Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold55
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: 4293517
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.26
Warning! 910309 characters in sequence are not A, C, G, or T
File 21 of 21
Found at i:4253642 original size:19 final size:20
Alignment explanation
Indices: 4253602--4253673 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
4253592 ACACCCAAAT
*
4253602 GTATCGATACATATTGCTTA
1 GTATCGATACATACTGCTTA
*
4253622 GTATCGATACATGCT-CTTA
1 GTATCGATACATACTGCTTA
**
4253641 GTATCGATACATACTTAATT-
1 GTATCGATACATAC-TGCTTA
4253661 GTATCGATACATA
1 GTATCGATACATA
4253674 AAACTCGCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.37
20 27 0.59
21 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATCGATACATACTGCTTA
Found at i:4253719 original size:13 final size:13
Alignment explanation
Indices: 4253701--4253725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4253691 AACTCACTAA
4253701 ATATCGATACATT
1 ATATCGATACATT
4253714 ATATCGATACAT
1 ATATCGATACAT
4253726 ACTTGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
ATATCGATACATT
Found at i:4254411 original size:20 final size:20
Alignment explanation
Indices: 4254386--4254459 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
4254376 ACCCTTAAAA
4254386 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4254406 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4254427 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4254447 GTATCGATACATG
1 GTATCGATACATG
4254460 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4254430 original size:21 final size:21
Alignment explanation
Indices: 4254404--4254479 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4254394 ACATGTTGCA
4254404 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4254425 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
4254445 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
4254466 ATGTATCGATACAT
1 ATGTATCGATACAT
4254480 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4254436 original size:41 final size:41
Alignment explanation
Indices: 4254386--4254479 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
4254376 ACCCTTAAAA
4254386 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
4254427 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
4254468 GTATCGATACAT
1 GTATCGATACAT
4254480 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:4254536 original size:13 final size:13
Alignment explanation
Indices: 4254518--4254543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4254508 TACAGCAAGT
4254518 ATGTATCGATACA
1 ATGTATCGATACA
4254531 ATGTATCGATACA
1 ATGTATCGATACA
4254544 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:4255064 original size:34 final size:35
Alignment explanation
Indices: 4255001--4255067 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
4254991 CTAAGTGATT
4255001 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
4255037 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
4255068 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:4258167 original size:13 final size:13
Alignment explanation
Indices: 4258149--4258173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4258139 TTTTCCAGAT
4258149 TGTATCGATACAA
1 TGTATCGATACAA
4258162 TGTATCGATACA
1 TGTATCGATACA
4258174 TTGCTTCAGT
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:4259355 original size:23 final size:23
Alignment explanation
Indices: 4259325--4259371 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4259315 GTGCAAATAA
4259325 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
4259348 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
4259371 A
1 A
4259372 AGGGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTTGATATGAATTACTTGATT
Found at i:4260016 original size:20 final size:20
Alignment explanation
Indices: 4259991--4260064 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
4259981 ACCCTTAAAA
4259991 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4260011 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4260032 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4260052 GTATCGATACATG
1 GTATCGATACATG
4260065 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4260035 original size:21 final size:21
Alignment explanation
Indices: 4260009--4260084 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4259999 ACATGTTGCA
4260009 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4260030 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
4260050 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
4260071 ATGTATCGATACAT
1 ATGTATCGATACAT
4260085 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4260041 original size:41 final size:41
Alignment explanation
Indices: 4259991--4260084 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
4259981 ACCCTTAAAA
4259991 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
4260032 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
4260073 GTATCGATACAT
1 GTATCGATACAT
4260085 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:4260141 original size:13 final size:13
Alignment explanation
Indices: 4260123--4260148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4260113 TACAGCAAGT
4260123 ATGTATCGATACA
1 ATGTATCGATACA
4260136 ATGTATCGATACA
1 ATGTATCGATACA
4260149 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:4260669 original size:34 final size:35
Alignment explanation
Indices: 4260606--4260672 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
4260596 CTAAGTGATT
4260606 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
4260642 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
4260673 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:4266306 original size:20 final size:20
Alignment explanation
Indices: 4266280--4266334 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
4266270 AAAAGGACAG
*
4266280 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
4266300 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
4266320 AATGCATCGATACAT
1 AATGTATCGATACAT
4266335 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:4267229 original size:31 final size:32
Alignment explanation
Indices: 4267184--4267267 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
4267174 AAAGAATGTC
* *
4267184 GCCACCAACTTGTGTGGGCTTTGGAAG-GGTT
1 GCCACCGACCTGTGTGGGCTTTGGAAGAGGTT
* *
4267215 GCCACCGACCTGTGTGGGCATTAGAAGAGGTT
1 GCCACCGACCTGTGTGGGCTTTGGAAGAGGTT
*
4267247 ACCACCGA-CT-TGTGGGCTTTG
1 GCCACCGACCTGTGTGGGCTTTG
4267268 AAAAGCTGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 9 0.20
31 25 0.56
32 11 0.24
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (32 bp):
GCCACCGACCTGTGTGGGCTTTGGAAGAGGTT
Found at i:4267284 original size:28 final size:28
Alignment explanation
Indices: 4267254--4267824 Score: 595
Period size: 28 Copynumber: 20.4 Consensus size: 28
4267244 GTTACCACCG
* *
4267254 ACTTGTGGGCTTTGAAAAGCTGCCACTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
*
4267282 ACTTATGGGCTTT-AAGAAGGTGCCACTA
1 ACTTGTGGGCTTTGAA-AAGGTGCCACTA
* * *
4267310 ACTTGTGGGCCTTGAAAAGGTGCCATTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
* *
4267338 ACTTGTAGGCTTTGAAAAGATGCCACTA
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
* *
4267366 ACTTGTGGGCTTTG-AAAGGATGCCATTG
1 ACTTGTGGGCTTTGAAAAGG-TGCCACTA
4267394 ACTTGTGGGCTTT-AAGAAGGTGCCACTA
1 ACTTGTGGGCTTTGAA-AAGGTGCCACTA
* *
4267422 ACTTGTGGGCTTTGAAAAGGTGCCCCTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
*
4267450 ACTTGTGAGCTTTGAAAAGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
*
4267478 ACTTGTGGGCTTTGAAAAGATGCCACTA
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
** *
4267506 ACTTGTGGGCTTTGAAAATATGCCACTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
* * *
4267534 ATTTGTGAGATTTG-AAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAAGG-TGCCACTA
* *
4267562 ACTTATGGGCTTT-AAGAAGGTGCCATTA
1 ACTTGTGGGCTTTGAA-AAGGTGCCACTA
* * *
4267590 ACTTATGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
**
4267618 ACTCATGGGCTTTG-AAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAAGG-TGCCACTA
4267646 ACTTGTGGGCTTT-AAAAGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
* *
4267673 GCTTGTGGGCTTTG-AAAGGATGCCA-TCG
1 ACTTGTGGGCTTTGAAAAGG-TGCCACT-A
* * *
4267701 ACTTATGGG-TTTTAAGTAGGTGCCACTA
1 ACTTGTGGGCTTTGAA-AAGGTGCCACTA
* * * *
4267729 ACTTGTAGGCTTTAAAAAGGCGCCACTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
** * *
4267757 ACCCGTGGGCTTTGAAAAGGTGCCATTG
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
* * *
4267785 AGTTGTGGGCTTTGGAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGGTGCCACTA
*
4267813 ACTTGTAGGCTT
1 ACTTGTGGGCTT
4267825 AAAAAGATGC
Statistics
Matches: 450, Mismatches: 74, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
27 42 0.09
28 385 0.86
29 23 0.05
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAAGGTGCCACTA
Found at i:4267349 original size:84 final size:82
Alignment explanation
Indices: 4267248--4267945 Score: 640
Period size: 84 Copynumber: 8.4 Consensus size: 82
4267238 GAAGAGGTTA
* * *
4267248 CCACCGACTTGTGGGCTTTGAAAAGCTGCCACTGACTTATGGGCTTTAAGAAGGTGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAA-AAGGTGCCACTAACT
*
4267313 TGTGGGCCTTGAAAAGGTG
65 TGTGGG-CTTTAAAAGGTG
* * * * * *
4267332 CCATTGACTTGTAGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAAGG-TGCCACTAACT
4267397 TGTGGGCTTTAAGAAGGTG
65 TGTGGGCTTTAA-AAGGTG
* * * *
4267416 CCACTAACTTGTGGGCTTTGAAAAGGTGCCCCTGACTTGTGAGCTTTGAAAAGGTGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT-AAAAGGTGCCACTAACT
*
4267481 TGTGGGCTTTGAAAAGATG
65 TGTGGGCTTT-AAAAGGTG
* * * * * *
4267500 CCACTAACTTGTGGGCTTTGAAAATATGCCACTGATTTGTGAGATTTGAAAGGATGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAAGG-TGCCACTAACT
*
4267565 TATGGGCTTTAAGAAGGTG
65 TGTGGGCTTTAA-AAGGTG
* * * * * ** *
4267584 CCATTAACTTATGGGCTTTGAAAGGGTGCCACTGACTCATGGGCTTTGAAAGGATGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAAGG-TGCCACTAACT
4267649 TGTGGGCTTTAAAAGGTG
65 TGTGGGCTTTAAAAGGTG
* * * *
4267667 CCACT-AGCTTGTGGGCTTTGAAAGGATGCCA-TCGACTTATGGGTTTTAAGTAGGTGCCACTAA
1 CCACTGA-CTTGTGGGCTTTGAAAAGATGCCACT-GACTTGTGGGCTTTAA-AAGGTGCCACTAA
* *
4267730 CTTGTAGGCTTTAAAAAGGCG
63 CTTGTGGGCTTT-AAAAGGTG
** * * * * *
4267751 CCACTGACCCGTGGGCTTTGAAAAGGTGCCATTGAGTTGTGGGCTTTGGAAGGGTGCCACTAACT
1 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT-AAAAGGTGCCACTAACT
* * *
4267816 TGTAGGCTTAAAAAGATG
65 TGTGGGCTTTAAAAGGTG
* * * * * * *
4267834 CCA-TGGAGTTGTAGAC-TTGAAAGGATGCCAC-GTAGTTGTGGAC-TTAAAAGGATGCCACGAA
1 CCACT-GACTTGTGGGCTTTGAAAAGATGCCACTG-ACTTGTGGGCTTTAAAAGG-TGCCACTAA
* *
4267895 GTTGTGGAC-TTAAAAGGATG
63 CTTGTGGGCTTTAAAAGG-TG
* * *
4267915 CCACGGAGTTGTGGAC-TT-AAAAGGATGCCAC
1 CCACTGACTTGTGGGCTTTGAAAA-GATGCCAC
4267946 GAAGTTGTGG
Statistics
Matches: 513, Mismatches: 82, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
80 13 0.03
81 42 0.08
82 24 0.05
83 96 0.19
84 328 0.64
85 10 0.02
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (82 bp):
CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGTGCCACTAACTT
GTGGGCTTTAAAAGGTG
Found at i:4267677 original size:27 final size:27
Alignment explanation
Indices: 4267255--4268214 Score: 428
Period size: 28 Copynumber: 34.9 Consensus size: 27
4267245 TTACCACCGA
*
4267255 CTTGTGGGCTTTGAAAAGCTGCCACT-G
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
* *
4267282 ACTTATGGGCTTTAAGAAGGTGCCACTAA
1 -CTTGTGGGCTTTAA-AAGGTGCCACTAG
* *
4267311 CTTGTGGGCCTTGAAAAGGTGCCA-TTG
1 CTTGTGGG-CTTTAAAAGGTGCCACTAG
* * *
4267338 ACTTGTAGGCTTTGAAAAGATGCCACTAA
1 -CTTGTGGGCTTT-AAAAGGTGCCACTAG
* *
4267367 CTTGTGGGCTTTGAAAGGATGCCA-TTG
1 CTTGTGGGCTTTAAAAGG-TGCCACTAG
*
4267394 ACTTGTGGGCTTTAAGAAGGTGCCACTAA
1 -CTTGTGGGCTTTAA-AAGGTGCCACTAG
*
4267423 CTTGTGGGCTTTGAAAAGGTGCCCCT-G
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
* *
4267450 ACTTGTGAGCTTTGAAAAGGTGCCACTAA
1 -CTTGTGGGCTTT-AAAAGGTGCCACTAG
* *
4267479 CTTGTGGGCTTTGAAAAGATGCCACTAA
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
**
4267507 CTTGTGGGCTTTGAAAATATGCCACT-G
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
* * * * *
4267534 ATTTGTGAGATTTGAAAGGATGCCACTAA
1 -CTTGTGGGCTTTAAAAGG-TGCCACTAG
* * *
4267563 CTTATGGGCTTTAAGAAGGTGCCATTAA
1 CTTGTGGGCTTTAA-AAGGTGCCACTAG
* *
4267591 CTTATGGGCTTTGAAAGGGTGCCACT-G
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
** * *
4267618 ACTCATGGGCTTTGAAAGGATGCCACTAA
1 -CTTGTGGGCTTTAAAAGG-TGCCACTAG
4267647 CTTGTGGGCTTTAAAAGGTGCCACTAG
1 CTTGTGGGCTTTAAAAGGTGCCACTAG
* *
4267674 CTTGTGGGCTTTGAAAGGATGCCA-TCG
1 CTTGTGGGCTTTAAAAGG-TGCCACTAG
* * * *
4267701 ACTTATGGGTTTTAAGTAGGTGCCACTAA
1 -CTTGTGGGCTTTAA-AAGGTGCCACTAG
* *
4267730 CTTGTAGGCTTTAAAAAGGCGCCACT-G
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
** *
4267757 ACCCGTGGGCTTTGAAAAGGTGCCATTGAG
1 -CTTGTGGGCTTT-AAAAGGTGCCACT-AG
* * *
4267787 -TTGTGGGCTTTGGAAGGGTGCCACTAA
1 CTTGTGGGCTTT-AAAAGGTGCCACTAG
* * *
4267814 CTTGTAGGCTTAAAAAGATGCCA-TGGAG
1 CTTGTGGGCTTTAAAAGGTGCCACT--AG
* * *
4267842 -TTGTAGAC-TTGAAAGGATGCCACGTAG
1 CTTGTGGGCTTTAAAAGG-TGCCAC-TAG
* *
4267869 -TTGTGGAC-TTAAAAGGATGCCACGAAG
1 CTTGTGGGCTTTAAAAGG-TGCCAC-TAG
* *
4267896 -TTGTGGAC-TTAAAAGGATGCCACGGAG
1 CTTGTGGGCTTTAAAAGG-TGCCAC-TAG
* *
4267923 -TTGTGGAC-TTAAAAGGATGCCACGAAG
1 CTTGTGGGCTTTAAAAGG-TGCCAC-TAG
* *
4267950 -TTGTGGAC-TTAAAAGGGTACCAC-AG
1 CTTGTGGGCTTTAAAA-GGTGCCACTAG
* * *
4267975 AGTTATGGAC-TTAAAAGGATGCCAC-AG
1 -CTTGTGGGCTTTAAAAGG-TGCCACTAG
* * * *
4268002 AGTTATGGAC-TTAAAAGGTGCCACGGAG
1 -CTTGTGGGCTTTAAAAGGTGCCAC-TAG
* *
4268030 -TTGTGGAC-TTAAAAGGGTGCCACGGAG
1 CTTGTGGGCTTTAAAA-GGTGCCAC-TAG
* *
4268057 -TTGTGGAC-TTAAAAGGGTGCCACGATG
1 CTTGTGGGCTTTAAAA-GGTGCCACTA-G
* *
4268084 -TTGTGGAC-TTAAAAGGGTGCCACGATG
1 CTTGTGGGCTTTAAAA-GGTGCCACTA-G
* *
4268111 -TTGTGGAC-TTAAAAGGGTGCCACGATG
1 CTTGTGGGCTTTAAAA-GGTGCCACTA-G
* * *
4268138 -TTGCGGACTTAAAAAGGTGCCA-TAG
1 CTTGTGGGCTTTAAAAGGTGCCACTAG
* * *
4268163 AGTTGTGGAC-TTAAAAGGGTGCCACGGAG
1 -CTTGTGGGCTTTAAAA-GGTGCCAC-TAG
*
4268192 -TTGTGGAC-TTAAAAGGATGCCAC
1 CTTGTGGGCTTTAAAAGG-TGCCAC
4268215 GAAGTTGTGG
Statistics
Matches: 778, Mismatches: 104, Indels: 101
0.79 0.11 0.10
Matches are distributed among these distances:
25 3 0.00
26 37 0.05
27 339 0.44
28 370 0.48
29 28 0.04
30 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (27 bp):
CTTGTGGGCTTTAAAAGGTGCCACTAG
Found at i:4268215 original size:27 final size:27
Alignment explanation
Indices: 4267800--4268740 Score: 1105
Period size: 27 Copynumber: 34.9 Consensus size: 27
4267790 TGGGCTTTGG
** *
4267800 AAGGGTGCCACTAACTTGTAGG-CTTAA
1 AAGGGTGCCACGGAGTTGT-GGACTTAA
* * * * *
4267827 AAAGATGCCATGGAGTTGTAGACTTGA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4267854 AAGGATGCCACGTAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4267881 AAGGATGCCACGAAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
*
4267908 AAGGATGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4267935 AAGGATGCCACGAAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4267962 AAGGGTACCACAGAGTTATGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4267989 AAGGATGCCACAGAGTTATGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
4268016 AA-GGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
4268042 AAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
4268069 AAGGGTGCCAC-GATGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
4268096 AAGGGTGCCAC-GATGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
*
4268123 AAGGGTGCCAC-GATGTTGCGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
* **
4268150 AAAGGTGCCATAGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
4268177 AAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4268204 AAGGATGCCACGAAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4268231 AAGGCTACCAC-GATGTTGTAGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
*
4268258 AAGGATGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* **
4268285 TAGGGTGCCACAAAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4268312 AAAGATGCCA-TGATGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
4268339 AAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * * *
4268366 AAAGGTGCCACAGAGTTATGGACGTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4268393 AACGATGCCA-TGATGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
*
4268420 AAGGGTGCCACAGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
4268447 AAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
*
4268474 AACGGTGCCAC-GATGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
* *
4268501 AAGGGTACCACAGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4268528 AAGGATGCCACAGAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * * **
4268555 AACGATGCCACGTAGTTGTAAACTT-A
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * * *
4268581 AACGATGCCATGTAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* *
4268608 AAGGGTGCCACAGAGTTGTGAACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
4268635 AAGGATGCCATGGAGTTGTAGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
**
4268662 AAGGGTGCCACAAAGTTGTGGACTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAA
*
4268689 AAGGGTGCCAC-AAGGTTGTGGACTTAA
1 AAGGGTGCCACGGA-GTTGTGGACTTAA
4268716 AAGGGTGCCAC-GATGTTGTGGACTT
1 AAGGGTGCCACGGA-GTTGTGGACTT
4268741 TAACAGAAAA
Statistics
Matches: 802, Mismatches: 98, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
26 57 0.07
27 735 0.92
28 10 0.01
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
AAGGGTGCCACGGAGTTGTGGACTTAA
Found at i:4268759 original size:34 final size:35
Alignment explanation
Indices: 4268714--4268784 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
4268704 TTGTGGACTT
*
4268714 AAAAGGGTGCCAC-GATGTTGTGGACTTT-AACAGA
1 AAAAGGGTGCCACAGA-GTTGTGGACTTTGAAAAGA
*
4268748 AAAAGGTTGCCACAGAGTTGTGGACTTTGAAAAGA
1 AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGA
4268783 AA
1 AA
4268785 TGTCACTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 24 0.73
35 9 0.27
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.23
Consensus pattern (35 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGA
Found at i:4272453 original size:52 final size:51
Alignment explanation
Indices: 4272368--4272491 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
4272358 ATATGAAAAG
* *
4272368 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
4272419 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
4272471 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
4272492 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:4272504 original size:51 final size:51
Alignment explanation
Indices: 4272368--4272511 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
4272358 ATATGAAAAG
*
4272368 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
4272420 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
4272471 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
4272512 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:4272518 original size:13 final size:13
Alignment explanation
Indices: 4272500--4272524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4272490 CAAAGATCAG
4272500 TGTATCGATACAA
1 TGTATCGATACAA
4272513 TGTATCGATACA
1 TGTATCGATACA
4272525 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4272602 original size:33 final size:33
Alignment explanation
Indices: 4272565--4272631 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4272555 AGTAGCTTAA
4272565 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
4272598 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
4272631 A
1 A
4272632 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:4272605 original size:13 final size:13
Alignment explanation
Indices: 4272587--4272611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4272577 CAAAAAAATA
4272587 TGTATCGATACAT
1 TGTATCGATACAT
4272600 TGTATCGATACA
1 TGTATCGATACA
4272612 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4273455 original size:49 final size:49
Alignment explanation
Indices: 4273338--4273894 Score: 787
Period size: 49 Copynumber: 11.7 Consensus size: 49
4273328 AAAATGATGT
* * *
4273338 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
4273390 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
4273439 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
4273488 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
4273530 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
4273579 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
4273628 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
4273670 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
4273719 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
4273768 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
4273810 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
4273859 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
4273895 GAAGGGTTGC
Statistics
Matches: 458, Mismatches: 26, Indels: 45
0.87 0.05 0.09
Matches are distributed among these distances:
42 93 0.20
43 21 0.05
45 9 0.02
46 6 0.01
48 21 0.05
49 270 0.59
51 1 0.00
52 37 0.08
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:4273589 original size:91 final size:94
Alignment explanation
Indices: 4273338--4273894 Score: 771
Period size: 91 Copynumber: 5.9 Consensus size: 94
4273328 AAAATGATGT
* * *
4273338 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
4273403 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
63 CAAGGCCAGCTATATTGGACTT-AA-AT--AGGTGC
* * *
4273439 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
4273504 GGCCAGCTATA-TGGACTT-AAT-GGTGC
66 GGCCAGCTATATTGGACTTAAATAGGTGC
*
4273530 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
4273595 GGCCAGCTATATTGGACTTAAAGATAAAGGTGC
66 GGCCAGCTATATTGGACTT-AA-AT--AGGTGC
* *
4273628 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTT--A-AT---GGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
4273686 GGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAAA--T--AGGTGC
* *
4273719 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
4273784 GGCCAGCTATA-TGGACTT-AAT-GGTGC
66 GGCCAGCTATATTGGACTTAAATAGGTGC
*
4273810 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
4273875 GGCCAGCTATATTGGGCTTA
66 GGCCAGCTATATTGGACTTA
4273895 GAAGGGTTGC
Statistics
Matches: 421, Mismatches: 17, Indels: 44
0.87 0.04 0.09
Matches are distributed among these distances:
89 1 0.00
90 2 0.00
91 229 0.54
92 20 0.05
94 6 0.01
95 6 0.01
96 2 0.00
97 21 0.05
98 95 0.23
101 39 0.09
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (94 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAATAGGTGC
Found at i:4273637 original size:140 final size:140
Alignment explanation
Indices: 4273385--4273894 Score: 957
Period size: 140 Copynumber: 3.6 Consensus size: 140
4273375 AGATGGAAAA
* * * *
4273385 GGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
* *
4273450 GTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
66 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
4273515 TGGACTTAAT
131 TGGACTTAAT
4273525 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
4273590 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
66 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
4273655 TGGACTTAAT
131 TGGACTTAAT
4273665 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
4273730 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
66 TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
4273795 TGGACTTAAT
131 TGGACTTAAT
4273805 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
1 GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
*
4273870 TTCAAGGCCAGCTATATTGGGCTTA
66 TTCAAGGCCAGCTATATTGGACTTA
4273895 GAAGGGTTGC
Statistics
Matches: 363, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 363 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (140 bp):
GGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGA
TTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
TGGACTTAAT
Found at i:4273998 original size:28 final size:28
Alignment explanation
Indices: 4273899--4274037 Score: 138
Period size: 28 Copynumber: 4.8 Consensus size: 28
4273889 GGCTTAGAAG
* *
4273899 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 GGTTGCCACTGAC-T-TGTGGGCTTT--TAAA
* * *
4273931 GGGTGCCACTGATTTGTGGGC-TTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTAAA
*
4273958 GATTGCCACTGACTTGTGGGCTTTTAAA
1 GGTTGCCACTGACTTGTGGGCTTTTAAA
4273986 GGTTGCCACTGACTTGTGGGCTTTTGAACA
1 GGTTGCCACTGACTTGTGGGCTTTT-AA-A
*
4274016 -ATATGCCACTGACTTGTGGGCT
1 GGT-TGCCACTGACTTGTGGGCT
4274038 GAAAAGAGTG
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
27 20 0.22
28 29 0.32
29 5 0.05
30 27 0.29
31 1 0.01
32 10 0.11
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (28 bp):
GGTTGCCACTGACTTGTGGGCTTTTAAA
Found at i:4274025 original size:30 final size:29
Alignment explanation
Indices: 4273915--4274250 Score: 217
Period size: 30 Copynumber: 11.5 Consensus size: 29
4273905 CACCGACTTG
* * *
4273915 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
4273945 TGTGGGC-TTTG--AAGATTGCCACTGACT
1 TGTGGGCTTTTGAAAAGA-TGCCACTGACT
* *
4273972 TGTGGGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
4274000 TGTGGGCTTTTGAACAATATGCCACTGACT
1 TGTGGGCTTTTGAA-AAGATGCCACTGACT
* *
4274030 TGTGGGC---TGAAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGA-TGCCACT-GACT
* ** * *
4274057 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTG-AAAAGA-TGCCACTGACT
* * * *
4274092 TGTGGACTTTGGAAAAGATGCCGCCGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
** * *
4274121 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
* *
4274151 TGTGGGC-TTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* * *
4274178 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
*
4274208 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
*
4274237 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
4274251 GGGTGATGAA
Statistics
Matches: 243, Mismatches: 41, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
26 5 0.02
27 54 0.22
28 30 0.12
29 59 0.24
30 71 0.29
31 1 0.00
34 1 0.00
35 22 0.09
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGATGCCACTGACT
Found at i:4274123 original size:29 final size:29
Alignment explanation
Indices: 4274074--4274246 Score: 161
Period size: 29 Copynumber: 5.9 Consensus size: 29
4274064 TTACAAAAGA
* * *
4274074 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* * *
4274104 AAAAGATGCCGCCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
4274133 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
4274162 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
4274191 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
4274220 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
4274247 TGAAGGGTGA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.18
28 2 0.02
29 50 0.42
30 46 0.39
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:4274201 original size:57 final size:57
Alignment explanation
Indices: 4273915--4274220 Score: 192
Period size: 57 Copynumber: 5.2 Consensus size: 57
4273905 CACCGACTTG
* * * *
4273915 TGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTT-G--AAGATTGCCACTGACT
1 TGTGGGCTTT-G--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACTGACT
* * * *
4273972 TGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAACAATATGCCACTGACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACTGACT
*** * * * * * * *
4274030 TGTGGGCTGAAAAGAG-TGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTC----GAAAAA-AATGCCACTGACT
* * * * * *** *
4274092 TGTGGACTTTGGAAAAGATGCCGCCGACTTGTGGGC-TTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-G-AAGGTTGCCACTGACTTGTGGGCTTTC-GAAAAAAATGCCACTGACT
*
4274151 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACTGACT
4274208 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
4274221 AAAAATGCCA
Statistics
Matches: 188, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
55 24 0.13
56 2 0.01
57 73 0.39
58 27 0.14
59 19 0.10
60 5 0.03
61 5 0.03
62 16 0.09
63 3 0.02
64 14 0.07
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACTGACT
Found at i:4275693 original size:1 final size:1
Alignment explanation
Indices: 4275689--4275809 Score: 71
Period size: 1 Copynumber: 121.0 Consensus size: 1
4275679 CCGGACCCCC
* * * * * * * * *
4275689 TTTTTTTGTTTTTGTTTGTTTTTTTTTATTGTTTTTGTTTTTGTTTTTTTTTTCTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ***** ** **
4275754 TGTTTTTTTTTGGGGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4275810 GGAGGACGCC
Statistics
Matches: 92, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (1 bp):
T
Found at i:4275720 original size:23 final size:22
Alignment explanation
Indices: 4275689--4275763 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 22
4275679 CCGGACCCCC
4275689 TTTTTTTGTTTTTGTTTGTTTT
1 TTTTTTTGTTTTTGTTTGTTTT
4275711 TTTTTATTGTTTTTGTTT-TTGTT
1 TTTTT-TTGTTTTTGTTTGTT-TT
*
4275734 TTTTTTT-TCTTTTGTTTTTTTGT
1 TTTTTTTGT-TTTTGTTTGTTT-T
4275757 TTTTTTT
1 TTTTTTT
4275764 TGGGGGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.02
22 18 0.38
23 29 0.60
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.87
Consensus pattern (22 bp):
TTTTTTTGTTTTTGTTTGTTTT
Found at i:4275740 original size:10 final size:10
Alignment explanation
Indices: 4275689--4275809 Score: 90
Period size: 10 Copynumber: 12.4 Consensus size: 10
4275679 CCGGACCCCC
4275689 TTTTTTTGTT
1 TTTTTTTGTT
*
4275699 TTTGTTTGTT
1 TTTTTTTGTT
*
4275709 TTTTTTT-AT
1 TTTTTTTGTT
*
4275718 TGTTTTTGTT
1 TTTTTTTGTT
4275728 TTTGTTTT-TT
1 TTT-TTTTGTT
*
4275738 TTTTCTTT-TG
1 TTTT-TTTGTT
4275748 TTTTTTTGTT
1 TTTTTTTGTT
**
4275758 TTTTTTTGGG
1 TTTTTTTGTT
** **
4275768 GGTTTTTCAT
1 TTTTTTTGTT
*
4275778 TTTTTTCGTT
1 TTTTTTTGTT
4275788 TTTTTTT-TT
1 TTTTTTTGTT
4275797 TTTTTTT-TT
1 TTTTTTTGTT
4275806 TTTT
1 TTTT
4275810 GGAGGACGCC
Statistics
Matches: 86, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
9 26 0.30
10 56 0.65
11 4 0.05
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:4275758 original size:59 final size:57
Alignment explanation
Indices: 4275689--4275809 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 57
4275679 CCGGACCCCC
*** *
4275689 TTTTTTTGTTTTTGTTT-GTTTTTTTTTATTGTTTTT-GTTTTTGTTTTTTTTTTCTTTT
1 TTTTTTTGTTTTTGTTTGGGGGTTTTTCATT-TTTTTCGTTTTT-TTTTTTTTTT-TTTT
*
4275747 GTTTTTTTGTTTTTTTTTGGGGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTT
1 -TTTTTTTGTTTTTGTTTGGGGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTT
4275805 TTTTT
1 TTTTT
4275810 GGAGGACGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
57 5 0.09
58 4 0.07
59 31 0.56
60 15 0.27
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (57 bp):
TTTTTTTGTTTTTGTTTGGGGGTTTTTCATTTTTTTCGTTTTTTTTTTTTTTTTTTT
Found at i:4275764 original size:23 final size:23
Alignment explanation
Indices: 4275692--4275764 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 23
4275682 GACCCCCTTT
4275692 TTTTGTTTTTGTTTGTTTTTTTTTA
1 TTTTG-TTTT-TTTGTTTTTTTTTA
* *
4275717 TTGTTTTTGTTTTTGTTTTTTTTTTC
1 TT-TTGTT-TTTTTG-TTTTTTTTTA
4275743 TTTTGTTTTTTTGTTTTTTTTT
1 TTTTGTTTTTTTGTTTTTTTTT
4275765 GGGGGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 9 0.21
24 6 0.14
25 12 0.29
26 15 0.36
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (23 bp):
TTTTGTTTTTTTGTTTTTTTTTA
Found at i:4285519 original size:10 final size:10
Alignment explanation
Indices: 4285504--4285530 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4285494 ATGTATCAAG
4285504 CAAAAACAAA
1 CAAAAACAAA
4285514 CAAAAACAAA
1 CAAAAACAAA
4285524 CAAAAAC
1 CAAAAAC
4285531 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:4289752 original size:51 final size:51
Alignment explanation
Indices: 4289646--4289766 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
4289636 ATATGAAAAG
* * *
4289646 TTGCTTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATAAATTAATAATGTATCGATACATCTGGGCAAAT
*
4289697 TTGCCTGCATGTATCGATAAATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATAAA-TTAATAATGTATCGATACATCTGGGCAAAT
4289748 TTGCCTGCATGTATCGATA
1 TTGCCTGCATGTATCGATA
4289767 CAAAGATCAG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
51 38 0.58
52 27 0.42
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATAAATTAATAATGTATCGATACATCTGGGCAAAT
Found at i:4289781 original size:51 final size:50
Alignment explanation
Indices: 4289646--4289788 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 50
4289636 ATATGAAAAG
* *
4289646 TTGCTTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-AAATAGTGTATCGATACATCTGGGCAAAT
* *
4289697 TTGCCTGCATGTATCGATA-AATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACAA---AATAGTGTATCGATACATCTGGGCAAAT
4289748 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
4289789 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
50 3 0.04
51 50 0.62
52 27 0.34
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:4289795 original size:13 final size:13
Alignment explanation
Indices: 4289777--4289801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4289767 CAAAGATCAG
4289777 TGTATCGATACAA
1 TGTATCGATACAA
4289790 TGTATCGATACA
1 TGTATCGATACA
4289802 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4289880 original size:13 final size:13
Alignment explanation
Indices: 4289862--4289886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4289852 CAAAAAAATA
4289862 TGTATCGATACAT
1 TGTATCGATACAT
4289875 TGTATCGATACA
1 TGTATCGATACA
4289887 ACATTTTTAT
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
Done.