Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 4 of 50
Found at i:2057047 original size:24 final size:26
Alignment explanation
Indices: 2056980--2057096 Score: 101
Period size: 30 Copynumber: 4.2 Consensus size: 26
2056970 TTCTTTAATA
* *
2056980 TAATTTTTTATATTATATATTTTATTT
1 TAATTTATTATATTATATA-TATATTT
* *
2057007 TAATTTCTTTTACTTATATTATATAATTTT
1 TAATTTATTATA-TTATA-TATAT-A-TTT
2057037 TAATTTATTATACTATATTATATTATATTT
1 TAATTTATTATA-T-TA-TATA-TATATTT
2057067 TAA-TTATTATATTATATATTATATTT
1 TAATTTATTATATTATATA-TATATTT
2057093 TAAT
1 TAAT
2057097 ATTTTTATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
26 15 0.19
27 12 0.16
28 8 0.10
29 11 0.14
30 21 0.27
31 5 0.06
32 5 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
TAATTTATTATATTATATATATATTT
Found at i:2057084 original size:26 final size:26
Alignment explanation
Indices: 2057020--2057096 Score: 97
Period size: 26 Copynumber: 2.9 Consensus size: 26
2057010 TTTCTTTTAC
2057020 TTATATTATATA--AT-TTTTAATTTA
1 TTATATTATATATTATATTTTAA-TTA
2057044 TTATACTATATTATATTATATTTTAATTA
1 TTATA-T-TA-TATATTATATTTTAATTA
2057073 TTATATTATATATTATATTTTAAT
1 TTATATTATATATTATATTTTAAT
2057097 ATTTTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.11
25 1 0.02
26 18 0.38
27 6 0.13
28 1 0.02
29 10 0.21
30 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTATATATTATATTTTAATTA
Found at i:2057091 original size:5 final size:5
Alignment explanation
Indices: 2057020--2057083 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
2057010 TTTCTTTTAC
* * * *
2057020 TTATA TTATA TAAT- TTTTAA TT-TA TTATA CTATA TTATA TTATA TTTTA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA
*
2057069 AT-TA TTATA TTATA T
1 TTATA TTATA TTATA T
2057084 ATTATATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
4 8 0.17
5 37 0.79
6 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:2057105 original size:26 final size:26
Alignment explanation
Indices: 2056923--2057114 Score: 89
Period size: 26 Copynumber: 7.2 Consensus size: 26
2056913 TTTAACATCA
* *
2056923 TATATTTTATTTATTTTTTATTATAATTT
1 TATATTTTA-ATA-TTTTTATTAT-ATAT
*
2056952 TATATATTT--TATTTTTATT-TCT-T
1 TATAT-TTTAATATTTTTATTATATAT
* *
2056975 TA-A-TATAATTTTTTATATTATATAT
1 TATATTTTAATATTTT-TATTATATAT
* *
2057000 TTTATTTTAATTTCTTTTACTTATAT-T
1 TATATTTTAATAT-TTTTA-TTATATAT
2057027 ATATAATTTTTAAT-TTATTATACTATATTATAT
1 -TAT-A-TTTTAATATT-TT-TA-T-TA-TATAT
*
2057060 TATATTTTAAT-TATTATATTATATAT
1 TATATTTTAATAT-TTTTATTATATAT
*
2057086 TATATTTTAATATTTTTATTTTA-AT
1 TATATTTTAATATTTTTATTATATAT
2057111 TATA
1 TATA
2057115 ATATTATAAA
Statistics
Matches: 133, Mismatches: 10, Indels: 44
0.71 0.05 0.24
Matches are distributed among these distances:
20 2 0.02
22 6 0.05
23 7 0.05
24 3 0.02
25 9 0.07
26 33 0.25
27 15 0.11
28 13 0.10
29 11 0.08
30 23 0.17
31 4 0.03
32 6 0.05
33 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TATATTTTAATATTTTTATTATATAT
Found at i:2057119 original size:14 final size:13
Alignment explanation
Indices: 2057056--2057110 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 13
2057046 ATACTATATT
2057056 ATATTATATTTTA
1 ATATTATATTTTA
*
2057069 ATTATTATATTAT-
1 A-TATTATATTTTA
2057082 ATATTATATTTTA
1 ATATTATATTTTA
*
2057095 ATATTTTTATTTTA
1 ATA-TTATATTTTA
2057109 AT
1 AT
2057111 TATAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 10 0.28
13 5 0.14
14 21 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTATATTTTA
Found at i:2058514 original size:160 final size:163
Alignment explanation
Indices: 2058299--2058606 Score: 446
Period size: 160 Copynumber: 1.9 Consensus size: 163
2058289 AAATAGATAT
* * * * *
2058299 GTGAAATAAGGAAGAGGAGGGAGGGGCACAAAAACATAAGATTACGGTGAGAGGAAGTGATGGTT
1 GTGAAAGAAGGAAGAGGAGAGAGAGGCACAAAAACATAAGATTACGATGAGAGGAAGTGATGATT
*
2058364 GTTTTTGAA-GGAAATTTCTTAG-AATTGAGTGAGAAGAAAAAAGAAAAACAAAATACCATTTCA
66 GTTTTTAAAGGGAAA--TCTTAGAAATTGAGTGAGAAGAAAAAAGAAAAACAAAATACCATTTCA
2058427 TTAAAATTG-AAAAAATATTTTAAAAGTAAAATAA
129 TTAAAATTGAAAAAAATATTTTAAAAGTAAAATAA
* ** *
2058461 GTGAAAGAAGGAAG-GGAGAGAGAGGCAC-AAAACATGAGATTTTGATTAGAGGAAGTGATGATT
1 GTGAAAGAAGGAAGAGGAGAGAGAGGCACAAAAACATAAGATTACGATGAGAGGAAGTGATGATT
* * *
2058524 GTTTTTAAAGGGAAATCTTGGAAATTGAGTGAGAAGAAAAAAGAAAAATAAAATACTATTTCATT
66 GTTTTTAAAGGGAAATCTTAGAAATTGAGTGAGAAGAAAAAAGAAAAACAAAATACCATTTCATT
2058589 AAAATTGAAAAAAATATT
131 AAAATTGAAAAAAATATT
2058607 CCAATCATGT
Statistics
Matches: 130, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
159 5 0.04
160 85 0.65
161 27 0.21
162 13 0.10
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (163 bp):
GTGAAAGAAGGAAGAGGAGAGAGAGGCACAAAAACATAAGATTACGATGAGAGGAAGTGATGATT
GTTTTTAAAGGGAAATCTTAGAAATTGAGTGAGAAGAAAAAAGAAAAACAAAATACCATTTCATT
AAAATTGAAAAAAATATTTTAAAAGTAAAATAA
Found at i:2059829 original size:13 final size:13
Alignment explanation
Indices: 2059811--2059841 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2059801 CAAAAATACT
2059811 ACACATGTCTTGG
1 ACACATGTCTTGG
2059824 ACACATGTCTTGG
1 ACACATGTCTTGG
2059837 ACACA
1 ACACA
2059842 ATTCAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (13 bp):
ACACATGTCTTGG
Found at i:2072080 original size:19 final size:18
Alignment explanation
Indices: 2072037--2072077 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
2072027 GGAGTGCTGT
2072037 GAATTTAA--AAGATATC
1 GAATTTAATTAAGATATC
2072053 GAATTTAATTAAGATTATC
1 GAATTTAATTAAGA-TATC
2072072 GCAATT
1 G-AATT
2072078 AATGCAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
18 4 0.19
19 5 0.24
20 4 0.19
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (18 bp):
GAATTTAATTAAGATATC
Found at i:2080621 original size:31 final size:30
Alignment explanation
Indices: 2080551--2080624 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
2080541 CTTTTTAATT
2080551 TTAT-TCAATTTAA-TCTTTATATTAAAAA
1 TTATATCAATTTAATTCTTTATATTAAAAA
* * *
2080579 TTAAAAT-AATTTAATTTTTTAATTTTAAAAA
1 TT-ATATCAATTTAATTCTTT-ATATTAAAAA
2080610 TTATATCAATTTAAT
1 TTATATCAATTTAAT
2080625 CTCTCCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 2 0.05
29 8 0.22
30 8 0.22
31 19 0.51
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATATCAATTTAATTCTTTATATTAAAAA
Found at i:2081397 original size:108 final size:108
Alignment explanation
Indices: 2081196--2081405 Score: 305
Period size: 108 Copynumber: 1.9 Consensus size: 108
2081186 TAATATAAAA
* *
2081196 TAACTAAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATTCTTTTGAAATTAT
1 TAACAAAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATTCTTTTGAAAGTAT
*
2081261 TCAACACTTATCCAATTAACATTTTATTTAAATTTACTCAAAT
66 TCAACACTTATCCAATTAACATTCTATTTAAATTTACTCAAAT
* * * *
2081304 TAACAAAATATGTTGATTTAGTTACAACTTTCACAATTTATAAATACACATTCTTTTGCAAGTAT
1 TAACAAAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATTCTTTTGAAAGTAT
** * *
2081369 TCAACTTTTA-CTCAATTTACCTTCTATTTAAATTTAC
66 TCAACACTTATC-CAATTAACATTCTATTTAAATTTAC
2081406 GTAAAAATTC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.01
108 89 0.99
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.42
Consensus pattern (108 bp):
TAACAAAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATTCTTTTGAAAGTAT
TCAACACTTATCCAATTAACATTCTATTTAAATTTACTCAAAT
Found at i:2086052 original size:27 final size:27
Alignment explanation
Indices: 2086014--2086068 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2086004 AGATAATAAG
2086014 TAGGTTTTCATGCGAATGGTTATATCT
1 TAGGTTTTCATGCGAATGGTTATATCT
2086041 TAGGTTTTCATGCGAATGGTTATATCT
1 TAGGTTTTCATGCGAATGGTTATATCT
2086068 T
1 T
2086069 TTGAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (27 bp):
TAGGTTTTCATGCGAATGGTTATATCT
Found at i:2087755 original size:48 final size:47
Alignment explanation
Indices: 2087617--2087761 Score: 157
Period size: 47 Copynumber: 3.0 Consensus size: 47
2087607 CCTAAACAGT
* *
2087617 ACCAGCTCTAAGGTTCTATTAAAAAACATTCATAACCAGTAACATTCATT
1 ACCAGCTCTAAGGTTCTATTAAAAAACATTCATATCCAGTAAC--TC-TG
* ** * * *
2087667 TCCAATTATAAGGTTTTATTAAAAAA-ATTCATATCTAGTAACTCTG
1 ACCAGCTCTAAGGTTCTATTAAAAAACATTCATATCCAGTAACTCTG
* *
2087713 ACGTAGCTCTAAGGTTGTATTAAAAAACATTCATATCCAGTAACTCTG
1 AC-CAGCTCTAAGGTTCTATTAAAAAACATTCATATCCAGTAACTCTG
2087761 A
1 A
2087762 TGTGAACCAG
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
46 2 0.03
47 21 0.27
48 20 0.26
49 14 0.18
50 21 0.27
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (47 bp):
ACCAGCTCTAAGGTTCTATTAAAAAACATTCATATCCAGTAACTCTG
Found at i:2088411 original size:25 final size:26
Alignment explanation
Indices: 2088365--2088423 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
2088355 ACATTCCAAG
2088365 CATAGAAGCGCTCAGGGGCGTTTCAAA
1 CATAGAAGCGC-CAGGGGCGTTTCAAA
*
2088392 CATAGAAGCG-CAGGGGCGTTTCAAG
1 CATAGAAGCGCCAGGGGCGTTTCAAA
2088417 CATAGAA
1 CATAGAA
2088424 AAGCCCAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 21 0.68
27 10 0.32
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (26 bp):
CATAGAAGCGCCAGGGGCGTTTCAAA
Found at i:2088427 original size:27 final size:27
Alignment explanation
Indices: 2088361--2088452 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 27
2088351 AGGAACATTC
** *
2088361 CAAGCATAGAAGCGCTCAGGGGCGTTT
1 CAAGCATAGAAAAGCCCAGGGGCGTTT
* *
2088388 CAAACATAG--AAGCGCAGGGGCGTTT
1 CAAGCATAGAAAAGCCCAGGGGCGTTT
* *
2088413 CAAGCATAGAAAAGCCCAAGGAGCGTTA
1 CAAGCATAGAAAAGCCC-AGGGGCGTTT
*
2088441 CAAGTATAGAAA
1 CAAGCATAGAAA
2088453 CACCGAGGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 21 0.40
27 13 0.25
28 19 0.36
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (27 bp):
CAAGCATAGAAAAGCCCAGGGGCGTTT
Found at i:2111416 original size:14 final size:13
Alignment explanation
Indices: 2111391--2111432 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2111381 AATAAAACTA
*
2111391 ATTTTTTATATAT
1 ATTTTATATATAT
2111404 A-TTTATATATAT
1 ATTTTATATATAT
*
2111416 AATTTTTTATATAT
1 -ATTTTATATATAT
2111430 ATT
1 ATT
2111433 AAGAAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTATATATAT
Found at i:2111604 original size:25 final size:24
Alignment explanation
Indices: 2111576--2111647 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 24
2111566 AATTATAAAT
*
2111576 TATATATTTTA-AATGATATAACTTA
1 TATATATTTTATAAT-ATATAA-TAA
2111601 TATATTAATTTTATAATATATAATAA
1 TATA-T-ATTTTATAATATATAATAA
*
2111627 TAAATATTTTAT-ATAT-TAATA
1 TATATATTTTATAATATATAATA
2111648 TGTTGTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 5 0.12
23 4 0.10
24 7 0.17
25 5 0.12
26 6 0.14
27 12 0.29
28 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
TATATATTTTATAATATATAATAA
Found at i:2111801 original size:39 final size:37
Alignment explanation
Indices: 2111721--2111801 Score: 85
Period size: 39 Copynumber: 2.1 Consensus size: 37
2111711 TGAAAAAATA
*
2111721 TTATATATATTTAATTTATATATAAACATTACTATAAC
1 TTATATAAATTTAATTTATATATAAACATTAC-ATAAC
*
2111759 TTATAATAAATTTTATTTATATGATTAAAC-TTA-ATAACC
1 TTAT-ATAAATTTAATTTATAT-A-TAAACATTACATAA-C
2111798 TTAT
1 TTAT
2111802 TAATTATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
38 8 0.22
39 20 0.54
40 4 0.11
41 5 0.14
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.48
Consensus pattern (37 bp):
TTATATAAATTTAATTTATATATAAACATTACATAAC
Found at i:2111992 original size:218 final size:218
Alignment explanation
Indices: 2111725--2112184 Score: 595
Period size: 218 Copynumber: 2.1 Consensus size: 218
2111715 AAAATATTAT
2111725 ATATATTTAATTTATATATAAACATTACTATAACTTATAATAAATTTTATTTATATGATTAAACT
1 ATATATTTAATTTATATATAAACATTACTATAACTTATAATAAATTTTATTTATATGATTAAACT
* * * *
2111790 TAATAACCTTATTAATTATCATCTTAGTTTTTATAATATGTTGTTTATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCATCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTTAT
* * * * *
2111855 ACAAATTTTGATAT-AAAA-T-A-TTATAACATATCAGTTATGTCATTAATTTTATATATACATA
131 ACAAATTTTAATATAAAAATTAAGTTATAACATATAAATTATATCATTAATTTCATATATACATA
*
2111916 ATAAAGTAATATAGCATATATAAAA
196 ATAAAATAATATA--ATATATAAAA
* * * *
2111941 ATATATTTAATTTATATATATAAGCATTACTGTAATTTATAATAGATTTTATTTATATGATTATA
1 ATATATTTAATTTATATATA-AA-CATTACTATAACTTATAATAAATTTTATTTATATGATTAAA
** * *
2112006 CTTAATAATTTTATTAGTTATCATTTTAATTTTTATAACATATTATTTATAATTAGTTATTATTT
64 CTTAATAACCTTATTAATTATCATCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTT
* *
2112071 ATATAAATTTTAATATAAAAATTAAAATGTTATAACATATAAATTATATTATTAATTTCATATAT
129 ATACAAATTTTAATATAAAAATT--AA-GTTATAACATATAAATTATATCATTAATTTCATATAT
* * * *
2112136 ATATAATAAAATAATATATTATATATAC
191 ACATAATAAAATAATATAATATATAAAA
* *
2112164 ACATATTTAATTTATACATAA
1 ATATATTTAATTTATATATAA
2112185 TTTATATATT
Statistics
Matches: 209, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
216 20 0.10
217 2 0.01
218 108 0.52
219 4 0.02
220 1 0.00
222 1 0.00
223 26 0.12
225 47 0.22
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (218 bp):
ATATATTTAATTTATATATAAACATTACTATAACTTATAATAAATTTTATTTATATGATTAAACT
TAATAACCTTATTAATTATCATCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTTAT
ACAAATTTTAATATAAAAATTAAGTTATAACATATAAATTATATCATTAATTTCATATATACATA
ATAAAATAATATAATATATAAAA
Found at i:2132327 original size:21 final size:21
Alignment explanation
Indices: 2132277--2132327 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2132267 TATCATATAT
2132277 TATAATATTAAAATATAAATTA
1 TATAAT-TTAAAATATAAATTA
*
2132299 TATCATTTAAAATATATAATT-
1 TATAATTTAAAATATA-AATTA
*
2132320 TGTAATTT
1 TATAATTT
2132328 TATATCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAATTTAAAATATAAATTA
Found at i:2132518 original size:28 final size:28
Alignment explanation
Indices: 2132459--2132519 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2132449 TCAATTCTTC
* * * *
2132459 TTAATATATATACAAATTATTATATATA
1 TTAATATATATAAAAAATATTAAAAATA
2132487 TTAATATATATAAAAAATATATAAAAAT-
1 TTAATATATATAAAAAATAT-TAAAAATA
2132515 TTAAT
1 TTAAT
2132520 TAATTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAATATATATAAAAAATATTAAAAATA
Found at i:2133231 original size:3 final size:3
Alignment explanation
Indices: 2133216--2133259 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2133206 TTGGTTCATT
*
2133216 AGG AGG GGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
2133260 AAGAGGGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:2143558 original size:17 final size:17
Alignment explanation
Indices: 2143532--2143571 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2143522 TTTAACATCA
2143532 TTTTCTTCTTTT-TCTT
1 TTTTCTTCTTTTCTCTT
2143548 TTTTCCTTCTTTTCTCTT
1 TTTT-CTTCTTTTCTCTT
*
2143566 TCTTCT
1 TTTTCT
2143572 CGAGTGGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTTCTTTTCTCTT
Found at i:2149071 original size:24 final size:24
Alignment explanation
Indices: 2149039--2149087 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2149029 CACGCCATAG
2149039 TTTCTGTTCTAGCACA-GTAGTAAT
1 TTTCTGTTCTAGCACATG-AGTAAT
*
2149063 TTTCTGTTCTGGCACATGAGTAAT
1 TTTCTGTTCTAGCACATGAGTAAT
2149087 T
1 T
2149088 ATATTTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (24 bp):
TTTCTGTTCTAGCACATGAGTAAT
Found at i:2149569 original size:13 final size:14
Alignment explanation
Indices: 2149553--2149585 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2149543 TTTTCTCCTT
2149553 TTCTTTTCTT-TCC
1 TTCTTTTCTTCTCC
2149566 TTCTTTTTCTTCTCC
1 TTC-TTTTCTTCTCC
2149581 TTCTT
1 TTCTT
2149586 CTCCCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 9 0.50
15 6 0.33
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTTTCTTCTCC
Found at i:2149581 original size:15 final size:15
Alignment explanation
Indices: 2149545--2149585 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2149535 ACCGTGAGTT
*
2149545 TTCTCCTTTTCTTTTC
1 TTCTCCTTCT-TTTTC
2149561 TT-TCCTTCTTTTTC
1 TTCTCCTTCTTTTTC
2149575 TTCTCCTTCTT
1 TTCTCCTTCTT
2149586 CTCCCTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 14 0.61
16 2 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCTCCTTCTTTTTC
Found at i:2159337 original size:30 final size:30
Alignment explanation
Indices: 2159301--2159358 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2159291 ATCAAGTCTT
2159301 TATATTTTTATTTTAAGTTAAATAAATTTA
1 TATATTTTTATTTTAAGTTAAATAAATTTA
2159331 TATATTTTTATTTTAAGTTAAATAAATT
1 TATATTTTTATTTTAAGTTAAATAAATT
2159359 ATTATGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
TATATTTTTATTTTAAGTTAAATAAATTTA
Found at i:2164182 original size:42 final size:42
Alignment explanation
Indices: 2164123--2164202 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
2164113 TCAAGGAAAG
* * * *
2164123 GCTGAATACAGGAAAGAATGTTCATATTGTTCGTAGTTGTTT
1 GCTGAACAAAGGAAAGAATGTTCACATTGTTCATAGTTGTTT
*
2164165 GCTGAACAAAGGAAAGAATGTTTACATTGTTCATAGTT
1 GCTGAACAAAGGAAAGAATGTTCACATTGTTCATAGTT
2164203 CTCTTCCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (42 bp):
GCTGAACAAAGGAAAGAATGTTCACATTGTTCATAGTTGTTT
Found at i:2169178 original size:3 final size:3
Alignment explanation
Indices: 2169172--2169208 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2169162 ACATCATCCA
*
2169172 TAT TAT TAT TAT TAT TAT TAT TAT TAA T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2169209 GAGGAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2169866 original size:2 final size:2
Alignment explanation
Indices: 2169859--2169886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2169849 AATATTTTAT
2169859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2169887 ACAGATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2189516 original size:60 final size:60
Alignment explanation
Indices: 2189423--2189720 Score: 388
Period size: 60 Copynumber: 5.0 Consensus size: 60
2189413 TTTGATTTAA
* *
2189423 AAAGGAGGACCTGAAGTCC-CGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAAGT
1 AAAGGAGGACCTGAAG-CCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
* *
2189483 AAAGGGGGACCTGAAGTCC-CAATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGAGGACCTGAAG-CCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
* *
2189543 AAATGAGGACCTGAAGCCTCGATTTATATATGGTGACGTGAGTAGTTCCCACGAGTAGGT
1 AAAGGAGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
* * * *
2189603 AAAAGAGGATCTGAAGCCTCGATTTATGTATGGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGAGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
* * * * *** *
2189663 AAAGGAGGACTTAAAGCCCCGA-TT-CATATGGTGACGTGAACAATTCCCACGAGTAGGT
1 AAAGGAGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
2189721 GATGATGTCT
Statistics
Matches: 212, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
58 27 0.13
59 4 0.02
60 181 0.85
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (60 bp):
AAAGGAGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGTAGTTCCCACGAGTAGGT
Found at i:2193425 original size:19 final size:17
Alignment explanation
Indices: 2193390--2193434 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2193380 AAAAATTTAT
*
2193390 TTAAATTTATTAAAATAA
1 TTAAATTTTTTAAAAT-A
2193408 TTAAATTTTTTAAAAATA
1 TTAAATTTTTT-AAAATA
*
2193426 TTATATTTT
1 TTAAATTTT
2193435 AAAAATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTTTTTAAAATA
Found at i:2193427 original size:27 final size:26
Alignment explanation
Indices: 2193375--2193428 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2193365 ACGTAATAAA
**
2193375 AAAATAAAAATTTATTTAAATTTATT
1 AAAATAAAAATTTATTTAAAAATATT
2193401 AAAATAATTAAATTT-TTTAAAAATATT
1 AAAATAA--AAATTTATTTAAAAATATT
2193428 A
1 A
2193429 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 11 0.46
28 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATAAAAATTTATTTAAAAATATT
Found at i:2193436 original size:16 final size:17
Alignment explanation
Indices: 2193415--2193446 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2193405 TAATTAAATT
2193415 TTTTAAAAATA-TTATA
1 TTTTAAAAATACTTATA
2193431 TTTTAAAAATACTTAT
1 TTTTAAAAATACTTAT
2193447 TCTCCATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAAATACTTATA
Found at i:2197491 original size:2 final size:2
Alignment explanation
Indices: 2197484--2197511 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2197474 GATGAGGTTA
2197484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2197512 TTGCAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2206862 original size:16 final size:15
Alignment explanation
Indices: 2206841--2206873 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
2206831 TGTTTGATAA
2206841 ATTTTTTTAATAAGTT
1 ATTTTTTT-ATAAGTT
2206857 ATTTTTTTATAAGTT
1 ATTTTTTTATAAGTT
2206872 AT
1 AT
2206874 AATTTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
ATTTTTTTATAAGTT
Found at i:2206879 original size:18 final size:17
Alignment explanation
Indices: 2206840--2206872 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2206830 TTGTTTGATA
2206840 AATTTTTTTAATAAGTT
1 AATTTTTTTAATAAGTT
2206857 -ATTTTTTT-ATAAGTT
1 AATTTTTTTAATAAGTT
2206872 A
1 A
2206873 TAATTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 3
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
AATTTTTTTAATAAGTT
Found at i:2232921 original size:33 final size:31
Alignment explanation
Indices: 2232884--2232956 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2232874 CTTTAATTTT
2232884 CATAAAAATAAAAGAAAATCATATAATTAGGAA
1 CATAAAAA-AAAA-AAAATCATATAATTAGGAA
* * ** *
2232917 CATAAAAAATAATATGTTATATAATTAGGAA
1 CATAAAAAAAAAAAAATCATATAATTAGGAA
2232948 CATAAAAAA
1 CATAAAAAA
2232957 TAATATGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 24 0.69
32 3 0.09
33 8 0.23
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (31 bp):
CATAAAAAAAAAAAAATCATATAATTAGGAA
Found at i:2232942 original size:31 final size:31
Alignment explanation
Indices: 2232904--2232965 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2232894 AAAGAAAATC
2232904 ATATAATTAGGAACATAAAAAATAATATGTT
1 ATATAATTAGGAACATAAAAAATAATATGTT
2232935 ATATAATTAGGAACATAAAAAATAATATGTT
1 ATATAATTAGGAACATAAAAAATAATATGTT
2232966 TACATGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32
Consensus pattern (31 bp):
ATATAATTAGGAACATAAAAAATAATATGTT
Found at i:2233076 original size:4 final size:4
Alignment explanation
Indices: 2233064--2233093 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
2233054 ATTTTGTATT
2233064 ATTA TATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA -ATTA ATTA ATTA ATTA ATTA ATTA A
2233094 AAAAACTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2266797 original size:2 final size:2
Alignment explanation
Indices: 2266792--2266823 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2266782 TTACAATCTG
2266792 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2266824 ANNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2266815 original size:15 final size:15
Alignment explanation
Indices: 2266795--2266823 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2266785 CAATCTGATA
2266795 TATATATATATATAT
1 TATATATATATATAT
2266810 TATATATATATATA
1 TATATATATATATA
2266824 ANNNNNNNNN
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:2266903 original size:2 final size:2
Alignment explanation
Indices: 2266896--2266935 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2266886 NNNNAATCTG
2266896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2266936 ATAATAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2272292 original size:9 final size:9
Alignment explanation
Indices: 2272263--2272300 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2272253 GAGGTTGTCA
2272263 TTTAATTTT
1 TTTAATTTT
*
2272272 ATTCAA-TTT
1 -TTTAATTTT
2272281 TTTAATTTT
1 TTTAATTTT
2272290 TTTAATTTT
1 TTTAATTTT
2272299 TT
1 TT
2272301 AAGTTTTCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTAATTTT
Found at i:2272298 original size:17 final size:18
Alignment explanation
Indices: 2272263--2272307 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
2272253 GAGGTTGTCA
2272263 TTTAATTTTATTCAATTT
1 TTTAATTTTATTCAATTT
*
2272281 TTTAATTTT-TTTAATTT
1 TTTAATTTTATTCAATTT
2272298 TTTAAGTTTT
1 TTTAA-TTTT
2272308 CCGACCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTAATTTTATTCAATTT
Found at i:2272307 original size:9 final size:8
Alignment explanation
Indices: 2272263--2272307 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
2272253 GAGGTTGTCA
2272263 TTTAATTT
1 TTTAATTT
2272271 TATTCAATTT
1 T-TT-AATTT
2272281 TTTAATTTT
1 TTTAA-TTT
2272290 TTTAATTT
1 TTTAATTT
*
2272298 TTTAAGTT
1 TTTAATTT
2272306 TT
1 TT
2272308 CCGACCCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 15 0.45
9 12 0.36
10 6 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTAATTT
Found at i:2272405 original size:4 final size:4
Alignment explanation
Indices: 2272366--2272417 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
2272356 TAAAGAGGTA
*
2272366 ATTT TTTT ATTT ATATT A-TT A-TT A-TT A-TT A-TT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2272410 ATTT ATTT
1 ATTT ATTT
2272418 CAATTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 15 0.34
4 26 0.59
5 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:2272423 original size:28 final size:27
Alignment explanation
Indices: 2272371--2272434 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
2272361 AGGTAATTTT
*
2272371 TTTATTTATATTATTATTATTATTATTA
1 TTTATTTATATTATTATTATAATTA-TA
2272399 TTTATTTAT-TTATTTATT-TCAATTATA
1 TTTATTTATATTA-TTATTAT-AATTATA
2272426 TTCTATTTA
1 TT-TATTTA
2272435 CTCATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTTATATTATTATTATAATTATA
Found at i:2272581 original size:15 final size:16
Alignment explanation
Indices: 2272561--2272591 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2272551 CTGTTATGTG
2272561 GATTTT-ATTTTTAAA
1 GATTTTAATTTTTAAA
2272576 GATTTTAATTTTTAAA
1 GATTTTAATTTTTAAA
2272592 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
GATTTTAATTTTTAAA
Found at i:2276472 original size:21 final size:21
Alignment explanation
Indices: 2276448--2276490 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2276438 TCATGCTTGC
*
2276448 TCTTTTGATTCCTTCCGATGA
1 TCTTTTGATTACTTCCGATGA
2276469 TCTTTTGATTACTTCCGATGA
1 TCTTTTGATTACTTCCGATGA
2276490 T
1 T
2276491 ATGTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (21 bp):
TCTTTTGATTACTTCCGATGA
Found at i:2310865 original size:15 final size:16
Alignment explanation
Indices: 2310845--2310874 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2310835 TGTTGGGATG
2310845 ATTAAAAA-TAAAAAA
1 ATTAAAAATTAAAAAA
2310860 ATTAAAAATTAAAAA
1 ATTAAAAATTAAAAA
2310875 TTTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
ATTAAAAATTAAAAAA
Found at i:2316295 original size:4 final size:4
Alignment explanation
Indices: 2316286--2316322 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2316276 AGGTGCTCCT
2316286 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
2316323 AGGATGTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:2321095 original size:108 final size:109
Alignment explanation
Indices: 2320940--2321150 Score: 282
Period size: 108 Copynumber: 1.9 Consensus size: 109
2320930 TGTAAGAATT
* ** * * *
2320940 TTTGAGTAAATTTGAATAAAAAGGTAAATTGGGTAAGTGTGGAATAATTTCAACAGAATTTGTAT
1 TTTGAGTAAATTTGAATAAAAAGGTAAATTAGGTAAAAGTGAAATAATTTCAAAAGAATGTGTAT
* * **
2321005 TTGTAAATTGTAAAAGTTGTAACTTAATCAACATATTTTGCTAA
66 TTATAAATTATAAAAGTTGTAACCAAATCAACATATTTTGCTAA
*
2321049 TTTGAGTAAATTT-AACT-AAAAGGTAAATTAGGTAAAAGTTAAATAATTTCAAAAGAATGTGTA
1 TTTGAGTAAATTTGAA-TAAAAAGGTAAATTAGGTAAAAGTGAAATAATTTCAAAAGAATGTGTA
* *
2321112 TTTATAAATTATGAAAGTTGTAACCAAATTAACATATTT
65 TTTATAAATTATAAAAGTTGTAACCAAATCAACATATTT
2321151 AGTCATTTTA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
108 74 0.84
109 14 0.16
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (109 bp):
TTTGAGTAAATTTGAATAAAAAGGTAAATTAGGTAAAAGTGAAATAATTTCAAAAGAATGTGTAT
TTATAAATTATAAAAGTTGTAACCAAATCAACATATTTTGCTAA
Found at i:2322976 original size:30 final size:29
Alignment explanation
Indices: 2322940--2323015 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
2322930 ATTTTAATTT
2322940 TTTAAAATTTTATAATTTT-AC-ATTTCAAA
1 TTTAAAATTTT-T-ATTTTCACTATTTCAAA
*
2322969 TATTAAAATTTTTATTTTCACTTTTTCAAA
1 T-TTAAAATTTTTATTTTCACTATTTCAAA
* *
2322999 TTTAAAATCTTAATTTT
1 TTTAAAATTTTTATTTT
2323016 ATCATTGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 18 0.44
30 18 0.44
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAAAATTTTTATTTTCACTATTTCAAA
Found at i:2344600 original size:29 final size:29
Alignment explanation
Indices: 2344566--2344627 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
2344556 AATTCAATCC
2344566 ATTGAATACTTACTCTCAAGTAACCAATT
1 ATTGAATACTTACTCTCAAGTAACCAATT
*
2344595 ATTGAATACTTACTCTCAAGTAGCCAATT
1 ATTGAATACTTACTCTCAAGTAACCAATT
2344624 ATTG
1 ATTG
2344628 CATGATATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (29 bp):
ATTGAATACTTACTCTCAAGTAACCAATT
Found at i:2344687 original size:18 final size:18
Alignment explanation
Indices: 2344664--2344702 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2344654 ACAAATTAGA
*
2344664 TATGATATGATTAATTAT
1 TATGATATGATCAATTAT
2344682 TATGATATGATCAATTAT
1 TATGATATGATCAATTAT
2344700 TAT
1 TAT
2344703 ATGATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (18 bp):
TATGATATGATCAATTAT
Found at i:2344704 original size:15 final size:15
Alignment explanation
Indices: 2344680--2344753 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
2344670 ATGATTAATT
2344680 ATTATGATATGATCA
1 ATTATGATATGATCA
*
2344695 ATTATTATATGAT-A
1 ATTATGATATGATCA
* *
2344709 TGTTGTGATATGACATCA
1 -ATTATGATATG--ATCA
*
2344727 ATTATTATATGATCA
1 ATTATGATATGATCA
*
2344742 A-TAAGATATGAT
1 ATTATGATATGAT
2344754 AGGATTATAG
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
14 10 0.22
15 25 0.54
17 10 0.22
18 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (15 bp):
ATTATGATATGATCA
Found at i:2345131 original size:45 final size:45
Alignment explanation
Indices: 2345079--2345200 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 45
2345069 CATATCATGA
* * *
2345079 TATTACACGTCATATACAAAAACATATTACACATCATGATTAGGT
1 TATTACACGCCATGTATAAAAACATATTACACATCATGATTAGGT
* * * ** *
2345124 TGTTACACGCCATGTATATAAACATATAACATGTCATGGTTAGGT
1 TATTACACGCCATGTATAAAAACATATTACACATCATGATTAGGT
* *
2345169 TATCACACGCCATGTATAAAAACATGTTACAC
1 TATTACACGCCATGTATAAAAACATATTACAC
2345201 GCCATGTACA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (45 bp):
TATTACACGCCATGTATAAAAACATATTACACATCATGATTAGGT
Found at i:2345201 original size:24 final size:24
Alignment explanation
Indices: 2345173--2345344 Score: 108
Period size: 24 Copynumber: 7.4 Consensus size: 24
2345163 TTAGGTTATC
2345173 ACACGCCATGTATAAAAACATGTT
1 ACACGCCATGTATAAAAACATGTT
* * *
2345197 ACACGCCATGTACAAAAATATGTG
1 ACACGCCATGTATAAAAACATGTT
*** **
2345221 ACACAAAATGGT-T---AAGTTGTT
1 ACACGCCAT-GTATAAAAACATGTT
*
2345242 ACACGTCATGTATAAAAACATGTT
1 ACACGCCATGTATAAAAACATGTT
* * *
2345266 ACACGTCATGTACAAAAACATGTG
1 ACACGCCATGTATAAAAACATGTT
* ***
2345290 ACACGTCATGGT-T---AGGTTGTT
1 ACACGCCAT-GTATAAAAACATGTT
* *
2345311 ACACGCCATGTACAAAAACATGTG
1 ACACGCCATGTATAAAAACATGTT
2345335 ACACGCCATG
1 ACACGCCATG
2345345 GTTAGGTTGT
Statistics
Matches: 110, Mismatches: 28, Indels: 20
0.70 0.18 0.13
Matches are distributed among these distances:
20 4 0.04
21 24 0.22
24 78 0.71
25 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (24 bp):
ACACGCCATGTATAAAAACATGTT
Found at i:2345246 original size:69 final size:69
Alignment explanation
Indices: 2345159--2345344 Score: 273
Period size: 69 Copynumber: 2.7 Consensus size: 69
2345149 ATAACATGTC
* * *
2345159 ATGGTTAGGTTATCACACGCCATGTATAAAAACATGTTACACGCCATGTACAAAAATATGTGACA
1 ATGGTTAGGTTGTTACACGCCATGTATAAAAACATGTTACACGCCATGTACAAAAACATGTGACA
2345224 CAAA
66 CAAA
* * *
2345228 ATGGTTAAGTTGTTACACGTCATGTATAAAAACATGTTACACGTCATGTACAAAAACATGTGACA
1 ATGGTTAGGTTGTTACACGCCATGTATAAAAACATGTTACACGCCATGTACAAAAACATGTGACA
***
2345293 CGTC
66 CAAA
* *
2345297 ATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACGCCATG
1 ATGGTTAGGTTGTTACACGCCATGTATAAAAACATGTTACACGCCATG
2345345 GTTAGGTTGT
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 103 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (69 bp):
ATGGTTAGGTTGTTACACGCCATGTATAAAAACATGTTACACGCCATGTACAAAAACATGTGACA
CAAA
Found at i:2345321 original size:45 final size:45
Alignment explanation
Indices: 2345262--2345423 Score: 245
Period size: 45 Copynumber: 3.6 Consensus size: 45
2345252 TATAAAAACA
*
2345262 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGTCATGGTTAGGT
*
2345307 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGTCATGGTTAGGT
* * **
2345352 TGTTACACGCCATGTACAAACATATGTGACACGGT-ATGGTTAAAT
1 TGTTACACGCCATGTACAAAAACATGTGACAC-GTCATGGTTAGGT
*
2345397 TGTTACACGTCATGTACAAAAACATGT
1 TGTTACACGCCATGTACAAAAACATGT
2345424 TATACGCTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 105 0.99
46 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTGACACGTCATGGTTAGGT
Found at i:2345381 original size:159 final size:159
Alignment explanation
Indices: 2345193--2345568 Score: 529
Period size: 159 Copynumber: 2.4 Consensus size: 159
2345183 TATAAAAACA
* *
2345193 TGTTACACGCCATGTACAAAAATATGTGACACAAAATGGTTAAGTTGTTACACGTCATGTATAAA
1 TGTTACACGCCATGTACAAAAATATGTGACACGAAATGGTTAAGTTGTTACACGTCATGTACAAA
* * * * *
2345258 AACATGTTACACG-TCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTACACGCCATGT
66 AACATGTTACACGCT-ATATACAAAAACATGTAACACGTCATGATTAGGTTGTCACACGCCATAT
*
2345322 ACAAAAACATGTGACACGCCATGGTTAGGT
130 ACAAAAACATGTGACACGCCATGGTTAGAT
* ** *
2345352 TGTTACACGCCATGTACAAACATATGTGACACGGTATGGTTAAATTGTTACACGTCATGTACAAA
1 TGTTACACGCCATGTACAAAAATATGTGACACGAAATGGTTAAGTTGTTACACGTCATGTACAAA
* * * *
2345417 AACATGTTATACGCTATATATAAAAATATGTAATACGTCATGATTAGGTTGTCACACGCCATATA
66 AACATGTTACACGCTATATACAAAAACATGTAACACGTCATGATTAGGTTGTCACACGCCATATA
* *
2345482 CAAAAATATGTGACACGTCATGGTTAGAT
131 CAAAAACATGTGACACGCCATGGTTAGAT
* * ***
2345511 TGTTACACACCATGTACAAAAACATGTGACACGCCGTGGTTAAGTTGTTACACGTCAT
1 TGTTACACGCCATGTACAAAAATATGTGACACGAAATGGTTAAGTTGTTACACGTCAT
2345569 ATTGAAAAAA
Statistics
Matches: 191, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
159 190 0.99
160 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (159 bp):
TGTTACACGCCATGTACAAAAATATGTGACACGAAATGGTTAAGTTGTTACACGTCATGTACAAA
AACATGTTACACGCTATATACAAAAACATGTAACACGTCATGATTAGGTTGTCACACGCCATATA
CAAAAACATGTGACACGCCATGGTTAGAT
Found at i:2345425 original size:114 final size:114
Alignment explanation
Indices: 2345081--2345545 Score: 384
Period size: 114 Copynumber: 4.1 Consensus size: 114
2345071 TATCATGATA
* * * * *
2345081 TTACACGTCATATACAAAAACATATTACACATCATGATTAGGTTGTTACACGCCATGTATATAAA
1 TTACACGCCATATACAAAAACATGTGACACATCATGATTAGGTTGTTACACGCCATGTACAAAAA
* * * * ** * * *
2345146 CATATAACATGTCATGGTTAGGTTATCACACGCCATGTATAAAAACATG
66 TATGTGACACGTCATGGTTAAATTGTTACACGCCATGTACAAAAACATG
* * ** * * * *
2345195 TTACACGCCATGTACAAAAATATGTGACACAAAATGGTTAAGTTGTTACACGTCATGTATAAAAA
1 TTACACGCCATATACAAAAACATGTGACACATCATGATTAGGTTGTTACACGCCATGTACAAAAA
* * * * * * * ***
2345260 CATGTTACACGTCAT-GTACAAAAACATGTGACACGTCATGGT----TAGGTTG
66 TATGTGACACGTCATGGT---TAAA-TTGTTACACGCCAT-GTACAAAAACATG
* ** * *
2345309 TTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTACACGCCATGTACAAACA
1 TTACACGCCATATACAAAAACATGTGACACATCATGATTAGGTTGTTACACGCCATGTACAAAAA
*
2345374 TATGTGACACGGT-ATGGTTAAATTGTTACACGTCATGTACAAAAACATG
66 TATGTGACAC-GTCATGGTTAAATTGTTACACGCCATGTACAAAAACATG
* * * * * * * * *
2345423 TTATACGCTATATATAAAAATATGTAATACGTCATGATTAGGTTGTCACACGCCATATACAAAAA
1 TTACACGCCATATACAAAAACATGTGACACATCATGATTAGGTTGTTACACGCCATGTACAAAAA
* *
2345488 TATGTGACACGTCATGGTTAGATTGTTACACACCATGTACAAAAACATG
66 TATGTGACACGTCATGGTTAAATTGTTACACGCCATGTACAAAAACATG
*
2345537 TGACACGCC
1 TTACACGCC
2345546 GTGGTTAAGT
Statistics
Matches: 279, Mismatches: 60, Indels: 24
0.77 0.17 0.07
Matches are distributed among these distances:
110 2 0.01
111 12 0.04
112 3 0.01
113 4 0.01
114 241 0.86
115 4 0.01
116 1 0.00
117 10 0.04
118 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (114 bp):
TTACACGCCATATACAAAAACATGTGACACATCATGATTAGGTTGTTACACGCCATGTACAAAAA
TATGTGACACGTCATGGTTAAATTGTTACACGCCATGTACAAAAACATG
Found at i:2345577 original size:45 final size:44
Alignment explanation
Indices: 2345421--2345570 Score: 138
Period size: 45 Copynumber: 3.3 Consensus size: 44
2345411 TACAAAAACA
* * * * * * * *
2345421 TGTTATACGCTATATATAAAAATATGTAATACGTCATGATTAGGT
1 TGTTACACGCCATATACAAAAACATGTGACACGCCATGGTTA-GT
* * *
2345466 TGTCACACGCCATATACAAAAATATGTGACACGTCATGGTTAGAT
1 TGTTACACGCCATATACAAAAACATGTGACACGCCATGGTTAG-T
* * *
2345511 TGTTACACACCATGTACAAAAACATGTGACACGCCGTGGTTAAGT
1 TGTTACACGCCATATACAAAAACATGTGACACGCCATGGTT-AGT
*
2345556 TGTTACACGTCATAT
1 TGTTACACGCCATAT
2345571 TGAAAAAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.01
45 84 0.97
46 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (44 bp):
TGTTACACGCCATATACAAAAACATGTGACACGCCATGGTTAGT
Found at i:2345593 original size:32 final size:32
Alignment explanation
Indices: 2345554--2345639 Score: 131
Period size: 30 Copynumber: 2.8 Consensus size: 32
2345544 CCGTGGTTAA
2345554 GTTGTTACACGTCATATTGAAAAAAAAAAATT
1 GTTGTTACACGTCATATTGAAAAAAAAAAATT
*
2345586 GTTGTTACACGTCATATTG--AAAAAAATATT
1 GTTGTTACACGTCATATTGAAAAAAAAAAATT
* *
2345616 GTTGTTACACGCCATATTCAAAAA
1 GTTGTTACACGTCATATTGAAAAA
2345640 CATTTTGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 27 0.55
32 22 0.45
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (32 bp):
GTTGTTACACGTCATATTGAAAAAAAAAAATT
Found at i:2345638 original size:27 final size:28
Alignment explanation
Indices: 2345576--2345649 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 28
2345566 CATATTGAAA
*
2345576 AAAAAAAATTGTTGTTACACGTCATATT
1 AAAAAAAATTGTTGTTACACGCCATATT
2345604 GAAAAAAATATTGTTGTTACACGCCATATT
1 -AAAAAAA-ATTGTTGTTACACGCCATATT
* *
2345634 CAAAAACATT-TTGTTA
1 AAAAAAAATTGTTGTTA
2345650 AACTTTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 6 0.15
28 3 0.07
29 12 0.29
30 20 0.49
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (28 bp):
AAAAAAAATTGTTGTTACACGCCATATT
Found at i:2352440 original size:122 final size:122
Alignment explanation
Indices: 2352220--2352443 Score: 306
Period size: 122 Copynumber: 1.8 Consensus size: 122
2352210 GGTACAATTG
* * * * * *
2352220 CGTGACAAATACAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCTTG
1 CGTGACAAATACAACCGTGCATGTGCAGAATGGGCAGTGCACACGCCGATAATGATGCTGTCATG
* * * *
2352285 ATAATTATAAACGTGCATGTGCGGAGTGGGCAGTGCATACGTCGGTAATGATGCTGT
66 ATAATTACAAACGTACATGTGCGGAGCGAGCAGTGCATACGTCGGTAATGATGCTGT
* * * *
2352342 CGTGATAATTACAACCGTGCATGTGCAGAATGGGCAGTGTACACGCCGATAATGATGTTGTCATG
1 CGTGACAAATACAACCGTGCATGTGCAGAATGGGCAGTGCACACGCCGATAATGATGCTGTCATG
2352407 ATAATTAC-AACAGTACATGTGCGGAGCGAGCAGTGCA
66 ATAATTACAAAC-GTACATGTGCGGAGCGAGCAGTGCA
2352444 CATGCCGGTG
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
121 3 0.03
122 84 0.97
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (122 bp):
CGTGACAAATACAACCGTGCATGTGCAGAATGGGCAGTGCACACGCCGATAATGATGCTGTCATG
ATAATTACAAACGTACATGTGCGGAGCGAGCAGTGCATACGTCGGTAATGATGCTGT
Found at i:2352460 original size:61 final size:61
Alignment explanation
Indices: 2352229--2352459 Score: 275
Period size: 61 Copynumber: 3.8 Consensus size: 61
2352219 GCGTGACAAA
* * * *
2352229 TACAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCTTGATAAT
1 TACAACAGTGCATGTGCGGAGTGGGCAGTGCACACGCCGGTAATGATGCTGTCATGATAAT
* * * *
2352290 TATAA-ACGTGCATGTGCGGAGTGGGCAGTGCATACGTCGGTAATGATGCTGTCGTGATAAT
1 TACAACA-GTGCATGTGCGGAGTGGGCAGTGCACACGCCGGTAATGATGCTGTCATGATAAT
* * * * * *
2352351 TACAACCGTGCATGTGCAGAATGGGCAGTGTACACGCCGATAATGATGTTGTCATGATAAT
1 TACAACAGTGCATGTGCGGAGTGGGCAGTGCACACGCCGGTAATGATGCTGTCATGATAAT
* * * * *
2352412 TACAACAGTACATGTGCGGAGCGAGCAGTGCACATGCCGGTGATGATG
1 TACAACAGTGCATGTGCGGAGTGGGCAGTGCACACGCCGGTAATGATG
2352460 TACATAAGCT
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
61 141 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (61 bp):
TACAACAGTGCATGTGCGGAGTGGGCAGTGCACACGCCGGTAATGATGCTGTCATGATAAT
Found at i:2356327 original size:17 final size:17
Alignment explanation
Indices: 2356307--2356356 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
2356297 TATACACTAA
2356307 ATATAATATATATATAT
1 ATATAATATATATATAT
*
2356324 ATATACTATATA-ATTAT
1 ATATAATATATATA-TAT
2356341 ATATTAAT-TATATATA
1 ATA-TAATATATATATA
2356357 GCAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 1 0.04
17 23 0.82
18 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:2356352 original size:19 final size:23
Alignment explanation
Indices: 2356307--2356356 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
2356297 TATACACTAA
2356307 ATATAATATATATATATATATACT
1 ATATAATATATATATATATATA-T
2356331 ATATAAT-TATATAT-TA-ATTAT
1 ATATAATATATATATATATA-TAT
2356352 ATATA
1 ATATA
2356357 GCAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.28
22 4 0.16
23 7 0.28
24 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATAATATATATATATATATAT
Found at i:2365576 original size:2 final size:2
Alignment explanation
Indices: 2365571--2365598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2365561 CCCCATATAT
2365571 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2365599 AAATACGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2367222 original size:27 final size:26
Alignment explanation
Indices: 2367192--2367259 Score: 64
Period size: 31 Copynumber: 2.4 Consensus size: 26
2367182 TTTAAATTTT
* *
2367192 TAAAAATTGAATTAATCGAATTCTTAA
1 TAAAAATTGAATCAATCGAATT-ATAA
*
2367219 TAAAACTAATTGAAATCAATTGAATTATAA
1 T-AAA--AATTG-AATCAATCGAATTATAA
2367249 TAAAAATTGAA
1 TAAAAATTGAA
2367260 AATAACCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
26 2 0.06
27 6 0.18
28 3 0.09
29 3 0.09
30 9 0.26
31 11 0.32
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (26 bp):
TAAAAATTGAATCAATCGAATTATAA
Found at i:2391151 original size:2 final size:2
Alignment explanation
Indices: 2391107--2391142 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2391097 CCTTCCCCCA
*
2391107 TC TC TC TC TC TC TC TC TC CC T- TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2391143 TTTTCTCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2396514 original size:17 final size:17
Alignment explanation
Indices: 2396483--2396528 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2396473 AAAATAATTT
2396483 AATTTTTTAATTTTAA-A
1 AATTTTTTAA-TTTAATA
2396500 AATTATTTTAATTTAATA
1 AATT-TTTTAATTTAATA
*
2396518 TATTTTTTAAT
1 AATTTTTTAAT
2396529 AATATCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTTAATTTAATA
Found at i:2397565 original size:6 final size:6
Alignment explanation
Indices: 2397526--2397550 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2397516 CTAAATTAAT
2397526 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
2397551 CATAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:2398412 original size:25 final size:26
Alignment explanation
Indices: 2398364--2398413 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2398354 TACCATTAAA
2398364 AAAATAATTAAATTTAAATAATTTTT
1 AAAATAATTAAATTTAAATAATTTTT
*
2398390 AAAATCAA-TAAA-TTAAATTATTTT
1 AAAAT-AATTAAATTTAAATAATTTT
2398414 AATTTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 9 0.41
27 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATAATTAAATTTAAATAATTTTT
Found at i:2399646 original size:18 final size:18
Alignment explanation
Indices: 2399610--2399658 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2399600 TGAAATTATA
* *
2399610 TAAAAAT-TAATTAATTT
1 TAAAAATATATTTTATTT
2399627 TAAATAA-ATATTTTATTT
1 TAAA-AATATATTTTATTT
2399645 TAAAAATATATTTT
1 TAAAAATATATTTT
2399659 TTAGACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAAATATATTTTATTT
Found at i:2407057 original size:29 final size:29
Alignment explanation
Indices: 2406996--2407067 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 29
2406986 TATTAAACAT
2406996 AATTTATTT-AACTTGAAATAAAAATATAAA
1 AATTTATTTGAA--TGAAATAAAAATATAAA
*
2407026 AATTTGA-TTGAATGAAATAGAAAA-ATATA
1 AATTT-ATTTGAATGAAATA-AAAATATAAA
2407055 AATTTATTTGAAT
1 AATTTATTTGAAT
2407068 TATCTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
29 22 0.59
30 11 0.30
31 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTTATTTGAATGAAATAAAAATATAAA
Found at i:2415605 original size:17 final size:18
Alignment explanation
Indices: 2415571--2415608 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2415561 TATTTAAATT
*
2415571 TAAAATATATAATTATAA
1 TAAAATATATAATAATAA
2415589 TAAAATA-ATAATAATAA
1 TAAAATATATAATAATAA
2415606 TAA
1 TAA
2415609 CATCAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATATATAATAATAA
Found at i:2415795 original size:18 final size:18
Alignment explanation
Indices: 2415774--2415813 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2415764 GTATACATGC
*
2415774 TTAAACACGATAATACGA
1 TTAAACACGATAACACGA
2415792 TTAAACACGATAACACGA
1 TTAAACACGATAACACGA
2415810 TTAA
1 TTAA
2415814 GTAAACGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (18 bp):
TTAAACACGATAACACGA
Found at i:2422947 original size:21 final size:19
Alignment explanation
Indices: 2422908--2422946 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2422898 TTTTGAAGTA
2422908 TGCTTAAAACCGTTCTCTC
1 TGCTTAAAACCGTTCTCTC
2422927 TGCTTAAAACCGTTCTCTC
1 TGCTTAAAACCGTTCTCTC
2422946 T
1 T
2422947 CCGTGCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (19 bp):
TGCTTAAAACCGTTCTCTC
Found at i:2423226 original size:2 final size:2
Alignment explanation
Indices: 2423221--2423250 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2423211 TTTCAGTTTC
2423221 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2423251 TTGGTGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2460826 original size:17 final size:18
Alignment explanation
Indices: 2460788--2460827 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2460778 TAATATTCTT
2460788 ATTTATTTTATATCATAA
1 ATTTATTTTATATCATAA
* *
2460806 ATTTATTTT-TTTCATAC
1 ATTTATTTTATATCATAA
2460823 ATTTA
1 ATTTA
2460828 AACTATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATTTTATATCATAA
Found at i:2460966 original size:20 final size:21
Alignment explanation
Indices: 2460926--2460967 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2460916 ACTTAATACT
* *
2460926 TTTATTTTTTATATTATAAAA
1 TTTATTTTTCATATTAAAAAA
2460947 TTTATTTTTCATA-TAAAAAA
1 TTTATTTTTCATATTAAAAAA
2460967 T
1 T
2460968 ATTGGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATTTTTCATATTAAAAAA
Found at i:2461606 original size:16 final size:14
Alignment explanation
Indices: 2461587--2461620 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
2461577 GAATTTTGAA
2461587 AAAATAAATTATAATG
1 AAAATAAA-TA-AATG
2461603 AAAATAAATAAATG
1 AAAATAAATAAATG
2461617 AAAA
1 AAAA
2461621 AGAAGTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAATAAATAAATG
Found at i:2472546 original size:31 final size:31
Alignment explanation
Indices: 2472508--2472570 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2472498 TTACTGACAT
*
2472508 TTTCTTATTCAATGACAACAGAGCATAAGGA
1 TTTCTTATTCAATGACAACAGAGAATAAGGA
2472539 TTTCTTATTCAATGACAACAGAGAATAAGGA
1 TTTCTTATTCAATGACAACAGAGAATAAGGA
2472570 T
1 T
2472571 ATAAGAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (31 bp):
TTTCTTATTCAATGACAACAGAGAATAAGGA
Found at i:2472892 original size:2 final size:2
Alignment explanation
Indices: 2472885--2472910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2472875 ATAGATAGAG
2472885 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2472911 CTATTGCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2477326 original size:23 final size:24
Alignment explanation
Indices: 2477300--2477347 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2477290 TTTTATCTTC
* *
2477300 ATTT-TTTTATATAAAAATTAAAT
1 ATTTATTTTATAAAAAAATAAAAT
2477323 ATTTATTTTATAAAAAAATAAAAT
1 ATTTATTTTATAAAAAAATAAAAT
2477347 A
1 A
2477348 CATAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTATTTTATAAAAAAATAAAAT
Found at i:2487883 original size:3 final size:3
Alignment explanation
Indices: 2487860--2487909 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
2487850 TTTCAGTCCT
*
2487860 TTC TTC TCC TTC TT- TTCC TTC TTC TTC TTC TTC TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
2487904 TCC TTC
1 TTC TTC
2487910 ACCTTCCTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:2497656 original size:2 final size:2
Alignment explanation
Indices: 2497649--2497675 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2497639 GAGAACCGTG
2497649 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2497676 GTTTGCTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2512294 original size:21 final size:21
Alignment explanation
Indices: 2512269--2512327 Score: 55
Period size: 26 Copynumber: 2.6 Consensus size: 21
2512259 TTAGTTTTAA
*
2512269 TATTTTGATATAATATTATTT
1 TATTTTGATAAAATATTATTT
2512290 TATTTGGTTTTGATAAAATATTATTT
1 TA-----TTTTGATAAAATATTATTT
*
2512316 TATTTTGTTAAA
1 TATTTTGATAAA
2512328 TAATAACGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
21 11 0.35
26 20 0.65
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (21 bp):
TATTTTGATAAAATATTATTT
Found at i:2512301 original size:26 final size:26
Alignment explanation
Indices: 2512271--2512320 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2512261 AGTTTTAATA
*
2512271 TTTTGATATAATATTATTTTATTTGG
1 TTTTGATAAAATATTATTTTATTTGG
2512297 TTTTGATAAAATATTATTTTATTT
1 TTTTGATAAAATATTATTTTATTT
2512321 TGTTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTTGATAAAATATTATTTTATTTGG
Found at i:2512538 original size:14 final size:14
Alignment explanation
Indices: 2512519--2512548 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2512509 AAATGGAAAA
*
2512519 AACCAACTTTAATT
1 AACCAAATTTAATT
2512533 AACCAAATTTAATT
1 AACCAAATTTAATT
2512547 AA
1 AA
2512549 TTTTGATAGC
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:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
AACCAAATTTAATT
Found at i:2516411 original size:36 final size:37
Alignment explanation
Indices: 2516342--2516411 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
2516332 AATTATAACA
* *
2516342 TATATAATAATATAAAATATATTATAGCGTATATATT
1 TATATAATAATATAAAATATATTATAACATATATATT
*
2516379 TATATGATAATAT-AAATATATTATAACATATAT
1 TATATAATAATATAAAATATATTATAACATATAT
2516412 CTATACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATAATAATATAAAATATATTATAACATATATATT
Found at i:2516798 original size:2 final size:2
Alignment explanation
Indices: 2516791--2516849 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
2516781 CTGGTACCTC
2516791 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
2516833 CT CT CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT C
2516850 AATTAGTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:2553062 original size:10 final size:10
Alignment explanation
Indices: 2553044--2553090 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
2553034 CTTTCTTTCC
2553044 CTCTCTCTGT
1 CTCTCTCTGT
*
2553054 CTCTGTCTGT
1 CTCTCTCTGT
*
2553064 CTCTCTCTCT
1 CTCTCTCTGT
*
2553074 CTCTCTCCGT
1 CTCTCTCTGT
2553084 CGTCTCT
1 C-TCTCT
2553091 TTCTGCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
10 26 0.84
11 5 0.16
ACGTcount: A:0.00, C:0.43, G:0.11, T:0.47
Consensus pattern (10 bp):
CTCTCTCTGT
Found at i:2554117 original size:23 final size:23
Alignment explanation
Indices: 2554091--2554158 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2554081 GAATTTAATA
2554091 TTTTTATATTAAAAATATTAAAT
1 TTTTTATATTAAAAATATTAAAT
*
2554114 TTTTTATAATT--AAATATTCAA-
1 TTTTTAT-ATTAAAAATATTAAAT
* *
2554135 TATTTATAGTAAAAATTATTAAAT
1 TTTTTATATTAAAAA-TATTAAAT
2554159 AACTGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 12 0.33
23 13 0.36
24 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
TTTTTATATTAAAAATATTAAAT
Found at i:2554139 original size:24 final size:23
Alignment explanation
Indices: 2554085--2554139 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
2554075 ATATTTGAAT
2554085 TTAATA-TTTTTATATTAAAAATA
1 TTAATATTTTTTATATT-AAAATA
2554108 TTAA-ATTTTTTATAATT-AAATA
1 TTAATATTTTTTAT-ATTAAAATA
2554130 TTCAATATTT
1 TT-AATATTT
2554140 ATAGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 8 0.29
23 13 0.46
24 7 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATTTTTTATATTAAAATA
Found at i:2554159 original size:23 final size:21
Alignment explanation
Indices: 2554093--2554159 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
2554083 ATTTAATATT
2554093 TTTATATTAAAAATATTAAAT-
1 TTTATA-TAAAAATATTAAATA
* *
2554114 TTTTTATAATTAAATATTCAATA
1 TTTATATAA--AAATATTAAATA
2554137 TTTATAGTAAAAATTATTAAATA
1 TTTATA-TAAAAA-TATTAAATA
2554160 ACTGAAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.08
21 5 0.14
22 13 0.35
23 13 0.35
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
TTTATATAAAAATATTAAATA
Found at i:2569033 original size:28 final size:28
Alignment explanation
Indices: 2568976--2569152 Score: 119
Period size: 28 Copynumber: 6.4 Consensus size: 28
2568966 AACAACTGAA
* * *
2568976 TTTTCAATATAACATATGAA-AACTACAT
1 TTTTCAATATGACATGT-AATAACTATAT
*
2569004 TTTTCAATATGACATGTAATAATTATAT
1 TTTTCAATATGACATGTAATAACTATAT
* ** *
2569032 TTTTCAACATGGTATGTAATAACTA-AA
1 TTTTCAATATGACATGTAATAACTATAT
* * ** *
2569059 TTTTCAACATAATGTGTAACAACTATAT
1 TTTTCAATATGACATGTAATAACTATAT
* * * * *
2569087 TTTTTAATATAACGTATAATAACTA-AA
1 TTTTCAATATGACATGTAATAACTATAT
* * * *
2569114 TTTTCAACATGAGATGTAACAATTATAT
1 TTTTCAATATGACATGTAATAACTATAT
2569142 TTTT-AATATGA
1 TTTTCAATATGA
2569153 TGTATAACAA
Statistics
Matches: 116, Mismatches: 30, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
27 48 0.41
28 68 0.59
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (28 bp):
TTTTCAATATGACATGTAATAACTATAT
Found at i:2569064 original size:55 final size:54
Alignment explanation
Indices: 2569004--2569179 Score: 167
Period size: 55 Copynumber: 3.2 Consensus size: 54
2568994 AAAACTACAT
* * *
2569004 TTTTCAATATGACATGTAATAATTATATTTTTCAACAT-GGTATGTAATAACTAAA
1 TTTTCAACATGACATGTAACAATTATATTTTTCAACATACGTA--TAATAACTAAA
* ** * * *
2569059 TTTTCAACATAATGTGTAACAACTATATTTTTTAATATAACGTATAATAACTAAA
1 TTTTCAACATGACATGTAACAATTATATTTTTCAACAT-ACGTATAATAACTAAA
* * * * *
2569114 TTTTCAACATGAGATGTAACAATTATATTTTT-AATATGATGTATAACAATTAAA
1 TTTTCAACATGACATGTAACAATTATATTTTTCAACAT-ACGTATAATAACTAAA
*
2569168 TTTTTAACATGA
1 TTTTCAACATGA
2569180 TAAAATAATA
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
54 29 0.29
55 69 0.68
57 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (54 bp):
TTTTCAACATGACATGTAACAATTATATTTTTCAACATACGTATAATAACTAAA
Found at i:2569076 original size:27 final size:28
Alignment explanation
Indices: 2569018--2569123 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 28
2569008 CAATATGACA
* * ** *
2569018 TGTAATAATTATATTTTTCAACATGGTA
1 TGTAATAACTATAATTTTCAACATAATG
2569046 TGTAATAACTA-AATTTTCAACATAATG
1 TGTAATAACTATAATTTTCAACATAATG
* * * * *
2569073 TGTAACAACTATATTTTTTAATATAACG
1 TGTAATAACTATAATTTTCAACATAATG
*
2569101 TATAATAACTA-AATTTTCAACAT
1 TGTAATAACTATAATTTTCAACAT
2569124 GAGATGTAAC
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
27 31 0.50
28 31 0.50
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (28 bp):
TGTAATAACTATAATTTTCAACATAATG
Found at i:2569083 original size:83 final size:82
Alignment explanation
Indices: 2568947--2569144 Score: 199
Period size: 83 Copynumber: 2.4 Consensus size: 82
2568937 TAATATGGTA
* * *
2568947 TAAA-TTT-AACATAGTATGTAACAACTGAATTTTCAATATAACATATGAAAACTACATTTTTCA
1 TAAATTTTCAACATGGTATGTAACAACTAAATTTTCAACATAACATATGAAAACTACATTTTTCA
* * *
2569010 ATATGACATGTAATAAT
66 ATATAACATATAATAAC
* * * *
2569027 TATATTTTTCAACATGGTATGTAATAACTAAATTTTCAACAT-A-ATGTGTAACAACTATATTTT
1 TA-AATTTTCAACATGGTATGTAACAACTAAATTTTCAACATAACATATG-AA-AACTACATTTT
* *
2569090 TTAATATAACGTATAATAAC
63 TCAATATAACATATAATAAC
* *
2569110 TAAATTTTCAACATGAG-ATGTAACAATTATATTTT
1 TAAATTTTCAACATG-GTATGTAACAACTAAATTTT
2569145 TAATATGATG
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
80 2 0.02
81 5 0.05
82 33 0.34
83 56 0.58
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (82 bp):
TAAATTTTCAACATGGTATGTAACAACTAAATTTTCAACATAACATATGAAAACTACATTTTTCA
ATATAACATATAATAAC
Found at i:2569143 original size:27 final size:27
Alignment explanation
Indices: 2569032--2569180 Score: 111
Period size: 27 Copynumber: 5.5 Consensus size: 27
2569022 ATAATTATAT
* * *
2569032 TTTTCAACATGGTATGTAATAACTAAA
1 TTTTCAACATGATGTGTAACAACTAAA
* *
2569059 TTTTCAACATAATGTGTAACAACTATAT
1 TTTTCAACATGATGTGTAACAACTA-AA
* * * * * *
2569087 TTTTTAATATAACGTATAATAACTAAA
1 TTTTCAACATGATGTGTAACAACTAAA
* *
2569114 TTTTCAACATGA-GATGTAACAATTATA
1 TTTTCAACATGATG-TGTAACAACTAAA
* * * *
2569141 TTTTTAATATGATGTATAACAATTAAA
1 TTTTCAACATGATGTGTAACAACTAAA
*
2569168 TTTTTAACATGAT
1 TTTTCAACATGAT
2569181 AAAATAATAT
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
26 1 0.01
27 73 0.76
28 22 0.23
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (27 bp):
TTTTCAACATGATGTGTAACAACTAAA
Found at i:2569198 original size:28 final size:27
Alignment explanation
Indices: 2569130--2569203 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
2569120 ACATGAGATG
* **
2569130 TAACAATTATATTTTTAATATGATGTA
1 TAACAATTATATTTTTAACATGATAAA
*
2569157 TAACAATTAAATTTTTAACATGATAAAA
1 TAACAATTATATTTTTAACATGAT-AAA
* *
2569185 TAATATTTATATTTTTAAC
1 TAACAATTATATTTTTAAC
2569204 TCAATTTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (27 bp):
TAACAATTATATTTTTAACATGATAAA
Found at i:2569198 original size:55 final size:54
Alignment explanation
Indices: 2569052--2569202 Score: 142
Period size: 55 Copynumber: 2.8 Consensus size: 54
2569042 GGTATGTAAT
*** * *
2569052 AACTAAATTTTCAACAT-AATGTGTAACAACTATATTTTTTAATATAACGTATAAT
1 AACTAAATTTTCAACATGAA-AAATAACAATTATA-TTTTTAATATAACGTATAAC
* ** * *
2569107 AACTAAATTTTCAACATGAGATGTAACAATTATATTTTTAATATGATGTATAAC
1 AACTAAATTTTCAACATGAAAAATAACAATTATATTTTTAATATAACGTATAAC
* * * *
2569161 AATTAAATTTTTAACATGATAAAATAATATTTATATTTTTAA
1 AACTAAATTTTCAACATGA-AAAATAACAATTATATTTTTAA
2569203 CTCAATTTTC
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 34 0.42
55 46 0.57
56 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (54 bp):
AACTAAATTTTCAACATGAAAAATAACAATTATATTTTTAATATAACGTATAAC
Found at i:2569459 original size:20 final size:21
Alignment explanation
Indices: 2569420--2569459 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2569410 TATTATTTTA
2569420 TTTTATTTTAAATTTTTAAAT
1 TTTTATTTTAAATTTTTAAAT
*
2569441 TTTTATTTT-TATTTTTAAA
1 TTTTATTTTAAATTTTTAAA
2569460 AATTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTTTAAATTTTTAAAT
Found at i:2569465 original size:21 final size:21
Alignment explanation
Indices: 2569419--2569467 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2569409 ATATTATTTT
2569419 ATTTTATTTTAAATTTTTAAA
1 ATTTTATTTTAAATTTTTAAA
* *
2569440 TTTTTATTTT-TATTTTTAAAA
1 ATTTTATTTTAAATTTTT-AAA
2569461 ATTTTAT
1 ATTTTAT
2569468 AATTTCATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTAAATTTTTAAA
Found at i:2570840 original size:15 final size:16
Alignment explanation
Indices: 2570822--2570851 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2570812 TATATATAAA
2570822 TATATTA-ATAATATT
1 TATATTACATAATATT
2570837 TATATTACATAATAT
1 TATATTACATAATAT
2570852 AATTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTACATAATATT
Found at i:2575107 original size:20 final size:20
Alignment explanation
Indices: 2575069--2575107 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2575059 TGTTAATATG
* *
2575069 ATATTAATTAAATATATTAT
1 ATATGAATTAAATAGATTAT
*
2575089 ATATGAATTACATAGATTA
1 ATATGAATTAAATAGATTA
2575108 ATCGCATAAG
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:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATGAATTAAATAGATTAT
Found at i:2586517 original size:20 final size:21
Alignment explanation
Indices: 2586483--2586523 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2586473 TTGTTATCAT
*
2586483 ACCCTTGTAAGAAAATTGTTC
1 ACCCTTGTAAAAAAATTGTTC
2586504 ACCC-TGTAAAAAAATTGTTC
1 ACCCTTGTAAAAAAATTGTTC
2586524 TACAGACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
ACCCTTGTAAAAAAATTGTTC
Found at i:2588633 original size:2 final size:2
Alignment explanation
Indices: 2588614--2588690 Score: 112
Period size: 2 Copynumber: 41.5 Consensus size: 2
2588604 CTTTAAGTAC
2588614 TA TA T- TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2588653 -A TA TA TA -A TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2588691 TTTAGGTGGT
Statistics
Matches: 69, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2588672 original size:35 final size:35
Alignment explanation
Indices: 2588614--2588689 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 35
2588604 CTTTAAGTAC
*
2588614 TATATTATATAATAATATATATATATATATATATA
1 TATAATATATAATAATATATATATATATATATATA
2588649 TATAATATATAATATATATTATATATATATATATATA
1 TATAATATATAATA-ATA-TATATATATATATATATA
2588686 TATA
1 TATA
2588690 TTTTAGGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 13 0.34
36 3 0.08
37 22 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATAATATATAATAATATATATATATATATATATA
Found at i:2589707 original size:53 final size:53
Alignment explanation
Indices: 2589624--2589727 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
2589614 TAGTGTAATA
* * *
2589624 TTGGGCCTAGTGGGTCAAAGTTGGGACAAGTTTT-TTTCTTCATAGGTCATTG
1 TTGGGCCTAGTGGGTCAAAGATGAGACAAGTTTTGTTTCTTAATAGGTCATTG
* * * *
2589676 TTGGGCCTCGGTGGGTCCAAGATGAGCCAAGTTTTGTTTCTTAATGGGTCAT
1 TTGGGCCT-AGTGGGTCAAAGATGAGACAAGTTTTGTTTCTTAATAGGTCAT
2589728 CGGTGGTACT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 8 0.19
53 21 0.49
54 14 0.33
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (53 bp):
TTGGGCCTAGTGGGTCAAAGATGAGACAAGTTTTGTTTCTTAATAGGTCATTG
Found at i:2595855 original size:29 final size:29
Alignment explanation
Indices: 2595813--2595873 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
2595803 CCTCTGGTTA
* *
2595813 TTGGGCTTTTATAATGTATCGGGTGAGTT
1 TTGGGCTTTGATAAAGTATCGGGTGAGTT
2595842 TTGGGCTTTGATAAAGTATCGGGTGAGTT
1 TTGGGCTTTGATAAAGTATCGGGTGAGTT
2595871 TTG
1 TTG
2595874 ATCCTAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.07, G:0.33, T:0.43
Consensus pattern (29 bp):
TTGGGCTTTGATAAAGTATCGGGTGAGTT
Found at i:2596308 original size:33 final size:33
Alignment explanation
Indices: 2596271--2596345 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
2596261 TGTTGACTTA
* **
2596271 ATATGTTAACATATTATAATTGCTTATAATGTG
1 ATATGTTAACATATTACAATTAATTATAATGTG
*
2596304 ATATGTCAACATATTACAATTAATTATAATGTG
1 ATATGTTAACATATTACAATTAATTATAATGTG
*
2596337 ACATGTTAA
1 ATATGTTAA
2596346 TTTGACATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (33 bp):
ATATGTTAACATATTACAATTAATTATAATGTG
Found at i:2602031 original size:2 final size:2
Alignment explanation
Indices: 2602026--2602117 Score: 78
Period size: 2 Copynumber: 44.5 Consensus size: 2
2602016 ATATATGTGT
* ** *
2602026 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ANC TC AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG
* * *
2602069 AT ATG TG -G TAG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG CAG
1 AG A-G AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG
2602113 AG AG A
1 AG AG A
2602118 ACAGGGTGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.01
2 72 0.95
3 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.43, T:0.05
Consensus pattern (2 bp):
AG
Found at i:2602652 original size:261 final size:261
Alignment explanation
Indices: 2602188--2602711 Score: 1039
Period size: 261 Copynumber: 2.0 Consensus size: 261
2602178 GTTGATGCCC
2602188 TTCTAAACTTGCTTGATCCAGAAGATTTATTGCTTCATCAAAATTTTCATATTCCAGCAATATCT
1 TTCTAAACTTGCTTGATCCAGAAGATTTATTGCTTCATCAAAATTTTCATATTCCAGCAATATCT
2602253 TCATAAAATAAAAAGCGTTAGAAACTGAACTCCGACCAATTACATGATAAATACTACTAATTGCT
66 TCATAAAATAAAAAGCGTTAGAAACTGAACTCCGACCAATTACATGATAAATACTACTAATTGCT
2602318 CCCCTCTCCTACTCACAAAAGGTATTCATAGTCGAGAGACAAATGTAAATTTTGCTTTAGCTGGA
131 CCCCTCTCCTACTCACAAAAGGTATTCATAGTCGAGAGACAAATGTAAATTTTGCTTTAGCTGGA
2602383 TATTTTCAGACAGGACAATCCTATGCTTTGTTATTATACATACTAAAAATATAGCAAGAAGACAG
196 TATTTTCAGACAGGACAATCCTATGCTTTGTTATTATACATACTAAAAATATAGCAAGAAGACAG
2602448 T
261 T
2602449 TTCTAAACTTGCTTGATCCAGAAGATTTATTGCTTCATCAAAATTTTCATATTCCAGCAATATCT
1 TTCTAAACTTGCTTGATCCAGAAGATTTATTGCTTCATCAAAATTTTCATATTCCAGCAATATCT
2602514 TCATAAAATAAAAAGCGTTAGAAACTGAACTCCGACCAATTACATGATAAATACTACTAATTGCT
66 TCATAAAATAAAAAGCGTTAGAAACTGAACTCCGACCAATTACATGATAAATACTACTAATTGCT
*
2602579 CCCCTCTGCTACTCACAAAAGGTATTCATAGTCGAGAGACAAATGTAAATTTTGCTTTAGCTGGA
131 CCCCTCTCCTACTCACAAAAGGTATTCATAGTCGAGAGACAAATGTAAATTTTGCTTTAGCTGGA
2602644 TATTTTCAGACAGGACAATCCTATGCTTTGTTATTATACATACTAAAAATATAGCAAGAAGACAG
196 TATTTTCAGACAGGACAATCCTATGCTTTGTTATTATACATACTAAAAATATAGCAAGAAGACAG
2602709 T
261 T
2602710 TT
1 TT
2602712 TGGGTGGTTA
Statistics
Matches: 262, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
261 262 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (261 bp):
TTCTAAACTTGCTTGATCCAGAAGATTTATTGCTTCATCAAAATTTTCATATTCCAGCAATATCT
TCATAAAATAAAAAGCGTTAGAAACTGAACTCCGACCAATTACATGATAAATACTACTAATTGCT
CCCCTCTCCTACTCACAAAAGGTATTCATAGTCGAGAGACAAATGTAAATTTTGCTTTAGCTGGA
TATTTTCAGACAGGACAATCCTATGCTTTGTTATTATACATACTAAAAATATAGCAAGAAGACAG
T
Found at i:2614981 original size:2 final size:2
Alignment explanation
Indices: 2614974--2615012 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2614964 ACTAAATGTA
*
2614974 TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2615013 CAGCTCGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:2626368 original size:2 final size:2
Alignment explanation
Indices: 2626361--2626395 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2626351 AAGCCTCTGT
* *
2626361 TC TC TC TC TC TC TC TC TC GC TC TC TC CC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2626396 GTCAATATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (2 bp):
TC
Found at i:2636660 original size:12 final size:12
Alignment explanation
Indices: 2636644--2636672 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2636634 GGTCAAATCT
2636644 TAAAAAAAAG-G
1 TAAAAAAAAGAG
2636655 TAAAAAAAAGAG
1 TAAAAAAAAGAG
2636667 TAAAAA
1 TAAAAA
2636673 TTCAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (12 bp):
TAAAAAAAAGAG
Done.