Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 163 of 322
Found at i:53507954 original size:17 final size:18
Alignment explanation
Indices: 53507917--53507961 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
53507907 AATCATATCT
*
53507917 TCTAAGATTGCATATCATA
1 TCTAAGATTG-ATACCATA
53507936 TCTAAGATTG-TACCATA
1 TCTAAGATTGATACCATA
53507953 TCTAAGATT
1 TCTAAGATT
53507962 TTATATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 15 0.60
19 10 0.40
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGATACCATA
Found at i:53508439 original size:44 final size:45
Alignment explanation
Indices: 53508335--53508520 Score: 221
Period size: 45 Copynumber: 4.2 Consensus size: 45
53508325 ACTATCTTTG
* * * *
53508335 ATCTGCTCCCCGTCTAATACAAAGACGTCAAATCTATTATCTTCG
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCA
* *
53508380 ATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGCT-TCTTCA
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCA
* *
53508424 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCA
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCA
* * * ** * **
53508469 ATTTGCTCCTCGTCTAATACAGAAATACCAAATCTGTCATCTTGG
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCA
53508514 ATCTGCT
1 ATCTGCT
53508521 TCGATGTAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
44 40 0.33
45 81 0.67
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (45 bp):
ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCA
Found at i:53508500 original size:89 final size:89
Alignment explanation
Indices: 53508335--53508504 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 89
53508325 ACTATCTTTG
* * *
53508335 ATCTGCTCCCCGTCTAATACAAAGACGTCAAATCTATTATCTTCGATCTGCTCCCTGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCAATCTGCTCCCTGTCTAATAC
* *
53508400 AGAGACGCCAAATCTGCTTCTTCA
66 AGAAACACCAAATCTGCTTCTTCA
* * * *
53508424 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCAATTTGCT-CCTCGTCTAATA
1 ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCAATCTGCTCCCT-GTCTAATA
*
53508488 CAGAAATACCAAATCTG
65 CAGAAACACCAAATCTG
53508505 TCATCTTGGA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
88 3 0.04
89 67 0.96
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.30
Consensus pattern (89 bp):
ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCAATCTGCTCCCTGTCTAATAC
AGAAACACCAAATCTGCTTCTTCA
Found at i:53508663 original size:78 final size:78
Alignment explanation
Indices: 53508534--53508750 Score: 292
Period size: 78 Copynumber: 2.8 Consensus size: 78
53508524 ATGTAAACAC
* * * **
53508534 ATGAAGGTCAGATCTGTGATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGTGAAATCATCT
1 ATGAAGGTCAGATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
53508599 TGGATCTACTTCA
66 TGGATCTACTTCA
*
53508612 ATGAAGGTCTA-ATCTGTTATGTCTTCAATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTC-AGATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
* *
53508676 TTTGATCTGCTTCA
65 TTGGATCTACTTCA
* * * * **
53508690 ATGAAGGTCAGATCTGCTATGTCTTCAATCTGTTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
53508751 TGTTTCTTCG
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
77 1 0.01
78 120 0.98
79 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTACTTCA
Found at i:53508870 original size:121 final size:121
Alignment explanation
Indices: 53508656--53508931 Score: 534
Period size: 121 Copynumber: 2.3 Consensus size: 121
53508646 CCCTGTCTAA
53508656 TACAGAGATGCCAAATCATCTTTGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCAATCT
1 TACAGAGATGCCAAATCATCTTTGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCAATCT
53508721 GTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAG
66 GTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAG
53508777 TACAGAGATGCCAAATCATCTTTGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCAATCT
1 TACAGAGATGCCAAATCATCTTTGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCAATCT
53508842 GTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAG
66 GTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAG
* *
53508898 TACAGAGATGCCAAATAATCTTAGATCTGCTTCA
1 TACAGAGATGCCAAATCATCTTTGATCTGCTTCA
53508932 GTGTAAACAC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 153 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (121 bp):
TACAGAGATGCCAAATCATCTTTGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCAATCT
GTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAG
Found at i:53509000 original size:88 final size:90
Alignment explanation
Indices: 53508898--53509091 Score: 268
Period size: 90 Copynumber: 2.2 Consensus size: 90
53508888 TCTCTGACAG
* * *
53508898 TACAGAGATGCCAAATAATCTTAGATCTGCTTC-A-GTGTAAACA-CGTGAAGGTTAGATCTGCT
1 TACAGAGATGCCAAATAATCTTAGATCTACTTCGATGTGAAAACATC-CGAAGGTTAGATCTGCT
*
53508960 ATGTCTTCGATCTACTCCCCGTCTAA
65 ATGTCTTCGATCTACTCCCCGTCGAA
* *
53508986 TACAGAGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTGCTA
1 TACAGAGATGCCAAATAATCTTAGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTGCTA
* *
53509051 TGTCTTCGATCTGCTCTCCGTCGAA
66 TGTCTTCGATCTACTCCCCGTCGAA
**
53509076 TATGGAGATGCCAAAT
1 TACAGAGATGCCAAAT
53509092 CTGTTTCTTC
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 30 0.32
89 1 0.01
90 61 0.66
91 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (90 bp):
TACAGAGATGCCAAATAATCTTAGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTGCTA
TGTCTTCGATCTACTCCCCGTCGAA
Found at i:53509104 original size:221 final size:220
Alignment explanation
Indices: 53508813--53509403 Score: 923
Period size: 220 Copynumber: 2.7 Consensus size: 220
53508803 CTGCTTCAAT
* * *
53508813 GAAGGTCAGATCTGCTATGTCTTCAATCTGTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* *
53508878 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATAATCTTAGATCTGCTTCAGTGTAAACACG
66 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* * *
53508943 TGAAGGTTAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTT
131 TGAAGGTCAAATCTGCTATGTCTTCGATCTACTCCCCGTC-AACACAGAGATGCCAAATCATCTT
53509008 GGATCTACTTCGATGTGAA-AACATCC
195 GGATCTACTTCGATGTGAAGAA-ATCC
53509034 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
53509099 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
66 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* * * *** ** *
53509164 TGAAGGTCAAATCTGTTGTGTCTTCGATCTGCTCTTTGTCAACGTAGGGATGCCAAATCATCTTG
131 TGAAGGTCAAATCTGCTATGTCTTCGATCTACTCCCCGTCAACACAGAGATGCCAAATCATCTTG
53509229 GATCTACTTCGATGTGAAGAAATCC
196 GATCTACTTCGATGTGAAGAAATCC
* * *
53509254 GAAGGTTAGATCTGTTATGTCTTCGATCTGCTTTCTGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* ** * * *
53509319 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTGGATCCGCTTCAGCGTAAACACC
66 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
53509384 TGAAGGTCAAATCTGCTATG
131 TGAAGGTCAAATCTGCTATG
53509404 CTTTAGCCTG
Statistics
Matches: 341, Mismatches: 28, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
220 182 0.53
221 159 0.47
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (220 bp):
GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
TGAAGGTCAAATCTGCTATGTCTTCGATCTACTCCCCGTCAACACAGAGATGCCAAATCATCTTG
GATCTACTTCGATGTGAAGAAATCC
Found at i:53518568 original size:39 final size:39
Alignment explanation
Indices: 53518524--53518682 Score: 282
Period size: 39 Copynumber: 4.1 Consensus size: 39
53518514 ATTATATTAT
* *
53518524 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
53518563 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
53518602 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
53518641 CAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
53518680 CAG
1 CAG
53518683 TGTCTTGCTT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 115 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:53521478 original size:10 final size:10
Alignment explanation
Indices: 53521463--53521493 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
53521453 TTAAATGCCA
53521463 AATGACATGC
1 AATGACATGC
53521473 AATGACATGC
1 AATGACATGC
53521483 AATGACA-GC
1 AATGACATGC
53521492 AA
1 AA
53521494 GTACTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (10 bp):
AATGACATGC
Found at i:53522931 original size:22 final size:21
Alignment explanation
Indices: 53522896--53522978 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 21
53522886 AAAAGGTATC
* *
53522896 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
53522917 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
53522940 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
53522959 TGC-AATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
53522977 TA
1 TA
53522979 TATCATATCT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
18 15 0.28
19 11 0.20
21 3 0.06
22 15 0.28
23 10 0.19
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:53522939 original size:23 final size:22
Alignment explanation
Indices: 53522896--53522953 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
53522886 AAAAGGTATC
* *
53522896 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
53522917 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
53522940 TGCATATCATATCT
1 TACAAATCATATCT
53522954 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:53522986 original size:35 final size:35
Alignment explanation
Indices: 53522925--53523015 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 35
53522915 ATTACAAAAT
53522925 CATATC-TTCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATTCTAAGATT--ATATCATATCTAAGATTG
53522961 CA-ATCATATCTAAGATTATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTATATCATATCTAAGATTG
*
53522996 CATATCATT-AAAGATTATAT
1 CATATCATTCTAAGATTATAT
53523016 TTCCATATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
34 10 0.20
35 24 0.47
36 8 0.16
37 9 0.18
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (35 bp):
CATATCATTCTAAGATTATATCATATCTAAGATTG
Found at i:53523011 original size:17 final size:19
Alignment explanation
Indices: 53522932--53523003 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
53522922 AATCATATCT
53522932 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53522951 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
53522969 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
53522986 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
53523004 TAAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.02
17 15 0.30
18 15 0.30
19 19 0.38
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53525021 original size:13 final size:14
Alignment explanation
Indices: 53524998--53525026 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53524988 TTGAGGGCAT
53524998 TTTTATATAAAATA
1 TTTTATATAAAATA
53525012 TTTT-TATAAAATA
1 TTTTATATAAAATA
53525025 TT
1 TT
53525027 ACTATGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTATATAAAATA
Found at i:53528571 original size:21 final size:21
Alignment explanation
Indices: 53528409--53528626 Score: 114
Period size: 21 Copynumber: 10.3 Consensus size: 21
53528399 ATGTTTTACT
* *
53528409 TTCTGTTTAGCTCTTTTCAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
53528430 TTCTATTTAACTCATATGAG-
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53528450 TTTTCATTCAGCTCTTTTGAGC
1 TTCT-GTTTAGCTCTTATGAGC
* * * * * *
53528472 TTTTGTTCAACTTTTATAAGT
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53528493 TTCCGTTCAGCTCTTTTAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
53528514 TTTTGTTCAACTTTTATGAGT
1 TTCTGTTTAGCTCTTATGAGC
* * *
53528535 TTCTATTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53528556 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* *
53528577 TTCCGTTTAGCTCTTATGATC
1 TTCTGTTTAGCTCTTATGAGC
53528598 TTCTAGTTTAGCTCTTATGAGC
1 TTCT-GTTTAGCTCTTATGAGC
53528620 TTCTGTT
1 TTCTGTT
53528627 CAGCCTCTGG
Statistics
Matches: 144, Mismatches: 50, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
20 3 0.02
21 117 0.81
22 24 0.17
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:53528573 original size:42 final size:42
Alignment explanation
Indices: 53528408--53528630 Score: 187
Period size: 42 Copynumber: 5.3 Consensus size: 42
53528398 CATGTTTTAC
* * * * *
53528408 TTTCTGTTTAGCTCTTTTCAGCTTCTATTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * * * *
53528450 TTT-TCATTCAGCTCTTTTGAGCTTTTGTTCAACTTTTATAAG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * * * *
53528492 TTTCCGTTCAGCTCTTTTAAGCTTTTGTTCAACTTTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * *
53528534 TTTCTATTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * *
53528576 TTTCCGTTTAGCTCTTATGATCTTCTAGTTTAGCTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCT-GTTTAACTCTTATGAG
*
53528619 CTTCTGTTCAGC
1 TTTCTGTTCAGC
53528631 CTCTGGGCTT
Statistics
Matches: 144, Mismatches: 34, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
41 1 0.01
42 121 0.84
43 22 0.15
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.48
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
Found at i:53528579 original size:84 final size:84
Alignment explanation
Indices: 53528408--53528591 Score: 208
Period size: 84 Copynumber: 2.2 Consensus size: 84
53528398 CATGTTTTAC
* * * **
53528408 TTTCTGTTTAGCTCTTTTCAGCTTCTATTTAACTCATATGAGTTTTCATTCAGCTCTTTTGAGCT
1 TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTCATTCAGCTCTTACGAGCT
* **
53528473 TTTGTTCAACTTTTATAAG
66 TCTGTTCAACCCTTATAAG
* * * **
53528492 TTTCCGTTCAGCTCTTTTAAGCTTTTGTTCAACTTTTATGAG-TTTCTATTCAGCTCTTACGAGC
1 TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTC-ATTCAGCTCTTACGAGC
* **
53528556 TTCTGTTTAACCCTTATGGG
65 TTCTGTTCAACCCTTATAAG
53528576 TTTCCGTTTAGCTCTT
1 TTTCCGTTTAGCTCTT
53528592 ATGATCTTCT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
83 4 0.05
84 78 0.95
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (84 bp):
TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTCATTCAGCTCTTACGAGCT
TCTGTTCAACCCTTATAAG
Found at i:53529778 original size:45 final size:45
Alignment explanation
Indices: 53529673--53529783 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 45
53529663 AATGGTAATA
* * * ** * *
53529673 GTAATAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
*
53529718 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTATTGAATCG
1 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
*
53529763 GTAACAGTAATGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
53529784 ATAGTAATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
Found at i:53532609 original size:21 final size:21
Alignment explanation
Indices: 53532447--53532664 Score: 114
Period size: 21 Copynumber: 10.3 Consensus size: 21
53532437 ATGTTTTACT
* *
53532447 TTCTGTTTAGCTCTTTTCAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
53532468 TTCTATTTAACTCATATGAG-
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53532488 TTTTCATTCAGCTCTTTTGAGC
1 TTCT-GTTTAGCTCTTATGAGC
* * * * * *
53532510 TTTTGTTCAACTTTTATAAGT
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53532531 TTCCGTTCAGCTCTTTTAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
53532552 TTTTGTTCAACTTTTATGAGT
1 TTCTGTTTAGCTCTTATGAGC
* * *
53532573 TTCTATTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
53532594 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* *
53532615 TTCCGTTTAGCTCTTATGATC
1 TTCTGTTTAGCTCTTATGAGC
53532636 TTCTAGTTTAGCTCTTATGAGC
1 TTCT-GTTTAGCTCTTATGAGC
53532658 TTCTGTT
1 TTCTGTT
53532665 CAGCCTCTGG
Statistics
Matches: 144, Mismatches: 50, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
20 3 0.02
21 117 0.81
22 24 0.17
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:53532611 original size:42 final size:42
Alignment explanation
Indices: 53532446--53532668 Score: 187
Period size: 42 Copynumber: 5.3 Consensus size: 42
53532436 CATGTTTTAC
* * * * *
53532446 TTTCTGTTTAGCTCTTTTCAGCTTCTATTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * * * *
53532488 TTT-TCATTCAGCTCTTTTGAGCTTTTGTTCAACTTTTATAAG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * * * *
53532530 TTTCCGTTCAGCTCTTTTAAGCTTTTGTTCAACTTTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * *
53532572 TTTCTATTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * *
53532614 TTTCCGTTTAGCTCTTATGATCTTCTAGTTTAGCTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCT-GTTTAACTCTTATGAG
*
53532657 CTTCTGTTCAGC
1 TTTCTGTTCAGC
53532669 CTCTGGGCTT
Statistics
Matches: 144, Mismatches: 34, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
41 1 0.01
42 121 0.84
43 22 0.15
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.48
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
Found at i:53532617 original size:84 final size:84
Alignment explanation
Indices: 53532446--53532629 Score: 208
Period size: 84 Copynumber: 2.2 Consensus size: 84
53532436 CATGTTTTAC
* * * **
53532446 TTTCTGTTTAGCTCTTTTCAGCTTCTATTTAACTCATATGAGTTTTCATTCAGCTCTTTTGAGCT
1 TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTCATTCAGCTCTTACGAGCT
* **
53532511 TTTGTTCAACTTTTATAAG
66 TCTGTTCAACCCTTATAAG
* * * **
53532530 TTTCCGTTCAGCTCTTTTAAGCTTTTGTTCAACTTTTATGAG-TTTCTATTCAGCTCTTACGAGC
1 TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTC-ATTCAGCTCTTACGAGC
* **
53532594 TTCTGTTTAACCCTTATGGG
65 TTCTGTTCAACCCTTATAAG
53532614 TTTCCGTTTAGCTCTT
1 TTTCCGTTTAGCTCTT
53532630 ATGATCTTCT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
83 4 0.05
84 78 0.95
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (84 bp):
TTTCCGTTTAGCTCTTTTAAGCTTCTATTCAACTCATATGAGTTTTCATTCAGCTCTTACGAGCT
TCTGTTCAACCCTTATAAG
Found at i:53533816 original size:45 final size:45
Alignment explanation
Indices: 53533711--53533821 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 45
53533701 AATGGTAATA
* * * ** * *
53533711 GTAATAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
*
53533756 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTATTGAATCG
1 GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
*
53533801 GTAACAGTAATGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
53533822 ATAGTAATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTTGACACACAAAGTACTGAATCG
Found at i:53538055 original size:25 final size:25
Alignment explanation
Indices: 53538027--53538092 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
53538017 ATTAATTGGG
*
53538027 AAGCTCATGAGAGCCAAATATCAGA
1 AAGCTCGTGAGAGCCAAATATCAGA
* *
53538052 AAGCTCGTGAGAGCCAAATATCTGG
1 AAGCTCGTGAGAGCCAAATATCAGA
53538077 AAGCTCGTGAGAGCCA
1 AAGCTCGTGAGAGCCA
53538093 TATAACGGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (25 bp):
AAGCTCGTGAGAGCCAAATATCAGA
Found at i:53538107 original size:25 final size:25
Alignment explanation
Indices: 53537945--53538132 Score: 103
Period size: 25 Copynumber: 7.6 Consensus size: 25
53537935 TGTAAGCTGT
* *
53537945 ATAACGGGAAGCTCTTGCGAGCCAA
1 ATAACGGGAAGCTCGTGAGAGCCAA
* * * * *
53537970 TTATCGGGAAGCTCAT-ACGAGACAT
1 ATAACGGGAAGCTCGTGA-GAGCCAA
* ** *
53537995 A-AACAGGAAGCTCAAGAAAGCC-A
1 ATAACGGGAAGCTCGTGAGAGCCAA
* * *
53538018 TTAATTGGGAAGCTCATGAGAGCCAA
1 ATAA-CGGGAAGCTCGTGAGAGCCAA
* * *
53538044 ATATCAGAAAGCTCGTGAGAGCCAA
1 ATAACGGGAAGCTCGTGAGAGCCAA
* * *
53538069 ATATCTGGAAGCTCGTGAGAGCCAT
1 ATAACGGGAAGCTCGTGAGAGCCAA
* * * *
53538094 ATAACGGGATGCTCATAAGAGCTAA
1 ATAACGGGAAGCTCGTGAGAGCCAA
* *
53538119 ATAATGGGACGCTC
1 ATAACGGGAAGCTC
53538133 TTGCGAGCTG
Statistics
Matches: 122, Mismatches: 36, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
24 16 0.13
25 103 0.84
26 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
ATAACGGGAAGCTCGTGAGAGCCAA
Found at i:53539900 original size:24 final size:25
Alignment explanation
Indices: 53539867--53539936 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
53539857 AGCTCTGAAT
* *
53539867 CGGTATGCTCTTATGAGCT--ATAAA
1 CGGTAAGCTCTTACGAGCTGAAT-AA
* *
53539891 CGGTAAGCTCATACGAGCTGAATAC
1 CGGTAAGCTCTTACGAGCTGAATAA
53539916 CGGTAAGCTCTCT-CGAGCTGA
1 CGGTAAGCTCT-TACGAGCTGA
53539937 GAATCGGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 16 0.42
25 19 0.50
26 3 0.08
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
CGGTAAGCTCTTACGAGCTGAATAA
Found at i:53540788 original size:21 final size:21
Alignment explanation
Indices: 53540764--53540805 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53540754 GAAATTAAAG
53540764 TGTTTTAATTT-CACTTTAATT
1 TGTTTTAATTTCCA-TTTAATT
53540785 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
53540806 ACAAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:53543041 original size:55 final size:56
Alignment explanation
Indices: 53542954--53543353 Score: 452
Period size: 56 Copynumber: 7.1 Consensus size: 56
53542944 ATAGACTAGT
* *
53542954 AAAAAAATT-AAATTTTTTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAGGTACG-
1 AAAAAAATTCAAA-TTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
* * * * *
53543009 AAAAAAATTCAATTTTTTTTAGGTGCTAGCCTTTTAATGACAGGCACCAGGTACGA
1 AAAAAAATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
* * * * *
53543065 AAAAAAATTCAAATTTTTTTAAGTGTTGGCCTTCTAATGGCCGACACAAGGTATGA
1 AAAAAAATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
* * *
53543121 AAAAAAATTCAAATTTTGTTAGGTGCTAGCCTTCTAATGGCCGGCACCAGGTGCGAA
1 AAAAAAATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACG-A
* * * *
53543178 AAAAAATATTCAAATTTTTTTAGGTCCTGGCCTTCTAATGGCCAGCACTAAGTACGA
1 AAAAAA-ATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
* * *
53543235 AAAAATATATTCAAA-TTTTTTAGGTGCTGGCCTTCTAATGGTCGAC-CTCATGTACG-
1 AAAAA-A-ATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCAC-CAGGTACGA
* * * * * *
53543291 AAAAAAATTCAATTTTTTTTAGGTGCTAGCTTTTTAATGGCCGGTACCAGATAC-A
1 AAAAAAATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
53543346 AAAAAAAT
1 AAAAAAAT
53543354 ATTTTTGTGT
Statistics
Matches: 289, Mismatches: 47, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
54 6 0.02
55 84 0.29
56 102 0.35
57 46 0.16
58 51 0.18
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (56 bp):
AAAAAAATTCAAATTTTTTTAGGTGCTGGCCTTCTAATGGCCGGCACCAGGTACGA
Found at i:53546667 original size:49 final size:46
Alignment explanation
Indices: 53546544--53546719 Score: 177
Period size: 47 Copynumber: 3.8 Consensus size: 46
53546534 AAATTACATA
* * *
53546544 GAAAGATAGATAATTTAAATGAAATGAGAAAAAAATTGAA-AT---
1 GAAAGAAAGATAATTTAAATGAAATGAGGAAAAAATTAAATATAAG
* *
53546586 GAACA-AAA-ATAATATAAATGAATTGA-GAAAAAATTTAAATTTATAAG
1 GAA-AGAAAGATAATTTAAATGAAATGAGGAAAAAA-TTAAA--TATAAG
* *
53546633 GAAATAAAGATAAATTTAAATGAAATGAGGAAAAAATTAAATATATG
1 GAAAGAAAGAT-AATTTAAATGAAATGAGGAAAAAATTAAATATAAG
*
53546680 GAAAGATAGATAATTTAAATGAAATGAGGAAAAAAATTAA
1 GAAAGAAAGATAATTTAAATGAAATGAGG-AAAAAATTAA
53546720 TTTAAATGAA
Statistics
Matches: 111, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
40 6 0.05
41 20 0.18
42 5 0.05
43 1 0.01
44 2 0.02
46 19 0.17
47 30 0.27
48 2 0.02
49 19 0.17
50 7 0.06
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.25
Consensus pattern (46 bp):
GAAAGAAAGATAATTTAAATGAAATGAGGAAAAAATTAAATATAAG
Found at i:53546722 original size:27 final size:27
Alignment explanation
Indices: 53546690--53546802 Score: 116
Period size: 27 Copynumber: 4.4 Consensus size: 27
53546680 GAAAGATAGA
53546690 TAATTTAAATGAAATGAGGAAAAAAAT
1 TAATTTAAATGAAATGAGGAAAAAAAT
53546717 TAATTTAAATGAAATGA-GAAGAAAAAT
1 TAATTTAAATGAAATGAGGAA-AAAAAT
* * *
53546744 TAAATT---TG-CAT--GGAAAGATAGA-
1 TAATTTAAATGAAATGAGGAAA-A-AAAT
53546766 TAATTTAAATGAAATGAGGAAAAAAAT
1 TAATTTAAATGAAATGAGGAAAAAAAT
53546793 TAATTTAAAT
1 TAATTTAAAT
53546803 AAAAATATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
21 1 0.01
22 9 0.13
23 4 0.06
24 2 0.03
25 2 0.03
26 7 0.10
27 39 0.57
28 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.15, T:0.28
Consensus pattern (27 bp):
TAATTTAAATGAAATGAGGAAAAAAAT
Found at i:53546722 original size:95 final size:91
Alignment explanation
Indices: 53546551--53546748 Score: 210
Period size: 95 Copynumber: 2.2 Consensus size: 91
53546541 ATAGAAAGAT
* *
53546551 AGAT-AATTTAAATGAAATGAGAAAAAAATTGAAATGAACAAAAATAATATAAATGAATTGAGAA
1 AGATAAATTTAAATGAAATGAGAAAAAAATTAAAATGAACAAAAATAATATAAATGAAATGAGAA
*
53546615 AAAATTTAAATTTATAAGGAAAT-A-A
66 AAAAATTAAATTTA-AAGGAAATGAGA
* * *
53546640 AGATAAATTTAAATGAAATGAGGAAAAAATTAAATATATGGAA-AGATAGATAATTTAAATGAAA
1 AGATAAATTTAAATGAAATGAGAAAAAAATT-AA-A-AT-GAACA-A-AAATAATATAAATGAAA
*
53546704 TGAGGAAAAAAATT-AATTTAAATGAAATGAGA
60 TGA-GAAAAAAATTAAATTTAAAGGAAATGAGA
*
53546736 AGA-AAAATTAAAT
1 AGATAAATTTAAAT
53546749 TTGCATGGAA
Statistics
Matches: 91, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
89 4 0.04
90 25 0.27
91 1 0.01
92 1 0.01
93 3 0.03
94 11 0.12
95 33 0.36
96 13 0.14
ACGTcount: A:0.60, C:0.01, G:0.14, T:0.26
Consensus pattern (91 bp):
AGATAAATTTAAATGAAATGAGAAAAAAATTAAAATGAACAAAAATAATATAAATGAAATGAGAA
AAAAATTAAATTTAAAGGAAATGAGA
Found at i:53546772 original size:76 final size:73
Alignment explanation
Indices: 53546631--53546802 Score: 272
Period size: 76 Copynumber: 2.3 Consensus size: 73
53546621 TAAATTTATA
* *
53546631 AGGAAATAAAGATAAATTTAAATGAAATGAGGAAAAAATTAAATATATGGAAAGATAGATAATTT
1 AGGAAA-AAA-ATTAATTTAAATGAAATGAGAAAAAAATTAAATATATGGAAAGATAGATAATTT
53546696 AAATGAAATG
64 AAATGAAATG
*
53546706 AGGAAAAAAATTAATTTAAATGAAATGAGAAGAAAAATTAAATTTGCATGGAAAGATAGATAATT
1 AGGAAAAAAATTAATTTAAATGAAATGAGAA-AAAAATTAAATAT--ATGGAAAGATAGATAATT
53546771 TAAATGAAATG
63 TAAATGAAATG
53546782 AGGAAAAAAATTAATTTAAAT
1 AGGAAAAAAATTAATTTAAAT
53546803 AAAAATATAT
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
73 20 0.22
74 15 0.16
75 6 0.07
76 50 0.55
ACGTcount: A:0.57, C:0.01, G:0.16, T:0.26
Consensus pattern (73 bp):
AGGAAAAAAATTAATTTAAATGAAATGAGAAAAAAATTAAATATATGGAAAGATAGATAATTTAA
ATGAAATG
Found at i:53546821 original size:41 final size:42
Alignment explanation
Indices: 53546765--53546868 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 42
53546755 GGAAAGATAG
*
53546765 ATAATTTAAATGAAATGAGGAAAAAAATTAATTTAAATAAAAAT
1 ATAA-TTAAATGAAATGAGGAAAAAAATTAAATTAAA-AAAAAT
*
53546809 AT-A-TAAATGAAAT-AAGAAAAAAATTAAATTAAAAAAAAT
1 ATAATTAAATGAAATGAGGAAAAAAATTAAATTAAAAAAAAT
53546848 ATAATTTAAATGAAATG-GGAA
1 ATAA-TTAAATGAAATGAGGAA
53546869 TGGAAATGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
39 8 0.15
40 19 0.36
41 10 0.19
42 13 0.25
43 1 0.02
44 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (42 bp):
ATAATTAAATGAAATGAGGAAAAAAATTAAATTAAAAAAAAT
Found at i:53546845 original size:15 final size:16
Alignment explanation
Indices: 53546825--53546857 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53546815 ATGAAATAAG
53546825 AAAAAAAT-TAAATTA
1 AAAAAAATATAAATTA
*
53546840 AAAAAAATATAATTTA
1 AAAAAAATATAAATTA
53546856 AA
1 AA
53546858 TGAAATGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAAATATAAATTA
Found at i:53546870 original size:11 final size:11
Alignment explanation
Indices: 53546855--53546912 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
53546845 AATATAATTT
53546855 AAATGAAATGG
1 AAATGAAATGG
*
53546866 GAATGGAAAT-G
1 AAAT-GAAATGG
53546877 AAATGAAATGG
1 AAATGAAATGG
53546888 AAATGAAATTGG
1 AAATGAAA-TGG
53546900 -AATGAAATGG
1 AAATGAAATGG
53546910 AAA
1 AAA
53546913 AAAAATTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 8 0.20
11 25 0.61
12 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:53546918 original size:22 final size:22
Alignment explanation
Indices: 53546878--53546920 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53546868 ATGGAAATGA
**
53546878 AATGAAATGGAAATGAAATTGG
1 AATGAAATGGAAAAAAAATTGG
53546900 AATGAAATGGAAAAAAAATTG
1 AATGAAATGGAAAAAAAATTG
53546921 ATGTGACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (22 bp):
AATGAAATGGAAAAAAAATTGG
Found at i:53547154 original size:30 final size:30
Alignment explanation
Indices: 53547098--53547178 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
53547088 TTAAATTGAC
*
53547098 AAAAATAAAATAT-AAA-AAAAT-TTAAATG
1 AAAAAT-AAATATGAAACAAAATGCTAAATG
* *
53547126 AAAAA-AATTAATGAAATAAAATGCTAAATG
1 AAAAATAAAT-ATGAAACAAAATGCTAAATG
53547156 AAAAATAAATATGAAACAAAATG
1 AAAAATAAATATGAAACAAAATG
53547179 TAATTTGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 8 0.18
29 5 0.11
30 23 0.52
31 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (30 bp):
AAAAATAAATATGAAACAAAATGCTAAATG
Found at i:53547155 original size:17 final size:14
Alignment explanation
Indices: 53547083--53547160 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 14
53547073 TAACAAATTT
* *
53547083 AAAATTTAAATTGAC
1 AAAAATTAAA-TGAA
* *
53547098 AAAAATAAAATATAA
1 AAAAATTAAAT-GAA
53547113 AAAAATTTAAATGAA
1 AAAAA-TTAAATGAA
53547128 AAAAATT-AATGAA
1 AAAAATTAAATGAA
53547141 ATAAAATGCTAAATGAA
1 A-AAAAT--TAAATGAA
53547158 AAA
1 AAA
53547161 TAAATATGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.14
14 8 0.16
15 21 0.41
16 8 0.16
17 7 0.14
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAAATTAAATGAA
Found at i:53547216 original size:12 final size:12
Alignment explanation
Indices: 53547199--53547233 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
53547189 TGAAAATGAA
53547199 ATTAAATGAAAT
1 ATTAAATGAAAT
53547211 ATTAAATG-AAT
1 ATTAAATGAAAT
*
53547222 ATAAAATGAAAT
1 ATTAAATGAAAT
53547234 GATGATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
ATTAAATGAAAT
Found at i:53547374 original size:11 final size:11
Alignment explanation
Indices: 53547358--53547400 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
53547348 ATAGATAATT
53547358 TAAATGAAATG
1 TAAATGAAATG
53547369 TAAATGTAAATG
1 TAAATG-AAATG
53547381 -AAATGAAAT-
1 TAAATGAAATG
53547390 TAAAATGAAAT
1 T-AAATGAAAT
53547401 TGGAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.14
11 20 0.69
12 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (11 bp):
TAAATGAAATG
Found at i:53547384 original size:5 final size:5
Alignment explanation
Indices: 53547359--53547415 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
53547349 TAGATAATTT
* *
53547359 AAATG AAATG TAAATG TAAATG AAATG AAATTA AAATG AAATTG GAATG
1 AAATG AAATG -AAATG -AAATG AAATG AAA-TG AAATG AAA-TG AAATG
53547408 AAATG AAA
1 AAATG AAA
53547416 AAAAAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 26 0.58
6 19 0.42
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.25
Consensus pattern (5 bp):
AAATG
Found at i:53547387 original size:22 final size:23
Alignment explanation
Indices: 53547354--53547417 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
53547344 AAGGATAGAT
*
53547354 AATTTAAATGAAATGT-AAATGTA
1 AATTGAAATGAAATGTAAAATG-A
53547377 AA-TGAAATGAAAT-TAAAATGA
1 AATTGAAATGAAATGTAAAATGA
* *
53547398 AATTGGAATGAAATGAAAAA
1 AATTGAAATGAAATGTAAAA
53547418 AAAAAAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 4 0.11
22 25 0.71
23 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.27
Consensus pattern (23 bp):
AATTGAAATGAAATGTAAAATGA
Found at i:53549773 original size:31 final size:31
Alignment explanation
Indices: 53549735--53549822 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
53549725 GATCGCAACA
* *
53549735 ATTTTAAATTTTTTCTGTTAATTTTTACTTT
1 ATTTTAAATTTTTTCTGTAAATATTTACTTT
* * *
53549766 ATTTTAAAATTATTCTGTAAATATTTATTTT
1 ATTTTAAATTTTTTCTGTAAATATTTACTTT
*
53549797 ATTGTTAAATTATTTT-TTTAAATATT
1 ATT-TTAAATT-TTTTCTGTAAATATT
53549823 AATTTAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 29 0.62
32 15 0.32
33 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (31 bp):
ATTTTAAATTTTTTCTGTAAATATTTACTTT
Found at i:53559017 original size:26 final size:28
Alignment explanation
Indices: 53558980--53559034 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
53558970 ACAATTGGGT
*
53558980 TAAAAAAGTTATATAAAAATAT-ATTTA
1 TAAAAAAGTTATATAAAAAAATAATTTA
*
53559007 TAAAAAA-TTATGTAAAAAAATAATTTA
1 TAAAAAAGTTATATAAAAAAATAATTTA
53559034 T
1 T
53559035 TGAAATGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (28 bp):
TAAAAAAGTTATATAAAAAAATAATTTA
Found at i:53561526 original size:13 final size:13
Alignment explanation
Indices: 53561503--53561536 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
53561493 AAACATATTA
53561503 TAAACATTTTGTGT
1 TAAA-ATTTTGTGT
53561517 TAAAATTTTGTGT
1 TAAAATTTTGTGT
53561530 TAGAAAT
1 TA-AAAT
53561537 AATAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (13 bp):
TAAAATTTTGTGT
Found at i:53561917 original size:39 final size:40
Alignment explanation
Indices: 53561816--53561917 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
53561806 TATTCGGATG
* * * *
53561816 ATATCAGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTGACT
53561856 ATATCCGGGCTAAGA-CCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAA-ATCCCGAAGGCATTTGTGCGAG-TGACT
53561896 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAATCCCGAAGG
53561918 TACTTGGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 1 0.02
39 14 0.25
40 38 0.69
41 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTGACT
Found at i:53573131 original size:46 final size:46
Alignment explanation
Indices: 53573079--53573341 Score: 339
Period size: 46 Copynumber: 5.7 Consensus size: 46
53573069 GCTCTCTGAT
* *
53573079 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
53573125 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAA
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
53573171 ATGAAATGAATAAGACCATGGTTGAAAGATGCCATGGCAACTTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
53573217 ATGAAATGAGTAAGAAAATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
53573263 GGGAAAATGAATAAAACTATGGTTGAAAGATACCATGGCAACATGAC
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
53573310 A-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATAC
53573342 TATGACATCA
Statistics
Matches: 193, Mismatches: 23, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
46 154 0.80
47 39 0.20
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:53576914 original size:10 final size:9
Alignment explanation
Indices: 53576884--53576932 Score: 62
Period size: 10 Copynumber: 5.1 Consensus size: 9
53576874 ATTTGGGACT
*
53576884 AATTTAAAA
1 AATTTGAAA
53576893 CAATTTGAAA
1 -AATTTGAAA
53576903 AATTTGAGAA
1 AATTTGA-AA
53576913 AATTTTGAAA
1 AA-TTTGAAA
53576923 AATTTGAAA
1 AATTTGAAA
53576932 A
1 A
53576933 TAGGGGTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 15 0.42
10 16 0.44
11 5 0.14
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (9 bp):
AATTTGAAA
Found at i:53578519 original size:46 final size:46
Alignment explanation
Indices: 53578418--53578505 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
53578408 TGTAACCCGC
* * * *
53578418 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
53578464 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
53578506 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:53590029 original size:14 final size:14
Alignment explanation
Indices: 53590012--53590038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53590002 TTATCAAATC
53590012 TTATTATTTTATTA
1 TTATTATTTTATTA
53590026 TTATTATTTTATT
1 TTATTATTTTATT
53590039 CCATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:53590280 original size:39 final size:39
Alignment explanation
Indices: 53590237--53590315 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
53590227 CTATTTTGAG
*
53590237 TTAATAAATTCTATCTGGGTTTTTCTTTTTAAGAATTTC
1 TTAATAAATTCTATCTGGGTTTTTCTTTTTAAAAATTTC
53590276 TTAATAAATTCTATCTGGGTTTTTCTTTTTAAAAATTTC
1 TTAATAAATTCTATCTGGGTTTTTCTTTTTAAAAATTTC
53590315 T
1 T
53590316 CTTAAGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (39 bp):
TTAATAAATTCTATCTGGGTTTTTCTTTTTAAAAATTTC
Found at i:53590556 original size:9 final size:9
Alignment explanation
Indices: 53590529--53590574 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
53590519 ATTATTCTAA
*
53590529 TATTTGATT
1 TATTTTATT
*
53590538 TATTAT-TT
1 TATTTTATT
53590546 TATTTTATT
1 TATTTTATT
*
53590555 TATTTTAAT
1 TATTTTATT
53590564 TATTTTATT
1 TATTTTATT
53590573 TA
1 TA
53590575 ACTTACATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
TATTTTATT
Found at i:53594697 original size:20 final size:20
Alignment explanation
Indices: 53594672--53594714 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
53594662 ATCAATATTC
53594672 TTATCCTGAATTTCAGGATT
1 TTATCCTGAATTTCAGGATT
*
53594692 TTATCCTGAATTTCAGTATT
1 TTATCCTGAATTTCAGGATT
53594712 TTA
1 TTA
53594715 ATTTGGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (20 bp):
TTATCCTGAATTTCAGGATT
Found at i:53600464 original size:18 final size:18
Alignment explanation
Indices: 53600441--53600493 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
53600431 GATAAATCCT
53600441 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
53600459 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
53600477 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
53600494 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:53608159 original size:36 final size:36
Alignment explanation
Indices: 53608108--53608177 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
53608098 GAGATTAGTC
* *
53608108 GATTTCTTGTGAGAAGATAGGAGATTGAGTTTGGCA
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
* *
53608144 GATTACTTGTTAGAAGTTAGGAGATTAAGTTTGG
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGG
53608178 ATTAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (36 bp):
GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
Found at i:53637713 original size:7 final size:7
Alignment explanation
Indices: 53637694--53637724 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
53637684 TTTTTAATTA
53637694 AATAAATT
1 AATAAA-T
53637702 AATAAAT
1 AATAAAT
53637709 AATAAAT
1 AATAAAT
53637716 AATAAAT
1 AATAAAT
53637723 AA
1 AA
53637725 AAGAGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:53640504 original size:18 final size:19
Alignment explanation
Indices: 53640462--53640505 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
53640452 ATGAAATATG
53640462 TATAAATATGCATAATAAAA
1 TATAAA-ATGCATAATAAAA
*
53640482 T-TAAAATGTATAA-AAAA
1 TATAAAATGCATAATAAAA
53640499 TATAAAA
1 TATAAAA
53640506 AAAACTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 4 0.18
20 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
TATAAAATGCATAATAAAA
Found at i:53640875 original size:31 final size:29
Alignment explanation
Indices: 53640840--53640903 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
53640830 CTTCTTTAAT
*
53640840 ATTTTAATGTTTTCTTAATTTTTTAAAAATA
1 ATTTTAATATTTTCTTAA-TTTTTAAAAA-A
* *
53640871 ATTTTTATATTTTTTTAATTTTTAAAAAA
1 ATTTTAATATTTTCTTAATTTTTAAAAAA
53640900 ATTT
1 ATTT
53640904 AAAAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 10 0.33
31 15 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTAATATTTTCTTAATTTTTAAAAAA
Found at i:53640895 original size:30 final size:32
Alignment explanation
Indices: 53640836--53640903 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
53640826 TATACTTCTT
53640836 TAATATTTTAATGTTTTCTTAATTTTTTAAAAA
1 TAAT-TTTTAATGTTTTCTTAATTTTTTAAAAA
53640869 TAATTTTTATAT-TTTT-TTAA-TTTTTAAAAA
1 TAATTTTTA-ATGTTTTCTTAATTTTTTAAAAA
53640899 -AATTT
1 TAATTT
53640904 AAAAAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 5 0.15
30 10 0.29
31 4 0.12
32 9 0.26
33 6 0.18
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (32 bp):
TAATTTTTAATGTTTTCTTAATTTTTTAAAAA
Found at i:53643965 original size:43 final size:43
Alignment explanation
Indices: 53643890--53644137 Score: 363
Period size: 43 Copynumber: 5.8 Consensus size: 43
53643880 ACGTCGCTAA
* * **
53643890 CTTTAGCAGCGC-TTTCCCACAAACGCCACTAAAGGTCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
*
53643932 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
*
53643975 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* * * * *
53644018 ATTTAGCGACGCTTTTCCGAGAAACGCCGCTAAAGACCCTGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* *
53644061 CTTTAGCGACGCTTTTCCCAAAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
*
53644104 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
53644138 ACATGGCTTT
Statistics
Matches: 186, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
42 11 0.06
43 175 0.94
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
Found at i:53646629 original size:62 final size:62
Alignment explanation
Indices: 53646532--53646656 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
53646522 CATATCATTC
53646532 AATGCACAAATATCATTTATATCAATTGAATCATCCATTTTGAATCACAAACTTACATATAT
1 AATGCACAAATATCATTTATATCAATTGAATCATCCATTTTGAATCACAAACTTACATATAT
53646594 AATGCACAAATATCATTTATATCAATTGAATCATCCATTTTGAATCACAAACTTACATATAT
1 AATGCACAAATATCATTTATATCAATTGAATCATCCATTTTGAATCACAAACTTACATATAT
53646656 A
1 A
53646657 GCGTTTAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (62 bp):
AATGCACAAATATCATTTATATCAATTGAATCATCCATTTTGAATCACAAACTTACATATAT
Found at i:53652262 original size:40 final size:40
Alignment explanation
Indices: 53652218--53652365 Score: 163
Period size: 40 Copynumber: 3.7 Consensus size: 40
53652208 ACTCGATATC
* *
53652218 TCACACACTAATTGCCGTAAATAGCCGAAGCTATCTC-AA
1 TCACACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
* * *
53652257 GTCACACACTAAGTGTCATATATAGCCGAAGCTATGTCGAA
1 -TCACACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
* * * * *
53652298 TCGCACACTAAGTGCCATACATAGCCGAAGCTATATTGTA
1 TCACACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
* * *
53652338 TCGCACACTAAGTGCCACAAATAACCGA
1 TCACACACTAAGTGCCATAAATAGCCGA
53652366 TTTATCGTCG
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 91 0.98
41 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
TCACACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
Found at i:53655018 original size:77 final size:77
Alignment explanation
Indices: 53654857--53655023 Score: 176
Period size: 77 Copynumber: 2.2 Consensus size: 77
53654847 CAAATTCATG
* * *
53654857 ACACTTTGGGAATTGGGACTATTTTATTCTGCCACCTCGGTTTGCCTGACAACAATGGCTTTTAA
1 ACACTCTGGGAATCGAGACTATTTTATTCTGCCACCTCGGTTTGCCTGACAACAATGGCTTTTAA
* *
53654922 TATCTGCCCACG
66 TATCTACCCACA
* ** * **
53654934 ACCCTCTGGGAATCGAGACTATTTTATTCTGTTACCTTGAG-TTG-CTCGACAATGATGGCTTTT
1 ACACTCTGGGAATCGAGACTATTTTATTCTGCCACCTCG-GTTTGCCT-GACAACAATGGCTTTT
* * *
53654997 AGTATCTATCTACA
64 AATATCTACCCACA
53655011 ACACTCTGGGAAT
1 ACACTCTGGGAAT
53655024 TGAGGCTGCG
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
76 2 0.03
77 70 0.96
78 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (77 bp):
ACACTCTGGGAATCGAGACTATTTTATTCTGCCACCTCGGTTTGCCTGACAACAATGGCTTTTAA
TATCTACCCACA
Found at i:53655523 original size:12 final size:12
Alignment explanation
Indices: 53655508--53655534 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53655498 TAATAATTAA
53655508 CAAAGGTATAGT
1 CAAAGGTATAGT
53655520 CAAAGGTATAGT
1 CAAAGGTATAGT
53655532 CAA
1 CAA
53655535 CAACCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (12 bp):
CAAAGGTATAGT
Found at i:53660493 original size:27 final size:27
Alignment explanation
Indices: 53660357--53660509 Score: 128
Period size: 28 Copynumber: 5.4 Consensus size: 27
53660347 GTTTTACAAA
*
53660357 TTTACAATTTTGCTCCTATTTTTTTTAGAAT
1 TTTACAATTTT-CCCCTA--TTTTTTAG-AT
* *
53660388 TTTACAATTTTCCCCTTACTTTTCAGAT
1 TTTACAATTTTCCCC-TATTTTTTAGAT
* * * * * *
53660416 TTTATAGTTTTGCACTTATTCTTCAGAT
1 TTTACAATTTT-CCCCTATTTTTTAGAT
53660444 TTTACAATTTTTCCCAC-ATTTTTTAGAT
1 TTTACAA-TTTTCCC-CTATTTTTTAGAT
*
53660472 TTTACAATTATCCCCTATTTTTTAGAT
1 TTTACAATTTTCCCCTATTTTTTAGAT
*
53660499 TTTACAGTTTT
1 TTTACAATTTT
53660510 GTCCCCTACT
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
27 26 0.26
28 44 0.44
29 12 0.12
30 3 0.03
31 13 0.13
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (27 bp):
TTTACAATTTTCCCCTATTTTTTAGAT
Found at i:53660834 original size:34 final size:34
Alignment explanation
Indices: 53660796--53660869 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
53660786 AAATACATGT
* *
53660796 TAAGCAAGTTTATTACTACTAT-TATAATTTGTTA
1 TAAGCAAGATAATTACTACTATATAT-ATTTGTTA
*
53660830 TAAGCATGATAATTACTACTATATATATTTGTTA
1 TAAGCAAGATAATTACTACTATATATATTTGTTA
53660864 TAAGCA
1 TAAGCA
53660870 TGTTATTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 33 0.92
35 3 0.08
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (34 bp):
TAAGCAAGATAATTACTACTATATATATTTGTTA
Found at i:53660870 original size:34 final size:34
Alignment explanation
Indices: 53660807--53660871 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
53660797 AAGCAAGTTT
53660807 ATTACTACTATTATAATTTGTTATAAGCATGATA
1 ATTACTACTATTATAATTTGTTATAAGCATGATA
53660841 ATTACTACTA-TATATATTTGTTATAAGCATG
1 ATTACTACTATTATA-ATTTGTTATAAGCATG
53660872 TTATTGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 4 0.13
34 26 0.87
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (34 bp):
ATTACTACTATTATAATTTGTTATAAGCATGATA
Found at i:53663488 original size:46 final size:46
Alignment explanation
Indices: 53663432--53663607 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53663422 TGGTTGAGCA
53663432 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53663478 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53663523 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53663571 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53663608 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53663588 original size:93 final size:93
Alignment explanation
Indices: 53663429--53663600 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53663419 GGATGGTTGA
* *
53663429 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53663494 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53663522 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53663587 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53663601 CTTATGGGCG
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:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53666038 original size:22 final size:23
Alignment explanation
Indices: 53665990--53666040 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
53665980 ATTCAATTTA
53665990 TTTTA-TTATATTATATATAAAT
1 TTTTATTTATATTATATATAAAT
* * *
53666012 ATTTATTTAT-TTATATTTATAT
1 TTTTATTTATATTATATATAAAT
53666034 TTTTATT
1 TTTTATT
53666041 CGCTAACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTATATTATATATAAAT
Found at i:53674978 original size:17 final size:18
Alignment explanation
Indices: 53674946--53674991 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
53674936 TATATTCACC
53674946 TTTTATG-AAATATTAT-
1 TTTTATGAAAATATTATA
*
53674962 TTTTATGAAAATTTTATCA
1 TTTTATGAAAATATTAT-A
53674981 TTTTAT-AAAAT
1 TTTTATGAAAAT
53674992 CAATGTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 5 0.19
19 6 0.23
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTTATGAAAATATTATA
Found at i:53676122 original size:38 final size:36
Alignment explanation
Indices: 53676045--53676128 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 36
53676035 GTAATATTGT
**
53676045 TGCTGGTATATTGTTGGTTATGTTGGTATACATGGC
1 TGCTGGTATATTGTTGGTTACATTGGTATACATGGC
* *
53676081 TGCTGGTATATTGTTGTTTAACATATGTTATACATGGC
1 TGCTGGTATATTGTTGGTT-ACAT-TGGTATACATGGC
53676119 TGCTGGTATA
1 TGCTGGTATA
53676129 CATGGCTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 18 0.43
37 2 0.05
38 22 0.52
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.44
Consensus pattern (36 bp):
TGCTGGTATATTGTTGGTTACATTGGTATACATGGC
Found at i:53676362 original size:23 final size:24
Alignment explanation
Indices: 53676315--53676362 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
53676305 AGATGAAAAA
*
53676315 ACACATATGTATTTCTCAATTCTC
1 ACACATATGTATTTCTCAATACTC
* *
53676339 ACACATTTGT-TTTTTCAATACTC
1 ACACATATGTATTTCTCAATACTC
53676362 A
1 A
53676363 TATGTTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (24 bp):
ACACATATGTATTTCTCAATACTC
Found at i:53677573 original size:25 final size:27
Alignment explanation
Indices: 53677518--53677576 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
53677508 CACACCCCCC
* *
53677518 TAAAAAACAATCACTATATGCATATTA
1 TAAAAAATAATCACTACATGCATATTA
*
53677545 TAAAAAATACTCACTACATGCATATTA
1 TAAAAAATAATCACTACATGCATATTA
53677572 -AAAAA
1 TAAAAA
53677577 TAGTCAACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.27
Consensus pattern (27 bp):
TAAAAAATAATCACTACATGCATATTA
Found at i:53677667 original size:22 final size:22
Alignment explanation
Indices: 53677642--53677688 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
53677632 CATGTGACCA
*
53677642 GCAACATAAAGTCAGAATAAAG
1 GCAACATAAAGTCAAAATAAAG
*
53677664 GCAACATGAAGTCAAAATAAAG
1 GCAACATAAAGTCAAAATAAAG
53677686 GCA
1 GCA
53677689 TTAGAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.15, G:0.19, T:0.13
Consensus pattern (22 bp):
GCAACATAAAGTCAAAATAAAG
Found at i:53679314 original size:15 final size:15
Alignment explanation
Indices: 53679302--53679331 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53679292 TTTTCAGATG
53679302 CATCACTACCAGACA
1 CATCACTACCAGACA
53679317 CATCACTACCAGACA
1 CATCACTACCAGACA
53679332 TGTCTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
CATCACTACCAGACA
Found at i:53679714 original size:89 final size:89
Alignment explanation
Indices: 53679604--53679783 Score: 297
Period size: 89 Copynumber: 2.0 Consensus size: 89
53679594 AGGTAAATAA
* * * *
53679604 CAAATTTTGATTTTGCTACATACAATATAGCAGCTTGGATATAAACAATGGCAGATATACAGAGC
1 CAAATTTTGATTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAAC
*
53679669 AAACATCAGTTTGATAATGACATT
66 AAACATCAATTTGATAATGACATT
53679693 CAAATTTTGATTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAAC
1 CAAATTTTGATTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAAC
* *
53679758 AAACATCAATTTGATATTGGCATT
66 AAACATCAATTTGATAATGACATT
53679782 CA
1 CA
53679784 TACAATGGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (89 bp):
CAAATTTTGATTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGGCAGATATACACAAC
AAACATCAATTTGATAATGACATT
Found at i:53679921 original size:18 final size:18
Alignment explanation
Indices: 53679892--53679934 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53679882 AGTGAGTGTT
*
53679892 TCAAAATTGAAACCAAAA
1 TCAAAATAGAAACCAAAA
* *
53679910 TCGAAATAGAAATCAAAA
1 TCAAAATAGAAACCAAAA
53679928 TCAAAAT
1 TCAAAAT
53679935 TAAAATCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (18 bp):
TCAAAATAGAAACCAAAA
Found at i:53679940 original size:18 final size:18
Alignment explanation
Indices: 53679892--53679946 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
53679882 AGTGAGTGTT
* *
53679892 TCAAAATTGAAACCAAAA
1 TCAAAATTAAAATCAAAA
*
53679910 TCGAAA-TAGAAATCAAAA
1 TCAAAATTA-AAATCAAAA
*
53679928 TCAAAATTAAAATCGAAA
1 TCAAAATTAAAATCAAAA
53679946 T
1 T
53679947 AACCCTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (18 bp):
TCAAAATTAAAATCAAAA
Found at i:53680416 original size:21 final size:21
Alignment explanation
Indices: 53680392--53680431 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53680382 AACGTGGCAA
53680392 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
53680413 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
53680432 AGTCCCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:53681207 original size:48 final size:48
Alignment explanation
Indices: 53681131--53681273 Score: 178
Period size: 48 Copynumber: 3.0 Consensus size: 48
53681121 AAGACATCCG
* * * * * *
53681131 ATCCCTTTGCTCTTGGCCCCAGCGACCGCTCGGATTCCCATACTCTCT
1 ATCCCTTTGTTCTCGACTCCAGCCACCGCTCGGATTCCCATAATCTCT
**
53681179 ATCCCTTTGTTCTCGACTCCAGCCACCGCTCGGATTCCTGTAATCTCT
1 ATCCCTTTGTTCTCGACTCCAGCCACCGCTCGGATTCCCATAATCTCT
* * * *
53681227 ATCCCTTTGTTCTCGACTCCAGCCGCCACTTGGATTCCCATTATCTC
1 ATCCCTTTGTTCTCGACTCCAGCCACCGCTCGGATTCCCATAATCTC
53681274 GACTCTTCCA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.14, C:0.39, G:0.15, T:0.32
Consensus pattern (48 bp):
ATCCCTTTGTTCTCGACTCCAGCCACCGCTCGGATTCCCATAATCTCT
Found at i:53694070 original size:42 final size:42
Alignment explanation
Indices: 53694011--53694094 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
53694001 AGAATATGAG
53694011 CCTAAAACCTAGTACTTAGAAAGGAAATAACCTAAACATATT
1 CCTAAAACCTAGTACTTAGAAAGGAAATAACCTAAACATATT
*
53694053 CCTAAAATCTAGTACTTAGAAAGGAAATAACCTAAACATATT
1 CCTAAAACCTAGTACTTAGAAAGGAAATAACCTAAACATATT
53694095 TTGAAATGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.25
Consensus pattern (42 bp):
CCTAAAACCTAGTACTTAGAAAGGAAATAACCTAAACATATT
Found at i:53695207 original size:11 final size:12
Alignment explanation
Indices: 53695191--53695219 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53695181 GTTTGAATAG
53695191 AGAAAAAA-AAA
1 AGAAAAAAGAAA
53695202 AGAAAAAAGAAA
1 AGAAAAAAGAAA
53695214 AGAAAA
1 AGAAAA
53695220 GCGGAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:53698549 original size:62 final size:62
Alignment explanation
Indices: 53698477--53698601 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
53698467 AAATAAAAAC
* ***
53698477 TAAATTAAGAAAGAAATTATTACAAAATTTTATTATTTATTCTTAGATCACATTTGTTGATA
1 TAAATTAAGAAAGAAATTATTACAAAAATTTATTACGCATTCTTAGATCACATTTGTTGATA
53698539 TAAATTAAGAAAGAAATTATTACAAAAATTTATTACGCATTCTTAGATCACATTTGTTGATA
1 TAAATTAAGAAAGAAATTATTACAAAAATTTATTACGCATTCTTAGATCACATTTGTTGATA
53698601 T
1 T
53698602 TTATAGTAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (62 bp):
TAAATTAAGAAAGAAATTATTACAAAAATTTATTACGCATTCTTAGATCACATTTGTTGATA
Found at i:53701873 original size:24 final size:23
Alignment explanation
Indices: 53701842--53701887 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
53701832 TTAAAAATAT
*
53701842 TAAAATTAAAAATTTTATTTTTA
1 TAAAATTAAAAATTTTAATTTTA
*
53701865 TAAATATTAAAACTTTTAATTTT
1 TAAA-ATTAAAAATTTTAATTTT
53701888 CTTTGTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAAATTAAAAATTTTAATTTTA
Found at i:53711675 original size:9 final size:9
Alignment explanation
Indices: 53711641--53711691 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
53711631 AATAATTATT
53711641 TTTTATATA
1 TTTTATATA
* *
53711650 TTTAAAAATA
1 TTT-TATATA
*
53711660 TTATATATA
1 TTTTATATA
53711669 TTTTATATA
1 TTTTATATA
*
53711678 TTATATATA
1 TTTTATATA
53711687 TTTTA
1 TTTTA
53711692 ATAATCAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTATATA
Found at i:53711680 original size:18 final size:18
Alignment explanation
Indices: 53711657--53711691 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53711647 ATATTTAAAA
53711657 ATATTATATATATTTTAT
1 ATATTATATATATTTTAT
53711675 ATATTATATATATTTTA
1 ATATTATATATATTTTA
53711692 ATAATCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTATATATATTTTAT
Found at i:53722842 original size:3 final size:3
Alignment explanation
Indices: 53722836--53722868 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53722826 TTATTTATAT
53722836 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
53722869 ATTTACGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:53722900 original size:3 final size:3
Alignment explanation
Indices: 53722884--53723150 Score: 139
Period size: 3 Copynumber: 89.3 Consensus size: 3
53722874 CGATTACTAT
* * * * * *
53722884 TTA TTA TCA ATA TTA TTA TTA CTA TTA TTA CTA TTT TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * * * *
53722932 CTA TTA ACA TTA TTA TTA TTA TCA TT- TTA TT- TTA CTA CTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
53722978 TTT TTA GTAA TTA TTA TTA CTA TTA TTA TT- TAA CATA TCA TTA TTG
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * ** ** ** * *
53723024 CTA TTA TTA TTA CTA TCA TTA TTA TTA TTT TTA CCA CCA CCA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
53723072 TTA TTA TTA TTA TTA TTA TTA TTT TCTA TTA CTA TTA TTA CTA GTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA
*
53723119 TT- TTA TTA TCA TTA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53723151 CATCATTCTT
Statistics
Matches: 197, Mismatches: 58, Indels: 18
0.72 0.21 0.07
Matches are distributed among these distances:
2 9 0.05
3 181 0.92
4 7 0.04
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:53722995 original size:22 final size:22
Alignment explanation
Indices: 53722943--53722996 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
53722933 TATTAACATT
* *
53722943 ATTATTATTATCATTTTATTTT
1 ATTATTATTATCATTTTATGTA
* *
53722965 ACTACTATTATCATTTT-TAGTA
1 ATTATTATTATCATTTTAT-GTA
53722987 ATTATTATTA
1 ATTATTATTA
53722997 CTATTATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTATTATCATTTTATGTA
Found at i:53730676 original size:81 final size:82
Alignment explanation
Indices: 53730585--53730745 Score: 243
Period size: 81 Copynumber: 2.0 Consensus size: 82
53730575 AATATTCTTT
* * * * *
53730585 TATTCTTTTATTTTTCATTCATAATCATATCATGCAAATAATTATTCTTAGATTATTTTGTTCTT
1 TATTCTTTTATTCTTCATTCATAATCATACCATGCAAATAATTATTCATAGAATATTTCGTTCTT
53730650 TGGACTTTT-CTTCAAA
66 TGGACTTTTCCTTCAAA
* *
53730666 TATTCTTTTATTCTTCATTCATAATCATACCATGTAAATAATTATTCATAGAATCTTTCGTTCTT
1 TATTCTTTTATTCTTCATTCATAATCATACCATGCAAATAATTATTCATAGAATATTTCGTTCTT
*
53730731 TGGATTTTTCCTTCA
66 TGGACTTTTCCTTCA
53730746 CCTCCATAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 66 0.93
82 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (82 bp):
TATTCTTTTATTCTTCATTCATAATCATACCATGCAAATAATTATTCATAGAATATTTCGTTCTT
TGGACTTTTCCTTCAAA
Found at i:53734294 original size:18 final size:17
Alignment explanation
Indices: 53734263--53734296 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53734253 GAGAACTTCT
53734263 AAAAAAAAAGAGAAAAG
1 AAAAAAAAAGAGAAAAG
*
53734280 AAAAGAAAAGAAGAAAA
1 AAAAAAAAAG-AGAAAA
53734297 TAGAGAGGCC
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGAAAAG
Found at i:53735316 original size:45 final size:45
Alignment explanation
Indices: 53735205--53736100 Score: 218
Period size: 44 Copynumber: 20.0 Consensus size: 45
53735195 ATCATTGCGA
* * * **
53735205 ATCTTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAG-CCGCAA-
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG-AAG
* * * * *
53735249 ACCTTATCTCTCT-AATGTTGCAGTGGAGCAGACTGAAGATAGTAG
1 ATCTTATATCCCTGAA-GTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * *
53735294 ATCTTATAGCCCTGAAGTTGCAGCGGAGTAGATCGAAGATAGCAA-
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG-AAG
* * * * * * *
53735339 ACCTTCTTTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGACACAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * *
53735384 -TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTTACAA
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AG--A-AG
* * * *** * * *
53735434 ATCTTATCTCTCTGAAGTTACAACAGAGCAGA-T-CATA-ACAA-
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * * * * *
53735475 ACCTTATCTCTCTGAAATTGCAGTAGAGCAGGTTGAAGTTATAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * * *
53735520 -TCTTATCTCCCTGAAGTTGCAATAGAGCAGACTAAAGATTA-CAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAGAAG
* * * * * * * * *
53735564 ATCTTATCTCTCTGAAGTTACAGTAGAGTA-AAT-CATA-ACAA-
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * * * * * *
53735605 ACCTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAG-TTG-CG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* *
53735648 AGTCTTATATCCCTGAAGTTGCAGTAGGAGCAGATT--ATA-ACAA-
1 A-TCTTATATCCCTGAAGTTGCAGT-GGAGCAGATTGAAGATAGAAG
* * * * * * * * * *
53735691 ACCTTATCTCTCTAAAATTGTAGTAGAGCAGGTTGAAGTTACAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * *
53735736 -TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATTA-CAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAGAAG
* * * * * * * *
53735780 ATCTTATCTCTCTGAAGTTACAGTAGAGCA-AAT-CATA-ACAA-
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * * *
53735821 ACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG-TTG-CG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * **
53735864 AGTCTTATCTCCCTGAAATTGCAGTAGGAGCAGACTGAAGATAGCGG
1 A-TCTTATATCCCTGAAGTTGCAGT-GGAGCAGATTGAAGATAGAAG
* * * * *
53735911 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
* * * * * * *
53735956 TTACAAATCTCATCTCTGAAGTTGTAGTGGAGCAGATTGAAGCTAAAAGTTACAA
1 AT-C--TTAT-ATCCCTGAAGTTGCAGTGGAGCAGATTGAAG---ATAG--A-AG
* * * * * *
53736011 ATCTCATATCCTTGAAGTTGTAGTGGAGTAGATTGGAA-CTACAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATT-GAAGATAGAAG
* * * *
53736056 -TCTTATTTCTCTAAAGTTGCAGTGGAGCGGATTGAAG-TAGTAAG
1 ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG-AAG
53736100 A
1 A
53736101 CACAGCAGAT
Statistics
Matches: 617, Mismatches: 178, Indels: 113
0.68 0.20 0.12
Matches are distributed among these distances:
41 88 0.14
42 23 0.04
43 20 0.03
44 208 0.34
45 153 0.25
46 30 0.05
47 4 0.01
48 3 0.00
49 28 0.05
50 2 0.00
51 49 0.08
52 5 0.01
54 2 0.00
55 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
ATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGAAG
Found at i:53735406 original size:44 final size:44
Alignment explanation
Indices: 53735206--53735997 Score: 410
Period size: 44 Copynumber: 17.8 Consensus size: 44
53735196 TCATTGCGAA
* * * *** *
53735206 TCTTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAGCCGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * * * **
53735250 CCTTATCTCTCT-AATGTTGCAGTGGAGCAGACTGAAGATAGTAG
1 TCTTATCTCCCTGAA-GTTGCAGTAGAGCAGATTGAAGATACAAG
** ** * * *
53735294 ATCTTATAGCCCTGAAGTTGCAGCGGAGTAGATCGAAGATAGCAAA
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATA-CAAG
* * * * * * *
53735340 CCTTCTTTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGACACAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * *
53735384 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAG-----A--TACAAG
* * ** * * *
53735435 TCTTATCTCTCTGAAGTTACAACAGAGCAGA-T-CATA-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * * * * *
53735476 CCTTATCTCTCTGAAATTGCAGTAGAGCAGGTTGAAGTTATAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * *
53735520 TCTTATCTCCCTGAAGTTGCAATAGAGCAGACTAAAGATTAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGA-TACAAG
* * * * * * *
53735564 ATCTTATCTCTCTGAAGTTACAGTAGAGTA-AAT-CATA-ACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * * * * * * *
53735606 CCTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAGTTGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * *
53735650 TCTTATATCCCTGAAGTTGCAGTAGGAGCAGATT--ATA-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTA-GAGCAGATTGAAGATACAAG
* * * * * * *
53735692 CCTTATCTCTCTAAAATTGTAGTAGAGCAGGTTGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* *
53735736 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATTAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGA-TACAAG
* * * * * *
53735780 ATCTTATCTCTCTGAAGTTACAGTAGAGCA-AAT-CATA-ACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * * * *
53735822 CCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
* * *
53735866 TCTTATCTCCCTGAAATTGCAGTAGGAGCAGACTGAAGATAGC-GG
1 TCTTATCTCCCTGAAGTTGCAGTA-GAGCAGATTGAAGATA-CAAG
* * * *
53735911 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
** * *
53735956 TTACAAATCTCATCTCTGAAGTTGTAGTGGAGCAGATTGAAG
1 -T-CTTATCTC--C-CTGAAGTTGCAGTAGAGCAGATTGAAG
53735998 CTAAAAGTTA
Statistics
Matches: 554, Mismatches: 156, Indels: 71
0.71 0.20 0.09
Matches are distributed among these distances:
41 92 0.17
42 25 0.05
43 11 0.02
44 188 0.34
45 149 0.27
46 32 0.06
48 1 0.00
49 26 0.05
50 1 0.00
51 29 0.05
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAG
Found at i:53735508 original size:136 final size:134
Alignment explanation
Indices: 53735336--53735683 Score: 429
Period size: 130 Copynumber: 2.6 Consensus size: 134
53735326 TCGAAGATAG
* * * **
53735336 CAAACCTTCTTTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGACACAAGTCTTATCTCCCTGAAGT
1 CAAACCTTATCTCCTTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGT
* *
53735401 TGCAGTGGAACAGATTGAAGCTATAAG-TTACAAATCTTATCTCTCTGAAGTTACAACAGAGCAG
66 TGCAGTGGAGCAGATTG-A-CTA-AAGATTACAAATCTTATCTCTCTGAAGTTACAACAGAGCAA
53735465 ATCATAA
128 ATCATAA
* *
53735472 CAAACCTTATCT-CTCTGAAATTGCAGTAGAGCAGGTTGAAGTTATAAGTCTTATCTCCCTGAAG
1 CAAACCTTATCTCCT-TGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAG
* * * ** *
53735536 TTGCAATAGAGC--A--GACTAAAGATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAAAT
65 TTGCAGTGGAGCAGATTGACTAAAGATTACAAATCTTATCTCTCTGAAGTTACAACAGAGCAAAT
53735597 CATAA
130 CATAA
* * * * *
53735602 CAAACCTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAGTTGCGAGTCTTATATCCCTGAAGT
1 CAAACCTTATCTCCTTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGT
53735667 TGCAGTAGGAGCAGATT
66 TGCAGT-GGAGCAGATT
53735684 ATAACAAACC
Statistics
Matches: 180, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
129 3 0.02
130 102 0.57
131 7 0.04
132 1 0.01
133 1 0.01
134 1 0.01
135 2 0.01
136 63 0.35
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (134 bp):
CAAACCTTATCTCCTTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGT
TGCAGTGGAGCAGATTGACTAAAGATTACAAATCTTATCTCTCTGAAGTTACAACAGAGCAAATC
ATAA
Found at i:53735632 original size:86 final size:86
Alignment explanation
Indices: 53735521--53735764 Score: 280
Period size: 86 Copynumber: 2.8 Consensus size: 86
53735511 AGTTATAAGT
* * * ** * * *
53735521 CTTATCTCCCTGAAGTTGCAATAGAGCAGACTAAAGATTACAGA-TCTTATCTCTCTGAAGTTAC
1 CTTATCTCCTTGAAGTTGTAGTAGAGCAGGTTGAAG-TTACAGAGTCTTATCTCCCTGAAGTTGC
*
53735585 AGTAGAGTAAATCATAACAAAC
65 AGTAGAGCAAATCATAACAAAC
* * *
53735607 CTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAGTTGC-GAGTCTTATATCCCTGAAGTTGCA
1 CTTATCTCCTTGAAGTTGTAGTAGAGCAGGTTGAAGTTACAGAGTCTTATCTCCCTGAAGTTGCA
* *
53735671 GTAGGAGCAGATTATAACAAAC
66 GTA-GAGCAAATCATAACAAAC
* * *
53735693 CTTATCT-CTCTAAAATTGTAGTAGAGCAGGTTGAAGTTACA-AGTCTTATCTCCCTAAAGTTGC
1 CTTATCTCCT-TGAAGTTGTAGTAGAGCAGGTTGAAGTTACAGAGTCTTATCTCCCTGAAGTTGC
53735756 AGTAGAGCA
65 AGTAGAGCA
53735765 GACTGAAGAT
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.01
85 31 0.23
86 101 0.75
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (86 bp):
CTTATCTCCTTGAAGTTGTAGTAGAGCAGGTTGAAGTTACAGAGTCTTATCTCCCTGAAGTTGCA
GTAGAGCAAATCATAACAAAC
Found at i:53735698 original size:216 final size:216
Alignment explanation
Indices: 53735459--53735897 Score: 761
Period size: 216 Copynumber: 2.0 Consensus size: 216
53735449 AGTTACAACA
* *
53735459 GAGCAGATCATAACAAACCTTATCTCTCTGAAATTGCAGTAGAGCAGGTTGAAGTTATAAGTCTT
1 GAGCAGATCATAACAAACCTTATCTCTCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAAGTCTT
*
53735524 ATCTCCCTGAAGTTGCAATAGAGCAGACTAAAGATTACAGATCTTATCTCTCTGAAGTTACAGTA
66 ATCTCCCTAAAGTTGCAATAGAGCAGACTAAAGATTACAGATCTTATCTCTCTGAAGTTACAGTA
* * * *
53735589 GAGTAAATCATAACAAACCTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAGTTGCGAGTCTT
131 GAGCAAATCATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAGTCTT
*
53735654 ATATCCCTGAAGTTGCAGTAG
196 ATATCCCTGAAATTGCAGTAG
* *
53735675 GAGCAGATTATAACAAACCTTATCTCTCTAAAATTGTAGTAGAGCAGGTTGAAGTTACAAGTCTT
1 GAGCAGATCATAACAAACCTTATCTCTCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAAGTCTT
* *
53735740 ATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATTACAGATCTTATCTCTCTGAAGTTACAGTA
66 ATCTCCCTAAAGTTGCAATAGAGCAGACTAAAGATTACAGATCTTATCTCTCTGAAGTTACAGTA
53735805 GAGCAAATCATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAGTCTT
131 GAGCAAATCATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAGTCTT
*
53735870 ATCTCCCTGAAATTGCAGTAG
196 ATATCCCTGAAATTGCAGTAG
53735891 GAGCAGA
1 GAGCAGA
53735898 CTGAAGATAG
Statistics
Matches: 210, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
216 210 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (216 bp):
GAGCAGATCATAACAAACCTTATCTCTCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAAGTCTT
ATCTCCCTAAAGTTGCAATAGAGCAGACTAAAGATTACAGATCTTATCTCTCTGAAGTTACAGTA
GAGCAAATCATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAGTCTT
ATATCCCTGAAATTGCAGTAG
Found at i:53735741 original size:130 final size:132
Alignment explanation
Indices: 53735607--53735945 Score: 438
Period size: 130 Copynumber: 2.6 Consensus size: 132
53735597 CATAACAAAC
* * * ** *
53735607 CTTATCTCCTTGAAGTTGTAGTAGAGTAGGTTGAAG-TTGCGAG-TCTTATATCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATTGCGAGATCTTATCTCCCTGAAGTTGC
* *
53735670 AGTAGGAGCAGATTATAACAAACCTTATCTCTCTAAAATTGTAGTAGAGCAGGTTGAAGTTACAA
66 AGTAGGAGCAGATTATAACAAACCTTATCTCCCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAA
53735735 GT
131 GT
* * * *
53735737 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATTAC-AGATCTTATCTCTCTGAAGTTAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATTGCGAGATCTTATCTCCCTGAAGTTGC
* * * * * *
53735801 AGTA-GAGCAAATCATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGA
66 AGTAGGAGCAGATTATAACAAACCTTATCTCCCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAA
53735865 GT
131 GT
* *
53735867 CTTATCTCCCTGAAATTGCAGTAGGAGCAGACTGAAGATAGCG-GATCTTATCTCCCTGAAGTTG
1 CTTATCTCCCTGAAGTTGCAGTA-GAGCAGACTGAAGATTGCGAGATCTTATCTCCCTGAAGTTG
*
53735931 CAGT-GGAGTAGATTA
65 CAGTAGGAGCAGATTA
53735946 AAGCTACAAG
Statistics
Matches: 177, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
130 107 0.60
131 70 0.40
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (132 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATTGCGAGATCTTATCTCCCTGAAGTTGC
AGTAGGAGCAGATTATAACAAACCTTATCTCCCTAAAATTGCAGTAGAGCAGGTTGAAGTTACAA
GT
Found at i:53735827 original size:86 final size:86
Alignment explanation
Indices: 53735737--53735895 Score: 223
Period size: 86 Copynumber: 1.8 Consensus size: 86
53735727 AGTTACAAGT
* *
53735737 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGATTAC-AGATCTTATCTCTCTGAAGTTAC
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAG-TTACGAG-TCTTATCTCCCTGAAATTAC
53735801 AGTA-GAGCAAATCATAACAAAC
64 AGTAGGAGCAAATCATAACAAAC
* ** * *
53735823 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTGCGAGTCTTATCTCCCTGAAATTGCAG
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGTTACGAGTCTTATCTCCCTGAAATTACAG
53735888 TAGGAGCA
66 TAGGAGCA
53735896 GACTGAAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
85 24 0.38
86 40 0.62
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (86 bp):
CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGTTACGAGTCTTATCTCCCTGAAATTACAG
TAGGAGCAAATCATAACAAAC
Found at i:53735985 original size:49 final size:50
Alignment explanation
Indices: 53735921--53736044 Score: 187
Period size: 49 Copynumber: 2.5 Consensus size: 50
53735911 ATCTTATCTC
* * *
53735921 CCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAGTTACAAATCTCATCT
1 CCTGAAGTTGTAGTGGAGTAGATTAAAGCTAAAAGTTACAAATCTCATAT
* *
53735971 -CTGAAGTTGTAGTGGAGCAGATTGAAGCTAAAAGTTACAAATCTCATAT
1 CCTGAAGTTGTAGTGGAGTAGATTAAAGCTAAAAGTTACAAATCTCATAT
53736020 CCTTGAAGTTGTAGTGGAGTAGATT
1 CC-TGAAGTTGTAGTGGAGTAGATT
53736045 GGAACTACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 44 0.67
50 1 0.02
51 21 0.32
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (50 bp):
CCTGAAGTTGTAGTGGAGTAGATTAAAGCTAAAAGTTACAAATCTCATAT
Found at i:53737585 original size:3 final size:3
Alignment explanation
Indices: 53737579--53737609 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53737569 TTATTTATAT
53737579 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
53737610 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:53737614 original size:3 final size:3
Alignment explanation
Indices: 53737608--53737922 Score: 214
Period size: 3 Copynumber: 105.7 Consensus size: 3
53737598 CATCATCATC
* * *
53737608 ATT ATT ATT ATT ATT ATT ATT ATT -TT ACT ATT -TT ACT ATT ACT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * * * * *
53737655 ATT ATC AAT ATT ATT ATT ATT ACT ATT TTT ATT TTT ATT TTT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
53737703 ATT AAC ATT ATT ATT ATC ATT -TT ATT -TT ATT ACT ATT ATC ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
53737749 AGTA ATT ATT ATT ACT ATT ATT ATT -TA ACAT ATT ATT ATT -TCT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT
* * * ** ** * * *
53737795 ATT ATT ACT ATC ATT ATT ATT ATT TTT ACC ACC ACT ACT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
53737843 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTCT ATT ACT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
*
53737889 AGTT ATT -TT ATT ATC ATT ATT ATT A-T ATT ATT AT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
53737923 CATCATCATT
Statistics
Matches: 240, Mismatches: 58, Indels: 28
0.74 0.18 0.09
Matches are distributed among these distances:
2 14 0.06
3 216 0.90
4 10 0.04
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:53737756 original size:22 final size:22
Alignment explanation
Indices: 53737709--53737762 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
53737699 TACTATTAAC
* *
53737709 ATTATTATTATCATTTTATTTT
1 ATTATTATTATCATTTTATGTA
*
53737731 ATTACTATTATCATTTT-TAGTA
1 ATTATTATTATCATTTTAT-GTA
53737753 ATTATTATTA
1 ATTATTATTA
53737763 CTATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTATTATTATCATTTTATGTA
Found at i:53738941 original size:20 final size:20
Alignment explanation
Indices: 53738916--53738989 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
53738906 AAAAATATAA
53738916 ATTTTGATTTTTTTATAAA-T
1 ATTTTGATTTTTTTA-AAACT
* *
53738936 ATTTTGA-ATTTTAAAAACT
1 ATTTTGATTTTTTTAAAACT
* * *
53738955 ATTTTGAATTTTTGAAAATT
1 ATTTTGATTTTTTTAAAACT
53738975 ATTTTGAATTTTTTT
1 ATTTTG-ATTTTTTT
53738990 GTAATTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.07
19 13 0.30
20 22 0.50
21 6 0.14
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTTGATTTTTTTAAAACT
Found at i:53738957 original size:19 final size:18
Alignment explanation
Indices: 53738926--53738986 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
53738916 ATTTTGATTT
*
53738926 TTTTATAAATATTTTGAA
1 TTTTAAAAATATTTTGAA
53738944 TTTTAAAAACTATTTTGAA
1 TTTTAAAAA-TATTTTGAA
*
53738963 TTTTTGAAAATTATTTTGAA
1 -TTTT-AAAAATATTTTGAA
53738983 TTTT
1 TTTT
53738987 TTTGTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 8 0.21
19 13 0.34
20 13 0.34
21 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTTAAAAATATTTTGAA
Found at i:53744221 original size:21 final size:23
Alignment explanation
Indices: 53744192--53744236 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
53744182 GTAGTATAGT
53744192 GGTTAGTTTT-CCCGCCTGTCAC
1 GGTTAGTTTTCCCCGCCTGTCAC
53744214 GGTT-GTTTTCCCCGCCTGTCAC
1 GGTTAGTTTTCCCCGCCTGTCAC
53744236 G
1 G
53744237 CGGGTGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.07, C:0.33, G:0.24, T:0.36
Consensus pattern (23 bp):
GGTTAGTTTTCCCCGCCTGTCAC
Found at i:53744393 original size:204 final size:212
Alignment explanation
Indices: 53744003--53744418 Score: 571
Period size: 204 Copynumber: 2.0 Consensus size: 212
53743993 GGTAAGTATT
*
53744003 CCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATCTTAATTTTTTAACCTT
1 CCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATCTTAATTTTTTAACCTC
53744068 TCAAAAGAGGGAAAAGATAGACAACTTATTTTTGTTCCTTGAAATGTAATAAACTTATGCATATT
66 TCAAAAGAGGG--AAGATAGA-AACTTATTTTTGTTCC-----ATGT-ATAAACTTATGCATATT
* * ** *
53744133 TATATTTCTTTAAAAAAAAAAGTTGTTACGGATTACCAAATAGGTCGTTGTAGTATAGTGGTTAG
122 TAGATTCCTTTAAAAAAAAAAGTTGTTACCAATTACCAAATAGGTCGTTGTAGTATAGTGGTAAG
*
53744198 TTTTCCCGCCTGTCACGGTTGTTTTC
187 TATTCCCGCCTGTCACGGTTGTTTTC
* * *
53744224 CCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGGT-TTTATTTTTTGACCTC
1 CCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATCTTAATTTTTTAACCTC
*
53744288 TCAAAAGAGGG-A-A-AG-AACTTATTTTTGTTCC-T-T-T-AACTTCTGCATATTTAGATTCCT
66 TCAAAAGAGGGAAGATAGAAACTTATTTTTGTTCCATGTATAAACTTATGCATATTTAGATTCCT
*
53744345 TTAAAACAAAAAAGTTGTTACCAATTAGCAAATAGGTCGTTGTAGTATAGTGGTAAGTATTCCCG
131 TTAAAA-AAAAAAGTTGTTACCAATTACCAAATAGGTCGTTGTAGTATAGTGGTAAGTATTCCCG
53744410 CCTGTCACG
195 CCTGTCACG
53744419 CGGGTGACCC
Statistics
Matches: 182, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
203 26 0.14
204 63 0.35
206 1 0.01
207 1 0.01
213 16 0.09
215 2 0.01
216 1 0.01
217 1 0.01
220 24 0.13
221 47 0.26
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (212 bp):
CCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATCTTAATTTTTTAACCTC
TCAAAAGAGGGAAGATAGAAACTTATTTTTGTTCCATGTATAAACTTATGCATATTTAGATTCCT
TTAAAAAAAAAAGTTGTTACCAATTACCAAATAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGC
CTGTCACGGTTGTTTTC
Found at i:53745509 original size:27 final size:27
Alignment explanation
Indices: 53745463--53745519 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
53745453 TATTTTATGT
*
53745463 AGTGGAGGGTGTCAAGTAGGCGGCACC
1 AGTGGAGGGTATCAAGTAGGCGGCACC
53745490 AGTGGAGGGTATC-AGATAGGCGGCACC
1 AGTGGAGGGTATCAAG-TAGGCGGCACC
53745517 AGT
1 AGT
53745520 TGTGCCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.25, C:0.18, G:0.42, T:0.16
Consensus pattern (27 bp):
AGTGGAGGGTATCAAGTAGGCGGCACC
Found at i:53746426 original size:9 final size:9
Alignment explanation
Indices: 53746412--53746479 Score: 84
Period size: 9 Copynumber: 7.6 Consensus size: 9
53746402 ATAAGTATAA
53746412 AATTAACCG
1 AATTAACCG
*
53746421 AATTAATCG
1 AATTAACCG
53746430 AATTAACCG
1 AATTAACCG
*
53746439 AATTACCCG
1 AATTAACCG
53746448 AATT-ACCTG
1 AATTAACC-G
* *
53746457 AATTACCCA
1 AATTAACCG
53746466 AATTAACCG
1 AATTAACCG
53746475 AATTA
1 AATTA
53746480 TTTGTATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 2 0.04
9 45 0.92
10 2 0.04
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:53746435 original size:18 final size:18
Alignment explanation
Indices: 53746412--53746479 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
53746402 ATAAGTATAA
**
53746412 AATTAACCGAATTAATCG
1 AATTAACCGAATTACCCG
53746430 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
53746448 AATT-ACCTGAATTACCCA
1 AATTAACC-GAATTACCCG
53746466 AATTAACCGAATTA
1 AATTAACCGAATTA
53746480 TTTGTATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
17 3 0.07
18 39 0.87
19 3 0.07
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:53746589 original size:17 final size:17
Alignment explanation
Indices: 53746567--53746599 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53746557 TTATGATTGA
53746567 GTTGGGTAATTGGGTTG
1 GTTGGGTAATTGGGTTG
*
53746584 GTTGGGTACTTGGGTT
1 GTTGGGTAATTGGGTT
53746600 AATATATATT
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:0.09, C:0.03, G:0.45, T:0.42
Consensus pattern (17 bp):
GTTGGGTAATTGGGTTG
Found at i:53754740 original size:121 final size:118
Alignment explanation
Indices: 53754555--53754788 Score: 328
Period size: 121 Copynumber: 2.0 Consensus size: 118
53754545 CCACATCAAA
* * * *
53754555 ATATTAAAATACTAAAAATAATATGCCAAAAATATATAAAAAAAAACATAACATAAACGATACAT
1 ATATTAAAATACTAAAAATAACATGCCAAAAACATAAAAAAAAAAACATAACATAAACAATACAT
* * *
53754620 GATAAATACGAATATTTTTATTACTATTTTAAAATGATAATAAGTAAATTATT
66 AATAAATACGAATATTTTTATTACTACTTTAAAATGAAAATAAGTAAATTATT
*
53754673 ATATTAAAATACTAAAAATAACATG-CAAATAACA-AAAACGTAATAAAAACATAACATAAGCAA
1 ATATTAAAATACTAAAAATAACATGCCAAA-AACATAAAA---AA-AAAAACATAACATAAACAA
*
53754736 TACATAATAAATACGAATATTTTTATTATTACTTTAAAATGAAAATAAGTAAA
61 TACATAATAAATACGAATATTTTTATTACTACTTTAAAATGAAAATAAGTAAA
53754789 CATTTTTGGT
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
117 7 0.07
118 27 0.26
120 2 0.02
121 66 0.65
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (118 bp):
ATATTAAAATACTAAAAATAACATGCCAAAAACATAAAAAAAAAAACATAACATAAACAATACAT
AATAAATACGAATATTTTTATTACTACTTTAAAATGAAAATAAGTAAATTATT
Found at i:53756595 original size:37 final size:36
Alignment explanation
Indices: 53756547--53756655 Score: 122
Period size: 37 Copynumber: 3.2 Consensus size: 36
53756537 GGCCGAATAC
*
53756547 ACATAT-TCACTTATACCCACCTATGCCGAATGCAT
1 ACATATATCACTTATATCCACCTATGCCGAATGCAT
* * *
53756582 ACATATATACACTTACATCTAACTATGCCGAATGCAT
1 ACATATAT-CACTTATATCCACCTATGCCGAATGCAT
*
53756619 ACA-A-AT-A--TATATCCACCTATGCCGAATGCCT
1 ACATATATCACTTATATCCACCTATGCCGAATGCAT
53756650 ACATAT
1 ACATAT
53756656 GCACACATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
31 23 0.37
32 1 0.02
33 1 0.02
35 8 0.13
36 2 0.03
37 27 0.44
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (36 bp):
ACATATATCACTTATATCCACCTATGCCGAATGCAT
Found at i:53770619 original size:3 final size:3
Alignment explanation
Indices: 53770572--53770609 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
53770562 TCCCCTTCCC
*
53770572 CTT CTT CTT CTT CTT CTT C-T CTT CTT -TT CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
53770610 CCTTTCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:53772116 original size:23 final size:23
Alignment explanation
Indices: 53772089--53772135 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53772079 GCAAGGCTTT
53772089 TGACCACAACAACAAAGAAGGCA
1 TGACCACAACAACAAAGAAGGCA
53772112 TGACCACAACAACAAAGAAGGCA
1 TGACCACAACAACAAAGAAGGCA
53772135 T
1 T
53772136 CAGCAGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.26, G:0.17, T:0.06
Consensus pattern (23 bp):
TGACCACAACAACAAAGAAGGCA
Found at i:53774959 original size:49 final size:49
Alignment explanation
Indices: 53774865--53774962 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
53774855 CATTTCAATC
* * *
53774865 CTTTTTATAATTTCTTGACATAGTTCATTCGAATACATACATTTCCTTT
1 CTTTTTATAACTTCATGACATAGTTCATTCGAACACATACATTTCCTTT
* *
53774914 CTTTTTATAACTTCATGACATAGTTCATTTGAACACATACTTTTCCTTT
1 CTTTTTATAACTTCATGACATAGTTCATTCGAACACATACATTTCCTTT
53774963 TTCATGCTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (49 bp):
CTTTTTATAACTTCATGACATAGTTCATTCGAACACATACATTTCCTTT
Found at i:53775349 original size:45 final size:45
Alignment explanation
Indices: 53775299--53775425 Score: 161
Period size: 45 Copynumber: 2.8 Consensus size: 45
53775289 CCTTTGATTT
* * *
53775299 GTGATGCCATAGCGTCTTTTAG-CTGTGGTCTTACTCGATAGAATCA
1 GTGATGCCATAACGTCTTTAAGTC-ATGGTCTTACTCGATAGAAT-A
*
53775345 -TGATGTCATAACGTCTTTAAGTCATGGTCTTACTCGATAGAATA
1 GTGATGCCATAACGTCTTTAAGTCATGGTCTTACTCGATAGAATA
*
53775389 GTGATGCCATAACATCTTTCAA-TCATGGTCTTACTCG
1 GTGATGCCATAACGTCTTT-AAGTCATGGTCTTACTCG
53775426 TTTCTTGTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 1 0.01
45 68 0.94
46 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (45 bp):
GTGATGCCATAACGTCTTTAAGTCATGGTCTTACTCGATAGAATA
Found at i:53775522 original size:15 final size:15
Alignment explanation
Indices: 53775493--53775526 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53775483 CCAATAAACT
53775493 CAATTCATATATAAA
1 CAATTCATATATAAA
53775508 CAATT-ATATATTAAA
1 CAATTCATATA-TAAA
53775523 CAAT
1 CAAT
53775527 CAAAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (15 bp):
CAATTCATATATAAA
Found at i:53776486 original size:56 final size:56
Alignment explanation
Indices: 53776410--53776524 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
53776400 TAAACATTAC
* *
53776410 AATTTCTTAACGAAACTTTAACACAACCTTAATAACACTTTGTAAATATTTATAAA
1 AATTTCTTAACGAAAATTTAACACAACCTTAATAACACTTCGTAAATATTTATAAA
* *
53776466 AATTTCTTAATGAAAATTTAATACAACCTTAATAACACTTCGTAAATATTTATAAA
1 AATTTCTTAACGAAAATTTAACACAACCTTAATAACACTTCGTAAATATTTATAAA
53776522 AAT
1 AAT
53776525 ATTCATGGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (56 bp):
AATTTCTTAACGAAAATTTAACACAACCTTAATAACACTTCGTAAATATTTATAAA
Found at i:53778789 original size:197 final size:197
Alignment explanation
Indices: 53778454--53778844 Score: 692
Period size: 197 Copynumber: 2.0 Consensus size: 197
53778444 ATAATGGGCA
* *
53778454 TGGCTTTATTTTCATTCTGATATAAATATATGGAGAAAGTCTTAGTTTTTTAGCTTTCAAACCAA
1 TGGCTTTATTTTCATTCTGATATAAATATATGGAGAAAGCCTTAGCTTTTTAGCTTTCAAACCAA
*
53778519 ACCCAATTTTTTTTGCTTCCCTTCTCTGCTTCTTTGTTTAAATTTTTACAATAAGTTATTATTAC
66 ACCCAATTTTTTTTGCTTCCCTTCTCTGCTTCTTTGTTTAAATTTTTACAAGAAGTTATTATTAC
*
53778584 GGTTGTTCAATCACAGTTGTATCCTGAAAACTTGAGTTTACTACATTGGCCCATGTGTGCCCTTG
131 GGTTGTTCAATCACAGTTGTATCCTGAAAACTTGAGTTTACTACATTGGCCCATGTGCGCCCTTG
53778649 CG
196 CG
*
53778651 TGGCTTTATTTTCATTCTGATATAAGTATATGGAGAAAGCCTTAGCTTTTTAGCTTTCAAACCAA
1 TGGCTTTATTTTCATTCTGATATAAATATATGGAGAAAGCCTTAGCTTTTTAGCTTTCAAACCAA
* * *
53778716 ACCCCATTTTTTTTGCTTCCCTTCTCTGCTTCTTTGTTTGAATTTTTACAAGAAGTTATTATTAT
66 ACCCAATTTTTTTTGCTTCCCTTCTCTGCTTCTTTGTTTAAATTTTTACAAGAAGTTATTATTAC
* *
53778781 GGTTGTTCAATCACAGTTGTATCCTGAAAACTTGGGTTTACTACCTTGGCCCATGTGCGCCCTT
131 GGTTGTTCAATCACAGTTGTATCCTGAAAACTTGAGTTTACTACATTGGCCCATGTGCGCCCTT
53778845 AAGGATTGGA
Statistics
Matches: 184, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
197 184 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (197 bp):
TGGCTTTATTTTCATTCTGATATAAATATATGGAGAAAGCCTTAGCTTTTTAGCTTTCAAACCAA
ACCCAATTTTTTTTGCTTCCCTTCTCTGCTTCTTTGTTTAAATTTTTACAAGAAGTTATTATTAC
GGTTGTTCAATCACAGTTGTATCCTGAAAACTTGAGTTTACTACATTGGCCCATGTGCGCCCTTG
CG
Found at i:53790895 original size:70 final size:74
Alignment explanation
Indices: 53790759--53790896 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 74
53790749 TACTTTCCCC
*
53790759 AAAAAAATTTTACTTCCCCCCAAACCCCTAAAACTTTTTTTCTTTTATTTTTCCTCCAAAACTTT
1 AAAAAAATTTTACTTCCCCCCAAACCCC-AAAACTTTTTTTCTTTTATTTCTCCTCCAAAACTTT
53790824 TACTTCTCTT
65 TACTTCTCTT
* * *
53790834 AAAAAAA-TTTAC-TCCCCTCAAACCCC-CAA-TTTTTTTCCTTTTACTTTCT-C-CCAAAATTT
1 AAAAAAATTTTACTTCCCCCCAAACCCCAAAACTTTTTTT-CTTTTA-TTTCTCCTCCAAAACTT
53790893 TTAC
64 TTAC
53790897 CTCCCGCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
70 19 0.33
71 9 0.16
72 4 0.07
73 13 0.23
74 5 0.09
75 7 0.12
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (74 bp):
AAAAAAATTTTACTTCCCCCCAAACCCCAAAACTTTTTTTCTTTTATTTCTCCTCCAAAACTTTT
ACTTCTCTT
Done.