Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 43 of 103
Found at i:16084220 original size:26 final size:26
Alignment explanation
Indices: 16084160--16084221 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
16084150 ACCATATACC
*
16084160 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
16084186 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
16084212 TATCATCATC
1 CATCATCATC
16084222 TCATATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:16084516 original size:42 final size:42
Alignment explanation
Indices: 16084456--16084579 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
16084446 ATGGGGGCAA
* *
16084456 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* * *
16084498 CAACGGCTTATATACACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
16084540 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
16084580 CAAATCAACA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:16091136 original size:29 final size:29
Alignment explanation
Indices: 16091102--16091281 Score: 224
Period size: 29 Copynumber: 6.2 Consensus size: 29
16091092 TATGTTTATA
16091102 TTAATTTAGATCAA-AAAACATGTTTTGTC
1 TTAATTTAGA-CAAGAAAACATGTTTTGTC
* *
16091131 TTAATTTAGACAAGAAAAAATGTTATGTC
1 TTAATTTAGACAAGAAAACATGTTTTGTC
16091160 TTAATTTAGAACAAGAAAACATGTTTTGTC
1 TTAATTTAG-ACAAGAAAACATGTTTTGTC
* * *
16091190 TTAATTTAGACAGGATAACATG-TTTCTC
1 TTAATTTAGACAAGAAAACATGTTTTGTC
*
16091218 TTAATGTAAGACAAGAAAACATG-TTTGTC
1 TTAAT-TTAGACAAGAAAACATGTTTTGTC
* *
16091247 TTTATTTAGACAA-AATAACATGTTTTATC
1 TTAATTTAGACAAGAA-AACATGTTTTGTC
16091276 TTAATT
1 TTAATT
16091282 AGAAACAAGA
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.02
28 26 0.20
29 76 0.58
30 27 0.21
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TTAATTTAGACAAGAAAACATGTTTTGTC
Found at i:16096152 original size:2 final size:2
Alignment explanation
Indices: 16096145--16096176 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16096135 TGGACATTTT
*
16096145 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16096177 GTTTTCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16096234 original size:2 final size:2
Alignment explanation
Indices: 16096227--16096260 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16096217 AAATACAAAN
16096227 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
16096261 GTTTTCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16096284 original size:84 final size:82
Alignment explanation
Indices: 16096145--16096309 Score: 294
Period size: 84 Copynumber: 2.0 Consensus size: 82
16096135 TGGACATTTT
16096145 AGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGGTTTTCCATAATAGCTTGACAAACTCTTGAAAA
1 AGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGGTTTTCCATAATAGCTTGACAAACTCTTGAAAA
16096210 GGAATTCAAATACAAANG
66 GGAATTCAAATACAAA-G
*
16096228 AGAGAGAGAGAGAGAGAGAAGAGAGAGAGAGAGGTTTTCCATAATAGCTTGACAAACTCTTGAAA
1 AGAGAGAGAGAAAGAGAG-AGAGAGAGAGAGAGGTTTTCCATAATAGCTTGACAAACTCTTGAAA
*
16096293 AGGAATTCAACTACAAA
65 AGGAATTCAAATACAAA
16096310 TTCACCAAGC
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
83 17 0.22
84 62 0.78
ACGTcount: A:0.45, C:0.10, G:0.27, T:0.17
Consensus pattern (82 bp):
AGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGGTTTTCCATAATAGCTTGACAAACTCTTGAAAA
GGAATTCAAATACAAAG
Found at i:16100862 original size:15 final size:16
Alignment explanation
Indices: 16100817--16100863 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
16100807 TGAAAGCCAA
*
16100817 GAACTAGCTATGAAAT
1 GAACTAGATATGAAAT
* *
16100833 GAA-GAGTTATGAAAT
1 GAACTAGATATGAAAT
16100848 GAACTAGATAT-AAAT
1 GAACTAGATATGAAAT
16100863 G
1 G
16100864 TTGATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (16 bp):
GAACTAGATATGAAAT
Found at i:16103344 original size:2 final size:2
Alignment explanation
Indices: 16103337--16103368 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16103327 CATTATGTTG
16103337 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
16103369 GAATAATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16103515 original size:42 final size:42
Alignment explanation
Indices: 16103391--16103516 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
16103381 ATAATGATAT
* * *
16103391 TGACCTAGCTATGTGCGAGTAGGAGTACGCATAAGCCGTTAC
1 TGACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
* * *
16103433 TGACCTGGTTATGTGCGAGTGGGAGTGCGCAAAAGCCGTTGC
1 TGACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
* *
16103475 TGA-CTCGGCTATGTGCGAGTAGGAGTGTGCATAAGTCGTTGC
1 TGACCT-GGCTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
16103517 ATATGAGCTG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 2 0.03
42 70 0.97
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.25
Consensus pattern (42 bp):
TGACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
Found at i:16110593 original size:2 final size:2
Alignment explanation
Indices: 16110586--16110624 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16110576 TNTTAGTATG
* *
16110586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16110625 GGTATATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16112743 original size:40 final size:39
Alignment explanation
Indices: 16112687--16112776 Score: 144
Period size: 40 Copynumber: 2.3 Consensus size: 39
16112677 ATGATGTATG
* *
16112687 TAATGTTTATGTATGTTTGATGGGTAAGACCCAATTGTTT
1 TAATGTTTATGCATGTTTGATGGGTAAAACCCAATTG-TT
16112727 TAATGTTTATGCATGTTTGATGGGTAAAACCCAATTGTT
1 TAATGTTTATGCATGTTTGATGGGTAAAACCCAATTGTT
*
16112766 TAAGGTTTATG
1 TAATGTTTATG
16112777 TATTCAAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.26
40 35 0.74
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (39 bp):
TAATGTTTATGCATGTTTGATGGGTAAAACCCAATTGTT
Found at i:16115203 original size:5 final size:5
Alignment explanation
Indices: 16115193--16115218 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16115183 TGAATAACTA
16115193 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
16115219 CAGCCTCTCA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:16115425 original size:17 final size:18
Alignment explanation
Indices: 16115385--16115428 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 18
16115375 TTTCAAGACA
16115385 ATTTATAAA-ATCATTTC
1 ATTTATAAACATCATTTC
*
16115402 A-TT-TAAACA-CATTTT
1 ATTTATAAACATCATTTC
16115417 ATTTATAAACAT
1 ATTTATAAACAT
16115429 AAAGATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
15 10 0.45
16 5 0.23
17 7 0.32
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTATAAACATCATTTC
Found at i:16116372 original size:11 final size:11
Alignment explanation
Indices: 16116343--16116375 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
16116333 CTAGGGTTTA
16116343 GTTCTTCCTTT
1 GTTCTTCCTTT
*
16116354 -TCCTTCCTTT
1 GTTCTTCCTTT
16116364 GTTCTTCCTTT
1 GTTCTTCCTTT
16116375 G
1 G
16116376 GCCTGCCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (11 bp):
GTTCTTCCTTT
Found at i:16118295 original size:35 final size:35
Alignment explanation
Indices: 16118256--16118336 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
16118246 ATCTTGATAG
*
16118256 AGGTTATGCCTGATCTTGAAAAAGACATGTTGTAA
1 AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
* ** * *
16118291 AGGTTACGTTTGATCTTGTAAAAGGCACGTTGTAA
1 AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
*
16118326 AAGTTATGCCT
1 AGGTTATGCCT
16118337 AACTCTATTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (35 bp):
AGGTTATGCCTGATCTTGAAAAAGACACGTTGTAA
Found at i:16122804 original size:35 final size:35
Alignment explanation
Indices: 16122763--16122905 Score: 189
Period size: 35 Copynumber: 4.1 Consensus size: 35
16122753 ATAGCCAGAG
* * *
16122763 TCATCGTGTGAAC-CCCCACATCACACACATCAACA
1 TCATCGTGTGCACTCCCTAC-TCGCACACATCAACA
* *
16122798 TCATCGTTTGCACTCCCTACTCGCACACATCATCA
1 TCATCGTGTGCACTCCCTACTCGCACACATCAACA
*
16122833 TCATCGTGTGCACTCCCTACTCGCACACATAAACA
1 TCATCGTGTGCACTCCCTACTCGCACACATCAACA
* * *
16122868 TCATCATGTGCACTCCTTACTCGCATACATCAACA
1 TCATCGTGTGCACTCCCTACTCGCACACATCAACA
16122903 TCA
1 TCA
16122906 CTATCCACAC
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 90 0.95
36 5 0.05
ACGTcount: A:0.29, C:0.38, G:0.09, T:0.24
Consensus pattern (35 bp):
TCATCGTGTGCACTCCCTACTCGCACACATCAACA
Found at i:16126776 original size:28 final size:28
Alignment explanation
Indices: 16126730--16126863 Score: 135
Period size: 28 Copynumber: 4.6 Consensus size: 28
16126720 TTACGACAAC
*
16126730 TCTTGTCTTTAATTAAGACAAATAT-TTT
1 TCTTGTC-TAAATTAAGACAAATATATTT
* *
16126758 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAATATATTT
* * * *
16126787 TCTTATCTAGATTTAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAATATA-TTT
*
16126817 TCTTGTCATAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAATATATTT
*
16126846 TCTTATCTAAATTAAGAC
1 TCTTGTCTAAATTAAGAC
16126864 TAAACATGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
28 41 0.46
29 24 0.27
30 15 0.17
31 9 0.10
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAATATATTT
Found at i:16126836 original size:59 final size:59
Alignment explanation
Indices: 16126749--16126863 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
16126739 TAATTAAGAC
* * * * *
16126749 AAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTATCTAGATTTAGACAAA
1 AAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACAAA
16126808 AAATATTTT-TCTTGTCATAAATTAAGACAAACATATTTTCTTATCTAAATTAAGAC
1 AAATATTTTATCTTGTC-TAAATTAAGACAAACATATTTTCTTATCTAAATTAAGAC
16126864 TAAACATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 7 0.14
59 43 0.86
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (59 bp):
AAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACAAA
Found at i:16126885 original size:59 final size:59
Alignment explanation
Indices: 16126749--16126886 Score: 143
Period size: 59 Copynumber: 2.3 Consensus size: 59
16126739 TAATTAAGAC
* * * * * * *
16126749 AAATATTTTATCTTGTC-TAAATTGAGACAAATATGTTTTCTTATCTAGATTTAGACAAA
1 AAATATTTTA-ATTCTCATAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACAAA
** * *
16126808 AAATATTTTTCTTGTCATAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACTAA
1 AAATATTTTAATTCTCATAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACAAA
* *
16126867 ACATGTTTTAATTCTCATAA
1 AAATATTTTAATTCTCATAA
16126887 CCCACTAGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 6 0.09
59 60 0.91
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (59 bp):
AAATATTTTAATTCTCATAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACAAA
Found at i:16130624 original size:40 final size:39
Alignment explanation
Indices: 16130569--16130656 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
16130559 AAATGCATTC
* * * *
16130569 TCGTTGCAGTGAGAAACTTTCTGTTTTCTGGGTTGCAATT
1 TCGTTGCAGCGAGAAACATTCTGTTTT-TGGGTAGAAATT
16130609 TCGTTGCAGCGAGAAACATTCTGTTTTTGGGTAGAAATT
1 TCGTTGCAGCGAGAAACATTCTGTTTTTGGGTAGAAATT
*
16130648 TCGCTGCAG
1 TCGTTGCAG
16130657 TGAATTCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 18 0.42
40 25 0.58
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (39 bp):
TCGTTGCAGCGAGAAACATTCTGTTTTTGGGTAGAAATT
Found at i:16141021 original size:11 final size:11
Alignment explanation
Indices: 16140988--16141022 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
16140978 CCTAGGGTTC
16140988 TTGTTCTTCCT
1 TTGTTCTTCCT
16140999 TT-TTCTTCCT
1 TTGTTCTTCCT
*
16141009 TTGTTCTTACT
1 TTGTTCTTCCT
16141020 TTG
1 TTG
16141023 GCCAGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.03, C:0.23, G:0.09, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:16145876 original size:22 final size:23
Alignment explanation
Indices: 16145851--16145897 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
16145841 ATTTCTATGC
16145851 ATTACTA-CAAGAACTAAACT-AA
1 ATTACTATCAA-AACTAAACTCAA
*
16145873 ATTACTATCAAAATTAAACTCAA
1 ATTACTATCAAAACTAAACTCAA
16145896 AT
1 AT
16145898 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAACTCAA
Found at i:16146031 original size:3 final size:3
Alignment explanation
Indices: 16146023--16146099 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
16146013 TAAATACAGT
* * * *
16146023 TAC TAC TAC TAC TAC TAC CAC TAT TAC TAC TAC TAC TAC TAT TAT TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* *
16146071 TAC TAC TAC TAT TAT TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
16146100 GAGATAAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (3 bp):
TAC
Found at i:16146045 original size:18 final size:18
Alignment explanation
Indices: 16146023--16146099 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
16146013 TAAATACAGT
*
16146023 TACTACTACTACTACTAC
1 TACTATTACTACTACTAC
*
16146041 CACTATTACTACTACTAC
1 TACTATTACTACTACTAC
*
16146059 TACTATTATTACTACTAC
1 TACTATTACTACTACTAC
*
16146077 TACTATTATTACTACTAC
1 TACTATTACTACTACTAC
16146095 TACTA
1 TACTA
16146100 GAGATAAAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (18 bp):
TACTATTACTACTACTAC
Found at i:16148120 original size:35 final size:35
Alignment explanation
Indices: 16148081--16148153 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
16148071 CTTACTCAGC
* *
16148081 TCATGTGCACTCCCTACACGCACATTTCCATATCA
1 TCATGTGCACTCCCTACACACACATTTCAATATCA
16148116 TCATGTGCACTCCCTACACACACATTTCAATATCA
1 TCATGTGCACTCCCTACACACACATTTCAATATCA
16148151 TCA
1 TCA
16148154 CACGTACTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACACACATTTCAATATCA
Found at i:16148163 original size:35 final size:35
Alignment explanation
Indices: 16148087--16148164 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
16148077 CAGCTCATGT
* * ***
16148087 GCACTCCCTACACGCACATTTCCATATCATCATGT
1 GCACTCCCTACACACACATTTCAATATCATCACAC
16148122 GCACTCCCTACACACACATTTCAATATCATCACAC
1 GCACTCCCTACACACACATTTCAATATCATCACAC
*
16148157 GTACTCCC
1 GCACTCCC
16148165 GCCCACATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.40, G:0.06, T:0.26
Consensus pattern (35 bp):
GCACTCCCTACACACACATTTCAATATCATCACAC
Found at i:16149440 original size:19 final size:19
Alignment explanation
Indices: 16149416--16149453 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16149406 GGTGCTAAGG
16149416 TGAAAATAGCATGAGAGCA
1 TGAAAATAGCATGAGAGCA
* *
16149435 TGAAAATGGCATGGGAGCA
1 TGAAAATAGCATGAGAGCA
16149454 CGAAGGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.16
Consensus pattern (19 bp):
TGAAAATAGCATGAGAGCA
Found at i:16165823 original size:43 final size:42
Alignment explanation
Indices: 16165702--16165810 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
16165692 TGACTCGGCT
* * * *
16165702 ATGTGCGAGTAGGGAGTACGCATAGGCCGATGATGACCCGGTC
1 ATGTGCGAGTAGGGAGTGCACATA-GCCGATGATGACCCAGCC
* * * *
16165745 AGGTGAGAGTAGGGAATGCACATAACCCGATGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCACAT-AGCCGATGATGACCCAGCC
16165788 ATGTGCGAGTAGGGAGTGCACAT
1 ATGTGCGAGTAGGGAGTGCACAT
16165811 GAGCTGGTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.35, T:0.17
Consensus pattern (42 bp):
ATGTGCGAGTAGGGAGTGCACATAGCCGATGATGACCCAGCC
Found at i:16167790 original size:2 final size:2
Alignment explanation
Indices: 16167785--16167819 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16167775 TTGTGTTATC
16167785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16167820 GGTTTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16168732 original size:12 final size:12
Alignment explanation
Indices: 16168715--16168739 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16168705 AAGAAAATGA
16168715 AATATTTTATTT
1 AATATTTTATTT
16168727 AATATTTTATTT
1 AATATTTTATTT
16168739 A
1 A
16168740 GTTTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:16170422 original size:4 final size:4
Alignment explanation
Indices: 16170408--16170460 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
16170398 TTCCTTTCTC
*
16170408 CTTT C-TT CTTT CTTT CTTT CTTT CCTTT C-TC CTTT C-TT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
*
16170454 CTCT CTT
1 CTTT CTT
16170461 CCAACCAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 8 0.20
4 29 0.71
5 4 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:16170432 original size:31 final size:31
Alignment explanation
Indices: 16170388--16170460 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
16170378 TCATTCTCTC
*
16170388 TCTTT-TTTTTTTCCTTTCTCCTTTCTTCTT
1 TCTTTCTTTCTTTCCTTTCTCCTTTCTTCTT
16170418 TCTTTCTTTCTTTCCTTTCTCCTTTCTTCTT
1 TCTTTCTTTCTTTCCTTTCTCCTTTCTTCTT
*
16170449 TCTTTCTCTCTT
1 TCTTTCTTTCTT
16170461 CCAACCAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (31 bp):
TCTTTCTTTCTTTCCTTTCTCCTTTCTTCTT
Found at i:16170452 original size:7 final size:7
Alignment explanation
Indices: 16170401--16170452 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
16170391 TTTTTTTTTC
*
16170401 CTTTCTC
1 CTTTCTT
16170408 CTTTCTT
1 CTTTCTT
16170415 CTTTCTTT
1 CTTTC-TT
16170423 CTTTCTTT
1 CTTTC-TT
*
16170431 CCTTTCTC
1 -CTTTCTT
16170439 CTTTCTT
1 CTTTCTT
16170446 CTTTCTT
1 CTTTCTT
16170453 TCTCTCTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
7 24 0.60
8 11 0.28
9 5 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (7 bp):
CTTTCTT
Found at i:16170752 original size:21 final size:21
Alignment explanation
Indices: 16170717--16170762 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16170707 TCTTCCTTGA
*
16170717 CTTTTCTTTCTTCCTTATTTG
1 CTTTTCTTTCTTCCTCATTTG
*
16170738 CTTTTCTTT-TCTCCTCATTTT
1 CTTTTCTTTCT-TCCTCATTTG
16170759 CTTT
1 CTTT
16170763 GTCATGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.67
Consensus pattern (21 bp):
CTTTTCTTTCTTCCTCATTTG
Found at i:16174183 original size:11 final size:12
Alignment explanation
Indices: 16174138--16174203 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
16174128 TTTGGCTGAA
*
16174138 TTTTT-TTTCCC
1 TTTTTCTTTCTC
16174149 TTTCTTCCTTTC-C
1 TTT-TT-CTTTCTC
*
16174162 TGTTTCTTTCTC
1 TTTTTCTTTCTC
16174174 TTTTTCTTCTGCTC
1 TTTTTCTT-T-CTC
*
16174188 TTCTTCTTTCTC
1 TTTTTCTTTCTC
16174200 TTTT
1 TTTT
16174204 CCTTCCTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 8 0.18
12 18 0.40
13 5 0.11
14 14 0.31
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:16176256 original size:21 final size:21
Alignment explanation
Indices: 16176227--16176302 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
16176217 TCAGTCCTTA
* *
16176227 TCATAAATGCATAAGTCTCTG
1 TCATGAATGCATAAGTCTTTG
* *
16176248 TTATGAATGCATTAGTCTTTG
1 TCATGAATGCATAAGTCTTTG
16176269 TCATGAATGCATCAA-TCTTTG
1 TCATGAATGCAT-AAGTCTTTG
16176290 TCATGAATTGCAT
1 TCATGAA-TGCAT
16176303 GAACATGTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 41 0.87
22 6 0.13
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
TCATGAATGCATAAGTCTTTG
Found at i:16182183 original size:28 final size:28
Alignment explanation
Indices: 16182146--16182271 Score: 117
Period size: 30 Copynumber: 4.3 Consensus size: 28
16182136 ATCATATTTG
* *
16182146 GTCTCAATTTAGACAAAAAAATATGTTT
1 GTCTTAATTTAGACAAAAAAATATTTTT
* *
16182174 GTCTTAATTTAAGATGAGAAAAATATTTTTT
1 GTCTTAATTT-AGA-CAAAAAAATA-TTTTT
* * * * *
16182205 GTCTTAATCTAGGCAAGAAAACATATTT
1 GTCTTAATTTAGACAAAAAAATATTTTT
*
16182233 GTCTCAATTTAGACAAGATAAAATATTTTT
1 GTCTTAATTTAGACAA-A-AAAATATTTTT
16182263 GTCTTAATT
1 GTCTTAATT
16182272 AAAGACAAGA
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
28 26 0.35
29 9 0.12
30 27 0.36
31 13 0.17
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
GTCTTAATTTAGACAAAAAAATATTTTT
Found at i:16182280 original size:31 final size:29
Alignment explanation
Indices: 16182128--16182281 Score: 120
Period size: 28 Copynumber: 5.2 Consensus size: 29
16182118 TCCCAACATG
* * * *
16182128 GACAAGAAATCATA-TTTGGTCTCAATTTA
1 GACAAGAAA-AATATTTTTGTCTTAATTAA
*
16182157 GACAA-AAAAATATGTTTGTCTTAATTTAA
1 GACAAGAAAAATATTTTTGTCTTAA-TTAA
**
16182186 GATGAGAAAAATATTTTTTGTCTTAATCT-A
1 GACAAGAAAAATA-TTTTTGTCTTAAT-TAA
* * *
16182216 GGCAAGAAAACATA--TTTGTCTCAATTTA
1 GACAAGAAAA-ATATTTTTGTCTTAATTAA
16182244 GACAAGATAAAATATTTTTGTCTTAATTAAA
1 GACAAGA-AAAATATTTTTGTCTTAATT-AA
16182275 GACAAGA
1 GACAAGA
16182282 GTTGTCTTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.04
28 31 0.31
29 14 0.14
30 27 0.27
31 23 0.23
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (29 bp):
GACAAGAAAAATATTTTTGTCTTAATTAA
Found at i:16182281 original size:59 final size:59
Alignment explanation
Indices: 16182146--16182270 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
16182136 ATCATATTTG
* * * * * * **
16182146 GTCTCAATTTAGACAAAAAAATATGTTTGTCTTAATTTAAGATGAGAAAAATATTTTTT
1 GTCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAGACAAGAAAAATATTTTTT
*
16182205 GTCTTAATCTAGGCAAGAAAACATATTTGTCTCAATTT-AGACAAGATAAAATA-TTTTT
1 GTCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAGACAAGA-AAAATATTTTTT
16182263 GTCTTAAT
1 GTCTTAAT
16182271 TAAAGACAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
58 19 0.34
59 37 0.66
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (59 bp):
GTCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAGACAAGAAAAATATTTTTT
Found at i:16184083 original size:6 final size:6
Alignment explanation
Indices: 16184072--16184097 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16184062 TCAAATTGGG
16184072 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
16184098 GGAGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:16192294 original size:21 final size:21
Alignment explanation
Indices: 16192265--16192307 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
16192255 GAGTAGTTTA
16192265 TTTAAGTTATTTTAG-TTAAAT
1 TTTAAGTTATTTT-GTTTAAAT
*
16192286 TTTATGTTATTTTGTTTAAAT
1 TTTAAGTTATTTTGTTTAAAT
16192307 T
1 T
16192308 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTAAGTTATTTTGTTTAAAT
Found at i:16195484 original size:18 final size:18
Alignment explanation
Indices: 16195451--16195485 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16195441 GAAGAAAGGG
* *
16195451 AAAAAGAAAGAGAAGAGA
1 AAAAAGAAAAAAAAGAGA
16195469 AAAAAGAAAAAAAAGAG
1 AAAAAGAAAAAAAAGAG
16195486 TGGGGGCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAGAGA
Found at i:16195739 original size:15 final size:16
Alignment explanation
Indices: 16195707--16195739 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16195697 GAAGAATAAG
16195707 GAGAAAGCAAAAACAA
1 GAGAAAGCAAAAACAA
*
16195723 GAGAAAG-AAAAAGAA
1 GAGAAAGCAAAAACAA
16195738 GA
1 GA
16195740 AAAAAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (16 bp):
GAGAAAGCAAAAACAA
Found at i:16195777 original size:69 final size:69
Alignment explanation
Indices: 16195682--16195845 Score: 179
Period size: 69 Copynumber: 2.4 Consensus size: 69
16195672 GCAGCGACGG
* * * * *
16195682 AAGAGCAACGACAAAGAAGAATAAGGAGAAAGCAA-AAACAAGAGAAAGAAAAAGAAGAA-AAAA
1 AAGAGCAACAACAGAGGAGAAAAAGGA-AAAGCAAGAAACAAGAGAAAGAAAAAAAAGAAGAAAA
16195745 GAGAGA
65 -AGAGA
* * * * *
16195751 AGGAGCAGCAACAGAGGAGAAAAAGGAAAGGGAAGAAAGAAGAGAAAGAAAAAAAAGAAGAAAAA
1 AAGAGCAACAACAGAGGAGAAAAAGGAAAAGCAAGAAACAAGAGAAAGAAAAAAAAGAAGAAAAA
16195816 GAGA
66 GAGA
* *
16195820 AAGAGCAACGATAGAGGAGAAGAAAG
1 AAGAGCAACAACAGAGGAGAA-AAAG
16195846 AAAGGGAAGT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
68 5 0.06
69 65 0.83
70 8 0.10
ACGTcount: A:0.63, C:0.06, G:0.29, T:0.01
Consensus pattern (69 bp):
AAGAGCAACAACAGAGGAGAAAAAGGAAAAGCAAGAAACAAGAGAAAGAAAAAAAAGAAGAAAAA
GAGA
Found at i:16195849 original size:69 final size:69
Alignment explanation
Indices: 16195721--16195860 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 69
16195711 AAGCAAAAAC
* * *
16195721 AAGAGAAAGAAAAAGAAGAAAAAAGAGAGAAGGAGCAGCAACAGAGGAGAAAAAGGAAAGGGAAG
1 AAGAGAAAGAAAAAAAAGAAAAAAGAGAGAAAGAGCAACAACAGAGGAGAAAAAGGAAAGGGAAG
16195786 AAAG
66 AAAG
* *
16195790 AAGAGAAAGAAAAAAAAGAAGAAAA-AGAGAAAGAGCAACGATAGAGGAGAAGAAA-GAAAGGGA
1 AAGAGAAAGAAAAAAAAGAA-AAAAGAGAGAAAGAGCAACAACAGAGGAGAA-AAAGGAAAGGGA
*
16195853 AGTAAG
64 AGAAAG
16195859 AA
1 AA
16195861 AAAAAATAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
69 56 0.89
70 7 0.11
ACGTcount: A:0.64, C:0.04, G:0.31, T:0.01
Consensus pattern (69 bp):
AAGAGAAAGAAAAAAAAGAAAAAAGAGAGAAAGAGCAACAACAGAGGAGAAAAAGGAAAGGGAAG
AAAG
Found at i:16196074 original size:2 final size:2
Alignment explanation
Indices: 16196065--16196098 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
16196055 TCTATTTTTT
*
16196065 TA TA -A TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16196099 CTACATGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:16196528 original size:59 final size:60
Alignment explanation
Indices: 16196421--16196627 Score: 319
Period size: 59 Copynumber: 3.5 Consensus size: 60
16196411 TTCATATTGA
*
16196421 GTGGCGTGGGTAGTTCCCACGAGTAGGTAAAAGGGGACTTGAAGCCCCGATTTATGTATG
1 GTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGCCCCGATTTATGTATG
*
16196481 GTGGCGTGGGTAGTTCCCA-GAGTAGGTAAAGGGGGACTTGAAGCCCCGATTTATGTATA
1 GTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGCCCCGATTTATGTATG
* * * *
16196540 GTGGCGTGGGTAGTTGCCACGAGTAGGTAAAGGGGGACCTGAAGCCTCGATTTA-ATATG
1 GTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGCCCCGATTTATGTATG
* *
16196599 GTGACGTGGGTAGTTTTCCACGAGTAGGT
1 GTGGCGTGGGTAG-TTCCCACGAGTAGGT
16196628 GATGATGTTT
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
59 71 0.52
60 65 0.48
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (60 bp):
GTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGGACTTGAAGCCCCGATTTATGTATG
Found at i:16209294 original size:15 final size:16
Alignment explanation
Indices: 16209274--16209304 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16209264 GAAAGGGAAG
16209274 AAAAAAGA-GAAAAGA
1 AAAAAAGAGGAAAAGA
16209289 AAAAAAGAGGAAAAGA
1 AAAAAAGAGGAAAAGA
16209305 GTGGGGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGGAAAAGA
Found at i:16209479 original size:16 final size:15
Alignment explanation
Indices: 16209434--16209482 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
16209424 CGGCGACGAG
* **
16209434 GAAAAAAAGGAGAGG
1 GAAAAAAAAGAGAAA
16209449 GAAGAAAAAAGAGAAA
1 GAA-AAAAAAGAGAAA
16209465 GAAAAAAAAGAAGAAA
1 GAAAAAAAAG-AGAAA
16209481 GA
1 GA
16209483 GAGAAGGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAGAAA
Found at i:16209576 original size:69 final size:67
Alignment explanation
Indices: 16209431--16209601 Score: 177
Period size: 69 Copynumber: 2.5 Consensus size: 67
16209421 GCACGGCGAC
* *
16209431 GAGGAAAAAAAGGAGAGGGAAGAAAAAAGAGAAAGAAAAAAAAGAAGAAAGAGAGAAGGAGTAGC
1 GAGGAGAAAAA-GAGAGGGAAGAAAAAA-AGAAAGAAAAAAAAGAAGAAAGAGAGAAGCAGTAGC
16209496 GATA
64 GATA
* * **
16209500 GAAGAGAAAAATGAGAGGGAAGAAAGAAAAGAAAGAAAGAGTAGAAGAATAAGAGAAGAAGCAGT
1 GAGGAGAAAAA-GAGAGGGAAGAAA-AAAAGAAAGAAAAAAAAGAAG-A-AAGAG-AGAAGCAGT
16209565 AGC-A-A
61 AGCGATA
* *
16209570 -AGGAGAAGAAAAAGAGGGAAGAAATAAAGAAA
1 GAGGAGAA-AAAGAGAGGGAAGAAAAAAAGAAA
16209602 TAATAATAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
68 7 0.08
69 55 0.63
70 8 0.09
71 6 0.07
72 11 0.13
ACGTcount: A:0.62, C:0.02, G:0.32, T:0.04
Consensus pattern (67 bp):
GAGGAGAAAAAGAGAGGGAAGAAAAAAAGAAAGAAAAAAAAGAAGAAAGAGAGAAGCAGTAGCGA
TA
Found at i:16210221 original size:60 final size:60
Alignment explanation
Indices: 16210130--16210365 Score: 314
Period size: 60 Copynumber: 3.9 Consensus size: 60
16210120 ATTTAAAAAA
* * *
16210130 GGGGACCTGAAGCCCCGATTCATAT-TGGGTGGCATGGTTAGTTCCCACGAGTAGGTAAAG
1 GGGGACCTGAAGCCCCGATTTATATAT-GGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAG
* *
16210190 GTGGACCTGAAGCCTCC-ATTTATGTATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAG
1 GGGGACCTGAAGCC-CCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAG
* * * *
16210250 GGGGACTTGAAGCCCCGATTTATGTATGGTGGTGTGGGTAGTTCCCACGAGTAAGTAAAG
1 GGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAG
* * * *
16210310 GGGGACCTGAAGCCCCGATTTATATATGATGGTGTGGGCAGTTTTCCACGAGTAGG
1 GGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAG-TTCCCACGAGTAGG
16210366 GGATGATGTT
Statistics
Matches: 157, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
59 2 0.01
60 140 0.89
61 15 0.10
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (60 bp):
GGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAG
Found at i:16211827 original size:80 final size:80
Alignment explanation
Indices: 16211738--16211963 Score: 337
Period size: 80 Copynumber: 2.8 Consensus size: 80
16211728 ATAACATTTC
* ** *
16211738 CATAAATCA-TCATCATGCTTAGCTCATAGTAAATATGACTATCTCAACACATATATCTCATTGC
1 CATAAATCATTCA-CATGCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGC
*
16211802 ATGCATTAGATAACCT
65 ATGCATTACATAACCT
* *
16211818 CATAAATCATTCACATTCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTACA
1 CATAAATCATTCACATGCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGCA
* *
16211883 TGCATTTCATAATCT
66 TGCATTACATAACCT
* *
16211898 CATAATTCATTCACATGCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCA
1 CATAAATCATTCACATGCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGCA
16211963 T
66 T
16211964 ACATATTACC
Statistics
Matches: 132, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 129 0.98
81 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.33
Consensus pattern (80 bp):
CATAAATCATTCACATGCTTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGCA
TGCATTACATAACCT
Found at i:16213793 original size:59 final size:59
Alignment explanation
Indices: 16213701--16213819 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
16213691 TAGTCATAGG
16213701 AGCTACTATCTTTGAGAAATCCTTAACGAATCTCCTATAATATCCAATCAACCCTAAGA
1 AGCTACTATCTTTGAGAAATCCTTAACGAATCTCCTATAATATCCAATCAACCCTAAGA
* *
16213760 AGCTATTATCTTTGAGAAATCCTTAACGAATCTCCTATAATATCCAATCAACTCTAAGA
1 AGCTACTATCTTTGAGAAATCCTTAACGAATCTCCTATAATATCCAATCAACCCTAAGA
16213819 A
1 A
16213820 ACTTTGTATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (59 bp):
AGCTACTATCTTTGAGAAATCCTTAACGAATCTCCTATAATATCCAATCAACCCTAAGA
Found at i:16216017 original size:52 final size:54
Alignment explanation
Indices: 16215954--16216072 Score: 127
Period size: 53 Copynumber: 2.3 Consensus size: 54
16215944 AAGATGAGAG
* ** *
16215954 TTAGTTGACTAAGAAGCT-GCTGCCAAAATCT-GGACTTCAAGACAAAACCGAC
1 TTAGTCGACTAAGAAGCTCGCTGCCAAAATCTAGGACTAAAAGACAAAACCAAC
* * * * *
16216006 TTAGTCGACTAA-ATGCTCTCTGCCAGAATCTATGACTAAAAGACAGAACCAAC
1 TTAGTCGACTAAGAAGCTCGCTGCCAAAATCTAGGACTAAAAGACAAAACCAAC
*
16216059 TTAGTCAACTAAGA
1 TTAGTCGACTAAGA
16216073 TGAAAGTTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
51 4 0.07
52 22 0.41
53 27 0.50
54 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (54 bp):
TTAGTCGACTAAGAAGCTCGCTGCCAAAATCTAGGACTAAAAGACAAAACCAAC
Found at i:16221126 original size:43 final size:43
Alignment explanation
Indices: 16221008--16221129 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
16220998 TGACTCGACT
* **
16221008 ATGTGCGAGTAGGGAGTGCACATAAGCCGAG-GATGACCAGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCAGGCC
*
16221051 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCTA-GCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACC-AGGCC
* *
16221094 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
16221130 TGATGATGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.01
43 68 0.97
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCAGGCC
Found at i:16224067 original size:43 final size:43
Alignment explanation
Indices: 16223949--16224070 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
16223939 TGACTCGACT
* **
16223949 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
16223992 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
16224035 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
16224071 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:16224081 original size:20 final size:20
Alignment explanation
Indices: 16224056--16224118 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
16224046 GGGAGTGCGC
16224056 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
16224076 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
16224096 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
16224115 ATGA
1 ATGA
16224119 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:16228447 original size:26 final size:26
Alignment explanation
Indices: 16228387--16228448 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
16228377 ACCATATACC
*
16228387 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
16228413 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
16228439 TATCATCATC
1 CATCATCATC
16228449 TCATATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:16228741 original size:42 final size:42
Alignment explanation
Indices: 16228683--16228806 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 42
16228673 ATGGGGGCAA
* *
16228683 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
16228725 CAACGGCTTATATGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
16228767 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
16228807 CAAATCAACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:16235636 original size:13 final size:13
Alignment explanation
Indices: 16235618--16235642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16235608 TTTCAGAAAA
16235618 TTTATAAAATCAT
1 TTTATAAAATCAT
16235631 TTTATAAAATCA
1 TTTATAAAATCA
16235643 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:16238878 original size:15 final size:15
Alignment explanation
Indices: 16238858--16238908 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
16238848 TTCTTAAAAC
16238858 AACTTTAAAA-CCGAA
1 AACTTTAAAATCC-AA
16238873 AACTTTAAAATCCAA
1 AACTTTAAAATCCAA
*
16238888 AGCTTTAAAAT-CAA
1 AACTTTAAAATCCAA
16238902 AATCTTT
1 AA-CTTT
16238909 GATCTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 4 0.12
15 26 0.81
16 2 0.06
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (15 bp):
AACTTTAAAATCCAA
Found at i:16243776 original size:43 final size:42
Alignment explanation
Indices: 16243695--16243828 Score: 196
Period size: 43 Copynumber: 3.1 Consensus size: 42
16243685 TTGTGTGATA
*
16243695 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGGGTGTGGGAGTGCACATGAGCTG
*
16243737 ATGATGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTA
1 ATGATGACCCAGCTATGTG-GGTGTGGGAGTGCACATGAGCTG
* * * *
16243780 ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACTTGAGCTG
1 ATGATGACCCAGCTATGTGGGTGT-GGGAGTGCACATGAGCTG
16243823 ATGATG
1 ATGATG
16243829 GTGGGATGGT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
42 22 0.27
43 61 0.73
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.25
Consensus pattern (42 bp):
ATGATGACCCAGCTATGTGGGTGTGGGAGTGCACATGAGCTG
Found at i:16247255 original size:22 final size:22
Alignment explanation
Indices: 16247229--16247277 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
16247219 GAAAAATGGA
16247229 TGCTGATATGTTTATGATATTT
1 TGCTGATATGTTTATGATATTT
*
16247251 TGCTGATATGTTTATGGTATTT
1 TGCTGATATGTTTATGATATTT
16247273 TGCTG
1 TGCTG
16247278 CTGATGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.06, G:0.22, T:0.53
Consensus pattern (22 bp):
TGCTGATATGTTTATGATATTT
Found at i:16248200 original size:73 final size:70
Alignment explanation
Indices: 16248005--16248201 Score: 211
Period size: 72 Copynumber: 2.7 Consensus size: 70
16247995 AATATTGAGA
* * *
16248005 AACAGAACAAACTTAGTCGACCAAGATGAGAGTTAGTCGACTAAGAAGCTATTGCCAAAATCTGG
1 AACAGAACCAACTTAGTCGACCAAGAAGAGAGTTAGTCGACTAAG-AGCTCTTGCCAAAATCTGG
16248070 ACTTCAG
65 AC-TCAG
* * * *
16248077 GACAGAACCAACTTAATCGACCAAGAA-ATGAGTTAGTCGACTAA-ATGCTCTCTGCTAGAATCT
1 AACAGAACCAACTTAGTCGACCAAGAAGA-GAGTTAGTCGACTAAGA-GCTCT-TGCCAAAATCT
16248140 GTGA-TCAG
63 G-GACTCAG
* * *
16248148 AAAATAGAACCAACATAGTCGACCAAGAAGAAAGTTAGTCGACTAAGAGCTCTT
1 --AACAGAACCAACTTAGTCGACCAAGAAGAGAGTTAGTCGACTAAGAGCTCTT
16248202 TGTCTGTAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
70 1 0.01
71 9 0.09
72 49 0.47
73 44 0.42
74 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (70 bp):
AACAGAACCAACTTAGTCGACCAAGAAGAGAGTTAGTCGACTAAGAGCTCTTGCCAAAATCTGGA
CTCAG
Found at i:16262649 original size:21 final size:21
Alignment explanation
Indices: 16262625--16262910 Score: 133
Period size: 22 Copynumber: 12.6 Consensus size: 21
16262615 TAACATGGCA
*
16262625 TGTAACATTTTTGAACTTGTG
1 TGTAACATTTTTGAACTTGCG
* *
16262646 TGTAACAATATTTGAACTTGCT
1 TGTAAC-ATTTTTGAACTTGCG
**
16262668 TGTAACATTTTTG-ACAAGGCG
1 TGTAACATTTTTGAAC-TTGCG
*
16262689 TGTAACAATTTTTGAACTTACG
1 TGTAAC-ATTTTTGAACTTGCG
* *
16262711 TGCAACATTTTTGAACAATGCG
1 TGTAACATTTTTGAAC-TTGCG
* * *
16262733 TATAGATAGCATAGTGTTGAACTTACG
1 --T-G-TAACAT--TTTTGAACTTGCG
*
16262760 TGTAACAATTTTTGAACTTACG
1 TGTAAC-ATTTTTGAACTTGCG
* *
16262782 TGCAACATTTTTGAACAATGCG
1 TGTAACATTTTTGAAC-TTGCG
* * *
16262804 TATAGATAGCATAGTGTTGAACTTGCA
1 --T-G-TAACAT--TTTTGAACTTGCG
* *
16262831 TGTAACATTTTTGCACATGGCG
1 TGTAACATTTTTGAAC-TTGCG
* * *
16262853 TGTAACATTTTTTAAACATGGCA
1 TGTAACA-TTTTTGAAC-TTGCG
* * *
16262876 TGTAACATTTTTAAACATGGCA
1 TGTAACATTTTTGAAC-TTGCG
16262898 TGTAACATATTTT
1 TGTAACAT-TTTT
16262911 AAACATGGTG
Statistics
Matches: 207, Mismatches: 36, Indels: 42
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.01
21 46 0.22
22 88 0.43
23 33 0.16
24 6 0.03
25 4 0.02
26 8 0.04
27 6 0.03
28 14 0.07
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTAACATTTTTGAACTTGCG
Found at i:16262672 original size:43 final size:44
Alignment explanation
Indices: 16262625--16262776 Score: 146
Period size: 43 Copynumber: 3.4 Consensus size: 44
16262615 TAACATGGCA
** * * *
16262625 TGTAACATTTTTGAAC-TTGTGTGTAACAATATTTGAACTTGCT
1 TGTAACATTTTTGAACAAGGCGTGTAACAATATTTGAACTTACG
*
16262668 TGTAACATTTTTG-ACAAGGCGTGTAACAATTTTTGAACTTACG
1 TGTAACATTTTTGAACAAGGCGTGTAACAATATTTGAACTTACG
* * * *
16262711 TGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAACTTACG
1 TGTAACATTTTTGAACAAGGCGTGTA-ACA--ATA-T-TTGAACTTACG
16262760 TGTAACAATTTTTGAAC
1 TGTAAC-ATTTTTGAAC
16262777 TTACGTGCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 46 0.52
44 10 0.11
45 2 0.02
47 2 0.02
48 1 0.01
49 16 0.18
50 10 0.11
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (44 bp):
TGTAACATTTTTGAACAAGGCGTGTAACAATATTTGAACTTACG
Found at i:16262769 original size:71 final size:71
Alignment explanation
Indices: 16262687--16262843 Score: 289
Period size: 71 Copynumber: 2.2 Consensus size: 71
16262677 TTTGACAAGG
16262687 CGTGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTG
1 CGTGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTG
16262752 AACTTA
66 AACTTA
16262758 CGTGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTG
1 CGTGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTG
*
16262823 AACTTG
66 AACTTA
*
16262829 CATGTAAC-ATTTTTG
1 CGTGTAACAATTTTTG
16262844 CACATGGCGT
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 7 0.08
71 77 0.92
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (71 bp):
CGTGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTG
AACTTA
Found at i:16262860 original size:71 final size:71
Alignment explanation
Indices: 16262689--16262864 Score: 273
Period size: 71 Copynumber: 2.5 Consensus size: 71
16262679 TGACAAGGCG
*
16262689 TGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAA
1 TGTAACAATTTTTGAACTGACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAA
*
16262754 CTTACG
66 CTTACA
*
16262760 TGTAACAATTTTTGAACTTACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAA
1 TGTAACAATTTTTGAACTGACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAA
*
16262825 CTTGCA
66 CTTACA
* * *
16262831 TGTAAC-ATTTTTGCACATGGCGTGTAACATTTTT
1 TGTAACAATTTTTGAAC-TGACGTGCAACATTTTT
16262865 TAAACATGGC
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
70 9 0.09
71 89 0.91
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (71 bp):
TGTAACAATTTTTGAACTGACGTGCAACATTTTTGAACAATGCGTATAGATAGCATAGTGTTGAA
CTTACA
Found at i:16262871 original size:23 final size:22
Alignment explanation
Indices: 16262828--16262927 Score: 137
Period size: 23 Copynumber: 4.5 Consensus size: 22
16262818 TGTTGAACTT
**
16262828 GCATGTAACATTTTTGCACATG
1 GCATGTAACATTTTTAAACATG
*
16262850 GCGTGTAACATTTTTTAAACATG
1 GCATGTAACA-TTTTTAAACATG
16262873 GCATGTAACATTTTTAAACATG
1 GCATGTAACATTTTTAAACATG
16262895 GCATGTAACATATTTTAAACATG
1 GCATGTAACAT-TTTTAAACATG
**
16262918 GTGTGTAACA
1 GCATGTAACA
16262928 ATATGGCTGA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
22 32 0.46
23 38 0.54
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (22 bp):
GCATGTAACATTTTTAAACATG
Found at i:16262882 original size:45 final size:45
Alignment explanation
Indices: 16262828--16262927 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
16262818 TGTTGAACTT
** * *
16262828 GCATGTAACATTTTTGCACATGGCGTGTAACATTTTTTAAACATG
1 GCATGTAACATTTTTAAACATGGCATGTAACATATTTTAAACATG
16262873 GCATGTAACATTTTTAAACATGGCATGTAACATATTTTAAACATG
1 GCATGTAACATTTTTAAACATGGCATGTAACATATTTTAAACATG
**
16262918 GTGTGTAACA
1 GCATGTAACA
16262928 ATATGGCTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (45 bp):
GCATGTAACATTTTTAAACATGGCATGTAACATATTTTAAACATG
Found at i:16265034 original size:29 final size:28
Alignment explanation
Indices: 16265002--16265144 Score: 119
Period size: 29 Copynumber: 4.9 Consensus size: 28
16264992 AAATATTTGA
* *
16265002 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAA-TTAAGACAAACATGTAT
** * * * *
16265031 TCTTCCCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTAT
16265061 TCTTGTCTTAAATTAAGACAAA-A-GTATTT
1 TCTTGTC-TAAATTAAGACAAACATGTA--T
* *
16265090 TCTTATCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTAT
16265119 TCTTGTCTAAATTAAGACAAACATGT
1 TCTTGTCTAAATTAAGACAAACATGT
16265145 TAAAGCTGCC
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.01
28 25 0.27
29 42 0.46
30 11 0.12
31 12 0.13
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTAT
Found at i:16265082 original size:59 final size:58
Alignment explanation
Indices: 16264984--16265144 Score: 175
Period size: 59 Copynumber: 2.7 Consensus size: 58
16264974 GTCGGTAATC
* * * *
16264984 AAGACAAAAAATATTTGATCTTGTCTAAATTTGAGACAAATATGTA-TTCTTCCCTAGATT
1 AAGACAAAAAATATTT-TTCTTGTCTAAA-TTAAGACAAA-ATGTATTTCTTACCTAAATT
*
16265044 AAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAAA-GTATTTTCTTATCTAAATT
1 AAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAAATGTA-TTTCTTACCTAAATT
* * *
16265103 AAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGT
1 AAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAA-ATGT
16265145 TAAAGCTGCC
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
57 17 0.19
58 12 0.14
59 39 0.44
60 20 0.23
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (58 bp):
AAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAAATGTATTTCTTACCTAAATT
Found at i:16270891 original size:127 final size:127
Alignment explanation
Indices: 16270656--16270917 Score: 488
Period size: 127 Copynumber: 2.1 Consensus size: 127
16270646 CTAACATTTC
* *
16270656 TAACCATTAAATATCAGCCAATTACCTTCTAAAATCATCAAAATGAGCTCACTTTCCTCCTTGAA
1 TAACAATTAAATATCAGCCAATAACCTTCTAAAATCATCAAAATGAGCTCACTTTCCTCCTTGAA
*
16270721 AAATTCGGTCAAAAATGGGACATTAACTCGGTTAATTTTTCACTTTGTTTTTCTATTACATT
66 AAATTCGGTCAAAAATGGGACATTAACTCGGTTAATTTTTCACTTTGTTTTTCTATCACATT
*
16270783 TAACAATTNAATATCAGCCAATAACCTTCTAAAATCATCAAAATGAGCTCACTTTCCTCCTTGAA
1 TAACAATTAAATATCAGCCAATAACCTTCTAAAATCATCAAAATGAGCTCACTTTCCTCCTTGAA
16270848 AAATTCGGTCAAAAATGGGACATTAACTCGGTTAATTTTTCACTTTGTTTTTCTATCACATT
66 AAATTCGGTCAAAAATGGGACATTAACTCGGTTAATTTTTCACTTTGTTTTTCTATCACATT
16270910 TAACAATT
1 TAACAATT
16270918 TTTCATCATT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (127 bp):
TAACAATTAAATATCAGCCAATAACCTTCTAAAATCATCAAAATGAGCTCACTTTCCTCCTTGAA
AAATTCGGTCAAAAATGGGACATTAACTCGGTTAATTTTTCACTTTGTTTTTCTATCACATT
Found at i:16276566 original size:20 final size:20
Alignment explanation
Indices: 16276521--16276558 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16276511 TTTTGGCCCC
16276521 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
16276541 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
16276559 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16279738 original size:17 final size:18
Alignment explanation
Indices: 16279703--16279744 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
16279693 AGGGAGAGCA
*
16279703 AAAGAAAAGCAAAAGAAG
1 AAAGAAAAGCAAAAAAAG
*
16279721 AAAGGAAAG-AAAAAAAG
1 AAAGAAAAGCAAAAAAAG
16279738 AAAGAAA
1 AAAGAAA
16279745 TAACCGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGCAAAAAAAG
Found at i:16281536 original size:20 final size:20
Alignment explanation
Indices: 16281511--16281557 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
16281501 TTTTGACCCC
16281511 ATTTGATTTATTGGAGTATA
1 ATTTGATTTATTGGAGTATA
* *
16281531 ATTTGACTTATTGGAGTATG
1 ATTTGATTTATTGGAGTATA
16281551 ATTTGAT
1 ATTTGAT
16281558 GTTTAGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTGATTTATTGGAGTATA
Found at i:16300717 original size:10 final size:10
Alignment explanation
Indices: 16300705--16300767 Score: 99
Period size: 10 Copynumber: 6.3 Consensus size: 10
16300695 AATATCATTC
* *
16300705 ATATAGATAC
1 ATATATATAT
16300715 ATATATATAT
1 ATATATATAT
16300725 ATATATATAT
1 ATATATATAT
16300735 ATATATATAT
1 ATATATATAT
16300745 ATATATATAT
1 ATATATATAT
*
16300755 ATATACATAT
1 ATATATATAT
16300765 ATA
1 ATA
16300768 ATAAGCCACA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:16300722 original size:4 final size:4
Alignment explanation
Indices: 16300705--16300767 Score: 99
Period size: 4 Copynumber: 15.8 Consensus size: 4
16300695 AATATCATTC
* *
16300705 ATAT AGAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
16300753 ATAT ATAC ATAT ATA
1 ATAT ATAT ATAT ATA
16300768 ATAAGCCACA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:16302580 original size:59 final size:58
Alignment explanation
Indices: 16302469--16302642 Score: 197
Period size: 59 Copynumber: 2.9 Consensus size: 58
16302459 TAAGACAATT
* * * *
16302469 CTTGTCCATAATTAAGACAAAAAATATTTGATCTTGTCTAAATTTGAGACAAATATGTATC
1 CTTGTCTA-AATTAAGACAAAAAATATTT-TTCTTGTCTAAA-TTAAGACAAACATGTATC
* * * *
16302530 CTTGTCTAGATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTT
1 CTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTATC
* * * *
16302589 CTTGTCTAAATTAAGACTAAACAT-GTTTTCTTGTCTAAATTAAAACAAACATGT
1 CTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
16302643 TAAAGCTGCC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
57 17 0.17
58 10 0.10
59 41 0.42
60 23 0.23
61 7 0.07
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (58 bp):
CTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTATC
Found at i:16302610 original size:29 final size:28
Alignment explanation
Indices: 16302467--16302640 Score: 168
Period size: 29 Copynumber: 5.9 Consensus size: 28
16302457 TTTAAGACAA
* *
16302467 TTCTTGTCCATAATTAAGACAAAAAATATT
1 TTCTTGTCTA-AATTAAGAC-AAACATATT
* * * *
16302497 TGATCTTGTCTAAATTTGAGACAAATATGTA
1 T--TCTTGTCTAAA-TTAAGACAAACATATT
* * *
16302528 TCCTTGTCTAGATTAAGACAAAAAATATTT
1 TTCTTGTCTAAATTAAGAC-AAACATA-TT
16302558 TTCTTGTCTTAAATTAAGACAAACATATT
1 TTCTTGTC-TAAATTAAGACAAACATATT
*
16302587 TTCTTGTCTAAATTAAGACTAAACATGTT
1 TTCTTGTCTAAATTAAGAC-AAACATATT
*
16302616 TTCTTGTCTAAATTAAAACAAACAT
1 TTCTTGTCTAAATTAAGACAAACAT
16302641 GTTAAAGCTG
Statistics
Matches: 121, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
28 23 0.19
29 50 0.41
30 15 0.12
31 19 0.16
32 14 0.12
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (28 bp):
TTCTTGTCTAAATTAAGACAAACATATT
Found at i:16304668 original size:29 final size:28
Alignment explanation
Indices: 16304623--16304764 Score: 185
Period size: 29 Copynumber: 4.9 Consensus size: 28
16304613 GGCAGCTTTG
16304623 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
16304651 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
16304680 ATATGTTTGCCTTAATTTAAGACAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAA
* * *
16304709 TATATTTTTTGTCTTAATTTAGTCAAGAAA
1 -ACA-TGTTTGTCTTAATTTAGACAAGAAA
* *
16304739 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
16304765 TAAAATATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
28 37 0.37
29 39 0.39
30 12 0.12
31 13 0.13
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:16304736 original size:59 final size:57
Alignment explanation
Indices: 16304623--16304797 Score: 215
Period size: 59 Copynumber: 3.0 Consensus size: 57
16304613 GGCAGCTTTG
* * *
16304623 ACATGTTTGTCTTAATTTAGACAAGAAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
16304680 ATATGTTTGCCTTAATTTAAGACAAGAAATATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAA-ATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
16304739 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAG--AAAATA-TTTTTTGTCTTAATT-TAGACAAGA
16304798 GTTGTCTTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 16 0.16
58 17 0.17
59 42 0.42
60 18 0.18
61 7 0.07
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (57 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:16304772 original size:28 final size:28
Alignment explanation
Indices: 16304623--16304774 Score: 171
Period size: 28 Copynumber: 5.3 Consensus size: 28
16304613 GGCAGCTTTG
*
16304623 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
16304651 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* * *
16304680 ATATGTTTGCCTTAATTTAAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
* * *
16304709 TATATTTTTTGTCTTAATTTAGTCAAGAAA
1 -ACA-TATTTGTCTTAATTTAGACAAGAAA
*
16304739 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
16304768 A-ATATTT
1 ACATATTT
16304775 TTTTGTCTTA
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
28 43 0.39
29 42 0.38
30 12 0.11
31 13 0.12
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:16312830 original size:15 final size:16
Alignment explanation
Indices: 16312806--16312835 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16312796 AACCTTTTTT
16312806 GTTTTATTATTTTATG
1 GTTTTATTATTTTATG
16312822 GTTTT-TTATTTTAT
1 GTTTTATTATTTTAT
16312836 AAAACAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
GTTTTATTATTTTATG
Found at i:16315467 original size:23 final size:23
Alignment explanation
Indices: 16315441--16315488 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
16315431 AAGGATTAGC
*
16315441 AACCCTATGACGCCCGTTCCATG
1 AACCCTATGACACCCGTTCCATG
* *
16315464 AACCCTGTGACACCCTTTCCATG
1 AACCCTATGACACCCGTTCCATG
16315487 AA
1 AA
16315489 TAGTACCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (23 bp):
AACCCTATGACACCCGTTCCATG
Found at i:16328201 original size:15 final size:15
Alignment explanation
Indices: 16328178--16328207 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16328168 TTTCTGGGTG
*
16328178 CTTTGTTTTTTTTTT
1 CTTTCTTTTTTTTTT
16328193 CTTTCTTTTTTTTTT
1 CTTTCTTTTTTTTTT
16328208 TCCTAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (15 bp):
CTTTCTTTTTTTTTT
Found at i:16328468 original size:7 final size:7
Alignment explanation
Indices: 16328458--16328499 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
16328448 TCCTTTTTTA
16328458 ATTTATT
1 ATTTATT
16328465 ATTTATT
1 ATTTATT
16328472 ATTTATT
1 ATTTATT
16328479 A-TTATT
1 ATTTATT
16328485 ATTT-TT
1 ATTTATT
16328491 ATATTATT
1 AT-TTATT
16328499 A
1 A
16328500 AAAAAAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 19 0.59
8 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:16328499 original size:17 final size:17
Alignment explanation
Indices: 16328460--16328498 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16328450 CTTTTTTAAT
16328460 TTATTATTTATTATTTA
1 TTATTATTTATTATTTA
16328477 TTATTA-TTATT-TTTA
1 TTATTATTTATTATTTA
16328492 -TATTATT
1 TTATTATT
16328499 AAAAAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 5 0.24
17 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTATTTATTATTTA
Found at i:16329835 original size:22 final size:22
Alignment explanation
Indices: 16329809--16329859 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
16329799 CCTAGGAGAA
16329809 GAAGAAAGAAAAAGAGAGAAAG
1 GAAGAAAGAAAAAGAGAGAAAG
16329831 GAAGAAAGAAAAAGAGAGAAAG
1 GAAGAAAGAAAAAGAGAGAAAG
16329853 GAAGAAA
1 GAAGAAA
16329860 AAGCTTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (22 bp):
GAAGAAAGAAAAAGAGAGAAAG
Found at i:16329836 original size:8 final size:7
Alignment explanation
Indices: 16329807--16329859 Score: 56
Period size: 8 Copynumber: 7.3 Consensus size: 7
16329797 ACCCTAGGAG
16329807 AAGAAGA
1 AAGAAGA
16329814 AAGAA-A
1 AAGAAGA
16329820 AAGAGAGA
1 AAGA-AGA
16329828 AAGGAAGA
1 AA-GAAGA
16329836 AAGAA-A
1 AAGAAGA
16329842 AAGAGAGA
1 AAGA-AGA
16329850 AAGGAAGA
1 AA-GAAGA
16329858 AA
1 AA
16329860 AAGCTTGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 10 0.25
7 10 0.25
8 16 0.40
9 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:16330951 original size:17 final size:19
Alignment explanation
Indices: 16330910--16330951 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
16330900 ATGTATATAT
16330910 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
16330931 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
16330948 ATGA
1 ATGA
16330952 TGATTGTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:16333664 original size:43 final size:43
Alignment explanation
Indices: 16333611--16333825 Score: 187
Period size: 43 Copynumber: 4.9 Consensus size: 43
16333601 AGGTCTCACA
* * *
16333611 ATGATGACCCAGCTATATGTGAGTAGAGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACATAAGCCG
* * * *
16333654 ATGATTACCCAGCTATGTGTCAGTAGGGAGTGCACATGAGCTGATG
1 ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACATAAGC---CG
*** * **
16333700 ATGATGACTTGGCTATGTGAGAGTAGGGAGTGTGCATAAGCCG
1 ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACATAAGCCG
* * * * *
16333743 ATGATGACTCAACTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
1 ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACATAAGC---CG
* * *
16333789 ATGATGACCGAGCTATGTGTAAATAGGGAGTGCACAT
1 ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACAT
16333826 GACGATGAAT
Statistics
Matches: 135, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
43 70 0.52
46 65 0.48
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.24
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGTGAGTAGGGAGTGCACATAAGCCG
Found at i:16333725 original size:46 final size:46
Alignment explanation
Indices: 16333665--16333827 Score: 174
Period size: 46 Copynumber: 3.6 Consensus size: 46
16333655 TGATTACCCA
** *
16333665 GCTATGTGTCAGTAGGGAGTGCACATGAGCTGATGATGATGACTTG
1 GCTATGTGAGAGTAGGGAGTGCACATGAGCTGATGATGATGACTCG
** * * *
16333711 GCTATGTGAGAGTAGGGAGTGTGCATAAGC---CGATGATGACTCA
1 GCTATGTGAGAGTAGGGAGTGCACATGAGCTGATGATGATGACTCG
* *
16333754 ACTATGTGCGAGTAGGGAGTGCACATGAGCTGATGATGATGAC-CG
1 GCTATGTGAGAGTAGGGAGTGCACATGAGCTGATGATGATGACTCG
*
16333799 AGCTATGTGTA-AATAGGGAGTGCACATGA
1 -GCTATGTG-AGAGTAGGGAGTGCACATGA
16333828 CGATGAATGA
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
43 35 0.37
45 1 0.01
46 58 0.62
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (46 bp):
GCTATGTGAGAGTAGGGAGTGCACATGAGCTGATGATGATGACTCG
Found at i:16333804 original size:89 final size:89
Alignment explanation
Indices: 16333611--16333821 Score: 284
Period size: 89 Copynumber: 2.4 Consensus size: 89
16333601 AGGTCTCACA
* * * * * *
16333611 ATGATGACCCAGCTATATGTGAGTAGAGAGTGCGCATAAGCCGATGATTACCCAGCTATGTGTCA
1 ATGATGACCGAGCTATGTGAGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAACTATGTGTCA
16333676 GTAGGGAGTGCACATGAGCTGATG
66 GTAGGGAGTGCACATGAGCTGATG
* * *
16333700 ATGATGACTTG-GCTATGTGAGAGTAGGGAGTGTGCATAAGCCGATGATGACTCAACTATGTG-C
1 ATGATGAC-CGAGCTATGTGAGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAACTATGTGTC
16333763 GAGTAGGGAGTGCACATGAGCTGATG
65 -AGTAGGGAGTGCACATGAGCTGATG
*
16333789 ATGATGACCGAGCTATGTGTA-AATAGGGAGTGC
1 ATGATGACCGAGCTATGTG-AGAGTAGGGAGTGC
16333822 ACATGACGAT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
88 2 0.02
89 103 0.97
90 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (89 bp):
ATGATGACCGAGCTATGTGAGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAACTATGTGTCA
GTAGGGAGTGCACATGAGCTGATG
Found at i:16334904 original size:31 final size:31
Alignment explanation
Indices: 16334705--16334905 Score: 296
Period size: 31 Copynumber: 6.5 Consensus size: 31
16334695 AAGAAAGAAA
* *
16334705 TAAAA-GTTGTTACATGCCACGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
*
16334735 TAAAATGTTGGTACACGCCATGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
* *
16334766 TAAAATGTTGGTACACGTCATGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
*
16334797 TAAAATGTTGGTACACGCCATGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
*
16334828 TCAAATGTTGTTACACGCCATGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
* *
16334859 TCAAATGTTTTTACACGCCATGCATATCAAG
1 TAAAATGTTGTTACACGCCATGCATATCAAG
* *
16334890 TCAAATGTTATTACAC
1 TAAAATGTTGTTACAC
16334906 ACCAACGCTG
Statistics
Matches: 161, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 5 0.03
31 156 0.97
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (31 bp):
TAAAATGTTGTTACACGCCATGCATATCAAG
Found at i:16335700 original size:47 final size:47
Alignment explanation
Indices: 16335573--16335779 Score: 261
Period size: 47 Copynumber: 4.4 Consensus size: 47
16335563 ACACACTCTA
* *
16335573 AACCTTGTCGTGTCACAAATTCCCTCCATGGCATGTCACAAAACTCTG
1 AACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAA-TCTG
* * * * * **
16335621 AACCCTACCATGTTACAGATTCCCTCCATGGCGTGTCACAAAATCAA
1 AACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTG
* *
16335668 AACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTTACAAAATCTG
1 AACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTG
* * * *
16335715 AACCCTGCCGTGTCACAGATTCCTTCCATGGCATGTCACAAATTTTG
1 AACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTG
*
16335762 AACCTTGTCGTGTCACAG
1 AACCTTGCCGTGTCACAG
16335780 CAGTGTCACA
Statistics
Matches: 135, Mismatches: 24, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 99 0.73
48 36 0.27
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (47 bp):
AACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTG
Found at i:16335766 original size:94 final size:95
Alignment explanation
Indices: 16335572--16335779 Score: 292
Period size: 94 Copynumber: 2.2 Consensus size: 95
16335562 TACACACTCT
* *
16335572 AAACCTTGTCGTGTCACAAATTCCCTCCATGGCATGTCACAAAACTCTGAACCCTACCATGTTAC
1 AAACCTTGTCGTGTCACAGATTCCCTCCATGGCATGTCACAAAACTCTGAACCCTACCATGTCAC
*
16335637 AGATTCCCTCCATGGCGTGTCACAAAATCA
66 AGATTCCCTCCATGGCATGTCACAAAATCA
* * * * *
16335667 AAACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTTACAAAA-TCTGAACCCTGCCGTGTCAC
1 AAACCTTGTCGTGTCACAGATTCCCTCCATGGCATGTCACAAAACTCTGAACCCTACCATGTCAC
* * **
16335731 AGATTCCTTCCATGGCATGTCACAAATTTT
66 AGATTCCCTCCATGGCATGTCACAAAATCA
*
16335761 GAACCTTGTCGTGTCACAG
1 AAACCTTGTCGTGTCACAG
16335780 CAGTGTCACA
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 59 0.60
95 40 0.40
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (95 bp):
AAACCTTGTCGTGTCACAGATTCCCTCCATGGCATGTCACAAAACTCTGAACCCTACCATGTCAC
AGATTCCCTCCATGGCATGTCACAAAATCA
Found at i:16335857 original size:47 final size:47
Alignment explanation
Indices: 16335796--16335902 Score: 178
Period size: 47 Copynumber: 2.3 Consensus size: 47
16335786 CACATGCTCG
*
16335796 CCCTGCCTTGTCACATATTCCCTCCATGGCATGTCACAAACTCTAAA
1 CCCTGCCGTGTCACATATTCCCTCCATGGCATGTCACAAACTCTAAA
* *
16335843 CCTTGCCGTGTCACATATTCCCTCCATGGTATGTCACAAACTCTAAA
1 CCCTGCCGTGTCACATATTCCCTCCATGGCATGTCACAAACTCTAAA
*
16335890 CCCTGTCGTGTCA
1 CCCTGCCGTGTCA
16335903 TAGTCGTGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (47 bp):
CCCTGCCGTGTCACATATTCCCTCCATGGCATGTCACAAACTCTAAA
Found at i:16335913 original size:126 final size:126
Alignment explanation
Indices: 16335673--16335902 Score: 334
Period size: 126 Copynumber: 1.8 Consensus size: 126
16335663 ATCAAAACCT
* * *
16335673 TGCCGTGTCACAGATTCCCTCCATGGCGTGTTACAAAATCTGAACCCTGCCGTGTCACAGATTCC
1 TGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTAAACCCTGCCGTGTCACAGATTCC
* * * * *
16335738 TTCCATGGCATGTCACAAATTTTGAACCTTGTCGTGTCACAGCAGTGTCACATGCTCGCCC
66 CTCCATGGCATGTCACAAACTCTAAACCCTGTCGTGTCACAGCAGTGTCACATGCTCGCCC
* * * * *
16335799 TGCCTTGTCACATATTCCCTCCATGGCATGTCACAAACTCTAAACCTTGCCGTGTCACATATTCC
1 TGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTAAACCCTGCCGTGTCACAGATTCC
*
16335864 CTCCATGGTATGTCACAAACTCTAAACCCTGTCGTGTCA
66 CTCCATGGCATGTCACAAACTCTAAACCCTGTCGTGTCA
16335903 TAGTCGTGTC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 90 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.29
Consensus pattern (126 bp):
TGCCGTGTCACAGATTCCCTCCATGGCATGTCACAAAATCTAAACCCTGCCGTGTCACAGATTCC
CTCCATGGCATGTCACAAACTCTAAACCCTGTCGTGTCACAGCAGTGTCACATGCTCGCCC
Found at i:16340260 original size:5 final size:5
Alignment explanation
Indices: 16340250--16340278 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16340240 ACATTTCTAC
16340250 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
16340279 TCAAATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:16340666 original size:24 final size:25
Alignment explanation
Indices: 16340621--16340668 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
16340611 ATAATCAGAC
*
16340621 ATAATATTTAAAAATTTAATTATTA
1 ATAATATTTAAAAAATTAATTATTA
16340646 ATAAT-TTTAAATAAATT-ATTATT
1 ATAATATTTAAA-AAATTAATTATT
16340669 TTTTATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATATTTAAAAAATTAATTATTA
Found at i:16341881 original size:2 final size:2
Alignment explanation
Indices: 16341874--16341905 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16341864 ATGTAAGGGA
16341874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16341906 GTATGATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16344977 original size:22 final size:22
Alignment explanation
Indices: 16344945--16345001 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
16344935 TAATCACCGT
*
16344945 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCATTAC
* *
16344967 GTGA-TTGGTTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
16344988 GTGACTAGTTTTTA
1 GTGACTAGTTTTTA
16345002 TACATTGCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.46
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:16345197 original size:26 final size:26
Alignment explanation
Indices: 16345054--16345406 Score: 215
Period size: 26 Copynumber: 14.7 Consensus size: 26
16345044 ATGTCTTATG
*
16345054 AACTAGTCACGCAATGCCTTA-C--T
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
16345077 AACAAGTCACGCAATACCTTA-C--T
1 AACTAGTCACGCAATGCCTTATCAAA
* *
16345100 AACAAGTCACGCAATGCCTTA-C--T
1 AACTAGTCACGCAATGCCTTATCAAA
* *
16345123 AACAAGTCACGCAATGCCTTA-C--T
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
16345146 AACAAGTCACGTAATACC-TATC---
1 AACTAGTCACGCAATGCCTTATCAAA
*
16345168 AACTAGTCATGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* *
16345194 AACTGGTCACACAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* *
16345220 AACTAGTTACGTAATGCC-TATC---
1 AACTAGTCACGCAATGCCTTATCAAA
*
16345242 AACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCAAA
*
16345268 AACTAGTCATGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
16345294 AATTAGTCACGTAATACC----CAAA
1 AACTAGTCACGCAATGCCTTATCAAA
** * *
16345316 GTC-AGTCACACAATGCC-TAT---T
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
16345337 AACTAGTCATGCAATTCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCAAA
*
16345363 AACTAGTCATGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAAA
* * *
16345389 AATTAGTCAAGTAATGCC
1 AACTAGTCACGCAATGCC
16345407 CAAAGTTTGT
Statistics
Matches: 271, Mismatches: 42, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.04
22 47 0.17
23 94 0.35
25 4 0.01
26 114 0.42
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (26 bp):
AACTAGTCACGCAATGCCTTATCAAA
Found at i:16345244 original size:74 final size:74
Alignment explanation
Indices: 16345054--16345311 Score: 266
Period size: 74 Copynumber: 3.6 Consensus size: 74
16345044 ATGTCTTATG
* * * * *
16345054 AACTAGTCACGCAATGCCTTA-C--TAACAAGTCACGCAATACCT-TACTAACAAGTCACGCAAT
1 AACTAGTCACACAATGCCTTATCAAAAACTAGTCACGTAATACCTAT-C-AACTAGTCACGCAAT
*
16345115 GCCTTA-C--T
64 GCCTTATCAAA
* * * * *
16345123 AACAAGTCACGCAATGCCTTA-C--TAACAAGTCACGTAATACCTATCAACTAGTCATGCAATGC
1 AACTAGTCACACAATGCCTTATCAAAAACTAGTCACGTAATACCTATCAACTAGTCACGCAATGC
16345185 CTTATCAAA
66 CTTATCAAA
* * *
16345194 AACTGGTCACACAATGCCTTATCAAAAACTAGTTACGTAATGCCTATCAACTAGTCACGCAATGC
1 AACTAGTCACACAATGCCTTATCAAAAACTAGTCACGTAATACCTATCAACTAGTCACGCAATGC
*
16345259 CTTATCAGA
66 CTTATCAAA
** *
16345268 AACTAGTCATGCAATGCCTTATCAAAAATTAGTCACGTAATACC
1 AACTAGTCACACAATGCCTTATCAAAAACTAGTCACGTAATACC
16345312 CAAAGTCAGT
Statistics
Matches: 162, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
68 19 0.12
69 42 0.26
70 1 0.01
71 18 0.11
72 1 0.01
74 81 0.50
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (74 bp):
AACTAGTCACACAATGCCTTATCAAAAACTAGTCACGTAATACCTATCAACTAGTCACGCAATGC
CTTATCAAA
Found at i:16345247 original size:22 final size:23
Alignment explanation
Indices: 16345035--16345387 Score: 222
Period size: 23 Copynumber: 14.9 Consensus size: 23
16345025 GCAATGCCTA
* * *
16345035 AGTCACACAATGTCTTATGAACT
1 AGTCACGCAATGCCTTATCAACT
*
16345058 AGTCACGCAATGCCTTA-CTAACA
1 AGTCACGCAATGCCTTATC-AACT
* *
16345081 AGTCACGCAATACCTTA-CTAACA
1 AGTCACGCAATGCCTTATC-AACT
*
16345104 AGTCACGCAATGCCTTA-CTAACA
1 AGTCACGCAATGCCTTATC-AACT
*
16345127 AGTCACGCAATGCCTTA-CTAACA
1 AGTCACGCAATGCCTTATC-AACT
* *
16345150 AGTCACGTAATACC-TATCAACT
1 AGTCACGCAATGCCTTATCAACT
*
16345172 AGTCATGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC---AACT
* *
16345198 GGTCACACAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC---AACT
* *
16345224 AGTTACGTAATGCC-TATCAACT
1 AGTCACGCAATGCCTTATCAACT
16345246 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATC---AACT
* *
16345272 AGTCATGCAATGCCTTATCAAAAATT
1 AGTCACGCAATGCCTTATC---AACT
* * * *
16345298 AGTCACGTAATACC-CA--AAGT
1 AGTCACGCAATGCCTTATCAACT
* *
16345318 CAGTCACACAATGCC-TATTAACT
1 -AGTCACGCAATGCCTTATCAACT
* *
16345341 AGTCATGCAATTCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATC---AACT
*
16345367 AGTCATGCAATGCCTTATCAA
1 AGTCACGCAATGCCTTATCAA
16345388 AAATTAGTCA
Statistics
Matches: 274, Mismatches: 39, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
20 3 0.01
21 12 0.04
22 43 0.16
23 114 0.42
25 5 0.02
26 97 0.35
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATGCCTTATCAACT
Found at i:16345419 original size:95 final size:95
Alignment explanation
Indices: 16345232--16345412 Score: 317
Period size: 95 Copynumber: 1.9 Consensus size: 95
16345222 CTAGTTACGT
16345232 AATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAAT
1 AATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAAT
*
16345297 TAGTCACGTAATACCCAAAGTCAGTCACAC
66 TAGTCAAGTAATACCCAAAGTCAGTCACAC
* * *
16345327 AATGCCTATTAACTAGTCATGCAATTCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAAT
1 AATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAAT
*
16345392 TAGTCAAGTAATGCCCAAAGT
66 TAGTCAAGTAATACCCAAAGT
16345413 TTGTCACGCA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (95 bp):
AATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAAT
TAGTCAAGTAATACCCAAAGTCAGTCACAC
Found at i:16345439 original size:21 final size:21
Alignment explanation
Indices: 16345406--16345445 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16345396 CAAGTAATGC
**
16345406 CCAAAGTTTGTCACGCAATAT
1 CCAAAGTCAGTCACGCAATAT
*
16345427 CCAAAGTCAGTCATGCAAT
1 CCAAAGTCAGTCACGCAAT
16345446 GCCTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
CCAAAGTCAGTCACGCAATAT
Found at i:16345459 original size:116 final size:118
Alignment explanation
Indices: 16345242--16345461 Score: 282
Period size: 116 Copynumber: 1.9 Consensus size: 118
16345232 AATGCCTATC
* * *
16345242 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGCCTTATCAAAAATTAGTCACGTA
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCAAGCAATGCC---TCAAAAATTAGTCACGCA
**
16345307 ATACCCAAAGTCAGTCACACAATGCCTATTAACTAGTCATGCAATTCCTTATCAGA
63 ATACCCAAAGTCAGTCACACAATGCCTAAAAACTAGTCATGCAATTCCTTATCAGA
* * * * *
16345363 AACTAGTCATGCAATGCCTTATCAAAAATTAGTCAAGTAATGCC-C-AAAGTTTGTCACGCAATA
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCAAGCAATGCCTCAAAAATTAGTCACGCAATA
* **
16345426 TCCAAAGTCAGTCATGCAATGCCTAAAAACTAGTCA
66 CCCAAAGTCAGTCACACAATGCCTAAAAACTAGTCA
16345462 CATAATTCTC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
116 46 0.53
117 1 0.01
121 39 0.45
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (118 bp):
AACTAGTCACGCAATGCCTTATCAAAAACTAGTCAAGCAATGCCTCAAAAATTAGTCACGCAATA
CCCAAAGTCAGTCACACAATGCCTAAAAACTAGTCATGCAATTCCTTATCAGA
Found at i:16349274 original size:68 final size:70
Alignment explanation
Indices: 16349125--16349333 Score: 173
Period size: 68 Copynumber: 3.1 Consensus size: 70
16349115 CTGTTGTCAA
* * * * *
16349125 AAAGTGTTGGAAAAACTCAAGAAAAGTTT-CTAACAAAAACTAATAA-AA-ATAACTT-GTAGTT
1 AAAGTGCTGGAAAAACTCAAGAAAAGTTTAC-AACAAAAAATAATAATAATAAAAATTCTTAGTT
***
16349186 TTCATC
65 TTTGCC
** * * * * *
16349192 AAAGTATTGAAAAAAC-CTAGGAAAAGTTTAC-ACACAAAAGTAATAATGA-AAAAA-TCTTATT
1 AAAGTGCTGGAAAAACTC-AAGAAAAGTTTACAACA-AAAAATAATAATAATAAAAATTCTTAGT
16349253 TTTTGCC
64 TTTTGCC
* *
16349260 AAAGTGCTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAATAATAAAAATTCTTAGTTT
1 AAAGTGCTGGAAAAACTCAAGAAAAGTTTACAACAAAAAATAATAATAATAAAAATTCTTAGTTT
*
16349325 TTGTC
66 TTGCC
16349330 AAAG
1 AAAG
16349334 GGTTGGGAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
66 4 0.04
67 35 0.32
68 47 0.42
69 9 0.08
70 16 0.14
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (70 bp):
AAAGTGCTGGAAAAACTCAAGAAAAGTTTACAACAAAAAATAATAATAATAAAAATTCTTAGTTT
TTGCC
Found at i:16349333 original size:70 final size:68
Alignment explanation
Indices: 16349125--16349378 Score: 212
Period size: 70 Copynumber: 3.7 Consensus size: 68
16349115 CTGTTGTCAA
* * * * * * *
16349125 AAAGTGTTGGAAAAACTCAAGAAAAGTTTCTAACAAAAACTAATAAAAATAACTT-GTAGTTTTC
1 AAAGTGTTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAAAAAAAAATTCTTAGTTTTT
*
16349189 ATC
66 GTC
* ** * * * * *
16349192 AAAGTATT-GAAAAAACCTAGGAAAAGTTTAC-ACACAAAAGTAATAATGAAAAAA-TCTTATTT
1 AAAGTGTTGGAAAAATTC-AAGAAAAGTTTCCAACA-AAAAATAATAA-AAAAAAATTCTTAGTT
*
16349254 TTTGCC
63 TTTGTC
*
16349260 AAAGTGCTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAATAATAAAAATTCTTAGTTT
1 AAAGTGTTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAA-AA-AAAAATTCTTAGTTT
16349325 TTGTC
64 TTGTC
* * * * * *
16349330 AAAGGGTTGGGAAAATTTAAGACAAGTTTCCAATATAAAA-AATAAAAAA
1 AAAGTGTTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAAAAAA
16349379 TAAAAGATAA
Statistics
Matches: 147, Mismatches: 32, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
66 10 0.07
67 30 0.20
68 42 0.29
69 20 0.14
70 45 0.31
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (68 bp):
AAAGTGTTGGAAAAATTCAAGAAAAGTTTCCAACAAAAAATAATAAAAAAAAATTCTTAGTTTTT
GTC
Found at i:16353836 original size:11 final size:11
Alignment explanation
Indices: 16353819--16353862 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
16353809 TATGGCCAGC
16353819 CAAAGGAA-AA
1 CAAAGGAAGAA
16353829 CAAAAGGAAGAA
1 C-AAAGGAAGAA
16353841 CAAAGGAAG-A
1 CAAAGGAAGAA
16353851 -AAA-GAAGAA
1 CAAAGGAAGAA
16353860 CAA
1 CAA
16353863 GAACCCTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 4 0.13
11 15 0.50
12 3 0.10
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:16357397 original size:2 final size:2
Alignment explanation
Indices: 16357385--16357430 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
16357375 ATTCTCTTAA
* *
16357385 CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16357427 CT CT
1 CT CT
16357431 TTTACCTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:16361144 original size:30 final size:30
Alignment explanation
Indices: 16361059--16361146 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 30
16361049 GTGAGTTAAG
16361059 GTGGTTATATCTTAGCCTTGAAAAGGTATAGA
1 GTGGTTATATCTTAGCCTTGAAAA-G-ATAGA
*
16361091 -T-GTTCTATCTTAGCCTTGAAAAGATAGA
1 GTGGTTATATCTTAGCCTTGAAAAGATAGA
* *
16361119 GTGGTTATATCTTTGCCTTTAAAAGATA
1 GTGGTTATATCTTAGCCTTGAAAAGATA
16361147 AAAAGGTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.10
29 2 0.04
30 42 0.84
31 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (30 bp):
GTGGTTATATCTTAGCCTTGAAAAGATAGA
Found at i:16367422 original size:35 final size:36
Alignment explanation
Indices: 16367383--16367453 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
16367373 TCTTTGCTCG
* *
16367383 TTGCTTCGGCATGTGCGTGATTTGTTT-TCTACCCA
1 TTGCTTCGGCACGTGCGTGATCTGTTTCTCTACCCA
* *
16367418 TTGCTTTGGCACGTGCGTGATCTGTTTCTCTCCCCA
1 TTGCTTCGGCACGTGCGTGATCTGTTTCTCTACCCA
16367454 ACTGCTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.41
Consensus pattern (36 bp):
TTGCTTCGGCACGTGCGTGATCTGTTTCTCTACCCA
Found at i:16370759 original size:24 final size:24
Alignment explanation
Indices: 16370732--16370799 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 24
16370722 GTGAATGGGG
16370732 ACATTTTGTATAATTTTTATCGAT
1 ACATTTTGTATAATTTTTATCGAT
** * *
16370756 ACA--TTGTCCAA-ATGTATCGAT
1 ACATTTTGTATAATTTTTATCGAT
16370777 ACATTTTGTATAATTTTTATCGA
1 ACATTTTGTATAATTTTTATCGA
16370800 GATATTGTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 11 0.33
22 6 0.18
23 6 0.18
24 10 0.30
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (24 bp):
ACATTTTGTATAATTTTTATCGAT
Found at i:16370774 original size:21 final size:21
Alignment explanation
Indices: 16370749--16370822 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
16370739 GTATAATTTT
16370749 TATCGATACATTGTCCAAATG
1 TATCGATACATTGTCCAAATG
** * *
16370770 TATCGATACATTTTGTATAATTTT
1 TATCGATACA--TTGTCCAA-ATG
* *
16370794 TATCGAGATATTGTCCAAATG
1 TATCGATACATTGTCCAAATG
16370815 TATCGATA
1 TATCGATA
16370823 GATTTGTGAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
21 18 0.46
22 6 0.15
23 6 0.15
24 9 0.23
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (21 bp):
TATCGATACATTGTCCAAATG
Found at i:16370796 original size:45 final size:45
Alignment explanation
Indices: 16370732--16370827 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
16370722 GTGAATGGGG
*
16370732 ACATTTTGTATAATTTTTATCGATACATTGTCCAAATGTATCGAT
1 ACATTTTGTATAATTTTTATCGAGACATTGTCCAAATGTATCGAT
*
16370777 ACATTTTGTATAATTTTTATCGAGATATTGTCCAAATGTATCGAT
1 ACATTTTGTATAATTTTTATCGAGACATTGTCCAAATGTATCGAT
*
16370822 AGATTT
1 ACATTT
16370828 GTGAAGGGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (45 bp):
ACATTTTGTATAATTTTTATCGAGACATTGTCCAAATGTATCGAT
Found at i:16370807 original size:106 final size:106
Alignment explanation
Indices: 16370671--16370888 Score: 314
Period size: 106 Copynumber: 2.1 Consensus size: 106
16370661 AACTAGGAGG
* * *
16370671 ACATTTTGTATAATTTTTATCTGTACATTGTCCAAATGTGTCGATA-ACTTTGTGAATGGGGACA
1 ACATTTTGTATAATTTTTATCTGGACATTGTCCAAATGTATCGATAGA-TTTGTGAAGGGGGACA
* * * **
16370735 TTTTGTATAATTTTTATCGATACATTGTCCAAATGTATCGAT
65 TTCTATATAATTTCTATCGATACATCATCCAAATGTATCGAT
*
16370777 ACATTTTGTATAATTTTTATC-GAGATATTGTCCAAATGTATCGATAGATTTGTGAAGGGGGACA
1 ACATTTTGTATAATTTTTATCTG-GACATTGTCCAAATGTATCGATAGATTTGTGAAGGGGGACA
16370841 TTCTATATAATTTCTATCGATACATCATCCAAATGTATCGAT
65 TTCTATATAATTTCTATCGATACATCATCCAAATGTATCGAT
*
16370883 AGATTT
1 ACATTT
16370889 GTAATGGAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
105 1 0.01
106 98 0.98
107 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (106 bp):
ACATTTTGTATAATTTTTATCTGGACATTGTCCAAATGTATCGATAGATTTGTGAAGGGGGACAT
TCTATATAATTTCTATCGATACATCATCCAAATGTATCGAT
Found at i:16370825 original size:23 final size:23
Alignment explanation
Indices: 16370758--16370829 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
16370748 TTATCGATAC
*
16370758 ATTGTCCAAATGTATCGATACAT
1 ATTGTCCAAATGTATCGATAGAT
* ** * *
16370781 TTTGTATAATTTTTATCG--AGAT
1 ATTGTCCAA-ATGTATCGATAGAT
16370803 ATTGTCCAAATGTATCGATAGAT
1 ATTGTCCAAATGTATCGATAGAT
16370826 -TTGT
1 ATTGT
16370830 GAAGGGGGAC
Statistics
Matches: 35, Mismatches: 11, Indels: 7
0.66 0.21 0.13
Matches are distributed among these distances:
21 6 0.17
22 13 0.37
23 10 0.29
24 6 0.17
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (23 bp):
ATTGTCCAAATGTATCGATAGAT
Done.