Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 48 of 186
Found at i:14550061 original size:41 final size:41
Alignment explanation
Indices: 14550010--14550158 Score: 226
Period size: 41 Copynumber: 3.6 Consensus size: 41
14550000 TTACTTTTTT
* *
14550010 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCATTTTTCCAAAAGCGCCGCTAAAACCTCGGCCTATA
* *
14550051 ACGGCATTTTTCCATAAGCGCCGCTAAAACCTCGGCCTATA
1 GCGGCATTTTTCCAAAAGCGCCGCTAAAACCTCGGCCTATA
* *
14550092 GCAGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGGCCTATA
1 GCGGCATTTTTCCAAAAGCGCCGCTAAAACCTCGGCCTATA
* *
14550133 GCGGCATTTTTCTAAAAGCGTCGCTA
1 GCGGCATTTTTCCAAAAGCGCCGCTA
14550159 TTGTACAGTT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (41 bp):
GCGGCATTTTTCCAAAAGCGCCGCTAAAACCTCGGCCTATA
Found at i:14564374 original size:19 final size:18
Alignment explanation
Indices: 14564341--14564377 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
14564331 TAAATGTAAA
*
14564341 TAAAAATAAAGATAATAG
1 TAAAAATAAAAATAATAG
14564359 TAAAAATAAAAAATAATAG
1 TAAAAAT-AAAAATAATAG
14564378 AATAAGCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (18 bp):
TAAAAATAAAAATAATAG
Found at i:14574846 original size:15 final size:15
Alignment explanation
Indices: 14574814--14574842 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14574804 ATTTTTTGTG
14574814 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
14574829 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
14574843 ATTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:14577253 original size:2 final size:2
Alignment explanation
Indices: 14577246--14577320 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
14577236 TCAAAGTATG
* * * * * *
14577246 TA TA TA TA TA TG TG TG TA TA TA TA TA TG TA TA TG TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
14577288 TA TA CA TA TA TA TA TA CA CA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14577321 TGAGGTGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (2 bp):
TA
Found at i:14577269 original size:20 final size:20
Alignment explanation
Indices: 14577241--14577298 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
14577231 TTATTTCAAA
* *
14577241 GTATGTATATATATATGTGT
1 GTATATATATATATATATGT
*
14577261 GTATATATATATGTATATGT
1 GTATATATATATATATATGT
*
14577281 GTATATATATACATATAT
1 GTATATATATATATATAT
14577299 ATATACACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (20 bp):
GTATATATATATATATATGT
Found at i:14577277 original size:22 final size:22
Alignment explanation
Indices: 14577246--14577300 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
14577236 TCAAAGTATG
*
14577246 TATATATATATGTGTGTATATA
1 TATATATATATGTGTATATATA
*
14577268 TATATGTATATGTGTATATATA
1 TATATATATATGTGTATATATA
*
14577290 TACATATATAT
1 TATATATATAT
14577301 ATACACACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (22 bp):
TATATATATATGTGTATATATA
Found at i:14590736 original size:15 final size:15
Alignment explanation
Indices: 14590716--14590746 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14590706 TAGAGAGAAA
14590716 TTAAAAATTTTGAAG
1 TTAAAAATTTTGAAG
14590731 TTAAAAATTTTGAAG
1 TTAAAAATTTTGAAG
14590746 T
1 T
14590747 CAAGGGTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
TTAAAAATTTTGAAG
Found at i:14591697 original size:40 final size:40
Alignment explanation
Indices: 14591648--14591736 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
14591638 TGATTTAGTG
* *
14591648 GTTTTGATAGGTATGGCTCTTAGGCTCATACAATTCAATA
1 GTTTTGATAGGTATGGCTCATAAGCTCATACAATTCAATA
* **
14591688 GTTTCGATAGGTATGGCTCATAAGCTCATATGATTCAATA
1 GTTTTGATAGGTATGGCTCATAAGCTCATACAATTCAATA
14591728 GTTTTGATA
1 GTTTTGATA
14591737 ACTATTCAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (40 bp):
GTTTTGATAGGTATGGCTCATAAGCTCATACAATTCAATA
Found at i:14596012 original size:26 final size:26
Alignment explanation
Indices: 14595983--14596035 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
14595973 TCAAACATGC
14595983 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
14596009 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
14596035 A
1 A
14596036 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:14597551 original size:26 final size:26
Alignment explanation
Indices: 14597522--14597573 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
14597512 ATTCCCATCT
14597522 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAAACCATTATCA
*
14597548 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAAACCATTATCA
14597574 ATTTGTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (26 bp):
TGGAACATTTACCTAAACCATTATCA
Found at i:14603073 original size:25 final size:27
Alignment explanation
Indices: 14603036--14603088 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
14603026 TCAAACATGC
14603036 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGTCAATTTAACTCCTAGGGGT
* *
14603062 ATTTCAGT-AATTTATCTCCTAGGGGT
1 ATTTAAGTCAATTTAACTCCTAGGGGT
14603088 A
1 A
14603089 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (27 bp):
ATTTAAGTCAATTTAACTCCTAGGGGT
Found at i:14607023 original size:2 final size:2
Alignment explanation
Indices: 14607016--14607042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14607006 ACTATTACAA
14607016 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
14607043 AATAACGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14615408 original size:56 final size:56
Alignment explanation
Indices: 14615351--14615558 Score: 326
Period size: 56 Copynumber: 3.7 Consensus size: 56
14615341 CAGATAGGGT
* * *
14615351 CTTACTCGTACACATATATCGGAGTCACATATCAATGCCAACGTATTAAACGTGGT
1 CTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGA
*
14615407 CTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATGAAACGTGGA
1 CTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGA
* * *
14615463 CTTACTCGTACACATATATCAGAGTCACATATCGATGACAACGTATTAAACGTGGA
1 CTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGA
* * *
14615519 CTTACTCGCACATAAATATCGGAGTCACATATTGATGCCA
1 CTTACTCGCACACATATATCGGAGTCACATATCGATGCCA
14615559 CATATACTTC
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 138 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (56 bp):
CTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGTGGA
Found at i:14619066 original size:42 final size:43
Alignment explanation
Indices: 14618968--14619085 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 43
14618958 AACGGGTACA
* * *
14618968 ATGCCGATGTCCCAGAC-GTGATCTTACATGTAATTCAGTATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATTCAGTATCG
** *
14619011 ATGCCTCTATCCCAGACAGGGTCTTACACG-AATTCAG-ATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATTCAGTAT-CG
* *
14619053 ATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAA
14619086 ATCTCAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.03
42 34 0.55
43 25 0.40
44 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATTCAGTATCG
Found at i:14643951 original size:10 final size:10
Alignment explanation
Indices: 14643932--14643981 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
14643922 TGAAATTCTA
14643932 AAAGATAAAT
1 AAAGATAAAT
14643942 ACAA-ATAAAT
1 A-AAGATAAAT
14643952 AAAGATAAAT
1 AAAGATAAAT
14643962 AAAGATAAAT
1 AAAGATAAAT
14643972 GAAA-ATAAAT
1 -AAAGATAAAT
14643982 CCTAGAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:14644621 original size:12 final size:13
Alignment explanation
Indices: 14644604--14644633 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14644594 TACCTCATTC
14644604 TTTTTTTTCT-TT
1 TTTTTTTTCTCTT
14644616 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
14644629 TTTTT
1 TTTTT
14644634 AATTCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:14644623 original size:14 final size:14
Alignment explanation
Indices: 14644604--14644633 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14644594 TACCTCATTC
14644604 TTTTTTT-TCTTTT
1 TTTTTTTCTCTTTT
14644617 TTTTTTTCTCTTTT
1 TTTTTTTCTCTTTT
14644631 TTT
1 TTT
14644634 AATTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTCTCTTTT
Found at i:14644815 original size:96 final size:97
Alignment explanation
Indices: 14644645--14644831 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 97
14644635 ATTCTATTTA
* * * *
14644645 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCA
** *
14644710 CCCTGGTTACTTAGCCCAACACATTCCTAATT
66 CCCCAGTTACTCAGCCCAACACATTCCTAATT
* * *
14644742 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACTCGAAAAGAGATGATAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCA
14644806 CCCCAGTTACTCAGCCCAACACATTC
66 CCCCAGTTACTCAGCCCAACACATTC
14644832 TTAAAAATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 71 0.89
97 9 0.11
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCA
CCCCAGTTACTCAGCCCAACACATTCCTAATT
Found at i:14645624 original size:18 final size:18
Alignment explanation
Indices: 14645591--14645645 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 18
14645581 TTAATATCTA
14645591 AAAATAATAA-AT--AAT
1 AAAATAATAAGATAAAAT
14645606 AAAATAATAAGATAAAAT
1 AAAATAATAAGATAAAAT
14645624 AAAAATAA-AAG-TAAAAGT
1 -AAAATAATAAGATAAAA-T
14645642 AAAA
1 AAAA
14645646 ATAAAAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.29
16 2 0.06
17 9 0.26
18 7 0.20
19 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAATAATAAGATAAAAT
Found at i:14645630 original size:6 final size:6
Alignment explanation
Indices: 14645589--14645653 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
14645579 TATTAATATC
* *
14645589 TAAAAA TAATAAA TAATAAAA TAATAAGA T-AAAA TAAAAA TAAAAG TAAAAG
1 TAAAAA TAA-AAA T-A-AAAA TAA-AA-A TAAAAA TAAAAA TAAAAA TAAAAA
14645641 TAAAAA TAAAAA T
1 TAAAAA TAAAAA T
14645654 TGGGTTGCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
5 2 0.04
6 33 0.65
7 8 0.16
8 7 0.14
9 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:14645646 original size:18 final size:18
Alignment explanation
Indices: 14645606--14645651 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
14645596 AATAAATAAT
14645606 AAAATAATAAGATAAAATA
1 AAAATAA-AAGATAAAATA
14645625 AAAATAAAAG-TAAAAGTA
1 AAAATAAAAGATAAAA-TA
14645643 AAAATAAAA
1 AAAATAAAA
14645652 ATTGGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAATAAAAGATAAAATA
Found at i:14645646 original size:24 final size:24
Alignment explanation
Indices: 14645596--14645653 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
14645586 ATCTAAAAAT
14645596 AATAAATAATAAAATAATAAGATAA
1 AATAAA-AATAAAATAATAAGATAA
14645621 AATAAAAATAAAAGTAA-AAG-TAAA
1 AATAAAAATAAAA-TAATAAGAT-AA
14645645 AATAAAAAT
1 AATAAAAAT
14645654 TGGGTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 1 0.03
24 21 0.68
25 9 0.29
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (24 bp):
AATAAAAATAAAATAATAAGATAA
Found at i:14648061 original size:11 final size:11
Alignment explanation
Indices: 14648045--14648080 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14648035 ATCAATAACT
14648045 TTTTGTTTTTG
1 TTTTGTTTTTG
14648056 TTTTGTTTTTTG
1 TTTTG-TTTTTG
*
14648068 TTGTGTTTTTG
1 TTTTGTTTTTG
14648079 TT
1 TT
14648081 GCTTTCCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:14648065 original size:12 final size:12
Alignment explanation
Indices: 14648045--14648077 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14648035 ATCAATAACT
14648045 TTTTG-TTTTTG
1 TTTTGTTTTTTG
14648056 TTTTGTTTTTTG
1 TTTTGTTTTTTG
*
14648068 TTGTGTTTTT
1 TTTTGTTTTT
14648078 GTTGCTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (12 bp):
TTTTGTTTTTTG
Found at i:14648926 original size:25 final size:26
Alignment explanation
Indices: 14648892--14648940 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
14648882 CAAAAAGGAT
*
14648892 TAGGTACATGA-GGGTATATGAATTC
1 TAGGTACATGATGGGCATATGAATTC
14648917 TAGGTACATGATGGGCATATGAAT
1 TAGGTACATGATGGGCATATGAAT
14648941 CCAAAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (26 bp):
TAGGTACATGATGGGCATATGAATTC
Found at i:14654234 original size:17 final size:18
Alignment explanation
Indices: 14654202--14654239 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
14654192 TGAATGACGG
14654202 ACAC-ATAAACCGAAAAC
1 ACACGATAAACCGAAAAC
14654219 ACACGATAAACC-AAAAC
1 ACACGATAAACCGAAAAC
14654236 -CACG
1 ACACG
14654240 CCATGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.55, C:0.32, G:0.08, T:0.05
Consensus pattern (18 bp):
ACACGATAAACCGAAAAC
Found at i:14665390 original size:18 final size:18
Alignment explanation
Indices: 14665363--14665404 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
14665353 TTTGAGTCCG
14665363 TTTA-TTTTACTATTATT
1 TTTATTTTTACTATTATT
* *
14665380 TTTATTTTTACTTTTCTT
1 TTTATTTTTACTATTATT
14665398 TTTATTT
1 TTTATTT
14665405 AAACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTACTATTATT
Found at i:14668239 original size:20 final size:20
Alignment explanation
Indices: 14668210--14668277 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
14668200 TAGATAATGT
14668210 ATTGATACTTAATCCCAAAG
1 ATTGATACTTAATCCCAAAG
* * *
14668230 ATTGAGACTTTAT---AATG
1 ATTGATACTTAATCCCAAAG
14668247 TATTGATACTTAATCCCAAAG
1 -ATTGATACTTAATCCCAAAG
*
14668268 ATTGAAACTT
1 ATTGATACTT
14668278 TATAAAGGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 3 0.08
18 11 0.30
20 20 0.54
21 3 0.08
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTGATACTTAATCCCAAAG
Found at i:14668254 original size:38 final size:38
Alignment explanation
Indices: 14668203--14668282 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
14668193 CTTAGGCTAG
*
14668203 ATAATGTATTGATACTTAATCCCAAAGATTGAGACTTT
1 ATAATGTATTGATACTTAATCCCAAAGATTGAAACTTT
14668241 ATAATGTATTGATACTTAATCCCAAAGATTGAAACTTT
1 ATAATGTATTGATACTTAATCCCAAAGATTGAAACTTT
14668279 ATAA
1 ATAA
14668283 AGGTATCGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (38 bp):
ATAATGTATTGATACTTAATCCCAAAGATTGAAACTTT
Found at i:14668257 original size:18 final size:18
Alignment explanation
Indices: 14668203--14668260 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
14668193 CTTAGGCTAG
14668203 ATAATGTATTGATACTTA
1 ATAATGTATTGATACTTA
* * *
14668221 ATCCCAAAG-ATTGAGACTTT
1 AT---AATGTATTGATACTTA
14668241 ATAATGTATTGATACTTA
1 ATAATGTATTGATACTTA
14668259 AT
1 AT
14668261 CCCAAAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
17 3 0.10
18 13 0.43
20 11 0.37
21 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (18 bp):
ATAATGTATTGATACTTA
Found at i:14670260 original size:23 final size:24
Alignment explanation
Indices: 14670230--14670318 Score: 72
Period size: 26 Copynumber: 3.5 Consensus size: 24
14670220 TGAAAGTTGA
14670230 AAAAATATTAAAAAAAAATT-TAT
1 AAAAATATTAAAAAAAAATTATAT
* * *
14670253 AAAAATATTATAAAAATATTGTAAAT
1 AAAAATATTA-AAAAAAAAT-TATAT
*
14670279 AAAAAAATTTAAAAAATACAATTATAT
1 AAAAATA-TTAAAAAA-A-AATTATAT
* *
14670306 AAAACTAATAAAA
1 AAAAATATTAAAA
14670319 GCTATAAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
23 10 0.20
24 7 0.14
25 1 0.02
26 18 0.36
27 12 0.24
28 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (24 bp):
AAAAATATTAAAAAAAAATTATAT
Found at i:14670277 original size:11 final size:11
Alignment explanation
Indices: 14670230--14670277 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
14670220 TGAAAGTTGA
*
14670230 AAAAATATTAA
1 AAAAATATTAT
*
14670241 AAAAAAATTTAT
1 AAAAATA-TTAT
14670253 AAAAATATTAT
1 AAAAATATTAT
*
14670264 AAAAATATTGT
1 AAAAATATTAT
14670275 AAA
1 AAA
14670278 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAAATATTAT
Found at i:14673845 original size:5 final size:5
Alignment explanation
Indices: 14673831--14673913 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
14673821 ATGGGGTAGA
* ** * * * *
14673831 ATATG ATATG TTATG ATATG ATATG ATAAA ATATG AAATGTG CTACG ACATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG --ATATG ATATG ATATG
14673883 ATATGG AATATG ATATG ATAAT- ATATG ATAT
1 ATAT-G -ATATG ATATG AT-ATG ATATG ATAT
14673914 AAGATATGCC
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
4 2 0.03
5 44 0.76
6 4 0.07
7 8 0.14
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (5 bp):
ATATG
Found at i:14673908 original size:22 final size:22
Alignment explanation
Indices: 14673846--14673921 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
14673836 ATATGTTATG
*
14673846 ATATGATATGATAAAATATGAA
1 ATATGATATGATAATATATGAA
* * * * *
14673868 ATGTGCTACGA-CATGATATGGA
1 ATATGATATGATAAT-ATATGAA
*
14673890 ATATGATATGATAATATATGAT
1 ATATGATATGATAATATATGAA
*
14673912 ATAAGATATG
1 ATATGATATG
14673922 CCCCATTATG
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 1 0.03
22 36 0.92
23 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (22 bp):
ATATGATATGATAATATATGAA
Found at i:14678878 original size:15 final size:15
Alignment explanation
Indices: 14678838--14678883 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
14678828 TAATAAAACT
*
14678838 AATAAAAATTATAAA
1 AATAAAAATTATATA
*
14678853 AATATAAAATTGTATA
1 AATA-AAAATTATATA
*
14678869 CATAAAAATTATATA
1 AATAAAAATTATATA
14678884 GAATTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAAAAATTATATA
Found at i:14678924 original size:9 final size:9
Alignment explanation
Indices: 14678805--14678931 Score: 82
Period size: 9 Copynumber: 13.7 Consensus size: 9
14678795 TAAATTTGTA
14678805 AAAAAT-AT
1 AAAAATAAT
*
14678813 AAAAATATTT
1 AAAAATA-AT
*
14678823 TAAAATAAT
1 AAAAATAAT
*
14678832 AAAACTAAT
1 AAAAATAAT
*
14678841 AAAAATTAT
1 AAAAATAAT
14678850 AAAAAT-AT
1 AAAAATAAT
14678858 AAAATTGTATACAT
1 AAAA----ATA-AT
*
14678872 AAAAATTAT
1 AAAAATAAT
* *
14678881 ATAGAATTAT
1 A-AAAATAAT
14678891 AAAAATAAT
1 AAAAATAAT
*
14678900 AAATAT-AT
1 AAAAATAAT
14678908 ATAAAATAAT
1 A-AAAATAAT
14678918 AAAAATAA-
1 AAAAATAAT
14678926 AAAAAT
1 AAAAAT
14678932 TAAAGAAAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
8 21 0.22
9 46 0.48
10 20 0.21
12 2 0.02
14 6 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATAAT
Found at i:14694179 original size:3 final size:3
Alignment explanation
Indices: 14694171--14694208 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
14694161 ATCACATGTT
14694171 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
14694209 TGGATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:14704249 original size:27 final size:26
Alignment explanation
Indices: 14704195--14704248 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14704185 CATACCATAA
14704195 TTACCTTTTTACTTAACAAATTTTTT
1 TTACCTTTTTACTTAACAAATTTTTT
14704221 TTACCTTTTTACTTAACAAATTTTTT
1 TTACCTTTTTACTTAACAAATTTTTT
14704247 TT
1 TT
14704249 TTCTTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (26 bp):
TTACCTTTTTACTTAACAAATTTTTT
Found at i:14704669 original size:204 final size:204
Alignment explanation
Indices: 14704319--14704728 Score: 820
Period size: 204 Copynumber: 2.0 Consensus size: 204
14704309 TCCCATCCTA
14704319 TACGCCAAAAGAAAAAATTGGGCAGATAACACTTCCCCAAATAGATTATTTCAATAGAATACACC
1 TACGCCAAAAGAAAAAATTGGGCAGATAACACTTCCCCAAATAGATTATTTCAATAGAATACACC
14704384 TAAATCCTAGATCTGCCAAATTTTGGGGTGTGACACCACGAACTGCTTCAAGTGTGGGCTCGAAC
66 TAAATCCTAGATCTGCCAAATTTTGGGGTGTGACACCACGAACTGCTTCAAGTGTGGGCTCGAAC
14704449 TAATTGAATCAAAATCCAAAACTAAAAAAAGTTTTCTTTTATCTTTTGCGTGAAAATGATAATTC
131 TAATTGAATCAAAATCCAAAACTAAAAAAAGTTTTCTTTTATCTTTTGCGTGAAAATGATAATTC
14704514 TCTCTTCTT
196 TCTCTTCTT
14704523 TACGCCAAAAGAAAAAATTGGGCAGATAACACTTCCCCAAATAGATTATTTCAATAGAATACACC
1 TACGCCAAAAGAAAAAATTGGGCAGATAACACTTCCCCAAATAGATTATTTCAATAGAATACACC
14704588 TAAATCCTAGATCTGCCAAATTTTGGGGTGTGACACCACGAACTGCTTCAAGTGTGGGCTCGAAC
66 TAAATCCTAGATCTGCCAAATTTTGGGGTGTGACACCACGAACTGCTTCAAGTGTGGGCTCGAAC
14704653 TAATTGAATCAAAATCCAAAACTAAAAAAAGTTTTCTTTTATCTTTTGCGTGAAAATGATAATTC
131 TAATTGAATCAAAATCCAAAACTAAAAAAAGTTTTCTTTTATCTTTTGCGTGAAAATGATAATTC
14704718 TCTCTTCTT
196 TCTCTTCTT
14704727 TA
1 TA
14704729 ATAATTGTTA
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 206 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (204 bp):
TACGCCAAAAGAAAAAATTGGGCAGATAACACTTCCCCAAATAGATTATTTCAATAGAATACACC
TAAATCCTAGATCTGCCAAATTTTGGGGTGTGACACCACGAACTGCTTCAAGTGTGGGCTCGAAC
TAATTGAATCAAAATCCAAAACTAAAAAAAGTTTTCTTTTATCTTTTGCGTGAAAATGATAATTC
TCTCTTCTT
Found at i:14718853 original size:14 final size:13
Alignment explanation
Indices: 14718833--14718864 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
14718823 AATATTTGAC
14718833 TTGTTCTTAATTA
1 TTGTTCTTAATTA
14718846 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
14718860 TTGTT
1 TTGTT
14718865 TTGATGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:14719300 original size:26 final size:26
Alignment explanation
Indices: 14719271--14719324 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14719261 TTTTTCTTTC
14719271 TATGCATTCTTAGTTAGTAATTAGTT
1 TATGCATTCTTAGTTAGTAATTAGTT
14719297 TATGCATTCTTAGTTAGTAATTAGTT
1 TATGCATTCTTAGTTAGTAATTAGTT
14719323 TA
1 TA
14719325 GACAACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (26 bp):
TATGCATTCTTAGTTAGTAATTAGTT
Found at i:14720567 original size:46 final size:46
Alignment explanation
Indices: 14720503--14720596 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 46
14720493 GTTCGATTAT
* *
14720503 ATATTGGCACTTATTGTGCG-AGACCAAAATAGCTTCGGCTATATAA
1 ATATTAGCACTTAGTGTGCGTA-ACCAAAATAGCTTCGGCTATATAA
*** *
14720549 ATATTAGCACTTAGTGTGCGTAATTGAGATAGCTTCGGCTATATAA
1 ATATTAGCACTTAGTGTGCGTAACCAAAATAGCTTCGGCTATATAA
14720595 AT
1 AT
14720597 TGTAACACCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 40 0.98
47 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (46 bp):
ATATTAGCACTTAGTGTGCGTAACCAAAATAGCTTCGGCTATATAA
Found at i:14723837 original size:26 final size:26
Alignment explanation
Indices: 14723806--14723913 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
14723796 TGAAATGCCC
*
14723806 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
14723832 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
14723858 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
14723884 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
14723910 ATCA
1 ATCA
14723914 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:14728222 original size:18 final size:18
Alignment explanation
Indices: 14728199--14728238 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14728189 CACCGCAAAT
14728199 CCGGCCCAGACGTAATGG
1 CCGGCCCAGACGTAATGG
*
14728217 CCGGCCCAGACGTTATGG
1 CCGGCCCAGACGTAATGG
14728235 CCGG
1 CCGG
14728239 ATCCGACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.12
Consensus pattern (18 bp):
CCGGCCCAGACGTAATGG
Found at i:14732575 original size:26 final size:26
Alignment explanation
Indices: 14732544--14732651 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
14732534 TGAAATGCCC
14732544 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
14732570 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAAACCATT
* *
14732596 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
14732622 ATCATGGAACATTTACCT-AACCGATT
1 ATCATGGAACATTTACCTAAACC-ATT
14732648 ATCA
1 ATCA
14732652 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
25 3 0.04
26 71 0.96
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:14732622 original size:52 final size:52
Alignment explanation
Indices: 14732544--14732651 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
14732534 TGAAATGCCC
14732544 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCG-TT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAA-CCGATT
* *
14732596 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCGATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCGATT
14732648 ATCA
1 ATCA
14732652 ATTTGTACCA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 3 0.06
52 50 0.94
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCGATT
Found at i:14734182 original size:41 final size:41
Alignment explanation
Indices: 14734112--14734286 Score: 235
Period size: 41 Copynumber: 4.3 Consensus size: 41
14734102 ATAAAATTTT
* * ***
14734112 CTAGGC-ATAAAGCCTAGTACAATACACCGGCACGGAGCCTG
1 CTAGGCAAT-AAGCCTAATATAATACACCGGCATAAAGCCTG
* * *
14734153 CTACGCAATAGGCCTAATATAATATACCGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
*
14734194 CTAGGCAATAAGCCTGATATAATACACCGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
* *
14734235 CTAGGCAATAAGCCTGATATAATACACTGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
14734276 CTAGGCAATAA
1 CTAGGCAATAA
14734287 AACCTGAATA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 118 0.98
42 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
Found at i:14744652 original size:13 final size:13
Alignment explanation
Indices: 14744634--14744658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14744624 TGTGGGTGCA
14744634 CATGGCCGTGTCG
1 CATGGCCGTGTCG
14744647 CATGGCCGTGTC
1 CATGGCCGTGTC
14744659 TTGCTTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:14748380 original size:13 final size:13
Alignment explanation
Indices: 14748362--14748390 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
14748352 TTTAGTTTAA
14748362 TTAGTTAATTAGT
1 TTAGTTAATTAGT
14748375 TTAGTTAATTAGT
1 TTAGTTAATTAGT
14748388 TTA
1 TTA
14748391 ATAAACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:14750092 original size:27 final size:27
Alignment explanation
Indices: 14750034--14750140 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
14750024 TGGCTGCAAA
* *
14750034 AACAGATAA-TGTGACAGAGTCACCAG
1 AACAGATAATTGTGGCAGAGCCACCAG
* **
14750060 ATACAGATAATCGTGGCAGAGCCTTCAG
1 A-ACAGATAATTGTGGCAGAGCCACCAG
*
14750088 AACAGA-AATATGTTGCAGAGCCACCAG
1 AACAGATAAT-TGTGGCAGAGCCACCAG
* *
14750115 ATCAGATAATTGTGGCATAGCCACCA
1 AACAGATAATTGTGGCAGAGCCACCA
14750141 AGACGCTTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
26 4 0.06
27 45 0.69
28 16 0.25
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (27 bp):
AACAGATAATTGTGGCAGAGCCACCAG
Found at i:14750412 original size:8 final size:8
Alignment explanation
Indices: 14750399--14750427 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
14750389 TACCGAATTG
14750399 GGCCCGTT
1 GGCCCGTT
14750407 GGCCCGTT
1 GGCCCGTT
14750415 GGCCCGTT
1 GGCCCGTT
14750423 GGCCC
1 GGCCC
14750428 ATTAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.38, T:0.21
Consensus pattern (8 bp):
GGCCCGTT
Found at i:14756787 original size:40 final size:40
Alignment explanation
Indices: 14756696--14756830 Score: 155
Period size: 41 Copynumber: 3.3 Consensus size: 40
14756686 ACATAAAATT
* *
14756696 TGCTAGGC-ATAAAGCCTAGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTAATATAATACACCGGCATA-AGCC
* * * *
14756737 TACTAGGCAATAGGTCTAATATAATATACCGGCATAAGCC
1 TGCTAGGCAATAAGCCTAATATAATACACCGGCATAAGCC
* *
14756777 TGCTAGGCAATAAGCCTGATATAATACAGCGGCATAAAGCC
1 TGCTAGGCAATAAGCCTAATATAATACACCGGCAT-AAGCC
*
14756818 TGCTAGTCAATAA
1 TGCTAGGCAATAA
14756831 AGCCCAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 33 0.42
41 44 0.56
42 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (40 bp):
TGCTAGGCAATAAGCCTAATATAATACACCGGCATAAGCC
Found at i:14767866 original size:16 final size:16
Alignment explanation
Indices: 14767847--14767877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14767837 CTTCTTCACT
14767847 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
14767863 TACTTACTTACTTAA
1 TACTCACTTACTTAA
14767878 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:14767883 original size:20 final size:20
Alignment explanation
Indices: 14767844--14767883 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14767834 AAACTTCTTC
* *
14767844 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
14767864 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
14767884 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:14772400 original size:16 final size:16
Alignment explanation
Indices: 14772381--14772411 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14772371 CTTCTTCACT
14772381 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
14772397 TACTTACTTACTTAA
1 TACTCACTTACTTAA
14772412 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:14772417 original size:20 final size:20
Alignment explanation
Indices: 14772378--14772417 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14772368 AAACTTCTTC
* *
14772378 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
14772398 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
14772418 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:14772786 original size:55 final size:54
Alignment explanation
Indices: 14772674--14772851 Score: 184
Period size: 55 Copynumber: 3.3 Consensus size: 54
14772664 CATGCCTCAA
* * *
14772674 CATGGTCTTACATGGTATCC-TAGCCTTATG-AA-CTCACCAATGCCATGCCTTGG
1 CATGGTCTTACATGGGA-CCTTTGCCTTA-GAAACCTTACCAATGCCATGCCTTGG
* * * *
14772727 CATGGTCTTACATGGGACCTTTGACTTCTAGAAA-CTTATCAATGCCATGTCTTGA
1 CATGGTCTTACATGGGACCTTTG-CCT-TAGAAACCTTACCAATGCCATGCCTTGG
** * *
14772782 CATGGTCTTACATGATATCTTTGCCTTAGAAACCTTACCAATTTCCATGCCTTGG
1 CATGGTCTTACATGGGACCTTTGCCTTAGAAACCTTACCAA-TGCCATGCCTTGG
14772837 CATGGTCTTACATGG
1 CATGGTCTTACATGG
14772852 TATCCTTAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 24 0.23
54 12 0.12
55 65 0.63
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
CATGGTCTTACATGGGACCTTTGCCTTAGAAACCTTACCAATGCCATGCCTTGG
Found at i:14779591 original size:48 final size:47
Alignment explanation
Indices: 14779437--14779601 Score: 192
Period size: 48 Copynumber: 3.5 Consensus size: 47
14779427 TTCAGTTATG
* *
14779437 TATTGGCACTTTGTGTGCGAGATTGAAATAGCTTCGACTACATATATA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATA-A
* *
14779485 TATTGGCACTTAGTGTGCGAGACTAAAATAGCTTCGACTATATA-AA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATAA
* *
14779531 TATTGGCACTTAGTGCGCGTA-ATTGAGATAGCTTCTG-CTATATATACA
1 TATTGGCACTTAGTGTGCG-AGATTGAAATAGCTTC-GACTATATATA-A
* * *
14779579 CATTGGCACTTAGCGTACGAGAT
1 TATTGGCACTTAGTGTGCGAGAT
14779602 CAATAGAGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 37 0.37
47 5 0.05
48 58 0.58
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (47 bp):
TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATAA
Found at i:14779615 original size:94 final size:94
Alignment explanation
Indices: 14779437--14779619 Score: 219
Period size: 94 Copynumber: 1.9 Consensus size: 94
14779427 TTCAGTTATG
* * * * * *
14779437 TATTGGCACTTTGTGTGCGAGATTGAAATAGCTTCGACTACATATATATATTGGCACTTAGTGTG
1 TATTGGCACTTAGTGCGCGAGATTGAAATAGCTTCGACTACATATACACATTGGCACTTAGCGTA
*
14779502 CGAGACTAAAATAGCTTCGACTATATAAA
66 CGAGACTAAAAGAGCTTCGACTATATAAA
* *
14779531 TATTGGCACTTAGTGCGCGTA-ATTGAGATAGCTTCTG-CTATATATACACATTGGCACTTAGCG
1 TATTGGCACTTAGTGCGCG-AGATTGAAATAGCTTC-GACTACATATACACATTGGCACTTAGCG
* *
14779594 TACGAGA-TCAATAGAGTTTCGACTAT
64 TACGAGACT-AAAAGAGCTTCGACTAT
14779620 TTATTTGGCA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
93 1 0.01
94 72 0.96
95 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (94 bp):
TATTGGCACTTAGTGCGCGAGATTGAAATAGCTTCGACTACATATACACATTGGCACTTAGCGTA
CGAGACTAAAAGAGCTTCGACTATATAAA
Found at i:14783050 original size:16 final size:16
Alignment explanation
Indices: 14783031--14783061 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14783021 CTTCGTCACT
14783031 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
14783047 TACTTACTTACTTAA
1 TACTCACTTACTTAA
14783062 TGAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:14783067 original size:20 final size:20
Alignment explanation
Indices: 14783028--14783067 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14783018 AAACTTCGTC
* *
14783028 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATGAAAT
*
14783048 ACTTACTTACTTAATGAAAT
1 ACTTACTCACTTAATGAAAT
14783068 TTATTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATGAAAT
Found at i:14783355 original size:53 final size:54
Alignment explanation
Indices: 14783247--14783480 Score: 259
Period size: 55 Copynumber: 4.4 Consensus size: 54
14783237 CATGAATTGT
* * * *
14783247 CATGGTCTTACGTGGTATCC-T---TT-TGAAACTTACCATTGCCATGTCTCGA
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGA
* *
14783296 CATGGTCTTACATGGTATCCTTGCCTTATG-AACTCACCAATGCCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGA
* * * *
14783349 CATGGTCTTACATGGGA-CCTTTGCCTTATAGAAACTTATCAATGACATGTCTTGA
1 CATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTTACCAATGCCATGCCTTGA
* * *
14783404 CATGGTCTTACATGATATCCTTGCCTTA-GAAACCTTACCAATTTCCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAA-CTTACCAA-TGCCATGCCTTGA
14783459 CATGGTCTTACATGGTATCCTT
1 CATGGTCTTACATGGTATCCTT
14783481 AAACCCCAAT
Statistics
Matches: 154, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
49 19 0.12
50 1 0.01
52 2 0.01
53 49 0.32
54 10 0.06
55 71 0.46
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGA
Found at i:14783426 original size:108 final size:110
Alignment explanation
Indices: 14783271--14783473 Score: 313
Period size: 108 Copynumber: 1.9 Consensus size: 110
14783261 GTATCCTTTT
* * *
14783271 GAAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGACATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACC
14783334 AA-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
65 AATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
* * *
14783379 GAAACTTATCAATGACATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGACATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
*
14783444 ATTTCCATGCCTTGGCATGGTCTTACATGG
66 ATTGCCATGCCTTGGCATGGTCTTACATGG
14783474 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.59
109 7 0.08
110 27 0.32
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (110 bp):
GAAACTTACCAATGACATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
ATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
Found at i:14786106 original size:26 final size:27
Alignment explanation
Indices: 14786056--14786109 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
14786046 TTGCCTCAAG
14786056 TTCAAATCTTTTTGAGTCATCAAATAT
1 TTCAAATCTTTTTGAGTCATCAAATAT
14786083 TTCAAA-CTTTTGTGA-TCAGT-AAATAT
1 TTCAAATCTTTT-TGAGTCA-TCAAATAT
14786109 T
1 T
14786110 CAGCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCATCAAATAT
Found at i:14798179 original size:26 final size:26
Alignment explanation
Indices: 14798143--14798193 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
14798133 TCGCAACCCG
14798143 ACTGACACTAGCATTTCTAGGATATA
1 ACTGACACTAGCATTTCTAGGATATA
*
14798169 ACTGGCACTAGCATTTCTAGGATAT
1 ACTGACACTAGCATTTCTAGGATAT
14798194 CTCGGAGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (26 bp):
ACTGACACTAGCATTTCTAGGATATA
Found at i:14799859 original size:41 final size:43
Alignment explanation
Indices: 14799801--14799893 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
14799791 TTTTTAGTTC
* * *
14799801 GTCTGGGACATTGGCATCG-TATTTGATTTCGTGTAAGAACCT
1 GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACCT
14799843 GTCT-GGACAGTGGCATCGATATTTGATTACATGTAAG-ACCAT
1 GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACC-T
*
14799885 GTTTGGGAC
1 GTCTGGGAC
14799894 GTTGGAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 16 0.36
42 24 0.55
43 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACCT
Found at i:14800231 original size:48 final size:48
Alignment explanation
Indices: 14800176--14800278 Score: 206
Period size: 48 Copynumber: 2.1 Consensus size: 48
14800166 TGGCTAAGGA
14800176 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
1 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
14800224 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
1 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
14800272 GTATATG
1 GTATATG
14800279 GCTTACTAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (48 bp):
GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
Found at i:14808517 original size:22 final size:22
Alignment explanation
Indices: 14808442--14808518 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
14808432 CATGGAAGGG
*
14808442 GGAGACACAC--CCATGTGAG-
1 GGAGACACACGGCCGTGTGAGA
*
14808461 GGA-ACACACGCCCGTGTGAGA
1 GGAGACACACGGCCGTGTGAGA
* *
14808482 GGAGGCACACGGCCGTGTGGGA
1 GGAGACACACGGCCGTGTGAGA
* *
14808504 GGAGATACATGGCCG
1 GGAGACACACGGCCG
14808519 AAGGCACATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.13
19 3 0.06
20 8 0.17
21 3 0.06
22 27 0.57
ACGTcount: A:0.26, C:0.25, G:0.39, T:0.10
Consensus pattern (22 bp):
GGAGACACACGGCCGTGTGAGA
Found at i:14809272 original size:3 final size:3
Alignment explanation
Indices: 14809264--14809289 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14809254 AAAATAGGAA
14809264 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
14809290 AACTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14811568 original size:6 final size:6
Alignment explanation
Indices: 14811557--14811585 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
14811547 ATATCAATCC
14811557 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
14811586 AGAATGCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:14813705 original size:25 final size:25
Alignment explanation
Indices: 14813669--14813724 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
14813659 GTGTTCTTGG
*
14813669 TTCTTTTTTATTTT-TATTTAGTTT-T
1 TTCTTTTGTATTTTCT-TTTA-TTTCT
14813694 TTCTTTTGTATTTTCTTTTATTTCT
1 TTCTTTTGTATTTTCTTTTATTTCT
14813719 TTCTTT
1 TTCTTT
14813725 CCCTTCGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 24 0.86
26 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.79
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTCT
Found at i:14814715 original size:3 final size:3
Alignment explanation
Indices: 14814709--14814803 Score: 86
Period size: 3 Copynumber: 31.7 Consensus size: 3
14814699 CATCATCATC
14814709 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
14814754 GTT ACTT TTT GTC ACT ATT GTC ATT ATT A-T ATT ATT ACT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14814799 ATT AT
1 ATT AT
14814804 ACTTATATTC
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.04
3 67 0.92
4 3 0.04
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:14818048 original size:13 final size:13
Alignment explanation
Indices: 14818032--14818056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14818022 CCATTACCAG
14818032 AAATAATAATAAC
1 AAATAATAATAAC
14818045 AAATAATAATAA
1 AAATAATAATAA
14818057 ATATCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:14818374 original size:2 final size:2
Alignment explanation
Indices: 14818367--14818424 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
14818357 TCTCCATGCA
14818367 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
14818409 CT CT CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
14818425 TTTCTGGCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:14831933 original size:23 final size:23
Alignment explanation
Indices: 14831907--14831957 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
14831897 TGATTTTTAA
*
14831907 ATTTAGAATTATTTAGTGATAGT
1 ATTTAGAATTATTTAGTGATAAT
14831930 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
14831953 ATTTA
1 ATTTA
14831958 AGAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:14845224 original size:6 final size:6
Alignment explanation
Indices: 14845213--14845251 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
14845203 TTTGAATCCC
14845213 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
14845252 CCCTTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:14857583 original size:13 final size:13
Alignment explanation
Indices: 14857565--14857604 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
14857555 AAAATAATCG
14857565 CACACGGGCGTGT
1 CACACGGGCGTGT
14857578 CACACGGGCGTGT
1 CACACGGGCGTGT
14857591 CACACGGGCGTGT
1 CACACGGGCGTGT
14857604 C
1 C
14857605 CCTCCCGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:14861356 original size:47 final size:47
Alignment explanation
Indices: 14861285--14861450 Score: 178
Period size: 47 Copynumber: 3.6 Consensus size: 47
14861275 ATCCATAAGT
14861285 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * * * *
14861332 GAACTTGGACTCAACTCAATGAGTTCGGA---C-ATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
* *
14861378 GAACTCGGACTCAACTTAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
14861425 AAACTCAGACTCAACTCAATGAGTTC
1 GAACTCGGACTCAACTCAACGAGTTC
14861451 ACCCAAATCT
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 25 0.27
47 48 0.52
48 2 0.02
49 2 0.02
50 6 0.06
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:14861406 original size:46 final size:46
Alignment explanation
Indices: 14861231--14861406 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
14861221 TGTAACCCGC
*** *
14861231 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * *
14861277 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* * * *
14861327 -C-TCA-CGAACTTGGACTCAACTCAATGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
14861370 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
14861407 TGCCTAGTTA
Statistics
Matches: 103, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.57
47 27 0.26
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:14861444 original size:93 final size:93
Alignment explanation
Indices: 14861240--14861450 Score: 323
Period size: 93 Copynumber: 2.3 Consensus size: 93
14861230 CCCATAAGCG
* * ***
14861240 AACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
* *
14861305 GAGTTCGGATGCCTAGTTACATCTCACG
66 GAGCTCGGATGCCTAGTTACATCTCACA
* * *
14861333 AACTTGGACTCAACTCAATGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTTAAC
1 AACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
14861398 GAGCTCGGATGCCTAGTTACATCTCACA
66 GAGCTCGGATGCCTAGTTACATCTCACA
*
14861426 AACTCAGACTCAACTCAATGAGTTC
1 AACTCGGACTCAACTCAATGAGTTC
14861451 ACCCAAATCT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 106 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (93 bp):
AACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCACA
Found at i:14871620 original size:144 final size:144
Alignment explanation
Indices: 14871360--14871647 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
14871350 GACAGATTAT
14871360 GAGAATTAAGTATTACTTGTCATATATGTATATGGCCGAATGGCAATTGTAATGGAAGTAAAATG
1 GAGAATTAAGTATTACTTGTCATATATGTATATGGCCGAATGGCAATTGTAATGGAAGTAAAATG
14871425 TGATATGCTTTTATGATCAAATGATAGTGTTAGATGAATATTAGTAAGATATTATGTGTAATCTA
66 TGATATGCTTTTATGATCAAATGATAGTGTTAGATGAATATTAGTAAGATATTATGTGTAATCTA
14871490 TCAAATGATAAACA
131 TCAAATGATAAACA
14871504 GAGAATTAAGTATTACTTGTCATATATGTATATGGCCGAATGGCAATTGTAATGGAAGTAAAATG
1 GAGAATTAAGTATTACTTGTCATATATGTATATGGCCGAATGGCAATTGTAATGGAAGTAAAATG
14871569 TGATATGCTTTTATGATCAAATGATAGTGTTAGATGAATATTAGTAAGATATTATGTGTAATCTA
66 TGATATGCTTTTATGATCAAATGATAGTGTTAGATGAATATTAGTAAGATATTATGTGTAATCTA
14871634 TCAAATGATAAACA
131 TCAAATGATAAACA
14871648 TGAGTGATGA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (144 bp):
GAGAATTAAGTATTACTTGTCATATATGTATATGGCCGAATGGCAATTGTAATGGAAGTAAAATG
TGATATGCTTTTATGATCAAATGATAGTGTTAGATGAATATTAGTAAGATATTATGTGTAATCTA
TCAAATGATAAACA
Found at i:14871829 original size:45 final size:45
Alignment explanation
Indices: 14871765--14871985 Score: 306
Period size: 45 Copynumber: 5.0 Consensus size: 45
14871755 ATATCGTACA
* *
14871765 ATACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCAGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
14871810 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
** **
14871855 ATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATAACGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
14871900 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * *
14871945 ATGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGTCGGTGA
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
14871986 ATGAATTCGG
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 9 0.06
43 17 0.11
44 5 0.03
45 127 0.80
46 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:14876510 original size:45 final size:45
Alignment explanation
Indices: 14876446--14876666 Score: 306
Period size: 45 Copynumber: 5.0 Consensus size: 45
14876436 ATATCGTACA
* *
14876446 ATACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCAGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
14876491 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
** **
14876536 ATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATAACGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
14876581 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * *
14876626 ATGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGTCGGTGA
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
14876667 ATGAATTCGG
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 9 0.06
43 17 0.11
44 5 0.03
45 127 0.80
46 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:14877226 original size:16 final size:18
Alignment explanation
Indices: 14877195--14877227 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
14877185 AACTCGTCAC
14877195 ACTATCTATCATTTTGGT
1 ACTATCTATCATTTTGGT
14877213 ACTA-CTAT-ATTTTGG
1 ACTATCTATCATTTTGG
14877228 AGCTAGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (18 bp):
ACTATCTATCATTTTGGT
Found at i:14899044 original size:5 final size:5
Alignment explanation
Indices: 14899034--14899061 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
14899024 GCAACTCACA
14899034 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
14899062 GAATTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:14904824 original size:11 final size:11
Alignment explanation
Indices: 14904808--14904832 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14904798 AAAGTTTCCT
14904808 TTAGATAAGCA
1 TTAGATAAGCA
14904819 TTAGATAAGCA
1 TTAGATAAGCA
14904830 TTA
1 TTA
14904833 AGAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (11 bp):
TTAGATAAGCA
Found at i:14906243 original size:25 final size:23
Alignment explanation
Indices: 14906209--14906254 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
14906199 TTTTCTATTC
14906209 TCTCTCTTTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
14906232 TCTCTCTTTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
14906255 ATAATTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (23 bp):
TCTCTCTTTTTTTACATTATAAG
Found at i:14910710 original size:2 final size:2
Alignment explanation
Indices: 14910703--14910730 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14910693 GCAATGCAGA
14910703 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14910731 GGAAAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14912467 original size:6 final size:7
Alignment explanation
Indices: 14912438--14912468 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
14912428 AGGAAAAAAA
14912438 TTATATT
1 TTATATT
14912445 TTATATT
1 TTATATT
14912452 TTATATT
1 TTATATT
14912459 TTA-ATT
1 TTATATT
14912465 TTAT
1 TTAT
14912469 TTGATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:14912985 original size:32 final size:32
Alignment explanation
Indices: 14912920--14912988 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
14912910 TACAAATTTC
* *
14912920 TAATTTTTTTAATTTCAACTTTCATATTCAAT
1 TAATTTTTTTAATTTCAACTTACAAATTCAAT
14912952 TAATTTTTTTAATTTCAAC-TACAAGAATT-AAT
1 TAATTTTTTTAATTTCAACTTAC-A-AATTCAAT
14912984 TAATT
1 TAATT
14912989 AATTTAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 28 0.85
33 3 0.09
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (32 bp):
TAATTTTTTTAATTTCAACTTACAAATTCAAT
Found at i:14919005 original size:44 final size:44
Alignment explanation
Indices: 14918942--14919029 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
14918932 CCCAAACGAG
* *
14918942 AGTCTTACAAACATTCACAAATTTTAGCTTCCCGAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
14918986 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
14919030 TTTGACAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (44 bp):
AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
Found at i:14926743 original size:22 final size:24
Alignment explanation
Indices: 14926713--14926770 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
14926703 ACCATTAAAT
*
14926713 ATTTGTAATTAGT-ATTTTAAAAA
1 ATTTGTAATTAATAATTTTAAAAA
* *
14926736 ATTT-TAATTAATAATTTTAACAC
1 ATTTGTAATTAATAATTTTAAAAA
14926759 ATTTGTAATTAA
1 ATTTGTAATTAA
14926771 GCACCAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 16 0.53
24 7 0.23
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTTGTAATTAATAATTTTAAAAA
Found at i:14927553 original size:32 final size:32
Alignment explanation
Indices: 14927517--14927582 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
14927507 GCAAGGTTTG
14927517 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
14927549 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
14927581 GA
1 GA
14927583 TAAATATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (32 bp):
GAGAAAGGCTGCCACATTAACAATGACTACCT
Found at i:14927984 original size:14 final size:14
Alignment explanation
Indices: 14927965--14927991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14927955 GATCGTACGA
14927965 TACATAGACATAAT
1 TACATAGACATAAT
14927979 TACATAGACATAA
1 TACATAGACATAA
14927992 ACATACTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
TACATAGACATAAT
Found at i:14937154 original size:42 final size:40
Alignment explanation
Indices: 14937068--14937155 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
14937058 ATGATTGTTG
* *
14937068 AATTGAATATATATATATTGAGAAAATGTGTTTATTGTCA
1 AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
* * * * *
14937108 AATTGAATATATGTTTATATGTGATAATATGTATATATGTGA
1 AATTGAATATATATATAT-TGAGAAAATATGTATAT-TGTCA
14937150 AATTGA
1 AATTGA
14937156 GACATTGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.41
41 13 0.33
42 10 0.26
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.43
Consensus pattern (40 bp):
AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
Found at i:14939419 original size:25 final size:26
Alignment explanation
Indices: 14939391--14939448 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
14939381 GGACACACCA
*
14939391 CAGCTCA-CATGAGTTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
14939416 CAGCT-AGCATGAGCTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
14939441 CAGCTCAG
1 CAGCTCAG
14939449 AAGAACTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 27 0.90
26 2 0.07
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
CAGCTCAGCATGAGCTTTCCGTTATT
Found at i:14952924 original size:69 final size:69
Alignment explanation
Indices: 14952842--14953001 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 69
14952832 CTTTTTAAGT
* * *
14952842 ATTAAAATT--ATTTTTAATGAAATTAGTAAAGAATTGAGCTATAAGAGTATTCTTT-GCTCAAT
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAG-TCAAT
14952904 GAAGG
65 GAAGG
**
14952909 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATGTGAGTATTCTTTAGTCAATG
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
**
14952974 TGGG
66 AAGG
* *
14952978 ATTAAAATTAACTTTTTTATGAAA
1 ATTAAAATTAAATTTTTAATGAAA
14953002 GTAGGGAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 9 0.11
69 71 0.88
70 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (69 bp):
ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
AAGG
Found at i:14954963 original size:20 final size:20
Alignment explanation
Indices: 14954938--14954975 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14954928 AATTTTGGAT
*
14954938 TTATTTTTAATTATCTTTAA
1 TTATTTGTAATTATCTTTAA
*
14954958 TTATTTGTATTTATCTTT
1 TTATTTGTAATTATCTTT
14954976 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTGTAATTATCTTTAA
Found at i:14961441 original size:5 final size:5
Alignment explanation
Indices: 14961421--14961475 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
14961411 GGGCAACTCA
* * *
14961421 ATTTT ATTTT -TATTT ATTTT ATTTA ATTTA ATTTT ATTATT -TATT ATTTT
1 ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT
14961471 ATTTT
1 ATTTT
14961476 TGGATGTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 3 0.07
5 36 0.86
6 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:14961441 original size:15 final size:15
Alignment explanation
Indices: 14961421--14961476 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
14961411 GGGCAACTCA
14961421 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
*
14961436 ATTTTA-TTTAATTT
1 ATTTTATTTTTATTT
14961450 AATTTTATTATTTA-TT
1 -ATTTTATT-TTTATTT
14961466 ATTTTATTTTT
1 ATTTTATTTTT
14961477 GGATGTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.28
15 20 0.56
16 3 0.08
17 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTATTTTTATTT
Found at i:14964294 original size:96 final size:96
Alignment explanation
Indices: 14964116--14964298 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
14964106 TTTTTAAGAA
* ** *
14964116 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCATGTCAAAAGGTTCG
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
14964181 ATATGTTCTTAAGAAAAATAAAAATTAGGAG
66 ATATGTTCTTAACAAAAATAAAAATTAGGAG
*** * * *
14964212 TATGTTGGGCTGAGTAATTGGGGTGAGGTGCTTGACTGTCATCTCTTTTCGCATCAAAAGGTTCA
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
14964277 ATATATT-TCTAACAAAAATAAA
66 ATATGTTCT-TAACAAAAATAAA
14964299 TAAATTAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 73 0.99
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (96 bp):
TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
ATATGTTCTTAACAAAAATAAAAATTAGGAG
Found at i:14964340 original size:8 final size:8
Alignment explanation
Indices: 14964327--14964351 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
14964317 AAAAAAAGAG
14964327 AAAGAAAA
1 AAAGAAAA
14964335 AAAGAAAA
1 AAAGAAAA
14964343 AAAGAAAA
1 AAAGAAAA
14964351 A
1 A
14964352 TTAATAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:14964933 original size:14 final size:13
Alignment explanation
Indices: 14964914--14964951 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
14964904 ATTTAATATT
14964914 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
14964928 TAATTATTAAGGA
1 TAATTATTTAGGA
14964941 TAATTATTTAG
1 TAATTATTTAG
14964952 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:14964990 original size:20 final size:20
Alignment explanation
Indices: 14964965--14965004 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
14964955 TAAATTTTAG
*
14964965 ATTTATTTTTAGTTATCTTT
1 ATTTATTTGTAGTTATCTTT
*
14964985 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTAGTTATCTTT
14965005 TAGAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTAGTTATCTTT
Found at i:14977045 original size:20 final size:20
Alignment explanation
Indices: 14977020--14977058 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14977010 AATTAGATTA
14977020 AAATTAGATACTGATAAATG
1 AAATTAGATACTGATAAATG
14977040 AAATTAGATACTGATAAAT
1 AAATTAGATACTGATAAAT
14977059 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (20 bp):
AAATTAGATACTGATAAATG
Found at i:14982309 original size:19 final size:19
Alignment explanation
Indices: 14982273--14982309 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14982263 TAATTAGGCT
* *
14982273 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
14982292 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
14982310 GAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:14984230 original size:23 final size:23
Alignment explanation
Indices: 14984186--14984230 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
14984176 TTATAATTGA
* *
14984186 AAAGTGATTTTAAATTCGAAATG
1 AAAGTGATTTGAAATTCAAAATG
14984209 AAAGTGATTTGAGAATT-AAAAT
1 AAAGTGATTTGA-AATTCAAAAT
14984231 ACCTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (23 bp):
AAAGTGATTTGAAATTCAAAATG
Found at i:14991459 original size:41 final size:40
Alignment explanation
Indices: 14991414--14991562 Score: 160
Period size: 41 Copynumber: 3.6 Consensus size: 40
14991404 CAAACATTAC
14991414 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTAA
* *
14991455 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTAA
* *
14991496 GTCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAA
1 GTCTAGCAGGCTTAA-TGCCGGTG-AAT-AATTCAGACTTTAA
* **
14991537 GCCTAGCAGGCAAAATGCCGGTGAAT
1 GTCTAGCAGGCTTAATGCCGGTGAAT
14991563 CTGTTTAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.02
40 7 0.08
41 78 0.85
42 2 0.02
43 2 0.02
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (40 bp):
GTCTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAA
Found at i:14999317 original size:29 final size:30
Alignment explanation
Indices: 14999269--14999360 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
14999259 ATAATCATGT
14999269 TATCTGTTTCCGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
14999299 TATCTGTTT-CGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
* *
14999328 TATCTATTTCCGTTATATCCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
14999358 TAT
1 TAT
14999361 GTCATATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 28 0.47
30 31 0.53
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (30 bp):
TATCTGTTTCCGTTATATTCTTTTTATAAG
Found at i:15005398 original size:7 final size:7
Alignment explanation
Indices: 15005386--15005410 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15005376 TATTCATGTC
15005386 CCTTCCA
1 CCTTCCA
15005393 CCTTCCA
1 CCTTCCA
15005400 CCTTCCA
1 CCTTCCA
15005407 CCTT
1 CCTT
15005411 TTAGCCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.56, G:0.00, T:0.32
Consensus pattern (7 bp):
CCTTCCA
Found at i:15013292 original size:25 final size:25
Alignment explanation
Indices: 15013263--15013313 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
15013253 GAAAATAATG
*
15013263 AAGAAATATCTAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
15013288 AAGAAATATATAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
15013313 A
1 A
15013314 TTTCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
AAGAAATATATAGATTTCTCATGAT
Found at i:15014380 original size:45 final size:45
Alignment explanation
Indices: 15014304--15014421 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
15014294 TGACACAGTT
* * * * * *
15014304 CGCACGTATGAGTCCGCCATATCTATTAATCTTCTTTTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
* *
15014349 CGTATGTATGAGTCCACTATATTTATGAATCTACTTCTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
*
15014394 CGCATGAATGAG-CTCACTATATCTATGA
1 CGCATGTATGAGTC-CACTATATCTATGA
15014422 GTATTCTTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (45 bp):
CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
Found at i:15015956 original size:7 final size:7
Alignment explanation
Indices: 15015944--15015977 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
15015934 CAAATTAATA
*
15015944 AAATATT
1 AAATATC
15015951 AAATATC
1 AAATATC
*
15015958 AATTATC
1 AAATATC
15015965 AAATATC
1 AAATATC
15015972 AAATAT
1 AAATAT
15015978 TATTGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (7 bp):
AAATATC
Found at i:15016231 original size:39 final size:39
Alignment explanation
Indices: 15016177--15016256 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
15016167 TAACAGAAGT
15016177 TAAAAAAATTGATGGTCAATCACATAGCG-CTACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGTC-ACGTGGCA
15016216 TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
15016255 TA
1 TA
15016257 TTTTTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (39 bp):
TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
Found at i:15016385 original size:18 final size:20
Alignment explanation
Indices: 15016349--15016386 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
15016339 AAAAATTCAT
*
15016349 AAAATATATATAATGTAGAA
1 AAAAAATATATAATGTAGAA
15016369 AAAAAATATA-AAT-TAGAA
1 AAAAAATATATAATGTAGAA
15016387 GAGAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAAAATATATAATGTAGAA
Found at i:15016492 original size:20 final size:19
Alignment explanation
Indices: 15016443--15016484 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15016433 GAAATTAGTT
15016443 AAAATTAATAATA--TTATA
1 AAAATT-ATAATATTTTATA
15016461 AAAATTATAATATTTTATA
1 AAAATTATAATATTTTATA
15016480 AAAAT
1 AAAAT
15016485 ATTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTATAATATTTTATA
Found at i:15016501 original size:20 final size:19
Alignment explanation
Indices: 15016447--15016502 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
15016437 TTAGTTAAAA
15016447 TTAATAATATTATAAAAATT
1 TTAATAA-ATTATAAAAATT
* **
15016467 ATAATATTTTATAAAAATAT
1 TTAATAAATTATAAAAAT-T
*
15016487 TTAATAAATTGTAAAA
1 TTAATAAATTATAAAA
15016503 TTATGAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAATAAATTATAAAAATT
Found at i:15019722 original size:12 final size:12
Alignment explanation
Indices: 15019705--15019746 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
15019695 CCTAAGATTA
15019705 TATTTTATTATG
1 TATTTTATTATG
*
15019717 TATTTTACTAT-
1 TATTTTATTATG
15019728 TATTTTATTATG
1 TATTTTATTATG
15019740 TATTTTA
1 TATTTTA
15019747 CTATCTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTTTATTATG
Found at i:15019731 original size:23 final size:23
Alignment explanation
Indices: 15019705--15019750 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15019695 CCTAAGATTA
15019705 TATTTTATTATGTATTTTACTAT
1 TATTTTATTATGTATTTTACTAT
15019728 TATTTTATTATGTATTTTACTAT
1 TATTTTATTATGTATTTTACTAT
15019751 CTAGTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATTATGTATTTTACTAT
Found at i:15024824 original size:12 final size:12
Alignment explanation
Indices: 15024807--15024833 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15024797 GGTGGGAAAG
15024807 AAGTTTTCATTA
1 AAGTTTTCATTA
15024819 AAGTTTTCATTA
1 AAGTTTTCATTA
15024831 AAG
1 AAG
15024834 CTATTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (12 bp):
AAGTTTTCATTA
Done.