Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 90 of 310
Found at i:28866422 original size:37 final size:37
Alignment explanation
Indices: 28866381--28866456 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 37
28866371 GTAATAAATT
*
28866381 TTCTCCGAAAAAAAAAGACAAAGATCAATAGTAAAGA
1 TTCTCCGAAAAAAAAAGACAAAGAACAATAGTAAAGA
* * * ** *
28866418 TTCTCTGCAAAGAAAAGACGGAGAAGAATAGTAAAGA
1 TTCTCCGAAAAAAAAAGACAAAGAACAATAGTAAAGA
28866455 TT
1 TT
28866457 TTTTTATAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.18
Consensus pattern (37 bp):
TTCTCCGAAAAAAAAAGACAAAGAACAATAGTAAAGA
Found at i:28866800 original size:56 final size:59
Alignment explanation
Indices: 28866708--28866838 Score: 178
Period size: 56 Copynumber: 2.2 Consensus size: 59
28866698 CCAAAATTTT
*
28866708 TTAACTTTCAAAAATTTAAGCTTTTGTTTTTCAAAAATTTAAATTCAAAATAAATAAAAA
1 TTAACTTTCAAAAATTTAAGC-TTTGTTTTTCAAAAATTTAAATTCAAAACAAATAAAAA
* * *
28866768 TTAACTTT-AAAAATTTTAG-TTT-TTTTTCAAAAATTTAAATTCAAAACAAATCAAAT
1 TTAACTTTCAAAAATTTAAGCTTTGTTTTTCAAAAATTTAAATTCAAAACAAATAAAAA
*
28866824 TTAAGTTTTCAAAAA
1 TTAA-CTTTCAAAAA
28866839 AATTTAATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
56 35 0.55
57 6 0.09
58 5 0.08
59 10 0.16
60 8 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (59 bp):
TTAACTTTCAAAAATTTAAGCTTTGTTTTTCAAAAATTTAAATTCAAAACAAATAAAAA
Found at i:28868045 original size:21 final size:21
Alignment explanation
Indices: 28868014--28868053 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28868004 ACAAAAAATC
28868014 TGTTATTTTTTATT-TTTTAA
1 TGTTATTTTTTATTGTTTTAA
28868034 TGTTATTTTTTTATTGTTTT
1 TGTTA-TTTTTTATTGTTTT
28868054 CTCCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (21 bp):
TGTTATTTTTTATTGTTTTAA
Found at i:28868094 original size:14 final size:14
Alignment explanation
Indices: 28868074--28868124 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
28868064 TGTTACCATT
*
28868074 TTATTATTATGTTA
1 TTATTATTTTGTTA
* *
28868088 CTATTATTTTGTTG
1 TTATTATTTTGTTA
28868102 TTATTATTTTGTTA
1 TTATTATTTTGTTA
28868116 TTATTATTT
1 TTATTATTT
28868125 GAATATTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (14 bp):
TTATTATTTTGTTA
Found at i:28870645 original size:22 final size:23
Alignment explanation
Indices: 28870620--28870663 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28870610 TTAAACATAC
*
28870620 CATTGTAATTGTAC-TATAATTA
1 CATTGTAATTATACTTATAATTA
*
28870642 CATTGTATTTATACTTATAATT
1 CATTGTAATTATACTTATAATT
28870664 TTTTATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (23 bp):
CATTGTAATTATACTTATAATTA
Found at i:28874465 original size:67 final size:67
Alignment explanation
Indices: 28874357--28874491 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
28874347 CCCAACATAC
*
28874357 TAAAAAAATACCCTAATAAATAACACACCTTTACTATAATTAATAATTAGTTATTAATTGTTATT
1 TAAAAAAACACCCTAATAAATAACACACCTTTACTATAATTAATAATTAGTTATTAATTGTTATT
28874422 AA
66 AA
28874424 TAAAAAAACACCCTAATAAATAACACACCTTTACTATAATTAATAATTAGTTATTAATTGTTATT
1 TAAAAAAACACCCTAATAAATAACACACCTTTACTATAATTAATAATTAGTTATTAATTGTTATT
28874489 AA
66 AA
28874491 T
1 T
28874492 TAATGTTCTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (67 bp):
TAAAAAAACACCCTAATAAATAACACACCTTTACTATAATTAATAATTAGTTATTAATTGTTATT
AA
Found at i:28874646 original size:19 final size:19
Alignment explanation
Indices: 28874622--28874681 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
28874612 ATTATTGTAT
28874622 TATTATTAAATATTATAAG
1 TATTATTAAATATTATAAG
*
28874641 TATTATT--ATAGTAT--G
1 TATTATTAAATATTATAAG
28874656 -ATTATTAAATATTATAAG
1 TATTATTAAATATTATAAG
28874674 TATTATTA
1 TATTATTA
28874682 TTATTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 6 0.18
17 6 0.18
18 1 0.03
19 14 0.41
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TATTATTAAATATTATAAG
Found at i:28874649 original size:33 final size:33
Alignment explanation
Indices: 28874610--28874710 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
28874600 AAACATATTT
28874610 TTATTATTGTATTATTATTAAATATTATAAGTA
1 TTATTATTGTATTATTATTAAATATTATAAGTA
* *
28874643 TTATTATAGTATGATTATTAAATATTATAAG--
1 TTATTATTGTATTATTATTAAATATTATAAGTA
*
28874674 -TATTA-T-TATTATTATTAAAGA-TATAAGTA
1 TTATTATTGTATTATTATTAAATATTATAAGTA
28874703 TTATTATT
1 TTATTATT
28874711 ATTCAACATA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
27 6 0.10
28 13 0.22
30 10 0.17
31 1 0.02
33 29 0.49
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (33 bp):
TTATTATTGTATTATTATTAAATATTATAAGTA
Found at i:28874708 original size:30 final size:31
Alignment explanation
Indices: 28874611--28874713 Score: 126
Period size: 30 Copynumber: 3.4 Consensus size: 31
28874601 AACATATTTT
*
28874611 TATTATT-GTATTATTATTAAATATTATAAG
1 TATTATTATTATTATTATTAAATATTATAAG
*
28874641 TATTATTATAGTATGATTATTAAATATTATAAG
1 TATTATTAT--TATTATTATTAAATATTATAAG
*
28874674 ---TATTATTATTATTATTAAAGA-TATAAG
1 TATTATTATTATTATTATTAAATATTATAAG
28874701 TATTATTATTATT
1 TATTATTATTATT
28874714 CAACATATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.10
28 13 0.21
30 23 0.37
33 21 0.33
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
TATTATTATTATTATTATTAAATATTATAAG
Found at i:28874710 original size:3 final size:3
Alignment explanation
Indices: 28874605--28874690 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
28874595 TTGTTAAACA
* * * * *
28874605 TAT TTT TAT TAT T-G TAT TAT TAT TAAA TAT TAT AAG TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
28874649 TAG TAT GAT TAT TAAA TAT TAT AAG TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
28874691 AAGATATAAG
Statistics
Matches: 60, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
2 3 0.05
3 53 0.88
4 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:28879192 original size:18 final size:18
Alignment explanation
Indices: 28879138--28879194 Score: 84
Period size: 17 Copynumber: 3.3 Consensus size: 18
28879128 CATGATCCAA
*
28879138 TTGAAAA-ATGAAAATTT
1 TTGAAAACACGAAAATTT
28879155 TT-AAAACACGAAAA-TT
1 TTGAAAACACGAAAATTT
28879171 TTGAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
28879189 TTGAAA
1 TTGAAA
28879195 CTTGAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 8 0.22
17 20 0.56
18 8 0.22
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.30
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:28879601 original size:70 final size:69
Alignment explanation
Indices: 28879472--28879610 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 69
28879462 ATACGTTGCC
* * *
28879472 TTATTTATTGAAATTAATTAGAATATGAGAAAAAAATATTCCTAAAGTGAGAAATTAAAAATAGA
1 TTATTTATTGAAATTAATTAGAACATGAAAAAAAAAAATTCCTAAAGTGAGAAATTAAAAATAGA
28879537 TAAA
66 TAAA
28879541 TTATTTATTGAAATTAATTAGAACATGACAAAAAAAAAATTCCTAAAGTGAGAAATTAAAAATAG
1 TTATTTATTGAAATTAATTAGAACATGA-AAAAAAAAAATTCCTAAAGTGAGAAATTAAAAATAG
28879606 ATAAA
65 ATAAA
28879611 GGACGCAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
69 27 0.41
70 39 0.59
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (69 bp):
TTATTTATTGAAATTAATTAGAACATGAAAAAAAAAAATTCCTAAAGTGAGAAATTAAAAATAGA
TAAA
Found at i:28881430 original size:12 final size:12
Alignment explanation
Indices: 28881413--28881443 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28881403 GTATTTTCAT
28881413 TATATATATATG
1 TATATATATATG
28881425 TATATATATATG
1 TATATATATATG
28881437 T-TATATA
1 TATATATA
28881444 GCATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:28881707 original size:22 final size:21
Alignment explanation
Indices: 28881677--28881719 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
28881667 TACTATGTAC
*
28881677 ACATATTATTATTTTTAATATAT
1 ACATATTA-TATGTTT-ATATAT
28881700 ACAT-TTATATGTTTATATAT
1 ACATATTATATGTTTATATAT
28881720 CGTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 3 0.16
23 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
ACATATTATATGTTTATATAT
Found at i:28881754 original size:17 final size:17
Alignment explanation
Indices: 28881721--28881754 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28881711 TTTATATATC
* *
28881721 GTTATTATTAGTCTTTT
1 GTTATTATTACTATTTT
28881738 GTTATTATTACTATTTT
1 GTTATTATTACTATTTT
28881755 TAATAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTATTATTACTATTTT
Found at i:28882972 original size:15 final size:17
Alignment explanation
Indices: 28882952--28882983 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28882942 TTAGGAAACG
28882952 TACATAA-A-AAATATA
1 TACATAATATAAATATA
28882967 TACATAATATAAATATA
1 TACATAATATAAATATA
28882984 ATATATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TACATAATATAAATATA
Found at i:28883533 original size:18 final size:18
Alignment explanation
Indices: 28883493--28883536 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28883483 AAATCATTTT
*
28883493 GAAGAGAGAAAGAAAAAA
1 GAAGGGAGAAAGAAAAAA
* * *
28883511 AAAGGGAGAAAGAAGAGA
1 GAAGGGAGAAAGAAAAAA
28883529 GAAGGGAG
1 GAAGGGAG
28883537 GGGGGAAAGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (18 bp):
GAAGGGAGAAAGAAAAAA
Found at i:28883611 original size:17 final size:18
Alignment explanation
Indices: 28883565--28883613 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
28883555 CCAAGGGGGG
* *
28883565 GCCGGTCACCGACCGATC
1 GCCGGCCACCGCCCGATC
* *
28883583 GTCGGCCGCCGCCCG-TC
1 GCCGGCCACCGCCCGATC
28883600 GCCGGCCACCGCCC
1 GCCGGCCACCGCCC
28883614 ACGGTGGCCG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.08, C:0.53, G:0.31, T:0.08
Consensus pattern (18 bp):
GCCGGCCACCGCCCGATC
Found at i:28884008 original size:19 final size:19
Alignment explanation
Indices: 28883984--28884034 Score: 95
Period size: 18 Copynumber: 2.7 Consensus size: 19
28883974 TTTCTTGGTT
28883984 TTTTTTTTTTGGGGTTAGG
1 TTTTTTTTTTGGGGTTAGG
28884003 TTTTTTTTTT-GGGTTAGG
1 TTTTTTTTTTGGGGTTAGG
28884021 TTTTTTTTTTGGGG
1 TTTTTTTTTTGGGG
28884035 GGAGGCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 18 0.58
19 13 0.42
ACGTcount: A:0.04, C:0.00, G:0.29, T:0.67
Consensus pattern (19 bp):
TTTTTTTTTTGGGGTTAGG
Found at i:28884892 original size:30 final size:30
Alignment explanation
Indices: 28884856--28884912 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28884846 TTTGAAAAAT
28884856 AGAAATT-AAAAGACTCAACTCAACTCTAGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTAGC
*
28884886 AGAAATTAAAAAGCTCAACTCACCTCT
1 AGAAATTAAAAAGCTCAACTCAACTCT
28884913 CGCAATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.21
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTAGC
Found at i:28885010 original size:24 final size:24
Alignment explanation
Indices: 28884983--28885031 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28884973 CCAAGGCTCA
*
28884983 ACTCACTTCTCGCAATATGAGTTG
1 ACTCACTTCTCGCAATATAAGTTG
28885007 ACTCACTTCTCGCAATATAAGTTG
1 ACTCACTTCTCGCAATATAAGTTG
28885031 A
1 A
28885032 TTTTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (24 bp):
ACTCACTTCTCGCAATATAAGTTG
Found at i:28885429 original size:75 final size:77
Alignment explanation
Indices: 28885304--28885468 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 77
28885294 TTGAAAAACG
* *
28885304 GAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCA-GTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTT
28885369 TTTTTT-ACAA-CA
65 TTTTTTGA-AAGCA
* * *
28885381 GAAATTGAAATTACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
28885445 TTTTTGAAAGGCA
66 TTTTTGAAA-GCA
28885458 GAAATTGAAAA
1 GAAATTGAAAA
28885469 ACGAAAATTG
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
75 48 0.61
76 1 0.01
77 30 0.38
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (77 bp):
GAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
TTTTTGAAAGCA
Found at i:28885617 original size:168 final size:167
Alignment explanation
Indices: 28885157--28885616 Score: 656
Period size: 167 Copynumber: 2.7 Consensus size: 167
28885147 ATACCTTAGT
* * * *
28885157 GTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAGACAGAAATTGA
1 GTGTGACCTGAGGCTCAACTCGCCTCTCGCAATATGAGTTGATTTTTTTGACA-ACAGAAATTGA
* * *** * * * * * * *
28885220 AAATAGCTCAGCACGTAAGCCAAGGTTCAACTTACCTCTTGTAATATAAGTCGA-TTTTTTTTGA
65 AATTACCTCAG--CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGA
*
28885284 AAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGC
128 AAGGCAGAAATTGAAAAACGAAAATTGAAAATACCTCGGC
* * *
28885324 ATGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTTTACAACAGAAATTGA
1 GTGTGACCTGAGGCTCAACTCGCCTCTCGCAATATGAGTTGA-TTTTTTTGACAACAGAAATTGA
*
28885389 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAA
65 AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAA
28885454 GGCAGAAATTGAAAAACGAAAATTGAAAATACCTCGGC
130 GGCAGAAATTGAAAAACGAAAATTGAAAATACCTCGGC
28885492 GTGTGACCTGAGGCTCAACTCGCCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAA
1 GTGTGACCTGAGGCTCAACTCGCCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAA
* *
28885557 ATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTGTCGCACTATGAGTTGATTTTTTTTT
66 ATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTT
28885617 TTTGAAAATA
Statistics
Matches: 262, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
167 146 0.56
168 89 0.34
169 20 0.08
170 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (167 bp):
GTGTGACCTGAGGCTCAACTCGCCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAA
ATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAG
GCAGAAATTGAAAAACGAAAATTGAAAATACCTCGGC
Found at i:28885662 original size:66 final size:66
Alignment explanation
Indices: 28885552--28885678 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
28885542 ACAACAGAAA
* * * *
28885552 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTGTCGCACTATGAGTTGATTTTTTTTT
1 TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTT
28885617 T
66 T
*
28885618 TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
28885679 GAAACATACG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (66 bp):
TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTT
T
Found at i:28893979 original size:12 final size:12
Alignment explanation
Indices: 28893957--28893992 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28893947 TGGGATATGC
*
28893957 AATGAATGAATG
1 AATGCATGAATG
*
28893969 GATGCATGAATG
1 AATGCATGAATG
28893981 AATGCATGAATG
1 AATGCATGAATG
28893993 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:28893979 original size:16 final size:17
Alignment explanation
Indices: 28893953--28893984 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28893943 AGTATGGGAT
28893953 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
28893970 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
28893985 CATGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:28895403 original size:18 final size:18
Alignment explanation
Indices: 28895361--28895405 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
28895351 AAAAAATGAG
28895361 AATTTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
28895378 AA-TTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
28895395 AATTTTTGAAA
1 AATTTTTGAAA
28895406 CCTGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 14 0.54
18 8 0.31
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:28896634 original size:19 final size:19
Alignment explanation
Indices: 28896598--28896636 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28896588 TTTTCATCAT
* *
28896598 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
28896617 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
28896636 A
1 A
28896637 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:28897130 original size:55 final size:55
Alignment explanation
Indices: 28897065--28897178 Score: 133
Period size: 55 Copynumber: 2.1 Consensus size: 55
28897055 AGCATGGCTG
* * * *
28897065 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-AGCCA
* * *
28897121 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCAAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCAAGCCA
28897175 CCAG
1 CCAG
28897179 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 8 0.16
55 21 0.42
56 21 0.42
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (55 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCAAGCCA
Found at i:28897174 original size:27 final size:28
Alignment explanation
Indices: 28897079--28897178 Score: 114
Period size: 27 Copynumber: 3.6 Consensus size: 28
28897069 ATACAGAAAA
* * *
28897079 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATAATT
* *
28897108 TGTGGCAGTGCCACCAGAACAGAT-ATA
1 TGTGGCAGAGCCACCAGAACAGATAATT
* *
28897135 CGTGGCAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
28897163 TGTGGCA-AGCCACCAG
1 TGTGGCAGAGCCACCAG
28897179 GACGCTTCCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 31 0.52
28 14 0.23
29 15 0.25
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGAACAGATAATT
Found at i:28897331 original size:28 final size:28
Alignment explanation
Indices: 28897284--28897348 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
28897274 AAATTAACCC
*
28897284 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
28897312 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
28897340 TAGGGGTAT
1 TAGGGGTAT
28897349 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:28899890 original size:12 final size:11
Alignment explanation
Indices: 28899873--28899902 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28899863 TATTCTATTG
28899873 AAAAAAATTAC
1 AAAAAAATTAC
28899884 AAAAAAATTAC
1 AAAAAAATTAC
28899895 AAAAAAAT
1 AAAAAAAT
28899903 CTTGTCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATTAC
Found at i:28903455 original size:49 final size:49
Alignment explanation
Indices: 28903385--28903756 Score: 489
Period size: 49 Copynumber: 7.5 Consensus size: 49
28903375 TGAGGTCATG
28903385 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATTGGTCGCA
* ** ***
28903434 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
28903484 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATTGGTCGCA
* ** ***
28903533 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
28903583 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATTGGTCGCA
* ** ***
28903632 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
28903682 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
28903731 TGTGTAGTACAAAGTGTAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28903757 TAATACCAGA
Statistics
Matches: 277, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
49 149 0.54
50 128 0.46
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:28903548 original size:99 final size:99
Alignment explanation
Indices: 28903377--28903756 Score: 726
Period size: 99 Copynumber: 3.8 Consensus size: 99
28903367 ATCTATTGTG
28903377 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
1 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
28903442 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
28903476 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
1 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
28903541 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
28903575 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
1 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
28903640 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
28903674 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AGATAATTGGTCGCATGTGTAG
1 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGA-ATAATTGGTCGCATGTGTAG
* *
28903738 TACAAAGTGTAGGCTACTA
65 TACTAAGTGCAGGCTACTA
28903757 TAATACCAGA
Statistics
Matches: 278, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
98 1 0.00
99 277 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (99 bp):
AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
Found at i:28903800 original size:198 final size:197
Alignment explanation
Indices: 28903377--28903801 Score: 651
Period size: 198 Copynumber: 2.1 Consensus size: 197
28903367 ATCTATTGTG
* * *
28903377 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
1 AGGTCAAGTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
28903442 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTGCAGGCTA
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTGCAGGCTA
* * *
28903507 CTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATG
131 CTACGTGTACCGAATAATTGGTCGCATGTGTAGTACAAAGTGCAGGCTACTAC-TATACCAGATG
*
28903572 GTT
195 CTT
* * *
28903575 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
1 AGGTCAAGTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
28903640 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTGCAGGCTA
66 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTGCAGGCTA
*
28903705 CTACGTGTACC-AGATAATTGGTCGCATGTGTAGTACAAAGTGTAGGCTACTA-TAATACCAGAT
131 CTACGTGTACCGA-ATAATTGGTCGCATGTGTAGTACAAAGTGCAGGCTACTACT-ATACCAGAT
28903768 AGCTT
194 -GCTT
* *
28903773 TGGCTACAAGTGTG-A-AAATATGTGCAGGC
1 AGG-T-CAAGTGTGTAGAAATAAGTGCAGGC
28903802 AACTGAGTAT
Statistics
Matches: 212, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
196 1 0.00
197 8 0.04
198 194 0.92
199 2 0.01
200 7 0.03
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (197 bp):
AGGTCAAGTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTGCAGGCTA
CTACGTGTACCGAATAATTGGTCGCATGTGTAGTACAAAGTGCAGGCTACTACTATACCAGATGC
TT
Found at i:28912290 original size:5 final size:5
Alignment explanation
Indices: 28912280--28912313 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
28912270 GATGCCAACC
28912280 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
28912314 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:28919182 original size:47 final size:47
Alignment explanation
Indices: 28919101--28919224 Score: 158
Period size: 47 Copynumber: 2.6 Consensus size: 47
28919091 ATGCCCTTCG
* * * * * *
28919101 GGACTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTC
1 GGACCTATCACATATATACACTTTCACATTCATCACATCGGCCACTA
* * *
28919148 GGCCCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 GGACCTATCACATATATACACTTTCACATTCATCACATCGGCCACTA
*
28919195 GGACTTATCACATATATACACTTTCACATT
1 GGACCTATCACATATATACACTTTCACATT
28919225 ACCAACCCTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
GGACCTATCACATATATACACTTTCACATTCATCACATCGGCCACTA
Found at i:28919554 original size:40 final size:40
Alignment explanation
Indices: 28919449--28919591 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
28919439 GCTACTCGTT
*
28919449 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28919489 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28919529 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28919570 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
28919592 AGACATCATT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
39 3 0.03
40 74 0.82
41 13 0.14
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28923465 original size:40 final size:40
Alignment explanation
Indices: 28923421--28923892 Score: 791
Period size: 40 Copynumber: 11.8 Consensus size: 40
28923411 CCAGCATGAT
* * * * *
28923421 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
28923461 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
28923501 TGCTCTTCGGAACTTAGCCTGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28923541 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28923581 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28923621 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28923661 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28923701 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28923741 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28923781 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28923821 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28923861 TGCTCTTCGAGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
28923893 CTTTCAAAAT
Statistics
Matches: 406, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 406 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28926806 original size:40 final size:40
Alignment explanation
Indices: 28926751--28927141 Score: 624
Period size: 40 Copynumber: 9.8 Consensus size: 40
28926741 CAGTATGTTA
28926751 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
28926791 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
** *
28926831 TATTTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
28926871 TATCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
28926911 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* * *
28926951 TATCCGGACTAGGTTCCGAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
** *
28926991 TATCCGGGCTAAGTCTTGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
* * *
28927031 TACCCGGGATAAGTCCCGAAGAGCATTCGTGCTGGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
28927071 TA-CCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
*
28927110 TATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
28927142 TGGACAAAAT
Statistics
Matches: 322, Mismatches: 28, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 47 0.15
40 275 0.85
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG
Found at i:28931152 original size:47 final size:47
Alignment explanation
Indices: 28931082--28931381 Score: 424
Period size: 47 Copynumber: 6.4 Consensus size: 47
28931072 GATGTACAAG
* * *
28931082 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* *
28931129 GTGTATATATATGTGAT-A-GCCTAATGGCCGATGTGATGAATGTGAAA
1 GTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
28931176 GTGTATATATGTGATAAGGCCGAATGGACAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* *
28931223 GTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
28931270 GTGTAGATATGAGATAAGACCTAATGGCCAATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
28931317 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
28931364 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
28931382 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
45 12 0.05
46 1 0.00
47 203 0.89
48 1 0.00
49 11 0.05
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:28943483 original size:11 final size:11
Alignment explanation
Indices: 28943469--28943498 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28943459 AGTTAATAAA
28943469 TCACTAATTTG
1 TCACTAATTTG
28943480 TCACTAATTTG
1 TCACTAATTTG
28943491 TCACTAAT
1 TCACTAAT
28943499 CATGCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (11 bp):
TCACTAATTTG
Found at i:28959125 original size:40 final size:40
Alignment explanation
Indices: 28959081--28959264 Score: 191
Period size: 40 Copynumber: 4.6 Consensus size: 40
28959071 GCTCCTCGTT
*
28959081 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
* *
28959121 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCA
*
28959161 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAAT-TCGCA
* ** * * *
28959200 CAAATGCCTTC-GGATCTTAGTCCGAATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCA
28959241 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28959265 ACATCACTCA
Statistics
Matches: 120, Mismatches: 14, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 29 0.24
40 73 0.61
41 14 0.12
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
Found at i:28959183 original size:79 final size:81
Alignment explanation
Indices: 28959081--28959265 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
28959071 GCTCCTCGTT
* *
28959081 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
* * *
28959143 CGGATTTAGTAAC-TCGCA
63 CGAATATAGTAACTTAGCA
**
28959161 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGA
* *
28959225 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
28959241 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28959266 CATCACTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 5 0.05
79 52 0.57
80 34 0.37
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGA
ATATAGTAACTTAGCA
Found at i:28966415 original size:40 final size:40
Alignment explanation
Indices: 28966371--28966715 Score: 491
Period size: 40 Copynumber: 8.7 Consensus size: 40
28966361 GCTCCTCGTT
* * *
28966371 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
28966411 CAAATGCCTTCGGAACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28966451 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28966491 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28966531 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28966571 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28966611 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
28966650 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
28966691 CAAA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28966716 CATCACTCAA
Statistics
Matches: 282, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
38 2 0.01
39 33 0.12
40 234 0.83
41 13 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28970578 original size:31 final size:31
Alignment explanation
Indices: 28970537--28970607 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
28970527 AATATTTTTA
28970537 ATTA-ATTTAATTGGTTAATTGAATTAAGTT
1 ATTATATTTAATTGGTTAATTGAATTAAGTT
28970567 ATTATATTTAATTGGTTAATTGAATTAAGTT
1 ATTATATTTAATTGGTTAATTGAATTAAGTT
28970598 ATTATATTTA
1 ATTATATTTA
28970608 GATTAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (31 bp):
ATTATATTTAATTGGTTAATTGAATTAAGTT
Found at i:28974651 original size:40 final size:40
Alignment explanation
Indices: 28974607--28975630 Score: 1862
Period size: 40 Copynumber: 25.6 Consensus size: 40
28974597 GCTCCTCGTT
* * * *
28974607 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28974647 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974687 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974727 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974767 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974807 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974847 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974887 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974927 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28974967 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975007 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975047 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975087 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975127 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975167 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975207 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975247 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975287 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975327 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975367 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975407 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975447 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28975487 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28975527 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
28975566 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
28975607 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28975631 CATCATTCAA
Statistics
Matches: 965, Mismatches: 13, Indels: 13
0.97 0.01 0.01
Matches are distributed among these distances:
38 2 0.00
39 49 0.05
40 905 0.94
41 9 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28984316 original size:22 final size:22
Alignment explanation
Indices: 28984288--28984352 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
28984278 GCAAATATGT
*
28984288 TTGGCACATAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
28984310 TTGGCACAAAGCAAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
28984332 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
28984353 AATAATTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:28984666 original size:98 final size:98
Alignment explanation
Indices: 28984494--28984677 Score: 332
Period size: 98 Copynumber: 1.9 Consensus size: 98
28984484 TGAAAGCCAC
*
28984494 CGGTGGATTCACGGTCGTCAAGCAACCATGCGATCCTCAATTTCTTCCTCTGTTTCATAATCCCC
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATTTCTTCCTCTGTTTCATAATCCCC
*
28984559 GACCCATGTGCATAATATTATGCGATCCTCAAT
66 CACCCATGTGCATAATATTATGCGATCCTCAAT
*
28984592 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATTTTTTCCTCTGTTTCATAATCCCC
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATTTCTTCCTCTGTTTCATAATCCCC
*
28984657 CACCTATGTGCATAATATTAT
66 CACCCATGTGCATAATATTAT
28984678 ATGAATGCAG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (98 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATTTCTTCCTCTGTTTCATAATCCCC
CACCCATGTGCATAATATTATGCGATCCTCAAT
Found at i:28984920 original size:27 final size:26
Alignment explanation
Indices: 28984890--28985255 Score: 268
Period size: 27 Copynumber: 13.6 Consensus size: 26
28984880 TGTAAATCTA
*
28984890 CAAACCAAGGGTATTTTGATAATTTTG
1 CAAATCAAGGGTATTTTG-TAATTTTG
* *
28984917 CAAACCAATGGTATTTCTGTAATTTTTG
1 CAAATCAAGGGTATTT-TGTAA-TTTTG
28984945 -AAAGTCAAGGGTATTTTTGTAATTTTG
1 CAAA-TCAAGGGTA-TTTTGTAATTTTG
* * *
28984972 TAAATCAGGGGTATTTCTGTAATTTTC
1 CAAATCAAGGGTATTT-TGTAATTTTG
28984999 CAAATCAAGGGTATTTTAGTAATTTT-
1 CAAATCAAGGGTATTTT-GTAATTTTG
* * *
28985025 CAAATTAGGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTT-GTAATTTTG
* * ** *
28985052 AAAATCAAGGGCATTTCAATAATTTTA
1 CAAATCAAGGGTATTT-TGTAATTTTG
** *
28985079 CACGTCAAGGGTATTTTAGTAATTTTA
1 CAAATCAAGGGTATTTT-GTAATTTTG
** * **
28985106 CAGGTCGAGGGTATTTTTGTAATTTAA
1 CAAATCAAGGGTA-TTTTGTAATTTTG
* *
28985133 CAAATCAGGGGTATTTTTGTAATTTTA
1 CAAATCAAGGGTA-TTTTGTAATTTTG
* * *
28985160 CGAACCAAGGGCATTTTGGTAATTTTG
1 CAAATCAAGGGTATTTT-GTAATTTTG
* *
28985187 CTAATCAAGGGTAATTTGGTAATTTTG
1 CAAATCAAGGGT-ATTTTGTAATTTTG
* * * **
28985214 TAAACCAACGGTATTCAGTAATTTTG
1 CAAATCAAGGGTATTTTGTAATTTTG
* *
28985240 TAAACCAAGGGTATTT
1 CAAATCAAGGGTATTT
28985256 CAGTAATTCT
Statistics
Matches: 279, Mismatches: 47, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
26 57 0.20
27 189 0.68
28 30 0.11
29 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (26 bp):
CAAATCAAGGGTATTTTGTAATTTTG
Found at i:28985227 original size:81 final size:81
Alignment explanation
Indices: 28984868--28985263 Score: 334
Period size: 81 Copynumber: 4.9 Consensus size: 81
28984858 TTTCACCCTA
* * * * * * * *
28984868 CAAGGGTGTTTTTGTAAATCTACAAACCAAGGGTATTT-TGATAATTTTGCAAACCAATGGTATT
1 CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTG-TAATTTTACAAACCAAGGGTATT
28984932 TCT-GTAATTTTTG-AAAGT
65 T-TAGTAA-TTTTGCAAA-T
* * * * *
28984950 CAAGGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTCTGTAATTTTCCAAATCAAGGGTATTT
1 CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTT
28985015 TAGTAATTTT-CAAAT
66 TAGTAATTTTGCAAAT
* * * * ** ***
28985030 TAGGGGTATTTTGGTAATTTTAAAAATCAAGGGCATTTCAATAATTTTACACGTCAAGGGTATTT
1 CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTT
* **
28985095 TAGTAATTTTACAGGT
66 TAGTAATTTTGCAAAT
* * * * * * * *
28985111 CGAGGGTATTTTTGTAATTTAACAAATCAGGGGTATTTTTGTAATTTTACGAACCAAGGGCATTT
1 CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTT
* *
28985176 TGGTAATTTTGCTAAT
66 TAGTAATTTTGCAAAT
* * * * * **
28985192 CAAGGGTAATTTGGTAATTTTGTAAACCAACGGTA-TTCAGTAATTTTGTAAACCAAGGGTATTT
1 CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTT
*
28985256 CAGTAATT
66 TAGTAATT
28985264 CTACCCTACA
Statistics
Matches: 248, Mismatches: 62, Indels: 10
0.77 0.19 0.03
Matches are distributed among these distances:
80 93 0.38
81 97 0.39
82 56 0.23
83 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (81 bp):
CAAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTT
TAGTAATTTTGCAAAT
Found at i:28985240 original size:26 final size:27
Alignment explanation
Indices: 28985205--28985263 Score: 102
Period size: 26 Copynumber: 2.2 Consensus size: 27
28985195 GGGTAATTTG
28985205 GTAATTTTGTAAACCAACGGTA-TTCA
1 GTAATTTTGTAAACCAACGGTATTTCA
*
28985231 GTAATTTTGTAAACCAAGGGTATTTCA
1 GTAATTTTGTAAACCAACGGTATTTCA
28985258 GTAATT
1 GTAATT
28985264 CTACCCTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (27 bp):
GTAATTTTGTAAACCAACGGTATTTCA
Found at i:28985275 original size:27 final size:27
Alignment explanation
Indices: 28985245--28985327 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
28985235 TTTTGTAAAC
*
28985245 CAAGGGTATTTCAGTAATTCTACCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
28985272 CAAGGGCATTTCAGTAATTCTACCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
* * * *
28985299 CTAGGGCATTTCAATAATACTAGCCTA
1 CAAGGGCATTTCAGTAATTCTACCCTA
28985326 CA
1 CA
28985328 GATATGAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (27 bp):
CAAGGGCATTTCAGTAATTCTACCCTA
Found at i:28989821 original size:48 final size:48
Alignment explanation
Indices: 28989761--28989939 Score: 322
Period size: 48 Copynumber: 3.7 Consensus size: 48
28989751 TCTCATATCG
28989761 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
** *
28989809 ATTTCATGTCCCAAACATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
28989857 ATGCCATGTCCCAGACATAGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
28989905 ATGCCATGTCCCAGACATGGTCTTACATGGGATCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCA
28989940 TAATGCCATA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 123 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
Found at i:28991497 original size:29 final size:29
Alignment explanation
Indices: 28991418--28991537 Score: 129
Period size: 29 Copynumber: 4.2 Consensus size: 29
28991408 ACCCCTACAT
* *
28991418 ATATGCATATGGCTCACTAGGCCCAATCTC
1 ATATTCATATGGCCCACTAGGCCCAAT-TC
* *
28991448 AT-TT-ATATGGTCCATCT-GGCCCAGTTC
1 ATATTCATATGGCCCA-CTAGGCCCAATTC
*
28991475 ATATTCTTATGGCCCACTAGGCCCAATTC
1 ATATTCATATGGCCCACTAGGCCCAATTC
* * *
28991504 ACATTCATATGGCCCATTAGGCCCAAATC
1 ATATTCATATGGCCCACTAGGCCCAATTC
28991533 ATATT
1 ATATT
28991538 ATACTCATGC
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
27 4 0.05
28 19 0.26
29 49 0.66
30 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (29 bp):
ATATTCATATGGCCCACTAGGCCCAATTC
Found at i:28991537 original size:58 final size:57
Alignment explanation
Indices: 28991425--28991537 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 57
28991415 CATATATGCA
* * * * **
28991425 TATGGCTCACTAGGCCCAATCTCATTTATATGGTCCATCTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCCAAATCATATTCT
28991482 TATGGCCCACTAGGCCCAATTCACATTCATATGGCCCAT-TAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATTCATATGGCCCATCT-GGCCCAAATCATATT
28991538 ATACTCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 19 0.40
58 29 0.60
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCCAAATCATATTCT
Found at i:28991632 original size:18 final size:19
Alignment explanation
Indices: 28991609--28991646 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28991599 ATGGGCCCAA
28991609 TAGCCCA-TCAGGCCCATT
1 TAGCCCATTCAGGCCCATT
*
28991627 TAGCCCATTCCGGCCCATT
1 TAGCCCATTCAGGCCCATT
28991646 T
1 T
28991647 GGCTAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.26
Consensus pattern (19 bp):
TAGCCCATTCAGGCCCATT
Found at i:28993056 original size:16 final size:16
Alignment explanation
Indices: 28993037--28993068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28993027 AAGTTTTGAA
28993037 TTTCAGAATTTTTGGG
1 TTTCAGAATTTTTGGG
*
28993053 TTTCAGGATTTTTGGG
1 TTTCAGAATTTTTGGG
28993069 GCATTACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCAGAATTTTTGGG
Found at i:28997305 original size:27 final size:27
Alignment explanation
Indices: 28997247--28997322 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
28997237 AATCTCATAT
* * * *
28997247 CTGTAGGCTAGCATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTAAAACACCC
* *
28997274 TTGTAGGGTAGAATTACTAAAACGCCC
1 CTGTAGGGTAGAATTACTAAAACACCC
*
28997301 CTGTAGGGTAGAATTACCAAAA
1 CTGTAGGGTAGAATTACTAAAA
28997323 TACCTTTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTAAAACACCC
Found at i:28997342 original size:27 final size:27
Alignment explanation
Indices: 28997312--28997483 Score: 175
Period size: 27 Copynumber: 6.4 Consensus size: 27
28997302 TGTAGGGTAG
* *
28997312 AATTACCAAAATACCTTTGGTTTATAA
1 AATTACCAAAATACCTCTGGTTTGTAA
*
28997339 AATTACCAAAATACCACTGGTTTGTAA
1 AATTACCAAAATACCTCTGGTTTGTAA
* *
28997366 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCTCTGGTTTGTAA
* *
28997393 AATTACCAAAATACCTCTGATTTGTGA
1 AATTACCAAAATACCTCTGGTTTGTAA
** * ***
28997420 AATTACTGAAATACCTTTGACCTGTAA
1 AATTACCAAAATACCTCTGGTTTGTAA
** **
28997447 AATTACTGAAATACC-CTCGACTTGTAA
1 AATTACCAAAATACCTCT-GGTTTGTAA
28997474 AATTACCAAA
1 AATTACCAAA
28997484 GGACCCACGA
Statistics
Matches: 125, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.01
27 124 0.99
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCTCTGGTTTGTAA
Found at i:28997423 original size:81 final size:81
Alignment explanation
Indices: 28997312--28997483 Score: 193
Period size: 81 Copynumber: 2.1 Consensus size: 81
28997302 TGTAGGGTAG
* * ***
28997312 AATTACCAAAATACCTTTGGTTTATAAAATTACCAAAATACCACTGGTTTGTAAAATTACCAAAA
1 AATTACCAAAATACCTCTGATTTATAAAATTACCAAAATACCACTGACCTGTAAAATTACCAAAA
*
28997377 TACCCCTAG-TTTGTAA
66 TA-CCCTAGACTTGTAA
* * ** ** **
28997393 AATTACCAAAATACCTCTGATTTGTGAAATTACTGAAATACCTTTGACCTGTAAAATTACTGAAA
1 AATTACCAAAATACCTCTGATTTATAAAATTACCAAAATACCACTGACCTGTAAAATTACCAAAA
*
28997458 TACCCTCGACTTGTAA
66 TACCCTAGACTTGTAA
28997474 AATTACCAAA
1 AATTACCAAA
28997484 GGACCCACGA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 5 0.07
81 70 0.93
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCTCTGATTTATAAAATTACCAAAATACCACTGACCTGTAAAATTACCAAAA
TACCCTAGACTTGTAA
Found at i:28997516 original size:27 final size:27
Alignment explanation
Indices: 28997486--28997840 Score: 410
Period size: 27 Copynumber: 13.1 Consensus size: 27
28997476 TTACCAAAGG
* * *
28997486 ACCCACGATTTATAGAATTATTGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
*
28997513 ACCCTCGATTTACAGAATTACTATTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
* * * *
28997540 ACCCTCAATTTAAAAAATTATTGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
*
28997567 ACCCTCGATTTACAGAATTACCGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
*
28997594 ACCCTCGATTTAAAGAATTACTGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
* * * *
28997621 ACCTTCAATTTACAAAATTA-TCATTTT
1 ACCCTCGATTTACAGAATTACT-GTTTT
*
28997648 ACCCTCGATTTACAGAATTACTATTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
* *
28997675 ACCCTCAATTTACAGAATTA-TCATTTT
1 ACCCTCGATTTACAGAATTACT-GTTTT
* *
28997702 ACCCTCGATTTACAAAATTACTATTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
* *
28997729 ATCCTCGATTTACAGAATTACAGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
*
28997756 ACCCTCGATTTATAGAATTACTGTTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
* *
28997783 ACCCTCAATTTACAGAAATA-TCGTTTT
1 ACCCTCGATTTACAGAATTACT-GTTTT
* * **
28997810 ACCCTCGATTTATAAAATTACCATTTT
1 ACCCTCGATTTACAGAATTACTGTTTT
28997837 ACCC
1 ACCC
28997841 CTAGGGTGTT
Statistics
Matches: 279, Mismatches: 43, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
26 3 0.01
27 274 0.98
28 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (27 bp):
ACCCTCGATTTACAGAATTACTGTTTT
Found at i:28998193 original size:33 final size:32
Alignment explanation
Indices: 28998143--28998206 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
28998133 CTCGCTGCAA
*
28998143 TCTGGTGGCTTCACCACACATATATATATCTGT
1 TCTGGTGGCCTCACCACA-ATATATATATCTGT
* *
28998176 TCTGGTGGCCT-AGCCACAATATCTGTATCTG
1 TCTGGTGGCCTCA-CCACAATATATATATCTG
28998207 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (32 bp):
TCTGGTGGCCTCACCACAATATATATATCTGT
Found at i:28998220 original size:27 final size:26
Alignment explanation
Indices: 28998168--28998227 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28998158 ACACATATAT
*
28998168 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28998194 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28998221 ATATCTG
1 ATATCTG
28998228 CCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28998381 original size:31 final size:31
Alignment explanation
Indices: 28998346--28998455 Score: 127
Period size: 31 Copynumber: 3.5 Consensus size: 31
28998336 TTGCATTCAC
*
28998346 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * *
28998377 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
28998408 ATTCTGATTCTGATTCTGATT--CTG-TCACCTG
1 ATTCTGATTCTGATTCTG-TTACCTGAT-A-CTG
28998439 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
28998456 CATTTTGATT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.01
30 2 0.03
31 63 0.94
32 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:28998385 original size:6 final size:6
Alignment explanation
Indices: 28998346--28998476 Score: 99
Period size: 6 Copynumber: 21.3 Consensus size: 6
28998336 TTGCATTCAC
* * *
28998346 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
28998395 -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* *
28998445 ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
28998477 AATGTTTCTT
Statistics
Matches: 98, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
5 5 0.05
6 81 0.83
7 9 0.09
8 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:28998465 original size:37 final size:37
Alignment explanation
Indices: 28998346--28998467 Score: 157
Period size: 37 Copynumber: 3.5 Consensus size: 37
28998336 TTGCATTCAC
* *
28998346 ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
*
28998383 ATTCT-A-----ATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
*
28998414 ATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
*
28998451 ATTCTCATTTTGATTCT
1 ATTCTGATTTTGATTCT
28998468 AGTTCTGATA
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
31 27 0.37
32 1 0.01
36 1 0.01
37 44 0.60
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (37 bp):
ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
Found at i:29000357 original size:27 final size:27
Alignment explanation
Indices: 29000327--29000436 Score: 148
Period size: 27 Copynumber: 4.1 Consensus size: 27
29000317 ATCTCATATC
* *
29000327 TGTAGGCTAAAATTACTAAAATACCCT
1 TGTAGGGTAGAATTACTAAAATACCCT
* * *
29000354 TGTAAGGTAGAATTACTGAAATGCCCT
1 TGTAGGGTAGAATTACTAAAATACCCT
* *
29000381 TGTAGGGTAGAATTACTGAAATGCCCT
1 TGTAGGGTAGAATTACTAAAATACCCT
*
29000408 TGTAGGGTAGAATTACCAAAATACCCT
1 TGTAGGGTAGAATTACTAAAATACCCT
29000435 TG
1 TG
29000437 GTTTACAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (27 bp):
TGTAGGGTAGAATTACTAAAATACCCT
Found at i:29000495 original size:27 final size:27
Alignment explanation
Indices: 29000418--29000575 Score: 167
Period size: 27 Copynumber: 5.9 Consensus size: 27
29000408 TGTAGGGTAG
* * **
29000418 AATTACCAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCTCGATTTGTAA
*
29000445 AATTACCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCCTCGA-TTTGTAA
*
29000472 AATTACCAAAATA-CCTCTGATTTGTGA
1 AATTACCAAAATACCCTC-GATTTGTAA
* **
29000499 AATTACTAAAATACCCTCGACCTGTAA
1 AATTACCAAAATACCCTCGATTTGTAA
** *
29000526 AATTACTGAAATACCCTCGACTTGTAA
1 AATTACCAAAATACCCTCGATTTGTAA
*
29000553 AATTACCAAAGTACCCTCGATTT
1 AATTACCAAAATACCCTCGATTT
29000576 ACAGAATTAT
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.02
27 103 0.94
28 5 0.05
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTTGTAA
Found at i:29000583 original size:27 final size:27
Alignment explanation
Indices: 29000564--29000946 Score: 453
Period size: 27 Copynumber: 14.2 Consensus size: 27
29000554 ATTACCAAAG
* *
29000564 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
29000591 TACCCTCGATTTACAAAATTATCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
29000618 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
***
29000645 TACCCTCGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29000672 TACCCTCGATTTACAAAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
**
29000699 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
29000726 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29000753 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* **
29000780 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29000807 TACCTTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
29000834 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29000861 TATCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29000888 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
29000915 TACCCTCGATTTATA-ATATTACCATTT
1 TACCCTCGATTTACAGA-ATTACCATTT
29000942 TACCC
1 TACCC
29000947 CTAGGGTGTT
Statistics
Matches: 318, Mismatches: 37, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.00
27 317 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:29000584 original size:54 final size:55
Alignment explanation
Indices: 29000526--29000640 Score: 126
Period size: 54 Copynumber: 2.1 Consensus size: 55
29000516 CGACCTGTAA
**
29000526 AATTACT-GAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTACAG
1 AATTACTCGAAATACCCTCGACTTACAAAATTACCAAAGTACCCTCGATTTACAG
*** * * ***
29000580 AATTA-TCGTTTTACCCTCGATTTACAAAATTATCATTTTACCCTCGATTTACAG
1 AATTACTCGAAATACCCTCGACTTACAAAATTACCAAAGTACCCTCGATTTACAG
29000634 AATTACT
1 AATTACT
29000641 ATTTTACCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.02
54 47 0.96
55 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (55 bp):
AATTACTCGAAATACCCTCGACTTACAAAATTACCAAAGTACCCTCGATTTACAG
Found at i:29000646 original size:54 final size:54
Alignment explanation
Indices: 29000564--29000946 Score: 504
Period size: 54 Copynumber: 7.1 Consensus size: 54
29000554 ATTACCAAAG
* * *
29000564 TACCCTCGATTTACAGAATTA-TCGTTTTACCCTCGATTTACAAAATTATCATTT
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAGAATTACCGTTT
* **
29000618 TACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* *
29000672 TACCCTCGATTTACAAAATTA-TCGTTTTACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAGAATTACCGTTT
* * * *
29000726 TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* * *
29000780 TACCCTCGATTTATAGAATTACTGTTTTACCTTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* * * *
29000834 TACCCTCGATTTACAAAATTACTATTTTATCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* * *
29000888 TACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTATA-ATATTACCATTT
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAGA-ATTACCGTTT
29000942 TACCC
1 TACCC
29000947 CTAGGGTGTT
Statistics
Matches: 294, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
53 3 0.01
54 289 0.98
55 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
Found at i:29000942 original size:81 final size:81
Alignment explanation
Indices: 29000564--29000946 Score: 588
Period size: 81 Copynumber: 4.7 Consensus size: 81
29000554 ATTACCAAAG
*
29000564 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTATCATTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
*
29000629 TACAGAATTACTATTT
66 TACAGAATTACTGTTT
* * *
29000645 TACCCTCGATTTACAGAATTATTGTTTTACCCTCGATTTACAAAATTATCGTTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
29000710 TACAGAATTACTGTTT
66 TACAGAATTACTGTTT
* * * *
29000726 TACCCTCGATTTATAGAATTA-CTATTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGAT
1 TACCCTCGATTTACAGAATTATC-GTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGAT
*
29000790 TTATAGAATTACTGTTT
65 TTACAGAATTACTGTTT
* * *
29000807 TACCTTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACTATTTTATCCTCGATT
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
* *
29000872 TATAGAATTACCGTTT
66 TACAGAATTACTGTTT
* * *
29000888 TACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTATAATATTACCATTTTACCC
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCC
29000947 CTAGGGTGTT
Statistics
Matches: 277, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
81 276 1.00
82 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
TACAGAATTACTGTTT
Found at i:29002868 original size:29 final size:29
Alignment explanation
Indices: 29002805--29002872 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29002795 TAATCAACCG
29002805 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29002834 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29002863 CGCACACTTA
1 CGCACACTTA
29002873 CCTTTTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29002985 original size:174 final size:174
Alignment explanation
Indices: 29002694--29003021 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
29002684 AACTCAAGGT
* *
29002694 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
29002759 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
29002824 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
* *
29002868 ACTTACCTTTTTCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
29002933 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
29002998 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
29003022 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:29003013 original size:29 final size:30
Alignment explanation
Indices: 29002974--29003052 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
29002964 CTTAATAATC
29002974 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
29003004 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
29003033 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29003053 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:29004678 original size:27 final size:26
Alignment explanation
Indices: 29004626--29004684 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
29004616 ACATATATAT
*
29004626 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
29004652 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
29004679 ATATCT
1 ATATCT
29004685 AGCAGCCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:29004843 original size:6 final size:6
Alignment explanation
Indices: 29004808--29004928 Score: 86
Period size: 6 Copynumber: 19.7 Consensus size: 6
29004798 ATTCACATTT
* * * *
29004808 TGATTT TGATTC TG-TTACC TGATAC TGATTC TGATTC TAATTC TG-TCACC
1 TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC TGATTC TGAT--TC
* **
29004858 TAATTC TGATTC TGATTC TGATTC TGACACC TGATTC TGATTC TGATTC
1 TGATTC TGATTC TGATTC TGATTC TGA-TTC TGATTC TGATTC TGATTC
* *
29004907 TCATTT TGATTC T-AGTTC TGAT
1 TGATTC TGATTC TGA-TTC TGAT
29004929 AATGTTTCTT
Statistics
Matches: 89, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
5 4 0.04
6 73 0.82
7 10 0.11
8 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (6 bp):
TGATTC
Found at i:29004851 original size:31 final size:31
Alignment explanation
Indices: 29004816--29004907 Score: 139
Period size: 31 Copynumber: 3.0 Consensus size: 31
29004806 TTTGATTTTG
* *
29004816 ATTCTGTTACCTGATACTGATTCTGATTCTA
1 ATTCTGTCACCTGATTCTGATTCTGATTCTA
* *
29004847 ATTCTGTCACCTAATTCTGATTCTGATTCTG
1 ATTCTGTCACCTGATTCTGATTCTGATTCTA
*
29004878 ATTCTGACACCTGATTCTGATTCTGATTCT
1 ATTCTGTCACCTGATTCTGATTCTGATTCT
29004908 CATTTTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.45
Consensus pattern (31 bp):
ATTCTGTCACCTGATTCTGATTCTGATTCTA
Found at i:29006556 original size:15 final size:17
Alignment explanation
Indices: 29006530--29006563 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29006520 TATTTAATTA
29006530 TTTATCATCTTTT-AAT
1 TTTATCATCTTTTCAAT
29006546 TTTATCA-CTTTTCAAT
1 TTTATCATCTTTTCAAT
29006562 TT
1 TT
29006564 AGTCCCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATCATCTTTTCAAT
Found at i:29008159 original size:23 final size:23
Alignment explanation
Indices: 29008129--29008173 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29008119 ATGTGGTCAT
29008129 AGGTTGTTACACAGCCTGGCGAG
1 AGGTTGTTACACAGCCTGGCGAG
*
29008152 AGGTTGTTACATAGCCTGGCGA
1 AGGTTGTTACACAGCCTGGCGA
29008174 CACATTCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (23 bp):
AGGTTGTTACACAGCCTGGCGAG
Found at i:29014850 original size:20 final size:19
Alignment explanation
Indices: 29014822--29014896 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
29014812 TTTTAAAATA
*
29014822 AAGTGAAAATGATTTTAACC
1 AAGTCAAAATGATTTTAA-C
*
29014842 AAGTCAAAATGATTTTCATC
1 AAGTCAAAATGATTTT-AAC
* *
29014862 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATGATTTTAAC
29014881 ATA-TCAAAATGATTTT
1 A-AGTCAAAATGATTTT
29014897 CAAAAAAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.30
20 31 0.67
21 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (19 bp):
AAGTCAAAATGATTTTAAC
Found at i:29014896 original size:39 final size:40
Alignment explanation
Indices: 29014822--29014898 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
29014812 TTTTAAAATA
*
29014822 AAGTGAAAATGATTTTAACCAAGTCAAAATGATTTTCATC
1 AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
*
29014862 AAGTTAAAATCATTTTAA-CATA-TCAAAATGATTTTCA
1 AAGTGAAAATCATTTTAACCA-AGTCAAAATGATTTTCA
29014899 AAAAAGTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (40 bp):
AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
Found at i:29014906 original size:40 final size:41
Alignment explanation
Indices: 29014811--29014907 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 41
29014801 TATTGAAACA
* * *
29014811 ATTTTAAAATAAAGTGAAAATGATTTTAACCAAGTCAAAATG
1 ATTTTCAAA-AAAGTTAAAATCATTTTAACCAAGTCAAAATG
**
29014853 ATTTTC-ATCAAGTTAAAATCATTTTAA-CATA-TCAAAATG
1 ATTTTCAAAAAAGTTAAAATCATTTTAACCA-AGTCAAAATG
29014892 ATTTTCAAAAAAGTTA
1 ATTTTCAAAAAAGTTA
29014908 GAATTGCTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 16 0.35
40 24 0.52
41 1 0.02
42 5 0.11
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (41 bp):
ATTTTCAAAAAAGTTAAAATCATTTTAACCAAGTCAAAATG
Found at i:29015074 original size:20 final size:22
Alignment explanation
Indices: 29015051--29015090 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
29015041 TTTTACCGAT
29015051 ATCGATA-CTTTC-TAAAAATA
1 ATCGATACCTTTCTTAAAAATA
29015071 ATCGATACCTTTCTTAAAAA
1 ATCGATACCTTTCTTAAAAA
29015091 CGATACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (22 bp):
ATCGATACCTTTCTTAAAAATA
Found at i:29022058 original size:28 final size:27
Alignment explanation
Indices: 29021994--29022145 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
29021984 TTATTAAGTC
* *
29021994 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
29022021 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
29022049 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
29022076 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
29022104 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
29022131 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29022146 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29022078 original size:55 final size:55
Alignment explanation
Indices: 29021994--29022170 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
29021984 TTATTAAGTC
* * *
29021994 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
29022049 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
29022104 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
29022160 CGCACACTTAG
1 CGCACACTTAG
29022171 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:29026471 original size:41 final size:41
Alignment explanation
Indices: 29026413--29026649 Score: 190
Period size: 41 Copynumber: 6.0 Consensus size: 41
29026403 AAAGTACATC
* * *
29026413 CAGGGGTACTGTAGTACAAACAGGGGCACATATGTGTAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
* * * *
29026454 TAGGGGTACCGAAGTACAAATAGAGGCACATAAGTGAAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
* * * *
29026495 CAAGGGTACCGAAGTACAAACAGGGGAACGTAAATGTAA-T
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
*
29026535 ------T--C-AA-TACAAATAGGGGCACATAAGTGTAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
* * * *** *
29026566 CAAGGGTATCAAAGTACAAACAGGGGCATGGAAGTGCAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
* * * *
29026607 CAGGGGTACCGAAGTACAAACAAGGGCACGTAATTGCAATT
1 CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
29026648 CA
1 CA
29026650 TCTTTTTTCT
Statistics
Matches: 154, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
30 21 0.14
31 3 0.02
32 1 0.01
34 1 0.01
37 1 0.01
39 1 0.01
40 3 0.02
41 123 0.80
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (41 bp):
CAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGTAATT
Found at i:29026550 original size:30 final size:30
Alignment explanation
Indices: 29026509--29026568 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29026499 GGTACCGAAG
*
29026509 TACAAACAGGGGAACGTAAATGTAATTCAA
1 TACAAACAGGGGAACATAAATGTAATTCAA
* * *
29026539 TACAAATAGGGGCACATAAGTGTAATTCAA
1 TACAAACAGGGGAACATAAATGTAATTCAA
29026569 GGGTATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (30 bp):
TACAAACAGGGGAACATAAATGTAATTCAA
Found at i:29026607 original size:71 final size:71
Alignment explanation
Indices: 29026468--29026608 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 71
29026458 GGTACCGAAG
* * *
29026468 TACAAATAGAGGCACATAAGTGAAATTCAAGGGTACCGAAGTACAAACAGGGGAACGTAAATGTA
1 TACAAATAGAGGCACATAAGTGAAATTCAAGGGTACCAAAGTACAAACAGGGGAACGGAAATGCA
29026533 ATTCAA
66 ATTCAA
* * * * * *
29026539 TACAAATAGGGGCACATAAGTGTAATTCAAGGGTATCAAAGTACAAACAGGGGCATGGAAGTGCA
1 TACAAATAGAGGCACATAAGTGAAATTCAAGGGTACCAAAGTACAAACAGGGGAACGGAAATGCA
29026604 ATTCA
66 ATTCA
29026609 GGGGTACCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (71 bp):
TACAAATAGAGGCACATAAGTGAAATTCAAGGGTACCAAAGTACAAACAGGGGAACGGAAATGCA
ATTCAA
Found at i:29026624 original size:112 final size:112
Alignment explanation
Indices: 29026427--29026649 Score: 293
Period size: 112 Copynumber: 2.0 Consensus size: 112
29026417 GGTACTGTAG
* * * * * *
29026427 TACAAACAGGGGCACATATGTGTAATTTAGGGGTACCGAAGTACAAATAGAGGCACATAAGTGAA
1 TACAAACAGGGGCACATAAGTGTAATTCAAGGGTACCAAAGTACAAACAGAGGCACAGAAGTGAA
* *
29026492 ATTCAAGGGTACCGAAGTACAAACAGGGGAACGTAAATGTAATTCAA
66 ATTCAAGGGTACCGAAGTACAAACAAGGGAACGTAAATGCAATTCAA
* * * ** *
29026539 TACAAATAGGGGCACATAAGTGTAATTCAAGGGTATCAAAGTACAAACAGGGGCATGGAAGTGCA
1 TACAAACAGGGGCACATAAGTGTAATTCAAGGGTACCAAAGTACAAACAGAGGCACAGAAGTGAA
* * *
29026604 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTAATTGCAATTCA
66 ATTCAAGGGTACCGAAGTACAAACAAGGGAACGTAAATGCAATTCA
29026650 TCTTTTTTCT
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
112 94 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (112 bp):
TACAAACAGGGGCACATAAGTGTAATTCAAGGGTACCAAAGTACAAACAGAGGCACAGAAGTGAA
ATTCAAGGGTACCGAAGTACAAACAAGGGAACGTAAATGCAATTCAA
Found at i:29027017 original size:48 final size:48
Alignment explanation
Indices: 29026964--29027061 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
29026954 GAAATCTAAG
**
29026964 CATTTTCATCCTTTTCTCAAGCTAATTGATTTTTCTAGGGATCTATAT
1 CATTTTCATCCTTTTCTCAAGCTAATCAATTTTTCTAGGGATCTATAT
*
29027012 CATTTTCGTCCTTTTCTCAAGCTAATCAATTTTTCTAGGGATCTATAT
1 CATTTTCATCCTTTTCTCAAGCTAATCAATTTTTCTAGGGATCTATAT
29027060 CA
1 CA
29027062 ACTCATACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.46
Consensus pattern (48 bp):
CATTTTCATCCTTTTCTCAAGCTAATCAATTTTTCTAGGGATCTATAT
Found at i:29028934 original size:27 final size:27
Alignment explanation
Indices: 29028897--29029301 Score: 517
Period size: 27 Copynumber: 15.0 Consensus size: 27
29028887 ATCAGTTATC
* *
29028897 TTACCATATAATGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
*
29028924 TTATCACATAAGGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
*
29028951 TTA-CACATAAGGGCAAAATAGTTATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29028977 TTACCTCATAAGGG-AAAATCAATCATT
1 TTACCACATAAGGGCAAAAT-AGTCATT
* *
29029004 TTACCTCAGAAGGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
** * * * *
29029031 TTACCTTATAAAGGCAAAACAGACGTT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029058 TTACCATATAAAGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029085 TTACCATATAAGGGCAAAACAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029112 TTACCACATAAAGGCAAAACAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029139 CTACCATATAAGGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
*
29029166 TTACCATATAAGGGCAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029193 TTACCACATAAAGGCAAAACAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029220 TTACCATATAAGGGGAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
* *
29029247 TTACCATATAAGGGCAAAACAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
*
29029274 TTACCACATAAGGGAAAAATAGTCATT
1 TTACCACATAAGGGCAAAATAGTCATT
29029301 T
1 T
29029302 ATCAATTTGG
Statistics
Matches: 335, Mismatches: 40, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
26 30 0.09
27 300 0.90
28 5 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (27 bp):
TTACCACATAAGGGCAAAATAGTCATT
Found at i:29030186 original size:23 final size:21
Alignment explanation
Indices: 29030138--29030186 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
29030128 GAATGAATGG
*
29030138 ATTCAAAATATAGAGAAACTA
1 ATTCAAAATATAGAGAAAATA
*
29030159 TTTCAAAACTATAGAGGAAAATA
1 ATTCAAAA-TATAGA-GAAAATA
29030182 ATTCA
1 ATTCA
29030187 CTCTCCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 6 0.26
23 10 0.43
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (21 bp):
ATTCAAAATATAGAGAAAATA
Found at i:29032595 original size:19 final size:20
Alignment explanation
Indices: 29032573--29032610 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29032563 AATAAAATTC
29032573 ATATATTAAATTA-TATTTT
1 ATATATTAAATTATTATTTT
*
29032592 ATATATTTAATTATTATTT
1 ATATATTAAATTATTATTT
29032611 AAGTAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTAAATTATTATTTT
Found at i:29032640 original size:19 final size:18
Alignment explanation
Indices: 29032574--29032646 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 18
29032564 ATAAAATTCA
*
29032574 TATATTAAATTATATT-T
1 TATATTATATTATATTAT
29032591 TATA-TAT-TTA-ATTAT
1 TATATTATATTATATTAT
*
29032606 TAT-TTA-AGTAAGTATTAT
1 TATATTATA-TTA-TATTAT
29032624 TATATTATATTAGTATTAT
1 TATATTATATTA-TATTAT
29032643 TATA
1 TATA
29032647 ATAAAACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
14 3 0.07
15 9 0.20
16 4 0.09
17 4 0.09
18 8 0.18
19 16 0.36
20 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATATTATATTATATTAT
Found at i:29032989 original size:18 final size:19
Alignment explanation
Indices: 29032960--29032995 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
29032950 GAGAAAATTT
29032960 TGAAATTTAGAGATTTAAG
1 TGAAATTTAGAGATTTAAG
29032979 TGAAA-TTAGAGATTTAA
1 TGAAATTTAGAGATTTAA
29032996 ATTTAGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (19 bp):
TGAAATTTAGAGATTTAAG
Found at i:29036087 original size:12 final size:13
Alignment explanation
Indices: 29036070--29036107 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29036060 ATCCTGGAAT
29036070 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
29036082 ATTAAGAACACATA
1 ATTAAGAACA-AGA
29036096 ATTAAGAACAAG
1 ATTAAGAACAAG
29036108 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:29044566 original size:44 final size:44
Alignment explanation
Indices: 29044503--29044591 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
29044493 GGTTTCATTC
*
29044503 CCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAA
1 CCCTTAGGTACTTAGGGGGTTTAGTTCATAATTATAAAAGAAAA
29044547 CCCTTAGGTACTTAGGGGGTTTAGTTCATAATTATAAAAGAAAA
1 CCCTTAGGTACTTAGGGGGTTTAGTTCATAATTATAAAAGAAAA
29044591 C
1 C
29044592 ATCTCAGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (44 bp):
CCCTTAGGTACTTAGGGGGTTTAGTTCATAATTATAAAAGAAAA
Found at i:29049591 original size:45 final size:44
Alignment explanation
Indices: 29049507--29049591 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
29049497 ATGTAATCTA
* **
29049507 AACTCATTGAGTTGTGTCTGAGTTTATGATATATGTGACATCCG
1 AACTCATTGAGTTGTGTCTGAGTTCATGATATACATGACATCCG
* *
29049551 AACTCATTGAGTTGTGGTCTGAGTTCGTGATATGCATGACA
1 AACTCATTGAGTTGT-GTCTGAGTTCATGATATACATGACA
29049592 CATGTTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 15 0.43
45 20 0.57
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (44 bp):
AACTCATTGAGTTGTGTCTGAGTTCATGATATACATGACATCCG
Found at i:29051003 original size:30 final size:30
Alignment explanation
Indices: 29050957--29051016 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29050947 TTCCTGAGCC
29050957 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
* *
29050987 TAGGGGCAAAAA-TGTAATTTTGCCAAAGTT
1 TAGGGG-AAAAAGTGTAATTATGCAAAAGTT
29051017 CATATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATGCAAAAGTT
Found at i:29051872 original size:31 final size:31
Alignment explanation
Indices: 29051832--29051915 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
29051822 TCAATCTCGA
29051832 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
29051862 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
29051893 CATATCACAGGGTCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
29051916 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:29052155 original size:24 final size:25
Alignment explanation
Indices: 29052128--29052205 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
29052118 GCCTAGCCTC
29052128 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
29052152 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *** *
29052177 CTTCGGTAAACTGGGGCATAG-CCT
1 TTTTAATAAACTGGGGCAAAGCCCT
29052201 TTTTA
1 TTTTA
29052206 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 11 0.24
25 34 0.76
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:29052163 original size:25 final size:25
Alignment explanation
Indices: 29052135--29052204 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
29052125 CTCTTTTAAT
29052135 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
* * *
29052160 AACTGGGGCAAAGCCCTCTTCGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
29052185 AACTGGGGCATAG-CCTTTTT
1 AACTGGGGCAAAGCCCTTTTT
29052205 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 5 0.13
25 34 0.87
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:29053043 original size:27 final size:27
Alignment explanation
Indices: 29053013--29053077 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29053003 GGGCATATTC
29053013 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
29053040 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
29053067 GTCTTTTTACC
1 GTCATTTTACC
29053078 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:29053170 original size:28 final size:28
Alignment explanation
Indices: 29053131--29053189 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
29053121 GTAAATCTAC
*
29053131 AAACCAAGGGTATT-TTAGTAATTTTGTA
1 AAACCAAGGGTATTCCTA-TAATTTTGTA
* *
29053159 AAACCAATGGTATTCCTATAATTTTTTA
1 AAACCAAGGGTATTCCTATAATTTTGTA
29053187 AAA
1 AAA
29053190 AAAGTCAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
AAACCAAGGGTATTCCTATAATTTTGTA
Found at i:29053268 original size:54 final size:53
Alignment explanation
Indices: 29053196--29053348 Score: 164
Period size: 54 Copynumber: 2.8 Consensus size: 53
29053186 AAAAAAAGTC
** *
29053196 AAGGGTATTTCTGA-AATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTC-GATAATTTTACAAA-CAGGGGTATTTTGGTAATTTTACAAACT
* * * * *
29053250 GAGGGTATTTCGATAATTTCACAAACCAGTGGTATTTCGATAATTTTACAAACT
1 AAGGGTATTTCGATAATTTTACAAA-CAGGGGTATTTTGGTAATTTTACAAACT
* * *
29053304 AAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTGGTAATT
1 AAGGGTATTTCGATAATTTTACAAAC-AGGGGTATTTTGGTAATT
29053349 CTATCCTACA
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
53 3 0.04
54 77 0.96
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (53 bp):
AAGGGTATTTCGATAATTTTACAAACAGGGGTATTTTGGTAATTTTACAAACT
Found at i:29053367 original size:27 final size:27
Alignment explanation
Indices: 29053225--29053351 Score: 132
Period size: 27 Copynumber: 4.7 Consensus size: 27
29053215 TGTAAATCAG
* * *
29053225 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTCTACAAACTAA
* * *
29053252 GGGTATTTCGATAATT-TCACAAAC-CA
1 GGGTATTTTGGTAATTCT-ACAAACTAA
* * *
29053278 GTGGTATTTCGATAATTTTACAAACTAA
1 G-GGTATTTTGGTAATTCTACAAACTAA
*
29053306 GGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTCTACAAACTAA
29053333 GGGTATTTTGGTAATTCTA
1 GGGTATTTTGGTAATTCTA
29053352 TCCTACAAGG
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.03
27 82 0.93
28 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTACAAACTAA
Found at i:29053417 original size:27 final size:27
Alignment explanation
Indices: 29053380--29053592 Score: 241
Period size: 27 Copynumber: 7.9 Consensus size: 27
29053370 GTAATTTCAC
*
29053380 AATCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
29053407 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTATA
* *
29053434 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
29053461 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
29053488 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* ** * *
29053515 AATTGAGGGTAAACCGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
** * *
29053542 AATCGA-GGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
** *
29053568 AATCGAGGGTACTATGGTTATTTTA
1 AATCGAGGGTAAAATGGTAATTTTA
29053593 CAAGTAGAGG
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 23 0.14
27 135 0.85
28 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:29053496 original size:81 final size:81
Alignment explanation
Indices: 29053380--29053578 Score: 278
Period size: 81 Copynumber: 2.5 Consensus size: 81
29053370 GTAATTTCAC
*
29053380 AATCGAGGGTAAAACGGTAATTTTATAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAACGGTAATTCTATAAATC-GAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
*
29053444 AAA-ATAGTAATTCTATA
65 AAACAGA-TAATTCTATA
* *
29053461 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
* * *
29053526 AACCGATAATTTTGTA
66 AACAGATAATTCTATA
* *
29053542 AATCGA-GGTAAAACAGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
29053579 CTATGGTTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
80 28 0.26
81 76 0.72
82 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
AACAGATAATTCTATA
Found at i:29053616 original size:80 final size:80
Alignment explanation
Indices: 29053380--29053619 Score: 241
Period size: 81 Copynumber: 3.0 Consensus size: 80
29053370 GTAATTTCAC
* * ** *
29053380 AATCGAGGGTAAAACGGTAATTTTATAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAACAGTAATTCTATAAATC-GAGGGTAAAATGGTAATTTTACAAATAGAGGGT
* *
29053444 AAAATAGTAATTCTATA
65 -AAACAGTAATTTTATA
** ** *
29053461 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTA
1 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTACAAATAGAGGGTA
* *
29053526 AACCGATAATTTTGTA
66 AACAG-TAATTTTATA
* ** * *
29053542 AATCGA-GGTAAAACAGTAATTCTGTAAATCGAGGGTACTATGGTTATTTTACAAGTAGAGGGTA
1 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTACAAATAGAGGGTA
**
29053606 TTTCAGTAATTTTA
66 -AACAGTAATTTTA
29053620 CAGGTTGAGG
Statistics
Matches: 135, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
80 59 0.44
81 75 0.56
82 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (80 bp):
AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTACAAATAGAGGGTA
AACAGTAATTTTATA
Found at i:29053617 original size:27 final size:27
Alignment explanation
Indices: 29053587--29053860 Score: 150
Period size: 27 Copynumber: 10.1 Consensus size: 27
29053577 TACTATGGTT
*
29053587 ATTTTACAAGTAGAGGGTATTTCAGTA
1 ATTTTACAAGTAGAGGGTATTTTAGTA
* *
29053614 ATTTTACAGGTTGAGGGTATTTTAGTA
1 ATTTTACAAGTAGAGGGTATTTTAGTA
* * *
29053641 ATTTCACAAATCAGA-GGTATTTTGGTA
1 ATTTTACAAGT-AGAGGGTATTTTAGTA
** *
29053668 ATTTTACAAACCAG-GGGTATTTTGGTA
1 ATTTTAC-AAGTAGAGGGTATTTTAGTA
* ** *
29053695 ATTTTATAAACCA-AGGGTATTTTGGTA
1 ATTTTA-CAAGTAGAGGGTATTTTAGTA
* * *
29053722 ATTTTACAAACTAG-GGGTATTTTGGTG
1 ATTTTAC-AAGTAGAGGGTATTTTAGTA
* ** *
29053749 ATTTTATAAACCA-AGAGTATTTTAGTA
1 ATTTTA-CAAGTAGAGGGTATTTTAGTA
** **
29053776 ATTTTACAAACCAG-GGGTATTTGGGTA
1 ATTTTAC-AAGTAGAGGGTATTTTAGTA
* ** *
29053803 ATTTTGAAAACCA-AGGGTATTTTGGTA
1 ATTTT-ACAAGTAGAGGGTATTTTAGTA
* *
29053830 ATTTTACAAGCCA-AGGGTATTTTGGTA
1 ATTTTACAAG-TAGAGGGTATTTTAGTA
29053857 ATTT
1 ATTT
29053861 GGTAAACTAA
Statistics
Matches: 205, Mismatches: 28, Indels: 28
0.79 0.11 0.11
Matches are distributed among these distances:
26 3 0.01
27 197 0.96
28 5 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
ATTTTACAAGTAGAGGGTATTTTAGTA
Found at i:29053628 original size:107 final size:108
Alignment explanation
Indices: 29053384--29053632 Score: 268
Period size: 107 Copynumber: 2.3 Consensus size: 108
29053374 TTTCACAATC
** * * * * *
29053384 GAGGGTAAAACGGTAATTTTATAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAAT
1 GAGGGTAAAATAGTAATTTTACAAATTGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAAC
* *
29053449 AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATC
66 AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACAAATA
* ** *
29053492 GAGGGTAAAATGGTAATTTTGTAAATTGAGGGTAAACCGATAATTTTGTAAATCGA-GGTAAAAC
1 GAGGGTAAAATAGTAATTTTACAAATTGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAAC
* ** * * *
29053556 AGTAATTCTGTAAATCGAGGGTACTATGGTTATTTTACAAGTA
66 AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACAAATA
** **
29053599 GAGGGT-ATTTCAGTAATTTTACAGGTTGAGGGTA
1 GAGGGTAAAAT-AGTAATTTTACAAATTGAGGGTA
29053633 TTTTAGTAAT
Statistics
Matches: 118, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
106 2 0.02
107 66 0.56
108 50 0.42
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (108 bp):
GAGGGTAAAATAGTAATTTTACAAATTGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAAC
AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTACAAATA
Found at i:29053686 original size:54 final size:54
Alignment explanation
Indices: 29053628--29053860 Score: 335
Period size: 54 Copynumber: 4.3 Consensus size: 54
29053618 TACAGGTTGA
* * * *
29053628 GGGTATTTTAGTAATTTCACAAATC-AGAGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAG-GGTATTTTGGTAATTTTACAAACCAG
*
29053682 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * *
29053736 GGGTATTTTGGTGATTTTATAAACCAAGAGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * *
29053790 GGGTATTTGGGTAATTTTGA-AAACCAAGGGTATTTTGGTAATTTTACAAGCCAA
1 GGGTATTTTGGTAATTTT-ATAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
29053844 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
29053861 GGTAAACTAA
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
54 158 0.98
55 3 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
Found at i:29053696 original size:81 final size:79
Alignment explanation
Indices: 29053600--29053860 Score: 265
Period size: 81 Copynumber: 3.2 Consensus size: 79
29053590 TTACAAGTAG
* **** *
29053600 AGGGTATTTCAGTAATTTTACAGGTTGAGGGTATTTTAGTAATTTCACAAATCAGAGGTATTTTG
1 AGGGTATTTTAGTAATTTTACA-AACAAGGGTATTTTGGTAATTTCACAAA-CAGAGGTATTTTG
29053665 GTAATTTTACAAACCA
64 GTAATTTTACAAACCA
* * * * *
29053681 GGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 AGGGTATTTTAGTAATTTTACAAA-CAAGGGTATTTTGGTAATTTCACAAAC-AGAGGTATTTTG
* *
29053746 GTGATTTTATAAACCA
64 GTAATTTTACAAACCA
* * * *
29053762 AGAGTATTTTAGTAATTTTACAAACCAGGGGTATTTGGGTAATTTTGA-AAACCA-AGGGTATTT
1 AGGGTATTTTAGTAATTTTACAAA-CAAGGGTATTTTGGTAA-TTTCACAAA-CAGA-GGTATTT
*
29053825 TGGTAATTTTACAAGCCA
62 TGGTAATTTTACAAACCA
*
29053843 AGGGTATTTTGGTAATTT
1 AGGGTATTTTAGTAATTT
29053861 GGTAAACTAA
Statistics
Matches: 149, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 143 0.96
82 5 0.03
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (79 bp):
AGGGTATTTTAGTAATTTTACAAACAAGGGTATTTTGGTAATTTCACAAACAGAGGTATTTTGGT
AATTTTACAAACCA
Found at i:29066601 original size:100 final size:101
Alignment explanation
Indices: 29066410--29066609 Score: 321
Period size: 101 Copynumber: 2.0 Consensus size: 101
29066400 CACTTGTAGC
* *
29066410 CGAAGCTATCTGGTAAGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATA
1 CGAAGCTATCAGGTAAGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATA
29066475 CACGTAGTAGCCTGCACTTAGTACTACACACGTGAT
66 CACGTAGTAGCCTGCACTTAGTACTACACACGTGAT
* * * ** *
29066511 CGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCTGGTA
1 CGAAGCTATCAGGTAAGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATA
29066575 CACGTAGTAGCCTGCACTTAGTACTACACACGTGA
66 CACGTAGTAGCCTGCACTTAGTACTACACACGTGA
29066610 CCTCACAATC
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 44 0.48
101 47 0.52
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (101 bp):
CGAAGCTATCAGGTAAGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATA
CACGTAGTAGCCTGCACTTAGTACTACACACGTGAT
Found at i:29068962 original size:27 final size:27
Alignment explanation
Indices: 29068903--29069241 Score: 359
Period size: 27 Copynumber: 12.7 Consensus size: 27
29068893 TAATAAAGAG
*
29068903 AAATTACCGAAGTACCCTCGA-TTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
29068929 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** *
29068956 ATTTTACCAAAATACCC-C-AGTTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTA
* *
29068982 AAATTACCGAAATACCCT-TAGTTTGCA
1 AAATTACCGAAATACCCTCGA-TTTGTA
* *
29069009 AAATTACTGAAATACCCTTGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
29069036 AAATTACCGAAATACCCTCGA-TTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
**
29069062 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
29069089 AAATTACCAAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
29069116 AAACTACTGAAGTACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
29069143 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
29069170 ACATTACCAAAACAACCC-CGATTTGTA
1 AAATTACCGAAA-TACCCTCGATTTGTA
* * * *
29069197 AAATTATCAAAATACTCTTG-TATTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
*
29069224 AAATTACTGAAATACCCT
1 AAATTACCGAAATACCCT
29069242 TGTAGTGTAA
Statistics
Matches: 261, Mismatches: 43, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
25 1 0.00
26 68 0.26
27 187 0.72
28 5 0.02
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:29069035 original size:80 final size:80
Alignment explanation
Indices: 29068903--29069242 Score: 337
Period size: 80 Copynumber: 4.2 Consensus size: 80
29068893 TAATAAAGAG
* * * ** **
29068903 AAATTACCGAAGTACCC-TCGATTGTAAAATTACTGAAATACCCTCGATTTGTAATTTTACCAAA
1 AAATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAA
29068967 ATACCC-CAGTTTGTA
66 ATACCCTC-GTTTGTA
* ** * *
29068982 AAATTACCGAAATACCCTTAGTTTGCAAAATTACTGAAATACCCTTGATTTGTAAAATTACCGAA
1 AAATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAA
*
29069047 ATACCCTCGATTGTA
66 ATACCCTCGTTTGTA
** * * * **
29069062 AAATTACTAAAATACCC-TCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAACTACTGA
1 AAATTACCGAAATACCCTTAG-TTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAA
*
29069126 AGTACCCTCGATTTGTA
65 AATACCCTCG-TTTGTA
* * * * * *
29069143 AAATTATCGAAATACCCTCAATTTGTAACATTACCAAAACAACCC-CGATTTGTAAAATTATCAA
1 AAATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAA-TACCCTCGATTTGTAAAATTACCAA
* *
29069207 AATACTCTTGTATTGTA
65 AATACCCTCGT-TTGTA
*
29069224 AAATTACTGAAATACCCTT
1 AAATTACCGAAATACCCTT
29069243 GTAGTGTAAA
Statistics
Matches: 215, Mismatches: 39, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
79 18 0.08
80 113 0.53
81 80 0.37
82 4 0.02
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (80 bp):
AAATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAA
ATACCCTCGTTTGTA
Found at i:29069265 original size:27 final size:27
Alignment explanation
Indices: 29069206--29069286 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
29069196 AAAATTATCA
* * *
29069206 AAATACTCTTGTATTGTAAAATTACTG
1 AAATACCCTTGTAGTGTAAAATGACTG
29069233 AAATACCCTTGTAGTGTAAAATGACT-
1 AAATACCCTTGTAGTGTAAAATGACTG
* *
29069259 AACATACCCCTGTAGGGTAAAATGACTG
1 AA-ATACCCTTGTAGTGTAAAATGACTG
29069287 TTTTGCCCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGTAGTGTAAAATGACTG
Found at i:29074379 original size:10 final size:10
Alignment explanation
Indices: 29074364--29074391 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29074354 ATATTACATG
29074364 TTTACTTTGT
1 TTTACTTTGT
29074374 TTTACTTTGT
1 TTTACTTTGT
29074384 TTTACTTT
1 TTTACTTT
29074392 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Done.