Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 12 of 172
Found at i:3856473 original size:46 final size:46
Alignment explanation
Indices: 3856420--3856595 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
3856410 TATTTGGGCA
3856420 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * * *
3856466 TCCGAACTTGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* * * *
3856513 TCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTCTGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
3856559 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3856596 GCGGGTTAGA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 64 0.61
47 30 0.29
48 1 0.01
50 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:3856575 original size:93 final size:93
Alignment explanation
Indices: 3856416--3856588 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
3856406 GGGATATTTG
* * * *
3856416 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTTGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3856481 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
3856509 GGCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTCTGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3856574 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
3856589 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:3862589 original size:21 final size:21
Alignment explanation
Indices: 3862549--3862606 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3862539 ATAATAAATC
*
3862549 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
3862569 AACA-AATATTAAAACAAATAA
1 AA-ATAATATTAAAACAAATAA
*
3862590 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
3862607 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:3862877 original size:42 final size:44
Alignment explanation
Indices: 3862819--3862942 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 44
3862809 GGCATTGACT
* *
3862819 TTTGATTTATGTGTAAGACCATGTTTGGTACA-TCGGCATCG-TA
1 TTTGATTTATGTGTAAGACCATGTCTGGGACAGT-GGCATCGATA
*
3862862 TTTGATTT-TGTGTAAGACCCTGTCTGGGACAGTGGCATCGATA
1 TTTGATTTATGTGTAAGACCATGTCTGGGACAGTGGCATCGATA
** * *
3862905 TTTGA-TTACATGTAAGACTACGTCTGGGAC-GTTGGCAT
1 TTTGATTTATGTGTAAGACCATGTCTGGGACAG-TGGCAT
3862943 TGTATGAGCT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
42 30 0.43
43 39 0.57
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (44 bp):
TTTGATTTATGTGTAAGACCATGTCTGGGACAGTGGCATCGATA
Found at i:3867490 original size:27 final size:27
Alignment explanation
Indices: 3867460--3867518 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3867450 ATTCTAATTC
3867460 TAAA-ATATACAAAGAAATATATAAAAA
1 TAAATATATACAAA-AAATATATAAAAA
* * *
3867487 TAAATATTTTCAAAAAATATATAATAA
1 TAAATATATACAAAAAATATATAAAAA
3867514 TAAAT
1 TAAAT
3867519 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
TAAATATATACAAAAAATATATAAAAA
Found at i:3867491 original size:14 final size:14
Alignment explanation
Indices: 3867460--3867518 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
3867450 ATTCTAATTC
*
3867460 TAAA-ATATACAAA
1 TAAATATATAAAAA
*
3867473 GAAATATATAAAAA
1 TAAATATATAAAAA
* **
3867487 TAAATATTTTCAAA
1 TAAATATATAAAAA
*
3867501 -AAATATATAATAA
1 TAAATATATAAAAA
3867514 TAAAT
1 TAAAT
3867519 TTAAATTTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
13 12 0.35
14 22 0.65
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (14 bp):
TAAATATATAAAAA
Found at i:3867907 original size:52 final size:53
Alignment explanation
Indices: 3867812--3867918 Score: 153
Period size: 52 Copynumber: 2.0 Consensus size: 53
3867802 ATTGAGACAA
* *
3867812 ATTTGATGAGATTTTATTTCTTTATTTCTTTAGGATGGGGTCAATCTTTGATTATC
1 ATTTGATGAGATTTTA--T-TTTATTTCTTTAGGATGGAGTCAATCGTTGATTATC
*
3867868 ATTTGATGAGATTTTA-TTTATTTCTTTAGGATTGAGTCAATCGTTGATTAT
1 ATTTGATGAGATTTTATTTTATTTCTTTAGGATGGAGTCAATCGTTGATTAT
3867919 AAGGATTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
52 32 0.67
56 16 0.33
ACGTcount: A:0.23, C:0.07, G:0.18, T:0.51
Consensus pattern (53 bp):
ATTTGATGAGATTTTATTTTATTTCTTTAGGATGGAGTCAATCGTTGATTATC
Found at i:3874900 original size:24 final size:23
Alignment explanation
Indices: 3874834--3874902 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 23
3874824 GGATTTTTAT
*
3874834 TTTATTTAATATTAA-ATTAATCATA
1 TTTAATTAATATTAATA-TAA--ATA
*
3874859 TTTATTTAATATTAATATAAATA
1 TTTAATTAATATTAATATAAATA
3874882 TTTAAATTAATTATTATATAT
1 TTT-AATTAA-TATTA-ATAT
3874903 TTTTAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 6 0.15
24 5 0.13
25 23 0.59
26 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAATTAATATTAATATAAATA
Found at i:3874904 original size:20 final size:19
Alignment explanation
Indices: 3874845--3874904 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
3874835 TTATTTAATA
* *
3874845 TTAAATTAATCATATTTAT
1 TTAAATTAATTATATATAT
*
3874864 TTAATATTAA-TATAAATAT
1 TTAA-ATTAATTATATATAT
3874883 TTAAATTAATTATTATATAT
1 TTAAATTAATTA-TATATAT
3874903 TT
1 TT
3874905 TTAATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.15
19 16 0.47
20 13 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATTAATTATATATAT
Found at i:3874930 original size:23 final size:22
Alignment explanation
Indices: 3874879--3874935 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
3874869 ATTAATATAA
* *
3874879 ATATTTAAATTAATTATTATAT
1 ATATTTAAATTTATTATTACAT
* *
3874901 ATTTTTAATATTTATTTTTACAT
1 ATATTTAA-ATTTATTATTACAT
3874924 ATATTTAAATTT
1 ATATTTAAATTT
3874936 TACATATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTAAATTTATTATTACAT
Found at i:3875087 original size:12 final size:12
Alignment explanation
Indices: 3875070--3875095 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3875060 ATTTAAAATG
3875070 AAAAAATTTGAA
1 AAAAAATTTGAA
3875082 AAAAAATTTGAA
1 AAAAAATTTGAA
3875094 AA
1 AA
3875096 TAATATAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAAATTTGAA
Found at i:3881053 original size:30 final size:30
Alignment explanation
Indices: 3881013--3881080 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
3881003 TAGAATAGGG
3881013 CCACACGGGTGTTTGGACCACCCGTATGGA
1 CCACACGGGTGTTTGGACCACCCGTATGGA
* *
3881043 CCACATGGGTGTTTGGGCCACCCGTATGGA
1 CCACACGGGTGTTTGGACCACCCGTATGGA
3881073 CCACACGG
1 CCACACGG
3881081 CCCCTTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (30 bp):
CCACACGGGTGTTTGGACCACCCGTATGGA
Found at i:3882815 original size:21 final size:22
Alignment explanation
Indices: 3882784--3882886 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 22
3882774 AGTATGATAC
3882784 AAATATTTTAATTATGATTTGA-
1 AAAT-TTTTAATTATGATTTGAG
*
3882806 AAATTTTTAATGT-T-A-TTAAG
1 AAATTTTTAAT-TATGATTTGAG
* * *
3882826 AAATTATTAATTTATAATATTGTAT
1 AAATTTTTAA-TTATGAT-TTG-AG
*
3882851 AAATTCTTTAATTATGATTTCA-
1 AAATT-TTTAATTATGATTTGAG
*
3882873 AAATTTTTCATTAT
1 AAATTTTTAATTAT
3882887 ATATCAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.05
20 11 0.17
21 18 0.28
22 11 0.17
23 1 0.02
24 4 0.06
25 12 0.19
26 4 0.06
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (22 bp):
AAATTTTTAATTATGATTTGAG
Found at i:3887725 original size:56 final size:56
Alignment explanation
Indices: 3887628--3887736 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
3887618 ACATTAGAGT
* * *
3887628 CGATATGTGTGTGCAAGTAAGACCATGTTTAATACGTTGGCATCGA-TATGTGACTC
1 CGATATATGTGTGCAAGTAAGACCATGTCTAAGACGTTGGCATC-ATTATGTGACTC
* * *
3887684 CGATATATGTGTGCGAGTAAGACCCTGTCTGAGACAG-TGGCATCATTATGTGA
1 CGATATATGTGTGCAAGTAAGACCATGTCTAAGAC-GTTGGCATCATTATGTGA
3887737 TTATATGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.02
56 43 0.96
57 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (56 bp):
CGATATATGTGTGCAAGTAAGACCATGTCTAAGACGTTGGCATCATTATGTGACTC
Found at i:3893401 original size:43 final size:43
Alignment explanation
Indices: 3893339--3893425 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
3893329 CAGTTTAATA
* * *
3893339 ATTTGCAAACACTAATGGTTTATCCATATCTTACTGGCAGTTT
1 ATTTGCAAACACTAATGGTTTATCCACAACGTACTGGCAGTTT
* *
3893382 ATTTGCAAACATTAGTGGTTTATCCACAACGTACTGGCAGTTT
1 ATTTGCAAACACTAATGGTTTATCCACAACGTACTGGCAGTTT
3893425 A
1 A
3893426 ACTGCAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (43 bp):
ATTTGCAAACACTAATGGTTTATCCACAACGTACTGGCAGTTT
Found at i:3896279 original size:27 final size:27
Alignment explanation
Indices: 3896249--3896353 Score: 102
Period size: 29 Copynumber: 3.7 Consensus size: 27
3896239 ATTTTGTTAT
3896249 AATTTAGTACCTAAACTTTTTTTATCC
1 AATTTAGTACCTAAACTTTTTTTATCC
* * *
3896276 AATTTAGTACCTGAACTTGATATTTTTTCTT
1 AATTTAGTACCTAAACTT--T-TTTTATC-C
*
3896307 AATTTGGTACCTAAACTTTTTTGTAGTCC
1 AATTTAGTACCTAAACTTTTTT-TA-TCC
* *
3896336 AATTTGGTACCTTAACTT
1 AATTTAGTACCTAAACTT
3896354 GGCATTTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
27 17 0.27
28 3 0.05
29 20 0.31
30 8 0.12
31 16 0.25
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (27 bp):
AATTTAGTACCTAAACTTTTTTTATCC
Found at i:3896371 original size:59 final size:59
Alignment explanation
Indices: 3896248--3896406 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 59
3896238 CATTTTGTTA
* * *
3896248 TAATTTAGTACCTAAACTTTTTTTA-TCCAATTTAGTACCTGAACTTGATATTTTTTCT
1 TAATTTGGTACCTAAACTTTTTTTAGTCCAATTTGGTACCTGAACTTGACATTTTTTCT
* *
3896306 TAATTTGGTACCTAAACTTTTTTGTAGTCCAATTTGGTACCTTAACTTGGCA-TTTTTCT
1 TAATTTGGTACCTAAACTTTTTT-TAGTCCAATTTGGTACCTGAACTTGACATTTTTTCT
** * *
3896365 TAATTTGGTACCTAAGTTTTTTTTAGGTTCAATTTGATACCT
1 TAATTTGGTACCTAAACTTTTTTTA-GTCCAATTTGGTACCT
3896407 CAATTTATTA
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
58 24 0.27
59 44 0.49
60 21 0.24
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (59 bp):
TAATTTGGTACCTAAACTTTTTTTAGTCCAATTTGGTACCTGAACTTGACATTTTTTCT
Found at i:3900465 original size:39 final size:40
Alignment explanation
Indices: 3900422--3900589 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
3900412 CTCGTTCAAG
* * * *
3900422 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
3900461 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
3900501 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
3900541 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
3900581 TGCCTTCGG
1 TGCCTTCGG
3900590 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:3900573 original size:80 final size:80
Alignment explanation
Indices: 3900457--3900642 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
3900447 AGTAACTCAT
* * *
3900457 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
3900521 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
3900536 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
3900600 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
3900617 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
3900643 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:3900602 original size:40 final size:40
Alignment explanation
Indices: 3900459--3900642 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
3900449 TAACTCATAC
* *
3900459 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
3900499 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
3900539 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
3900579 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
3900620 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3900643 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:3907987 original size:27 final size:27
Alignment explanation
Indices: 3907957--3908134 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3907947 ATATTGAGTC
* * * *
3907957 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
3907984 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3908011 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
3908039 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
3908066 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
3908093 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3908120 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3908135 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:3908096 original size:82 final size:81
Alignment explanation
Indices: 3907978--3908133 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3907968 TGCTATATAA
* *
3907978 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
3908043 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3908060 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
3908124 CACTTAGTGC
65 CACTTAGTGC
3908134 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:3914214 original size:83 final size:83
Alignment explanation
Indices: 3914075--3914240 Score: 323
Period size: 83 Copynumber: 2.0 Consensus size: 83
3914065 AACATTAACA
3914075 TTCGGCATGTATAGCTAGACTCATACGCACTATGGTAGTCCTAGAACCGACTAAACCATAGCTCT
1 TTCGGCATGTATAGCTAGACTCATACGCACTATGGTAGTCCTAGAACCGACTAAACCATAGCTCT
3914140 GATACCAATCAAATGTAG
66 GATACCAATCAAATGTAG
*
3914158 TTCGGCATGTATAGCTAGACTCATACGCGCTATGGTAGTCCTAGAACCGACTAAACCATAGCTCT
1 TTCGGCATGTATAGCTAGACTCATACGCACTATGGTAGTCCTAGAACCGACTAAACCATAGCTCT
3914223 GATACCAATCAAATGTAG
66 GATACCAATCAAATGTAG
3914241 CACCCCGAAC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
TTCGGCATGTATAGCTAGACTCATACGCACTATGGTAGTCCTAGAACCGACTAAACCATAGCTCT
GATACCAATCAAATGTAG
Found at i:3915619 original size:27 final size:27
Alignment explanation
Indices: 3915586--3915763 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
3915576 ATATTGAGTC
* *
3915586 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
3915613 CGTACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3915640 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
3915668 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
3915695 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
3915722 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
3915749 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3915764 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3915746 original size:54 final size:55
Alignment explanation
Indices: 3915586--3915763 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 55
3915576 ATATTGAGTC
* * * * * * *
3915586 CGCACACTCAGTGCTATATAATC-AACTCGTACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
3915640 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
3915695 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
3915749 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3915764 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 60 0.58
55 44 0.42
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:3917317 original size:84 final size:83
Alignment explanation
Indices: 3917166--3917331 Score: 323
Period size: 84 Copynumber: 2.0 Consensus size: 83
3917156 CATTTTTTTT
3917166 TTTTCTTTCCTCAACTCACGGCAACAAGGGGGGTATGGATGAGACCATTTTTTTTTCATCACCCT
1 TTTTCTTTCCTCAACTCACGGCAACAAGGGGGGTATGGATGAGACCATTTTTTTTTCATCACCCT
3917231 TCCTTTTCATTGTTTAAG
66 TCCTTTTCATTGTTTAAG
3917249 TTTTCTTTCCTCAACTCACGGCAACAAGGGGGGGTATGGATGAGACCATTTTTTTTTCATCACCC
1 TTTTCTTTCCTCAACTCACGGCAACAA-GGGGGGTATGGATGAGACCATTTTTTTTTCATCACCC
3917314 TTCCTTTTCATTGTTTAA
65 TTCCTTTTCATTGTTTAA
3917332 TTACCATGCT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 27 0.33
84 55 0.67
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (83 bp):
TTTTCTTTCCTCAACTCACGGCAACAAGGGGGGTATGGATGAGACCATTTTTTTTTCATCACCCT
TCCTTTTCATTGTTTAAG
Found at i:3923109 original size:27 final size:27
Alignment explanation
Indices: 3923051--3923227 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
3923041 TAAATTGTAC
* *
3923051 AGCACTATGTGTGCG-ATTTACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
3923077 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
3923103 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
3923131 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
3923159 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
3923186 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
3923213 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3923228 GACTCAATAT
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
26 13 0.10
27 91 0.72
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:3923164 original size:82 final size:80
Alignment explanation
Indices: 3923052--3923206 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 80
3923042 AAATTGTACA
* * *
3923052 GCACTATGTGTGCGATTTACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGT
3923116 GCGAATTGACCATGCG
65 GCGAATTGACCATGCG
** *
3923132 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3923197 TGCGAGTTGA
64 TGCGAATTGA
3923207 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 14 0.22
81 3 0.05
82 47 0.72
83 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
GCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
CGAATTGACCATGCG
Found at i:3923218 original size:82 final size:80
Alignment explanation
Indices: 3923048--3923227 Score: 209
Period size: 82 Copynumber: 2.2 Consensus size: 80
3923038 GATTAAATTG
* * *
3923048 TACAGCACTATGTGTGCGATTTACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
3923113 TGTGCGAATTGACCA
66 TGTGCGAATTGACCA
* * ** *
3923128 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3923192 AAGTGTGCGAGTTGATTA
63 AAGTGTGCGAATTGACCA
* *
3923210 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3923228 GACTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 16 0.20
81 4 0.05
82 62 0.76
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGAATTGACCA
Found at i:3926676 original size:38 final size:38
Alignment explanation
Indices: 3926633--3926841 Score: 148
Period size: 38 Copynumber: 5.0 Consensus size: 38
3926623 TTTCAAATTA
*
3926633 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
*
3926671 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* * * *
3926712 GAATCGATATATGTAACCGTGGCATATCCACATAGCACCATGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* *
3926756 ACATGTATCAATATGTGTAATCGTGGTATATCCACTGAGCACCACGTT
1 ACATG------TA----TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
3926804 ACACGTATAACCATGGTATATCCACTTAGCGCCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
3926842 TTTCCATTCC
Statistics
Matches: 136, Mismatches: 18, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
38 61 0.45
39 1 0.01
40 2 0.01
41 2 0.01
42 3 0.02
43 1 0.01
44 2 0.01
45 3 0.02
46 3 0.02
47 26 0.19
48 32 0.24
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:3926732 original size:47 final size:48
Alignment explanation
Indices: 3926678--3926806 Score: 179
Period size: 48 Copynumber: 2.7 Consensus size: 48
3926668 GTTACATGTT
*
3926678 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCGATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * * * *
3926725 TAACCGTGGCATATCCACATAGCACCATGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* *
3926773 TAATCGTGGTATATCCACTGAGCACCACGTTACA
1 TAACCGTGGTATATCCACTTAGCACCACGTTACA
3926807 CGTATAACCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
47 29 0.41
48 41 0.59
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:3928169 original size:100 final size:100
Alignment explanation
Indices: 3927996--3928191 Score: 392
Period size: 100 Copynumber: 2.0 Consensus size: 100
3927986 GTACTAGTCG
3927996 TTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAAACTA
1 TTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAAACTA
3928061 GACTCATGTGCCCATCTATGTATTTTTTTCTGTCA
66 GACTCATGTGCCCATCTATGTATTTTTTTCTGTCA
3928096 TTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAAACTA
1 TTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAAACTA
3928161 GACTCATGTGCCCATCTATGTATTTTTTTCT
66 GACTCATGTGCCCATCTATGTATTTTTTTCT
3928192 AGAATTTTTG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (100 bp):
TTTTAAAAATCATATCTTGAGTTTCGTAACTCGAAAATCAGTTTCGTAATTTTTCCCAGAAACTA
GACTCATGTGCCCATCTATGTATTTTTTTCTGTCA
Found at i:3929364 original size:27 final size:27
Alignment explanation
Indices: 3929334--3929502 Score: 155
Period size: 27 Copynumber: 6.3 Consensus size: 27
3929324 ATATTGAGTC
* *
3929334 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3929361 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3929388 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** **
3929416 CGCACACTTAGTGCCGCATGGTCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
* **
3929442 ACGCACACTTAGTGC-ATCATATTCATTT
1 -CGCACACTTAGTGCTA-CATAATCAACT
* * *
3929470 CGCACACTTAGTGCAACATAGT-AAAT
1 CGCACACTTAGTGCTACATAATCAACT
3929496 CGCACAC
1 CGCACAC
3929503 ATGGTGCTGT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
26 10 0.08
27 85 0.71
28 25 0.21
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3929426 original size:55 final size:54
Alignment explanation
Indices: 3929334--3929502 Score: 182
Period size: 54 Copynumber: 3.1 Consensus size: 54
3929324 ATATTGAGTC
* * * * *
3929334 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
3929388 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTC-AAT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
3929442 ACGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGT-AAAT
1 -CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
3929496 CGCACAC
1 CGCACAC
3929503 ATGGTGCTGT
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
53 7 0.07
54 48 0.49
55 42 0.43
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:3936427 original size:21 final size:21
Alignment explanation
Indices: 3936381--3936428 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3936371 CCTAACCCCT
*
3936381 AAACCCTTAACCCTTAACTAC
1 AAACCCATAACCCTTAACTAC
* *
3936402 TAACCCATAATCCTTAACCT-C
1 AAACCCATAACCCTTAA-CTAC
3936423 AAACCC
1 AAACCC
3936429 CTAAATCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCATAACCCTTAACTAC
Found at i:3936533 original size:14 final size:14
Alignment explanation
Indices: 3936513--3936557 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
3936503 TTTTAAACCT
3936513 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
3936527 TATACCCTAAA-TCA
1 TAAACCCTAAACT-A
3936541 TAAACCCTAAACTA
1 TAAACCCTAAACTA
3936555 TAA
1 TAA
3936558 TCATAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:3937922 original size:60 final size:60
Alignment explanation
Indices: 3937843--3937961 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
3937833 AATTTTTTTA
* * *
3937843 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAATTATTGTGTTTG
3937903 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAATTATTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAATTATTGTGTTT
3937962 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAATTATTGTGTTTG
Found at i:3937952 original size:34 final size:32
Alignment explanation
Indices: 3937845--3937953 Score: 97
Period size: 33 Copynumber: 3.5 Consensus size: 32
3937835 TTTTTTTATA
3937845 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTAAAATTAATTT-TTAGTAATTTAGG
* *
3937878 ATTATGTTATAAATT--TTTGT-GT--TTGTA--
1 ATTATTTTA-AAATTAATTTTTAGTAATT-TAGG
3937905 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTT-TTAGTAATTTAGG
*
3937938 ATTATATTATAAATTA
1 ATTATTTTA-AAATTA
3937954 TTGTGTTTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
26 5 0.08
27 8 0.13
28 5 0.08
29 3 0.05
30 4 0.07
31 3 0.05
32 5 0.08
33 16 0.27
34 11 0.18
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTATTTTAAAATTAATTTTTAGTAATTTAGG
Found at i:3938282 original size:107 final size:102
Alignment explanation
Indices: 3938157--3938347 Score: 251
Period size: 107 Copynumber: 1.8 Consensus size: 102
3938147 CTATAGTTAT
3938157 TTATTTTGTTAATAATTTATGGGATTAG-GT-TACAAATTGTTAGTGTTTAGTGGTTTAGGGTAT
1 TTATTTTGTTAATAATTTAT--GATTAGAGTATACAAATTGTTAGTGTTTA---GTTTAGGGTAT
*
3938220 TGTTATTTTTTAGTAATGTAATTTTTTAAAAAACAATTTTATAG
61 TGTGATTTTTT--TAATGTAATTTTTTAAAAAACAATTTTATAG
* * * * *
3938264 TTATTTTGTTAGTAATTTATGATTAGATTATATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
1 TTATTTTGTTAATAATTTATGATTAGAGTATACAAATTGTTAGTGTTTAGTTTAGGGTATTGTGA
3938329 TTTTTTTAATGTAATTTTT
66 TTTTTTTAATGTAATTTTT
3938348 ATATAATGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
102 13 0.17
104 19 0.25
105 6 0.08
106 1 0.01
107 37 0.49
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (102 bp):
TTATTTTGTTAATAATTTATGATTAGAGTATACAAATTGTTAGTGTTTAGTTTAGGGTATTGTGA
TTTTTTTAATGTAATTTTTTAAAAAACAATTTTATAG
Found at i:3938362 original size:15 final size:16
Alignment explanation
Indices: 3938335--3938366 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3938325 GTGATTTTTT
3938335 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
3938351 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
3938366 T
1 T
3938367 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:3938511 original size:17 final size:17
Alignment explanation
Indices: 3938474--3938511 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3938464 GGTATGTTTC
*
3938474 TATTTCTATTTTTTTTA
1 TATTTCTATGTTTTTTA
*
3938491 -ATTTGTATGTTTTTTA
1 TATTTCTATGTTTTTTA
3938507 TATTT
1 TATTT
3938512 AGATAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (17 bp):
TATTTCTATGTTTTTTA
Found at i:3940760 original size:17 final size:18
Alignment explanation
Indices: 3940728--3940763 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3940718 ATTTTTTGGC
3940728 ATTTTATTTATCAATTTA
1 ATTTTATTTATCAATTTA
*
3940746 ATTTT-TTTTTCAATTTA
1 ATTTTATTTATCAATTTA
3940763 A
1 A
3940764 ATATTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTATTTATCAATTTA
Found at i:3940783 original size:73 final size:75
Alignment explanation
Indices: 3940704--3940843 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 75
3940694 AATAACTTCA
*
3940704 TATTTATGTAATGAA-TTTTTTGGCATTTTATTTATCAATTTAAT-TTTTTTTTCAATTTAAATA
1 TATTTATGTAATGAATTTTTTTGCCATTTTATTTATCAATTTAATGTTTTTTTTCAATTTAAATA
3940767 TTCAACTTTG
66 TTCAACTTTG
*
3940777 TATTTATGTAATGAATTTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTCAATTTAAA
1 TATTTATGTAATGAATTTTTTTGCCATTTTATTTATCAATTTAAT--GTTTTTTTTCAATTTAAA
3940842 TA
64 TA
3940844 AATAACCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
73 15 0.25
74 27 0.44
77 19 0.31
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (75 bp):
TATTTATGTAATGAATTTTTTTGCCATTTTATTTATCAATTTAATGTTTTTTTTCAATTTAAATA
TTCAACTTTG
Found at i:3946180 original size:22 final size:22
Alignment explanation
Indices: 3946140--3946199 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
3946130 TTAGCCATTT
*
3946140 TTTTATTTTTATTGCAATT-TAA
1 TTTT-TTTTTATTTCAATTATAA
*
3946162 TTTTGTTTTTATTTTAATTACTAA
1 TTTT-TTTTTATTTCAATTA-TAA
3946186 TTTTTCTTTTATTT
1 TTTTT-TTTTATTT
3946200 ACTTCTGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 16 0.50
23 1 0.03
24 15 0.47
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTTTTTTTATTTCAATTATAA
Found at i:3967474 original size:20 final size:20
Alignment explanation
Indices: 3967437--3967475 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3967427 GGGCACACGC
**
3967437 CCGTGTGGCCTGGGACATGT
1 CCGTGTGGCCTGAAACATGT
*
3967457 CCGTGTGGCTTGAAACATG
1 CCGTGTGGCCTGAAACATG
3967476 GTTGTGGGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (20 bp):
CCGTGTGGCCTGAAACATGT
Found at i:3970322 original size:14 final size:15
Alignment explanation
Indices: 3970287--3970315 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3970277 GAATTATTTC
3970287 CTATTA-TGTACTTT
1 CTATTATTGTACTTT
3970301 CTATTATTGTACTTT
1 CTATTATTGTACTTT
3970316 TCTTATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
CTATTATTGTACTTT
Found at i:3971220 original size:30 final size:30
Alignment explanation
Indices: 3971185--3971241 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3971175 TAGGCACTTT
* *
3971185 CACACAGGTAAACCACACGCTCGTGTGAGA
1 CACACAGGCAAACCACACGCCCGTGTGAGA
**
3971215 CACACAGGCAGGCCACACGCCCGTGTG
1 CACACAGGCAAACCACACGCCCGTGTG
3971242 TCACGGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.35, G:0.26, T:0.11
Consensus pattern (30 bp):
CACACAGGCAAACCACACGCCCGTGTGAGA
Found at i:3978317 original size:17 final size:16
Alignment explanation
Indices: 3978294--3978381 Score: 67
Period size: 17 Copynumber: 5.4 Consensus size: 16
3978284 CCGAATGTGT
3978294 GAGCTCACCAAGACTGC
1 GAGCTCACCAAGA-TGC
*
3978311 AAGCTCACC-AGAAT--
1 GAGCTCACCAAG-ATGC
*
3978325 -AGCTCATCAAGATCGC
1 GAGCTCACCAAGAT-GC
*
3978341 GAGCTCACCAACATTGC
1 GAGCTCACCAAGA-TGC
*
3978358 GAGCTCACCAAGAATGA
1 GAGCTCACCAAG-ATGC
3978375 GAGCTCA
1 GAGCTCA
3978382 TCTTCGAGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
13 9 0.16
14 2 0.04
16 3 0.05
17 41 0.72
18 2 0.04
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.15
Consensus pattern (16 bp):
GAGCTCACCAAGATGC
Found at i:3978704 original size:35 final size:36
Alignment explanation
Indices: 3978648--3978716 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
3978638 TTTCATCTTT
* *
3978648 TGCTTTTGTTTTAATCTCTCCTTCATAAAAAATCCA
1 TGCTTTTGTTCTAACCTCTCCTTCATAAAAAATCCA
3978684 TGCTTTT-TTCTAACCTCTCCTTCATAAAAAATC
1 TGCTTTTGTTCTAACCTCTCCTTCATAAAAAATC
3978717 TAACGGTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.28, C:0.25, G:0.04, T:0.43
Consensus pattern (36 bp):
TGCTTTTGTTCTAACCTCTCCTTCATAAAAAATCCA
Found at i:3981016 original size:134 final size:136
Alignment explanation
Indices: 3980757--3981028 Score: 431
Period size: 134 Copynumber: 2.0 Consensus size: 136
3980747 CAAAAGATAA
* * *
3980757 AATCTCTAATTATTATTAAATTATTTGGAGTTCCTATTGTTATTGGACATATTCAAATTAAGTGA
1 AATCTCTAATTATTATTAAATTATTTGGAGTTCCGATAGTTATTGGACATATCCAAATTAAGTG-
* *
3980822 AAGGGAAAATCCTTAAGGCACTACTATATAAGTCTAGAAATTACATTAGAAAAAAGATGACACCT
65 AAGAGAAAATCCTTAAGGCACTACTATATAAGTCTAGAAATTACATTAGAAAAAACATGACACCT
*
3980887 TTCAAGC
130 TTAAAGC
*
3980894 AATCTCTAATTATTATTAATTTATTTGGAGTTCCGATAGTTATTGGACATATCCAAATTAAGTG-
1 AATCTCTAATTATTATTAAATTATTTGGAGTTCCGATAGTTATTGGACATATCCAAATTAAGTGA
* * *
3980958 AGAG-AAATCCTTAAGGCACTACTATGTAAGTCTAGAAGTTACATTAGAAACAACATGACACCTT
66 AGAGAAAATCCTTAAGGCACTACTATATAAGTCTAGAAATTACATTAGAAAAAACATGACACCTT
3981022 TAAAGC
131 TAAAGC
3981028 A
1 A
3981029 TAGTCACCAA
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 62 0.50
135 3 0.02
137 60 0.48
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (136 bp):
AATCTCTAATTATTATTAAATTATTTGGAGTTCCGATAGTTATTGGACATATCCAAATTAAGTGA
AGAGAAAATCCTTAAGGCACTACTATATAAGTCTAGAAATTACATTAGAAAAAACATGACACCTT
TAAAGC
Found at i:3984387 original size:27 final size:27
Alignment explanation
Indices: 3984330--3984444 Score: 97
Period size: 27 Copynumber: 4.1 Consensus size: 27
3984320 TTTCAAATAT
* ** *
3984330 TAAAAATTAAAAAATATATAAAAAATCA
1 TAAAAATTATAAAAT-TATAAAATTTTA
* *
3984358 TAAAAATTGTAAAATTGTAAAATTTTA
1 TAAAAATTATAAAATTATAAAATTTTA
* *
3984385 TAAAAATCATAATGAATTATAAAA-TATA
1 TAAAAATTATAA--AATTATAAAATTTTA
* *
3984413 TAGAAATATAAAAAATTATAAAATTTTA
1 TAAAAAT-TATAAAATTATAAAATTTTA
3984441 TAAA
1 TAAA
3984445 GTCGTAAGAA
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
27 28 0.41
28 28 0.41
29 12 0.18
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
TAAAAATTATAAAATTATAAAATTTTA
Found at i:3984419 original size:10 final size:9
Alignment explanation
Indices: 3984340--3984436 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 9
3984330 TAAAAATTAA
3984340 AAAATATAT
1 AAAATATAT
*
3984349 AAAAAATCAT
1 AAAATAT-AT
*
3984359 AAAA-ATTGT
1 AAAATA-TAT
*
3984368 AAAAT-TGT
1 AAAATATAT
*
3984376 AAAATTTTAT
1 AAAA-TATAT
3984386 AAAA-ATCAT
1 AAAATAT-AT
3984395 AATGAAT-TAT
1 AA--AATATAT
3984405 AAAATATAT
1 AAAATATAT
*
3984414 AGAAATATAA
1 A-AAATATAT
3984424 AAAAT-TAT
1 AAAATATAT
3984432 AAAAT
1 AAAAT
3984437 TTTATAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
8 18 0.25
9 25 0.35
10 25 0.35
11 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:3984435 original size:8 final size:8
Alignment explanation
Indices: 3984314--3984437 Score: 54
Period size: 8 Copynumber: 14.0 Consensus size: 8
3984304 ATTAATTTTA
3984314 ATAAAATT
1 ATAAAATT
3984322 -TCAAATATT
1 AT-AAA-ATT
3984331 A-AAAATT
1 ATAAAATT
*
3984338 AAAAAATAT
1 ATAAAAT-T
*
3984347 ATAAAAAATC
1 AT--AAAATT
3984357 ATAAAAATT
1 AT-AAAATT
*
3984366 GTAAAATT
1 ATAAAATT
*
3984374 GTAAAATTTT
1 ATAAAA--TT
*
3984384 ATAAAAATC
1 AT-AAAATT
3984393 ATAATGAATT
1 ATAA--AATT
3984403 ATAAAATAT
1 ATAAAAT-T
3984412 ATAGAAATAT
1 ATA-AAAT-T
*
3984422 AAAAAATT
1 ATAAAATT
3984430 ATAAAATT
1 ATAAAATT
3984438 TTATAAAGTC
Statistics
Matches: 93, Mismatches: 9, Indels: 28
0.72 0.07 0.22
Matches are distributed among these distances:
7 5 0.05
8 36 0.39
9 23 0.25
10 20 0.22
11 9 0.10
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (8 bp):
ATAAAATT
Found at i:3984789 original size:19 final size:20
Alignment explanation
Indices: 3984767--3984821 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
3984757 AATAAATTTG
3984767 AAAATTTTATATTTTTAT-T
1 AAAATTTTATATTTTTATCT
* *
3984786 AAAATTTAATA-ATTTATCT
1 AAAATTTTATATTTTTATCT
*
3984805 AAAATTTATTTATTTTT
1 AAAATTT-TATATTTTT
3984822 CTAATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 2 0.07
21 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTTATATTTTTATCT
Found at i:3984790 original size:27 final size:25
Alignment explanation
Indices: 3984741--3984800 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
3984731 TTTTTATAAA
3984741 AAAATTTCTAATTTTTAATAAATTT
1 AAAATTTCTAATTTTTAATAAATTT
*
3984766 GAAAATTT-TATATTTTTATTAAAATTT
1 -AAAATTTCTA-ATTTTTAAT-AAATTT
3984793 AATAATTT
1 AA-AATTT
3984801 ATCTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 17 0.57
27 11 0.37
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
AAAATTTCTAATTTTTAATAAATTT
Found at i:3984832 original size:38 final size:35
Alignment explanation
Indices: 3984745--3984835 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 35
3984735 TATAAAAAAA
3984745 TTTCTAATTTTTAATAAATTTGAAAATTTTATATT
1 TTTCTAATTTTTAATAAATTTGAAAATTTTATATT
* ** * * *
3984780 TTTATTAAAATTTAATAATTTATCTAAAATTTATTTATT
1 TTT-CTAATTTTTAATAAATT-T-GAAAATTT-TATATT
3984819 TTTCTAATTTTTAATAA
1 TTTCTAATTTTTAATAA
3984836 GAGCATGGCC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
35 3 0.07
36 13 0.30
37 1 0.02
38 18 0.42
39 8 0.19
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTCTAATTTTTAATAAATTTGAAAATTTTATATT
Found at i:3984980 original size:90 final size:94
Alignment explanation
Indices: 3984877--3985047 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 94
3984867 TTTGAGTGTA
* * *
3984877 TTTTTGATGCATTTTAAAAGTTCAAGT-ATCCAATTGAGTGAAAAAAAAAA-A-G-GA-ACTTAA
1 TTTTTAATACATTTTAAAAGTTCAAGTGCT-CAATTGAGTGAAAAAAAAAAGAGGAGAGACTTAA
3984937 CTGCTTTTTTTTTAAAGAAATTTGAGGGCC
65 CTGCTTTTTTTTTAAAGAAATTTGAGGGCC
* * *
3984967 TTTTTAATACATTTTGAAAGTTCAAGTGCTCAATTGAGTGAAAAAAAAAAGAGGAGAGATTTAAT
1 TTTTTAATACATTTTAAAAGTTCAAGTGCTCAATTGAGTGAAAAAAAAAAGAGGAGAGACTTAAC
3985032 TGCTTTTTTTTTAAAG
66 TGCTTTTTTTTTAAAG
3985048 TTTGACGGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
90 44 0.63
91 2 0.03
92 1 0.01
93 2 0.03
94 21 0.30
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (94 bp):
TTTTTAATACATTTTAAAAGTTCAAGTGCTCAATTGAGTGAAAAAAAAAAGAGGAGAGACTTAAC
TGCTTTTTTTTTAAAGAAATTTGAGGGCC
Found at i:3985631 original size:19 final size:18
Alignment explanation
Indices: 3985580--3985631 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
3985570 CCCTCTCAAC
3985580 AAAA-ATTTA-AAAAATT
1 AAAATATTTATAAAAATT
* *
3985596 AAAAGTAATTTTTAAAATTT
1 AAAA-T-ATTTATAAAAATT
3985616 AAAATATTTATAAAAA
1 AAAATATTTATAAAAA
3985632 ATTCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 4 0.14
18 9 0.32
19 5 0.18
20 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAATATTTATAAAAATT
Found at i:3985671 original size:18 final size:19
Alignment explanation
Indices: 3985648--3985683 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3985638 AATTTATATT
3985648 ATTTAAAAA-TTCTAATAA
1 ATTTAAAAATTTCTAATAA
3985666 ATTTAAAAATTTCTAATA
1 ATTTAAAAATTTCTAATA
3985684 TAAAGGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAAAATTTCTAATAA
Found at i:3988151 original size:21 final size:21
Alignment explanation
Indices: 3988127--3988197 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
3988117 AACGTATGCG
3988127 ATATTAAACATGATAACAATA
1 ATATTAAACATGATAACAATA
** ** *
3988148 ATATT-AA-ATGCGAAGTATGCG
1 ATATTAAACATGATAACAAT--A
3988169 ATATTAAACATGATAACAATA
1 ATATTAAACATGATAACAATA
3988190 ATATTAAA
1 ATATTAAA
3988198 TGCGAAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 7 0.19
20 2 0.06
21 18 0.50
22 2 0.06
23 7 0.19
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (21 bp):
ATATTAAACATGATAACAATA
Found at i:3988167 original size:42 final size:42
Alignment explanation
Indices: 3988120--3988203 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3988110 CAATAACAAC
3988120 GTATGCGATATTAAACATGATAACAATAATATTAAATGCGAA
1 GTATGCGATATTAAACATGATAACAATAATATTAAATGCGAA
3988162 GTATGCGATATTAAACATGATAACAATAATATTAAATGCGAA
1 GTATGCGATATTAAACATGATAACAATAATATTAAATGCGAA
3988204 ATAAGGATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (42 bp):
GTATGCGATATTAAACATGATAACAATAATATTAAATGCGAA
Found at i:3988642 original size:21 final size:21
Alignment explanation
Indices: 3988613--3988653 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3988603 TTATTAATAG
*
3988613 TAAACATATACATATATATAT
1 TAAACATATACACATATATAT
* *
3988634 TAAAGATATATACATATATA
1 TAAACATATACACATATATA
3988654 ATAGAACACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAACATATACACATATATAT
Found at i:3988698 original size:3 final size:3
Alignment explanation
Indices: 3988692--3989412 Score: 1442
Period size: 3 Copynumber: 240.3 Consensus size: 3
3988682 TAATAATAAT
3988692 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988740 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988788 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988836 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988884 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988932 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3988980 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989028 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989076 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989124 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989172 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989220 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989268 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989316 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989364 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3989412 A
1 A
3989413 GGGCGGTGCC
Statistics
Matches: 718, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 718 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3989431 original size:19 final size:19
Alignment explanation
Indices: 3989404--3989450 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3989394 AAGAAGAAGA
* *
3989404 AGAAGAAGAGGGCGGTGCC
1 AGAAAAAGAGGGCAGTGCC
*
3989423 AGAAAAAGAGGGTAGTGCC
1 AGAAAAAGAGGGCAGTGCC
*
3989442 AGGAAAAGA
1 AGAAAAAGA
3989451 AAAGAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.40, T:0.06
Consensus pattern (19 bp):
AGAAAAAGAGGGCAGTGCC
Found at i:3989499 original size:20 final size:19
Alignment explanation
Indices: 3989442--3989500 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
3989432 GGGTAGTGCC
3989442 AGGA-AAAGAAAAGAA-AA
1 AGGAGAAAGAAAAGAAGAA
3989459 AGAGAGAAAGAGAATAG-AGAA
1 AG-GAGAAAGA-AA-AGAAGAA
3989480 AGGAGAAAGAAAGAGAAGAA
1 AGGAGAAAGAAA-AGAAGAA
3989500 A
1 A
3989501 AAAAATAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 9 0.26
20 16 0.46
21 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (19 bp):
AGGAGAAAGAAAAGAAGAA
Found at i:3989510 original size:24 final size:23
Alignment explanation
Indices: 3989447--3989511 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
3989437 GTGCCAGGAA
*
3989447 AAGAAAAGAAAAAGAGAGAAAGAG
1 AAGAAAA-AAAAAGAAAGAAAGAG
* * **
3989471 AATAGAGAAAGGAGAAAGAAAGAG
1 AAGA-AAAAAAAAGAAAGAAAGAG
3989495 AAGAAAAAAAATAGAAA
1 AAGAAAAAAAA-AGAAA
3989512 AATAAGGTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 4 0.13
24 24 0.80
25 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAGAAAGAG
Found at i:3989866 original size:40 final size:42
Alignment explanation
Indices: 3989811--3989896 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 42
3989801 TTATATTATT
**
3989811 GTTAGTTATTATTTTTAGTAAAACCCTAATTATT-TT-TGTTA
1 GTTAGTTATTATTTTTAGTAAAAAACT-ATTATTATTGTGTTA
3989852 GTTAG-TATTATTTTTAGTAAAAAACTATTATTATTGTGTTA
1 GTTAGTTATTATTTTTAGTAAAAAACTATTATTATTGTGTTA
3989893 GTTA
1 GTTA
3989897 TTAGAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 6 0.15
40 21 0.51
41 14 0.34
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (42 bp):
GTTAGTTATTATTTTTAGTAAAAAACTATTATTATTGTGTTA
Found at i:3989880 original size:20 final size:20
Alignment explanation
Indices: 3989817--3989883 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
3989807 TATTGTTAGT
**
3989817 TATTATTTTTAGTAAAACCC
1 TATTATTTTTAGTAAAAAAC
* *** *
3989837 TAATTATTTTT-GTTAGTTAG
1 T-ATTATTTTTAGTAAAAAAC
3989857 TATTATTTTTAGTAAAAAAC
1 TATTATTTTTAGTAAAAAAC
3989877 TATTATT
1 TATTATT
3989884 ATTGTGTTAG
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
19 9 0.26
20 16 0.47
21 9 0.26
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.52
Consensus pattern (20 bp):
TATTATTTTTAGTAAAAAAC
Found at i:3989884 original size:76 final size:79
Alignment explanation
Indices: 3989679--3989905 Score: 239
Period size: 76 Copynumber: 2.9 Consensus size: 79
3989669 GTTTAGTTAT
* * *
3989679 TAATAATTATTGTTACTTAGTATTATTGCTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTATTAT-GTTAGTTAT
3989744 TAGGATTAGTAAAAACCC
62 TAGGATTAGTAAAAACCC
* **** *
3989762 TAATTATTATT-TTAGTTAGTATGATTGTTAGT-TTTTA-TATTA-TATTATTGTTAGTTATTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTA-TGTTAGTTATTAG
**
3989823 TTTTAGT-AAAACCC
65 GATTAGTAAAAACCC
* * * *
3989837 TAATTATTTTTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTGTGTTAGTTATTAGA
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATGTTAGTTATTAGG
3989902 ATTA
66 ATTA
3989906 ATGGTTAAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
75 17 0.15
76 40 0.34
77 7 0.06
78 20 0.17
79 4 0.03
81 1 0.01
82 18 0.15
83 10 0.09
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (79 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATGTTAGTTATTAGG
ATTAGTAAAAACCC
Found at i:3992792 original size:8 final size:8
Alignment explanation
Indices: 3992762--3992807 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
3992752 AATTGAGCTT
3992762 ATGTTGTA
1 ATGTTGTA
* *
3992770 AAGTTGTT
1 ATGTTGTA
3992778 ATG-TGTA
1 ATGTTGTA
3992785 ATGTTGTA
1 ATGTTGTA
3992793 ATGTTGTA
1 ATGTTGTA
3992801 ATGTTGT
1 ATGTTGT
3992808 TGTAACACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
ATGTTGTA
Found at i:3995306 original size:161 final size:159
Alignment explanation
Indices: 3995122--3995530 Score: 633
Period size: 161 Copynumber: 2.6 Consensus size: 159
3995112 ACTTCAAAAC
3995122 AAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCAGATTTTAT
1 AAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCC-GATTTTAT
3995187 TACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
65 TACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
* * *
3995252 AAATGTATTAATTTAGTGTGTTTTTTTATAT
130 AAATGTATTAATTTAGTAT-ATTTTTTAAAT
* *
3995283 AAATTTAGTAAAAAAAATCTTATTTTGGCCCTTTATTCGTATTTTTCTTTTTTCCCGAATTTTAT
1 AAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCG-ATTTTAT
* * *
3995348 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTGCATTATGTTTG
65 TACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
*
3995413 AAATGTATTATTTTAGTATATTTTTTAAAT
130 AAATGTATTAATTTAGTATATTTTTTAAAT
* * * *
3995443 AAATTTAAT-AAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTT-CGGATTTTAT
1 AAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTT-TTTTCCCGATTTTAT
**
3995506 TACTTTCAGTAAATATACTATTTTC
65 TACTTTCAAAAAATATACTATTTTC
3995531 GTTTCTTTTC
Statistics
Matches: 229, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
158 30 0.13
159 37 0.16
160 22 0.10
161 140 0.61
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (159 bp):
AAATTTAGTAAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGATTTTATT
ACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
AATGTATTAATTTAGTATATTTTTTAAAT
Found at i:3995582 original size:16 final size:16
Alignment explanation
Indices: 3995536--3995585 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3995526 TTTTCGTTTC
3995536 TTTTC-GTATTTTATT
1 TTTTCAGTATTTTATT
***
3995551 TTTTCA-TAAACATATT
1 TTTTCAGT-ATTTTATT
3995567 TTTTCAGTATTTTATT
1 TTTTCAGTATTTTATT
3995583 TTT
1 TTT
3995586 AATCCTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 6 0.23
16 19 0.73
17 1 0.04
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (16 bp):
TTTTCAGTATTTTATT
Found at i:3995790 original size:20 final size:20
Alignment explanation
Indices: 3995765--3995802 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3995755 TTTTTTACAC
3995765 AAATAATACAAAAAAAATTA
1 AAATAATACAAAAAAAATTA
*
3995785 AAATAATACAAAGAAAAT
1 AAATAATACAAAAAAAAT
3995803 ACCTTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAATACAAAAAAAATTA
Found at i:3995940 original size:20 final size:20
Alignment explanation
Indices: 3995917--3995959 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3995907 CTTTTCTTTT
*
3995917 CTTT-CTTTTTCTTTCTTCTC
1 CTTTCCTTTTT-TATCTTCTC
3995937 CTTTCCTTTTTTATCTTCTC
1 CTTTCCTTTTTTATCTTCTC
3995957 CTT
1 CTT
3995960 CAGTCGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (20 bp):
CTTTCCTTTTTTATCTTCTC
Found at i:3995959 original size:15 final size:16
Alignment explanation
Indices: 3995886--3995940 Score: 73
Period size: 15 Copynumber: 3.6 Consensus size: 16
3995876 CCTACGCCTC
3995886 CTTCTCCTTTTTC-TT
1 CTTCTCCTTTTTCTTT
3995901 CTTCTCC-TTTTCTTTT
1 CTTCTCCTTTTTC-TTT
3995917 CTT-T-CTTTTTCTTT
1 CTTCTCCTTTTTCTTT
3995931 CTTCTCCTTT
1 CTTCTCCTTT
3995941 CCTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.34
15 14 0.40
16 9 0.26
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTCTCCTTTTTCTTT
Found at i:3997267 original size:6 final size:6
Alignment explanation
Indices: 3997256--3997293 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
3997246 TGCAATGCCG
3997256 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA
3997294 ACCAAAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:4004613 original size:26 final size:26
Alignment explanation
Indices: 4004583--4004649 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
4004573 TGTTATTGGT
4004583 AGCTTTGCTGCGATACTGA-TACTGGC
1 AGCTTTGCTGCGATACT-ATTACTGGC
** * *
4004609 AGCTTCACTACAATACTATTACTGGC
1 AGCTTTGCTGCGATACTATTACTGGC
4004635 AGCTTTGCTGCGATA
1 AGCTTTGCTGCGATA
4004650 TTAGTGTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (26 bp):
AGCTTTGCTGCGATACTATTACTGGC
Found at i:4004809 original size:28 final size:28
Alignment explanation
Indices: 4004756--4004810 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
4004746 CACTATACTA
* **
4004756 TTACTGTATTGGGCTAAGTCTGACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
4004784 TTACTGTATTGGGCTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
4004811 ATACTGTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:4007670 original size:13 final size:13
Alignment explanation
Indices: 4007620--4007728 Score: 65
Period size: 13 Copynumber: 8.3 Consensus size: 13
4007610 GTTAACACTT
*
4007620 TGAAATGGCTATA
1 TGAAATGGTTATA
* *
4007633 CGAAATGGCTATA
1 TGAAATGGTTATA
* **
4007646 TGAATTTTTTATA
1 TGAAATGGTTATA
*
4007659 TGAAATGGTTATG
1 TGAAATGGTTATA
* *
4007672 TAAAATGATTATA
1 TGAAATGGTTATA
* *
4007685 AGAATTGGTTATA
1 TGAAATGGTTATA
***
4007698 TAGAAATAAATATA
1 T-GAAATGGTTATA
* *
4007712 CGAAATGCTTATA
1 TGAAATGGTTATA
4007725 TGAA
1 TGAA
4007729 TCAATTATAT
Statistics
Matches: 68, Mismatches: 27, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
13 60 0.88
14 8 0.12
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (13 bp):
TGAAATGGTTATA
Found at i:4007777 original size:13 final size:13
Alignment explanation
Indices: 4007754--4007818 Score: 69
Period size: 13 Copynumber: 5.0 Consensus size: 13
4007744 CAGATGAACA
*
4007754 AAATAATTATATG
1 AAATGATTATATG
*
4007767 AATTGATTATATG
1 AAATGATTATATG
*
4007780 AAAATAATTATATG
1 -AAATGATTATATG
*
4007794 AAGTG-TTATATG
1 AAATGATTATATG
*
4007806 AAATGTTTATATG
1 AAATGATTATATG
4007819 GATAGATATG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 11 0.26
13 21 0.49
14 11 0.26
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.42
Consensus pattern (13 bp):
AAATGATTATATG
Found at i:4007783 original size:27 final size:26
Alignment explanation
Indices: 4007753--4007808 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
4007743 ACAGATGAAC
*
4007753 AAAATAATTATATGAATTGATTATATG
1 AAAATAATTATATGAAGTG-TTATATG
4007780 AAAATAATTATATGAAGTGTTATATG
1 AAAATAATTATATGAAGTGTTATATG
4007806 AAA
1 AAA
4007809 TGTTTATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (26 bp):
AAAATAATTATATGAAGTGTTATATG
Found at i:4007791 original size:14 final size:14
Alignment explanation
Indices: 4007753--4007795 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
4007743 ACAGATGAAC
4007753 AAAATAATTATATG
1 AAAATAATTATATG
* *
4007767 -AATTGATTATATG
1 AAAATAATTATATG
4007780 AAAATAATTATATG
1 AAAATAATTATATG
4007794 AA
1 AA
4007796 GTGTTATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (14 bp):
AAAATAATTATATG
Found at i:4009798 original size:50 final size:50
Alignment explanation
Indices: 4009687--4009809 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
4009677 TGGTATGCTT
*
4009687 ATACGAG-CATATAATCGGGAACCTCTTCCAAGCCATGTAACGAGAAGCTC
1 ATACGAGCCATATAAT-GGGAAGCTCTTCCAAGCCATGTAACGAGAAGCTC
* * * *
4009737 A-AGTGATCCATATAATGGGAAGCTCTTGCAAGCCAAT-TATCGAGAAGCTC
1 ATA-CGAGCCATATAATGGGAAGCTCTTCCAAGCC-ATGTAACGAGAAGCTC
*
4009787 ATACGAGCCATA-AACGGGAAGCT
1 ATACGAGCCATATAATGGGAAGCT
4009810 TAAGAGAGCC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
49 11 0.18
50 39 0.64
51 11 0.18
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (50 bp):
ATACGAGCCATATAATGGGAAGCTCTTCCAAGCCATGTAACGAGAAGCTC
Found at i:4009873 original size:24 final size:24
Alignment explanation
Indices: 4009775--4009893 Score: 80
Period size: 24 Copynumber: 4.9 Consensus size: 24
4009765 CAAGCCAATT
* *
4009775 ATCGAGAAGCTCATACGAGCCATA
1 ATCGGGAAGCTCATAAGAGCCATA
* * *
4009799 AACGGGAAGCTTA-AGAGAGCCAAA
1 ATCGGGAAGCTCATA-AGAGCCATA
* * * *
4009823 TATCAGAAAGCTCATGAG-GGCATTA
1 -ATCGGGAAGCTCATAAGAGCCA-TA
*
4009848 ATCGGGAAGCTCATAAGAGCCGTA
1 ATCGGGAAGCTCATAAGAGCCATA
* * *
4009872 ATTGGAAAGCTCATACGAGCCA
1 ATCGGGAAGCTCATAAGAGCCA
4009894 ATATTGAGAA
Statistics
Matches: 69, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
23 1 0.01
24 54 0.78
25 14 0.20
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (24 bp):
ATCGGGAAGCTCATAAGAGCCATA
Found at i:4009939 original size:25 final size:25
Alignment explanation
Indices: 4009851--4009940 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 25
4009841 GGCATTAATC
* *
4009851 GGGAAGCTCATAAGAGCCGTA-ATT
1 GGGAAGCTCATTAGAGCCATATATT
*
4009875 GGAAAGCTCA-TACGAGCCA-ATATT
1 GGGAAGCTCATTA-GAGCCATATATT
* * *** *
4009899 GAGAAGGTCCGGAGAGCCATATACT
1 GGGAAGCTCATTAGAGCCATATATT
4009924 GGGAAGCTCATTAGAGC
1 GGGAAGCTCATTAGAGC
4009941 TAAATAACGA
Statistics
Matches: 48, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
23 2 0.04
24 29 0.60
25 17 0.35
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (25 bp):
GGGAAGCTCATTAGAGCCATATATT
Found at i:4017618 original size:29 final size:30
Alignment explanation
Indices: 4017559--4017617 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4017549 ATTTTTGGGT
4017559 TTTTGGGTTTTTATAAATTAAACAAAAAAA
1 TTTTGGGTTTTTATAAATTAAACAAAAAAA
4017589 TTTTGGGTTTTTATAAATTAAACAAAAAA
1 TTTTGGGTTTTTATAAATTAAACAAAAAA
4017618 TAAATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTTGGGTTTTTATAAATTAAACAAAAAAA
Found at i:4021922 original size:14 final size:14
Alignment explanation
Indices: 4021903--4021950 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
4021893 ATTTGATGAC
4021903 ACATGGTCTAGGGG
1 ACATGGTCTAGGGG
**
4021917 ACATGGTCGT-GTAG
1 ACATGGTC-TAGGGG
4021931 ACATGGTCTAGGGG
1 ACATGGTCTAGGGG
4021945 ACATGG
1 ACATGG
4021951 ACGTGTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.23
Consensus pattern (14 bp):
ACATGGTCTAGGGG
Found at i:4021943 original size:28 final size:28
Alignment explanation
Indices: 4021903--4021958 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4021893 ATTTGATGAC
*
4021903 ACATGGTCTAGGGGACATGGTCGTGTAG
1 ACATGGTCTAGGGGACATGGACGTGTAG
4021931 ACATGGTCTAGGGGACATGGACGTGTAG
1 ACATGGTCTAGGGGACATGGACGTGTAG
4021959 GTTTTTGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.23
Consensus pattern (28 bp):
ACATGGTCTAGGGGACATGGACGTGTAG
Found at i:4027476 original size:17 final size:17
Alignment explanation
Indices: 4027454--4027486 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4027444 TATCAAATTT
4027454 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
4027471 TGATACCCATATCTTT
1 TGATACCCATATCTTT
4027487 GAATTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:4029605 original size:200 final size:200
Alignment explanation
Indices: 4029262--4029659 Score: 778
Period size: 200 Copynumber: 2.0 Consensus size: 200
4029252 AATAGTATAG
4029262 GTTATTCCTTCTTGTGTCTTTCATTACTGTCAATACCCCAGCTACTACCTTTAGTAATCCATCTC
1 GTTATTCCTTCTTGTGTCTTTCATTACTGTCAATACCCCAGCTACTACCTTTAGTAATCCATCTC
*
4029327 TCAAAGTGATTGTGAGCCCTTTAGATTCTAGGACCCCTAACGAGATGAGATTTTTCTTCAAGCTA
66 TCAAAGTGATTGTGAGCCCCTTAGATTCTAGGACCCCTAACGAGATGAGATTTTTCTTCAAGCTA
4029392 GGTATGTAGCGAACATCTGTGAAGACTTGAATTGAGCCGTCCTGATTCTTCAATTGGATTGTACC
131 GGTATGTAGCGAACATCTGTGAAGACTTGAATTGAGCCGTCCTGATTCTTCAATTGGATTGTACC
4029457 TACAA
196 TACAA
4029462 GTTATTCCTTCTTGTGTCTTTCATTACTGTCAATACCCCAGCTACTACCTTTAGTAATCCATCTC
1 GTTATTCCTTCTTGTGTCTTTCATTACTGTCAATACCCCAGCTACTACCTTTAGTAATCCATCTC
*
4029527 TCAAAGTGATTGTGAGCCCCTTAGATTCTAGGACCCCTAATGAGATGAGATTTTTCTTCAAGCTA
66 TCAAAGTGATTGTGAGCCCCTTAGATTCTAGGACCCCTAACGAGATGAGATTTTTCTTCAAGCTA
4029592 GGTATGTAGCGAACATCTGTGAAGACTTGAATTGAGCCGTCCTGATTCTTCAATTGGATTGTACC
131 GGTATGTAGCGAACATCTGTGAAGACTTGAATTGAGCCGTCCTGATTCTTCAATTGGATTGTACC
4029657 TAC
196 TAC
4029660 TCCCATTGTC
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 196 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (200 bp):
GTTATTCCTTCTTGTGTCTTTCATTACTGTCAATACCCCAGCTACTACCTTTAGTAATCCATCTC
TCAAAGTGATTGTGAGCCCCTTAGATTCTAGGACCCCTAACGAGATGAGATTTTTCTTCAAGCTA
GGTATGTAGCGAACATCTGTGAAGACTTGAATTGAGCCGTCCTGATTCTTCAATTGGATTGTACC
TACAA
Found at i:4031195 original size:17 final size:17
Alignment explanation
Indices: 4031173--4031222 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
4031163 TCTCAGATTT
4031173 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
4031190 TGATACCAATATCTTTC
1 TGATACCCATATCTTTC
4031207 TGATACCCATATCTTT
1 TGATACCCATATCTTT
4031223 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:4031889 original size:17 final size:19
Alignment explanation
Indices: 4031866--4031910 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
4031856 AAATTTGTCA
4031866 AAATTTAAATATAATAA-T
1 AAATTTAAATATAATAAGT
*
4031884 -AATTT--ATTTAATAAGT
1 AAATTTAAATATAATAAGT
4031900 AAATTTAAATA
1 AAATTTAAATA
4031911 ATTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 7
0.70 0.07 0.23
Matches are distributed among these distances:
15 8 0.38
16 1 0.05
17 10 0.48
19 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTTAAATATAATAAGT
Found at i:4033477 original size:20 final size:19
Alignment explanation
Indices: 4033435--4033483 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
4033425 TTCTTTATCA
*
4033435 TCAATTAT-ATAAATGCAT
1 TCAATTATAATAAATCCAT
*
4033453 CCAATTATAATCAAATCCAT
1 TCAATTATAAT-AAATCCAT
*
4033473 TCAATGATAAT
1 TCAATTATAAT
4033484 TCAATTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 7 0.28
19 2 0.08
20 16 0.64
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (19 bp):
TCAATTATAATAAATCCAT
Found at i:4035557 original size:70 final size:67
Alignment explanation
Indices: 4035436--4035577 Score: 171
Period size: 70 Copynumber: 2.1 Consensus size: 67
4035426 ACTTCCTAAT
* *
4035436 ATTAATTTTTAATGAAAATAGTAAAAAAGTGAGTATAGAAGTATTCTCTAGTTAATATAAGATTA
1 ATTAATTTTTAATGAAAATAGTAAAAAAGTGAGAATAGAAGTATTCTCTAGTCAATATAAGATTA
4035501 AA
66 AA
* * **
4035503 ATTAACTTTTCTAATGAAAATAGTGAAGAAA-TGAGCAAT-GAGAGTATTCTCTAGTCAATGTGG
1 ATTAA-TTTT-TAATGAAAATAGT-AAAAAAGTGAG-AATAGA-AGTATTCTCTAGTCAATATAA
4035566 GATTAAA
61 GATTAAA
4035573 ATTAA
1 ATTAA
4035578 AATGTAACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
67 5 0.08
68 4 0.06
69 19 0.30
70 36 0.56
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (67 bp):
ATTAATTTTTAATGAAAATAGTAAAAAAGTGAGAATAGAAGTATTCTCTAGTCAATATAAGATTA
AA
Found at i:4041295 original size:20 final size:21
Alignment explanation
Indices: 4041251--4041298 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
4041241 GAACATGTTA
4041251 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
4041273 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
4041293 ATTTTT
1 ATTTTT
4041299 TACAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:4041871 original size:14 final size:14
Alignment explanation
Indices: 4041848--4041877 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4041838 CATCCCTCAT
*
4041848 TCACATCTCTTCTC
1 TCACAACTCTTCTC
4041862 TCACAACTCTTCTC
1 TCACAACTCTTCTC
4041876 TC
1 TC
4041878 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:4043352 original size:36 final size:36
Alignment explanation
Indices: 4043304--4043374 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
4043294 ATCAAGGGCT
4043304 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
* * *
4043340 ACAATTAGAAGCTGTATATAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGA
4043375 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:4058414 original size:92 final size:93
Alignment explanation
Indices: 4058292--4058521 Score: 311
Period size: 95 Copynumber: 2.5 Consensus size: 93
4058282 AGTGTGAGAT
* * * * * *
4058292 ATGAGAGTGTTCTCTAGTCAATATTGGATTAAAATTAACTTTTAATGAAAATAGTG-AAGAAAGT
1 ATGAGAGTGTTTTCTAGCCAATGTAGGATTAAAATTAACTTTTAATGAAAATAGTGAAAAAAACT
** *
4058356 AACACTTATTTATTGAGCAAGTACGAGC
66 AACACTTATTTATAAAGCAAATACGAGC
*
4058384 ATGAGAGTGTTTTCTAGCCAATGTAAGATTAAAATTAACTTTTTAATGAAAATAGTGAAAAAAAA
1 ATGAGAGTGTTTTCTAGCCAATGTAGGATTAAAATTAAC-TTTTAATGAAAATAGTG-AAAAAAA
*
4058449 CTAACACTTATTTATAAAGCAAATGCGAGC
64 CTAACACTTATTTATAAAGCAAATACGAGC
*
4058479 ATGGGAGTGTTCTT-TAGCCAATGTAGGATTAAAATTAACTTTT
1 ATGAGAGTGTT-TTCTAGCCAATGTAGGATTAAAATTAACTTTT
4058522 TAAGGGAGCA
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
92 34 0.28
93 17 0.14
94 4 0.03
95 64 0.53
96 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (93 bp):
ATGAGAGTGTTTTCTAGCCAATGTAGGATTAAAATTAACTTTTAATGAAAATAGTGAAAAAAACT
AACACTTATTTATAAAGCAAATACGAGC
Found at i:4059998 original size:42 final size:40
Alignment explanation
Indices: 4059952--4060042 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 40
4059942 TTAAAAGTAT
* * *
4059952 TTATATTAAAAAAATACTACCATAAAGATAATAAATGTTTTA
1 TTATATTAAAAAAACAC-A-AATAAAGATAATAAATATTTTA
*
4059994 TTATATT-AAAAAACACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACACAAATAAAGATAATAAATATTTTA
4060033 TTATATTAAA
1 TTATATTAAA
4060043 TATAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 26 0.59
40 3 0.07
41 8 0.18
42 7 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.37
Consensus pattern (40 bp):
TTATATTAAAAAAACACAAATAAAGATAATAAATATTTTA
Found at i:4066841 original size:54 final size:54
Alignment explanation
Indices: 4066777--4066895 Score: 238
Period size: 54 Copynumber: 2.2 Consensus size: 54
4066767 ATAATGTCAA
4066777 AAATTATATAATGCCAATAAAATAGGGTTTTATTGGCATTGTTAAAATATTGAT
1 AAATTATATAATGCCAATAAAATAGGGTTTTATTGGCATTGTTAAAATATTGAT
4066831 AAATTATATAATGCCAATAAAATAGGGTTTTATTGGCATTGTTAAAATATTGAT
1 AAATTATATAATGCCAATAAAATAGGGTTTTATTGGCATTGTTAAAATATTGAT
4066885 AAATTATATAA
1 AAATTATATAA
4066896 CTTTATACCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (54 bp):
AAATTATATAATGCCAATAAAATAGGGTTTTATTGGCATTGTTAAAATATTGAT
Found at i:4080635 original size:22 final size:23
Alignment explanation
Indices: 4080592--4080635 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
4080582 AAAAATTATT
*
4080592 AAATTATAAATTTATATATAATA
1 AAATTATAAATTTAAATATAATA
* *
4080615 AAATTAT-ACTTTAAATTTAAT
1 AAATTATAAATTTAAATATAAT
4080636 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATTATAAATTTAAATATAATA
Found at i:4086243 original size:203 final size:203
Alignment explanation
Indices: 4085894--4086270 Score: 666
Period size: 203 Copynumber: 1.9 Consensus size: 203
4085884 TGAGAATTGT
4085894 AGTCTGGTAGTAGAAAAGTTGAGGAACTGATAAACTTCCTTACCTCTCTGTACTTGTAGATTGAA
1 AGTCTGGTAGTAGAAAAGTTGAGGAACTGATAAACTTCCTTACCTCTCTGTACTTGTAGATTGAA
* *
4085959 GAGAGAAGTAGAGTAAGAATACTTAAAAGCTTCTATATAATTATGGATTATGGGTTTTTAAGGGT
66 GAGAGAAGTAGAGTAAAAATACTTAAAAGCTTCTATATAATTATGGATTATAGGTTTTTAAGGGT
4086024 TGAACACCTTTAGTTTAACCAATAAATGGTTGTCATGCTTAGCTTTGCATGTCGCAACCATCATG
131 TGAACACCTTTAGTTTAACCAATAAATGGTTGTCATGCTTAGCTTTGCATGTCGCAACCATCATG
4086089 AAAACTGA
196 AAAACTGA
* * * *
4086097 AGTCTGGTATTAGATAAGTTGAGGAACTGGTAAACTTCCTTACCTCTCTGTACTTGTGGATTGAA
1 AGTCTGGTAGTAGAAAAGTTGAGGAACTGATAAACTTCCTTACCTCTCTGTACTTGTAGATTGAA
*
4086162 GAGAGAAGTAGAGTAAAAACT-CTTAAAAGCTTCTATATAATTATGGATTCTAGGTTTTTAAGGG
66 GAGAGAAGTAGAGTAAAAA-TACTTAAAAGCTTCTATATAATTATGGATTATAGGTTTTTAAGGG
*
4086226 TTGAACACCTTTAGTTTAACCGATAAATGGTTGTCATGCTTAGCT
130 TTGAACACCTTTAGTTTAACCAATAAATGGTTGTCATGCTTAGCT
4086271 ATCAAGACAA
Statistics
Matches: 165, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
203 164 0.99
204 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (203 bp):
AGTCTGGTAGTAGAAAAGTTGAGGAACTGATAAACTTCCTTACCTCTCTGTACTTGTAGATTGAA
GAGAGAAGTAGAGTAAAAATACTTAAAAGCTTCTATATAATTATGGATTATAGGTTTTTAAGGGT
TGAACACCTTTAGTTTAACCAATAAATGGTTGTCATGCTTAGCTTTGCATGTCGCAACCATCATG
AAAACTGA
Found at i:4088277 original size:20 final size:20
Alignment explanation
Indices: 4088243--4088305 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
4088233 TTGTACAGGA
* *
4088243 TTGCACTTCGATGCCTCTAT
1 TTGCACTTTGGTGCCTCTAT
*
4088263 TTGCACTTTGGTGCCACTGTAT
1 TTGCACTTTGGTG-C-CTCTAT
*
4088285 TTGCACTATGGTGCCTCTAT
1 TTGCACTTTGGTGCCTCTAT
4088305 T
1 T
4088306 AGCATTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
22 17 0.47
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTAT
Found at i:4092379 original size:51 final size:51
Alignment explanation
Indices: 4092255--4092416 Score: 234
Period size: 51 Copynumber: 3.1 Consensus size: 51
4092245 TTTGAGTACT
* * *
4092255 TCTGATTAGTGACAAGTGACAAGTGACAAGTAGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
4092306 TCTGATCAGTACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTG---A-T-C-AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
4092363 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
4092414 TCT
1 TCT
4092417 TTAAAGCTAC
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
51 50 0.50
52 1 0.01
53 1 0.01
54 2 0.02
55 1 0.01
57 45 0.45
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:4094770 original size:24 final size:24
Alignment explanation
Indices: 4094742--4094792 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
4094732 AACATCCACT
4094742 ATCACCTCATTTTGTCTAATTACC
1 ATCACCTCATTTTGTCTAATTACC
4094766 ATCACCTCATTTTGTCTAATTACC
1 ATCACCTCATTTTGTCTAATTACC
4094790 ATC
1 ATC
4094793 CAAGTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.41
Consensus pattern (24 bp):
ATCACCTCATTTTGTCTAATTACC
Found at i:4095197 original size:36 final size:36
Alignment explanation
Indices: 4095150--4095220 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
4095140 TATGTTTTGT
* *
4095150 TCTTGAGCTTATGTTTATGGATGGTTGAATATGAGG
1 TCTTGAGCTTATGTTTAAGAATGGTTGAATATGAGG
4095186 TCTTGAGCTTATGTTTAAGAATGGTTGAATATGAG
1 TCTTGAGCTTATGTTTAAGAATGGTTGAATATGAG
4095221 AAGAAACAAA
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:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (36 bp):
TCTTGAGCTTATGTTTAAGAATGGTTGAATATGAGG
Found at i:4095446 original size:19 final size:19
Alignment explanation
Indices: 4095422--4095485 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
4095412 AATCTTCAAG
* *
4095422 GATATGTAATCTTAGCTAT
1 GATATGCAATCTTAGATAT
4095441 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4095460 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
4095481 GATAT
1 GATAT
4095486 ATACAATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 22 0.54
21 19 0.46
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4095468 original size:21 final size:21
Alignment explanation
Indices: 4095423--4095498 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
4095413 ATCTTCAAGG
* *
4095423 ATATGTAATCTTAGCTATG--
1 ATATGCAATCTTAGATATGAT
4095442 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
4095463 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
4095484 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
4095499 AGATATGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 17 0.33
21 35 0.67
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:4095751 original size:23 final size:23
Alignment explanation
Indices: 4095707--4095751 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4095697 TCTTATTTTG
* *
4095707 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
4095730 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
4095752 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:4096067 original size:23 final size:22
Alignment explanation
Indices: 4096027--4096086 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
4096017 TTTTATGTAA
*
4096027 TATATATATTGTTTTATATATAG
1 TATACATA-TGTTTTATATATAG
* **
4096050 TATACGTATGTTTATATATATTT
1 TATACATATGTTT-TATATATAG
4096073 TATACATATGTTTT
1 TATACATATGTTTT
4096087 TATTTTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (22 bp):
TATACATATGTTTTATATATAG
Found at i:4098132 original size:69 final size:69
Alignment explanation
Indices: 4098004--4098147 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
4097994 TCCAGTGAGG
** *
4098004 TATAAGGTATAAGACCATAGCTCAGCTATGGAAACTAATAAAGTTCATCAGGATTGTAAACACGG
1 TATAAGGTATAAGACCATAGCTCAGCTATGGAAACTAATAAAGTTCATCAGGACAGTAAACACAG
4098069 GGAT
66 GGAT
* * * * * *
4098073 TATAAGGTGTAAGATCATAGCTCCGCTATGGCAACTAATAGAGTTTATC-GAGACAGTAAACACA
1 TATAAGGTATAAGACCATAGCTCAGCTATGGAAACTAATAAAGTTCATCAG-GACAGTAAACACA
4098137 GGGAT
65 GGGAT
4098142 TATAAG
1 TATAAG
4098148 CTATGAAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (69 bp):
TATAAGGTATAAGACCATAGCTCAGCTATGGAAACTAATAAAGTTCATCAGGACAGTAAACACAG
GGAT
Found at i:4099220 original size:23 final size:23
Alignment explanation
Indices: 4099177--4099220 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4099167 TTATTTAAAA
**
4099177 TAAAAATCAACCAATTTAACATT
1 TAAAAATCAACCAATAAAACATT
4099200 TAAAAAT-AATCCAATAAAACA
1 TAAAAATCAA-CCAATAAAACA
4099221 GTCTGAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAAATCAACCAATAAAACATT
Found at i:4107602 original size:42 final size:42
Alignment explanation
Indices: 4107556--4107658 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
4107546 GCAATCATGG
* * * *
4107556 TGGCACGTAAGTGCATCATTAGATGTACCGAAGTAAAGATAC
1 TGGCACATAAGTGCATCATTAGATATACCAAAGCAAAGATAC
* * * **
4107598 TGGCACATAAGTCCATCATTGGATATACTAAAGCAATTATAC
1 TGGCACATAAGTGCATCATTAGATATACCAAAGCAAAGATAC
4107640 TGGCACATAAGTGCATCAT
1 TGGCACATAAGTGCATCAT
4107659 CGGCTAAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (42 bp):
TGGCACATAAGTGCATCATTAGATATACCAAAGCAAAGATAC
Found at i:4108112 original size:189 final size:189
Alignment explanation
Indices: 4107792--4108361 Score: 1027
Period size: 189 Copynumber: 3.0 Consensus size: 189
4107782 TAACATAAGC
* * *
4107792 TCATTTTATACTAATTTCTTATATTAGCTAAGACATACAAATTTCTATTCAATTTAGTCCCTATC
1 TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
4107857 T-GAATATT-CAATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGA
66 TCG-ATATTAC-ATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGA
*
4107920 CGTTATGGCCAAATCTAGAGTTGTTACGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
129 CGTTATGGCCAAATCTGGAGTTGTTACGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
4107981 TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
1 TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
4108046 TCGATATTACATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGACG
66 TCGATATTACATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGACG
*
4108111 TTATGGCCAAATCTGGAGTTGTTTCGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
131 TTATGGCCAAATCTGGAGTTGTTACGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
4108170 TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
1 TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
4108235 TCGATATTACATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGACG
66 TCGATATTACATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGACG
* * * *
4108300 TTATGTCCAAATCTGGAGATGTTACGTAAAGCAGTTGTAAATTCAATTTTCAAAACCTT
131 TTATGGCCAAATCTGGAGTTGTTACGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
4108359 TCA
1 TCA
4108362 AAAATGTCAT
Statistics
Matches: 369, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
189 367 0.99
190 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (189 bp):
TCATTTTATACTAATTCCTTATATCAGCTAAGACATACAAATTTCTATTCAATTTTGTCCCTATC
TCGATATTACATTTCAACCATAGCATTTCAAGTCAATATGTAACACCCCAAACTCAACCTAGACG
TTATGGCCAAATCTGGAGTTGTTACGTAAAGCAGTTGTAAATCCAGTTTTCAAAACCTT
Found at i:4108754 original size:57 final size:57
Alignment explanation
Indices: 4108683--4108790 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
4108673 ATTGTAACTG
*
4108683 AGTCAAATAGAATATGAGTTTACGAAACTCAGTATGTAACAATAACTTGAAAATACC
1 AGTCAAATAGAATATGAGTTTACGAAACTCAATATGTAACAATAACTTGAAAATACC
* *
4108740 AGTCAAATAGAATATGAGTTTTCGAAACTCAATGTGTAACAATAACTTGAA
1 AGTCAAATAGAATATGAGTTTACGAAACTCAATATGTAACAATAACTTGAA
4108791 CAATTAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (57 bp):
AGTCAAATAGAATATGAGTTTACGAAACTCAATATGTAACAATAACTTGAAAATACC
Found at i:4114763 original size:18 final size:17
Alignment explanation
Indices: 4114711--4114773 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
4114701 AATGTGATTT
* *
4114711 GAAAGATAACAGAAAAA
1 GAAAGAAAAAAGAAAAA
* *
4114728 GAAAGAATAAAGGTAAAA
1 GAAAGAA-AAAAGAAAAA
4114746 GAAAGGAAAAAAGAAAAA
1 GAAA-GAAAAAAGAAAAA
4114764 GAAAAGAAAA
1 G-AAAGAAAA
4114774 GAATGGCAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 6 0.16
18 25 0.68
19 6 0.16
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.05
Consensus pattern (17 bp):
GAAAGAAAAAAGAAAAA
Found at i:4121308 original size:20 final size:21
Alignment explanation
Indices: 4121262--4121311 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4121252 GAATGAGCAT
**
4121262 GTATCGATATTTTTATCATGA
1 GTATCGATATTCGTATCATGA
*
4121283 GTATCGATATTCGTAT-ATGG
1 GTATCGATATTCGTATCATGA
4121303 GTATCGATA
1 GTATCGATA
4121312 CCAAAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (21 bp):
GTATCGATATTCGTATCATGA
Found at i:4122313 original size:29 final size:29
Alignment explanation
Indices: 4122271--4122331 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
4122261 ACCAATATGT
4122271 CCTGCTGAATGGAGCTTAGCTCGACATCC
1 CCTGCTGAATGGAGCTTAGCTCGACATCC
*
4122300 CCTGCTGAATGGAGCTTAGCTCGACATTC
1 CCTGCTGAATGGAGCTTAGCTCGACATCC
4122329 CCT
1 CCT
4122332 TATCTCTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (29 bp):
CCTGCTGAATGGAGCTTAGCTCGACATCC
Found at i:4122699 original size:50 final size:50
Alignment explanation
Indices: 4122622--4122722 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
4122612 ACATTATTCT
* * *
4122622 AATCAATGTCAAATAGAAGGAGTGTAGTTCTATACGGATTCTACTTGTGC
1 AATCAATGTCAAATAAAAGAAGAGTAGTTCTATACGGATTCTACTTGTGC
4122672 AATCAATGTCAAATAAAAGAAGAGTAGTTCTATACGGATTCTACTTGTGC
1 AATCAATGTCAAATAAAAGAAGAGTAGTTCTATACGGATTCTACTTGTGC
4122722 A
1 A
4122723 GCTTGGTCTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (50 bp):
AATCAATGTCAAATAAAAGAAGAGTAGTTCTATACGGATTCTACTTGTGC
Found at i:4125348 original size:82 final size:82
Alignment explanation
Indices: 4125221--4125376 Score: 249
Period size: 82 Copynumber: 1.9 Consensus size: 82
4125211 TATTTTGGAC
* *
4125221 TGCATCATGCTTGAACAACTATGTATATTATTGACGTCATTTGGTACCTACGCTATTTTTGTCCC
1 TGCATCATGCTTGAACAACTATGTATATTATTGACGTCATTTGGTACCTACACTATTTTTCTCCC
4125286 AATTTGGTATTTCGAAA
66 AATTTGGTATTTCGAAA
* * * * *
4125303 TGCATCATGCTTGAGCAACTATGTATATTGTTGATGTCATTTGGTACCTACATTTTTTTTCTCCC
1 TGCATCATGCTTGAACAACTATGTATATTATTGACGTCATTTGGTACCTACACTATTTTTCTCCC
4125368 AATTTGGTA
66 AATTTGGTA
4125377 CCTAAGTTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (82 bp):
TGCATCATGCTTGAACAACTATGTATATTATTGACGTCATTTGGTACCTACACTATTTTTCTCCC
AATTTGGTATTTCGAAA
Done.