Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 144 of 168
Found at i:42364208 original size:12 final size:13
Alignment explanation
Indices: 42364177--42364210 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
42364167 TTTTCATATA
42364177 TTTATTTTTCAGTT
1 TTTATTTTTCAG-T
42364191 TTTATTTTTCAG-
1 TTTATTTTTCAGT
42364203 TTTATTTT
1 TTTATTTT
42364211 GCTCATTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
14 12 0.60
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTATTTTTCAGT
Found at i:42364584 original size:7 final size:7
Alignment explanation
Indices: 42364572--42364600 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
42364562 ATGACTATAT
42364572 TAAATTA
1 TAAATTA
42364579 TAAATTA
1 TAAATTA
42364586 TAAATTA
1 TAAATTA
42364593 -AAATTA
1 TAAATTA
42364599 TA
1 TA
42364601 TACAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAATTA
Found at i:42364598 original size:13 final size:14
Alignment explanation
Indices: 42364572--42364600 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42364562 ATGACTATAT
42364572 TAAATTATAAATTA
1 TAAATTATAAATTA
42364586 TAAATTA-AAATTA
1 TAAATTATAAATTA
42364599 TA
1 TA
42364601 TACAACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTATAAATTA
Found at i:42377308 original size:116 final size:116
Alignment explanation
Indices: 42377104--42377329 Score: 452
Period size: 116 Copynumber: 1.9 Consensus size: 116
42377094 AGCAACAAAC
42377104 TGTTGCTCAGTCTACTGCTGAAGCTGAATACATAGCAGCAGCTGCAGCAGTGAATCAAGCTATTT
1 TGTTGCTCAGTCTACTGCTGAAGCTGAATACATAGCAGCAGCTGCAGCAGTGAATCAAGCTATTT
42377169 GGCTTAGGAAGTTGCTATGTGATATGAATGAAGAACAGCTTGAGCAACAGT
66 GGCTTAGGAAGTTGCTATGTGATATGAATGAAGAACAGCTTGAGCAACAGT
42377220 TGTTGCTCAGTCTACTGCTGAAGCTGAATACATAGCAGCAGCTGCAGCAGTGAATCAAGCTATTT
1 TGTTGCTCAGTCTACTGCTGAAGCTGAATACATAGCAGCAGCTGCAGCAGTGAATCAAGCTATTT
42377285 GGCTTAGGAAGTTGCTATGTGATATGAATGAAGAACAGCTTGAGC
66 GGCTTAGGAAGTTGCTATGTGATATGAATGAAGAACAGCTTGAGC
42377330 CTACTGAAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (116 bp):
TGTTGCTCAGTCTACTGCTGAAGCTGAATACATAGCAGCAGCTGCAGCAGTGAATCAAGCTATTT
GGCTTAGGAAGTTGCTATGTGATATGAATGAAGAACAGCTTGAGCAACAGT
Found at i:42379219 original size:93 final size:95
Alignment explanation
Indices: 42379078--42379347 Score: 321
Period size: 99 Copynumber: 2.8 Consensus size: 95
42379068 TTTTTTTCAT
* *
42379078 GCCATTTACAGGTCAGCACCCAAATTTTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGAC
1 GCCATTGACAGGCCAGCA-CCAAA--TTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGAC
******
42379143 ACAAA-TTTTTTTTTAAATTGTACTGGGTGCCA
63 ACAAAGAAAAAATTTAAATTGTACTGGGTGCCA
42379175 GCCATTGACAGGCCAGCACCAGAATTTTTTTA-TTTTTT-GTATACTGATATCTGATTCTGACAC
1 GCCATTGACAGGCCAGCACCA-AATTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACAC
*
42379238 GAAAAAAGGAAAAAATTTAAATTGTACTGGGTGCCG
65 ----AAA-GAAAAAATTTAAATTGTACTGGGTGCCA
* * *
42379274 GCCATTGACAGGCCAACACCAAAATTTTTTTATTTTTTTCGTATACCGATATCTGACTCTGACAC
1 GCCATTGACAGGCCAGCACC-AAATTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACAC
42379339 AAAGAAAAA
65 AAAGAAAAA
42379348 GAATTTTTTT
Statistics
Matches: 151, Mismatches: 12, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
93 25 0.17
94 6 0.04
95 8 0.05
96 9 0.06
97 24 0.16
99 49 0.32
100 7 0.05
101 23 0.15
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (95 bp):
GCCATTGACAGGCCAGCACCAAATTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACA
AAGAAAAAATTTAAATTGTACTGGGTGCCA
Found at i:42379383 original size:107 final size:102
Alignment explanation
Indices: 42379146--42379416 Score: 343
Period size: 99 Copynumber: 2.6 Consensus size: 102
42379136 TTCTGACACA
* *
42379146 AATTTTTTTTTAAATTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCAGAATTTTTTTA-TTT
1 AATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTATTTT
* * * *
42379210 TTTGTATACTGATATCTGATTCTGACACGAAAAAAGG
66 TTTGTATACCGATATCTGACTCTGACACAAAAAAAAG
**** *
42379247 AA--AAAATTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTATTTT
1 AATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTATTTT
42379310 TTTCGTATACCGATATCTGACTCTGACACAAAGAAAAAG
66 TTT-GTATACCGATATCTGACTCTGACACAAA-AAAAAG
* *
42379349 AATTTTTTTTTAAAAAATTGTACTGGGTTCCGGCCATTGACAGACCAGCACCCAAAATTTTTTT-
1 AATTTTTTTTT---AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAATTTTTTTA
42379413 TTTT
62 TTTT
42379417 CTTTTTTCTT
Statistics
Matches: 143, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
99 50 0.35
100 6 0.04
101 27 0.19
102 7 0.05
104 3 0.02
107 37 0.26
108 13 0.09
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (102 bp):
AATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTATTTT
TTTGTATACCGATATCTGACTCTGACACAAAAAAAAG
Found at i:42379440 original size:18 final size:18
Alignment explanation
Indices: 42379407--42379442 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42379397 CACCCAAAAT
* *
42379407 TTTTTTTTTTCTTTTTTC
1 TTTTTTTTTCCCTTTTTC
42379425 TTTTTTTTTCCCTTTTTC
1 TTTTTTTTTCCCTTTTTC
42379443 ATATATCAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTCCCTTTTTC
Found at i:42383144 original size:15 final size:15
Alignment explanation
Indices: 42383121--42383163 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42383111 TAATTGTGAT
*
42383121 TAAGATTTAATTAAC
1 TAAGGTTTAATTAAC
* *
42383136 TAAGGTTTAACTAAT
1 TAAGGTTTAATTAAC
42383151 TAAGG-TTAATTAA
1 TAAGGTTTAATTAA
42383164 GGTTTAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (15 bp):
TAAGGTTTAATTAAC
Found at i:42385839 original size:43 final size:43
Alignment explanation
Indices: 42385778--42385950 Score: 183
Period size: 43 Copynumber: 4.1 Consensus size: 43
42385768 CATATAATTT
* * *
42385778 TCGATATGTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * * * *
42385821 TCGATTTGTGTTTACGTGTAAGACCATGTCTGGGACATCGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
42385864 TCG-TATTTGATT-CGTGTAAGACC-CTGCCTGGGACAG-TGGCA
1 TCGATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* * *
42385905 TTGATATATGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
42385948 TCG
1 TCG
42385951 TACGAGTTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 25 0.24
42 15 0.14
43 65 0.61
44 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:42391071 original size:16 final size:16
Alignment explanation
Indices: 42391029--42391074 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42391019 AACTAAAACC
*
42391029 TTGTTCTGAAC-ATAG
1 TTGTTCTGAACAACAG
*
42391044 TTATTCTCGAACAACAG
1 TTGTTCT-GAACAACAG
42391061 TTGTTCTGAACAAC
1 TTGTTCTGAACAAC
42391075 TATTCTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.23
16 11 0.42
17 9 0.35
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (16 bp):
TTGTTCTGAACAACAG
Found at i:42392928 original size:9 final size:9
Alignment explanation
Indices: 42392914--42392944 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42392904 GTTAAACGAA
42392914 TCGAGTTAT
1 TCGAGTTAT
*
42392923 TCGAGTTAA
1 TCGAGTTAT
42392932 TCGAGTTAT
1 TCGAGTTAT
42392941 TCGA
1 TCGA
42392945 ATCAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42393022 original size:9 final size:9
Alignment explanation
Indices: 42392998--42393034 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42392988 TGAGTTTTCG
*
42392998 AATTCAAAT
1 AATTCGAAT
*
42393007 AACTCGAAT
1 AATTCGAAT
42393016 AATTCGAAT
1 AATTCGAAT
42393025 AATTCGAAT
1 AATTCGAAT
42393034 A
1 A
42393035 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42393284 original size:30 final size:31
Alignment explanation
Indices: 42393248--42393307 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
42393238 AAACTTTTTA
**
42393248 TTTTCCCCTAAAGTTTTTACTCCC-TCCCAC
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
*
42393278 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
42393308 TCCCACCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.18, C:0.38, G:0.02, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:42394627 original size:3 final size:3
Alignment explanation
Indices: 42394619--42394698 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
42394609 TGTATCATGC
*
42394619 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42394667 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42394699 AGGAAATGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42407313 original size:16 final size:16
Alignment explanation
Indices: 42407284--42407337 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
42407274 TTTGGTTCGC
* *
42407284 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
42407300 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
42407316 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
42407332 TGTAAT
1 TGTAAT
42407338 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:42407382 original size:45 final size:44
Alignment explanation
Indices: 42407316--42407406 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
42407306 GGAATAGAGG
*
42407316 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
42407361 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
42407405 TG
1 TG
42407407 GAATAGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:42407591 original size:18 final size:17
Alignment explanation
Indices: 42407570--42407604 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42407560 TTATTATTAA
*
42407570 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42407588 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42407605 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42407767 original size:119 final size:120
Alignment explanation
Indices: 42407550--42407836 Score: 470
Period size: 119 Copynumber: 2.4 Consensus size: 120
42407540 TTAATCATAT
42407550 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
42407615 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
42407669 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
42407733 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
42407789 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA
42407837 TCATCATACT
Statistics
Matches: 154, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
119 103 0.67
120 51 0.33
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:42407782 original size:61 final size:60
Alignment explanation
Indices: 42407585--42407784 Score: 146
Period size: 61 Copynumber: 3.3 Consensus size: 60
42407575 TTTTAATTAA
* * * *
42407585 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCT-AAATCAT
* * * * * * * *
42407646 AATATATGATACT-AT-AAA-T-ATAAT-TTGAAATAAT-TAATATTAAATATATT-TTAATTAA
1 AATATATAAT-CTAATAAAATTCTTAATATT-AAATATTCTTATA-TGAAT-T-TTCTAAATCAT
* *
42407704 AATATATGATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCT-AAATCAT
42407765 AATATATAATACT-ATAAAAT
1 AATATATAAT-CTAATAAAAT
42407785 ATAATTTAAC
Statistics
Matches: 103, Mismatches: 22, Indels: 28
0.67 0.14 0.18
Matches are distributed among these distances:
57 6 0.06
58 29 0.28
59 8 0.08
60 7 0.07
61 45 0.44
62 8 0.08
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAATCAT
Found at i:42418965 original size:3 final size:3
Alignment explanation
Indices: 42418957--42418983 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42418947 AGACCAGTGT
42418957 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
42418984 AATCCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42419128 original size:3 final size:3
Alignment explanation
Indices: 42419120--42419157 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42419110 AAGAACTTCA
42419120 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
42419158 AACAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42429230 original size:13 final size:14
Alignment explanation
Indices: 42429207--42429237 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
42429197 GTTAGGAATC
42429207 TAATAATAATTAAA
1 TAATAATAATTAAA
42429221 TAAT-ATAATTAAA
1 TAATAATAATTAAA
42429234 TAAT
1 TAAT
42429238 GGATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAATAATTAAA
Found at i:42434634 original size:29 final size:29
Alignment explanation
Indices: 42434592--42434651 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
42434582 AATTCCAAAT
42434592 AGATTATACATTTATGGTGGGTTCTTTAA
1 AGATTATACATTTATGGTGGGTTCTTTAA
42434621 AGATTATACATTTATGGTGGGTTCTTTAA
1 AGATTATACATTTATGGTGGGTTCTTTAA
42434650 AG
1 AG
42434652 GGCTCCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (29 bp):
AGATTATACATTTATGGTGGGTTCTTTAA
Found at i:42437568 original size:36 final size:36
Alignment explanation
Indices: 42437521--42437590 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
42437511 GTACCTAAAT
*
42437521 TATACCCTTTTCCTTAAGTTGGCATCTCCGTTAAGC
1 TATACCATTTTCCTTAAGTTGGCATCTCCGTTAAGC
42437557 TATACCATTTTCCTTAAGTTGGCATCTCCGTTAA
1 TATACCATTTTCCTTAAGTTGGCATCTCCGTTAA
42437591 TCCAACTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (36 bp):
TATACCATTTTCCTTAAGTTGGCATCTCCGTTAAGC
Found at i:42439197 original size:30 final size:30
Alignment explanation
Indices: 42439158--42439214 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
42439148 TTTTATAAAT
42439158 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
42439188 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
42439215 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:42439405 original size:13 final size:13
Alignment explanation
Indices: 42439389--42439439 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
42439379 TTTAAACTAA
42439389 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
42439402 ACTTCTCAAAAGT
1 ACTTTTCAAAAGT
* * *
42439415 ACTTTTCCACAGC
1 ACTTTTCAAAAGT
42439428 ACTTTTCAAAAG
1 ACTTTTCAAAAG
42439440 CAATGAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:42447897 original size:21 final size:21
Alignment explanation
Indices: 42447867--42447906 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42447857 CCATGTATAA
*
42447867 TTGATGAGTTATAAGATTGTG
1 TTGATAAGTTATAAGATTGTG
42447888 TTGATAAGTTATAAGATTG
1 TTGATAAGTTATAAGATTG
42447907 ATAGCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (21 bp):
TTGATAAGTTATAAGATTGTG
Found at i:42447915 original size:21 final size:21
Alignment explanation
Indices: 42447873--42447915 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42447863 ATAATTGATG
* *
42447873 AGTTATAAGATTGTGTTGATA
1 AGTTATAAGATTGTATAGATA
42447894 AGTTATAAGATTG-ATAGCATA
1 AGTTATAAGATTGTATAG-ATA
42447915 A
1 A
42447916 ATTTTTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (21 bp):
AGTTATAAGATTGTATAGATA
Found at i:42448339 original size:2 final size:2
Alignment explanation
Indices: 42448332--42448362 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
42448322 TTTTGGTTAC
*
42448332 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42448363 TACATGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42451457 original size:83 final size:82
Alignment explanation
Indices: 42451360--42451524 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 82
42451350 GAGACCAAAT
* * * * * **
42451360 TATGTTAGAGATTAAATTATAAGGATTAAAAATCTCAAATTTAAGCATATT-GATTGACCAAAAC
1 TATGTTAGAAATTAAAATATAAGGATT--AAATATCAAATTTAAACATATTAAAAAGACCAAAAC
*
42451424 TGAAAATTAACCACTTTTA
64 TAAAAATTAACCACTTTTA
*
42451443 TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAAAAAGACCAAAATTA
1 TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAAAAAGACCAAAACTA
42451508 AAAATTAACCACTTTTA
66 AAAATTAACCACTTTTA
42451525 CAAAATGTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.28
82 27 0.38
83 25 0.35
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (82 bp):
TATGTTAGAAATTAAAATATAAGGATTAAATATCAAATTTAAACATATTAAAAAGACCAAAACTA
AAAATTAACCACTTTTA
Found at i:42451754 original size:29 final size:29
Alignment explanation
Indices: 42451714--42451773 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
42451704 TAGTAATGAT
** *
42451714 AAAATTGTATTTTGTCTTCTAAAATTATA
1 AAAATTGTATTTAATATTCTAAAATTATA
*
42451743 AAAATT-TGATTTAATATTTTAAAATTATA
1 AAAATTGT-ATTTAATATTCTAAAATTATA
42451772 AA
1 AA
42451774 GATATAGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (29 bp):
AAAATTGTATTTAATATTCTAAAATTATA
Found at i:42454003 original size:30 final size:30
Alignment explanation
Indices: 42453969--42454031 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
42453959 ATTTATTTGT
* *
42453969 TTTTACTATCACTGTATATAT-GATTTTTAA
1 TTTTA-TATAACTGTATATATAAATTTTTAA
* *
42453999 TTTTATATAATTTTATATATAAATTTTTAA
1 TTTTATATAACTGTATATATAAATTTTTAA
42454029 TTT
1 TTT
42454032 GATTCAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTATATAACTGTATATATAAATTTTTAA
Found at i:42454950 original size:20 final size:19
Alignment explanation
Indices: 42454927--42454968 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
42454917 TGGTATCGTA
42454927 TTTAAATT-TCTATTATTTCT
1 TTTAAATTATCT-TT-TTTCT
*
42454947 TTTAAGTTATCTTTTTTCT
1 TTTAAATTATCTTTTTTCT
42454966 TTT
1 TTT
42454969 TGGTATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTAAATTATCTTTTTTCT
Found at i:42466926 original size:27 final size:27
Alignment explanation
Indices: 42466876--42466937 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
42466866 CCACTCTCCC
* *
42466876 TATAATTTAATTATAAATGAATTTTTG
1 TATAATTTAATTATAAATCAATTTTTA
* *
42466903 TTTAATTTAATTTTAAA-CATATTTTTA
1 TATAATTTAATTATAAATCA-ATTTTTA
42466930 TATAATTT
1 TATAATTT
42466938 CTTTCGCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TATAATTTAATTATAAATCAATTTTTA
Found at i:42467137 original size:22 final size:20
Alignment explanation
Indices: 42467091--42467144 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
42467081 GAATACTATA
* *
42467091 AAAATTATAAAAAAAATTTG
1 AAAATAATAAAAAAAATTTC
*
42467111 TAAATAATAAGAAAAATATTTC
1 AAAATAATAA-AAAAA-ATTTC
42467133 AAAAT-ATAAAAA
1 AAAATAATAAAAA
42467145 TTCATTAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
21 9 0.32
22 8 0.29
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
AAAATAATAAAAAAAATTTC
Found at i:42467636 original size:18 final size:18
Alignment explanation
Indices: 42467613--42467664 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
42467603 ATGGACTTAG
42467613 ATAATTTTTAATAATTTC
1 ATAATTTTTAATAATTTC
* *
42467631 ATAATTTTTTTATAAATTTT
1 ATAA-TTTTTAAT-AATTTC
42467651 AT-ATTTTTAATAAT
1 ATAATTTTTAATAAT
42467665 GATTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 8 0.28
20 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTTTAATAATTTC
Found at i:42467657 original size:17 final size:18
Alignment explanation
Indices: 42467616--42467680 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
42467606 GACTTAGATA
*
42467616 ATTTTTAATAAT-TTCAT
1 ATTTTTAATAATATTTAT
*
42467633 AATTTTTTTATAA-ATTTTAT
1 -A-TTTTTAATAATA-TTTAT
42467653 ATTTTTAATAATGATTTAT
1 ATTTTTAATAAT-ATTTAT
42467672 ATTTTTAAT
1 ATTTTTAAT
42467681 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.26
19 24 0.62
20 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTAATAATATTTAT
Found at i:42472204 original size:30 final size:31
Alignment explanation
Indices: 42472133--42472204 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
42472123 TAAAAATCAA
*
42472133 ATATCGAATC-TTCCTAAGCTCCTGAACGAG
1 ATATCGAGTCTTTCCTAAGCTCCTGAACGAG
42472163 ATATCGAGTCTTTCC-AAGCTCCTGAACGAG
1 ATATCGAGTCTTTCCTAAGCTCCTGAACGAG
*
42472193 ATATCGTGTCTT
1 ATATCGAGTCTT
42472205 CTCAAGTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (31 bp):
ATATCGAGTCTTTCCTAAGCTCCTGAACGAG
Found at i:42474876 original size:51 final size:50
Alignment explanation
Indices: 42474795--42474903 Score: 182
Period size: 51 Copynumber: 2.2 Consensus size: 50
42474785 CGGATCACAT
* * *
42474795 TTATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACCGATCAGATAAGTGTAACT-AAGCTACCAC
42474846 TTATCACTTGTCACTTGTCACCGATCAGATAAGTGTAACTAAGCTACCAC
1 TTATCACTTGTCACTTGTCACCGATCAGATAAGTGTAACTAAGCTACCAC
42474896 TTATCACT
1 TTATCACT
42474904 GATCAGATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 18 0.33
51 37 0.67
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTTGTCACCGATCAGATAAGTGTAACTAAGCTACCAC
Found at i:42474908 original size:36 final size:37
Alignment explanation
Indices: 42474857--42474940 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 37
42474847 TATCACTTGT
* * *
42474857 CACTTGTCACCGATCAGATAAGTGTAACT-AAGCTAC
1 CACTTATCACTGATCAGATAAGTGCAACTAAAGCTAC
*
42474893 CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTGATCAGATAAGTGCAACTAAAGCTAC
42474930 CACTTATCACT
1 CACTTATCACT
42474941 TGTCACTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 25 0.58
37 18 0.42
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (37 bp):
CACTTATCACTGATCAGATAAGTGCAACTAAAGCTAC
Found at i:42474959 original size:87 final size:87
Alignment explanation
Indices: 42474806--42474990 Score: 307
Period size: 87 Copynumber: 2.1 Consensus size: 87
42474796 TATCACTTGT
* * * *
42474806 CACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACCGAT
1 CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTATCACCGAT
*
42474871 CAGATAAGTGTAACTAAGCTAC
66 CAGATAAGTGTAACTAAACTAC
*
42474893 CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTATCACTGAT
1 CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTATCACCGAT
*
42474958 CAGATAAGTGTAGCTAAACTAC
66 CAGATAAGTGTAACTAAACTAC
42474980 CACTTATCACT
1 CACTTATCACT
42474991 TGTCACTGAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (87 bp):
CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTATCACCGAT
CAGATAAGTGTAACTAAACTAC
Found at i:42474973 original size:51 final size:50
Alignment explanation
Indices: 42474893--42475002 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 50
42474883 ACTAAGCTAC
42474893 CACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGT
1 CACTTATCACTGATCAGATAAGTGCAGCTAAA-CTACCACTTATCACTTGT
*
42474944 CACTTATCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGT
1 CACTTATCACTGATCAGATAAGTGCAGCTAAACTACCACTTATCACTTGT
*
42474994 CACTGATCA
1 CACTTATCA
42475003 GAAGTACTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 26 0.46
51 31 0.54
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (50 bp):
CACTTATCACTGATCAGATAAGTGCAGCTAAACTACCACTTATCACTTGT
Found at i:42480476 original size:6 final size:6
Alignment explanation
Indices: 42480465--42480491 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42480455 TTGCCTCTTA
42480465 CCACTG CCACTG CCACTG CCACTG CCA
1 CCACTG CCACTG CCACTG CCACTG CCA
42480492 GAGATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.15, T:0.15
Consensus pattern (6 bp):
CCACTG
Found at i:42486793 original size:21 final size:20
Alignment explanation
Indices: 42486764--42486803 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42486754 GGACTAAAAT
* *
42486764 ATATTTTTTAAGATTTTTTAA
1 ATATATTTT-AGAATTTTTAA
42486785 ATATATTTTAGAATTTTTA
1 ATATATTTTAGAATTTTTA
42486804 GAATTAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
ATATATTTTAGAATTTTTAA
Found at i:42486994 original size:23 final size:24
Alignment explanation
Indices: 42486946--42486994 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
42486936 TTAATAACTA
**
42486946 AACCAAAAATAATAATAATTTTGT
1 AACCAAAAATAATAATAATTAGGT
42486970 AACCAAAATATAA-AA-AATTAGGT
1 AACCAAAA-ATAATAATAATTAGGT
42486993 AA
1 AA
42486995 TTAGGTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 10 0.45
25 4 0.18
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (24 bp):
AACCAAAAATAATAATAATTAGGT
Found at i:42492970 original size:34 final size:34
Alignment explanation
Indices: 42492927--42492997 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
42492917 ACCAACAAGA
*
42492927 ATGTTCTTTGGTTAAAGTTCTATAGCATAAAGTG
1 ATGTTCTTTGGTTAAAGTCCTATAGCATAAAGTG
42492961 ATGTTCTTTGGTTAAAGTCCTATAGCATAAAGTG
1 ATGTTCTTTGGTTAAAGTCCTATAGCATAAAGTG
42492995 ATG
1 ATG
42492998 ATATTTGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (34 bp):
ATGTTCTTTGGTTAAAGTCCTATAGCATAAAGTG
Found at i:42495363 original size:23 final size:25
Alignment explanation
Indices: 42495329--42495377 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
42495319 GCTCGGCCCG
42495329 TTTTTAATTAAAATTA-AAATTATT
1 TTTTTAATTAAAATTACAAATTATT
42495353 TTTTTAA-TAAAATTATCAAATTATT
1 TTTTTAATTAAAATTA-CAAATTATT
42495378 AATTGTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.35
24 7 0.30
25 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTTAATTAAAATTACAAATTATT
Found at i:42495452 original size:9 final size:9
Alignment explanation
Indices: 42495440--42495483 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
42495430 ATTATCAAAT
42495440 TATTAATTG
1 TATTAATTG
42495449 TATTAATTG
1 TATTAATTG
42495458 --TTAATTG
1 TATTAATTG
*
42495465 AATTAATTG
1 TATTAATTG
42495474 TATTAATTG
1 TATTAATTG
42495483 T
1 T
42495484 TGTAACAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 7 0.22
9 25 0.78
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:42495461 original size:16 final size:16
Alignment explanation
Indices: 42495437--42495474 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42495427 AAAATTATCA
* *
42495437 AATTATTAATTGTATT
1 AATTGTTAATTGAATT
42495453 AATTGTTAATTGAATT
1 AATTGTTAATTGAATT
42495469 AATTGT
1 AATTGT
42495475 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTGTTAATTGAATT
Found at i:42495580 original size:68 final size:69
Alignment explanation
Indices: 42495470--42495615 Score: 267
Period size: 68 Copynumber: 2.1 Consensus size: 69
42495460 AATTGAATTA
42495470 ATTGTATTAATTGTTGTAACAAAATCAAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
1 ATTGTATTAATTGTTGTAACAAAATCAAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
42495535 TATT
66 TATT
*
42495539 -TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
1 ATTGTATTAATTGTTGTAACAAAATCAAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
42495603 TATT
66 TATT
*
42495607 ATTTTATTA
1 ATTGTATTA
42495616 TTATTATTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 67 0.91
69 7 0.09
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (69 bp):
ATTGTATTAATTGTTGTAACAAAATCAAACATTTGATTAGTAAAATAAACTTGATGTTTTATTAT
TATT
Found at i:42495613 original size:14 final size:14
Alignment explanation
Indices: 42495594--42495625 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42495584 AAACTTGATG
42495594 TTTTATTATTATTA
1 TTTTATTATTATTA
42495608 TTTTATTATTATTA
1 TTTTATTATTATTA
42495622 TTTT
1 TTTT
42495626 GTAACTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:42496221 original size:36 final size:36
Alignment explanation
Indices: 42496181--42496249 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
42496171 TAATGTAGTG
* *
42496181 ATGAGATTGGATGCTATAGCAGTGAGATTAAAAGTA
1 ATGAGATTGAATGCTATAGCACTGAGATTAAAAGTA
*
42496217 ATGAGATTGAATGCTATATCACTGAGATTAAAA
1 ATGAGATTGAATGCTATAGCACTGAGATTAAAA
42496250 ATAGCTGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (36 bp):
ATGAGATTGAATGCTATAGCACTGAGATTAAAAGTA
Found at i:42496829 original size:14 final size:14
Alignment explanation
Indices: 42496810--42496837 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42496800 CGATTGCATA
42496810 ATTTTCAATATAGG
1 ATTTTCAATATAGG
42496824 ATTTTCAATATAGG
1 ATTTTCAATATAGG
42496838 TCTCATTGTC
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:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTTTCAATATAGG
Found at i:42496906 original size:20 final size:20
Alignment explanation
Indices: 42496881--42496918 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42496871 AGAACCCATG
42496881 TTTGATTCTCAATTTTTCGA
1 TTTGATTCTCAATTTTTCGA
*
42496901 TTTGATTCTCAGTTTTTC
1 TTTGATTCTCAATTTTTC
42496919 ATACAAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTGATTCTCAATTTTTCGA
Found at i:42498416 original size:33 final size:32
Alignment explanation
Indices: 42498344--42498455 Score: 91
Period size: 33 Copynumber: 3.4 Consensus size: 32
42498334 CATAGTCCAA
* * * *
42498344 CTATGGTCTTACA-CATGCATTGCCATAGCCCTG
1 CTATGGTCTTACATCA-G-AATGTCATAACCCAG
* ** *
42498377 CCATGGTCTTACATTTGTAGTGTCATAACCCAG
1 CTATGGTCTTACATCAG-AATGTCATAACCCAG
* *
42498410 TTATGGTCTTATCATCAGAATGTCATAGCCCAG
1 CTATGGTCTTA-CATCAGAATGTCATAACCCAG
42498443 CTATGGTCTTACA
1 CTATGGTCTTACA
42498456 CATGTATCTA
Statistics
Matches: 62, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
32 2 0.03
33 56 0.90
34 4 0.06
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (32 bp):
CTATGGTCTTACATCAGAATGTCATAACCCAG
Found at i:42502910 original size:4 final size:4
Alignment explanation
Indices: 42502901--42502925 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42502891 GGCACTTCTC
42502901 CTAT CTAT CTAT CTAT CTAT CTAT C
1 CTAT CTAT CTAT CTAT CTAT CTAT C
42502926 CATCCATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CTAT
Found at i:42506386 original size:19 final size:19
Alignment explanation
Indices: 42506359--42506397 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42506349 AAAAAAATTA
42506359 TATTATTTTGGTATT-TTTT
1 TATTATTTT-GTATTATTTT
*
42506378 TATTTTTTTGTATTATTTT
1 TATTATTTTGTATTATTTT
42506397 T
1 T
42506398 GTAAAAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (19 bp):
TATTATTTTGTATTATTTT
Found at i:42512886 original size:87 final size:87
Alignment explanation
Indices: 42512754--42512946 Score: 228
Period size: 88 Copynumber: 2.2 Consensus size: 87
42512744 TTAAAAGGCG
* * * * *
42512754 ATTAAACCCCTACTTAATTTTTTCATTCATTTGAGTACTTGAACTTT-AAAATGTATCAAAAAGG
1 ATTAAGCCCCTACTT--TTTTTTCACTCAATTGAGTACTTAAACTTTCAAAATGCATC-AAAAGG
* *
42512818 CTCTTAAACCTTTT-AAAAAAAGCA
63 CCCTCAAACCTTTTCAAAAAAAGCA
* *
42512842 ATTAAGCTCCTACTTTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAGGCC
1 ATTAAGCCCCTACTTTTTTTT-CACTCAATTGAGTACTTAAACTTTCAAAATGCATCAAAAGGCC
* *
42512907 CTCAAACTTTTTCAGAAAAAGCA
65 CTCAAACCTTTTCAAAAAAAGCA
*
42512930 ATTAAGCCCCTGCTTTT
1 ATTAAGCCCCTACTTTT
42512947 ATTAAAAATT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
86 6 0.07
87 37 0.42
88 46 0.52
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (87 bp):
ATTAAGCCCCTACTTTTTTTTCACTCAATTGAGTACTTAAACTTTCAAAATGCATCAAAAGGCCC
TCAAACCTTTTCAAAAAAAGCA
Found at i:42513089 original size:29 final size:29
Alignment explanation
Indices: 42513022--42513119 Score: 71
Period size: 29 Copynumber: 3.5 Consensus size: 29
42513012 TTTCAAATAT
* *
42513022 TAAAATTATAAAAATTATAAAAAAATGTA
1 TAAAATTATAAAAATCACAAAAAAATGTA
* *
42513051 -AAATTTTATAAAAATCGCAAAAAAAT-TA
1 TAAA-ATTATAAAAATCACAAAAAAATGTA
* *
42513079 TAAAATATATAGAAAT-A-TAAAAAAT-TA
1 TAAAAT-TATAAAAATCACAAAAAAATGTA
* *
42513106 CAAAATTTTAAAAA
1 TAAAATTATAAAAA
42513120 GTTGTAAGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
26 6 0.11
27 14 0.25
28 6 0.11
29 29 0.53
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
TAAAATTATAAAAATCACAAAAAAATGTA
Found at i:42516142 original size:17 final size:18
Alignment explanation
Indices: 42516112--42516145 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
42516102 TTCGATCAAA
42516112 AAATTATATTTTTAAAAG
1 AAATTATATTTTTAAAAG
42516130 AAATTAT-TTTTTAAAA
1 AAATTATATTTTTAAAA
42516146 TTTTTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTATATTTTTAAAAG
Found at i:42516786 original size:21 final size:21
Alignment explanation
Indices: 42516761--42516800 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42516751 TATTTTATTC
42516761 AATGAAA-ATAATTTTTAATAA
1 AATGAAATAT-ATTTTTAATAA
*
42516782 AATGAATTATATTTTTAAT
1 AATGAAATATATTTTTAAT
42516801 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
AATGAAATATATTTTTAATAA
Found at i:42517161 original size:17 final size:17
Alignment explanation
Indices: 42517135--42517168 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42517125 TCAATTATTT
*
42517135 TAAATATTATAATTAAA
1 TAAATATTATAAATAAA
*
42517152 TAAATTTTATAAATAAA
1 TAAATATTATAAATAAA
42517169 ATATTCCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATTATAAATAAA
Found at i:42527207 original size:21 final size:20
Alignment explanation
Indices: 42527168--42527207 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42527158 TTAATAAATT
*
42527168 TATATTTAAAATTATTTATA
1 TATATTTAAAATAATTTATA
*
42527188 TATATATTACAATAATTTAT
1 TATAT-TTAAAATAATTTAT
42527208 TTATGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTTAAAATAATTTATA
Found at i:42528433 original size:32 final size:32
Alignment explanation
Indices: 42528387--42528467 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
42528377 TGTCAATCAT
*
42528387 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAACTTAAAACATAATAAA
* * * *
42528419 TTCAATATCTAACAAATTTAAGACATAATAAT
1 TTCAATATCCAACAAACTTAAAACATAATAAA
*
42528451 TTCAA-AACCAACAAACT
1 TTCAATATCCAACAAACT
42528468 AATTTTTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 9 0.22
32 32 0.78
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (32 bp):
TTCAATATCCAACAAACTTAAAACATAATAAA
Found at i:42533334 original size:15 final size:16
Alignment explanation
Indices: 42533302--42533334 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42533292 TTATGATTTT
*
42533302 TTTTAAATAATCAAAA
1 TTTTAAAAAATCAAAA
42533318 TTTTAAAAAAT-AAAA
1 TTTTAAAAAATCAAAA
42533333 TT
1 TT
42533335 GAAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTAAAAAATCAAAA
Found at i:42533855 original size:18 final size:19
Alignment explanation
Indices: 42533832--42533870 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
42533822 CAAAAATTAA
42533832 AAAAAAT-AAAATTTTTAT
1 AAAAAATCAAAATTTTTAT
*
42533850 AAAAAATCCCAAATTTTTAT
1 AAAAAAT-CAAAATTTTTAT
42533870 A
1 A
42533871 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATCAAAATTTTTAT
Found at i:42535870 original size:32 final size:33
Alignment explanation
Indices: 42535828--42535896 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
42535818 TCCAAACAAT
42535828 AAATTGTATTTACAAAACCAT-AAAAATTTTAA
1 AAATTGTATTTACAAAACCATAAAAAATTTTAA
* *
42535860 AAATTTTATTTACAAAATCATAAAAAATTTTAA
1 AAATTGTATTTACAAAACCATAAAAAATTTTAA
42535893 AAAT
1 AAAT
42535897 ATTAACCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (33 bp):
AAATTGTATTTACAAAACCATAAAAAATTTTAA
Found at i:42543579 original size:15 final size:15
Alignment explanation
Indices: 42543559--42543592 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42543549 ACCAAGGAAC
* *
42543559 GGAAAGAGAGGAGGA
1 GGAAAGAAAGGAAGA
42543574 GGAAAGAAAGGAAGA
1 GGAAAGAAAGGAAGA
42543589 GGAA
1 GGAA
42543593 TGTGAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGGAAGA
Found at i:42553448 original size:105 final size:101
Alignment explanation
Indices: 42553286--42553482 Score: 286
Period size: 105 Copynumber: 1.9 Consensus size: 101
42553276 ACACTCGTAA
**
42553286 TGCCATAACCCAGTTATGGTCTTATCATTAGGATGCCATAGCCCAACTATGGTCTTACACGTATA
1 TGCCATAACCCAGTTATGGTCTTATCATTAAAATGCCATAGCCCAACTATGGTCTTACA--TATA
**
42553351 CATTTATTGCCATAGTCCAACCATGGTCTTACGTTTAAAG
64 -A-ACATTGCCATAGTCCAACCATGGTCTTACGTTTAAAG
* * *
42553391 TGCCATAACCCAGTTATGGTCTTTTCATTAAAATGTCATAGCCCAACTATGGTCTTACATTTAAA
1 TGCCATAACCCAGTTATGGTCTTATCATTAAAATGCCATAGCCCAACTATGGTCTTACATATAAA
*
42553456 CATTGCCATGGTCCAACCATGGTCTTA
66 CATTGCCATAGTCCAACCATGGTCTTA
42553483 TCTGTCAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 25 0.30
102 1 0.01
103 3 0.04
105 55 0.65
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATTAAAATGCCATAGCCCAACTATGGTCTTACATATAAA
CATTGCCATAGTCCAACCATGGTCTTACGTTTAAAG
Found at i:42553455 original size:33 final size:33
Alignment explanation
Indices: 42553358--42553482 Score: 108
Period size: 33 Copynumber: 3.7 Consensus size: 33
42553348 ATACATTTAT
* * *
42553358 TGCCATAGTCCAACCATGGTCTTACGTTTAAAG
1 TGCCATAGCCCAACCATGGTCTTACATTTAAAA
* *** *
42553391 TGCCATAACCCAGTTATGGTCTTTTCA-TTAAAA
1 TGCCATAGCCCAACCATGGTC-TTACATTTAAAA
* *
42553424 TGTCATAGCCCAACTATGGTCTTACATTTAAACA
1 TGCCATAGCCCAACCATGGTCTTACATTTAAA-A
* *
42553458 TTGCCATGGTCCAACCATGGTCTTA
1 -TGCCATAGCCCAACCATGGTCTTA
42553483 TCTGTCAATT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
32 4 0.06
33 43 0.61
34 4 0.06
35 20 0.28
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (33 bp):
TGCCATAGCCCAACCATGGTCTTACATTTAAAA
Found at i:42555310 original size:19 final size:20
Alignment explanation
Indices: 42555268--42555315 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
42555258 AAATTATTTA
* *
42555268 TAAAATTTAATTTAAACATG
1 TAAAATATATTTTAAACATG
* *
42555288 TAAACTATATTTTAAATAT-
1 TAAAATATATTTTAAACATG
42555307 TAAAATATA
1 TAAAATATA
42555316 ATATTTCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATATATTTTAAACATG
Found at i:42555765 original size:12 final size:12
Alignment explanation
Indices: 42555748--42555780 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
42555738 TGACCCGCCC
42555748 ATATTAATTTTT
1 ATATTAATTTTT
42555760 ATATT-ATTTTT
1 ATATTAATTTTT
42555771 ATA-TAATTTT
1 ATATTAATTTT
42555781 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:42555936 original size:30 final size:30
Alignment explanation
Indices: 42555902--42555964 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
42555892 ACTTAATAAG
*
42555902 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTATAAAATAATAACAAAATTAA
**
42555932 CAAATGTCTATAAAATAATAACAAAATTAA
1 CAAATACCTATAAAATAATAACAAAATTAA
42555962 CAA
1 CAA
42555965 TAAAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTATAAAATAATAACAAAATTAA
Found at i:42555985 original size:19 final size:19
Alignment explanation
Indices: 42555940--42555985 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
42555930 AACAAATGTC
*
42555940 TATAAAATAATAACAAAAT
1 TATACAATAATAACAAAAT
42555959 TA-ACAATAA-AACAAAATT
1 TATACAATAATAACAAAA-T
42555977 TATACAATA
1 TATACAATA
42555986 TCCAAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (19 bp):
TATACAATAATAACAAAAT
Found at i:42556490 original size:16 final size:18
Alignment explanation
Indices: 42556471--42556510 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
42556461 ATTTTTTTTA
42556471 TTTTAAATTTT-AAAT-T
1 TTTTAAATTTTAAAATAT
42556487 TTTT-AATTTTAAAATAT
1 TTTTAAATTTTAAAATAT
42556504 TTTTAAA
1 TTTTAAA
42556511 ATACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 5 0.24
18 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAAATTTTAAAATAT
Found at i:42556505 original size:32 final size:31
Alignment explanation
Indices: 42556481--42556580 Score: 91
Period size: 32 Copynumber: 3.3 Consensus size: 31
42556471 TTTTAAATTT
42556481 TAAATTTTT-TAATTTTAAAATATTTTTAAAA
1 TAAATTTTTCTAATTTTAAAATA-TTTTAAAA
**
42556512 TACTTTTTTCTAATTTTAAAATATTTTTAAAA
1 TAAATTTTTCTAATTTTAAAATA-TTTTAAAA
* * ***
42556544 T-ACTTTTT-AAATTTTTTTAT-TTTTAAAA
1 TAAATTTTTCTAATTTTAAAATATTTTAAAA
42556572 TAAATTTTT
1 TAAATTTTT
42556581 GGTGTTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 9 0.16
29 6 0.10
30 8 0.14
31 12 0.21
32 23 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TAAATTTTTCTAATTTTAAAATATTTTAAAA
Found at i:42556509 original size:11 final size:11
Alignment explanation
Indices: 42556493--42556554 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
42556483 AATTTTTTAA
42556493 TTTTAAAATAT
1 TTTTAAAATAT
42556504 TTTTAAAATACT
1 TTTTAAAATA-T
** *
42556516 TTTT--TCTAA
1 TTTTAAAATAT
42556525 TTTTAAAATAT
1 TTTTAAAATAT
42556536 TTTTAAAATACT
1 TTTTAAAATA-T
42556548 TTTTAAA
1 TTTTAAA
42556555 TTTTTTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.10
10 2 0.05
11 22 0.54
12 13 0.32
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:42559322 original size:33 final size:33
Alignment explanation
Indices: 42559284--42559347 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
42559274 GCATAATGTA
42559284 TTTTTTAATAAATATACA-TTTACATAAAAAAAG
1 TTTTTTAATAAATATA-ATTTTACATAAAAAAAG
* * *
42559317 TTTTTTTATAAGTGTAATTTTACATAAAAAA
1 TTTTTTAATAAATATAATTTTACATAAAAAA
42559348 TTCACCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (33 bp):
TTTTTTAATAAATATAATTTTACATAAAAAAAG
Found at i:42567099 original size:2 final size:2
Alignment explanation
Indices: 42567092--42567118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42567082 GATTTATGGT
42567092 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42567119 TTCTGTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42567473 original size:16 final size:17
Alignment explanation
Indices: 42567447--42567484 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
42567437 TTAACTAACT
42567447 ATATTATTAAATATAAA
1 ATATTATTAAATATAAA
*
42567464 ATATTA-TAAATCTAAA
1 ATATTATTAAATATAAA
42567480 A-ATTA
1 ATATTA
42567485 AATATCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTATTAAATATAAA
Found at i:42568572 original size:51 final size:51
Alignment explanation
Indices: 42568512--42568626 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
42568502 TCCTCTCTAA
42568512 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
42568563 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
42568614 TCCCCTCAATTTC
1 TCCTCTCAATTTC
42568627 ATTTTTGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:42568650 original size:10 final size:10
Alignment explanation
Indices: 42568635--42568678 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
42568625 TCATTTTTGA
42568635 AAATAATTTT
1 AAATAATTTT
42568645 AAATAATTTT
1 AAATAATTTT
*
42568655 AAAT-TTTTT
1 AAATAATTTT
42568664 AAAATAATTTT
1 -AAATAATTTT
42568675 AAAT
1 AAAT
42568679 TTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.13
10 22 0.73
11 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATAATTTT
Found at i:42568668 original size:20 final size:20
Alignment explanation
Indices: 42568641--42568684 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
42568631 TTGAAAATAA
42568641 TTTT-AAATAATTTTAAATT
1 TTTTAAAATAATTTTAAATT
42568660 TTTTAAAATAATTTTAAATT
1 TTTTAAAATAATTTTAAATT
42568680 TTTTA
1 TTTTA
42568685 TATTTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAAATAATTTTAAATT
Found at i:42570728 original size:23 final size:23
Alignment explanation
Indices: 42570701--42570799 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
42570691 AGTGTTATTG
* *
42570701 ATCAGTGGTAGCTTTGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
42570724 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
42570747 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
42570770 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
42570793 ATCAGTG
1 ATCAGTG
42570800 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:42571058 original size:15 final size:16
Alignment explanation
Indices: 42571028--42571060 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42571018 TAGTTATATG
42571028 TTAAAAGAGTTAATTA
1 TTAAAAGAGTTAATTA
*
42571044 TTAAATGAG-TAATTA
1 TTAAAAGAGTTAATTA
42571059 TT
1 TT
42571061 GTTTACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (16 bp):
TTAAAAGAGTTAATTA
Found at i:42573556 original size:25 final size:25
Alignment explanation
Indices: 42573528--42573596 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
42573518 TTTAAATTTA
*
42573528 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* * *
42573553 TTATTTAATATAGTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
42573578 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
42573597 ACCCTAACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 22 0.61
26 14 0.39
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:42573615 original size:18 final size:18
Alignment explanation
Indices: 42573592--42574036 Score: 482
Period size: 18 Copynumber: 25.1 Consensus size: 18
42573582 TTTGATGTAA
42573592 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573610 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
42573628 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
* *
42573646 TAAAAACCTTAATTTAAT
1 TAAAAACCCTAACTTAAT
*
42573664 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
42573682 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573700 TAAAAACCTTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573718 TAAAAACCCTAAC-T--C
1 TAAAAACCCTAACTTAAT
*
42573733 T---AA-CCTAATTTAAT
1 TAAAAACCCTAACTTAAT
42573747 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
**
42573765 TAAAAACCCTAAC---CC
1 TAAAAACCCTAACTTAAT
42573780 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
42573794 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573812 TAAAAACACTAACTTAAT
1 TAAAAACCCTAACTTAAT
42573830 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
42573848 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAA-C----TTAAT
*
42573871 TAAAAACCCTAAC---CT
1 TAAAAACCCTAACTTAAT
42573886 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
42573900 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573918 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
42573936 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
42573954 TAAAAGCTCTAACCTAACTTAAT
1 TAAAA-----ACCCTAACTTAAT
*
42573977 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
42573995 TAAAAACACTAACCTAACTTAAT
1 T-AAAA-AC---CCTAACTTAAT
42574018 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
42574036 T
1 T
42574037 TTACTAACCA
Statistics
Matches: 365, Mismatches: 26, Indels: 72
0.79 0.06 0.16
Matches are distributed among these distances:
11 17 0.05
12 7 0.02
14 4 0.01
15 4 0.01
17 7 0.02
18 267 0.73
19 5 0.01
20 2 0.01
21 2 0.01
22 5 0.01
23 45 0.12
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:42573760 original size:47 final size:46
Alignment explanation
Indices: 42573689--42574036 Score: 265
Period size: 47 Copynumber: 7.7 Consensus size: 46
42573679 AATTAAAAAC
*
42573689 CCTAACTTAATTAAAAACCTTAACTTAATTAAAAACCCTAACTCTAA
1 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAA-CCTAACTCTAA
* *
42573736 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAA-CCTAACTCTAA
42573783 CCTAACTTAATTAAAAACCCTAACTTAATT--AAA---AA--C--A
1 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCTAACTCTAA
42573820 -CTAACTTAATTAAAAACCCTAACTTAATTAAAAA-C---C-CTAA
1 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCTAACTCTAA
* * * * **
42573860 CCTAATTTAATTAAAAACCCTAACCTTAACCT---AACTTAATTAAAAA
1 CCTAACTTAATTAAAAACCCTAA-CTTAA-TTAAAAACCTAACT-CTAA
*
42573906 CCCTAACTTAATTAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAGCTCTAA
1 -CCTAACTTAATTAAAAACCCTAACTTAATTAAAAA--C---C-----T--AA-CTCTAA
*
42573966 CCTAACTTAATTAAAAACCCTAATTTAATTAAAAA-C--A--CTAA
1 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCTAACTCTAA
42574007 CCTAACTTAATTAAAAACCCTAACTTAATT
1 CCTAACTTAATTAAAAACCCTAACTTAATT
42574037 TTACTAACCA
Statistics
Matches: 251, Mismatches: 18, Indels: 70
0.74 0.05 0.21
Matches are distributed among these distances:
36 29 0.12
37 1 0.00
38 4 0.02
39 1 0.00
40 3 0.01
41 56 0.22
42 5 0.02
43 1 0.00
44 1 0.00
45 4 0.02
46 6 0.02
47 95 0.38
48 2 0.01
50 1 0.00
53 1 0.00
58 1 0.00
59 35 0.14
60 4 0.02
61 1 0.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.29
Consensus pattern (46 bp):
CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCTAACTCTAA
Found at i:42573889 original size:29 final size:29
Alignment explanation
Indices: 42573852--42573952 Score: 105
Period size: 29 Copynumber: 3.3 Consensus size: 29
42573842 CTTAATTAAA
*
42573852 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
*
42573881 AACCTTAACCTAACTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
*
42573910 AACTTAATTAAAAACCCTAATTTAATTAAAAACCCT
1 AAC---CTT---AA-CCTAATTTAATTAAAAACCCT
42573946 AA-CTTAA
1 AACCTTAA
42573953 TTAAAAGCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
29 32 0.53
32 4 0.07
35 2 0.03
36 22 0.37
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCTTAACCTAATTTAATTAAAAACCCT
Found at i:42573909 original size:106 final size:98
Alignment explanation
Indices: 42573599--42574036 Score: 249
Period size: 106 Copynumber: 4.5 Consensus size: 98
42573589 TAATAAAAAC
* * * *
42573599 CCTAACTTAATTAAAAACCCTAA-T--TTAA-TTAAAAACCCTAACTTAATTAAAAACCTTAATT
1 CCTAATTTAATTAAAAACCCTAACTAATTAACCTAAAAACCCTAACTTAATTAAAAACCCTAACT
*
42573660 TAATTAAAAACCCTAATTTAATTAAAAA-C---
66 TAATTAAAAACCCTAACTTAATTAAAAACCTAA
* * * *
42573689 CCTAACTTAATTAAAAACCTTAACTTAATTAAAAACCCTAACTCTAA-CCTAATTTAATTAAAAA
1 CCTAATTTAATTAAAAACCCTAAC-TAATT---AA-CCTAA---AAACCCTAACTTAATTAAAAA
42573753 CCCTAACTTAATTAAAAACCCTAAC-----------CCTAA
58 CCCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCTAA
* * *
42573783 CCTAACTTAATTAAAAACCCTAAC---TTAA-TTAAAAACACTAACTTAATTAAAAACCCTAACT
1 CCTAATTTAATTAAAAACCCTAACTAATTAACCTAAAAACCCTAACTTAATTAAAAACCCTAACT
42573844 TAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
66 TAATTAAAAACCCTAA-C----TTAATTAAAAA-CCTAA
* *
42573883 CCTTAACCTAACTTAATTAAAAACCCTAAC---TTAA-TTAAAAACCCTAATTTAATTAAAAACC
1 CC-TAA--T---TTAATTAAAAACCCTAACTAATTAACCTAAAAACCCTAACTTAATTAAAAACC
*
42573944 CTAACTTAATTAAAAGCTCTAACCTAACTTAATTAAAAA-C---
60 CTAACTTAATTAAAA-----ACCCTAACTTAATTAAAAACCTAA
* *
42573984 CCTAATTTAATTAAAAACACTAACCTAACTTAA-TTAAAAACCCTAACTTAATT
1 CCTAATTTAATTAAAAACCCTAA-CTAA-TTAACCTAAAAACCCTAACTTAATT
42574037 TTACTAACCA
Statistics
Matches: 280, Mismatches: 18, Indels: 90
0.72 0.05 0.23
Matches are distributed among these distances:
82 2 0.01
83 39 0.14
84 1 0.00
85 3 0.01
87 2 0.01
90 24 0.09
91 1 0.00
92 1 0.00
94 25 0.09
95 16 0.06
96 1 0.00
97 2 0.01
98 1 0.00
99 3 0.01
100 33 0.12
101 43 0.15
102 2 0.01
104 1 0.00
106 73 0.26
110 1 0.00
111 6 0.02
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (98 bp):
CCTAATTTAATTAAAAACCCTAACTAATTAACCTAAAAACCCTAACTTAATTAAAAACCCTAACT
TAATTAAAAACCCTAACTTAATTAAAAACCTAA
Found at i:42574057 original size:21 final size:21
Alignment explanation
Indices: 42574033--42574104 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
42574023 ACCCTAACTT
*
42574033 AATTTTACTAACCATTAGCAC
1 AATTTTACTAACCATTAACAC
** * *
42574054 AATTGTTGGACTTAATAATTTATCAT
1 AATT-TT--AC-TAACCA-TTAACAC
42574080 AATTTTACTAACCATTAACAC
1 AATTTTACTAACCATTAACAC
42574101 AATT
1 AATT
42574105 GTTGGACTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 13 0.34
22 6 0.16
23 2 0.05
24 2 0.05
25 6 0.16
26 9 0.24
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (21 bp):
AATTTTACTAACCATTAACAC
Found at i:42574102 original size:47 final size:47
Alignment explanation
Indices: 42574027--42574131 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
42574017 TTAAAAACCC
* *
42574027 TAACTTAATTTTACTAACCATTAGCACAATTGTTGGACTTAATAATT
1 TAACATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATT
*
42574074 TATCATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATT
1 TAACATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATT
42574121 TAACATAATTT
1 TAACATAATTT
42574132 GATAATTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (47 bp):
TAACATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATT
Found at i:42574123 original size:26 final size:26
Alignment explanation
Indices: 42574051--42574130 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
42574041 TAACCATTAG
*
42574051 CACAATTGTTGGACTTAATAATTTAT
1 CACAATTGTTGGACTTAATAATTTAA
* **
42574077 CATAATT-TT--AC-TAACCA-TTAA
1 CACAATTGTTGGACTTAATAATTTAA
42574098 CACAATTGTTGGACTTAATAATTTAA
1 CACAATTGTTGGACTTAATAATTTAA
*
42574124 CATAATT
1 CACAATT
42574131 TGATAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 2 0.05
24 2 0.05
25 6 0.15
26 16 0.39
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (26 bp):
CACAATTGTTGGACTTAATAATTTAA
Found at i:42574154 original size:55 final size:56
Alignment explanation
Indices: 42574078--42574906 Score: 432
Period size: 55 Copynumber: 14.0 Consensus size: 56
42574068 ATAATTTATC
* * *
42574078 ATAATTTTA-CTAACCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTG
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
* *
42574133 ATAATTTTA-CTAACCATTAACAAAAATTTGGGACTTAATAATTTTACATAATTTG
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
* * *
42574188 ATAATTTTACCTAA--TTTAATTAAAATTTTTTGGCTTAATAATTTTATATAATTTTACATAATT
1 ATAATTTTACCTAACCATTAA-CAAAA-TTTTTGG-------A-CTTA-ATAATTTTACATAATT
42574251 TG
55 TG
** * *
42574253 ATAATTTTACCT-A-GTTTAATTAAAATTTTTTTGG-CTTAATAATTTTACATAATTTTAC
1 ATAATTTTACCTAACCATTAA-CAAAA--TTTTTGGACTTAATAATTTTACATAA-TTT-G
** * **
42574311 ATAATTTGATAATTTTACCTAGTTTAATTACAATTTTTTTGG-CTTAATAATTTTACATAATTTT
1 ATAATTT--T-ACCTAACC-A--TT-A--ACAAAATTTTTGGACTTAATAATTTTACATAA-TTT
*
42574375 AC
56 -G
** * **
42574377 ATAATTTGATAGTTATA-CAGGGGTTTAATTAAAATTTTTTGGGGTTAATAATTTTACATAATTT
1 ATAATTT--TACCTA-ACCA-----TTAA-CAAAA-TTTTTGGACTTAATAATTTTACATAATTT
42574441 G
56 G
*
42574442 ATAATTTTA-CTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTG
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
** * ** *
42574497 ATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTACATAATTTTACATAATTT
1 ATAATTTTACCTAA--CCATT-AACAAAATTT---TT--GGA-CTTA-ATAATTTTACATAATTT
42574562 G
56 G
***
42574563 ATAATTTTACCTAGTTTAATTAA-AAAATTTTTGG-CTTAATAATTTTACATAATTTG
1 ATAATTTTACCTA--ACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
*
42574619 ATAATTTTA-CTAACCATTAACAAAATTTTGGGACTTAATAA-TTT---T-A--T-
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
*
42574666 ATAATTTTA-CTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTG
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
* * *
42574721 ATAATTTTACCTAA--TTTAATTCAAATTTTTTTGG-CTTAATAATTTTACATAATTTTAC
1 ATAATTTTACCTAACCATTAA--CAAA-ATTTTTGGACTTAATAATTTTACATAA-TTT-G
** * * *
42574779 ATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTA
1 ATAATTT--T-ACCTAACC-A--TTAA-CAAAA--TTTTTGG-------A-CTTA-ATAATTTTA
42574844 CATAATTTG
48 CATAATTTG
*
42574853 ATAATTTTA-CTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTT
1 ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTT
42574907 TACATAATGT
Statistics
Matches: 627, Mismatches: 63, Indels: 168
0.73 0.07 0.20
Matches are distributed among these distances:
47 41 0.07
48 4 0.01
50 1 0.00
51 2 0.00
52 1 0.00
53 5 0.01
54 22 0.04
55 136 0.22
56 87 0.14
57 23 0.04
58 17 0.03
59 9 0.01
60 2 0.00
61 8 0.01
62 6 0.01
63 3 0.00
64 20 0.03
65 63 0.10
66 114 0.18
67 26 0.04
68 2 0.00
69 2 0.00
70 4 0.01
71 1 0.00
72 1 0.00
74 7 0.01
75 6 0.01
76 14 0.02
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (56 bp):
ATAATTTTACCTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTG
Found at i:42574193 original size:18 final size:18
Alignment explanation
Indices: 42574170--42574204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42574160 TTGGGACTTA
42574170 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
42574188 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
42574205 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:42574296 original size:38 final size:38
Alignment explanation
Indices: 42574253--42574366 Score: 104
Period size: 38 Copynumber: 3.3 Consensus size: 38
42574243 ACATAATTTG
42574253 ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
1 ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
* * * **
42574291 ATAATTTTACATA-ATT--TT-ACA-TAATTT-G----
1 ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
*
42574319 ATAATTTTACCTAGTTTAATTACAATTTTTTTGGCTTA
1 ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
42574357 ATAATTTTAC
1 ATAATTTTAC
42574367 ATAATTTTAC
Statistics
Matches: 55, Mismatches: 11, Indels: 20
0.64 0.13 0.23
Matches are distributed among these distances:
28 12 0.22
29 2 0.04
31 2 0.04
32 2 0.04
33 8 0.15
34 3 0.05
35 2 0.04
37 2 0.04
38 22 0.40
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (38 bp):
ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
Found at i:42574297 original size:56 final size:56
Alignment explanation
Indices: 42574235--42574841 Score: 404
Period size: 66 Copynumber: 10.3 Consensus size: 56
42574225 ATAATTTTAT
42574235 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGC---------TTA
*
42574300 CATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTACAATTTTTTTGGCTTA
1 -ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
* ** * *
42574357 ATAATTTTACATAATTTTACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGGT
1 ATAATTTTACATAA-TTT-GATAATTT--TA--CCT--A---GTTTAATTAAAATTTTTTTGGCT
42574422 TA
55 TA
** * *
42574424 ATAATTTTACATAATTTGATAATTTTA-CTAACCATTAA-CAAAA--TTTTGGGACTTA
1 ATAATTTTACATAATTTGATAATTTTACCT-A-GTTTAATTAAAATTTTTTTGG-CTTA
* ****
42574479 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATT----AAAATTT---TT--TTGGCTTA
**
42574544 CATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTA
1 -ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
** * *
42574601 ATAATTTTACATAATTTGATAATTTTA-CTAACCATTAA-CAAAA--TTTTGGGACTTA
1 ATAATTTTACATAATTTGATAATTTTACCT-A-GTTTAATTAAAATTTTTTTGG-CTTA
* * * * *
42574656 ATAATTTTATATAATTT--T-A-CTAACC-A--TTAA-CAAAA--TTTTGGGACTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGG-CTTA
* *
42574703 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGC---------TTA
42574768 CATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
1 -ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
42574825 ATAATTTTACATAATTT
1 ATAATTTTACATAATTT
42574842 TACATAATTT
Statistics
Matches: 447, Mismatches: 44, Indels: 110
0.74 0.07 0.18
Matches are distributed among these distances:
47 37 0.08
49 1 0.00
50 2 0.00
51 6 0.01
52 3 0.01
53 1 0.00
54 21 0.05
55 56 0.13
56 70 0.16
57 27 0.06
58 7 0.02
59 7 0.02
60 3 0.01
61 1 0.00
62 6 0.01
63 2 0.00
64 3 0.01
65 13 0.03
66 145 0.32
67 36 0.08
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
Found at i:42574306 original size:10 final size:10
Alignment explanation
Indices: 42574291--42574317 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42574281 TTTTGGCTTA
42574291 ATAATTTTAC
1 ATAATTTTAC
42574301 ATAATTTTAC
1 ATAATTTTAC
42574311 ATAATTT
1 ATAATTT
42574318 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574319 original size:66 final size:66
Alignment explanation
Indices: 42574170--42574617 Score: 519
Period size: 66 Copynumber: 7.1 Consensus size: 66
42574160 TTGGGACTTA
*
42574170 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAA-TTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
*
42574234 T
66 C
42574235 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
42574300 C
66 C
*
42574301 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTACAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
42574366 C
66 C
* * *** * *
42574367 ATAATTTTACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGGTTAATAATTTT
1 ATAATTTTACATAATTTGATAATTTTAC-CTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTT
42574432 AC
65 AC
* * * * *
42574434 ATAA-TTT-GATAATTT--T-A-CTAACC-A--TTAA-CAAAA--TTTTGGGAC-T--TAA----
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGG-CTTAATAATTTT
42574480 --
65 AC
* ****
42574480 -TAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
42574544 C
66 C
**
42574545 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
42574610 C
66 C
42574611 ATAATTT
1 ATAATTT
42574618 GATAATTTTA
Statistics
Matches: 328, Mismatches: 30, Indels: 49
0.81 0.07 0.12
Matches are distributed among these distances:
45 3 0.01
46 3 0.01
47 7 0.02
49 1 0.00
50 1 0.00
51 4 0.01
52 4 0.01
54 12 0.04
55 4 0.01
56 5 0.02
57 9 0.03
59 3 0.01
61 2 0.01
63 1 0.00
65 49 0.15
66 184 0.56
67 36 0.11
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (66 bp):
ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
C
Found at i:42574372 original size:10 final size:10
Alignment explanation
Indices: 42574357--42574383 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42574347 TTTTGGCTTA
42574357 ATAATTTTAC
1 ATAATTTTAC
42574367 ATAATTTTAC
1 ATAATTTTAC
42574377 ATAATTT
1 ATAATTT
42574384 GATAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574502 original size:18 final size:18
Alignment explanation
Indices: 42574479--42574513 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42574469 TTGGGACTTA
42574479 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
42574497 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
42574514 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:42574539 original size:38 final size:38
Alignment explanation
Indices: 42574497--42574617 Score: 109
Period size: 38 Copynumber: 3.4 Consensus size: 38
42574487 ACATAATTTG
*
42574497 ATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTA
1 ATAATTTTACATAATTTAATTAAAAAAAATTTGGCTTA
* *
42574535 ATAATTTTACATAA-TT--TT--ACATAATTT-G----
1 ATAATTTTACATAATTTAATTAAAAAAAATTTGGCTTA
* * **
42574563 ATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTA
1 ATAATTTTACATAATTTAATTAAAAAAAATTTGGCTTA
42574601 ATAATTTTACATAATTT
1 ATAATTTTACATAATTT
42574618 GATAATTTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
28 12 0.19
29 2 0.03
31 2 0.03
32 1 0.02
33 12 0.19
34 1 0.02
35 2 0.03
37 2 0.03
38 28 0.45
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (38 bp):
ATAATTTTACATAATTTAATTAAAAAAAATTTGGCTTA
Found at i:42574550 original size:10 final size:10
Alignment explanation
Indices: 42574535--42574561 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42574525 ATTTGGCTTA
42574535 ATAATTTTAC
1 ATAATTTTAC
42574545 ATAATTTTAC
1 ATAATTTTAC
42574555 ATAATTT
1 ATAATTT
42574562 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574647 original size:21 final size:21
Alignment explanation
Indices: 42574621--42574694 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
42574611 ATAATTTGAT
42574621 AATTTTACTAACCATTAACAA
1 AATTTTACTAACCATTAACAA
** * * *
42574642 AATTTTGGGACTTAATAATTTTATAT
1 AATTTT---AC-TAACCA-TTAACAA
42574668 AATTTTACTAACCATTAACAA
1 AATTTTACTAACCATTAACAA
42574689 AATTTT
1 AATTTT
42574695 GGGACTTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
21 16 0.42
22 4 0.11
23 2 0.05
24 2 0.05
25 4 0.11
26 10 0.26
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTTTACTAACCATTAACAA
Found at i:42574672 original size:26 final size:26
Alignment explanation
Indices: 42574642--42574719 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
42574632 CCATTAACAA
*
42574642 AATTTTGGGACTTAATAATTTTATAT
1 AATTTTGGGACTTAATAATTTTACAT
** * *
42574668 AATTTT---AC-TAACCA-TTAACAA
1 AATTTTGGGACTTAATAATTTTACAT
42574689 AATTTTGGGACTTAATAATTTTACAT
1 AATTTTGGGACTTAATAATTTTACAT
42574715 AATTT
1 AATTT
42574720 GATAATTTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
21 10 0.26
22 4 0.11
23 2 0.05
24 2 0.05
25 4 0.11
26 16 0.42
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (26 bp):
AATTTTGGGACTTAATAATTTTACAT
Found at i:42574672 original size:177 final size:178
Alignment explanation
Indices: 42574301--42574672 Score: 595
Period size: 178 Copynumber: 2.1 Consensus size: 178
42574291 ATAATTTTAC
* * ****
42574301 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTACAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
* * * * *
42574366 CATAATTTTACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGGTTAATAATTT
66 CATAATTTTACATAATTTGATAATTATACACGAGTTTAATTAAAAATTTTTGGGCTTAATAATTT
42574431 TACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTA
131 TACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTA
42574479 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
* *
42574544 CATAATTTTACATAATTTGATAATTTTAC-CTAGTTTAATTAAAAAATTTTT-GGCTTAATAATT
66 CATAATTTTACATAATTTGATAATTATACACGAGTTTAATT-AAAAATTTTTGGGCTTAATAATT
42574607 TTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTA
130 TTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTA
*
42574656 ATAATTTTATATAATTT
1 ATAATTTTACATAATTT
42574673 TACTAACCAT
Statistics
Matches: 179, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
177 84 0.47
178 95 0.53
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (178 bp):
ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTA
CATAATTTTACATAATTTGATAATTATACACGAGTTTAATTAAAAATTTTTGGGCTTAATAATTT
TACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTA
Found at i:42574672 original size:309 final size:307
Alignment explanation
Indices: 42574112--42574675 Score: 830
Period size: 309 Copynumber: 1.8 Consensus size: 307
42574102 ATTGTTGGAC
42574112 TTAATAATTTAACATAATTTGATAATTTTACTAACCATTAACAAAAATTTGGGACTTAATAATTT
1 TTAATAATTTAACATAATTTGATAATTTTACTAACCATTAACAAAAATTTGGGACTTAATAATTT
*** *
42574177 TACATAATTTGATAATTTTACCTAATTTAATTAAAATTTTTTGGCTTAATAATTTTATATAATTT
66 TACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTTGGCTTAATAATTTTACATAATTT
**
42574242 TACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATT
131 TACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTAATAATTTTACATAATT
* * ** * ** ** *
42574307 TTACATAATTTGATAATTTTACCTAGTTTAATTACAATTTTTTTGGCTTAATAATTTTACATAAT
196 TTACATAATTTGATAAATTAACAAAATTTAAGGACAATAATTTT-G-ATAATAATTTTACATAAT
42574372 TTTACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGG
259 TTTACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGG
* *
42574421 TTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTT
1 TTAATAATTTAACATAATTTGATAATTTTACTAACCATTAACAAAAATTTGGGACTTAATAATTT
42574486 TACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTACATAATT
66 TACATAATTTGATAATTTTACCTAATTTAATT-AAAAAAATTTGGCTTAATAATTTTACATAATT
42574551 TTACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTAATAATTTTACATAA-
130 TTACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTAATAATTTTACATAAT
* * **
42574615 TTT-GATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTT-AT-ATAATTTTAC
195 TTTACATAATTTGA-TAA--ATTAACAAAATTTAAGGAC--AATAATTTTGATAATAATTTTAC
42574676 TAACCATTAA
Statistics
Matches: 227, Mismatches: 22, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
308 8 0.04
309 111 0.49
310 91 0.40
311 10 0.04
313 7 0.03
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (307 bp):
TTAATAATTTAACATAATTTGATAATTTTACTAACCATTAACAAAAATTTGGGACTTAATAATTT
TACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTTGGCTTAATAATTTTACATAATTT
TACATAATTTGATAATTTTACCTAGTTTAATTAAAAAATTTTTGGCTTAATAATTTTACATAATT
TTACATAATTTGATAAATTAACAAAATTTAAGGACAATAATTTTGATAATAATTTTACATAATTT
TACATAATTTGATAGTTATACAGGGGTTTAATTAAAATTTTTTGGGG
Found at i:42574678 original size:47 final size:47
Alignment explanation
Indices: 42574619--42574719 Score: 193
Period size: 47 Copynumber: 2.1 Consensus size: 47
42574609 ACATAATTTG
*
42574619 ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAT
1 ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
42574666 ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
1 ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
42574713 ATAATTT
1 ATAATTT
42574720 GATAATTTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.43
Consensus pattern (47 bp):
ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
Found at i:42574696 original size:224 final size:224
Alignment explanation
Indices: 42574101--42574909 Score: 929
Period size: 224 Copynumber: 3.4 Consensus size: 224
42574091 CCATTAACAC
* * *
42574101 AATTGTTGGACTTAATAATTTAACATAATTTGATAATTTTACTAACCATTAACAAAAATTTGGGA
1 AATTTTTGG-CTTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGA
* * * * *
42574166 CTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAATTTTTTGGCTTAATAATT
65 CTTAATAATTTTACATAATTT--T-A-CTAACC--A-TTAA-CAAAA--TTTTGG------GA-C
*
42574231 TTATATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAAT
113 TTA-ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAAT
*
42574296 TTTACATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTACAA
177 TTTACATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAA
** * * *
42574344 TTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATAGTTATA-CAGGGGTTTAATTA
1 AATTTTTGGCTTAATAATTTTACATAA-TTT-GATAATTT--TA-CTA-ACCA-----TTAA-CA
*
42574408 AAATTTTTTGGG-GTTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTG
54 AAA--TTTTGGGACTTAATAATTTTAC--------ATAATTTTACTAACCATTAACAAAATTTTG
****
42574472 GGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAAATTTGGCTTAAT
109 GGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAATTTTTTTGGCTTAAT
42574537 AATTTTACATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAA
174 AATTTTACATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAA
42574588 AATTTTTGGCTTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGAC
1 AATTTTTGGCTTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGAC
*
42574653 TTAATAATTTTATATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAAT
66 TTAATAATTTTACATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAAT
*
42574718 TTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAA
131 TTGATAATTTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAA
42574783 TTTGATAATTTTACCTAGTTTAATTAAAA
196 TTTGATAATTTTACCTAGTTTAATTAAAA
**
42574812 TTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAA
1 AATTTTTGGC---------TTA-ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAA
42574877 ATTTTGGGACTTAATAATTTTACATAATTTTAC
56 ATTTTGGGACTTAATAATTTTACATAATTTTAC
42574910 ATAATGTTAG
Statistics
Matches: 497, Mismatches: 35, Indels: 77
0.82 0.06 0.13
Matches are distributed among these distances:
224 149 0.30
231 7 0.01
232 12 0.02
233 7 0.01
234 78 0.16
238 1 0.00
239 4 0.01
240 2 0.00
242 24 0.05
243 12 0.02
244 135 0.27
245 3 0.01
246 3 0.01
247 4 0.01
248 1 0.00
252 10 0.02
253 4 0.01
254 17 0.03
255 10 0.02
256 1 0.00
258 4 0.01
259 1 0.00
260 1 0.00
262 7 0.01
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (224 bp):
AATTTTTGGCTTAATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGAC
TTAATAATTTTACATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAAT
TTGATAATTTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAA
TTTGATAATTTTACCTAGTTTAATTAAAA
Found at i:42574726 original size:18 final size:18
Alignment explanation
Indices: 42574703--42574737 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42574693 TTGGGACTTA
42574703 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
42574721 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
42574738 AATTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:42574764 original size:38 final size:38
Alignment explanation
Indices: 42574721--42574841 Score: 111
Period size: 38 Copynumber: 3.4 Consensus size: 38
42574711 ACATAATTTG
*
42574721 ATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTA
1 ATAATTTTACATAATTTAATTCAAATTTTTTTGGCTTA
*
42574759 ATAATTTTACATAATTT--TACATAA----TTT-G----
1 ATAATTTTACATAATTTAATTCA-AATTTTTTTGGCTTA
* * *
42574787 ATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTA
1 ATAATTTTACATAATTTAATTCAAATTTTTTTGGCTTA
42574825 ATAATTTTACATAATTT
1 ATAATTTTACATAATTT
42574842 TACATAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 24
0.66 0.08 0.25
Matches are distributed among these distances:
28 15 0.24
29 2 0.03
30 2 0.03
32 1 0.02
33 6 0.10
34 1 0.02
36 3 0.05
37 2 0.03
38 31 0.49
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (38 bp):
ATAATTTTACATAATTTAATTCAAATTTTTTTGGCTTA
Found at i:42574774 original size:10 final size:10
Alignment explanation
Indices: 42574759--42574785 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42574749 TTTTGGCTTA
42574759 ATAATTTTAC
1 ATAATTTTAC
42574769 ATAATTTTAC
1 ATAATTTTAC
42574779 ATAATTT
1 ATAATTT
42574786 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574783 original size:66 final size:66
Alignment explanation
Indices: 42574703--42574914 Score: 324
Period size: 66 Copynumber: 3.2 Consensus size: 66
42574693 TTGGGACTTA
42574703 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTA
42574768 C
66 C
* *
42574769 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTA
42574834 C
66 C
* * *
42574835 ATAATTTTACATAATTTGATAATTTTA-CTAACCATTAA--CAAA-ATTTTGGGACTTAATAATT
1 ATAATTTTACATAATTTGATAATTTTACCTAA--TTTAATTCAAATTTTTTTGG-CTTAATAATT
42574896 TTAC
63 TTAC
42574900 ATAATTTTACATAAT
1 ATAATTTTACATAAT
42574915 GTTAGATTTG
Statistics
Matches: 136, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
64 6 0.04
65 35 0.26
66 91 0.67
67 4 0.03
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (66 bp):
ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTA
C
Found at i:42574840 original size:10 final size:10
Alignment explanation
Indices: 42574825--42574851 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42574815 TTTTGGCTTA
42574825 ATAATTTTAC
1 ATAATTTTAC
42574835 ATAATTTTAC
1 ATAATTTTAC
42574845 ATAATTT
1 ATAATTT
42574852 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574905 original size:10 final size:10
Alignment explanation
Indices: 42574890--42574914 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42574880 TTGGGACTTA
42574890 ATAATTTTAC
1 ATAATTTTAC
42574900 ATAATTTTAC
1 ATAATTTTAC
42574910 ATAAT
1 ATAAT
42574915 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42574971 original size:234 final size:229
Alignment explanation
Indices: 42574258--42574940 Score: 654
Period size: 234 Copynumber: 2.9 Consensus size: 229
42574248 ATTTGATAAT
*
42574258 TTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATAA
1 TTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATAA
*
42574323 TTTTACCTAGTTTAATTACAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
66 TTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
* * **** * * * *
42574388 GTTATAC-AGGGGTTTAATTAAAATTTTTTGGG-GTTAATAATTTTACATAA-TTT-GATAATTT
131 ATTTTACTA-ACCATTAA-CAAAA--TTTTGGGACTTAATAATTTTACATAATTTTACATAATAT
** * *
42574449 TACTAACCAT--TAACAAAATTTTGGGACTTAATAATTTTACATAATTTGATAA
192 TA--AA-TTTGGTAA-AATATTTT--GAC-T--T-A---TA-A-AATTAGA-AA
****
42574501 TTTTACCTAATTTAATTAAAAAAAATTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
1 -TTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
**
42574566 ATTTTACCTAGTTTAATTAAAAAATTTTTGGC---------TTA-ATAATTTTACATAATTTGAT
65 ATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGAT
* *
42574621 AATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTATATAATTTTAC-TAACCATTA
130 AATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTTACATAA-TATT-
* * *
42574685 ACAAAATTTTGGGACTTAATAATTTT-AC--AT--AATTTGATAA
193 ---AAA-TTTGGTA--AAAT-ATTTTGACTTATAAAATTAGA-AA
*
42574725 TTTTACCTAATTTAATTCAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
1 -TTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
42574790 ATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGAT
65 ATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGAT
* *
42574855 AATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTTACATAATGTTAG
130 AATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTTACATAATATTAA
42574920 ATTTGGTAAAATATTTTGACT
195 ATTTGGTAAAATATTTTGACT
42574941 GGTACTAACA
Statistics
Matches: 373, Mismatches: 39, Indels: 70
0.77 0.08 0.15
Matches are distributed among these distances:
224 100 0.27
226 5 0.01
227 5 0.01
228 1 0.00
229 6 0.02
230 2 0.01
231 8 0.02
232 16 0.04
233 13 0.03
234 108 0.29
235 7 0.02
236 3 0.01
237 2 0.01
238 2 0.01
239 2 0.01
240 5 0.01
244 88 0.24
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.47
Consensus pattern (229 bp):
TTTACCTAATTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATAA
TTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTACATAATTTTACATAATTTGATA
ATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTTACATAATATTAAA
TTTGGTAAAATATTTTGACTTATAAAATTAGAAA
Found at i:42581723 original size:9 final size:9
Alignment explanation
Indices: 42581709--42581736 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42581699 TATAGTTTGA
42581709 TATTCGAAT
1 TATTCGAAT
42581718 TATTCGAAT
1 TATTCGAAT
42581727 TATTCGAAT
1 TATTCGAAT
42581736 T
1 T
42581737 TGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42583384 original size:25 final size:25
Alignment explanation
Indices: 42583343--42583390 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
42583333 TATTTGTTTA
* *
42583343 CACTTTTACTTTTAAAATTAATTCT
1 CACTTTTACTTTAAAAAATAATTCT
42583368 CACTTTTA-TATTAAAAAATAATT
1 CACTTTTACT-TTAAAAAATAATT
42583391 TATTAGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (25 bp):
CACTTTTACTTTAAAAAATAATTCT
Found at i:42584625 original size:60 final size:60
Alignment explanation
Indices: 42584523--42584635 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
42584513 TTAATATAAC
* * *
42584523 ATTTGGTACCTGAACTTGACATTTGTTCTTAATTTGGTACCTAAACTTCTTTTGGGTCCA
1 ATTTGGTACCCGAACTTGACATTTGTTCTTAACTTGGCACCTAAACTTCTTTTGGGTCCA
* * * * *
42584583 ATTTGGTACCCGAAGTTGGCATTT-TTTTCTAACTTGGCACCTAAGCTTTTTTT
1 ATTTGGTACCCGAACTTGACATTTGTTCT-TAACTTGGCACCTAAACTTCTTTT
42584636 TTTTAGGTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 3 0.07
60 41 0.93
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (60 bp):
ATTTGGTACCCGAACTTGACATTTGTTCTTAACTTGGCACCTAAACTTCTTTTGGGTCCA
Found at i:42585113 original size:25 final size:25
Alignment explanation
Indices: 42585078--42585126 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
42585068 AAAAAGTGAC
* *
42585078 AAGTTTGGGTACCAAATTGGAAAAA
1 AAGTTTAGGTACCAAATTAGAAAAA
42585103 AAGTTTAGGTACCAAATTAGAAAA
1 AAGTTTAGGTACCAAATTAGAAAA
42585127 TATTAAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.24
Consensus pattern (25 bp):
AAGTTTAGGTACCAAATTAGAAAAA
Done.