Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 10 of 210
Found at i:3837060 original size:14 final size:14
Alignment explanation
Indices: 3837043--3837088 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
3837033 AATAAAATTT
3837043 TAAATTTTAAATAA
1 TAAATTTTAAATAA
* *
3837057 TAAATCTTAAATCA
1 TAAATTTTAAATAA
*
3837071 TAAATTTTAAATAG
1 TAAATTTTAAATAA
3837085 TAAA
1 TAAA
3837089 CTTAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (14 bp):
TAAATTTTAAATAA
Found at i:3837074 original size:21 final size:22
Alignment explanation
Indices: 3837031--3837075 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3837021 TGTGGGTGTG
* **
3837031 ATAATAAAATTTTAAATTTTAA
1 ATAATAAAATCTTAAATCATAA
3837053 ATAAT-AAATCTTAAATCATAA
1 ATAATAAAATCTTAAATCATAA
3837074 AT
1 AT
3837076 TTTAAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAAAATCTTAAATCATAA
Found at i:3837074 original size:28 final size:27
Alignment explanation
Indices: 3837043--3837095 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
3837033 AATAAAATTT
3837043 TAAATTTTAAATAATAAATCTTAAATCA
1 TAAATTTTAAATAATAAA-CTTAAATCA
*
3837071 TAAATTTTAAATAGTAAACTTAAAT
1 TAAATTTTAAATAATAAACTTAAAT
3837096 TTTAAAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTTAAATAATAAACTTAAATCA
Found at i:3844630 original size:165 final size:164
Alignment explanation
Indices: 3844359--3844880 Score: 810
Period size: 165 Copynumber: 3.2 Consensus size: 164
3844349 ATTTTTGTTT
* * * ** *
3844359 ACCGATGATCCACCGCCATGCTACTGTACATCACCAGCCGTTTTAGCTCAGCCGGTAGAGCGCGT
1 ACCGATGATCCACCACTATGCTACTGTCCATCAATAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
* *
3844424 GGCTTTTAACCACGTGGTCGTGGGTTCAATTCCCACAGACGGCGTTGTGTTTTGTAAATTCTGTT
66 GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTTGTGTTTTGT-AATTCTATT
*
3844489 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAT
130 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
*
3844524 ACCGATGATCCACCACTATGTTACTGTCCATCAATAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
1 ACCGATGATCCACCACTATGCTACTGTCCATCAATAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
* **
3844589 GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTTGAGTTTTGTTGTTACTATT
66 GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTTGTGTTTTGTAATT-CTATT
3844654 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
130 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
* * *
3844689 ACCGATGATCCAGCACTATGCTACTGTCTATCAGTAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
1 ACCGATGATCCACCACTATGCTACTGTCCATCAATAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
* **
3844754 GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTCGTGTTTTGTTGTTTCTATT
66 GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTTGTGTTTTG-TAATTCTATT
3844819 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
130 TTACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
* * * *
3844854 ACTGGTGATCCACCGCTATACTACTGT
1 ACCGATGATCCACCACTATGCTACTGT
3844881 GCGCCATCTA
Statistics
Matches: 329, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
164 2 0.01
165 324 0.98
166 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (164 bp):
ACCGATGATCCACCACTATGCTACTGTCCATCAATAGCCGTCTTAGCTCAGCCGGTAGAGCGCGT
GGCTTTTAACCACGTGGTCGTGGGTTCGATTCCCACAGACGGCGTTGTGTTTTGTAATTCTATTT
TACATTTTTGTTTACCGAAGAGAAGAGGGAGAAC
Found at i:3851842 original size:18 final size:19
Alignment explanation
Indices: 3851819--3851856 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3851809 AATTTTGGAG
3851819 AGTAAAAGTTT-GAGGGAA
1 AGTAAAAGTTTGGAGGGAA
*
3851837 AGTAAAATTTTGGAGGGAA
1 AGTAAAAGTTTGGAGGGAA
3851856 A
1 A
3851857 ATATTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.24
Consensus pattern (19 bp):
AGTAAAAGTTTGGAGGGAA
Found at i:3852748 original size:24 final size:24
Alignment explanation
Indices: 3852693--3852738 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3852683 TTTTTTGGAT
*
3852693 ATATATTTATAAAATTATTGAAAA
1 ATATTTTTATAAAATTATTGAAAA
3852717 ATATTTTTATAAATATT-TTGAA
1 ATATTTTTATAAA-ATTATTGAA
3852739 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATATTTTTATAAAATTATTGAAAA
Found at i:3853803 original size:31 final size:31
Alignment explanation
Indices: 3853741--3853803 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
3853731 TACTAGAAAA
*
3853741 ATTTTAAAATTTTAACTTTCTTTATATATAT
1 ATTTTAAAATTTTAACTTTCTTTATAAATAT
*
3853772 ATTTTAATATTTTAAAACTTT-TTTA-AAATAT
1 ATTTTAAAATTTT--AACTTTCTTTATAAATAT
3853803 A
1 A
3853804 AATTTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 18 0.64
32 4 0.14
33 6 0.21
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTTAAAATTTTAACTTTCTTTATAAATAT
Found at i:3853821 original size:18 final size:17
Alignment explanation
Indices: 3853800--3853843 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3853790 TTTTTTAAAA
*
3853800 TATAAATTTTGGAATTTT
1 TATAAAATTT-GAATTTT
3853818 TATAAAAATTTGAATTTT
1 TAT-AAAATTTGAATTTT
3853836 T-TAAAATT
1 TATAAAATT
3853844 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 1 0.04
18 11 0.46
19 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAAATTTGAATTTT
Found at i:3853847 original size:19 final size:18
Alignment explanation
Indices: 3853803--3853857 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
3853793 TTTAAAATAT
3853803 AAATTTTGGAATTTTTATAA
1 AAATTTT-GAATTTTT-TAA
3853823 AAA-TTTGAATTTTTTAA
1 AAATTTTGAATTTTTTAA
*
3853840 AATTATTTTAAATTTTTT
1 AA--ATTTTGAATTTTTT
3853858 GTGGAGAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 4 0.13
20 14 0.45
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
AAATTTTGAATTTTTTAA
Found at i:3866250 original size:2 final size:2
Alignment explanation
Indices: 3866245--3866278 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3866235 ATATTCTCTC
3866245 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
3866279 TTCTAGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3868076 original size:6 final size:7
Alignment explanation
Indices: 3868057--3868083 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3868047 TTTGTAAATT
3868057 ATAAAAA
1 ATAAAAA
3868064 ATAAAAA
1 ATAAAAA
3868071 ATAAAAA
1 ATAAAAA
3868078 ATAAAA
1 ATAAAA
3868084 TGGAAAGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:3872417 original size:27 final size:28
Alignment explanation
Indices: 3872381--3872451 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
3872371 GTGGAGGGGC
3872381 TGCCACAGGCGGCACCAG-TGGTGCCAG
1 TGCCACAGGCGGCACCAGATGGTGCCAG
** * *
3872408 TGGTAGAGGCGGCACC-GATGGTGCCAT
1 TGCCACAGGCGGCACCAGATGGTGCCAG
3872435 TGCCACAGGCGGCACCA
1 TGCCACAGGCGGCACCA
3872452 CCCCCCTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.03
27 34 0.97
ACGTcount: A:0.20, C:0.31, G:0.37, T:0.13
Consensus pattern (28 bp):
TGCCACAGGCGGCACCAGATGGTGCCAG
Found at i:3872532 original size:34 final size:33
Alignment explanation
Indices: 3872493--3872611 Score: 102
Period size: 38 Copynumber: 3.5 Consensus size: 33
3872483 GTGGATGGAG
*
3872493 AAGAAAAGGAGAGGGAAAGGAGAAGAAAGAAAGA
1 AAGAAAAGGAGA-AGAAAGGAGAAGAAAGAAAGA
*
3872527 AAGAAAATGAAAGAAAATGAAAGGAGAAGAAAGAAAGAA
1 AAGAAAA-G---GAGAA-GAAAGGAGAAGAAAGAAAG-A
*
3872566 AAGTAAAGGAGAAG-AA--AGAA-AAAGAAAGGA
1 AAGAAAAGGAGAAGAAAGGAGAAGAAAGAAA-GA
*
3872596 AAGGAAAGGAGAAGAA
1 AAGAAAAGGAGAAGAA
3872612 GAAGACCAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
30 21 0.29
31 6 0.08
33 2 0.03
34 8 0.11
35 5 0.07
38 23 0.32
39 7 0.10
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (33 bp):
AAGAAAAGGAGAAGAAAGGAGAAGAAAGAAAGA
Found at i:3872538 original size:10 final size:9
Alignment explanation
Indices: 3872515--3872603 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
3872505 GGGAAAGGAG
3872515 AAGAAAG-A
1 AAGAAAGAA
3872523 AAGAAAGAA
1 AAGAAAGAA
3872532 AATGAAAGAA
1 AA-GAAAGAA
3872542 AATGAAAG--
1 AA-GAAAGAA
*
3872550 GAG-AAG-A
1 AAGAAAGAA
3872557 AAGAAAGAA
1 AAGAAAGAA
*
3872566 AAGTAAAGGAG
1 AAG-AAA-GAA
3872577 AAGAAAGAAA
1 AAGAAAG-AA
3872587 AAGAAAGGAA
1 AAGAAA-GAA
*
3872597 AGGAAAG
1 AAGAAAG
3872604 GAGAAGAAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
6 3 0.04
7 3 0.04
8 11 0.16
9 9 0.13
10 35 0.52
11 6 0.09
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:3872562 original size:24 final size:23
Alignment explanation
Indices: 3872518--3872600 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 23
3872508 AAAGGAGAAG
3872518 AAAGAAA-GA-AAGAAAATGAAAGA
1 AAAGAAAGGAGAAG-AAA-GAAAGA
3872541 AAATGAAAGGAGAAGAAAGAAAGA
1 AAA-GAAAGGAGAAGAAAGAAAGA
3872565 AAAGTAAAGGAGAAGAAAGAAAAAGA
1 AAAG-AAAGGAGAAGAAAG--AAAGA
*
3872591 AAGGAAAGGA
1 AAAGAAAGGA
3872601 AAGGAGAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
23 4 0.08
24 27 0.51
25 11 0.21
26 11 0.21
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.04
Consensus pattern (23 bp):
AAAGAAAGGAGAAGAAAGAAAGA
Found at i:3872573 original size:5 final size:4
Alignment explanation
Indices: 3872515--3872603 Score: 56
Period size: 5 Copynumber: 19.8 Consensus size: 4
3872505 GGGAAAGGAG
3872515 AAGA AAGA AAGA AAGAA AATGA AAGAA AATGA AAGGA GAAGA AAGA AAGAA
1 AAGA AAGA AAGA AAG-A AA-GA AAG-A AA-GA AA-GA -AAGA AAGA AAG-A
3872566 AAGTA AAGGA GAAGA AAG- AA-A AAGA AAGGA AAGGA AAG
1 AAG-A AA-GA -AAGA AAGA AAGA AAGA AA-GA AA-GA AAG
3872604 GAGAAGAAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
3 4 0.06
4 26 0.36
5 35 0.49
6 7 0.10
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:3872604 original size:10 final size:10
Alignment explanation
Indices: 3872506--3872605 Score: 59
Period size: 10 Copynumber: 10.3 Consensus size: 10
3872496 AAAAGGAGAG
3872506 GGAAAGGAGAA
1 GGAAAGGA-AA
3872517 -GAAA-GAAA
1 GGAAAGGAAA
*
3872525 -GAAAGAAAA
1 GGAAAGGAAA
* *
3872534 TGAAAGAAAA
1 GGAAAGGAAA
*
3872544 TGAAAGGAGAA
1 GGAAAGGA-AA
3872555 -GAAA-GAAA
1 GGAAAGGAAA
* *
3872563 GAAAAGTAAA
1 GGAAAGGAAA
3872573 GGAGAA-GAAA
1 GGA-AAGGAAA
* *
3872583 GAAAAAGAAA
1 GGAAAGGAAA
3872593 GGAAAGGAAA
1 GGAAAGGAAA
3872603 GGA
1 GGA
3872606 GAAGAAGAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
8 8 0.11
9 12 0.16
10 49 0.67
11 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (10 bp):
GGAAAGGAAA
Found at i:3872635 original size:54 final size:54
Alignment explanation
Indices: 3872522--3872648 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
3872512 GAGAAGAAAG
* *
3872522 AAAGAAAGAAAATGAAAGAAAATGAAAGGAGAAGAAAGAAAGAAAAGTAAAGGA
1 AAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGAAAGAAAAGTAAAGGA
* * *
3872576 GAAGAAAGAAAAAGAAAGGAAAGGAAAGGAGAAG-AAG-AAGACCAAAG-GAAGGAA
1 AAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGAAAGA--AAAGTAAAGG-A
*
3872630 AAAGAAAGGAAAA-AAAGAA
1 AAAGAAAGAAAAAGAAAGAA
3872649 GTAAAGGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
52 4 0.06
53 12 0.19
54 46 0.74
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (54 bp):
AAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGAAAGAAAAGTAAAGGA
Found at i:3872648 original size:34 final size:33
Alignment explanation
Indices: 3872586--3872649 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
3872576 GAAGAAAGAA
* * *
3872586 AAAGAAAGGAAAGGAAAGGAGAAGAAGAAGACC
1 AAAGAAAGGAAAAGAAAGGAAAAAAAGAAGACC
*
3872619 AAAGGAAGGAAAAAGAAAGGAAAAAAAGAAG
1 AAAGAAAGG-AAAAGAAAGGAAAAAAAGAAG
3872650 TAAAGGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 8 0.31
34 18 0.69
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (33 bp):
AAAGAAAGGAAAAGAAAGGAAAAAAAGAAGACC
Found at i:3873064 original size:13 final size:13
Alignment explanation
Indices: 3873031--3873082 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
3873021 TAATACATTT
* *
3873031 CAAACATAATGTA
1 CAAAAATAATATA
*
3873044 CTAAAATAATATA
1 CAAAAATAATATA
*
3873057 -AAATAATAAAATA
1 CAAA-AATAATATA
3873070 CAAAAATAATATA
1 CAAAAATAATATA
3873083 TTTTTATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
CAAAAATAATATA
Found at i:3873194 original size:156 final size:154
Alignment explanation
Indices: 3872957--3873314 Score: 510
Period size: 156 Copynumber: 2.3 Consensus size: 154
3872947 CGAAAGTAAT
* *
3872957 AAAATACGAACAAAGGGCCGAAATAAGGG-TATTTTACTAAATATTTTTAAAAAACAGAATTAAT
1 AAAATACGAACAAA-GGCCGAAATAAGGGTTATTTTACTAAAT-TTTTTAAAAAACACAATAAAT
3873021 TAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTT
64 TAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTT
3873086 TTATTGAAAGTAATAAAATCC-GGG-AA
129 TT-TT-AAAGTAATAAAATCCGGGGAAA
* * *
3873112 AAAATACGAGCAAAGAGCCGAAATAAGGGTTATTTTTCTAAATTTATTTAAAAAACACACTAAAT
1 AAAATACGAACAAAG-GCCGAAATAAGGGTTATTTTACTAAATTT-TTTAAAAAACACAATAAAT
* *** *
3873177 TAATGA-ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTGGAAAATAGTATATT
64 TAAT-ACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATT
3873241 TTTTTAAAGTAATAAAATCCGGGGAAA
128 TTTTTAAAGTAATAAAATCCGGGGAAA
*
3873268 AAAATACGAACAAAGGTCCGAAATAACGGTT-TTTTACTAAATTTTTT
1 AAAATACGAACAAAGG-CCGAAATAAGGGTTATTTTACTAAATTTTTT
3873315 TTGAAGTTGC
Statistics
Matches: 183, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
154 19 0.10
155 46 0.25
156 117 0.64
157 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (154 bp):
AAAATACGAACAAAGGCCGAAATAAGGGTTATTTTACTAAATTTTTTAAAAAACACAATAAATTA
ATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTT
TTAAAGTAATAAAATCCGGGGAAA
Found at i:3875813 original size:39 final size:38
Alignment explanation
Indices: 3875769--3875896 Score: 141
Period size: 39 Copynumber: 3.3 Consensus size: 38
3875759 ACTAACACAA
3875769 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGTTTTTTACT-AAAATAATACTAAC
**
3875808 TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAC
1 TAACAATAATAA-TAGTTTTTTACT-AAAATAAT-ACTAAC
* * * **
3875849 -CATAATAATATTAGTTTTTTACTAACAATAATACTAGG
1 TAACAATAATAATAGTTTTTTACTAA-AATAATACTAAC
3875887 TAACAATAAT
1 TAACAATAAT
3875897 TATTAATAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 6 0.08
39 35 0.48
40 26 0.36
41 6 0.08
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.35
Consensus pattern (38 bp):
TAACAATAATAATAGTTTTTTACTAAAATAATACTAAC
Found at i:3875854 original size:37 final size:39
Alignment explanation
Indices: 3875786--3875881 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
3875776 AATAATAGTT
* *
3875786 TTTTACTCAAAATAAT-ACTAACTAACAATAATAATTAGGG
1 TTTTACTAAAAATAATAACTAAC-AATAATAAT-ATTAGGG
* **
3875826 TTTTACTAAAAATAATAACTAACCATAATAATATTAGTT
1 TTTTACTAAAAATAATAACTAACAATAATAATATTAGGG
*
3875865 TTTTACTAACAATAATA
1 TTTTACTAAAAATAATA
3875882 CTAGGTAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 21 0.43
40 22 0.45
41 6 0.12
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.36
Consensus pattern (39 bp):
TTTTACTAAAAATAATAACTAACAATAATAATATTAGGG
Found at i:3876285 original size:24 final size:23
Alignment explanation
Indices: 3876245--3876293 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
3876235 TTTAGTAAAT
3876245 AATTTTTTTATTATATTATTT-TA
1 AATTTTTTTATTATATT-TTTGTA
3876268 AATTTTTTT-TGTATTATTTTTGTA
1 AATTTTTTTAT-TA-TATTTTTGTA
3876292 AA
1 AA
3876294 AGACCCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 1 0.04
23 14 0.61
24 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
AATTTTTTTATTATATTTTTGTA
Found at i:3885923 original size:16 final size:16
Alignment explanation
Indices: 3885904--3885934 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3885894 AGATTTTATT
3885904 TTTTAAAATATATAAC
1 TTTTAAAATATATAAC
*
3885920 TTTTAAAATTTATAA
1 TTTTAAAATATATAA
3885935 TCCATTTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAATATATAAC
Found at i:3888293 original size:2 final size:2
Alignment explanation
Indices: 3888286--3888332 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3888276 CAATCGAAGA
3888286 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
3888328 AT AT A
1 AT AT A
3888333 CGTGCTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3894954 original size:12 final size:11
Alignment explanation
Indices: 3894930--3894963 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
3894920 GTGTATGAAT
3894930 TATATTTTTTA
1 TATATTTTTTA
3894941 TA-ATTTTTTA
1 TATATTTTTTA
3894951 TATATTTATTTA
1 TATATTT-TTTA
3894963 T
1 T
3894964 CTTTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 6 0.29
12 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:3906923 original size:19 final size:18
Alignment explanation
Indices: 3906896--3906932 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3906886 TTTATTTTTT
3906896 AAAAATATAAAAGAATAA
1 AAAAATATAAAAGAATAA
*
3906914 AAAAATTATAAAATAATAA
1 AAAAA-TATAAAAGAATAA
3906933 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATATAAAAGAATAA
Found at i:3908346 original size:21 final size:21
Alignment explanation
Indices: 3908296--3908339 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3908286 TTTTTATGTT
* * *
3908296 AAAAGAGATGGAGAAGAGAGG
1 AAAATAGAAGGAGAAGAGAAG
3908317 AAAATAGAAGGAGAAGTAGAAG
1 AAAATAGAAGGAGAAG-AGAAG
3908339 A
1 A
3908340 GAAAGAACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (21 bp):
AAAATAGAAGGAGAAGAGAAG
Found at i:3910189 original size:22 final size:22
Alignment explanation
Indices: 3910154--3910203 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3910144 AAACAAGAAC
*
3910154 AATAATATTAAAAT-AGTAGCAA
1 AATAATAATAAAATGA-TAGCAA
* *
3910176 CATAATAATGAAATGATAGCAA
1 AATAATAATAAAATGATAGCAA
3910198 AATAAT
1 AATAAT
3910204 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (22 bp):
AATAATAATAAAATGATAGCAA
Found at i:3914450 original size:8 final size:8
Alignment explanation
Indices: 3914437--3914467 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3914427 TTAAATTTAA
3914437 ATTAAAAT
1 ATTAAAAT
3914445 ATTAAAAT
1 ATTAAAAT
3914453 ATTAAAAT
1 ATTAAAAT
*
3914461 AATAAAA
1 ATTAAAA
3914468 AAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
ATTAAAAT
Found at i:3917837 original size:19 final size:18
Alignment explanation
Indices: 3917815--3917886 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
3917805 ACAAAAATTG
3917815 TAAAATTTTATAAAAATCA
1 TAAAATTTTATAAAAAT-A
**
3917834 TAAAAAATTATAAAATATA
1 TAAAATTTTATAAAA-ATA
* *
3917853 TAGAAA-TATAGAAAAAATTA
1 TA-AAATTTTA-TAAAAA-TA
3917873 TAAAATTTTATAAA
1 TAAAATTTTATAAA
3917887 GTCATAAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAATTTTATAAAAATA
Found at i:3917869 original size:58 final size:59
Alignment explanation
Indices: 3917807--3917922 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
3917797 ATAAAATCAC
* *
3917807 AAAAATTGTAAAATTTTATAAAAATCATAA-AAAATTAT-AAAATATATAGAAATATAGA
1 AAAAATTATAAAATTTTAT-AAAATCATAAGAAAATTATAAAAATATAAAGAAATATAGA
* *
3917865 AAAAATTATAAAATTTTATAAAGTCATAAGAAAGTTATAAAAAATATAAAGAAATATA
1 AAAAATTATAAAATTTTATAAAATCATAAGAAAATTAT-AAAAATATAAAGAAATATA
3917923 AAATTCGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 9 0.18
58 25 0.49
60 17 0.33
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (59 bp):
AAAAATTATAAAATTTTATAAAATCATAAGAAAATTATAAAAATATAAAGAAATATAGA
Found at i:3917876 original size:39 final size:39
Alignment explanation
Indices: 3917826--3917926 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
3917816 AAAATTTTAT
*
3917826 AAAAATCATAAAAAATTATAAAAT-ATATAGAAA-TATAGA
1 AAAAATTATAAAAAATTATAAAATCATA-AGAAAGT-TAGA
** * *
3917865 AAAAATTATAAAATTTTATAAAGTCATAAGAAAGTTATA
1 AAAAATTATAAAAAATTATAAAATCATAAGAAAGTTAGA
3917904 AAAAA-TATAAAGAAA-TATAAAAT
1 AAAAATTATAAA-AAATTATAAAAT
3917927 TCGTAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
38 13 0.25
39 34 0.67
40 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (39 bp):
AAAAATTATAAAAAATTATAAAATCATAAGAAAGTTAGA
Found at i:3917902 original size:29 final size:28
Alignment explanation
Indices: 3917795--3917906 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 28
3917785 AGAAGAAAAA
* *
3917795 TTATAAAATCA-CAAAAATTGTAAAATT
1 TTATAAAATCATAAAAAATTATAAAATT
3917822 TTATAAAAATCATAAAAAATTATAAAA-T
1 TTAT-AAAATCATAAAAAATTATAAAATT
*
3917850 ATATAGAAAT-ATAGAAAAAATTATAAAATT
1 TTATA-AAATCAT--AAAAAATTATAAAATT
* *
3917880 TTATAAAGTCATAAGAAAGTTATAAAA
1 TTATAAAATCATAA-AAAATTATAAAA
3917907 AATATAAAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
27 7 0.10
28 17 0.24
29 40 0.56
30 7 0.10
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (28 bp):
TTATAAAATCATAAAAAATTATAAAATT
Found at i:3917943 original size:10 final size:10
Alignment explanation
Indices: 3917807--3917949 Score: 63
Period size: 10 Copynumber: 14.9 Consensus size: 10
3917797 ATAAAATCAC
*
3917807 AAAAATTGTA
1 AAAAATTATA
**
3917817 AAATTTTAT-
1 AAAAATTATA
*
3917826 AAAAATCATA
1 AAAAATTATA
3917836 AAAAATTATA
1 AAAAATTATA
*
3917846 AAATA-TAT-
1 AAAAATTATA
* *
3917854 AGAAATATAGA
1 AAAAAT-TATA
3917865 AAAAATTAT-
1 AAAAATTATA
*
3917874 -AAAATTTTA
1 AAAAATTATA
* * *
3917883 TAAAGTCATA
1 AAAAATTATA
*
3917893 AGAAAGTTATA
1 A-AAAATTATA
3917904 AAAAA-TATA
1 AAAAATTATA
3917913 AAGAAA-TAT-
1 AA-AAATTATA
*
3917922 -AAAATTCGTA
1 AAAAATT-ATA
3917932 AAAAATTAT-
1 AAAAATTATA
3917941 AAAAATTAT
1 AAAAATTAT
3917950 CGTACTAAAA
Statistics
Matches: 99, Mismatches: 22, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
7 3 0.03
8 12 0.12
9 25 0.25
10 39 0.39
11 20 0.20
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:3918221 original size:30 final size:28
Alignment explanation
Indices: 3918165--3918245 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
3918155 CAATATCTTA
* * *
3918165 TAATTTTTCTTCTAATTTTTAATAAAATTT
1 TAATTTTT-TTATACTTTTTATTAAAA-TT
*
3918195 TAATATTTTTTATCCTTTTTATTAAAATT
1 TAAT-TTTTTTATACTTTTTATTAAAATT
*
3918224 TAATTTTTTTATATTTTTTATT
1 TAATTTTTTTATACTTTTTATT
3918246 GATTTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 16 0.36
29 6 0.14
30 18 0.41
31 4 0.09
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
TAATTTTTTTATACTTTTTATTAAAATT
Found at i:3918253 original size:28 final size:28
Alignment explanation
Indices: 3918165--3918269 Score: 88
Period size: 28 Copynumber: 3.7 Consensus size: 28
3918155 CAATATCTTA
* * *
3918165 TAATTTTTCTTCTAATTTTTAATAAAATTT
1 TAATTTTT-TTAT-ATTTTTTATTAAATTT
** *
3918195 TAATATTTTTTATCCTTTTTATTAAAATT
1 TAAT-TTTTTTATATTTTTTATTAAATTT
*
3918224 TAATTTTTTTATATTTTTTATT-GATTT
1 TAATTTTTTTATATTTTTTATTAAATTT
*
3918251 TTA-TTTTTTATAATTTTTT
1 TAATTTTTTTAT-ATTTTTT
3918270 GCCACATGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.13
27 12 0.19
28 16 0.26
29 15 0.24
30 7 0.11
31 4 0.06
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.68
Consensus pattern (28 bp):
TAATTTTTTTATATTTTTTATTAAATTT
Found at i:3918268 original size:17 final size:18
Alignment explanation
Indices: 3918229--3918269 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
3918219 AAATTTAATT
*
3918229 TTTTTATATTTTTTATTGA
1 TTTTT-TATTTTTTATTAA
3918248 -TTTTTATTTTTTA-TAA
1 TTTTTTATTTTTTATTAA
3918264 TTTTTT
1 TTTTTT
3918270 GCCACATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 14 0.70
18 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTATTTTTTATTAA
Found at i:3918543 original size:95 final size:89
Alignment explanation
Indices: 3918374--3918635 Score: 267
Period size: 90 Copynumber: 2.9 Consensus size: 89
3918364 GTCAAATATT
* * * **
3918374 ATTTTTGATACATTTT-ACAGTTCAAATACCTAATTGAGTGCAAGAAAAAATTAAGGACTTAATT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAA-AAAAAAAAAAGGACTTAATT
***
3918438 GCTTTTTTTGAAAAAATTTTGAGGGC
65 GCTTTTTTTGAAAAAATTTT-ACAAC
* *
3918464 ATTTTTAATACATTTTGAAAGTTCGAGTACCCAATTGAGTGCAAAAAAAAAAAAGGCATGGCCTT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAAGG-A----CTT
*
3918529 AATTGCTTTTTTTGAAAAAGTTTTACAAC
61 AATTGCTTTTTTTGAAAAAATTTTACAAC
* ** * * *
3918558 TTTTTTAATGTATTTTGAAAGTTTAAATACCCAATTGAGTG-AAAAAAAAGAGTAAGAACTTAAT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAA-A-AAAGGACTTAAT
*
3918622 TACTTTTTTTGAAA
64 TGCTTTTTTTGAAA
3918636 TGTTTAAAGG
Statistics
Matches: 144, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
90 44 0.31
91 24 0.17
93 8 0.06
94 39 0.27
95 29 0.20
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (89 bp):
ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAAGGACTTAATTG
CTTTTTTTGAAAAAATTTTACAAC
Found at i:3918573 original size:94 final size:94
Alignment explanation
Indices: 3918374--3918606 Score: 255
Period size: 94 Copynumber: 2.5 Consensus size: 94
3918364 GTCAAATATT
* * * **
3918374 ATTTTTGATACATTTT-ACAGTTCAAATACCTAATTGAGTGCAAGAAAAAATTAAGG-A----CT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTG-AA-AAAAAAAAAAGGCATGGCCT
***
3918433 TAATTGCTTTTTTTGAAAAAATTTTGAGGGC
64 TAATTGCTTTTTTTGAAAAAATTTTGACAAC
* *
3918464 ATTTTTAATACATTTTGAAAGTTCGAGTACCCAATTGAGTGCAAAAAAAAAAAAGGCATGGCCTT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTG-AAAAAAAAAAAAGGCATGGCCTT
*
3918529 AATTGCTTTTTTTGAAAAAGTTTT-ACAAC
65 AATTGCTTTTTTTGAAAAAATTTTGACAAC
* ** *
3918558 TTTTTTAATGTATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAAA
1 ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGAAAAAAAA
3918607 GAGTAAGAAC
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
90 25 0.21
91 24 0.20
93 8 0.07
94 37 0.31
95 26 0.22
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (94 bp):
ATTTTTAATACATTTTGAAAGTTCAAATACCCAATTGAGTGAAAAAAAAAAAAGGCATGGCCTTA
ATTGCTTTTTTTGAAAAAATTTTGACAAC
Found at i:3933576 original size:18 final size:16
Alignment explanation
Indices: 3933553--3933594 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
3933543 TCACCTAAGT
3933553 TTGAGTATTAATTGTGAA
1 TTGAGTATTAATT-TG-A
*
3933571 TTGAGTCTTAATTTGA
1 TTGAGTATTAATTTGA
3933587 TTGA-TATT
1 TTGAGTATT
3933595 GATATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 2 0.09
18 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (16 bp):
TTGAGTATTAATTTGA
Found at i:3941410 original size:19 final size:18
Alignment explanation
Indices: 3941386--3941447 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
3941376 AAGCCCATAA
3941386 TTTTTAATAGTTTTAATAT
1 TTTTTAATAGTTTT-ATAT
*
3941405 TTTTTAATA-ATTTATATT
1 TTTTTAATAGTTTTATA-T
*
3941423 TATTTTAA-AGTTTTTTTAT
1 T-TTTTAATAG-TTTTATAT
3941442 TTTTTA
1 TTTTTA
3941448 GAATTAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 11 0.31
19 17 0.47
20 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTAATAGTTTTATAT
Found at i:3943130 original size:23 final size:24
Alignment explanation
Indices: 3943083--3943132 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3943073 ATTATTAAAA
* *
3943083 TATTATTTTAGTTATTTATTTAATT
1 TATTATTTTA-TTAGTTATTGAATT
3943108 TATTATTTT-TTAGTTATTGAATT
1 TATTATTTTATTAGTTATTGAATT
3943131 TA
1 TA
3943133 CAATAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (24 bp):
TATTATTTTATTAGTTATTGAATT
Found at i:3945765 original size:14 final size:14
Alignment explanation
Indices: 3945748--3945777 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3945738 TCCACAAGGT
*
3945748 TTTAAACATAAACA
1 TTTAAACACAAACA
3945762 TTTAAACACAAACA
1 TTTAAACACAAACA
3945776 TT
1 TT
3945778 CCTCCCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
TTTAAACACAAACA
Found at i:3948477 original size:138 final size:138
Alignment explanation
Indices: 3948219--3948492 Score: 433
Period size: 138 Copynumber: 2.0 Consensus size: 138
3948209 GACGCTACCG
* * *
3948219 ATGCTGATATCTCGTTAGAATTGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
1 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
* * * * *
3948284 CGTAACAATCATTATAAACTGAATATCAATGAAGCCCTTACTTTGGCAACTACGAGTGATAATTT
66 CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
3948349 TACATCCA
131 TACATCCA
* * *
3948357 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAATAAACCCC-CAGGGTTTGAAGTTGGTGA
1 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGG-TTGAAGTCGGTGA
3948421 ACGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGT
65 ACGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGT
3948486 TTACATC
130 TTACATC
3948493 GAAGAAAAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 4 0.03
138 120 0.97
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (138 bp):
ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
TACATCCA
Found at i:3948535 original size:138 final size:137
Alignment explanation
Indices: 3948249--3948522 Score: 306
Period size: 138 Copynumber: 2.0 Consensus size: 137
3948239 TTGTCTCTTT
* * *
3948249 CAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATTATAAACTGAATATCAAT
1 CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
* * * * * * * *
3948314 GAAGCCCTTACTTTGGCAACTACGAGTGATAATTTTACATCCAATGCCGATAGCTCGTTAGAATG
66 GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATG-CAAAAGCACGTAACAATG
*** **
3948379 GTCTCTTT
130 GAAACTGA
* *
3948387 CAATGAATAAACCCC-CAGGGTTTGAAGTTGGTGAACGTAACAATCATCATAAACTGAAGATCAA
1 CAATGAATAAACCCCAAAGGG-TTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAA
*
3948451 TGAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCGAA-G-AAAAG-ACG-AACAATG
65 TGAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAAT-
3948512 GGGAAACTGA
129 -GGAAACTGA
3948522 C
1 C
3948523 GAATAGAAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
133 4 0.04
134 2 0.02
135 8 0.07
137 5 0.04
138 95 0.83
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (137 bp):
CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAATGG
AAACTGA
Found at i:3961265 original size:17 final size:17
Alignment explanation
Indices: 3961243--3961280 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3961233 TAATAAACAA
3961243 ATGATTAGCAAATGATC
1 ATGATTAGCAAATGATC
3961260 ATGATTAGCAAATGATC
1 ATGATTAGCAAATGATC
3961277 ATGA
1 ATGA
3961281 AGCTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGATTAGCAAATGATC
Found at i:3970672 original size:21 final size:21
Alignment explanation
Indices: 3970648--3970691 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3970638 CATGTTTTGG
3970648 TTTCTGTATTAAGTTGATGTT
1 TTTCTGTATTAAGTTGATGTT
3970669 TTTCTGTATTAAGTTGATGTT
1 TTTCTGTATTAAGTTGATGTT
3970690 TT
1 TT
3970692 CCGTTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (21 bp):
TTTCTGTATTAAGTTGATGTT
Found at i:3970749 original size:21 final size:21
Alignment explanation
Indices: 3970708--3970750 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3970698 GTGTTTATGG
*
3970708 ATTATATATAATTTTTATAGT
1 ATTATATATAATATTTATAGT
*
3970729 ATTATATATTATGATTT-TAGT
1 ATTATATATAAT-ATTTATAGT
3970750 A
1 A
3970751 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATATAATATTTATAGT
Found at i:3970792 original size:17 final size:18
Alignment explanation
Indices: 3970767--3970812 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3970757 TATAAGAATG
*
3970767 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
3970784 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
3970802 ATTAAATTATA
1 ATTAAATTATA
3970813 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:3970809 original size:55 final size:54
Alignment explanation
Indices: 3970743--3970848 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
3970733 TATATTATGA
* * *
3970743 TTTTAGTAAATTCATA-TAAGAATGATTATATTAAGAATTTTATTAAATTATATAT
1 TTTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAAATTATATAT
* * *
3970798 TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTAT
1 TTTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAAATTAT
3970849 TTATATTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 3 0.07
55 25 0.58
56 15 0.35
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (54 bp):
TTTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAAATTATATAT
Found at i:3971054 original size:44 final size:44
Alignment explanation
Indices: 3970966--3971057 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
3970956 ATTACAACAT
* *
3970966 CATTCCATTCAACCAAAGACAAGAATACTATTATAGTTCTATTC
1 CATTCCATTCAACCAAAGACAAGAATACTATTACAGCTCTATTC
*
3971010 CATTCCATTCAACC-AA-ACAATTGAATTGCTATTACAGCTC-ATTC
1 CATTCCATTCAACCAAAGACAA--GAA-TACTATTACAGCTCTATTC
3971054 CATT
1 CATT
3971058 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.10
43 2 0.05
44 25 0.60
45 11 0.26
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAAGACAAGAATACTATTACAGCTCTATTC
Found at i:3971060 original size:15 final size:16
Alignment explanation
Indices: 3971040--3971078 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3971030 TTGAATTGCT
3971040 ATTACAGCTC-ATTCC
1 ATTACAGCTCTATTCC
3971055 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
3971071 ATTACAGC
1 ATTACAGC
3971079 AAACCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:3971271 original size:23 final size:23
Alignment explanation
Indices: 3971217--3971284 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
3971207 ATTAACATTT
**
3971217 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTTGATTA-ATG
** *
3971241 TTTATGAACATGTTTGTTTAATG
1 TTCGTGAACATGTTTGATTAATG
3971264 TTCGTGAACATGTTTGATTAA
1 TTCGTGAACATGTTTGATTAA
3971285 GTTAAATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (23 bp):
TTCGTGAACATGTTTGATTAATG
Found at i:3971294 original size:23 final size:23
Alignment explanation
Indices: 3971221--3971300 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
3971211 ACATTTTTCG
** *
3971221 TGAACATGTTCAATTATATGTTTA
1 TGAACATGTTTGATTA-ATGTTAA
* **
3971245 TGAACATGTTTGTTTAATGTTCG
1 TGAACATGTTTGATTAATGTTAA
3971268 TGAACATGTTTGATTAA-GTTAAA
1 TGAACATGTTTGATTAATGTT-AA
3971291 TGAACATGTT
1 TGAACATGTT
3971301 CGTGAATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.66
24 13 0.28
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (23 bp):
TGAACATGTTTGATTAATGTTAA
Found at i:3979047 original size:4 final size:4
Alignment explanation
Indices: 3979038--3979190 Score: 297
Period size: 4 Copynumber: 38.2 Consensus size: 4
3979028 AAATTTCATG
*
3979038 TACA TACA TACA TGCA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3979086 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3979134 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3979182 TACA TACA T
1 TACA TACA T
3979191 TCAAGACCTT
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 147 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:3985440 original size:75 final size:76
Alignment explanation
Indices: 3985351--3985501 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 76
3985341 CAGATTGGCA
*
3985351 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAATGGGGAAATA-GGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
3985415 ATATCAAATAG
66 ATATCAAATAG
3985426 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
3985491 ATATCAAATAG
66 ATATCAAATAG
3985502 AGGAGTTTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 52 0.70
76 22 0.30
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (76 bp):
TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
ATATCAAATAG
Found at i:3993722 original size:28 final size:28
Alignment explanation
Indices: 3993691--3993751 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
3993681 ATATGGTCCA
3993691 GTTGAAACATTCTTAGATAATTG-TGGTT
1 GTTGAAACATTCTTAGATAATTGCT-GTT
3993719 GTTGAAACATTCTTAGATAATTGCTGTT
1 GTTGAAACATTCTTAGATAATTGCTGTT
3993747 GTTGA
1 GTTGA
3993752 TGAACTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (28 bp):
GTTGAAACATTCTTAGATAATTGCTGTT
Found at i:4004006 original size:51 final size:51
Alignment explanation
Indices: 4003943--4004077 Score: 146
Period size: 55 Copynumber: 2.5 Consensus size: 51
4003933 TGATAATCAT
*
4003943 TTATTTGAGCAAAGAATCCAC-CTTTTTTCAACTCGAGAGCAAGTTTTACAA
1 TTATTTGTGCAAA-AATCCACTCTTTTTTCAACTCGAGAGCAAGTTTTACAA
* * * * *
4003994 TTATTTGTGCAAAAATTCCACTTTTTTTTTTTCAATTTGAGAGCAAGTTTTCCAT
1 TTATTTGTGCAAAAA-TCCAC---TCTTTTTTCAACTCGAGAGCAAGTTTTACAA
*
4004049 TTATTTGTGCAAAAAATCCACTATTTTTT
1 TTATTTGTGC-AAAAATCCACTCTTTTTT
4004078 TTTTCAACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
50 2 0.03
51 17 0.24
52 7 0.10
55 40 0.56
56 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (51 bp):
TTATTTGTGCAAAAATCCACTCTTTTTTCAACTCGAGAGCAAGTTTTACAA
Found at i:4004053 original size:55 final size:56
Alignment explanation
Indices: 4003965--4004085 Score: 190
Period size: 55 Copynumber: 2.2 Consensus size: 56
4003955 AGAATCCACC
*
4003965 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAATTCCACT-TTTT
1 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
* * * *
4004020 TTTTTTCAATTTGAGAGCAAGTTTTCCATTTATTTGTGCAAAAAATCCACTATTTT
1 TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
4004076 TTTTTTCAAC
1 TTTTTTCAAC
4004086 AAGGAAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 46 0.78
56 13 0.22
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (56 bp):
TTTTTTCAACTCGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTTT
Found at i:4007065 original size:11 final size:11
Alignment explanation
Indices: 4007049--4007075 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4007039 AGTTGGAGTA
4007049 GGGGTGGGGGT
1 GGGGTGGGGGT
4007060 GGGGTGGGGGT
1 GGGGTGGGGGT
4007071 GGGGT
1 GGGGT
4007076 TTAGGGAGAG
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:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (11 bp):
GGGGTGGGGGT
Found at i:4007625 original size:13 final size:13
Alignment explanation
Indices: 4007609--4007633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4007599 AAACAATTAT
4007609 TTTATTTTTATAC
1 TTTATTTTTATAC
4007622 TTTATTTTTATA
1 TTTATTTTTATA
4007634 AAATTTAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTATAC
Found at i:4020088 original size:6 final size:6
Alignment explanation
Indices: 4020077--4020119 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
4020067 TTCAAACCCA
* * *
4020077 TTTATT TTTATTT TTTATT TCTATT TTTATT TCTATT TCTATT
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT
4020120 CCAGTCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:4020105 original size:12 final size:12
Alignment explanation
Indices: 4020077--4020119 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4020067 TTCAAACCCA
*
4020077 TTTATTTTTATTT
1 TTTATTTCTA-TT
4020090 TTTATTTCTATT
1 TTTATTTCTATT
4020102 TTTATTTCTATT
1 TTTATTTCTATT
*
4020114 TCTATT
1 TTTATT
4020120 CCAGTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTCTATT
Found at i:4020113 original size:18 final size:19
Alignment explanation
Indices: 4020079--4020119 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
4020069 CAAACCCATT
*
4020079 TATTTTTATTTTTTATTTC
1 TATTTTTATTTTCTATTTC
4020098 TATTTTTA-TTTCTATTTC
1 TATTTTTATTTTCTATTTC
4020116 TATT
1 TATT
4020120 CCAGTCTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTATTTTCTATTTC
Found at i:4021099 original size:21 final size:22
Alignment explanation
Indices: 4021054--4021098 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
4021044 CTAAATAGAG
4021054 ATTTAATTTTTCTATAATTTAT
1 ATTTAATTTTTCTATAATTTAT
4021076 ATTT-ATTTTATCATATAATTTAT
1 ATTTAATTTT-TC-TATAATTTAT
4021099 TAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 6 0.29
23 10 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTAATTTTTCTATAATTTAT
Found at i:4021577 original size:7 final size:7
Alignment explanation
Indices: 4021565--4021590 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4021555 TACTAAAATC
4021565 ATTTTAA
1 ATTTTAA
4021572 ATTTTAA
1 ATTTTAA
4021579 ATTTTAA
1 ATTTTAA
4021586 ATTTT
1 ATTTT
4021591 CATTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:4021597 original size:14 final size:14
Alignment explanation
Indices: 4021566--4021610 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
4021556 ACTAAAATCA
* *
4021566 TTTTAAATTTTAAA
1 TTTTAAATTTTCAT
4021580 TTTTAAATTTTCAT
1 TTTTAAATTTTCAT
4021594 TTTTACAAATTTTCAT
1 TTTT--AAATTTTCAT
4021610 T
1 T
4021611 ATAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 16 0.59
16 11 0.41
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAATTTTCAT
Found at i:4021984 original size:21 final size:21
Alignment explanation
Indices: 4021954--4022009 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
4021944 AACAGCGGTG
* *
4021954 GCGGTGAGATTAGTTACTGTA
1 GCGGTAAGATTAGATACTGTA
*
4021975 GCGGTAAGATTGGATACTGTA
1 GCGGTAAGATTAGATACTGTA
*
4021996 GCGGTAAAATTAGA
1 GCGGTAAGATTAGA
4022010 AACAGCGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (21 bp):
GCGGTAAGATTAGATACTGTA
Found at i:4022788 original size:113 final size:113
Alignment explanation
Indices: 4022590--4022817 Score: 438
Period size: 113 Copynumber: 2.0 Consensus size: 113
4022580 AGACTATATC
*
4022590 CCCATACCTATTCCAAATATATGCCGAAAGATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
4022655 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
4022703 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
*
4022768 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
4022816 CC
1 CC
4022818 ATGATTGAAG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (113 bp):
CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
TATATCACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
Found at i:4026638 original size:2 final size:2
Alignment explanation
Indices: 4026626--4026655 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4026616 GGCACATGTC
4026626 AT AT A- 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
4026656 ACAAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4027397 original size:17 final size:17
Alignment explanation
Indices: 4027375--4027407 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4027365 ATAGAAAGTC
*
4027375 AAAGATATTGGTATCAG
1 AAAGATATGGGTATCAG
4027392 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
4027408 AAATCTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:4030897 original size:17 final size:17
Alignment explanation
Indices: 4030875--4030907 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4030865 ATAGAAAGTC
*
4030875 AAAGATATGGGTATCAG
1 AAAGATATAGGTATCAG
4030892 AAAGATATAGGTATCA
1 AAAGATATAGGTATCA
4030908 AAATCTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAGATATAGGTATCAG
Found at i:4032203 original size:25 final size:26
Alignment explanation
Indices: 4032158--4032208 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4032148 AGCCCGGCCC
* *
4032158 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAACAATAAAAAATT
4032184 ATTTTAAAAATAAA-AATAAAAAATT
1 ATTTTAAAAATAAACAATAAAAAATT
4032209 TTAAAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTTAAAAATAAACAATAAAAAATT
Found at i:4032253 original size:33 final size:33
Alignment explanation
Indices: 4032161--4032253 Score: 77
Period size: 33 Copynumber: 2.8 Consensus size: 33
4032151 CCGGCCCATT
4032161 TTTAAAATAAACATTAAAAA-AT-TATTTTAAAAA
1 TTTAAAATAAA-A-TAAAAATATATATTTTAAAAA
* *** *
4032194 -TAAAAATAAAA-AATTTTAAAAGTATTTTAAAAA
1 TTTAAAATAAAATAAAAAT-ATA-TATTTTAAAAA
4032227 TTTAAAATAAAATAAAAATATATATTT
1 TTTAAAATAAAATAAAAATATATATTT
4032254 ATTATATTCG
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
29 2 0.05
31 2 0.05
32 9 0.20
33 16 0.36
34 12 0.27
35 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
TTTAAAATAAAATAAAAATATATATTTTAAAAA
Found at i:4032790 original size:23 final size:23
Alignment explanation
Indices: 4032764--4032807 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4032754 ATTTTAATAG
*
4032764 TTTTTATTTTTTAAAA-TAATTT
1 TTTTTAATTTTTAAAATTAATTT
4032786 TTTTTAATTTTTAAAATTAATT
1 TTTTTAATTTTTAAAATTAATT
4032808 AATTGATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAATTTTTAAAATTAATTT
Found at i:4033164 original size:35 final size:35
Alignment explanation
Indices: 4033114--4033185 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
4033104 AAATACTCAC
4033114 AATCTTATATAGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
*
4033149 AATCTTATATTGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
4033184 AA
1 AA
4033186 GGTTTATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (35 bp):
AATCTTATATAGATCAAGAATAATGTATAAAAATG
Found at i:4034596 original size:2 final size:2
Alignment explanation
Indices: 4034589--4034639 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4034579 TCCTTAGAAT
4034589 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
4034631 TA TA TA TA T
1 TA TA TA TA T
4034640 GTATGTTAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4036839 original size:24 final size:23
Alignment explanation
Indices: 4036812--4036857 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
4036802 TTTGGAGAAT
4036812 TTTGTGTTT-ACGTTTTGAGGGTTA
1 TTTGT-TTTGACGTTTTG-GGGTTA
*
4036836 TTTGTTTTGAGGTTTTGGGGTT
1 TTTGTTTTGACGTTTTGGGGTT
4036858 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.02, G:0.33, T:0.57
Consensus pattern (23 bp):
TTTGTTTTGACGTTTTGGGGTTA
Found at i:4037799 original size:42 final size:43
Alignment explanation
Indices: 4037743--4037863 Score: 147
Period size: 42 Copynumber: 2.8 Consensus size: 43
4037733 TTCCAATATG
*
4037743 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
* * *
4037785 TGATTACGTGTAAGAGCC-TGTCTGGGACAGTGGCATCATTATT
1 TGATTACGTGTAAGA-CCATGTCTGGGACATTGGCATCAGTATA
* * **
4037828 TGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
4037864 TATTCGAGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 34 0.51
43 33 0.49
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
Found at i:4037862 original size:43 final size:42
Alignment explanation
Indices: 4037751--4037863 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
4037741 TGTGATTTCG
*
4037751 TGTAAGACCATGTCTGGGACA-TTGGCATCGTATATGATTACG
1 TGTAAGACCATGTCTGGGA-AGTTGGCATCGTATATGATTACA
* *
4037793 TGTAAGAGCC-TGTCTGGGACAG-TGGCATCATTATTTGATTACA
1 TGTAAGA-CCATGTCTGGGA-AGTTGGCATC-GTATATGATTACA
* *
4037836 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGAAGTTGGCAT
4037864 TATTCGAGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
42 28 0.46
43 33 0.54
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGAAGTTGGCATCGTATATGATTACA
Found at i:4039709 original size:2 final size:2
Alignment explanation
Indices: 4039696--4039736 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4039686 TATCTCTTTA
*
4039696 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4039737 ACAGTTCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4044884 original size:20 final size:22
Alignment explanation
Indices: 4044860--4044901 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4044850 TTATGATTTT
4044860 AAAAAA-AATATATTGATTAAC
1 AAAAAATAATATATTGATTAAC
*
4044881 AAAAAATAATATTTTGATTAA
1 AAAAAATAATATATTGATTAA
4044902 TGGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAAATAATATATTGATTAAC
Found at i:4044958 original size:22 final size:19
Alignment explanation
Indices: 4044909--4044959 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
4044899 TAATGGAAAA
4044909 TAATTTTTTTAAAAATAAC
1 TAATTTTTTTAAAAATAAC
*
4044928 T-TTTCTTTTTAAAAAGCATAAC
1 TAATT-TTTTT-AAAA--ATAAC
4044950 TAATTTTTTT
1 TAATTTTTTT
4044960 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 4 0.16
22 11 0.44
23 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTTTTTTAAAAATAAC
Found at i:4050967 original size:54 final size:54
Alignment explanation
Indices: 4050865--4050970 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
4050855 CTAAGTTGTC
* *
4050865 GGGCTTGGTGTGTGGAGGAGATGGGAAAGAGGTGGTTGCTGCCACGGGCGGCCG
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCCG
*
4050919 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGGTA-CACCGGGCGGC
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCA-CGGGCGGC
4050971 GGAGCTGGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 2 0.04
54 46 0.96
ACGTcount: A:0.17, C:0.13, G:0.51, T:0.19
Consensus pattern (54 bp):
GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCCG
Found at i:4054783 original size:4 final size:4
Alignment explanation
Indices: 4054774--4054808 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
4054764 GAAGAAGAAG
4054774 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
4054809 GCATTAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:4063441 original size:12 final size:12
Alignment explanation
Indices: 4063424--4063453 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4063414 TTGAGAAAGG
*
4063424 GAAATGAAATGT
1 GAAATGAAATAT
4063436 GAAATGAAATAT
1 GAAATGAAATAT
4063448 GAAATG
1 GAAATG
4063454 GTGGATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
GAAATGAAATAT
Found at i:4065846 original size:23 final size:24
Alignment explanation
Indices: 4065810--4065857 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4065800 TGATCCCCAT
4065810 ATTTTTTTCGTTTTAAGTAATTTA
1 ATTTTTTTCGTTTTAAGTAATTTA
* *
4065834 ATTTTTTTC-TTTTATGTTATTTA
1 ATTTTTTTCGTTTTAAGTAATTTA
4065857 A
1 A
4065858 ACTTTCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (24 bp):
ATTTTTTTCGTTTTAAGTAATTTA
Found at i:4068364 original size:30 final size:30
Alignment explanation
Indices: 4068330--4068392 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
4068320 ACTTAACAAG
4068330 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** * *
4068360 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
4068390 CAA
1 CAA
4068393 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:4071429 original size:11 final size:13
Alignment explanation
Indices: 4071398--4071422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4071388 TCTAAAGAAT
4071398 CCATATTTGACAA
1 CCATATTTGACAA
4071411 CCATATTTGACA
1 CCATATTTGACA
4071423 CATATTTAGA
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:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
CCATATTTGACAA
Found at i:4073117 original size:34 final size:34
Alignment explanation
Indices: 4073074--4073142 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
4073064 CTGCTTACTC
*
4073074 ATGGGGAAAATATGGAAAGGAAAAGGGAAAACAG
1 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
4073108 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
1 ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
4073142 A
1 A
4073143 GGATGGTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.54, C:0.03, G:0.36, T:0.07
Consensus pattern (34 bp):
ATGGGGAAAAGATGGAAAGGAAAAGGGAAAACAG
Found at i:4079175 original size:18 final size:17
Alignment explanation
Indices: 4079135--4079182 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4079125 TATTATTAAG
*
4079135 TTTA-TATAAGATATTA
1 TTTATTATAAAATATTA
4079151 TTTATTATAAAATATTA
1 TTTATTATAAAATATTA
*
4079168 TCTTATTAAAAAATA
1 T-TTATTATAAAATA
4079183 AATTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTATTATAAAATATTA
Found at i:4079410 original size:40 final size:40
Alignment explanation
Indices: 4079365--4079497 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
4079355 AATAGTGAAG
4079365 AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
1 AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
*** **
4079405 AAAATATGTTTGACTAAAAATTTTAATTTTCTTAGAAAATAGTGAA
1 AAAATATGTTTGACTAAAAATTTTAA--AAATT---AAATTTTG-A
*
4079451 GAAAATATGTTTGACTAAAAATTTTAAAAATTAATTTTTGA
1 -AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
4079492 AAAATA
1 AAAATA
4079498 AAAATATGTG
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
40 32 0.43
41 1 0.01
42 7 0.09
45 8 0.11
46 1 0.01
47 26 0.35
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (40 bp):
AAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTTGA
Found at i:4079440 original size:87 final size:87
Alignment explanation
Indices: 4079338--4079497 Score: 311
Period size: 87 Copynumber: 1.8 Consensus size: 87
4079328 GTTATTTTCG
4079338 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
4079403 GAAAAATATGTTTGACTAAAAA
66 GAAAAATATGTTTGACTAAAAA
*
4079425 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAATTTTT
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
4079490 GAAAAATA
66 GAAAAATA
4079498 AAAATATGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (87 bp):
TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAATTTTAAAAATTAAATTTT
GAAAAATATGTTTGACTAAAAA
Found at i:4079457 original size:47 final size:47
Alignment explanation
Indices: 4079338--4079477 Score: 186
Period size: 47 Copynumber: 3.1 Consensus size: 47
4079328 GTTATTTTCG
4079338 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
*** **
4079385 TTTTAA--AAATT---AAATTTTG-A-AAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
4079425 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
1 TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
4079472 TTTTAA
1 TTTTAA
4079478 AAATTAATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
40 26 0.34
41 1 0.01
42 8 0.11
45 8 0.11
46 1 0.01
47 32 0.42
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (47 bp):
TTTTAATTTTCTTAGAAAATAGTGAAGAAAATATGTTTGACTAAAAA
Found at i:4080169 original size:31 final size:31
Alignment explanation
Indices: 4080117--4080215 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
4080107 TTAGGTAAAC
* * *
4080117 TACACTTTTAGTCACTAAACTATAGGAAAGTT
1 TACA-TTTTAGTCAGTTAACTATAAGAAAGTT
* *
4080149 TTCATTTTAGTCAGTTAACTA-AAAAAAG-T
1 TACATTTTAGTCAGTTAACTATAAGAAAGTT
* * **
4080178 TACAATTTAATCAGTTAACTATTCGAAAGTT
1 TACATTTTAGTCAGTTAACTATAAGAAAGTT
*
4080209 TCCATTT
1 TACATTT
4080216 AAGTGACAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 19 0.37
30 9 0.17
31 21 0.40
32 3 0.06
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (31 bp):
TACATTTTAGTCAGTTAACTATAAGAAAGTT
Found at i:4091738 original size:9 final size:9
Alignment explanation
Indices: 4091671--4091863 Score: 108
Period size: 9 Copynumber: 20.6 Consensus size: 9
4091661 GTTTTCCATA
*
4091671 AAAAATTTT
1 AAAAATTAT
*
4091680 AAAAA-AAT
1 AAAAATTAT
*
4091688 TAAAATATAT
1 AAAAAT-TAT
*
4091698 GAAAATTGAT
1 AAAAATT-AT
4091708 ATAAAATTAT
1 A-AAAATTAT
* *
4091718 AAATATTTT
1 AAAAATTAT
4091727 AAAAATTAT
1 AAAAATTAT
4091736 AAAAATCTA-
1 AAAAAT-TAT
*
4091745 AGAAATTAT
1 AAAAATTAT
4091754 -AAAA-TAT
1 AAAAATTAT
*
4091761 ATAATATTAAT
1 A-AAAATT-AT
*
4091772 AAAATATATTT
1 AAAA-AT-TAT
*
4091783 AAAATTTTAT
1 AAAA-ATTAT
*
4091793 AAAAAGTAT
1 AAAAATTAT
*
4091802 -AAAATCAT
1 AAAAATTAT
4091810 AAAAATAATAT
1 AAAAAT--TAT
*
4091821 AAAAAGTAT
1 AAAAATTAT
*
4091830 TAAAATTGAT
1 AAAAATT-AT
4091840 ATAAAATTAT
1 A-AAAATTAT
4091850 AAAAATTAT
1 AAAAATTAT
4091859 AAAAA
1 AAAAA
4091864 AAATCGTAAT
Statistics
Matches: 141, Mismatches: 26, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
7 3 0.02
8 16 0.11
9 62 0.44
10 28 0.20
11 31 0.22
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4091823 original size:28 final size:28
Alignment explanation
Indices: 4091789--4091862 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
4091779 ATTTAAAATT
4091789 TTATAAAAAGTATAAAA-TCATA-AAAA
1 TTATAAAAAGTATAAAATTCATATAAAA
*
4091815 TAATATAAAAAGTATTAAAATTGATATAAAA
1 T--TATAAAAAGTA-TAAAATTCATATAAAA
*
4091846 TTATAAAAATTATAAAA
1 TTATAAAAAGTATAAAA
4091863 AAAATCGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 1 0.02
28 16 0.39
29 15 0.37
30 4 0.10
31 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
TTATAAAAAGTATAAAATTCATATAAAA
Found at i:4091855 original size:49 final size:47
Alignment explanation
Indices: 4091747--4091863 Score: 114
Period size: 48 Copynumber: 2.4 Consensus size: 47
4091737 AAAATCTAAG
* * * *
4091747 AAATTATAAAATATATAATATTAATAAAATATATTTAAAATTTTATAA
1 AAATTATAAAA-ATATAAAAATAATAAAAAATATTTAAAATTATATAA
*
4091795 AAAGTAT-AAAATCATAAAAATAATATAAAAAGTA-TTAAAATTGATAT-A
1 AAATTATAAAAAT-ATAAAAATAATA-AAAAA-TATTTAAAATT-ATATAA
4091843 AAATTATAAAAATTATAAAAA
1 AAATTATAAAAA-TATAAAAA
4091864 AAATCGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
46 2 0.04
47 13 0.23
48 25 0.44
49 16 0.28
50 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (47 bp):
AAATTATAAAAATATAAAAATAATAAAAAATATTTAAAATTATATAA
Found at i:4091865 original size:20 final size:20
Alignment explanation
Indices: 4091802--4091865 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
4091792 TAAAAAGTAT
* * *
4091802 AAAATCATAAAAATAATATA
1 AAAATTATAAAAATTATAAA
* * *
4091822 AAAAGTATTAAAATTGAT-AT
1 AAAATTATAAAAATT-ATAAA
4091842 AAAATTATAAAAATTATAAA
1 AAAATTATAAAAATTATAAA
4091862 AAAA
1 AAAA
4091866 ATCGTAATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAAATTATAAA
Found at i:4092318 original size:19 final size:19
Alignment explanation
Indices: 4092296--4092410 Score: 54
Period size: 16 Copynumber: 6.3 Consensus size: 19
4092286 GTTTATATCA
4092296 ATTTTAATATATTTTTATT
1 ATTTTAATATATTTTTATT
* * *
4092315 ATTTTTAAAAAATTTAATACTT
1 A-TTTTAATATATTT-TTA-TT
4092337 -TTTTAATAT-TTTTTA--
1 ATTTTAATATATTTTTATT
4092352 ATTATT-ATAT-TTTTTA-T
1 ATT-TTAATATATTTTTATT
*
4092369 ATTTTACA-ATA--TTTATA
1 ATTTTA-ATATATTTTTATT
*
4092386 ATTTT-ATATCATTTTTAAT
1 ATTTTAATAT-ATTTTTATT
4092405 ATTTTA
1 ATTTTA
4092411 CAATTTTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 29
0.65 0.08 0.26
Matches are distributed among these distances:
15 1 0.01
16 20 0.28
17 13 0.18
18 3 0.04
19 13 0.18
20 18 0.25
21 2 0.03
22 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAATATATTTTTATT
Found at i:4092348 original size:9 final size:9
Alignment explanation
Indices: 4092304--4092438 Score: 59
Period size: 9 Copynumber: 14.9 Consensus size: 9
4092294 CAATTTTAAT
4092304 ATATTTTTA
1 ATATTTTTA
*
4092313 TTATTTTTA
1 ATATTTTTA
* **
4092322 AAAAATTTA
1 ATATTTTTA
4092331 ATACTTTTTTA
1 ATA--TTTTTA
*
4092342 ATATTTTTT
1 ATATTTTTA
*
4092351 A-ATTATT-
1 ATATTTTTA
*
4092358 ATATTTTTT
1 ATATTTTTA
*
4092367 ATATTTTACA
1 ATATTTT-TA
*
4092377 ATATTTATA
1 ATATTTTTA
*
4092386 AT-TTTAT-
1 ATATTTTTA
4092393 ATCATTTTTA
1 AT-ATTTTTA
4092403 ATA-TTTTA
1 ATATTTTTA
4092411 CA-ATTTTT-
1 -ATATTTTTA
4092419 ATGATTTGTTA
1 AT-ATTT-TTA
4092430 ATAATTTTT
1 AT-ATTTTT
4092439 TATGGGAAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 27
0.68 0.12 0.19
Matches are distributed among these distances:
7 4 0.04
8 21 0.22
9 45 0.47
10 12 0.13
11 13 0.14
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
ATATTTTTA
Found at i:4092425 original size:17 final size:16
Alignment explanation
Indices: 4092362--4092425 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 16
4092352 ATTATTATAT
4092362 TTTTTATATTTTACAA
1 TTTTTATATTTTACAA
* *
4092378 TATTTATAATTTTATATCA
1 TTTTTAT-ATTTTACA--A
4092397 TTTTTAATATTTTACAA
1 TTTTT-ATATTTTACAA
4092414 TTTTTATGATTT
1 TTTTTAT-ATTT
4092426 GTTAATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 8 0.21
17 17 0.44
19 12 0.31
20 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTTATATTTTACAA
Found at i:4095679 original size:10 final size:10
Alignment explanation
Indices: 4095657--4095823 Score: 89
Period size: 10 Copynumber: 16.8 Consensus size: 10
4095647 GTTTTTCCAT
4095657 TAAAAAATT-
1 TAAAAAATTA
4095666 TAAAAAATTA
1 TAAAAAATTA
*
4095676 T-AAATATT-
1 TAAAAAATTA
4095684 TCAAAAAA-TA
1 T-AAAAAATTA
4095694 TAAAAAA-TA
1 TAAAAAATTA
*
4095703 TAAGAAATTA
1 TAAAAAATTA
*
4095713 TAAAAAAATA
1 TAAAAAATTA
*
4095723 TTAATAAAACATA
1 -TAA-AAAA-TTA
** *
4095736 TTTAAAATTT
1 TAAAAAATTA
**
4095746 TATAAAACGTA
1 TA-AAAAATTA
*
4095757 T--AAAATCA
1 TAAAAAATTA
*
4095765 TAAAAATAATA
1 TAAAAA-ATTA
*
4095776 TAAAAAAGTA
1 TAAAAAATTA
*
4095786 T-TAAAATTGA
1 TAAAAAATT-A
*
4095796 TATAAAATTA
1 TAAAAAATTA
4095806 TAAAAAATTA
1 TAAAAAATTA
4095816 TAAAAAAT
1 TAAAAAAT
4095824 CGTAAGAACT
Statistics
Matches: 121, Mismatches: 23, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.05
9 35 0.29
10 45 0.37
11 27 0.22
12 5 0.04
13 3 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:4095716 original size:19 final size:18
Alignment explanation
Indices: 4095657--4095719 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
4095647 GTTTTTCCAT
4095657 TAAAAAATTTAAAAAATTA
1 TAAAAAATTT-AAAAATTA
* *
4095676 T-AAATATTTCAAAAAATA
1 TAAAAAATTT-AAAAATTA
*
4095694 TAAAAAATATAAGAAATTA
1 TAAAAAATTTAA-AAATTA
4095713 TAAAAAA
1 TAAAAAA
4095720 ATATTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 17 0.47
19 19 0.53
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAAATTTAAAAATTA
Found at i:4095820 original size:9 final size:9
Alignment explanation
Indices: 4095655--4095821 Score: 63
Period size: 9 Copynumber: 17.1 Consensus size: 9
4095645 TAGTTTTTCC
4095655 ATTA-AAAA
1 ATTATAAAA
4095663 ATT-TAAAAA
1 ATTAT-AAAA
*
4095672 ATTATAAAT
1 ATTATAAAA
4095681 ATT-TCAAAA
1 ATTAT-AAAA
*
4095690 AATATAAAA
1 ATTATAAAA
*
4095699 AATATAAGAA
1 ATTATAA-AA
4095709 ATTATAAAAAAA
1 ATTAT---AAAA
4095721 TATTAATAAAA
1 -ATT-ATAAAA
*
4095732 CATATTTAAAA
1 -AT-TATAAAA
*
4095743 TTTTATAAAA
1 -ATTATAAAA
**
4095753 CGTAT-AAA
1 ATTATAAAA
*
4095761 ATCATAAAA
1 ATTATAAAA
4095770 ATAATATAAAAA
1 AT--TAT-AAAA
* *
4095782 AGTATTAAA
1 ATTATAAAA
4095791 ATTGATATAAA
1 ATT-ATA-AAA
4095802 ATTATAAAAA
1 ATTAT-AAAA
4095812 ATTATAAAA
1 ATTATAAAA
4095821 A
1 A
4095822 ATCGTAAGAA
Statistics
Matches: 121, Mismatches: 19, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
8 9 0.07
9 47 0.39
10 29 0.24
11 21 0.17
12 8 0.07
13 5 0.04
14 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
ATTATAAAA
Found at i:4096198 original size:27 final size:28
Alignment explanation
Indices: 4096170--4096247 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
4096160 TTTATATCAA
*
4096170 TTTTAATATTTTTTATTATTTTTAAAAT
1 TTTTAATATTTTTTATTATTTTTAAAAG
* *
4096198 TTTTAATATGTTTT-TTAATTTTAAATAGG
1 TTTTAATATTTTTTATTATTTTTAAA-A-G
4096227 TTTTAATATTTTTTAATTATT
1 TTTTAATATTTTTT-ATTATT
4096248 ATATTTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.24
28 14 0.34
29 13 0.32
31 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTAATATTTTTTATTATTTTTAAAAG
Found at i:4096247 original size:11 final size:10
Alignment explanation
Indices: 4096170--4096243 Score: 57
Period size: 10 Copynumber: 7.7 Consensus size: 10
4096160 TTTATATCAA
4096170 TTTTAATATT
1 TTTTAATATT
*
4096180 TTTTATTA-T
1 TTTTAATATT
*
4096189 TTTTAA-AAT
1 TTTTAATATT
4096198 TTTTAATATGT
1 TTTTAATAT-T
*
4096209 TTTT--TAAT
1 TTTTAATATT
* **
4096217 TTTAAATAGG
1 TTTTAATATT
4096227 TTTTAATATT
1 TTTTAATATT
4096237 TTTTAAT
1 TTTTAAT
4096244 TATTATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
8 5 0.10
9 15 0.31
10 24 0.49
11 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTAATATT
Found at i:4096292 original size:17 final size:17
Alignment explanation
Indices: 4096169--4096327 Score: 85
Period size: 19 Copynumber: 8.9 Consensus size: 17
4096159 GTTTATATCA
* *
4096169 ATTTTAATATTTTTTATT
1 ATTTT-ATAATTTTTAAT
*
4096187 ATTTTTAAAATTTTTAAT
1 A-TTTTATAATTTTTAAT
* *
4096205 ATGTTTTTTAATTTTAAAT
1 A--TTTTATAATTTTTAAT
*
4096224 AGGTTTTAATATTTTTTAAT
1 A--TTTT-ATAATTTTTAAT
*
4096244 -TATTAT-A-TTTT-AT
1 ATTTTATAATTTTTAAT
*
4096257 ATTTTACAA-TTTTAAT
1 ATTTTATAATTTTTAAT
4096273 AATTTTATATCATTTTTAAT
1 -ATTTTATA--ATTTTTAAT
4096293 ATTTTATAATTTTTATGAT
1 ATTTTATAATTTTTA--AT
*
4096312 TTTTTAATAATTTTTA
1 ATTTT-ATAATTTTTA
4096328 TGGGAAACAT
Statistics
Matches: 111, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
13 2 0.02
14 8 0.07
15 5 0.05
16 4 0.04
17 17 0.15
18 11 0.10
19 38 0.34
20 26 0.23
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTATAATTTTTAAT
Found at i:4096325 original size:9 final size:9
Alignment explanation
Indices: 4096147--4096325 Score: 56
Period size: 9 Copynumber: 19.8 Consensus size: 9
4096137 TTTATTTTTG
*
4096147 TAATTTTTA
1 TAATTTTAA
*
4096156 TAAGTTTATA
1 TAATTTTA-A
4096166 TCAATTTTAA
1 T-AATTTTAA
* *
4096176 TATTTTTTAT
1 TA-ATTTTAA
*
4096186 TATTTTTAA
1 TAATTTTAA
4096195 -AATTTTTAA
1 TAA-TTTTAA
**
4096204 T-ATGTTTTT
1 TAAT-TTTAA
4096213 TAATTTTAAA
1 TAATTTT-AA
*
4096223 TAGGTTTTAA
1 TA-ATTTTAA
*
4096233 T-ATTTT-T
1 TAATTTTAA
4096240 TAATTATT-A
1 TAATT-TTAA
4096249 T-ATTTT-A
1 TAATTTTAA
4096256 T-ATTTT-A
1 TAATTTTAA
*
4096263 CAATTTTAA
1 TAATTTTAA
4096272 TAATTTTATA
1 TAATTTTA-A
*
4096282 TCATTTTTAA
1 T-AATTTTAA
4096292 T-ATTTT-A
1 TAATTTTAA
*
4096299 TAATTTTTA
1 TAATTTTAA
*
4096308 TGATTTTTTAA
1 T-A-ATTTTAA
4096319 TAATTTT
1 TAATTTT
4096326 TATGGGAAAC
Statistics
Matches: 129, Mismatches: 22, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
7 13 0.10
8 26 0.20
9 44 0.34
10 24 0.19
11 22 0.17
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TAATTTTAA
Found at i:4104834 original size:25 final size:25
Alignment explanation
Indices: 4104799--4104846 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4104789 TTATTATTTA
*
4104799 AAATAAATTTTTATTTCTATTTATC
1 AAATAAATTTTTATTTCAATTTATC
* *
4104824 AAATAAGTTTTTTTTTCAATTTA
1 AAATAAATTTTTATTTCAATTTA
4104847 AAAATGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (25 bp):
AAATAAATTTTTATTTCAATTTATC
Found at i:4104851 original size:24 final size:24
Alignment explanation
Indices: 4104794--4104851 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
4104784 TATTTTTATT
*
4104794 ATTT-AAAATAAATTTTTATTTCT
1 ATTTAAAAATAAATTTTTATTTCA
* * *
4104817 ATTTATCAAATAAGTTTTTTTTTCA
1 ATTTA-AAAATAAATTTTTATTTCA
4104842 ATTTAAAAAT
1 ATTTAAAAAT
4104852 GTAAAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 20 0.71
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTAAAAATAAATTTTTATTTCA
Found at i:4105904 original size:21 final size:19
Alignment explanation
Indices: 4105880--4105922 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4105870 GATTTAATAG
4105880 TTTCTAGGCAATTCTTCATGT
1 TTTCTAGG-AA-TCTTCATGT
* *
4105901 TTTCTTGGAATGTTCATGT
1 TTTCTAGGAATCTTCATGT
4105920 TTT
1 TTT
4105923 TAAGACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.53
Consensus pattern (19 bp):
TTTCTAGGAATCTTCATGT
Found at i:4109269 original size:19 final size:18
Alignment explanation
Indices: 4109247--4109285 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
4109237 TATACTTTTC
*
4109247 TATAAATTTTGTCTAATTT
1 TATAAATTTTG-ATAATTT
4109266 TATAAATTTTGATAATTT
1 TATAAATTTTGATAATTT
4109284 TA
1 TA
4109286 ATTCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (18 bp):
TATAAATTTTGATAATTT
Found at i:4109311 original size:10 final size:10
Alignment explanation
Indices: 4109213--4109316 Score: 50
Period size: 9 Copynumber: 11.3 Consensus size: 10
4109203 TTTAATATTT
4109213 TAATTTTATA
1 TAATTTTATA
*
4109223 T-ATATT-TA
1 TAATTTTATA
*
4109231 TACTTTTATA
1 TAATTTTATA
4109241 CT--TTTCTATA
1 -TAATTT-TATA
* *
4109251 -AATTTTGTC
1 TAATTTTATA
4109260 TAATTTTATA
1 TAATTTTATA
*
4109270 -AATTTT-GA
1 TAATTTTATA
4109278 TAATTTTA-A
1 TAATTTTATA
**
4109287 TTCTTTTA-A
1 TAATTTTATA
4109296 -AATTTTATA
1 TAATTTTATA
4109305 TAATTTT-TA
1 TAATTTTATA
4109314 TAA
1 TAA
4109317 AAAAATAATA
Statistics
Matches: 71, Mismatches: 12, Indels: 23
0.67 0.11 0.22
Matches are distributed among these distances:
8 9 0.13
9 38 0.54
10 23 0.32
11 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (10 bp):
TAATTTTATA
Found at i:4121335 original size:62 final size:60
Alignment explanation
Indices: 4121262--4121380 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 60
4121252 AACTACGTCA
* *
4121262 AGAAACATAAAAGGTAAAAAAATAGAAAATCAATCTTTTTACTTTTTTTGTGTTTTTTTAG
1 AGAAACATAAAAGGTAAAAAAATAGAAAATCAATATTTTT-CTTTTTTTATGTTTTTTTAG
* *
4121323 AGAATACATAAAAGGTAAAAATATAGAAAATCAATATTTTTTTTTTTTTATGTTTTTT
1 AGAA-ACATAAAAGGTAAAAAAATAGAAAATCAATATTTTTCTTTTTTTATGTTTTTT
4121381 AGGGAATGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 19 0.36
62 34 0.64
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (60 bp):
AGAAACATAAAAGGTAAAAAAATAGAAAATCAATATTTTTCTTTTTTTATGTTTTTTTAG
Found at i:4130252 original size:46 final size:47
Alignment explanation
Indices: 4130168--4130534 Score: 397
Period size: 46 Copynumber: 7.6 Consensus size: 47
4130158 TTTGAGTACT
* *
4130168 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * *
4130214 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
4130266 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
4130312 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
4130358 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
4130410 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * *
4130462 TCTGATCAAGAGACAAAGTGATAAGTAATAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
4130508 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
4130535 GCTACACTTA
Statistics
Matches: 292, Mismatches: 17, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
46 157 0.54
52 135 0.46
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (47 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
Found at i:4130288 original size:98 final size:97
Alignment explanation
Indices: 4130168--4130534 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
4130158 TTTGAGTACT
* *
4130168 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
4130233 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
4130266 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
4130326 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
4130358 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
4130423 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
4130462 TCTGATCAAGAGACAAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
4130527 GATAAGTG
65 GA-AAGTG
4130535 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 43 0.18
98 144 0.60
99 10 0.04
104 43 0.18
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:4130516 original size:196 final size:196
Alignment explanation
Indices: 4130182--4130534 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
4130172 ATCAAGTGAC
* * *
4130182 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
4130247 ATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTA
*
4130312 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
4130377 G
196 G
* *
4130378 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
4130443 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTA
4130508 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
4130535 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Done.