Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008015.1 Hibiscus syriacus cultivar Beakdansim tig00110481_pilon, whole genome shotgun sequence
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: 961110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:221953 original size:33 final size:33
Alignment explanation
Indices: 221911--221981 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
221901 AATACTAACT
*
221911 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
221944 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
221977 TGAAA
1 TGAAA
221982 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:222215 original size:22 final size:22
Alignment explanation
Indices: 222163--222217 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
222153 TGGTTGTGAG
**
222163 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
222185 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
222207 GGATTTCTTCG
1 GGATTTCTTCG
222218 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:222388 original size:20 final size:20
Alignment explanation
Indices: 222363--222555 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
222353 CTTTAAATAT
222363 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
222383 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
222405 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
222424 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
222444 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
222464 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
222484 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
222504 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
222524 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
222544 CGCGTTGCGATT
1 CGCGTTGCGATT
222556 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:222550 original size:60 final size:60
Alignment explanation
Indices: 222363--222555 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
222353 CTTTAAATAT
**
222363 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
222424 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
222484 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
222544 CGCGTTGCGATT
1 CGCGTTGCGATT
222556 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:222636 original size:20 final size:20
Alignment explanation
Indices: 222611--222662 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
222601 AAGAATCGCG
*
222611 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
222631 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
222651 TTGCGATTCTGG
1 TTGCGATTCTGG
222663 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:225809 original size:2 final size:2
Alignment explanation
Indices: 225732--225789 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
225722 ATCCTAACTC
* *
225732 AT AT AT AT AT AT AC AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225774 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
225790 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:226722 original size:29 final size:29
Alignment explanation
Indices: 226687--226745 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
226677 CTTCAACTAC
* **
226687 TAAAAGTTATAAAATTATCATTTGATTAT
1 TAAAAGTTACAAAATTATCATCCGATTAT
226716 TAAAAGTTACAAAATTATCATCCGATTAT
1 TAAAAGTTACAAAATTATCATCCGATTAT
226745 T
1 T
226746 CATTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (29 bp):
TAAAAGTTACAAAATTATCATCCGATTAT
Found at i:238739 original size:14 final size:13
Alignment explanation
Indices: 238716--238748 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
238706 ATATTTATAG
238716 TTAA-TTTTTTTA
1 TTAATTTTTTTTA
238728 TTTAATTTTTTTTA
1 -TTAATTTTTTTTA
238742 TTAATTT
1 TTAATTT
238749 AGACTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTAATTTTTTTTA
Found at i:238938 original size:23 final size:23
Alignment explanation
Indices: 238912--239013 Score: 71
Period size: 23 Copynumber: 4.4 Consensus size: 23
238902 ATTTGTGTTC
*
238912 GTTTATTTATTGTTCACGAATAT
1 GTTTATTTAGTGTTCACGAATAT
* * ** *
238935 GTTTACTCAGTGTTCGTGAATGT
1 GTTTATTTAGTGTTCACGAATAT
* * *
238958 GCTTGTTTATATGTTCACGAACT-T
1 GTTTATTTA-GTGTTCACGAA-TAT
* * *
238982 ATTCATTTAGTGTTCACAAATAT
1 GTTTATTTAGTGTTCACGAATAT
239005 GTTTATTTA
1 GTTTATTTA
239014 AAAAATGTAT
Statistics
Matches: 55, Mismatches: 21, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
22 1 0.02
23 39 0.71
24 14 0.25
25 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.48
Consensus pattern (23 bp):
GTTTATTTAGTGTTCACGAATAT
Found at i:239287 original size:12 final size:12
Alignment explanation
Indices: 239272--239329 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
239262 AATGAGTTGT
*
239272 TAAATGAGCTCA
1 TAAACGAGCTCA
*
239284 TAAACGAGCTTA
1 TAAACGAGCTCA
*
239296 TAAATGAGCTCA
1 TAAACGAGCTCA
* *
239308 TAGACGAGGTCA
1 TAAACGAGCTCA
239320 TAAACGAGCT
1 TAAACGAGCT
239330 TTTTCATCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (12 bp):
TAAACGAGCTCA
Found at i:239299 original size:24 final size:24
Alignment explanation
Indices: 239272--239329 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
239262 AATGAGTTGT
*
239272 TAAATGAGCTCATAAACGAGCTTA
1 TAAATGAGCTCATAAACGAGCTCA
* *
239296 TAAATGAGCTCATAGACGAGGTCA
1 TAAATGAGCTCATAAACGAGCTCA
*
239320 TAAACGAGCT
1 TAAATGAGCT
239330 TTTTCATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (24 bp):
TAAATGAGCTCATAAACGAGCTCA
Found at i:261551 original size:21 final size:20
Alignment explanation
Indices: 261527--261599 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 20
261517 AACCTCATGC
261527 TATAATATTCAGACAATTATT
1 TATAATATTCAGA-AATTATT
* *
261548 TAT-A-CTT--GATATTTATT
1 TATAATATTCAGA-AATTATT
261565 TA--ATATTCATGAAATTATT
1 TATAATATTCA-GAAATTATT
261584 TATAATATTCATGAAA
1 TATAATATTCA-GAAA
261600 ATGTTAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
16 1 0.02
17 12 0.29
19 10 0.24
20 3 0.07
21 15 0.37
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (20 bp):
TATAATATTCAGAAATTATT
Found at i:262666 original size:60 final size:60
Alignment explanation
Indices: 262539--262694 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 60
262529 AGTTATAACT
* * * * * *
262539 CTCATTTTAAATTAGTCCTTAAA-TTTTAAATGTTCTAATTTCACCCTCAAACTATGACT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTGCACCCTCAAACTATGACA
* * *
262598 TTCATTCTAAATTAATCTTTAAACTTTTGAATATTTTAATTGCATCCCT-AAACTATGACA
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTGCA-CCCTCAAACTATGACA
* * * **
262658 CTCTTTCTAATTTGGTCCCCAAACTTTTGAATATTTT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTT
262695 GATTTTTATC
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 19 0.24
60 55 0.71
61 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTTAATTGCACCCTCAAACTATGACA
Found at i:264093 original size:21 final size:21
Alignment explanation
Indices: 264051--264093 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
264041 TTTCTGGGCT
* * *
264051 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
264072 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
264093 A
1 A
264094 ACGAACTAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:264166 original size:23 final size:22
Alignment explanation
Indices: 264122--264166 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
264112 AATGTCATGG
*
264122 GGAAACCGATACCCCCACAGGA
1 GGAAACCGATACCCCCAAAGGA
*
264144 GGAAACCGATTCCCCCTAAAGGA
1 GGAAACCGATACCCCC-AAAGGA
264167 AAGTTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.33, G:0.22, T:0.09
Consensus pattern (22 bp):
GGAAACCGATACCCCCAAAGGA
Found at i:264234 original size:21 final size:21
Alignment explanation
Indices: 264208--264254 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
264198 TAAGTTGCTA
264208 GTATCCAATTACAAGGTGTAG
1 GTATCCAATTACAAGGTGTAG
*
264229 GTATCCAATTACAAGGTTTAG
1 GTATCCAATTACAAGGTGTAG
264250 GTATC
1 GTATC
264255 TAATAATTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (21 bp):
GTATCCAATTACAAGGTGTAG
Found at i:265773 original size:23 final size:23
Alignment explanation
Indices: 265743--265786 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
265733 ATGGAACTAC
265743 GGTGCAATTCTAAGCGGCACTCT
1 GGTGCAATTCTAAGCGGCACTCT
* *
265766 GGTGCAATTCTACGTGGCACT
1 GGTGCAATTCTAAGCGGCACT
265787 TCGATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTAAGCGGCACTCT
Found at i:275764 original size:38 final size:38
Alignment explanation
Indices: 275686--275764 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
275676 TCCTGACCCA
* * **
275686 ACCTGAAAATTATACATCTTTCACTCGACCCAAAGTTG
1 ACCTGAAAATTATACACCTTCCACTCGACCCAAACCTG
*
275724 ACCTGATAAA-TATACACCTTCCACTCGACTCAAACCTG
1 ACCTGA-AAATTATACACCTTCCACTCGACCCAAACCTG
275762 ACC
1 ACC
275765 CAACCCGACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 32 0.91
39 3 0.09
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (38 bp):
ACCTGAAAATTATACACCTTCCACTCGACCCAAACCTG
Found at i:276969 original size:24 final size:23
Alignment explanation
Indices: 276942--277009 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
276932 ATGCTAAACA
* *
276942 AACATATAAGCGAACATGTTCTCG
1 AACAT-TAAACGAACATGTTCACG
* *
276966 AACATTTAAAAGAACGTGTTCACG
1 AACA-TTAAACGAACATGTTCACG
*
276990 AACATTAAACGAACACGTTC
1 AACATTAAACGAACATGTTC
277010 GTGAACGTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 13 0.36
24 22 0.61
25 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (23 bp):
AACATTAAACGAACATGTTCACG
Found at i:279451 original size:31 final size:31
Alignment explanation
Indices: 279416--279478 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
279406 AATTTGGTGA
279416 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
*
279447 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
279478 A
1 A
279479 AAATCTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:280896 original size:14 final size:14
Alignment explanation
Indices: 280879--280908 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
280869 TACCATTGTT
280879 CTCATATAGATCTC
1 CTCATATAGATCTC
*
280893 CTCATCTAGATCTC
1 CTCATATAGATCTC
280907 CT
1 CT
280909 TTCAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:282753 original size:22 final size:22
Alignment explanation
Indices: 282722--282764 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
282712 CGTTTAAAAT
282722 ACTAACATTTATATAGCTATTA
1 ACTAACATTTATATAGCTATTA
* *
282744 ACTAATATTTATATAGTTATT
1 ACTAACATTTATATAGCTATT
282765 TAATAAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATTA
Found at i:285983 original size:20 final size:22
Alignment explanation
Indices: 285938--285995 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
285928 GCATGGGTAG
285938 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
285962 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
285982 TGCATCGATGCACT
1 TGCATCGATGCACT
285996 TCAAGGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:287144 original size:2 final size:2
Alignment explanation
Indices: 287064--287133 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
287054 ATGCGTGGAT
287064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
287106 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
287134 GATGAATATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:293629 original size:3 final size:3
Alignment explanation
Indices: 293621--293670 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
293611 TATCCCAATT
* *
293621 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTT TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
293668 TTA
1 TTA
293671 ATAAATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:293969 original size:19 final size:18
Alignment explanation
Indices: 293945--293983 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
293935 GTCACCATTT
*
293945 TTCGGTGAGTCACCACAAG
1 TTCGGTGACTCACCA-AAG
293964 TTCGGTGACTCACCAAAG
1 TTCGGTGACTCACCAAAG
293982 TT
1 TT
293984 TGCTCCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (18 bp):
TTCGGTGACTCACCAAAG
Found at i:295001 original size:3 final size:3
Alignment explanation
Indices: 294993--295040 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
294983 AATATATTTA
294993 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
295041 TAGTCATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:295278 original size:2 final size:2
Alignment explanation
Indices: 295271--295295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
295261 TTTTATAAAT
295271 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
295296 TAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:295355 original size:147 final size:151
Alignment explanation
Indices: 295170--295444 Score: 416
Period size: 147 Copynumber: 1.8 Consensus size: 151
295160 TCATATTTTG
* * *
295170 ATATTTATTTATTTTTTAATATTAAAAAAATGATTGTCTTAAAACAATTAGAAGTCTTTTTCTGA
1 ATATTTATTTATTTTTTAATATTAAAAAAATGAATGTCTTAAAACAACTAGAAGTCTTTTTCTAA
* * *
295235 TATTTCTAAATAACTAAATATCCTACTTT-TATAAAT-T-ATATATATATATATATATATATATT
66 TATTTCTAAATAAATAAATATCCTA-TTTATAAAAATATAAAATATATATATATATATATATATT
295297 AATTTATTTTAATGTTTTATTA
130 AATTTATTTTAATGTTTTATTA
* *
295319 ATATTTATTTA-TTTTT-ATATTAAGAAAATGAATGTCTTAAAGCAACTAGAAGTCTTTTTCTAA
1 ATATTTATTTATTTTTTAATATTAAAAAAATGAATGTCTTAAAACAACTAGAAGTCTTTTTCTAA
* *
295382 TATTTCTAAGTAAATAAATATCTTATTTATAAAAATATAAAATATATATATATATATATATAT
66 TATTTCTAAATAAATAAATATCCTATTTATAAAAATATAAAATATATATATATATATATATAT
295445 ATATATATAT
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
146 3 0.03
147 70 0.62
148 6 0.05
149 34 0.30
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (151 bp):
ATATTTATTTATTTTTTAATATTAAAAAAATGAATGTCTTAAAACAACTAGAAGTCTTTTTCTAA
TATTTCTAAATAAATAAATATCCTATTTATAAAAATATAAAATATATATATATATATATATATTA
ATTTATTTTAATGTTTTATTA
Found at i:295464 original size:2 final size:2
Alignment explanation
Indices: 295423--295454 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
295413 AAAATATAAA
295423 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
295455 GTTAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:296002 original size:21 final size:21
Alignment explanation
Indices: 295972--296018 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
295962 TGGTAAGAAC
*
295972 AATATCAATTTATGTAAATAT
1 AATATCAATTTATGTAAAAAT
*
295993 ATATAT-AATTTATTTAAAAAT
1 A-ATATCAATTTATGTAAAAAT
296014 AATAT
1 AATAT
296019 TTGAATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATATCAATTTATGTAAAAAT
Found at i:299737 original size:9 final size:9
Alignment explanation
Indices: 299720--299759 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
299710 TATTTAAATA
299720 AAAAATATT
1 AAAAATATT
*
299729 AAAATTATT
1 AAAAATATT
299738 AAAAATATAT
1 AAAAATAT-T
299748 AAAAAT-TT
1 AAAAATATT
299756 AAAA
1 AAAA
299760 TTTTTAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 5 0.18
9 16 0.57
10 7 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATATT
Found at i:299979 original size:15 final size:15
Alignment explanation
Indices: 299959--299988 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
299949 AAAAATTACA
299959 TTAAAAGTATATAAT
1 TTAAAAGTATATAAT
*
299974 TTAAAAGTCTATAAT
1 TTAAAAGTATATAAT
299989 ACATTATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAAAAGTATATAAT
Found at i:303147 original size:16 final size:16
Alignment explanation
Indices: 303113--303150 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
303103 AACGTGAAAT
*
303113 AAAAATAAAATTAATA
1 AAAAATAAAATGAATA
*
303129 AAAAATAAAA-GAATG
1 AAAAATAAAATGAATA
303144 AAAAATA
1 AAAAATA
303151 TAATATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATGAATA
Found at i:307247 original size:35 final size:34
Alignment explanation
Indices: 307162--307248 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
307152 AATATAATTT
*
307162 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
307196 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
307234 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
307249 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:309813 original size:30 final size:29
Alignment explanation
Indices: 309751--309813 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
309741 TACTGCTACG
*
309751 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTCACC
*
309780 GGTGTTAGATCGATAAATATACCAT-TCACC
1 GGTGTTAGATCGAGAAATATA--ATCTCACC
309810 GGTG
1 GGTG
309814 ATTTTTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 20 0.67
30 8 0.27
31 2 0.07
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATCTCACC
Found at i:310164 original size:21 final size:20
Alignment explanation
Indices: 310078--310235 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
310068 AAATGACCAA
**
310078 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
310097 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
310117 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
310137 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
310158 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
310179 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
310199 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
310220 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
310236 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:310264 original size:20 final size:20
Alignment explanation
Indices: 310202--310395 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
310192 CGATTTTCCA
* ** *
310202 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
310222 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
310242 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
310262 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
310282 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
310302 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
310322 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
310342 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
*
310362 AAAATCGCAATGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
310383 AAATCGCAACGCG
1 AAATCGCAACGCG
310396 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:310286 original size:60 final size:60
Alignment explanation
Indices: 310202--310395 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
310192 CGATTTTCCA
* ** * * *
310202 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
310262 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* **
310322 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
310383 AAATCGCAACGCG
1 AAATCGCAACGCG
310396 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 81 0.72
61 32 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:310816 original size:33 final size:33
Alignment explanation
Indices: 310777--310847 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
310767 TTCACTTAGA
* *
310777 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
310810 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
310843 TTTCA
1 TTTCA
310848 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:310953 original size:21 final size:20
Alignment explanation
Indices: 310927--311032 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
310917 TGCAGAAGAG
310927 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
310948 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
310968 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
310989 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
311003 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
311022 TCGCAACGAGA
1 TCGCAACGAGA
311033 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:310971 original size:20 final size:21
Alignment explanation
Indices: 310925--311003 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
310915 TTTGCAGAAG
*
310925 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
310947 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
310966 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
310988 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
311004 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:310984 original size:41 final size:38
Alignment explanation
Indices: 310920--311036 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
310910 TTCAATTTGC
* *
310920 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
310958 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
310999 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
311032 AGAAT
1 AGAAT
311037 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:311009 original size:14 final size:14
Alignment explanation
Indices: 310990--311043 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
310980 AAATGAAAAG
310990 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
311004 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
311023 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
311037 CGCAACG
1 CGCAACG
311044 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:311019 original size:33 final size:33
Alignment explanation
Indices: 310979--311048 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
310969 CGCAACGAGA
310979 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
311012 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
311045 GAAA
1 GAAA
311049 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:311055 original size:33 final size:33
Alignment explanation
Indices: 310985--311059 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
310975 GAGAGAAATG
* **
310985 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
311018 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
311051 AAAATCGCA
1 AAAATCGCA
311060 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:311077 original size:19 final size:19
Alignment explanation
Indices: 311055--311152 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
311045 GAAACCAAAA
*
311055 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
311074 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
311088 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
311107 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
311121 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
311140 TCGCGTTGCGATT
1 TCGCGTTGCGATT
311153 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:311096 original size:14 final size:14
Alignment explanation
Indices: 311077--311166 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
311067 TTTCATTTCG
311077 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
311091 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
311110 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
311124 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
311141 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
311157 CGTTGCGATT
1 CGTTGCGATT
311167 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:311102 original size:33 final size:33
Alignment explanation
Indices: 311060--311174 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
311050 CAAAATCGCA
311060 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
311093 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
311126 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
311159 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
311175 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:313031 original size:93 final size:93
Alignment explanation
Indices: 312872--313252 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
312862 TAGATTGCTT
*
312872 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312937 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
312965 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313030 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
313058 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313123 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313151 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
313216 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
313244 AGTAAATTT
1 AGTAAATTT
313253 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:313287 original size:19 final size:19
Alignment explanation
Indices: 313265--313394 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
313255 CCATTCAAGA
313265 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
313284 TTGCGA--TTC-TTT--CG
1 TTGCGATTTTCATTTCGCG
*
313298 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
313317 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
313331 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
313350 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
313369 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
313389 TTGCGA
1 TTGCGA
313395 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 42 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:313301 original size:14 final size:14
Alignment explanation
Indices: 313282--313338 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
313272 TTTCATTTCG
313282 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
313296 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
313313 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
313329 CGTTGCGATT
1 CGTTGCGATT
313339 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:313307 original size:33 final size:33
Alignment explanation
Indices: 313265--313357 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
313255 CCATTCAAGA
*
313265 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
313298 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
313331 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
313358 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:315307 original size:14 final size:14
Alignment explanation
Indices: 315288--315323 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
315278 ATTGTTTAAT
315288 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
315302 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
315316 TGATTTGT
1 TGATTTGT
315324 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:315454 original size:19 final size:19
Alignment explanation
Indices: 315430--315529 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
315420 AAAATTGACT
315430 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
315449 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
315468 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
315482 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
315501 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
315521 ATCGCAATG
1 ATCGCAATG
315530 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.53
20 18 0.25
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:315559 original size:53 final size:53
Alignment explanation
Indices: 315430--315546 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
315420 AAAATTGACT
*
315430 ATCGCAATGCGAAATGAAAATCGCAATAC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
315482 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
315535 ATCGCAATGCGA
1 ATCGCAATGCGA
315547 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 28 0.46
53 33 0.54
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:315564 original size:19 final size:19
Alignment explanation
Indices: 315536--315684 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
315526 AATGGGAGAA
* *
315536 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
315555 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
315571 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
315588 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
315607 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
315623 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
315640 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
315656 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
315673 TCCGCATTGCGA
1 T-CGCATTGCGA
315685 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:315599 original size:52 final size:52
Alignment explanation
Indices: 315536--315652 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
315526 AATGGGAGAA
*
315536 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
315588 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
315640 TCGCATTGCGATT
1 TCGCATTGCGATT
315653 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:315630 original size:33 final size:33
Alignment explanation
Indices: 315593--315684 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
315583 TCATTTCGCA
315593 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
315626 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
315659 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
315685 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:315631 original size:14 final size:14
Alignment explanation
Indices: 315612--315666 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
315602 TCATTTCGCA
315612 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
315626 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
315643 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
315659 TTGCGATT
1 TTGCGATT
315667 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:315767 original size:19 final size:19
Alignment explanation
Indices: 315743--315840 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
315733 AAAATTGACT
315743 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
315762 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
315781 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
315795 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
315814 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
315834 ATCGCAA
1 ATCGCAA
315841 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:315872 original size:53 final size:53
Alignment explanation
Indices: 315743--315859 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
315733 AAAATTGACT
315743 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
315795 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
315848 ATCGCAATGCGA
1 ATCGCAATGCGA
315860 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:318427 original size:24 final size:24
Alignment explanation
Indices: 318387--318441 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
318377 AAAATCCGTG
* * *
318387 TATTGACCAATATCAAAGTTCGGA
1 TATTGACCAAGACCAAAGTTCGAA
*
318411 TATTGACCAAGACCAAATTTCGAA
1 TATTGACCAAGACCAAAGTTCGAA
*
318435 TACTGAC
1 TATTGAC
318442 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGACCAAAGTTCGAA
Found at i:319130 original size:20 final size:20
Alignment explanation
Indices: 319115--319351 Score: 260
Period size: 20 Copynumber: 11.8 Consensus size: 20
319105 GTGATTTATA
*
319115 GATTCTCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACG
** *
319135 GATTATCGTTGCGATTTACA
1 GATTCGCGTTGCGATTTACG
*
319155 GATTCTCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACG
** *
319175 GATTATCGTTGCGATTTACA
1 GATTCGCGTTGCGATTTACG
*
319195 GATTCTCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACG
* *
319215 GATACGCGTTGCGATATACG
1 GATTCGCGTTGCGATTTACG
* * *
319235 GATACGCATTGCGATTTACC
1 GATTCGCGTTGCGATTTACG
* *
319255 CATACGCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACG
*
319275 GATACGCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACG
* *
319295 GATACGCGTTGCGATTTATG
1 GATTCGCGTTGCGATTTACG
* *
319315 TG-TTCGCGTTGCGATTTTCA
1 -GATTCGCGTTGCGATTTACG
*
319335 TATTCGCGTTGCGATTT
1 GATTCGCGTTGCGATTT
319352 TGGAAAATCG
Statistics
Matches: 191, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 190 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GATTCGCGTTGCGATTTACG
Found at i:319368 original size:21 final size:21
Alignment explanation
Indices: 319338--319420 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
319328 ATTTTCATAT
*
319338 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
319359 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
319380 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
319401 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
319421 CTGATTTGTG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:319411 original size:42 final size:43
Alignment explanation
Indices: 319318--319416 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
319308 ATTTATGTGT
* *
319318 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
319359 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
319401 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
319417 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:320104 original size:10 final size:10
Alignment explanation
Indices: 320089--320113 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
320079 TTCATCACAC
320089 CAAATTCTCT
1 CAAATTCTCT
320099 CAAATTCTCT
1 CAAATTCTCT
320109 CAAAT
1 CAAAT
320114 ACACTCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:320196 original size:17 final size:18
Alignment explanation
Indices: 320161--320201 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
320151 ATATTATGTA
*
320161 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
320179 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
320196 TTTACT
1 TTTACT
320202 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:343339 original size:13 final size:13
Alignment explanation
Indices: 343321--343346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343311 ATCATTCAAT
343321 CATGTATTGACAC
1 CATGTATTGACAC
343334 CATGTATTGACAC
1 CATGTATTGACAC
343347 GTGTTAAGTT
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CATGTATTGACAC
Found at i:347898 original size:72 final size:72
Alignment explanation
Indices: 347775--347985 Score: 255
Period size: 72 Copynumber: 2.9 Consensus size: 72
347765 CTTCAGCTAT
* * * * * * *
347775 AGTTGCTACGCCTTCACAGTCTGTGTTTGGTAACACCAATCCGGGCCTGGTGTTTGGGTCAACTC
1 AGTTGCTATGCCATCGCAGTCTGTGTTTGCTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
*
347840 CTGCTGC
66 CAGCTGC
* *
347847 AGTTGCTATGCCATCGCAGTCCGTGTTTGCTAACACCAGTCCCGGCTTGGTGTTTGGGTCAACTC
1 AGTTGCTATGCCATCGCAGTCTGTGTTTGCTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
347912 CAGCTGC
66 CAGCTGC
* ** * *
347919 AGGTGCTACT-CCATCGCAGAATGTGTTTGGC-AACACCAGTTCAGGCTTGGTGTTTGGGTTAAC
1 AGTTGCTA-TGCCATCGCAGTCTGTGTTT-GCTAACACCAGTCCAGGCTTGGTGTTTGGGTCAAC
347982 TCCA
64 TCCA
347986 TCTAGTAATA
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
72 118 0.98
73 3 0.02
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (72 bp):
AGTTGCTATGCCATCGCAGTCTGTGTTTGCTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
CAGCTGC
Found at i:371562 original size:35 final size:33
Alignment explanation
Indices: 371510--371581 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 33
371500 CTTACAAACT
*
371510 CCCTAGTTTTTCCGGGCTAAACTAGAACATTTC
1 CCCTAGTTTTACCGGGCTAAACTAGAACATTTC
* *
371543 CCCTAGCTTTTACACGGGCTAAGCTAGAACCTTTC
1 CCCTAG-TTTTAC-CGGGCTAAACTAGAACATTTC
371578 CCCT
1 CCCT
371582 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 6 0.18
34 5 0.15
35 23 0.68
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.31
Consensus pattern (33 bp):
CCCTAGTTTTACCGGGCTAAACTAGAACATTTC
Found at i:371888 original size:21 final size:21
Alignment explanation
Indices: 371862--371903 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
371852 CCAGAATGGG
*
371862 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
371883 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
371904 ATATTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:372004 original size:29 final size:31
Alignment explanation
Indices: 371972--372031 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
371962 AAATTTTGAA
371972 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
372001 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
372032 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:375341 original size:30 final size:29
Alignment explanation
Indices: 375306--375371 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
375296 ATCTTTAATA
** *
375306 AAATATATTCATATTTTATAAAAACAAAT
1 AAATATATAAATATATTATAAAAACAAAT
*
375335 ACAATATATAAATATATTATTAAAACAAAT
1 A-AATATATAAATATATTATAAAAACAAAT
375365 AAATATA
1 AAATATA
375372 AGCTTGACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (29 bp):
AAATATATAAATATATTATAAAAACAAAT
Found at i:377376 original size:63 final size:63
Alignment explanation
Indices: 377277--377405 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
377267 TCTTCTCATT
377277 ATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATCGAGTGAAATGTTG
1 ATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATCGAGTGAAATGTTG
377340 ATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATCGAGTGAAATGTTG
1 ATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATCGAGTGAAATGTTG
377403 ATG
1 ATG
377406 TTGATCTAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (63 bp):
ATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATCGAGTGAAATGTTG
Found at i:389826 original size:31 final size:31
Alignment explanation
Indices: 389781--389865 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
389771 AAATCATGCG
* * *
389781 TTTAATACTT-AACTATTAATTTTGTTCTGT
1 TTTAGTACTTAAACTATTAATTTTGCTCTAT
* *
389811 TTTAGTATTTAAACTATTAGTTTTGCTCTAT
1 TTTAGTACTTAAACTATTAATTTTGCTCTAT
*
389842 TTTAGTACTTAAACTTTTAATTTT
1 TTTAGTACTTAAACTATTAATTTT
389866 ATCAAATCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
30 8 0.17
31 38 0.83
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTAGTACTTAAACTATTAATTTTGCTCTAT
Found at i:391129 original size:184 final size:187
Alignment explanation
Indices: 390819--391190 Score: 723
Period size: 184 Copynumber: 2.0 Consensus size: 187
390809 ATAACACCAC
390819 TTTCAATCGTGAATATATGGACGGAAGCAAGATTTTACTTTAGAGGAAAACTTTATAAAATTTTT
1 TTTCAATCGTGAATATATGGACGGAAGCAAGATTTTACTTTAGAGGAAAACTTTATAAAATTTTT
390884 GGGACGAAAATAGATTATGGATAGAAAATACAAAAAGAATATATAAAGGATAATTTGGTTGTTAA
66 GGGACGAAAATAGATTATGGATAGAAAATACAAAAAGAATATATAAAGGATAATTTGGTTGTTAA
390949 TGGCGTTAAAATGGACTGTTATATAGATGCAAAACGATGTCG-TTT-GTGAAAATTT
131 TGGCGTTAAAATGGACTGTTATATAGATGCAAAACGATGTCGTTTTGGTGAAAATTT
391004 TTTCAATCGTGAATATATGGACGGAAGCAAGA-TTTACTTTAGAGGAAAACTTTATAAAATTTTT
1 TTTCAATCGTGAATATATGGACGGAAGCAAGATTTTACTTTAGAGGAAAACTTTATAAAATTTTT
391068 GGGACGAAAATAGATTATGGATAGAAAATACAAAAAGAATATATAAAGGATAATTTGGTTGTTAA
66 GGGACGAAAATAGATTATGGATAGAAAATACAAAAAGAATATATAAAGGATAATTTGGTTGTTAA
391133 TGGCGTTAAAATGGACTGTTATATAGATGCAAAACGATGTCGTTTTGGTGAAAATTT
131 TGGCGTTAAAATGGACTGTTATATAGATGCAAAACGATGTCGTTTTGGTGAAAATTT
391190 T
1 T
391191 GTTTTTATAA
Statistics
Matches: 185, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
184 139 0.75
185 35 0.19
186 11 0.06
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (187 bp):
TTTCAATCGTGAATATATGGACGGAAGCAAGATTTTACTTTAGAGGAAAACTTTATAAAATTTTT
GGGACGAAAATAGATTATGGATAGAAAATACAAAAAGAATATATAAAGGATAATTTGGTTGTTAA
TGGCGTTAAAATGGACTGTTATATAGATGCAAAACGATGTCGTTTTGGTGAAAATTT
Found at i:400155 original size:15 final size:16
Alignment explanation
Indices: 400135--400171 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
400125 TCCGTCCCCC
*
400135 TATTTTAAA-AGTCAA
1 TATTTTAAACAATCAA
400150 TATTTTAAACAATCAA
1 TATTTTAAACAATCAA
400166 -ATTTTA
1 TATTTTA
400172 TAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (16 bp):
TATTTTAAACAATCAA
Found at i:401624 original size:23 final size:23
Alignment explanation
Indices: 401597--401640 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
401587 ATAAAATTTC
*
401597 TAAAAATATTTTTTTTAAAAACA
1 TAAAAATATTTTTTATAAAAACA
*
401620 TAAAATTATTTTTTATAAAAA
1 TAAAAATATTTTTTATAAAAA
401641 AAACTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATATTTTTTATAAAAACA
Found at i:402075 original size:20 final size:19
Alignment explanation
Indices: 402046--402084 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
402036 TAGTTTTTTA
*
402046 TTTTTTATAAAAATAATAT
1 TTTTTTATAAAAAAAATAT
402065 TTTTATTATAAAAAAAATAT
1 TTTT-TTATAAAAAAAATAT
402085 AACGGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTTATAAAAAAAATAT
Found at i:402171 original size:23 final size:23
Alignment explanation
Indices: 402141--402188 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
402131 TTTTATCGAA
402141 AAATTCTTTAGACACCAAAAGTC
1 AAATTCTTTAGACACCAAAAGTC
402164 AAATTCTTTAGACACCAAAAGTC
1 AAATTCTTTAGACACCAAAAGTC
402187 AA
1 AA
402189 TTTACAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (23 bp):
AAATTCTTTAGACACCAAAAGTC
Found at i:404802 original size:36 final size:36
Alignment explanation
Indices: 404762--404847 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
404752 ATTAACTTTG
404762 CTCTTAAAATTTTAGTATTTTATAAATTTAAATTCA
1 CTCTTAAAATTTTAGTATTTTATAAATTTAAATTCA
* *
404798 CTCTTAAAATTTTAGTGTTTTATAAATTTAAATTCG
1 CTCTTAAAATTTTAGTATTTTATAAATTTAAATTCA
404834 CTCTTAAAATTTTA
1 CTCTTAAAATTTTA
404848 AAAATTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (36 bp):
CTCTTAAAATTTTAGTATTTTATAAATTTAAATTCA
Found at i:406757 original size:28 final size:28
Alignment explanation
Indices: 406704--406759 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
406694 AGTAAAATAA
* *
406704 TAATTATTAATTAATAATTTAGTATTTT
1 TAATTATTAATTAATAAATTAATATTTT
*
406732 TAATTATTTATTAGA-AAATTAATATTTT
1 TAATTATTAATTA-ATAAATTAATATTTT
406760 AGCAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TAATTATTAATTAATAAATTAATATTTT
Found at i:408828 original size:17 final size:18
Alignment explanation
Indices: 408806--408848 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
408796 ATATATCCGG
408806 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
408823 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
408843 TATCAT
1 TATCAT
408849 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:408866 original size:20 final size:19
Alignment explanation
Indices: 408811--408857 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
408801 TCCGGTATCA
408811 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
408830 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
408851 TTTTACC
1 TTTTACC
408858 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:409008 original size:20 final size:20
Alignment explanation
Indices: 408979--409024 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
408969 CACTTTTAAA
*
408979 TTTACTGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
408998 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
409019 TTTACC
1 TTTACC
409025 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:413217 original size:6 final size:6
Alignment explanation
Indices: 413208--413283 Score: 61
Period size: 6 Copynumber: 12.7 Consensus size: 6
413198 TTTAGTTTTA
* *
413208 AAAAAT AAAAAT ATCAAAT AAAAAT ATAAAA- AAAAGT AAAAA- AACAAAGT
1 AAAAAT AAAAAT A-AAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AA-AAA-T
*
413258 -AAAAT AAAAAT -AAAAT AAACAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
413284 TAGGAGTACC
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
5 11 0.20
6 35 0.62
7 10 0.18
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:413262 original size:30 final size:29
Alignment explanation
Indices: 413207--413281 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
413197 ATTTAGTTTT
*
413207 AAAAAATAAAAATATCAAATAAAAATATAA
1 AAAAAATAAAAATAACAAATAAAAATA-AA
413237 AAAAAAGTAAAAA-AACAAAGT-AAAATAAA
1 AAAAAA-TAAAAATAACAAA-TAAAAATAAA
*
413266 AATAAAATAAACATAA
1 AA-AAAATAAAAATAA
413282 AATAGGAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.23
30 23 0.59
31 7 0.18
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.16
Consensus pattern (29 bp):
AAAAAATAAAAATAACAAATAAAAATAAA
Found at i:413273 original size:11 final size:11
Alignment explanation
Indices: 413209--413285 Score: 75
Period size: 11 Copynumber: 6.5 Consensus size: 11
413199 TTAGTTTTAA
413209 AAAATAAAAAT
1 AAAATAAAAAT
413220 ATCAAATAAAAAT
1 A--AAATAAAAAT
413233 ATAAA-AAAAAGT
1 A-AAATAAAAA-T
*
413245 AAAAAAACAAAGT
1 AAAATAA-AAA-T
413258 AAAATAAAAAT
1 AAAATAAAAAT
*
413269 AAAATAAACAT
1 AAAATAAAAAT
413280 AAAATA
1 AAAATA
413286 GGAGTACCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
11 26 0.45
12 10 0.17
13 22 0.38
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:416352 original size:31 final size:31
Alignment explanation
Indices: 416316--416375 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
416306 AAACTTAAAA
**
416316 TAGTTTTACAATATTGGGATTTAAATAATTT
1 TAGTTTTACAATATTGAAATTTAAATAATTT
416347 TAGTTTTACAATATTGAAATTTAAATAAT
1 TAGTTTTACAATATTGAAATTTAAATAAT
416376 CCATACAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (31 bp):
TAGTTTTACAATATTGAAATTTAAATAATTT
Found at i:416541 original size:32 final size:32
Alignment explanation
Indices: 416502--417039 Score: 225
Period size: 32 Copynumber: 18.7 Consensus size: 32
416492 CAATCTATAT
*
416502 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416534 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
416556 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
416588 TTTATAATAAATCAAT---T--T-AT--ATT-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
416611 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
416643 TTTAAAATAAACCAATCCATATTTTAAAATAAATCA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATTA
* * * *
416679 TTTCATACTAATAAAT-TAT--TTA-AAATAAATCAA
1 TTT-A-A--AATAAATCAATCCATACTAATAAAT-TA
* * ** **
416712 TCCATACAACTACAAT-AATAAAT-C-AATCCATAT-
1 T--TTA-AAATA-AATCAATCCATACTAATAAAT-TA
416745 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416777 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
416799 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
416831 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
416861 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416886 -------TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416911 TTTAAAATAAATCAA--C---CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416933 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416965 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
416987 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
417019 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
417040 TTTTAAAATA
Statistics
Matches: 389, Mismatches: 37, Indels: 160
0.66 0.06 0.27
Matches are distributed among these distances:
22 73 0.19
23 26 0.07
24 8 0.02
25 6 0.02
26 30 0.08
27 8 0.02
28 14 0.04
29 7 0.02
30 15 0.04
31 14 0.04
32 147 0.38
33 8 0.02
34 8 0.02
35 2 0.01
36 11 0.03
37 3 0.01
38 1 0.00
39 2 0.01
40 6 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:416547 original size:54 final size:54
Alignment explanation
Indices: 416485--417061 Score: 625
Period size: 54 Copynumber: 10.7 Consensus size: 54
416475 TAACTACAAT
*
416485 AATAAATCAATCTATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
416539 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
416593 AATAAATCAATTTATATTTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCTATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * *
416648 AATAAACCAATCCATATTTTAAAATAAATCATTTCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * ** **
416702 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTTAAA--A--T-A
1 AATAAATCAAT-C-TA-TATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
* * * **
416754 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA-TTTTAAA--A--T-A
1 AATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
416808 AATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
416862 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
416916 AATAAATCAACCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
416970 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
417024 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATA
417062 TTTTATAATA
Statistics
Matches: 460, Mismatches: 44, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
48 25 0.05
49 3 0.01
50 2 0.00
51 1 0.00
52 15 0.03
53 4 0.01
54 328 0.71
55 58 0.13
56 1 0.00
57 9 0.02
58 14 0.03
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:416560 original size:22 final size:22
Alignment explanation
Indices: 416534--416576 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
416524 TAATAAATTA
416534 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
416556 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
416577 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:416585 original size:22 final size:22
Alignment explanation
Indices: 416536--416584 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
416526 ATAAATTATT
***
416536 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
416558 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
416581 TAAA
1 TAAA
416585 TTATTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:416774 original size:22 final size:23
Alignment explanation
Indices: 416699--416773 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
416689 ATAAATTATT
416699 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
416721 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
416747 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
416770 TAAA
1 TAAA
416774 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:416784 original size:134 final size:133
Alignment explanation
Indices: 416591--416981 Score: 667
Period size: 134 Copynumber: 2.9 Consensus size: 133
416581 TAAATTATTT
* * *
416591 ATAATAAATCAATTTATATTTTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAACC
1 ATAATAAATCAATCTATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
416656 AATCCATATTTTAAAATAAATCATTTCATACTAATAAATTATTTAAAATAAATCAATCCATACAA
65 AATCCATATTTTAAAATAAATCA-TTCATACTAATAAATTATTTAAAATAAATCAATCCATACAA
416721 CTACA
129 CTACA
*
416726 ATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 ATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
416791 ATTCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
66 ATCCATATTTTAAAATAAATCATTC-ATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
416856 TACA
130 TACA
416860 ATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 ATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
416925 A-CCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
66 ATCC-ATATTTTAAAATAAATC-ATTCATACTAATAAATTATTTAAAATAAATCAATC
416982 TATATTTTAA
Statistics
Matches: 243, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
133 3 0.01
134 222 0.91
135 18 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (133 bp):
ATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
ATCCATATTTTAAAATAAATCATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
ACA
Found at i:416908 original size:22 final size:23
Alignment explanation
Indices: 416833--416907 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
416823 ATAAATTATT
416833 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
416855 CTACAATAATAAATCAATCTATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
416881 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
416904 TAAA
1 TAAA
416908 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:417016 original size:22 final size:22
Alignment explanation
Indices: 416967--417015 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
416957 ATAAATTATT
* **
416967 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
416989 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
417012 TAAA
1 TAAA
417016 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:417045 original size:22 final size:22
Alignment explanation
Indices: 417019--417072 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
417009 TAATAAATTA
417019 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
417041 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
417063 TTTATAATAA
1 TTTAAAATAA
417073 TTTATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:417080 original size:15 final size:15
Alignment explanation
Indices: 417060--417149 Score: 126
Period size: 15 Copynumber: 6.0 Consensus size: 15
417050 AATCAATCCA
* *
417060 TATTTTATAATAATT
1 TATTTTAAAATAAAT
*
417075 TATTTTAAAATAATT
1 TATTTTAAAATAAAT
*
417090 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
417105 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
* *
417120 TAGTTTATAATAAAT
1 TATTTTAAAATAAAT
417135 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
417150 AACCTTATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:417096 original size:30 final size:30
Alignment explanation
Indices: 417060--417149 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
417050 AATCAATCCA
* *
417060 TATTTTATAATAATTTATTTTAAAATAATT
1 TATTTTATAATAAATTATTTTAAAATAAAT
417090 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
417120 TAGTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
417150 AACCTTATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:417651 original size:21 final size:21
Alignment explanation
Indices: 417625--417665 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
417615 CCCACGATGG
*
417625 CCGCAATAGCGTCCGTGACAT
1 CCGCAATAGCGTCCGCGACAT
417646 CCGCAATAGCGTCCGCGACA
1 CCGCAATAGCGTCCGCGACA
417666 GTCGTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.15
Consensus pattern (21 bp):
CCGCAATAGCGTCCGCGACAT
Found at i:421919 original size:3 final size:3
Alignment explanation
Indices: 421913--421964 Score: 54
Period size: 3 Copynumber: 16.7 Consensus size: 3
421903 AAGTTTTTTT
421913 TAA TAA TAA T-A TATA TAA TATA TATA TATA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TA-A TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA
421960 TAA TA
1 TAA TA
421965 CTTAAATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 27 0.60
4 14 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:421932 original size:9 final size:10
Alignment explanation
Indices: 421915--421961 Score: 66
Period size: 9 Copynumber: 5.1 Consensus size: 10
421905 GTTTTTTTTA
421915 ATAATAATAT
1 ATAATAATAT
421925 AT-ATAATAT
1 ATAATAATAT
421934 AT-AT-ATAT
1 ATAATAATAT
421942 ATAATAATA-
1 ATAATAATAT
421951 ATAATAATAT
1 ATAATAATAT
421961 A
1 A
421962 ATACTTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.18
9 22 0.65
10 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATAATAT
Found at i:422399 original size:39 final size:35
Alignment explanation
Indices: 422330--422420 Score: 123
Period size: 36 Copynumber: 2.5 Consensus size: 35
422320 TTGAATAAGC
*
422330 TCTTCTCATTGTGAA--CTTTTTCTTCAGATGATGAGT
1 TCTTCTCATTATGAACTCTTTTTCTTCAGATGA--A-T
422366 TCTTCTCATTATGAACTTCTTTTTCTTCAGATGAAT
1 TCTTCTCATTATGAAC-TCTTTTTCTTCAGATGAAT
422402 TCTTCTCATTATGAACTCT
1 TCTTCTCATTATGAACTCT
422421 ACCTGGCAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
35 3 0.06
36 31 0.61
37 1 0.02
39 16 0.31
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (35 bp):
TCTTCTCATTATGAACTCTTTTTCTTCAGATGAAT
Found at i:422545 original size:38 final size:39
Alignment explanation
Indices: 422472--422570 Score: 137
Period size: 38 Copynumber: 2.5 Consensus size: 39
422462 AGGTTGAACA
422472 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACG
1 AATTCTTCTCATTATG-A---ATTCTTCCTTCTTCAGATGACG
422515 AATTCTTCTCATTATGAATTCTT-CTTCTTCAGATGACG
1 AATTCTTCTCATTATGAATTCTTCCTTCTTCAGATGACG
* *
422553 AGTTCTTCTGATTATGAA
1 AATTCTTCTCATTATGAA
422571 CTCTATTTGG
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 31 0.57
39 6 0.11
42 1 0.02
43 16 0.30
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (39 bp):
AATTCTTCTCATTATGAATTCTTCCTTCTTCAGATGACG
Found at i:422558 original size:19 final size:19
Alignment explanation
Indices: 422500--422561 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
422490 CTTATTCTTC
422500 CTTCTTCAGATGACGAATT
1 CTTCTTCAGATGACGAATT
* ****
422519 CTTC-TCATTATGAATTCTT
1 CTTCTTCA-GATGACGAATT
*
422538 CTTCTTCAGATGACGAGTT
1 CTTCTTCAGATGACGAATT
422557 CTTCT
1 CTTCT
422562 GATTATGAAC
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (19 bp):
CTTCTTCAGATGACGAATT
Found at i:422597 original size:154 final size:150
Alignment explanation
Indices: 422349--422685 Score: 507
Period size: 154 Copynumber: 2.2 Consensus size: 150
422339 TGTGAACTTT
*
422349 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTTCTTTTTCTTCAGATGAATTCTTCTCATTAT
1 TTCTTCAGATGA-GA-TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAATTCTTCTCATTAT
* *
422414 GAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTT
64 GAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAACTCTT
422479 CTCATTATGAACTTATTCTTCC
129 CTCATTATGAACTTATTCTTCC
*
422501 TTCTTCAGATGACGAATTCTTCTCATTATGAA-TTCTTCTTCTTCAGATGACGAGTTCTTCTGAT
1 TTCTTCAGATGA-G-ATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGA--A-TTCTTCTCAT
** * * *
422565 TATGAACTCTATTTGGCAATGTTAATCTATCAATTGATGAATTTAAACAAAAGGTTGAACAAGCT
61 TATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAACT
*
422630 CTTCTCATTATGAACTTCTTCTTCC
126 CTTCTCATTATGAACTTATTCTTCC
422655 TTCTTCAGATGAG-TTCTTCTCATTATGAACT
1 TTCTTCAGATGAGATTCTTCTCATTATGAACT
422686 CTCTCAGGAA
Statistics
Matches: 169, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
151 33 0.20
152 30 0.18
153 3 0.02
154 103 0.61
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (150 bp):
TTCTTCAGATGAGATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAATTCTTCTCATTATGA
ACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAACTCTTCT
CATTATGAACTTATTCTTCC
Found at i:423025 original size:113 final size:112
Alignment explanation
Indices: 422515--423025 Score: 679
Period size: 113 Copynumber: 4.5 Consensus size: 112
422505 TCAGATGACG
** * * * *
422515 AATTCTTCTCATTATGAA-TTCTTCTT-CTTC-AGATGACGAGTTCTTCTGATTATGAACTCTAT
1 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTTTCT
* * * * * * * *
422577 TTGGCAATGTTAATCTATCAATTGATGAATTTAAACAAAAGGTTGAACA
65 CTGGAAAAGCTAATCCATCAA-TGATGGATTTGAGCAAAAGGTTGAACA
** * *
422626 AGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTC
1 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
422691 AGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACA
66 TGGAAAAGCTAATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACA
*
422739 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTC
1 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
422804 TGAAAAAGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAATA
66 TGGAAAAGCTAATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACA
**
422852 AGCTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* *
422916 CTGGCAAAGCTAATCCATCAAGTGATGGCTTTGAGCAAAAGGTTGAACA
65 CTGGAAAAGCTAATCCATCAA-TGATGGATTTGAGCAAAAGGTTGAACA
*
422965 AATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
423026 AACTGACATT
Statistics
Matches: 356, Mismatches: 37, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
111 16 0.04
112 13 0.04
113 321 0.90
114 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTAATCCATCAATGATGGATTTGAGCAAAAGGTTGAACA
Found at i:424145 original size:83 final size:83
Alignment explanation
Indices: 423997--424723 Score: 1150
Period size: 83 Copynumber: 8.6 Consensus size: 83
423987 GGTTTCATAT
* * *
423997 CAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
424062 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
424080 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
424145 TTCAATGATTGGTTTTAC
66 TTCAATAACTGGTTTTAC
* * *
424163 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
424228 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
*
424246 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
424311 TTCAATGATTGGTTTTAC
66 TTCAATAACTGGTTTTAC
424329 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
424394 TTCAATGATTGGTTCTATGGTTTCATAT
66 TTCAAT-A-----AC--TGGTTT--TAC
* * *
424422 CAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
424486 ATTCAATAACTGGTTTTAC
65 ATTCAATAACTGGTTTTAC
424505 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
424570 TTCAATGATTGGTTTTAC
66 TTCAATAACTGGTTTTAC
* *
424588 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
424653 TTCAATGATTGGTTTTAC
66 TTCAATAACTGGTTTTAC
424671 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
424724 GGCATTTGTT
Statistics
Matches: 598, Mismatches: 34, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
82 2 0.00
83 513 0.86
85 6 0.01
87 1 0.00
91 6 0.01
92 1 0.00
93 67 0.11
94 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATAACTGGTTTTAC
Found at i:425879 original size:11 final size:11
Alignment explanation
Indices: 425863--425889 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
425853 TTGACCCCCC
425863 TTTTTTCTTTT
1 TTTTTTCTTTT
425874 TTTTTTCTTTT
1 TTTTTTCTTTT
425885 TTTTT
1 TTTTT
425890 CTGTTCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:437759 original size:3 final size:3
Alignment explanation
Indices: 437747--437824 Score: 122
Period size: 3 Copynumber: 25.7 Consensus size: 3
437737 AAATTTTTTT
*
437747 TAA TAC TAA TAA TAA TAA TAA TAA TAA TATA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA
437794 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
437825 CTTAAATGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
2 2 0.03
3 62 0.89
4 6 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:440823 original size:31 final size:30
Alignment explanation
Indices: 440754--440855 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 30
440744 GTGGTAAGAA
* *
440754 ATTATTTTTATGTTAGTAT-TTT-TTAAAT
1 ATTATTTTTATATTAATATATTTATTAAAT
440782 AGTTTATTTTTATATTAATATATTTATGTAAAT
1 A--TTATTTTTATATTAATATATTTAT-TAAAT
* *
440815 ATTATTTTTTTATTAAAATAATATTTATATAATT
1 ATTATTTTTATATT--AAT-ATATTTAT-TAAAT
440849 ATTATTT
1 ATTATTT
440856 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.02
30 16 0.26
31 15 0.25
32 1 0.02
33 9 0.15
34 19 0.31
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTATTTTTATATTAATATATTTATTAAAT
Found at i:442601 original size:21 final size:21
Alignment explanation
Indices: 442571--442618 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
442561 GCAGGGGTAC
* *
442571 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
442592 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
442613 ATGCCA
1 ATGCCA
442619 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:442648 original size:21 final size:21
Alignment explanation
Indices: 442622--442715 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
442612 TATGCCATCT
* *
442622 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
442643 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
442664 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
442685 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
442706 CCGCAGGGTT
1 CCGCAGGGTT
442716 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:443301 original size:33 final size:35
Alignment explanation
Indices: 443237--443325 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 35
443227 TTTAAAATAC
*
443237 AAATTATATTATTCAAAATTTAAAATAAAATAAAA
1 AAATAATATTATTCAAAATTTAAAATAAAATAAAA
* * *
443272 AAATAATA-TATTC-AAATTTAAATTTAAAT--AT
1 AAATAATATTATTCAAAATTTAAAATAAAATAAAA
* *
443303 AAATTATAGTATTCAAAATTTAA
1 AAATAATATTATTCAAAATTTAA
443326 CATTAATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
31 8 0.17
32 5 0.11
33 22 0.47
34 5 0.11
35 7 0.15
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (35 bp):
AAATAATATTATTCAAAATTTAAAATAAAATAAAA
Found at i:444227 original size:128 final size:128
Alignment explanation
Indices: 443723--444986 Score: 2252
Period size: 128 Copynumber: 9.9 Consensus size: 128
443713 TTACCTGATT
443723 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
443788 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCCTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
443851 TACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
443916 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
443977 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT-ACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
444041 TAACGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
444104 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
444169 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444232 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
****
444297 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
444360 TACTGATATATCTAGTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
444425 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444488 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
444553 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444616 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
444680 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATATGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444743 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
444808 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
444870 TACTGATATATCTAGTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
444935 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
444987 ACTCCGATTA
Statistics
Matches: 1098, Mismatches: 33, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
125 31 0.03
126 92 0.08
127 334 0.30
128 641 0.58
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:444818 original size:255 final size:256
Alignment explanation
Indices: 443723--444986 Score: 2252
Period size: 255 Copynumber: 5.0 Consensus size: 256
443713 TTACCTGATT
443723 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
443788 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCCTCATGTCCCCT-GAGAAATAATAGGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
*
443852 ACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
130 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*** *
443917 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCT-GAGAAATAATAGG
195 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
443977 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT-ACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
444041 TAACGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
444106 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
444171 ATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444232 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
****
444297 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
444362 CTGATATATCTAGTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
444427 ATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444488 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
444553 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
444618 CTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
444682 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATATGAATAGTGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
444743 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
444808 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
444872 CTGATATATCTAGTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
444937 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTGAATAGT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
444987 ACTCCGATTA
Statistics
Matches: 969, Mismatches: 36, Indels: 9
0.96 0.04 0.01
Matches are distributed among these distances:
252 1 0.00
253 148 0.15
254 136 0.14
255 350 0.36
256 334 0.34
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (256 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:445068 original size:8 final size:8
Alignment explanation
Indices: 445055--445095 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
445045 TCACAATCTT
445055 TCAAATTC
1 TCAAATTC
445063 TCAAATTC
1 TCAAATTC
* *
445071 CCAAACTC
1 TCAAATTC
445079 T-AAATTC
1 TCAAATTC
445086 TCAAATTC
1 TCAAATTC
445094 TC
1 TC
445096 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:448105 original size:21 final size:20
Alignment explanation
Indices: 448067--448107 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
448057 TTTAAATACA
448067 TAAATATATAATATATTATT
1 TAAATATATAATATATTATT
448087 TAAATA-ATAATTAATATTATT
1 TAAATATATAA-T-ATATTATT
448108 AGTTATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATATAATATATTATT
Done.