Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 118 of 290
Found at i:40195396 original size:31 final size:31
Alignment explanation
Indices: 40195361--40195454 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 31
40195351 ATGTGTCCGC
40195361 TCGTGTCGGTATTCGAAATAGGGTCACACGG
1 TCGTGTCGGTATTCGAAATAGGGTCACACGG
* * ** * *
40195392 TCGTGTC-CTA-GC-CCAT-GTGT--C-CGC
1 TCGTGTCGGTATTCGAAATAGGGTCACACGG
*
40195416 TCGTGTGGGTATTCGAAATAGGGTCACACGG
1 TCGTGTCGGTATTCGAAATAGGGTCACACGG
40195447 TCGTGTCG
1 TCGTGTCG
40195455 TAGGTGTGTG
Statistics
Matches: 42, Mismatches: 14, Indels: 14
0.60 0.20 0.20
Matches are distributed among these distances:
24 8 0.19
25 3 0.07
26 1 0.02
27 5 0.12
28 5 0.12
29 1 0.02
30 3 0.07
31 16 0.38
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.28
Consensus pattern (31 bp):
TCGTGTCGGTATTCGAAATAGGGTCACACGG
Found at i:40195399 original size:55 final size:55
Alignment explanation
Indices: 40195331--40195453 Score: 237
Period size: 55 Copynumber: 2.2 Consensus size: 55
40195321 AAGTATGGAA
40195331 ACACGGTCGTGTCCTAGCCCATGTGTCCGCTCGTGTCGGTATTCGAAATAGGGTC
1 ACACGGTCGTGTCCTAGCCCATGTGTCCGCTCGTGTCGGTATTCGAAATAGGGTC
*
40195386 ACACGGTCGTGTCCTAGCCCATGTGTCCGCTCGTGTGGGTATTCGAAATAGGGTC
1 ACACGGTCGTGTCCTAGCCCATGTGTCCGCTCGTGTCGGTATTCGAAATAGGGTC
40195441 ACACGGTCGTGTC
1 ACACGGTCGTGTC
40195454 GTAGGTGTGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (55 bp):
ACACGGTCGTGTCCTAGCCCATGTGTCCGCTCGTGTCGGTATTCGAAATAGGGTC
Found at i:40196007 original size:18 final size:18
Alignment explanation
Indices: 40195984--40196031 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
40195974 TTCAAGGATC
* *
40195984 AATTTTTAAAAAATATAA
1 AATTTTGAAAAAATAGAA
*
40196002 AATTTTGGAAAAACTAGAA
1 AATTTT-GAAAAAATAGAA
40196021 AATTTTGAAAA
1 AATTTTGAAAA
40196032 TAAGGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (18 bp):
AATTTTGAAAAAATAGAA
Found at i:40205671 original size:522 final size:522
Alignment explanation
Indices: 40204687--40205729 Score: 2086
Period size: 522 Copynumber: 2.0 Consensus size: 522
40204677 TTCTTAATTT
40204687 TGTGTTCATAATTCTTGCTTTAATATTTTAGGATATTGATTCAAGTATTGATGTGCTTATTCAGA
1 TGTGTTCATAATTCTTGCTTTAATATTTTAGGATATTGATTCAAGTATTGATGTGCTTATTCAGA
40204752 GGAGCAAAAGTTATTGTCTAAGAGTAGATCTAGCATAATTAAGCGGAGTTGATTGCACCCTTAGA
66 GGAGCAAAAGTTATTGTCTAAGAGTAGATCTAGCATAATTAAGCGGAGTTGATTGCACCCTTAGA
40204817 CATAGGGCGACATAAATCTGCCGGATTAGGGTCAAACCTAATAAGGGAATCCATAAATCGAGTTA
131 CATAGGGCGACATAAATCTGCCGGATTAGGGTCAAACCTAATAAGGGAATCCATAAATCGAGTTA
40204882 ATGCAACACTAGGGGTTTTAATTAGAAAGGGATTTCAATTAATCAACCTAGGGTTAGAAATTGTT
196 ATGCAACACTAGGGGTTTTAATTAGAAAGGGATTTCAATTAATCAACCTAGGGTTAGAAATTGTT
40204947 AGTCTCGAGAGAGATAATAATATAAATTAGGGATTTCTACAGATCAAGTCAAGTGAATAAATCGT
261 AGTCTCGAGAGAGATAATAATATAAATTAGGGATTTCTACAGATCAAGTCAAGTGAATAAATCGT
40205012 CTAGTTCAGAGTCAAATAACAAGTGAAGTCTAGGTGGATTCTTCCTTGGGTATTGTCTAAATCAA
326 CTAGTTCAGAGTCAAATAACAAGTGAAGTCTAGGTGGATTCTTCCTTGGGTATTGTCTAAATCAA
40205077 TAAGTTTTCCCAAAAGTATTTCCCCAATTTATGTCTTGTGCATTCTTAGTTTAGTTAATTAGTTT
391 TAAGTTTTCCCAAAAGTATTTCCCCAATTTATGTCTTGTGCATTCTTAGTTTAGTTAATTAGTTT
40205142 AGATAAAACAAATCCTATTATTTTTAAGCTAGATAATAAAAAGAAGGTTAATACTAGTACTTTTA
456 AGATAAAACAAATCCTATTATTTTTAAGCTAGATAATAAAAAGAAGGTTAATACTAGTACTTTTA
40205207 GA
521 GA
40205209 TGTGTTCATAATTCTTGCTTTAATATTTTAGGATATTGATTCAAGTATTGATGTGCTTATTCAGA
1 TGTGTTCATAATTCTTGCTTTAATATTTTAGGATATTGATTCAAGTATTGATGTGCTTATTCAGA
40205274 GGAGCAAAAGTTATTGTCTAAGAGTAGATCTAGCATAATTAAGCGGAGTTGATTGCACCCTTAGA
66 GGAGCAAAAGTTATTGTCTAAGAGTAGATCTAGCATAATTAAGCGGAGTTGATTGCACCCTTAGA
40205339 CATAGGGCGACATAAATCTGCCGGATTAGGGTCAAACCTAATAAGGGAATCCATAAATCGAGTTA
131 CATAGGGCGACATAAATCTGCCGGATTAGGGTCAAACCTAATAAGGGAATCCATAAATCGAGTTA
40205404 ATGCAACACTAGGGGTTTTAATTAGAAAGGGATTTCAATTAATCAACCTAGGGTTAGAAATTGTT
196 ATGCAACACTAGGGGTTTTAATTAGAAAGGGATTTCAATTAATCAACCTAGGGTTAGAAATTGTT
40205469 AGTCTCGAGAGAGATAATAATATAAATTAGGGATTTCTACAGATCAAGTCAAGTGAATAAATCGT
261 AGTCTCGAGAGAGATAATAATATAAATTAGGGATTTCTACAGATCAAGTCAAGTGAATAAATCGT
40205534 CTAGTTCAGAGTCAAATAACAAGTGAAGTCTAGGTGGATTCTTCCTTGGGTATTGTCTAAATCAA
326 CTAGTTCAGAGTCAAATAACAAGTGAAGTCTAGGTGGATTCTTCCTTGGGTATTGTCTAAATCAA
40205599 TAAGTTTTCCCAAAAGTATTTCCCCAATTTATGTCTTGTGCATTCTTAGTTTAGTTAATTAGTTT
391 TAAGTTTTCCCAAAAGTATTTCCCCAATTTATGTCTTGTGCATTCTTAGTTTAGTTAATTAGTTT
40205664 AGATAAAACAAATCCTATTATTTTTAAGCTAGATAATAAAAAGAAGGTTAATACTAGTACTTTTA
456 AGATAAAACAAATCCTATTATTTTTAAGCTAGATAATAAAAAGAAGGTTAATACTAGTACTTTTA
40205729 G
521 G
40205730 TTCCTGTGGG
Statistics
Matches: 521, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
522 521 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (522 bp):
TGTGTTCATAATTCTTGCTTTAATATTTTAGGATATTGATTCAAGTATTGATGTGCTTATTCAGA
GGAGCAAAAGTTATTGTCTAAGAGTAGATCTAGCATAATTAAGCGGAGTTGATTGCACCCTTAGA
CATAGGGCGACATAAATCTGCCGGATTAGGGTCAAACCTAATAAGGGAATCCATAAATCGAGTTA
ATGCAACACTAGGGGTTTTAATTAGAAAGGGATTTCAATTAATCAACCTAGGGTTAGAAATTGTT
AGTCTCGAGAGAGATAATAATATAAATTAGGGATTTCTACAGATCAAGTCAAGTGAATAAATCGT
CTAGTTCAGAGTCAAATAACAAGTGAAGTCTAGGTGGATTCTTCCTTGGGTATTGTCTAAATCAA
TAAGTTTTCCCAAAAGTATTTCCCCAATTTATGTCTTGTGCATTCTTAGTTTAGTTAATTAGTTT
AGATAAAACAAATCCTATTATTTTTAAGCTAGATAATAAAAAGAAGGTTAATACTAGTACTTTTA
GA
Found at i:40206786 original size:16 final size:16
Alignment explanation
Indices: 40206759--40206802 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
40206749 TAATATTTGC
*
40206759 ATAACATTTTCAATCA
1 ATAACCTTTTCAATCA
* *
40206775 ATACCCTTTTCAATCG
1 ATAACCTTTTCAATCA
40206791 ATAACCTTTTCA
1 ATAACCTTTTCA
40206803 TCATTTTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAACCTTTTCAATCA
Found at i:40219284 original size:37 final size:37
Alignment explanation
Indices: 40219221--40219292 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
40219211 TACACTTTCT
**
40219221 CAATTCAATATACATTTCAATTATTCACATA-TAATCA
1 CAATTCAATATACATTTCAACAATTCA-ATACTAATCA
*
40219258 CAATTCAATTTA-ATTTCATACAATTCAATACTAAT
1 CAATTCAATATACATTTCA-ACAATTCAATACTAAT
40219293 ACTTACCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (37 bp):
CAATTCAATATACATTTCAACAATTCAATACTAATCA
Found at i:40220077 original size:13 final size:13
Alignment explanation
Indices: 40220045--40220077 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40220035 AAACCCTAAA
*
40220045 TTTCTTCTTTTCT
1 TTTCTTTTTTTCT
40220058 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
40220071 TTTCTTT
1 TTTCTTT
40220078 CTGTTTCGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:40220142 original size:5 final size:5
Alignment explanation
Indices: 40220129--40220180 Score: 95
Period size: 5 Copynumber: 10.2 Consensus size: 5
40220119 TTCTTTAGTT
40220129 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
40220180 T
1 T
40220181 TAAAACATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 42 0.91
6 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:40220224 original size:10 final size:9
Alignment explanation
Indices: 40220130--40220224 Score: 67
Period size: 10 Copynumber: 10.7 Consensus size: 9
40220120 TCTTTAGTTT
40220130 ATATATATA
1 ATATATATA
40220139 ATATAATATA
1 ATAT-ATATA
40220149 ATATAATATA
1 ATAT-ATATA
40220159 ATATAATATA
1 ATAT-ATATA
40220169 ATATAATATA
1 ATAT-ATATA
40220179 AT-TA-A-A
1 ATATATATA
*
40220185 ACATA-A-A
1 ATATATATA
* *
40220192 ATATCTTTA
1 ATATATATA
*
40220201 TTATATAATA
1 ATATAT-ATA
40220211 ATATA-ATA
1 ATATATATA
40220219 ATATAT
1 ATATAT
40220225 TAAACATAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.03
7 8 0.11
8 9 0.12
9 10 0.14
10 43 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATATATA
Found at i:40224481 original size:25 final size:27
Alignment explanation
Indices: 40224430--40224483 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40224420 CATTTAAAAA
* *
40224430 AATATTTATATTATATTTTTTAATATTT
1 AATAATTATATTACATTTTTT-ATATTT
40224458 AATAATTATA-TACATTTTTT-TATTT
1 AATAATTATATTACATTTTTTATATTT
40224483 A
1 A
40224484 TTTGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
27 9 0.38
28 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
AATAATTATATTACATTTTTTATATTT
Found at i:40226275 original size:19 final size:20
Alignment explanation
Indices: 40226251--40226289 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
40226241 AATGTGTATA
*
40226251 AATATACCAAATTA-AAATT
1 AATATACAAAATTACAAATT
*
40226270 AATATATAAAATTACAAATT
1 AATATACAAAATTACAAATT
40226290 GTATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATACAAAATTACAAATT
Found at i:40226888 original size:15 final size:17
Alignment explanation
Indices: 40226856--40226892 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40226846 TCTATCTATC
40226856 TTTTTTGTTCTTCCATTT
1 TTTTTTGTTCTT-CATTT
40226874 TTTTTTGTT-TT-ATTT
1 TTTTTTGTTCTTCATTT
40226889 TTTT
1 TTTT
40226893 CTCTACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTTTGTTCTTCATTT
Found at i:40227727 original size:28 final size:26
Alignment explanation
Indices: 40227696--40227781 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 26
40227686 TTTTAGCATT
*
40227696 TTTTATATTTTTTAGAAACTTTTTAAA
1 TTTTATATTTTTTA-AAAATTTTTAAA
* * * *
40227723 CTTTTATAAATTTTAAAAAATATATAAA
1 -TTTTAT-ATTTTTTAAAAATTTTTAAA
*
40227751 TTTTATAATTTTTTATAAATATTTTAAA
1 TTTTAT-ATTTTTTAAAAAT-TTTTAAA
40227779 TTT
1 TTT
40227782 GTTATGTGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
27 17 0.37
28 23 0.50
29 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTTATATTTTTTAAAAATTTTTAAA
Found at i:40230725 original size:34 final size:34
Alignment explanation
Indices: 40230678--40230746 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
40230668 TATTTCAAAA
*
40230678 AACACAATACTTAGATTATTCAGCAAGATATGAT
1 AACACAATACTTAGATTATTCAGCAAAATATGAT
*
40230712 AACACAATGCTTAGATTATTCAGCAAAATATGAT
1 AACACAATACTTAGATTATTCAGCAAAATATGAT
40230746 A
1 A
40230747 GTTTTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (34 bp):
AACACAATACTTAGATTATTCAGCAAAATATGAT
Found at i:40231452 original size:4 final size:4
Alignment explanation
Indices: 40231445--40231472 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40231435 AATAAAATAA
40231445 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
40231473 CAAGTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:40232144 original size:5 final size:5
Alignment explanation
Indices: 40232136--40232161 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40232126 AAAATTTGAT
40232136 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
40232162 GGGTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:40236457 original size:17 final size:17
Alignment explanation
Indices: 40236437--40236469 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40236427 CTTAAATTAA
*
40236437 TAAATTAATTTCTCAAT
1 TAAATAAATTTCTCAAT
40236454 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
40236470 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:40238967 original size:46 final size:46
Alignment explanation
Indices: 40238881--40239057 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
40238871 ACATATCCGT
* * * *
40238881 GCCGATGCTGTGTCCCAGACATGGTCTTACACT-GAC--ACATTTTGTA
1 GCCGATGC-ATGTCCTAGACAT-GTCTTACACTAG-CTTACATTTCGAA
40238927 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
* *
40238973 GCCGATGCATGTCTTAGACATGTCTTACACTGGCTTACATTTCGAA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
* * *
40239019 GCCGATGCATGTCTTAGACATGTTTTACACTAGCATACA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACA
40239058 ATTAACCTGA
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
44 11 0.09
45 12 0.10
46 96 0.81
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (46 bp):
GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
Found at i:40246573 original size:46 final size:48
Alignment explanation
Indices: 40246324--40246642 Score: 233
Period size: 46 Copynumber: 6.8 Consensus size: 48
40246314 CATAGGGTAT
* * *
40246324 AATGCCAATGCCATGTCCCAGACATGGTCTTACATTGGCTCATC-TATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATATC
* * *
40246372 AA-GTCGATGCCATGTCCCAAACATGGTCTTTCACT-GACTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCT--CATATC
** * * *
40246421 CGTGCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATTTTGC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-TAT-C
** *
40246469 -A-GCCGATG-CATGTAACAGACAT-GTCTTACACTAGCT-TACATCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATC
* *
40246513 GA-GACCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-TTATC
1 AATG-CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
* * *
40246558 AATGCCGATGCCATGTCCCAGACATGGTTTTACACTGGCTCTCGTA--
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
* *
40246604 ATGTGGCCAATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 A-AT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
40246643 ACACAATTAA
Statistics
Matches: 221, Mismatches: 31, Indels: 40
0.76 0.11 0.14
Matches are distributed among these distances:
44 11 0.05
45 27 0.12
46 72 0.33
47 63 0.29
48 13 0.06
49 4 0.02
50 31 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
Found at i:40248222 original size:22 final size:21
Alignment explanation
Indices: 40248196--40248239 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40248186 TTCACCCGTT
40248196 AGGCTTCAGTGTCGCGACACCC
1 AGGCTTCAGTGTCGCGAC-CCC
**
40248218 AGGCTTTGGTGTCGCGACCCC
1 AGGCTTCAGTGTCGCGACCCC
40248239 A
1 A
40248240 CGACAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.16, C:0.34, G:0.30, T:0.20
Consensus pattern (21 bp):
AGGCTTCAGTGTCGCGACCCC
Found at i:40252150 original size:52 final size:48
Alignment explanation
Indices: 40252131--40252333 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
40252121 TGACAAGTGG
* *
40252131 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
40252177 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
40252229 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
40252275 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
40252321 AAAGTGATAAGTG
1 AAAGTGATAAGTG
40252334 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:40252185 original size:98 final size:98
Alignment explanation
Indices: 40252065--40252333 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
40252055 TTTGAGTACT
*
40252065 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
40252130 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
40252163 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
40252228 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
40252261 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
40252326 GATAAGTG
65 GAAAAGTG
40252334 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:40252341 original size:37 final size:37
Alignment explanation
Indices: 40252297--40252442 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
40252287 GATAGCTTTA
*
40252297 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40252334 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
40252371 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40252408 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40252443 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40254819 original size:47 final size:48
Alignment explanation
Indices: 40254703--40254831 Score: 215
Period size: 48 Copynumber: 2.7 Consensus size: 48
40254693 GTGCGAGCGA
*
40254703 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
* *
40254751 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCGG-GATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
*
40254798 TACCTAGATTTGGCTATGGGCCATGGTATAGGTA
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTA
40254832 CTTATCGATT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 37 0.49
48 39 0.51
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (48 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
Found at i:40254899 original size:29 final size:29
Alignment explanation
Indices: 40254857--40254914 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40254847 TATTAAATAT
40254857 CCAATTTCTATTCTGAATGGTTCAACGGG
1 CCAATTTCTATTCTGAATGGTTCAACGGG
40254886 CCAATTTCTATTCTGAATGGTTCAACGGG
1 CCAATTTCTATTCTGAATGGTTCAACGGG
40254915 TCAACGAATG
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:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
CCAATTTCTATTCTGAATGGTTCAACGGG
Found at i:40259675 original size:104 final size:104
Alignment explanation
Indices: 40259494--40259698 Score: 293
Period size: 104 Copynumber: 2.0 Consensus size: 104
40259484 CTGTCTGTTT
* * * * *
40259494 TTGTCCCCTCAAATAGTCCAGATTGCACATGTTATTTCCTTGTACTTATCCTTAGAATGCACAAA
1 TTGTCCCCGCAAATAGCCCAGATTGAACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
*
40259559 TAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
66 GAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
* * *
40259598 TTGTCCCCGCAAATAGCCCAGATTGAACATGTTATTTATTTGCACTTATCCTTAGACTGCATAAA
1 TTGTCCCCGCAAATAGCCCAGATTGAACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
* * * *
40259663 GAACAGCTAGTCCATCCATTGTTTGTATCTCTCATT
66 GAACAACCAGTCCATCCACTGTCTGTATCTCTCATT
40259699 AAACTAATTT
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (104 bp):
TTGTCCCCGCAAATAGCCCAGATTGAACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
GAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
Found at i:40263689 original size:23 final size:23
Alignment explanation
Indices: 40263607--40263693 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
40263597 CCTGATCAGT
*
40263607 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
40263629 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
40263649 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
40263672 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
40263694 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:40265222 original size:27 final size:30
Alignment explanation
Indices: 40265177--40265231 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
40265167 GCTCGAATGC
*
40265177 TTTCTGTTCTCTTTTCTCT-ATTCTTTTTG
1 TTTCTGTTCTCTTTACTCTGATTCTTTTTG
*
40265206 TTTCT-TT-TCTTTACTCTGTTTCTTTT
1 TTTCTGTTCTCTTTACTCTGATTCTTTT
40265232 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (30 bp):
TTTCTGTTCTCTTTACTCTGATTCTTTTTG
Found at i:40267769 original size:128 final size:127
Alignment explanation
Indices: 40267625--40267873 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 127
40267615 AAGTGTGTGC
* * * *
40267625 ACAACTCGAGTTGGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACTACATCCAGCACGTT
1 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
*
40267690 AGGACACGATATTTTAAGCCTCCAAAAAACTGAGATCACCTCATGATTTTCAAAACATGCAAA
66 AGGACACGATATTTTAAGCCTCC-AAAAACTGAGATCACCACATGATTTTCAAAACATGCAAA
* *
40267753 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCAGATCTAGCACGTT
1 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
* *
40267818 AGGACACGATATTTTAAGCCTCCAAAAATTGAGATCACCACATGATTTTCGAAACA
66 AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCACATGATTTTCAAAACA
40267874 CGTGACAAAA
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 30 0.27
128 82 0.73
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (127 bp):
ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCACATGATTTTCAAAACATGCAAA
Found at i:40270386 original size:178 final size:177
Alignment explanation
Indices: 40270062--40270525 Score: 563
Period size: 178 Copynumber: 2.6 Consensus size: 177
40270052 CACTGCAACT
* * * *
40270062 TCAGAGAGACAAGG-TCGGTGGCTAAAATCTACTCCATAGCCGATACATGGAGATAAGACTCGCT
1 TCAGAGAGATAAGGCT-GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCC
* * * *
40270126 ATTTTTTA-TCTG-TTC----C-ATACATGGATATAAGCTCTGTAACTTTCAATTTGCTTCCTTG
65 A-TTTTCAGTCTGCTTCATAGCGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTG
* *
40270184 CTACCTCAGGAAGACAATACTTGTATCTCCAACCTACTCTCTTGCTACC
129 CTACCTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCCTGCTACC
*
40270233 TCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCACAGCCGATACATGGAGATAAGACTCTCCA
1 TCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCA
*
40270298 TTTTCAGTCTGCTTCATAGTCGATACATGGAGATAAGATCTGTAACTTTCAGTCTGCTTCCTTGC
66 TTTTCAGTCTGCTTCATAG-CGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTGC
* * * * *
40270363 TATCTGAGGAAGATAAGACTTGTATCTTCAACCTGCTCTCCTGCTACC
130 TACCTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCCTGCTACC
* * * * *
40270411 TCAGAGAGATAAGGCTAGTGGCTCAAATTTGCTCCATAGCTGATACATGGAGATAAGA-TTTGCC
1 TCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCT-CC
* * * *
40270475 ATCTTC-GATCTGCTCCATAGCCGATACATAGAGATAAGATCTGCAA-TTTCA
65 ATTTTCAG-TCTGCTTCATAG-CGATACATGGAGATAAGATCTGTAACTTTCA
40270526 CTGATGTCGC
Statistics
Matches: 254, Mismatches: 28, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
170 5 0.02
171 62 0.24
172 4 0.02
177 9 0.04
178 174 0.69
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (177 bp):
TCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCA
TTTTCAGTCTGCTTCATAGCGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTGCT
ACCTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCCTGCTACC
Found at i:40275189 original size:21 final size:21
Alignment explanation
Indices: 40275164--40275207 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40275154 GAAATGCAAG
*
40275164 AAAAGAAAATTTGCTCAAGAT
1 AAAAGAAAATTTGCTCAAAAT
*
40275185 AAAAGAATATTTGCTCAAAAT
1 AAAAGAAAATTTGCTCAAAAT
40275206 AA
1 AA
40275208 GACATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (21 bp):
AAAAGAAAATTTGCTCAAAAT
Found at i:40282045 original size:100 final size:99
Alignment explanation
Indices: 40281872--40282068 Score: 358
Period size: 100 Copynumber: 2.0 Consensus size: 99
40281862 AAGTGTGTGC
* *
40281872 ACAACTCGAGTTAGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
1 ACAACTCAAGTTAGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
40281937 AGGACACGATATTTTAAGCCTCCAAAAAACTGAGA
66 AGGACACGATATTTTAAGCCTCC-AAAAACTGAGA
*
40281972 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
1 ACAACTCAAGTTAGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
40282037 AGGACACGATATTTTAAGCCTCCAAAAACTGA
66 AGGACACGATATTTTAAGCCTCCAAAAACTGA
40282069 TATCACCACA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
99 9 0.10
100 85 0.90
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (99 bp):
ACAACTCAAGTTAGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
AGGACACGATATTTTAAGCCTCCAAAAACTGAGA
Found at i:40285713 original size:43 final size:43
Alignment explanation
Indices: 40285652--40285765 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 43
40285642 TGCCTTCAAT
* * **
40285652 CTGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTACAAACTCGAC
* * * * *
40285695 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTACAAATTTGGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTACAAACTCGAC
* *
40285738 TTGCTACCCTACTGCTTAGGGGGTTAAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAG
40285766 GCCTGTGAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTACAAACTCGAC
Found at i:40297703 original size:3 final size:3
Alignment explanation
Indices: 40297695--40297756 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
40297685 ATAAAAGATG
* * * * *
40297695 ATA ATA ATA ATG ATA ATA ATA AT- GTA GTA CCT- ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
40297739 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
40297757 CTATTAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.94
4 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40298026 original size:14 final size:14
Alignment explanation
Indices: 40297984--40298027 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
40297974 AACAACTATA
40297984 AGTATATACATAAAT
1 AGTATATACAT-AAT
*
40297999 AGATATATA-GTAAT
1 AG-TATATACATAAT
40298013 AGTATATACATAAT
1 AGTATATACATAAT
40298027 A
1 A
40298028 TAGTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 6 0.24
14 10 0.40
15 3 0.12
16 6 0.24
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (14 bp):
AGTATATACATAAT
Found at i:40298056 original size:26 final size:25
Alignment explanation
Indices: 40297983--40298072 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 25
40297973 AAACAACTAT
40297983 AAGTATATACATAA-ATAGATATATAGTA
1 AAGTATATACATAAGATAG-TATA-A--A
* *
40298011 ATAGTATATACATAATATAGTTATTAA
1 A-AGTATATACATAAGATAG-TATAAA
**
40298038 AAGTATATATGTAAGATAGTATAAA
1 AAGTATATACATAAGATAGTATAAA
40298063 AATGTATATA
1 AA-GTATATA
40298073 ATATAGTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 7 0.13
26 22 0.42
27 2 0.04
28 1 0.02
29 14 0.26
30 7 0.13
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (25 bp):
AAGTATATACATAAGATAGTATAAA
Found at i:40300180 original size:13 final size:13
Alignment explanation
Indices: 40300162--40300186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40300152 AACTTGGCTT
40300162 GTATTTTGGGCCA
1 GTATTTTGGGCCA
40300175 GTATTTTGGGCC
1 GTATTTTGGGCC
40300187 GGGTTTTGTA
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:0.12, C:0.16, G:0.32, T:0.40
Consensus pattern (13 bp):
GTATTTTGGGCCA
Found at i:40306007 original size:2 final size:2
Alignment explanation
Indices: 40306002--40306028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40305992 TTACACACAC
40306002 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
40306029 GAAAAAGCAT
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:40308582 original size:20 final size:20
Alignment explanation
Indices: 40308557--40308600 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40308547 TTAGTTTTGA
*
40308557 ATTTTTTTAATTTTCAAAAT
1 ATTTTTATAATTTTCAAAAT
* *
40308577 ATTTTTATAATTTTTAAATT
1 ATTTTTATAATTTTCAAAAT
40308597 ATTT
1 ATTT
40308601 GTTGATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTATAATTTTCAAAAT
Found at i:40308789 original size:19 final size:18
Alignment explanation
Indices: 40308743--40308789 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
40308733 AATTAATGAT
*
40308743 TAAAT-TTAACTAAAAAA
1 TAAATGTTAAATAAAAAA
* *
40308760 TAAAAGCTAAATAAATAAA
1 TAAATGTTAAATAAA-AAA
40308779 TAAATGTTAAA
1 TAAATGTTAAA
40308790 ACCTAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (18 bp):
TAAATGTTAAATAAAAAA
Found at i:40310614 original size:22 final size:23
Alignment explanation
Indices: 40310586--40310640 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
40310576 AATTTTTTTA
40310586 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
40310608 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
40310632 -TA-ATATTAT
1 ATATATATTAT
40310641 CAGTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
23 9 0.32
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:40323223 original size:75 final size:75
Alignment explanation
Indices: 40323116--40323337 Score: 408
Period size: 75 Copynumber: 2.9 Consensus size: 75
40323106 TATGTTTTCC
* *
40323116 AAAAATCAGCTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
40323181 TGCTTTTCAA
66 TGCTTTTCAA
40323191 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
40323256 TGCTTTTCAA
66 TGCTTTTCAA
*
40323266 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
40323331 TTGCTTT
66 -TGCTTT
40323338 CCAATTTCTG
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
75 137 0.96
76 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTC
TGCTTTTCAA
Found at i:40323598 original size:73 final size:72
Alignment explanation
Indices: 40323442--40323745 Score: 313
Period size: 72 Copynumber: 4.0 Consensus size: 72
40323432 TTTTTTTTTT
* * * *
40323442 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTTAACCTCC
1 AAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCT
*
40323507 GTTTTCGA
65 GTTTTCAA
*
40323515 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCTG
40323580 TTTGTCAA
66 TTT-TCAA
** *
40323588 AAATCAACTCATATCACGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGG-----T-AA---
* *
40323652 TTTTTTAATTTCTGTTTTTCAA
54 --TTTCAATCTCTG-TTTTCAA
* *
40323674 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTC
1 A--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTC
40323739 TGTTTTC
64 TGTTTTC
40323746 TCCAATTTAT
Statistics
Matches: 197, Mismatches: 15, Indels: 37
0.79 0.06 0.15
Matches are distributed among these distances:
72 53 0.27
73 49 0.25
74 5 0.03
75 20 0.10
80 3 0.02
81 3 0.02
86 27 0.14
87 3 0.02
88 32 0.16
89 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (72 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCTG
TTTTCAA
Found at i:40323790 original size:89 final size:85
Alignment explanation
Indices: 40323568--40323863 Score: 321
Period size: 89 Copynumber: 3.4 Consensus size: 85
40323558 GCTGAGGTAA
* * **
40323568 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
*
40323632 TGCTGAGGTCTTTTCAATT-T-TT
63 TGCTGAGGT-ATTTCAATTCTGTT
* * *
40323654 TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAT
1 TTTCAATTTATGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
40323719 GCTGAGGTAATTTCAATCTCTGTT
64 GCTGAGGT-ATTTCAAT-TCTGTT
* * * *
40323743 TTCTCCAATTTATGTTTTTCAAAAATCAGCTCAAATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TT-T-CAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
*
40323808 GCTGAGGTATTCTCGATTTCTGTT
64 GCTGAGGTATT-TC-AATTCTGTT
* *
40323832 TTTCAATTTATG-TTTCCAAAAATCAATTCATA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATA
40323864 GCACTAAAGG
Statistics
Matches: 181, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
86 51 0.28
87 10 0.06
88 40 0.22
89 64 0.35
90 3 0.02
91 13 0.07
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (85 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
TGAGGTATTTCAATTCTGTT
Found at i:40323884 original size:408 final size:400
Alignment explanation
Indices: 40323111--40324248 Score: 1075
Period size: 408 Copynumber: 2.8 Consensus size: 400
40323101 CAATTTATGT
* * * *
40323111 TTTCCAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTA
1 TTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
40323176 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
66 ATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGA
40323241 GG----T--A----TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
128 GGTTTTTCAATTTTTTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
* * ** * * *
40323296 TGAGCCTCAGGGCACGCTGAGGTATTTTTGATTTCT-TGCTTTCCAATTTCTGCCTTTCAAAAAA
193 TGAGCCTCAGGACATGCTGAGGTATTTTCAATATCTGT-TTTTCCAATTT-TG-TTTTC-AAAAA
* * *
40323360 TCAACTCATATGGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGTCACTTTCAATTTCTGT
254 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACG-GCTGAGTCACTTTCAATTTCTGT
**** *** * *
40323425 TTTTATGTTTTTTTTTTAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGACACACT-
318 TTTTATGTTTTTTCCAAAAATCAACTCATAAGCACGAAAGGTGAATTGAGCCTCAGGACACA-TA
*
40323489 GAGGTAATTTT-AACCTCCG
382 GAGGT-ATTTTCAACCTACG
* * *
40323508 TTTTCGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
** *
40323573 ATTTCTGTTTGTC-AAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCTG
66 ATTTCTGTTT-TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GCAC--GCTG
* *
40323637 AGGTCTTTTCAATTTTTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGA
127 AGGT-TTTTCAATTTTTTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
* *
40323702 GTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTCCAATTTATGTTTTTCAAAA
191 GTTGAGCCTCAGGACATGCTGAGGTATTTTCAATATCTGTTTT-TCCAATTT-TG-TTTTCAAAA
* * *
40323767 ATCAGCTCAAATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC-GCTGAGGT-A-TTCTCGATTTC
253 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCGCACGGCTGA-GTCACTT-TCAATTTC
* * * *
40323828 TGTTTTTCAAT-TTATGTTTCCAAAAATCAATTCAT-AGCACTAAAGGTGAATTGAGCCTCGGGT
315 TGTTTTT--ATGTT-T-TTTCCAAAAATCAACTCATAAGCACGAAAGGTGAATTGAGCCTCAGGA
** *
40323891 CACATAGCGAGGTATTTTCAATTTATG
376 CACATA--GAGGTATTTTCAACCTACG
* *** * * * * *
40323918 TTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACACGCTGAGGTGTTTT
1 TTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTT
* *
40323983 CAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGAGCACGCT
64 CAATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GCACGCT
* *
40324048 GAGGTATTTTCAATTAATGTTTTTTCAA-TTCATGCTTTTC--AAGAATCAACTCATATTACGAG
126 GAGGT-TTTTCAATT--T-TTTTTT-AATTTC-TGCTTTTCAAAAAAATCAACTCATATTGCGAG
** ** * * * * *
40324110 AAATGAGTTGAGCCTTGGGTCACATACCGAGGTATTTTCAAAATCTGTTTTACAAATTTTGTTTT
185 AGGTGAGTTGAGCCTCAGG--ACATGCTGAGGTATTTTCAATATCTGTTTTTCCAATTTTGTTTT
* * * * *
40324175 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATTGGCTCACGTGCTGAG-CTATTTTCAA
248 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACG-GCTGAGTC-ACTTTCAA
*
40324238 TTTATGTTTTT
311 TTTCTGTTTTT
40324249 GATTTCTGTT
Statistics
Matches: 608, Mismatches: 87, Indels: 75
0.79 0.11 0.10
Matches are distributed among these distances:
394 2 0.00
395 39 0.06
396 3 0.00
397 74 0.12
402 1 0.00
404 1 0.00
405 2 0.00
406 20 0.03
407 5 0.01
408 145 0.24
409 36 0.06
410 45 0.07
411 2 0.00
412 78 0.13
413 8 0.01
414 96 0.16
415 17 0.03
416 34 0.06
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (400 bp):
TTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGT
TTTTCAATTTTTTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCAGGACATGCTGAGGTATTTTCAATATCTGTTTTTCCAATTTTGTTTTCAAAAATCAACTC
ATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGGCTGAGTCACTTTCAATTTCTGTTTTTATGT
TTTTTCCAAAAATCAACTCATAAGCACGAAAGGTGAATTGAGCCTCAGGACACATAGAGGTATTT
TCAACCTACG
Found at i:40323912 original size:177 final size:175
Alignment explanation
Indices: 40323571--40323912 Score: 381
Period size: 177 Copynumber: 1.9 Consensus size: 175
40323561 GAGGTAATTT
* * *
40323571 CAATTTCTGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCT
1 CAATTTATGTTTGTCAAAAATCAACTCAAATCACGAGAGGTGAGTTGAGCCTCGGCGCACA-GCT
* * * * *
40323636 GAGGTCTTTTCAATTTTTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTG
65 GAGGTATTCTCAATTTTTTTTTAATTTATG-TTTTCAAAAAAATCAACTCATACTACGAAAGGTG
*
40323701 AGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
129 AATTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
* * **
40323748 CAATTTATGTTTTTCAAAAATCAGCTCAAATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC-GCT
1 CAATTTATGTTTGTCAAAAATCAACTCAAATCACGAGAGGTGAGTTGAGCCTC-GGCGCACAGCT
* * * *
40323811 GAGGTATTCTCGATTTCTGTTTTTCAATTTATG-TTTC-CAAAAATCAATTCATAGC-ACTAAAG
65 GAGGTATTCTCAATTT-T-TTTTT-AATTTATGTTTTCAAAAAAATCAACTCATA-CTACGAAAG
* *
40323873 GTGAATTGAGCCTCGGGTCACATAGC-GAGGTATTTTCAAT
126 GTGAATTGAGCCTCAGG--ACAT-GCTGAGGTAATTTCAAT
40323913 TTATGTTTCC
Statistics
Matches: 138, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
175 49 0.36
176 6 0.04
177 72 0.52
178 11 0.08
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (175 bp):
CAATTTATGTTTGTCAAAAATCAACTCAAATCACGAGAGGTGAGTTGAGCCTCGGCGCACAGCTG
AGGTATTCTCAATTTTTTTTTAATTTATGTTTTCAAAAAAATCAACTCATACTACGAAAGGTGAA
TTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
Found at i:40323952 original size:74 final size:74
Alignment explanation
Indices: 40323831--40324069 Score: 299
Period size: 74 Copynumber: 3.2 Consensus size: 74
40323821 CGATTTCTGT
40323831 TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACAT
1 TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACA-
40323896 AGC-GAGGTA
65 AGCTGAGGTA
*
40323905 TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACAC
1 TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACAA
*
40323970 GCTGAGGTG
66 GCTGAGGTA
* * *** * *
40323979 TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGT-AAGTTGAGCCTCGGAG-
1 TTTTCAATTTATG--TTTC-CAAAAATCAATTCATAGCACTAAAGGTGAA-TTGAGCCTCGG-GT
40324042 CAC--GCTGAGGTA
61 CACAAGCTGAGGTA
*
40324054 TTTTCAATTAATGTTT
1 TTTTCAATTTATGTTT
40324070 TTTCAATTCA
Statistics
Matches: 148, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
73 5 0.03
74 82 0.55
75 20 0.14
76 6 0.04
77 34 0.23
78 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (74 bp):
TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACAA
GCTGAGGTA
Found at i:40324197 original size:87 final size:85
Alignment explanation
Indices: 40323977--40324296 Score: 277
Period size: 87 Copynumber: 3.6 Consensus size: 85
40323967 CACGCTGAGG
* ** * *
40323977 TGTTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGAG
1 TGTTTTCAATTT-TGCTTTT---AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGG-G
*
40324042 -CAC-GCTGAGGTATTTTCAATTAATG
61 TCACTGCTGAGGTATTTTCAA--AATA
* * * *
40324067 TTTTTTCAATTCATGCTTTTCAAGAATCAACTCATATTACGAGAAATGAGTTGAGCCTTGGGTCA
1 TGTTTTCAATT-TTGCTTTT-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGTCA
* * *
40324132 CATACCGAGGTATTTTCAAAATC
64 C-TGCTGAGGTATTTTCAAAATA
* * *
40324155 TGTTTTACAAATTTTG-TTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATTGGCTCA
1 TGTTTT-C-AATTTTGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGTCA
* **
40324219 CGTGCTGAGCTATTTTCAATTTA
64 C-TGCTGAGGTATTTTCAAAATA
** * * *
40324242 TGTTTTTGATTTCTGTTTTTAAAAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TGTTTTCAATTT-TGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
40324297 TCAGGATCAC
Statistics
Matches: 190, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
85 4 0.02
86 2 0.01
87 98 0.52
88 49 0.26
89 3 0.02
90 34 0.18
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (85 bp):
TGTTTTCAATTTTGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGTCACT
GCTGAGGTATTTTCAAAATA
Found at i:40324235 original size:326 final size:328
Alignment explanation
Indices: 40323514--40324246 Score: 772
Period size: 326 Copynumber: 2.2 Consensus size: 328
40323504 TCCGTTTTCG
* * * *
40323514 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC-GCTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGTCACTGCTGAGGTATTTTCAATTTA
* * * * *
40323578 TGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCT
65 TGTTTGCCAAAAATCAACTCATAGCACGAAAGGTGAATTGAGCCTCGGCTCACACGCTGAGGTCT
*
40323643 TTTCAATTTTTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAG
130 TTTCAA-----TTTTAA--T-TGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAG
* * * * *
40323708 CCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTCCAATTTATGTTTTTCAAAAATCAGC
187 CCTCAGGACACGCTGAGGTAATTTCAATCTATGTTTTCTCCAATTCATGCTTTTCAAAAATCAAC
* ** * * * ** *
40323773 TCAAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTCTCGATTTCTGTTTTTCAA
252 TCAAATTACGAGAAATGAGTTGAGCCTCAGGGCACACCGAGGTATTCTCAAAATCTGTTTTACAA
40323838 TTTATGTTTCCA
317 TTTATGTTTCCA
* *** * * *
40323850 AAAATCAATTCATAGCACTA-AAGGTGAATTGAGCCTCGGGTCACATAGC-GAGGTATTTTCAAT
1 AAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCT-AGGTCAC-T-GCTGAGGTATTTTCAAT
* * *
40323913 TTATGTTT-CCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACACGCTGAGG
62 TTATGTTTGCCAAAAATCAACTCATAGCACGAAAGGTGAATTGAGCCTCGGCTCACACGCTGAGG
* *
40323977 TGTTTTCAA-TTT-A-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-
127 TCTTTTCAATTTTAATTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCA
* * *
40324038 GGAGCACGCTGAGGTATTTTCAAT-TAATGTTTT-TTCAATTCATGCTTTTCAAGAATCAACTCA
192 GGA-CACGCTGAGGTAATTTCAATCT-ATGTTTTCTCCAATTCATGCTTTTCAAAAATCAACTCA
* * *
40324101 TATTACGAGAAATGAGTTGAGCCT-TGGGTCACATACCGAGGTATTTTCAAAATCTGTTTTACAA
255 AATTACGAGAAATGAGTTGAGCCTCAGGG-CAC--ACCGAGGTATTCTCAAAATCTGTTTTAC-A
*
40324165 ATTT-TGTTT-TA
316 ATTTATGTTTCCA
* * *
40324176 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATTGGCTCACGTGCTGAGCTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGG-TCAC-TGCTGAGGTATTTTCAATTT
40324241 ATGTTT
64 ATGTTT
40324247 TTGATTTCTG
Statistics
Matches: 331, Mismatches: 53, Indels: 36
0.79 0.13 0.09
Matches are distributed among these distances:
324 3 0.01
325 56 0.17
326 123 0.37
327 28 0.08
328 5 0.02
330 1 0.00
331 3 0.01
335 1 0.00
336 33 0.10
337 56 0.17
338 20 0.06
339 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (328 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGTCACTGCTGAGGTATTTTCAATTTAT
GTTTGCCAAAAATCAACTCATAGCACGAAAGGTGAATTGAGCCTCGGCTCACACGCTGAGGTCTT
TTCAATTTTAATTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAGGAC
ACGCTGAGGTAATTTCAATCTATGTTTTCTCCAATTCATGCTTTTCAAAAATCAACTCAAATTAC
GAGAAATGAGTTGAGCCTCAGGGCACACCGAGGTATTCTCAAAATCTGTTTTACAATTTATGTTT
CCA
Found at i:40325199 original size:19 final size:18
Alignment explanation
Indices: 40325172--40325219 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
40325162 TACATATATT
* *
40325172 AAAACATAAAAGAAAATA
1 AAAAAATAAAAAAAAATA
40325190 CAAAAAATAAAAAAAAATA
1 -AAAAAATAAAAAAAAATA
40325209 AAAAATATAAA
1 AAAAA-ATAAA
40325220 TTTTTACCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAAAAAATA
Found at i:40325206 original size:10 final size:10
Alignment explanation
Indices: 40325172--40325213 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
40325162 TACATATATT
*
40325172 AAAACATAAA
1 AAAAAATAAA
* *
40325182 AGAAAAT-AC
1 AAAAAATAAA
40325191 AAAAAATAAA
1 AAAAAATAAA
40325201 AAAAAATAAA
1 AAAAAATAAA
40325211 AAA
1 AAA
40325214 TATAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:40325327 original size:11 final size:11
Alignment explanation
Indices: 40325311--40325345 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
40325301 CCCTTTCCCC
40325311 CTCCCTTCTCT
1 CTCCCTTCTCT
40325322 CTCCCTTCTCT
1 CTCCCTTCTCT
40325333 CTTCCC-TCTCT
1 C-TCCCTTCTCT
40325344 CT
1 CT
40325346 TTTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:40325831 original size:3 final size:3
Alignment explanation
Indices: 40325823--40325857 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
40325813 TGTATTTCAA
* *
40325823 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40325858 ACATTACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40326074 original size:22 final size:23
Alignment explanation
Indices: 40326046--40326100 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
40326036 AATTTTTTTA
40326046 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
40326068 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
40326092 -TA-ATATTAT
1 ATATATATTAT
40326101 CAGTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
23 9 0.32
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:40330706 original size:32 final size:32
Alignment explanation
Indices: 40330640--40330707 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
40330630 TTTTTGTTAA
* * *
40330640 TGTTGGATTCTGAAATTTTAGTTTATTATGTT
1 TGTTGGATTCTAAAATTTTAGTCTATGATGTT
40330672 TGTTGGATTCTAAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATGTT
40330704 TGTT
1 TGTT
40330708 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATGTT
Found at i:40330733 original size:27 final size:27
Alignment explanation
Indices: 40330703--40330775 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
40330693 TGTCTTGATT
40330703 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
40330730 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
40330762 TTGTTGGATATTGA
1 TTGTTAGATATTGA
40330776 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:40330755 original size:32 final size:32
Alignment explanation
Indices: 40330716--40330776 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
40330706 TTAGATATTG
40330716 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
40330748 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
40330777 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:40331787 original size:22 final size:22
Alignment explanation
Indices: 40331756--40331804 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
40331746 GGACAATGTT
40331756 GTTATAATGTGCTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
* *
40331778 GTTATCATGTGGTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
40331800 GTTAT
1 GTTAT
40331805 GCACTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
GTTATAATGTGCTGTAATATTA
Found at i:40331817 original size:22 final size:22
Alignment explanation
Indices: 40331720--40331817 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
40331710 ATATTGATAA
40331720 TGTGGTATAATATTAGTTATGCAC
1 TGTGG-ATAATATTAGTTAT-CAC
* * *
40331744 T-TGGACAATGTT-GTTAT-AA
1 TGTGGATAATATTAGTTATCAC
40331763 TGTGCTG-TAATATTAGTTATCA-
1 TGTG--GATAATATTAGTTATCAC
*
40331785 TGTGGTGTAATATTAGTTATGCAC
1 TGTGG-ATAATATTAGTTAT-CAC
40331809 T-TGGATAAT
1 TGTGGATAAT
40331818 GTTGTTGTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 10 0.17
22 33 0.56
23 9 0.15
24 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (22 bp):
TGTGGATAATATTAGTTATCAC
Found at i:40332282 original size:15 final size:14
Alignment explanation
Indices: 40332248--40332314 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
40332238 CCAGAAAAGT
*
40332248 AAATCATTTTCCAG
1 AAATTATTTTCCAG
40332262 AAATTATTTTCCAG
1 AAATTATTTTCCAG
40332276 AAAATTATTTTCCAG
1 -AAATTATTTTCCAG
* *
40332291 AAATCATTTTCCGG
1 AAATTATTTTCCAG
*
40332305 AAAATATTTT
1 AAATTATTTT
40332315 ACCTGCAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 33 0.70
15 14 0.30
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:40332285 original size:29 final size:29
Alignment explanation
Indices: 40332248--40332314 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
40332238 CCAGAAAAGT
* *
40332248 AAATCATTTTCCAGAAATTATTTTCCAGA
1 AAATTATTTTCCAGAAATCATTTTCCAGA
*
40332277 AAATTATTTTCCAGAAATCATTTTCCGGA
1 AAATTATTTTCCAGAAATCATTTTCCAGA
40332306 AAA-TATTTT
1 AAATTATTTT
40332315 ACCTGCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (29 bp):
AAATTATTTTCCAGAAATCATTTTCCAGA
Found at i:40334829 original size:19 final size:20
Alignment explanation
Indices: 40334790--40334830 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40334780 ATATATATAA
*
40334790 TTTTGTTAAAATATGAGTAT
1 TTTTCTTAAAATATGAGTAT
*
40334810 TTTTCTTAAAATTTGA-TAT
1 TTTTCTTAAAATATGAGTAT
40334829 TT
1 TT
40334831 AGTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTTCTTAAAATATGAGTAT
Found at i:40335062 original size:30 final size:31
Alignment explanation
Indices: 40335019--40335079 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
40335009 AATGCTAAAC
* *
40335019 TTTAAAATTTAAAAAATA-AATGAATTAAATT
1 TTTAAAATATAAAAAATATAAAG-ATTAAATT
40335050 TTTAAAA-ATAAAAAATATAAAGATTAAATT
1 TTTAAAATATAAAAAATATAAAGATTAAATT
40335080 CTATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
TTTAAAATATAAAAAATATAAAGATTAAATT
Found at i:40335070 original size:23 final size:23
Alignment explanation
Indices: 40335020--40335070 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
40335010 ATGCTAAACT
*
40335020 TTAAAATTTAAAAAATAAATGAA
1 TTAAAATTTAAAAAATAAATAAA
* *
40335043 TTAAATTTTTAAAAATAAA-AAA
1 TTAAAATTTAAAAAATAAATAAA
40335065 TATAAA
1 T-TAAA
40335071 GATTAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAATTTAAAAAATAAATAAA
Found at i:40338535 original size:20 final size:20
Alignment explanation
Indices: 40338510--40338549 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40338500 TTAAGAACAA
40338510 AGATAATTAAAAATTAGCAG
1 AGATAATTAAAAATTAGCAG
40338530 AGATAATTAAAAATTAGCAG
1 AGATAATTAAAAATTAGCAG
40338550 TTAAGGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
AGATAATTAAAAATTAGCAG
Found at i:40345822 original size:185 final size:186
Alignment explanation
Indices: 40345580--40345940 Score: 467
Period size: 186 Copynumber: 1.9 Consensus size: 186
40345570 TGATTATGAT
* * * * *
40345580 GATGATGATGATCATGATCATGAAGCAGCGGCAACTACGACTCTTACTGTACTTACACTTATA-T
1 GATGATAATGATCATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTACACA
* * * * * * *
40345644 GTTTTTTTTCCTTTCT-TATTTCAATTAATGGTTTTTTCATTTGTGTTCTTTTGTTACATATATG
66 CTTTTTTTTCCTTT-TGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACATAAG
* * * *
40345708 TACACATTCGCATTTACTTTTTCATTTTA-CCATGAACATGTAAAAGTGTGGAAATTC
130 TAAACACTCACACTTACTTTTTC-TTTTATCCATGAACATGTAAAAGTGTGGAAATTC
* * * * *
40345765 GATGATAATGATGATGATTATGAAGCAGCGACAGCTACGACTCTCACTTTGCTTACACTTACACA
1 GATGATAATGATCATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTACACA
* *
40345830 CTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCGTTTCTTTTCTTCTGTGACACATAAGT
66 CTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACATAAGT
*
40345895 AAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAAAGT
131 AAACACTCACACTTACTTTTTCTTTTATCCATGAACATGTAAAAGT
40345941 ATAAAACCCC
Statistics
Matches: 149, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
185 60 0.40
186 89 0.60
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (186 bp):
GATGATAATGATCATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTACACA
CTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACATAAGT
AAACACTCACACTTACTTTTTCTTTTATCCATGAACATGTAAAAGTGTGGAAATTC
Found at i:40346583 original size:410 final size:413
Alignment explanation
Indices: 40345808--40346590 Score: 1056
Period size: 410 Copynumber: 1.9 Consensus size: 413
40345798 GCTACGACTC
* * *
40345808 TCACTTTGCTTACACTTACACACTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCGTTTC
1 TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTCAATTAATGGTTTTGTCGTTTC
*
40345873 TTTTCTTCTGTGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAA
66 TTTTCTTCTATGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAA
* * ** * * *
40345938 AGTATAAAACCCCTTTATGACTCACATGTGCACGCGTATACTCTATCTTACTTACCTTTCCCCCT
131 ACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCCCCT
* * * ** ** * *
40346003 ACCCCATTTATTTTTCGTTATTGTTTAGTTTTATTCTATGAACCGAAATTAATTTCTAAATAGTA
196 ACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAAATAATTCCTAAATAGTA
* * * * * *
40346068 TTATAATTATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATATTGTTTGGAAGTGGCAGGA
261 TTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGAAAGA
* * *
40346133 AATGATCTACTTCAAAAGGCAAGCATTAAAACTGTTATGTGCATGATTTGTGAATGATTCATGTA
326 AATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATTTGTGAATGATTCATGTA
40346198 TTATGATGCATCAAGAGCAACTT
391 TTATGATGCATCAAGAGCAACTT
* * *
40346221 TCACTTTACTTACACTTATACACATTTTTTTCCTTATGTA-TTCAAATTAGTGGTTTT-TCTTTT
1 TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTC-AATTAATGGTTTTGTCGTTT
* * * ** *
40346284 GTTTTCTTCTATTACACATACA-TATACACTTGCACTTATTTTTTCTTTT-TACCGTGAACATGT
65 CTTTTCTTCTATGACACATA-AGTAAACACTCACACTTACTTTTTCTTTTAT-CCGTGAACATGT
* * * *
40346347 AAAACTATAAAACCCCCTTATGGCTCCCACATGCATACGTATACTCTGCCTTACTTACCCTTCCC
128 AAAACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCC
* *
40346412 CC-ACCCCCTTTATTTTTCATTA-TCTTCAGTTTTATTCTACAAACAAAAAATAATTCCTAGATA
193 CCTACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAAATAATTCCTAAATA
* * *
40346475 GTATTATGATAATGGCGTAAAGAAAAATAAAGCATTGGTGAGGTTGATACTATTTGGAAATGGAA
258 GTATTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGAA
* *
40346540 AGAAATGATCTATTTCAAAAGGCAAGAATCAGAACTATTATGTGCATGATT
323 AGAAATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATT
40346591 CGTGCATTAT
Statistics
Matches: 318, Mismatches: 49, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
410 134 0.42
411 19 0.06
412 116 0.36
413 49 0.15
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (413 bp):
TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTCAATTAATGGTTTTGTCGTTTC
TTTTCTTCTATGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAA
ACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCCCCT
ACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAAATAATTCCTAAATAGTA
TTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGAAAGA
AATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATTTGTGAATGATTCATGTA
TTATGATGCATCAAGAGCAACTT
Found at i:40349257 original size:29 final size:29
Alignment explanation
Indices: 40349225--40349320 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 29
40349215 TGTGTGTGTG
40349225 TGATTCGTGCATTATGTTTTGTGCATTAA
1 TGATTCGTGCATTATGTTTTGTGCATTAA
* ** *
40349254 TGA-TC-T---TT-TGTATGTGTGTGTGT-G
1 TGATTCGTGCATTATGT-TTTGTGCAT-TAA
40349278 TGATTCGTGCATTATGTTTTGTGCATTAA
1 TGATTCGTGCATTATGTTTTGTGCATTAA
*
40349307 TGATTCATGCATTA
1 TGATTCGTGCATTA
40349321 ATTGTTTGTG
Statistics
Matches: 49, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
23 3 0.06
24 11 0.22
25 3 0.06
26 1 0.02
27 1 0.02
28 3 0.06
29 24 0.49
30 3 0.06
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (29 bp):
TGATTCGTGCATTATGTTTTGTGCATTAA
Found at i:40349287 original size:53 final size:53
Alignment explanation
Indices: 40349207--40349310 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
40349197 CCTTATTGCC
40349207 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
1 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
40349260 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGAT
1 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGAT
40349311 TCATGCATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.15, C:0.07, G:0.27, T:0.51
Consensus pattern (53 bp):
TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
Found at i:40356866 original size:6 final size:6
Alignment explanation
Indices: 40356855--40356884 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40356845 TCCTCTTGAG
40356855 CATTCA CATTCA CATTCA CATTCA CATTCA
1 CATTCA CATTCA CATTCA CATTCA CATTCA
40356885 TGCGTCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CATTCA
Found at i:40366678 original size:30 final size:30
Alignment explanation
Indices: 40366643--40366699 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
40366633 AGGCACTTCT
40366643 ACACGGGT-GATCCACACGCCCGTGTGTGAC
1 ACACGGGTAGA-CCACACGCCCGTGTGTGAC
40366673 ACACGGGTAGACCACACGCCCGTGTGT
1 ACACGGGTAGACCACACGCCCGTGTGT
40366700 TATGGCCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.16
Consensus pattern (30 bp):
ACACGGGTAGACCACACGCCCGTGTGTGAC
Found at i:40366769 original size:19 final size:19
Alignment explanation
Indices: 40366732--40366769 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40366722 CAAGTAAGAA
*
40366732 TTGCACACAGCTTGAGCAC
1 TTGCACACAGCGTGAGCAC
40366751 TTGCACACGAGCGTG-GCAC
1 TTGCACAC-AGCGTGAGCAC
40366770 ACGGCAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (19 bp):
TTGCACACAGCGTGAGCAC
Found at i:40370965 original size:30 final size:29
Alignment explanation
Indices: 40370922--40370982 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
40370912 CAAACAGGCG
40370922 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
*
40370951 AAGCTAGTTTAAATCGCACTCTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
40370981 AA
1 AA
40370983 ACTTTCGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:40389279 original size:18 final size:18
Alignment explanation
Indices: 40389256--40389299 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
40389246 TGTGGTAAGC
*
40389256 CGTGTGATGGAACACGGG
1 CGTGTGATGGAACACGGA
40389274 CGTGTGATGGAACACGGA
1 CGTGTGATGGAACACGGA
40389292 CGTGTGAT
1 CGTGTGAT
40389300 CGACGAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (18 bp):
CGTGTGATGGAACACGGA
Found at i:40389911 original size:18 final size:19
Alignment explanation
Indices: 40389874--40389912 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40389864 TAGGATTTGA
* *
40389874 TACTGTATATCTGTTACTG
1 TACTGAATATCTGATACTG
40389893 TACTGAATAT-TGATACTG
1 TACTGAATATCTGATACTG
40389911 TA
1 TA
40389913 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
TACTGAATATCTGATACTG
Found at i:40390736 original size:11 final size:11
Alignment explanation
Indices: 40390720--40390744 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40390710 GTGTGTTTAA
40390720 AATGGTTAATT
1 AATGGTTAATT
40390731 AATGGTTAATT
1 AATGGTTAATT
40390742 AAT
1 AAT
40390745 AGGTATAATG
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
AATGGTTAATT
Found at i:40403692 original size:24 final size:24
Alignment explanation
Indices: 40403665--40403721 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
40403655 TAGCGATTAA
40403665 CTTTCATTATTTTATAATTTAGTT
1 CTTTCATTATTTTATAATTTAGTT
40403689 CTTTCATTATTTTATAATTTAGTT
1 CTTTCATTATTTTATAATTTAGTT
*
40403713 CTTCCATTA
1 CTTTCATTA
40403722 GAATTAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (24 bp):
CTTTCATTATTTTATAATTTAGTT
Found at i:40403757 original size:17 final size:18
Alignment explanation
Indices: 40403735--40403773 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
40403725 TTAGTTACTA
40403735 ATTTAAAA-AAATTATCT
1 ATTTAAAATAAATTATCT
40403752 ATTTAAAATTCAAATTATCT
1 ATTTAAAA-T-AAATTATCT
40403772 AT
1 AT
40403774 ATAATAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAAATAAATTATCT
Found at i:40404302 original size:19 final size:18
Alignment explanation
Indices: 40404251--40404304 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
40404241 TATTAAATAT
40404251 TATAATATTATGTTAT-AC
1 TATAATATTA-GTTATAAC
*
40404269 TATATATTTTA-TTATAATC
1 TATA-ATATTAGTTATAA-C
40404288 TATAATATTAGTTATAA
1 TATAATATTAGTTATAA
40404305 ATAGGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.13
18 10 0.33
19 16 0.53
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TATAATATTAGTTATAAC
Found at i:40416111 original size:83 final size:82
Alignment explanation
Indices: 40415972--40416133 Score: 306
Period size: 83 Copynumber: 2.0 Consensus size: 82
40415962 GCCCCTGAGA
*
40415972 ATATGTAGAAAACTACCTTCGTAACAATGTGGGGAACATTCTGCTACAAGGTGATGCCATTTGGG
1 ATATGGAGAAAACTACCTTCGTAACAATGTGGGGAACATTCTGCTACAAGGTGATGCCATTTGGG
40416037 TTAAAGAATGCTGNGAGG
66 TTAAAGAATGCTG-GAGG
40416055 ATATGGAGAAAACTACCTTCGTAACAATGTGGGGAACATTCTGCTACAAGGTGATGCCATTTGGG
1 ATATGGAGAAAACTACCTTCGTAACAATGTGGGGAACATTCTGCTACAAGGTGATGCCATTTGGG
40416120 TTAAAGAATGCTGG
66 TTAAAGAATGCTGG
40416134 GGCACCATAT
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 1 0.01
83 77 0.99
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (82 bp):
ATATGGAGAAAACTACCTTCGTAACAATGTGGGGAACATTCTGCTACAAGGTGATGCCATTTGGG
TTAAAGAATGCTGGAGG
Found at i:40419881 original size:83 final size:82
Alignment explanation
Indices: 40419735--40419898 Score: 199
Period size: 83 Copynumber: 2.0 Consensus size: 82
40419725 TCAACTCATA
* * *
40419735 ATTGCGAAAGGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTCAAATTCTACTTTAAAAAAAA
1 ATTGCGAAAGGTGAGTTGAGCCTCAGGACACGTCGAGGTAATTTCAAATTCTACTTT-AAAAAAA
*
40419800 TCAACTCATATTGCGAGT
65 TCAACTCATATCGCGAGT
* * **
40419818 ATTGC-AAGAGGTGAGTTGAGCCTCAGGACACG-CTGAGGTAATTTCAATTTCT-GTTTGTCAAA
1 ATTGCGAA-AGGTGAGTTGAGCCTCAGGACACGTC-GAGGTAATTTCAAATTCTACTTT-AAAAA
40419880 AATCAACTCATATCGCGAG
63 AATCAACTCATATCGCGAG
40419899 AGGTGAGTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
82 27 0.39
83 43 0.61
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (82 bp):
ATTGCGAAAGGTGAGTTGAGCCTCAGGACACGTCGAGGTAATTTCAAATTCTACTTTAAAAAAAT
CAACTCATATCGCGAGT
Found at i:40420016 original size:161 final size:166
Alignment explanation
Indices: 40419820--40420179 Score: 451
Period size: 177 Copynumber: 2.1 Consensus size: 166
40419810 TTGCGAGTAT
40419820 TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TT-TG-TCAAAAA
1 TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTATGTTCAAAAA
* *
40419882 TCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTCTTTTCAATTTCT-A
66 TCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTATGA
* *
40419946 TTTTT-AATTTCTGTTTTTCAAAAATCAACTCATAC
131 TTTTTCAATTTATATTTTTCAAAAATCAACTCATAC
*
40419981 TGCAAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCTGTTTTCTCCAATTTA
1 TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG----------TTTA
** * *
40420046 TGTTTTTCAAAAATCAGTTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTAT
56 TG---TTCAAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTAT
* * *
40420111 TTTCAATTTATGTTTTTTCAATTTATATTTTTCAAAGATCAACTCATAT
118 TTTCAATTTATGATTTTTCAATTTATATTTTTCAAAAATCAACTCATAC
*
40420160 TGCGAGAGGTGAGTTGAGCC
1 TGCAAGAGGTGAGTTGAGCC
40420180 GTGGGTTCAC
Statistics
Matches: 168, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
161 50 0.30
172 2 0.01
173 2 0.01
177 64 0.38
178 5 0.03
179 45 0.27
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (166 bp):
TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTATGTTCAAAAA
TCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTATGA
TTTTTCAATTTATATTTTTCAAAAATCAACTCATAC
Found at i:40420130 original size:15 final size:15
Alignment explanation
Indices: 40420110--40420142 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40420100 TGCTGAGGTA
*
40420110 TTTTCAATTTATGTT
1 TTTTCAATTTATATT
40420125 TTTTCAATTTATATT
1 TTTTCAATTTATATT
40420140 TTT
1 TTT
40420143 CAAAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:40420164 original size:90 final size:90
Alignment explanation
Indices: 40419859--40420179 Score: 445
Period size: 89 Copynumber: 3.6 Consensus size: 90
40419849 GCTGAGGTAA
* * * *
40419859 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACAT
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
* *
40419924 GCTGAGGTCTTTTCAATTTCT-ATT
66 GCTGAGGTATTTTCAATTTCTGTTT
* * *
40419948 TTT-AATTTCTGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGG---ACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACA
*
40420009 TGCTGAGGTAATTTCAATTTCTGTTT
65 TGCTGAGGTATTTTCAATTTCTGTTT
* **
40420035 TCTCCAATTTATGTTTTTCAAAAATCAGTTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
1 T-TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
*
40420100 TGCTGAGGTATTTTCAATTTATGTTT
65 TGCTGAGGTATTTTCAATTTCTGTTT
* *
40420126 TTTCAATTTATATTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
40420180 GTGGGTTCAC
Statistics
Matches: 204, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
86 23 0.11
87 3 0.01
88 50 0.25
89 52 0.25
90 48 0.24
91 28 0.14
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (90 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
GCTGAGGTATTTTCAATTTCTGTTT
Found at i:40422018 original size:53 final size:51
Alignment explanation
Indices: 40421948--40422046 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 51
40421938 TACTTGGGTA
40421948 TTATATTATATATATTTTTATATGTTATA-TA-TATACTTTTAATATTGTATT
1 TTATATTATATATATTTTTA-ATGTTATATTATTATA-TTTTAATATTGTATT
*
40421999 TTATATATATCATATATTTTTAATGTTGTATTATTATATTTTAATATT
1 TTATAT-TAT-ATATATTTTTAATGTTATATTATTATATTTTAATATT
40422047 ATACTACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
51 6 0.14
52 10 0.23
53 23 0.53
54 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (51 bp):
TTATATTATATATATTTTTAATGTTATATTATTATATTTTAATATTGTATT
Found at i:40422020 original size:32 final size:32
Alignment explanation
Indices: 40421973--40422037 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
40421963 TTTTATATGT
40421973 TATATATATACTTTTAATATTGTATT-TTATA
1 TATATATATACTTTTAATATTGTATTATTATA
* *
40422004 TATATCATATATTTTTAATGTTGTATTATTATA
1 TATAT-ATATACTTTTAATATTGTATTATTATA
40422037 T
1 T
40422038 TTTAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 19 0.63
33 6 0.20
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (32 bp):
TATATATATACTTTTAATATTGTATTATTATA
Found at i:40422058 original size:53 final size:52
Alignment explanation
Indices: 40421949--40422059 Score: 127
Period size: 53 Copynumber: 2.1 Consensus size: 52
40421939 ACTTGGGTAT
* * **
40421949 TATATTATATATATTTTTATATGTTATATATATACTTTTAATATTGTATTTTA
1 TATA-TATATATATTTTTATATGTTATATATATACTTTTAATATTATACTACA
*
40422002 TATATATCATATATTTTTA-ATGTTGTATTATTATA-TTTTAATATTATACTACA
1 TATATAT-ATATATTTTTATATGTTATA-TA-TATACTTTTAATATTATACTACA
40422055 TATAT
1 TATAT
40422060 TTTCATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
52 10 0.20
53 36 0.72
54 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (52 bp):
TATATATATATATTTTTATATGTTATATATATACTTTTAATATTATACTACA
Found at i:40422086 original size:26 final size:26
Alignment explanation
Indices: 40422044--40422132 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 26
40422034 ATATTTTAAT
40422044 ATTATACTACATATATTTTCATATTAC
1 ATTATA-TACATATATTTTCATATTAC
* *
40422071 ATTATATACATATATTTTTATA-TAT
1 ATTATATACATATATTTTCATATTAC
** *
40422096 ATTATCATGTATATATTTTGATATTAC
1 ATTAT-ATACATATATTTTCATATTAC
40422123 TAGTTATATA
1 -A-TTATATA
40422133 TTACTTATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.14
26 29 0.57
27 8 0.16
28 3 0.06
29 4 0.08
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATATACATATATTTTCATATTAC
Found at i:40424009 original size:21 final size:22
Alignment explanation
Indices: 40423973--40424029 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
40423963 ATATCAAATA
* **
40423973 ATATATAATATATTAAT-ATTTT
1 ATATAT-ATGTATTAATGATTAG
40423995 ATATATATGTATTAATGATTAG
1 ATATATATGTATTAATGATTAG
40424017 ATAT-TATGTATTA
1 ATATATATGTATTA
40424030 TGTGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATATATGTATTAATGATTAG
Found at i:40425142 original size:18 final size:20
Alignment explanation
Indices: 40425119--40425158 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
40425109 ATGATTAGAC
40425119 ATTATAT-TATTATT-TAAT
1 ATTATATCTATTATTATAAT
*
40425137 ATTATATCTTTTATTATAAT
1 ATTATATCTATTATTATAAT
40425157 AT
1 AT
40425159 ATAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATCTATTATTATAAT
Found at i:40425189 original size:32 final size:31
Alignment explanation
Indices: 40425153--40425223 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
40425143 TCTTTTATTA
*
40425153 TAATATATAATA-TAATAGTTATATATATGTAT
1 TAATATAT-ATAGTAATAGTTATATAT-TATAT
*
40425185 TAATAGT-TTTAGTAATAGTTATATATTATAT
1 TAATA-TATATAGTAATAGTTATATATTATAT
*
40425216 TATTATAT
1 TAATATAT
40425224 TATTATATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.03
31 11 0.33
32 20 0.61
33 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (31 bp):
TAATATATATAGTAATAGTTATATATTATAT
Found at i:40425221 original size:8 final size:8
Alignment explanation
Indices: 40425119--40425231 Score: 58
Period size: 8 Copynumber: 13.9 Consensus size: 8
40425109 ATGATTAGAC
40425119 ATTATATT
1 ATTATATT
40425127 ATTAT-TT
1 ATTATATT
40425134 A--ATATT
1 ATTATATT
* *
40425140 ATATCTTTT
1 AT-TATATT
*
40425149 ATTATAAT
1 ATTATATT
*
40425157 A-TATAAT
1 ATTATATT
*
40425164 ATAATAGTT
1 ATTATA-TT
40425173 ATATATATGT
1 AT-TATAT-T
40425183 ATTAATAGTT
1 ATT-ATA-TT
*
40425193 -TTAGTAAT
1 ATTA-TATT
40425201 AGTTATA-T
1 A-TTATATT
40425209 ATTATATT
1 ATTATATT
40425217 ATTATATT
1 ATTATATT
40425225 ATTATAT
1 ATTATAT
40425232 GATGTAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
5 2 0.02
6 3 0.04
7 15 0.18
8 32 0.39
9 16 0.20
10 13 0.16
11 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (8 bp):
ATTATATT
Found at i:40428251 original size:17 final size:17
Alignment explanation
Indices: 40428168--40428251 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 17
40428158 ATTACATTAA
40428168 TATATTATTTCATTATATGTT
1 TATA-TATTT-ATTA-AT-TT
*
40428189 T-TATATTATCATTAAATT
1 TATATATT-T-ATTAATTT
* *
40428207 TAAATA-TTATAAATTT
1 TATATATTTATTAATTT
40428223 TGATA-A-TTATTAATTT
1 T-ATATATTTATTAATTT
40428239 TATATATTTATTA
1 TATATATTTATTA
40428252 TACATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
15 3 0.06
16 19 0.37
17 9 0.17
18 4 0.08
19 8 0.15
20 8 0.15
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATATTTATTAATTT
Found at i:40437334 original size:31 final size:31
Alignment explanation
Indices: 40437299--40437360 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40437289 AAAATTATAA
40437299 TTCATGGTCTAAATGCATGATGTCGTATCTG
1 TTCATGGTCTAAATGCATGATGTCGTATCTG
40437330 TTCATGGTCTAAATGCATGATGTCGTATCTG
1 TTCATGGTCTAAATGCATGATGTCGTATCTG
40437361 CAAGGCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (31 bp):
TTCATGGTCTAAATGCATGATGTCGTATCTG
Found at i:40444140 original size:125 final size:125
Alignment explanation
Indices: 40443949--40444187 Score: 442
Period size: 125 Copynumber: 1.9 Consensus size: 125
40443939 AGGTCTAAGG
40443949 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTATGG
1 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTATGG
*
40444014 AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTATATCATTATAAAAATTGTAGA
66 AGTACCTAGATCAATAAAATGATTAAATTTGTAAATTTATATCATTATAAAAATTGTAGA
* *
40444074 GTAAAATGGTCATTTTGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTCTGG
1 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTATGG
*
40444139 AGTACCTAGATCAATAAAATGATTAAATTTGTAAATTTTTATCATTATA
66 AGTACCTAGATCAATAAAATGATTAAATTTGTAAATTTATATCATTATA
40444188 GATCAAGAAT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (125 bp):
GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTATGG
AGTACCTAGATCAATAAAATGATTAAATTTGTAAATTTATATCATTATAAAAATTGTAGA
Found at i:40444558 original size:46 final size:46
Alignment explanation
Indices: 40444451--40444580 Score: 138
Period size: 46 Copynumber: 2.8 Consensus size: 46
40444441 TCGGGTTATT
* * * *
40444451 TGTATGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGA
1 TGTAAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCATTCAGA
* * *
40444499 CG-AGAGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTTCAGA
1 TGTA-AGCCAGTGTAAGACATGTCTAGGACATGCATCAGCATTCAGA
*
40444545 TGTAAGCCAGTGTAAGACATGTC-AGGGACATACATC
1 TGTAAGCCAGTGTAAGACATGTCTA-GGACATGCATC
40444581 GGCTACGAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 41 0.59
47 15 0.22
48 12 0.17
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (46 bp):
TGTAAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCATTCAGA
Found at i:40444619 original size:45 final size:46
Alignment explanation
Indices: 40444553--40444680 Score: 136
Period size: 48 Copynumber: 2.8 Consensus size: 46
40444543 GATGTAAGCC
* * *
40444553 AGTGTAA-GACATGTCAGGGACAT-ACATCGGCTACG-AGATGTGTT
1 AGTGTAAGGCCATGTCTGGGACATGACATCGGC-ACGTAGAGGTGTT
*
40444597 AGTGTAAGGCCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTT
1 AGTGTAAGGCCATGTCTGGGACATGACATCGGCACG--TAGAGGTGTT
* * * *
40444645 AGTGTAAGACCATGTCTTGGACATGGCATCGACACG
1 AGTGTAAGGCCATGTCTGGGACATGACATCGGCACG
40444681 GATATGTGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 7 0.10
45 17 0.24
46 7 0.10
48 41 0.57
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
AGTGTAAGGCCATGTCTGGGACATGACATCGGCACGTAGAGGTGTT
Found at i:40444652 original size:48 final size:50
Alignment explanation
Indices: 40444587--40444774 Score: 188
Period size: 48 Copynumber: 3.8 Consensus size: 50
40444577 CATCGGCTAC
* *
40444587 GAGATGTGTTAGTGTAAGGCCATGTCTGGGACATGGCATCGGCACGTATA-
1 GAGA-GTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATAT
* *
40444637 GAG-GTGTTAGTGTAAGACCATGTCTTGGACATGGCATCGACACGGATAT
1 GAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATAT
* * * * * *
40444686 GTGAGAGCTAGTGTAAGACCATGCCTGGGACATGGCGTCGGC-CTCGAT-T
1 GAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGATAT
** * *
40444735 TTGA-TAGTCAGTGTAAGACCATGCCTGGGACATGGCATCG
1 GAGAGT-GTTAGTGTAAGACCATGTCTGGGACATGGCATCG
40444775 ACAACATACC
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
48 41 0.35
49 38 0.32
50 38 0.32
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (50 bp):
GAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATAT
Found at i:40452092 original size:10 final size:10
Alignment explanation
Indices: 40452073--40452109 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
40452063 AATTTTAGCT
*
40452073 TTTATTTCTA
1 TTTATCTCTA
40452083 TTTATCTCTA
1 TTTATCTCTA
*
40452093 TTTATCTTTA
1 TTTATCTCTA
40452103 TTTATCT
1 TTTATCT
40452110 TTTAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATCTCTA
Found at i:40456479 original size:16 final size:16
Alignment explanation
Indices: 40456458--40456525 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
40456448 TTTGGTTCGC
40456458 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40456474 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40456490 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
40456506 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40456522 TGTA
1 TGTA
40456526 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40456781 original size:16 final size:16
Alignment explanation
Indices: 40456741--40456795 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
40456731 TTAATCATAT
*
40456741 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
40456757 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
40456772 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
40456790 -TAAAAT
1 TTAAAAT
40456796 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:40456788 original size:18 final size:17
Alignment explanation
Indices: 40456761--40456795 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40456751 TTTTTATTAA
*
40456761 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40456779 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40456796 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40456908 original size:18 final size:17
Alignment explanation
Indices: 40456881--40456915 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40456871 TTACTATTAA
*
40456881 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40456899 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40456916 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40456961 original size:61 final size:60
Alignment explanation
Indices: 40456776--40456966 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
40456766 TTTTAATTAA
* *
40456776 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
40456837 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
40456895 A
60 T
*
40456896 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
40456957 AATATATAAT
1 AATATATAAT
40456967 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:40457044 original size:120 final size:120
Alignment explanation
Indices: 40456739--40457022 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
40456729 ATTTAATCAT
*
40456739 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
40456804 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
40456860 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
40456925 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
40456980 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
40457023 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:40458958 original size:19 final size:19
Alignment explanation
Indices: 40458934--40458970 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40458924 ATAAAATATT
40458934 ATCGTTCAGGTACATATAC
1 ATCGTTCAGGTACATATAC
*
40458953 ATCGTTCAGGTGCATATA
1 ATCGTTCAGGTACATATA
40458971 GAGGTCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
ATCGTTCAGGTACATATAC
Found at i:40460673 original size:21 final size:21
Alignment explanation
Indices: 40460648--40460688 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40460638 ATACAAAGTC
40460648 AGTCTATACATATCATGCCAG
1 AGTCTATACATATCATGCCAG
40460669 AGTCTATACATATCATGCCA
1 AGTCTATACATATCATGCCA
40460689 TTAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (21 bp):
AGTCTATACATATCATGCCAG
Found at i:40460855 original size:20 final size:21
Alignment explanation
Indices: 40460830--40460872 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
40460820 ATTGAGAATC
40460830 ATCTTCATATGATTATA-ATT
1 ATCTTCATATGATTATAGATT
*
40460850 ATCTTCGTATGATTATAGATT
1 ATCTTCATATGATTATAGATT
40460871 AT
1 AT
40460873 TCAAACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
ATCTTCATATGATTATAGATT
Found at i:40467711 original size:25 final size:26
Alignment explanation
Indices: 40467683--40467733 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
40467673 ATTTGTAATT
* *
40467683 TAATACATTT-AAAATATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
40467708 TAATAAATTTAAAAAAATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
40467734 ATTATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAAATTTAAAAAAATTAAATATA
Found at i:40474226 original size:16 final size:17
Alignment explanation
Indices: 40474195--40474228 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40474185 ATTGTGCATA
40474195 AAAAGAAAGAAAAATAT
1 AAAAGAAAGAAAAATAT
*
40474212 AAAAG-AAGGAAAATAT
1 AAAAGAAAGAAAAATAT
40474228 A
1 A
40474229 GTGAGGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
AAAAGAAAGAAAAATAT
Found at i:40477558 original size:15 final size:16
Alignment explanation
Indices: 40477533--40477566 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40477523 AAATTACAGT
40477533 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
40477549 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
40477564 TTT
1 TTT
40477567 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:40479468 original size:20 final size:21
Alignment explanation
Indices: 40479440--40479479 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40479430 CTTTTATACC
40479440 AATAAATAC-ATAAAATAAAA
1 AATAAATACTATAAAATAAAA
*
40479460 AATATATACTATAAAATAAA
1 AATAAATACTATAAAATAAA
40479480 TTAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAATACTATAAAATAAAA
Found at i:40480389 original size:17 final size:17
Alignment explanation
Indices: 40480369--40480423 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
40480359 TTATTTCTTT
*
40480369 TATATATTTATATATTC
1 TATATATTTATATATTA
* * *
40480386 TATAAATTTATATTTTT
1 TATATATTTATATATTA
*
40480403 TTTA-ATTTATATATTA
1 TATATATTTATATATTA
40480419 TATAT
1 TATAT
40480424 TTTTCAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTTATATATTA
Found at i:40480416 original size:33 final size:37
Alignment explanation
Indices: 40480327--40480422 Score: 112
Period size: 36 Copynumber: 2.7 Consensus size: 37
40480317 TGCTTTTTAG
* * * *
40480327 TTCTTATATATATTTGTA-ATTTTATAAATTTTTTAT
1 TTCTTTTATATATTTATATATTATATAAATTTTATAT
*
40480363 TTCTTTTATATATTTATATATTCTATAAA-TTTATAT
1 TTCTTTTATATATTTATATATTATATAAATTTTATAT
40480399 TT-TTTT-TA-ATTTATATATTATATA
1 TTCTTTTATATATTTATATATTATATA
40480423 TTTTTCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 15 0.28
34 2 0.04
35 4 0.07
36 24 0.44
37 9 0.17
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (37 bp):
TTCTTTTATATATTTATATATTATATAAATTTTATAT
Found at i:40485177 original size:19 final size:18
Alignment explanation
Indices: 40485153--40485196 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40485143 ATAGACATGC
40485153 ATAATA-TCAAATAATAATA
1 ATAATATTCAAA-AATAA-A
40485172 ATAATATTCAAAAATAAA
1 ATAATATTCAAAAATAAA
40485190 AT-ATATT
1 ATAATATT
40485197 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.21
18 3 0.12
19 11 0.46
20 5 0.21
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATATTCAAAAATAAA
Found at i:40505659 original size:13 final size:13
Alignment explanation
Indices: 40505629--40505664 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
40505619 ATTGGTTGAG
*
40505629 AAATTAATTTAGTT
1 AAATTAA-TTAATT
40505643 AAATTAATTAATT
1 AAATTAATTAATT
40505656 AAATTAATT
1 AAATTAATT
40505665 GATTGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:40507965 original size:3 final size:3
Alignment explanation
Indices: 40507957--40507992 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
40507947 TTTAATTGTA
40507957 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40507993 TGATAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40509855 original size:31 final size:33
Alignment explanation
Indices: 40509802--40509905 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 33
40509792 TTTTGCATTA
* *
40509802 ATTTATATTTTATGTATCATTATA-TT-AAATT
1 ATTTAAATATTATGTATCATTATATTTAAAATT
* *
40509833 ATTTAAATATTATTTATTATTATATTTAAAATT
1 ATTTAAATATTATGTATCATTATATTTAAAATT
* * * *
40509866 -TTAAAATATTTCATGTATAATTAAATTTACAAATA
1 ATTTAAATA-TT-ATGTATCATTATATTTA-AAATT
40509901 ATTTA
1 ATTTA
40509906 CTAATTATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
31 20 0.35
32 9 0.16
33 7 0.12
34 14 0.25
35 4 0.07
36 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (33 bp):
ATTTAAATATTATGTATCATTATATTTAAAATT
Found at i:40511155 original size:80 final size:80
Alignment explanation
Indices: 40511058--40511217 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
40511048 TACTGACTAA
40511058 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAATGCACATCATGTTAGT
1 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAATGCACATCATGTTAGT
40511123 ATAACACCATTTGTT
66 ATAACACCATTTGTT
*
40511138 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCACATCATGTTAGT
1 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAATGCACATCATGTTAGT
40511203 ATAACACCATTTGTT
66 ATAACACCATTTGTT
40511218 TTATATGTCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (80 bp):
AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAATGCACATCATGTTAGT
ATAACACCATTTGTT
Found at i:40511294 original size:16 final size:16
Alignment explanation
Indices: 40511244--40511295 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
40511234 TAAATAATTA
*
40511244 AAAATTTTAAAAAAAT
1 AAAATTTTAAAAATAT
** *
40511260 AAAATACATCAAAAT-T
1 AAAAT-TTTAAAAATAT
40511276 AAAATTTTAAAAATAT
1 AAAATTTTAAAAATAT
40511292 AAAA
1 AAAA
40511296 AGTTCATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTTAAAAATAT
Done.