Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 18 of 198
Found at i:5423216 original size:19 final size:20
Alignment explanation
Indices: 5423192--5423238 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
5423182 TTCCTATACA
*
5423192 TATATATGCGCATA-GTTTT
1 TATATATGCACATACGTTTT
*
5423211 TATATAATGTACATACGTTTT
1 TATAT-ATGCACATACGTTTT
5423232 TATATAT
1 TATATAT
5423239 AGTATACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 10 0.42
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
TATATATGCACATACGTTTT
Found at i:5423245 original size:19 final size:18
Alignment explanation
Indices: 5423223--5423262 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5423213 TATAATGTAC
* *
5423223 ATACGTTTTTATATATAGT
1 ATACGTTTATACATATA-T
5423242 ATACGTTTATACATATAT
1 ATACGTTTATACATATAT
5423260 ATA
1 ATA
5423263 TAAGTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
ATACGTTTATACATATAT
Found at i:5423480 original size:18 final size:18
Alignment explanation
Indices: 5423435--5423480 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5423425 CACATGCACG
5423435 TTTTAAAATACACATGTT
1 TTTTAAAATACACATGTT
* *
5423453 TTTCAAAATACACATTTT
1 TTTTAAAATACACATGTT
*
5423471 TTTTATAATA
1 TTTTAAAATA
5423481 GATATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTAAAATACACATGTT
Found at i:5426339 original size:15 final size:15
Alignment explanation
Indices: 5426321--5426367 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5426311 ATATATTTAT
5426321 AAATTAAAATATAAA
1 AAATTAAAATATAAA
* **
5426336 AAATTAAATTATACT
1 AAATTAAAATATAAA
5426351 AAATTAAAATATAAA
1 AAATTAAAATATAAA
5426366 AA
1 AA
5426368 TCAAATTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAATATAAA
Found at i:5426393 original size:36 final size:36
Alignment explanation
Indices: 5426353--5426442 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
5426343 ATTATACTAA
5426353 ATTAAAATATA-AAAATCA-AATTCTAAATTTTAACAT
1 ATTAAAATATACAAAATCATAATT-TAAATTTTAA-AT
* *
5426389 ATTAAAA-AAACCAAAATCATAATTTAACTTTTAAAT
1 ATTAAAATATA-CAAAATCATAATTTAAATTTTAAAT
* *
5426425 ATTAATATATCCAAAATC
1 ATTAAAATATACAAAATC
5426443 GTAAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
35 2 0.04
36 22 0.49
37 17 0.38
38 4 0.09
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (36 bp):
ATTAAAATATACAAAATCATAATTTAAATTTTAAAT
Found at i:5427085 original size:26 final size:25
Alignment explanation
Indices: 5427023--5427089 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
5427013 ATTGATATGA
*
5427023 TTTATA-ATTTTTTAAGTTATTTTT
1 TTTATATATTTTTTAAATTATTTTT
*
5427047 TTTATATA-ATTTTATAATT-TTTATT
1 TTTATATATTTTTTA-AATTATTT-TT
5427072 TTTATATATTTTTTAAAT
1 TTTATATATTTTTTAAAT
5427090 AATATCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 14 0.39
25 17 0.47
26 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTATATATTTTTTAAATTATTTTT
Found at i:5427094 original size:16 final size:16
Alignment explanation
Indices: 5427075--5427108 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5427065 TTTTATTTTT
5427075 ATAT-ATTTTTTAAATA
1 ATATCATTTTTT-AATA
5427091 ATATCATTTTTTAATA
1 ATATCATTTTTTAATA
5427107 AT
1 AT
5427109 TTTAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATCATTTTTTAATA
Found at i:5435004 original size:17 final size:17
Alignment explanation
Indices: 5434982--5435045 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
5434972 AATCTTAGAG
5434982 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* *
5434999 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
*
5435018 TTCCAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
5435035 TTTTAATTGTA
1 TTCTAATTGTA
5435046 GCCCTTGATG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.58
18 2 0.06
19 11 0.31
20 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:5435026 original size:36 final size:36
Alignment explanation
Indices: 5434974--5435044 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
5434964 GATTATGTAA
*
5434974 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCCAATTGTATACAACTTCTAATTGTG
*
5435010 TCTTAGAGTTCCAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCCAATTGTATACAACTTCTAATTGT
5435045 AGCCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (36 bp):
TCTTAGAGTTCCAATTGTATACAACTTCTAATTGTG
Found at i:5440084 original size:17 final size:17
Alignment explanation
Indices: 5440062--5440106 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5440052 AATCTTAGAG
5440062 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
5440079 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAAC
*
5440096 TTTTAATTGTA
1 TTCTAATTGTA
5440107 GCCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:5442369 original size:15 final size:16
Alignment explanation
Indices: 5442349--5442389 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
5442339 AAATCATGTC
5442349 TATATTAAA-TAATAA
1 TATATTAAATTAATAA
5442364 TATATTATAAATTAATAA
1 TATA-T-TAAATTAATAA
5442382 TA-ATTAAA
1 TATATTAAA
5442390 AGGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 5 0.22
18 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATTAAATTAATAA
Found at i:5454528 original size:14 final size:13
Alignment explanation
Indices: 5454509--5454568 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
5454499 TGAATCAAAT
5454509 TAAAATATCATATA
1 TAAAAT-TCATATA
*
5454523 TAAAATTGCATAAAA
1 TAAAATT-CAT-ATA
5454538 TCAAAATTCATATA
1 T-AAAATTCATATA
*
5454552 TAACATTGCATAT-
1 TAAAATT-CATATA
5454565 TAAA
1 TAAA
5454569 CTAAAGTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 9 0.24
14 17 0.45
15 6 0.16
16 6 0.16
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (13 bp):
TAAAATTCATATA
Found at i:5454549 original size:29 final size:30
Alignment explanation
Indices: 5454490--5454563 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
5454480 GCTAGTAGTT
* * *
5454490 TATAAAATTTGAATCAAATTAAAATATCATA
1 TATAAAA-TTGCATAAAATCAAAATATCATA
5454521 TATAAAATTGCATAAAATCAAAAT-TCATA
1 TATAAAATTGCATAAAATCAAAATATCATA
*
5454550 TATAACATTGCATA
1 TATAAAATTGCATA
5454564 TTAAACTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 18 0.46
30 14 0.36
31 7 0.18
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (30 bp):
TATAAAATTGCATAAAATCAAAATATCATA
Found at i:5455634 original size:29 final size:29
Alignment explanation
Indices: 5455568--5455635 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
5455558 ATAAAAATAT
*
5455568 ATTTTTTAAAAAAATTAAAATTCTAAAGA
1 ATTTTATAAAAAAATTAAAATTCTAAAGA
* * *
5455597 A-TGTATAAACAAAGTTAAAATTTTAAA-A
1 ATTTTATAAA-AAAATTAAAATTCTAAAGA
*
5455625 ATTTTCTAAAA
1 ATTTTATAAAA
5455636 TAATAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (29 bp):
ATTTTATAAAAAAATTAAAATTCTAAAGA
Found at i:5466712 original size:29 final size:30
Alignment explanation
Indices: 5466672--5466741 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
5466662 TTAAAATTTT
5466672 ATGTATAAAATT-ACATAAAATCAAAATCC
1 ATGTATAAAATTAACATAAAATCAAAATCC
* *
5466701 ATGTTTAAAATTACACATTAAATCAAAATCC
1 ATGTATAAAATTA-ACATAAAATCAAAATCC
5466732 AT-TGATAAAA
1 ATGT-ATAAAA
5466742 ATTTATCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 1 0.03
31 23 0.66
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (30 bp):
ATGTATAAAATTAACATAAAATCAAAATCC
Found at i:5468965 original size:22 final size:22
Alignment explanation
Indices: 5468922--5468974 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
5468912 ATTTTGATTT
** **
5468922 TTTTTAAAAATTTTAACTATAA
1 TTTTTAAAAAAATTAAAAATAA
5468944 TTTTTAAAAAAATTAAAAATAA
1 TTTTTAAAAAAATTAAAAATAA
*
5468966 -TCTTAAAAA
1 TTTTTAAAAA
5468975 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTTAAAAAAATTAAAAATAA
Found at i:5469399 original size:8 final size:8
Alignment explanation
Indices: 5469386--5469414 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5469376 TCAATAAATA
5469386 AAATTATT
1 AAATTATT
5469394 AAATTATT
1 AAATTATT
5469402 AAA-TATT
1 AAATTATT
5469409 AAATTA
1 AAATTA
5469415 AAATAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:5476580 original size:50 final size:50
Alignment explanation
Indices: 5476501--5476595 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
5476491 GCCTTATTCT
* * * *
5476501 AATCAATGTCAAATAGAAGGAGAGAAGTTCTATATGGATTCTACTTGTAC
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
*
5476551 AATCAATATCAAATAGAAGAAGAGTAGTTCTATACGAATTCTACT
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACT
5476596 CGTATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (50 bp):
AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
Found at i:5478960 original size:3 final size:3
Alignment explanation
Indices: 5478954--5478988 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5478944 GCTGGGGTTG
* *
5478954 TCT TCT TCT TCT TCT TCT CCT TCT CCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5478989 CTCAGACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:5491917 original size:26 final size:26
Alignment explanation
Indices: 5491887--5491939 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5491877 AAAAAGAAAG
5491887 TTAAAAGACAATTTTATTCTGCTATC
1 TTAAAAGACAATTTTATTCTGCTATC
5491913 TTAAAAGACAATTTTATTCTGCTATC
1 TTAAAAGACAATTTTATTCTGCTATC
5491939 T
1 T
5491940 CTATTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (26 bp):
TTAAAAGACAATTTTATTCTGCTATC
Found at i:5499801 original size:48 final size:48
Alignment explanation
Indices: 5499681--5499837 Score: 199
Period size: 48 Copynumber: 3.2 Consensus size: 48
5499671 TTGCACATCG
* * * * *
5499681 TCACATATCACACACCGAAGCCATAGCCTAGCTATGGTCTTACACGGAAA
1 TCACATAT--CACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
* *
5499731 -CACAAATCACACCGATGTCATATCCCATATATGGTCTTACACGGAAA
1 TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
* * *
5499778 TCACATATCACACCGATGTCATATCCTAGATATGATCTTACACAGAAA
1 TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
5499826 TCACATATCACA
1 TCACATATCACA
5499838 TCACACCAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
47 34 0.36
48 54 0.57
49 6 0.06
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (48 bp):
TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
Found at i:5499876 original size:53 final size:53
Alignment explanation
Indices: 5499691--5499923 Score: 220
Period size: 53 Copynumber: 4.6 Consensus size: 53
5499681 TCACATATCA
* *
5499691 CACACCGAAGCCATAGCCTAGCTATGGTCTTACACGGAAA-CAC--A--A-AT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * ** *
5499738 CACACCGATGTCATATCCCATATATGGTCTTACACGGAAATCAC--AT---AT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * *
5499786 CACACCGATGTCATATCCTAGATATGATCTTACACAGAAATCACATATCACAT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * *
5499839 CACACCAATGCCATAGCCCAGCTATGGTCTTATACAG-AAGCACATAGTCACAT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATA-TCACAT
*
5499892 CACACCGATGACATAGCCTAGCTATGGTCTTA
1 CACACCGATGCCATAGCCTAGCTATGGTCTTA
5499924 TACGGAAGCA
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
47 34 0.22
48 46 0.29
50 2 0.01
52 8 0.05
53 67 0.43
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.23
Consensus pattern (53 bp):
CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
Found at i:5504843 original size:21 final size:21
Alignment explanation
Indices: 5504813--5504870 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5504803 GCTTCTGTTT
5504813 AACCCTTATGGGTTTCCATTC
1 AACCCTTATGGGTTTCCATTC
* * *
5504834 AACTCTTATGAGCTTT-CGTTC
1 AACCCTTATG-GGTTTCCATTC
5504855 AACCCTTATGGGTTTC
1 AACCCTTATGGGTTTC
5504871 TGTTTAGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCATTC
Found at i:5504884 original size:42 final size:43
Alignment explanation
Indices: 5504763--5504897 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 43
5504753 TTTCACTAGC
* * * * * *
5504763 TTCTGTTTAACTCATATGAGTTTCCGTTTAGCTTTTTTGAGC-
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
* * * *
5504805 TTCTGTTTAACCCTTATGGGTTTCCATTCAACTCTTATGAGCT
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
* * *
5504848 TTC-GTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGC-
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
5504889 TTCTGTTCA
1 TTCTGTTCA
5504898 GCCTTCAGGC
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.04
42 70 0.92
43 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (43 bp):
TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
Found at i:5507290 original size:85 final size:85
Alignment explanation
Indices: 5507187--5507353 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 85
5507177 CTCAACATAC
* ** * * *
5507187 TTGTGTTGTTGCAGGTATGTCACAAGATCATCTGAAATTGGATTCTGACCTTATCTCTAACATTG
1 TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
*
5507252 TCTTATCTATAGTGAAATAT
66 TCTTACCTATAGTGAAATAT
* * **
5507272 TTGTGTTGTTACATGTATGTCACAAGATCATCCAAAATTGAACTCTTACATTATCTCTCGCATTG
1 TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
*
5507337 TCTTACCTATGGTGAAA
66 TCTTACCTATAGTGAAA
5507354 GTGAATCCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (85 bp):
TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
TCTTACCTATAGTGAAATAT
Found at i:5511544 original size:10 final size:10
Alignment explanation
Indices: 5511529--5511560 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5511519 AATTTTATTG
5511529 TTTTTATCTC
1 TTTTTATCTC
5511539 TTTTTAT-T-
1 TTTTTATCTC
5511547 TTTTTATCTC
1 TTTTTATCTC
5511557 TTTT
1 TTTT
5511561 ATTTTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATCTC
Found at i:5511565 original size:16 final size:18
Alignment explanation
Indices: 5511521--5511565 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
5511511 CTTGTTTCAA
5511521 TTTTATTGTTTTTATCTCT
1 TTTTATT-TTTTTATCTCT
5511540 TTTTATTTTTTTATCTC-
1 TTTTATTTTTTTATCTCT
5511557 TTTTATTTT
1 TTTTATTTT
5511566 CGTTTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTTATCTCT
Found at i:5512545 original size:2 final size:2
Alignment explanation
Indices: 5512540--5512588 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
5512530 TTCAAATTGT
* *
5512540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5512582 TA TA TA T
1 TA TA TA T
5512589 TAAAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5520499 original size:2 final size:2
Alignment explanation
Indices: 5520492--5520536 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5520482 TTTTATATTT
5520492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5520534 TA T
1 TA T
5520537 TANNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5520847 original size:22 final size:22
Alignment explanation
Indices: 5520802--5520847 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5520792 TTAAAGGGCA
**
5520802 TTTTTATGCATTTTATAATCTT
1 TTTTTATGCATTTTATAAAATT
5520824 TTTTTATG-ATTTTTATAAAATT
1 TTTTTATGCA-TTTTATAAAATT
5520846 TT
1 TT
5520848 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTATGCATTTTATAAAATT
Found at i:5520857 original size:21 final size:21
Alignment explanation
Indices: 5520833--5520872 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5520823 TTTTTTATGA
*
5520833 TTTTTATAAAATTTTATAATT
1 TTTTTATAAAATTTAATAATT
* *
5520854 TTTTTCTAATATTTAATAA
1 TTTTTATAAAATTTAATAA
5520873 AAAATAAATA
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTATAAAATTTAATAATT
Found at i:5521179 original size:92 final size:89
Alignment explanation
Indices: 5521043--5521208 Score: 226
Period size: 92 Copynumber: 1.8 Consensus size: 89
5521033 ATTGAGTGCA
*
5521043 AAAAAAAAAGTAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
1 AAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
**
5521108 GTAGTTCAAATACTTAAATGAATG
66 AAAGTTCAAATACTTAAATGAATG
* * * *
5521132 AAAAAAAAA-CAGGGGCTTAATTGTTTTATTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGTAT
1 AAAAAAAAAGCAGGGGCTTAA-T-TATT-TTTTTTTG-AAAAGTTTGAGAGCATTTTTGATATAT
5521196 TTTGAAAGTTCAA
62 TTTGAAAGTTCAA
5521209 GTACCCAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
88 10 0.15
89 10 0.15
90 3 0.05
91 8 0.12
92 35 0.53
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (89 bp):
AAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
AAAGTTCAAATACTTAAATGAATG
Found at i:5521228 original size:92 final size:89
Alignment explanation
Indices: 5521032--5521230 Score: 220
Period size: 92 Copynumber: 2.2 Consensus size: 89
5521022 TTATTTTGGA
*
5521032 AATTGAGTGCAAAAAAAAAAGTAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTT
1 AATTGAGT--AAAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTT
** **
5521097 GATATATTTTGGTAGTTCAAATACTT
64 GATATATTTTGAAAGTTCAAATACCC
* * * * *
5521123 AAATGAATGAAAAAAAAA-CAGGGGCTTAATTGTTTTATTTTTTTGAAAAAGTTTGAGAGCCTTT
1 AATTGAGTAAAAAAAAAAGCAGGGGCTTAA-T-TATT-TTTTTTTG-AAAAGTTTGAGAGCATTT
* * *
5521187 TTTATGTATTTTGAAAGTTCAAGTACCC
62 TTGATATATTTTGAAAGTTCAAATACCC
5521215 AATTGAGTAAAAAAAA
1 AATTGAGTAAAAAAAA
5521231 GCAGCAACTT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
88 10 0.11
89 10 0.11
90 3 0.03
91 14 0.16
92 51 0.58
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (89 bp):
AATTGAGTAAAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGA
TATATTTTGAAAGTTCAAATACCC
Found at i:5521257 original size:92 final size:91
Alignment explanation
Indices: 5521069--5521264 Score: 214
Period size: 92 Copynumber: 2.1 Consensus size: 91
5521059 CTTAATTATT
** **
5521069 TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGGTAGTTCAAATACTTAAATGAATGAA
1 TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGAA
***
5521134 AAAAAAACAGGGGCTTAATTGTTTTA
66 AAAAAAACAGCAACTTAATTGTTTTA
* * * * * *
5521160 TTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGTATTTTGAAAGTTCAAGTACCCAATTGAGT-A
1 TTTTTTTG-AAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGA
* *
5521224 AAAAAAAGCAGCAACTTAATTGTCTTTTCT
65 AAAAAAAACAGCAACTTAATTG--TTTT-A
5521254 TTTTTTTGAAA
1 TTTTTTTGAAA
5521265 TGATGCAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
91 27 0.31
92 44 0.51
93 7 0.08
94 8 0.09
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (91 bp):
TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGAA
AAAAAAACAGCAACTTAATTGTTTTA
Found at i:5523341 original size:12 final size:13
Alignment explanation
Indices: 5523322--5523359 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5523312 TCGGTCAATA
5523322 ATTAGTTTTAATT
1 ATTAGTTTTAATT
* *
5523335 ATT-GTTTCATTT
1 ATTAGTTTTAATT
5523347 ATTAGTTTTAATT
1 ATTAGTTTTAATT
5523360 CTTTTTCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:5523377 original size:24 final size:25
Alignment explanation
Indices: 5523316--5523378 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
5523306 TTAAATTCGG
5523316 TCAATAATTAGTTTTAATTATTGTT
1 TCAATAATTAGTTTTAATTATTGTT
* * *
5523341 TCATTTATTAGTTTTAATTCTT-TT
1 TCAATAATTAGTTTTAATTATTGTT
*
5523365 TCAATAATCAGTTT
1 TCAATAATTAGTTT
5523379 GTACTTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (25 bp):
TCAATAATTAGTTTTAATTATTGTT
Found at i:5531963 original size:21 final size:22
Alignment explanation
Indices: 5531922--5531972 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
5531912 ATTTTCTCCC
* **
5531922 ATTATTTATTATTATTGTTA-T
1 ATTATTTATTATCATCATTATT
5531943 ATTATTTATTATCATCATTATT
1 ATTATTTATTATCATCATTATT
5531965 ATT-TTTAT
1 ATTATTTAT
5531973 ATTTGTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATTTATTATCATCATTATT
Found at i:5534605 original size:24 final size:24
Alignment explanation
Indices: 5534554--5534607 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
5534544 AGCTCAGGCA
* * *
5534554 AGCCAATAACGGGTAGCTCTGAAG
1 AGCCATTAACGAGAAGCTCTGAAG
* *
5534578 AGCCATTAACGAGAAGCTCTGGAT
1 AGCCATTAACGAGAAGCTCTGAAG
5534602 AGCCAT
1 AGCCAT
5534608 ATATCAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
AGCCATTAACGAGAAGCTCTGAAG
Found at i:5534721 original size:26 final size:27
Alignment explanation
Indices: 5534633--5534722 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 27
5534623 AGCAAGTTAT
*
5534633 ATCGGGAAGCTC-CGGAGAGCCAT-TA
1 ATCGGGAAGCTCACGAAGAGCCATATA
* * *
5534658 ATCAGGAAGCTCACAAAGAGCC-TTTA
1 ATCGGGAAGCTCACGAAGAGCCATATA
* *
5534684 ATTGGGTAGCTCACGAAGAGCCATAT-
1 ATCGGGAAGCTCACGAAGAGCCATATA
*
5534710 ATCGGGACGCTCA
1 ATCGGGAAGCTCA
5534723 TAAGAGCTGT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
25 12 0.24
26 37 0.73
27 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (27 bp):
ATCGGGAAGCTCACGAAGAGCCATATA
Found at i:5539174 original size:48 final size:48
Alignment explanation
Indices: 5539098--5539195 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
5539088 CATATGTTCC
*
5539098 ACCAGAGAACATTGAGAACATTATTTCTGCTCATGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
5539146 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
5539194 AC
1 AC
5539196 GAAATCCTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (48 bp):
ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
Found at i:5545079 original size:12 final size:12
Alignment explanation
Indices: 5545062--5545094 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5545052 CTCTTGAAAT
5545062 ACTTGTGTCCAC
1 ACTTGTGTCCAC
5545074 ACTTGTGTCCAC
1 ACTTGTGTCCAC
5545086 ACTTGTGTC
1 ACTTGTGTC
5545095 TGACACACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.36
Consensus pattern (12 bp):
ACTTGTGTCCAC
Found at i:5548086 original size:21 final size:21
Alignment explanation
Indices: 5548062--5548102 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5548052 ATTATTTGGG
5548062 AAAATGTA-AAAAAAATTTAAA
1 AAAAT-TATAAAAAAATTTAAA
*
5548083 AAAATTATAAATAAATTTAA
1 AAAATTATAAAAAAATTTAA
5548103 TATTTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTATAAAAAAATTTAAA
Found at i:5548810 original size:13 final size:13
Alignment explanation
Indices: 5548794--5548818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5548784 TTATGAAAAA
5548794 ATTATTATTATTT
1 ATTATTATTATTT
5548807 ATTATTATTATT
1 ATTATTATTATT
5548819 AAAATGTGTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:5555588 original size:13 final size:13
Alignment explanation
Indices: 5555570--5555594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5555560 AAATAGTAAA
5555570 TATATTTAAATTT
1 TATATTTAAATTT
5555583 TATATTTAAATT
1 TATATTTAAATT
5555595 ATAATAATAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAAATTT
Found at i:5557744 original size:41 final size:41
Alignment explanation
Indices: 5557676--5557876 Score: 271
Period size: 41 Copynumber: 4.9 Consensus size: 41
5557666 TGAGTTTTTG
* * * *
5557676 GGGCATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTG
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
5557717 GGGCCTCTAGCGACGCTTTTT-AGAAAGCGCCGCTAATGCTA
1 GGGCCTTTAGCGACG-TTTTTGAGAAAGCGCCGCTAATGCTC
*
5557758 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
5557799 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
5557840 GGGCCTTTAGC-AGCGTTTTTGAAAAAGTGCCGCTAAT
1 GGGCCTTTAGCGA-CGTTTTTGAGAAAGCGCCGCTAAT
5557877 AATAAAAAAA
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 5 0.03
41 134 0.93
42 5 0.03
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (41 bp):
GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
Found at i:5557824 original size:82 final size:82
Alignment explanation
Indices: 5557676--5557876 Score: 305
Period size: 82 Copynumber: 2.5 Consensus size: 82
5557666 TGAGTTTTTG
* *
5557676 GGGCATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGCCTCTAGCGACGCTTTTTAGA
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTTAGA
*
5557741 AAGCGCCGCTAATGCTA
66 AAGCGCCACTAATGCTA
* * *
5557758 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCG-TTTTTGAG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTT-AG
*
5557822 AAAGCGCCACTAATGCTC
65 AAAGCGCCACTAATGCTA
* *
5557840 GGGCCTTTAGCAGCGTTTTTGAAAAAGTGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
5557877 AATAAAAAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 5 0.05
82 103 0.95
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (82 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTTAGA
AAGCGCCACTAATGCTA
Found at i:5558786 original size:33 final size:33
Alignment explanation
Indices: 5558740--5558812 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
5558730 ATTAAATAAT
* * * *
5558740 GTTTAGGGGTTAGGGATTCGGGGTTGGGTTAGG
1 GTTTAGGGATTAGGAATTCAGGGTCGGGTTAGG
5558773 GTTTAGGGATTAGGAATTCAGGGTCGGGTTAGG
1 GTTTAGGGATTAGGAATTCAGGGTCGGGTTAGG
5558806 GTTTAGG
1 GTTTAGG
5558813 ATTTAGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.33
Consensus pattern (33 bp):
GTTTAGGGATTAGGAATTCAGGGTCGGGTTAGG
Found at i:5560626 original size:2 final size:2
Alignment explanation
Indices: 5560619--5560644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5560609 AATTTAGCTG
5560619 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
5560645 TTAGCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5563071 original size:50 final size:51
Alignment explanation
Indices: 5562975--5563074 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 51
5562965 TCAAAATTTT
5562975 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
1 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
* *
5563026 AAAATTTTCATTTAATCTCTTTAA-ATCTTTAATTATATCAGTTTTAATT
1 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATT
5563075 AGAATAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 25 0.53
51 22 0.47
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (51 bp):
AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
Found at i:5564071 original size:91 final size:91
Alignment explanation
Indices: 5563916--5564129 Score: 286
Period size: 91 Copynumber: 2.4 Consensus size: 91
5563906 TGATACATCG
* * * * * *
5563916 ATTGATAGTTCAAGTACCACATTGAACATTTTCCAAGTATAAGTACCACGTTGGGCAATTTATGA
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGACAATTTATGA
* **
5563981 AAGTACATGTGTCAAATAAGACACAA
66 AAGTACAGGTACCAAATAAGACACAA
* * *
5564007 ATTGATAGTTCAAGTATCACATTGGACATTTTCAAAGTAC-AGATATCACATTAGACATTTTATG
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAG-TACCACATTAGACAATTTATG
*
5564071 AAAGTACAGGTACCAAATAATACACAA
65 AAAGTACAGGTACCAAATAAGACACAA
*
5564098 ATTAATAGTTCAAGTACCACATTGGACATTTT
1 ATTGATAGTTCAAGTACCACATTGGACATTTT
5564130 ATGAAAGTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 2 0.02
91 105 0.98
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (91 bp):
ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGACAATTTATGA
AAGTACAGGTACCAAATAAGACACAA
Found at i:5566776 original size:2 final size:2
Alignment explanation
Indices: 5566769--5566823 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5566759 CAAAGATGGA
5566769 AT AT AT 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 AT AT AT
5566811 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5566824 AAATGCATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5567250 original size:41 final size:40
Alignment explanation
Indices: 5567192--5567333 Score: 212
Period size: 41 Copynumber: 3.5 Consensus size: 40
5567182 AAATATATTT
* *
5567192 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
5567232 ATTTTTTTAATTTTTAAAATATTTTTAAAATACTTTTTAAA
1 ATTTTTTTAA-TTTTAAAATATTTTTAAAATACTTTTTTAA
* *
5567273 ATTTTTTTAATTTTAAAATATTTTGAAAATATTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
5567313 ATTTTTTAAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
5567334 AATATGGGCC
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 46 0.49
41 47 0.51
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:5567257 original size:40 final size:39
Alignment explanation
Indices: 5567192--5567333 Score: 194
Period size: 40 Copynumber: 3.5 Consensus size: 39
5567182 AAATATATTT
*
5567192 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATA-TTTTTAAATACTTTTTTAA
*
5567232 ATTTTTTTAATTTTTAAAATATTTTTAAAATACTTTTTAAA
1 ATTTTTTTAA-TTTTAAAATATTTTT-AAATACTTTTTTAA
* *
5567273 ATTTTTTTAATTTTAAAATATTTTGAAAATATTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTT-TAAATACTTTTTTAA
*
5567313 ATTTTTTAAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
5567334 AATATGGGCC
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
40 50 0.54
41 42 0.46
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAATACTTTTTTAA
Found at i:5567286 original size:29 final size:29
Alignment explanation
Indices: 5567254--5567309 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
5567244 TTTAAAATAT
*
5567254 TTTTAAAATACTTTTTAAAAT-TTTTTTAA
1 TTTTAAAATA-TTTTGAAAATATTTTTTAA
5567283 TTTTAAAATATTTTGAAAATATTTTTT
1 TTTTAAAATATTTTGAAAATATTTTTT
5567310 TAAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAAATATTTTGAAAATATTTTTTAA
Found at i:5567326 original size:8 final size:9
Alignment explanation
Indices: 5567192--5567332 Score: 68
Period size: 9 Copynumber: 14.2 Consensus size: 9
5567182 AAATATATTT
*
5567192 ATTTTTTTA
1 ATTTTTTAA
**
5567201 ATTTTAAAA
1 ATTTTTTAA
5567210 TATTTTTTACA
1 -ATTTTTTA-A
5567221 TACTTTTTTAA
1 -A-TTTTTTAA
*
5567232 ATTTTTTTA
1 ATTTTTTAA
*
5567241 ATTTTTAAA
1 ATTTTTTAA
5567250 ATATTTTTAAA
1 AT-TTTTT-AA
5567261 ATACTTTTTAAA
1 AT--TTTTT-AA
*
5567273 ATTTTTTTA
1 ATTTTTTAA
*
5567282 A-TTTTAAA
1 ATTTTTTAA
*
5567290 ATATTTTGAAAA
1 AT-TTTT--TAA
5567302 TATTTTTTTAA
1 -A-TTTTTTAA
5567313 ATTTTTTAA
1 ATTTTTTAA
*
5567322 ATTTTTAAA
1 ATTTTTTAA
5567331 AT
1 AT
5567333 AAATATGGGC
Statistics
Matches: 105, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
8 6 0.06
9 42 0.40
10 21 0.20
11 10 0.10
12 20 0.19
13 5 0.05
14 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:5567713 original size:12 final size:12
Alignment explanation
Indices: 5567696--5567727 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5567686 ATATGAATGG
5567696 AATAATAATATT
1 AATAATAATATT
5567708 AATAATAATATT
1 AATAATAATATT
5567720 AATAATAA
1 AATAATAA
5567728 CAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAATAATATT
Found at i:5573649 original size:21 final size:21
Alignment explanation
Indices: 5573608--5573651 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5573598 TTTTTGTACT
* * *
5573608 TTTTAATAATTTTTAATATAA
1 TTTTAAAAATTTTAAAAATAA
5573629 TTTTAAAAATTTTAAAAATAA
1 TTTTAAAAATTTTAAAAATAA
5573650 TT
1 TT
5573652 AATTGCACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATTTTAAAAATAA
Found at i:5580712 original size:14 final size:15
Alignment explanation
Indices: 5580693--5580725 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5580683 AAATAAAGGG
5580693 CTTTTTCTTT-TTTT
1 CTTTTTCTTTATTTT
5580707 CTTTTTCTTTATTTT
1 CTTTTTCTTTATTTT
5580722 -TTTT
1 CTTTT
5580726 AACCTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTTCTTTATTTT
Found at i:5581415 original size:31 final size:31
Alignment explanation
Indices: 5581374--5581435 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5581364 AAAAAATAGA
5581374 TACAAACGTATAGCTGCTTGTAGAAACTCCC
1 TACAAACGTATAGCTGCTTGTAGAAACTCCC
*
5581405 TACAATCGTATAGCTGCTTGTAGAAACTCCC
1 TACAAACGTATAGCTGCTTGTAGAAACTCCC
5581436 CTCAACCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (31 bp):
TACAAACGTATAGCTGCTTGTAGAAACTCCC
Found at i:5583925 original size:40 final size:39
Alignment explanation
Indices: 5583870--5583991 Score: 217
Period size: 40 Copynumber: 3.1 Consensus size: 39
5583860 TGTTGCACTT
5583870 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTATTT-AACCCTAGTATTCTTGCTCTAAGGATTTTAC
5583910 TTCTATATTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTAT-TTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
5583950 TTCTATTTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTA-TTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
5583990 TT
1 TT
5583992 TGCTCCATCA
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
40 77 0.96
41 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (39 bp):
TTCTATTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
Found at i:5590302 original size:53 final size:54
Alignment explanation
Indices: 5590198--5590303 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 54
5590188 TATTCCTCTG
* *
5590198 AAAGCTTGGAAGCAGGAATAAGGCCCCCCTTAACAGAAATTGCAAAACTTTCCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCCC
5590252 AAAGCTTAGAAGCAGGAATAAGG-CCCCCTCAACAGAAATTGCAAAACTTTCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCC
5590304 GAACTATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 28 0.56
54 22 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (54 bp):
AAAGCTTAGAAGCAGGAATAAGGCCCCCCTCAACAGAAATTGCAAAACTTTCCC
Found at i:5595226 original size:4 final size:4
Alignment explanation
Indices: 5595217--5595364 Score: 52
Period size: 4 Copynumber: 37.8 Consensus size: 4
5595207 GGGAAAGGAG
* *
5595217 AAGA AAG- AA-A AAGA AAG- AA-A AAGA AAGGA AAGGA GAGGG AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AA-GA -AAGA AAGA AAGA
*
5595263 AA-A AAGA ATGA AAGAA AAGGA AAG- AAG- AAGA AA-A AAGA AAG- AA-A
1 AAGA AAGA AAGA AAG-A AA-GA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* ** *
5595307 AAGA AGGA AAGAA AAGGA AAGGA GAAG- AAG- AAGA GGGA AGGAA AAGA
1 AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA AAG-A AAGA
5595354 AAGA AAGA AAG
1 AAGA AAGA AAG
5595365 GTAATTTTTG
Statistics
Matches: 113, Mismatches: 12, Indels: 38
0.69 0.07 0.23
Matches are distributed among these distances:
3 31 0.27
4 50 0.44
5 27 0.24
6 5 0.04
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:5595302 original size:27 final size:31
Alignment explanation
Indices: 5595227--5595307 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 31
5595217 AAGAAAGAAA
* *
5595227 AAGAAAG--AAAAAGAAAGGAAAGGAGAGGG
1 AAGAAAGAAAAAAAGAAAGAAAAGGAGAGAG
5595256 AAGAAAGAAAAAGAATGAAAGAAAAGGA-A-AG
1 AAGAAAGAAAAA-AA-GAAAGAAAAGGAGAGAG
5595287 AAG-AAG-AAAAAAGAAAGAAAA
1 AAGAAAGAAAAAAAGAAAGAAAA
5595308 AGAAGGAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
27 9 0.20
28 2 0.04
29 11 0.24
30 3 0.07
31 7 0.15
32 3 0.07
33 11 0.24
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (31 bp):
AAGAAAGAAAAAAAGAAAGAAAAGGAGAGAG
Found at i:5595323 original size:10 final size:11
Alignment explanation
Indices: 5595217--5595362 Score: 82
Period size: 10 Copynumber: 13.8 Consensus size: 11
5595207 GGGAAAGGAG
5595217 AAGAAAGAA-A
1 AAGAAAGAAGA
5595227 AAGAAAGAA-A
1 AAGAAAGAAGA
5595237 AAGAAAG--GA
1 AAGAAAGAAGA
*
5595246 AAGGAGAGGGAAGA
1 AA-GA-A-AGAAGA
5595260 AAGAAA-AAGA
1 AAGAAAGAAGA
*
5595270 ATGAAAGAA-A
1 AAGAAAGAAGA
*
5595280 AGGAAAGAAG-
1 AAGAAAGAAGA
*
5595290 AAGAAAAAAGA
1 AAGAAAGAAGA
5595301 AAGAAA-AAGA
1 AAGAAAGAAGA
*
5595311 AGGAAAGAA-A
1 AAGAAAGAAGA
* *
5595321 AGGAAAGGAG-
1 AAGAAAGAAGA
5595331 AAG-AAGAAGA
1 AAGAAAGAAGA
*
5595341 GGGAAGGAA-AAGA
1 ---AAGAAAGAAGA
5595354 AAGAAAGAA
1 AAGAAAGAA
5595363 AGGTAATTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
9 8 0.07
10 70 0.65
11 13 0.12
12 2 0.02
13 9 0.08
14 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:5596066 original size:309 final size:312
Alignment explanation
Indices: 5595689--5596322 Score: 951
Period size: 307 Copynumber: 2.0 Consensus size: 312
5595679 AAAAATGGTA
* * * *
5595689 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAATA
* * *
5595754 AAATTAAAAATTATGGTATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAATAAATAGCC
66 AAATTAAAAATTATGATA-TTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAACAAAGAGCC
* *
5595819 GAAGTAAGAGAGTTTTACTAAATTTTTAAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
129 GAAGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACA
5595884 AAATGTACTG-G-AA-T-AAT-ATAAAATAAT-AAAATAATATATTTTTATTGAAAGTAATAAAA
194 AAATGTACTGAGTAAGTAAATAATAAAAT-ATGAAAATAATATATTTTTATTGAAAGTAATAAAA
*
5595943 TTCGAGAAAATAATACGAGCAAAAGGCAGGAATACGGG-TTTTTTTACACTAAAT
258 TTCGAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
* *
5595997 TAATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTAT
1 T-ATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAAT
* * * *
5596062 AAAATTAGAAATTATGATATTTTTAAAGTAATAAAATGCTGAGAAAAAATACGAACAAAGGGCTG
65 AAAATTAAAAATTATGATATTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGAGCCG
* * *
5596127 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
130 AAGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACAA
5596192 AATGTACTGAAGTAATGTAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAA
195 AATGTACTG-AGTAA-GT-AAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAA
* * *
5596257 ATTCGAGAAAATTATACGAGTAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAAT
257 ATTCGAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
5596313 T-TTTAAAAAT
1 TATTTAAAAAT
5596323 TTATATTGAA
Statistics
Matches: 293, Mismatches: 22, Indels: 16
0.89 0.07 0.05
Matches are distributed among these distances:
307 87 0.30
308 24 0.08
309 75 0.26
310 2 0.01
312 1 0.00
314 14 0.05
315 73 0.25
316 17 0.06
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (312 bp):
TATTTAAAAATCAAACTAAATTAATAAATTTCAAACATAATGCACTAAAATAATATAAAATAATA
AAATTAAAAATTATGATATTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGAGCCGA
AGTAAGAGACTTTTACTAAATTTTTAAAAAATTCAAAAATAATGAATACAAATATTTCAAACAAA
ATGTACTGAGTAAGTAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTC
GAGAAAATAATACGAGCAAAAGGCAGGAATAAGGGTTTTTTTTACACTAAAT
Found at i:5596238 original size:156 final size:152
Alignment explanation
Indices: 5595716--5596267 Score: 534
Period size: 156 Copynumber: 3.5 Consensus size: 152
5595706 AAATTAATAA
* * * *
5595716 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAAAAATTATGGTATTTTTTAAA
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATT-AAAATTATGATA-TTTTTAAA
* **
5595781 GTAATAAAATGCGGAGAAAAAAATACGAATAAATA-GCCGAAGTAAGAGAGTTTTACTAAATTTT
64 GTAATAAAATGC-GAG-AAAAAATACGAACAAA-AGGCCGAAGTAAGAGTCTTTTACTAAATTTT
*
5595845 TAAAAAATTCAAAAATAATTAATACAAAT
126 TTAAAAATTC-AAAATAA-TAATACAAAT
* *
5595874 ATTTCAAACAAAATGTACTGGAATAATATAAAATAATAAAA-T--AA-TAT-ATTTTTATTGAAA
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTAAAATTATGATATTT-TT-AAA
* * * * * *
5595934 GTAATAAAATTCGAGAAAATAATACGAGCAAAAGGCAGGAA-TACGGGTTTTTTTACACTAAATT
64 GTAATAAAATGCGAGAAAA-AATACGAACAAAAGGC-CGAAGTAAGAG-TCTTTT--ACTAAATT
* * *
5595998 AATTTAAAAA-TCAAACTAA-ATTA-ATAA-
124 -TTTTAAAAATTCAAAATAATAATACA-AAT
* * *
5596025 ATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTAGAAATTATGATATTTTTAAAG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTA-AAATTATGATATTTTTAAAG
* *
5596090 TAATAAAATGCTGAGAAAAAATACGAACAAAGGGCTGAAGTAAGAGTCTTTTACTAAATTTTTTA
65 TAATAAAATGC-GAGAAAAAATACGAACAAAAGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTA
5596155 AAAATTCAGAAATAATGAATACAAAT
129 AAAATTCA-AAATAAT-AATACAAAT
* * *
5596181 ATTTCAAACAAAATGTACTGAAGTAATGTAAAATAATAAAATATGAAAATAATAT-ATTTTTATT
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAAT-T-AAAAT--TATGATATTT-TT
*
5596245 GAAAGTAATAAAATTCGAGAAAA
61 -AAAGTAATAAAATGCGAGAAAA
5596268 TTATACGAGT
Statistics
Matches: 324, Mismatches: 40, Indels: 59
0.77 0.09 0.14
Matches are distributed among these distances:
151 54 0.17
152 39 0.12
153 29 0.09
154 16 0.05
155 49 0.15
156 57 0.18
157 11 0.03
158 43 0.13
159 12 0.04
160 14 0.04
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.31
Consensus pattern (152 bp):
ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATTAAAATTATGATATTTTTAAAGT
AATAAAATGCGAGAAAAAATACGAACAAAAGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAA
AATTCAAAATAATAATACAAAT
Found at i:5598368 original size:9 final size:9
Alignment explanation
Indices: 5598349--5598388 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
5598339 TTTGGTTAAA
*
5598349 AATTAATCG
1 AATTAACCG
*
5598358 AATTACCCG
1 AATTAACCG
5598367 AATTAACCG
1 AATTAACCG
5598376 AATTAACCG
1 AATTAACCG
5598385 AATT
1 AATT
5598389 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:5598372 original size:18 final size:18
Alignment explanation
Indices: 5598349--5598393 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5598339 TTTGGTTAAA
*
5598349 AATTAATCGAATTACCCG
1 AATTAATCGAATTAACCG
*
5598367 AATTAACCGAATTAACCG
1 AATTAATCGAATTAACCG
5598385 AATTGAATC
1 AATT-AATC
5598394 ACTACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTAATCGAATTAACCG
Found at i:5598452 original size:13 final size:13
Alignment explanation
Indices: 5598420--5598452 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5598410 ATTTTTAGAC
*
5598420 TTTTAGACTTTAG
1 TTTTAGTCTTTAG
5598433 TTTTAGTCTTTAG
1 TTTTAGTCTTTAG
5598446 TTTTAGT
1 TTTTAGT
5598453 AATTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61
Consensus pattern (13 bp):
TTTTAGTCTTTAG
Found at i:5601294 original size:40 final size:41
Alignment explanation
Indices: 5601227--5601332 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
5601217 AATAGTCTTA
*
5601227 TACTCAAAATAATACTAACTAACAATAATAAT-TAGGGTTT
1 TACTAAAAATAATACTAACTAACAATAATAATATAGGGTTT
* * **
5601267 TACTAAAAATAATAACTAAC-CATAATAATAATACTAGTTTTT
1 TACTAAAAATAAT-ACTAACTAACAATAATAATA-TAGGGTTT
* *
5601309 TACTAACAATAATACTAAGTAACA
1 TACTAAAAATAATACTAACTAACA
5601333 TTTAAACCCT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
40 22 0.42
41 11 0.21
42 20 0.38
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (41 bp):
TACTAAAAATAATACTAACTAACAATAATAATATAGGGTTT
Found at i:5601357 original size:3 final size:3
Alignment explanation
Indices: 5601349--5601392 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5601339 CCCTAAAAAC
5601349 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5601393 CTAACTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5601546 original size:10 final size:10
Alignment explanation
Indices: 5601518--5601554 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5601508 AAATACATTT
5601518 TTTTTCTCTTC
1 TTTTTCTC-TC
*
5601529 TCTTTCTCTC
1 TTTTTCTCTC
5601539 TTTTTCTCTC
1 TTTTTCTCTC
5601549 TTTTTC
1 TTTTTC
5601555 CGGCAGCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:5602690 original size:21 final size:20
Alignment explanation
Indices: 5602652--5602690 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5602642 AATATATTAT
*
5602652 TATTTTATTTTAATATTTAA
1 TATTTTATTTTAAAATTTAA
*
5602672 TATTTTTTTATTAAAATTT
1 TATTTTATT-TTAAAATTT
5602691 TTTATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTATTTTAAAATTTAA
Found at i:5604525 original size:22 final size:22
Alignment explanation
Indices: 5604500--5604551 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5604490 TCAGCACGTC
* *
5604500 GGTGTCTACTG-TCCAATACTTT
1 GGTGCCTACTGCT-CAACACTTT
5604522 GGTGCCTACTGCTCAACACTTT
1 GGTGCCTACTGCTCAACACTTT
5604544 GGTGCCTA
1 GGTGCCTA
5604552 TTGGTGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (22 bp):
GGTGCCTACTGCTCAACACTTT
Found at i:5617333 original size:12 final size:12
Alignment explanation
Indices: 5617318--5617362 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5617308 TGAGTAAATA
*
5617318 ATAATAATGATG
1 ATAATAATAATG
5617330 ATAATAATAATG
1 ATAATAATAATG
5617342 -TAAT-ATAAT-
1 ATAATAATAATG
5617351 AGTAATAATAAT
1 A-TAATAATAAT
5617363 TGGGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 5 0.17
11 8 0.28
12 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:5617843 original size:83 final size:84
Alignment explanation
Indices: 5617730--5618228 Score: 415
Period size: 87 Copynumber: 5.8 Consensus size: 84
5617720 GTTTTAATCG
** * *
5617730 GCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCTG-TCTGCTTCACTACTGCTTAGGGA
1 GCTCCACTACTGC-TTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGA
*
5617794 GATAATACTTGGTGCGATCT
65 GATAAGACTTGGTGCGATCT
* * *
5617814 GCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTG-TCTGCTCCATTACTGCTTAGGGAG
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGAG
* *
5617878 ATAAGACTTGATGTGATCT
66 ATAAGACTTGGTGCGATCT
* * * *
5617897 ACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTT-TGACCTGCTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTCTGATCTGCTCCACTACTGCTTAGGGA
* *
5617960 GATAGGAC-TGGTGGCTTAAATCT
65 GATAAGACTTGGT-GC---GATCT
* * **
5617983 GCTTCACTACTGCTTAGGAAGATAAGATTCGCCATT-TTC-GATCTGCTCCACTACTGCTTAGGG
1 GCTCCACTACTGCTTAGGGAGATAAGATT-G-GTTTCTTCTGATCTGCTCCACTACTGCTTAGGG
* * ** *
5618046 AGATAAGATCTACCGTATTTGACCT
64 AGATAAGA-CT--TG-GTGCGATCT
**** * *
5618071 GCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC-GACCTACTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGA
* *
5618135 GATAGGAC-TGGTGGCTTAAATCT
65 GATAAGACTTGGT-GC---GATCT
* * * * * *
5618158 ACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTC-GATCTACTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTCTGATCTGCTCCACTACTGCTTAGGGA
5618222 GATAAGA
65 GATAAGA
5618229 TCTACCATCT
Statistics
Matches: 336, Mismatches: 57, Indels: 41
0.77 0.13 0.09
Matches are distributed among these distances:
82 31 0.09
83 98 0.29
84 12 0.04
86 7 0.02
87 122 0.36
88 63 0.19
89 1 0.00
91 1 0.00
92 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (84 bp):
GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTCTGATCTGCTCCACTACTGCTTAGGGAG
ATAAGACTTGGTGCGATCT
Found at i:5617870 original size:43 final size:42
Alignment explanation
Indices: 5617730--5618269 Score: 299
Period size: 44 Copynumber: 12.6 Consensus size: 42
5617720 GTTTTAATCG
** *
5617730 GCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCT
1 GCTCCACTACTGC-TTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * *
5617774 GCTTCACTACTGCTTAGGGAGATAATACTTGG-TGC---GATCT
1 GCTCCACTACTGCTTAGGGAGATAAGA-TTGGTTTCTTTG-TCT
*
5617814 GCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTGTCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTC-TTTGTCT
* * *
5617857 GCTCCATTACTGCTTAGGGAGATAAGACTT-G---ATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGA-TTGGTTTCTTTG-TCT
* * * *
5617897 ACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTTG-TCT
* * ** **
5617940 GCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * ** *
5617983 GCTTCACTACTGCTTAGGAAGATAAGATTCGCCATT-TTCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATT-G-GTTTCTTTG-TCT
**** * *
5618027 GCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
**** * *
5618071 GCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
* * * ** **
5618115 ACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTT-TGTCT
* * * * * *
5618158 ACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTGGT-TTCTTTG-TCT
* **** *
5618202 ACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCT
1 GCTCCACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTTG-TCT
*
5618246 GCACCACTACTGCTTAGGGAGATA
1 GCTCCACTACTGCTTAGGGAGATA
5618270 GGACTACTAG
Statistics
Matches: 394, Mismatches: 77, Indels: 50
0.76 0.15 0.10
Matches are distributed among these distances:
38 2 0.01
39 31 0.08
40 34 0.09
43 116 0.29
44 209 0.53
45 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
GCTCCACTACTGCTTAGGGAGATAAGATTGGTTTCTTTGTCT
Found at i:5618052 original size:44 final size:43
Alignment explanation
Indices: 5617809--5618269 Score: 330
Period size: 44 Copynumber: 10.7 Consensus size: 43
5617799 TACTTGGTGC
* * *
5617809 GATCTGCTCCACTACTGCTTAGGGATATAAGATTGGTTTC-TTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCG--CCATTTT
* *
5617853 G-TCTGCTCCATTACTGCTTAGGGAGATAAGACTT-G--A-TGT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-TTCGCCATTTT
* * *
5617892 GATCTACT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCAT-TTT
* * * * **** *
5617935 GACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* * *
5617978 AATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* *
5618021 CGATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTACCGTATTT
1 -GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* * *
5618066 GACCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTACCATCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* * * * * **** *
5618110 GACCTACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
* * * * * * *
5618153 AATCTACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCAT-TTT
* *
5618197 GATCTACTCCACTACTGCTTAGGGAGATAAGA-TCTACCATCTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGATTC-GCCAT-TTT
* *
5618241 GACCTGCACCACTACTGCTTAGGGAGATA
1 GATCTGCTCCACTACTGCTTAGGGAGATA
5618270 GGACTACTAG
Statistics
Matches: 337, Mismatches: 65, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.01
39 26 0.08
40 5 0.01
41 1 0.00
43 107 0.32
44 192 0.57
45 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
GATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGCCATTTT
Found at i:5618085 original size:131 final size:126
Alignment explanation
Indices: 5617812--5618097 Score: 349
Period size: 126 Copynumber: 2.2 Consensus size: 126
5617802 TTGGTGCGAT
* * ** *** * *
5617812 CTGCTCCACTACTGCTTAGGGATATAAGATTGGTTTCTTTTGTCTGCTCCATTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
* ** *
5617877 GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGAC
66 GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATCTACCATATTTGAC
* *
5617938 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
* * *
5618003 GATAAGA-TTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTG
66 GATAAGACTT-G--A-TGT-GATCTACT-CACTACTGCTTAGGGAGATAAGATCTACCATATTTG
5618067 AC
125 AC
5618069 CTGCTCCACTACTGCTTAGGGAGATAAGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGA
5618098 TCTACCATCT
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
125 2 0.01
126 62 0.46
128 1 0.01
129 2 0.01
130 7 0.05
131 61 0.45
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (126 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTACTGCTTAGGAA
GATAAGACTTGATGTGATCTACTCACTACTGCTTAGGGAGATAAGATCTACCATATTTGAC
Found at i:5618122 original size:175 final size:174
Alignment explanation
Indices: 5617778--5618269 Score: 646
Period size: 175 Copynumber: 2.9 Consensus size: 174
5617768 CTGTCTGCTT
** * * * *
5617778 CACTACTGCTTAGGGAGATAATACTTGGT-GC---GATCTGCTCCACTACTGCTTAGGGATATAA
1 CACTACTGCTTAGGGAGATAGGAC-TGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAA
* * * * * *
5617839 GATTGGTTTCTTTT-G-TCTGCTCCATTACTGCTTAGGGAGATAAGA-CT--TG-ATGTGATCTA
65 GATTCG--TCTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTG
* ** * *
5617898 CT-CACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCTGCTC
128 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
5617944 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
1 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
*
5618009 ATTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
66 ATTCGTC-TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
5618074 CCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
130 CCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
*
5618119 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAG
1 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
* * * * *
5618184 ATTCGTCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCA
66 ATTCGTC-TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCT
5618249 CCACTACTGCTTAGGGAGATA
130 CCACTACTGCTTAGGGAGATA
5618270 GGACTACTAG
Statistics
Matches: 288, Mismatches: 26, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
165 4 0.01
166 24 0.08
167 1 0.00
168 4 0.01
169 32 0.11
170 29 0.10
171 2 0.01
173 1 0.00
174 9 0.03
175 182 0.63
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (174 bp):
CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAG
ATTCGTCTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTACTC
Found at i:5618166 original size:131 final size:130
Alignment explanation
Indices: 5617893--5618274 Score: 401
Period size: 131 Copynumber: 2.9 Consensus size: 130
5617883 ACTTGATGTG
* *
5617893 ATCTAC-TCACTACTGCTTAGGGAGATAAGATTTGTCATCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGA-TT-CCGTCTTTGACCTGCTCCACTACTGCTTAG
* ***** * * * * * * **
5617957 GGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCATTTT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTT
**
5618021 CG
129 AA
* * *
5618023 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCGTATTTGACCTGCTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGAT-T-CCGTCTTTGACCTGCTCCACTACTGCTTAG
* * ***
5618088 GGAGATAAGATCTACCATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGACT-GGTGGCTT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTT
5618152 AA
129 AA
* * * *
5618154 ATCTACTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGATCTACTCCACTACTGCTTAG
1 ATCTACTTCACTACTGCTTAGGGAGATAAGATTC--CGTCTTTGACCTGCTCCACTACTGCTTAG
* *
5618219 GGAGATAAGATCTACCATCTTTGACCTGCACCACTACTGCTTAGGGAGATAGGACT
64 GGAGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACT
5618275 ACTAGCTTCA
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
129 1 0.00
130 7 0.03
131 170 0.81
132 32 0.15
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (130 bp):
ATCTACTTCACTACTGCTTAGGGAGATAAGATTCCGTCTTTGACCTGCTCCACTACTGCTTAGGG
AGATAAGATCTACCATCTTAGACCTGCTCCACTACTGCTTAGGGAGATAGGACTCGCCAGCTTAA
Found at i:5618478 original size:46 final size:46
Alignment explanation
Indices: 5618414--5618938 Score: 269
Period size: 46 Copynumber: 11.7 Consensus size: 46
5618404 ACTAGCTTTA
*
5618414 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
* * * *
5618460 GTCTGTTCCACTGTAATCTCAGGGAAATAAGATCTG--A---TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
* * * **** *
5618501 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCTTTGGTT-TT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAATTCTTCG
* * * * * *
5618545 ATCCGCTCCACTGTAATATCAGAGAGAT-AGCAT-T--ACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAG-ATCTGAAAT-TCTTCG
* * *
5618589 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCAGAAATTATTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
* * * * * *
5618635 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CTTG-CA-TATTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC-TGAAATTCTTCG
* * * * *
5618679 ACCTGCCCCACTGTAA-CTTCAGGGAAATAAGGT-TCG---TGGCTTCG
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCT-GAAAT-TCTTCG
**
5618723 ATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
* * * * * *
5618769 GTCTACTCCACTGTAACCTCAGGGAGATAA-AACTTGCATATTC-T-A
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC-TG-AAATTCTTCG
* * * *
5618814 ACCT-CGTCCCACCTCGTAA-CTTCA-GGAGATAAGGT-T-TAGTTGCTTCG
1 ATCTGC-T-CCA-CT-GTAATC-TCAGGGAGATAAGATCTGAAATT-CTTCG
**
5618861 ATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
* * *
5618907 GTCTACTCCACTGTAACCTCAGGGAGATAAGA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA
5618939 CTTGCATATT
Statistics
Matches: 357, Mismatches: 81, Indels: 82
0.69 0.16 0.16
Matches are distributed among these distances:
40 1 0.00
41 31 0.09
43 7 0.02
44 122 0.34
45 26 0.07
46 136 0.38
47 26 0.07
48 8 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (46 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
Found at i:5618483 original size:175 final size:175
Alignment explanation
Indices: 5618295--5618667 Score: 579
Period size: 175 Copynumber: 2.1 Consensus size: 175
5618285 ATTTGCTCTG
5618295 CTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGCAACTTCAGAGAAATAAGATC
1 CTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGCAACTTCAGAGAAATAAGAT-
* * *
5618360 CTTT-ATTTTAATCCGCTCCACTGTAATCTCA-AGGAGATAGGATTACTAGCTTTAATCTGCTCC
65 CTTTGATTTTAATCCGCTCCACTGTAATATCAGA-GAGATAGCATTACTAGCTTCAATCTGCTCC
* * **
5618423 GCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCA
129 GCTGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCA
* * * * * *
5618470 CTGTAATCTCAGGGAAATAAGATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGCAACTTCAGAGAAATAAGATC
*
5618535 TTTGGTTTTAATCCGCTCCACTGTAATATCAGAGAGATAGCATTACTAGCTTCAATCTGCTCCGC
66 TTTGATTTTAATCCGCTCCACTGTAATATCAGAGAGATAGCATTACTAGCTTCAATCTGCTCCGC
5618600 TGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCA
131 TGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCA
*
5618645 CTGTAACCTCAGGGAGATAAGAC
1 CTGTAATCTCAGGGAGATAAGAC
5618668 TTGCATATTC
Statistics
Matches: 179, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
174 4 0.02
175 174 0.97
176 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (175 bp):
CTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGCAACTTCAGAGAAATAAGATC
TTTGATTTTAATCCGCTCCACTGTAATATCAGAGAGATAGCATTACTAGCTTCAATCTGCTCCGC
TGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCA
Found at i:5618690 original size:134 final size:134
Alignment explanation
Indices: 5618470--5618982 Score: 636
Period size: 134 Copynumber: 3.8 Consensus size: 134
5618460 GTCTGTTCCA
* * * * * *
5618470 CTGTAATCTCAGGGAAATAAGATCTG--A---TGCGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
* * * * *
5618530 AGATCTTTG-GT-TTTAATCC-GCTCCACTGTAA-TATCAGAGAGAT-AGCATTACTAGCTTCAA
66 AGA-C-TTGCATATTCAA-CCTGCCCCACTGTAACT-TCAGGGAGATAAG-ATTACTAGCTTCGA
**
5618590 TCTGCTCCG
126 TCTGCTCTT
* *
5618599 CTGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
* * *
5618664 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTT-CGTGGCTTCGATCTG
66 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGATTAC-TAGCTTCGATCTG
5618728 CTCTT
130 CTCTT
5618733 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
* * * * *
5618798 AAACTTGCATATTCTAACCTCGTCCCACCTCGTAACTTCA-GGAGATAAGGTTTAGTTGCTTCGA
66 AGACTTGCATATTC-AACCT-GCCCCA-CT-GTAACTTCAGGGAGATAA-GATTACTAGCTTCGA
5618862 TCTGCTCTT
126 TCTGCTCTT
5618871 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
5618936 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGA
66 AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGA
5618983 CTTTATGCGA
Statistics
Matches: 338, Mismatches: 28, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
129 24 0.07
131 1 0.00
132 3 0.01
133 5 0.01
134 156 0.46
135 18 0.05
136 10 0.03
137 14 0.04
138 107 0.32
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (134 bp):
CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
AGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCGATCTGC
TCTT
Found at i:5618692 original size:44 final size:44
Alignment explanation
Indices: 5618640--5618985 Score: 188
Period size: 44 Copynumber: 7.7 Consensus size: 44
5618630 ATTCGGTCTA
5618640 CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTG
* * * * * * * *
5618684 CCCCACTGTAACTTCAGGGAAATAAG-GTT-CGTGGCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACTTGCAT--ATTCAACCTG
** * * ** *
5618728 CTCTTCTGTAATCTCAGGGAGATAAGA-TCTG-AAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACT-TGCATATTCAAC---CTG
*
5618774 CTCCACTGTAACCTCAGGGAGATAAAACTTGCATATTCTAACCT-
1 CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTC-AACCTG
* ** * * * *
5618818 CGTCCCACCTCGTAACTTCA-GGAGATAAGGTTTAG-TTGCTTCGATCTG
1 C-T-CCA-CT-GTAACCTCAGGGAGATAAGACTT-GCAT-ATTCAACCTG
** * * ** *
5618866 CTCTTCTGTAATCTCAGGGAGATAAGA-TCTG-AAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACT-TGCATATTCAAC---CTG
5618912 CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTG
* *
5618956 CCCCACTGTAACTTCAGGGAGATAAGACTT
1 CTCCACTGTAACCTCAGGGAGATAAGACTT
5618986 TATGCGACCT
Statistics
Matches: 220, Mismatches: 57, Indels: 50
0.67 0.17 0.15
Matches are distributed among these distances:
42 2 0.01
43 8 0.04
44 91 0.41
45 16 0.07
46 59 0.27
47 30 0.14
48 14 0.06
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTG
Found at i:5618895 original size:138 final size:134
Alignment explanation
Indices: 5618583--5618981 Score: 656
Period size: 138 Copynumber: 2.9 Consensus size: 134
5618573 AGCATTACTA
* ** * *
5618583 GCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCAGAAATTATTCGGTCTACTCCACTG
1 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
*
5618648 TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAAATAAGGTT
66 TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTT
*
5618713 CGTG
131 AGTG
5618717 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
1 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
* *
5618782 TAACCTCAGGGAGATAAAACTTGCATATTCTAACCTCGTCCCACCTCGTAACTTCA-GGAGATAA
66 TAACCTCAGGGAGATAAGACTTGCATATTC-AACCT-GCCCCA-CT-GTAACTTCAGGGAGATAA
*
5618846 GGTTTAGTT
127 GG-TTAGTG
5618855 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
1 GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
5618920 TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAG
66 TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAG
5618982 ACTTTATGCG
Statistics
Matches: 247, Mismatches: 12, Indels: 11
0.91 0.04 0.04
Matches are distributed among these distances:
134 98 0.40
135 16 0.06
136 10 0.04
137 16 0.06
138 107 0.43
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (134 bp):
GCTTCGATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
TAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGTT
AGTG
Found at i:5619008 original size:41 final size:42
Alignment explanation
Indices: 5618914--5619010 Score: 124
Period size: 44 Copynumber: 2.3 Consensus size: 42
5618904 TCGGTCTACT
* *
5618914 CCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCC
1 CCACTGTAACTTCAGGGAGATAAGACTT--ATATGCAACCTGCC
* *
5618958 CCACTGTAACTTCAGGGAGATAAGACTT-TATGCGACCTGCT
1 CCACTGTAACTTCAGGGAGATAAGACTTATATGCAACCTGCC
*
5618999 CTACTGTAACTT
1 CCACTGTAACTT
5619011 TAGAGAGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 21 0.44
44 27 0.56
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (42 bp):
CCACTGTAACTTCAGGGAGATAAGACTTATATGCAACCTGCC
Found at i:5620401 original size:7 final size:7
Alignment explanation
Indices: 5620386--5620441 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
5620376 TTAGCCTCTC
5620386 CATTTTT
1 CATTTTT
*
5620393 CAATTTT
1 CATTTTT
5620400 CA-TTTT
1 CATTTTT
*
5620406 CTTTTTT
1 CATTTTT
*
5620413 TATTTTT
1 CATTTTT
5620420 CA-TTTT
1 CATTTTT
5620426 CATTTTT
1 CATTTTT
5620433 CATTTTT
1 CATTTTT
5620440 CA
1 CA
5620442 GAGTGCCCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 11 0.26
7 31 0.74
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:5620419 original size:20 final size:20
Alignment explanation
Indices: 5620386--5620441 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5620376 TTAGCCTCTC
*
5620386 CATTTTTCAATTTTCATTTT
1 CATTTTTCATTTTTCATTTT
* *
5620406 CTTTTTTTATTTTTCATTTT
1 CATTTTTCATTTTTCATTTT
5620426 CATTTTTCATTTTTCA
1 CATTTTTCATTTTTCA
5620442 GAGTGCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTTTCATTTTTCATTTT
Found at i:5621458 original size:39 final size:40
Alignment explanation
Indices: 5621364--5621476 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 40
5621354 TTTTTCTCAG
* * *
5621364 TTTCATTTTCATTTTGATCTTGATTTTGATTTTTTTCTTC
1 TTTCATTTTCATTTTAATTTTGATTTTGATTTTTTTCCTC
* * *
5621404 TTTC-TTCTT-TTTTTTATTTTTATTTTTGATTTTTTTCCT-
1 TTTCATT-TTCATTTTAATTTTGA-TTTTGATTTTTTTCCTC
*
5621443 TTTCATTTTCATTTTAACTTTGATTTTGATTTTT
1 TTTCATTTTCATTTTAATTTTGATTTTGATTTTT
5621477 ATTTTTCTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
39 28 0.47
40 32 0.53
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (40 bp):
TTTCATTTTCATTTTAATTTTGATTTTGATTTTTTTCCTC
Found at i:5622159 original size:26 final size:28
Alignment explanation
Indices: 5622130--5622185 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
5622120 TGAAATAATC
*
5622130 AGAAATAATTATTCAAAAA-GAATG-AA
1 AGAAATAATTACTCAAAAAGGAATGCAA
* *
5622156 AG-AATATTTGCTCAAAAAGGAATGCAA
1 AGAAATAATTACTCAAAAAGGAATGCAA
5622183 AGA
1 AGA
5622186 TGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (28 bp):
AGAAATAATTACTCAAAAAGGAATGCAA
Found at i:5625408 original size:2 final size:2
Alignment explanation
Indices: 5625401--5625425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5625391 GTATAAAAAG
5625401 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5625426 GAGTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5629766 original size:83 final size:84
Alignment explanation
Indices: 5629606--5630023 Score: 245
Period size: 86 Copynumber: 4.9 Consensus size: 84
5629596 CTTAACTAAA
* * *
5629606 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTTCGCTAAGTTAATAGCAAAATCATTGTTGAC
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
*
5629671 CTTTTAAGGCACTTAGCGG
66 CTCTTAAGGCACTTAGCGG
* * * **
5629690 TTTATTTGA-GCACACACCTTTT-AAGGGTATTGTCCGCTAAGTTAATAGTAGAATTTTTGCTAA
1 TTTATTTCAGGCACACA-CTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAA
* **
5629753 CCTCTTAATGCACTTAGCCAAA
65 CCTCTTAAGGCACTTAG-C-GG
* * * * * * * * * * * *
5629775 TTTATTTGAAGCACAC-CCTAT-GAGAGTATTGTTCACTAAGTTGATAGCAGAACCACTGCTAAC
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
* * **
5629838 CTCTCAATGCACTTAGTCAAA
66 CTCTTAAGGCACTTAG-C-GG
* * ** * * * * * * *
5629859 TTTATTTAAGGCGCACACCCTACAAGGGTA-TGACTTGCTAAGTCAATAGTAGAATCATTGCTAG
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTC-CGCTAAGTTAATAGCAAAATCATTGCTAA
* * *
5629923 CCTCCTAAGACACTTAGCGAAA
65 CCTCTTAAGGCACTTAGCG--G
* * * * * * * * * *
5629945 TTTATTTAAGGCACACACCTTACGAGGGTGTTG-CTAGTTAAGTTAATAGCAAAAACGTTGCTAG
1 TTTATTTCAGGCACACACTTTTCAAGGGTATTGTC-CGCTAAGTTAATAGCAAAATCATTGCTAA
5630009 CCTCTTAAGGCACTT
65 CCTCTTAAGGCACTT
5630024 GGCTAAGTTT
Statistics
Matches: 262, Mismatches: 62, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
83 56 0.21
84 81 0.31
85 14 0.05
86 109 0.42
87 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (84 bp):
TTTATTTCAGGCACACACTTTTCAAGGGTATTGTCCGCTAAGTTAATAGCAAAATCATTGCTAAC
CTCTTAAGGCACTTAGCGG
Found at i:5629937 original size:86 final size:85
Alignment explanation
Indices: 5629847--5630142 Score: 263
Period size: 86 Copynumber: 3.5 Consensus size: 85
5629837 CCTCTCAATG
* * * * *
5629847 CACTTAGTC-AAATTTATTTAAGGCGCACACCCTACAAGGGTATGACTTGCTAAGTCAATAGTAG
1 CACTTAG-CGAAATTTATTTAAGGCACACACCCTACGAGGGTATG-CTAGCTAAGTCAATAGCAA
*
5629911 AATCATTGCTAGCCTCCTAAGA
64 AAACATTGCTAGCCTCCTAAGA
* * * *
5629933 CACTTAGCGAAATTTATTTAAGGCACACACCTTACGAGGGTGTTGCTAGTTAAGTTAATAGCAAA
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGT-ATGCTAGCTAAGTCAATAGCAAA
* * *
5629998 AACGTTGCTAGCCTCTTAAGG
65 AACATTGCTAGCCTCCTAAGA
* * * * * * * *
5630019 CACTTGGCTAAGTTTATTTAAAGCACAAACCCTACGAGGGTATTGCCA-CTAAGCCAATAACAAA
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGTA-TGCTAGCTAAGTCAATAGCAAA
* ** * * * *
5630083 ATCGCTACTAGCTTTCTAAGC
65 AACATTGCTAGCCTCCTAAGA
* * *
5630104 CATTTAGCGATATTTATTTAAGGCACACACCCTATGAGG
1 CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGG
5630143 ATATTACCCT
Statistics
Matches: 167, Mismatches: 40, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
85 58 0.35
86 107 0.64
87 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (85 bp):
CACTTAGCGAAATTTATTTAAGGCACACACCCTACGAGGGTATGCTAGCTAAGTCAATAGCAAAA
ACATTGCTAGCCTCCTAAGA
Found at i:5638936 original size:18 final size:19
Alignment explanation
Indices: 5638915--5638955 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5638905 GGAGAATACC
*
5638915 AAAAGAATGAAAAATA-GA
1 AAAAGAAAGAAAAATATGA
*
5638933 AAAAGAAAGGAAAATATGA
1 AAAAGAAAGAAAAATATGA
5638952 AAAA
1 AAAA
5638956 AAATAGCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAAGAAAGAAAAATATGA
Found at i:5640292 original size:25 final size:26
Alignment explanation
Indices: 5640264--5640317 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5640254 AAAATTAAAT
5640264 TAATATAT-AAAACTAAAAATTGTTA
1 TAATATATAAAAACTAAAAATTGTTA
* *
5640289 TAATATATAAAAATTGAAAATTGTTA
1 TAATATATAAAAACTAAAAATTGTTA
5640315 TAA
1 TAA
5640318 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TAATATATAAAAACTAAAAATTGTTA
Found at i:5640326 original size:27 final size:26
Alignment explanation
Indices: 5640265--5640330 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
5640255 AAATTAAATT
* *
5640265 AATATATAAAACTAAAAATTGTTATAA
1 AATATA-AAAATTGAAAATTGTTATAA
*
5640292 TATATAAAAATTGAAAATTGTTATAA
1 AATATAAAAATTGAAAATTGTTATAA
*
5640318 AATTTTAAAAATT
1 AA-TATAAAAATT
5640331 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (26 bp):
AATATAAAAATTGAAAATTGTTATAA
Found at i:5640565 original size:22 final size:22
Alignment explanation
Indices: 5640538--5640583 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5640528 ATAAAATTAT
*
5640538 TAAATA-TGAAAATAATATAATA
1 TAAATATTGAAAAGAA-ATAATA
*
5640560 TAAATATTTAAAAGAAATAATA
1 TAAATATTGAAAAGAAATAATA
5640582 TA
1 TA
5640584 GACGAGCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAATATTGAAAAGAAATAATA
Found at i:5647019 original size:17 final size:15
Alignment explanation
Indices: 5646988--5647017 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5646978 TAGGTATACT
5646988 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
5647003 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
5647018 AAGAGAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATATTAAAAAAA
Found at i:5649664 original size:3 final size:3
Alignment explanation
Indices: 5649656--5649681 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5649646 CTAATATCTT
5649656 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5649682 CACATTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5655570 original size:21 final size:20
Alignment explanation
Indices: 5655542--5655580 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5655532 ATTTTTTTTG
5655542 AATTGAGTCGAGTAAAATGA
1 AATTGAGTCGAGTAAAATGA
*
5655562 AATTCGAGTCGAGTTAAAT
1 AATT-GAGTCGAGTAAAAT
5655581 TGAATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (20 bp):
AATTGAGTCGAGTAAAATGA
Found at i:5655835 original size:9 final size:9
Alignment explanation
Indices: 5655789--5655852 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
5655779 CTATTATTTC
5655789 ATATTTTTA
1 ATATTTTTA
*
5655798 A-ATTTTTTT
1 ATA-TTTTTA
5655807 ATATTCTTT-
1 ATATT-TTTA
5655816 ATATTTTTTA
1 ATA-TTTTTA
5655826 ATATTTTTA
1 ATATTTTTA
* *
5655835 AAATTTATA
1 ATATTTTTA
5655844 AT-TTTTTA
1 ATATTTTTA
5655852 A
1 A
5655853 AAAAATATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.16
9 29 0.64
10 9 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
ATATTTTTA
Found at i:5655845 original size:18 final size:18
Alignment explanation
Indices: 5655789--5655854 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
5655779 CTATTATTTC
* *
5655789 ATATTTTTAAATTTTTTT
1 ATATTTTTAAAATTTTTA
* *
5655807 ATATTCTTTATATTTTTTA
1 ATATT-TTTAAAATTTTTA
*
5655826 ATATTTTTAAAATTTATA
1 ATATTTTTAAAATTTTTA
5655844 AT-TTTTTAAAA
1 ATATTTTTAAAA
5655855 AAATATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 9 0.21
18 17 0.40
19 16 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTAAAATTTTTA
Found at i:5655849 original size:27 final size:27
Alignment explanation
Indices: 5655818--5655887 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5655808 TATTCTTTAT
*
5655818 ATTTTTT-AATATTTTTAAAATTTATA
1 ATTTTTTAAATATTTTTAAAATTTAGA
* ** *
5655844 ATTTTTTAAAAAAATATAAAATTTAGA
1 ATTTTTTAAATATTTTTAAAATTTAGA
5655871 ATTTTTATAAATATTTT
1 ATTTTT-TAAATATTTT
5655888 GAATTTTAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
26 7 0.21
27 20 0.61
28 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTTTTTAAATATTTTTAAAATTTAGA
Found at i:5655879 original size:18 final size:19
Alignment explanation
Indices: 5655858--5655894 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5655848 TTTAAAAAAA
5655858 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
5655876 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
5655895 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:5657421 original size:166 final size:170
Alignment explanation
Indices: 5657101--5657481 Score: 450
Period size: 168 Copynumber: 2.2 Consensus size: 170
5657091 GGTCAGTTGG
* * *
5657101 CTGATTTTGAAACATCTAGAGCTAAATTCAATTGGTTTTTGTAAAGATTTCAATCTTACTCTTTG
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
* * * * * *
5657166 TTTCTATAAATATTTGAAGCTGAATTCAACTACAATTTTCTAAATAATTCCTGGATAATGACAAC
66 TTTCTATAAAGAATTGAAGCTGAATTCAACTACAATTCTCTAAAGAATTCATCG--AATGACAAC
5657231 ATTTGCAGAATGATACCTCATAAGACT-TGT-TCTATTTTGAA
129 ATTTGCAGAATGATACCTCATAAGACTATGTCT-TATTTTGAA
* * * * * * *
5657272 CTGGTTTTGAAACATCTAGGGCTAAATTGAACTGGCTTTTGTAAATATTCCTATCTT-TTCTTT-
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
* * * * *
5657335 TTTCTATATAGAATTGAAGTTGAA-TCTAACTGCAATTCTGTAAAGATTTCATCG-ATGACAACA
66 TTTCTATAAAGAATTGAAGCTGAATTC-AACTACAATTCTCTAAAGAATTCATCGAATGACAACA
* *
5657398 TTTGCAGAATGATGCCTCATAAGACTAATGTCTTATTTTTAA
130 TTTGCAGAATGATACCTCATAAGACT-ATGTCTTATTTTGAA
* *
5657440 CTGATGTTGAAACAACTAGAGCTAAATTGAAATGGTTTTTGT
1 CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGT
5657482 TTCTGTAAAG
Statistics
Matches: 178, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
166 34 0.19
168 49 0.28
169 41 0.23
170 5 0.03
171 49 0.28
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (170 bp):
CTGATTTTGAAACATCTAGAGCTAAATTGAAATGGTTTTTGTAAAGATTCCAATCTTACTCTTTG
TTTCTATAAAGAATTGAAGCTGAATTCAACTACAATTCTCTAAAGAATTCATCGAATGACAACAT
TTGCAGAATGATACCTCATAAGACTATGTCTTATTTTGAA
Found at i:5660944 original size:109 final size:109
Alignment explanation
Indices: 5660753--5660963 Score: 386
Period size: 109 Copynumber: 1.9 Consensus size: 109
5660743 GACTTCAATA
* *
5660753 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGATTTACTCCTCTCTTCTTATCTTTATCA
1 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
5660818 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
66 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
* *
5660862 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGCTTACTCCTCTCTTCTTATCGTTGTCA
1 GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
5660927 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAAT
66 TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAAT
5660964 TACATTTTTC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (109 bp):
GTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGACTTACTCCTCTCTTCTTATCGTTATCA
TATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATCACGTTG
Found at i:5667694 original size:19 final size:20
Alignment explanation
Indices: 5667660--5667698 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5667650 AAGAAATTTG
*
5667660 TCTAATATGATTAAAAATAT
1 TCTAAAATGATTAAAAATAT
5667680 TCTAAAATG-TTAAAAATAT
1 TCTAAAATGATTAAAAATAT
5667699 ATATGTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TCTAAAATGATTAAAAATAT
Found at i:5674102 original size:33 final size:33
Alignment explanation
Indices: 5674061--5674181 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 33
5674051 CTATATCAAC
5674061 TTGTTATAAGCATGATATTTCTACCATATTGAT
1 TTGTTATAAGCATGATATTTCTACCATATTGAT
* ** ** *
5674094 TTGTTATAAGCATGTTATGTTGCATTGCATGGGGTGACAAC
1 TTGTTATAAGCATGATAT-TT-C-TACCAT--ATTG---AT
5674135 TTGTTATAAGCATGATATTTCTACCATATTGAT
1 TTGTTATAAGCATGATATTTCTACCATATTGAT
5674168 TTGTTATAAGCATG
1 TTGTTATAAGCATG
5674182 TTATGTTGCA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
33 32 0.47
34 2 0.03
35 1 0.01
36 6 0.09
38 6 0.09
39 1 0.01
40 2 0.03
41 18 0.26
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (33 bp):
TTGTTATAAGCATGATATTTCTACCATATTGAT
Found at i:5674140 original size:74 final size:74
Alignment explanation
Indices: 5674057--5674204 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
5674047 GCTACTATAT
5674057 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
1 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
*
5674122 ATGGGGTGA
66 ATGGAGTGA
5674131 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
1 CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
5674196 ATGGAGTGA
66 ATGGAGTGA
5674205 GACGATATGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (74 bp):
CAACTTGTTATAAGCATGATATTTCTACCATATTGATTTGTTATAAGCATGTTATGTTGCATTGC
ATGGAGTGA
Found at i:5676496 original size:64 final size:64
Alignment explanation
Indices: 5676421--5676592 Score: 308
Period size: 64 Copynumber: 2.7 Consensus size: 64
5676411 TCATATGAAA
* *
5676421 CTTTATGGTACAATAACTCATATTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
* *
5676485 CTTTATAGTACAATGACCCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
5676549 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGG
1 CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGG
5676593 TAATAATTCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 102 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (64 bp):
CTTTATAGTACAATAACTCATACTGACACTAATTAAAGTAAAGGCATCCAAAGCTTATCCAAAG
Found at i:5680145 original size:16 final size:17
Alignment explanation
Indices: 5680124--5680157 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5680114 GAGATATAGT
5680124 TAAATA-TTAAAAAAAA
1 TAAATATTTAAAAAAAA
5680140 TAAATATTTTAAAAAAAA
1 TAAATA-TTTAAAAAAAA
5680158 ATACATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATATTTAAAAAAAA
Found at i:5683164 original size:16 final size:17
Alignment explanation
Indices: 5683124--5683164 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5683114 TTCAAAATTT
5683124 AAATTTTAAAATTATAA
1 AAATTTTAAAATTATAA
*
5683141 AAAGTTTAAAA-TA-AA
1 AAATTTTAAAATTATAA
5683156 AAATATTTA
1 AAAT-TTTA
5683165 GAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTTAAAATTATAA
Found at i:5683235 original size:15 final size:15
Alignment explanation
Indices: 5683203--5683235 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5683193 ATTAAATTAC
*
5683203 AAATATTTTTTAATA
1 AAATATTTTTTAAAA
5683218 AAATATTTTTTAAAA
1 AAATATTTTTTAAAA
5683233 AAA
1 AAA
5683236 GTAGCGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTTTTAAAA
Found at i:5691231 original size:19 final size:20
Alignment explanation
Indices: 5691207--5691246 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5691197 GTTGGTAAAT
5691207 ACATGTGTA-ATAATAATAA
1 ACATGTGTATATAATAATAA
*
5691226 ACATGTGTATTTAATAATAA
1 ACATGTGTATATAATAATAA
5691246 A
1 A
5691247 ATATGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
ACATGTGTATATAATAATAA
Found at i:5691242 original size:20 final size:20
Alignment explanation
Indices: 5691207--5691255 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5691197 GTTGGTAAAT
*
5691207 ACATGTGTA-ATAATAATAA
1 ACATGTGTATTTAATAATAA
5691226 ACATGTGTATTTAATAATAA
1 ACATGTGTATTTAATAATAA
*
5691246 A-ATATGTATT
1 ACATGTGTATT
5691256 GCTTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (20 bp):
ACATGTGTATTTAATAATAA
Found at i:5691253 original size:19 final size:20
Alignment explanation
Indices: 5691217--5691255 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5691207 ACATGTGTAA
*
5691217 TAATAATAAACATGTGTATT
1 TAATAATAAACATATGTATT
5691237 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
5691256 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:5691392 original size:16 final size:15
Alignment explanation
Indices: 5691366--5691398 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5691356 CAAAACAGGG
5691366 AGAAAAAAGAAAGAA
1 AGAAAAAAGAAAGAA
5691381 AGAAAAAGAGAAAGAA
1 AGAAAAA-AGAAAGAA
5691397 AG
1 AG
5691399 GAGGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAGAA
Found at i:5692079 original size:24 final size:24
Alignment explanation
Indices: 5692052--5692098 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5692042 ATTGAAATGG
5692052 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
5692076 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
5692099 GATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:5693806 original size:24 final size:24
Alignment explanation
Indices: 5693759--5693806 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5693749 GATGAATTAT
* *
5693759 AATTTAAAGTATATTGGTTGAATA
1 AATTTAAAGTATAATGATTGAATA
5693783 AATTTAAAGTATGAATGATT-AATA
1 AATTTAAAGTAT-AATGATTGAATA
5693807 TACTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTTAAAGTATAATGATTGAATA
Done.