Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold510
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: 507550
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 4
Found at i:269621 original size:33 final size:33
Alignment explanation
Indices: 269579--269645 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
269569 GCCAAGGAAA
***
269579 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
269612 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
269645 T
1 T
269646 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:272162 original size:28 final size:27
Alignment explanation
Indices: 272095--272167 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
272085 CTTCACAATC
* *
272095 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
272122 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
272150 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
272168 GTTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:272288 original size:28 final size:28
Alignment explanation
Indices: 272252--272333 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
272242 ATTTTTCACA
*
272252 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
272280 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
272308 -T-GAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
272334 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 41 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:284729 original size:10 final size:10
Alignment explanation
Indices: 284710--284772 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
284700 CCTTCTCTTC
284710 AAAA-AAAAA
1 AAAAGAAAAA
284719 AAAAGAAAAA
1 AAAAGAAAAA
*
284729 AAAACAAAAA
1 AAAAGAAAAA
*
284739 AAAA-CAAAA
1 AAAAGAAAAA
*
284748 CAAAGAAAAA
1 AAAAGAAAAA
* *
284758 GAGAGAAAAGA
1 AAAAGAAAA-A
284769 AAAA
1 AAAA
284773 ACCTACTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 11 0.26
10 29 0.67
11 3 0.07
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:284730 original size:15 final size:15
Alignment explanation
Indices: 284710--284773 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
284700 CCTTCTCTTC
284710 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
284725 AAAAAAAACAAAA-A
1 AAAAAAAAAAAAAGA
* *
284739 AAAACAAAACAAAGA
1 AAAAAAAAAAAAAGA
* * *
284754 AAAAGAGAGAAAAGA
1 AAAAAAAAAAAAAGA
284769 AAAAA
1 AAAAA
284774 CCTACTTAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 11 0.28
15 28 0.72
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:284773 original size:1 final size:1
Alignment explanation
Indices: 284710--284757 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
284700 CCTTCTCTTC
* * * * *
284710 AAAAAAAAAAAAAGAAAAAAAAACAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
284758 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:285822 original size:55 final size:55
Alignment explanation
Indices: 285731--286414 Score: 1028
Period size: 55 Copynumber: 12.4 Consensus size: 55
285721 TCTCCTTCCG
* *
285731 CTTTTTAGTCCTCAAAGAGCAGGACACGTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
285786 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
285841 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
285896 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
285951 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
286006 -TTGTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTT-TTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
286061 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
286116 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
286171 -TTTTCCAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
286226 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
286281 CCTTTCATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
286336 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
286391 CTTTTTACTCCTCAATGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
286415 TACAACTTAT
Statistics
Matches: 588, Mismatches: 29, Indels: 24
0.92 0.05 0.04
Matches are distributed among these distances:
54 14 0.02
55 561 0.95
56 13 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (55 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:287016 original size:1 final size:1
Alignment explanation
Indices: 287010--287055 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
287000 AAAGTGTTTG
***
287010 AAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
287056 TTTAAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:287030 original size:18 final size:18
Alignment explanation
Indices: 287007--287055 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
286997 GATAAAGTGT
287007 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
287025 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
287043 ---AAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
287056 TTTAAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.42
18 18 0.58
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (18 bp):
TTGAAAAAAAAAAAAAAA
Found at i:287084 original size:21 final size:21
Alignment explanation
Indices: 287060--287116 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
287050 AAAAAATTTA
287060 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
287081 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
287102 AATGTATCGATACAT
1 AATGTATCGATACAT
287117 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:287196 original size:19 final size:19
Alignment explanation
Indices: 287172--287239 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
287162 AATTCAACAA
287172 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
287191 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
287206 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
287223 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
287240 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:287211 original size:13 final size:13
Alignment explanation
Indices: 287193--287217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
287183 ACATAAGTTT
287193 TGTATCGATACAA
1 TGTATCGATACAA
287206 TGTATCGATACA
1 TGTATCGATACA
287218 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:287215 original size:32 final size:32
Alignment explanation
Indices: 287174--287236 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
287164 TTCAACAATT
*
287174 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
287206 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
287237 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:287297 original size:13 final size:13
Alignment explanation
Indices: 287279--287304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287269 CATTTTTCTG
287279 TGTATCGATACAT
1 TGTATCGATACAT
287292 TGTATCGATACAT
1 TGTATCGATACAT
287305 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:287301 original size:33 final size:33
Alignment explanation
Indices: 287259--287325 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
287249 GCCAAGGAAA
***
287259 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
287292 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
287325 T
1 T
287326 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:289841 original size:28 final size:27
Alignment explanation
Indices: 289774--289846 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
289764 CTTCACAATC
* *
289774 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
289801 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
289829 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
289847 GTTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:289967 original size:28 final size:28
Alignment explanation
Indices: 289931--290012 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
289921 ATTTTTCACA
*
289931 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
289959 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
289987 -T-GAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
290013 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 41 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:292538 original size:12 final size:12
Alignment explanation
Indices: 292517--292551 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
292507 TAGTTGATGC
*
292517 TTTTACAATTTT
1 TTTTAAAATTTT
292529 TTTTAAAATTTT
1 TTTTAAAATTTT
292541 TTTCTAAAATT
1 TTT-TAAAATT
292552 ATAAGAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:292732 original size:25 final size:23
Alignment explanation
Indices: 292700--292746 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
292690 TAATTAATTT
*
292700 ATAAATAAAATATTATTAAATTAAG
1 ATAAATAAAA-ATT-TAAAATTAAG
292725 ATAAATAAAAATTTAAAATTAA
1 ATAAATAAAAATTTAAAATTAA
292747 ATGCTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAAATAAAAATTTAAAATTAAG
Found at i:297422 original size:21 final size:21
Alignment explanation
Indices: 297384--297442 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
297374 TAATATTCTT
*
297384 GAAAA-AAAATTAAGTGAATTA
1 GAAAAGAAAA-TAAATGAATTA
297405 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
297426 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
297443 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:298543 original size:20 final size:20
Alignment explanation
Indices: 298520--298584 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
298510 ATACCTAGAT
298520 GTATCGATACATTTTGCTTA
1 GTATCGATACATTTTGCTTA
298540 GTATCGATACA------TT-
1 GTATCGATACATTTTGCTTA
298553 GTATCGATACATTTTGCTTA
1 GTATCGATACATTTTGCTTA
*
298573 GTATTGATACAT
1 GTATCGATACAT
298585 AAATAGGCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.30
14 2 0.05
19 2 0.05
20 22 0.59
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTTTGCTTA
Found at i:298558 original size:13 final size:13
Alignment explanation
Indices: 298540--298565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
298530 ATTTTGCTTA
298540 GTATCGATACATT
1 GTATCGATACATT
298553 GTATCGATACATT
1 GTATCGATACATT
298566 TTGCTTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:298561 original size:33 final size:33
Alignment explanation
Indices: 298519--298584 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
298509 CATACCTAGA
298519 TGTATCGATACATTTTGCTTAGTATCGATACAT
1 TGTATCGATACATTTTGCTTAGTATCGATACAT
*
298552 TGTATCGATACATTTTGCTTAGTATTGATACAT
1 TGTATCGATACATTTTGCTTAGTATCGATACAT
298585 AAATAGGCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTTTGCTTAGTATCGATACAT
Found at i:298685 original size:17 final size:17
Alignment explanation
Indices: 298663--298700 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
298653 TATCGATACA
*
298663 TCACTGTTCATCACTAT
1 TCACTGTTCATAACTAT
*
298680 TCACTGTTCATAACTGT
1 TCACTGTTCATAACTAT
298697 TCAC
1 TCAC
298701 ATATCACTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (17 bp):
TCACTGTTCATAACTAT
Found at i:298707 original size:24 final size:27
Alignment explanation
Indices: 298665--298720 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 27
298655 TCGATACATC
*
298665 ACTGTTCATCACTATTCACTGTTCATA
1 ACTGTTCATCACTATTCACTGTTCACA
298692 ACTGTTCA-CA-TA-TCACTGTTCACA
1 ACTGTTCATCACTATTCACTGTTCACA
298716 ACTGT
1 ACTGT
298721 ATCGATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 16 0.57
25 2 0.07
26 2 0.07
27 8 0.29
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (27 bp):
ACTGTTCATCACTATTCACTGTTCACA
Found at i:300159 original size:3 final size:3
Alignment explanation
Indices: 300151--300176 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
300141 AATCTAACCC
300151 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
300177 GAATGAGATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:303588 original size:165 final size:164
Alignment explanation
Indices: 303315--303777 Score: 526
Period size: 165 Copynumber: 2.8 Consensus size: 164
303305 TGATTTTCTT
* * * *
303315 TTGAAATTCCTCTTATTTTTAAATTACGGGGTTTTTTT-CTCCGTCAATTTTTTTGGGAGGA-TT
1 TTGAAATT-CTCTTATTTTTAAAATAC-TGATTTTTTTACTCCGTAAATTTTTTTGGG-GGATTT
* ** *
303378 TTCATGGGTTCAAAATTTTAAAAATTCATCAAATATAATTATTTATTTCATATTAAATCTA-TTT
63 TTC-TTGGTTTTAAATTTTTAAAATTCATCAAATATAATTATTTATTTCATATTAAAT-TAGTTT
303442 TAAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTCC
126 TAAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTCC
* *
303481 TTGAAATTCTCCTATTTTTAAAATACTGATTTTTTTACTCCATAAAATTTTTTTGGGGGATTTTT
1 TTGAAATTCTCTTATTTTTAAAATACTGATTTTTTTACTCCGT-AAATTTTTTTGGGGGATTTTT
* * * *
303546 CTTGGTTTTTAATTTTTAAAATTCATGAAATATTATTATTTATTTCATATTAAATTAGTTTTCAA
65 CTTGGTTTTAAATTTTTAAAATTCATCAAATATAATTATTTATTTCATATTAAATTAGTTTTAAA
303611 AAATTCATTCATTTTCATGAGTTTTTCATTTTTCC
130 AAATTCATTCATTTTCATGAGTTTTTCATTTTTCC
* * * * * *
303646 TTAAAATT-TCTTTATTTCTACAAA-A-TCGA-GTTTTTATTCCGTAAATGTTTTTGGAGGGGTT
1 TTGAAATTCTC-TTATTTTTA-AAATACT-GATTTTTTTACTCCGTAAATTTTTTTGG-GGGATT
* * ** * * * *
303707 TTTCTTGGTTTTAAACTTTTAAAATTCATCTAATATTGTCATTAAATTCACATTAAATTAGTTTT
62 TTTCTTGGTTTTAAATTTTTAAAATTCATCAAATATAATTATTTATTTCATATTAAATTAGTTTT
*
303772 GAAAAA
127 AAAAAA
303778 CTCAAATTAT
Statistics
Matches: 257, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
163 11 0.04
164 89 0.35
165 129 0.50
166 28 0.11
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (164 bp):
TTGAAATTCTCTTATTTTTAAAATACTGATTTTTTTACTCCGTAAATTTTTTTGGGGGATTTTTC
TTGGTTTTAAATTTTTAAAATTCATCAAATATAATTATTTATTTCATATTAAATTAGTTTTAAAA
AATTCATTCATTTTCATGAGTTTTTCATTTTTCC
Found at i:304499 original size:20 final size:21
Alignment explanation
Indices: 304468--304507 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
304458 ATCTGGGTTT
304468 TTTCAGATGTATCGATACATC
1 TTTCAGATGTATCGATACATC
304489 TTTCA-ATGTATCGATACAT
1 TTTCAGATGTATCGATACAT
304508 TCTAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTCAGATGTATCGATACATC
Found at i:314515 original size:20 final size:20
Alignment explanation
Indices: 314473--314526 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
314463 TTCAATAATT
* *
314473 TGTATCAATACAATAAGGCAA
1 TGTATCGATAC-ATAAGGAAA
*
314494 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAGGAAA
314514 TGTATCGATACAT
1 TGTATCGATACAT
314527 GCCTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGGAAA
Found at i:314533 original size:20 final size:21
Alignment explanation
Indices: 314492--314544 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
314482 ACAATAAGGC
*
314492 AATGTATCGATACATAAGT-A
1 AATGTATCGATACATAACTAA
**
314512 AATGTATCGATACATGCCTAA
1 AATGTATCGATACATAACTAA
314533 AATGTATCGATA
1 AATGTATCGATA
314545 TAAGATCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACATAACTAA
Found at i:314638 original size:20 final size:19
Alignment explanation
Indices: 314613--314650 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
314603 TAAATAAGAA
*
314613 ATTATATTGATACATTTCTC
1 ATTATATCGATAC-TTTCTC
314633 ATTATATCGATACTTTCT
1 ATTATATCGATACTTTCT
314651 AGGTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTATATCGATACTTTCTC
Found at i:316379 original size:168 final size:168
Alignment explanation
Indices: 316101--316438 Score: 667
Period size: 168 Copynumber: 2.0 Consensus size: 168
316091 CAAGCTATTT
*
316101 CATCATCCCAAACTACTCCGAAATTATGTAAATGAGTTTGTGATGCTCATACCACTCTTTTTTTC
1 CATCATCCCAAACTACTCCAAAATTATGTAAATGAGTTTGTGATGCTCATACCACTCTTTTTTTC
316166 CTTTCATGAATGTATGAATGTCCATGCCTCGAGTTTAGACCCATAAACACCAAAACAACCGAAGC
66 CTTTCATGAATGTATGAATGTCCATGCCTCGAGTTTAGACCCATAAACACCAAAACAACCGAAGC
316231 CATACCTAGTTTTCCTCTATTTCAAGCTGGCAGCATAG
131 CATACCTAGTTTTCCTCTATTTCAAGCTGGCAGCATAG
316269 CATCATCCCAAACTACTCCAAAATTATGTAAATGAGTTTGTGATGCTCATACCACTCTTTTTTTC
1 CATCATCCCAAACTACTCCAAAATTATGTAAATGAGTTTGTGATGCTCATACCACTCTTTTTTTC
316334 CTTTCATGAATGTATGAATGTCCATGCCTCGAGTTTAGACCCATAAACACCAAAACAACCGAAGC
66 CTTTCATGAATGTATGAATGTCCATGCCTCGAGTTTAGACCCATAAACACCAAAACAACCGAAGC
316399 CATACCTAGTTTTCCTCTATTTCAAGCTGGCAGCATAG
131 CATACCTAGTTTTCCTCTATTTCAAGCTGGCAGCATAG
316437 CA
1 CA
316439 GTTAGTATTT
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (168 bp):
CATCATCCCAAACTACTCCAAAATTATGTAAATGAGTTTGTGATGCTCATACCACTCTTTTTTTC
CTTTCATGAATGTATGAATGTCCATGCCTCGAGTTTAGACCCATAAACACCAAAACAACCGAAGC
CATACCTAGTTTTCCTCTATTTCAAGCTGGCAGCATAG
Found at i:318190 original size:40 final size:40
Alignment explanation
Indices: 318114--318191 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
318104 AAAACCTAGA
*
318114 ATGTATCGATACAATGAGAAATGTATCAATACAATTTCTT
1 ATGTATCGATACAATGAAAAATGTATCAATACAATTTCTT
* *
318154 ATGTATCGATATAATTAAAAACTGTATCAATA-AATTTC
1 ATGTATCGATACAATGAAAAA-TGTATCAATACAATTTC
318192 CTTCCAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 24 0.71
41 10 0.29
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (40 bp):
ATGTATCGATACAATGAAAAATGTATCAATACAATTTCTT
Found at i:318239 original size:20 final size:21
Alignment explanation
Indices: 318213--318263 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
318203 CCACATGGTC
*
318213 TTGTATCGATACATTTACTTA
1 TTGTATCGATACATTGACTTA
* *
318234 -TGTATCAATACATTGCCTTA
1 TTGTATCGATACATTGACTTA
318254 TTGTATCGAT
1 TTGTATCGAT
318264 GCAAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (21 bp):
TTGTATCGATACATTGACTTA
Found at i:320699 original size:38 final size:40
Alignment explanation
Indices: 320618--320699 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 40
320608 TCCTCTGTGG
* *
320618 AAAGAAAAAAATGAGATAAAGAAAGAAAACAGAAAATGCA
1 AAAGAAAAAAATGAGATAAAGAAAGAAAACAGAAAAGGAA
**
320658 AAAGAAAAAAATG-GA-AAATCAAGAAAA-AGACAAAGGAA
1 AAAGAAAAAAATGAGATAAAGAAAGAAAACAGA-AAAGGAA
320696 AAAG
1 AAAG
320700 CGCATATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 3 0.08
38 19 0.51
39 2 0.05
40 13 0.35
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.06
Consensus pattern (40 bp):
AAAGAAAAAAATGAGATAAAGAAAGAAAACAGAAAAGGAA
Found at i:321477 original size:16 final size:15
Alignment explanation
Indices: 321452--321481 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
321442 AATAACCTCT
321452 TGAACTTGATCTTGA
1 TGAACTTGATCTTGA
321467 TGAACCTTGATCTTG
1 TGAA-CTTGATCTTG
321482 TTAGGCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (15 bp):
TGAACTTGATCTTGA
Found at i:322525 original size:44 final size:43
Alignment explanation
Indices: 322476--323060 Score: 296
Period size: 44 Copynumber: 13.4 Consensus size: 43
322466 TTATTCTTGC
* *
322476 TTGACATATGGTTACCACCTTGGTCAAACTCTTTTCATTTCCAT
1 TTGACATATGGTTACCACCCTGGTCAAA-TCTTTTCATTTCGAT
* * *
322520 TTGACATATGATTACCACTCTGGTCAAATGCTTCTT-ATTTCGGT
1 TTGACATATGGTTACCACCCTGGTCAAAT-CTT-TTCATTTCGAT
* *
322564 TTGACGTATGGTTACCACCCTAGTCAAAATCTTTTCATTAT-GAT
1 TTGACATATGGTTACCACCCTGGTC-AAATCTTTTCATT-TCGAT
** * ** * *
322608 TTGATGTATGGTTATCGTCCTGGTCAAATATACTTT-ATTTCTAT
1 TTGACATATGGTTACCACCCTGGTCAAATCT--TTTCATTTCGAT
* * * ** ** *
322652 TTGATATGTGGTTACCAACCTCATCAAATCTACCTCATTTCTAT
1 TTGACATATGGTTACCACCCTGGTCAAATCT-TTTCATTTCGAT
* * * *
322696 TTGACAAATGGTTACCACCCTGGTCAAACTCTTCTCATTTTGGT
1 TTGACATATGGTTACCACCCTGGTCAAA-TCTTTTCATTTCGAT
* * * * *
322740 GTGACGTATGGTTACCACCTTGGTCAGAT-TGGTTTCA-TTCTAAT
1 TTGACATATGGTTACCACCCTGGTCAAATCT--TTTCATTTC-GAT
* *** *
322784 TTGACATATGGTTACCACCCTAGTCAAATTCACCTCTTTTCTG-T
1 TTGACATATGGTTACCACCCTGGTCAAA-TCTTTTCATTTC-GAT
* ** * *
322828 TTGACGTATCATTACCACCCTAGTCAAA-CTCTTC---TC-AGT
1 TTGACATATGGTTACCACCCTGGTCAAATCTTTTCATTTCGA-T
* * * * **
322867 TTGACATATGGTCACCACCCTAGTCAGATTCTTTTTATTTTAAT
1 TTGACATATGGTTACCACCCTGGTCA-AATCTTTTCATTTCGAT
* * * ** *
322911 TTGACGTATGGTTACTACCCTAGTCAAATC-TGCCTATTTCTTAT
1 TTGACATATGGTTACCACCCTGGTCAAATCTTTTC-ATTTC-GAT
** * * * *
322955 TTGACATACAGTTACCACCCTAGTCAAACTCCTCTT-ATTTTGGT
1 TTGACATATGGTTACCACCCTGGTCAAA-T-CTTTTCATTTCGAT
* * ** * *
322999 CTAATGTATGGTTACCACCCTGGTCAGATTCTTTTCATTTTGAT
1 TTGACATATGGTTACCACCCTGGTCA-AATCTTTTCATTTCGAT
*
323043 TTGACGTATGGTTACCAC
1 TTGACATATGGTTACCAC
323061 TTGTCGCAAC
Statistics
Matches: 408, Mismatches: 102, Indels: 62
0.71 0.18 0.11
Matches are distributed among these distances:
39 25 0.06
40 1 0.00
41 4 0.01
42 6 0.01
43 24 0.06
44 322 0.79
45 25 0.06
46 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (43 bp):
TTGACATATGGTTACCACCCTGGTCAAATCTTTTCATTTCGAT
Found at i:322871 original size:39 final size:39
Alignment explanation
Indices: 322817--322892 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
322807 TCAAATTCAC
* * * *
322817 CTCTTTTCTGTTTGACGTATCATTACCACCCTAGTCAAA
1 CTCTTCTCAGTTTGACATATCATCACCACCCTAGTCAAA
**
322856 CTCTTCTCAGTTTGACATATGGTCACCACCCTAGTCA
1 CTCTTCTCAGTTTGACATATCATCACCACCCTAGTCA
322893 GATTCTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (39 bp):
CTCTTCTCAGTTTGACATATCATCACCACCCTAGTCAAA
Found at i:322914 original size:83 final size:82
Alignment explanation
Indices: 322783--322938 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 82
322773 TTCATTCTAA
* *
322783 TTTGACATATGGTTACCACCCTAGTCAAATTCACCTCTTTTCTGTTTGACGTATCATTACCACCC
1 TTTGACATATGGTCACCACCCTAGTCAAATT-ACCTCTTTTCTATTTGACGTATCATTACCACCC
322848 TAGTCAAACTCTTCTCAG
65 TAGTCAAACTCTTCTCAG
* * * * ** *
322866 TTTGACATATGGTCACCACCCTAGTCAGATT-CTTTTTATTTTAATTTGACGTATGGTTACTACC
1 TTTGACATATGGTCACCACCCTAGTCAAATTACCTCTT-TTCT-ATTTGACGTATCATTACCACC
322930 CTAGTCAAA
64 CTAGTCAAA
322939 TCTGCCTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 4 0.06
82 3 0.05
83 55 0.89
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (82 bp):
TTTGACATATGGTCACCACCCTAGTCAAATTACCTCTTTTCTATTTGACGTATCATTACCACCCT
AGTCAAACTCTTCTCAG
Found at i:322935 original size:127 final size:127
Alignment explanation
Indices: 322476--323060 Score: 423
Period size: 132 Copynumber: 4.5 Consensus size: 127
322466 TTATTCTTGC
* * * ** * * *
322476 TTGACATATGGTTACCACCTTGGTCAAACTCTTTTCATTTCCATTTGACATATGATTACCACTCT
1 TTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTTTAATTTGACGTATGGTTACCACCCT
* * * ** * ** * *
322541 GGTCAAATGCTTCTTATTTC-GGTTTGACGTATGGTTACCACCCTAGTCAAAATCTTTTCATTAT
66 AGTCAAAT-CTACCTATTTCTTATTTGACATACAGTTACCACCCTAGTC-AAA-CTCTTC-TCA-
322605 GAT
126 G-T
** * ** * ** * *
322608 TTGATGTATGGTTATCGTCCTGGTCAAATATAC-TTT-ATTTCT-ATTTGATATGTGGTTACCAA
1 TTGACATATGGTTACCACCCTGGTCAGAT-T-CTTTTCATTT-TAATTTGACGTATGGTTACCAC
* ** *
322670 CCTCA-TCAAATCTACCTCATTTC-TATTTGACAAATGGTTACCACCCTGGTCAAACTCTTCTCA
63 CCT-AGTCAAATCTACCT-ATTTCTTATTTGACATACAGTTACCACCCTAGTCAAACTCTTCTCA
322733 TTTTGGT
126 -----GT
* * * ** * *
322740 GTGACGTATGGTTACCACCTTGGTCAGATTGGTTTCATTCTAATTTGACATATGGTTACCACCCT
1 TTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTTTAATTTGACGTATGGTTACCACCCT
* * *
322805 AGTCAAAT-TCACCTCTTT-TCTGTTTGACGTATCA-TTACCACCCTAGTCAAACTCTTCTCAGT
66 AGTCAAATCT-ACCTATTTCT-TATTTGACATA-CAGTTACCACCCTAGTCAAACTCTTCTCAGT
* * * *
322867 TTGACATATGGTCACCACCCTAGTCAGATTCTTTTTATTTTAATTTGACGTATGGTTACTACCCT
1 TTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTTTAATTTGACGTATGGTTACCACCCT
* * * *
322932 AGTCAAATCTGCCTATTTCTTATTTGACATACAGTTACCACCCTAGTCAAACTCCTCTTATT
66 AGTCAAATCTACCTATTTCTTATTTGACATACAGTTACCACCCTAGTCAAACTCTTCTCAGT
* *
322994 TTGGTCTAATGTATGGTTACCACCCTGGTCAGATTCTTTTCATTTTGATTTGACGTATGGTTACC
1 TT-GAC--A--TATGGTTACCACCCTGGTCAGATTCTTTTCATTTTAATTTGACGTATGGTTACC
323059 AC
61 AC
323061 TTGTCGCAAC
Statistics
Matches: 361, Mismatches: 67, Indels: 50
0.76 0.14 0.10
Matches are distributed among these distances:
126 2 0.01
127 106 0.29
128 4 0.01
129 2 0.01
130 6 0.02
131 17 0.05
132 218 0.60
133 5 0.01
134 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (127 bp):
TTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTTTAATTTGACGTATGGTTACCACCCT
AGTCAAATCTACCTATTTCTTATTTGACATACAGTTACCACCCTAGTCAAACTCTTCTCAGT
Found at i:324395 original size:98 final size:98
Alignment explanation
Indices: 324249--324433 Score: 221
Period size: 98 Copynumber: 1.9 Consensus size: 98
324239 AAGATAAAAA
* * *** *
324249 TTAAATCTTGATAAGCTTAAAAATGGGGTTGGAGTATCTTTTCAAAAGA-ATAGGGTTAGAGTAT
1 TTAAATCTTGATAAGCTTAAAAATAGGGTTAGAGTATCCCCTCAAAAGAGAGA-GGTTAGAGTAT
* *
324313 CCCTAATGAAGGAAA-TTTAAGCAAAATTAAGGT
65 CCCCAACGAAGGAAATTTTAAGCAAAATTAAGGT
* * * * *
324346 TTAAATTTTGATAAGTTTCAAAAATAGGGTTAGAGTATCCCCTCGAAAGAGCGAGGTTGGAGTAT
1 TTAAATCTTGATAAGCTT-AAAAATAGGGTTAGAGTATCCCCTCAAAAGAGAGAGGTTAGAGTAT
324411 CCCCAACGAAGGAAATTTTAAGC
65 CCCCAACGAAGGAAATTTTAAGC
324434 TTTTTATGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
97 16 0.22
98 48 0.67
99 8 0.11
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (98 bp):
TTAAATCTTGATAAGCTTAAAAATAGGGTTAGAGTATCCCCTCAAAAGAGAGAGGTTAGAGTATC
CCCAACGAAGGAAATTTTAAGCAAAATTAAGGT
Found at i:333049 original size:13 final size:13
Alignment explanation
Indices: 333031--333056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
333021 ACAAAGATCC
333031 ATGTATCGATACA
1 ATGTATCGATACA
333044 ATGTATCGATACA
1 ATGTATCGATACA
333057 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:333053 original size:33 final size:33
Alignment explanation
Indices: 333011--333076 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
333001 AACTTCCTAG
***
333011 ATGTATCGATACAAAGATCCATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
*
333044 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
333077 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:333223 original size:21 final size:21
Alignment explanation
Indices: 333167--333223 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
333157 GTTGGGACCC
*
333167 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTTCACAAA
*
333188 TGTATCGATACATTTTACAAA
1 TGTATCGATACATTTCACAAA
333209 TGTATCGATACATTT
1 TGTATCGATACATTT
333224 GGATAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTCACAAA
Found at i:335099 original size:8 final size:8
Alignment explanation
Indices: 335086--335205 Score: 62
Period size: 8 Copynumber: 15.4 Consensus size: 8
335076 TCAGAAAGTC
335086 AAATAATA
1 AAATAATA
335094 AAATAATA
1 AAATAATA
335102 AGTACA-AATCA
1 A--A-ATAAT-A
*
335113 AAA-ATTA
1 AAATAATA
*
335120 AAAATAAAA
1 -AAATAATA
335129 AAATTAATA
1 AAA-TAATA
335138 AAATAAT-
1 AAATAATA
335145 -AATAA-A
1 AAATAATA
*
335151 AATTAAT-
1 AAATAATA
*
335158 AAA-AATC
1 AAATAATA
335165 AAATAATA
1 AAATAATA
335173 AAATAATA
1 AAATAATA
*
335181 ACAATGA-A
1 A-AATAATA
335189 AAATAA-A
1 AAATAATA
335196 AAATAA-A
1 AAATAATA
335203 AAA
1 AAA
335206 AAATCATGAA
Statistics
Matches: 90, Mismatches: 9, Indels: 27
0.71 0.07 0.21
Matches are distributed among these distances:
6 8 0.09
7 25 0.28
8 36 0.40
9 14 0.16
10 4 0.04
11 3 0.03
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:335109 original size:21 final size:22
Alignment explanation
Indices: 335089--335161 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
335079 GAAAGTCAAA
*
335089 TAATAAAATAATAAGTACAAAT
1 TAATAAAATAATAAGTAAAAAT
* * *
335111 CAA-AAATTAA-AAATAAAAAAAT
1 TAATAAAATAATAAGT--AAAAAT
335133 TAATAAAATAATAA-TAAAAAT
1 TAATAAAATAATAAGTAAAAAT
335154 TAATAAAA
1 TAATAAAA
335162 ATCAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.07
21 20 0.49
22 9 0.22
23 7 0.17
24 2 0.05
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (22 bp):
TAATAAAATAATAAGTAAAAAT
Found at i:335137 original size:12 final size:12
Alignment explanation
Indices: 335122--335162 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
335112 AAAAATTAAA
335122 AATAAAAAAATT
1 AATAAAAAAATT
*
335134 AATAAAATAA-T
1 AATAAAAAAATT
335145 AAT--AAAAATT
1 AATAAAAAAATT
335155 AATAAAAA
1 AATAAAAA
335163 TCAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 4 0.17
12 12 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:335140 original size:24 final size:24
Alignment explanation
Indices: 335113--335198 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 24
335103 GTACAAATCA
335113 AAAATTAAAAATAAAAAAATTAAT
1 AAAATTAAAAATAAAAAAATTAAT
*
335137 AAAA-TAATAAT--AAAAATTAAT
1 AAAATTAAAAATAAAAAAATTAAT
* * *
335158 AAAAAT-CAAATAATAAAA-TAAT
1 AAAATTAAAAATAAAAAAATTAAT
*
335180 AACAATGAAAAATAAAAAA
1 AA-AATTAAAAATAAAAAA
335199 TAAAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
21 17 0.35
22 7 0.14
23 12 0.24
24 13 0.27
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.22
Consensus pattern (24 bp):
AAAATTAAAAATAAAAAAATTAAT
Found at i:335157 original size:10 final size:10
Alignment explanation
Indices: 335118--335163 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
335108 AATCAAAAAT
335118 TAAAAA-TAA
1 TAAAAATTAA
335127 -AAAAATTAA
1 TAAAAATTAA
*
335136 TAAAATAATAA
1 TAAAA-ATTAA
335147 TAAAAATTAA
1 TAAAAATTAA
335157 TAAAAAT
1 TAAAAAT
335164 CAAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 15 0.47
11 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:335169 original size:21 final size:22
Alignment explanation
Indices: 335122--335207 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
335112 AAAAATTAAA
335122 AATAA-AAAAATTAAT-AAAAT
1 AATAATAAAAATTAATAAAAAT
335142 AATAATAAAAATTAATAAAAAT
1 AATAATAAAAATTAATAAAAAT
*
335164 CAAATAAT-AAAA-TAATAACAAT
1 --AATAATAAAAATTAATAAAAAT
* * *
335186 GAAAAATAAAAAATAAAAAAAA
1 -AATAATAAAAATTAATAAAAA
335208 ATCATGAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.09
21 15 0.27
22 18 0.33
23 11 0.20
24 6 0.11
ACGTcount: A:0.76, C:0.02, G:0.01, T:0.21
Consensus pattern (22 bp):
AATAATAAAAATTAATAAAAAT
Found at i:335194 original size:35 final size:31
Alignment explanation
Indices: 335119--335198 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 31
335109 ATCAAAAATT
* *
335119 AAAAATAAAAAAATTAATAAAATAATAATAA
1 AAAAATAAAAAAAATAATAAAATAATAACAA
335150 AAATTAATAAAAATCAAATAATAAAATAATAACAA
1 AAA--AATAAAAA--AAATAATAAAATAATAACAA
335185 TGAAAAATAAAAAA
1 --AAAAATAAAAAA
335199 TAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
31 3 0.07
33 9 0.22
35 26 0.63
37 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (31 bp):
AAAAATAAAAAAAATAATAAAATAATAACAA
Found at i:338573 original size:31 final size:31
Alignment explanation
Indices: 338520--338578 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
338510 TACATTGAAT
* *
338520 AATGTATTGATATATCTAGGTAAAAAGATAG
1 AATGTATCGATACATCTAGGTAAAAAGATAG
* *
338551 AATGTATCGATACATGTGGGTAAAAAGA
1 AATGTATCGATACATCTAGGTAAAAAGA
338579 CATCTATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (31 bp):
AATGTATCGATACATCTAGGTAAAAAGATAG
Found at i:339400 original size:28 final size:28
Alignment explanation
Indices: 339342--339697 Score: 320
Period size: 28 Copynumber: 12.5 Consensus size: 28
339332 CACCAACTTG
* * *
339342 TGTGGGCTTTAGAAGGGTTGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTAACT
* * *
339371 TGTGGGCTTCGAAAGGGTGCCATTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
339399 TGTGAGCTTTGAAAGGTTACCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
339427 TATGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * **
339455 TGTGGGCTTTGAAAAAGGTTACCACCGACT
1 TGTGGGCTTTG--AAAGGATGCCACTAACT
*
339485 TGTGGGCTTTAAGAAGGATGCCACTAACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACT
* *
339514 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
339542 TGTGGGCTTTGAAAAGATGCTACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
339570 TGTGGGCTTTGAAAAGATGCTACTAACA
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* **
339598 TGTGGGCTTTG-TAGTGATGCCACCGACTT
1 TGTGGGCTTTGAAAG-GATGCCACTAAC-T
* *
339627 GTGTGGGCTTCGAAAAGG-TGCCACTGACT
1 -TGTGGGCTTTG-AAAGGATGCCACTAACT
* ** ** *
339656 TGTGAGCTTCAAAAGTTTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
339684 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
339698 ATGTGAACAT
Statistics
Matches: 273, Mismatches: 45, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.02
28 190 0.70
29 33 0.12
30 42 0.15
31 1 0.00
32 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTAACT
Found at i:339507 original size:115 final size:114
Alignment explanation
Indices: 339324--339584 Score: 317
Period size: 115 Copynumber: 2.3 Consensus size: 114
339314 GGCTTCAGAG
* * * * * * *
339324 AAGATTGCCACCAACTTGTGTGGGCTTT-AGAAGGGTTGCCACTGACTTGTGGGCTTCGAAAGGG
1 AAGA-TGCCACTAAC-T-TGTGGGCTTTGAAAAAGGTTACCACCGACTTGTGGGCTTCAAAAGGA
* * *
339388 TGCCATTAACTTGTGAGCTTTGAAAGGTTACCACTAACTTATGGGCTTTGAA
63 TGCCACTAACTTGTGAGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAA
* * *
339440 AGGGTGCCACTAACTTGTGGGCTTTGAAAAAGGTTACCACCGACTTGTGGGCTTTAAGAAGGATG
1 AAGATGCCACTAACTTGTGGGCTTTGAAAAAGGTTACCACCGACTTGTGGGCTTCAA-AAGGATG
* * * *
339505 CCACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
65 CCACTAACTTGTGAGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAA
*
339555 AAGATGCTACTAACTTGTGGGCTTTGAAAA
1 AAGATGCCACTAACTTGTGGGCTTTGAAAA
339585 GATGCTACTA
Statistics
Matches: 123, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
113 10 0.08
114 26 0.21
115 85 0.69
116 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (114 bp):
AAGATGCCACTAACTTGTGGGCTTTGAAAAAGGTTACCACCGACTTGTGGGCTTCAAAAGGATGC
CACTAACTTGTGAGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAA
Found at i:339552 original size:143 final size:142
Alignment explanation
Indices: 339331--339698 Score: 406
Period size: 143 Copynumber: 2.6 Consensus size: 142
339321 GAGAAGATTG
* * * * *
339331 CCACCAACTTGTGTGGGCTTT-AGAAGGGTTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCATT
1 CCACCGACTTGTGTGGGCTTTAAGAA-GG-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACT
* * * * * * *
339395 AACTTGTGAGCTTTGAAAGGTTACCACTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGG
64 GACTTGTGGGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAAAAGATGCCACTAACATGTGG
*
339460 GCTTTGAAAAAG-GTTA
129 GCTTTG---AAGTGATA
*
339476 CCACCGAC-T-TGTGGGCTTTAAGAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTG
1 CCACCGACTTGTGTGGGCTTTAAGAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTG
* * * *
339539 ACTTGTGGGCTTTGAAAAGATGCTACTAACTTGTGGGCTTTGAAAAGATGCTACTAACATGTGGG
65 ACTTGTGGGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAAAAGATGCCACTAACATGTGGG
* *
339604 CTTTGTAGTGATG
130 CTTTGAAGTGATA
* * * *
339617 CCACCGACTTGTGTGGGCTTCGAA-AAGGTGCCACTGACTTGTGAGC-TTCAAAAGTTTGCCACT
1 CCACCGACTTGTGTGGGCTT-TAAGAAGGTGCCACTGACTTGTGGGCTTTGAAAAG-ATGCCACT
339680 GACTTGTGGGCTTTGAAAA
64 GACTTGTGGGCTTTGAAAA
339699 TGTGAACATT
Statistics
Matches: 191, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
140 2 0.01
141 17 0.09
142 43 0.23
143 115 0.60
144 7 0.04
145 7 0.04
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (142 bp):
CCACCGACTTGTGTGGGCTTTAAGAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGA
CTTGTGGGCTTTGAAAAGATACCACTAACTTATGGGCTTTGAAAAGATGCCACTAACATGTGGGC
TTTGAAGTGATA
Found at i:339658 original size:114 final size:112
Alignment explanation
Indices: 339395--339698 Score: 308
Period size: 115 Copynumber: 2.7 Consensus size: 112
339385 GGGTGCCATT
* * * * * * * * *
339395 AACTTGTGAGCTTTGAAAGGTTACCACTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGG
1 AACTTGTGGGCTTCGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
* * *
339460 GCTTTGAAAAAGGTTACCACCGACTTGTGGGCTTTAAGAAGGATGCCACT
66 GCTTTGAAAAAGGCTACCA-C-ACATGTGGGCTTT-AGAAGGATGCCACC
* *
339510 AACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCTACTAACTTGTGG
1 AACTTGTGGGCTTCGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
* * *
339575 GCTTTGAAAAGATGCTACTA-ACATGTGGGCTTT-GTAGTGATGCCACC
66 GCTTTGAAAA-AGGCTACCACACATGTGGGCTTTAGAAG-GATGCCACC
* * * * * *
339622 GACTTGTGTGGGCTTCGAAAAGGTGCCACTGACTTGTGAGC-TTCAAAAGTTTGCCACTGACTTG
1 AAC-T-TGTGGGCTTCGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAG-ATGCCACTAACTTG
339686 TGGGCTTTGAAAA
63 TGGGCTTTGAAAA
339699 TGTGAACATT
Statistics
Matches: 161, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
111 3 0.02
112 10 0.06
113 20 0.12
114 56 0.35
115 66 0.41
116 6 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (112 bp):
AACTTGTGGGCTTCGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
GCTTTGAAAAAGGCTACCACACATGTGGGCTTTAGAAGGATGCCACC
Found at i:340972 original size:1 final size:1
Alignment explanation
Indices: 340961--341027 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
340951 TCTGGACCCC
* * * * * * * * *
340961 TTTTTTGTTTTTTTTTTGTTGTTTTTTTTGTTGTTTTTTGTTGTTTTTTGTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
341026 TT
1 TT
341028 CTTGGTTGTT
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:341039 original size:12 final size:10
Alignment explanation
Indices: 340961--341048 Score: 74
Period size: 10 Copynumber: 8.5 Consensus size: 10
340951 TCTGGACCCC
*
340961 TTTTTTGTTTT
1 TTTTTTG-TTG
340972 TTTTTTGTTG
1 TTTTTTGTTG
340982 TTTTTTTTGTTG
1 --TTTTTTGTTG
340994 TTTTTTGTTG
1 TTTTTTGTTG
341004 TTTTTTGTT-
1 TTTTTTGTTG
341013 TTTTGTT-TT-
1 TTTT-TTGTTG
*
341022 TTTTTTCTTGG
1 TTTTTTGTT-G
*
341033 TTGTTTTCTTG
1 TT-TTTTGTTG
341044 TTTTT
1 TTTTT
341049 ATTGGTATGA
Statistics
Matches: 69, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
8 2 0.03
9 12 0.17
10 26 0.38
11 12 0.17
12 17 0.25
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (10 bp):
TTTTTTGTTG
Found at i:341039 original size:32 final size:31
Alignment explanation
Indices: 340962--341026 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
340952 CTGGACCCCT
340962 TTTTTGTTTTTTTTTTGTTGTTTTTT-TTGT
1 TTTTTGTTTTTTTTTTGTTGTTTTTTGTTGT
* * *
340992 TGTTTT-TTGTTGTTTT-TTGTTTTTTGTTTT
1 T-TTTTGTTTTTTTTTTGTTGTTTTTTGTTGT
341022 TTTTT
1 TTTTT
341027 TCTTGGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 13 0.43
30 13 0.43
31 4 0.13
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (31 bp):
TTTTTGTTTTTTTTTTGTTGTTTTTTGTTGT
Found at i:341048 original size:32 final size:29
Alignment explanation
Indices: 340961--341048 Score: 72
Period size: 32 Copynumber: 2.9 Consensus size: 29
340951 TCTGGACCCC
*
340961 TTTTTTGTTTTTTTTTTGTTGTTTTTTTTGTT
1 TTTTTTG-TTGTTTTTTGTTG--TTTTTTGTT
340993 GTTTTTTGTTGTTTTTTGTT-TTTTGTT-TT
1 -TTTTTTGTTGTTTTTTGTTGTTTT-TTGTT
* *
341022 TTTTTTCTTGGTTGTTTTCTTGTTTTT
1 TTTTTTGTT-GTT-TTTTGTTGTTTTT
341049 ATTGGTATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
28 8 0.17
29 9 0.19
30 9 0.19
31 4 0.08
32 11 0.23
33 7 0.15
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (29 bp):
TTTTTTGTTGTTTTTTGTTGTTTTTTGTT
Found at i:343028 original size:20 final size:19
Alignment explanation
Indices: 342999--343037 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
342989 AGGTTAAAAC
342999 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
343018 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
343038 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:343151 original size:13 final size:13
Alignment explanation
Indices: 343133--343157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343123 CTTAACTGTT
343133 TGTATCGATACAG
1 TGTATCGATACAG
343146 TGTATCGATACA
1 TGTATCGATACA
343158 TCCTAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:349029 original size:8 final size:8
Alignment explanation
Indices: 349016--349047 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
349006 ATTTGATTAA
349016 ATTTTGTG
1 ATTTTGTG
349024 ATTTTGTG
1 ATTTTGTG
349032 ATTTTGTG
1 ATTTTGTG
349040 ATGTTTGT
1 AT-TTTGT
349048 TGTTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:349262 original size:13 final size:13
Alignment explanation
Indices: 349244--349282 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
349234 CAGCATTCTC
*
349244 TGTATCGATACAT
1 TGTATCGATACAA
349257 TGTATCGATACAA
1 TGTATCGATACAA
349270 TGTATCGATACAA
1 TGTATCGATACAA
349283 AGGGTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:351746 original size:13 final size:13
Alignment explanation
Indices: 351728--351752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351718 ACAATGCACA
351728 GTATCGATACATT
1 GTATCGATACATT
351741 GTATCGATACAT
1 GTATCGATACAT
351753 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:351765 original size:20 final size:21
Alignment explanation
Indices: 351740--351792 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
351730 ATCGATACAT
*
351740 TGTATCGATACATGAC-CAAA
1 TGTATCGATACATGACAAAAA
*
351760 TGTATCGATAC-TTACGAAAAA
1 TGTATCGATACATGAC-AAAAA
351781 TGTATCGATACA
1 TGTATCGATACA
351793 GGTGCTTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 11 0.39
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGACAAAAA
Found at i:367921 original size:15 final size:15
Alignment explanation
Indices: 367901--367935 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
367891 AATCATCAAA
367901 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
367916 GATGATGACGATAAT
1 GATGATGAAGATAAT
367931 GATGA
1 GATGA
367936 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.29, T:0.26
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:371753 original size:9 final size:9
Alignment explanation
Indices: 371739--371764 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
371729 CTTTATCCTA
371739 AAAAAAAAC
1 AAAAAAAAC
371748 AAAAAAAAC
1 AAAAAAAAC
371757 AAAAAAAA
1 AAAAAAAA
371765 AGAAGGGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:373027 original size:28 final size:28
Alignment explanation
Indices: 372993--373399 Score: 390
Period size: 28 Copynumber: 14.1 Consensus size: 28
372983 CGTTCATCTC
* * *
372993 TTCAAAGCCCACAGGTGAGTTGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
373021 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
**
373048 CTTCACAAAACCACAAGTCAGTGGCATCCT
1 -TTCA-AAGCCCACAAGTCAGTGGCATCCT
* *
373078 TTCAAAGCCCGCAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
373106 TCTCAAAGCCCATAAGTCAGTGGCATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
* *
373135 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
373163 TTCAAAGCCCACAAGTCAGTGGC-TCCCTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CC-T
*
373192 TTCAAAGCCCACAAGTTAGTGGC-TCCCTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CC-T
* * **
373221 TTCAAAGCCCACAAGCCAGTGGTAACTTTT
1 TTCAAAGCCCACAAGTCAGTGG-CA-TCCT
* * *
373251 TTCAAAGTCCATACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* * *
373283 TTCAAAGACCACACAAATCGGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* *
373313 TCCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
373341 TTCAAAGCTCAAAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
373369 TTCAAAGCCCACCCAAGTTAGTGGCA-CCT
1 TTCAAAGCCCA--CAAGTCAGTGGCATCCT
373398 TT
1 TT
373400 TTTTTAAAGC
Statistics
Matches: 323, Mismatches: 42, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.01
28 146 0.45
29 104 0.32
30 29 0.09
31 3 0.01
32 38 0.12
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:373075 original size:57 final size:57
Alignment explanation
Indices: 372987--373394 Score: 357
Period size: 57 Copynumber: 7.0 Consensus size: 57
372977 CTAGAGCGTT
* * * *
372987 CATCTC-T-TCAAAGCCCACAGGTGAGTTGCATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCTCAAA-CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* * *
373043 CATCTCTTCACAAAACCACAAGTCAGTGGCATCCTTTCAAAGCCCGCAAGTTAGTGG
1 CATCTCTTCTCAAACCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
*
373100 CATC-CTTCTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCTCTTCTCAAA-CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
373157 CATCT-TT-TCAAAGCCCACAAGTCAGTGGC-TCCCTTTTCAAAGCCCACAAGTTAGTGG
1 CATCTCTTCTCAAA-CCCACAAGTCAGTGGCAT-CC-TTTCAAAGCCCACAAGTTAGTGG
* * * * ** * **
373214 C-TCCCTTTTCAAAGCCCACAAGCCAGTGGTAACTTTTTTCAAAGTCCATACAAGTCGGTGG
1 CATCTCTTCTCAAA-CCCACAAGTCAGTGG-CA-TCCTTTCAAAG-CC-CACAAGTTAGTGG
* * * * * * *
373275 CAACTCTTTTCAAAGACCACACAAATCGGTGGCACCCTTCCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCTC-AA-ACC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* * * *
373335 CA-CCCTT-TCAAAGCTCAAAAGTCAGTGGCACCCTTTCAAAGCCCACCCAAGTTAGTGG
1 CATCTCTTCTCAAA-CCCACAAGTCAGTGGCATCCTTTCAAAGCCCA--CAAGTTAGTGG
373393 CA
1 CA
373395 CCTTTTTTTT
Statistics
Matches: 293, Mismatches: 39, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
55 1 0.00
56 66 0.23
57 117 0.40
58 38 0.13
59 12 0.04
60 15 0.05
61 14 0.05
62 14 0.05
63 5 0.02
64 11 0.04
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (57 bp):
CATCTCTTCTCAAACCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
Found at i:373849 original size:12 final size:12
Alignment explanation
Indices: 373832--373861 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
373822 ACTTATTTTT
373832 TAAAAAAATAAA
1 TAAAAAAATAAA
373844 TAAAAAAATAAA
1 TAAAAAAATAAA
373856 -AAAAAA
1 TAAAAAA
373862 TGAGTGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:374432 original size:20 final size:20
Alignment explanation
Indices: 374407--374478 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
374397 TACCTAGATC
*
374407 TATCGATACATTTTTTAATG
1 TATCGATACATTTTTCAATG
* * *
374427 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
*
374447 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
374467 TATCGATACATT
1 TATCGATACATT
374479 CTCTCGTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:374512 original size:90 final size:91
Alignment explanation
Indices: 374354--374528 Score: 237
Period size: 90 Copynumber: 1.9 Consensus size: 91
374344 TTTTACCTAG
* * * * * * *
374354 ATGTATTGATACATTTTTTAATGTATCGATACATTCTGTCTTTTACCTAGATCTATCGATACATT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTCTCTTTTACCGAAATCTATCAATACATT
*
374419 TTTT-AATGTATCGATACATGTATGA
66 TTTTCAATATATCGATACATGTATGA
* *
374444 ATGTATCGATACATTCTTCAATGTATCGATACATTCTCTCGTTTTACCGAAATGTATTAATACA-
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTCTC-TTTTACCGAAATCTATCAATACAT
374508 TTTTTCAATATATCGATACAT
65 TTTTTCAATATATCGATACAT
374529 CTAGTTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
90 41 0.56
91 32 0.44
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (91 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTCTCTTTTACCGAAATCTATCAATACATT
TTTTCAATATATCGATACATGTATGA
Found at i:381305 original size:20 final size:20
Alignment explanation
Indices: 381282--381343 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
381272 TGCTTCGTAT
*
381282 TGATACATTGTATCGATACG
1 TGATACATTGTATCGATACA
381302 TGAT-CATTGTATCGATACA
1 TGATACATTGTATCGATACA
381321 TGA-ACAATTGTATCGATACA
1 TGATAC-ATTGTATCGATACA
381341 TGA
1 TGA
381344 AACTGGTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:381344 original size:20 final size:19
Alignment explanation
Indices: 381286--381344 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
381276 TCGTATTGAT
*
381286 ACATTGTATCGATACGTGA
1 ACATTGTATCGATACATGA
*
381305 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
381324 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
381344 A
1 A
381345 ACTGGTAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:382327 original size:20 final size:21
Alignment explanation
Indices: 382302--382355 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
382292 AATTTTAGGC
*
382302 ATGTATCGATACATTCACT-T
1 ATGTATCAATACATTCACTAT
*
382322 ATGTATCAATACATTTACTAT
1 ATGTATCAATACATTCACTAT
*
382343 TTGTATCAATACA
1 ATGTATCAATACA
382356 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
ATGTATCAATACATTCACTAT
Found at i:382922 original size:61 final size:61
Alignment explanation
Indices: 382783--383509 Score: 668
Period size: 61 Copynumber: 12.0 Consensus size: 61
382773 AGACACCTTG
* * * * * * * * ** *
382783 CTCTTTGAGGACTAGAAGGTGCCACTAGCTTATGTGGACTTTAAAAGAAAAAAAAGTGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG--GAAAAGGCATCCTA
* *
382846 CTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
* * * * * *
382907 CTTTTTGAGGACTAAAAGGTGACACCAGCTTGTGTAGGG-TTT-TAAGGGAAAGTG--TCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGT-GGGCTTTGAAAGGAAAAG-GCATCCTA
* * * * * * ***
382966 CTCTTTAAGGACTAAAAGGTACTACCAAGTTGTGTGGGCTTTAAAAGAAAAAAAAATGTCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCA--TCCTA
* * *
383029 CTCTTT-AGGGACTAAAAGGTGCCACCAACTTGTGTGGCCTTTGAAAAGAAAATGCATCCTA
1 CTCTTTGA-GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
* * * *
383090 CTCTTTCAGGACTAAAAGGTGCCACCAACGTGTGTGGGCTTTGAAAGGAAAAGGCATTCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
* *
383151 CTCTTTGAGAACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGG-AAAGTG--TCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG-GCATCCTA
* * * * * * ** *
383210 CTTTTTGAAGATTGAAAGGTGCCATCAACTTGTATGGGCTTTGAAAGGAAAAGGTGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
* * * * * **
383271 CTCTTTGAGGACTAAAAAGTGCCACAAACTTGTGTGGGCTTTCAAAGGGAAATGTGTCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
* * *
383332 CTCTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGCA-CCTTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC-TA
* * * * * *
383393 CTCTTTTAGGACTAAAAGGTGCCATCAGCTTGTGTAGGCTTTTAAAGG-AAAGTG--TCTTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG-GCATCCTA
* * * * * *
383452 CTTTTTGAAGACTAAAAGGTGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGGCATC
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATC
383510 TTGCCATCAA
Statistics
Matches: 543, Mismatches: 101, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
58 3 0.01
59 121 0.22
60 32 0.06
61 295 0.54
62 4 0.01
63 88 0.16
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (61 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
Found at i:382999 original size:120 final size:119
Alignment explanation
Indices: 382781--383509 Score: 737
Period size: 120 Copynumber: 6.0 Consensus size: 119
382771 AAAGACACCT
* * * * ** *
382781 TGCTCTTTGAGGACTAGAAGGTGCCACTAGCTTATGTGGACTTTAAAAGAAAAAAAAGTGTCCTG
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGG-GTTT----GAAAGGAAAGTGTCCTA
* * *
382846 CTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCC
61 CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
* * * * * *
382905 TACTTTTTGAGGACTAAAAGGTGACACCAGCTTGTGTAGGGTTTTAAGGGAAAGTGTCCTGCTCT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGT-GGGTTTGAAAGGAAAGTGTCCTACTCT
* * * * * ***
382970 TTAAGGACTAAAAGGTACTACCAAGTTGTGTGGGCTTTAAAAGAAAAAAAAATGTCC
65 TTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCA--TCC
* * * * *
383027 TACTCTTT-AGGGACTAAAAGGTGCCACCAACTTGTGTGGCCTTTGAAAAGAAAATGCATCCTAC
1 TGCTCTTTGA-GGACTAAAAGGTGCCACCAGCTTGTGTGG-GTTTGAAAGGAAAGTG--TCCTAC
* * *
383091 TCTTTCAGGACTAAAAGGTGCCACCAACGTGTGTGGGCTTTGAAAGGAAAAGGCATTC
62 TCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
* *
383149 TGCTCTTTGAGAACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGAAAGTGTCCTACTTT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGG-TTTGAAAGGAAAGTGTCCTACTCT
* * * * **
383214 TTGAA-GATTGAAAGGTGCCATCAACTTGTATGGGCTTTGAAAGGAAAAGGTGTCC
65 TT-AAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
* * * *
383269 TGCTCTTTGAGGACTAAAAAGTGCCACAAACTTGTGTGGGCTTTCAAAGGGAAATGTGTCCTACT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGG-TTTGAAA-GGAAA-GTGTCCTACT
* * *
383334 CTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGCA-CC
63 CTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
* * * * * *
383390 TTGCTCTTTTAGGACTAAAAGGTGCCATCAGCTTGTGTAGGCTTTTAAAGGAAAGTGTCTTACTT
1 -TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGT-GGGTTTGAAAGGAAAGTGTCCTACTC
* * * *
383455 TTTGAA-GACTAAAAGGTGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGGCATC
64 TTT-AAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATC
383510 TTGCCATCAA
Statistics
Matches: 501, Mismatches: 87, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
120 206 0.41
121 19 0.04
122 187 0.37
123 3 0.01
124 84 0.17
125 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (119 bp):
TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGTTTGAAAGGAAAGTGTCCTACTCTT
TAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
Found at i:383371 original size:242 final size:242
Alignment explanation
Indices: 382781--383505 Score: 902
Period size: 242 Copynumber: 3.0 Consensus size: 242
382771 AAAGACACCT
* * * * * * *
382781 TGCTCTTTGAGGACTAGAAGGTGCCACTAGCTTATGTGGACTTTAAAAGAAAAAAAAGTGTCCTG
1 TGCTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTGGACTTTAAAAG--GAAAATGTGTCCTA
* * * *
382846 CTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCCTACTTT
64 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCT
* * * *
382911 TTGAGGACTAAAAGGTGACACCAGCTTGTGTAGGG-TTTTAAGGGAAAGTGTCCTGCTCTTT-AA
129 TTGAGGACTAAAAGGTGCCACCAGCTTGTGT-GGGCTTTTAAAGGAAAGTGTCCTACTTTTTGAA
* * * * * * **
382974 GGACTAAAAGGTACTACCAAGTTGTGTGGGCTTTAAAAGAAAAAAAAATGTCC
193 -GACTAAAAGGTGCCATCAACTTGTATGGGCTTTAAAAG--GAAAAGGTGTCC
* * * **
383027 TACTCTTT-AGGGACTAAAAGGTGCCACCAACTTGTGTGGCCTTTGAAAA-GAAAATGCATCCTA
1 TGCTCTTTGA-GGACTAAAAGGTGCCACAAACTTGTGTGGACTTT-AAAAGGAAAATGTGTCCTA
* * *
383090 CTCTTTCAGGACTAAAAGGTGCCACCAACGTGTGTGGGCTTTGAAAGGAAAAGGCATTCTGCTCT
64 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCT
* *
383155 TTGAGAACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGAAAGTGTCCTACTTTTTGAAG
129 TTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTTAAAGGAAAGTGTCCTACTTTTTGAAG
* * *
383220 ATTGAAAGGTGCCATCAACTTGTATGGGCTTTGAAAGGAAAAGGTGTCC
194 ACTAAAAGGTGCCATCAACTTGTATGGGCTTTAAAAGGAAAAGGTGTCC
* * * *
383269 TGCTCTTTGAGGACTAAAAAGTGCCACAAACTTGTGTGGGCTTTCAAAGGGAAATGTGTCCTACT
1 TGCTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTGGACTTTAAAAGGAAAATGTGTCCTACT
* *
383334 CTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGCA-CCTTGCTCTT
66 CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC-TGCTCTT
* * * *
383398 TTAGGACTAAAAGGTGCCATCAGCTTGTGTAGGCTTTTAAAGGAAAGTGTCTTACTTTTTGAAGA
130 TGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTTAAAGGAAAGTGTCCTACTTTTTGAAGA
* *
383463 CTAAAAGGTGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGG
195 CTAAAAGGTGCCATCAACTTGTATGGGCTTTAAAAGGAAAAGG
383506 CATCTTGCCA
Statistics
Matches: 413, Mismatches: 59, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
241 4 0.01
242 214 0.52
243 4 0.01
244 148 0.36
245 3 0.01
246 36 0.09
247 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (242 bp):
TGCTCTTTGAGGACTAAAAGGTGCCACAAACTTGTGTGGACTTTAAAAGGAAAATGTGTCCTACT
CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTT
GAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTTAAAGGAAAGTGTCCTACTTTTTGAAGAC
TAAAAGGTGCCATCAACTTGTATGGGCTTTAAAAGGAAAAGGTGTCC
Found at i:383530 original size:40 final size:40
Alignment explanation
Indices: 383471--383553 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
383461 GACTAAAAGG
383471 TGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGGCATCT
1 TGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGGCATCT
* *
383511 TGCCATCAACTT-TTGTGGGCTTTAAAATGAAAAGGCGTCT
1 TGCCATCAACTTATT-TGGGCTTTAAAAGGAAAAGGCATCT
383551 TGC
1 TGC
383554 TCTTTAAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 2 0.05
40 38 0.95
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (40 bp):
TGCCATCAACTTATTTGGGCTTTAAAAGGAAAAGGCATCT
Found at i:383555 original size:160 final size:161
Alignment explanation
Indices: 383351--383671 Score: 421
Period size: 160 Copynumber: 2.0 Consensus size: 161
383341 GATTAAAAGG
* * *
383351 TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGCACCTTGCTCTTTTAGGACTAAAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCACCTTGCTCTTTAAGGACTAAAAGGTGCC
* * * * * *
383416 ATCAGCTTGTGTAGGCTTTTAAAGG-AAAGTG-TCTTACTTTTTGAAGACTAAAAGGTGCCATCA
66 ACCAACTTGTGTAGGCTTTGAAAGGAAAAG-GATCCTACTCTTTGAAGACTAAAAGGTGCCACCA
*
383479 ACTTATTTGGGCTTTAAAAGGAAAAGGCATCT
130 ACTTATGTGGGCTTTAAAAGGAAAAGGCATCT
* * * **
383511 TGCCATCAACTTTTGTGGGCTTTAAAATGAAAAGGCGTCTTGCTCTTTAAGGACTAAAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCACCTTGCTCTTTAAGGACTAAAAGGTGCC
* * * *
383576 ACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTTGAGGAGTAAAAGGTGCCACCA
66 ACCAACTTGTGTAGGCTTTGAAAGGAAAAGG-ATCCTACTCTTTGAAGACTAAAAGGTGCCACCA
* *
383641 GCTTGTGTGGGCTTTAAAAGGAAAAGGCATC
130 ACTTATGTGGGCTTTAAAAGGAAAAGGCATC
383672 CTGCTTTTCT
Statistics
Matches: 137, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
160 79 0.58
161 4 0.03
162 54 0.39
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (161 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCACCTTGCTCTTTAAGGACTAAAAGGTGCC
ACCAACTTGTGTAGGCTTTGAAAGGAAAAGGATCCTACTCTTTGAAGACTAAAAGGTGCCACCAA
CTTATGTGGGCTTTAAAAGGAAAAGGCATCT
Found at i:383589 original size:61 final size:61
Alignment explanation
Indices: 383511--383676 Score: 251
Period size: 61 Copynumber: 2.7 Consensus size: 61
383501 AAAGGCATCT
* * * * *
383511 TGCCATCAACTTTTGTGGGCTTTAAAATGAAAAGGCGTCTTGCTCTTTAAGGACTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAAGG
* * *
383572 TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTCTTTGAGGAGTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAAGG
*
383633 TGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCT
383677 TTTCTCATTA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (61 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAAGG
Found at i:383895 original size:44 final size:44
Alignment explanation
Indices: 383786--383895 Score: 168
Period size: 44 Copynumber: 2.5 Consensus size: 44
383776 TGTTTGGCGT
* *
383786 ATGGTTACCACCCTAGTCAAACTCTTCTTATTTTAATCTGACAT
1 ATGGTTACCACCCTAGTCAAATTCTTCTTATTTTAATCTGACAC
* *
383830 ATGGTTACCACCCTAGTCAAATTCTT-TTCATTTTGATTTGACAC
1 ATGGTTACCACCCTAGTCAAATTCTTCTT-ATTTTAATCTGACAC
383874 ATGGTTACCACCCTAGTCAAAT
1 ATGGTTACCACCCTAGTCAAAT
383896 CTGCCTCCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 2 0.03
44 59 0.97
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (44 bp):
ATGGTTACCACCCTAGTCAAATTCTTCTTATTTTAATCTGACAC
Found at i:383913 original size:44 final size:44
Alignment explanation
Indices: 383785--383938 Score: 141
Period size: 44 Copynumber: 3.5 Consensus size: 44
383775 CTGTTTGGCG
* * * * * *
383785 TATGGTTACCACCCTAGTCAAACTCTTCTTATTTTAATCTGACA
1 TATGGTTACCACCCTAGTCAAATTCTCCTCATTCTGATTTGACA
** *
383829 TATGGTTACCACCCTAGTCAAATTCTTTTCATTTTGATTTGACA
1 TATGGTTACCACCCTAGTCAAATTCTCCTCATTCTGATTTGACA
* * *
383873 CATGGTTACCACCCTAGTCAAA-TCTGCCTCCTTCCT-ATTTGACG
1 TATGGTTACCACCCTAGTCAAATTCT-CCTCATT-CTGATTTGACA
* * *
383917 TTTGGTTACCACCTTGGTCAAA
1 TATGGTTACCACCCTAGTCAAA
383939 CGATTTGTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.03
44 89 0.96
45 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (44 bp):
TATGGTTACCACCCTAGTCAAATTCTCCTCATTCTGATTTGACA
Found at i:384148 original size:82 final size:83
Alignment explanation
Indices: 384040--384240 Score: 244
Period size: 82 Copynumber: 2.4 Consensus size: 83
384030 GTCGGCTTAA
* * ** * *
384040 TCTTTAGTGAACTCTTTTACCTTTTGTTGACTTATTGGTGCAGCCTTGGTC-CTTTTTATCCTTT
1 TCTTTAGTGAACTCCTTTACCCTTTGTTGACTTATCAGTGCAGCCCTGGTCACCTTTTATCCTTT
***
384104 ATCTACCTGTTGGCTCAG
66 ATCTACCTGTCAACTCAG
* *
384122 TCTTTAGTGAACTCCTTTCCCCTTTGTTGACTTATCAGTTCAGCCCTGGTCAACCTTTTATCCTT
1 TCTTTAGTGAACTCCTTTACCCTTTGTTGACTTATCAGTGCAGCCCTGGTC-ACCTTTTATCCTT
*
384187 TGTCTACCTGTCAACTCAG
65 TATCTACCTGTCAACTCAG
** *
384206 TCCCTGGTGAACT-CTTTACCCTTTGTTGACTTATC
1 TCTTTAGTGAACTCCTTTACCCTTTGTTGACTTATC
384241 GATTTAGCCT
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
82 44 0.44
83 21 0.21
84 36 0.36
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (83 bp):
TCTTTAGTGAACTCCTTTACCCTTTGTTGACTTATCAGTGCAGCCCTGGTCACCTTTTATCCTTT
ATCTACCTGTCAACTCAG
Found at i:384187 original size:41 final size:42
Alignment explanation
Indices: 384131--384240 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
384121 GTCTTTAGTG
* **
384131 AACTCCTTTCCCCTTTGTTGACTTATCAGTTCAG-CCCTGGTC
1 AACT-CTTTACCCTTTGTTGACTTATCAACTCAGTCCCTGGTC
* * * *
384173 AAC-CTTTTATCCTTTGTCT-ACCTGTCAACTCAGTCCCTGGTG
1 AACTC-TTTACCCTTTGT-TGACTTATCAACTCAGTCCCTGGTC
384215 AACTCTTTACCCTTTGTTGACTTATC
1 AACTCTTTACCCTTTGTTGACTTATC
384241 GATTTAGCCT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
40 1 0.02
41 21 0.40
42 30 0.57
43 1 0.02
ACGTcount: A:0.16, C:0.31, G:0.13, T:0.40
Consensus pattern (42 bp):
AACTCTTTACCCTTTGTTGACTTATCAACTCAGTCCCTGGTC
Found at i:384278 original size:83 final size:84
Alignment explanation
Indices: 384128--384291 Score: 208
Period size: 83 Copynumber: 2.0 Consensus size: 84
384118 TCAGTCTTTA
* * * *
384128 GTGAACTCCTTTCCCCTTTGTTGACTTATCAGTTCAGCCCTGGTCAACCTTTTATCCTTTGTCTA
1 GTGAACTCCTTTACCCTTTGTTGACTTATCAGTTCAGCCCTGATCAACCTTTCATCCCTTGTCTA
384193 CCTGTCAACTCAGTCCCTG
66 CCTGTCAACTCAGTCCCTG
* * *
384212 GTGAACT-CTTTACCCTTTGTTGACTTATC-GATTTAG-CCTGCATTAACCTTTCATCCCTTGTT
1 GTGAACTCCTTTACCCTTTGTTGACTTATCAG-TTCAGCCCTG-ATCAACCTTTCATCCCTTGTC
* *
384274 TACCTGTCAGCTTAGTCC
64 TACCTGTCAACTCAGTCC
384292 TGGGTAAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
82 5 0.07
83 57 0.83
84 7 0.10
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.40
Consensus pattern (84 bp):
GTGAACTCCTTTACCCTTTGTTGACTTATCAGTTCAGCCCTGATCAACCTTTCATCCCTTGTCTA
CCTGTCAACTCAGTCCCTG
Found at i:385585 original size:13 final size:13
Alignment explanation
Indices: 385567--385591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385557 TTCATAAGTT
385567 TTAAAATTTTTCC
1 TTAAAATTTTTCC
385580 TTAAAATTTTTC
1 TTAAAATTTTTC
385592 TATTTTCGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTTTTCC
Found at i:385628 original size:166 final size:166
Alignment explanation
Indices: 385445--385847 Score: 417
Period size: 167 Copynumber: 2.4 Consensus size: 166
385435 ATTACAGGGC
* *
385445 TTTCTTCTCCGTAAATTTTTTCGGAAGGA-TTTTCATGGGTTTAAAATTTTAAAAATTCATCAAA
1 TTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTC-TGGGTTTAAAATTTT-AAAATTCATCAAA
385509 TATTATTT-TCTATTTCATATTAAATCAGATTTT-AAAAATTCATTCA-TCTTCATAAG-TTTTA
64 TATTATTTATCTATTTCATATTAAATCAG-TTTTCAAAAATTCA-TCAGTCTTCATAAGTTTTTA
* *
385570 AAATTTTTCCTTAAAAT-TTTTCTATTTTCGAAATATTGAGT
127 AAATTTTTCC-T-AAATGTTTTCTATTTTCGAAAAATCGAGT
* * **
385611 TTTCTACTCCATAAATTTTTTTCAGG-GGGATTTTTCTTGGTTTTTAATTTGTAAAATTCATCAA
1 TTTCTACTCCGTAAA-TTTTTTC-GGAGGGATTTTTCTGGGTTTAAAATTT-TAAAATTCATCAA
* * * * * * *
385675 ATATT-TTTATTTATTTCATATTGAATTAGTTTTCAAAAATTCATGAGTTTTCATGAGTTTTTTA
63 ATATTATTTATCTATTTCATATTAAATCAGTTTTCAAAAATTCATCAGTCTTCATAAGTTTTTAA
* * * *
385739 TATTTTTTCTAAATGTTTTTTATTTTTGAAAAATCGAGT
128 AATTTTTCCTAAATGTTTTCTATTTTCGAAAAATCGAGT
* * * * ** * *
385778 TTTCTGCACCGTAAATGTTTTCAGAGGGATTTTTCTTGATTTTAAACTTTTAAAATTCATCTAAT
1 TTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTC-TGGGTTTAAAATTTTAAAATTCATCAAAT
385843 ATTAT
65 ATTAT
385848 CATTAAATTC
Statistics
Matches: 194, Mismatches: 31, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
165 1 0.01
166 59 0.30
167 114 0.59
168 20 0.10
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (166 bp):
TTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCTGGGTTTAAAATTTTAAAATTCATCAAATA
TTATTTATCTATTTCATATTAAATCAGTTTTCAAAAATTCATCAGTCTTCATAAGTTTTTAAAAT
TTTTCCTAAATGTTTTCTATTTTCGAAAAATCGAGT
Found at i:386349 original size:10 final size:10
Alignment explanation
Indices: 386330--386372 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
386320 GTTCAGCGAA
386330 AAAAAAAGAG
1 AAAAAAAGAG
*
386340 AAAAAGAGAG
1 AAAAAAAGAG
386350 AAAAAAA-AG
1 AAAAAAAGAG
386359 AAAGAAAA-AG
1 AAA-AAAAGAG
386369 AAAA
1 AAAA
386373 GGAAATAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 6 0.20
10 24 0.80
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:386364 original size:23 final size:22
Alignment explanation
Indices: 386327--386369 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
386317 TTAGTTCAGC
*
386327 GAAAAAAAAAGAGAAAAAGAGA
1 GAAAAAAAAAAAGAAAAAGAGA
386349 GAAAAAAAAGAAAGAAAAAGA
1 GAAAAAAAA-AAAGAAAAAGA
386370 AAAGGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAAAGAAAAAGAGA
Found at i:388547 original size:79 final size:80
Alignment explanation
Indices: 388412--388833 Score: 435
Period size: 79 Copynumber: 5.3 Consensus size: 80
388402 TCAACGAGGC
* * * ** * * *
388412 TGGAGTATCCCCTGACTATGGAAAATCGGTGTTTTAGAAATAAAA-TCGAGATTGGAGTATCCCC
1 TGGAGTATCCCC-GATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCC
*
388476 TCGAAAATAACGGGGT
65 TCGAAAATAACAGGGT
* * ** *
388492 TGGAGTATCCCTGATTGTGAAAAATTAATGTTTTGGAAATAAAACT-GGGGCTGGAGTATCCCCT
1 TGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCCT
388556 C-AGAAATAACAGGGT
66 CGA-AAATAACAGGGT
* * *** * *
388571 TGAAGTATCCCCGATTGTGATAAATTGGTGTTTTGAAAATAAAA-TCGGGGTTAGAGTATCCCCT
1 TGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCCT
388635 CGAAAATAACAGGGT
66 CGAAAATAACAGGGT
* * ** * * ** * *
388650 TGGAGTATCCTCGATTATGGTAAATCGATGCTTTAAAAATAAGGCT-GGGGTTGGAGTACCCCCG
1 TGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCCT
388714 CGAAAATAACAGGGT
66 CGAAAATAACAGGGT
* * * * *
388729 TGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAAT-AAAGTCGGGGTTTGAGTATCCCCT
1 TGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCCT
*
388793 C-AGAAATAACGGGGT
66 CGA-AAATAACAGGGT
388808 TGGAGTATCCCCGATTGTGAAAAATC
1 TGGAGTATCCCCGATTGTGAAAAATC
388834 TAGAAATTTA
Statistics
Matches: 286, Mismatches: 49, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
78 5 0.02
79 267 0.93
80 14 0.05
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (80 bp):
TGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACTCGGGGTTGGAGTATCCCCT
CGAAAATAACAGGGT
Found at i:388727 original size:158 final size:157
Alignment explanation
Indices: 388434--388833 Score: 491
Period size: 158 Copynumber: 2.5 Consensus size: 157
388424 TGACTATGGA
* * *
388434 AAATCGGTGTTTTAGAAATAAAATCGAGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTA
1 AAATCGGTGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTA
* * * ** * *
388499 TCCCTGATTGTGAAAAATTAATGTTTTGGAAATAAAACTGGGGCTGGAGTATCCCCTCAGAAATA
66 TCCC-GATTATGAAAAATCAATGCTTTAAAAATAAAACTGGGGCTGGAGTACCCCCGCAGAAATA
*
388564 ACAGGGTTGAAGTATCCCCGATTGTGAT
130 ACAGGGTTGAAGTATCCCCGATTGTGAG
* *
388592 AAATTGGTGTTTT-GAAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGT
1 AAATCGGTGTTTTAG-AAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
** * ** *
388656 ATCCTCGATTATGGTAAATCGATGCTTTAAAAATAAGGCTGGGGTTGGAGTACCCCCGC-GAAAA
65 ATCC-CGATTATGAAAAATCAATGCTTTAAAAATAAAACTGGGGCTGGAGTACCCCCGCAG-AAA
*
388720 TAACAGGGTTGGAGTATCCCCGATTGTGAG
128 TAACAGGGTTGAAGTATCCCCGATTGTGAG
** * * *
388750 AAATCAATATTTTAGAAATAAAGTCGGGGTTTGAGTATCCCCTC-AGAAATAACGGGGTTGGAGT
1 AAATCGGTGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGA-AAATAACGGGGTTGGAGT
*
388814 ATCCCCGATTGTGAAAAATC
65 AT-CCCGATTATGAAAAATC
388834 TAGAAATTTA
Statistics
Matches: 206, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
157 3 0.01
158 199 0.97
159 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (157 bp):
AAATCGGTGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTA
TCCCGATTATGAAAAATCAATGCTTTAAAAATAAAACTGGGGCTGGAGTACCCCCGCAGAAATAA
CAGGGTTGAAGTATCCCCGATTGTGAG
Found at i:391897 original size:61 final size:60
Alignment explanation
Indices: 391786--391901 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 60
391776 AAATGGGTCC
* **
391786 TGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCTTTGCAAGGAGAAAGCATCA
1 TGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCCTTAAAAGGA-AAAGCATCA
* * * *
391847 TGCT-CTTTGAGGACTAGAAGGTGCCACTAGCTTGTGTGGGCCTTAAAAGGAAAAG
1 TGCTCCTTTG-GGACTAGAAGGTGCCACCAACTTGTATGAGCCTTAAAAGGAAAAG
391902 GTGTCCTGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
60 9 0.19
61 38 0.81
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (60 bp):
TGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCCTTAAAAGGAAAAGCATCA
Found at i:391984 original size:18 final size:18
Alignment explanation
Indices: 391961--392015 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
391951 TTAAAAGGAA
*
391961 AAGGCGTCATGCTCTTTG
1 AAGGCGTCCTGCTCTTTG
391979 AAGGCGTCCTGCTCTTTG
1 AAGGCGTCCTGCTCTTTG
391997 AAGGCGTCCTGCTCTTTG
1 AAGGCGTCCTGCTCTTTG
392015 A
1 A
392016 GGACTAGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (18 bp):
AAGGCGTCCTGCTCTTTG
Found at i:392113 original size:61 final size:62
Alignment explanation
Indices: 391997--392516 Score: 743
Period size: 61 Copynumber: 8.5 Consensus size: 62
391987 CTGCTCTTTG
*
391997 AAGGCGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * *
392058 AAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTAAAAAGAAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * * * *
392120 AAGGCATCCTACTCCTTGAGGAGT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * *
392181 AAGGCATCTTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * *
392243 AAGGCGTCCTGCTCTTTAAGGACT-GAAAAATG---CCAACTTGTGTGAGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* *
392301 AAGGCATCCTGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * *
392362 AAGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAA
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * * * *
392424 AAGGTGTCCTGCTCCTTGAGGACTA-AAAAGTGCTACCAATTTGTGTGGGCTTTAAAAGGAG
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
*
392485 AAGGCGTCTTGCTCTTTGAGGACT-GAAAAGTG
1 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTG
392517 AAAGAAGAAA
Statistics
Matches: 413, Mismatches: 39, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
58 53 0.13
61 194 0.47
62 166 0.40
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (62 bp):
AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
Found at i:392164 original size:123 final size:123
Alignment explanation
Indices: 391997--392513 Score: 722
Period size: 123 Copynumber: 4.2 Consensus size: 123
391987 CTGCTCTTTG
* * **
391997 AAGGCGTCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAGGCATCCTACTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
** * * *
392061 GTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTAAAAAGAAA
65 GCATCCTGCTCCTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* *
392120 AAGGCATCCTACTCCTTGAGGAGTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
1 AAGGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * *
392185 CATCTTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAA
66 CATCCTGCTCCTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * * *
392243 AAGGCGTCCTGCTCTTTAAGGACTGAAAAATG---CCAACTTGTGTGAGCTTTAAAAGGAAAAGG
1 AAGGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
392305 CATCCTGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
66 CATCCTGCTCCTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* *
392362 AAGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAG
1 AAGGCATCCTACTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
** * * *
392427 GTGTCCTGCTCCTTGAGGACTA-AAAAGTGCTACCAATTTGTGTGGGCTTTAAAAGGAG
65 GCATCCTGCTCCTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * *
392485 AAGGCGTCTTGCTCTTTGAGGACTGAAAA
1 AAGGCATCCTACTCTTTGAGGACTGAAAA
392514 GTGAAAGAAG
Statistics
Matches: 353, Mismatches: 35, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
119 57 0.16
120 54 0.15
122 5 0.01
123 236 0.67
124 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (123 bp):
AAGGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
CATCCTGCTCCTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
Found at i:392173 original size:220 final size:220
Alignment explanation
Indices: 391782--392199 Score: 567
Period size: 220 Copynumber: 1.9 Consensus size: 220
391772 AATGAAATGG
**
391782 GTCCTGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCTTTGCAAGGAGAAAGCATCA
1 GTCCTGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCTTTAAAAGGAGAAAGCATCA
* * * * ** *
391847 TGCTCTTTGAGGACTAGAAGGTGCCACTAGCTTGTGTGGGCCTTAAAAGGAAAAGGTGTCCTGCC
66 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCCTTAAAAGAAAAAGGCATCCTACC
* * *
391912 CTTTAAGGATTGGAAAAGTGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGGCGTCATGCTCTT
131 CTTTAAGGAGTGGAAAAATGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGGCATCATGCTCTT
391977 TGAAGGCGTCCTGCTCTTTGAAGGC
196 TGAAGGCGTCCTGCTCTTTGAAGGC
* * **
392002 GTCCTGCT-CTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGTGT
1 GTCCTGCTCCTTTG-GGACTAGAAGGTGCCACCAACTTGTATGAGCTTTAAAAGGAGAAA-GCAT
*
392065 CCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGG-CTTAAAAAGAAAAAGGCATCC
64 CATGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCCTT-AAAAGAAAAAGGCATCC
* * * *
392129 TACTCC-TTGAGGAGT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTG
127 TAC-CCTTTAAGGAGTGGAAAAATGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGGCATCATG
392192 CTCTTTGA
191 CTCTTTGA
392200 GGACTAGAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
219 8 0.05
220 119 0.69
221 43 0.25
222 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (220 bp):
GTCCTGCTCCTTTGGGACTAGAAGGTGCCACCAACTTGTATGAGCTTTAAAAGGAGAAAGCATCA
TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCCTTAAAAGAAAAAGGCATCCTACC
CTTTAAGGAGTGGAAAAATGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGGCATCATGCTCTT
TGAAGGCGTCCTGCTCTTTGAAGGC
Found at i:393672 original size:28 final size:28
Alignment explanation
Indices: 393616--393687 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
393606 GGAATAAAGC
** *
393616 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
393644 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
393672 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
393688 TCGACTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:393740 original size:52 final size:51
Alignment explanation
Indices: 393675--393896 Score: 212
Period size: 52 Copynumber: 4.3 Consensus size: 51
393665 GAAATAACAA
* * * * * *
393675 GGTTGGAGTATCCTCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTAGAAATAAAACCGG
* * * * * *
393727 AGTTGGAGTATCCTCGATTAAAGGAAAATTGGTG-TTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTAG-AAATAAAACCGG
* *
393779 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * * **
393831 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
393882 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
393897 TCGGAAATAA
Statistics
Matches: 140, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
51 41 0.29
52 84 0.60
53 15 0.11
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:393913 original size:28 final size:28
Alignment explanation
Indices: 393879--393951 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
393869 GAAATAAAGT
393879 CGGGGTTGGAGTATCCCCTCGGA-AAT-AA
1 CGGGGTTGGAGTATCCCC-C-GATAATCAA
*
393907 CGGGGTTGGAGTA-CCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCCGATAATCAA
393934 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
393952 GATTGTGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
25 2 0.05
26 3 0.07
27 19 0.46
28 17 0.41
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGATAATCAA
Found at i:394056 original size:263 final size:262
Alignment explanation
Indices: 393571--394065 Score: 735
Period size: 263 Copynumber: 1.9 Consensus size: 262
393561 ATAACGGGGC
* * * *
393571 TGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTC
1 TGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTC
* * *
393636 GGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTATGAAAA
66 GGAAATAACGGGGTTGGAGTACCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTATGAAAA
* * *
393701 ATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTCG
130 ATTGGTATTTTTGGAAATAAAATCGGAGTTGGACTATCCCCGATTAAAGGAAAATTAGTGTTTCG
* *
393766 AAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
195 AAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
393831 GAT
260 GAT
* *
393834 TGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTC
1 TGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTC
** * *
393899 GGAAATAACGGGGTTGGAGTACCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTGTGAAGA
66 GGAAATAACGGGGTTGGAGTACCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTATGAA-A
* *
393963 AATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGACTATCCCCGATTATA-GAAAATTAGTGTCT
129 AATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGACTATCCCCGATTAAAGGAAAATTAGTGT-T
*
394027 T-GAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
192 TCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
394066 GAATTGAGGA
Statistics
Matches: 207, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
261 2 0.01
262 24 0.12
263 141 0.68
264 40 0.19
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (262 bp):
TGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTC
GGAAATAACGGGGTTGGAGTACCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTATGAAAAA
TTGGTATTTTTGGAAATAAAATCGGAGTTGGACTATCCCCGATTAAAGGAAAATTAGTGTTTCGA
AAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGG
AT
Found at i:396447 original size:13 final size:13
Alignment explanation
Indices: 396429--396454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
396419 ACAAAGATCC
396429 ATGTATCGATACA
1 ATGTATCGATACA
396442 ATGTATCGATACA
1 ATGTATCGATACA
396455 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:396450 original size:33 final size:33
Alignment explanation
Indices: 396408--396474 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
396398 AAAATTTCCA
***
396408 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
396441 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
396474 A
1 A
396475 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:396518 original size:19 final size:18
Alignment explanation
Indices: 396494--396561 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
396484 CAGTAGCTAA
396494 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
396513 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
396528 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
396545 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
396562 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:396534 original size:13 final size:13
Alignment explanation
Indices: 396516--396540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396506 ACAATACTTA
396516 TGTATCGATACAT
1 TGTATCGATACAT
396529 TGTATCGATACA
1 TGTATCGATACA
396541 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:396538 original size:32 final size:32
Alignment explanation
Indices: 396497--396559 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
396487 TAGCTAATTA
*
396497 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
396529 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
396560 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:397800 original size:14 final size:13
Alignment explanation
Indices: 397763--397811 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
397753 CTTTTCTCTC
*
397763 TTTTTTTTCTTTG
1 TTTTTTTTTTTTG
397776 TTTTGTTTTTTTTG
1 TTTT-TTTTTTTTG
397790 TTTTTTGTTTTTT-
1 TTTTTT-TTTTTTG
397803 TATTTTTTT
1 T-TTTTTTT
397812 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:397802 original size:9 final size:9
Alignment explanation
Indices: 397763--397803 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
397753 CTTTTCTCTC
*
397763 TTTTTTTTC
1 TTTTTTTTG
*
397772 TTTGTTTTG
1 TTTTTTTTG
397781 TTTTTTTTG
1 TTTTTTTTG
397790 --TTTTTTG
1 TTTTTTTTG
397797 TTTTTTT
1 TTTTTTT
397804 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
7 7 0.26
9 20 0.74
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:397809 original size:16 final size:15
Alignment explanation
Indices: 397764--397811 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 15
397754 TTTTCTCTCT
397764 TTTTTTTCTTTGTTTTG
1 TTTTTTT-TTT-TTTTG
397781 TTTTTTTTGTTTTTTG
1 TTTTTTTT-TTTTTTG
397797 TTTTTTTATTTTTTT
1 TTTTTTT-TTTTTTT
397812 AAAAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:401315 original size:16 final size:14
Alignment explanation
Indices: 401293--401335 Score: 61
Period size: 13 Copynumber: 3.0 Consensus size: 14
401283 AATTGCCTGC
401293 ATGTATCGATACAT
1 ATGTATCGATACAT
401307 CAGTGTATCGATACA-
1 -A-TGTATCGATACAT
401322 ATGTATCGATACAT
1 ATGTATCGATACAT
401336 TTGAGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 12 0.46
14 1 0.04
15 1 0.04
16 12 0.46
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (14 bp):
ATGTATCGATACAT
Found at i:412217 original size:79 final size:78
Alignment explanation
Indices: 412045--412460 Score: 374
Period size: 79 Copynumber: 5.3 Consensus size: 78
412035 GGATGACAAA
* * * * * * * * * *
412045 GGGGCTGGAGTATCCCCTGACTATGGAAAATCGGTGTTCTGGAAGTAAAATCGAGATTGGAGTAT
1 GGGGTTGGAGTATCCCC-GATTGTGAAAAATCGATGTTTTGAAAATAAACT-GGGATTGGAGTAT
* *
412110 CTCCTCAAAAATAAT
64 CCCCTCAAAAATAAC
412125 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAACTGGGATTGGAGTATCC
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAACTGGGATTGGAGTATCC
*
412190 CCTCAAAAAAAAAC
66 CCTC-AAAAATAAC
* * * * *
412204 GGGGTTGGAGTATCCCCGATTTTGATAAAT-TAGTGTTTTGAAAATAAAATCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGA-TGTTTTGAAAATAAACT-GGGATTGGAGTAT
*
412268 CCCCTAAAAAATAAC
64 CCCCTCAAAAATAAC
* * ** * * *
412283 GGGATTAGAGTATCCTTGATTGTGAAAAATTGATGCTTT-AGAAATAAGGCTGAGG-TTGGAGTA
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGA-AAATAA-ACTG-GGATTGGAGTA
*
412346 TCCCCGCAAAAATAAC
63 TCCCCTCAAAAATAAC
*** * * * *
412362 CAAGTTGGAGTATCCCCAATTGTGAAAAATCAATATTTT-AGAAATAAAGCCGGGGATT-GAGTA
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGA-AAATAAA--CTGGGATTGGAGTA
*
412425 TCCCCTCAGAAATAAC
63 TCCCCTCAAAAATAAC
*
412441 GAGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
412461 GATATAATGG
Statistics
Matches: 275, Mismatches: 51, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
78 19 0.07
79 215 0.78
80 41 0.15
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAACTGGGATTGGAGTATCC
CCTCAAAAATAAC
Found at i:418298 original size:138 final size:138
Alignment explanation
Indices: 418050--418327 Score: 479
Period size: 138 Copynumber: 2.0 Consensus size: 138
418040 CATGGATCAC
*
418050 GGTAAAATACAAGTTTATGCATGAACATTCTTATGAAATGTTGACTTGAACACTAACTATATGTT
1 GGTAAAATACAAGTTTATGCATGAACATTCTTATGAAATGCTGACTTGAACACTAACTATATGTT
*
418115 AGACATGTTAAGATGCATGGAACATGGTACAAAATGCATGATCAAGGGCTGTTAAGATGAT-GAT
66 AGACATGTTAAAATGCATGGAACATGGTACAAAATGCATGATCAAGGGCTGTTAAGATGATGGA-
418179 CATGAATAT
130 CATGAATAT
* *
418188 GGTAAAATACAAGTTTATGCATGCACATTCTTAT-AAGATGCTGACTTGAACATTAACTATATGT
1 GGTAAAATACAAGTTTATGCATGAACATTCTTATGAA-ATGCTGACTTGAACACTAACTATATGT
*
418252 TAGACATGTTAAAATGCATGGAACATGGTACAAAATGCATGATCAAGGGTTGTTAAGATGATGGA
65 TAGACATGTTAAAATGCATGGAACATGGTACAAAATGCATGATCAAGGGCTGTTAAGATGATGGA
418317 CATGAATAT
130 CATGAATAT
418326 GG
1 GG
418328 CATTTTAGTC
Statistics
Matches: 133, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
137 2 0.02
138 129 0.97
139 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (138 bp):
GGTAAAATACAAGTTTATGCATGAACATTCTTATGAAATGCTGACTTGAACACTAACTATATGTT
AGACATGTTAAAATGCATGGAACATGGTACAAAATGCATGATCAAGGGCTGTTAAGATGATGGAC
ATGAATAT
Found at i:419195 original size:21 final size:21
Alignment explanation
Indices: 419171--419232 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
419161 ATGTGTAAAT
419171 TTGCCTGTATGTATCGATACA
1 TTGCCTGTATGTATCGATACA
** * *
419192 TTGCAAGCATGTATCGATGCA
1 TTGCCTGTATGTATCGATACA
** *
419213 TTTACT-TATGTATTGATACA
1 TTGCCTGTATGTATCGATACA
419233 ATGTTTTCAA
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGCCTGTATGTATCGATACA
Found at i:419342 original size:21 final size:20
Alignment explanation
Indices: 419291--419344 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
419281 CATTTCAAGC
*
419291 ATGTATTGATACATTTACTT
1 ATGTATTGATACATTAACTT
419311 ATGTATTGATACATTAACTT
1 ATGTATTGATACATTAACTT
*
419331 ATTGTATCGATACA
1 A-TGTATTGATACA
419345 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATTGATACATTAACTT
Found at i:424554 original size:13 final size:13
Alignment explanation
Indices: 424536--424560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424526 TAAATACCAG
424536 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
424549 AGAAAAAAGAAA
1 AGAAAAAAGAAA
424561 GTAAAAAAGA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:426023 original size:33 final size:33
Alignment explanation
Indices: 425981--426048 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
425971 GTTGTTGGGC
*
425981 ACAATGTATCGATACT-TT-TCACTATGTATCGAT
1 ACAATGTATCGATA-TATTGT-ACCATGTATCGAT
426014 ACAATGTATCGATATATTGTACCATGTATCGAT
1 ACAATGTATCGATATATTGTACCATGTATCGAT
426047 AC
1 AC
426049 GAACAGTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 1 0.03
33 30 0.94
34 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (33 bp):
ACAATGTATCGATATATTGTACCATGTATCGAT
Found at i:426946 original size:13 final size:13
Alignment explanation
Indices: 426927--426965 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
426917 ACTATTTATG
426927 ATGTATCGATACA
1 ATGTATCGATACA
* *
426940 CTGTATCGATATA
1 ATGTATCGATACA
426953 ATGTATCGATACA
1 ATGTATCGATACA
426966 TGAATAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:427051 original size:21 final size:22
Alignment explanation
Indices: 427020--427070 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
427010 GTGAACAGTG
427020 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
427042 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
427063 TGAACAGT
1 TGAACAGT
427071 AATGAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:427180 original size:53 final size:53
Alignment explanation
Indices: 427116--427252 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
427106 CTACTTCCAA
427116 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
427169 TGTATCGATACATATTGTGTGTATTGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
427222 TGTATCGATACATATTTATGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
427253 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Done.