Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 25 of 25
Found at i:4028150 original size:3 final size:3
Alignment explanation
Indices: 4028142--4028180 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4028132 TCTTTGCTCG
4028142 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4028181 AATATTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4029687 original size:31 final size:30
Alignment explanation
Indices: 4029635--4029692 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4029625 TGTGCAAAAG
*
4029635 AAAAAAAAAATGAAAAGTGAAAGAAAATGA
1 AAAAAAAAAATGAAAAGTGAAAAAAAATGA
*
4029665 AAAAAAAAAATTGGCAAA-TGAAAAAAAA
1 AAAAAAAAAA-T-GAAAAGTGAAAAAAAA
4029693 AACCCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 10 0.42
32 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (30 bp):
AAAAAAAAAATGAAAAGTGAAAAAAAATGA
Found at i:4033330 original size:16 final size:17
Alignment explanation
Indices: 4033306--4033338 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4033296 TTGAAATTAC
4033306 TTAAATTAA-AAAAATA
1 TTAAATTAATAAAAATA
*
4033322 TTAATTTAATAAAAATA
1 TTAAATTAATAAAAATA
4033339 ATAACTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATTAATAAAAATA
Found at i:4035842 original size:2 final size:2
Alignment explanation
Indices: 4035835--4035872 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4035825 TTGGTGGATA
4035835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4035873 GAGATTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4036523 original size:2 final size:2
Alignment explanation
Indices: 4036518--4036557 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4036508 TTTCACACAC
4036518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4036558 TGGATGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4045839 original size:27 final size:28
Alignment explanation
Indices: 4045786--4045840 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
4045776 AATTTTAATC
* *
4045786 ATAAAAAATAAATAAAACTTATTTAAGA
1 ATAAAAAATAAATAAAACATATCTAAGA
* *
4045814 ATAAAAATTAAATAAAA-ATCTCTAAGA
1 ATAAAAAATAAATAAAACATATCTAAGA
4045841 TTCAGCTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (28 bp):
ATAAAAAATAAATAAAACATATCTAAGA
Found at i:4046170 original size:25 final size:27
Alignment explanation
Indices: 4046142--4046204 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
4046132 AGTCTTACAC
4046142 TATTTTTTTA-TGTGTGTGAAT-TTTT
1 TATTTTTTTAGTGTGTGTGAATCTTTT
* * *
4046167 TATTTATTTTAGTTTGTGTTACTCTTTT
1 TATTT-TTTTAGTGTGTGTGAATCTTTT
4046195 TAATTTTTTT
1 T-ATTTTTTT
4046205 TATTGTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 5 0.16
26 5 0.16
27 8 0.26
28 9 0.29
29 4 0.13
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.70
Consensus pattern (27 bp):
TATTTTTTTAGTGTGTGTGAATCTTTT
Found at i:4046210 original size:27 final size:25
Alignment explanation
Indices: 4046144--4046211 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 25
4046134 TCTTACACTA
4046144 TTTTTTTATGTGTGTGAATTTTTTAT
1 TTTTTTTAT-TGTGTGAATTTTTTAT
* * *
4046170 TTATTTTAGTTTGTGTTACTCTTTTTAAT
1 TTTTTTTA--TTGTGTGAAT-TTTTT-AT
4046199 TTTTTTTATTGTG
1 TTTTTTTATTGTG
4046212 ATTTTAGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
26 7 0.21
27 12 0.35
28 6 0.18
29 9 0.26
ACGTcount: A:0.15, C:0.03, G:0.13, T:0.69
Consensus pattern (25 bp):
TTTTTTTATTGTGTGAATTTTTTAT
Found at i:4046331 original size:25 final size:25
Alignment explanation
Indices: 4046297--4046353 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
4046287 AATCTAAGTA
4046297 TGACATTGTAATTATTTATTAATCT
1 TGACATTGTAATTATTTATTAATCT
*
4046322 TGACATTGTAATTATTTATTGATCT
1 TGACATTGTAATTATTTATTAATCT
4046347 TGACATT
1 TGACATT
4046354 TAGGAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (25 bp):
TGACATTGTAATTATTTATTAATCT
Found at i:4048756 original size:2 final size:2
Alignment explanation
Indices: 4048749--4048781 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4048739 ACCTAGTTAA
4048749 TC TC 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 TC TC T
4048782 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4055620 original size:110 final size:110
Alignment explanation
Indices: 4055427--4055646 Score: 422
Period size: 110 Copynumber: 2.0 Consensus size: 110
4055417 CATCCATTAG
4055427 AGCCAACTTTTGATAATGGAGTCCCACTAGAAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAA
1 AGCCAACTTTTGATAATGGAGTCCCACTAGAAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAA
*
4055492 TTTCAAGACAACCTACTTGCCTTTGCCTAATGGCATGTAGAGATC
66 TTTCAAGACAACCTACTTGCCTTTGCCCAATGGCATGTAGAGATC
*
4055537 AGCCAACTTTTGATAATGGAGTCCCACTAGAAATCCTTGCATTTTTCTTGCTTATTTTGTGTAAA
1 AGCCAACTTTTGATAATGGAGTCCCACTAGAAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAA
4055602 TTTCAAGACAACCTACTTGCCTTTGCCCAATGGCATGTAGAGATC
66 TTTCAAGACAACCTACTTGCCTTTGCCCAATGGCATGTAGAGATC
4055647 TTGTGCAATG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (110 bp):
AGCCAACTTTTGATAATGGAGTCCCACTAGAAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAA
TTTCAAGACAACCTACTTGCCTTTGCCCAATGGCATGTAGAGATC
Found at i:4057722 original size:27 final size:27
Alignment explanation
Indices: 4057651--4058443 Score: 773
Period size: 27 Copynumber: 28.9 Consensus size: 27
4057641 TGGCATTTCT
* * *
4057651 TTTTAAAGTTCACAACTTCGTTGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* * * *
4057679 TTCTAAAGTCCATAACTCCATGGCATCG
1 TT-TTAAGTCCACAACTCCGTGGCATCC
* **
4057707 TTTTAAGTCCGCAACTTTGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
4057734 TTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
4057761 TTTTAAAGTCCCCAACTCCATGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* *
4057789 TTTTAAGTCCACAACTCCATGGCATCT
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * *
4057816 TTTTAAGTCCAAAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * * * ** *
4057843 TTTCAAAGCCCACGATTTAGTGGCATTTCA
1 TTT-TAAGTCCACAACTCCGTGGCA--TCC
*
4057873 TTTTAAAGTCCACAACTCCGTGGCATCT
1 TTTT-AAGTCCACAACTCCGTGGCATCC
*
4057901 TTTTACGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
4057928 TTTTGAAGTCCATAACTCCGTGGCATCA
1 TTTT-AAGTCCACAACTCCGTGGCATCC
4057956 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
4057983 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
4058010 TTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
*** * *
4058037 TTTGTAAGTTTGCAACTCTGTGGCATCG
1 TTT-TAAGTCCACAACTCCGTGGCATCC
* *
4058065 TTTTAAGTCTACAACT-CGTGGCATCT
1 TTTTAAGTCCACAACTCCGTGGCATCC
* **
4058091 TTTTAAGTCCATAACTTTGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
** *
4058118 TTTTAAAGTCTGCAACTTCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* *
4058146 TTTTAAGTCTACAACTCCATGGCAT-C
1 TTTTAAGTCCACAACTCCGTGGCATCC
* ** *
4058172 TTTTAAGTCCATAACTCTATGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * *
4058199 TTTTAAAGTCCACCACTCTGTGGCATGC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
*
4058227 TTTTAAGTCCACAACTTCGT-GCATCCC
1 TTTTAAGTCCACAACTCCGTGGCAT-CC
* *
4058254 TTTTTAAGTCCACAACTCCGTGCCACCC
1 -TTTTAAGTCCACAACTCCGTGGCATCC
* ** *
4058282 CTTTAAGTCCACAACTTTGTGGCAGCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * *
4058309 TTTAAAGTCCACAACTCCATGGCAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-TCC
* * *
4058337 TTTTAAAGTCCATAGCTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* *
4058365 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
4058392 TTTTAGGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
*
4058419 TTTTAAAGTCTACAACTCCGTGGCA
1 TTTT-AAGTCCACAACTCCGTGGCA
4058444 AGTCTACAAC
Statistics
Matches: 634, Mismatches: 113, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
26 48 0.08
27 341 0.54
28 206 0.32
29 20 0.03
30 19 0.03
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCATCC
Found at i:4057733 original size:55 final size:54
Alignment explanation
Indices: 4057651--4058443 Score: 739
Period size: 55 Copynumber: 14.4 Consensus size: 54
4057641 TGGCATTTCT
* * * * * *
4057651 TTTTAAAGTTCACAACTTCGTTGCATCCTTCTAAAGTCCATAACTCCATGGCATCG
1 TTTT-AAGTCCACAACTCCGTGGCATCCTT-TTAAGTCCACAACTCCATGGCATCC
* ** *
4057707 TTTTAAGTCCGCAACTTTGTGGCATCCTTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* * *
4057761 TTTTAAAGTCCCCAACTCCATGGCATCCTTTTAAGTCCACAACTCCATGGCATCT
1 TTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* * * * * * ** *
4057816 TTTTAAGTCCAAAACTCTGTGGCACCCTTTCAAAGCCCACGA-TTTAGTGGCATTTCA
1 TTTTAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTCCA-TGGCA--TCC
* * *
4057873 TTTTAAAGTCCACAACTCCGTGGCATCTTTTTACGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* * *
4057928 TTTTGAAGTCCATAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
*
4057983 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
*** * * * * *
4058037 TTTGTAAGTTTGCAACTCTGTGGCATCGTTTTAAGTCTACAACT-CGTGGCATCT
1 TTT-TAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* ** ** * *
4058091 TTTTAAGTCCATAACTTTGTGGCATCCTTTTAAAGTCTGCAACTTCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCATGGCATCC
* * * * *
4058146 TTTTAAGTCTACAACTCCATGGCAT-CTTTTAAGTCCATAACTCTATGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* * * * *
4058199 TTTTAAAGTCCACCACTCTGTGGCATGCTTTTAAGTCCACAACTTCGT-GCATCCC
1 TTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCAT-CC
* * * *** *
4058254 TTTTTAAGTCCACAACTCCGTGCCACCCCTTTAAGTCCACAACTTTGTGGCAGCC
1 -TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
* * * * * * *
4058309 TTTAAAGTCCACAACTCCATGGCAGCCCTTTTAAAGTCCATAGCTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCA-TCCTTTT-AAGTCCACAACTCCATGGCATCC
* * * * *
4058365 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAGGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
*
4058419 TTTTAAAGTCTACAACTCCGTGGCA
1 TTTT-AAGTCCACAACTCCGTGGCA
4058444 AGTCTACAAC
Statistics
Matches: 613, Mismatches: 106, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
53 42 0.07
54 191 0.31
55 289 0.47
56 50 0.08
57 18 0.03
58 23 0.04
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (54 bp):
TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCATGGCATCC
Found at i:4057768 original size:82 final size:82
Alignment explanation
Indices: 4057651--4058443 Score: 810
Period size: 82 Copynumber: 9.6 Consensus size: 82
4057641 TGGCATTTCT
* * * * *
4057651 TTTTAAAGTTCACAACTTCGTTGCATCCTTCTAAAGTCCATAACTCCATGGCATCGTTTTAAGTC
1 TTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTC
* *
4057716 CGCAACTTTGTGGCATCC
65 CACAACTCTGTGGCATCC
* * **
4057734 TTTTAAGTCCATAACTCCATGGCATCCTTTTAAAGTCCCCAACTCCATGGCATCCTTTTAAGTCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTCC
** *
4057799 ACAACTCCATGGCATCT
66 ACAACTCTGTGGCATCC
* * * * * ** ** *
4057816 TTTTAAGTCCAAAACTCTGTGGCACCCTTTCAAAGCCCACGA-TTTAGTGGCATTTCATTTTAAA
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCA-TGGCA--TCCTTTT-AA
* *
4057880 GTCCACAACTCCGTGGCATCT
62 GTCCACAACTCTGTGGCATCC
* * * *
4057901 TTTTACGTCCACAACTCCGTGGCATCCTTTTGAAGTCCATAACTCCGTGGCATCATTTTAAGTCC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTCC
*
4057966 ACAACTCCGTGGCATCC
66 ACAACTCTGTGGCATCC
*
4057983 TTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCATAACTCCATGGCATCCTTTGTAAGTT
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTT-TAAGTC
** *
4058047 TGCAACTCTGTGGCATCG
65 CACAACTCTGTGGCATCC
* * ***
4058065 TTTTAAGTCTACAACT-CGTGGCAT-CTTTTTAAGTCCATAACTTTGTGGCATCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTT-AAGTC
**
4058128 TGCAACT-TCGTGGCATCC
65 CACAACTCT-GTGGCATCC
* * * *
4058146 TTTTAAGTCTACAACTCCATGGCAT-CTTTT-AAGTCCATAACTCTATGGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTT-AAGTC
* *
4058209 CACCACTCTGTGGCATGC
65 CACAACTCTGTGGCATCC
* * * * * * *
4058227 TTTTAAGTCCACAACTTCGT-GCATCCCTTTTTAAGTCCACAACTCCGTGCCACCCCTTTAAGTC
1 TTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTC
* *
4058291 CACAACTTTGTGGCAGCC
65 CACAACTCTGTGGCATCC
* * * * * *
4058309 TTTAAAGTCCACAACTCCATGGCAGCCCTTTTAAAGTCCATAGCTCCGTGGCACCCTTTTAAGTC
1 TTTTAAGTCCACAACTCCGTGGCA-TCCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTC
*
4058374 CACAACTCTGTGGCACCC
65 CACAACTCTGTGGCATCC
* * * * *
4058392 TTTTAGGTCCACAACTCCGTGGCACCCTTTTAAAGTCTACAACTCCGTGGCA
1 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCA
4058444 AGTCTACAAC
Statistics
Matches: 604, Mismatches: 90, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
80 11 0.02
81 151 0.25
82 268 0.44
83 107 0.18
84 6 0.01
85 60 0.10
86 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (82 bp):
TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCATGGCATCCTTTTAAGTCC
ACAACTCTGTGGCATCC
Found at i:4058448 original size:19 final size:19
Alignment explanation
Indices: 4058424--4058462 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4058414 CACCCTTTTA
4058424 AAGTCTACAACTCCGTGGC
1 AAGTCTACAACTCCGTGGC
*
4058443 AAGTCTACAACTCTGTGGC
1 AAGTCTACAACTCCGTGGC
4058462 A
1 A
4058463 CCTTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (19 bp):
AAGTCTACAACTCCGTGGC
Found at i:4058508 original size:28 final size:28
Alignment explanation
Indices: 4058474--4059378 Score: 550
Period size: 28 Copynumber: 31.2 Consensus size: 28
4058464 CTTTTTAAGT
*
4058474 CCACAAGTCAGTGGCATCATTTCAAAAC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * * *
4058502 GCACAAGTTAGTGGCATCAATTCAAAGA
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
4058530 CCACAGGTTAGTGGCA-CTATTTCAAAGC
1 CCACAAGTCAGTGGCATC-ATTTCAAAGC
* * * *
4058558 CCACAAGTTAGTAGCATCTTTTGAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * * *
4058586 CCACAAGTCAGTGGCACCTTTTTTAATGC
1 CCACAAGTCAGTGGCATC-ATTTCAAAGC
* * *
4058615 CCACAAGTTAGTGGCATCCTTTTTAAAGC
1 CCACAAGTCAGTGGCAT-CATTTCAAAGC
* * * *
4058644 CCACAAGTCAGTGACTTCCTTTTAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
4058672 CCACAAGTCAGTAGCAGCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
4058700 CCACAAGTCAGTAGCAGCCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCATTTCAAAGC
* * *
4058729 CTACAAGTTAGTGGCAACTCTTTTCAAAGTC
1 CCACAAGTCAGTGGC-A-TCATTTCAAAG-C
* * *
4058760 CACACAAGTCAATGGTAACTCTTTTCAAAGCC
1 C-CACAAGTCAGTGG-CA-TCATTTCAAAG-C
* * *
4058792 CACACAAATCAGTGGTA-CCTTTCCAAAGC
1 C-CACAAGTCAGTGGCATCATTT-CAAAGC
* * * *
4058821 CCATAAGTTAGTGGCAACCTTT-AAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * * * *
4058848 CCATAAATCAGTAGCACCCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCATTTCAAAGC
* * *
4058877 CCACTAGTCAGTGGAAACTCTTTTCAAAGTC
1 CCACAAGTCAGTGG-CA-TCATTTCAAAG-C
* * *
4058908 CACACAAGTCGGTGCCAGCTCTTTTCAAAGCC
1 C-CACAAGTCAGTGGCA--TCATTTCAAAG-C
* * *
4058940 CACACAAATCGGTGGCA-CCTTTCCAAAGC
1 C-CACAAGTCAGTGGCATCATTT-CAAAGC
*
4058969 CCACAAGTCAGTGGC-TCTTTTTCAAAGC
1 CCACAAGTCAGTGGCATC-ATTTCAAAGC
* * *
4058997 CCACAAGTTAGTGGCATACCCTTT-TAAGC
1 CCACAAGTCAGTGGCAT--CATTTCAAAGC
* *
4059026 CCACAAGTCAGTGGCATCCTTTTCAAAAC
1 CCACAAGTCAGTGGCAT-CATTTCAAAGC
* *
4059055 CTACAAGTCAGTGGCAACTCTTTTCAAAGTC
1 CCACAAGTCAGTGGC-A-TCATTTCAAAG-C
* *
4059086 CACACAAGTC-GATAGCAACTCTTTTCAAAGCC
1 C-CACAAGTCAG-TGGC-A-TCATTTCAAAG-C
* * *
4059118 CACACAAATCGGTGGCA-CTTTTCCAAAGC
1 C-CACAAGTCAGTGGCATCATTT-CAAAGC
* *
4059147 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
4059175 CCACAAGTCAGTGGCATACCTTTTCAAAGC
1 CCACAAGTCAGTGGCAT--CATTTCAAAGC
* * *
4059205 CCACAAGTCAGTGTCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
4059233 CCACAAGACAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
4059261 CCATAAGTGAGTGGCATCATTTTCAAAGC
1 CCACAAGTCAGTGGCATCA-TTTCAAAGC
* * ** * *
4059290 CCAAAAGTCAATGATACCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * * * *
4059318 TCACGAGACAGTGGCATCTTTTTAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
** *
4059346 CCATTAGTCAATGGCACTC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-TCATTTCAAAGC
4059374 CCACA
1 CCACA
4059379 CAAGTCGATA
Statistics
Matches: 717, Mismatches: 124, Indels: 72
0.79 0.14 0.08
Matches are distributed among these distances:
27 19 0.03
28 320 0.45
29 176 0.25
30 77 0.11
31 12 0.02
32 112 0.16
33 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCATTTCAAAGC
Found at i:4058869 original size:148 final size:147
Alignment explanation
Indices: 4058549--4059381 Score: 746
Period size: 148 Copynumber: 5.7 Consensus size: 147
4058539 AGTGGCACTA
* * * **
4058549 TTTCAAAGCCCACAAGTTAGTAGCA-TCTTTTGAAAGCCCACAAGTCAGTGGC-ACCTTTTTTAA
1 TTTCAAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAAA
* * * * * * *
4058612 -TGCCCACAAGTTAGTGGCATC-CTTTTTAAAG-CC-CACAAGTCAGTGACTTCCTTT-TAAAGC
66 GT-CCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAGTGGC-ACCTTTCCAAAGC
* *
4058672 CCACAAGTCAGTAGCAGCC
129 CCACAAGTCAGTGGCAACC
* * *
4058691 TTTCAAAGCCCACAAGTCAGTAGCAGCCTTTTCAAAGCCTACAAGTTAGTGGCAACTCTTTTCAA
1 TTTCAAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAAC-CTTTTCAA
* * *
4058756 AGTCCACACAAGTCAATGGTAACTCTTTTCAAAGCCCACACAAATCAGTGGTACCTTTCCAAAGC
65 AGTCC-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGC
* *
4058821 CCATAAGTTAGTGGCAACC
129 CCACAAGTCAGTGGCAACC
* * * *
4058840 TTT-AAAGCCCATAAATCAGTAGCACCCTTTTCAAAGCCCACTAGTCAGTGGAAACTCTTTTCAA
1 TTTCAAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAAC-CTTTTCAA
* * * *
4058904 AGTCCACACAAGTCGGTGCCAGCTCTTTTCAAAGCCCACACAAATCGGTGGCACCTTTCCAAAGC
65 AGTCC-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGC
* *
4058969 CCACAAGTCAGTGGC-TCTT
129 CCACAAGTCAGTGGCAAC-C
* * *
4058988 TTTCAAAGCCCACAAGTTAGTGGCATACCCTTTT--AAGCCCACAAGTCAGTGGCATCCTTTTCA
1 TTTCAAAGCCCACAAGTCAGTAGC--ACCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTTCA
* * * * * *
4059051 AA-ACCTACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTC-GATAGCAACTCTTTTCAA
64 AAGTCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAG-TGGC-AC-CTTTCCAA
* * *
4059114 AGCCCACACAAATCGGTGGC-ACT
126 AG-CC-CACAAGTCAGTGGCAACC
*
4059137 TTTCCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCATACCTTTTCA
1 TTT-CAAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTTTCA
* * * *
4059201 AAG-CCCACAAGTCAGTGTC-AC-CTTTTCAAAGCCCACA-AGA-CAGTGGCATCTTTTCAAAGC
64 AAGTCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGC
* * * *
4059261 CCATAAGTGAGTGGCATCAT
129 CCACAAGTCAGTGGCAAC-C
* * * * * * * *
4059281 TTTCAAAGCCCAAAAGTCAAT-G-ATACCTTTTCAAAGCTCACGAGACAGTGGC-ATCTTTTTAA
1 TTTCAAAGCCCACAAGTCAGTAGCA-CCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAA
** *
4059343 AG-CCCATTAGTCAATGGC-ACTC-TTTCAAAGCCCACACAA
65 AGTCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAA
4059382 GTCGATAGCA
Statistics
Matches: 576, Mismatches: 85, Indels: 60
0.80 0.12 0.08
Matches are distributed among these distances:
141 39 0.07
142 39 0.07
143 63 0.11
144 16 0.03
145 11 0.02
146 55 0.10
147 19 0.03
148 172 0.30
149 97 0.17
150 57 0.10
151 8 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (147 bp):
TTTCAAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTTCAAA
GTCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGCCC
ACAAGTCAGTGGCAACC
Found at i:4059049 original size:178 final size:177
Alignment explanation
Indices: 4058457--4059259 Score: 776
Period size: 178 Copynumber: 4.6 Consensus size: 177
4058447 CTACAACTCT
* * * * * * * * *
4058457 GTGGC-ACCTTTT-TAAGTCCACAAGTCAGTGGCAT-CATTTCAAAACGCACAAGTTAGTGGCAT
1 GTGGCTACCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTAAAGCCCACAAGTCAGTAGCAC
** * * * * **
4058519 CAATTCAAAGACCACAGGTTAGTGGC-ACT-ATTTCAAAG-CC-CACAAGTTAGTAGC-A-TCTT
66 CTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGGT-GCAACTCTT
* * ** * *
4058578 TTGAAAG-CC-CACAAGTCAGTGGCACCTTTTTTAATGCCCACAAGTTA
130 TTCAAAGCCCACACAAATCAGTGGCACC-TTTCCAAAGCCCACAAGTCA
* * *
4058625 GTGGC-ATCCTTTTTAAAGCCCACAAGTCAGTGAC-TTCCTTTTAAAGCCCACAAGTCAGTAGCA
1 GTGGCTA-CCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTAAAGCCCACAAGTCAGTAGCA
* * * **
4058688 GCC-TTTCAAAGCCCACAAGTCAGTAGCAGC-CTTTTCAAAG-CC-TACAAGTTAGTGGCAACTC
65 -CCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGGT-GCAACTC
* * * * * *
4058749 TTTTCAAAGTCCACACAAGTCAATGGTAACTCTTTTCAAAGCCCACACAAATCA
128 TTTTCAAAGCCCACACAAATCAGTGG-CAC-CTTTCCAAAG-CC-CACAAGTCA
* * * * *
4058803 GTGG-TACCTTTCCAAAGCCCATAAGTTAGTGGCA-ACC-TTTAAAGCCCATAAATCAGTAGCAC
1 GTGGCTACCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTAAAGCCCACAAGTCAGTAGCA-
* * *
4058865 CCTTTTCAAAGCCCACTAGTCAGTGGAAACTCTTTTCAAAGTCCACACAAGTCGGTGCCAGCTCT
65 CCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGGTG-CAACTCT
*
4058930 TTTCAAAGCCCACACAAATCGGTGGCACCTTTCCAAAGCCCACAAGTCA
129 TTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGCCCACAAGTCA
* * *
4058979 GTGGCT-CTTTTTCAAAGCCCACAAGTTAGTGGCATACCCTTTT-AAGCCCACAAGTCAGTGGCA
1 GTGGCTACCTTTTCAAAGCCCACAAGTCAGTGGCATA-CCTTTTAAAGCCCACAAGTCAGTAGCA
* * *
4059042 TCCTTTTCAAAACCTACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGATAGCAACTC
65 -CCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGGT-GCAACTC
* *
4059107 TTTTCAAAGCCCACACAAATCGGTGGCACTTTTCCAAAGCCCACAAGTCA
128 TTTTCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGCCCACAAGTCA
*
4059157 GTGGC-ACCCTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTCAAAGCCCACAAGTCAGT-GTC
1 GTGGCTACCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTT-AAAGCCCACAAGTCAGTAG-C
*
4059220 ACCTTTTCAAAGCCCACAAGACAGTGGC-A-TCTTTTCAAAG
64 ACCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAG
4059260 CCCATAAGTG
Statistics
Matches: 535, Mismatches: 70, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
168 6 0.01
169 7 0.01
170 57 0.11
171 24 0.04
172 1 0.00
173 10 0.02
174 2 0.00
175 12 0.02
176 81 0.15
177 61 0.11
178 212 0.40
179 27 0.05
180 35 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (177 bp):
GTGGCTACCTTTTCAAAGCCCACAAGTCAGTGGCATACCTTTTAAAGCCCACAAGTCAGTAGCAC
CTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGTCCACACAAGTCGGTGCAACTCTTT
TCAAAGCCCACACAAATCAGTGGCACCTTTCCAAAGCCCACAAGTCA
Found at i:4059556 original size:45 final size:46
Alignment explanation
Indices: 4059501--4059621 Score: 136
Period size: 49 Copynumber: 2.6 Consensus size: 46
4059491 TCTGATATCG
* *
4059501 CTAGCATTGAATCAGCATATTGGCACTTTT-ATTAGCCTAATGTCA
1 CTAGCCTTGAATCAGCATATTGGCACTTTTCATTAGCCCAATGTCA
* * *
4059546 CTAGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCG
1 CTAGCCTTGAATCAGCATATTGG--CACTTTT-CATTAGCCCAATGTCA
* **
4059595 CTGGCCTTGAATTGGCATATTGGCACT
1 CTAGCCTTGAATCAGCATATTGGCACT
4059622 CCTCTCATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
45 21 0.33
47 11 0.17
49 31 0.49
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (46 bp):
CTAGCCTTGAATCAGCATATTGGCACTTTTCATTAGCCCAATGTCA
Found at i:4063049 original size:12 final size:14
Alignment explanation
Indices: 4063021--4063065 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
4063011 TGTAATTTTT
4063021 ATTTTTATAATTTA
1 ATTTTTATAATTTA
4063035 ATTTTT-TAA-TTA
1 ATTTTTATAATTTA
**
4063047 ATTTTTATGGTTTA
1 ATTTTTATAATTTA
4063061 ATTTT
1 ATTTT
4063066 GCAAATATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 9 0.33
13 4 0.15
14 14 0.52
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
ATTTTTATAATTTA
Found at i:4064592 original size:21 final size:21
Alignment explanation
Indices: 4064551--4064594 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4064541 CTCTCCTTTA
* *
4064551 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
4064572 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
4064593 TC
1 TC
4064595 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:4066256 original size:21 final size:21
Alignment explanation
Indices: 4066232--4066278 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4066222 TTTGATGCTG
4066232 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
4066252 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
4066273 ATTTTG
1 ATTTTG
4066279 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4066417 original size:13 final size:13
Alignment explanation
Indices: 4066399--4066437 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
4066389 ATAATCACTC
4066399 TGTATCGATACAA
1 TGTATCGATACAA
4066412 TGTATCGATACAA
1 TGTATCGATACAA
4066425 TGTATCGATACAA
1 TGTATCGATACAA
4066438 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:4068536 original size:15 final size:15
Alignment explanation
Indices: 4068516--4068546 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4068506 ATTTCGTTTG
*
4068516 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4068531 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4068546 G
1 G
4068547 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4070359 original size:21 final size:21
Alignment explanation
Indices: 4070330--4070374 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4070320 AAGTTTTCAT
*
4070330 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4070350 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4070372 TTT
1 TTT
4070375 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4078404 original size:13 final size:13
Alignment explanation
Indices: 4078386--4078411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4078376 CAATTTTTTG
4078386 TGTATCGATACAT
1 TGTATCGATACAT
4078399 TGTATCGATACAT
1 TGTATCGATACAT
4078412 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:4082978 original size:15 final size:15
Alignment explanation
Indices: 4082958--4082988 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4082948 ATTTCGTTTG
*
4082958 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4082973 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4082988 G
1 G
4082989 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4084814 original size:21 final size:21
Alignment explanation
Indices: 4084785--4084829 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4084775 AAGTTTTCAT
*
4084785 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4084805 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4084827 TTT
1 TTT
4084830 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4087064 original size:13 final size:13
Alignment explanation
Indices: 4087046--4087071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4087036 CAATTTTTTG
4087046 TGTATCGATACAT
1 TGTATCGATACAT
4087059 TGTATCGATACAT
1 TGTATCGATACAT
4087072 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:4087155 original size:20 final size:21
Alignment explanation
Indices: 4087110--4087162 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
4087100 CTACCAAGAA
* **
4087110 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
4087131 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
4087151 ATGTATCGATAC
1 ATGTATCGATAC
4087163 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Found at i:4090834 original size:48 final size:47
Alignment explanation
Indices: 4090729--4090834 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 47
4090719 TTAATAAATA
* **
4090729 TATCGATACATTCTAAAAACCTAGATGTATCAATACATTATTCATTG
1 TATCGATACATTCTAAAAACCTAGATATATCAATACATTATTCAAAG
* **
4090776 TAT-TATTACATTCTGAAAAA-CTGAGATATATTGATACATTATTCAAAG
1 TATCGA-TACATTCT-AAAAACCT-AGATATATCAATACATTATTCAAAG
4090824 TATCGATACAT
1 TATCGATACAT
4090835 AAACCTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
46 1 0.02
47 13 0.27
48 33 0.69
49 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (47 bp):
TATCGATACATTCTAAAAACCTAGATATATCAATACATTATTCAAAG
Found at i:4093173 original size:33 final size:33
Alignment explanation
Indices: 4093136--4093200 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4093126 TACAAGCCAA
*
4093136 TGTATCGATACAATA-TTTTGTGTATCGATACAT
1 TGTATCGATAC-ATACTTTGGTGTATCGATACAT
4093169 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
4093201 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:4093174 original size:13 final size:13
Alignment explanation
Indices: 4093156--4093181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4093146 CAATATTTTG
4093156 TGTATCGATACAT
1 TGTATCGATACAT
4093169 TGTATCGATACAT
1 TGTATCGATACAT
4093182 ACTTTGGTGT
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:4093903 original size:39 final size:39
Alignment explanation
Indices: 4093828--4093918 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
4093818 TTTTCTTTCT
4093828 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCG-ACATTCTCC
* *
4093868 CCCTTAA-TAAGGTAATTTTAGCAAATTTACG-CATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAA-TT-CGACATTCTCC
* *
4093907 CCTTTTATTAAA
1 CCCTTAATTAAA
4093919 AAAATCTCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 29 0.67
40 12 0.28
41 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (39 bp):
CCCTTAATTAAAGTAATTTTAACAAATTCGACATTCTCC
Found at i:4095298 original size:21 final size:20
Alignment explanation
Indices: 4095269--4095311 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4095259 GGCTAGTATG
*
4095269 GGGACTGCCCGGTTACGACCT
1 GGGACTG-CCGGTCACGACCT
* *
4095290 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCACGACCT
4095310 GG
1 GG
4095312 TGGTGCTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCACGACCT
Found at i:4095770 original size:13 final size:13
Alignment explanation
Indices: 4095752--4095777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4095742 ATAATCCCCC
4095752 TGTATCGATACAA
1 TGTATCGATACAA
4095765 TGTATCGATACAA
1 TGTATCGATACAA
4095778 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4101952 original size:20 final size:21
Alignment explanation
Indices: 4101927--4101979 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
4101917 TACAAGCCAA
* *
4101927 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
4101947 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
4101967 TGTATCGATACAA
1 TGTATCGATACAA
4101980 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:4101984 original size:19 final size:19
Alignment explanation
Indices: 4101927--4101985 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
4101917 TACAAGCCAA
* *
4101927 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
4101947 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
4101967 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
4101986 CTACTGCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:4102077 original size:20 final size:20
Alignment explanation
Indices: 4102030--4102085 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4102020 ACATCTATTT
*
4102030 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
4102050 CATCTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
4102069 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
4102086 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:4108839 original size:20 final size:20
Alignment explanation
Indices: 4108814--4108887 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
4108804 CATTTGAGAC
4108814 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
4108834 ATGTATCAATACATTCACTT
1 ATGTATCGATACATTCACTT
*
4108854 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTT
4108874 ATTGTATCGATACA
1 A-TGTATCGATACA
4108888 AATTGTAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
20 38 0.76
21 12 0.24
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:4109678 original size:20 final size:20
Alignment explanation
Indices: 4109617--4109685 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
4109607 TAGCTTAGAC
* *
4109617 TATCGATACATTTTTAGATG
1 TATCGATACATTTTGATATG
* * *
4109637 TACCGATATATTGTG-TATTG
1 TATCGATACATTTTGATA-TG
4109657 TATCGATACATTTTGATATG
1 TATCGATACATTTTGATATG
4109677 TAT-GATACA
1 TATCGATACA
4109686 AATGAGGGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 7 0.18
20 30 0.77
21 2 0.05
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTTGATATG
Found at i:4114054 original size:27 final size:28
Alignment explanation
Indices: 4114024--4114087 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
4114014 TTAAGCGATG
*
4114024 AATTAAAATTTTA-TATGTGAT-AAATCC
1 AATTAAAATTTAATTATGT-ATGAAATCC
*
4114051 AATTAAGAATTTAATTATGTATGAATTCC
1 AATTAA-AATTTAATTATGTATGAAATCC
4114080 AATTAAAA
1 AATTAAAA
4114088 ATTCATAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 10 0.31
29 16 0.50
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (28 bp):
AATTAAAATTTAATTATGTATGAAATCC
Found at i:4114115 original size:15 final size:15
Alignment explanation
Indices: 4114097--4114130 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4114087 AATTCATAAG
*
4114097 AAAAAATTGA-ATTA
1 AAAAAATTGACATGA
4114111 AAAAAATTGACATGA
1 AAAAAATTGACATGA
4114126 AAAAA
1 AAAAA
4114131 TTCATTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAAATTGACATGA
Found at i:4114128 original size:27 final size:27
Alignment explanation
Indices: 4114096--4114157 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
4114086 AAATTCATAA
4114096 GAAAAAATTGAATTAAAAAAATTGACAT
1 GAAAAAATT-AATTAAAAAAATTGACAT
* * **
4114124 GAAAAAATTCATTAAGAAAATTTTCAT
1 GAAAAAATTAATTAAAAAAATTGACAT
4114151 GAAAAAA
1 GAAAAAA
4114158 GAATTTAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.26
Consensus pattern (27 bp):
GAAAAAATTAATTAAAAAAATTGACAT
Found at i:4114142 original size:15 final size:14
Alignment explanation
Indices: 4114084--4114143 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
4114074 AATTCCAATT
4114084 AAAAATTCATAAGA
1 AAAAATTCATAAGA
* *
4114098 AAAAATTGAATTA-A
1 AAAAATT-CATAAGA
* * *
4114112 AAAAATTGACATGA
1 AAAAATTCATAAGA
4114126 AAAAATTCATTAAGA
1 AAAAATTCA-TAAGA
4114141 AAA
1 AAA
4114144 TTTTCATGAA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
13 1 0.03
14 24 0.71
15 9 0.26
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.23
Consensus pattern (14 bp):
AAAAATTCATAAGA
Found at i:4115547 original size:40 final size:40
Alignment explanation
Indices: 4115472--4115547 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
4115462 CAATACAATG
* * *
4115472 TATCGATATAAAGTGAGTTTTAGCTACTGCCAGTTTCATC
1 TATCAATACAAAGTGAGTTTTAGCTACTACCAGTTTCATC
*
4115512 TATCAATACAAAGTGAGTTTTAGCTACTACTAGTTT
1 TATCAATACAAAGTGAGTTTTAGCTACTACCAGTTT
4115548 TATGTATCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (40 bp):
TATCAATACAAAGTGAGTTTTAGCTACTACCAGTTTCATC
Found at i:4115613 original size:20 final size:19
Alignment explanation
Indices: 4115570--4115619 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4115560 TATTTTAATG
*
4115570 TGTATCGATACAATGAACA
1 TGTATCGATACAAAGAACA
*
4115589 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAG-AACA
*
4115609 TGTATTGATAC
1 TGTATCGATAC
4115620 TTTCAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAGAACA
Found at i:4117648 original size:35 final size:35
Alignment explanation
Indices: 4117602--4117671 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
4117592 AATTTACATT
4117602 AATAATTGAATATTCCTATGTCTAATCTTATTAGC
1 AATAATTGAATATTCCTATGTCTAATCTTATTAGC
4117637 AATAATTGAATATTCCTATGTCTAATCTTATTAGC
1 AATAATTGAATATTCCTATGTCTAATCTTATTAGC
4117672 TTTAGAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (35 bp):
AATAATTGAATATTCCTATGTCTAATCTTATTAGC
Found at i:4118062 original size:39 final size:39
Alignment explanation
Indices: 4118018--4118093 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
4118008 GTTGTCTATC
*
4118018 TATTTAAG-TTTTGGGGATAATTGATTACTCAACTTAACT
1 TATTTAAGCTTTT-GGGATAATTGATCACTCAACTTAACT
4118057 TATTTAAGCTTTTGGGATAATTGATCACTCAACTTAA
1 TATTTAAGCTTTTGGGATAATTGATCACTCAACTTAA
4118094 TATAGTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 31 0.89
40 4 0.11
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (39 bp):
TATTTAAGCTTTTGGGATAATTGATCACTCAACTTAACT
Found at i:4121137 original size:31 final size:29
Alignment explanation
Indices: 4121086--4121146 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 29
4121076 ACATAAATTT
*
4121086 AATAATATATCAAAAAAT-AAATAATGTAA
1 AATAACATATCAAAAAATAAAAT-ATGTAA
4121115 AATAACATATCGAATAAAATAAAATATGTAA
1 AATAACATATC-AA-AAAATAAAATATGTAA
4121146 A
1 A
4121147 TTTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.36
30 2 0.07
31 12 0.43
32 4 0.14
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (29 bp):
AATAACATATCAAAAAATAAAATATGTAA
Done.