Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 202 of 322
Found at i:66236628 original size:24 final size:22
Alignment explanation
Indices: 66236560--66236628 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 22
66236550 TTTTAGAATT
*
66236560 ATATATTTTAGAATTTTATAAAA
1 ATATATTTTA-AATTTTTTAAAA
*
66236583 A-ATTATTTTAAACCTTTCTTAAAA
1 ATA-TATTTTAAA--TTTTTTAAAA
66236607 ATATATCTTTACAATTTTTTAA
1 ATATAT-TTTA-AATTTTTTAA
66236629 TAATTTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
24 19 0.51
25 5 0.14
26 2 0.05
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.49
Consensus pattern (22 bp):
ATATATTTTAAATTTTTTAAAA
Found at i:66241583 original size:4 final size:4
Alignment explanation
Indices: 66241554--66241608 Score: 76
Period size: 4 Copynumber: 13.2 Consensus size: 4
66241544 AGAGCTCATG
66241554 CTAA CTAA TCTAA C-AGA CTAAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA
1 CTAA CTAA -CTAA CTA-A CT-AA CTAA CTAA CTAA CTAA CTAA CTAA CTAA
66241604 CTAA C
1 CTAA C
66241609 AATTAACCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 1 0.02
4 38 0.81
5 7 0.15
6 1 0.02
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.24
Consensus pattern (4 bp):
CTAA
Found at i:66252742 original size:33 final size:33
Alignment explanation
Indices: 66252705--66252770 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
66252695 AAGAGTAAGT
66252705 ACATGTTTGTGATGGTTAAGTATAGAGTTGTGA
1 ACATGTTTGTGATGGTTAAGTATAGAGTTGTGA
66252738 ACATGTTTGTGATGGTTAAGTATAGAGTTGTGA
1 ACATGTTTGTGATGGTTAAGTATAGAGTTGTGA
66252771 TTATTACGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.39
Consensus pattern (33 bp):
ACATGTTTGTGATGGTTAAGTATAGAGTTGTGA
Found at i:66252805 original size:17 final size:16
Alignment explanation
Indices: 66252783--66252829 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
66252773 ATTACGCCAA
66252783 TTGGCGAACTCTTAGCT
1 TTGGCGAACTCTT-GCT
*
66252800 TTGGCGAGA-TCTGTGGT
1 TTGGCGA-ACTCT-TGCT
66252817 TTGGCGAACTCTT
1 TTGGCGAACTCTT
66252830 TTGTTAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (16 bp):
TTGGCGAACTCTTGCT
Found at i:66260507 original size:6 final size:6
Alignment explanation
Indices: 66260489--66260532 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
66260479 TACAAATTAA
* *
66260489 TCATTT CTCATTT TCATTT TCATTT CCATTT CCATTT TCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT T
66260533 GAAAAAACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (6 bp):
TCATTT
Found at i:66260524 original size:18 final size:19
Alignment explanation
Indices: 66260489--66260531 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
66260479 TACAAATTAA
*
66260489 TCATTTCTCATTTTCATTT
1 TCATTTCTCATTTCCATTT
66260508 TCATTTC-CATTTCCATTT
1 TCATTTCTCATTTCCATTT
66260526 TCATTT
1 TCATTT
66260532 TGAAAAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (19 bp):
TCATTTCTCATTTCCATTT
Found at i:66264034 original size:31 final size:31
Alignment explanation
Indices: 66263970--66264034 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
66263960 CAAACATTTC
* * * *
66263970 AAAATGGTCAAATAAGGGCTAGACCTTTTCA
1 AAAATGCTCAAATAAGAGCTAAACCTTTCCA
*
66264001 AAAATGCTCAAATAAGAGCTAAATCTTTCCA
1 AAAATGCTCAAATAAGAGCTAAACCTTTCCA
66264032 AAA
1 AAA
66264035 GTACTTCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (31 bp):
AAAATGCTCAAATAAGAGCTAAACCTTTCCA
Found at i:66265826 original size:16 final size:16
Alignment explanation
Indices: 66265805--66265835 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66265795 CATGTGAAAA
66265805 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
66265821 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
66265836 AAAGAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:66271272 original size:6 final size:6
Alignment explanation
Indices: 66271261--66271294 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
66271251 AATTTGTGAA
*
66271261 AAAAAT AAAAAT AAAAAT AAAAAA ATAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT AAA
66271295 GAACACATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:66272508 original size:31 final size:31
Alignment explanation
Indices: 66272430--66272509 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
66272420 AATTATGAAT
* * *
66272430 AAATTTTTATTTTAGTCATTAAACTATTTAA
1 AAATTTTTATTTAAGTTACTAAACTATTTAA
*
66272461 AATTTTTTATTTAAGTTACTAAACTATTTAA
1 AAATTTTTATTTAAGTTACTAAACTATTTAA
66272492 AAATTTTTATTTAAGTTA
1 AAATTTTTATTTAAGTTA
66272510 TTTGGCCGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (31 bp):
AAATTTTTATTTAAGTTACTAAACTATTTAA
Found at i:66273453 original size:70 final size:70
Alignment explanation
Indices: 66273312--66273454 Score: 162
Period size: 70 Copynumber: 2.0 Consensus size: 70
66273302 GTGCTTAACG
* * * *
66273312 GTACATCTAAAGTAATGAGTGCTCAACACTCATTGGAATGTCTGAAATAATATGCACCTAGCACT
1 GTACATCTAAAGTAATGAGTGCCCAACACTCATAGGAATGTCTGAAATAATATGCACCCAACACT
**
66273377 TCTCA
66 GATCA
* * ** **
66273382 GTACAT-TCAAAGTAATGTGTGCCCAACACTCATAGGAATGTCTGAAGTAATATGTGCCCAATGC
1 GTACATCT-AAAGTAATGAGTGCCCAACACTCATAGGAATGTCTGAAATAATATGCACCCAACAC
66273446 TGATCA
65 TGATCA
66273452 GTA
1 GTA
66273455 TAAATTGGAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
69 1 0.02
70 59 0.98
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (70 bp):
GTACATCTAAAGTAATGAGTGCCCAACACTCATAGGAATGTCTGAAATAATATGCACCCAACACT
GATCA
Found at i:66273636 original size:14 final size:14
Alignment explanation
Indices: 66273617--66273644 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
66273607 CATATAAGCA
66273617 TTCAATTTAAACCT
1 TTCAATTTAAACCT
66273631 TTCAATTTAAACCT
1 TTCAATTTAAACCT
66273645 ATTTTACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
TTCAATTTAAACCT
Found at i:66277087 original size:23 final size:23
Alignment explanation
Indices: 66277059--66277103 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
66277049 CAACGTAACT
66277059 TTAGTCTCGGACCCTAATCTTAC
1 TTAGTCTCGGACCCTAATCTTAC
66277082 TTAGTCTCGGACCCTAATCTTA
1 TTAGTCTCGGACCCTAATCTTA
66277104 GTATTTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (23 bp):
TTAGTCTCGGACCCTAATCTTAC
Found at i:66281988 original size:27 final size:27
Alignment explanation
Indices: 66281955--66282181 Score: 203
Period size: 27 Copynumber: 8.6 Consensus size: 27
66281945 AAACTGTACA
* *
66281955 GCACTAAGTGTGCGATATGACTATGTT
1 GCACTAAGTGTGCGAAATGAATATGTT
* *
66281982 GCACTAAGTGTGCGAAATGAATACGAT
1 GCACTAAGTGTGCGAAATGAATATGTT
* * *
66282009 ACACTAAGTGTGCGAAATGAATACGAT
1 GCACTAAGTGTGCGAAATGAATATGTT
66282036 GCACTAAGTGTGCGAAATG---A--TT
1 GCACTAAGTGTGCGAAATGAATATGTT
* *
66282058 GCACTCAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGAATATGTT
* ** **
66282085 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAAATGAATATGTT
** * *
66282112 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-AATGAATATGTT
** * * *
66282140 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAAATGAATATGTT
66282167 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
66282182 GTTGATTATA
Statistics
Matches: 170, Mismatches: 24, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
22 19 0.11
24 1 0.01
25 1 0.01
27 127 0.75
28 22 0.13
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (27 bp):
GCACTAAGTGTGCGAAATGAATATGTT
Found at i:66282016 original size:54 final size:53
Alignment explanation
Indices: 66281955--66282207 Score: 230
Period size: 54 Copynumber: 4.8 Consensus size: 53
66281945 AAACTGTACA
*
66281955 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATACGAT
1 GCACTAAGTGTGCGATATGAATATGTTGCACTAAGTGTGCGAAATGAATACG-T
* * * *
66282009 ACACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGAAATG-AT---T
1 GCACTAAGTGTGCGATATGAATATGTTGCACTAAGTGTGCGAAATGAATACGT
* * * * *
66282058 GCACTCAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG-
1 GCACTAAGTGTGCGATATGAATATGTTGCACTAAGTGTGCGAAATGA--ATACGT
* * * ** *
66282112 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT
1 GCACTAAGTGTGCGA-TATGAATATGTTGCACTAAGTGTGCGAAATGAATACGT
* * * *
66282166 GGCACTAAGTGTGCGAGT-TGATTATATAGCACTGAGTGTGCG
1 -GCACTAAGTGTGCGA-TATGAATATGTTGCACTAAGTGTGCG
66282208 GGCTCAATAT
Statistics
Matches: 169, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
49 43 0.25
52 2 0.01
53 5 0.03
54 76 0.45
55 43 0.25
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
GCACTAAGTGTGCGATATGAATATGTTGCACTAAGTGTGCGAAATGAATACGT
Found at i:66282090 original size:76 final size:75
Alignment explanation
Indices: 66281980--66282126 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 75
66281970 TATGACTATG
66281980 TTGCACTAAGTGTGCGAAATGAATACGATACACTAAGTGTGCGAAATGA-ATACGATGCACTAAG
1 TTGCACTAAGTGTGCGAAATGAATACGATACACTAAGTGTGCGAAATGACATACG--GCACTAAG
66282044 TGTGCGAAATGA
64 TGTGCGAAATGA
* * * * *
66282056 TTGCACTCAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGT
1 TTGCACTAAGTGTGCGAAATGAATACGATACACTAAGTGTGCGAAATGA-CATACGGCACTAAGT
66282121 GTGCGA
65 GTGCGA
66282127 GTCTGACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
76 60 0.94
78 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (75 bp):
TTGCACTAAGTGTGCGAAATGAATACGATACACTAAGTGTGCGAAATGACATACGGCACTAAGTG
TGCGAAATGA
Found at i:66282186 original size:27 final size:26
Alignment explanation
Indices: 66281955--66282207 Score: 192
Period size: 27 Copynumber: 9.5 Consensus size: 26
66281945 AAACTGTACA
*
66281955 GCACTAAGTGTGCG-ATATGACTATGTT
1 GCACTAAGTGTGCGAAT-TGAATATG-T
* *
66281982 GCACTAAGTGTGCGAAATGAATACGAT
1 GCACTAAGTGTGCGAATTGAATATG-T
* * *
66282009 ACACTAAGTGTGCGAAATGAATACGAT
1 GCACTAAGTGTGCGAATTGAATATG-T
*
66282036 GCACTAAGTGTGCGAAATG---AT-T
1 GCACTAAGTGTGCGAATTGAATATGT
* *
66282058 GCACTCAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGAATATG-T
** *
66282085 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGAATATG-T
* *
66282112 GCACTAAGTGTGCGAGTCTGACTATGT
1 GCACTAAGTGTGCGAAT-TGAATATGT
* * *
66282139 AGCACTAAGTGTGCGATTTGATTACGT
1 -GCACTAAGTGTGCGAATTGAATATGT
* * *
66282166 GGCACTAAGTGTGCGAGTTGATTATAT
1 -GCACTAAGTGTGCGAATTGAATATGT
*
66282193 AGCACTGAGTGTGCG
1 -GCACTAAGTGTGCG
66282208 GGCTCAATAT
Statistics
Matches: 192, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.10
24 1 0.01
25 2 0.01
27 146 0.76
28 24 0.12
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (26 bp):
GCACTAAGTGTGCGAATTGAATATGT
Found at i:66282584 original size:74 final size:74
Alignment explanation
Indices: 66282496--66282637 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
66282486 TATAGAATGC
* *
66282496 GAATGCATGAATTGATATGAAATTGAATTGATAAGTTGGAGGAACTATGGTATGGTTCGGTATGG
1 GAATGCATGAATTGATATGAAATTGAATCGATAAGTTGGAGGAACTATGGCATGGTTCGGTATGG
66282561 ATGAATTGT
66 ATGAATTGT
*
66282570 GAATGCATGAATTGATATGAAATTGAATCGATAGGTTGGAGGAACTATGGCATGGTTCGGTATGG
1 GAATGCATGAATTGATATGAAATTGAATCGATAAGTTGGAGGAACTATGGCATGGTTCGGTATGG
66282635 ATG
66 ATG
66282638 GAGTAAATTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.32, C:0.06, G:0.31, T:0.32
Consensus pattern (74 bp):
GAATGCATGAATTGATATGAAATTGAATCGATAAGTTGGAGGAACTATGGCATGGTTCGGTATGG
ATGAATTGT
Found at i:66282813 original size:63 final size:63
Alignment explanation
Indices: 66282736--66282862 Score: 218
Period size: 63 Copynumber: 2.0 Consensus size: 63
66282726 ACTCACCCGG
*
66282736 TGTTTCCTTGTCACCCATTATAGGTTGCTTGGACTCACCAATTTTTGCGGGGTCGGGCCGTCA
1 TGTTTCCTTGTCACCCACTATAGGTTGCTTGGACTCACCAATTTTTGCGGGGTCGGGCCGTCA
* * *
66282799 TGTTTCCTTGTCACCCACTATAGGTTGCTTGGACTCATCTATTTTTGTGGGGTCGGGCCGTCA
1 TGTTTCCTTGTCACCCACTATAGGTTGCTTGGACTCACCAATTTTTGCGGGGTCGGGCCGTCA
66282862 T
1 T
66282863 TGAAGTCATC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.37
Consensus pattern (63 bp):
TGTTTCCTTGTCACCCACTATAGGTTGCTTGGACTCACCAATTTTTGCGGGGTCGGGCCGTCA
Found at i:66287213 original size:46 final size:46
Alignment explanation
Indices: 66287146--66287413 Score: 282
Period size: 46 Copynumber: 5.8 Consensus size: 46
66287136 TGTAACCCGC
66287146 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
66287192 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* *
66287242 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
66287285 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * *
66287335 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
66287378 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
66287414 ATGCTCAACC
Statistics
Matches: 185, Mismatches: 19, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
42 5 0.03
43 6 0.03
44 4 0.02
45 5 0.03
46 90 0.49
47 53 0.29
48 6 0.03
49 4 0.02
50 6 0.03
51 6 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:66287266 original size:93 final size:93
Alignment explanation
Indices: 66287154--66287417 Score: 483
Period size: 93 Copynumber: 2.8 Consensus size: 93
66287144 GCCCATAAGT
66287154 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
66287219 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
66287247 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
66287312 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
66287340 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
66287405 CGAGTTCGGATGC
66 CGAGCTCGGATGC
66287418 TCAACCATCC
Statistics
Matches: 166, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 166 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:66287268 original size:47 final size:47
Alignment explanation
Indices: 66287200--66287368 Score: 213
Period size: 47 Copynumber: 3.6 Consensus size: 47
66287190 ATCCATAAGT
66287200 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
66287247 GAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-C
66287293 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
* *
66287340 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCAGACTCAACTCAACGAGCTCGGA
66287369 CATTCGCATC
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 3 0.03
46 27 0.26
47 54 0.52
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:66288250 original size:22 final size:22
Alignment explanation
Indices: 66288225--66288278 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
66288215 ATTAAAAACA
66288225 GGGCTTGGAATCACTTACTATG
1 GGGCTTGGAATCACTTACTATG
66288247 GGGCTTGGAATCACTTACTATG
1 GGGCTTGGAATCACTTACTATG
*
66288269 GAGCTTGGAA
1 GGGCTTGGAA
66288279 GCTTGAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (22 bp):
GGGCTTGGAATCACTTACTATG
Found at i:66303259 original size:159 final size:159
Alignment explanation
Indices: 66302970--66303289 Score: 552
Period size: 159 Copynumber: 2.0 Consensus size: 159
66302960 AATCTTTGGG
*
66302970 CTATGATTCTAGCAGATACATTGGGCGGCAACAAGCTCATATTTGATATCCAAACTGCTTAGTGC
1 CTATGATTCTAGCAGATACATTGGGCAGCAACAAGCTCATATTTGATATCCAAACTGCTTAGTGC
* *
66303035 AACATATCTTCGAGATTGGTTTGCATGGAATCAAGACAATCGACTTCCCAAAACTTGGAAGTATA
66 AACATATCTTAGAGATTGGTTTACATGGAATCAAGACAATCGACTTCCCAAAACTTGGAAGTATA
*
66303100 TCCTAAATATTCTAGACTTATCCTAAGCC
131 TCCTAAATATTCTAGACTTATCCCAAGCC
* *
66303129 CTATGATTCTAGCAGATACTTTGGGCAGCAACAAGC-CTATATTTGATATCCAAATTGCTTAGTG
1 CTATGATTCTAGCAGATACATTGGGCAGCAACAAGCTC-ATATTTGATATCCAAACTGCTTAGTG
**
66303193 CAACATATCTTAGAGATTGGTTTACATGGAATCAAGGTAATCGACTTCCCAAAACTTGGAAGTAT
65 CAACATATCTTAGAGATTGGTTTACATGGAATCAAGACAATCGACTTCCCAAAACTTGGAAGTAT
66303258 ATCCTAAATATTCTAGACTTATCCCAAGCC
130 ATCCTAAATATTCTAGACTTATCCCAAGCC
66303288 CT
1 CT
66303290 TTGAGGATAT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
158 1 0.01
159 151 0.99
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (159 bp):
CTATGATTCTAGCAGATACATTGGGCAGCAACAAGCTCATATTTGATATCCAAACTGCTTAGTGC
AACATATCTTAGAGATTGGTTTACATGGAATCAAGACAATCGACTTCCCAAAACTTGGAAGTATA
TCCTAAATATTCTAGACTTATCCCAAGCC
Found at i:66308312 original size:37 final size:37
Alignment explanation
Indices: 66308271--66308345 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
66308261 TTTAAATGCC
*
66308271 TTGATATTTCATAAATTGTGAATTACGAATTTGCGGA
1 TTGATATTGCATAAATTGTGAATTACGAATTTGCGGA
*
66308308 TTGATATTGGATAAATTGTGAATTACGAATTTGCGGA
1 TTGATATTGCATAAATTGTGAATTACGAATTTGCGGA
66308345 T
1 T
66308346 ACATTCGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (37 bp):
TTGATATTGCATAAATTGTGAATTACGAATTTGCGGA
Found at i:66308499 original size:48 final size:48
Alignment explanation
Indices: 66308428--66308606 Score: 286
Period size: 48 Copynumber: 3.7 Consensus size: 48
66308418 CATTAGGGAA
*
66308428 TACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCAGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATTGGCACTTTAGGTGCGAGT
* * *
66308476 TACATTGATTTGGCTTTGGGCCATGATTTTGGCACTTTGGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATTGGCACTTTAGGTGCGAGT
* *
66308524 TACATTGATTTGGCTTCGGGCCATGATATTGGAACTTTAGGCGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATTGGCACTTTAGGTGCGAGT
* *
66308572 TACATTGATTTGGCTTCGGGTCATGATATTAGCAC
1 TACATTGATTTGGCTTCGGGCCATGATATTGGCAC
66308607 CTAGGGTGCG
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (48 bp):
TACATTGATTTGGCTTCGGGCCATGATATTGGCACTTTAGGTGCGAGT
Found at i:66317073 original size:15 final size:15
Alignment explanation
Indices: 66317053--66317090 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
66317043 GATTTTGAGT
66317053 TAATGATTTTGTCAA
1 TAATGATTTTGTCAA
66317068 TAATGATTTTGTCAA
1 TAATGATTTTGTCAA
66317083 TAAT-ATTT
1 TAATGATTT
66317091 CTGAGCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (15 bp):
TAATGATTTTGTCAA
Found at i:66329831 original size:15 final size:15
Alignment explanation
Indices: 66329811--66329842 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66329801 AATAAGTATC
66329811 ATTTTTCGAGAATTG
1 ATTTTTCGAGAATTG
*
66329826 ATTTTTTGAGAATTG
1 ATTTTTCGAGAATTG
66329841 AT
1 AT
66329843 GATTTGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (15 bp):
ATTTTTCGAGAATTG
Found at i:66336724 original size:35 final size:35
Alignment explanation
Indices: 66336681--66336785 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
66336671 CATAAGTATG
* *
66336681 TACATGTGAGGTCATATTGAGTTTGTATATTCGGC
1 TACATGTGAGGTTATATTGAATTTGTATATTCGGC
* * * * **
66336716 TGCTTGTGAAGTTATATTGAACTTGTATATTCGAT
1 TACATGTGAGGTTATATTGAATTTGTATATTCGGC
*
66336751 TACATATGAGGTTATATTGAATTTGTATATTCGGC
1 TACATGTGAGGTTATATTGAATTTGTATATTCGGC
66336786 CATATGAGAT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.43
Consensus pattern (35 bp):
TACATGTGAGGTTATATTGAATTTGTATATTCGGC
Found at i:66336809 original size:70 final size:71
Alignment explanation
Indices: 66336681--66336866 Score: 175
Period size: 70 Copynumber: 2.6 Consensus size: 71
66336671 CATAAGTATG
* * * * *
66336681 TACATGTGAGGTCATATTGAGTTTGTATATTCGGCTGC-T-TGTGA-AGTTATATTGAACTTGTA
1 TACATGTGAGGTTATATTGAATTTGTATATTCGGC--CATATGAGATAGTTATATTAAACTTGAA
* *
66336743 TATTCGAT
64 CATTAGAT
* *
66336751 TACATATGAGGTTATATTGAATTTGTATATTCGGCCATATGAGATA-TTTTATTAAACTTGAACA
1 TACATGTGAGGTTATATTGAATTTGTATATTCGGCCATATGAGATAGTTATATTAAACTTGAACA
*
66336815 TTAGGT
66 TTAGAT
* * * * *
66336821 TACATGTGATGATA-ACTTGAACTTATATATTCAGCCATATGAGATA
1 TACATGTGAGGTTATA-TTGAATTTGTATATTCGGCCATATGAGATA
66336867 ATATAATGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
68 1 0.01
69 2 0.02
70 92 0.96
71 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (71 bp):
TACATGTGAGGTTATATTGAATTTGTATATTCGGCCATATGAGATAGTTATATTAAACTTGAACA
TTAGAT
Found at i:66342896 original size:24 final size:24
Alignment explanation
Indices: 66342864--66342912 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
66342854 GAGAATGCAA
66342864 TGAAAGAACGTCATCCAAACCTAT
1 TGAAAGAACGTCATCCAAACCTAT
66342888 TGAAAGAACGTCATCCAAACCTAT
1 TGAAAGAACGTCATCCAAACCTAT
66342912 T
1 T
66342913 CACCGGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (24 bp):
TGAAAGAACGTCATCCAAACCTAT
Found at i:66346156 original size:15 final size:15
Alignment explanation
Indices: 66346136--66346167 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66346126 AATAAGTATC
66346136 ATTTTTCGAGAATTG
1 ATTTTTCGAGAATTG
*
66346151 ATTTTTTGAGAATTG
1 ATTTTTCGAGAATTG
66346166 AT
1 AT
66346168 GATTTGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (15 bp):
ATTTTTCGAGAATTG
Found at i:66353112 original size:28 final size:28
Alignment explanation
Indices: 66353049--66353199 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
66353039 ATATTAAGTC
*
66353049 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
66353076 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
66353104 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
66353132 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
66353160 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
66353189 CGCACACTTAG
1 CGCACACTTAG
66353200 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:66365644 original size:20 final size:20
Alignment explanation
Indices: 66365619--66365660 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
66365609 TAATTAAACT
*
66365619 TACTAAATTAAAATGTAACC
1 TACTAAATGAAAATGTAACC
*
66365639 TACTAAATGAAAATTTAACC
1 TACTAAATGAAAATGTAACC
66365659 TA
1 TA
66365661 TGTATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (20 bp):
TACTAAATGAAAATGTAACC
Found at i:66366397 original size:2 final size:2
Alignment explanation
Indices: 66366390--66366446 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
66366380 GAATTGTATA
66366390 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
66366432 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
66366447 ATTTATGTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:66367946 original size:6 final size:6
Alignment explanation
Indices: 66367914--66367963 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
66367904 ACAGTACCTA
* *
66367914 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
66367963 A
1 A
66367964 TTCAACACAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:66367994 original size:45 final size:45
Alignment explanation
Indices: 66367943--66368050 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 45
66367933 AGCAGTAACA
* * *
66367943 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCT
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTC-AAATCG
* *
66367988 GTAACAGTAACGGTAAAAGTATTCGACACACAAAGTGTCAAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCAAATCG
66368033 GTAACAGTAACGGTAACA
1 GTAACAGTAACGGTAACA
66368051 ATAACAGTAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCAAATCG
Found at i:66368693 original size:14 final size:14
Alignment explanation
Indices: 66368674--66368727 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
66368664 TTTAGCTTTG
*
66368674 TTTCTTTTATTTTT
1 TTTCTTTTATTTTC
*
66368688 TTTCTTTTCTTTTC
1 TTTCTTTTATTTTC
*
66368702 TTTCTATTTCATTTAC
1 TTTCT-TTT-ATTTTC
*
66368718 TTTATTTTAT
1 TTTCTTTTAT
66368728 ATTTAAGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 19 0.58
15 6 0.18
16 8 0.24
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTTATTTTC
Found at i:66369030 original size:25 final size:23
Alignment explanation
Indices: 66368986--66369046 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
66368976 ATTTTGATTT
*
66368986 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
66369010 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
66369034 ATATAAATTATAT
1 AT-TTAATTATAT
66369047 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:66369049 original size:35 final size:35
Alignment explanation
Indices: 66368994--66369073 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
66368984 TTATTTAATA
* *
66368994 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
66369028 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
66369063 ATATAAT-TAAA
1 ATATAATATAAA
66369074 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:66370564 original size:26 final size:26
Alignment explanation
Indices: 66370525--66370632 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
66370515 TGATACAAAT
*
66370525 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
* *
66370551 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
* *
66370577 CGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
66370603 TGATAAT-AGTTTAGGTAAATGTTCCA
1 TGATAATGAG-TTAGGTAAATGTTCCA
66370629 TGAT
1 TGAT
66370633 GGGAATTTCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
25 1 0.01
26 71 0.99
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.35
Consensus pattern (26 bp):
TGATAATGAGTTAGGTAAATGTTCCA
Found at i:66370583 original size:52 final size:52
Alignment explanation
Indices: 66370526--66370628 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
66370516 GATACAAATT
66370526 GATAATGGGTTAGGTAAATGTTCCATGATAAT-GAATTAGGTAAATATTCCAC
1 GATAATGGGTTAGGTAAATGTTCCATGATAATAG-ATTAGGTAAATATTCCAC
* *
66370578 GATAATGGGTTAGGTAAATGTTCCATGATAATAGTTTAGGTAAATGTTCCA
1 GATAATGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCA
66370629 TGATGGGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (52 bp):
GATAATGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCAC
Found at i:66377267 original size:20 final size:20
Alignment explanation
Indices: 66377229--66377267 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
66377219 TAAATTATGT
66377229 ATATTGATATGTTTGAATTAA
1 ATATTGATATG-TTGAATTAA
66377250 ATATTGTATATG-TGAATT
1 ATATTG-ATATGTTGAATT
66377268 GTGTAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATTGATATGTTGAATTAA
Found at i:66377275 original size:28 final size:26
Alignment explanation
Indices: 66377210--66377275 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 26
66377200 CAAGGTAAGT
*
66377210 TTGTGTAACTAAATTATGTATATTGA
1 TTGTGTAATTAAATTATGTATATTGA
*
66377236 TATGTTTGAATTAAA-TATTGTATATGTGAA
1 T-TGTGT-AATTAAATTA-TGTATAT-TG-A
66377266 TTGTGTAATT
1 TTGTGTAATT
66377276 GTTATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
26 1 0.03
27 6 0.19
28 17 0.53
29 6 0.19
30 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (26 bp):
TTGTGTAATTAAATTATGTATATTGA
Found at i:66377455 original size:24 final size:25
Alignment explanation
Indices: 66377428--66377478 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
66377418 AGCATCCCGA
*
66377428 TATATGG-CCTTTTGAGCTTCCTGT
1 TATATGGTCCTTGTGAGCTTCCTGT
*
66377452 TATATGGTTCTTGTGAGCTTCCTGT
1 TATATGGTCCTTGTGAGCTTCCTGT
66377477 TA
1 TA
66377479 ATAGCTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.47
Consensus pattern (25 bp):
TATATGGTCCTTGTGAGCTTCCTGT
Found at i:66383991 original size:17 final size:18
Alignment explanation
Indices: 66383960--66383993 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
66383950 CGTGACCCTT
66383960 GCCCGTGTGGGCCCACAG
1 GCCCGTGTGGGCCCACAG
66383978 GCCCGTGT-GGCCCACA
1 GCCCGTGTGGGCCCACA
66383994 TAGCCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.41, G:0.35, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGGGCCCACAG
Found at i:66383999 original size:18 final size:18
Alignment explanation
Indices: 66383960--66383999 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
66383950 CGTGACCCTT
*
66383960 GCCCGTGTGGGCCCACAG
1 GCCCGTGTGGGCCCACAA
66383978 GCCCGTGT-GGCCCACATA
1 GCCCGTGTGGGCCCACA-A
66383996 GCCC
1 GCCC
66384000 AAATTAGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.12, C:0.42, G:0.33, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGGGCCCACAA
Found at i:66398720 original size:23 final size:23
Alignment explanation
Indices: 66398617--66398724 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 23
66398607 CCTGATCAGT
66398617 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
66398639 A-ACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
** * *
66398660 A-ACGACACACGAGGTACCTG--
1 ATACGACACATAAAGTGCCTGAA
** *
66398680 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
66398703 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
66398725 TCAATAAAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 1 0.01
21 53 0.72
22 1 0.01
23 19 0.26
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:66399120 original size:15 final size:15
Alignment explanation
Indices: 66399095--66399152 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
66399085 TCGTATATAT
*
66399095 TATATAATTCAATCAG
1 TATA-AATTCAATCAA
66399111 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
66399126 AATAATTTCAATCAA
1 TATAAATTCAATCAA
66399141 TATAAATTCAAT
1 TATAAATTCAAT
66399153 AAATTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:66400435 original size:5 final size:5
Alignment explanation
Indices: 66400422--66400463 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
66400412 TTCTTTAGTT
66400422 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
66400464 TAAAACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:66413222 original size:1 final size:1
Alignment explanation
Indices: 66413216--66413250 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
66413206 ACACTTAAGC
*
66413216 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
66413251 CAAGCATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:66420112 original size:263 final size:263
Alignment explanation
Indices: 66419645--66420170 Score: 989
Period size: 263 Copynumber: 2.0 Consensus size: 263
66419635 TCGCATCATC
*
66419645 AGCCGATGCAAACGTTACATAACCAAAACCACGGGATCGACCCGTAGTTCGCTCCTGGACAATAG
1 AGCCGATGCAAACGTTACATAACCAAAACCACGGGATCGACCCGTAGTTCGCTCCTAGACAATAG
* *
66419710 AAAAACATAATCAATGAACAACATTAAATAAAAAAAGAATCGAATAAAGAAAAGAAATGAAAGAA
66 AAAAACATAATCAATGAACAACATAAAATAAAAAAAGAATCGAATAAAGAAAAGAAAGGAAAGAA
*
66419775 AGTTAGGTTATTTAGCAGTTGGTCAAGCTCGCAAACTAGCAATAACACTAGTAGACAAACTTGTA
131 AGATAGGTTATTTAGCAGTTGGTCAAGCTCGCAAACTAGCAATAACACTAGTAGACAAACTTGTA
66419840 TAGAAGAAAGCTTAAAAGAGTTCATGCCCCAGCTTGGGCTATTTAAACATAGAGTGAAGGTTCTA
196 TAGAAGAAAGCTTAAAAGAGTTCATGCCCCAGCTTGGGCTATTTAAACATAGAGTGAAGGTTCTA
66419905 AAA
261 AAA
*
66419908 AGCCGATGCAAACGTTACATAACCAAAACCACGGGATTGACCCGTAGTTCGCTCCTAGACAATAG
1 AGCCGATGCAAACGTTACATAACCAAAACCACGGGATCGACCCGTAGTTCGCTCCTAGACAATAG
*
66419973 AAAAACATAATCAATGAACAACATAAAATAAAAAAGGAATCGAATAAAGAAAAGAAAGGAAAGAA
66 AAAAACATAATCAATGAACAACATAAAATAAAAAAAGAATCGAATAAAGAAAAGAAAGGAAAGAA
66420038 AGATAGGTTATTTAGCAGTTGGTCAAGCTCGCAAACTAGCAATAACACTAGTAGACAAACTTGTA
131 AGATAGGTTATTTAGCAGTTGGTCAAGCTCGCAAACTAGCAATAACACTAGTAGACAAACTTGTA
*
66420103 TAGAAGAAAGCTTAAAAGAGTTCATGCCCCAGCTTGGGCTATTTAAACATAGAGTGAAGGTTGTA
196 TAGAAGAAAGCTTAAAAGAGTTCATGCCCCAGCTTGGGCTATTTAAACATAGAGTGAAGGTTCTA
66420168 AAA
261 AAA
66420171 GTCCTAGTAT
Statistics
Matches: 256, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
263 256 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.21
Consensus pattern (263 bp):
AGCCGATGCAAACGTTACATAACCAAAACCACGGGATCGACCCGTAGTTCGCTCCTAGACAATAG
AAAAACATAATCAATGAACAACATAAAATAAAAAAAGAATCGAATAAAGAAAAGAAAGGAAAGAA
AGATAGGTTATTTAGCAGTTGGTCAAGCTCGCAAACTAGCAATAACACTAGTAGACAAACTTGTA
TAGAAGAAAGCTTAAAAGAGTTCATGCCCCAGCTTGGGCTATTTAAACATAGAGTGAAGGTTCTA
AAA
Found at i:66424324 original size:52 final size:53
Alignment explanation
Indices: 66424246--66424383 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 53
66424236 CCATGGCAAT
* * *
66424246 TATAAGACCATAGCTAGACTATGGCATCGGTGTGATGAGA-TA-TGTGCTTCCG
1 TATAAGACTATAGCTAGGCTATGGCATCGGTGAGATGAGATTATTG-GCTTCCG
**
66424298 TATAAGACTATAGCTAGGCTATGGCATCGGTGAGATTTGATTATTGGCTTCCG
1 TATAAGACTATAGCTAGGCTATGGCATCGGTGAGATGAGATTATTGGCTTCCG
* *
66424351 TATAAGACTATATCT-GAGATATGGCATCGGTGA
1 TATAAGACTATAGCTAG-GCTATGGCATCGGTGA
66424384 TATATGTGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
52 36 0.47
53 38 0.50
54 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (53 bp):
TATAAGACTATAGCTAGGCTATGGCATCGGTGAGATGAGATTATTGGCTTCCG
Found at i:66425481 original size:22 final size:20
Alignment explanation
Indices: 66425437--66425475 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66425427 GACTACACGG
*
66425437 CCTACCCACATGGGTGTGTC
1 CCTACCCACACGGGTGTGTC
*
66425457 CCTATCCACACGGGTGTGT
1 CCTACCCACACGGGTGTGT
66425476 GACCCTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (20 bp):
CCTACCCACACGGGTGTGTC
Found at i:66431616 original size:20 final size:19
Alignment explanation
Indices: 66431578--66431634 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
66431568 ATCTTTTGCG
*
66431578 TTTTTTATCTGCTTCTTTCAT
1 TTTTTTATCTGCAT-TTTC-T
*
66431599 TTTTTTATGTGCATTTTCT
1 TTTTTTATCTGCATTTTCT
*
66431618 TTTATTTATTTGCATTT
1 TTT-TTTATCTGCATTT
66431635 AAAAACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 16 0.50
21 12 0.38
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (19 bp):
TTTTTTATCTGCATTTTCT
Found at i:66433661 original size:127 final size:128
Alignment explanation
Indices: 66433392--66433677 Score: 330
Period size: 127 Copynumber: 2.2 Consensus size: 128
66433382 GTTTGGGAAC
* * * * * *
66433392 TCGAGGAATCGTGCCCAACCGTGCTGGGTTTCGATTTTCTGTTTGCCCAAATAATTAAATATTCC
1 TCGAGGAATCGTGCCCTA-CGTGCTGGGTTGCAATTTACCGTTTGCCCAAATAATCAAATATTCC
* * *
66433457 TTTGAAATTTCATCCGTACTTTGAAAATTCCTTAAAACGAAGACAATGTTCGATGTTTAGAAAT
65 TTTGAAATTTCATCCATACTTTCAAAATTCCTTAAAACGAAGACAATGTTCAATGTTTAGAAAT
* * * *
66433521 TCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTACCGTTTGTTCGAAATAATCGAATATTC
1 TCGAGGAATCGTGCCCTA-CGTGCTGGGTTGCAATTTACCGTTTG-CCCAAATAATCAAATATTC
* * *
66433586 CTTT-AGAATTTCA-CTCATATTTTCTAAATT-C-TAAAAC-AAGGCAATGTTCAATGTTTAGAA
64 CTTTGA-AATTTCATC-CATACTTTCAAAATTCCTTAAAACGAAGACAATGTTCAATGTTTAGAA
66433646 AT
127 AT
*
66433648 TTGAGGAATCGTGCCCTACTGTGCTGGGTT
1 TCGAGGAATCGTGCCCTAC-GTGCTGGGTT
66433678 TCAGTTTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
126 1 0.01
127 49 0.37
128 6 0.04
129 41 0.31
130 37 0.28
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (128 bp):
TCGAGGAATCGTGCCCTACGTGCTGGGTTGCAATTTACCGTTTGCCCAAATAATCAAATATTCCT
TTGAAATTTCATCCATACTTTCAAAATTCCTTAAAACGAAGACAATGTTCAATGTTTAGAAAT
Found at i:66435862 original size:55 final size:53
Alignment explanation
Indices: 66435778--66435887 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 53
66435768 TTTGAATAAT
66435778 GTATTGTGAAGCTTCTTATCAACTCAAAGACAGAGTTTATCCTCATCGGCACTGC
1 GTATTGTGAAGCTTCTTATCAACTCAAAGAC--AGTTTATCCTCATCGGCACTGC
66435833 GTATTGTGAAGCTTCTTATCAACTCAAAGACAGTTTATCCTCATCGGCACTGC
1 GTATTGTGAAGCTTCTTATCAACTCAAAGACAGTTTATCCTCATCGGCACTGC
66435886 GT
1 GT
66435888 GTAGTACCGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 24 0.44
55 31 0.56
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (53 bp):
GTATTGTGAAGCTTCTTATCAACTCAAAGACAGTTTATCCTCATCGGCACTGC
Found at i:66439349 original size:20 final size:21
Alignment explanation
Indices: 66439321--66439364 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66439311 AATAATATTC
* *
66439321 TTAATATAA-TTATTTTTATA
1 TTAAAATAATTTATTTTTAAA
66439341 TTAAAATAATTTATTTTTAAA
1 TTAAAATAATTTATTTTTAAA
66439362 TTA
1 TTA
66439365 TATTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAATAATTTATTTTTAAA
Found at i:66450328 original size:2 final size:2
Alignment explanation
Indices: 66450321--66450347 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66450311 GATAATAATA
66450321 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
66450348 AAGATAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66466186 original size:58 final size:58
Alignment explanation
Indices: 66466116--66466230 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
66466106 AACTTTACTT
* * *
66466116 GTTAAATTTAAAAATT-TCATTAACAGTATATTAAATAATCAAAGAAAAATATTTATTC
1 GTTAAATCTAAAAATTCT-ACTAACAATATATTAAATAATCAAAGAAAAATATTTATTC
* * *
66466174 GTTAAATCTAAAAATTCTACTAACAATATATTAAATAATCTAATAAAAATCTTTATT
1 GTTAAATCTAAAAATTCTACTAACAATATATTAAATAATCAAAGAAAAATATTTATT
66466231 AGAAAAAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 49 0.98
59 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (58 bp):
GTTAAATCTAAAAATTCTACTAACAATATATTAAATAATCAAAGAAAAATATTTATTC
Found at i:66467721 original size:21 final size:21
Alignment explanation
Indices: 66467689--66467768 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 21
66467679 GATAATAACG
66467689 AAAAAATAAAAATAAGATAAAT
1 AAAAAAT-AAAATAAGATAAAT
66467711 AAAAAATAAAATAAGCCAATTAAAT
1 AAAAAATAAAATAAG---A-TAAAT
**
66467736 AAAAAGCAATAATAA-ATAAAT
1 AAAAAATAA-AATAAGATAAAT
66467757 AAACAAATAAAA
1 AAA-AAATAAAA
66467769 ACTAAAAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
21 18 0.38
22 12 0.25
24 1 0.02
25 12 0.25
26 5 0.10
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAATAAGATAAAT
Found at i:66467872 original size:15 final size:15
Alignment explanation
Indices: 66467826--66467865 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
66467816 TAAAACAGTT
66467826 TAAAAA-AATAATGA
1 TAAAAATAATAATGA
66467840 TAAAAATAATAATGA
1 TAAAAATAATAATGA
66467855 TAAAAATAATA
1 TAAAAATAATA
66467866 GTAATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
TAAAAATAATAATGA
Found at i:66467897 original size:23 final size:23
Alignment explanation
Indices: 66467839--66467894 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
66467829 AAAAATAATG
* *
66467839 ATAAAAATAATAATGATAAAAATA
1 ATAATAATAAT-ATTATAAAAATA
*
66467863 ATAGTAATAATATTATAAAAAT-
1 ATAATAATAATATTATAAAAATA
66467885 ATAATAATAA
1 ATAATAATAA
66467895 ATAAGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 10 0.36
24 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
ATAATAATAATATTATAAAAATA
Found at i:66467903 original size:22 final size:23
Alignment explanation
Indices: 66467839--66467903 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
66467829 AAAAATAATG
* *
66467839 ATAAAAATAATAATGATAAAAATA
1 ATAATAATAAT-ATAATAAAAATA
* *
66467863 ATAGTAATAATATTATAAAAAT-
1 ATAATAATAATATAATAAAAATA
66467885 ATAATAATAA-ATAAGTAAA
1 ATAATAATAATATAA-TAAA
66467904 TAAAACACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.09
22 13 0.37
23 10 0.29
24 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (23 bp):
ATAATAATAATATAATAAAAATA
Found at i:66469419 original size:20 final size:20
Alignment explanation
Indices: 66469396--66469434 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
66469386 AATTACAAAA
*
66469396 AAAAACTCAAAATAATTTTC
1 AAAAACTCAAAACAATTTTC
* *
66469416 AAAAATTTAAAACAATTTT
1 AAAAACTCAAAACAATTTT
66469435 TTAATTTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAACTCAAAACAATTTTC
Found at i:66470960 original size:17 final size:17
Alignment explanation
Indices: 66470935--66470985 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
66470925 TTGTTGAAGA
66470935 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
* *
66470952 ATCTATTT-G--TTT-A
1 ATCTGTTTGGATTTTGC
66470965 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
66470982 ATCT
1 ATCT
66470986 TTCAACTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
16 4 0.15
17 11 0.42
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (17 bp):
ATCTGTTTGGATTTTGC
Found at i:66472390 original size:13 final size:13
Alignment explanation
Indices: 66472372--66472398 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
66472362 TAATCAAAAC
66472372 TCAATTAATATAG
1 TCAATTAATATAG
66472385 TCAATTAATATAG
1 TCAATTAATATAG
66472398 T
1 T
66472399 TTTTGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TCAATTAATATAG
Found at i:66482532 original size:97 final size:97
Alignment explanation
Indices: 66482431--66482625 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
66482421 TGAAGAAAAG
66482431 AAAAAAAAAATTGTTCATCCTTTTTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAAGGAG
1 AAAAAAAAAATTGTTCATCCTTTTTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAAGGAG
66482496 TTCTTGCTTCATGTTTGGTTTGGAAGAGGATT
66 TTCTTGCTTCATGTTTGGTTTGGAAGAGGATT
*
66482528 AAAAAAAAATTTGTTCATCCTTTTTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAAGGAG
1 AAAAAAAAAATTGTTCATCCTTTTTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAAGGAG
66482593 TTCTTGCTTCATGTTTGGTTTGGAAGAGGATT
66 TTCTTGCTTCATGTTTGGTTTGGAAGAGGATT
66482625 A
1 A
66482626 GGAGGAGGTT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (97 bp):
AAAAAAAAAATTGTTCATCCTTTTTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAAGGAG
TTCTTGCTTCATGTTTGGTTTGGAAGAGGATT
Found at i:66483869 original size:40 final size:40
Alignment explanation
Indices: 66483775--66483919 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
66483765 TACTCGAATG
* *
66483775 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
66483816 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
66483856 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
66483896 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
66483920 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:66484316 original size:59 final size:59
Alignment explanation
Indices: 66484245--66484361 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
66484235 ATCCCTTGCT
*
66484245 CAAAACTTACTAAGCATAAATTGCTTACTCCGTTTCTTTGTTTCTCTGTTTTATAGATA
1 CAAAACTTACTAAGCAAAAATTGCTTACTCCGTTTCTTTGTTTCTCTGTTTTATAGATA
66484304 CAAAACTTACTAAGCAAAAATTGCTTACTCCGTTTCTTTGTTTCTCTGTTTTATAGAT
1 CAAAACTTACTAAGCAAAAATTGCTTACTCCGTTTCTTTGTTTCTCTGTTTTATAGAT
66484362 TTTGGCTCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (59 bp):
CAAAACTTACTAAGCAAAAATTGCTTACTCCGTTTCTTTGTTTCTCTGTTTTATAGATA
Found at i:66491260 original size:40 final size:40
Alignment explanation
Indices: 66491166--66491310 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
66491156 TACTCGAATG
*
66491166 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
66491207 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
66491247 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
66491287 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
66491311 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:66494180 original size:39 final size:40
Alignment explanation
Indices: 66494072--66494256 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
66494062 TCGAATGATG
* * * *
66494072 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
66494112 TCCGGACTAAGAT-CCGAAGACATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
66494152 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
66494191 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
66494232 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
66494257 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:66494238 original size:79 final size:81
Alignment explanation
Indices: 66494073--66494254 Score: 203
Period size: 79 Copynumber: 2.3 Consensus size: 81
66494063 CGAATGATGT
* *
66494073 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGACATTT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGACATTT
*
66494137 GTGCGAGTTACTAATT
66 GTGCGAGTTACTAATA
* * * * ** *
66494153 CTGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGACATT
66494215 TGTGCGAGTTACT-ATAA
65 TGTGCGAGTTACTAAT-A
* *
66494232 CCGGGCTATGTCCCAAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
66494255 TGAACGAGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.04
79 56 0.66
80 26 0.31
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGACATTT
GTGCGAGTTACTAATA
Found at i:66494278 original size:79 final size:79
Alignment explanation
Indices: 66494125--66494289 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
66494115 GGACTAAGAT
* * * * **
66494125 CCGAAGACATTTGTGCGAGTTACTAATTCTGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
*
66494190 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
66494204 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
* *
66494267 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
66494283 CCGAAGG
1 CCGAAGG
66494290 TACGTGATTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:66495810 original size:32 final size:32
Alignment explanation
Indices: 66495761--66495844 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
66495751 TTGAAATTTT
*
66495761 AGTTTGTTGGATTTTGAAATTATCATGTCTTGA
1 AGTTTGTTGGATATTGAAATTATCATGT-TTGA
* * * *
66495794 A-TTTGTTAGATATTGAATTTATTATGTTTTA
1 AGTTTGTTGGATATTGAAATTATCATGTTTGA
*
66495825 AGCTTGTTGGATATTGAAAT
1 AGTTTGTTGGATATTGAAAT
66495845 CATTGACAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 4 0.10
32 37 0.88
33 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (32 bp):
AGTTTGTTGGATATTGAAATTATCATGTTTGA
Found at i:66497306 original size:20 final size:19
Alignment explanation
Indices: 66497262--66497306 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
66497252 TCCAAACACC
*
66497262 AGAAAAGTAAATCATTTCT
1 AGAAAAGTAAATCATTTCG
*
66497281 AAAAAAGTAAATCATTTTCG
1 AGAAAAGTAAATCA-TTTCG
66497301 AGAAAA
1 AGAAAA
66497307 TATTTTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTCG
Found at i:66511131 original size:30 final size:31
Alignment explanation
Indices: 66511066--66511132 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
66511056 GAAATAAAGA
*
66511066 AAGATATGATATGATATTGTGCTAATTAATT
1 AAGATATAATATGATATTGTGCTAATTAATT
66511097 -AGATATAATATGATA-TGT-CTAA-TAATGCT
1 AAGATATAATATGATATTGTGCTAATTAAT--T
66511126 AAGATAT
1 AAGATAT
66511133 TCACTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
29 4 0.12
30 20 0.62
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (31 bp):
AAGATATAATATGATATTGTGCTAATTAATT
Found at i:66515431 original size:31 final size:31
Alignment explanation
Indices: 66515388--66515450 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
66515378 ATAAAATGAC
*
66515388 CACTGAATTATTTGAAAGTTTTCATTTAAGT
1 CACTAAATTATTTGAAAGTTTTCATTTAAGT
* *
66515419 CACTAAATTATTTGAAATTTTTTATTTAAGT
1 CACTAAATTATTTGAAAGTTTTCATTTAAGT
66515450 C
1 C
66515451 GCTGGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (31 bp):
CACTAAATTATTTGAAAGTTTTCATTTAAGT
Found at i:66521645 original size:21 final size:21
Alignment explanation
Indices: 66521621--66521676 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
66521611 AACAGCGGTG
*
66521621 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
66521642 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
66521663 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
66521677 AACAGCGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:66523716 original size:32 final size:32
Alignment explanation
Indices: 66523677--66523836 Score: 266
Period size: 32 Copynumber: 5.0 Consensus size: 32
66523667 CATAAAAAAT
*
66523677 ATCATACATTAGGTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
66523709 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
66523741 ATCATACATTAGGTTCACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
66523773 ATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
66523805 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
66523837 CATAGTTATA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 117 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:66523750 original size:64 final size:64
Alignment explanation
Indices: 66523677--66523836 Score: 293
Period size: 64 Copynumber: 2.5 Consensus size: 64
66523667 CATAAAAAAT
66523677 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
* *
66523741 ATCATACATTAGGTTCACATATAAAAAAGTAGATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
*
66523805 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAG
66523837 CATAGTTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 92 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (64 bp):
ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
Found at i:66529064 original size:18 final size:19
Alignment explanation
Indices: 66529027--66529064 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
66529017 TCATTTACAT
66529027 ACATTTGGGTGCCTACCAA
1 ACATTTGGGTGCCTACCAA
*
66529046 ACATTTGGGT-CCTATCAA
1 ACATTTGGGTGCCTACCAA
66529064 A
1 A
66529065 GGTTGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (19 bp):
ACATTTGGGTGCCTACCAA
Found at i:66530674 original size:16 final size:17
Alignment explanation
Indices: 66530647--66530707 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 17
66530637 AACCGAGCCC
66530647 ATAAATAAAGAATAATT
1 ATAAATAAAGAATAATT
66530664 ATAAA-AAAGAATAATT
1 ATAAATAAAGAATAATT
66530680 ATATTAATAATA-AATAA-T
1 ATA--AATAA-AGAATAATT
66530698 ATAAA-AAAGA
1 ATAAATAAAGA
66530708 TCCAATATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 3 0.08
16 16 0.41
17 5 0.13
18 6 0.15
19 7 0.18
20 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
ATAAATAAAGAATAATT
Found at i:66530765 original size:28 final size:29
Alignment explanation
Indices: 66530733--66530795 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 29
66530723 CTTATATTTG
66530733 TAAAAATTTATAAATAGT-T-TTA-ATAAAA
1 TAAAAATTT-TAAAT-GTATATTATATAAAA
*
66530761 T-AAAATTTTAAATGTATATTATATTAAA
1 TAAAAATTTTAAATGTATATTATATAAAA
66530789 TAAAAAT
1 TAAAAAT
66530796 AAATTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
27 10 0.33
28 7 0.23
29 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
TAAAAATTTTAAATGTATATTATATAAAA
Found at i:66532524 original size:40 final size:40
Alignment explanation
Indices: 66532464--66532555 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
66532454 TACTTTTGTA
* * * *
66532464 CTCCTTATAGCACATTCGTGCT-TCTGTTAGCATTACAGTG
1 CTCCTAATAGCACATCCGTGCTCT-TGTTAACACTACAGTG
*
66532504 CTCCTAATCGCACATCCGTGCTCTTGTTAACACTACAGTG
1 CTCCTAATAGCACATCCGTGCTCTTGTTAACACTACAGTG
* *
66532544 CTCTTGATAGCA
1 CTCCTAATAGCA
66532556 TATTCATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 42 0.98
41 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (40 bp):
CTCCTAATAGCACATCCGTGCTCTTGTTAACACTACAGTG
Found at i:66545292 original size:39 final size:38
Alignment explanation
Indices: 66545225--66545447 Score: 277
Period size: 39 Copynumber: 5.7 Consensus size: 38
66545215 ACAAAGCATG
* ** *
66545225 CGGGACTTTAAGCCCGGATATAATACCAGCACAAACCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAATGCCTT
66545265 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCAC-AATGCCTT
* *
66545305 CGGGGCTTAGCCCGGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCA-CAATGCCTT
* *
66545344 CGGGACTTTA-CCCGAATATAACACCAGCATGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCA-CAATGCCTT
* *
66545383 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCAC-AATGCCTT
66545422 CGGGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
66545448 TTATAAAGTC
Statistics
Matches: 165, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
38 3 0.02
39 140 0.85
40 22 0.13
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (38 bp):
CGGGACTTAGCCCGGATATAACACCAGCACAATGCCTT
Found at i:66545553 original size:28 final size:28
Alignment explanation
Indices: 66545520--66545584 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
66545510 ATTTAATCAT
*
66545520 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTTGCACACTAAGTGACATTC
* *
66545548 TCAATATCTTGCACATTAAGTGACATTC
1 TCAATATTTTGCACACTAAGTGACATTC
66545576 TCAATATTT
1 TCAATATTT
66545585 CGTACACTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (28 bp):
TCAATATTTTGCACACTAAGTGACATTC
Found at i:66551781 original size:39 final size:38
Alignment explanation
Indices: 66551697--66551936 Score: 273
Period size: 39 Copynumber: 6.1 Consensus size: 38
66551687 CAAATCCAAT
* * *
66551697 CACCACCACAAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACAAAGCCTTCGGGAC-TT-AGCCCGGATATAA
* * * *
66551737 TACCAGCACAAACCCTGCGGGACTTTATCCCGGATATAA
1 CACCAGCACAAAGCCTTCGGGAC-TTAGCCCGGATATAA
*
66551776 CACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTAGCCCGGATATAA
* *
66551815 CACCAGCACGAATGCCTTCGGGACTTGGCCCGGATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAA
* * *
66551854 CACCAGCATGAATGCCTTCAGGACTTAGCCCGGATATAA
1 CACCAGCA-CAAAGCCTTCGGGACTTAGCCCGGATATAA
* * *
66551893 CACCAACACGAATGCCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAA
66551932 CACCA
1 CACCA
66551937 TTATAAAGTC
Statistics
Matches: 176, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 144 0.82
40 32 0.18
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (38 bp):
CACCAGCACAAAGCCTTCGGGACTTAGCCCGGATATAA
Found at i:66551847 original size:78 final size:78
Alignment explanation
Indices: 66551724--66551936 Score: 302
Period size: 78 Copynumber: 2.7 Consensus size: 78
66551714 CGGGACTTTA
* ** * *
66551724 AGCCCGGATATAATACCAGCAC-AAACCCTGCGGGACTTTATCCCGGATATAACACCAGCACAAA
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACAAA
* *
66551788 TGCCTTCGGGGCTT
65 TGCCTTCAGGACTT
* **
66551802 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTGGCCCGGATATAACACCAGCATGAAT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
66551867 GCCTTCAGGACTT
66 GCCTTCAGGACTT
* *
66551880 AGCCCGGATATAACACCAACACGAATGCCTTCGAGACTTAGCCCGGATATAACACCA
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA
66551937 TTATAAAGTC
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
78 110 0.91
79 11 0.09
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (78 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACAAAT
GCCTTCAGGACTT
Found at i:66551931 original size:117 final size:117
Alignment explanation
Indices: 66551725--66551936 Score: 309
Period size: 117 Copynumber: 1.8 Consensus size: 117
66551715 GGGACTTTAA
* * * *
66551725 GCCCGGATATAATACCAGCACAAACCCTGCGGGACTTTATCCCGGATATAACACCAGCACAAATG
1 GCCCGGATATAACACCAGCACAAACCCTGCAGGACTTTAGCCCGGATATAACACCAACACAAATG
* *
66551790 CCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTG
66 CCTTCGAGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTG
* ** * *
66551842 GCCCGGATATAACACCAGCATGAATGCCTTCAGGAC-TTAGCCCGGATATAACACCAACACGAAT
1 GCCCGGATATAACACCAGCA-CAAACCCTGCAGGACTTTAGCCCGGATATAACACCAACACAAAT
66551906 GCCTTCGAGACTTAGCCCGGATATAACACCA
65 GCCTTCGAGACTTAGCCCGGATATAACACCA
66551937 TTATAAAGTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
117 73 0.88
118 10 0.12
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (117 bp):
GCCCGGATATAACACCAGCACAAACCCTGCAGGACTTTAGCCCGGATATAACACCAACACAAATG
CCTTCGAGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTG
Found at i:66552042 original size:28 final size:28
Alignment explanation
Indices: 66552009--66552090 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
66551999 ATTTAATCAT
*
66552009 TCAATATTTTGCACACTAAGTGT-CATTC
1 TCAATATTTCGCACACTAAGT-TCCATTC
* *
66552037 TCAATATCTCGCACATTAAGTTCCATTC
1 TCAATATTTCGCACACTAAGTTCCATTC
* * *
66552065 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTTCCAT
66552091 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTTCCATTC
Found at i:66556710 original size:79 final size:83
Alignment explanation
Indices: 66556614--66556874 Score: 208
Period size: 90 Copynumber: 3.0 Consensus size: 83
66556604 CTTTTCTTTT
* * *
66556614 CTTTTTTTTTTGCACTCAATTG-A-GCAC-T-AATGCATCAAAAAGGCCCTCAAACTTATTCGAT
1 CTTTTTTTTTT-CACTCAATTGTATGAACTTAAATGCATCAAAAAGGCCATCAAACTTATTCGAA
* *
66556675 AAAAGTAATTAAGCCATTG
65 AAAAGCAATTAAGCCACTG
*
66556694 CTTTTTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGGCCATCAAACTTC
1 CTTTTTTTTTTCACTCAATT--GTA--TGAAC-TT--AAATGCATCAAAAAGGCCATCAAACTTA
* *
66556759 TTTGAAAAAAGCAATTAAGCCCCTG
59 TTCGAAAAAAGCAATTAAGCCACTG
* * * * *
66556784 CTTTTTTTTTTCATTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCGTCAAATTTT
1 CTTTTTTTTTTCACTCAATT--GTA--TGAAC-TT--AAATGCATCAAAAAGGCCATCAAACTTA
* * *
66556849 TTC-AAAAAAGTAATGAAGCCCCTG
59 TTCGAAAAAAGCAATTAAGCCACTG
66556873 CT
1 CT
66556875 CTTATTAAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
79 9 0.06
80 11 0.07
81 1 0.01
82 1 0.01
85 3 0.02
87 1 0.01
89 21 0.14
90 107 0.69
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34
Consensus pattern (83 bp):
CTTTTTTTTTTCACTCAATTGTATGAACTTAAATGCATCAAAAAGGCCATCAAACTTATTCGAAA
AAAGCAATTAAGCCACTG
Found at i:66556736 original size:90 final size:90
Alignment explanation
Indices: 66556642--66556874 Score: 333
Period size: 90 Copynumber: 2.6 Consensus size: 90
66556632 ATTGAGCACT
* * *
66556642 AATGCATCAAAAAGGCCCTCAAACTTATTCGATAAAAGTAATTAAGCCATTGCTTTTTTTTTTCA
1 AATGCATCAAAAAGGCCATCAAACTTATTCGAAAAAAGTAATTAAGCCACTGCTTTTTTTTTTCA
66556707 CTCAATTGGGTACTTGAACTTTCAA
66 CTCAATTGGGTACTTGAACTTTCAA
* * * *
66556732 AATGCATCAAAAAGGCCATCAAACTTCTTTGAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTTCA
1 AATGCATCAAAAAGGCCATCAAACTTATTCGAAAAAAGTAATTAAGCCACTGCTTTTTTTTTTCA
*
66556797 TTCAATTGGGTACTTGAACTTTCAA
66 CTCAATTGGGTACTTGAACTTTCAA
* * * * * *
66556822 AATGCATCAAAAAGACCGTCAAATTTTTTC-AAAAAAGTAATGAAGCCCCTGCT
1 AATGCATCAAAAAGGCCATCAAACTTATTCGAAAAAAGTAATTAAGCCACTGCT
66556875 CTTATTAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 21 0.16
90 107 0.84
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (90 bp):
AATGCATCAAAAAGGCCATCAAACTTATTCGAAAAAAGTAATTAAGCCACTGCTTTTTTTTTTCA
CTCAATTGGGTACTTGAACTTTCAA
Found at i:66556990 original size:27 final size:28
Alignment explanation
Indices: 66556935--66556992 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
66556925 AATTGTTAAA
*
66556935 TTTTAATAAAAATATAAAAAATAATAAT
1 TTTTAATAAAAATATAAAAAATAAGAAT
66556963 TTTTAATAAAAAT-TAAAAAA-ATAGAAT
1 TTTTAATAAAAATATAAAAAATA-AGAAT
66556990 TTT
1 TTT
66556993 AAAATCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.04
27 14 0.50
28 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TTTTAATAAAAATATAAAAAATAAGAAT
Found at i:66557234 original size:20 final size:22
Alignment explanation
Indices: 66557206--66557250 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
66557196 GAAATTTATA
* *
66557206 TTTCTTTAC-ATTTTGTATAAT
1 TTTCTTTACGACTTTGTAAAAT
66557227 TTTC-TTACGACTTTGTAAAAT
1 TTTCTTTACGACTTTGTAAAAT
66557248 TTT
1 TTT
66557251 ATATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTCTTTACGACTTTGTAAAAT
Found at i:66557274 original size:10 final size:9
Alignment explanation
Indices: 66557246--66557358 Score: 81
Period size: 10 Copynumber: 12.2 Consensus size: 9
66557236 ACTTTGTAAA
66557246 ATTTTATAT
1 ATTTTATAT
66557255 ATTTTATAT
1 ATTTTATAT
66557264 ATTTCTATAT
1 ATTT-TATAT
66557274 ATTTTATAGT
1 ATTTTATA-T
*
66557284 ATTTTA-AG
1 ATTTTATAT
*
66557292 ATTTTTATAAA
1 A-TTTTAT-AT
*
66557303 ATTTTATAAA
1 ATTTTAT-AT
66557313 ATTTTATAT
1 ATTTTATAT
66557322 -TTTT-TACT
1 ATTTTATA-T
66557330 ATTATTATAT
1 ATT-TTATAT
* *
66557340 TTTTTCTAT
1 ATTTTATAT
*
66557349 TTTTTA-AT
1 ATTTTATAT
66557357 AT
1 AT
66557359 CTAAATTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
7 2 0.02
8 9 0.10
9 36 0.41
10 37 0.42
11 4 0.05
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTATAT
Found at i:66557274 original size:19 final size:19
Alignment explanation
Indices: 66557246--66557320 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
66557236 ACTTTGTAAA
66557246 ATTTTATATATTTTATA-T
1 ATTTTATATATTTTATAGT
66557264 ATTTCTATATATTTTATAGT
1 ATTT-TATATATTTTATAGT
* **
66557284 ATTTTA-AGATTTTTATAAA
1 ATTTTATATA-TTTTATAGT
*
66557303 ATTTTATAAAATTTTATA
1 ATTTTAT-ATATTTTATA
66557321 TTTTTTACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.12
19 28 0.58
20 12 0.25
21 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTATATATTTTATAGT
Found at i:66557342 original size:17 final size:18
Alignment explanation
Indices: 66557316--66557349 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
66557306 TTATAAAATT
66557316 TTATATTTTTTACTATTA
1 TTATATTTTTTACTATTA
66557334 TTATATTTTTT-CTATT
1 TTATATTTTTTACTATT
66557350 TTTTAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTTTTACTATTA
Found at i:66559530 original size:46 final size:46
Alignment explanation
Indices: 66559478--66559653 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
66559468 TGGTTGAGCA
*
66559478 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
66559524 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
66559569 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
66559617 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66559654 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:66559634 original size:93 final size:93
Alignment explanation
Indices: 66559475--66559645 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
66559465 GGATGGTTGA
* * **
66559475 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66559540 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
66559568 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
66559633 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
66559646 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:66561980 original size:40 final size:39
Alignment explanation
Indices: 66561826--66561982 Score: 235
Period size: 40 Copynumber: 4.0 Consensus size: 39
66561816 TTGATTCCAC
* * * *
66561826 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
*
66561865 T-CCCCATACTATTTTGTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
*
66561903 TCTCCCATACTATTTTGTTTTCATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTGTTTT-ATTATTAATTAAAACCAT
66561943 TCCCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
66561983 ACTTTATTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
38 35 0.32
39 19 0.17
40 51 0.47
41 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (39 bp):
TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
Found at i:66563097 original size:13 final size:13
Alignment explanation
Indices: 66563079--66563103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66563069 GAGTTTTGAG
66563079 TTCTTCGATCTGC
1 TTCTTCGATCTGC
66563092 TTCTTCGATCTG
1 TTCTTCGATCTG
66563104 TTCCCTATAA
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:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (13 bp):
TTCTTCGATCTGC
Found at i:66563150 original size:44 final size:43
Alignment explanation
Indices: 66563086--66563171 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 43
66563076 GAGTTCTTCG
*
66563086 ATCTGCTTCTTCGATCTGTTCCCTATAAACACAAGGATGCCAA
1 ATCTGCTTCTTCAATCTGTTCCCTATAAACACAAGGATGCCAA
*
66563129 ATCTGCTATCTTCAA-CTTGTTCCCTATAAACACAGGGATGCCA
1 ATCTGCT-TCTTCAATC-TGTTCCCTATAAACACAAGGATGCCA
66563172 TGCTGAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 8 0.21
44 31 0.79
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (43 bp):
ATCTGCTTCTTCAATCTGTTCCCTATAAACACAAGGATGCCAA
Found at i:66563621 original size:205 final size:205
Alignment explanation
Indices: 66563269--66563850 Score: 990
Period size: 205 Copynumber: 2.8 Consensus size: 205
66563259 AAATCTATTT
* * *
66563269 CTTCGATTTGTTCCCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCATAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
*
66563334 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATTCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66563399 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
66563464 AGATGCCAAA
196 AGATGCCAAA
*
66563474 CTTCGATTCGTTCTTTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
66563539 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66563604 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
*
66563669 AGATGGCAAA
196 AGATGCCAAA
* * *
66563679 CTTCGATTCATTCTCTAACGATACAGAGACGACAAATCATCTTAGATTTGC-TCCATCGTAATCA
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTC-TCGTAATCA
* *
66563743 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACTATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
* * * *
66563808 TGGGTCTGCTTCAGT-ATAA-CATTTGAAGGCCAGATCTGTTATG
130 TGGATCTGCTTCAGTGA-AATCATCTGAAGGCGAGATCTGCTATG
66563851 CTGCGGCCTA
Statistics
Matches: 359, Mismatches: 16, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
204 24 0.07
205 335 0.93
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
AGATGCCAAA
Found at i:66571800 original size:13 final size:15
Alignment explanation
Indices: 66571770--66571800 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
66571760 TTCCAGATTT
66571770 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
66571785 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
66571800 T
1 T
66571801 GGAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:66571886 original size:15 final size:14
Alignment explanation
Indices: 66571844--66571893 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
66571834 ATAACTTTGA
*
66571844 ATGCAAATGATGTG
1 ATGCAAATGATGAG
66571858 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
66571873 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
66571887 ATGCAAA
1 ATGCAAA
66571894 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:66576335 original size:39 final size:39
Alignment explanation
Indices: 66576277--66576432 Score: 231
Period size: 39 Copynumber: 3.9 Consensus size: 39
66576267 AGTTGATTCC
** *
66576277 ACTCCCCCATGTTACTTTGTTTTATTATTAATTAAAACT
1 ACTCCCCCATACTATTTTGTTTTATTATTAATTAAAACT
*
66576316 ACTCCCCCATACTATTTTGTTTTATTATTAATTAAAATT
1 ACTCCCCCATACTATTTTGTTTTATTATTAATTAAAACT
* *
66576355 ATTCCCCCATATTATTTTGTTTTCATTATTAATTAAAACT
1 ACTCCCCCATACTATTTTGTTTT-ATTATTAATTAAAACT
*
66576395 ATTCCCCCATACTATTTTGTTTTTATTATTAATTAAAA
1 ACTCCCCCATACTATTTTG-TTTTATTATTAATTAAAA
66576433 ACATACTTTA
Statistics
Matches: 107, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
39 56 0.52
40 47 0.44
41 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (39 bp):
ACTCCCCCATACTATTTTGTTTTATTATTAATTAAAACT
Found at i:66576398 original size:40 final size:39
Alignment explanation
Indices: 66576292--66576432 Score: 237
Period size: 40 Copynumber: 3.6 Consensus size: 39
66576282 CCCATGTTAC
*
66576292 TTTGTTTTATTATTAATTAAAACTACTCCCCCATACTAT
1 TTTGTTTTATTATTAATTAAAACTATTCCCCCATACTAT
* *
66576331 TTTGTTTTATTATTAATTAAAATTATTCCCCCATATTAT
1 TTTGTTTTATTATTAATTAAAACTATTCCCCCATACTAT
66576370 TTTGTTTTCATTATTAATTAAAACTATTCCCCCATACTAT
1 TTTGTTTT-ATTATTAATTAAAACTATTCCCCCATACTAT
66576410 TTTGTTTTTATTATTAATTAAAA
1 TTTG-TTTTATTATTAATTAAAA
66576433 ACATACTTTA
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 44 0.46
40 47 0.49
41 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (39 bp):
TTTGTTTTATTATTAATTAAAACTATTCCCCCATACTAT
Found at i:66576407 original size:79 final size:79
Alignment explanation
Indices: 66576279--66576432 Score: 265
Period size: 79 Copynumber: 1.9 Consensus size: 79
66576269 TTGATTCCAC
*
66576279 TCCCCCATGTTACTTTGTTTTATTATTAATTAAAACTACTCCCCCATACTATTTTG-TTTTATTA
1 TCCCCCATATTACTTTGTTTTATTATTAATTAAAACTACTCCCCCATACTATTTTGTTTTTATTA
66576343 TTAATTAAAATTAT
66 TTAATTAAAATTAT
* *
66576357 TCCCCCATATTATTTTGTTTTCATTATTAATTAAAACTATTCCCCCATACTATTTTGTTTTTATT
1 TCCCCCATATTACTTTGTTTT-ATTATTAATTAAAACTACTCCCCCATACTATTTTGTTTTTATT
66576422 ATTAATTAAAA
65 ATTAATTAAAA
66576433 ACATACTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 19 0.27
79 34 0.48
80 18 0.25
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (79 bp):
TCCCCCATATTACTTTGTTTTATTATTAATTAAAACTACTCCCCCATACTATTTTGTTTTTATTA
TTAATTAAAATTAT
Found at i:66576608 original size:12 final size:12
Alignment explanation
Indices: 66576591--66576623 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
66576581 TTCCCCTCCT
66576591 CCGGTCATCGGA
1 CCGGTCATCGGA
66576603 CCGGTCATCGGA
1 CCGGTCATCGGA
*
66576615 CCGGCCATC
1 CCGGTCATC
66576624 AACCGTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.39, G:0.30, T:0.15
Consensus pattern (12 bp):
CCGGTCATCGGA
Found at i:66579012 original size:18 final size:18
Alignment explanation
Indices: 66578947--66579061 Score: 97
Period size: 18 Copynumber: 6.3 Consensus size: 18
66578937 AGCAATTAAT
*
66578947 CAATCAGTAATATTCATTAA
1 CAATCAGT--TATTCAGTAA
* *
66578967 CAATCAGTCAATCAG-AA
1 CAATCAGTTATTCAGTAA
* *
66578984 CAATTATTTATTCAGTAA
1 CAATCAGTTATTCAGTAA
* *
66579002 CAGTCAGTTATTCGGTAA
1 CAATCAGTTATTCAGTAA
* *
66579020 CAATCAATTATTCAATAA
1 CAATCAGTTATTCAGTAA
* * *
66579038 TAATCAGTTATTTAGTAT
1 CAATCAGTTATTCAGTAA
66579056 CAATCA
1 CAATCA
66579062 ATTGATCGAT
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
17 13 0.18
18 52 0.71
20 8 0.11
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (18 bp):
CAATCAGTTATTCAGTAA
Found at i:66579031 original size:36 final size:36
Alignment explanation
Indices: 66578957--66579064 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
66578947 CAATCAGTAA
* * * * *
66578957 TATTCATTAACAATCAGTCAATCAG-AACAATTATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * *
66578992 TATTCAGTAACAGTCAGTTATTCGGTAACAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * *
66579028 TATTCAATAATAATCAGTTATTTAGTATCAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
66579064 T
1 T
66579065 GATCGATTAT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 20 0.34
36 39 0.66
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (36 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
Found at i:66579097 original size:18 final size:18
Alignment explanation
Indices: 66579070--66579141 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
66579060 CAATTGATCG
*
66579070 ATTATCCAGTAACAGTCA
1 ATTATTCAGTAACAGTCA
* *
66579088 ATTATTCAGTAAAAATCA
1 ATTATTCAGTAACAGTCA
* * *
66579106 GA-TATACAGTAACAATTAA
1 -ATTATTCAGTAAC-AGTCA
*
66579125 ATTATTCAGTAATAGTC
1 ATTATTCAGTAACAGTC
66579142 GATCTTTCCA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
18 27 0.68
19 13 0.32
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (18 bp):
ATTATTCAGTAACAGTCA
Found at i:66579136 original size:19 final size:19
Alignment explanation
Indices: 66579087--66579136 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
66579077 AGTAACAGTC
66579087 AATTATTCAGTAAAAATCA
1 AATTATTCAGTAAAAATCA
* * * *
66579106 GA-TATACAGTAACAATTA
1 AATTATTCAGTAAAAATCA
66579124 AATTATTCAGTAA
1 AATTATTCAGTAA
66579137 TAGTCGATCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTATTCAGTAAAAATCA
Found at i:66583700 original size:24 final size:24
Alignment explanation
Indices: 66583673--66583726 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
66583663 ATGAGATATT
* *
66583673 GACCTTTACGTTGATATCCTTTTC
1 GACCTTTACATTGATATCATTTTC
* *
66583697 GACCTTTTCATTTATATCATTTTC
1 GACCTTTACATTGATATCATTTTC
*
66583721 AACCTT
1 GACCTT
66583727 CTTTGATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.48
Consensus pattern (24 bp):
GACCTTTACATTGATATCATTTTC
Found at i:66583943 original size:40 final size:40
Alignment explanation
Indices: 66583895--66584064 Score: 154
Period size: 40 Copynumber: 4.3 Consensus size: 40
66583885 GCGTCCAGTG
*
66583895 CTAGTCGGATAAATTGACAATATCAAATGTGTGCCCAACA
1 CTAGTCGGATAAACTGACAATATCAAATGTGTGCCCAACA
** *
66583935 CTAGTCGGATAAACTGATGATATCAAATGTGTGCCCAGCA
1 CTAGTCGGATAAACTGACAATATCAAATGTGTGCCCAACA
* ** ** * * *
66583975 CTAGTTGGATAAACCAACAATGAT----T-TGAACCTAGCG
1 CTAGTCGGATAAACTGACAAT-ATCAAATGTGTGCCCAACA
*
66584011 CTAGTCGGATAAACCGACAATATCAAATGTGTGCCCAGA-A
1 CTAGTCGGATAAACTGACAATATCAAATGTGTGCCCA-ACA
*
66584051 CTAGTCAGATAAAC
1 CTAGTCGGATAAAC
66584065 CGAAAATGAT
Statistics
Matches: 102, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
35 2 0.02
36 26 0.25
37 1 0.01
39 1 0.01
40 70 0.69
41 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (40 bp):
CTAGTCGGATAAACTGACAATATCAAATGTGTGCCCAACA
Found at i:66583986 original size:116 final size:116
Alignment explanation
Indices: 66583847--66584064 Score: 300
Period size: 116 Copynumber: 1.9 Consensus size: 116
66583837 CCGACGATAG
* ** * **
66583847 GTGTGCCCTACACTAGTTAGATAAACCGACAAT-ATTTTGCGTCC-AGTGCTAGTCGGATAAATT
1 GTGTGCCCTACACTAGTTAGATAAACCAACAATGA-TTTG-AACCTAGCGCTAGTCGGATAAACC
*
66583910 GACAATATCAAATGTGTGCCCA-ACACTAGTCGGATAAACTGATGATATCAAAT
64 GACAATATCAAATGTGTGCCCAGA-ACTAGTCAGATAAACTGATGATATCAAAT
*
66583963 GTGTGCCC-AGCACTAGTTGGATAAACCAACAATGATTTGAACCTAGCGCTAGTCGGATAAACCG
1 GTGTGCCCTA-CACTAGTTAGATAAACCAACAATGATTTGAACCTAGCGCTAGTCGGATAAACCG
66584027 ACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAAC
65 ACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAAC
66584065 CGAAAATGAT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
115 3 0.03
116 85 0.94
117 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (116 bp):
GTGTGCCCTACACTAGTTAGATAAACCAACAATGATTTGAACCTAGCGCTAGTCGGATAAACCGA
CAATATCAAATGTGTGCCCAGAACTAGTCAGATAAACTGATGATATCAAAT
Found at i:66584020 original size:76 final size:76
Alignment explanation
Indices: 66583928--66584106 Score: 225
Period size: 76 Copynumber: 2.4 Consensus size: 76
66583918 CAAATGTGTG
* * ** * **
66583928 CCCAACACTAGTCGGATAAACTGATGATATCAAATGTGTGCCCAGCACTAGTTGGATAAACC-AA
1 CCCAACGCTAGTCGGATAAACCGACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAACCGAA
66583992 CAATGATTTGAA
66 -AATGATTTGAA
* *
66584004 CCTAGCGCTAGTCGGATAAACCGACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAACCGAA
1 CCCAACGCTAGTCGGATAAACCGACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAACCGAA
*
66584069 AATGATTTGCA
66 AATGATTTGAA
* * *
66584080 CCCAATGCTAGTTGGATAAACCAACAA
1 CCCAACGCTAGTCGGATAAACCGACAA
66584107 ATACATACGT
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 85 0.98
77 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (76 bp):
CCCAACGCTAGTCGGATAAACCGACAATATCAAATGTGTGCCCAGAACTAGTCAGATAAACCGAA
AATGATTTGAA
Found at i:66585774 original size:20 final size:20
Alignment explanation
Indices: 66585751--66585814 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
66585741 CTGCACATTT
66585751 GTGCTTTTGTTAGCACTATG
1 GTGCTTTTGTTAGCACTATG
** * *
66585771 GTGCTCCT-ATAGCAC-ATTT
1 GTGCTTTTGTTAGCACTA-TG
*
66585790 GTGCTTTTGTTGGCACTATG
1 GTGCTTTTGTTAGCACTATG
66585810 GTGCT
1 GTGCT
66585815 CCTATAGCAC
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 17 0.53
21 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
GTGCTTTTGTTAGCACTATG
Found at i:66585785 original size:19 final size:19
Alignment explanation
Indices: 66585761--66585824 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
66585751 GTGCTTTTGT
66585761 TAGCACTATGGTGCTCCTA
1 TAGCACTATGGTGCTCCTA
* ** *
66585780 TAGCAC-ATTTGTGCTTTTGT
1 TAGCACTA-TGGTGCTCCT-A
*
66585800 TGGCACTATGGTGCTCCTA
1 TAGCACTATGGTGCTCCTA
66585819 TAGCAC
1 TAGCAC
66585825 ATTTGTACTC
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 12 0.38
21 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (19 bp):
TAGCACTATGGTGCTCCTA
Done.