Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 19 of 311
Found at i:5386391 original size:87 final size:87
Alignment explanation
Indices: 5386221--5386392 Score: 190
Period size: 87 Copynumber: 2.0 Consensus size: 87
5386211 GACGCCAAAC
* * * * *
5386221 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTTCTTCATCGTAAGCACG
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCATCATAAACACA
5386286 TGAAAGCCAAATCAGCTATGAT
66 TGAAAGCCAAATCAGCTATGAT
*
5386308 TTCGATTTGTT-TCTTGTA-AATACA-AGGATGCCAAATCATCTTGGATCTGCTTCAGT-ATAAA
1 TTCGATTTGTTCTC-TG-ACAATACAGA-GATGCCAAATCATCTTAGATCTGCTTCA-TCATAAA
* * * *
5386369 CATATGAAGGCCAGATCTGCTATG
62 CACATGAAAGCCAAATCAGCTATG
5386393 TGTCTACTCT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
86 3 0.04
87 66 0.93
88 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (87 bp):
TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCATCATAAACACA
TGAAAGCCAAATCAGCTATGAT
Found at i:5386458 original size:206 final size:207
Alignment explanation
Indices: 5386017--5386567 Score: 813
Period size: 206 Copynumber: 2.7 Consensus size: 207
5386007 CTGCTTCTTT
* *
5386017 GATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTTAGT-GTAAGCACGCG
1 GATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCA-TCGTAAGCACGTG
* * * * *
5386081 AAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATACCAAACCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGA
* * ** * *
5386146 TCTTGCTTCAGTGAAATCATCTAAAGGTGAGATCTGCTATGTGTCTGCCCTCCGTCGAATATGGA
130 TCTTGCTTCAGTGAAAACATATAAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGGA
5386211 GACGCCAAACTTC
195 GACGCCAAACTTC
* *
5386224 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTTCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
5386289 AAGCCAAATCAGCTATGAT-TTCGATTTGTTTCTTGTAAATACAAGGATGCCAAATCATCTTGGA
66 AAGCCAAATCAGCTATG-TCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGA
* *
5386353 TC-TGCTTCAGT-ATAAACATATGAAGGCCAGATCTGCTATGTGTCTACTCTCCATCGAATATGG
130 TCTTGCTTCAGTGA-AAACATATAAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGG
5386416 AGACGCCAAACTTC
194 AGACGCCAAACTTC
* * * *
5386430 GATTTGTTCTTTGACAATACATAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * *
5386495 AAGCCAAATCAGCTATGTCTTCGGTTTGTTTCTTGTAAGTACAAGGATGCCATACCATCTTAGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGAT
5386560 CTTGCTTC
131 CTTGCTTC
5386568 TGCCAGATCT
Statistics
Matches: 310, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
205 2 0.01
206 185 0.60
207 122 0.39
208 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (207 bp):
GATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGAT
CTTGCTTCAGTGAAAACATATAAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGGAG
ACGCCAAACTTC
Found at i:5388709 original size:45 final size:45
Alignment explanation
Indices: 5388645--5388733 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
5388635 GTCTTTCCGT
*
5388645 GTCTTGTACAAGATATCTCCGTCTGAGACATAGTCGCAAGCTAAA
1 GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAAA
*
5388690 GTCTTGTATAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAA
1 GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAA
5388734 CCTCCTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (45 bp):
GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAAA
Found at i:5394726 original size:14 final size:16
Alignment explanation
Indices: 5394691--5394727 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5394681 CAAACGATGC
5394691 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
5394706 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
5394721 -ATGCAAA
1 GATGCAAA
5394728 AGGATATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:5394770 original size:14 final size:14
Alignment explanation
Indices: 5394747--5394776 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5394737 ATTCTGGTAC
5394747 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
5394761 AACTTTATTTAGAA
1 AACTTCATTTAGAA
5394775 AA
1 AA
5394777 ATAATATATT
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:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:5398549 original size:19 final size:19
Alignment explanation
Indices: 5398497--5398549 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
5398487 TAATATACAA
* *
5398497 TATATAATATAAAAA-AAT
1 TATATAAAACAAAAATAAT
* *
5398515 T-TATAAAAGAATAATAAT
1 TATATAAAACAAAAATAAT
5398533 TATATAAAACAAAAATA
1 TATATAAAACAAAAATA
5398550 TAATGATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 13 0.46
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TATATAAAACAAAAATAAT
Found at i:5398792 original size:23 final size:23
Alignment explanation
Indices: 5398733--5398792 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
5398723 GTAATAATAG
*
5398733 AATATAAG-TAAAATAATTATTA
1 AATATAAGTTAAAATAAGTATTA
* *
5398755 ACATATAAATAAAAATAAGTA-TA
1 A-ATATAAGTTAAAATAAGTATTA
5398778 TAATATAAGTTAAAA
1 -AATATAAGTTAAAA
5398793 CTTTTAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 19 0.63
24 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
AATATAAGTTAAAATAAGTATTA
Found at i:5398931 original size:14 final size:14
Alignment explanation
Indices: 5398912--5398950 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5398902 AATATAATAT
5398912 ATATAAATAATACA
1 ATATAAATAATACA
**
5398926 ATAT-AATAATATT
1 ATATAAATAATACA
5398939 ATATAAATAATA
1 ATATAAATAATA
5398951 ATGTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAATAATACA
Found at i:5398960 original size:27 final size:26
Alignment explanation
Indices: 5398905--5398963 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
5398895 GTAAAAAAAT
*
5398905 ATAATATATATAAATAATACAATATA
1 ATAATATATATAAATAATACAATAAA
*
5398931 ATAATATTATATAAATAATA-ATGTAAA
1 ATAATA-TATATAAATAATACA-ATAAA
5398958 ATAATA
1 ATAATA
5398964 CTAATTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATAATATATATAAATAATACAATAAA
Found at i:5398997 original size:3 final size:3
Alignment explanation
Indices: 5398977--5399040 Score: 51
Period size: 3 Copynumber: 20.3 Consensus size: 3
5398967 ATTTGTGAAA
*
5398977 AAT AAT ATAT AGT AAAT AAT AAT AAT ACA- AAT AAT ATAT AAT AAT -AT
1 AAT AAT A-AT AAT -AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT
*
5399024 AAT TAT AAT ATAT AAT A
1 AAT AAT AAT A-AT AAT A
5399041 CAAAGATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
2 3 0.06
3 35 0.70
4 12 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:5399019 original size:19 final size:20
Alignment explanation
Indices: 5398902--5399040 Score: 71
Period size: 20 Copynumber: 7.0 Consensus size: 20
5398892 TATGTAAAAA
*
5398902 AATATAATAT-ATATA-AAT
1 AATACAATATAATATATAAT
*
5398920 AATACAATATAATA-ATATT
1 AATACAATATAATATATAAT
* *
5398939 ATATA-AATAATAATGTAAAAT
1 A-ATACAAT-ATAATATATAAT
** *
5398960 AATACTAAT-TTGTGA-AAAAT
1 AATAC-AATATAAT-ATATAAT
*
5398980 AATA-TATAGTAA-ATAATAAT
1 AATACAATA-TAATAT-ATAAT
5399000 AATACAA-ATAATATATAAT
1 AATACAATATAATATATAAT
*
5399019 AATATAATTATAATATATAAT
1 AATACAA-TATAATATATAAT
5399040 A
1 A
5399041 CAAAGATATA
Statistics
Matches: 91, Mismatches: 14, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
18 13 0.14
19 23 0.25
20 34 0.37
21 18 0.20
22 3 0.03
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (20 bp):
AATACAATATAATATATAAT
Found at i:5400903 original size:78 final size:78
Alignment explanation
Indices: 5400768--5401391 Score: 869
Period size: 78 Copynumber: 8.0 Consensus size: 78
5400758 GTGTTTACGC
* * * ** * * *
5400768 TGAAGCAGATCTAAGATGATATGGCTTCTCCATATTCGACGGAAAGCAGATCAAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5400833 ATCTGACCTTCAT
66 ATCTGACCTTCAT
* * **
5400846 TGAAGCAGATCCAAGATGATTTAGCATCTCTGTATTAGACAGAGAGCAGATCGAAGACACGGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
*
5400911 AT-TGGACCTTTAT
66 ATCT-GACCTTCAT
* ** *
5400924 TGAAGTAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5400989 ATCTGACCTTCAT
66 ATCTGACCTTCAT
* * * * *
5401002 TGAAGCAGATCCAAGATGGTTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACATCAA
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5401067 AT-TGCACCTTCAT
66 ATCTG-ACCTTCAT
** *
5401080 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5401145 ATCTGACCTTCAT
66 ATCTGACCTTCAT
* * *
5401158 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGTAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5401223 ATCTGACCTTCAT
66 ATCTGACCTTCAT
* * * * *
5401236 TGAAGCAGATCCAAGATGATTTGGCATCTTTGTATTAGATAGG-GAGCAGATCAAAGCCATAACA
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGA-CGGAGAGCAGATCGAAGACATAGCA
5401300 GAT-TGGACCTTCAT
65 GATCT-GACCTTCAT
* *
5401314 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
5401379 ATCTGACCTTCAT
66 ATCTGACCTTCAT
5401392 GTGTTTACAT
Statistics
Matches: 480, Mismatches: 58, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
77 6 0.01
78 468 0.98
79 6 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (78 bp):
TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACATAGCAG
ATCTGACCTTCAT
Found at i:5401533 original size:45 final size:45
Alignment explanation
Indices: 5401331--5401559 Score: 225
Period size: 45 Copynumber: 5.1 Consensus size: 45
5401321 GATCCAAGAT
*
5401331 GATTTGGCATCTCTGTATTAAACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAGCA
* * * * * * *
5401378 GATCTGACCT-TCATGTGTTTACATC--GAAGCAGATCCAAGAT-GACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAG-CA
* *
5401423 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
* * *
5401467 GTTTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
* * *
5401512 GATTTGGCGTCTCTGTATTAGACGGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
5401557 GAT
1 GAT
5401560 ATCGCCTTCT
Statistics
Matches: 146, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 43 0.29
45 71 0.49
46 4 0.03
47 22 0.15
48 4 0.03
49 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
Found at i:5401931 original size:14 final size:15
Alignment explanation
Indices: 5401912--5401967 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
5401902 AATCTTTAAT
5401912 GATATG-CAATCTTA
1 GATATGACAATCTTA
5401926 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
5401943 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
5401961 GATATGA
1 GATATGA
5401968 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:5401934 original size:19 final size:19
Alignment explanation
Indices: 5401910--5401981 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
5401900 ATAATCTTTA
5401910 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5401929 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5401946 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5401964 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5401982 ATATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5401956 original size:35 final size:37
Alignment explanation
Indices: 5401910--5401988 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
5401900 ATAATCTTTA
5401910 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
5401946 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
5401982 AT-ATATG
1 ATGATATG
5401989 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 21 0.52
36 9 0.22
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:5402220 original size:18 final size:19
Alignment explanation
Indices: 5402180--5402221 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5402170 TCCCTCTTAC
5402180 GTTCTTATTTTATACGGTTT
1 GTTCTTATTTTATAC-GTTT
*
5402200 GTTCTTATTTTATTC-TTT
1 GTTCTTATTTTATACGTTT
5402218 GTTC
1 GTTC
5402222 ATCTTCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (19 bp):
GTTCTTATTTTATACGTTT
Found at i:5402295 original size:17 final size:17
Alignment explanation
Indices: 5402271--5402305 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5402261 TGTTTCCCTG
*
5402271 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
5402289 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
5402306 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:5412711 original size:23 final size:23
Alignment explanation
Indices: 5412685--5412732 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5412675 TGAAGAGAAG
*
5412685 AAGCGTAAGGATTGAAAGGCGTT
1 AAGCGTAAGGATCGAAAGGCGTT
*
5412708 AAGCGTAAGGATCGAAAGGTGTT
1 AAGCGTAAGGATCGAAAGGCGTT
5412731 AA
1 AA
5412733 CACAATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (23 bp):
AAGCGTAAGGATCGAAAGGCGTT
Found at i:5423412 original size:85 final size:85
Alignment explanation
Indices: 5423293--5423458 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 85
5423283 TAAGTCTTCG
* * * * *
5423293 TTTGGAAAAAAATTAATATTGAATAAAATCTTGTTAAACGACGGGAATAAATCCTGAAATAGATT
1 TTTGAAAAAAAATTAAAATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGATT
5423358 TTATTTAA-TTTAATTCTAA
66 TTATTTAATTTTAATTCTAA
* * ** *
5423377 TTTGAAAACAAAATTAAAATCGAATAGAATCTTGTTAATCGGTGGGAATAAATCCTAAAACATAT
1 TTTGAAAA-AAAATTAAAATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGAT
5423442 TTTATTTAATTTTAATT
65 TTTATTTAATTTTAATT
5423459 TCTCATTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
84 7 0.10
85 56 0.80
86 7 0.10
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (85 bp):
TTTGAAAAAAAATTAAAATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGATT
TTATTTAATTTTAATTCTAA
Found at i:5423799 original size:19 final size:20
Alignment explanation
Indices: 5423771--5423811 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5423761 AAATAGATAA
5423771 ATATAAAT-AAAT-ATTTAT
1 ATATAAATAAAATAATTTAT
5423789 ATATAAAATAAAATAATTTAT
1 ATAT-AAATAAAATAATTTAT
5423810 AT
1 AT
5423812 TCCAATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 4 0.20
21 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAATAAAATAATTTAT
Found at i:5429662 original size:19 final size:19
Alignment explanation
Indices: 5429638--5429687 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
5429628 AATCTTTAAG
5429638 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5429657 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5429676 GATATGCAATCT
1 GATATGCAATCT
5429688 CGAAGATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5430087 original size:4 final size:4
Alignment explanation
Indices: 5430078--5430102 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5430068 AAACAAAAGA
5430078 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
5430103 TCTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5431319 original size:21 final size:22
Alignment explanation
Indices: 5431293--5431335 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5431283 GATCCTCCCA
5431293 CATTTT-TT-ATTTTTATAATTT
1 CATTTTATTCATTTTTA-AATTT
5431314 CATTTTATTCATTTTTAAATTT
1 CATTTTATTCATTTTTAAATTT
5431336 AGCTCTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
CATTTTATTCATTTTTAAATTT
Found at i:5431681 original size:25 final size:24
Alignment explanation
Indices: 5431653--5431705 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
5431643 ATATAAATTT
5431653 TATTA-TATGTTATATATATTTATTA
1 TATTACTATGTTAT-TATATTT-TTA
*
5431678 TATTACTTATTTTATTATATTTTTA
1 TATTAC-TATGTTATTATATTTTTA
5431703 TAT
1 TAT
5431706 GTAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 11 0.44
26 7 0.28
27 7 0.28
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTACTATGTTATTATATTTTTA
Found at i:5431703 original size:8 final size:9
Alignment explanation
Indices: 5431651--5431768 Score: 66
Period size: 9 Copynumber: 12.7 Consensus size: 9
5431641 ATATATAAAT
5431651 TTTATTATA
1 TTTATTATA
5431660 TGTTATATATA
1 T-TTAT-TATA
5431671 TTTATTATA
1 TTTATTATA
5431680 -TTACTTAT-
1 TTTA-TTATA
5431688 TTTATTATA
1 TTTATTATA
5431697 TTT-TTATA
1 TTTATTATA
* **
5431705 TGTAAAATA
1 TTTATTATA
* *
5431714 TTTGTTACA
1 TTTATTATA
5431723 -TTATTAT-
1 TTTATTATA
*
5431730 TATTATACATA
1 T-TTAT-TATA
5431741 TTTCATATTATA
1 -TT--TATTATA
5431753 TTTCATTATA
1 TTT-ATTATA
5431763 TTTATT
1 TTTATT
5431769 TAAGTTTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
8 19 0.23
9 30 0.36
10 19 0.23
11 8 0.10
12 4 0.05
13 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTATTATA
Found at i:5435722 original size:12 final size:12
Alignment explanation
Indices: 5435705--5435737 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
5435695 TAAAGTTATT
5435705 AAAAAGAGAAAG
1 AAAAAGAGAAAG
5435717 AAAAAGAGAAAG
1 AAAAAGAGAAAG
5435729 AGAAAAGAG
1 A-AAAAGAG
5435738 GGTCACCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:5438290 original size:21 final size:21
Alignment explanation
Indices: 5438266--5438335 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
5438256 TTCTATTTAA
5438266 AAAAAAG-GAAAAAAAGAAAAG
1 AAAAAAGAGAAAAAAA-AAAAG
*
5438287 -AAAAAGAGAAAAAAAATTAA-
1 AAAAAAGAGAAAAAAAA-AAAG
5438307 AAAAAAGAGAAAAAATAAAAAAG
1 AAAAAAGAG-AAAAA-AAAAAAG
5438330 AAAAAA
1 AAAAAA
5438336 TGGAGAGGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 7 0.17
21 18 0.44
22 7 0.17
23 9 0.22
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAGAGAAAAAAAAAAAG
Found at i:5438319 original size:11 final size:11
Alignment explanation
Indices: 5438264--5438321 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
5438254 ACTTCTATTT
5438264 AAAAAAAAG-G
1 AAAAAAAAGAG
5438274 -AAAAAAAGA-
1 AAAAAAAAGAG
5438283 AAAGAAAAAGAG
1 AAA-AAAAAGAG
**
5438295 AAAAAAAA-TT
1 AAAAAAAAGAG
5438305 AAAAAAAAGAG
1 AAAAAAAAGAG
5438316 AAAAAA
1 AAAAAA
5438322 TAAAAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 8 0.21
10 10 0.26
11 18 0.46
12 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:5439340 original size:44 final size:44
Alignment explanation
Indices: 5439290--5439391 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
5439280 AGCGCCTTAA
* *
5439290 TCCCCTAAGTAGTAGGGTAACAGGTTAAATTTACAGATCTTATC
1 TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
* * *
5439334 TCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGGATCTTATC
1 TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
*
5439378 T-CCTTAAGTAGTAG
1 TCCCCTAAGTAGTAG
5439392 TGGAGTAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 11 0.22
44 40 0.78
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
Found at i:5439616 original size:87 final size:87
Alignment explanation
Indices: 5439453--5439621 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
5439443 TAAAGTATAG
* ** * *
5439453 CAGATCTGGCCTTCAGGTGTTCATGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
1 CAGATCTGACCTTCAGGTGTTCACACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTATTTAC
*
5439518 AAGGAGCAAATCAAAGACATAA
66 AAGAAGCAAATCAAAGACATAA
* *
5439540 CAGATTTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATATC-TGTATTGT
1 CAGATCTGACCTTCAGGTGTTCACACTGAAGCAGATCCAAGATGATTTGGCAT-TCTTGTATT-T
5439604 -CAGAGAAG-AAATCAAAGA
64 ACA-AGAAGCAAATCAAAGA
5439622 AACAGATTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
87 64 0.90
88 7 0.10
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (87 bp):
CAGATCTGACCTTCAGGTGTTCACACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTATTTAC
AAGAAGCAAATCAAAGACATAA
Found at i:5439862 original size:220 final size:220
Alignment explanation
Indices: 5439480--5440299 Score: 1327
Period size: 220 Copynumber: 3.7 Consensus size: 220
5439470 TGTTCATGCT
* *
5439480 GAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAACAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
* * *
5439545 TTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATATCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
* *
5439610 AGAAATCAAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
5439675 TCTGACCTTTGGATGTTTTCACATC
196 TCTGACCTTTGGATGTTTTCACATC
5439700 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
* * *
5439765 CTGACCTTTAGGTGTTTACATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
* *
5439830 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTTGATAGAGAGCAGATCGAAGACATAGCAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
5439895 TCTGACCTTTGGATGTTTTCACATC
196 TCTGACCTTTGGATGTTTTCACATC
**
5439920 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCGTAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
*
5439985 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATGTCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
* * * *
5440050 ACAAATTGAATAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATTGAAGACATAGCAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
* * *
5440115 TCTGACCTTCGGATATTTTCACATT
196 TCTGACCTTTGGATGTTTTCACATC
* * * *
5440140 GAAGCAGATCCAAGATGATTTAGCATCCTTGTGTTTACAAGGAGCAAATCGAAGACATAGTAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
* *
5440205 CTGACCTTCAGGTGTTTACGCTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTATCA-AGG
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGA-G
* * * *
5440269 AACGAATCGAAGGTAGCAGATTTGACATCTC
130 AACAAATCGAA-GAAACAGATTTGGCATCTC
5440300 TGTATTTGAC
Statistics
Matches: 560, Mismatches: 38, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
219 1 0.00
220 544 0.97
221 15 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (220 bp):
GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
TCTGACCTTTGGATGTTTTCACATC
Found at i:5440055 original size:87 final size:89
Alignment explanation
Indices: 5439869--5440055 Score: 233
Period size: 87 Copynumber: 2.1 Consensus size: 89
5439859 CATATTTGAT
* * *
5439869 AGAGAGCAGATCGAAGACATAGCAGATCTGACCTTTGGATGTTTTCACATCGAAGCAGATCCAAG
1 AGAGAGCAAATCGAAGACATAGCAGATCTGACCTTAGGATGTTTACACATCGAAGCAGATCCAAG
* *
5439934 ATGATTTGGCATTCTTGTGTTTAC
66 ATGATTTGACATTCTTGTATTTAC
*
5439958 A-AGGAGCAAATCGTAGACATAGCAGATCTGACCTTCAGG-TGTTTACAC-T-GAAGCAGATCCA
1 AGA-GAGCAAATCGAAGACATAGCAGATCTGACCTT-AGGATGTTTACACATCGAAGCAGATCCA
5440019 AGATGATTTGACATGTC-TGTATTGT-C
64 AGATGATTTGACAT-TCTTGTATT-TAC
*
5440045 AGAGAACAAAT
1 AGAGAGCAAAT
5440056 TGAATAAACA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
87 39 0.45
88 6 0.07
89 39 0.45
90 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (89 bp):
AGAGAGCAAATCGAAGACATAGCAGATCTGACCTTAGGATGTTTACACATCGAAGCAGATCCAAG
ATGATTTGACATTCTTGTATTTAC
Found at i:5440269 original size:87 final size:89
Alignment explanation
Indices: 5440092--5440280 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 89
5440082 ATTCGACGGA
* * * *
5440092 GAGCAGATTGAAGACATAGCAGATCTGACCTTCGGATATTTTCACATTGAAGCAGATCCAAGATG
1 GAGCAAATCGAAGACATAGCAGATCTGACCTTCGGATAGTTTCACACTGAAGCAGATCCAAGATG
*
5440157 ATTTAGCATCCTTGTGTTTACAAG
66 ATTTAGCATCCTTGTATTTACAAG
* *
5440181 GAGCAAATCGAAGACATAGTAGATCTGACCTTCAGG-T-GTTT-ACGCTGAAGCAGATCCAAGAT
1 GAGCAAATCGAAGACATAGCAGATCTGACCTTC-GGATAGTTTCACACTGAAGCAGATCCAAGAT
5440243 GATTT-GACAT-CTCTGTA-TTATCAAG
65 GATTTAG-CATCCT-TGTATTTA-CAAG
* *
5440268 GAACGAATCGAAG
1 GAGCAAATCGAAG
5440281 GTAGCAGATT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
86 6 0.07
87 45 0.52
88 3 0.03
89 31 0.36
90 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (89 bp):
GAGCAAATCGAAGACATAGCAGATCTGACCTTCGGATAGTTTCACACTGAAGCAGATCCAAGATG
ATTTAGCATCCTTGTATTTACAAG
Found at i:5440698 original size:16 final size:17
Alignment explanation
Indices: 5440648--5440698 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
5440638 ATGGAAATAT
*
5440648 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
5440665 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
5440684 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
5440699 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:5440717 original size:22 final size:21
Alignment explanation
Indices: 5440658--5440700 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
5440648 AATCTTTAAG
5440658 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
5440677 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
5440698 GAT
1 GAT
5440701 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:5441328 original size:20 final size:22
Alignment explanation
Indices: 5441289--5441329 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5441279 TGCATGCATT
*
5441289 ATGTTTTTCTTTTAGTTTATTC
1 ATGTTTTTCATTTAGTTTATTC
5441311 ATGTTTTT-ATTT-GTTTATT
1 ATGTTTTTCATTTAGTTTATT
5441330 ATCTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (22 bp):
ATGTTTTTCATTTAGTTTATTC
Found at i:5443333 original size:28 final size:28
Alignment explanation
Indices: 5443293--5443381 Score: 115
Period size: 28 Copynumber: 3.2 Consensus size: 28
5443283 CCAAAGGTGG
*
5443293 GTGCAAGCCAAAGTGGTGGACAGTCTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
* *
5443321 GTGCAAGCCAAAGTGGCGGAGATTCTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
* * * *
5443349 ATGCAAGTCAAAGTGGCAGACAGTTTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
5443377 GTGCA
1 GTGCA
5443382 CTCCAAAAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (28 bp):
GTGCAAGCCAAAGTGGCGGACAGTCTAA
Found at i:5443388 original size:28 final size:28
Alignment explanation
Indices: 5443293--5443393 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 28
5443283 CCAAAGGTGG
* * *
5443293 GTGCAAGCCAAAGTGGTGGACAGTCTAA
1 GTGCAATCCAAAGTGGCGGACAGTTTAA
* *
5443321 GTGCAAGCCAAAGTGGCGGAGA-TTCTAA
1 GTGCAATCCAAAGTGGCGGACAGTT-TAA
* *
5443349 ATGCAAGT-CAAAGTGGCAGACAGTTTAA
1 GTGCAA-TCCAAAGTGGCGGACAGTTTAA
*
5443377 GTGCACTCCAAAAGTGG
1 GTGCAATCC-AAAGTGG
5443394 GTGAAAGTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
27 2 0.03
28 48 0.81
29 9 0.15
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.19
Consensus pattern (28 bp):
GTGCAATCCAAAGTGGCGGACAGTTTAA
Found at i:5443443 original size:28 final size:28
Alignment explanation
Indices: 5443402--5443461 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
5443392 GGGTGAAAGT
* * *
5443402 CAAAGTGGCAGATAGTCTAAGTGCAAGC
1 CAAAATGGAAGATAGTCTAAATGCAAGC
*
5443430 CAAAATGGAAGATAGTCTAAATGCAAGT
1 CAAAATGGAAGATAGTCTAAATGCAAGC
5443458 CAAA
1 CAAA
5443462 GTTAGTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.18
Consensus pattern (28 bp):
CAAAATGGAAGATAGTCTAAATGCAAGC
Found at i:5447898 original size:56 final size:56
Alignment explanation
Indices: 5447812--5447931 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
5447802 ACAAGGGATG
5447812 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
5447868 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
5447924 ATGGGCAA
1 ATGGGCAA
5447932 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:5449143 original size:40 final size:39
Alignment explanation
Indices: 5449059--5449243 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 39
5449049 TCGAATGATG
* * * *
5449059 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5449099 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
5449139 TCCGGGCTAAGCCCGAAGGCA-TTGCTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTG-TGCGAGTTACTAAA
*
5449178 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
5449219 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
5449244 AATGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.02
39 31 0.25
40 77 0.62
41 13 0.10
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5449195 original size:79 final size:80
Alignment explanation
Indices: 5449059--5449241 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
5449049 TCGAATGATG
* *
5449059 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
5449124 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
5449138 TTCCGGGCTAAG-CCCGAAGGCATTGCTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTG-TGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
5449200 TTTGTGCGAGTTACTATA
63 TTTGTGCGAGATACTATA
* *
5449218 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
5449242 TGAATGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 61 0.69
80 27 0.30
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:5449274 original size:79 final size:78
Alignment explanation
Indices: 5449111--5449276 Score: 187
Period size: 79 Copynumber: 2.1 Consensus size: 78
5449101 CGGACTAAGA
*
5449111 TCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGCTGCGAGTTACTA
1 TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATT-CTGCGAGTTACTA
*
5449176 AATCCGGGTTAAGT
65 AATCCGGGTTAAAT
* * * *
5449190 CCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT-TGAATGAG-TA
1 TCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTCTG--CGAGTTA
*
5449252 GCTATATCC-GGTTAAAT
62 -CTAAATCCGGGTTAAAT
5449269 TCCGAAGG
1 TCCGAAGG
5449277 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
78 4 0.05
79 48 0.65
80 22 0.30
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTCTGCGAGTTACTAA
ATCCGGGTTAAAT
Found at i:5451235 original size:14 final size:14
Alignment explanation
Indices: 5451214--5451254 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5451204 TTGCAACTTG
5451214 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
5451228 TGCAACTTGCAAAT
1 CACAACTTGCACAT
5451242 CACAACTTGCACA
1 CACAACTTGCACA
5451255 ATTAGGTTAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:5456463 original size:4 final size:4
Alignment explanation
Indices: 5456454--5456508 Score: 92
Period size: 4 Copynumber: 13.8 Consensus size: 4
5456444 GAAATAAAAT
*
5456454 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
5456502 ATGC ATA
1 ATAC ATA
5456509 TAAATGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:5456680 original size:40 final size:40
Alignment explanation
Indices: 5456634--5456712 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
5456624 AAACAGTAAT
5456634 TAGATAGTAATGAAACAAAGTTAACCTTGGGTTTTTGTAC
1 TAGATAGTAATGAAACAAAGTTAACCTTGGGTTTTTGTAC
5456674 TAGATAGTAATGAAACAAAGTTAACCTTGGGTTTTTGTA
1 TAGATAGTAATGAAACAAAGTTAACCTTGGGTTTTTGTA
5456713 TTTTACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (40 bp):
TAGATAGTAATGAAACAAAGTTAACCTTGGGTTTTTGTAC
Found at i:5457777 original size:48 final size:48
Alignment explanation
Indices: 5457724--5457832 Score: 110
Period size: 49 Copynumber: 2.2 Consensus size: 48
5457714 ATGACTCGAT
* * *
5457724 AATGATGATTTTACTGTTTGCATATTCTACCATCCCGAGTGGCCCAAC
1 AATGATGATTTTAATATTTGCATATTCTACCATCCCGAGCGGCCCAAC
* * * * ** *
5457772 AATGATGGCTTTGAATATTTGCATGTTCTATCATCTTGAGCGGCCTAAC
1 AATGAT-GATTTTAATATTTGCATATTCTACCATCCCGAGCGGCCCAAC
*
5457821 AATGATGGTTTT
1 AATGATGATTTT
5457833 GAATCATTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
48 10 0.21
49 38 0.79
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (48 bp):
AATGATGATTTTAATATTTGCATATTCTACCATCCCGAGCGGCCCAAC
Found at i:5457822 original size:49 final size:49
Alignment explanation
Indices: 5457740--5457836 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
5457730 GATTTTACTG
*
5457740 TTTGCATATTCTACCATCCCGAGTGGCCCAACAATGATGGCTTTGAATA
1 TTTGCATATTCTACCATCCCGAGCGGCCCAACAATGATGGCTTTGAATA
* * ** * *
5457789 TTTGCATGTTCTATCATCTTGAGCGGCCTAACAATGATGGTTTTGAAT
1 TTTGCATATTCTACCATCCCGAGCGGCCCAACAATGATGGCTTTGAAT
5457837 CATTATATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (49 bp):
TTTGCATATTCTACCATCCCGAGCGGCCCAACAATGATGGCTTTGAATA
Found at i:5458701 original size:20 final size:20
Alignment explanation
Indices: 5458658--5458697 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5458648 GGTTAACATT
5458658 AGTTAAATATTAATTAATTA
1 AGTTAAATATTAATTAATTA
*
5458678 AGTTAATTA-TAATTAATTA
1 AGTTAAATATTAATTAATTA
5458697 A
1 A
5458698 AGTTTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AGTTAAATATTAATTAATTA
Found at i:5461062 original size:35 final size:35
Alignment explanation
Indices: 5461019--5461183 Score: 233
Period size: 35 Copynumber: 4.7 Consensus size: 35
5461009 TCCATAGAAA
* *
5461019 AGTTGTGAAATGTAGGTATGGTATCATCCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
* *
5461054 ATTTGTGAAACGTAGGTATGGTATTAACCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
5461089 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
** **
5461124 AGTTAAGAAACGTAGGTATGAAATT-TCCCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTAT-CCATACTG
*
5461159 AGTTGTGAAATGTAGGTATGGTATT
1 AGTTGTGAAACGTAGGTATGGTATT
5461184 TCAACGAGGA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 1 0.01
35 113 0.99
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (35 bp):
AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
Found at i:5461584 original size:5 final size:5
Alignment explanation
Indices: 5461574--5461605 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5461564 TTGTGTGTTC
5461574 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5461606 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5461593 original size:14 final size:14
Alignment explanation
Indices: 5461574--5461604 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5461564 TTGTGTGTTC
5461574 TTTATTTTATTTTA
1 TTTATTTTATTTTA
5461588 TTTATTTTATTTTA
1 TTTATTTTATTTTA
5461602 TTT
1 TTT
5461605 TTCACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:5466039 original size:5 final size:5
Alignment explanation
Indices: 5466029--5466060 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5466019 TTGTGTGTTC
5466029 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5466061 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5466048 original size:14 final size:14
Alignment explanation
Indices: 5466029--5466059 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5466019 TTGTGTGTTC
5466029 TTTATTTTATTTTA
1 TTTATTTTATTTTA
5466043 TTTATTTTATTTTA
1 TTTATTTTATTTTA
5466057 TTT
1 TTT
5466060 TTCACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:5466340 original size:5 final size:5
Alignment explanation
Indices: 5466330--5466361 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5466320 TTGTGTGTTC
5466330 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5466362 TCATAGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5466344 original size:9 final size:9
Alignment explanation
Indices: 5466330--5466360 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5466320 TTGTGTGTTC
5466330 TTTATTTTA
1 TTTATTTTA
5466339 TTTATTTTA
1 TTTATTTTA
5466348 TTTTATTTTA
1 -TTTATTTTA
5466358 TTT
1 TTT
5466361 TTCATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5473378 original size:56 final size:56
Alignment explanation
Indices: 5473312--5473425 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
5473302 AGAAACAGTA
*
5473312 TAGACATTGTCTAAGCCTTTGTTCCAGTCCATAACAAAGCTTTTATCTATCATGGC
1 TAGAAATTGTCTAAGCCTTTGTTCCAGTCCATAACAAAGCTTTTATCTATCATGGC
*
5473368 TAGAAATTGTCTAAGCCTTTGTTCCAGTCTATAACAAAGCTTTTATCTATCATGGC
1 TAGAAATTGTCTAAGCCTTTGTTCCAGTCCATAACAAAGCTTTTATCTATCATGGC
5473424 TA
1 TA
5473426 CTGTCATGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (56 bp):
TAGAAATTGTCTAAGCCTTTGTTCCAGTCCATAACAAAGCTTTTATCTATCATGGC
Found at i:5481429 original size:5 final size:4
Alignment explanation
Indices: 5481395--5481436 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
5481385 TAAGGTTAAC
*
5481395 ATTA GTTA ATT- ATTA ATTA ATTA ACTTA ATATA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A-TTA AT-TA ATTA ATTA A
5481437 AGTTTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 3 0.09
4 22 0.67
5 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:5482568 original size:23 final size:21
Alignment explanation
Indices: 5482518--5482568 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5482508 AGCAAGTTAG
*
5482518 ATAGAAGGTCTGAGTAAGAAA
1 ATAGATGGTCTGAGTAAGAAA
* *
5482539 ATTGATGGTTTGAGTAAGAATAA
1 ATAGATGGTCTGAGTAAG-A-AA
5482562 ATAGATG
1 ATAGATG
5482569 AATCCAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.27, T:0.27
Consensus pattern (21 bp):
ATAGATGGTCTGAGTAAGAAA
Found at i:5494173 original size:59 final size:59
Alignment explanation
Indices: 5494096--5494219 Score: 221
Period size: 59 Copynumber: 2.1 Consensus size: 59
5494086 TGAGCAAATT
5494096 ACTTAAACACAAGGCATAAGTCAGGGATTTTCAAATAATCATATAAATAACCTCCCCAC
1 ACTTAAACACAAGGCATAAGTCAGGGATTTTCAAATAATCATATAAATAACCTCCCCAC
* *
5494155 ACTTAAACATAAGGCATAAGTCAGGGATTTTCAAATAATCATATAAATAACCTCCCTAC
1 ACTTAAACACAAGGCATAAGTCAGGGATTTTCAAATAATCATATAAATAACCTCCCCAC
*
5494214 ATTTAA
1 ACTTAA
5494220 GATGTACATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (59 bp):
ACTTAAACACAAGGCATAAGTCAGGGATTTTCAAATAATCATATAAATAACCTCCCCAC
Found at i:5494493 original size:6 final size:6
Alignment explanation
Indices: 5494468--5494578 Score: 98
Period size: 6 Copynumber: 18.5 Consensus size: 6
5494458 AATAAAGTTC
* * * **
5494468 AAAATAT AAAAA- CAAAAT AAACAT AAAAAG AAAAAT AAAAAT AAACCT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * **
5494516 AAAAAT AAACAT AAAGAG AAAAAT AAAAAT AACGAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
5494564 AAACAT AAAGAT AAA
1 AAAAAT AAAAAT AAA
5494579 TGTACTCAAT
Statistics
Matches: 82, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
5 4 0.05
6 74 0.90
7 4 0.05
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:5494522 original size:36 final size:36
Alignment explanation
Indices: 5494481--5494566 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
5494471 ATATAAAAAC
*
5494481 AAAATAAACATAAAAAGAAAAATAAAAATAAAC-CTA
1 AAAATAAACATAAAAAGAAAAATAAAAAT-AACGATA
*
5494517 AAAATAAACATAAAGAGAAAAATAAAAATAACGATA
1 AAAATAAACATAAAAAGAAAAATAAAAATAACGATA
*
5494553 AAAATAAAAATAAA
1 AAAATAAACATAAA
5494567 CATAAAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.07
36 43 0.93
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.14
Consensus pattern (36 bp):
AAAATAAACATAAAAAGAAAAATAAAAATAACGATA
Found at i:5494571 original size:18 final size:18
Alignment explanation
Indices: 5494481--5494578 Score: 108
Period size: 18 Copynumber: 5.4 Consensus size: 18
5494471 ATATAAAAAC
* * *
5494481 AAAATAAACATAAAAAGA
1 AAAATAAAAATAAACATA
*
5494499 AAAATAAAAATAAACCTA
1 AAAATAAAAATAAACATA
* * *
5494517 AAAATAAACATAAAGAGA
1 AAAATAAAAATAAACATA
5494535 AAAATAAAAAT-AACGATA
1 AAAATAAAAATAAAC-ATA
5494553 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACATA
*
5494571 AAGATAAA
1 AAAATAAA
5494579 TGTACTCAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
17 2 0.03
18 61 0.92
19 3 0.05
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAATAAAAATAAACATA
Found at i:5496451 original size:18 final size:17
Alignment explanation
Indices: 5496428--5496469 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
5496418 CCGTGCGGGT
5496428 AAGAGGAAAATGGGGAGA
1 AAGAGGAAAA-GGGGAGA
*
5496446 AAGAGG-AGAGGGGAGA
1 AAGAGGAAAAGGGGAGA
5496462 AAG-GGAAA
1 AAGAGGAAA
5496470 GAAAGGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.10
16 11 0.52
17 2 0.10
18 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (17 bp):
AAGAGGAAAAGGGGAGA
Found at i:5501858 original size:35 final size:35
Alignment explanation
Indices: 5501835--5502000 Score: 136
Period size: 35 Copynumber: 4.7 Consensus size: 35
5501825 GATCCATGGA
*
5501835 AAAGTTGTGAAACTTAGGTATGGTATCATCCATAC
1 AAAGTTGTGAAACGTAGGTATGGTATCATCCATAC
** * *
5501870 TGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
1 AAAGTTGTGAAACGTAGGTATGGTATCATCCATAC
** * *
5501905 TGAGTTGTGGAACGTAGGTATGGTATTATCCATAC
1 AAAGTTGTGAAACGTAGGTATGGTATCATCCATAC
** ** ** * *
5501940 TGAGTTAAGAAACGTAGGTACCGCAT-TTCCCATAC
1 AAAGTTGTGAAACGTAGGTATGGTATCAT-CCATAC
** *
5501975 CGAGTTGTGAAATGTAGGTATGGTAT
1 AAAGTTGTGAAACGTAGGTATGGTAT
5502001 GTCAATGAGG
Statistics
Matches: 109, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
34 1 0.01
35 108 0.99
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (35 bp):
AAAGTTGTGAAACGTAGGTATGGTATCATCCATAC
Found at i:5501936 original size:70 final size:70
Alignment explanation
Indices: 5501837--5502000 Score: 220
Period size: 70 Copynumber: 2.3 Consensus size: 70
5501827 TCCATGGAAA
* ** ** *
5501837 AGTTGTGAAACTTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCA
1 AGTTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTACCGCATTAACCA
*
5501902 TACTG
66 TACCG
* * **
5501907 AGTTGTGGAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAACGTAGGTACCGCATTTCCCA
1 AGTTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTACCGCATTAACCA
5501972 TACCG
66 TACCG
*
5501977 AGTTGTGAAATGTAGGTATGGTAT
1 AGTTGTGAAACGTAGGTATGGTAT
5502001 GTCAATGAGG
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 81 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (70 bp):
AGTTGTGAAACGTAGGTATGGTATCATCCATACTGAGTTAAGAAACGTAGGTACCGCATTAACCA
TACCG
Found at i:5508235 original size:12 final size:12
Alignment explanation
Indices: 5508220--5508251 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5508210 ATCGAACCAT
5508220 AAATATTTTTAA
1 AAATATTTTTAA
*
5508232 AAATATTTTTAG
1 AAATATTTTTAA
5508244 AAATATTT
1 AAATATTT
5508252 ATGGCATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
AAATATTTTTAA
Found at i:5509040 original size:13 final size:13
Alignment explanation
Indices: 5509024--5509049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5509014 CTCAGCACTT
5509024 GCACACGGATGTG
1 GCACACGGATGTG
5509037 GCACACGGATGTG
1 GCACACGGATGTG
5509050 TCCCTGTCAA
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:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
GCACACGGATGTG
Found at i:5519120 original size:35 final size:35
Alignment explanation
Indices: 5519081--5519242 Score: 218
Period size: 35 Copynumber: 4.6 Consensus size: 35
5519071 ATAGAAAAGC
* *
5519081 TGTGAAACGTAGGTATGGTATCATCCATACTGATT
1 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
*
5519116 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
5519151 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
** ** *
5519186 TAAGAAACGTAGGTATGACATT-TCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAT-CCATACTGAGT
* *
5519221 TGTGAAATGCAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
5519243 TCAATAAGGA
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
34 1 0.01
35 110 0.99
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
Found at i:5524226 original size:4 final size:4
Alignment explanation
Indices: 5524217--5524247 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5524207 GAAATCAAAT
5524217 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
5524248 TAAATGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:5530648 original size:49 final size:49
Alignment explanation
Indices: 5530595--5530691 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
5530585 ACTTTTACTG
5530595 TTTGCATATTCTACCATCCCAAGTGGCCCAACAATGATGGCTTTGAATA
1 TTTGCATATTCTACCATCCCAAGTGGCCCAACAATGATGGCTTTGAATA
* * *** *
5530644 TTTGCATATTTTATCATCTTGAGTGGCCTAACAATGATGGCTTTGAAT
1 TTTGCATATTCTACCATCCCAAGTGGCCCAACAATGATGGCTTTGAAT
5530692 CATTATATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (49 bp):
TTTGCATATTCTACCATCCCAAGTGGCCCAACAATGATGGCTTTGAATA
Found at i:5531565 original size:23 final size:20
Alignment explanation
Indices: 5531514--5531553 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5531504 GGTTAACATT
5531514 AGTTAATTATTAATTAATTA
1 AGTTAATTATTAATTAATTA
5531534 AGTTAATTA-TAATTAATTA
1 AGTTAATTATTAATTAATTA
5531553 A
1 A
5531554 AGTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AGTTAATTATTAATTAATTA
Found at i:5547883 original size:9 final size:9
Alignment explanation
Indices: 5547869--5547926 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 9
5547859 GGCTTCATTG
5547869 CAACTTGCA
1 CAACTTGCA
5547878 CAACTTGCA
1 CAACTTGCA
5547887 CAACTTGCA
1 CAACTTGCA
5547896 C-A-TTG--
1 CAACTTGCA
5547901 CAACTTGCA
1 CAACTTGCA
5547910 -AA--T-CA
1 CAACTTGCA
5547915 CAACTTGCA
1 CAACTTGCA
5547924 CAA
1 CAA
5547927 TTAGGTTAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
5 3 0.07
6 4 0.10
7 6 0.15
8 4 0.10
9 24 0.59
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.22
Consensus pattern (9 bp):
CAACTTGCA
Found at i:5547906 original size:14 final size:14
Alignment explanation
Indices: 5547864--5547925 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
5547854 TTTTAGGCTT
5547864 CATTGCAACTTGCA
1 CATTGCAACTTGCA
5547878 CAACTTGCACAACTTGCA
1 C-A-TTG--CAACTTGCA
5547896 CATTGCAACTTGCA
1 CATTGCAACTTGCA
* **
5547910 AATCACAACTTGCA
1 CATTGCAACTTGCA
5547924 CA
1 CA
5547926 ATTAGGTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 22 0.55
15 1 0.03
16 6 0.15
17 1 0.03
18 10 0.25
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.24
Consensus pattern (14 bp):
CATTGCAACTTGCA
Found at i:5549660 original size:93 final size:93
Alignment explanation
Indices: 5549501--5549671 Score: 227
Period size: 93 Copynumber: 1.8 Consensus size: 93
5549491 GGATGGTTGA
* * **** * *
5549501 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCATTAAGT
5549566 TGAGT-TCGAGTTCGTGAGATGTAACTAG
66 TGAGTCT-GAGTTCGTGAGATGTAACTAG
* * *
5549594 GCATCCGAACTCATTGATTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCATTAAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCATTAAGT
5549659 TGAGTCTGAGTTC
66 TGAGTCTGAGTTC
5549672 ACTTAGGGGC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
93 65 0.98
94 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCATTAAGT
TGAGTCTGAGTTCGTGAGATGTAACTAG
Found at i:5557132 original size:46 final size:45
Alignment explanation
Indices: 5557080--5557254 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
5557070 TGGTTGAGCA
5557080 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * * *
5557126 TTCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
* *
5557171 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * *
5557219 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
5557255 GGCGGGTTAC
Statistics
Matches: 104, Mismatches: 16, Indels: 19
0.75 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 57 0.55
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:5557236 original size:93 final size:93
Alignment explanation
Indices: 5557077--5557247 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
5557067 GGATGGTTGA
* ** *
5557077 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCATTGAGT
*
5557142 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
5557170 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCATTGAGT
5557235 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5557248 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5560982 original size:14 final size:14
Alignment explanation
Indices: 5560961--5561001 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5560951 TTGCAACTTG
5560961 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
5560975 TGCAACTTGCAAAT
1 CACAACTTGCACAT
5560989 CACAACTTGCACA
1 CACAACTTGCACA
5561002 ATCAGGTTAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:5562249 original size:4 final size:4
Alignment explanation
Indices: 5562140--5562241 Score: 141
Period size: 4 Copynumber: 25.5 Consensus size: 4
5562130 GAAATCAAAT
* *
5562140 ATAC ATAC ATAC AAAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
5562188 ATGC ATGC ATAC ATAC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5562236 ATAC AT
1 ATAC AT
5562242 GCATGCATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 90 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:5562694 original size:19 final size:19
Alignment explanation
Indices: 5562659--5562700 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
5562649 TATGGTTAAC
5562659 ATTAGTTAATTATTAATTA
1 ATTAGTTAATTATTAATTA
5562678 ATTATGTTAATTA-TAATTA
1 ATTA-GTTAATTATTAATTA
5562697 ATTA
1 ATTA
5562701 AAGTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTAGTTAATTATTAATTA
Found at i:5564381 original size:90 final size:90
Alignment explanation
Indices: 5564218--5564408 Score: 310
Period size: 90 Copynumber: 2.1 Consensus size: 90
5564208 ACACCCAACT
* * * *
5564218 TTAAAAAATCATTTTTTATAGGTTTTTCTGGCATTCTAAGACATATGGTTGACCAAAATAAGAAG
1 TTAAGAAATCACTATTTATAGGTTTTTCGGGCATTCTAAGACATATGGTTGACCAAAATAAGAAG
* *
5564283 ATATGAGTGAATTGTCATAAAATGA
66 ATAGGAGTGAATTGTCATAAAATAA
* *
5564308 TTAAGAAATCACTATTTATAGGTTTTTCGGGCATTCTAAGACGTATGGTTGACCAAAATAAGAAT
1 TTAAGAAATCACTATTTATAGGTTTTTCGGGCATTCTAAGACATATGGTTGACCAAAATAAGAAG
5564373 ATAGGAGTGAATTGTCATAAAATAA
66 ATAGGAGTGAATTGTCATAAAATAA
5564398 TTAAGAAATCA
1 TTAAGAAATCA
5564409 ACTTGAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (90 bp):
TTAAGAAATCACTATTTATAGGTTTTTCGGGCATTCTAAGACATATGGTTGACCAAAATAAGAAG
ATAGGAGTGAATTGTCATAAAATAA
Found at i:5577197 original size:4 final size:4
Alignment explanation
Indices: 5577104--5577177 Score: 130
Period size: 4 Copynumber: 18.5 Consensus size: 4
5577094 GAAATCAAAT
* *
5577104 ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5577152 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
5577178 GCATGCATGC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:5577977 original size:20 final size:20
Alignment explanation
Indices: 5577930--5577993 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
5577920 TAAACTTGTA
5577930 ATTTACAATA--TTTTAA-T
1 ATTTACAATATTTTTTAAGT
*
5577947 ATTT-TAATATTTTTTAAGT
1 ATTTACAATATTTTTTAAGT
5577966 ATTTACAATATTTTTTAAGT
1 ATTTACAATATTTTTTAAGT
5577986 ATTTACAA
1 ATTTACAA
5577994 CATGATTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
16 4 0.10
17 4 0.10
18 6 0.15
19 5 0.12
20 22 0.54
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTACAATATTTTTTAAGT
Found at i:5585074 original size:10 final size:10
Alignment explanation
Indices: 5585047--5585095 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
5585037 TTAAATTCTA
5585047 AAAGATAAAT
1 AAAGATAAAT
*
5585057 ATAA-ATAATT
1 A-AAGATAAAT
*
5585067 AAAGATAATT
1 AAAGATAAAT
5585077 AAAGATAAAT
1 AAAGATAAAT
5585087 AAA-ATAAAT
1 AAAGATAAAT
5585096 CCTAAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.23
10 25 0.71
11 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5585145 original size:14 final size:13
Alignment explanation
Indices: 5585108--5585146 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5585098 TAAATTCAAA
5585108 TCTAAATAATTAT
1 TCTAAATAATTAT
* *
5585121 CCTTAATAATTAT
1 TCTAAATAATTAT
5585134 TCTAATATAATTA
1 TCTAA-ATAATTA
5585147 AACATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (13 bp):
TCTAAATAATTAT
Found at i:5585736 original size:13 final size:13
Alignment explanation
Indices: 5585718--5585742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5585708 AATATGTCTT
5585718 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
5585731 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5585743 TTATTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:5585930 original size:96 final size:97
Alignment explanation
Indices: 5585760--5585943 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 97
5585750 ATTTAATTTA
** * * *
5585760 TTTATTTTTACTTAGGAATATATCAAGCCCTTTGACACGAAGAGAGATAACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAAAACATATCAAACCCTTTGACACGAAGAGAGATAACAACCAAGCACCCCA
* * *
5585825 CCTCGGTTACTTAGCCCAACATACTCCTAATT
66 CCCCAGTTACTCAGCCCAACATACTCCTAATT
* * * * *
5585857 TTTATTTTT-CTTAAAAACATATCAAACCTTTTGGCGCGAAGAGAGATGACAACCAAGCACCTCA
1 TTTATTTTTACTTAAAAACATATCAAACCCTTTGACACGAAGAGAGATAACAACCAAGCACCCCA
5585921 CCCCAGTTACTCAGCCCAACATA
66 CCCCAGTTACTCAGCCCAACATA
5585944 TTCTTAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
96 65 0.88
97 9 0.12
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (97 bp):
TTTATTTTTACTTAAAAACATATCAAACCCTTTGACACGAAGAGAGATAACAACCAAGCACCCCA
CCCCAGTTACTCAGCCCAACATACTCCTAATT
Found at i:5591387 original size:40 final size:41
Alignment explanation
Indices: 5591332--5591517 Score: 249
Period size: 40 Copynumber: 4.7 Consensus size: 41
5591322 TGATTATTCG
*
5591332 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTA-TT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
5591372 GACTATATCCGGGCTAAGTCCCGAAGGC-GTTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCGAGTT
** *
5591413 G-CTATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAG-T
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
** *
5591452 GACTATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
*
5591493 G-CTATATCC-GGCTAAATCCCGAAGG
1 GACTATATCCGGGCTAAGTCCCGAAGG
5591518 TACTTGGGTT
Statistics
Matches: 133, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
39 18 0.14
40 110 0.83
41 5 0.04
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
Found at i:5591467 original size:80 final size:80
Alignment explanation
Indices: 5591334--5591517 Score: 298
Period size: 80 Copynumber: 2.3 Consensus size: 80
5591324 ATTATTCGGA
* **
5591334 CTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGG
*
5591399 CGTTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
**
5591414 CTATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGG
5591479 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
*
5591494 CTATATCC-GGCTAAATCCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGG
5591518 TACTTGGGTT
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 15 0.15
80 82 0.85
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (80 bp):
CTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGG
CATTTGTGCGAGTTG
Found at i:5599674 original size:40 final size:41
Alignment explanation
Indices: 5599619--5599808 Score: 169
Period size: 40 Copynumber: 4.7 Consensus size: 41
5599609 TGATTATTCG
* * *
5599619 GACTATATCCAGGCTAAGTCCCGAAGGCAGTTGTGCTA-CT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
5599659 GACTATATCCGGGCTAAGTCCCGAAGGC-GTTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCGAGTT
* ** *
5599700 G-CTAATATCCGAGCTAAGTCCCGAAGGCTTTTGTGCTA-TAGT
1 GACT-ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGT--T
* * * *
5599742 GATCTATAT-CGGGCTAAGACCCAAAAGCATTTGTGCGAGTT
1 GA-CTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
*
5599783 G-CTATATCC-GGCTAAAATCCCGAAGG
1 GACTATATCCGGGCT-AAGTCCCGAAGG
5599809 TACTTGGGGT
Statistics
Matches: 123, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
39 11 0.09
40 46 0.37
41 34 0.28
42 25 0.20
43 5 0.04
44 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (41 bp):
GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
Found at i:5601515 original size:12 final size:11
Alignment explanation
Indices: 5601507--5601551 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 11
5601497 AAAATAAAGT
5601507 AATAAATAATA
1 AATAAATAATA
*
5601518 AATAAAGTAATG
1 AATAAA-TAATA
5601530 AATAAA-AA-A
1 AATAAATAATA
5601539 AATAAATAA-A
1 AATAAATAATA
5601549 AAT
1 AAT
5601552 TGGGTTGCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 6 0.20
10 8 0.27
11 6 0.20
12 10 0.33
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (11 bp):
AATAAATAATA
Found at i:5601522 original size:19 final size:19
Alignment explanation
Indices: 5601498--5601534 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5601488 TCACCCAACA
5601498 AAATAAAGTAATAAATAAT
1 AAATAAAGTAATAAATAAT
*
5601517 AAATAAAGTAATGAATAA
1 AAATAAAGTAATAAATAA
5601535 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAAAGTAATAAATAAT
Found at i:5602133 original size:93 final size:91
Alignment explanation
Indices: 5602014--5602194 Score: 272
Period size: 93 Copynumber: 2.0 Consensus size: 91
5602004 AGTGCCATAA
*
5602014 ACGTTAAACTTCACGATCTCCCCATCAAACTCCATCATAAGGGTTCCGCTTCGTACGTCAATCTT
1 ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGG-TCCGCTTCGTACGTCAATCTT
* *
5602079 AGTATTTGCAATACTAAGGAAAGGTCGC
65 AGCA-TTGCAATACTAAGAAAAGGTCGC
* * * *
5602107 ACGTTATACTTCACAATCTCTCCATCAAACTCCATCGTGAGGGTCCGCTTCGTACGTCAATCTTA
1 ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGGTCCGCTTCGTACGTCAATCTTA
*
5602172 GCATTGCAGTACTAAGAAAAGGT
66 GCATTGCAATACTAAGAAAAGGT
5602195 TGCCCAACAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 18 0.22
92 24 0.30
93 38 0.47
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (91 bp):
ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGGTCCGCTTCGTACGTCAATCTTA
GCATTGCAATACTAAGAAAAGGTCGC
Found at i:5609365 original size:41 final size:40
Alignment explanation
Indices: 5609297--5609453 Score: 130
Period size: 40 Copynumber: 3.9 Consensus size: 40
5609287 TGATTATTCG
5609297 GACTATATCCAGGCTAAGTCCCGAAGGCAG-TTGTGCTACT
1 GACTATATCCAGGCTAAGTCCCGAAGGC-GTTTGTGCTACT
* *
5609337 GACTATATCC-GGCTACAGTTCCCGAAGGCGTTTGTGCGAGTTT
1 GACTATATCCAGGCTA-AG-TCCCGAAGGCGTTTGTGCTA--CT
* *
5609380 G-CTATATCC-GAGC-AAGTCCCGAAGGCTTTTGTGCTAGT
1 GACTATATCCAG-GCTAAGTCCCGAAGGCGTTTGTGCTACT
* * *
5609418 GA-TATATCTCCCGGCTAAGACCC-AAGGCATTTGTGC
1 GACTATA--TCCAGGCTAAGTCCCGAAGGCGTTTGTGC
5609454 CGAGGTTTGC
Statistics
Matches: 99, Mismatches: 7, Indels: 22
0.77 0.05 0.17
Matches are distributed among these distances:
38 6 0.06
39 5 0.05
40 48 0.48
41 26 0.26
42 10 0.10
43 4 0.04
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (40 bp):
GACTATATCCAGGCTAAGTCCCGAAGGCGTTTGTGCTACT
Found at i:5610756 original size:40 final size:41
Alignment explanation
Indices: 5610701--5610884 Score: 283
Period size: 40 Copynumber: 4.7 Consensus size: 41
5610691 ATGATTATTC
*
5610701 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-T
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
5610741 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
5610782 G-CTATATCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAG-T
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
5610819 GACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
5610860 G-CTATATCC-GGCTAAATCCCGAAGG
1 GACTATATCCGGGCTAAGTCCCGAAGG
5610885 TACTTGGGTT
Statistics
Matches: 133, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
37 2 0.02
38 25 0.19
39 30 0.23
40 72 0.54
41 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
Found at i:5610834 original size:78 final size:80
Alignment explanation
Indices: 5610703--5610884 Score: 325
Period size: 78 Copynumber: 2.3 Consensus size: 80
5610693 GATTATTCGA
*
5610703 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
5610768 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
5610783 CTATATCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
5610846 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
*
5610861 CTATATCC-GGCTAAATCCCGAAGG
1 CTATATCCGGGCTAAGTCCCGAAGG
5610885 TACTTGGGTT
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
77 7 0.07
78 67 0.68
79 8 0.08
80 17 0.17
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
CATTTGTGCGAGTTG
Found at i:5619087 original size:40 final size:41
Alignment explanation
Indices: 5619032--5619217 Score: 222
Period size: 40 Copynumber: 4.7 Consensus size: 41
5619022 TGATTATTCG
* * *
5619032 GACTATATCCAGGCTAAGTCCCGAAGGCAGTTGTGCTA-CT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
5619072 GACTATATCCGGGCTAAGTCCCGAAGGC-GTTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCGAGTT
* ** *
5619113 G-CTATATCCGAGCTAAGTCCCGAAGGCTTTTGTGCTAG-T
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
* * *
5619152 GACTATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
*
5619193 G-CTATATCC-GGCTAAATCCCGAAGG
1 GACTATATCCGGGCTAAGTCCCGAAGG
5619218 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
39 16 0.13
40 107 0.84
41 4 0.03
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (41 bp):
GACTATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCGAGTT
Found at i:5619167 original size:80 final size:80
Alignment explanation
Indices: 5619034--5619217 Score: 282
Period size: 80 Copynumber: 2.3 Consensus size: 80
5619024 ATTATTCGGA
* *
5619034 CTATATCC-AGGCTAAGTCCCGAAGGCAGTTGTGCTACTGACTATATCCGGGCTAAGTCCCGAAG
1 CTATATCCGA-GCTAAGTCCCGAAGGCAGTTGTGCTACTGACTATATCCGGGCTAAGACCCAAAG
*
5619098 GCGTTTGTGCGAGTTG
65 GCATTTGTGCGAGTTG
** *
5619114 CTATATCCGAGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACTATATCCGGGCTAAGACCCAAAGG
1 CTATATCCGAGCTAAGTCCCGAAGGCAGTTGTGCTACTGACTATATCCGGGCTAAGACCCAAAGG
5619179 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
*
5619194 CTATATCCG-GCTAAATCCCGAAGG
1 CTATATCCGAGCTAAGTCCCGAAGG
5619218 TACTTGGGTT
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
79 14 0.15
80 81 0.84
81 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (80 bp):
CTATATCCGAGCTAAGTCCCGAAGGCAGTTGTGCTACTGACTATATCCGGGCTAAGACCCAAAGG
CATTTGTGCGAGTTG
Found at i:5620958 original size:20 final size:19
Alignment explanation
Indices: 5620933--5620978 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
5620923 TCACCCAAAC
5620933 AAAATAAAGTAATAAATAA
1 AAAATAAAGTAATAAATAA
*
5620952 TAAAATAAAGTAATGAATAA
1 -AAAATAAAGTAATAAATAA
5620972 AAAATAA
1 AAAATAA
5620979 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAATAAAGTAATAAATAA
Found at i:5621577 original size:93 final size:93
Alignment explanation
Indices: 5621458--5621640 Score: 294
Period size: 93 Copynumber: 2.0 Consensus size: 93
5621448 AGTGCCATAA
*
5621458 ACGTTAAACTTCACGATCTCCCCATCAAACTCCATCATAAGGGTTCCGCTTCGTACGTCAATCTT
1 ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGGTTCCGCTTCGTACGTCAATCTT
* *
5621523 AGTATTTGCAATACTAAGGAAAGGTCGC
66 AGCATTTGCAATACTAAGAAAAGGTCGC
* * * *
5621551 ACGTTATACTTCACAATCTCTCCATCAAACTCCATCGTGAGGGTTCCGCTTCGTACGTCAATCTT
1 ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGGTTCCGCTTCGTACGTCAATCTT
*
5621616 AGCATTTGCAGTACTAAGAAAAGGT
66 AGCATTTGCAATACTAAGAAAAGGT
5621641 TGCCCCAACA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (93 bp):
ACGTTAAACTTCACAATCTCCCCATCAAACTCCATCATAAGGGTTCCGCTTCGTACGTCAATCTT
AGCATTTGCAATACTAAGAAAAGGTCGC
Found at i:5624735 original size:10 final size:10
Alignment explanation
Indices: 5624708--5624757 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
5624698 TTAAATTCTA
5624708 AAAGATAAAT
1 AAAGATAAAT
*
5624718 ACAA-ATAATT
1 A-AAGATAAAT
*
5624728 AAAGATAATT
1 AAAGATAAAT
5624738 AAAGATAAAT
1 AAAGATAAAT
*
5624748 AAAAATAAAT
1 AAAGATAAAT
5624758 CTTAAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5624807 original size:14 final size:13
Alignment explanation
Indices: 5624771--5624808 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
5624761 AAATTCAAAT
5624771 CTAAATAATTATC
1 CTAAATAATTATC
*
5624784 CTTAATAATTATC
1 CTAAATAATTATC
5624797 CTAACATAATTA
1 CTAA-ATAATTA
5624809 AACATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:5630184 original size:86 final size:86
Alignment explanation
Indices: 5630006--5630194 Score: 222
Period size: 86 Copynumber: 2.2 Consensus size: 86
5629996 CGCAGCTATA
* * * * * *
5630006 GCAAACGCCGCTAAAGATCATGACTTTTAGTGGCACTTTTTCCACAAGCGCCACTAAAGATCATG
1 GCAAACGCCGCTAAAGACCATGACCTTTAGTCGCACTTTTTCCACAAACACCACTAAAGACCATG
*
5630071 ACCTTTAGCGACGCTTTTTCC
66 ACCTTTAGCGACGCTTTTCCC
** **
5630092 AAAAACGCCGCTAAAGACCATGACCTTTAG-CG-ACGTTTTTCCTACAAACACCGTTAAAGACCA
1 GCAAACGCCGCTAAAGACCATGACCTTTAGTCGCAC-TTTTTCC-ACAAACACCACTAAAGACCA
*
5630155 TGACCTTTAGTGACGC-TTTCCC
64 TGACCTTTAGCGACGCTTTTCCC
5630177 TGCAAACGCCGCTAAAGA
1 -GCAAACGCCGCTAAAGA
5630195 ATATAACCTT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
84 2 0.02
85 13 0.15
86 71 0.83
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (86 bp):
GCAAACGCCGCTAAAGACCATGACCTTTAGTCGCACTTTTTCCACAAACACCACTAAAGACCATG
ACCTTTAGCGACGCTTTTCCC
Found at i:5630205 original size:43 final size:43
Alignment explanation
Indices: 5630007--5630194 Score: 191
Period size: 43 Copynumber: 4.4 Consensus size: 43
5629997 GCAGCTATAG
* * * * * *
5630007 CAAACGCCGCTAAAGATCATGACTTTTAGTGGCACTTTTTCC-A
1 CAAACGCCGCTAAAGACCATGACCTTTAGCGACGC-TTTCCCTA
* * * *
5630050 CAAGCGCCACTAAAGATCATGACCTTTAGCGACGCTTTTTCC-A
1 CAAACGCCGCTAAAGACCATGACCTTTAGCGACGC-TTTCCCTA
* * *
5630093 AAAACGCCGCTAAAGACCATGACCTTTAGCGACGTTTTTCCTA
1 CAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTCCCTA
* * * *
5630136 CAAACACCGTTAAAGACCATGACCTTTAGTGACGCTTTCCCTG
1 CAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTCCCTA
5630179 CAAACGCCGCTAAAGA
1 CAAACGCCGCTAAAGA
5630195 ATATAACCTT
Statistics
Matches: 124, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
42 6 0.05
43 118 0.95
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
CAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTCCCTA
Found at i:5636137 original size:3 final size:3
Alignment explanation
Indices: 5636113--5636172 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
5636103 TATATCTTTG
*
5636113 TAT TA- TAT TAT AAT TA- TAT TAT TAT ATAT TATT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA-T
*
5636159 TAC TAT ATAT TAT T
1 TAT TAT -TAT TAT T
5636173 TTTCACAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 4 0.09
3 31 0.66
4 12 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5636137 original size:14 final size:14
Alignment explanation
Indices: 5636113--5636251 Score: 92
Period size: 14 Copynumber: 9.7 Consensus size: 14
5636103 TATATCTTTG
5636113 TATTATATTATA-AT
1 TATT-TATTATATAT
5636127 TATATTATTATATAT
1 TAT-TTATTATATAT
5636142 TATTTATTAT-TAT
1 TATTTATTATATAT
*
5636155 TATTTACTATATAT
1 TATTTATTATATAT
* *
5636169 TATTT-TTCACAAAT
1 TATTTATT-ATATAT
* *
5636183 TAGTATTATTTTACAT
1 TA-T-TTATTATATAT
5636199 TA-TTATT-TATAT
1 TATTTATTATATAT
*
5636211 AATATTATTATATTGTAT
1 TAT-TTATTATA---TAT
5636229 TATTTA-TATATAT
1 TATTTATTATATAT
*
5636242 TATATATTAT
1 TATTTATTAT
5636252 TTTTACATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
12 5 0.05
13 26 0.26
14 39 0.39
15 9 0.09
16 11 0.11
17 5 0.05
18 5 0.05
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (14 bp):
TATTTATTATATAT
Found at i:5636154 original size:20 final size:20
Alignment explanation
Indices: 5636116--5636283 Score: 82
Period size: 20 Copynumber: 8.4 Consensus size: 20
5636106 ATCTTTGTAT
5636116 TATATTATAATTA-TATTATTA
1 TATATTAT--TTATTATTATTA
5636137 TATATTATTTATTATTATTA
1 TATATTATTTATTATTATTA
* * * *
5636157 TTTACTATATATTATTTTTCA
1 TATATTATTTATTATTATT-A
* * *
5636178 CAAATTA-GTATTATT-TTA
1 TATATTATTTATTATTATTA
* *
5636196 CATTATTATTTATATAATATTA
1 TA-TATTATTTAT-TATTATTA
5636218 T-TA-TATTGTATTATT-TATA
1 TATATTATT-TATTATTAT-TA
* *
5636237 TATATTATATATTATTTTTA
1 TATATTATTTATTATTATTA
* * *
5636257 CATATATACTT-TCA-TATTA
1 TATAT-TATTTATTATTATTA
5636276 TATATTAT
1 TATATTAT
5636284 AATTATTTTA
Statistics
Matches: 113, Mismatches: 22, Indels: 27
0.70 0.14 0.17
Matches are distributed among these distances:
18 6 0.05
19 27 0.24
20 55 0.49
21 22 0.19
22 3 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (20 bp):
TATATTATTTATTATTATTA
Found at i:5636218 original size:27 final size:26
Alignment explanation
Indices: 5636186--5636263 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
5636176 CACAAATTAG
*
5636186 TATTATTTTACAT-TATTATTTATATAA
1 TATTATTATA-ATGTATTATTTATAT-A
*
5636213 TATTATTATATTGTATTATTTATATA
1 TATTATTATAATGTATTATTTATATA
*
5636239 TATTA-TAT-AT-TATT-TTTACATA
1 TATTATTATAATGTATTATTTATATA
5636261 TAT
1 TAT
5636264 ACTTTCATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 10 0.22
23 4 0.09
24 1 0.02
25 3 0.07
26 7 0.15
27 21 0.46
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (26 bp):
TATTATTATAATGTATTATTTATATA
Found at i:5636221 original size:13 final size:13
Alignment explanation
Indices: 5636199--5636252 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
5636189 TATTTTACAT
5636199 TATTATTTATATAA
1 TATTA-TTATATAA
**
5636213 TATTATTATATTG
1 TATTATTATATAA
5636226 TATTATT-TAT-A
1 TATTATTATATAA
*
5636237 TA-TATTATATAT
1 TATTATTATATAA
5636249 TATT
1 TATT
5636253 TTTACATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 5 0.15
13 14 0.42
14 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATAA
Found at i:5636300 original size:48 final size:49
Alignment explanation
Indices: 5636117--5636302 Score: 117
Period size: 50 Copynumber: 3.9 Consensus size: 49
5636107 TCTTTGTATT
*
5636117 ATATTAT-A-ATTATATTATTATATATTA-TTTATTATTATTATTTAC-TA
1 ATATTATCATATTATATTATT-TATATTATTTTA-AATTATTATTTACATA
** * * *
5636164 TATATTAT--T-TT-TCACAAATTAGTATTATTTTACATTATTATTTATATA
1 -ATATTATCATATTAT-ATTATTTA-TATTATTTTAAATTATTATTTACATA
* * * *
5636212 ATATTATTATATTGTATTATTTATATATATTATATATTATT-TTTACATA
1 ATATTATCATATTATATTATTTATAT-TATTTTAAATTATTATTTACATA
5636261 TATACTT-TCATATTATA-TA-TTATAATTATTTTAAATTATTAT
1 -ATA-TTATCATATTATATTATTTAT-ATTATTTTAAATTATTAT
5636303 GTCATTTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
46 3 0.03
47 28 0.26
48 29 0.27
49 16 0.15
50 30 0.28
51 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (49 bp):
ATATTATCATATTATATTATTTATATTATTTTAAATTATTATTTACATA
Found at i:5640336 original size:14 final size:14
Alignment explanation
Indices: 5640317--5640346 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5640307 AAGATATTCT
5640317 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
5640331 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
5640345 TT
1 TT
5640347 GAACCAGAAT
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:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:5640385 original size:14 final size:16
Alignment explanation
Indices: 5640366--5640402 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5640356 TCGATATCCT
5640366 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
5640380 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
5640396 TTT-CATC
1 TTTGCATC
5640403 GCATCGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:5648942 original size:207 final size:207
Alignment explanation
Indices: 5648425--5648979 Score: 832
Period size: 206 Copynumber: 2.7 Consensus size: 207
5648415 AGATCTGGCG
* *
5648425 GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTACTTACAAGGAACAAACCGAAGACATAGCTGA
1 GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGA
* * * * *
5648490 TTCGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAATTTGGCATCTCTGTATTGTCAAAG
66 TTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
** * **
5648555 AACAAATCGAAGTTTGGCGTCTCCATATTCGGTGGAAAGCAGACACATTACAGATTTGGCCTTCA
131 AACAAATCGAAGTTTGGCGTCTCCATATTCGGACGAAAGCAGACACATTACAGATCTCACCTTCA
* *
5648620 TATGTTTATACT
196 GATGTTTACACT
* * *
5648632 GAAGC-AGATCCAAGATGATTTAGCATCCTTGTGTTTACAAGGAACAAATCGAA-ATCATAGCTG
1 GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CATAGCTG
*
5648695 ATTTGGCTTTCACGTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
65 ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
5648760 GAACAAATTGAAGTTTGGCGTCTCCATATTC-GACGAAAGACAGACACA-TAGCAGATCTCACCT
130 GAACAAATCGAAGTTTGGCGTCTCCATATTCGGACGAAAG-CAGACACATTA-CAGATCTCACCT
5648823 TCAGATGATTT-CACT
193 TCAGATG-TTTACACT
*
5648838 GAAGCAAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGA
1 GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGA
* * *
5648903 TTTGGTTTTCGCGTGTTTACGCTAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
66 TTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
5648968 AACAAATCGAAG
131 AACAAATCGAAG
5648980 AAGCAGATTT
Statistics
Matches: 314, Mismatches: 28, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
205 9 0.03
206 171 0.54
207 133 0.42
208 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (207 bp):
GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGA
TTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
AACAAATCGAAGTTTGGCGTCTCCATATTCGGACGAAAGCAGACACATTACAGATCTCACCTTCA
GATGTTTACACT
Found at i:5649678 original size:21 final size:20
Alignment explanation
Indices: 5649641--5649679 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5649631 TTATACATTA
*
5649641 TTTTTTTTAAATCATTATAT
1 TTTTTTTTAAATAATTATAT
*
5649661 TTTTGTTTTATATAATTAT
1 TTTT-TTTTAAATAATTAT
5649680 TATTCTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTTTTAAATAATTATAT
Found at i:5650986 original size:7 final size:7
Alignment explanation
Indices: 5650966--5651045 Score: 106
Period size: 7 Copynumber: 11.0 Consensus size: 7
5650956 TTAAATATTA
5650966 AATTTTT
1 AATTTTT
5650973 AAGTTTTT
1 AA-TTTTT
*
5650981 TATTTTT
1 AATTTTT
*
5650988 TATTTTCT
1 AATTTT-T
*
5650996 TATTTTT
1 AATTTTT
5651003 AATTTTT
1 AATTTTT
5651010 AATTTTT
1 AATTTTT
5651017 AATTTTT
1 AATTTTT
5651024 AATTTTT
1 AATTTTT
5651031 AATTTTT
1 AATTTTT
5651038 AAATTTTT
1 -AATTTTT
5651046 TTTGAAGATT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
7 48 0.71
8 20 0.29
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (7 bp):
AATTTTT
Found at i:5650993 original size:21 final size:21
Alignment explanation
Indices: 5650966--5651045 Score: 106
Period size: 22 Copynumber: 3.7 Consensus size: 21
5650956 TTAAATATTA
*
5650966 AATTTTTAAGTTTTTTATTTTT
1 AATTTTTAA-TTTTTAATTTTT
* *
5650988 TATTTTCTTATTTTTAATTTTT
1 AATTTT-TAATTTTTAATTTTT
5651010 AATTTTTAATTTTTAATTTTT
1 AATTTTTAATTTTTAATTTTT
5651031 AATTTTTAAATTTTT
1 AATTTTT-AATTTTT
5651046 TTTGAAGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 21 0.41
22 28 0.55
23 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (21 bp):
AATTTTTAATTTTTAATTTTT
Found at i:5651666 original size:15 final size:15
Alignment explanation
Indices: 5651633--5651675 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5651623 TTATCTCTTA
*
5651633 CATAA-CCATAAA-T
1 CATAATCCATAAACC
*
5651646 CATAATCCCTAAACC
1 CATAATCCATAAACC
5651661 CATAATCCATAAACC
1 CATAATCCATAAACC
5651676 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.20
14 6 0.24
15 14 0.56
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:5651680 original size:22 final size:22
Alignment explanation
Indices: 5651638--5651724 Score: 52
Period size: 22 Copynumber: 4.0 Consensus size: 22
5651628 TCTTACATAA
*
5651638 CCATAAATCATAATCCCTAAAC
1 CCATAAATCATAAACCCTAAAC
* *
5651660 CCAT-AATCCATAAACCTTAAAA
1 CCATAAAT-CATAAACCCTAAAC
** * * **
5651682 TAATAACTCATACACTTTAAAC
1 CCATAAATCATAAACCCTAAAC
* *
5651704 CC-TAAACCATATACCCTAAAC
1 CCATAAATCATAAACCCTAAAC
5651725 TATAAACCCT
Statistics
Matches: 47, Mismatches: 16, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
21 17 0.36
22 28 0.60
23 2 0.04
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (22 bp):
CCATAAATCATAAACCCTAAAC
Found at i:5651721 original size:14 final size:14
Alignment explanation
Indices: 5651699--5651743 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5651689 TCATACACTT
5651699 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
5651713 TATACCCTAAACTA
1 TAAACCCTAAACCA
*
5651727 TAAACCCTAAACTA
1 TAAACCCTAAACCA
5651741 TAA
1 TAA
5651744 TGATAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Done.