Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 136 of 325
Found at i:41261905 original size:34 final size:34
Alignment explanation
Indices: 41261866--41261931 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
41261856 ATGGTTGAAG
41261866 AATGATTTTGTATATAAGTTAAGCCATGTGATAC
1 AATGATTTTGTATATAAGTTAAGCCATGTGATAC
41261900 AATGATTTTGTATATAAGTTAAGCCATGTGAT
1 AATGATTTTGTATATAAGTTAAGCCATGTGAT
41261932 TTGGCTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (34 bp):
AATGATTTTGTATATAAGTTAAGCCATGTGATAC
Found at i:41269266 original size:43 final size:42
Alignment explanation
Indices: 41269219--41269317 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
41269209 TCCCAGACGT
*
41269219 GGTCTTACATGTAATTAAATATCGATG-CCACTATCCCAGATAG
1 GGTCTTACATGTAATCAAATA-CGATGTCCA-TATCCCAGATAG
* * * * *
41269262 GGTCTTACATGAAATCAAATACGATGTCGATGTCCCATATAT
1 GGTCTTACATGTAATCAAATACGATGTCCATATCCCAGATAG
41269304 GGTCTTACATGTAA
1 GGTCTTACATGTAA
41269318 ATCATAAGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 27 0.56
43 21 0.44
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAATACGATGTCCATATCCCAGATAG
Found at i:41269321 original size:43 final size:44
Alignment explanation
Indices: 41269209--41269371 Score: 131
Period size: 43 Copynumber: 3.8 Consensus size: 44
41269199 AATGCCAACG
** *
41269209 TCCCAGACGTGGTCTTACATGT-AATTAAATATCGATGCCACTA
1 TCCCAGATATGGTCTTACATGTAAATCAAATATCGATGCCACTA
* * *
41269252 TCCCAGATAGGGTCTTACATG-AAATCAAATA-CGATGTCGA-TG
1 TCCCAGATATGGTCTTACATGTAAATCAAATATCGATG-CCACTA
* * * * *
41269294 TCCCATATATGGTCTTACATGTAAATCATAA-GTCCATGCCAATG
1 TCCCAGATATGGTCTTACATGTAAATCA-AATATCGATGCCACTA
** * *
41269338 TCCCAGACGTGGTCTTACATG-AAAACACATATCG
1 TCCCAGATATGGTCTTACATGTAAATCAAATATCG
41269372 GATCCTATGT
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
42 26 0.27
43 43 0.45
44 26 0.27
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (44 bp):
TCCCAGATATGGTCTTACATGTAAATCAAATATCGATGCCACTA
Found at i:41271188 original size:40 final size:39
Alignment explanation
Indices: 41271077--41271227 Score: 151
Period size: 40 Copynumber: 3.8 Consensus size: 39
41271067 TATAACATGT
* ** *
41271077 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
*
41271117 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* *** *
41271157 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* *
41271197 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAT
41271228 CATTCAATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 15 0.16
40 80 0.84
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
Found at i:41271211 original size:80 final size:79
Alignment explanation
Indices: 41271077--41271227 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41271067 TATAACATGT
*
41271077 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGG-CTTAGCC
41271142 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41271157 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGCTTAGC
41271220 CCGGATAT
64 CCGGATAT
41271228 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41272558 original size:19 final size:19
Alignment explanation
Indices: 41272516--41272551 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41272506 ATGAACACTT
*
41272516 TTTTTTTTTTCATTACTCA
1 TTTTTTTTTCCATTACTCA
41272535 TTTTTTTTTCCA-TACTC
1 TTTTTTTTTCCATTACTC
41272552 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTTTTCCATTACTCA
Found at i:41278998 original size:40 final size:40
Alignment explanation
Indices: 41278953--41279081 Score: 133
Period size: 40 Copynumber: 3.2 Consensus size: 40
41278943 CGGAATATAA
41278953 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
* * *
41278993 CCGGATAGAATG-ACT-CGCACGAATGCCTTCGGGTCTTAG-
1 CCGGATATAA-GCA-TGTGCACAAATGCCTTCGGGTCTTAGC
* * *
41279032 CCGGATAT-AGC-CGCTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAGCATG-T-GCACAAATGCCTTCGGGTCTTAGC
41279072 CCGGATATAA
1 CCGGATATAA
41279082 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 27 0.38
40 40 0.56
41 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (40 bp):
CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41279096 original size:40 final size:40
Alignment explanation
Indices: 41278969--41279119 Score: 128
Period size: 40 Copynumber: 3.8 Consensus size: 40
41278959 ATAAGCATGT
* * * *
41278969 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC-
1 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATCAC-CA
* ** * *
41279009 GCACGAA-TGCCTTCGGGTCTT-AGCCGGATATAGCCGCTA
1 GCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATCACCA
**
41279048 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATCACCA
* * * *
41279088 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAACCCGGATAT
41279120 CATTCAATTT
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.02
39 27 0.30
40 58 0.65
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAACCCGGATATAATCACCA
Found at i:41279102 original size:79 final size:80
Alignment explanation
Indices: 41278969--41279119 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
41278959 ATAAGCATGT
* *
41278969 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAG-C
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
41279033 CGGATATAGCCGCTA
66 CGGATATAGCCGCTA
* * ** * *
41279048 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
41279111 CCCGGATAT
64 CCCGGATAT
41279120 CATTCAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 50 0.82
80 8 0.13
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCGCTA
Found at i:41284351 original size:24 final size:24
Alignment explanation
Indices: 41284293--41284368 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 24
41284283 AGACATGGCC
*
41284293 AGTAAGCTCT-TCATGAGCTGATAAAT
1 AGTAAGCTCTAT--TGAGTTGA-AAAT
41284319 AGTAAGCTCTATTGAGTTGAAAAT
1 AGTAAGCTCTATTGAGTTGAAAAT
* *
41284343 GGTACGCTCTATTGAGTTGAACAAT
1 AGTAAGCTCTATTGAGTTGAA-AAT
41284368 A
1 A
41284369 AGCTCCAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 23 0.52
25 10 0.23
26 10 0.23
27 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (24 bp):
AGTAAGCTCTATTGAGTTGAAAAT
Found at i:41286626 original size:43 final size:43
Alignment explanation
Indices: 41286577--41286709 Score: 176
Period size: 43 Copynumber: 3.1 Consensus size: 43
41286567 ACATATCGTA
* * *
41286577 CAATGCCAACGTCCCAGACGTGGTCTTACACATTATTACATAT
1 CAATGCCAACGTCCCAAACATGGTCTTACACATAATTACATAT
* * * *
41286620 CAATGCCAAGGTCCCATACTTGGTCTTACATATAATTACATAT
1 CAATGCCAACGTCCCAAACATGGTCTTACACATAATTACATAT
** *
41286663 TGATGCCAATGTCCCAAACATGGTCTTACACATAATTACATAT
1 CAATGCCAACGTCCCAAACATGGTCTTACACATAATTACATAT
41286706 CAAT
1 CAAT
41286710 ATCACATATA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (43 bp):
CAATGCCAACGTCCCAAACATGGTCTTACACATAATTACATAT
Found at i:41292425 original size:12 final size:13
Alignment explanation
Indices: 41292391--41292428 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
41292381 TTTTTTTAAG
41292391 TAGTTTATTGATA
1 TAGTTTATTGATA
41292404 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
41292418 TAGTTTATTGA
1 TAGTTTATTGA
41292429 GAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 7 0.32
15 5 0.23
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:41296610 original size:43 final size:43
Alignment explanation
Indices: 41296550--41296771 Score: 327
Period size: 43 Copynumber: 5.2 Consensus size: 43
41296540 GCATGAAACT
* * * *
41296550 CGGTGATGTGTATTCGGGCCTTCATGCCTAGCGGGCTTTGTGT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
41296593 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * *
41296636 CAGTGATGTGTATTCGGGCCTTCGTACCTAGTAGGCTTCATGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
41296679 CGGTGATGTGTATTCAGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * **
41296722 CAGTGATGTGTATTCGGGTCTTCGTGCCTAGCAGGCTTAATGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
41296765 CGGTGAT
1 CGGTGAT
41296772 TCTAGCAAGG
Statistics
Matches: 160, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.13, C:0.23, G:0.32, T:0.32
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:41297045 original size:28 final size:28
Alignment explanation
Indices: 41296957--41297053 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
41296947 CTTTAACCGA
*
41296957 GCACTATGTGTGCGAGATCAGT-AATTGAG
1 GCACTATGTGTGCGAGATC-GTCAACTG-G
* * * * *
41296986 GCACTGTGTGTGCGAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGATCGTCAACTGG
*
41297014 GCACTATGTGTGTGAGATCGGTCAA-TGG
1 GCACTATGTGTGCGAGATC-GTCAACTGG
*
41297042 GCACTAAGTGTG
1 GCACTATGTGTG
41297054 TGAAATGAGA
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
28 29 0.55
29 24 0.45
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTCAACTGG
Found at i:41298581 original size:12 final size:13
Alignment explanation
Indices: 41298547--41298586 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
41298537 TTTTTTTAAG
41298547 TAGTTTATTGATA
1 TAGTTTATTGATA
41298560 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
41298574 TAGTTTATTGATA
1 TAGTTTATTGATA
41298587 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:41310641 original size:37 final size:37
Alignment explanation
Indices: 41310592--41310666 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
41310582 ATTCAAGGAG
41310592 TTCATTCATCATTCAGGAAGTTTCACCTCTCTCCCTA
1 TTCATTCATCATTCAGGAAGTTTCACCTCTCTCCCTA
41310629 TTCATTCATCATTCAGGAAGTTTCACCTCTCTCCCTA
1 TTCATTCATCATTCAGGAAGTTTCACCTCTCTCCCTA
41310666 T
1 T
41310667 CTTATGATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.32, G:0.08, T:0.39
Consensus pattern (37 bp):
TTCATTCATCATTCAGGAAGTTTCACCTCTCTCCCTA
Found at i:41314408 original size:93 final size:93
Alignment explanation
Indices: 41314295--41314466 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
41314285 CGCCCATAAG
*
41314295 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
41314360 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
41314388 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
41314453 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41314467 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:41314463 original size:46 final size:46
Alignment explanation
Indices: 41314288--41314463 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
41314278 TGTAACCCGC
* *
41314288 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
41314334 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
41314384 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41314427 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
41314464 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 28 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41324835 original size:39 final size:40
Alignment explanation
Indices: 41324658--41324835 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
41324648 CGGATGATAA
* *
41324658 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
41324698 TCGAGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41324738 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41324778 CCGGGCTAAGTCTCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
41324818 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41324836 TACTTGGTTT
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
39 17 0.14
40 104 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41329903 original size:29 final size:29
Alignment explanation
Indices: 41329813--41329972 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
41329803 ACTCGATTTC
* * **
41329813 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
41329842 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
41329870 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
41329900 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41329929 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41329958 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41329973 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41337952 original size:29 final size:29
Alignment explanation
Indices: 41337862--41338021 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
41337852 ACTCGATTTC
* * **
41337862 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
41337891 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
41337919 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
41337949 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41337978 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41338007 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41338022 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41340781 original size:23 final size:23
Alignment explanation
Indices: 41340749--41340793 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
41340739 TAAATAGATA
41340749 ATAGTATGATAGACTTCACTGAG
1 ATAGTATGATAGACTTCACTGAG
*
41340772 ATAGTGTGATAGACTTCACTGA
1 ATAGTATGATAGACTTCACTGA
41340794 CAATCCCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (23 bp):
ATAGTATGATAGACTTCACTGAG
Found at i:41346076 original size:43 final size:43
Alignment explanation
Indices: 41346029--41346146 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
41346019 ACTGCCAACA
* * * *
41346029 TCCCAGACTTGGTCTTACATGTA-ATCACATATCGATGCCACTG
1 TCCCAGACATGGTCTTACACG-AGAACACATATCGATGCCAATG
* *
41346072 TCCCAGACAAGGTCTTACACGAGAACACATATCGATGCTAATG
1 TCCCAGACATGGTCTTACACGAGAACACATATCGATGCCAATG
* *
41346115 TCCTAGACATGGTCCTACACGAGAACACATAT
1 TCCCAGACATGGTCTTACACGAGAACACATAT
41346147 TGGAAATCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAGAACACATATCGATGCCAATG
Found at i:41350456 original size:17 final size:18
Alignment explanation
Indices: 41350414--41350462 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
41350404 AGTTGAAAAG
41350414 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
41350433 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
41350450 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
41350463 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:41351350 original size:40 final size:40
Alignment explanation
Indices: 41351284--41351450 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41351274 AAATTGAATG
* * *
41351284 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41351323 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41351363 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41351403 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41351443 ATATCCGG
1 ATATCCGG
41351451 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41358465 original size:17 final size:18
Alignment explanation
Indices: 41358423--41358471 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
41358413 AGTTGAAAAG
41358423 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
41358442 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
41358459 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
41358472 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:41359359 original size:40 final size:40
Alignment explanation
Indices: 41359293--41359459 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41359283 AAATTGAATG
* * *
41359293 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41359332 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41359372 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41359412 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41359452 ATATCCGG
1 ATATCCGG
41359460 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41361153 original size:24 final size:24
Alignment explanation
Indices: 41361093--41361188 Score: 111
Period size: 24 Copynumber: 3.9 Consensus size: 24
41361083 GAGACATAGT
* *
41361093 CGGTAAGCTCTTCTTAAGTTGATAAA
1 CGGTAAGCTC-TATTAAGCTGA-AAA
*
41361119 CAGTAAGCTCTATTAAGCTGAAAA
1 CGGTAAGCTCTATTAAGCTGAAAA
* * *
41361143 TGGTAAGCTCTATTGAGCTAAAAA
1 CGGTAAGCTCTATTAAGCTGAAAA
*
41361167 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTAAGCTGAA
41361189 CAGTAAGCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 43 0.70
25 9 0.15
26 9 0.15
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (24 bp):
CGGTAAGCTCTATTAAGCTGAAAA
Found at i:41361179 original size:48 final size:46
Alignment explanation
Indices: 41361116--41361221 Score: 135
Period size: 48 Copynumber: 2.3 Consensus size: 46
41361106 TTAAGTTGAT
* *
41361116 AAACAGTAAGCTCTATTAAGCTGAAAATGGTAAGCTCTATTGAGCTAA
1 AAACAGTAAGCTCTATTAAGCTGAAAA--GTAAGCTCCAATGAGCTAA
* * *
41361164 AAACGGTAAGCTCTATTGAGCTGAACAGTAAGCTCCAATGAGCT--
1 AAACAGTAAGCTCTATTAAGCTGAAAAGTAAGCTCCAATGAGCTAA
41361208 AAACAGTAAGCTCT
1 AAACAGTAAGCTCT
41361222 TACGAGCTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 13 0.25
46 15 0.29
48 24 0.46
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (46 bp):
AAACAGTAAGCTCTATTAAGCTGAAAAGTAAGCTCCAATGAGCTAA
Found at i:41361197 original size:22 final size:22
Alignment explanation
Indices: 41361115--41361221 Score: 117
Period size: 24 Copynumber: 4.7 Consensus size: 22
41361105 CTTAAGTTGA
*
41361115 TAAACAGTAAGCTCTATTAAGC
1 TAAACAGTAAGCTCTATTGAGC
41361137 TGAAA-ATGGTAAGCTCTATTGAGC
1 T-AAACA--GTAAGCTCTATTGAGC
*
41361161 TAAAAACGGTAAGCTCTATTGAGC
1 T--AAACAGTAAGCTCTATTGAGC
* * *
41361185 TGAACAGTAAGCTCCAATGAGC
1 TAAACAGTAAGCTCTATTGAGC
41361207 TAAACAGTAAGCTCT
1 TAAACAGTAAGCTCT
41361222 TACGAGCTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
22 32 0.45
23 3 0.04
24 33 0.46
25 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (22 bp):
TAAACAGTAAGCTCTATTGAGC
Found at i:41361228 original size:22 final size:21
Alignment explanation
Indices: 41361115--41361230 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 21
41361105 CTTAAGTTGA
*
41361115 TAAACAGTAAGCTCTATTAAGC
1 TAAACAGTAAGCTCTA-TGAGC
41361137 TGAAA-ATGGTAAGCTCTATTGAGC
1 T-AAACA--GTAAGCTCTA-TGAGC
*
41361161 TAAAAACGGTAAGCTCTATTGAGC
1 T--AAACAGTAAGCTCTA-TGAGC
* *
41361185 TGAACAGTAAGCTCCAATGAGC
1 TAAACAGTAAGCT-CTATGAGC
*
41361207 TAAACAGTAAGCTCTTACGAGC
1 TAAACAGTAAGCTC-TATGAGC
41361229 TA
1 TA
41361231 TGGTGAGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.01
22 36 0.46
23 5 0.06
24 33 0.42
25 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (21 bp):
TAAACAGTAAGCTCTATGAGC
Found at i:41364979 original size:30 final size:30
Alignment explanation
Indices: 41364945--41365015 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
41364935 ACCCTAGGGG
41364945 ACACACGGCTGTGAAACATACCCGTGTGTC
1 ACACACGGCTGTGAAACATACCCGTGTGTC
*
41364975 ACACACGGCTGTGTAACATACCCGTGTGTC
1 ACACACGGCTGTGAAACATACCCGTGTGTC
*
41365005 ACACACAGCTG
1 ACACACGGCTG
41365016 AGACACACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.20
Consensus pattern (30 bp):
ACACACGGCTGTGAAACATACCCGTGTGTC
Found at i:41369702 original size:40 final size:40
Alignment explanation
Indices: 41369646--41369813 Score: 184
Period size: 40 Copynumber: 4.2 Consensus size: 40
41369636 CAATTGAATG
* *
41369646 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
41369687 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * *
41369726 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
** *
41369766 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
41369806 ATATCCGG
1 ATATCCGG
41369814 TTGTATTCCG
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 98 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:41369779 original size:80 final size:79
Alignment explanation
Indices: 41369646--41369813 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 79
41369636 CAATTGAATG
* *
41369646 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
41369711 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
41369726 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
41369790 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
41369806 ATATCCGG
1 ATATCCGG
41369814 TTGTATTCCG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 2 0.03
80 76 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:41377670 original size:40 final size:40
Alignment explanation
Indices: 41377614--41377781 Score: 184
Period size: 40 Copynumber: 4.2 Consensus size: 40
41377604 CAATTGAATG
* *
41377614 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
41377655 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * *
41377694 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
** *
41377734 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
41377774 ATATCCGG
1 ATATCCGG
41377782 TTGTATTCCG
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 98 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:41377747 original size:80 final size:79
Alignment explanation
Indices: 41377614--41377781 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 79
41377604 CAATTGAATG
* *
41377614 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
41377679 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
41377694 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
41377758 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
41377774 ATATCCGG
1 ATATCCGG
41377782 TTGTATTCCG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 2 0.03
80 76 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:41383296 original size:40 final size:40
Alignment explanation
Indices: 41383251--41383417 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41383241 CGGAATATAA
41383251 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41383291 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41383331 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41383371 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41383410 CCGGATAT
1 CCGGATAT
41383418 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41391291 original size:40 final size:40
Alignment explanation
Indices: 41391246--41391413 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41391236 CGGAATATAA
41391246 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41391286 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41391326 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
41391366 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41391406 CCGGATAT
1 CCGGATAT
41391414 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41407061 original size:42 final size:43
Alignment explanation
Indices: 41406953--41407109 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 43
41406943 AGCTTGTACA
* * *
41406953 ATGCCAACGTCCCAGATGTGGTCTTACATGTAAACAAATATCG
1 ATGCCAATGTCCCAGATATGGTCTTACACGTAAACAAATATCG
* * * * *
41406996 ATGCCACTATCCTAAATAGGGTCTTACACG-AAATCAAATA-CG
1 ATGCCAATGTCCCAGATATGGTCTTACACGTAAA-CAAATATCG
* * * *
41407038 ATGCCAATGTCCCAGACATGGTCTTACTCATAAAACATAA-GTCG
1 ATGCCAATGTCCCAGATATGGTCTTACACGT-AAACA-AATATCG
* * * *
41407082 ATGTCAATGTCCTAGAAAAGGTCTTACA
1 ATGCCAATGTCCCAGATATGGTCTTACA
41407110 TGAAAACACA
Statistics
Matches: 87, Mismatches: 22, Indels: 9
0.74 0.19 0.08
Matches are distributed among these distances:
42 27 0.31
43 30 0.34
44 30 0.34
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATATGGTCTTACACGTAAACAAATATCG
Found at i:41409484 original size:17 final size:18
Alignment explanation
Indices: 41409462--41409495 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41409452 TTTTAATTAA
*
41409462 GGTTAATTTGG-TAATTT
1 GGTTAATATGGTTAATTT
41409479 GGTTAATATGGTTAATT
1 GGTTAATATGGTTAATT
41409496 GAATGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (18 bp):
GGTTAATATGGTTAATTT
Found at i:41409490 original size:9 final size:9
Alignment explanation
Indices: 41409462--41409495 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41409452 TTTTAATTAA
41409462 GGTTAATTT
1 GGTTAATTT
41409471 GG-TAATTT
1 GGTTAATTT
*
41409479 GGTTAATAT
1 GGTTAATTT
41409488 GGTTAATT
1 GGTTAATT
41409496 GAATGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (9 bp):
GGTTAATTT
Found at i:41410424 original size:24 final size:24
Alignment explanation
Indices: 41410387--41410461 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
41410377 AGACTCACCG
* * * *
41410387 CAGCTCGTATGAGATTGCTGTTTT
1 CAGCTTGTAAGAGATTACTGTTCT
41410411 CAGCTTGTAAGAGATTACTGTTCT
1 CAGCTTGTAAGAGATTACTGTTCT
* *
41410435 CAGCTTGTATGAGCTTACTG--CT
1 CAGCTTGTAAGAGATTACTGTTCT
41410457 CAGCT
1 CAGCT
41410462 CATCAGAGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.16
24 38 0.84
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (24 bp):
CAGCTTGTAAGAGATTACTGTTCT
Found at i:41412145 original size:27 final size:27
Alignment explanation
Indices: 41412115--41412188 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
41412105 ATATATACTG
* *
41412115 CACATAGGGGTAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
41412142 CACATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGGCAAAACAGTCATCTTAC
41412169 CACATAATGGGCAAAACAGT
1 CACATAA-GGGCAAAACAGT
41412189 TTGCCACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATCTTAC
Found at i:41412195 original size:24 final size:25
Alignment explanation
Indices: 41412141--41412207 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 25
41412131 AGTCATCTTA
41412141 CCACATAA-GGGCAAAACAGTCATTTTG
1 CCACATAATGGGCAAAACAG---TTTTG
41412168 CCACATAATGGGCAAAACAG-TTTG
1 CCACATAATGGGCAAAACAGTTTTG
41412192 CCACATAATGGGCAAA
1 CCACATAATGGGCAAA
41412208 TTAGTCATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 20 0.51
27 8 0.21
28 11 0.28
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (25 bp):
CCACATAATGGGCAAAACAGTTTTG
Found at i:41415853 original size:29 final size:28
Alignment explanation
Indices: 41415810--41415894 Score: 104
Period size: 27 Copynumber: 3.1 Consensus size: 28
41415800 ATATATACTG
41415810 CACATAAGGGCAAAAAATAGTAATTTTAC
1 CACATAAGGG-AAAAAATAGTAATTTTAC
*
41415839 CACATAAGGGAAAAACA-A-TCATTTTAC
1 CACATAAGGGAAAAA-ATAGTAATTTTAC
* *
41415866 CACATAAGGG-TAAAATAGTTATTTTAC
1 CACATAAGGGAAAAAATAGTAATTTTAC
41415893 CA
1 CA
41415895 TTTAGGGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 28 0.56
28 6 0.12
29 11 0.22
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (28 bp):
CACATAAGGGAAAAAATAGTAATTTTAC
Found at i:41420977 original size:8 final size:8
Alignment explanation
Indices: 41420954--41420991 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
41420944 ATAAAATATT
*
41420954 AATAATTC
1 AATAATTA
41420962 AATAAATTA
1 AAT-AATTA
41420971 AATAATTA
1 AATAATTA
41420979 AATAATTA
1 AATAATTA
41420987 AATAA
1 AATAA
41420992 AATTGAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAATTA
Found at i:41423507 original size:46 final size:46
Alignment explanation
Indices: 41423380--41423508 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
41423370 TGTAACCCGC
* * *
41423380 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGAACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
41423426 CCATAAGTGAACTCGGGCTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
41423472 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
41423509 TGCCCAAATA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:41430969 original size:65 final size:65
Alignment explanation
Indices: 41430865--41430992 Score: 238
Period size: 65 Copynumber: 2.0 Consensus size: 65
41430855 CCCCTAGGGT
* *
41430865 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATATTTGACTGTTAATATTTACTGCATGCCATGTTATTATTATCTGA
41430930 TAAGGTTGACCTGAATGCATATTTGACTGTTAATATTTACTGCATGCCATGTTATTATTATCT
1 TAAGGTTGACCTGAATGCATATTTGACTGTTAATATTTACTGCATGCCATGTTATTATTATCT
41430993 AATGCATGGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATATTTGACTGTTAATATTTACTGCATGCCATGTTATTATTATCTGA
Found at i:41435067 original size:65 final size:65
Alignment explanation
Indices: 41434957--41435080 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 65
41434947 TAGGGTTGAG
41434957 GTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACGCCATGTTATTATTATCTGATAAA
1 GTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACGCCATGTTATTATTATCTGATAAA
* *
41435022 GTTGTCCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCT
1 GTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACGCCATGTTATTATTATCT
41435081 AATGCATGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (65 bp):
GTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCACGCCATGTTATTATTATCTGATAAA
Found at i:41440304 original size:19 final size:20
Alignment explanation
Indices: 41440280--41440317 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41440270 GGTACCACCA
41440280 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41440299 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41440318 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41440714 original size:46 final size:46
Alignment explanation
Indices: 41440542--41440714 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
41440532 AACCCGCCCC
* * * * * *
41440542 TAAGTGAAATCGGACTCAACTCAATGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
*
41440588 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACATCCA
* * *
41440636 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
*
41440681 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41440715 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 58 0.55
47 29 0.27
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
Found at i:41445484 original size:42 final size:42
Alignment explanation
Indices: 41445425--41445546 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
41445415 TAGGGTTAGT
41445425 TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
41445467 TGAGATTTTGTGTAAGACCATAGCTGGGATAATGGCATCTATA
1 TGAGATTATGTGTAAGACCATATCTGGGAT-ATGGCATCGATA
**** *
41445510 TGAGATCCCATGTAAGACCATATCTTGGATATGGCAT
1 TGAGATTATGTGTAAGACCATATCTGGGATATGGCAT
41445547 TGGTATGGTA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 35 0.50
43 35 0.50
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:41445524 original size:43 final size:42
Alignment explanation
Indices: 41445435--41445546 Score: 152
Period size: 43 Copynumber: 2.6 Consensus size: 42
41445425 TGAGATTATG
****
41445435 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTTG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCCCA
* *
41445477 TGTAAGACCATAGCTGGGATAATGGCATCTATATGAGATCCCA
1 TGTAAGACCATATCTGGGAT-ATGGCATCGATATGAGATCCCA
*
41445520 TGTAAGACCATATCTTGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
41445547 TGGTATGGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 26 0.43
43 35 0.57
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCCCA
Found at i:41447821 original size:100 final size:100
Alignment explanation
Indices: 41447648--41447831 Score: 305
Period size: 100 Copynumber: 1.8 Consensus size: 100
41447638 GTGAGGTCAC
* **
41447648 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTAGTCGCATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTAGTCGCATGTGTAGTACTAAGT
*
41447713 GTAGGCTACTATGCGTACCTAAAAACAGTGATCAT
66 GCAGGCTACTATGCGTACCTAAAAACAGTGATCAT
* * *
41447748 GTGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAGATTATTGGTCGCATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTAGTCGCATGTGTAGTACTAAGT
41447813 GCAGGCTACTATGCGTACC
66 GCAGGCTACTATGCGTACC
41447832 AGATAGCTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (100 bp):
GTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTAGTCGCATGTGTAGTACTAAGT
GCAGGCTACTATGCGTACCTAAAAACAGTGATCAT
Found at i:41447831 original size:49 final size:49
Alignment explanation
Indices: 41447649--41447836 Score: 214
Period size: 49 Copynumber: 3.8 Consensus size: 49
41447639 TGAGGTCACG
* * ** *
41447649 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
* * * * * ***
41447698 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCTAAAAACAGTGATCATG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-AGATA-ATTGGTCGCA
* * *
41447749 TGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
41447798 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
41447837 GCTTCAACTA
Statistics
Matches: 110, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
49 71 0.65
50 4 0.04
51 35 0.32
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
Found at i:41449795 original size:29 final size:29
Alignment explanation
Indices: 41449753--41449826 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
41449743 CGGGTTAGGG
* *
41449753 ACATGGCCGTGTGACCACATGGCCTACCC
1 ACATGGGCGTGTGACCACATAGCCTACCC
*
41449782 ACATGGGCTTGTGACCACATAGCCTACCC
1 ACATGGGCGTGTGACCACATAGCCTACCC
*
41449811 ACACGGGCGTGTGACC
1 ACATGGGCGTGTGACC
41449827 CCTGTTCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.18
Consensus pattern (29 bp):
ACATGGGCGTGTGACCACATAGCCTACCC
Found at i:41454529 original size:40 final size:40
Alignment explanation
Indices: 41454459--41454676 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
41454449 AACCCAAGTA
* *
41454459 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
41454498 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41454538 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
41454578 CCTTCGGGACGTAGCCCGAATTTAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
41454618 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41454658 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41454677 TTATCATCCG
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 14 0.09
40 148 0.91
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41462628 original size:40 final size:40
Alignment explanation
Indices: 41462558--41462775 Score: 291
Period size: 40 Copynumber: 5.5 Consensus size: 40
41462548 AACCCAAGTA
* * *
41462558 CCTTCGGGATTTAG-CCGGATCTAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
41462597 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
41462637 CCTTTGGGAATTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41462677 CCTTCGGGA-TGTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACT-TAGCCCGGATATAGTAACTCGCACAAATG
* * *
41462717 CCTTCAGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41462757 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41462776 TTATCATCTG
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.09
40 144 0.90
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41464848 original size:40 final size:40
Alignment explanation
Indices: 41464803--41464970 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
41464793 CGGAATACAA
41464803 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * * *
41464843 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* **
41464883 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* *
41464923 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC
41464963 CCGGATAT
1 CCGGATAT
41464971 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
Found at i:41464943 original size:80 final size:80
Alignment explanation
Indices: 41464803--41464970 Score: 241
Period size: 80 Copynumber: 2.1 Consensus size: 80
41464793 CGGAATACAA
* *
41464803 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
41464868 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
41464883 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAA
*
41464946 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
41464963 CCGGATAT
1 CCGGATAT
41464971 CATTCAATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 76 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:41472812 original size:40 final size:40
Alignment explanation
Indices: 41472767--41472934 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
41472757 CGGAATACAA
41472767 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * * *
41472807 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* **
41472847 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* *
41472887 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC
41472927 CCGGATAT
1 CCGGATAT
41472935 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
Found at i:41472907 original size:80 final size:80
Alignment explanation
Indices: 41472767--41472934 Score: 241
Period size: 80 Copynumber: 2.1 Consensus size: 80
41472757 CGGAATACAA
* *
41472767 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
41472832 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
41472847 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAA
*
41472910 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
41472927 CCGGATAT
1 CCGGATAT
41472935 CATTCAATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 76 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:41483762 original size:29 final size:29
Alignment explanation
Indices: 41483723--41483797 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
41483713 GGTTGAGAGA
* *
41483723 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
41483752 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
41483781 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
41483798 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:41488439 original size:41 final size:40
Alignment explanation
Indices: 41488366--41488463 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 40
41488356 AGAATGATTC
*
41488366 CGCACACTTAGTGCCACCTCAAATAACCAAAGCTATCTCGATAT
1 CGCACACTTAGTG---CCTCAAATAACCAAAGCTAT-TCCATAT
* *
41488410 CGCACACTTAGTGCCTCATATAACCAAAGCTATTCCATTT
1 CGCACACTTAGTGCCTCAAATAACCAAAGCTATTCCATAT
*
41488450 CGTACACTTAGTGC
1 CGCACACTTAGTGC
41488464 TATTTATAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 18 0.36
41 19 0.38
44 13 0.26
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (40 bp):
CGCACACTTAGTGCCTCAAATAACCAAAGCTATTCCATAT
Found at i:41488472 original size:40 final size:40
Alignment explanation
Indices: 41488366--41488503 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 40
41488356 AGAATGATTC
* *
41488366 CGCACACTTAGTGCCACCTCAAATAACCAAAGCTATCTCGATAT
1 CGCACACTTAGTG---CCTCATATAACCAAAGCTAT-TCCATAT
*
41488410 CGCACACTTAGTGCCTCATATAACCAAAGCTATTCCATTT
1 CGCACACTTAGTGCCTCATATAACCAAAGCTATTCCATAT
* * *
41488450 CGTACACTTAGTG-CT-ATTTATAACCGAAA-CTATTTCAAAT
1 CGCACACTTAGTGCCTCA--TATAACC-AAAGCTATTCCATAT
*
41488490 CACACACTTAGTGC
1 CGCACACTTAGTGC
41488504 GATCATAGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 43 0.53
41 22 0.27
44 13 0.16
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (40 bp):
CGCACACTTAGTGCCTCATATAACCAAAGCTATTCCATAT
Found at i:41489565 original size:19 final size:19
Alignment explanation
Indices: 41489529--41489567 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41489519 TTTTCATCAT
* *
41489529 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
41489548 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
41489567 A
1 A
41489568 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:41490077 original size:28 final size:28
Alignment explanation
Indices: 41490029--41490147 Score: 211
Period size: 28 Copynumber: 4.2 Consensus size: 28
41490019 GTGACAGAGT
* *
41490029 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGGGC
41490058 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
41490086 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
41490114 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
41490142 CACCAG
1 CACCAG
41490148 GACGCTTCCT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
28 81 0.92
29 7 0.08
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGGGC
Found at i:41490291 original size:28 final size:28
Alignment explanation
Indices: 41490251--41490317 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
41490241 CAAAATTAAC
*
41490251 CATAGGGGTATAAAGGTCATTTTGCATA
1 CATAGGGGTATAAAGGTAATTTTGCATA
*
41490279 CATAGGGGTATAATGGTAATTTTGCATA
1 CATAGGGGTATAAAGGTAATTTTGCATA
41490307 CATAGGGGTAT
1 CATAGGGGTAT
41490318 TCTAGTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (28 bp):
CATAGGGGTATAAAGGTAATTTTGCATA
Found at i:41501896 original size:43 final size:43
Alignment explanation
Indices: 41501849--41501939 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
41501839 TCTTATATGT
* *
41501849 AATCAAATATCGATGTCACTGTACCAGACAG-GGTCTTACACG-A
1 AATCAAATAT-GATGCCAATGTACCAGA-AGTGGTCTTACACGTA
* *
41501892 AATCAAATATGATGCCAATGTCCCAGAGGTGGTCTTACACGTA
1 AATCAAATATGATGCCAATGTACCAGAAGTGGTCTTACACGTA
41501935 AATCA
1 AATCA
41501940 TAAGTCGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.02
42 25 0.60
43 16 0.38
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (43 bp):
AATCAAATATGATGCCAATGTACCAGAAGTGGTCTTACACGTA
Found at i:41501929 original size:42 final size:43
Alignment explanation
Indices: 41501818--41501975 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 43
41501808 AGCTCGTACA
** * * * *
41501818 ATGCCAACATCCCAGACGTGCTCTTATATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGAAGTGGTCTTACACGTAAATCAAATAT-G
* * *
41501861 ATGTCACTGTACCAGACAG-GGTCTTACACG-AAATCAAATATG
1 ATGCCAATGTCCCAGA-AGTGGTCTTACACGTAAATCAAATATG
* *
41501903 ATGCCAATGTCCCAGAGGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGAAGTGGTCTTACACGTAAATCA-AA-TATG
* *
41501947 ATGCCAACGTCTCA-AACGTGGTCTTACAC
1 ATGCCAATGTCCCAGAA-GTGGTCTTACAC
41501976 AAAAACACAT
Statistics
Matches: 91, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.27
43 36 0.40
44 28 0.31
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGAAGTGGTCTTACACGTAAATCAAATATG
Found at i:41506468 original size:41 final size:40
Alignment explanation
Indices: 41506250--41506469 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
41506240 GCTCGATTGT
* * * *
41506250 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
*
41506290 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
41506330 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41506370 CTTCGAGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41506410 CTTCGGGAGTT-GACCCGGATTTAGTCACTGAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAACT-CGCACAAATGC
41506451 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
41506470 CACCATTCGA
Statistics
Matches: 157, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
40 129 0.82
41 27 0.17
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:41514184 original size:40 final size:40
Alignment explanation
Indices: 41514140--41514358 Score: 215
Period size: 40 Copynumber: 5.5 Consensus size: 40
41514130 ACTCGATTGT
* * * * *
41514140 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGACATAACCCGGTTTTAGTAACTCGCACAAATGC
* * *
41514180 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACA-TAACCCGGTTTTAGTAACTCGCACAAATGC
* *
41514220 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAACCCGGTTTTAGTAACTCGCACAAATGC
* *
41514260 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAACCCGGTTTTAGTAACTCGCACAAATGC
** * ** * * *
41514300 CTTCGGGAGTTGACCCGAATTTAGTCACTGAGCACAAAAGC
1 CTTCGGGACATAACCCGGTTTTAGTAACT-CGCACAAATGC
* *
41514341 CTTCGGGACTTAGCCCGG
1 CTTCGGGACATAACCCGG
41514359 ACACCATTTG
Statistics
Matches: 153, Mismatches: 23, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.84
41 23 0.15
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
CTTCGGGACATAACCCGGTTTTAGTAACTCGCACAAATGC
Found at i:41517733 original size:27 final size:28
Alignment explanation
Indices: 41517686--41517738 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
41517676 GCTGGCCAAG
41517686 GGTCTTTAGTATAGGCAAA-TTCGGCTC
1 GGTCTTTAGTATAGGCAAATTTCGGCTC
**
41517713 GGTCATTTAGTAT-GGGGAATTTCGGC
1 GGTC-TTTAGTATAGGCAAATTTCGGC
41517739 ATTTGGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (28 bp):
GGTCTTTAGTATAGGCAAATTTCGGCTC
Found at i:41518924 original size:27 final size:27
Alignment explanation
Indices: 41518894--41518957 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
41518884 ATTTACTAAA
*
41518894 ATACCCCTAAGAAT-GAAAATTACCATT
1 ATACCCCTAAG-ATGGAAAATGACCATT
*
41518921 ATACCCCT-AGGTGGAAAATGACCATT
1 ATACCCCTAAGATGGAAAATGACCATT
41518947 ATACCCCTAAG
1 ATACCCCTAAG
41518958 GTTAATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 22 0.67
27 10 0.30
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.23
Consensus pattern (27 bp):
ATACCCCTAAGATGGAAAATGACCATT
Found at i:41519107 original size:28 final size:28
Alignment explanation
Indices: 41519060--41519113 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
41519050 GGAGGAAGCG
* *
41519060 TTCTGGTGGCTATGCGACAAATATCTGT
1 TTCTGGTGGCTACGCCACAAATATCTGT
41519088 TTCTGGTGGCTACGCCACAAATATCT
1 TTCTGGTGGCTACGCCACAAATATCT
41519114 ACTCTGGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (28 bp):
TTCTGGTGGCTACGCCACAAATATCTGT
Found at i:41519146 original size:27 final size:27
Alignment explanation
Indices: 41519061--41519155 Score: 81
Period size: 27 Copynumber: 3.5 Consensus size: 27
41519051 GAGGAAGCGT
* *
41519061 TCTGGTGGCTATGCGACAAATATCTGTT
1 TCTGGTGGCTCTGCG-CAAATATCTGTA
*
41519089 TCTGGTGGCTAC-GCCACAAATATC--TA
1 TCTGGTGGCT-CTG-CGCAAATATCTGTA
41519115 CTCTGGTGGCTCTGCTGC-AATATCTGTA
1 -TCTGGTGGCTCTGC-GCAAATATCTGTA
*
41519143 TCTGGTGACTCTG
1 TCTGGTGGCTCTG
41519156 TCACAATATC
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
26 9 0.16
27 24 0.44
28 21 0.38
29 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCGCAAATATCTGTA
Found at i:41519161 original size:54 final size:54
Alignment explanation
Indices: 41519061--41519173 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
41519051 GAGGAAGCGT
* *
41519061 TCTGGTGGCTATGCGACAAATATCTGTTTCTGGTGGCTACGCCACAAATATCTAC
1 TCTGGTGGCTATGCGACAAATATCTGTATCTGGTGACTACGCCAC-AATATCTAC
* * *
41519116 TCTGGTGGCTCTGCTG-C-AATATCTGTATCTGGTGACT-CTGTCACAATATCTAT
1 TCTGGTGGCTATGC-GACAAATATCTGTATCTGGTGACTAC-GCCACAATATCTAC
41519169 TCTGG
1 TCTGG
41519174 CAGCCACGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 14 0.27
54 22 0.43
55 14 0.27
56 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (54 bp):
TCTGGTGGCTATGCGACAAATATCTGTATCTGGTGACTACGCCACAATATCTAC
Found at i:41526324 original size:41 final size:41
Alignment explanation
Indices: 41526267--41526353 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
41526257 GGTGTTGTAT
41526267 GTGCTAGTGTGGACAAGGGGCCGTACAATGAAGGGCTTGAA
1 GTGCTAGTGTGGACAAGGGGCCGTACAATGAAGGGCTTGAA
* *
41526308 GTGCTAGTGTGGACAAGGGGGCGTACAGTGAAGGGCTTGAA
1 GTGCTAGTGTGGACAAGGGGCCGTACAATGAAGGGCTTGAA
41526349 G-GCTA
1 GTGCTA
41526354 ACTCGATTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.25, C:0.14, G:0.41, T:0.20
Consensus pattern (41 bp):
GTGCTAGTGTGGACAAGGGGCCGTACAATGAAGGGCTTGAA
Found at i:41526888 original size:27 final size:27
Alignment explanation
Indices: 41526858--41526919 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
41526848 ATTTACTAAA
**
41526858 ATACCCCTAAGAATG-AAAATTACCATT
1 ATACCCCTAAG-ATGTAAAAGGACCATT
* *
41526885 ATACCTCT-AGGTGTAAAAGGACCATT
1 ATACCCCTAAGATGTAAAAGGACCATT
41526911 ATACCCCTA
1 ATACCCCTA
41526920 GGGTTAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 2 0.07
26 19 0.68
27 7 0.25
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGTAAAAGGACCATT
Found at i:41527069 original size:28 final size:28
Alignment explanation
Indices: 41527028--41527104 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
41527018 AAGCGTTCTG
* *
41527028 GTGGCTCTGTCACAAATATCTGTTTCTA
1 GTGGCTCTGCCACAAATATCTGTCTCTA
*
41527056 GTGGCTAC-GCCACAAATATCTG-CTCTG
1 GTGGCT-CTGCCACAAATATCTGTCTCTA
41527083 GTGGCTCTGCCAC-AATATCTGT
1 GTGGCTCTGCCACAAATATCTGT
41527105 ATCTGGGGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 9 0.21
27 14 0.33
28 19 0.44
29 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
GTGGCTCTGCCACAAATATCTGTCTCTA
Found at i:41527094 original size:27 final size:28
Alignment explanation
Indices: 41527024--41527136 Score: 112
Period size: 27 Copynumber: 4.2 Consensus size: 28
41527014 GAGGAAGCGT
* *
41527024 TCTGGTGGCTCTGTCACAAATATCTGTT
1 TCTGGTGGCTCTGCCACAAATATCTGTC
*
41527052 TCTAGTGGCTAC-GCCACAAATATCTG-C
1 TCTGGTGGCT-CTGCCACAAATATCTGTC
*
41527079 TCTGGTGGCTCTGCCAC-AATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTC
**
41527106 TCTGG-GGACTCTGTTAC-AATATCTGT-
1 TCTGGTGG-CTCTGCCACAAATATCTGTC
41527132 TCTGG
1 TCTGG
41527137 CAGCCACGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
26 16 0.22
27 35 0.47
28 22 0.30
29 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTGTC
Found at i:41529441 original size:35 final size:35
Alignment explanation
Indices: 41529367--41529546 Score: 171
Period size: 35 Copynumber: 5.1 Consensus size: 35
41529357 TACTTACTTG
* * * * *
41529367 TATGGCCAAATACACATGGTTCATTATACCATCACA
1 TATGGCCGAATATACA-AGTTCAATATAACATCACA
* * *
41529403 TATGGCCGAATATACAAGTACAATATATCATCATA
1 TATGGCCGAATATACAAGTTCAATATAACATCACA
* * * *
41529438 TATGACTGAATATACAAGTTCAATAAAACGTCACA
1 TATGGCCGAATATACAAGTTCAATATAACATCACA
* * * * *
41529473 TGTAGTCGAATATTCAAGTTTAATATAACATCACA
1 TATGGCCGAATATACAAGTTCAATATAACATCACA
* * *
41529508 TATGGCCAAATATACAAGTTCAATACATCATCACA
1 TATGGCCGAATATACAAGTTCAATATAACATCACA
41529543 TATG
1 TATG
41529547 TACATACCTA
Statistics
Matches: 113, Mismatches: 31, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
35 99 0.88
36 14 0.12
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (35 bp):
TATGGCCGAATATACAAGTTCAATATAACATCACA
Found at i:41535154 original size:28 final size:29
Alignment explanation
Indices: 41535119--41535217 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 29
41535109 ATAATAAGCC
* *
41535119 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
*
41535147 CGTACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
* ** *
41535175 CGCACACTTAGTGC-TATACAATTTGAACC
1 CGCACACTTAGTGCTTATATAA-TCAAACT
41535204 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41535218 CAATTCATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.03
28 41 0.67
29 18 0.30
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTTATATAATCAAACT
Found at i:41541343 original size:40 final size:40
Alignment explanation
Indices: 41541178--41541345 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
41541168 CAATTGAATG
* * ** * ***
41541178 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGGTT
* * *
41541218 ATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGGTT
* *
41541258 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGGTT
*
41541298 CTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGGTT
41541338 ATATCCGG
1 ATATCCGG
41541346 TTGTATTCCG
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 4 0.04
40 101 0.94
41 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGGTT
Found at i:41541344 original size:80 final size:80
Alignment explanation
Indices: 41541178--41541345 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 80
41541168 CAATTGAATG
* * * *
41541178 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCA
41541243 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * *** *
41541258 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCGTTCTATCCGGGCTAAGACCCGAAGGC-
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCA
*
41541322 ATTCGTGC-ACGTGGTT
66 ATT-GTGCTA-GTGGCT
41541338 ATATCCGG
1 ATATCCGG
41541346 TTGTATTCCG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
79 4 0.05
80 69 0.95
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:41548532 original size:40 final size:40
Alignment explanation
Indices: 41548406--41548534 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
41548396 ATGCTGGAAA
* *
41548406 TTATAT-CGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
41548445 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
41548485 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
41548525 TTATATCCGG
1 TTATATCCGG
41548535 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.10
40 69 0.90
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:41556818 original size:28 final size:29
Alignment explanation
Indices: 41556786--41556884 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
41556776 ATAATAAGCC
*
41556786 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
41556814 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
41556842 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
41556871 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41556885 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:41567201 original size:43 final size:43
Alignment explanation
Indices: 41567140--41567277 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 43
41567130 TCCCAGATGT
* *
41567140 GGTCTTACATGTAATCAAATATCGATGCCACTGTCAC-AGACAG
1 GGTCTTACATGAAATCAAATATCGATGCCAATGTC-CTAGACAG
* * *
41567183 GGTCTTACACGAAATCAAATA-CAATGCCAATGTCCTAGACAT
1 GGTCTTACATGAAATCAAATATCGATGCCAATGTCCTAGACAG
* * *
41567225 GGTCTTACATGTAAATCATAA-GTCGATGCCAACGTCTTAGAC-G
1 GGTCTTACATG-AAATCA-AATATCGATGCCAATGTCCTAGACAG
41567268 TGGTCTTACA
1 -GGTCTTACA
41567278 CAAAAACACA
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 26 0.33
43 25 0.32
44 27 0.34
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGAAATCAAATATCGATGCCAATGTCCTAGACAG
Found at i:41567310 original size:86 final size:85
Alignment explanation
Indices: 41567139--41567310 Score: 183
Period size: 86 Copynumber: 2.0 Consensus size: 85
41567129 GTCCCAGATG
* *
41567139 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCACAGACAGGGTCTTACACGAAATCAAATA
1 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCACAGACAGGGTCTTACACAAAAACAAATA
*
41567204 CAATGCCAATGTCCTAGACA
66 CAATGCCAATGTCATAGACA
* **
41567224 TGGTCTTACATGTAAATCATAA-GTCGATGCCAAC-GTCTTAGAC-GTGGTCTTACACAAAAACA
1 TGGTCTTACATGT-AATCA-AATATCGATGCC-ACTGTCACAGACAG-GGTCTTACACAAAAACA
* *
41567286 CATATCAGAT-CCTATGTCAT-GACA
62 AATA-CA-ATGCCAATGTCATAGACA
41567310 T
1 T
41567311 ATGTATCCTA
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
85 14 0.19
86 43 0.59
87 14 0.19
88 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (85 bp):
TGGTCTTACATGTAATCAAATATCGATGCCACTGTCACAGACAGGGTCTTACACAAAAACAAATA
CAATGCCAATGTCATAGACA
Found at i:41570773 original size:40 final size:39
Alignment explanation
Indices: 41570728--41570895 Score: 137
Period size: 40 Copynumber: 4.2 Consensus size: 39
41570718 CGGAATATAA
41570728 CCGGATATAACTATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACTAT-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41570768 CCGGATAGAA-TGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACTAT-T-GCACAAATGCCTTCGGGTCTTAGC
* * * * * *
41570808 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACTA-TTGCACAAATGCCTTCGGGTCTTAGC
* *
41570848 CCGGATATAA-T-TTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAACTATTGCA-CA-AA-TGCCTTCGGG-TCTTAGC
41570888 CCGGATAT
1 CCGGATAT
41570896 CATTCAATTT
Statistics
Matches: 100, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
37 3 0.03
38 2 0.02
39 4 0.04
40 89 0.89
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (39 bp):
CCGGATATAACTATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41570878 original size:80 final size:80
Alignment explanation
Indices: 41570744--41570893 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
41570734 ATAACTATGT
*
41570744 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
41570808 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
41570824 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
41570887 CCCGGAT
64 CCCGGAT
41570894 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:41582001 original size:40 final size:40
Alignment explanation
Indices: 41581946--41582153 Score: 231
Period size: 40 Copynumber: 5.2 Consensus size: 40
41581936 TGAATGATAC
*
41581946 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
41581986 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
** *
41582026 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT
* * * ** *
41582066 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
* * * * * * *
41582106 CTGGGTTAAGATCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
41582146 CC-GGCTAA
1 CCGGGCTAA
41582154 ATTCTGAAGA
Statistics
Matches: 143, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 6 0.04
40 135 0.94
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
Found at i:41587301 original size:27 final size:28
Alignment explanation
Indices: 41587241--41587303 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
41587231 TCAAAAATTA
41587241 TTATAATATTAAGTATAATTCAACATGT
1 TTATAATATTAAGTATAATTCAACATGT
* *
41587269 TAATAAT-TTAAGTA-AAGTTTAACTAT-T
1 TTATAATATTAAGTATAA-TTCAAC-ATGT
41587296 TTATAATA
1 TTATAATA
41587304 ATTATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (28 bp):
TTATAATATTAAGTATAATTCAACATGT
Found at i:41588407 original size:17 final size:17
Alignment explanation
Indices: 41588385--41588418 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41588375 TAACTTTATT
41588385 TTATTTT-TGTTCTTAGG
1 TTATTTTATGTT-TTAGG
41588402 TTATTTTATGTTTTAGG
1 TTATTTTATGTTTTAGG
41588419 ATTAGGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.15, C:0.03, G:0.18, T:0.65
Consensus pattern (17 bp):
TTATTTTATGTTTTAGG
Found at i:41589261 original size:17 final size:17
Alignment explanation
Indices: 41589239--41589271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41589229 AATTCTCATG
41589239 AAAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAGAA
*
41589256 AAAAAAAGAGAAAAGA
1 AAAAAAAGAAAAAAGA
41589272 GCATACGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAGAA
Found at i:41596613 original size:19 final size:20
Alignment explanation
Indices: 41596581--41596619 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
41596571 ACTTCGGTAT
41596581 ATTTGGGTTTAATGGGCCAA
1 ATTTGGGTTTAATGGGCCAA
41596601 ATTTGGG-TTAATGGGCCAA
1 ATTTGGGTTTAATGGGCCAA
41596620 CGGGCCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.33
Consensus pattern (20 bp):
ATTTGGGTTTAATGGGCCAA
Found at i:41596942 original size:27 final size:27
Alignment explanation
Indices: 41596884--41596964 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
41596874 GTAGAAGCAT
* *
41596884 TCTGGTGGCTCTGCTACAAATATCTGTT
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
41596912 TCTGGTGGCTCTGCCACAATATCTGTA
1 TCTGGTGGCTCTGCCACAATATCTGTA
* *
41596939 TCTGGTGACTCTGTCACAATATCTGT
1 TCTGGTGGCTCTGCCACAATATCTGT
41596965 TTTGGCAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 33 0.67
28 16 0.33
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAATATCTGTA
Found at i:41603213 original size:13 final size:13
Alignment explanation
Indices: 41603197--41603229 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41603187 TTTAATTAAA
*
41603197 TTAGTTAATTAGT
1 TTAGATAATTAGT
41603210 TTAGATAATTAGT
1 TTAGATAATTAGT
41603223 TTA-ATAA
1 TTAGATAA
41603230 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:41614267 original size:40 final size:40
Alignment explanation
Indices: 41614208--41614415 Score: 276
Period size: 40 Copynumber: 5.2 Consensus size: 40
41614198 TGAATGATAC
* * *
41614208 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
41614248 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
41614288 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
41614328 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
41614368 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
41614408 CC-GGCTAA
1 CCGGGCTAA
41614416 ATTCCGAAGA
Statistics
Matches: 149, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
39 5 0.03
40 142 0.95
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:41619923 original size:40 final size:40
Alignment explanation
Indices: 41619864--41620031 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
41619854 TGAATGATAC
* * * *
41619864 CCGGGCTGAGTCCCTAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
41619904 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
41619944 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
41619984 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
41620024 CC-GGCTAA
1 CCGGGCTAA
41620032 ATTCCGAAGA
Statistics
Matches: 104, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
39 6 0.06
40 96 0.92
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:41623178 original size:24 final size:24
Alignment explanation
Indices: 41622911--41623176 Score: 471
Period size: 24 Copynumber: 11.1 Consensus size: 24
41622901 GCAAAGACCA
41622911 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41622935 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41622959 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
41622983 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41623007 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41623031 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41623055 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41623079 TATGGCACTATGTGTGCGA-TTAC
1 TATGGCACTATGTGTGCGATTTAC
41623102 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41623126 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
41623150 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
41623174 TAT
1 TAT
41623177 AGTCACATTC
Statistics
Matches: 235, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
23 23 0.10
24 212 0.90
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:41626840 original size:29 final size:29
Alignment explanation
Indices: 41626807--41626880 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41626797 CCTTCGAGCT
41626807 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
41626836 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41626865 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41626881 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41626841 original size:58 final size:58
Alignment explanation
Indices: 41626748--41626880 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
41626738 ATACTCGATT
* * * * *
41626748 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
41626806 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
41626864 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
41626881 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:41634718 original size:29 final size:29
Alignment explanation
Indices: 41634685--41634758 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41634675 CCTTCGAGCT
41634685 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
41634714 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41634743 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41634759 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41634719 original size:58 final size:58
Alignment explanation
Indices: 41634626--41634758 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
41634616 ATACTCGATT
* * * * *
41634626 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
41634684 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
41634742 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
41634759 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:41637517 original size:39 final size:41
Alignment explanation
Indices: 41637457--41637533 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 41
41637447 ACCTACGTAC
41637457 CTGGAAAAGAAATAAGAAAAAACAAAATTAAAAGTTTTAAT
1 CTGGAAAAGAAATAAGAAAAAACAAAATTAAAAGTTTTAAT
* *
41637498 CTGG-AAA-AAATAA-ATAAAAATAGAATTAAAAGTTTT
1 CTGGAAAAGAAATAAGA-AAAAACAAAATTAAAAGTTTT
41637534 GATTGGGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 1 0.03
39 25 0.76
40 3 0.09
41 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.25
Consensus pattern (41 bp):
CTGGAAAAGAAATAAGAAAAAACAAAATTAAAAGTTTTAAT
Found at i:41643263 original size:16 final size:16
Alignment explanation
Indices: 41643214--41643263 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
41643204 ATGGAAATAT
*
41643214 AATCTTTAAGGATATGC
1 AATCTTGAA-GATATGC
*
41643231 AATCTTAGATTGATATGC
1 AATCTT-GA-AGATATGC
41643249 AATCTTGAAGATATG
1 AATCTTGAAGATATG
41643264 ATCTTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 14 0.50
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (16 bp):
AATCTTGAAGATATGC
Found at i:41644016 original size:32 final size:33
Alignment explanation
Indices: 41643980--41644047 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
41643970 TTGTATGGAA
41643980 ATGTTAGAATA-TTTGTACATCTATGCTTCATG
1 ATGTTAGAATATTTTGTACATCTATGCTTCATG
41644012 ATGTTAGAATATTTTGTACATCTATGCTTCATG
1 ATGTTAGAATATTTTGTACATCTATGCTTCATG
41644045 ATG
1 ATG
41644048 CATTAATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 11 0.31
33 24 0.69
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
ATGTTAGAATATTTTGTACATCTATGCTTCATG
Found at i:41654565 original size:28 final size:29
Alignment explanation
Indices: 41654533--41654631 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
41654523 ATAATAAGCC
*
41654533 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
41654561 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
41654589 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
41654618 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41654632 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:41658360 original size:40 final size:40
Alignment explanation
Indices: 41658296--41658463 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
41658286 TCTTCGGAAT
* ** * **
41658296 TTAG-CCGGATATAACCACAAGCACAATTGTTTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
41658335 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
41658375 TTAGCCCAGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
41658415 TTAGCCCGAATATAATC-ACTAGCATAAATGCCTTCGAGG-C
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCG-GGTC
41658455 TTAGCCCGG
1 TTAGCCCGG
41658464 GTATCATTCA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.03
40 102 0.94
41 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:41660868 original size:16 final size:18
Alignment explanation
Indices: 41660847--41660884 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
41660837 CAGTCTCTAG
41660847 CAGTTT-ACTATAG-TTT
1 CAGTTTAACTATAGTTTT
41660863 CAGTTTAACTATAGTTTT
1 CAGTTTAACTATAGTTTT
41660881 CAGT
1 CAGT
41660885 ATATACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 7 0.35
18 7 0.35
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (18 bp):
CAGTTTAACTATAGTTTT
Found at i:41660913 original size:27 final size:27
Alignment explanation
Indices: 41660881--41660934 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41660871 CTATAGTTTT
*
41660881 CAGTATATACTAACTAAAGTATTTTCA
1 CAGTATATACTAACTAAAGTAGTTTCA
* *
41660908 CAGTATATACTACCTATAGTAGTTTCA
1 CAGTATATACTAACTAAAGTAGTTTCA
41660935 GAATAGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (27 bp):
CAGTATATACTAACTAAAGTAGTTTCA
Found at i:41664718 original size:88 final size:87
Alignment explanation
Indices: 41664455--41664718 Score: 309
Period size: 87 Copynumber: 3.0 Consensus size: 87
41664445 ACTTATCAAT
* * * *
41664455 AAGTTCAGAGTTCAAATGAAAAAAAAAATGGATTGATTTCAAGTGTAAAGGTGAAAAAGGAAAAC
1 AAGTTCAGAGTTCAAATG-AAAAAAATAT--ACTGATTTCAAGTATAAAGGTGAAAAAGGAAAAT
* *
41664520 TACCATCTGAACTCCAAATTAAGTA
63 TACCATTTGAACTCTAAATTAAGTA
* * * *
41664545 AAGTTC-GAATTCAACTGAAAAAAATAAAACTAATTTCAAGTATAAAGGTGAAAAAGGAAAATTA
1 AAGTTCAGAGTTCAAATGAAAAAAAT-ATACTGATTTCAAGTATAAAGGTGAAAAAGGAAAATTA
*
41664609 CCATTTGAA-TTTCAAATTAAGTA
65 CCATTTGAACTCT-AAATTAAGTA
* * *
41664632 CAAGTACAGAGTTCAATTGAACAAAAATATACTGATTTCAAGTATAAAGGTG-AAAAGAAAAATT
1 -AAGTTCAGAGTTCAAATGAA-AAAAATATACTGATTTCAAGTATAAAGGTGAAAAAGGAAAATT
*
41664696 ACCATTTTAACTCTAAATTAAGT
64 ACCATTTGAACTCTAAATTAAGT
41664719 GGTGTGAAAT
Statistics
Matches: 149, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
86 1 0.01
87 50 0.34
88 41 0.28
89 45 0.30
90 12 0.08
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (87 bp):
AAGTTCAGAGTTCAAATGAAAAAAATATACTGATTTCAAGTATAAAGGTGAAAAAGGAAAATTAC
CATTTGAACTCTAAATTAAGTA
Found at i:41664963 original size:2 final size:2
Alignment explanation
Indices: 41664952--41664997 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
41664942 TGTTAATTCC
*
41664952 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
41664993 TT AT A
1 AT AT A
41664998 CACACACGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:41665507 original size:31 final size:31
Alignment explanation
Indices: 41665447--41665518 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
41665437 ATGGAAATAT
* *
41665447 AAAAAAAT-ATATAAATTTATTAAATATTAA
1 AAAAAAATAATAAAAATATATTAAATATTAA
*
41665477 ATAAAAATAATAAAAATATATTTAAA-ATTAA
1 AAAAAAATAATAAAAATATA-TTAAATATTAA
41665508 AAAAAAATAAT
1 AAAAAAATAAT
41665519 GAATGGACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 7 0.19
31 24 0.67
32 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAAAATAATAAAAATATATTAAATATTAA
Found at i:41665917 original size:13 final size:13
Alignment explanation
Indices: 41665901--41665937 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
41665891 GGCCTACCCA
41665901 ATATTAATTTTTT
1 ATATTAATTTTTT
41665914 ATATT-A-TTTTT
1 ATATTAATTTTTT
41665925 ATA-TAATTTTTT
1 ATATTAATTTTTT
41665937 A
1 A
41665938 ATATATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.41
12 7 0.32
13 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:41665941 original size:13 final size:12
Alignment explanation
Indices: 41665905--41665942 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
41665895 TACCCAATAT
41665905 TAATTTTTTATA
1 TAATTTTTTATA
*
41665917 TTA-TTTTTATA
1 TAATTTTTTATA
41665928 TAATTTTTTAATA
1 TAATTTTTT-ATA
41665941 TA
1 TA
41665943 TGTATAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:41666096 original size:30 final size:30
Alignment explanation
Indices: 41666060--41666122 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
41666050 ACTTAACAAG
41666060 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
41666090 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
41666120 CAA
1 CAA
41666123 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41666177 original size:22 final size:22
Alignment explanation
Indices: 41666152--41666194 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41666142 TATCCGAATA
41666152 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
41666174 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
41666195 AATAGAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:41666198 original size:11 final size:11
Alignment explanation
Indices: 41666159--41666199 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41666149 ATAATAACAA
41666159 CAAAATAGTAG
1 CAAAATAGTAG
* *
41666170 CAACATAATAG
1 CAAAATAGTAG
*
41666181 TAAAATAGTAG
1 CAAAATAGTAG
41666192 CAAAATAG
1 CAAAATAG
41666200 AAAGTAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Done.