Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009584.1 Hibiscus syriacus cultivar Beakdansim tig00116961_pilon, whole genome shotgun sequence
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: 2003061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:848789 original size:19 final size:19
Alignment explanation
Indices: 848765--848802 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
848755 CTTTGTATTT
*
848765 TAGTTTAAATAGGTTTTAG
1 TAGTTTAAATAAGTTTTAG
*
848784 TAGTTTAATTAAGTTTTAG
1 TAGTTTAAATAAGTTTTAG
848803 GATGTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (19 bp):
TAGTTTAAATAAGTTTTAG
Found at i:848813 original size:75 final size:73
Alignment explanation
Indices: 848734--848941 Score: 217
Period size: 75 Copynumber: 2.8 Consensus size: 73
848724 TTAGGATAAG
* ** *
848734 ATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAAGTT
1 ATTTTAAATATTATATTTT-T-TAGGTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAAGAT
* *
848799 TTAGGATGTC
64 TTAGAATATC
* * * * *
848809 ATTTTTATATTTTATCATTGTTTAGGTATTTTAGTTTAAATAGGTTTTAG-AATCTTAATTAGGA
1 A-TTTTAAATATTAT-ATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAGT-TTAATTAAGA
*
848873 TTTAGAATATT
63 TTTAGAATATC
848884 ATTTTAAATATTA-ATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT-GTTTTAATTA
1 ATTTTAAATATTATATTTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTAG-TTTAATTA
848942 GGATATAAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
71 5 0.05
72 34 0.31
73 1 0.01
74 12 0.11
75 44 0.40
76 11 0.10
77 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.54
Consensus pattern (73 bp):
ATTTTAAATATTATATTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAGTTTAATTAAGATTT
AGAATATC
Found at i:848871 original size:19 final size:19
Alignment explanation
Indices: 848844--848880 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
848834 GTATTTTAGT
*
848844 TTAAATAGGTTTTAGAATC
1 TTAAATAGGATTTAGAATC
*
848863 TTAATTAGGATTTAGAAT
1 TTAAATAGGATTTAGAAT
848881 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (19 bp):
TTAAATAGGATTTAGAATC
Found at i:848939 original size:72 final size:74
Alignment explanation
Indices: 848759--848945 Score: 220
Period size: 75 Copynumber: 2.5 Consensus size: 74
848749 TTTTATCTTT
* * * * * *
848759 GTATTTTAGTTTAAATAGGTTTTAGTAG-TTTAATTAAGTTTTAGGATGTCATTTTTATATTTTA
1 GTATTTTAGTTTAAATAGGTTTTAGT-GTTTTAATTAGGATTTAGAATATCATTTTTAAATATTA
848823 TCATTGTTTAG
65 -CATTGTTTAG
** * *
848834 GTATTTTAGTTTAAATAGGTTTTAGAATCTTAATTAGGATTTAGAATATTA-TTTTAAATATTA-
1 GTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATCATTTTTAAATATTAC
*
848897 ATTTTTTAG
66 ATTGTTTAG
848906 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGAT
1 GTATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGAT
848946 ATAAGATGTT
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
71 5 0.05
72 39 0.41
74 10 0.10
75 42 0.44
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (74 bp):
GTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATCATTTTTAAATATTAC
ATTGTTTAG
Found at i:849663 original size:14 final size:14
Alignment explanation
Indices: 849597--849665 Score: 54
Period size: 14 Copynumber: 4.8 Consensus size: 14
849587 TAAAAACCCT
849597 TTTTATTTTA-CTA
1 TTTTATTTTATCTA
849610 TTATTA-TTTAT-TA
1 TT-TTATTTTATCTA
* *
849623 TTTTATTATTTTCCCTT
1 TTTTATT-TTAT--CTA
849640 TTTTATTTTTATCTA
1 TTTTA-TTTTATCTA
849655 TTTTATTTTAT
1 TTTTATTTTAT
849666 TAAATCTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
12 3 0.07
13 11 0.25
14 12 0.27
15 7 0.16
17 9 0.20
18 2 0.05
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATTTTATCTA
Found at i:850681 original size:13 final size:13
Alignment explanation
Indices: 850635--850679 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
850625 GTCATAAATC
850635 TATGACACGCATT
1 TATGACACGCATT
850648 TATGACACGCATT
1 TATGACACGCATT
*
850661 TATGACGCGCATT
1 TATGACACGCATT
850674 TATGAC
1 TATGAC
850680 GCCCATTACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:850686 original size:13 final size:13
Alignment explanation
Indices: 850635--850686 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
850625 GTCATAAATC
*
850635 TATGACACGCATT
1 TATGACGCGCATT
*
850648 TATGACACGCATT
1 TATGACGCGCATT
850661 TATGACGCGCATT
1 TATGACGCGCATT
*
850674 TATGACGCCCATT
1 TATGACGCGCATT
850687 ACGCGTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:850865 original size:2 final size:2
Alignment explanation
Indices: 850858--850920 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
850848 TTTCGTAAAT
850858 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
850900 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
850921 GTAGATTGAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:853878 original size:16 final size:16
Alignment explanation
Indices: 853857--853891 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
853847 GATCATCAAC
*
853857 TTGCAGCTAGAAACCT
1 TTGCAGCTAAAAACCT
*
853873 TTGCAGTTAAAAACCT
1 TTGCAGCTAAAAACCT
853889 TTG
1 TTG
853892 AAGTGTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (16 bp):
TTGCAGCTAAAAACCT
Found at i:853967 original size:2 final size:2
Alignment explanation
Indices: 853960--854019 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
853950 ATTGAAATCA
853960 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
854002 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
854020 GTCTAATATC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:855657 original size:15 final size:15
Alignment explanation
Indices: 855639--855667 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
855629 CTCCTAGAGA
855639 CAGCACGAAGCCACC
1 CAGCACGAAGCCACC
855654 CAGCACGAAGCCAC
1 CAGCACGAAGCCAC
855668 GCCTGTTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.45, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGCACGAAGCCACC
Found at i:868983 original size:24 final size:25
Alignment explanation
Indices: 868955--869059 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 25
868945 GCTTGAAGAT
868955 AAAAAAAG--AAAAAGAAAAAAAGG
1 AAAAAAAGAAAAAAAGAAAAAAAGG
* *
868978 AGAAAAAATAAAAAAAGAAAAAAATG
1 A-AAAAAAGAAAAAAAGAAAAAAAGG
*
869004 -AAAAAAGAAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAG-AAAAAAAGG
869029 AAAAAGAATGAAAAAAAG--AAAAAGG
1 AAAAA-AA-GAAAAAAAGAAAAAAAGG
869054 AAAAAA
1 AAAAAA
869060 TGAAGGAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
23 1 0.01
24 21 0.30
25 19 0.27
26 18 0.26
27 2 0.03
28 9 0.13
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAGAAAAAAAGG
Found at i:869012 original size:42 final size:43
Alignment explanation
Indices: 868955--869075 Score: 149
Period size: 42 Copynumber: 2.8 Consensus size: 43
868945 GCTTGAAGAT
* * *
868955 AAAAAAAG-AAAAAGAAAAAAAGGAGAAAAAATAAAAA-AA-G
1 AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAGAATG
868995 AAAAAAATGAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAGAATG
1 AAAAAAA-GAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAGAATG
* *
869039 AAAAAAAGAAAAAGGAAAAAATGAAGGAAAAAAAGAA
1 AAAAAAAGAAAAAAGAAAAAAAGAA--AAAAAAAGAA
869076 GGGTTCAAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
40 7 0.10
41 1 0.01
42 26 0.37
43 18 0.26
44 8 0.11
45 10 0.14
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (43 bp):
AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAGAATG
Found at i:869026 original size:18 final size:18
Alignment explanation
Indices: 868958--869051 Score: 95
Period size: 18 Copynumber: 5.3 Consensus size: 18
868948 TGAAGATAAA
868958 AAAAGAAAAAGAAAAAAAG
1 AAAA-AAAAAGAAAAAAAG
* * *
868977 GAGAAAAAATAAAAAAAG
1 AAAAAAAAAGAAAAAAAG
*
868995 -AAAAAAATG-AAAAAAG
1 AAAAAAAAAGAAAAAAAG
869011 AAAAAAAGAA-AAAAAAAG
1 AAAAAAA-AAGAAAAAAAG
* *
869029 AAAAAGAATGAAAAAAAG
1 AAAAAAAAAGAAAAAAAG
869047 AAAAA
1 AAAAA
869052 GGAAAAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
16 7 0.11
17 13 0.21
18 40 0.65
19 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAG
Found at i:869051 original size:1 final size:1
Alignment explanation
Indices: 868955--869033 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
868945 GCTTGAAGAT
* * ** * * * ** * *
868955 AAAAAAAGAAAAAGAAAAAAAGGAGAAAAAATAAAAAAAGAAAAAAATGAAAAAAGAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
869020 AAAAAAAAGAAAAA
1 AAAAAAAAAAAAAA
869034 GAATGAAAAA
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (1 bp):
A
Found at i:869059 original size:8 final size:8
Alignment explanation
Indices: 868955--869051 Score: 101
Period size: 8 Copynumber: 11.6 Consensus size: 8
868945 GCTTGAAGAT
868955 AAAAAAAG
1 AAAAAAAG
868963 --AAAAAG
1 AAAAAAAG
868969 AAAAAAAGG
1 AAAAAAA-G
*
868978 AGAAAAAAT
1 A-AAAAAAG
868987 AAAAAAAG
1 AAAAAAAG
868995 AAAAAAATG
1 AAAAAAA-G
869004 -AAAAAAG
1 AAAAAAAG
869011 AAAAAAAG
1 AAAAAAAG
869019 AAAAAAAAAG
1 --AAAAAAAG
869029 AAAAAGAATG
1 AAAAA-AA-G
869039 AAAAAAAG
1 AAAAAAAG
869047 AAAAA
1 AAAAA
869052 GGAAAAAATG
Statistics
Matches: 77, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
6 6 0.08
7 1 0.01
8 42 0.55
9 8 0.10
10 20 0.26
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:869065 original size:12 final size:12
Alignment explanation
Indices: 869029--869077 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
869019 AAAAAAAAAG
*
869029 AAAAAGAATGAA
1 AAAAAGAAGGAA
869041 AAAAAGAAAAAGGAA
1 AAAAAG---AAGGAA
*
869056 AAAATGAAGGAA
1 AAAAAGAAGGAA
869068 AAAAAGAAGG
1 AAAAAGAAGG
869078 GTTCAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 21 0.68
15 10 0.32
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (12 bp):
AAAAAGAAGGAA
Found at i:869075 original size:27 final size:28
Alignment explanation
Indices: 868968--869059 Score: 56
Period size: 26 Copynumber: 3.5 Consensus size: 28
868958 AAAAGAAAAA
* * *
868968 GAAAAAAAGGAGAAAAAATAAAAA-AA-
1 GAAAAAAAGAAAAAAAAAGAAAAAGAAG
*
868994 GAAAAAAATGAAAAAAGAA-AAAAAGAA-
1 GAAAAAAA-GAAAAAAAAAGAAAAAGAAG
* *
869021 -AAAAAAAGAAAAAGAATGAAAAA-AA-
1 GAAAAAAAGAAAAAAAAAGAAAAAGAAG
*
869046 G-AAAAAGGAAAAAA
1 GAAAAAAAGAAAAAA
869060 TGAAGGAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
25 20 0.37
26 25 0.46
27 9 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (28 bp):
GAAAAAAAGAAAAAAAAAGAAAAAGAAG
Found at i:870460 original size:54 final size:54
Alignment explanation
Indices: 870392--871204 Score: 909
Period size: 54 Copynumber: 15.1 Consensus size: 54
870382 TGAAGCAAAT
* * * *
870392 GAAGATTGTTCGAGTTTCTTCTCCCTAAAGAAAGAGGGACCGAACCCATTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * * *
870446 GAATATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACACGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * *
870500 GAAGATTGTTTGAGTTCCTACTCCCTAAAGAAAGAGGGAACGAACCCGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * * *
870554 GAAGATTGTTCGAGATCCTACTCCTTAAAGAAAGAGGGAGCGAACTCGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * *
870608 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAACAGGGAGCGAACCTGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
*
870662 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCATTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * *
870716 GAAGATTGTTTGAGTTCGTACTCCCTAAAGAAAGAGAGAGCGAACCCGTTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* ** * *
870770 GAAGATTGTTCGAGTTCTTACTCCCTAAAGAAAGAGTTAACGAACCCATTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* *
870824 GAAGATTGATCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCAGTTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * *
870878 GAAGATTGTTCAAGTTCCTACTCCCTAAATAGAGAGGGAGCGAACCCGTTGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * * * *
870932 GAATATTGTTTGAGTTCCTACTCCCTAAAGAAAGCGGGAGCAAACCCGTTAGAA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * ** * ** *
870986 GAAGATTATTTGAGTTCCTACTGTCTAAAGAAAGA-GGAGCAAACCCGTAAGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * * * *
871039 TAAGATTGTTTGAGTTCCTACTCCTTAAAAGAAAGA--G-GCGAACCCATCGATA
1 GAAGATTGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * * ** * *
871091 GAAGATTGTTTGAGTTCCCACT-CCTCAAAGAAAGAAGGAGTGAACCTATAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTGGTA
* * * ** * * **
871145 GAAGAGTGCTCGAGTT-CTACTCCCTGAAGCGATAGGGAGCAAACCCGTTTTTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
871198 GAAGATT
1 GAAGATT
871205 CTCTTCAAGT
Statistics
Matches: 649, Mismatches: 105, Indels: 11
0.85 0.14 0.01
Matches are distributed among these distances:
51 11 0.02
52 29 0.04
53 64 0.10
54 545 0.84
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTA
Found at i:878430 original size:22 final size:20
Alignment explanation
Indices: 878395--878438 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
878385 AAAATAAAAT
878395 AATAAAAATGAATTAATTATC
1 AATAAAAATGAATTAATT-TC
* *
878416 AATATAAAATTAATTTATTTC
1 AATA-AAAATGAATTAATTTC
878437 AA
1 AA
878439 GTTCACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
AATAAAAATGAATTAATTTC
Found at i:889412 original size:22 final size:22
Alignment explanation
Indices: 889384--889427 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
889374 AATTTGTGTT
* *
889384 GGGTCTGGGTTGAGTCTGGATC
1 GGGTCTGGATCGAGTCTGGATC
*
889406 GGGTCTGTATCGAGTCTGGATC
1 GGGTCTGGATCGAGTCTGGATC
889428 TTGGGTCGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.41, T:0.32
Consensus pattern (22 bp):
GGGTCTGGATCGAGTCTGGATC
Found at i:889577 original size:3 final size:3
Alignment explanation
Indices: 889569--889622 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
889559 TGAAAAATGT
889569 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
889617 ATA ATA
1 ATA ATA
889623 TATATATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:901995 original size:23 final size:23
Alignment explanation
Indices: 901964--902008 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
901954 TTTGATATTT
*
901964 TTTCTTTTTTTGTTCTCTTTTTC
1 TTTCATTTTTTGTTCTCTTTTTC
*
901987 TTTCATTTTTTGTTTTCTTTTT
1 TTTCATTTTTTGTTCTCTTTTT
902009 TCCTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTCATTTTTTGTTCTCTTTTTC
Found at i:903212 original size:134 final size:132
Alignment explanation
Indices: 902865--903221 Score: 346
Period size: 134 Copynumber: 2.7 Consensus size: 132
902855 TGTTGTTTAT
* * * * * *
902865 GGGTGACACGGCTCCTACGTGAC-GAGAAGATTTGGTCGATGGATGACATGGTTCCTACGTGGTA
1 GGGTGACTCGGCTCCTACGTG-CTGAGGAGATATGGTC-ATGGATGACA-CGTTCCTACGTGATG
* * * * * *
902929 AGGA-TGACTGGCCATCTTTATGGATGATGATTACATGGTTCCTATACGATGAGGACGGCTGGTT
63 AGGACAGA-TGGCCATCTTTAGGGATGATGATTACACGGTTCCTACACGATGAGGACGACTAGTT
902993 ATCTAA
127 ATCTAA
* * * * * **
902999 GGTTGACTCGGCTCCTACGTGATGATGAGATCTGGTCAGTGGATGGCACGATTCCTACACGATGA
1 GGGTGACTCGGCTCCTACGTGCTGAGGAGATATGGTCA-TGGATGACACG-TTCCTACGTGATG-
* * * *
903064 AGG-CAGCTGACCATCTTTAGGGATGATGA-TAGCACGGTTCTTACGCGATGAGGACGACTAGTT
63 AGGACAGATGGCCATCTTTAGGGATGATGATTA-CACGGTTCCTACACGATGAGGACGACTAGTT
903127 ATCTAA
127 ATCTAA
* *
903133 GGGTGACGT-GTCTCCTACGTGCTGAGGAGATATGGTCATTGGATGACACAGTTCCTACGTAATG
1 GGGTGAC-TCGGCTCCTACGTGCTGAGGAGATATGGTCA-TGGATGACAC-GTTCCTACGTGATG
*
903197 AGGACGGATGGCCATCTTTAGGGAT
63 AGGACAGATGGCCATCTTTAGGGAT
903222 AATATTTCAA
Statistics
Matches: 179, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
133 7 0.04
134 166 0.93
135 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (132 bp):
GGGTGACTCGGCTCCTACGTGCTGAGGAGATATGGTCATGGATGACACGTTCCTACGTGATGAGG
ACAGATGGCCATCTTTAGGGATGATGATTACACGGTTCCTACACGATGAGGACGACTAGTTATCT
AA
Found at i:903462 original size:131 final size:131
Alignment explanation
Indices: 903233--903567 Score: 338
Period size: 131 Copynumber: 2.5 Consensus size: 131
903223 ATATTTCAAG
* *
903233 AGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGTTAATGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACACTCTCAAAGTTAATGTTTCAAG
* * * * * *
903298 AGAATCTGTATCAAGAGAGACAAAATTCCTTTTAAGGGAGACGAGACTCAAAGATCTTTGTTTCA
66 AGAAACTATATAAAGAGACACAAAAATCCTTTTAAGGGAAACGA-ACTCAAAGATCTTTGTTTCA
903363 TA
130 TA
* * * *
903365 AGAAACTGTCTGAAGGGAGACAATATTTATTTCAA-GGAAACGA-TCTCAAA-TGTGATGTTTCA
1 AGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAC-ACTCTCAAAGT-TAATGTTTCA
* * * **
903427 AGAGAAACTATCTAAAGAGACACAAAAATCGTTTTAAGGGAAACGATCTCAAAGAT-GATGTTTC
64 AGAGAAACTATATAAAGAGACACAAAAATCCTTTTAAGGGAAACGAACTCAAAGATCTTTGTTTC
903491 A-A
129 ATA
* * * * * ** * *
903493 GAGAAATTGTCTCAAAAGAGATAAAATTCATTTAAAGGGAAACGAGACTCAAAGATATTTGTTTC
1 -AGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAC-ACTCTCAAAGTTA-ATGTTTC
*
903558 AAGATAAACT
63 AAGAGAAACT
903568 GTCTCAAGAG
Statistics
Matches: 166, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
128 1 0.01
129 34 0.20
130 18 0.11
131 67 0.40
132 46 0.28
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (131 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACACTCTCAAAGTTAATGTTTCAAG
AGAAACTATATAAAGAGACACAAAAATCCTTTTAAGGGAAACGAACTCAAAGATCTTTGTTTCAT
A
Found at i:903569 original size:196 final size:196
Alignment explanation
Indices: 903226--903580 Score: 491
Period size: 196 Copynumber: 1.8 Consensus size: 196
903216 AGGGATAATA
* * * * * * *
903226 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGTTAATG
1 TTTCAAGAGAAACTATCTAAAGAGACACAAAAATCGTTTCAAGGGAAACACTCTCAAAGATAATG
* * * * *
903291 TTTCAAGAGAATCTGTATCAAGAGAGACAAAATTCCTTTTAAGGGAGACGAGACTCAAAGATCTT
66 TTTCAAGAGAATCTGTATCAAAAGAGACAAAATTCATTTAAAGGGAAACGAGACTCAAAGATATT
* *
903356 TGTTTCATAAGAAACTGTCTGAAGGGAGACAATATTTATTTCAAGGAAACGATCTCAAATGTGAT
131 TGTTTCATAAGAAACTGTCTCAAGAGAGACAATATTTATTTCAAGGAAACGATCTCAAATGTGAT
903421 G
196 G
* *
903422 TTTCAAGAGAAACTATCTAAAGAGACACAAAAATCGTTTTAAGGGAAACGA-TCTCAAAGATGAT
1 TTTCAAGAGAAACTATCTAAAGAGACACAAAAATCGTTTCAAGGGAAAC-ACTCTCAAAGATAAT
* *
903486 GTTTCAAGAGAAAT-TGTCTCAAAAGAGATAAAATTCATTTAAAGGGAAACGAGACTCAAAGATA
65 GTTTCAAGAG-AATCTGTATCAAAAGAGACAAAATTCATTTAAAGGGAAACGAGACTCAAAGATA
*
903550 TTTGTTTCA-AGATAAACTGTCTCAAGAGAGA
129 TTTGTTTCATA-AGAAACTGTCTCAAGAGAGA
903581 TAAAACTATG
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
195 1 0.01
196 132 0.96
197 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (196 bp):
TTTCAAGAGAAACTATCTAAAGAGACACAAAAATCGTTTCAAGGGAAACACTCTCAAAGATAATG
TTTCAAGAGAATCTGTATCAAAAGAGACAAAATTCATTTAAAGGGAAACGAGACTCAAAGATATT
TGTTTCATAAGAAACTGTCTCAAGAGAGACAATATTTATTTCAAGGAAACGATCTCAAATGTGAT
G
Found at i:903571 original size:67 final size:65
Alignment explanation
Indices: 903226--903612 Score: 347
Period size: 65 Copynumber: 5.9 Consensus size: 65
903216 AGGGATAATA
* * * * *
903226 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-ACTCTCAAAGTTAAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA-ACTCAAAGATATT
903290 G
65 G
* * * * * *
903291 TTTCAAGAGAATCTGTATCAAGAGAGACAAAATTCCTTTTAAGGGAGACGAGACTCAAAGATCTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA-ACTCAAAGAT-AT
903356 TG
64 TG
* * * ** *
903358 TTTCATA-AGAAACTGTCTGAAGGGAGACAATATTTATTTCAA-GGAAACGATCTCAAATG-TGA
1 TTTCA-AGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGAACTCAAA-GAT-A
903420 -TG
63 TTG
* * * * * *
903422 TTTCAAGAGAAACTATCTAAAGAGACACAAAAATCGTTTTAAGGGAAACGATCTCAAAGATGA-T
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGAACTCAAAGAT-ATT
903486 G
65 G
* * * * *
903487 TTTCAAGAGAAATTGTCTCAAAAGAGATAAAATTCATTTAAAGGGAAACGAGACTCAAAGATATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA-ACTCAAAGATA-T
903552 TG
64 TG
* * *
903554 TTTCAAGATAAACTGTCTCAAGAGAGATAAAACTAT-GTTTCAAGGGAAACAAACTCAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-T-TCGTTTCAAGGGAAACGAACTCAAA
903613 ATTTTTTGTT
Statistics
Matches: 261, Mismatches: 49, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
63 1 0.00
64 34 0.13
65 112 0.43
66 26 0.10
67 72 0.28
68 15 0.06
69 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGAACTCAAAGATATTG
Found at i:903648 original size:29 final size:30
Alignment explanation
Indices: 903589--903649 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
903579 GATAAAACTA
903589 TGTTTCAAGGGAAACAAACTCAAAATTTTT
1 TGTTTCAAGGGAAACAAACTCAAAATTTTT
* *
903619 TGTTTCAAGTGAAAC-AACTTCCAAATTTTT
1 TGTTTCAAGGGAAACAAAC-TCAAAATTTTT
903649 T
1 T
903650 ATTTTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (30 bp):
TGTTTCAAGGGAAACAAACTCAAAATTTTT
Found at i:909646 original size:22 final size:20
Alignment explanation
Indices: 909609--909660 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
909599 TTTTGCTATT
909609 TTTTTCTTTTTGTTGTTCTC
1 TTTTTCTTTTTGTTGTTCTC
* * *
909629 TTTTTCTTTCCTTTTTGTTGTT
1 TTTTTCTTT--TTGTTGTTCTC
909651 TTTTTCTTTT
1 TTTTTCTTTT
909661 GAATTTTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTTGTTGTTCTC
Found at i:910304 original size:2 final size:2
Alignment explanation
Indices: 910297--910359 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
910287 AATAATAATA
910297 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
910339 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
910360 ATTTTTTTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:911683 original size:21 final size:22
Alignment explanation
Indices: 911640--911683 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
911630 TTGTCGAGGC
* *
911640 AATGTTAAAAGTTTTCTCATGA
1 AATGATAAAAGTTATCTCATGA
911662 AATGATAAAAGTTATC-CATGA
1 AATGATAAAAGTTATCTCATGA
911683 A
1 A
911684 GACTTACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AATGATAAAAGTTATCTCATGA
Found at i:919849 original size:16 final size:16
Alignment explanation
Indices: 919830--919862 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
919820 TTATTGCTCA
919830 ACAATTTTATGAGGTG
1 ACAATTTTATGAGGTG
919846 ACAATTTTATGAGGTG
1 ACAATTTTATGAGGTG
919862 A
1 A
919863 ATTAGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
ACAATTTTATGAGGTG
Found at i:923059 original size:13 final size:13
Alignment explanation
Indices: 923041--923085 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
923031 GCTATTTTTT
923041 TCTTTTTTTGTTC
1 TCTTTTTTTGTTC
*
923054 TCTTTTTCT-TTC
1 TCTTTTTTTGTTC
*
923066 -CTTTTTTTGTTT
1 TCTTTTTTTGTTC
923078 TCTTTTTT
1 TCTTTTTT
923086 CCTTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.26
12 5 0.19
13 15 0.56
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TCTTTTTTTGTTC
Found at i:923074 original size:24 final size:22
Alignment explanation
Indices: 923035--923085 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
923025 CCTTTTGCTA
923035 TTTTTTTCTTTTTTTGTTCTCT
1 TTTTTTTCTTTTTTTGTTCTCT
*
923057 TTTTCTTTCCTTTTTTTGTTTTCT
1 TTTT-TTT-CTTTTTTTGTTCTCT
923081 TTTTT
1 TTTTT
923086 CCTTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTGTTCTCT
Found at i:924188 original size:134 final size:134
Alignment explanation
Indices: 924013--924295 Score: 347
Period size: 134 Copynumber: 2.1 Consensus size: 134
924003 AGGATAACTA
* * * *
924013 ACCATCTTTAGGGATGATGATTACACGGTTCCTATACGATGAGGACAGCTGGTTATCTAAGGTTG
1 ACCATCTTTAGGGATGATGAATACACGGTTCCTACACGATGAGGACAGCTAGTTATCTAAGGGTG
* * *
924078 ACATG-G-CTTCTACGTGATGATGAGATCTGGTCGGTGGATGACACGATTCCTACACGATGAAGA
66 --ATGCGTCTCCTACGTGACGAGGAGATCTGGTCGGTGGATGACACGATTCCTACACGATGAAGA
* *
924141 TGGTTG
129 CGGATG
** *
924147 ACCATCTTTAGGGATGAT-AATAGCACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGT
1 ACCATCTTTAGGGATGATGAATA-CACGGTTCCTACACGATGAGGACAGCTAGTTATCTAAGGGT
* * * ** *
924211 GATGCGTCTCCTATGTGCCGAGGAGATCTGGTCGTTGGATGACACGATTCCTACGTGATGAGGAC
65 GATGCGTCTCCTACGTGACGAGGAGATCTGGTCGGTGGATGACACGATTCCTACACGATGAAGAC
924276 GGATG
130 GGATG
*
924281 GCCATCTTTAGGGAT
1 ACCATCTTTAGGGAT
924296 AATATTTCAA
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
132 3 0.02
133 4 0.03
134 120 0.94
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (134 bp):
ACCATCTTTAGGGATGATGAATACACGGTTCCTACACGATGAGGACAGCTAGTTATCTAAGGGTG
ATGCGTCTCCTACGTGACGAGGAGATCTGGTCGGTGGATGACACGATTCCTACACGATGAAGACG
GATG
Found at i:924549 original size:65 final size:65
Alignment explanation
Indices: 924302--924671 Score: 354
Period size: 65 Copynumber: 5.6 Consensus size: 65
924292 GGATAATATT
** * * *
924302 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACGCTCTCAAAGTTGATGTTTCAAGAGAAACTGTA
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTGTC
* * * * ** *
924367 TCAAGAGATACAAAATTCCTTTCAAGGGAGACGAGACTCAAAGATCTTTGTTTCATGAGAAACTG
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAACGA-TCTCAAAGAT-GATGTTTCAAGAGAAACTG
924432 TC
64 TC
* * * * *
924434 TGAAGGGAGACAATATTTATTTCAA-AGAAACGATCTCAAATG-TGATGTTTCAAGAGAAACTGT
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAA-GATGATGTTTCAAGAGAAACTGT
924497 C
65 C
* * * * *
924498 TGAAGAGACACAAAAATCATTTTAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAATTGTC
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTGTC
* * * * *
924563 TCAAAAGAGACAAAATTGATTTAAATGGAAACAAGA-CTCAAAGAT-ATTTGTTTCAAGATAAAC
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAAC--GATCTCAAAGATGA--TGTTTCAAGAGAAAC
924626 TGTC
62 TGTC
* * *
924630 TCAAGAGAGACAAAACTAT-GTTTCAAGGGAAACAAACTCAAA
1 TCAAGAGAGACAAAA-T-TCATTTCAAGGGAAACGATCTCAAA
924672 AATTTTTGTT
Statistics
Matches: 248, Mismatches: 45, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
64 38 0.15
65 97 0.39
66 25 0.10
67 75 0.30
68 12 0.05
69 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (65 bp):
TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTGTC
Found at i:931976 original size:11 final size:11
Alignment explanation
Indices: 931960--931984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
931950 GTCGAGTCTA
931960 GATCGGGTATG
1 GATCGGGTATG
931971 GATCGGGTATG
1 GATCGGGTATG
931982 GAT
1 GAT
931985 TGGATCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.44, T:0.28
Consensus pattern (11 bp):
GATCGGGTATG
Found at i:932138 original size:3 final size:3
Alignment explanation
Indices: 932130--932176 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
932120 GCAAAAATGT
*
932130 ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
932177 TTTTAAGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:942355 original size:20 final size:20
Alignment explanation
Indices: 942330--942374 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
942320 GAAGGATTAG
942330 AACACCTATCCAAGCAATCA
1 AACACCTATCCAAGCAATCA
942350 AACACCTATCCAAGCAATCA
1 AACACCTATCCAAGCAATCA
942370 AACAC
1 AACAC
942375 AAGAGAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.36, G:0.04, T:0.13
Consensus pattern (20 bp):
AACACCTATCCAAGCAATCA
Found at i:944050 original size:25 final size:25
Alignment explanation
Indices: 943965--944043 Score: 149
Period size: 25 Copynumber: 3.2 Consensus size: 25
943955 CCAAATATAA
943965 GAAATTAATTTCAAAACATAAAGTT
1 GAAATTAATTTCAAAACATAAAGTT
943990 GAAATTAATTTCAAAACATAAAGTT
1 GAAATTAATTTCAAAACATAAAGTT
*
944015 GAAATTAATTTCAAAACATAAATTT
1 GAAATTAATTTCAAAACATAAAGTT
944040 GAAA
1 GAAA
944044 ATGATTTGGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (25 bp):
GAAATTAATTTCAAAACATAAAGTT
Found at i:947150 original size:19 final size:19
Alignment explanation
Indices: 947126--947162 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
947116 TTTTCAAAGG
947126 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
*
947145 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
947163 GATTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
CATGCACCGATGCACTCTC
Found at i:947267 original size:65 final size:64
Alignment explanation
Indices: 947126--947269 Score: 166
Period size: 65 Copynumber: 2.2 Consensus size: 64
947116 TTTTCAAAGG
* ** * *
947126 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCAAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTAATTAAAACATCAAATGCACTT
* * * *
947190 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTTCAAACATCGAATGCAC
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTAATTAAAACATCAAATGCAC
947253 TT
63 TT
947255 CATGCATCGATGCAC
1 CATGCATCGATGCAC
947270 TCTTAGTGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
64 29 0.43
65 32 0.48
66 4 0.06
67 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTAATTAAAACATCAAATGCACTT
Found at i:947269 original size:17 final size:19
Alignment explanation
Indices: 947241--947289 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
947231 TTTTTTCAAA
947241 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
947259 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
947278 CACCGATGCACT
1 CATCGATGCACT
947290 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:969957 original size:53 final size:55
Alignment explanation
Indices: 969888--971004 Score: 269
Period size: 55 Copynumber: 20.7 Consensus size: 55
969878 TTCCTACAGG
* * * *
969888 TCTGCTCTCTTTTTCTTCAGGGAG-AT-GGAACTCGAA-CATATTCAACAATCGTA
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAG-ACTCGAATCATATTCAACAAACGTA
* * *
969941 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATCTTCAACAAACTTG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATATTCAACAAACGTA
* * * * *
969996 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATCATCTTCAACAAACTTG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATATTCAACAAACGTA
* * * * * * * ** **
970051 TATGAC-CCCTATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCGATTGCG
1 TCTG-CTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATATTCAACAAACGTA
* * * * * ** ** **
970104 TCTGCCCCCTATTTCTTCAAAGAGTATAAGAC-C-CA-CAATCTTCAATGATTGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * * **
970157 TCTGCCCCCTATTTCTTTAGAGAGTATAAGAC-C-AA-CAATCTTCATCAATCGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * ** ** **
970210 TCTGAC-CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAATGATTGCG
1 TCTG-CTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * * *
970265 TCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CA-CA-ACCTTCATCAATCATG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATA--TTCAACAAACGTA
* * * *
970318 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACGATTACG--
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAAC-A-AACGTA
* * * * * * * **
970373 TCTGCCCCCTATTTCTTCAGAAAGTATAAGAC-C-CA-CAATCTTCATCAATCGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * ** ** **
970426 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTTAATGATTGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * *
970481 TCTG-TCCCCTATTTCTTCAGAGAGTATAAGAC-C-CA-CAATCTTCATCAATCACG--
1 TCTGCT-CTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAA--ACGTA
* * * ** ** **
970534 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAATGATTGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * **
970589 TCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-AA-CAATCTTCATCAATCGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * *
970642 TCTGCCCCCTATTTCTTCAAAGAGTATAAGACTCGAA-CAATCTTCAATGATTACG--
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAA-CA-AACGTA
* * * * * * * **
970697 TCTGCCCCCTATTTCTTCAAAGAGTATAAGAC-C-CA-CAATCTTCATCAATCGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * ** ** **
970750 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAATGATTGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * **
970805 TCTGC-CCCATATTTCTTCAGAGAGTATAAGAC-C-CA-CAATCTTCATCAATCGCG
1 TCTGCTCTC-TATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * ** ** **
970858 TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAATGATTGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * * * * * * * **
970913 TCTACCCCCTATTTCTTCATAGAGTATAAGACTC-AAACAATCTTCAACGATCGCG
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATC-ATATTCAACAAACGTA
* * *
970968 TCTGCCCCCTATTTCTTCAAAGAGTATAAGACTCGAA
1 TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAA
971005 CAATCTTCTT
Statistics
Matches: 908, Mismatches: 112, Indels: 85
0.82 0.10 0.08
Matches are distributed among these distances:
51 4 0.00
52 4 0.00
53 409 0.45
54 33 0.04
55 449 0.49
56 6 0.01
57 3 0.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (55 bp):
TCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAATCATATTCAACAAACGTA
Found at i:970118 original size:108 final size:107
Alignment explanation
Indices: 969949--971012 Score: 1634
Period size: 108 Copynumber: 9.8 Consensus size: 107
969939 TATCTGCTCT
* * * **
969949 CTATTTCTTCAGAGAGTATAAGACTCGA-ATCATCTTCAACAAACTTGTCTGCCCCCTATTTCTT
1 CTATTTCTTCAGAGAGTATAAGAC-CCACA--ATCTTCATCAATCGCGTCTGCCCCCTATTTCTT
** * *
970013 CAGAGAGTATAAGACTCGAATC-ATCTTCAACAAACTT-GTATGACCC
63 CAGAGAGTATAAGACTCGAA-CAATCTTCAA-TGA-TTCGTCTGCCCC
* * * *
970059 CTATTTCTTCAGAGAGTATAAGACCCATAATCTTCATCGATTGCGTCTGCCCCCTATTTCTTCAA
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
*
970124 AGAGTATAAGAC-C-CACAATCTTCAATGATTGCGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
* * *
970165 CTATTTCTTTAGAGAGTATAAGACCAACAATCTTCATCAATCGCGTCTGACCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
970230 AGAGTATAAGACTCGAACAATCTTCAATGATTGCGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
* **
970273 CTATTTCTTCAGAGAGTATAAGACCCACAACCTTCATCAATCATGTCTGCCCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
*
970338 AGAGTATAAGACTCGAACAATCTTCAACGATTACGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
*
970381 CTATTTCTTCAGAAAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
* *
970446 AGAGTATAAGACTCGAACAATCTTTAATGATTGCGTCTGTCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
*
970489 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
970554 AGAGTATAAGACTCGAACAATCTTCAATGATTGCGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
* *
970597 CTATTTCTTCAGAGAGTATAAGACCAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAA
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
970662 AGAGTATAAGACTCGAACAATCTTCAATGATTACGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
*
970705 CTATTTCTTCAAAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
970770 AGAGTATAAGACTCGAACAATCTTCAATGATTGCGTCTGCCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
*
970813 ATATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
1 CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
*
970878 AGAGTATAAGACTCGAACAATCTTCAATGATTGCGTCTACCCC
66 AGAGTATAAGACTCGAACAATCTTCAATGATT-CGTCTGCCCC
* * * *
970921 CTATTTCTTCATAGAGTATAAGACTCAAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1 CTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
*
970986 AAAGAGTATAAGACTCGAACAATCTTC
64 AGAGAGTATAAGACTCGAACAATCTTC
971013 TTTTGCTTCA
Statistics
Matches: 888, Mismatches: 58, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
104 2 0.00
105 2 0.00
106 86 0.10
107 2 0.00
108 707 0.80
109 3 0.00
110 86 0.10
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (107 bp):
CTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAG
AGAGTATAAGACTCGAACAATCTTCAATGATTCGTCTGCCCC
Found at i:972548 original size:124 final size:124
Alignment explanation
Indices: 972328--972553 Score: 328
Period size: 124 Copynumber: 1.8 Consensus size: 124
972318 ATCATCTTAT
* * * **
972328 ACTGGTACGAGCCTTCAAAATGCCTCAACATCTCAGATTGTAAGGCTTACTCTTAATGCCTTTTT
1 ACTGGTACGAGCCTTCAAAATGCCTCAACACCTCAAATTGTAAGGCTCACTCTTAATGCCTCCTT
* *
972393 GGTCTAAATCTTGTCCTCTCAATATGATGTGGGTTCAGTCATTCCCCATCAGCGTTTTA
66 GGTCGAAATCTTGTCCTCTCAACATGATGTGGGTTCAGTCATTCCCCATCAGCGTTTTA
* * * *
972452 ACTGGTACGGGCCTTCAAAATGCCTCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTCCTT
1 ACTGGTACGAGCCTTCAAAATGCCTCAACACCTCAAATTGTAAGGCTCACTCTTAATGCCTCCTT
*
972517 GGTCGGAATCTTG-CCATCTCAACATGATGTGGGTTCA
66 GGTCGAAATCTTGTCC-TCTCAACATGATGTGGGTTCA
972554 TTCGACCCCC
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 2 0.02
124 87 0.98
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (124 bp):
ACTGGTACGAGCCTTCAAAATGCCTCAACACCTCAAATTGTAAGGCTCACTCTTAATGCCTCCTT
GGTCGAAATCTTGTCCTCTCAACATGATGTGGGTTCAGTCATTCCCCATCAGCGTTTTA
Found at i:976214 original size:6 final size:6
Alignment explanation
Indices: 976203--976227 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
976193 ATGCAATGAA
976203 AAATGC AAATGC AAATGC AAATGC A
1 AAATGC AAATGC AAATGC AAATGC A
976228 CGAGGTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:983708 original size:71 final size:74
Alignment explanation
Indices: 983526--983715 Score: 257
Period size: 76 Copynumber: 2.6 Consensus size: 74
983516 TTTTATCTTT
* *
983526 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAG-TTTCATGATATTATTTTTATATTTTA
1 GTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTT-ATGATATTATTTTTAAATTTTA
983590 TCTTTGTTTAAG
64 -CTTTGTTTAAG
983602 GTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAGGATTTA-GAATATTA-TTTTAAATTTTA
1 GTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAGGATTTATG-ATATTATTTTTAAATTTTA
983665 -TTT-TTT-AG
64 CTTTGTTTAAG
*
983673 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
983716 AGAAGCTTTA
Statistics
Matches: 107, Mismatches: 3, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
70 6 0.06
71 37 0.35
72 3 0.03
73 3 0.03
75 12 0.11
76 42 0.39
77 4 0.04
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (74 bp):
GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTATGATATTATTTTTAAATTTTACT
TTGTTTAAG
Found at i:984328 original size:17 final size:18
Alignment explanation
Indices: 984306--984347 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
984296 CTTTAAATTA
984306 TTTATTTAATTATT-TAT
1 TTTATTTAATTATTATAT
* *
984323 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATAT
984341 TTTATTT
1 TTTATTT
984348 TAAAAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:984420 original size:20 final size:20
Alignment explanation
Indices: 984372--984448 Score: 55
Period size: 23 Copynumber: 3.6 Consensus size: 20
984362 TAAAACCCCT
* * * *
984372 TTTTATTTTACTACTATTAT
1 TTTTATTTTATTATTATCAA
* **
984392 TTATTATTTTATTATTTTCCC
1 TT-TTATTTTATTATTATCAA
984413 TTTTATTTATTTATTATTATCAA
1 TTTTA--T-TTTATTATTATCAA
984436 TTTTATTTTATTA
1 TTTTATTTTATTA
984449 AATCTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 12 0.27
21 15 0.34
22 1 0.02
23 16 0.36
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTTATTATTATCAA
Found at i:984439 original size:23 final size:24
Alignment explanation
Indices: 984391--984443 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
984381 ACTACTATTA
* **
984391 TTTA-TTATTTTATTATTTTCCCT
1 TTTATTTATTTTATTATTATCAAT
984414 TTTATTTA-TTTATTATTATCAAT
1 TTTATTTATTTTATTATTATCAAT
984437 TTTATTT
1 TTTATTT
984444 TATTAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATTTATTTTATTATTATCAAT
Found at i:987368 original size:27 final size:27
Alignment explanation
Indices: 987330--987468 Score: 260
Period size: 27 Copynumber: 5.1 Consensus size: 27
987320 ATAATCTATT
987330 CGATATCGGATAGTAATTGGGTAAATC
1 CGATATCGGATAGTAATTGGGTAAATC
987357 CGATATCGGATAGTAATTGGGTAAATC
1 CGATATCGGATAGTAATTGGGTAAATC
987384 CGATATCGGATAGTAATTGGGTAAATC
1 CGATATCGGATAGTAATTGGGTAAATC
987411 CGATATCGGATAGTAATTGGGTAAATC
1 CGATATCGGATAGTAATTGGGTAAATC
* *
987438 CGATATCGGATAGTAATTGAGTAAGTC
1 CGATATCGGATAGTAATTGGGTAAATC
987465 CGAT
1 CGAT
987469 TCATGTGGTT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (27 bp):
CGATATCGGATAGTAATTGGGTAAATC
Found at i:990026 original size:22 final size:21
Alignment explanation
Indices: 989998--990048 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
989988 GAGGCAACCC
989998 ATTTCATTCTATTCTAT-ATTTT
1 ATTTCATTCTATT-T-TCATTTT
* *
990020 ATTTCATTTTATTTTCGTTTT
1 ATTTCATTCTATTTTCATTTT
990041 ATTTCATT
1 ATTTCATT
990049 TTTTAACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTCATTCTATTTTCATTTT
Found at i:990051 original size:11 final size:10
Alignment explanation
Indices: 990015--990050 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
990005 TCTATTCTAT
990015 ATTTTATTTC
1 ATTTTATTTC
990025 ATTTTATTTTC
1 ATTTTA-TTTC
*
990036 GTTTTATTTC
1 ATTTTATTTC
990046 ATTTT
1 ATTTT
990051 TTAACATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (10 bp):
ATTTTATTTC
Found at i:990097 original size:20 final size:20
Alignment explanation
Indices: 990072--990119 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
990062 TTTAACAAAC
990072 TTTATTTTCATT-ATATTTAT
1 TTTATTTTCATTAAT-TTTAT
990092 TTTATTTTCATTAATTTTAT
1 TTTATTTTCATTAATTTTAT
990112 TTTATTTT
1 TTTATTTT
990120 TTCTCTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTCATTAATTTTAT
Found at i:990258 original size:30 final size:30
Alignment explanation
Indices: 990215--990285 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
990205 AATTCGAATA
* * * *
990215 GAACAGTGTAGAAAAATACACAGCATATTC
1 GAACAATGCAGAAAAATACAAAGCAGATTC
*
990245 GAACAATGCAGAAAAATACAAAGTAGATTC
1 GAACAATGCAGAAAAATACAAAGCAGATTC
990275 GAACAATGCAG
1 GAACAATGCAG
990286 TGTAGGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.17
Consensus pattern (30 bp):
GAACAATGCAGAAAAATACAAAGCAGATTC
Found at i:992057 original size:12 final size:13
Alignment explanation
Indices: 992034--992062 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
992024 CTTAATTAGG
992034 ATTTAGAATATTA
1 ATTTAGAATATTA
992047 ATTTA-AATATTA
1 ATTTAGAATATTA
992059 ATTT
1 ATTT
992063 TTTAGGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATTTAGAATATTA
Found at i:997004 original size:22 final size:20
Alignment explanation
Indices: 996969--997012 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
996959 AAAATAAAAT
*
996969 AATAAAAATGAATTAATTATC
1 AATAAAAATCAATTAATT-TC
*
996990 AATATAAAATCAATTTATTTC
1 AATA-AAAATCAATTAATTTC
997011 AA
1 AA
997013 GTTCACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
AATAAAAATCAATTAATTTC
Found at i:998062 original size:22 final size:23
Alignment explanation
Indices: 998034--998094 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
998024 CCCCTTTTTG
*
998034 CTATTTT-TTTCTTTTTGTTGTT
1 CTATTTTCTTTCTTTTTCTTGTT
998056 CTATTTTTCTTTCTTTTTCTTGTT
1 CTA-TTTTCTTTCTTTTTCTTGTT
*
998080 -TTTTTTCTTTCTTTT
1 CTATTTTCTTTCTTTT
998095 GAATTTTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 16 0.46
23 5 0.14
24 14 0.40
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (23 bp):
CTATTTTCTTTCTTTTTCTTGTT
Found at i:998727 original size:3 final size:3
Alignment explanation
Indices: 998719--998766 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
998709 GTATAATATA
* *
998719 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAG AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
998767 GTTTTAAGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:999142 original size:134 final size:134
Alignment explanation
Indices: 998952--999311 Score: 420
Period size: 133 Copynumber: 2.7 Consensus size: 134
998942 TTCTGGTCAC
* * * *
998952 CTAAGGGTAACACGGCTCCTACGTGACAAGGAGA-ATTGGTCGGTGGATGACACGGTTCCTACAT
1 CTAAGGGTGACGCGGCTCCTACGTGATAAGGAGATA-TGATCGGTGGATGACACGGTTCCTACAT
* * *
999016 GATGAGGATGGCTAGCCAGCTTTAGGGATGATGATAACATAGTTTCTACGCGATGAGGACGTCTG
65 GATGAGGATGGCTAGCCATCTTTAGGGATGATGATAACATAGTTCCTACGCGATGAGGACGGCTG
999081 GTTAT
130 GTTAT
* * * * * * * *
999086 TTAAGGTTGAGGCGGCTCCTACGTGATGAGGAGATATCATCGGTGGATGGCCCGGTTCTTACATG
1 CTAAGGGTGACGCGGCTCCTACGTGATAAGGAGATATGATCGGTGGATGACACGGTTCCTACATG
* ** * * * *
999151 ATGAAGA-CACTGGCCATCTTTAGGGATGATGATAACATGGTTCCTACGTGATGAGGATGGCTGG
66 ATGAGGATGGCTAGCCATCTTTAGGGATGATGATAACATAGTTCCTACGCGATGAGGACGGCTGG
999215 TTAT
131 TTAT
* * * * * *
999219 CTAAGGGTGACGCGGCTCCTACATGATTAA-GAGATCTGATCGGTGGATGAAACTGATCCTACGT
1 CTAAGGGTGACGCGGCTCCTACGTGA-TAAGGAGATATGATCGGTGGATGACACGGTTCCTACAT
*
999283 GATGAGGATGGCTAACCATCTTTAGGGAT
65 GATGAGGATGGCTAGCCATCTTTAGGGAT
999312 AATGTTTCAA
Statistics
Matches: 182, Mismatches: 41, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
133 106 0.58
134 75 0.41
135 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
CTAAGGGTGACGCGGCTCCTACGTGATAAGGAGATATGATCGGTGGATGACACGGTTCCTACATG
ATGAGGATGGCTAGCCATCTTTAGGGATGATGATAACATAGTTCCTACGCGATGAGGACGGCTGG
TTAT
Found at i:999466 original size:67 final size:67
Alignment explanation
Indices: 999313--999628 Score: 369
Period size: 65 Copynumber: 4.8 Consensus size: 67
999303 TTTAGGGATA
* * ** * *
999313 ATGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATAT-CAAAAT-
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGAGATCCAAAATA
999376 TG
66 TG
*
999378 ATGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAATATTTGTTTCAAGGGAAATAAGATCCAAATA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ATTTGTTTCAAGGGAAATGAGATCCAAA-A
999442 TAT-
64 TATG
* * * *
999445 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTTGTTTCAAGGGAAA-CA-ATCTAAAATA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGAGATCCAAAATA
999508 TG
66 TG
* * * *
999510 ATGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTCGTTTCAAGGGGAATGGGA-CTCAAAGA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGAGATC-CAAA-A
*
999574 TCT-
64 TATG
* *
999577 TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAA
999629 CATACTAAAA
Statistics
Matches: 215, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
64 7 0.03
65 98 0.46
66 6 0.03
67 83 0.39
68 21 0.10
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (67 bp):
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGAGATCCAAAATA
TG
Found at i:999552 original size:132 final size:131
Alignment explanation
Indices: 999314--999641 Score: 450
Period size: 132 Copynumber: 2.5 Consensus size: 131
999304 TTAGGGATAA
* * *
999314 TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATATC-AAAAT-T
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-GTTTCAAGGGAAAC-A-ATCTAAAATAT
* *
999377 GATGTTTCAAGAGAAACTGTCTCAAGAGAGAAAATATTTGTTTCAAGGGAAATAAGA-TCCAAAT
63 GATGTTTCAAGAGAAACTGTCTCAAGAGAGAAAATATTCGTTTCAAGGGAAATAAGACT-CAAAG
999441 ATATT
127 ATATT
999446 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTTGTTTCAAGGGAAACAATCTAAAATATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAACAATCTAAAATATGA
* **
999511 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAA-ATTCGTTTCAAGGGGAATGGGACTCAAAGAT
65 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAATATTCGTTTCAAGGGAAATAAGACTCAAAGAT
*
999575 CTT
129 ATT
*
999578 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-ATACTAAAATAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--TTGTTTCAAGGGAAACAAT-CTAAAATAT
999642 TTTTGTTTCA
Statistics
Matches: 178, Mismatches: 11, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
130 3 0.02
131 6 0.03
132 138 0.78
133 31 0.17
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (131 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGTTTCAAGGGAAACAATCTAAAATATGAT
GTTTCAAGAGAAACTGTCTCAAGAGAGAAAATATTCGTTTCAAGGGAAATAAGACTCAAAGATAT
T
Found at i:999651 original size:67 final size:65
Alignment explanation
Indices: 999314--999658 Score: 365
Period size: 67 Copynumber: 5.2 Consensus size: 65
999304 TTAGGGATAA
* * **
999314 TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGATA-TCAAA-ATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-A-ACTCAAATATT
**
999377 GA
64 TT
* *
999379 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAATATTTGTTTCAAGGGAAATAAGATCCAAATAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ATTTGTTTCAAGGGAAACAA-CT-CAAATAT
*
999443 ATT
63 TTT
* * *
999446 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTTGTTTCAAGGGAAACAATCTAAAATA-TG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAA-CTCAAATATTT
*
999510 A
65 T
* * *** * *
999511 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTCGTTTCAAGGGGAATGGGACTCAAAGATC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GGGAA-ACAACTCAAATATT
999576 TT
64 TT
* *
999578 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATACTAAAATATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACA-ACTCAAATATT
999643 TT
64 TT
*
999645 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
999659 TAATTTCTAA
Statistics
Matches: 231, Mismatches: 38, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.00
64 4 0.02
65 84 0.36
66 20 0.09
67 110 0.48
68 12 0.05
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAACTCAAATATTTT
Found at i:1000958 original size:2 final size:2
Alignment explanation
Indices: 1000940--1001000 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1000930 ATCTTTAATG
* *
1000940 TA TA CA TA TA CA 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
1000982 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1001001 TTTCTGGGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1003025 original size:14 final size:14
Alignment explanation
Indices: 1003006--1003042 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1002996 AATGCCGTGC
1003006 AAAATGCAATGATG
1 AAAATGCAATGATG
1003020 AAAATGCAATGATG
1 AAAATGCAATGATG
1003034 AAAATGCAA
1 AAAATGCAA
1003043 ATGCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.19
Consensus pattern (14 bp):
AAAATGCAATGATG
Found at i:1004467 original size:18 final size:18
Alignment explanation
Indices: 1004444--1004515 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
1004434 CATAACCATT
1004444 TTTTAAAAAACAATTATG
1 TTTTAAAAAACAATTATG
1004462 TTTTAAAAAACAATTATG
1 TTTTAAAAAACAATTATG
*
1004480 TTTTAAATAACAATTATG
1 TTTTAAAAAACAATTATG
1004498 TTTTAAAAAACAATTATG
1 TTTTAAAAAACAATTATG
1004516 ACTTTTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTTAAAAAACAATTATG
Found at i:1006859 original size:3 final size:3
Alignment explanation
Indices: 1006851--1006887 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1006841 TTTGGCCTTC
1006851 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1006888 TTTTTTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1012318 original size:24 final size:24
Alignment explanation
Indices: 1012291--1012399 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 24
1012281 GTTAACCGAG
1012291 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
1012315 ATATAAGATATCATAACAGAA-TC
1 ATATCAGAAATCAAAACAGAATTC
* * *
1012338 TAGATAAGAAATCAGAACAGAATTC
1 -ATATCAGAAATCAAAACAGAATTC
** *
1012363 A-AGTCAGGTA-CAAGAACATAATTC
1 ATA-TCAGAAATCAA-AACAGAATTC
*
1012387 AAATCAGAAATCA
1 ATATCAGAAATCA
1012400 GATAAAACAT
Statistics
Matches: 66, Mismatches: 13, Indels: 11
0.73 0.14 0.12
Matches are distributed among these distances:
23 5 0.08
24 56 0.85
25 5 0.08
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:1014259 original size:11 final size:11
Alignment explanation
Indices: 1014243--1014276 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1014233 TCAAAGTTAA
1014243 CGGTCAATGGT
1 CGGTCAATGGT
1014254 CGGTCAATGGT
1 CGGTCAATGGT
1014265 CGGTCAATGGT
1 CGGTCAATGGT
1014276 C
1 C
1014277 AACGATCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.35, T:0.26
Consensus pattern (11 bp):
CGGTCAATGGT
Found at i:1022088 original size:12 final size:12
Alignment explanation
Indices: 1022072--1022110 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1022062 TGTGAACTTC
1022072 ATTCTGAATTTG
1 ATTCTGAATTTG
*
1022084 GTTCTGAATTTG
1 ATTCTGAATTTG
*
1022096 ATTATGAATTTG
1 ATTCTGAATTTG
1022108 ATT
1 ATT
1022111 ATGGATCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (12 bp):
ATTCTGAATTTG
Found at i:1022153 original size:15 final size:16
Alignment explanation
Indices: 1022133--1022162 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1022123 CTAAATATGA
1022133 TTGTTGTTG-ATCCTC
1 TTGTTGTTGTATCCTC
1022148 TTGTTGTTGTATCCT
1 TTGTTGTTGTATCCT
1022163 TCTTTCTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.17, G:0.20, T:0.57
Consensus pattern (16 bp):
TTGTTGTTGTATCCTC
Found at i:1023417 original size:26 final size:26
Alignment explanation
Indices: 1023388--1023437 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1023378 CACATTTAAA
* *
1023388 GTTGCTGACTAGATCTTCCAGAAAAT
1 GTTGCTGACTAGACCTTCAAGAAAAT
*
1023414 GTTGTTGACTAGACCTTCAAGAAA
1 GTTGCTGACTAGACCTTCAAGAAA
1023438 CTGCCACGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (26 bp):
GTTGCTGACTAGACCTTCAAGAAAAT
Found at i:1031804 original size:11 final size:11
Alignment explanation
Indices: 1031788--1031826 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1031778 TCGATACATA
*
1031788 GCTACAGTACT
1 GCTACATTACT
*
1031799 GCTACATTAAT
1 GCTACATTACT
1031810 GCTACATTACT
1 GCTACATTACT
1031821 GCTACA
1 GCTACA
1031827 ATATTTCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (11 bp):
GCTACATTACT
Found at i:1032308 original size:59 final size:59
Alignment explanation
Indices: 1032245--1032386 Score: 164
Period size: 59 Copynumber: 2.4 Consensus size: 59
1032235 TCTGGAAGAT
* * * *
1032245 CATACACA-TAGTATGCTTCCTCTT-TCATTTTAGCACACAAAGTGCCCTAT-TCGAAAATC
1 CATAC-CATTAGTATGATT-CTCTTACCATTTCAGCACACAAAATGCCCTATGT-GAAAATC
* * *
1032304 CATACCATTAGTATGATTTTGTTACCATTTCAGCACATAAAATGCCCTATGTGAAAATC
1 CATACCATTAGTATGATTCTCTTACCATTTCAGCACACAAAATGCCCTATGTGAAAATC
*
1032363 CATACCATTAGTATGATTTTCTTA
1 CATACCATTAGTATGATTCTCTTA
1032387 TCCTTATAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.07
59 66 0.92
60 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (59 bp):
CATACCATTAGTATGATTCTCTTACCATTTCAGCACACAAAATGCCCTATGTGAAAATC
Found at i:1032516 original size:59 final size:59
Alignment explanation
Indices: 1032358--1032504 Score: 235
Period size: 59 Copynumber: 2.5 Consensus size: 59
1032348 CCCTATGTGA
* * *
1032358 AAATCCATAC-CATTAGTATGATTTTCTTATCCTTATAGCACGCTTAGTGCTTTATCTGG
1 AAATCCATACAC-TCAGTATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
1032417 AAATCCATACACTCA-TAATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
1 AAATCCATACACTCAGT-ATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
1032476 AAATCCATACACTCAGTATGATTTCCTTA
1 AAATCCATACACTCAGTATGATTTCCTTA
1032505 CCATTTTAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
58 1 0.01
59 79 0.96
60 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (59 bp):
AAATCCATACACTCAGTATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
Found at i:1032536 original size:59 final size:58
Alignment explanation
Indices: 1032270--1032634 Score: 215
Period size: 59 Copynumber: 6.2 Consensus size: 58
1032260 CTTCCTCTTT
* * * **
1032270 CATTTTAGCACACAAAGTGCCCTAT-TCGAAAATCCATAC-CATTAGTATGATTTTGTTAC
1 CATTTTAGCACATAAA-TGCCCTATAT-GGAAATCCATACAC-TCAGTATGATTTCCTTAC
* * * * *
1032329 CATTTCAGCACATAAAATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTTCTTATC
1 CATTTTAGCACAT-AAATGCCCTATATGGAAATCCATACAC-TCAGTATGATTTCCTTA-C
* * * * ** *
1032389 C-TTATAGCACGCTTAGTGCTTTATCTGGAAATCCATACACTCA-TAATGATTTCCTTATC
1 CATTTTAGCAC-ATAAATGCCCTATATGGAAATCCATACACTCAGT-ATGATTTCCTTA-C
* * * * ** *
1032448 C-TTATAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTTCCTTAC
1 CATTTTAGCA-CATAAATGCCCTATATGGAAATCCATACACTCAGTATGATTTCCTTAC
*** * * * *
1032506 CATTTTAGCACATAACATGCCCTATATGGAAATCCATATTTTTAATATGATTTCTTTAT
1 CATTTTAGCACATAA-ATGCCCTATATGGAAATCCATACACTCAGTATGATTTCCTTAC
** * * * *
1032565 CA-TTTAGCACACTAAGCGCACTATATGGAAATCTATACACTCAATAT-AGTTTCCTTAT
1 CATTTTAGCACA-TAAATGCCCTATATGGAAATCCATACACTCAGTATGA-TTTCCTTAC
*
1032623 CGTTTTAGCACA
1 CATTTTAGCACA
1032635 CAAAATGCTC
Statistics
Matches: 255, Mismatches: 38, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.00
58 48 0.19
59 196 0.77
60 10 0.04
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (58 bp):
CATTTTAGCACATAAATGCCCTATATGGAAATCCATACACTCAGTATGATTTCCTTAC
Found at i:1032557 original size:177 final size:176
Alignment explanation
Indices: 1032299--1032633 Score: 408
Period size: 177 Copynumber: 1.9 Consensus size: 176
1032289 CCCTATTCGA
* ** *
1032299 AAATCCATACCATTAGTATGATTTTGTTACCATTTCAGCACATAAAATGCCCTATGTGAAAATCC
1 AAATCCATACCATCAGTATGATTTCCTTACCATTTCAGCACATAAAATGCCCTATATGAAAATCC
* * * * * ** *
1032364 ATACCATTAGTATGATTT-TCTTATCCTTATAGCACGCTTAGTGCTTTATCTGGAAATCCATACA
66 ATACCATTAATATGATTTCT-TTATCATT-TAGCACACTAAGCGCACTATATGGAAATCCATACA
1032428 CTC-ATA-ATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
129 CTCAATATA-G-TTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
* * *
1032476 AAATCCATA-CACTCAGTATGATTTCCTTACCATTTTAGCACATAACATGCCCTATATGGAAATC
1 AAATCCATACCA-TCAGTATGATTTCCTTACCATTTCAGCACATAAAATGCCCTATATGAAAATC
*** *
1032540 CATATTTTTAATATGATTTCTTTATCATTTAGCACACTAAGCGCACTATATGGAAATCTATACAC
65 CATACCATTAATATGATTTCTTTATCATTTAGCACACTAAGCGCACTATATGGAAATCCATACAC
* *
1032605 TCAATATAGTTTCCTTATCGTTTTAGCAC
130 TCAATATAGTTTCCTTATCCTTATAGCAC
1032634 ACAAAATGCT
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
176 51 0.38
177 80 0.60
178 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (176 bp):
AAATCCATACCATCAGTATGATTTCCTTACCATTTCAGCACATAAAATGCCCTATATGAAAATCC
ATACCATTAATATGATTTCTTTATCATTTAGCACACTAAGCGCACTATATGGAAATCCATACACT
CAATATAGTTTCCTTATCCTTATAGCACCCTTAGTGCTTTATCTGG
Found at i:1033045 original size:63 final size:62
Alignment explanation
Indices: 1032976--1033136 Score: 175
Period size: 63 Copynumber: 2.5 Consensus size: 62
1032966 TTCTCTCACA
*
1032976 GATGCATCGGTGCACAACCTATGCATCGATGCATATATTACATTCGATG-TT-TTCATCTTAAGG
1 GATGCATCGGTGCACAACCTATGCATCGATGCATA-ACTACATTCGATGTTTATTCAT-TTAA-G
* * * *
1033039 GATGCATCGAG-GCACTACCTGTGCATCGATGCACTAACTACCTTCGATGTTTATTTATTTAAG
1 GATGCATCG-GTGCACAACCTATGCATCGATGCA-TAACTACATTCGATGTTTATTCATTTAAG
* * *
1033102 TATGCATCGGTGCACTCACTTATGCATCGATGCAT
1 GATGCATCGGTGCAC-AACCTATGCATCGATGCAT
1033137 CTTGCCCAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 54 0.65
64 24 0.29
65 4 0.05
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (62 bp):
GATGCATCGGTGCACAACCTATGCATCGATGCATAACTACATTCGATGTTTATTCATTTAAG
Found at i:1039004 original size:11 final size:11
Alignment explanation
Indices: 1038988--1039026 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1038978 TCGATACATA
1038988 GCTACAGTACT
1 GCTACAGTACT
* *
1038999 GCTACATTAAT
1 GCTACAGTACT
1039010 GCTACAGTACT
1 GCTACAGTACT
1039021 GCTACA
1 GCTACA
1039027 ATATTTCTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (11 bp):
GCTACAGTACT
Found at i:1039531 original size:59 final size:59
Alignment explanation
Indices: 1039468--1039580 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
1039458 CTTCATATTT
* * *
1039468 CATTTTAGCACACGAAGTGCCCTAT-TCGAAAATTCATACCATTAGTATGATTTTGATAC
1 CATTTTAGCACACAAAATGCCCTATGT-GAAAATCCATACCATTAGTATGATTTTGATAC
*
1039527 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTT
1 CATTTTAGCACACAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTT
1039581 CTTATCCTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTTGATAC
Found at i:1039595 original size:59 final size:59
Alignment explanation
Indices: 1039524--1039819 Score: 205
Period size: 59 Copynumber: 5.0 Consensus size: 59
1039514 ATGATTTTGA
* * * * *
1039524 TACCATTTTAGCA-CATAAAATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTTCT
1 TACCATTATAGCACCAT-AAATGCCCTATCTGGAAATCCATACAC-TCAGTATGATTTCCT
* * * **
1039583 TATCC-TTATAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTTCCT
1 TA-CCATTATAGCACCATAAATGCCCTATCTGGAAATCCATACACTCAGTATGATTTCCT
* * * * **
1039642 TATCC-TTATAGTACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTTCCT
1 TA-CCATTATAGCACCATAAATGCCCTATCTGGAAATCCATACACTCAGTATGATTTCCT
* * *** * * *
1039701 TACCATTTTAGCA-CATAACATGCCCTATATGGAAATCCATATTTTTAATATGATTTCTT
1 TACCATTATAGCACCATAA-ATGCCCTATCTGGAAATCCATACACTCAGTATGATTTCCT
* * * *
1039760 TATCATT-TAGCA-CACTAAGTGCTCC-ATATGGAAATCTATACACTCAGTAT-AGTTTCCT
1 TACCATTATAGCACCA-TAAATGC-CCTATCTGGAAATCCATACACTCAGTATGA-TTTCCT
1039818 TA
1 TA
1039820 TTGTTTTAGC
Statistics
Matches: 195, Mismatches: 34, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.01
58 41 0.21
59 148 0.76
60 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (59 bp):
TACCATTATAGCACCATAAATGCCCTATCTGGAAATCCATACACTCAGTATGATTTCCT
Found at i:1044074 original size:19 final size:19
Alignment explanation
Indices: 1044013--1044074 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1044003 GTTAAACAAG
* *
1044013 TTCTTCTCATTATAAACTTC
1 TTCTTCTCATTATGATC-TC
***
1044033 TTCTTCCTCATTA-GATGAG
1 TTCTT-CTCATTATGATCTC
1044052 TTCTTCTCATTATGATCTC
1 TTCTTCTCATTATGATCTC
1044071 TTCT
1 TTCT
1044075 GGAAATATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 6 0.19
21 7 0.22
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.50
Consensus pattern (19 bp):
TTCTTCTCATTATGATCTC
Found at i:1044354 original size:136 final size:136
Alignment explanation
Indices: 1044123--1044904 Score: 1081
Period size: 136 Copynumber: 5.8 Consensus size: 136
1044113 AGGAACATGT
* * * *
1044123 TCTTCTCATTATGAA-TT-TTCT-CCT-T-TAGGATGCGTTCTTCTTATTATGAACTCTCCATTA
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * * * *
1044183 AAAAT-TTCAATCCCTCAAGAGAGGCATCGCTGATTCAAAATACCGTGAATCGAGTGATAGGTCG
66 GAAATGTT-AATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCG
1044247 AACAAGC
130 AACAAGC
* * * * *
1044254 TCTTCTCAATATGAACTTATTCTCTCTCTATTGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * *
1044319 GAAATGTTAATCCCTCAAGCGAGGTGTCACTGATTCAAAAGGTCATGAATCGAGTGATAGGTCGA
66 GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
1044384 ACAAGC
131 ACAAGC
*
1044390 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * * * *
1044455 GAAATGTTGATCCCTCAAGCCAGGCGTCACTAATTCAAAATGGCGTGAATCGACTGATAGGTCGA
66 GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
1044520 ACAAGC
131 ACAAGC
*
1044526 TCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * * * * *
1044591 GAAATGTCAATCCTTCAAGCGAGGTGTCAGTGATTCGAAATGCCATAAATCGAGTGATAGGTTGA
66 GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
*
1044656 ATAAGC
131 ACAAGC
* * * *
1044662 TCTTCTCATTATAAACTTCTTCTCCCTTTGTCGGATGAGTTCTTCTCAGTATGAACTCTCTATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * *
1044727 GAAATATTGATCCCTCAAGTGAGGCATCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
66 GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
*
1044792 AGAAGC
131 ACAAGC
*
1044798 TCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * **
1044863 GAAATGTTGATCCCTCAAGTGAGGTTTCACTGATTCAAAATG
66 GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATG
1044905 ATGTGAATCG
Statistics
Matches: 575, Mismatches: 70, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
131 14 0.02
132 2 0.00
133 4 0.01
134 2 0.00
135 1 0.00
136 550 0.96
137 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
GAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGATAGGTCGA
ACAAGC
Found at i:1045091 original size:90 final size:90
Alignment explanation
Indices: 1044938--1045201 Score: 478
Period size: 90 Copynumber: 2.9 Consensus size: 90
1044928 TTGAAAACAT
*
1044938 ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGATTTACAAATCAAGAAACCCCCGAAGGC
1 ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
1045003 TTAGTTTTTAAAATCTCATTTGAAA
66 TTAGTTTTTAAAATCTCATTTGAAA
1045028 ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
1 ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
*
1045093 TTAGTTTCTAAAATCTCATTTGAAA
66 TTAGTTTTTAAAATCTCATTTGAAA
*
1045118 ACATCCAACACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
1 ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
1045183 TTAGTTTCTT--AATCTCATT
66 TTAGTTT-TTAAAATCTCATT
1045202 CGAGAAAAAA
Statistics
Matches: 169, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
89 9 0.05
90 159 0.94
91 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (90 bp):
ACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
TTAGTTTTTAAAATCTCATTTGAAA
Found at i:1045582 original size:96 final size:96
Alignment explanation
Indices: 1045467--1045659 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 96
1045457 GATGCATGAA
1045467 TGCAATGGATATGTATCTAAATGTAATGTATGATTTTATTATATGCAAATGATGTTCTTATGAAT
1 TGCAATGGATATGTATCTAAATGTAATGTATGATTTTATTATATGCAAATGATGTTCTTATGAAT
**
1045532 GCATAAATGTTGATGCAATCTTTGTTTGACT
66 GCATAAATGTTGATGCAATCTTCATTTGACT
*
1045563 TGCAATGGATATGTATCTAAATGTAATGTATGATTTTCTTATATGCAAATGATGTTCTTATGAAT
1 TGCAATGGATATGTATCTAAATGTAATGTATGATTTTATTATATGCAAATGATGTTCTTATGAAT
1045628 GCATAAATGTTGATGCAATCTTCATTTGACT
66 GCATAAATGTTGATGCAATCTTCATTTGACT
1045659 T
1 T
1045660 CAAAGTGGTG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (96 bp):
TGCAATGGATATGTATCTAAATGTAATGTATGATTTTATTATATGCAAATGATGTTCTTATGAAT
GCATAAATGTTGATGCAATCTTCATTTGACT
Found at i:1055004 original size:3 final size:3
Alignment explanation
Indices: 1054990--1055029 Score: 53
Period size: 3 Copynumber: 12.3 Consensus size: 3
1054980 TGTAAAAAGC
1054990 AAT AATT AAT AAT AAT AAT AAT AAT AAT ATAT AATT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT A
1055030 TTTTTAATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 25 0.74
4 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1063980 original size:12 final size:13
Alignment explanation
Indices: 1063955--1063980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1063945 CTTCCTGTAG
1063955 TTGTTACTTTTTT
1 TTGTTACTTTTTT
1063968 TTGTTACTTTTTT
1 TTGTTACTTTTTT
1063981 ATTCTACTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (13 bp):
TTGTTACTTTTTT
Found at i:1069123 original size:87 final size:87
Alignment explanation
Indices: 1069008--1069176 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
1068998 AAGTTGATGT
* * * * *
1069008 TGATCCAACTCTTTATGTGCTGGATTTGAGTGAAATGAAAATGTCGATCCCCCTCCTTCTGTGAT
1 TGATCCAACTCCTTATGTGCTGGATTTGAATGAAATAAAAATGTCGATCCCCCTCATTCTATGAT
*
1069073 GGAATCGAACGAGATGTCGTAC
66 GGAATCAAACGAGATGTCGTAC
* *
1069095 TGATCCAACTCCTTATGTGTTGGATTTGAATGAAATAAAAATTTCGATCCCCCTCATTCTATGAT
1 TGATCCAACTCCTTATGTGCTGGATTTGAATGAAATAAAAATGTCGATCCCCCTCATTCTATGAT
1069160 GGAATCAAACGAGATGT
66 GGAATCAAACGAGATGT
1069177 TGGTGCTGAT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (87 bp):
TGATCCAACTCCTTATGTGCTGGATTTGAATGAAATAAAAATGTCGATCCCCCTCATTCTATGAT
GGAATCAAACGAGATGTCGTAC
Found at i:1069355 original size:120 final size:120
Alignment explanation
Indices: 1069132--1069463 Score: 416
Period size: 120 Copynumber: 2.8 Consensus size: 120
1069122 GAATGAAATA
* * * * * * *
1069132 AAAATTTCGATCCCCCTCATTCTATGATGGAATCAAACGAGATGTTGGTGCTGATCTACCTCCTT
1 AAAATGTCGATCCACCTCCTTATGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCCTT
** * *
1069197 CTACGATAGAATTGAGCAAAAATTGATGATAACCCAACTCCTTATGTGCTGGATG
66 CTGTGATAGAATTGAGCAAAAGTTGATGATAACCCAACTCCTTATGCGCTGGATG
* * * * *
1069252 AAAGTGTCGATCGACCTCCTTATTTGATGGAATCGAACGATATGTTGGTGTTGATCTACCTTCTT
1 AAAATGTCGATCCACCTCCTTATGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCCTT
* * *
1069317 ATGTGATAGAATTGAGCACAAAGTTGAT-ACTGA-TCAACTCCTTATGCGCTGGATG
66 CTGTGATAGAATTGAGCA-AAAGTTGATGA-TAACCCAACTCCTTATGCGCTGGATG
* * *
1069372 AAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAATGAGATGTTGGTGTTGACCTACCTCCTT
1 AAAATGTCGATCCACCTCCTTATGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCCTT
*
1069437 CTGTGATAGAATCGAGCAAAAAGTTGA
66 CTGTGATAGAATTGAGC-AAAAGTTGA
1069464 ACAAGTTCTC
Statistics
Matches: 181, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
120 170 0.94
121 11 0.06
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (120 bp):
AAAATGTCGATCCACCTCCTTATGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCCTT
CTGTGATAGAATTGAGCAAAAGTTGATGATAACCCAACTCCTTATGCGCTGGATG
Found at i:1069974 original size:37 final size:37
Alignment explanation
Indices: 1069867--1069984 Score: 132
Period size: 37 Copynumber: 3.2 Consensus size: 37
1069857 TCAAAAGAAA
** * *
1069867 TTTGTTTGAAGAGAAACTATCTCAAGTGAGATAAAA-
1 TTTGTTTCCAGAGAAACTATCTCAAGAGAGACAAAAC
* *
1069903 TTTGATTT-CAGTGAAACTATCTCTAGAGAGACAAAAC
1 TTTG-TTTCCAGAGAAACTATCTCAAGAGAGACAAAAC
* * *
1069940 TTTGTTTCCAGAGAAACTGTCTCAAGGGACACAAAAC
1 TTTGTTTCCAGAGAAACTATCTCAAGAGAGACAAAAC
1069977 TTTGTTTC
1 TTTGTTTC
1069985 AAGGGAAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
36 30 0.43
37 39 0.57
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (37 bp):
TTTGTTTCCAGAGAAACTATCTCAAGAGAGACAAAAC
Found at i:1070102 original size:66 final size:68
Alignment explanation
Indices: 1069942--1070102 Score: 220
Period size: 68 Copynumber: 2.4 Consensus size: 68
1069932 GACAAAACTT
* * * *
1069942 TGTTTCCAGAGAAACTGTCTCAAGGGACACAAAACTTTGTTTCAAGGGAAATAAATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAACTTTGTTTCAAGGGAAACAAATGCAAAGATT
1070007 TCA
66 TCA
* *
1070010 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGTAAACAAATGCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAACTTTGTTTCAAGGGAAACAAATGCAAAGATT
*
1070074 T-T
66 TCA
*
1070076 TGTTTTAAG-GCAAACTGTCTCAAGAGA
1 TGTTTCAAGAG-AAACTGTCTCAAGAGA
1070103 AATTGTCTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 24 0.29
67 28 0.33
68 31 0.37
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (68 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAACTTTGTTTCAAGGGAAACAAATGCAAAGATT
TCA
Found at i:1070202 original size:65 final size:65
Alignment explanation
Indices: 1070095--1070346 Score: 256
Period size: 65 Copynumber: 3.7 Consensus size: 65
1070085 GCAAACTGTC
* * * *
1070095 TCAAGAGAAATTGTCTCAAGGGAGACGAAATTTGTTTTAAGGGAAACATATTCAAAGATTTTGCT
1 TCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGCT
* *
1070160 TCAAGGGAAATT-TGCTCATGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGT
1 TCAAGGGAAATTGT-CTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGC
1070224 T
65 T
* * *
1070225 TCAAGGGAAACTGTCTCAAGAGAGAGACAAAATTTAGTTTCAAGAGAAACTG-TCTCAAGGGAGA
1 TCAAGGGAAATTGTCTCAAG-G-GAGACAAAATTT-GTTTCAAGGGAAACAGAT-TCAA---AGA
*
1070289 TGAAATTTGTT
59 T----TTTGCT
* * * *
1070300 TCAAGGGAAACTGTATCAAGGGAGACAAAACTTGTTTTAAGGGAAAC
1 TCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1070347 TGTCTTAAGG
Statistics
Matches: 160, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
64 1 0.01
65 73 0.46
66 2 0.01
67 13 0.08
68 18 0.11
71 4 0.03
72 12 0.08
73 11 0.07
74 1 0.01
75 25 0.16
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (65 bp):
TCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGCT
Found at i:1070310 original size:36 final size:36
Alignment explanation
Indices: 1070219--1070591 Score: 395
Period size: 36 Copynumber: 10.5 Consensus size: 36
1070209 ATTCAAAGAT
1070219 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAG-G-GAGACAAAA
* **
1070257 TTTAGTTTCAAGAGAAACTGTCTCAAGGGAGATGAAA
1 TTT-GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
*
1070294 TTTGTTTCAAGGGAAACTGTATCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* * * *
1070330 CTTGTTTTAAGGGAAACTGTCTTAAGGGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
** * * *
1070366 CGTGTTTCAAGGGAAATTGTTTCAAGGGAGACAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* * * *
1070402 CTTGTTTCAAGGTAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* * *
1070438 TTTGATTCAAGGGAAACTGTCTCAAGAGAAACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* * *
1070474 TTCGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
* *
1070510 TTCGTTTCAAGGGAAA-TGTTCTCAA---AG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAA
*
1070538 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
*
1070575 TTTGTTTCAAGAGAAAC
1 TTTGTTTCAAGGGAAAC
1070592 AATCTCAAAG
Statistics
Matches: 285, Mismatches: 38, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.01
29 18 0.06
30 2 0.01
32 2 0.01
33 2 0.01
35 1 0.00
36 220 0.77
37 12 0.04
38 4 0.01
39 22 0.08
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
Found at i:1070582 original size:65 final size:65
Alignment explanation
Indices: 1070477--1070606 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
1070467 AACAAAATTC
* * ***
1070477 GTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGTTCTCAAAGTTTAT
1 GTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATCTCAAAGTTTAT
* * *
1070542 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTAT
1 GTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATCTCAAAGTTTAT
1070607 CAAATTTGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (65 bp):
GTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATCTCAAAGTTTAT
Found at i:1075823 original size:32 final size:34
Alignment explanation
Indices: 1075780--1075848 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
1075770 TTTAAATAAG
1075780 TTTTAGTATTTTAAT-TATGTTTTAGG-ATATTAT
1 TTTTAGTATTTT-ATCTATGTTTTAGGTATATTAT
* *
1075813 TTTTA-TATTTTATCTTTGTTTTAGGTATTTTAT
1 TTTTAGTATTTTATCTATGTTTTAGGTATATTAT
1075846 TTT
1 TTT
1075849 AAATAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 16 0.50
33 14 0.44
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (34 bp):
TTTTAGTATTTTATCTATGTTTTAGGTATATTAT
Found at i:1076647 original size:19 final size:20
Alignment explanation
Indices: 1076596--1076668 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 20
1076586 TAAAATCCCC
* *
1076596 TTTTATTTTACTACTAT-TA
1 TTTTATTTTATTATTATCTA
*
1076615 TTTATTATTTTATTATTTTC-A
1 -TT-TTATTTTATTATTATCTA
1076636 CTTTTA-TTTATTATTATCTA
1 -TTTTATTTTATTATTATCTA
1076656 TTTTATTTTATTA
1 TTTTATTTTATTA
1076669 AATCTTTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 16 0.36
20 13 0.30
21 15 0.34
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTTATTATTATCTA
Found at i:1083860 original size:19 final size:19
Alignment explanation
Indices: 1083833--1083869 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1083823 GTATTTTAGT
*
1083833 TTAAATAGGTTTTAGAATC
1 TTAAATAGGATTTAGAATC
*
1083852 TTAATTAGGATTTAGAAT
1 TTAAATAGGATTTAGAAT
1083870 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (19 bp):
TTAAATAGGATTTAGAATC
Found at i:1083928 original size:72 final size:74
Alignment explanation
Indices: 1083747--1083937 Score: 226
Period size: 76 Copynumber: 2.6 Consensus size: 74
1083737 TTTTATCTTT
* * * * * * **
1083747 TTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATGTTATTTTTATATTTTAT
1 TTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAAAAATTA-
1083812 CTTTGTTTTAG
65 -TTTGTTTTAG
* * *
1083823 GTATTTTAGTTTAAATAGGTTTTAGAATCTTAATTAGGATTTAGAATATTATTTTAAAAAATTA-
1 TTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAAAAATTAT
1083887 TT-TTTTAG
66 TTGTTTTAG
*
1083895 TTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
1083938 AGATGTTTTA
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
71 5 0.05
72 39 0.39
73 2 0.02
76 53 0.54
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.55
Consensus pattern (74 bp):
TTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAAAAATTAT
TTGTTTTAG
Found at i:1085594 original size:59 final size:59
Alignment explanation
Indices: 1085501--1085632 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 59
1085491 CACCATAATG
* * * *
1085501 CAATCCCGAGTATGACACATAAGGTCGTATCCACCATCTATACTAGGTATCCTTAAGTA
1 CAATCCCGAATATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
* * * *
1085560 CAATCCCGAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTG
1 CAATCCCGAATATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
* *
1085619 TATTCCCGAATATG
1 CAATCCCGAATATG
1085633 CAGCCTGCTG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (59 bp):
CAATCCCGAATATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
Found at i:1093863 original size:23 final size:23
Alignment explanation
Indices: 1093829--1093885 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
1093819 CCTTTTTCTA
1093829 TTTC-TTCTTTTTATTGATCTC-TT
1 TTTCTTTC-TTTT-TTGATCTCTTT
* *
1093852 TTTCTTTCTTTTTTGTTTTCTTT
1 TTTCTTTCTTTTTTGATCTCTTT
*
1093875 TTTATTTCTTT
1 TTTCTTTCTTT
1093886 AGAATTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 6 0.21
23 20 0.69
24 3 0.10
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (23 bp):
TTTCTTTCTTTTTTGATCTCTTT
Found at i:1093875 original size:11 final size:11
Alignment explanation
Indices: 1093820--1093885 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 11
1093810 AACCTTCTCC
1093820 CTTTTTCTATTT
1 CTTTTT-TATTT
1093832 CTTCTTTTTATTGAT
1 C-T-TTTTTATT--T
*
1093847 CTCTTTTTCTTT
1 CT-TTTTTATTT
*
1093859 CTTTTTTGTTTT
1 CTTTTTT-ATTT
1093871 CTTTTTTATTT
1 CTTTTTTATTT
1093882 CTTT
1 CTTT
1093886 AGAATTTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 12 0.26
12 14 0.30
13 5 0.11
14 13 0.28
15 2 0.04
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (11 bp):
CTTTTTTATTT
Found at i:1094957 original size:134 final size:134
Alignment explanation
Indices: 1094670--1095074 Score: 440
Period size: 134 Copynumber: 3.0 Consensus size: 134
1094660 GTTGAGGATG
* * * * * *
1094670 ACACAGCTCATACGTGATGAAGAGTTATGGTCGTCTAAGGGTAACATGGCTCTTACGTGATGAGG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGG
* * * * *
1094735 AGATTTGGTCGGTGGATGACATGGTTCCTACGTGATGAGGATGGTTGGCCATTTTTAGGGATGAT
66 AGATTTGGTCGGTGGATGACACGATTCCTAAGTGATGAGGATGGCTGGCCATCTTTAGGGATGAT
*
1094800 GATG
131 GATA
* ** * *
1094804 ACACTGCTCATACGTGATGAAGAGTTCTGGTCATCTAAGGGTGACACAACTCCTATGTGATGAAG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGG
* *
1094869 AGATTTGGTTGGTGGATAACACGATTCCTAAGTGATGAGGATGGCTGGCCATCTTTAGGGATGAT
66 AGATTTGGTCGGTGGATGACACGATTCCTAAGTGATGAGGATGGCTGGCCATCTTTAGGGATGAT
1094934 GATA
131 GATA
* * * * * * * **
1094938 ACACGGTTCCTACGCGATGATGA-TGGCTGGTTATCTAAGGTTGATGCGGCTCCTACGTGATGAG
1 ACACGGCTCATACGTGATGAAGAGT-TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAG
* * * * **
1095002 GAGATATCGTCGGTGGATGACACGGA-TCCTACA-CGATGAAGA-CACTGGCCATCTTTAGGGAT
65 GAGATTTGGTCGGTGGATGACAC-GATTCCTA-AGTGATGAGGATGGCTGGCCATCTTTAGGGAT
*
1095064 GTTGATA
128 GATGATA
1095071 ACAC
1 ACAC
1095075 AATTTCTACA
Statistics
Matches: 227, Mismatches: 41, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
133 29 0.13
134 195 0.86
135 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (134 bp):
ACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGG
AGATTTGGTCGGTGGATGACACGATTCCTAAGTGATGAGGATGGCTGGCCATCTTTAGGGATGAT
GATA
Found at i:1095230 original size:50 final size:50
Alignment explanation
Indices: 1095107--1095265 Score: 187
Period size: 50 Copynumber: 3.1 Consensus size: 50
1095097 TTGGTTATCT
* * * * *
1095107 AAGAGAGAC-AAATTTCTTTCAAGGGAGATGAGACTCAAAGAT-ATTTTTTTC
1 AAGAGAGACAAAATTTATTTCAAGGGAAACGA-TCTCAAAGATGA--TGTTTC
* *
1095158 AAGAGAGAGACAAAAATAATTTCAAGGGAAACGATCTCAAAGATGATGTTTC
1 -A-AGAGAGACAAAATTTATTTCAAGGGAAACGATCTCAAAGATGATGTTTC
*
1095210 AAGAGAGACAAAATTTATTTCAAGGGAAACGATCTCAAATATGATGTTTC
1 AAGAGAGACAAAATTTATTTCAAGGGAAACGATCTCAAAGATGATGTTTC
1095260 AAGAGA
1 AAGAGA
1095266 AACTGTCTCA
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
50 52 0.55
51 1 0.01
52 6 0.06
53 17 0.18
54 18 0.19
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (50 bp):
AAGAGAGACAAAATTTATTTCAAGGGAAACGATCTCAAAGATGATGTTTC
Found at i:1095295 original size:36 final size:36
Alignment explanation
Indices: 1095255--1095365 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
1095245 CAAATATGAT
*
1095255 GTTTCAAGAGAAACTGTCTCAAGAGAGTCAAAATTC
1 GTTTCAAGAGAAACTGACTCAAGAGAGTCAAAATTC
* * *
1095291 GTTTCAAGGGAAACGAGACTCAA-AGA-TC--TA-TC
1 GTTTCAAGAGAAAC-TGACTCAAGAGAGTCAAAATTC
* *
1095323 -TTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTT
1 GTTTCAAGAGAAACTGACTCAAGAGAGTCAAAA-TTC
1095359 GTTTCAA
1 GTTTCAA
1095366 ATGAAACATA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
30 7 0.12
31 15 0.26
32 3 0.05
33 1 0.02
34 1 0.02
35 2 0.03
36 17 0.29
37 12 0.21
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGACTCAAGAGAGTCAAAATTC
Found at i:1095346 original size:67 final size:65
Alignment explanation
Indices: 1095208--1095402 Score: 230
Period size: 67 Copynumber: 2.9 Consensus size: 65
1095198 AGATGATGTT
* * * * *
1095208 TCAAGAGAGACAAAATTTATTTCAAGGGAAACGATCTCAAATATGATGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACGAACTCAAAGATTATGTTTCAAGAGAAACTGAC
* * *
1095273 TCAAGAGAGTCAAAATTCGTTTCAAGGGAAACGAGACTCAAAGATCTATCTTTCAAGAGAAACTG
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACGA-ACTCAAAGAT-TATGTTTCAAGAGAAACTG
1095338 AC
64 AC
** * *
1095340 TCAAGAGAGACAAAACTTTGTTTCAAATGAAAC-ATACTCAAAGATTTTTGTTTCAAGTGAAAC
1 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACGA-ACTCAAAGA-TTATGTTTCAAGAGAAAC
1095403 AATTTCCAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 31 0.28
66 8 0.07
67 56 0.51
68 15 0.14
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (65 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACGAACTCAAAGATTATGTTTCAAGAGAAACTGAC
Found at i:1099611 original size:21 final size:19
Alignment explanation
Indices: 1099568--1099613 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1099558 CATAAACATT
* *
1099568 TTTTTGAAAAACAATTAAG
1 TTTTTAAAAAACAATTAAC
1099587 TTTTTAAAAAACAATTATGAC
1 TTTTTAAAAAACAATTA--AC
1099608 TTTTTA
1 TTTTTA
1099614 TTTGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
21 7 0.30
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (19 bp):
TTTTTAAAAAACAATTAAC
Found at i:1105884 original size:17 final size:18
Alignment explanation
Indices: 1105854--1105888 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1105844 CTTTTTCGCA
1105854 CTTTTGTTGTTTTTCTGT
1 CTTTTGTTGTTTTTCTGT
*
1105872 CTTTTTTTG-TTTTCTGT
1 CTTTTGTTGTTTTTCTGT
1105889 TTCTATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (18 bp):
CTTTTGTTGTTTTTCTGT
Found at i:1119809 original size:16 final size:15
Alignment explanation
Indices: 1119772--1119845 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
1119762 ATTCTTTTTC
*
1119772 ATATATCATTATTATTT
1 ATATAT-ATTTTTA-TT
1119789 ATATATATTTTTATT
1 ATATATATTTTTATT
* *
1119804 ACTATA-ATTATAAGTT
1 A-TATATATTTTTA-TT
1119820 ATATATATTTATTATT
1 ATATATATTT-TTATT
*
1119836 TTATATATTT
1 ATATATATTT
1119846 CATTTTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 12 0.26
16 27 0.57
17 8 0.17
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (15 bp):
ATATATATTTTTATT
Found at i:1119868 original size:15 final size:15
Alignment explanation
Indices: 1119848--1119879 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1119838 ATATATTTCA
*
1119848 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
1119863 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
1119878 TT
1 TT
1119880 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:1119896 original size:20 final size:20
Alignment explanation
Indices: 1119849--1119902 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1119839 TATATTTCAT
*
1119849 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
1119870 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
1119890 TGTTATTGTTATT
1 T-TTATTTTTATT
1119903 ATATTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:1119946 original size:33 final size:32
Alignment explanation
Indices: 1119875--1119951 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1119865 TTATCTTCTA
1119875 TTTTTATTTTTGTATTGTTATTGTTATTATAT
1 TTTTTATTTTTGTATTGTTATTGTTATTATAT
*
1119907 TCTTTATTTTATGTATT-TTATT-TATATATATAT
1 TTTTTATTTT-TGTATTGTTATTGT-TAT-TATAT
*
1119940 TTTTTATATTTG
1 TTTTTATTTTTG
1119952 ATTTTGTGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 1 0.03
32 19 0.49
33 19 0.49
ACGTcount: A:0.22, C:0.01, G:0.06, T:0.70
Consensus pattern (32 bp):
TTTTTATTTTTGTATTGTTATTGTTATTATAT
Found at i:1130708 original size:20 final size:20
Alignment explanation
Indices: 1130683--1130728 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1130673 GAAAGGTTGT
1130683 ACTCTCCTAAATATTGTCGC
1 ACTCTCCTAAATATTGTCGC
*
1130703 ACTCTCCTAAATGTTGTCGC
1 ACTCTCCTAAATATTGTCGC
1130723 ACTCTC
1 ACTCTC
1130729 AAAGATCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.35
Consensus pattern (20 bp):
ACTCTCCTAAATATTGTCGC
Found at i:1131748 original size:110 final size:110
Alignment explanation
Indices: 1131550--1131753 Score: 320
Period size: 110 Copynumber: 1.9 Consensus size: 110
1131540 GCTTCCCAGT
* *
1131550 TTCAGAGCCAATTTTAACTTCACAGCGAGAGATATTGGACTCAAGACAACACAAGCTCAACATCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGAACTCAAGACAACACAAGCTCAACATCA
*
1131615 CAACGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAATTTTA
66 CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAATTTTA
* * *
1131660 TTCAGAGTCAATTTCAACTTCACAGCGA-AGGATATTGAACTCGAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAGA-GATATTGAACTCAAGACAACACAAGCTCAACATC
* *
1131724 ACAGCGAAGGGGGGACTGACTGTCAACAAA
65 ACAACGAAGGGGCGACTGACTGTCAACAAA
1131754 CAATTTCCAG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
109 1 0.01
110 84 0.99
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGAACTCAAGACAACACAAGCTCAACATCA
CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAATTTTA
Found at i:1133333 original size:16 final size:15
Alignment explanation
Indices: 1133296--1133369 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
1133286 ATTCTTTTTC
*
1133296 ATATATCATTATTATTT
1 ATATAT-ATTTTTA-TT
1133313 ATATATATTTTTATT
1 ATATATATTTTTATT
* *
1133328 ACTATA-ATTATATGTT
1 A-TATATATT-TTTATT
1133344 ATATATATTTATTATT
1 ATATATATTT-TTATT
*
1133360 TTATATATTT
1 ATATATATTT
1133370 CATTTTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 11 0.23
16 30 0.64
17 6 0.13
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATATATTTTTATT
Found at i:1138444 original size:18 final size:18
Alignment explanation
Indices: 1138412--1138446 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1138402 TCCTTTATTC
*
1138412 ATTTAATCTCCTTTTACT
1 ATTTAATCTCATTTTACT
*
1138430 ATTTAATCTTATTTTAC
1 ATTTAATCTCATTTTAC
1138447 CGAACCCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAATCTCATTTTACT
Found at i:1142095 original size:44 final size:43
Alignment explanation
Indices: 1142045--1142161 Score: 162
Period size: 46 Copynumber: 2.6 Consensus size: 43
1142035 GTAAGCATAC
*
1142045 AAATAAGCTTACGAGCTTTTGGAATAATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTAT-TGGGTA
* *
1142089 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATTGGGTA
*
1142135 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
1142162 ATGGTAAGGG
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
43 2 0.03
44 24 0.36
46 29 0.44
47 11 0.17
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.31
Consensus pattern (43 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATTGGGTA
Found at i:1142150 original size:46 final size:45
Alignment explanation
Indices: 1142045--1142169 Score: 182
Period size: 44 Copynumber: 2.8 Consensus size: 45
1142035 GTAAGCATAC
* *
1142045 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
*
1142089 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
*
1142135 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1142170 GGATTTTATA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
44 34 0.46
46 29 0.39
47 11 0.15
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:1143487 original size:18 final size:18
Alignment explanation
Indices: 1143451--1143487 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1143441 GTTGAAAATG
* *
1143451 ATTTGGTTTTGAAAGAAA
1 ATTTGATTTTGAAAAAAA
1143469 ATTTGATTTTGAAAAAAA
1 ATTTGATTTTGAAAAAAA
1143487 A
1 A
1143488 AATCATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (18 bp):
ATTTGATTTTGAAAAAAA
Found at i:1150473 original size:55 final size:55
Alignment explanation
Indices: 1150371--1150597 Score: 213
Period size: 55 Copynumber: 4.1 Consensus size: 55
1150361 AGCAACTTTG
* * * * ** *
1150371 TGCTTCAATCGAGAACTGACATCTCTGTGTAGCCAAAAGA-GATTGAGCACCTCTA
1 TGCTTCAATCAAGAACTGACACCTCTATGCAGTTAAAA-ATGACTGAGCACCTCTA
* * *
1150426 TGTTTCAATCAAGAAATGACACCTCTATGCAGTTAAAAATGACTGAGCACCTCTG
1 TGCTTCAATCAAGAACTGACACCTCTATGCAGTTAAAAATGACTGAGCACCTCTA
* ** * ** * * * *
1150481 GGCTTCAGCCAAGAGCTGACACCTCTATATAGCTAAGACTGATTGAGCACCTCTA
1 TGCTTCAATCAAGAACTGACACCTCTATGCAGTTAAAAATGACTGAGCACCTCTA
* * * * *
1150536 TGCTTCAATCAAGGACTTACACCTCTGTGCAGTAAAAAATGACTGAGCACCTCTG
1 TGCTTCAATCAAGAACTGACACCTCTATGCAGTTAAAAATGACTGAGCACCTCTA
1150591 TGCTTCA
1 TGCTTCA
1150598 GTCTAAAAGT
Statistics
Matches: 133, Mismatches: 38, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
54 1 0.01
55 132 0.99
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (55 bp):
TGCTTCAATCAAGAACTGACACCTCTATGCAGTTAAAAATGACTGAGCACCTCTA
Done.