Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold113
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: 3764034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 4009 characters in sequence are not A, C, G, or T
File 10 of 23
Found at i:1525934 original size:13 final size:13
Alignment explanation
Indices: 1525916--1525941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1525906 GAAATCAAAA
1525916 AGGTACCAATTTC
1 AGGTACCAATTTC
1525929 AGGTACCAATTTC
1 AGGTACCAATTTC
1525942 TGGGCACCAC
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
AGGTACCAATTTC
Found at i:1536539 original size:21 final size:22
Alignment explanation
Indices: 1536497--1536539 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1536487 GCAGATAGTG
* *
1536497 TAAAAAAATATTATGCATAAAA
1 TAAAAAAATATTATGAAAAAAA
*
1536519 TAAAAAAA-ATTTTGAAAAAAA
1 TAAAAAAATATTATGAAAAAAA
1536540 GGGGTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
TAAAAAAATATTATGAAAAAAA
Found at i:1537672 original size:42 final size:43
Alignment explanation
Indices: 1537606--1537686 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
1537596 CTCACTAAAC
* *
1537606 TTCATCTTTTTATTTTCCCGTCGATTTAGACC-TGGGAAATTTT
1 TTCATCTTTTTATTTTCCCATCGATTCA-ACCTTGGGAAATTTT
1537649 TTCA-CTTTTTATTTTCCCATCGATTCAACCTTGGGAAA
1 TTCATCTTTTTATTTTCCCATCGATTCAACCTTGGGAAA
1537687 CAACCTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 3 0.09
42 28 0.80
43 4 0.11
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (43 bp):
TTCATCTTTTTATTTTCCCATCGATTCAACCTTGGGAAATTTT
Found at i:1537991 original size:42 final size:42
Alignment explanation
Indices: 1537873--1538424 Score: 311
Period size: 42 Copynumber: 13.0 Consensus size: 42
1537863 GACCATATGA
* *
1537873 ACTTTCCTACCATAAAGTCTGCTTGTC-GACTTTGACCCTAGAG
1 ACTTTCCTATC-TAAAGTCTGCCTGTCAG-CTTTGACCCTAGAG
** * *
1537916 ACTTTCCTATCCTTTAGTCTGTCTGTCAACTTTGACCCTAGAG
1 ACTTTCCTAT-CTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* ** * * *
1537959 ACTTTTCTATCTAAAGTCTGTTTGTTAGCTTTGACCTTGGAG
1 ACTTTCCTATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
** * * * * *
1538001 ACTTTCCTATCCTTCATTCTACATATCGGCTTTGACCCTAGAG
1 ACTTTCCTAT-CTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* * * *
1538044 ACTGT-CTCATCTAAAGTTTGCTTGTC-GACTTTGACCTTAGAG
1 ACTTTCCT-ATCTAAAGTCTGCCTGTCAG-CTTTGACCCTAGAG
** * *
1538086 ACTGTT-CTATCCTTTAGTCTACCTGTCAGCTTTGACCCTGGAG
1 ACT-TTCCTAT-CTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* * * * *
1538129 AC-TGCCTCATCTAAAGTCTG-CTGTCGGTTTTAACCTTAGAG
1 ACTTTCCT-ATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* * * * *
1538170 ACTGT-CTCATCTTAAGTCTACCTGTCAACTTTGACCCTTGAG
1 ACTTTCCT-ATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* * * * ** * *
1538212 ACTTTTCTACCCT-CAGTCTGCTTGTTGGCTTTGACCGTGGAG
1 ACTTTCCTA-TCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
**
1538254 AC-AACCTCATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
1 ACTTTCCT-ATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
** * * * * *
1538296 ACTTTCCTATCCTTTAGTTTGCCTATCGGCTTTGATCTTAGAG
1 ACTTTCCTAT-CTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
* * *
1538339 AC-TGCCTCATCTAAAGTTTGCCTGTC-GACTTTGACCCTGGAG
1 ACTTTCCT-ATCTAAAGTCTGCCTGTCAG-CTTTGACCCTAGAG
* * *
1538381 ACTTT-CTAATCCTTCAA-TCTGCCTGTCAGCTTTAACCCTGGAG
1 ACTTTCCT-AT-C-TAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
1538424 A
1 A
1538425 TTGTCTCATC
Statistics
Matches: 382, Mismatches: 103, Indels: 48
0.72 0.19 0.09
Matches are distributed among these distances:
41 38 0.10
42 177 0.46
43 161 0.42
44 6 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (42 bp):
ACTTTCCTATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAG
Found at i:1538361 original size:85 final size:85
Alignment explanation
Indices: 1537887--1538442 Score: 346
Period size: 85 Copynumber: 6.6 Consensus size: 85
1537877 TCCTACCATA
* * * * ** ** *
1537887 AAGTCTGCTTGTCGACTTTGACCCTAGAGACTTTCCT-ATCCTTTAGTCTGTCTGTCAACTTTGA
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGAC-TGCCTCAT-CTAAAGTCTACCTGTCAGCTTTGA
*
1537951 CCCTAGAGACTTT-TCTAT-CTA
64 CCCTAGAGACTTTCTC-ATCCTT
** ** * * ** * * * *
1537972 AAGTCTGTTTGTTAGCTTTGACCTTGGAGACTTTCCT-ATCCTTCATTCTACATATCGGCTTTGA
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGAC-TGCCTCAT-CTAAAGTCTACCTGTCAGCTTTGA
* *
1538036 CCCTAGAGACTGTCTCAT-CTA
64 CCCTAGAGACTTTCTCATCCTT
* * * * **
1538057 AAGTTTGCTTGTCGACTTTGACCTTAGAGACTG-TTCTATCCTTTAGTCTACCTGTCAGCTTTGA
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC-AT-CTAAAGTCTACCTGTCAGCTTTGA
* ** *
1538121 CCCTGGAGACTGCCTCAT-CTA
64 CCCTAGAGACTTTCTCATCCTT
* * * * *
1538142 AAGTCTG-CTGTCGGTTTTAACCTTAGAGACTGTCTCATCTTAAGTCTACCTGTCAACTTTGACC
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTAAAGTCTACCTGTCAGCTTTGACC
* *
1538206 CTTGAGACTTT-TC-TACCCT
66 CTAGAGACTTTCTCAT-CCTT
* * * * * ** *
1538225 CAGTCTGCTTGTTGGCTTTGACCGTGGAGACAACCTCATCTAAAGTCTGCCTGTCAGCTTTGACC
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTAAAGTCTACCTGTCAGCTTTGACC
1538290 CTAGAGACTTTC-CTATCCTT
66 CTAGAGACTTTCTC-ATCCTT
* * * * * *
1538310 TAGTTTGCCTATCGGCTTTGATCTTAGAGACTGCCTCATCTAAAGTTTGCCTGTC-GACTTTGAC
1 AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTAAAGTCTACCTGTCAG-CTTTGAC
* *
1538374 CCTGGAGACTTTCTAATCCTT
65 CCTAGAGACTTTCTCATCCTT
* * * * * * *
1538395 CAA-TCTGCCTGTCAGCTTTAACCCTGGAGATTGTCTCATCTTAAGTCT
1 -AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTAAAGTCT
1538443 GTTTGTCGAC
Statistics
Matches: 375, Mismatches: 83, Indels: 26
0.77 0.17 0.05
Matches are distributed among these distances:
81 1 0.00
82 2 0.01
83 40 0.11
84 81 0.22
85 247 0.66
86 4 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (85 bp):
AAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTAAAGTCTACCTGTCAGCTTTGACC
CTAGAGACTTTCTCATCCTT
Found at i:1539463 original size:18 final size:17
Alignment explanation
Indices: 1539430--1539463 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1539420 ACAAGGAAGA
*
1539430 AAGTGGAAGACAAAGCT
1 AAGTGGAACACAAAGCT
1539447 AAGTGGAACAGCAAAGC
1 AAGTGGAACA-CAAAGC
1539464 AACAAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.15, G:0.29, T:0.09
Consensus pattern (17 bp):
AAGTGGAACACAAAGCT
Found at i:1539615 original size:68 final size:68
Alignment explanation
Indices: 1539540--1539836 Score: 280
Period size: 68 Copynumber: 4.5 Consensus size: 68
1539530 ACCAACACCT
** * * *
1539540 GCAGCAGCTTCTAGCAGTTCAGCAACCACCGCAATCTTCAACAACTTCAAGCAGCTCCCACAGCT
1 GCAGCAGCAACTAGCAGCTCAGCAACCACCGCAATCTCCAGCAACTTCAAGCAGCTCCCACAGCT
*
1539605 CTA
66 CCA
* * *
1539608 GCAGCAGCCAA-TAGCAGCTCAGCAACCACCTCAATCTCCAGCAACTTCCAGCAGCTCCCACAAC
1 GCAGCAG-CAACTAGCAGCTCAGCAACCACCGCAATCTCCAGCAACTTCAAGCAGCTCCCACAGC
1539672 TCCA
65 TCCA
* *
1539676 GCAGCAGCCAAC-AGCAGCTCCGCAACCACCGCAACCTCCAGCAACTTCCAA-CAGCTCCCACAG
1 GCAGCAG-CAACTAGCAGCTCAGCAACCACCGCAATCTCCAGCAACTT-CAAGCAGCTCCCACAG
1539739 -T---
64 CTCCA
* * * * * * *
1539740 --AGC--CAAC-AGTAGCTGAGTAACCACTGCAACCCCCAGCAACTTCCAGCAGCTCCCACAGCT
1 GCAGCAGCAACTAGCAGCTCAGCAACCACCGCAATCTCCAGCAACTTCAAGCAGCTCCCACAGCT
1539800 CCCA
66 -CCA
*
1539804 -CAGCAGCCAA-TAGCAGCTTAGCAACCACCGCAA
1 GCAGCAG-CAACTAGCAGCTCAGCAACCACCGCAA
1539837 CCTCTAGTAG
Statistics
Matches: 190, Mismatches: 25, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.01
59 45 0.24
60 1 0.01
62 3 0.02
65 3 0.02
67 1 0.01
68 132 0.69
69 3 0.02
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (68 bp):
GCAGCAGCAACTAGCAGCTCAGCAACCACCGCAATCTCCAGCAACTTCAAGCAGCTCCCACAGCT
CCA
Found at i:1539762 original size:59 final size:59
Alignment explanation
Indices: 1539681--1539797 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
1539671 CTCCAGCAGC
* *
1539681 AGCCAACAGCAGCTCCGCAACCACCGCAACCTCCAGCAACTTCCAACAGCTCCCACAGT
1 AGCCAACAGCAGCTCAGCAACCACCGCAACCCCCAGCAACTTCCAACAGCTCCCACAGT
* * * * *
1539740 AGCCAACAGTAGCTGAGTAACCACTGCAACCCCCAGCAACTTCCAGCAGCTCCCACAG
1 AGCCAACAGCAGCTCAGCAACCACCGCAACCCCCAGCAACTTCCAACAGCTCCCACAG
1539798 CTCCCACAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.31, C:0.43, G:0.15, T:0.11
Consensus pattern (59 bp):
AGCCAACAGCAGCTCAGCAACCACCGCAACCCCCAGCAACTTCCAACAGCTCCCACAGT
Found at i:1539945 original size:49 final size:49
Alignment explanation
Indices: 1539814--1539929 Score: 205
Period size: 49 Copynumber: 2.4 Consensus size: 49
1539804 CAGCAGCCAA
* *
1539814 TAGCAGCTTAGCAACCACCGCAACCTCTAGTAGCTTCCACAACAGTTTC
1 TAGCAGCTCAGCAACCACCGGAACCTCTAGTAGCTTCCACAACAGTTTC
1539863 TAGCAGCTCAGCAACCACCGGAACCTCTAGTAGCTTCCACAACAGTTTC
1 TAGCAGCTCAGCAACCACCGGAACCTCTAGTAGCTTCCACAACAGTTTC
*
1539912 TAGTAGCTCAGCAACCAC
1 TAGCAGCTCAGCAACCAC
1539930 GAGCAGCTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (49 bp):
TAGCAGCTCAGCAACCACCGGAACCTCTAGTAGCTTCCACAACAGTTTC
Found at i:1540077 original size:37 final size:38
Alignment explanation
Indices: 1540007--1540079 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
1539997 CAACCTTCAG
*
1540007 CAACTTCTAGTAGCTCCCACAACAGCCATCAGCAACGA
1 CAACTTCTAGTAGCTCCCACAACAACCATCAGCAACGA
* *
1540045 CAACTT-TAGTAGCTTCTACAACAACC-TCCAGCAAC
1 CAACTTCTAGTAGCTCCCACAACAACCAT-CAGCAAC
1540080 TTCTAGTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.03
37 24 0.77
38 6 0.19
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.19
Consensus pattern (38 bp):
CAACTTCTAGTAGCTCCCACAACAACCATCAGCAACGA
Found at i:1540263 original size:24 final size:24
Alignment explanation
Indices: 1540227--1540272 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1540217 AAACTAAGGT
**
1540227 AAATCTTTTTTTTTCTTTTTCAAC
1 AAATCTTTTTTTTAATTTTTCAAC
1540251 AAAT-TTTTGTTTTAATTTTTCA
1 AAATCTTTT-TTTTAATTTTTCA
1540273 TGTTGTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (24 bp):
AAATCTTTTTTTTAATTTTTCAAC
Found at i:1543856 original size:35 final size:36
Alignment explanation
Indices: 1543817--1543888 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
1543807 TTCAACTATG
1543817 TGTATCGATACATAAAATGTTTTGTATCGA-TACAA
1 TGTATCGATACATAAAATGTTTTGTATCGATTACAA
*** *
1543852 TGTATCGATACATATTTTTTTTTGTATCGATTACAA
1 TGTATCGATACATAAAATGTTTTGTATCGATTACAA
1543888 T
1 T
1543889 TTAAGCTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 26 0.81
36 6 0.19
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (36 bp):
TGTATCGATACATAAAATGTTTTGTATCGATTACAA
Found at i:1543857 original size:13 final size:13
Alignment explanation
Indices: 1543839--1543863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1543829 TAAAATGTTT
1543839 TGTATCGATACAA
1 TGTATCGATACAA
1543852 TGTATCGATACA
1 TGTATCGATACA
1543864 TATTTTTTTT
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:1544093 original size:52 final size:52
Alignment explanation
Indices: 1543965--1544085 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1543955 ACATGATCTT
*
1543965 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1544017 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1544069 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1544086 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1550504 original size:21 final size:21
Alignment explanation
Indices: 1550480--1550545 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1550470 TTGATATATG
1550480 TGGTAATTCTTTATATGATTT
1 TGGTAATTCTTTATATGATTT
* *
1550501 TGGTAA-GCTTTGATATAATTT
1 TGGTAATTCTTT-ATATGATTT
* *
1550522 TGGTAATTTTTTTTA-G-TTT
1 TGGTAATTCTTTATATGATTT
1550541 TGGTA
1 TGGTA
1550546 CTTTTGATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.22
20 4 0.11
21 22 0.59
22 3 0.08
ACGTcount: A:0.23, C:0.03, G:0.18, T:0.56
Consensus pattern (21 bp):
TGGTAATTCTTTATATGATTT
Found at i:1550542 original size:40 final size:40
Alignment explanation
Indices: 1550449--1550562 Score: 110
Period size: 39 Copynumber: 2.9 Consensus size: 40
1550439 ATTTAATAGC
* * *
1550449 CTTTGATATAATTTTGATACTTTGATAT-A-TGTGGTAATT
1 CTTT-ATATGATTTTGGTACTTTGATATAATTTTGGTAATT
1550488 CTTTATATGATTTTGGTAAGCTTTGATATAATTTTGGTAATT
1 CTTTATATGATTTTGGT-A-CTTTGATATAATTTTGGTAATT
* * *
1550530 TTTTTTA-G-TTTTGGTACTTTTGATAAAATTTTG
1 CTTTATATGATTTTGGTAC-TTTGATATAATTTTG
1550563 ATAACATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
38 12 0.19
39 20 0.31
40 16 0.25
41 2 0.03
42 14 0.22
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.54
Consensus pattern (40 bp):
CTTTATATGATTTTGGTACTTTGATATAATTTTGGTAATT
Found at i:1550581 original size:21 final size:21
Alignment explanation
Indices: 1550556--1550624 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1550546 CTTTTGATAA
*
1550556 AATTTTGATAACATTTACAAT
1 AATTTTGGTAACATTTACAAT
*
1550577 AATTTTGGTAA-ATCTTAGATAT
1 AATTTTGGTAACAT-TTACA-AT
* * *
1550599 ACTTTTGGTAACATTTGCTAT
1 AATTTTGGTAACATTTACAAT
1550620 AATTT
1 AATTT
1550625 CAATAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 2 0.05
21 20 0.53
22 14 0.37
23 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (21 bp):
AATTTTGGTAACATTTACAAT
Found at i:1550863 original size:21 final size:21
Alignment explanation
Indices: 1550814--1550869 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1550804 TTTAACAACT
*
1550814 TTTGATATAGTTTGTGTAACC
1 TTTGATATAGTTTGTATAACC
*** *
1550835 TCAAATATAGTTTTTATAACC
1 TTTGATATAGTTTGTATAACC
*
1550856 TTTGATATAATTTG
1 TTTGATATAGTTTG
1550870 GTAATTTTTA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (21 bp):
TTTGATATAGTTTGTATAACC
Found at i:1550899 original size:21 final size:21
Alignment explanation
Indices: 1550875--1550916 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1550865 ATTTGGTAAT
* *
1550875 TTTTAATTTGATTTTAATAAC
1 TTTTAATCTAATTTTAATAAC
*
1550896 TTTTAATCTAATTTTGATAAC
1 TTTTAATCTAATTTTAATAAC
1550917 CTTGATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTAATCTAATTTTAATAAC
Found at i:1551039 original size:42 final size:42
Alignment explanation
Indices: 1550990--1551073 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1550980 ATAAATATTA
* *
1550990 ATATAATTTTGATAATTTTTCATATAAGTTTGGTAACATTTG
1 ATATAATTTTGATAACTTTTCATATAAGTTTGATAACATTTG
* * *
1551032 ATATAATTTTGATAACTTTTGATATAATTTTGATAATATTTG
1 ATATAATTTTGATAACTTTTCATATAAGTTTGATAACATTTG
1551074 CAATATTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (42 bp):
ATATAATTTTGATAACTTTTCATATAAGTTTGATAACATTTG
Found at i:1551072 original size:11 final size:11
Alignment explanation
Indices: 1550954--1551066 Score: 94
Period size: 11 Copynumber: 10.6 Consensus size: 11
1550944 TTGTTTAACC
1550954 TTTGATATAAT
1 TTTGATATAAT
1550965 TTTGATA-AAT
1 TTTGATATAAT
*
1550975 TTT-TTATAAAT
1 TTTGATAT-AAT
* *
1550986 ATTAATATAAT
1 TTTGATATAAT
*
1550997 TTTGATA-ATT
1 TTTGATATAAT
* *
1551007 TTTCATATAAG
1 TTTGATATAAT
*
1551018 TTTGGTA-ACA-
1 TTTGATATA-AT
1551028 TTTGATATAAT
1 TTTGATATAAT
*
1551039 TTTGATA-ACT
1 TTTGATATAAT
1551049 TTTGATATAAT
1 TTTGATATAAT
1551060 TTTGATA
1 TTTGATA
1551067 ATATTTGCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
9 2 0.03
10 31 0.39
11 44 0.55
12 3 0.04
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (11 bp):
TTTGATATAAT
Found at i:1551073 original size:21 final size:21
Alignment explanation
Indices: 1550960--1551073 Score: 110
Period size: 21 Copynumber: 5.5 Consensus size: 21
1550950 AACCTTTGAT
*
1550960 ATAAT-TTTGATA-AATTTTTT
1 ATAATATTTGATATAA-TTTTG
*
1550980 ATAA-ATATTAATATAATTTTG
1 ATAATAT-TTGATATAATTTTG
* * *
1551001 ATAATTTTTCATATAAGTTTG
1 ATAATATTTGATATAATTTTG
* *
1551022 GTAACATTTGATATAATTTTG
1 ATAATATTTGATATAATTTTG
1551043 ATAACT-TTTGATATAATTTTG
1 ATAA-TATTTGATATAATTTTG
1551064 ATAATATTTG
1 ATAATATTTG
1551074 CAATATTTGG
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
20 6 0.08
21 67 0.88
22 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.52
Consensus pattern (21 bp):
ATAATATTTGATATAATTTTG
Found at i:1551495 original size:17 final size:18
Alignment explanation
Indices: 1551475--1551509 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1551465 TAAAATATAG
1551475 ATATAAATA-ACACAAAT
1 ATATAAATACACACAAAT
*
1551492 ATATGAATACACACAAAT
1 ATATAAATACACACAAAT
1551510 CTAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAAATACACACAAAT
Found at i:1553056 original size:2 final size:2
Alignment explanation
Indices: 1553049--1553083 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1553039 ATACAAATGC
*
1553049 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1553084 GCTTCATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1553826 original size:13 final size:13
Alignment explanation
Indices: 1553808--1553836 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1553798 CATATTCTTG
1553808 TTCATGAATAAGT
1 TTCATGAATAAGT
1553821 TTCATGAATAAGT
1 TTCATGAATAAGT
1553834 TTC
1 TTC
1553837 GTTAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (13 bp):
TTCATGAATAAGT
Found at i:1557820 original size:15 final size:15
Alignment explanation
Indices: 1557786--1557829 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1557776 TTTATGTTAC
*
1557786 TAAAATT-AAAATTT
1 TAAAATTCAACATTT
1557800 TAAAATTCAACATTT
1 TAAAATTCAACATTT
* *
1557815 TTAAATTCAATATTT
1 TAAAATTCAACATTT
1557830 ATAGTAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTCAACATTT
Found at i:1558635 original size:2 final size:2
Alignment explanation
Indices: 1558628--1558656 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1558618 AAACCCATCT
1558628 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1558657 GATATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1559234 original size:7 final size:7
Alignment explanation
Indices: 1559222--1559248 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1559212 AACTGAAAAG
1559222 AATTTTC
1 AATTTTC
1559229 AATTTTC
1 AATTTTC
1559236 AATTTTC
1 AATTTTC
1559243 AATTTT
1 AATTTT
1559249 TCTTATCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTC
Found at i:1563661 original size:16 final size:16
Alignment explanation
Indices: 1563636--1563712 Score: 68
Period size: 16 Copynumber: 4.9 Consensus size: 16
1563626 GATCGATTCG
1563636 AAAC-CGAAATGACCC
1 AAACTCGAAATGACCC
* * *
1563651 GAACTCAAAATGATCC
1 AAACTCGAAATGACCC
* *
1563667 AAACCCGAAATAACCC
1 AAACTCGAAATGACCC
*
1563683 AAAC-CTGAAATGATCC
1 AAACTC-GAAATGACCC
*
1563699 GAACTCGAAATGAC
1 AAACTCGAAATGAC
1563713 TAGAACAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 4 0.09
16 42 0.89
17 1 0.02
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (16 bp):
AAACTCGAAATGACCC
Found at i:1563676 original size:32 final size:32
Alignment explanation
Indices: 1563639--1563712 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1563629 CGATTCGAAA
*
1563639 CCGAAATGACCCGAA-CTCAAAATGATCCAAAC
1 CCGAAATGACCCAAACCT-AAAATGATCCAAAC
* * *
1563671 CCGAAATAACCCAAACCTGAAATGATCCGAAC
1 CCGAAATGACCCAAACCTAAAATGATCCAAAC
*
1563703 TCGAAATGAC
1 CCGAAATGAC
1563713 TAGAACAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.14
Consensus pattern (32 bp):
CCGAAATGACCCAAACCTAAAATGATCCAAAC
Found at i:1564914 original size:28 final size:29
Alignment explanation
Indices: 1564848--1564918 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
1564838 TAAAATATTT
* *
1564848 AATTATTTGATTAATAATTTTGAAAGGTA
1 AATTATTTAATTAATAATTTTGAAAAGTA
1564877 AATTATTTAATTAATAATTTT-AAAAGTA
1 AATTATTTAATTAATAATTTTGAAAAGTA
1564905 AATTATTTAATTAA
1 AATTATTTAATTAA
1564919 AAAGTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 20 0.50
29 20 0.50
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (29 bp):
AATTATTTAATTAATAATTTTGAAAAGTA
Found at i:1564921 original size:20 final size:20
Alignment explanation
Indices: 1564898--1564937 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1564888 TAATAATTTT
* *
1564898 AAAAGTAAATTATTTAATTA
1 AAAAGTAAACTAATTAATTA
1564918 AAAAGTAAACTAATTAATTA
1 AAAAGTAAACTAATTAATTA
1564938 TGTTTCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAAGTAAACTAATTAATTA
Found at i:1566689 original size:13 final size:12
Alignment explanation
Indices: 1566664--1566714 Score: 63
Period size: 13 Copynumber: 4.3 Consensus size: 12
1566654 TTTTTTAAAC
1566664 TTTTCAAAAATAA
1 TTTT-AAAAATAA
1566677 TTTTAAAAGATAA
1 TTTTAAAA-ATAA
1566690 TTTT-AAAAT--
1 TTTTAAAAATAA
1566699 TTTTAAAAATAA
1 TTTTAAAAATAA
1566711 TTTT
1 TTTT
1566715 TTATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 2 0.06
12 11 0.32
13 12 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:1566727 original size:21 final size:21
Alignment explanation
Indices: 1566675--1566714 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1566665 TTTCAAAAAT
1566675 AATTTTAAAAGATAATTTTAA
1 AATTTTAAAAGATAATTTTAA
1566696 AATTTTTAAAA-ATAATTTT
1 AA-TTTTAAAAGATAATTTT
1566715 TTATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AATTTTAAAAGATAATTTTAA
Found at i:1568967 original size:22 final size:20
Alignment explanation
Indices: 1568925--1568967 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1568915 TAATTTTATT
**
1568925 ATTTTAAAATTTAAATCTAA
1 ATTTTAAAATTTAAAAATAA
1568945 ATTTATAAATATTTAAAAATAA
1 ATTT-TAAA-ATTTAAAAATAA
1568967 A
1 A
1568968 GTTCATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTAAAATTTAAAAATAA
Found at i:1569029 original size:109 final size:105
Alignment explanation
Indices: 1568828--1569062 Score: 267
Period size: 109 Copynumber: 2.2 Consensus size: 105
1568818 TATTATTTTA
** * * *
1568828 AAATTTAAATTAATAAATATTTTGAAATAAAGTTCACATGATATTAATTTACTTTAAAGTTAATA
1 AAATTTAAATTAATAAATATTTAAAAATAAAGTTCACATGATATTAATCTACATTAAAATTAATA
* *
1568893 AAAAAATTCTTATTTATATATATAATTTTATTATTTTAAAATTT
66 AAAAAATTCATATTTATATATATAA-TTTATTAATTT---ATTT
* * * *
1568937 AAATCTAAATTTATAAATATTTAAAAATAAAGTTCATATTATATTAATCTACATTAAAATTAAT-
1 AAATTTAAATTAATAAATATTTAAAAATAAAGTTCACATGATATTAATCTACATTAAAATTAATA
** *
1569001 AAAATTTTCATATTT-TAATATGTAAATTTATTAATTTATTT
66 AAAAAATTCATATTTAT-ATATAT-AATTTATTAATTTATTT
*
1569042 AAATTTAAACTAATAAATATT
1 AAATTTAAATTAATAAATATT
1569063 AGAATCCACA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
105 22 0.21
107 1 0.01
108 27 0.25
109 57 0.53
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (105 bp):
AAATTTAAATTAATAAATATTTAAAAATAAAGTTCACATGATATTAATCTACATTAAAATTAATA
AAAAAATTCATATTTATATATATAATTTATTAATTTATTT
Found at i:1573727 original size:51 final size:51
Alignment explanation
Indices: 1573669--1573788 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 51
1573659 CCAACTTATG
* *
1573669 TGGATTTATACTCTATAAGGCTTGTCCTT-TCTATACAAGTGCTAGCTAATT
1 TGGATTTAGACTCTATAAGGCTTGACCTTCT-TATACAAGTGCTAGCTAATT
* * * *
1573720 TGGATTTAGACTTTATAGGGCTTGACCTTCTTATACATGTGCTAGCTAATG
1 TGGATTTAGACTCTATAAGGCTTGACCTTCTTATACAAGTGCTAGCTAATT
*
1573771 TAGACTTT-GACTCTATAA
1 TGGA-TTTAGACTCTATAA
1573789 ACCTTGATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
51 54 0.93
52 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (51 bp):
TGGATTTAGACTCTATAAGGCTTGACCTTCTTATACAAGTGCTAGCTAATT
Found at i:1573847 original size:52 final size:52
Alignment explanation
Indices: 1573700--1573853 Score: 118
Period size: 52 Copynumber: 3.0 Consensus size: 52
1573690 TTGTCCTTTC
* * * * *
1573700 TATACAAGTGCTAGCTAATTTGGA-TTTAGACTTTATAGGGCTTGAC-CTTCT
1 TATACATGTGCCAACTAATATGGACTTT-GACTTTATAGGGCTTGACTCTTAT
* * * * * ***
1573751 TATACATGTGCTAGCTAATGTAGACTTTGACTCTATAAACCTTGATCTCTCTAT
1 TATACATGTGCCAACTAATATGGACTTTGACTTTATAGGGCTTGA-CTCT-TAT
*
1573805 TATA-A-GTTCCAACTAATATGGACTTTGACTTTATAGGGCTTGACCTCTT
1 TATACATGTGCCAACTAATATGGACTTTGACTTTATAGGGCTTGA-CTCTT
1573854 TGTGCTAGCT
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
51 35 0.43
52 37 0.46
53 3 0.04
54 6 0.07
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (52 bp):
TATACATGTGCCAACTAATATGGACTTTGACTTTATAGGGCTTGACTCTTAT
Found at i:1574917 original size:39 final size:39
Alignment explanation
Indices: 1574863--1574940 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1574853 CACCCAGTAA
1574863 TTACCTAGGACTAGGTTTTATAGGAAAACTTAATAGGAT
1 TTACCTAGGACTAGGTTTTATAGGAAAACTTAATAGGAT
1574902 TTACCTAGGACTAGGTTTTATAGGAAAACTTAATAGGAT
1 TTACCTAGGACTAGGTTTTATAGGAAAACTTAATAGGAT
1574941 ATCCCTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (39 bp):
TTACCTAGGACTAGGTTTTATAGGAAAACTTAATAGGAT
Found at i:1576246 original size:22 final size:22
Alignment explanation
Indices: 1576221--1576309 Score: 57
Period size: 22 Copynumber: 4.2 Consensus size: 22
1576211 AATATGATAA
1576221 ATAAAACATATCAATAAAATCT
1 ATAAAACATATCAATAAAATCT
*
1576243 AT-AAAC-TATTGCAATGAAAATCA
1 ATAAAACATA-T-CAAT-AAAATCT
* * **
1576266 AGACAA-ATA-CACCAAAA---
1 ATAAAACATATCAATAAAATCT
1576283 ATAAAACATATCAATAAAATCT
1 ATAAAACATATCAATAAAATCT
1576305 ATAAA
1 ATAAA
1576310 CTAGGATCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 20
0.62 0.12 0.26
Matches are distributed among these distances:
17 4 0.08
18 3 0.06
19 6 0.12
20 6 0.12
21 7 0.15
22 11 0.23
23 7 0.15
24 4 0.08
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.22
Consensus pattern (22 bp):
ATAAAACATATCAATAAAATCT
Found at i:1577772 original size:10 final size:11
Alignment explanation
Indices: 1577756--1577782 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1577746 GAGTTTTTCA
1577756 AAAAAAATCTC
1 AAAAAAATCTC
1577767 AAAAAAATCTC
1 AAAAAAATCTC
1577778 AAAAA
1 AAAAA
1577783 TAGAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATCTC
Found at i:1578481 original size:35 final size:35
Alignment explanation
Indices: 1578442--1578512 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1578432 AGAGATGTTC
* * *
1578442 TAAAGTGCAATGCAAGATATCTTTGAAAGAGGCTT
1 TAAAGTGCAAAGCAAGATATCCTCGAAAGAGGCTT
* *
1578477 TAAAGTGTAAAGCGAGATATCCTCGAAAGAGGCTT
1 TAAAGTGCAAAGCAAGATATCCTCGAAAGAGGCTT
1578512 T
1 T
1578513 TGGGATATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (35 bp):
TAAAGTGCAAAGCAAGATATCCTCGAAAGAGGCTT
Found at i:1578598 original size:71 final size:71
Alignment explanation
Indices: 1578520--1578692 Score: 195
Period size: 71 Copynumber: 2.4 Consensus size: 71
1578510 TTTTGGGATA
*
1578520 TCTTTGTTGAAACATCCTTAAGAGAGTTTTTAAAAGTTTTGGAT-GAATATCCTTAAGAGAAGCT
1 TCTTTGTT-AAACATCCTTAAGAGAGGTTTTAAAAGTTTTGGATGGAATATCCTTAAGAGAAGCT
*
1578584 TTGGAAG
65 TTAGAAG
** * * * * * * * * *
1578591 TCTTTGTTAAGTATCCTTGAGAGTGGCTTTAAAGGTTTTTGATGGACTATCTTTATGAGAGGCTT
1 TCTTTGTTAAACATCCTTAAGAGAGGTTTTAAAAGTTTTGGATGGAATATCCTTAAGAGAAGCTT
1578656 TAGAAG
66 TAGAAG
*
1578662 TCTTTGATAAAACATCCTTAAGAGAGGTTTT
1 TCTTTG-TTAAACATCCTTAAGAGAGGTTTT
1578693 GAAATATCCA
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
70 27 0.33
71 36 0.44
72 18 0.22
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (71 bp):
TCTTTGTTAAACATCCTTAAGAGAGGTTTTAAAAGTTTTGGATGGAATATCCTTAAGAGAAGCTT
TAGAAG
Found at i:1578687 original size:36 final size:34
Alignment explanation
Indices: 1578529--1578943 Score: 155
Period size: 36 Copynumber: 11.9 Consensus size: 34
1578519 ATCTTTGTTG
** *
1578529 AAACATCCTTAAGAGAGTTTTTAAAAGTTTTGGAT
1 AAACATCCTTAAGAGAGGCTTTAGAAGTTTT-GAT
* * * * *
1578564 GAATATCCTTAAGAGAAGCTTTGGAAGTCTTTGTT
1 AAACATCCTTAAGAGAGGCTTTAGAAGT-TTTGAT
** * *
1578599 AAGTATCCTTGAGAGTGGCTTTA-AAGGTTTTTGAT
1 AAACATCCTTAAGAGAGGCTTTAGAA-G-TTTTGAT
** * *
1578634 GGACTATCTTTATGAGAGGCTTTAGAAGTCTTTGAT
1 AAAC-ATCCTTAAGAGAGGCTTTAGAAGT-TTTGAT
* * ***
1578670 AAAACATCCTTAAGAGAGG-TTTTGAAATATCCAAT
1 -AAACATCCTTAAGAGAGGCTTTAGAAGT-TTTGAT
* * ** * *
1578705 AAATATACTCGAGAGAGGCTTTAGAGGTTTTTA-
1 AAACATCCTTAAGAGAGGCTTTAGAAGTTTTGAT
* * * *
1578738 AAATATCCTCAAGAGAGACTTT-GAAAGTTTTTAAT
1 AAACATCCTTAAGAGAGGCTTTAG-AAG-TTTTGAT
* * * *
1578773 GGAGCATCCTTAAAAGAGGCTTTGGAAG-TTT-AT
1 -AAACATCCTTAAGAGAGGCTTTAGAAGTTTTGAT
* * *
1578806 GAAATATCCTCAAGAGAGGCTTTTA-AAGTATTTAAT
1 -AAACATCCTTAAGAGAGGC-TTTAGAAGT-TTTGAT
*
1578842 ACAACATCCTTAAGAGAGGCTTTAAAAGTTTTTGAT
1 A-AACATCCTTAAGAGAGGCTTTAGAAG-TTTTGAT
* **
1578878 GAA-ATGTTTTCAAGAGAGGCTTT-GAAAGTTTTTGAT
1 AAACAT-CCTT-AAGAGAGGCTTTAG-AAG-TTTTGAT
** * * *
1578914 GAAATGTCCTCAAGAAAGGCTTTGGAAGTT
1 -AAACATCCTTAAGAGAGGCTTTAGAAGTT
1578944 ACTTTTTTAT
Statistics
Matches: 281, Mismatches: 73, Indels: 52
0.69 0.18 0.13
Matches are distributed among these distances:
32 1 0.00
33 41 0.15
34 31 0.11
35 77 0.27
36 120 0.43
37 10 0.04
38 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (34 bp):
AAACATCCTTAAGAGAGGCTTTAGAAGTTTTGAT
Found at i:1578811 original size:69 final size:69
Alignment explanation
Indices: 1578718--1578910 Score: 224
Period size: 69 Copynumber: 2.8 Consensus size: 69
1578708 TATACTCGAG
* * * * ** *
1578718 AGAGGCTTTAGAGGTTTTTAAAATATCCTCAAGAGAGACTTTGAAAGTTTTTAATGGAGCATCCT
1 AGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAGAGGCTTTGAAAGTTTTTAATACAACATCCT
1578783 TAAA
66 TAAA
* * *
1578787 AGAGGCTTTGGAAGTTTATGAAATATCCTCAAGAGAGGCTTTTAAAGTATTTAATACAACATCCT
1 AGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAGAGGCTTTGAAAGTTTTTAATACAACATCCT
*
1578852 TAAG
66 TAAA
* * **
1578856 AGAGGCTTTAAAAGTTTTTGATGAAATGTTTTCAAGAGAGGCTTTGAAAGTTTTT
1 AGAGGCTTTAGAAG--TTT-ATGAAATATCCTCAAGAGAGGCTTTGAAAGTTTTT
1578911 GATGAAATGT
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
69 70 0.68
71 3 0.03
72 30 0.29
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (69 bp):
AGAGGCTTTAGAAGTTTATGAAATATCCTCAAGAGAGGCTTTGAAAGTTTTTAATACAACATCCT
TAAA
Found at i:1578934 original size:72 final size:75
Alignment explanation
Indices: 1578815--1579007 Score: 182
Period size: 76 Copynumber: 2.6 Consensus size: 75
1578805 TGAAATATCC
* * * ** * * *
1578815 TCAAGAGAGGCTTTTAAAGTATTTAAT-ACAACATCCTTAAGAGAGGCTTT-AA-AAGTTTTTGA
1 TCAAGAGAGGCTTTGAAAGTTTTTGATGA-AATGTCCTCAAGAAAGGCTTTGAAGAACTTTTTGA
1578877 TGAAATGT-TT
65 TGAAATGTCTT
* *
1578887 TCAAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCCTCAAGAAAGGCTTTGGAAGTTACTTTTTT
1 TCAAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCCTCAAGAAAGGCTTT-GAAG-AACTTTTTG
1578952 ATGAAATGTCTT
64 ATGAAATGTCTT
* * * *
1578964 T-GAGAAAGGCTTTG-AAGATTTTTGGTGTAATGTCCTCAAGAAAG
1 TCAAGAGAGGCTTTGAAAG-TTTTTGATGAAATGTCCTCAAGAAAG
1579008 TGTAGATACT
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
72 41 0.41
73 1 0.01
74 2 0.02
75 3 0.03
76 50 0.50
77 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (75 bp):
TCAAGAGAGGCTTTGAAAGTTTTTGATGAAATGTCCTCAAGAAAGGCTTTGAAGAACTTTTTGAT
GAAATGTCTT
Found at i:1578996 original size:36 final size:37
Alignment explanation
Indices: 1578848--1579007 Score: 146
Period size: 36 Copynumber: 4.3 Consensus size: 37
1578838 TAATACAACA
* * * *
1578848 TCCTTAAGAGAGGCTTT-AAAAGTTTTTGATGAAATG
1 TCCTCAAGAAAGGCTTTGAAGACTTTTTGATGAAATG
** * *
1578884 TTTTCAAGAGAGGCTTTGAA-AGTTTTTGATGAAATG
1 TCCTCAAGAAAGGCTTTGAAGACTTTTTGATGAAATG
*
1578920 TCCTCAAGAAAGGCTTTGGAAGTTACTTTTTTATGAAATG
1 TCCTCAAGAAAGGCTTT-GAAG--ACTTTTTGATGAAATG
* ** * *
1578960 TCTTTGAGAAAGGCTTTGAAGA-TTTTTGGTGTAATG
1 TCCTCAAGAAAGGCTTTGAAGACTTTTTGATGAAATG
1578996 TCCTCAAGAAAG
1 TCCTCAAGAAAG
1579008 TGTAGATACT
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
36 64 0.63
37 6 0.06
39 4 0.04
40 28 0.27
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (37 bp):
TCCTCAAGAAAGGCTTTGAAGACTTTTTGATGAAATG
Found at i:1580080 original size:20 final size:20
Alignment explanation
Indices: 1580047--1580090 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1580037 CAAAATATTA
1580047 TTTATGATTATTAATTTTAAT
1 TTTATGATTATTAATTTT-AT
*
1580068 TTTAT-ATTTTTAATTTTAT
1 TTTATGATTATTAATTTTAT
1580087 TTTA
1 TTTA
1580091 GTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTATGATTATTAATTTTAT
Found at i:1580556 original size:20 final size:20
Alignment explanation
Indices: 1580533--1580605 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1580523 ACAATTCAAA
1580533 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1580553 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1580574 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1580594 GTATCGATACAT
1 GTATCGATACAT
1580606 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1580577 original size:21 final size:21
Alignment explanation
Indices: 1580551--1580626 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1580541 ACATGTTGCA
1580551 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1580572 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1580592 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1580613 ATGTATCGATACAT
1 ATGTATCGATACAT
1580627 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1580584 original size:41 final size:41
Alignment explanation
Indices: 1580533--1580626 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1580523 ACAATTCAAA
*
1580533 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1580574 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1580615 GTATCGATACAT
1 GTATCGATACAT
1580627 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1580683 original size:13 final size:13
Alignment explanation
Indices: 1580665--1580690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1580655 TACAGCAAGT
1580665 ATGTATCGATACA
1 ATGTATCGATACA
1580678 ATGTATCGATACA
1 ATGTATCGATACA
1580691 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:1582850 original size:13 final size:13
Alignment explanation
Indices: 1582832--1582857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1582822 CAATTTTTTG
1582832 TGTATCGATACAT
1 TGTATCGATACAT
1582845 TGTATCGATACAT
1 TGTATCGATACAT
1582858 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:1584898 original size:13 final size:13
Alignment explanation
Indices: 1584880--1584904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1584870 ACTGAAGCAA
1584880 TGTATCGATACAT
1 TGTATCGATACAT
1584893 TGTATCGATACA
1 TGTATCGATACA
1584905 ATCTGGAAAA
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:1588643 original size:13 final size:13
Alignment explanation
Indices: 1588625--1588650 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1588615 CAATTTTTTG
1588625 TGTATCGATACAT
1 TGTATCGATACAT
1588638 TGTATCGATACAT
1 TGTATCGATACAT
1588651 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:1591752 original size:15 final size:15
Alignment explanation
Indices: 1591732--1591762 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1591722 TAAAAATGTC
*
1591732 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1591747 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1591762 C
1 C
1591763 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:1593859 original size:13 final size:13
Alignment explanation
Indices: 1593841--1593878 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1593831 CATTTTTATT
1593841 TGTATCGATACAA
1 TGTATCGATACAA
*
1593854 TGTATCGATACAC
1 TGTATCGATACAA
1593867 TGTATCGATACA
1 TGTATCGATACA
1593879 GGGTGTTTAT
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:1595707 original size:32 final size:32
Alignment explanation
Indices: 1595671--1595732 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
1595661 AATTTTGATA
1595671 TGAATTACTTGATTAAGGGGGAGATTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTT
1595703 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
1595733 AATAAACGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (32 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTT
Found at i:1596377 original size:20 final size:20
Alignment explanation
Indices: 1596354--1596426 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1596344 ACAATTCAAA
1596354 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1596374 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1596395 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1596415 GTATCGATACAT
1 GTATCGATACAT
1596427 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1596398 original size:21 final size:21
Alignment explanation
Indices: 1596372--1596447 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1596362 ACATGTTGCA
1596372 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1596393 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1596413 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1596434 ATGTATCGATACAT
1 ATGTATCGATACAT
1596448 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1596405 original size:41 final size:41
Alignment explanation
Indices: 1596354--1596447 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1596344 ACAATTCAAA
*
1596354 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1596395 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1596436 GTATCGATACAT
1 GTATCGATACAT
1596448 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1596504 original size:13 final size:13
Alignment explanation
Indices: 1596486--1596511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1596476 TACAGCAAGT
1596486 ATGTATCGATACA
1 ATGTATCGATACA
1596499 ATGTATCGATACA
1 ATGTATCGATACA
1596512 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:1597302 original size:13 final size:13
Alignment explanation
Indices: 1597281--1597318 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1597271 TATCTTTAGT
*
1597281 TAATTATAAAAAA
1 TAATAATAAAAAA
1597294 TAATAAT-AAAAA
1 TAATAATAAAAAA
1597306 TAATGAATAAAAA
1 TAAT-AATAAAAA
1597319 GTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 9 0.41
13 9 0.41
14 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
TAATAATAAAAAA
Found at i:1597306 original size:12 final size:13
Alignment explanation
Indices: 1597289--1597318 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1597279 GTTAATTATA
1597289 AAAAATAAT-AAT
1 AAAAATAATGAAT
1597301 AAAAATAATGAAT
1 AAAAATAATGAAT
1597314 AAAAA
1 AAAAA
1597319 GTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAAATAATGAAT
Found at i:1600156 original size:66 final size:66
Alignment explanation
Indices: 1600048--1600184 Score: 215
Period size: 66 Copynumber: 2.1 Consensus size: 66
1600038 TGTACAGCCT
* *
1600048 AGGGTACCAGCCTCTCCACCTATTATTGTTATCAACCTCGAAATGGTACCTCAAGAATCTAACCC
1 AGGGTACCAACCTCTCCACCTATTATTGTTATCAACCTCGAAATGGTACCTCAAGAAACTAACCC
1600113 A
66 A
*
1600114 AGGGTACCAACAC-CTCCACCTATTATTGTTATCAA-CTCCGAAATGGTACTTCAAGAAACTAAC
1 AGGGTACCAAC-CTCTCCACCTATTATTGTTATCAACCT-CGAAATGGTACCTCAAGAAACTAAC
1600177 CCA
64 CCA
1600180 AGGGT
1 AGGGT
1600185 CAATCTTGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
65 2 0.03
66 63 0.95
67 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (66 bp):
AGGGTACCAACCTCTCCACCTATTATTGTTATCAACCTCGAAATGGTACCTCAAGAAACTAACCC
A
Found at i:1608837 original size:19 final size:20
Alignment explanation
Indices: 1608794--1608844 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1608784 TACAAGCCAA
*
1608794 TGTATCGATACATTTTATGG
1 TGTATCGATACATCTTATGG
1608814 TGTATCGATACATACTT-T-G
1 TGTATCGATACAT-CTTATGG
1608833 TGTATCGATACA
1 TGTATCGATACA
1608845 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATCTTATGG
Found at i:1609670 original size:46 final size:46
Alignment explanation
Indices: 1609617--1609708 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1609607 TTTGTTATAG
1609617 CAAAAATGCAATTTTAGAGAGATAATCAATTATTTCCATAAAACAA
1 CAAAAATGCAATTTTAGAGAGATAATCAATTATTTCCATAAAACAA
1609663 CAAAAATGCAATTTTAGAGAGATAATCAATTATTTCCATAAAACAA
1 CAAAAATGCAATTTTAGAGAGATAATCAATTATTTCCATAAAACAA
1609709 ACATTTTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (46 bp):
CAAAAATGCAATTTTAGAGAGATAATCAATTATTTCCATAAAACAA
Found at i:1611305 original size:23 final size:24
Alignment explanation
Indices: 1611260--1611306 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1611250 CAGAGAATTG
*
1611260 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1611284 AACAC-AATTCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1611307 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1612682 original size:21 final size:21
Alignment explanation
Indices: 1612658--1612699 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1612648 AGCTATTTCT
* *
1612658 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
1612679 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
1612700 ACGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:1613830 original size:34 final size:35
Alignment explanation
Indices: 1613792--1613858 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
1613782 CCTTACAACA
*
1613792 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAAATAG-AACCTCTCTCT
1613826 CTATCTTTTTCAAAGGCTAAAATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAAATAGAACCTCTC
1613859 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAAATAGAACCTCTCTCT
Found at i:1614336 original size:13 final size:13
Alignment explanation
Indices: 1614318--1614342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1614308 CATTTTATGG
1614318 TGTATCGATACAA
1 TGTATCGATACAA
1614331 TGTATCGATACA
1 TGTATCGATACA
1614343 TACTTTGTGT
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:1614358 original size:32 final size:33
Alignment explanation
Indices: 1614295--1614362 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1614285 CGTTACAAGC
*
1614295 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATCTTATGGTGTATCGATA
1614328 CAATGTATCGATACATACTT-T-GTGTATCGATA
1 CAATGTATCGATACAT-CTTATGGTGTATCGATA
1614360 CAA
1 CAA
1614363 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATCTTATGGTGTATCGATA
Found at i:1615120 original size:44 final size:44
Alignment explanation
Indices: 1615029--1615573 Score: 274
Period size: 44 Copynumber: 12.4 Consensus size: 44
1615019 CTATTTTACA
* * * * * *
1615029 TATGGTTACCACCTTGGTCA-AATCTTTTCCTT-TCTATCTGACA
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTAT-GATTTGACG
* *
1615072 TATGGTTGCCACCCTGGCCAGATTCTTTTCATTATGATTTGACG
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTGACG
* * * * * *
1615116 TATGGTTACCACCCTAGTCA-AGTCTTTTCCTTTTTG-TCTAACG
1 TATGGTTACCACCCTGGTCAGATTCTTTT-CATTATGATTTGACG
* * * *
1615159 TATGGTTACCACCTTGGTCAGATTCTTTTCATTCTGATGTGACA
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTGACG
* * *
1615203 TATGGTTACCACCCTGGTCAAATT-TTCCTCTC-TTCTG-TTTGATG
1 TATGGTTACCACCCTGGTCAGATTCTT--T-TCATTATGATTTGACG
* * * * * * * *
1615247 TATGGTTACTATCCTGGTCAAACTCTTCTCATTTTAGGA-CTGATG
1 TATGGTTACCACCCTGGTCAGATTCTTTTCA--TTATGATTTGACG
*
1615292 TATGGTTACCACCCAGGTCAGATTCTTTTCATTATGATTTGACG
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTGACG
* * * * * * *
1615336 TATGGTTACTACCTTGGTCAAATT-TTTCTCTTTTCTG-TTTAAAG
1 TATGGTTACCACCCTGGTCAGATTCTTT-TC-ATTATGATTTGACG
* * * * * *
1615380 TATGGTTACCACCCTAGTCAAACTCTTTTCATT-TCAGGTCTAACG
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTAT--GATTTGACG
* * * * *
1615425 TATGGTTACCACCCT-ATCTGATTCTCTTCATTCTGATTT-AAG
1 TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTGACG
* * * ** * * * * * *
1615467 ATATGGTTACTACTCTGGTCA-AATCTGCCTCTTTCTTATCTAACA
1 -TATGGTTACCACCCTGGTCAGATTCT-TTTCATTATGATTTGACG
* * * *
1615512 TATGGTTATCACCCTGGTCAAAATT-TTTTCATTCTGATTTGATG
1 TATGGTTACCACCCTGGTC-AGATTCTTTTCATTATGATTTGACG
* *
1615556 TATGGTTATCACCTTGGT
1 TATGGTTACCACCCTGGT
1615574 TAAATCTGCC
Statistics
Matches: 383, Mismatches: 92, Indels: 53
0.73 0.17 0.10
Matches are distributed among these distances:
42 5 0.01
43 84 0.22
44 217 0.57
45 73 0.19
46 4 0.01
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (44 bp):
TATGGTTACCACCCTGGTCAGATTCTTTTCATTATGATTTGACG
Found at i:1615163 original size:87 final size:87
Alignment explanation
Indices: 1615026--1615580 Score: 284
Period size: 87 Copynumber: 6.3 Consensus size: 87
1615016 CTTCTATTTT
* * *
1615026 ACATATGGTTACCACCTTGGTCAAATCTTTTCCTTTCTATCTGACATATGGTTGCCACCCTGGCC
1 ACATATGGTTACCACCCTGGTCAAATCTTTTCCTTTCTATCTAACATATGGTTACCACCCTGGCC
*
1615091 AGATTCTTTTCATTATGATTTG
66 AGATTCTTTTCATTATGATGTG
* * * * * * * *
1615113 ACGTATGGTTACCACCCTAGTCAAGTCTTTTCCTTTTTGTCTAACGTATGGTTACCACCTTGGTC
1 ACATATGGTTACCACCCTGGTCAAATCTTTTCCTTTCTATCTAACATATGGTTACCACCCTGGCC
*
1615178 AGATTCTTTTCATTCTGATGTG
66 AGATTCTTTTCATTATGATGTG
* * * * ** * *
1615200 ACATATGGTTACCACCCTGGTCAAAT-TTTCCTCTCTTCTGTTTGATGTATGGTTACTATCCTGG
1 ACATATGGTTACCACCCTGGTCAAATCTTTTC-CT-TTCTATCTAACATATGGTTACCACCCTGG
* * * * * *
1615264 TCAAACTCTTCTCATTTTAGGA-CTG
64 CCAGATTCTTTTCA--TTATGATGTG
** * * * * * * * * *
1615289 ATGTATGGTTACCACCCAGGTCAGATTCTTTTCATTAT-GATTTGACGTATGGTTACTACCTTGG
1 ACATATGGTTACCACCCTGGTCA-AATCTTTTCCTT-TCTATCTAACATATGGTTACCACCCTGG
* * ** *
1615353 TCAAATT-TTTCTC-TT-TTCTGTTT
64 CCAGATTCTTT-TCATTATGATG-TG
* * * *
1615376 AAAGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTC-AGGTCTAACGTATGGTTACCACCCT
1 ACA-TATGGTTACCACCCTGGTCAAA-TCTTTTCCTTTCTA--TCTAACATATGGTTACCACCCT
** * * * * *
1615440 -ATCTGATTCTCTTCATTCTGATTTA
62 GGCCAGATTCTTTTCATTATGATGTG
* * * ** *
1615465 AGATATGGTTACTACTCTGGTCAAATC-TGCCTCTTTCTTATCTAACATATGGTTATCACCCTGG
1 ACATATGGTTACCACCCTGGTCAAATCTTTTC-CTTTC-TATCTAACATATGGTTACCACCCTGG
* * * *
1615529 TCAAAATT-TTTTCATTCTGATTTG
64 -CCAGATTCTTTTCATTATGATGTG
** * * *
1615553 ATGTATGGTTATCACCTTGGTTAAATCT
1 ACATATGGTTACCACCCTGGTCAAATCT
1615581 GCCTTCTTCC
Statistics
Matches: 356, Mismatches: 88, Indels: 46
0.73 0.18 0.09
Matches are distributed among these distances:
86 8 0.02
87 130 0.37
88 123 0.35
89 81 0.23
90 10 0.03
91 4 0.01
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (87 bp):
ACATATGGTTACCACCCTGGTCAAATCTTTTCCTTTCTATCTAACATATGGTTACCACCCTGGCC
AGATTCTTTTCATTATGATGTG
Found at i:1615340 original size:133 final size:133
Alignment explanation
Indices: 1615115--1615533 Score: 440
Period size: 133 Copynumber: 3.2 Consensus size: 133
1615105 ATGATTTGAC
* * * ** * **
1615115 GTATGGTTACCACCCTAGTC-AAGTCTTTTCCTTT-TTGTCTAACGTATGGTTACCACCTTGGTC
1 GTATGGTTACCACCCTAGTCAAACTCTTCTCATTTCAGGACTAACGTATGGTTACCACCCAGGTC
* * *
1615178 AGATTCTTTTCATTCTGATGTGACATATGGTTACCACCCTGGTCAAATTTTCCTCTCTTCTGTTT
66 AGATTCTTTTCATTCTGATTTGACGTATGGTTACTACCCTGGTCAAATTTTCCTCTCTTCTGTTT
* *
1615243 GAT
131 AAA
* * * * * *
1615246 GTATGGTTACTATCCTGGTCAAACTCTTCTCATTTTAGGACTGATGTATGGTTACCACCCAGGTC
1 GTATGGTTACCACCCTAGTCAAACTCTTCTCATTTCAGGACTAACGTATGGTTACCACCCAGGTC
* * * *
1615311 AGATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATTTTTCTCTTTTCTGTTT
66 AGATTCTTTTCATTCTGATTTGACGTATGGTTACTACCCTGGTCAAATTTTCCTCTCTTCTGTTT
1615376 AAA
131 AAA
* *
1615379 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAGGTCTAACGTATGGTTACCACCCTA--T
1 GTATGGTTACCACCCTAGTCAAACTCTTCTCATTTCAGGACTAACGTATGGTTACCACCC-AGGT
* * * * * *
1615442 CTGATTCTCTTCATTCTGATTT-AAGATATGGTTACTACTCTGGTCAAATCTGCCTCT-TTCT-T
65 CAGATTCTTTTCATTCTGATTTGACG-TATGGTTACTACCCTGGTCAAATTTTCCTCTCTTCTGT
1615504 ATCTAACA
129 -T-TAA-A
* *
1615512 -TATGGTTATCACCCTGGTCAAA
1 GTATGGTTACCACCCTAGTCAAA
1615534 ATTTTTTCAT
Statistics
Matches: 240, Mismatches: 41, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.00
131 24 0.10
132 80 0.33
133 134 0.56
134 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (133 bp):
GTATGGTTACCACCCTAGTCAAACTCTTCTCATTTCAGGACTAACGTATGGTTACCACCCAGGTC
AGATTCTTTTCATTCTGATTTGACGTATGGTTACTACCCTGGTCAAATTTTCCTCTCTTCTGTTT
AAA
Found at i:1615426 original size:89 final size:87
Alignment explanation
Indices: 1615115--1615433 Score: 222
Period size: 89 Copynumber: 3.6 Consensus size: 87
1615105 ATGATTTGAC
* * ** * *
1615115 GTATGGTTACCACCCTAGTCAAGTCTTTTCCTTTTTGTCTAACGTATGGTTACCACCTTGGTCAG
1 GTATGGTTACCACCCTAGTCAAATCTTTTCATTTAGGTCTAACGTATGGTTACTACCTTGGTCAA
* * *
1615180 ATTCTTT-TC-ATTCTGATGTGACA
66 ATT-TTTCTCTTTTCTG-T-TTAAA
* ** * * *
1615203 -TATGGTTACCACCCTGGTCAAAT-TTTCCTC-TCTTCTGTTTGATGTATGGTTACTATCC-TGG
1 GTATGGTTACCACCCTAGTCAAATCTTT--TCAT-TTAGGTCTAACGTATGGTTACTA-CCTTGG
* * ** ** * *
1615264 TCAAACTCTTCTCATTTTAGGACTGAT
62 TCAAATTTTTCTC-TTTTCTGTTTAAA
* * * *
1615291 GTATGGTTACCACCC-AGGTCAGATTCTTTTCA-TTATGATTTGACGTATGGTTACTACCTTGGT
1 GTATGGTTACCACCCTA-GTCA-AATCTTTTCATTTA-GGTCTAACGTATGGTTACTACCTTGGT
1615354 CAAATTTTTCTCTTTTCTGTTTAAA
63 CAAATTTTTCTCTTTTCTGTTTAAA
1615379 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAGGTCTAACGTATGGTTAC
1 GTATGGTTACCACCCTAGTCAAA-TCTTTTCATTT-AGGTCTAACGTATGGTTAC
1615434 CACCCTATCT
Statistics
Matches: 176, Mismatches: 37, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
86 3 0.02
87 25 0.14
88 68 0.39
89 71 0.40
90 6 0.03
91 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (87 bp):
GTATGGTTACCACCCTAGTCAAATCTTTTCATTTAGGTCTAACGTATGGTTACTACCTTGGTCAA
ATTTTTCTCTTTTCTGTTTAAA
Found at i:1615543 original size:220 final size:219
Alignment explanation
Indices: 1615028--1615580 Score: 572
Period size: 220 Copynumber: 2.5 Consensus size: 219
1615018 TCTATTTTAC
* * * *
1615028 ATATGGTTACCAC-CTTGGTCAAATCTTTTCCTTTC-TATCTGACATATGGTTGCCACCCTGGCC
1 ATATGGTTACTACTC-TGGTCAAATCTTCT-CTTTCTTATCTGACATATGGTTACCACCCTGGTC
* * * *
1615091 AGATTCTTTTCATTATGATTTGACGTATGGTTACCACCCTAGTCAAGTCTTTTCCTTTTTGTCTA
64 AGATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTCCTTTTTGTCTA
* * * * * * * * *
1615156 ACGTATGGTTACCACCTTGGTCAGATTCTTTTCATTCTGATGTGACATATGGTTACCACCCTGGT
129 AAGTATGGTTACCACCCTAGTCAAACTCTTTTCATTCAGATCTAACATATGGTTACCACCCTGAT
* *
1615221 CAAATTTTCCTCTCTTCTGTTTGATG
194 CAAATTCTCCTCTCTTCTGTTTGAAG
* * ** *
1615247 -TATGGTTACTA-TCCTGGTCAAACTCTTCTCATT-TTAGGACTGATGTATGGTTACCACCCAGG
1 ATATGGTTACTACT-CTGGTCAAA-TCTTCTCTTTCTTA--TCTGACATATGGTTACCACCCTGG
1615309 TCAGATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAAT-TTTTCTCTTTTCTG
62 TCAGATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTC-CTTTT-TG
* * *
1615373 TTTAAAGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTCAGGTCTAACGTATGGTTACCACC
125 TCTAAAGTATGGTTACCACCCTAGTCAAACTCTTTTCA-TTCAGATCTAACATATGGTTACCACC
**
1615438 CT-ATCTGATTCT-CT-TCATTCTGATTT-AAG
189 CTGATCAAATTCTCCTCTC-TTCTG-TTTGAAG
* * *
1615467 ATATGGTTACTACTCTGGTCAAATCTGCCTCTTTCTTATCTAACATATGGTTATCACCCTGGTCA
1 ATATGGTTACTACTCTGGTCAAATCT-TCTCTTTCTTATCTGACATATGGTTACCACCCTGGTC-
* * * *
1615532 AAATT-TTTTCATTCTGATTTGATGTATGGTTA-TCACCTTGGTTAAATCT
64 AGATTCTTTTCATTATGATTTGACGTATGGTTACT-ACCTTGGTCAAATCT
1615581 GCCTTCTTCC
Statistics
Matches: 275, Mismatches: 41, Indels: 34
0.79 0.12 0.10
Matches are distributed among these distances:
218 23 0.08
219 14 0.05
220 138 0.50
221 73 0.27
222 27 0.10
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (219 bp):
ATATGGTTACTACTCTGGTCAAATCTTCTCTTTCTTATCTGACATATGGTTACCACCCTGGTCAG
ATTCTTTTCATTATGATTTGACGTATGGTTACTACCTTGGTCAAATCTTTTCCTTTTTGTCTAAA
GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCAGATCTAACATATGGTTACCACCCTGATCA
AATTCTCCTCTCTTCTGTTTGAAG
Found at i:1615601 original size:88 final size:88
Alignment explanation
Indices: 1615451--1615614 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
1615441 TCTGATTCTC
* *
1615451 TTCATTCTGATTTAAGATATGGTTACTACTCTGGTCAAATCTGCCTCTTTCTTATCTAACATATG
1 TTCATTCTGATTTAAGATATGGTTACTACTCTGGTCAAATCTGCCTCTTTCCTATCTAACATATA
1615516 GTTATCACCCTGGTCAAAATTTT
66 GTTATCACCCTGGTCAAAATTTT
* * * *
1615539 TTCATTCTGATTTGATG-TATGGTTA-TCAC-CTTGGTTAAATCTGCCT-TCTTCCTATTTGACA
1 TTCATTCTGATTT-AAGATATGGTTACT-ACTC-TGGTCAAATCTGCCTCT-TTCCTATCTAACA
*
1615600 TATAGTTGTCACCCT
62 TATAGTTATCACCCT
1615615 AATCAAATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
87 3 0.05
88 60 0.92
89 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (88 bp):
TTCATTCTGATTTAAGATATGGTTACTACTCTGGTCAAATCTGCCTCTTTCCTATCTAACATATA
GTTATCACCCTGGTCAAAATTTT
Found at i:1617012 original size:167 final size:167
Alignment explanation
Indices: 1616799--1617571 Score: 920
Period size: 167 Copynumber: 4.6 Consensus size: 167
1616789 CAAATTACGA
* *
1616799 AGTTTTCTACT-C-TATGATTTTTTCAGGGGGGATTTTTCTTGGTTTTTAAATTTTAAAATTCAT
1 AGTTTTCTACTCCGTA-AATTTTTTCA-GGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCAT
* * * * *
1616862 CAAATACCATTATTTATATGACATTAAATTAGTTTTCAATAATTCCTTCATTTTCTTTAGTTTTT
64 CAAATATCATTATTTATATCACATTAAATCAGTTTTCAAAAATTCCTTCATTTTCTTGAGTTTTT
* *
1616927 AGATTTTTTCTTTTAAA-TTCCCATATTTTCGAAAAACAG
129 AGATTTTTTCCTTTAAATTTTCC-TATTTTCGAAAAACAG
* * * *
1616966 AGTTTTTTACTTCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTCATTTTTAAAATTCATCA
1 AGTTTTCTACTCCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCA
* * *
1617031 AATATTATTATTTATATCACATTAAATCAATTTTCAAAAATTCCTTCATTTTATTGAGTTTTT-G
66 AATATCATTATTTATATCACATTAAATCAGTTTTCAAAAATTCCTTCATTTTCTTGAGTTTTTAG
* * *
1617095 AATTTTTTCCTTCAAATTTTCCTATTTTTGAAAAATAG
131 -ATTTTTTCCTTTAAATTTTCCTATTTTCGAAAAACAG
* *
1617133 AGTTTTTTACTCCGTAAATTTTTTCA-GGAGGATTTTTCTTGGTTTTT-AATTTTCAAAGTTCAT
1 AGTTTTCTACTCCGTAAATTTTTTCAGGGA-GATTTTTCTTGGTTTTTAAATTTT-AAAATTCAT
* * *
1617196 CAAATATCATTATTTATATCATATTAAATCCA-TTTTCAAATATTCCTTCATTTTCTTAAGTTTT
64 CAAATATCATTATTTATATCACATTAAAT-CAGTTTTCAAAAATTCCTTCATTTTCTTGAGTTTT
* * * * *
1617260 TATAATTTTTTCCTTTAAATTTTTCT-GTTTCTAAAAAAATGG
128 TA-GATTTTTTCCTTTAAATTTTCCTATTTTCGAAAAACA--G
* ** * *
1617302 AGTTTTCTACTCCATAAATTTTTTGGGGGATATTTTTCTTGGATTTTAAATTTTAAAATTCATCA
1 AGTTTTCTACTCCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCA
* * **
1617367 AATATCATTTTTTATATCACATTAAATCAGTTTTCAAAAATTTCTTCATTTTCTTGAGTTTTTTC
66 AATATCATTATTTATATCACATTAAATCAGTTTTCAAAAATTCCTTCATTTTCTTGAGTTTTTAG
* * * *
1617432 ATTTTTT-CTTTAAATTTTTCTGTTTCCGAAAAACGG
131 ATTTTTTCCTTTAAATTTTCCTATTTTCGAAAAACAG
* * * * *
1617468 AGTTTTCTACTTCGTAAATTTTTT-TGGAAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATC
1 AGTTTTCTACTCCGTAAATTTTTTCAGGGA-GATTTTTCTTGGTTTTTAAATTTTAAAATTCATC
* *
1617532 AAATATCATTATTCAT-TCCATATTAAATCAGTTTTCAAAA
65 AAATATCATTATTTATAT-CACATTAAATCAGTTTTCAAAA
1617572 GGAATTCATT
Statistics
Matches: 526, Mismatches: 63, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
165 4 0.01
166 97 0.18
167 258 0.49
168 53 0.10
169 105 0.20
170 9 0.02
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (167 bp):
AGTTTTCTACTCCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAAATTTTAAAATTCATCA
AATATCATTATTTATATCACATTAAATCAGTTTTCAAAAATTCCTTCATTTTCTTGAGTTTTTAG
ATTTTTTCCTTTAAATTTTCCTATTTTCGAAAAACAG
Found at i:1617418 original size:336 final size:333
Alignment explanation
Indices: 1616799--1617570 Score: 977
Period size: 335 Copynumber: 2.3 Consensus size: 333
1616789 CAAATTACGA
* *
1616799 AGTTTTCTACT-C-TATGATTTTTTCAGGGGGGATTTTTCTTGGTTTTTAAATTTTAAAATTCAT
1 AGTTTTCTACTCCGTA-AATTTTTTCA-GGAGGATTTTTCTTGGTTTTT-AATTTTAAAATTCAT
* * * * *
1616862 CAAATACCATTATTTATATGACATTAAATTAGTTTTC-AATAATTCCTTCATTTTCTTTAGTTTT
63 CAAATATCATTATTTATATCATATTAAATCAGTTTTCAAATAATTCCTTCATTTTCTTAAGTTTT
* * * * * * *
1616926 TAGATTTTTTCTTTTAAATTCCCATATTTTCGAAAAACAGAGTTTTTTACTTCGTAAATTTTTTC
128 TAAATTTTTTCCTTTAAATTCCCATAGTTTCGAAAAAAAGAGTTTTCTACTCCATAAATTTTTTC
* * * *
1616991 AGGGAGATTTTTCTTGGTTTTTCATTTTTAAAATTCATCAAATATTATTATTTATATCACATTAA
193 AGGGAGATTTTTCTTGGATTTTAAATTTTAAAATTCATCAAATATCATTATTTATATCACATTAA
1617056 ATCAATTTTCAAAAATTCCTTCATTTTATTGAGTTTTTGAATTTTTTCCTTCAAATTTTCCTATT
258 ATCAATTTTCAAAAATTCCTTCATTTTATTGAGTTTTTGAATTTTTT-CTTCAAATTTTCCTATT
** *
1617121 TTTGAAAAATAG
322 TCCGAAAAACAG
* *
1617133 AGTTTTTTACTCCGTAAATTTTTTCAGGAGGATTTTTCTTGGTTTTTAATTTTCAAAGTTCATCA
1 AGTTTTCTACTCCGTAAATTTTTTCAGGAGGATTTTTCTTGGTTTTTAATTTT-AAAATTCATCA
1617198 AATATCATTATTTATATCATATTAAATCCA-TTTTCAAAT-ATTCCTTCATTTTCTTAAGTTTTT
65 AATATCATTATTTATATCATATTAAAT-CAGTTTTCAAATAATTCCTTCATTTTCTTAAGTTTTT
** *
1617261 ATAATTTTTTCCTTTAAATTTTTC-T-GTTTCTAAAAAAATGGAGTTTTCTACTCCATAAATTTT
129 A-AATTTTTTCCTTTAAA-TTCCCATAGTTTCGAAAAAAA--GAGTTTTCTACTCCATAAATTTT
** * *
1617324 TTGGGGGATATTTTTCTTGGATTTTAAATTTTAAAATTCATCAAATATCATTTTTTATATCACAT
190 TTCAGGGAGATTTTTCTTGGATTTTAAATTTTAAAATTCATCAAATATCATTATTTATATCACAT
* * * ** * * *
1617389 TAAATCAGTTTTCAAAAATTTCTTCATTTTCTTGAGTTTTTTCATTTTTTCTTTAAATTTTTCTG
255 TAAATCAATTTTCAAAAATTCCTTCATTTTATTGAGTTTTTGAATTTTTTCTTCAAATTTTCCTA
*
1617454 TTTCCGAAAAACGG
320 TTTCCGAAAAACAG
* * *
1617468 AGTTTTCTACTTCGTAAATTTTTT-TGGAAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATC
1 AGTTTTCTACTCCGTAAATTTTTTCAGG-AGGATTTTTCTTGGTTTTTAA-TTTTAAAATTCATC
*
1617532 AAATATCATTATTCAT-TCCATATTAAATCAGTTTTCAAA
64 AAATATCATTATTTATAT-CATATTAAATCAGTTTTCAAA
1617571 AGGAATTCAT
Statistics
Matches: 380, Mismatches: 45, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
333 6 0.02
334 108 0.28
335 135 0.36
336 131 0.34
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (333 bp):
AGTTTTCTACTCCGTAAATTTTTTCAGGAGGATTTTTCTTGGTTTTTAATTTTAAAATTCATCAA
ATATCATTATTTATATCATATTAAATCAGTTTTCAAATAATTCCTTCATTTTCTTAAGTTTTTAA
ATTTTTTCCTTTAAATTCCCATAGTTTCGAAAAAAAGAGTTTTCTACTCCATAAATTTTTTCAGG
GAGATTTTTCTTGGATTTTAAATTTTAAAATTCATCAAATATCATTATTTATATCACATTAAATC
AATTTTCAAAAATTCCTTCATTTTATTGAGTTTTTGAATTTTTTCTTCAAATTTTCCTATTTCCG
AAAAACAG
Found at i:1618235 original size:22 final size:22
Alignment explanation
Indices: 1618207--1618258 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1618197 GCTTTTAATT
*
1618207 GAAAGAAGAA-AGAGAAAAGATA
1 GAAAGAA-AAGAGAGAAAAAATA
1618229 GAAAGAAAAGAGAGAAAAAATA
1 GAAAGAAAAGAGAGAAAAAATA
1618251 G-AAGAAAA
1 GAAAGAAAA
1618259 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (22 bp):
GAAAGAAAAGAGAGAAAAAATA
Found at i:1619486 original size:162 final size:161
Alignment explanation
Indices: 1619204--1619524 Score: 432
Period size: 162 Copynumber: 2.0 Consensus size: 161
1619194 ACGGATTAAT
* *
1619204 TTTTTTCTTAATCTTTTATATTCCTATAGGCATCCATAGAGATATCAAAGATTTTAAAAATATTT
1 TTTTTTCTTAATCTTTTATATTCCTATAGGCATCCATAGAGATATAAAAGATTTTAAAAATATTC
* **
1619269 CATATCCTTTTAGGCTTCCATTAGGGTATGAAATGGTATTTTCGAAAATAAATAAAATTAAATTG
66 CATATCCTTTCAGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATAAATAAAATTAAATTG
* *
1619334 AATTAATACTTTC-AGGATAAATTTTAATTA
131 AATTAATACTTTCGAGAAAAAATTTTAATTA
* * * *
1619364 TTTTTTC-TAATCTTTTATATTCTTATGGGCATTCGA-AGGGATATAAAAGATTTATAAAAAAAT
1 TTTTTTCTTAATCTTTTATATTCCTATAGGCA-TCCATAGAGATATAAAAGATTT-T--AAAAAT
* * * * *
1619427 ATTCCGTATCCTTTCGGGCTTCTATTAGGGTACAAAATGGTGTTTTTGAAAATAAATAAAATTAA
62 ATTCCATATCCTTTCAGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATAAATAAAATTAA
*
1619492 GTTGAATTAATACTTTCGAGAAAAAATTTTAAT
127 ATTGAATTAATACTTTCGAGAAAAAATTTTAAT
1619525 CTTTTATATT
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
159 37 0.27
160 11 0.08
162 78 0.56
163 13 0.09
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (161 bp):
TTTTTTCTTAATCTTTTATATTCCTATAGGCATCCATAGAGATATAAAAGATTTTAAAAATATTC
CATATCCTTTCAGGCTTCCATTAGGGTACAAAATGGTATTTTCGAAAATAAATAAAATTAAATTG
AATTAATACTTTCGAGAAAAAATTTTAATTA
Found at i:1621278 original size:32 final size:33
Alignment explanation
Indices: 1621212--1621278 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1621202 GTTACAAGCT
1621212 AATGTATCGATACAATTTGTGGTGCATCGATAC
1 AATGTATCGATACAATTTGTGGTGCATCGATAC
* *
1621245 AATGTATTGATAC-ATATTGT-GTGTATCGATAC
1 AATGTATCGATACAAT-TTGTGGTGCATCGATAC
1621277 AA
1 AA
1621279 ATTTGGCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACAATTTGTGGTGCATCGATAC
Found at i:1621368 original size:13 final size:13
Alignment explanation
Indices: 1621350--1621375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1621340 ACAATTGGTC
1621350 ATGTATCGATACA
1 ATGTATCGATACA
1621363 ATGTATCGATACA
1 ATGTATCGATACA
1621376 TTTAAATGTG
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:1623634 original size:20 final size:21
Alignment explanation
Indices: 1623605--1623645 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1623595 TGTTTTTGTT
1623605 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1623624 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1623646 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1623795 original size:13 final size:13
Alignment explanation
Indices: 1623777--1623815 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1623767 ATAAACCCCT
*
1623777 TGTATCGATACAC
1 TGTATCGATACAA
1623790 TGTATCGATACAA
1 TGTATCGATACAA
1623803 TGTATCGATACAA
1 TGTATCGATACAA
1623816 AGAATTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1628360 original size:9 final size:9
Alignment explanation
Indices: 1628346--1628375 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1628336 TCTGAGTCAC
*
1628346 CATCATCAT
1 CATCATCTT
1628355 CATCATCTT
1 CATCATCTT
1628364 CATCATCTT
1 CATCATCTT
1628373 CAT
1 CAT
1628376 TGTCCTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (9 bp):
CATCATCTT
Found at i:1630001 original size:13 final size:13
Alignment explanation
Indices: 1629983--1630007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1629973 CAATTTGTGG
1629983 TGTATCGATACAA
1 TGTATCGATACAA
1629996 TGTATCGATACA
1 TGTATCGATACA
1630008 TATTGTGTGT
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:1630023 original size:32 final size:33
Alignment explanation
Indices: 1629960--1630027 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1629950 CGTTACAAGC
1629960 CAATGTATCGATACAATTTGTGGTGTATCGATA
1 CAATGTATCGATACAATTTGTGGTGTATCGATA
1629993 CAATGTATCGATAC-ATATTGT-GTGTATCGATA
1 CAATGTATCGATACAAT-TTGTGGTGTATCGATA
1630025 CAA
1 CAA
1630028 ATTTGGCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACAATTTGTGGTGTATCGATA
Found at i:1630106 original size:20 final size:21
Alignment explanation
Indices: 1630059--1630111 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1630049 GCCAATGACC
**
1630059 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
1630080 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
1630100 TGTATCGATACA
1 TGTATCGATACA
1630112 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:1630117 original size:13 final size:13
Alignment explanation
Indices: 1630099--1630127 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1630089 ACATTTGGTC
1630099 ATGTATCGATACA
1 ATGTATCGATACA
1630112 ATGTATCGATACA
1 ATGTATCGATACA
1630125 ATG
1 ATG
1630128 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1630138 original size:20 final size:20
Alignment explanation
Indices: 1630113--1630163 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1630103 ATCGATACAA
*
1630113 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
1630133 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
1630153 TGTATCGATAC
1 TGTATCGATAC
1630164 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:1634066 original size:4 final size:4
Alignment explanation
Indices: 1634059--1634155 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
1634049 TTTAACATTT
* * * * *
1634059 ATAA ATAA A-AA ATAT A-AA ATAT A-AA ATAA ATAA ATAA A-AGT GTAT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA
* * * * *
1634104 ATAA A-AA ATAT ATATA ACAT ATAA ATAA ATAA ATAA ACAA AGAA ATAA
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1634152 ATAA
1 ATAA
1634156 TAATAAAAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
3 11 0.16
4 55 0.80
5 3 0.04
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1634142 original size:20 final size:21
Alignment explanation
Indices: 1634058--1634155 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 21
1634048 ATTTAACATT
*
1634058 TATAAATAAA-AAATATAAAA
1 TATAAATAAATAAATATAACA
* *
1634078 TATAAAATAAATAAATAAAAGTGTA
1 TAT-AAATAAATAAATATAA---CA
*
1634103 TATAAA-AAATATATATAACA
1 TATAAATAAATAAATATAACA
1634123 TATAAATAAATAAATA-AACA
1 TATAAATAAATAAATATAACA
* *
1634143 AAGAAATAAATAA
1 TATAAATAAATAA
1634156 TAATAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
20 25 0.39
21 15 0.23
22 7 0.11
23 10 0.16
24 3 0.05
25 4 0.06
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (21 bp):
TATAAATAAATAAATATAACA
Found at i:1634152 original size:44 final size:41
Alignment explanation
Indices: 1634060--1634163 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 41
1634050 TTAACATTTA
* **
1634060 TAAATAAAAAATATAAAATATAAAATAAATAAATAAAAGTG
1 TAAATAAAAAATATAAAACATAAAATAAATAAATAAAAAAG
*
1634101 TATATAAAAAATATATATAACATATAAATAAATAAATAAACAAAG
1 TAAATAAAAAATATA-A-AACATA-AAATAAATAAATAAA-AAAG
*
1634146 -AAATAAATAATAATAAAA
1 TAAATAAAAAAT-ATAAAA
1634164 AAACTCAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 14 0.27
42 1 0.02
43 7 0.13
44 25 0.48
45 5 0.10
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (41 bp):
TAAATAAAAAATATAAAACATAAAATAAATAAATAAAAAAG
Found at i:1634258 original size:38 final size:38
Alignment explanation
Indices: 1634202--1634284 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
1634192 ATATTGCATG
*
1634202 CATTTCATGCATTCCATGCATGCATTTTACGTAATTTT
1 CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
* *
1634240 CATTTTATGCATTACATGCATGCATTTTATGTAATTTT
1 CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
1634278 CATTTCA
1 CATTTCA
1634285 AGCAATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (38 bp):
CATTTCATGCATTACATGCATGCATTTTACGTAATTTT
Found at i:1634340 original size:12 final size:12
Alignment explanation
Indices: 1634319--1634375 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
1634309 ATGCATTATA
1634319 TTTCATGCATAC
1 TTTCATGCATAC
*
1634331 TTTCACGCATAC
1 TTTCATGCATAC
*
1634343 CTTCATGCATAC
1 TTTCATGCATAC
**
1634355 TTTCATGCATGT
1 TTTCATGCATAC
1634367 TTTCATGCA
1 TTTCATGCA
1634376 AATGAAATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (12 bp):
TTTCATGCATAC
Found at i:1634875 original size:23 final size:24
Alignment explanation
Indices: 1634819--1634890 Score: 101
Period size: 23 Copynumber: 3.0 Consensus size: 24
1634809 AAGCAAGTAG
*
1634819 CAACATCGAGCACCAACAGCAGCAA
1 CAACATCGAGCACCAACAGCAAC-A
*
1634844 CAACATCGAGCACCAATAGCAACA
1 CAACATCGAGCACCAACAGCAACA
*
1634868 -AACATCGAGCGCCAACAGCAACA
1 CAACATCGAGCACCAACAGCAACA
1634891 TCACAGCAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 21 0.49
24 1 0.02
25 21 0.49
ACGTcount: A:0.44, C:0.35, G:0.15, T:0.06
Consensus pattern (24 bp):
CAACATCGAGCACCAACAGCAACA
Found at i:1641637 original size:13 final size:13
Alignment explanation
Indices: 1641619--1641657 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1641609 TACACAAAAT
1641619 ATGTATCGATACA
1 ATGTATCGATACA
1641632 ATGTATCGATACA
1 ATGTATCGATACA
1641645 ATGTATCGATACA
1 ATGTATCGATACA
1641658 CAAAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1648006 original size:20 final size:20
Alignment explanation
Indices: 1647963--1648008 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1647953 AAATCTTTTG
1647963 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1647984 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1648004 CAAAA
1 CAAAA
1648009 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:1650295 original size:20 final size:20
Alignment explanation
Indices: 1650270--1650322 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1650260 ACCCTTAAAA
1650270 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1650290 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1650310 GTATCGATACATG
1 GTATCGATACATG
1650323 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1650398 original size:19 final size:18
Alignment explanation
Indices: 1650374--1650436 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1650364 TAGCCAAACT
1650374 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
1650393 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
1650406 TGTATCGATACACAAAAA
1 TGTATCGATACACAAAAA
1650424 GTGTATCGATACA
1 -TGTATCGATACA
1650437 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
18 2 0.05
19 21 0.55
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:1650410 original size:13 final size:13
Alignment explanation
Indices: 1650392--1650417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1650382 TACACAAAAT
1650392 ATGTATCGATACA
1 ATGTATCGATACA
1650405 ATGTATCGATACA
1 ATGTATCGATACA
1650418 CAAAAAGTGT
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:1650415 original size:32 final size:32
Alignment explanation
Indices: 1650374--1650436 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1650364 TAGCCAAACT
1650374 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAA-AGTGTATCGATACAA
1650406 TGTATCGATACACAAAAAGTGTATCGATACA
1 TGTATCGATACACAAAAAGTGTATCGATACA
1650437 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAAGTGTATCGATACAA
Found at i:1658968 original size:85 final size:83
Alignment explanation
Indices: 1658865--1659211 Score: 328
Period size: 85 Copynumber: 4.1 Consensus size: 83
1658855 TGAATTTTTT
* * *
1658865 TACCC-TCAGTCTGCCTGTCGTCTTTAACCTGGAGACTACCTCATTTAAAGTCTACCTGACGGCT
1 TACCCTTCAGTCTGTCTGTCG-CTTTAACCTGGAGACTACCTCATCTAAAGTCTATCTGACGGCT
1658929 TTGACCCTAAAGACTTTCC
65 TTGACCCTAAAGACTTTCC
*
1658948 TACCCCTTCAGTCTGTCTGTCAGCTTTGACTCTGGAGACTACCTCATCTAAAGTCTATCT-ATCG
1 TA-CCCTTCAGTCTGTCTGTC-GCTTTAAC-CTGGAGACTACCTCATCTAAAGTCTATCTGA-CG
*
1659012 GCTTTGACCCTGGAA-ACTTTCC
62 GCTTTGACCCT-AAAGACTTTCC
* * * * * * *
1659034 TACCCTTCAGTCTG-CTTGTCGGCTTTAACCTTGGAGACTGCCTCACCTAATGTCTGTATGTCGA
1 TACCCTTCAGTCTGTC-TGTC-GCTTTAACC-TGGAGACTACCTCATCTAAAGTCTATCTGACGG
* *
1659098 TTTTGACCCTAGAGACTTTCC
63 CTTTGACCCTAAAGACTTTCC
* * * * * * *
1659119 TACCC-TCAGTCTGTCTGTCGACTTTGACCCTAGAGACTGCCTCACCTAAAGTTTGTCT-ATCAG
1 TACCCTTCAGTCTGTCTGTCG-CTTT-AACCTGGAGACTACCTCATCTAAAGTCTATCTGA-CGG
* **
1659182 CTTTGACCCTGAAGACTTTTT
63 CTTTGACCCTAAAGACTTTCC
1659203 TACCCTTCA
1 TACCCTTCA
1659212 ATTTGCATGT
Statistics
Matches: 219, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
83 3 0.01
84 68 0.31
85 96 0.44
86 50 0.23
87 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (83 bp):
TACCCTTCAGTCTGTCTGTCGCTTTAACCTGGAGACTACCTCATCTAAAGTCTATCTGACGGCTT
TGACCCTAAAGACTTTCC
Found at i:1659222 original size:127 final size:126
Alignment explanation
Indices: 1659099--1659444 Score: 358
Period size: 127 Copynumber: 2.7 Consensus size: 126
1659089 GTATGTCGAT
* *
1659099 TTTGACCCTAGAGACTTTCCTACCCTCAGTCTGTCTGTCGACTTTGACCCTAGAGACTGCCTCAC
1 TTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTAAC
* * *
1659164 CTAAAGT-TTGTCTATCAGCTTTGACCCTGAAGACTTTTTTACCCTTCAATTTGCATGTCGGC
66 CTAAAGTCTT-CCTATCAGCTTTGACCCTGAAGACTTTTCTACCC-TCAATCTGCATGTCGGC
* * * * * * *
1659226 TTTGACCTTGGAGACTTTCTTACCCTCAGTTTGCCTGTCGGCTTTGACCCTAAAGACTGCCTAAT
1 TTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTAAC
* ** * * *
1659291 CTAAAGTCTTCCTGTTGGCTTTGACCCTGGAGACTTTTCTACCCTCAATCTGCCTATCGGC
66 CTAAAGTCTTCCTATCAGCTTTGACCCTGAAGACTTTTCTACCCTCAATCTGCATGTCGGC
* * * * * *
1659352 TTTAACCCTAGAGACTGT-CT-CATCTAAAGTCTGCCTGTCAACTTTGACCCTAGAGACTTTCCT
1 TTTGACCCTAGAGACTTTCCTAC-CCT-CAGTCTGCCTGTCGACTTTGACCCTAGAGAC-TGCCT
*** * *
1659415 -ACCCCCAGTCTACCTATCAGTTTTGACCCT
63 AACCTAAAGTCTTCCTATCAGCTTTGACCCT
1659445 AGAGATGTCT
Statistics
Matches: 176, Mismatches: 39, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
124 1 0.01
125 3 0.02
126 75 0.43
127 95 0.54
128 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (126 bp):
TTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTAAC
CTAAAGTCTTCCTATCAGCTTTGACCCTGAAGACTTTTCTACCCTCAATCTGCATGTCGGC
Found at i:1659274 original size:169 final size:171
Alignment explanation
Indices: 1658865--1659283 Score: 474
Period size: 169 Copynumber: 2.5 Consensus size: 171
1658855 TGAATTTTTT
* * * * ** * * *
1658865 TACCC-TCAGTCTGCCTGTCGTCTTTAACC-TGGAGACTACCTCATTTAAAGTCTACCTGACGGC
1 TACCCTTCAATCTGCATGTCGGCTTTAACCTTGGAGACTGCCTCACCTAATGTCTGCCTGTCGGC
* *
1658928 TTTGACCCTAAAGACTTTCCTACCCCTTCAGTCTGTCTGTCAGCTTTGACTCTGGAGACTACCTC
66 TTTGACCCTAAAGACTTTCCTACCCCTTCAGTCTGTCTGTCAGCTTTGACCCTAGAGACTACCTC
* *
1658993 ATCTAAAGTCTATCTATCGGCTTTGACCCTGGAAACTTTCC
131 ACCTAAAGTCTATCTATCAGCTTTGACCCTGGAAACTTTCC
* * ** **
1659034 TACCCTTCAGTCTGCTTGTCGGCTTTAACCTTGGAGACTGCCTCACCTAATGTCTGTATGTCGAT
1 TACCCTTCAATCTGCATGTCGGCTTTAACCTTGGAGACTGCCTCACCTAATGTCTGCCTGTCGGC
* *
1659099 TTTGACCCTAGAGACTTTCCTA-CCC-TCAGTCTGTCTGTC-GACTTTGACCCTAGAGACTGCCT
66 TTTGACCCTAAAGACTTTCCTACCCCTTCAGTCTGTCTGTCAG-CTTTGACCCTAGAGACTACCT
* * **
1659161 CACCTAAAGTTTGTCTATCAGCTTTGACCCT-GAAGACTTTTT
130 CACCTAAAGTCTATCTATCAGCTTTGACCCTGGAA-ACTTTCC
* * ** * * *
1659203 TACCCTTCAATTTGCATGTCGGCTTTGACCTTGGAGACTTTCTTACCCTCA-GTTTGCCTGTCGG
1 TACCCTTCAATCTGCATGTCGGCTTTAACCTTGGAGACTGCCTCA-CCTAATGTCTGCCTGTCGG
1659267 CTTTGACCCTAAAGACT
65 CTTTGACCCTAAAGACT
1659284 GCCTAATCTA
Statistics
Matches: 209, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
168 4 0.02
169 131 0.63
170 29 0.14
171 45 0.22
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.34
Consensus pattern (171 bp):
TACCCTTCAATCTGCATGTCGGCTTTAACCTTGGAGACTGCCTCACCTAATGTCTGCCTGTCGGC
TTTGACCCTAAAGACTTTCCTACCCCTTCAGTCTGTCTGTCAGCTTTGACCCTAGAGACTACCTC
ACCTAAAGTCTATCTATCAGCTTTGACCCTGGAAACTTTCC
Found at i:1659335 original size:211 final size:212
Alignment explanation
Indices: 1659009--1659411 Score: 506
Period size: 211 Copynumber: 1.9 Consensus size: 212
1658999 AGTCTATCTA
* * **
1659009 TCGGCTTTGACCCTGGAAACTTTCCTACCCTTCAGTCTGCTTGTCGGCTTTAACCTTGGAGACTG
1 TCGGCTTTGACCCTGGAAACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTAACCCTAAAGACTG
* * * * * *
1659074 CCTCACCTAATGTCTGTATGTCGATTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGTCTGTCG
66 CCTAACCTAAAGTCTGTATGTCGACTTTGACCCTAGAGACTTTCCTACCCTCAATCTGCCTATCG
* * * *
1659139 ACTTTGACCCTAGAGACTGCCTCACCTAAAGTTTGTCTATCAGCTTTGACCCT-GAAGACTTTTT
131 ACTTTAACCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCAACTTTGACCCTAG-AGACTTTTT
1659203 TACCCTTCAATTTGCATG
195 TACCCTTCAATTTGCATG
* * * * *
1659221 TCGGCTTTGACCTTGGAGACTTTCTTACCC-TCAGTTTGCCTGTCGGCTTTGACCCTAAAGACTG
1 TCGGCTTTGACCCTGGAAACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTAACCCTAAAGACTG
* * * * * *
1659285 CCTAATCTAAAGTCT-TCCTGTTGGCTTTGACCCTGGAGACTTTTCTACCCTCAATCTGCCTATC
66 CCTAACCTAAAGTCTGT-ATGTCGACTTTGACCCTAGAGACTTTCCTACCCTCAATCTGCCTATC
* * * *
1659349 GGCTTTAACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCAACTTTGACCCTAGAGACTTT
130 GACTTTAACCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCAACTTTGACCCTAGAGACTTT
1659412 CCTACCCCCA
Statistics
Matches: 160, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
210 1 0.01
211 131 0.82
212 28 0.17
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (212 bp):
TCGGCTTTGACCCTGGAAACTTTCCTACCCTTCAGTCTGCCTGTCGGCTTTAACCCTAAAGACTG
CCTAACCTAAAGTCTGTATGTCGACTTTGACCCTAGAGACTTTCCTACCCTCAATCTGCCTATCG
ACTTTAACCCTAGAGACTGCCTCACCTAAAGTCTGCCTATCAACTTTGACCCTAGAGACTTTTTT
ACCCTTCAATTTGCATG
Found at i:1659425 original size:42 final size:42
Alignment explanation
Indices: 1658913--1659494 Score: 306
Period size: 42 Copynumber: 13.8 Consensus size: 42
1658903 CCTCATTTAA
* * *
1658913 AGTCTACCTGACGGCTTTGACCCTAAAGACTTTCCTACCCCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTA-CCC-TC
* * * * * * *
1658957 AGTCTGTCTGTCAGCTTTGACTCTGGAGAC-TACCT-CATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTAC-CCT-C
** * * *
1658999 AGTCTATCTATCGGCTTTGACCCTGGAAACTTTCCTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCC-TC
* * * * * *
1659042 AGTCTGCTTGTCGGCTTTAACCTTGGAGAC-TGCCT-CACCTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTAC-CCTC
** **
1659083 ATGTCTGTATGTCGATTTTGACCCTAGAGACTTTCCTACCCTC
1 A-GTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTC
* * * *
1659126 AGTCTGTCTGTCGACTTTGACCCTAGAGAC-TGCCT-CACCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTAC-CCT-C
* * * * **
1659168 AGTTTGTCTATCAGCTTTGACCCT-GAAGACTTTTTTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTTCCTACCC-TC
* * * * * *
1659211 AATTTGCATGTCGGCTTTGACCTTGGAGACTTTCTTACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTC
* * * ** *
1659253 AGTTTGCCTGTCGGCTTTGACCCTAAAGAC-TGCCTAATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCT-C
* * * *
1659295 AGTCTTCCTGTTGGCTTTGACCCTGGAGACTTTTCTACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTC
* * * * * *
1659337 AATCTGCCTATCGGCTTTAACCCTAGAGACTGT-CT-CATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTAC-CCT-C
** *
1659379 AGTCTGCCTGTCAACTTTGACCCTAGAGACTTTCCTACCCCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTC
* * * * * * * *
1659421 AGTCTACCTATCAGTTTTGACCCTAGAGA-TGT-CTCATCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-ACCCTC
* * *
1659462 AGTCTGCCTATTGGCTTTGACCCTAAAGACTTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTT
1659495 TTCACCTTTT
Statistics
Matches: 406, Mismatches: 108, Indels: 50
0.72 0.19 0.09
Matches are distributed among these distances:
40 4 0.01
41 51 0.13
42 237 0.58
43 84 0.21
44 30 0.07
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTC
Found at i:1660026 original size:4 final size:4
Alignment explanation
Indices: 1660019--1660084 Score: 64
Period size: 4 Copynumber: 16.0 Consensus size: 4
1660009 TTTAACATTT
* *
1660019 ATAA ATAA A-AA ATAT A-AA ATAA ATAA ATAAA AGTAA ATATA AAAA TATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA A-TAA ATA-A ATAA -ATAA
1660069 ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA
1660085 TAATAAACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 5 0.10
4 34 0.65
5 12 0.23
6 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1660040 original size:14 final size:15
Alignment explanation
Indices: 1660021--1660091 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 15
1660011 TAACATTTAT
1660021 AAATAAA-AAATATA
1 AAATAAATAAATATA
1660035 AAATAAATAAATA-A
1 AAATAAATAAATATA
* *
1660049 AAGTAAATATAAAAATA
1 AAAT-AA-ATAAATATA
1660066 TAAATAAATAAATA-A
1 -AAATAAATAAATATA
1660081 ATAAT-AATAAA
1 A-AATAAATAAA
1660092 CTCGAATGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 18 0.38
15 11 0.23
16 12 0.26
17 3 0.06
18 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (15 bp):
AAATAAATAAATATA
Found at i:1660057 original size:10 final size:9
Alignment explanation
Indices: 1660021--1660091 Score: 60
Period size: 10 Copynumber: 7.8 Consensus size: 9
1660011 TAACATTTAT
1660021 AAATAAA-A
1 AAATAAATA
1660029 AATATAAA-A
1 AA-ATAAATA
1660038 TAAATAAATA
1 -AAATAAATA
1660048 AAAGTAAATA
1 AAA-TAAATA
*
1660058 TAA-AAATA
1 AAATAAATA
1660066 TAAATAAAT-
1 -AAATAAATA
1660075 AAATAAATA
1 AAATAAATA
1660084 ATAATAAA
1 A-AATAAA
1660092 CTCGAATGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
8 15 0.28
9 17 0.32
10 21 0.40
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:1660071 original size:32 final size:32
Alignment explanation
Indices: 1660020--1660081 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
1660010 TTAACATTTA
1660020 TAAATAAAAAATATAAAATAAATAAATAAAAG
1 TAAATAAAAAATATAAAATAAATAAATAAAAG
1660052 TAAATATAAAAATAT-AAATAAATAAATAAA
1 TAAATA-AAAAATATAAAATAAATAAATAAA
1660082 TAATAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (32 bp):
TAAATAAAAAATATAAAATAAATAAATAAAAG
Found at i:1660089 original size:18 final size:18
Alignment explanation
Indices: 1660019--1660091 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
1660009 TTTAACATTT
*
1660019 ATAAATAAAAAAT-ATAAA
1 ATAAATAAATAATAAT-AA
1660037 ATAAATAAATAA-AAGTAA
1 ATAAATAAATAATAA-TAA
1660055 ATATAA-AAAT-ATAAATAA
1 ATA-AATAAATAAT-AATAA
1660073 ATAAATAAATAATAATAA
1 ATAAATAAATAATAATAA
1660091 A
1 A
1660092 CTCGAATGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
17 3 0.06
18 37 0.79
19 7 0.15
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (18 bp):
ATAAATAAATAATAATAA
Found at i:1660231 original size:14 final size:14
Alignment explanation
Indices: 1660191--1660236 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1660181 TTTACGTAAT
*
1660191 TTTCAATTCATGCAA
1 TTTCATTTCATGC-A
1660206 TGTTCATTTCATGCA
1 T-TTCATTTCATGCA
*
1660221 TTTCTTTTCATGCA
1 TTTCATTTCATGCA
1660235 TT
1 TT
1660237 GCATGCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 14 0.50
15 3 0.11
16 11 0.39
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.50
Consensus pattern (14 bp):
TTTCATTTCATGCA
Found at i:1660241 original size:23 final size:23
Alignment explanation
Indices: 1660210--1660258 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1660200 ATGCAATGTT
* * *
1660210 CATTTCATGCATTTCTTTTCATG
1 CATTGCATGCATTACATTTCATG
1660233 CATTGCATGCATTACATTTCATG
1 CATTGCATGCATTACATTTCATG
1660256 CAT
1 CAT
1660259 ACTTTCACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (23 bp):
CATTGCATGCATTACATTTCATG
Found at i:1660775 original size:36 final size:36
Alignment explanation
Indices: 1660728--1660798 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1660718 AAGCAAGCGA
*
1660728 CAACATCGAGCACCAACAGCAACAACACAGCAGCAG
1 CAACATCGAGCACCAACAGCAACAACACAACAGCAG
*
1660764 CAACATCGAGCACCAACAGCAACATCACAACAGCA
1 CAACATCGAGCACCAACAGCAACAACACAACAGCA
1660799 ACAATGACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.45, C:0.37, G:0.14, T:0.04
Consensus pattern (36 bp):
CAACATCGAGCACCAACAGCAACAACACAACAGCAG
Found at i:1660785 original size:19 final size:19
Alignment explanation
Indices: 1660728--1660789 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
1660718 AAGCAAGCGA
1660728 CAACATCGAGCACCAACAG
1 CAACATCGAGCACCAACAG
* * *
1660747 CAACAAC-A-CAGCAGCAG
1 CAACATCGAGCACCAACAG
1660764 CAACATCGAGCACCAACAG
1 CAACATCGAGCACCAACAG
1660783 CAACATC
1 CAACATC
1660790 ACAACAGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 13 0.37
18 2 0.06
19 20 0.57
ACGTcount: A:0.44, C:0.37, G:0.15, T:0.05
Consensus pattern (19 bp):
CAACATCGAGCACCAACAG
Found at i:1661535 original size:9 final size:9
Alignment explanation
Indices: 1661521--1661558 Score: 58
Period size: 9 Copynumber: 4.0 Consensus size: 9
1661511 CTTTGCTCGA
1661521 TTGGATGTT
1 TTGGATGTT
1661530 TTGGATGTT
1 TTGGATGTT
1661539 TTGGATGTT
1 TTGGATGTT
1661548 CTTGGTATGTT
1 -TTGG-ATGTT
1661559 GTCAAGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.67
10 4 0.15
11 5 0.19
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.55
Consensus pattern (9 bp):
TTGGATGTT
Found at i:1664449 original size:32 final size:33
Alignment explanation
Indices: 1664408--1664475 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1664398 CCTTAACTAT
* * *
1664408 TTGTATCGATACA-CACAATATTTATCGATACA
1 TTGTATCGATACATCACAAAATGTACCGATACA
*
1664440 TTGTATCGATACATCCCAAAATGTACCGATACA
1 TTGTATCGATACATCACAAAATGTACCGATACA
1664473 TTG
1 TTG
1664476 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTACCGATACA
Done.