Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 51 of 187
Found at i:15178211 original size:42 final size:42
Alignment explanation
Indices: 15178094--15178275 Score: 242
Period size: 42 Copynumber: 4.3 Consensus size: 42
15178084 AAGAACATGA
* *
15178094 CGCTTAGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGG
1 CGCTTAGAAAAAAACGCCACTAAAGACAATGTTCTTTAGCGG
* *
15178136 CGCTTAGAAAAAAAACG-CAGCTAAAGGCAATGTTCTTTAGTGG
1 CGCTTAG-AAAAAAACGCCA-CTAAAGACAATGTTCTTTAGCGG
* *
15178179 CGCTTAGAAAGAAACGCCACTAAAGACCATGTTCTTTCA-CGG
1 CGCTTAGAAAAAAACGCCACTAAAGACAATGTTCTTT-AGCGG
* * *
15178221 CGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGG
1 CGCTTAGAAAAAAACGCCACTAAAGACAATGTTCTTTAGCGG
15178263 CGCTTAGAAAAAA
1 CGCTTAGAAAAAA
15178276 CGCTGCAAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
41 1 0.01
42 84 0.68
43 39 0.31
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (42 bp):
CGCTTAGAAAAAAACGCCACTAAAGACAATGTTCTTTAGCGG
Found at i:15179490 original size:26 final size:27
Alignment explanation
Indices: 15179461--15179512 Score: 88
Period size: 26 Copynumber: 1.9 Consensus size: 27
15179451 AAGGTCTCAA
15179461 AAAATTTAAAAATTT-TATCTCTTTAG
1 AAAATTTAAAAATTTATATCTCTTTAG
15179487 AAAATTTAAAAATTTAATATCTCTTT
1 AAAATTTAAAAATTT-ATATCTCTTT
15179513 TTCAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAATTTAAAAATTTATATCTCTTTAG
Found at i:15180049 original size:18 final size:18
Alignment explanation
Indices: 15180007--15180062 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
15179997 ATGTAAGTCA
* *
15180007 TGTTAATAATTAATTAAAT
1 TGTTAAAAATTAA-AAAAT
*
15180026 TTTTAAAAATTAAAAAAT
1 TGTTAAAAATTAAAAAAT
*
15180044 TGTTAACAATTTAAAAAAT
1 TGTTAA-AAATTAAAAAAT
15180063 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (18 bp):
TGTTAAAAATTAAAAAAT
Found at i:15180103 original size:16 final size:16
Alignment explanation
Indices: 15180082--15180116 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15180072 TTTAATTATA
15180082 TAAAAATAATAAAAAT
1 TAAAAATAATAAAAAT
*
15180098 TAAAAATGATAAAAAT
1 TAAAAATAATAAAAAT
15180114 TAA
1 TAA
15180117 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAATAATAAAAAT
Found at i:15183498 original size:30 final size:30
Alignment explanation
Indices: 15183462--15183522 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
15183452 AAGACAAAGG
*
15183462 ATTGTCACTAGTTTTGGACCTAATTTCCTT
1 ATTGTCACTAGTTTCGGACCTAATTTCCTT
15183492 ATTGTCACTAGTTTCGGACCTAATTTCCTT
1 ATTGTCACTAGTTTCGGACCTAATTTCCTT
15183522 A
1 A
15183523 CTTCTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.44
Consensus pattern (30 bp):
ATTGTCACTAGTTTCGGACCTAATTTCCTT
Found at i:15185713 original size:15 final size:15
Alignment explanation
Indices: 15185693--15185728 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
15185683 GGATTCACTC
15185693 AGTTCATTATGTACT
1 AGTTCATTATGTACT
15185708 AGTTCATTATGTACT
1 AGTTCATTATGTACT
15185723 AGTTCA
1 AGTTCA
15185729 AATCCACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (15 bp):
AGTTCATTATGTACT
Found at i:15187807 original size:36 final size:35
Alignment explanation
Indices: 15187764--15187840 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
15187754 AATCTTTATA
*
15187764 TTTTAT-AA-TTCATAATTTTTTATATTATTAAAATTT
1 TTTTATAAATTTCATAATTTTTTAAATT-TT--AATTT
*
15187800 TTTTATAAAATTTTATAATTTTTTAAATTTTAATTT
1 TTTTAT-AAATTTCATAATTTTTTAAATTTTAATTT
15187836 TTTTA
1 TTTTA
15187841 AATAATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 16 0.44
38 4 0.11
39 16 0.44
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (35 bp):
TTTTATAAATTTCATAATTTTTTAAATTTTAATTT
Found at i:15187839 original size:16 final size:17
Alignment explanation
Indices: 15187749--15187843 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 17
15187739 TATTTTTTAC
15187749 TTTTAAATCTTTAT-ATT
1 TTTTAAAT-TTTATAATT
* *
15187766 TTAT-AA-TTCATAATT
1 TTTTAAATTTTATAATT
* *
15187781 TTTTATATTATTAAAATTTT
1 TTTTAAATT-TTATAA--TT
15187801 TTTATAAAATTTTATAATT
1 TTT-T-AAATTTTATAATT
*
15187820 TTTTAAATTTTA-ATTT
1 TTTTAAATTTTATAATT
15187836 TTTTAAAT
1 TTTTAAAT
15187844 AATTATTGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.07
15 6 0.10
16 14 0.23
17 12 0.20
18 5 0.08
19 5 0.08
20 5 0.08
21 6 0.10
22 4 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTTATAATT
Found at i:15189989 original size:27 final size:27
Alignment explanation
Indices: 15189959--15190085 Score: 146
Period size: 27 Copynumber: 4.7 Consensus size: 27
15189949 AAGTCCTTAT
* * **
15189959 TACAGAATACGCCACAAAGGTGATCCA
1 TACAGAGTATGCCACAAAGGTGATATA
*** *
15189986 TACAGAGTACATCACAAAGGTTATATA
1 TACAGAGTATGCCACAAAGGTGATATA
* * * *
15190013 TAGAGAGTATACCACAAAGGCGACATA
1 TACAGAGTATGCCACAAAGGTGATATA
15190040 TACAGAGTATGCCACAAAGGTGATATA
1 TACAGAGTATGCCACAAAGGTGATATA
15190067 TACAGAGTATGCCACAAAG
1 TACAGAGTATGCCACAAAG
15190086 ACAATTCATT
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.19
Consensus pattern (27 bp):
TACAGAGTATGCCACAAAGGTGATATA
Found at i:15190099 original size:27 final size:27
Alignment explanation
Indices: 15190008--15190112 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
15189998 CACAAAGGTT
* * * *
15190008 ATATATAGAGAGTATACCACAAAGGCG
1 ATATATACAGAGTATGCCACAAAGACA
* ***
15190035 ACATATACAGAGTATGCCACAAAGGTG
1 ATATATACAGAGTATGCCACAAAGACA
15190062 ATATATACAGAGTATGCCACAAAGACA
1 ATATATACAGAGTATGCCACAAAGACA
* * *
15190089 AT-TCATTCAGAGTACGCCATAAAG
1 ATAT-ATACAGAGTATGCCACAAAG
15190113 GCTGACAGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 65 0.98
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (27 bp):
ATATATACAGAGTATGCCACAAAGACA
Found at i:15190100 original size:54 final size:54
Alignment explanation
Indices: 15189985--15190113 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
15189975 AAGGTGATCC
** * * *
15189985 ATACAGAGTACATCACAAAGGTTATATATAGAGAGTATACCACAAAGGCGACAT
1 ATACAGAGTACGCCACAAAGGTGATATATACAGAGTATACCACAAAGACGACAT
* *
15190039 ATACAGAGTATGCCACAAAGGTGATATATACAGAGTATGCCACAAAGAC-A-ATT
1 ATACAGAGTACGCCACAAAGGTGATATATACAGAGTATACCACAAAGACGACA-T
* *
15190092 CATTCAGAGTACGCCATAAAGG
1 -ATACAGAGTACGCCACAAAGG
15190114 CTGACAGGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
52 1 0.02
53 2 0.03
54 60 0.95
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (54 bp):
ATACAGAGTACGCCACAAAGGTGATATATACAGAGTATACCACAAAGACGACAT
Found at i:15190611 original size:18 final size:18
Alignment explanation
Indices: 15190585--15190821 Score: 156
Period size: 18 Copynumber: 13.4 Consensus size: 18
15190575 CGATCAGATC
* *
15190585 AAAATACGAGAATTTTTA
1 AAAACACGAGAATTTTTG
15190603 AAAACACGA-AGATTTTTG
1 AAAACACGAGA-ATTTTTG
** **
15190621 -AAACATTTA-TTTTTTTG
1 AAAACA-CGAGAATTTTTG
*
15190638 AAAACACGAAAAATTTTT-
1 AAAACACG-AGAATTTTTG
*
15190656 AAAACACGAGAATTTTAG
1 AAAACACGAGAATTTTTG
* * * *
15190674 -AGACACGAAAATTCTTA
1 AAAACACGAGAATTTTTG
* *
15190691 AAAATACGAAAATTTTTG
1 AAAACACGAGAATTTTTG
15190709 AAAACACG-GAAATTTTT-
1 AAAACACGAG-AATTTTTG
15190726 AAAACAC-AGGAATTTTTG
1 AAAACACGA-GAATTTTTG
* *
15190744 AAAACATGAAAATTTTTG
1 AAAACACGAGAATTTTTG
15190762 -AAACACCG-GAA-TTTTG
1 AAAACA-CGAGAATTTTTG
* *
15190778 AAAACACGAGGATTCTTG
1 AAAACACGAGAATTTTTG
*
15190796 AAAACACGA-AGATTTTTT
1 AAAACACGAGA-ATTTTTG
15190814 AAAACACG
1 AAAACACG
15190822 GAAGAAAATA
Statistics
Matches: 170, Mismatches: 32, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
16 7 0.04
17 59 0.35
18 98 0.58
19 6 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
AAAACACGAGAATTTTTG
Found at i:15190680 original size:35 final size:35
Alignment explanation
Indices: 15190585--15190821 Score: 189
Period size: 35 Copynumber: 6.7 Consensus size: 35
15190575 CGATCAGATC
* * *
15190585 AAAATACGAGAATTTTTAAAAACACGAAGATTTTT
1 AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
* ** **
15190620 GAAACATTTA-TTTTTTTGAAAACACGAAAAATTTTT
1 AAAACA-CGAGAATTTTTGAAAACACG-AAAATTTTT
* * *
15190656 AAAACACGAGAATTTTAG-AGACACGAAAATTCTTA
1 AAAACACGAGAATTTTTGAAAACACGAAAATT-TTT
* * *
15190691 AAAATACGAAAATTTTTGAAAACACGGAAATTTTT
1 AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
*
15190726 AAAACAC-AGGAATTTTTGAAAACATGAAAATTTTT
1 AAAACACGA-GAATTTTTGAAAACACGAAAATTTTT
* ** *
15190761 GAAACACCG-GAA-TTTTGAAAACACGAGGATTCTTG
1 AAAACA-CGAGAATTTTTGAAAACACGAAAATT-TTT
*
15190796 AAAACACGA-AGATTTTTTAAAACACG
1 AAAACACGAGA-ATTTTTGAAAACACG
15190822 GAAGAAAATA
Statistics
Matches: 157, Mismatches: 33, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
34 26 0.17
35 88 0.56
36 43 0.27
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
Found at i:15190755 original size:53 final size:53
Alignment explanation
Indices: 15190635--15190824 Score: 196
Period size: 53 Copynumber: 3.6 Consensus size: 53
15190625 ATTTATTTTT
* *
15190635 TTGAAAACACGAAAAATTTTT-AAAACAC-GAGAA-TTTTAGAGACAC-GAAAATTC
1 TTGAAAACACG-AAAATTTTTGAAAACACGGA-AATTTTTA-AAACACAG-GAATTC
* * *
15190688 TTAAAAATACGAAAATTTTTGAAAACACGGAAATTTTTAAAACACAGGAATTT
1 TTGAAAACACGAAAATTTTTGAAAACACGGAAATTTTTAAAACACAGGAATTC
* *
15190741 TTGAAAACATGAAAATTTTTG-AAACACCGG-AATTTTGAAAACACGAGG-ATTC
1 TTGAAAACACGAAAATTTTTGAAAACA-CGGAAATTTTTAAAACAC-AGGAATTC
* *
15190793 TTGAAAACACGAAGATTTTTTAAAACACGGAA
1 TTGAAAACACGAAAATTTTTGAAAACACGGAA
15190825 GAAAATACAG
Statistics
Matches: 116, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
52 51 0.44
53 57 0.49
54 8 0.07
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (53 bp):
TTGAAAACACGAAAATTTTTGAAAACACGGAAATTTTTAAAACACAGGAATTC
Found at i:15192169 original size:18 final size:18
Alignment explanation
Indices: 15192128--15192182 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
15192118 GTCGCCGGCG
* *
15192128 TCTCCTCTTCTCTCCTTCT
1 TCTCTTCTTCTCTTCTT-T
15192147 T-TCTTCTTCTCTTCTTT
1 TCTCTTCTTCTCTTCTTT
*
15192164 TCTCTT-TTCCTTTTCTTT
1 TCTCTTCTT-CTCTTCTTT
15192182 T
1 T
15192183 TGGTTGCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.13
18 26 0.84
19 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTCTTCTTCTCTTCTTT
Found at i:15193293 original size:74 final size:74
Alignment explanation
Indices: 15193194--15194064 Score: 731
Period size: 77 Copynumber: 11.6 Consensus size: 74
15193184 GCTAGCCCAT
* * *
15193194 AAATTGAAAAATACATC-GACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTAAAAAATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
15193258 TGAAAAGCAA
65 TGAAAAACAA
* * *
15193268 AAATTAAAAAATACCTCAACATGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
15193333 GAAAAAACAG
66 G-AAAAACAA
* * *
15193343 AAATTGAAAAGAATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
1 AAATT-AAAA-AATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
***
15193408 TTTT----TTGAA
62 TTTTGAAAAACAA
** ** * * *
15193417 AAA-T---ACCT-CAGCA-TGTGACCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
15193476 GAACAACAGA
66 GAAAAACA-A
* * * * * *
15193486 AATTTAAACGAAATACCTCGGCATGACCCGAGACTCAACTCACCTCT-GTATTATGAGTTGATTT
1 AAATTAAA--AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
15193550 TTGAAAAACAT
64 TTGAAAAACAA
* * * * * *
15193561 AAATTGAAAAGAAATACCTCGGCCTACGACCCGAGGATCAACTCACCCCTCGCAGTATGAATTGA
1 AAATT--AAA-AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
15193626 TTTTTGAAAAATAGA
61 TTTTTGAAAAACA-A
* * * ** *
15193641 AATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAATT-AAA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---
15193706 TTTTTATGAAAAACAGA
61 -TTTT-TGAAAAACA-A
* *
15193723 AATTTAAAAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATT-AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
15193788 TGAAAAAAAAACAG
65 TG----AAAAACAA
* * **
15193802 AAATT-AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAA
1 AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
15193866 AAAAAGACAT
66 GAAAA-ACAA
*
15193876 AAATT-AAAAATACCTCAGCGTGACCCGAGGCTCAACTCA-CTCT-G-TATATGAGTTGA-TTTT
1 AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
15193936 -AAAAAAAA
66 GAAAAACAA
* * * *
15193944 AGACATAAATAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC-GGTATTATGAGTTGAT
1 A-A-AT-TA-AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
15194008 TTTTAAAAAAAAGGCAT
62 TTTT--GAAAAA--CAA
15194025 AAATT-AAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
1 AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
15194065 NNNNNNNNNN
Statistics
Matches: 657, Mismatches: 91, Indels: 96
0.78 0.11 0.11
Matches are distributed among these distances:
64 41 0.06
67 2 0.00
68 5 0.01
69 9 0.01
70 5 0.01
71 10 0.02
72 1 0.00
73 43 0.07
74 111 0.17
75 27 0.04
76 85 0.13
77 122 0.19
78 20 0.03
79 93 0.14
80 12 0.02
81 52 0.08
82 19 0.03
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (74 bp):
AAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAAACAA
Found at i:15193449 original size:64 final size:64
Alignment explanation
Indices: 15193354--15193475 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
15193344 AATTGAAAAG
*
15193354 AATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAA
1 AATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAA
* * * *
15193418 AATACCTCAGCATGTGACCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 AATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTT
15193476 GAACAACAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (64 bp):
AATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAA
Found at i:15193465 original size:143 final size:138
Alignment explanation
Indices: 15193274--15193551 Score: 405
Period size: 143 Copynumber: 2.0 Consensus size: 138
15193264 GCAAAAATTA
*
15193274 AAAAATACCTCAACATGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAAAATACCTCAACATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
*
15193339 ACAGAAATTGAAAAG-AATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAG
65 ACAGAAATTGAAAAGAAATACCTCGGCAT--GACCCGAGACTCAACTCACCTCT-GCAATATGAG
15193403 TTGATTTTTTTG
127 TTGATTTTTTTG
* * * *
15193415 AAAAATACCTCAGCATGTGACCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAC
1 AAAAATACCTCAACA--TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
* * * *
15193480 AACAGAAATTTAAACGAAATACCTCGGCATGACCCGAGACTCAACTCACCTCTGTATTATGAGTT
64 AACAGAAATTGAAAAGAAATACCTCGGCATGACCCGAGACTCAACTCACCTCTGCAATATGAGTT
15193545 GATTTTT
129 GATTTTT
15193552 GAAAAACATA
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
140 17 0.14
141 36 0.29
142 16 0.13
143 55 0.44
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (138 bp):
AAAAATACCTCAACATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
CAGAAATTGAAAAGAAATACCTCGGCATGACCCGAGACTCAACTCACCTCTGCAATATGAGTTGA
TTTTTTTG
Found at i:15195061 original size:1 final size:1
Alignment explanation
Indices: 15195050--15195144 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
15195040 TTCATCTTGA
* * * * * * * * * *
15195050 TTTTTTCTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTGTCTGTTTTTTGTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
15195115 TTTTTTTTGTTTTTTTTGTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15195145 AAGCATAATA
Statistics
Matches: 68, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (1 bp):
T
Found at i:15195061 original size:8 final size:8
Alignment explanation
Indices: 15195058--15195143 Score: 106
Period size: 8 Copynumber: 10.9 Consensus size: 8
15195048 GATTTTTTCT
15195058 TTTTTTTG
1 TTTTTTTG
15195066 TTTTTTTTG
1 -TTTTTTTG
15195075 TTTTTTTG
1 TTTTTTTG
15195083 TTTTTTTG
1 TTTTTTTG
*
15195091 TTTTGTCTG
1 TTTT-TTTG
15195100 -TTTTTTG
1 TTTTTTTG
15195107 TTTTTTTG
1 TTTTTTTG
15195115 TTTTTTT-
1 TTTTTTTG
*
15195122 TGTTTTT-
1 TTTTTTTG
*
15195129 TTTGTTTG
1 TTTTTTTG
15195137 TTTTTTT
1 TTTTTTT
15195144 TAAGCATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
7 14 0.21
8 43 0.63
9 11 0.16
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:15195064 original size:9 final size:9
Alignment explanation
Indices: 15195050--15195141 Score: 113
Period size: 9 Copynumber: 10.7 Consensus size: 9
15195040 TTCATCTTGA
*
15195050 TTTTTTCTT
1 TTTTTTGTT
15195059 TTTTTTGTT
1 TTTTTTGTT
15195068 TTTTTTG-T
1 TTTTTTGTT
15195076 TTTTTTG-T
1 TTTTTTGTT
15195084 TTTTTTGTT
1 TTTTTTGTT
* *
15195093 TTGTCTG--
1 TTTTTTGTT
15195100 TTTTTTG-T
1 TTTTTTGTT
15195108 TTTTTTGTT
1 TTTTTTGTT
15195117 TTTTTTGTT
1 TTTTTTGTT
15195126 TTTTTTGTT
1 TTTTTTGTT
15195135 TGTTTTT
1 T-TTTTT
15195142 TTTAAGCATA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
7 5 0.07
8 23 0.31
9 41 0.55
10 5 0.07
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:15195137 original size:41 final size:39
Alignment explanation
Indices: 15195052--15195144 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 39
15195042 CATCTTGATT
*
15195052 TTTTCTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTG
1 TTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTG
15195091 TTTTGTCTGTTTTTTG-TTTTTTTGTTTTTTTTGTTTTTTT-
1 TTTTGT-T-TTTTTTGTTTTTTTTG-TTTTTTTGTTTTTTTG
15195131 TGTTTGTTTTTTTT
1 T-TTTGTTTTTTTT
15195145 AAGCATAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
39 11 0.22
40 11 0.22
41 27 0.55
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (39 bp):
TTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTG
Found at i:15206159 original size:18 final size:17
Alignment explanation
Indices: 15206133--15206365 Score: 127
Period size: 18 Copynumber: 13.2 Consensus size: 17
15206123 CGATCAGATC
*
15206133 AAAATACGAGAATTTTT
1 AAAACACGAGAATTTTT
15206150 AAAAACACGA-AGATTTTT
1 -AAAACACGAGA-ATTTTT
* *** *
15206168 GAAACA-TTTATTTTTTT
1 AAAACACGAGAAT-TTTT
*
15206185 GAAAACACGAAAAATTTTT
1 -AAAACACG-AGAATTTTT
15206204 AAAACACGAGAA-TTTT
1 AAAACACGAGAATTTTT
* * *
15206220 AGAGACACGAAAATTCTTA
1 A-AAACACGAGAATT-TTT
* * *
15206239 AAAATATGAAAATTTTT
1 AAAACACGAGAATTTTT
15206256 GAAAACACG-GAAATTTTT
1 -AAAACACGAG-AATTTTT
*
15206274 AAAACACGGGAATTTTT
1 AAAACACGAGAATTTTT
* *
15206291 GAAAACATGAAAATTTTT
1 -AAAACACGAGAATTTTT
* *
15206309 GAAACACCG-GAATTTTG
1 AAAACA-CGAGAATTTTT
*
15206326 AAAACACGAAGATTTTTT
1 AAAACACG-AGAATTTTT
15206344 AAAACACG-GAAATTTTT
1 AAAACACGAG-AATTTTT
15206361 GAAAA
1 -AAAA
15206366 TACAGAAATT
Statistics
Matches: 165, Mismatches: 32, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
16 9 0.05
17 62 0.38
18 85 0.52
19 7 0.04
20 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (17 bp):
AAAACACGAGAATTTTT
Found at i:15206228 original size:35 final size:34
Alignment explanation
Indices: 15206133--15206365 Score: 200
Period size: 35 Copynumber: 6.6 Consensus size: 34
15206123 CGATCAGATC
* * *
15206133 AAAATACGAGAATTTTTAAAAACACGAAGATTTTT
1 AAAACACG-GAATTTTTGAAAACACGAAAATTTTT
* *** *
15206168 GAAACATTTATTTTTTTGAAAACACGAAAAATTTTT
1 AAAACACGGA-ATTTTTGAAAACACG-AAAATTTTT
* * *
15206204 AAAACACGAGAATTTTAG-AGACACGAAAATTCTTA
1 AAAACACG-GAATTTTTGAAAACACGAAAATT-TTT
* * * *
15206239 AAAATATGAAAATTTTTGAAAACACGGAAATTTTT
1 AAAACACG-GAATTTTTGAAAACACGAAAATTTTT
*
15206274 AAAACACGGGAATTTTTGAAAACATGAAAATTTTT
1 AAAACAC-GGAATTTTTGAAAACACGAAAATTTTT
* *
15206309 GAAACACCGGAA-TTTTGAAAACACGAAGATTTTTT
1 AAAACA-CGGAATTTTTGAAAACACGAA-AATTTTT
15206344 AAAACACGGAAATTTTTGAAAA
1 AAAACACGG-AATTTTTGAAAA
15206366 TACAGAAATT
Statistics
Matches: 156, Mismatches: 32, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
34 24 0.15
35 91 0.58
36 40 0.26
37 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (34 bp):
AAAACACGGAATTTTTGAAAACACGAAAATTTTT
Found at i:15206373 original size:18 final size:18
Alignment explanation
Indices: 15206180--15206376 Score: 128
Period size: 18 Copynumber: 11.2 Consensus size: 18
15206170 AACATTTATT
*
15206180 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACAC-AGAAA
15206199 TTTTT-AAAACAC-GAGAA
1 TTTTTGAAAACACAGA-AA
* *
15206216 TTTTAG-AGACAC-GAAAA
1 TTTTTGAAAACACAG-AAA
* *
15206233 TTCTT-AAAA-ATATGAAAA
1 TTTTTGAAAACACA-G-AAA
*
15206251 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACAGAAA
* *
15206269 TTTTT-AAAACACGGGAA
1 TTTTTGAAAACACAGAAA
*
15206286 TTTTTGAAAACA-TGAAAA
1 TTTTTGAAAACACAG-AAA
* *
15206304 TTTTTG-AAACACCGGAA
1 TTTTTGAAAACACAGAAA
15206321 -TTTTGAAAACAC-GAAGA
1 TTTTTGAAAACACAGAA-A
* *
15206338 TTTTTTAAAACACGGAAA
1 TTTTTGAAAACACAGAAA
*
15206356 TTTTTGAAAATACAGAAA
1 TTTTTGAAAACACAGAAA
15206374 TTT
1 TTT
15206377 GAAATACAGA
Statistics
Matches: 143, Mismatches: 20, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.06
17 50 0.35
18 70 0.49
19 13 0.09
20 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACAGAAA
Found at i:15206378 original size:52 final size:51
Alignment explanation
Indices: 15206180--15206434 Score: 167
Period size: 53 Copynumber: 4.7 Consensus size: 51
15206170 AACATTTATT
* * *
15206180 TTTTTGAAAACACGAAAAATTTTT-AAAACAC-GAGAATTTTAGAGACACGAAAA
1 TTTTTGAAAACACG-AAAATTTTTGAAAA-ACGGA-AATTTGA-AAACACGAGAA
* * * * * *
15206233 TTCTTAAAAATATGAAAATTTTTGAAAACACGGAAATTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAAA-ACGGAAA-TTTGAAAACACGAGAA
* * *
15206286 TTTTTGAAAACATGAAAATTTTTGAAACACCGGAATTTTGAAAACACGA-AGA
1 TTTTTGAAAACACGAAAATTTTTGAAA-AACGGAAATTTGAAAACACGAGA-A
* * * *
15206338 TTTTTTAAAACACGGAAATTTTTGAAAATACAGAAATTTGAAATACA-GAAATTA
1 TTTTTGAAAACACGAAAATTTTTGAAAA-ACGGAAATTTGAAA-ACACGAGA--A
* *
15206392 TTTTTAAAAAACAAGAATATATTTTTTGAAAAACGGTAAATTT
1 TTTTT-GAAAACACGAA-A-A-TTTTTGAAAAACGG-AAATTT
15206435 CATTATTATT
Statistics
Matches: 163, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
51 2 0.01
52 58 0.36
53 60 0.37
54 14 0.09
55 8 0.05
56 1 0.01
57 4 0.02
58 16 0.10
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (51 bp):
TTTTTGAAAACACGAAAATTTTTGAAAAACGGAAATTTGAAAACACGAGAA
Found at i:15206383 original size:15 final size:16
Alignment explanation
Indices: 15206358--15206390 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
15206348 CACGGAAATT
15206358 TTTGAAAATACAGAAA
1 TTTGAAAATACAGAAA
15206374 TTTG-AAATACAGAAA
1 TTTGAAAATACAGAAA
15206389 TT
1 TT
15206391 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (16 bp):
TTTGAAAATACAGAAA
Found at i:15206394 original size:18 final size:19
Alignment explanation
Indices: 15206322--15206394 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 19
15206312 ACACCGGAAT
*
15206322 TTTGAAAACAC-GAAGATT-
1 TTTGAAAATACAGAA-ATTA
* * *
15206340 TTTTAAAACACGGAAATT-
1 TTTGAAAATACAGAAATTA
15206358 TTTGAAAATACAG-AA--A
1 TTTGAAAATACAGAAATTA
15206374 TTTG-AAATACAGAAATTA
1 TTTGAAAATACAGAAATTA
15206392 TTT
1 TTT
15206395 TTAAAAAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
15 8 0.17
16 6 0.13
17 2 0.04
18 27 0.59
19 3 0.07
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (19 bp):
TTTGAAAATACAGAAATTA
Found at i:15206994 original size:15 final size:15
Alignment explanation
Indices: 15206959--15206994 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
15206949 GCAATTCGGG
15206959 CCTTTTTTGTTTTTT
1 CCTTTTTTGTTTTTT
**
15206974 GTTTTTTTGTTTTTT
1 CCTTTTTTGTTTTTT
15206989 CCTTTT
1 CCTTTT
15206995 CTCCTCTTTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (15 bp):
CCTTTTTTGTTTTTT
Found at i:15207294 original size:9 final size:9
Alignment explanation
Indices: 15207280--15207338 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
15207270 CTGTAATGTA
15207280 TTTCTTTTT
1 TTTCTTTTT
15207289 TTTC-TTTT
1 TTTCTTTTT
*
15207297 TTTC-TTTC
1 TTTCTTTTT
*
15207305 TCTCTTTTT
1 TTTCTTTTT
*
15207314 TCTT-TCTTT
1 T-TTCTTTTT
*
15207323 TTTCTCTTT
1 TTTCTTTTT
15207332 TTTCTTT
1 TTTCTTT
15207339 CTTTCTTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 16 0.39
9 24 0.59
10 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:15207304 original size:4 final size:4
Alignment explanation
Indices: 15207289--15207349 Score: 72
Period size: 4 Copynumber: 15.5 Consensus size: 4
15207279 ATTTCTTTTT
* * *
15207289 TTTC TTTT TTTC TTTC TCTC TTT- TTTC TTTC TTT- TTTC TCTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC
15207336 TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TT
15207350 CTTCCTTCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 6 0.12
4 39 0.81
5 3 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:15207333 original size:35 final size:36
Alignment explanation
Indices: 15207280--15207352 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 36
15207270 CTGTAATGTA
* *
15207280 TTTCTTTTTTTTCTTTTTTTCTTTCTCTCTTTTTTC
1 TTTCTTTTTTCTCTTTTTTTCTTTCTCTCTTTCTTC
*
15207316 TTTCTTTTTTCTC-TTTTTTCTTTCTTTCTTTCTTC
1 TTTCTTTTTTCTCTTTTTTTCTTTCTCTCTTTCTTC
15207351 TT
1 TT
15207353 CCTTCCCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 22 0.65
36 12 0.35
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTCTTTTTTCTCTTTTTTTCTTTCTCTCTTTCTTC
Found at i:15207651 original size:23 final size:23
Alignment explanation
Indices: 15207607--15207651 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
15207597 GCCCTTTGGC
* *
15207607 TTGCTGCTTTTTGTTTGATTTTT
1 TTGCTGCTTTTTCTTAGATTTTT
15207630 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
15207652 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.04, C:0.11, G:0.18, T:0.67
Consensus pattern (23 bp):
TTGCTGCTTTTTCTTAGATTTTT
Found at i:15207964 original size:30 final size:29
Alignment explanation
Indices: 15207911--15208066 Score: 131
Period size: 30 Copynumber: 5.2 Consensus size: 29
15207901 AAATATGGGC
* * *
15207911 CAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAATGAAATTT-TAGAAAGTTTAGGGGT
* * *
15207941 CAAAGTGCAATTTTGAGAAAGTTTAAGGGT
1 CAAAATGAAATTTT-AGAAAGTTTAGGGGT
*
15207971 CGAAAT-ATAATTTTAGAAAGTTTTA-GGGT
1 CAAAATGA-AATTTTAGAAAG-TTTAGGGGT
15208000 CAAAATGTAAATTTTAGAAAAGTTT-GGGGT
1 CAAAATG-AAATTTTAG-AAAGTTTAGGGGT
*
15208030 CAAAATGTAAATTTT-GAAAAGTATAGGGGT
1 CAAAATG-AAATTTTAG-AAAGTTTAGGGGT
*
15208060 TAAAATG
1 CAAAATG
15208067 CAAAAAATAA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
29 24 0.22
30 78 0.73
31 5 0.05
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (29 bp):
CAAAATGAAATTTTAGAAAGTTTAGGGGT
Found at i:15213631 original size:38 final size:38
Alignment explanation
Indices: 15213580--15213692 Score: 127
Period size: 38 Copynumber: 3.0 Consensus size: 38
15213570 GTTATATCGT
* * *
15213580 TATTCAAGTTTTGTGCATAGCAGGCTTAGTGCTGGTGA
1 TATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTGA
* ** *
15213618 TATTCAGGATTTGTGCCTAGCATGCTTAGTGCCAGTGT
1 TATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTGA
* * * *
15213656 TATTCAGGCTTAGTGCCTAGCAGGTTTATTGCTGGTG
1 TATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTG
15213693 TAATTAAAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 61 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (38 bp):
TATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTGA
Found at i:15217700 original size:11 final size:11
Alignment explanation
Indices: 15217684--15217717 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
15217674 AAGGTTTTTG
15217684 AATTATTAATT
1 AATTATTAATT
15217695 AATTATTAATT
1 AATTATTAATT
15217706 AATTA-TAATT
1 AATTATTAATT
15217716 AA
1 AA
15217718 ATAATTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTATTAATT
Found at i:15219881 original size:41 final size:41
Alignment explanation
Indices: 15219769--15219888 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
15219759 TGATAATCGA
* * * * *
15219769 GCTTTGTGCCTAGTAGGCTTTATGCCGGTGAATTATATCAG
1 GCTTTATGCCTAGCAGGCTTAATGCCGGTGTATCATATCAG
** * *
15219810 ATTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATATCAG
1 GCTTTATGCCTAGCAGGCTTAATGCCGGTGTATCATATCAG
**
15219851 GCTTTATGCCTAGCAGGCTTCGTGCCGGTGTATCATAT
1 GCTTTATGCCTAGCAGGCTTAATGCCGGTGTATCATAT
15219889 TAAGATTTGT
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (41 bp):
GCTTTATGCCTAGCAGGCTTAATGCCGGTGTATCATATCAG
Found at i:15231951 original size:6 final size:6
Alignment explanation
Indices: 15231918--15231942 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15231908 AATAAATATA
15231918 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
15231943 TAATTTTAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:15233787 original size:15 final size:16
Alignment explanation
Indices: 15233730--15233785 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
15233720 ATTTTAATAG
15233730 TTTAATATTAATATTAA
1 TTTAATATT-ATATTAA
*
15233747 TTTAATACTTATCTTAA
1 TTTAATA-TTATATTAA
*
15233764 --TAGTATT-TATTAA
1 TTTAATATTATATTAA
15233777 TTTAATATT
1 TTTAATATT
15233786 TAAGTGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 10 0.31
17 13 0.41
18 2 0.06
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAATATTATATTAA
Found at i:15233788 original size:25 final size:24
Alignment explanation
Indices: 15233714--15233788 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 24
15233704 TTCCAAAAAA
* *
15233714 AATATTATTTTAATAGTTTAATATT
1 AATATTAATTTAATA-TTTAATAGT
15233739 AATATTAATTTAATACTTATCTTAATAGT
1 AATATTAATTT-A-A--TAT-TTAATAGT
*
15233768 ATTTATTAATTTAATATTTAA
1 A-ATATTAATTTAATATTTAA
15233789 GTGATTATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
25 14 0.34
26 4 0.10
27 1 0.02
28 2 0.05
29 11 0.27
30 9 0.22
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
AATATTAATTTAATATTTAATAGT
Found at i:15233807 original size:67 final size:64
Alignment explanation
Indices: 15233730--15233926 Score: 168
Period size: 67 Copynumber: 3.0 Consensus size: 64
15233720 ATTTTAATAG
*
15233730 TTTAATATTAATATTAATTTAATACTTATCTTAATAGTATTTATTAATTTAATATTTAAGTGATT
1 TTTAATATTAA-ATTAATTTAATATTTATCTT-ATAGTATTTATTAATTTAATATTTAAGTGATT
15233795 A
64 A
* * * * * ** * *
15233796 TCTTAATATTAAAATAAATTTAATGTTTATATTGTAG-A-TAAACAATTTATTATTTTAA-T-AA
1 T-TTAATATT-AAATTAATTTAATATTTATCTTATAGTATTTATTAATTTAATA-TTTAAGTGAT
15233857 TA
63 TA
* * *
15233859 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAA-TTAATTTAATATTTATCTT-AT-AGTATT-TATTAATTTAATATTTAAGTGA
15233924 TTA
62 TTA
15233927 GGTTTAATCA
Statistics
Matches: 98, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
61 3 0.03
62 23 0.23
63 5 0.05
64 12 0.12
65 7 0.07
66 9 0.09
67 34 0.35
68 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (64 bp):
TTTAATATTAAATTAATTTAATATTTATCTTATAGTATTTATTAATTTAATATTTAAGTGATTA
Found at i:15234053 original size:25 final size:24
Alignment explanation
Indices: 15234024--15234072 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
15234014 AGTTGCAAAG
15234024 AGAAAA-TTCTTAAAGAGATTATTTC
1 AGAAAATTTC-TAAAGAGATT-TTTC
*
15234049 AGAAAATTTCTAAAGATATTTTTC
1 AGAAAATTTCTAAAGAGATTTTTC
15234073 TGATTTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 15 0.68
26 3 0.14
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (24 bp):
AGAAAATTTCTAAAGAGATTTTTC
Found at i:15237079 original size:5 final size:5
Alignment explanation
Indices: 15237058--15237113 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
15237048 TTTTTTGAAG
* *
15237058 TATAT TATTAT TTTAT TATATT GTAAAT TATAT TATAT TATAT TATTAT
1 TATAT TA-TAT TATAT TATA-T -TATAT TATAT TATAT TATAT TA-TAT
15237107 TATAT TA
1 TATAT TA
15237114 GGTAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 29 0.67
6 11 0.26
7 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:15237347 original size:13 final size:13
Alignment explanation
Indices: 15237316--15237356 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
15237306 GACGAAACAG
*
15237316 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
15237328 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
15237341 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
15237354 AGA
1 AGA
15237357 GAAAATTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:15238692 original size:37 final size:37
Alignment explanation
Indices: 15238591--15238692 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 37
15238581 CGACCTTGAG
15238591 TCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATA-AT
** ** *
15238632 TCGATGAGGTACTGGGTACCAACTTACTTCGG-T-TT
1 TCGATGAGACACTGGGTGTCAACTTACTTCGGATAAT
15238667 TGCCGATGAGACACTGGGTGTCAACT
1 T--CGATGAGACACTGGGTGTCAACT
15238693 ATTGCTTCGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
35 2 0.04
37 20 0.40
38 9 0.18
40 2 0.04
41 17 0.34
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (37 bp):
TCGATGAGACACTGGGTGTCAACTTACTTCGGATAAT
Found at i:15245652 original size:45 final size:46
Alignment explanation
Indices: 15245557--15245654 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
15245547 TGTGTATATC
* *
15245557 TATTTTCTTTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
15245603 TATTTTGTTTTAATTAGGAGATTAGATGCT-AAGTTTAAGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
15245648 TATTTTG
1 TATTTTG
15245655 GTTTCTATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 21 0.42
46 29 0.58
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (46 bp):
TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
Found at i:15250242 original size:45 final size:46
Alignment explanation
Indices: 15250147--15250244 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
15250137 TGTGTATATC
* *
15250147 TATTTTCTTTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
15250193 TATTTTGTTTTAATTAGGAGATTAGATGCT-AAGTTTAAGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
15250238 TATTTTG
1 TATTTTG
15250245 GTTTCTATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 21 0.42
46 29 0.58
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (46 bp):
TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
Found at i:15258191 original size:20 final size:20
Alignment explanation
Indices: 15258166--15258205 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15258156 CGTAAAATGA
*
15258166 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
15258186 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
15258206 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:15258195 original size:34 final size:35
Alignment explanation
Indices: 15258151--15258217 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
15258141 CAATAAAATA
* *
15258151 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
15258185 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
15258218 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:15260000 original size:14 final size:14
Alignment explanation
Indices: 15259981--15260010 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15259971 AGGTGAACTA
15259981 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
15259995 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
15260009 GC
1 GC
15260011 TGCAATCGTT
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:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:15260058 original size:33 final size:33
Alignment explanation
Indices: 15260021--15260087 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
15260011 TGCAATCGTT
15260021 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
* *
15260054 AGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
15260087 A
1 A
15260088 ATGTCTTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.45, T:0.13
Consensus pattern (33 bp):
AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
Found at i:15262776 original size:30 final size:30
Alignment explanation
Indices: 15262710--15262777 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
15262700 GACGACGACG
15262710 CAGGCCCATCAACGAGGCCCAGAAATTCAC
1 CAGGCCCATCAACGAGGCCCAGAAATTCAC
* * * * *
15262740 CCGGCCCATCATC-AGTGCCCATAACTTCAT
1 CAGGCCCATCAACGAG-GCCCAGAAATTCAC
15262770 CAGGCCCA
1 CAGGCCCA
15262778 GCAATAGCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.15
Consensus pattern (30 bp):
CAGGCCCATCAACGAGGCCCAGAAATTCAC
Found at i:15262884 original size:18 final size:18
Alignment explanation
Indices: 15262861--15262903 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15262851 TGCCAGGTGC
* *
15262861 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
15262879 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
15262897 GTTTCCT
1 GTATCCT
15262904 TTTCCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:15263340 original size:49 final size:49
Alignment explanation
Indices: 15263285--15263454 Score: 295
Period size: 49 Copynumber: 3.5 Consensus size: 49
15263275 GTTTATATTA
* *
15263285 ATGTAATAAAGTACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
15263334 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATAATTTT
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
15263383 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
*
15263432 ATTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
15263455 AATATTCTTA
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 115 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
Found at i:15266775 original size:125 final size:125
Alignment explanation
Indices: 15266553--15266965 Score: 673
Period size: 125 Copynumber: 3.3 Consensus size: 125
15266543 CCCAAACATG
*
15266553 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTTTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
15266618 TTGAAGCGTTTTTTATACTATTTGCTTAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* *
15266678 CTACTGTAGCAAAAGTGCGTCCACATGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
15266743 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGAAT
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
15266803 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTGATTTCAGAAATTCTTCTGATAAAACATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
15266868 TTGAAACTTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
15266928 CTACTGTATCAAAAACGCGTCAACGTAGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
15266966 CTTAATAAAT
Statistics
Matches: 266, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 266 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:15267154 original size:6 final size:6
Alignment explanation
Indices: 15267143--15267174 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
15267133 AAAAACCTTA
15267143 AACCCT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AA
15267175 AAACCCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:15268621 original size:19 final size:18
Alignment explanation
Indices: 15268592--15268627 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
15268582 AGTCAAAATG
15268592 CAAAAATGGTATCGATAT
1 CAAAAATGGTATCGATAT
15268610 CAAAAGATGGTATCGATA
1 CAAAA-ATGGTATCGATA
15268628 AAAATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (18 bp):
CAAAAATGGTATCGATAT
Found at i:15272159 original size:41 final size:40
Alignment explanation
Indices: 15272112--15272219 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 40
15272102 ACCGGCACGT
* * *
15272112 AGCCTGCTAGGCTTGAAGCCTGATTCAGTACACCGGCATTA
1 AGCCTGCTAGGCATAAAGCCTGATT-AGTACACCAGCATTA
* * * * * *
15272153 AGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAGCATTA
1 AGCCTGCTAGGCATAAAGCCTG-ATTAGTACACCAGCATTA
15272194 AGCCTGCTAGGCATAAAGCCTGATTA
1 AGCCTGCTAGGCATAAAGCCTGATTA
15272220 TCTCAGATAC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
40 3 0.06
41 49 0.91
42 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (40 bp):
AGCCTGCTAGGCATAAAGCCTGATTAGTACACCAGCATTA
Found at i:15272350 original size:2 final size:2
Alignment explanation
Indices: 15272345--15272379 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15272335 TTCAAACCAC
15272345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15272380 ATTCACAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15272451 original size:67 final size:66
Alignment explanation
Indices: 15272368--15272578 Score: 291
Period size: 67 Copynumber: 3.2 Consensus size: 66
15272358 TATATATATA
* * *
15272368 TATATATATATAATTCACAACATTAAATTCAGCTCACAGAGATTGAAACATATATTCGAACCACA
1 TATATATATATAATTCATAACATTAAATTCAGCTCA-AGAAATTGAAACATACATTCGAACCACA
15272433 TG
65 TG
* * * * * * *
15272435 TATGTATATATAATTCATAACATTAAGTTCAGCTAAAAAAATTTGTAACATACATTCCAACCTCA
1 TATATATATATAATTCATAACATTAAATTCAGCTCAAGAAA-TTGAAACATACATTCGAACCACA
15272500 --
65 TG
15272500 TATATATATATAATTCATAACATTAAATTCAGCTCAAGGAAATTGAAACATACATTCGAACCACA
1 TATATATATATAATTCATAACATTAAATTCAGCTCAA-GAAATTGAAACATACATTCGAACCACA
15272565 TG
65 TG
15272567 TATATATATATA
1 TATATATATATA
15272579 TATTATACTA
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
65 54 0.44
66 6 0.05
67 63 0.51
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (66 bp):
TATATATATATAATTCATAACATTAAATTCAGCTCAAGAAATTGAAACATACATTCGAACCACAT
G
Found at i:15272531 original size:65 final size:65
Alignment explanation
Indices: 15272367--15272576 Score: 278
Period size: 65 Copynumber: 3.2 Consensus size: 65
15272357 ATATATATAT
* * * *
15272367 ATATATATATATAATTCACAACATTAAATTCAGCTCACAGAGATTGAAACATATATTCGAACCAC
1 ATATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTGAAACATACATTCGAACCAC
* * * * *
15272432 ATGTATGTATATATAATTCATAACATTAAGTTCAGCT-AAAAAAATTTGTAACATACATTCCAAC
1 A--TATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAA-TTGAAACATACATTCGAAC
*
15272496 CTC
63 CAC
*
15272499 ATATATATATATAATTCATAACATTAAATTCAGCTCAAGGAAATTGAAACATACATTCGAACCAC
1 ATATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTGAAACATACATTCGAACCAC
*
15272564 ATGTATATATATA
1 ATATATATATATA
15272577 TATATTATAC
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
65 64 0.52
66 9 0.07
67 50 0.41
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (65 bp):
ATATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTGAAACATACATTCGAACCAC
Found at i:15274257 original size:126 final size:126
Alignment explanation
Indices: 15274029--15274280 Score: 441
Period size: 126 Copynumber: 2.0 Consensus size: 126
15274019 AAACAACGTG
* * *
15274029 TAGGCAAAGGTTTTAAAAAAAAATTTCAAAATTTTGACTAAGTTTAGGTAACCTCCTACAAGAAA
1 TAGGCAAAGGGTTTAAAAAAAAATTTCAAAATTTTAACTAAGTTTAGGCAACCTCCTACAAGAAA
*
15274094 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTCAACCAATAATTTGATAAA
66 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
* *
15274155 TAGGCAAAGGGTTTAAAGAAAATTTTCAAAATTTTAACTAAGTTTAGGCAACCTCCTACAAGAAA
1 TAGGCAAAGGGTTTAAAAAAAAATTTCAAAATTTTAACTAAGTTTAGGCAACCTCCTACAAGAAA
*
15274220 ATACAATATATAGGTTCCAAATAAACCTAAAACCATAATTTTAAACCAATAATTTGATAAA
66 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
15274281 AATTCAATAA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (126 bp):
TAGGCAAAGGGTTTAAAAAAAAATTTCAAAATTTTAACTAAGTTTAGGCAACCTCCTACAAGAAA
ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
Found at i:15276357 original size:23 final size:23
Alignment explanation
Indices: 15276313--15276357 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
15276303 TCTTATTTTG
* *
15276313 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
15276336 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
15276358 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:15276827 original size:23 final size:22
Alignment explanation
Indices: 15276798--15276841 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
15276788 ATAATTCACA
*
15276798 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
15276821 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
15276842 TTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:15280920 original size:57 final size:57
Alignment explanation
Indices: 15280809--15280947 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 57
15280799 TTTAATTCAT
* * * *
15280809 ATAATAATTATATTAAGAATGTTATTAAATTATATTTTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGATTAAATTATATTTTATTTTAATAAAATATATTTA
*
15280867 ATAATAATTATGTTAAAATATGATTAAATTAT-TTATT-TTTTAAATAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTATATT-TTATTTT-AATAAAATATATTTA
* * *
15280924 ACAATAATTTTATTAAAATTTGAT
1 ATAATAATTATATTAAAATATGAT
15280948 AACAAACAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
56 6 0.09
57 49 0.70
58 15 0.21
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAATTATATTTTATTTTAATAAAATATATTTA
Found at i:15280941 original size:26 final size:26
Alignment explanation
Indices: 15280847--15280942 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
15280837 ATTATATTTT
*
15280847 ATTTTATTAAATTATATTTAATAATA
1 ATTTTATTAAAATATATTTAATAATA
* * * *
15280873 ATTATGTTAAAATATGATTAAATTATTTA
1 ATTTTATTAAAATAT-ATTTAA-TA-ATA
* * *
15280902 TTTTTTAAATAAAATATATTTAACAATA
1 -ATTTT-ATTAAAATATATTTAATAATA
15280930 ATTTTATTAAAAT
1 ATTTTATTAAAAT
15280943 TTGATAACAA
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
26 19 0.37
27 9 0.18
28 4 0.08
29 3 0.06
30 8 0.16
31 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTTATTAAAATATATTTAATAATA
Found at i:15281104 original size:44 final size:45
Alignment explanation
Indices: 15281035--15281123 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 45
15281025 TATAACATCT
* *
15281035 ATTCCATTCATCTAAACACAAGAATT-TTATTACAGCTCTATTCC
1 ATTCCATTCAACTAAACACAAGAATTATGATTACAGCTCTATTCC
*
15281079 ATTCCATTCAAC-AAA-ACAATTGAATTACTGATTATAGCTCTATTC
1 ATTCCATTCAACTAAACACAA--GAATTA-TGATTACAGCTCTATTC
15281124 AATTACAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
42 4 0.11
43 3 0.08
44 16 0.42
46 15 0.39
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (45 bp):
ATTCCATTCAACTAAACACAAGAATTATGATTACAGCTCTATTCC
Found at i:15281106 original size:39 final size:39
Alignment explanation
Indices: 15281032--15281106 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
15281022 TATTATAACA
* * **
15281032 TCTATTCCATTCATCTAAACACAAGAATTTTATTACAGC
1 TCTATTCCATTCATCTAAACAAAACAATTGAATTACAGC
*
15281071 TCTATTCCATTCCAT-TCAACAAAACAATTGAATTAC
1 TCTATTCCATT-CATCTAAACAAAACAATTGAATTAC
15281107 TGATTATAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 27 0.90
40 3 0.10
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (39 bp):
TCTATTCCATTCATCTAAACAAAACAATTGAATTACAGC
Found at i:15281189 original size:16 final size:16
Alignment explanation
Indices: 15281168--15281206 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
15281158 GTACCCTAAG
15281168 TTTCATTACAGCTCTA
1 TTTCATTACAGCTCTA
15281184 TTTCATTACAGCTCTA
1 TTTCATTACAGCTCTA
15281200 TTTCATT
1 TTTCATT
15281207 TCAATTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (16 bp):
TTTCATTACAGCTCTA
Found at i:15281215 original size:22 final size:21
Alignment explanation
Indices: 15281183--15281225 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
15281173 TTACAGCTCT
15281183 ATTTCATTACAGCTCTATTTC
1 ATTTCATTACAGCTCTATTTC
15281204 ATTTCAATTACAGCTCTATTTC
1 ATTTC-ATTACAGCTCTATTTC
15281226 TTCTTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTCATTACAGCTCTATTTC
Found at i:15282419 original size:16 final size:17
Alignment explanation
Indices: 15282384--15282418 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15282374 CGCATATTAT
* *
15282384 AATAAGCATTTTTAAAA
1 AATAAACATTTATAAAA
15282401 AATAAACATTTATAAAA
1 AATAAACATTTATAAAA
15282418 A
1 A
15282419 TTTAATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AATAAACATTTATAAAA
Found at i:15291141 original size:3 final size:3
Alignment explanation
Indices: 15291133--15291166 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
15291123 CTTTAAAAAC
15291133 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
15291167 CATGATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15295447 original size:3 final size:3
Alignment explanation
Indices: 15295439--15295469 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15295429 GCGCTGAGAA
15295439 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
15295470 ACTACGTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:15300841 original size:5 final size:6
Alignment explanation
Indices: 15300823--15300847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15300813 AAATATAGGG
15300823 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
15300848 TGGTGTATTT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:15302779 original size:25 final size:25
Alignment explanation
Indices: 15302736--15302817 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
15302726 AATACTCATA
*
15302736 CGAG-CATGTAATCGGGAAGCTCTTT
1 CGAGCCATGTAA-CGAGAAGCTCTTT
*
15302761 CGAGCCATGTAACGAGAAGCTCATGT
1 CGAGCCATGTAACGAGAAGCTC-TTT
* * *
15302787 -GAGCCATTTATCGAGAAGCTCTTG
1 CGAGCCATGTAACGAGAAGCTCTTT
15302811 CGAGCCA
1 CGAGCCA
15302818 ATTATCAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 38 0.79
26 9 0.19
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (25 bp):
CGAGCCATGTAACGAGAAGCTCTTT
Found at i:15302822 original size:25 final size:24
Alignment explanation
Indices: 15302746--15302869 Score: 106
Period size: 25 Copynumber: 5.0 Consensus size: 24
15302736 CGAGCATGTA
* * *
15302746 ATCGGGAAGCTCTTTCGAGCCATGT
1 ATCGAGAAGCTCATGCGAGCCAT-T
* *
15302771 AACGAGAAGCTCATGTGAGCCATTT
1 ATCGAGAAGCTCATGCGAGCCA-TT
*
15302796 ATCGAGAAGCTCTTGCGAGCCAATT
1 ATCGAGAAGCTCATGCGAGCC-ATT
* *
15302821 ATC-AGGAAGCTCATACGAGCCATA
1 ATCGA-GAAGCTCATGCGAGCCATT
* * *
15302845 ATCGAGAAACTCAAGAGAGCCATT
1 ATCGAGAAGCTCATGCGAGCCATT
15302869 A
1 A
15302870 ATCGGGAAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
24 21 0.27
25 56 0.71
26 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (24 bp):
ATCGAGAAGCTCATGCGAGCCATT
Found at i:15302830 original size:50 final size:49
Alignment explanation
Indices: 15302746--15302931 Score: 123
Period size: 50 Copynumber: 3.7 Consensus size: 49
15302736 CGAGCATGTA
* * * *
15302746 ATCGGGAAGCTCTTTCGAGCCATGTAAC-GAGAAGCTCATGTGAGCCATTT
1 ATCGAGAAGCTCTTGCGAGCCAT-TATCAG-GAAGCTCATGAGAGCCATTT
*
15302796 ATCGAGAAGCTCTTGCGAGCCAATTATCAGGAAGCTCAT-ACGAGCCA-TA
1 ATCGAGAAGCTCTTGCGAGCC-ATTATCAGGAAGCTCATGA-GAGCCATTT
* ** * * * *
15302845 ATCGAGAAACTCAAGAGAGCCATTAATCGGGAAACT-ACGGAGAGCCATTT
1 ATCGAGAAGCTCTTGCGAGCCATT-ATCAGGAAGCTCA-TGAGAGCCATTT
* *
15302895 ATC-AGGAAGCTCATT-TGAGCCAATTATTAGGAAGCTC
1 ATCGA-GAAGCTC-TTGCGAGCC-ATTATCAGGAAGCTC
15302932 CGAAGAGCTA
Statistics
Matches: 105, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
48 4 0.04
49 34 0.32
50 61 0.58
51 6 0.06
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (49 bp):
ATCGAGAAGCTCTTGCGAGCCATTATCAGGAAGCTCATGAGAGCCATTT
Found at i:15302914 original size:25 final size:24
Alignment explanation
Indices: 15302762--15302931 Score: 92
Period size: 25 Copynumber: 6.8 Consensus size: 24
15302752 AAGCTCTTTC
* *
15302762 GAGCCATGTAACGAGAAGCTCATGT
1 GAGCCATTTATCG-GAAGCTCATGT
* *
15302787 GAGCCATTTATCGAGAAGCTCTTGC
1 GAGCCATTTATCG-GAAGCTCATGT
* **
15302812 GAGCCAATTATCAGGAAGCTCATAC
1 GAGCCATTTATC-GGAAGCTCATGT
* * * *
15302837 GAGCCA-TAATCGAGAAACTCAAGA
1 GAGCCATTTATCG-GAAGCTCATGT
* * * *
15302861 GAGCCATTAATCGGGAAACT-ACGGA
1 GAGCCATTTATC-GGAAGCTCA-TGT
*
15302886 GAGCCATTTATCAGGAAGCTCATTT
1 GAGCCATTTATC-GGAAGCTCATGT
* *
15302911 GAGCCAATTATTAGGAAGCTC
1 GAGCCATTTA-TCGGAAGCTC
15302932 CGAAGAGCTA
Statistics
Matches: 117, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.01
24 18 0.15
25 94 0.80
26 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (24 bp):
GAGCCATTTATCGGAAGCTCATGT
Found at i:15303306 original size:21 final size:21
Alignment explanation
Indices: 15303282--15303323 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15303272 TGAATTTATC
*
15303282 TCAACTTAATACAATTCACAT
1 TCAACTTAATACAATACACAT
* *
15303303 TCAATTTAATCCAATACACAT
1 TCAACTTAATACAATACACAT
15303324 CTTTGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
TCAACTTAATACAATACACAT
Found at i:15305928 original size:23 final size:25
Alignment explanation
Indices: 15305902--15305983 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
15305892 CATATATCGA
* *
15305902 GAAGTTCAAGCGAGCCA-T-ATCAG
1 GAAGCTCAAGAGAGCCATTAATCAG
*
15305925 GAAGCTCCAGAGAGCCATTAATCAG
1 GAAGCTCAAGAGAGCCATTAATCAG
* *
15305950 GAAGCTCACAGAGAGTCTTTAAT-AG
1 GAAGCTCA-AGAGAGCCATTAATCAG
15305975 AGAAGCTCA
1 -GAAGCTCA
15305984 CGAAGAGCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 14 0.29
24 1 0.02
25 14 0.29
26 20 0.41
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCAAGAGAGCCATTAATCAG
Found at i:15305971 original size:26 final size:26
Alignment explanation
Indices: 15305913--15305984 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
15305903 AAGTTCAAGC
15305913 GAGCCA-T-ATCAGGAAGCTC-CAGA
1 GAGCCATTAATCAGGAAGCTCACAGA
15305936 GAGCCATTAATCAGGAAGCTCACAGA
1 GAGCCATTAATCAGGAAGCTCACAGA
* *
15305962 GAGTCTTTAAT-AGAGAAGCTCAC
1 GAGCCATTAATCAG-GAAGCTCAC
15305985 GAAGAGCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 6 0.14
24 1 0.02
25 14 0.33
26 22 0.51
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAGA
Found at i:15311853 original size:198 final size:198
Alignment explanation
Indices: 15311515--15311914 Score: 764
Period size: 198 Copynumber: 2.0 Consensus size: 198
15311505 ATATAATGGC
*
15311515 ATGTATAACTAGACTGTACATTCTACGTTATTCTGAGAATCGACTAAACCGTATCTCTGATACCA
1 ATGTATAACTAGACTGTACATGCTACGTTATTCTGAGAATCGACTAAACCGTATCTCTGATACCA
15311580 ATAAATGTAACACCCCTAACCTATATATGCCGCCAGAATAGTGTTACGAAACATTACCAAAATTT
66 ATAAATGTAACACCCCTAACCTATATATGCCGCCAGAATAGTGTTACGAAACATTACCAAAATTT
15311645 ACAGAACCAATAACAGACTTTTCATATCATTTAGCACTTATATAATAAACCAGTTGTAATCAAGC
131 ACAGAACCAATAACAGACTTTTCATATCATTTAGCACTTATATAATAAACCAGTTGTAATCAAGC
15311710 ATA
196 ATA
15311713 ATGTATAACTAGACTGTACATGCTACGTTATTCTGAGAATCGACTAAACCGTATCTCTGATACCA
1 ATGTATAACTAGACTGTACATGCTACGTTATTCTGAGAATCGACTAAACCGTATCTCTGATACCA
* * *
15311778 ATAAATGTAACACCCTTAACCTATATATGTCGCCAGAATAGTGTTACGAAGCATTACCAAAATTT
66 ATAAATGTAACACCCCTAACCTATATATGCCGCCAGAATAGTGTTACGAAACATTACCAAAATTT
15311843 ACAGAACCAATAACAGACTTTTCATATCATTTAGCACTTATATAATAAACCAGTTGTAATCAAGC
131 ACAGAACCAATAACAGACTTTTCATATCATTTAGCACTTATATAATAAACCAGTTGTAATCAAGC
15311908 ATA
196 ATA
15311911 ATGT
1 ATGT
15311915 CCCTTATTTG
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (198 bp):
ATGTATAACTAGACTGTACATGCTACGTTATTCTGAGAATCGACTAAACCGTATCTCTGATACCA
ATAAATGTAACACCCCTAACCTATATATGCCGCCAGAATAGTGTTACGAAACATTACCAAAATTT
ACAGAACCAATAACAGACTTTTCATATCATTTAGCACTTATATAATAAACCAGTTGTAATCAAGC
ATA
Found at i:15314092 original size:18 final size:19
Alignment explanation
Indices: 15314054--15314092 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15314044 TTTATAGTTT
*
15314054 TATAATTTTTATTTCTTTA
1 TATAATTTTTATTTCTGTA
*
15314073 TATATTTTTTATTT-TGTA
1 TATAATTTTTATTTCTGTA
15314091 TA
1 TA
15314093 AATGTATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TATAATTTTTATTTCTGTA
Found at i:15314778 original size:13 final size:13
Alignment explanation
Indices: 15314755--15314786 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
15314745 GATTCAATTA
15314755 GCTTGATGAAGCTT
1 GCTT-ATGAAGCTT
15314769 GCTTATGAAGCTT
1 GCTTATGAAGCTT
15314782 GCTTA
1 GCTTA
15314787 AGACAAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (13 bp):
GCTTATGAAGCTT
Found at i:15318774 original size:43 final size:43
Alignment explanation
Indices: 15318699--15318864 Score: 160
Period size: 43 Copynumber: 4.0 Consensus size: 43
15318689 AAACACATAT
* * * * *
15318699 ATCACATA-CAATGCC-ATATCCCAAATATGGTCTTACATGTT
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACATGTA
** * * **
15318740 ATCACATATCGATGCCTCTATCCCAGACAGGGTCTTACA-CAA
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACATGTA
* * * *
15318782 ATCATATA-CGGTGCCAATGTCCTAGACATGGTCTTACACGTA
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACATGTA
*
15318824 ATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACATG
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACATG
15318865 AAACCACACC
Statistics
Matches: 99, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 32 0.32
42 20 0.20
43 47 0.47
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACATGTA
Found at i:15320357 original size:30 final size:30
Alignment explanation
Indices: 15320323--15320386 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
15320313 TCAATTAGAC
** *
15320323 TAAGGAAATGTGTAGGTTTTTCTACTAATA
1 TAAGGAAATGTGTAGGTTCATCTACCAATA
* *
15320353 TAAGGACATGTTTAGGTTCATCTACCAATA
1 TAAGGAAATGTGTAGGTTCATCTACCAATA
15320383 TAAG
1 TAAG
15320387 TTGTCTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (30 bp):
TAAGGAAATGTGTAGGTTCATCTACCAATA
Found at i:15326570 original size:21 final size:17
Alignment explanation
Indices: 15326544--15326598 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 17
15326534 TATAAAATTT
15326544 GTTTAATTTTTTTAGAAA
1 GTTTAATTTTTTTA-AAA
15326562 CTGTTTTAAGTTTTTTTAAAA
1 --G-TTTAA-TTTTTTTAAAA
15326583 GTTTAATTTTTATTAA
1 GTTTAATTTTT-TTAA
15326599 TCTGTTTCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.16
18 9 0.28
19 1 0.03
20 1 0.03
21 8 0.25
22 8 0.25
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (17 bp):
GTTTAATTTTTTTAAAA
Found at i:15331378 original size:2 final size:2
Alignment explanation
Indices: 15331371--15331408 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15331361 TCTCAATCCA
15331371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15331409 TTCAATCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15334425 original size:17 final size:17
Alignment explanation
Indices: 15334392--15334425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15334382 ACTACAAAAT
*
15334392 CAAATCTTCTAATATTA
1 CAAATCTTCTAAGATTA
*
15334409 CAAATCTTTTAAGATTA
1 CAAATCTTCTAAGATTA
15334426 GTTTTCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:15335239 original size:21 final size:21
Alignment explanation
Indices: 15335197--15335239 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
15335187 ACAAACACAA
* **
15335197 CTCTGCCTCTGTCACCTGCGC
1 CTCTGCCTCTGCCACCAACGC
*
15335218 CTCTTCCTCTGCCACCAACGC
1 CTCTGCCTCTGCCACCAACGC
15335239 C
1 C
15335240 ACGCCTGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.51, G:0.14, T:0.26
Consensus pattern (21 bp):
CTCTGCCTCTGCCACCAACGC
Found at i:15340910 original size:35 final size:34
Alignment explanation
Indices: 15340867--15340934 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
15340857 CTATTGAATT
15340867 AAATTTTAAATTATATTCT-AATTTAATGCATATG
1 AAATTTTAAATTATATTCTCAATTTAAT-CATATG
* *
15340901 AAATATTTAAATTTTATTTTCAATTTAATCATAT
1 AAAT-TTTAAATTATATTCTCAATTTAATCATAT
15340935 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 4 0.13
35 18 0.60
36 8 0.27
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (34 bp):
AAATTTTAAATTATATTCTCAATTTAATCATATG
Found at i:15343986 original size:20 final size:22
Alignment explanation
Indices: 15343961--15344002 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
15343951 TATTGTTTTC
15343961 AAAAAAA-CCAAAAGTT-TGTT
1 AAAAAAAGCCAAAAGTTGTGTT
*
15343981 AAAAAAAGTCAAAAGTTGTGTT
1 AAAAAAAGCCAAAAGTTGTGTT
15344003 TTGAAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAAAAAGCCAAAAGTTGTGTT
Found at i:15348584 original size:22 final size:19
Alignment explanation
Indices: 15348532--15348573 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
15348522 ATGGGAAATT
15348532 TCATGTGGAAATCTTTTTA
1 TCATGTGGAAATCTTTTTA
15348551 TCATGTGGAAATCTTTTTA
1 TCATGTGGAAATCTTTTTA
15348570 TCAT
1 TCAT
15348574 CAAGGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (19 bp):
TCATGTGGAAATCTTTTTA
Found at i:15349431 original size:12 final size:12
Alignment explanation
Indices: 15349414--15349439 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15349404 TAATGTTCTA
15349414 TTTATTTAAAAT
1 TTTATTTAAAAT
15349426 TTTATTTAAAAT
1 TTTATTTAAAAT
15349438 TT
1 TT
15349440 AATTACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTTAAAAT
Found at i:15356951 original size:16 final size:19
Alignment explanation
Indices: 15356915--15356951 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
15356905 CAACTTAAAC
15356915 AATTATACATTTCATAATA
1 AATTATACATTTCATAATA
15356934 AATTAT-CA-TTCA-AATA
1 AATTATACATTTCATAATA
15356950 AA
1 AA
15356952 AAACTATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 2 0.11
19 6 0.33
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATACATTTCATAATA
Found at i:15359966 original size:43 final size:43
Alignment explanation
Indices: 15359914--15360056 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 43
15359904 ATGCTATTAC
* * * * * *
15359914 GTGCTAGTATGATTA-TTCCAGTTTATCTAATGATGCACTATGT
1 GTGCCAGTATAATTACTT-CAGTTTATCCAATAATGAACTACGT
*
15359957 GTGCCAGTATAATTACTTCAGTTTATCCAATAATGAATTACGT
1 GTGCCAGTATAATTACTTCAGTTTATCCAATAATGAACTACGT
* ** * * * *
15360000 GTGCCAGTATAATTGCTTTGGTTCATCCAATGATGCACTTCGT
1 GTGCCAGTATAATTACTTCAGTTTATCCAATAATGAACTACGT
*
15360043 GTGCCAATATAATT
1 GTGCCAGTATAATT
15360057 GCTTTGGTTC
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 81 0.98
44 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (43 bp):
GTGCCAGTATAATTACTTCAGTTTATCCAATAATGAACTACGT
Found at i:15360057 original size:43 final size:43
Alignment explanation
Indices: 15359942--15360102 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
15359932 CAGTTTATCT
* * ** *
15359942 AATGATGCACTAT-GTGTGCCAGTATAATTACTTCAGTTTATCC
1 AATGATGCACT-TCGTGTGCCAATATAATTGCTTTGGTTCATCC
* * *
15359985 AATAATG-AATTACGTGTGCCAGTATAATTGCTTTGGTTCATCC
1 AATGATGCACTT-CGTGTGCCAATATAATTGCTTTGGTTCATCC
*
15360028 AATGATGCACTTCGTGTGCCAATATAATTGCTTTGGTTCATTC
1 AATGATGCACTTCGTGTGCCAATATAATTGCTTTGGTTCATCC
* * *
15360071 GATGATGCACCTCGTGTGCCAATACAATTGCT
1 AATGATGCACTTCGTGTGCCAATATAATTGCT
15360103 GCGACTTGCT
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 96 0.94
44 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (43 bp):
AATGATGCACTTCGTGTGCCAATATAATTGCTTTGGTTCATCC
Found at i:15360116 original size:43 final size:42
Alignment explanation
Indices: 15359997--15360122 Score: 110
Period size: 43 Copynumber: 2.9 Consensus size: 42
15359987 TAATGAATTA
* * ** * * *
15359997 CGTGTGCCAGTATAATTGCTTTGGTTCATCCAATGATGCACTT
1 CGTGTGCCAATACAATTGCTGCGCTTCAT-CGATGATGCACCT
* ** *
15360040 CGTGTGCCAATATAATTGCTTTGGTTCATTCGATGATGCACCT
1 CGTGTGCCAATACAATTGCTGCGCTTCA-TCGATGATGCACCT
15360083 CGTGTGCCAATACAATTGCTGCGACTTGC-TCGATGATGCA
1 CGTGTGCCAATACAATTGCTGCG-CTT-CATCGATGATGCA
15360123 TTATGTGTGC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 69 0.95
44 3 0.04
45 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
CGTGTGCCAATACAATTGCTGCGCTTCATCGATGATGCACCT
Found at i:15363057 original size:9 final size:9
Alignment explanation
Indices: 15363037--15363111 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
15363027 GTAGTGATTC
*
15363037 AATTTGGTT
1 AATTCGGTT
*
15363046 AATTCGGGT
1 AATTCGGTT
15363055 AATTCGGTT
1 AATTCGGTT
*
15363064 AATTCGGGT
1 AATTCGGTT
*
15363073 AATCCGGTT
1 AATTCGGTT
15363082 AATTCTGG-T
1 AATTC-GGTT
15363091 AATT-GGTT
1 AATTCGGTT
15363099 AATTCGGTT
1 AATTCGGTT
15363108 AATT
1 AATT
15363112 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 47 0.84
10 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:15363063 original size:18 final size:18
Alignment explanation
Indices: 15363037--15363111 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
15363027 GTAGTGATTC
*
15363037 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
15363055 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
* *
15363073 AATCCGGTTAATTCTGGT
1 AATTCGGTTAATTCGGGT
*
15363091 AATT-GGTTAATTCGGTT
1 AATTCGGTTAATTCGGGT
15363108 AATT
1 AATT
15363112 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 15 0.29
18 36 0.71
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:15369099 original size:7 final size:7
Alignment explanation
Indices: 15369087--15369123 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
15369077 TAATTACTAT
15369087 AATTTAA
1 AATTTAA
15369094 AATTTAA
1 AATTTAA
15369101 AATTTAA
1 AATTTAA
15369108 AATTTAA
1 AATTTAA
15369115 AATTTAA
1 AATTTAA
15369122 AA
1 AA
15369124 AATTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTTAA
Found at i:15369592 original size:3 final size:3
Alignment explanation
Indices: 15369586--15369616 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15369576 CCATCTTCGA
15369586 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
15369617 GTCAATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:15375229 original size:27 final size:27
Alignment explanation
Indices: 15375191--15375244 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
15375181 AACATCGTCC
15375191 GCGTCATCACTTTCCCCAAACGGTGGT
1 GCGTCATCACTTTCCCCAAACGGTGGT
15375218 GCGTCATCACTTTCCCCAAACGGTGGT
1 GCGTCATCACTTTCCCCAAACGGTGGT
15375245 CTTACCTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.26
Consensus pattern (27 bp):
GCGTCATCACTTTCCCCAAACGGTGGT
Found at i:15378189 original size:25 final size:25
Alignment explanation
Indices: 15378183--15378289 Score: 133
Period size: 25 Copynumber: 4.0 Consensus size: 25
15378173 GGAACAAATA
*
15378183 ACCAGCAGAGGAACAAAAAACCAGC
1 ACCAGCAGAGGAACAAAGAACCAGC
15378208 ACCAGCAGAGGAACAAAGAACCAGC
1 ACCAGCAGAGGAACAAAGAACCAGC
15378233 ACCAGCACTAGCAGAAGAACAAAGAACCAGC
1 ACCAG--C-AG-AG--GAACAAAGAACCAGC
* *
15378264 ACCAGCAGAGGATCAAAGAAGCAGC
1 ACCAGCAGAGGAACAAAGAACCAGC
15378289 A
1 A
15378290 GAGAACAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
25 43 0.59
27 3 0.04
28 4 0.05
29 3 0.04
31 20 0.27
ACGTcount: A:0.49, C:0.27, G:0.22, T:0.02
Consensus pattern (25 bp):
ACCAGCAGAGGAACAAAGAACCAGC
Found at i:15378233 original size:19 final size:19
Alignment explanation
Indices: 15378151--15378208 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
15378141 GTGGTGGAGA
**
15378151 AGAGGAACAAAGCACCAGC
1 AGAGGAACAAAAAACCAGC
*
15378170 AGAGGAACAAATAACCAGC
1 AGAGGAACAAAAAACCAGC
15378189 AGAGGAACAAAAAACCAGC
1 AGAGGAACAAAAAACCAGC
15378208 A
1 A
15378209 CCAGCAGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.53, C:0.22, G:0.22, T:0.02
Consensus pattern (19 bp):
AGAGGAACAAAAAACCAGC
Found at i:15378240 original size:31 final size:31
Alignment explanation
Indices: 15378202--15378270 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
15378192 GGAACAAAAA
*
15378202 ACCAGCACCAGCAGAGGAACAAAGAACCAGC
1 ACCAGCACCAGCAGAAGAACAAAGAACCAGC
*
15378233 ACCAGCACTAGCAGAAGAACAAAGAACCAGC
1 ACCAGCACCAGCAGAAGAACAAAGAACCAGC
15378264 ACCAGCA
1 ACCAGCA
15378271 GAGGATCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.46, C:0.32, G:0.20, T:0.01
Consensus pattern (31 bp):
ACCAGCACCAGCAGAAGAACAAAGAACCAGC
Found at i:15378306 original size:18 final size:19
Alignment explanation
Indices: 15378264--15378307 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
15378254 AAGAACCAGC
* *
15378264 ACCAGCAGAGGATCAAAGA
1 ACCAGCAGAGGAACAAAAA
*
15378283 AGCAGCAGA-GAACAAAAA
1 ACCAGCAGAGGAACAAAAA
15378301 ACCAGCA
1 ACCAGCA
15378308 ATGAGAGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.52, C:0.23, G:0.23, T:0.02
Consensus pattern (19 bp):
ACCAGCAGAGGAACAAAAA
Found at i:15402623 original size:25 final size:25
Alignment explanation
Indices: 15402595--15402654 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
15402585 TATAATGAAT
15402595 TTTACAATTTTTT-CCTAATTTGATA
1 TTTA-AATTTTTTACCTAATTTGATA
* *
15402620 TTTAATTTTTTTAGTCTAATTTGATA
1 TTTAAATTTTTTA-CCTAATTTGATA
* *
15402646 CTTGAATTT
1 TTTAAATTT
15402655 GACATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
26 17 0.61
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (25 bp):
TTTAAATTTTTTACCTAATTTGATA
Found at i:15413478 original size:2 final size:2
Alignment explanation
Indices: 15413471--15413497 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15413461 ATTATACATG
15413471 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
15413498 TAACCTAACT
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:15413849 original size:41 final size:41
Alignment explanation
Indices: 15413778--15413883 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
15413768 NNNNNNNATT
* * *
15413778 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
* *
15413819 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGTATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
15413860 AGCCTGTTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
15413884 TTATCTCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:15419357 original size:22 final size:22
Alignment explanation
Indices: 15419333--15419375 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
15419323 GCCTATATAT
*
15419333 AAAACTATAAAGCATTATTATTA
1 AAAAATATAAAGC-TTATTATTA
*
15419356 AAAAATTTAAAGCTTATTAT
1 AAAAATATAAAGCTTATTAT
15419376 ATGTATATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAAATATAAAGCTTATTATTA
Found at i:15421273 original size:3 final size:3
Alignment explanation
Indices: 15421260--15421289 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
15421250 AATACACCAT
15421260 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TT
15421290 TTGGGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:15422102 original size:2 final size:2
Alignment explanation
Indices: 15422095--15422132 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15422085 AAGGGTGCTC
15422095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15422133 TTGTTATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15422613 original size:40 final size:38
Alignment explanation
Indices: 15422546--15422664 Score: 114
Period size: 42 Copynumber: 3.0 Consensus size: 38
15422536 ACATCAACAA
* *
15422546 TTAATTATTTTTTAAAATTTTAAATTTTAAAATATATGT
1 TTAATT-TTTTTAAAAATATTAAATTTTAAAATATATGT
* *
15422585 TATAATTTTTTTAAAAATATATATATTTTTTAAAATATGTGCT
1 T-TAATTTTTTTAAAAATAT-TA-A-ATTTTAAAATATATG-T
* * *
15422628 TTAA-TTTTTTAAAATTATTAAATTTAAAAATCTATGT
1 TTAATTTTTTTAAAAATATTAAATTTTAAAATATATGT
15422665 GGCAATATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
37 1 0.02
38 11 0.17
39 13 0.20
40 9 0.14
41 14 0.21
42 16 0.24
43 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (38 bp):
TTAATTTTTTTAAAAATATTAAATTTTAAAATATATGT
Found at i:15422665 original size:40 final size:38
Alignment explanation
Indices: 15422552--15422665 Score: 108
Period size: 40 Copynumber: 2.9 Consensus size: 38
15422542 ACAATTAATT
15422552 ATTTTTTAAAATT-TTAAATTTTAAAATATATGT-TATA
1 ATTTTTTAAAATTATTAAATTTTAAAAT-TATGTGTATA
** *
15422589 ATTTTTTTAAAAATATATATATTTTTTAAAA-TATGTGCTTTA
1 A-TTTTTT-AAAAT-TAT-TAAATTTTAAAATTATGTG-TATA
*
15422631 ATTTTTTAAAATTATTAAATTTAAAAATCTATGTG
1 ATTTTTTAAAATTATTAAATTTTAAAAT-TATGTG
15422666 GCAATATTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
37 1 0.02
38 15 0.24
39 8 0.13
40 17 0.27
41 7 0.11
42 14 0.23
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (38 bp):
ATTTTTTAAAATTATTAAATTTTAAAATTATGTGTATA
Found at i:15432011 original size:23 final size:23
Alignment explanation
Indices: 15431981--15432026 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15431971 GGTCTGGTGT
15431981 ACAACCCCAATTTTCACTCTTAA
1 ACAACCCCAATTTTCACTCTTAA
15432004 ACAACCCCAATTTTCACTCTTAA
1 ACAACCCCAATTTTCACTCTTAA
15432027 CATTTGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (23 bp):
ACAACCCCAATTTTCACTCTTAA
Found at i:15433982 original size:46 final size:44
Alignment explanation
Indices: 15433879--15434194 Score: 351
Period size: 46 Copynumber: 7.6 Consensus size: 44
15433869 TACGTATGAT
*
15433879 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTA-GCTAC
15433922 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
15433968 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT--AGCTAC
*
15434014 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TA---A-
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGCTAC
15434050 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGCTAC
15434086 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGCTAC
15434122 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* *
15434168 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
15434195 AGTACTCAAA
Statistics
Matches: 253, Mismatches: 5, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
36 100 0.40
37 1 0.00
38 3 0.01
40 2 0.01
42 3 0.01
43 10 0.04
44 7 0.03
45 21 0.08
46 104 0.41
47 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (44 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:15434055 original size:36 final size:36
Alignment explanation
Indices: 15434014--15434158 Score: 263
Period size: 36 Copynumber: 4.0 Consensus size: 36
15434004 CTAAAGCTAC
* *
15434014 CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
15434050 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
15434086 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
15434122 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
15434158 C
1 C
15434159 TAAAGCTACC
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 106 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:15444590 original size:29 final size:29
Alignment explanation
Indices: 15444549--15444631 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 29
15444539 TTGTTCTGGG
* *
15444549 AAAAATAATTTTGACAAGATGGGTTCTGA
1 AAAAATAAATTTGACAAGATGGATTCTGA
* * *
15444578 AAAAATAAATTTGACATGATGTATTTTGA
1 AAAAATAAATTTGACAAGATGGATTCTGA
* * **
15444607 AAAAATTATTTTGATGAGATGGATT
1 AAAAATAAATTTGACAAGATGGATT
15444632 TTTTTTTGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (29 bp):
AAAAATAAATTTGACAAGATGGATTCTGA
Found at i:15444769 original size:59 final size:59
Alignment explanation
Indices: 15444672--15444875 Score: 327
Period size: 59 Copynumber: 3.4 Consensus size: 59
15444662 CACAGCCAGT
*
15444672 AATATATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
* *
15444732 AATAATTTGTACAAAATTATTCAAAAGAACTTCTATTTTATTAAATAAAACAATATTAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
* *
15444791 AATAATTTTTACAAAAATATTGAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
* * *
15444850 AACAATTTGTATAAAAAAATTCAAAA
1 AATAATTTGTACAAAAATATTCAAAA
15444876 ATAAATCAAT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 128 0.97
60 4 0.03
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
Done.