Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 125 of 141
Found at i:39856412 original size:9 final size:10
Alignment explanation
Indices: 39856385--39856448 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
39856375 TTTAATTTCC
*
39856385 TAAAATTATA
1 TAAAATTTTA
39856395 TAAAATTTT-
1 TAAAATTTTA
*
39856404 TAAAGTTTTA
1 TAAAATTTTA
*
39856414 TAAAA-TTCA
1 TAAAATTTTA
*
39856423 AAAAATATTT-
1 TAAAAT-TTTA
39856433 TAAAATTTTA
1 TAAAATTTTA
*
39856443 GAAAAT
1 TAAAAT
39856449 ATGAAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 18 0.43
10 22 0.52
11 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (10 bp):
TAAAATTTTA
Found at i:39857103 original size:5 final size:5
Alignment explanation
Indices: 39857093--39857121 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39857083 TAGTCTCTAT
39857093 ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATAT
39857122 TTTATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:39857886 original size:6 final size:6
Alignment explanation
Indices: 39857862--39857899 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
39857852 CGAGTCTCTC
39857862 TTTATT TTT-TT GCTTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT --TTTATT TTTATT TTTATT TTTATT T
39857900 ATCTTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 2 0.07
6 22 0.76
7 3 0.10
8 2 0.07
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:39857896 original size:18 final size:18
Alignment explanation
Indices: 39857862--39857899 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39857852 CGAGTCTCTC
39857862 TTTATTTTTTTGCTTTATT
1 TTTATTTTTTT-CTTTATT
39857881 TTTATTTTTATT-TTTATT
1 TTTATTTTT-TTCTTTATT
39857899 T
1 T
39857900 ATCTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTATTTTTTTCTTTATT
Found at i:39858753 original size:3 final size:3
Alignment explanation
Indices: 39858745--39858782 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
39858735 TTTAACCTTG
39858745 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39858783 AATTTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39858957 original size:13 final size:13
Alignment explanation
Indices: 39858941--39858965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39858931 GATTTATCCC
39858941 TTTTATTTATTTA
1 TTTTATTTATTTA
39858954 TTTTATTTATTT
1 TTTTATTTATTT
39858966 TTGTTGCTAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:39859338 original size:74 final size:74
Alignment explanation
Indices: 39859194--39859338 Score: 224
Period size: 72 Copynumber: 2.0 Consensus size: 74
39859184 TCTTTTCAAA
* *
39859194 CTCAAGTTTTAAACCGATCTTGGGATTAAGAAGAGAGATCGTGTCCTAACTTACTGGGCATGATC
1 CTCAAGTTTTAAACCGATCTCGGGATTAAGAAGAGAGATCGTGTCCTAACTTACTAGGCATGATC
39859259 CTTTTTTTT
66 CTTTTTTTT
*
39859268 CTCAAGTTTTAAA-TGATCTCGGGAATTAAGAA-A-AGATCGTGTCCTAACTTACTAGGCATGAT
1 CTCAAGTTTTAAACCGATCTCGGG-ATTAAGAAGAGAGATCGTGTCCTAACTTACTAGGCATGAT
*
39859330 CCATTTTTT
65 CCTTTTTTT
39859339 AAATCCGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
72 36 0.55
73 9 0.14
74 21 0.32
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (74 bp):
CTCAAGTTTTAAACCGATCTCGGGATTAAGAAGAGAGATCGTGTCCTAACTTACTAGGCATGATC
CTTTTTTTT
Found at i:39865602 original size:15 final size:15
Alignment explanation
Indices: 39865582--39865612 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39865572 TAATTTGGCA
39865582 TAAACATGTGCATTT
1 TAAACATGTGCATTT
39865597 TAAACATGTGCATTT
1 TAAACATGTGCATTT
39865612 T
1 T
39865613 TTCATTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TAAACATGTGCATTT
Found at i:39867054 original size:2 final size:2
Alignment explanation
Indices: 39867047--39867075 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39867037 TAAGCAGTGG
39867047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39867076 GAATGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39868131 original size:14 final size:14
Alignment explanation
Indices: 39868112--39868138 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39868102 TTTTAGTGGC
39868112 TTGATAATGGTGTT
1 TTGATAATGGTGTT
39868126 TTGATAATGGTGT
1 TTGATAATGGTGT
39868139 AAACAACACA
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:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
TTGATAATGGTGTT
Found at i:39869008 original size:24 final size:24
Alignment explanation
Indices: 39868973--39869053 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
39868963 TAGACTAATT
* *
39868973 AGAGTTTGATTGAAATAAATAAGC
1 AGAGTTTAATTGAAACAAATAAGC
* *
39868997 GGAGTTTAATTGAAACAAATAAGT
1 AGAGTTTAATTGAAACAAATAAGC
* *
39869021 AGAGTTAAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAGC
39869045 AGAGTTTAA
1 AGAGTTTAA
39869054 CTGGAAGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAGC
Found at i:39870306 original size:40 final size:40
Alignment explanation
Indices: 39870258--39870348 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
39870248 CGTGTCCTAT
** * *
39870258 TGGA-GCGTTTTGCTGATTGTGCAAGAAAGCGTACCTCAC
1 TGGACGCGTTTTGCAAACTGTGCAAGAAAGCGCACCTCAC
* * *
39870297 TGGACGCGTTTTGCAAACTGTGCAGGAAAGCGCGCCTCGC
1 TGGACGCGTTTTGCAAACTGTGCAAGAAAGCGCACCTCAC
*
39870337 TGGACACGTTTT
1 TGGACGCGTTTT
39870349 CCCCAACTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (40 bp):
TGGACGCGTTTTGCAAACTGTGCAAGAAAGCGCACCTCAC
Found at i:39879702 original size:3 final size:3
Alignment explanation
Indices: 39879694--39879729 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39879684 CATTGAACCA
*
39879694 ATC ATC ATC ATC ATC ATC ATC ATC AAC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
39879730 TCCATGACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:39888464 original size:61 final size:59
Alignment explanation
Indices: 39888390--39888506 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 59
39888380 AGTGATTATC
39888390 TTAATATTAAATTTAGTT-TAATATTTATCTTATATATAAATATTATACTAATTTAATAGAT
1 TTAATATTAAATTTA-TTCTAATATTTATCTT-TA-ATAAATATTATACTAATTTAATAGAT
* *
39888451 TTAATATTAAATTTATTCTAATATTTATCTTTAATAAGTATTATACTATTTTAATA
1 TTAATATTAAATTTATTCTAATATTTATCTTTAATAAATATTATACTAATTTAATA
39888507 TTAGAGTGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 21 0.40
60 4 0.08
61 28 0.53
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTATTCTAATATTTATCTTTAATAAATATTATACTAATTTAATAGAT
Found at i:39891177 original size:19 final size:17
Alignment explanation
Indices: 39891145--39891179 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
39891135 ATTCACATTC
39891145 CATCATTCTCAATTCAA
1 CATCATTCTCAATTCAA
39891162 CATCAATTCGTCAATTCA
1 CATC-ATTC-TCAATTCA
39891180 TCATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (17 bp):
CATCATTCTCAATTCAA
Found at i:39891563 original size:9 final size:9
Alignment explanation
Indices: 39891546--39891582 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39891536 TGAGTTTTCG
39891546 AATTCGAAT
1 AATTCGAAT
*
39891555 AACTCGAAT
1 AATTCGAAT
39891564 AATTCGAAT
1 AATTCGAAT
39891573 AATTCGAAT
1 AATTCGAAT
39891582 A
1 A
39891583 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39895644 original size:21 final size:23
Alignment explanation
Indices: 39895615--39895662 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
39895605 AGAGTATAAG
*
39895615 ATAATATTATTA-AATTATTAA-
1 ATAAAATTATTATAATTATTAAT
*
39895636 ATAAAATTATTATTATTATTAAT
1 ATAAAATTATTATAATTATTAAT
39895659 ATAA
1 ATAA
39895663 TATTCTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 8 0.35
23 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATTATTATAATTATTAAT
Found at i:39896797 original size:20 final size:22
Alignment explanation
Indices: 39896758--39896812 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
39896748 ATTCATGAAG
* *
39896758 TTAAAAAAATAACTCTTAATT-
1 TTAAAAAAATAACACGTAATTA
39896779 TTAAAAAAATAA-ACGTAATTA
1 TTAAAAAAATAACACGTAATTA
39896800 TCTAAAGAAAATA
1 T-TAAA-AAAATA
39896813 GCTCATAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.21
21 13 0.45
22 4 0.14
23 6 0.21
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (22 bp):
TTAAAAAAATAACACGTAATTA
Found at i:39907792 original size:24 final size:24
Alignment explanation
Indices: 39907760--39907812 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
39907750 GTTTTAAGAG
39907760 AATGTTTACATACTCTTGAAGTAT
1 AATGTTTACATACTCTTGAAGTAT
39907784 AATGTTTACATACTCTTGAAGTAT
1 AATGTTTACATACTCTTGAAGTAT
39907808 -ATGTT
1 AATGTT
39907813 AAACCTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (24 bp):
AATGTTTACATACTCTTGAAGTAT
Found at i:39910620 original size:23 final size:22
Alignment explanation
Indices: 39910594--39910650 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
39910584 AGTAAAAATG
39910594 AATGCAAAATAATAAATGATGAC
1 AATGCAAAATAATAAATGAT-AC
*
39910617 AATG-TAAAT-A-AAATGATAC
1 AATGCAAAATAATAAATGATAC
*
39910636 AA-GCAAAACAATAAA
1 AATGCAAAATAATAAA
39910651 CAATAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 1 0.04
19 7 0.25
20 8 0.29
21 4 0.14
22 4 0.14
23 4 0.14
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AATGCAAAATAATAAATGATAC
Found at i:39911165 original size:18 final size:18
Alignment explanation
Indices: 39911065--39911165 Score: 73
Period size: 18 Copynumber: 5.7 Consensus size: 18
39911055 CAACAACAAC
*
39911065 AATAATAATAATAATAAT
1 AATAATAATATTAATAAT
* *
39911083 AATAATAAAAGTAATAA-
1 AATAATAATATTAATAAT
* **
39911100 AGATAATAATACT-ATAGC
1 A-ATAATAATATTAATAAT
* * *
39911118 AATGATGACATTAATAAT
1 AATAATAATATTAATAAT
*
39911136 AATAATACTATTAATAAT
1 AATAATAATATTAATAAT
39911154 -ATAAATAATATT
1 AAT-AATAATATT
39911166 GCTACTAATA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
17 13 0.21
18 50 0.79
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (18 bp):
AATAATAATATTAATAAT
Found at i:39911174 original size:24 final size:24
Alignment explanation
Indices: 39911133--39911185 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
39911123 TGACATTAAT
* *
39911133 AATAATAATACTATTAATAATATA
1 AATAATAATACTACTAATAATAGA
* *
39911157 AATAATATTGCTACTAATAATAGA
1 AATAATAATACTACTAATAATAGA
39911181 AATAA
1 AATAA
39911186 CGATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (24 bp):
AATAATAATACTACTAATAATAGA
Found at i:39911178 original size:3 final size:3
Alignment explanation
Indices: 39911065--39911163 Score: 62
Period size: 3 Copynumber: 33.3 Consensus size: 3
39911055 CAACAACAAC
39911065 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAGT AAT AA- AGAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT
* ** * * * * * *
39911110 ACT -AT AGC AAT GAT GAC ATT AAT AAT AAT AAT ACT ATT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39911156 AAAT AAT A
1 -AAT AAT A
39911164 TTGCTACTAA
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
2 6 0.08
3 63 0.85
4 5 0.07
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39912274 original size:27 final size:28
Alignment explanation
Indices: 39912224--39912280 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
39912214 TAGTTTTGGG
*
39912224 TTTGTTGGGTATTTGGGCTTGGTT-TAA
1 TTTGTTGGGTACTTGGGCTTGGTTGTAA
*
39912251 TTTGTTGGGT-CTTGGGTTTGGGTTGTAA
1 TTTGTTGGGTACTTGGGCTT-GGTTGTAA
39912279 TT
1 TT
39912281 GGGTTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.09, C:0.04, G:0.35, T:0.53
Consensus pattern (28 bp):
TTTGTTGGGTACTTGGGCTTGGTTGTAA
Found at i:39919047 original size:98 final size:99
Alignment explanation
Indices: 39918932--39919131 Score: 393
Period size: 98 Copynumber: 2.0 Consensus size: 99
39918922 TTTAATCTCT
39918932 TTATGCTTTTTTATAAATATAAGTCTAATTATTAATATTATTGAAAATTTTATGTTAAATTTAGA
1 TTATGCTTTTTTATAAATATAAGTCTAATTATTAATATTATTGAAAATTTTATGTTAAATTTAGA
39918997 TCTATTACAATACTATTTTTATGTTACACGATTA
66 TCTATTACAATACTATTTTTATGTTACACGATTA
39919031 TTATGC-TTTTTATAAATATAAGTCTAATTATTAATATTATTGAAAATTTTATGTTAAATTTAGA
1 TTATGCTTTTTTATAAATATAAGTCTAATTATTAATATTATTGAAAATTTTATGTTAAATTTAGA
39919095 TCTATTACAATACTATTTTTATGTTACACGATTA
66 TCTATTACAATACTATTTTTATGTTACACGATTA
39919129 TTA
1 TTA
39919132 AATAAGTATT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 95 0.94
99 6 0.06
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.49
Consensus pattern (99 bp):
TTATGCTTTTTTATAAATATAAGTCTAATTATTAATATTATTGAAAATTTTATGTTAAATTTAGA
TCTATTACAATACTATTTTTATGTTACACGATTA
Found at i:39923379 original size:143 final size:143
Alignment explanation
Indices: 39923116--39923385 Score: 344
Period size: 143 Copynumber: 1.9 Consensus size: 143
39923106 AACTCTTCCA
* * * * *** * * *
39923116 ACCTTCTAAGATCATGTGAAGGATTGTTATCTGCCATCATAGGTGCTGGAAAGGAGGCTTTGATG
1 ACCTTCTAAGACCATGTGAAGGATTGTTATCCGCCATCACAAGTGCCAAAAAGGAGGCTCTAATA
* * ** *
39923181 CCAATTTGGTGTGCGGTTTAATTAAAGATAAAGAAATTACTAAGGAAGTTGAGATGAAGAACAAC
66 CCAATTTGGTGCGCGGTTTAATCAAAGATAAAGAAATTACTAAGGAAACTAAGATGAAGAACAAC
39923246 AATTCAGAGTAAT
131 AATTCAGAGTAAT
* *
39923259 ACCTTCTAATACCATGTGAATGATTGTTATCCGCCATCACAAGTGCCAAAAAGGAGGCTCTAATA
1 ACCTTCTAAGACCATGTGAAGGATTGTTATCCGCCATCACAAGTGCCAAAAAGGAGGCTCTAATA
* * *
39923324 CTAATTTGGTGCGTGGTTTAATCAAAGATAAAG-ATTTACTCAAGGAAACTAAGATGAAGAAC
66 CCAATTTGGTGCGCGGTTTAATCAAAGATAAAGAAATTACT-AAGGAAACTAAGATGAAGAAC
39923386 TACATCTGAG
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
142 6 0.06
143 100 0.94
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (143 bp):
ACCTTCTAAGACCATGTGAAGGATTGTTATCCGCCATCACAAGTGCCAAAAAGGAGGCTCTAATA
CCAATTTGGTGCGCGGTTTAATCAAAGATAAAGAAATTACTAAGGAAACTAAGATGAAGAACAAC
AATTCAGAGTAAT
Found at i:39925012 original size:170 final size:171
Alignment explanation
Indices: 39924716--39925031 Score: 483
Period size: 170 Copynumber: 1.9 Consensus size: 171
39924706 CTACATCTTA
* *
39924716 ATTTAAGATTAACTTTTTTCCCTTTTAGTGAGGTTTGGTCATTCAAAAAAGCGTATACGGATTTC
1 ATTTAAGATTAAATTTTTTCCCTTTTAGTGAGGTTTGGTCATTCAAAAAAGCATATACGGATTTC
* *
39924781 AGTTTTAATTATGATTATACTCACCATATATGGATTTCATTTTTCTTTGATATTAACTTTCTGTT
66 AGTTTTAATTATGATTATACTCACCATATATGGATTTCATTTATCTTTGATATGAACTTTCTGTT
39924846 GCTGCCACTC-CTGTTGCATTTCCAATTTAAGATTAATTGG
131 GCTGCCACTCACTGTTGCATTTCCAATTTAAGATTAATTGG
* ** **
39924886 ATTT-AGATTAAATCTTTTTCCCTTTTATTGAGGTTTGGTCATTTGAAAAAGCATATTTGGATTT
1 ATTTAAGATTAAAT-TTTTTCCCTTTTAGTGAGGTTTGGTCATTCAAAAAAGCATATACGGATTT
* * * *
39924950 CATTTTTAATTATGATTATACTTACCGTATATGGATTTCATTTATCTTTGATGTGAACTTTCTGT
65 CAGTTTTAATTATGATTATACTCACCATATATGGATTTCATTTATCTTTGATATGAACTTTCTGT
*
39925015 TGCTGCCGCTCACTGTT
130 TGCTGCCACTCACTGTT
39925032 CCTGATGGTC
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
169 8 0.06
170 117 0.90
171 5 0.04
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (171 bp):
ATTTAAGATTAAATTTTTTCCCTTTTAGTGAGGTTTGGTCATTCAAAAAAGCATATACGGATTTC
AGTTTTAATTATGATTATACTCACCATATATGGATTTCATTTATCTTTGATATGAACTTTCTGTT
GCTGCCACTCACTGTTGCATTTCCAATTTAAGATTAATTGG
Found at i:39930709 original size:35 final size:32
Alignment explanation
Indices: 39930649--39930712 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
39930639 AATTGAACTT
* *
39930649 TTTTTTTTAATTTTATAATATAAATGATATTA
1 TTTTTTGTAATTTTATAATAAAAATGATATTA
39930681 TTTTTTGTAATTTCTATCATATAAAAATGATA
1 TTTTTTGTAATTT-TAT-A-ATAAAAATGATA
39930713 ACATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
33 3 0.11
34 1 0.04
35 11 0.41
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (32 bp):
TTTTTTGTAATTTTATAATAAAAATGATATTA
Found at i:39941795 original size:26 final size:28
Alignment explanation
Indices: 39941730--39941800 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
39941720 ATAAGAAAAT
* *
39941730 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
*
39941760 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
39941787 TTATT-TTAAATTAT
1 TTATTATTAAATTAT
39941801 TACGCCTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 9 0.24
27 6 0.16
28 14 0.37
29 1 0.03
30 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:39941865 original size:16 final size:16
Alignment explanation
Indices: 39941844--39941908 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
39941834 TTGATTTGCT
39941844 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
39941860 ATTACGCCTCTAATT-C
1 ATTACGCCTCT-ATTCC
*
39941876 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
39941892 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
39941908 A
1 A
39941909 ATACAGCGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.04
16 40 0.89
17 3 0.07
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39943947 original size:14 final size:14
Alignment explanation
Indices: 39943928--39943957 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39943918 AACATTATGA
39943928 AATATTTCAAAGGT
1 AATATTTCAAAGGT
*
39943942 AATATTTCAAGGGT
1 AATATTTCAAAGGT
39943956 AA
1 AA
39943958 ACTACACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (14 bp):
AATATTTCAAAGGT
Found at i:39944462 original size:29 final size:29
Alignment explanation
Indices: 39944420--39944478 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39944410 AAAAAATAGG
39944420 ATAGTTTAATGATTCTTTTATAACTTTTA
1 ATAGTTTAATGATTCTTTTATAACTTTTA
39944449 ATAGTTTAATGATTCTTTTATAACTTTTA
1 ATAGTTTAATGATTCTTTTATAACTTTTA
39944478 A
1 A
39944479 ATTGAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (29 bp):
ATAGTTTAATGATTCTTTTATAACTTTTA
Found at i:39946711 original size:36 final size:36
Alignment explanation
Indices: 39946664--39946736 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
39946654 CTTGATTGAT
* *
39946664 ATTGGTATCGTTATGAATGTAAAATGACGTGAATTA
1 ATTGGTATCGTTATAAATATAAAATGACGTGAATTA
*
39946700 ATTGGTATCGTTATAAATATAAAATGAGGTGAATTA
1 ATTGGTATCGTTATAAATATAAAATGACGTGAATTA
39946736 A
1 A
39946737 AGTGCATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.36
Consensus pattern (36 bp):
ATTGGTATCGTTATAAATATAAAATGACGTGAATTA
Found at i:39948457 original size:26 final size:26
Alignment explanation
Indices: 39948410--39948459 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
39948400 TTAAATAAAC
* * *
39948410 AATTAATGGAATCAGTTGATCAAATT
1 AATTAATAGAATCAATTAATCAAATT
*
39948436 AATTAATAGAATTAATTAATCAAA
1 AATTAATAGAATCAATTAATCAAA
39948460 CCAACCACTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (26 bp):
AATTAATAGAATCAATTAATCAAATT
Found at i:39949406 original size:21 final size:21
Alignment explanation
Indices: 39949382--39949421 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39949372 ATTTTTTAAC
39949382 ATTTTATATATTTT-TTCTTGA
1 ATTTTA-ATATTTTATTCTTGA
*
39949403 ATTTTAATTTTTTATTCTT
1 ATTTTAATATTTTATTCTT
39949422 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (21 bp):
ATTTTAATATTTTATTCTTGA
Found at i:39950291 original size:33 final size:32
Alignment explanation
Indices: 39950219--39950292 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
39950209 ATTTCTCAAC
* * *
39950219 TTTATAAGATTTTATAAATATTTTTAATACAA
1 TTTATAAAACTTTATAAATATATTTAATACAA
* **
39950251 TTT-TAAAACTTTATAAATATATTTGATTTAA
1 TTTATAAAACTTTATAAATATATTTAATACAA
39950282 TTTTATAAAAC
1 -TTTATAAAAC
39950293 ACTAACATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 22 0.65
32 6 0.18
33 6 0.18
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (32 bp):
TTTATAAAACTTTATAAATATATTTAATACAA
Found at i:39951283 original size:19 final size:19
Alignment explanation
Indices: 39951261--39951315 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
39951251 AATATAAAAT
39951261 AATTCAAAATAATTT-TCAAA
1 AATTCAAAAT-ATTTAT-AAA
* *
39951281 ATTTTAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
39951300 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
39951316 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.24
19 13 0.45
20 9 0.31
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:39953069 original size:2 final size:2
Alignment explanation
Indices: 39953064--39953105 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39953054 TATATATATA
39953064 TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39953105 T
1 T
39953106 TCTATTATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:39959842 original size:50 final size:50
Alignment explanation
Indices: 39959700--39959894 Score: 160
Period size: 50 Copynumber: 3.9 Consensus size: 50
39959690 GATAATAACA
* * * ** * * *
39959700 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * **
39959749 TGCCAATGCCATATCCCATATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGG
* * * ** * *
39959799 TGCCCATGCTATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGG
* *
39959849 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATA
39959895 ATCTCAATGA
Statistics
Matches: 115, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 77 0.67
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:39960320 original size:30 final size:30
Alignment explanation
Indices: 39960286--39960346 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39960276 TTGACTCGAT
* * *
39960286 TTTTGCAAAATTACAGTTTTGCCCCTAAAC
1 TTTTGCAAAATTACACTTTTACCCCAAAAC
* *
39960316 TTTTGCATATTTACACTTTTACCCCAAAAC
1 TTTTGCAAAATTACACTTTTACCCCAAAAC
39960346 T
1 T
39960347 CAGAAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACACTTTTACCCCAAAAC
Found at i:39972853 original size:2 final size:2
Alignment explanation
Indices: 39972846--39972877 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39972836 TTGACTTGAG
39972846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39972878 TCAAAAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39973147 original size:2 final size:2
Alignment explanation
Indices: 39973140--39973174 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39973130 TATTTATATT
39973140 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39973175 GCGTTGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:39977770 original size:18 final size:17
Alignment explanation
Indices: 39977737--39977775 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39977727 TTTTATAAAT
39977737 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39977755 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39977772 TGTG
1 TGTG
39977776 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39978032 original size:23 final size:23
Alignment explanation
Indices: 39978001--39978073 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
39977991 AATGTTATTG
*
39978001 ATCAATGGTAGCTTCGGTTAAAT
1 ATCAATGGTAGCTTCGGCTAAAT
* * * *
39978024 TTCAGTGGTAGCTACGGCTACAT
1 ATCAATGGTAGCTTCGGCTAAAT
* *
39978047 ATCAATGGTAACTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTAAAT
39978070 ATCA
1 ATCA
39978074 GTGTGGCACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (23 bp):
ATCAATGGTAGCTTCGGCTAAAT
Found at i:39988445 original size:21 final size:21
Alignment explanation
Indices: 39988418--39988468 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
39988408 AGCGGTGACG
*
39988418 GTGAGATTAGTTACTGTAGCTA
1 GTGAGATTAGATACTGTAGC-A
*
39988440 -TGAGATTGGATACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
39988460 GTGAGATTA
1 GTGAGATTA
39988469 AAAATAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.33
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:39989445 original size:17 final size:17
Alignment explanation
Indices: 39989415--39989448 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39989405 TTTATAGATA
*
39989415 TATTTGTTACATAATTT
1 TATTTGTTAAATAATTT
*
39989432 TATTTTTTAAATAATTT
1 TATTTGTTAAATAATTT
39989449 AATATTTAAT
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:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTGTTAAATAATTT
Found at i:39990376 original size:19 final size:18
Alignment explanation
Indices: 39990335--39990379 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
39990325 GTGTGGAGGG
**
39990335 TTAAAATAAAATTAAAATT
1 TTAAAA-AAAATTAAAAAA
39990354 TTAAAAAAATATTAAAAAA
1 TTAAAAAAA-ATTAAAAAA
39990373 TTAAAAA
1 TTAAAAA
39990380 TTTAGCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAAAATTAAAAAA
Found at i:40005774 original size:565 final size:566
Alignment explanation
Indices: 40004695--40005825 Score: 2255
Period size: 565 Copynumber: 2.0 Consensus size: 566
40004685 TTAATTTAAA
40004695 TAAATAGCATTTTAAAATTATTTTTAAAATTTAAATATTATAATAAATTTTGTCAAATTATAATT
1 TAAATAGCATTTTAAAATTATTTTTAAAATTTAAATATTATAATAAATTTTGTCAAATTATAATT
40004760 TTATATATAGTTTCTAACTTAATTTTAATTATTGATTAGTGGATATAGATTTTTAATTAAATTTT
66 TTATATATAGTTTCTAACTTAATTTTAATTATTGATTAGTGGATATAGATTTTTAATTAAATTTT
40004825 GCGACCACTAAATAATTTATTGTAACATTATTTATATATTTAAAATATCTATTTCAATTTTAGTA
131 GCGACCACTAAATAATTTATTGTAACATTATTTATATATTTAAAATATCTATTTCAATTTTAGTA
40004890 GTATATTTAATTTGTAAAAATATTAATAAACTTAAAAAGATTTTTGAAACAATTTCAAAATTTAA
196 GTATATTTAATTTGTAAAAATATTAATAAACTTAAAAAGATTTTTGAAACAATTTCAAAATTTAA
40004955 AATGTATATAAAATTGTAAGTTAAATTATTGAATATAAGCAAATTAGAAAGACTTATTATGAATT
261 AATGTATATAAAATTGTAAGTTAAATTATTGAATATAAGCAAATTAGAAAGACTTATTATGAATT
40005020 ATACGAAAAAAGTTCCTCCACGAATGTTTTCCTTTTTCTATTGCTACATGTCAAAAAAAAAAAAT
326 ATACGAAAAAAGTTCCTCCACGAATGTTTTCCTTTTTCTATTGCTACATGTCAAAAAAAAAAAAT
40005085 AGTATTATCATTTTAAAAACTTAAAAATCTCTCTTCCCATATGTATACTAAAGCAAGCAGATTAT
391 AGTATTATCATTTTAAAAACTTAAAAATCTCTCTTCCCATATGTATACTAAAGCAAGCAGATTAT
40005150 TTGAATGTTAATAAAATTTTTGTTTTCCGTTCTCTTTTGTTTCTTTCTCTATTTTTCTCCCTTCT
456 TTGAATGTTAATAAAATTTTTGTTTTCCGTTCTCTTTTGTTTCTTTCTCTATTTTTCTCCCTTCT
40005215 TTATTTTTTTAACGTAGTTTCTTTATATTTTTCATTTGTTAAAATT
521 TTATTTTTTTAACGTAGTTTCTTTATATTTTTCATTTGTTAAAATT
40005261 TAAATAGCA-TTTAAAATTATTTTTAAAATTTAAATATTATAATAAATTTTGTCAAATTATAATT
1 TAAATAGCATTTTAAAATTATTTTTAAAATTTAAATATTATAATAAATTTTGTCAAATTATAATT
40005325 TTATATATAGTTTCTAACTTAATTTTAATTATTGATTAGTGGATATAGATTTTTAATTAAATTTT
66 TTATATATAGTTTCTAACTTAATTTTAATTATTGATTAGTGGATATAGATTTTTAATTAAATTTT
40005390 GCGACCACTAAATAATTTATTGTAACATTATTTATATATTTAAAATATCTATTTCAATTTTAGTA
131 GCGACCACTAAATAATTTATTGTAACATTATTTATATATTTAAAATATCTATTTCAATTTTAGTA
40005455 GTATATTTAATTTGTAAAAATATTAATAAACTTAAAAAGATTTTTGAAACAATTTCAAAATTTAA
196 GTATATTTAATTTGTAAAAATATTAATAAACTTAAAAAGATTTTTGAAACAATTTCAAAATTTAA
40005520 AATGTATATAAAATTGTAAGTTAAATTATTGAATATAAGCAAATTAGAAAGACTTATTATGAATT
261 AATGTATATAAAATTGTAAGTTAAATTATTGAATATAAGCAAATTAGAAAGACTTATTATGAATT
40005585 ATACGAAAAAAGTTCCTCCACGAATGTTTTCCTTTTTCTATTGCTACATGTCAAAAAAAAAAAAT
326 ATACGAAAAAAGTTCCTCCACGAATGTTTTCCTTTTTCTATTGCTACATGTCAAAAAAAAAAAAT
40005650 AGTATTATCATTTTAAAAACTTAAAAATCTCTCTTCCCATATGTATACTAAAGCAAGCAGATTAT
391 AGTATTATCATTTTAAAAACTTAAAAATCTCTCTTCCCATATGTATACTAAAGCAAGCAGATTAT
40005715 TTGAATGTTAATAAAATTTTTGTTTTCCGTTCTCTTTTGTTTCTTTCTCTATTTTTCTCCCTTCT
456 TTGAATGTTAATAAAATTTTTGTTTTCCGTTCTCTTTTGTTTCTTTCTCTATTTTTCTCCCTTCT
40005780 TTATTTTTTTAACGTAGTTTCTTTATATTTTTCATTTGTTAAAATT
521 TTATTTTTTTAACGTAGTTTCTTTATATTTTTCATTTGTTAAAATT
40005826 AGTTCAAAAG
Statistics
Matches: 565, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
565 556 0.98
566 9 0.02
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (566 bp):
TAAATAGCATTTTAAAATTATTTTTAAAATTTAAATATTATAATAAATTTTGTCAAATTATAATT
TTATATATAGTTTCTAACTTAATTTTAATTATTGATTAGTGGATATAGATTTTTAATTAAATTTT
GCGACCACTAAATAATTTATTGTAACATTATTTATATATTTAAAATATCTATTTCAATTTTAGTA
GTATATTTAATTTGTAAAAATATTAATAAACTTAAAAAGATTTTTGAAACAATTTCAAAATTTAA
AATGTATATAAAATTGTAAGTTAAATTATTGAATATAAGCAAATTAGAAAGACTTATTATGAATT
ATACGAAAAAAGTTCCTCCACGAATGTTTTCCTTTTTCTATTGCTACATGTCAAAAAAAAAAAAT
AGTATTATCATTTTAAAAACTTAAAAATCTCTCTTCCCATATGTATACTAAAGCAAGCAGATTAT
TTGAATGTTAATAAAATTTTTGTTTTCCGTTCTCTTTTGTTTCTTTCTCTATTTTTCTCCCTTCT
TTATTTTTTTAACGTAGTTTCTTTATATTTTTCATTTGTTAAAATT
Found at i:40011473 original size:21 final size:21
Alignment explanation
Indices: 40011439--40011478 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40011429 CCAAAACAAG
*
40011439 GGAAAATGGGTTACATTTTAA
1 GGAAAATGGATTACATTTTAA
* *
40011460 GGAAAATGTATTACCTTTT
1 GGAAAATGGATTACATTTT
40011479 CAATTTCCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
GGAAAATGGATTACATTTTAA
Found at i:40048237 original size:15 final size:16
Alignment explanation
Indices: 40048217--40048250 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40048207 GACTATGAGC
40048217 TTACTTGAAT-ACATT
1 TTACTTGAATCACATT
*
40048232 TTACTTGATTCACATT
1 TTACTTGAATCACATT
40048248 TTA
1 TTA
40048251 TGTTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTACTTGAATCACATT
Found at i:40048697 original size:13 final size:13
Alignment explanation
Indices: 40048658--40048697 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
40048648 AGTTCTTCAT
*
40048658 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
40048671 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
40048684 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40048697 T
1 T
40048698 TTGGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40049174 original size:20 final size:19
Alignment explanation
Indices: 40049133--40049176 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
40049123 TTCTTAAGAC
40049133 TAAATTAAAAAAAAAACCCT
1 TAAATTAAAAAAAAAA-CCT
40049153 TAAATTAAAAAGAAAGAA-CT
1 TAAATTAAAAA-AAA-AACCT
40049173 TAAA
1 TAAA
40049177 AATAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 17 0.77
21 3 0.14
22 2 0.09
ACGTcount: A:0.66, C:0.09, G:0.05, T:0.20
Consensus pattern (19 bp):
TAAATTAAAAAAAAAACCT
Found at i:40055337 original size:17 final size:17
Alignment explanation
Indices: 40055311--40055353 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
40055301 TAGAACACAT
*
40055311 TAAA-AAAAACTTATAA
1 TAAATAAAAACTTACAA
* *
40055327 TATATAAAAACTTCCAA
1 TAAATAAAAACTTACAA
40055344 TAAATAAAAA
1 TAAATAAAAA
40055354 AATATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAATAAAAACTTACAA
Found at i:40055375 original size:5 final size:5
Alignment explanation
Indices: 40055365--40055391 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40055355 ATATAAATTT
40055365 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
40055392 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:40055408 original size:28 final size:29
Alignment explanation
Indices: 40055345--40055406 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
40055335 AACTTCCAAT
*
40055345 AAAT-AAA-AAAATATAAATTTTAAAATA
1 AAATAAAATAAAATATAAATATTAAAATA
40055372 AAATAAAATAAAATA-AAATATTAAAA-A
1 AAATAAAATAAAATATAAATATTAAAATA
*
40055399 AATTAAAA
1 AAATAAAA
40055407 ATTAATATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.39
28 13 0.42
29 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (29 bp):
AAATAAAATAAAATATAAATATTAAAATA
Found at i:40055410 original size:16 final size:17
Alignment explanation
Indices: 40055365--40055411 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
40055355 ATATAAATTT
40055365 TAAAAT-AAAA-TAAAA
1 TAAAATAAAAATTAAAA
40055380 TAAAATAAAATATTAAAA
1 TAAAATAAAA-ATTAAAA
*
40055398 -AAATTAAAAATTAA
1 TAAAATAAAAATTAA
40055412 TATAGGCGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 9 0.32
18 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAAAAATTAAAA
Found at i:40058355 original size:24 final size:23
Alignment explanation
Indices: 40058296--40058355 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
40058286 TAGACCCGTC
40058296 AATATTTTTT-TTAATTTTTAAA
1 AATATTTTTTATTAATTTTTAAA
* *
40058318 AATATATTTATATTAA-TTTTAACTT
1 AATAT-TTTTTATTAATTTTTAA--A
40058343 AATATTTTTTATT
1 AATATTTTTTATT
40058356 TGTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.16
23 10 0.32
24 11 0.35
25 5 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATTTTTTATTAATTTTTAAA
Found at i:40065583 original size:30 final size:30
Alignment explanation
Indices: 40065549--40065614 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
40065539 ATGCTTGGGG
* *
40065549 CTTAAGCTCTTCAATTTTTTGAAAATGTTA
1 CTTAAGCCCTTAAATTTTTTGAAAATGTTA
* *
40065579 CTTAAACCCTTAAATTTTTTGAAAATTTTA
1 CTTAAGCCCTTAAATTTTTTGAAAATGTTA
*
40065609 GTTAAG
1 CTTAAG
40065615 TTCTACAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (30 bp):
CTTAAGCCCTTAAATTTTTTGAAAATGTTA
Found at i:40065689 original size:22 final size:20
Alignment explanation
Indices: 40065654--40065693 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40065644 ACCTTCAAAA
*
40065654 TTTTTGAAAATTCTCATTACT
1 TTTTTAAAAATTCT-ATTACT
40065675 TTTTTAAAAATTTCTATTA
1 TTTTTAAAAA-TTCTATTA
40065694 AACCTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAATTCTATTACT
Found at i:40075470 original size:7 final size:7
Alignment explanation
Indices: 40075460--40075485 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40075450 GTGTTTTTTT
40075460 TTTTGCA
1 TTTTGCA
40075467 TTTTGCA
1 TTTTGCA
40075474 TTTTGCA
1 TTTTGCA
40075481 TTTTG
1 TTTTG
40075486 GTGAAGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (7 bp):
TTTTGCA
Found at i:40078574 original size:35 final size:36
Alignment explanation
Indices: 40078526--40078594 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
40078516 ATTTGTTAGA
40078526 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
*
40078562 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAA
40078595 ATGATTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
Found at i:40079870 original size:20 final size:19
Alignment explanation
Indices: 40079842--40079884 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
40079832 CAATTTTAAA
40079842 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATA-G
*
40079862 TATATAAATTTATTAATAG
1 TATAAAAATTTATTAATAG
40079881 TATA
1 TATA
40079885 GGTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TATAAAAATTTATTAATAG
Found at i:40079898 original size:3 final size:3
Alignment explanation
Indices: 40079890--40079919 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40079880 GTATAGGTAT
40079890 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40079920 GCCAAGGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40089750 original size:20 final size:20
Alignment explanation
Indices: 40089727--40089767 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40089717 TTTAAATTTA
*
40089727 GGGTTTTAGGTTTA-GGTTTG
1 GGGTTTT-GATTTAGGGTTTG
40089747 GGGTTTTGATTTAGGGTTTG
1 GGGTTTTGATTTAGGGTTTG
40089767 G
1 G
40089768 TACTCAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.49
Consensus pattern (20 bp):
GGGTTTTGATTTAGGGTTTG
Found at i:40095086 original size:20 final size:20
Alignment explanation
Indices: 40095056--40095101 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
40095046 TGTATTTCCT
40095056 TATGATGGCTCTTTCAACAGG
1 TATG-TGGCTCTTTCAACAGG
40095077 TATGTGGCTCTTTCAACAGG
1 TATGTGGCTCTTTCAACAGG
40095097 TATGT
1 TATGT
40095102 CTTACTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
TATGTGGCTCTTTCAACAGG
Found at i:40102459 original size:42 final size:42
Alignment explanation
Indices: 40102400--40102569 Score: 340
Period size: 42 Copynumber: 4.0 Consensus size: 42
40102390 AGCTGGTTTG
40102400 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
1 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
40102442 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
1 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
40102484 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
1 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
40102526 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
1 ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
40102568 AT
1 AT
40102570 ATATACCTGA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (42 bp):
ATTGATGGTTTTAAACAGAATTCAGAAATTCAGTATATATAT
Found at i:40106188 original size:22 final size:20
Alignment explanation
Indices: 40106163--40106203 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
40106153 ATTCTAAAGG
40106163 ATTAATTAGAATTAATAAAAAA
1 ATTAATTAG--TTAATAAAAAA
*
40106185 ATTAATTCGTTAATAAAAA
1 ATTAATTAGTTAATAAAAA
40106204 TAACATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTAATTAGTTAATAAAAAA
Found at i:40106212 original size:22 final size:20
Alignment explanation
Indices: 40106174--40106213 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40106164 TTAATTAGAA
*
40106174 TTAATAAAAAAATTAATTCG
1 TTAATAAAAAAAATAATTCG
40106194 TTAATAAAAATAACATAATT
1 TTAATAAAAA-AA-ATAATT
40106214 AAATCCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 2 0.12
22 5 0.29
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAATAAAAAAAATAATTCG
Found at i:40107085 original size:3 final size:3
Alignment explanation
Indices: 40107079--40107131 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
40107069 ACTTCTTCTT
* * *
40107079 CAC CAC CAC CAC CAC CAC CAC CAT CAC CAT CAC CAT CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
40107127 CAC CA
1 CAC CA
40107132 GAGTCAACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.60, G:0.00, T:0.06
Consensus pattern (3 bp):
CAC
Found at i:40107145 original size:30 final size:30
Alignment explanation
Indices: 40107079--40107202 Score: 88
Period size: 30 Copynumber: 4.1 Consensus size: 30
40107069 ACTTCTTCTT
* *
40107079 CACCACCACCACCACCACCACCATCACCAT
1 CACCATCACCACCACCACCACCATCACCAA
* *
40107109 CACCATCACCACCACCACCACCA-GAGTCAA
1 CACCATCACCACCACCACCACCATCA-CCAA
* * * * * * **
40107139 CTCCATCGCCACCCCCACCATCAACATCGC
1 CACCATCACCACCACCACCACCATCACCAA
* * * *
40107169 CACCATCACCATCACCGCCACCGTCACCAC
1 CACCATCACCACCACCACCACCATCACCAA
40107199 CACC
1 CACC
40107203 CCCATCTAAG
Statistics
Matches: 71, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
29 1 0.01
30 69 0.97
31 1 0.01
ACGTcount: A:0.30, C:0.56, G:0.05, T:0.09
Consensus pattern (30 bp):
CACCATCACCACCACCACCACCATCACCAA
Found at i:40107166 original size:21 final size:21
Alignment explanation
Indices: 40107142--40107182 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40107132 GAGTCAACTC
*
40107142 CATCGCCACCCCCACCATCAA
1 CATCGCCACCACCACCATCAA
*
40107163 CATCGCCACCATCACCATCA
1 CATCGCCACCACCACCATCA
40107183 CCGCCACCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.54, G:0.05, T:0.12
Consensus pattern (21 bp):
CATCGCCACCACCACCATCAA
Found at i:40111950 original size:60 final size:60
Alignment explanation
Indices: 40111886--40112012 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
40111876 TCTTTTTTAA
* * ** *
40111886 AATTTTTAGAATTAAAATTAAAATGATAAATTTTGTAAATGTTGA-GCGCTAAATTTATTG
1 AATTTTTAGAATTAAAACTAAAATGACAAATTTTGTAAACATTAATG-GCTAAATTTATTG
* *
40111946 AATTTTTAGAATTCAAACTCAAATGACAAATTTTGTAAACATTAATGGCTAAATTTATTG
1 AATTTTTAGAATTAAAACTAAAATGACAAATTTTGTAAACATTAATGGCTAAATTTATTG
*
40112006 ATTTTTT
1 AATTTTT
40112013 TTAGTTTTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (60 bp):
AATTTTTAGAATTAAAACTAAAATGACAAATTTTGTAAACATTAATGGCTAAATTTATTG
Found at i:40123188 original size:13 final size:13
Alignment explanation
Indices: 40123170--40123194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40123160 TCTTCCTAAG
40123170 ATTTTTTATTATT
1 ATTTTTTATTATT
40123183 ATTTTTTATTAT
1 ATTTTTTATTAT
40123195 AATTATTTTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTATTATT
Found at i:40123203 original size:15 final size:15
Alignment explanation
Indices: 40123171--40123214 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 15
40123161 CTTCCTAAGA
*
40123171 TTTTTTATTATTATT
1 TTTTTTATAATTATT
40123186 TTTTATTATAATTATT
1 TTTT-TTATAATTATT
40123202 TTTTTTATAATTA
1 TTTTTTATAATTA
40123215 AGAGTGGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTATAATTATT
Found at i:40145134 original size:13 final size:13
Alignment explanation
Indices: 40145116--40145142 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40145106 AAAGTTTTTT
40145116 TTTCAAACTAACA
1 TTTCAAACTAACA
40145129 TTTCAAACTAACA
1 TTTCAAACTAACA
40145142 T
1 T
40145143 GCACATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (13 bp):
TTTCAAACTAACA
Found at i:40146196 original size:16 final size:16
Alignment explanation
Indices: 40146131--40146197 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
40146121 TCATTTTATG
40146131 TTTAATTAATAACTCT
1 TTTAATTAATAACTCT
* *
40146147 TTT-ATTTATAAAT-T
1 TTTAATTAATAACTCT
** *
40146161 TTATGTTTAATTA-TCTT
1 TT-TAATTAATAACTC-T
40146178 TTTAATTAATAACTCT
1 TTTAATTAATAACTCT
40146194 TTTA
1 TTTA
40146198 TTTATAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
14 3 0.08
15 10 0.26
16 20 0.53
17 5 0.13
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAATTAATAACTCT
Found at i:40146422 original size:25 final size:22
Alignment explanation
Indices: 40146379--40146426 Score: 53
Period size: 24 Copynumber: 2.0 Consensus size: 22
40146369 TATCATTTAA
40146379 TTTTATAAAAAAAGAGTTATAAT
1 TTTTATAAAAAAAGAGTTA-AAT
40146402 TTTTATATAAAATCAAG-GTTAAAT
1 TTTTATA-AAAA--AAGAGTTAAAT
40146426 T
1 T
40146427 GAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
23 7 0.32
24 8 0.36
25 4 0.18
26 3 0.14
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (22 bp):
TTTTATAAAAAAAGAGTTAAAT
Found at i:40149172 original size:144 final size:145
Alignment explanation
Indices: 40148910--40149197 Score: 479
Period size: 144 Copynumber: 2.0 Consensus size: 145
40148900 TCTACTCAAA
* *
40148910 AACCTTAAGCAAACCCTTACAAATATGATAAATAATAACAATGATTGAAGACATCTCTCAAGGAA
1 AACCTTAAGCAAACCCTTACAAATATGATAAATAATAACAATGATTAAAGACACCTCTCAAGGAA
* *
40148975 GATATTACAATGATAAAGCTCGCTCAATGACAATACAACAATTGAAAAGAATAAAAGAGA-TGGT
66 GATATTACAATGATAAAGCTCACTCAATAACAATACAACAATTGAAAAGAATAAAAGAGACTGGT
40149039 TACCCAAGTGTGTGT
131 TACCCAAGTGTGTGT
*
40149054 AACCTTAAGCAACCCCTTACAAATATGATAAATAATAACAATGATTAAAGACACCTCTCAAGGAA
1 AACCTTAAGCAAACCCTTACAAATATGATAAATAATAACAATGATTAAAGACACCTCTCAAGGAA
* * *
40149119 GATATTACAATGATAAAGCTCACTCAATAACAGTACAACACTTGAAAATAATAAAAGAGATCTGG
66 GATATTACAATGATAAAGCTCACTCAATAACAATACAACAATTGAAAAGAATAAAAGAGA-CTGG
*
40149184 TTACCCGAGTGTGT
130 TTACCCAAGTGTGT
40149198 ATAAAGAACA
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
144 117 0.88
146 16 0.12
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (145 bp):
AACCTTAAGCAAACCCTTACAAATATGATAAATAATAACAATGATTAAAGACACCTCTCAAGGAA
GATATTACAATGATAAAGCTCACTCAATAACAATACAACAATTGAAAAGAATAAAAGAGACTGGT
TACCCAAGTGTGTGT
Found at i:40150440 original size:29 final size:29
Alignment explanation
Indices: 40150398--40150455 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40150388 GTATGATATG
40150398 AATCCTAACATACCACGTGTTCCATCATT
1 AATCCTAACATACCACGTGTTCCATCATT
40150427 AATCCTAACATACCACGTGTTCCATCATT
1 AATCCTAACATACCACGTGTTCCATCATT
40150456 CTTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (29 bp):
AATCCTAACATACCACGTGTTCCATCATT
Found at i:40154621 original size:40 final size:41
Alignment explanation
Indices: 40154567--40154652 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 41
40154557 TACTAAGATT
40154567 ACAACAATAAATGAC-AGTACCAAAGGGGTAGTTTATTCTA
1 ACAACAATAAATGACAAGTACCAAAGGGGTAGTTTATTCTA
*
40154607 ACAACAATAAATGACAGAGTACTAAAGGGGTAGTTTATTCTA
1 ACAACAATAAATGACA-AGTACCAAAGGGGTAGTTTATTCTA
40154649 ACAA
1 ACAA
40154653 GATCGCGGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 15 0.35
42 28 0.65
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (41 bp):
ACAACAATAAATGACAAGTACCAAAGGGGTAGTTTATTCTA
Found at i:40155815 original size:17 final size:17
Alignment explanation
Indices: 40155771--40155821 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
40155761 AACTTGATCC
* *
40155771 AAATATATTATGTTATAA
1 AAATATATT-TATAATAA
40155789 AAA-ATA-TTATAATAA
1 AAATATATTTATAATAA
*
40155804 AAATATATTTATATTAA
1 AAATATATTTATAATAA
40155821 A
1 A
40155822 TTACTAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 12 0.43
18 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATATATTTATAATAA
Found at i:40164379 original size:21 final size:21
Alignment explanation
Indices: 40164355--40164407 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
40164345 TTTAGCTCCA
*
40164355 GTGAGATTAGTTACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
*
40164376 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
40164397 GTGAGATTAGA
1 GTGAGATTAGA
40164408 AACAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:40177566 original size:81 final size:81
Alignment explanation
Indices: 40177473--40177634 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
40177463 CCTTTTGTTG
40177473 AAGACTCAAACCCGAAAAAGGAAATTTTTCCCCCCC-AAAAAAAGCTCTTACCTTGATGCACCAA
1 AAGACTCAAACCCGAAAAAGGAAATTTTTCCCCCCCAAAAAAAAGCTCTT-CCTTGATGCACCAA
40177537 AGCTCTTTTTTTTTTTT
65 AGCTCTTTTTTTTTTTT
40177554 AAGACTCAAACCCGAAAAAGGAAATTTTTCCCCCCCAAAAAAAAGCTCTTCCTTGATGCACCAAA
1 AAGACTCAAACCCGAAAAAGGAAATTTTTCCCCCCCAAAAAAAAGCTCTTCCTTGATGCACCAAA
40177619 GCTCTTTTTTTTTTTT
66 GCTCTTTTTTTTTTTT
40177635 CTTCAAAACT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 67 0.84
82 13 0.16
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (81 bp):
AAGACTCAAACCCGAAAAAGGAAATTTTTCCCCCCCAAAAAAAAGCTCTTCCTTGATGCACCAAA
GCTCTTTTTTTTTTTT
Found at i:40178820 original size:18 final size:19
Alignment explanation
Indices: 40178794--40178839 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
40178784 TGTTTAAAAC
40178794 TTTTAAAAAT-ATTTATAT
1 TTTTAAAAATAATTTATAT
* *
40178812 TTTTCAAAATAATTTTTAT
1 TTTTAAAAATAATTTATAT
40178831 TTATTAAAA
1 TT-TTAAAA
40178840 CATTAACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 9 0.39
20 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATAATTTATAT
Found at i:40179323 original size:3 final size:3
Alignment explanation
Indices: 40179285--40179309 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40179275 TTCAAAGCAA
40179285 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
40179310 CTTTAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40184206 original size:317 final size:318
Alignment explanation
Indices: 40183621--40184255 Score: 1263
Period size: 317 Copynumber: 2.0 Consensus size: 318
40183611 CTATTTTAGA
40183621 GGTATTTGCTTGTTAAGTTACATTTATCTTAATATTTTAAAATTTATTTTCAATTTGTTATGTTT
1 GGTATTTGCTTGTTAAGTTACATTTATCTTAATATTTTAAAATTTATTTTCAATTTGTTATGTTT
40183686 TTAGTATATTTTTATGTATTATATATTTTAAAATTTTTATATAAAAAATTAATTCGAGCAGGTCA
66 TTAGTATATTTTTATGTATTATATATTTTAAAATTTTTATATAAAAAATTAATTCGAGCAGGTCA
40183751 AGCTCAGGCCTAGCAATTCTAGGCCTGATTTTTAGGCCCATGGACAAGTCTAGTTCTGGTTGGAC
131 AGCTCAGGCCTAGCAATTCTAGGCCTGATTTTTAGGCCCATGGACAAGTCTAGTTCTGGTTGGAC
40183816 AGATGCAGAATTTTAGGTCCGCTTTTTAGGTTTGAATTTGATCCAAAAATAGGCTTAAAATTCTA
196 AGATGCAGAATTTTAGGTCCGCTTTTTAGGTTTGAATTTGATCCAAAAATAGGCTTAAAATTCTA
40183881 TTTAAGCTCGACGTAGATTCAAAATACTAAACTCAAACTTTATTCGATTAGCCTGTTT
261 TTTAAGCTCGACGTAGATTCAAAATACTAAACTCAAACTTTATTCGATTAGCCTGTTT
40183939 GGTATTTGC-TGTTAAGTTACATTTATCTTAATATTTTAAAATTTATTTTCAATTTGTTATGTTT
1 GGTATTTGCTTGTTAAGTTACATTTATCTTAATATTTTAAAATTTATTTTCAATTTGTTATGTTT
40184003 TTAGTATATTTTTATGTATTATATATTTTAAAATTTTTATATAAAAAATTAATTCGAGCAGGTCA
66 TTAGTATATTTTTATGTATTATATATTTTAAAATTTTTATATAAAAAATTAATTCGAGCAGGTCA
40184068 AGCTCAGGCCTAGCAATTCTAGGCCTGATTTTTAGGCCCATGGACAAGTCTAGTTCTGGTTGGAC
131 AGCTCAGGCCTAGCAATTCTAGGCCTGATTTTTAGGCCCATGGACAAGTCTAGTTCTGGTTGGAC
40184133 AGATGCAGAATTTTAGGTCCGCTTTTTAGGTTTGAATTTGATCCAAAAATAGGCTTAAAATTCTA
196 AGATGCAGAATTTTAGGTCCGCTTTTTAGGTTTGAATTTGATCCAAAAATAGGCTTAAAATTCTA
40184198 TTTAAGCTCGACGTAGATTCAAAATACTAAACTCAAACTTTATTCGATTAGCCTGTTT
261 TTTAAGCTCGACGTAGATTCAAAATACTAAACTCAAACTTTATTCGATTAGCCTGTTT
40184256 TAAAAAAAAT
Statistics
Matches: 317, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
317 308 0.97
318 9 0.03
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (318 bp):
GGTATTTGCTTGTTAAGTTACATTTATCTTAATATTTTAAAATTTATTTTCAATTTGTTATGTTT
TTAGTATATTTTTATGTATTATATATTTTAAAATTTTTATATAAAAAATTAATTCGAGCAGGTCA
AGCTCAGGCCTAGCAATTCTAGGCCTGATTTTTAGGCCCATGGACAAGTCTAGTTCTGGTTGGAC
AGATGCAGAATTTTAGGTCCGCTTTTTAGGTTTGAATTTGATCCAAAAATAGGCTTAAAATTCTA
TTTAAGCTCGACGTAGATTCAAAATACTAAACTCAAACTTTATTCGATTAGCCTGTTT
Found at i:40185461 original size:91 final size:88
Alignment explanation
Indices: 40185188--40185458 Score: 354
Period size: 85 Copynumber: 3.1 Consensus size: 88
40185178 TTAAGGGTGC
* * * *
40185188 AAAAAGCCCTCAAATTTTTTGAAAAAATA-CAATTAAGCCCCTGTTTTTTTTTTGCACTCATTTG
1 AAAAAGCCCTCAAACTTTTTCAAAAAA-AGCAATTAAGCCCCT-TTTTTTTTTTGCATTCAATTG
* *
40185252 GATACTTGAACTTTCAAAATGTATCA
64 GGTACTTGAACTTTCAAAATGCAT-A
* *
40185278 AAAAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAGGCCCC----TTTTTTTGCATTCAATTGGG
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTTTTTTTTTTTGCATTCAATTGGG
* *
40185339 TATTTGAACTTTTAAAATGCATA
66 TACTTGAACTTTCAAAATGCATA
40185362 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTGTTGCATTCAATT
1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCT-TTTTTTTT-TTGCATTCAATT
*
40185427 GGGTACTTGAACTTTCAATATGCATA
63 GGGTACTTGAACTTTCAAAATGCATA
40185453 AAAAAG
1 AAAAAG
40185459 ACCTTTTTCA
Statistics
Matches: 158, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
84 7 0.04
85 69 0.44
89 1 0.01
90 40 0.25
91 41 0.26
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (88 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTTTTTTTTTTTGCATTCAATTGGG
TACTTGAACTTTCAAAATGCATA
Found at i:40185479 original size:91 final size:90
Alignment explanation
Indices: 40185217--40185518 Score: 262
Period size: 85 Copynumber: 3.4 Consensus size: 90
40185207 TGAAAAAATA
** * * * *
40185217 CAATTAAGCCCCTGTTTTTTTTTTGCACTCATTTGGATACTTGAACTTTCAAAATGTATCAAAAA
1 CAATTAAGCCCCTACTTTTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATGCAT-AAAAA
* ****
40185282 AG-CCCTCAAACCTTTTCAAAAA-AAG
65 AGACCCTCAAA-ATAAAAAAAAAGAAG
* * *
40185307 CAATT-AGGCCC--C--TTTTTTTGCATTCAATTGGGTATTTGAACTTTTAAAATGCATAAAAAA
1 CAATTAAGCCCCTACTTTTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAA
* ****
40185367 GACCCTCAAACTTTTTCAAAAA-AAG
66 GACCCTCAAA-ATAAAAAAAAAGAAG
* *
40185392 CAATTAAGCCCCTATTTTTTTTGTTGCATTCAATTGGGTACTTGAACTTTCAATATGCATAAAAA
1 CAATTAAGCCCCTACTTTTTTT-TTGCATTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAA
* *
40185457 AGACCTTTTTCAAAAAAAAAAAAAAGAAG
65 AGACC---CTCAAAATAAAAAAAAAGAAG
*
40185486 CAATTAAGCCCCTGCTTTTTTTTT-CATTCAATT
1 CAATTAAGCCCCTACTTTTTTTTTGCATTCAATT
40185519 AGGTGCTCGA
Statistics
Matches: 178, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
84 7 0.04
85 63 0.35
86 5 0.03
89 5 0.03
90 10 0.06
91 44 0.25
92 9 0.05
93 7 0.04
94 28 0.16
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (90 bp):
CAATTAAGCCCCTACTTTTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAA
GACCCTCAAAATAAAAAAAAAGAAG
Found at i:40185756 original size:19 final size:18
Alignment explanation
Indices: 40185728--40185769 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
40185718 ATTTATGTTT
40185728 TTTATAATTTTAT-TAAAA
1 TTTATAATTTT-TCTAAAA
40185746 TTTAGTAATTTTTCTAAAA
1 TTTA-TAATTTTTCTAAAA
40185765 TTTAT
1 TTTAT
40185770 TATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTATAATTTTTCTAAAA
Found at i:40185757 original size:27 final size:29
Alignment explanation
Indices: 40185697--40185757 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
40185687 TTTTTATAAA
*
40185697 AATTTTCTAATTTTTAATAAAATTTATGT
1 AATTTTATAATTTTTAATAAAATTTATGT
* *
40185726 -TTTTTATAA-TTTTATTAAAATTTA-GT
1 AATTTTATAATTTTTAATAAAATTTATGT
40185752 AATTTT
1 AATTTT
40185758 TCTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 18 0.67
28 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTTATAATTTTTAATAAAATTTATGT
Found at i:40185757 original size:28 final size:28
Alignment explanation
Indices: 40185699--40185796 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
40185689 TTTATAAAAA
*
40185699 TTTTCTAATTTTTAATAAAATTTATGT--T
1 TTTTCTAA-TTTTATTAAAATTTA-GTAAT
*
40185727 TTTTATAATTTTATTAAAATTTAGTAAT
1 TTTTCTAATTTTATTAAAATTTAGTAAT
* **
40185755 TTTTCTAAAATTTATTATTATTTA-TAATTT
1 TTTTCT-AATTTTATTAAAATTTAGTAA--T
40185785 TTTTCTAATTTT
1 TTTTCTAATTTT
40185797 TAATAAGAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
26 2 0.03
27 14 0.24
28 16 0.28
29 19 0.33
30 7 0.12
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCTAATTTTATTAAAATTTAGTAAT
Found at i:40185795 original size:47 final size:47
Alignment explanation
Indices: 40185677--40185785 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
40185667 GGTTGTTAAT
* * **
40185677 TTTTTTATGATTTTTATAAAAATTTTCTAATTTTTAATAAAATTTATG
1 TTTTTTAT-AATTTTATTAAAATTTAGTAATTTTTAATAAAATTTATG
*
40185725 TTTTTTATAATTTTATTAAAATTTAGTAATTTTT-CTAAAATTTAT-
1 TTTTTTATAATTTTATTAAAATTTAGTAATTTTTAATAAAATTTATG
40185770 TATTATTTATAATTTT
1 T-TT-TTTATAATTTT
40185786 TTTCTAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 1 0.02
46 12 0.22
47 33 0.61
48 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (47 bp):
TTTTTTATAATTTTATTAAAATTTAGTAATTTTTAATAAAATTTATG
Found at i:40187026 original size:6 final size:6
Alignment explanation
Indices: 40187015--40187039 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40187005 ATAACTATTT
40187015 AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC A
40187040 GTAGCCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:40191137 original size:31 final size:31
Alignment explanation
Indices: 40191101--40191164 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
40191091 AATGTGTTAG
40191101 AATGCGTAATAGAATAAGAAAAGCTAAAAAC
1 AATGCGTAATAGAATAAGAAAAGCTAAAAAC
40191132 AATGCGTAATAGAATAAGAAAAGCTAAAAAC
1 AATGCGTAATAGAATAAGAAAAGCTAAAAAC
40191163 AA
1 AA
40191165 AAGAATACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (31 bp):
AATGCGTAATAGAATAAGAAAAGCTAAAAAC
Found at i:40191618 original size:14 final size:14
Alignment explanation
Indices: 40191599--40191629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
40191589 CAAAATATAT
40191599 CAAAAAAAAAACAAA
1 CAAAAAAAAAA-AAA
40191614 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
40191628 CA
1 CA
40191630 TGACACCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:40191733 original size:26 final size:28
Alignment explanation
Indices: 40191654--40191734 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 28
40191644 TCAGGCCAAT
*
40191654 TAAATTGGCGGCACCAAAGGTGCCAAA-
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
40191681 TAAATTGGTGGCACCAATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
40191709 T-CATTGGCGGCACC-ATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
40191735 GAAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 12 0.24
27 36 0.73
28 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (28 bp):
TAAATTGGCGGCACCAATGGTGCCAAAG
Found at i:40191837 original size:19 final size:19
Alignment explanation
Indices: 40191810--40191879 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
40191800 TCAACTCATT
*
40191810 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
40191829 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
40191847 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
40191866 TTTTAATTTAATAA
1 TTTTAATTTAATAA
40191880 AATATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:40191860 original size:37 final size:37
Alignment explanation
Indices: 40191815--40191885 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
40191805 TCATTTTTTT
*
40191815 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
40191852 ATTTAATAACTCTATTTTAATTTAATAAAATATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
40191886 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:40192119 original size:71 final size:72
Alignment explanation
Indices: 40192002--40192146 Score: 256
Period size: 71 Copynumber: 2.0 Consensus size: 72
40191992 GCCACATTTC
*
40192002 AATTTTAGTGCGCAAGCAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAATTTGCATGTTAGG
1 AATTTTAGTGCGCAAGCAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAATTTGCATGTCAGG
40192067 TCCTTGA
66 TCCTTGA
* *
40192074 AATTTTAGTGC-CAAGCAGGAGCAATTCACTTTCAAAATTCAAAATGGTAAATTTTCATGTCAGG
1 AATTTTAGTGCGCAAGCAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAATTTGCATGTCAGG
40192138 TCCTTGA
66 TCCTTGA
40192145 AA
1 AA
40192147 CTGCAGGTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 59 0.84
72 11 0.16
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (72 bp):
AATTTTAGTGCGCAAGCAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAATTTGCATGTCAGG
TCCTTGA
Found at i:40192296 original size:19 final size:19
Alignment explanation
Indices: 40192227--40192295 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
40192217 ACTTAATATT
*
40192227 TTATTAAATTAAAGTAGAG
1 TTATTAAATTAAAATAGAG
* * * *
40192246 TTATTAAATGAGAACA-AT
1 TTATTAAATTAAAATAGAG
40192264 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
40192283 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
40192296 AAATGAGTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 19 0.47
19 21 0.52
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:40192303 original size:20 final size:19
Alignment explanation
Indices: 40192227--40192304 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
40192217 ACTTAATATT
* **
40192227 TTATTAAATTAAAGTAGAG
1 TTATTAAATAAAAAAAGAG
* * * *
40192246 TTATTAAATGAGAACA-AT
1 TTATTAAATAAAAAAAGAG
* *
40192264 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
40192283 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
40192303 TT
1 TT
40192305 GAAGGGGAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
18 14 0.30
19 27 0.59
20 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:40192502 original size:23 final size:23
Alignment explanation
Indices: 40192472--40192516 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40192462 GTTTTTTTTG
40192472 ATATATTTTAGTAAATAAAAAAA
1 ATATATTTTAGTAAATAAAAAAA
*
40192495 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTAGTAAATAAAAAA
40192517 TGATAACATT
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:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
ATATATTTTAGTAAATAAAAAAA
Found at i:40203741 original size:18 final size:18
Alignment explanation
Indices: 40203718--40203754 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40203708 TTCTCTCTAC
*
40203718 AACTTTCTTTTAAATTTA
1 AACTTTCTCTTAAATTTA
40203736 AACTTTCTCTTAAATTTA
1 AACTTTCTCTTAAATTTA
40203754 A
1 A
40203755 GTGTGTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AACTTTCTCTTAAATTTA
Found at i:40206606 original size:59 final size:55
Alignment explanation
Indices: 40206494--40206606 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 55
40206484 TGATTTATTC
* * * *
40206494 ATTTTCGTTTTGGAGAAACACATTTATTTCTAAATGTTTCTATTTCTCCATTTTA
1 ATTTTCATATTGGAGAAACAAATTTATTTCCAAATGTTTCTATTTCTCCATTTTA
40206549 ATTTTCATATTGGAGAAAACCAAATTTCATTTCCAAATGTTTCCTATTTCTCCATTTT
1 ATTTTCATATTGGAG-AAA-CAAATTT-ATTTCCAAATGTTT-CTATTTCTCCATTTT
40206607 CACTATTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 13 0.26
56 3 0.06
57 6 0.12
58 13 0.26
59 15 0.30
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (55 bp):
ATTTTCATATTGGAGAAACAAATTTATTTCCAAATGTTTCTATTTCTCCATTTTA
Found at i:40214844 original size:12 final size:12
Alignment explanation
Indices: 40214827--40214855 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40214817 CCTAAACTGG
40214827 ACTGATACTAAT
1 ACTGATACTAAT
40214839 ACTGATACTAAT
1 ACTGATACTAAT
40214851 ACTGA
1 ACTGA
40214856 AAAGGGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (12 bp):
ACTGATACTAAT
Found at i:40215297 original size:18 final size:19
Alignment explanation
Indices: 40215256--40215300 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
40215246 TAATAAAAAC
40215256 ATTTTGAAATTGAATAACT
1 ATTTTGAAATTGAATAACT
40215275 A-TTTGTAAA-TGAATAA-T
1 ATTTTG-AAATTGAATAACT
40215292 ATTTTGAAA
1 ATTTTGAAA
40215301 ACGAACAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 15 0.62
19 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAACT
Found at i:40215818 original size:20 final size:20
Alignment explanation
Indices: 40215781--40215819 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40215771 GGGAATTAAC
40215781 TGGATTTTATAAGAAAAACT
1 TGGATTTTATAAGAAAAACT
*
40215801 TGGATCTTTATAGGAAAAA
1 TGGAT-TTTATAAGAAAAA
40215820 TTATTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (20 bp):
TGGATTTTATAAGAAAAACT
Found at i:40233552 original size:20 final size:20
Alignment explanation
Indices: 40233518--40233559 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40233508 CACTATTTAA
** *
40233518 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
40233538 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
40233558 AT
1 AT
40233560 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:40233656 original size:15 final size:15
Alignment explanation
Indices: 40233636--40233666 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40233626 ACATGAAAAC
40233636 ACACCAACAAATTCT
1 ACACCAACAAATTCT
40233651 ACACCAACAAATTCT
1 ACACCAACAAATTCT
40233666 A
1 A
40233667 ATATTATTTC
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:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
ACACCAACAAATTCT
Found at i:40245737 original size:15 final size:15
Alignment explanation
Indices: 40245717--40245750 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40245707 TCCTCCTCCT
*
40245717 CATCTTCTTCTTCAC
1 CATCTTCATCTTCAC
*
40245732 CATCTTCATCTTCTC
1 CATCTTCATCTTCAC
40245747 CATC
1 CATC
40245751 ATCGTCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (15 bp):
CATCTTCATCTTCAC
Found at i:40245761 original size:3 final size:3
Alignment explanation
Indices: 40245747--40245814 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
40245737 TCATCTTCTC
* * * *
40245747 CAT CAT CGT CAT CAT CAT TAT CCT C-T AATT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA-T CAT CAT CAT CAT CAT
40245792 CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CA
40245815 CCAATAGCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.31, C:0.32, G:0.01, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:40253250 original size:26 final size:28
Alignment explanation
Indices: 40253166--40253275 Score: 70
Period size: 26 Copynumber: 4.1 Consensus size: 28
40253156 CGTAAAAATC
* * *
40253166 TAAAATAAATAATATACATAAAACAGTT
1 TAAAATAAATAATATATATCAAACAATT
* * *
40253194 TAAGAT-AA-AATA-ATA-GAAAGTAATT
1 TAAAATAAATAATATATATCAAA-CAATT
** *
40253219 CGAAATAAATAA-A-ATATGAAACAATT
1 TAAAATAAATAATATATATCAAACAATT
* *
40253245 TAAAATAGATAATATATATCAAACAGTT
1 TAAAATAAATAATATATATCAAACAATT
40253273 TAA
1 TAA
40253276 TATGAACAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.05
25 8 0.13
26 23 0.37
27 9 0.15
28 19 0.31
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.28
Consensus pattern (28 bp):
TAAAATAAATAATATATATCAAACAATT
Found at i:40253377 original size:24 final size:27
Alignment explanation
Indices: 40253324--40253374 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
40253314 ATCTGCTAAA
40253324 AAATAATAATAATGAATATAAAAATTT
1 AAATAATAATAATGAATATAAAAATTT
40253351 AAATAA-AATAAT-AA-ATAACAAATT
1 AAATAATAATAATGAATATAA-AAATT
40253375 AAAGGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 7 0.30
26 6 0.26
27 6 0.26
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
AAATAATAATAATGAATATAAAAATTT
Found at i:40254522 original size:18 final size:18
Alignment explanation
Indices: 40254487--40254524 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40254477 CTGAAAATTT
*
40254487 TTTAGTTTTGGGCTAGGG
1 TTTAGTTTTGGCCTAGGG
40254505 TTTAG-TTTGGCCTAAGGG
1 TTTAGTTTTGGCCT-AGGG
40254523 TT
1 TT
40254525 AATTTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.13, C:0.08, G:0.34, T:0.45
Consensus pattern (18 bp):
TTTAGTTTTGGCCTAGGG
Found at i:40255502 original size:30 final size:28
Alignment explanation
Indices: 40255477--40255533 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
40255467 TCTTTTTGTC
40255477 TTTCT-TTTTACAATTTTTTTCCTTTTATT
1 TTTCTATTTTAC-ATTTTTTT-CTTTTATT
*
40255506 TTTTTATTTTACATTTTTTTCTTTTATT
1 TTTCTATTTTACATTTTTTTCTTTTATT
40255534 ACGATTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 12 0.46
30 6 0.23
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTCTATTTTACATTTTTTTCTTTTATT
Found at i:40255521 original size:15 final size:15
Alignment explanation
Indices: 40255477--40255531 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
40255467 TCTTTTTGTC
40255477 TTTCTTTTTACAATTTT
1 TTTC-TTTTAC-ATTTT
40255494 TTTCCTTTT--ATTTT
1 TTT-CTTTTACATTTT
*
40255508 TTTATTTTACATTTT
1 TTTCTTTTACATTTT
40255523 TTTCTTTTA
1 TTTCTTTTA
40255532 TTACGATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 4 0.12
14 8 0.24
15 13 0.39
17 7 0.21
18 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTTTTACATTTT
Found at i:40257102 original size:65 final size:64
Alignment explanation
Indices: 40256994--40257116 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 64
40256984 TGACAAATGC
* *
40256994 CCCCCAAAATTTTGGAAACTTTTGATTTCTCTCTTGAAATTTTTAGAAAATTTTAATTAATTAGA
1 CCCCCAAAATTTTGGAAAATTTTCATTTCTCTCTTGAAATTTTTAGAAAA-TTTAATTAATTAGA
* * * *
40257059 CCCCCAAAGTTTTTGAAAATTTTCATTTCT-TCTTTGAAGTTTTTAGCAAATTTAATTA
1 CCCCCAAAATTTTGGAAAATTTTCATTTCTCTC-TTGAAATTTTTAGAAAATTTAATTA
40257117 GGCTCCTCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 10 0.20
65 41 0.80
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.45
Consensus pattern (64 bp):
CCCCCAAAATTTTGGAAAATTTTCATTTCTCTCTTGAAATTTTTAGAAAATTTAATTAATTAGA
Found at i:40264626 original size:27 final size:27
Alignment explanation
Indices: 40264547--40264637 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
40264537 GGGGGAAGTG
* * * * *
40264547 GGTGTCGCCTATTGGGATGGCGTGACC
1 GGTGCCGCCTATAGAGAAGGCGTGATC
*
40264574 AGTGCCGCCTATAGAGAAGGCGTGATC
1 GGTGCCGCCTATAGAGAAGGCGTGATC
*
40264601 GGTGCCGCCTATCAGA-AAGGCGTGATT
1 GGTGCCGCCTAT-AGAGAAGGCGTGATC
*
40264628 GGTGCTGCCT
1 GGTGCCGCCT
40264638 CTTCCCTAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 51 0.94
28 3 0.06
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (27 bp):
GGTGCCGCCTATAGAGAAGGCGTGATC
Found at i:40268940 original size:2 final size:2
Alignment explanation
Indices: 40268933--40268957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40268923 TAGTATCGTG
40268933 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40268958 TTGATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40274077 original size:18 final size:18
Alignment explanation
Indices: 40274056--40274094 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40274046 TATTTATTAT
40274056 TAATAAGTCTA-TATAAAA
1 TAATAAGT-TATTATAAAA
*
40274074 TAATTAGTTATTATAAAA
1 TAATAAGTTATTATAAAA
40274092 TAA
1 TAA
40274095 ATTTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
TAATAAGTTATTATAAAA
Done.