Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 70 of 187
Found at i:20514397 original size:53 final size:53
Alignment explanation
Indices: 20514316--20514423 Score: 175
Period size: 53 Copynumber: 2.0 Consensus size: 53
20514306 CTCCTAAGTA
*
20514316 TAGAAACATGAATTTAAAAGATTGGGAGCAT-AAAGTTCACTAATTTACATAAT
1 TAGAAACATGAATTTAAAAGATTAGGAGCATCAAA-TTCACTAATTTACATAAT
20514369 TAGAAACATGAATTT-AAAGCATTAGGAGCATCAAATTCACTAATTTACATAAT
1 TAGAAACATGAATTTAAAAG-ATTAGGAGCATCAAATTCACTAATTTACATAAT
20514422 TA
1 TA
20514424 ATCATCCAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 4 0.08
53 45 0.87
54 3 0.06
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (53 bp):
TAGAAACATGAATTTAAAAGATTAGGAGCATCAAATTCACTAATTTACATAAT
Found at i:20515537 original size:148 final size:148
Alignment explanation
Indices: 20515263--20515550 Score: 407
Period size: 148 Copynumber: 1.9 Consensus size: 148
20515253 AATTAGGACT
* * *
20515263 AAACCGTAATGTTTATAAAATTTTAGGTTGACATCGCGAAGTTATAGGGTTCCTTGTCACGACAC
1 AAACCGTAATGTTTACAAAATTTTAGGTTGACATCACGAAGTTATAGGGTTCCTCGTCACGACAC
* * * * ** *
20515328 AATATAGTAACTAGGTCTCATCTCAACAACCTATGCTTGACATCGTGTCGTGGCATAGTGGCCCG
66 AACATACTAACTAGGTCTCATCTAAACAACCCATGCTTGACATCGCATCATGGCATAGTGGCCCG
20515393 ATCTCGTCGCGATATGAC
131 ATCTCGTCGCGATATGAC
* * **
20515411 AAACTGTAATGTTTACAAAATTTTAGGTTGACGTCACGAAGTTAT-GAGGTTCCTCGTCGTGACA
1 AAACCGTAATGTTTACAAAATTTTAGGTTGACATCACGAAGTTATAG-GGTTCCTCGTCACGACA
* *
20515475 CAACATACTAACTAGGTCTCATCTAAACAACCCATGCTTGACATCGCATCATGGCATGGTGGCCT
65 CAACATACTAACTAGGTCTCATCTAAACAACCCATGCTTGACATCGCATCATGGCATAGTGGCCC
*
20515540 GATCTTGTCGC
130 GATCTCGTCGC
20515551 AACGATCTAC
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
147 1 0.01
148 121 0.99
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (148 bp):
AAACCGTAATGTTTACAAAATTTTAGGTTGACATCACGAAGTTATAGGGTTCCTCGTCACGACAC
AACATACTAACTAGGTCTCATCTAAACAACCCATGCTTGACATCGCATCATGGCATAGTGGCCCG
ATCTCGTCGCGATATGAC
Found at i:20519773 original size:21 final size:21
Alignment explanation
Indices: 20519749--20519792 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20519739 TTATATATGT
*
20519749 TTAATTAAGC-TTTAGTTAATA
1 TTAATTAA-CTTTTAATTAATA
20519770 TTAATTAACTTTTAATTAATA
1 TTAATTAACTTTTAATTAATA
20519791 TT
1 TT
20519793 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAATTAACTTTTAATTAATA
Found at i:20525177 original size:27 final size:27
Alignment explanation
Indices: 20525139--20525192 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20525129 TTACCATCAG
20525139 AAAGCCTGATATAAGTTTTGATGATTT
1 AAAGCCTGATATAAGTTTTGATGATTT
*
20525166 AAAGCCTTATATAAGTTTTGATGATTT
1 AAAGCCTGATATAAGTTTTGATGATTT
20525193 CTGGAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (27 bp):
AAAGCCTGATATAAGTTTTGATGATTT
Found at i:20531654 original size:14 final size:13
Alignment explanation
Indices: 20531635--20531680 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 13
20531625 GTTTTGAGTA
20531635 TTTTTTTCTTTTAT
1 TTTTTTTCTTTT-T
*
20531649 TTTTTTAACTTTCTT
1 TTTTTT-TCTTT-TT
20531664 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
20531677 TTTT
1 TTTT
20531681 CTATTCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 11 0.39
16 1 0.04
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:20537016 original size:20 final size:21
Alignment explanation
Indices: 20536991--20537032 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
20536981 TCAATTGGTC
*
20536991 ATAATACTCTATATA-AACAA
1 ATAATAATCTATATATAACAA
20537011 ATAATAATCTATATATAACAA
1 ATAATAATCTATATATAACAA
20537032 A
1 A
20537033 GTAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAATCTATATATAACAA
Found at i:20537028 original size:22 final size:22
Alignment explanation
Indices: 20536991--20537032 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20536981 TCAATTGGTC
*
20536991 ATAATACTCTATATAAACAAATA
1 ATAATACTATATAT-AACAAATA
20537014 ATAAT-CTATATATAACAAA
1 ATAATACTATATATAACAAA
20537033 GTAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATACTATATATAACAAATA
Found at i:20537446 original size:16 final size:16
Alignment explanation
Indices: 20537425--20537456 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20537415 TTTAACTGCC
20537425 ACGTTAATTGAACTAT
1 ACGTTAATTGAACTAT
20537441 ACGTTAATTGAACTAT
1 ACGTTAATTGAACTAT
20537457 GTACCGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
ACGTTAATTGAACTAT
Found at i:20537583 original size:31 final size:29
Alignment explanation
Indices: 20537548--20537637 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
20537538 AATCTCAAAA
*
20537548 TTATACATGAACTTTGGTCTAATGTGCAATT
1 TTATACATGAACTTTGAT-T-ATGTGCAATT
*
20537579 TTATACAT-AGACTTTGATTTTGTGCAATT
1 TTATACATGA-ACTTTGATTATGTGCAATT
*
20537608 TTATACATGAAAATTTGATT-TGATGCAATT
1 TTATACATG-AACTTTGATTATG-TGCAATT
20537638 CTCACAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 19 0.37
30 17 0.33
31 16 0.31
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (29 bp):
TTATACATGAACTTTGATTATGTGCAATT
Found at i:20537816 original size:31 final size:30
Alignment explanation
Indices: 20537772--20537840 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
20537762 AATTGAATTA
* *
20537772 AAATTAAATTTTCATGTATA-CATTTGAACC
1 AAATCAAAATTTCATGTATATCA-TTGAACC
*
20537802 ACAATCAAAATTTCATGTGTATCATTGAACC
1 A-AATCAAAATTTCATGTATATCATTGAACC
20537833 AAATCAAA
1 AAATCAAA
20537841 GTTCGTGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATATCATTGAACC
Found at i:20549067 original size:18 final size:18
Alignment explanation
Indices: 20549044--20549081 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20549034 AAACAAGTTC
*
20549044 ATATAAA-AATCAAAATAT
1 ATATAAATAAT-AAAACAT
20549062 ATATAAATAATAAAACAT
1 ATATAAATAATAAAACAT
20549080 AT
1 AT
20549082 GATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATAAATAATAAAACAT
Found at i:20552274 original size:33 final size:33
Alignment explanation
Indices: 20552232--20552301 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
20552222 AGCCTAAGGT
20552232 ATGAGCCGTGTTATTCGCTTATCTCTTAACATG
1 ATGAGCCGTGTTATTCGCTTATCTCTTAACATG
*
20552265 ATGAGCCGTGTTATTCGCTTCTCTCTTAACATG
1 ATGAGCCGTGTTATTCGCTTATCTCTTAACATG
20552298 ATGA
1 ATGA
20552302 AAAGTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (33 bp):
ATGAGCCGTGTTATTCGCTTATCTCTTAACATG
Found at i:20552494 original size:18 final size:18
Alignment explanation
Indices: 20552469--20552534 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
20552459 CTAAAAAAGG
20552469 TTTT-TTTTTAAAAAATA
1 TTTTATTTTTAAAAAATA
* **
20552486 TTTTATTTTTTAATTATA
1 TTTTATTTTTAAAAAATA
* * *
20552504 ATTTATTTTATAATTAATTA
1 TTTTATTTT-TAA-AAAATA
20552524 TTTTATTTTTA
1 TTTTATTTTTA
20552535 GGAAGTCTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
17 4 0.11
18 18 0.50
19 4 0.11
20 10 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTTTTAAAAAATA
Found at i:20553301 original size:11 final size:10
Alignment explanation
Indices: 20553283--20553317 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 10
20553273 CAAATAATTT
20553283 AAAAATTATA
1 AAAAATTATA
20553293 AAAATATTATA
1 AAAA-ATTATA
20553304 AAAAATT-TA
1 AAAAATTATA
20553313 AAAAA
1 AAAAA
20553318 ACTTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.29
10 7 0.29
11 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:20559684 original size:16 final size:16
Alignment explanation
Indices: 20559663--20559699 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20559653 TACATTTGTA
*
20559663 TTTTTTTTATTTCAAG
1 TTTTTTCTATTTCAAG
*
20559679 TTTTTTCTATTTCATG
1 TTTTTTCTATTTCAAG
20559695 TTTTT
1 TTTTT
20559700 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTTTTCTATTTCAAG
Found at i:20564291 original size:21 final size:21
Alignment explanation
Indices: 20564265--20564304 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20564255 ACCTTTTCTA
20564265 AAGTTAAAA-GACAAAACTATT
1 AAGTTAAAAGGA-AAAACTATT
20564286 AAGTTAAAAGGAAAAACTA
1 AAGTTAAAAGGAAAAACTA
20564305 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGAAAAACTATT
Found at i:20564983 original size:31 final size:32
Alignment explanation
Indices: 20564927--20564992 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
20564917 CTCAATTTCA
*
20564927 TTTTTTAAAATAATTTTAATTTTTTTTTATAT
1 TTTTTTAAAATAATTTTAATATTTTTTTATAT
20564959 TTTTTTAAAATAATTTTAA-ATTTTTTTATAT
1 TTTTTTAAAATAATTTTAATATTTTTTTATAT
20564990 TTT
1 TTT
20564993 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (32 bp):
TTTTTTAAAATAATTTTAATATTTTTTTATAT
Found at i:20566075 original size:7 final size:7
Alignment explanation
Indices: 20566063--20566087 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20566053 AGTCGATTGA
20566063 TATTTAG
1 TATTTAG
20566070 TATTTAG
1 TATTTAG
20566077 TATTTAG
1 TATTTAG
20566084 TATT
1 TATT
20566088 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20566940 original size:25 final size:25
Alignment explanation
Indices: 20566912--20566981 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
20566902 ATTTAATTTT
*
20566912 TTTATCTGATGTAATAAAATAGAAG
1 TTTATTTGATGTAATAAAATAGAAG
* *
20566937 TTTATTTAATATAATAAAATAGAAG
1 TTTATTTGATGTAATAAAATAGAAG
20566962 TTCTATTTGATGTAATAAAA
1 TT-TATTTGATGTAATAAAA
20566982 ACCCTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 24 0.62
26 15 0.38
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (25 bp):
TTTATTTGATGTAATAAAATAGAAG
Found at i:20567000 original size:18 final size:18
Alignment explanation
Indices: 20566977--20567025 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
20566967 TTTGATGTAA
*
20566977 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
20566995 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
20567013 TAAAAACCCTAAC
1 TAAAAACCCTAAC
20567026 CCTAACCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:20567044 original size:29 final size:29
Alignment explanation
Indices: 20567002--20567282 Score: 230
Period size: 29 Copynumber: 9.3 Consensus size: 29
20566992 AATTAAAAAC
*
20567002 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
20567031 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
20567060 CCTAGTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20567089 CCCTAACTTAATTTAATTAAAAACCCTAACCCTAA
1 --C---C-TAATTTAATTAAAAACCCTAACCCTAA
*
20567124 CCTAATTTAATTAAAAACCCTAA-CTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * * * **
20567152 -TTAA--AAACCCTAACCCTAA-CCTAACTTAATTAAAA
1 CCTAATTTAA--TTAA---AAACCCTAAC---CCT--AA
*
20567187 CCCTAACTTAATTAAAAACCCTAACCCTAA
1 -CCTAATTTAATTAAAAACCCTAACCCTAA
* *
20567217 CCTAACTTAATTAAAAACCCTAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * *
20567246 CGTAACTTAATTGAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20567275 CCTAATTT
1 CCTAATTT
20567283 TACATAATTT
Statistics
Matches: 207, Mismatches: 23, Indels: 44
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.01
27 6 0.03
28 4 0.02
29 140 0.68
30 5 0.02
31 1 0.00
32 1 0.00
33 3 0.01
34 3 0.01
35 34 0.16
37 6 0.03
39 2 0.01
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:20567084 original size:23 final size:23
Alignment explanation
Indices: 20566984--20567084 Score: 82
Period size: 29 Copynumber: 4.1 Consensus size: 23
20566974 TAATAAAAAC
20566984 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
*
20567007 CTTAA-TTAA--AAACCCTAACCCTAA
1 CCTAATTTAATTAAA----AACCCTAA
20567031 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
20567054 CTCTAACCTAGTTTAATTAAAAACCCTAA
1 C-CT-A---A-TTTAATTAAAAACCCTAA
20567083 CC
1 CC
20567085 CTAACCCTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
20 3 0.05
22 4 0.06
23 13 0.21
24 14 0.22
25 5 0.08
27 3 0.05
28 2 0.03
29 19 0.30
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.29
Consensus pattern (23 bp):
CCTAATTTAATTAAAAACCCTAA
Found at i:20567092 original size:64 final size:64
Alignment explanation
Indices: 20567017--20567147 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
20567007 CTTAATTAAA
* *
20567017 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACTCTAACCTAGTTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
*
20567081 AACCCTAACCCTAACTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
20567145 AAC
1 AAC
20567148 TTAATTAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (64 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:20567151 original size:18 final size:18
Alignment explanation
Indices: 20567124--20567211 Score: 93
Period size: 18 Copynumber: 5.3 Consensus size: 18
20567114 CTAACCCTAA
*
20567124 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
20567142 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
20567160 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
20567171 CCTAACTTAATT-AAAAC
1 CCTAACTTAATTAAAAAC
20567188 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
20567206 CCTAAC
1 CCTAAC
20567212 CCTAACCTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
11 6 0.10
12 2 0.03
14 1 0.02
15 1 0.02
16 2 0.03
17 12 0.21
18 34 0.59
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:20567204 original size:46 final size:47
Alignment explanation
Indices: 20567101--20567245 Score: 265
Period size: 46 Copynumber: 3.1 Consensus size: 47
20567091 CTAACTTAAT
*
20567101 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAC
1 TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAAC
20567148 TTAATTAAAAACCCTAACCCTAACCTAACTTAATT-AAAACCCTAAC
1 TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAAC
20567194 TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAA-C
20567242 TTAA
1 TTAA
20567246 CGTAACTTAA
Statistics
Matches: 95, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
46 46 0.48
47 44 0.46
48 5 0.05
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (47 bp):
TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAAC
Found at i:20567268 original size:93 final size:92
Alignment explanation
Indices: 20566977--20567269 Score: 317
Period size: 93 Copynumber: 3.1 Consensus size: 92
20566967 TTTGATGTAA
*
20566977 TAAAAACCCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACTTAATT-AAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
**
20567042 TAAAAACCCTAACTCTAACCTAGTTTAAT
65 TAAAAACCCTAACT-TAACCTAACTTAAT
* **** * *
20567071 TAAAAACCCTAACCCTAACCCTAA-CTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAA-CTTAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
* * *
20567135 TAAAAACCCTAACTTAA-TTAA--AAACCC
65 TAAAAACCCTAACTTAACCTAACTTAA--T
* *
20567162 TAACCCTAA-CCTAACTTAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTA
1 TAA---AAACCCTAACTTAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTA
*
20567226 ATTAAAAACCCTAACCTTAACGTAACTTAAT
63 ATTAAAAACCCTAA-CTTAACCTAACTTAAT
*
20567257 TGAAAACCCTAAC
1 TAAAAACCCTAAC
20567270 CCTAACCTAA
Statistics
Matches: 161, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
89 2 0.01
91 5 0.03
92 11 0.07
93 112 0.70
94 21 0.13
95 8 0.05
97 2 0.01
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.27
Consensus pattern (92 bp):
TAAAAACCCTAACTTAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
AAAAACCCTAACTTAACCTAACTTAAT
Found at i:20567271 original size:64 final size:64
Alignment explanation
Indices: 20567017--20567276 Score: 201
Period size: 64 Copynumber: 4.2 Consensus size: 64
20567007 CTTAATTAAA
* **
20567017 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CTCTAACCTAGTTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCT-TAACCTAACTTAATTAAAAACCCT
* * * *
20567081 AACCCTAACCCTAACTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCTTAACCTAACTTAATTAAAAACCCT
** * *
20567145 AACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA----AA-C----CCTAACTTAATTA
1 AAC---CCT---AACCCTAA-CCTAACTTAA-TTAA-AAACCCTAACCTTAACCTAACTTAATTA
20567201 AAAACCCT
57 AAAACCCT
* *
20567209 AA--C----CCTAACCTAACTTAATTAAAAACCCTAACCTTAACGTAACTTAATTGAAAACCCT
1 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCTTAACCTAACTTAATTAAAAACCCT
20567267 AACCCTAACC
1 AACCCTAACC
20567277 TAATTTTACA
Statistics
Matches: 156, Mismatches: 15, Indels: 50
0.71 0.07 0.23
Matches are distributed among these distances:
49 2 0.01
50 4 0.03
51 9 0.06
52 5 0.03
53 2 0.01
54 1 0.01
58 21 0.13
60 1 0.01
64 85 0.54
65 1 0.01
67 1 0.01
68 1 0.01
69 2 0.01
70 8 0.05
71 7 0.04
72 4 0.03
73 2 0.01
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (64 bp):
AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCTTAACCTAACTTAATTAAAAACCCT
Found at i:20567361 original size:55 final size:55
Alignment explanation
Indices: 20567277--20567400 Score: 223
Period size: 55 Copynumber: 2.3 Consensus size: 55
20567267 AACCCTAACC
*
20567277 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTT-GGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATT-TTAGGACTTAA
20567332 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTAGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTAGGACTTAA
20567387 TAATTTTACATAAT
1 TAATTTTACATAAT
20567401 GTTAGATTTG
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
54 2 0.03
55 65 0.97
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTAGGACTTAA
Found at i:20570164 original size:123 final size:123
Alignment explanation
Indices: 20569945--20570169 Score: 398
Period size: 123 Copynumber: 1.8 Consensus size: 123
20569935 CCCAAACTTG
*
20569945 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAACAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
20570010 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
* * *
20570068 CTACTGTAACAAAATCGCGTCTACGAGGGCGCGATTTCACAATTTTTTCTCAAATAGCATCTTGG
1 CTACTGTAACAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
20570133 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
20570170 CTCGAAATAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
123 96 0.99
124 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (123 bp):
CTACTGTAACAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
Found at i:20573291 original size:23 final size:21
Alignment explanation
Indices: 20573265--20573309 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
20573255 AATTTTTGTT
20573265 TTCAAAAAAATGATTTCGACAGC
1 TTCAAAAAAAT-ATTTCGA-AGC
**
20573288 TTCAAATTAATATTTCGAAGC
1 TTCAAAAAAATATTTCGAAGC
20573309 T
1 T
20573310 ATACAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (21 bp):
TTCAAAAAAATATTTCGAAGC
Found at i:20573365 original size:30 final size:31
Alignment explanation
Indices: 20573324--20573383 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20573314 AAATATGGCT
*
20573324 ATATAAAAGTA-TTAACAACCATATTATTATA
1 ATATAAAAGTATTTAACAACCACATT-TTATA
*
20573355 ATAT-AAAGTATTTCACAACCACATTTTAT
1 ATATAAAAGTATTTAACAACCACATTTTAT
20573384 GGTTGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (31 bp):
ATATAAAAGTATTTAACAACCACATTTTATA
Found at i:20575278 original size:13 final size:13
Alignment explanation
Indices: 20575247--20575284 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20575237 GTTACAATAG
*
20575247 TAATATT-TTAAT
1 TAATATTATTTAT
20575259 TAATATTATTTAT
1 TAATATTATTTAT
*
20575272 TATTATTATTTAT
1 TAATATTATTTAT
20575285 ACTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATATTATTTAT
Found at i:20588900 original size:45 final size:45
Alignment explanation
Indices: 20588851--20588938 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
20588841 ATATTTTGAA
* *
20588851 TATTTTGATATTATTTTATATAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATATAATAAAATAGAAATTTATTTGAGT
* *
20588896 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATATAATAAAATAGAAATTTATTTGA
20588939 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (45 bp):
TATTTTGATATTATTTGATATAATAAAATAGAAATTTATTTGAGT
Found at i:20588934 original size:25 final size:25
Alignment explanation
Indices: 20588906--20588963 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
20588896 TATTTTGATA
*
20588906 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
20588931 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
*
20588956 TTTTTTGA
1 TTATTTGA
20588964 GTTATTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:20591771 original size:41 final size:41
Alignment explanation
Indices: 20591726--20591991 Score: 469
Period size: 41 Copynumber: 6.5 Consensus size: 41
20591716 AGCACTTCAT
* * * * *
20591726 CTGCTAGGTTTAAAGTCTAATTCAGTTCACTGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
20591767 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
20591808 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
20591849 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
*
20591890 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
*
20591931 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
20591972 CTGCTAGGCTTATAGCCTGA
1 CTGCTAGGCTTATAGCCTGA
20591992 ATAATTTCAC
Statistics
Matches: 219, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 219 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
Found at i:20593342 original size:40 final size:39
Alignment explanation
Indices: 20593275--20593384 Score: 130
Period size: 40 Copynumber: 2.8 Consensus size: 39
20593265 GTGTTTGGAT
*
20593275 AAAAAATGCCGCTAAAAATAAGCATTAGCGGTGCTATTA
1 AAAAAACGCCGCTAAAAATAAGCATTAGCGGTGCTATTA
* * * *
20593314 AAAAAACGCCGCTAAAGATCAAGTATTAGCGGTGCTTTTT
1 AAAAAACGCCGCTAAAAAT-AAGCATTAGCGGTGCTATTA
** * *
20593354 GGAAAACGCCGTTAAAAATGAGCATTAGCGG
1 AAAAAACGCCGCTAAAAATAAGCATTAGCGG
20593385 CGTTTTTCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 27 0.46
40 32 0.54
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATAAGCATTAGCGGTGCTATTA
Found at i:20593658 original size:21 final size:22
Alignment explanation
Indices: 20593634--20593678 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
20593624 GCCATTTTAT
*
20593634 CCCCAAATTTCC-CCCCTGAAA
1 CCCCAAATTTCCTCCCCTAAAA
*
20593655 CCCCTAATTTCCTCCCCTAAAA
1 CCCCAAATTTCCTCCCCTAAAA
20593677 CC
1 CC
20593679 TTTAACTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.49, G:0.02, T:0.22
Consensus pattern (22 bp):
CCCCAAATTTCCTCCCCTAAAA
Found at i:20596171 original size:17 final size:18
Alignment explanation
Indices: 20596149--20596182 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20596139 ATGAGTAAAG
20596149 AAAAAC-TTTTTTATTTA
1 AAAAACTTTTTTTATTTA
20596166 AAAAACTTTTTTTATTT
1 AAAAACTTTTTTTATTT
20596183 TATAGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAAACTTTTTTTATTTA
Found at i:20597620 original size:43 final size:42
Alignment explanation
Indices: 20597550--20597776 Score: 233
Period size: 43 Copynumber: 5.3 Consensus size: 42
20597540 AAGTCATGTT
* * * * *
20597550 TTTAGTGGCATTTGTGAAAAAACGCCGCTAAAGGTCATGAGT-
1 TTTAGTGGCGTTTGTGGAGAAGCGCCGCTAAAGGTCACGA-TC
** * *
20597592 TTTAGTGTTGTTTGTGGTAGAAGCGCCGCTAAAGGCCAAGATC
1 TTTAGTGGCGTTTGTGG-AGAAGCGCCGCTAAAGGTCACGATC
* *
20597635 TTTAGCGGCGTTTGTTGGAGAAGCGCCGCTAAAGGTCACGAGC
1 TTTAGTGGCGTTTG-TGGAGAAGCGCCGCTAAAGGTCACGATC
** * *
20597678 TTTAGCAGCGTTTGTGGGGGAAGCGCCACTAAAGGTCACGATC
1 TTTAGTGGCGTTTGT-GGAGAAGCGCCGCTAAAGGTCACGATC
*
20597721 TTTAGTGGCGATTGTGTGG-GAAGTGCCGCTAAAGGTCACGATC
1 TTTAGTGGCG-TT-TGTGGAGAAGCGCCGCTAAAGGTCACGATC
*
20597764 TTTAGCGGCGTTT
1 TTTAGTGGCGTTT
20597777 TTCCAAATAA
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 17 0.11
43 128 0.82
44 7 0.04
45 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (42 bp):
TTTAGTGGCGTTTGTGGAGAAGCGCCGCTAAAGGTCACGATC
Found at i:20597871 original size:22 final size:22
Alignment explanation
Indices: 20597846--20597887 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
20597836 TTGTTAAAGC
20597846 GCCGTTAAAAGCCTAAAAAAAT
1 GCCGTTAAAAGCCTAAAAAAAT
20597868 GCCGTTAAAAGCCTAAAAAA
1 GCCGTTAAAAGCCTAAAAAA
20597888 CGCCGCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (22 bp):
GCCGTTAAAAGCCTAAAAAAAT
Found at i:20597887 original size:21 final size:22
Alignment explanation
Indices: 20597845--20597899 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
20597835 CTTGTTAAAG
20597845 CGCCGTTAAAAGCCTAAAAAAA
1 CGCCGTTAAAAGCCTAAAAAAA
*
20597867 TGCCGTTAAAAGCCT-AAAAAA
1 CGCCGTTAAAAGCCTAAAAAAA
*
20597888 CGCCGCTAAAAG
1 CGCCGTTAAAAG
20597900 TCTTTTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (22 bp):
CGCCGTTAAAAGCCTAAAAAAA
Found at i:20605159 original size:39 final size:39
Alignment explanation
Indices: 20605062--20605159 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
20605052 GGCGTTTGGA
* *
20605062 ACAAAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTT
1 ACAAAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTT
* * *
20605101 CCAAGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGATTT
1 ACAA-AAGCGCCACAAAAAATAGAGAATTAGCGGCGATTT
*
20605140 ATATAAAGCGCCACAAAAAA
1 ACA-AAAGCGCCACAAAAAA
20605160 CCTAAGACCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
39 32 0.67
40 16 0.33
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.15
Consensus pattern (39 bp):
ACAAAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTT
Found at i:20605333 original size:41 final size:41
Alignment explanation
Indices: 20605288--20605504 Score: 167
Period size: 41 Copynumber: 5.3 Consensus size: 41
20605278 TTTTTATATG
* * *
20605288 AGCGCCGTTAAAT-CTCTGGCCTTTAGCGACGTTTTTGTCCA
1 AGCGCCGCT-AATCCTCTGGCCTTTAGTGGCGTTTTTGTCCA
* * *
20605329 AGCGCCGCTAATGCTC-GGAGCTTTAGTGGCGTTTTTATCTC-
1 AGCGCCGCTAATCCTCTGG-CCTTTAGTGGCGTTTTTGTC-CA
* *
20605370 AGCGCCACTAATCCTCTGGCCTTTAGTGGCGTTTTTGTCTA
1 AGCGCCGCTAATCCTCTGGCCTTTAGTGGCGTTTTTGTCCA
* * * * **
20605411 AGCGCCGCTAATGCTC-GGATCTTTAGTGACGTTTTTATCTG
1 AGCGCCGCTAATCCTCTGG-CCTTTAGTGGCGTTTTTGTCCA
* * * *
20605452 AGCGCCACTAATTCTCCT-GCCTTTAGCGGCGTTTGTT-TCTA
1 AGCGCCGCTAATCCT-CTGGCCTTTAGTGGCGTTT-TTGTCCA
*
20605493 TGCGCCGCTAAT
1 AGCGCCGCTAAT
20605505 AGTAACAAAA
Statistics
Matches: 143, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
40 7 0.05
41 129 0.90
42 7 0.05
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (41 bp):
AGCGCCGCTAATCCTCTGGCCTTTAGTGGCGTTTTTGTCCA
Found at i:20605390 original size:82 final size:81
Alignment explanation
Indices: 20605253--20605504 Score: 330
Period size: 82 Copynumber: 3.1 Consensus size: 81
20605243 GTGGCATGCT
* * ** *
20605253 GCTAATGCTCCGATCTTTAGCT-GCGTTTTTATATGAGCGCCGTTAAATCTCTGGCCTTTAGCGA
1 GCTAATGCTCGGATCTTTAG-TGGCGTTTTTATCTGAGCGCCACT-AATCTCTGGCCTTTAGCGG
*
20605317 CGTTTTTGTCCAAGCGCC
64 CGTTTTTGTCTAAGCGCC
* * *
20605335 GCTAATGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGGCCTTTAGTGGC
1 GCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAAT-CTCTGGCCTTTAGCGGC
20605400 GTTTTTGTCTAAGCGCC
65 GTTTTTGTCTAAGCGCC
*
20605417 GCTAATGCTCGGATCTTTAGTGACGTTTTTATCTGAGCGCCACTAATTCTCCT-GCCTTTAGCGG
1 GCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAA-TCT-CTGGCCTTTAGCGG
*
20605481 CGTTTGTT-TCTATGCGCC
64 CGTTT-TTGTCTAAGCGCC
20605499 GCTAAT
1 GCTAAT
20605505 AGTAACAAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
81 4 0.03
82 142 0.94
83 5 0.03
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (81 bp):
GCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATCTCTGGCCTTTAGCGGCG
TTTTTGTCTAAGCGCC
Found at i:20607208 original size:52 final size:52
Alignment explanation
Indices: 20607144--20607249 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
20607134 AATTAAAAAC
**
20607144 ATTTAACCCAAATTAATGGCCATTTGATATATATTTTGATATATATGGATAT
1 ATTTAACCCAAATTAACAGCCATTTGATATATATTTTGATATATATGGATAT
* *
20607196 ATTTAGCCCAAATTAACAGCCATTTGATATATTTTTTGATATATATGGATAT
1 ATTTAACCCAAATTAACAGCCATTTGATATATATTTTGATATATATGGATAT
20607248 AT
1 AT
20607250 ATATAGTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (52 bp):
ATTTAACCCAAATTAACAGCCATTTGATATATATTTTGATATATATGGATAT
Found at i:20607349 original size:27 final size:27
Alignment explanation
Indices: 20607319--20607370 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20607309 AATAAACAAA
* *
20607319 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTAATTATTTGT
**
20607346 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATAAGTAATTAATTATTT
20607371 AAATGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (27 bp):
TAAATAAATAAGTAATTAATTATTTGT
Found at i:20608235 original size:11 final size:11
Alignment explanation
Indices: 20608219--20608245 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20608209 TTTGTTTAAT
20608219 TTACTTTCATA
1 TTACTTTCATA
20608230 TTACTTTCATA
1 TTACTTTCATA
20608241 TTACT
1 TTACT
20608246 GGTTGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (11 bp):
TTACTTTCATA
Found at i:20610192 original size:21 final size:21
Alignment explanation
Indices: 20610163--20610215 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
20610153 ACATCTTTGA
* *
20610163 TATATATATTTATATACAGTTT
1 TATATATATTTAT-TAAAATTT
20610185 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
20610205 TATATATATTT
1 TATATATATTT
20610216 GAAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:20610324 original size:16 final size:16
Alignment explanation
Indices: 20610263--20610708 Score: 169
Period size: 16 Copynumber: 26.9 Consensus size: 16
20610253 ACACATAGCC
* *
20610263 TACATGACTTACTTAA
1 TACATAACTTACATAA
* *
20610279 TACACAACTTAAATAA
1 TACATAACTTACATAA
*
20610295 TTTAAATAACTTACATAA
1 --TACATAACTTACATAA
20610313 TACATAACTTACAT--
1 TACATAACTTACATAA
20610327 T-CATAACTTACATAA
1 TACATAACTTACATAA
20610342 -ACTTATATGTTACCTTACATAA
1 TAC--ATA----A-CTTACATAA
*
20610364 TACATAACTTATATAA
1 TACATAACTTACATAA
** *
20610380 -A-AT-TTTTATATAAA
1 TACATAACTTACAT-AA
20610394 CTTACATAA--TACATAGCA
1 --TACATAACTTACATA--A
20610412 TACATAACTTACATAA
1 TACATAACTTACATAA
*
20610428 TACAAAACTTACATAA
1 TACATAACTTACATAA
* * *
20610444 CTTAAATATCTTACACAA
1 --TACATAACTTACATAA
*
20610462 CTTACATAACCTACATAA
1 --TACATAACTTACATAA
20610480 TACATAACTTACATAA
1 TACATAACTTACATAA
20610496 CTTACATAACTTACATAA
1 --TACATAACTTACATAA
*
20610514 TACATAA-TAAC-T--
1 TACATAACTTACATAA
20610526 TAC--AACTTACATAACA
1 TACATAACTTACAT-A-A
**
20610542 TACATTAA-TTTGATAA
1 TACA-TAACTTACATAA
*
20610558 CTTACATAAGTTACATAA
1 --TACATAACTTACATAA
*
20610576 TACATAACTTACA-ACT
1 TACATAACTTACATA-A
*
20610592 TACATAACATACATTAA
1 TACATAACTTACA-TAA
***
20610609 TTTGGTAACTTACATAA
1 -TACATAACTTACATAA
20610626 GTTACATAA--TACATAA
1 --TACATAACTTACATAA
20610642 CTTAC--AACTTACATAACA
1 --TACATAACTTACAT-A-A
* **
20610660 TACATTACTTTGATAA
1 TACATAACTTACATAA
*
20610676 CTTACATAAGTTACATAA
1 --TACATAACTTACATAA
*
20610694 TACACAACTTACATA
1 TACATAACTTACATA
20610709 GCTTACTTAA
Statistics
Matches: 328, Mismatches: 50, Indels: 104
0.68 0.10 0.22
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 4 0.01
13 18 0.05
14 8 0.02
15 6 0.02
16 140 0.43
17 18 0.05
18 112 0.34
19 2 0.01
21 4 0.01
22 9 0.03
23 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:20610325 original size:9 final size:9
Alignment explanation
Indices: 20610279--20610765 Score: 277
Period size: 9 Copynumber: 56.3 Consensus size: 9
20610269 ACTTACTTAA
*
20610279 TACACAACT
1 TACATAACT
* *
20610288 TAAATAATT
1 TACATAACT
*
20610297 TAAATAACT
1 TACATAACT
20610306 TACATAA--
1 TACATAACT
20610313 TACATAACT
1 TACATAACT
20610322 TAC---A-T
1 TACATAACT
20610327 T-CATAACT
1 TACATAACT
20610335 TACATAAACT
1 TACAT-AACT
* *
20610345 TATATGTTACCT
1 TACA---TAACT
20610357 TACATAA--
1 TACATAACT
20610364 TACATAACT
1 TACATAACT
* *
20610373 TATATAAAATTTT
1 TACAT--AA--CT
*
20610386 TATATAAACT
1 TACAT-AACT
20610396 TACATAA--
1 TACATAACT
* *
20610403 TACATAGCA
1 TACATAACT
20610412 TACATAACT
1 TACATAACT
20610421 TACATAA--
1 TACATAACT
*
20610428 TACAAAACT
1 TACATAACT
20610437 TACATAACT
1 TACATAACT
* *
20610446 TAAATATCT
1 TACATAACT
*
20610455 TACACAACT
1 TACATAACT
*
20610464 TACATAACC
1 TACATAACT
20610473 TACATAA--
1 TACATAACT
20610480 TACATAACT
1 TACATAACT
20610489 TACATAACT
1 TACATAACT
20610498 TACATAACT
1 TACATAACT
*
20610507 TACATAATACA
1 TACAT-A-ACT
20610518 TA-ATAACT
1 TACATAACT
20610526 TAC--AACT
1 TACATAACT
*
20610533 TACATAACA
1 TACATAACT
20610542 TACATTAA-T
1 TACA-TAACT
**
20610551 TTGATAACT
1 TACATAACT
*
20610560 TACATAAGT
1 TACATAACT
20610569 TACATAA--
1 TACATAACT
20610576 TACATAACT
1 TACATAACT
20610585 TAC--AACT
1 TACATAACT
*
20610592 TACATAACA
1 TACATAACT
20610601 TACATTAA-T
1 TACA-TAACT
***
20610610 TTGGTAACT
1 TACATAACT
*
20610619 TACATAAGT
1 TACATAACT
20610628 TACATAA--
1 TACATAACT
20610635 TACATAACT
1 TACATAACT
20610644 TAC--AACT
1 TACATAACT
*
20610651 TACATAACA
1 TACATAACT
*
20610660 TACATTACT
1 TACATAACT
**
20610669 TTGATAACT
1 TACATAACT
*
20610678 TACATAAGT
1 TACATAACT
20610687 TACATAA--
1 TACATAACT
*
20610694 TACACAACT
1 TACATAACT
*
20610703 TACATAGCT
1 TACATAACT
*
20610712 TACTTAA--
1 TACATAACT
*
20610719 TACATGACT
1 TACATAACT
20610728 TACATAACT
1 TACATAACT
*
20610737 T--ATACACG
1 TACATA-ACT
20610745 TACATAACT
1 TACATAACT
*
20610754 TACATAATT
1 TACATAACT
20610763 TAC
1 TAC
20610766 TTAATACATA
Statistics
Matches: 368, Mismatches: 63, Indels: 94
0.70 0.12 0.18
Matches are distributed among these distances:
4 1 0.00
5 2 0.01
6 1 0.00
7 83 0.23
8 15 0.04
9 220 0.60
10 24 0.07
11 6 0.02
12 9 0.02
13 7 0.02
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (9 bp):
TACATAACT
Found at i:20610333 original size:13 final size:15
Alignment explanation
Indices: 20610300--20610340 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
20610290 AATAATTTAA
20610300 ATAACTTACATAATAC
1 ATAACTTACAT-ATAC
20610316 ATAACTTACAT-T-C
1 ATAACTTACATATAC
20610329 ATAACTTACATA
1 ATAACTTACATA
20610341 AACTTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAACTTACATATAC
Found at i:20610372 original size:38 final size:38
Alignment explanation
Indices: 20610328--20610520 Score: 125
Period size: 34 Copynumber: 5.1 Consensus size: 38
20610318 AACTTACATT
* * *
20610328 CATAACTTACATAAACTTATATGTTACCTTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
* * *
20610366 CATAACTTATATAAAATTTTTATATAAACTTACATAATA
1 CATAACTTACAT-AAACTTATATATAAACTTACATAATA
* * *
20610405 CATAGCATACAT-AACTTACATAATACAAAACTTACATAACTTA
1 CATAACTTACATAAACTT--AT-ATA-TAAACTTACATAA--TA
* * * * *
20610448 AATATCTTACA-CAAC-T-TACAT-AACCTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
*
20610482 CATAACTTACAT-AAC-T-TACAT-AACTTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
20610516 CATAA
1 CATAA
20610521 TAACTTACAA
Statistics
Matches: 125, Mismatches: 21, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
34 37 0.30
36 10 0.08
37 4 0.03
38 13 0.10
39 32 0.26
40 3 0.02
41 12 0.10
42 1 0.01
43 13 0.10
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (38 bp):
CATAACTTACATAAACTTATATATAAACTTACATAATA
Found at i:20610420 original size:25 final size:25
Alignment explanation
Indices: 20610392--20610761 Score: 201
Period size: 25 Copynumber: 14.5 Consensus size: 25
20610382 TTTTTATATA
* *
20610392 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACATAACTTACAT
*
20610417 AACTTACATAATACAAAACTTACAT
1 AACTTACATAATACATAACTTACAT
* * *
20610442 AACTTAAATATCTTACACAACTTACAT
1 AACTTACATA--ATACATAACTTACAT
*
20610469 AACCTACATAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
*
20610494 AACTTACATAACTTACATAATACATA-AT
1 AACTTACATAA--TACAT-A-ACTTACAT
* *
20610522 AACTTACA-ACTTACATAACATACATT
1 AACTTACATA-ATACATAACTTACA-T
** *
20610548 AA-TTTGATAACTTACATAAGTTACAT
1 AACTTACATAA--TACATAACTTACAT
20610574 AA--TACATAACTTAC--AACTTACAT
1 AACTTACATAA--TACATAACTTACAT
* ***
20610597 AACATACATTAATTTGGTAACTTACAT
1 AACTTACA-TAA-TACATAACTTACAT
*
20610624 AAGTTACATAATACATAACTTAC--
1 AACTTACATAATACATAACTTACAT
* **
20610647 AACTTACATAACATACATTACTTTGAT
1 AACTTACAT-A-ATACATAACTTACAT
*
20610674 AACTTACATAAGTTACATAA--TACAC
1 AACTTACATAA--TACATAACTTACAT
* *
20610699 AACTTACATAGCTTACTTAA--TACAT
1 AACTTACATA--ATACATAACTTACAT
* * *
20610724 GACTTACATAACT-TATACACGTACAT
1 AACTTACATAA-TACATA-ACTTACAT
20610750 AACTTACATAAT
1 AACTTACATAAT
20610762 TTACTTAATA
Statistics
Matches: 272, Mismatches: 44, Indels: 58
0.73 0.12 0.16
Matches are distributed among these distances:
23 20 0.07
24 8 0.03
25 127 0.47
26 34 0.12
27 68 0.25
28 11 0.04
29 4 0.01
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:20610470 original size:52 final size:52
Alignment explanation
Indices: 20610412--20610510 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
20610402 ATACATAGCA
* *
20610412 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACT
1 TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACACAACT
* *
20610464 TACATAACCTACATAATACATAACTTACATAACTTACATAACTTACA
1 TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACA
20610511 TAATACATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.30
Consensus pattern (52 bp):
TACATAACCTACATAATACAAAACTTACATAACTTAAATAACTTACACAACT
Found at i:20610484 original size:43 final size:41
Alignment explanation
Indices: 20610412--20610776 Score: 168
Period size: 43 Copynumber: 8.7 Consensus size: 41
20610402 ATACATAGCA
* *
20610412 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCT
1 TACATAACTTACATAATACATAA--TACATAACTTAAATAACT
* *
20610455 TACACAACTTACATAACCTACATAATACATAACTTACATAACT
1 TACATAACTTACATAA--TACATAATACATAACTTAAATAACT
*
20610498 TACATAACTTACATAATAC---ATA-ATAACTT--ACAACT
1 TACATAACTTACATAATACATAATACATAACTTAAATAACT
* ** * *
20610533 TACATAACATACATTAATTTGATAACTTACATAAGTTACATAA--
1 TACATAACTTACA-TAA-TACATAA--TACATAACTTAAATAACT
* ***
20610576 TACATAACTTACA-ACTTACATAACATACATTAA-TTTGGTAACT
1 TACATAACTTACATA-ATACAT-A-ATACA-TAACTTAAATAACT
* * *
20610619 TACATAAGTTACATAATACATAACTTAC--AACTTACATAACA
1 TACATAACTTACATAATACATAA--TACATAACTTAAATAACT
* ** * *
20610660 TACATTACTTTGATAACTTACATAAGTTACATAA--TACACAACT
1 TACATAACTTACATAA--TACATAA--TACATAACTTAAATAACT
* * * *
20610703 TACATAGCTTACTTAATACATGACTTACATAACTT--ATACACG
1 TACATAACTTACATAATACAT-A-ATACATAACTTAAATA-ACT
*
20610745 TACATAACTTACATAATTTACTTAATACATAA
1 TACATAACTTACATAA--TACATAATACATAA
20610777 ATTATGTAAC
Statistics
Matches: 246, Mismatches: 43, Indels: 67
0.69 0.12 0.19
Matches are distributed among these distances:
35 17 0.07
36 3 0.01
37 8 0.03
38 3 0.01
40 3 0.01
41 49 0.20
42 31 0.13
43 116 0.47
44 5 0.02
45 11 0.04
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (41 bp):
TACATAACTTACATAATACATAATACATAACTTAAATAACT
Found at i:20610608 original size:59 final size:59
Alignment explanation
Indices: 20610492--20610706 Score: 367
Period size: 59 Copynumber: 3.6 Consensus size: 59
20610482 CATAACTTAC
*
20610492 ATAACTTACATAACTTACATAATACATAATAACTTACAACTTACATAACATACATTAATTTG
1 ATAACTTACATAAGTTACATAATAC---ATAACTTACAACTTACATAACATACATTAATTTG
20610554 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTAATTTG
1 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTAATTTG
* *
20610613 GTAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTACTTTG
1 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTAATTTG
*
20610672 ATAACTTACATAAGTTACATAATACACAACTTACA
1 ATAACTTACATAAGTTACATAATACATAACTTACA
20610707 TAGCTTACTT
Statistics
Matches: 148, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
59 124 0.84
62 24 0.16
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (59 bp):
ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTAATTTG
Found at i:20610722 original size:118 final size:119
Alignment explanation
Indices: 20610455--20610738 Score: 389
Period size: 118 Copynumber: 2.4 Consensus size: 119
20610445 TTAAATATCT
* *
20610455 TACACAACTTACATAACCTACATAATACA-TAACTTACATAACTTACATAACTTACATAATACAT
1 TACACAACTTACAT-ACTTACTTAATACATTAACTTACATAACTTACATAACTTACATAATAC--
20610519 AATAACTTACAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAA
63 AATAACTTACAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAA
* * *** *
20610576 TACATAACTTACA-ACTTACATAACATACATTAA-TTTGGTAACTTACATAAGTTACATAATAC-
1 TACACAACTTACATACTTAC-TTA-ATACATTAACTTACATAACTTACATAACTTACATAATACA
*
20610638 ATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAAGTTACATAA
64 ATAACTTACAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAA
*
20610694 TACACAACTTACATAGCTTACTTAATACA-TGACTTACATAACTTA
1 TACACAACTTACATA-CTTACTTAATACATTAACTTACATAACTTA
20610739 TACACGTACA
Statistics
Matches: 142, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
117 2 0.01
118 81 0.57
119 8 0.06
120 6 0.04
121 42 0.30
122 3 0.02
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (119 bp):
TACACAACTTACATACTTACTTAATACATTAACTTACATAACTTACATAACTTACATAATACAAT
AACTTACAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAA
Found at i:20610735 original size:59 final size:59
Alignment explanation
Indices: 20610479--20610738 Score: 335
Period size: 59 Copynumber: 4.4 Consensus size: 59
20610469 AACCTACATA
* *
20610479 ATACATAACTTACATAACTTACATAACTTACATAATACATAATAACTTACAACTTACATAAC
1 ATACATTACTTACATAACTTACATAAGTTACATAATAC---ATAACTTACAACTTACATAAC
* **
20610541 ATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAAC
1 ATACATTACTTACATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAAC
* ***
20610600 ATACATTAATTTGGTAACTTACATAAGTTACATAATACATAACTTACAACTTACATAAC
1 ATACATTACTTACATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAAC
** * *
20610659 ATACATTACTTTGATAACTTACATAAGTTACATAATACACAACTTACATAGCTTAC-TTA-
1 ATACATTACTTACATAACTTACATAAGTTACATAATACATAACTTACA-A-CTTACATAAC
*
20610718 ATACATGACTTACATAACTTA
1 ATACATTACTTACATAACTTA
20610739 TACACGTACA
Statistics
Matches: 183, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
59 142 0.78
60 3 0.02
61 5 0.03
62 33 0.18
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (59 bp):
ATACATTACTTACATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAAC
Found at i:20613790 original size:29 final size:29
Alignment explanation
Indices: 20613748--20613807 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
20613738 AATACTGAGA
*
20613748 TCTCATTCGCGCTCCCGAAGAACACAGCT
1 TCTCATTCGCGCTCCCGAAGAACACAACT
*
20613777 TCTCGTTCGCGCTCCCGAAGAACACAACT
1 TCTCATTCGCGCTCCCGAAGAACACAACT
20613806 TC
1 TC
20613808 GAGACATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.22
Consensus pattern (29 bp):
TCTCATTCGCGCTCCCGAAGAACACAACT
Found at i:20617211 original size:98 final size:97
Alignment explanation
Indices: 20617042--20617229 Score: 340
Period size: 98 Copynumber: 1.9 Consensus size: 97
20617032 AAAGTTGGAT
*
20617042 GCCTTCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCA
1 GCCTTCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAAACCTATGACTCCTGAAGCTGCA
*
20617107 GAAATTATGGTACGTTTGCTTAATNAGTTAGAC
66 GAAATTATGGTACGTTCGCTTAAT-AGTTAGAC
*
20617140 GCCTTCAACTTTTTTACATTACACATAGGAAGAAAGATGGAAAACCTATGACTCCTGAAGCTGCA
1 GCCTTCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAAACCTATGACTCCTGAAGCTGCA
20617205 GAAATTATGGTACGTTCGCTTAATA
66 GAAATTATGGTACGTTCGCTTAATA
20617230 CAATTTGACT
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
97 1 0.01
98 86 0.99
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (97 bp):
GCCTTCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAAACCTATGACTCCTGAAGCTGCA
GAAATTATGGTACGTTCGCTTAATAGTTAGAC
Found at i:20617706 original size:21 final size:21
Alignment explanation
Indices: 20617682--20617732 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20617672 CTACAACTTA
* *
20617682 AAGCAGATGCGGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
*
20617703 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAG
*
20617724 AAGCTGAGG
1 AAGCAGAGG
20617733 TTCAACGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:20617785 original size:21 final size:21
Alignment explanation
Indices: 20617761--20617819 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
20617751 AACTCCAGCA
*
20617761 GCAGCGAGAGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
* ** *
20617782 GCAGTGAGGGAATTAAAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
*
20617803 GCAACGAGGGAAGCAGA
1 GCAGCGAGGGAAGCAGA
20617820 ACAGCGTAAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.41, T:0.08
Consensus pattern (21 bp):
GCAGCGAGGGAAGCAGAGGCT
Found at i:20618191 original size:43 final size:43
Alignment explanation
Indices: 20618126--20618638 Score: 636
Period size: 43 Copynumber: 11.9 Consensus size: 43
20618116 CAAAATTAGC
** * * *
20618126 GGCGTTTTTTGGGTAAGCGCCGCTAAAGAACACGGCCTATAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
20618169 GGCATTTTTCGTATAAGCGCCGCTAAAGACCTTGGTCTATAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
20618212 GACGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTCTAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
20618255 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATCGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
20618298 GGC-TTTTTTGGCTAAGCGCTGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
20618340 GGCGTTTTTTGTCTAAACGCCGCTAAAGACAATGGCCTATAAT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
20618383 GGCGTTTTTTTGTCCAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCG-TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * * *
20618427 GGCGTTTTTTGTCCAATCGCCGCTAAAAAACACGGTCTATAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
20618470 GGCATTTTTTGTCCAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
20618513 GGCGTTTTATGTAC-AAACGCCGCTAAAAGACCATGATCTATAGT
1 GGCGTTTTTTGT-CTAAGCGCCGCT-AAAGACCATGGTCTATAGT
* * * * * *
20618557 GGCGTTTTTTGTAT-AGCGGCGCGAAAGACTATGGCCTATAGC
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
20618599 GGCGTTTTTTGTGTAAGCGCCGCTAAAGACCATAGTCTAT
1 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTAT
20618639 TGCGGCGCTT
Statistics
Matches: 403, Mismatches: 61, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
42 67 0.17
43 268 0.67
44 68 0.17
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:20628370 original size:27 final size:26
Alignment explanation
Indices: 20628336--20628447 Score: 93
Period size: 26 Copynumber: 4.1 Consensus size: 26
20628326 AAAATTTTGA
*
20628336 AAATTTAAAAAAATATAAAAATTATT
1 AAATATAAAAAAATATAAAAATTATT
* *
20628362 AAATCTTAAAAAAATATGAAAATTGATAT
1 AAAT-ATAAAAAAATATAAAAATT-AT-T
*
20628391 AGAATCATAAAAAAA-ATTATAAAATTATA
1 A-AAT-ATAAAAAAATA-TA-AAAATTATT
*
20628420 AAATAT-AAAAAATCTAATAAATTATT
1 AAATATAAAAAAATATAA-AAATTATT
20628446 AA
1 AA
20628448 TAAAACATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.01
26 21 0.29
27 20 0.28
28 5 0.07
29 4 0.06
30 15 0.21
31 6 0.08
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
AAATATAAAAAAATATAAAAATTATT
Found at i:20628404 original size:30 final size:27
Alignment explanation
Indices: 20628341--20628447 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
20628331 TTTGAAAATT
*
20628341 TAAAAAAATATAAAAATTATTAAATCT
1 TAAAAAAATATAAAAATTATTAAATCA
*
20628368 TAAAAAAATATGAAAATTGATATAGAATCA
1 TAAAAAAATATAAAAATT-AT-TA-AATCA
*
20628398 TAAAAAAA-ATTATAAAATTATAAAAT-A
1 TAAAAAAATA-TA-AAAATTATTAAATCA
*
20628425 T-AAAAAATCTAATAAATTATTAA
1 TAAAAAAATATAA-AAATTATTAA
20628448 TAAAACATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.01
26 17 0.25
27 19 0.28
28 5 0.07
29 4 0.06
30 15 0.22
31 6 0.09
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAAAAAATATAAAAATTATTAAATCA
Found at i:20628471 original size:21 final size:23
Alignment explanation
Indices: 20628438--20628484 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
20628428 AAAATCTAAT
20628438 AAATTATTAATAAAACATATTTA
1 AAATTATTAATAAAACATATTTA
*
20628461 AAATT-TT-ATAAAACCTATTTA
1 AAATTATTAATAAAACATATTTA
20628482 AAA
1 AAA
20628485 ACTATACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 2 0.09
23 5 0.22
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTATTAATAAAACATATTTA
Found at i:20628550 original size:10 final size:9
Alignment explanation
Indices: 20628297--20628559 Score: 74
Period size: 9 Copynumber: 27.6 Consensus size: 9
20628287 TTTTTTCATA
20628297 AAAATATTA-
1 AAAA-ATTAT
20628306 AAAAATTAT
1 AAAAATTAT
* *
20628315 AAGGAATTAG
1 AA-AAATTAT
*
20628325 AAAAATTTT
1 AAAAATTAT
*
20628334 GAAAATT-T
1 AAAAATTAT
*
20628342 AAAAAAATAT
1 -AAAAATTAT
20628352 AAAAATTATT
1 AAAAATTA-T
**
20628362 AAATCTTA-
1 AAAAATTAT
*
20628370 AAAAAATAT
1 AAAAATTAT
*
20628379 GAAAATTGAT
1 AAAAATT-AT
* *
20628389 ATAGAATCATAAA
1 A-A-AA--ATTAT
20628402 AAAAATTAT
1 AAAAATTAT
20628411 -AAAATTAT
1 AAAAATTAT
20628419 -AAAA-TAT
1 AAAAATTAT
20628426 AAAAAATCTAAT
1 -AAAAAT-T-AT
*
20628438 AAATTATTAAT
1 AAA-AATT-AT
*
20628449 AAAACATATTT
1 AAAA-AT-TAT
*
20628460 AAAATTTTAT
1 AAAA-ATTAT
20628470 AAAACCTATT-T
1 AAAA---ATTAT
*
20628481 AAAAACTAT
1 AAAAATTAT
* *
20628490 ACAAATCAT
1 AAAAATTAT
20628499 AAAAATTAT
1 AAAAATTAT
20628508 AAAAA-TAT
1 AAAAATTAT
* *
20628516 TAAAAGTAT
1 AAAAATTAT
*
20628525 GAAAATTGAT
1 AAAAATT-AT
*
20628535 ATAAATTTAT
1 A-AAAATTAT
20628545 AAAAATTATT
1 AAAAATTA-T
20628555 AAAAA
1 AAAAA
20628560 AACATAAAGA
Statistics
Matches: 188, Mismatches: 40, Indels: 51
0.67 0.14 0.18
Matches are distributed among these distances:
7 3 0.02
8 31 0.16
9 73 0.39
10 34 0.18
11 32 0.17
12 11 0.06
13 2 0.01
14 2 0.01
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20629442 original size:23 final size:24
Alignment explanation
Indices: 20629415--20629462 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
20629405 TTTTTAATTA
* *
20629415 TTTTAAAGAACTCT-AATAAGTTT
1 TTTTAAAAAAATCTAAATAAGTTT
*
20629438 TTTTAAAAAAATTTAAATAAGTTT
1 TTTTAAAAAAATCTAAATAAGTTT
20629462 T
1 T
20629463 ACTAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
TTTTAAAAAAATCTAAATAAGTTT
Found at i:20629577 original size:18 final size:19
Alignment explanation
Indices: 20629551--20629595 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
20629541 TTTTAATATT
*
20629551 TAATATTTA-ATATTTTTA
1 TAATTTTTAGATATTTTTA
*
20629569 TAATTTTTATGATTTTTTTA
1 TAATTTTTA-GATATTTTTA
20629589 TAATTTT
1 TAATTTT
20629596 AATGAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TAATTTTTAGATATTTTTA
Found at i:20629588 original size:20 final size:20
Alignment explanation
Indices: 20629563--20629600 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20629553 ATATTTAATA
*
20629563 TTTTTATAATTTTTATGATT
1 TTTTTATAATTTTAATGATT
20629583 TTTTTATAATTTTAATGA
1 TTTTTATAATTTTAATGA
20629601 AAATATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTTATAATTTTAATGATT
Found at i:20637785 original size:54 final size:54
Alignment explanation
Indices: 20637681--20637785 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
20637671 AAACAGGGGT
* * * * *
20637681 CACACGGTTGTGTCCCAGCCTGTGTCTCTACTCATGTAACTCACTGACTTGAGA
1 CACAAGGTCGTGTCCCAGCCCGTGTCTCTACCCATGTAACTCACTAACTTGAGA
* * * *
20637735 CACAAGGTCGTGTCCCAGCCCGTGTCTTTGCCCGTGTAACTCATTAACTTG
1 CACAAGGTCGTGTCCCAGCCCGTGTCTCTACCCATGTAACTCACTAACTTG
20637786 GGTCACACGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (54 bp):
CACAAGGTCGTGTCCCAGCCCGTGTCTCTACCCATGTAACTCACTAACTTGAGA
Found at i:20641641 original size:11 final size:10
Alignment explanation
Indices: 20641628--20641696 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
20641618 TAAAAAAAGT
20641628 ATTTTAAAAA
1 ATTTTAAAAA
20641638 TATTTT--AAA
1 -ATTTTAAAAA
*
20641647 A-TTAAAAAA
1 ATTTTAAAAA
**
20641656 ATTAAAAAAA
1 ATTTTAAAAA
20641666 GTATTTTAAAAA
1 --ATTTTAAAAA
*
20641678 AATTTAAAAA
1 ATTTTAAAAA
20641688 ATTTTAAAA
1 ATTTTAAAA
20641697 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 7 0.15
10 24 0.51
11 5 0.11
12 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:20641663 original size:10 final size:9
Alignment explanation
Indices: 20641644--20641715 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
20641634 AAAATATTTT
20641644 AAAATTAAA
1 AAAATTAAA
20641653 AAAATTAAAA
1 AAAATT-AAA
20641663 AAAGTATTTTAAA
1 AAA--A--TTAAA
*
20641676 AAAATTTAA
1 AAAATTAAA
**
20641685 AAAATT-TT
1 AAAATTAAA
20641693 AAAATTAAA
1 AAAATTAAA
20641702 AAAATTTAAA
1 AAAA-TTAAA
20641712 AAAA
1 AAAA
20641716 GTATTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
8 6 0.12
9 20 0.39
10 15 0.29
11 1 0.02
12 1 0.02
13 6 0.12
14 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAATTAAA
Found at i:20641664 original size:40 final size:39
Alignment explanation
Indices: 20641605--20641744 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 39
20641595 ATTTCAAAAA
20641605 TTAAAA-T-AAAAATTAAAAAAAGTATTTTAAAAATATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
*
20641642 TTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAATT
1 TTAAAATT-AAAAAATTAAAAAAAGTATTTTAAAAATATT
* ** **
20641682 TAAAAAATTTTAAAATTAAAAAAA-T-TTAAAAAAAGTATT
1 T-TAAAATTAAAAAATTAAAAAAAGTATTTTAAAAA-TATT
*
20641721 TTAAAATTTAAAAAATAAAAAAAA
1 TTAAAA-TTAAAAAATTAAAAAAA
20641745 ATAAAAATAT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
37 6 0.07
38 12 0.14
39 19 0.22
40 43 0.50
41 6 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (39 bp):
TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
Found at i:20641696 original size:49 final size:51
Alignment explanation
Indices: 20641630--20641726 Score: 180
Period size: 50 Copynumber: 1.9 Consensus size: 51
20641620 AAAAAAGTAT
20641630 TTTAAAAATATTTTAAAATTAAAAAAA-TTAAAAAAAGTATTTTAAAAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAAAA
20641680 TTTAAAAA-ATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAA
20641727 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 18 0.39
50 28 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (51 bp):
TTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAAAA
Found at i:20641727 original size:30 final size:28
Alignment explanation
Indices: 20641671--20641746 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 28
20641661 AAAAAGTATT
20641671 TTAAAAAAATTT--AAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAAAAATTTTAAAA
20641697 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTTAAAAAAA--ATTTTAAAA
* *
20641727 TTTAAAAAA-TAAAAAAAAAT
1 TTAAAAAAATTTAAAAAAAAT
20641747 AAAAATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 12 0.27
27 2 0.05
28 5 0.11
29 8 0.18
30 17 0.39
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
TTAAAAAAATTTAAAAAAAATTTTAAAA
Found at i:20641745 original size:40 final size:40
Alignment explanation
Indices: 20641650--20641751 Score: 100
Period size: 50 Copynumber: 2.4 Consensus size: 40
20641640 TTTTAAAATT
20641650 AAAAAAATTAAAAAAAGTATTTTAAAAAAATTTAAAAAATTTTAAAA
1 AAAAAAATTAAAAAAAGTATTTT--AAAAATTTAAAAAA---T--AA
20641697 TTAAAAAAATTTAAAAAAAGTATTTT-AAAATTTAAAAAATAA
1 --AAAAAAA-TTAAAAAAAGTATTTTAAAAATTTAAAAAATAA
20641739 AAAAAAA-TAAAAA
1 AAAAAAATTAAAAA
20641752 TATTTATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
38 6 0.12
40 7 0.13
42 2 0.04
44 1 0.02
47 13 0.25
49 7 0.13
50 16 0.31
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (40 bp):
AAAAAAATTAAAAAAAGTATTTTAAAAATTTAAAAAATAA
Found at i:20643560 original size:26 final size:27
Alignment explanation
Indices: 20643517--20643570 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
20643507 AAACTAAATT
*
20643517 ATAATTATTTTTAAATGTGTAATTATC
1 ATAATTATTTTTAAATGTATAATTATC
20643544 ATAATT-TTTTTAAATGTATAATTATC
1 ATAATTATTTTTAAATGTATAATTATC
20643570 A
1 A
20643571 CAACTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (27 bp):
ATAATTATTTTTAAATGTATAATTATC
Found at i:20645802 original size:3 final size:3
Alignment explanation
Indices: 20645794--20645834 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
20645784 AAGGGCTAGC
*
20645794 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20645835 TTCTTGAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20647564 original size:18 final size:17
Alignment explanation
Indices: 20647538--20647573 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20647528 TTTGGTTATA
20647538 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
20647556 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
20647573 T
1 T
20647574 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:20654687 original size:25 final size:25
Alignment explanation
Indices: 20654642--20654698 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
20654632 AGCTCTTTCT
* * **
20654642 AGCTGAATAATGGGAACCTCATGCG
1 AGCTGAATAACGGAAACCTCATAAG
*
20654667 AGCTGAATAACGGAAAGCTCATAAG
1 AGCTGAATAACGGAAACCTCATAAG
20654692 AGCTGAA
1 AGCTGAA
20654699 ATCGGTGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.18
Consensus pattern (25 bp):
AGCTGAATAACGGAAACCTCATAAG
Found at i:20662127 original size:25 final size:25
Alignment explanation
Indices: 20662098--20662156 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
20662088 TAAGCTCTTT
*
20662098 CGAGCTGAATAACGGGAACCTCATG
1 CGAGCTGAATAACGGGAACCTCATA
* *
20662123 CGAGCTGAATAACGTGAAGCTCATA
1 CGAGCTGAATAACGGGAACCTCATA
*
20662148 AGAGCTGAA
1 CGAGCTGAA
20662157 ATCAGTGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (25 bp):
CGAGCTGAATAACGGGAACCTCATA
Found at i:20669811 original size:22 final size:24
Alignment explanation
Indices: 20669769--20669813 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
20669759 CTACTAAGTT
20669769 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
20669793 TACTT-CTTTTCT-ACTTAATTC
1 TACTTACTTTTCTAACTTAATTC
20669814 TTTGCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.53
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:20670132 original size:12 final size:12
Alignment explanation
Indices: 20670115--20670147 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
20670105 TAGTTTTTCC
20670115 TTTCTTTCTCTT
1 TTTCTTTCTCTT
20670127 TTTCTTTCTCTT
1 TTTCTTTCTCTT
20670139 TTTCTTTCT
1 TTTCTTTCT
20670148 TTCTCCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTTCTCTT
Found at i:20670133 original size:16 final size:16
Alignment explanation
Indices: 20670108--20670152 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 16
20670098 TAAACCCTAG
20670108 TTTTTCCTTTCTTTCTC
1 TTTTT-CTTTCTTTCTC
20670125 ---TT-TTTCTTTCTC
1 TTTTTCTTTCTTTCTC
20670137 TTTTTCTTTCTTTCTC
1 TTTTTCTTTCTTTCTC
20670153 CCCTATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
12 10 0.42
14 2 0.08
15 2 0.08
16 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTCTTTCTC
Found at i:20670244 original size:19 final size:19
Alignment explanation
Indices: 20670197--20670233 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20670187 CTGTTTCTTT
20670197 CTTTCTTTTATTTCATTTG
1 CTTTCTTTTATTTCATTTG
20670216 CTTTCTTTTATTTCATTT
1 CTTTCTTTTATTTCATTT
20670234 CATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.16, G:0.03, T:0.70
Consensus pattern (19 bp):
CTTTCTTTTATTTCATTTG
Found at i:20672449 original size:10 final size:10
Alignment explanation
Indices: 20672434--20672460 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20672424 ATTTTCCACC
20672434 GTACCATGCT
1 GTACCATGCT
20672444 GTACCATGCT
1 GTACCATGCT
20672454 GTACCAT
1 GTACCAT
20672461 TTCCCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (10 bp):
GTACCATGCT
Found at i:20673151 original size:15 final size:15
Alignment explanation
Indices: 20673131--20673167 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
20673121 TGTAAGTAAA
20673131 CTTTTACCCTTTACT
1 CTTTTACCCTTTACT
20673146 CTTTTACCCTTTACT
1 CTTTTACCCTTTACT
20673161 CTATTTA
1 CT-TTTA
20673168 ATCATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.54
Consensus pattern (15 bp):
CTTTTACCCTTTACT
Found at i:20678205 original size:16 final size:16
Alignment explanation
Indices: 20678172--20678218 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
20678162 AAACTTTTAA
*
20678172 GTTCTTTGTT-TTTGTT
1 GTTCTTTCTTCTTT-TT
20678188 GTTCTTTCTTCTTTTT
1 GTTCTTTCTTCTTTTT
*
20678204 GTTTTTTCTTCTTTT
1 GTTCTTTCTTCTTTT
20678219 CTGCGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.77
Consensus pattern (16 bp):
GTTCTTTCTTCTTTTT
Found at i:20680156 original size:15 final size:16
Alignment explanation
Indices: 20680136--20680165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20680126 TGGTACGTTG
20680136 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
20680151 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
20680166 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:20687630 original size:79 final size:79
Alignment explanation
Indices: 20687547--20687706 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 79
20687537 AATCTCATCA
* *
20687547 AATCAATTATACTTAATATAATAATACAAAAGATCATAAAATCAACTTATATCTTCATGGATTAC
1 AATCAATTATACTTAATATAAGAATACAAAAGATCATAAAATCAACTCATATCTTCATGGATTAC
*
20687612 ATATCTCAATATAT
66 ATATCTCAACATAT
* * * * * * **
20687626 AATCAATTGTCCTTAATATAAGGATACAAAAGATCATAAAGTTATCTCATATCTTCATGGATTGT
1 AATCAATTATACTTAATATAAGAATACAAAAGATCATAAAATCAACTCATATCTTCATGGATTAC
20687691 ATATCTCAACATAT
66 ATATCTCAACATAT
20687705 AA
1 AA
20687707 GGTAAATGGA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (79 bp):
AATCAATTATACTTAATATAAGAATACAAAAGATCATAAAATCAACTCATATCTTCATGGATTAC
ATATCTCAACATAT
Found at i:20704112 original size:20 final size:21
Alignment explanation
Indices: 20704087--20704138 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20704077 CAGCCTTTAT
20704087 GGCTCAACATA-GGTTGATGG
1 GGCTCAACATAGGGTTGATGG
* *
20704107 GGCTCAACATAGGGTTGCTGT
1 GGCTCAACATAGGGTTGATGG
*
20704128 GGCTCAGCATA
1 GGCTCAACATA
20704139 AGGCTACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
GGCTCAACATAGGGTTGATGG
Found at i:20708465 original size:5 final size:5
Alignment explanation
Indices: 20708445--20708500 Score: 62
Period size: 5 Copynumber: 11.2 Consensus size: 5
20708435 AGTTCTATGC
* *
20708445 TTTAT TTATTT TTTAT TTTA- TTTA- TTTAGA TTTAT TTTAT TTTAT TTTAT
1 TTTAT TT-TAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
20708495 TTTAT T
1 TTTAT T
20708501 ATGCACTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
4 8 0.18
5 29 0.64
6 8 0.18
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:20712416 original size:11 final size:11
Alignment explanation
Indices: 20712400--20712424 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20712390 CATTTAAGAG
20712400 AAAATGAGTGA
1 AAAATGAGTGA
20712411 AAAATGAGTGA
1 AAAATGAGTGA
20712422 AAA
1 AAA
20712425 CAGAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAATGAGTGA
Found at i:20717992 original size:5 final size:6
Alignment explanation
Indices: 20717975--20717999 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20717965 AGGTAGTTTA
20717975 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
20718000 TTCCTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:20718767 original size:21 final size:22
Alignment explanation
Indices: 20718743--20718813 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 22
20718733 TTAGATTTCA
**
20718743 ATTTATTTTTGTAATTTAT-TT
1 ATTTATTTTTAAAATTTATATT
20718764 ATTTA-TTTTAAAATTTATATT
1 ATTTATTTTTAAAATTTATATT
*
20718785 ATTTA-TTTTAAAATTTTCTATT
1 ATTTATTTTTAAAA-TTTATATT
20718807 A-TTATTT
1 ATTTATTT
20718814 ATTTTAAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
20 11 0.25
21 23 0.52
22 10 0.23
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
ATTTATTTTTAAAATTTATATT
Found at i:20718809 original size:22 final size:21
Alignment explanation
Indices: 20718755--20718820 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 21
20718745 TTATTTTTGT
20718755 AATTTAT-TTATTTATTTTAA
1 AATTTATATTATTTATTTTAA
20718775 AATTTATATTATTTATTTTAA
1 AATTTATATTATTTATTTTAA
20718796 AATTTTCTATTATTATTTATTTTAA
1 AA--TT-TA-TATTATTTATTTTAA
20718821 GTTTTTCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.17
21 15 0.37
23 2 0.05
24 2 0.05
25 15 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTATATTATTTATTTTAA
Found at i:20718826 original size:25 final size:25
Alignment explanation
Indices: 20718762--20718846 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
20718752 TGTAATTTAT
20718762 TTATTTATTTTAAAA--TT--TATA
1 TTATTTATTTTAAAATTTTCATATA
20718783 TTATTTATTTTAAAATTTTC-TATTA
1 TTATTTATTTTAAAATTTTCATA-TA
**
20718808 TTATTTATTTTAAGTTTTTCATATA
1 TTATTTATTTTAAAATTTTCATATA
**
20718833 TTATCCATTTTAAA
1 TTATTTATTTTAAA
20718847 CTATTATATG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 15 0.28
23 2 0.04
24 2 0.04
25 33 0.61
26 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (25 bp):
TTATTTATTTTAAAATTTTCATATA
Found at i:20722301 original size:65 final size:64
Alignment explanation
Indices: 20722197--20722371 Score: 219
Period size: 65 Copynumber: 2.7 Consensus size: 64
20722187 TATTCTATTA
* ** * *
20722197 TTACCTTAATGAGGTAAAGCCA-TTTTAAAGAACTGTGCTATCTAAGTTTGCTTTAATGAA-CAG
1 TTACCTTAA-GAGGTAAAGCCACTTTT-AAGAAGTGTGCTATCTAAGTCCGCTTCAAAGAAGCA-
20722260 TG
63 TG
*
20722262 TTACCTTCAAGAGGTAAAGCCACTTTTAAGAAGTGTGCTATCTATGTCCGCTTCAAAGAAGCATG
1 TTACCTT-AAGAGGTAAAGCCACTTTTAAGAAGTGTGCTATCTAAGTCCGCTTCAAAGAAGCATG
* *
20722327 TTACCTTAAAGAGGTAAAGTCACTTTAAAGAAGTGTGCTATCTAA
1 TTACCTT-AAGAGGTAAAGCCACTTTTAAGAAGTGTGCTATCTAA
20722372 ATCCTCTTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
65 89 0.92
66 8 0.08
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (64 bp):
TTACCTTAAGAGGTAAAGCCACTTTTAAGAAGTGTGCTATCTAAGTCCGCTTCAAAGAAGCATG
Found at i:20722387 original size:16 final size:16
Alignment explanation
Indices: 20722366--20722398 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20722356 GAAGTGTGCT
20722366 ATCTAAATCCTCTTTA
1 ATCTAAATCCTCTTTA
*
20722382 ATCTAAATCCTTTTTA
1 ATCTAAATCCTCTTTA
20722398 A
1 A
20722399 AGAAGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (16 bp):
ATCTAAATCCTCTTTA
Found at i:20727300 original size:24 final size:23
Alignment explanation
Indices: 20727239--20727302 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 23
20727229 TTCTGACCCA
20727239 CAGCTCGTGTGAGCATTCTGATT
1 CAGCTCGTGTGAGCATTCTGATT
* *
20727262 CATAGCTCGTTTGAGCATTTTGATTT
1 C--AGCTCGTGTGAGCATTCTGA-TT
20727288 CAGCTCGTGTGAGCA
1 CAGCTCGTGTGAGCA
20727303 AACATTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 13 0.37
25 18 0.51
26 3 0.09
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (23 bp):
CAGCTCGTGTGAGCATTCTGATT
Found at i:20735430 original size:49 final size:47
Alignment explanation
Indices: 20735209--20735711 Score: 853
Period size: 47 Copynumber: 10.6 Consensus size: 47
20735199 CCCTTCGGGA
* * * * * *
20735209 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20735256 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20735303 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20735350 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735397 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735446 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735493 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735542 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735591 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20735638 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20735685 CCTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
20735712 TATTCAAATA
Statistics
Matches: 439, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
47 296 0.67
49 143 0.33
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20735438 original size:96 final size:94
Alignment explanation
Indices: 20735209--20735711 Score: 853
Period size: 96 Copynumber: 5.3 Consensus size: 94
20735199 CCCTTCGGGA
* * * * * * * *
20735209 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
20735274 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
20735303 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
20735368 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
20735397 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
20735462 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
20735493 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
20735558 ACACTTTCACATTCATCACATCGGCCATTAGGC
62 ACACTTTCACATTCATCACATCGGCCATTAGGC
20735591 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
20735656 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
20735685 CCTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
20735712 TATTCAAATA
Statistics
Matches: 392, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
94 156 0.40
96 189 0.48
98 47 0.12
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:20766416 original size:16 final size:16
Alignment explanation
Indices: 20766395--20766464 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
20766385 TTTGGTTCGC
* *
20766395 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
20766411 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
20766427 TGTAATAGAATAGAGG
1 TGTAATGGAATAGAGG
20766443 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
20766459 TGTAAT
1 TGTAAT
20766465 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:20766441 original size:32 final size:32
Alignment explanation
Indices: 20766405--20766466 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
20766395 TGTATTGGAT
* *
20766405 TAGAGGTGTATTGGATTAGAGGTGTAATAGAA
1 TAGAGGTGTAATGGAATAGAGGTGTAATAGAA
20766437 TAGAGGTGTAATGGAATAGAGGTGTAATAG
1 TAGAGGTGTAATGGAATAGAGGTGTAATAG
20766467 CAAATCAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (32 bp):
TAGAGGTGTAATGGAATAGAGGTGTAATAGAA
Found at i:20766497 original size:45 final size:44
Alignment explanation
Indices: 20766443--20766537 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
20766433 AGAATAGAGG
*
20766443 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
20766488 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
20766532 TGTAAT
1 TGTAAT
20766538 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:20766718 original size:18 final size:17
Alignment explanation
Indices: 20766697--20766731 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20766687 TTATTATTAA
*
20766697 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20766715 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20766732 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20770959 original size:44 final size:44
Alignment explanation
Indices: 20770909--20771059 Score: 257
Period size: 44 Copynumber: 3.4 Consensus size: 44
20770899 TTGTCCCTTG
* *
20770909 TCACTTGTCACTGGTCAGATAAGTGTAGCTAAAGCTACCATTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
*
20770953 TCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
*
20770997 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
*
20771041 ACACTTGTCACTGATCAGA
1 TCACTTGTCACTGATCAGA
20771060 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 101 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (44 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
Found at i:20775751 original size:17 final size:18
Alignment explanation
Indices: 20775726--20775762 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20775716 ATTTGACACT
*
20775726 TTTTTTCACTAT-CCAAA
1 TTTTCTCACTATACCAAA
20775743 TTTTCTCACTATACCAAA
1 TTTTCTCACTATACCAAA
20775761 TT
1 TT
20775763 AAAACCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTCTCACTATACCAAA
Found at i:20778017 original size:15 final size:16
Alignment explanation
Indices: 20777997--20778030 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20777987 TTTTTTTTTC
20777997 TTAC-AATTTAGTCAT
1 TTACAAATTTAGTCAT
*
20778012 TTACAAATTTAGTTAT
1 TTACAAATTTAGTCAT
20778028 TTA
1 TTA
20778031 ATTGATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (16 bp):
TTACAAATTTAGTCAT
Found at i:20788851 original size:50 final size:50
Alignment explanation
Indices: 20788670--20788945 Score: 233
Period size: 50 Copynumber: 5.6 Consensus size: 50
20788660 TTTTCTGTAC
* * * ** * *
20788670 TGCCAATGCCATATCCCAGATATGGTCTTACTTGGGAGTTATCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * **
20788720 TGCCCATGCCATGTCCCAAACATGGTCTTAC-GGGGTACCTCTCATCTTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATATCGG
* * *
20788770 TGCCAACGCCATGTTCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
20788820 TGCCAACGCCATATCCCAGACATGGTCTTACACT-GG--CTCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATATCGG
* * * * *
20788868 TGTCGATGCCATGTCCCAGACATGGTCTTACACT-TG--CTCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATATCGG
* *
20788916 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
20788946 TACGAGATCG
Statistics
Matches: 196, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
48 82 0.42
49 3 0.02
50 107 0.55
51 4 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:20788892 original size:48 final size:48
Alignment explanation
Indices: 20788777--20788945 Score: 223
Period size: 48 Copynumber: 3.5 Consensus size: 48
20788767 TAGTGCCAAC
* * * * * * *
20788777 GCCATGTTCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCGATGTCGAT
*
20788827 GCCATATCCCAGACATGGTCTTACACTGGCTCACATATCGATGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGATGTCGAT
*
20788875 GCCATGTCCCAGACATGGTCTTACACTTGCTCACATATCGATGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGATGTCGAT
20788923 GCCATGTCCCAGACATGGTCTTA
1 GCCATGTCCCAGACATGGTCTTA
20788946 TACGAGATCG
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
48 82 0.76
50 25 0.23
51 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGATGTCGAT
Found at i:20788965 original size:48 final size:48
Alignment explanation
Indices: 20788827--20788967 Score: 158
Period size: 48 Copynumber: 2.9 Consensus size: 48
20788817 CGGTGCCAAC
* * * *
20788827 GCCATATCCCAGACATGGTCTTACACTG-GCTCACATATCGATGTCGAT
1 GCCATGTCCCAGACATGGTCTTACAC-GAGATCACACACCGATGTCGAT
** * * *
20788875 GCCATGTCCCAGACATGGTCTTACACTTGCTCACATATCGATGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATGTCGAT
* * *
20788923 GCCATGTCCCAGACATGGTCTTATACGAGATCGCACGCCGATGTC
1 GCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATGTC
20788968 ATATCTCAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATGTCGAT
Found at i:20791204 original size:28 final size:28
Alignment explanation
Indices: 20791173--20791227 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
20791163 AATCTTGATG
20791173 TTCTTACCTTGTGCTATTGATTTCAATT
1 TTCTTACCTTGTGCTATTGATTTCAATT
20791201 TTCTTACCTTGTGCTATTGATTTCAAT
1 TTCTTACCTTGTGCTATTGATTTCAAT
20791228 CTTTAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (28 bp):
TTCTTACCTTGTGCTATTGATTTCAATT
Found at i:20791835 original size:30 final size:31
Alignment explanation
Indices: 20791780--20791847 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
20791770 ACCCCTAAAA
** * **
20791780 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
20791811 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
20791841 TATTTAC
1 TATTTAC
20791848 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:20808006 original size:7 final size:7
Alignment explanation
Indices: 20807994--20808018 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20807984 CTCCTACTAC
20807994 ATTTATT
1 ATTTATT
20808001 ATTTATT
1 ATTTATT
20808008 ATTTATT
1 ATTTATT
20808015 ATTT
1 ATTT
20808019 CTAAGTCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:20808741 original size:29 final size:29
Alignment explanation
Indices: 20808699--20808759 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
20808689 TAGTTTAGTC
20808699 ATTTCTTATTTTGGTAAGTGAGGGAGTTG
1 ATTTCTTATTTTGGTAAGTGAGGGAGTTG
20808728 ATTTCTTATTTTGGTAAGTGAGGGAGTTG
1 ATTTCTTATTTTGGTAAGTGAGGGAGTTG
20808757 ATT
1 ATT
20808760 CATGGTCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.46
Consensus pattern (29 bp):
ATTTCTTATTTTGGTAAGTGAGGGAGTTG
Found at i:20809912 original size:29 final size:31
Alignment explanation
Indices: 20809858--20809918 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
20809848 GAATCAAAGT
*
20809858 TAAGAAATTATTTTTTTAATA-TTTTTTATA
1 TAAGAAATTACTTTTTTAATAGTTTTTTATA
20809888 TAAGAAATT-CTTTTTTAATAGTTTTTTATA
1 TAAGAAATTACTTTTTTAATAGTTTTTTATA
20809918 T
1 T
20809919 TATTAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (31 bp):
TAAGAAATTACTTTTTTAATAGTTTTTTATA
Found at i:20810245 original size:18 final size:18
Alignment explanation
Indices: 20810224--20810264 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20810214 AAATAAACTT
20810224 TTTTTGAAATATAATTTA
1 TTTTTGAAATATAATTTA
** *
20810242 TTTTTGTTATGTAATTTA
1 TTTTTGAAATATAATTTA
20810260 TTTTT
1 TTTTT
20810265 ACTCTACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTTTGAAATATAATTTA
Found at i:20812145 original size:53 final size:53
Alignment explanation
Indices: 20812070--20812177 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
20812060 ACTATGCAAT
* * *
20812070 TGATATTGTTACTGTTACTGTATTGACTAGCATGTTGTGCTATATGACTGATA
1 TGATATTGTTACTGTTACTGTATTGACTAGCATGATATGCTACATGACTGATA
* ** *
20812123 TGATATTGTTACTGTTATTGTATTGTTTAGCATGATATGCTACATGATTGATA
1 TGATATTGTTACTGTTACTGTATTGACTAGCATGATATGCTACATGACTGATA
20812176 TG
1 TG
20812178 CCATTATTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.45
Consensus pattern (53 bp):
TGATATTGTTACTGTTACTGTATTGACTAGCATGATATGCTACATGACTGATA
Done.