Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 10 of 198
Found at i:3383863 original size:34 final size:35
Alignment explanation
Indices: 3383819--3383885 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3383809 CAGTAAAATG
*
3383819 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3383853 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3383886 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3383889 original size:14 final size:15
Alignment explanation
Indices: 3383813--3383889 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3383803 GATTGGCAGT
* *
3383813 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
3383827 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3383841 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3383861 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3383876 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3383890 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3383997 original size:20 final size:20
Alignment explanation
Indices: 3383972--3384010 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3383962 GTTTTTACAT
3383972 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
3383992 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
3384011 TTTTAAATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:3386621 original size:18 final size:18
Alignment explanation
Indices: 3386600--3386650 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3386590 AGGAATGAAG
*
3386600 GAAGGGAGAAGAATGGGT
1 GAAGGGAGAAGAATGGAT
*** *
3386618 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
3386636 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
3386651 CCTGACAGCT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.45, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:3389857 original size:2 final size:2
Alignment explanation
Indices: 3389852--3389883 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3389842 TTTAGTCATA
3389852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3389884 GAAAGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3390126 original size:35 final size:35
Alignment explanation
Indices: 3390060--3390154 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
3390050 ATTTGTTAAT
*
3390060 ATTTTGATTCACATGTTAAGCATGCTATTA-TTCG
1 ATTTTGATTCACATGTTAAACATGCTATTATTTCG
* * * *
3390094 AATTTTGATTCGCATGTTAATCATG-TCGTTATTTTG
1 -ATTTTGATTCACATGTTAAACATGCT-ATTATTTCG
* *
3390130 ATTTTGAGTCTCATGTTAAACATGC
1 ATTTTGATTCACATGTTAAACATGC
3390155 CACTGTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 1 0.02
35 46 0.92
36 3 0.06
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (35 bp):
ATTTTGATTCACATGTTAAACATGCTATTATTTCG
Found at i:3397410 original size:42 final size:42
Alignment explanation
Indices: 3397363--3397447 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
3397353 CGTAAAGCCT
3397363 ATACAATAAGGAGTTTTCAATCATTGTACTGCTTGTGGACTG
1 ATACAATAAGGAGTTTTCAATCATTGTACTGCTTGTGGACTG
3397405 ATACAATAAGGAGTTTTCAATCATTGTACTGCTTGTGGACTG
1 ATACAATAAGGAGTTTTCAATCATTGTACTGCTTGTGGACTG
3397447 A
1 A
3397448 CTCCATGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
ATACAATAAGGAGTTTTCAATCATTGTACTGCTTGTGGACTG
Found at i:3402207 original size:22 final size:22
Alignment explanation
Indices: 3402179--3402220 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3402169 TTTATTGTTC
3402179 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
3402201 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
3402221 CAAAAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:3410413 original size:22 final size:22
Alignment explanation
Indices: 3410351--3410415 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
3410341 CTCTGATTAT
* * *
3410351 TAGCACGTCAGTGCTCTCCGTT
1 TAGCACATCAGTGCTCTCTGTA
*
3410373 TAGCACATCTGTGCTCTCTGTA
1 TAGCACATCAGTGCTCTCTGTA
*
3410395 TAGCACTTCAGTGCTCTCTGT
1 TAGCACATCAGTGCTCTCTGT
3410416 TCATTAGTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.35
Consensus pattern (22 bp):
TAGCACATCAGTGCTCTCTGTA
Found at i:3410541 original size:31 final size:31
Alignment explanation
Indices: 3410506--3410564 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3410496 AAGAATATGA
* *
3410506 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAACAGAATATGAAAAAC
3410537 GATAGTGAATTGAAAACAGAATATGAAA
1 GATAGTGAATTGAAAACAGAATATGAAA
3410565 TACGTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.22, T:0.22
Consensus pattern (31 bp):
GATAGTGAATTGAAAACAGAATATGAAAAAC
Found at i:3417305 original size:15 final size:16
Alignment explanation
Indices: 3417285--3417316 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3417275 AATTGAAGTG
3417285 GAATATATATAT-TAT
1 GAATATATATATATAT
3417300 GAATATATATATATAT
1 GAATATATATATATAT
3417316 G
1 G
3417317 TATAAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
GAATATATATATATAT
Found at i:3417479 original size:25 final size:24
Alignment explanation
Indices: 3417451--3417538 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 24
3417441 ACCTTAGCGC
3417451 GCTCTCTGATTATTAGCACGTCAGT
1 GCTCTCTG-TTATTAGCACGTCAGT
* *
3417476 GCTCTCCGTTTATTAGCACGTCTGT
1 GCTCTCTG-TTATTAGCACGTCAGT
*
3417501 GCTCTCTG-TA-TAGCACTTCAGT
1 GCTCTCTGTTATTAGCACGTCAGT
3417523 GCTCTCTGTTCATTAG
1 GCTCTCTGTT-ATTAG
3417539 TGCTTAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 18 0.33
23 3 0.06
24 1 0.02
25 32 0.59
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACGTCAGT
Found at i:3417680 original size:31 final size:31
Alignment explanation
Indices: 3417622--3417680 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3417612 AAGAATATGA
* **
3417622 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAACAGAACATGAAAAAC
3417653 GATAGTGAATTGAAAACAGAACATGAAA
1 GATAGTGAATTGAAAACAGAACATGAAA
3417681 TACGTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (31 bp):
GATAGTGAATTGAAAACAGAACATGAAAAAC
Found at i:3458715 original size:73 final size:73
Alignment explanation
Indices: 3458626--3458793 Score: 300
Period size: 73 Copynumber: 2.3 Consensus size: 73
3458616 CACACGACCT
**
3458626 GCCACACGGCTGTGTCCCCCCTGTGGGTTGATTTTTGAAATTTTCACATGGCCTTAGTCTGTTAA
1 GCCACACAACTGTGTCCCCCCTGTGGGTTGATTTTTGAAATTTTCACATGGCCTTAGTCTGTTAA
3458691 ACGGGCGA
66 ACGGGCGA
3458699 GCCACACAACTGTGTCCCCCCTGTGGGTTGATTTTTGAAATTTTCACATGGCCTTAGTCTGTTAA
1 GCCACACAACTGTGTCCCCCCTGTGGGTTGATTTTTGAAATTTTCACATGGCCTTAGTCTGTTAA
3458764 ACGGGCGA
66 ACGGGCGA
* *
3458772 GCCACACAACCGTGTACCCCCT
1 GCCACACAACTGTGTCCCCCCT
3458794 CCACACGGTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (73 bp):
GCCACACAACTGTGTCCCCCCTGTGGGTTGATTTTTGAAATTTTCACATGGCCTTAGTCTGTTAA
ACGGGCGA
Found at i:3462452 original size:48 final size:48
Alignment explanation
Indices: 3462400--3462496 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
3462390 CTTTTATATA
*
3462400 AAAATAGAAATATAAATACATATCTAATAATATAAAGCCTTTTTATCG
1 AAAATAGAAATATAAATACATATCTAATAATATAAAACCTTTTTATCG
* * *
3462448 AAAATAGAAATATAAATACATCTCTACTAATATAAAACTTTTTTATCG
1 AAAATAGAAATATAAATACATATCTAATAATATAAAACCTTTTTATCG
3462496 A
1 A
3462497 GTTTGGTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (48 bp):
AAAATAGAAATATAAATACATATCTAATAATATAAAACCTTTTTATCG
Found at i:3471788 original size:6 final size:6
Alignment explanation
Indices: 3471773--3471805 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3471763 AAAAGATAGT
3471773 TTGA-C TTGAGC TTGAGC TTGAGC TTGAGC TTGA
1 TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC TTGA
3471806 TCTAGGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (6 bp):
TTGAGC
Found at i:3474264 original size:24 final size:24
Alignment explanation
Indices: 3474224--3474269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3474214 ATAAATTTGA
*
3474224 AATTTAATTTATGTATTTTTTATG
1 AATTTAATTTATGTATTGTTTATG
* *
3474248 AATTTAATTTTTTTATTGTTTA
1 AATTTAATTTATGTATTGTTTA
3474270 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (24 bp):
AATTTAATTTATGTATTGTTTATG
Found at i:3474290 original size:20 final size:21
Alignment explanation
Indices: 3474265--3474318 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
3474255 TTTTTTTATT
3474265 GTTTAAATT-TTAA-ATTTTAA
1 GTTT-AATTATTAATATTTTAA
3474285 GTTTAATTATTAATATTTTAA
1 GTTTAATTATTAATATTTTAA
* *
3474306 ATTT-TTTATTAAT
1 GTTTAATTATTAAT
3474319 TTTGTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 16 0.53
21 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
GTTTAATTATTAATATTTTAA
Found at i:3482061 original size:11 final size:11
Alignment explanation
Indices: 3482035--3482075 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
3482025 GGCCCATTTT
3482035 TATTTT-AAAA
1 TATTTTAAAAA
3482045 -ATTTTAAAAA
1 TATTTTAAAAA
3482055 TATTTTAAAAA
1 TATTTTAAAAA
3482066 TATTTTAAAA
1 TATTTTAAAA
3482076 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.17
10 4 0.14
11 20 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:3482121 original size:9 final size:10
Alignment explanation
Indices: 3482072--3482124 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
3482062 AAAATATTTT
3482072 AAAATT-AAA
1 AAAATTAAAA
3482081 AAAATTAAAA
1 AAAATTAAAA
* ***
3482091 AAAAGTATTTT
1 AAAATTA-AAA
3482102 AAAATTAAAA
1 AAAATTAAAA
3482112 AAAATTAAAA
1 AAAATTAAAA
3482122 AAA
1 AAA
3482125 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
9 6 0.18
10 22 0.65
11 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:3482150 original size:11 final size:12
Alignment explanation
Indices: 3482136--3482175 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
3482126 TATTTTAAAA
3482136 TTAAAAAAT-TT
1 TTAAAAAATATT
*
3482147 TTAAAAAGTATT
1 TTAAAAAATATT
3482159 TT-AAAAATATT
1 TTAAAAAATATT
3482170 TTAAAA
1 TTAAAA
3482176 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:3482166 original size:30 final size:30
Alignment explanation
Indices: 3482048--3482164 Score: 159
Period size: 30 Copynumber: 4.0 Consensus size: 30
3482038 TTTAAAAATT
* *
3482048 TTAAAAATATTT-TAAAAA-TATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
*
3482076 TTAAAAAAATTAAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
*
3482106 TTAAAAAAAATTAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
**
3482136 TT-AAAAAATTTTTAAAAAGTATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
3482165 ATATTTTAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 10 0.13
29 29 0.37
30 40 0.51
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
TTAAAAAAATTTAAAAAAAGTATTTTAAAA
Found at i:3482193 original size:40 final size:41
Alignment explanation
Indices: 3482119--3482218 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
3482109 AAAAAAATTA
* *** *
3482119 AAAAAAGTATTTTAAAATT-AAAAAATTTTTAAAAAGTATTT
1 AAAAAA-TATTTTAAAATTAAAAAAAATAAAAAAAAGTATGT
*
3482160 TAAAAATATTTTAAAATTAAAAAAAATAAAAAAAAGTATGT
1 AAAAAATATTTTAAAATTAAAAAAAATAAAAAAAAGTATGT
3482201 AAAAAATATTTTAAAATT
1 AAAAAATATTTTAAAATT
3482219 TTAAAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 12 0.24
41 39 0.76
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (41 bp):
AAAAAATATTTTAAAATTAAAAAAAATAAAAAAAAGTATGT
Found at i:3482259 original size:5 final size:5
Alignment explanation
Indices: 3482246--3482282 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
3482236 TTTATTATAT
*
3482246 CGGGT CGGGC CGGGC CGGGC CGGGC CGGGC CTGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGC C-GGGC C
3482283 AAAAAAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.38, G:0.57, T:0.05
Consensus pattern (5 bp):
CGGGC
Found at i:3484262 original size:20 final size:20
Alignment explanation
Indices: 3484211--3484264 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3484201 GACATTGGAC
* * *
3484211 TTAAATAACTTATATTTATT
1 TTAAATAATTTAAATATATT
*
3484231 TTATAA-ATTTTAAATATATT
1 TTA-AATAATTTAAATATATT
3484251 TTAAATAATTTAAA
1 TTAAATAATTTAAA
3484265 AAAATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATAATTTAAATATATT
Found at i:3487729 original size:22 final size:20
Alignment explanation
Indices: 3487694--3487767 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
3487684 ACATTAAAAA
3487694 ATATAAAAATAGAAATAAAT
1 ATATAAAAATAGAAATAAAT
3487714 ATATAAAAAATCAGAAAT--AT
1 ATAT-AAAAAT-AGAAATAAAT
**
3487734 ATAT-AATCTAGAAATAAAT
1 ATATAAAAATAGAAATAAAT
*
3487753 TTATAAAAATA-AAAT
1 ATATAAAAATAGAAAT
3487768 TACAAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.14
18 3 0.07
19 9 0.20
20 14 0.32
21 6 0.14
22 6 0.14
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (20 bp):
ATATAAAAATAGAAATAAAT
Found at i:3488271 original size:20 final size:22
Alignment explanation
Indices: 3488216--3488271 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
3488206 TTTTTAAATT
3488216 ATTTAA-ATATTTAATATTATA
1 ATTTAATATATTTAATATTATA
** *
3488237 ACTTTTTTATTTTTAATA-TA-A
1 A-TTTAATATATTTAATATTATA
3488258 ATTTAATATATTTA
1 ATTTAATATATTTA
3488272 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
20 10 0.37
21 3 0.11
22 5 0.19
23 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAATATATTTAATATTATA
Found at i:3492674 original size:2 final size:2
Alignment explanation
Indices: 3492667--3492702 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3492657 CTGCAACAAA
*
3492667 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3492703 TTTGTTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3499919 original size:13 final size:13
Alignment explanation
Indices: 3499901--3499925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3499891 AAAATAAAAA
3499901 TATTTATAATTTT
1 TATTTATAATTTT
3499914 TATTTATAATTT
1 TATTTATAATTT
3499926 AGCATAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTATAATTTT
Found at i:3499943 original size:36 final size:37
Alignment explanation
Indices: 3499894--3499981 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
3499884 TTTACTAAAA
* *
3499894 ATAAAAAT-ATTTATAATTTTTA-TTTATAATTT-AG
1 ATAAATATAATTTATAATTTATATTTTATAATTTGAG
*
3499928 CATAAATATAATTTAT-ATTTATATTTTATTATTTGAG
1 -ATAAATATAATTTATAATTTATATTTTATAATTTGAG
*
3499965 TTAAATATAATTTATAA
1 ATAAATATAATTTATAA
3499982 AATATTTTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 13 0.29
36 29 0.64
37 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (37 bp):
ATAAATATAATTTATAATTTATATTTTATAATTTGAG
Found at i:3518635 original size:26 final size:26
Alignment explanation
Indices: 3518606--3518655 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3518596 TCTGATTTTG
3518606 CTTTTTG-GAATTTTCTTAATAGAATA
1 CTTTTTGTGAATTTTCTTAA-AGAATA
**
3518632 CTTTTTGTTCATTTTCTTAAAGAA
1 CTTTTTGTGAATTTTCTTAAAGAA
3518656 CTTGAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (26 bp):
CTTTTTGTGAATTTTCTTAAAGAATA
Found at i:3519854 original size:32 final size:29
Alignment explanation
Indices: 3519795--3519852 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3519785 TGGGATAAAA
3519795 TTAGTTTTTGTATTATTAAATAGATTAAT
1 TTAGTTTTTGTATTATTAAATAGATTAAT
* *
3519824 TTAGTTTTTTTATTATTAAA-AAATTAAT
1 TTAGTTTTTGTATTATTAAATAGATTAAT
3519852 T
1 T
3519853 AAATATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (29 bp):
TTAGTTTTTGTATTATTAAATAGATTAAT
Found at i:3525535 original size:15 final size:15
Alignment explanation
Indices: 3525515--3525545 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3525505 ATGACAATGT
3525515 ATGGTTGACTTACTC
1 ATGGTTGACTTACTC
3525530 ATGGTTGACTTACTC
1 ATGGTTGACTTACTC
3525545 A
1 A
3525546 ACTTCACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
ATGGTTGACTTACTC
Found at i:3538237 original size:28 final size:29
Alignment explanation
Indices: 3538192--3538248 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
3538182 AAACTTTCTC
3538192 CTTTTATTTTTTATTTATTCTCATGGTTG
1 CTTTTATTTTTTATTTATTCTCATGGTTG
*
3538221 CTTTTA-TTTTTATTTATTCTCATTGTTG
1 CTTTTATTTTTTATTTATTCTCATGGTTG
3538249 TTGAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.14, C:0.11, G:0.09, T:0.67
Consensus pattern (29 bp):
CTTTTATTTTTTATTTATTCTCATGGTTG
Found at i:3538257 original size:28 final size:28
Alignment explanation
Indices: 3538199--3538257 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3538189 CTCCTTTTAT
**
3538199 TTTTTATTTATTCTCATGGTTGCTTTTA
1 TTTTTATTTATTCTCATGGTTGCTTAAA
*
3538227 TTTTTATTTATTCTCATTGTTG-TTGAAA
1 TTTTTATTTATTCTCATGGTTGCTT-AAA
3538255 TTT
1 TTT
3538258 AAGGTGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.17, C:0.08, G:0.10, T:0.64
Consensus pattern (28 bp):
TTTTTATTTATTCTCATGGTTGCTTAAA
Found at i:3538750 original size:30 final size:30
Alignment explanation
Indices: 3538716--3538786 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
3538706 AAGTAATAAT
*
3538716 AAAATTAACAAGTGTCTTTAAAATAACAAC
1 AAAATTAACAAATGTCTTTAAAATAACAAC
*
3538746 AAAATTAACAAATGTCTTTAAAATAATAAC
1 AAAATTAACAAATGTCTTTAAAATAACAAC
3538776 AAAATTAACAA
1 AAAATTAACAA
3538787 TAAAATATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (30 bp):
AAAATTAACAAATGTCTTTAAAATAACAAC
Found at i:3540375 original size:18 final size:20
Alignment explanation
Indices: 3540352--3540390 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3540342 GTAAATTAGT
3540352 AAATTA-TTAAAAAA-TAAA
1 AAATTATTTAAAAAATTAAA
3540370 AAATTATTTAAAAAATTAAA
1 AAATTATTTAAAAAATTAAA
3540390 A
1 A
3540391 GCTACACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTATTTAAAAAATTAAA
Found at i:3547575 original size:19 final size:19
Alignment explanation
Indices: 3547541--3547585 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3547531 ACAAATGACC
* *
3547541 TAAATTTTTATTTTAT-AT
1 TAAATTCTTATATTATAAT
3547559 TAATATTCTTATATTATAAT
1 TAA-ATTCTTATATTATAAT
3547579 TAAATTC
1 TAAATTC
3547586 AAGTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAATTCTTATATTATAAT
Found at i:3549613 original size:15 final size:15
Alignment explanation
Indices: 3549593--3549622 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3549583 CCTGAAGACG
*
3549593 ATAATAATATATTAA
1 ATAATAACATATTAA
3549608 ATAATAACATATTAA
1 ATAATAACATATTAA
3549623 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATAACATATTAA
Found at i:3550711 original size:21 final size:21
Alignment explanation
Indices: 3550672--3550711 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3550662 TAATATTTTA
* *
3550672 ATAAAAATATTTATTATAATT
1 ATAAAAATATTAATAATAATT
*
3550693 ATAAATATATTAATAATAA
1 ATAAAAATATTAATAATAA
3550712 ATATTTTGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAAATATTAATAATAATT
Found at i:3552061 original size:2 final size:2
Alignment explanation
Indices: 3552054--3552079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3552044 TGCCTAGTTG
3552054 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3552080 GCATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3556608 original size:23 final size:22
Alignment explanation
Indices: 3556582--3556647 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
3556572 TTCATTTAAC
3556582 TTAATCGAACATGTTCACGGACA
1 TTAATC-AACATGTTCACGGACA
* * *
3556605 TTAAACAAGCATGTTCATGTACA
1 TTAATCAA-CATGTTCACGGACA
*
3556628 TATAATTAAACATGTTCACG
1 T-TAA-TCAACATGTTCACG
3556648 AACAATGTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.06
23 18 0.53
24 12 0.35
25 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
TTAATCAACATGTTCACGGACA
Found at i:3556861 original size:12 final size:12
Alignment explanation
Indices: 3556832--3556885 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
3556822 ATCATTATTA
3556832 AATAAACGAGTC
1 AATAAACGAGTC
3556844 -ATAAACGAGTC
1 AATAAACGAGTC
*
3556855 AATAAACAAG-C
1 AATAAACGAGTC
* *
3556866 TTATAAACGAGCC
1 -AATAAACGAGTC
3556879 AATAAAC
1 AATAAAC
3556886 AAGCTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 12 0.34
12 22 0.63
13 1 0.03
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:3556874 original size:24 final size:24
Alignment explanation
Indices: 3556844--3556899 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
3556834 TAAACGAGTC
*
3556844 ATAAACGAGTCAATAAACAAGCTT
1 ATAAACGAGCCAATAAACAAGCTT
3556868 ATAAACGAGCCAATAAACAAGCTT
1 ATAAACGAGCCAATAAACAAGCTT
*
3556892 TTAAACGA
1 ATAAACGA
3556900 ACTTGTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACAAGCTT
Found at i:3566626 original size:27 final size:25
Alignment explanation
Indices: 3566588--3566639 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
3566578 TAATTTTAAT
3566588 TTAAAATAAGAATAATTTTTTAATATA
1 TTAAAATAAGAAT--TTTTTTAATATA
3566615 TTAACAAT-AGAATTTTTTTAATATA
1 TTAA-AATAAGAATTTTTTTAATATA
3566640 AAAGGTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 12 0.50
27 9 0.38
28 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAAAATAAGAATTTTTTTAATATA
Found at i:3567377 original size:3 final size:3
Alignment explanation
Indices: 3567369--3567396 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3567359 TGTACACAGA
3567369 AGC AGC AGC AGC AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC A
3567397 CTTGGATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:3568341 original size:29 final size:29
Alignment explanation
Indices: 3568278--3568349 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
3568268 ATTCACAATA
* *
3568278 AATTGAGCCTTCAACATCTATTTTCATGC
1 AATTGACCCTTCAACATCTATTTTCATCC
*
3568307 ATTTGAACCCTTCAA-ATCTATTTTCATCC
1 AATTG-ACCCTTCAACATCTATTTTCATCC
*
3568336 AATTGAGCCTTCAA
1 AATTGACCCTTCAA
3568350 TCTGACGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 21 0.57
30 8 0.22
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTGACCCTTCAACATCTATTTTCATCC
Found at i:3578967 original size:15 final size:15
Alignment explanation
Indices: 3578947--3578980 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3578937 AACCTTCTGA
3578947 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
3578962 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
3578977 TGAT
1 TGAT
3578981 GCAATGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (15 bp):
TGATTCTCTACCAGT
Found at i:3591876 original size:19 final size:17
Alignment explanation
Indices: 3591852--3591897 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3591842 ATTTAAATAA
3591852 TATTAAAAAATTATTTT
1 TATTAAAAAATTATTTT
*
3591869 ATATT-TAAAATATATTTT
1 -TATTAAAAAAT-TATTTT
3591887 TA-TAAAAAATT
1 TATTAAAAAATT
3591898 TAAAACAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAAAAATTATTTT
Found at i:3601193 original size:43 final size:44
Alignment explanation
Indices: 3601127--3601285 Score: 157
Period size: 43 Copynumber: 3.7 Consensus size: 44
3601117 AGCTCGTATA
* *
3601127 ATGCCA-TCGTCCAAGACATGGTCTTACATGTAA-TCAAATATCG
1 ATGCCACT-GTCCTAGACATGGTCTTACACGTAAGTCAAATATCG
* *
3601170 ATGCCACTGTCCTAGACAGGGTCTTATACG-AAGTCAAATA-CG
1 ATGCCACTGTCCTAGACATGGTCTTACACGTAAGTCAAATATCG
* * * ***
3601212 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTTTCATATCG
1 ATGCCACTGTCCTAGACATGGTCTTACACGTAAGTCAAATATCG
**
3601256 ATGCCAAC-GTCCTAGATGTGGTCTTACACG
1 ATGCC-ACTGTCCTAGACATGGTCTTACACG
3601286 AAATCACATA
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.32
43 37 0.39
44 27 0.28
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ATGCCACTGTCCTAGACATGGTCTTACACGTAAGTCAAATATCG
Found at i:3601280 original size:86 final size:85
Alignment explanation
Indices: 3601127--3601296 Score: 202
Period size: 86 Copynumber: 2.0 Consensus size: 85
3601117 AGCTCGTATA
*
3601127 ATGCCATCGTCCAAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTCCTAGACAGGGT
1 ATGCCATCGTCCAAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCTAGACAGGGT
* *
3601192 CTTATACGAAGTCAAATACG
66 CTTACACGAAATCAAATACG
* *** *
3601212 ATGCCAAT-GTCCCAGACATGGTCTTACACGTAATTTTCATATCGATGCCAAC-GTCCTAGA-TG
1 ATGCC-ATCGTCCAAGACATGGTCTTACACGTAA-TCAAATATCGATGCC-ACTGTCCTAGACAG
*
3601274 TGGTCTTACACGAAATCACATAC
63 -GGTCTTACACGAAATCAAATAC
3601297 CAGAATCCTA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 29 0.40
86 41 0.57
87 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (85 bp):
ATGCCATCGTCCAAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCTAGACAGGGT
CTTACACGAAATCAAATACG
Found at i:3602886 original size:30 final size:30
Alignment explanation
Indices: 3602845--3602907 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3602835 ACTTAGCAAG
3602845 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
3602875 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
3602905 CAA
1 CAA
3602908 TAAAATAAGT
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:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:3611278 original size:21 final size:21
Alignment explanation
Indices: 3611235--3611295 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3611225 TAATAAATCA
3611235 TAAAA-TTTATAAAACATATT
1 TAAAATTTTATAAAACATATT
*
3611255 TAAAATTTTATTAAAACGTA-T
1 TAAAATTTTA-TAAAACATATT
3611276 TAAAATTTTATAAAACATAT
1 TAAAATTTTATAAAACATAT
3611296 AAATCATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 13 0.36
21 15 0.42
22 8 0.22
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAATTTTATAAAACATATT
Found at i:3611821 original size:29 final size:26
Alignment explanation
Indices: 3611761--3611823 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 26
3611751 AGTTTATATC
*
3611761 AATTTTAATATTTTATAATTTTTTTT
1 AATTTTAATATTTAATAATTTTTTTT
*
3611787 ATTTTTAATGATTCTAATACATTTTTTTT
1 AATTTTAAT-ATT-TAATA-ATTTTTTTT
3611816 AATTTTAA
1 AATTTTAA
3611824 ATAAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.26
27 3 0.10
28 4 0.13
29 16 0.52
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
AATTTTAATATTTAATAATTTTTTTT
Found at i:3611902 original size:55 final size:54
Alignment explanation
Indices: 3611808--3611912 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 54
3611798 TTCTAATACA
*
3611808 TTTTTTTTAATTTTAAATAAGTTTTATTAAAAATTATATTTTATAATATTTATAG
1 TTTTTTATAATTTTAAATAAGTTTTATTAAAAATTATATTTT-TAATATTTATAG
** *
3611863 TTTTTTATAATTTT-AATAAG-TTTATATAAATTTTAATATTTTTACTATTT
1 TTTTTTATAATTTTAAATAAGTTTTAT-TAAAAATT-ATATTTTTAATATTT
3611913 TTAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
53 5 0.11
54 19 0.43
55 20 0.45
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (54 bp):
TTTTTTATAATTTTAAATAAGTTTTATTAAAAATTATATTTTTAATATTTATAG
Found at i:3611905 original size:29 final size:27
Alignment explanation
Indices: 3611830--3611959 Score: 74
Period size: 29 Copynumber: 4.8 Consensus size: 27
3611820 TTAAATAAGT
**
3611830 TTTATTAAAAATT-ATATTTTATAATA-
1 TTTATTAAATTTTAATATTTT-TAATAG
** * *
3611856 TTTA-TAGTTTTTTATAATTTTAATAAG
1 TTTATTAAATTTTAATATTTTTAAT-AG
*
3611883 TTTATATAAATTTTAATATTTTTACTA-
1 TTTAT-TAAATTTTAATATTTTTAATAG
*
3611910 TTT-TT-AATATTTAATATTTTTTATAG
1 TTTATTAAAT-TTTAATATTTTTAATAG
* *
3611936 TTATATTTAGATTTTTATATTTTT
1 TT-TA-TTAAATTTTAATATTTTT
3611960 TGAGATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
24 3 0.04
25 23 0.29
26 14 0.18
27 8 0.10
28 1 0.01
29 28 0.35
30 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTATTAAATTTTAATATTTTTAATAG
Found at i:3611906 original size:20 final size:19
Alignment explanation
Indices: 3611849--3611921 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 19
3611839 AATTATATTT
3611849 TATAATATTT-ATAGTTTTT-
1 TATAAT-TTTAATA-TTTTTA
**
3611868 TATAATTTTAATAAGTTTA
1 TATAATTTTAATATTTTTA
3611887 TATAAATTTTAATATTTTTA
1 TAT-AATTTTAATATTTTTA
3611907 CTAT--TTTTAATATTT
1 -TATAATTTTAATATTT
3611922 AATATTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 17 0.37
19 12 0.26
20 14 0.30
21 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (19 bp):
TATAATTTTAATATTTTTA
Found at i:3611927 original size:16 final size:16
Alignment explanation
Indices: 3611893--3611943 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3611883 TTTATATAAA
*
3611893 TTTTAATATTTTTACTAT
1 TTTTAATA--TTTAATAT
3611911 TTTTAATATTTAATAT
1 TTTTAATATTTAATAT
* *
3611927 TTTTTATAGTT-ATAT
1 TTTTAATATTTAATAT
3611942 TT
1 TT
3611944 AGATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.20
16 16 0.53
18 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTAATATTTAATAT
Found at i:3611967 original size:18 final size:19
Alignment explanation
Indices: 3611944--3611979 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3611934 AGTTATATTT
3611944 AGATTTTTAT-ATTTTTTG
1 AGATTTTTATAATTTTTTG
3611962 AGATTTTTATAATTTTTT
1 AGATTTTTATAATTTTTT
3611980 ATGGGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
AGATTTTTATAATTTTTTG
Found at i:3611976 original size:9 final size:9
Alignment explanation
Indices: 3611846--3611978 Score: 55
Period size: 9 Copynumber: 14.4 Consensus size: 9
3611836 AAAAATTATA
3611846 TTTTATAAT
1 TTTTATAAT
* *
3611855 ATTTATAGTT
1 TTTTATA-AT
3611865 TTTTATAAT
1 TTTTATAAT
*
3611874 TTTAATAAGT
1 TTTTATAA-T
* *
3611884 TTATATAAA
1 TTTTATAAT
3611893 TTTTA-ATAT
1 TTTTATA-AT
3611902 TTTTACT-A-
1 TTTTA-TAAT
3611910 TTTT-TAAT
1 TTTTATAAT
* *
3611918 ATTTAATATT
1 -TTTTATAAT
*
3611928 TTTTATAGT
1 TTTTATAAT
3611937 TATATT-TAGAT
1 T-T-TTATA-AT
3611948 TTTTAT-AT
1 TTTTATAAT
3611956 TTTT-TGAGAT
1 TTTTAT-A-AT
3611966 TTTTATAAT
1 TTTTATAAT
3611975 TTTT
1 TTTT
3611979 TATGGGAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 34
0.65 0.11 0.24
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 11 0.12
9 44 0.48
10 29 0.32
11 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:3624827 original size:13 final size:14
Alignment explanation
Indices: 3624801--3624827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3624791 TTGTTAATAC
3624801 CATTAAATTTTTTT
1 CATTAAATTTTTTT
3624815 CATTAAATTTTTT
1 CATTAAATTTTTT
3624828 GGTATGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
CATTAAATTTTTTT
Found at i:3625218 original size:16 final size:16
Alignment explanation
Indices: 3625197--3625227 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3625187 AATAAAAATA
3625197 AAAATAAAATAATTTC
1 AAAATAAAATAATTTC
*
3625213 AAAATAATATAATTT
1 AAAATAAAATAATTT
3625228 ACTTTGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAAAATAATTTC
Found at i:3626602 original size:2 final size:2
Alignment explanation
Indices: 3626595--3626632 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3626585 AGTATACTCC
3626595 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
3626633 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3627483 original size:17 final size:16
Alignment explanation
Indices: 3627460--3627498 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3627450 CCGTCAACGG
* *
3627460 AATTTATCAAACAAAT
1 AATTTATAAAAAAAAT
3627476 ATATTTATAAAAAAAAT
1 A-ATTTATAAAAAAAAT
3627493 AATTTA
1 AATTTA
3627499 AAGATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTATAAAAAAAAT
Found at i:3629121 original size:2 final size:2
Alignment explanation
Indices: 3629114--3629159 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3629104 TTACCCTTTA
* * * *
3629114 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT GT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3629156 AT AT
1 AT AT
3629160 GAATTAATAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3632689 original size:11 final size:11
Alignment explanation
Indices: 3632675--3632700 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3632665 AAAAATTAAA
3632675 AAAAACATTTT
1 AAAAACATTTT
3632686 AAAAACATTTT
1 AAAAACATTTT
3632697 AAAA
1 AAAA
3632701 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAACATTTT
Found at i:3632718 original size:29 final size:28
Alignment explanation
Indices: 3632686--3632746 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
3632676 AAAACATTTT
3632686 AAAAACATTTT-AAAATTAAAAAATAATA
1 AAAAACATTTTAAAAATTAAAAAAT-ATA
* *
3632714 AAAAATATTTTAAAAATTAAAAAATTTA
1 AAAAACATTTTAAAAATTAAAAAATATA
3632742 AAAAA
1 AAAAA
3632747 TAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAACATTTTAAAAATTAAAAAATATA
Found at i:3632746 original size:39 final size:39
Alignment explanation
Indices: 3632662--3632750 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
3632652 AAAAATTTAT
* **
3632662 TTTAAAAATTAAAAAAAACATTTTAAAAACATTTTAAAA
1 TTTAAAAAATAAAAAAAACATTTTAAAAACATTAAAAAA
*
3632701 -TTAAAAAATAATAAAAAATATTTT-AAAA-ATTAAAAAA
1 TTTAAAAAATAA-AAAAAACATTTTAAAAACATTAAAAAA
3632738 TTTAAAAAATAAA
1 TTTAAAAAATAAA
3632751 TATATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
37 8 0.18
38 25 0.57
39 11 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.31
Consensus pattern (39 bp):
TTTAAAAAATAAAAAAAACATTTTAAAAACATTAAAAAA
Found at i:3632758 original size:17 final size:17
Alignment explanation
Indices: 3632716--3632758 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3632706 AAATAATAAA
*
3632716 AAATAT-TTTAAAAATT
1 AAATATATTTAAAAAAT
*
3632732 AAA-AAATTTAAAAAAT
1 AAATATATTTAAAAAAT
3632748 AAATATATTTA
1 AAATATATTTA
3632759 TTATATCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 15 0.68
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATTTAAAAAAT
Found at i:3632912 original size:18 final size:18
Alignment explanation
Indices: 3632889--3632923 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3632879 CCCATATTTC
3632889 GGTCGGGCCGTCGGGCCA
1 GGTCGGGCCGTCGGGCCA
*
3632907 GGTCGGGCTGTCGGGCC
1 GGTCGGGCCGTCGGGCC
3632924 GCCCGGCCCA
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:0.31, G:0.51, T:0.14
Consensus pattern (18 bp):
GGTCGGGCCGTCGGGCCA
Found at i:3640974 original size:28 final size:28
Alignment explanation
Indices: 3640934--3640988 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3640924 TTCTCACGCC
3640934 TTGTCATGAGATATGTCACAAAAATACT
1 TTGTCATGAGATATGTCACAAAAATACT
3640962 TTGTCATGAGATATGTCACAAAAATAC
1 TTGTCATGAGATATGTCACAAAAATAC
3640989 AATAGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (28 bp):
TTGTCATGAGATATGTCACAAAAATACT
Found at i:3642298 original size:13 final size:13
Alignment explanation
Indices: 3642282--3642309 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3642272 ATAAAATCCG
3642282 AAATCTGTACACA
1 AAATCTGTACACA
3642295 AAATCTGTACACA
1 AAATCTGTACACA
3642308 AA
1 AA
3642310 CTACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATCTGTACACA
Found at i:3644513 original size:20 final size:20
Alignment explanation
Indices: 3644490--3644532 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3644480 TATTTTAAGA
*
3644490 TTTA-GAATTATAGTTTATAG
1 TTTAGGAATTAAAGTTT-TAG
*
3644510 TTTAGGATTTAAAGTTTTAG
1 TTTAGGAATTAAAGTTTTAG
3644530 TTT
1 TTT
3644533 TAGAGTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTAGGAATTAAAGTTTTAG
Found at i:3644513 original size:27 final size:26
Alignment explanation
Indices: 3644478--3644575 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 26
3644468 AAAGTTATAC
* *
3644478 TATATTTTAAGATTTAGAATTATAGTT
1 TATAGTTTAAGATTTA-AATTTTAGTT
*
3644505 TATAGTTTAGGATTTAAAGTTTTAGTTT
1 TATAGTTTAAGATTTAAA-TTTTAG-TT
*
3644533 TAGAGTTTAA-AGTTTAAATTTTAAGTT
1 TATAGTTTAAGA-TTTAAATTTT-AGTT
*
3644560 TA-GGTTTTAAGATTTA
1 TATAG-TTTAAGATTTA
3644576 GGGTTTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
26 3 0.05
27 37 0.63
28 19 0.32
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (26 bp):
TATAGTTTAAGATTTAAATTTTAGTT
Found at i:3644526 original size:21 final size:22
Alignment explanation
Indices: 3644501--3644561 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
3644491 TTAGAATTAT
3644501 AGTTTATAG-TTTAG-GATTTAA
1 AGTTTATAGTTTTAGAG-TTTAA
3644522 AGTTT-TAGTTTTAGAGTTTAA
1 AGTTTATAGTTTTAGAGTTTAA
*
3644543 AGTTTA-AATTTTA-AGTTTA
1 AGTTTATAGTTTTAGAGTTTA
3644562 GGTTTTAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 9 0.25
21 26 0.72
22 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
AGTTTATAGTTTTAGAGTTTAA
Found at i:3644548 original size:14 final size:14
Alignment explanation
Indices: 3644482--3644582 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
3644472 TTATACTATA
*
3644482 TTTTAAGATTTAGAA
1 TTTTAAG-TTTAGAG
* *
3644497 TTAT-AGTTTATAG
1 TTTTAAGTTTAGAG
* *
3644510 -TTTAGGATTTAAAG
1 TTTTAAG-TTTAGAG
3644524 TTTT-AGTTTTAGAG
1 TTTTAAG-TTTAGAG
* *
3644538 TTTAAAGTTTA-AA
1 TTTTAAGTTTAGAG
3644551 TTTTAAGTTTAG-G
1 TTTTAAGTTTAGAG
*
3644564 TTTTAAGATTTAGGG
1 TTTTAAG-TTTAGAG
3644579 TTTT
1 TTTT
3644583 TAAAATAAGT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
12 2 0.03
13 24 0.36
14 27 0.41
15 13 0.20
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (14 bp):
TTTTAAGTTTAGAG
Found at i:3645127 original size:21 final size:21
Alignment explanation
Indices: 3645101--3645149 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3645091 TGCTTAGACT
3645101 TGGCCCAAACCCAGCTCGACC
1 TGGCCCAAACCCAGCTCGACC
3645122 TGGCCCAAACCCAGCTCGACC
1 TGGCCCAAACCCAGCTCGACC
3645143 TGGCCCA
1 TGGCCCA
3645150 TGAGCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.47, G:0.20, T:0.10
Consensus pattern (21 bp):
TGGCCCAAACCCAGCTCGACC
Found at i:3646750 original size:2 final size:2
Alignment explanation
Indices: 3646743--3646785 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3646733 AAATCCGGAG
*
3646743 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3646785 A
1 A
3646786 AAGAGGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3648199 original size:29 final size:30
Alignment explanation
Indices: 3648156--3648235 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
3648146 GAATTGGATC
*
3648156 AAATCGAAATTTCATGTATAAAATT-ACATA
1 AAATC-AAAGTTCATGTATAAAATTCACATA
* *
3648186 AAATCAAAGTTCATGTATATAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATT-CACATA
*
3648217 AAATCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
3648236 GTTTTGGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 5 0.11
31 22 0.50
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTCACATA
Found at i:3654032 original size:33 final size:33
Alignment explanation
Indices: 3653981--3654215 Score: 151
Period size: 33 Copynumber: 6.7 Consensus size: 33
3653971 TTGTCCGTTA
* *
3653981 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
3654015 TCGGGGAATCAGCACTTAGCAACCTCTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAACCAC---CA-A--T--GAT
* * *
3654056 ACGGTGGGATCAGCACTTAGCAACCACCAATGAG
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
3654090 TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT
3654131 AT-GGTGGAATCAGCACTTAGCAACCACCAATGAT
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
3654165 TCGGGGAATCAGCATTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
*
3654192 TGGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
3654216 CCCTTTATAT
Statistics
Matches: 164, Mismatches: 17, Indels: 47
0.72 0.07 0.21
Matches are distributed among these distances:
27 23 0.14
32 2 0.01
33 57 0.35
34 16 0.10
36 6 0.04
37 1 0.01
38 2 0.01
39 6 0.04
41 12 0.07
42 39 0.24
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:3654105 original size:75 final size:75
Alignment explanation
Indices: 3653982--3654190 Score: 330
Period size: 75 Copynumber: 2.8 Consensus size: 75
3653972 TGTCCGTTAT
* * *
3653982 CGGT-GGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCTCTTTCA
1 CGGTGGGA-TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTCA
*
3654046 CATTTAAGATA
65 CATTTAAAATA
*
3654057 CGGTGGGATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCCTTCAC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTCAC
3654122 ATTTAAAATA
66 ATTTAAAATA
* * *
3654132 TGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCATTTAGCAACCCC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCC
3654191 TTGGGGGAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 121 0.98
76 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.22
Consensus pattern (75 bp):
CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAAATA
Found at i:3656603 original size:20 final size:20
Alignment explanation
Indices: 3656578--3656618 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3656568 AGTGGCGAGG
3656578 GAAGAACGA-GAAAGAAAAAC
1 GAAGAAC-ATGAAAGAAAAAC
3656598 GAAGAACATTGAAAGAAAAAC
1 GAAGAACA-TGAAAGAAAAAC
3656619 AACAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 7 0.37
21 11 0.58
ACGTcount: A:0.63, C:0.10, G:0.22, T:0.05
Consensus pattern (20 bp):
GAAGAACATGAAAGAAAAAC
Found at i:3660424 original size:21 final size:19
Alignment explanation
Indices: 3660387--3660438 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3660377 AACTCAAACG
**
3660387 GAAAAAGATGAGTAAACCTA
1 GAAAAAGAAAAGTAAA-CTA
3660407 GAAAAAGAAAAGTGAAACTA
1 GAAAAAGAAAAGT-AAACTA
3660427 GAAAAATGAAAA
1 GAAAAA-GAAAA
3660439 ACCGAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.63, C:0.06, G:0.19, T:0.12
Consensus pattern (19 bp):
GAAAAAGAAAAGTAAACTA
Found at i:3673215 original size:3 final size:3
Alignment explanation
Indices: 3673207--3673235 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3673197 TCTATCCTTT
3673207 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
3673236 TTCTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:3673501 original size:19 final size:18
Alignment explanation
Indices: 3673460--3673517 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3673450 TAAACTTATA
*
3673460 AAAATATATATAATAGTAT
1 AAAATAT-TATAATAATAT
3673479 -AAATATTATAATAAATAT
1 AAAATATTATAAT-AATAT
*
3673497 AAAATTTTATAA-AAT-T
1 AAAATATTATAATAATAT
3673513 AAAAT
1 AAAAT
3673518 TATATAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 6 0.17
17 9 0.26
18 10 0.29
19 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATTATAATAATAT
Found at i:3673515 original size:16 final size:17
Alignment explanation
Indices: 3673460--3673546 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 17
3673450 TAAACTTATA
*
3673460 AAAATATATATAATAGTAT
1 AAAAT-TATATAA-AATAT
3673479 AAATATTATA-ATAAATAT
1 AAA-ATTATATA-AAATAT
*
3673497 AAAATTTTATAAAAT-T
1 AAAATTATATAAAATAT
*
3673513 AAAATTATATAAACTTAT
1 AAAATTATATAAA-ATAT
3673531 AAAAATTATTATAAAA
1 -AAAATTA-TATAAAA
3673547 ACTTGACCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
16 13 0.23
17 10 0.18
18 10 0.18
19 15 0.27
20 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
AAAATTATATAAAATAT
Found at i:3673525 original size:10 final size:10
Alignment explanation
Indices: 3673447--3673546 Score: 51
Period size: 10 Copynumber: 10.8 Consensus size: 10
3673437 TATTTAAAAA
*
3673447 ATATAAACTT
1 ATATAAAATT
3673457 ATA-AAAA-T
1 ATATAAAATT
*
3673465 ATATATAA-T
1 ATATAAAATT
3673474 AGTATAAATATT
1 A-TATAAA-ATT
*
3673486 ATA-ATAA--
1 ATATAAAATT
3673493 ATATAAAATT
1 ATATAAAATT
*
3673503 TTAT-AAA--
1 ATATAAAATT
3673510 AT-TAAAATT
1 ATATAAAATT
*
3673519 ATATAAACTT
1 ATATAAAATT
3673529 ATA-AAAATT
1 ATATAAAATT
3673538 ATTATAAAA
1 A-TATAAAA
3673547 ACTTGACCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 25
0.67 0.09 0.25
Matches are distributed among these distances:
6 1 0.01
7 7 0.10
8 7 0.10
9 20 0.29
10 24 0.35
11 7 0.10
12 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (10 bp):
ATATAAAATT
Found at i:3673543 original size:36 final size:38
Alignment explanation
Indices: 3673447--3673546 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 38
3673437 TATTTAAAAA
*
3673447 ATATAAACTTATAAAAA-TATATATAATAGTATAAATATT
1 ATATAAACTTATAAAAATTAT-TATAA-AATATAAATATT
3673486 ATAATAAA--TAT-AAAATT-TTATAAAAT-TAAA-ATT
1 AT-ATAAACTTATAAAAATTATTATAAAATATAAATATT
3673519 ATATAAACTTATAAAAATTATTATAAAA
1 ATATAAACTTATAAAAATTATTATAAAA
3673547 ACTTGACCTA
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
32 5 0.09
33 5 0.09
34 7 0.13
35 8 0.15
36 13 0.24
37 5 0.09
38 4 0.07
39 2 0.04
40 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (38 bp):
ATATAAACTTATAAAAATTATTATAAAATATAAATATT
Found at i:3682347 original size:33 final size:34
Alignment explanation
Indices: 3682286--3682357 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
3682276 TTACTTATAA
* * * *
3682286 AAAAATAAAAAATTTATATTTTTTAAAAAATTAT
1 AAAAATAAAAAAATGATATATTTAAAAAAATTAT
*
3682320 AAAAATAAAAAAATGATA-ATTTAAAAAACTTAT
1 AAAAATAAAAAAATGATATATTTAAAAAAATTAT
*
3682353 TAAAA
1 AAAAA
3682358 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (34 bp):
AAAAATAAAAAAATGATATATTTAAAAAAATTAT
Found at i:3685594 original size:15 final size:15
Alignment explanation
Indices: 3685576--3685606 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3685566 TAAAATTAAG
3685576 ATTTTTAAAATATCC
1 ATTTTTAAAATATCC
*
3685591 ATTTTTACAATATCC
1 ATTTTTAAAATATCC
3685606 A
1 A
3685607 AAATTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTTAAAATATCC
Found at i:3685810 original size:2 final size:2
Alignment explanation
Indices: 3685803--3685836 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3685793 AATATTAATG
* *
3685803 AT AT AT AT AA AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3685837 CATACAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3685999 original size:2 final size:2
Alignment explanation
Indices: 3685992--3686016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3685982 ATATGCGAAG
3685992 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3686017 GATTAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3687716 original size:274 final size:274
Alignment explanation
Indices: 3687208--3688037 Score: 1567
Period size: 274 Copynumber: 3.0 Consensus size: 274
3687198 CTTTTTCCTC
3687208 ATTTAATCTAAAATACCAAAAAAAAAAAAGAGGGTATGCACACTTGCACTACAC--AAAATTTAA
1 ATTTAATCTAAAATACC--AAAAAAAAAA-A-GGTATGCACACTTGCACTACACTGAAAATTTAA
3687271 TTTAATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTT
62 TTTAATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTT
3687336 CTTTTCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGT
127 CTTTTCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGT
3687401 CTTGAACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTCCCGTACTTCAAAAAGAA
192 CTTGAACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTCCCGTACTTCAAAAAGAA
3687466 CCTAAAAAGATTTACGGA
257 CCTAAAAAGATTTACGGA
3687484 ATTTAATCTAAAATACCAAAAAAAAAAAGGTATGCACACTTGCACTACACTGAAAATTTAATTTA
1 ATTTAATCTAAAATACCAAAAAAAAAAAGGTATGCACACTTGCACTACACTGAAAATTTAATTTA
3687549 ATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTTCTTT
66 ATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTTCTTT
3687614 TCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGTCTTG
131 TCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGTCTTG
3687679 AACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTCCCGTACTTCAAAAAGAACCTA
196 AACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTCCCGTACTTCAAAAAGAACCTA
3687744 AAAAGATTTACGGA
261 AAAAGATTTACGGA
3687758 ATTTAATCTAAAATACCAAAAAAAAAAAGGTATGCACACTTGCACTACACTGAAAATTTAATTTA
1 ATTTAATCTAAAATACCAAAAAAAAAAAGGTATGCACACTTGCACTACACTGAAAATTTAATTTA
3687823 ATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTTCTTT
66 ATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTTCTTT
*
3687888 TCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAACCATTTTTATTAAGGAGAGAGTCTTG
131 TCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGTCTTG
* *
3687953 AACCCTTGACAGAAAATATTATTATCATGATAAGATCTTGTC-CTCCGTACTTCAAAAAGAACCT
196 AACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTC-CCGTACTTCAAAAAGAACCT
3688017 AAAAAGATTTACGGA
260 AAAAAGATTTACGGA
3688032 ATTTAA
1 ATTTAA
3688038 AAAACACCTC
Statistics
Matches: 548, Mismatches: 3, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
272 22 0.04
273 2 0.00
274 507 0.93
276 17 0.03
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (274 bp):
ATTTAATCTAAAATACCAAAAAAAAAAAGGTATGCACACTTGCACTACACTGAAAATTTAATTTA
ATCTATTAATTTGCACTAAGTTAAAGCTTTTAAGTCCAATTTTTGTACCCACAAGTCATTTCTTT
TCACTAGTTTTTTACTCAATATTTTTAAGTATCGAAAAATCATTTTTATTAAGGAGAGAGTCTTG
AACCCTTGACAGAAAGTATTATTATCATGATAAGATTTTGTCTCCCGTACTTCAAAAAGAACCTA
AAAAGATTTACGGA
Found at i:3688679 original size:33 final size:33
Alignment explanation
Indices: 3688642--3688718 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
3688632 TTTGCTCAGT
*
3688642 CCACTCCCCACCATCCCGACTCCAGCACTGACA
1 CCACTTCCCACCATCCCGACTCCAGCACTGACA
3688675 CCACTTCCCACCATCCCGACTCCAGCACTGACA
1 CCACTTCCCACCATCCCGACTCCAGCACTGACA
3688708 CCACTTCCCAC
1 CCACTTCCCAC
3688719 AAGTCCAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.23, C:0.55, G:0.08, T:0.14
Consensus pattern (33 bp):
CCACTTCCCACCATCCCGACTCCAGCACTGACA
Found at i:3688730 original size:33 final size:33
Alignment explanation
Indices: 3688642--3688732 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
3688632 TTTGCTCAGT
* * *
3688642 CCACTCCCCACCATCCCGACTCCAGCACTGACA
1 CCACTTCCCACAATCCCAACTCCAGCACTGACA
* *
3688675 CCACTTCCCACCATCCCGACTCCAGCACTGACA
1 CCACTTCCCACAATCCCAACTCCAGCACTGACA
3688708 CCACTTCCCACAAGT-CCAACTCCAG
1 CCACTTCCCACAA-TCCCAACTCCAG
3688733 TACCGATACC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.25, C:0.52, G:0.09, T:0.14
Consensus pattern (33 bp):
CCACTTCCCACAATCCCAACTCCAGCACTGACA
Found at i:3705125 original size:12 final size:12
Alignment explanation
Indices: 3705108--3705180 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
3705098 ATAAATAAAA
3705108 AACTATAATAAT
1 AACTATAATAAT
3705120 AACTATAATAAT
1 AACTATAATAAT
* *
3705132 -AGTAAAGATAAT
1 AACTATA-ATAAT
3705144 AA-TAGTAATAAT
1 AACTA-TAATAAT
*
3705156 AGA-TATAATAAA
1 A-ACTATAATAAT
3705168 AACTA-AATAAT
1 AACTATAATAAT
3705179 AA
1 AA
3705181 AATTGCTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
11 12 0.24
12 34 0.67
13 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (12 bp):
AACTATAATAAT
Found at i:3706835 original size:132 final size:132
Alignment explanation
Indices: 3706616--3706871 Score: 424
Period size: 132 Copynumber: 1.9 Consensus size: 132
3706606 CAACTATCGT
** * *
3706616 TTAGGGATACAGAATCTACAATCTTTGATCTATTCCACTACTGCTTAGGGTGATAGGACTAATCG
1 TTAGGGATACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATCG
* *
3706681 TTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACT
66 CTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTACT
3706746 GC
131 GC
* *
3706748 TTAGGG-TGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG
1 TTAGGGAT-ACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATC
3706812 GCTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTACTCC
65 GCTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTACTCC
3706872 GCTGCCAAAT
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
131 1 0.01
132 114 0.99
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (132 bp):
TTAGGGATACAGAATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATCG
CTTAAATCTGCTTCTCCACTGTATTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTACT
GC
Found at i:3706907 original size:46 final size:46
Alignment explanation
Indices: 3706856--3707413 Score: 882
Period size: 46 Copynumber: 12.1 Consensus size: 46
3706846 AAGATTCACC
* *
3706856 ATCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGTT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
3706902 ATCTTCGATCTCCTCCACTGCCAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
3706948 ATCTTCGATCTCCTCCGCTGCCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
3706994 ATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
3707040 ATCTTTGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
3707086 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
3707132 ATCTTCGATCTACTCTGCTGCCAAATACAGCAAGACAAGATTCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGA-TCTGCT
* *
3707179 ATCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
3707225 ATCTTCGATCTCTTCTGCTGCCAAATACAGGAATACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
3707271 ATCTTCGATCTCTTCTGCTGCCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
3707317 ATCTTCGATCTACTCCACTGCCAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
3707363 ATCTTCGATCTCCTCCACTGCCAAACACAGGAAGACAATACCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
3707409 ATCTT
1 ATCTT
3707414 TATTGATCTG
Statistics
Matches: 479, Mismatches: 32, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
46 434 0.91
47 45 0.09
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (46 bp):
ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
Found at i:3708566 original size:45 final size:43
Alignment explanation
Indices: 3708515--3708615 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 43
3708505 CCCGATCTGA
3708515 TCAAAATTTGAGCT-GCTCTGATCACTACCATGCCCCTAATTTGAT
1 TCAAAATTTGAGCTCGCTCTGATCACT-CCATGCCCC-AATTTG-T
* * * *
3708560 TCAAAATTTAAG-TCGCTCTGATCACTTCGTGCCCCATTTTGT
1 TCAAAATTTGAGCTCGCTCTGATCACTCCATGCCCCAATTTGT
3708602 TCCAAAATTTGAGC
1 T-CAAAATTTGAGC
3708616 CGTCCTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
42 2 0.04
43 15 0.31
44 8 0.17
45 23 0.48
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (43 bp):
TCAAAATTTGAGCTCGCTCTGATCACTCCATGCCCCAATTTGT
Found at i:3708708 original size:12 final size:14
Alignment explanation
Indices: 3708691--3708750 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
3708681 TTGGCCTCTC
3708691 CTTTTTC-CTT-TT
1 CTTTTTCTCTTCTT
3708703 CTTTTTCTCTTCTT
1 CTTTTTCTCTTCTT
*
3708717 CTTCTTCTTCTTC-T
1 CTTTTTC-TCTTCTT
*
3708731 CTTTTTTTCATTCTT
1 CTTTTTCTC-TTCTT
3708746 -TTTTT
1 CTTTTT
3708751 TGTTTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.17
13 5 0.12
14 22 0.55
15 6 0.15
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTTTCTCTTCTT
Found at i:3708744 original size:20 final size:20
Alignment explanation
Indices: 3708701--3708796 Score: 85
Period size: 20 Copynumber: 4.9 Consensus size: 20
3708691 CTTTTTCCTT
*
3708701 TTCTTTTTCTCTTCTTCTTC-
1 TTCTTTTTCTCTT-TTTTTCA
*
3708721 TTCTTCTTCTCTTTTTTTCA
1 TTCTTTTTCTCTTTTTTTCA
3708741 TTCTTTTT-T-TTGTTTTT-A
1 TTCTTTTTCTCTT-TTTTTCA
* *
3708759 TTCTTTTTTTATTTTTTTCTA
1 TTCTTTTTCTCTTTTTTTC-A
*
3708780 TT-TTTTTCTGTTTTTTT
1 TTCTTTTTCTCTTTTTTT
3708797 AGCTTGCATC
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.17
19 17 0.26
20 34 0.52
21 3 0.05
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (20 bp):
TTCTTTTTCTCTTTTTTTCA
Found at i:3708749 original size:11 final size:9
Alignment explanation
Indices: 3708732--3708796 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
3708722 TCTTCTTCTC
*
3708732 TTTTTTTCA
1 TTTTTTTTA
3708741 TTCTTTTTT-
1 TT-TTTTTTA
*
3708750 TTGTTTTTA
1 TTTTTTTTA
3708759 TTCTTTTTTTA
1 -T-TTTTTTTA
3708770 TTTTTTTCTA
1 TTTTTTT-TA
*
3708780 TTTTTTTCTG
1 TTTTTTT-TA
3708790 TTTTTTT
1 TTTTTTT
3708797 AGCTTGCATC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
8 5 0.11
9 10 0.21
10 25 0.53
11 7 0.15
ACGTcount: A:0.06, C:0.08, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3708757 original size:10 final size:10
Alignment explanation
Indices: 3708744--3708796 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
3708734 TTTTTCATTC
*
3708744 TTTTT-TTTG
1 TTTTTATTTT
3708753 TTTTTATTCTT
1 TTTTTATT-TT
3708764 TTTTTATTTT
1 TTTTTATTTT
*
3708774 TTTCTATTTT
1 TTTTTATTTT
* *
3708784 TTTCTGTTTT
1 TTTTTATTTT
3708794 TTT
1 TTT
3708797 AGCTTGCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 5 0.13
10 25 0.64
11 9 0.23
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.85
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:3708761 original size:18 final size:18
Alignment explanation
Indices: 3708734--3708786 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
3708724 TTCTTCTCTT
*
3708734 TTTTTCATTCTTTTTTTTG
1 TTTTT-ATTCTTTTTTTTA
3708753 TTTTTATTC-TTTTTTTA
1 TTTTTATTCTTTTTTTTA
3708770 TTTTT-TTCTATTTTTTT
1 TTTTTATTCT-TTTTTTT
3708787 CTGTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 11 0.35
19 5 0.16
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTATTCTTTTTTTTA
Found at i:3708793 original size:18 final size:18
Alignment explanation
Indices: 3708744--3708794 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3708734 TTTTTCATTC
* *
3708744 TTTTTTTTGTTTTTATTC
1 TTTTTTTTGTTTTTACTA
*
3708762 TTTTTTTAT-TTTTTTCTA
1 TTTTTTT-TGTTTTTACTA
3708780 TTTTTTTCTGTTTTT
1 TTTTTTT-TGTTTTT
3708795 TTAGCTTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.84
Consensus pattern (18 bp):
TTTTTTTTGTTTTTACTA
Found at i:3711634 original size:19 final size:19
Alignment explanation
Indices: 3711610--3711646 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3711600 TTATGAAGTT
3711610 GATGTATG-TATGTAATGCG
1 GATGTATGATATG-AATGCG
3711629 GATGTATGATATGAATGC
1 GATGTATGATATGAATGC
3711647 AAAAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (19 bp):
GATGTATGATATGAATGCG
Found at i:3713911 original size:3 final size:3
Alignment explanation
Indices: 3713865--3713898 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3713855 TTATATTAGT
*
3713865 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3713899 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3715538 original size:13 final size:13
Alignment explanation
Indices: 3715502--3715539 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3715492 CAAGGAAGAA
3715502 AACAAAAAA-AGC
1 AACAAAAAATAGC
*
3715514 AACCAAACAATAGC
1 AA-CAAAAAATAGC
3715528 AACAAAAAATAG
1 AACAAAAAATAG
3715540 AAAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 15 0.68
14 5 0.23
ACGTcount: A:0.68, C:0.18, G:0.08, T:0.05
Consensus pattern (13 bp):
AACAAAAAATAGC
Found at i:3715699 original size:17 final size:18
Alignment explanation
Indices: 3715662--3715699 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3715652 TTGAAGGTGA
**
3715662 TTTTGCTTTTCTTTTTTT
1 TTTTGCTTTTCTTTTACT
3715680 TTTTG-TTTTCTTTTACT
1 TTTTGCTTTTCTTTTACT
3715697 TTT
1 TTT
3715700 CACATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.03, C:0.11, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTGCTTTTCTTTTACT
Found at i:3716431 original size:3 final size:3
Alignment explanation
Indices: 3716414--3716495 Score: 55
Period size: 3 Copynumber: 26.7 Consensus size: 3
3716404 TTTAGCAATT
*
3716414 TTA TTA TTTA GTTA TTA TTA -TA TCTA TTA TTA CTA TTA TTA TCT- TTA
1 TTA TTA -TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA
* *
3716461 CTA TTA TTA -TA GTTA TTA TTA -TA GTTA TTT TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TT
3716496 TATATTTACC
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
2 7 0.11
3 42 0.67
4 14 0.22
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3716443 original size:12 final size:11
Alignment explanation
Indices: 3716414--3716498 Score: 75
Period size: 12 Copynumber: 7.4 Consensus size: 11
3716404 TTTAGCAATT
3716414 TTATTATT-TA
1 TTATTATTATA
3716424 GTTATTATTATA
1 -TTATTATTATA
3716436 TCTATTATTACTA
1 T-TATTATTA-TA
*
3716449 TTATTATCTTTA
1 TTATTAT-TATA
*
3716461 CTATTATTATA
1 TTATTATTATA
3716472 GTTATTATTATA
1 -TTATTATTATA
*
3716484 GTTATTTTTAT-
1 -TTATTATTATA
3716495 TTAT
1 TTAT
3716499 ATTTACCTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
10 4 0.06
11 12 0.19
12 44 0.69
13 4 0.06
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (11 bp):
TTATTATTATA
Found at i:3719941 original size:126 final size:126
Alignment explanation
Indices: 3719742--3719989 Score: 426
Period size: 126 Copynumber: 2.0 Consensus size: 126
3719732 TAACAATTTA
3719742 ATAATATAATCATAAATAAATAGTATTTTTTATTTATTTTAAAGTTTCTTCACTTTAAAGGTCTA
1 ATAATATAATCATAAATAAATAGTATTTTTTATTTATTTTAAAGTTTCTTCACTTTAAAGGTCTA
3719807 ATTCCAGATTCAGTATCTATACTCTTTGAATTTCTAAAATTTAATTCTTTAATTTTTTAATT
66 ATTCCAGATTCAGTATCTATACTCTTTGAATTT-TAAAATTTAATTCTTTAATTTTTTAATT
* * *
3719869 ATAATATAATCATCAATAAATAGTA-TTTTTATTTATTTTAAAGTTTCTTCTCTTTAAAGGTTTA
1 ATAATATAATCATAAATAAATAGTATTTTTTATTTATTTTAAAGTTTCTTCACTTTAAAGGTCTA
* * *
3719933 ATTCCAGATTCAGTATCTATACTCTTTGAATTTTAGATTTTAATTCTTTTATTTTTT
66 ATTCCAGATTCAGTATCTATACTCTTTGAATTTTAAAATTTAATTCTTTAATTTTTT
3719990 TTAATTTCAA
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
125 21 0.18
126 70 0.61
127 24 0.21
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (126 bp):
ATAATATAATCATAAATAAATAGTATTTTTTATTTATTTTAAAGTTTCTTCACTTTAAAGGTCTA
ATTCCAGATTCAGTATCTATACTCTTTGAATTTTAAAATTTAATTCTTTAATTTTTTAATT
Found at i:3728970 original size:2 final size:2
Alignment explanation
Indices: 3728965--3728989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3728955 ATTTGATATA
3728965 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3728990 ATAGATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3731086 original size:52 final size:52
Alignment explanation
Indices: 3731008--3731127 Score: 231
Period size: 52 Copynumber: 2.3 Consensus size: 52
3730998 ATAACAACTT
3731008 TAACCCTCAACTTTTATGTATTATGTCAATTTAGTCTTGATTCTAAAAAGTC
1 TAACCCTCAACTTTTATGTATTATGTCAATTTAGTCTTGATTCTAAAAAGTC
3731060 TAACCCTCAACTTTTATGTATTATGTCAATTTAGTCTTGATTCTAAAAAGTC
1 TAACCCTCAACTTTTATGTATTATGTCAATTTAGTCTTGATTCTAAAAAGTC
*
3731112 TAACCCTCAACATTTA
1 TAACCCTCAACTTTTA
3731128 CACATTGTGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (52 bp):
TAACCCTCAACTTTTATGTATTATGTCAATTTAGTCTTGATTCTAAAAAGTC
Found at i:3731858 original size:17 final size:18
Alignment explanation
Indices: 3731836--3731870 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3731826 TTACACTTTA
*
3731836 AATTTATAA-TTTATATT
1 AATTTAAAATTTTATATT
3731853 AATTTAAAATTTTATATT
1 AATTTAAAATTTTATATT
3731871 TTTTACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTAAAATTTTATATT
Found at i:3739190 original size:30 final size:31
Alignment explanation
Indices: 3739142--3739222 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
3739132 ATTTTCAAAA
*
3739142 ATATAATAA-TAACTTTAAATATATATAAAT
1 ATATAATAATTAACATTAAATATATATAAAT
* *
3739172 ATATAATAATTAA-ATTAAATTTTATATTAAT
1 ATATAATAATTAACATTAAA-TATATATAAAT
* *
3739203 AGAT-AT-ATTAATATTAAATA
1 ATATAATAATTAACATTAAATA
3739223 AAAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 6 0.14
30 22 0.51
31 15 0.35
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
ATATAATAATTAACATTAAATATATATAAAT
Found at i:3740811 original size:42 final size:42
Alignment explanation
Indices: 3740752--3740834 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
3740742 AATTTCAAAG
3740752 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
3740794 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
3740835 CACACATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:3744779 original size:46 final size:46
Alignment explanation
Indices: 3744712--3744811 Score: 182
Period size: 46 Copynumber: 2.2 Consensus size: 46
3744702 CGATTTCTAA
*
3744712 TCCCTTGCAAAAGCAAAGATTAGGTAATCGGTGTCTCATTTACCCT
1 TCCCTTGCAAAAGCAAAGATTAGGTAATCGATGTCTCATTTACCCT
3744758 TCCCTTGCAAAAGCAAAGATTAGGTAATCGATGTCTCATTTACCCT
1 TCCCTTGCAAAAGCAAAGATTAGGTAATCGATGTCTCATTTACCCT
*
3744804 CCCCTTGC
1 TCCCTTGC
3744812 CGAAATCGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (46 bp):
TCCCTTGCAAAAGCAAAGATTAGGTAATCGATGTCTCATTTACCCT
Found at i:3745164 original size:21 final size:22
Alignment explanation
Indices: 3745133--3745187 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3745123 TTTCCCCCCA
*
3745133 TTGCATGTGGCTATACAA-TTGT
1 TTGCA-GTGGCTATACAATTTAT
*
3745155 TTGCAGTGGCTATATAATTTAT
1 TTGCAGTGGCTATACAATTTAT
3745177 TTGCAGTGGCT
1 TTGCAGTGGCT
3745188 CCATCTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (22 bp):
TTGCAGTGGCTATACAATTTAT
Found at i:3747041 original size:23 final size:23
Alignment explanation
Indices: 3746972--3747044 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
3746962 GTATATTAAA
3746972 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
3746995 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
3747015 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
3747038 ATATAAT
1 ATATAAT
3747045 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Done.