Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold382
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: 2572505
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 16
Found at i:113858 original size:2 final size:2
Alignment explanation
Indices: 113851--113889 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
113841 TTTTACTACA
113851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
113890 GTTGGCTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115385 original size:20 final size:20
Alignment explanation
Indices: 115360--115398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
115350 TAATTAGTTA
*
115360 TTAATTTAGAGTTTTAATTG
1 TTAATTTAGAGTTCTAATTG
*
115380 TTAATTTATAGTTCTAATT
1 TTAATTTAGAGTTCTAATT
115399 TATTTATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (20 bp):
TTAATTTAGAGTTCTAATTG
Found at i:116191 original size:16 final size:16
Alignment explanation
Indices: 116170--116240 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 16
116160 TATTAACGCG
116170 TAAAAATTTATATAAA
1 TAAAAATTTATATAAA
116186 TAAAAATTTATATACATTTA
1 TAAAAATTTATATA-A---A
* *
116206 TAACACTTTGAATTATAAA
1 TAAAAATTT--A-TATAAA
116225 TAAAAATTTATATAAA
1 TAAAAATTTATATAAA
116241 AGGGTCAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
16 20 0.45
17 2 0.05
19 8 0.18
20 8 0.18
22 2 0.05
23 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAAAATTTATATAAA
Found at i:116591 original size:22 final size:22
Alignment explanation
Indices: 116566--116613 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
116556 TTTTTTATTA
*
116566 AAAT-TTAATTATAAAAATATAT
1 AAATATTAA-TATAAAAAAATAT
*
116588 AAATATTAATATAAAAAAATTT
1 AAATATTAATATAAAAAAATAT
116610 AAAT
1 AAAT
116614 GATGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTAATATAAAAAAATAT
Found at i:117260 original size:38 final size:37
Alignment explanation
Indices: 117217--117301 Score: 91
Period size: 38 Copynumber: 2.3 Consensus size: 37
117207 ATGTAAATAT
* * *
117217 TAAAATATATGTTAAATTATTTAAAATTTAAAACTTAA
1 TAAAATATATATTAAAATA-TTAAAAATTAAAACTTAA
* **
117255 TAAAATAAAATATTAAAATATTAAAAATTAAATTTTAA
1 TAAAAT-ATATATTAAAATATTAAAAATTAAAACTTAA
117293 -AAAATATAT
1 TAAAATATAT
117302 TTCCTTAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 3 0.08
37 5 0.13
38 21 0.54
39 10 0.26
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (37 bp):
TAAAATATATATTAAAATATTAAAAATTAAAACTTAA
Found at i:117264 original size:22 final size:22
Alignment explanation
Indices: 117238--117294 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
117228 TTAAATTATT
*
117238 TAAAATTTAAAA-CTTAATAAAA
1 TAAAATTTAAAATATTAA-AAAA
*
117260 TAAAATATTAAAATATTAAAAAT
1 TAAAAT-TTAAAATATTAAAAAA
*
117283 TAAATTTTAAAA
1 TAAAATTTAAAA
117295 AATATATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.40
23 14 0.47
24 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATTTAAAATATTAAAAAA
Found at i:117332 original size:17 final size:17
Alignment explanation
Indices: 117292--117337 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
117282 TTAAATTTTA
117292 AAAAATATATTTCC-TT
1 AAAAATATATTTCCTTT
117308 AGAAAATATA-TTCCTTT
1 A-AAAATATATTTCCTTT
*
117325 AAACAATAAATTT
1 AAA-AATATATTT
117338 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAAATATATTTCCTTT
Found at i:118291 original size:19 final size:19
Alignment explanation
Indices: 118267--118304 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
118257 AATCTTAGTT
118267 GGGTTATTGTAGTTTCTTA
1 GGGTTATTGTAGTTTCTTA
118286 GGGTTATTGTAGTTTCTTA
1 GGGTTATTGTAGTTTCTTA
118305 TAAAGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (19 bp):
GGGTTATTGTAGTTTCTTA
Found at i:118600 original size:16 final size:16
Alignment explanation
Indices: 118593--118714 Score: 56
Period size: 16 Copynumber: 7.5 Consensus size: 16
118583 AAATAATTTA
118593 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
* *
118609 TATTTAAACTTAAAAT
1 AATTTAAATTTAAAAT
* *
118625 ATTTTAAACAATTAACTCAAATT
1 AATTT--A-AATT---T-AAAAT
* *
118648 AA-TTCAACTTAAAAT
1 AATTTAAATTTAAAAT
*
118663 AA-TAAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
118678 -A-TTAAATTT-AATT
1 AATTTAAATTTAAAAT
**
118691 AATTTAAATAAAAAAT
1 AATTTAAATTTAAAAT
118707 AATTTAAA
1 AATTTAAA
118715 AATTTAAAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
13 3 0.04
14 9 0.12
15 22 0.28
16 29 0.37
18 1 0.01
19 6 0.08
22 3 0.04
23 5 0.06
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:118606 original size:22 final size:22
Alignment explanation
Indices: 118572--118622 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
118562 AATTGAAATG
*
118572 ATTTTAATATAAAATAATTTAA
1 ATTTAAATATAAAATAATTTAA
* *
118594 ATTTAAATTTAAAATTATTTAA
1 ATTTAAATATAAAATAATTTAA
*
118616 ACTTAAA
1 ATTTAAA
118623 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAATATAAAATAATTTAA
Found at i:118686 original size:14 final size:15
Alignment explanation
Indices: 118656--118688 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
118646 TTAATTCAAC
118656 TTAAAATAATAAAAT
1 TTAAAATAATAAAAT
*
118671 TTAAAAT-ATTAAAT
1 TTAAAATAATAAAAT
118685 TTAA
1 TTAA
118689 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAATAATAAAAT
Found at i:121120 original size:15 final size:15
Alignment explanation
Indices: 121100--121132 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
121090 AATTGAAGTT
121100 AGTCAAGTACAATTA
1 AGTCAAGTACAATTA
*
121115 AGTCAAGTGCAATTA
1 AGTCAAGTACAATTA
121130 AGT
1 AGT
121133 TAACTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (15 bp):
AGTCAAGTACAATTA
Found at i:123436 original size:14 final size:13
Alignment explanation
Indices: 123417--123458 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
123407 TTGCCTCCAA
123417 CCTTCTATCACCTT
1 CCTTCTATC-CCTT
*
123431 CCTTCTCTCCCTT
1 CCTTCTATCCCTT
*
123444 CCTT-TTTCCCTT
1 CCTTCTATCCCTT
123456 CCT
1 CCT
123459 CTTTTCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 8 0.31
14 8 0.31
ACGTcount: A:0.05, C:0.48, G:0.00, T:0.48
Consensus pattern (13 bp):
CCTTCTATCCCTT
Found at i:123467 original size:12 final size:12
Alignment explanation
Indices: 123427--123465 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
123417 CCTTCTATCA
*
123427 CCTTCCTTCTCTC
1 CCTTCCTT-TTTC
123440 CCTTCCTTTTTC
1 CCTTCCTTTTTC
123452 CCTTCCTCTTTTC
1 CCTTCCT-TTTTC
123465 C
1 C
123466 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (12 bp):
CCTTCCTTTTTC
Found at i:133246 original size:15 final size:14
Alignment explanation
Indices: 133226--133264 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
133216 TAATAAAGAA
133226 AATATTTTTAAGTTT
1 AATATTTTTAA-TTT
133241 AATATTTTT-ATTT
1 AATATTTTTAATTT
*
133254 AATTTTTTTAA
1 AATATTTTTAA
133265 AATATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
AATATTTTTAATTT
Found at i:133802 original size:105 final size:105
Alignment explanation
Indices: 133612--133807 Score: 221
Period size: 105 Copynumber: 1.9 Consensus size: 105
133602 GTTTTCTGCA
* * * * * * * *
133612 GGTTTAGCTACTCCTCCATTGTCGTCAACTAACTTTTCTTCTTCACTTTTCGCAGCAGTAACCGC
1 GGTTTAGCTACGCCTCCATTGGCGTCAACCAACTTCTCTTCATCACTTTTAGCAGCACTAACCAC
* * *
133677 ACTGGTCTTTTCGTCTATGGCAGCTTCATCCCGGCTTTCT
66 ACTGATCTGTTCGTCCATGGCAGCTTCATCCCGGCTTTCT
* * * * * *
133717 GGTTTAGCTTCGCTTCCATTGGCGTCAACCAACTTCTCTTCATCATTTTTAGCAGCTCTCATCAC
1 GGTTTAGCTACGCCTCCATTGGCGTCAACCAACTTCTCTTCATCACTTTTAGCAGCACTAACCAC
* *
133782 ACTGATCTGTTCTTCCATGGCCGCTT
66 ACTGATCTGTTCGTCCATGGCAGCTT
133808 TATCAGGGCG
Statistics
Matches: 72, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
105 72 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.38
Consensus pattern (105 bp):
GGTTTAGCTACGCCTCCATTGGCGTCAACCAACTTCTCTTCATCACTTTTAGCAGCACTAACCAC
ACTGATCTGTTCGTCCATGGCAGCTTCATCCCGGCTTTCT
Found at i:135124 original size:6 final size:6
Alignment explanation
Indices: 135113--135156 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
135103 TAGACACCCC
135113 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
135157 GAGATAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:135886 original size:3 final size:3
Alignment explanation
Indices: 135878--135909 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
135868 TCAAAAGCAA
135878 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
135910 AATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:137365 original size:25 final size:25
Alignment explanation
Indices: 137337--137384 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
137327 AAGTTTTATA
137337 AAAAATAAAAAAATTTCAAAAAACT
1 AAAAATAAAAAAATTTCAAAAAACT
* * *
137362 AAAAGTATAAAAATTTTAAAAAA
1 AAAAATAAAAAAATTTCAAAAAA
137385 ATTATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAAATAAAAAAATTTCAAAAAACT
Found at i:138102 original size:25 final size:25
Alignment explanation
Indices: 138060--138144 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
138050 ATAACTTAAT
*
138060 TTAATATATTAAAA-TTTTAAAAAAA
1 TTAAAATA-TAAAATTTTTAAAAAAA
** *
138085 TTAAAATATAAAATTTTTATTAATA
1 TTAAAATATAAAATTTTTAAAAAAA
***
138110 TTAAAAATTATGACTTTTTTTAAAAAAA
1 TT-AAAA-TAT-AAAATTTTTAAAAAAA
138138 TTAAAAT
1 TTAAAAT
138145 TAAGACTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
24 5 0.11
25 17 0.37
26 5 0.11
27 7 0.15
28 12 0.26
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
TTAAAATATAAAATTTTTAAAAAAA
Found at i:138143 original size:27 final size:27
Alignment explanation
Indices: 138074--138152 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
138064 TATATTAAAA
***
138074 TTTTAAAAAAATTAAAA-TAT-AAAAT
1 TTTTAAAAAAATTAAAATTATGACTTT
** *
138099 TTTTATTAATATTAAAAATTATGACTTT
1 TTTTAAAAAAATT-AAAATTATGACTTT
*
138127 TTTTAAAAAAATTAAAATTAAGACTT
1 TTTTAAAAAAATTAAAATTATGACTT
138153 AACAAATCTA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 10 0.24
26 4 0.10
27 15 0.37
28 12 0.29
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTTAAAAAAATTAAAATTATGACTTT
Found at i:138776 original size:3 final size:3
Alignment explanation
Indices: 138770--138806 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
138760 CTACTACTAC
* *
138770 TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
138807 GACCCTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:143098 original size:20 final size:20
Alignment explanation
Indices: 143043--143099 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
143033 AATGATAGGG
* *
143043 AATTGATGGAATTTGATGTGT
1 AATTGA-GGAATTTGAAGAGT
*
143064 AATTGAAGAAATTTGAAGAGT
1 AATTG-AGGAATTTGAAGAGT
*
143085 ATTTGAGGAATTTGA
1 AATTGAGGAATTTGA
143100 GGATTGATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 9 0.30
21 20 0.67
22 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (20 bp):
AATTGAGGAATTTGAAGAGT
Found at i:147311 original size:22 final size:22
Alignment explanation
Indices: 147286--147342 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
147276 ACCAAGGAAA
147286 TGTATTGATACATCCGTCAAAT
1 TGTATTGATACATCCGTCAAAT
* * *
147308 TGTATCGATACATGCTTCAAAT
1 TGTATTGATACATCCGTCAAAT
147330 TGTATTGATACAT
1 TGTATTGATACAT
147343 TATTCAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (22 bp):
TGTATTGATACATCCGTCAAAT
Found at i:147348 original size:22 final size:22
Alignment explanation
Indices: 147286--147362 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
147276 ACCAAGGAAA
* *
147286 TGTATTGATACATCCGTCAAAT
1 TGTATCGATACATCCTTCAAAT
*
147308 TGTATCGATACATGCTTCAAAT
1 TGTATCGATACATCCTTCAAAT
* **
147330 TGTATTGATACATTATTC-AA-
1 TGTATCGATACATCCTTCAAAT
147350 TGTATCGATACAT
1 TGTATCGATACAT
147363 GCATGCATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.25
21 2 0.04
22 34 0.71
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (22 bp):
TGTATCGATACATCCTTCAAAT
Found at i:150407 original size:61 final size:61
Alignment explanation
Indices: 150308--150444 Score: 213
Period size: 61 Copynumber: 2.2 Consensus size: 61
150298 TAAAGATGAT
* *
150308 AAGATGAGAAGAATGATAAAGGTGTCAATATGCAGATTCTAA-GCCAGCGATATTGGGCTTA
1 AAGATGAGAAAAATGATAAAGGTGCCAATATGCAGATTC-AAGGCCAGCGATATTGGGCTTA
**
150369 AAGATGAGAAAAATGATAAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTA
1 AAGATGAGAAAAATGATAAAGGTGCCAATATGCAGATTCAAGGCCAGCGATATTGGGCTTA
*
150430 AAGATGCGAAAAATG
1 AAGATGAGAAAAATG
150445 CCAGTGTGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 2 0.03
61 68 0.97
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.23
Consensus pattern (61 bp):
AAGATGAGAAAAATGATAAAGGTGCCAATATGCAGATTCAAGGCCAGCGATATTGGGCTTA
Found at i:152746 original size:20 final size:20
Alignment explanation
Indices: 152721--152792 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
152711 TTTGCCTACA
152721 TATCGATACAATGATAAATG
1 TATCGATACAATGATAAATG
* *
152741 TATCGATCCAATTTGA-AGCATG
1 TATCGATACAA--TGATA-AATG
* * *
152763 TATCGATACATTTATTAATG
1 TATCGATACAATGATAAATG
152783 TATCGATACA
1 TATCGATACA
152793 TTTCCTTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 25 0.61
21 1 0.02
22 15 0.37
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACAATGATAAATG
Found at i:152837 original size:13 final size:13
Alignment explanation
Indices: 152819--152844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152809 CAAGGTAGTT
152819 TTGTATCGATACA
1 TTGTATCGATACA
152832 TTGTATCGATACA
1 TTGTATCGATACA
152845 AAACTTATGT
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):
TTGTATCGATACA
Found at i:154892 original size:27 final size:26
Alignment explanation
Indices: 154845--154897 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
154835 TATCATTGTC
154845 GGGGACACTCCAACCCTATTTCTTTAA
1 GGGGACACTCCAACCCTATTT-TTTAA
154872 GGGGACACTCCAA-CCTCATTTTTTAA
1 GGGGACACTCCAACCCT-ATTTTTTAA
154898 CCAAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (26 bp):
GGGGACACTCCAACCCTATTTTTTAA
Found at i:159624 original size:17 final size:18
Alignment explanation
Indices: 159604--159705 Score: 71
Period size: 16 Copynumber: 6.1 Consensus size: 18
159594 TGAAAAAGTC
* *
159604 AAAAGCAAAAGCACAAAA
1 AAAAGCAAAAACAAAAAA
159622 AAAAG-AAAAACAAAAAA
1 AAAAGCAAAAACAAAAAA
*
159639 AAAA-C--AAA-AAAACA
1 AAAAGCAAAAACAAAAAA
159653 AAAA-CAAAAAC-AAAAA
1 AAAAGCAAAAACAAAAAA
*
159669 AAAA-CAAAAA-ATAAAA
1 AAAAGCAAAAACAAAAAA
*
159685 AACAG-AAACAACCAAAAAA
1 AAAAGCAAA-AA-CAAAAAA
159704 AA
1 AA
159706 TTAAAAAATG
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.15
15 3 0.04
16 27 0.40
17 16 0.24
18 5 0.07
19 7 0.10
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (18 bp):
AAAAGCAAAAACAAAAAA
Found at i:159636 original size:14 final size:13
Alignment explanation
Indices: 159616--159688 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 13
159606 AAGCAAAAGC
159616 ACAAAAAAAAGAAA
1 ACAAAAAAAA-AAA
*
159630 A-ACAAAAAAAAA
1 ACAAAAAAAAAAA
159642 ACAAAAAAACAAAA
1 ACAAAAAAA-AAAA
159656 ACAAAAACAAAAAAAA
1 AC--AAA-AAAAAAAA
159672 ACAAAAAATAAAAA
1 ACAAAAAA-AAAAA
159686 ACA
1 ACA
159689 GAAACAACCA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
12 4 0.08
13 16 0.31
14 18 0.35
16 9 0.18
17 4 0.08
ACGTcount: A:0.86, C:0.11, G:0.01, T:0.01
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:159638 original size:25 final size:22
Alignment explanation
Indices: 159604--159678 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
159594 TGAAAAAGTC
* *
159604 AAAAGCAAAAGCACAAAA-AAAA
1 AAAAACAAAAACA-AAAACAAAA
159626 GAAAAACAAAAA-AAAAAC--AA
1 -AAAAACAAAAACAAAAACAAAA
159646 AAAAACAAAAACAAAAACAAAA
1 AAAAACAAAAACAAAAACAAAA
159668 AAAAACAAAAA
1 AAAAACAAAAA
159679 ATAAAAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
19 11 0.24
20 8 0.17
21 4 0.09
22 14 0.30
23 9 0.20
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAACAAAAACAAAAACAAAA
Found at i:159639 original size:26 final size:25
Alignment explanation
Indices: 159619--159695 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
159609 CAAAAGCACA
*
159619 AAAAAAAGAAAAACAAAAAAAAAAC
1 AAAAAAACAAAAACAAAAAAAAAAC
*
159644 AAAAAAACAAAAACAAAAACAAAA-
1 AAAAAAACAAAAACAAAAAAAAAAC
* *
159668 AAAAACA-AAAAATAAAAAACAGAAAC
1 AAAAAAACAAAAACAAAAAA-A-AAAC
159694 AA
1 AA
159696 CCAAAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 10 0.23
24 7 0.16
25 25 0.57
26 2 0.05
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (25 bp):
AAAAAAACAAAAACAAAAAAAAAAC
Found at i:159670 original size:30 final size:30
Alignment explanation
Indices: 159620--159704 Score: 109
Period size: 30 Copynumber: 2.7 Consensus size: 30
159610 AAAAGCACAA
*
159620 AAAAAAGAAAAACAAAAAAAAAACAAAAAA-
1 AAAAAACAAAAAC-AAAAAAAAACAAAAAAT
159650 ACAAAAACAAAAACAAAAAAAAACAAAAAAT
1 A-AAAAACAAAAACAAAAAAAAACAAAAAAT
*
159681 AAAAAACAGAAACAACCAAAAAAA
1 AAAAAACAAAAACAA--AAAAAAA
159705 ATTAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
30 30 0.61
31 12 0.24
32 7 0.14
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (30 bp):
AAAAAACAAAAACAAAAAAAAACAAAAAAT
Found at i:159685 original size:6 final size:6
Alignment explanation
Indices: 159603--159678 Score: 70
Period size: 6 Copynumber: 13.0 Consensus size: 6
159593 ATGAAAAAGT
* * * *
159603 CAAAAG CAAAAG CACAAA -AAAAA GAAAAA CAAAAA -AAAAA CAAAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C--AAAAA
159651 CAAAAA CAAAAA C-AAAA -AAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
159679 ATAAAAAACA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 17 0.28
6 37 0.62
8 6 0.10
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:159685 original size:36 final size:37
Alignment explanation
Indices: 159621--159695 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
159611 AAAGCACAAA
*
159621 AAAAAGAAAAACAAAAAAAAAACAAAAAAACAAAAAC
1 AAAAACAAAAACAAAAAAAAAACAAAAAAACAAAAAC
* *
159658 AAAAACAAAAA-AAAACAAAAAA-TAAAAAACAGAAAC
1 AAAAACAAAAACAAAA-AAAAAACAAAAAAACAAAAAC
159694 AA
1 AA
159696 CCAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (37 bp):
AAAAACAAAAACAAAAAAAAAACAAAAAAACAAAAAC
Found at i:159704 original size:36 final size:33
Alignment explanation
Indices: 159616--159705 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 33
159606 AAGCAAAAGC
*
159616 ACAAAAA-AAAGAAAAACAAAAAAAAAACAAAAAA
1 ACAAAAACAAA-AAAAA-AAAAAAAAAAAAAAAAA
159650 ACAAAAACAAAAACAAAAAAAAACAAAAAATAAAAA
1 ACAAAAACAAAAA-AAAAAAAAA-AAAAAA-AAAAA
* **
159686 ACAGAAACAACCAAAAAAAA
1 ACAAAAACAAAAAAAAAAAA
159706 TTAAAAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 15 0.31
35 18 0.38
36 15 0.31
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (33 bp):
ACAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:159705 original size:1 final size:1
Alignment explanation
Indices: 159618--159686 Score: 66
Period size: 1 Copynumber: 69.0 Consensus size: 1
159608 GCAAAAGCAC
* * * * * * * *
159618 AAAAAAAAGAAAAACAAAAAAAAAACAAAAAAACAAAAACAAAAACAAAAAAAAACAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
159683 AAAA
1 AAAA
159687 CAGAAACAAC
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.88, C:0.09, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:164627 original size:20 final size:20
Alignment explanation
Indices: 164583--164633 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
164573 TATCAATATA
164583 ATGTATCGATACTTAGCAAT
1 ATGTATCGATACTTAGCAAT
*
164603 TTGTATCGATACATCT-GC-AT
1 ATGTATCGATAC-T-TAGCAAT
164623 ATGTATCGATA
1 ATGTATCGATA
164634 TATTTAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 23 0.85
21 3 0.11
22 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACTTAGCAAT
Found at i:165069 original size:16 final size:18
Alignment explanation
Indices: 165044--165083 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
165034 AATAAAATGT
165044 ATTT-TTTTT-AT-TATA
1 ATTTATTTTTAATATATA
165059 ATTTATTTTTAATATATA
1 ATTTATTTTTAATATATA
165077 ATTTATT
1 ATTTATT
165084 AATTTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 5 0.23
17 2 0.09
18 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTATTTTTAATATATA
Found at i:166849 original size:20 final size:20
Alignment explanation
Indices: 166824--166867 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
166814 GGATCATTCT
*
166824 CTATTTTTTTTAGTATTTTA
1 CTATTTTTTTTAGTAGTTTA
166844 CTA-TTTTTTTAGTAGTTTA
1 CTATTTTTTTTAGTAGTTTA
166863 -TATTT
1 CTATTT
166868 AACATTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 17 0.77
20 3 0.14
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
CTATTTTTTTTAGTAGTTTA
Found at i:167280 original size:49 final size:48
Alignment explanation
Indices: 167227--167327 Score: 107
Period size: 51 Copynumber: 2.1 Consensus size: 48
167217 CTCTTATTAC
*
167227 TTATACTCAT-T-GTTTATAATTAATAAAAACTAAAAAATTATTTTGTTAT
1 TTATACTCATATAGTTTATAATTAATAAAAA-TAAAAAA-TATTTT-TTAA
* * * **
167276 TTATATTTATATATTTTATAATTAATTTAAATAAAAAATATTTTTTAA
1 TTATACTCATATAGTTTATAATTAATAAAAATAAAAAATATTTTTTAA
167324 TTAT
1 TTAT
167328 TAAATATCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
48 7 0.16
49 14 0.32
50 8 0.18
51 15 0.34
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (48 bp):
TTATACTCATATAGTTTATAATTAATAAAAATAAAAAATATTTTTTAA
Found at i:169246 original size:2 final size:2
Alignment explanation
Indices: 169239--169288 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
169229 TGTAAGAAAG
*
169239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169281 AT AT AT AT
1 AT AT AT AT
169289 GAAATAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:170413 original size:21 final size:23
Alignment explanation
Indices: 170387--170440 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
170377 TTCGATCTAG
*
170387 ATTAATTTAAA-TTATTATTT-A
1 ATTAATTAAAATTTATTATTTAA
*
170408 ATTAA-TAAAATTTTTTATTTAA
1 ATTAATTAAAATTTATTATTTAA
170430 ATTAATTAAAA
1 ATTAATTAAAA
170441 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 6 0.21
23 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTAATTAAAATTTATTATTTAA
Found at i:170449 original size:22 final size:22
Alignment explanation
Indices: 170424--170468 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
170414 AAAATTTTTT
170424 ATTTAAATTAATTAAA-AATAAA
1 ATTTAAA-TAATTAAACAATAAA
* *
170446 ATTTTAATATTTAAACAATAAA
1 ATTTAAATAATTAAACAATAAA
170468 A
1 A
170469 CCTTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAAATAATTAAACAATAAA
Found at i:172627 original size:13 final size:13
Alignment explanation
Indices: 172609--172633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172599 AATTTATGTT
172609 TATTAAATTTAAA
1 TATTAAATTTAAA
172622 TATTAAATTTAA
1 TATTAAATTTAA
172634 TGATTTCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTAAATTTAAA
Found at i:173091 original size:5 final size:5
Alignment explanation
Indices: 173081--173113 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
173071 TTTGTGCTAT
173081 AAACA AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAA
173114 TACATGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:173541 original size:13 final size:13
Alignment explanation
Indices: 173523--173547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173513 ATATACTTGA
173523 CAAAAATGTTCTC
1 CAAAAATGTTCTC
173536 CAAAAATGTTCT
1 CAAAAATGTTCT
173548 TTTTTTTTTT
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
CAAAAATGTTCTC
Found at i:174787 original size:2 final size:2
Alignment explanation
Indices: 174748--174775 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
174738 CATATCAGAC
174748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174776 GACACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183460 original size:2 final size:2
Alignment explanation
Indices: 183453--183490 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
183443 TCACAAGAAA
*
183453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183491 TAATTATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184244 original size:18 final size:19
Alignment explanation
Indices: 184217--184268 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
184207 AAAAAATGTC
*
184217 AAAAAGGAAACAAAAACAA
1 AAAAAGAAAACAAAAACAA
*
184236 AAAAAGAAAACAAAAATAA
1 AAAAAGAAAACAAAAACAA
*
184255 AAAAA-AAAAGAAAA
1 AAAAAGAAAACAAAA
184269 TGAATGGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAACAAAAACAA
Found at i:184247 original size:13 final size:13
Alignment explanation
Indices: 184229--184268 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
184219 AAAGGAAACA
184229 AAAACAAAAAAAG
1 AAAACAAAAAAAG
*
184242 AAAAC--AAAAAT
1 AAAACAAAAAAAG
184253 AAAA-AAAAAAAG
1 AAAACAAAAAAAG
184265 AAAA
1 AAAA
184269 TGAATGGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.39
12 9 0.39
13 5 0.22
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.03
Consensus pattern (13 bp):
AAAACAAAAAAAG
Found at i:186647 original size:97 final size:96
Alignment explanation
Indices: 186504--186693 Score: 299
Period size: 97 Copynumber: 2.0 Consensus size: 96
186494 AGATACTCCA
* * * *
186504 ACCCTATTCCTCCGAGGGATACTCCAACCTCGCTTTTAAACACATCAAAGTTTAAATCTTATTCT
1 ACCCCATTCCTCCGAGGAATACTCCAACCTCACTTTTAAACACATCAAAATTTAAATCTTATTCT
186569 CACTTAAATTGTCATCATCGGGGACACTTCG
66 CACTTAAATTGTCATCATCGGGGACACTTCG
* * * *
186600 ACCCCATTCCTCCGAGATAATACTCCAATCTCACTTTTAAACGCATCAAAATTTAAATTTTATTC
1 ACCCCATTCCTCCGAG-GAATACTCCAACCTCACTTTTAAACACATCAAAATTTAAATCTTATTC
186665 TCACTTAAATTGTCATCATCGGGGACACT
65 TCACTTAAATTGTCATCATCGGGGACACT
186694 CCAACCTCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 15 0.18
97 70 0.82
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (96 bp):
ACCCCATTCCTCCGAGGAATACTCCAACCTCACTTTTAAACACATCAAAATTTAAATCTTATTCT
CACTTAAATTGTCATCATCGGGGACACTTCG
Found at i:191521 original size:22 final size:21
Alignment explanation
Indices: 191474--191546 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 21
191464 ATAAAAGCAT
*
191474 AAAAAATGAAAGAG-AAAACAA
1 AAAAAATGAAA-AGCAAAATAA
191495 CAAAAAATGCAAAAGCAAAATAA
1 -AAAAAATG-AAAAGCAAAATAA
191518 AAAAAGA-GAAGAA-CAAAAATAA
1 AAAAA-ATGAA-AAGC-AAAATAA
191540 AAAAAAT
1 AAAAAAT
191547 AAGGACATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 4 0.09
22 30 0.68
23 10 0.23
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAAAATGAAAAGCAAAATAA
Found at i:192956 original size:28 final size:27
Alignment explanation
Indices: 192925--193399 Score: 421
Period size: 28 Copynumber: 17.1 Consensus size: 27
192915 GTGGAACCTT
* * *
192925 TTTTAAGTCCATAACACCGTGACACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
192952 GTTTTAAGTTCACAACTCAGTGGCACCT
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* *
192980 TTTTAAGTCTACAACTCCGTGGCACCAA
1 TTTTAAGTCCACAACTCCGTGGCACC-C
* *
193008 TTTAAAGTCCACAACTCTGTGGCATTCCC
1 TTTTAAGTCCACAACTCCGTGGCA--CCC
* * * *
193037 TTTTAAGTCCATAACTCTGTGACATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
193064 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
193092 TTTTAAAGTCCACAACTCCATGGTACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
193120 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * * *
193148 TTTTAAATCCATAACTCTGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
** * *
193175 TTTTAAAGTCCATTACTCTGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
193203 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
193230 TTTTAAAGTCCACAACTTCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
193258 TTTTAAAGTTCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
193286 TTTTAAGTCCACAACTTCGTGGCA-TC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * * *
193312 TTTTCAAAGCCCACAAGTCAGTAGCATCC
1 TTTT--AAGTCCACAACTCCGTGGCACCC
* * * *
193341 TTTTAAAGCCCACAAGTCAGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * * * *
193369 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTT-TAAGTCCACAACTCCGTGGCACCC
193397 TTT
1 TTT
193400 CAAAGCTCGC
Statistics
Matches: 383, Mismatches: 54, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.01
27 93 0.24
28 257 0.67
29 26 0.07
30 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:193000 original size:55 final size:56
Alignment explanation
Indices: 192924--193404 Score: 456
Period size: 55 Copynumber: 8.6 Consensus size: 56
192914 AGTGGAACCT
* * * * *
192924 TTTTTAAGTCCATAACACCGTGACACCCGTTTT-AAGTTCACAACTCAGTGGCA-CC
1 TTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAAGTCCACAACTCTGTGGCATCC
* **
192979 TTTTTAAGTCTACAACTCCGTGGCACCAATTTAAAGTCCACAACTCTGTGGCATTCC
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCA-TCC
* * * * * * *
193036 CTTTTAAGTCCATAACTCTGTGACATCCTTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCC
* * *
193092 TTTTAAAGTCCACAACTCCATGGTACCCTTTTAAAGTCCACAACTCTGTGGCA-CC
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCC
* * * * * **
193147 CTTTTAAATCCATAACTCTGTGGCACCTTTTTAAAGTCCATTACTCTGTGGCATCC
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCC
*
193203 -TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-TCGTGGCACCC
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCT-GTGGCATCC
* * *
193258 TTTTAAAGTTCACAACTCTGTGGCACCCTTTT-AAGTCCACAACT-TCGTGGCAT-C
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCT-GTGGCATCC
* * * * * * * * *
193312 TTTTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC
1 TTTT-TAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCC
** * * * * *
193369 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
1 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAG
193405 CTCGCAAGTT
Statistics
Matches: 356, Mismatches: 60, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
54 9 0.03
55 174 0.49
56 123 0.35
57 50 0.14
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (56 bp):
TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCC
Found at i:193179 original size:83 final size:83
Alignment explanation
Indices: 192915--193404 Score: 493
Period size: 83 Copynumber: 5.9 Consensus size: 83
192905 CCATGATTTA
* * * * * * * * *
192915 GTGGAACCTTTTTTAAGTCCATAACACCGTGACACCCGTTTTAAGTTCACAACTCAGTGGCA-CC
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCC-TTTTAAGTCCACAACTCTGTGGCACCC
* *
192979 TTTTTAAGTCTACAACTCC
65 TTTTAAAGTCCACAACTCC
** * * *
192998 GTGGCACCAATTTAAAGTCCACAACTCTGTGGCATTCCCTTTTAAGTCCATAACTCTGTGACATC
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCA--CCCTTTTAAGTCCACAACTCTGTGGCACC
193063 CTTTTAAAGTCCACAACTCC
64 CTTTTAAAGTCCACAACTCC
** *
193083 GTGGCACCCTTTTAAAGTCCACAACTCCATGGTACCCTTTTAAAGTCCACAACTCTGTGGCACCC
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCC
* *
193148 TTTTAAA-TCCATAACTCT
65 TTTTAAAGTCCACAACTCC
* ** * *
193166 GTGGCACCTTTTTAAAGTCCATTACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCT
*
193231 TTTAAAGTCCACAACTTC
66 TTTAAAGTCCACAACTCC
* *
193249 GTGGCACCCTTTTAAAGTTCACAACTCTGTGGCACCCTTTTAAGTCCACAACT-TCGTGGCA-TC
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCT-GTGGCACCC
* * *
193312 TTTTCAAAGCCCACAAGTCA
65 TTTT-AAAGTCCACAACTCC
* * * * * * * * * * *
193332 GTAGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
1 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACCC
*
193397 TTTCAAAG
65 TTTTAAAG
193405 CTCGCAAGTT
Statistics
Matches: 338, Mismatches: 59, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
82 34 0.10
83 182 0.54
84 67 0.20
85 55 0.16
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (83 bp):
GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCT
TTTAAAGTCCACAACTCC
Found at i:193366 original size:56 final size:56
Alignment explanation
Indices: 193059--193720 Score: 423
Period size: 56 Copynumber: 11.7 Consensus size: 56
193049 AACTCTGTGA
* * * * * *
193059 CATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCCA-TGG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGT-CAGTGG
* * * * * * * * * *
193115 TACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTT-AAA-TCCATAACTCTGTGG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGG
* ** * * * * *
193170 CA-CCTTTTTAAAGTCCATTACTCTGTGGCATCCTTTT--AAGTCCACAACTCCGTGG
1 CATCC-TTTTAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCAGTGG
* * * * ** * *
193225 CACCCTTTTAAAGTCCACAACTTC-GTGGCACCCTTTT-AAAGTTCACAACTCTGTGG
1 CATCCTTTTAAAGCCCACAA-GTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
193281 CACCCTTTT-AAGTCCACAACTTC-GTGGCATCTTTTCAAAGCCCACAAGTCAGTAG
1 CATCCTTTTAAAGCCCACAA-GTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
*
193336 CATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* * * * * * * * *
193392 CATCCTTTCAAAGCTCGCAAGTTATTGGCATATTTTCAAAGCCTATAAGTTAGTGG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* ** * * *
193448 CAT-CTTTTCAAAGCCCACACAAGTCGGTGATAACTCTTTTCAAAGTCCACAAGTTAGTAG
1 CATCCTTTT-AAAG-CC-CACAAGTCAGTG-GCA-TCTTTTCAAAGCCCACAAGTCAGTGG
* * *
193508 CATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAATGG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* * * * *
193564 CATCATTTCAAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTAG
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
193620 TAT-CTTTTCAAAGCCCACAAGTCAATGGCATACCCTTTCAAAGCTCACACAAGTCGGTGG
1 CATCCTTTT-AAAGCCCACAAGTCAGTGGCAT--CTTTTCAAAGC-C-CACAAGTCAGTGG
* * * *
193680 CAACTCTTTTTAAAACCCACACAAGTTAGTGGCACCTTTTC
1 C-A-TCCTTTT-AAAGCC-CACAAGTCAGTGGCATCTTTTC
193721 TTAAAGTCCA
Statistics
Matches: 500, Mismatches: 80, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
54 10 0.02
55 130 0.26
56 252 0.50
57 2 0.00
58 30 0.06
59 4 0.01
60 39 0.08
61 5 0.01
62 6 0.01
63 9 0.02
64 13 0.03
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (56 bp):
CATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:193400 original size:28 final size:28
Alignment explanation
Indices: 193194--193681 Score: 435
Period size: 28 Copynumber: 17.2 Consensus size: 28
193184 CCATTACTCT
* * * *
193194 GTGGCATCCTTT-TAAGTCCACAACTCC
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
193221 GTGGCACCCTTTTAAAGTCCACAACTTC-
1 GTGGCATCCTTTCAAAGCCCACAA-GTCA
* * ** * *
193249 GTGGCACCCTTTTAAAGTTCACAACTCT
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
193277 GTGGCACCCTTT-TAAGTCCACAACTTC-
1 GTGGCATCCTTTCAAAGCCCACAA-GTCA
*
193304 GTGGCATCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
193332 GTAGCATCCTTTTAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
193360 GTGGCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
193388 GTGGCATCCTTTCAAAGCTCGCAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* ** * * *
193416 TTGGCATATTTTCAAAGCCTATAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
193444 GTGGCATCTTTTCAAAGCCCACACAAGTCG
1 GTGGCATCCTTTCAAAG-CC-CACAAGTCA
** * * *
193474 GTGATAACTCTTTTCAAAGTCCACAAGTTA
1 GTG-GCA-TCCTTTCAAAGCCCACAAGTCA
*
193504 GTAGCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
193532 GTGGCATCATTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
193560 ATGGCATCATTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
193588 GTGGTATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
193616 GTAGTATCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
193644 ATGGCATACCCTTTCAAAGCTCACACAAGTCG
1 GTGGCAT--CCTTTCAAAGC-C-CACAAGTCA
193676 GTGGCA
1 GTGGCA
193682 ACTCTTTTTA
Statistics
Matches: 388, Mismatches: 59, Indels: 23
0.83 0.13 0.05
Matches are distributed among these distances:
27 34 0.09
28 295 0.76
29 5 0.01
30 27 0.07
31 3 0.01
32 24 0.06
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (28 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:193510 original size:172 final size:172
Alignment explanation
Indices: 193310--193638 Score: 496
Period size: 172 Copynumber: 1.9 Consensus size: 172
193300 CTTCGTGGCA
* *
193310 TCTTTTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAA
* * * * * * * * *
193375 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCTCGCAAGTTATTGGCATATTTTCAAAGCCTATAA
66 AGCCCACAAGTCAATGGCATCATTTCAAAGCCCACAAGTCAGTGGCATACTTTCAAAGCCCACAA
* *
193440 GTTAGTGGCATCTTTTCAAAGCCCACACAAGTCGGTGATAAC
131 GTCAGTAGCATCTTTTCAAAGCCCACACAAGTCGGTGATAAC
* *
193482 TCTTTTCAAAGTCCACAAGTTAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAA
* *
193547 AGCCCACAAGTCAATGGCATCATTTCAAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAA
66 AGCCCACAAGTCAATGGCATCATTTCAAAGCCCACAAGTCAGTGGCATACTTTCAAAGCCCACAA
*
193612 GTCAGTAGTATCTTTTCAAAGCCCACA
131 GTCAGTAGCATCTTTTCAAAGCCCACA
193639 AGTCAATGGC
Statistics
Matches: 139, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
172 139 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (172 bp):
TCTTTTCAAAGCCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAA
AGCCCACAAGTCAATGGCATCATTTCAAAGCCCACAAGTCAGTGGCATACTTTCAAAGCCCACAA
GTCAGTAGCATCTTTTCAAAGCCCACACAAGTCGGTGATAAC
Found at i:193701 original size:32 final size:33
Alignment explanation
Indices: 193665--193757 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 33
193655 TTTCAAAGCT
193665 CACACAAGTCGGTGGCAACTCTTT-TTAAAACC
1 CACACAAGTCGGTGGCAACTCTTTCTTAAAACC
** * **
193697 CACACAAGTTAGTGGCACCT-TTTCTTAAAGTC
1 CACACAAGTCGGTGGCAACTCTTTCTTAAAACC
* *
193729 CACGCAAGTCGGTGGCAAC-CTTTGTTAAA
1 CACACAAGTCGGTGGCAACTCTTTCTTAAA
193758 TCACCACTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 3 0.06
32 46 0.94
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (33 bp):
CACACAAGTCGGTGGCAACTCTTTCTTAAAACC
Found at i:193713 original size:64 final size:63
Alignment explanation
Indices: 193635--193757 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 63
193625 TTTCAAAGCC
193635 CACAAGTCAATGGCATACCCTTTC-AAAG-CTCACACAAGTCGGTGGCAACTCTTT-TTAAAACC
1 CACAAGTCAATGGC--ACCCTTTCTAAAGTC-CACACAAGTCGGTGGCAAC-CTTTGTTAAAACC
193697 CA
62 CA
* * * *
193699 CACAAGTTAGTGGCACCTTTTCTTAAAGTCCACGCAAGTCGGTGGCAACCTTTGTTAAA
1 CACAAGTCAATGGCACCCTTTC-TAAAGTCCACACAAGTCGGTGGCAACCTTTGTTAAA
193758 TCACCACTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
62 7 0.14
63 4 0.08
64 39 0.76
65 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (63 bp):
CACAAGTCAATGGCACCCTTTCTAAAGTCCACACAAGTCGGTGGCAACCTTTGTTAAAACCCA
Found at i:196644 original size:97 final size:97
Alignment explanation
Indices: 196493--196720 Score: 357
Period size: 97 Copynumber: 2.4 Consensus size: 97
196483 TATCAAGAAT
* * * *
196493 ACTCCAACCCTATTCCTCTGAAGGGATACTCCAATCCTGGTTTTAAACACATCAAAGTTTAAATA
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAATCCCGCTTTTAAACACATCAAAGTTTAAATA
196558 TTATTCTCACTTAAATTGTCATCATCAGGGAC
66 TTATTCTCACTTAAATTGTCATCATCAGGGAC
* * ** *
196590 ATTTCAACCCCATTCCTCTGAGGGGATACTCCAATCCCGCTTTTAAACGTATCAAAGTTTAAATT
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAATCCCGCTTTTAAACACATCAAAGTTTAAATA
*
196655 TTATTCTCACTTAAATTGTCATCATCGGGGAC
66 TTATTCTCACTTAAATTGTCATCATCAGGGAC
*
196687 ACTCCAACCCCATTCCTCCGAGGGGATACTCCAA
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAA
196721 CCCTGTTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 118 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (97 bp):
ACTCCAACCCCATTCCTCTGAGGGGATACTCCAATCCCGCTTTTAAACACATCAAAGTTTAAATA
TTATTCTCACTTAAATTGTCATCATCAGGGAC
Found at i:199237 original size:21 final size:21
Alignment explanation
Indices: 199213--199259 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
199203 CTTATCTTGG
199213 AATCATCAATATCATTTTTCA
1 AATCATCAATATCATTTTTCA
* * * *
199234 AATCATTATTTTCATTTTTTA
1 AATCATCAATATCATTTTTCA
199255 AATCA
1 AATCA
199260 ATTTTAGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
AATCATCAATATCATTTTTCA
Found at i:205258 original size:20 final size:17
Alignment explanation
Indices: 205225--205263 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 17
205215 ATTAATTATC
205225 TTAGTTTATTTTAAGATT
1 TTAGTTTATTTTAAG-TT
205243 TTAGTTTACTTTTTAAGTT
1 TTAGTTTA--TTTTAAGTT
205262 TT
1 TT
205264 CATTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (17 bp):
TTAGTTTATTTTAAGTT
Found at i:206122 original size:2 final size:2
Alignment explanation
Indices: 206101--206147 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
206091 ACTTTTCTTT
* *
206101 TA TA -A TA TA CA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
206142 TA TA TA
1 TA TA TA
206148 CACAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:206669 original size:11 final size:11
Alignment explanation
Indices: 206648--206682 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
206638 TAATTCATAG
206648 TAATT-ATAAA
1 TAATTAATAAA
206658 TAATTAATAAA
1 TAATTAATAAA
*
206669 TAGTTAATAAA
1 TAATTAATAAA
206680 TAA
1 TAA
206683 GATCGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TAATTAATAAA
Found at i:207193 original size:20 final size:20
Alignment explanation
Indices: 207153--207193 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
207143 ATGAAAGTCA
**
207153 TAAAAATTTAAATTTTCATT
1 TAAAAATTTAAATTTGAATT
*
207173 TAAAAATTTAGATTTGAATT
1 TAAAAATTTAAATTTGAATT
207193 T
1 T
207194 GGATTTCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAAATTTAAATTTGAATT
Found at i:207941 original size:14 final size:14
Alignment explanation
Indices: 207919--207979 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
207909 AAACATATTA
207919 TTATCATATTATAT
1 TTATCATATTATAT
* *
207933 TTATTATATTATTT
1 TTATCATATTATAT
*
207947 TTATAATTCATTATAT
1 TTATCA-T-ATTATAT
*
207963 ATATC-TATTCATAT
1 TTATCATATT-ATAT
207977 TTA
1 TTA
207980 CTTTTATATC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 24 0.65
15 1 0.03
16 9 0.24
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATCATATTATAT
Found at i:209009 original size:13 final size:13
Alignment explanation
Indices: 208991--209016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208981 CTTTTGGTGC
208991 AGTCATTTTTTAT
1 AGTCATTTTTTAT
209004 AGTCATTTTTTAT
1 AGTCATTTTTTAT
209017 TTCTATGACA
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:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
AGTCATTTTTTAT
Found at i:210134 original size:2 final size:2
Alignment explanation
Indices: 210122--210173 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
210112 CTAAGATAAT
*
210122 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
210164 TA TA TA TA TA
1 TA TA TA TA TA
210174 CACACACTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:211726 original size:4 final size:4
Alignment explanation
Indices: 211711--211739 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
211701 ATCCCAAGAC
211711 AATA AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
211740 AGGTAGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:211880 original size:23 final size:23
Alignment explanation
Indices: 211854--211897 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
211844 TTTAATAATA
211854 TTATCTA-TGTATTCATATTATTT
1 TTATCTATTGTATT-ATATTATTT
* *
211877 TTATGTATTTTATTATATTAT
1 TTATCTATTGTATTATATTAT
211898 ACTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (23 bp):
TTATCTATTGTATTATATTATTT
Found at i:211925 original size:9 final size:9
Alignment explanation
Indices: 211907--211989 Score: 64
Period size: 9 Copynumber: 8.9 Consensus size: 9
211897 TACTAACATT
*
211907 TTTTAAATA
1 TTTTATATA
211916 TTTTATATA
1 TTTTATATA
211925 -TTTATATTAA
1 TTTTATA-T-A
211935 TTTTA-ATA
1 TTTTATATA
211943 TATTTATATA
1 T-TTTATATA
211953 TTTATATCATA
1 TTT-TAT-ATA
211964 TTTTA-ATTA
1 TTTTATA-TA
*
211973 TTTTATTTA
1 TTTTATATA
*
211982 TATTATAT
1 TTTTATAT
211990 TTATATAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
8 9 0.15
9 31 0.51
10 11 0.18
11 10 0.16
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTATATA
Found at i:211930 original size:8 final size:8
Alignment explanation
Indices: 211913--211959 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
211903 CATTTTTTAA
211913 ATAT-TTT
1 ATATATTT
211920 ATATATTT
1 ATATATTT
211928 ATATTAATTTT
1 ATA-T-A-TTT
211939 AATATATTT
1 -ATATATTT
211948 ATATATTT
1 ATATATTT
211956 ATAT
1 ATAT
211960 CATATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.11
8 18 0.51
9 4 0.11
10 2 0.06
11 4 0.11
12 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:211943 original size:20 final size:19
Alignment explanation
Indices: 211915--211990 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
211905 TTTTTTAAAT
211915 ATTTTATATATTTATATTA
1 ATTTTATATATTTATATTA
211934 ATTTTAATATATTTATA-T-
1 ATTTT-ATATATTTATATTA
211952 ATTTATATCATATTT-TAATT-
1 ATTT-TAT-ATATTTAT-ATTA
*
211972 ATTTTATTTATATTATATT
1 ATTTTATATAT-TTATATT
211991 TATATAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
18 10 0.20
19 22 0.45
20 17 0.35
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATATATTTATATTA
Found at i:211948 original size:28 final size:30
Alignment explanation
Indices: 211843--211995 Score: 120
Period size: 29 Copynumber: 5.0 Consensus size: 30
211833 TAATATAAAT
* *
211843 TTTTAATAATATTATCTATGTATTCATATTAT-
1 TTTTAAT-ATATT-T-TATATATTTATATTATA
* ** *
211875 TTTT-ATGTATTTTATTATATTATACTAACATT
1 TTTTAATATATTTTA-TATATT-TA-TATTATA
211907 TTTTAA-ATATTTTATATATTTATATTA-A
1 TTTTAATATATTTTATATATTTATATTATA
*
211935 TTTTAATATA-TTTATATATTTATATCATA
1 TTTTAATATATTTTATATATTTATATTATA
*
211964 TTTTAAT-TATTTTATTTATATTATATTTATA
1 TTTTAATATATTTTATATAT-TTATA-TTATA
211995 T
1 T
211996 AATTACTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
28 26 0.26
29 28 0.28
30 12 0.12
31 17 0.17
32 15 0.15
33 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTAATATATTTTATATATTTATATTATA
Found at i:211966 original size:11 final size:11
Alignment explanation
Indices: 211913--211995 Score: 63
Period size: 11 Copynumber: 7.9 Consensus size: 11
211903 CATTTTTTAA
211913 ATATTT-TA-T
1 ATATTTATATT
211922 ATATTTATATT
1 ATATTTATATT
*
211933 A-ATTT-TAAT
1 ATATTTATATT
211942 ATA-TT-TA-T
1 ATATTTATATT
*
211950 ATATTTATATC
1 ATATTTATATT
211961 ATATTTTAATTATT
1 ATA-TTT-A-TATT
*
211975 TTATTTATATT
1 ATATTTATATT
211986 ATATTTATAT
1 ATATTTATAT
211996 AATTACTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
8 4 0.07
9 16 0.27
10 9 0.15
11 18 0.30
12 4 0.07
13 4 0.07
14 5 0.08
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTATATT
Found at i:211993 original size:20 final size:20
Alignment explanation
Indices: 211914--211993 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
211904 ATTTTTTAAA
211914 TATTTTATATAT-TTATATT
1 TATTTTATATATATTATATT
* *
211933 AATTTTA-ATATATT-TATA
1 TATTTTATATATATTATATT
* *
211951 TA-TTTATATCATATTTTAAT
1 TATTTTATAT-ATATTATATT
*
211971 TATTTTATTTATATTATATT
1 TATTTTATATATATTATATT
211991 TAT
1 TAT
211994 ATAATTACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 4 0.08
18 10 0.21
19 13 0.27
20 15 0.31
21 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTATATATATTATATT
Found at i:212431 original size:14 final size:14
Alignment explanation
Indices: 212412--212454 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
212402 CATATATTAT
*
212412 TTTTTTTAAATTTA
1 TTTTTTAAAATTTA
212426 TTTTTTAAAATTTA
1 TTTTTTAAAATTTA
* *
212440 ATCTTTAATAATTTA
1 TTTTTTAA-AATTTA
212455 ATATTGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTAAAATTTA
Found at i:216021 original size:20 final size:20
Alignment explanation
Indices: 215996--216033 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
215986 TCCACAAATT
*
215996 CAAATATCAGTATGATTAAA
1 CAAATATCACTATGATTAAA
*
216016 CAAATATTACTATGATTA
1 CAAATATCACTATGATTA
216034 TTATTCAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (20 bp):
CAAATATCACTATGATTAAA
Found at i:216997 original size:17 final size:20
Alignment explanation
Indices: 216975--217018 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 20
216965 TTATTTTTTT
216975 ATAAAAAA-TTTAAAA-AA-
1 ATAAAAAATTTTAAAATAAC
216992 ATAAAAAATTTTAAAATAAC
1 ATAAAAAATTTTAAAATAAC
217012 ATAAAAA
1 ATAAAAA
217019 CTTATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 2 0.08
20 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAAAAAATTTTAAAATAAC
Found at i:216998 original size:18 final size:20
Alignment explanation
Indices: 216977--217018 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
216967 ATTTTTTTAT
216977 AAAAAATTTAAAA-AA-ATA
1 AAAAAATTTAAAATAACATA
*
216995 AAAAATTTTAAAATAACATA
1 AAAAAATTTAAAATAACATA
217015 AAAA
1 AAAA
217019 CTTATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 2 0.10
20 7 0.33
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATTTAAAATAACATA
Found at i:217042 original size:15 final size:15
Alignment explanation
Indices: 217022--217065 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
217012 ATAAAAACTT
217022 ATTATAAATTTATAA
1 ATTATAAATTTATAA
**
217037 ATTATAAATAGAT-A
1 ATTATAAATTTATAA
217051 A-TATAAATTTATAA
1 ATTATAAATTTATAA
217065 A
1 A
217066 AGCCTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTATAAATTTATAA
Found at i:217043 original size:28 final size:28
Alignment explanation
Indices: 217012--217065 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
217002 TTAAAATAAC
* *
217012 ATAAAAACTTATTATAAATTTATAAATT
1 ATAAAAACATAATATAAATTTATAAATT
* *
217040 ATAAATAGATAATATAAATTTATAAA
1 ATAAAAACATAATATAAATTTATAAA
217066 AGCCTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAAAAACATAATATAAATTTATAAATT
Found at i:217064 original size:21 final size:21
Alignment explanation
Indices: 217032--217082 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
217022 ATTATAAATT
217032 TATAAA-TTATAAATAG-ATAA
1 TATAAATTTATAAA-AGCATAA
* *
217052 TATAAATTTATAAAAGCCTAT
1 TATAAATTTATAAAAGCATAA
217073 TATAAATTTA
1 TATAAATTTA
217083 CTTTGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
TATAAATTTATAAAAGCATAA
Found at i:218363 original size:13 final size:13
Alignment explanation
Indices: 218345--218369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218335 TAAAATTCAC
218345 ATTGTATCGATAT
1 ATTGTATCGATAT
218358 ATTGTATCGATA
1 ATTGTATCGATA
218370 CATGGTAAAC
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:219612 original size:22 final size:22
Alignment explanation
Indices: 219587--219628 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
219577 ATTTAAATAG
219587 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
219609 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
219629 AATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:220324 original size:16 final size:16
Alignment explanation
Indices: 220303--220341 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
220293 CATGAAAAAA
*
220303 ATAATAAAAATATAAT
1 ATAATAAAAAAATAAT
220319 ATAATAAAAAAATAAT
1 ATAATAAAAAAATAAT
220335 ATGAATA
1 AT-AATA
220342 TGACACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
ATAATAAAAAAATAAT
Found at i:220352 original size:25 final size:25
Alignment explanation
Indices: 220278--220361 Score: 62
Period size: 27 Copynumber: 3.3 Consensus size: 25
220268 AATATTAGAC
* **
220278 ATAATATGAACATGACATGAAAAAA
1 ATAATATGAATATGACAAAAAAAAA
** * *
220303 ATAATAAAAATATAATATAATAAAAAA
1 ATAATATGAATATGACA-AA-AAAAAA
*
220330 ATAATATGAATATGACACAAAAATAA
1 ATAATATGAATATGACA-AAAAAAAA
220356 A-AATAT
1 ATAATAT
220362 TTTAAATTTA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
25 17 0.39
26 6 0.14
27 21 0.48
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (25 bp):
ATAATATGAATATGACAAAAAAAAA
Found at i:220531 original size:13 final size:13
Alignment explanation
Indices: 220502--220532 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
220492 CCTCTTTTCT
220502 TTTTC-TTTTTTG
1 TTTTCTTTTTTTG
220514 TTTTCTTTTTTTG
1 TTTTCTTTTTTTG
220527 TTTTCT
1 TTTTCT
220533 CCTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTTTTG
Found at i:220874 original size:29 final size:29
Alignment explanation
Indices: 220820--220875 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
220810 TCTATAAATA
*
220820 ATTAATTTTATAAAAAAATATTTATTTAC
1 ATTAATTTTATAAAAAAATATCTATTTAC
*
220849 ATTAATTTTA-ACAAAAATAATCTATTT
1 ATTAATTTTATAAAAAAAT-ATCTATTT
220876 TTTTGTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTAATTTTATAAAAAAATATCTATTTAC
Found at i:222123 original size:2 final size:2
Alignment explanation
Indices: 222118--222144 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
222108 TTAGTGTGTG
222118 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
222145 GTTTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:222180 original size:15 final size:16
Alignment explanation
Indices: 222160--222192 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
222150 TTAAATTAAA
222160 TTATTTAATTTA-TAT
1 TTATTTAATTTATTAT
222175 TTATTTAATTTATTAT
1 TTATTTAATTTATTAT
222191 TT
1 TT
222193 TTATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTAATTTATTAT
Found at i:222184 original size:28 final size:28
Alignment explanation
Indices: 222146--222201 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
222136 TATATATATG
222146 TTTATTAAATTAAATTA-TTTAATTTATA
1 TTTATTAAATT-AATTATTTTAATTTATA
* * *
222174 TTTATTTAATTTATTATTTTTATTTATA
1 TTTATTAAATTAATTATTTTAATTTATA
222202 ACTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTATTAAATTAATTATTTTAATTTATA
Found at i:225649 original size:2 final size:2
Alignment explanation
Indices: 225644--225683 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
225634 AAATAACAAG
225644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225684 TGTGCAAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228014 original size:29 final size:27
Alignment explanation
Indices: 227973--228029 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
227963 TTTATAAAAT
*
227973 TATATTTTTAAATTAAGATTAATTTGA
1 TATATTTTTAAATTAAGATTAATATGA
* *
228000 TATATTTTATGAAATTTATATTAATATGA
1 TATATTTT-T-AAATTAAGATTAATATGA
228029 T
1 T
228030 CTGAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 1 0.04
29 16 0.64
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (27 bp):
TATATTTTTAAATTAAGATTAATATGA
Found at i:229435 original size:32 final size:31
Alignment explanation
Indices: 229394--229468 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
229384 AAATTTGAGT
* * *
229394 TAATATAAATTT-AGATTGTTTTAAGTTTAAA
1 TAATTTAAATTTGA-ATTATTTTAACTTTAAA
*
229425 TCAATTTAAATTTGAATTATTTTAACTTTAAG
1 T-AATTTAAATTTGAATTATTTTAACTTTAAA
*
229457 TAATTTGAATTT
1 TAATTTAAATTT
229469 CATTATCAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 11 0.30
32 25 0.68
33 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (31 bp):
TAATTTAAATTTGAATTATTTTAACTTTAAA
Found at i:236242 original size:11 final size:11
Alignment explanation
Indices: 236225--236257 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
236215 TGGTAAATTA
236225 AATAATTATTT
1 AATAATTATTT
*
236236 GATAATTATTT
1 AATAATTATTT
236247 AATAA-TATTT
1 AATAATTATTT
236257 A
1 A
236258 CATGAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AATAATTATTT
Found at i:239063 original size:185 final size:184
Alignment explanation
Indices: 238822--239158 Score: 477
Period size: 185 Copynumber: 1.8 Consensus size: 184
238812 AAAAGTTCTA
** *
238822 ACATAACCCTAATGAACATGTATCGACTCAAACGTCCTTACATGATCCTCAGGACTC-AGTTATA
1 ACATAACCCTAACAAACATGTATCGACTCAAACGTCCTTACATGATCCTAAGGACTCGA-TTATA
* *
238886 AGGTAATATTACCTGAATGCACCTAATGGACATGTTTCGACATGAAAATTATCACATGATTCTAA
65 AGGTAATATTACCTAAATACACCTAATGGACATGTTT-GACATGAAAATTATCACATGATTC-AA
238951 AGA-CTCGATT-TTAAAGTAGTATTACTTAAATATCCCTAATGGACACGAAGATTTCC
128 AGATCTCG-TTATTAAAGTAGTATTACTTAAATATCCCTAATGGACACGAAGATTTCC
* *
239007 ACATAACCCTAACAAACATGTATTGACATGAAA-GTTCC-TACATGATCCTAAGGACTCGATTAT
1 ACATAACCCTAACAAACATGTATCGAC-TCAAACG-TCCTTACATGATCCTAAGGACTCGATTAT
** * *
239070 AAGGTAATATTACCTAAATATGCCTAATGGACATGTTTGACATGAAAATTCTCACATGATTCGAA
64 AAGGTAATATTACCTAAATACACCTAATGGACATGTTTGACATGAAAATTATCACATGATTCAAA
*
239135 GATCTTGTTATTAAAGTAGTATTA
129 GATCTCGTTATTAAAGTAGTATTA
239159 TGTTTGTAGA
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
183 6 0.04
184 40 0.30
185 81 0.60
186 8 0.06
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (184 bp):
ACATAACCCTAACAAACATGTATCGACTCAAACGTCCTTACATGATCCTAAGGACTCGATTATAA
GGTAATATTACCTAAATACACCTAATGGACATGTTTGACATGAAAATTATCACATGATTCAAAGA
TCTCGTTATTAAAGTAGTATTACTTAAATATCCCTAATGGACACGAAGATTTCC
Found at i:239492 original size:13 final size:13
Alignment explanation
Indices: 239474--239498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
239464 ACATTATTCA
239474 TTGTATCGATACG
1 TTGTATCGATACG
239487 TTGTATCGATAC
1 TTGTATCGATAC
239499 ATCTGGGTCA
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:242119 original size:79 final size:79
Alignment explanation
Indices: 241951--242535 Score: 554
Period size: 79 Copynumber: 7.4 Consensus size: 79
241941 AAACAATCGA
* * * * * *
241951 GGATACTCTAACCTCGATTTTACTTCCAAAACATCGATTTTTTATAATCGGAGGATACTCCAACC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGG-GGATACTCCAACC
* * *
242016 CCGTTGTTTTAGAGG
65 CTGTTATTTTCGAGG
* * * * * *
242031 AGATACTCCAACCCCGATTTTATTTCTAAAACATCGGTTTTCCATAATCGAGGATACTCTAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
* **
242096 TGTTATTTTCAAAA
66 TGTTATTTTCGAGG
* * * *
242110 GGATACTCCAACCCCGATTTTACTTCCAAAACATCAATTTTTCACAATCGGGAATAC-CCAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
**
242174 CATTATTTTCGAGG
66 TGTTATTTTCGAGG
* * * * * *
242188 GGATACTCCAACCCCGGTTTCATTTCCAAAAAACCAATTTTTCACAATCGGGGATACTCCAA-CC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
* *
242252 TCGTTATTTCCAAGG
66 T-GTTATTTTCGAGG
* * *
242267 GGATACTCCAA-CCCTAGTTTTATTTTTAAAACATTGATTTTTCACAATCGGGGATACGT-CAA-
1 GGATACTCCAACCCCGA-TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATAC-TCCAAC
*
242329 CCTCGTTATTTTTGAGG
64 CCT-GTTATTTTCGAGG
** * * * *
242346 GGATACTCCAACCCTAATTTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCTAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
*
242411 CGTTA-TTTCTGAGG
66 TGTTATTTTC-GAGG
* * * * * *
242425 GGATACTCTAACCCCGATTTTATTT-TCAAACATCGATTTTCCATAATCGGGGATACTCTGACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTC-CAACC
* *
242489 CTGTTATTTTTGAAG
65 CTGTTATTTTCGAGG
* * **
242504 GGATACCCCCAACCTCGATTTTACCTCTAAAA
1 GGATA-CTCCAACCCCGATTTTATTTCTAAAA
242536 TATTAAACTT
Statistics
Matches: 410, Mismatches: 83, Indels: 23
0.79 0.16 0.04
Matches are distributed among these distances:
78 102 0.25
79 238 0.58
80 66 0.16
81 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
TGTTATTTTCGAGG
Found at i:242259 original size:157 final size:157
Alignment explanation
Indices: 241949--242535 Score: 606
Period size: 157 Copynumber: 3.7 Consensus size: 157
241939 TTAAACAATC
* * * * *
241949 GAGGATACTCTAACCTCGATTTTACTTCCAAAACATCGATTTTTTATAATCGGAGGATACTCCAA
1 GAGGATACTCCAACCCCGATTTTACTTCCAAAACATCGATTTTTCACAATCGG-GGATACGCCAA
* * * ** * *
242014 CCCCGTTGTTTTAGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACATCGGTTTTCCATAAT
65 CCCCGTTATTTTAGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAAT
*
242079 CGAGGATACTCTAACCCTGTTATTTTCAA
130 CGGGGATACTCTAACCC-GTTATTTTCAA
* * *
242108 AAGGATACTCCAACCCCGATTTTACTTCCAAAACATCAATTTTTCACAATCGGGAATAC-CCAAC
1 GAGGATACTCCAACCCCGATTTTACTTCCAAAACATCGATTTTTCACAATCGGGGATACGCCAAC
* * * * * *
242172 CCCATTATTTTCGAGGGGATACTCCAACCCCGGTTTCATTTCCAAAAAACCAATTTTTCACAATC
66 CCCGTTATTTTAGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATC
* *
242237 GGGGATACTCCAACCTCGTTATTTCCAA
131 GGGGATACTCTAACC-CGTTATTTTCAA
* * * ** * *
242265 GGGGATACTCCAA-CCCTAGTTTTATTTTTAAAACATTGATTTTTCACAATCGGGGATACGTCAA
1 GAGGATACTCCAACCCCGA-TTTTACTTCCAAAACATCGATTTTTCACAATCGGGGATACGCCAA
* * **
242329 CCTCGTTATTTTTGAGGGGATACTCCAACCCTAATTTTATTTCTAAAACACCAATTTTTCACAAT
65 CCCCGTTATTTTAGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAAT
* *
242394 CGGAGATACTCTAACCCCGTTA-TTTCTGA
130 CGGGGATACTCTAA-CCCGTTATTTTC-AA
* * * * * * * **
242423 GGGGATACTCTAACCCCGATTTTATTTTC-AAACATCGATTTTCCATAATCGGGGATACTCTGAC
1 GAGGATACTCCAACCCCGATTTTACTTCCAAAACATCGATTTTTCACAATCGGGGATACGCCAAC
* * * * **
242487 CCCTGTTATTTTTGAAGGGATACCCCCAACCTCGATTTTACCTCTAAAA
66 CCC-GTTATTTTAGAGGGGATA-CTCCAACCCCGATTTTATTTCTAAAA
242536 TATTAAACTT
Statistics
Matches: 356, Mismatches: 64, Indels: 16
0.82 0.15 0.04
Matches are distributed among these distances:
156 4 0.01
157 158 0.44
158 121 0.34
159 73 0.21
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (157 bp):
GAGGATACTCCAACCCCGATTTTACTTCCAAAACATCGATTTTTCACAATCGGGGATACGCCAAC
CCCGTTATTTTAGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATC
GGGGATACTCTAACCCGTTATTTTCAA
Found at i:242299 original size:236 final size:237
Alignment explanation
Indices: 241951--242497 Score: 642
Period size: 236 Copynumber: 2.3 Consensus size: 237
241941 AAACAATCGA
* * *
241951 GGATACTCTAACCTCGATTTTACTTCCAAAACATCGATTTTTTATAATCGGAGGATACTCCAACC
1 GGATACTCTAACCCCGATTTTATTTCCAAAACATCGATTTTTCATAATCGG-GGATACTCCAACC
* * * * *
242016 CCGTTGTTTTAGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACATCGGTTTTCCATAATCG
65 CCGTTATTTCAGAGGAGATACTCCAACCCAGATTTTATTTCTAAAACATCGATTTTCCACAATCG
* *
242081 AGGATAC-TCTAACC-CTGTTATTTTCAAAAGGATACTCCAACCCCGATTTTACTTCCAAAACAT
130 AGGATACGTC-AACCTC-GTTATTTTCAAAAGGATACTCCAACCCCAATTTTACTTCCAAAACAC
242144 CAATTTTTCACAATCGG-GAATAC-CCAACCCCATTATTT-TCGAGG
193 CAATTTTTCACAATCGGAG-ATACTCCAACCCCATTATTTCT-GAGG
* * * * * * * *
242188 GGATACTCCAACCCCGGTTTCATTTCCAAAAAACCAATTTTTCACAATCGGGGATACTCCAACCT
1 GGATACTCTAACCCCGATTTTATTTCCAAAACATCGATTTTTCATAATCGGGGATACTCCAACCC
* * * *
242253 CGTTATTTCCA-AGGGGATACTCCAACCCTAG-TTTTATTTTTAAAACATTGATTTTTCACAATC
66 CGTTATTT-CAGAGGAGATACTCCAACCC-AGATTTTATTTCTAAAACATCGATTTTCCACAATC
* ** ** * * *
242316 GGGGATACGTCAACCTCGTTATTTTTGAGGGGATACTCCAACCCTAATTTTATTTCTAAAACACC
129 GAGGATACGTCAACCTCGTTATTTTCAAAAGGATACTCCAACCCCAATTTTACTTCCAAAACACC
* *
242381 AATTTTTCACAATCGGAGATACTCTAACCCCGTTATTTCTGAGG
194 AATTTTTCACAATCGGAGATACTCCAACCCCATTATTTCTGAGG
* * **
242425 GGATACTCTAACCCCGATTTTATTTTC-AAACATCGATTTTCCATAATCGGGGATACTCTGACCC
1 GGATACTCTAACCCCGATTTTATTTCCAAAACATCGATTTTTCATAATCGGGGATACTCCAACCC
242489 CTGTTATTT
66 C-GTTATTT
242498 TTGAAGGGAT
Statistics
Matches: 258, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
236 163 0.63
237 94 0.36
238 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (237 bp):
GGATACTCTAACCCCGATTTTATTTCCAAAACATCGATTTTTCATAATCGGGGATACTCCAACCC
CGTTATTTCAGAGGAGATACTCCAACCCAGATTTTATTTCTAAAACATCGATTTTCCACAATCGA
GGATACGTCAACCTCGTTATTTTCAAAAGGATACTCCAACCCCAATTTTACTTCCAAAACACCAA
TTTTTCACAATCGGAGATACTCCAACCCCATTATTTCTGAGG
Found at i:243688 original size:78 final size:76
Alignment explanation
Indices: 243547--243793 Score: 252
Period size: 77 Copynumber: 3.2 Consensus size: 76
243537 ACACGAAAGG
* * * * *
243547 TCCCAGATGATCCTAAAGACTTGA-TATAAGGTAATATTACCTAAATACGCCTACTGGACATGTT
1 TCCCACATGATCCT-AAGACTTGATTTTAAGGTAGTATTACCTAAATAC-CCTAATAGACATGTT
*
243611 TTGACATGCAA-AT
64 TCGACATG-AAGAT
* *
243624 TCCCACATGATTCTAAGTACTTGATTTTAAGGTAGTATTACCTTAATATCCCTAATAGACATGTT
1 TCCCACATGATCCTAAG-ACTTGATTTTAAGGTAGTATTACCTAAATA-CCCTAATAGACATGTT
*
243689 TCGACATGAAGGT
64 TCGACATGAAGAT
* *
243702 T-CCACATGATCCTAAGGAC-TCAGTTTTAAGG-AGTATTACCTAAATACCCCTAATAAACATGT
1 TCCCACATGATCCTAA-GACTTGA-TTTTAAGGTAGTATTACCTAAATA-CCCTAATAGACATGT
* *
243764 TTGGACATAAAGAT
63 TTCGACATGAAGAT
* *
243778 TTCCACATAATCCTAA
1 TCCCACATGATCCTAA
243794 AGATTCGATA
Statistics
Matches: 145, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
76 45 0.31
77 56 0.39
78 43 0.30
79 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (76 bp):
TCCCACATGATCCTAAGACTTGATTTTAAGGTAGTATTACCTAAATACCCTAATAGACATGTTTC
GACATGAAGAT
Found at i:243961 original size:78 final size:77
Alignment explanation
Indices: 243517--243969 Score: 264
Period size: 78 Copynumber: 5.8 Consensus size: 77
243507 TTTCCACATA
* * ** * * * *
243517 ACCCTAAT-GAACATGTATTGACACGAAAGGTCCCAGATGATCCTAA-AGACT-TGATATAAGGT
1 ACCCTAATAG-ACATGTTTTGACATGAAAATTCCCACATGATCCTAAGA-ACTCAGTTTTAAGGT
*
243579 AATATTACCTAAAT
64 AGTATTACCTAAAT
* * * * * *
243593 ACGCCTACTGGACATGTTTTGACATGCAAATTCCCACATGATTCTAAGTACT-TGATTTTAAGGT
1 AC-CCTAATAGACATGTTTTGACATGAAAATTCCCACATGATCCTAAGAACTCAG-TTTTAAGGT
*
243657 AGTATTACCTTAAT
64 AGTATTACCTAAAT
* ** *
243671 ATCCCTAATAGACATGTTTCGACATGAAGGTT-CCACATGATCCTAAGGACTCAGTTTTAAGG-A
1 A-CCCTAATAGACATGTTTTGACATGAAAATTCCCACATGATCCTAAGAACTCAGTTTTAAGGTA
243734 GTATTACCTAAAT
65 GTATTACCTAAAT
* * * * *
243747 ACCCCTAATAAACATGTTTGGACAT-AAAGATTTCCACATAATCCTAAAGATTCGATACATGTTC
1 A-CCCTAATAGACATGTTTTGACATGAAA-ATTCCCACATGATCCT-AAGA-AC--T-CA-GTT-
* *** * *
243811 TGACACAAAG-GTT--CTCACAAC
57 TTA-AGGTAGTATTACCT-A-AAT
* * * * * * * *
243832 ACCGTAACA-ACATATATTGACATGAAAGTTCTCAGATGATCCTAA-AGACTCAGTTGTAAGGTA
1 ACCCTAATAGACATGTTTTGACATGAAAATTCCCACATGATCCTAAGA-ACTCAGTTTTAAGGTA
243895 GTATTACCTAAAT
65 GTATTACCTAAAT
* * *
243908 ACGCCTAATAGACATTTTTTGACATGAAAATTCCCGCATGATTCTAAGAACTCAGCTTTTAA
1 AC-CCTAATAGACATGTTTTGACATGAAAATTCCCACATGATCCTAAGAACTCAG-TTTTAA
243970 ATGGTATTAT
Statistics
Matches: 285, Mismatches: 65, Indels: 51
0.71 0.16 0.13
Matches are distributed among these distances:
75 5 0.02
76 46 0.16
77 84 0.29
78 87 0.31
79 9 0.03
81 3 0.01
82 4 0.01
83 27 0.09
84 12 0.04
85 6 0.02
86 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (77 bp):
ACCCTAATAGACATGTTTTGACATGAAAATTCCCACATGATCCTAAGAACTCAGTTTTAAGGTAG
TATTACCTAAAT
Found at i:246653 original size:40 final size:40
Alignment explanation
Indices: 246579--246655 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
246569 ATATATACAA
* * *
246579 CATGGCCATCAAAATATTTTATTATTGTATATGCATATTC
1 CATGGCCATCAAAATATTTTATTACTATACATGCATATTC
** *
246619 CATGGCCATTTAAATTTTTTATTACTATACATGCATA
1 CATGGCCATCAAAATATTTTATTACTATACATGCATA
246656 CTTCAAAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (40 bp):
CATGGCCATCAAAATATTTTATTACTATACATGCATATTC
Found at i:247988 original size:20 final size:20
Alignment explanation
Indices: 247965--248089 Score: 81
Period size: 20 Copynumber: 6.7 Consensus size: 20
247955 CACATCTAGA
*
247965 TGTATCGATACATTATGCCT
1 TGTATCGATACATTATGCAT
*
247985 TGTATCGATACA-T-TGTAT
1 TGTATCGATACATTATGCAT
* *
248003 CG-AT--ACACATCTA-G-A-
1 TGTATCGATACAT-TATGCAT
*
248018 TGTATCGATACATTATGCCT
1 TGTATCGATACATTATGCAT
**
248038 TGTATCGATACATGCT-CAT
1 TGTATCGATACATTATGCAT
*
248057 TGTATCGATACA-TATCCAAT
1 TGTATCGATACATTATGC-AT
*
248077 TGCATCGATACAT
1 TGTATCGATACAT
248090 GAAACTGGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
15 5 0.06
16 3 0.04
17 6 0.08
18 11 0.14
19 16 0.20
20 39 0.49
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:248002 original size:13 final size:13
Alignment explanation
Indices: 247984--248009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247974 ACATTATGCC
247984 TTGTATCGATACA
1 TTGTATCGATACA
247997 TTGTATCGATACA
1 TTGTATCGATACA
248010 CATCTAGATG
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):
TTGTATCGATACA
Found at i:248089 original size:59 final size:53
Alignment explanation
Indices: 247946--248050 Score: 210
Period size: 53 Copynumber: 2.0 Consensus size: 53
247936 ACCCTTGAAA
247946 GTATCGATACACATCTAGATGTATCGATACATTATGCCTTGTATCGATACATT
1 GTATCGATACACATCTAGATGTATCGATACATTATGCCTTGTATCGATACATT
247999 GTATCGATACACATCTAGATGTATCGATACATTATGCCTTGTATCGATACAT
1 GTATCGATACACATCTAGATGTATCGATACATTATGCCTTGTATCGATACAT
248051 GCTCATTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (53 bp):
GTATCGATACACATCTAGATGTATCGATACATTATGCCTTGTATCGATACATT
Found at i:254422 original size:21 final size:20
Alignment explanation
Indices: 254375--254423 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
254365 ACAAAATATT
254375 CATCAAATTTCTTCAAATCA
1 CATCAAATTTCTTCAAATCA
*
254395 -ATTTCAAATTTCTTCAATTTCA
1 CA--TCAAATTTCTTCAA-ATCA
254417 CATCAAA
1 CATCAAA
254424 ACATTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 1 0.04
21 19 0.79
22 3 0.12
23 1 0.04
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (20 bp):
CATCAAATTTCTTCAAATCA
Found at i:256603 original size:21 final size:21
Alignment explanation
Indices: 256579--256633 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
256569 TTTCAATATC
256579 AATAAATGTTTT-AGAG-TTATA
1 AATAAATGTTTTCA-AGCTT-TA
*
256600 AATATATGTTTTCAAGCTTTA
1 AATAAATGTTTTCAAGCTTTA
256621 AATCAAATGTTTT
1 AAT-AAATGTTTT
256634 TTAAGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (21 bp):
AATAAATGTTTTCAAGCTTTA
Found at i:256810 original size:20 final size:19
Alignment explanation
Indices: 256763--256816 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
256753 ACATTATGCC
* *
256763 TTGTATCAATACATGCTCA
1 TTGTATCGATACATGCTAA
* *
256782 TTATATCGATACATATCTAA
1 TTGTATCGATACAT-GCTAA
256802 TTGTATCGATACATG
1 TTGTATCGATACATG
256817 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGCTAA
Found at i:264717 original size:28 final size:30
Alignment explanation
Indices: 264659--264753 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 30
264649 ATTTTAAAAA
** *
264659 TAAAATATTAAAATATTTTTTTAATATTAT
1 TAAAATATTAAAATATTTTTAAAATAATAT
264689 TAAAAT-TTAAAAT-TTTTTAAAATAATAT
1 TAAAATATTAAAATATTTTTAAAATAATAT
*
264717 T----TATT-AAATATTTTTAAATATGATATT
1 TAAAATATTAAAATATTTTTAAA-ATAATA-T
*
264744 TATAATATTA
1 TAAAATATTA
264754 TTTTTATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
24 5 0.10
25 10 0.19
26 5 0.10
27 2 0.04
28 13 0.25
29 7 0.13
30 6 0.12
31 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TAAAATATTAAAATATTTTTAAAATAATAT
Found at i:264723 original size:15 final size:16
Alignment explanation
Indices: 264679--264724 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
264669 AAATATTTTT
264679 TTAATA-TTATTAAAA
1 TTAATATTTATTAAAA
* *
264694 TTTAAAATTTTTTAAAA
1 -TTAATATTTATTAAAA
264711 -TAATATTTATTAAA
1 TTAATATTTATTAAA
264725 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 12 0.48
16 5 0.20
17 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATATTTATTAAAA
Found at i:264725 original size:24 final size:26
Alignment explanation
Indices: 264698--264759 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
264688 TTAAAATTTA
264698 AAAT-TTTTTAAA-ATAATATTTATT
1 AAATATTTTTAAATATAATATTTATT
*
264722 AAATATTTTTAAATATGATATTTA-T
1 AAATATTTTTAAATATAATATTTATT
264747 AATATTATTTTTA
1 AA-A-TATTTTTA
264760 TTTAAGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 4 0.12
25 11 0.33
26 10 0.30
27 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AAATATTTTTAAATATAATATTTATT
Found at i:264836 original size:39 final size:39
Alignment explanation
Indices: 264793--264870 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
264783 ATAATTTATT
*
264793 ATATTATTTATATATA-AAAATAT-AAAATATTATTTATAA
1 ATATT-TTTATAAATATAAAATATGAAAAT-TTATTTATAA
* * *
264832 ATATTTTTTTAAATATATAGTATGAAAATTTATTTATAA
1 ATATTTTTATAAATATAAAATATGAAAATTTATTTATAA
264871 TTAAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
38 8 0.24
39 20 0.61
40 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (39 bp):
ATATTTTTATAAATATAAAATATGAAAATTTATTTATAA
Found at i:264989 original size:26 final size:26
Alignment explanation
Indices: 264908--264997 Score: 84
Period size: 25 Copynumber: 3.7 Consensus size: 26
264898 TTGATATATT
* *
264908 AATAATATTTTAT-ATAAAATAA-AA
1 AATAATATTTTTTAATTAAATAATAA
*
264932 AATAAATATATTTTAA-TAAAT--TAA
1 AAT-AATATTTTTTAATTAAATAATAA
*
264956 AAT-TTATTTTTTAATTAAATAATAA
1 AATAATATTTTTTAATTAAATAATAA
*
264981 AATAATATTTTTAAATT
1 AATAATATTTTTTAATT
264998 TATTATTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 9 0.17
23 5 0.10
24 8 0.15
25 18 0.35
26 12 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATAATATTTTTTAATTAAATAATAA
Found at i:265009 original size:4 final size:4
Alignment explanation
Indices: 264995--265028 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
264985 ATATTTTTAA
264995 ATTT A-TT ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
265029 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:266126 original size:1 final size:1
Alignment explanation
Indices: 266120--266148 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
266110 GATCTTTGCA
266120 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
266149 GTGTTTGGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.