Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 190 of 199
Found at i:55469914 original size:38 final size:36
Alignment explanation
Indices: 55469839--55469914 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
55469829 TAGTACTTTC
* * *
55469839 CTGCAAATCTTTCTTTGTGGAAATACGGTCAATTTT
1 CTGCAAATCTTTCTTTGTGGAAATACAGCCAAATTT
*
55469875 CTGCAAGTCTTTCTTTGTGGAAAAATACAGCCAAATTT
1 CTGCAAATCTTTCTTTGTGG--AAATACAGCCAAATTT
55469913 CT
1 CT
55469915 TAGTACTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 19 0.56
38 15 0.44
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (36 bp):
CTGCAAATCTTTCTTTGTGGAAATACAGCCAAATTT
Found at i:55470183 original size:16 final size:17
Alignment explanation
Indices: 55470156--55470189 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
55470146 TCTTATATAC
55470156 AAATACAAATAAAAATA
1 AAATACAAATAAAAATA
55470173 AAATA-AAATAAAAATA
1 AAATACAAATAAAAATA
55470189 A
1 A
55470190 TTTAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATACAAATAAAAATA
Found at i:55474657 original size:51 final size:51
Alignment explanation
Indices: 55474585--55474706 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 51
55474575 TGTACTATTT
** * * *
55474585 CTTCTGGTCATATATCCTCTACTCCATCCGGGTTAGTTAAAAGTTTTTCTA
1 CTTCTGGTCATACGTCATCTACTCCATCCGGGTTACTTAAAAGTTCTTCTA
***
55474636 CTTCTGGTCATACGTCATCTACTCCATCCGGGTTACTTAGGGGTTCTTCTA
1 CTTCTGGTCATACGTCATCTACTCCATCCGGGTTACTTAAAAGTTCTTCTA
* * *
55474687 TTTCTAGTTATACGTCATCT
1 CTTCTGGTCATACGTCATCT
55474707 GAGTTAATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (51 bp):
CTTCTGGTCATACGTCATCTACTCCATCCGGGTTACTTAAAAGTTCTTCTA
Found at i:55477472 original size:69 final size:69
Alignment explanation
Indices: 55477373--55477564 Score: 199
Period size: 69 Copynumber: 2.8 Consensus size: 69
55477363 TAGACTCTTG
** * * * * *
55477373 AGATATAT-TTCCAGAAAACTTATCGGAAGAGAGATCTAAATACTCTAGTGATGTTAAATTTTTA
1 AGATATATCTT-CAGAAAAAATATTGAAAGAGATATCTAAATACTCGAGTGATGTTAAATTCTTA
*
55477437 AGCAC
65 AACAC
* *
55477442 AGATATATCTTCA-AAAAAACTGTTGAAAGAGATATCTAAATAGTCGAGTGATGTTAAATTCTTA
1 AGATATATCTTCAGAAAAAA-TATTGAAAGAGATATCTAAATACTCGAGTGATGTTAAATTCTTA
*
55477506 AACAT
65 AACAC
* * * * * *
55477511 AGATATATTTTTAGAAAAAATATTGGAAGAGATATTTAAATACTTGAGGGATGT
1 AGATATATCTTCAGAAAAAATATTGAAAGAGATATCTAAATACTCGAGTGATGT
55477565 GAGTTCAAAG
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
68 4 0.04
69 89 0.88
70 8 0.08
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.33
Consensus pattern (69 bp):
AGATATATCTTCAGAAAAAATATTGAAAGAGATATCTAAATACTCGAGTGATGTTAAATTCTTAA
ACAC
Found at i:55477896 original size:53 final size:55
Alignment explanation
Indices: 55477815--55477921 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
55477805 CAAAATAATG
* *
55477815 TTAATTGTTTATTTTGGTGTTC-TATATATAAGGCATAATAACAAGTTTAGCCCT
1 TTAATTGCTTATTTTGGTGTTCATATATATAAGGCATAATAACAAATTTAGCCCT
55477869 TTAATTGCTTA-TTTGGTGTTCTATATATATAAGGCATAATAACAAATTTAGCC
1 TTAATTGCTTATTTTGGTGTTC-ATATATATAAGGCATAATAACAAATTTAGCC
55477922 TTCAACCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
53 10 0.20
54 10 0.20
55 29 0.59
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (55 bp):
TTAATTGCTTATTTTGGTGTTCATATATATAAGGCATAATAACAAATTTAGCCCT
Found at i:55492315 original size:17 final size:17
Alignment explanation
Indices: 55492271--55492305 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55492261 AACATAAAAT
*
55492271 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
55492288 AAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
55492305 A
1 A
55492306 GAATAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:55493008 original size:3 final size:3
Alignment explanation
Indices: 55493000--55493055 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
55492990 GTGAGGTAAG
55493000 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55493048 TAT TAT TA
1 TAT TAT TA
55493056 GTGAGAATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55493394 original size:23 final size:22
Alignment explanation
Indices: 55493367--55493451 Score: 95
Period size: 21 Copynumber: 4.0 Consensus size: 22
55493357 GGCCTTGCCG
*
55493367 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTCATGTGTCGT-T
* * *
55493390 ATCAGGCACCTCGTGTGCCG-T
1 ATCAGGCACTTCATGTGTCGTT
*
55493411 ATCAGGCACTTCGTGTGTCGTT
1 ATCAGGCACTTCATGTGTCGTT
55493433 -TCAGGCACTT-ATGTGTCGT
1 ATCAGGCACTTCATGTGTCGT
55493452 ATACTGATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 8 0.15
21 29 0.54
22 1 0.02
23 16 0.30
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
ATCAGGCACTTCATGTGTCGTT
Found at i:55503941 original size:13 final size:13
Alignment explanation
Indices: 55503923--55503969 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
55503913 ATGTCAAACA
55503923 CTCAAAAGTACTT
1 CTCAAAAGTACTT
*
55503936 CTCAAAAGCACTT
1 CTCAAAAGTACTT
55503949 CTCAAAAGTACTT
1 CTCAAAAGTACTT
55503962 CTCAAAAG
1 CTCAAAAG
55503970 CAATGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (13 bp):
CTCAAAAGTACTT
Found at i:55504097 original size:47 final size:47
Alignment explanation
Indices: 55504045--55504135 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
55504035 CAAAATTGTA
* *
55504045 ATATATAAATTGTCTTATATATTTGAACTGATGTTATTGGAATTGCT
1 ATATATAAATTGTCTCAAATATTTGAACTGATGTTATTGGAATTGCT
*
55504092 ATATATAAATTGTCTCAAATATTTGAACTGATGTTGTTGGAATT
1 ATATATAAATTGTCTCAAATATTTGAACTGATGTTATTGGAATT
55504136 TATATTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (47 bp):
ATATATAAATTGTCTCAAATATTTGAACTGATGTTATTGGAATTGCT
Found at i:55510706 original size:69 final size:69
Alignment explanation
Indices: 55510649--55510833 Score: 203
Period size: 68 Copynumber: 2.7 Consensus size: 69
55510639 TCTTAAGAAG
* *
55510649 AGATATATCTCCAAAAAATTTATAGGAAGAAATATCTAAATACTCGAGTGATATTAGATTATTAA
1 AGATATATTTCCAAAAAATTTATAGAAAGAAATATCTAAATACTCGAGTGATATTAGATTATTAA
* *
55510714 ATAT
66 ACAC
* * * * * * * * *
55510718 AGATATATTTTCAAGAAAGTTATTGTAAGAAAAATCTAAATACT-GGGTGTTATTAGATTTTTAA
1 AGATATATTTCCAAAAAATTTATAGAAAGAAATATCTAAATACTCGAGTGATATTAGATTATTAA
55510782 ACAC
66 ACAC
* * *
55510786 AGATATATTTCTAAAAAATCTATTA-AAAGAAATATCTAAATGCTCGAG
1 AGATATATTTCCAAAAAATTTA-TAGAAAGAAATATCTAAATACTCGAG
55510834 GAATGTGAGT
Statistics
Matches: 92, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
68 52 0.57
69 40 0.43
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (69 bp):
AGATATATTTCCAAAAAATTTATAGAAAGAAATATCTAAATACTCGAGTGATATTAGATTATTAA
ACAC
Found at i:55513477 original size:47 final size:47
Alignment explanation
Indices: 55513422--55513543 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
55513412 TTTTCGAACC
*
55513422 TTATATATAAATTGTCTTATATATTTGAACTGATATTATTAGAATTG
1 TTATATATAAATTGTCTTATATATTTGAACCGATATTATTAGAATTG
* * *
55513469 TTGTATATAAATTGTCTTATATATTTGAACCGATGTTATTGGAATTG
1 TTATATATAAATTGTCTTATATATTTGAACCGATATTATTAGAATTG
* * *
55513516 TTATATATAACTTGTTTTAAATATTTGA
1 TTATATATAAATTGTCTTATATATTTGA
55513544 GGAATTTATA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (47 bp):
TTATATATAAATTGTCTTATATATTTGAACCGATATTATTAGAATTG
Found at i:55516033 original size:69 final size:68
Alignment explanation
Indices: 55515941--55516150 Score: 258
Period size: 69 Copynumber: 3.0 Consensus size: 68
55515931 CTAAAATGAG
* * *
55515941 ATATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAAAC
1 ATATATCTCCAAAAAAATTATTGGA-GAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAAC
*
55516006 ACAT
65 ACAA
* * * * * *
55516010 ATATATTTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTTGAGTGAGGTTAGATTCTTGAAC
1 ATATATCTCCAAAAAAATTATTGG-AGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAAC
*
55516075 ACAG
65 ACAA
* * *
55516079 ATATATCTCCAGAAAATTTATTGTGAGAGAGATCTAAAAACTCAAGTGACGTTAGATTCTTAAAC
1 ATATATCTCCAAAAAAATTATTG-GAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAAC
*
55516144 ATAA
65 ACAA
55516148 ATA
1 ATA
55516151 CATTTTCAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
69 116 0.98
70 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (68 bp):
ATATATCTCCAAAAAAATTATTGGAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAACA
CAA
Found at i:55516177 original size:69 final size:69
Alignment explanation
Indices: 55515941--55516185 Score: 244
Period size: 69 Copynumber: 3.6 Consensus size: 69
55515931 CTAAAATGAG
* * * * *
55515941 ATATATCTCCAGAAAA-CTTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAAA
1 ATATATTTCCA-AAAATATTATTGAAAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAA
*
55516005 CACAT
65 CACAA
* * * * *
55516010 ATATATTTCCAAAAAAATTATTGGAAA-AGAGATCTAAATACTTGAGTGAGGTTAGATTCTTGAA
1 ATATATTTCCAAAAATATTATT-GAAAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAA
*
55516074 CACAG
65 CACAA
* ** *
55516079 ATATATCTCCAGAAAAT-TTATTGTGAGAGAGATCTAAAAACTCAAGTGACGTTAGATTCTTAAA
1 ATATATTTCCA-AAAATATTATTGAAAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAA
*
55516143 CATAA
65 CACAA
* * ** *
55516148 ATACATTTTCAAAAATACCATTGAAAGAGATATCTAAA
1 ATATATTTCCAAAAATATTATTGAAAGAGAGATCTAAA
55516186 TGCTTAAGTG
Statistics
Matches: 142, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
68 11 0.08
69 125 0.88
70 6 0.04
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (69 bp):
ATATATTTCCAAAAATATTATTGAAAGAGAGATCTAAAAACTCGAGTGACGTTAGATTCTTAAAC
ACAA
Found at i:55516196 original size:138 final size:138
Alignment explanation
Indices: 55515939--55516196 Score: 367
Period size: 138 Copynumber: 1.9 Consensus size: 138
55515929 TTCTAAAATG
*
55515939 AGATATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCGAGTGACCTTAGATTCTTAA
1 AGATATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTAA
* * ** *
55516004 ACACATATATATTTCCAAAAAAATTATTGGAAAAGAGATCTAAATACTTGAGTGAGGTTAGATTC
66 ACACAAATACATTTCCAAAAAAACCATTGGAAAAGAGATCTAAATACTTAAGTGAGGTTAGATTC
55516069 TTGAACAC
131 TTGAACAC
* *
55516077 AGATATATCTCCAGAAAATTTATTGTGA-GAGAGATCTAAAAACTCAAGTGACGTTAGATTCTTA
1 AGATATATCTCCAGAAAACTTATTG-GACGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTA
* * * * *
55516141 AACATAAATACATTTTCAAAAATACCATT-GAAAGAGATATCTAAATGCTTAAGTGA
65 AACACAAATACATTTCCAAAAAAACCATTGGAAA-AGAGATCTAAATACTTAAGTGA
55516197 TATGAGTTCA
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 4 0.04
138 99 0.94
139 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (138 bp):
AGATATATCTCCAGAAAACTTATTGGACGAGAGATCTAAAAACTCAAGTGACCTTAGATTCTTAA
ACACAAATACATTTCCAAAAAAACCATTGGAAAAGAGATCTAAATACTTAAGTGAGGTTAGATTC
TTGAACAC
Found at i:55517943 original size:17 final size:18
Alignment explanation
Indices: 55517918--55517951 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55517908 GTTTTTGGCT
55517918 AAACCAAAAA-GAAAAAA
1 AAACCAAAAATGAAAAAA
*
55517935 AAACGAAAAATGAAAAA
1 AAACCAAAAATGAAAAA
55517952 GATGTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.03
Consensus pattern (18 bp):
AAACCAAAAATGAAAAAA
Found at i:55522054 original size:10 final size:10
Alignment explanation
Indices: 55522023--55522070 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
55522013 GAAAAGTCTT
55522023 AAATTATAAA
1 AAATTATAAA
*
55522033 AAAGTTACAAA
1 AAA-TTATAAA
55522044 AAATTAT-AA
1 AAATTATAAA
55522053 AAATT-TAAA
1 AAATTATAAA
55522062 AAATATATA
1 AAAT-TATA
55522071 TAATAAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 1 0.03
9 13 0.41
10 7 0.22
11 11 0.34
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AAATTATAAA
Found at i:55522072 original size:21 final size:22
Alignment explanation
Indices: 55522023--55522073 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
55522013 GAAAAGTCTT
55522023 AAAT-TATA-AAAAAGTTACAA
1 AAATATATATAAAAAGTTACAA
*
55522043 AAA-AT-TATAAAAATTTA-AA
1 AAATATATATAAAAAGTTACAA
55522062 AAATATATATAA
1 AAATATATATAA
55522074 TAAACGGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATATATATAAAAAGTTACAA
Found at i:55527628 original size:44 final size:44
Alignment explanation
Indices: 55527531--55527629 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
55527521 TCATTAAAGC
* * * *
55527531 AATAAC-TCTATTAAATTGTAATTATTTTTAAATTTATAATTAT
1 AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
* * * *
55527574 CACAATTTCTATCAAATTATAAATCTTTTTAAATGTATAATTAT
1 AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
55527618 AATAACTTCTAT
1 AATAACTTCTAT
55527630 TTTACTTCAA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.47
Consensus pattern (44 bp):
AATAACTTCTATCAAATTATAAATATTTTTAAATGTATAATTAT
Found at i:55537426 original size:18 final size:18
Alignment explanation
Indices: 55537403--55537437 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55537393 CTTTTTTGAA
55537403 AATTTTAATAAAATTTTC
1 AATTTTAATAAAATTTTC
* *
55537421 AATTTTTATACAATTTT
1 AATTTTAATAAAATTTT
55537438 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTAATAAAATTTTC
Found at i:55551219 original size:2 final size:2
Alignment explanation
Indices: 55551212--55551236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55551202 ACACGAGTGA
55551212 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55551237 AATGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55551887 original size:34 final size:35
Alignment explanation
Indices: 55551849--55551915 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
55551839 AGTAAAATAT
* *
55551849 TTTTCCGTAAAATGATTT-CTGTAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
55551883 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
55551916 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:55551889 original size:20 final size:20
Alignment explanation
Indices: 55551864--55551903 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55551854 CGTAAAATGA
*
55551864 TTTCTGTAAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
55551884 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
55551904 GGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:55553005 original size:22 final size:22
Alignment explanation
Indices: 55552943--55553006 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
55552933 AAAGCAATAA
* *
55552943 AAATATTAATTTTGTTAAACATT
1 AAATA-TAATTTTATTAAACACT
* * *
55552966 AAATGATCATTTTTTTAAGCACT
1 AAAT-ATAATTTTATTAAACACT
55552989 AAATATAATTTTATTAAA
1 AAATATAATTTTATTAAA
55553007 ATTTGATCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 11 0.33
23 21 0.64
24 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATATAATTTTATTAAACACT
Found at i:55553528 original size:2 final size:2
Alignment explanation
Indices: 55553521--55553562 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
55553511 CGAATCTAGA
*
55553521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55553563 GTTTAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55559733 original size:9 final size:10
Alignment explanation
Indices: 55559708--55559736 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
55559698 AAAAGCTGGT
55559708 GGCCAAAAAA
1 GGCCAAAAAA
55559718 GGCCAAAAAA
1 GGCCAAAAAA
55559728 GG-CAAAAAA
1 GGCCAAAAAA
55559737 ATATAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.62, C:0.17, G:0.21, T:0.00
Consensus pattern (10 bp):
GGCCAAAAAA
Found at i:55560392 original size:18 final size:20
Alignment explanation
Indices: 55560355--55560398 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
55560345 GAGTAACATT
55560355 GAAATATAAATACGTATATAA
1 GAAATATAAATAC-TATATAA
55560376 GAAATA-AAATA-TATATAA
1 GAAATATAAATACTATATAA
*
55560394 AAAAT
1 GAAAT
55560399 TCACATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
20 5 0.23
21 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
GAAATATAAATACTATATAA
Found at i:55564694 original size:25 final size:25
Alignment explanation
Indices: 55564630--55564752 Score: 81
Period size: 25 Copynumber: 5.0 Consensus size: 25
55564620 GTCATTAGAG
* * *
55564630 TTACCGAT-TTCAACTCTTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* *
55564654 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* * * * *
55564679 TTACTGTTATTTAGCTTGGA-GAAGT
1 TTACCGTTATTCAGCTCGTATG-AGC
* * * *
55564704 TTACTGTTATTCAGCTAGGAAGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
*
55564729 TTACCGTT-TACAGCTCGTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
55564753 ATACATGTAC
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
24 21 0.27
25 56 0.72
26 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (25 bp):
TTACCGTTATTCAGCTCGTATGAGC
Found at i:55567692 original size:45 final size:45
Alignment explanation
Indices: 55567617--55567892 Score: 306
Period size: 45 Copynumber: 6.4 Consensus size: 45
55567607 TAACGGTAGT
* * *
55567617 AGTAACAGTAACAGTAACAGTGTTCAACACACAAAGTACTGAATC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC
* * * *
55567662 TGTAACAGTAACAGTAACTGTATTTGACACACAAAGTGCCGAATC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC
* *
55567707 -G-----GTAATAGTAACGGT-TT-GACACAC--AGTG-TCGAATC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATC
* *
55567742 GGTAACAGTAACAATAACAGTATTCGACACACAAAGTGCTGAATC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC
*
55567787 AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTG-TCGAATC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATC
* * *
55567832 AGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAACC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC
*
55567877 AGTAACAGTAATAGTA
1 AGTAACAGTAACAGTA
55567893 GTCGGCACAT
Statistics
Matches: 195, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
35 9 0.05
36 1 0.01
37 7 0.04
38 2 0.01
39 12 0.06
41 11 0.06
42 2 0.01
43 7 0.04
44 2 0.01
45 141 0.72
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATC
Found at i:55567740 original size:35 final size:36
Alignment explanation
Indices: 55567669--55567753 Score: 109
Period size: 35 Copynumber: 2.3 Consensus size: 36
55567659 ATCTGTAACA
*
55567669 GTAACAGTAACTGTATTTGACACACAAAGTGCCGAATCG
1 GTAACAGTAAC-G-GTTTGACACAC-AAGTGCCGAATCG
* *
55567708 GTAATAGTAACGGTTTGACACAC-AGTGTCGAATCG
1 GTAACAGTAACGGTTTGACACACAAGTGCCGAATCG
55567743 GTAACAGTAAC
1 GTAACAGTAAC
55567754 AATAACAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 21 0.50
37 10 0.24
38 1 0.02
39 10 0.24
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (36 bp):
GTAACAGTAACGGTTTGACACACAAGTGCCGAATCG
Found at i:55567842 original size:125 final size:125
Alignment explanation
Indices: 55567618--55567846 Score: 359
Period size: 125 Copynumber: 1.8 Consensus size: 125
55567608 AACGGTAGTA
* * * *
55567618 GTAACAGTAACAGTAACAGTGTTCAACACACAAAGTACTGAATCTGTAACAGTAACAGTAACTGT
1 GTAACAGTAACAATAACAGTATTCAACACACAAAGTACTGAATCAGTAACAGTAACAGTAACAGT
** * *
55567683 ATTTGACACACAAAGTGCCGAATCGGTAATAGTAACGGTTTGACACACAGTGTCGAATCG
66 ATTCAACACACAAAGTGCCGAATCAGTAACAGTAACGGTTTGACACACAGTGTCGAATCG
* *
55567743 GTAACAGTAACAATAACAGTATTCGACACACAAAGTGCTGAATCAGTAACAGTAACAGTAACAGT
1 GTAACAGTAACAATAACAGTATTCAACACACAAAGTACTGAATCAGTAACAGTAACAGTAACAGT
*
55567808 ATTCAACACACAAAGTGTCGAATCAGTAACAGTAACGGT
66 ATTCAACACACAAAGTGCCGAATCAGTAACAGTAACGGT
55567847 AACAGTATTC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
125 93 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (125 bp):
GTAACAGTAACAATAACAGTATTCAACACACAAAGTACTGAATCAGTAACAGTAACAGTAACAGT
ATTCAACACACAAAGTGCCGAATCAGTAACAGTAACGGTTTGACACACAGTGTCGAATCG
Found at i:55572708 original size:32 final size:36
Alignment explanation
Indices: 55572667--55572732 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 36
55572657 TTAAATTAAA
*
55572667 AATTATT-AAATCAATATTA-TT-TAATT-TTTATT
1 AATTATTAAAATCAAAATTACTTATAATTATTTATT
55572699 AATTATTAAAATCAAAATTACTTATAATTATTTA
1 AATTATTAAAATCAAAATTACTTATAATTATTTA
55572733 GAAATAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.24
33 11 0.38
34 2 0.07
35 5 0.17
36 4 0.14
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (36 bp):
AATTATTAAAATCAAAATTACTTATAATTATTTATT
Found at i:55574543 original size:35 final size:38
Alignment explanation
Indices: 55574461--55574543 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
55574451 AAAATTTATA
* ** *
55574461 TTTAATACAATAAAGTATTTATTATACTTATTTGTGTT
1 TTTAATATAATAAAACATTTATTATACTTATATGTGTT
55574499 TTTAATATAATAAAACATTTATTATA-TT-TATGT-TT
1 TTTAATATAATAAAACATTTATTATACTTATATGTGTT
55574534 TTTAATATAA
1 TTTAATATAA
55574544 ATATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 12 0.29
36 4 0.10
37 2 0.05
38 23 0.56
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATACTTATATGTGTT
Found at i:55580676 original size:24 final size:22
Alignment explanation
Indices: 55580649--55580693 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
55580639 ATTGTGAAGT
55580649 TATAAATTTAAATAATTCTAAAAC
1 TATAAATTT-AATAATT-TAAAAC
* *
55580673 TATATATTTTATAATTTAAAA
1 TATAAATTTAATAATTTAAAA
55580694 AGATTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAAATTTAATAATTTAAAAC
Found at i:55597609 original size:21 final size:19
Alignment explanation
Indices: 55597573--55597616 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
55597563 TTTTCCATGA
55597573 TTTTTAAGTTATTGATTGTG
1 TTTTTAAGTTATTGA-TGTG
55597593 TTTTTACATGTTA-TGATGTG
1 TTTTTA-A-GTTATTGATGTG
55597613 TTTT
1 TTTT
55597617 GGTTTGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.64
21 4 0.18
22 4 0.18
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (19 bp):
TTTTTAAGTTATTGATGTG
Found at i:55600782 original size:40 final size:40
Alignment explanation
Indices: 55600643--55600783 Score: 119
Period size: 40 Copynumber: 3.6 Consensus size: 40
55600633 ACTTTGAGTT
* * * * *
55600643 GATGAGACACTAGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTAGGTGCCAAATTATTACTTCGTATT-ATCC
* * *
55600684 GATGAGGCACTAGGTGCC-AA-T-TTACTTCGGT-TTAGCT
1 GATGAGACACTAGGTGCCAAATTATTACTTC-GTATTATCC
* **
55600721 GATGAGACACTGGGTTTCAAATTATTACTTCGTATTATCC
1 GATGAGACACTAGGTGCCAAATTATTACTTCGTATTATCC
* *
55600761 GATGAGGCACTGGGTGCCAAATT
1 GATGAGACACTAGGTGCCAAATT
55600784 GGTGTGTTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
37 15 0.19
38 10 0.13
39 5 0.06
40 32 0.41
41 16 0.21
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (40 bp):
GATGAGACACTAGGTGCCAAATTATTACTTCGTATTATCC
Found at i:55608836 original size:27 final size:27
Alignment explanation
Indices: 55608806--55608867 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
55608796 CCTATCAGGT
55608806 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
55608833 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
55608860 AGGCGCCA
1 AGGCGCCA
55608868 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:55609581 original size:49 final size:49
Alignment explanation
Indices: 55609509--55609652 Score: 188
Period size: 49 Copynumber: 3.0 Consensus size: 49
55609499 NNNNNNNNNN
*
55609509 TATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTG
1 TATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTG
* **
55609558 TATGAATATTGTAATATTATAATTTTGTATGAATATTGTAA--TGTCGG
1 TATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTG
* *
55609605 TAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTT
1 TATGAATATTGTAATATTATAA--TTTTGTATGAATATTGTAATTTTTTT
55609653 ATAATTAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
45 16 0.20
47 25 0.30
49 41 0.50
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
TATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTG
Found at i:55609591 original size:27 final size:27
Alignment explanation
Indices: 55609509--55609599 Score: 138
Period size: 27 Copynumber: 3.6 Consensus size: 27
55609499 NNNNNNNNNN
55609509 TATGAATATTGTAATATTATAATTTTG
1 TATGAATATTGTAATATTATAATTTTG
*
55609536 TATGAATATTG-CA-ATT-T--TTTTG
1 TATGAATATTGTAATATTATAATTTTG
55609558 TATGAATATTGTAATATTATAATTTTG
1 TATGAATATTGTAATATTATAATTTTG
55609585 TATGAATATTGTAAT
1 TATGAATATTGTAAT
55609600 GTCGGTATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.28
23 1 0.02
24 4 0.07
25 4 0.07
26 1 0.02
27 31 0.54
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (27 bp):
TATGAATATTGTAATATTATAATTTTG
Found at i:55609717 original size:19 final size:19
Alignment explanation
Indices: 55609695--55609732 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55609685 TATAAATTTA
*
55609695 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
55609714 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
55609733 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:55617027 original size:9 final size:9
Alignment explanation
Indices: 55617015--55617049 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
55617005 TGAAGATGTT
55617015 GAAGGTTGA
1 GAAGGTTGA
55617024 GAAGGTTGA
1 GAAGGTTGA
55617033 GAAGGTTGA
1 GAAGGTTGA
55617042 GAAGGTTG
1 GAAGGTTG
55617050 TGAAACTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (9 bp):
GAAGGTTGA
Found at i:55628058 original size:27 final size:27
Alignment explanation
Indices: 55628008--55628061 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
55627998 TAGCAATGCT
55628008 CTTTACAGTTACAAGTATAAAACCTCA
1 CTTTACAGTTACAAGTATAAAACCTCA
55628035 CTTTACAGTTACAAGTATAAAACCTCA
1 CTTTACAGTTACAAGTATAAAACCTCA
55628062 GATTACATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (27 bp):
CTTTACAGTTACAAGTATAAAACCTCA
Found at i:55628067 original size:27 final size:27
Alignment explanation
Indices: 55628010--55628068 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
55628000 GCAATGCTCT
*
55628010 TTACAGTTACAAGTATAAAACCTCACT
1 TTACAGTTACAAGTATAAAACCTCACA
*
55628037 TTACAGTTACAAGTATAAAACCTCAGA
1 TTACAGTTACAAGTATAAAACCTCACA
55628064 TTACA
1 TTACA
55628069 TAGAATTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (27 bp):
TTACAGTTACAAGTATAAAACCTCACA
Found at i:55636391 original size:18 final size:19
Alignment explanation
Indices: 55636368--55636408 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
55636358 CATTGACTAT
*
55636368 AAAGAAAAACTAAAGGAA-
1 AAAGAAAAACAAAAGGAAG
*
55636386 AAAGAAAAAGAAAAGGAAG
1 AAAGAAAAACAAAAGGAAG
55636405 AAAG
1 AAAG
55636409 GAAGATGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAGAAAAACAAAAGGAAG
Found at i:55641983 original size:47 final size:48
Alignment explanation
Indices: 55641889--55641984 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 48
55641879 TGCATGTATT
* * *
55641889 TATATATTTTAAAATTATGAAATATATATGAAAGAAACATATGTATGTA
1 TATATATTTTAAAATTACGAAATATAGA-GAAAGAAACATAAGTATGTA
* * * *
55641938 TATATATTTTAAAATTACGAAATATGGA-AAATATATATAAGTATGTA
1 TATATATTTTAAAATTACGAAATATAGAGAAAGAAACATAAGTATGTA
55641985 CATGTATATC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 15 0.38
49 25 0.62
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (48 bp):
TATATATTTTAAAATTACGAAATATAGAGAAAGAAACATAAGTATGTA
Found at i:55644202 original size:12 final size:12
Alignment explanation
Indices: 55644185--55644209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55644175 CTCAAACTCA
55644185 ATCAATAATATT
1 ATCAATAATATT
55644197 ATCAATAATATT
1 ATCAATAATATT
55644209 A
1 A
55644210 AAAGTTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCAATAATATT
Found at i:55651631 original size:17 final size:18
Alignment explanation
Indices: 55651609--55651645 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
55651599 CTTTAAAATA
55651609 TAATAT-TTATTTA-ATTT
1 TAATATATT-TTTATATTT
55651626 TAATATATTTTTATATTT
1 TAATATATTTTTATATTT
55651644 TA
1 TA
55651646 TAGTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATATATTTTTATATTT
Found at i:55651726 original size:31 final size:32
Alignment explanation
Indices: 55651691--55651755 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
55651681 CTATATTGCA
* * *
55651691 TTTTTAT-ATTATTTATTTTAATATCATT-AAT
1 TTTTTATAACTATTT-TTATAAAATCATTGAAT
55651722 TTTTTATAACTATTTTTATAAAATCATTGAAT
1 TTTTTATAACTATTTTTATAAAATCATTGAAT
55651754 TT
1 TT
55651756 CATTAACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (32 bp):
TTTTTATAACTATTTTTATAAAATCATTGAAT
Found at i:55658802 original size:12 final size:11
Alignment explanation
Indices: 55658787--55658828 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
55658777 GTGAGAGTAT
55658787 AATAAAAGAAA
1 AATAAAAGAAA
*
55658798 TAATAAAATAAA
1 -AATAAAAGAAA
55658810 AATAAAAGTAAA
1 AATAAAAG-AAA
55658822 AATAAAA
1 AATAAAA
55658829 CAATAACCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AATAAAAGAAA
Found at i:55666624 original size:17 final size:17
Alignment explanation
Indices: 55666592--55666634 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
55666582 ATTCTAAAAG
55666592 AATAA-AAAAAACTAAT
1 AATAATAAAAAACTAAT
55666608 AATAATAAAATAA-TAAT
1 AATAATAAAA-AACTAAT
*
55666625 AACAATAAAA
1 AATAATAAAA
55666635 CGTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAATAAAAAACTAAT
Found at i:55666831 original size:3 final size:3
Alignment explanation
Indices: 55666823--55666884 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
55666813 AAACATAAAC
** * * * * * *
55666823 AAT AAT AAT AGC AAA AAT AGT ATT AAT GAT AAT AAT AAT AGT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55666871 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
55666885 GGTATTAATT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55668778 original size:100 final size:100
Alignment explanation
Indices: 55668605--55669111 Score: 763
Period size: 100 Copynumber: 5.1 Consensus size: 100
55668595 GGGAAATGAG
* * * * *
55668605 ATTGCAATGTC-AGGGAAGGGAGATTCGTCGTTGTAGCTTCAATCTATTCCACTGCA-TCGCCTG
1 ATTGCAATGTCGA-GGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT-ACCAG
* *
55668668 GGAAAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTA
64 GGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
*
55668705 ATTGCAATGTCGAGGAAGCGAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGGG
1 ATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGGG
55668770 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
* * *
55668805 ATTGCAATGTCGGGGAAGCGAGATTAGCCGTTGTAGCTTCAATTTGTTCCACTGCACTACCAGGG
1 ATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGGG
*
55668870 AAAGTAAGATTCACCGTTGTGGCCTCAATCTTATA
66 AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
55668905 ATTGCAATGTC-AGCGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGG
1 ATTGCAATGTCGAG-GAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGG
*
55668969 GAAAGTAAGATTCACCGTTGTGGCCTCAATCTTATA
65 GAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
* * * *
55669005 ATTGCAATGTCGGGGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCATTGCA-TCGCCAGG
1 ATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT-ACCAGG
* *
55669069 G-AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA
65 GAAAGTAAGATTCGCCGTTGTGGCCTCAATC-TTATA
55669105 ATTGCAA
1 ATTGCAA
55669112 ACTATGGTGT
Statistics
Matches: 378, Mismatches: 23, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
99 29 0.08
100 346 0.92
101 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (100 bp):
ATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTACCAGGG
AAAGTAAGATTCGCCGTTGTGGCCTCAATCTTATA
Found at i:55669192 original size:45 final size:45
Alignment explanation
Indices: 55669121--55669258 Score: 170
Period size: 45 Copynumber: 3.1 Consensus size: 45
55669111 AACTATGGTG
* * *
55669121 TCTTCGATCTGCTTCACCGTCAGTACAAGAAGACAAGATCTGCTA
1 TCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * * *
55669166 TTTTCAGTCTGCTCCGCCGTCAGTACAGGGAGGCAAGA-CTGGTG
1 TCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTA
*
55669210 TCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTA
1 TCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTA
55669255 TCTT
1 TCTT
55669259 TATTGATCTG
Statistics
Matches: 74, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
44 36 0.49
45 38 0.51
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTA
Found at i:55669236 original size:44 final size:45
Alignment explanation
Indices: 55669116--55669251 Score: 166
Period size: 44 Copynumber: 3.0 Consensus size: 45
55669106 TTGCAAACTA
* * *
55669116 TGGTGTCTTCGATCTGCTTCACCGTCAGTACAAGAAGACAAGATC
1 TGGTGTCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATC
* * * * * * *
55669161 TGCTATTTTCAGTCTGCTCCGCCGTCAGTACAGGGAGGCAAGA-C
1 TGGTGTCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATC
*
55669205 TGGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATC
1 TGGTGTCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATC
55669250 TG
1 TG
55669252 CTATCTTTAT
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 36 0.50
45 36 0.50
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (45 bp):
TGGTGTCTTCAATCTGCTTCACCGTCAGTACAGGAAGGCAAGATC
Found at i:55675242 original size:21 final size:21
Alignment explanation
Indices: 55675218--55675259 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55675208 AATTATGGTG
*
55675218 TTAATATGCATAATG-GAATAA
1 TTAACATG-ATAATGTGAATAA
55675239 TTAACATGATAATGTGAATAA
1 TTAACATGATAATGTGAATAA
55675260 AAATAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (21 bp):
TTAACATGATAATGTGAATAA
Found at i:55675535 original size:3 final size:3
Alignment explanation
Indices: 55675527--55675565 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55675517 TAAATGAGTA
55675527 AAT 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
55675566 TATTATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55677678 original size:44 final size:44
Alignment explanation
Indices: 55677500--55677696 Score: 136
Period size: 44 Copynumber: 4.5 Consensus size: 44
55677490 ATGCGATCTG
* *
55677500 CTCCACTACTGCTTAGGGTGATAAGATCTACAATCTTTAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTAACCTA
* **** * ** *
55677544 CTCCACTACTG-TTCAGGGAGATAGGA-CTGGTGGCTTAAATTTG
1 CTCCACTACTGCTT-AGGGAGATAAGATCTGCAATCTTTAACCTA
* * * * ** * *
55677587 CTTC-CTACAT-CTCAGGAAGATAAGAT-T-CACCGTCTTCGATCTG
1 CTCCACTAC-TGCTTAGGGAGATAAGATCTGCA--ATCTTTAACCTA
55677630 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTAACCTA
*
55677674 CTCCACTATTGCTTAGGGAGATA
1 CTCCACTACTGCTTAGGGAGATA
55677697 GGATTGGTGG
Statistics
Matches: 113, Mismatches: 30, Indels: 20
0.69 0.18 0.12
Matches are distributed among these distances:
42 15 0.13
43 27 0.24
44 68 0.60
45 1 0.01
46 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTAACCTA
Found at i:55677766 original size:122 final size:125
Alignment explanation
Indices: 55677493--55677954 Score: 597
Period size: 122 Copynumber: 3.6 Consensus size: 125
55677483 AGACTGGATG
* * *
55677493 CGATCTGCTCCACTACTGCTTAGGGTGATAAGATCTACAATCTTTAACCTACTCCACTACTGTTC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTC
* * *
55677558 AGGGAGATAGGACTGGTGGCTTAAATTTGCTTCCTACATCTCAGGAAGATAAGATTCACCGTCTT
66 AGGGAGATAGGACTGGTGGCTTAAA-TT-CCT-CT--ATCTCGGGAAGATAAGATTCGCCGTCTT
* * * *
55677623 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTAACCTACTCCACTATTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTC
* *
55677688 AGGGAGATAGGATTGGTGGCTTAAA-T-CT-TATCTCGGGAAGATAAGATTCGTCGTCTT
66 AGGGAGATAGGACTGGTGGCTTAAATTCCTCTATCTCGGGAAGATAAGATTCGCCGTCTT
* * * * **
55677745 TGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTACTCCATTGTTGCTC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTC
* *
55677810 AGGGAGATAGAACTGGTGGCTTAAATCTGCTTCCTACTATCTCGGAAAGATAAGATTCGCCGTCT
66 AGGGAGATAGGACTGGTGGCTTAAA-----TTCCT-CTATCTCGGGAAGATAAGATTCGCCGTCT
55677875 T
125 T
* *
55677876 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTC
*
55677941 AGAGAGATAGGACT
66 AGGGAGATAGGACT
55677955 TGTTATGATG
Statistics
Matches: 293, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
122 105 0.36
124 1 0.00
126 1 0.00
128 2 0.01
129 2 0.01
130 84 0.29
131 98 0.33
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (125 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTC
AGGGAGATAGGACTGGTGGCTTAAATTCCTCTATCTCGGGAAGATAAGATTCGCCGTCTT
Found at i:55688958 original size:23 final size:23
Alignment explanation
Indices: 55688932--55688979 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
55688922 TGTTCAAAAA
55688932 GAATATCACATCCAACACATTAG
1 GAATATCACATCCAACACATTAG
*
55688955 GAATATCACATCCAGCACATTAG
1 GAATATCACATCCAACACATTAG
55688978 GA
1 GA
55688980 TACGATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (23 bp):
GAATATCACATCCAACACATTAG
Found at i:55689204 original size:15 final size:15
Alignment explanation
Indices: 55689186--55689216 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55689176 AATTAACATG
55689186 ATAATATGAACAAAA
1 ATAATATGAACAAAA
*
55689201 ATAATATGAGCAAAA
1 ATAATATGAACAAAA
55689216 A
1 A
55689217 CGAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (15 bp):
ATAATATGAACAAAA
Found at i:55689476 original size:3 final size:3
Alignment explanation
Indices: 55689468--55689497 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55689458 TAAATGAGTA
55689468 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55689498 TTGAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55692605 original size:64 final size:64
Alignment explanation
Indices: 55692501--55692634 Score: 214
Period size: 64 Copynumber: 2.1 Consensus size: 64
55692491 TTAATTCTTG
* * * *
55692501 GTTTAATATTTCTAGAGTATTGATCCATGTTTGATTTGCTTAAATCCAAGGTTGAATAGACCTT
1 GTTTAATATTTCTAGAGTATTGATCCATGTATGATGTGCTTAAATCAAAGGTTGAATAGACCCT
* *
55692565 GTTTAATATTTCTAGAGTATTGATCTATGTATGATGTGCTTAAATCAAAGTTTGAATAGACCCT
1 GTTTAATATTTCTAGAGTATTGATCCATGTATGATGTGCTTAAATCAAAGGTTGAATAGACCCT
55692629 GTTTAA
1 GTTTAA
55692635 GAGTAGATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (64 bp):
GTTTAATATTTCTAGAGTATTGATCCATGTATGATGTGCTTAAATCAAAGGTTGAATAGACCCT
Found at i:55693614 original size:5 final size:5
Alignment explanation
Indices: 55693604--55693657 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
55693594 CTAATACTCA
*
55693604 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAG AGAAAT AAAA- AAAA- ACAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT A-AAAT
55693654 AAAA
1 AAAA
55693658 GATTCAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
4 5 0.11
5 34 0.77
6 5 0.11
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:55693666 original size:26 final size:26
Alignment explanation
Indices: 55693610--55693659 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
55693600 CTCAAAAATA
55693610 AAATAAAATAAAATAAAATAAAAGAG
1 AAATAAAATAAAATAAAATAAAAGAG
55693636 AAATAAAA-AAAA-ACAAATAAAAGA
1 AAATAAAATAAAATA-AAATAAAAGA
55693660 TTCAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 14 0.61
26 8 0.35
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (26 bp):
AAATAAAATAAAATAAAATAAAAGAG
Found at i:55694446 original size:40 final size:40
Alignment explanation
Indices: 55694391--55694471 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55694381 TACTACAATT
55694391 ATACAATTATTAACAAGCTAAAACATAGTAATGGATTTCG
1 ATACAATTATTAACAAGCTAAAACATAGTAATGGATTTCG
55694431 ATACAATTATTAACAAGCTAAAACATAGTAATGGATTTCG
1 ATACAATTATTAACAAGCTAAAACATAGTAATGGATTTCG
55694471 A
1 A
55694472 GTATAGGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (40 bp):
ATACAATTATTAACAAGCTAAAACATAGTAATGGATTTCG
Found at i:55696429 original size:26 final size:26
Alignment explanation
Indices: 55696397--55696449 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
55696387 TGAATATAAT
*
55696397 AACATCAACAATTTGACAAAAAAATA
1 AACATCAACAATGTGACAAAAAAATA
* * *
55696423 AACATCAACCATGTGACTAAATAATA
1 AACATCAACAATGTGACAAAAAAATA
55696449 A
1 A
55696450 TAGTAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.21
Consensus pattern (26 bp):
AACATCAACAATGTGACAAAAAAATA
Found at i:55710262 original size:13 final size:13
Alignment explanation
Indices: 55710244--55710303 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
55710234 CCTGACTTGT
55710244 TTTTATTATTTCC
1 TTTTATTATTTCC
**
55710257 TTTTATTATTTTG
1 TTTTATTATTTCC
*
55710270 TTTGT-TTATTGTTC
1 TTT-TATTATT-TCC
55710284 TTTTATTATTTCC
1 TTTTATTATTTCC
*
55710297 ATTTATT
1 TTTTATT
55710304 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 28 0.72
14 11 0.28
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTCC
Found at i:55714517 original size:36 final size:36
Alignment explanation
Indices: 55714476--55714666 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
55714466 GGTAGCATTA
*
55714476 GCTACATTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55714512 GCTACACTTATCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
55714557 AGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
55714594 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55714630 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
55714666 G
1 G
55714667 GTAGCCTTAG
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 99 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:55714543 original size:82 final size:82
Alignment explanation
Indices: 55714440--55714630 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
55714430 TTTGAGTACT
*
55714440 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACATTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
55714505 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* * *
55714522 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
55714587 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
*
55714604 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTG
55714631 CTATACTTAT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 102 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:55714614 original size:21 final size:20
Alignment explanation
Indices: 55714586--55714651 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
55714576 AGTGAGAAAG
55714586 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
55714606 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
55714622 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
55714642 TGATCAAGTG
1 TGAT-AAGTG
55714652 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:55714691 original size:118 final size:118
Alignment explanation
Indices: 55714483--55714704 Score: 399
Period size: 118 Copynumber: 1.9 Consensus size: 118
55714473 TTAGCTACAT
*
55714483 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGATAAAGTGATAAGT
1 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
55714548 GGTAGCTTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGCTATAC
66 GGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTATAC
* *
55714601 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
55714666 GGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
66 GGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
55714705 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (118 bp):
TTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
GGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTATAC
Found at i:55716068 original size:49 final size:49
Alignment explanation
Indices: 55716007--55716199 Score: 305
Period size: 49 Copynumber: 3.9 Consensus size: 49
55715997 ATGTGAACAT
*
55716007 GTGATTATGTGATTCCGTGTAAGACCATAGCTGAGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
*
55716057 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGATAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
55716106 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
55716155 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
55716200 AGAAAACGAA
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 130 0.97
50 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:55718652 original size:3 final size:3
Alignment explanation
Indices: 55718644--55718671 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55718634 AAATAGAAAT
55718644 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55718672 ACAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55719353 original size:44 final size:44
Alignment explanation
Indices: 55719290--55719709 Score: 180
Period size: 44 Copynumber: 9.4 Consensus size: 44
55719280 TCCGACCTGG
* * * *
55719290 TGCAACTTCAGAGG-TATAGGATTCATTGTTTTAGTCCGCTCCAC
1 TGCAACTTCAG-GGAGATAGGATTAATTGTTTTAATCTGCTCCAC
* * * *
55719334 TGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCAT
1 TGCAACTTCAGGGAGATAGGATTAATTGTTTTAATCTGCTCCAC
* * *
55719378 TGCAACTTCAGGGAGA-A-AATT--TTAGTATCTTCAA-CTTGTTTCAC
1 TGCAACTTCAGGGAGATAGGATTAATT-GT-T-TT-AATC-TGCTCCAC
* ** * *
55719422 TACAACTTCAGGGAGATAAGG-TTTGTGGTTTTAGTCTGCTCCAC
1 TGCAACTTCAGGGAGAT-AGGATTAATTGTTTTAATCTGCTCCAC
* * * * * *
55719466 TGCAACGTCAGGGAGATAAGACTTTTTATGGTAGATTTAATCCGAC-CTAC
1 TGCAACTTCAGGGAGATAGGA---TTAAT--T-GTTTTAATCTG-CTCCAC
* * *
55719516 TGCAACTTCAGAGG-TATAGGATTCATCGTTTTAATCTGCTCCAC
1 TGCAACTTCAG-GGAGATAGGATTAATTGTTTTAATCTGCTCCAC
* * * * * *
55719560 TGCAACTTTAAGGAGATAGGATTAATAGCTTCAATCTGCTTCAC
1 TGCAACTTCAGGGAGATAGGATTAATTGTTTTAATCTGCTCCAC
* * ** * *
55719604 TACAACTTCAGGGAGATAAGATTGGTT-TCTTCAACCTGCTCCAC
1 TGCAACTTCAGGGAGATAGGATTAATTGT-TTTAATCTGCTCCAC
* * ** * * *
55719648 TGCAA-TTTAGAGAGATAAGG-TTGGTTATCTTCAGTCTGCTCCAC
1 TGCAACTTCAGGGAGAT-AGGATTAATTGT-TTTAATCTGCTCCAC
* *
55719692 TGCAATTTTAGGGAGATA
1 TGCAACTTCAGGGAGATA
55719710 ATACTTGTTA
Statistics
Matches: 286, Mismatches: 63, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 4 0.01
43 25 0.09
44 198 0.69
45 13 0.05
46 4 0.01
47 10 0.03
48 1 0.00
50 26 0.09
51 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAGGATTAATTGTTTTAATCTGCTCCAC
Found at i:55719637 original size:226 final size:226
Alignment explanation
Indices: 55719222--55719723 Score: 673
Period size: 226 Copynumber: 2.2 Consensus size: 226
55719212 AAGATCTGCT
* * * *
55719222 ATCTACAGTCTACTCCACTACAACTTTAGGGAGATAAGACTTGTTATGATAGACTTAATCCGACC
1 ATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACC
** * * *
55719287 TGGTGCAACTTCAGAGGTATAGGATTCATTGTTTTAGTCCGCTCCACTGCAACTTCAGGGAGATA
66 TACTGCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATA
* * ** * *
55719352 GGATTAATAGCTTCAATCTGCTCCATTGCAACTTCAGGGAGAAAATTTTAGTATCTTCAACTTGT
131 GGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAGAAAAGATTAGTATCTTCAACCTGC
* * *
55719417 TTCACTACAACTTCAGGGAGATAAGGTTTGTG
196 TCCACTACAA-TTCAGAGAGATAAGGTTGGTG
* * * * * *
55719449 GT-TTTAGTCTGCTCCACTGCAACGTCAGGGAGATAAGACTTTTTATGGTAGATTTAATCCGACC
1 ATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACC
* *
55719513 TACTGCAACTTCAGAGGTATAGGATTCATCGTTTTAATCTGCTCCACTGCAACTTTAAGGAGATA
66 TACTGCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATA
* * * *
55719578 GGATTAATAGCTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGATTGGTTTCTTCAACCTGC
131 GGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAGAAAAGATTAGTATCTTCAACCTGC
* * *
55719643 TCCACTGCAATTTAGAGAGATAAGGTTGGTT
196 TCCACTACAATTCAGAGAGATAAGGTTGGTG
* *
55719674 ATCTTCAGTCTGCTCCACTGCAATTTTAGGGAGATAATACTTGTTATGGT
1 ATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGT
55719724 GTGATCTGCT
Statistics
Matches: 234, Mismatches: 40, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
225 18 0.08
226 215 0.92
227 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (226 bp):
ATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACC
TACTGCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATA
GGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAGAAAAGATTAGTATCTTCAACCTGC
TCCACTACAATTCAGAGAGATAAGGTTGGTG
Found at i:55719672 original size:43 final size:45
Alignment explanation
Indices: 55719548--55719803 Score: 209
Period size: 44 Copynumber: 5.7 Consensus size: 45
55719538 TCATCGTTTT
* * ** *
55719548 AATCTGCTCCACTGCAACTTTAAGGAGATAGGATT-AATAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTATCTTC
* * *
55719592 AATCTGCTTCACTACAACTTCAGGGAGATAAGATTGGTT-TCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTATCTTC
* * *
55719636 AACCTGCTCCACTGCAA-TTTAGAGAGATAAGGTTGGTTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTATCTTC
* * * *
55719680 AGTCTGCTCCACTGCAATTTTAGGGAGATAATACTT-GTTATGGTGT-
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGGTTAT-CT-TC
* * * *
55719726 GATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT-GCTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGGTTATCTTC
* * * * * *
55719771 AGTCTACTCTACTGCAACATCAGTGAGATAAGA
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA
55719804 CTTGTAGCTT
Statistics
Matches: 170, Mismatches: 34, Indels: 15
0.78 0.16 0.07
Matches are distributed among these distances:
43 18 0.11
44 69 0.41
45 47 0.28
46 35 0.21
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTATCTTC
Found at i:55719799 original size:91 final size:90
Alignment explanation
Indices: 55719639--55719808 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 90
55719629 TTTCTTCAAC
* * * ** *
55719639 CTGCTCCACTGCAATTTAGAGAGATAAGGTTGGTTATCTTCAGTCTGCTCCACTGCAATTTTAGG
1 CTGCTCCACTGCAATTTAGAGAGATAAGATTGGCTATCTTCAGTCTACTCCACTGCAACATCAGG
*
55719704 GAGATAATACTTGTTATGGTGTGAT
66 GAGATAAGACTTGTTATGGTGTGAT
* *
55719729 CTGCTCTACTGCAACTTTAGAGAGATAAGATCT-GCTATCTTCAGTCTACTCTACTGCAACATCA
1 CTGCTCCACTGCAA-TTTAGAGAGATAAGAT-TGGCTATCTTCAGTCTACTCCACTGCAACATCA
*
55719793 GTGAGATAAGACTTGT
64 GGGAGATAAGACTTGT
55719809 AGCTTCAACT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
90 13 0.19
91 54 0.79
92 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (90 bp):
CTGCTCCACTGCAATTTAGAGAGATAAGATTGGCTATCTTCAGTCTACTCCACTGCAACATCAGG
GAGATAAGACTTGTTATGGTGTGAT
Found at i:55719941 original size:44 final size:45
Alignment explanation
Indices: 55719893--55720098 Score: 238
Period size: 44 Copynumber: 4.6 Consensus size: 45
55719883 ATTTTATGCC
*
55719893 GCTCCACTGCAACTTCAGGGAGATAGGACTAG-TAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAGTTAACTTCAATCT
*
55719937 GCTCCACTGCAACTTCAGGGAGATAGGACTAG-TAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAGTTAACTTCAATCT
* * * * * *
55719981 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTTA-GTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAG-TTAACTTCAATCT
* * * * * ** *
55720026 GTTCCTCTGTAACTTCAGGAAGATAAGACTTGTTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAGTTAACTTCAATCT
55720071 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
55720099 TATGCCATCT
Statistics
Matches: 136, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
44 74 0.54
45 60 0.44
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTAGTTAACTTCAATCT
Found at i:55720099 original size:90 final size:88
Alignment explanation
Indices: 55719893--55720099 Score: 236
Period size: 90 Copynumber: 2.3 Consensus size: 88
55719883 ATTTTATGCC
* * * *
55719893 GCTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTCAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAACGTCAATCTGCTCCACTGCAACTTCAGGAA
*
55719958 GATAGGACTAGTAACTTCAATCT
66 GATAAGACTAGTAACTTCAATCT
* * * * * * *
55719981 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTTA-GTCAGTCTGTTCCTCTGTAACTTCAGG
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG--TAACGTCAATCTGCTCCACTGCAACTTCAGG
* ** *
55720045 AAGATAAGACTTGTTGGCTTTAATCT
64 AAGATAAGACTAG-TAACTTCAATCT
55720071 GCTCCACTGCAACTTCAGGGAGATAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT
55720100 ATGCCATCTT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
88 28 0.28
89 32 0.32
90 39 0.39
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (88 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAACGTCAATCTGCTCCACTGCAACTTCAGGAA
GATAAGACTAGTAACTTCAATCT
Found at i:55720111 original size:45 final size:45
Alignment explanation
Indices: 55719893--55720143 Score: 212
Period size: 44 Copynumber: 5.7 Consensus size: 45
55719883 ATTTTATGCC
* *
55719893 GCTCCACTGCAACTTCAGGGAGATAGGACTA-GTAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATGTAACTTTAATCT
* *
55719937 GCTCCACTGCAACTTCAGGGAGATAGGACTA-GTAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATGTAACTTTAATCT
* * * * * * * *
55719981 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTTA-GTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-ATGTAACTTTAATCT
* * * * **
55720026 GTTCCTCTGTAACTTCAGGAAGATAAGACT-TGTTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATG-TAACTTTAATCT
* * *
55720071 GCTCCACTGCAACTTCAGGGAGATAAGA-TATGCCATCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATG-TAACTTTAATCT
*
55720116 G-TCTCACTGC--CTTCAGGGGGATAAGACT
1 GCTC-CACTGCAACTTCAGGGAGATAAGACT
55720144 TACTTTCTTC
Statistics
Matches: 170, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
43 16 0.09
44 76 0.45
45 76 0.45
46 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTATGTAACTTTAATCT
Found at i:55720115 original size:90 final size:87
Alignment explanation
Indices: 55719893--55720143 Score: 224
Period size: 90 Copynumber: 2.8 Consensus size: 87
55719883 ATTTTATGCC
* * * * * *
55719893 GCTCCACTGCAACTTCAGGGAGATAGGACTA-GTAACTTCAATCTGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TATG-ATCTTTAGTCTGTTCCACTGCAACTTCAGGA
*
55719957 AGATAGGACTAGTAACTTCAATCT
64 AGATAAGACTAGTAACTTCAATCT
* * * * *
55719981 GCTCCACTGCAACTTCAGAGAGATAAGAT-TGGTTTTAGTCAGTCTGTTCCTCTGTAACTTCAGG
1 GCTCCACTGCAACTTCAGGGAGATAAGATATGATCTT--T-AGTCTGTTCCACTGCAACTTCAGG
* ** *
55720045 AAGATAAGACTTGTTGGCTTTAATCT
63 AAGATAAGACTAG-TAACTTCAATCT
55720071 GCTCCACTGCAACTTCAGGGAGATAAGATATGCCATCTTTAGTCTG-TCTCACTGC--CTTCAGG
1 GCTCCACTGCAACTTCAGGGAGATAAGATATG--ATCTTTAGTCTGTTC-CACTGCAACTTCAGG
**
55720133 GGGATAAGACT
63 AAGATAAGACT
55720144 TACTTTCTTC
Statistics
Matches: 131, Mismatches: 23, Indels: 18
0.76 0.13 0.10
Matches are distributed among these distances:
86 2 0.02
87 2 0.02
88 42 0.32
89 32 0.24
90 47 0.36
91 3 0.02
93 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATATGATCTTTAGTCTGTTCCACTGCAACTTCAGGAAG
ATAAGACTAGTAACTTCAATCT
Found at i:55720176 original size:36 final size:36
Alignment explanation
Indices: 55720129--55720197 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
55720119 TCACTGCCTT
* *
55720129 CAGGGGGATAAGACTT-ACTTTCTTCAACTTTAACAC
1 CAGGGAGATAAGA-TTCACTTCCTTCAACTTTAACAC
*
55720165 CAGGGAGATAAGATTCGCTTCCTTCAACTTTAA
1 CAGGGAGATAAGATTCACTTCCTTCAACTTTAA
55720198 TCTGCTCCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (36 bp):
CAGGGAGATAAGATTCACTTCCTTCAACTTTAACAC
Found at i:55720406 original size:123 final size:122
Alignment explanation
Indices: 55720180--55720409 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 122
55720170 AGATAAGATT
* * *
55720180 CGCTTCCTTCAACTTTAATCTGCTCCGCTGCAATGCCAGGAAAACAAGATTCGCTACCTTTAGCT
1 CGCTTCCTTCAACTTTAATCTACTCCACTACAATGCCAGGAAAACAAGATTCGCTACCTTTAGCT
* * *
55720245 TTAATCTGTTCCACTGTAACGACAAGGAGATAGAATTTGCTGCCTTCAGCATTAATC
66 TTAATCTGTTCCACTGCAACAACAAGGAAATAGAATTTGCTGCCTTCAGCATTAATC
* * *
55720302 CGCTTCACTTCAACTTTAATCTATTCCACTACAATGCCAGGGAAACAAGATTCGCTACCTTTAGT
1 CGCTTC-CTTCAACTTTAATCTACTCCACTACAATGCCAGGAAAACAAGATTCGCTACCTTTAGC
* *
55720367 TTTAATTTGTTCCACTGCAA-AACCAGGGAAATA-AGATTTGCTG
65 TTTAATCTGTTCCACTGCAACAA-CAAGGAAATAGA-ATTTGCTG
55720410 TCTTTGATCT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
122 8 0.09
123 86 0.91
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (122 bp):
CGCTTCCTTCAACTTTAATCTACTCCACTACAATGCCAGGAAAACAAGATTCGCTACCTTTAGCT
TTAATCTGTTCCACTGCAACAACAAGGAAATAGAATTTGCTGCCTTCAGCATTAATC
Found at i:55720537 original size:88 final size:88
Alignment explanation
Indices: 55720439--55720731 Score: 408
Period size: 88 Copynumber: 3.3 Consensus size: 88
55720429 CTGTTTAGGG
* * * * * *
55720439 AGACAGGATCTACAATCTTCGACCCACTCCACTGCTGCTCAGGGAGA-CAGGACTAGTATTTTCA
1 AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGG-CTAGTGTTTTCA
* * *
55720503 ATCTGCTTCACTACTAGTACAAGA
65 ATCTGCTTCACTGCCAGTACAGGA
*
55720527 AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGTTTTCGA
1 AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGTTTTCAA
*
55720592 TCTGCCTCACTGCCAGTACAGGA
66 TCTGCTTCACTGCCAGTACAGGA
* * *** *
55720615 AGATAAGATATACAATCTTCAACCTACTCCACTACAATTCAGGGAGATAAGGCTGGTGTTTTCAA
1 AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGTTTTCAA
*
55720680 TCTGCTTTACTGCCAGTACAGGA
66 TCTGCTTCACTGCCAGTACAGGA
55720703 AGACAAGATCTACAATCTTCAACCTACTC
1 AGACAAGATCTACAATCTTCAACCTACTC
55720732 TGTAACAGCC
Statistics
Matches: 182, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 179 0.98
89 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (88 bp):
AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGTTTTCAA
TCTGCTTCACTGCCAGTACAGGA
Found at i:55723065 original size:47 final size:47
Alignment explanation
Indices: 55723014--55723113 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
55723004 TGGTTGGACC
* *
55723014 ATGGCAAC-ATGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCT
1 ATGGCAACGATGTGATATGTG-CTACCGTATAAGACCATAGCTGGGCT
** * * * *
55723061 ATGGCTTCGGTGTTATATGTGCTACTGTGTAAGACCATAGCTGGGCT
1 ATGGCAACGATGTGATATGTGCTACCGTATAAGACCATAGCTGGGCT
55723108 ATGGCA
1 ATGGCA
55723114 TTAGTATGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
47 33 0.77
48 10 0.23
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (47 bp):
ATGGCAACGATGTGATATGTGCTACCGTATAAGACCATAGCTGGGCT
Found at i:55723148 original size:49 final size:47
Alignment explanation
Indices: 55723043--55723159 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 47
55723033 GATTTCCGTA
* * *
55723043 TAAGACCATAGCTGGGCTATGGCTTCGGTGTTATATGTGCTACTGTG
1 TAAGACCATAGCTGGGCTATGGCTTAGATGTTATATGTGCTACAGTG
*
55723090 TAAGACCATAGCTGGGCTATGGCATTAGTATGTGT-TATGTGATTA-AGTG
1 TAAGACCATAGCTGGGCTATGGC-TTAG-ATGT-TATATGTG-CTACAGTG
* *
55723139 TAAGACCATAGTTGGACTATG
1 TAAGACCATAGCTGGGCTATG
55723160 ACATCGAGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
47 23 0.38
48 3 0.05
49 31 0.52
50 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCTTAGATGTTATATGTGCTACAGTG
Found at i:55726420 original size:43 final size:43
Alignment explanation
Indices: 55726286--55726420 Score: 101
Period size: 44 Copynumber: 3.1 Consensus size: 43
55726276 TTACATACTC
55726286 CACTACTGCTCAGGGAGATAAGGCTGGTGTTTTT-GATCTGCTT
1 CACTACTGCTCAGGGAGATAAGGCTGGT-TTTTTCGATCTGCTT
* *** * * * **** * * * *
55726329 CACTGCCAATACAGGAAGACAAGATCTACAATCTTCAACCTACTT
1 CACTACTGCT-CAGGGAGATAAG-GCTGGTTTTTTCGATCTGCTT
55726374 CACTACTGCTCAGGGAGATAAGGCTGGTTTTTTCGATCTGCTT
1 CACTACTGCTCAGGGAGATAAGGCTGGTTTTTTCGATCTGCTT
55726417 CACT
1 CACT
55726421 GCCAGTACAG
Statistics
Matches: 59, Mismatches: 30, Indels: 6
0.62 0.32 0.06
Matches are distributed among these distances:
43 22 0.37
44 23 0.39
45 14 0.24
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
CACTACTGCTCAGGGAGATAAGGCTGGTTTTTTCGATCTGCTT
Found at i:55726435 original size:88 final size:88
Alignment explanation
Indices: 55726281--55726620 Score: 547
Period size: 88 Copynumber: 3.9 Consensus size: 88
55726271 GGGTGTTACA
*
55726281 TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAATACAGGAA
1 TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAA
55726346 GACAAGATCTACAATCTTCAACC
66 GACAAGATCTACAATCTTCAACC
*
55726369 TACTTCACTACTGCTCAGGGAGATAAGGCTGGT-TTTTTCGATCTGCTTCACTGCCAGTACAGGA
1 TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTT-GATCTGCTTCACTGCCAGTACAGGA
55726433 AGACAAGATCTACAATCTTCAACC
65 AGACAAGATCTACAATCTTCAACC
* * * * *
55726457 TACTCCACTGCTGCTCAGGGAGATAAGACTGGTGTTTTTTATCTGCTTTATTGCCAGTACAGGAA
1 TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAA
55726522 GACAAGATCTACAATCTTCAACC
66 GACAAGATCTACAATCTTCAACC
** * * * *
55726545 TACTCCACTGTTGCTCAGGGAGATAAGGCTAGTGTTTTTTATCTGCTTTACTGCTAGTACAGGAA
1 TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAA
55726610 GACAAGATCTA
66 GACAAGATCTA
55726621 TAATATTCTT
Statistics
Matches: 237, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
87 5 0.02
88 227 0.96
89 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (88 bp):
TACTCCACTACTGCTCAGGGAGATAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAA
GACAAGATCTACAATCTTCAACC
Found at i:55726967 original size:24 final size:24
Alignment explanation
Indices: 55726934--55726991 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
55726924 GGATTGCCCC
*
55726934 CCACTCTAATCTTCAAGGCTCAAT
1 CCACTGTAATCTTCAAGGCTCAAT
* *
55726958 CCACTGTAATCTTCAAGGTTCAGT
1 CCACTGTAATCTTCAAGGCTCAAT
*
55726982 CCAATGTAAT
1 CCACTGTAAT
55726992 TTTGGGACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGCTCAAT
Found at i:55738553 original size:4 final size:4
Alignment explanation
Indices: 55738544--55738573 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
55738534 ACAAATTGTT
*
55738544 TTTA TTTA TTTA TTCA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
55738574 ACTCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:55738679 original size:15 final size:14
Alignment explanation
Indices: 55738641--55738706 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 14
55738631 ATTATCGTTA
* *
55738641 TTATATTATTTTTA
1 TTATTTTATTTTTG
*
55738655 TTTTTATTATTTCTTG
1 TTATT-TTATTT-TTG
*
55738671 TTATTTTATTATTTC
1 TTATTTTATT-TTTG
*
55738686 TTAATTTATTTTTG
1 TTATTTTATTTTTG
*
55738700 ATATTTT
1 TTATTTT
55738707 CATGTCATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
14 11 0.28
15 22 0.55
16 7 0.17
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (14 bp):
TTATTTTATTTTTG
Found at i:55741500 original size:26 final size:26
Alignment explanation
Indices: 55741458--55741532 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 26
55741448 AAAAGATTTC
*
55741458 AAATAAACAATATATAAAAAAAACTTA
1 AAATAAATAATA-ATAAAAAAAACTTA
* *
55741485 AAATGAATAATAAT---AAAAATTTA
1 AAATAAATAATAATAAAAAAAACTTA
55741508 AAATAAATAATAATATGAAAAAAAC
1 AAATAAATAATAATA--AAAAAAAC
55741533 ATATAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
23 21 0.55
26 2 0.05
27 10 0.26
28 5 0.13
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (26 bp):
AAATAAATAATAATAAAAAAAACTTA
Found at i:55741502 original size:23 final size:23
Alignment explanation
Indices: 55741466--55741522 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
55741456 TCAAATAAAC
* *
55741466 AATATATAAAAAAAACTTAAAATG
1 AATA-ATAATAAAAACTTAAAATA
*
55741490 AATAATAATAAAAATTTAAAATA
1 AATAATAATAAAAACTTAAAATA
55741513 AATAATAATA
1 AATAATAATA
55741523 TGAAAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAATAATAAAAACTTAAAATA
Found at i:55741630 original size:25 final size:24
Alignment explanation
Indices: 55741551--55741668 Score: 94
Period size: 25 Copynumber: 4.8 Consensus size: 24
55741541 CAGTTTCTTT
* *
55741551 TTTTAAAAATATAATATATAAAAA
1 TTTTAAATAGATAATATATAAAAA
* * *
55741575 ATTTAAA-AGATAATATATAATAG
1 TTTTAAATAGATAATATATAAAAA
* *
55741598 TCTAAAATAGATAATATAATAAAAA
1 TTTTAAATAGATAATAT-ATAAAAA
* **
55741623 TTTTAAATAAATAATACGTAAAACA
1 TTTTAAATAGATAATATATAAAA-A
* *
55741648 GTTTAGAATAAATAATATATA
1 TTTTA-AATAGATAATATATA
55741669 TATATATATA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
23 17 0.23
24 20 0.27
25 23 0.32
26 13 0.18
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (24 bp):
TTTTAAATAGATAATATATAAAAA
Found at i:55743911 original size:16 final size:17
Alignment explanation
Indices: 55743892--55743929 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
55743882 TTAAAAGGTA
55743892 AATAATGGGA-TACAAT
1 AATAATGGGATTACAAT
* *
55743908 AATAATGTGATTATAAT
1 AATAATGGGATTACAAT
55743925 AATAA
1 AATAA
55743930 CACCAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (17 bp):
AATAATGGGATTACAAT
Found at i:55744067 original size:13 final size:13
Alignment explanation
Indices: 55744049--55744076 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55744039 TATAACTTGA
55744049 GAGTAATAAAGGT
1 GAGTAATAAAGGT
55744062 GAGTAATAAAGGT
1 GAGTAATAAAGGT
55744075 GA
1 GA
55744077 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.21
Consensus pattern (13 bp):
GAGTAATAAAGGT
Found at i:55744084 original size:14 final size:13
Alignment explanation
Indices: 55744052--55744085 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
55744042 AACTTGAGAG
*
55744052 TAATAAAGGTGAG
1 TAATAAAGGTGAA
55744065 TAATAAAGGTGATA
1 TAATAAAGGTGA-A
55744079 TAATAAA
1 TAATAAA
55744086 AATAAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (13 bp):
TAATAAAGGTGAA
Found at i:55744212 original size:12 final size:11
Alignment explanation
Indices: 55744190--55744214 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55744180 TAATAAGGCA
55744190 TTTGATTTTTT
1 TTTGATTTTTT
55744201 TTTGATTTTTT
1 TTTGATTTTTT
55744212 TTT
1 TTT
55744215 AAAAAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTGATTTTTT
Found at i:55746204 original size:44 final size:44
Alignment explanation
Indices: 55746035--55746204 Score: 223
Period size: 44 Copynumber: 3.9 Consensus size: 44
55746025 TCATTGTTTT
* *
55746035 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
** * * *
55746079 AATCTGCTCCACTGCAACTTCAAAGAGACAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * * * *
55746123 AACCTGCTCCATTGCAACTTTAGGGAGATAAGGTTTGTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
55746167 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT
55746205 TGTAACAGCC
Statistics
Matches: 105, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
Found at i:55747528 original size:27 final size:26
Alignment explanation
Indices: 55747487--55747539 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
55747477 AATATGAAAG
*
55747487 GGGGTTGCTATGTGCTGATTCTCCCGA
1 GGGGTTGCTAAGTGCTGATTC-CCCGA
55747514 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
55747540 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:55747590 original size:105 final size:104
Alignment explanation
Indices: 55747409--55747780 Score: 577
Period size: 105 Copynumber: 3.6 Consensus size: 104
55747399 TGTATATAAA
** * *
55747409 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTAGGTGCG-TGATCCACCATACCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTACCT
* *
55747473 TTGAAATATGAAAGGGGGTTGCTATGTGCTGATTCTCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
55747513 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
*
55747578 TTGAAATGTGAAAGGGGGTTGCTACGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
55747618 AGGGGTTGCTAAGTGCTGAATCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
*
55747683 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
55747722 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCG
55747781 ATAACGGTTA
Statistics
Matches: 250, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
103 29 0.12
104 80 0.32
105 140 0.56
106 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:55752868 original size:3 final size:3
Alignment explanation
Indices: 55752835--55752910 Score: 66
Period size: 3 Copynumber: 25.0 Consensus size: 3
55752825 TTTAGCACAT
* * *
55752835 TTA TTA TCTA GTTAA TTA TT- TTA ATA ATA TTA TTA TTA TTA TTG TTA
1 TTA TTA T-TA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
55752882 TCA TTA TTA TTA TTA CTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55752911 ATATAATTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.07
3 49 0.82
4 5 0.08
5 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:55753105 original size:33 final size:34
Alignment explanation
Indices: 55753067--55753152 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 34
55753057 TTTTCATAAA
55753067 TATATATATATACATACTTACATATTTT-TAATT
1 TATATATATATACATACTTACATATTTTATAATT
* * * *
55753100 TATATATATGTACATGCTTATATATTTTATACTT
1 TATATATATATACATACTTACATATTTTATAATT
55753134 TATACTTTATATATACATA
1 TATA---TATATATACATA
55753153 TATATACATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 25 0.58
34 8 0.19
37 10 0.23
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (34 bp):
TATATATATATACATACTTACATATTTTATAATT
Found at i:55757802 original size:22 final size:22
Alignment explanation
Indices: 55757777--55757820 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55757767 TTCATATTTA
55757777 AAAT-TTAATTATAAAATTATAT
1 AAATGTTAA-TATAAAATTATAT
*
55757799 AAATGTTAATATTAAATTATAT
1 AAATGTTAATATAAAATTATAT
55757821 TATTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATGTTAATATAAAATTATAT
Found at i:55759811 original size:20 final size:21
Alignment explanation
Indices: 55759768--55759812 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
55759758 GTATGGTGTT
*
55759768 AATATGCATAATGGAATAATA
1 AATATGCATAATGGAACAATA
55759789 AATATG-ATAATGTGAACAA-A
1 AATATGCATAATG-GAACAATA
55759809 AATA
1 AATA
55759813 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (21 bp):
AATATGCATAATGGAACAATA
Found at i:55760064 original size:16 final size:15
Alignment explanation
Indices: 55760043--55760073 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
55760033 GAATATATAT
55760043 ATATAAAAATTATAAG
1 ATATAAAAA-TATAAG
55760059 ATATAAAAATATAAG
1 ATATAAAAATATAAG
55760074 TATTTACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
ATATAAAAATATAAG
Found at i:55760071 original size:30 final size:30
Alignment explanation
Indices: 55760008--55760071 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
55759998 ACTATATATG
* *
55760008 TATATACATAAAATTATGAAAATATGAATA
1 TATATACATAAAATTATGAAAATATAAAAA
* *
55760038 TATATATATAAAAATTAT-AAGATATAAAAA
1 TATATACAT-AAAATTATGAAAATATAAAAA
55760068 TATA
1 TATA
55760072 AGTATTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (30 bp):
TATATACATAAAATTATGAAAATATAAAAA
Found at i:55760429 original size:3 final size:3
Alignment explanation
Indices: 55760421--55760465 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
55760411 AAATGAACAT
* * * *
55760421 ATA ATA ATA ATA ACA ATA ACA TTA ATA TTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55760466 TTATTATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55760457 original size:24 final size:24
Alignment explanation
Indices: 55760425--55760474 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
55760415 GAACATATAA
55760425 TAATAATAACAATAACATTAATAT
1 TAATAATAACAATAACATTAATAT
* * *
55760449 TAATAATAATAATAATATTATTAT
1 TAATAATAACAATAACATTAATAT
55760473 TA
1 TA
55760475 TTATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAATAACAATAACATTAATAT
Found at i:55760471 original size:27 final size:27
Alignment explanation
Indices: 55760422--55760488 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
55760412 AATGAACATA
*
55760422 TAATAATAATAACAATAACATTAATAT
1 TAATAATAATAATAATAACATTAATAT
** *
55760449 TAATAATAATAATAATATTATTATTAT
1 TAATAATAATAATAATAACATTAATAT
* *
55760476 TATTAAAAATAAT
1 TAATAATAATAAT
55760489 GAACTGAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATAATAATAATAATAACATTAATAT
Found at i:55760928 original size:2 final size:2
Alignment explanation
Indices: 55760923--55760973 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
55760913 AGAGAGAAGG
55760923 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
55760965 CT CT CT CT C
1 CT CT CT CT C
55760974 GGTTTCTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:55762328 original size:63 final size:63
Alignment explanation
Indices: 55762200--55762318 Score: 202
Period size: 63 Copynumber: 1.9 Consensus size: 63
55762190 AAAAAGGTCA
*
55762200 AGCCATTTAAGATTTCTCACAATTCGATATTAAAAATAGAACAATTCCCGAAAAATCTATAGG
1 AGCCATTCAAGATTTCTCACAATTCGATATTAAAAATAGAACAATTCCCGAAAAATCTATAGG
* * *
55762263 AGCCATTCAAGATTTCTCACAATTTGATATTAAATATGGAACAATTCCCGAAAAAT
1 AGCCATTCAAGATTTCTCACAATTCGATATTAAAAATAGAACAATTCCCGAAAAAT
55762319 TTACTGGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (63 bp):
AGCCATTCAAGATTTCTCACAATTCGATATTAAAAATAGAACAATTCCCGAAAAATCTATAGG
Found at i:55762641 original size:3 final size:3
Alignment explanation
Indices: 55762633--55762670 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
55762623 ACTAGTGGTC
55762633 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55762671 TATTATTATT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55762677 original size:3 final size:3
Alignment explanation
Indices: 55762671--55762704 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55762661 AATAATAATA
55762671 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55762705 GTCGCCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55764021 original size:21 final size:22
Alignment explanation
Indices: 55763981--55764027 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
55763971 GATATAAGGG
55763981 TTTAGGGTTTAAGGTATTAG-A
1 TTTAGGGTTTAAGGTATTAGCA
*
55764002 TTTAGGGTTT-AGAGTTTTAGCA
1 TTTAGGGTTTAAG-GTATTAGCA
55764024 TTTA
1 TTTA
55764028 TTTATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.47
Consensus pattern (22 bp):
TTTAGGGTTTAAGGTATTAGCA
Found at i:55765808 original size:14 final size:14
Alignment explanation
Indices: 55765789--55765818 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55765779 ACATGTACAA
55765789 ACATGGGCTGGGAC
1 ACATGGGCTGGGAC
55765803 ACATGGGCTGGGAC
1 ACATGGGCTGGGAC
55765817 AC
1 AC
55765819 CGCCGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.40, T:0.13
Consensus pattern (14 bp):
ACATGGGCTGGGAC
Found at i:55768387 original size:13 final size:13
Alignment explanation
Indices: 55768361--55768408 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
55768351 CCCTTAAAAT
55768361 TTTAAAAATATATA
1 TTTAAAAAT-TATA
55768375 TTTAAAAATTATA
1 TTTAAAAATTATA
* *
55768388 TATATAAATTA-A
1 TTTAAAAATTATA
55768400 TGTTAAAAA
1 T-TTAAAAA
55768409 ATACGCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 2 0.07
13 18 0.62
14 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TTTAAAAATTATA
Found at i:55770848 original size:13 final size:14
Alignment explanation
Indices: 55770828--55770867 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
55770818 TATGCAATTT
55770828 ATATATAAAAAATA
1 ATATATAAAAAATA
*
55770842 A-ATATAAAAATTA
1 ATATATAAAAAATA
55770855 ATATATTAAAAAA
1 ATATA-TAAAAAA
55770868 GTTAATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 12 0.55
14 4 0.18
15 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATATAAAAAATA
Found at i:55772958 original size:9 final size:9
Alignment explanation
Indices: 55772946--55772971 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55772936 AAAATATATT
55772946 AAATGTAAA
1 AAATGTAAA
55772955 AAATGTAAA
1 AAATGTAAA
55772964 AAATGTAA
1 AAATGTAA
55772972 TTTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (9 bp):
AAATGTAAA
Found at i:55775834 original size:13 final size:13
Alignment explanation
Indices: 55775812--55775849 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
55775802 GTGATATTTA
55775812 TTTT-TTTTCTTT
1 TTTTCTTTTCTTT
55775824 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
*
55775837 TATTCTTCTTCTT
1 TTTTCTT-TTCTT
55775850 CCCCTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 4 0.17
13 14 0.61
14 5 0.22
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Done.