Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 73 of 208
Found at i:21301810 original size:51 final size:49
Alignment explanation
Indices: 21301715--21301887 Score: 150
Period size: 51 Copynumber: 3.4 Consensus size: 49
21301705 TTTTAACATT
* **
21301715 GATGGCAGGCACCAGTGTATTTAAAAAAAAATTTTGGTGCTGGCCATGTA
1 GATGGCTGGCACCAGTACATTTAAAAAAAAATTTTGGTGCTGGCCA-GTA
*
21301765 -ATGGCTGGCACCAAGTACATTTAATAAAAAAATTTTGGTGTTGGCCAGTA
1 GATGGCTGGCACC-AGTACATTTAA-AAAAAAATTTTGGTGCTGGCCAGTA
* * ** ** *
21301815 GATGGGTGGCACTAGTGTATTTGAAAAAAAAAATATTTATATGCTGGCTAGTA
1 GATGGCTGGCACCAGTACATTT--AAAAAAAAAT-TTT-GGTGCTGGCCAGTA
* *
21301868 GATGGCCGGCATCAAGTACA
1 GATGGCTGGCA-CCAGTACA
21301888 ATTTTTAGCT
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
49 11 0.11
50 19 0.19
51 39 0.40
52 5 0.05
53 19 0.19
54 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (49 bp):
GATGGCTGGCACCAGTACATTTAAAAAAAAATTTTGGTGCTGGCCAGTA
Found at i:21302848 original size:86 final size:87
Alignment explanation
Indices: 21302736--21302929 Score: 214
Period size: 91 Copynumber: 2.2 Consensus size: 87
21302726 CCTAGTATCG
* * * *
21302736 GCCAATGGATTCCCAAATTCAAAAAAATTTATTATTTTTAAAGCCTG-C-AT-CAGGCAATAATA
1 GCCATTGGGTTCCCAAACTCAAAAAAAATTA-T-TTTTTAAAGCCTGACAATACAGGCAATAATA
*
21302798 GGGCCAAAACACTAGGTAGTGCCA
64 GGGACAAAACACTAGGTAGTGCCA
* * * *
21302822 GTCATTGGGTTCCTAAACTCAAAAAAAATTATTTTTTAAAGCCTGATACAATCAACATGCAATCA
1 GCCATTGGGTTCCCAAACTCAAAAAAAATTATTTTTTAAAGCCTG--ACAAT--ACAGGCAATAA
* *
21302887 TGGGGACAAAACACTAGGTAGTGCCG
62 TAGGGACAAAACACTAGGTAGTGCCA
21302913 GCCATTGGGTTCCCAAA
1 GCCATTGGGTTCCCAAA
21302930 ACTTAAATCT
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
84 13 0.15
85 1 0.01
86 25 0.28
87 1 0.01
88 2 0.02
91 46 0.52
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (87 bp):
GCCATTGGGTTCCCAAACTCAAAAAAAATTATTTTTTAAAGCCTGACAATACAGGCAATAATAGG
GACAAAACACTAGGTAGTGCCA
Found at i:21304349 original size:21 final size:21
Alignment explanation
Indices: 21304323--21304376 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
21304313 TAGCGGTGGT
*
21304323 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
21304344 GGTGAGATTAAATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
21304365 GGTGAGATTAGA
1 GGTGAGATTAGA
21304377 AACAATGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:21304606 original size:30 final size:30
Alignment explanation
Indices: 21304544--21304724 Score: 257
Period size: 30 Copynumber: 6.2 Consensus size: 30
21304534 ATTCATTTAA
*
21304544 TAAAATACACTACATATA----TATA-TTT
1 TAAAATACACTACATATATTTTTTTATTTT
*
21304569 TAAAATACACTACATATATTTTTTTATTTC
1 TAAAATACACTACATATATTTTTTTATTTT
*
21304599 TAGAATACACTACATATA-TTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
21304628 TAAAATACACTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
*
21304658 TAAAATACACTACATGTATTTTTTTTATTTT
1 TAAAATACACTACATATA-TTTTTTTATTTT
* *
21304689 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
21304719 TAAAAT
1 TAAAAT
21304725 TTTAAATACA
Statistics
Matches: 140, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
25 18 0.13
29 30 0.21
30 65 0.46
31 27 0.19
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (30 bp):
TAAAATACACTACATATATTTTTTTATTTT
Found at i:21304692 original size:61 final size:59
Alignment explanation
Indices: 21304544--21304724 Score: 262
Period size: 61 Copynumber: 3.1 Consensus size: 59
21304534 ATTCATTTAA
* *
21304544 TAAAATACACTACATATA---TATA-TTTTAAAATACACTACATATATTTTTTTATTTC
1 TAAAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTT
*
21304599 TAGAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTT
* * *
21304658 TAAAATACACTACATGTATTTTTTTTATTTTTAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACA--TATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTT
21304719 TAAAAT
1 TAAAAT
21304725 TTTAAATACA
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
55 17 0.15
58 3 0.03
59 45 0.40
61 48 0.42
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (59 bp):
TAAAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTT
Found at i:21304926 original size:6 final size:6
Alignment explanation
Indices: 21304915--21304949 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
21304905 TCTCTCCTCT
21304915 CATTCC CATTCC CATTTCC CATTCC CATTCC CATT
1 CATTCC CATTCC CA-TTCC CATTCC CATTCC CATT
21304950 ATCAACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.46, G:0.00, T:0.37
Consensus pattern (6 bp):
CATTCC
Found at i:21304935 original size:13 final size:12
Alignment explanation
Indices: 21304915--21304949 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
21304905 TCTCTCCTCT
21304915 CATTCCCATTCC
1 CATTCCCATTCC
21304927 CATTTCCCATTCC
1 CA-TTCCCATTCC
21304940 CATTCCCATT
1 CATTCCCATT
21304950 ATCAACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.17, C:0.46, G:0.00, T:0.37
Consensus pattern (12 bp):
CATTCCCATTCC
Found at i:21306709 original size:45 final size:45
Alignment explanation
Indices: 21306640--21306731 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
21306630 CTTTCCTCTT
21306640 ATAGCCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
1 ATAGCCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
*
21306685 ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
1 ATAGCCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
21306730 AT
1 AT
21306732 CAATCTCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (45 bp):
ATAGCCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
Found at i:21310073 original size:44 final size:45
Alignment explanation
Indices: 21310009--21310097 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
21309999 TGATAAAATA
21310009 TTATTAATATAAAATAAAAATAATTATAATTAT-TTTATATTATT
1 TTATTAATATAAAATAAAAATAATTATAATTATCTTTATATTATT
* * *
21310053 TTATTAATAGTAATAT-AAAATAATTTTAATTATCTTTATTTTATT
1 TTATTAATA-TAAAATAAAAATAATTATAATTATCTTTATATTATT
21310098 AATTATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 25 0.62
45 15 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (45 bp):
TTATTAATATAAAATAAAAATAATTATAATTATCTTTATATTATT
Found at i:21310101 original size:18 final size:19
Alignment explanation
Indices: 21310078--21310113 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21310068 TAAAATAATT
21310078 TTAATTATCTTT-ATTTTA
1 TTAATTATCTTTCATTTTA
*
21310096 TTAATTATTTTTCATTTT
1 TTAATTATCTTTCATTTT
21310114 TAGTATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAATTATCTTTCATTTTA
Found at i:21312601 original size:12 final size:12
Alignment explanation
Indices: 21312584--21312608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21312574 GGGACAACAG
21312584 ACCCTCACTACA
1 ACCCTCACTACA
21312596 ACCCTCACTACA
1 ACCCTCACTACA
21312608 A
1 A
21312609 ATTAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (12 bp):
ACCCTCACTACA
Found at i:21313316 original size:44 final size:44
Alignment explanation
Indices: 21313261--21313349 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
21313251 AATTTATAGC
* * * *
21313261 TTCAGTTATGCTTCTTTTAACTCCTTGTAAAACCAGTTCGGTGT
1 TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
*
21313305 TTCAATTATGCTTCTCTCAACTCATTGTAAAACTAGTTCGGTGT
1 TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
21313349 T
1 T
21313350 GCTTATACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (44 bp):
TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
Found at i:21319684 original size:17 final size:17
Alignment explanation
Indices: 21319659--21319695 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
21319649 TCCAATTATC
*
21319659 TAAAAATATTAAAATTT
1 TAAAAATATTAAAATGT
*
21319676 TAAAGATATTAAAATGT
1 TAAAAATATTAAAATGT
21319693 TAA
1 TAA
21319696 TTTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAAAATATTAAAATGT
Found at i:21325169 original size:15 final size:15
Alignment explanation
Indices: 21325149--21325178 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21325139 AATTTCATGC
21325149 TTCAATCACCATGTT
1 TTCAATCACCATGTT
21325164 TTCAATCACCATGTT
1 TTCAATCACCATGTT
21325179 ATCACTTAGA
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:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:21327580 original size:20 final size:21
Alignment explanation
Indices: 21327555--21327593 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
21327545 TATAAAATTA
*
21327555 ATTTTTCTAAA-AATATTTTT
1 ATTTTTCAAAATAATATTTTT
21327575 ATTTTTCAAAATAATATTT
1 ATTTTTCAAAATAATATTT
21327594 CCCAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTCAAAATAATATTTTT
Found at i:21332736 original size:21 final size:21
Alignment explanation
Indices: 21332702--21332756 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
21332692 TATTAAACAG
* *
21332702 CTAA-GGTTCGCATATAATTT
1 CTAAGGGTTCACATATAACTT
*
21332722 CTATGGGTTCACATATAACTT
1 CTAAGGGTTCACATATAACTT
*
21332743 CTAAGTGTTCACAT
1 CTAAGGGTTCACAT
21332757 TACAATTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (21 bp):
CTAAGGGTTCACATATAACTT
Found at i:21332788 original size:23 final size:22
Alignment explanation
Indices: 21332762--21332806 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21332752 CACATTACAA
* *
21332762 TTCCTATAGTGTTCGCATGTTAT
1 TTCCTATAG-GTTCACATATTAT
*
21332785 TTCCTCTAGGTTCACATATTAT
1 TTCCTATAGGTTCACATATTAT
21332807 ACTGTTCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (22 bp):
TTCCTATAGGTTCACATATTAT
Found at i:21332806 original size:22 final size:23
Alignment explanation
Indices: 21332707--21332806 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 23
21332697 AACAGCTAAG
* * *
21332707 GTTCGCATATAATTT-CTAT-GG
1 GTTCACATATTATTTCCTATAGT
* *
21332728 GTTCACATATAACTT-CTA-AGT
1 GTTCACATATTATTTCCTATAGT
* *
21332749 GTTCACAT-TACAATTCCTATAGT
1 GTTCACATAT-TATTTCCTATAGT
* * *
21332772 GTTCGCATGTTATTTCCTCTAG-
1 GTTCACATATTATTTCCTATAGT
21332794 GTTCACATATTAT
1 GTTCACATATTAT
21332807 ACTGTTCACG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.02
21 28 0.44
22 14 0.22
23 19 0.30
24 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (23 bp):
GTTCACATATTATTTCCTATAGT
Found at i:21333092 original size:19 final size:20
Alignment explanation
Indices: 21333054--21333092 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
21333044 TGGGTTTTGA
21333054 AGAAAAAATAGAGAATAAAT
1 AGAAAAAATAGAGAATAAAT
* *
21333074 AGAAAGAAT-GAGGATAAAT
1 AGAAAAAATAGAGAATAAAT
21333093 TCTATTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
AGAAAAAATAGAGAATAAAT
Found at i:21336118 original size:15 final size:15
Alignment explanation
Indices: 21336098--21336128 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21336088 ATCCAGGAAG
21336098 TTGGTCACATATAAT
1 TTGGTCACATATAAT
21336113 TTGGTCACATATAAT
1 TTGGTCACATATAAT
21336128 T
1 T
21336129 GGTAATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTGGTCACATATAAT
Found at i:21343792 original size:32 final size:33
Alignment explanation
Indices: 21343729--21343792 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
21343719 ATAAAGATCT
* *
21343729 AAAATAAAATATTTGTAATATTTCAGTAATAAC
1 AAAATAAAATATTTGTAATATGTCAGAAATAAC
21343762 AAAATAAAATA-TTGTATATATGT-AGAAATAA
1 AAAATAAAATATTTGTA-ATATGTCAGAAATAA
21343793 ATAAACATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (33 bp):
AAAATAAAATATTTGTAATATGTCAGAAATAAC
Found at i:21345022 original size:26 final size:27
Alignment explanation
Indices: 21344993--21345043 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
21344983 CCACATTAGC
*
21344993 TGGGCTAGGTTAATTGGGT-TTTGGTT
1 TGGGCTAGGTTAAGTGGGTATTTGGTT
21345019 TGGGCTAGGTTAAGTGGGTATTTGG
1 TGGGCTAGGTTAAGTGGGTATTTGG
21345044 GATCTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.14, C:0.04, G:0.41, T:0.41
Consensus pattern (27 bp):
TGGGCTAGGTTAAGTGGGTATTTGGTT
Found at i:21352929 original size:48 final size:48
Alignment explanation
Indices: 21352859--21352955 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
21352849 TTCTTTGCTT
21352859 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
1 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
* * * *
21352907 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAGA
1 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
21352955 A
1 A
21352956 TTCCCTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (48 bp):
AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
Found at i:21353198 original size:36 final size:36
Alignment explanation
Indices: 21353158--21353228 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
21353148 ATCAAAGGCT
*
21353158 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
21353194 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
21353229 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:21353199 original size:19 final size:19
Alignment explanation
Indices: 21353175--21353228 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
21353165 AAAGTTGTAT
21353175 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
21353194 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
21353211 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
21353229 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:21353216 original size:17 final size:17
Alignment explanation
Indices: 21353157--21353220 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
21353147 CATCAAAGGC
* *
21353157 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
21353174 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
21353193 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
21353210 TACAATTAGAA
1 TACAATTAGAA
21353221 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:21356055 original size:17 final size:17
Alignment explanation
Indices: 21356033--21356096 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
21356023 CATCAAAGGC
*
21356033 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
21356050 TACAATTAGAA-CTCGAAGA
1 TACAATTAGAAGCT-G--TA
*
21356069 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
21356086 TACAATTAGAA
1 TACAATTAGAA
21356097 TTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
19 12 0.32
20 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:21357429 original size:23 final size:23
Alignment explanation
Indices: 21357402--21357461 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
21357392 TACTTAAATT
*
21357402 TATTTCAAATATATAA-AATTATA
1 TATTT-AAATATATAATAACTATA
*
21357425 TATTTAAATTTATAATAACTATA
1 TATTTAAATATATAATAACTATA
21357448 T-TTTAAATTATATA
1 TATTTAAA-TATATA
21357462 TTCAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTAAATATATAATAACTATA
Found at i:21357438 original size:22 final size:23
Alignment explanation
Indices: 21357402--21357461 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
21357392 TACTTAAATT
* *
21357402 TATTTCAAATATATAA-AATTATA
1 TATTT-AAATTTATAATAACTATA
21357425 TATTTAAATTTATAATAACTATA
1 TATTTAAATTTATAATAACTATA
21357448 T-TTTAAATTATATA
1 TATTTAAATT-TATA
21357462 TTCAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTAAATTTATAATAACTATA
Found at i:21357892 original size:9 final size:9
Alignment explanation
Indices: 21357880--21357931 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
21357870 TTTTGTGAAC
21357880 TTTTTTTTA
1 TTTTTTTTA
*
21357889 TTTTTTTAA
1 TTTTTTTTA
*
21357898 TTTTGATTTA
1 TTTT-TTTTA
*
21357908 TATTTTTTA
1 TTTTTTTTA
* *
21357917 TTTTTATAA
1 TTTTTTTTA
21357926 TTTTTT
1 TTTTTT
21357932 ATTTATTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:21357901 original size:15 final size:15
Alignment explanation
Indices: 21357883--21357935 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21357873 TGTGAACTTT
*
21357883 TTTTTATTTTTTTAA
1 TTTTTATTTTTATAA
* *
21357898 TTTTGA--TTTATAT
1 TTTTTATTTTTATAA
21357911 TTTTTATTTTTATAA
1 TTTTTATTTTTATAA
21357926 TTTTTTATTT
1 -TTTTTATTT
21357936 ATTTGTTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 10 0.33
15 11 0.37
16 9 0.30
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTATAA
Found at i:21365408 original size:63 final size:63
Alignment explanation
Indices: 21365341--21365467 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
21365331 AGTAAAAAAA
*
21365341 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTGTTTATATAGGAATTAGCCTGTAATTCC
1 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
21365404 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
1 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
21365467 A
1 A
21365468 CTATAACTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (63 bp):
AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
Found at i:21366775 original size:24 final size:24
Alignment explanation
Indices: 21366730--21366775 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
21366720 AACAAAAATT
* * **
21366730 TAAATATTCCTAACAATTTAAACA
1 TAAAAATTCCAAACAAACTAAACA
21366754 TAAAAATTCCAAACAAACTAAA
1 TAAAAATTCCAAACAAACTAAA
21366776 ACTTCAATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (24 bp):
TAAAAATTCCAAACAAACTAAACA
Found at i:21368849 original size:41 final size:41
Alignment explanation
Indices: 21368764--21368921 Score: 183
Period size: 41 Copynumber: 3.8 Consensus size: 41
21368754 GTCTGACCTT
* * *
21368764 TCGGGGCTTTAGCGACATTTTTCGAAAAAGCGCCGCTAAAGC
1 TCGGGGATTTAGCGACGTTTTT-GAAAAAGCGCCGCTAATGC
* *
21368806 TCGGGGATATAGCGACGTTTTTGAAAAAGCGACGCTAATGC
1 TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
21368847 TC-GGAACTTTAGCGGCGTTTTTGAAAAAGCGCCCCTAATTC
1 TCGGGGA-TTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
* * *
21368888 TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCG
1 TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCG
21368922 AAAAAATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
40 3 0.03
41 76 0.77
42 20 0.20
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:21369306 original size:50 final size:55
Alignment explanation
Indices: 21369245--21369566 Score: 449
Period size: 58 Copynumber: 5.7 Consensus size: 55
21369235 AAAATTTAAA
*
21369245 AAATATTAGTTTAAATAGAATTAATAAATAAGATTAAAT-AA-A-A-T-ATATTT
1 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAATATATTAATATTT
21369295 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAATATTT
1 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAAT-AAATATA-TT-AATATTT
21369353 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAATATTT
1 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAAT-AAATATA-TT-AATATTT
*
21369411 AAATATTAGTTTAAATAGAATTAATAATTAAGTTTAAATAAAATATATTTAAATATTT
1 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAAT-AAATATA-TT-AATATTT
* *
21369469 AAATATTAGTTTAAATAAAATTAATAATTAAGTTTAAATAAAATATATTTAAATATTT
1 AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAAT-AAATATA-TT-AATATTT
21369527 AAATATTAGTTTAAATAGAATTAATAAATATA-TTTAAATA
1 AAATATTAGTTTAAATAGAATTAATAAATA-AGTTTAAATA
21369567 TTAGTTTAAA
Statistics
Matches: 258, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
50 38 0.15
52 2 0.01
53 1 0.00
54 1 0.00
56 1 0.00
57 1 0.00
58 213 0.83
59 1 0.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (55 bp):
AAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAATATATTAATATTT
Found at i:21369328 original size:23 final size:23
Alignment explanation
Indices: 21369252--21369334 Score: 103
Period size: 23 Copynumber: 3.4 Consensus size: 23
21369242 AAAAAATATT
21369252 AGTTTAAATAGAATTAATAAATA
1 AGTTTAAATAGAATTAATAAATA
* * *
21369275 AGATTAAATAAAATATATTTAAATA
1 AGTTTAAATAGAAT-TA-ATAAATA
21369300 TTAGTTTAAATAGAATTAATAAATA
1 --AGTTTAAATAGAATTAATAAATA
21369325 AGTTTAAATA
1 AGTTTAAATA
21369335 AAATATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 22 0.44
24 2 0.04
25 12 0.24
26 2 0.04
27 12 0.24
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
AGTTTAAATAGAATTAATAAATA
Found at i:21369353 original size:23 final size:24
Alignment explanation
Indices: 21369251--21369473 Score: 91
Period size: 23 Copynumber: 9.5 Consensus size: 24
21369241 TAAAAAATAT
* *
21369251 TAGTTTAAATAGAAT-TA-ATAAA
1 TAGTTTAAATAAAATATATTTAAA
*
21369273 TAAGATTAAATAAAATATATTTAAATA
1 T-AGTTTAAATAAAATATATTT-AA-A
* *
21369300 TTAGTTTAAATAGAAT-TA-ATAAA
1 -TAGTTTAAATAAAATATATTTAAA
21369323 TAAGTTTAAATAAAATATATTTAAA
1 T-AGTTTAAATAAAATATATTTAAA
21369348 TA-TTTAAAT---AT-TAGTTTAAA
1 TAGTTTAAATAAAATATA-TTTAAA
*
21369368 TAGAATT-AAT-AAATA-AGTTTAAA
1 TAG-TTTAAATAAAATATA-TTTAAA
*** * * *
21369391 TAAAATATATTTAAATAT-TTAAATA
1 TAGTTTA-AATAAAATATATTTAA-A
* * *
21369416 TTAGTTTAAATAGAAT-TA-ATAAT
1 -TAGTTTAAATAAAATATATTTAAA
21369439 TAAGTTTAAATAAAATATATTTAAA
1 T-AGTTTAAATAAAATATATTTAAA
21369464 TA-TTTAAATA
1 TAGTTTAAATA
21369474 TTAGTTTAAA
Statistics
Matches: 151, Mismatches: 25, Indels: 49
0.67 0.11 0.22
Matches are distributed among these distances:
19 2 0.01
20 10 0.07
21 3 0.02
22 7 0.05
23 66 0.44
24 19 0.13
25 22 0.15
26 8 0.05
27 13 0.09
28 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
TAGTTTAAATAAAATATATTTAAA
Found at i:21369360 original size:58 final size:58
Alignment explanation
Indices: 21369289--21369566 Score: 513
Period size: 58 Copynumber: 4.8 Consensus size: 58
21369279 TAAATAAAAT
21369289 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
1 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
21369347 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
1 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
*
21369405 ATATTTAAATATTAGTTTAAATAGAATTAATAATTAAGTTTAAATAAAATATATTTAA
1 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
* *
21369463 ATATTTAAATATTAGTTTAAATAAAATTAATAATTAAGTTTAAATAAAATATATTTAA
1 ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
21369521 ATATTTAAATATTAGTTTAAATAGAATTAATAAATATA-TTTAAATA
1 ATATTTAAATATTAGTTTAAATAGAATTAATAAATA-AGTTTAAATA
21369567 TTAGTTTAAA
Statistics
Matches: 215, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
58 214 1.00
59 1 0.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (58 bp):
ATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAA
Found at i:21369364 original size:35 final size:37
Alignment explanation
Indices: 21369325--21369489 Score: 148
Period size: 35 Copynumber: 4.4 Consensus size: 37
21369315 TTAATAAATA
21369325 AGTTTAAATAAAATATATTTAAAT-ATTTAAAT-ATT
1 AGTTTAAATAAAATATATTTAAATAATTTAAATAATT
* *
21369360 AGTTTAAATAGAAT-TA-ATAAATAAGTTTAAATAAAATAT
1 AGTTTAAATAAAATATATTTAAATAA-TTTAAAT--AAT-T
*
21369399 A-TTTAAATATTTAAATATTAGTTTAAATAGAATT-AATAATT
1 AGTTTAAATA---AAATA-TA-TTTAAATA-ATTTAAATAATT
21369440 AAGTTTAAATAAAATATATTTAAAT-ATTTAAAT-ATT
1 -AGTTTAAATAAAATATATTTAAATAATTTAAATAATT
21369476 AGTTTAAATAAAAT
1 AGTTTAAATAAAAT
21369490 TAATAATTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 34
0.73 0.04 0.23
Matches are distributed among these distances:
33 5 0.05
34 3 0.03
35 34 0.32
36 6 0.06
37 3 0.03
38 17 0.16
39 4 0.04
40 5 0.05
41 4 0.04
42 4 0.04
43 10 0.09
44 3 0.03
45 8 0.07
46 1 0.01
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (37 bp):
AGTTTAAATAAAATATATTTAAATAATTTAAATAATT
Found at i:21369463 original size:15 final size:17
Alignment explanation
Indices: 21369325--21369543 Score: 103
Period size: 15 Copynumber: 11.6 Consensus size: 17
21369315 TTAATAAATA
21369325 AGTTTAAATAAAATA-T
1 AGTTTAAATAAAATATT
21369341 A-TTTAAATATTTAAATATT
1 AGTTTAAATA---AAATATT
*
21369360 AGTTTAAATAGAATTAATAAATA
1 AGTTTAAAT--AA--AAT--ATT
21369383 AGTTTAAATAAAATA-T
1 AGTTTAAATAAAATATT
21369399 A-TTTAAATATTTAAATATT
1 AGTTTAAATA---AAATATT
21369418 AGTTTAAATAGAATTAATAATT
1 AGTTTAAAT--AA--AAT-ATT
21369440 AAGTTTAAATAAAATA-T
1 -AGTTTAAATAAAATATT
21369457 A-TTTAAATATTTAAATATT
1 AGTTTAAATA---AAATATT
21369476 AGTTTAAATAAAATTAATAATT
1 AGTTTAAAT--AA--AAT-ATT
21369498 AAGTTTAAATAAAATA-T
1 -AGTTTAAATAAAATATT
21369515 A-TTTAAATATTTAAATATT
1 AGTTTAAATA---AAATATT
21369534 AGTTTAAATA
1 AGTTTAAATA
21369544 GAATTAATAA
Statistics
Matches: 163, Mismatches: 2, Indels: 72
0.69 0.01 0.30
Matches are distributed among these distances:
15 32 0.20
16 4 0.02
17 3 0.02
18 22 0.13
19 20 0.12
20 29 0.18
21 15 0.09
22 9 0.06
23 29 0.18
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AGTTTAAATAAAATATT
Found at i:21369538 original size:35 final size:35
Alignment explanation
Indices: 21369499--21369582 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
21369489 TTAATAATTA
* *
21369499 AGTTTAAATAAAATATATTTAA-ATATTTAAATATT
1 AGTTTAAATAAAAT-TAATAAATATATTTAAATATT
*
21369534 AGTTTAAATAGAATTAATAAATATATTTAAATATT
1 AGTTTAAATAAAATTAATAAATATATTTAAATATT
21369569 AGTTTAAATAAAAT
1 AGTTTAAATAAAAT
21369583 GATTTTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 5 0.11
35 39 0.89
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (35 bp):
AGTTTAAATAAAATTAATAAATATATTTAAATATT
Found at i:21369541 original size:12 final size:11
Alignment explanation
Indices: 21369509--21369578 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
21369499 AGTTTAAATA
21369509 AAATATA-TTT
1 AAATATAGTTT
21369519 -AA-ATA-TTT
1 AAATATAGTTT
21369527 AAATATTAGTTT
1 AAATA-TAGTTT
* *
21369539 AAATAGAATTAAT
1 AAATATAGTT--T
21369552 AAATATA-TTT
1 AAATATAGTTT
21369562 AAATATTAGTTT
1 AAATA-TAGTTT
21369574 AAATA
1 AAATA
21369579 AAATGATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
8 6 0.12
9 4 0.08
10 7 0.14
11 7 0.14
12 18 0.37
13 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (11 bp):
AAATATAGTTT
Found at i:21372956 original size:6 final size:6
Alignment explanation
Indices: 21372945--21372970 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21372935 AACATAATAT
21372945 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
21372971 CATTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:21373256 original size:43 final size:42
Alignment explanation
Indices: 21373142--21373322 Score: 186
Period size: 43 Copynumber: 4.3 Consensus size: 42
21373132 AAAAGTCATG
* * * *
21373142 TTTTTAGCGGCATTTGTGAAAAAGTGCCGCTAAAAGTTAT--
1 TTTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTTATGA
* *
21373182 TTTTATAGCGGCGTTTGTAATAGAAGCGCCGCTAAAGGTTATGA
1 TTTT-TAGCGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTTATGA
* * *
21373226 TTTTTAGCGACGTTTGTGGTAAAAGTGCCGCTAAAGGTCATGA
1 TTTTTAGCGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTTATGA
* ***
21373269 TTTTTAGCGGCGTTTGTGTGAAAAGCGCTGCTAAAGACCATGA
1 TTTTTAGCGGCGTTTGTGT-AAAAGCGCCGCTAAAGGTTATGA
*
21373312 TCTTTAGCGGC
1 TTTTTAGCGGC
21373323 ATTTTTTCAC
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
40 4 0.03
41 12 0.10
42 20 0.17
43 78 0.66
44 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TTTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTTATGA
Found at i:21373924 original size:19 final size:19
Alignment explanation
Indices: 21373900--21373943 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21373890 ATATAAAGAT
21373900 TAATATAAATTTTTAAATA-
1 TAATAT-AATTTTTAAATAG
* *
21373919 TAATATTATTTTTAGATAG
1 TAATATAATTTTTAAATAG
21373938 TAATAT
1 TAATAT
21373944 GGTTTTGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TAATATAATTTTTAAATAG
Found at i:21373931 original size:18 final size:19
Alignment explanation
Indices: 21373908--21373943 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21373898 ATTAATATAA
21373908 ATTTTTAAATA-TAATATT
1 ATTTTTAAATAGTAATATT
*
21373926 ATTTTTAGATAGTAATAT
1 ATTTTTAAATAGTAATAT
21373944 GGTTTTGCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTTAAATAGTAATATT
Found at i:21375992 original size:22 final size:23
Alignment explanation
Indices: 21375967--21376010 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21375957 AAAATTTAAA
21375967 TAATATG-AAATAAAAATAACAT
1 TAATATGCAAATAAAAATAACAT
**
21375989 TAATATGCTTATAAAAATAACA
1 TAATATGCAAATAAAAATAACA
21376011 GAATCTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (23 bp):
TAATATGCAAATAAAAATAACAT
Found at i:21376250 original size:31 final size:32
Alignment explanation
Indices: 21376202--21376275 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
21376192 CCATCTAACG
* * * *
21376202 AAAAAATT-AATATCTTAAA-AAACATTAATT
1 AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
*
21376232 AAAAAATTAAAAAGCTTAAAGTAACATGAAAT
1 AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
21376264 AAAAAA-TAAAAA
1 AAAAAATTAAAAA
21376276 TATGAGTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 8 0.22
31 15 0.41
32 14 0.38
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.24
Consensus pattern (32 bp):
AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
Found at i:21376282 original size:140 final size:138
Alignment explanation
Indices: 21376041--21376390 Score: 375
Period size: 140 Copynumber: 2.5 Consensus size: 138
21376031 CATTCGTAAT
*
21376041 TATCTAACCATCTAACAAAATGAGTTAATATGTTAAAAATATTAATTAAAAATAAAAATAAAAAA
1 TATCTAACCATCTAACAAAA-GAGTTAATATGTTAAAAA-ATTAATT---AA-AAAATTAAAAAA
* * * *
21376106 CTTGAAGCAACATTAAATAAAAAATACAAATGTGAGT-AGTAAA-AGAATAAAACTCGAGACTCA
60 CTTAAAGCAACATGAAATAAAAAATAAAAATATGAGTAAG-AAAGA-AATAAAACTCGAGACTCA
* *
21376169 ATGTTGTAATTACAAC
123 AGGATGTAATTACAAC
* * * *
21376185 TATCTTACCATCTAACGAAAA-AATTAATATCTTAAAAAACATTAATTAAAAAATTAAAAAGCTT
1 TATCTAACCATCTAAC-AAAAGAGTTAATATGTT-AAAAA-ATTAATTAAAAAATTAAAAAACTT
* * *
21376249 AAAGTAACATGAAATAAAAAATAAAAATATGAGTAAGAGAGAAATTAAACTCGAGACTCAAGGAT
63 AAAGCAACATGAAATAAAAAATAAAAATATGAGTAAGAAAGAAATAAAACTCGAGACTCAAGGAT
*
21376314 GTAATTGCAAC
128 GTAATTACAAC
* * * *
21376325 TAAT-TAAACAATCTAACAAAAGAGCTAATATGTTAAAAAATTAATTAAAAATTTTAAAAATCTT
1 T-ATCT-AACCATCTAACAAAAGAGTTAATATGTTAAAAAATTAATTAAAAA-ATTAAAAAACTT
21376389 AA
63 AA
21376391 CATGAAATTA
Statistics
Matches: 175, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
139 12 0.07
140 97 0.55
141 25 0.14
143 10 0.06
144 27 0.15
145 4 0.02
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (138 bp):
TATCTAACCATCTAACAAAAGAGTTAATATGTTAAAAAATTAATTAAAAAATTAAAAAACTTAAA
GCAACATGAAATAAAAAATAAAAATATGAGTAAGAAAGAAATAAAACTCGAGACTCAAGGATGTA
ATTACAAC
Found at i:21377443 original size:23 final size:23
Alignment explanation
Indices: 21377417--21377463 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
21377407 TAAATTTTGA
*
21377417 ATTATTTAGTGATAATCTTTAGG
1 ATTATTTAGTGATAATATTTAGG
21377440 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
21377463 A
1 A
21377464 AAAATCTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:21377460 original size:13 final size:13
Alignment explanation
Indices: 21377419--21377461 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
21377409 AATTTTGAAT
21377419 TATTTAGTGATAA
1 TATTTAGTGATAA
*
21377432 TCTTTAG-GAT--
1 TATTTAGTGATAA
21377442 TATTTAGTGATAA
1 TATTTAGTGATAA
21377455 TATTTAG
1 TATTTAG
21377462 GAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:21380815 original size:49 final size:49
Alignment explanation
Indices: 21380760--21380858 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
21380750 AATTTCTCAC
21380760 TTTTTCTCATTTTTTCCTTTTTCACTAATCAAAGTCAATTCCTTGTCTT
1 TTTTTCTCATTTTTTCCTTTTTCACTAATCAAAGTCAATTCCTTGTCTT
21380809 TTTTTCTCATTTTTTCCTTTTTCACTAATCAAAGTCAATTCCTTGTCTT
1 TTTTTCTCATTTTTTCCTTTTTCACTAATCAAAGTCAATTCCTTGTCTT
21380858 T
1 T
21380859 CTTGACTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (49 bp):
TTTTTCTCATTTTTTCCTTTTTCACTAATCAAAGTCAATTCCTTGTCTT
Found at i:21386146 original size:13 final size:13
Alignment explanation
Indices: 21386128--21386183 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
21386118 AAATTTGAAT
21386128 TATTTAGTGATAA
1 TATTTAGTGATAA
*
21386141 TATTTAGTGATCA
1 TATTTAGTGATAA
21386154 TATTTAG-GAT--
1 TATTTAGTGATAA
21386164 TATTTAGTGATAA
1 TATTTAGTGATAA
21386177 TATTTAG
1 TATTTAG
21386184 AAAAAATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 7 0.18
11 3 0.08
12 3 0.08
13 26 0.67
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:21387390 original size:21 final size:22
Alignment explanation
Indices: 21387366--21387406 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21387356 TAATAACTAA
*
21387366 ATATTTTA-TATAATTTTTTTC
1 ATATTTTATTAGAATTTTTTTC
21387387 ATATTTTATTAGAATTTTTT
1 ATATTTTATTAGAATTTTTT
21387407 AAGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTTTATTAGAATTTTTTTC
Found at i:21387507 original size:19 final size:19
Alignment explanation
Indices: 21387485--21387543 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
21387475 TATTAAAATT
21387485 TTTATTAAGTTTTATAATA
1 TTTATTAAGTTTTATAATA
* * *
21387504 TTTATAAATTTTTATGAT-
1 TTTATTAAGTTTTATAATA
21387522 TCTT-TTAAGTTTTTATAA-A
1 T-TTATTAAG-TTTTATAATA
21387541 TTT
1 TTT
21387544 TGTAATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATTAAGTTTTATAATA
Found at i:21387517 original size:10 final size:10
Alignment explanation
Indices: 21387464--21387600 Score: 71
Period size: 10 Copynumber: 14.5 Consensus size: 10
21387454 TTTATTGCTT
21387464 TTTTTAT-AA
1 TTTTTATAAA
21387473 TTTATTA-AAA
1 TTT-TTATAAA
*
21387483 TTTTTATTAA
1 TTTTTATAAA
*
21387493 GTTTTAT-AA
1 TTTTTATAAA
*
21387502 TATTTATAAA
1 TTTTTATAAA
*
21387512 TTTTTAT-GA
1 TTTTTATAAA
*
21387521 TTCTTT-TAAG
1 TT-TTTATAAA
21387531 TTTTTATAAA
1 TTTTTATAAA
*
21387541 -TTTTGT-AA
1 TTTTTATAAA
* *
21387549 --TTTCTAAG
1 TTTTTATAAA
*
21387557 TTTATATAAA
1 TTTTTATAAA
21387567 TTTTTAGT--A
1 TTTTTA-TAAA
21387576 TTTTTATAAA
1 TTTTTATAAA
* *
21387586 TTTTAATAAC
1 TTTTTATAAA
21387596 TTTTT
1 TTTTT
21387601 TATTATAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 25
0.69 0.14 0.18
Matches are distributed among these distances:
7 4 0.04
8 4 0.04
9 32 0.33
10 55 0.57
11 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:21388323 original size:27 final size:27
Alignment explanation
Indices: 21388285--21388339 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21388275 TCTAGTATTG
21388285 TATAAAAAAGAACATATATGATAAGAA
1 TATAAAAAAGAACATATATGATAAGAA
21388312 TATAAAAAAGAACATATATGATAAGAA
1 TATAAAAAAGAACATATATGATAAGAA
21388339 T
1 T
21388340 CTATAGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.24
Consensus pattern (27 bp):
TATAAAAAAGAACATATATGATAAGAA
Found at i:21391187 original size:45 final size:45
Alignment explanation
Indices: 21391115--21391208 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
21391105 AACAGATACT
* *
21391115 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* * *
21391160 CGGTGGAATCAGCACATTGCAATCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
21391205 CGGT
1 CGGT
21391209 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:21391320 original size:51 final size:51
Alignment explanation
Indices: 21391211--21391320 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 51
21391201 TGTTCGGTTC
* * *
21391211 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATAA
* * * *
21391262 ACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTAA
1 ACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCGATAA
21391313 ACATAGTA
1 ACATAGTA
21391321 CTACACATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
51 48 0.96
52 2 0.04
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATAA
Found at i:21393652 original size:9 final size:9
Alignment explanation
Indices: 21393635--21393671 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
21393625 TGAGTTTTTG
21393635 AATTCGAAT
1 AATTCGAAT
*
21393644 AACTCGAAT
1 AATTCGAAT
21393653 AATTCGAAT
1 AATTCGAAT
21393662 AATTCGAAT
1 AATTCGAAT
21393671 A
1 A
21393672 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21394663 original size:5 final size:5
Alignment explanation
Indices: 21394653--21394679 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21394643 TTCAAAAATT
21394653 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
21394680 GAATGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:21397553 original size:2 final size:2
Alignment explanation
Indices: 21397536--21397582 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
21397526 AAGGGGGCGA
* *
21397536 AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21397578 AT AT A
1 AT AT A
21397583 CACTTATGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21397784 original size:2 final size:2
Alignment explanation
Indices: 21397777--21397805 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21397767 TTAGCCTAAC
21397777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21397806 ACTATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21405102 original size:13 final size:13
Alignment explanation
Indices: 21405084--21405111 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21405074 TGTGATTAAT
21405084 TAGCTTAAAACCA
1 TAGCTTAAAACCA
21405097 TAGCTTAAAACCA
1 TAGCTTAAAACCA
21405110 TA
1 TA
21405112 TGTTTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (13 bp):
TAGCTTAAAACCA
Found at i:21406263 original size:27 final size:27
Alignment explanation
Indices: 21406207--21406271 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
21406197 TGGCAAACAA
** *
21406207 GTGTATGCCATTAGGTCTGGCGAGTAG
1 GTGTATGCCAGCAGGTCTGGCAAGTAG
21406234 GTGTATGCCAGCAGGTCTGGCAAGCT-G
1 GTGTATGCCAGCAGGTCTGGCAAG-TAG
*
21406261 GTGTTTGCCAG
1 GTGTATGCCAG
21406272 TGGATTTGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (27 bp):
GTGTATGCCAGCAGGTCTGGCAAGTAG
Found at i:21409473 original size:8 final size:8
Alignment explanation
Indices: 21409456--21409617 Score: 64
Period size: 10 Copynumber: 18.4 Consensus size: 8
21409446 TATTTTCTTA
*
21409456 TAAAATAT
1 TAAAAAAT
21409464 TAAAAAAT
1 TAAAAAAT
21409472 T-AAAAA-
1 TAAAAAAT
21409478 TAAAAAAGT
1 TAAAAAA-T
21409487 ATAAAAAGTAT
1 -TAAAAA--AT
*
21409498 T-AAATAT
1 TAAAAAAT
21409505 TAAAAATAT
1 TAAAAA-AT
21409514 T--AAAAT
1 TAAAAAAT
21409520 TGATATAAAAT
1 T-A-A-AAAAT
21409531 TATAAAAAT
1 TA-AAAAAT
21409540 TATTAAAAAT
1 TA--AAAAAT
*
21409550 GATAAAAACT
1 --TAAAAAAT
21409560 TAAAAATAT
1 TAAAAA-AT
21409569 TAGAAAAAAT
1 T--AAAAAAT
21409579 ATATAAAAAT
1 -TA-AAAAAT
*
21409589 CTAATAAAT
1 -TAAAAAAT
21409598 TATAAAAAT
1 TA-AAAAAT
*
21409607 TATAAAAT
1 TAAAAAAT
21409615 TAA
1 TAA
21409618 TAAAGCATAT
Statistics
Matches: 122, Mismatches: 10, Indels: 44
0.69 0.06 0.25
Matches are distributed among these distances:
6 4 0.03
7 16 0.13
8 26 0.21
9 28 0.23
10 32 0.26
11 13 0.11
12 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (8 bp):
TAAAAAAT
Found at i:21409491 original size:16 final size:16
Alignment explanation
Indices: 21409466--21409614 Score: 67
Period size: 19 Copynumber: 8.9 Consensus size: 16
21409456 TAAAATATTA
21409466 AAAAATT-AAAAATA-
1 AAAAATTAAAAAATAT
*
21409480 AAAAAGTATAAAAAGTATT
1 AAAAA-T-TAAAAAATA-T
*
21409499 AAATATT-AAAAATAT
1 AAAAATTAAAAAATAT
*
21409514 TAAAATTGATATAAAATTAT
1 AAAAATT-A-A-AAAA-TAT
21409534 AAAAATTATTAAAAATGAT
1 AAAAATTA--AAAAAT-AT
21409553 AAAAACTT-AAAAATAT
1 AAAAA-TTAAAAAATAT
* * *
21409569 TAGAA--AAAATATAT
1 AAAAATTAAAAAATAT
*
21409583 AAAAATCTAATAAATTAT
1 AAAAAT-TAA-AAAATAT
*
21409601 AAAAATTATAAAAT
1 AAAAATTAAAAAAT
21409615 TAATAAAGCA
Statistics
Matches: 102, Mismatches: 15, Indels: 34
0.68 0.10 0.23
Matches are distributed among these distances:
14 15 0.15
15 7 0.07
16 16 0.16
17 17 0.17
18 14 0.14
19 20 0.20
20 13 0.13
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAATTAAAAAATAT
Found at i:21409509 original size:26 final size:25
Alignment explanation
Indices: 21409457--21409518 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
21409447 ATTTTCTTAT
21409457 AAAATATTAAAAA--ATTAAAAATAA
1 AAAATA-TAAAAAGTATTAAAAATAA
* *
21409481 AAAAGTATAAAAAGTATTAAATATTA
1 AAAA-TATAAAAAGTATTAAAAATAA
*
21409507 AAAATATTAAAA
1 AAAATATAAAAA
21409519 TTGATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 10 0.31
25 9 0.28
26 13 0.41
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (25 bp):
AAAATATAAAAAGTATTAAAAATAA
Found at i:21409546 original size:29 final size:29
Alignment explanation
Indices: 21409505--21409621 Score: 95
Period size: 29 Copynumber: 4.1 Consensus size: 29
21409495 TATTAAATAT
* *
21409505 TAAAAA-TATTAAAATTGATATAAAATTA
1 TAAAAATTATAAAAAATGATATAAAATTA
*
21409533 TAAAAATTATTAAAAATGATA-AAAACTTA
1 TAAAAATTATAAAAAATGATATAAAA-TTA
* * *
21409562 -AAAATATTAGAAAAAAT-ATATAAAAATC
1 TAAAA-ATTATAAAAAATGATATAAAATTA
21409590 TAATAAATTAT-AAAAAT--TATAAAATTAA
1 TAA-AAATTATAAAAAATGATATAAAATT-A
21409618 TAAA
1 TAAA
21409622 GCATATTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
27 9 0.12
28 27 0.36
29 36 0.49
30 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAAAATTATAAAAAATGATATAAAATTA
Found at i:21409581 original size:55 final size:53
Alignment explanation
Indices: 21409452--21409613 Score: 145
Period size: 57 Copynumber: 3.0 Consensus size: 53
21409442 TTAATATTTT
* *
21409452 CTTATAAAATATT-AAAAAAT-TAAAAATA-AAAAAGTATAAAAA-GTATTAAATA
1 CTTA-AAAATATTAAAAAAATATAAAAATATAAAAATTATAAAAATG-A-TAAAAA
** *
21409504 -TTAAAAATATTAAAATTGATATAAAATTATAAAAATTATTAAAAATGATAAAAA
1 CTTAAAAATATTAAAA-AAATATAAAAATATAAAAATTA-TAAAAATGATAAAAA
* *
21409558 CTTAAAAATATTAGAAAAAATATATAAAAATCTAATAAATTATAAAAATTATAAAA
1 CTTAAAAATATT--AAAAAA-ATATAAAAATATAA-AAATTATAAAAATGATAAAA
21409614 TTAATAAAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
50 8 0.09
51 6 0.07
52 2 0.02
53 7 0.08
54 12 0.13
55 18 0.20
56 1 0.01
57 29 0.33
58 6 0.07
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (53 bp):
CTTAAAAATATTAAAAAAATATAAAAATATAAAAATTATAAAAATGATAAAAA
Found at i:21409701 original size:9 final size:9
Alignment explanation
Indices: 21409453--21409883 Score: 126
Period size: 9 Copynumber: 46.0 Consensus size: 9
21409443 TAATATTTTC
21409453 TTATAAAATA
1 TTATAAAA-A
21409463 TTA-AAAAA
1 TTATAAAAA
21409471 -T-TAAAAA
1 TTATAAAAA
21409478 -TA-AAAAA
1 TTATAAAAA
*
21409485 GTATAAAAA
1 TTATAAAAA
* *
21409494 GTAT-TAAA
1 TTATAAAAA
21409502 -TATTAAAAA
1 TTA-TAAAAA
*
21409511 -TATTAAAA
1 TTATAAAAA
21409519 TTGATATAAAA
1 TT-ATA-AAAA
21409530 TTATAAAAA
1 TTATAAAAA
21409539 TTATTAAAAA
1 TTA-TAAAAA
*
21409549 TGATAAAAA
1 TTATAAAAA
21409558 CTTA-AAAATA
1 -TTATAAAA-A
*
21409568 TTAGAAAAAA
1 TTA-TAAAAA
21409578 TATATAAAAA
1 T-TATAAAAA
*
21409588 TCTA-ATAAA
1 T-TATAAAAA
21409597 TTATAAAAA
1 TTATAAAAA
21409606 TTAT-AAAA
1 TTATAAAAA
21409614 TTAATAAAGCATA
1 TT-ATAAA--A-A
21409627 TT-TAAAATA
1 TTATAAAA-A
*
21409636 TT-TAAAATT
1 TTATAAAA-A
21409645 TTATAAAAA
1 TTATAAAAA
*
21409654 CGTATAAAAA
1 -TTATAAAAA
* *
21409664 TTCTTTAAAAC
1 -T-TATAAAAA
21409675 TTATAAAAAA
1 TTAT-AAAAA
*
21409685 TCAT-AAAA
1 TTATAAAAA
21409693 TTATAAAAA
1 TTATAAAAA
* *
21409702 -AATTAAATA
1 TTA-TAAAAA
**
21409711 TTATAAATG
1 TTATAAAAA
*
21409720 TTAT-TAAA
1 TTATAAAAA
* *
21409728 -TATTAAAT
1 TTATAAAAA
*
21409736 TTGATATAAAC
1 TT-ATA-AAAA
21409747 TTATAAAAA
1 TTATAAAAA
*
21409756 TTATTAACCAGA
1 TTA-TAA--AAA
*
21409768 TCATAAAAA
1 TTATAAAAA
*
21409777 CTTATAAATA
1 -TTATAAAAA
*
21409787 TTGTAAAAA
1 TTATAAAAA
21409796 -TATAAAAA
1 TTATAAAAA
*
21409804 TCTAATAAATTAT
1 T-T-ATAAA--AA
*
21409817 TTATAAAAT
1 TTATAAAAA
21409826 TTATAAAATA
1 TTATAAAA-A
* *
21409836 TATTTAAAATT
1 T-TATAAAA-A
21409847 TTATAAAAA
1 TTATAAAAA
* *
21409856 CCTGT-AAAA
1 -TTATAAAAA
*
21409865 TATAAAAAAA
1 T-TATAAAAA
21409875 TTATAAAAA
1 TTATAAAAA
21409884 ATTCATTTAA
Statistics
Matches: 322, Mismatches: 53, Indels: 93
0.69 0.11 0.20
Matches are distributed among these distances:
7 17 0.05
8 38 0.12
9 125 0.39
10 83 0.26
11 48 0.15
12 6 0.02
13 5 0.02
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:21409834 original size:21 final size:21
Alignment explanation
Indices: 21409810--21409854 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21409800 AAAATCTAAT
21409810 AAAT-TATTTATAAAATTTATA
1 AAATATATTTA-AAAATTTATA
*
21409831 AAATATATTTAAAATTTTATA
1 AAATATATTTAAAAATTTATA
21409852 AAA
1 AAA
21409855 ACCTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATATTTAAAAATTTATA
Found at i:21413114 original size:26 final size:26
Alignment explanation
Indices: 21413062--21413115 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
21413052 TCGAACCGAG
** *
21413062 TAAGATGGAATTAGAATTGAATTGAA
1 TAAGATGGAATTAGAATCAAATCGAA
*
21413088 TAAGATGGAATTCGAATCAAATCGAA
1 TAAGATGGAATTAGAATCAAATCGAA
21413114 TA
1 TA
21413116 TATTTGTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (26 bp):
TAAGATGGAATTAGAATCAAATCGAA
Found at i:21417443 original size:27 final size:29
Alignment explanation
Indices: 21417395--21417458 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
21417385 TAAAAATGTA
*
21417395 TTAAAAATATTTTTA-TAATTTTT-AATT
1 TTAAAAATATTTCTATTAATTTTTGAATT
*
21417422 TTAAAAATAATTTCTATT-TTTTTTGAATT
1 TTAAAAAT-ATTTCTATTAATTTTTGAATT
*
21417451 TTTAAAAT
1 TTAAAAAT
21417459 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 11 0.35
29 12 0.39
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTAAAAATATTTCTATTAATTTTTGAATT
Found at i:21417444 original size:28 final size:28
Alignment explanation
Indices: 21417395--21417458 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
21417385 TAAAAATGTA
*
21417395 TTAAAAATATTTTTATAATTTTT-AATT
1 TTAAAAATATTTCTATAATTTTTGAATT
**
21417422 TTAAAAATAATTTCTATTTTTTTTGAATT
1 TTAAAAAT-ATTTCTATAATTTTTGAATT
*
21417451 TTTAAAAT
1 TTAAAAAT
21417459 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.26
28 12 0.39
29 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTAAAAATATTTCTATAATTTTTGAATT
Found at i:21417631 original size:3 final size:3
Alignment explanation
Indices: 21417623--21417653 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21417613 TTAAATTGAC
21417623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21417654 AAAGTTGAGA
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21418151 original size:38 final size:38
Alignment explanation
Indices: 21418108--21418224 Score: 112
Period size: 38 Copynumber: 3.0 Consensus size: 38
21418098 AAATTAGTTC
21418108 AAATCTTATGAACATTAAAATTTAATAGTTGGATATTA
1 AAATCTTATGAACATTAAAATTTAATAGTTGGATATTA
* * ** *
21418146 AAATCTTACG-ACTATTAAAATTTAATTGTTAAAAATTA
1 AAATCTTATGAAC-ATTAAAATTTAATAGTTGGATATTA
*
21418184 ACAATACTGTTATGACCATTAAAATTTAA-AGGTTGGATATT
1 A-AAT-C--TTATGAACATTAAAATTTAATA-GTTGGATATT
21418225 GTTATTTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
37 2 0.03
38 31 0.51
39 3 0.05
40 1 0.02
42 23 0.38
43 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (38 bp):
AAATCTTATGAACATTAAAATTTAATAGTTGGATATTA
Found at i:21419234 original size:14 final size:14
Alignment explanation
Indices: 21419215--21419243 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21419205 ATAGAAACAC
21419215 TCAAAAACCCAATA
1 TCAAAAACCCAATA
21419229 TCAAAAACCCAATA
1 TCAAAAACCCAATA
21419243 T
1 T
21419244 ATGTATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (14 bp):
TCAAAAACCCAATA
Found at i:21423063 original size:102 final size:102
Alignment explanation
Indices: 21422939--21423141 Score: 388
Period size: 102 Copynumber: 2.0 Consensus size: 102
21422929 GAGATTGACA
*
21422939 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACATGAATGATCTCAATGGC
1 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
*
21423004 AATCTAAATGATCACATTGAGAATCTTCACATGGGCT
66 AATCTAAATGATCACATTGAGAATCCTCACATGGGCT
21423041 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
1 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
21423106 AATCTAAATGATCACATTGAGAATCCTCACATGGGC
66 AATCTAAATGATCACATTGAGAATCCTCACATGGGC
21423142 CGTGTGGTGG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (102 bp):
GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
AATCTAAATGATCACATTGAGAATCCTCACATGGGCT
Found at i:21425626 original size:12 final size:12
Alignment explanation
Indices: 21425609--21425636 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21425599 GACCTATCAG
21425609 TTTTGATGAACA
1 TTTTGATGAACA
21425621 TTTTGATGAACA
1 TTTTGATGAACA
21425633 TTTT
1 TTTT
21425637 TTGGTAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (12 bp):
TTTTGATGAACA
Found at i:21438603 original size:27 final size:27
Alignment explanation
Indices: 21438573--21438634 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
21438563 ACCTAAATCC
21438573 AAATGTAAAAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
* *
21438600 AAATGGAAAACCCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
21438627 AAATGTAA
1 AAATGTAA
21438635 TACCTACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (27 bp):
AAATGTAAAAACCTTATGGTTTCATTA
Found at i:21439576 original size:27 final size:27
Alignment explanation
Indices: 21439520--21439577 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
21439510 AGGTCAAAAC
* * *
21439520 TTTATTTTAAAAATTTAAAATTTTTAT
1 TTTATTTTAAAAATCTAAAATCTCTAT
* *
21439547 TTTATTTTTAAAAATCTAAACTCTCTTT
1 TTTA-TTTTAAAAATCTAAAATCTCTAT
21439575 TTT
1 TTT
21439578 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATTTTAAAAATCTAAAATCTCTAT
Found at i:21439877 original size:148 final size:149
Alignment explanation
Indices: 21439545--21439884 Score: 424
Period size: 148 Copynumber: 2.3 Consensus size: 149
21439535 TAAAATTTTT
*
21439545 ATTTTATTTTT-AAAAATCTAAAC--TCTC-TTTTTTTAAAAAAAAAGTCACTATTTTTCTTAAA
1 ATTTT-TTTTTGAAAAATCTAAACTTTCTCATTTTTTT---TAAAAAGTCACTATTTTTCTTAAA
* * * * *
21439606 AGTTAAAGCTTTATTTCGAAATGGTTGAACAAGATCAAAACGTTGTTGTAAAAAATTTAAACTTT
62 AATCAAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTT
21439671 TCCTTTAAAATGACTAAAAAAAG
127 TCCTTTAAAATGACTAAAAAAAG
*
21439694 ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTTAAAA-TCACTATTTTTCTTAAAAATC
1 ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTAAAAAGTCACTATTTTTCTTAAAAATC
* * * *
21439758 AAAACTTTATTTCGAAATTGTTGAAAAAGATTAAAACTTTGTT-TTAAAAATTTAAAATTTTCCT
66 AAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTTTCCT
* * *
21439822 TTAATATGACTAAAAACAT
131 TTAAAATGACTAAAAAAAG
* * *
21439841 ATTTTTATTTT-AAAACTTTAAACTTTCTCTTTTTTTTTTAAAAA
1 ATTTTT-TTTTGAAAAATCTAAACTTTCTC-ATTTTTTTTAAAAA
21439885 AAAGATCAAA
Statistics
Matches: 167, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
147 57 0.34
148 78 0.47
149 21 0.13
151 4 0.02
152 7 0.04
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (149 bp):
ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTAAAAAGTCACTATTTTTCTTAAAAATC
AAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTTTCCT
TTAAAATGACTAAAAAAAG
Found at i:21440208 original size:39 final size:39
Alignment explanation
Indices: 21440153--21440354 Score: 273
Period size: 39 Copynumber: 5.2 Consensus size: 39
21440143 TAGTAGATAA
*
21440153 CTGTTGTACTTCGGTACCCCTGACCGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* *
21440192 CTGTTGTACTTTGGTACCCCTGATTGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * *
21440231 TTGTTGTACTTCGGTACCCCTGATCAG-ACTTACGTTCCC
1 CTGTTGTACTTCGGTACCCCTGA-CTGCACTTACGTGCCC
21440270 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * * * *
21440309 CTGTTGTACTTCAGTA-CCCTTATTTGCACTCATGTGCCC
1 CTGTTGTACTTCGGTACCCCTGA-CTGCACTTACGTGCCC
21440348 CTGTTGT
1 CTGTTGT
21440355 TCGGTACGCC
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
38 7 0.05
39 136 0.94
40 1 0.01
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (39 bp):
CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
Found at i:21440261 original size:20 final size:20
Alignment explanation
Indices: 21440158--21440292 Score: 68
Period size: 19 Copynumber: 6.9 Consensus size: 20
21440148 GATAACTGTT
**
21440158 GTACTTCGGTACCCCTGACC
1 GTACTTCGGTACCCCTGATA
* * *
21440178 GCACTTAC-GTGCCCCTG-TT
1 GTACTT-CGGTACCCCTGATA
* *
21440197 GTACTTTGGTACCCCTGATT
1 GTACTTCGGTACCCCTGATA
* * * *
21440217 GCACTTAC-GTGCCCTTG-TT
1 GTACTT-CGGTACCCCTGATA
21440236 GTACTTCGGTACCCCTGATCA
1 GTACTTCGGTACCCCTGAT-A
* *
21440257 G-ACTTAC-GTTCCCCTG-TT
1 GTACTT-CGGTACCCCTGATA
21440275 GTACTTCGGTACCCCTGA
1 GTACTTCGGTACCCCTGA
21440293 CTGCACTTAC
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
18 3 0.03
19 40 0.47
20 40 0.47
21 3 0.03
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (20 bp):
GTACTTCGGTACCCCTGATA
Found at i:21440309 original size:20 final size:20
Alignment explanation
Indices: 21440166--21440311 Score: 97
Period size: 20 Copynumber: 7.5 Consensus size: 20
21440156 TTGTACTTCG
**
21440166 GTACCCCTGACCGCACTTAC
1 GTACCCCTGATTGCACTTAC
* * **
21440186 GTGCCCCTG-TTGTACTTTG
1 GTACCCCTGATTGCACTTAC
21440205 GTACCCCTGATTGCACTTAC
1 GTACCCCTGATTGCACTTAC
* * *
21440225 GTGCCCTTG-TTGTACTT-C
1 GTACCCCTGATTGCACTTAC
*
21440243 GGTACCCCTGATCAG-ACTTAC
1 -GTACCCCTGAT-TGCACTTAC
* *
21440264 GTTCCCCTG-TTGTACTT-C
1 GTACCCCTGATTGCACTTAC
*
21440282 GGTACCCCTGACTGCACTTAC
1 -GTACCCCTGATTGCACTTAC
*
21440303 GTGCCCCTG
1 GTACCCCTG
21440312 TTGTACTTCA
Statistics
Matches: 95, Mismatches: 22, Indels: 18
0.70 0.16 0.13
Matches are distributed among these distances:
18 3 0.03
19 40 0.42
20 49 0.52
21 3 0.03
ACGTcount: A:0.14, C:0.35, G:0.20, T:0.32
Consensus pattern (20 bp):
GTACCCCTGATTGCACTTAC
Found at i:21447522 original size:31 final size:28
Alignment explanation
Indices: 21447484--21447565 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 28
21447474 TGCATGTTTT
21447484 AATGAGTTCAAACTATATCAAATGGATATCA
1 AATGAGTTCAAACTATATCAAAT-G-T-TCA
* **
21447515 AATGAGTTCAAACTATATTAAAATGTTTT
1 AATGAGTTCAAACTATA-TCAAATGTTCA
*
21447544 AATGAGTTCAAACTATTTCAAA
1 AATGAGTTCAAACTATATCAAA
21447566 AGAAATATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 1 0.02
31 18 0.40
32 5 0.11
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (28 bp):
AATGAGTTCAAACTATATCAAATGTTCA
Found at i:21454158 original size:21 final size:21
Alignment explanation
Indices: 21454132--21454177 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21454122 CATGGGTGAG
** *
21454132 CACACGGGTGTGTGGAGTAGC
1 CACACGGGCATGTGGAATAGC
21454153 CACACGGGCATGTGGAATAGC
1 CACACGGGCATGTGGAATAGC
21454174 CACA
1 CACA
21454178 TGGCCTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.35, T:0.15
Consensus pattern (21 bp):
CACACGGGCATGTGGAATAGC
Found at i:21455364 original size:15 final size:15
Alignment explanation
Indices: 21455346--21455390 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
21455336 ACATATTGAG
* *
21455346 ATTAAACATCATTTC
1 ATTAAAGATCATGTC
21455361 ATTAAAGATCATGTC
1 ATTAAAGATCATGTC
21455376 ATTAAAGATCATGTC
1 ATTAAAGATCATGTC
21455391 CAAAAAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (15 bp):
ATTAAAGATCATGTC
Found at i:21456004 original size:21 final size:21
Alignment explanation
Indices: 21455958--21455998 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21455948 ACAATTTTAG
*
21455958 CGATAC-T-TTTAAAAATTAT
1 CGATACTTGTTTAAAAAGTAT
21455977 CGATACTTGTTTAAAAAGTAT
1 CGATACTTGTTTAAAAAGTAT
21455998 C
1 C
21455999 AGTACTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
CGATACTTGTTTAAAAAGTAT
Found at i:21470675 original size:29 final size:31
Alignment explanation
Indices: 21470627--21470691 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
21470617 TTGATAATTT
* * *
21470627 AAGTATCACATTAGACA-TTT-TTAATATAC
1 AAGTATCACATGAAACATTTTATTAAAATAC
*
21470656 AAGTATCACATGAAATATTTTATTAAAATAC
1 AAGTATCACATGAAACATTTTATTAAAATAC
21470687 AAGTA
1 AAGTA
21470692 CCAAATGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 3 0.10
31 13 0.43
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (31 bp):
AAGTATCACATGAAACATTTTATTAAAATAC
Found at i:21475512 original size:14 final size:14
Alignment explanation
Indices: 21475495--21475533 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
21475485 ACCTCATATA
21475495 AATTTTCTATAAAT
1 AATTTTCTATAAAT
*
21475509 AATTTT-TAAAAAT
1 AATTTTCTATAAAT
21475522 AATTTTCTATAA
1 AATTTTCTATAA
21475534 TTATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTCTATAAAT
Found at i:21475660 original size:19 final size:20
Alignment explanation
Indices: 21475638--21475694 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
21475628 CATTTTCAAC
21475638 ATTATTTTTAATAATTT-TT
1 ATTATTTTTAATAATTTCTT
* *
21475657 ATTAATTTTAACAATTTCTT
1 ATTATTTTTAATAATTTCTT
* *
21475677 ATCATTTTAAATAATTTC
1 ATTATTTTTAATAATTTC
21475695 CTTTTTTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTTTTAATAATTTCTT
Found at i:21475692 original size:20 final size:20
Alignment explanation
Indices: 21475638--21475694 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
21475628 CATTTTCAAC
*
21475638 ATTATTTTTAATAATTT-TT
1 ATTAATTTTAATAATTTCTT
*
21475657 ATTAATTTTAACAATTTCTT
1 ATTAATTTTAATAATTTCTT
*
21475677 A-TCATTTTAAATAATTTC
1 ATTAATTTT-AATAATTTC
21475695 CTTTTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAATTTTAATAATTTCTT
Found at i:21476531 original size:21 final size:21
Alignment explanation
Indices: 21476502--21476542 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21476492 TGCTTTTGTT
*
21476502 CTTTTATACTTTTATATAATC
1 CTTTCATACTTTTATATAATC
21476523 CTTTCATACTTTTATATAAT
1 CTTTCATACTTTTATATAAT
21476543 TTATATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (21 bp):
CTTTCATACTTTTATATAATC
Found at i:21480885 original size:29 final size:30
Alignment explanation
Indices: 21480849--21481035 Score: 183
Period size: 29 Copynumber: 6.4 Consensus size: 30
21480839 TGTATAAGTG
*
21480849 AGCCTTTGTGGCT-ATCTCTGTTAAATGGA
1 AGCCTTTGTGGCTGATCTATGTTAAATGGA
* * *
21480878 AGTCTTTGTGGC-CATCTATGTTCAATGGA
1 AGCCTTTGTGGCTGATCTATGTTAAATGGA
21480907 AGCCTTTGTGGC-GATCTATGTTAATATGGA
1 AGCCTTTGTGGCTGATCTATGTTAA-ATGGA
* *
21480937 AGCCTTTGTGG-TGATCTCTGTTATAA-GAA
1 AGCCTTTGTGGCTGATCTATGTTA-AATGGA
** *
21480966 AGTGTTTGTGG-TGATCTATGTTATAA-GAA
1 AGCCTTTGTGGCTGATCTATGTTA-AATGGA
* *
21480995 AGCCTTTGTGG-TGATCTCTGTTAAAAGGA
1 AGCCTTTGTGGCTGATCTATGTTAAATGGA
*
21481024 AGCCTTTATGGC
1 AGCCTTTGTGGC
21481036 AACCTTTGCT
Statistics
Matches: 136, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.01
29 106 0.78
30 27 0.20
31 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (30 bp):
AGCCTTTGTGGCTGATCTATGTTAAATGGA
Found at i:21480998 original size:88 final size:87
Alignment explanation
Indices: 21480849--21481035 Score: 227
Period size: 88 Copynumber: 2.1 Consensus size: 87
21480839 TGTATAAGTG
* * *
21480849 AGCCTTTGTGGCTATCTCTGTTAAATGGAAGTCTTTGTGGCCATCTATGTTCAATGGAAGCCTTT
1 AGCCTTTGTGGCTATCTCTGTTAAATGAAAGTCTTTGTGGCCATCTATGTTCAAAGAAAGCCTTT
*
21480914 GTGGCGATCTATGTTAATATGGA
66 GTGGCGATCTATGTTAA-AAGGA
* **
21480937 AGCCTTTGTGG-TGATCTCTGTTATAA-GAAAGTGTTTGTGGTGATCTATGTT-ATAAGAAAGCC
1 AGCCTTTGTGGCT-ATCTCTGTTA-AATGAAAGTCTTTGTGGCCATCTATGTTCA-AAGAAAGCC
* *
21480999 TTTGTGGTGATCTCTGTTAAAAGGA
63 TTTGTGGCGATCTATGTTAAAAGGA
*
21481024 AGCCTTTATGGC
1 AGCCTTTGTGGC
21481036 AACCTTTGCT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
87 16 0.19
88 67 0.79
89 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (87 bp):
AGCCTTTGTGGCTATCTCTGTTAAATGAAAGTCTTTGTGGCCATCTATGTTCAAAGAAAGCCTTT
GTGGCGATCTATGTTAAAAGGA
Found at i:21499840 original size:184 final size:184
Alignment explanation
Indices: 21499531--21499888 Score: 603
Period size: 184 Copynumber: 1.9 Consensus size: 184
21499521 CTTGCGACAA
* * *
21499531 CCATCACATACCATCAACCCTATTGATCATATATCAGCTGCCTCTTTCAGGATCAATCGAGTCCT
1 CCATCACATACCATCAACCCTATTGATCACATATCAGCGGCCTCTTTCAGGATCAATCGAGTCCC
* *
21499596 AGCAAGCTCTGTCGATTACCATCGTCAACAATTGGAAGCAATCGGGACCTGTAGAACCTTGTGCG
66 AGCAAGCCCTATCGATTACCATCGTCAACAATTGGAAGCAATCGGGACCTGTAGAACCTTGTGCG
21499661 CCACCAGTCAACGACAACAGCAGAATTTTTTCAATAGTTTCCTTGGAGAGGCAG
131 CCACCAGTCAACGACAACAGCAGAATTTTTTCAATAGTTTCCTTGGAGAGGCAG
* * *
21499715 CCATCACATACCATTGATCCCTATTGATCACATA-CAGCGGCCTCTTTCGGGCA-CAATCGAGTC
1 CCATCACATACCA-TCAACCCTATTGATCACATATCAGCGGCCTCTTTCAGG-ATCAATCGAGTC
21499778 CCAGCAAGCCCTATCGATTACCATCGTCAACAATTGGAAGCAATCGGGACCTGTAGAACCTTGTG
64 CCAGCAAGCCCTATCGATTACCATCGTCAACAATTGGAAGCAATCGGGACCTGTAGAACCTTGTG
*
21499843 CGCCACCAGTCAACGGCAACAGCAGAATTTTTTCAATAGTTTCCTT
129 CGCCACCAGTCAACGACAACAGCAGAATTTTTTCAATAGTTTCCTT
21499889 AGATATTGTG
Statistics
Matches: 163, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
184 145 0.89
185 18 0.11
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (184 bp):
CCATCACATACCATCAACCCTATTGATCACATATCAGCGGCCTCTTTCAGGATCAATCGAGTCCC
AGCAAGCCCTATCGATTACCATCGTCAACAATTGGAAGCAATCGGGACCTGTAGAACCTTGTGCG
CCACCAGTCAACGACAACAGCAGAATTTTTTCAATAGTTTCCTTGGAGAGGCAG
Found at i:21502036 original size:20 final size:20
Alignment explanation
Indices: 21502011--21502063 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
21502001 TTATGTTAAC
* *
21502011 TTCAAATCATGTTGTTCATT
1 TTCAAATCATATTCTTCATT
21502031 TTCAAA--ATATTCTTCATT
1 TTCAAATCATATTCTTCATT
*
21502049 TACAAATCATTATTC
1 TTCAAATCA-TATTC
21502064 AATTTCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.56
20 7 0.26
21 5 0.19
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (20 bp):
TTCAAATCATATTCTTCATT
Found at i:21502048 original size:18 final size:19
Alignment explanation
Indices: 21502025--21502072 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
21502015 AATCATGTTG
*
21502025 TTCATTTTCAAAAT-ATTC
1 TTCATTTTCAAAATCATTA
*
21502043 TTCATTTAC-AAATCATTA
1 TTCATTTTCAAAATCATTA
*
21502061 TTCAATTTCAAA
1 TTCATTTTCAAA
21502073 TTTCAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (19 bp):
TTCATTTTCAAAATCATTA
Found at i:21505161 original size:12 final size:11
Alignment explanation
Indices: 21505134--21505171 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
21505124 GAAAATAGTC
21505134 AAAATTAATA-
1 AAAATTAATAT
21505144 AAAATTAACTAT
1 AAAATTAA-TAT
21505156 AAAATTAAT-T
1 AAAATTAATAT
21505166 AAAATT
1 AAAATT
21505172 CATCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:21510590 original size:40 final size:41
Alignment explanation
Indices: 21510525--21510614 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
21510515 TGAATTATGG
* *
21510525 AATT-CTGAATATTGTTTTTGAGTACTGAATTGAATTGTGA
1 AATTACTGAATATTGTTTATGAGTACTGAATTGAACTGTGA
* * *
21510565 AGTTACTGAATATTG-TTATGTGTACTGCATTGAACTGTGA
1 AATTACTGAATATTGTTTATGAGTACTGAATTGAACTGTGA
*
21510605 AATTATTGAA
1 AATTACTGAA
21510615 GTAATGAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 32 0.76
41 10 0.24
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (41 bp):
AATTACTGAATATTGTTTATGAGTACTGAATTGAACTGTGA
Found at i:21510886 original size:45 final size:45
Alignment explanation
Indices: 21510818--21510918 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
21510808 GCCAACTACT
* **
21510818 GTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACC
* *
21510863 GTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACC
21510908 GTTACTGTTAC
1 GTTACTGTTAC
21510919 TGCCACCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACC
Found at i:21511608 original size:21 final size:21
Alignment explanation
Indices: 21511584--21511627 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21511574 AATATTAGAG
21511584 TTATTTAAAATCCTACTAAGC
1 TTATTTAAAATCCTACTAAGC
21511605 TTATTTAAAATCCTACTAAGC
1 TTATTTAAAATCCTACTAAGC
21511626 TT
1 TT
21511628 GGGATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (21 bp):
TTATTTAAAATCCTACTAAGC
Found at i:21515141 original size:22 final size:22
Alignment explanation
Indices: 21515116--21515163 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
21515106 TTCTCTAATC
21515116 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21515138 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21515160 CTCT
1 CTCT
21515164 GAAACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:21515194 original size:51 final size:51
Alignment explanation
Indices: 21515138--21515250 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
21515128 TTCCAAAATT
*
21515138 CTCTCAATTTCCTTCCAAAATTCTCTGAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
* *
21515189 CTCTCAATTTCCTTCGAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
21515240 CCCTCAATTTC
1 CTCTCAATTTC
21515251 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:21515278 original size:10 final size:10
Alignment explanation
Indices: 21515251--21515316 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
21515241 CCTCAATTTC
*
21515251 ATTTTTTAAA
1 ATTTTTTTAA
**
21515261 ATAATTTTAA
1 ATTTTTTTAA
*
21515271 ATTTTTTTAT
1 ATTTTTTTAA
21515281 ATTTTTTTAAA
1 ATTTTTTT-AA
**
21515292 ATAATTTTAA
1 ATTTTTTTAA
*
21515302 ATTTTTTTAT
1 ATTTTTTTAA
21515312 ATTTT
1 ATTTT
21515317 CATCAATGGC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:21515290 original size:31 final size:31
Alignment explanation
Indices: 21515252--21515316 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
21515242 CTCAATTTCA
21515252 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
21515283 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
21515314 TTT
1 TTT
21515317 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATAT
Found at i:21517060 original size:18 final size:18
Alignment explanation
Indices: 21517034--21517068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21517024 ATGTGTGTTT
* *
21517034 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
21517052 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
21517069 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:21517600 original size:29 final size:29
Alignment explanation
Indices: 21517561--21517642 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
21517551 TAACACAATT
*
21517561 AACTAACTTAATTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTA
*
21517590 ACCTAATTTAATTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTA
21517619 AACTAATTTAATTAAAAACCCTAA
1 AACTAATTTAATTAAAAACCCTAA
21517643 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (29 bp):
AACTAATTTAATTAAAAACCCTAACCCTA
Found at i:21517686 original size:29 final size:28
Alignment explanation
Indices: 21517660--21517873 Score: 127
Period size: 29 Copynumber: 7.9 Consensus size: 28
21517650 TTACTAACAA
*
21517660 TTAACTAGTTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
21517688 CTAACCTAATTTAATTAAAAACCCTAACCC
1 TTAA-CTAATTTAATTAAAAACCCTAA-CC
*
21517718 TAAAC-AACTTTAATTAAAAACCCTAA--
1 TTAACTAA-TTTAATTAAAAACCCTAACC
* * * *
21517744 TT---TAATTTTACTAACAA--TTAA-C
1 TTAACTAATTTAATTAAAAACCCTAACC
** **
21517766 -TAACTTAA-TTAAAAACCCTAACCCTAA-C
1 TTAAC-TAATTTAATTA--AAAACCCTAACC
21517794 ----CTAATTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
21517818 CTAACCTAATTTAATTAAAAACCCTAACTC
1 TTAA-CTAATTTAATTAAAAACCCTAAC-C
*
21517848 TAAACTAATTTAATTAAAAACCCTAA
1 TTAACTAATTTAATTAAAAACCCTAA
21517874 TTTAATTTTA
Statistics
Matches: 144, Mismatches: 21, Indels: 41
0.70 0.10 0.20
Matches are distributed among these distances:
21 4 0.03
23 17 0.12
24 10 0.07
25 9 0.06
26 3 0.02
28 9 0.06
29 85 0.59
30 7 0.05
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
TTAACTAATTTAATTAAAAACCCTAACC
Found at i:21517705 original size:101 final size:101
Alignment explanation
Indices: 21517528--21518234 Score: 780
Period size: 101 Copynumber: 7.1 Consensus size: 101
21517518 TTTGATGTCA
21517528 TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
1 TAAAAACCCTAATTTAATTTTACT-A-ACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
*
21517593 TAATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
64 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
**
21517631 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAGTTTAATTAAAAACCCTAACCCTAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
*
21517696 ATTTAATTAAAAACCCTAACCCTAAAC-AACTTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACCTAA-TTTAAT
21517732 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
21517797 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
* * * * ***** **
21517833 TAAAAACCCTAACTCTAA----ACTAATTTAATTAA-AAACCCTAATTTAATTTTACTAACAATT
1 TAAAAACCCTAA-TTTAATTTTACTAA--CAATTAACTAA-CTTAA-TTAAAAACCCTAAC-CCT
*
21517893 AA-CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
60 AACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
** ** * ** * * ***** **
21517934 TAAAAACCCTAACCCTAA-CCTAAT-TTAATTAA-AAACCCTAATTTAATTTTACTAACAATTAA
1 TAAAAACCCTAA-TTTAATTTTACTAACAATTAACTAA-CTTAA-TTAAAAACCCTAAC-CCTAA
21517996 -CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
62 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
21518035 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
*
21518100 ATTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
** *
21518136 TAAAAACCC-----TAA---CCCTAAC------CTAACTTAATTAAAAACCCTAACCCTAAACTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
* *
21518187 ACTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
21518223 TAAAAACCCTAA
1 TAAAAACCCTAA
21518235 CCATTAACAC
Statistics
Matches: 542, Mismatches: 44, Indels: 49
0.85 0.07 0.08
Matches are distributed among these distances:
87 73 0.13
93 5 0.01
96 3 0.01
98 5 0.01
99 2 0.00
100 18 0.03
101 388 0.72
102 20 0.04
103 26 0.05
104 2 0.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (101 bp):
TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
ATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
Found at i:21517709 original size:130 final size:127
Alignment explanation
Indices: 21517563--21518236 Score: 556
Period size: 130 Copynumber: 5.2 Consensus size: 127
21517553 ACACAATTAA
* *
21517563 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA-ACTAATT
1 CTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAA-CCTAATACTAA--
* **** * *
21517627 TAATTAA-AAACCCTAATTTAATTTTACTAACAATTAA-CTAGTTTAATTAAAAACCCTAACCCT
63 CAATTAACAAA-CCTAA-TTAAAAACACTAAC-ACTAACCTAATTTAATTAAAAACCCTAACCCT
21517690 AAC
125 AAC
**
21517693 CTAATTTAATTAAAAACCCTAACCCTAAAC-AACTTTAATTAAAAACCCTAATTTAATTTTACTA
1 CTAATTTAATTAAAAACCCTAACCCTAAACTAA-TTTAATTAAAAACCCTAACCTAA---TACTA
* * * *
21517757 ACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
62 ACAATTAACAAACCTAATTAAAAACACTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAA
21517822 C
127 C
* **
21517823 CTAATTTAATTAAAAACCCTAACTCTAAACTAATTTAATTAAAAACCCTAATTTAATTTTACTAA
1 CTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCTAA---TACTAA
* * * *
21517888 CAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAC
63 CAATTAACAAACCTAATTAAAAACACTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAAC
* *
21517953 CTAATTTAATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAATTTAATTAAAAACCCTAA
1 CTAATTTAATTAAAAACCC-----T-A----AC---C-CTAAACTAATTTAATTAAAAACCCTAA
* * **** * *
21518018 CCCTAA-CCTAATTTAATTAA-AAACCCTAATTTAATTTTACTAACAATTAA-CTAACTTAATTA
52 -CCTAATACTAA--CAATTAACAAA-CCTAA-TTAAAAACACTAAC-ACTAACCTAATTTAATTA
21518080 AAAACCCTAACCCTAAC
111 AAAACCCTAACCCTAAC
* *
21518097 CTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACC-----CTAAC--
1 CTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCTAATACTAACAA
* * * * * * *
21518155 ----CTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAAA
66 TTAACAAACCTAATTAAAAACACTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAAC
21518213 CTAATTTAATTAAAAACCCTAACC
1 CTAATTTAATTAAAAACCCTAACC
21518237 ATTAACACAA
Statistics
Matches: 467, Mismatches: 47, Indels: 74
0.79 0.08 0.13
Matches are distributed among these distances:
115 3 0.01
116 61 0.13
117 4 0.01
118 2 0.00
125 4 0.01
129 10 0.02
130 252 0.54
131 13 0.03
132 2 0.00
133 5 0.01
134 2 0.00
135 1 0.00
136 1 0.00
138 1 0.00
139 1 0.00
140 2 0.00
141 4 0.01
142 2 0.00
143 10 0.02
144 81 0.17
145 6 0.01
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (127 bp):
CTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCTAATACTAACAA
TTAACAAACCTAATTAAAAACACTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAAC
Found at i:21517793 original size:35 final size:29
Alignment explanation
Indices: 21517765--21517873 Score: 173
Period size: 29 Copynumber: 3.8 Consensus size: 29
21517755 TAACAATTAA
21517765 CTAACTTAATTAAAAACCCTAACCCTAAC
1 CTAACTTAATTAAAAACCCTAACCCTAAC
*
21517794 CTAATTTAATTAAAAACCCTAACCCTAAC
1 CTAACTTAATTAAAAACCCTAACCCTAAC
* * *
21517823 CTAATTTAATTAAAAACCCTAACTCTAAA
1 CTAACTTAATTAAAAACCCTAACCCTAAC
*
21517852 CTAATTTAATTAAAAACCCTAA
1 CTAACTTAATTAAAAACCCTAA
21517874 TTTAATTTTA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (29 bp):
CTAACTTAATTAAAAACCCTAACCCTAAC
Found at i:21517917 original size:29 final size:29
Alignment explanation
Indices: 21517895--21517974 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
21517885 TAACAATTAA
*
21517895 CTAACTTAATTAAAAACCCTAACCCTAAC
1 CTAATTTAATTAAAAACCCTAACCCTAAC
21517924 CTAATTTAATTAAAAACCCTAACCCTAAC
1 CTAATTTAATTAAAAACCCTAACCCTAAC
21517953 CTAATTTAATTAAAAACCCTAA
1 CTAATTTAATTAAAAACCCTAA
21517975 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (29 bp):
CTAATTTAATTAAAAACCCTAACCCTAAC
Found at i:21517971 original size:231 final size:231
Alignment explanation
Indices: 21517563--21518046 Score: 898
Period size: 231 Copynumber: 2.1 Consensus size: 231
21517553 ACACAATTAA
*
21517563 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
1 CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
**
21517628 AATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAGTTTAATTAAAAACCCTAACCCTAAC
66 AATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
21517693 CTAATTTAATTAAAAACCCTAACCCTAAACAACTTTAATTAAAAACCCTAATTTAATTTTACTAA
131 CTAATTTAATTAAAAACCCTAACCCTAAACAACTTTAATTAAAAACCCTAATTTAATTTTACTAA
21517758 CAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
196 CAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
*
21517794 CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACTCTAAACTAATTT
1 CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
21517859 AATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
66 AATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
*
21517924 CTAATTTAATTAAAAACCCTAACCCTAACCTAA-TTTAATTAAAAACCCTAATTTAATTTTACTA
131 CTAATTTAATTAAAAACCCTAACCCTAAAC-AACTTTAATTAAAAACCCTAATTTAATTTTACTA
*
21517988 ACAATTAACTAATTTAATTAAAAACCCTAACCCTAAC
195 ACAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
21518025 CTAATTTAATTAAAAACCCTAA
1 CTAATTTAATTAAAAACCCTAA
21518047 TTTAATTTTA
Statistics
Matches: 246, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
231 244 0.99
232 2 0.01
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (231 bp):
CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
AATTAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
CTAATTTAATTAAAAACCCTAACCCTAAACAACTTTAATTAAAAACCCTAATTTAATTTTACTAA
CAATTAACTAACTTAATTAAAAACCCTAACCCTAAC
Found at i:21518090 original size:29 final size:28
Alignment explanation
Indices: 21518064--21518242 Score: 241
Period size: 29 Copynumber: 6.2 Consensus size: 28
21518054 TTACTAACAA
21518064 TTAACTAACTTAATTAAAAACCCTAACC
1 TTAACTAACTTAATTAAAAACCCTAACC
* *
21518092 CTAACCTAATTTAATTAAAAACCCTAACC
1 TTAA-CTAACTTAATTAAAAACCCTAACC
*
21518121 TTAACCTAATTTAATTAAAAACCCTAACC
1 TTAA-CTAACTTAATTAAAAACCCTAACC
*
21518150 CTAACCTAACTTAATTAAAAACCCTAACCC
1 TTAA-CTAACTTAATTAAAAACCCTAA-CC
*
21518180 TAAACTAACTTAATTAAAAACCCTAACCC
1 TTAACTAACTTAATTAAAAACCCTAA-CC
* *
21518209 TAAACTAATTTAATTAAAAACCCTAACC
1 TTAACTAACTTAATTAAAAACCCTAACC
21518237 ATTAAC
1 -TTAAC
21518243 ACAATTTTTG
Statistics
Matches: 139, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
28 5 0.04
29 130 0.94
30 4 0.03
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.27
Consensus pattern (28 bp):
TTAACTAACTTAATTAAAAACCCTAACC
Found at i:21518137 original size:58 final size:58
Alignment explanation
Indices: 21518064--21518242 Score: 297
Period size: 58 Copynumber: 3.1 Consensus size: 58
21518054 TTACTAACAA
21518064 TTAA-CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 TTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
* *
21518121 TTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 TTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
* * *
21518179 CTAAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACC
1 TTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
21518237 ATTAAC
1 -TTAAC
21518243 ACAATTTTTG
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 4 0.04
58 104 0.94
59 3 0.03
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.27
Consensus pattern (58 bp):
TTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
Found at i:21518166 original size:87 final size:87
Alignment explanation
Indices: 21518068--21518236 Score: 302
Period size: 87 Copynumber: 1.9 Consensus size: 87
21518058 TAACAATTAA
* * * *
21518068 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTT
1 CTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTT
21518133 AATTAAAAACCCTAACCCTAAC
66 AATTAAAAACCCTAACCCTAAC
21518155 CTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTT
1 CTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTT
21518220 AATTAAAAACCCTAACC
66 AATTAAAAACCCTAACC
21518237 ATTAACACAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (87 bp):
CTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTT
AATTAAAAACCCTAACCCTAAC
Found at i:21518299 original size:55 final size:55
Alignment explanation
Indices: 21518231--21518386 Score: 251
Period size: 55 Copynumber: 2.8 Consensus size: 55
21518221 ATTAAAAACC
*
21518231 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATATTA
*
21518286 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATATTTTGATAATATTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATATTA
* *
21518341 CTAACCATTAACAAAAAAATTTTGG-CTTAATAATTTTACATAATTT
1 CTAACCATTAAC--ACAATTTTTGGACTTAATAATTTTACATAATTT
21518387 TACATAATGT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
55 65 0.69
56 20 0.21
57 9 0.10
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (55 bp):
CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATATTA
Done.