Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 135 of 295
Found at i:41429730 original size:48 final size:48
Alignment explanation
Indices: 41429670--41429895 Score: 175
Period size: 48 Copynumber: 4.7 Consensus size: 48
41429660 ATGTGAGTAT
* *
41429670 TGAGATCCCGTGTAAGACCATATTTGGGATATGGTATTGGCATCAAGA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGCATTGGCATCAAGA
* * * ** *** * *
41429718 TGAGATCTCGTGTAAGACCGTATCTAGGATATAACACCAGCATCGATA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGCATTGGCATCAAGA
* ** * *
41429766 TGAGATCCCGTATAAGACCATGCCTGGGACATGGCATTGGCATCATTG-
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGCATTGGCATCA-AGA
* * * * * * *
41429814 TGAGATCCCATGTAAGATCATATCTGGGATATGGTATTGGTACCGATA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGCATTGGCATCAAGA
* * * * *
41429862 TCAGGTCCCGTCTAAGACCATGTCTGGGACATGG
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGG
41429896 TATCGGCACC
Statistics
Matches: 130, Mismatches: 46, Indels: 4
0.72 0.26 0.02
Matches are distributed among these distances:
48 130 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (48 bp):
TGAGATCCCGTGTAAGACCATATCTGGGATATGGCATTGGCATCAAGA
Found at i:41429818 original size:96 final size:96
Alignment explanation
Indices: 41429670--41429845 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 96
41429660 ATGTGAGTAT
* ** * * * *
41429670 TGAGATCCCGTGTAAGACCATATTTGGGATATGGTATTGGCATCAAGATGAGATCTCGTGTAAGA
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTGGCATCAAGATGAGATCCCATGTAAGA
*
41429735 CCGTATCTAGGATATAACACCAGCATCGATA
66 CCATATCTAGGATATAACACCAGCATCGATA
* *
41429766 TGAGATCCCGTATAAGACCATGCCTGGGACATGGCATTGGCATCATTG-TGAGATCCCATGTAAG
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTGGCATCA-AGATGAGATCCCATGTAAG
* *
41429830 ATCATATCTGGGATAT
65 ACCATATCTAGGATAT
41429846 GGTATTGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 66 0.99
97 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (96 bp):
TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTGGCATCAAGATGAGATCCCATGTAAGA
CCATATCTAGGATATAACACCAGCATCGATA
Found at i:41434445 original size:47 final size:47
Alignment explanation
Indices: 41434387--41434517 Score: 138
Period size: 47 Copynumber: 2.8 Consensus size: 47
41434377 GTACGAATAA
* * **
41434387 TACCTTAATTTGGCTACGAGCCATGATATAGGTATTTTGAGA-AGAGG
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATA-AGG
* ** * * * *
41434434 TACCTTGATTTGGTTGTGGGCCATGGTATAGGTACTCCAAGATAAGT
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATAAGG
*
41434481 TACCTTGATTTGGCTACAAGCCATGGTATAGGTATTT
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTT
41434518 ATCTATTATG
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
47 64 0.98
48 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATAAGG
Found at i:41437381 original size:15 final size:14
Alignment explanation
Indices: 41437363--41437392 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
41437353 TTAATAGCAT
41437363 TTATGTTAACTTACA
1 TTATGTTAA-TTACA
41437378 TTATGTTAATTACA
1 TTATGTTAATTACA
41437392 T
1 T
41437393 ATTAAAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (14 bp):
TTATGTTAATTACA
Found at i:41439634 original size:21 final size:21
Alignment explanation
Indices: 41439608--41439649 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41439598 TAGTACAGAC
41439608 GATTTTGAATGAAGCACACAA
1 GATTTTGAATGAAGCACACAA
41439629 GATTTTGAATGAAGCACACAA
1 GATTTTGAATGAAGCACACAA
41439650 TGGTAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (21 bp):
GATTTTGAATGAAGCACACAA
Found at i:41450960 original size:13 final size:13
Alignment explanation
Indices: 41450936--41450960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41450926 TACAAAAAGG
41450936 TTTTACTAAAATA
1 TTTTACTAAAATA
41450949 TTTTACTAAAAT
1 TTTTACTAAAAT
41450961 TGTGGTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTACTAAAATA
Found at i:41454012 original size:107 final size:107
Alignment explanation
Indices: 41453880--41454100 Score: 424
Period size: 107 Copynumber: 2.1 Consensus size: 107
41453870 GTTGGTGATT
41453880 TTCACTTTAAAAAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCC
1 TTCA-TTTAAAAAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCC
41453945 CTTCGAATCTTTTGTATCAAGTTGAGCCTTTCAATTCACAAAA
65 CTTCGAATCTTTTGTATCAAGTTGAGCCTTTCAATTCACAAAA
*
41453988 TTCATTTTAAAAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCC
1 TTCATTTAAAAAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCC
41454053 TTCGAATCTTTTGTATCAAGTTGAGCCTTTCAATTCACAAAA
66 TTCGAATCTTTTGTATCAAGTTGAGCCTTTCAATTCACAAAA
41454095 TTCATT
1 TTCATT
41454101 AATTAAGTCC
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 108 0.96
108 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (107 bp):
TTCATTTAAAAAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCC
TTCGAATCTTTTGTATCAAGTTGAGCCTTTCAATTCACAAAA
Found at i:41455686 original size:89 final size:89
Alignment explanation
Indices: 41455580--41455756 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
41455570 AGTACTAAAC
41455580 AAATAGTGATGTTAACATATATAATAACGC-AAATATG-TAGGAATCATATCTCTTACAACAAAA
1 AAATAGTGATGTTAACATATATAATAAC-CTAAATATGTTA-GAATCATATCTCTTACAACAAAA
*
41455643 AGCAACAAAGAAAAAGACAGAAAGAT
64 AACAACAAAGAAAAAGACAGAAAGAT
*
41455669 AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATTATATCTCTTACAACAAAAAA
1 AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAAAA
*
41455734 CAATAAAGAAAAAGACAGAAAGA
66 CAACAAAGAAAAAGACAGAAAGA
41455757 AAGAAACAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
88 1 0.01
89 80 0.96
90 2 0.02
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (89 bp):
AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAAAA
CAACAAAGAAAAAGACAGAAAGAT
Found at i:41456348 original size:3 final size:3
Alignment explanation
Indices: 41456340--41456368 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41456330 GTGATTCAAT
41456340 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41456369 GTGTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41457463 original size:16 final size:17
Alignment explanation
Indices: 41457424--41457463 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
41457414 AATTAAAATG
41457424 TAATTTTATCATTATAA
1 TAATTTTATCATTATAA
41457441 TAA-TTTAT-ATT-TATA
1 TAATTTTATCATTATA-A
41457456 TAATTTTA
1 TAATTTTA
41457464 AGAAGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 7 0.33
16 9 0.43
17 3 0.14
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTATCATTATAA
Found at i:41460304 original size:21 final size:19
Alignment explanation
Indices: 41460266--41460304 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
41460256 AATAATTAAT
*
41460266 GTAAATATTATTTTTTTTA
1 GTAAATATTATTTATTTTA
41460285 GTAAATATAATATTTATTTT
1 GTAAATAT--TATTTATTTT
41460305 TCAATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
GTAAATATTATTTATTTTA
Found at i:41463606 original size:28 final size:27
Alignment explanation
Indices: 41463573--41463632 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
41463563 TTAATAATTA
41463573 ATTTTTAAAATTTAAAAATTATAAAAACT
1 ATTTTTAAAA-TT-AAAATTATAAAAACT
* *
41463602 ATTTTTTAAAATTAAAATTATTAAAATT
1 A-TTTTTAAAATTAAAATTATAAAAACT
41463630 ATT
1 ATT
41463633 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 14 0.50
29 3 0.11
30 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATTAAAATTATAAAAACT
Found at i:41463626 original size:9 final size:9
Alignment explanation
Indices: 41463612--41463636 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41463602 ATTTTTTAAA
41463612 ATTAAAATT
1 ATTAAAATT
41463621 ATTAAAATT
1 ATTAAAATT
41463630 ATTAAAA
1 ATTAAAA
41463637 AATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTAAAATT
Found at i:41463647 original size:36 final size:35
Alignment explanation
Indices: 41463577--41463647 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
41463567 TAATTAATTT
**
41463577 TTAAAATTTAAAAATTATAAAAACTATTTTTTAAAA
1 TTAAAATTTAAAAATTATAAAAAC-ATTAATTAAAA
*
41463613 TTAAAATTATTAAAATTATTAAAAA-ATTAATTAAA
1 TTAAAATT-TAAAAATTA-TAAAAACATTAATTAAA
41463648 TGCTACGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 16 0.53
37 8 0.27
38 6 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
TTAAAATTTAAAAATTATAAAAACATTAATTAAAA
Found at i:41469350 original size:16 final size:17
Alignment explanation
Indices: 41469324--41469358 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41469314 TAGAATTGGG
*
41469324 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
41469341 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
41469357 TT
1 TT
41469359 TAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:41470457 original size:30 final size:31
Alignment explanation
Indices: 41470423--41470524 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 31
41470413 TAAAAAATAA
*
41470423 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* * *
41470453 AAATTTCATTTTGACCCTTAAA-ATTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
41470483 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
41470513 AAATTTCATTTT
1 AAATTTCATTTT
41470525 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 4 0.07
30 55 0.92
31 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:41470538 original size:29 final size:28
Alignment explanation
Indices: 41470423--41470539 Score: 92
Period size: 30 Copynumber: 4.0 Consensus size: 28
41470413 TAAAAAATAA
* * *
41470423 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTT-AACCCTAAA-TTTTCTT
* *
41470453 AAATTTCATTTTGACCCTTAAAATTTCTTT
1 AAATTTCATTTTAACCC-TAAATTTTC-TT
* *
41470483 AAATTTCA-CTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTA-A-CCCTAAATTTTC-TT
*
41470513 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTAACCCTAAATTTTCT
41470540 AAAAATTACA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.01
29 19 0.27
30 44 0.63
31 6 0.09
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (28 bp):
AAATTTCATTTTAACCCTAAATTTTCTT
Found at i:41470807 original size:10 final size:10
Alignment explanation
Indices: 41470788--41470817 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41470778 TTTTTCGAAG
*
41470788 GAAAAAAGAA
1 GAAAAGAGAA
41470798 GAAAAGAGAA
1 GAAAAGAGAA
41470808 GAAAAGAGAA
1 GAAAAGAGAA
41470818 AGAGGAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:41470909 original size:3 final size:3
Alignment explanation
Indices: 41470903--41470937 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
41470893 GTGTAGGAGG
41470903 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
41470938 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41471122 original size:17 final size:16
Alignment explanation
Indices: 41471099--41471158 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
41471089 AAACTAAAGC
41471099 AAAAAAAGCAGCCCAA
1 AAAAAAAGCAGCCCAA
*
41471115 AAAGAAAAG--GCCAAA
1 AAA-AAAAGCAGCCCAA
*
41471130 AAAAAAAACAGCCCAGA
1 AAAAAAAGCAGCCCA-A
41471147 AAAAAGAAGCAG
1 AAAAA-AAGCAG
41471159 GCCACAGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.11
15 8 0.23
16 7 0.20
17 11 0.31
18 5 0.14
ACGTcount: A:0.65, C:0.18, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAGCAGCCCAA
Found at i:41471272 original size:7 final size:7
Alignment explanation
Indices: 41471244--41471345 Score: 107
Period size: 7 Copynumber: 14.0 Consensus size: 7
41471234 AGCAGGCCAG
41471244 GAAAAAA
1 GAAAAAA
*
41471251 GAGAGAAA
1 GA-AAAAA
41471259 G-AAAAA
1 GAAAAAA
41471265 GAAAAAA
1 GAAAAAA
*
41471272 GAAAGAA
1 GAAAAAA
*
41471279 GAAAGAA
1 GAAAAAA
41471286 GAAAAAA
1 GAAAAAA
*
41471293 GAAAAGA
1 GAAAAAA
41471300 GAAAAAA
1 GAAAAAA
*
41471307 GGAAAAAG
1 -GAAAAAA
41471315 GAAAAAA
1 GAAAAAA
41471322 GGAAAAAGAA
1 -G-AAAA-AA
41471332 GAAAAAA
1 GAAAAAA
41471339 GAAAAAA
1 GAAAAAA
41471346 AAAGAGTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
6 5 0.06
7 53 0.65
8 16 0.20
9 5 0.06
10 2 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:41471276 original size:17 final size:17
Alignment explanation
Indices: 41471254--41471350 Score: 96
Period size: 17 Copynumber: 5.8 Consensus size: 17
41471244 GAAAAAAGAG
41471254 AGAAAGAAAAAGAAAAA
1 AGAAAGAAAAAGAAAAA
*
41471271 AGAAAGAAGAAAGAAGAA
1 AGAAAGAA-AAAGAAAAA
41471289 A-AAAGAAAAGAGAAAAA
1 AGAAAGAAAA-AGAAAAA
41471306 AG---GAAAAAGGAAAAA
1 AGAAAGAAAAA-GAAAAA
*
41471321 AGGAAA-AAGAAGAAAAA
1 A-GAAAGAAAAAGAAAAA
*
41471338 AGAAAAAAAAAGA
1 AGAAAGAAAAAGA
41471351 GTTTCAATTC
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
14 1 0.01
15 12 0.18
16 7 0.10
17 34 0.51
18 13 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAGAAAAA
Found at i:41471932 original size:19 final size:21
Alignment explanation
Indices: 41471893--41471933 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41471883 AATTTTGTGT
*
41471893 AAAAAATCCAGTGTTTTCAAA
1 AAAAAATCCAGTGTTTCCAAA
41471914 AAAAAATCCA-T-TTTCCAAA
1 AAAAAATCCAGTGTTTCCAAA
41471933 A
1 A
41471934 TTTTTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAATCCAGTGTTTCCAAA
Found at i:41472003 original size:18 final size:17
Alignment explanation
Indices: 41471929--41472084 Score: 154
Period size: 17 Copynumber: 9.0 Consensus size: 17
41471919 ATCCATTTTC
* *
41471929 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
41471947 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
41471965 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
41471981 CAAAAATTTTCGTGTTT
1 CAAAAATTTTCGTGTTT
41471998 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
41472016 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
41472033 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
41472051 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
** *
41472068 TGAAAATTTTCATGTTT
1 CAAAAATTTTCGTGTTT
41472085 TTAAAAAAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
16 16 0.14
17 54 0.47
18 34 0.29
19 12 0.10
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:41472026 original size:35 final size:34
Alignment explanation
Indices: 41471950--41472090 Score: 153
Period size: 35 Copynumber: 4.1 Consensus size: 34
41471940 GTGTCTTCTA
41471950 AAAATTTTT-GTGTTTCAAAAATTTTC-GTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCTGTTTTC
*
41471982 AAAAATTTTCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTC-TGTTTTC
* **
41472017 AAAATTTTTCGTATTTCAAAAATCCTCTTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTC-TGTTTTC
* ** *
41472052 AAAA-ATTTCGGTGTTTTGAAAATTTTCATGTTTTT
1 AAAATTTTTC-GTGTTTCAAAAATTTTC-TGTTTTC
41472087 AAAA
1 AAAA
41472091 AAAAAATCTC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
32 8 0.09
33 17 0.19
34 4 0.04
35 62 0.68
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (34 bp):
AAAATTTTTCGTGTTTCAAAAATTTTCTGTTTTC
Found at i:41472091 original size:35 final size:34
Alignment explanation
Indices: 41471925--41472091 Score: 149
Period size: 35 Copynumber: 4.8 Consensus size: 34
41471915 AAAAATCCAT
* * * *
41471925 TTTCCAAAATTTTTAGTGTCTTCTAAAAATTTTTGTG
1 TTTCAAAAATTTTCA-TGTTTTC-AAAAA-TTTCGTG
41471962 TTTCAAAAATTTTC--GTTTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCATGTTTTCAAAAA-TTTCGTG
* * *
41471995 TTTCAAAAATTTTCGTGTTTTCAAAATTTTTCGTA
1 TTTCAAAAATTTTCATGTTTTCAAAA-ATTTCGTG
** *
41472030 TTTCAAAAATCCTCTTGTTTTCAAAAATTTCGGTG
1 TTTCAAAAATTTTCATGTTTTCAAAAATTTC-GTG
** *
41472065 TTTTGAAAATTTTCATGTTTTTAAAAA
1 TTTCAAAAATTTTCATGTTTTCAAAAA
41472092 AAAAATCTCG
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
33 26 0.24
34 9 0.08
35 62 0.57
37 12 0.11
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (34 bp):
TTTCAAAAATTTTCATGTTTTCAAAAATTTCGTG
Found at i:41484185 original size:192 final size:192
Alignment explanation
Indices: 41483858--41484660 Score: 1533
Period size: 192 Copynumber: 4.2 Consensus size: 192
41483848 CTTTCCAAGG
41483858 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41483923 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
41483988 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
41484050 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41484115 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
41484180 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
41484242 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41484307 TT-AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
41484370 TTTATGTTTTAAATTGACTCAT-TTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
41484431 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41484496 TTAAAAAAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
41484560 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
41484623 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
41484661 GGCTCACATG
Statistics
Matches: 603, Mismatches: 3, Indels: 9
0.98 0.00 0.01
Matches are distributed among these distances:
189 106 0.18
190 57 0.09
191 108 0.18
192 298 0.49
193 34 0.06
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:41484338 original size:122 final size:122
Alignment explanation
Indices: 41484120--41484346 Score: 305
Period size: 122 Copynumber: 1.9 Consensus size: 122
41484110 ATTTTTTAAA
* ** * *
41484120 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
** ** *
41484185 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
**
41484242 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT-
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT-AATTTA
*
41484306 T-TTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
65 TGTT-AAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCT
41484347 CGGGGCACGC
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
121 2 0.02
122 84 0.93
123 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (122 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:41484564 original size:381 final size:385
Alignment explanation
Indices: 41483858--41484660 Score: 1535
Period size: 381 Copynumber: 2.1 Consensus size: 385
41483848 CTTTCCAAGG
41483858 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41483923 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
41483988 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
41484053 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
41484118 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTT
261 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTT
41484183 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-
326 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
41484242 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
41484307 TT-AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
41484370 TTTATGTTTTAAATTGACTCAT-TTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
41484434 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT-
41484499 AAAAAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTT
260 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTT
41484563 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
325 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
* **
41484624 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
41484661 GGCTCACATG
Statistics
Matches: 414, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
381 204 0.49
382 88 0.21
383 55 0.13
384 67 0.16
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (385 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTT
ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
Found at i:41484700 original size:16 final size:17
Alignment explanation
Indices: 41484679--41484712 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41484669 TGCTGAGGTA
*
41484679 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
41484695 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
41484712 T
1 T
41484713 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:41484876 original size:85 final size:88
Alignment explanation
Indices: 41484618--41484876 Score: 309
Period size: 91 Copynumber: 2.9 Consensus size: 88
41484608 TAATTTTTGT
*
41484618 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
41484682 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
41484709 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
**
41484771 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* *
41484796 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
41484860 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
41484877 TCTGTTTTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 29 0.20
88 2 0.01
89 31 0.21
91 41 0.28
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:41484879 original size:13 final size:13
Alignment explanation
Indices: 41484863--41484896 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
41484853 TCTTTTCAAA
41484863 TTCTGTTTTTAAT
1 TTCTGTTTTTAAT
41484876 TTCTGTTTTTTTAAT
1 TTCTG--TTTTTAAT
41484891 TTCTGT
1 TTCTGT
41484897 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (13 bp):
TTCTGTTTTTAAT
Found at i:41484888 original size:15 final size:15
Alignment explanation
Indices: 41484868--41484896 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41484858 TCAAATTCTG
41484868 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
41484883 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
41484897 GTTTCAAAAA
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:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:41485057 original size:54 final size:55
Alignment explanation
Indices: 41484973--41485190 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
41484963 TCAATTTCTA
*
41484973 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
41485028 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
41485082 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
41485133 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
41485188 CTT
1 CTT
41485191 GGCTCACGTG
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 12 0.08
51 35 0.23
52 2 0.01
53 2 0.01
54 48 0.32
55 42 0.28
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:41485456 original size:13 final size:15
Alignment explanation
Indices: 41485432--41485465 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41485422 TTTAATTTTC
41485432 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
41485446 AAAATTT-AAAAATA
1 AAAATTTCAAAAATA
41485460 AAAATT
1 AAAATT
41485466 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:41485495 original size:30 final size:31
Alignment explanation
Indices: 41485461--41485562 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
41485451 TTAAAAATAA
*
41485461 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
41485491 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
41485521 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
41485551 AAATTTCATTTT
1 AAATTTCATTTT
41485563 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:41485844 original size:10 final size:10
Alignment explanation
Indices: 41485825--41485874 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
41485815 TTTTTCGAAG
*
41485825 GAAAAAAGAA
1 GAAAAGAGAA
41485835 GAAAAGAGAA
1 GAAAAGAGAA
41485845 GAAAAGAGAA
1 GAAAAGAGAA
* *
41485855 -AGAGGAGAA
1 GAAAAGAGAA
41485864 GAAAAGA-AA
1 GAAAAGAGAA
41485873 GA
1 GA
41485875 GTACCGGGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:41485875 original size:17 final size:19
Alignment explanation
Indices: 41485828--41485870 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
41485818 TTCGAAGGAA
41485828 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
41485846 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
41485865 AAAAGA
1 AAAAGA
41485871 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:41485945 original size:3 final size:3
Alignment explanation
Indices: 41485939--41485973 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
41485929 GTGTAGGAGG
41485939 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
41485974 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41486156 original size:15 final size:14
Alignment explanation
Indices: 41486108--41486176 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
41486098 CAACACAAAA
41486108 AAAAACAAATCAGCCC
1 AAAAA-AAA-CAGCCC
***
41486124 AAAAAAAACCAAAGC
1 AAAAAAAA-CAGCCC
41486139 AAAAAAAAGCAGCCC
1 AAAAAAAA-CAGCCC
41486154 AAAAAGAAA-AGGCCC
1 AAAAA-AAACA-GCCC
41486169 AAAAAAAA
1 AAAAAAAA
41486177 AGAAAAAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 4 0.09
15 31 0.72
16 8 0.19
ACGTcount: A:0.67, C:0.22, G:0.10, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAGCCC
Found at i:41486178 original size:14 final size:15
Alignment explanation
Indices: 41486139--41486179 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
41486129 AAACCAAAGC
41486139 AAAAAAAAGCAGCCCA
1 AAAAAAAAG-AGCCCA
41486155 AAAAGAAAAG-GCCCA
1 AAAA-AAAAGAGCCCA
41486170 AAAAAAAAGA
1 AAAAAAAAGA
41486180 AAAAACAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGCCCA
Found at i:41486290 original size:7 final size:7
Alignment explanation
Indices: 41486267--41486355 Score: 97
Period size: 7 Copynumber: 11.9 Consensus size: 7
41486257 CAGGCCAGGA
41486267 AAAAAAG
1 AAAAAAG
*
41486274 AGAGAAAG
1 A-AAAAAG
41486282 AAAAAAG
1 AAAAAAG
41486289 AAAAAAG
1 AAAAAAG
*
41486296 AAAGAAG
1 AAAAAAG
41486303 AAAAAAAG
1 -AAAAAAG
*
41486311 AAAAGAG
1 AAAAAAG
41486318 AAAAAAGG
1 AAAAAA-G
41486326 AAAAAAGG
1 AAAAAA-G
41486334 AAAAAGAAG
1 -AAAA-AAG
41486343 AAAAAAG
1 AAAAAAG
41486350 AAAAAA
1 AAAAAA
41486356 AAAGAGTTTC
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
7 39 0.55
8 25 0.35
9 5 0.07
10 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:41486295 original size:22 final size:21
Alignment explanation
Indices: 41486289--41486361 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 21
41486279 AAGAAAAAAG
*
41486289 AAAAAAGAAAG-AAGAAAAAA
1 AAAAAAGAGAGAAAGAAAAAA
* *
41486309 AGAAAAGAGAAAAAAGGAAAAAA
1 AAAAAAGAG-AGAAA-GAAAAAA
*
41486332 GGAAAAAGA-AGAAA-AAAGAAA
1 -AAAAAAGAGAGAAAGAAA-AAA
41486353 AAAAAAGAG
1 AAAAAAGAG
41486362 TTTCAATTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
20 17 0.43
21 4 0.10
22 6 0.15
23 7 0.17
24 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAAGAGAGAAAGAAAAAA
Found at i:41486341 original size:44 final size:42
Alignment explanation
Indices: 41486266--41486361 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 42
41486256 GCAGGCCAGG
* *
41486266 AAAAAAAGAGAGAAAGAAAAAAGAAAAAAGAAAGAAGAAA-AA
1 AAAAAAAGAGAAAAAGAAAAAAGAAAAAAG-AAGAAAAAAGAA
* *
41486308 AAGAAAAGAGAAAAAAGGAAAAAAGGAAAAAGAAGAAAAAAGAA
1 AAAAAAAGAG-AAAAA-GAAAAAAGAAAAAAGAAGAAAAAAGAA
41486352 AAAAAAAGAG
1 AAAAAAAGAG
41486362 TTTCAATTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 9 0.20
43 12 0.26
44 25 0.54
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (42 bp):
AAAAAAAGAGAAAAAGAAAAAAGAAAAAAGAAGAAAAAAGAA
Found at i:41486941 original size:20 final size:22
Alignment explanation
Indices: 41486900--41486942 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41486890 AATTTTGTGT
*
41486900 AAAAAAATCCAGTGTTTTCAAA
1 AAAAAAATCCAGTGTTTCCAAA
41486922 AAAAAAATCCA-T-TTTCCAAA
1 AAAAAAATCCAGTGTTTCCAAA
41486942 A
1 A
41486943 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAAATCCAGTGTTTCCAAA
Found at i:41487012 original size:18 final size:17
Alignment explanation
Indices: 41486938--41487100 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
41486928 ATCCATTTTC
* *
41486938 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
41486956 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
41486974 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
41486990 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
41487007 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
41487025 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
41487042 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
41487060 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
41487077 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
41487095 CAAAAA
1 CAAAAA
41487101 AAAATCTCGT
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:41487100 original size:35 final size:34
Alignment explanation
Indices: 41486938--41487100 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
41486928 ATCCATTTTC
* * * *
41486938 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
41486974 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
41487007 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
41487042 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
41487077 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
41487101 AAAATCTCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:41491567 original size:19 final size:19
Alignment explanation
Indices: 41491545--41491716 Score: 90
Period size: 19 Copynumber: 9.1 Consensus size: 19
41491535 TAAACTTATT
41491545 AAATTATAAAAAATATAAA
1 AAATTATAAAAAATATAAA
*
41491564 AAATTAT-AAAAGTAATAAA
1 AAATTATAAAAAAT-ATAAA
* ** **
41491583 AACTTATTTAAAATATTTA
1 AAATTATAAAAAATATAAA
*
41491602 AAATTA-AATAAAAGTAT-TA
1 AAATTATAA-AAAA-TATAAA
*
41491621 GAATTATTAAAAAA-ATAAA
1 AAATTA-TAAAAAATATAAA
* *
41491640 AAATTGTAAAAACTATAAA
1 AAATTATAAAAAATATAAA
* * *
41491659 ATA-TATTAAAAATAT-TA
1 AAATTATAAAAAATATAAA
* *
41491676 AAATTGAT-ATAAATTTATAA
1 AAATT-ATAAAAAATATA-AA
41491696 AAATT-TAAAAAATCATAAA
1 AAATTATAAAAAAT-ATAAA
41491715 AA
1 AA
41491717 CTTGAACCAG
Statistics
Matches: 114, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
17 3 0.03
18 30 0.26
19 60 0.53
20 19 0.17
21 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAAATATAAA
Found at i:41491596 original size:38 final size:36
Alignment explanation
Indices: 41491545--41491716 Score: 125
Period size: 38 Copynumber: 4.6 Consensus size: 36
41491535 TAAACTTATT
*
41491545 AAATTATAAAAAATATAAAAAATTATAAAAGTAATAA
1 AAATTATTAAAAATATAAAAAATTATAAAAGT-ATAA
* ** *
41491582 AAACTTATTTAAAATATTTAAAATTAAATAAAAGTATTA
1 AAA-TTATTAAAAATATAAAAAATT--ATAAAAGTATAA
* * * *
41491621 GAATTATTAAAAAAATAAAAAATTGTAAAAACTAT-A
1 AAATTATTAAAAATATAAAAAATTAT-AAAAGTATAA
* *
41491657 AAATATATTAAAAATAT-TAAAATTGATATAAATTTATAA
1 AAAT-TATTAAAAATATAAAAAATT-ATA-AAA-GTATAA
*
41491696 AAATT-TAAAAAATCATAAAAA
1 AAATTATTAAAAAT-ATAAAAA
41491717 CTTGAACCAG
Statistics
Matches: 105, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
36 12 0.11
37 32 0.30
38 40 0.38
39 13 0.12
40 8 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (36 bp):
AAATTATTAAAAATATAAAAAATTATAAAAGTATAA
Found at i:41491678 original size:8 final size:9
Alignment explanation
Indices: 41491453--41491678 Score: 76
Period size: 9 Copynumber: 24.6 Consensus size: 9
41491443 TATTTTCTCA
41491453 TAAAAATGAT
1 TAAAAAT-AT
41491463 TACAAAA-A-
1 TA-AAAATAT
41491471 TAAAAA-AT
1 TAAAAATAT
*
41491479 TATAAAATCT
1 TA-AAAATAT
*
41491489 GAAACAATAT
1 TAAA-AATAT
*
41491499 TAGAAATAT
1 TAAAAATAT
*
41491508 TAAAAA-CT
1 TAAAAATAT
*
41491516 TAAAAA-AA
1 TAAAAATAT
*
41491524 TAAAATTGAT
1 TAAAAAT-AT
**
41491534 ATAAACTTAT
1 -TAAAAATAT
*
41491544 T-AAATTAT
1 TAAAAATAT
*
41491552 AAAAAATA-
1 TAAAAATAT
41491560 TAAAAA-AT
1 TAAAAATAT
*
41491568 TATAAAAGTAA
1 TA-AAAA-TAT
41491579 TAAAAACTTAT
1 TAAAAA--TAT
*
41491590 TTAAAATATT
1 TAAAAATA-T
* *
41491600 TAAAATTAAA
1 TAAAAAT-AT
*
41491610 TAAAAGTAT
1 TAAAAATAT
* *
41491619 TAGAATTAT
1 TAAAAATAT
*
41491628 TAAAAAAAT
1 TAAAAATAT
*
41491637 AAAAAAT-T
1 TAAAAATAT
41491645 GTAAAAACTA-
1 -TAAAAA-TAT
41491655 TAAAATATAT
1 TAAAA-ATAT
41491665 TAAAAATAT
1 TAAAAATAT
41491674 TAAAA
1 TAAAA
41491679 TTGATATAAA
Statistics
Matches: 162, Mismatches: 33, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.04
8 30 0.19
9 69 0.43
10 36 0.22
11 21 0.13
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:41491706 original size:28 final size:27
Alignment explanation
Indices: 41491638--41491715 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
41491628 TAAAAAAATA
41491638 AAAAATTGTAAAAACTATAAAATATATT
1 AAAAATT-TAAAAACTATAAAATATATT
* *
41491666 AAAAATATT-AAAATTGATATAAATTTA-T
1 AAAAAT-TTAAAAACT-ATA-AAATATATT
*
41491694 AAAAATTTAAAAAATCATAAAA
1 AAAAATTTAAAAACT-ATAAAA
41491716 ACTTGAACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
27 10 0.24
28 25 0.60
29 7 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAAATTTAAAAACTATAAAATATATT
Found at i:41492121 original size:19 final size:18
Alignment explanation
Indices: 41492074--41492129 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
41492064 GTTTTATTAA
*
41492074 AAATAATTTTTCTAATTT
1 AAATAATTTTTATAATTT
* * *
41492092 AAATCAGTTTTAATACTTT
1 AAAT-AATTTTTATAATTT
41492111 AAATAATTTTTTATAATTT
1 AAATAA-TTTTTATAATTT
41492130 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATAATTTTTATAATTT
Found at i:41492241 original size:29 final size:28
Alignment explanation
Indices: 41492181--41492299 Score: 82
Period size: 28 Copynumber: 4.1 Consensus size: 28
41492171 TATAAATTTC
* * *
41492181 TTTTTATAA-TTTATTAGAATTTTTATAT
1 TTTTTATAATTTTAATA-AGTTTTTACAT
*
41492209 TTTTTATAGTATTTAA-AAGTTTTTACAT
1 TTTTTATAAT-TTTAATAAGTTTTTACAT
* *
41492237 GTTTTTATAATTTTAATAAGTTTATATCAA
1 -TTTTTATAATTTTAATAAGTTTTTA-CAT
* * *
41492267 TTTTAAT-ATTTTTATAATTTTTTAATCAT
1 TTTTTATAATTTTAATAAGTTTTT-A-CAT
41492296 TTTT
1 TTTT
41492300 AGGGGAAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
28 35 0.48
29 32 0.44
30 6 0.08
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTTTATAATTTTAATAAGTTTTTACAT
Found at i:41492250 original size:9 final size:9
Alignment explanation
Indices: 41492181--41492292 Score: 75
Period size: 9 Copynumber: 12.1 Consensus size: 9
41492171 TATAAATTTC
41492181 TTTTTATAA
1 TTTTTATAA
*
41492190 TTTATTAGAA
1 TTT-TTATAA
*
41492200 TTTTTATAT
1 TTTTTATAA
*
41492209 TTTTTATAG
1 TTTTTATAA
* *
41492218 TATTTAAAA
1 TTTTTATAA
* *
41492227 GTTTTTACATG
1 -TTTTTATA-A
41492238 TTTTTATAA
1 TTTTTATAA
*
41492247 TTTTAATAA
1 TTTTTATAA
*
41492256 GTTTATATCAA
1 -TTTTTAT-AA
*
41492267 TTTTAAT-A
1 TTTTTATAA
41492275 TTTTTATAA
1 TTTTTATAA
41492284 TTTTT-TAA
1 TTTTTATAA
41492292 T
1 T
41492293 CATTTTTAGG
Statistics
Matches: 79, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
8 11 0.14
9 35 0.44
10 31 0.39
11 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41501067 original size:5 final size:5
Alignment explanation
Indices: 41501057--41501084 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41501047 GGTTTTGTGA
41501057 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
41501085 GAACACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41505514 original size:5 final size:5
Alignment explanation
Indices: 41505504--41505536 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
41505494 CTATTTGTGA
41505504 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
41505537 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41506699 original size:51 final size:51
Alignment explanation
Indices: 41506630--41506728 Score: 198
Period size: 51 Copynumber: 1.9 Consensus size: 51
41506620 GGATTAAAGT
41506630 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
41506681 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA
1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA
41506729 CATTTGCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (51 bp):
CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
Found at i:41511283 original size:23 final size:24
Alignment explanation
Indices: 41511238--41511283 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
41511228 GTAATAAAAT
41511238 AATAATACATAAAAACAAGTTTAA
1 AATAATACATAAAAACAAGTTTAA
* *
41511262 AATAATATAT-AAAGCAAGTTTA
1 AATAATACATAAAAACAAGTTTA
41511284 GAGTAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (24 bp):
AATAATACATAAAAACAAGTTTAA
Found at i:41511478 original size:26 final size:25
Alignment explanation
Indices: 41511449--41511506 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
41511439 CTTTAAAGTA
** *
41511449 AATAATATATAAAAAGTTTTAACATG
1 AATAATATATAAAAA-ACTTAAAATG
*
41511475 AATAAAATATAAAAAACTTAAAATG
1 AATAATATATAAAAAACTTAAAATG
41511500 AATAATA
1 AATAATA
41511507 ACAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (25 bp):
AATAATATATAAAAAACTTAAAATG
Found at i:41511495 original size:25 final size:26
Alignment explanation
Indices: 41511405--41511504 Score: 69
Period size: 26 Copynumber: 3.8 Consensus size: 26
41511395 AAAATAATGT
* * *
41511405 AAAAG-CTTAAAATAAATAATATGTGGA
1 AAAAGACTTAAAATGAATAAAATAT--A
* * *
41511432 AAAAGAACTTTAAAGTAAATAATATATA
1 AAAAG-AC-TTAAAATGAATAAAATATA
** *
41511460 AAAAGTTTTAACATGAATAAAATATA
1 AAAAGACTTAAAATGAATAAAATATA
41511486 AAAA-ACTTAAAATGAATAA
1 AAAAGACTTAAAATGAATAA
41511505 TAACAATAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
25 12 0.20
26 19 0.32
27 5 0.08
28 6 0.10
29 1 0.02
30 16 0.27
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (26 bp):
AAAAGACTTAAAATGAATAAAATATA
Found at i:41512337 original size:24 final size:26
Alignment explanation
Indices: 41512310--41512376 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
41512300 AATCGATTTA
*
41512310 AAATACAAATAAGAAAAAA-GA-AAG
1 AAATACAAAAAAGAAAAAATGAGAAG
41512334 AAAT-CGAAAAAAGGAAAAAATGAGAAG
1 AAATAC-AAAAAA-GAAAAAATGAGAAG
*
41512361 AAA-ACAAAGAAGAAAA
1 AAATACAAAAAAGAAAA
41512377 TCGAAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 1 0.03
24 9 0.25
25 12 0.33
26 7 0.19
27 7 0.19
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (26 bp):
AAATACAAAAAAGAAAAAATGAGAAG
Found at i:41519504 original size:119 final size:120
Alignment explanation
Indices: 41519322--41519537 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 120
41519312 TCCTCGTTCA
*
41519322 AATGCCTTCGGGACATAGCCCGGTTATAGTAGCTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
41519387 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
41519442 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGGACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAGCTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
41519504 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
41519538 GCTCGGACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 59 0.71
120 20 0.24
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41519538 original size:40 final size:40
Alignment explanation
Indices: 41519320--41519544 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
41519310 GCTCCTCGTT
* * *
41519320 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41519360 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41519400 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
41519440 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
41519479 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
*
41519520 CAAA-GCCTTCGGGACTTAGCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41519545 CATCATTCAA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 117 0.73
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41521648 original size:17 final size:17
Alignment explanation
Indices: 41521626--41521659 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41521616 CAAGGGACAA
41521626 TTTCTACATACTTGGTC
1 TTTCTACATACTTGGTC
41521643 TTTCTACATACTTGGTC
1 TTTCTACATACTTGGTC
41521660 AACTAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTCTACATACTTGGTC
Found at i:41529989 original size:39 final size:40
Alignment explanation
Indices: 41529890--41530113 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
41529880 TTGAATGATG
* * * *
41529890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
41529930 TCCGGATTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
41529970 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGGTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41530009 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC-AAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
41530048 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41530089 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41530114 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 71 0.45
40 76 0.48
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41530026 original size:79 final size:79
Alignment explanation
Indices: 41529890--41530113 Score: 258
Period size: 79 Copynumber: 2.8 Consensus size: 79
41529880 TTGAATGATG
* * * * *
41529890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGATTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGT-ACTAAATCCGGGTTAAG-TCCCGAAGGCAT
*
41529953 TTGTGCGAGATACTAAT
64 TTGTGCGAGATAC-AAA
* *
41529970 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
*
41530034 GTGCGAGTTACAAA
66 GTGCGAGATACAAA
* * * * *
41530048 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
41530112 TG
65 TG
41530114 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
78 12 0.10
79 91 0.73
80 21 0.17
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
GTGCGAGATACAAA
Found at i:41530144 original size:79 final size:79
Alignment explanation
Indices: 41529981--41530146 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
41529971 CTGGGCTAAG
* ** *
41529981 CCCGAAGGCATTGGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACA
1 CCCGAAGGCATTGGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACA
*
41530046 AATCCGGGTTAAGT
66 AATCCGGGTTAAAT
* * * *
41530060 CCCGAAGGCATTTGTGTGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCCGAAGGCATTGGTGCGAGGTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-
*
41530123 CTATATCC-GGTTAAAT
64 C-AAATCCGGGTTAAAT
*
41530139 TCCGAAGG
1 CCCGAAGG
41530147 TACGTGATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 65 0.89
80 7 0.10
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (79 bp):
CCCGAAGGCATTGGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACA
AATCCGGGTTAAAT
Found at i:41537898 original size:76 final size:78
Alignment explanation
Indices: 41537779--41537998 Score: 245
Period size: 76 Copynumber: 2.8 Consensus size: 78
41537769 TTGAATGATG
* * * *
41537779 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC-GGATAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGATAAG-TCCCG-AGGCAT
* *
41537841 TTGTGCGAGATACTAT
63 TTGTGCGAGATACAAA
* *
41537857 TCC-GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGATAAGTCCCGAGGCATTTG
*
41537920 TGCGAGTTACAAA
66 TGCGAGATACAAA
* * *
41537933 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGATAAGTCCCG-AGGCATT
41537997 TG
64 TG
41537999 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
76 42 0.34
77 28 0.23
78 41 0.34
79 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGATAAGTCCCGAGGCATTTG
TGCGAGATACAAA
Found at i:41537923 original size:39 final size:40
Alignment explanation
Indices: 41537779--41537998 Score: 251
Period size: 39 Copynumber: 5.7 Consensus size: 40
41537769 TTGAATGATG
* * * *
41537779 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41537819 TCC-GGATAAGAT-CCGAAGGCATTTGTGCGAGATACT-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41537857 TCC-GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41537895 TCCGGGTTAAGTCCCG-AGGCATTTGTGCGAGTTAC-AAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41537933 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41537974 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41537999 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 15, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
37 22 0.14
38 32 0.21
39 61 0.39
40 39 0.25
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41543932 original size:22 final size:22
Alignment explanation
Indices: 41543907--41543948 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
41543897 ATACAATGAT
41543907 TAATAGAAAATTTTAACTAAAC
1 TAATAGAAAATTTTAACTAAAC
41543929 TAATAGAAAATTTTAACTAA
1 TAATAGAAAATTTTAACTAA
41543949 GTTATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
TAATAGAAAATTTTAACTAAAC
Found at i:41545962 original size:32 final size:31
Alignment explanation
Indices: 41545926--41545990 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
41545916 AATAAGGTTT
* **
41545926 ATAATTTTTTATTTTTATTTTTTATATTTTAA
1 ATAATTTTTTATTATTATTTAATAT-TTTTAA
41545958 ATAATTTTTTATTATTATTTAATATTTTTAA
1 ATAATTTTTTATTATTATTTAATATTTTTAA
41545989 AT
1 AT
41545991 TTAAGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
ATAATTTTTTATTATTATTTAATATTTTTAA
Found at i:41545973 original size:20 final size:19
Alignment explanation
Indices: 41545941--41545986 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
41545931 TTTTTATTTT
41545941 TATTTTTTATATT-TTAAA
1 TATTTTTTATATTATTAAA
*
41545959 TAATTTTTTATTATTATTTAA
1 T-ATTTTTTA-TATTATTAAA
41545980 TATTTTT
1 TATTTTT
41545987 AAATTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 8 0.33
20 10 0.42
21 5 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTTATATTATTAAA
Found at i:41547740 original size:7 final size:7
Alignment explanation
Indices: 41547726--41547866 Score: 117
Period size: 7 Copynumber: 20.6 Consensus size: 7
41547716 CTTAATCCTA
41547726 AATTCTC
1 AATTCTC
*
41547733 AATCCTC
1 AATTCTC
*
41547740 AATTTTC
1 AATTCTC
41547747 -ATTCTC
1 AATTCTC
41547753 AATTCTC
1 AATTCTC
*
41547760 ATTTCTC
1 AATTCTC
* *
41547767 -ATCCTT
1 AATTCTC
* *
41547773 AATCCTA
1 AATTCTC
41547780 AATTCTC
1 AATTCTC
*
41547787 -ATCCTC
1 AATTCTC
*
41547793 AATTTTC
1 AATTCTC
*
41547800 ATTTCTC
1 AATTCTC
41547807 AATTCTC
1 AATTCTC
*
41547814 ATTTCTC
1 AATTCTC
* *
41547821 GATCCTC
1 AATTCTC
*
41547828 AATCCTC
1 AATTCTC
*
41547835 AATCCTC
1 AATTCTC
*
41547842 AATTCTT
1 AATTCTC
41547849 AATTCTC
1 AATTCTC
41547856 AATTCTC
1 AATTCTC
41547863 AATT
1 AATT
41547867 AATTTTTTAA
Statistics
Matches: 106, Mismatches: 25, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
6 13 0.12
7 93 0.88
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.44
Consensus pattern (7 bp):
AATTCTC
Found at i:41547768 original size:54 final size:54
Alignment explanation
Indices: 41547710--41547866 Score: 226
Period size: 54 Copynumber: 2.9 Consensus size: 54
41547700 ATACCCAATA
41547710 CTCATCCTTAATCCTAAATTCTCAATCCTCAATTTTCATTCTCAATTCTCATTT
1 CTCATCCTTAATCCTAAATTCTCAATCCTCAATTTTCATTCTCAATTCTCATTT
41547764 CTCATCCTTAATCCTAAATTCTC-ATCCTCAATTTTCATTTCTCAATTCTCATTT
1 CTCATCCTTAATCCTAAATTCTCAATCCTCAATTTTCA-TTCTCAATTCTCATTT
* * * * * *
41547818 CTCGATCCTCAATCCTCAATCCTCAATTCTTAATTCTCAATTCTCAATT
1 CTC-ATCCTTAATCCTAAATTCTCAATCCTCAATTTTC-ATTCTCAATT
41547867 AATTTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
53 14 0.15
54 42 0.45
55 17 0.18
56 19 0.20
57 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (54 bp):
CTCATCCTTAATCCTAAATTCTCAATCCTCAATTTTCATTCTCAATTCTCATTT
Found at i:41547788 original size:27 final size:27
Alignment explanation
Indices: 41547710--41547793 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
41547700 ATACCCAATA
*
41547710 CTCATCCTTAATCCTAAATTCTCAATC
1 CTCATCCTTAATCCTAAATTCTCATTC
* * * * *
41547737 CTCAAT-TTTCATTCTCAATTCTCATTT
1 CTC-ATCCTTAATCCTAAATTCTCATTC
41547764 CTCATCCTTAATCCTAAATTCTCA-TC
1 CTCATCCTTAATCCTAAATTCTCATTC
41547790 CTCA
1 CTCA
41547794 ATTTTCATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
26 7 0.16
27 35 0.80
28 2 0.05
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (27 bp):
CTCATCCTTAATCCTAAATTCTCATTC
Found at i:41547828 original size:21 final size:21
Alignment explanation
Indices: 41547726--41547866 Score: 108
Period size: 20 Copynumber: 6.9 Consensus size: 21
41547716 CTTAATCCTA
*
41547726 AATTCTCAATCCTCAATTTTC
1 AATTCTCAATCCTCAATTCTC
* *
41547747 -ATTCTCAATTCTCATTTCTC
1 AATTCTCAATCCTCAATTCTC
* * *
41547767 -ATCCTTAATCCTAAATTCTC
1 AATTCTCAATCCTCAATTCTC
* ** *
41547787 -ATCCTCAATTTTCATTTCTC
1 AATTCTCAATCCTCAATTCTC
* * * *
41547807 AATTCTCATTTCTCGATCCTC
1 AATTCTCAATCCTCAATTCTC
* *
41547828 AATCCTCAATCCTCAATTCTT
1 AATTCTCAATCCTCAATTCTC
*
41547849 AATTCTCAATTCTCAATT
1 AATTCTCAATCCTCAATT
41547867 AATTTTTTAA
Statistics
Matches: 92, Mismatches: 27, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 47 0.51
21 45 0.49
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.44
Consensus pattern (21 bp):
AATTCTCAATCCTCAATTCTC
Found at i:41558676 original size:46 final size:46
Alignment explanation
Indices: 41558540--41558809 Score: 182
Period size: 46 Copynumber: 5.7 Consensus size: 46
41558530 CGAAATCGAG
* * * *
41558540 GCCGATGTCATGTCCCATATATGGTCATACACTAGCTCTCACATATCTGT-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-T-ACATCTC-GTA
41558590 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GAC--ACATCTCGTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTACATCTCGTA
*
41558636 GCCGATGCATGTCCCAGACAT-ACTTTACACTAGCTTACATCTCG-A
1 GCCGATGCATGTCCCAGACATGTC-TTACACTAGCTTACATCTCGTA
* *
41558681 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTC-AA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCT-TACATCTCGTA
* * * * * *
41558727 TGCCGATGCCATGTACCAGACACGGTCTTACACTGGCTCT-CATAAT-ATG
1 -GCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCT-TACAT-CTCGTA
** *
41558776 GCCGACACATGTCCCAAACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
41558810 ACACAAGTAA
Statistics
Matches: 184, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 8 0.04
45 18 0.10
46 78 0.42
47 25 0.14
48 22 0.12
49 2 0.01
50 30 0.16
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGTA
Found at i:41558759 original size:94 final size:92
Alignment explanation
Indices: 41558567--41558814 Score: 229
Period size: 94 Copynumber: 2.7 Consensus size: 92
41558557 TATATGGTCA
* *
41558567 TACACTAGCTCTCACATATCTGTGCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACAT
1 TACACTAGCTCTCATA-ATATG-GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACACAT
* * *
41558630 CTCGTAGCCGATGCATGTCCCAGACATACTT
62 CTCATAGCCGATGCATGTACCAGACACACTT
* * * *
41558661 TACACTAGCT-TACAT-CTCGA-GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTC
1 TACACTAGCTCT-CATAAT--ATGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATC
**
41558723 TCA-ATGCCGATGCCATGTACCAGACACGGTCT
63 TCATA-GCCGATG-CATGTACCAGACACACT-T
* ** *
41558755 TACACTGGCTCTCATAATATGGCCGACACATGTCCCAAACATGTCTTACACTAGCACACA
1 TACACTAGCTCTCATAATATGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACACA
41558815 AGTAACCCAA
Statistics
Matches: 124, Mismatches: 19, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
90 10 0.08
91 16 0.13
92 21 0.17
93 16 0.13
94 59 0.48
95 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (92 bp):
TACACTAGCTCTCATAATATGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCA
TAGCCGATGCATGTACCAGACACACTT
Found at i:41558805 original size:140 final size:141
Alignment explanation
Indices: 41558535--41558809 Score: 317
Period size: 140 Copynumber: 2.0 Consensus size: 141
41558525 ACTATCGAAA
* * **
41558535 TCGAGGCCGATGTCATGTCCCATATATGGTCATACACTAGCTCTCACATATCTGTGCCGATGCCA
1 TCGAGGCCGATGTCATGTCCCAGACATGGTCATACACTAGCTCT-ACATATCAATGCCGATGCCA
* * ** ** *
41558600 TGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGCATGTCCCAGACATACTTTACA
65 TGTACCAGACACGGTCTTACACTGACACATCTAATAGCCGACACATGTCCCAAACATACTTTACA
41558665 CTAGCTTACATC
130 CTAGCTTACATC
* * *
41558677 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCAT
1 TCGAGGCCGATGTCATGTCCCAGACATGGTCATACACTAGCTCTACATATCAATGCCGATGCCAT
* * *
41558739 GTACCAGACACGGTCTTACACTGGCTC-TCATAATATGGCCGACACATGTCCCAAACAT-GTCTT
66 GTACCAGACACGGTCTTACACTGACACATC-TAATA--GCCGACACATGTCCCAAACATACT-TT
41558802 ACACTAGC
127 ACACTAGC
41558810 ACACAAGTAA
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
137 2 0.02
138 42 0.38
139 1 0.01
140 43 0.38
141 12 0.11
142 12 0.11
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (141 bp):
TCGAGGCCGATGTCATGTCCCAGACATGGTCATACACTAGCTCTACATATCAATGCCGATGCCAT
GTACCAGACACGGTCTTACACTGACACATCTAATAGCCGACACATGTCCCAAACATACTTTACAC
TAGCTTACATC
Found at i:41562322 original size:15 final size:16
Alignment explanation
Indices: 41562304--41562333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41562294 AATTGTTATA
41562304 TTACA-AATTTCACTC
1 TTACATAATTTCACTC
41562319 TTACATAATTTCACT
1 TTACATAATTTCACT
41562334 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (16 bp):
TTACATAATTTCACTC
Found at i:41577529 original size:27 final size:27
Alignment explanation
Indices: 41577499--41577676 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
41577489 ATATTGAGCC
* *
41577499 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
41577526 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41577553 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** ** *
41577581 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41577608 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
41577635 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41577662 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
41577677 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41577638 original size:82 final size:81
Alignment explanation
Indices: 41577520--41577675 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
41577510 TGCTATATAA
* * *
41577520 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
*
41577585 CTCTTAGTGCCGCATGG
65 CCCTTAGTGCCGCATGG
* * **
41577602 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41577666 CCCTTAGTGC
65 CCCTTAGTGC
41577676 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
CCTTAGTGCCGCATGG
Found at i:41582138 original size:40 final size:40
Alignment explanation
Indices: 41582094--41582318 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
41582084 GCTCCTCGTT
* * * *
41582094 CAAATGCCTTTGGGCCATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
41582134 CAAATGCCTTCGGGACTTAACCCGGATTTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41582174 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
41582214 CCAATGCCTTCGGG-CTTAGCCCGGAATCAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
41582253 CAAATGCCTTC-GGATCTTAATCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41582294 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41582319 CATCATTCAA
Statistics
Matches: 157, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.20
40 111 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41582272 original size:119 final size:120
Alignment explanation
Indices: 41582096--41582318 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
41582086 TCCTCGTTCA
* *
41582096 AATGCCTTTGGGCCATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGCCATAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
41582161 TTTGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATGGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
41582216 AATGCCTTCGGG-CTTAGCCCGG-AATCAGTATCTCGCACAAATGCCTTC-GGATCTTAATCCGG
1 AATGCCTTCGGGCCATAGCCCGGTAAT-AGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
41582278 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
41582319 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 5 0.06
119 66 0.73
120 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGCCATAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41590157 original size:39 final size:40
Alignment explanation
Indices: 41590000--41590217 Score: 273
Period size: 40 Copynumber: 5.5 Consensus size: 40
41589990 GCTCCTCGTT
* *
41590000 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
41590040 CAAATGCCTTCGGGACTTAACCCGGATTTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41590080 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
41590120 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
41590159 CAAATGCCTTC-GGATCTTAATCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
41590200 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
41590218 GCCGGACATC
Statistics
Matches: 156, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.21
40 109 0.70
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41590178 original size:119 final size:120
Alignment explanation
Indices: 41590002--41590217 Score: 305
Period size: 119 Copynumber: 1.8 Consensus size: 120
41589992 TCCTCGTTCA
*
41590002 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
41590067 TTTGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATGGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
41590122 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAATCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
*
41590184 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATGGTAACTTAGCACAAAGCCTTCGGGACTTA
41590218 GCCGGACATC
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 4 0.05
119 61 0.72
120 20 0.24
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41590223 original size:79 final size:78
Alignment explanation
Indices: 41590000--41590223 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 78
41589990 GCTCCTCGTT
* * * * *
41590000 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA-GCCTTCGGGACTT-AGCCGG
* *
41590065 ATTTTGTAACTCGCA
64 AATTAGTAACTCGCA
* * *
41590080 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAG-CCGG
*
41590144 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * *
41590159 CAAATGCCTTC-GGATCTTAATCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCGG
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCGG
41590223 A
64 A
41590224 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.03
79 63 0.51
80 54 0.44
81 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCGGAA
TTAGTAACTCGCA
Found at i:41594466 original size:47 final size:47
Alignment explanation
Indices: 41594306--41594475 Score: 181
Period size: 45 Copynumber: 3.7 Consensus size: 47
41594296 GCTACCAGTA
* *
41594306 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGG-TG-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGGATGCTT-GCAT
* * * *
41594352 CC-TAAGTGAACTCGGACTCAACTC-ACGAG-CTCGGATGCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGGATGCTTGCAT
* *** *
41594395 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGGACGCTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTTGGGATGCTTGCAT
41594443 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
41594476 CGGATGGCCC
Statistics
Matches: 99, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
43 4 0.04
44 10 0.10
45 40 0.40
46 7 0.07
47 33 0.33
48 5 0.05
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGGATGCTTGCAT
Found at i:41594826 original size:27 final size:27
Alignment explanation
Indices: 41594768--41594832 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
41594758 TATTTTGGAA
* **
41594768 AAATTACAATTTTGCCCCTAAACTTTT
1 AAATTACACTTTTGCCCCTAAACTCGT
*
41594795 GAATTACACTTTTG-CCCTAAAGCTCGT
1 AAATTACACTTTTGCCCCTAAA-CTCGT
*
41594822 AAATTAAACTT
1 AAATTACACTT
41594833 CAGCCTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
AAATTACACTTTTGCCCCTAAACTCGT
Found at i:41611205 original size:38 final size:39
Alignment explanation
Indices: 41611162--41611244 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
41611152 CTCTTCATGC
41611162 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
41611201 -CTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
41611239 ACTATA
1 ACTATA
41611245 TGACCGTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 38 0.88
39 5 0.12
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (39 bp):
ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
Found at i:41612787 original size:14 final size:15
Alignment explanation
Indices: 41612750--41612794 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
41612740 AAGCTTCTAA
41612750 AGTGCTAAATACCCT
1 AGTGCTAAATACCCT
*
41612765 AGTGCTAAATTCCCT
1 AGTGCTAAATACCCT
41612780 AG-GCTAAATACCCT
1 AGTGCTAAATACCCT
41612794 A
1 A
41612795 AACCCTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
AGTGCTAAATACCCT
Found at i:41615560 original size:15 final size:15
Alignment explanation
Indices: 41615540--41615570 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41615530 TTCACTATTA
*
41615540 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
41615555 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
41615570 T
1 T
41615571 CATTAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:41617493 original size:44 final size:42
Alignment explanation
Indices: 41617356--41617515 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 42
41617346 AGCTCGTACA
* * * * * *
41617356 ATGCAAACGTCCTAGACGTGGTCTTACATGTAATTAAATATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGAAATCAAATA-CG
* *
41617399 ATGCC-ACTGTCCCAAACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAAC-GTCCCAGA-TGTGGTCTTACACGAAATCAAATACG
*
41617441 ATGCCAACGTCCTAGATGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAACGTCCCAGATGTGGTCTTACACG-AAATCA-AA-TACG
41617485 ATGCCAACGTCCCAGATGTGGTCTTACACGA
1 ATGCCAACGTCCCAGATGTGGTCTTACACGA
41617516 TAACACATAT
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 37 0.37
44 34 0.34
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGAAATCAAATACG
Found at i:41617510 original size:86 final size:85
Alignment explanation
Indices: 41617356--41617515 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 85
41617346 AGCTCGTACA
* *
41617356 ATGCAAACGTCCTAGACGTGGTCTTACATGTAATTAAATATCGATGCCACTGTCCCAAACAGGGT
1 ATGCAAACGTCCTAGACGTGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAACAGGGT
41617421 CTTACACGAAATCAAATACG
66 CTTACACGAAATCAAATACG
* * * * *
41617441 ATGCCAACGTCCTAGATGTGGTCTTACACGTAAATCATAA-GTCGATGCCAAC-GTCCCAGA-TG
1 ATGCAAACGTCCTAGACGTGGTCTTACACGT-AATCA-AATATCGATGCC-ACTGTCCCAAACAG
41617503 TGGTCTTACACGA
63 -GGTCTTACACGA
41617516 TAACACATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
85 29 0.45
86 31 0.48
87 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (85 bp):
ATGCAAACGTCCTAGACGTGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAACAGGGT
CTTACACGAAATCAAATACG
Found at i:41623828 original size:40 final size:40
Alignment explanation
Indices: 41623747--41623967 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
41623737 AAACCAAGTA
** * *
41623747 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
41623786 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
41623826 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACTATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41623866 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41623906 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
41623946 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
41623968 CAATCGAATA
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 26 0.15
40 142 0.85
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:41633546 original size:27 final size:27
Alignment explanation
Indices: 41633516--41633818 Score: 362
Period size: 27 Copynumber: 11.2 Consensus size: 27
41633506 TGATTTACAA
* *
41633516 AATTATTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
41633543 AATTACCGAAGTACCCCTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
41633570 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
41633597 AATTATTGAAATACCCCTATATGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
41633624 AATTACTAAAATACCCCTGTAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
41633651 AATTA-TCGAAATATCCCTGTAAGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
41633678 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
41633705 AATTA-TCGAGATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
41633732 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
41633759 AATTACCGAAATA-CCCTCGTAGGGTAGG
1 AATTACTGAAATACCCCT-GTAGGGTA-G
**
41633787 AA-TACTGAAATACCCCTGTAGTATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
41633813 AATTAC
1 AATTAC
41633819 CGAGAAACCC
Statistics
Matches: 233, Mismatches: 35, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.03
27 217 0.93
28 8 0.03
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:41634257 original size:6 final size:6
Alignment explanation
Indices: 41634248--41634398 Score: 96
Period size: 6 Copynumber: 24.3 Consensus size: 6
41634238 TTGCATTCAC
* *
41634248 ATTCTG ATTCTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTC-TG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
41634298 -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCCG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * *
41634348 ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTA ATTCTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
41634397 AT
1 AT
41634399 AATGTTTCTT
Statistics
Matches: 112, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
5 8 0.07
6 82 0.73
7 18 0.16
8 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:41634281 original size:19 final size:19
Alignment explanation
Indices: 41634259--41634316 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
41634249 TTCTGATTCT
41634259 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
41634278 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
41634290 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
41634309 TGATTCTG
1 TGATTCTG
41634317 ATTTTGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:41634296 original size:31 final size:31
Alignment explanation
Indices: 41634248--41634389 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
41634238 TTGCATTCAC
41634248 ATTCTGATTCTTGATTCTGTTACCTGATACTG
1 ATTCTGATT-TTGATTCTGTTACCTGATACTG
41634280 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
41634311 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * * *
41634342 ATTCCGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* *
41634373 ATTCTAATTCTGATTCT
1 ATTCTGATTTTGATTCT
41634390 AGTTCTGATA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 94 0.91
32 9 0.09
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:41637139 original size:79 final size:80
Alignment explanation
Indices: 41637040--41637207 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
41637030 CTCGTTCAAG
* * ** * *
41637040 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCTTAC-AATGCCTTCGGGACTTAACCCAGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCGCACAAAGGCCTTCGGGACTTAACCCAGA-A
*
41637103 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
41637119 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCGCACAAAGGCCTTCGGGACTTAACCCAGAATT
41637184 AATAACTCGCACAAA
66 AATAACTCGCACAAA
41637199 TGCCTTCGG
1 TGCCTTCGG
41637208 ATCTTAGTCC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 33 0.43
80 43 0.57
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCGCACAAAGGCCTTCGGGACTTAACCCAGAATT
AATAACTCGCACAAA
Found at i:41637191 original size:80 final size:80
Alignment explanation
Indices: 41637075--41637260 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
41637065 AGTAACTCTT
* * * *
41637075 ACAATGCCTTCGGGACTTAACCCAGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
41637139 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
41637154 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
41637218 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
41637235 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
41637261 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 11 0.12
80 71 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:41637220 original size:40 final size:40
Alignment explanation
Indices: 41637077--41637260 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
41637067 TAACTCTTAC
* * *
41637077 AATGCCTTCGGGACTTAACCCAGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
41637117 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
41637157 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
41637197 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
41637238 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41637261 CAGCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
39 8 0.07
40 104 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:41640200 original size:47 final size:48
Alignment explanation
Indices: 41639996--41640354 Score: 253
Period size: 47 Copynumber: 7.6 Consensus size: 48
41639986 GTTTCAATGC
* *
41639996 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATAGAGGCGGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * * * *
41640044 CCATGTCCCAGACATGGTTTTACACTAGC--TCTT-ATATGTACATGCTGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTATCTTCAT-CG---AGGCCGATG
* * * *
41640094 CATGTCCCAAACAT-GTCTTACACTAGC-A-CTACCCTC-A-GCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTATCT-TCATCGAGGCCGATG
*
41640138 CATGTCCCAAACAT-GTCTTACACTGGCTATCTTCATCGAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * ** * * *
41640185 CATGTCCCAGACAT-GTTTTATACTGGCGCTCATC-TCTATGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * * *
41640231 CCATGTCCCAGACATGGTCTTACACTGGCTAT-TATAAT-GTGGCTGATA
1 -CATGTCCCAGACATGGTCTTACACTGGCTATCT-TCATCGAGGCCGATG
* ** * * **
41640279 CATGTCCCAGACAT-GTCTTACACTAGCCCTCGTC-TCAATACCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATG
*
41640325 CCATGTCCCAAACATGGTCTTACACTGGCT
1 -CATGTCCCAGACATGGTCTTACACTGGCT
41640355 CTCACATAAC
Statistics
Matches: 244, Mismatches: 47, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
44 32 0.13
45 6 0.02
46 33 0.14
47 81 0.33
48 44 0.18
49 40 0.16
50 8 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATG
Found at i:41640283 original size:94 final size:93
Alignment explanation
Indices: 41639996--41640354 Score: 345
Period size: 94 Copynumber: 3.8 Consensus size: 93
41639986 GTTTCAATGC
* * ** * * *
41639996 CATGTCCCAGACATGGTCTTACACTGGCTA-TCTTCATAGAGGCGGATGCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TCTATGCCGATGCCATGTCCCAAACATG
* * * *
41640060 GTTTTACACTAGCTCTTATATGTACATGCTGATG
63 GTCTTACACTGGCTATTATATGT---GGCTGATG
* *
41640094 CATGTCCCAAACATGTCTTACACTAGCACT-A-CCCTCA-GCCGATG-CATGTCCCAAACAT-GT
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCT-ATGCCGATGCCATGTCCCAAACATGGT
* *
41640154 CTTACACTGGCTATCT-TCATCGAGGCCGATG
65 CTTACACTGGCTAT-TAT-AT-GTGGCTGATG
* * * * *
41640185 CATGTCCCAGACATGTTTTATACTGGCGCTCATCTCTATGCCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
*
41640250 TTACACTGGCTATTATAATGTGGCTGATA
66 TTACACTGGCTATTAT-ATGTGGCTGATG
* * * *
41640279 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATACCGATGCCATGTCCCAAACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
41640344 TTACACTGGCT
66 TTACACTGGCT
41640355 CTCACATAAC
Statistics
Matches: 217, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
91 31 0.14
92 16 0.07
93 26 0.12
94 96 0.44
95 21 0.10
96 1 0.00
97 13 0.06
98 13 0.06
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
TTACACTGGCTATTATATGTGGCTGATG
Found at i:41640283 original size:141 final size:140
Alignment explanation
Indices: 41639996--41640350 Score: 362
Period size: 141 Copynumber: 2.5 Consensus size: 140
41639986 GTTTCAATGC
*
41639996 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATAGAGGCGGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACAT-GTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGG
* * * *
41640061 TTTTACACTAGCTCTTATATGTACATGCTGATGCATGTCCCAAACATGTCTTACACTAGCACTAC
65 TTTTACACTAGCGCTCATATCTA-ATGCCGATGCATGTCCCAAACATGTCTTACACTAGCACTAC
** *
41640126 CCTCAGCCGATG
129 AATCAGCCGATA
* *
41640138 CATGTCCCAAACATGTCTTACACTGGCTATCTTCATCGAGGCCGATG-CATGTCCCAGACAT-GT
1 CATGTCCCAGACATGTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGGT
* * * * * *
41640201 TTTATACTGGCGCTCATCTCT-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTA
66 TTTACACTAGCGCTCATATCTAATGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGC-ACTA
* ** *
41640265 TAATGTGGCTGATA
128 CAAT-CAGCCGATA
* ** * *
41640279 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCA-ATA--CCGATGCCATGTCCCAAACATG
1 CATGTCCCAGACATGTCTTACACTGGCTATC-T-TCATAGAGGCCGATGCCATGTCCCAGACATG
*
41640341 GTCTTACACT
64 GTTTTACACT
41640351 GGCTCTCACA
Statistics
Matches: 176, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
137 8 0.05
138 13 0.07
139 29 0.16
140 24 0.14
141 76 0.43
142 23 0.13
143 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACATGTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGGT
TTTACACTAGCGCTCATATCTAATGCCGATGCATGTCCCAAACATGTCTTACACTAGCACTACAA
TCAGCCGATA
Found at i:41669806 original size:21 final size:23
Alignment explanation
Indices: 41669781--41669831 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
41669771 CAGAGGTACT
41669781 CGTGGAAG-GG-GT-ACAAGAGGC
1 CGTGGAAGAGGCGTGAC-AGAGGC
41669802 CGTGGAAGAGGCCGTGACAGAGGC
1 CGTGGAAGAGG-CGTGACAGAGGC
41669826 CGTGGA
1 CGTGGA
41669832 GGTGCTCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
24 14 0.54
25 2 0.08
ACGTcount: A:0.25, C:0.18, G:0.47, T:0.10
Consensus pattern (23 bp):
CGTGGAAGAGGCGTGACAGAGGC
Found at i:41669812 original size:12 final size:12
Alignment explanation
Indices: 41669795--41669831 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
41669785 GAAGGGGTAC
41669795 AAGAGGCCGTGG
1 AAGAGGCCGTGG
41669807 AAGAGGCCGT-G
1 AAGAGGCCGTGG
41669818 ACAGAGGCCGTGG
1 A-AGAGGCCGTGG
41669831 A
1 A
41669832 GGTGCTCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.27, C:0.19, G:0.46, T:0.08
Consensus pattern (12 bp):
AAGAGGCCGTGG
Found at i:41673465 original size:27 final size:27
Alignment explanation
Indices: 41673435--41673496 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
41673425 TTTACAAAAC
41673435 TACCCCTAAGTATG-AAAATTACCATTA
1 TACCCCTAAG-ATGCAAAATTACCATTA
41673462 TACCCCCT-AGATGCAAAATTACCATTA
1 TA-CCCCTAAGATGCAAAATTACCATTA
41673489 TACCCCTA
1 TACCCCTA
41673497 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 19 0.59
28 5 0.16
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (27 bp):
TACCCCTAAGATGCAAAATTACCATTA
Found at i:41673700 original size:26 final size:26
Alignment explanation
Indices: 41673604--41673711 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 26
41673594 GGAAGCGTTT
*
41673604 TGGTGGCTATGCCACAAATATCTATTTC
1 TGGTGGCTCTGCCAC-AATATCT-TTTC
* *
41673632 TGGTGGCTATGCCACAAATATCTGTTC
1 TGGTGGCTCTGCCAC-AATATCTTTTC
41673659 TGGTGGCTCTGCCACAATATCTTTATC
1 TGGTGGCTCTGCCACAATATCTTT-TC
* *
41673686 TGGTGACTCTG-CACAATATCTGTTC
1 TGGTGGCTCTGCCACAATATCTTTTC
41673711 T
1 T
41673712 AGCAGCCATG
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.04
26 19 0.26
27 29 0.39
28 23 0.31
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (26 bp):
TGGTGGCTCTGCCACAATATCTTTTC
Found at i:41682458 original size:34 final size:34
Alignment explanation
Indices: 41682420--41682484 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
41682410 TTCACTCAGA
41682420 TAAAATCATCATTCATACTTGCATACAAACTGTC
1 TAAAATCATCATTCATACTTGCATACAAACTGTC
41682454 TAAAATCATCATTCATACTTGCATACAAACT
1 TAAAATCATCATTCATACTTGCATACAAACT
41682485 ATCTCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (34 bp):
TAAAATCATCATTCATACTTGCATACAAACTGTC
Found at i:41692926 original size:34 final size:34
Alignment explanation
Indices: 41692883--41692952 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
41692873 AATTTTCAAA
*
41692883 AGAATGACCTTCCCCATGATACACACAGGAAACT
1 AGAATGACCTTCCCCACGATACACACAGGAAACT
41692917 AGAATGACCTTCCCCACGATACACACAGGAAACT
1 AGAATGACCTTCCCCACGATACACACAGGAAACT
41692951 AG
1 AG
41692953 TTCAAACGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.16
Consensus pattern (34 bp):
AGAATGACCTTCCCCACGATACACACAGGAAACT
Found at i:41698294 original size:16 final size:16
Alignment explanation
Indices: 41698263--41698312 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
41698253 TTAATTAATT
*
41698263 TTTTAAAATTTAAAAA
1 TTTTAAAAATTAAAAA
41698279 TTTTAAAAATTCAAAAA
1 TTTTAAAAATT-AAAAA
**
41698296 AATTAAAACATTAAAAA
1 TTTTAAAA-ATTAAAAA
41698313 ATATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.34
17 16 0.55
18 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTTAAAAATTAAAAA
Found at i:41698321 original size:18 final size:17
Alignment explanation
Indices: 41698283--41698327 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
41698273 TAAAAATTTT
*
41698283 AAAAATTCAAAAAAATTA
1 AAAAATT-AAAAAAATAA
*
41698301 AAACATTAAAAAATATAA
1 AAAAATTAAAAAA-ATAA
41698319 AAAAATTAA
1 AAAAATTAA
41698328 TATTGTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATTAAAAAAATAA
Found at i:41699368 original size:16 final size:17
Alignment explanation
Indices: 41699335--41699368 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41699325 GTAATTAATA
*
41699335 AAATATTGTAAAATTAT
1 AAATATTGTAAAACTAT
41699352 AAATATT-TAAAACTAT
1 AAATATTGTAAAACTAT
41699368 A
1 A
41699369 CAAATCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATATTGTAAAACTAT
Found at i:41699828 original size:33 final size:33
Alignment explanation
Indices: 41699791--41699857 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41699781 TTGGTGAAAG
41699791 TTCAATTAATAAATGATGAATACGTATATCATT
1 TTCAATTAATAAATGATGAATACGTATATCATT
41699824 TTCAATTAATAAATGATGAATACGTATATCATT
1 TTCAATTAATAAATGATGAATACGTATATCATT
41699857 T
1 T
41699858 GGTGTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (33 bp):
TTCAATTAATAAATGATGAATACGTATATCATT
Found at i:41706961 original size:17 final size:16
Alignment explanation
Indices: 41706922--41706961 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
41706912 AACATAGTCC
41706922 AATATATATATAAAGA
1 AATATATATATAAAGA
*
41706938 AATTATATATATACAGA
1 AA-TATATATATAAAGA
41706955 ACATATA
1 A-ATATA
41706962 ACGGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AATATATATATAAAGA
Found at i:41711681 original size:28 final size:26
Alignment explanation
Indices: 41711650--41711711 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
41711640 TTACTTGAAT
* *
41711650 ACCCCTATGTATGGAAAATTACTATTAC
1 ACCCCTA-G-ATGCAAAATTACCATTAC
* *
41711678 ACCCCTAGGTGCAAAATTACCATTAT
1 ACCCCTAGATGCAAAATTACCATTAC
41711704 ACCCCTAG
1 ACCCCTAG
41711712 GGTTACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.73
27 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (26 bp):
ACCCCTAGATGCAAAATTACCATTAC
Found at i:41711856 original size:27 final size:26
Alignment explanation
Indices: 41711816--41711926 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
41711806 AGGAAGCGTC
*
41711816 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
41711843 GTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
41711870 CTGGTGGCTCTGCCATGATTATCT-ATT
1 CTGGTGGCTCTGCCA-CATTATCTGA-T
* * *
41711897 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
41711923 CTGG
1 CTGG
41711927 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
26 14 0.20
27 54 0.77
28 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:41711902 original size:54 final size:53
Alignment explanation
Indices: 41711816--41711926 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
41711806 AGGAAGCGTC
* *
41711816 CTGGTGGCTATGCCACAATTATCTGATGTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* ** *
41711870 CTGGTGGCTCTGCCATGATTATCT-ATTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGA-TCTGGTGACTCTGCCACATTATCTGTT
41711923 CTGG
1 CTGG
41711927 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 13 0.26
54 37 0.74
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:41720497 original size:41 final size:40
Alignment explanation
Indices: 41720444--41720613 Score: 143
Period size: 41 Copynumber: 4.2 Consensus size: 40
41720434 AGTCCGACTC
* *
41720444 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
41720483 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA
* * *
41720523 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
*
41720568 TTAG-CACTGGCTCAAAAGCCCTTTGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
41720607 TTTAGAC
1 -TTAGAC
41720614 CCCGATTAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
39 5 0.05
40 18 0.17
41 49 0.47
42 19 0.18
43 10 0.10
44 1 0.01
45 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Done.