Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 54 of 444
Found at i:13046483 original size:29 final size:29
Alignment explanation
Indices: 13046449--13046530 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
13046439 TAAATTTTAT
*
13046449 AATTAATATTATTGAATAATTATTGTATA
1 AATTAATATTATTAAATAATTATTGTATA
13046478 AATTAATATTATTAAATAATTATTGTATA
1 AATTAATATTATTAAATAATTATTGTATA
*
13046507 AATTAATATTATTAAATAAATATT
1 AATTAATATTATTAAATAATTATT
13046531 ATCCAATCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
AATTAATATTATTAAATAATTATTGTATA
Found at i:13046490 original size:18 final size:18
Alignment explanation
Indices: 13046467--13046519 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
13046457 TTATTGAATA
13046467 ATTATTGTATAAATTAAT
1 ATTATTGTATAAATTAAT
13046485 ATTA---T-TAAA-T-A-
1 ATTATTGTATAAATTAAT
13046496 ATTATTGTATAAATTAAT
1 ATTATTGTATAAATTAAT
13046514 ATTATT
1 ATTATT
13046520 AAATAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
11 4 0.14
12 1 0.04
13 1 0.04
14 5 0.18
15 5 0.18
16 1 0.04
17 1 0.04
18 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTATTGTATAAATTAAT
Found at i:13046501 original size:14 final size:13
Alignment explanation
Indices: 13046452--13046532 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 13
13046442 ATTTTATAAT
*
13046452 TAATATTATTGAA
1 TAATATTATTAAA
*
13046465 TAATTATTGTATAAA
1 TAA-TATTAT-TAAA
13046480 TTAATATTATTAAA
1 -TAATATTATTAAA
*
13046494 TAATTATTGTATAAA
1 TAA-TATTAT-TAAA
13046509 TTAATATTATTAAA
1 -TAATATTATTAAA
13046523 TAAATATTAT
1 T-AATATTAT
13046533 CCAATCATCC
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
13 7 0.12
14 26 0.46
15 17 0.30
16 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TAATATTATTAAA
Found at i:13052102 original size:2 final size:2
Alignment explanation
Indices: 13052095--13052149 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
13052085 AGTCAATAGA
13052095 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13052137 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
13052150 ATTGAAGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13053997 original size:10 final size:10
Alignment explanation
Indices: 13053982--13054007 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13053972 ATTTTCATAT
13053982 AAATATCAAG
1 AAATATCAAG
13053992 AAATATCAAG
1 AAATATCAAG
13054002 AAATAT
1 AAATAT
13054008 TTGTCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATATCAAG
Found at i:13056707 original size:18 final size:18
Alignment explanation
Indices: 13056684--13056733 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
13056674 GAGTTAAACG
*
13056684 AATCGAGTTATTTGAGTT
1 AATCGAATTATTTGAGTT
*
13056702 AATCGAATTATTTGAGTC
1 AATCGAATTATTTGAGTT
*
13056720 AACTCAAATTATTT
1 AA-TCGAATTATTT
13056734 TTCGAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (18 bp):
AATCGAATTATTTGAGTT
Found at i:13057032 original size:20 final size:20
Alignment explanation
Indices: 13056997--13057038 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13056987 CCCCCAACCT
*
13056997 CTAAACTTTTTATTTTCTCC
1 CTAAACTTTTTATTTTCACC
13057017 CTAAAC-TTTTATTTTTCACC
1 CTAAACTTTTTA-TTTTCACC
13057037 CT
1 CT
13057039 TTACCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.52
Consensus pattern (20 bp):
CTAAACTTTTTATTTTCACC
Found at i:13058293 original size:2 final size:2
Alignment explanation
Indices: 13058286--13058323 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13058276 CTAATTTCAC
13058286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13058324 TAAAATTAGA
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):
AT
Found at i:13058870 original size:56 final size:57
Alignment explanation
Indices: 13058808--13058919 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 57
13058798 ACAATCCAAA
* * *
13058808 TTAAGATTTTGCAAATGAATG-GTGATTCCAATTCACTGCACTTAAT-CACCAAATTG
1 TTAAGATTTTGCAAATGAATGAGTGATTACAATACAATGCACTT-ATCCACCAAATTG
13058864 TTAAGATTTTGCAAATGAATGTCAGTGATTACAATACAATGCACTTATCCACCAAA
1 TTAAGATTTTGCAAATGAATG--AGTGATTACAATACAATGCACTTATCCACCAAA
13058920 AGGACATGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
56 21 0.43
58 2 0.04
59 26 0.53
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (57 bp):
TTAAGATTTTGCAAATGAATGAGTGATTACAATACAATGCACTTATCCACCAAATTG
Found at i:13067118 original size:22 final size:21
Alignment explanation
Indices: 13067068--13067118 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
13067058 ATAATATTAC
* *
13067068 TTTTTTTCTTTCTTTTCTCTG
1 TTTTTTTGTCTCTTTTCTCTG
* *
13067089 CTTCTTTGTCTCTATTTCTCTG
1 TTTTTTTGTCTCT-TTTCTCTG
13067111 TTTTTTTG
1 TTTTTTTG
13067119 CAGGTGGTGG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.71
Consensus pattern (21 bp):
TTTTTTTGTCTCTTTTCTCTG
Found at i:13067645 original size:41 final size:40
Alignment explanation
Indices: 13067578--13067925 Score: 407
Period size: 41 Copynumber: 8.6 Consensus size: 40
13067568 TAATAAACAT
* *
13067578 TAGCGGCG--TTTGGCCGAAACGCCACTAAAAACTGAACAA
1 TAGCGGCGTTTTTGTCC-AAACGCCACTAAAAACTGATCAA
* * *
13067617 TAGCGGCGTTTTTTTCCAAAACGCCACTAAAAACAGGTCAA
1 TAGCGGCGTTTTTGTCC-AAACGCCACTAAAAACTGATCAA
* *
13067658 TAGCGGCGTTTTTGGCCAAACGCCACTAAAACCTGATCAA
1 TAGCGGCGTTTTTGTCCAAACGCCACTAAAAACTGATCAA
*
13067698 TAGCGGCGTTTTTATCCCAAACGCCACTAAAAACTGATCAA
1 TAGCGGCGTTTTTGT-CCAAACGCCACTAAAAACTGATCAA
* * *
13067739 TAGCGGCGTTTCTGGCCAAACGCCACTAAAAACCGATCAA
1 TAGCGGCGTTTTTGTCCAAACGCCACTAAAAACTGATCAA
* *** *
13067779 TAGCGGCGTTTTTTTGCCAGGTGCCACTAAAAACTGATTAA
1 TAGCGGCGTTTTTGT-CCAAACGCCACTAAAAACTGATCAA
* * *
13067820 TAGCGGCGTTTTTCTTCCAAACGCCACGAAAAACTTG-TGAA
1 TAGCGGCGTTTTT-GTCCAAACGCCACTAAAAAC-TGATCAA
* *
13067861 TAGCGGCGTTTTTAGT-CAAACGCCACAAAAAACTGATCAG
1 TAGCGGCGTTTTT-GTCCAAACGCCACTAAAAACTGATCAA
13067901 TAGCGGCGTTTTTGATCCAAACGCC
1 TAGCGGCGTTTTTG-TCCAAACGCC
13067926 GCAAAAAGTT
Statistics
Matches: 264, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
39 11 0.04
40 101 0.38
41 148 0.56
42 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (40 bp):
TAGCGGCGTTTTTGTCCAAACGCCACTAAAAACTGATCAA
Found at i:13067699 original size:81 final size:80
Alignment explanation
Indices: 13067578--13067925 Score: 409
Period size: 81 Copynumber: 4.3 Consensus size: 80
13067568 TAATAAACAT
* *
13067578 TAGCGGCG--TTTGGCCGAAACGCCACTAAAAACTGAACAATAGCGGCGTTTTTTTCCAAAACGC
1 TAGCGGCGTTTTTGGCC-AAACGCCACTAAAACCTGATCAATAGCGGCGTTTTTTTCC-AAACGC
* *
13067641 CACTAAAAACAGGTCAA
64 CACTAAAAACTGATCAA
*
13067658 TAGCGGCGTTTTTGGCCAAACGCCACTAAAACCTGATCAATAGCGGCGTTTTTATCCCAAACGCC
1 TAGCGGCGTTTTTGGCCAAACGCCACTAAAACCTGATCAATAGCGGCGTTTTT-TTCCAAACGCC
13067723 ACTAAAAACTGATCAA
65 ACTAAAAACTGATCAA
* ***
13067739 TAGCGGCGTTTCTGGCCAAACGCCACTAAAAACC-GATCAATAGCGGCGTTTTTTTGCCAGGTGC
1 TAGCGGCGTTTTTGGCCAAACGCCACT-AAAACCTGATCAATAGCGGCGTTTTTTT-CCAAACGC
*
13067803 CACTAAAAACTGATTAA
64 CACTAAAAACTGATCAA
** * * * *
13067820 TAGCGGCGTTTTTCTTCCAAACGCCACGAAAAACTTG-TGAATAGCGGCGTTTTTAGT-CAAACG
1 TAGCGGCGTTTTT-GGCCAAACGCCAC-TAAAACCTGATCAATAGCGGCGTTTTT-TTCCAAACG
* *
13067883 CCACAAAAAACTGATCAG
63 CCACTAAAAACTGATCAA
*
13067901 TAGCGGCGTTTTTGATCCAAACGCC
1 TAGCGGCGTTTTTG-GCCAAACGCC
13067926 GCAAAAAGTT
Statistics
Matches: 233, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
80 9 0.04
81 174 0.75
82 48 0.21
83 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (80 bp):
TAGCGGCGTTTTTGGCCAAACGCCACTAAAACCTGATCAATAGCGGCGTTTTTTTCCAAACGCCA
CTAAAAACTGATCAA
Found at i:13067758 original size:122 final size:121
Alignment explanation
Indices: 13067594--13067925 Score: 423
Period size: 122 Copynumber: 2.7 Consensus size: 121
13067584 CGTTTGGCCG
* ** *
13067594 AAACGCCACTAAAAACTGAACAATAGCGGCGTTTTTTTCCAAAACGCCACTAAAAACAGGTCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC-AAACGCCACTAAAAACAGATCAAT
*
13067659 AGCGGCGTTTTTGGCCAAACGCCACTAAAACCTGATCAATAGCGGCGTTTTTATCCC
65 AGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCCC
* * *
13067716 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTCTGGCCAAACGCCACTAAAAACCGATCAATA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCCAAACGCCACTAAAAACAGATCAATA
* *** * * *
13067781 GCGGCGTTTTTTTGCCAGGTGCCACTAAAAACTGATTAATAGCGGCGTTTTTCTTCC
66 GCGGCG-TTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCCC
* * * * * *
13067838 AAACGCCACGAAAAACTTG-TGAATAGCGGCGTTTTTAGTCAAACGCCACAAAAAACTGATCAGT
1 AAACGCCACTAAAAAC-TGATCAATAGCGGCGTTTTTAGCCAAACGCCACTAAAAACAGATCAAT
*
13067902 AGCGGCGTTTTTGATCCAAACGCC
65 AGCGGCGTTTTTG-GCCAAACGCC
13067926 GCAAAAAGTT
Statistics
Matches: 180, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
121 34 0.19
122 144 0.80
123 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (121 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCCAAACGCCACTAAAAACAGATCAATA
GCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCCC
Found at i:13068264 original size:29 final size:30
Alignment explanation
Indices: 13068218--13068274 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
13068208 TGGCTTTTTG
13068218 TAAACCCTTAAATCTTAAAA-ATTAAACCCC
1 TAAACCCTTAAATCTTAAAACA-TAAACCCC
*
13068248 TAAACCC-TAAATTTTAAAACATAAACC
1 TAAACCCTTAAATCTTAAAACATAAACC
13068275 ATAAACACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAACCCTTAAATCTTAAAACATAAACCCC
Found at i:13070258 original size:18 final size:19
Alignment explanation
Indices: 13070224--13070259 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13070214 CTTCTTTCTG
13070224 TAGAATTGCAAAGATGAAA
1 TAGAATTGCAAAGATGAAA
*
13070243 TAGAATTG-AGAGATGAA
1 TAGAATTGCAAAGATGAA
13070260 GAATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.22
Consensus pattern (19 bp):
TAGAATTGCAAAGATGAAA
Found at i:13072268 original size:22 final size:22
Alignment explanation
Indices: 13072240--13072287 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
13072230 TTTACGTTTG
* * *
13072240 CTGCATCGCCTTCGGTAGTCCT
1 CTGCATCGCCGTCGGCAGCCCT
*
13072262 CTGCATCGTCGTCGGCAGCCCT
1 CTGCATCGCCGTCGGCAGCCCT
13072284 CTGC
1 CTGC
13072288 TACATCTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.08, C:0.40, G:0.25, T:0.27
Consensus pattern (22 bp):
CTGCATCGCCGTCGGCAGCCCT
Found at i:13072345 original size:25 final size:25
Alignment explanation
Indices: 13072271--13072338 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
13072261 TCTGCATCGT
*
13072271 CGTCGGCAGCCCTCTGCTACATCTC
1 CGTCGGCATCCCTCTGCTACATCTC
* *
13072296 CATCGGCATCCCTCTTCTACATCTC
1 CGTCGGCATCCCTCTGCTACATCTC
13072321 CGTCGGCATCCCTCTGCT
1 CGTCGGCATCCCTCTGCT
13072339 GCTTCTCTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.12, C:0.44, G:0.16, T:0.28
Consensus pattern (25 bp):
CGTCGGCATCCCTCTGCTACATCTC
Found at i:13072703 original size:10 final size:10
Alignment explanation
Indices: 13072690--13072731 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
13072680 TTTAAATATT
13072690 TTTATCAATA
1 TTTATCAATA
13072700 TTTATCAATA
1 TTTATCAATA
*
13072710 -TAAT-AATA
1 TTTATCAATA
*
13072718 TTTATCATTA
1 TTTATCAATA
13072728 TTTA
1 TTTA
13072732 AATTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 4 0.15
9 6 0.22
10 17 0.63
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTATCAATA
Found at i:13072953 original size:40 final size:40
Alignment explanation
Indices: 13072907--13072988 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
13072897 ATTAATAATG
13072907 TTTGATTTTAATATTTAATATTTTTAAATGTTTTTAAGAC
1 TTTGATTTTAATATTTAATATTTTTAAATGTTTTTAAGAC
13072947 TTTGATTTTAATATTTAATATTTTTAAATGTTTTTAAGAC
1 TTTGATTTTAATATTTAATATTTTTAAATGTTTTTAAGAC
13072987 TT
1 TT
13072989 ATAAATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (40 bp):
TTTGATTTTAATATTTAATATTTTTAAATGTTTTTAAGAC
Found at i:13073300 original size:9 final size:9
Alignment explanation
Indices: 13073283--13073443 Score: 87
Period size: 9 Copynumber: 18.9 Consensus size: 9
13073273 ATCTAATTTT
*
13073283 ATAACTTAC
1 ATAATTTAC
13073292 ATAATTTAC
1 ATAATTTAC
*
13073301 ATAACTTAC
1 ATAATTTAC
13073310 ATAA--TAC
1 ATAATTTAC
* *
13073317 ATGAGTTAC
1 ATAATTTAC
*
13073326 ATAATTTAAAG
1 ATAATTT--AC
13073337 ATCAAATTT-C
1 AT--AATTTAC
* *
13073347 ATAACTTAT
1 ATAATTTAC
13073356 ATAA--TAC
1 ATAATTTAC
*
13073363 ATAACTTAC
1 ATAATTTAC
13073372 ATAATTT--
1 ATAATTTAC
*
13073379 A-AATAT-C
1 ATAATTTAC
13073386 A-AATTT-C
1 ATAATTTAC
*
13073393 ATAACTTAC
1 ATAATTTAC
13073402 ATAATTTAC
1 ATAATTTAC
*
13073411 ATAACTTAC
1 ATAATTTAC
13073420 ATAA--TAC
1 ATAATTTAC
*
13073427 ATAACTTAC
1 ATAATTTAC
13073436 ATAATTTA
1 ATAATTTA
13073444 AAGATCAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
6 4 0.03
7 27 0.22
8 8 0.07
9 72 0.60
10 2 0.02
11 3 0.02
13 5 0.04
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAATTTAC
Found at i:13073362 original size:46 final size:46
Alignment explanation
Indices: 13073294--13073558 Score: 242
Period size: 46 Copynumber: 5.3 Consensus size: 46
13073284 TAACTTACAT
13073294 AATTTACATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
1 AATTT-CATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
* * * *
13073341 AATTTCATAACTTATATAATACATAACTTACATAATTTAAATATCA
1 AATTTCATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
* * ** **
13073387 AATTTCATAACTTACATAATTTACATAACTTACATAATACATAACTTACA
1 AATTTCATAACTTACATAA--TACATGAGTTACATAATTTA-AAGAT-CA
* *
13073437 TAATTTAAAGATCAAATTTCATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
1 -AATTT---CAT--AA---C-TT----ACATAATACATGAGTTACATAATTTAAAGATCA
*
13073497 AATTTCAAAACTTACATAATACATGAGTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
13073543 AATTTCATAACTTACA
1 AATTTCATAACTTACA
13073559 GCTTTTACAT
Statistics
Matches: 179, Mismatches: 21, Indels: 37
0.76 0.09 0.16
Matches are distributed among these distances:
46 103 0.58
47 5 0.03
48 18 0.10
49 3 0.02
50 3 0.02
51 6 0.03
54 4 0.02
56 3 0.02
59 6 0.03
60 3 0.02
61 3 0.02
62 16 0.09
64 6 0.03
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (46 bp):
AATTTCATAACTTACATAATACATGAGTTACATAATTTAAAGATCA
Found at i:13073396 original size:30 final size:30
Alignment explanation
Indices: 13073362--13073470 Score: 139
Period size: 30 Copynumber: 3.5 Consensus size: 30
13073352 TTATATAATA
13073362 CATAACTTACATAATTTAAATATCAAATTT
1 CATAACTTACATAATTTAAATATCAAATTT
* *
13073392 CATAACTTACATAATTTACATAACTTACATAA-TA
1 CATAACTTACATAATTTAAAT-A--T-CA-AATTT
*
13073426 CATAACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAATATCAAATTT
13073456 CATAACTTACATAAT
1 CATAACTTACATAAT
13073471 ACATGAGTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
29 2 0.03
30 38 0.56
31 2 0.03
33 2 0.03
34 22 0.32
35 2 0.03
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.37
Consensus pattern (30 bp):
CATAACTTACATAATTTAAATATCAAATTT
Found at i:13073440 original size:110 final size:110
Alignment explanation
Indices: 13073242--13073532 Score: 460
Period size: 110 Copynumber: 2.7 Consensus size: 110
13073232 TTTTTAAATA
* * *
13073242 TTATTTAATACATAACTTACATAATTTAAAGATCTAATTTTATAACTTACATAATTTACATAACT
1 TTATATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
* *
13073307 TACATAATACATGAGTTACATAATTTAAAGATCAAATTTCATAAC
66 TACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAAC
*
13073352 TTATATAATACATAACTTACATAATTTAAATATCAAATTTCATAACTTACATAATTTACATAACT
1 TTATATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
13073417 TACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAAC
66 TACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAAC
* * * * * *
13073462 TTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATAA--TACATGAGT
1 TTATATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
13073525 TACATAAT
66 TACATAAT
13073533 TTAAAGATCA
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 15 0.09
110 153 0.91
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.37
Consensus pattern (110 bp):
TTATATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
TACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAAC
Found at i:13073528 original size:156 final size:157
Alignment explanation
Indices: 13073294--13073600 Score: 526
Period size: 156 Copynumber: 2.0 Consensus size: 157
13073284 TAACTTACAT
* *
13073294 AATTTACATAACTTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCATAACTTATATA
1 AATTTACATAACTTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATA
* *
13073359 ATACATAACTTACATAATTTAAATATCAAATTTCATAACTTACATAATTTACATAACTTACATAA
66 ATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAGAATTTACATAACTTACATAA
*
13073424 TACATAACTTACATAATTTAAAGATCA
131 TACATAACTTACATAACTTAAAGATCA
13073451 AATTT-CATAACTTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATA
1 AATTTACATAACTTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATA
* * **
13073515 ATACATGAGTTACATAATTTAAAGATCAAATTTCATAACTTACAGCTTTTACATAACTTACATAA
66 ATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAGAATTTACATAACTTACATAA
13073580 TACATAACTTACATAACTTAA
131 TACATAACTTACATAACTTAA
13073601 TTATACTTAT
Statistics
Matches: 141, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
156 136 0.96
157 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (157 bp):
AATTTACATAACTTACATAATACATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATA
ATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAGAATTTACATAACTTACATAA
TACATAACTTACATAACTTAAAGATCA
Found at i:13073575 original size:9 final size:9
Alignment explanation
Indices: 13073563--13073599 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
13073553 CTTACAGCTT
13073563 TTACATAAC
1 TTACATAAC
13073572 TTACATAA-
1 TTACATAAC
13073580 -TACATAAC
1 TTACATAAC
13073588 TTACATAAC
1 TTACATAAC
13073597 TTA
1 TTA
13073600 ATTATACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
9 19 0.73
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:13076797 original size:942 final size:942
Alignment explanation
Indices: 13074974--13076861 Score: 3535
Period size: 942 Copynumber: 2.0 Consensus size: 942
13074964 AGAACTTTAA
*
13074974 TTTACGTACAGCTTTGTTGTGGACAATTAATGATTTCCCGGCTTATGCTAATTTATCGAGTTGGA
1 TTTACGTACAGCTTTGTTGTGGACAATTAATGATTTCCCGGCTTATGCTAATTTATCGAGTTAGA
13075039 GTACTAAAGAACGTTATGCCTGTCCTTGTTGTGCTGCACAAACTTGTTCGAAGTGGTTGTATAAT
66 GTACTAAAGAACGTTATGCCTGTCCTTGTTGTGCTGCACAAACTTGTTCGAAGTGGTTGTATAAT
13075104 GGGAAGAAGTTCTCTTACATGGGCCATCTTCGGTGGTTAGATGGAAATCATAAATTTAGATTTCA
131 GGGAAGAAGTTCTCTTACATGGGCCATCTTCGGTGGTTAGATGGAAATCATAAATTTAGATTTCA
*
13075169 GAGGACTCTATTTGACAGTACTGAAGAGTACAGAGGAGCTCCTGAGCAAACCGTTGGATCTGAAA
196 GAGGACTCTATTTGACAGTACTGAAGAGTACAGAGGAGCTCCTGAGCAAACCGTTGGATCTAAAA
*
13075234 TCTTGTTTATGTTAAAAGATATCATCTTTAGTTACGGGAAGATGAATCAACCACCTAACACGCAA
261 TCTTGTTTATGTTAAAAGATATCACCTTTAGTTACGGGAAGATGAATCAACCACCTAACACGCAA
13075299 ACAAAGAGAAGATCGATGGATGAATCTGATGATGAATCTGACGAAGAGGATGATCCTAATGAGGC
326 ACAAAGAGAAGATCGATGGATGAATCTGATGATGAATCTGACGAAGAGGATGATCCTAATGAGGC
13075364 AGAATTGTGGAAAAAAAGAGTATTTTTTTTGAGTTGCCTTATTGGAAGCACAACATTTTACGCCA
391 AGAATTGTGGAAAAAAAGAGTATTTTTTTTGAGTTGCCTTATTGGAAGCACAACATTTTACGCCA
*
13075429 CAATCTTGATGCCATGCATATTGAGAAGAATGTCTGCGAGAACATAATTGGGACAATTTTGAATG
456 CAATCTTGATGCCATGCATATTGAGAAGAATGTCTACGAGAACATAATTGGGACAATTTTGAATG
*
13075494 TCGATGGAAAATCAAAAGACAATCTTCAAAGTTGACTTGATTTAGTTAACATGAGAATTCGGCGT
521 TCGATGGAAAATCAAAAGACAATCTTCAAAGTCGACTTGATTTAGTTAACATGAGAATTCGGCGT
13075559 GATCTTCATCCTCAAGTACTTCCTAATGGGAAATATCGGTTGCCACCTTCTATTTTTTTCAATGT
586 GATCTTCATCCTCAAGTACTTCCTAATGGGAAATATCGGTTGCCACCTTCTATTTTTTTCAATGT
13075624 CAAAGAAAGAGAAAGAGGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAAATGCGTATACG
651 CAAAGAAAGAGAAAGAGGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAAATGCGTATACG
13075689 TCAAATATATCTCCATGTGTAAGTCTTAAAGATCGAAGATTATATTCATTGAAATTACATGATTA
716 TCAAATATATCTCCATGTGTAAGTCTTAAAGATCGAAGATTATATTCATTGAAATTACATGATTA
* *
13075754 CCACATCTTGATGCAAGATTTACTCTCAGTTGCTTTACGGTGCTGCATGTCAAAAAATGTGACAT
781 CCACATCTTGATGCAAGATTTACTCCCAGTTGCTATACGGTGCTGCATGTCAAAAAATGTGACAT
*
13075819 CTTGTATAATTGAACTATCCAATATAATGAAAGCTATTTGTGGCAAAGTTTTGGATGTTGAAGAA
846 CTTGTATAATTGAACTATCCAATATAATGAAAGCTATTTGTGGCAAAGTTTTAGATGTTGAAGAA
* * *
13075884 CTTAAGAAAGTACATGATCGAGCTGTTTTGAT
911 CATAAGAAAGTACATGATCGAGCTGCTTTGAC
* *
13075916 TTTACGTGCAGCTTTGTTGTGGACAATTAATGATTTCCCGGCTTATGCTAATTTATCGGGTTAGA
1 TTTACGTACAGCTTTGTTGTGGACAATTAATGATTTCCCGGCTTATGCTAATTTATCGAGTTAGA
* *
13075981 GTACTAAAGGACGTTATGCCTGTCCTTGTTGTGCTGCGCAAACTTGTTCGAAGTGGTTGTATAAT
66 GTACTAAAGAACGTTATGCCTGTCCTTGTTGTGCTGCACAAACTTGTTCGAAGTGGTTGTATAAT
13076046 GGGAAGAAGTTCTCTTACATGGGCCATCTTCGGTGGTTAGATGGAAATCATAAATTTAGATTTCA
131 GGGAAGAAGTTCTCTTACATGGGCCATCTTCGGTGGTTAGATGGAAATCATAAATTTAGATTTCA
13076111 GAGGACTCTATTTGACAGTACTGAAGAGTACAGAGGAGCTCCTGAGCAAACCGTTGGATCTAAAA
196 GAGGACTCTATTTGACAGTACTGAAGAGTACAGAGGAGCTCCTGAGCAAACCGTTGGATCTAAAA
*
13076176 TCTTGTTTATGTTAAAAGATATCACCTTTAGTTATGGGAAGATGAATCAACCACCTAACACGCAA
261 TCTTGTTTATGTTAAAAGATATCACCTTTAGTTACGGGAAGATGAATCAACCACCTAACACGCAA
13076241 ACAAAGAGAAGATCGATGGATGAATCTGATGATGAATCTGACGAAGAGGATGATCCTAATGAGGC
326 ACAAAGAGAAGATCGATGGATGAATCTGATGATGAATCTGACGAAGAGGATGATCCTAATGAGGC
* * *
13076306 GGAATTGTGGAAAAAAAAGGGTATTTTTTTTTAGTTGCCTTATTGGAAGCACAACATTTTACGCC
391 AGAATTGTGG-AAAAAAAGAGTATTTTTTTTGAGTTGCCTTATTGGAAGCACAACATTTTACGCC
13076371 ACAATCTTGATGCCATGCATATTGAGAAGAATGTCTACGAGAACATAATTGGGACAATTTTGAAT
455 ACAATCTTGATGCCATGCATATTGAGAAGAATGTCTACGAGAACATAATTGGGACAATTTTGAAT
*
13076436 GTCGATGGAAAATCAAAAGACAATCTTCAAAGTCGACTTGATTTAGTTGACATGAGAATTCGGCG
520 GTCGATGGAAAATCAAAAGACAATCTTCAAAGTCGACTTGATTTAGTTAACATGAGAATTCGGCG
13076501 TGATCTTCATCCTCAAGTACTTCCTAATGGGAAATATCGGTTGCCACCTTCTA-TTTTTTCAATG
585 TGATCTTCATCCTCAAGTACTTCCTAATGGGAAATATCGGTTGCCACCTTCTATTTTTTTCAATG
*
13076565 TCAAAGAAAGAGAAAGAGGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCGTATAC
650 TCAAAGAAAGAGAAAGAGGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAAATGCGTATAC
* * *
13076630 GTCGAATATATCTCGATGTGTAAGTCTTAAAGATCGAAGATTATATTTATTGAAATTACATGATT
715 GTCAAATATATCTCCATGTGTAAGTCTTAAAGATCGAAGATTATATTCATTGAAATTACATGATT
*
13076695 ACCACATCTTGATGCAAGATTTACTCCCAGTTGCTATACGGTGCTGCATGTCAAAAAATGTGACG
780 ACCACATCTTGATGCAAGATTTACTCCCAGTTGCTATACGGTGCTGCATGTCAAAAAATGTGACA
13076760 TCTTGTATAATTGAACTATCCAATATAATGAAAGCTATTTGTGGCAAAGTTTTAGATGTTGAAGA
845 TCTTGTATAATTGAACTATCCAATATAATGAAAGCTATTTGTGGCAAAGTTTTAGATGTTGAAGA
13076825 ACATAAGAAAGTACATGATCGAGCTGCTTTGAC
910 ACATAAGAAAGTACATGATCGAGCTGCTTTGAC
13076858 TTTA
1 TTTA
13076862 TGCAATTTGG
Statistics
Matches: 920, Mismatches: 25, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
942 688 0.75
943 232 0.25
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (942 bp):
TTTACGTACAGCTTTGTTGTGGACAATTAATGATTTCCCGGCTTATGCTAATTTATCGAGTTAGA
GTACTAAAGAACGTTATGCCTGTCCTTGTTGTGCTGCACAAACTTGTTCGAAGTGGTTGTATAAT
GGGAAGAAGTTCTCTTACATGGGCCATCTTCGGTGGTTAGATGGAAATCATAAATTTAGATTTCA
GAGGACTCTATTTGACAGTACTGAAGAGTACAGAGGAGCTCCTGAGCAAACCGTTGGATCTAAAA
TCTTGTTTATGTTAAAAGATATCACCTTTAGTTACGGGAAGATGAATCAACCACCTAACACGCAA
ACAAAGAGAAGATCGATGGATGAATCTGATGATGAATCTGACGAAGAGGATGATCCTAATGAGGC
AGAATTGTGGAAAAAAAGAGTATTTTTTTTGAGTTGCCTTATTGGAAGCACAACATTTTACGCCA
CAATCTTGATGCCATGCATATTGAGAAGAATGTCTACGAGAACATAATTGGGACAATTTTGAATG
TCGATGGAAAATCAAAAGACAATCTTCAAAGTCGACTTGATTTAGTTAACATGAGAATTCGGCGT
GATCTTCATCCTCAAGTACTTCCTAATGGGAAATATCGGTTGCCACCTTCTATTTTTTTCAATGT
CAAAGAAAGAGAAAGAGGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAAATGCGTATACG
TCAAATATATCTCCATGTGTAAGTCTTAAAGATCGAAGATTATATTCATTGAAATTACATGATTA
CCACATCTTGATGCAAGATTTACTCCCAGTTGCTATACGGTGCTGCATGTCAAAAAATGTGACAT
CTTGTATAATTGAACTATCCAATATAATGAAAGCTATTTGTGGCAAAGTTTTAGATGTTGAAGAA
CATAAGAAAGTACATGATCGAGCTGCTTTGAC
Found at i:13080348 original size:33 final size:33
Alignment explanation
Indices: 13080298--13080379 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
13080288 TTAGAATTAA
*
13080298 TGTTTTTGGTTGTATTTTTTATACTAAATTTGC
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
* * *
13080331 TGTTTTTGGCTGCA--TTTTATACTATATTTGT
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
* *
13080362 TGTATTTGGTTGGATTTT
1 TGTTTTTGGTTGCATTTT
13080380 AAGGCAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.16, C:0.06, G:0.18, T:0.60
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
Found at i:13082478 original size:24 final size:23
Alignment explanation
Indices: 13082450--13082502 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
13082440 TACATATATG
*
13082450 ATATAGTATTTTTACAATATTAAA
1 ATATAGTATTTTAACAATA-TAAA
* * *
13082474 ATATAATATTTTAATAATATACA
1 ATATAGTATTTTAACAATATAAA
13082497 ATATAG
1 ATATAG
13082503 AATATTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
ATATAGTATTTTAACAATATAAA
Found at i:13082761 original size:2 final size:2
Alignment explanation
Indices: 13082754--13082802 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
13082744 TTGCAATGTG
13082754 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
*
13082796 AA TA TA T
1 TA TA TA T
13082803 TCAAATGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13087184 original size:23 final size:23
Alignment explanation
Indices: 13087158--13087204 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
13087148 CAAATATAAT
*
13087158 AGAATAGTAAGA-ACAAAGATGGG
1 AGAATAATAAGACAC-AAGATGGG
13087181 AGAATAATAAGACACAAGATGGG
1 AGAATAATAAGACACAAGATGGG
13087204 A
1 A
13087205 AACTTGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.13
Consensus pattern (23 bp):
AGAATAATAAGACACAAGATGGG
Found at i:13095575 original size:26 final size:26
Alignment explanation
Indices: 13095536--13095589 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
13095526 GTTGTGAGAG
*
13095536 TTGAAAAGATATCCACTTATAAAATA
1 TTGAAAAGACATCCACTTATAAAATA
*
13095562 TTGAAAGGACATCCACTTATAAAATA
1 TTGAAAAGACATCCACTTATAAAATA
13095588 TT
1 TT
13095590 TACAACACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (26 bp):
TTGAAAAGACATCCACTTATAAAATA
Found at i:13096741 original size:63 final size:63
Alignment explanation
Indices: 13096627--13096752 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 63
13096617 GCCAGGGACA
* * *
13096627 TAACTCACTGTTTGAGGTGTAAAAACCACACGGCCAGGGACATGAATGTGTGCCCAGGCCGTG
1 TAACTCACTGTTTGAGGTGTAAAAACCACACGGCCAGGCACATGAACGTGTGCCAAGGCCGTG
* ** *
13096690 TAACTCACTGTTTG-GGCT-TAAAAACCACACGGCCAATGCACATGGGCGTGTGCCAAGGTCGTG
1 TAACTCACTGTTTGAGG-TGTAAAAACCACACGGCC-AGGCACATGAACGTGTGCCAAGGCCGTG
13096753 CGGCAGGATG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 18 0.33
63 36 0.67
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (63 bp):
TAACTCACTGTTTGAGGTGTAAAAACCACACGGCCAGGCACATGAACGTGTGCCAAGGCCGTG
Found at i:13097736 original size:26 final size:26
Alignment explanation
Indices: 13097706--13097767 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
13097696 TCTCATCCAT
*
13097706 ATTTTACCCCCAATAAAATTTTGACG
1 ATTTTACCCCCAATAAAATTTTGACA
* * **
13097732 ATTTTACGCCCGATAATTTTTTGACA
1 ATTTTACCCCCAATAAAATTTTGACA
13097758 ATTTTACCCC
1 ATTTTACCCC
13097768 TGGTAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCAATAAAATTTTGACA
Found at i:13099928 original size:3 final size:3
Alignment explanation
Indices: 13099920--13100019 Score: 71
Period size: 3 Copynumber: 33.0 Consensus size: 3
13099910 GTGATAATAC
* * * * *
13099920 AAT AAT AAT AA- AGT AGAA AAT AAC AAT AAT ACT ACATT AAT AAG AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
* *
13099967 AAT AAT AAT -AT AAT AAT AAT AAT AAGA AAT AAT AAT -AT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
*
13100011 AAG AAT AAT
1 AAT AAT AAT
13100020 TACAGCAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
2 5 0.07
3 63 0.85
4 4 0.05
5 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13099929 original size:11 final size:11
Alignment explanation
Indices: 13099913--13099987 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
13099903 AATGATAGTG
13099913 ATAATACAATA
1 ATAATACAATA
13099924 ATAATA-AAGTA
1 ATAATACAA-TA
*
13099935 GAAAATAACAATA
1 -ATAAT-ACAATA
* *
13099948 ATACTACATTA
1 ATAATACAATA
* *
13099959 ATAAGAATAATA
1 ATAA-TACAATA
*
13099971 ATAATATAATA
1 ATAATACAATA
13099982 ATAATA
1 ATAATA
13099988 ATAAGAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
10 2 0.04
11 28 0.56
12 15 0.30
13 3 0.06
14 2 0.04
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (11 bp):
ATAATACAATA
Found at i:13099967 original size:20 final size:20
Alignment explanation
Indices: 13099938--13100001 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
13099928 TAAAGTAGAA
*
13099938 AATAACAATAATACTACAT-T
1 AATAACAATAATAATA-ATAT
*
13099958 AATAAGAATAATAATAATAT
1 AATAACAATAATAATAATAT
* *
13099978 AATAATAATAATAAGAA-AT
1 AATAACAATAATAATAATAT
13099997 AATAA
1 AATAA
13100002 TATATTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AATAACAATAATAATAATAT
Found at i:13100005 original size:27 final size:29
Alignment explanation
Indices: 13099957--13100019 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
13099947 AATACTACAT
13099957 TAATAAGAATAATAATAATATAATAATAA
1 TAATAAGAATAATAATAATATAATAATAA
*
13099986 TAATAAGAAATAATAAT-ATATTAATAAGAA
1 TAATAAG-AATAATAATAATA-TAATAATAA
13100016 TAAT
1 TAAT
13100020 TACAGCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (29 bp):
TAATAAGAATAATAATAATATAATAATAA
Found at i:13100252 original size:3 final size:3
Alignment explanation
Indices: 13100246--13100307 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
13100236 TAATGAAAAA
* * ** *
13100246 AAT AAT ATT AAT AAT GAT GCT AAT AAT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
13100294 ATT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT
13100308 TTAAAGAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:13101975 original size:30 final size:30
Alignment explanation
Indices: 13101940--13102000 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
13101930 TTTTTTGCAT
13101940 GCAAAAACCATTTGAGGACAATAATACAAA
1 GCAAAAACCATTTGAGGACAATAATACAAA
13101970 GCAAAAACCATTTGAGGACAATAATACAAA
1 GCAAAAACCATTTGAGGACAATAATACAAA
13102000 G
1 G
13102001 TATTAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.16
Consensus pattern (30 bp):
GCAAAAACCATTTGAGGACAATAATACAAA
Found at i:13109985 original size:15 final size:14
Alignment explanation
Indices: 13109965--13110012 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
13109955 GAATAGGTAC
13109965 ATAATAGGATAATA
1 ATAATAGGATAATA
*
13109979 TATAATAAGATAATA
1 -ATAATAGGATAATA
*
13109994 ATAATGAGGACAATA
1 ATAAT-AGGATAATA
13110009 ATAA
1 ATAA
13110013 AATAAAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.27
Consensus pattern (14 bp):
ATAATAGGATAATA
Found at i:13110155 original size:3 final size:3
Alignment explanation
Indices: 13110142--13110318 Score: 119
Period size: 3 Copynumber: 59.7 Consensus size: 3
13110132 ATTTAAAAAA
* * * * *
13110142 AAT AAT GAT AAT AAA AAT AAT AGT AAT AAT AAT ACT AAT AAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
13110189 AAT AAT GAC AGT AGT GAT AA- AAT AAT AAT AAT AAT AAT AAC AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * *
13110236 AAT AAA AAT AGT AGT AAC AGT AAT AAC AGA- CAT AAT AAT ACT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
13110281 AAT AAT AAT AA- ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
13110319 ATATAAAACT
Statistics
Matches: 131, Mismatches: 37, Indels: 12
0.73 0.21 0.07
Matches are distributed among these distances:
2 5 0.04
3 124 0.95
4 2 0.02
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13110324 original size:12 final size:12
Alignment explanation
Indices: 13110270--13110324 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
13110260 AACAGACATA
* *
13110270 ATAATACTAAAA
1 ATAATAATAAAT
13110282 ATAATAATAAAT
1 ATAATAATAAAT
13110294 ATAATAATAATAAT
1 ATAATAAT-A-AAT
13110308 AATAATAATAAAT
1 -ATAATAATAAAT
13110321 ATAA
1 ATAA
13110325 AACTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 22 0.58
13 4 0.11
14 4 0.11
15 8 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:13111632 original size:45 final size:46
Alignment explanation
Indices: 13111581--13111958 Score: 248
Period size: 45 Copynumber: 8.5 Consensus size: 46
13111571 AACATGCTCT
* * *
13111581 CTGCAACTTTAGAGAGATAAGGTTTGCCAT-TTTCGATCTGCTCCG
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* * * * * *
13111626 CTGCAACTTTA-AGGAAATAAGATCTACTATCTTTAG-TCTGCTCCA
1 CTGCAACTTCAGA-GAGATAAGATTTGCTATCTTTCGATCTGCTCCG
** ** * * * *
13111671 CTGCAACTTCAGAGAGATGTGACATG-TAAC-TTCAACCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* *
13111714 CAGTAACTTCAGAGAGATAAGATTTGCTATCTTT-GATCTGCTCCG
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* * * ** * * * * * *
13111759 CTACAACTTTAGGGAGATGGGATCT-ATAAC-TTCAACCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* * *
13111802 CTGCAACTTCAAAGAGATAAGGTTTGCTATCTTT-GATCTACTCCG
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* * * * *
13111847 CTGCAACTTCAGGGAGATGAGATCTGCTAT-TTTCAATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
* *
13111892 CTGCAACTTCA-AGGAGATAAGACTCGCTATC-TTC-AGTCTGCTCCG
1 CTGCAACTTCAGA-GAGATAAGATTTGCTATCTTTCGA-TCTGCTCCG
13111937 CTGCAACTTCA-AGGAGATAAGA
1 CTGCAACTTCAGA-GAGATAAGA
13111959 CTGGTGACTT
Statistics
Matches: 248, Mismatches: 70, Indels: 30
0.71 0.20 0.09
Matches are distributed among these distances:
43 43 0.17
44 39 0.16
45 161 0.65
46 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (46 bp):
CTGCAACTTCAGAGAGATAAGATTTGCTATCTTTCGATCTGCTCCG
Found at i:13111736 original size:88 final size:87
Alignment explanation
Indices: 13111628--13111954 Score: 331
Period size: 88 Copynumber: 3.7 Consensus size: 87
13111618 CTGCTCCGCT
* * * * * *
13111628 GCAACTTTAAGGAAATAAGATCTACTATCTTT-AGTCTGCTCCACTGCAACTTCAGAGAGATGTG
1 GCAACTTCAA-GAGATAAGATCTGCTATCTTTGA-TCTGCTCCGCTGCAACTTCAGGGAGATGAG
13111692 A-CATGTAACTTCAACCTGCTCTCA
64 ATC-TGTAACTTCAACCTGCTCTCA
* * * * *
13111716 GTAACTTCAGAGAGATAAGATTTGCTATCTTTGATCTGCTCCGCTACAACTTTAGGGAGATGGGA
1 GCAACTTCA-AGAGATAAGATCTGCTATCTTTGATCTGCTCCGCTGCAACTTCAGGGAGATGAGA
* *
13111781 TCTATAACTTCAACCTGCTCTCT
65 TCTGTAACTTCAACCTGCTCTCA
* * *
13111804 GCAACTTCAAAGAGATAAGGTTTGCTATCTTTGATCTACTCCGCTGCAACTTCAGGGAGATGAGA
1 GCAACTTC-AAGAGATAAGATCTGCTATCTTTGATCTGCTCCGCTGCAACTTCAGGGAGATGAGA
** *
13111869 TCTGCTATTTTCAATCTGCTC-CA
65 TCTG-TAACTTCAACCTGCTCTCA
* *
13111892 CTGCAACTTCAAGGAGATAAGA-CTCGCTATC-TTCAGTCTGCTCCGCTGCAACTTCAAGGAGAT
1 --GCAACTTCAA-GAGATAAGATCT-GCTATCTTTGA-TCTGCTCCGCTGCAACTTCAGGGAGAT
13111955 AAGACTGGTG
Statistics
Matches: 201, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
88 131 0.65
89 23 0.11
90 47 0.23
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (87 bp):
GCAACTTCAAGAGATAAGATCTGCTATCTTTGATCTGCTCCGCTGCAACTTCAGGGAGATGAGAT
CTGTAACTTCAACCTGCTCTCA
Found at i:13111818 original size:133 final size:133
Alignment explanation
Indices: 13111562--13111819 Score: 333
Period size: 133 Copynumber: 2.0 Consensus size: 133
13111552 AGATAGGACT
* * *
13111562 TGTAACTTCAACATGCTCTCTGCAACTTTAGAGAGATAAGGTTTGCCATTTTCGATCTGCTCCGC
1 TGTAACTTCAACATGCTCTCAGCAACTTCAGAGAGATAAGATTTGCCATTTTCGATCTGCTCCGC
* * * **
13111627 TGCAACTTTAAGGAAATAAGATCTACTATCTTTAGTCTGCTCCACTGCAACTTCAGAGAGATGTG
66 TACAACTTTAAGGAAATAAGATCTACTAACTTCAACCTGCTCCACTGCAACTTCAGAGAGATGTG
13111692 ACA
131 ACA
* * *
13111695 TGTAACTTCAACCTGCTCTCAGTAACTTCAGAGAGATAAGATTTGCTATCTTT-GATCTGCTCCG
1 TGTAACTTCAACATGCTCTCAGCAACTTCAGAGAGATAAGATTTGCCAT-TTTCGATCTGCTCCG
* * ** * *
13111759 CTACAACTTTAGGGAGATGGGATCTA-TAACTTCAACCTGCT-CTCTGCAACTTCAAAGAGAT
65 CTACAACTTTAAGGAAATAAGATCTACTAACTTCAACCTGCTCCACTGCAACTTCAGAGAGAT
13111820 AAGGTTTGCT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 18 0.17
132 11 0.10
133 75 0.70
134 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (133 bp):
TGTAACTTCAACATGCTCTCAGCAACTTCAGAGAGATAAGATTTGCCATTTTCGATCTGCTCCGC
TACAACTTTAAGGAAATAAGATCTACTAACTTCAACCTGCTCCACTGCAACTTCAGAGAGATGTG
ACA
Found at i:13112014 original size:89 final size:90
Alignment explanation
Indices: 13111830--13112050 Score: 232
Period size: 89 Copynumber: 2.5 Consensus size: 90
13111820 AAGGTTTGCT
* * * * *
13111830 ATCTTTGATCTACTCCGCTGCAACTTCAGGGAGATGAGATCTGCTATTTTCAATCTGCTCCACTG
1 ATCTTCGATCTACTCCGCTGCAACTTCAAGGAGATAAGATCTGCTATCTTAAATCTGCTCCACTG
* * *
13111895 CAACTTCAAGGAGATAAGACTCGCT
66 CAACTACAAGGAGATAAGACTCACC
* * *
13111920 ATCTTC-AGTCTGCTCCGCTGCAACTTCAAGGAGATAAGA-CTGGTGA-CTTAAATCTGCTCCAT
1 ATCTTCGA-TCTACTCCGCTGCAACTTCAAGGAGATAAGATCTGCT-ATCTTAAATCTGCTCCAC
** * *
13111982 TGCCGCTACATGGAGATAAGATTCACC
64 TGCAACTACAAGGAGATAAGACTCACC
* ** *
13112009 GTCTTCGATCTACTCTACTGCTACTTCAAGGAGATAAGATCT
1 ATCTTCGATCTACTCCGCTGCAACTTCAAGGAGATAAGATCT
13112051 ACAATCTTTA
Statistics
Matches: 107, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
89 70 0.65
90 37 0.35
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (90 bp):
ATCTTCGATCTACTCCGCTGCAACTTCAAGGAGATAAGATCTGCTATCTTAAATCTGCTCCACTG
CAACTACAAGGAGATAAGACTCACC
Found at i:13116588 original size:21 final size:23
Alignment explanation
Indices: 13116558--13116604 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
13116548 AAATGAAATG
*
13116558 CAGGAATAAAAG-AATATTTGCT
1 CAGGAATAAAAGAAATATATGCT
13116580 CAGG-ATAAAAGAAATATATGCT
1 CAGGAATAAAAGAAATATATGCT
13116602 CAG
1 CAG
13116605 AATGAGACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (23 bp):
CAGGAATAAAAGAAATATATGCT
Found at i:13123620 original size:15 final size:14
Alignment explanation
Indices: 13123600--13123638 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
13123590 GAATAGGTAC
13123600 ATAATAGGATAATA
1 ATAATAGGATAATA
*
13123614 TATAATAAGATAATA
1 -ATAATAGGATAATA
13123629 ATAATGAGGA
1 ATAAT-AGGA
13123639 CAAGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (14 bp):
ATAATAGGATAATA
Found at i:13123791 original size:3 final size:3
Alignment explanation
Indices: 13123778--13123913 Score: 125
Period size: 3 Copynumber: 45.7 Consensus size: 3
13123768 TTTTAAAAAA
* * * * *
13123778 AAT AAT GAT AAT AAA AAT ATT AGT AAT AAT AAT ACT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
13123826 GAC AGT AGT GAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
13123873 AAT AAT AAT ACT AAA AAT AAT AAT AA- ATAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
13123914 ATATAAAACT
Statistics
Matches: 107, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
2 4 0.04
3 101 0.94
4 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:13127746 original size:20 final size:20
Alignment explanation
Indices: 13127721--13127759 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13127711 GCCTGGTCCC
13127721 ATGGCCATGTCCCAAGCCAT
1 ATGGCCATGTCCCAAGCCAT
*
13127741 ATGGCCATGTCCCAGGCCA
1 ATGGCCATGTCCCAAGCCA
13127760 CACGGGCGTG
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:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (20 bp):
ATGGCCATGTCCCAAGCCAT
Found at i:13128078 original size:18 final size:19
Alignment explanation
Indices: 13128038--13128084 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
13128028 ATAGATATAC
13128038 AATTAAAATGTGCATAATAA
1 AATTAAAATGT-CATAATAA
13128058 AATTAAAATGT-ATAA-ATA
1 AATTAAAATGTCATAATA-A
13128076 AATTAAAAT
1 AATTAAAAT
13128085 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
20 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (19 bp):
AATTAAAATGTCATAATAA
Found at i:13139151 original size:6 final size:5
Alignment explanation
Indices: 13139116--13139150 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
13139106 GAAGGAAAAG
13139116 AAATA AAATA AAATA AAATAA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAAT-A AAAT-A AAATA AAA
13139151 AGGACAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:13139681 original size:17 final size:17
Alignment explanation
Indices: 13139661--13139693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13139651 TTAAAAATTG
13139661 TAAA-AATATAAATTATT
1 TAAACAATA-AAATTATT
13139678 TAAACAATAAAATTAT
1 TAAACAATAAAATTAT
13139694 ACTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAACAATAAAATTATT
Found at i:13139747 original size:5 final size:5
Alignment explanation
Indices: 13139737--13139765 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13139727 CGATTCAATA
13139737 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
13139766 GGGTTCGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:13140144 original size:16 final size:17
Alignment explanation
Indices: 13140118--13140149 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13140108 TTTTTTGCCA
13140118 TCAACATTTATTTTTTT
1 TCAACATTTATTTTTTT
13140135 TCAA-ATTTATTTTTT
1 TCAACATTTATTTTTT
13140150 AATAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TCAACATTTATTTTTTT
Found at i:13152466 original size:39 final size:37
Alignment explanation
Indices: 13152422--13152530 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 37
13152412 ATAAAGTATG
*
13152422 GTTTTAATTAATAATAAAACAAAATGGTATGAGAAAGT
1 GTTTTAATTAATAATAAAACAAAATAGTATG-GAAAGT
* **
13152460 AGTTTTAATTAACAATAAAACAAAATAGTATGGGGAGT
1 -GTTTTAATTAATAATAAAACAAAATAGTATGGAAAGT
* * *
13152498 GCTTTTGATTAATAATAAAACAAAGTAGCATGG
1 G-TTTTAATTAATAATAAAACAAAATAGTATGG
13152531 GGGAGTGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
37 1 0.02
38 31 0.51
39 29 0.48
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (37 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGAAAGT
Found at i:13152518 original size:38 final size:37
Alignment explanation
Indices: 13152422--13152537 Score: 133
Period size: 39 Copynumber: 3.0 Consensus size: 37
13152412 ATAAAGTATG
* **
13152422 GTTTTAATTAATAATAAAACAAAATGGTATGAGAAAGT
1 GTTTTAATTAATAATAAAACAAAATAGTATG-GGGAGT
*
13152460 AGTTTTAATTAACAATAAAACAAAATAGTATGGGGAGT
1 -GTTTTAATTAATAATAAAACAAAATAGTATGGGGAGT
* * *
13152498 GCTTTTGATTAATAATAAAACAAAGTAGCATGGGGGAGT
1 G-TTTTAATTAATAATAAAACAAAATAGTAT-GGGGAGT
13152537 G
1 G
13152538 AAATCAGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
38 29 0.43
39 37 0.55
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (37 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGGGAGT
Found at i:13153073 original size:24 final size:26
Alignment explanation
Indices: 13153046--13153094 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
13153036 TGTATATACC
*
13153046 ATGTAAATATTTTA-ATAT-TATATT
1 ATGTAAACATTTTATATATATATATT
*
13153070 ATGTATACATTTTATATATATATAT
1 ATGTAAACATTTTATATATATATAT
13153095 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 4 0.19
26 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATGTAAACATTTTATATATATATATT
Found at i:13153089 original size:2 final size:2
Alignment explanation
Indices: 13153082--13153108 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13153072 GTATACATTT
13153082 TA 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 TA T
13153109 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13155667 original size:58 final size:55
Alignment explanation
Indices: 13155543--13155667 Score: 153
Period size: 58 Copynumber: 2.2 Consensus size: 55
13155533 TTATTAAATA
*
13155543 TTATTAAGAATGATATTAAATTATATATATTTTATTAAATTGTATTTAATAATAAT
1 TTATTAA-AATGATATTAAATTATATATATTTTATTAAATTATATTTAATAATAAT
** *
13155599 TATAGGAAAAT-ATGATTAAATTATTTATTATTTTTATTAAATTATATTTAATAATAAT
1 T-TATTAAAATGAT-ATTAAATTATATA-TA-TTTTATTAAATTATATTTAATAATAAT
13155657 CTTATTAAAAT
1 -TTATTAAAAT
13155668 TTAATAACAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
55 2 0.03
56 16 0.28
57 6 0.10
58 33 0.57
59 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (55 bp):
TTATTAAAATGATATTAAATTATATATATTTTATTAAATTATATTTAATAATAAT
Found at i:13157093 original size:21 final size:21
Alignment explanation
Indices: 13157067--13157106 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13157057 ATTCTCCCTA
13157067 TATATTTATTA-ATTATTAATC
1 TATA-TTATTATATTATTAATC
*
13157088 TATATTATTATTTTATTAA
1 TATATTATTATATTATTAA
13157107 ATTGGTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATTATATTATTAATC
Found at i:13159184 original size:8 final size:8
Alignment explanation
Indices: 13159173--13159348 Score: 82
Period size: 8 Copynumber: 21.6 Consensus size: 8
13159163 AACAATAACG
*
13159173 TAATATTA
1 TAATATAA
*
13159181 TAATGTAA
1 TAATATAA
13159189 TAATATAA
1 TAATATAA
13159197 -AAT-TAA
1 TAATATAA
13159203 TTAGAT-TAA
1 -TA-ATATAA
* **
13159212 TGATATGG
1 TAATATAA
13159220 TAA--TAA
1 TAATATAA
*
13159226 TAATAGTGA
1 TAATA-TAA
*
13159235 TAATACAA
1 TAATATAA
13159243 TAATAATAA
1 TAAT-ATAA
13159252 TAA-AGTAGA
1 TAATA-TA-A
13159261 -AA-ATAA
1 TAATATAA
*
13159267 CAATAATAA
1 TAAT-ATAA
13159276 TACAT-TAA
1 TA-ATATAA
13159284 TAATAATAA
1 TAAT-ATAA
13159293 TAATAATAA
1 TAAT-ATAA
13159302 TAATAATAA
1 TAAT-ATAA
13159311 TAATATAA
1 TAATATAA
*
13159319 TAATAGAA
1 TAATATAA
*
13159327 AAATAATAA
1 TAAT-ATAA
*
13159336 TAATATAT
1 TAATATAA
13159344 TAATA
1 TAATA
13159349 AGAATGATTA
Statistics
Matches: 132, Mismatches: 19, Indels: 34
0.71 0.10 0.18
Matches are distributed among these distances:
6 8 0.06
7 12 0.09
8 55 0.42
9 55 0.42
10 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (8 bp):
TAATATAA
Found at i:13159228 original size:3 final size:3
Alignment explanation
Indices: 13159220--13159489 Score: 141
Period size: 3 Copynumber: 91.0 Consensus size: 3
13159210 AATGATATGG
* * * * *
13159220 TAA TAA TAA TAG TGA TAA T-A CAA TAA TAA TAA TAA -AG TAGA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
*
13159264 TAA CAA TAA TAA TACA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
13159311 TAA T-A TAA TAA TAGA -AA -AA TAA TAA TAA T-A TAT TAA TAA GAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * ** *
13159353 TGA TTA TAG T-A TAA -AA AAA TAA TAG TAA AAA TAA TTT TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
13159399 GAA TAA TAA -AA GTAA AAA TAA TGAA T-G TAA TAG TAA CATA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA
* * * *
13159445 TAA TAA TGAA T-A CAA TAG TAA TAT TAT TAA -AA TAA TTAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
13159490 AAATGTTCAA
Statistics
Matches: 200, Mismatches: 47, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
2 18 0.09
3 163 0.81
4 17 0.09
5 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:13159276 original size:38 final size:38
Alignment explanation
Indices: 13159234--13159338 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 38
13159224 AATAATAGTG
*
13159234 ATAATACAATAATAATAATAA-AGTAGAAAATAACAATA
1 ATAATACAATAATAATAATAATAATA-AAAATAACAATA
* * *
13159272 ATAATACATTAATAATAATAATAATAATAATAATAATA
1 ATAATACAATAATAATAATAATAATAAAAATAACAATA
* *
13159310 ATAATATAATAATAGAAAAATAATAATAA
1 ATAATACAATAAT--AATAATAATAATAA
13159339 TATATTAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 41 0.72
39 3 0.05
40 13 0.23
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (38 bp):
ATAATACAATAATAATAATAATAATAAAAATAACAATA
Found at i:13160144 original size:4 final size:4
Alignment explanation
Indices: 13160135--13160164 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
13160125 TTTTAAGGAA
13160135 AAAT AAAT -AAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
13160165 AAGAAAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:13162923 original size:38 final size:38
Alignment explanation
Indices: 13162871--13162977 Score: 164
Period size: 36 Copynumber: 2.9 Consensus size: 38
13162861 ATAAAATTTC
* * *
13162871 GTCCCTGGCAGAGAATAGATAGACTTTGACTTTTTTTT
1 GTCCCTGGCGGAGAATAGATAGACTTTGGCTTTTTTTA
13162909 GTCCCTGGCGGAGAATAGATAGACTTTGGC--TTTTTA
1 GTCCCTGGCGGAGAATAGATAGACTTTGGCTTTTTTTA
*
13162945 GTCCCTGGCGAAGAATAGATAGACTTTGGCTTT
1 GTCCCTGGCGGAGAATAGATAGACTTTGGCTTT
13162978 ATTTGATATG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
36 34 0.54
38 29 0.46
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (38 bp):
GTCCCTGGCGGAGAATAGATAGACTTTGGCTTTTTTTA
Found at i:13165598 original size:30 final size:30
Alignment explanation
Indices: 13165561--13165646 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
13165551 AAAACCCTAG
*
13165561 CCACCTTGCTTCCCACTTGCACCTACTTCA
1 CCACCTTGCTTCCCACTTGCACCTACTCCA
* *
13165591 TCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCTTCCCACTTGCACCTACTCCA
13165621 CCACCTTG-TCTCCCACTTGCACCTAC
1 CCACCTTGCT-TCCCACTTGCACCTAC
13165647 ACCATCAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.28
Consensus pattern (30 bp):
CCACCTTGCTTCCCACTTGCACCTACTCCA
Found at i:13166166 original size:9 final size:9
Alignment explanation
Indices: 13166141--13166219 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
13166131 GAGCTTTGTT
*
13166141 TTATTTTTT
1 TTATTTTTA
13166150 TTA-TTTTA
1 TTATTTTTA
13166158 TTATTTTTA
1 TTATTTTTA
*
13166167 CTATTATTTA
1 TTATT-TTTA
*
13166177 -TATTATTA
1 TTATTTTTA
*
13166185 TTATTTCTCA
1 TTATTT-TTA
*
13166195 TGTATATATTA
1 T-TAT-TTTTA
*
13166206 TTATTTATA
1 TTATTTTTA
13166215 TTATT
1 TTATT
13166220 ATATATTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.18
9 28 0.51
10 10 0.18
11 6 0.11
12 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (9 bp):
TTATTTTTA
Found at i:13166171 original size:17 final size:14
Alignment explanation
Indices: 13166139--13166190 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
13166129 TGGAGCTTTG
13166139 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
*
13166153 TTTTATTATTTTTA
1 TTTTATTTTTTTTA
* * *
13166167 CTATTATTTATATTA
1 -TTTTATTTTTTTTA
13166182 TTATTATTT
1 TT-TTATTT
13166191 CTCATGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:13166186 original size:15 final size:15
Alignment explanation
Indices: 13166168--13166372 Score: 78
Period size: 15 Copynumber: 12.4 Consensus size: 15
13166158 TTATTTTTAC
13166168 TATTATTTATATTAT
1 TATTATTTATATTAT
13166183 TATTATTTCTCATGTATATAT
1 TATTA-TT-T-A--TAT-TAT
13166204 TATTATTTATATTAT
1 TATTATTTATATTAT
*
13166219 TATATATTATATATACCAT
1 TAT-TATT-TATAT--TAT
13166238 CTCCA-TATTTAT-TTA-
1 -T--ATTATTTATATTAT
13166253 TATTATTACTATCATTAT
1 TATTATT--TAT-ATTAT
* * *
13166271 TGTTACTTCTATTATT
1 TATTATTTATATTA-T
* * *
13166287 TTTTATTTCTGACTAT
1 TATTATTTAT-ATTAT
13166303 TATATATATATATATGTAT
1 TAT-TAT-T-TATAT-TAT
* *
13166322 TATTGTTTGTATTAT
1 TATTATTTATATTAT
13166337 TATTA-TTATTATTAT
1 TATTATTTA-TATTAT
13166352 TATTA-TTATTATTAT
1 TATTATTTA-TATTAT
13166367 TATTAT
1 TATTAT
13166373 CACCCCTATT
Statistics
Matches: 148, Mismatches: 15, Indels: 53
0.69 0.07 0.25
Matches are distributed among these distances:
12 1 0.01
13 4 0.03
14 3 0.02
15 51 0.34
16 28 0.19
17 16 0.11
18 12 0.08
19 14 0.09
20 10 0.07
21 8 0.05
22 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (15 bp):
TATTATTTATATTAT
Found at i:13166216 original size:12 final size:12
Alignment explanation
Indices: 13166149--13166221 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
13166139 TTTTATTTTT
*
13166149 TTTATTTTATTA
1 TTTATATTATTA
* *
13166161 TTTTTACTATTA
1 TTTATATTATTA
13166173 TTTATATTATTA
1 TTTATATTATTA
* *
13166185 -TTAT-TTCTCA
1 TTTATATTATTA
13166195 TGTATATATTATTA
1 T-T-TATATTATTA
13166209 TTTATATTATTA
1 TTTATATTATTA
13166221 T
1 T
13166222 ATATTATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 4 0.08
11 4 0.08
12 31 0.65
13 4 0.08
14 5 0.10
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:13166337 original size:3 final size:3
Alignment explanation
Indices: 13166300--13166372 Score: 85
Period size: 3 Copynumber: 23.0 Consensus size: 3
13166290 TATTTCTGAC
*
13166300 TAT TAT ATAT ATAT ATAT GTAT TAT TGT T-T GTAT TAT TAT TAT TAT
1 TAT TAT -TAT -TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT
13166346 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
13166373 CACCCCTATT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 1 0.02
3 49 0.75
4 15 0.23
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13166576 original size:3 final size:3
Alignment explanation
Indices: 13166568--13166607 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13166558 ATTTCTATAT
13166568 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13166608 ATAGTAGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13167539 original size:21 final size:18
Alignment explanation
Indices: 13167476--13167542 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
13167466 GACAAAAAAA
*
13167476 TTATAAAAATTATTAAATT
1 TTATAAAAA-TATAAAATT
13167495 TTAATAAAAATATAAAATT
1 TT-ATAAAAATATAAAATT
*
13167514 TTATAAATATCATAAAATAAT
1 TTATAAAAAT-ATAAAAT--T
13167535 TTATAAAA
1 TTATAAAA
13167543 TGCATCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.17
19 19 0.46
20 7 0.17
21 8 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
TTATAAAAATATAAAATT
Found at i:13169000 original size:30 final size:28
Alignment explanation
Indices: 13168955--13169028 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 28
13168945 TTTACAATTT
* *
13168955 TATTTTTTGAATTTTTAATAAAATTTAAA
1 TATTTTTTTATTTTTTAATAAAATTT-AA
*
13168984 TATTTTTTTTATTTTTTATTAAAATTTAA
1 TA-TTTTTTTATTTTTTAATAAAATTTAA
*
13169013 TA-ATTTTTATTTTTTA
1 TATTTTTTTATTTTTTA
13169029 TCATTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 13 0.32
29 6 0.15
30 21 0.52
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTTTTTTATTTTTTAATAAAATTTAA
Found at i:13170083 original size:28 final size:27
Alignment explanation
Indices: 13170023--13170106 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
13170013 AAATTTTCTT
* * *
13170023 TTTTCAATTTTTTAAAATTTAAATACTTT
1 TTTT-AATTTTTAAAAATTTATATA-TTA
13170052 TTTTAATTTTTAAAAATATTATATATTA
1 TTTTAATTTTTAAAAAT-TTATATATTA
* *
13170080 TTTTGAGTTTTAAAAATTTATAT-TTA
1 TTTTAATTTTTAAAAATTTATATATTA
13170106 T
1 T
13170107 ACATTTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 29 0.59
29 10 0.20
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTAATTTTTAAAAATTTATATATTA
Found at i:13170302 original size:20 final size:20
Alignment explanation
Indices: 13170258--13170306 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13170248 CATGTGGATG
* *
13170258 ATCAACAATGGTCAACGCTA
1 ATCAACAATGGTCAACACCA
*
13170278 ATCAACTATGGTCAACACCA
1 ATCAACAATGGTCAACACCA
*
13170298 GTCAACAAT
1 ATCAACAAT
13170307 CAATCAATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (20 bp):
ATCAACAATGGTCAACACCA
Found at i:13170343 original size:21 final size:23
Alignment explanation
Indices: 13170305--13170350 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
13170295 CCAGTCAACA
*
13170305 ATCAATCAATGATGGTCAATATCG
1 ATCAATCAATGA-GGTCAAAATCG
13170329 ATCAA-CAATGA-GTCAAAATCG
1 ATCAATCAATGAGGTCAAAATCG
13170350 A
1 A
13170351 AGGTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
23 6 0.29
24 5 0.24
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (23 bp):
ATCAATCAATGAGGTCAAAATCG
Found at i:13171901 original size:3 final size:3
Alignment explanation
Indices: 13171825--13171888 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
13171815 ATATATGTAA
* * *
13171825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -CT GAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
13171872 AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
13171889 CCATAGAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13172004 original size:3 final size:3
Alignment explanation
Indices: 13171996--13172021 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13171986 TGATTAAATA
13171996 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
13172022 ATATGTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:13172339 original size:13 final size:13
Alignment explanation
Indices: 13172321--13172345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13172311 GAAACTTAAA
13172321 ATAAAATTAAAAG
1 ATAAAATTAAAAG
13172334 ATAAAATTAAAA
1 ATAAAATTAAAA
13172346 AAAAAACAGA
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
ATAAAATTAAAAG
Found at i:13173180 original size:22 final size:22
Alignment explanation
Indices: 13173155--13173198 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13173145 ACATTTTGAA
13173155 AATAGTCT-TGCTTTTTTAGATT
1 AATAGTCTCT-CTTTTTTAGATT
* *
13173177 AATATTCTCTCTTTTTTTGATT
1 AATAGTCTCTCTTTTTTAGATT
13173199 GATTGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (22 bp):
AATAGTCTCTCTTTTTTAGATT
Found at i:13173817 original size:11 final size:11
Alignment explanation
Indices: 13173803--13173847 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
13173793 ATATAAATAT
13173803 TATTTTATTAA
1 TATTTTATTAA
*
13173814 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
13173827 TATTTTATTAT
1 TATTTTATTAA
13173838 TATTTTATTA
1 TATTTTATTA
13173848 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:13178169 original size:21 final size:21
Alignment explanation
Indices: 13178145--13178216 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
13178135 CTTTCTGAAA
13178145 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
13178166 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
13178190 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
13178212 TGAAA
1 TGAAA
13178217 GATGCCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:13178196 original size:46 final size:46
Alignment explanation
Indices: 13178144--13178555 Score: 511
Period size: 46 Copynumber: 9.0 Consensus size: 46
13178134 GCTTTCTGAA
*
13178144 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
13178190 ATGAAATGTGTAAGACCATGGTTGAAAGATGCCATGGCAATATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
13178236 ATGAAATGTGTAAGACCATGGTTGATAGATACCATAGTAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
13178282 ATGAAATGTGTAAGACCATGGATGAAAGATACAATGGCAACACGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
13178328 ATGAAATGTGTAAGACAATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** ** * * *
13178374 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCATTAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
13178420 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** *
13178466 ATGAAATGAACAAGACCATGGTTAAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * * * *
13178511 CGGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
13178556 TCAAAGATAA
Statistics
Matches: 322, Mismatches: 43, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 321 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:13178857 original size:16 final size:17
Alignment explanation
Indices: 13178836--13178868 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13178826 ATGATGGAGC
13178836 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
13178852 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
13178869 TACTTATGAA
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:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:13183903 original size:93 final size:93
Alignment explanation
Indices: 13183796--13183967 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
13183786 GCCCATAAGT
* *
13183796 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
13183861 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
13183889 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAA
13183954 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
13183968 CAAATATTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:13183963 original size:46 final size:46
Alignment explanation
Indices: 13183788--13183963 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
13183778 TGTAACCCGC
* * *
13183788 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * *
13183834 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
13183884 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
13183927 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
13183964 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.62
47 30 0.27
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:13190831 original size:27 final size:27
Alignment explanation
Indices: 13190790--13190917 Score: 148
Period size: 27 Copynumber: 4.7 Consensus size: 27
13190780 AACACGTCAG
* *
13190790 GAAAGAGTAGCCTTTGTGGCAAAATAT
1 GAAAGAATAGCCTTTGTGGCGAAATAT
* ** * *
13190817 GAAAGAGTAATCTTTGTGGCGGAATAC
1 GAAAGAATAGCCTTTGTGGCGAAATAT
13190844 GAAAGAATAGCCTTTGTGGCGAAATAT
1 GAAAGAATAGCCTTTGTGGCGAAATAT
* **
13190871 GAAAAAATAGCCTTTGTAACGAAATAT
1 GAAAGAATAGCCTTTGTGGCGAAATAT
* *
13190898 GAAAGAATAACCTGTGTGGC
1 GAAAGAATAGCCTTTGTGGC
13190918 AAACCCTGTA
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
GAAAGAATAGCCTTTGTGGCGAAATAT
Found at i:13196799 original size:2 final size:2
Alignment explanation
Indices: 13196792--13196816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13196782 CCATAACTAC
13196792 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
13196817 TAACGAAAGC
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:13203077 original size:16 final size:16
Alignment explanation
Indices: 13203058--13203088 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13203048 TATATATACT
13203058 AAAACATGAGATGAGA
1 AAAACATGAGATGAGA
13203074 AAAACATGAGATGAG
1 AAAACATGAGATGAG
13203089 GTGACATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (16 bp):
AAAACATGAGATGAGA
Found at i:13209357 original size:32 final size:32
Alignment explanation
Indices: 13209321--13209388 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
13209311 TGAAACGTTA
13209321 TTTTAATTGATGATGAGAATTAT-GATATTGTT
1 TTTTAATTGATGATGAGAATTATGGA-ATTGTT
*
13209353 TTTTAATTGATTATGAGAATTATGGAATTGTT
1 TTTTAATTGATGATGAGAATTATGGAATTGTT
13209385 TTTT
1 TTTT
13209389 TTAAGTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (32 bp):
TTTTAATTGATGATGAGAATTATGGAATTGTT
Found at i:13211807 original size:41 final size:41
Alignment explanation
Indices: 13211761--13211889 Score: 170
Period size: 41 Copynumber: 3.2 Consensus size: 41
13211751 TTTAATCCAA
* * * * **
13211761 TATTTTTATGGTTTATTTGATTATTAGTTATAATTGTTGGT
1 TATTTTGATGGATTATTTGATAATTAGTTATATTTGTTAAT
13211802 TATTTTGATGGATTATTTGATAATTAGTTATATTTGTTAAT
1 TATTTTGATGGATTATTTGATAATTAGTTATATTTGTTAAT
* * *
13211843 TATTTTGATGGATT-GTTGATGATTAATTATATTTGTTAAT
1 TATTTTGATGGATTATTTGATAATTAGTTATATTTGTTAAT
13211883 TATTTTG
1 TATTTTG
13211890 GTTGGTAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 30 0.38
41 49 0.62
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (41 bp):
TATTTTGATGGATTATTTGATAATTAGTTATATTTGTTAAT
Found at i:13213049 original size:22 final size:23
Alignment explanation
Indices: 13213024--13213069 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
13213014 CAACCAAATC
13213024 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
13213046 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
13213069 A
1 A
13213070 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:13213075 original size:23 final size:23
Alignment explanation
Indices: 13213031--13213075 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13213021 ATCAATTCAA
*
13213031 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
13213054 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
13213076 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:13218154 original size:51 final size:51
Alignment explanation
Indices: 13218094--13218195 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
13218084 TGAAGGTGTC
13218094 AAGGTTCGTTCATTTATCTTCATATAATTATGTTTGGGGTACATGAGAGAA
1 AAGGTTCGTTCATTTATCTTCATATAATTATGTTTGGGGTACATGAGAGAA
13218145 AAGGTTCGTTCATTTATCTTCATATAATTATGTTTGGGGTACATGAGAGAA
1 AAGGTTCGTTCATTTATCTTCATATAATTATGTTTGGGGTACATGAGAGAA
13218196 CTTTAAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (51 bp):
AAGGTTCGTTCATTTATCTTCATATAATTATGTTTGGGGTACATGAGAGAA
Found at i:13222057 original size:18 final size:16
Alignment explanation
Indices: 13222026--13222068 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
13222016 TTTTTGAATT
13222026 ATATTTTTTATTTTTA
1 ATATTTTTTATTTTTA
13222042 ATATTTTATGTATTTTTA
1 ATATTTT-T-TATTTTTA
*
13222060 AAATTTTTT
1 ATATTTTTT
13222069 TATTGTACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
ATATTTTTTATTTTTA
Found at i:13223559 original size:13 final size:13
Alignment explanation
Indices: 13223537--13223572 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
13223527 AGCAAGAAAC
13223537 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
* *
13223550 AAAAATAAAAATG
1 AAAAAGAAAAAGG
13223563 AAAAAGAAAA
1 AAAAAGAAAA
13223573 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAAAGAAAAAGG
Found at i:13238683 original size:13 final size:13
Alignment explanation
Indices: 13238665--13238689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13238655 AAATTTCATC
13238665 TGTTTCAAAGCTA
1 TGTTTCAAAGCTA
13238678 TGTTTCAAAGCT
1 TGTTTCAAAGCT
13238690 CCCCAACTAT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTTTCAAAGCTA
Found at i:13247871 original size:23 final size:21
Alignment explanation
Indices: 13247842--13247885 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
13247832 ATTATATTAA
*
13247842 AATTAAAATTAAAATATAAATAT
1 AATTAAAAATAAAA-A-AAATAT
13247865 AATTAAAAATAAAAAAAATAT
1 AATTAAAAATAAAAAAAATAT
13247886 TTATTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
23 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAAAAATAAAAAAAATAT
Found at i:13249783 original size:20 final size:19
Alignment explanation
Indices: 13249758--13249823 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
13249748 ACGAGCTTCC
13249758 GTTAACTCATATGAGTTTCA
1 GTTAACTC-TATGAGTTTCA
* * *
13249778 GTTAACCCTTTTGGGGTTTCA
1 GTTAACTC-TAT-GAGTTTCA
*
13249799 GTTCAACTCTGATGAGCTTCA
1 GTT-AACTCT-ATGAGTTTCA
13249820 GTTA
1 GTTA
13249824 GCCTTCGGGC
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 10 0.29
21 20 0.57
22 5 0.14
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (19 bp):
GTTAACTCTATGAGTTTCA
Found at i:13249857 original size:21 final size:21
Alignment explanation
Indices: 13249832--13249896 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
13249822 TAGCCTTCGG
13249832 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* ** *
13249853 GCTTCAG-TTAGC-C-TCCGG
1 GCTTCCGTTTAGCACTTATGT
13249871 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
13249892 GCTTC
1 GCTTC
13249897 AGCTAGATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 6 0.18
21 13 0.39
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:13249860 original size:39 final size:39
Alignment explanation
Indices: 13249814--13249913 Score: 164
Period size: 39 Copynumber: 2.6 Consensus size: 39
13249804 ACTCTGATGA
13249814 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
13249853 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
13249892 GCTTCAGCTAGATTTCGGGCTT
1 GCTTCAGTTAGCCTTCGGGCTT
13249914 TAGATCACGA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:13254248 original size:15 final size:14
Alignment explanation
Indices: 13254223--13254305 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 14
13254213 TCTAATACTA
*
13254223 TTATTTTTATCTAAT
1 TTATATTTATCT-AT
*
13254238 TTTTATTTATCTAT
1 TTATATTTATCTAT
*
13254252 TTATATTTCAACTA-
1 TTATATTT-ATCTAT
13254266 TTATTATATT-TCTAT
1 TTA-TAT-TTATCTAT
13254281 TTATTATATT-TCTAT
1 TTA-TAT-TTATCTAT
13254296 TTATATTTAT
1 TTATATTTAT
13254306 ATACTAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
13 2 0.03
14 19 0.33
15 35 0.60
16 2 0.03
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATTTATCTAT
Found at i:13254301 original size:44 final size:44
Alignment explanation
Indices: 13254217--13254347 Score: 130
Period size: 44 Copynumber: 3.0 Consensus size: 44
13254207 TGTTATTCTA
13254217 ATACTATTATT-TTTATCTAATTT-TTATTTATCTATTTATATTT-C
1 ATACTATTATTATTT-TCT-ATTTATTATTT-TCTATTTATATTTAC
*
13254261 A-ACTATTATTATATTTCTATTTATTATATTTCTATTTATATTTAT
1 ATACTATTATTAT-TTTCTATTTATTAT-TTTCTATTTATATTTAC
* *
13254306 ATACTAATATTATTTTC-A-TTATTATTTTTCTTATATATATTT
1 ATACTATTATTATTTTCTATTTATTA-TTTTC-TATTTATATTT
13254348 TTTACTCTTG
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
43 23 0.30
44 34 0.45
45 9 0.12
46 10 0.13
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.63
Consensus pattern (44 bp):
ATACTATTATTATTTTCTATTTATTATTTTCTATTTATATTTAC
Found at i:13254462 original size:25 final size:25
Alignment explanation
Indices: 13254434--13254482 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
13254424 TTCATTTCAA
* *
13254434 ATTTTTATACATTATTTACTTTAAT
1 ATTTTCATACATTATGTACTTTAAT
* *
13254459 ATTTTCATATATTATGTATTTTAA
1 ATTTTCATACATTATGTACTTTAA
13254483 ACTTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTTCATACATTATGTACTTTAAT
Found at i:13262996 original size:21 final size:22
Alignment explanation
Indices: 13262970--13263012 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
13262960 ATATGCATGT
13262970 TGCTTTTGTTT-CTTTCCTTTG
1 TGCTTTTGTTTGCTTTCCTTTG
*
13262991 TGCTTTTTTTTGCTTTCCTTTG
1 TGCTTTTGTTTGCTTTCCTTTG
13263013 GTACATGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.00, C:0.19, G:0.14, T:0.67
Consensus pattern (22 bp):
TGCTTTTGTTTGCTTTCCTTTG
Found at i:13266874 original size:15 final size:15
Alignment explanation
Indices: 13266854--13266886 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
13266844 GTATTTCATG
13266854 TTAAATT-TTTTAATT
1 TTAAATTATTTT-ATT
13266869 TTAAATTATTTTATT
1 TTAAATTATTTTATT
13266884 TTA
1 TTA
13266887 TTTTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAAATTATTTTATT
Found at i:13269249 original size:11 final size:12
Alignment explanation
Indices: 13269233--13269266 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
13269223 ATATATATTT
13269233 AAAAATAATA-A
1 AAAAATAATATA
13269244 AAAAATAATATA
1 AAAAATAATATA
13269256 AAAAATTAATA
1 AAAAA-TAATA
13269267 CGGGCGGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 6 0.29
13 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:13270115 original size:20 final size:20
Alignment explanation
Indices: 13270077--13270124 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13270067 TAAATTCTAA
* **
13270077 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
13270097 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
13270117 AAA-ATAAA
1 AAAGATAAA
13270125 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:13271981 original size:42 final size:42
Alignment explanation
Indices: 13271922--13272030 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
13271912 GGTTTTGGGG
* * *
13271922 ATTCTAGGGCTGGAATAGGATTGTTCGGCTGCAGAAATATGGC
1 ATTCT-GGGCTGGAATAGAACTGTTCGGCAGCAGAAATATGGC
* **
13271965 ATTCTGGGCTGGAATAGAACTGTTTGGCAGCAGGGATATGGC
1 ATTCTGGGCTGGAATAGAACTGTTCGGCAGCAGAAATATGGC
* * *
13272007 ATTTTGGGTTGGAATTGAACTGTT
1 ATTCTGGGCTGGAATAGAACTGTT
13272031 TGGTACCATG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
42 52 0.91
43 5 0.09
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (42 bp):
ATTCTGGGCTGGAATAGAACTGTTCGGCAGCAGAAATATGGC
Found at i:13272153 original size:10 final size:10
Alignment explanation
Indices: 13272140--13272220 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 10
13272130 AATATTTAAC
13272140 TAAAATAAAA
1 TAAAATAAAA
13272150 TAAAAATAAAA
1 T-AAAATAAAA
13272161 TAATAAATAATAA
1 T-A-AAATAA-AA
*
13272174 -ATAATAAAA
1 TAAAATAAAA
*
13272183 TAAAATAAAG
1 TAAAATAAAA
*
13272193 GAAAATAATAAA
1 TAAAAT-A-AAA
13272205 TAAAAATAAAAA
1 T-AAAAT-AAAA
13272217 TAAA
1 TAAA
13272221 GATTGGGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.03
10 18 0.31
11 17 0.29
12 12 0.21
13 9 0.16
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:13272170 original size:7 final size:7
Alignment explanation
Indices: 13272148--13272219 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
13272138 ACTAAAATAA
13272148 AATAAA-
1 AATAAAT
13272154 AATAAAAT
1 AAT-AAAT
13272162 AATAAAT
1 AATAAAT
13272169 AATAAAT
1 AATAAAT
13272176 AATAAAAT
1 AAT-AAAT
*
13272184 AAAATAAAG
1 --AATAAAT
*
13272193 GA-AAAT
1 AATAAAT
13272199 AATAAAT
1 AATAAAT
13272206 AA-AAAT
1 AATAAAT
13272212 AA-AAAT
1 AATAAAT
13272218 AA
1 AA
13272220 AGATTGGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
6 19 0.34
7 24 0.43
8 7 0.12
9 3 0.05
10 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (7 bp):
AATAAAT
Found at i:13272181 original size:33 final size:32
Alignment explanation
Indices: 13272143--13272220 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 32
13272133 ATTTAACTAA
*
13272143 AATAAAATAAAAATAAAATAATAAATAATAAAT
1 AATAAAATAAAAATAAAAGAA-AAATAATAAAT
*
13272176 AATAAAAT-AAAAT-AAAGGAAAATAATAAAT
1 AATAAAATAAAAATAAAAGAAAAATAATAAAT
13272206 -A-AAAATAAAAATAAA
1 AATAAAATAAAAATAAA
13272221 GATTGGGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.12
29 6 0.15
30 13 0.32
31 4 0.10
32 5 0.12
33 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (32 bp):
AATAAAATAAAAATAAAAGAAAAATAATAAAT
Found at i:13278573 original size:20 final size:20
Alignment explanation
Indices: 13278535--13278582 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13278525 TAAATTCTAA
* **
13278535 AAAGATAAATATATTTAATT
1 AAAGATAAATAAAGATAATT
13278555 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
13278575 AAA-ATAAA
1 AAAGATAAA
13278583 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:13280350 original size:126 final size:126
Alignment explanation
Indices: 13280120--13280360 Score: 356
Period size: 126 Copynumber: 1.9 Consensus size: 126
13280110 AATTAACGAT
*
13280120 ATAGGTTATAGATTATGGACAAGCATGAACAAATATAAATAAAAGGTTAAAATATGAAGTAAATT
1 ATAGATTATAGATTATGGACAAGCATGAACAAATATAAATAAAAGGTTAAAATATGAAGTAAATT
* *
13280185 TATGTAGCTTTCGTAAATTTAGAATTTAATTTATATACTTTAATTACTAAAATATTTTTAA
66 TATGTAGCTTTCGTAAATTTAAAATTTAATTAATATACTTTAATTACTAAAATATTTTTAA
* * * * *
13280246 ATAGATTATAGATTATGGACAAGCATGTACAGATATAAATGAAAGGTTAAAATATGTAGTAAGTT
1 ATAGATTATAGATTATGGACAAGCATGAACAAATATAAATAAAAGGTTAAAATATGAAGTAAATT
** * * * *
13280311 TATGTATTTTTCGTAAATTTAAAATTTAGTTAATGTACTTTTATTCCTAA
66 TATGTAGCTTTCGTAAATTTAAAATTTAATTAATATACTTTAATTACTAA
13280361 GAATTTAGTC
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 101 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (126 bp):
ATAGATTATAGATTATGGACAAGCATGAACAAATATAAATAAAAGGTTAAAATATGAAGTAAATT
TATGTAGCTTTCGTAAATTTAAAATTTAATTAATATACTTTAATTACTAAAATATTTTTAA
Found at i:13282151 original size:14 final size:14
Alignment explanation
Indices: 13282132--13282161 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13282122 ATGTATATTC
13282132 TAAATATATATATA
1 TAAATATATATATA
13282146 TAAATATATATATA
1 TAAATATATATATA
13282160 TA
1 TA
13282162 TAAGAAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:13288828 original size:28 final size:28
Alignment explanation
Indices: 13288735--13288827 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
13288725 CAAATATGGT
*
13288735 ACTTAGTGTACGAAATATTGAGAATGGC
1 ACTTAGTGTACGAAATATTGAGAATGAC
*
13288763 ACCTAGTGTACGAAATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
* *
13288791 ACTTAGTGTGCGAGATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
13288819 ACTTAGTGT
1 ACTTAGTGT
13288828 GTAAAATATC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (28 bp):
ACTTAGTGTACGAAATATTGAGAATGAC
Found at i:13295381 original size:46 final size:46
Alignment explanation
Indices: 13295314--13295529 Score: 306
Period size: 46 Copynumber: 4.7 Consensus size: 46
13295304 GGCAACCTGA
*
13295314 GTGTAAGACCATGGTTGAAAGATACCATGACAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
13295360 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
13295406 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
13295452 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
13295498 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
13295530 TCATGTCAAA
Statistics
Matches: 155, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 155 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:13295515 original size:138 final size:130
Alignment explanation
Indices: 13295264--13295529 Score: 370
Period size: 138 Copynumber: 2.0 Consensus size: 130
13295254 AGTGTGCTCT
*
13295264 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
13295329 TGAAAGATACCATGACAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGACAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
13295394 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
* *
13295459 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
13295524 ATGGCA
123 ATGGCA
13295530 TCATGTCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
130 48 0.41
132 1 0.01
133 1 0.01
136 2 0.02
138 66 0.56
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGACAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Done.