Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 77 of 106
Found at i:29414800 original size:29 final size:29
Alignment explanation
Indices: 29414768--29414823 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29414758 ATTAAAATAA
29414768 TTTTTT-ATTTTATTT-T-ATTTTATTTCTC
1 TTTTTTCATTTT-TTTCTCATTTT-TTTCTC
29414796 TTTTTTCATTTTTTTCTCATTTTTTTCT
1 TTTTTTCATTTTTTTCTCATTTTTTTCT
29414824 GTTCTTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTTTTCATTTTTTTCTCATTTTTTTCTC
Found at i:29414809 original size:10 final size:10
Alignment explanation
Indices: 29414768--29414821 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
29414758 ATTAAAATAA
29414768 TTTTTT-ATT
1 TTTTTTCATT
29414777 TTATTTT-ATT
1 TT-TTTTCATT
* *
29414787 TTATTTC-TC
1 TTTTTTCATT
29414796 TTTTTTCATT
1 TTTTTTCATT
29414806 TTTTTCTCATT
1 TTTTT-TCATT
29414817 TTTTT
1 TTTTT
29414822 CTGTTCTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 12 0.32
10 15 0.41
11 10 0.27
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:29414811 original size:18 final size:19
Alignment explanation
Indices: 29414780--29414820 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29414770 TTTTATTTTA
29414780 TTTTATTTTATTTCTC-TT
1 TTTTATTTTATTTCTCATT
29414798 TTTTCATTTT-TTTCTCATT
1 TTTT-ATTTTATTTCTCATT
29414817 TTTT
1 TTTT
29414821 TCTGTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTATTTCTCATT
Found at i:29415818 original size:20 final size:18
Alignment explanation
Indices: 29415793--29415861 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
29415783 AATTACACAA
*
29415793 TATATTAAATAGTATATATT
1 TATATTAAATA-T-TATAAT
*
29415813 TATATTTAATATTATAAT
1 TATATTAAATATTATAAT
*
29415831 TATATAAAATA-T-TAAT
1 TATATTAAATATTATAAT
*
29415847 TATGATTTAATATTA
1 TAT-ATTAAATATTA
29415862 ATTTTTCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 15 0.38
19 1 0.03
20 10 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTAAATATTATAAT
Found at i:29416599 original size:2 final size:2
Alignment explanation
Indices: 29416594--29416629 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29416584 ACACGCATGA
29416594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29416630 CTGTGTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29423374 original size:24 final size:24
Alignment explanation
Indices: 29423327--29423374 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29423317 TAAATAACAA
*
29423327 TATTTAAATTAAATATAATTTTAT
1 TATTTAAATTAAATATAATGTTAT
29423351 TATTTAAATTAAAT-TAATAGTTAT
1 TATTTAAATTAAATATAAT-GTTAT
29423375 AAAAACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTAAATTAAATATAATGTTAT
Found at i:29425472 original size:26 final size:25
Alignment explanation
Indices: 29425443--29425529 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
29425433 ATGTTTTAGT
* *
29425443 ACATGGCATGTAATATGTTTTTTTGA
1 ACATGGCATGTAACA-ATTTTTTTGA
*
29425469 ACATGGCGTGTAACAATTTTTTTGA
1 ACATGGCATGTAACAATTTTTTTGA
* * * * *
29425494 ATATGGCGTGCAACAAATTTTTTCA
1 ACATGGCATGTAACAATTTTTTTGA
*
29425519 ACATAGCATGT
1 ACATGGCATGT
29425530 CGTGTAACAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
25 37 0.74
26 13 0.26
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (25 bp):
ACATGGCATGTAACAATTTTTTTGA
Found at i:29425488 original size:25 final size:25
Alignment explanation
Indices: 29425460--29425522 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
29425450 ATGTAATATG
*
29425460 TTTTTTTGAACATGGCGTGTAACAA
1 TTTTTTTGAACATGGCGTGCAACAA
*
29425485 TTTTTTTGAATATGGCGTGCAACAA
1 TTTTTTTGAACATGGCGTGCAACAA
* *
29425510 ATTTTTTCAACAT
1 TTTTTTTGAACAT
29425523 AGCATGTCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (25 bp):
TTTTTTTGAACATGGCGTGCAACAA
Found at i:29429007 original size:15 final size:15
Alignment explanation
Indices: 29428964--29429012 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
29428954 TCTGTTCTTT
*
29428964 TTTTTTTAATTTTAT
1 TTTTTTTAATTTTAA
29428979 TATTTTTTAA--TTAA
1 T-TTTTTTAATTTTAA
29428993 TTTTTTTAATTTTAA
1 TTTTTTTAATTTTAA
29429008 TTTTT
1 TTTTT
29429013 ATTATGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
15 10 0.33
16 8 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTAATTTTAA
Found at i:29429024 original size:29 final size:28
Alignment explanation
Indices: 29428964--29429043 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
29428954 TCTGTTCTTT
*
29428964 TTTTTTTAATTTTATTATTTTT-TAATTAA
1 TTTTTTTAATTTTA--ATTTTTATTATTAA
*
29428993 TTTTTTTAATTTTAATTTTTATTATGTTA
1 TTTTTTTAATTTTAATTTTTATTAT-TAA
** *
29429022 TTTGATT-ATTTTATTTTTTATT
1 TTTTTTTAATTTTAATTTTTATT
29429044 TTTTTTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.14
28 17 0.39
29 21 0.48
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (28 bp):
TTTTTTTAATTTTAATTTTTATTATTAA
Found at i:29429789 original size:22 final size:22
Alignment explanation
Indices: 29429764--29429822 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
29429754 CGAGAGTTTC
*
29429764 TCGCTGCAGTGAGAATCCATTT
1 TCGCTGCAGCGAGAATCCATTT
* *
29429786 TCGCTGCAGCGAGAATTCTTTT
1 TCGCTGCAGCGAGAATCCATTT
* *
29429808 TCCCTGCAGCTAGAA
1 TCGCTGCAGCGAGAA
29429823 ACAGGGTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (22 bp):
TCGCTGCAGCGAGAATCCATTT
Found at i:29430163 original size:36 final size:36
Alignment explanation
Indices: 29430107--29430193 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
29430097 ATTATGTTTG
* *
29430107 TGTGCTCCCCCATATCGCGCACAACTAATGCCATCA
1 TGTGCTCCCCCACATAGCGCACAACTAATGCCATCA
*
29430143 TGTGCTCCCTCACATAGCGCACAACTAATGCCATCA
1 TGTGCTCCCCCACATAGCGCACAACTAATGCCATCA
29430179 TGTGCTCCCCCACAT
1 TGTGCTCCCCCACAT
29430194 CGCGTACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.23
Consensus pattern (36 bp):
TGTGCTCCCCCACATAGCGCACAACTAATGCCATCA
Found at i:29430228 original size:44 final size:44
Alignment explanation
Indices: 29430179--29430262 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
29430169 AATGCCATCA
* *
29430179 TGTGCTCCCCCACATCGCGTACATAGGCAATATCATCATCATTG
1 TGTGCTCCCCCACATCGCGCACATAAGCAATATCATCATCATTG
29430223 TGTGCTCCCCCACATCGCGCACATAAGCAATATCATCATC
1 TGTGCTCCCCCACATCGCGCACATAAGCAATATCATCATC
29430263 CACACTCCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (44 bp):
TGTGCTCCCCCACATCGCGCACATAAGCAATATCATCATCATTG
Found at i:29430367 original size:2 final size:2
Alignment explanation
Indices: 29430360--29430384 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29430350 AATGCACAAC
29430360 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 A
29430385 CCAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29433201 original size:23 final size:23
Alignment explanation
Indices: 29433169--29433417 Score: 189
Period size: 23 Copynumber: 10.7 Consensus size: 23
29433159 AACCTTACCA
29433169 TGTCACATATTCTCACCATGTCG
1 TGTCACATATTCTCACCATGTCG
* *
29433192 TCTCACATATTCTTACCATGTCG
1 TGTCACATATTCTCACCATGTCG
* *
29433215 TGTCACATATTCT-ATCCATATTG
1 TGTCACATATTCTCA-CCATGTCG
* * ** *
29433238 TCTCACATATTCCCTTCATGGCG
1 TGTCACATATTCTCACCATGTCG
* * *
29433261 TGTCACATACTCTCACCCTATCG
1 TGTCACATATTCTCACCATGTCG
* * **
29433284 TGTCGCATATTCTCACCCTACCG
1 TGTCACATATTCTCACCATGTCG
* *
29433307 TGTCTCACATATTCTTACAATGTCG
1 TG--TCACATATTCTCACCATGTCG
* *
29433332 TGTCACATATTC-CATCCATATTG
1 TGTCACATATTCTCA-CCATGTCG
* * *
29433355 TCTCACATATTC-CTTCCATGGCG
1 TGTCACATATTCTC-ACCATGTCG
* * *
29433378 TGTCACATACTCTCACCCTATCG
1 TGTCACATATTCTCACCATGTCG
*
29433401 TGTCACATATTTTCACC
1 TGTCACATATTCTCACC
29433418 CTACCGTGTC
Statistics
Matches: 173, Mismatches: 46, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
22 2 0.01
23 153 0.88
24 1 0.01
25 17 0.10
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (23 bp):
TGTCACATATTCTCACCATGTCG
Found at i:29433397 original size:117 final size:117
Alignment explanation
Indices: 29433169--29433427 Score: 427
Period size: 117 Copynumber: 2.2 Consensus size: 117
29433159 AACCTTACCA
* * *
29433169 TGTCACATATTCTCA-CC-A-TGTCGTCTCACATATTCTTACCATGTCGTGTCACATATTCTATC
1 TGTCACATATTCTCACCCTACCGT-GTCTCACATATTCTTACAATGTCGTGTCACATATTCCATC
29433231 CATATTGTCTCACATATTCCCTTCATGGCGTGTCACATACTCTCACCCTATCG
65 CATATTGTCTCACATATTCCCTTCATGGCGTGTCACATACTCTCACCCTATCG
*
29433284 TGTCGCATATTCTCACCCTACCGTGTCTCACATATTCTTACAATGTCGTGTCACATATTCCATCC
1 TGTCACATATTCTCACCCTACCGTGTCTCACATATTCTTACAATGTCGTGTCACATATTCCATCC
29433349 ATATTGTCTCACATATT-CCTTCCATGGCGTGTCACATACTCTCACCCTATCG
66 ATATTGTCTCACATATTCCCTT-CATGGCGTGTCACATACTCTCACCCTATCG
*
29433401 TGTCACATATTTTCACCCTACCGTGTC
1 TGTCACATATTCTCACCCTACCGTGTC
29433428 ACTATTAGAT
Statistics
Matches: 134, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
115 14 0.10
116 6 0.04
117 112 0.84
118 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (117 bp):
TGTCACATATTCTCACCCTACCGTGTCTCACATATTCTTACAATGTCGTGTCACATATTCCATCC
ATATTGTCTCACATATTCCCTTCATGGCGTGTCACATACTCTCACCCTATCG
Found at i:29437439 original size:27 final size:26
Alignment explanation
Indices: 29437407--29437463 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
29437397 TATTAATATT
*
29437407 TAAATTATTAATCT-TTAATATTTTAAA
1 TAAATTATAAAT-TATTAATA-TTTAAA
29437434 TAAATTATAAATTATTAATATTTAAA
1 TAAATTATAAATTATTAATATTTAAA
29437460 -AAAT
1 TAAAT
29437464 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 7 0.25
27 17 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATTATAAATTATTAATATTTAAA
Found at i:29437469 original size:34 final size:35
Alignment explanation
Indices: 29437389--29437478 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 35
29437379 TTTAAACTAT
* * *
29437389 AAATAAAATATTAATATTTAAATTATTAATCTTTAAT
1 AAATAAAATA--AATATATAAATTATTAATATTTAAA
** *
29437426 ATTTTAAATAAAT-TATAAATTATTAATATTTAAA
1 AAATAAAATAAATATATAAATTATTAATATTTAAA
29437460 AAATAAAATAAA-A-ATAAAT
1 AAATAAAATAAATATATAAAT
29437479 AATCATATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
33 6 0.14
34 27 0.63
35 3 0.07
37 7 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
AAATAAAATAAATATATAAATTATTAATATTTAAA
Found at i:29458416 original size:5 final size:5
Alignment explanation
Indices: 29458408--29458433 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29458398 CAGAAACAGG
29458408 AGAGA AGAGA AGAGA AGAGA AGAGA A
1 AGAGA AGAGA AGAGA AGAGA AGAGA A
29458434 TATTTAACAA
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:29474182 original size:10 final size:10
Alignment explanation
Indices: 29474167--29474191 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29474157 AATCTAGACT
29474167 TTTTTTTTTA
1 TTTTTTTTTA
29474177 TTTTTTTTTA
1 TTTTTTTTTA
29474187 TTTTT
1 TTTTT
29474192 CATGTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:29475380 original size:21 final size:21
Alignment explanation
Indices: 29475350--29475417 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
29475340 GGATATGTTC
29475350 ATGCAATTCATGACAAAGACTG
1 ATGC-ATTCATGACAAAGACTG
*
29475372 ATGCATTCATAACAAAGACTG
1 ATGCATTCATGACAAAGACTG
* * *
29475393 ATGCATTTATGATAAGGACTG
1 ATGCATTCATGACAAAGACTG
29475414 ATGC
1 ATGC
29475418 CTCCATTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:29476882 original size:14 final size:14
Alignment explanation
Indices: 29476846--29476884 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29476836 TTTGTGCAGG
29476846 TTCATAAAAAAAAT
1 TTCATAAAAAAAAT
**
29476860 TTTTTAAAAAAAAT
1 TTCATAAAAAAAAT
29476874 TTCA-AAAAAAA
1 TTCATAAAAAAA
29476885 TTCAAAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (14 bp):
TTCATAAAAAAAAT
Found at i:29477293 original size:9 final size:8
Alignment explanation
Indices: 29477250--29477318 Score: 79
Period size: 8 Copynumber: 8.8 Consensus size: 8
29477240 TTATTTGAAC
29477250 TACCCA-T
1 TACCCATT
29477257 TACCCATT
1 TACCCATT
*
29477265 TACCCAAT
1 TACCCATT
29477273 TACCCATT
1 TACCCATT
29477281 TACCCACTT
1 TACCCA-TT
*
29477290 TACCCACT
1 TACCCATT
*
29477298 AACCCATT
1 TACCCATT
*
29477306 TACGCA-T
1 TACCCATT
29477313 TACCCA
1 TACCCA
29477319 ACAAAAACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
7 12 0.23
8 32 0.62
9 8 0.15
ACGTcount: A:0.29, C:0.41, G:0.01, T:0.29
Consensus pattern (8 bp):
TACCCATT
Found at i:29483434 original size:23 final size:23
Alignment explanation
Indices: 29483362--29483434 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
29483352 TTAGTACATG
*
29483362 AACATTTTTATTGAAAATGGTGTGT
1 AACA-TTTT-TTGAACATGGTGTGT
** * * *
29483387 AACACGTTATCAACATGGTGGGT
1 AACATTTTTTGAACATGGTGTGT
*
29483410 AACATTTTTTGAACATGATGTGT
1 AACATTTTTTGAACATGGTGTGT
29483433 AA
1 AA
29483435 GAAAATTTTT
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
23 30 0.83
24 2 0.06
25 4 0.11
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (23 bp):
AACATTTTTTGAACATGGTGTGT
Found at i:29483459 original size:26 final size:26
Alignment explanation
Indices: 29483413--29483474 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
29483403 GGTGGGTAAC
* ** *
29483413 ATTTTTTGAACATGATGTGTAAGAAA
1 ATTTTTTCAACATGACATGTAACAAA
*
29483439 ATTTTTTCAACATGACATGTAACAAC
1 ATTTTTTCAACATGACATGTAACAAA
*
29483465 ATGTTTTCAA
1 ATTTTTTCAA
29483475 TAGGGCGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (26 bp):
ATTTTTTCAACATGACATGTAACAAA
Found at i:29488809 original size:77 final size:77
Alignment explanation
Indices: 29488561--29489272 Score: 594
Period size: 77 Copynumber: 9.4 Consensus size: 77
29488551 ACACTAAAAA
* *** *
29488561 TGTTAGATGTCATTGACATCTTGTCATGACACATCGCCATGTTATTGTAGTATTATAAGGTGACA
1 TGTTAGATGTCGTTGACATCTTGTCATGACACA-CATGA-GTCATTGTAGTATTATAAGGTGACA
*
29488626 CACCACT-CTCCAAT
64 CGCCA-TGCTCCAAT
* * ** *
29488640 TGTTAGATGCCGTTGACATCTTGTCGTGACATGCATGA---ATTGCAGTATTATAAGGTGACACG
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACACG
*
29488702 TCACT-CTCCAA-
66 CCA-TGCTCCAAT
* * * *
29488713 ----AGATGTCGTTGACATCTTGTCATGACACACATAAGTCGTTATAGTATTAT-AGGATGACAT
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGG-TGACAC
29488773 GCCATGCTCCAAT
65 GCCATGCTCCAAT
* * ** *
29488786 TGTTAGATGTCGTTGACATCTTGTTATGACACTCTACCATGTCATTGTAGTATTATAAGGTGACG
1 TGTTAGATGTCGTTGACATCTTGTCATGACACAC-ATGA-GTCATTGTAGTATTATAAGGTGACA
*
29488851 CGTCACT-CTCCAA-
64 CGCCA-TGCTCCAAT
* * *
29488864 ----AGATGTAGTTGACATCTTTTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACATG
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACACG
29488925 CCATGCTCCAAT
66 CCATGCTCCAAT
* ** * ** ** *
29488937 TGTTAGATGTTGTTGACATCTTGTTGTGGCATGCATGAGTCATTACAGTATTGTAAGGTGACACG
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACACG
29489002 CCACT-CTCCAAT
66 CCA-TGCTCCAAT
* ** * *
29489014 TGTTAGATGTCGTAGACATCTTGTTGTGACACACTTGAGTCATTATAGTAATTATAAGGTGACAC
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGT-ATTATAAGGTGACAC
**
29489079 GCCACACTCCAAT
65 GCCATGCTCCAAT
* * * * * * * * *
29489092 TGTTAGATGTCATTAACAT-TTGGTCGTGACATAC-CGCCTTGTCGTTGCAGTATTATAGGGTGA
1 TGTTAGATGTCGTTGACATCTT-GTCATGACACACATG---AGTCATTGTAGTATTATAAGGTGA
29489155 CACGCCATGCTCCAA-
62 CACGCCATGCTCCAAT
* * * * * *
29489170 ----AGATGTCGTTGACATCTTGTCGTGACACA-TTGGGTCATTGTAGTATTATAGGGTGGCATG
1 TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACACG
*
29489230 CCAAGCTCCAAT
66 CCATGCTCCAAT
*
29489242 TGTTATATGTCGTTGACATCTTGTCATGACA
1 TGTTAGATGTCGTTGACATCTTGTCATGACA
29489273 TGCTGCCACA
Statistics
Matches: 515, Mismatches: 84, Indels: 71
0.77 0.13 0.11
Matches are distributed among these distances:
69 29 0.06
71 38 0.07
72 57 0.11
73 2 0.00
74 82 0.16
75 2 0.00
76 25 0.05
77 133 0.26
78 56 0.11
79 79 0.15
80 12 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (77 bp):
TGTTAGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACACG
CCATGCTCCAAT
Found at i:29488887 original size:151 final size:151
Alignment explanation
Indices: 29488565--29489273 Score: 733
Period size: 151 Copynumber: 4.7 Consensus size: 151
29488555 TAAAAATGTT
* *** * * **
29488565 AGATGTCATTGACATCTTGTCATGACACATCGCCATGTTATTGTAGTATTATAAGGTGACACACC
1 AGATGTCGTTGACATCTTGTCATGACACA-CATGA-GTCATTATAGTATTATAAGGTGACATGCC
* * *
29488630 ACT-CTCCAATTGTTAGATGCCGTTGACATCTTGTCGTGAC--A-T-GCATG-AATTGCAGTATT
64 A-TGCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACATACTACCATGTCATTGCAGTATT
*
29488689 ATAAGGTGACACGTCACTCTCCAA
128 ATAAGGTGACACGCCACTCTCCAA
* *
29488713 AGATGTCGTTGACATCTTGTCATGACACACATAAGTCGTTATAGTATTAT-AGGATGACATGCCA
1 AGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTATAGTATTATAAGG-TGACATGCCA
** *
29488777 TGCTCCAATTGTTAGATGTCGTTGACATCTTGTTATGACACT-CTACCATGTCATTGTAGTATTA
65 TGCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACA-TACTACCATGTCATTGCAGTATTA
* *
29488841 TAAGGTGACGCGTCACTCTCCAA
129 TAAGGTGACACGCCACTCTCCAA
* * *
29488864 AGATGTAGTTGACATCTTTTCATGACACACATGAGTCATTGTAGTATTATAAGGTGACATGCCAT
1 AGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTATAGTATTATAAGGTGACATGCCAT
* * * * ** * *
29488929 GCTCCAATTGTTAGATGTTGTTGACATCTTGTTGTGGCATGC-ATGA-GTCATTACAGTATTGTA
66 GCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACATACTACCATGTCATTGCAGTATTATA
29488992 AGGTGACACGCCACTCTCCAA
131 AGGTGACACGCCACTCTCCAA
* ** *
29489013 TTGTTAGATGTCGTAGACATCTTGTTGTGACACACTTGAGTCATTATAGTAATTATAAGGTGACA
1 -----AGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTATAGT-ATTATAAGGTGACA
* ** * * ** * *
29489078 CGCCACACTCCAATTGTTAGATGTCATTAACAT-TTGGTCGTGACATACCGCCTTGTCGTTGCAG
60 TGCCATGCTCCAATTGTTAGATGTCGTTGACATCTT-GTCGTGACATACTACCATGTCATTGCAG
*
29489142 TATTATAGGGTGACACGCCA-TGCTCCAA
124 TATTATAAGGTGACACGCCACT-CTCCAA
* * * * * * *
29489170 AGATGTCGTTGACATCTTGTCGTGACACA-TTGGGTCATTGTAGTATTATAGGGTGGCATGCCAA
1 AGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTATAGTATTATAAGGTGACATGCCAT
* *
29489234 GCTCCAATTGTTATATGTCGTTGACATCTTGTCATGACAT
66 GCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACAT
29489274 GCTGCCACAT
Statistics
Matches: 472, Mismatches: 68, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
145 4 0.01
146 55 0.12
147 2 0.00
148 28 0.06
149 34 0.07
150 55 0.12
151 141 0.30
152 30 0.06
154 40 0.08
155 50 0.11
156 1 0.00
157 32 0.07
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (151 bp):
AGATGTCGTTGACATCTTGTCATGACACACATGAGTCATTATAGTATTATAAGGTGACATGCCAT
GCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACATACTACCATGTCATTGCAGTATTATA
AGGTGACACGCCACTCTCCAA
Found at i:29489034 original size:228 final size:220
Alignment explanation
Indices: 29488561--29489272 Score: 614
Period size: 228 Copynumber: 3.1 Consensus size: 220
29488551 ACACTAAAAA
* * * *
29488561 TGTTAGATGTCATTGACATCTTGTCATGACACATCGCCATGTTATTGTAGTATTATAAGGTGACA
1 TGTTAGATGTCGTTGACATCTTGTTATGACAC-TCTCCATGTCATTGTAGTATTATAAGGTGACA
* * * **
29488626 CACCACTCTCCAATTGTTAGATGCCGTTGACATCTTGTCGTGACATGCATGAATTGCAGTATTAT
65 CGCCACTCTCCAA----TAGATGCAGTTGACATCTTGTCATGACACACATGAATTGCAGTATTAT
* * *
29488691 AAGGTGACACGTCACTCTCCAAAGATGTCGTTGACATCTTGTCATGACACACATAAGTCGTTATA
126 AAGGTGACACGCCACTCTCCAAAGATGTCGTTGACATCTTGTCATGACACACATAAGTCATTACA
*
29488756 GTATTATAGGATGACATGCCATGCTCCAAT
191 GTATTATAGGATGACACGCCATGCTCCAAT
*
29488786 TGTTAGATGTCGTTGACATCTTGTTATGACACTCTACCATGTCATTGTAGTATTATAAGGTGACG
1 TGTTAGATGTCGTTGACATCTTGTTATGACACTCT-CCATGTCATTGTAGTATTATAAGGTGACA
* * * *
29488851 CGTCACTCTCCAA-AGATGTAGTTGACATCTTTTCATGACACACATGAGTCATTGTAGTATTATA
65 CGCCACTCTCCAATAGATGCAGTTGACATCTTGTCATGACACACATGA---ATTGCAGTATTATA
* * ** * ** *
29488915 AGGTGACATGCCA-TGCTCCAATTGTTAGATGTTGTTGACATCTTGTTGTGGCATGCATGAGTCA
127 AGGTGACACGCCACT-CTCCAA-----AGATGTCGTTGACATCTTGTCATGACACACATAAGTCA
*
29488979 TTACAGTATTGTAAGG-TGACACGCCACT-CTCCAAT
186 TTACAGTATTAT-AGGATGACACGCCA-TGCTCCAAT
* * * ** *
29489014 TGTTAGATGTCGTAGACATCTTGTTGTGACACACTTGA-GTCATTATAGTAATTATAAGGTGACA
1 TGTTAGATGTCGTTGACATCTTGTTATGACACTCTCCATGTCATTGTAGT-ATTATAAGGTGACA
* * * * * **
29489078 CGCCACACTCCAATTGTTAGATGTCA-TTAACAT-TTGGTCGTGACATACCGCCTTGTCGTTGCA
65 CGCCACTCTCCAA----TAGATG-CAGTTGACATCTT-GTCATGAC--A-C-ACATG-AATTGCA
* * * **
29489141 GTATTATAGGGTGACACGCCA-TGCTCCAAAGATGTCGTTGACATCTTGTCGTGACACA-TTGGG
119 GTATTATAAGGTGACACGCCACT-CTCCAAAGATGTCGTTGACATCTTGTCATGACACACATAAG
** * * * *
29489204 TCATTGTAGTATTATAGGGTGGCATGCCAAGCTCCAAT
183 TCATTACAGTATTATAGGATGACACGCCATGCTCCAAT
* *
29489242 TGTTATATGTCGTTGACATCTTGTCATGACA
1 TGTTAGATGTCGTTGACATCTTGTTATGACA
29489273 TGCTGCCACA
Statistics
Matches: 396, Mismatches: 64, Indels: 51
0.77 0.13 0.10
Matches are distributed among these distances:
220 28 0.07
222 1 0.00
223 30 0.08
224 2 0.01
225 68 0.17
226 10 0.03
227 28 0.07
228 145 0.37
229 28 0.07
231 2 0.01
232 17 0.04
233 1 0.00
234 32 0.08
235 1 0.00
236 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (220 bp):
TGTTAGATGTCGTTGACATCTTGTTATGACACTCTCCATGTCATTGTAGTATTATAAGGTGACAC
GCCACTCTCCAATAGATGCAGTTGACATCTTGTCATGACACACATGAATTGCAGTATTATAAGGT
GACACGCCACTCTCCAAAGATGTCGTTGACATCTTGTCATGACACACATAAGTCATTACAGTATT
ATAGGATGACACGCCATGCTCCAAT
Found at i:29492678 original size:41 final size:41
Alignment explanation
Indices: 29492633--29492716 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 41
29492623 TTGTATGATA
* *
29492633 ATGATG-ACCCAGCTATATGCGGTGTAGGGAGTGCACATGAG
1 ATGATGAACCCAACTATATGCGGTGT-GGGAATGCACATGAG
*
29492674 ATGATGATAACCCAACTATGTGCGGTGTGGGAATGCACATGAG
1 ATGATG--AACCCAACTATATGCGGTGTGGGAATGCACATGAG
29492717 CTTATGATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 6 0.16
43 14 0.38
44 17 0.46
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.23
Consensus pattern (41 bp):
ATGATGAACCCAACTATATGCGGTGTGGGAATGCACATGAG
Found at i:29492725 original size:43 final size:44
Alignment explanation
Indices: 29492633--29492726 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 44
29492623 TTGTATGATA
* * *
29492633 ATGATGACCCAGCTATATGCGGTGTAGGGAGTGCACATGAGATG
1 ATGATAACCCAACTATATGCGGTGTAGGGAATGCACATGAGATG
* * *
29492677 ATGATAACCCAACTATGTGCGGTGT-GGGAATGCACATGAGCTT
1 ATGATAACCCAACTATATGCGGTGTAGGGAATGCACATGAGATG
29492720 ATGATAA
1 ATGATAA
29492727 TGATATTGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 22 0.50
44 22 0.50
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (44 bp):
ATGATAACCCAACTATATGCGGTGTAGGGAATGCACATGAGATG
Found at i:29513258 original size:13 final size:13
Alignment explanation
Indices: 29513240--29513264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29513230 TTTCAGAAAA
29513240 TTTATAAAATCAT
1 TTTATAAAATCAT
29513253 TTTATAAAATCA
1 TTTATAAAATCA
29513265 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:29514660 original size:19 final size:19
Alignment explanation
Indices: 29514636--29514673 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29514626 CTGCCAAACC
*
29514636 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
29514655 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
29514674 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:29515362 original size:246 final size:245
Alignment explanation
Indices: 29514928--29515419 Score: 912
Period size: 246 Copynumber: 2.0 Consensus size: 245
29514918 AACAATTCTT
*
29514928 CGAACTTCCTAAATATGCAAACATTCTATTGAGCATATAAATGACGTTGTAATTATTTTATAGAA
1 CGAACTTCCTAAATATGCAAACATTCTATTGAGCATACAAATGACGTTGTAATTATTTTATAGAA
*
29514993 CAGGGTTTGACAACACTACCCCCCTTAAAATAAAATTTTGTCCTCAAAATTTCACTTATCAACTC
66 CAGGGTTGGACAACACTACCCCCCTTAAAATAAAATTTTGTCCTCAAAATTTCACTTATCAACTC
* *
29515058 CAAGAAAATGCGGGGTATTATCTTTTATTCGATACTCAACTTCTCCTGTTATCTCCTTTATAGGG
131 AAAGAAAATGCAGGGTATTATCTTTTATTCGATACTCAACTTCTCCTGTTATCTCCTTTATAGGG
29515123 AATCTTGTGTTGCTCCTCGTATTTATTTCCAACTCAACTTGAATACTTCA
196 AATCTTGTGTTGCTCCTCGTATTTATTTCCAACTCAACTTGAATACTTCA
* *
29515173 NCGAACTTCGTAAATATGCAAACATTCTATTGAGCATACAAATGACGTTTTAATTATTTTATAGA
1 -CGAACTTCCTAAATATGCAAACATTCTATTGAGCATACAAATGACGTTGTAATTATTTTATAGA
*
29515238 ACAGGGTTGGACAACACTACCCCCCTTAAAATAAATTTTTGTCCTCAAAATTTCACTTATCAACT
65 ACAGGGTTGGACAACACTACCCCCCTTAAAATAAAATTTTGTCCTCAAAATTTCACTTATCAACT
29515303 CAAAGAAAATGCAGGGTATTATCTTTTATTCGATACTCAACTTCTCCTGTTATCTCCTTTATAGG
130 CAAAGAAAATGCAGGGTATTATCTTTTATTCGATACTCAACTTCTCCTGTTATCTCCTTTATAGG
29515368 GAATCTTGTGTTGCTCCTCGTATTTATTTCCAACTCAACTTGAATACTTCA
195 GAATCTTGTGTTGCTCCTCGTATTTATTTCCAACTCAACTTGAATACTTCA
29515419 C
1 C
29515420 TTATATATAT
Statistics
Matches: 239, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
245 1 0.00
246 238 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (245 bp):
CGAACTTCCTAAATATGCAAACATTCTATTGAGCATACAAATGACGTTGTAATTATTTTATAGAA
CAGGGTTGGACAACACTACCCCCCTTAAAATAAAATTTTGTCCTCAAAATTTCACTTATCAACTC
AAAGAAAATGCAGGGTATTATCTTTTATTCGATACTCAACTTCTCCTGTTATCTCCTTTATAGGG
AATCTTGTGTTGCTCCTCGTATTTATTTCCAACTCAACTTGAATACTTCA
Found at i:29516978 original size:15 final size:15
Alignment explanation
Indices: 29516958--29517008 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
29516948 TTCTTAAAAC
29516958 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
29516973 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
29516988 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
*
29517003 ATCTTT
1 AACTTT
29517009 GATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:29517380 original size:208 final size:208
Alignment explanation
Indices: 29517022--29517458 Score: 678
Period size: 208 Copynumber: 2.1 Consensus size: 208
29517012 CTTTAAACCA
*
29517022 TGCTCTGATACCACTCGAATTCGACTCAACCCCGCAGGACATAATAGCATCCAATGGTACCTATC
1 TGCTCTGATACCAATCGAATTCGACTCAACCCCGCAGGACATAATAGCATCCAATGGTACCTATC
* * * *
29517087 AGAGCATTCGGTAAGAGGTGCACTTCACTCCGGAACGCACCGGGAGCAGTCCCTTCCCTCCTCTT
66 AAAGCACTCGGCAAGAGGTGCACTTCACTCCGGAACGCACCGGAAGCAGTCCCTTCCCTCCTCTT
*
29517152 CCAAGCTCCTGAGCGGAGAGTCATACTTCACCATAGATCATATGCGAGAGTTCCTAGGA-ATAGG
131 CCAAGCTCCTGAGCGGAGAGTCATACTTCACCATAGATCATATGCGAGAGTTCCCA-GATATAGG
*
29517216 GTTATCTTTTCCAT
195 GTTATCTTTCCCAT
* * * *
29517230 TGCTCTGATACCAATCGAATTCGACTCAACCTCGCAGGGCATAATCGCATCTAATGGTACCTATC
1 TGCTCTGATACCAATCGAATTCGACTCAACCCCGCAGGACATAATAGCATCCAATGGTACCTATC
* * *
29517295 AAAGCACTCGGCAAGAGGTGCACTTCACTTCGGGACGCACTGGAAGCAGTCCCTTCCCTCCTCTT
66 AAAGCACTCGGCAAGAGGTGCACTTCACTCCGGAACGCACCGGAAGCAGTCCCTTCCCTCCTCTT
* * *
29517360 CCAAGCTCCTGGGTGGAGAGTCATACTTCGCCATAGATCATATGCGAGAGTTCCCAGATATAGGG
131 CCAAGCTCCTGAGCGGAGAGTCATACTTCACCATAGATCATATGCGAGAGTTCCCAGATATAGGG
*
29517425 TTATCTTTCCCTT
196 TTATCTTTCCCAT
* *
29517438 TGCTCTGATGCCAACCGAATT
1 TGCTCTGATACCAATCGAATT
29517459 GTCACGACCC
Statistics
Matches: 208, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
207 2 0.01
208 206 0.99
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (208 bp):
TGCTCTGATACCAATCGAATTCGACTCAACCCCGCAGGACATAATAGCATCCAATGGTACCTATC
AAAGCACTCGGCAAGAGGTGCACTTCACTCCGGAACGCACCGGAAGCAGTCCCTTCCCTCCTCTT
CCAAGCTCCTGAGCGGAGAGTCATACTTCACCATAGATCATATGCGAGAGTTCCCAGATATAGGG
TTATCTTTCCCAT
Found at i:29518625 original size:13 final size:13
Alignment explanation
Indices: 29518607--29518631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29518597 TTTCAGAAAA
29518607 TTTATAAAATCAT
1 TTTATAAAATCAT
29518620 TTTATAAAATCA
1 TTTATAAAATCA
29518632 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:29522391 original size:19 final size:19
Alignment explanation
Indices: 29522367--29522403 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
29522357 CCATTTGACT
29522367 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
29522386 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
29522404 AGTTTATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:29531969 original size:15 final size:17
Alignment explanation
Indices: 29531943--29531985 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 17
29531933 CACATGAGCT
29531943 AAAAATGAAAGAAG-AAG
1 AAAAA-GAAAGAAGCAAG
29531960 -AAAAGAAAGAAGCTAAG
1 AAAAAGAAAGAAGC-AAG
29531977 AAAAAGAAA
1 AAAAAGAAA
29531986 AAAAAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.35
16 4 0.17
17 3 0.13
18 8 0.35
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAGAAGCAAG
Found at i:29536060 original size:35 final size:35
Alignment explanation
Indices: 29536005--29536075 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
29535995 AGTTAGTTTG
* * *
29536005 GGTTTTGGTTGATCTCGGTAAAAACCATTGTGAAA
1 GGTTTTGGCTGAGCTCGGTAAAAACCATTGTAAAA
* *
29536040 GGTTTTGGCTGAGCTTGGTAAAAGCCATTGTAAAA
1 GGTTTTGGCTGAGCTCGGTAAAAACCATTGTAAAA
29536075 G
1 G
29536076 TGTCATGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (35 bp):
GGTTTTGGCTGAGCTCGGTAAAAACCATTGTAAAA
Found at i:29545266 original size:21 final size:21
Alignment explanation
Indices: 29545230--29545278 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29545220 TATGGTAAAA
*
29545230 AGTTTAAGGGATAACTAAGGAC
1 AGTTT-AGGGAGAACTAAGGAC
*
29545252 AGTTTAGGGAGAACTAGGGAC
1 AGTTTAGGGAGAACTAAGGAC
*
29545273 AATTTA
1 AGTTTA
29545279 AGAACAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (21 bp):
AGTTTAGGGAGAACTAAGGAC
Found at i:29545335 original size:20 final size:19
Alignment explanation
Indices: 29545295--29545333 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29545285 AAACAATGAC
*
29545295 TACTTTTTTTGCTGTTTTT
1 TACTTTTTCTGCTGTTTTT
*
29545314 TACTTTTTCTGCTATTTTT
1 TACTTTTTCTGCTGTTTTT
29545333 T
1 T
29545334 TATGTTGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (19 bp):
TACTTTTTCTGCTGTTTTT
Found at i:29545807 original size:17 final size:17
Alignment explanation
Indices: 29545785--29545817 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29545775 GTAAAATAAG
29545785 CACACACTAAGGGGGAA
1 CACACACTAAGGGGGAA
*
29545802 CACACACTTAGGGGGA
1 CACACACTAAGGGGGA
29545818 GAAATCCTCA
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:0.36, C:0.24, G:0.30, T:0.09
Consensus pattern (17 bp):
CACACACTAAGGGGGAA
Found at i:29552211 original size:96 final size:95
Alignment explanation
Indices: 29552047--29552237 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 95
29552037 AATGTGTTCA
29552047 CTTTGATGTGCAATATGGTAGGGATGGATTTTGTGGCATGTGAAAACCCCTTATTTATCATTTGC
1 CTTTGATGTGCAATATGGTAGGGATGGATTTTGTGGCATGTGAAAACCCCTTATTTATCATTTGC
29552112 CCTGAATCTCACTGCAGTGAGAATGCATTC
66 CCTGAATCTCACTGCAGTGAGAATGCATTC
29552142 NCTTTGATGTGCAATATGGTAGGGATGGATTTTGTGGCATGTGAAAACCCCTTATTTATCATTTG
1 -CTTTGATGTGCAATATGGTAGGGATGGATTTTGTGGCATGTGAAAACCCCTTATTTATCATTTG
29552207 CCCTGAATCTCACTGCAGTGAGAATGCATTC
65 CCCTGAATCTCACTGCAGTGAGAATGCATTC
29552238 TTGCTGCAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (95 bp):
CTTTGATGTGCAATATGGTAGGGATGGATTTTGTGGCATGTGAAAACCCCTTATTTATCATTTGC
CCTGAATCTCACTGCAGTGAGAATGCATTC
Found at i:29553085 original size:23 final size:23
Alignment explanation
Indices: 29553055--29553101 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
29553045 ACTGTAAGGT
*
29553055 GGCAAATGAGTGATATTATGTTA
1 GGCAAATGAGTGATACTATGTTA
*
29553078 GGCAAATGATTGATACTATGTTA
1 GGCAAATGAGTGATACTATGTTA
29553101 G
1 G
29553102 CATAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (23 bp):
GGCAAATGAGTGATACTATGTTA
Found at i:29558654 original size:2 final size:2
Alignment explanation
Indices: 29558602--29558646 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
29558592 TATTATGTTG
29558602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29558643 AT AT
1 AT AT
29558647 GAATATATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29558729 original size:56 final size:55
Alignment explanation
Indices: 29558662--29558772 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 55
29558652 TATGCTGTGC
29558662 ATTGACGAATAATGTTGTGTAATGATATTGACCTGGCTACGTGCAAGTAGAAGTG
1 ATTGACGAATAATGTTGTGTAATGATATTGACCTGGCTACGTGCAAGTAGAAGTG
*
29558717 NATTGACGAATAATGTTGTGTAATGATATTGACCTGGCTATGTGCAAGTAGAAGTG
1 -ATTGACGAATAATGTTGTGTAATGATATTGACCTGGCTACGTGCAAGTAGAAGTG
29558773 CGCATAAGCC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (55 bp):
ATTGACGAATAATGTTGTGTAATGATATTGACCTGGCTACGTGCAAGTAGAAGTG
Found at i:29558809 original size:42 final size:43
Alignment explanation
Indices: 29558746--29558829 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
29558736 GTAATGATAT
* *
29558746 TGACCTGGCTATGTGCAAGTA-GAAGTGCGCATAAGCCGATGC
1 TGACCTGACTATGTGCAAGTAGGAAGTGCACATAAGCCGATGC
* *
29558788 TGACCTGACTATGTGCGAGTAGGGAGTGCACATAAGCCGATG
1 TGACCTGACTATGTGCAAGTAGGAAGTGCACATAAGCCGATG
29558830 ATGATGATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.21
Consensus pattern (43 bp):
TGACCTGACTATGTGCAAGTAGGAAGTGCACATAAGCCGATGC
Found at i:29562219 original size:19 final size:19
Alignment explanation
Indices: 29562195--29562232 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29562185 TGTTTATATA
29562195 TGATTAAAGGTTGTTCTTG
1 TGATTAAAGGTTGTTCTTG
*
29562214 TGATTAAATGTTGTTCTTG
1 TGATTAAAGGTTGTTCTTG
29562233 GAAATTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (19 bp):
TGATTAAAGGTTGTTCTTG
Found at i:29564428 original size:11 final size:11
Alignment explanation
Indices: 29564412--29564437 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29564402 AGAATTTTGA
29564412 AATAAAATATT
1 AATAAAATATT
29564423 AATAAAATATT
1 AATAAAATATT
29564434 AATA
1 AATA
29564438 TTTTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:29565344 original size:56 final size:56
Alignment explanation
Indices: 29565231--29565344 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
29565221 GCAAAGTGGT
*** **
29565231 CAAATGAAAACAAAGGAAAATTGGTGCATGTGTTATGATTGGTTTGAAAGGGAGGC
1 CAAATGAAAACAAAGGAAAATTGGTGCATGAAATATGATTGGTTCCAAAGGGAGGC
* * * *
29565287 CAAATGAAAACAAAGGAAAATTTGTGCATGAAATGTGATTGGTTCCAATGGGCGGC
1 CAAATGAAAACAAAGGAAAATTGGTGCATGAAATATGATTGGTTCCAAAGGGAGGC
29565343 CA
1 CA
29565345 TATAAATACT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.24
Consensus pattern (56 bp):
CAAATGAAAACAAAGGAAAATTGGTGCATGAAATATGATTGGTTCCAAAGGGAGGC
Found at i:29565491 original size:13 final size:13
Alignment explanation
Indices: 29565460--29565495 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
29565450 AGTTCCACCC
*
29565460 GAGAGGAAGAAAA
1 GAGAGAAAGAAAA
29565473 -AGAGAAAGAAAA
1 GAGAGAAAGAAAA
29565485 GAGAGAAAGAA
1 GAGAGAAAGAA
29565496 GGGAAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GAGAGAAAGAAAA
Found at i:29577844 original size:37 final size:37
Alignment explanation
Indices: 29577803--29577949 Score: 269
Period size: 37 Copynumber: 4.0 Consensus size: 37
29577793 ATGATGTTGA
29577803 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
29577840 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
*
29577877 AGTGTGCGAGTAGGGAGTGCACACATGATGATG-TTG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
29577913 AAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
1 -AGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
29577950 TTGCTTTGAG
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
36 2 0.02
37 103 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.22
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
Found at i:29585608 original size:37 final size:38
Alignment explanation
Indices: 29585550--29585671 Score: 160
Period size: 37 Copynumber: 3.3 Consensus size: 38
29585540 TAATGTTGTG
* * * *
29585550 TGATGATG-TTGAAGTGCGCGAGAAGGGAGTGCACACA
1 TGATGATGATAGAAGGGTGCGAGTAGGGAGTGCACACA
*
29585587 TGATGATGATAG-AGGGTGCGAGTAGGGGGTGCACACA
1 TGATGATGATAGAAGGGTGCGAGTAGGGAGTGCACACA
* *
29585624 TGATGAT-ATTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATAGAAGGGTGCGAGTAGGGAGTGCACACA
29585661 TGATGATGATA
1 TGATGATGATA
29585672 TTGCATTGAG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
36 3 0.04
37 66 0.90
38 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.38, T:0.22
Consensus pattern (38 bp):
TGATGATGATAGAAGGGTGCGAGTAGGGAGTGCACACA
Found at i:29589604 original size:40 final size:37
Alignment explanation
Indices: 29589551--29589658 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 37
29589541 CACACCCAAC
*
29589551 TCATGTACATCCCCCCACATCATGCACAT-AGCTGGCACCA
1 TCATGTACATCCCCCCACATCATGCACATCA-AT-G--CCA
* * *
29589591 TCGTGTGCATCCCCCCCTACATCGTGCACAATCAATGCCA
1 TCATGTACAT-CCCCCC-ACATCATGCAC-ATCAATGCCA
29589631 TCATGTACATCCCCCCACATCATGCACA
1 TCATGTACATCCCCCCACATCATGCACA
29589659 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
37 1 0.02
38 10 0.18
39 6 0.11
40 19 0.33
41 6 0.11
42 11 0.19
43 3 0.05
44 1 0.02
ACGTcount: A:0.26, C:0.41, G:0.12, T:0.21
Consensus pattern (37 bp):
TCATGTACATCCCCCCACATCATGCACATCAATGCCA
Found at i:29591775 original size:43 final size:43
Alignment explanation
Indices: 29591715--29591807 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
29591705 TTATGTGATA
*
29591715 ATGATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGGTGTAGGAGTGCACATGAGCTG
* *
29591758 ATGATGACCCAATTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGGTGTAGGAGTGCACATGAGCTG
29591801 ATGATGA
1 ATGATGA
29591808 TGATATTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAACTATGTGCGGTGTAGGAGTGCACATGAGCTG
Found at i:29595526 original size:22 final size:22
Alignment explanation
Indices: 29595484--29595524 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29595474 TACCTTTTGT
*
29595484 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
29595506 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
29595525 TCCACCAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:29604582 original size:17 final size:18
Alignment explanation
Indices: 29604552--29604585 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29604542 TAAAAAGAAA
29604552 AACATTTTCATGAAATAC
1 AACATTTTCATGAAATAC
*
29604570 AACA-TTTCTTGAAATA
1 AACATTTTCATGAAATA
29604586 AATTATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (18 bp):
AACATTTTCATGAAATAC
Found at i:29608929 original size:17 final size:17
Alignment explanation
Indices: 29608882--29608997 Score: 96
Period size: 17 Copynumber: 6.8 Consensus size: 17
29608872 GAGCCTTGCC
29608882 TTCCTTTCTCTCTTT-TT
1 TTCCTTTCT-TCTTTCTT
* *
29608899 CTTCATTTTTTTCTTTCTT
1 -TTC-CTTTCTTCTTTCTT
*
29608918 TTCTTTTCTTCTTTCTT
1 TTCCTTTCTTCTTTCTT
* *
29608935 CTCCTTTC-TCTTT-TC
1 TTCCTTTCTTCTTTCTT
*
29608950 TTCATTTCTTTCTTTCTT
1 TTCCTTTC-TTCTTTCTT
29608968 TTCCTTTCTTCTTTCTT
1 TTCCTTTCTTCTTTCTT
**
29608985 CACCTTTC-TCTTT
1 TTCCTTTCTTCTTT
29608998 TCTTCTTGGT
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.09
16 10 0.12
17 39 0.48
18 19 0.23
19 6 0.07
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCCTTTCTTCTTTCTT
Found at i:29608947 original size:33 final size:35
Alignment explanation
Indices: 29608909--29608984 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 35
29608899 CTTCATTTTT
*
29608909 TTCTTTCTTTTCTTTTC-TTCTTTCTTCTCCTTTC
1 TTCTTTCTTTTCATTTCTTTCTTTCTTCTCCTTTC
* *
29608943 -TCTTT-TCTTCATTTCTTTCTTTCTTTTCCTTTC
1 TTCTTTCTTTTCATTTCTTTCTTTCTTCTCCTTTC
29608976 TTCTTTCTT
1 TTCTTTCTT
29608985 CACCTTTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 8 0.23
33 21 0.60
34 5 0.14
35 1 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (35 bp):
TTCTTTCTTTTCATTTCTTTCTTTCTTCTCCTTTC
Found at i:29608962 original size:50 final size:50
Alignment explanation
Indices: 29608890--29609002 Score: 190
Period size: 50 Copynumber: 2.2 Consensus size: 50
29608880 CCTTCCTTTC
* * *
29608890 TCTCTTTTTCTTCATTTTTTTCTTTCTTTTCTTTTCTTCTTTCTTCTCCTT
1 TCTC-TTTTCTTCATTTCTTTCTTTCTTTTCCTTTCTTCTTTCTTCACCTT
29608941 TCTCTTTTCTTCATTTCTTTCTTTCTTTTCCTTTCTTCTTTCTTCACCTT
1 TCTCTTTTCTTCATTTCTTTCTTTCTTTTCCTTTCTTCTTTCTTCACCTT
29608991 TCTCTTTTCTTC
1 TCTCTTTTCTTC
29609003 TTGGTTATGG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
50 55 0.93
51 4 0.07
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (50 bp):
TCTCTTTTCTTCATTTCTTTCTTTCTTTTCCTTTCTTCTTTCTTCACCTT
Found at i:29608985 original size:33 final size:32
Alignment explanation
Indices: 29608922--29609003 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
29608912 TTTCTTTTCT
29608922 TTTCTTCTTTCTTCTCCTTTCTCTTTTCTTCA
1 TTTCTTCTTTCTTCTCCTTTCTCTTTTCTTCA
*
29608954 TTTCTTTCTTTCTTTTCCTTTCT-TCTTTCTTCA
1 TTTC-TTCTTTCTTCTCCTTTCTCT-TTTCTTCA
29608987 CCTTTC-TCTTTTCTTCT
1 --TTTCTTC-TTTCTTCT
29609004 TGGTTATGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 5 0.12
33 27 0.63
34 7 0.16
35 4 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (32 bp):
TTTCTTCTTTCTTCTCCTTTCTCTTTTCTTCA
Found at i:29612041 original size:39 final size:39
Alignment explanation
Indices: 29611953--29612129 Score: 218
Period size: 39 Copynumber: 4.6 Consensus size: 39
29611943 TCATCTCAGC
* * * * *
29611953 TCATATGCACTCCTACACCGCACATAGC-TA-AT-ATCC
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * *
29611989 TCATGTGCACTCCCACACGGCACATGGCAAATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
*
29612028 TCATGTGTTCTCCCACACCGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
29612067 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCTA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATC-A
* *
29612107 T-GTGTGCTCTCTCACACCGCACA
1 TCATGTGCTCTCCCACACCGCACA
29612130 CTACTAGCAC
Statistics
Matches: 124, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
36 24 0.19
37 1 0.01
38 2 0.02
39 95 0.77
40 2 0.02
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
Found at i:29612083 original size:78 final size:74
Alignment explanation
Indices: 29611962--29612165 Score: 232
Period size: 78 Copynumber: 2.7 Consensus size: 74
29611952 CTCATATGCA
* * *
29611962 CTCCTACACCGCACATAGCTAATATCCTCATGTGCACTCCCACACGGCACATGGCAAATATCATC
1 CTCCCACACCGCACATAGCTAATATCATCATGTGCACTCCCACACCGCACATGGCAAATATCATC
29612027 ATCATGTGT-T
66 -T-ATGTGTCT
* * *
29612037 CTCCCACACCGCACATGGCATATATCATCATCATGTGCTCTCCCACACCGCACATGGCATATATC
1 CTCCCACACCGCACATAGC-TA-AT-ATCATCATGTGCACTCCCACACCGCACATGGCAAATATC
29612102 ATCTATGTGTGCT
63 ATCTATGTGT-CT
* ** * *
29612115 CTCTCACACCGCACACTA-CTAGCACCATCATGTGCACTCCCACACCACACA
1 CTCCCACACCGCACA-TAGCTAATATCATCATGTGCACTCCCACACCGCACA
29612166 CGCACGATTA
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
75 42 0.38
76 8 0.07
77 5 0.05
78 54 0.49
79 1 0.01
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (74 bp):
CTCCCACACCGCACATAGCTAATATCATCATGTGCACTCCCACACCGCACATGGCAAATATCATC
TATGTGTCT
Found at i:29613532 original size:18 final size:19
Alignment explanation
Indices: 29613493--29613532 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
29613483 TTAATATTTT
29613493 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
29613512 AATATTATTTTATTC-TAA
1 AATATTATTTTATTCATAA
29613530 AAT
1 AAT
29613533 TCTCCACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:29619026 original size:28 final size:28
Alignment explanation
Indices: 29618994--29619054 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
29618984 TTGAGCCTAG
29618994 CCTTAAAATAAAATGACAATTTTGCAAC
1 CCTTAAAATAAAATGACAATTTTGCAAC
29619022 CCTTAAAATAAAATGACAATTTTGCAAC
1 CCTTAAAATAAAATGACAATTTTGCAAC
29619050 CCTTA
1 CCTTA
29619055 CTTCTAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.30
Consensus pattern (28 bp):
CCTTAAAATAAAATGACAATTTTGCAAC
Found at i:29621569 original size:2 final size:2
Alignment explanation
Indices: 29621562--29621589 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29621552 CATTATGATG
29621562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29621590 GTTGTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29621675 original size:95 final size:94
Alignment explanation
Indices: 29621566--29621751 Score: 363
Period size: 95 Copynumber: 2.0 Consensus size: 94
29621556 ATGATGATAT
29621566 ATATATATATATATATATATATATGTTGTGCATGATAGTTGATATTGTGTATGTTGACTATAACC
1 ATATATATATATATATATATATATGTTGTGCATGATAGTTGATATTGTGTATGTTGACTATAACC
29621631 GTGTGTGTGCACGATGTGAGGGGANTGATG
66 GTGTGTGTGCACGATGTGAGGGGA-TGATG
29621661 ATATATATATATATATATATATATGTTGTGCATGATAGTTGATATTGTGTATGTTGACTATAACC
1 ATATATATATATATATATATATATGTTGTGCATGATAGTTGATATTGTGTATGTTGACTATAACC
29621726 GTGTGTGTGCACGATGTGAGGGGATG
66 GTGTGTGTGCACGATGTGAGGGGATG
29621752 CACATGCCGG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 2 0.02
95 89 0.98
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.39
Consensus pattern (94 bp):
ATATATATATATATATATATATATGTTGTGCATGATAGTTGATATTGTGTATGTTGACTATAACC
GTGTGTGTGCACGATGTGAGGGGATGATG
Found at i:29621906 original size:40 final size:38
Alignment explanation
Indices: 29621802--29621907 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 38
29621792 ATAGTGCCCG
**
29621802 TGTGCACGATGTGGGGGGATGTACACCATGGAACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGAACTGAT
* * *
29621840 TGTGCACGATGTGGGGGGATGCACATGATGGCATCTGCT
1 TGTGCACGATGTGGGGGGATGTACATGATGG-AACTGAT
*
29621879 ATGTGCACGATGTGGGGGGATATACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
29621908 GCCGGGTGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 28 0.47
39 5 0.08
40 26 0.44
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGAACTGAT
Found at i:29624558 original size:20 final size:20
Alignment explanation
Indices: 29624529--29624571 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
29624519 CAAGAGGAAA
29624529 TTTTTGGAATAAAATAATAT
1 TTTTTGGAATAAAATAATAT
*
29624549 TTTTTTGAATAAAATAATAT
1 TTTTTGGAATAAAATAATAT
29624569 TTT
1 TTT
29624572 ATTCATGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTTTGGAATAAAATAATAT
Found at i:29626193 original size:42 final size:42
Alignment explanation
Indices: 29626131--29626295 Score: 226
Period size: 42 Copynumber: 3.9 Consensus size: 42
29626121 GTGATAATTA
*
29626131 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATAAGCTGTGC
* *
29626173 TGACCTAGCCATGT-CTGGTGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGC-GGTGTAGGAGTGCACATAAGCTGTGC
* * *
29626215 TAACCCAGCCATGTGCGGTGTATGAGTGCACATAAGTTGTGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATAAGCTGTGC
* *
29626257 TGACCCGGCTATGTGCGGTGT-GGTAGTGCACATAAGCTG
1 TGACCCAGCCATGTGCGGTGTAGG-AGTGCACATAAGCTG
29626296 AGATAGAGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
41 2 0.02
42 106 0.97
43 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (42 bp):
TGACCCAGCCATGTGCGGTGTAGGAGTGCACATAAGCTGTGC
Found at i:29626331 original size:2 final size:2
Alignment explanation
Indices: 29626324--29626379 Score: 53
Period size: 2 Copynumber: 28.0 Consensus size: 2
29626314 GGTCGGTGGT
* * *
29626324 TA TA TA TA TA TT TA TA TA TGG TA TA -A TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
29626366 TA TA T- TGA TA TA TA
1 TA TA TA T-A TA TA TA
29626380 GAGGTTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29628383 original size:20 final size:20
Alignment explanation
Indices: 29628358--29628396 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29628348 CATTCTGCTA
*
29628358 AGAATGTATCGATACATTTG
1 AGAATGTATCAATACATTTG
*
29628378 AGAATGTATTAATACATTT
1 AGAATGTATCAATACATTT
29628397 TTCCCTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (20 bp):
AGAATGTATCAATACATTTG
Found at i:29635411 original size:22 final size:21
Alignment explanation
Indices: 29635386--29635441 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
29635376 TTAATCACTC
*
29635386 TGTGACTAGTTTTTAGGCATTA
1 TGTGA-TAGATTTTAGGCATTA
*
29635408 TGTGATTGATTTTAGGCATTA
1 TGTGATAGATTTTAGGCATTA
* *
29635429 CGTGATTGATTTT
1 TGTGATAGATTTT
29635442 TAAACATTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.48
Consensus pattern (21 bp):
TGTGATAGATTTTAGGCATTA
Found at i:29635422 original size:21 final size:21
Alignment explanation
Indices: 29635396--29635441 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
29635386 TGTGACTAGT
*
29635396 TTTTAGGCATTATGTGATTGA
1 TTTTAGGCATTACGTGATTGA
29635417 TTTTAGGCATTACGTGATTGA
1 TTTTAGGCATTACGTGATTGA
29635438 TTTT
1 TTTT
29635442 TAAACATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.50
Consensus pattern (21 bp):
TTTTAGGCATTACGTGATTGA
Found at i:29635449 original size:22 final size:22
Alignment explanation
Indices: 29635403--29635466 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
29635393 AGTTTTTAGG
* **
29635403 CATTATGTGATTGA-TTTTAGG
1 CATTACGTGATTGATTTTTAAA
29635424 CATTACGTGATTGATTTTTAAA
1 CATTACGTGATTGATTTTTAAA
* *
29635446 CATTGCGTGACTGATTTTTAA
1 CATTACGTGATTGATTTTTAA
29635467 GCAATACCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (22 bp):
CATTACGTGATTGATTTTTAAA
Found at i:29635507 original size:23 final size:23
Alignment explanation
Indices: 29635476--29635584 Score: 132
Period size: 23 Copynumber: 4.8 Consensus size: 23
29635466 AGCAATACCT
*
29635476 AAGTCACGCAATGCCTTACTAGC
1 AAGTCACGCAATGCCTTACTAAC
*
29635499 TAGTCACGCAATGCCTTACTAAC
1 AAGTCACGCAATGCCTTACTAAC
* **
29635522 AAGTTATACAATGCCTTACTAAC
1 AAGTCACGCAATGCCTTACTAAC
*
29635545 AAGTCACACAATGCC-TA-TCAAC
1 AAGTCACGCAATGCCTTACT-AAC
*
29635567 TAGTCACGCAATGCCTTA
1 AAGTCACGCAATGCCTTA
29635585 TCAGAAACTA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.01
22 18 0.24
23 55 0.74
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (23 bp):
AAGTCACGCAATGCCTTACTAAC
Found at i:29635593 original size:26 final size:26
Alignment explanation
Indices: 29635564--29635706 Score: 161
Period size: 26 Copynumber: 5.7 Consensus size: 26
29635554 AATGCCTATC
*
29635564 AACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
29635590 AACTAATCACACAATGTCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
*
29635616 AACTACTCACGCAATG-C---TCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
29635638 ATC-AGTCATGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCAAA
*
29635663 AACTAGTCACGTAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
*
29635689 AACTAGTCATGCAATGCC
1 AACTAGTCACGCAATGCC
29635707 CAAAGTCAGT
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
21 10 0.10
22 8 0.08
25 7 0.07
26 71 0.74
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (26 bp):
AACTAGTCACGCAATGCCTTATCAAA
Found at i:29635652 original size:73 final size:73
Alignment explanation
Indices: 29635568--29635719 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 73
29635558 CCTATCAACT
*
29635568 AGTCACGCAATGCCTTATCAGAAACTAATCACACAATGTCTTATCAAAAACTACTCACGCAATGC
1 AGTCACGCAATGCCTTATCAGAAACTAATCACACAATGCCTTATCAAAAACTACTCACGCAATGC
*
29635633 TCAAAATC
66 CCAAAATC
* * ** * *
29635641 AGTCATGCAATGCCTTATCAGAAACTAGTCACGTAATGCCTTATCAAAAACTAGTCATGCAATGC
1 AGTCACGCAATGCCTTATCAGAAACTAATCACACAATGCCTTATCAAAAACTACTCACGCAATGC
*
29635706 CCAAAGTC
66 CCAAAATC
29635714 AGTCAC
1 AGTCAC
29635720 ATAATATCCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (73 bp):
AGTCACGCAATGCCTTATCAGAAACTAATCACACAATGCCTTATCAAAAACTACTCACGCAATGC
CCAAAATC
Found at i:29635658 original size:47 final size:50
Alignment explanation
Indices: 29635564--29635706 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 50
29635554 AATGCCTATC
* * * ** *
29635564 AACTAGTCACGCAATGCCTTATCAGAAACTAATCACACAATGTCTTATCAAA
1 AACTACTCACGCAATGCC-T-TCAAAAACTAGTCATGCAATGCCTTATCAAA
* *
29635616 AACTACTCACGCAATG-C-TCAAAATC-AGTCATGCAATGCCTTATCAGA
1 AACTACTCACGCAATGCCTTCAAAAACTAGTCATGCAATGCCTTATCAAA
* *
29635663 AACTAGTCACGTAATGCCTTATCAAAAACTAGTCATGCAATGCC
1 AACTACTCACGCAATGCC-T-TCAAAAACTAGTCATGCAATGCC
29635707 CAAAGTCAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
47 31 0.41
48 7 0.09
51 8 0.11
52 29 0.39
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (50 bp):
AACTACTCACGCAATGCCTTCAAAAACTAGTCATGCAATGCCTTATCAAA
Found at i:29635775 original size:22 final size:22
Alignment explanation
Indices: 29635612--29635776 Score: 75
Period size: 21 Copynumber: 7.3 Consensus size: 22
29635602 AATGTCTTAT
* *
29635612 CAAAAACTACTCACGCAATGCT
1 CAAAAACTAGTCACGCAATGCC
* *
29635634 CAAAATC-AGTCATGCAATGCC
1 CAAAAACTAGTCACGCAATGCC
* *
29635655 TTATCAGAAACTAGTCACGTAATGCC
1 ----CAAAAACTAGTCACGCAATGCC
*
29635681 TTATCAAAAACTAGTCATGCAATGCC
1 ----CAAAAACTAGTCACGCAATGCC
** ** **
29635707 CAAAGTC-AGTCACATAATATC
1 CAAAAACTAGTCACGCAATGCC
**
29635728 CAAAGTC-AGTCACGCAATGCC
1 CAAAAACTAGTCACGCAATGCC
* * *
29635749 TAAAAACTAGTCACGTAATTCC
1 CAAAAACTAGTCACGCAATGCC
29635771 CAAAAA
1 CAAAAA
29635777 TCACCAAAAC
Statistics
Matches: 109, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
21 41 0.38
22 28 0.26
25 5 0.05
26 35 0.32
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (22 bp):
CAAAAACTAGTCACGCAATGCC
Found at i:29643867 original size:22 final size:21
Alignment explanation
Indices: 29643842--29643882 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29643832 AGTGGCAAGC
29643842 AAAACAATAAATTGGCTAAAGA
1 AAAACAATAAATTGG-TAAAGA
*
29643864 AAAACAATATATTGGTAAA
1 AAAACAATAAATTGGTAAA
29643883 ATATGGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAACAATAAATTGGTAAAGA
Found at i:29646924 original size:36 final size:36
Alignment explanation
Indices: 29646847--29646936 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
29646837 AGGGTACACT
* * * * * *
29646847 TGATCTTG-TAAAATGTATGTTGTGAAGGTTATGCT
1 TGATCTTGTTAAAAGGCATGTTGTAAAAGTTACGCC
*
29646882 TAATCTTGTTAAAAGGCATGTTGTAAAAGTTACGCC
1 TGATCTTGTTAAAAGGCATGTTGTAAAAGTTACGCC
*
29646918 TGATCTTATTGAAAAGGCA
1 TGATCTTGTT-AAAAGGCA
29646937 AGCTGATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 7 0.16
36 29 0.66
37 8 0.18
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (36 bp):
TGATCTTGTTAAAAGGCATGTTGTAAAAGTTACGCC
Found at i:29647773 original size:22 final size:22
Alignment explanation
Indices: 29647718--29647775 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
29647708 GCAATTCCCA
* *
29647718 AAACTAGTCACACAATGCCTAC
1 AAACAAGTCACGCAATGCCTAC
29647740 AAACAAGTCACGCAATGCCTAC
1 AAACAAGTCACGCAATGCCTAC
*
29647762 AAACCAGTCACGCA
1 AAACAAGTCACGCA
29647776 TTGCACAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.33, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGTCACGCAATGCCTAC
Found at i:29649857 original size:46 final size:46
Alignment explanation
Indices: 29649783--29649917 Score: 234
Period size: 46 Copynumber: 2.9 Consensus size: 46
29649773 GTTGGCAGAT
29649783 TAGTTACAGCCACTTAATTAGCCGCGCAACTGTGAACACGAGCCTG
1 TAGTTACAGCCACTTAATTAGCCGCGCAACTGTGAACACGAGCCTG
* *
29649829 TATTTACAGCCACTTAATTAGCCACGCAACTGTGAACACGAGCCTG
1 TAGTTACAGCCACTTAATTAGCCGCGCAACTGTGAACACGAGCCTG
* *
29649875 TAGTTACAGCCACTTAATTAGCCGCTCAAGTGTGAACACGAGC
1 TAGTTACAGCCACTTAATTAGCCGCGCAACTGTGAACACGAGC
29649918 TTTTTTCTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAGTTACAGCCACTTAATTAGCCGCGCAACTGTGAACACGAGCCTG
Found at i:29650779 original size:26 final size:27
Alignment explanation
Indices: 29650740--29650796 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
29650730 ATATATGAAC
* ** *
29650740 AAATAGAATATAATTGAAAAAATAAAT
1 AAATACAATATAATAAAAAAAATAAAA
29650767 AAATACAA-ATAATAAAAAAAATAAAA
1 AAATACAATATAATAAAAAAAATAAAA
29650793 AAAT
1 AAAT
29650797 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (27 bp):
AAATACAATATAATAAAAAAAATAAAA
Found at i:29651653 original size:22 final size:23
Alignment explanation
Indices: 29651627--29651676 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
29651617 ATGTTTCATA
*
29651627 ATATAAAA-TGTTATGAATATA-T
1 ATATAAAATTG-TATAAATATATT
*
29651649 ATATATAATTGTATAAATATATT
1 ATATAAAATTGTATAAATATATT
29651672 ATATA
1 ATATA
29651677 TACATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATAAAATTGTATAAATATATT
Found at i:29651729 original size:22 final size:22
Alignment explanation
Indices: 29651678--29651732 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
29651668 TATTATATAT
29651678 ACATATATTTAATTTATACATAA
1 ACAT-TATTTAATTTATACATAA
*
29651701 GCATTATTATAATTTATA-ATAA
1 ACATTATT-TAATTTATACATAA
*
29651723 ACTTTATTTA
1 ACATTATTTA
29651733 TATGATTNTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.07
22 14 0.50
23 12 0.43
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
ACATTATTTAATTTATACATAA
Found at i:29661868 original size:13 final size:13
Alignment explanation
Indices: 29661850--29661874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29661840 TGAAAATAGG
29661850 TTTTATTGATTTC
1 TTTTATTGATTTC
29661863 TTTTATTGATTT
1 TTTTATTGATTT
29661875 TAGTAGGGGT
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:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTATTGATTTC
Found at i:29662596 original size:2 final size:2
Alignment explanation
Indices: 29662589--29662639 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
29662579 TAATTTTATC
* *
29662589 TA TA TA TA TA TA -A TA AA GTCA TC TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA
29662631 TA TA TA TA T
1 TA TA TA TA T
29662640 TTAATTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 1 0.02
4 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29665367 original size:35 final size:35
Alignment explanation
Indices: 29665339--29665567 Score: 224
Period size: 35 Copynumber: 6.5 Consensus size: 35
29665329 CTTAATTGTT
* *
29665339 TAATTTAATCAATTAGGCCTAATAACTTAATCAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
29665374 TAATTTAATTAATTAAGCCCAACAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
29665409 CAATTTTAATCAACTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAA
* ***
29665445 CAAATTTAATCAATTAGGCCCAATAACTTAATTGTT
1 -TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
29665481 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * ** * *
29665516 CAATTTAATTAATTAGATCCAATTATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
29665551 CAATTTAGTTAATTAGG
1 TAATTTAATCAATTAGG
29665568 AACAACTTAA
Statistics
Matches: 160, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
35 105 0.66
36 53 0.33
37 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:29665470 original size:107 final size:105
Alignment explanation
Indices: 29665340--29665567 Score: 285
Period size: 107 Copynumber: 2.2 Consensus size: 105
29665330 TTAATTGTTT
* *
29665340 AATTTAATCAATTAGGCCTAATAACTTAATCAAATAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATCAAATAATTTAATTAATTAAGCCCAACAACTTAAT
*
29665405 TAAACAATTTTAATCAACTAGGCCCAATGACTTAATTAAAC
66 TAAACAA-TTTAATCAACTAGACCCAATGACTTAATTAAAC
**** * **
29665446 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAA
1 -AATTTAATCAATTAGGCCCAATAACTTAATCAAATAATTTAATTAATTAAGCCCAACAACTTAA
* * * * *
29665511 TTAAACAATTTAATTAATTAGATCCAATTATTTAATTAAAC
65 TTAAACAATTTAATCAACTAGACCCAATGACTTAATTAAAC
* *
29665552 AATTTAGTTAATTAGG
1 AATTTAATCAATTAGG
29665568 AACAACTTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
105 14 0.13
106 27 0.26
107 63 0.61
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATCAAATAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTAATCAACTAGACCCAATGACTTAATTAAAC
Found at i:29670114 original size:16 final size:16
Alignment explanation
Indices: 29670086--29670120 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29670076 AACAAAAAAT
29670086 AATTAAAAGAAATAAA
1 AATTAAAAGAAATAAA
29670102 AATTGAAAA-AAATAAA
1 AATT-AAAAGAAATAAA
29670118 AAT
1 AAT
29670121 GAAGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (16 bp):
AATTAAAAGAAATAAA
Found at i:29671694 original size:17 final size:18
Alignment explanation
Indices: 29671672--29671709 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29671662 AAATAAATTG
29671672 TTACAT-TA-ATTATTATT
1 TTACATATATATTA-TATT
29671689 TTACATATATATTATATT
1 TTACATATATATTATATT
29671707 TTA
1 TTA
29671710 ATGGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TTACATATATATTATATT
Found at i:29672592 original size:7 final size:7
Alignment explanation
Indices: 29672575--29672629 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
29672565 TGTTATTTGC
29672575 TATTTTAT
1 TATTTT-T
29672583 TATTTTT
1 TATTTTT
29672590 TATCTTTT
1 TAT-TTTT
*
29672598 TATTATT
1 TATTTTT
*
29672605 TATTTAT
1 TATTTTT
29672612 TA-TTTT
1 TATTTTT
*
29672618 TATTTAT
1 TATTTTT
29672625 TATTT
1 TATTT
29672630 CGTTTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
6 5 0.12
7 22 0.55
8 13 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTTTT
Found at i:29672636 original size:13 final size:11
Alignment explanation
Indices: 29672579--29672646 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 11
29672569 ATTTGCTATT
*
29672579 TTATTATTTT-
1 TTATTTTTTTA
*
29672589 TTATCTTTTTA
1 TTATTTTTTTA
*
29672600 TTATTTATTTA
1 TTATTTTTTTA
29672611 TTATTTTTATTTA
1 TTA-TTTT-TTTA
29672624 TTATTTCGTTTTA
1 TTATTT--TTTTA
29672637 -TATTTTTTTA
1 TTATTTTTTTA
29672647 AAACAATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
10 13 0.27
11 12 0.25
12 11 0.23
13 11 0.23
14 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:29672835 original size:16 final size:16
Alignment explanation
Indices: 29672806--29672855 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
29672796 TATATTTTAT
*
29672806 TATTTACTTATTATTTC
1 TATTT-CTTTTTATTTC
29672823 TATTTCTTTTTATTAT-
1 TATTTCTTTTTATT-TC
29672839 TATATT-TTTTTATTTC
1 TAT-TTCTTTTTATTTC
29672855 T
1 T
29672856 TTATTCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.03
16 20 0.69
17 8 0.28
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTCTTTTTATTTC
Found at i:29672863 original size:33 final size:31
Alignment explanation
Indices: 29672800--29672880 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 31
29672790 AAAATGTATA
* *
29672800 TTTTATTATTTA-CTTATTATTTCTATTTCT
1 TTTTATTATTTATTTTTTTATTTCTATTTCT
*
29672830 TTTTATTATTATATTTTTTTATTTCTTTATTCT
1 TTTTATTATT-TATTTTTTTATTTCTAT-TTCT
* *
29672863 TCTTCATAATTTATTTTT
1 T-TTTATTATTTATTTTT
29672881 ACTTTTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 10 0.24
31 2 0.05
32 11 0.26
33 12 0.29
34 7 0.17
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTATTATTTATTTTTTTATTTCTATTTCT
Found at i:29673237 original size:9 final size:9
Alignment explanation
Indices: 29673225--29673267 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
29673215 AACCTTTTCC
29673225 TTCTTTTTT
1 TTCTTTTTT
*
29673234 TTCTTTTCT
1 TTCTTTTTT
29673243 TTCTTTCTTT
1 TTCTTT-TTT
*
29673253 TCCTTTTTCT
1 TTCTTTTT-T
29673263 TTCTT
1 TTCTT
29673268 CTTCTCTCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:29673241 original size:18 final size:19
Alignment explanation
Indices: 29673217--29673259 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
29673207 TGACCCAAAA
29673217 CCTTTTCCTTCTTT-TTTT
1 CCTTTTCCTTCTTTCTTTT
* *
29673235 TCTTTTCTTTCTTTCTTTT
1 CCTTTTCCTTCTTTCTTTT
29673254 CCTTTT
1 CCTTTT
29673260 TCTTTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
CCTTTTCCTTCTTTCTTTT
Found at i:29673249 original size:13 final size:12
Alignment explanation
Indices: 29673231--29673264 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29673221 TTCCTTCTTT
*
29673231 TTTTTCTTTTCT
1 TTTTTCTTTTCC
29673243 TTCTTTCTTTTCC
1 TT-TTTCTTTTCC
29673256 TTTTTCTTT
1 TTTTTCTTT
29673265 CTTCTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTTCC
Found at i:29673360 original size:70 final size:70
Alignment explanation
Indices: 29673230--29673366 Score: 165
Period size: 70 Copynumber: 2.0 Consensus size: 70
29673220 TTTCCTTCTT
* * *
29673230 TTTTTTCTTTTCTTTCTTTCTTTTCCTTTTTCTTTCTTCTTCTCTCCCAGCCGCTCCTTCTTTCT
1 TTTTTTCTTTTCTTTCTTTCTTTTCCCTTTCCTTTCTTCTTCTCTCCCAGCAGCTCCTTCTTTCT
29673295 TTTTC
66 TTTTC
* *
29673300 TTTTTTCTTTTTTTTCTTCTCTTTCTCTCCTTTCCTTTC-TC-TCTC-CCC-GCTAGCTTCTTCT
1 TTTTTTCTTTTCTTTCTT-TCTTT-TC-CCTTTCCTTTCTTCTTCTCTCCCAGC-AGCTCCTTCT
29673361 TTCTTT
62 TTCTTT
29673367 CTCCTTCTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
69 2 0.03
70 34 0.59
71 9 0.16
72 4 0.07
73 9 0.16
ACGTcount: A:0.01, C:0.32, G:0.03, T:0.64
Consensus pattern (70 bp):
TTTTTTCTTTTCTTTCTTTCTTTTCCCTTTCCTTTCTTCTTCTCTCCCAGCAGCTCCTTCTTTCT
TTTTC
Found at i:29673917 original size:17 final size:16
Alignment explanation
Indices: 29673889--29673949 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
29673879 ACCATTCCTC
* *
29673889 TTTTTTTTTTATTATA
1 TTTTTATTTTATTTTA
*
29673905 TATATTATTTTATTTTA
1 T-TTTTATTTTATTTTA
29673922 TTTTATATTTTATTTTA
1 TTTT-TATTTTATTTTA
29673939 TTTTTTATTTT
1 -TTTTTATTTT
29673950 TTGAGGTGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 3 0.08
17 31 0.82
18 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:29673920 original size:22 final size:22
Alignment explanation
Indices: 29673890--29673946 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
29673880 CCATTCCTCT
*
29673890 TTTTTTTTTATTATATATATTA
1 TTTTATTTTATTATATATATTA
* *
29673912 TTTTATTTTATTTTATATTTTA
1 TTTTATTTTATTATATATATTA
29673934 TTTTATTTT-TTAT
1 TTTTATTTTATTAT
29673947 TTTTTGAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATTTTATTATATATATTA
Found at i:29673930 original size:12 final size:12
Alignment explanation
Indices: 29673895--29673949 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
29673885 CCTCTTTTTT
*
29673895 TTTTATTATATA
1 TTTTATTTTATA
*
29673907 TATTA-TTT-TA
1 TTTTATTTTATA
29673917 TTTTATTTTATA
1 TTTTATTTTATA
*
29673929 TTTTATTTTATT
1 TTTTATTTTATA
29673941 TTTTATTTT
1 TTTTATTTT
29673950 TTGAGGTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 6 0.16
11 5 0.14
12 26 0.70
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:29673949 original size:5 final size:5
Alignment explanation
Indices: 29673890--29673942 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
29673880 CCATTCCTCT
* *
29673890 TTTTT TTTTA TTATATA TATTA TTTTA TTTTA TTTTATA TTTTA TTTTA
1 TTTTA TTTTA TT-T-TA TTTTA TTTTA TTTTA -TTT-TA TTTTA TTTTA
29673939 TTTT
1 TTTT
29673943 TTATTTTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 28 0.68
6 8 0.20
7 5 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:29680465 original size:14 final size:14
Alignment explanation
Indices: 29680446--29680472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29680436 TTTCTATTCA
29680446 TTCTTTATTTTTTT
1 TTCTTTATTTTTTT
29680460 TTCTTTATTTTTT
1 TTCTTTATTTTTT
29680473 AATTTTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTATTTTTTT
Found at i:29683313 original size:20 final size:20
Alignment explanation
Indices: 29683288--29683332 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
29683278 CGTCATTTCT
29683288 CCAATTTGAAATTTGGTCAA
1 CCAATTTGAAATTTGGTCAA
29683308 CCAATTTGAAATTTGGTCAA
1 CCAATTTGAAATTTGGTCAA
29683328 CCAAT
1 CCAAT
29683333 ATTCTTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CCAATTTGAAATTTGGTCAA
Found at i:29696404 original size:24 final size:24
Alignment explanation
Indices: 29696350--29696404 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
29696340 CATGGTGCTT
*
29696350 TTGCTGCTCATCATGCTACTACTC
1 TTGCTGCTCATCATCCTACTACTC
* * * * *
29696374 TTACTGCTGATCCTCCTACTTCTG
1 TTGCTGCTCATCATCCTACTACTC
29696398 TTGCTGC
1 TTGCTGC
29696405 CCTTCCTTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.13, C:0.33, G:0.15, T:0.40
Consensus pattern (24 bp):
TTGCTGCTCATCATCCTACTACTC
Found at i:29696619 original size:24 final size:24
Alignment explanation
Indices: 29696565--29696621 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29696555 GCAGATACAT
29696565 GCAATGCAATTGAAGATCCAGCAG
1 GCAATGCAATTGAAGATCCAGCAG
* *
29696589 TCAATGCAATT-AGAGATCCAGCGG
1 GCAATGCAATTGA-AGATCCAGCAG
*
29696613 GCGATGCAA
1 GCAATGCAA
29696622 ATGCAGATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (24 bp):
GCAATGCAATTGAAGATCCAGCAG
Found at i:29698272 original size:26 final size:26
Alignment explanation
Indices: 29698232--29698283 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29698222 AACATTATTC
*
29698232 TGTATCATTTCCATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
29698258 TGTATCATTTACATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
29698284 ATTCATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (26 bp):
TGTATCATTTACATATTATTCTTTGT
Found at i:29698283 original size:23 final size:23
Alignment explanation
Indices: 29698225--29698290 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 23
29698215 TGTAAATAAC
*
29698225 ATTATTC--TGTATCATTTCCAT
1 ATTATTCTTTGTATCATTTACAT
29698246 ATTATTCTTTGTTGTATCATTTACAT
1 ATTATTC--T-TTGTATCATTTACAT
29698272 ATTATTCTTTGTATTCATT
1 ATTATTCTTTGTA-TCATT
29698291 CATGTGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 7 0.18
23 5 0.13
24 6 0.16
26 20 0.53
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTATTCTTTGTATCATTTACAT
Found at i:29698647 original size:22 final size:23
Alignment explanation
Indices: 29698577--29698649 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
29698567 TATGGAGTCA
* ** *
29698577 CGTGAGTACTAAATTTTGAATCA
1 CGTGAGTAGTAAATAATGAATCG
** *
29698600 CGCCAGTAGTTAATAATGAATCG
1 CGTGAGTAGTAAATAATGAATCG
*
29698623 CGTGAGTAGTAAAT-ATGGATCG
1 CGTGAGTAGTAAATAATGAATCG
29698645 CGTGA
1 CGTGA
29698650 ACCGTTAAGA
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (23 bp):
CGTGAGTAGTAAATAATGAATCG
Found at i:29698732 original size:23 final size:23
Alignment explanation
Indices: 29698706--29698942 Score: 92
Period size: 23 Copynumber: 10.3 Consensus size: 23
29698696 GAGTAGTACA
* *
29698706 TATGGAGTGGCGTTACTAGTTAT
1 TATGGAGTCGCGTGACTAGTTAT
* *
29698729 TATGGAAG-CACGTGACTAGTTTT
1 TATGG-AGTCGCGTGACTAGTTAT
*
29698752 TGTGGAAG-CGCGTGACTAGTTGA-
1 TATGG-AGTCGCGTGACTAGTT-AT
* * * *
29698775 TATTGACTCGCGTGAGTA-ATAT
1 TATGGAGTCGCGTGACTAGTTAT
* *
29698797 ATATGGAGTGGCGTTACTAGTTAT
1 -TATGGAGTCGCGTGACTAGTTAT
* * * *
29698821 TATGGAATGGCGTGAGTATTTAT
1 TATGGAGTCGCGTGACTAGTTAT
* ** * * * * *
29698844 TCTAAAATCACGTGAGTAG-AAA
1 TATGGAGTCGCGTGACTAGTTAT
* * *
29698866 AATGGAGTTGCGTGACTGGTTAT
1 TATGGAGTCGCGTGACTAGTTAT
* * * *
29698889 TATGGAATTGCATTACTAGTTGA-
1 TATGGAGTCGCGTGACTAGTT-AT
*
29698912 TATGGAGTCGCGTGAGTAG-TAT
1 TATGGAGTCGCGTGACTAGTTAT
29698934 ATATGGAGT
1 -TATGGAGT
29698943 GGCATTACCA
Statistics
Matches: 153, Mismatches: 51, Indels: 20
0.68 0.23 0.09
Matches are distributed among these distances:
21 2 0.01
22 14 0.09
23 131 0.86
24 6 0.04
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (23 bp):
TATGGAGTCGCGTGACTAGTTAT
Found at i:29698816 original size:46 final size:46
Alignment explanation
Indices: 29698686--29698838 Score: 130
Period size: 46 Copynumber: 3.3 Consensus size: 46
29698676 TAGGGTATAC
* *
29698686 TGACTCGTGTGAGTAGTACATATGGAGTGGCGTTACTAGTTATTAT
1 TGACTCGCGTGAGTAGTATATATGGAGTGGCGTTACTAGTTATTAT
* ** * * * * * * *
29698732 GGAAGCACGTGACTAGTTTTTGTGGAAG-CGCGTGACTAGTTGA-TAT
1 TGACTCGCGTGAGTAGTATATATGG-AGTGGCGTTACTAGTT-ATTAT
*
29698778 TGACTCGCGTGAGTAATATATATGGAGTGGCGTTACTAGTTATTAT
1 TGACTCGCGTGAGTAGTATATATGGAGTGGCGTTACTAGTTATTAT
* * *
29698824 GGAATGGCGTGAGTA
1 TGACTCGCGTGAGTA
29698839 TTTATTCTAA
Statistics
Matches: 77, Mismatches: 26, Indels: 8
0.69 0.23 0.07
Matches are distributed among these distances:
45 3 0.04
46 71 0.92
47 3 0.04
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (46 bp):
TGACTCGCGTGAGTAGTATATATGGAGTGGCGTTACTAGTTATTAT
Found at i:29698858 original size:92 final size:92
Alignment explanation
Indices: 29698686--29698858 Score: 224
Period size: 92 Copynumber: 1.9 Consensus size: 92
29698676 TAGGGTATAC
* *
29698686 TGACTCGTGTGAGTAGTACATATGGAGTGGCGTTACTAGTTATTATGGAAGCACGTGACTAGTTT
1 TGACTCGCGTGAGTAATACATATGGAGTGGCGTTACTAGTTATTATGGAAGCACGTGACTAGTTT
* ** *
29698751 TTGTGGAAGCGCGTGACTAGTTGATAT
66 TTCTAAAAGCACGTGACTAGTTGATAT
* * *
29698778 TGACTCGCGTGAGTAATATATATGGAGTGGCGTTACTAGTTATTATGGAATG-GCGTGAGTA-TT
1 TGACTCGCGTGAGTAATACATATGGAGTGGCGTTACTAGTTATTATGGAA-GCACGTGACTAGTT
*
29698841 TATTCTAAAATCACGTGA
65 T-TTCTAAAAGCACGTGA
29698859 GTAGAAAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
91 3 0.04
92 65 0.94
93 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (92 bp):
TGACTCGCGTGAGTAATACATATGGAGTGGCGTTACTAGTTATTATGGAAGCACGTGACTAGTTT
TTCTAAAAGCACGTGACTAGTTGATAT
Found at i:29699015 original size:23 final size:23
Alignment explanation
Indices: 29698964--29699016 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
29698954 TTCCAAAGGA
* *
29698964 ATCGCATGACTAAATGATATGGG
1 ATCGCGTGACTAAATGATATCGG
*
29698987 ATCGCGTGACTAGATGATATCGG
1 ATCGCGTGACTAAATGATATCGG
29699010 ATCGCGT
1 ATCGCGT
29699017 CACTCACCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (23 bp):
ATCGCGTGACTAAATGATATCGG
Found at i:29701181 original size:61 final size:60
Alignment explanation
Indices: 29701098--29701383 Score: 209
Period size: 61 Copynumber: 4.6 Consensus size: 60
29701088 GAAACTGTAT
**
29701098 CTATCGATATATTTATCCTCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAATGGCAA
1 CTATCGATATATTTATAATCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAA-GGCAA
* * * * * ** *
29701159 CTATCGATATGTTTAAAATCTATCAATATAAA-TTGGAATACTT-AGAAGATGAAAGAAACGATA
1 CTATCGATATATTTATAATCTATCGATAGAAATTTCGAATGGTTCA-AAGATGAAAG--GC-A-A
** *
29701222 TCTATCGATATATTTATCTTCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAACGGCAG
1 -CTATCGATATATTTATAATCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAA-GGCAA
* * * * * ** ** *
29701284 CTATCGATATGTTTAGAATCTATTGATATAAA-TTGGAATACTTGGAAGATGAAAGAAACGATA
1 CTATCGATATATTTATAATCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAAG--GC-A-A
**
29701347 TCTATCGATATATTTATCTTCTATCGATAGAAATTTC
1 -CTATCGATATATTTATAATCTATCGATAGAAATTTC
29701384 AAATCGACAG
Statistics
Matches: 169, Mismatches: 41, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
59 3 0.02
60 34 0.20
61 54 0.32
62 2 0.01
63 2 0.01
64 53 0.31
65 19 0.11
66 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (60 bp):
CTATCGATATATTTATAATCTATCGATAGAAATTTCGAATGGTTCAAAGATGAAAGGCAA
Found at i:29701293 original size:125 final size:125
Alignment explanation
Indices: 29701071--29701383 Score: 547
Period size: 125 Copynumber: 2.5 Consensus size: 125
29701061 ACTTGGACTC
*
29701071 ATACTTGGAAGATGAAAGAAACTG-TATCTATCGATATATTTATCCTCTATCGATAGAAATTTCG
1 ATACTTGGAAGATGAAAGAAAC-GATATCTATCGATATATTTATCTTCTATCGATAGAAATTTCG
*
29701135 AATGGTTCAAAGATGAAATGGCAACTATCGATATGTTTAAAATCTATCAATATAAATTGGA
65 AATGGTTCAAAGATGAAACGGCAACTATCGATATGTTTAAAATCTATCAATATAAATTGGA
*
29701196 ATACTTAGAAGATGAAAGAAACGATATCTATCGATATATTTATCTTCTATCGATAGAAATTTCGA
1 ATACTTGGAAGATGAAAGAAACGATATCTATCGATATATTTATCTTCTATCGATAGAAATTTCGA
* * **
29701261 ATGGTTCAAAGATGAAACGGCAGCTATCGATATGTTTAGAATCTATTGATATAAATTGGA
66 ATGGTTCAAAGATGAAACGGCAACTATCGATATGTTTAAAATCTATCAATATAAATTGGA
29701321 ATACTTGGAAGATGAAAGAAACGATATCTATCGATATATTTATCTTCTATCGATAGAAATTTC
1 ATACTTGGAAGATGAAAGAAACGATATCTATCGATATATTTATCTTCTATCGATAGAAATTTC
29701384 AAATCGACAG
Statistics
Matches: 179, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 1 0.01
125 178 0.99
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (125 bp):
ATACTTGGAAGATGAAAGAAACGATATCTATCGATATATTTATCTTCTATCGATAGAAATTTCGA
ATGGTTCAAAGATGAAACGGCAACTATCGATATGTTTAAAATCTATCAATATAAATTGGA
Found at i:29701430 original size:110 final size:110
Alignment explanation
Indices: 29701281--29701513 Score: 369
Period size: 110 Copynumber: 2.1 Consensus size: 110
29701271 GATGAAACGG
*
29701281 CAGCTATCGATATGTTTAGAATCTATTGATATAAATTGGAATACTTGGAAGATGAAAGAAAC-GA
1 CAGCTATCGATATGTTTAGAATCTATCGATATAAATTGGAATACTTGGAAGATGAAAGAAACTG-
*
29701345 TATCTATCGATATATTTATCTTCTATCGATAGAAATTTCAAATCGA
65 TATCTATCAATATATTTATCTTCTATCGATAGAAATTTCAAATCGA
* ** *
29701391 CAGCTGTCGATATGTTTATCATTTATCGATATAAATTGGAATACTTGGAAGATGAAAGAAACTGT
1 CAGCTATCGATATGTTTAGAATCTATCGATATAAATTGGAATACTTGGAAGATGAAAGAAACTGT
* *
29701456 ATCTATCAATATATTTATCTTCTATCGATAGAAATTTCGAATCGG
66 ATCTATCAATATATTTATCTTCTATCGATAGAAATTTCAAATCGA
*
29701501 CAACTATCGATAT
1 CAGCTATCGATAT
29701514 AAATTGGAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 111 0.99
111 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (110 bp):
CAGCTATCGATATGTTTAGAATCTATCGATATAAATTGGAATACTTGGAAGATGAAAGAAACTGT
ATCTATCAATATATTTATCTTCTATCGATAGAAATTTCAAATCGA
Found at i:29701522 original size:91 final size:91
Alignment explanation
Indices: 29701414--29701600 Score: 311
Period size: 91 Copynumber: 2.1 Consensus size: 91
29701404 GTTTATCATT
* *
29701414 TATCGATATAAATTGGAATACTTGGAAGATGAAAGAAACTGTATCTATCAATATATTTATCTTCT
1 TATCGATATAAATTGGAATACTTGGAAGATAAAAGAAACGGTATCTATCAATATATTTATCTTCT
*
29701479 ATCGATAGAAATTTCGAATCGGCAAC
66 ATCGATAGAAATTTCGAATCGACAAC
* *
29701505 TATCGATATAAATTGGAATACTTGGAATATAAAAGAAACGGTATCTATCGATATATTTATCTTCT
1 TATCGATATAAATTGGAATACTTGGAAGATAAAAGAAACGGTATCTATCAATATATTTATCTTCT
* *
29701570 ATCGATAGATATTTCGAATCGACAGC
66 ATCGATAGAAATTTCGAATCGACAAC
29701596 TATCG
1 TATCG
29701601 CTATGTTTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (91 bp):
TATCGATATAAATTGGAATACTTGGAAGATAAAAGAAACGGTATCTATCAATATATTTATCTTCT
ATCGATAGAAATTTCGAATCGACAAC
Done.