Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 12 of 255
Found at i:3467428 original size:21 final size:20
Alignment explanation
Indices: 3467371--3467428 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
3467361 TAATATATAT
* * *
3467371 ATTTAGGGTTTAGGGTGTAA
1 ATTTATGGTTTAGGATTTAA
* *
3467391 ATTTATGGTCTAAGATTTAA
1 ATTTATGGTTTAGGATTTAA
3467411 GATTTATGGTTTAGGATT
1 -ATTTATGGTTTAGGATT
3467429 CGGAGTTTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.45
Consensus pattern (20 bp):
ATTTATGGTTTAGGATTTAA
Found at i:3468099 original size:8 final size:8
Alignment explanation
Indices: 3468086--3468114 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3468076 AATCTTTAAA
3468086 AAAATTTT
1 AAAATTTT
3468094 AAAATTTT
1 AAAATTTT
3468102 AAAATTTT
1 AAAATTTT
3468110 AAAAT
1 AAAAT
3468115 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAAATTTT
Found at i:3468126 original size:8 final size:7
Alignment explanation
Indices: 3468110--3468156 Score: 76
Period size: 7 Copynumber: 6.4 Consensus size: 7
3468100 TTAAAATTTT
3468110 AAAATAA
1 AAAATAA
3468117 AAAATAA
1 AAAATAA
3468124 AAAATAA
1 AAAATAA
3468131 AAAATAAA
1 AAAAT-AA
3468139 AAAATAAA
1 AAAAT-AA
3468147 AAAATAA
1 AAAATAA
3468154 AAA
1 AAA
3468157 TTTAATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 24 0.62
8 15 0.38
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:3468157 original size:14 final size:14
Alignment explanation
Indices: 3468110--3468157 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
3468100 TTAAAATTTT
3468110 AAAAT-AAAAAATAA
1 AAAATAAAAAAAT-A
*
3468124 AAAATAAAAAATAAA
1 AAAATAAAAAA-ATA
3468139 AAAATAAAAAAATA
1 AAAATAAAAAAATA
3468153 AAAAT
1 AAAAT
3468158 TTAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.40
15 17 0.57
16 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:3468301 original size:18 final size:18
Alignment explanation
Indices: 3468255--3468312 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
3468245 AAAACTTTTG
* *
3468255 AAAAAAAAATAGAAAAAT
1 AAAATAAAATTGAAAAAT
3468273 AATATATTAAAATTGAAAAAT
1 AA-A-A-TAAAATTGAAAAAT
*
3468294 AAAATAAAATTGAACAAT
1 AAAATAAAATTGAAAAAT
3468312 A
1 A
3468313 GTAGCAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 16 0.47
19 2 0.06
20 2 0.06
21 14 0.41
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAATAAAATTGAAAAAT
Found at i:3469132 original size:18 final size:18
Alignment explanation
Indices: 3469106--3469144 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3469096 GGTCAAGTTG
* *
3469106 AATTTGAATAATTTAAAT
1 AATTCGAATAACTTAAAT
3469124 AATTCGAATAACTTAAAT
1 AATTCGAATAACTTAAAT
3469142 AAT
1 AAT
3469145 AGATTGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTCGAATAACTTAAAT
Found at i:3482801 original size:15 final size:15
Alignment explanation
Indices: 3482781--3482810 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3482771 AAGTGTTTAC
3482781 TGTATTAGAATTTGA
1 TGTATTAGAATTTGA
3482796 TGTATTAGAATTTGA
1 TGTATTAGAATTTGA
3482811 AGTGTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
TGTATTAGAATTTGA
Found at i:3507474 original size:13 final size:14
Alignment explanation
Indices: 3507451--3507479 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3507441 TAAAAACTAA
3507451 AAATAATAAAAATT
1 AAATAATAAAAATT
3507465 AAAT-ATAAAAATT
1 AAATAATAAAAATT
3507478 AA
1 AA
3507480 GTATGGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATAAAAATT
Found at i:3507744 original size:48 final size:48
Alignment explanation
Indices: 3507687--3507783 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3507677 ATTGTATCTT
3507687 CCTAATGATTAATATGATCATTGTCAATCAAATGATTGTGATCAATTG
1 CCTAATGATTAATATGATCATTGTCAATCAAATGATTGTGATCAATTG
3507735 CCTAATGATTAATATGATCATTGTCAATCAAATGATTGTGATCAATTG
1 CCTAATGATTAATATGATCATTGTCAATCAAATGATTGTGATCAATTG
3507783 C
1 C
3507784 TTGTTCGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (48 bp):
CCTAATGATTAATATGATCATTGTCAATCAAATGATTGTGATCAATTG
Found at i:3507776 original size:24 final size:24
Alignment explanation
Indices: 3507701--3507778 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
3507691 ATGATTAATA
3507701 TGATCATTGTCAATCAAATGATTG
1 TGATCATTGTCAATCAAATGATTG
* * * * *
3507725 TGATCAATTGCCTAAT--GATTAATA
1 TGATC-ATTGTC-AATCAAATGATTG
3507749 TGATCATTGTCAATCAAATGATTG
1 TGATCATTGTCAATCAAATGATTG
3507773 TGATCA
1 TGATCA
3507779 ATTGCTTGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
22 3 0.08
23 5 0.12
24 24 0.60
25 5 0.12
26 3 0.08
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (24 bp):
TGATCATTGTCAATCAAATGATTG
Found at i:3508424 original size:17 final size:16
Alignment explanation
Indices: 3508402--3508433 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3508392 ATCTCTCTGG
3508402 ATAAAAAATAATAAAAA
1 ATAAAAAATAA-AAAAA
3508419 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
3508434 TCCAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAAAATAAAAAAA
Found at i:3508430 original size:14 final size:15
Alignment explanation
Indices: 3508406--3508434 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3508396 CTCTGGATAA
3508406 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
3508421 AAAA-AATAAAAAAT
1 AAAATAATAAAAAAT
3508435 CCAAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:3509963 original size:17 final size:18
Alignment explanation
Indices: 3509926--3509965 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3509916 CCATCCCCTG
*
3509926 GCCACCCCCATACCGTCT
1 GCCACCACCATACCGTCT
*
3509944 GCCACCACCATGCC-TCT
1 GCCACCACCATACCGTCT
3509961 GCCAC
1 GCCAC
3509966 ACCTGCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.55, G:0.12, T:0.15
Consensus pattern (18 bp):
GCCACCACCATACCGTCT
Found at i:3530465 original size:21 final size:22
Alignment explanation
Indices: 3530435--3530480 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
3530425 ATACTGAAGC
*
3530435 AAATCCAAGAGAAAAAAAAAAA
1 AAATCCAAGAAAAAAAAAAAAA
3530457 AAAT-CAAGAAAAAAAAAAAAA
1 AAATCCAAGAAAAAAAAAAAAA
3530478 AAA
1 AAA
3530481 AAAGATCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.04
Consensus pattern (22 bp):
AAATCCAAGAAAAAAAAAAAAA
Found at i:3530785 original size:132 final size:131
Alignment explanation
Indices: 3530586--3530824 Score: 309
Period size: 132 Copynumber: 1.8 Consensus size: 131
3530576 TCCGTATTGT
* * *
3530586 TAGGGAACAAGTTGAAAACAGTAGATTTGGCATCCATGTGCTAATAGGGAACAGATCGAATATAG
1 TAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCATGTGCTAATAGGGAACAGATCGAAGACAG
* *
3530651 CAGATCTGACATTCCTGTGCTTACGGTGAAGCAGATCAAAGATTTCAGCATGGAATCCCTGTGCT
66 CAGATCTGACATCCCTGTGCTTACGGGGAA-CAGATCAAAGATTTCAGCATGGAATCCCTGTGCT
3530716 TA
130 TA
* * * * * *
3530718 TAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGACA
1 TAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCATGTGCTAATAGGGAACAGA-TCGAAGACA
* * * * *
3530782 GCAGATTTGGCATCCCTGTGTTTATGGGGAACAGATCGAAGAT
65 GCAGATCTGACATCCCTGTGCTTACGGGGAACAGATCAAAGAT
3530825 GCAGATCAAG
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
131 12 0.13
132 78 0.87
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (131 bp):
TAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCATGTGCTAATAGGGAACAGATCGAAGACAG
CAGATCTGACATCCCTGTGCTTACGGGGAACAGATCAAAGATTTCAGCATGGAATCCCTGTGCTT
A
Found at i:3530797 original size:88 final size:88
Alignment explanation
Indices: 3530565--3530830 Score: 233
Period size: 88 Copynumber: 3.0 Consensus size: 88
3530555 GATCTAAGAT
* * * *
3530565 GATTTGGCATCTCC-GTATTGT-TAGGGAACAAGTTGAAAACAGTAGATTTGGCATCCATGTGCT
1 GATTTGGCATC-CCTGTGTT-TATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCT
* *
3530628 AATAGGGAACAGATCGAATATAGCA
64 TATAGGGAACAGATCGAAGATAGCA
* * * * * ** *** *
3530653 GATCTGACATTCCTGTGCTTA-CGGTGAAGC-AGATCAAAGATTTCAGCA--TGGAATCCCTGTG
1 GATTTGGCATCCCTGTGTTTATAGG-GAA-CAAG-TTGAAGACAGCAG-ATTTGGCATCCCTGTG
*
3530714 CTTATAGGGAACA-AGTTGAAGATAGCA
62 CTTATAGGGAACAGA-TCGAAGATAGCA
*
3530741 GATTTGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTA
1 GATTTGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCTTA
*
3530806 TGGGGAACAGATCGAAGAT-GCA
66 TAGGGAACAGATCGAAGATAGCA
3530828 GAT
1 GAT
3530831 CAAGAACTCA
Statistics
Matches: 134, Mismatches: 32, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
86 1 0.01
87 21 0.16
88 101 0.75
89 10 0.07
90 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (88 bp):
GATTTGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCTTA
TAGGGAACAGATCGAAGATAGCA
Found at i:3530823 original size:44 final size:44
Alignment explanation
Indices: 3530608--3530830 Score: 206
Period size: 44 Copynumber: 5.1 Consensus size: 44
3530598 TGAAAACAGT
* * *
3530608 AGATTTGGCATCCATGTGCTAATAGGGAACAGATCGAATATAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGC
* * * * * **
3530652 AGATCTGACATTCCTGTGCTTA-CGGTGAAGCAGATCAAAGATTTC
1 AGATTTGGCATCCCTGTGCTTATAGG-GAA-CAGATCGAAGATAGC
* *
3530697 AGCA--TGGAATCCCTGTGCTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGC
* * *
3530740 AGATTTGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGACAGC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGC
* *
3530784 AGATTTGGCATCCCTGTGTTTATGGGGAACAGATCGAAGAT-GC
1 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGC
3530827 AGAT
1 AGAT
3530831 CAAGAACTCA
Statistics
Matches: 147, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.01
43 19 0.13
44 109 0.74
45 16 0.11
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGC
Found at i:3531345 original size:29 final size:30
Alignment explanation
Indices: 3531284--3531366 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 30
3531274 AGAGAATAGA
3531284 TTTTTTTTTTTGAGATTCAAGAAAAGATTTT
1 TTTTTTTTTTTGAGATTCAAGAAAAGA-TTT
***
3531315 TTTTTTTTTTTGAGATTCAAGAGGGGA-TT
1 TTTTTTTTTTTGAGATTCAAGAAAAGATTT
*
3531344 TTTCTTTTTTTGAGATTCAAGAA
1 TTTTTTTTTTTGAGATTCAAGAA
3531367 CAAAAAATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.49
31 24 0.51
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (30 bp):
TTTTTTTTTTTGAGATTCAAGAAAAGATTT
Found at i:3532080 original size:16 final size:15
Alignment explanation
Indices: 3532049--3532091 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3532039 CCTTCATTCC
*
3532049 ATTATTATTATTACT
1 ATTATTATTTTTACT
3532064 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
3532080 ATCATTATTTTT
1 ATTATTATTTTT
3532092 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:3532217 original size:16 final size:16
Alignment explanation
Indices: 3532196--3532227 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3532186 CTATTGTTAC
3532196 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
3532212 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
3532228 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:3532269 original size:11 final size:13
Alignment explanation
Indices: 3532239--3532270 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3532229 TTATTATAAT
3532239 TTATTATTGTTAC
1 TTATTATTGTTAC
3532252 TTATTATT-TTAC
1 TTATTATTGTTAC
3532264 -TATTATT
1 TTATTATT
3532271 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:3532455 original size:22 final size:22
Alignment explanation
Indices: 3532425--3532485 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3532415 TTATTATATC
*
3532425 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
3532447 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* *
3532469 TTTTCCT-TTATTTTTGT
1 TTTTACTATTATTATTGT
3532486 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:3532459 original size:3 final size:3
Alignment explanation
Indices: 3532227--3532440 Score: 52
Period size: 3 Copynumber: 72.3 Consensus size: 3
3532217 TTCTCATCAC
* * *
3532227 TAT TAT TAT AATT TAT TAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
3532273 CTAA TA- TAT CAT CAT TAT CAT TAT T-T CAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * * *
3532317 TAT TAT TAT TAT TAT TAG CAC TACT T-T TAT TAC TAT TAT T-T AAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * ** * * * *
3532361 ATAT TAT TTT TAC TAT TAT CGT CA- TAT TGT TAC TAT TAC TAT TA-
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3532405 TAT TAT TA- TGT TAT TA- TAT CTTT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T
3532441 GTTGTATTTT
Statistics
Matches: 147, Mismatches: 47, Indels: 34
0.64 0.21 0.15
Matches are distributed among these distances:
2 15 0.10
3 118 0.80
4 14 0.10
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:3532762 original size:18 final size:17
Alignment explanation
Indices: 3532734--3532767 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3532724 TCCTGTTATG
3532734 GTTATCATTTTTTATTT
1 GTTATCATTTTTTATTT
3532751 GTTATGCATTTTTTATT
1 GTTAT-CATTTTTTATT
3532768 ATCTCGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (17 bp):
GTTATCATTTTTTATTT
Found at i:3533763 original size:12 final size:12
Alignment explanation
Indices: 3533746--3533770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3533736 ACCCAAAACC
3533746 CTTAGCCCAAAA
1 CTTAGCCCAAAA
3533758 CTTAGCCCAAAA
1 CTTAGCCCAAAA
3533770 C
1 C
3533771 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTTAGCCCAAAA
Found at i:3533857 original size:38 final size:38
Alignment explanation
Indices: 3533806--3533894 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
3533796 AACCCTAATC
*
3533806 CCACCTACTCCACCACCCTTGTTGGCTACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
3533844 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
3533882 CCACCTACACCAC
1 CCACCTACTCCAC
3533895 TATGCCGCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.18, C:0.51, G:0.11, T:0.20
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:3534603 original size:28 final size:28
Alignment explanation
Indices: 3534563--3534617 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3534553 TGTATATATT
* * *
3534563 ATATTGTTGTTATTATTACTATTTTTAA
1 ATATTCTTATTATTACTACTATTTTTAA
*
3534591 ATATTCTTATTATTACTATTATTTTTA
1 ATATTCTTATTATTACTACTATTTTTA
3534618 TTCCTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (28 bp):
ATATTCTTATTATTACTACTATTTTTAA
Found at i:3534953 original size:22 final size:22
Alignment explanation
Indices: 3534927--3534968 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3534917 TAACGTGCTA
* *
3534927 TTATTACTATTATTTTTATTTG
1 TTATTACCATTATTGTTATTTG
3534949 TTATTACCATTATTGTTATT
1 TTATTACCATTATTGTTATT
3534969 GTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
TTATTACCATTATTGTTATTTG
Found at i:3537736 original size:19 final size:19
Alignment explanation
Indices: 3537714--3537760 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
3537704 CTTCCTTTCT
3537714 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTCCA-ACA
*
3537733 TTTGCATTACATTGCAACA
1 TTTGCATTACATTCCAACA
3537752 TTTGCATTA
1 TTTGCATTA
3537761 AACTTTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCAACA
Found at i:3541016 original size:17 final size:17
Alignment explanation
Indices: 3540996--3541032 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3540986 CTTTAAGACC
3540996 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
3541013 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
3541030 AAA
1 AAA
3541033 GGAGAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:3542167 original size:61 final size:64
Alignment explanation
Indices: 3542091--3542209 Score: 192
Period size: 61 Copynumber: 1.9 Consensus size: 64
3542081 ATAACACATC
3542091 TAGTTAGGAGCATTTGATTCATTTC-AT-A-A-CATCCTAATTATTTGACATAAAGCATCACAGT
1 TAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACAT-AAGCATCACAGT
*
3542152 TAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGGCATAAGCAT
1 TAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
3542210 AGATACATGA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
61 25 0.47
62 2 0.04
63 1 0.02
64 7 0.13
65 18 0.34
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (64 bp):
TAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCATCACAGT
Found at i:3542719 original size:205 final size:205
Alignment explanation
Indices: 3542354--3542842 Score: 757
Period size: 205 Copynumber: 2.4 Consensus size: 205
3542344 ATCAGGCGGA
* * *
3542354 GAGCAGATCGAACACATAGCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAATCTAAGATAAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAAT
*
3542419 TTGGCATCTTTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCATATCGATGGAAGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCATATCGATGGAAGGCAGA
* ** *
3542484 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTTGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
3542549 TGCTTACAAG
196 TGCTTACAAG
* * *
3542559 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAAT
* * * *
3542624 TTGGCATCTCTGTATTGTTAGAGAACAAATTGAAGTCTGGCATCTCCACT-TCGATGG-AGGTTA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCA-TATCGATGGAAGG-CA
3542687 GACACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCT
129 GACACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCT
3542752 TGTGCTTACAAG
194 TGTGCTTACAAG
* * * * *
3542764 CAGTAAATTGAAGACATGGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCCAAGATAAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAAT
*
3542829 TTGGCGTCTCTGTA
66 TTGGCATCTCTGTA
3542843 GCGGCAGAGA
Statistics
Matches: 258, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
204 3 0.01
205 254 0.98
206 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (205 bp):
GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATAAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCATATCGATGGAAGGCAGA
CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
TGCTTACAAG
Found at i:3543104 original size:132 final size:132
Alignment explanation
Indices: 3542867--3543656 Score: 1357
Period size: 132 Copynumber: 6.0 Consensus size: 132
3542857 ATCGAAGATT
*
3542867 GCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* *
3542932 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
3542997 CA
131 CA
3542999 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
3543064 TTACGGTGAAGTAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
3543129 CA
131 CA
* **
3543131 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCAAAGATAATAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
3543196 TTACGGTGAAGCAGATCGAAGATTTCAGCATGGA-ATCCATGTGCTTACAGGGAACAAGTTGAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCAT-GACATCCCTGTGCTTATAGGGAACAAGTTGAAA
*
3543260 ATA
130 ACA
* *
3543263 GCAGATTTGGCATCCATGTGCTTATAGGGAACAGATCGAAGATAGCAAATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
*
3543328 TTGCAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
3543393 CA
131 CA
*
3543395 GCAGATTTGGCATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
3543460 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
3543525 CA
131 CA
* * *
3543527 GCAGATTTGGCATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATATGGCATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
3543592 TTACAGTAAAGCAGATTGAATATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
3543657 TACTTAATTT
Statistics
Matches: 625, Mismatches: 31, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
131 2 0.00
132 622 1.00
133 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
TTACAGTGAAGCAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAA
CA
Found at i:3543725 original size:173 final size:173
Alignment explanation
Indices: 3543496--3543861 Score: 624
Period size: 173 Copynumber: 2.1 Consensus size: 173
3543486 AGCATGACAT
*
3543496 CCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACGG
1 CCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGCGCTTATAGGGAACGG
* ** * *
3543561 ATCGAAGATAGCAGATATGGCATTCCTGTGCTTACAGTAAAGCAGATTGAATATTTCAGCATGAC
66 ATCGAAGATAGCAGACATAACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCATGAC
3543626 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
131 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
* * *
3543669 CTCTGTGCTTATAGGGAATAAGTTGAAAACAGCATATTTGGCATCCCTGCGCTTATAGGGAACGG
1 CCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGCGCTTATAGGGAACGG
* * *
3543734 ATCGAAGATAGCAGACCTAACATTCCTGTGCTTACAGTGAAGTAGATCGAAGATTTCAGCATGAC
66 ATCGAAGATAGCAGACATAACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCATGAC
3543799 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
131 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
3543842 CCCTGTGCTTATAGGGAACA
1 CCCTGTGCTTATAGGGAACA
3543862 GATCAAAAAT
Statistics
Matches: 179, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
173 179 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (173 bp):
CCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGCGCTTATAGGGAACGG
ATCGAAGATAGCAGACATAACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCATGAC
ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
Found at i:3543728 original size:44 final size:42
Alignment explanation
Indices: 3543625--3543731 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 42
3543615 TTCAGCATGA
* *
3543625 CATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTT
1 CATCCCTGTGCTTATAGGGAACAAGTTGAAAACACATAATTT
* * *
3543667 -AACTCTGTGCTTATAGGGAATAAGTTGAAAACAGCAT-ATTT
1 CATCCCTGTGCTTATAGGGAACAAGTTGAAAACA-CATAATTT
*
3543708 GGCATCCCTGCGCTTATAGGGAAC
1 --CATCCCTGTGCTTATAGGGAAC
3543732 GGATCGAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 33 0.63
42 2 0.04
44 17 0.33
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (42 bp):
CATCCCTGTGCTTATAGGGAACAAGTTGAAAACACATAATTT
Found at i:3543767 original size:44 final size:44
Alignment explanation
Indices: 3543710--3543819 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
3543700 GCATATTTGG
* *
3543710 CATCCCTGCGCTTATAGGGAACG-GATCGAAGATAGCAGACCTAA
1 CATCCCTGTGCTTATAGGGAACGAGATCGAAGATAGCAG-CATAA
* * * ** *
3543754 CATTCCTGTGCTTACAGTGAA-GTAGATCGAAGATTTCAGCATGA
1 CATCCCTGTGCTTATAGGGAACG-AGATCGAAGATAGCAGCATAA
3543798 CATCCCTGTGCTTATAGGGAAC
1 CATCCCTGTGCTTATAGGGAAC
3543820 AAGTTGAAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
43 1 0.02
44 38 0.73
45 13 0.25
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
CATCCCTGTGCTTATAGGGAACGAGATCGAAGATAGCAGCATAA
Found at i:3543947 original size:173 final size:173
Alignment explanation
Indices: 3542968--3543958 Score: 574
Period size: 176 Copynumber: 5.7 Consensus size: 173
3542958 AGCATGGCAT
* ** * * * *
3542968 CCCTGTGTTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAG
1 CCCTGTGCTTATAGGGAACAAGTCAAAAACAACAGATTTGGCATCCCTGCGATTAGAGGGAACAG
* * * * *
3543033 ATCGAAGATAGCAGATCT-GACATTCCTGTGCTTACGGTGAAGTAGATCGAAGATTTCAGCATGG
66 ATCGAAGATAGCAGATATAG-CATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTCAGCATGA
* *
3543097 CATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGC--AGATTTGGCAT
130 CATCCCTGTGCTTATAGGGAACAAGTTGAAAATA-CTTA-ATTT---AA
* * * * * * * * *
3543144 CCCTGTGCTTATAGGGAAC-AGATCAAAGATAATAGATCTGACATTCCTGTGCTTACG-GTGAAG
1 CCCTGTGCTTATAGGGAACAAG-TCAAAAACAACAGATTTGGCATCCCTGCGATTA-GAGGGAA-
** * * * * * **
3543207 CAGATCGAAGATTTCAG-CAT-GGAATCCATGTGCTTACAGGGAA-CA-AGTTGAAAATAGCAG-
63 CAGATCGAAGATAGCAGATATAGCATTCC-TGTGCTTACAGTGAAGCAGA-TTGAAGATTTCAGC
* * * * * *
3543267 ATTTGGCATCCATGTGCTTATAGGGAAC-AGATCGAAGATAGC-AAATCTGACA
126 A--TGACATCCCTGTGCTTATAGGGAACAAG-TTGAAAATA-CTTAAT-TTA-A
* ** * * * *** * * * *
3543319 TTCCTGTGCTTGCAGTGAAGC-AGATCGAAGATTTCAGCA--TGACATCCCTGTGCTTATAGGGA
1 -CCCTGTGCTTATAGGGAA-CAAG-TCAAAAACAACAG-ATTTGGCATCCCTGCGATTAGAGGGA
* * * * * * * * * * **
3543381 ACA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CGGATCGAAGATAGCAG-
62 ACAGA-TCGAAGATAGCAGATATAGCATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTCAGC
* * * * * *
3543443 ATCTGACATTCCTGTGCTTACAGTGAAGC-AGATCGAAGAT--TTCAGCA-TGACA
126 A--TGACATCCCTGTGCTTATAGGGAA-CAAG-TTGAAAATACTT-A--ATTTA-A
** * * * * *
3543495 TCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACG
1 -CCCTGTGCTTATAGGGAACAAGTCAAAAACAACAGATTTGGCATCCCTGCGATTAGAGGGAACA
* * *
3543560 GATCGAAGATAGCAGATATGGCATTCCTGTGCTTACAGTAAAGCAGATTGAATATTTCAGCATGA
65 GATCGAAGATAGCAGATATAGCATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTCAGCATGA
3543625 CATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
130 CATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
* * ** * * * * *
3543669 CTCTGTGCTTATAGGGAATAAGTTGAAAACAGCATATTTGGCATCCCTGCGCTTATAGGGAACGG
1 CCCTGTGCTTATAGGGAACAAGTCAAAAACAACAGATTTGGCATCCCTGCGATTAGAGGGAACAG
** * * *
3543734 ATCGAAGATAGCAGACCTAACATTCCTGTGCTTACAGTGAAGTAGATCGAAGATTTCAGCATGAC
66 ATCGAAGATAGCAGATATAGCATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTCAGCATGAC
3543799 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
131 ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
* * * * *
3543842 CCCTGTGCTTATAGGGAAC-AGATCAAAAATAACAGATTTGGCGTCTCTG-TATTAGACGGGGAG
1 CCCTGTGCTTATAGGGAACAAG-TCAAAAACAACAGATTTGGCATCCCTGCGATTAGA--GGGAA
* * * * *
3543905 CAGATCAAAGATAGCAGATATCGCCTTCCTGAG-TTGCAGTGAAGCAGATTGAAG
63 CAGATCGAAGATAGCAGATATAGCATTCCTGTGCTTACAGTGAAGCAGATTGAAG
3543959 TCGTCAAGAG
Statistics
Matches: 649, Mismatches: 129, Indels: 77
0.76 0.15 0.09
Matches are distributed among these distances:
172 6 0.01
173 216 0.33
174 36 0.06
175 46 0.07
176 280 0.43
177 62 0.10
178 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (173 bp):
CCCTGTGCTTATAGGGAACAAGTCAAAAACAACAGATTTGGCATCCCTGCGATTAGAGGGAACAG
ATCGAAGATAGCAGATATAGCATTCCTGTGCTTACAGTGAAGCAGATTGAAGATTTCAGCATGAC
ATCCCTGTGCTTATAGGGAACAAGTTGAAAATACTTAATTTAA
Found at i:3544271 original size:38 final size:38
Alignment explanation
Indices: 3544220--3544308 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
3544210 AACCCTAATC
*
3544220 CCACCTACTCCACCACCCTTGTTGGCTACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
3544258 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
3544296 CCACCTACACCAC
1 CCACCTACTCCAC
3544309 TATGCCACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.18, C:0.51, G:0.11, T:0.20
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:3544551 original size:13 final size:13
Alignment explanation
Indices: 3544533--3544571 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
3544523 GGCTAAGGTT
*
3544533 TTCTTTTCTTTTC
1 TTCTTTTATTTTC
3544546 TTCTTTTATTTTTC
1 TTCTTTTA-TTTTC
*
3544560 TTTTTTTATTTT
1 TTCTTTTATTTT
3544572 TTTGAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTATTTTC
Found at i:3544560 original size:14 final size:14
Alignment explanation
Indices: 3544541--3544572 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3544531 TTTTCTTTTC
3544541 TTTTCTTCTTTTAT
1 TTTTCTTCTTTTAT
*
3544555 TTTTCTTTTTTTAT
1 TTTTCTTCTTTTAT
3544569 TTTT
1 TTTT
3544573 TTGAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTCTTTTAT
Found at i:3547528 original size:12 final size:12
Alignment explanation
Indices: 3547511--3547538 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3547501 TTTTTTTTAA
3547511 ATATATAAAATT
1 ATATATAAAATT
3547523 ATATATAAAATT
1 ATATATAAAATT
3547535 ATAT
1 ATAT
3547539 TAACATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATAAAATT
Found at i:3553578 original size:20 final size:20
Alignment explanation
Indices: 3553553--3553602 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3553543 TGGCTTAAAA
3553553 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3553573 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3553590 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3553603 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3558217 original size:20 final size:20
Alignment explanation
Indices: 3558192--3558241 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3558182 TGGCTTAAAA
3558192 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3558212 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3558229 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3558242 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3563062 original size:38 final size:38
Alignment explanation
Indices: 3563020--3563095 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3563010 AGTAACGGAG
3563020 ATAGGGCGATGCGCATTCCATTGCCTGGTTTGTCACAT
1 ATAGGGCGATGCGCATTCCATTGCCTGGTTTGTCACAT
*
3563058 ATAGGGTGATGCGCATTCCATTGCCTGGTTTGTCACAT
1 ATAGGGCGATGCGCATTCCATTGCCTGGTTTGTCACAT
3563096 TTTCGACAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.33
Consensus pattern (38 bp):
ATAGGGCGATGCGCATTCCATTGCCTGGTTTGTCACAT
Found at i:3563933 original size:158 final size:155
Alignment explanation
Indices: 3563614--3563938 Score: 384
Period size: 158 Copynumber: 2.1 Consensus size: 155
3563604 AAAAAAAGAA
* *
3563614 TTTTTTTCCCCTTAATTGAGACAGAATAGAAGAAATTGTGAAAACTGAAAAACAAAGAGTGAAAA
1 TTTTTTT-CCCTTAATTGAGACAGAATACAAGAAAATGTGAAAACTGAAAAACAAAGAGTGAAAA
*
3563679 CGATCAGAAACACAGATTTGAGAATTTGAAAGCAAAAAACAATTCGGATGATGAAAAAACAATGG
65 CGATCAGAAACACAGATTTGAGAATTTGAAAGCAAAAAACAATTCGGATGAAGAAAAAACAATGG
** ** * ** *
3563744 ATTTGAAAGCAGGTTTTTTTTTTGTTT
130 AAGTGAAAG-AGGTTTACTTTATAATG
* *
3563771 TTTTTTTCCCTTAATTGACAGACAGAATACAAGAAAATGTGAAAATTGAAAAACAAAGAGTGGAA
1 TTTTTTTCCCTTAATTG--AGACAGAATACAAGAAAATGTGAAAACTGAAAAACAAAGAGTGAAA
* * * *
3563836 ATGATCAGAAACACAGATTTGAGAATTTGAAAGCAAAAAAGACTTTTGGATGAAGAAAAAACAAT
64 ACGATCAGAAACACAGATTTGAGAATTTGAAAGCAAAAAACA-ATTCGGATGAAGAAAAAACAAT
***
3563901 GGCAAGT-CTTG-GGTTTAACTTTATAATG
128 GG-AAGTGAAAGAGGTTT-ACTTTATAATG
3563929 TTTTTCTTCC
1 TTTTT-TTCC
3563939 TCATTAGTTT
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
156 10 0.07
157 12 0.08
158 92 0.65
159 26 0.18
160 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (155 bp):
TTTTTTTCCCTTAATTGAGACAGAATACAAGAAAATGTGAAAACTGAAAAACAAAGAGTGAAAAC
GATCAGAAACACAGATTTGAGAATTTGAAAGCAAAAAACAATTCGGATGAAGAAAAAACAATGGA
AGTGAAAGAGGTTTACTTTATAATG
Found at i:3571588 original size:20 final size:20
Alignment explanation
Indices: 3571560--3571601 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3571550 AAGGTAAATA
3571560 TAAAAATATTTTAATA-TTTT
1 TAAAAATATTTT-ATACTTTT
*
3571580 TAAATATATTTTATACTTTT
1 TAAAAATATTTTATACTTTT
3571600 TA
1 TA
3571602 GAATTCGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAAAATATTTTATACTTTT
Found at i:3574599 original size:30 final size:30
Alignment explanation
Indices: 3574545--3574607 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
3574535 TGACGAAAAT
* *
3574545 ATGAGAGAATAAGAAACGTAAATAACTAAGTA
1 ATGAGAAAATAAGAAAAGTAAATAA-TAA-TA
3574577 ATGAGAAAATAA-AAAAGT-AATAATAATA
1 ATGAGAAAATAAGAAAAGTAAATAATAATA
3574605 ATG
1 ATG
3574608 CAATGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 3 0.10
30 5 0.17
31 5 0.17
32 11 0.38
ACGTcount: A:0.60, C:0.03, G:0.16, T:0.21
Consensus pattern (30 bp):
ATGAGAAAATAAGAAAAGTAAATAATAATA
Found at i:3577935 original size:17 final size:17
Alignment explanation
Indices: 3577910--3577942 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3577900 TTTATATAAA
3577910 TTTAAAAAAATTAAAAT
1 TTTAAAAAAATTAAAAT
*
3577927 TTTATAAAAATTAAAA
1 TTTAAAAAAATTAAAA
3577943 AATAGAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAAAAATTAAAAT
Found at i:3582608 original size:17 final size:18
Alignment explanation
Indices: 3582586--3582621 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3582576 GGTACATTAC
3582586 AATTGATTTAAATT-AAA
1 AATTGATTTAAATTCAAA
3582603 AATTGATTTAAATTCAAA
1 AATTGATTTAAATTCAAA
3582621 A
1 A
3582622 CAAATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (18 bp):
AATTGATTTAAATTCAAA
Found at i:3583497 original size:17 final size:17
Alignment explanation
Indices: 3583477--3583518 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3583467 TTTAATCGTC
3583477 TTTTATTTCAGGTATAG
1 TTTTATTTCAGGTATAG
3583494 TTTTATTTCAGGTATAG
1 TTTTATTTCAGGTATAG
3583511 TTTTATTT
1 TTTTATTT
3583519 TTATTTCAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTTATTTCAGGTATAG
Found at i:3587807 original size:19 final size:19
Alignment explanation
Indices: 3587783--3587819 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3587773 AGAAGATTAT
3587783 CAATTGTGACAAATAAAAG
1 CAATTGTGACAAATAAAAG
3587802 CAATTGTGACAAATAAAA
1 CAATTGTGACAAATAAAA
3587820 TCGAATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.22
Consensus pattern (19 bp):
CAATTGTGACAAATAAAAG
Found at i:3589993 original size:16 final size:15
Alignment explanation
Indices: 3589972--3590019 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3589962 GATGTGAATA
3589972 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
3589988 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
3590003 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3590019 A
1 A
3590020 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3589995 original size:24 final size:24
Alignment explanation
Indices: 3589968--3590023 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3589958 TAATGATGTG
*
3589968 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
3589992 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
3590016 AATAATAA
1 AATAATAA
3590024 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:3590002 original size:8 final size:8
Alignment explanation
Indices: 3589968--3590019 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3589958 TAATGATGTG
*
3589968 AATAATAA
1 AATATTAA
3589976 AATATATAA
1 AATAT-TAA
3589985 AATA-TAA
1 AATATTAA
3589992 AATATTAA
1 AATATTAA
*
3590000 AATATCAA
1 AATATTAA
*
3590008 AATATTAG
1 AATATTAA
3590016 AATA
1 AATA
3590020 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:3590195 original size:25 final size:25
Alignment explanation
Indices: 3590167--3590378 Score: 131
Period size: 25 Copynumber: 8.7 Consensus size: 25
3590157 TAAATACGTG
*
3590167 ATAGTATTAAAAATATGTACATAAT
1 ATAGTATTAAAAATATATACATAAT
* *
3590192 ATAGTGTTAAAAATACATACATAAT
1 ATAGTATTAAAAATATATACATAAT
* *
3590217 ATAG--TT-AAGATATATACATAAG
1 ATAGTATTAAAAATATATACATAAT
** *
3590239 ATAACATGTAAAATATATATATAAATAAT
1 ATAGTAT-T-AAA-A-ATATATACATAAT
* * *
3590268 ATAATATTAAAGATATATACATAAA
1 ATAGTATTAAAAATATATACATAAT
* *
3590293 ATAGTA-T-AATATATATACGTAAT
1 ATAGTATTAAAAATATATACATAAT
* * *
3590316 ATAGAATT-TAAA-ATATACCT-A-
1 ATAGTATTAAAAATATATACATAAT
*
3590337 ATA-TATTAAAAGA-ATATATATAAT
1 ATAGTATTAAAA-ATATATACATAAT
*
3590361 ATAATATTAAGAAATATA
1 ATAGTATTAA-AAATATA
3590379 ATAATAACAA
Statistics
Matches: 146, Mismatches: 26, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
20 3 0.02
21 5 0.03
22 24 0.16
23 28 0.19
24 8 0.05
25 50 0.34
26 5 0.03
27 5 0.03
28 1 0.01
29 17 0.12
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (25 bp):
ATAGTATTAAAAATATATACATAAT
Found at i:3590266 original size:29 final size:29
Alignment explanation
Indices: 3590226--3590292 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3590216 TATAGTTAAG
*
3590226 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* *
3590255 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
*
3590284 ATACATAAA
1 ATATATAAA
3590293 ATAGTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:3590267 original size:76 final size:77
Alignment explanation
Indices: 3590187--3590332 Score: 188
Period size: 76 Copynumber: 1.9 Consensus size: 77
3590177 AAATATGTAC
* * *
3590187 ATAATATAGTGTTAAAAATACATACATAATATAGT-TAAGATATATACATAAGATA-ACATGTAA
1 ATAATATAATATTAAAAATACATACATAAAATAGTATAAGATATATACATAAGATAGA-ATGTAA
3590250 AATATATATATAA
65 AATATATATATAA
* * * * * *
3590263 ATAATATAATATTAAAGATATATACATAAAATAGTATAATATATATACGTAATATAGAATTTAAA
1 ATAATATAATATTAAAAATACATACATAAAATAGTATAAGATATATACATAAGATAGAATGTAAA
3590328 ATATA
66 ATATA
3590333 CCTAATATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
76 30 0.51
77 28 0.47
78 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (77 bp):
ATAATATAATATTAAAAATACATACATAAAATAGTATAAGATATATACATAAGATAGAATGTAAA
ATATATATATAA
Found at i:3590283 original size:27 final size:29
Alignment explanation
Indices: 3590226--3590304 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
3590216 TATAGTTAAG
* * * *
3590226 ATATATACATAAGATAACATGTAAAATAT
1 ATATATAAATAATATAATATGTAAAAGAT
3590255 ATATATAAATAATATAATAT-T-AAAGAT
1 ATATATAAATAATATAATATGTAAAAGAT
*
3590282 ATATACATAAAATAGTATAATAT
1 ATAT--AT-AAATAATATAATAT
3590305 ATATACGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
27 9 0.21
28 1 0.02
29 19 0.45
30 13 0.31
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (29 bp):
ATATATAAATAATATAATATGTAAAAGAT
Found at i:3590382 original size:23 final size:24
Alignment explanation
Indices: 3590171--3590384 Score: 88
Period size: 23 Copynumber: 8.9 Consensus size: 24
3590161 TACGTGATAG
*
3590171 TATTAA-AAATATGTACATAATATAG
1 TATTAAGAAATA--TACATAATATAA
*
3590196 TGTTAA-AAATACATACATAATAT-A
1 TATTAAGAAAT--ATACATAATATAA
* * *
3590220 -GTTAAGATATATACATAAGATAA
1 TATTAAGAAATATACATAATATAA
* * *
3590243 CATGTAAAATATATATATAAATAATATAA
1 TAT-T--AAGA-A-ATATACATAATATAA
* * *
3590272 TATTAAAGATATATACATAAAATAG
1 TATT-AAGAAATATACATAATATAA
* * *
3590297 TA-TAATATATATACGTAATATAGA
1 TATTAAGAAATATACATAATATA-A
* * *
3590321 -ATTTA-AAATATACCTAATATAT
1 TATTAAGAAATATACATAATATAA
* *
3590343 TA-AAAG-AATATATATAATATAA
1 TATTAAGAAATATACATAATATAA
3590365 TATTAAGAAATATA-ATAATA
1 TATTAAGAAATATACATAATA
3590385 ACAAAAAAAG
Statistics
Matches: 144, Mismatches: 29, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
22 26 0.18
23 47 0.33
24 13 0.09
25 34 0.24
27 8 0.06
28 1 0.01
29 15 0.10
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
TATTAAGAAATATACATAATATAA
Found at i:3590816 original size:30 final size:30
Alignment explanation
Indices: 3590780--3590924 Score: 245
Period size: 30 Copynumber: 4.8 Consensus size: 30
3590770 TAGGTACAAG
* *
3590780 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
3590810 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
3590840 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
3590870 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
3590900 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
3590925 TGAGAAAAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 109 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:3591692 original size:14 final size:14
Alignment explanation
Indices: 3591673--3591722 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3591663 GAGTTGATTT
* *
3591673 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
3591687 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
3591702 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
3591716 TT-AAAAA
1 TTGAAAAA
3591723 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:3593407 original size:12 final size:12
Alignment explanation
Indices: 3593387--3593422 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3593377 TGGGATATGC
*
3593387 AATGTATGAATG
1 AATGCATGAATG
3593399 AATGCATGAATG
1 AATGCATGAATG
3593411 AATGCATGAATG
1 AATGCATGAATG
3593423 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:3594972 original size:16 final size:15
Alignment explanation
Indices: 3594951--3594998 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3594941 GATGTGAATA
3594951 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
3594967 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
3594982 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3594998 A
1 A
3594999 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3594974 original size:24 final size:24
Alignment explanation
Indices: 3594947--3595002 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3594937 TAATGATGTG
*
3594947 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
3594971 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
3594995 AATAATAA
1 AATAATAA
3595003 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:3594981 original size:8 final size:8
Alignment explanation
Indices: 3594947--3594998 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3594937 TAATGATGTG
*
3594947 AATAATAA
1 AATATTAA
3594955 AATATATAA
1 AATAT-TAA
3594964 AATA-TAA
1 AATATTAA
3594971 AATATTAA
1 AATATTAA
*
3594979 AATATCAA
1 AATATTAA
*
3594987 AATATTAG
1 AATATTAA
3594995 AATA
1 AATA
3594999 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:3595212 original size:22 final size:24
Alignment explanation
Indices: 3595149--3595213 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
3595139 CGTGATAATA
*
3595149 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
3595174 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
3595197 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
3595214 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:3595238 original size:30 final size:29
Alignment explanation
Indices: 3595202--3595269 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
3595192 TATAGTTAAG
*
3595202 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
3595232 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
*
3595261 ATACATAAA
1 ATATATAAA
3595270 ATAGTATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:3595260 original size:25 final size:24
Alignment explanation
Indices: 3595143--3595361 Score: 96
Period size: 23 Copynumber: 9.0 Consensus size: 24
3595133 TAAATACGTG
* *
3595143 ATAATATTAAAAATATGTACATAAT
1 ATAATATT-AAGATATATACATAAT
* * * *
3595168 ATAGTGTTAAAAATACATACATAAT
1 ATAATATT-AAGATATATACATAAT
* *
3595193 AT-A-GTTAAGATATATACATAAG
1 ATAATATTAAGATATATACATAAT
* * *
3595215 ATAACATGTAAAAATATATATATAAATAAT
1 ATAATAT-T----A-AGATATATACATAAT
*
3595245 ATAATATTAAAGATATATACATAAA
1 ATAATATT-AAGATATATACATAAT
* * *
3595270 ATAGTA-TAATATATATACGTAAT
1 ATAATATTAAGATATATACATAAT
*
3595293 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATA-TTAAGATATATACATAAT
* * *
3595316 ATATTA-AAAGA-ATATATATAAT
1 ATAATATTAAGATATATACATAAT
*
3595338 ATAATATTAAGAAATATA-ATAAT
1 ATAATATTAAGATATATACATAAT
3595361 A
1 A
3595362 ACAAAAAAGG
Statistics
Matches: 151, Mismatches: 28, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
21 2 0.01
22 30 0.20
23 45 0.30
24 8 0.05
25 44 0.29
26 2 0.01
29 2 0.01
30 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
ATAATATTAAGATATATACATAAT
Found at i:3595886 original size:30 final size:30
Alignment explanation
Indices: 3595850--3595934 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
3595840 TAGGTACAAG
* *
3595850 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAAT
3595880 TGGTGGTGGAAAAGGTGTGGCTAGTGGAAT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAAT
*
3595910 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
3595935 TGAGAAAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAAT
Found at i:3597956 original size:22 final size:22
Alignment explanation
Indices: 3597929--3597984 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
3597919 CGGGGTGACA
3597929 ACACAGGCGTGTCACCTAGGCC
1 ACACAGGCGTGTCACCTAGGCC
3597951 ACACAGGCGTGTCACCTAGGCC
1 ACACAGGCGTGTCACCTAGGCC
3597973 ACACAGGCGTGT
1 ACACAGGCGTGT
3597985 GGTACTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.34, G:0.29, T:0.14
Consensus pattern (22 bp):
ACACAGGCGTGTCACCTAGGCC
Found at i:3610011 original size:6 final size:6
Alignment explanation
Indices: 3610002--3610044 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
3609992 TGTCTTTAGA
3610002 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT
3610045 ATCCTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:3618385 original size:136 final size:136
Alignment explanation
Indices: 3618141--3618414 Score: 548
Period size: 136 Copynumber: 2.0 Consensus size: 136
3618131 TAAACAAAAA
3618141 TAACTATTTTAATAGTTTACTCTAAAAATTAATAATAGAATTTATCCATAGATAAGAGTTCGATA
1 TAACTATTTTAATAGTTTACTCTAAAAATTAATAATAGAATTTATCCATAGATAAGAGTTCGATA
3618206 AAGTCTTACTTTTTGGAGTATTTTCTTTACAATATCCTTAATAAATTAGTGGAAGATAAAGACAT
66 AAGTCTTACTTTTTGGAGTATTTTCTTTACAATATCCTTAATAAATTAGTGGAAGATAAAGACAT
3618271 CCTCTT
131 CCTCTT
3618277 TAACTATTTTAATAGTTTACTCTAAAAATTAATAATAGAATTTATCCATAGATAAGAGTTCGATA
1 TAACTATTTTAATAGTTTACTCTAAAAATTAATAATAGAATTTATCCATAGATAAGAGTTCGATA
3618342 AAGTCTTACTTTTTGGAGTATTTTCTTTACAATATCCTTAATAAATTAGTGGAAGATAAAGACAT
66 AAGTCTTACTTTTTGGAGTATTTTCTTTACAATATCCTTAATAAATTAGTGGAAGATAAAGACAT
3618407 CCTCTT
131 CCTCTT
3618413 TA
1 TA
3618415 TCTTTATTTG
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 138 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (136 bp):
TAACTATTTTAATAGTTTACTCTAAAAATTAATAATAGAATTTATCCATAGATAAGAGTTCGATA
AAGTCTTACTTTTTGGAGTATTTTCTTTACAATATCCTTAATAAATTAGTGGAAGATAAAGACAT
CCTCTT
Found at i:3620131 original size:15 final size:15
Alignment explanation
Indices: 3620107--3620154 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3620097 ACGACCATTT
*
3620107 AAAATTTTAAAATTCA
1 AAAATATTAAAATT-A
3620123 AAAA-ATTAAAAATTA
1 AAAATATT-AAAATTA
*
3620138 AAAATAATAAAATTA
1 AAAATATTAAAATTA
3620153 AA
1 AA
3620155 GAAAAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATTAAAATTA
Found at i:3620531 original size:20 final size:20
Alignment explanation
Indices: 3620488--3620532 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
3620478 TTTCATTTTT
*
3620488 TATTTTTTTAATATTTTCTG
1 TATTTTTTGAATATTTTCTG
3620508 -ATTTTTTGAA-ATTCTTCTG
1 TATTTTTTGAATATT-TTCTG
3620527 TATTTT
1 TATTTT
3620533 ATCTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (20 bp):
TATTTTTTGAATATTTTCTG
Found at i:3624807 original size:21 final size:23
Alignment explanation
Indices: 3624781--3624823 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
3624771 AGATTTTAAT
3624781 AATTAAAAAT-AT-TAAATATTA
1 AATTAAAAATAATATAAATATTA
3624802 AATTAAAAATAATATAAATATT
1 AATTAAAAATAATATAAATATT
3624824 TCAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTAAAAATAATATAAATATTA
Found at i:3625975 original size:3 final size:3
Alignment explanation
Indices: 3625967--3626001 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3625957 ATATAGATAG
3625967 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3626002 GGTAGTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3627408 original size:20 final size:20
Alignment explanation
Indices: 3627379--3627421 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3627369 GTTCCTGCTC
* * *
3627379 TGCTTTGTTTCTGTCTTGTT
1 TGCTTCGTTTCTATCTCGTT
3627399 TGCTTCGTTTCTATCTCGTT
1 TGCTTCGTTTCTATCTCGTT
3627419 TGC
1 TGC
3627422 AGGCGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.21, G:0.19, T:0.58
Consensus pattern (20 bp):
TGCTTCGTTTCTATCTCGTT
Found at i:3640627 original size:350 final size:341
Alignment explanation
Indices: 3639968--3640627 Score: 900
Period size: 350 Copynumber: 1.9 Consensus size: 341
3639958 TACTTATATT
*
3639968 ACTGTTACAAACTCTTAGGCTTAATTCTATGATTTTATTTTATTTTTTCTTTATTTAGACTTGTT
1 ACTGTTACAAACTCTTAGGCTTAATTCTAGGATTTTATTTTATTTTTTCTTTATTTAGACTTGTT
3640033 GTGAATATAAAAATAGATAAATCATGTTAGAGTTTATATTAATGCCTACTTCTTTACCTAGTTAA
66 GTGAATATAAAAATAGATAAATCATGTTAGAGTTTATATTAATGCCTACTTCTTTACCTAGTTAA
* *
3640098 ACTCTTGTAACTTGTACAATGTTCCCATGAGTAAATCTATGAGGTTTTCTTTCAAATTCTACTTT
131 ACTCTTGTAACTTGTACAATGTTCCCATGAGTAAATCTATAAGGTTTTCTCTCAAATTCTACTTT
** *
3640163 TGTTACATGGAATCAGAGCTAAGGGATCGATTTTAGAGTATAAGTCTCATCGAATTAATCGCAAA
196 CATTACATGGAATCAGAGCTAAGGGATCAATTTTAGAGTATAAGTCTCATCGAATTAATCGCAAA
* **
3640228 ATAGTGAGTTTTTAGGGTATTTTCGTTAACTACCAAGGGTTGTCCTTTTTATCTCACCACCAGCC
261 ATAGCGAGTTTAGAGGGTATTTTCGTTAACTACCAAGGGTTGTCCTTTTTATCTCACCACCAGCC
3640293 TAGGGAGGTGCGCAAG
326 TAGGGAGGTGCGCAAG
*
3640309 ACTGTTACAAACTCTTAGGCTTAATTCTAGGATTTTATTTTCTTTTCTT-TTCGTATTTAGACTT
1 ACTGTTACAAACTCTTAGGCTTAATTCTAGGATTTTATTTTATTTT-TTCTT--TATTTAGACTT
* * * * **
3640373 GTTGTGAATA-AAATATTAGATATATCATGTTCGGGTTTATATTAACT-TTTACTTCTTT-CTCT
63 GTTGTGAATATAAA-AATAGATAAATCATGTTAGAGTTTATATTAA-TGCCTACTTCTTTAC-CT
* *
3640435 AGTTAAACTCTTGTAACTTGTATATATGTAAATATTCCCATGTGTAAATCTATAAGGTTTTCTCT
125 AGTTAAACTCTTGTAACTTGTACA-ATG------TTCCCATGAGTAAATCTATAAGGTTTTCTCT
* * * * * *
3640500 CAAATTCTACTTTCATTACATGGTA-CTGGAGCTAAGGGATCAATTTTAGAGTCTGAGTTTCATT
183 CAAATTCTACTTTCATTACATGGAATC-AGAGCTAAGGGATCAATTTTAGAGTATAAGTCTCATC
* * *
3640564 GAATTTATCGCAAAATAGCGAGTTCTAGAGGGTATTTTTGTTGACTACCAAGGGTTG-CCTTTTT
247 GAATTAATCGCAAAATAGCGAGTT-TAGAGGGTATTTTCGTTAACTACCAAGGGTTGTCCTTTTT
3640628 TAATCTCATC
Statistics
Matches: 277, Mismatches: 27, Indels: 21
0.85 0.08 0.06
Matches are distributed among these distances:
341 46 0.17
342 6 0.02
343 82 0.30
344 4 0.01
349 1 0.00
350 110 0.40
351 28 0.10
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (341 bp):
ACTGTTACAAACTCTTAGGCTTAATTCTAGGATTTTATTTTATTTTTTCTTTATTTAGACTTGTT
GTGAATATAAAAATAGATAAATCATGTTAGAGTTTATATTAATGCCTACTTCTTTACCTAGTTAA
ACTCTTGTAACTTGTACAATGTTCCCATGAGTAAATCTATAAGGTTTTCTCTCAAATTCTACTTT
CATTACATGGAATCAGAGCTAAGGGATCAATTTTAGAGTATAAGTCTCATCGAATTAATCGCAAA
ATAGCGAGTTTAGAGGGTATTTTCGTTAACTACCAAGGGTTGTCCTTTTTATCTCACCACCAGCC
TAGGGAGGTGCGCAAG
Found at i:3642514 original size:42 final size:42
Alignment explanation
Indices: 3642467--3642555 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
3642457 TCCTAATTGG
*
3642467 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
3642509 GAAAATAGTTCTCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
3642551 TAAAA
1 GAAAA
3642556 ATATTTCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:3642575 original size:43 final size:42
Alignment explanation
Indices: 3642482--3642577 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
3642472 TAGTTCCCTT
* * ***
3642482 ATTCTAATAAACTACTAAAATATAAAAGAAAATAGTTCTCTT
1 ATTCTAATAAACTACTAAAAGATAAAAAAAAATAGTTCTAGA
*
3642524 ATTCTAATAAACTACTAAAAGATAAAATAAAAATATTTCTAGA
1 ATTCTAATAAACTACTAAAAGATAAAA-AAAAATAGTTCTAGA
3642567 ATAT-TAATAAA
1 AT-TCTAATAAA
3642578 ACTTGTCTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 26 0.57
43 19 0.41
44 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (42 bp):
ATTCTAATAAACTACTAAAAGATAAAAAAAAATAGTTCTAGA
Found at i:3642605 original size:19 final size:18
Alignment explanation
Indices: 3642583--3642619 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3642573 ATAAAACTTG
3642583 TCTACCTAAATAAGATTTA
1 TCTACCTAAATAA-ATTTA
3642602 TCTACCTAAATAAATTTA
1 TCTACCTAAATAAATTTA
3642620 AAATATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (18 bp):
TCTACCTAAATAAATTTA
Found at i:3646478 original size:42 final size:42
Alignment explanation
Indices: 3646419--3646507 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
3646409 TCCTAATTGG
*
3646419 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
* *
3646461 GAAAATAGTTCTCTTATTCTAATAAATTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
3646503 TAAAA
1 GAAAA
3646508 ATATTCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:3646554 original size:19 final size:18
Alignment explanation
Indices: 3646532--3646571 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
3646522 TTAATAAAAC
3646532 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
3646551 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
3646569 TTA
1 TTA
3646572 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:3665052 original size:19 final size:20
Alignment explanation
Indices: 3665028--3665065 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3665018 TAATTAGATT
3665028 TTAATTAA-GTAAATTTAGC
1 TTAATTAAGGTAAATTTAGC
*
3665047 TTAATTAAGGTTAATTTAG
1 TTAATTAAGGTAAATTTAG
3665066 TGAAAGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (20 bp):
TTAATTAAGGTAAATTTAGC
Found at i:3668894 original size:20 final size:20
Alignment explanation
Indices: 3668869--3668948 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 20
3668859 TCAAACGGTA
3668869 TTTTTAATAATTTTAAATATTTTT
1 TTTTTAATAATTTTAAATA----T
**
3668893 TATTTTAATAATTTTTTATAT
1 T-TTTTAATAATTTTAAATAT
3668914 TTTTTAAATAATTTTATAAT-T
1 TTTTT-AATAATTTTA-AATAT
*
3668935 TTTATAATAATTTT
1 TTTTTAATAATTTT
3668949 TTAATAATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.27
21 16 0.33
22 2 0.04
24 1 0.02
25 16 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAATAATTTTAAATAT
Found at i:3668899 original size:16 final size:16
Alignment explanation
Indices: 3668878--3668911 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3668868 ATTTTTAATA
3668878 ATTTTAA-ATATTTTTT
1 ATTTTAATA-ATTTTTT
3668894 ATTTTAATAATTTTTT
1 ATTTTAATAATTTTTT
3668910 AT
1 AT
3668912 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTAATAATTTTTT
Found at i:3668902 original size:25 final size:25
Alignment explanation
Indices: 3668870--3668919 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3668860 CAAACGGTAT
3668870 TTTTAATAATTTTAAATATTTTTTA
1 TTTTAATAATTTTAAATATTTTTTA
**
3668895 TTTTAATAATTTTTTATATTTTTTA
1 TTTTAATAATTTTAAATATTTTTTA
3668920 AATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTAATAATTTTAAATATTTTTTA
Found at i:3668909 original size:11 final size:11
Alignment explanation
Indices: 3668895--3668956 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
3668885 ATATTTTTTA
3668895 TTTTAATAATT
1 TTTTAATAATT
3668906 TTTT-AT-ATT
1 TTTTAATAATT
3668915 TTTTAAATAA--
1 TTTT-AATAATT
3668925 TTTT-ATAATT
1 TTTTAATAATT
3668935 TTTATAATAATT
1 TTT-TAATAATT
3668947 TTTTAATAAT
1 TTTTAATAAT
3668957 CATTTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
8 4 0.09
9 7 0.16
10 9 0.20
11 14 0.32
12 10 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:3668925 original size:21 final size:21
Alignment explanation
Indices: 3668868--3668956 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 21
3668858 TTCAAACGGT
*
3668868 ATTTTTAATAA-TTTTAAAT-
1 ATTTTTTATAATTTTTAAATA
3668887 A-TTTTT-T-A-TTTT-AATA
1 ATTTTTTATAATTTTTAAATA
*
3668903 ATTTTTTATATTTTTTAAATA
1 ATTTTTTATAATTTTTAAATA
3668924 A--TTTTATAATTTTTATAATA
1 ATTTTTTATAATTTTTA-AATA
3668944 ATTTTTTAATAAT
1 ATTTTTT-ATAAT
3668957 CATTTAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
15 3 0.05
16 6 0.11
17 6 0.11
18 5 0.09
19 14 0.25
20 9 0.16
21 5 0.09
22 4 0.07
23 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTTATAATTTTTAAATA
Found at i:3668953 original size:20 final size:19
Alignment explanation
Indices: 3668895--3668953 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 19
3668885 ATATTTTTTA
3668895 TTTTAATAATTTTTTATATT
1 TTTTAATAATTTTTTA-ATT
*
3668915 TTTTAAATAATTTTATAATT
1 TTTT-AATAATTTTTTAATT
3668935 TTTATAATAATTTTTTAAT
1 TTT-TAATAATTTTTTAAT
3668954 AATCATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAATAATTTTTTAATT
Found at i:3673084 original size:19 final size:18
Alignment explanation
Indices: 3673033--3673088 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
3673023 TGAAAATAAA
3673033 TATAATTG-TAATAATTT
1 TATAATTGTTAATAATTT
*
3673050 T-TAATCAT-TTATTAATTT
1 TATAAT--TGTTAATAATTT
3673068 TATAATTGTTAAATAATTT
1 TATAATTGTT-AATAATTT
3673087 TA
1 TA
3673089 AAAATTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 4 0.13
17 2 0.06
18 12 0.39
19 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TATAATTGTTAATAATTT
Found at i:3673226 original size:21 final size:21
Alignment explanation
Indices: 3673202--3673252 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3673192 CGCTGTTTCT
* *
3673202 AATCTCACTGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
3673223 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
3673244 AATCTCACC
1 AATCTCACC
3673253 ACCACCGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.37, G:0.08, T:0.24
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:3674740 original size:23 final size:23
Alignment explanation
Indices: 3674714--3674783 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
3674704 GAATCTATGT
3674714 AATATAGTATTGAAAATATATAC
1 AATATAGTATTGAAAATATATAC
*
3674737 AATAT-GATATTGAAAGGATAGATATAT
1 AATATAG-TATTGAAA--AT--ATATAC
3674764 AATATAGTA-TGAAAAGTATA
1 AATATAGTATTGAAAA-TATA
3674784 GGTACATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
22 1 0.03
23 16 0.41
24 1 0.03
25 3 0.08
26 5 0.13
27 12 0.31
28 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.33
Consensus pattern (23 bp):
AATATAGTATTGAAAATATATAC
Found at i:3675462 original size:22 final size:23
Alignment explanation
Indices: 3675436--3675508 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 23
3675426 GTACAAAGGG
3675436 TATATA-ACTAATAATAT-TAAAA
1 TATATACA-TAATAATATATAAAA
*
3675458 TATATACATAATAGTATATAAAA
1 TATATACATAATAATATATAAAA
* *
3675481 -A-AAACATAATACTA-A-AAATA
1 TATATACATAATAATATATAAA-A
3675501 TATATACA
1 TATATACA
3675509 CATAATACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 3 0.07
20 2 0.05
21 12 0.29
22 19 0.45
23 6 0.14
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (23 bp):
TATATACATAATAATATATAAAA
Found at i:3675643 original size:3 final size:3
Alignment explanation
Indices: 3675635--3675696 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
3675625 TTACTAATGT
*
3675635 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3675683 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
3675697 TTGGAATGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3683501 original size:3 final size:3
Alignment explanation
Indices: 3683493--3683520 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3683483 ATGCATTTGC
3683493 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3683521 AAATTGTCTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3691411 original size:15 final size:15
Alignment explanation
Indices: 3691387--3691436 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3691377 TTGGCCTAAC
3691387 ATCAGGAGCTTTGGA
1 ATCAGGAGCTTTGGA
* **
3691402 ATCAGCAGCTTCAGA
1 ATCAGGAGCTTTGGA
* *
3691417 TTCAGGAACTTTGGA
1 ATCAGGAGCTTTGGA
3691432 ATCAG
1 ATCAG
3691437 AAGGGGCTGG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (15 bp):
ATCAGGAGCTTTGGA
Found at i:3691474 original size:6 final size:6
Alignment explanation
Indices: 3691460--3691554 Score: 91
Period size: 6 Copynumber: 15.8 Consensus size: 6
3691450 CAGATTTGGG
* * * * * * *
3691460 GATGAT GATGGT GATGAT GATGGA GATGGA GATGGG GATGAT GATGGG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
* * * *
3691508 GATGAT GATGGT GATGAT GATGGG GATGAT GATGGT GATGGT GATGG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGG
3691555 GCCTAAGTCC
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.25, C:0.00, G:0.47, T:0.27
Consensus pattern (6 bp):
GATGGT
Found at i:3691475 original size:12 final size:12
Alignment explanation
Indices: 3691456--3691555 Score: 139
Period size: 12 Copynumber: 8.3 Consensus size: 12
3691446 GGGCCAGATT
3691456 TGGGGATGATGA
1 TGGGGATGATGA
*
3691468 TGGTGATGATGA
1 TGGGGATGATGA
*
3691480 TGGAGATGGA-GA
1 TGGGGAT-GATGA
3691492 TGGGGATGATGA
1 TGGGGATGATGA
3691504 TGGGGATGATGA
1 TGGGGATGATGA
*
3691516 TGGTGATGATGA
1 TGGGGATGATGA
3691528 TGGGGATGATGA
1 TGGGGATGATGA
* *
3691540 TGGTGATGGTGA
1 TGGGGATGATGA
3691552 TGGG
1 TGGG
3691556 CCTAAGTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
11 2 0.03
12 74 0.95
13 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.49, T:0.27
Consensus pattern (12 bp):
TGGGGATGATGA
Found at i:3691493 original size:24 final size:24
Alignment explanation
Indices: 3691456--3691555 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
3691446 GGGCCAGATT
3691456 TGGGGATGATGATGGTGATGATGA
1 TGGGGATGATGATGGTGATGATGA
* *
3691480 TGGAGATGGA-GATGGGGATGATGA
1 TGGGGAT-GATGATGGTGATGATGA
3691504 TGGGGATGATGATGGTGATGATGA
1 TGGGGATGATGATGGTGATGATGA
*
3691528 TGGGGATGATGATGGTGATGGTGA
1 TGGGGATGATGATGGTGATGATGA
3691552 TGGG
1 TGGG
3691556 CCTAAGTCCG
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
23 2 0.03
24 65 0.94
25 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.49, T:0.27
Consensus pattern (24 bp):
TGGGGATGATGATGGTGATGATGA
Found at i:3696416 original size:30 final size:28
Alignment explanation
Indices: 3696380--3696446 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
3696370 CAATTGGACC
3696380 TTAAATTTTAA-AATCTAAAAATAAAAAAAA
1 TTAAATTTTAAGAA--TAAAAAT-AAAAAAA
* *
3696410 TTAAATTCTTAAGAATAAATATAAAATAA
1 TTAAATT-TTAAGAATAAAAATAAAAAAA
3696439 TTAAATTT
1 TTAAATTT
3696447 CAATTTTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.03
29 13 0.39
30 13 0.39
31 4 0.12
32 2 0.06
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (28 bp):
TTAAATTTTAAGAATAAAAATAAAAAAA
Found at i:3703423 original size:23 final size:23
Alignment explanation
Indices: 3703380--3703423 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3703370 ATTTAATTAT
* *
3703380 ATTTTATTTTTATTTTGAATTTG
1 ATTTGATTTTTATTTTAAATTTG
3703403 ATTTGATTTTT-TTCTTAAATT
1 ATTTGATTTTTATT-TTAAATT
3703424 ATACATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTGATTTTTATTTTAAATTTG
Found at i:3713585 original size:24 final size:24
Alignment explanation
Indices: 3713552--3713610 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
3713542 ATCTCTTAAG
*
3713552 ATTTAGTAGAACAATATA-TTTAGC
1 ATTTATTAGAACAATATATTTTA-C
*
3713576 ATTTATTAGAATAATATATTTTAC
1 ATTTATTAGAACAATATATTTTAC
*
3713600 ATTAATTAGAA
1 ATTTATTAGAA
3713611 TTAGGCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (24 bp):
ATTTATTAGAACAATATATTTTAC
Found at i:3714016 original size:20 final size:20
Alignment explanation
Indices: 3713976--3714015 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3713966 TGTCACTAAA
*
3713976 TAATCAAATTAAATTTATTT
1 TAATCAAATTAAATTAATTT
3713996 TAATCAAA-TAAATTAATTT
1 TAATCAAATTAAATTAATTT
3714015 T
1 T
3714016 TTGACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATCAAATTAAATTAATTT
Found at i:3719074 original size:32 final size:32
Alignment explanation
Indices: 3719038--3719102 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3719028 TGTATGCATT
3719038 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
3719070 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
3719102 T
1 T
3719103 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:3720612 original size:26 final size:26
Alignment explanation
Indices: 3720583--3720635 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3720573 TTTACAATTT
3720583 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* * *
3720609 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3720635 T
1 T
3720636 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3725496 original size:9 final size:9
Alignment explanation
Indices: 3725476--3725508 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3725466 ATAATGTATA
3725476 ATATAA-AT
1 ATATAAGAT
3725484 ATATAAGAT
1 ATATAAGAT
*
3725493 ATATGAGAT
1 ATATAAGAT
3725502 ATATAAG
1 ATATAAG
3725509 TTAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (9 bp):
ATATAAGAT
Found at i:3725837 original size:18 final size:19
Alignment explanation
Indices: 3725814--3725859 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3725804 TAATATATAG
*
3725814 ATAAAAATG-CGTAATAAT
1 ATAAAAATGACGTAATAAC
*
3725832 ATAAAAATGACTTAATAAC
1 ATAAAAATGACGTAATAAC
3725851 ATATAAAAT
1 ATA-AAAAT
3725860 AATTACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 10 0.42
20 5 0.21
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (19 bp):
ATAAAAATGACGTAATAAC
Found at i:3725904 original size:11 final size:11
Alignment explanation
Indices: 3725888--3725966 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
3725878 AAAAGCATAT
3725888 ATATATAAATA
1 ATATATAAATA
3725899 ATATAT-AATA
1 ATATATAAATA
*
3725909 A-ATAATAAACA
1 ATAT-ATAAATA
3725920 TATAATATAATAATA
1 -AT-ATAT-A-AATA
3725935 ATATATAAATA
1 ATATATAAATA
3725946 ATGATGATAAAATA
1 AT-AT-AT-AAATA
3725960 ATA-ATAA
1 ATATATAA
3725967 CTTGTGAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 21
0.71 0.03 0.27
Matches are distributed among these distances:
9 2 0.04
10 9 0.16
11 17 0.30
12 4 0.07
13 9 0.16
14 12 0.21
15 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (11 bp):
ATATATAAATA
Found at i:3725909 original size:3 final size:3
Alignment explanation
Indices: 3725895--3726022 Score: 61
Period size: 3 Copynumber: 41.0 Consensus size: 3
3725885 TATATATATA
3725895 AAT AAT ATAT AAT AAAT AAT AA- ACAT -AT AAT -AT AAT AAT AAT ATAT
1 AAT AAT A-AT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT
* * ** *
3725941 AAAT AAT GAT GAT AA- AAT AAT AAT AACT TGT GAAA AAT AAT ATAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT -AAT AAT AAT A-AT AAT
*
3725989 AAAT AAT AAT -AT AAAT AAT GTAT AAT AA- AAT AAT
1 -AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT
3726023 TTTATGATAT
Statistics
Matches: 98, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
2 11 0.11
3 65 0.66
4 21 0.21
5 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3725940 original size:18 final size:18
Alignment explanation
Indices: 3725844--3725947 Score: 94
Period size: 18 Copynumber: 6.1 Consensus size: 18
3725834 AAAAATGACT
* *
3725844 TAATAACATATAAAATAA
1 TAATAATATATAATATAA
* *
3725862 TTACAATATATAATATAA
1 TAATAATATATAATATAA
**
3725880 -AAGCATATAT-ATAT-A
1 TAATAATATATAATATAA
3725895 -AATAATATATAATA-AA
1 TAATAATATATAATATAA
*
3725911 TAATAAACATATAATATAA
1 TAAT-AATATATAATATAA
3725930 TAATAATATATAA-ATAA
1 TAATAATATATAATATAA
3725947 T
1 T
3725948 GATGATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
15 9 0.13
16 8 0.11
17 15 0.21
18 32 0.46
19 6 0.09
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.34
Consensus pattern (18 bp):
TAATAATATATAATATAA
Found at i:3726012 original size:28 final size:28
Alignment explanation
Indices: 3725924--3726012 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
3725914 TAAACATATA
3725924 ATATAAT-AATAAT-ATATAAATAATG-
1 ATATAATAAATAATAATATAAATAATGT
* * *
3725949 ATGATAAAATAATAATAACTTGTGAAA-AATAAT
1 AT-ATAATA-AATAATAA--TAT-AAATAAT-GT
3725982 ATATAATAAATAATAATATAAATAATGT
1 ATATAATAAATAATAATATAAATAATGT
3726010 ATA
1 ATA
3726013 ATAAAATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
28 13 0.27
29 6 0.12
31 13 0.27
32 8 0.17
33 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.34
Consensus pattern (28 bp):
ATATAATAAATAATAATATAAATAATGT
Found at i:3728429 original size:411 final size:410
Alignment explanation
Indices: 3727663--3728800 Score: 1663
Period size: 411 Copynumber: 2.8 Consensus size: 410
3727653 AAATCTGCTT
*
3727663 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATA-GTAAGCA
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-ACGTAAGCA
*
3727727 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * * ** * * * *
3727792 TGGATCTTGCTTCAGTCTAATCGTCTGAAAATCAGATCTGCCATGTTTCTACTCTCCGTCGAAGT
130 TGGATC-TGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGT
3727857 GGAGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTT
194 GGAGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTT
*
3727922 CAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCATAAGGATG
259 CAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATG
* * *
3727987 CCAAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGTTTGGATCTTCTATGTGTCTGCCCT
324 CCAAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGAATCTGCTATGTGTCTGCCCT
*
3728052 CTGTCGAAGTGGAGATGCCAGA
389 CCGTCGAAGTGGAGATGCCAGA
* * * *
3728074 CTTTGATTTGTTCTCTGACAATAAAGAGATGCCAAATCATCTTAGACTTGTTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
3728139 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * *
3728204 GGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCTGTCGAAGTGG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGG
* *
3728269 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGTTTCA
196 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA
3728334 ACGTAAGCACGTGAAAGCCAAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGC
261 ACGTAAGCACGTGAAAGCC-AAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGC
3728399 CAAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGAATCTGCTATGTGTCTGCCCTC
325 CAAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGAATCTGCTATGTGTCTGCCCTC
3728464 CGTCGAAGTGGAGATGCCAGA
390 CGTCGAAGTGGAGATGCCAGA
*
3728485 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * ** * * * *
3728550 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAAAGAT---AAGATCT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTG--TAA-GCACAAGGATGCCAA-A-C-
** * * * * *
3728612 GTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTGTTATGCGTCTGCCTTCCAT
125 --CATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCCTCCGT
* * * * * *
3728677 CAAAGTGGAAATGCCAGAGTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGAC
188 CGAAGTGGAGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGAT
* * * * * * *
3728742 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAGTTATTTCTTTGATCTGCTCCCTGTA
253 TTGCTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTA
3728801 GAATACAGAG
Statistics
Matches: 655, Mismatches: 62, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
410 131 0.20
411 350 0.53
412 1 0.00
413 3 0.00
414 7 0.01
415 27 0.04
416 136 0.21
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (410 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGG
AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA
ACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCC
AAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGAATCTGCTATGTGTCTGCCCTCC
GTCGAAGTGGAGATGCCAGA
Found at i:3728471 original size:206 final size:206
Alignment explanation
Indices: 3727663--3728800 Score: 1637
Period size: 205 Copynumber: 5.5 Consensus size: 206
3727653 AAATCTGCTT
*
3727663 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATA-GTAAGCA
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-ACGTAAGCA
*
3727727 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * * * ** * * * * *
3727792 TGGATCTTGCTTCAGTCTAATCGTCTGAA-AATCAGATCTGCCATGTTTCTACTCTCCGTCGAAG
130 TGGATC-TACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCGTCGAAG
3727856 TGGAGATGCCAGA
194 TGGAGATGCCAGA
3727869 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
*
3727934 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCATAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * *
3727999 GGATCTACTTCAGTATAAACATCTGAAGTTTG-GATCTTCTATGTGTCTGCCCTCTGTCGAAGTG
131 GGATCTACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTG
3728063 GAGATGCCAGA
196 GAGATGCCAGA
* * * *
3728074 CTTTGATTTGTTCTCTGACAATAAAGAGATGCCAAATCATCTTAGACTTGTTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
3728139 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
3728204 GGATCTACTTCAGTATAAACATCTGAAGGTT-AGATCTGCTATGTGTCTGCCCTCTGTCGAAGTG
131 GGATCTACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTG
3728268 GAGATGCCAGA
196 GAGATGCCAGA
* *
3728279 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGTTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
3728344 GTGAAAGCCAAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 GTGAAAGCC-AAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCT
3728409 TGGATCTACTTCAGTATAAACATCTGAAGGTTGA-ATCTGCTATGTGTCTGCCCTCCGTCGAAGT
130 TGGATCTACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCGTCGAAGT
3728473 GGAGATGCCAGA
195 GGAGATGCCAGA
*
3728485 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * ** * * * *
3728550 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAAAGAT---AAGATCT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTG--TAA-GCACAAGGATGCCAA-A-C-
* ** * * * *
3728612 GTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGG-TGAGATCTGTTATGCGTCTGCCTTCCA
125 --CATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCG
* *
3728676 TCAAAGTGGAAATGCCAGA
188 TCGAAGTGGAGATGCCAGA
* * * * * *
3728695 GTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGACTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * * * *
3728760 GTGAAAGCCAAATCAGTTATTTCTTTGATCTGCTCCCTGTA
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTA
3728801 GAATACAGAG
Statistics
Matches: 860, Mismatches: 58, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
205 351 0.41
206 331 0.38
207 4 0.00
208 8 0.01
209 3 0.00
210 163 0.19
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTATAAACATCTGAAGGTTGAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTG
GAGATGCCAGA
Found at i:3737452 original size:26 final size:26
Alignment explanation
Indices: 3737420--3737527 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
3737410 TGGTACAAAT
*
3737420 TGATAATGGGTTAGGTAAATGTTACA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
3737446 CGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3737472 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
**
3737498 TGATAATGATTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3737524 TGAT
1 TGAT
3737528 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3743906 original size:9 final size:9
Alignment explanation
Indices: 3743886--3743918 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3743876 ATAATGTATA
3743886 ATATAA-AT
1 ATATAAGAT
3743894 ATATAAGAT
1 ATATAAGAT
*
3743903 ATATGAGAT
1 ATATAAGAT
3743912 ATATAAG
1 ATATAAG
3743919 TTAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (9 bp):
ATATAAGAT
Found at i:3744246 original size:17 final size:18
Alignment explanation
Indices: 3744224--3744262 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3744214 TAATATATAG
3744224 ATAAAATG-CGTAATAAT
1 ATAAAATGACGTAATAAT
*
3744241 ATAAAAATGACTTAATAAT
1 AT-AAAATGACGTAATAAT
3744260 ATA
1 ATA
3744263 TAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.11
18 7 0.37
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (18 bp):
ATAAAATGACGTAATAAT
Found at i:3744259 original size:3 final size:3
Alignment explanation
Indices: 3744253--3744434 Score: 67
Period size: 3 Copynumber: 58.3 Consensus size: 3
3744243 AAAAATGACT
* * **
3744253 TAA TAA TATA TAA -AA TAA TTA CAA TATA TAA T-A TAA -AA GCA TATA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A
3744298 TATA TAAA TAA TATA TAA TAAA TAA TAA -ACA T-A TAA T-A TAA TAA
1 TA-A TA-A TAA TA-A TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA
* * ** *
3744342 TAA TATA TAAA TAA TGA TGA TAA -AA TAA TAA TAA CTTG TGAA AAA TAA
1 TAA TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA -TAA T-AA TAA TAA
*
3744390 TATA TAA TAAA TAA TAA TAA T-A TAAA TAA TGTA TAA TAA -AA TAA T
1 TA-A TAA T-AA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA T
3744435 TTTATGATAT
Statistics
Matches: 138, Mismatches: 18, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
2 17 0.12
3 83 0.60
4 37 0.27
5 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3744314 original size:50 final size:46
Alignment explanation
Indices: 3744254--3744370 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 46
3744244 AAAATGACTT
*
3744254 AATAATATATAAAATAATTACAATATATAATATAAAAGCATATATATATA
1 AATAATATATAAAATAATTA-AACATATAATATAAAA--ATA-ATATATA
*
3744304 AATAATATATAATAAATAA-TAAACATATAATATAATAATAATATATA
1 AATAATATAT-A-AAATAATTAAACATATAATATAAAAATAATATATA
3744351 AATAATGATGATAAAATAAT
1 AATAAT-AT-ATAAAATAAT
3744371 AATAACTTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
47 19 0.32
48 6 0.10
49 2 0.03
50 24 0.40
51 3 0.05
52 6 0.10
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (46 bp):
AATAATATATAAAATAATTAAACATATAATATAAAAATAATATATA
Found at i:3744349 original size:18 final size:18
Alignment explanation
Indices: 3744253--3744356 Score: 103
Period size: 18 Copynumber: 6.1 Consensus size: 18
3744243 AAAAATGACT
*
3744253 TAATAATATATAAAATAA
1 TAATAATATATAATATAA
* *
3744271 TTACAATATATAATATAA
1 TAATAATATATAATATAA
**
3744289 -AAGCATATAT-ATAT-A
1 TAATAATATATAATATAA
3744304 -AATAATATATAATA-AA
1 TAATAATATATAATATAA
*
3744320 TAATAAACATATAATATAA
1 TAAT-AATATATAATATAA
3744339 TAATAATATATAA-ATAA
1 TAATAATATATAATATAA
3744356 T
1 T
3744357 GATGATAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
15 9 0.13
16 8 0.11
17 15 0.21
18 33 0.46
19 6 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAATAATATATAATATAA
Done.