Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:224122 original size:12 final size:12
Alignment explanation
Indices: 224105--224138 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
224095 CCAACTGGGT
224105 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
224117 TTTTTTCTTTTC
1 TTTTTTTTTTTC
224129 TTTTCTTTTT
1 TTTT-TTTTT
224139 GTATCTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:224132 original size:17 final size:15
Alignment explanation
Indices: 224104--224138 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
224094 GCCAACTGGG
224104 TTTTTTTTTTTTCTT
1 TTTTTTTTTTTTCTT
224119 TTTTCTTTTCTTTTCTT
1 TTTT-TTTT-TTTTCTT
224136 TTT
1 TTT
224139 GTATCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 4 0.22
17 10 0.56
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTTCTT
Found at i:224673 original size:3 final size:3
Alignment explanation
Indices: 224665--224691 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
224655 TTTAGTATAT
224665 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
224692 TTCTTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:225634 original size:3 final size:3
Alignment explanation
Indices: 225626--225660 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
225616 AAAAATATAG
225626 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
225661 ATATCATCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:227929 original size:3 final size:3
Alignment explanation
Indices: 227923--227985 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
227913 CGAAAAAAAT
* * * * * * *
227923 GCA GCA GCA GCA GCA GCA ACA GCA ACA GCA TCA ACA ACA ACA GCA ACA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
227971 GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA
227986 ACATTATAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.43, C:0.33, G:0.22, T:0.02
Consensus pattern (3 bp):
GCA
Found at i:228172 original size:2 final size:2
Alignment explanation
Indices: 228165--228208 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
228155 GTAACGTAAG
*
228165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228207 TA
1 TA
228209 AAAACAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:229077 original size:13 final size:13
Alignment explanation
Indices: 229040--229084 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
229030 ATAATATTTG
229040 TTTTAAAA-A-AA
1 TTTTAAAATATAA
229051 TTTTAAATATATAA
1 TTTTAAA-ATATAA
229065 TTTTAAAATATAA
1 TTTTAAAATATAA
229078 TTGTTAA
1 TT-TTAA
229085 GATGATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.23
12 1 0.03
13 9 0.30
14 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TTTTAAAATATAA
Found at i:229813 original size:19 final size:20
Alignment explanation
Indices: 229789--229836 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
229779 GAAAAAGAAC
229789 AAAAGGAAA-AAGAAG-AAAG
1 AAAAGGAAAGAA-AAGAAAAG
229808 AAAAGGAAAGAAAAGAAAAG
1 AAAAGGAAAGAAAAGAAAAG
229828 AAAA-GAAAG
1 AAAAGGAAAG
229837 CAGGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAAGGAAAGAAAAGAAAAG
Found at i:229817 original size:5 final size:5
Alignment explanation
Indices: 229804--229835 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
229794 GAAAAAGAAG
*
229804 AAAGA AAAGG AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
229836 GCAGGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:229818 original size:10 final size:10
Alignment explanation
Indices: 229789--229836 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
229779 GAAAAAGAAC
229789 AAAAGGAAA-
1 AAAAGGAAAG
229798 AAGAA-GAAAG
1 AA-AAGGAAAG
229808 AAAAGGAAAG
1 AAAAGGAAAG
*
229818 AAAAGAAAAG
1 AAAAGGAAAG
229828 AAAA-GAAAG
1 AAAAGGAAAG
229837 CAGGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 12 0.35
10 22 0.65
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AAAAGGAAAG
Found at i:231393 original size:5 final size:5
Alignment explanation
Indices: 231383--231415 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
231373 TTAATACTAC
231383 TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
231416 ATAGAGAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:234582 original size:83 final size:83
Alignment explanation
Indices: 234443--234610 Score: 300
Period size: 83 Copynumber: 2.0 Consensus size: 83
234433 TAGTTTTCCT
*
234443 TCCGTTTCTGTCATACACACTTGGACAGATAATTATCAGACCCCTACAATCTATACTTATTTGCT
1 TCCGTTTCTGTCATACACACTTGAACAGATAATTATCAGACCCCTACAATCTATACTTATTTGCT
234508 TTTTCTGTACAAGCAACA
66 TTTTCTGTACAAGCAACA
* * *
234526 TCCGTTTCTGTCATACACACTTGAACAGATATTTATCAGACCTCTATAATCTATACTTATTTGCT
1 TCCGTTTCTGTCATACACACTTGAACAGATAATTATCAGACCCCTACAATCTATACTTATTTGCT
234591 TTTTCTGTACAAGCAACA
66 TTTTCTGTACAAGCAACA
234609 TC
1 TC
234611 AACAACAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (83 bp):
TCCGTTTCTGTCATACACACTTGAACAGATAATTATCAGACCCCTACAATCTATACTTATTTGCT
TTTTCTGTACAAGCAACA
Found at i:237526 original size:15 final size:15
Alignment explanation
Indices: 237508--237551 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
237498 AATTTTAATT
237508 TTAATTTATTAAATA
1 TTAATTTATTAAATA
*
237523 TTAATTTTTTAAA-A
1 TTAATTTATTAAATA
*
237537 TTTATTTATATAAAT
1 TTAATTTAT-TAAAT
237552 GAATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTTATTAAATA
Found at i:237611 original size:2 final size:2
Alignment explanation
Indices: 237604--237630 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
237594 CTATTGAAAT
237604 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
237631 TTTTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:237962 original size:2 final size:2
Alignment explanation
Indices: 237955--237979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
237945 AAGTATTAAT
237955 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
237980 GAATGTCAGT
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:239148 original size:16 final size:17
Alignment explanation
Indices: 239127--239160 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
239117 ATCATGGATA
*
239127 AATTTTAATAATT-TTT
1 AATTTTAAAAATTATTT
239143 AATTTTAAAAATTATTT
1 AATTTTAAAAATTATTT
239160 A
1 A
239161 TGTTATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTAAAAATTATTT
Found at i:239914 original size:23 final size:22
Alignment explanation
Indices: 239888--239997 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 22
239878 TAAATATGAC
239888 ATTTAAATAGATATAAATATATA
1 ATTTAAATA-ATATAAATATATA
*
239911 ATTTAAA-AATTTTATAATATA-A
1 ATTTAAATAA-TATA-AATATATA
239933 ATTATAAAT-ATATTAAA-ATATA
1 ATT-TAAATAATA-TAAATATATA
*
239955 ATTATAATATAATA-ACATATATA
1 ATT-TAA-ATAATATAAATATATA
239978 A-TT--ATAATATAAATATATA
1 ATTTAAATAATATAAATATATA
239997 A
1 A
239998 ATTATCGTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
18 6 0.08
19 9 0.12
21 5 0.07
22 22 0.30
23 28 0.38
24 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
ATTTAAATAATATAAATATATA
Found at i:239958 original size:11 final size:11
Alignment explanation
Indices: 239926--239989 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
239916 AAAATTTTAT
239926 AATATAAATTATA
1 AATAT-AATTA-A
239939 AATAT-ATTAA
1 AATATAATTAA
*
239949 AATATAATTAT
1 AATATAATTAA
239960 AATATAA-TAA
1 AATATAATTAA
*
239970 CATATATAATTAT
1 -A-ATATAATTAA
239983 AATATAA
1 AATATAA
239990 ATATATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.18
11 22 0.50
12 7 0.16
13 7 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAATTAA
Found at i:239960 original size:29 final size:26
Alignment explanation
Indices: 239923--239999 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 26
239913 TTAAAAATTT
239923 TATAATATAAATTATAAATATATTAAAA
1 TATAATATAAATTATAAATATA-T-AAA
* *
239951 TATAATTATAATATAATAACATATATAAT
1 TATAA-TATAA-ATTATAA-ATATATAAA
239980 TATAATATAAATATATAAAT
1 TATAATATAAAT-TATAAAT
240000 TATCGTATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
27 4 0.10
28 14 0.33
29 12 0.29
30 7 0.17
31 5 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
TATAATATAAATTATAAATATATAAA
Found at i:239987 original size:34 final size:34
Alignment explanation
Indices: 239922--239994 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
239912 TTTAAAAATT
**
239922 TTATAATATAAATTATAAATATATTAAAATATAA
1 TTATAATATAAAACATAAATATATTAAAATATAA
* *
239956 TTATAATATAATAACATATATA-ATTATAATATAA
1 TTATAATATAA-AACATAAATATATTAAAATATAA
*
239990 ATATA
1 TTATA
239995 TAAATTATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
TTATAATATAAAACATAAATATATTAAAATATAA
Found at i:245471 original size:22 final size:21
Alignment explanation
Indices: 245440--245481 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
245430 TACAAAAGTA
245440 TAATCATAAATAATATAATAAC
1 TAATCATAAATAATA-AATAAC
* *
245462 TAATCTTAAATATTAAATAA
1 TAATCATAAATAATAAATAA
245482 TATCTAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATCATAAATAATAAATAAC
Found at i:247459 original size:14 final size:15
Alignment explanation
Indices: 247440--247473 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
247430 ATATTATAAT
247440 AATATAAAT-AATTA
1 AATATAAATCAATTA
247454 AATAT-AATCAATTA
1 AATATAAATCAATTA
247468 AATATA
1 AATATA
247474 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAAATCAATTA
Found at i:256652 original size:22 final size:23
Alignment explanation
Indices: 256624--256679 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
256614 TGGACATGTT
256624 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
256646 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
256669 AAAAATGCATG
1 AAAAATGCATG
256680 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:257637 original size:20 final size:20
Alignment explanation
Indices: 257590--257664 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
257580 AAAAAGACAT
*
257590 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
257609 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
257630 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTCATA
257650 AATGTATCGATACAT
1 AATGTATCGATACAT
257665 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:257658 original size:40 final size:39
Alignment explanation
Indices: 257587--257664 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
257577 GGTAAAAAGA
** *
257587 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAAAATATATCGATACATT
* *
257626 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTAAAAAATATATCGATACAT
257665 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAAAATATATCGATACATT
Found at i:261121 original size:18 final size:18
Alignment explanation
Indices: 261087--261124 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
261077 GTCACATTAA
*
261087 AACCATACCAACTTTGGG
1 AACCATACCAACGTTGGG
261105 AACCATATCCAA-GTTGGG
1 AACCATA-CCAACGTTGGG
261123 AA
1 AA
261125 ATATGTGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (18 bp):
AACCATACCAACGTTGGG
Found at i:261822 original size:30 final size:28
Alignment explanation
Indices: 261753--261822 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
261743 GAAGAGAAAG
*
261753 TTTAAATTA-TTTTATATTTATAATTTA
1 TTTAAAATATTTTTATATTTATAATTTA
261780 TTTAATATATATTTTTATATATTATAATTATA
1 TTTAA-A-ATATTTTTATAT-TTATAATT-TA
261812 TTTAAAATATT
1 TTTAAAATATT
261823 ACATATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 2 0.05
30 13 0.35
31 9 0.24
32 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTAAAATATTTTTATATTTATAATTTA
Found at i:261830 original size:37 final size:32
Alignment explanation
Indices: 261762--261821 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
261752 GTTTAAATTA
261762 TTTTATAT-TTATAATT-TATTTAATATATAT
1 TTTTATATATTATAATTATATTTAATATATAT
*
261792 TTTTATATATTATAATTATATTTAAAATAT
1 TTTTATATATTATAATTATATTTAATATAT
261822 TACATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.30
31 8 0.30
32 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTATATATTATAATTATATTTAATATATAT
Found at i:261849 original size:16 final size:14
Alignment explanation
Indices: 261830--261863 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
261820 ATTACATATT
261830 TATATAAATTTTAA
1 TATATAAATTTTAA
261844 TATATAAATTTTAA
1 TATATAAATTTTAA
*
261858 TTTATA
1 TATATA
261864 CTTGTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:262117 original size:14 final size:14
Alignment explanation
Indices: 262100--262145 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
262090 TATTATATAT
262100 TTATATAAATTTTA
1 TTATATAAATTTTA
262114 TTATATTAATAATTTATA
1 TTATA-T-A-AATTT-TA
262132 TTATATAAATTTTA
1 TTATATAAATTTTA
262146 ATATGTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 2 0.07
17 6 0.21
18 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:262154 original size:18 final size:18
Alignment explanation
Indices: 262081--262155 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 18
262071 GTCATTATCA
*
262081 TATATAAGATATTATATATT
1 TATATAA-ATTTTATATA-T
262101 TATATAAATTTTATTATAT
1 TATATAAATTTTA-TATAT
262120 TA-AT-AA--TT-TATAT
1 TATATAAATTTTATATAT
262133 TATATAAATTTTA-ATAT
1 TATATAAATTTTATATAT
262150 GTATAT
1 -TATAT
262156 GTATTTATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
13 7 0.15
14 2 0.04
15 4 0.09
17 8 0.17
18 7 0.15
19 8 0.17
20 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATAAATTTTATATAT
Found at i:262162 original size:33 final size:31
Alignment explanation
Indices: 262090--262168 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 31
262080 ATATATAAGA
262090 TATTATATATTTATATAAATTTTATTATATTAAT
1 TATT-TATA-TTATATAAATTTTA-TATATTAAT
*
262124 AATTTATATTATATAAATTTTA-ATATGTATAT
1 TATTTATATTATATAAATTTTATATAT-TA-AT
*
262156 GTATTTATGTTAT
1 -TATTTATATTAT
262169 TTTGTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.10
31 2 0.05
32 16 0.41
33 14 0.36
34 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (31 bp):
TATTTATATTATATAAATTTTATATATTAAT
Found at i:262421 original size:23 final size:23
Alignment explanation
Indices: 262391--262451 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 23
262381 TTTATGGTTT
262391 TATATTATATTTATATATTTTTA
1 TATATTATATTTATATATTTTTA
262414 TATATTATA---AT-TATTTTTA
1 TATATTATATTTATATATTTTTA
*
262433 AAGTATTAATATTTATATA
1 TA-TATT-ATATTTATATA
262452 AATTTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
19 9 0.29
20 6 0.19
21 3 0.10
23 9 0.29
24 2 0.06
25 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TATATTATATTTATATATTTTTA
Found at i:263572 original size:18 final size:19
Alignment explanation
Indices: 263540--263584 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
263530 CATTTAAAAA
*
263540 ATATAAAA-AAATTAT-TT
1 ATATAAAATTAATTATATT
263557 ATATAAAATTAATTATATT
1 ATATAAAATTAATTATATT
263576 -TATAAAATT
1 ATATAAAATT
263585 TAAAAATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 15 0.60
19 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAAATTAATTATATT
Found at i:268281 original size:22 final size:24
Alignment explanation
Indices: 268241--268330 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 24
268231 CATCACTTGC
268241 AAAATATATAATATAAAATATTAT
1 AAAATATATAATATAAAATATTAT
268265 AAAA-ATATAA-ATAAAATA-T-T
1 AAAATATATAATATAAAATATTAT
* * *
268285 AATATAT-TATTTTAAAAT-TTAT
1 AAAATATATAATATAAAATATTAT
*
268307 ATAATATA-AATTATTAAAATATTA
1 AAAATATATAA-TA-TAAAATATTA
268331 AAATTTATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
20 6 0.12
21 10 0.20
22 15 0.29
23 7 0.14
24 10 0.20
25 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATATATAATATAAAATATTAT
Found at i:268344 original size:18 final size:18
Alignment explanation
Indices: 268296--268344 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
268286 ATATATTATT
268296 TTAAAATTTATAT-AATA
1 TTAAAATTTATATAAATA
268313 -T-AAA-TTAT-TAAAATA
1 TTAAAATTTATAT-AAATA
268328 TTAAAATTTATATAAAT
1 TTAAAATTTATATAAAT
268345 GTAAAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 11
0.70 0.00 0.30
Matches are distributed among these distances:
13 1 0.04
14 4 0.15
15 7 0.27
16 2 0.08
17 3 0.12
18 8 0.31
19 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAAATTTATATAAATA
Found at i:272931 original size:3 final size:3
Alignment explanation
Indices: 272923--272958 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
272913 ATGTAAATAG
272923 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
272959 TTGATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:273815 original size:23 final size:24
Alignment explanation
Indices: 273789--273878 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 24
273779 AATGAATTCG
* *
273789 TTTATGAATAT-TAAATAAATATA
1 TTTATAAATATATAAATAAACATA
*
273812 TTTATAAATATATAATTAAACATA
1 TTTATAAATATATAAATAAACATA
* * * *
273836 TTTTTAAGTA-ATTAA-AAATATA
1 TTTATAAATATATAAATAAACATA
* *
273858 TTAATAAATA-ATAAATTAACA
1 TTTATAAATATATAAATAAACA
273879 ATTACGGTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
22 17 0.33
23 16 0.31
24 18 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTATAAATATATAAATAAACATA
Found at i:273869 original size:22 final size:21
Alignment explanation
Indices: 273818--273869 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
273808 TATATTTATA
* *
273818 AATATATAATTAAACATATTT
1 AATAAATAATTAAAAATATTT
* *
273839 -TTAAGTAATTAAAAATATATT
1 AATAAATAATTAAAAATAT-TT
273860 AATAAATAAT
1 AATAAATAAT
273870 AAATTAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAAATAATTAAAAATATTT
Found at i:274395 original size:18 final size:18
Alignment explanation
Indices: 274358--274399 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
274348 TTTAAATTAT
*
274358 TATTTAAAAATATTAATA
1 TATTAAAAAATATTAATA
**
274376 TATTAAAAAATATTTGTA
1 TATTAAAAAATATTAATA
274394 TATTAA
1 TATTAA
274400 TATTTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATTAAAAAATATTAATA
Found at i:274420 original size:22 final size:21
Alignment explanation
Indices: 274385--274426 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
274375 ATATTAAAAA
274385 ATATTTGTATATTAATATTTAT
1 ATATTTGTATATTAA-ATTTAT
274407 ATATTT-TATAATTAAATTTA
1 ATATTTGTAT-ATTAAATTTA
274427 AATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATTTGTATATTAAATTTAT
Found at i:274438 original size:17 final size:17
Alignment explanation
Indices: 274416--274487 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 17
274406 TATATTTTAT
274416 AATTAAATTTAAATAAA
1 AATTAAATTTAAATAAA
* *
274433 AATT-AATTTTATTAAA
1 AATTAAATTTAAATAAA
*
274449 AA-TAATTATTTAAAT-CA
1 AATTAA--ATTTAAATAAA
*
274466 AATT-AATTTAAAATATA
1 AATTAAATTT-AAATAAA
274483 AATTA
1 AATTA
274488 TAAAATACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.12
16 17 0.40
17 13 0.31
18 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATTTAAATAAA
Found at i:276871 original size:15 final size:14
Alignment explanation
Indices: 276851--276910 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
276841 TATGCCGTCA
*
276851 TAAAATTATATATTT
1 TAAAATT-TATATAT
276866 TAAAATTTATATAAT
1 TAAAATTTATAT-AT
*
276881 ATAAATTATTAATATAT
1 -TAAA--ATTTATATAT
276898 TAAAATTTATATA
1 TAAAATTTATATA
276911 AATATAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.34
15 8 0.21
16 8 0.21
17 2 0.05
18 7 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATTTATATAT
Found at i:276877 original size:16 final size:16
Alignment explanation
Indices: 276851--276910 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
276841 TATGCCGTCA
276851 TAAAA-TTATATATTT
1 TAAAATTTATATATTT
* *
276866 TAAAATTTATATAATA
1 TAAAATTTATATATTT
* *
276882 TAAATTATTA-ATATAT
1 TAAAAT-TTATATATTT
276898 TAAAATTTATATA
1 TAAAATTTATATA
276911 AATATAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 8 0.23
16 24 0.69
17 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATTTATATATTT
Found at i:276903 original size:32 final size:33
Alignment explanation
Indices: 276855--276933 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
276845 CCGTCATAAA
* *
276855 ATTATATATTTTAAAATTTATAT-AATATAAATT
1 ATTA-ATATATTAAAATTTATATAAATATAAAAT
276888 ATTAATATATTAAAATTTATATAAATATAAAAT
1 ATTAATATATTAAAATTTATATAAATATAAAAT
*
276921 ATTTTATATATTA
1 A-TTAATATATTA
276934 TTATAACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
32 17 0.41
33 14 0.34
34 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTAATATATTAAAATTTATATAAATATAAAAT
Found at i:276907 original size:18 final size:19
Alignment explanation
Indices: 276885--276933 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
276875 TATAATATAA
276885 ATTATTAATATATTAAAAT
1 ATTATTAATATATTAAAAT
276904 -TTATATAA-ATA-TAAAAT
1 ATTAT-TAATATATTAAAAT
276921 ATT-TT-ATATATTA
1 ATTATTAATATATTA
276934 TTATAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
15 1 0.04
16 4 0.15
17 9 0.35
18 9 0.35
19 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTAATATATTAAAAT
Found at i:276918 original size:17 final size:17
Alignment explanation
Indices: 276866--276920 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
276856 TTATATATTT
276866 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
276882 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
276897 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
276915 TAAAAT
1 TAAAAT
276921 ATTTTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:279403 original size:2 final size:2
Alignment explanation
Indices: 279396--279424 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
279386 ATTTCTTTTC
279396 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
279425 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:281800 original size:16 final size:15
Alignment explanation
Indices: 281779--281810 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
281769 TAAATTTTAA
281779 ATTTTATTTTATTATT
1 ATTTTATTTTA-TATT
281795 ATTTTATTTTATATT
1 ATTTTATTTTATATT
281810 A
1 A
281811 ATATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTATTTTATATT
Found at i:281805 original size:21 final size:21
Alignment explanation
Indices: 281779--281835 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
281769 TAAATTTTAA
* **
281779 ATTTTATTTTATTATTATTTT
1 ATTTTATTTTAATATTAAGTT
*
281800 ATTTTATATTAATATTAAGTT
1 ATTTTATTTTAATATTAAGTT
*
281821 ATTTTTATTTAAATA
1 A-TTTTATTTTAATA
281836 AAAGTAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTATTTTAATATTAAGTT
Found at i:282408 original size:2 final size:2
Alignment explanation
Indices: 282397--282430 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
282387 CTTTCATCTA
*
282397 AT AT -T AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
282431 CCAAGCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:282511 original size:2 final size:2
Alignment explanation
Indices: 282504--282536 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
282494 CTTTTATCTA
282504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
282537 CACACCAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:282568 original size:110 final size:108
Alignment explanation
Indices: 282320--282644 Score: 555
Period size: 110 Copynumber: 3.0 Consensus size: 108
282310 TGTTCTTTTC
* **
282320 ATAC-CCAAGCAAGTCTCTATGTAGGTGGAATTGGCGGCCTTTGATACAACTTTTGGGGTTTCAA
1 ATACACCAAGCAAATCTCTATGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTCAA
* *
282384 CATCTTTCATCTAATAT-TATATATATATATATATGTATATAT
66 CATCTTTTATCTAATATATATATATATATATATATATATATAT
* *
282426 ATATACCAAGCAAATCTCTACGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTCAA
1 ATACACCAAGCAAATCTCTATGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTCAA
282491 CATCTTTTATCTAATATATATATATATATATATATATATATAT
66 CATCTTTTATCTAATATATATATATATATATATATATATATAT
282534 ATACACACCAAGCAAATCTCTATGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTC
1 AT--ACACCAAGCAAATCTCTATGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTC
282599 AACATCTTTTATCTAATATATATATATATATATATATATATATAT
64 AACATCTTTTATCTAATATATATATATATATATATATATATATAT
282644 A
1 A
282645 CACAATTGTC
Statistics
Matches: 206, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
106 3 0.01
107 72 0.35
108 26 0.13
110 105 0.51
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (108 bp):
ATACACCAAGCAAATCTCTATGTAGGTGGAATTGGCATCCTTTGATACAACTTTTGGGGTTTCAA
CATCTTTTATCTAATATATATATATATATATATATATATATAT
Found at i:282621 original size:2 final size:2
Alignment explanation
Indices: 282614--282644 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
282604 CTTTTATCTA
282614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
282645 CACAATTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:283077 original size:29 final size:31
Alignment explanation
Indices: 283045--283102 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
283035 ATTTTTAAAA
283045 AATTAAATTT-TTTAT-TTAAATT-TATTTTC
1 AATTAAATTTATTTATATT-AATTATATTTTC
*
283074 AATTCAATTTATTTATATTAATTATATTT
1 AATTAAATTTATTTATATTAATTATATTT
283103 AATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 9 0.36
30 9 0.36
31 7 0.28
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
AATTAAATTTATTTATATTAATTATATTTTC
Found at i:284880 original size:16 final size:16
Alignment explanation
Indices: 284830--284887 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
284820 CAACTTAAAT
*
284830 AAAATTTAAAATAATT
1 AAAATTTAAAATAATC
* * *
284846 TAAA-TT-AAACAACC
1 AAAATTTAAAATAATC
284860 AAAATTTAAAATAATC
1 AAAATTTAAAATAATC
284876 AAAATTTTAAAA
1 AAAA-TTTAAAA
284888 AGTCAGAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
16 13 0.41
17 7 0.22
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTTAAAATAATC
Found at i:286595 original size:49 final size:49
Alignment explanation
Indices: 286526--286624 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
286516 AACAGTTGGC
*
286526 AAACAACATCAGAAGAAAAATAGGAATAAAACATAAGAAATCTTCAGCA
1 AAACAACATCAGAAGAAAAATAGGAATAAAACATAAGAAACCTTCAGCA
** * *
286575 AAACAACATCAGAATTAAAATGGGAATAAAACATTAGAAACCTTCAGCA
1 AAACAACATCAGAAGAAAAATAGGAATAAAACATAAGAAACCTTCAGCA
286624 A
1 A
286625 TAAAATGTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.16
Consensus pattern (49 bp):
AAACAACATCAGAAGAAAAATAGGAATAAAACATAAGAAACCTTCAGCA
Found at i:288907 original size:2 final size:2
Alignment explanation
Indices: 288900--288928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
288890 AATTTAAAGG
288900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
288929 GAGTTGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:290253 original size:6 final size:6
Alignment explanation
Indices: 290242--290269 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
290232 AGGACTGACA
290242 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
290270 ACCGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:290733 original size:34 final size:34
Alignment explanation
Indices: 290695--290759 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
290685 ATTAATAATT
* ** *
290695 ATTTTATTTTAATTTTAAATATATAAAAATAAAA
1 ATTTTAATTTAATAATAAAAATATAAAAATAAAA
*
290729 ATTTTAATTTAATAATAAAAATATTAAAATA
1 ATTTTAATTTAATAATAAAAATATAAAAATA
290760 TATTTTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
ATTTTAATTTAATAATAAAAATATAAAAATAAAA
Found at i:290882 original size:18 final size:20
Alignment explanation
Indices: 290832--290873 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
290822 ATATTTTATT
290832 TTAAATTAAATATTTAA-TAA
1 TTAAATT-AATATTTAATTAA
290852 TTAAATTAATATTTAATTAA
1 TTAAATTAATATTTAATTAA
290872 TT
1 TT
290874 CATAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTAATATTTAATTAA
Found at i:293506 original size:22 final size:21
Alignment explanation
Indices: 293464--293506 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
293454 AAATTCAATT
293464 ATATATTTTAATTTTGATATTA
1 ATATATTTTAATTTT-ATATTA
293486 ATATATTATGTAATTTT-TATT
1 ATATATT-T-TAATTTTATATT
293507 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATATATTTTAATTTTATATTA
Found at i:293702 original size:9 final size:9
Alignment explanation
Indices: 293657--293702 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
293647 AAACATAAAA
293657 TATATTTTT
1 TATATTTTT
*
293666 TATATGTTT
1 TATATTTTT
293675 TATATTTTT
1 TATATTTTT
293684 T-TATTCTTT
1 TATATT-TTT
293693 TATATTTTT
1 TATATTTTT
293702 T
1 T
293703 TAACCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 4 0.12
9 25 0.76
10 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (9 bp):
TATATTTTT
Found at i:294019 original size:48 final size:48
Alignment explanation
Indices: 293960--294067 Score: 189
Period size: 48 Copynumber: 2.2 Consensus size: 48
293950 TATATTTATC
* * *
293960 TTTTTATTTAAAATTAACTTATAAATAATAATTTAGGAGGTAAATTTA
1 TTTTTAATTAAAATTAACTTATAAATAATAATTTAAGAGGTAAATATA
294008 TTTTTAATTAAAATTAACTTATAAATAATAATTTAAGAGGTAAATATA
1 TTTTTAATTAAAATTAACTTATAAATAATAATTTAAGAGGTAAATATA
294056 TTTTTAATTAAA
1 TTTTTAATTAAA
294068 CTCTAAAGGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (48 bp):
TTTTTAATTAAAATTAACTTATAAATAATAATTTAAGAGGTAAATATA
Found at i:298199 original size:13 final size:13
Alignment explanation
Indices: 298183--298207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
298173 TGATTTTTTG
298183 CATTATATTTGCT
1 CATTATATTTGCT
298196 CATTATATTTGC
1 CATTATATTTGC
298208 CTTTATTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
CATTATATTTGCT
Found at i:302185 original size:28 final size:28
Alignment explanation
Indices: 302153--302208 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
302143 GCAAGTAAGT
302153 GCTCTTATTTATTCCAAATTATATTCTA
1 GCTCTTATTTATTCCAAATTATATTCTA
302181 GCTCTTATTTATTCCAAATTATATTCTA
1 GCTCTTATTTATTCCAAATTATATTCTA
302209 TCTTTGTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.50
Consensus pattern (28 bp):
GCTCTTATTTATTCCAAATTATATTCTA
Found at i:305360 original size:3 final size:3
Alignment explanation
Indices: 305354--305378 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
305344 AATAATAGTA
305354 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
305379 TGAATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:305580 original size:2 final size:2
Alignment explanation
Indices: 305573--305603 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
305563 AGATAGACTG
305573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
305604 AGATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:306276 original size:2 final size:2
Alignment explanation
Indices: 306269--306294 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
306259 TTCAACGACA
306269 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
306295 CACTTTGCCA
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:307655 original size:18 final size:17
Alignment explanation
Indices: 307622--307662 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
307612 TTTAATATAT
307622 TTTTATATAAATATAAA
1 TTTTATATAAATATAAA
307639 TTTTA-ATAAAT-TAATA
1 TTTTATATAAATATAA-A
*
307655 ATTTATAT
1 TTTTATAT
307663 TTTATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTATATAAATATAAA
Found at i:307684 original size:23 final size:22
Alignment explanation
Indices: 307630--307687 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
307620 ATTTTTATAT
*
307630 AAATATAAATTTTAATAAATTA
1 AAATATATATTTTAATAAATTA
*
307652 ATAATTTATATTTT-ATAAATATTA
1 A-AATATATATTTTAAT-AA-ATTA
307676 AAATATATATTT
1 AAATATATATTT
307688 ATACTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.10
23 22 0.73
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATATATTTTAATAAATTA
Found at i:311759 original size:37 final size:37
Alignment explanation
Indices: 311718--311791 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
311708 TCCAGAAGAA
* *
311718 AGAGTGGCAAAGCTACACAACCTTCTTGATGACATTC
1 AGAGTAGCAAAGCTACACAACCTTCTCGATGACATTC
*
311755 AGAGTAGCAAAGCTGCACAACCTTCTCGATGACATTC
1 AGAGTAGCAAAGCTACACAACCTTCTCGATGACATTC
311792 TGATGAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (37 bp):
AGAGTAGCAAAGCTACACAACCTTCTCGATGACATTC
Found at i:315975 original size:16 final size:17
Alignment explanation
Indices: 315954--315987 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
315944 TAAATGAAAA
315954 TTTAATTTAATA-TAAT
1 TTTAATTTAATAGTAAT
*
315970 TTTAATTTGATAGTAAT
1 TTTAATTTAATAGTAAT
315987 T
1 T
315988 AAAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAATTTAATAGTAAT
Found at i:317154 original size:27 final size:26
Alignment explanation
Indices: 317133--317193 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
317123 TTTTATTTTA
*
317133 TTTATTTTTAATTAAATATTTAAAATTT
1 TTTA-TTTTAAATAAATATTT-AAATTT
*
317161 TTTATTTTAAATAAATATTTTAA-TT
1 TTTATTTTAAATAAATATTTAAATTT
317186 TTTATTTT
1 TTTATTTT
317194 TATCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 10 0.32
26 2 0.06
27 15 0.48
28 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATTTTAAATAAATATTTAAATTT
Found at i:317160 original size:25 final size:25
Alignment explanation
Indices: 317132--317203 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 25
317122 TTTTTATTTT
317132 ATTTATTTTTAATTAAATATTTAAA
1 ATTTATTTTTAATTAAATATTTAAA
* * *
317157 ATTTTTTATTTTAAATAAATATTTTAAT
1 A-TTTAT-TTTTAATTAAATA-TTTAAA
* *
317185 TTTTATTTTT-ATCAAATAT
1 ATTTATTTTTAATTAAATAT
317204 AAAAATATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
24 1 0.03
25 7 0.19
26 8 0.22
27 16 0.43
28 5 0.14
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTATTTTTAATTAAATATTTAAA
Found at i:317354 original size:24 final size:23
Alignment explanation
Indices: 317306--317387 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
317296 TCAACTTTTA
* *
317306 AAATGTAAAA-AAA-TAAAATAA
1 AAATTTAAAATAAATTAAAATAT
317327 AAATTTAAAATATAATTAAAATAT
1 AAATTTAAAATA-AATTAAAATAT
*
317351 AAATTTTTAAA-AAATTAAAA-AT
1 AAA-TTTAAAATAAATTAAAATAT
*
317373 ATAATTAAAAATAAA
1 A-AATTTAAAATAAA
317388 AATTTAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 9 0.18
22 9 0.18
23 15 0.30
24 11 0.22
25 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (23 bp):
AAATTTAAAATAAATTAAAATAT
Found at i:317362 original size:34 final size:33
Alignment explanation
Indices: 317302--317403 Score: 108
Period size: 35 Copynumber: 3.2 Consensus size: 33
317292 ATTATCAACT
*
317302 TTTAAAATGTAA--AAAAAT-AAAA--TAAAAA
1 TTTAAAATATAATTAAAAATAAAAATTTAAAAA
**
317330 TTTAAAATATAATTAAAATATAAATTTTTAAAAAA
1 TTTAAAATATAATTAAAA-ATAAAAATTT-AAAAA
*
317365 TTAAAAATATAATTAAAAATAAAAATTT-AAAA
1 TTTAAAATATAATTAAAAATAAAAATTTAAAAA
317397 TTTAAAA
1 TTTAAAA
317404 ACCCCCCCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 11 0.18
30 4 0.07
31 2 0.03
32 12 0.20
34 9 0.15
35 22 0.37
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (33 bp):
TTTAAAATATAATTAAAAATAAAAATTTAAAAA
Found at i:317382 original size:18 final size:18
Alignment explanation
Indices: 317314--317390 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 18
317304 TAAAATGTAA
* *
317314 AAAAATAAAATAAAAATT
1 AAAAATATAATTAAAATT
*
317332 TAAAATATAATTAAAATAT
1 AAAAATATAATTAAAAT-T
** *
317351 AAATTTTTAA--AAAATT
1 AAAAATATAATTAAAATT
*
317367 AAAAATATAATTAAAAAT
1 AAAAATATAATTAAAATT
317385 AAAAAT
1 AAAAAT
317391 TTAAAATTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
16 8 0.18
17 5 0.11
18 25 0.56
19 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATAATTAAAATT
Found at i:317866 original size:17 final size:17
Alignment explanation
Indices: 317844--317876 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
317834 TGGGGGATAT
317844 AGCTCGGAACAGAAAAA
1 AGCTCGGAACAGAAAAA
317861 AGCTCGGAACAGAAAA
1 AGCTCGGAACAGAAAA
317877 TAGAGGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (17 bp):
AGCTCGGAACAGAAAAA
Found at i:318811 original size:6 final size:6
Alignment explanation
Indices: 318800--318831 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
318790 ATTTTTATTA
318800 AAAAAT AAAAAT --AAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
318832 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:318821 original size:16 final size:16
Alignment explanation
Indices: 318800--318830 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
318790 ATTTTTATTA
318800 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
318816 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
318831 ATTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:319411 original size:16 final size:17
Alignment explanation
Indices: 319392--319438 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
319382 TATTAATTTT
319392 AATTTTAATATAT-TAA
1 AATTTTAATATATATAA
*
319408 AATTTT-ATAT-TATAT
1 AATTTTAATATATATAA
*
319423 AATTTTAAAATATATA
1 AATTTTAATATATATA
319439 TTCATACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 9 0.35
17 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTAATATATATAA
Found at i:319727 original size:21 final size:22
Alignment explanation
Indices: 319702--319749 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
319692 AATCAATAAC
319702 TAAATTAACATAAAATTAAA-T
1 TAAATTAACATAAAATTAAATT
* * *
319723 TAAATTTACGTATAATTAAATT
1 TAAATTAACATAAAATTAAATT
319745 TAAAT
1 TAAAT
319750 CTCATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTAACATAAAATTAAATT
Found at i:322075 original size:3 final size:3
Alignment explanation
Indices: 322067--322094 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
322057 ATACATTGAT
322067 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
322095 ATCGTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:322276 original size:2 final size:2
Alignment explanation
Indices: 322269--322296 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
322259 CTTGACAGAA
322269 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
322297 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322917 original size:20 final size:21
Alignment explanation
Indices: 322879--322919 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
322869 TTTAGTTGAT
322879 ATAAGATTTATTTAGATACAA
1 ATAAGATTTATTTAGATACAA
322900 ATAAG-TTTATTT-GAATACAA
1 ATAAGATTTATTTAG-ATACAA
322920 TAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 13 0.68
21 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (21 bp):
ATAAGATTTATTTAGATACAA
Found at i:324107 original size:23 final size:25
Alignment explanation
Indices: 324081--324128 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
324071 AAAAACAAAA
324081 TTAAAAAAAATTT-A-ATTTAAATT
1 TTAAAAAAAATTTAATATTTAAATT
* *
324104 TTAAAAACATTTTAATATTTAAATT
1 TTAAAAAAAATTTAATATTTAAATT
324129 AACAAATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 1 0.05
25 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAAAAAAATTTAATATTTAAATT
Found at i:324403 original size:23 final size:24
Alignment explanation
Indices: 324377--324429 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
324367 AGACGTAATA
324377 TTTAATAAAT-TTAAATTTTAAAT
1 TTTAATAAATATTAAATTTTAAAT
** *
324400 TTTAATATTTATTAATTTTTAAAT
1 TTTAATAAATATTAAATTTTAAAT
*
324424 TATAAT
1 TTTAAT
324430 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAATAAATATTAAATTTTAAAT
Found at i:324406 original size:30 final size:31
Alignment explanation
Indices: 324372--324433 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
324362 TTTTAAGACG
*
324372 TAATATTTAATAA-ATTTAAATTTTAAATTT
1 TAATATTTAATAATATTTAAATTATAAATTT
* * *
324402 TAATATTTATTAATTTTTAAATTATAATTTT
1 TAATATTTAATAATATTTAAATTATAAATTT
324433 T
1 T
324434 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TAATATTTAATAATATTTAAATTATAAATTT
Found at i:324827 original size:37 final size:37
Alignment explanation
Indices: 324777--324882 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 37
324767 AATATAAATA
324777 AAATTATATTTATATTTAATAATAATTAAAAATTATT
1 AAATTATATTTATATTTAATAATAATTAAAAATTATT
*
324814 AAATGATATTTATA-TT-A-AA-AA-TAAATAATTA--
1 AAATTATATTTATATTTAATAATAATTAAA-AATTATT
* **
324845 AAATTATATTTATATTAAATAATTGTTAAAATATTATT
1 AAATTATATTTATATTTAATAATAATTAAAA-ATTATT
324883 TACATTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
31 13 0.24
32 5 0.09
33 8 0.15
34 4 0.07
35 2 0.04
36 10 0.18
37 13 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
AAATTATATTTATATTTAATAATAATTAAAAATTATT
Found at i:324867 original size:68 final size:72
Alignment explanation
Indices: 324724--324882 Score: 193
Period size: 68 Copynumber: 2.2 Consensus size: 72
324714 AAATATGATA
*
324724 AATAATTTAAAATTATTAAAAATATATTTAAAGTAGATAATATAATATAAATAAAATTATATTTA
1 AATAATTAAAAATTATT-AAAATATATTTAAAGTAGATAATATAATATAAATAAAATTATATTTA
*
324789 TATTTAAT
65 TATTAAAT
* * *
324797 AATAATTAAAAATTATT-AAATGATATTTATATTA-A-AA-ATAA-ATAATTAAAATTATATTTA
1 AATAATTAAAAATTATTAAAAT-ATATTTAAAGTAGATAATATAATATAAATAAAATTATATTTA
324857 TATTAAAT
65 TATTAAAT
**
324865 AATTGTTAAAATATTATT
1 AATAATTAAAA-ATTATT
324883 TACATTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
68 34 0.44
69 10 0.13
70 2 0.03
71 5 0.06
72 10 0.13
73 16 0.21
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (72 bp):
AATAATTAAAAATTATTAAAATATATTTAAAGTAGATAATATAATATAAATAAAATTATATTTAT
ATTAAAT
Found at i:324901 original size:28 final size:29
Alignment explanation
Indices: 324801--324901 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 29
324791 TTTAATAATA
*
324801 ATTAAAAAT--TATT-AAATGATATTTAT
1 ATTAAAAATAATATTAAAATTATATTTAT
324827 ATTAAAAATAAATAATTAAAATTATATTTAT
1 ATTAAAAAT-AAT-ATTAAAATTATATTTAT
* *
324858 ATT--AAATAATTGTTAAAA-TATTATTTAC
1 ATTAAAAATAA-TATTAAAATTA-TATTTAT
324886 ATTAAAAATAAT-TTAA
1 ATTAAAAATAATATTAA
324902 TAAAAAAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
26 9 0.14
27 2 0.03
28 21 0.33
29 7 0.11
30 9 0.14
31 15 0.24
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTAAAAATAATATTAAAATTATATTTAT
Found at i:326048 original size:5 final size:5
Alignment explanation
Indices: 326040--326069 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
326030 AACATAAATA
326040 TAGCC TAGCC TAGCC TAGCC TAGCC TAGCC
1 TAGCC TAGCC TAGCC TAGCC TAGCC TAGCC
326070 CAGCAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
TAGCC
Found at i:326203 original size:2 final size:2
Alignment explanation
Indices: 326196--326227 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
326186 TTGAAAGAAT
*
326196 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
326228 TTTAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:330445 original size:3 final size:3
Alignment explanation
Indices: 330423--330464 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
330413 GCCCCACTCT
* *
330423 ATA ATA GTA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
330465 TTGCTGGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:333845 original size:41 final size:40
Alignment explanation
Indices: 333760--333855 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
333750 TATTAATATT
*
333760 ATTT-ATTTTATTT-AAATTTGGTTAGTTTAAAATAAAAA
1 ATTTAATTTTATTTAAAATTTGGTTAATTTAAAATAAAAA
* *
333798 ATTTTAATTTTATTTAAAATTT-TTTATATTTATAAATAAATA
1 A-TTTAATTTTATTTAAAATTTGGTTA-ATTTA-AAATAAAAA
*
333840 ATTTAAATTTATTTAA
1 ATTTAATTTTATTTAA
333856 TTGATCCATA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 12 0.24
41 24 0.49
42 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (40 bp):
ATTTAATTTTATTTAAAATTTGGTTAATTTAAAATAAAAA
Found at i:334436 original size:15 final size:15
Alignment explanation
Indices: 334418--334468 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
334408 CTATTTTATA
334418 TTTAATTAATAAATT
1 TTTAATTAATAAATT
*
334433 TTTAA-TAAAAAATT
1 TTTAATTAATAAATT
*
334447 TATTAATTTTAATAAAAT
1 T-TTAA--TTAATAAATT
334465 TTTA
1 TTTA
334469 CTAACAATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.31
15 9 0.31
17 3 0.10
18 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAATTAATAAATT
Found at i:336890 original size:18 final size:19
Alignment explanation
Indices: 336867--336907 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
336857 AATATTTTAA
336867 TTTTTAAA-AAATTATTAT
1 TTTTTAAATAAATTATTAT
* *
336885 TTTTTAAATTAATTTTTAT
1 TTTTTAAATAAATTATTAT
336904 TTTT
1 TTTT
336908 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTAAATAAATTATTAT
Found at i:336908 original size:18 final size:17
Alignment explanation
Indices: 336860--336908 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
336850 TTGATATAAT
*
336860 ATTTTAATTTTTAAAAA
1 ATTTTTATTTTTAAAAA
* *
336877 ATTATTATTTTTTAAATTA
1 ATTTTTA-TTTTTAAA-AA
336896 ATTTTTATTTTTA
1 ATTTTTATTTTTA
336909 TTTTTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTTATTTTTAAAAA
Found at i:336922 original size:13 final size:13
Alignment explanation
Indices: 336880--336922 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
336870 TTAAAAAATT
336880 ATTATTTTTTA-A
1 ATTATTTTTTATA
* *
336892 ATTAATTTTTATT
1 ATTATTTTTTATA
*
336905 TTTATTTTTTATA
1 ATTATTTTTTATA
336918 ATTAT
1 ATTAT
336923 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTATTTTTTATA
Found at i:337808 original size:2 final size:2
Alignment explanation
Indices: 337801--337833 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
337791 TAATACTAAC
337801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
337834 ATTGTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338387 original size:3 final size:3
Alignment explanation
Indices: 338376--338412 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
338366 AAAAGAATAA
338376 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
338413 CATTGAACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:339813 original size:2 final size:2
Alignment explanation
Indices: 339808--339832 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
339798 ATATATATAT
339808 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
339833 CACGTGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:342666 original size:15 final size:15
Alignment explanation
Indices: 342648--342683 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
342638 TGTCTGTGCC
342648 AAAGTACTTGTGTCA
1 AAAGTACTTGTGTCA
342663 AAAGTACTTGTGTCA
1 AAAGTACTTGTGTCA
342678 AAAGTA
1 AAAGTA
342684 TTTATATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (15 bp):
AAAGTACTTGTGTCA
Found at i:342693 original size:15 final size:15
Alignment explanation
Indices: 342648--342711 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
342638 TGTCTGTGCC
* *
342648 AAAGTACTTGTGTCA
1 AAAGTACTTATATCA
* *
342663 AAAGTACTTGTGTCA
1 AAAGTACTTATATCA
*
342678 AAAGTATTTATATC-
1 AAAGTACTTATATCA
*
342692 AAAGTACTTATATTA
1 AAAGTACTTATATCA
342707 AAAGT
1 AAAGT
342712 GTCTATGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (15 bp):
AAAGTACTTATATCA
Found at i:342936 original size:14 final size:14
Alignment explanation
Indices: 342914--342958 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
342904 CTTGTGTCAG
342914 GTACTTGTACCAAA
1 GTACTTGTACCAAA
* *
342928 GTGCTTGTA-CTAA
1 GTACTTGTACCAAA
342941 GTACTTGTACCAAA
1 GTACTTGTACCAAA
342955 GTAC
1 GTAC
342959 CTATGTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (14 bp):
GTACTTGTACCAAA
Found at i:342970 original size:41 final size:40
Alignment explanation
Indices: 342923--343009 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
342913 GGTACTTGTA
* * *
342923 CCAAAGTGCTTGTACTAAGTACTTGTACCAAAGTACCTATG
1 CCAAAGTGCTTATACCAAGCACTTGTACC-AAGTACCTATG
* * * *
342964 TCAAAGTGCTTATACCGAGCACTTGTGCCAAGTACTTATG
1 CCAAAGTGCTTATACCAAGCACTTGTACCAAGTACCTATG
343004 CCAAAG
1 CCAAAG
343010 GTAGCCAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
CCAAAGTGCTTATACCAAGCACTTGTACCAAGTACCTATG
Found at i:343801 original size:37 final size:37
Alignment explanation
Indices: 343751--343826 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
343741 GTCTGTCAAC
343751 ATGCTTTCTTTGAAGGAAACATGTCCATGTTCCTTCA
1 ATGCTTTCTTTGAAGGAAACATGTCCATGTTCCTTCA
343788 ATGCTTTCTTTGAAGGAAACATGTCCATGTTCCTTCA
1 ATGCTTTCTTTGAAGGAAACATGTCCATGTTCCTTCA
343825 AT
1 AT
343827 TGTCCCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
ATGCTTTCTTTGAAGGAAACATGTCCATGTTCCTTCA
Found at i:345764 original size:102 final size:103
Alignment explanation
Indices: 345571--345774 Score: 356
Period size: 102 Copynumber: 2.0 Consensus size: 103
345561 TTGATTCATG
* *
345571 GTATGGGAATTTTCTGGTGCCAGTTGTTCCATCACGGGCAGAACTAAACGGTTAAGTACTTCTTG
1 GTATGGGAATTTTCTGGTGCCAGTTGCTCCATCACGGGCAGAACTAAAC-GATAAGTACTTCTTG
345636 CACCTCATTGATTTTGATCTAATTTTATCTGCTGACATC
65 CACCTCATTGATTTTGATCTAATTTTATCTGCTGACATC
* *
345675 GTATGGGAATTTTCTGGTGCCAGTTGCTCTATCATGGGCAGAACTAAAC-ATAAGTACTTCTTGC
1 GTATGGGAATTTTCTGGTGCCAGTTGCTCCATCACGGGCAGAACTAAACGATAAGTACTTCTTGC
345739 ACCTCATTGATTTTGATCTAATTTTATCTGCTGACA
66 ACCTCATTGATTTTGATCTAATTTTATCTGCTGACA
345775 ATGCAACTGC
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 50 0.52
104 46 0.48
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (103 bp):
GTATGGGAATTTTCTGGTGCCAGTTGCTCCATCACGGGCAGAACTAAACGATAAGTACTTCTTGC
ACCTCATTGATTTTGATCTAATTTTATCTGCTGACATC
Found at i:347374 original size:24 final size:23
Alignment explanation
Indices: 347347--347412 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
347337 ATAATTTTTA
* *
347347 ATAATTTAATTATTATTATTTAAC
1 ATAATATAATT-TTAATATTTAAC
*
347371 ATAAATATAATTTTAATATTTAAT
1 AT-AATATAATTTTAATATTTAAC
*
347395 ATAAATATTATTTTAATA
1 AT-AATATAATTTTAATA
347413 GTTTTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 29 0.78
25 8 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATATAATTTTAATATTTAAC
Found at i:347424 original size:59 final size:63
Alignment explanation
Indices: 347315--347454 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 63
347305 TTCAATTTTA
347315 AATTTTAT-TTTAATATAAATATATAATTTTTAATAATTTAATTATTATTATTTAACATAAATAT
1 AATTTTATATTTAATATAAATATATAATTTTTAATAATTT-ATTA-TATTATTTAACATAAATAT
* ** *
347379 AATTTTAATATTTAATATAAATAT-T-A-TTTTAATAGTTT-TTA-ATTATTTATTATATATAT
1 AATTTT-ATATTTAATATAAATATATAATTTTTAATAATTTATTATATTATTTAACATAAATAT
347438 ACATTTTA-ATTTAATAT
1 A-ATTTTATATTTAATAT
347455 TTTTAGTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
58 9 0.13
59 17 0.25
60 5 0.07
61 3 0.04
63 11 0.16
64 7 0.10
65 3 0.04
66 14 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (63 bp):
AATTTTATATTTAATATAAATATATAATTTTTAATAATTTATTATATTATTTAACATAAATAT
Found at i:347448 original size:66 final size:66
Alignment explanation
Indices: 347308--347456 Score: 159
Period size: 65 Copynumber: 2.3 Consensus size: 66
347298 CTGTTTATTC
*
347308 AATTTTAAATTTT-AT-TTTAATATAAATATATAATTTTTAATAATTTAATTATTATTATTTAAC
1 AATTTT-AATTTTAATATTTAATATAAATATATAATTTTTAATAATTTAATTATTATTATATAAC
347371 AT
65 AT
* * *
347373 AAATATAATTTTAATATTTAATATAAATAT-T-A-TTTTAATAGTTTTTAATTATTTATTATAT-
1 AATTTTAATTTTAATATTTAATATAAATATATAATTTTTAATA--ATTTAATTA-TTATTATATA
*
347434 ATAT
63 ACAT
347438 ACATTTTAA-TTTAATATTT
1 A-ATTTTAATTTTAATATTT
347457 TTAGTTATCA
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
63 8 0.11
64 7 0.10
65 29 0.41
66 27 0.38
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (66 bp):
AATTTTAATTTTAATATTTAATATAAATATATAATTTTTAATAATTTAATTATTATTATATAACA
T
Found at i:347559 original size:21 final size:21
Alignment explanation
Indices: 347534--347606 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
347524 TATACCATTA
*
347534 ATTTAATTTGATTATTATAAT
1 ATTTAATTTTATTATTATAAT
347555 ATTTAATTTTATTATTATAAT
1 ATTTAATTTTATTATTATAAT
*
347576 -TATTAATTTTATCATTATAAT
1 AT-TTAATTTTATTATTATAAT
347597 ATTTAATTTT
1 ATTTAATTTT
347607 TACCGTTCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (21 bp):
ATTTAATTTTATTATTATAAT
Found at i:347584 original size:26 final size:23
Alignment explanation
Indices: 347521--347605 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 23
347511 TCTAAATGGA
347521 TATTATACCATTAATTTAATTTGAT
1 TATTATA--ATTAATTTAATTTGAT
*
347546 TATTATAA-T-ATTTAATTTTAT
1 TATTATAATTAATTTAATTTGAT
*
347567 TATTATAATT-A-TTAATTTTAT
1 TATTATAATTAATTTAATTTGAT
*
347588 CATTATAA-T-ATTTAATTT
1 TATTATAATTAATTTAATTT
347606 TTACCGTTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.04
21 43 0.77
22 3 0.05
23 1 0.02
25 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (23 bp):
TATTATAATTAATTTAATTTGAT
Found at i:347625 original size:43 final size:42
Alignment explanation
Indices: 347536--347633 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 42
347526 TACCATTAAT
* * ** *
347536 TTAATTTGATTATTATAATATTTAATTTTATTATTATAATTA
1 TTAATTTCATCATTATAATATTTAATTTTACCATTATAATGA
* * *
347578 TTAATTTTATCATTATAATATTTAATTTTTACCGTTCTAATGA
1 TTAATTTCATCATTATAATATTTAA-TTTTACCATTATAATGA
347621 TTAATTTCATCAT
1 TTAATTTCATCAT
347634 AATTTATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 23 0.49
43 24 0.51
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (42 bp):
TTAATTTCATCATTATAATATTTAATTTTACCATTATAATGA
Found at i:347905 original size:21 final size:20
Alignment explanation
Indices: 347879--347935 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
347869 AATTAATTCG
347879 ATTTAAATTAAATTATTATTT
1 ATTTAAATTAAATTATT-TTT
* *
347900 ATTT-AATAAAAATAATTTTT
1 ATTTAAAT-TAAATTATTTTT
* *
347920 ATCTAAATTTAATTAT
1 ATTTAAATTAAATTAT
347936 AAAAATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATTAAATTATTTTT
Found at i:348138 original size:2 final size:2
Alignment explanation
Indices: 348120--348161 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
348110 CGACTAAAAG
* *
348120 AT AT CT AT AT CT 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
348162 TTGTGGCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:348718 original size:9 final size:9
Alignment explanation
Indices: 348706--348776 Score: 81
Period size: 9 Copynumber: 7.4 Consensus size: 9
348696 ATTTATGTTA
348706 TTTTTTAAT
1 TTTTTTAAT
348715 TTTTTCTAAGT
1 TTTTT-TAA-T
348726 TTTTTCTAAT
1 TTTTT-TAAT
*
348736 TTTTCTAAT
1 TTTTTTAAT
348745 TTTTTATAAT
1 TTTTT-TAAT
348755 ATTTTTTAA-
1 -TTTTTTAAT
348764 TTTTTTAAT
1 TTTTTTAAT
348773 TTTT
1 TTTT
348777 CTCAATTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.15
9 17 0.31
10 15 0.27
11 15 0.27
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:348728 original size:10 final size:9
Alignment explanation
Indices: 348705--348783 Score: 72
Period size: 10 Copynumber: 8.3 Consensus size: 9
348695 TATTTATGTT
348705 ATTTTT-TA
1 ATTTTTCTA
348713 ATTTTTTCTA
1 A-TTTTTCTA
348723 AGTTTTTTCTA
1 A--TTTTTCTA
348734 ATTTTTCTA
1 ATTTTTCTA
*
348743 ATTTTTTATA
1 A-TTTTTCTA
*
348753 ATATTTTTTA
1 AT-TTTTCTA
348763 ATTTTT-TA
1 ATTTTTCTA
348771 ATTTTTCTCA
1 ATTTTTCT-A
348781 ATT
1 ATT
348784 ATTTTTTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
8 9 0.15
9 20 0.32
10 23 0.37
11 10 0.16
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTTCTA
Found at i:348738 original size:20 final size:18
Alignment explanation
Indices: 348706--348789 Score: 89
Period size: 20 Copynumber: 4.3 Consensus size: 18
348696 ATTTATGTTA
348706 TTTTTTAATTTTTTCTAAGT
1 TTTTTTAA-TTTTTCTAA-T
348726 TTTTTCTAATTTTTCTAAT
1 TTTTT-TAATTTTTCTAAT
*
348745 TTTTTATAATATTTTTTAA-
1 TTTTT-TAAT-TTTTCTAAT
348764 TTTTTTAATTTTTCTCAAT
1 TTTTTTAATTTTTCT-AAT
348783 TATTTTT
1 T-TTTTT
348790 TTAATTTCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
17 5 0.09
18 6 0.11
19 16 0.29
20 26 0.46
21 3 0.05
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTTTTAATTTTTCTAAT
Done.