Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 13 of 349
Found at i:3919275 original size:17 final size:17
Alignment explanation
Indices: 3919253--3919285 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3919243 GATATGATAC
3919253 TAAAA-TTATTAAAAAAT
1 TAAAATTTA-TAAAAAAT
3919270 TAAAATTTATAAAAAA
1 TAAAATTTATAAAAAA
3919286 AATCAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTTATAAAAAAT
Found at i:3919284 original size:18 final size:17
Alignment explanation
Indices: 3919253--3919286 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3919243 GATATGATAC
*
3919253 TAAAATTATTAAAAAAT
1 TAAAATTATAAAAAAAT
3919270 TAAAATTTATAAAAAAA
1 TAAAA-TTATAAAAAAA
3919287 ATCAAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:3919577 original size:22 final size:22
Alignment explanation
Indices: 3919542--3919599 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3919532 AAAAGGTATC
* *
3919542 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
3919563 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
3919586 TGCATATCATATCT
1 TACAAATCATATCT
3919600 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:3919634 original size:35 final size:37
Alignment explanation
Indices: 3919571--3919649 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
3919561 ATTACAAAAT
3919571 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
3919607 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
3919642 CATATCAT
1 CATATCAT
3919650 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:3919647 original size:14 final size:15
Alignment explanation
Indices: 3919592--3919647 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
3919582 AGATTGCATA
3919592 TCATATCTAAGATTG
1 TCATATCTAAGATTG
3919607 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
3919625 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
3919642 -CATATC
1 TCATATC
3919648 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:3919657 original size:17 final size:19
Alignment explanation
Indices: 3919578--3919649 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
3919568 AATCATATCT
3919578 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3919597 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
3919615 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
3919632 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
3919650 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3919806 original size:21 final size:20
Alignment explanation
Indices: 3919768--3919807 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3919758 TTGGACTTCG
**
3919768 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
3919788 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
3919808 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:3927464 original size:20 final size:20
Alignment explanation
Indices: 3927422--3927477 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
3927412 CCTTTTTTAG
* * *
3927422 AATAATAATTAAATATACGAA
1 AATAAT-ATTATATACACAAA
3927443 AATAATATTATATACACAAA
1 AATAATATTATATACACAAA
*
3927463 AAT-GTA-TATATACAC
1 AATAATATTATATACAC
3927478 TTATGGTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 9 0.29
19 2 0.06
20 14 0.45
21 6 0.19
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (20 bp):
AATAATATTATATACACAAA
Found at i:3928458 original size:11 final size:11
Alignment explanation
Indices: 3928417--3928450 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3928407 AGAAAAAAAA
*
3928417 AGAGAG-AGGA
1 AGAGAGAAGGG
3928427 AGAGAGAAGGG
1 AGAGAGAAGGG
3928438 AGAGAGAAGGG
1 AGAGAGAAGGG
3928449 AG
1 AG
3928451 GGGGAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (11 bp):
AGAGAGAAGGG
Found at i:3928588 original size:13 final size:13
Alignment explanation
Indices: 3928540--3928590 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
3928530 CGCGTGGTAA
3928540 TTTTTT-TTATAT
1 TTTTTTATTATAT
*
3928552 TTGTTTTGTATATAT
1 TT-TTTTAT-TATAT
*
3928567 ATTTTTATTATAT
1 TTTTTTATTATAT
3928580 TTTTTTATTAT
1 TTTTTTATTAT
3928591 GATGTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 6 0.18
15 6 0.18
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTATTATAT
Found at i:3929002 original size:18 final size:18
Alignment explanation
Indices: 3928979--3929013 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3928969 AGGGTTTCTT
3928979 GGTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTGGGTTA
*
3928997 GGTTTTTTTTTTTGGTT
1 GGTTTTTTTTTTGGGTT
3929014 TAATGGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.71
Consensus pattern (18 bp):
GGTTTTTTTTTTGGGTTA
Found at i:3930405 original size:21 final size:23
Alignment explanation
Indices: 3930357--3930400 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3930347 AATAATCCTT
*
3930357 AAAATCATTATCTAAAAAGGAAA
1 AAAATCAATATCTAAAAAGGAAA
3930380 AAAATCAATAT-TAAAAAGGAA
1 AAAATCAATATCTAAAAAGGAA
3930401 CAAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATCAATATCTAAAAAGGAAA
Found at i:3930752 original size:13 final size:13
Alignment explanation
Indices: 3930734--3930758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3930724 GGTTTGGGAA
3930734 CATCCATTGCTTT
1 CATCCATTGCTTT
3930747 CATCCATTGCTT
1 CATCCATTGCTT
3930759 GTTACTTCGA
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:0.16, C:0.32, G:0.08, T:0.44
Consensus pattern (13 bp):
CATCCATTGCTTT
Found at i:3932616 original size:30 final size:30
Alignment explanation
Indices: 3932582--3932638 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3932572 CAGTATAATC
3932582 ATTAGTTCTCGACTCAACTCATTTGATTGG
1 ATTAGTTCTCGACTCAACTCATTTGATTGG
*
3932612 ATTAGTTCTCGATTCAACTCATTTGAT
1 ATTAGTTCTCGACTCAACTCATTTGAT
3932639 CGGTTCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (30 bp):
ATTAGTTCTCGACTCAACTCATTTGATTGG
Found at i:3933121 original size:26 final size:27
Alignment explanation
Indices: 3933091--3933151 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
3933081 TTCTTAGTCC
*
3933091 AATCAATCCAA-CCAACCAACCAATCA
1 AATCAATCCAATCCAACCAACCAAACA
* *
3933117 AATCAAT-CAATCTAACCAACCAAACC
1 AATCAATCCAATCCAACCAACCAAACA
3933143 AATCAATCC
1 AATCAATCC
3933152 TATTCCAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 3 0.10
26 26 0.87
27 1 0.03
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (27 bp):
AATCAATCCAATCCAACCAACCAAACA
Found at i:3933133 original size:22 final size:22
Alignment explanation
Indices: 3933108--3933150 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3933098 CCAACCAACC
* *
3933108 AACCAATCAAATCAATCAATCT
1 AACCAACCAAACCAATCAATCT
3933130 AACCAACCAAACCAATCAATC
1 AACCAACCAAACCAATCAATC
3933151 CTATTCCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (22 bp):
AACCAACCAAACCAATCAATCT
Found at i:3934686 original size:20 final size:20
Alignment explanation
Indices: 3934661--3934699 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3934651 TATATTAAAC
3934661 CATAATTCATAAATTGTACA
1 CATAATTCATAAATTGTACA
3934681 CATAATTCATAAATTGTAC
1 CATAATTCATAAATTGTAC
3934700 GAAGTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (20 bp):
CATAATTCATAAATTGTACA
Found at i:3937207 original size:20 final size:21
Alignment explanation
Indices: 3937160--3937207 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3937150 CAAAAGGAGT
3937160 AAATTATGTAAAGTGGATACC
1 AAATTATGTAAAGTGGATACC
3937181 AAATTATGTAAAGTGGATACC
1 AAATTATGTAAAGTGGATACC
3937202 -AATTAT
1 AAATTAT
3937208 TCTAACCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (21 bp):
AAATTATGTAAAGTGGATACC
Found at i:3942009 original size:14 final size:15
Alignment explanation
Indices: 3941981--3942013 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3941971 ACGAAATTTA
*
3941981 AAATCTAAAACTATT
1 AAATCTAAAAATATT
3941996 AAAT-TAAAAATATT
1 AAATCTAAAAATATT
3942010 AAAT
1 AAAT
3942014 GAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATCTAAAAATATT
Found at i:3954473 original size:44 final size:45
Alignment explanation
Indices: 3954402--3954515 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
3954392 TTGATCCGAC
* * *
3954402 CTACTACAACTTCAGAG-GTATAGGATTTG-TAGCGTTAATCTTCT
1 CTACTGCAACTTCAGAGAG-ATAAGATTTGCTAGCGTTAATCTACT
* * *
3954446 CTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTTAGTCTACT
1 CTACTGCAACTTCAGAGAGATAAGATTTGCTAGCGTTAATCTACT
* *
3954491 CCACTGCAACTTCAGGGAGATAAGA
1 CTACTGCAACTTCAGAGAGATAAGA
3954516 CTCATAACTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 25 0.42
45 35 0.58
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (45 bp):
CTACTGCAACTTCAGAGAGATAAGATTTGCTAGCGTTAATCTACT
Found at i:3954609 original size:140 final size:140
Alignment explanation
Indices: 3954425--3954705 Score: 393
Period size: 140 Copynumber: 2.0 Consensus size: 140
3954415 AGAGGTATAG
* * *
3954425 GATTTGTAGCGTTAATCTTCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTTAGTCTAC
1 GATTTGTAGCGTTAATCTTCTCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTTAGGCTAC
* * * * * *
3954490 TCCACTGCAACTTCAGGGAGATAAGACTCATAACTTCAACTTGCTCCACTGTAACTTTAGGGAGA
66 TCCACTGCAACTTCAAGAAGATAAGACTCATAACTTCAACCTGCCCCACTGCAACTTCAGGGAGA
3954555 TAAAGTTTGT
131 TAAAGTTTGT
* * * *
3954565 GATTTGTAGCTTTAATCTGT-TCCACTTCATCTTCAGGGAAATAAGATTTGCTATCTTTAGGCTA
1 GATTTGTAGCGTTAATCT-TCTCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTTAGGCTA
** *
3954629 CTCCACTGCAACTTCAAGAAGATAAGACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGGGGG
65 CTCCACTGCAACTTCAAGAAGATAAGACTCATAACTTCAACCTGCCCCACTGCAACTTCAGGGAG
*
3954694 ATAATGTTTGT
130 ATAAAGTTTGT
3954705 G
1 G
3954706 GCTTCAACCT
Statistics
Matches: 123, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
140 122 0.99
141 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (140 bp):
GATTTGTAGCGTTAATCTTCTCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTTAGGCTAC
TCCACTGCAACTTCAAGAAGATAAGACTCATAACTTCAACCTGCCCCACTGCAACTTCAGGGAGA
TAAAGTTTGT
Found at i:3954681 original size:44 final size:44
Alignment explanation
Indices: 3954565--3954921 Score: 183
Period size: 44 Copynumber: 8.2 Consensus size: 44
3954555 TAAAGTTTGT
* * * * * * * *
3954565 GATTTGTAGCTTTAATCTGTTCCACTTCATCTTCAGGGAAATAA
1 GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
* * ** * *
3954609 GATTTGCTATCTTTAGGCTACTCCACTGCAACTTCAAGAAGATAA
1 GATTTG-TAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
* * * *
3954654 GACTTGTAACTTCAACCTGCCCCACTGCAACTTCAGGGGGATAA
1 GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
** * * * * *
3954698 TG-TTTGTGGCTTCAACCTACTCCATTACAACTTCAGGGAGATTA
1 -GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
** * * * * *
3954742 G----GTAGA-TTTGATCTGAC-CTACTACAACTTCAGAGG-TATAG
1 GATTTGTA-ACTTCAACCTG-CTCCACTGCAACTTCA-AGGAGATAA
* * * * *
3954782 GGTTTGTAGCTTTAATCTGCTCTACTGCAACTTC-AGAGAGATAA
1 GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAG-GAGATAA
* ** *
3954826 GATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAA
1 GATTTG-TAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
* * *
3954871 GACTCGTAACTTCAACCTGCTCCACTGCAATTTCAAGGAGATAA
1 GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
*
3954915 GGTTTGT
1 GATTTGT
3954922 GATTTGTAGC
Statistics
Matches: 236, Mismatches: 62, Indels: 30
0.72 0.19 0.09
Matches are distributed among these distances:
40 22 0.09
41 3 0.01
42 2 0.01
43 3 0.01
44 136 0.58
45 68 0.29
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
GATTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
Found at i:3955272 original size:64 final size:64
Alignment explanation
Indices: 3955170--3955291 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
3955160 TCATGTATCT
3955170 ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAAATGTG
* *
3955234 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAACTGCTCCTAACTA
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTA
3955292 GATATGTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (64 bp):
ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:3959865 original size:19 final size:19
Alignment explanation
Indices: 3959830--3959867 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3959820 ATGCAATGCA
*
3959830 AATGCAAATGCATGGAATG
1 AATGCAAAAGCATGGAATG
3959849 AATGCAAAAG-ATAGGAATG
1 AATGCAAAAGCAT-GGAATG
3959868 CGTTGATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.47, C:0.08, G:0.26, T:0.18
Consensus pattern (19 bp):
AATGCAAAAGCATGGAATG
Found at i:3965257 original size:12 final size:12
Alignment explanation
Indices: 3965240--3965268 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3965230 TTGTCATTTC
3965240 TTTATTATTATT
1 TTTATTATTATT
3965252 TTTATTATTATT
1 TTTATTATTATT
3965264 TTTAT
1 TTTAT
3965269 CGTTACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:3965388 original size:3 final size:3
Alignment explanation
Indices: 3965380--3965409 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3965370 AAAAAATTAG
3965380 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3965410 CGTTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3966524 original size:40 final size:40
Alignment explanation
Indices: 3966432--3966568 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 40
3966422 TGTAACAACC
*
3966432 AGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAACC
1 AGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAACT
* *
3966472 CGTACGAATGCCTTCGGGACTTAACCCGGTTATAATAACT
1 AGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAACT
* ** *
3966512 AGCAC-AATTGCCTTC-GGATCTT-ACTCTGAATATAGTAACT
1 AGCACGAA-TGCCTTCGGGA-CTTAAC-CCGGTTATAATAACT
*
3966552 AGCACAAATGCCTTCGG
1 AGCACGAATGCCTTCGG
3966569 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
39 7 0.08
40 73 0.88
41 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (40 bp):
AGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAACT
Found at i:3969472 original size:177 final size:177
Alignment explanation
Indices: 3969167--3969641 Score: 702
Period size: 177 Copynumber: 2.7 Consensus size: 177
3969157 GAATTCACAA
* *
3969167 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAAATTGTAGTCTTATCTTCCTAAGGTAGCA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
* *
3969232 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAATATGGC
66 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
3969297 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAGATTTTAGCCACCAG
131 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAGATTTTAGCCACCAG
** * * *
3969344 CCTTATCTCTCTAAGGTAGCGCGAGAGCTGGTTGAAGATTGAAGTCTTATCTTCTTGAGGTAGCA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
* **
3969409 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAATATGGA
66 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
* * * * *
3969474 GATTCTTATCTTCCCGTGGTAGTAGGGGAGCAGATTTTTGCCACCAG
131 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAGATTTTAGCCACCAG
* * * *
3969521 CCTTATCTCTCTGAGTTAGCAAGAGAGCAGGTTAAAGATTGTAGTCTTATCTTCCTGAGGTAGTA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
* * *
3969586 AGGAAGCAGACTGAAGATT-ACAAATCTTATCTCCCTACGC-GATAGTGGAGCAGATC
66 AGGAAGCAGACTAAAGATTGA-AGATCTTATCTCCCTAAGCAG-TAGTGGAGCAGATC
3969642 GAAGACGATG
Statistics
Matches: 265, Mismatches: 31, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
176 2 0.01
177 263 0.99
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (177 bp):
CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAGATTTTAGCCACCAG
Found at i:3969584 original size:88 final size:87
Alignment explanation
Indices: 3969167--3969595 Score: 245
Period size: 88 Copynumber: 4.9 Consensus size: 87
3969157 GAATTCACAA
* * **
3969167 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAAATTGTAGTCTTATCTTCCTAAGGTAGCA
1 CCTTATCTCTCTAA-GTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCCGAGGTAGCA
* ** *****
3969232 AGGAAGCAGACTAAAGATTGAAG
65 AGGAAGCAGATTTTAGCCACCAG
* * * * * * * ** * *
3969255 ATCTTATCTCCCTAAGCAG-TAGTGGAGTAGATCAAATATGGCGAA-TCTTATCTTCCCGAGGTA
1 -CCTTATCTCTCTAAGTAGCAAG-AGAGCAGGTTGAAGAT--TGAAGTCTTATCTTCCCGAGGTA
3969318 GC-AGGAGAGCAGATTTTAGCCACCAG
62 GCAAGGA-AGCAGATTTTAGCCACCAG
** * **
3969344 CCTTATCTCTCTAAGGTAGCGCGAGAGCTGGTTGAAGATTGAAGTCTTATCTTCTTGAGGTAGCA
1 CCTTATCTCTCTAA-GTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCCGAGGTAGCA
* ** *****
3969409 AGGAAGCAGACTAAAGATTGAAG
65 AGGAAGCAGATTTTAGCCACCAG
* * * * * * * * *
3969432 ATCTTATCTCCCTAAGCAG-TAGTAGAGCAGATTGAATATGGAGATTCTTATCTTCCCGTGGTAG
1 -CCTTATCTCTCTAAGTAGCAAG-AGAGCAGGTTGAAGATTGA-AGTCTTATCTTCCCGAGGTAG
* * * *
3969496 TAGGGGAGCAGATTTTTGCCACCAG
63 CAAGGAAGCAGATTTTAGCCACCAG
* * * * *
3969521 CCTTATCTCTCTGAGTTAGCAAGAGAGCAGGTTAAAGATTGTAGTCTTATCTTCCTGAGGTAGTA
1 CCTTATCTCTCTAAG-TAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCCGAGGTAGCA
3969586 AGGAAGCAGA
65 AGGAAGCAGA
3969596 CTGAAGATTA
Statistics
Matches: 242, Mismatches: 85, Indels: 27
0.68 0.24 0.08
Matches are distributed among these distances:
87 6 0.02
88 116 0.48
89 115 0.48
90 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (87 bp):
CCTTATCTCTCTAAGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCCGAGGTAGCAA
GGAAGCAGATTTTAGCCACCAG
Found at i:3969638 original size:44 final size:44
Alignment explanation
Indices: 3969593--3970155 Score: 353
Period size: 44 Copynumber: 13.0 Consensus size: 44
3969583 GTAAGGAAGC
* * *
3969593 AGACTGAAGATTACAAATCTTATCTCCCTACGC-GATAGTGGAGC
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAG-TAGTGGAGT
* ** * *
3969637 AGA-TCGAAGACGATGAATCTTGTCTCCCTAAGCAGTAGTAGAGT
1 AGACT-GAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * * * * * *
3969681 AGGCTAAAGATTACAGATCTTATCTCCCTAAACAATAGTGAAGC
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * ** * * * *
3969725 AGA-TCAAAGACGATGAATCTTGTTTCCCTAAGCAATAGTAGAGT
1 AGACT-GAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * * *
3969769 AGATTTAAG-CCAC-CATCCTATCTCCCTAAGCAGTAGTGGAGT
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * *
3969811 AGGCTGAAGA-T-TAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
** * * * * *
3969853 AGA-TCGAAGACGGCGAATCTTGTCTCTCTAAGCAGCAGTGGAGA
1 AGACT-GAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * * *
3969897 AGATTTAAG-CCAC-CATCCTATCTCCCTAAGCAGTAGTGGAGT
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * *
3969939 AGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGT
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * * * *
3969983 AGA-TCGAAGACGACGAATCTTGTCTCCCTAAGCAATAATGGAGC
1 AGACT-GAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * * * * *
3970027 AGATTTAAG-CCAC-CATCCTATTTCCCTAAGCAGTAGTGGAGT
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
* * *
3970069 AGGCTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGGAGT
1 AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
** * * * *
3970113 AGA-TCGAAGACGGCGAATTTTGTCTCTCTAAGCAGTAGTGGAG
1 AGACT-GAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAG
3970156 CATATTTAAG
Statistics
Matches: 390, Mismatches: 111, Indels: 36
0.73 0.21 0.07
Matches are distributed among these distances:
41 1 0.00
42 119 0.31
43 15 0.04
44 250 0.64
45 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
AGACTGAAGACTACAAATCTTATCTCCCTAAGCAGTAGTGGAGT
Found at i:3969823 original size:130 final size:130
Alignment explanation
Indices: 3969659--3970206 Score: 812
Period size: 130 Copynumber: 4.2 Consensus size: 130
3969649 ATGAATCTTG
* * * * *
3969659 TCTCCCTAAGCAGTAGTAGAGTAGGCTAAAGATTACAGATCTTATCTCCCTAAACAATAGTGAAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * * * *
3969724 CAGATCAAAGACGATGAATCTTGTTTCCCTAAGCAATAGTAGAGTAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTTAAGCCACCATCCTA
3969789 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT--AGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * ** *
3969852 CAGATCGAAGACGGCGAATCTTGTCTCTCTAAGCAGCAGTGGAGAAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTTAAGCCACCATCCTA
3969917 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* *
3969982 TAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAATGGAGCAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTTAAGCCACCATCCTA
* * *
3970047 TTTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * * * * * *
3970112 TAGATCGAAGACGGCGAATTTTGTCTCTCTAAGCAGTAGTGGAGCATATTTAAGTCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTTAAGCCACCATCCTA
* * *
3970177 TCTCCCTAAGCAGTGGTGGAGCAGGTTGAA
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAA
3970207 ATCAACAATT
Statistics
Matches: 381, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
128 116 0.30
130 265 0.70
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (130 bp):
TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTTAAGCCACCATCCTA
Found at i:3969895 original size:86 final size:86
Alignment explanation
Indices: 3969787--3970200 Score: 327
Period size: 86 Copynumber: 4.8 Consensus size: 86
3969777 GCCACCATCC
*
3969787 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTA-GATCTTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGACTACGATCTTATCTCCCTAAGCAGTAGTGGA
*
3969851 GCAGATCGAAGACGGCGAATCT
66 GCAGATCGAAGACGAC-AATCT
* * * * ** * * * *
3969873 TGTCTCTCTAAGCAGCAGTGGAGAAGATTTAAG-CCACCATCCTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGACTACGATCTTATCTCCCTAAGCAGTAGTGGA
* * **
3969937 GTAG-GCTGAAGATTACAGATCT
66 GCAGATC-GAAGACGACA-ATCT
* * * * *
3969959 TATCTCCCTAAGCAGTAGTGGAGTA-GATCGAAGACGACGAATCTTGTCTCCCTAAGCAATAATG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCT-GAAGACTACG-ATCTTATCTCCCTAAGCAGTAGTG
** * * *
3970023 GAGCAGATTTAAG-CCACCATCC
64 GAGCAGATCGAAGACGACAATCT
* * * *
3970045 TATTTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGACTAC-GATCTTATCTCCCTAAGCAGTAGTGG
* * *
3970110 AGTAGATCGAAGACGGCGAATTT
65 AGCAGATCGAAGACGAC-AATCT
* * * *** * * * * *
3970133 TGTCTCTCTAAGCAGTAGTGGAGCATATTTAAGTC-ACCATCCTATCTCCCTAAGCAGTGGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGACTACGATCTTATCTCCCTAAGCAGTAGTGGA
3970197 GCAG
66 GCAG
3970201 GTTGAAATCA
Statistics
Matches: 248, Mismatches: 69, Indels: 22
0.73 0.20 0.06
Matches are distributed among these distances:
85 4 0.02
86 178 0.72
87 11 0.04
88 55 0.22
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (86 bp):
TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGACTACGATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGACGACAATCT
Found at i:3970297 original size:44 final size:44
Alignment explanation
Indices: 3970240--3970629 Score: 139
Period size: 44 Copynumber: 8.9 Consensus size: 44
3970230 AGTTTCAGGG
*
3970240 GAGTAAATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
* * * * * *** ***
3970284 GAGCT-GCTCGAAGCCACAATTCT-TATCTCCTTGAAGTTTTAGGG
1 GAG-TAGATCGAAGCTACAAATCTCT-TCTCCCTGAAATGACATTA
* *
3970328 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGACATTG
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
* * * * * * * * ** *
3970372 GAGTGGCTCGTAGCCACAATTCT-TATTTCCTTGAAGTTCCAGCGTA
1 GAGTAGATCGAAGCTACAAATCTCT-TCTCCCTGAAATGACA--TTA
* * * *
3970418 -A-TAGATCGAAGCTACAAATCTCTTCTTCCTAAAATGGCATTG
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
* * * * * * ** ***
3970460 GAGTGGCTCGAAGCCAC-AAT-TGTTATCTCCTTAAAGTTCCAGCG
1 GAGTAGATCGAAGCTACAAATCTCTTCTC-CCTGAAA-TGACATTA
* * **
3970504 GAGTAGATCGAAGTTACAAATCTCTTCTCCTTGAAATGGTATTA
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
** * * * * * ** ***
3970548 GAGCGGCTCGAAGCCACAATTCT-TATCTCCTTGAAGTTTCAACG
1 GAGTAGATCGAAGCTACAAATCTCT-TCTCCCTGAAATGACATTA
*
3970592 GAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATG
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATG
3970630 GTATTGGAGC
Statistics
Matches: 233, Mismatches: 97, Indels: 32
0.64 0.27 0.09
Matches are distributed among these distances:
42 5 0.02
43 14 0.06
44 195 0.84
45 13 0.06
46 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATTA
Found at i:3970328 original size:88 final size:88
Alignment explanation
Indices: 3970211--3970654 Score: 604
Period size: 88 Copynumber: 5.0 Consensus size: 88
3970201 GTTGAAATCA
* *
3970211 ACAATTCTTATCTCCTTGAAGTTTCAGGGGAGTAAATCGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
3970276 TGACATTAGAGCTGCTCGAAGCC
66 TGGCATTGGAGCTGCTCGAAGCC
* * *
3970299 ACAATTCTTATCTCCTTGAAGTTTTAGGGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
3970364 TGACATTGGAG-TGGCTCGTAGCC
66 TGGCATTGGAGCT-GCTCGAAGCC
* * * * * *
3970387 ACAATTCTTATTTCCTTGAAGTTCCAGCGTAATAGATCGAAGCTACAAATCTCTTCTTCCTAAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
3970452 TGGCATTGGAG-TGGCTCGAAGCC
66 TGGCATTGGAGCT-GCTCGAAGCC
* * * * *
3970475 ACAATTGTTATCTCCTTAAAGTTCCAGCGGAGTAGATCGAAGTTACAAATCTCTTCTCCTTGAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* * *
3970540 TGGTATTAGAGCGGCTCGAAGCC
66 TGGCATTGGAGCTGCTCGAAGCC
* *
3970563 ACAATTCTTATCTCCTTGAAGTTTCAACGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* * *
3970628 TGGTATTGGAGCGGCTCAAAGCC
66 TGGCATTGGAGCTGCTCGAAGCC
3970651 ACAA
1 ACAA
3970655 ATCACAAACC
Statistics
Matches: 319, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 1 0.00
88 318 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (88 bp):
ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
TGGCATTGGAGCTGCTCGAAGCC
Found at i:3970777 original size:65 final size:65
Alignment explanation
Indices: 3970673--3970804 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
3970663 CCTTATCTCC
* *
3970673 CTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
*
3970738 CTAAAGTTGCAGTGGAGTAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
1 CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
3970803 CT
1 CT
3970805 GAAGATAGCG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (65 bp):
CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
Found at i:3970918 original size:44 final size:44
Alignment explanation
Indices: 3970741--3970897 Score: 192
Period size: 44 Copynumber: 3.5 Consensus size: 44
3970731 GAGCAGACTA
* *
3970741 AAGTTGCAGTGGAGTA-AGTTGAAGTTAC-AAGTCTTATCTCCCTA
1 AAGTTGCAGTGGAGCAGA-TTGAAGTTACGAA-TCTTATCTCCCTG
* *
3970785 AAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGTTA-CGAATCTTATCTCCCTG
* * *
3970830 AAGTTGCAATAGAGCAGGTTGAAGTTACGAATCTTATCTCCCTG
1 AAGTTGCAGTGGAGCAGATTGAAGTTACGAATCTTATCTCCCTG
* *
3970874 AAGTTGTAGTGGAGTAGATTGAAG
1 AAGTTGCAGTGGAGCAGATTGAAG
3970898 CCACTAGTCT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
44 58 0.60
45 36 0.38
46 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (44 bp):
AAGTTGCAGTGGAGCAGATTGAAGTTACGAATCTTATCTCCCTG
Found at i:3972478 original size:6 final size:6
Alignment explanation
Indices: 3972467--3972493 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3972457 ATTCAACCCC
3972467 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
3972494 AAGATTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:3972776 original size:3 final size:3
Alignment explanation
Indices: 3972768--3972827 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
3972758 AAAAAATTAG
3972768 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3972816 ATT ATT ATT ATT
1 ATT ATT ATT ATT
3972828 CGTTTATTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3972912 original size:23 final size:24
Alignment explanation
Indices: 3972878--3972922 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3972868 ATTTGAACCT
*
3972878 TTTATTTTTTTATTT-TTATTTCA
1 TTTATTTATTTATTTCTTATTTCA
3972901 TTTATTTATTTATTTCTTATTT
1 TTTATTTATTTATTTCTTATTT
3972923 ATAATTAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTATTTATTTCTTATTTCA
Found at i:3973043 original size:3 final size:3
Alignment explanation
Indices: 3973035--3973080 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3973025 CAAAGTTTAG
3973035 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3973081 CCTTCTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3980313 original size:40 final size:40
Alignment explanation
Indices: 3980264--3980370 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
3980254 CGGATGTAAC
*
3980264 AACCAGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
*
3980304 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
*
3980344 AA-CTAGCAC-AATTGCCTTCGGATCTTA
1 AACCT-GCACGAA-TGCCTTCGGAACTTA
3980371 GTCCGAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 4 0.07
40 57 0.93
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (40 bp):
AACCTGCACGAATGCCTTCGGAACTTAACCCGGTTATAAT
Found at i:3980387 original size:40 final size:40
Alignment explanation
Indices: 3980268--3980420 Score: 130
Period size: 40 Copynumber: 3.8 Consensus size: 40
3980258 TGTAACAACC
* * ** **
3980268 AGCACGAATGCCTTCGGAACTTAACCCGGTTATAATAACCT
1 AGCACAAATGCCTTCGGATCTTAGTCCGAATATAATAA-CT
* ** **
3980309 -GCACGAATGCCTTCGGGA-CTTAACCCGGTTATAATAACT
1 AGCACAAATGCCTTC-GGATCTTAGTCCGAATATAATAACT
* *
3980348 AGCACAATTGCCTTCGGATCTTAGTCCGAATATAGTAACT
1 AGCACAAATGCCTTCGGATCTTAGTCCGAATATAATAACT
* * *
3980388 AGCACAAATGCCTTCTGATCTTATTCCGGATAT
1 AGCACAAATGCCTTCGGATCTTAGTCCGAATAT
3980421 CATCCGAATA
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
39 5 0.05
40 90 0.92
41 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGATCTTAGTCCGAATATAATAACT
Found at i:3982090 original size:40 final size:40
Alignment explanation
Indices: 3981986--3982215 Score: 178
Period size: 41 Copynumber: 5.9 Consensus size: 40
3981976 CGTTTGTCCG
* * * * * **
3981986 AAACGCCACTAAAAGCTAAACTATAGCGGCATTTTTGGCAA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTCTC-A
*
3982027 AAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCTCA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTCTCA
*
3982067 AAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTAATCTC-
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTT--TCTCA
* * *
3982108 AAACGCCACT---AA---AT---TA-CGGCATTTTTGTCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTCT-CA
* * *
3982139 AAACGCCA-TAAAAAACTGATCAATTGTGGCGTTTTTATCCA
1 AAACGCCACT-AAAAACTGATCAATAGCGGCGTTTTTCT-CA
*
3982180 AAACGCCACTAAAAACTGATTAATAGCGGCGTTTTT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT
3982216 GGTCCAAACG
Statistics
Matches: 152, Mismatches: 21, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
29 2 0.01
30 2 0.01
31 16 0.11
32 2 0.01
34 2 0.01
35 2 0.01
37 2 0.01
38 1 0.01
40 35 0.23
41 83 0.55
42 5 0.03
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (40 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTCTCA
Found at i:3982225 original size:41 final size:40
Alignment explanation
Indices: 3982124--3982227 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 40
3982114 CACTAAATTA
* *
3982124 CGGCATTTTTGTCCCAAACGCCATAAAAAACTGATCAATTG
1 CGGCGTTTTTGT-CCAAACGCCATAAAAAACTGATCAATAG
* * *
3982165 TGGCGTTTTTATCCAAAACGCCACT-AAAAACTGATTAATAG
1 CGGCGTTTTTGTCC-AAACGCCA-TAAAAAACTGATCAATAG
3982206 CGGCGTTTTTGGTCCAAACGCC
1 CGGCGTTTTT-GTCCAAACGCC
3982228 GCAAAAAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.04
41 47 0.89
42 4 0.08
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (40 bp):
CGGCGTTTTTGTCCAAACGCCATAAAAAACTGATCAATAG
Found at i:3982227 original size:113 final size:112
Alignment explanation
Indices: 3982012--3982214 Score: 300
Period size: 112 Copynumber: 1.8 Consensus size: 112
3982002 TAAACTATAG
* *
3982012 CGGCATTTTTGGCAAAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCTCAAAACGCCACT
1 CGGCATTTTTGGCAAAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCAAAACGCCACT
*
3982077 AAAAGCTGATCAATAGCGGCGTTTTAATCTCAAACGCCACTAAATTA
66 AAAAACTGATCAATAGCGGCGTTTTAATCTCAAACGCCACTAAATTA
* ** * *
3982124 CGGCATTTTTGTCCCAAACGCCA-TAAAAAACTGATCAATTGTGGCGTTTTTATCCAAAACGCCA
1 CGGCATTTTTGGCAAAAACGCCACT-AAAAACTGATCAATAGCGGCGTTTTTAT-CAAAACGCCA
*
3982188 CTAAAAACTGATTAATAGCGGCGTTTT
64 CTAAAAACTGATCAATAGCGGCGTTTT
3982215 TGGTCCAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
111 1 0.01
112 44 0.55
113 35 0.44
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (112 bp):
CGGCATTTTTGGCAAAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCAAAACGCCACT
AAAAACTGATCAATAGCGGCGTTTTAATCTCAAACGCCACTAAATTA
Found at i:3984556 original size:14 final size:15
Alignment explanation
Indices: 3984537--3984566 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3984527 TGTGTTTATA
3984537 TAAATACAT-AATTC
1 TAAATACATAAATTC
3984551 TAAATACATAAATTC
1 TAAATACATAAATTC
3984566 T
1 T
3984567 GAAGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATACATAAATTC
Found at i:3987087 original size:23 final size:23
Alignment explanation
Indices: 3987057--3987106 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
3987047 AACATTAACC
3987057 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
3987080 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
3987103 AAAT
1 AAAT
3987107 AAATTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:3987715 original size:242 final size:241
Alignment explanation
Indices: 3987224--3987661 Score: 767
Period size: 241 Copynumber: 1.8 Consensus size: 241
3987214 TAAGTATGAA
3987224 TTAAT-TTTATTACATGTAGATTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCA
1 TTAATATTTATTACATGTAGATTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCA
3987288 ACCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTAT
66 ACCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTAT
*
3987353 ATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTTTAACAACGCCACGTATGATGAATCTTAAA
131 ATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAA
* * * *
3987418 AAATTCAAGAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTAT
196 AAATTCAACAAGACTTCAAAAAAGTTCTATCGAGATAATTTACTAT
* *
3987464 TGAATATTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCC
1 TTAATATTTATTA-CATGTAGATTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCC
3987529 AA-CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
65 AACCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
3987593 TATCGAGCTGTAAGATAATAATGGATCCT-CCTA-GTGTAACAACGCCACGTATGATGAATCTTA
130 TATCGAGCTGTAAGAT-ATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTA
3987656 AAAAAT
194 AAAAAT
3987662 GACTATATTC
Statistics
Matches: 192, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
240 39 0.20
241 89 0.46
242 64 0.33
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (241 bp):
TTAATATTTATTACATGTAGATTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCA
ACCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTAT
ATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAA
AAATTCAACAAGACTTCAAAAAAGTTCTATCGAGATAATTTACTAT
Found at i:3987803 original size:9 final size:9
Alignment explanation
Indices: 3987780--3987906 Score: 128
Period size: 9 Copynumber: 13.6 Consensus size: 9
3987770 ATTGATCATT
*
3987780 ACTTAAATA
1 ACTTACATA
*
3987789 AATTACATA
1 ACTTACATA
3987798 ACTTACATA
1 ACTTACATA
* *
3987807 ACTCATATA
1 ACTTACATA
3987816 ACTTACATA
1 ACTTACATA
*
3987825 ATTTACATAA
1 ACTTACAT-A
3987835 CACTTACATA
1 -ACTTACATA
*
3987845 ACTCACATA
1 ACTTACATA
3987854 ACTTACATA
1 ACTTACATA
*
3987863 ATTTACATA
1 ACTTACATA
*
3987872 ACTCACATA
1 ACTTACATA
*
3987881 ACGTACATAACA
1 ACTTACAT---A
3987893 ACTTACATA
1 ACTTACATA
3987902 ACTTA
1 ACTTA
3987907 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
9 79 0.82
10 2 0.02
11 7 0.07
12 8 0.08
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:3987849 original size:38 final size:38
Alignment explanation
Indices: 3987780--3987873 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
3987770 ATTGATCATT
* * *
3987780 ACTTAAATAAATTACAT-A-ACTTACATAACTCATATA
1 ACTTACATAATTTACATAACACTTACATAACTCACATA
3987816 ACTTACATAATTTACATAACACTTACATAACTCACATA
1 ACTTACATAATTTACATAACACTTACATAACTCACATA
3987854 ACTTACATAATTTACATAAC
1 ACTTACATAATTTACATAAC
3987874 TCACATAACG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
36 15 0.28
37 1 0.02
38 37 0.70
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (38 bp):
ACTTACATAATTTACATAACACTTACATAACTCACATA
Found at i:3988006 original size:15 final size:16
Alignment explanation
Indices: 3987969--3988006 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
3987959 GTTTAAATTT
3987969 CATAACTTACATAATCTA
1 CATAACTTACATAA--TA
3987987 CATAACTTACATAA-A
1 CATAACTTACATAATA
3988002 CATAA
1 CATAA
3988007 AGATATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
18 14 0.70
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:3992258 original size:15 final size:16
Alignment explanation
Indices: 3992233--3992263 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3992223 GCAACAACTT
3992233 AGAGCGGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
3992249 AGAG-GGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
3992264 CTGCAGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (16 bp):
AGAGCGGAGGCAGCAG
Found at i:3992575 original size:31 final size:31
Alignment explanation
Indices: 3992540--3992606 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
3992530 TTTTGTTGTT
* *
3992540 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
3992571 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
3992602 TTTTA
1 TTTTA
3992607 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:3992706 original size:43 final size:42
Alignment explanation
Indices: 3992680--3992838 Score: 237
Period size: 43 Copynumber: 3.7 Consensus size: 42
3992670 TGTAAAAAAG
3992680 CGCCGCTAAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCT-AAAAGCCTTGACCTTTAGCGGCGCTTTT-CCACAAA
* *
3992724 TGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTTGCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGC-TTTTCCACAAA
* *
3992767 CGCCGCTAAAAGGCTTGACCTTTAGCGGCGCTTATCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTT-TTCCACAAA
*
3992810 CGCCACTAAAAGCCTTGACCTTTAGCGGC
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGC
3992839 ATTTTTTTCC
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
42 2 0.02
43 93 0.89
44 10 0.10
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (42 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCACAAA
Found at i:3992805 original size:86 final size:87
Alignment explanation
Indices: 3992680--3992838 Score: 275
Period size: 86 Copynumber: 1.8 Consensus size: 87
3992670 TGTAAAAAAG
* * *
3992680 CGCCGCTAAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAAGCCTTGACCT
1 CGCCGCTAAAAAGCCTTGACCTTTAGCGGCGCTTATCCCACAAACGCCACTAAAAGCCTTGACCT
3992745 TTAGCGGCGCTTTTTGCACAAA
66 TTAGCGGCGCTTTTTGCACAAA
*
3992767 CGCCGCT-AAAAGGCTTGACCTTTAGCGGCGCTTATCCCACAAACGCCACTAAAAGCCTTGACCT
1 CGCCGCTAAAAAGCCTTGACCTTTAGCGGCGCTTATCCCACAAACGCCACTAAAAGCCTTGACCT
3992831 TTAGCGGC
66 TTAGCGGC
3992839 ATTTTTTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
86 61 0.90
87 7 0.10
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (87 bp):
CGCCGCTAAAAAGCCTTGACCTTTAGCGGCGCTTATCCCACAAACGCCACTAAAAGCCTTGACCT
TTAGCGGCGCTTTTTGCACAAA
Found at i:3999487 original size:40 final size:40
Alignment explanation
Indices: 3999438--3999538 Score: 168
Period size: 40 Copynumber: 2.5 Consensus size: 40
3999428 CGGATGTAAC
3999438 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
3999478 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
3999518 AACTAGCAC-AATTGCCTTCGG
1 AACCAGCACGAA-TGCCTTCGG
3999539 ATCTTAGTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 2 0.04
40 55 0.96
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:3999561 original size:40 final size:40
Alignment explanation
Indices: 3999512--3999587 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
3999502 TTAACCCGGT
*
3999512 TATAATAACTAGCACAATTGCCTTCGGATCTTAGTCTGAA
1 TATAATAACTAGCACAAATGCCTTCGGATCTTAGTCTGAA
*
3999552 TATAGTAACTAGCACAAATGCCTTCGGATCTTAGTC
1 TATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
3999588 CGGATATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (40 bp):
TATAATAACTAGCACAAATGCCTTCGGATCTTAGTCTGAA
Found at i:4002479 original size:177 final size:177
Alignment explanation
Indices: 4002174--4002647 Score: 684
Period size: 177 Copynumber: 2.7 Consensus size: 177
4002164 GAATTCACAA
* *
4002174 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAAATTGTAGTCTTATCTTCCTAAGGTAGCA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
* *
4002239 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAATATGGC
66 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
4002304 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAAATTTTAGCCACCAG
131 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAAATTTTAGCCACCAG
** * * * *
4002351 CCTTATCTCTCTAAGGTAGCGCGAGAGCTGGTTGAAGATTGAAGTCTTATCTTCTTGAGATAGCA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
**
4002416 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAATATGGA
66 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
* * * * * *
4002481 GATTCTTATCTTCCCGTGGTAGTAGGGGAGCAGATTTTTGCCACCAG
131 GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAAATTTTAGCCACCAG
* * * *
4002528 CCTTATCTCTCTGAGTTAGCAAGAGAGCAGGTTAAAGATTGTAGTCTTATCTTCCTGAGGTAGTA
1 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
* * *
4002593 AGGAAGCAGACTGAAGATT-ACAAATCTTATCTCCCTACGC-GATAGTGG-GCAGATC
66 AGGAAGCAGACTAAAGATTGA-AGATCTTATCTCCCTAAGCAG-TAGTGGAGCAGATC
4002648 GAAGATGATG
Statistics
Matches: 263, Mismatches: 32, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
176 8 0.03
177 255 0.97
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (177 bp):
CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCA
AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGA
GAATCTTATCTTCCCGAGGTAGCAGGAGAGCAAATTTTAGCCACCAG
Found at i:4002707 original size:44 final size:42
Alignment explanation
Indices: 4002616--4003203 Score: 301
Period size: 44 Copynumber: 13.6 Consensus size: 42
4002606 AAGATTACAA
* * * * *
4002616 ATCTTATCTCCCTACGC-GATAGTGG-GCAGATCGAAGATGATG
1 ATCTTATCTCCCTAAGCAG-TAGTGGAGTAGCT-GAAGACGACG
* * * **
4002658 AATCTTGTCTCCCTAAGCAGTAGTAGAGTATGCTAAAGATTACAG
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GCTGAAGACGAC-G
* * * * * * *
4002703 ATCTTATCTCCCTAAACAATAGTGAAGCAGATCAAAGACGATG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGCT-GAAGACGACG
* * * * * * * *
4002746 AATCTTGTTTCCCTAAGCAATAGTAGAGTAGATTTAAG-CCACC
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAG-CTGAAGACGACG
* **
4002789 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTA-G
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GCTGAAGACGACG
* * *
4002831 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGCT-GAAGACGACG
* * * * * * * *
4002874 AATCTTGTCTCTCTAAGCAGCAGTGGAGAAGATTTAAG-CCACC
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAG-CTGAAGACGACG
* **
4002917 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GCTGAAGACGAC-G
*
4002961 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGACG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGCT-GAAGACGACG
* * * * * * *
4003004 AATCTTGTCTCCCTAAGCAGTAATGGAGCAGATTTAAG-CCACC
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAG-CTGAAGACGACG
* * ** *
4003047 ATCCTATTTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTA-GCTGAAGACGAC-G
* * * **
4003091 ATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGTG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGCT-GAAGACGACG
* * * * * * *
4003134 AATTTTGTCTCTCTAAGCAGTAGTGGAGCATA-TTTAAGTC-ACC
1 -ATCTTATCTCCCTAAGCAGTAGTGGAG--TAGCTGAAGACGACG
*
4003177 ATCTTATCTCCCTAAGCAGTGGTGGAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAG
4003204 CAGGTTGAAA
Statistics
Matches: 411, Mismatches: 108, Indels: 53
0.72 0.19 0.09
Matches are distributed among these distances:
41 2 0.00
42 139 0.34
43 44 0.11
44 217 0.53
45 7 0.02
46 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGCTGAAGACGACG
Found at i:4002805 original size:42 final size:43
Alignment explanation
Indices: 4002755--4003212 Score: 332
Period size: 44 Copynumber: 10.7 Consensus size: 43
4002745 GAATCTTGTT
* * * *
4002755 TCCCTAAGCAATAGTAGAGTAGATTTAAG-CCACCATCCTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
** ** *
4002797 TCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTA-GATCTTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
* * ** * *
4002839 TCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTGTC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCAC-CATCTTATC
* * * * *
4002883 TCTCTAAGCAGCAGTGGAGAAGATTTAAG-CCACCATCCTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
** ** *
4002925 TCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCAC-CATCTTATC
* * * *
4002969 TCCCTAAGCAGTAGTGGAGTAGATCGAAGACGACGAATCTTGTC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCAC-CATCTTATC
* * * * *
4003013 TCCCTAAGCAGTAATGGAGCAGATTTAAG-CCACCATCCTATT
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
** ** *
4003055 TCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAAATCTTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCAC-CATCTTATC
* * ***** * *
4003099 TCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGTGAATTTTGTC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CCACCATCTTATC
* * * * *
4003143 TCTCTAAGCAGTAGTGGAGCATATTTAAG-TCACCATCTTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
* * *
4003185 TCCCTAAGCAGTGGTGGAGCAGGTTGAA
1 TCCCTAAGCAGTAGTGGAGTAGATTGAA
4003213 ATCAACAATT
Statistics
Matches: 315, Mismatches: 93, Indels: 16
0.74 0.22 0.04
Matches are distributed among these distances:
42 144 0.46
43 10 0.03
44 161 0.51
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (43 bp):
TCCCTAAGCAGTAGTGGAGTAGATTGAAGACCACCATCTTATC
Found at i:4002829 original size:130 final size:130
Alignment explanation
Indices: 4002665--4003212 Score: 785
Period size: 130 Copynumber: 4.2 Consensus size: 130
4002655 ATGAATCTTG
* * * * * *
4002665 TCTCCCTAAGCAGTAGTAGAGTATGCTAAAGATTACAGATCTTATCTCCCTAAACAATAGTGAAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * * * * *
4002730 CAGATCAAAGACGATGAATCTTGTTTCCCTAAGCAATAGTAGAGTAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTA
4002795 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT--AGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * * *
4002858 CAGATCGAAGACGGCGAATCTTGTCTCTCTAAGCAGCAGTGGAGAAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTA
4002923 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* *
4002988 TAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAATGGAGCAGATTTAAGCCACCATCCTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTA
* * *
4003053 TTTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * ** * * * * *
4003118 TAGATCGAAGATGGTGAATTTTGTCTCTCTAAGCAGTAGTGGAGCATATTTAAGTCACCATCTTA
66 CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTA
* * *
4003183 TCTCCCTAAGCAGTGGTGGAGCAGGTTGAA
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAA
4003213 ATCAACAATT
Statistics
Matches: 379, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
128 116 0.31
130 263 0.69
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (130 bp):
TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATCGAAGACGACGAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTA
Found at i:4002901 original size:86 final size:86
Alignment explanation
Indices: 4002793--4003206 Score: 329
Period size: 86 Copynumber: 4.8 Consensus size: 86
4002783 GCCACCATCC
* *
4002793 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTA-GATCTTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATCACCATCTTATCTCCCTAAGCAGTAGTGGA
*
4002857 GCAGATCGAAGACGGCGAATCT
66 GCAGATCGAAGACGAC-AATCT
* * * * ** * * *
4002879 TGTCTCTCTAAGCAGCAGTGGAGAAGATTTAAG-CCACCATCCTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATCACCATCTTATCTCCCTAAGCAGTAGTGGA
* * **
4002943 GTAG-GCTGAAGATTACAGATCT
66 GCAGATC-GAAGACGACA-ATCT
* * * *
4002965 TATCTCCCTAAGCAGTAGTGGAGTA-GATCGAAGA-CGACGAATCTTGTCTCCCTAAGCAGTAAT
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCT-GAAGATC-AC-CATCTTATCTCCCTAAGCAGTAGT
** * * *
4003028 GGAGCAGATTTAAG-CCACCATCC
63 GGAGCAGATCGAAGACGACAATCT
* * * *
4003051 TATTTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATCAC-CATCTTATCTCCCTAAGCAGTAGTGG
* * ** *
4003116 AGTAGATCGAAGATGGTGAATTT
65 AGCAGATCGAAGA-CGACAATCT
* * * *** * *
4003139 TGTCTCTCTAAGCAGTAGTGGAGCATATTTAAG-TCACCATCTTATCTCCCTAAGCAGTGGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATCACCATCTTATCTCCCTAAGCAGTAGTGGA
4003203 GCAG
66 GCAG
4003207 GTTGAAATCA
Statistics
Matches: 251, Mismatches: 65, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
85 4 0.02
86 182 0.73
87 9 0.04
88 56 0.22
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (86 bp):
TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATCACCATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGACGACAATCT
Found at i:4003303 original size:44 final size:44
Alignment explanation
Indices: 4003245--4003556 Score: 125
Period size: 44 Copynumber: 7.1 Consensus size: 44
4003235 AAGTTTCAGC
*
4003245 AGAGTAAATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
1 AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
* * * * * *** **
4003289 AGAGCT-GCTCGAAGCCACAATTCT-TATCTCCTTGAAGTTTTAGG
1 AGAG-TAGATCGAAGCTACAAATCTCT-TCTCCCTGAAATGACATT
* *
4003333 GGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGACATT
1 AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
* * * * * * * * ** *
4003377 AGAGTGGCTCGTAGCCACAATTCT-TATTTCCTTGAAGTTCCAGCGT
1 AGAGTAGATCGAAGCTACAAATCTCT-TCTCCCTGAAATGACA--TT
* * *
4003423 A-A-TAGATCGAAGCTACAAATCTCTTCTTCCTAAAATGGCATT
1 AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
* * * * * * * ** **
4003465 GGAGTGGCTCGAAGCCAC-AAT-TGTTATCTCCTTAAAGTTCCAGC
1 AGAGTAGATCGAAGCTACAAATCTCTTCTC-CCTGAAA-TGACATT
* * * **
4003509 GGAGTAGATCGAAGTTACAAATCTCTTCTCCTTGAAATGGTATT
1 AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
4003553 AGAG
1 AGAG
4003557 CGGCTCGAAG
Statistics
Matches: 179, Mismatches: 75, Indels: 28
0.63 0.27 0.10
Matches are distributed among these distances:
42 5 0.03
43 13 0.07
44 142 0.79
45 12 0.07
46 7 0.04
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGACATT
Found at i:4003338 original size:88 final size:88
Alignment explanation
Indices: 4003217--4003660 Score: 586
Period size: 88 Copynumber: 5.0 Consensus size: 88
4003207 GTTGAAATCA
* * *
4003217 ACAATTCTTATCTCCTTGAAGTTTCAGCAGAGTAAATCGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
*
4003282 TGACATTAGAGCTGCTCGAAGCC
66 TGGCATTAGAGCTGCTCGAAGCC
* *
4003305 ACAATTCTTATCTCCTTGAAGTTTTAGGGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
* *
4003370 TGACATTAGAG-TGGCTCGTAGCC
66 TGGCATTAGAGCT-GCTCGAAGCC
* * * * *
4003393 ACAATTCTTATTTCCTTGAAGTTCCAGCGTAATAGATCGAAGCTACAAATCTCTTCTTCCTAAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
*
4003458 TGGCATTGGAG-TGGCTCGAAGCC
66 TGGCATTAGAGCT-GCTCGAAGCC
* * * * * *
4003481 ACAATTGTTATCTCCTTAAAGTTCCAGCGGAGTAGATCGAAGTTACAAATCTCTTCTCCTTGAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
* *
4003546 TGGTATTAGAGCGGCTCGAAGCC
66 TGGCATTAGAGCTGCTCGAAGCC
* * * *
4003569 CCAATTCTTATCTCCTTGAAGTTTCAACGGATTAGATTGAAGCTACAAATCTCTTCTCCCTAAAA
1 ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
* * * *
4003634 TGGTATTGGAGCGGCTCAAAGCC
66 TGGCATTAGAGCTGCTCGAAGCC
4003657 ACAA
1 ACAA
4003661 ATCACAAACC
Statistics
Matches: 313, Mismatches: 41, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
87 1 0.00
88 312 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (88 bp):
ACAATTCTTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAA
TGGCATTAGAGCTGCTCGAAGCC
Found at i:4003783 original size:65 final size:65
Alignment explanation
Indices: 4003679--4003810 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
4003669 CCTTATCTCC
* *
4003679 CTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
*
4003744 CTAAAGTTGCAGTGGAGTAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
1 CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
4003809 CT
1 CT
4003811 GAAGATAGCG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (65 bp):
CTAAAGTTGCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
Found at i:4003792 original size:44 final size:44
Alignment explanation
Indices: 4003744--4003903 Score: 182
Period size: 44 Copynumber: 3.6 Consensus size: 44
4003734 GTGGAGCAGA
4003744 CTAAAGTTGCAGTGGAGTAAGTTGAAGTTAC-AAGTCTTATCTCC
1 CTAAAGTTGCAGTGGAGTAAGTTGAAGTTACGAA-TCTTATCTCC
* * *
4003788 CTAAAGTTGCAGTGGAG-CAGACTGAAGATAGCGAATCTTATCTCC
1 CTAAAGTTGCAGTGGAGTAAG-TTGAAGTTA-CGAATCTTATCTCC
* * * *
4003833 CTGAAGTTGCAGTAGAGCAGGTTGAAGTTACGAATCTTATCTCC
1 CTAAAGTTGCAGTGGAGTAAGTTGAAGTTACGAATCTTATCTCC
* *
4003877 CTGAAGTTGTAGTGGAGTACA-TTGAAG
1 CTAAAGTTGCAGTGGAGTA-AGTTGAAG
4003904 CCGCTAGTCT
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
43 2 0.02
44 60 0.61
45 33 0.34
46 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
CTAAAGTTGCAGTGGAGTAAGTTGAAGTTACGAATCTTATCTCC
Found at i:4005776 original size:3 final size:3
Alignment explanation
Indices: 4005768--4005848 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
4005758 CAAAAATTAG
4005768 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4005816 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4005849 CGTTTCATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4005934 original size:23 final size:24
Alignment explanation
Indices: 4005900--4005944 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
4005890 ATTTGAACCT
*
4005900 TTTATTTTTTTATTT-TTATTTCA
1 TTTATTTATTTATTTCTTATTTCA
4005923 TTTATTTATTTATTTCTTATTT
1 TTTATTTATTTATTTCTTATTT
4005945 ATAATTAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTATTTATTTCTTATTTCA
Found at i:4006065 original size:3 final size:3
Alignment explanation
Indices: 4006057--4006090 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4006047 CAAAGTTTAG
4006057 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4006091 CCTTCTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4007618 original size:52 final size:51
Alignment explanation
Indices: 4007560--4007657 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 51
4007550 TAACCTCAAA
* * * *
4007560 TAGATATTACAATTATTTAAGTTTATTTGTTATCAAACTAATATTTAAATAT
1 TAGATATGACAATCATTTAAATTTATTT-TTATCAAAATAATATTTAAATAT
* *
4007612 TAGATATGATAATCATTTAAATTTATTTTTATTAAAATAATATTTA
1 TAGATATGACAATCATTTAAATTTATTTTTATCAAAATAATATTTA
4007658 GATACTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 16 0.40
52 24 0.60
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (51 bp):
TAGATATGACAATCATTTAAATTTATTTTTATCAAAATAATATTTAAATAT
Found at i:4007657 original size:27 final size:30
Alignment explanation
Indices: 4007620--4007675 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
4007610 ATTAGATATG
*
4007620 ATAATCATTTAAAT-TTATTTT-TATTAAA
1 ATAATCATTTAAATACTATTTTATATTAAA
*
4007648 ATAAT-ATTTAGATACTATTTTATATTAA
1 ATAATCATTTAAATACTATTTTATATTAA
4007676 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 11 0.46
29 6 0.25
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (30 bp):
ATAATCATTTAAATACTATTTTATATTAAA
Found at i:4008485 original size:44 final size:44
Alignment explanation
Indices: 4008437--4008525 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
4008427 ATAATAATTT
4008437 TATATTCAAATGGTTTAATGTAACTATTTTGAATTTCATTATAA
1 TATATTCAAATGGTTTAATGTAACTATTTTGAATTTCATTATAA
4008481 TATATTCAAATGGTTTAATGTAACTATTTTGAATTTCATTATAA
1 TATATTCAAATGGTTTAATGTAACTATTTTGAATTTCATTATAA
4008525 T
1 T
4008526 GACTTATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (44 bp):
TATATTCAAATGGTTTAATGTAACTATTTTGAATTTCATTATAA
Found at i:4009546 original size:28 final size:26
Alignment explanation
Indices: 4009499--4009554 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
4009489 TAGTTGATAT
*
4009499 TTTAAATATATTTATAATTAAATTTAAA
1 TTTAAAAATATTTATAATT--ATTTAAA
* *
4009527 TTTAAAAATATTTTTTATTATTTAAA
1 TTTAAAAATATTTATAATTATTTAAA
4009553 TT
1 TT
4009555 GAAATACAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
28 16 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAAAAATATTTATAATTATTTAAA
Found at i:4018945 original size:18 final size:18
Alignment explanation
Indices: 4018924--4018965 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4018914 TAATGCTAAC
*
4018924 AATAACCA-TAAACATAGT
1 AATAACCATTAAA-ATAAT
*
4018942 AATAACGATTAAAATAAT
1 AATAACCATTAAAATAAT
4018960 AATAAC
1 AATAAC
4018966 AACAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAACCATTAAAATAAT
Found at i:4019151 original size:3 final size:3
Alignment explanation
Indices: 4019143--4019303 Score: 86
Period size: 3 Copynumber: 54.3 Consensus size: 3
4019133 TAGTACCATT
* * *
4019143 ATA ATA ATA AAA ATA ATA ATA ATA A-A ATA ATA A-A ATA ACA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
4019188 TTT CTA ATA ATA ATA ATAA ATAA ATA ATG GTA ATA A-A TATA TATA A-A
1 ATA ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA ATA
* * *
4019235 ATA ATA GTA ACA GTA ATA A-A ATA A-A TATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * *
4019278 TATA ATA ATA ACA ATA TTA AAA ATA A
1 -ATA ATA ATA ATA ATA ATA ATA ATA A
4019304 CACTCTTCCC
Statistics
Matches: 121, Mismatches: 25, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
2 14 0.12
3 91 0.75
4 16 0.13
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4025102 original size:16 final size:16
Alignment explanation
Indices: 4025064--4025105 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4025054 TGTGTAAATA
4025064 ATTTTTATTTGTTTAT
1 ATTTTTATTTGTTTAT
*
4025080 ATATTTA-TTGTTTTAT
1 ATTTTTATTTG-TTTAT
*
4025096 TTTTTTATTT
1 ATTTTTATTT
4025106 CAAAAGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
ATTTTTATTTGTTTAT
Found at i:4030275 original size:54 final size:54
Alignment explanation
Indices: 4030215--4030320 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
4030205 TGAAGGACAC
*
4030215 AACAACATAGATGACGAAGATGTGAACAATCCCATTAAGCACGGTAATGGAATG
1 AACAACATAGATGACGAAGATGTGAACAATCCCATTAAGCACAGTAATGGAATG
*
4030269 AACAACATAGATGACGAAGATGTGAACAATCCCATTAAGCTCAGTAATGGAA
1 AACAACATAGATGACGAAGATGTGAACAATCCCATTAAGCACAGTAATGGAA
4030321 CGAATGAGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (54 bp):
AACAACATAGATGACGAAGATGTGAACAATCCCATTAAGCACAGTAATGGAATG
Found at i:4043145 original size:6 final size:6
Alignment explanation
Indices: 4043136--4043174 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
4043126 ACCCGCATCC
* *
4043136 GCAACA GCAACA GCACCA GCACCA GCAACA GCAACA GCA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCA
4043175 CCATGTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.44, C:0.38, G:0.18, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:4043163 original size:18 final size:18
Alignment explanation
Indices: 4043140--4043177 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4043130 GCATCCGCAA
*
4043140 CAGCAACAGCACCAGCAC
1 CAGCAACAGCAACAGCAC
4043158 CAGCAACAGCAACAGCAC
1 CAGCAACAGCAACAGCAC
4043176 CA
1 CA
4043178 TGTGCCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.16, T:0.00
Consensus pattern (18 bp):
CAGCAACAGCAACAGCAC
Found at i:4044501 original size:73 final size:73
Alignment explanation
Indices: 4044382--4044640 Score: 473
Period size: 73 Copynumber: 3.5 Consensus size: 73
4044372 TATTATTATT
**
4044382 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
4044447 ATTTTAAG
66 ATTTTAAG
4044455 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
4044520 ATTTTAAG
66 ATTTTAAG
* *
4044528 TGGATGTAATTATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGATAGTAGGTGGTGATTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
4044593 ATTTTAAG
66 ATTTTAAG
*
4044601 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTT
4044641 GTCAAGTTGT
Statistics
Matches: 180, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 180 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:4049005 original size:73 final size:73
Alignment explanation
Indices: 4048886--4049071 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
4048876 TATTATTATT
*
4048886 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
4048951 ATTTTAAG
66 ATTTTAAG
*
4048959 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
4049024 ATTTTAAG
66 ATTTTAAG
4049032 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
4049072 GTCAAGTTGT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:4055957 original size:16 final size:16
Alignment explanation
Indices: 4055926--4055958 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4055916 AAAATAATTA
4055926 AATATGTATGTTTAAT
1 AATATGTATGTTTAAT
4055942 AATAT-TATGTTATAAT
1 AATATGTATGTT-TAAT
4055958 A
1 A
4055959 TTCATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
AATATGTATGTTTAAT
Found at i:4060758 original size:30 final size:30
Alignment explanation
Indices: 4060724--4060786 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4060714 CCTTATTTTA
4060724 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
4060754 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
4060784 TTG
1 TTG
4060787 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:4062030 original size:20 final size:20
Alignment explanation
Indices: 4062005--4062044 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4061995 ACAGCATGTA
4062005 AGTTCAATTCTTGATTATTT
1 AGTTCAATTCTTGATTATTT
4062025 AGTTCAATTCTTGATTATTT
1 AGTTCAATTCTTGATTATTT
4062045 CTTGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
AGTTCAATTCTTGATTATTT
Found at i:4062833 original size:52 final size:50
Alignment explanation
Indices: 4062772--4062982 Score: 216
Period size: 52 Copynumber: 4.2 Consensus size: 50
4062762 ATGGAAAAGG
*
4062772 TGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAA
1 TGTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG--A
* * *
4062824 TGTGATATGTGCTCCTGTATAAGACTATAGTTGGGCTATGGCATCGGTGTGA
1 TGTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATC-G-GTGA
* * * ** *
4062876 TGTGATAATGTGCTTCTGTAAAAGACCATATTTGGGATATGGCATCGGT-A
1 TGTGAT-ATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGA
* * * *
4062926 --TGATATGTG-ACCCGTGTAAGACCATAACTGGGCTATGGCTTCGGTG-
1 TGTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGA
4062972 TGTGATATGTG
1 TGTGATATGTG
4062983 ACTATGTGCA
Statistics
Matches: 135, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
46 27 0.20
47 5 0.04
48 13 0.10
50 1 0.01
51 2 0.01
52 49 0.36
53 35 0.26
54 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (50 bp):
TGTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGA
Found at i:4063956 original size:20 final size:20
Alignment explanation
Indices: 4063928--4063966 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4063918 GACCACACAG
4063928 CCTACCCACACGGGCGTGTC
1 CCTACCCACACGGGCGTGTC
*
4063948 CCTATCCACACGGGCGTGT
1 CCTACCCACACGGGCGTGT
4063967 GGCCCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACACGGGCGTGTC
Found at i:4064369 original size:18 final size:18
Alignment explanation
Indices: 4064346--4064383 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4064336 TGCTTGGAAA
4064346 GAAATAATGCAACTTAGT
1 GAAATAATGCAACTTAGT
4064364 GAAATAATGCAACTTAGT
1 GAAATAATGCAACTTAGT
4064382 GA
1 GA
4064384 TAGCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (18 bp):
GAAATAATGCAACTTAGT
Found at i:4065309 original size:22 final size:21
Alignment explanation
Indices: 4065284--4065355 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
4065274 TTTCAATAAT
4065284 ATATTAAAAATATTAAAATTTA
1 ATATTAAAAATA-TAAAATTTA
** *
4065306 ATATTATTATTACTAAAA-TTA
1 ATATTAAAAATA-TAAAATTTA
* *
4065327 ATTATT-AAAATAAAAAATGTA
1 A-TATTAAAAATATAAAATTTA
4065348 ATATTAAA
1 ATATTAAA
4065356 TAATTTATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
20 8 0.21
21 12 0.32
22 18 0.47
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATATTAAAAATATAAAATTTA
Found at i:4075895 original size:16 final size:15
Alignment explanation
Indices: 4075867--4075896 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
4075857 ATTAAAAATT
4075867 TAAAATTATTATTAC
1 TAAAATTATTATTAC
4075882 TAAAATTAATTATTA
1 TAAAATT-ATTATTA
4075897 AAATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATTATTATTAC
Found at i:4093962 original size:2 final size:2
Alignment explanation
Indices: 4093955--4093999 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4093945 TATCAAGTTT
4093955 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
4093997 TA T
1 TA T
4094000 CACTTAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4105044 original size:46 final size:46
Alignment explanation
Indices: 4104991--4105109 Score: 211
Period size: 46 Copynumber: 2.6 Consensus size: 46
4104981 ATACTCGGAC
*
4104991 GAACTCGGACTCAACTCAAAGAGTTCGGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
* *
4105037 TAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
4105083 GAACTCGGACTCAACTCAACGAGTTCG
1 GAACTCGGACTCAACTCAACGAGTTCG
4105110 AATACCTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
Found at i:4116514 original size:12 final size:12
Alignment explanation
Indices: 4116497--4116521 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4116487 GAATAATTAT
4116497 ATAAAATTTTTA
1 ATAAAATTTTTA
4116509 ATAAAATTTTTA
1 ATAAAATTTTTA
4116521 A
1 A
4116522 AACAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAAAATTTTTA
Found at i:4119399 original size:12 final size:12
Alignment explanation
Indices: 4119382--4119408 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4119372 CATTTAATCT
4119382 TCATGCAATTTG
1 TCATGCAATTTG
4119394 TCATGCAATTTG
1 TCATGCAATTTG
4119406 TCA
1 TCA
4119409 ATAATCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (12 bp):
TCATGCAATTTG
Found at i:4121386 original size:21 final size:21
Alignment explanation
Indices: 4121360--4121400 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4121350 ACCTACTTAA
*
4121360 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
4121381 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
4121401 TCGCTTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:4124256 original size:12 final size:12
Alignment explanation
Indices: 4124239--4124265 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4124229 CATTTAATCT
4124239 TCATGCAATTTG
1 TCATGCAATTTG
4124251 TCATGCAATTTG
1 TCATGCAATTTG
4124263 TCA
1 TCA
4124266 ACAATCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (12 bp):
TCATGCAATTTG
Found at i:4125433 original size:20 final size:20
Alignment explanation
Indices: 4125410--4125452 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4125400 TTATATATAA
* *
4125410 TTTTTAACATTATATTTATG
1 TTTTAAACATTAGATTTATG
* *
4125430 TTTTAAAGATTAGATTTGTG
1 TTTTAAACATTAGATTTATG
4125450 TTT
1 TTT
4125453 AATTGTTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTTAAACATTAGATTTATG
Found at i:4131431 original size:6 final size:6
Alignment explanation
Indices: 4131422--4131461 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
4131412 GGATTTTTTA
* *
4131422 AAATGG AAATGG AAATGG AAATGG AAATGA AAATGA AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
4131462 AAAAATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:4131466 original size:6 final size:6
Alignment explanation
Indices: 4131421--4131474 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
4131411 TGGATTTTTT
* * * * *
4131421 AAAATG GAAATG GAAATG GAAATG GAAATG AAAATG AAAATA AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
4131469 AGAAAT
1 A-AAAT
4131475 AATTCATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 39 0.91
7 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:4132852 original size:11 final size:11
Alignment explanation
Indices: 4132836--4132860 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4132826 AAAAGGCTAA
4132836 TTTTGGACTAT
1 TTTTGGACTAT
4132847 TTTTGGACTAT
1 TTTTGGACTAT
4132858 TTT
1 TTT
4132861 GGGCATTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTGGACTAT
Found at i:4133355 original size:20 final size:21
Alignment explanation
Indices: 4133308--4133357 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
4133298 TAGAGATAGG
4133308 ACAAATCTACCGGATTAGAGT
1 ACAAATCTACCGGATTAGAGT
4133329 ACAAATCTACCGGATTAGAGT
1 ACAAATCTACCGGATTAGAGT
4133350 -CAAATCTA
1 ACAAATCTA
4133358 ATAAGGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (21 bp):
ACAAATCTACCGGATTAGAGT
Found at i:4141805 original size:9 final size:9
Alignment explanation
Indices: 4141700--4141799 Score: 69
Period size: 9 Copynumber: 10.9 Consensus size: 9
4141690 CAGCAAAAAG
4141700 TTATGTAAA
1 TTATGTAAA
*
4141709 TTATGTAAG
1 TTATGTAAA
* * **
4141718 TTGTTTATC
1 TTATGTAAA
4141727 TTATGTAAA
1 TTATGTAAA
4141736 TTATGTAACA
1 TTATGTAA-A
* *
4141746 TGTGATATATAT
1 T-T-ATGTA-AA
4141758 TTATGT-AA
1 TTATGTAAA
* *
4141766 TT-GGTAAG
1 TTATGTAAA
4141774 TTATGTAAA
1 TTATGTAAA
4141783 TTATGTAAA
1 TTATGTAAA
4141792 TTATGTAA
1 TTATGTAA
4141800 GATATGATAT
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
7 2 0.03
8 6 0.09
9 47 0.69
10 5 0.07
11 2 0.03
12 5 0.07
13 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (9 bp):
TTATGTAAA
Found at i:4141805 original size:27 final size:27
Alignment explanation
Indices: 4141700--4141805 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
4141690 CAGCAAAAAG
* * * **
4141700 TTATGTAAATTATGTAAGTTGTTTATC
1 TTATGTAAATTATGTAAGATATGTAAA
* *
4141727 TTATGTAAATTATGTAACATGTGATATATA
1 TTATGTAAATTATGTAAGATATG-TA-A-A
* *
4141757 TTTATGT-AATT-GGTAAGTTATGTAAA
1 -TTATGTAAATTATGTAAGATATGTAAA
4141783 TTATGTAAATTATGTAAGATATG
1 TTATGTAAATTATGTAAGATATG
4141806 ATATATATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
25 6 0.10
26 5 0.08
27 30 0.48
28 4 0.06
29 7 0.11
30 4 0.06
31 6 0.10
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (27 bp):
TTATGTAAATTATGTAAGATATGTAAA
Found at i:4142390 original size:205 final size:202
Alignment explanation
Indices: 4142062--4142458 Score: 580
Period size: 205 Copynumber: 2.0 Consensus size: 202
4142052 AATTTGTTGA
* *
4142062 ACAATTAATTTAATTAGGTTATTTAACAAAAAAATAAAAGTAAACAAAATATTTTTCGTAATTAA
1 ACAATTAACTTAATTAGGTAATTTAACAAAAAAATAAAAGTAAACAAAATATTTTTCGTAATTAA
*
4142127 AATAAAATAAAAAAATATTTAAAAAAACTTCAAATATAATGTAATTTAACTAGGTAATTTAAAAA
66 AATAAAATAAAAAAATATTTAAAAAAACTTCAAATACAATGTAATTTAACTAGGTAATTTAAAAA
* * * * *
4142192 TAAAATAAGAGTAGACATAATATTTTTTGTTATTAAAATAAAATACAATAAAATATTTAAAAAAC
131 TAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAAAATATTCAAAAAAC
4142257 TTTAAAT
196 TTTAAAT
* * * * *
4142264 ACAATTTAACTTAATTAGGTAATTTAA-AAATAAAATAAGAGTAGACATAATATTTTTTGTGATT
1 ACAA-TTAACTTAATTAGGTAATTTAACAAA-AAAATAAAAGTAAACAAAATATTTTTCGTAATT
* * * * *
4142328 AAAATAAAATGCAATAAAATATTTAAAAAAACTTTAAATACAATTTAATTTAATTTGGTAATTTA
64 AAAATAAAAT--AAAAAAATATTTAAAAAAACTTCAAATACAATGTAATTTAACTAGGTAATTTA
*
4142393 AAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTCAAA
127 AAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAAAATATTCAAA
4142458 A
192 A
4142459 TAAAACTATG
Statistics
Matches: 172, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
202 7 0.04
203 58 0.34
205 107 0.62
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (202 bp):
ACAATTAACTTAATTAGGTAATTTAACAAAAAAATAAAAGTAAACAAAATATTTTTCGTAATTAA
AATAAAATAAAAAAATATTTAAAAAAACTTCAAATACAATGTAATTTAACTAGGTAATTTAAAAA
TAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAAAATATTCAAAAAAC
TTTAAAT
Found at i:4142393 original size:103 final size:103
Alignment explanation
Indices: 4142062--4142458 Score: 579
Period size: 103 Copynumber: 3.9 Consensus size: 103
4142052 AATTTGTTGA
* * * *
4142062 ACAA-TTAATTTAATTAGGTTATTTAACAAA-AAAATAAAAGTAAACAAAATATTTTTCGTAATT
1 ACAATTTAATTTAATTAGGTAATTTAA-AAATAAAATAAAAGTAGACAAAATATTTTTTGTGATT
*
4142125 AAAATAAAATA-AA-AAAATATTTAAAAAAACTTCAAAT
65 AAAATAAAATACAATAAAATATTTAAAAAAACTTTAAAT
* * * * * *
4142162 ATAATGTAATTTAACTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTTATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
4142227 AAATAAAATACAATAAAATATTT-AAAAAACTTTAAAT
66 AAATAAAATACAATAAAATATTTAAAAAAACTTTAAAT
* * *
4142264 ACAATTTAACTTAATTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
*
4142329 AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
66 AAATAAAATACAATAAAATATTTAAAAAAACTTTAAAT
*
4142367 ACAATTTAATTTAATTTGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
* * *
4142432 AAATAAAATAAAATAACATATTCAAAA
66 AAATAAAATACAATAAAATATTTAAAA
4142459 TAAAACTATG
Statistics
Matches: 268, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
100 6 0.02
101 58 0.22
102 97 0.36
103 107 0.40
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (103 bp):
ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
AAATAAAATACAATAAAATATTTAAAAAAACTTTAAAT
Found at i:4145904 original size:21 final size:22
Alignment explanation
Indices: 4145880--4145920 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4145870 ATTCATATTC
4145880 AAATA-TATTTGT-TTTATTTTA
1 AAATACTATTT-TCTTTATTTTA
4145901 AAATACTATTTTCTTTATTT
1 AAATACTATTTTCTTTATTT
4145921 AACAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATACTATTTTCTTTATTTTA
Found at i:4149904 original size:20 final size:20
Alignment explanation
Indices: 4149837--4149978 Score: 93
Period size: 20 Copynumber: 7.0 Consensus size: 20
4149827 TAAATTAATT
4149837 TTATTAAACTTTTAAATAAAA
1 TTATTAAACTTTT-AATAAAA
* *
4149858 TAAAATT-AA-TTTGT-ATAAAT
1 T--TATTAAACTTT-TAATAAAA
4149878 TTA-TAAACTTTTAATAAAA
1 TTATTAAACTTTTAATAAAA
*
4149897 TTATTAAAATTTTAAATAAAA
1 TTATTAAACTTTT-AATAAAA
* **
4149918 TAAAATT-AA-TTTGT-ATAATT
1 T--TATTAAACTTT-TAATAAAA
4149938 TTA-TAAACTTTTAATAAAA
1 TTATTAAACTTTTAATAAAA
4149957 TTATTAAACTTTTAAATAAAA
1 TTATTAAACTTTT-AATAAAA
4149978 T
1 T
4149979 AAAATTAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
17 2 0.02
18 8 0.09
19 21 0.22
20 28 0.30
21 23 0.24
22 6 0.06
23 6 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (20 bp):
TTATTAAACTTTTAATAAAA
Found at i:4149910 original size:60 final size:60
Alignment explanation
Indices: 4149837--4150011 Score: 316
Period size: 60 Copynumber: 2.9 Consensus size: 60
4149827 TAAATTAATT
4149837 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATTTATAAACTTTTAATAAAA
1 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATTTATAAACTTTTAATAAAA
* *
4149897 TTATTAAAATTTTAAATAAAATAAAATTAATTTGTATAATTTTATAAACTTTTAATAAAA
1 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATTTATAAACTTTTAATAAAA
4149957 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTAT-AATTATATAAACTTTTAA
1 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATT-TATAAACTTTTAA
4150012 ATTATTTTAT
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
59 3 0.03
60 107 0.97
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (60 bp):
TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATTTATAAACTTTTAATAAAA
Found at i:4150517 original size:21 final size:21
Alignment explanation
Indices: 4150493--4150546 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4150483 TATATACCCT
4150493 AAACCTTAAACCCAAAATAAC
1 AAACCTTAAACCCAAAATAAC
** *
4150514 AAACCCCAAGCCCAAAATAAC
1 AAACCTTAAACCCAAAATAAC
4150535 AAACCTTAAACC
1 AAACCTTAAACC
4150547 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.33, G:0.02, T:0.11
Consensus pattern (21 bp):
AAACCTTAAACCCAAAATAAC
Found at i:4150558 original size:28 final size:28
Alignment explanation
Indices: 4150527--4150581 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4150517 CCCCAAGCCC
*
4150527 AAAATAAC-AAACCTTAAACCATAAATTT
1 AAAAT-ACTAAACATTAAACCATAAATTT
*
4150555 AAAATACTAAACATTAAACCCTAAATT
1 AAAATACTAAACATTAAACCATAAATT
4150582 GTAAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.25
Consensus pattern (28 bp):
AAAATACTAAACATTAAACCATAAATTT
Found at i:4151272 original size:18 final size:17
Alignment explanation
Indices: 4151249--4151283 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4151239 AAAGTCAGTT
*
4151249 TCAAATATCAAAATAAAA
1 TCAAAT-TCAAAACAAAA
4151267 TCAAATTCAAAACAAAA
1 TCAAATTCAAAACAAAA
4151284 ATAAGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (17 bp):
TCAAATTCAAAACAAAA
Found at i:4152239 original size:16 final size:17
Alignment explanation
Indices: 4152218--4152252 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
4152208 TAATGTCTAG
4152218 GAAAATTA-TTAATTGA
1 GAAAATTAGTTAATTGA
4152234 GAAAATTAGTTTAATTGA
1 GAAAATTAG-TTAATTGA
4152252 G
1 G
4152253 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
GAAAATTAGTTAATTGA
Found at i:4153732 original size:41 final size:41
Alignment explanation
Indices: 4153687--4154090 Score: 531
Period size: 41 Copynumber: 9.9 Consensus size: 41
4153677 GTTTTAACCA
*
4153687 GAAACGCCACTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
** * *
4153728 GAAACGCTACTGTTGCTCAGTTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* * *
4153769 GAAATGCCGCTATTGCTCGGTTTTTAGTGGCATTTGGACAT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* *
4153810 GAAACGCCTCTATTGCTCGGTTTTTAGTGGCGTTTGGACAT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* *
4153851 GAAACGCCGCTATTGTTCAGTTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* * * * *
4153892 GAAACGCTGCAATTGCTCTGTTTTTAGTTGCATTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* ** **
4153933 AAAACGCCGCTATTGCTTTGTTTTTAGTGGCGTTTTAACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* *
4153974 GAAACGTCGCTATTGCTCAGTTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
*
4154015 -AAAGCGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACTT
1 GAAA-CGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* ** *
4154056 GAAACACCGCTATTGCTTTGTTTTTAGCGGCGTTT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTT
4154091 TAATGCTCAG
Statistics
Matches: 317, Mismatches: 44, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
40 3 0.01
41 311 0.98
42 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
Found at i:4164543 original size:20 final size:20
Alignment explanation
Indices: 4164502--4164541 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4164492 AACAAGGTTA
*
4164502 CAAAACATTACCAACAATTT
1 CAAAACATTACAAACAATTT
*
4164522 CAAAACAATTACAAATAATT
1 CAAAAC-ATTACAAACAATT
4164542 CAGATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (20 bp):
CAAAACATTACAAACAATTT
Found at i:4166343 original size:16 final size:17
Alignment explanation
Indices: 4166312--4166344 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4166302 TTCATAAGAA
4166312 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
4166329 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
4166345 GCTCTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:4166787 original size:92 final size:92
Alignment explanation
Indices: 4166630--4166856 Score: 355
Period size: 92 Copynumber: 2.5 Consensus size: 92
4166620 TTTGACATGA
* * * *
4166630 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
*** *
4166695 CATGGTCTTGTTCATTTCATATCACGT
66 CATGGTCTTACACATTTCATATCAAGT
*
4166722 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
4166787 CATGGTCTTACACATTTCATATCAAGT
66 CATGGTCTTACACATTTCATATCAAGT
* *
4166814 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCA
4166857 GAGAGCACAC
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 123 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAAGT
Found at i:4166850 original size:46 final size:46
Alignment explanation
Indices: 4166625--4166852 Score: 314
Period size: 46 Copynumber: 5.0 Consensus size: 46
4166615 TTATCTTTGA
* * * * *
4166625 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
**
4166671 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * * *
4166717 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
4166763 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
4166809 CAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
4166853 GTCAGAGAGC
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 160 0.98
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:4175379 original size:6 final size:6
Alignment explanation
Indices: 4175365--4175400 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
4175355 TTAAAATTAA
4175365 AAATA- AAATAT AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT A
4175401 TATTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:4182089 original size:22 final size:22
Alignment explanation
Indices: 4182061--4182102 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4182051 ATATTTTAAA
4182061 ATTTATATATTTTAAAATTTAT
1 ATTTATATATTTTAAAATTTAT
*
4182083 ATTTATATATTTTAGAATTT
1 ATTTATATATTTTAAAATTT
4182103 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATATATTTTAAAATTTAT
Found at i:4182091 original size:8 final size:7
Alignment explanation
Indices: 4182033--4182106 Score: 51
Period size: 8 Copynumber: 10.1 Consensus size: 7
4182023 AAAATTTTCA
4182033 ATTTTAT
1 ATTTTAT
*
4182040 ATATTAT
1 ATTTTAT
*
4182047 -TTTGAT
1 ATTTTAT
*
4182053 ATTTTAAA
1 ATTTT-AT
4182061 ATTTATAT
1 ATTT-TAT
*
4182069 ATTTTAA
1 ATTTTAT
*
4182076 AATTTAT
1 ATTTTAT
4182083 ATTTATAT
1 ATTT-TAT
*
4182091 ATTTTAGA
1 ATTTTA-T
4182099 ATTTTAT
1 ATTTTAT
4182106 A
1 A
4182107 AAAAATTATT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
6 4 0.08
7 22 0.44
8 23 0.46
9 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
ATTTTAT
Found at i:4182102 original size:16 final size:16
Alignment explanation
Indices: 4182051--4182084 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4182041 TATTATTTTG
4182051 ATATTTTAAAATTTAT
1 ATATTTTAAAATTTAT
4182067 ATATTTTAAAATTTAT
1 ATATTTTAAAATTTAT
4182083 AT
1 AT
4182085 TTATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTAAAATTTAT
Done.