
Period size: 87 Copynumber: 3.2 Consensus size: 86
1616179 GGTTGCACCA
* *
1616189 ACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTG
1 ACTTGTGGGCTTTTGAAGGATGCCACTGACTTGTGGGCTTTGG-AAAGGGTGCCACTGACTTGTG
1616254 GGCTTTGGAAAAGATGCCACTG
65 GGCTTTGGAAAAGATGCCACTG
* *
1616276 ACTTGTGGGCTTTTGAAGGATCCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGT
1 ACTTGTGGGCTTTTGAAGGATGCCACTGACTTGTGGGCTTT-GGA-AAGGGTGCCACTGACTTGT
* *
1616341 GGGCTTT-G-AAGGTTGCCACTG
64 GGGCTTTGGAAAAGATGCCACTG
* * * *
1616362 ACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTT-G-AAGGTTGCCACTGACTTG
1 ACTTGTGGGCTTT---TGAAGGATGCCACTGACTTGTGGGCTTTGGAAAGGGTGCCACTGACTTG
*
1616425 TGGGCTTTGAAAAAGATGCCACTG
63 TGGGCTTTGGAAAAGATGCCACTG
*
1616449 ACTTGTAGGCTTTTGAAGG
1 ACTTGTGGGCTTTTGAAGG
1616468 GTGAGGTAAT
Statistics
Matches: 168, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
84 5 0.03
85 24 0.14
86 24 0.14
87 64 0.38
88 27 0.16
89 24 0.14
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (86 bp):
ACTTGTGGGCTTTTGAAGGATGCCACTGACTTGTGGGCTTTGGAAAGGGTGCCACTGACTTGTGG
GCTTTGGAAAAGATGCCACTG
Found at i:1617920 original size:12 final size:11
Alignment explanation
Indices: 1617905--1618013 Score: 96
Period size: 12 Copynumber: 9.3 Consensus size: 11
1617895 TTTGTTGTTG
1617905 TTGTTTTTGTTT
1 TTGTTTTT-TTT
*
1617917 TTG-TTTTTTG
1 TTGTTTTTTTT
1617927 TTG-TTTTTTT
1 TTGTTTTTTTT
1617937 TTGCTTTTTTTT
1 TTG-TTTTTTTT
1617949 TTGCTTTGTTTTT
1 TTG-TTT-TTTTT
1617962 TTGTTTTTTTT
1 TTGTTTTTTTT
1617973 TTGTCTTCTTCTTT
1 TTGT-TT-TT-TTT
*
1617987 TTTTTTTGTTTAT
1 TTGTTTT-TTT-T
*
1618000 TTGGTTTTTTT
1 TTGTTTTTTTT
1618011 TTG
1 TTG
1618014 GTGGAGGACG
Statistics
Matches: 84, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
10 14 0.17
11 17 0.20
12 28 0.33
13 19 0.23
14 6 0.07
ACGTcount: A:0.01, C:0.05, G:0.13, T:0.82
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:1617927 original size:22 final size:21
Alignment explanation
Indices: 1617893--1617996 Score: 79
Period size: 22 Copynumber: 4.7 Consensus size: 21
1617883 ATCCGGACCC
*
1617893 TTTTTG-TTGTTGTTGTTTTT
1 TTTTTGTTTTTTGTTGTTTTT
1617913 GTTTTTGTTTTTTGTTG-TTTT
1 -TTTTTGTTTTTTGTTGTTTTT
*
1617934 TTTTTGCTTTTTTTTTTGCTTTGTT
1 TTTTTG--TTTTTTGTTG-TTT-TT
*
1617959 TTTTTGTTTTTTTTTTGTCTTCTT
1 TTTTTG-TTTTTTGTTGT-TT-TT
*
1617983 CTTTT-TTTTTTGTT
1 TTTTTGTTTTTTGTT
1617997 TATTTGGTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
20 6 0.08
21 10 0.14
22 25 0.35
23 1 0.01
24 21 0.30
25 8 0.11
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (21 bp):
TTTTTGTTTTTTGTTGTTTTT
Found at i:1617935 original size:38 final size:37
Alignment explanation
Indices: 1617893--1618011 Score: 111
Period size: 38 Copynumber: 3.1 Consensus size: 37
1617883 ATCCGGACCC
*
1617893 TTTTTGTTG-TTGTTGTTTTTGTTTTTGTTTTTTGTTGT
1 TTTTTGTTGCTT-TTCTTTTTGTTTTTGTTTTTTGTT-T
* * *
1617931 TTTTTTTTGCTTTTTTTTTTG-CTTTGTTTTTTTGTTT
1 TTTTTGTTGCTTTTCTTTTTGTTTTTG-TTTTTTGTTT
1617968 TTTTT-TTGTCTTCTTCTTTTT-TTTTTGTTTATTTGGTTT
1 TTTTTGTTG-CTT-TTCTTTTTGTTTTTGTTT-TTT-GTTT
1618007 TTTTT
1 TTTTT
1618012 TGGTGGAGGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
36 3 0.04
37 16 0.23
38 39 0.57
39 11 0.16
ACGTcount: A:0.01, C:0.04, G:0.13, T:0.82
Consensus pattern (37 bp):
TTTTTGTTGCTTTTCTTTTTGTTTTTGTTTTTTGTTT
Found at i:1617936 original size:25 final size:23
Alignment explanation
Indices: 1617893--1618013 Score: 93
Period size: 25 Copynumber: 4.9 Consensus size: 23
1617883 ATCCGGACCC
* *
1617893 TTTTTGTTGTTGTTGTTTTTGTTT
1 TTTTTTTTGTT-TTTTTTTTGTTT
*
1617917 TTGTTTTTTGTTGTTTTTTTTTGCTT
1 TT-TTTTTTG-T-TTTTTTTTTGTTT
1617943 TTTTTTTTGCTTTGTTTTTTTG-TT
1 TTTTTTTTG-TTT-TTTTTTTGTTT
1617967 TTTTTTTTGTCTTCTTCTTTTT-TTT
1 TTTTTTTTGT-TT-TT-TTTTTGTTT
*
1617992 TTGTTTATTTGGTTTTTTTTTG
1 TT-TTT-TTTGTTTTTTTTTTG
1618014 GTGGAGGACG
Statistics
Matches: 81, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.01
24 24 0.30
25 33 0.41
26 18 0.22
27 5 0.06
ACGTcount: A:0.01, C:0.04, G:0.14, T:0.81
Consensus pattern (23 bp):
TTTTTTTTGTTTTTTTTTTGTTT
Found at i:1618012 original size:38 final size:34
Alignment explanation
Indices: 1617908--1618013 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 34
1617898 GTTGTTGTTG
*
1617908 TTTTTGTTTTTGTTTTTTGTTGTTTTTTTTTGCTTT
1 TTTTTTTTTTTGTTTTTTG--GTTTTTTTTTGCTTT
* *
1617944 TTTTTTTGCTTTGTTTTTTTGTTTTTTTTTTGTCTTCT
1 TTTTTTT-TTTTG-TTTTTTGGTTTTTTTTTG-CTT-T
1617982 TCTTTTTTTTTTGTTTATTTGGTTTTTTTTTG
1 T-TTTTTTTTTTGTTT-TTTGGTTTTTTTTTG
1618014 GTGGAGGACG
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
36 16 0.27
37 10 0.17
38 27 0.46
39 6 0.10
ACGTcount: A:0.01, C:0.05, G:0.12, T:0.82
Consensus pattern (34 bp):
TTTTTTTTTTTGTTTTTTGGTTTTTTTTTGCTTT
Found at i:1618012 original size:51 final size:50
Alignment explanation
Indices: 1617902--1618012 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 50
1617892 CTTTTTGTTG
* * *
1617902 TTGTTGTTTTTGTTTTTGTTTTTTGTTGTTTTTTTTTGCTTTTTTTTTTGCT
1 TTGTT-TTTTTGTTTTTGTTTTTTCTTCTTTTTTTTT-CTTTTTTATTTGCT
*
1617954 TTGTTTTTTTGTTTTT-TTTTTGTCTTCTTCTTTTTTT-TTTGTTTATTTGGT
1 TTGTTTTTTTGTTTTTGTTTTT-TCTTCTT-TTTTTTTCTTT-TTTATTTGCT
1618005 TT-TTTTTT
1 TTGTTTTTT
1618013 GGTGGAGGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
50 14 0.27
51 26 0.50
52 12 0.23
ACGTcount: A:0.01, C:0.05, G:0.13, T:0.82
Consensus pattern (50 bp):
TTGTTTTTTTGTTTTTGTTTTTTCTTCTTTTTTTTTCTTTTTTATTTGCT
Found at i:1631633 original size:52 final size:52
Alignment explanation
Indices: 1631485--1631613 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1631475 CGAAATATGA
* *
1631485 AAATTTGCCTGCATGTGTCGATACATTTCATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
1631537 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1631589 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1631614 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:1631640 original size:13 final size:13
Alignment explanation
Indices: 1631622--1631646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1631612 CAAAGATCAG
1631622 TGTATCGATACAA
1 TGTATCGATACAA
1631635 TGTATCGATACA
1 TGTATCGATACA
1631647 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:1631713 original size:19 final size:19
Alignment explanation
Indices: 1631689--1631738 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1631679 TAGCTTACAT
*
1631689 TGTATCAATATAAAACTTA
1 TGTATCAATACAAAACTTA
* *
1631708 TGTATCGATACAACACTTA
1 TGTATCAATACAAAACTTA
*
1631727 TGTATCGATACA
1 TGTATCAATACA
1631739 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (19 bp):
TGTATCAATACAAAACTTA
Found at i:1631745 original size:13 final size:13
Alignment explanation
Indices: 1631727--1631751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1631717 ACAACACTTA
1631727 TGTATCGATACAT
1 TGTATCGATACAT
1631740 TGTATCGATACA
1 TGTATCGATACA
1631752 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:1631749 original size:32 final size:33
Alignment explanation
Indices: 1631708--1631771 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1631698 ATAAAACTTA
1631708 TGTATCGATACAACAC-TTATGTATCGATACAT
1 TGTATCGATACAACACTTTATGTATCGATACAT
*
1631740 TGTATCGATACAACACTTTATGTATTGATACA
1 TGTATCGATACAACACTTTATGTATCGATACA
1631772 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAACACTTTATGTATCGATACAT
Found at i:1637563 original size:13 final size:13
Alignment explanation
Indices: 1637545--1637570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1637535 TACACAAAGT
1637545 ATGTATCGATACA
1 ATGTATCGATACA
1637558 ATGTATCGATACA
1 ATGTATCGATACA
1637571 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:1637568 original size:32 final size:33
Alignment explanation
Indices: 1637527--1637590 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1637517 TAGCCAAACT
**
1637527 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1637559 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1637591 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:1638489 original size:20 final size:20
Alignment explanation
Indices: 1638464--1638587 Score: 124
Period size: 20 Copynumber: 5.8 Consensus size: 20
1638454 TTTTCACAAT
*
1638464 TTGTATCGTTACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1638484 TTGTATCGGTACATTGTTCA
1 TTGTATCGATACATTGTTCA
1638504 TTGTATCGATACATTCTGGGTTTACA
1 TTGTATCGATACA-T-T--G-TT-CA
1638530 TAGATGTATCGATACATT-TTGCA
1 T---TGTATCGATACATTGTT-CA
*
1638553 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1638573 TTGTATCGATACATT
1 TTGTATCGATACATT
1638588 TTACAATGTA
Statistics
Matches: 90, Mismatches: 4, Indels: 20
0.79 0.04 0.18
Matches are distributed among these distances:
20 62 0.69
21 2 0.02
22 1 0.01
23 5 0.06
24 1 0.01
25 2 0.02
26 3 0.03
27 1 0.01
28 1 0.01
29 12 0.13
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1638597 original size:20 final size:19
Alignment explanation
Indices: 1638533--1638608 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
1638523 GTTTACATAG
1638533 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTT-CA
* *
1638553 TTGTATCGATACATTGCTCA
1 ATGTATCGATACATT-TTCA
*
1638573 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTTT-CA
* *
1638593 ATGTATTGATATATTT
1 ATGTATCGATACATTT
1638609 AGGCATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:1640985 original size:51 final size:50
Alignment explanation
Indices: 1640910--1641074 Score: 186
Period size: 51 Copynumber: 3.2 Consensus size: 50
1640900 TTCATCTCGA
* * *
1640910 GGATACTCCAACCCCGGTTCCATTTCCAAAACATCAATTTTTCCTAATCGG
1 GGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCC-AATCGG
* * * * ** *
1640961 GGATACTCTAACTCCGATTTCATTTCTAAAGCATCGATTTACCGCAATGGG
1 GGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTC-CAATCGG
* * *
1641012 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGG
1 GGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTC-CAATCGG
1641063 GGATACTCCAAC
1 GGATACTCCAAC
1641075 CCCATTATTT
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 92 0.99
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (50 bp):
GGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCCAATCGG
Found at i:1641117 original size:26 final size:28
Alignment explanation
Indices: 1641062--1641131 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1641052 TTCACAATTG
*
1641062 GGGATACTCCAACCCCATTATTTCATCGA
1 GGGATACTCCAACCACATTATTTCA-CGA
**
1641091 -GGATACTCCAACCATGTTATTTC-CGA
1 GGGATACTCCAACCACATTATTTCACGA
1641117 GGGGATACTCCAACC
1 -GGGATACTCCAACC
1641132 TCGGCTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.08
28 33 0.92
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (28 bp):
GGGATACTCCAACCACATTATTTCACGA
Found at i:1641208 original size:28 final size:30
Alignment explanation
Indices: 1641169--1641242 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
1641159 TTTTTTCATA
1641169 ATCGTGGG-TACTCCAACT-CCA-TTATTTC
1 ATCG-GGGATACTCCAACTCCCAGTTATTTC
1641197 ATCGGGGATACTCCAA-TCCCAGTTATTTC
1 ATCGGGGATACTCCAACTCCCAGTTATTTC
***
1641226 CGAGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
1641243 CCCGATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.10
28 15 0.38
29 20 0.51
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (30 bp):
ATCGGGGATACTCCAACTCCCAGTTATTTC
Found at i:1641284 original size:51 final size:51
Alignment explanation
Indices: 1641229--1641400 Score: 204
Period size: 51 Copynumber: 3.4 Consensus size: 51
1641219 TTATTTCCGA
* *
1641229 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTCCACAATC
* * * *
1641280 GGGGATACTCCAACTCCGATTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTC-CACAATC
* *** *
1641331 GGGGGATACTTCAACCCCGGCCTTATTTCT-AAATCATCGATTTTTCACAATC
1 -GGGGATACTCCAACCCCGATTTTATTTCTAAAAT-ATCGATTTTCCACAATC
1641383 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1641401 TTATTTTCGA
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.04
51 61 0.60
52 33 0.33
53 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTCCACAATC
Found at i:1641307 original size:111 final size:107
Alignment explanation
Indices: 1641010--1641296 Score: 362
Period size: 111 Copynumber: 2.6 Consensus size: 107
1641000 TACCGCAATG
* * * *
1641010 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
*
1641075 CCCATTATTTCATCGAGGATACTCCAACCATGTTATTTCCGA
66 TCCATTATTTCATCGAGGATACTCCAACCATGTTATTTCCGA
* ** * ** * *
1641117 GGGGATACTCCAACCTCGGCTTTATATCTAAAAATATTGATGTTTTTTCATAATCGTGGG-TACT
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAATA-CCA--ATTTTTCACAATCG-GGGATACT
*
1641181 CCAACTCCATTATTTCATCGGGGATACTCCAATCCCA-GTTATTTCCGA
61 CCAACTCCATTATTTCATCGAGGATACTCCAA--CCATGTTATTTCCGA
*
1641229 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1641294 TCC
66 TCC
1641297 GATTTTATTT
Statistics
Matches: 149, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
107 26 0.17
108 28 0.19
109 1 0.01
110 1 0.01
111 51 0.34
112 39 0.26
113 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
TCCATTATTTCATCGAGGATACTCCAACCATGTTATTTCCGA
Found at i:1641467 original size:79 final size:80
Alignment explanation
Indices: 1641332--1641516 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 80
1641322 CTCATAATCG
* ** * *
1641332 GGGGATACTTCAACCCCGGCCTTA-TTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAATCATCGATTTTTCACAATCAGGGATACTCCAA
* *
1641396 CCCCGTTATTTTCGA
66 CCCCGTTATTTCCAA
* *
1641411 GGGGATACTCCAACCCCGATTTTATTTTCAAAAT-ATCGA-TTTTCTATAATCAGGGATACTCCA
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAATCATCGATTTTTC-ACAATCAGGGATACTCCA
*
1641474 ACCCTGTTATTTCCAA
65 ACCCCGTTATTTCCAA
*
1641490 GGGAATACTCCAACCCCGGTTTTATTT
1 GGGGATACTCCAACCCCGGTTTTATTT
1641517 CTGGAACACC
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 5 0.05
79 79 0.86
80 8 0.09
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGGTTTTATTTTCAAAATCATCGATTTTTCACAATCAGGGATACTCCAA
CCCCGTTATTTCCAA
Found at i:1641532 original size:79 final size:78
Alignment explanation
Indices: 1641370--1641560 Score: 213
Period size: 79 Copynumber: 2.4 Consensus size: 78
1641360 TAAATCATCG
* * * * *
1641370 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTCCATAATC-GGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTA
* * *
1641435 TTTTCAAAATATCG
65 TTTTCAAAACACCA
* * *
1641449 ATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGGTTTTA
1 ATTTTCCATAATC-GGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTA
**
1641514 -TTTCTGGAACACCA
65 TTTTC-AAAACACCA
*
1641528 ATTTTCCATAATCGGAGATACTCCAGCCCCGTT
1 ATTTTCCATAATCGG-GATACTCCAACCCCGTT
1641561 GTTATCTCAA
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
78 6 0.06
79 87 0.94
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (78 bp):
ATTTTCCATAATCGGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTAT
TTTCAAAACACCA
Found at i:1647328 original size:15 final size:15
Alignment explanation
Indices: 1647308--1647338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1647298 TAAAAATGTC
*
1647308 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1647323 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1647338 C
1 C
1647339 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1649437 original size:13 final size:13
Alignment explanation
Indices: 1649419--1649456 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1649409 CATTTTTCTT
1649419 TGTATCGATACAA
1 TGTATCGATACAA
*
1649432 TGTATCGATACAC
1 TGTATCGATACAA
1649445 TGTATCGATACA
1 TGTATCGATACA
1649457 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1649611 original size:20 final size:20
Alignment explanation
Indices: 1649568--1649613 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1649558 AAATCTTTTG
1649568 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1649589 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1649609 CAAAA
1 CAAAA
1649614 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1651357 original size:39 final size:40
Alignment explanation
Indices: 1651290--1651380 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
1651280 GGGAGATTTT
* * *
1651290 TTTAGTAAAAGGGGAGAATGCGTAAATTTGCTAAAATTA-
1 TTTAGTTAAGGGGGAGAATGCATAAATTTGCTAAAATTAC
* * *
1651329 TCTTA-TTAAGGGGGAGAATGTATGAATTTGTTAAAATTAC
1 T-TTAGTTAAGGGGGAGAATGCATAAATTTGCTAAAATTAC
1651369 TTTAGTTAAGGG
1 TTTAGTTAAGGG
1651381 AGAAAGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.74
40 11 0.26
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (40 bp):
TTTAGTTAAGGGGGAGAATGCATAAATTTGCTAAAATTAC
Found at i:1651928 original size:20 final size:20
Alignment explanation
Indices: 1651900--1651953 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1651890 AAAACCCTTA
*
1651900 AAAGGATCGATACACAATT-C
1 AAAGTATCGATACA-AATTGC
*
1651920 AAAGTATCGATACAAGTTGC
1 AAAGTATCGATACAAATTGC
*
1651940 AATGTATCGATACA
1 AAAGTATCGATACA
1651954 TGAAAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
AAAGTATCGATACAAATTGC
Found at i:1653542 original size:4 final size:4
Alignment explanation
Indices: 1653533--1653563 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1653523 TTTTGAGGTG
*
1653533 TTTA TTTA TTTA TTTA TTTA TTTG TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1653564 TGTTTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1663885 original size:11 final size:11
Alignment explanation
Indices: 1663869--1663897 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1663859 TTTTTTTTAG
1663869 AAAAAAACAAC
1 AAAAAAACAAC
1663880 AAAAAAACAAC
1 AAAAAAACAAC
1663891 AAAAAAA
1 AAAAAAA
1663898 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:1663904 original size:7 final size:7
Alignment explanation
Indices: 1663892--1663925 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
1663882 AAAAACAACA
1663892 AAAAAAG
1 AAAAAAG
1663899 AAAAAAG
1 AAAAAAG
1663906 AAAAAAG
1 AAAAAAG
1663913 AAAGAAAAG
1 -AA-AAAAG
1663922 AAAA
1 AAAA
1663926 GAACTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 16 0.64
8 4 0.16
9 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1663904 original size:18 final size:18
Alignment explanation
Indices: 1663881--1663920 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1663871 AAAAACAACA
1663881 AAAAAACAACAAAA-AAAG
1 AAAAAACAA-AAAAGAAAG
*
1663899 AAAAAAGAAAAAAGAAAG
1 AAAAAACAAAAAAGAAAG
1663917 AAAA
1 AAAA
1663921 GAAAAGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAGAAAG
Found at i:1663928 original size:14 final size:14
Alignment explanation
Indices: 1663892--1663925 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
1663882 AAAAACAACA
1663892 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
1663906 AAAAAAGAAAGAAAAG
1 AAAAAAG-AA-AAAAG
1663922 AAAA
1 AAAA
1663926 GAACTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:1665017 original size:61 final size:59
Alignment explanation
Indices: 1664919--1665142 Score: 223
Period size: 61 Copynumber: 3.9 Consensus size: 59
1664909 AGTAGGATGC
* * *
1664919 CTTTTAAAGCCCACACAAGTTGGTGGCACGTCCCAGTCCTCAAAGAGTAGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCC-TTT
* *
1664979 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
1 C-TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTT
* * ** ** *
1665039 C----AAACCCCACACAAGCTGGTGGCATTTTTTTAGTCCTCAAAGAGCGGGATG-C---
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCCAGTCCTCAAAGAGCAGGATGCCTTT
* *
1665091 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTTAAAGAACAGGA
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGA
1665143 CGCTCTCTCC
Statistics
Matches: 137, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
52 1 0.01
54 2 0.01
55 37 0.27
56 42 0.31
60 5 0.04
61 50 0.36
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (59 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTT
Found at i:1665226 original size:56 final size:58
Alignment explanation
Indices: 1665165--1665415 Score: 291
Period size: 61 Copynumber: 4.3 Consensus size: 58
1665155 TCGCCCTTTT
* *
1665165 GTCCTCAAAGAGTAGGACGC-CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTA
1 GTCCTCAAAGAGCAGGACGCTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCA
*
1665221 GTCCTCAAAGAGCAGGACGC-C-TTTCAAAGCCCACACAAGTCGGTGGCA-TTTTCCA
1 GTCCTCAAAGAGCAGGACGCTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCA
* * *
1665276 GTCCTCAAAGAGCAGCATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCCA
1 GTCCTCAAAGAGCAGGACGC--TC-TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCCA
* * *
1665337 GTCCTCAAAGAGCAAGACGTCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TA
1 GTCCTCAAAGAGCAGGACG-C---TCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCA
*
1665398 GTCCTCAAAAAGCAGGAC
1 GTCCTCAAAGAGCAGGAC
1665416 ACACTTTATT
Statistics
Matches: 169, Mismatches: 15, Indels: 17
0.84 0.07 0.08
Matches are distributed among these distances:
55 27 0.16
56 42 0.25
58 1 0.01
60 3 0.02
61 85 0.50
62 7 0.04
63 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (58 bp):
GTCCTCAAAGAGCAGGACGCTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCA
Found at i:1665286 original size:150 final size:150
Alignment explanation
Indices: 1665015--1665286 Score: 427
Period size: 150 Copynumber: 1.8 Consensus size: 150
1665005 GCACCTTTCA
* *
1665015 GTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCTGGTGGCATTTTTTTAGTCCTCAAA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAA
* * * * *
1665080 GAGCGGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTTAAAGAACAGGACG
66 GAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTCCCAGTCCTCAAAGAACAGGACG
1665145 CTCTCTCCTTTCGCCCTTTT
131 CTCTCTCCTTTCGCCCTTTT
* * * *
1665165 GTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAA
* *
1665230 GAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGA
66 GAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTCCCAGTCCTCAAAGA
1665287 GCAGCATGCT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
150 109 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (150 bp):
GTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAA
GAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTCCCAGTCCTCAAAGAACAGGACG
CTCTCTCCTTTCGCCCTTTT
Found at i:1665444 original size:42 final size:41
Alignment explanation
Indices: 1665393--1665635 Score: 152
Period size: 46 Copynumber: 5.5 Consensus size: 41
1665383 TGGTGGCACT
*
1665393 TTTTAGTCCTCAAAAAGCAGGACACACTTT-ATTTTCCTCTTTA
1 TTTT-GTCCTCAAAGAGCAGGACACA-TTTCATTTTCCT-TTTA
* * *
1665436 TTTTGTCCTCAAAGAGCAGGACGCATTTCGTTTTCCTTTTT
1 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTA
* * ** *
1665477 TCCTTTGTCTTCAAAGAGCAGGACACATTCCATTCCCTTATTTTCTCC
1 T--TTTGTCCTCAAAGAGCAGGACACATTTCATT---TTCCTTT-T-A
* * *
1665525 TTTTGTCCTCAAAGAGCAGGACGCACTTCA-TTTCCTTCTTT
1 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTT-TTA
* *
1665566 TCCCTTCTAGTCCTTAAAGAGCAGGACACATTTTATTTTCCCTTTT-
1 T---TT-T-GTCCTCAAAGAGCAGGACACATTTCATTTT-CCTTTTA
1665612 TCCTTTGTCCTCGAAA-AGCAGGAC
1 T--TTTGTCCTC-AAAGAGCAGGAC
1665636 GTACTCTTTT
Statistics
Matches: 160, Mismatches: 23, Indels: 34
0.74 0.11 0.16
Matches are distributed among these distances:
41 8 0.05
42 31 0.19
43 45 0.28
44 6 0.04
45 6 0.04
46 53 0.33
47 6 0.04
48 5 0.03
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (41 bp):
TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTA
Found at i:1665543 original size:46 final size:46
Alignment explanation
Indices: 1665436--1665635 Score: 170
Period size: 46 Copynumber: 4.5 Consensus size: 46
1665426 TTCCTCTTTA
* * **
1665436 TTTTGTCCTCAAAGAGCAGGACGCATTTCGTTTTCC-TTTTT-TCC
1 TTTTGTCCTCAAAGAGCAGGACACACTTCCATTTCCTTTTTTCTCC
* *
1665480 -TTTGTCTTCAAAGAGCAGGACACA-TTCCATTCCCTTATTTTCTCC
1 TTTTGTCCTCAAAGAGCAGGACACACTTCCATTTCCTT-TTTTCTCC
*
1665525 TTTTGTCCTCAAAGAGCAGGACGCACTT-CATTTCCTTCTTTTC-CC
1 TTTTGTCCTCAAAGAGCAGGACACACTTCCATTTCCTT-TTTTCTCC
* * ** *
1665570 TTCTAGTCCTTAAAGAGCAGGACACA-TTTTATTTTCC-CTTTT-TCC
1 TT-TTGTCCTCAAAGAGCAGGACACACTTCCA-TTTCCTTTTTTCTCC
1665615 -TTTGTCCTCGAAA-AGCAGGAC
1 TTTTGTCCTC-AAAGAGCAGGAC
1665636 GTACTCTTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 21
0.78 0.10 0.13
Matches are distributed among these distances:
42 7 0.05
43 37 0.28
44 8 0.06
45 15 0.12
46 56 0.43
47 7 0.05
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (46 bp):
TTTTGTCCTCAAAGAGCAGGACACACTTCCATTTCCTTTTTTCTCC
Found at i:1665619 original size:89 final size:87
Alignment explanation
Indices: 1665394--1665636 Score: 259
Period size: 89 Copynumber: 2.8 Consensus size: 87
1665384 GGTGGCACTT
* * * *
1665394 TTTAGTCCTCAAAAAGCAGGACACACTTTATTTTCCTCTTTAT--TTTGTCCTCAAAGAGCAGGA
1 TTTAGTCCTTAAAGAGCAGGACACATTTTATTTTCC-CTTTTTCCTTTGTCCTCAAAGAGCAGGA
* *
1665457 CGCATTTCGTTTTCCTTTTTTCC
65 CGCACTTCGATTTCCTTTTTTCC
**
1665480 TTT-GT-CTTCAAAGAGCAGGACACATTCCA--TTCCCTTATTTTCTCCTTTTGTCCTCAAAGAG
1 TTTAGTCCTT-AAAGAGCAGGACACATTTTATTTTCCC---TTTT-TCC-TTTGTCCTCAAAGAG
1665541 CAGGACGCACTTC-ATTTCCTTCTTTTCCC
60 CAGGACGCACTTCGATTTCCTT-TTTT-CC
1665570 TTCTAGTCCTTAAAGAGCAGGACACATTTTATTTTCCCTTTTTCCTTTGTCCTCGAAA-AGCAGG
1 TT-TAGTCCTTAAAGAGCAGGACACATTTTATTTTCCCTTTTTCCTTTGTCCTC-AAAGAGCAGG
1665634 ACG
64 ACG
1665637 TACTCTTTTC
Statistics
Matches: 131, Mismatches: 10, Indels: 29
0.77 0.06 0.17
Matches are distributed among these distances:
82 1 0.01
83 4 0.03
84 2 0.02
85 21 0.16
86 4 0.03
88 7 0.05
89 49 0.37
90 10 0.08
91 5 0.04
92 20 0.15
93 3 0.02
94 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (87 bp):
TTTAGTCCTTAAAGAGCAGGACACATTTTATTTTCCCTTTTTCCTTTGTCCTCAAAGAGCAGGAC
GCACTTCGATTTCCTTTTTTCC
Found at i:1666352 original size:20 final size:20
Alignment explanation
Indices: 1666327--1666380 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1666317 TTTACCCAGA
*
1666327 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
1666347 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
1666367 TGTATCGATACATT
1 TGTATCGATACATT
1666381 CAGGCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:1668783 original size:51 final size:51
Alignment explanation
Indices: 1668683--1668847 Score: 154
Period size: 51 Copynumber: 3.2 Consensus size: 51
1668673 TTCATCTTGG
* * * *
1668683 GGATACTCCAACCCCGGTTCCATTTTCAAAACATCAATTCTTCCTAATCGA
1 GGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTATTCCTAATCGA
* * * * * *
1668734 TGATACTCCAACTCCGATTTCATTTTTAAAGCATCGATTTATTGC-AATCGG
1 GGATACTCCAACTCCGATTTCATTTTCAAAACATC-AATTATTCCTAATCGA
* * * * * *
1668785 GGATACTCTAACTCCGATTTTATTTTCAAAACACCAATTTTTCAC-AATTGG
1 GGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTATTC-CTAATCGA
1668836 GGATACTCCAAC
1 GGATACTCCAAC
1668848 CCCGTTATTT
Statistics
Matches: 91, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
50 5 0.05
51 80 0.88
52 6 0.07
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTATTCCTAATCGA
Found at i:1668952 original size:28 final size:28
Alignment explanation
Indices: 1668913--1668989 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1668903 TTTTTTCATA
* *
1668913 ATCGGGGGTACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
1668941 ATCGGGGATACTCCAATCCCATTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
1668969 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1668990 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:1669034 original size:51 final size:51
Alignment explanation
Indices: 1668972--1669092 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
1668962 TTATTTCCGA
* *
1668972 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTCTCATAATC
* ***
1669023 GGGGATACTCCAACTCCGATTTTATTTCCAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTCTCATAATC
*
1669074 GGAGGATACTTCAACCCCG
1 GG-GGATACTCCAACCCCG
1669093 GGGATATTCC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
51 47 0.77
52 14 0.23
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTCTCATAATC
Found at i:1669050 original size:110 final size:110
Alignment explanation
Indices: 1668834--1669036 Score: 286
Period size: 110 Copynumber: 1.9 Consensus size: 110
1668824 TTTCACAATT
* * *
1668834 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATATCTAAAAATAT
1 GGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAAATAT
** * * *
1668899 TGATTTTTTTCATAATCGGGGGTACTCTAACCCCGTTATTTCATC
66 CCATATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCATC
* * *
1668944 GGGGATACTCCAATCCCATTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCT-AAAATA-
1 GGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAAATAT
1669007 CCA-ATTTTTCATAATCGGGGATACTCCAAC
66 CCATATTTTTCATAATCGGGGATACTCCAAC
1669037 TCCGATTTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
107 24 0.29
108 1 0.01
109 6 0.07
110 51 0.62
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (110 bp):
GGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAAATAT
CCATATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCATC
Found at i:1669241 original size:79 final size:79
Alignment explanation
Indices: 1669093--1669260 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 79
1669083 TTCAACCCCG
* * * * * * * *
1669093 GGGATATTCCAACCCTGTTATTTTCGAGGGGCTACTCCAACCCCAATTTTATTTTCAAAATATCG
1 GGGATACTCCAACCCTATTATTTTCAAGAGGATACTCCAACCCCAATTTTATTTTCAAAACACCA
*
1669158 ATTTTCTATAATCA
66 ATTTTCCATAATCA
* **
1669172 GGGATACTCCAACCCTATTATTTTCAAGAGGATACTCCAACCCCGATTTTA-TTTCTGGAACACC
1 GGGATACTCCAACCCTATTATTTTCAAGAGGATACTCCAACCCCAATTTTATTTTC-AAAACACC
*
1669236 AATTTTCCATAATCG
65 AATTTTCCATAATCA
1669251 GGGATACTCC
1 GGGATACTCC
1669261 GGCCCCGTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
78 4 0.05
79 71 0.95
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCTATTATTTTCAAGAGGATACTCCAACCCCAATTTTATTTTCAAAACACCA
ATTTTCCATAATCA
Found at i:1672563 original size:10 final size:10
Alignment explanation
Indices: 1672548--1672613 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
1672538 CGTCTTCCGT
1672548 AAAAAAAACA
1 AAAAAAAACA
1672558 AAAAAAAGACA
1 AAAAAAA-ACA
*
1672569 AAAAAATA-A
1 AAAAAAAACA
*
1672578 AAAACAAA-A
1 AAAAAAAACA
*
1672587 AACAAAAACA
1 AAAAAAAACA
*
1672597 ATAAAAAACA
1 AAAAAAAACA
*
1672607 ATAAAAA
1 AAAAAAA
1672614 GGATCCGAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
9 14 0.30
10 24 0.51
11 9 0.19
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.05
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1672586 original size:23 final size:22
Alignment explanation
Indices: 1672548--1672612 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
1672538 CGTCTTCCGT
* *
1672548 AAAAAAA-ACAAAA-AAAAGAC
1 AAAAAAATAAAAAACAAAAAAC
1672568 AAAAAAATAAAAAACAAAAAAC
1 AAAAAAATAAAAAACAAAAAAC
1672590 AAAAACAATAAAAAACAATAAAA
1 AAAAA-AATAAAAAACAA-AAAA
1672613 AGGATCCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.18
21 5 0.13
22 11 0.28
23 12 0.31
24 4 0.10
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.05
Consensus pattern (22 bp):
AAAAAAATAAAAAACAAAAAAC
Found at i:1672592 original size:33 final size:33
Alignment explanation
Indices: 1672550--1672613 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1672540 TCTTCCGTAA
1672550 AAAAAACAAAAAAAAGACAAAAA-AATAAAAAAC
1 AAAAAACAAAAAAAAGA-AAAAACAATAAAAAAC
* *
1672583 AAAAAACAAAAACAATAAAAAACAATAAAAA
1 AAAAAACAAAAAAAAGAAAAAACAATAAAAA
1672614 GGATCCGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (33 bp):
AAAAAACAAAAAAAAGAAAAAACAATAAAAAAC
Found at i:1673679 original size:37 final size:37
Alignment explanation
Indices: 1673638--1673719 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
1673628 TGCCACAATC
1673638 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1673675 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1673712 ATGCATTT
1 ATGCATTT
1673720 ATGCTTCATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:1674162 original size:29 final size:29
Alignment explanation
Indices: 1674088--1674805 Score: 787
Period size: 29 Copynumber: 25.3 Consensus size: 29
1674078 CTCACCTTCC
* *
1674088 AAAGCCCACAAGTTAGTGGCACATTTTC-
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
* *
1674116 AAAGCCCACAAGTTAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674145 AAAGCCTACAAGTCAGTGGCAACC--TTC-
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
*
1674172 AAAGCCCATAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
* *
1674200 GAAGCCCACAAGTCGGTGGCACCTTTTTC-
1 AAAGCCCACAAGTCAGTGGCACC-TTTTCA
1674229 AAA-CCCTACAAGTCAGTGGCACCCTTTTC-
1 AAAGCCC-ACAAGTCAGTGGCA-CCTTTTCA
* * *
1674258 AAAGTCCACAAGTCAAG-GGTATCTTTTCA
1 AAAGCCCACAAGTC-AGTGGCACCTTTTCA
*
1674287 AAAGCCCACAAGTCAATGGCACCTTTTC-
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674315 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
1674344 AAAGCCCACAAGTCAGTGGCAACC--TTC-
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
*
1674371 AAAGGCCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
* ** *
1674399 GAAGCCCACAAGTTGGTGGCACTTTTTTC-
1 AAAGCCCACAAGTCAGTGGCAC-CTTTTCA
*
1674428 AAAGCCCACAAATCAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCA
*
1674458 AAA-CCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674486 AAAGCCCACAAGTCAGTGGCACATTTTC-
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674514 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
1674543 AAAGCCCACAAGTCAGTGGCAACC--TTC-
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
*
1674570 AAAGGCCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
* *
1674598 GAAGCCCACAAGTCGGTGGCACCTTTTTC-
1 AAAGCCCACAAGTCAGTGGCACC-TTTTCA
1674627 AAAGCCCACAAGTCAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCA
* *
1674657 AAA-CCCACAAGTCAGTGACATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674685 AAAGCCCATAAGTCAGTGGCACCTTTTC-
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
* *
1674713 AAAGCCCATAAGTCA-TGGCACCTTTT-T
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
1674740 AAAGCCCACAAGTCAGTGGCAAC-TTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
* * *
1674768 GAAGCCCACAAGTCAGTGGCA-ATCTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
1674796 AAAGCCCACA
1 AAAGCCCACA
1674806 CAAGTTGGGG
Statistics
Matches: 598, Mismatches: 58, Indels: 68
0.83 0.08 0.09
Matches are distributed among these distances:
27 113 0.19
28 221 0.37
29 234 0.39
30 30 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTCA
Found at i:1674428 original size:199 final size:199
Alignment explanation
Indices: 1674088--1674805 Score: 1174
Period size: 199 Copynumber: 3.6 Consensus size: 199
1674078 CTCACCTTCC
* * *
1674088 AAAGCCCACAAGTTAGTGGCACATTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCTA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
*
1674153 CAAGTCAGTGGCAACCTTCAAAGCCCATAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
66 CAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
** *
1674218 GCACCTTTTTCAAA-CCCTACAAGTCAGTGGCACCCTTTTCAAAGTCCACAAGTCAAG-GGTATC
131 GCACCTTTTTCAAAGCCC-ACAAGTCAGTGGCACCCTTTTCAAAACCCACAAGTC-AGTGGCATC
1674281 TTTTCA
194 TTTTCA
* *
1674287 AAAGCCCACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
* *
1674352 CAAGTCAGTGGCAACCTTCAAAGGCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTTGGTG
66 CAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
* *
1674417 GCACTTTTTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCATCTT
131 GCACCTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCATCTT
1674482 TTCA
196 TTCA
1674486 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
*
1674551 CAAGTCAGTGGCAACCTTCAAAGGCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
66 CAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
*
1674616 GCACCTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGACATCTT
131 GCACCTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCATCTT
1674681 TTCA
196 TTCA
* * * * *
1674685 AAAGCCCATAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCA-TGGCACCTTTT-TAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
* * *
1674748 CAAGTCAGTGGCAACTTTCAGAAGCCCACAAGTCAGTGGCAATCTTCAAAAGCCCACA
66 CAAGTCAGTGGCAACCTTCA-AAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACA
1674806 CAAGTTGGGG
Statistics
Matches: 488, Mismatches: 28, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
197 27 0.06
198 46 0.09
199 412 0.84
200 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (199 bp):
AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCA
CAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGTG
GCACCTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCATCTT
TTCA
Found at i:1674810 original size:142 final size:142
Alignment explanation
Indices: 1674087--1674805 Score: 826
Period size: 142 Copynumber: 5.1 Consensus size: 142
1674077 CCTCACCTTC
* * *
1674087 CAAAGCCCACAAGTTAGTGGCA-CATTTTC-AAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGC
1 CAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGC
* * * *
1674150 CTACAAGTCAGTGGCAACC--TTCAAAGCCCATAAGTCAGTGGCAAC-CTTCAGAAGCCCACAAG
64 CCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCAACTTTTCAAAAGCCCACAAG
* *
1674212 TCGGTGGCACCTTTTT
128 TCAGTGGCA-CATTTT
* * * *
1674228 CAAA-CCCTACAAGTCAGTGGCACCCTTTTC-AAAGTCCACAAGTCAAG-GGTATCTTTTCAAAA
1 CAAAGCCC-ACAAGTCAGTGGCA-TCTTTTCAAAAGCCCACAAGTC-AGTGGCACCTTTTC-AAA
* *
1674290 GCCCACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAA
62 GCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACTTTTCAAAAGCCCACAA
**
1674355 GTCAGTGGCA-ACCTT
127 GTCAGTGGCACATTTT
* * * * ** *
1674370 CAAAGGCCACAAGTCAGTGGCAAC-CTTCAGAAGCCCACAAGTTGGTGGCACTTTTTTCAAAGCC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCC
* * *
1674434 CACAAATCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGT
65 CACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAACTTTTCAAAAGCCCACAAGT
1674499 CAGTGGCACATTTT
129 CAGTGGCACATTTT
*
1674513 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAGGC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCC
* *
1674576 CACAAGTCAGTGGCAACC--TTCAGAAGCCCACAAGTCGGTGGCACCTTTTTC-AAAGCCCACAA
65 CACAAGTCAGTGGC-ACCTTTTCA-AAGCCCACAAGTCAGTGGCAAC-TTTTCAAAAGCCCACAA
*
1674638 GTCAGTGGCACCCTTTT
127 GTCAGTGGCA-CATTTT
* * *
1674655 CAAAACCCACAAGTCAGTGACATCTTTTCAAAAGCCCATAAGTCAGTGGCACCTTTTCAAAGCCC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
* * *
1674720 ATAAGTCA-TGGCACCTTTTTAAAGCCCACAAGTCAGTGGCAAC-TTTCAGAAGCCCACAAGTCA
66 ACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACTTTTCAAAAGCCCACAAGTCA
*
1674783 GTGGCA-ATCTT
131 GTGGCACATTTT
1674794 CAAAAGCCCACA
1 C-AAAGCCCACA
1674806 CAAGTTGGGG
Statistics
Matches: 499, Mismatches: 54, Indels: 51
0.83 0.09 0.08
Matches are distributed among these distances:
139 4 0.01
140 24 0.05
141 120 0.24
142 231 0.46
143 74 0.15
144 44 0.09
145 2 0.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (142 bp):
CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
ACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACTTTTCAAAAGCCCACAAGTCA
GTGGCACATTTT
Found at i:1675000 original size:101 final size:98
Alignment explanation
Indices: 1674815--1675373 Score: 516
Period size: 101 Copynumber: 5.5 Consensus size: 98
1674805 ACAAGTTGGG
* * * *
1674815 GGCACCTTCA-CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCT
1 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTT-TCATCT
* *
1674879 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATT
63 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
*
1674915 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGTGCATTTGTCATCT
1 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTT-TCATCT
1674980 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
63 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
* * * * **
1675016 GGCACCTTCACCTTTAAGTCCAATATTGCTGGTCTTGAGTCAGCACATTGGCACCTTCATCTTTA
1 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTA
*
1675081 AGTCCAATATCGCTGGCCTTGAATCAGCATATT
66 AGTCCAATGTCGCTGGCCTTGAATCAGCATATT
* * * * ** *
1675114 GGCGCCTTTGTCATCTTTAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCT
1 GGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCT
** * *
1675179 TTAAGTCCAAAATCACTAGCCTTGAATCAGCATATT
63 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
* * ** * *
1675215 GGCA-TTGGTAACAT-TCCTAAACCCAATGTCGCTAGCCTTGAATCAGCACATTGGCATTCTTCT
1 GGCACCT--T--CATCT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-T-TT-T
* * * * * *
1675278 CATCTTCAAGTCTAATGTCGCTGACCATGAATCAACACATT
58 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
* * * * *
1675319 GACATTCTTTACATCTTTAAGCCCAAT-TCACTGGTCC-TGAATCAGCATATTGGCA
1 GGCA--CCTT-CATCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCA
1675374 CCTTTATCAC
Statistics
Matches: 389, Mismatches: 54, Indels: 29
0.82 0.11 0.06
Matches are distributed among these distances:
98 47 0.12
99 6 0.02
100 13 0.03
101 247 0.63
103 23 0.06
104 49 0.13
105 2 0.01
107 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (98 bp):
GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTA
AGTCCAATGTCGCTGGCCTTGAATCAGCATATT
Found at i:1675067 original size:150 final size:150
Alignment explanation
Indices: 1674825--1675218 Score: 599
Period size: 150 Copynumber: 2.6 Consensus size: 150
1674815 GGCACCTTCA
* *
1674825 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCACCTTTAAGTCCAAT
*
1674890 GTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
63 ATTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
1674955 CAGCATATTAGTGCATTTGTCAT
128 CAGCATATTAGCGCATTTGTCAT
*
1674978 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATT
* *
1675043 GCTGGTCTTGAGTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
* *
1675108 CATATTGGCGCCTTTGTCAT
131 CATATTAGCGCATTTGTCAT
* * * * * *
1675128 CTTTAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATT
* * *
1675193 ACTAGCCTTGAATCAGCATATTGGCA
66 GCTGGCCTTGAATCAGCACATTGGCA
1675219 TTGGTAACAT
Statistics
Matches: 220, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
150 178 0.81
151 1 0.00
153 41 0.19
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (150 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATT
GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
CATATTAGCGCATTTGTCAT
Found at i:1675270 original size:251 final size:250
Alignment explanation
Indices: 1674815--1675270 Score: 702
Period size: 251 Copynumber: 1.8 Consensus size: 250
1674805 ACAAGTTGGG
1674815 GGCACCTTCACTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTT
1 GGCACCTTCACTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTT
*** * * * * *
1674880 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
66 TAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCACT
* * * ** *
1674945 GGCCTTGAATCAGCATATTAGTGCATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAG
131 AGCCTTGAATCAGCATATTAGTGCATTGGTCATCTCTAAACCCAATGTCGCTAGCCTTGAATCAG
*
1675010 CATATTGGCACCTTCACCTTTAAGTCCAATATTGCTGGTCTTGAGTCAGCACATT
196 CACATTGGCACCTTCACCTTTAAGTCCAATATTGCTGGTCTTGAGTCAGCACATT
* *
1675065 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
1 GGCACCTTCA-CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCT
1675130 TTAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCAC
65 TTAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCAC
1675195 TAGCCTTGAATCAGCATATT-G-GCATTGGTAACAT-TCCTAAACCCAATGTCGCTAGCCTTGAA
130 TAGCCTTGAATCAGCATATTAGTGCATTGGT--CATCT-CTAAACCCAATGTCGCTAGCCTTGAA
1675257 TCAGCACATTGGCA
192 TCAGCACATTGGCA
1675271 TTCTTCTCAT
Statistics
Matches: 185, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
249 7 0.04
250 12 0.06
251 166 0.90
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (250 bp):
GGCACCTTCACTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTT
TAAGTCCAATAACGCTAGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCACT
AGCCTTGAATCAGCATATTAGTGCATTGGTCATCTCTAAACCCAATGTCGCTAGCCTTGAATCAG
CACATTGGCACCTTCACCTTTAAGTCCAATATTGCTGGTCTTGAGTCAGCACATT
Found at i:1675295 original size:52 final size:49
Alignment explanation
Indices: 1674815--1675374 Score: 500
Period size: 52 Copynumber: 11.1 Consensus size: 49
1674805 ACAAGTTGGG
* * *
1674815 GGCACCTTCA-CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATT
1 GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * * *
1674863 GGCGCCTTTGTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATT
1 GGC-AC-TT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* *
1674915 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
1 GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * *
1674964 AGTGCATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT
1 -G-GCACTT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * * * *
1675016 GGCACCTTCACCTTTAAGTCCAATATTGCTGGTCTTGAGTCAGCACATT
1 GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* *
1675065 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
1 GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * *
1675114 GGCGCCTTTGTCATCTTTAAGTCCAATAACGCTAGCCTTGAATCAGCACATT
1 GGC-AC-TT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * * * * * *
1675166 AGCACCTTCACCTTTAAGTCCAAAATCACTAGCCTTGAATCAGCATATT
1 GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* ** * *
1675215 GGCA-TTGGTAACAT-TCCTAAACCCAATGTCGCTAGCCTTGAATCAGCACATT
1 GGCACTT--T--CATCT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * * * * *
1675267 GGCATTCTTCTCATCTTCAAGTCTAATGTCGCTGACCATGAATCAACACATT
1 GGCA--CTT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
* * * *
1675319 GACATTCTTTACATCTTTAAGCCCAAT-TCACTGGTCC-TGAATCAGCATATT
1 GGCA--CTTT-CATCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATT
1675370 GGCAC
1 GGCAC
1675375 CTTTATCACT
Statistics
Matches: 421, Mismatches: 70, Indels: 41
0.79 0.13 0.08
Matches are distributed among these distances:
48 4 0.01
49 163 0.39
50 10 0.02
51 33 0.08
52 207 0.49
53 1 0.00
54 1 0.00
55 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (49 bp):
GGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
Found at i:1675990 original size:13 final size:13
Alignment explanation
Indices: 1675972--1675997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1675962 ACATAAGTGT
1675972 TGTATCGATACAA
1 TGTATCGATACAA
1675985 TGTATCGATACAA
1 TGTATCGATACAA
1675998 AGCTACCCTG
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):
TGTATCGATACAA
Found at i:1684669 original size:14 final size:14
Alignment explanation
Indices: 1684652--1684680 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1684642 TGCATAAGGG
1684652 ACTAGGTGATGGGC
1 ACTAGGTGATGGGC
1684666 ACTAGGTGATGGGC
1 ACTAGGTGATGGGC
1684680 A
1 A
1684681 TTTATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.21
Consensus pattern (14 bp):
ACTAGGTGATGGGC
Found at i:1686596 original size:18 final size:18
Alignment explanation
Indices: 1686573--1686607 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1686563 TCATCATCAT
*
1686573 GCTGTCAATTAAGTTTTG
1 GCTGTCAATAAAGTTTTG
1686591 GCTGTCAATAAAGTTTT
1 GCTGTCAATAAAGTTTT
1686608 TCCCTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (18 bp):
GCTGTCAATAAAGTTTTG
Found at i:1691412 original size:19 final size:18
Alignment explanation
Indices: 1691388--1691446 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
1691378 ATCGATACAT
1691388 TGTATCGAAATAATACTTA
1 TGTATCGAAA-AATACTTA
*
1691407 TGTATCG----ATACAT-
1 TGTATCGAAAAATACTTA
1691420 TGTATCGAAACAATACTTA
1 TGTATCGAAA-AATACTTA
1691439 TGTATCGA
1 TGTATCGA
1691447 TATATTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 7 0.22
14 5 0.16
18 5 0.16
19 15 0.47
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (18 bp):
TGTATCGAAAAATACTTA
Found at i:1691418 original size:32 final size:32
Alignment explanation
Indices: 1691377--1691448 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1691367 GGCAACTTTA
*
1691377 TATCGATACATTGTATCGAAATAATACTTATG
1 TATCGATACATTGTATCGAAACAATACTTATG
1691409 TATCGATACATTGTATCGAAACAATACTTATG
1 TATCGATACATTGTATCGAAACAATACTTATG
1691441 TATCGATA
1 TATCGATA
1691449 TATTTACTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (32 bp):
TATCGATACATTGTATCGAAACAATACTTATG
Found at i:1692178 original size:6 final size:6
Alignment explanation
Indices: 1692159--1692193 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1692149 AATGGCGACC
* *
1692159 ATTACT ATTCCT ATTACT ATTACT ATTACC ATTAC
1 ATTACT ATTACT ATTACT ATTACT ATTACT ATTAC
1692194 CATCTTATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTACT
Found at i:1692192 original size:18 final size:18
Alignment explanation
Indices: 1692156--1692196 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1692146 GACAATGGCG
1692156 ACCATTACTATT-CCTATT
1 ACCATTACTATTACC-ATT
*
1692174 ACTATTACTATTACCATT
1 ACCATTACTATTACCATT
1692192 ACCAT
1 ACCAT
1692197 CTTATGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (18 bp):
ACCATTACTATTACCATT
Found at i:1693017 original size:26 final size:26
Alignment explanation
Indices: 1692969--1693018 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1692959 TTGATTTGGT
*
1692969 TTTTTATTAATATATATAAAATCAGA
1 TTTTTATTAATATAGATAAAATCAGA
*
1692995 TTTTTATTGAAT-TAGATAGAATCA
1 TTTTTATT-AATATAGATAAAATCA
1693019 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTTATTAATATAGATAAAATCAGA
Found at i:1693266 original size:2 final size:2
Alignment explanation
Indices: 1693259--1693283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1693249 TTTATAAACT
1693259 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1693284 TAAATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1693386 original size:20 final size:20
Alignment explanation
Indices: 1693361--1693400 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1693351 ATTAAAAATT
1693361 TATTTTTAT-ATTAATATTTA
1 TATTTTTATAATTAA-ATTTA
1693381 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1693401 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATAATTAAATTTA
Found at i:1693494 original size:31 final size:31
Alignment explanation
Indices: 1693456--1693517 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1693446 AAATAAAAAA
*
1693456 AATTATATTCAAAGCCAGACACTTATATTTT
1 AATTATATTCAAAGCCAGACACCTATATTTT
*
1693487 AATTATATTCAAAGCCTGACACCTATATTTT
1 AATTATATTCAAAGCCAGACACCTATATTTT
1693518 GATTCTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (31 bp):
AATTATATTCAAAGCCAGACACCTATATTTT
Found at i:1699140 original size:34 final size:34
Alignment explanation
Indices: 1699099--1699235 Score: 132
Period size: 41 Copynumber: 3.8 Consensus size: 34
1699089 CTTACAACAC
*
1699099 TATCTTTTCACAGGCTAAGATAGAACGTCTTCCT
1 TATCTTTTCACAGGCTAAGATAGAACATCTTCCT
*
1699133 TATCTTTTCACAAGCTACAGGCTAAGATAGAACATCTTCCC
1 TATCTTTT------C-ACAGGCTAAGATAGAACATCTTCCT
* *
1699174 TATCTTTTCACAGGTTAAGATAGAACCT-TTCTTCT
1 TATCTTTTCACAGGCTAAGATAGAACATCTTC--CT
*
1699209 TATCTTTTTCAAAGGCTAAGATAGAAC
1 TATC-TTTTCACAGGCTAAGATAGAAC
1699236 CTCTCAATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
33 3 0.03
34 25 0.29
35 6 0.07
36 20 0.23
40 1 0.01
41 31 0.36
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (34 bp):
TATCTTTTCACAGGCTAAGATAGAACATCTTCCT
Found at i:1699165 original size:41 final size:41
Alignment explanation
Indices: 1699108--1699185 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1699098 CTATCTTTTC
* *
1699108 ACAGGCTAAGATAGAACGTCTTCCTTATCTTTTCACAAGCT
1 ACAGGCTAAGATAGAACATCTTCCCTATCTTTTCACAAGCT
1699149 ACAGGCTAAGATAGAACATCTTCCCTATCTTTTCACA
1 ACAGGCTAAGATAGAACATCTTCCCTATCTTTTCACA
1699186 GGTTAAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (41 bp):
ACAGGCTAAGATAGAACATCTTCCCTATCTTTTCACAAGCT
Found at i:1699218 original size:36 final size:36
Alignment explanation
Indices: 1699149--1699237 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
1699139 TTCACAAGCT
1699149 ACAGGCTAAGATAGAA-C-ATCTTCCCTATCTTTTC
1 ACAGGCTAAGATAGAACCTATCTTCCCTATCTTTTC
* * *
1699183 ACAGGTTAAGATAGAACCTTTCTT-CTTATCTTTTTC
1 ACAGGCTAAGATAGAACCTATCTTCCCTATC-TTTTC
*
1699219 AAAGGCTAAGATAGAACCT
1 ACAGGCTAAGATAGAACCT
1699238 CTCAATTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 15 0.32
35 6 0.13
36 26 0.55
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (36 bp):
ACAGGCTAAGATAGAACCTATCTTCCCTATCTTTTC
Found at i:1704162 original size:24 final size:24
Alignment explanation
Indices: 1704134--1704185 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1704124 ACCTATGAGT
1704134 TCATCCAAGGACAGTGTGTTTGGA
1 TCATCCAAGGACAGTGTGTTTGGA
1704158 TCATCCAAGGACAGTGTGTTTGGA
1 TCATCCAAGGACAGTGTGTTTGGA
1704182 TCAT
1 TCAT
1704186 TGGATTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (24 bp):
TCATCCAAGGACAGTGTGTTTGGA
Found at i:1705251 original size:34 final size:34
Alignment explanation
Indices: 1705174--1705293 Score: 138
Period size: 34 Copynumber: 3.6 Consensus size: 34
1705164 TATCTTTTGA
*
1705174 AGGCTAAGATAGAACCTC--CC-TATCTTTTCAC
1 AGGCTAAGATAGAACCTCTTCCTTATTTTTTCAC
* * *
1705205 AAGATAAAATAGAACCTCTTCCTTATTTTTTCAC
1 AGGCTAAGATAGAACCTCTTCCTTATTTTTTCAC
* *
1705239 AGGCTAAGATAGAACCTTTCTCCTTATCTTTTTCAA
1 AGGCTAAGATAGAACCTCT-TCCTTAT-TTTTTCAC
*
1705275 AGGCTAAGATAAAACCTCT
1 AGGCTAAGATAGAACCTCT
1705294 CAATCACTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 15 0.21
33 2 0.03
34 25 0.34
35 7 0.10
36 24 0.33
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (34 bp):
AGGCTAAGATAGAACCTCTTCCTTATTTTTTCAC
Found at i:1705279 original size:36 final size:35
Alignment explanation
Indices: 1705173--1705291 Score: 126
Period size: 36 Copynumber: 3.5 Consensus size: 35
1705163 CTATCTTTTG
1705173 AAGGCTAAGATAGAACC-TC-CC-TATC-TTTTCA
1 AAGGCTAAGATAGAACCTTCTCCTTATCTTTTTCA
* *
1705204 CAA-GATAAAATAGAACC-TCTTCCTTAT-TTTTTCA
1 -AAGGCTAAGATAGAACCTTC-TCCTTATCTTTTTCA
*
1705238 CAGGCTAAGATAGAACCTTTCTCCTTATCTTTTTCA
1 AAGGCTAAGATAGAACC-TTCTCCTTATCTTTTTCA
*
1705274 AAGGCTAAGATAAAACCT
1 AAGGCTAAGATAGAACCT
1705292 CTCAATCACT
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
31 14 0.19
32 2 0.03
33 3 0.04
34 21 0.29
35 8 0.11
36 24 0.33
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (35 bp):
AAGGCTAAGATAGAACCTTCTCCTTATCTTTTTCA
Found at i:1710604 original size:52 final size:52
Alignment explanation
Indices: 1710517--1710624 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
1710507 ATGCATTTGA
* * * *
1710517 AATTCTAGCCATTGGACTCAATGTATCGGTACAATTCATAATGTATCGATAC
1 AATTATAGCCATTGGACTCAATGTATCGATACAATTCACAATATATCGATAC
* * * *
1710569 AATTATAGTCATTGGACTTAATGTATCGATACAATTTACCATATATCGATAC
1 AATTATAGCCATTGGACTCAATGTATCGATACAATTCACAATATATCGATAC
1710621 AATT
1 AATT
1710625 CACTTAGGCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (52 bp):
AATTATAGCCATTGGACTCAATGTATCGATACAATTCACAATATATCGATAC
Found at i:1710864 original size:24 final size:23
Alignment explanation
Indices: 1710820--1710864 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1710810 AATTATTTTA
*
1710820 CTTGAAAAATATTTGATTTATTG
1 CTTGAAAAATATTTGACTTATTG
1710843 CTTGAAAAATATTTGAACTTAT
1 CTTGAAAAATATTTG-ACTTAT
1710865 CTCTAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
CTTGAAAAATATTTGACTTATTG
Found at i:1712980 original size:12 final size:12
Alignment explanation
Indices: 1712963--1712988 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1712953 GGGATGTGGG
1712963 TTTTTGAAGGGA
1 TTTTTGAAGGGA
1712975 TTTTTGAAGGGA
1 TTTTTGAAGGGA
1712987 TT
1 TT
1712989 AGAAAGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTTGAAGGGA
Found at i:1717081 original size:9 final size:9
Alignment explanation
Indices: 1717067--1717097 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1717057 ACCTCTTCAC
1717067 CATTATCAT
1 CATTATCAT
*
1717076 CATTATCTT
1 CATTATCAT
1717085 CATTATCAT
1 CATTATCAT
1717094 CATT
1 CATT
1717098 GATGGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (9 bp):
CATTATCAT
Found at i:1718759 original size:20 final size:20
Alignment explanation
Indices: 1718734--1718772 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1718724 ATTGGACTTA
*
1718734 ATGTATCGAGACAGTTTACC
1 ATGTATCGAGACAATTTACC
*
1718754 ATGTATCGATACAATTTAC
1 ATGTATCGAGACAATTTAC
1718773 TTAGGGTAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGAGACAATTTACC
Found at i:1718853 original size:13 final size:13
Alignment explanation
Indices: 1718835--1718859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1718825 TACAAAAAAC
1718835 ATGTATCGATACA
1 ATGTATCGATACA
1718848 ATGTATCGATAC
1 ATGTATCGATAC
1718860 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:1719005 original size:25 final size:23
Alignment explanation
Indices: 1718971--1719029 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 23
1718961 GTATCGATAC
1718971 TTTGAATTATTTTACTTGAAAAACA
1 TTTGAATTA--TTACTTGAAAAACA
* *
1718996 TTTGATTTATTGCTTGAAAAACA
1 TTTGAATTATTACTTGAAAAACA
1719019 TTTGAACTTAT
1 TTTGAA-TTAT
1719030 CTCTAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.60
24 4 0.13
25 8 0.27
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (23 bp):
TTTGAATTATTACTTGAAAAACA
Done.