Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 31 of 318
Found at i:11573620 original size:47 final size:47
Alignment explanation
Indices: 11573530--11573656 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 47
11573520 TCTTTACATA
* * * * *
11573530 ATGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTC
1 ATGATGCCATATCCCAGATATGGTCTTATACAGTAAGCACATATCAC
* *
11573576 ACTGATGTCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC
1 A-TGATGCCATATCCCAGATATGGTCTTATACAGTAAGCACATATCAC
*
11573623 ATCGATGCCTTATCCCAGATATGGTCTTATACAG
1 AT-GATGCCATATCCCAGATATGGTCTTATACAG
11573657 AAATCACTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 2 0.03
47 65 0.94
48 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (47 bp):
ATGATGCCATATCCCAGATATGGTCTTATACAGTAAGCACATATCAC
Found at i:11573715 original size:31 final size:31
Alignment explanation
Indices: 11573680--11573888 Score: 301
Period size: 31 Copynumber: 6.7 Consensus size: 31
11573670 CTTGTCACTT
* *
11573680 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
11573711 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
11573742 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
11573773 GTAGCCGAAGCTACCACTTTTCACTAATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
11573804 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
11573835 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
11573866 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
11573889 GTTGTCATTT
Statistics
Matches: 160, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 160 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:11573965 original size:50 final size:50
Alignment explanation
Indices: 11573866--11574042 Score: 212
Period size: 50 Copynumber: 3.5 Consensus size: 50
11573856 CACTGATCAG
* * * * * *
11573866 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCC-TTAATCAGATAAGT
*
11573917 GTAGCCGAAACTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
* * * * * *
11573967 GTAGTCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATAAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
11574017 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
11574043 GTTTCCATGG
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
50 85 0.79
51 23 0.21
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
Found at i:11576108 original size:43 final size:42
Alignment explanation
Indices: 11576047--11576186 Score: 190
Period size: 43 Copynumber: 3.2 Consensus size: 42
11576037 AGGCTGTTAC
*
11576047 AACGCCGTTATAGACCTGTACTTTTAGCGGCGCTTTTTTAAAA
1 AACGCCGCTAT-GACCTGTACTTTTAGCGGCGCTTTTTTAAAA
*
11576090 AACGCCGCTATCGACCTGTACTTTTAGCGGCGCTTTTATAAAAA
1 AACGCCGCTAT-GACCTGTACTTTTAGCGGCGCTTTT-TTAAAA
* * * *
11576134 AACGCCGCTAATGACCAGGACCTTTAGCAGCGCTTTTTTAAAA
1 AACGCCGCT-ATGACCTGTACTTTTAGCGGCGCTTTTTTAAAA
11576177 AACGCCGCTA
1 AACGCCGCTA
11576187 ATTTGCGCAG
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
42 1 0.01
43 49 0.56
44 35 0.40
45 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
AACGCCGCTATGACCTGTACTTTTAGCGGCGCTTTTTTAAAA
Found at i:11576160 original size:44 final size:44
Alignment explanation
Indices: 11576069--11576188 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 44
11576059 GACCTGTACT
* * *
11576069 TTTAGCGGCGCTTTTTTAAAAAACGCCGCT-ATCGACCTGTACT
1 TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAATCGACCAGGACC
*
11576112 TTTAGCGGCGCTTTTATAAAAAAACGCCGCTAAT-GACCAGGACC
1 TTTAGCGGCGCTTTT-TTAAAAAACGCCGCTAATCGACCAGGACC
*
11576156 TTTAGCAGCGCTTTTTTAAAAAACGCCGCTAAT
1 TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAAT
11576189 TTGCGCAGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 32 0.46
44 35 0.51
45 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
TTTAGCGGCGCTTTTTTAAAAAACGCCGCTAATCGACCAGGACC
Found at i:11576514 original size:21 final size:21
Alignment explanation
Indices: 11576490--11576530 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11576480 GTTCTGCTCC
11576490 GCCTCCCTCGCTGCTGCCTCA
1 GCCTCCCTCGCTGCTGCCTCA
11576511 GCCTCCCTCGCTGCTGCCTC
1 GCCTCCCTCGCTGCTGCCTC
11576531 CGCTCTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.54, G:0.20, T:0.24
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCA
Found at i:11577121 original size:18 final size:18
Alignment explanation
Indices: 11577089--11577126 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
11577079 TACAATATAG
11577089 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
11577108 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
11577125 TA
1 TA
11577127 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:11581463 original size:15 final size:15
Alignment explanation
Indices: 11581445--11581476 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11581435 AAATAACATT
*
11581445 TTATATATATTTATC
1 TTATATACATTTATC
11581460 TTATATACATTTATC
1 TTATATACATTTATC
11581475 TT
1 TT
11581477 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:11581504 original size:25 final size:28
Alignment explanation
Indices: 11581476--11581534 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
11581466 ACATTTATCT
*
11581476 TCTAAA-TTAAAATCCAAAAT-T-ATAC
1 TCTAAATTTAAAACCCAAAATCTAATAC
*
11581501 TCTAAATTTAAAACCCTAAATCTAATAC
1 TCTAAATTTAAAACCCAAAATCTAATAC
11581529 TCTAAA
1 TCTAAA
11581535 CACTAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 12 0.41
27 1 0.03
28 10 0.34
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (28 bp):
TCTAAATTTAAAACCCAAAATCTAATAC
Found at i:11582363 original size:14 final size:14
Alignment explanation
Indices: 11582344--11582383 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11582334 ATTAAACCTG
* *
11582344 CTTAAACCATATAT
1 CTTAAACCATAAAC
11582358 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
11582372 CTTAAACTATAA
1 CTTAAACCATAA
11582384 TGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:11582573 original size:41 final size:40
Alignment explanation
Indices: 11582527--11582704 Score: 184
Period size: 41 Copynumber: 4.4 Consensus size: 40
11582517 GGTTATGGGA
11582527 TTTTTAGCGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTA-CAAAAGCGCCGCTAATGCTCTGG
* * *
11582568 TTTTTAGCGGCGTTTTACCGAAAGTGCCGCTAATGCTC-AG
1 TTTTTAGCGGCGTTTTA-CAAAAGCGCCGCTAATGCTCTGG
** *
11582608 TTTTTAGCGGCGTTTTATTGAAAGCGCCGCTAATGCTATGG
1 TTTTTAGCGGCGTTTTA-CAAAAGCGCCGCTAATGCTCTGG
* **
11582649 -TTTTAGCGGCATTTTTTACTAAAA-CGCCGCTGTTGCTCT-G
1 TTTTTAGCGGC--GTTTTAC-AAAAGCGCCGCTAATGCTCTGG
*
11582689 TTTTTACCGGCGTTTT
1 TTTTTAGCGGCGTTTT
11582705 TTTTAAAACG
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
39 4 0.03
40 46 0.40
41 57 0.50
42 8 0.07
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTACAAAAGCGCCGCTAATGCTCTGG
Found at i:11582678 original size:81 final size:81
Alignment explanation
Indices: 11582527--11582725 Score: 224
Period size: 81 Copynumber: 2.5 Consensus size: 81
11582517 GGTTATGGGA
** * *
11582527 TTTTTAGCGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAG
1 TTTTTAGCGGCGTTTTATTAAAAGCGCCGCTAATGCTATGGTTTTTAGCGGCGTTTTACCGAAAA
*
11582592 TGCCGCTAATGCTCAG
66 CGCCGCTAATGCTCAG
* * *
11582608 TTTTTAGCGGCGTTTTATTGAAAGCGCCGCTAATGCTATGG-TTTTAGCGGCATTTTTTA-CTAA
1 TTTTTAGCGGCGTTTTATTAAAAGCGCCGCTAATGCTATGGTTTTTAGCGGC--GTTTTACCGAA
** *
11582671 AACGCCGCTGTTGCTCTG
64 AACGCCGCTAATGCTCAG
* * *
11582689 TTTTTACCGGCGTTTTTTTTAAAA-CGCCGCTATTGCT
1 TTTTTAGCGGCG-TTTTATTAAAAGCGCCGCTAATGCT
11582726 CTGAATTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 10 0.10
81 76 0.76
82 14 0.14
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (81 bp):
TTTTTAGCGGCGTTTTATTAAAAGCGCCGCTAATGCTATGGTTTTTAGCGGCGTTTTACCGAAAA
CGCCGCTAATGCTCAG
Found at i:11582705 original size:40 final size:39
Alignment explanation
Indices: 11582527--11582728 Score: 190
Period size: 40 Copynumber: 5.0 Consensus size: 39
11582517 GGTTATGGGA
11582527 TTTTTAGCGGCGTTTTAGC-AAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTA-CTAAAA-CGCCGCTAATGCTCT-G
* ** *
11582568 TTTTTAGCGGCGTTTTACCGAAAGTGCCGCTAATGCTCAG
1 TTTTTAGCGGCGTTTTA-CTAAAACGCCGCTAATGCTCTG
* * *
11582608 TTTTTAGCGGCGTTTTATTGAAAGCGCCGCTAATGCTATG
1 TTTTTAGCGGCGTTTTACT-AAAACGCCGCTAATGCTCTG
* * **
11582648 GTTTTAGCGGCATTTTTTACTAAAACGCCGCTGTTGCTCTG
1 TTTTTAGCGGC--GTTTTACTAAAACGCCGCTAATGCTCTG
* ** *
11582689 TTTTTACCGGCGTTTTTTTTAAAACGCCGCTATTGCTCTG
1 TTTTTAGCGGCG-TTTTACTAAAACGCCGCTAATGCTCTG
11582729 AATTTTAAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
40 69 0.51
41 56 0.42
42 9 0.07
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.37
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTACTAAAACGCCGCTAATGCTCTG
Found at i:11586029 original size:24 final size:24
Alignment explanation
Indices: 11585901--11586059 Score: 124
Period size: 24 Copynumber: 6.6 Consensus size: 24
11585891 AACCGATTTT
* ** *
11585901 GCACACATAGTGCTAAACAAATTC
1 GCACACATAGTGCCATTCAAATCC
* *
11585925 GCACACATAGTGCCATGCTACA-CC
1 GCACACATAGTGCCATTC-AAATCC
* *
11585949 GCACACATAGTGCC-TTGAAGATTC
1 GCACACATAGTGCCATTCAA-ATCC
* * ** * * * *
11585973 ACTCATGTATTGACATCCAAATCA
1 GCACACATAGTGCCATTCAAATCC
*
11585997 GCACACATAGTGCCATTCAATTCC
1 GCACACATAGTGCCATTCAAATCC
11586021 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
*
11586045 GCACACTTAGTGCCA
1 GCACACATAGTGCCA
11586060 ATGTTGACCC
Statistics
Matches: 101, Mismatches: 30, Indels: 8
0.73 0.22 0.06
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 93 0.92
25 5 0.05
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (24 bp):
GCACACATAGTGCCATTCAAATCC
Found at i:11590651 original size:3 final size:3
Alignment explanation
Indices: 11590645--11590721 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
11590635 ATCTAAAATT
* ** *
11590645 TTA TTA TTA TTAA TTA TTA GTA TGG TT- TTA -TA TTA -AA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11590688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11590722 GGTTTCATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 5 0.08
3 55 0.87
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:11590987 original size:23 final size:22
Alignment explanation
Indices: 11590961--11591017 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
11590951 ATAATGACAA
*
11590961 TTGTAATAAAA-ATATTGGTACAT
1 TTGTAATAAAAGATA-T-GTACAC
11590984 TTGTAATAAATAGATATGTACAC
1 TTGTAATAAA-AGATATGTACAC
11591007 TTGTAATAAAA
1 TTGTAATAAAA
11591018 TAACTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 25 0.81
24 2 0.06
25 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (22 bp):
TTGTAATAAAAGATATGTACAC
Found at i:11591245 original size:22 final size:21
Alignment explanation
Indices: 11591213--11591253 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
11591203 TAAACAAAGT
11591213 AAATAAAAGAATA-AAAGAATG
1 AAATAAAAGAA-ACAAAGAATG
11591234 AAATAAAAAGAAACAAAGAA
1 AAAT-AAAAGAAACAAAGAA
11591254 AAGAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (21 bp):
AAATAAAAGAAACAAAGAATG
Found at i:11592021 original size:16 final size:17
Alignment explanation
Indices: 11592000--11592031 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11591990 TGAATATGTA
11592000 TTGAAATTG-AATTGAG
1 TTGAAATTGAAATTGAG
11592016 TTGAAATTGAAATTGA
1 TTGAAATTGAAATTGA
11592032 AAAGTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
TTGAAATTGAAATTGAG
Found at i:11592189 original size:20 final size:22
Alignment explanation
Indices: 11592136--11592192 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
11592126 GCCGATCAGA
11592136 CACTTTATGTGTCGTATTTTAGG
1 CACTTTATGTGTCG-ATTTTAGG
* **
11592159 CACCTCGTGTGTC-A-TTTAGG
1 CACTTTATGTGTCGATTTTAGG
11592179 CACTTTATGTGTCG
1 CACTTTATGTGTCG
11592193 GGTATTCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
23 10 0.37
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (22 bp):
CACTTTATGTGTCGATTTTAGG
Found at i:11593977 original size:35 final size:35
Alignment explanation
Indices: 11593938--11594010 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
11593928 AACATCTAAT
11593938 GTCCATCAATGAAAACTTCCAAAATTTTTAATAAA
1 GTCCATCAATGAAAACTTCCAAAATTTTTAATAAA
11593973 GTCCATCAATGAAAACTTCCAAAATTTTTAATAAA
1 GTCCATCAATGAAAACTTCCAAAATTTTTAATAAA
11594008 GTC
1 GTC
11594011 AAAAACAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (35 bp):
GTCCATCAATGAAAACTTCCAAAATTTTTAATAAA
Found at i:11595674 original size:19 final size:20
Alignment explanation
Indices: 11595647--11595686 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11595637 AAATATTAAA
*
11595647 AACTCAATTA-TAATAATAT
1 AACTCAATTACTAAAAATAT
*
11595666 AACTTAATTACTAAAAATAT
1 AACTCAATTACTAAAAATAT
11595686 A
1 A
11595687 TTTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
AACTCAATTACTAAAAATAT
Found at i:11596630 original size:15 final size:14
Alignment explanation
Indices: 11596599--11596651 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
11596589 TAAATCAAGA
11596599 TTTTAACAACTTTTAT
1 TTTTAA-AA-TTTTAT
11596615 TTTTAAAATTTATAT
1 TTTTAAAATTT-TAT
** *
11596630 TTTTTTAATTTTTT
1 TTTTAAAATTTTAT
11596644 TTTTAAAA
1 TTTTAAAA
11596652 AATTGAAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 11 0.35
15 14 0.45
16 6 0.19
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAATTTTAT
Found at i:11596964 original size:21 final size:21
Alignment explanation
Indices: 11596939--11596978 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11596929 GCATTTAAGG
11596939 TTACATTAGCCTTTTTAACAA
1 TTACATTAGCCTTTTTAACAA
11596960 TTACATTAGCCTTTTTAAC
1 TTACATTAGCCTTTTTAAC
11596979 CCTCCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (21 bp):
TTACATTAGCCTTTTTAACAA
Found at i:11599426 original size:21 final size:21
Alignment explanation
Indices: 11599387--11599427 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11599377 ATCTGCTCAA
* * *
11599387 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTAGAGTAC
11599408 ACTCCACCTGCTGTAGAGTA
1 ACTCCACCTGCTGTAGAGTA
11599428 TTGCTCATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTAGAGTAC
Found at i:11603131 original size:27 final size:27
Alignment explanation
Indices: 11603097--11603159 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
11603087 TGTCTCTTCT
*
11603097 CCTCCACCTTCATCACCACCCCCCTCC
1 CCTCCACCTTCATCACAACCCCCCTCC
11603124 CCTCCACCTTCATCACAACCCCCCTCC
1 CCTCCACCTTCATCACAACCCCCCTCC
11603151 CCTCCACCT
1 CCTCCACCT
11603160 CAATCCCCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.65, G:0.00, T:0.19
Consensus pattern (27 bp):
CCTCCACCTTCATCACAACCCCCCTCC
Found at i:11604389 original size:21 final size:21
Alignment explanation
Indices: 11604363--11604405 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11604353 AAAATAAATA
11604363 AGGTTTTAGTCAGGGTGGGAG
1 AGGTTTTAGTCAGGGTGGGAG
11604384 AGGTTTTAGTCAGGGTGGGAG
1 AGGTTTTAGTCAGGGTGGGAG
11604405 A
1 A
11604406 TAAGTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.47, T:0.28
Consensus pattern (21 bp):
AGGTTTTAGTCAGGGTGGGAG
Found at i:11607876 original size:20 final size:19
Alignment explanation
Indices: 11607851--11607896 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
11607841 CCGCAACAAT
11607851 AAAAAAAAGAACTGAAAAAG
1 AAAAAAAA-AACTGAAAAAG
* *
11607871 AAAAAAAACACTGAAAACG
1 AAAAAAAAAACTGAAAAAG
11607890 AAAAAAA
1 AAAAAAA
11607897 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.76, C:0.09, G:0.11, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAACTGAAAAAG
Found at i:11608054 original size:25 final size:24
Alignment explanation
Indices: 11608020--11608082 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
11608010 AATCAGCAGC
**
11608020 AAGGAGAAGAAAATAAAGGGAAAG
1 AAGGAGAAGAAAATAAAGAAAAAG
* *
11608044 AAAGGAGAAGAGAATGAAGAAAAAG
1 -AAGGAGAAGAAAATAAAGAAAAAG
11608069 AAGGAGAAGGAAAA
1 AAGGAGAA-GAAAA
11608083 CAGAAAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (24 bp):
AAGGAGAAGAAAATAAAGAAAAAG
Found at i:11608077 original size:15 final size:15
Alignment explanation
Indices: 11608020--11608105 Score: 50
Period size: 16 Copynumber: 5.3 Consensus size: 15
11608010 AATCAGCAGC
11608020 AAGGAGAAGAAAATA-
1 AAGGAGAAGAAAA-AG
*
11608035 AAGG-GAAAGAAAGGAG
1 AAGGAG-AAGAAA-AAG
11608051 AAGAGAATGAAGAAAAAG
1 AAG-G-A-GAAGAAAAAG
11608069 AAGGAGAAGGAAAACAG
1 AAGGAGAA-GAAAA-AG
* *
11608086 AAAGAAAAGAAAAAAG
1 AAGGAGAAG-AAAAAG
11608102 AAGG
1 AAGG
11608106 TATAAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
14 1 0.02
15 14 0.25
16 15 0.27
17 14 0.25
18 5 0.09
19 6 0.11
20 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.31, T:0.02
Consensus pattern (15 bp):
AAGGAGAAGAAAAAG
Found at i:11608253 original size:26 final size:26
Alignment explanation
Indices: 11608197--11608254 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
11608187 GTTGTTAGTT
* * * * *
11608197 ATTAATATTGTTAGTAAAAAATCTTT
1 ATTATTATTATTAGTAAAAAACCATA
*
11608223 GTTATTATTATTAGTAAAAAACCATA
1 ATTATTATTATTAGTAAAAAACCATA
11608249 ATTATT
1 ATTATT
11608255 GTTAGTTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (26 bp):
ATTATTATTATTAGTAAAAAACCATA
Found at i:11608829 original size:29 final size:29
Alignment explanation
Indices: 11608787--11608844 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
11608777 ACATTAATAG
11608787 AACGAGAACATCAAATCGTTTTAGACCAA
1 AACGAGAACATCAAATCGTTTTAGACCAA
11608816 AACGAGAACATCAAATCGTTTTAGACCAA
1 AACGAGAACATCAAATCGTTTTAGACCAA
11608845 CTTTGGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (29 bp):
AACGAGAACATCAAATCGTTTTAGACCAA
Found at i:11614283 original size:46 final size:45
Alignment explanation
Indices: 11614179--11614396 Score: 190
Period size: 46 Copynumber: 4.8 Consensus size: 45
11614169 AGATTTGTGT
* * * * *
11614179 GCCAGTGTAAGACCATGTATGGGACATGGCATC-GGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA--CAGATGAGA
*
11614227 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGA
* * **
11614273 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGA
* * * * *
11614319 GCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GA
* * *
11614363 GCTAGTGTAAGACATGTCTGGAACATGCGTCAGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGC
11614397 ACGGTTACAT
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
43 1 0.01
44 32 0.22
45 2 0.01
46 80 0.56
47 18 0.12
48 11 0.08
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.22
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGA
Found at i:11614338 original size:92 final size:90
Alignment explanation
Indices: 11614179--11614390 Score: 237
Period size: 92 Copynumber: 2.3 Consensus size: 90
11614169 AGATTTGTGT
* * * *
11614179 GCCAGTGTAAGACCATGTATGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT
11614244 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACGAG-AT--GA
* * ** *
11614273 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTAGCCAGTGTCAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
* * * *
11614338 GGGACATGCGTCGGCTACGAGATGT
66 GGGACATGCATCAGCCACGAGATGA
* *
11614363 GCTAGTGTAAGACATGTCTGGAACATGC
1 GCCAGTGTAAGACATGTCTGGGACATGC
11614391 GTCAGCACGG
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 27 0.26
92 48 0.47
93 15 0.15
94 12 0.12
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA
Found at i:11619093 original size:50 final size:50
Alignment explanation
Indices: 11619035--11619139 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
11619025 TTTTAATGTG
11619035 AGTA-TGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
11619084 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
11619134 AGTATT
1 AGTATT
11619140 AGTCATGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 4 0.07
50 51 0.93
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (50 bp):
AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
Found at i:11620915 original size:18 final size:17
Alignment explanation
Indices: 11620874--11620915 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11620864 TAAATTTCGG
11620874 TTATTA-ATTTTAATAT
1 TTATTAGATTTTAATAT
11620890 TTGA-TAGATTTTAAATAT
1 TT-ATTAGATTTT-AATAT
11620908 TTATTAGA
1 TTATTAGA
11620916 ATAACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TTATTAGATTTTAATAT
Found at i:11621299 original size:147 final size:147
Alignment explanation
Indices: 11621041--11622238 Score: 1409
Period size: 147 Copynumber: 8.2 Consensus size: 147
11621031 ATAAGTAAAA
* * * * *
11621041 TATTTTCGTATATTA-TT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAG-T
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
* **
11621103 GTTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTTTC-TTCGTATTTTTTTCGTAT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAG-CAC-TTCATTCGTATTTTTTTCGTAT
11621166 CTTATTTTTTAAAATATAT
129 CTTATTTTTTAAAATATAT
* * **
11621185 TATTTTCATATTTTATTTCTTTATATCATTTTAGTACATAATGTTTTGAATGTATTATTTAAGTT
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
11621250 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTATTTTTTTCGTATCT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTATTTTTTTCGTATCT
11621315 TATTTTTTAAAATATAT
131 TATTTTTTAAAATATAT
* *
11621332 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATATTTTAAATGTATTATTTAAG-T
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
* ** * *
11621396 GTTTTTTATA-TTTTTTAATAAATAAGTCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATAT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTATTTTTTTCGTATCT
11621460 TATTTTTTAAAATATAT
131 TATTTTTTAAAATATAT
* * * * * *
11621477 TATTTTCGTATTTTATTT-TTTATATTATCTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
** * *
11621541 TTTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTT-TTTCATATTTTTATTTTCGT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAG-CACTTCATTCGTA--TTT-TTTTCGT
*
11621604 AACTTA-TTTTTAAAATATAT
127 ATCTTATTTTTTAAAATATAT
*
11621624 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAG-T
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
* * * * * *
11621688 ATTATTTATATTTTTTCAATAAATAACCTTGATTTTAGCACTTTATTCGTATTTTTTTCGTATAT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTATTTTTTTCGTATCT
11621753 TATTTTTTAAAATATAT
131 TATTTTTTAAAATATAT
* * * * *
11621770 TATTTTCGTATTTTATTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTACTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
* **
11621834 TTTCTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTTTC-TTCGTAATTTTTTTTATT
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAG-CAC-TTCATTCGT-A-----TTT-TT
11621897 TTCGTATCTTATTTTTTAAAATATAT
122 TTCGTATCTTATTTTTTAAAATATAT
*
11621923 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
* * *
11621988 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCATATTTTTTTTCGTATA
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTA-TTTTTTTCGTATC
11622053 TTATTTTTTAAAATATAT
130 TTATTTTTTAAAATATAT
** *
11622071 TATTTTCGTATTTTA------T-T-TTA--GCA-TA-A-AATCTTTCAAATGTATTATTTAAG--
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
** * * * *
11622121 -TTTTTTATATTAATTTAATAAATAACCCTGACTTTGGCACCTTGTTCATAT-TTTTTTATTTTC
66 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCA-C---TTCAT-TCGTATTT-TTTTC
* * *
11622184 GAATTTTATTTTTTAAAATATAC
125 GTATCTTATTTTTTAAAATATAT
*
11622207 TATTTTCATATTTTATTT-TTTATATTATTTTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTA
11622239 ACAAAAAACT
Statistics
Matches: 916, Mismatches: 95, Indels: 85
0.84 0.09 0.08
Matches are distributed among these distances:
132 35 0.04
133 1 0.00
135 26 0.03
136 45 0.05
137 3 0.00
138 1 0.00
140 3 0.00
141 2 0.00
142 2 0.00
143 3 0.00
144 50 0.05
145 154 0.17
146 149 0.16
147 206 0.22
148 98 0.11
149 4 0.00
152 3 0.00
153 48 0.05
154 82 0.09
155 1 0.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (147 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTT
TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTCATTCGTATTTTTTTCGTATCT
TATTTTTTAAAATATAT
Found at i:11621653 original size:29 final size:28
Alignment explanation
Indices: 11621582--11621653 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
11621572 ATTTTGACAC
*
11621582 TTTTTCATATTTTTATTTTCGTAACTTA
1 TTTTTCATATTATTATTTTCGTAACTTA
* * **
11621610 TTTTTAAAATATATTATTTTCGTATTTTA
1 TTTTTCATAT-TATTATTTTCGTAACTTA
11621639 TTTCTTCATATTATT
1 TTT-TTCATATTATT
11621654 TTAGTACATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
28 8 0.23
29 22 0.63
30 5 0.14
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTTCATATTATTATTTTCGTAACTTA
Found at i:11621776 original size:293 final size:293
Alignment explanation
Indices: 11621041--11622238 Score: 1663
Period size: 293 Copynumber: 4.1 Consensus size: 293
11621031 ATAAGTAAAA
* * * * *
11621041 TATTTTCGTATATTA-TT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* * *
11621104 TTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTTTCTTCGTATTTTTTTCGTATCT
66 TTTTTTATATT-TTTTAATAAATAACCCTGATTTTAG-CACTTTATTCGTATTTTTTTCGTATAT
* * * * * **
11621168 TATTTTTTAAAATATATTATTTTCATATTTTATTTCTTTATATCATTTTAGTACATAATGTTTTG
129 TATTTTTTAAAATATATTATTTTCGTATTTTATTT-TTTATATTATTTTAGCAAAAAATGTTTCA
* ** *
11621233 AATGTATTATTTAAGTTTTTTTTTATATTTTTTTAATAAATAACCCTGATTTT-AGCACTTCATT
193 AATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGA-CACTT-TTT
* *
11621297 CGTA--TTT-TTTTCGTATCTTATTTTTTAAAATATAT
256 CATATTTTTATTTTCGTAACTTATTTTTTAAAATATAT
* *
11621332 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATATTTTAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
**
11621397 TTTTTTATATTTTTTAATAAATAAGTCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATTA
66 TTTTTTATATTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATTA
*
11621462 TTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATCTTAGCAAAAAATGTTTCAAAT
131 TTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAAT
*
11621527 GTATTATGTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTTTCATAT
196 GTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTTTCATAT
11621592 TTTTATTTTCGTAACTTA-TTTTTAAAATATAT
261 TTTTATTTTCGTAACTTATTTTTTAAAATATAT
* *
11621624 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
11621689 TTATTTATATTTTTTCAATAAATAACCTTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
66 TTTTTTATATTTTTT-AATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
11621754 ATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAA
130 ATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAA
* *
11621819 TGTATTACTTAAGTGTTTCTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGT
195 TGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTT-TTC--
* *
11621884 AATTTTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
257 -A-TATTTTTATTTTCGTAACTTATTTTTTAAAATATAT
11621923 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
*
11621988 TTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCATATTTTTTTTCGTATA
66 -TTTTTTATA-TTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA-TTTTTTTCGTATA
* *
11622053 TTATTTTTTAAAATATATTATTTTCG-----TA-----T-T-TTATTTTAGCATAAAATCTTTCA
128 TTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCA
* * *
11622106 AATGTATTATTTAA--G-TTTTTTATATTAATTTAATAAATAACCCTGACTTTGGCACCTTGTTC
193 AATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACA-CTTTTTC
* *
11622168 ATATTTTTTTATTTTCG-AATTTTATTTTTTAAAATATAC
257 ATA--TTTTTATTTTCGTAA-CTTATTTTTTAAAATATAT
*
11622207 TATTTTCATATTTTATTT-TTTATATTATTTTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTA
11622239 ACAAAAAACT
Statistics
Matches: 828, Mismatches: 58, Indels: 50
0.88 0.06 0.05
Matches are distributed among these distances:
282 1 0.00
283 16 0.02
284 46 0.06
286 39 0.05
287 4 0.00
289 34 0.04
290 6 0.01
291 91 0.11
292 174 0.21
293 230 0.28
294 3 0.00
296 2 0.00
297 1 0.00
298 19 0.02
299 77 0.09
300 40 0.05
301 45 0.05
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (293 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
TTTTTTATATTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATTA
TTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAAT
GTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTTTCATAT
TTTTATTTTCGTAACTTATTTTTTAAAATATAT
Found at i:11622044 original size:132 final size:131
Alignment explanation
Indices: 11621908--11622178 Score: 300
Period size: 132 Copynumber: 2.1 Consensus size: 131
11621898 TCGTATCTTA
* * * *
11621908 TTTTTTAAAATATATTATTTTCGT-AT-T-TTA-TTTCTTTATATTATTTTAGTACATAATGTTT
1 TTTTTTAAAATATATTATTTT-GTAATATATTATTTTC-GTATATTATTTTAGCACAAAATCTTT
** * *
11621969 CAAATGTATTATTTAAGTGTTTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTAT
64 CAAATGTATTATTTAA--G-TTTTTTATATTAATTTAATAAATAACCCTGACTTTAGCACCTTAT
11622034 TCATAT
126 TCATAT
*** * * *
11622040 TTTTTT-TCGTATATTATTTTTTAAAATATATTATTTTCGTATTTTATTTTAGCATAAAATCTTT
1 TTTTTTAAAATATATTATTTTGT--AATATATTATTTTCGTATATTATTTTAGCACAAAATCTTT
* *
11622104 CAAATGTATTATTTAAGTTTTTTATATTAATTTAATAAATAACCCTGACTTTGGCACCTTGTTCA
64 CAAATGTATTATTTAAGTTTTTTATATTAATTTAATAAATAACCCTGACTTTAGCACCTTATTCA
11622169 TAT
129 TAT
11622172 TTTTTTA
1 TTTTTTA
11622179 TTTTCGAATT
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
130 1 0.01
131 11 0.09
132 57 0.49
133 3 0.03
134 1 0.01
135 39 0.34
136 4 0.03
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (131 bp):
TTTTTTAAAATATATTATTTTGTAATATATTATTTTCGTATATTATTTTAGCACAAAATCTTTCA
AATGTATTATTTAAGTTTTTTATATTAATTTAATAAATAACCCTGACTTTAGCACCTTATTCATA
T
Found at i:11622221 original size:136 final size:134
Alignment explanation
Indices: 11621948--11622225 Score: 371
Period size: 132 Copynumber: 2.1 Consensus size: 134
11621938 TTTCTTTATA
* * * **
11621948 TTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATTTTTTTAATAAATA
1 TTATTTTAGCACAAAATCTTTCAAATGTATTATTTAAG-GTTTTTTTATATTAATTTAATAAATA
* * * *
11622013 ACCCTGATTTTAGCACTTTATTCATATTTTTTTTCGTATATTATTTTTTAAAATATATTATTTTC
65 ACCCTGACTTTAGCACCTTATTCATATTTTTTTTCGAATATTATTTTTTAAAATATACTATTTTC
*
11622078 GTATT
130 ATATT
*
11622083 TTATTTTAGCATAAAATCTTTCAAATGTATTATTTAA-G-TTTTTTATATTAATTTAATAAATAA
1 TTATTTTAGCACAAAATCTTTCAAATGTATTATTTAAGGTTTTTTTATATTAATTTAATAAATAA
* * *
11622146 CCCTGACTTTGGCACCTTGTTCATATTTTTTTATTTTCGAATTTTATTTTTTAAAATATACTATT
66 CCCTGACTTTAGCACCTTATTCATA---TTTT-TTTTCGAATATTATTTTTTAAAATATACTATT
11622211 TTCATATT
127 TTCATATT
11622219 TTATTTT
1 TTATTTT
11622226 TTATATTATT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
132 44 0.35
133 1 0.01
135 37 0.30
136 43 0.34
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (134 bp):
TTATTTTAGCACAAAATCTTTCAAATGTATTATTTAAGGTTTTTTTATATTAATTTAATAAATAA
CCCTGACTTTAGCACCTTATTCATATTTTTTTTCGAATATTATTTTTTAAAATATACTATTTTCA
TATT
Found at i:11622736 original size:17 final size:18
Alignment explanation
Indices: 11622714--11622760 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
11622704 CCTTTTTTTC
11622714 CTTCTTTTTCCTTC-CCT
1 CTTCTTTTTCCTTCTCCT
*
11622731 CTTCTTCTTCTCCTTCTCTT
1 CTTCTT-TT-TCCTTCTCCT
*
11622751 TTTCTTTTTC
1 CTTCTTTTTC
11622761 TTTTTTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 8 0.32
20 7 0.28
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTCTTTTTCCTTCTCCT
Found at i:11622823 original size:16 final size:17
Alignment explanation
Indices: 11622802--11622849 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
11622792 TCCTCCTCCC
11622802 CTTCTTTTTCTTT-CTT
1 CTTCTTTTTCTTTCCTT
11622818 CTTCTTCTCTTCTTTCCTT
1 CTTCTT-T-TTCTTTCCTT
*
11622837 CTTCTCTTTCTTT
1 CTTCTTTTTCTTT
11622850 TCTTTTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 7 0.25
19 8 0.29
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTCTTTTTCTTTCCTT
Found at i:11622830 original size:11 final size:10
Alignment explanation
Indices: 11622803--11622858 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
11622793 CCTCCTCCCC
*
11622803 TTCTTTTTCT
1 TTCTTCTTCT
11622813 TTCTTCTTCT
1 TTCTTCTTCT
*
11622823 TCTCTTCTTTCC
1 T-TCTTC-TTCT
11622835 TTCTTC-TCT
1 TTCTTCTTCT
11622844 TTCTT-TTCT
1 TTCTTCTTCT
11622853 TT-TTCT
1 TTCTTCT
11622859 CCGCCTTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.05
9 13 0.33
10 10 0.26
11 10 0.26
12 4 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:11622838 original size:22 final size:22
Alignment explanation
Indices: 11622804--11622854 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11622794 CTCCTCCCCT
*
11622804 TCTT-TTTCTTTCTTCT-TCTTC
1 TCTTCTTTCCTTCTTCTCT-TTC
11622825 TCTTCTTTCCTTCTTCTCTTTC
1 TCTTCTTTCCTTCTTCTCTTTC
*
11622847 TTTTCTTT
1 TCTTCTTT
11622855 TTCTCCGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
TCTTCTTTCCTTCTTCTCTTTC
Found at i:11623042 original size:18 final size:18
Alignment explanation
Indices: 11623019--11623060 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
11623009 TTTATTTTTA
*
11623019 TTTTTTCGTTTTCAGTGTT
1 TTTTTTCGTTTTCAAT-TT
*
11623038 TTTTTTCTTTTTCAATTT
1 TTTTTTCGTTTTCAATTT
11623056 TTTTT
1 TTTTT
11623061 ACTGTTACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTTCGTTTTCAATTT
Found at i:11629718 original size:26 final size:29
Alignment explanation
Indices: 11629672--11629740 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 29
11629662 TTAATTGTTA
* * *
11629672 TTTGATAAATTAAGATTTTAATAA-TA-T
1 TTTGAAAAATTAAGATATTAAAAATTATT
11629699 TTTGAAAAATTAA-ATATTAAAAATTATT
1 TTTGAAAAATTAAGATATTAAAAATTATT
*
11629727 TTTAAAAAATTAAG
1 TTTGAAAAATTAAG
11629741 TATAGAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.23
27 14 0.40
28 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTGAAAAATTAAGATATTAAAAATTATT
Found at i:11631254 original size:19 final size:19
Alignment explanation
Indices: 11631230--11631266 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11631220 TTAAATGTTA
11631230 AAATTTTAATTTAATATAT
1 AAATTTTAATTTAATATAT
*
11631249 AAATTTTAATTTGATATA
1 AAATTTTAATTTAATATA
11631267 ATTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
AAATTTTAATTTAATATAT
Found at i:11641398 original size:18 final size:18
Alignment explanation
Indices: 11641375--11641447 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
11641365 TTTAGTATTT
11641375 TTTTAAATTATTATAAAA
1 TTTTAAATTATTATAAAA
* *
11641393 TTTTAAAATAATAT-AAA
1 TTTTAAATTATTATAAAA
*
11641410 TTTTAGAATTTTTATAAATA
1 TTTTA-AATTATTATAAA-A
*
11641430 TTTTGAATT-TTA-AAAA
1 TTTTAAATTATTATAAAA
11641446 TT
1 TT
11641448 ATTTTGAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.07
17 11 0.24
18 21 0.46
19 6 0.13
20 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTAAATTATTATAAAA
Found at i:11641439 original size:19 final size:19
Alignment explanation
Indices: 11641404--11641460 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
11641394 TTTAAAATAA
*
11641404 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
11641422 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
11641440 TAAAAATTATTTTGAATTTT
1 TATAAA-TATTTTGAATTTT
11641460 T
1 T
11641461 TTTTTGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 15 0.44
19 15 0.44
20 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:11643387 original size:31 final size:33
Alignment explanation
Indices: 11643352--11643429 Score: 133
Period size: 31 Copynumber: 2.4 Consensus size: 33
11643342 CAGCAGACAA
11643352 TACTTACCTTTCAAATTTTTT-TTTTG-TTTTT
1 TACTTACCTTTCAAATTTTTTATTTTGTTTTTT
*
11643383 TACTTACCTTTCAATTTTTTTATTTTGTTTTTT
1 TACTTACCTTTCAAATTTTTTATTTTGTTTTTT
11643416 TACTTACCTTTCAA
1 TACTTACCTTTCAA
11643430 TTTACACGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 20 0.45
32 5 0.11
33 19 0.43
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (33 bp):
TACTTACCTTTCAAATTTTTTATTTTGTTTTTT
Found at i:11643420 original size:33 final size:31
Alignment explanation
Indices: 11643352--11643432 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 31
11643342 CAGCAGACAA
*
11643352 TACTTACCTTTCAAATTTTTTTTTTGTTTTT
1 TACTTACCTTTCAATTTTTTTTTTTGTTTTT
11643383 TACTTACCTTTCAATTTTTTTATTTTGTTTTTT
1 TACTTACCTTTCAATTTTTTT-TTTTG-TTTTT
11643416 TACTTACCTTTCAATTT
1 TACTTACCTTTCAATTT
11643433 ACACGTACGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 20 0.43
32 5 0.11
33 22 0.47
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.65
Consensus pattern (31 bp):
TACTTACCTTTCAATTTTTTTTTTTGTTTTT
Found at i:11652366 original size:26 final size:25
Alignment explanation
Indices: 11652337--11652427 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
11652327 ATATTTAATT
11652337 ATTTTTTA-AAATTTTAAAAATATATA
1 ATTTTTTATAAATTTTAAAAAT-T-TA
*
11652363 A-TTTTTATAATTTTTAATAAATTTA
1 ATTTTTTATAAATTTTAA-AAATTTA
** *
11652388 ATGATTTATAATTTTTAAAAATTTTA
1 ATTTTTTATAAATTTTAAAAA-TTTA
* *
11652414 AATTTTTAAAAATT
1 ATTTTTTATAAATT
11652428 AAATAAATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
25 12 0.23
26 37 0.70
27 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
ATTTTTTATAAATTTTAAAAATTTA
Found at i:11652385 original size:11 final size:9
Alignment explanation
Indices: 11652359--11652421 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
11652349 TTTAAAAATA
11652359 TATAATTTT
1 TATAATTTT
11652368 TATAATTTT
1 TATAATTTT
*
11652377 TAATAAATTT
1 T-ATAATTTT
* *
11652387 AATGA--TT
1 TATAATTTT
11652394 TATAATTTT
1 TATAATTTT
* *
11652403 TAAAAATTT
1 TATAATTTT
11652412 TA-AATTTT
1 TATAATTTT
11652420 TA
1 TA
11652422 AAAATTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
7 5 0.12
8 7 0.16
9 24 0.56
10 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATAATTTT
Found at i:11652388 original size:35 final size:34
Alignment explanation
Indices: 11652339--11652426 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 34
11652329 ATTTAATTAT
* *
11652339 TTTTTAAAATTTTAAAAATATATAATTTTTATAA
1 TTTTTAAAAATTTAAAAATATATAATTTTTAAAA
** *
11652373 TTTTTAATAAATTTAATGATTTATAATTTTTAAAA
1 TTTTTAA-AAATTTAAAAATATATAATTTTTAAAA
* **
11652408 ATTTTAAATTTTTAAAAAT
1 TTTTTAAAAATTTAAAAAT
11652427 TAAATAAATA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 15 0.35
35 28 0.65
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
TTTTTAAAAATTTAAAAATATATAATTTTTAAAA
Found at i:11652411 original size:17 final size:17
Alignment explanation
Indices: 11652348--11652427 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
11652338 TTTTTTAAAA
*
11652348 TTTTAAAAATATATAAT
1 TTTTAAAAATTTATAAT
* *
11652365 TTTT-ATAATTTTTAAT
1 TTTTAAAAATTTATAAT
* **
11652381 AAATTTAATGATTTATAAT
1 --TTTTAAAAATTTATAAT
11652400 TTTTAAAAATTT-TAAAT
1 TTTTAAAAATTTAT-AAT
11652417 TTTTAAAAATT
1 TTTTAAAAATT
11652428 AAATAAATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
16 10 0.20
17 27 0.54
18 3 0.06
19 10 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTTAAAAATTTATAAT
Found at i:11667901 original size:3 final size:3
Alignment explanation
Indices: 11667853--11667886 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
11667843 GCTTCCTCAA
*
11667853 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
11667887 TATATCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.35, G:0.29, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:11669026 original size:95 final size:95
Alignment explanation
Indices: 11668863--11669053 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
11668853 CATCATCAAG
11668863 TATGTTTTTGAATTTTTGCAGTTACATACTGTTGCTCTTTGCCTTATTTCTTTGTTGCTTTCTGA
1 TATGTTTTTGAATTTTTGCAGTTACATACTGTTGCTCTTTGCCTTATTTCTTTGTTGCTTTCTGA
11668928 TATTGTGTTATTTAACTGATCTTTAAATAT
66 TATTGTGTTATTTAACTGATCTTTAAATAT
11668958 TATGTTTTTGAATTTTTGCAGTTACATACTGTTGCTCTTTGCCTTATTTCTTTGTTGCTTTCTGA
1 TATGTTTTTGAATTTTTGCAGTTACATACTGTTGCTCTTTGCCTTATTTCTTTGTTGCTTTCTGA
11669023 TATTGTGTTATTTAACTGATCTTTAAATAT
66 TATTGTGTTATTTAACTGATCTTTAAATAT
11669053 T
1 T
11669054 TCCTCAGATA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.55
Consensus pattern (95 bp):
TATGTTTTTGAATTTTTGCAGTTACATACTGTTGCTCTTTGCCTTATTTCTTTGTTGCTTTCTGA
TATTGTGTTATTTAACTGATCTTTAAATAT
Found at i:11672564 original size:24 final size:24
Alignment explanation
Indices: 11672537--11672588 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11672527 TCAGATTATG
* *
11672537 CAGCAGAAGCATCAA-CTAATGCAA
1 CAGCAGAAGCAGCAAGC-AAAGCAA
*
11672561 CAGCAGCAGCAGCAAGCAAAGCAA
1 CAGCAGAAGCAGCAAGCAAAGCAA
11672585 CAGC
1 CAGC
11672589 TGCCCACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (24 bp):
CAGCAGAAGCAGCAAGCAAAGCAA
Found at i:11686444 original size:22 final size:23
Alignment explanation
Indices: 11686418--11686461 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11686408 AAAAATGATA
11686418 TAAATATTTTT-AGGA-ATAAATC
1 TAAAT-TTTTTAAGGATATAAATC
11686440 TAAATTTTTTAAGGATATAAAT
1 TAAATTTTTTAAGGATATAAAT
11686462 ACACAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 9 0.45
23 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TAAATTTTTTAAGGATATAAATC
Found at i:11686629 original size:18 final size:18
Alignment explanation
Indices: 11686588--11686629 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
11686578 ATTTTGATAA
11686588 TTCAA-ATAATTAATATT
1 TTCAATATAATTAATATT
*
11686605 TTTAATATAATT-ATATT
1 TTCAATATAATTAATATT
11686622 TGTCAATA
1 T-TCAATA
11686630 ATATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (18 bp):
TTCAATATAATTAATATT
Found at i:11687418 original size:17 final size:18
Alignment explanation
Indices: 11687384--11687423 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
11687374 CTTTTTTAGT
11687384 AAAACTTAATTCAAAGTAA
1 AAAACTTAATTC-AAGTAA
*
11687403 AAAATTTAATTC-AGTAA
1 AAAACTTAATTCAAGTAA
11687420 AAAA
1 AAAA
11687424 ATTTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAACTTAATTCAAGTAA
Found at i:11688012 original size:22 final size:23
Alignment explanation
Indices: 11687981--11688029 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
11687971 CTTAATTCGA
* *
11687981 TTTTAGTTAAATTTAA-CATTAT
1 TTTTAGTTAAACTTAATCATAAT
*
11688003 TTTTATTTAAACTTAATCATAAT
1 TTTTAGTTAAACTTAATCATAAT
11688026 TTTT
1 TTTT
11688030 TAAAAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAGTTAAACTTAATCATAAT
Found at i:11693191 original size:19 final size:19
Alignment explanation
Indices: 11693169--11693213 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11693159 TGAGTTAATG
*
11693169 TAAAAAAT-ATTTTGAATTA
1 TAAAAAATAATATT-AATTA
*
11693188 TAAATAATAATATTAATTA
1 TAAAAAATAATATTAATTA
11693207 TAAAAAA
1 TAAAAAA
11693214 ATAAGTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAAAATAATATTAATTA
Found at i:11694592 original size:22 final size:21
Alignment explanation
Indices: 11694562--11694608 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
11694552 GGTTGATAAG
* *
11694562 AAAAAGTAAATATAAATTGTA
1 AAAAAGTAAAAATAAATTATA
*
11694583 AAAAAGGTAAAAATATATTATA
1 AAAAA-GTAAAAATAAATTATA
11694605 AAAA
1 AAAA
11694609 TTTAAAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAAAGTAAAAATAAATTATA
Found at i:11695584 original size:3 final size:3
Alignment explanation
Indices: 11695576--11695603 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11695566 TATTTTAACG
11695576 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11695604 TAATTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11710131 original size:11 final size:12
Alignment explanation
Indices: 11710100--11710132 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11710090 TTTTACATTG
11710100 GTTTCTTTTCCA
1 GTTTCTTTTCCA
*
11710112 GTTTTTTTTCCA
1 GTTTCTTTTCCA
11710124 -TTTCTTTTC
1 GTTTCTTTTC
11710133 TAAGATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.67
Consensus pattern (12 bp):
GTTTCTTTTCCA
Found at i:11724346 original size:32 final size:32
Alignment explanation
Indices: 11724298--11724381 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 32
11724288 TTATAATTAA
11724298 TATAATTTATTATTTTAATAAAACCA-TTTAATAT
1 TATAA-TT-TTATTTTAATAAAA-CATTTTAATAT
* *
11724332 TATAATTTTATTTTAATAATACATTTTAATGT
1 TATAATTTTATTTTAATAAAACATTTTAATAT
*
11724364 TAATAATTTAAATTTTAA
1 T-ATAATTT-TATTTTAA
11724382 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.05
32 21 0.48
33 9 0.20
34 12 0.27
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (32 bp):
TATAATTTTATTTTAATAAAACATTTTAATAT
Found at i:11728119 original size:29 final size:30
Alignment explanation
Indices: 11728077--11728133 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
11728067 TCTCGGCCCT
11728077 CTTTAAAAATG-AAAAAAAAATTCATATCC
1 CTTTAAAAATGAAAAAAAAAATTCATATCC
11728106 CTTTAAAAATGAAAAAAAAAATTCATAT
1 CTTTAAAAATGAAAAAAAAAATTCATAT
11728134 AGCCAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.28
Consensus pattern (30 bp):
CTTTAAAAATGAAAAAAAAAATTCATATCC
Found at i:11738306 original size:112 final size:111
Alignment explanation
Indices: 11738109--11738337 Score: 334
Period size: 112 Copynumber: 2.0 Consensus size: 111
11738099 AATATTTGAG
*
11738109 TATACAATTATAGATGGACCATAAGGAACCGTACATATTGACTAATAAAAACATTGCATGTTTTG
1 TATACAATTATAGATGGACCATAAGGAACCATACA-ATTGACTAATAAAAACATTGCATGTTTTG
* * * *
11738174 TAAATAAATTAGACCACACTTTAGAGCTTATTGTATGTCTTATGCTT
65 TAAATAAACTAAACCACACTTTAGAGCTTATTATATGTCGTATGCTT
* *
11738221 TATACATATATATGGATGTACCATAAGGAACCATAC-ATTGACTAATAAAAACATTGCATGTTTT
1 TATACA-AT-TATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCATGTTTT
* * *
11738285 GTAGATAAACTAAACCACACTTTGGAGTTTATTATATGTCGTATGCTT
64 GTAAATAAACTAAACCACACTTTAGAGCTTATTATATGTCGTATGCTT
11738333 TATAC
1 TATAC
11738338 GTGCATATAG
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
112 80 0.76
113 2 0.02
114 23 0.22
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (111 bp):
TATACAATTATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCATGTTTTGT
AAATAAACTAAACCACACTTTAGAGCTTATTATATGTCGTATGCTT
Found at i:11741825 original size:9 final size:8
Alignment explanation
Indices: 11741806--11741843 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
11741796 AATATTTTAA
11741806 AAAAATAT
1 AAAAATAT
11741814 AAAAATAGT
1 AAAAATA-T
11741823 AAAAAATAT
1 -AAAAATAT
11741832 AAAAATA-
1 AAAAATAT
11741839 AAAAA
1 AAAAA
11741844 AATATTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.18
8 14 0.50
9 2 0.07
10 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (8 bp):
AAAAATAT
Found at i:11741828 original size:18 final size:17
Alignment explanation
Indices: 11741804--11741848 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
11741794 TTAATATTTT
11741804 AAAAAAATATAAAAATA
1 AAAAAAATATAAAAATA
*
11741821 GTAAAAAATATAAAAATA
1 -AAAAAAATATAAAAATA
11741839 AAAAAAATAT
1 AAAAAAATAT
11741849 TGTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAAATATAAAAATA
Found at i:11742300 original size:25 final size:24
Alignment explanation
Indices: 11742267--11742339 Score: 78
Period size: 22 Copynumber: 3.1 Consensus size: 24
11742257 TTTAACGGTC
*
11742267 AACCGTTAAAGTTAACGGTTAAAG
1 AACCGTTAAAGTTAACGGTCAAAG
* **
11742291 AATTCGTTAACTTTAACGGTCAAAG
1 AA-CCGTTAAAGTTAACGGTCAAAG
*
11742316 --CCGTTAAAGTTAACGATCAAAG
1 AACCGTTAAAGTTAACGGTCAAAG
11742338 AA
1 AA
11742340 ATTTTTTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 18 0.47
24 2 0.05
25 18 0.47
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (24 bp):
AACCGTTAAAGTTAACGGTCAAAG
Found at i:11742304 original size:45 final size:46
Alignment explanation
Indices: 11742241--11742339 Score: 150
Period size: 47 Copynumber: 2.2 Consensus size: 46
11742231 ACTTAAAAAA
11742241 ATTAAAG-ATTGTTAACTTTAACGGTC-AA-CCGTTAAAGTTAACG
1 ATTAAAGAATTGTTAACTTTAACGGTCAAAGCCGTTAAAGTTAACG
*
11742284 GTTAAAGAATTCGTTAACTTTAACGGTCAAAGCCGTTAAAGTTAACG
1 ATTAAAGAATT-GTTAACTTTAACGGTCAAAGCCGTTAAAGTTAACG
*
11742331 ATCAAAGAA
1 ATTAAAGAA
11742340 ATTTTTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 6 0.12
44 3 0.06
45 16 0.33
46 2 0.04
47 22 0.45
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (46 bp):
ATTAAAGAATTGTTAACTTTAACGGTCAAAGCCGTTAAAGTTAACG
Found at i:11742328 original size:22 final size:22
Alignment explanation
Indices: 11742258--11742337 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
11742248 ATTGTTAACT
11742258 TTAACGGTC-AA-CCGTTAAAG
1 TTAACGGTCAAAGCCGTTAAAG
* * **
11742278 TTAACGGTTAAAGAATTCGTTAACT
1 TTAACGGTCAAAG---CCGTTAAAG
11742303 TTAACGGTCAAAGCCGTTAAAG
1 TTAACGGTCAAAGCCGTTAAAG
*
11742325 TTAACGATCAAAG
1 TTAACGGTCAAAG
11742338 AAATTTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 8 0.17
21 2 0.04
22 18 0.39
25 18 0.39
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (22 bp):
TTAACGGTCAAAGCCGTTAAAG
Found at i:11746697 original size:84 final size:84
Alignment explanation
Indices: 11746559--11746726 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
11746549 ACTTAAAATT
11746559 TTCTCTGCAATTAATCTACCCCTATGAAGAGAGAAGACAAAAAGCACTCAAATTTATACTATATA
1 TTCTCTGCAATTAATCTACCCCTATGAAGAGAGAAGACAAAAAGCACTCAAATTTATACTATATA
11746624 TAAACAAAGAAAAAAGAAA
66 TAAACAAAGAAAAAAGAAA
11746643 TTCTCTGCAATTAATCTACCCCTATGAAGAGAGAAGACAAAAAGCACTCAAATTTATACTATATA
1 TTCTCTGCAATTAATCTACCCCTATGAAGAGAGAAGACAAAAAGCACTCAAATTTATACTATATA
11746708 TAAACAAAGAAAAAAGAAA
66 TAAACAAAGAAAAAAGAAA
11746727 GTCTGTCTGC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.23
Consensus pattern (84 bp):
TTCTCTGCAATTAATCTACCCCTATGAAGAGAGAAGACAAAAAGCACTCAAATTTATACTATATA
TAAACAAAGAAAAAAGAAA
Found at i:11750028 original size:9 final size:9
Alignment explanation
Indices: 11750008--11750052 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
11749998 ATTTTAATTT
11750008 AATTAT-AA
1 AATTATAAA
11750016 AATTATAAA
1 AATTATAAA
11750025 AATTATAAA
1 AATTATAAA
*
11750034 ATATATATACA
1 A-AT-TATAAA
11750045 AATTATAA
1 AATTATAA
11750053 TATTTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 6 0.19
9 16 0.50
10 4 0.12
11 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AATTATAAA
Found at i:11750047 original size:20 final size:17
Alignment explanation
Indices: 11750008--11750052 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
11749998 ATTTTAATTT
11750008 AATTATAAAATTATAAA
1 AATTATAAAATTATAAA
11750025 AATTATAAAATATATATACA
1 AATTATAAAAT-TATA-A-A
11750045 AATTATAA
1 AATTATAA
11750053 TATTTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 1 0.04
20 9 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATAAAATTATAAA
Found at i:11750754 original size:31 final size:31
Alignment explanation
Indices: 11750678--11750757 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
11750668 CCAATAATTT
* *
11750678 AAATAAAAA-TTTCTAAATAATTTAGTGACTT
1 AAATAAAAACTTT-TAAATAATTTAATGACTC
11750709 AAATAAAAACTTTTAAATAATTTAATGA-TC
1 AAATAAAAACTTTTAAATAATTTAATGACTC
* *
11750739 AAATTATAACTTTTTAAAT
1 AAATAAAAAC-TTTTAAAT
11750758 TAAGTGATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.21
31 31 0.72
32 3 0.07
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATAAAAACTTTTAAATAATTTAATGACTC
Found at i:11754436 original size:18 final size:19
Alignment explanation
Indices: 11754415--11754456 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
11754405 TTCCGGATTT
*
11754415 TTTTATAACTA-TTAAGTA
1 TTTTATAACTATTTAAGAA
*
11754433 TTTTA-AATTATTTAAGAA
1 TTTTATAACTATTTAAGAA
11754451 TTTTAT
1 TTTTAT
11754457 GTCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTATAACTATTTAAGAA
Found at i:11757880 original size:183 final size:183
Alignment explanation
Indices: 11757560--11757929 Score: 542
Period size: 183 Copynumber: 2.0 Consensus size: 183
11757550 CAACTGGCAC
11757560 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTAC
* ** * * *
11757625 ATCCTGAGACCTGACAGACTGAGTAACAGGTCCCTTTCGCAACGCTTGCTGCTCTTCGAACTCAC
66 ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* *
11757690 AGAGGGCATATTGAATTCCTTGGCCATGTTCCAAACTATCACTAGTCTTTGAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAACTATCACTAGTCTTTAAT
* *** * *
11757743 AAATTGTCCCATGAACTGGTTCTGTGTTCTAAGGGGATCTTTGGTTGATTTGAAGTCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTAC
* * * *
11757808 ATCTTGAAACCTGGCAGACTGAGTAACAGACCCCTTTTGCAACCCTTGCAGCTCTTCAAACTCGC
66 ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* ** *
11757873 TGAGGGCATATTGAATTCCTTGGCCATATTCTGAGCTATCACTAGTCTTTAAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAACTATCACTAGTCTTTAAT
11757926 AAAT
1 AAAT
11757930 GACTGATTCT
Statistics
Matches: 165, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (183 bp):
AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTAC
ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
AGAGGGCATATTGAATTCCTTGGCCATATTCCAAACTATCACTAGTCTTTAAT
Found at i:11766237 original size:27 final size:27
Alignment explanation
Indices: 11766188--11766257 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
11766178 AAATAAATAA
* *
11766188 AAAAATATAAATATTTAACTTTAACTT
1 AAAAATATAAATATTTAAATTTAAATT
*
11766215 AAAAATAT-AATTTTTAAAATTTAAATT
1 AAAAATATAAATATTT-AAATTTAAATT
* *
11766242 TAAAATTTAAAATATT
1 AAAAATAT-AAATATT
11766258 ACACTTAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.18
27 23 0.68
29 5 0.15
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAAATATAAATATTTAAATTTAAATT
Found at i:11766245 original size:13 final size:13
Alignment explanation
Indices: 11766227--11766252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11766217 AAATATAATT
11766227 TTTAAAATTTAAA
1 TTTAAAATTTAAA
11766240 TTTAAAATTTAAA
1 TTTAAAATTTAAA
11766253 ATATTACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:11766852 original size:93 final size:93
Alignment explanation
Indices: 11766715--11766901 Score: 275
Period size: 93 Copynumber: 2.0 Consensus size: 93
11766705 GACAACTGTG
* * * * * * * *
11766715 AATCTCAAATATTGACCGTAAAACGGACATGAAATATACAAAAAATAAAAGAATCTATTGAATGT
1 AATCTCAAACATGGACAGTAAAACAGACATAAAACATACAAAAAATAAAAGAAACAATTGAATGT
11766780 TTTATGATTTGTAAAATTTAACGTTTCA
66 TTTATGATTTGTAAAATTTAACGTTTCA
* * *
11766808 AATCTCAAACATGGACAGTAAAATAGACATAAAACATACCAAAAATAAAATAAACAATTGAATGT
1 AATCTCAAACATGGACAGTAAAACAGACATAAAACATACAAAAAATAAAAGAAACAATTGAATGT
11766873 TTTATGATTTGTAAAATTTAACGTTTCA
66 TTTATGATTTGTAAAATTTAACGTTTCA
11766901 A
1 A
11766902 TTCAATCTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (93 bp):
AATCTCAAACATGGACAGTAAAACAGACATAAAACATACAAAAAATAAAAGAAACAATTGAATGT
TTTATGATTTGTAAAATTTAACGTTTCA
Found at i:11768328 original size:71 final size:75
Alignment explanation
Indices: 11768248--11768393 Score: 237
Period size: 75 Copynumber: 2.0 Consensus size: 75
11768238 CTTTAAATTT
*
11768248 TAAATTATAATTTTAATAG-GTTGTGATTATT-AAAA-AA-ATTTATTAATATTAAAATAGTTTT
1 TAAATTATAATTTTAATAGAGTTGTGATTATTAAAAATAACATATATTAATATTAAAATAGTTTT
11768309 ATCTAAAAAA
66 ATCTAAAAAA
* *
11768319 TAAATTATAATTTTAATAGATTTGTGATTATTAAAAATAACATATATTAATGTTAAAATAGTTTT
1 TAAATTATAATTTTAATAGAGTTGTGATTATTAAAAATAACATATATTAATATTAAAATAGTTTT
11768384 ATCTAAAAAA
66 ATCTAAAAAA
11768394 AATGTAAAGG
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
71 19 0.28
72 11 0.16
73 4 0.06
74 2 0.03
75 32 0.47
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (75 bp):
TAAATTATAATTTTAATAGAGTTGTGATTATTAAAAATAACATATATTAATATTAAAATAGTTTT
ATCTAAAAAA
Found at i:11769634 original size:19 final size:21
Alignment explanation
Indices: 11769596--11769634 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11769586 TCTGAGTGAA
*
11769596 AATAAAATTGTAATATATTGG
1 AATAAAAATGTAATATATTGG
11769617 AATAAAAAT-TAA-ATATTG
1 AATAAAAATGTAATATATTG
11769635 TGTTGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
AATAAAAATGTAATATATTGG
Found at i:11774691 original size:19 final size:19
Alignment explanation
Indices: 11774667--11774703 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11774657 CATCTCATCA
11774667 TTGGCCTTGTTGGAATTTG
1 TTGGCCTTGTTGGAATTTG
11774686 TTGGCCTTGTTGGAATTT
1 TTGGCCTTGTTGGAATTT
11774704 ATAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.30, T:0.49
Consensus pattern (19 bp):
TTGGCCTTGTTGGAATTTG
Found at i:11797326 original size:27 final size:27
Alignment explanation
Indices: 11797296--11797352 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
11797286 AATTACGGTT
* *
11797296 TATTCAAAATAATTAT-TCAATTTAACA
1 TATTCAAAATAATAATAACAA-TTAACA
*
11797323 TATTCAAATTAATAATAACAATTAACA
1 TATTCAAAATAATAATAACAATTAACA
11797350 TAT
1 TAT
11797353 ACGAATCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (27 bp):
TATTCAAAATAATAATAACAATTAACA
Found at i:11797768 original size:35 final size:35
Alignment explanation
Indices: 11797722--11797793 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
11797712 CATCTCCGGA
*
11797722 GCTTGGCAAATATGAAAAGTA-ATCTTCAAAGATAT
1 GCTTGGCAAATATG-AAAGGAGATCTTCAAAGATAT
*
11797757 GCTTGGCAAATATGGAAGGAGATCTTCAAAGATAT
1 GCTTGGCAAATATGAAAGGAGATCTTCAAAGATAT
11797792 GC
1 GC
11797794 AATCTTAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGAAAGGAGATCTTCAAAGATAT
Found at i:11802919 original size:35 final size:35
Alignment explanation
Indices: 11802880--11802951 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
11802870 CATCTCTGGA
*
11802880 GCTTGGCAAATATGGAAAGTA-ATCTTCAAAGATAT
1 GCTTGGCAAATATGG-AAGGAGATCTTCAAAGATAT
*
11802915 GCTTGGCAAATATGGGAGGAGATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAGGAGATCTTCAAAGATAT
11802950 GC
1 GC
11802952 AATCTTAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAGGAGATCTTCAAAGATAT
Found at i:11803951 original size:16 final size:16
Alignment explanation
Indices: 11803918--11803951 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11803908 TATGGGTGTT
* *
11803918 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
11803934 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
11803950 AA
1 AA
11803952 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:11806777 original size:21 final size:21
Alignment explanation
Indices: 11806751--11806791 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11806741 AGACGAGCAA
* *
11806751 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
11806772 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
11806792 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:11808730 original size:16 final size:16
Alignment explanation
Indices: 11808697--11808730 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11808687 GGAGATTGTT
* *
11808697 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
11808713 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
11808729 AA
1 AA
11808731 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:11810930 original size:40 final size:39
Alignment explanation
Indices: 11810900--11811014 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 39
11810890 GACTAAGATT
*
11810900 CGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCC
1 CGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAG-TC
*
11810940 CGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGT-C
* * *
11810980 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTA
1 CGAAGGCATTTGTGCGAGATACTAAATCCGGGTTA
11811015 GCATTGTGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 64 0.96
41 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
CGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:11819812 original size:20 final size:20
Alignment explanation
Indices: 11819800--11819855 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
11819790 AAAAATATAT
* *
11819800 AAATATATATAAATATTTTG
1 AAATATATATAAAAATTTTA
* *
11819820 AAATATGTATAATAATTTTA
1 AAATATATATAAAAATTTTA
11819840 AAATATATATAAAAAT
1 AAATATATATAAAAAT
11819856 AAAAATATGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
AAATATATATAAAAATTTTA
Found at i:11820851 original size:22 final size:23
Alignment explanation
Indices: 11820808--11820852 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
11820798 AATTCCTTTT
**
11820808 TAATGTATAAAATTTTAAATTAA
1 TAATGTATAAAATTACAAATTAA
*
11820831 TAATG-ATAAAATTACATATTAA
1 TAATGTATAAAATTACAAATTAA
11820853 CCCTCTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TAATGTATAAAATTACAAATTAA
Found at i:11823605 original size:22 final size:22
Alignment explanation
Indices: 11823580--11823624 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11823570 ACAAAAAAAG
11823580 TCTTCCAATTTTTTTCCCAGTT
1 TCTTCCAATTTTTTTCCCAGTT
11823602 TCTTCCAATTTTTTTCCCAGTT
1 TCTTCCAATTTTTTTCCCAGTT
11823624 T
1 T
11823625 TTCTTTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.27, G:0.04, T:0.56
Consensus pattern (22 bp):
TCTTCCAATTTTTTTCCCAGTT
Found at i:11827186 original size:4 final size:4
Alignment explanation
Indices: 11827177--11827203 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11827167 ATTTTTTTAA
11827177 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
11827204 ATACTCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:11827264 original size:23 final size:25
Alignment explanation
Indices: 11827222--11827269 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
11827212 TCGTGTAGTC
11827222 CAAATGAAAAAAAACTTTA-TGATA
1 CAAATGAAAAAAAACTTTATTGATA
11827246 CAAAT-AAAAAAAA-TATTATTGATA
1 CAAATGAAAAAAAACT-TTATTGATA
11827270 TGATATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.05
23 11 0.50
24 10 0.45
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (25 bp):
CAAATGAAAAAAAACTTTATTGATA
Found at i:11830718 original size:16 final size:16
Alignment explanation
Indices: 11830697--11830729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11830687 TTCATACATG
11830697 TTAATTTAATATGTAT
1 TTAATTTAATATGTAT
11830713 TTAATTTAATATGTAT
1 TTAATTTAATATGTAT
11830729 T
1 T
11830730 CATTATGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAATTTAATATGTAT
Found at i:11831160 original size:31 final size:30
Alignment explanation
Indices: 11831117--11831177 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
11831107 AATAAGTTTC
11831117 TTTTAATAA-TTTTATAGTTTATTTTACCTTT
1 TTTTAATAATTTTTATA-TTT-TTTTACCTTT
* *
11831148 TTTTGATAATTTTTATATTTTTTTAGCTTT
1 TTTTAATAATTTTTATATTTTTTTACCTTT
11831178 ATAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 11 0.41
32 7 0.26
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (30 bp):
TTTTAATAATTTTTATATTTTTTTACCTTT
Found at i:11831790 original size:21 final size:21
Alignment explanation
Indices: 11831740--11831791 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
11831730 ATATCTTTAT
*
11831740 AATTTTTAAAGGATTAAATTA
1 AATTTTTATAGGATTAAATTA
11831761 AATTTTTATAGGATTAAATTA
1 AATTTTTATAGGATTAAATTA
11831782 AATTTTTATA
1 AATTTTTATA
11831792 ATTTTTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (21 bp):
AATTTTTATAGGATTAAATTA
Found at i:11852806 original size:30 final size:30
Alignment explanation
Indices: 11852743--11852805 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
11852733 AATAGGTATA
*
11852743 TTTATAATTTTTAAAAAATTAAATTAAATT
1 TTTATAATTTTTAAAAAATAAAATTAAATT
11852773 TTTAT-ATTTTTAAGAAAATCAAAATGT-AATT
1 TTTATAATTTTTAA-AAAAT-AAAAT-TAAATT
11852804 TT
1 TT
11852806 ACCTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 8 0.28
30 10 0.34
31 10 0.34
32 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATAAAATTAAATT
Found at i:11862417 original size:31 final size:30
Alignment explanation
Indices: 11862393--11862467 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
11862383 AAAATAATTT
11862393 AACAATTCAATGACTTAAATAAAAATTTTCA
1 AACAATTCAATGACTTAAATAAAAATTTT-A
* * *
11862424 AATAATTTAGTGACTTAAATAAAAATTTTGA
1 AACAATTCAATGACTTAAATAAAAATTTT-A
* *
11862455 AATAATTGAATGA
1 AACAATTCAATGA
11862468 TAATTTCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.35
Consensus pattern (30 bp):
AACAATTCAATGACTTAAATAAAAATTTTA
Found at i:11863892 original size:22 final size:22
Alignment explanation
Indices: 11863867--11863908 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11863857 AGGCATGTGA
*
11863867 TTTAAGGTTTAAGGTATAGGAT
1 TTTAAGGTTTAAGATATAGGAT
* *
11863889 TTTAGGGTTTATGATATAGG
1 TTTAAGGTTTAAGATATAGG
11863909 GCTTGTGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (22 bp):
TTTAAGGTTTAAGATATAGGAT
Found at i:11866525 original size:53 final size:53
Alignment explanation
Indices: 11866444--11866594 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
11866434 CTTACACGGT
* *
11866444 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
11866499 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
11866552 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
11866595 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:11868473 original size:5 final size:5
Alignment explanation
Indices: 11868463--11868497 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
11868453 AAATTTAAAG
*
11868463 TTATA TTATA TTTTA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA
11868498 ATGATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:11868528 original size:4 final size:4
Alignment explanation
Indices: 11868521--11868594 Score: 64
Period size: 4 Copynumber: 18.0 Consensus size: 4
11868511 GAATAAATAA
*
11868521 AAAG AAAG AAAG ATAG AAACG AAACG AAACAG AAAG -AA- AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G AAA-G -AA-AG AAAG AAAG AAAG AAAG
*
11868567 AAAG AAAG AAAAG AAA- AATG AAAG AAAG
1 AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
11868595 GAAGGAGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
3 6 0.10
4 37 0.63
5 12 0.20
6 3 0.05
7 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:11868573 original size:34 final size:34
Alignment explanation
Indices: 11868508--11868593 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
11868498 ATGATAAAAT
*
11868508 AAAGAATAAAT-AAA-AAGAAAGAAAGATAGAAACGA
1 AAAGAA-AAATGAAAGAA-AAAGAAAGAAAGAAA-GA
* *
11868543 AACGAAACA-GAAAGAAAAAGAAAGAAAGAAAGA
1 AAAGAAAAATGAAAGAAAAAGAAAGAAAGAAAGA
11868576 AAAGAAAAATGAAAGAAA
1 AAAGAAAAATGAAAGAAA
11868594 GGAAGGAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 9 0.21
34 27 0.63
35 7 0.16
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (34 bp):
AAAGAAAAATGAAAGAAAAAGAAAGAAAGAAAGA
Found at i:11868917 original size:18 final size:19
Alignment explanation
Indices: 11868882--11868919 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11868872 ATGAAAATTT
* *
11868882 TGAAATTTAGGGATTTAAA
1 TGAAATTTAGAGAGTTAAA
11868901 TGAAA-TTAGAGAGTTAAA
1 TGAAATTTAGAGAGTTAAA
11868919 T
1 T
11868920 CTAGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (19 bp):
TGAAATTTAGAGAGTTAAA
Found at i:11870720 original size:20 final size:20
Alignment explanation
Indices: 11870673--11870721 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11870663 TTCCCTTTAA
*
11870673 ATTATTTTATTTATAAGGTT
1 ATTATTTTATTTATAAGATT
* *
11870693 GTTGTTTTATTTAT-AGAATT
1 ATTATTTTATTTATAAG-ATT
11870713 ATTATTTTA
1 ATTATTTTA
11870722 ATAAATAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (20 bp):
ATTATTTTATTTATAAGATT
Found at i:11870865 original size:20 final size:20
Alignment explanation
Indices: 11870829--11870869 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
11870819 TTTTTATTGA
11870829 AAAATGAAATTTTATTTTTT
1 AAAATGAAATTTTATTTTTT
*
11870849 AAAAT-AAATTTTAATTTTT
1 AAAATGAAATTTTATTTTTT
11870868 AA
1 AA
11870870 GAATCAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAAATGAAATTTTATTTTTT
Found at i:11873530 original size:12 final size:12
Alignment explanation
Indices: 11873513--11873546 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11873503 TGGCCCGCCG
11873513 ATATTAATTTTT
1 ATATTAATTTTT
*
11873525 ATATTATTTTTT
1 ATATTAATTTTT
11873537 ATA-TAATTTT
1 ATATTAATTTT
11873547 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:11873704 original size:30 final size:30
Alignment explanation
Indices: 11873669--11873730 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
11873659 CTTAACAAGT
11873669 AAATATCTCTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
* * *
11873699 AAATATCTTTAATATAATAATAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
11873729 AA
1 AA
11873731 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (30 bp):
AAATATCTCTAAAATAATAACAAAATTAAC
Found at i:11874610 original size:18 final size:18
Alignment explanation
Indices: 11874567--11874601 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11874557 ATAAATGATG
*
11874567 ATTGAA-TTTGTTAATTA
1 ATTGAAGTTAGTTAATTA
11874584 ATTGAAGTTAGTTAATTA
1 ATTGAAGTTAGTTAATTA
11874602 GTTTGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTGAAGTTAGTTAATTA
Found at i:11876479 original size:26 final size:25
Alignment explanation
Indices: 11876446--11876497 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
11876436 AGAAAAGTAA
*
11876446 ATATGATATTAATACATATATATAT
1 ATATGATATTAATACATATAGATAT
*
11876471 ATATAGATATTGATACATATAGATAT
1 ATAT-GATATTAATACATATAGATAT
11876497 A
1 A
11876498 ACAGCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
ATATGATATTAATACATATAGATAT
Found at i:11885496 original size:17 final size:18
Alignment explanation
Indices: 11885458--11885505 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
11885448 CATATGGCGA
11885458 GTTCTTTTTT-TAATTATT
1 GTTCTTTTTTAT-ATTATT
11885476 -TTCTTTTTTATATT-TT
1 GTTCTTTTTTATATTATT
*
11885492 GTTCTTTGTTATAT
1 GTTCTTTTTTATAT
11885506 GAGAGGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 24 0.89
18 1 0.04
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (18 bp):
GTTCTTTTTTATATTATT
Found at i:11887832 original size:193 final size:193
Alignment explanation
Indices: 11887480--11887835 Score: 523
Period size: 193 Copynumber: 1.8 Consensus size: 193
11887470 TTCGAGAGCG
* * *
11887480 TCATTATTTTCTGTCAGCTTACCCAAAGCAATATTGAAGAGCGCTTGTAACATGTCCATATTGGA
1 TCATTATTTTCTGTCAACTTACCCAAAGCAATATTGAAGAGCGCTTATAACACGTCCATATTGGA
* *
11887545 ACTAAAGGCCTCCGCAACATATTCCTCAAGTTGCTCTTTCATCAAGTCCAGCTCATTAATGCGTC
66 ACTAAAGGCCTCCACAACATATTCCTCAAGTTGCTCTTTCATCAAGTCCAACTCATTAATGCGTC
*
11887610 CCTCAACTATCTCGAATGTTTCATTCACCTCACCCATGGATTCTTCAACTAAGGGCTTCCGCA
131 CCTCAACTATCTCGAATATTTCATTCACCTCACCCATGGATTCTTCAACTAAGGGCTTCCGCA
* ** * * * * *
11887673 TCATTCTTTTCTGTCAACTTACCCGGAGCAGTATTGAGGAGTGTTTATAATACGTCCATATTGGA
1 TCATTATTTTCTGTCAACTTACCCAAAGCAATATTGAAGAGCGCTTATAACACGTCCATATTGGA
* * * *
11887738 ACTAAGGGCCTCCATAACATATTCCTCAAGTTGCTCTTTCATCGAGTCCAACTTATTAATGCGTC
66 ACTAAAGGCCTCCACAACATATTCCTCAAGTTGCTCTTTCATCAAGTCCAACTCATTAATGCGTC
* * *
11887803 CCTCAACTATCTTGAGTATTTCCTTCACCTCAC
131 CCTCAACTATCTCGAATATTTCATTCACCTCAC
11887836 TTACAAGTTT
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
193 142 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.33
Consensus pattern (193 bp):
TCATTATTTTCTGTCAACTTACCCAAAGCAATATTGAAGAGCGCTTATAACACGTCCATATTGGA
ACTAAAGGCCTCCACAACATATTCCTCAAGTTGCTCTTTCATCAAGTCCAACTCATTAATGCGTC
CCTCAACTATCTCGAATATTTCATTCACCTCACCCATGGATTCTTCAACTAAGGGCTTCCGCA
Found at i:11888851 original size:20 final size:20
Alignment explanation
Indices: 11888828--11888876 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11888818 TATTTATAAA
*
11888828 TATTTTTATAATTAT-ATATG
1 TATTTTTATAA-AATCATATG
* *
11888848 TATTTTTGTAAAATCTTATG
1 TATTTTTATAAAATCATATG
11888868 TATTTTTAT
1 TATTTTTAT
11888877 TGAAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
TATTTTTATAAAATCATATG
Found at i:11893611 original size:20 final size:21
Alignment explanation
Indices: 11893574--11893617 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11893564 TAAGTATCTT
*
11893574 TTTTTAAAAATCAAAATATTA
1 TTTTTAAAAATCAAAATATAA
*
11893595 TTTTTAAAAAT-ATAATATAA
1 TTTTTAAAAATCAAAATATAA
11893615 TTT
1 TTT
11893618 CATAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTTAAAAATCAAAATATAA
Found at i:11898280 original size:20 final size:21
Alignment explanation
Indices: 11898242--11898281 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11898232 TCTTCAGTAT
* *
11898242 CCATGATGGTAAAGCATAGGC
1 CCATGAAGGTAAAGAATAGGC
11898263 CCATGAAGG-AAAGAATAGG
1 CCATGAAGGTAAAGAATAGG
11898282 AGGTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
CCATGAAGGTAAAGAATAGGC
Done.