Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold26
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: 1656043
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 334368 characters in sequence are not A, C, G, or T
File 5 of 8
Found at i:1005067 original size:42 final size:42
Alignment explanation
Indices: 1005012--1005130 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1005002 TTCTTCTCTC
* *
1005012 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1005054 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1005096 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1005131 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1005071 original size:12 final size:11
Alignment explanation
Indices: 1005045--1005120 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1005035 TCTATTATCT
*
1005045 CTCCTGTCTCTC
1 CTCCTATCTC-C
1005057 CTCCTATCATCC
1 CTCCTATC-TCC
1005069 CTCCTATCT--
1 CTCCTATCTCC
*
1005078 CTACTATCT--
1 CTCCTATCTCC
*
1005087 CTCCTGTCTCTC
1 CTCCTATCTC-C
1005099 CTCCTATCATCC
1 CTCCTATC-TCC
*
1005111 CTCCTCTCTC
1 CTCCTATCTC
1005121 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1005072 original size:24 final size:24
Alignment explanation
Indices: 1005036--1005121 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1005026 CCTCCTCTCT
* *
1005036 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1005060 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1005081 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1005102 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1005122 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1005096 original size:18 final size:18
Alignment explanation
Indices: 1005027--1005097 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1005017 CCTGTCATCC
* *
1005027 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1005045 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1005067 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1005087 CTCCTGTCTCT
1 CTCCTGTCTCT
1005098 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1006878 original size:79 final size:78
Alignment explanation
Indices: 1006772--1006956 Score: 237
Period size: 79 Copynumber: 2.3 Consensus size: 78
1006762 TCTAAAGCAT
* * * *
1006772 CAATTTTTCACAATCGGGGATATTCCAATCCC-GTTATTTTCGAGGGGATACTCCAACCCCGATT
1 CAATTTTCCATAATC-GGGATACTCCAA-CCCTGTTATTTTCGAGGGAATACTCCAACCCCGATT
1006836 TTATTTTCAAAACAC
64 TTATTTTCAAAACAC
* * *
1006851 CAATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACTCTGATTT
1 CAATTTTCCATAATC-GGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTT
* *
1006916 TATTTTTAGAACAC
65 TATTTTCAAAACAC
*
1006930 CGATTTTCCATAATCGAGGATACTCCA
1 CAATTTTCCATAATCG-GGATACTCCA
1006957 GCCCCGTTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 4 0.04
79 88 0.96
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
CAATTTTCCATAATCGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTT
ATTTTCAAAACAC
Found at i:1013814 original size:19 final size:20
Alignment explanation
Indices: 1013789--1013843 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1013779 TGTATTGATA
* **
1013789 AATTGTATCGATATATGTTC
1 AATTGTATCGATACATACTC
*
1013809 -ATTGTATTGATACATACTC
1 AATTGTATCGATACATACTC
1013828 AATTGTATCGATACAT
1 AATTGTATCGATACAT
1013844 GAAAGTGGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
AATTGTATCGATACATACTC
Found at i:1013911 original size:13 final size:13
Alignment explanation
Indices: 1013893--1013919 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1013883 TATGGGACAA
1013893 TGTATCGATACAT
1 TGTATCGATACAT
1013906 TGTATCGATACAT
1 TGTATCGATACAT
1013919 T
1 T
1013920 ATGCCCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1017736 original size:18 final size:17
Alignment explanation
Indices: 1017703--1017737 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1017693 TTAAAATACA
*
1017703 AAAAATAAATAGTATTT
1 AAAAATAAATACTATTT
1017720 AAAAATAAATATCTATTT
1 AAAAATAAATA-CTATTT
1017738 GACTCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAAATAAATACTATTT
Found at i:1018915 original size:9 final size:9
Alignment explanation
Indices: 1018901--1018947 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1018891 ACCAAATATT
1018901 TATTATTAA
1 TATTATTAA
1018910 TATTATTAA
1 TATTATTAA
*
1018919 -AATATTAAA
1 TATTATT-AA
*
1018928 TATT-TTTA
1 TATTATTAA
1018936 TATTATTAA
1 TATTATTAA
1018945 TAT
1 TAT
1018948 CTTGAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 10 0.32
9 19 0.61
10 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTATTAA
Found at i:1023993 original size:2 final size:2
Alignment explanation
Indices: 1023918--1023974 Score: 60
Period size: 2 Copynumber: 27.5 Consensus size: 2
1023908 AAAACTTGAA
* * * *
1023918 AT AT AT AT AT AT AT AT AT AT GAGT TT AT AT TT GT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT
1023962 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1023975 CACACATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 44 0.96
3 1 0.02
4 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1029202 original size:48 final size:46
Alignment explanation
Indices: 1029080--1029203 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 46
1029070 ATTTCTTAGT
* * *
1029080 TAATTTAATTAGAGATAAAAT-TACTTTATTTATCTCTTAATTAATT
1 TAATTTAATTAGAGAAAAAATAT-TTTTATTTATCTCTTAATTAATA
* *
1029126 TAATTTAATTTA-ATTAAAAATATTTTTTTATTTATCTCTTAATTAATA
1 TAATTTAA-TTAGA-GAAAAA-ATATTTTTATTTATCTCTTAATTAATA
1029174 TAATTTAATTAGAGACAAAAATGATTTTTA
1 TAATTTAATTAGAGA-AAAAAT-ATTTTTA
1029204 AAGAATTTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
46 9 0.14
47 13 0.20
48 42 0.65
49 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (46 bp):
TAATTTAATTAGAGAAAAAATATTTTTATTTATCTCTTAATTAATA
Found at i:1039921 original size:15 final size:14
Alignment explanation
Indices: 1039898--1039955 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
1039888 GCTAAACTTG
1039898 AAATGACCTAAAAC
1 AAATGACCTAAAAC
*
1039912 AAAGTGACCTAAACTC
1 AAA-TGACCTAAA-AC
*
1039928 GAAATGACCTGAAAC
1 -AAATGACCTAAAAC
*
1039943 AAAATGACTTAAA
1 -AAATGACCTAAA
1039956 CCCAAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 3 0.09
15 20 0.57
16 9 0.26
17 3 0.09
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (14 bp):
AAATGACCTAAAAC
Found at i:1039932 original size:31 final size:31
Alignment explanation
Indices: 1039871--1039956 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
1039861 AACCAAGAAA
* * * *
1039871 ACCTAAAATCGAAATAAGCTAAACTTGAAATG
1 ACCTAAAA-CAAAATGACCTAAACTCGAAATG
*
1039903 ACCTAAAACAAAGTGACCTAAACTCGAAATG
1 ACCTAAAACAAAATGACCTAAACTCGAAATG
* *
1039934 ACCTGAAACAAAATGACTTAAAC
1 ACCTAAAACAAAATGACCTAAAC
1039957 CCAAAAATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
31 38 0.83
32 8 0.17
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.19
Consensus pattern (31 bp):
ACCTAAAACAAAATGACCTAAACTCGAAATG
Found at i:1043474 original size:26 final size:25
Alignment explanation
Indices: 1043430--1043482 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1043420 TCTGGTTTTT
1043430 TTAAATATTTTTCTAAAAGCTA-CA
1 TTAAATATTTTTCTAAAAGCTATCA
*
1043454 TTAAATTTTCTTTCTTAAAAGCTATCA
1 TTAAATATT-TTTC-TAAAAGCTATCA
1043481 TT
1 TT
1043483 TGATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 4 0.16
26 9 0.36
27 4 0.16
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (25 bp):
TTAAATATTTTTCTAAAAGCTATCA
Found at i:1045126 original size:16 final size:16
Alignment explanation
Indices: 1045105--1045144 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1045095 ATTTTTTTCA
1045105 AAAATATTTGCATACG
1 AAAATATTTGCATACG
* **
1045121 AAAATATTTTCATATT
1 AAAATATTTGCATACG
1045137 AAAATATT
1 AAAATATT
1045145 ATAAGTTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (16 bp):
AAAATATTTGCATACG
Found at i:1046147 original size:4 final size:4
Alignment explanation
Indices: 1046138--1046162 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1046128 AAGAACTTTG
1046138 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
1046163 GAGATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1047704 original size:3 final size:3
Alignment explanation
Indices: 1047696--1047728 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1047686 TAAGTATATT
1047696 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1047729 CAAGCAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1048153 original size:23 final size:24
Alignment explanation
Indices: 1048123--1048179 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
1048113 TTATTAAAAC
*
1048123 ATAA-TATAATAAATAA-ATTTAT
1 ATAATTATAATAAATAATATTTAA
1048145 ATAATTAT-A-AAATAATTATTTAA
1 ATAATTATAATAAATAA-TATTTAA
*
1048168 ATAATTAAAATA
1 ATAATTATAATA
1048180 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 6 0.21
22 5 0.18
23 15 0.54
24 1 0.04
25 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATTATAATAAATAATATTTAA
Found at i:1048176 original size:21 final size:21
Alignment explanation
Indices: 1048150--1048202 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1048140 TTTATATAAT
**
1048150 TATAAAATAATTATTTAAATA
1 TATAAAATAATTAAATAAATA
*
1048171 -ATTAAAATATTTAAATAAATA
1 TA-TAAAATAATTAAATAAATA
1048192 TATAAAATAAT
1 TATAAAATAAT
1048203 ATTATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAATAATTAAATAAATA
Found at i:1048235 original size:23 final size:23
Alignment explanation
Indices: 1048189--1048235 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1048179 ATTTAAATAA
*
1048189 ATATATAAAATAATATTATTAAT
1 ATATATAAAATAATATTATCAAT
*
1048212 ATATATATAATTAATA-TATCAAT
1 ATATATA-AAATAATATTATCAAT
1048235 A
1 A
1048236 AACTCTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATAAAATAATATTATCAAT
Found at i:1048236 original size:15 final size:15
Alignment explanation
Indices: 1048201--1048230 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1048191 ATATAAAATA
*
1048201 ATATTATTAATATAT
1 ATATAATTAATATAT
1048216 ATATAATTAATATAT
1 ATATAATTAATATAT
1048231 CAATAAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATTAATATAT
Found at i:1048459 original size:28 final size:29
Alignment explanation
Indices: 1048428--1048487 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
1048418 TTTTATAGTA
*
1048428 TTTAATAAAAAATTATT-TTAAATTAAAT
1 TTTAATAAAAAATAATTATTAAATTAAAT
* * * *
1048456 TTTATTAAATAATAATTATTTATTTAAAT
1 TTTAATAAAAAATAATTATTAAATTAAAT
1048485 TTT
1 TTT
1048488 GCATTTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAATAAAAAATAATTATTAAATTAAAT
Found at i:1049090 original size:15 final size:15
Alignment explanation
Indices: 1049059--1049100 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1049049 TTCATTATTT
*
1049059 AAAA-TAAAATTTAAA
1 AAAACTAAAATAT-AA
*
1049074 AAAACTTAAATATAA
1 AAAACTAAAATATAA
1049089 AAAACTAAAATA
1 AAAACTAAAATA
1049101 ATTAGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAACTAAAATATAA
Found at i:1055277 original size:29 final size:29
Alignment explanation
Indices: 1055242--1055306 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1055232 TGAAAGCGTC
1055242 TATTTTTAAATAT-TTACAAAAAAATATATT
1 TATTTTTAAATATCTTA-AAAAAAAT-TATT
** *
1055272 TATTTTTTTATATCTTAAAAATAATTATT
1 TATTTTTAAATATCTTAAAAAAAATTATT
1055301 TATTTT
1 TATTTT
1055307 ATTAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.32
30 18 0.58
31 3 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTTTTAAATATCTTAAAAAAAATTATT
Found at i:1055367 original size:11 final size:12
Alignment explanation
Indices: 1055331--1055364 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
1055321 AAAATTATAC
1055331 TTAATTTTTAAA
1 TTAATTTTTAAA
1055343 TTATTATTTTTAAA
1 TTA--ATTTTTAAA
1055357 TTAATTTT
1 TTAATTTT
1055365 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.40
14 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTAATTTTTAAA
Found at i:1055877 original size:12 final size:12
Alignment explanation
Indices: 1055860--1055909 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1055850 AACTTAACAT
1055860 ATTAATATTAAA
1 ATTAATATTAAA
*
1055872 ATTAATATATATA
1 ATTAATAT-TAAA
*
1055885 ATTGA-ATTAAA
1 ATTAATATTAAA
1055896 TATTAAT-TTAAA
1 -ATTAATATTAAA
1055908 AT
1 AT
1055910 ATTTTTAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 5 0.16
12 19 0.61
13 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTAATATTAAA
Found at i:1057525 original size:17 final size:17
Alignment explanation
Indices: 1057486--1057527 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1057476 AAAATTTTAA
**
1057486 TTTTTTATTTTTATTGT
1 TTTTTTATTTTTATACT
*
1057503 TGTTTTATTTTTATACT
1 TTTTTTATTTTTATACT
1057520 TTTTTTAT
1 TTTTTTAT
1057528 GAATTATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTTATACT
Found at i:1059248 original size:17 final size:17
Alignment explanation
Indices: 1059228--1059270 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1059218 TTGCCTCCCT
1059228 TTTTCAAAAGCCTTTTA
1 TTTTCAAAAGCCTTTTA
*
1059245 TTTTCAGAAGCCTTTTA
1 TTTTCAAAAGCCTTTTA
1059262 TTTTCAAAA
1 TTTTCAAAA
1059271 ATTTCTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (17 bp):
TTTTCAAAAGCCTTTTA
Found at i:1067082 original size:13 final size:13
Alignment explanation
Indices: 1067061--1067090 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1067051 ACTTTTCAAC
*
1067061 ATGTTTCGATACA
1 ATGTATCGATACA
1067074 ATGTATCGATACA
1 ATGTATCGATACA
1067087 ATGT
1 ATGT
1067091 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1067180 original size:19 final size:20
Alignment explanation
Indices: 1067156--1067207 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1067146 AAAATTGAGT
*
1067156 ATGTATCGATACAATG-A-A
1 ATGTATCGATACAAAGCATA
*
1067174 CATGTATTGATACAAAGCATA
1 -ATGTATCGATACAAAGCATA
1067195 ATGTATCGATACA
1 ATGTATCGATACA
1067208 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.50
20 13 0.46
21 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:1067612 original size:11 final size:11
Alignment explanation
Indices: 1067596--1067622 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1067586 TTAAATCATG
1067596 ATTTAAAAATA
1 ATTTAAAAATA
1067607 ATTTAAAAATA
1 ATTTAAAAATA
1067618 ATTTA
1 ATTTA
1067623 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:1068050 original size:74 final size:72
Alignment explanation
Indices: 1067929--1068077 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 72
1067919 AAAAATAGAA
** *
1067929 AAATCAAGAAAAAATAGTTGTAGTTTCTTTATATTATTGTTGTTTTAATTTTTTTTATAATTTAT
1 AAATCAAGAAAAAATAGTTACAGTTTCTTTATATTATTGTTATTTTAA--TTTTTTATAATTTAT
1067994 TATTTTCAT
64 TATTTTCAT
*
1068003 AAATCAAGACAAAATAGTTACAGTTTCTTTATATTATTGTTATTTTAATTTTTTATAATTTATTA
1 AAATCAAGAAAAAATAGTTACAGTTTCTTTATATTATTGTTATTTTAATTTTTTATAATTTATTA
*
1068068 TTTTTAT
66 TTTTCAT
1068075 AAA
1 AAA
1068078 AACTAAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 26 0.37
74 44 0.63
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.54
Consensus pattern (72 bp):
AAATCAAGAAAAAATAGTTACAGTTTCTTTATATTATTGTTATTTTAATTTTTTATAATTTATTA
TTTTCAT
Found at i:1068192 original size:3 final size:3
Alignment explanation
Indices: 1068186--1068229 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1068176 AAATATGAAT
*
1068186 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1068230 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1068234 original size:3 final size:3
Alignment explanation
Indices: 1068228--1068264 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1068218 ATAATAATAA
1068228 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1068265 TGATTTAATT
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:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:1068418 original size:53 final size:53
Alignment explanation
Indices: 1068357--1068460 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
1068347 ATTAAGAAAG
*
1068357 TTAAAGTTGCTAAATATGTGCTTAAGAGTAAGGTTGCTCGGCAAGTTCAAGTA
1 TTAAAGTTGCTAAATATATGCTTAAGAGTAAGGTTGCTCGGCAAGTTCAAGTA
* * * *
1068410 TTAAAGTTGTTAAGTATATGCTTAAGAGTAAGGTTGTTTGGCAAGTTCAAG
1 TTAAAGTTGCTAAATATATGCTTAAGAGTAAGGTTGCTCGGCAAGTTCAAG
1068461 CATCCCAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.35
Consensus pattern (53 bp):
TTAAAGTTGCTAAATATATGCTTAAGAGTAAGGTTGCTCGGCAAGTTCAAGTA
Found at i:1078657 original size:19 final size:20
Alignment explanation
Indices: 1078614--1078666 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
1078604 CTGCAAGTTT
*
1078614 CATGTATCGATACAATTGTA
1 CATGTATCGATACAATTGAA
*
1078634 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1078653 CATGTATCGATACA
1 CATGTATCGATACA
1078667 TTTAGGTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1079259 original size:22 final size:20
Alignment explanation
Indices: 1079220--1079262 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1079210 GGCTCTCGTT
*
1079220 AAAAAATTTTCTCTTTGATA
1 AAAAAATTTTCTCCTTGATA
1079240 AAAAAATTTCTCCTCCTTGATA
1 AAAAAATTT-T-CTCCTTGATA
1079262 A
1 A
1079263 TCGGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 1 0.05
22 10 0.50
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAAAATTTTCTCCTTGATA
Found at i:1080794 original size:22 final size:21
Alignment explanation
Indices: 1080759--1080808 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1080749 TTTGTTGATG
*
1080759 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1080779 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1080800 AATTTGAAG
1 ATTTTGAAG
1080809 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1080805 original size:21 final size:22
Alignment explanation
Indices: 1080766--1080808 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1080756 ATGATTTTGA
* *
1080766 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1080788 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1080809 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1085496 original size:3 final size:3
Alignment explanation
Indices: 1085488--1085524 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1085478 TCCGAGTCAC
*
1085488 CAT CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1085525 TTTGATAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:1086962 original size:13 final size:13
Alignment explanation
Indices: 1086944--1086968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1086934 ACAATGAATA
1086944 TGTATCGATACAT
1 TGTATCGATACAT
1086957 TGTATCGATACA
1 TGTATCGATACA
1086969 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1089179 original size:50 final size:49
Alignment explanation
Indices: 1089103--1089237 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 49
1089093 TTCCACTATT
* * *
1089103 TGTATCGATACATTCTTCATTATATCGATATATTCTGGGTTTAACCTAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGGGTTTAACCCAGA
*
1089153 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGGGTTTAACCCAGA
*
1089203 TGTATCGATACATTTCTCAATGTATCGATACATTC
1 TGTATCGATACATTT-TCATTGTATCGATACATTC
1089238 AGGCATTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 77 0.99
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTTTCATTGTATCGATACATTCTGGGTTTAACCCAGA
Found at i:1091933 original size:163 final size:159
Alignment explanation
Indices: 1091613--1091981 Score: 428
Period size: 163 Copynumber: 2.3 Consensus size: 159
1091603 AATTTCCCAT
* *
1091613 GAAGGGATACTCTAATTCTGGTTTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCC
1 GAAGGG-TACTCCAATCCTGGTTTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCC
* * *
1091678 AACCCTGTTATTTCTGAGAGGATACTCCAACCCTGATTTTTATTTCCAAAACACCTATTTTTCAC
65 AACCCCGTTATTTCTGAGAGGATACTCAAACCCTGATTTTTATTTCCAAAACACCGATTTTTCAC
1091743 AATTGGGGATACTCCAATCCCGTTATTTCC
130 AATTGGGGATACTCCAATCCCGTTATTTCC
* * * * *
1091773 GAGAGGGTACTCCAATCCTGGTTTTTATTTCTAAGACATCGGTTTTTTTTCACCAT-TGGAGATA
1 GA-AGGGTACTCCAATCCTGGTTTTTATTTCCAAAACATC-G--ATTTTTCACAATCAGG-GATA
*
1091837 CTCCAACCCCGTTATTT-TCGA-AGGGATACTCAAACCCT-AGTTTTTATTTCCGAAACACCGAT
61 CTCCAACCCCGTTATTTCT-GAGA-GGATACTCAAACCCTGA-TTTTTATTTCCAAAACACCGAT
*
1091899 TTTTCATAATCT-GGGATACTCCAA-CCCTGTTATTTCC
123 TTTTCACAAT-TGGGGATACTCCAATCCC-GTTATTTCC
* * * *
1091936 GAAGAGATACTCCAA-CCTTAGTTTTTATTTCCAATACATCAATTTT
1 GAAG-GGTACTCCAATCC-TGGTTTTTATTTCCAAAACATCGATTTT
1091982 CCACCATTGG
Statistics
Matches: 179, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
160 35 0.20
161 5 0.03
162 12 0.07
163 126 0.70
164 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (159 bp):
GAAGGGTACTCCAATCCTGGTTTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCA
ACCCCGTTATTTCTGAGAGGATACTCAAACCCTGATTTTTATTTCCAAAACACCGATTTTTCACA
ATTGGGGATACTCCAATCCCGTTATTTCC
Found at i:1091981 original size:80 final size:79
Alignment explanation
Indices: 1091633--1091991 Score: 393
Period size: 80 Copynumber: 4.5 Consensus size: 79
1091623 TCTAATTCTG
* *
1091633 GTTTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCCTGTTATTTCTGAGAG
1 GTTTTTATTTCCAAAACATCGATTTTTCACAAT-TGGGATACTCCAACCCTGTTATTTCCGAGAG
1091698 GATACTCCAACCCT-
65 GATACTCCAACCCTA
* *
1091712 GATTTTTATTTCCAAAACACCTATTTTTCACAATTGGGGATACTCCAATCCC-GTTATTTCCGAG
1 G-TTTTTATTTCCAAAACATCGATTTTTCACAATT-GGGATACTCCAA-CCCTGTTATTTCCGAG
* * *
1091776 AGGGTACTCCAATCCTG
63 AGGATACTCCAACCCTA
* * * * * *
1091793 GTTTTTATTTCTAAGACATCGGTTTTTTTTCACCATTGGAGATACTCCAACCCCGTTATTTTCGA
1 GTTTTTATTTCCAAAACATC-G--ATTTTTCACAATTGG-GATACTCCAACCCTGTTATTTCCGA
*
1091858 -AGGGATACTCAAACCCTA
62 GA-GGATACTCCAACCCTA
* * *
1091876 GTTTTTATTTCCGAAACACCGATTTTTCATAATCTGGGATACTCCAACCCTGTTATTTCCGA-AG
1 GTTTTTATTTCCAAAACATCGATTTTTCACAAT-TGGGATACTCCAACCCTGTTATTTCCGAGAG
*
1091940 AGATACTCCAACCTTA
65 -GATACTCCAACCCTA
* * * *
1091956 GTTTTTATTTCCAATACATCAATTTTCCACCATTGG
1 GTTTTTATTTCCAAAACATCGATTTTTCACAATTGG
1091992 AGAATGTACT
Statistics
Matches: 233, Mismatches: 35, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
79 5 0.02
80 155 0.67
81 7 0.03
82 7 0.03
83 59 0.25
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (79 bp):
GTTTTTATTTCCAAAACATCGATTTTTCACAATTGGGATACTCCAACCCTGTTATTTCCGAGAGG
ATACTCCAACCCTA
Found at i:1093167 original size:14 final size:14
Alignment explanation
Indices: 1093129--1093170 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1093119 TGATATCAAA
1093129 ATTAATTTTATTTC
1 ATTAATTTTATTTC
* *
1093143 ATTTATCTTATTTC
1 ATTAATTTTATTTC
1093157 -TTAAATTTTATTTC
1 ATT-AATTTTATTTC
1093171 CATGTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTAATTTTATTTC
Found at i:1094814 original size:155 final size:156
Alignment explanation
Indices: 1094585--1094870 Score: 375
Period size: 156 Copynumber: 1.8 Consensus size: 156
1094575 ATGATTGTCG
* * * * *
1094585 TTTCATATTATTATTGAGTCCTTTAGAGTTATCGAGATAGTTTTATGTTGAAGGTATATTTTAGG
1 TTTCATATTATTATCGAGTCCTTTAGAGCTATCGAGATACTTTCATGTTGAAGGTATATTTTAAG
* * * *
1094650 AGGTATTTTAGTAGTTTT-CCTTAGAACTAAGTCTT-TTATG-GTCACCGAGATGCTTTCATGTT
66 AGGTATTTTAGTAATTTTACCTTAAAACCAAGT-TTATTA-GAGTCACCGAGATACTTTCATG-T
1094712 AAAAGTGTACTTTAGAGATAGGTTGGTCA
128 AAAAGTGTACTTTAGAGATAGGTTGGTCA
* * *
1094741 TTTCATGA-TATTATCGAGTCTTTTAGGGCTATCGGGATACTTTCAT-TTGAAGGTATATTTTAA
1 TTTCAT-ATTATTATCGAGTCCTTTAGAGCTATCGAGATACTTTCATGTTGAAGGTATATTTTAA
* *
1094804 GAGGTATTTTAGTAATTTTACCTTAAAACCGAGTTTATTAGAGTCACTGAGATACTTTCATGTAA
65 GAGGTATTTTAGTAATTTTACCTTAAAACCAAGTTTATTAGAGTCACCGAGATACTTTCATGTAA
1094869 AA
130 AA
1094871 TATACACTTA
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
155 42 0.38
156 69 0.62
157 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (156 bp):
TTTCATATTATTATCGAGTCCTTTAGAGCTATCGAGATACTTTCATGTTGAAGGTATATTTTAAG
AGGTATTTTAGTAATTTTACCTTAAAACCAAGTTTATTAGAGTCACCGAGATACTTTCATGTAAA
AGTGTACTTTAGAGATAGGTTGGTCA
Found at i:1097847 original size:25 final size:25
Alignment explanation
Indices: 1097812--1097879 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
1097802 TTATTTTATT
*
1097812 TTTAAATAAAAATAATATTATAT-A
1 TTTAATTAAAAATAATATTATATAA
*
1097836 -TTAATATCAAAATTAATA-TATATAA
1 TTTAAT-T-AAAAATAATATTATATAA
1097861 TTTAATTAAAAATAA-ATTA
1 TTTAATTAAAAATAATATTA
1097880 AAATATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
23 5 0.14
24 15 0.42
25 11 0.31
26 5 0.14
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTAATTAAAAATAATATTATATAA
Found at i:1097871 original size:24 final size:22
Alignment explanation
Indices: 1097807--1097879 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 22
1097797 AATAATTATT
* *
1097807 TTATTTTTAAATAAAAATAATA
1 TTATATTTAATTAAAAATAATA
*
1097829 TTATATATTAATATCAAAATTAATA
1 TTATAT-TTAAT-T-AAAAATAATA
1097854 TATATAATTTAATTAAAAATAA-A
1 T-TAT-ATTTAATTAAAAATAATA
1097877 TTA
1 TTA
1097880 AAATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 7 0.17
23 6 0.14
24 8 0.19
25 11 0.26
26 8 0.19
27 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATTTAATTAAAAATAATA
Found at i:1100339 original size:16 final size:17
Alignment explanation
Indices: 1100309--1100397 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 17
1100299 ATATTTTATT
1100309 ATATATATTTAAATTAAA
1 ATATA-ATTTAAATTAAA
*
1100327 ATATAATTT-AATTATA
1 ATATAATTTAAATTAAA
*
1100343 ATTTAATTTGATAATGATTAAA
1 ATATAA-TT--TAA--ATTAAA
1100365 A-ATAATTTTATAATTAAA
1 ATATAA-TTTA-AATTAAA
1100383 ATAT--TTTAAA-TAAA
1 ATATAATTTAAATTAAA
1100397 A
1 A
1100398 AATATTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 15 0.25
17 6 0.10
18 12 0.20
19 5 0.08
20 2 0.03
21 6 0.10
22 6 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATAATTTAAATTAAA
Found at i:1100382 original size:18 final size:17
Alignment explanation
Indices: 1100359--1100401 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1100349 TTTGATAATG
1100359 ATTAAAAATAATTTTATA
1 ATTAAAAATAATTTTA-A
1100377 ATT-AAAAT-ATTTTAA
1 ATTAAAAATAATTTTAA
*
1100392 ATAAAAAATA
1 ATTAAAAATA
1100402 TTAATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 11 0.50
17 5 0.23
18 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAAATAATTTTAA
Found at i:1100807 original size:18 final size:17
Alignment explanation
Indices: 1100788--1100850 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
1100778 TTTTAAATAT
1100788 TTTATATTTATATAAAA
1 TTTATATTTATATAAAA
*
1100805 TTTA-ATATAT-TAATAA
1 TTTATATTTATATAA-AA
*
1100821 TTTATA-TTATATAAAT
1 TTTATATTTATATAAAA
*
1100837 TTTAAAATTTATAT
1 TTT-ATATTTATAT
1100851 CATATTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.08
16 18 0.49
17 10 0.27
18 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTATATTTATATAAAA
Found at i:1100840 original size:16 final size:16
Alignment explanation
Indices: 1100786--1100840 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 16
1100776 TTTTTTAAAT
1100786 ATTTTATATTTATATAAA
1 ATTTTATA-TTATAT-AA
1100804 ATTTAATATATTA-AT-A
1 ATTT--TATATTATATAA
1100820 A-TTTATATTATATAA
1 ATTTTATATTATATAA
1100835 ATTTTA
1 ATTTTA
1100841 AAATTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 4 0.12
16 6 0.19
18 6 0.19
19 3 0.09
20 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:1100872 original size:16 final size:16
Alignment explanation
Indices: 1100853--1100911 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
1100843 ATTTATATCA
*
1100853 TATTAATATTATTTTT
1 TATTTATATTATTTTT
*
1100869 TATTTA-ATTATATTT
1 TATTTATATTATTTTT
* * *
1100884 TAATTATTTTATTTTA
1 TATTTATATTATTTTT
1100900 TATTTATATTAT
1 TATTTATATTAT
1100912 ATAATTATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 13 0.38
16 21 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATATTATTTTT
Found at i:1100884 original size:15 final size:14
Alignment explanation
Indices: 1100859--1100922 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1100849 ATCATATTAA
*
1100859 TATTATTTTTTATT
1 TATTATATTTTATT
*
1100873 TAATTATATTTTAAT
1 T-ATTATATTTTATT
* *
1100888 TATTTTATTTTATA
1 TATTATATTTTATT
*
1100902 T-TTATATTATA-T
1 TATTATATTTTATT
*
1100914 AATTATATT
1 TATTATATT
1100923 ACGTCTATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 15 0.38
14 12 0.31
15 12 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATATTTTATT
Found at i:1102597 original size:185 final size:186
Alignment explanation
Indices: 1102284--1102654 Score: 717
Period size: 185 Copynumber: 2.0 Consensus size: 186
1102274 AAAAGAAAAA
1102284 ACTGGTAGAAAGAAAAACCCAACAGAATAGGAAAATCTAGTAATATTTTTTTTTTAATAAAATTT
1 ACTGGTAGAAAGAAAAACCCAACAGAATAGGAAAATCTAGTAATATTTTTTTTTTAATAAAATTT
1102349 TCTTGTTTTTTAAACTTAATTATCTTTTAATTTTGATATATGAATTTGGGTTCCTGCTTAACAAC
66 TCTTGTTTTTTAAACTTAATTATCTTTTAATTTTGATATATGAATTTGGGTTCCTGCTTAACAAC
1102414 TTGGATAATAATTTGGAGTTAATTGAGATGCCCTTTATTTACTTTGGTATCATTTC
131 TTGGATAATAATTTGGAGTTAATTGAGATGCCCTTTATTTACTTTGGTATCATTTC
1102470 ACTGGTAGAAAGAAAAACCCAACAGAATAGGAAAATCTAGTAATA-TTTTTTTTTAATAAAATTT
1 ACTGGTAGAAAGAAAAACCCAACAGAATAGGAAAATCTAGTAATATTTTTTTTTTAATAAAATTT
* *
1102534 TCTTGTTTTTTAAACTTAGTTATTTTTTAATTTTGATATATGAATTTGGGTTCCTGCTTAACAAC
66 TCTTGTTTTTTAAACTTAATTATCTTTTAATTTTGATATATGAATTTGGGTTCCTGCTTAACAAC
1102599 TTGGATAATAATTTGGAGTTAATTGAGATGCCCTTTATTTACTTTGGTATCATTTC
131 TTGGATAATAATTTGGAGTTAATTGAGATGCCCTTTATTTACTTTGGTATCATTTC
1102655 CTTGCATTGT
Statistics
Matches: 183, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 138 0.75
186 45 0.25
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.43
Consensus pattern (186 bp):
ACTGGTAGAAAGAAAAACCCAACAGAATAGGAAAATCTAGTAATATTTTTTTTTTAATAAAATTT
TCTTGTTTTTTAAACTTAATTATCTTTTAATTTTGATATATGAATTTGGGTTCCTGCTTAACAAC
TTGGATAATAATTTGGAGTTAATTGAGATGCCCTTTATTTACTTTGGTATCATTTC
Found at i:1103766 original size:21 final size:19
Alignment explanation
Indices: 1103719--1103769 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
1103709 TCATGCTATT
*
1103719 TTTATATTTAAA-ATTTAA
1 TTTATATTCAAATATTTAA
*
1103737 TTT-TTTTCAAATATTTCATA
1 TTTATATTCAAATATTT-A-A
1103757 TTTATATTCAAAT
1 TTTATATTCAAAT
1103770 CAAAAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 1 0.04
20 4 0.15
21 8 0.31
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTCAAATATTTAA
Found at i:1103874 original size:37 final size:37
Alignment explanation
Indices: 1103822--1103892 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1103812 ACATAGAGTT
* *
1103822 TAATAAAAATTAGGGTAAAAATGTAAAATTAAAACTC
1 TAATAAAAATAAGGGTAAAAATATAAAATTAAAACTC
1103859 TAATAAAAATAAGGGTAAAAATATAAAATTAAAA
1 TAATAAAAATAAGGGTAAAAATATAAAATTAAAA
1103893 GTTTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (37 bp):
TAATAAAAATAAGGGTAAAAATATAAAATTAAAACTC
Found at i:1104036 original size:15 final size:16
Alignment explanation
Indices: 1104007--1104037 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1103997 AAAATTCAAC
1104007 ACTTAATTATTTCAGT
1 ACTTAATTATTTCAGT
1104023 ACTTAATT-TTTCAGT
1 ACTTAATTATTTCAGT
1104038 TTATCAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (16 bp):
ACTTAATTATTTCAGT
Found at i:1104448 original size:29 final size:30
Alignment explanation
Indices: 1104403--1104460 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1104393 ACTAACCCTT
* * *
1104403 TTGATTTTCTTGCCGATTGATACTCCCTAG
1 TTGATTTTCTTACCGATCGACACTCCCTAG
1104433 TTGATTTTC-TACCGATCGACACTCCCTA
1 TTGATTTTCTTACCGATCGACACTCCCTA
1104461 CTGTTAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (30 bp):
TTGATTTTCTTACCGATCGACACTCCCTAG
Found at i:1106386 original size:4 final size:4
Alignment explanation
Indices: 1106377--1106430 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
1106367 TTATTGGTGA
* * *
1106377 AAAG AAAG AAAG AAAG AAAAGG AGAG AAGAA AAAG AATG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG -AAA-G AAAG AA-AG AAAG AAAG AAAG AAAG AAAG
1106428 AAA
1 AAA
1106431 AAAATGCAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 32 0.78
5 8 0.20
6 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:1110859 original size:160 final size:160
Alignment explanation
Indices: 1110678--1110998 Score: 536
Period size: 160 Copynumber: 2.0 Consensus size: 160
1110668 TTTAGATAAA
* * * * *
1110678 ATTAATTTTGTAATTAATGCCATTAGTTTTTTATGAAATATTTAACTATAGTATGTGAAAGAATA
1 ATTAATTTTGTAATTAATGCCATTAGTATTTTATGAAATATTTAACTACACTACGT-AAAAAATA
* *
1110743 TATTTC-AACTAATAAAAATAAAGTGTATTTATTATCAAATTTTAAAGAGGTTTTTATATTATTC
65 TATTTCAAACTAATAAAAATAAAATGTATTTATTATCAAACTTTAAAGAGGTTTTTATATTATTC
*
1110807 AAAATAAATAAAAAGAATTTAGTGTGTTTTT
130 AAAATAAATAAAAAGAATTTAGTATGTTTTT
*
1110838 ATTAATTTTGTAATTAATGCCATTAGTATTTTATGAAATGTTTAACTACACTACGTAAAAAATAT
1 ATTAATTTTGTAATTAATGCCATTAGTATTTTATGAAATATTTAACTACACTACGTAAAAAATAT
*
1110903 CTTTCAAACTAATAAAAATAAAATGTATTTATTATCAAACTTTAAAGAGGTTTTTATATTATTCA
66 ATTTCAAACTAATAAAAATAAAATGTATTTATTATCAAACTTTAAAGAGGTTTTTATATTATTCA
1110968 AAATAAATAAAAAGAATTTAGTATGTTTTT
131 AAATAAATAAAAAGAATTTAGTATGTTTTT
1110998 A
1 A
1110999 AGTGGAATTA
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 12 0.08
160 138 0.92
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (160 bp):
ATTAATTTTGTAATTAATGCCATTAGTATTTTATGAAATATTTAACTACACTACGTAAAAAATAT
ATTTCAAACTAATAAAAATAAAATGTATTTATTATCAAACTTTAAAGAGGTTTTTATATTATTCA
AAATAAATAAAAAGAATTTAGTATGTTTTT
Found at i:1111689 original size:257 final size:259
Alignment explanation
Indices: 1111228--1111744 Score: 914
Period size: 257 Copynumber: 2.0 Consensus size: 259
1111218 GGTAAATTCT
*
1111228 TAGTGCACTTGGTTGACTTGAAACCATGTGATTGGATGGCAAATTTGTTGCCATCTTATTTGCTG
1 TAGTACACTTGGTTGACTTGAAACCATGTGATTGGATGGCAAATTTGTTGCCATCTTATTTGCTG
* *
1111293 CCATGAATCAATCTTTGGCTGCACCCAATGAGCTTTTTTAGTACCAAAAATAGCCCTTAAACACC
66 CCATGAATCAATCTTTGGCAGCACCCAATGAGCTTTTTTAGCACCAAAAATAGCCCTTAAACACC
* * * *
1111358 TGCCAAAGGTGGTGATCAAAGGTCATCAACATGGACGCAGAGATCACCTATACCAAGAACAACTT
131 TGCCAAAAGTGGCGATCAAAGGTCATAAACATGGACGAAGAGATCACCTATACCAAGAACAACTT
1111423 GGTAGAGTGTTACTTCTAT-GGAACTAATCTTCTATTAGGAATAAAATTC-TAAAAGTTGAGAA
196 GGTAGAGTGTTACTTCTATAGGAACTAATCTTCTATTAGGAATAAAATTCTTAAAAGTTGAGAA
1111485 TAGTACACTTGGTTGACTTGAAACCATGTGATTGGATGGCAAATTTGTTGCCATCTTATTTGCTG
1 TAGTACACTTGGTTGACTTGAAACCATGTGATTGGATGGCAAATTTGTTGCCATCTTATTTGCTG
*
1111550 CCATGGATCAATCTTTGGCAGCACCCAATGAG-TTTTTCTAGCACCAAAAATAGCCCTTAAACAC
66 CCATGAATCAATCTTTGGCAGCACCCAATGAGCTTTTT-TAGCACCAAAAATAGCCCTTAAACAC
*
1111614 CTGCCAAAAGTGGCGATCAAAGGTCATAAACATGGCCGAAGAGATCACCTATACCAAGAACAACT
130 CTGCCAAAAGTGGCGATCAAAGGTCATAAACATGGACGAAGAGATCACCTATACCAAGAACAACT
*
1111679 TGGTAGAGTGTTACTTCTATAGGAACTAATCTTCTATTAGGAATAAAATTCTTAGAAGTTGAGAA
195 TGGTAGAGTGTTACTTCTATAGGAACTAATCTTCTATTAGGAATAAAATTCTTAAAAGTTGAGAA
1111744 T
1 T
1111745 TTAATTCCTT
Statistics
Matches: 247, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
256 5 0.02
257 199 0.81
258 30 0.12
259 13 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (259 bp):
TAGTACACTTGGTTGACTTGAAACCATGTGATTGGATGGCAAATTTGTTGCCATCTTATTTGCTG
CCATGAATCAATCTTTGGCAGCACCCAATGAGCTTTTTTAGCACCAAAAATAGCCCTTAAACACC
TGCCAAAAGTGGCGATCAAAGGTCATAAACATGGACGAAGAGATCACCTATACCAAGAACAACTT
GGTAGAGTGTTACTTCTATAGGAACTAATCTTCTATTAGGAATAAAATTCTTAAAAGTTGAGAA
Found at i:1116366 original size:2 final size:2
Alignment explanation
Indices: 1116361--1116391 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1116351 TGTTATGAAC
1116361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1116392 CTTTTGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1119603 original size:31 final size:31
Alignment explanation
Indices: 1119568--1119630 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1119558 TTAACAATTT
1119568 TTATAGTTATTTTTATTTAATGCTTTTGAAA
1 TTATAGTTATTTTTATTTAATGCTTTTGAAA
1119599 TTATAGTTATTTTTATTTAATGCTTTTGAAA
1 TTATAGTTATTTTTATTTAATGCTTTTGAAA
1119630 T
1 T
1119631 GTAACTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.59
Consensus pattern (31 bp):
TTATAGTTATTTTTATTTAATGCTTTTGAAA
Found at i:1123938 original size:24 final size:25
Alignment explanation
Indices: 1123910--1123957 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1123900 ATAGAAAATT
1123910 TCAAAGAAAAAAATAAAA-ATAAAA
1 TCAAAGAAAAAAATAAAATATAAAA
***
1123934 TCAAATTTAAAAATAAAATATAAA
1 TCAAAGAAAAAAATAAAATATAAA
1123958 GAAAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (25 bp):
TCAAAGAAAAAAATAAAATATAAAA
Found at i:1124397 original size:23 final size:24
Alignment explanation
Indices: 1124366--1124413 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1124356 TCAAAATCCC
* *
1124366 TTCAAATTTTTTTG-AATTTTTTT
1 TTCAAATTTTTCTGCAAATTTTTT
*
1124389 TTCATATTTTTCTGCAAATTTTTT
1 TTCAAATTTTTCTGCAAATTTTTT
1124413 T
1 T
1124414 ATTTTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (24 bp):
TTCAAATTTTTCTGCAAATTTTTT
Found at i:1126743 original size:3 final size:3
Alignment explanation
Indices: 1126735--1126769 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1126725 ATGAAATTTT
1126735 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1126770 ATATTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1127499 original size:154 final size:155
Alignment explanation
Indices: 1127146--1127684 Score: 561
Period size: 154 Copynumber: 3.5 Consensus size: 155
1127136 TTCCTTCATG
* * * * * * *
1127146 TTTTTAAGTCCTTT-AGGTTTATTAGGTACTTTTACGTTAAAGGTATCCCTTATGG-GCATCTTG
1 TTTTTAAGTCCTTTAAGG-GTATCAGGTACTTTCACATTGAAGGTATCCCTTA-GGAGCATTTTC
* * * *
1127209 GTAATTTTTTTAGAACCGAGTCTTAGGTGGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATT
64 GTAATTTTTTTAAAACCAAGTCTTAGGTTGTCACC-GGTCCGCTTTTATGCCGAAGGTGGGTATT
*
1127274 TAGGATAGGTTTGTCCCTTTTAAAATCC
128 TAGGATAGGTTCGTCCCTTTTAAAATCC
* * * *
1127302 TTTTTAAGTTCTTTAGGGGTATCGGGTACTCTT-ACGA-TAAAGGTATCCCTTAGGAGCATTTTC
1 TTTTTAAGTCCTTTAAGGGTATCAGGTACT-TTCAC-ATTGAAGGTATCCCTTAGGAGCATTTTC
* * * * * *
1127365 GTAA-TTTTTTATAACCAATTCCTAGGTTGTCACTGGTCCGCTTTTATGCCGAAGGTGAGTGTTT
64 GTAATTTTTTTAAAACCAAGTCTTAGGTTGTCACCGGTCCGCTTTTATGCCGAAGGTGGGTATTT
* * * * *
1127429 AGGATAGGTTCATCTCATCTATAATCC
129 AGGATAGGTTCGTCCCTTTTAAAATCC
* * * * *
1127456 -TTTTAAGTCCTTTAAGGGTACCAAGATACTTTCACATTGAAGGTATCCCTTAGAAGTATTTTTG
1 TTTTTAAGTCCTTTAAGGGTATC-AGGTACTTTCACATTGAAGGTATCCCTTAGGAGCATTTTCG
* * * *
1127520 TAATTTTTTTCAAAACTAAGTCTTAGGTTATCACCGGATCCACTTTTATGCTGAAGGTGGGTATT
65 TAATTTTTTT-AAAACCAAGTCTTAGGTTGTCACCGG-TCCGCTTTTATGCCGAAGGTGGGTATT
1127585 TAGGATAGGTTCGTCCCTTTTAAAATCC
128 TAGGATAGGTTCGTCCCTTTTAAAATCC
* * * * *
1127613 TTTTTTAAGTCCTTTAAGGGTATCAGGTAC-TTCAACGTCGAAGATATCCCCTAGGGGCATTTTC
1 -TTTTTAAGTCCTTTAAGGGTATCAGGTACTTTC-ACATTGAAGGTATCCCTTAGGAGCATTTTC
*
1127677 ATAATTTT
64 GTAATTTT
1127685 ACTTGAACTT
Statistics
Matches: 312, Mismatches: 58, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
153 22 0.07
154 81 0.26
155 32 0.10
156 69 0.22
157 53 0.17
158 34 0.11
159 21 0.07
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (155 bp):
TTTTTAAGTCCTTTAAGGGTATCAGGTACTTTCACATTGAAGGTATCCCTTAGGAGCATTTTCGT
AATTTTTTTAAAACCAAGTCTTAGGTTGTCACCGGTCCGCTTTTATGCCGAAGGTGGGTATTTAG
GATAGGTTCGTCCCTTTTAAAATCC
Found at i:1130773 original size:13 final size:13
Alignment explanation
Indices: 1130752--1130784 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1130742 AATGAATTGA
*
1130752 AGAGAGATACTTG
1 AGAGGGATACTTG
1130765 AGAGGGATACTTG
1 AGAGGGATACTTG
1130778 AGAGGGA
1 AGAGGGA
1130785 AGAGGGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.39, T:0.18
Consensus pattern (13 bp):
AGAGGGATACTTG
Found at i:1130900 original size:27 final size:27
Alignment explanation
Indices: 1130864--1130938 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
1130854 AAACAACATG
*
1130864 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* *
1130891 CCACCATTTTTGACAAACACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
*
1130918 CTACCATTTTTGACAAACAAA
1 CCACCATTTTTGACAAACAAA
1130939 GGGTGACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:1135345 original size:13 final size:13
Alignment explanation
Indices: 1135329--1135362 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1135319 AAAGATACAA
1135329 GAGAGGGATACCT
1 GAGAGGGATACCT
*
1135342 GAGAGGGATACTT
1 GAGAGGGATACCT
1135355 GAGAGGGA
1 GAGAGGGA
1135363 GGAGGGAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.44, T:0.15
Consensus pattern (13 bp):
GAGAGGGATACCT
Found at i:1136504 original size:22 final size:22
Alignment explanation
Indices: 1136489--1136532 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1136479 AAATAGTAAT
1136489 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
*
1136511 TTATTAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
1136533 AGAAGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:1136685 original size:27 final size:27
Alignment explanation
Indices: 1136655--1136710 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1136645 TTAAGTACTT
1136655 ATTTGAATATGTTAGACTAGCAATATA
1 ATTTGAATATGTTAGACTAGCAATATA
**
1136682 ATTTTTATATGTTAGACTAGCAATATA
1 ATTTGAATATGTTAGACTAGCAATATA
1136709 AT
1 AT
1136711 AGAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (27 bp):
ATTTGAATATGTTAGACTAGCAATATA
Found at i:1137668 original size:19 final size:19
Alignment explanation
Indices: 1137644--1137709 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
1137634 TGTCAACGAT
1137644 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1137663 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1137677 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1137695 TTGTATCGATACATA
1 TTGTATCGATACATA
1137710 TGAAGCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1137681 original size:32 final size:32
Alignment explanation
Indices: 1137645--1137707 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1137635 GTCAACGATT
1137645 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1137677 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1137708 TATGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1137682 original size:13 final size:13
Alignment explanation
Indices: 1137664--1137688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1137654 ACATAAGTGT
1137664 TGTATCGATACAA
1 TGTATCGATACAA
1137677 TGTATCGATACA
1 TGTATCGATACA
1137689 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1139996 original size:24 final size:27
Alignment explanation
Indices: 1139969--1140017 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1139959 TCAAAAATTT
1139969 ATTCAT-CG-GGG-ACACTCCAACCAC
1 ATTCATCCGAGGGAACACTCCAACCAC
*
1139993 ATTCTTCCGAGGGAACACTCCAACC
1 ATTCATCCGAGGGAACACTCCAACC
1140018 CCGTTTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 2 0.10
26 3 0.14
27 11 0.52
ACGTcount: A:0.29, C:0.37, G:0.16, T:0.18
Consensus pattern (27 bp):
ATTCATCCGAGGGAACACTCCAACCAC
Found at i:1151717 original size:1 final size:1
Alignment explanation
Indices: 1151711--1151830 Score: 78
Period size: 1 Copynumber: 120.0 Consensus size: 1
1151701 GTCCTTCGCC
* * * * * * * * * * *
1151711 AAAAAAAAAAAAACAAAACAGAAAAGAAAAAAAGAGACAAAAAAAAAACAACAAGAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** *
1151776 AAAAAACAAAAAAAACAAACAAAAAAAAAAGAAAAAAAAAGCAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1151831 GGGTCCGGAT
Statistics
Matches: 84, Mismatches: 35, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1151760 original size:35 final size:34
Alignment explanation
Indices: 1151714--1151824 Score: 143
Period size: 34 Copynumber: 3.2 Consensus size: 34
1151704 CTTCGCCAAA
*
1151714 AAAAAAAAAACAAAACAGAAAAGAAAAAAAGAGAC
1 AAAAAAAAAACAAAA-AGAAAAGAAAAAAAAAGAC
* * *
1151749 AAAAAAAAAACAACAAGAAAACAAAAAAAAAAAC
1 AAAAAAAAAACAAAAAGAAAAGAAAAAAAAAGAC
*
1151783 AAAAAAAACAAACAAAAAAAAAAGAAAAAAAAAG-C
1 -AAAAAAA-AAACAAAAAGAAAAGAAAAAAAAAGAC
1151818 AAAAAAA
1 AAAAAAA
1151825 CAAAAAGGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 23 0.35
35 22 0.33
36 21 0.32
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAACAAAAAGAAAAGAAAAAAAAAGAC
Found at i:1151825 original size:34 final size:35
Alignment explanation
Indices: 1151713--1151828 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 35
1151703 CCTTCGCCAA
* * *
1151713 AAAAAAAAAAACAAAACAGAAAAGAAAAAAAGAGAC
1 AAAAAAACAAACAAAACAAAAAAGAAAAAAAAAG-C
*
1151749 AAAAAAA-AAACAACAAGAAAACAA-AAAAAAAAA-C
1 AAAAAAACAAACAA-AACAAAA-AAGAAAAAAAAAGC
1151783 AAAAAAAACAAACAAAA-AAAAAAGAAAAAAAAAGC
1 -AAAAAAACAAACAAAACAAAAAAGAAAAAAAAAGC
1151818 AAAAAAACAAA
1 AAAAAAACAAA
1151829 AAGGGTCCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
33 2 0.03
34 25 0.35
35 16 0.23
36 26 0.37
37 2 0.03
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (35 bp):
AAAAAAACAAACAAAACAAAAAAGAAAAAAAAAGC
Found at i:1153301 original size:28 final size:28
Alignment explanation
Indices: 1153261--1153494 Score: 333
Period size: 28 Copynumber: 8.1 Consensus size: 28
1153251 CATCCCTCAC
1153261 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1153289 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1153317 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1153345 CCTTTTCCAAAGCCCACAAATCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
* *
1153375 CCTTCAAAAGCCAACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1153403 CCTTTTCAAAAGCCCACAAGTCAGTGGCAC
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
* *
1153433 CCTTTTCCAAAGCCCACAAATCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
*
1153463 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1153491 CCTT
1 CCTT
1153495 TTCTGAAGCC
Statistics
Matches: 187, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
28 108 0.58
30 79 0.42
ACGTcount: A:0.33, C:0.34, G:0.16, T:0.17
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1153449 original size:88 final size:88
Alignment explanation
Indices: 1153267--1153526 Score: 427
Period size: 88 Copynumber: 3.0 Consensus size: 88
1153257 TCACCCTTCA
* *
1153267 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCC
1153330 ACAAGTCAGTGGCACCCTTTTCC
66 ACAAGTCAGTGGCACCCTTTTCC
*
1153353 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCAACAAGTCAGTGGCACCCTTTTCAAAAGCCC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCC
1153418 ACAAGTCAGTGGCACCCTTTTCC
66 ACAAGTCAGTGGCACCCTTTTCC
**
1153441 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTGAAGCCC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCC
* *
1153506 ACAATTCCA-TGGCACCATTTT
66 ACAAGT-CAGTGGCACCCTTTT
1153527 TCTTTTTAAG
Statistics
Matches: 163, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
86 49 0.30
88 112 0.69
89 2 0.01
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.18
Consensus pattern (88 bp):
AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCC
ACAAGTCAGTGGCACCCTTTTCC
Found at i:1153519 original size:58 final size:57
Alignment explanation
Indices: 1153261--1153494 Score: 337
Period size: 58 Copynumber: 4.1 Consensus size: 57
1153251 CATCCCTCAC
1153261 CCTTCAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
1153317 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
1153375 CCTTCAAAAGCCAACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
1153433 CCTTTTCCAAAGCCCACAAATCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCAC
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCAA
1153491 CCTT
1 CCTT
1153495 TTCTGAAGCC
Statistics
Matches: 163, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
56 31 0.19
58 108 0.66
60 24 0.15
ACGTcount: A:0.33, C:0.34, G:0.16, T:0.17
Consensus pattern (57 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1153540 original size:34 final size:34
Alignment explanation
Indices: 1153500--1153596 Score: 151
Period size: 34 Copynumber: 2.9 Consensus size: 34
1153490 CCCTTTTCTG
* *
1153500 AAGCCCACAATTCCATGGCAC-CATTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTC-TTTTTCTTTTT
*
1153534 AAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
1153568 AAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAGCCCACAACTCCGTGGCACTCTTTTTC
1153597 CTTCTAAGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 57 0.98
35 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
Found at i:1153620 original size:34 final size:34
Alignment explanation
Indices: 1153495--1153622 Score: 132
Period size: 34 Copynumber: 3.7 Consensus size: 34
1153485 TGGCACCCTT
* ** *
1153495 TTCTGAAGCCCACAATTCCATGGCAC-CATTTTTCT
1 TTCT-AAGCCCACAACTCTGTGGCACTC-TTTTTCC
* *
1153530 TTTTAAGCCCACAACTCTGTGGCACTCTTTTTCT
1 TTCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
* *
1153564 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 TTCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
* * *
1153598 TTCTAAGTCCACGAGTCTGTGGCAC
1 TTCTAAGCCCACAACTCTGTGGCAC
1153623 CCTTATCTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
34 77 0.95
35 4 0.05
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (34 bp):
TTCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
Found at i:1153694 original size:43 final size:43
Alignment explanation
Indices: 1153629--1153720 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
1153619 GCACCCTTAT
* *
1153629 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * ** *
1153672 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1153715 CTTTAA
1 CTTTAA
1153721 CATCCCTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1153803 original size:47 final size:48
Alignment explanation
Indices: 1153725--1153968 Score: 186
Period size: 47 Copynumber: 4.9 Consensus size: 48
1153715 CTTTAACATC
* * **
1153725 CCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGACATTTTTCT
1 CCTAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACATTTTTCT
* *
1153773 CC-AAGCCTAATGCCGTTGACCGTGAATCAGCACATTGACATCCTTTTTCT
1 CCTAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACA---TTTTTCT
* * * ** *
1153823 CATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAACAT
1 C--C--TAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACATTTTT--C-T
* * ** *
1153878 CCCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCT
1 -CCTAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACATTTTTCT
* * * *
1153927 -CTAAGTCTAATGTCGCTGACCGCGAATCAGCACATTGACATT
1 CCTAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACATT
1153969 CTTTACATCT
Statistics
Matches: 155, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
47 66 0.43
48 2 0.01
49 1 0.01
50 9 0.06
52 43 0.28
54 2 0.01
55 31 0.20
56 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (48 bp):
CCTAAGCCCAATGTCGTTGACCGTGAATCAGCACATTGACATTTTTCT
Found at i:1153889 original size:52 final size:52
Alignment explanation
Indices: 1153675--1153989 Score: 238
Period size: 52 Copynumber: 6.2 Consensus size: 52
1153665 TTGGCACCTT
* * ** * *
1153675 TAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATTTTTAACATCCC
**
1153727 TAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGACATTTTT--C-T-CC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATTTTTAACATCCC
* * * * ** **
1153775 -AAGCCTAATGCCGTTGACCGTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACA---TTTTTAACATCCC
* ** *
1153829 TAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAACATCCC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATTTTTAACATCCC
** *
1153881 TAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTT--C-T--C
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATTTTTAACATCCC
* * * * ** **
1153928 TAAGTCTAATGTCGCTGACCGCGAATCAGCACATTGACATTCTTT-ACATCTT
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATT-TTTAACATCCC
1153980 TAAGCCCAAT
1 TAAGCCCAAT
1153990 ATCACTGGTC
Statistics
Matches: 203, Mismatches: 47, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
47 66 0.33
48 4 0.02
49 3 0.01
50 8 0.04
52 91 0.45
53 1 0.00
55 30 0.15
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (52 bp):
TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATTTTTAACATCCC
Found at i:1153954 original size:154 final size:151
Alignment explanation
Indices: 1153672--1154024 Score: 528
Period size: 154 Copynumber: 2.3 Consensus size: 151
1153662 ACATTGGCAC
*
1153672 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAAT
1 CTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAAT
* * *
1153737 GTCGTTGGCCTTGTCTCAGCACATTGACATTTTTCTCCAAGCCTAATGCCGTTGACCGTGAATCA
66 GTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGCCTAATGCCGCTGACCGCGAATCA
* *
1153802 GCACATTGACATCCTTTTTCTCAT
131 GCACATTGACAT--TCTTT-ACAT
*
1153826 CTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAACATCCCTAAGCCCAAT
1 CTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAAT
* * *
1153891 GTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCTAAGTCTAATGTCGCTGACCGCGAATCA
66 GTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGCCTAATGCCGCTGACCGCGAATCA
1153956 GCACATTGACATTCTTTACAT
131 GCACATTGACATTCTTTACAT
** * * *
1153977 CTTTAAGCCCAATATCACTGGTCC-TGAATCAACATATTGGCACCTTTA
1 CTTTAAGCCCAATATCGTTGG-CCTTGAATCAGCGTATTGGCATCTTTA
1154025 TCACTTTTCT
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
151 42 0.23
152 6 0.03
154 134 0.74
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (151 bp):
CTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAAT
GTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGCCTAATGCCGCTGACCGCGAATCA
GCACATTGACATTCTTTACAT
Found at i:1155055 original size:19 final size:19
Alignment explanation
Indices: 1155031--1155128 Score: 112
Period size: 19 Copynumber: 5.8 Consensus size: 19
1155021 TGTCAACGAT
1155031 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1155050 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1155064 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1155082 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1155096 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1155114 TTGTATCGATACATA
1 TTGTATCGATACATA
1155129 TGAAGCTACT
Statistics
Matches: 67, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 37 0.55
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1155068 original size:32 final size:32
Alignment explanation
Indices: 1155032--1155126 Score: 190
Period size: 32 Copynumber: 3.0 Consensus size: 32
1155022 GTCAACGATT
1155032 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1155064 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1155096 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1155127 TATGAAGCTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1155069 original size:13 final size:13
Alignment explanation
Indices: 1155051--1155107 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1155041 ACATAAGTGT
1155051 TGTATCGATACAA
1 TGTATCGATACAA
1155064 TGTATCGATACATAA
1 TGTATCGATAC--AA
1155079 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1155096 TGTATCGATACA
1 TGTATCGATACA
1155108 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1155193 original size:33 final size:33
Alignment explanation
Indices: 1155151--1155214 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
1155141 CAAGAAAATG
*
1155151 TATCGATACA-TTACTCTTTGTATCGATACATTA
1 TATCGATACACTGA-TCTTTGTATCGATACATTA
1155184 TATCGATACACTGATCTTTGTATCGATACAT
1 TATCGATACACTGATCTTTGTATCGATACAT
1155215 GCAGGCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (33 bp):
TATCGATACACTGATCTTTGTATCGATACATTA
Found at i:1159599 original size:155 final size:155
Alignment explanation
Indices: 1159183--1159822 Score: 472
Period size: 155 Copynumber: 4.1 Consensus size: 155
1159173 TACGAAAATG
* * **
1159183 CCCCTAGGGGATAACTTCGACATAAA-A--A-TACCTGATACCCCTAAAGGACTTAAAAAGGATT
1 CCCCTAAGGGATACCTTCGACATAAAGATGAGTACCCAATA-CCCTAAAGGACTTAAAAA-GA-T
* * * * *
1159244 ATAGAAGGGATGAACCTACCCTAAATATCTACCTTCGACATAAAAGCAGACCCAGTGACAACCTA
63 ATAGATGGGATGAACCTATCCTAAATATC-ACCTTTGACATAAAAACGGACCCAGTGACAACCTA
* *
1159309 GGATTTGATTCTAAAAAATTACGAAATTA
127 GGACTTGATTCTAAAAAATTATGAAATTA
1159338 CCCCTAAGGGATACCTTCGACATAAAGTACTGAGTACCCAATACTCCTAAAGGACTTAAAAAGAT
1 CCCCTAAGGGATACCTTCGACATAAAG-A-TGAGTACCCAATAC-CCTAAAGGACTTAAAAAGAT
* * * * *
1159403 -TAGAAATGGGATGAACCTATCCTAAAT-GCCCACTTTCGACATAAAAATGGACCCAATGACGAC
63 ATAG--ATGGGATGAACCTATCCTAAATATCAC-CTTT-GACATAAAAACGGACCCAGTGACAAC
* *
1159466 CTAGGAGTTGGTT-TAAAAAATTATGAAATTA
124 CTAGGACTTGATTCTAAAAAATTATGAAATTA
* * * * ** *
1159497 CCCCTATGGGTTTACTTTCGACGTGAAAG-T-A-T-CCCGGTAACCCTAAAAGACTTAAAACAGA
1 CCCCTAAGGG-ATACCTTCGACAT-AAAGATGAGTACCCAAT-ACCCTAAAGGACTTAAAA-AGA
* * * *
1159558 TATAGATTGGG-TGAACCTATCCGAAATAATCACCTTTGACATGAAAACGGATCTAGTGACAACC
62 TATAGA-TGGGATGAACCTATCCTAAAT-ATCACCTTTGACATAAAAACGGACCCAGTGACAACC
* * *
1159622 TAGGACTCGATTCTAAAAAATTATGAAAATG
125 TAGGACTTGATTCTAAAAAATTATGAAATTA
* * * *
1159653 CCCCT-AGAGGATA-TTTCGA-ATAAA-A--A-TACCCAATACTCTTAAAAGATTTAAAAAGATT
1 CCCCTAAG-GGATACCTTCGACATAAAGATGAGTACCCAATAC-CCTAAAGGACTTAAAAAGA-T
* * * * * * * ** *
1159711 CATAAAAGGGATGAATCTATCCTAAATATCTACATTTGGCATAAAAGCGGACCCGGCAACGACCT
63 -ATAGATGGGATGAACCTATCCTAAATATC-ACCTTTGACATAAAAACGGACCCAGTGACAACCT
* * * **
1159776 AGGAGTTGGTTCTAAAAAATTATAAAAAGA
126 AGGACTTGATTCTAAAAAATTATGAAATTA
* *
1159806 CCCATAGGGGATACCTT
1 CCCCTAAGGGATACCTT
1159823 TAACGTAAAA
Statistics
Matches: 387, Mismatches: 68, Indels: 61
0.75 0.13 0.12
Matches are distributed among these distances:
151 7 0.02
152 28 0.07
153 76 0.20
154 9 0.02
155 92 0.24
156 38 0.10
157 7 0.02
158 5 0.01
159 31 0.08
160 66 0.17
161 28 0.07
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (155 bp):
CCCCTAAGGGATACCTTCGACATAAAGATGAGTACCCAATACCCTAAAGGACTTAAAAAGATATA
GATGGGATGAACCTATCCTAAATATCACCTTTGACATAAAAACGGACCCAGTGACAACCTAGGAC
TTGATTCTAAAAAATTATGAAATTA
Found at i:1159885 original size:155 final size:154
Alignment explanation
Indices: 1159672--1160015 Score: 429
Period size: 155 Copynumber: 2.2 Consensus size: 154
1159662 GATATTTCGA
* * * *
1159672 ATAAAAATACCCAATACTCTTAAAAGATTTAAAAAGATTCATAAAAGGGATGAATCTATCCTAAA
1 ATAAAAGTACCCGATACCCTTAAGAGATTTAAAAAGATTCATAAAAGGGATGAATCTATCCTAAA
* * * * *
1159737 TATCTACATTTGGCATAAAAGCGGACCCGGCAACGACCTAGGAGTTGGTTCTAAAAAATTATAAA
66 TATCTACATTCGGCATAAAAGCAGACCCGACAACGACATAGGAGTTAGTTCTAAAAAATTATAAA
*
1159802 AAGACCCATAGGGGATACCTTTAAC
131 AAGACCCATA-GAGATACCTTTAAC
* * * *
1159827 GTAAAAGTACCCGATACCCCTAAGAGATTTAAAGAGGATT-TTAAAAGGGATGAATCTATCCTAA
1 ATAAAAGTACCCGATACCCTTAAGAGATTTAAA-AAGATTCATAAAAGGGATGAATCTATCCTAA
* * * * *
1159891 ATATCTACATTCGGCATAAAAGCATACTCGACGATGATATAGGAGTTAGTTCTAAAAAATTATAA
65 ATATCTACATTCGGCATAAAAGCAGACCCGACAACGACATAGGAGTTAGTTCTAAAAAATTATAA
* * *
1159956 AAATACCCCTAGAGATACCTTTGAC
130 AAAGACCCATAGAGATACCTTTAAC
** * *
1159981 ATAAAAGTACTTGATGCCCTTAAGGGATTTAAAAA
1 ATAAAAGTACCCGATACCCTTAAGAGATTTAAAAA
1160016 CATAAGAGAA
Statistics
Matches: 159, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
153 1 0.01
154 39 0.25
155 114 0.72
156 5 0.03
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (154 bp):
ATAAAAGTACCCGATACCCTTAAGAGATTTAAAAAGATTCATAAAAGGGATGAATCTATCCTAAA
TATCTACATTCGGCATAAAAGCAGACCCGACAACGACATAGGAGTTAGTTCTAAAAAATTATAAA
AAGACCCATAGAGATACCTTTAAC
Found at i:1160597 original size:166 final size:166
Alignment explanation
Indices: 1160229--1160651 Score: 495
Period size: 166 Copynumber: 2.5 Consensus size: 166
1160219 GATAATTTTT
* * * * * *
1160229 ATTTGATTTTTTTCATTTAC-AAAAATTC-ATTTCGTACCTTAATGG-AATTCCAAAAAGATATG
1 ATTTAATTTTATTCATTTTCGAAAAATACTATTTCGTACCTTAATGGAAACT-CGAAAAGATATG
1160291 AAAAGTTTTTTAAAATCTTTTATACCCCTACGGACCCCCATAGGAATATAAAAGATTAGAAAAGA
65 AAAAG--TTTTAAAATCTTTTATACCCCTACGGACCCCCATAGGAATATAAAAGATTAGAAAAGA
** * *
1160356 AAGATTTAAATTTATCTTGGTTATGAAAGTGTTGATTTA
128 AAGATTTAAATTTATCTTAATTATGAAAGTATTAATTTA
** *
1160395 ATTTAATTTTATTTGTTTTCGAAAAATA-TCATTTCGTACCTTAATGGAAACTCGAAAAGATACG
1 ATTTAATTTTATTCATTTTCGAAAAATACT-ATTTCGTACCTTAATGGAAACTCGAAAAGATATG
** *
1160459 AAAAGTTTTAAAATCTTTTATACCTTTACGGA-CCCCATAGGAATATAAAAGATTA-AAAA-AAT
65 AAAAGTTTTAAAATCTTTTATACCCCTACGGACCCCCATAGGAATATAAAAGATTAGAAAAGAAA
1160521 GA-TTAATATTTAT-TTCAATTATGAAAGTATTAATTTA
130 GATTTAA-ATTTATCTT-AATTATGAAAGTATTAATTTA
* * * *
1160558 ATTTTATTTATTTATTCATTTTTGAAAAATACTATTTCGTACTTTAATGGAAACCCGAAAAGATA
1 A-TTTA-AT-TTTATTCATTTTCGAAAAATACTATTTCGTACCTTAATGGAAACTCGAAAAGATA
* *
1160623 TGAAAAGTTTTTAAATATTTCTATACCCC
63 TGAAAAGTTTTAAAATCTTT-TATACCCC
1160652 ACAGATACCT
Statistics
Matches: 219, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
162 6 0.03
163 28 0.13
164 8 0.04
165 24 0.11
166 105 0.48
167 13 0.06
168 32 0.15
169 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (166 bp):
ATTTAATTTTATTCATTTTCGAAAAATACTATTTCGTACCTTAATGGAAACTCGAAAAGATATGA
AAAGTTTTAAAATCTTTTATACCCCTACGGACCCCCATAGGAATATAAAAGATTAGAAAAGAAAG
ATTTAAATTTATCTTAATTATGAAAGTATTAATTTA
Found at i:1161666 original size:16 final size:16
Alignment explanation
Indices: 1161645--1161753 Score: 103
Period size: 16 Copynumber: 6.8 Consensus size: 16
1161635 TCCAAATTCA
1161645 AAATGACCCGAACCCG
1 AAATGACCCGAACCCG
* *
1161661 AAATGACTCGAATCC-
1 AAATGACCCGAACCCG
*
1161676 AGAATAACCCGAACCCG
1 A-AATGACCCGAACCCG
* * **
1161693 AAATGACTCGAATCTA
1 AAATGACCCGAACCCG
*
1161709 AAATGACCTGAACCCG
1 AAATGACCCGAACCCG
* *
1161725 AAATGACCCGAATCCA
1 AAATGACCCGAACCCG
*
1161741 AAATGACCTGAAC
1 AAATGACCCGAAC
1161754 TTAAATTAAG
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
15 1 0.01
16 69 0.97
17 1 0.01
ACGTcount: A:0.41, C:0.29, G:0.16, T:0.14
Consensus pattern (16 bp):
AAATGACCCGAACCCG
Found at i:1161691 original size:32 final size:32
Alignment explanation
Indices: 1161643--1161753 Score: 150
Period size: 32 Copynumber: 3.5 Consensus size: 32
1161633 AATCCAAATT
*
1161643 CAAAATGACCCGAACCCGAAATGACTCGAATC
1 CAAAATAACCCGAACCCGAAATGACTCGAATC
*
1161675 CAGAATAACCCGAACCCGAAATGACTCGAATC
1 CAAAATAACCCGAACCCGAAATGACTCGAATC
* * * *
1161707 TAAAATGACCTGAACCCGAAATGACCCGAATC
1 CAAAATAACCCGAACCCGAAATGACTCGAATC
* *
1161739 CAAAATGACCTGAAC
1 CAAAATAACCCGAAC
1161754 TTAAATTAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.14
Consensus pattern (32 bp):
CAAAATAACCCGAACCCGAAATGACTCGAATC
Found at i:1162826 original size:32 final size:32
Alignment explanation
Indices: 1162781--1162901 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
1162771 AACTCGATTG
*
1162781 ACCCGAACCCGAAATGACTCGAATCTGAAATA
1 ACCCGAACCCGAAATGACTCGAACCTGAAATA
* * *
1162813 ACTCGAACTCGAAATGACTTGAACCTGAAATA
1 ACCCGAACCCGAAATGACTCGAACCTGAAATA
* * * * *
1162845 ACCCGAATCTGAAGTGACTCGAACCCGAAATG
1 ACCCGAACCCGAAATGACTCGAACCTGAAATA
*
1162877 ACCCGAACCCAAAATGACTCGAACC
1 ACCCGAACCCGAAATGACTCGAACC
1162902 CAAAAACAAC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.16
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACTCGAACCTGAAATA
Found at i:1162885 original size:48 final size:48
Alignment explanation
Indices: 1162779--1162891 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 48
1162769 TAAACTCGAT
* * *
1162779 TGACCCGAACCCGAAATGACTCGAATCTGAAATAACTCGAACTCGAAA
1 TGACCCGAACCCGAAATAACCCGAATCTGAAATAACTCGAACCCGAAA
** * * *
1162827 TGACTTGAACCTGAAATAACCCGAATCTGAAGTGACTCGAACCCGAAA
1 TGACCCGAACCCGAAATAACCCGAATCTGAAATAACTCGAACCCGAAA
*
1162875 TGACCCGAACCCAAAAT
1 TGACCCGAACCCGAAAT
1162892 GACTCGAACC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (48 bp):
TGACCCGAACCCGAAATAACCCGAATCTGAAATAACTCGAACCCGAAA
Found at i:1162902 original size:32 final size:32
Alignment explanation
Indices: 1162781--1162916 Score: 146
Period size: 32 Copynumber: 4.2 Consensus size: 32
1162771 AACTCGATTG
* *
1162781 ACCCGAACCCGAAATGACTCGAATCTGAAATA
1 ACCCGAACCCGAAATGACTCGAACCCGAAATA
* * * *
1162813 ACTCGAACTCGAAATGACTTGAACCTGAAATA
1 ACCCGAACCCGAAATGACTCGAACCCGAAATA
* * * *
1162845 ACCCGAATCTGAAGTGACTCGAACCCGAAATG
1 ACCCGAACCCGAAATGACTCGAACCCGAAATA
* * *
1162877 ACCCGAACCCAAAATGACTCGAACCCAAAAACA
1 ACCCGAACCCGAAATGACTCGAACCC-GAAATA
1162910 ACCCGAA
1 ACCCGAA
1162917 ACTTTTATAA
Statistics
Matches: 84, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
32 74 0.88
33 10 0.12
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.14
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACTCGAACCCGAAATA
Found at i:1162906 original size:16 final size:16
Alignment explanation
Indices: 1162779--1162902 Score: 122
Period size: 16 Copynumber: 7.8 Consensus size: 16
1162769 TAAACTCGAT
*
1162779 TGACCCGAACCCGAAA
1 TGACTCGAACCCGAAA
* *
1162795 TGACTCGAATCTGAAA
1 TGACTCGAACCCGAAA
* *
1162811 TAACTCGAACTCGAAA
1 TGACTCGAACCCGAAA
* *
1162827 TGACTTGAACCTGAAA
1 TGACTCGAACCCGAAA
* * * * *
1162843 TAACCCGAATCTGAAG
1 TGACTCGAACCCGAAA
1162859 TGACTCGAACCCGAAA
1 TGACTCGAACCCGAAA
* *
1162875 TGACCCGAACCCAAAA
1 TGACTCGAACCCGAAA
1162891 TGACTCGAACCC
1 TGACTCGAACCC
1162903 AAAAACAACC
Statistics
Matches: 84, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 84 1.00
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.16
Consensus pattern (16 bp):
TGACTCGAACCCGAAA
Found at i:1164113 original size:18 final size:19
Alignment explanation
Indices: 1164078--1164119 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1164068 TTTCAAGGAA
*
1164078 AAATTCAATTTATGAAAAT
1 AAATTCAATTTATAAAAAT
*
1164097 AAATT-AATTTTTAAAAAT
1 AAATTCAATTTATAAAAAT
*
1164115 TAATT
1 AAATT
1164120 TAATATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTCAATTTATAAAAAT
Found at i:1164175 original size:163 final size:165
Alignment explanation
Indices: 1163841--1164224 Score: 445
Period size: 163 Copynumber: 2.3 Consensus size: 165
1163831 ATTTTCGACC
* * * * **
1163841 AAAAAAATCCT-CCTAAAAATATTTATGGAATA-AAAAATTCAGTTTTTCAAAAACAAGAGAATT
1 AAAAAAATCCTCCCGAAAAA-ATTTACGGAGTAGAAAACTTCA-TTTTTTGAAAACAAGAGAATT
* * * * *
1163904 TCAAGGAAAAATTCAAATATTTATGAAAATGAATGCACTTTTGAAAACTGATTTACTATAAATTA
64 TCAAGGAAAAATTC-AATATTTATGAAAATAAATGAACTTTTAAAAACTAATTTAATATAAATTA
*
1163969 AATAATAATATTTGATAAATTTAAAAAAATAAAAACTA
128 AATAACAATATTTGATAAATTTAAAAAAATAAAAACTA
*
1164007 AAAAAAATCCTCCCGAAAAAATTTACGGAGTAGAAAACTTCATTTTTTGAAAATAAGAGAATTTC
1 AAAAAAATCCTCCCGAAAAAATTTACGGAGTAGAAAACTTCATTTTTTGAAAACAAGAGAATTTC
* * * *
1164072 AAGGAAAAATTC-A-ATTTATGAAAATAAATTAATTTTTAAAAATTAATTTAATATGAATTAAAT
66 AAGGAAAAATTCAATATTTATGAAAATAAATGAACTTTTAAAAACTAATTTAATATAAATTAAAT
* * **
1164135 AACAATATTTGATGAATTTTAAAATTTAAAAA-TAA
131 AACAATATTTGATAAATTTAAAAAAATAAAAACT-A
* ** * * **
1164170 AAAAAAATTCTCTTGAAAAAATTTACGGAGAAGAAAACCTCATAATTTGAAAACA
1 AAAAAAATCCTCCCGAAAAAATTTACGGAGTAGAAAACTTCATTTTTTGAAAACA
1164225 TAAGGAATTC
Statistics
Matches: 186, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
162 1 0.01
163 116 0.62
164 1 0.01
166 53 0.28
167 15 0.08
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (165 bp):
AAAAAAATCCTCCCGAAAAAATTTACGGAGTAGAAAACTTCATTTTTTGAAAACAAGAGAATTTC
AAGGAAAAATTCAATATTTATGAAAATAAATGAACTTTTAAAAACTAATTTAATATAAATTAAAT
AACAATATTTGATAAATTTAAAAAAATAAAAACTA
Found at i:1167202 original size:2 final size:2
Alignment explanation
Indices: 1167191--1167250 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
1167181 ACAATAACTT
*
1167191 TA TA -A TA TA TA TA CA TA TA T- TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1167228 TA T- TA TA TA TA AA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1167251 CACGCACATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
1 6 0.13
2 41 0.87
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1167214 original size:5 final size:5
Alignment explanation
Indices: 1167206--1167235 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1167196 TATATATACA
1167206 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
1167236 ATAAACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1167214 original size:15 final size:14
Alignment explanation
Indices: 1167191--1167239 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1167181 ACAATAACTT
*
1167191 TATAATATATATACA
1 TATAATATAT-TATA
*
1167206 TATATTATATTATA
1 TATAATATATTATA
*
1167220 TTATATTATATTATA
1 -TATAATATATTATA
1167235 TATAA
1 TATAA
1167240 ACATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATAATATATTATA
Found at i:1167461 original size:4 final size:4
Alignment explanation
Indices: 1167452--1167477 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1167442 ATCACATCTC
1167452 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
1167478 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:1168160 original size:63 final size:62
Alignment explanation
Indices: 1168076--1168197 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 62
1168066 AAGTTTGGGT
* * * *
1168076 TTTTACTGATTATAAGAAAAATAAGGGTTGCGATTACTAAAGGGAAAAAATTAGGTTTTGAGA
1 TTTTACTGATGATAAGAAAAATAAGAGTTGCGACTACTAAA-GGAAAAAAATAGGTTTTGAGA
* *
1168139 TTTTACTGATGCTAAGGAAAATAAGAGTTGCGACTACTAAAGGAAAAAAATAGGTTTTG
1 TTTTACTGATGATAAGAAAAATAAGAGTTGCGACTACTAAAGGAAAAAAATAGGTTTTG
1168198 GGTTTTAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 17 0.32
63 36 0.68
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (62 bp):
TTTTACTGATGATAAGAAAAATAAGAGTTGCGACTACTAAAGGAAAAAAATAGGTTTTGAGA
Found at i:1168763 original size:16 final size:16
Alignment explanation
Indices: 1168736--1168804 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
1168726 TGAAAAAGCT
* *
1168736 CAAACACGAATAA-GT
1 CAAACTCGAATAAGGC
1168751 CAGAACTCGAATAAGGC
1 CA-AACTCGAATAAGGC
*
1168768 CAAACTCGAATAGGGC
1 CAAACTCGAATAAGGC
* *
1168784 CGAACCCGAAT-AGGCC
1 CAAACTCGAATAAGG-C
1168800 CAAAC
1 CAAAC
1168805 CCAAAAGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.09
16 37 0.84
17 3 0.07
ACGTcount: A:0.42, C:0.28, G:0.20, T:0.10
Consensus pattern (16 bp):
CAAACTCGAATAAGGC
Found at i:1169494 original size:19 final size:19
Alignment explanation
Indices: 1169466--1169527 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1169456 TATTTTTTTA
*
1169466 TTTAATAAAATAATAATTT
1 TTTAAAAAAATAATAATTT
* *
1169485 TTTAAAAAAATTATAGTTTT
1 TTTAAAAAAATAATA-ATTT
* *
1169505 TTTAAAAAAATGATAGTTT
1 TTTAAAAAAATAATAATTT
1169524 TTTA
1 TTTA
1169528 TTTGAGTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
TTTAAAAAAATAATAATTT
Found at i:1169507 original size:20 final size:20
Alignment explanation
Indices: 1169482--1169526 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1169472 AAAATAATAA
*
1169482 TTTTTTAAAAAAATTATAGT
1 TTTTTTAAAAAAATGATAGT
1169502 TTTTTTAAAAAAATGATAGT
1 TTTTTTAAAAAAATGATAGT
1169522 TTTTT
1 TTTTT
1169527 ATTTGAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTTTAAAAAAATGATAGT
Found at i:1170887 original size:32 final size:32
Alignment explanation
Indices: 1170846--1170909 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1170836 TTTTTTTGAA
* *
1170846 GAGTAAGGTTAGAGTGTCCCCTCGGAGGAATG
1 GAGTAAGGTTAGAGTGTCCCCTCAGACGAATG
*
1170878 GAGTAAGGTTAGAGTGTTCCCTCAGACGAATG
1 GAGTAAGGTTAGAGTGTCCCCTCAGACGAATG
1170910 AGATGGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (32 bp):
GAGTAAGGTTAGAGTGTCCCCTCAGACGAATG
Found at i:1171138 original size:97 final size:99
Alignment explanation
Indices: 1170958--1171149 Score: 223
Period size: 97 Copynumber: 2.0 Consensus size: 99
1170948 ATTTGATTTT
* *
1170958 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAGTGGGGATGGAGCTTCCCCAAAGGTAAAAT
1 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAATGGGGATGGAGCTTCCCCAAAGGAAAAAT
** * *
1171023 TATATTAAGGAAATTTTGA-TTTTTTGAAAGAAA
66 TATACGAAGAAAAATTTGATTTTTTTGAAAGAAA
* * * * *
1171056 TCTT-AAAGAAGGGTTGGAATGTCCT-TTCGAAGGAATGGGGATGGCA-TTTCTCCAAA-GAAAA
1 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAG-AGGAATGGGGATGG-AGCTTCCCCAAAGGAAAA
1171117 AGTTATACGAAGAAAAATTTGATTTTTTTGAAA
64 A-TTATACGAAGAAAAATTTGATTTTTTTGAAA
1171150 AACGAGGTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
96 8 0.10
97 56 0.71
98 15 0.19
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (99 bp):
TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAATGGGGATGGAGCTTCCCCAAAGGAAAAAT
TATACGAAGAAAAATTTGATTTTTTTGAAAGAAA
Found at i:1173428 original size:21 final size:20
Alignment explanation
Indices: 1173386--1173435 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1173376 CAGGTTAATA
*
1173386 TATCGATACATAAGTGAATG
1 TATCGATATATAAGTGAATG
1173406 TATCGATATATGAA-TGCAATG
1 TATCGATATAT-AAGTG-AATG
1173427 TATCGATAT
1 TATCGATAT
1173436 TGGACCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATATATAAGTGAATG
Found at i:1173526 original size:20 final size:21
Alignment explanation
Indices: 1173473--1173529 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
1173463 TTCTAAAAAA
**
1173473 ATTGTATTGATACATGCTTGC
1 ATTGTATTGATACATTATTGC
* **
1173494 AATGTATCAATACATTATT-C
1 ATTGTATTGATACATTATTGC
1173514 ATTGTATTGATACATT
1 ATTGTATTGATACATT
1173530 CTGGGTTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
ATTGTATTGATACATTATTGC
Found at i:1174337 original size:27 final size:22
Alignment explanation
Indices: 1174276--1174350 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
1174266 CAGACTTGTC
*
1174276 ACTTTCATTTTTTATTTTAGCT
1 ACTTTCATCTTTTATTTTAGCT
1174298 ACTTTCATCTTTTATTTTAGCT
1 ACTTTCATCTTTTATTTTAGCT
* *
1174320 ACTTTCATCTTCTGTTTTAGCT
1 ACTTTCATCTTTTATTTTAGCT
*
1174342 ACTTCCATC
1 ACTTTCATC
1174351 ATCTTAGTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.56
Consensus pattern (22 bp):
ACTTTCATCTTTTATTTTAGCT
Found at i:1177719 original size:68 final size:68
Alignment explanation
Indices: 1177562--1177914 Score: 252
Period size: 68 Copynumber: 5.2 Consensus size: 68
1177552 GGGAATTGAG
* * * * * * *
1177562 GTAGATGGGTGCCACAAGCTTGTGTGGGCTTTGAGAAAGAAAAAAAGCGTCCTGCTCCCTAGGGA
1 GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTAAGGAA-AAAAATA-CATCCTGCTCCTTAAGGA
*
1177627 -TTGA
64 CTAGA
* * * *
1177631 GGTAGATAAGTGCCATAAGCTTGTGTGGGCTTTAAGGAAAAAAATACATCTTGCTTCTTAAGGAC
1 -GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTAAGGAAAAAAATACATCCTGCTCCTTAAGGAC
1177696 TAGA
65 TAGA
* * * * *
1177700 GTAGATAGGCGCCACAAGCTTGTGT-GGCGTTTAATGAAAAAAATGCATCTTTCTCCTTAAGGAC
1 GTAGATAGGTGCCACAAGCTTGTGTGGGC-TTTAAGGAAAAAAATACATCCTGCTCCTTAAGGAC
1177764 TAGA
65 TAGA
* * * * * ** * **
1177768 ATAGATAGGTGGCACTAA-CTTGTGTGAGCTTTGAA-GAAGAAAAGATGTCCTACTTTTTAAGGA
1 GTAGATAGGTGCCAC-AAGCTTGTGTGGGCTTT-AAGGAAAAAAATACATCCTGCTCCTTAAGGA
1177831 CTAGA
64 CTAGA
* * * ** * * *
1177836 GTAGATAGGTTCCACAAACTT-TATGGGCTTTGAA--AAAGAAAAGGCATCCTACTCTTTAAAGA
1 GTAGATAGGTGCCACAAGCTTGTGTGGGCTTT-AAGGAAA-AAAATACATCCTGCTCCTTAAGGA
*
1177898 CTAAA
64 CTAGA
*
1177903 GTAGAGAGGTGC
1 GTAGATAGGTGC
1177915 TAGCAATTTA
Statistics
Matches: 230, Mismatches: 46, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
66 2 0.01
67 49 0.21
68 131 0.57
69 15 0.07
70 33 0.14
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (68 bp):
GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTAAGGAAAAAAATACATCCTGCTCCTTAAGGACT
AGA
Found at i:1178166 original size:68 final size:68
Alignment explanation
Indices: 1178056--1178233 Score: 211
Period size: 68 Copynumber: 2.6 Consensus size: 68
1178046 AAAAAACATC
* * * ** * *
1178056 ATGCTCTTTGAGGATTGGAGTAGATAAGTGTTGCCAAGTTGTGTGGGCTTTGAGGAACAAAATA-
1 ATGCTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGA--AACAAAAAAG
1178120 TGT-T
64 TGTCT
*
1178124 ATGCTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAATAAAAAAGGT
1 ATGCTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAACAAAAAA-GT
1178189 GTCT
65 GTCT
*
1178193 -TGCTCTTTGAGGACTAGAAG-AGATAGGTGCCACCAACTTGT
1 ATGCTCTTTGAGGACT-GAAGTAGATAGGTGTCACCAACTTGT
1178234 ACAGACTTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
66 7 0.07
68 85 0.88
69 5 0.05
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (68 bp):
ATGCTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAACAAAAAAGTG
TCT
Found at i:1178243 original size:68 final size:69
Alignment explanation
Indices: 1178125--1178278 Score: 186
Period size: 68 Copynumber: 2.3 Consensus size: 69
1178115 AAATATGTTA
* *** * * *
1178125 TGCTCTTTGAGGACT-GAAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAATAAAAAAGGT
1 TGCTCTTTGAGGACTAGAAGTAGATAGGTGCCACCAACTTGTACAGACTTTGAAAGAAAAAAGGC
*
1178189 GTCT
66 ATCT
* * *
1178193 TGCTCTTTGAGGACTAGAAG-AGATAGGTGCCACCAACTTGTACAGACTTTGAAGGAGAAGAGGC
1 TGCTCTTTGAGGACTAGAAGTAGATAGGTGCCACCAACTTGTACAGACTTTGAAAGAAAAAAGGC
1178257 ATCT
66 ATCT
*
1178261 TGCTCTTTGAGGATTAGA
1 TGCTCTTTGAGGACTAGA
1178279 GGAAAATAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 69 0.95
69 4 0.05
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (69 bp):
TGCTCTTTGAGGACTAGAAGTAGATAGGTGCCACCAACTTGTACAGACTTTGAAAGAAAAAAGGC
ATCT
Done.