Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 170 of 226
Found at i:54366079 original size:124 final size:124
Alignment explanation
Indices: 54365859--54366104 Score: 465
Period size: 124 Copynumber: 2.0 Consensus size: 124
54365849 GATACAATCA
54365859 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATA
1 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATA
* *
54365924 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATATAAT
66 ATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGCAAATTCATATAAT
54365983 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATA
1 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATA
*
54366048 ATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATA
66 ATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGCAAATTCATATA
54366105 TTTTATTAAA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (124 bp):
TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATA
ATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGCAAATTCATATAAT
Found at i:54366105 original size:41 final size:40
Alignment explanation
Indices: 54365936--54366123 Score: 127
Period size: 41 Copynumber: 4.6 Consensus size: 40
54365926 TATTTTAAAT
* * *
54365936 TATATTTTATAGTATTATATATTATGATTTTAGCAAATTCA
1 TATATTTTATAATATTATATATTATAATTTTAGTAAATT-A
* * * * * *
54365977 TATAATTAAGAATATT-TAATACTAAGAATTTTATTAAATTA
1 TATATTTTATAATATTAT-ATA-TTATAATTTTAGTAAATTA
* **
54366018 TATATTTTTGTTAA-ATTATAT-TTAATAATAATTATTTTAAA-T-
1 TATA-TTTT-ATAATATTATATATT-ATAAT--TT-TAGTAAATTA
54366060 TATATTTTATAATATTATATATTATAATTTTAGTAAATTCA
1 TATATTTTATAATATTATATATTATAATTTTAGTAAATT-A
54366101 TATATTTTATTAA-ATTATATATT
1 TATATTTTA-TAATATTATATATT
54366124 TTTATTAAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 30
0.70 0.12 0.19
Matches are distributed among these distances:
38 5 0.04
39 3 0.03
40 5 0.04
41 59 0.52
42 29 0.26
43 6 0.05
44 6 0.05
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (40 bp):
TATATTTTATAATATTATATATTATAATTTTAGTAAATTA
Found at i:54366358 original size:44 final size:45
Alignment explanation
Indices: 54366295--54366391 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
54366285 CTATTACACC
*
54366295 TCCATTCCATTCAACCAAACACA-AGA-TTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATTTACTATTACGCCTCTAT
* * *
54366339 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTTTAT
1 TCCATTACATTCAACCAAACAATAGATTTACTATTACGCCTCTAT
54366384 TCCATTAC
1 TCCATTAC
54366392 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATTTACTATTACGCCTCTAT
Found at i:54366392 original size:16 final size:16
Alignment explanation
Indices: 54366371--54366403 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54366361 TTGATTTGCT
*
54366371 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
54366387 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54366403 A
1 A
54366404 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54366824 original size:3 final size:3
Alignment explanation
Indices: 54366816--54366853 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54366806 CACATTTAGT
54366816 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54366854 TAAACAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54368389 original size:13 final size:13
Alignment explanation
Indices: 54368371--54368399 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54368361 TCAAGATTAT
54368371 TTAACAAATGAAA
1 TTAACAAATGAAA
54368384 TTAACAAATGAAA
1 TTAACAAATGAAA
54368397 TTA
1 TTA
54368400 TATGAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (13 bp):
TTAACAAATGAAA
Found at i:54372895 original size:68 final size:68
Alignment explanation
Indices: 54372713--54372896 Score: 224
Period size: 68 Copynumber: 2.7 Consensus size: 68
54372703 TTTAATATGC
* * * * * * * *
54372713 AAGACTATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAATATGAGTTTATAATG
1 AAGACCATAGCTAGGCTATGGCAACATATAGAGTCCGCCAGGACAGTAAACATGAGTTTATAATG
54372778 TGT
66 TGT
* * * * * *
54372781 AAAACCATAGCTAGGCTATGGAAACATATAGAGTCTGCCAGAACAGTAAACATGGGTTTGTAATG
1 AAGACCATAGCTAGGCTATGGCAACATATAGAGTCCGCCAGGACAGTAAACATGAGTTTATAATG
54372846 TGT
66 TGT
* *
54372849 AAGACCATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTA
1 AAGACCATAGCTAGGCTATGGCAACATATAGAGTCCGCCAGGACAGTA
54372897 GTATGATTGT
Statistics
Matches: 96, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.25
Consensus pattern (68 bp):
AAGACCATAGCTAGGCTATGGCAACATATAGAGTCCGCCAGGACAGTAAACATGAGTTTATAATG
TGT
Found at i:54373346 original size:68 final size:68
Alignment explanation
Indices: 54373224--54373469 Score: 312
Period size: 68 Copynumber: 3.6 Consensus size: 68
54373214 GAGAGAGGTT
* * * * * *
54373224 TAATATGTAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGGATAGTAAACATGGGT
54373289 TTA
66 TTA
* * * *
54373292 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAATAGTAAACATAGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGGATAGTAAACATGGGT
*
54373357 TTG
66 TTA
* * * * * * *
54373360 TAATGTGTGAGACTATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGGATAGTAAACATGGGT
54373425 TTA
66 TTA
* *
54373428 TAATATGTAAGACCATAACTAGGCTATGGAAATATATAGAGT
1 TAATATGTAAGACCATAGCTAGGCTATGGAAACATATAGAGT
54373470 TCTCTAGGAC
Statistics
Matches: 150, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 150 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (68 bp):
TAATATGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGGATAGTAAACATGGGT
TTA
Found at i:54373362 original size:519 final size:519
Alignment explanation
Indices: 54372383--54373415 Score: 1877
Period size: 519 Copynumber: 2.0 Consensus size: 519
54372373 TATAAGTACA
*
54372383 ATTGTTGAATGAAATATGGTGTTTGAATAAATGGCATACTATGTATTTTATAATAAGTACCTTGC
1 ATTGTTGAATGAAATATGGTGTTTGAATAAATGGCATACTATGTATTTTATAATAAGTAACTTGC
54372448 TCGTGTGTCTAATGCATGATTATATTATACACAAAGTACAAAGGTAATTTATCTGGATGGGTAGA
66 TCGTGTGTCTAATGCATGATTATATTATACACAAAGTACAAAGGTAATTTATCTGGATGGGTAGA
54372513 TGAAGTTAGGAATAATTAGCAGAATGGAGGAATGAGTCGATTGTTAAGGGAATAAAAGGGAGTAA
131 TGAAGTTAGGAATAATTAGCAGAATGGAGGAATGAGTCGATTGTTAAGGGAATAAAAGGGAGTAA
* * *
54372578 GGAAGTGTCGTGGGATGCTATCGACTGACTCGCTAGAGTGAAACCGTGACAATAGTCTATTGACT
196 GAAAGTGTCGTGGAATGCTATCGACTAACTCGCTAGAGTGAAACCGTGACAATAGTCTATTGACT
54372643 CTATGGAGTGACACAGTGACAGGGGTTTATAAGTCCTATGGGGCGACATCTCGAGAGAGGTTTAA
261 CTATGGAGTGACACAGTGACAGGGGTTTATAAGTCCTATGGGGCGACATCTCGAGAGAGGTTTAA
* *
54372708 TATGCAAGACTATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAATATGAGTTTA
326 TATGCAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGAGTTTA
* *
54372773 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCTGCCAGAACAGTAAACATGGGT
391 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAACAGTAAACATAGGT
54372838 TTGTAATGTGTAAGACCATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTAGTATG
456 TTGTAATGTGTAAGACCATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTAGTATG
54372902 ATTGTTGAATGAAATATGGTGTTTGAATAAATGGCATACTATGTATTTTATAATAAGTAACTTGC
1 ATTGTTGAATGAAATATGGTGTTTGAATAAATGGCATACTATGTATTTTATAATAAGTAACTTGC
*
54372967 TCGTGTGTGTAATGCATGATTATATTATACACAAAGTACAAAGGTAATTTATCTGGATGGGTAGA
66 TCGTGTGTCTAATGCATGATTATATTATACACAAAGTACAAAGGTAATTTATCTGGATGGGTAGA
*
54373032 TGAAGTTAGGAATAATTAGCAGAATGGAGGAATGAGTCGATTGTTAAGGGAATATAAGGGAGTAA
131 TGAAGTTAGGAATAATTAGCAGAATGGAGGAATGAGTCGATTGTTAAGGGAATAAAAGGGAGTAA
* * *
54373097 GAAAGTGTCGTGGAATGCTATCGATTAACTCGCTAGAGTGAAACCTTGGCAATAGTCTATTGACT
196 GAAAGTGTCGTGGAATGCTATCGACTAACTCGCTAGAGTGAAACCGTGACAATAGTCTATTGACT
* * *
54373162 CTATGGAGTGACACCGTGACAGGGGTTTATAGGTCCTATGGGGTGACATCTCGAGAGAGGTTTAA
261 CTATGGAGTGACACAGTGACAGGGGTTTATAAGTCCTATGGGGCGACATCTCGAGAGAGGTTTAA
* *
54373227 TATGTAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGGGTTTA
326 TATGCAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGAGTTTA
*
54373292 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAATAGTAAACATAGGT
391 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAACAGTAAACATAGGT
* *
54373357 TTGTAATGTGTGAGACTATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTA
456 TTGTAATGTGTAAGACCATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTA
54373416 AACATGGGTT
Statistics
Matches: 493, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
519 493 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (519 bp):
ATTGTTGAATGAAATATGGTGTTTGAATAAATGGCATACTATGTATTTTATAATAAGTAACTTGC
TCGTGTGTCTAATGCATGATTATATTATACACAAAGTACAAAGGTAATTTATCTGGATGGGTAGA
TGAAGTTAGGAATAATTAGCAGAATGGAGGAATGAGTCGATTGTTAAGGGAATAAAAGGGAGTAA
GAAAGTGTCGTGGAATGCTATCGACTAACTCGCTAGAGTGAAACCGTGACAATAGTCTATTGACT
CTATGGAGTGACACAGTGACAGGGGTTTATAAGTCCTATGGGGCGACATCTCGAGAGAGGTTTAA
TATGCAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGAGTTTA
TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAACAGTAAACATAGGT
TTGTAATGTGTAAGACCATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTAGTATG
Found at i:54373488 original size:136 final size:136
Alignment explanation
Indices: 54373224--54373469 Score: 348
Period size: 136 Copynumber: 1.8 Consensus size: 136
54373214 GAGAGAGGTT
* ** * *
54373224 TAATATGTAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCTGGATAGTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGACTATGGCAACATAAAGAGCCCGCCAGGACAGTAAACATGGGT
* * *
54373289 TTATAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCGCCAGAATAGTAAACATA
66 TTATAATATGTAAAACCATAACTAGGCTATGGAAACATATAGAGTCCGCCAGAACAGTAAACATA
54373354 GGTTTG
131 GGTTTG
* * * * * *
54373360 TAATGTGTGAGACTATAGCTAGGCTATGGCAACATATAGAGCCCGTCAGGACAGTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGACTATGGCAACATAAAGAGCCCGCCAGGACAGTAAACATGGGT
* *
54373425 TTATAATATGTAAGACCATAACTAGGCTATGGAAATATATAGAGT
66 TTATAATATGTAAAACCATAACTAGGCTATGGAAACATATAGAGT
54373470 TCTCTAGGAC
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
136 95 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (136 bp):
TAATATGTAAGACCATAGCTAGACTATGGCAACATAAAGAGCCCGCCAGGACAGTAAACATGGGT
TTATAATATGTAAAACCATAACTAGGCTATGGAAACATATAGAGTCCGCCAGAACAGTAAACATA
GGTTTG
Found at i:54373505 original size:68 final size:69
Alignment explanation
Indices: 54373224--54373511 Score: 305
Period size: 68 Copynumber: 4.2 Consensus size: 69
54373214 GAGAGAGGTT
* * * * * * * *
54373224 TAATATGTAAGACCATAGCTAGACTATGGCAATATAAAGAGTTCGCCT-GGATAGTAAACATGGG
1 TAATGTGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGTCTAGGACAGTAAACATGGG
54373288 TTTA
66 TTTA
* * * * *
54373292 TAATGTGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCCG-CCAGAATAGTAAACATAGG
1 TAATGTGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGTCTAGGACAGTAAACATGGG
*
54373356 TTTG
66 TTTA
* * * *
54373360 TAATGTGTGAGACTATAGCTAGGCTATGGCAACATATAGAGCCCGTC-AGGACAGTAAACATGGG
1 TAATGTGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGTCTAGGACAGTAAACATGGG
54373424 TTTA
66 TTTA
* * * * *
54373428 TAATATGTAAGACCATAACTAGGCTATGGAAATATATAGAGTTC-TCTAGGACATTAAACATGGG
1 TAATGTGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGTCTAGGACAGTAAACATGGG
* *
54373492 CTCA
66 TTTA
**
54373496 TACCGTGTAAGACCAT
1 TAATGTGTAAGACCAT
54373512 GGCCAGACTA
Statistics
Matches: 183, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
67 3 0.02
68 179 0.98
69 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (69 bp):
TAATGTGTAAGACCATAGCTAGGCTATGGAAACATATAGAGTCCGTCTAGGACAGTAAACATGGG
TTTA
Found at i:54377489 original size:22 final size:23
Alignment explanation
Indices: 54377461--54377504 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
54377451 TAATGTAAAT
*
54377461 TTATTT-CAGCAGTTACAAACCA
1 TTATTTCCAACAGTTACAAACCA
54377483 TTATTTCCAACAGTTACAAACC
1 TTATTTCCAACAGTTACAAACC
54377505 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (23 bp):
TTATTTCCAACAGTTACAAACCA
Found at i:54379187 original size:12 final size:10
Alignment explanation
Indices: 54379163--54379208 Score: 65
Period size: 11 Copynumber: 4.3 Consensus size: 10
54379153 ACTTAATCCT
54379163 TTCTCTCAAA
1 TTCTCTCAAA
54379173 TTCTCTCTAATA
1 TTCTCTC-AA-A
54379185 TTCTCTCAAA
1 TTCTCTCAAA
54379195 TTCTTCTCAAA
1 TTC-TCTCAAA
54379206 TTC
1 TTC
54379209 CTATTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.33
11 14 0.42
12 8 0.24
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:54379261 original size:28 final size:28
Alignment explanation
Indices: 54379212--54379270 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
54379202 CAAATTCCTA
**
54379212 TTTAAAAAAGTTTTGATTTTTTAATTATT
1 TTTAAAAAAGTTTTGAAATTTT-ATTATT
*
54379241 TTTAAAAAAGTTTT-AAATTTTATTTTT
1 TTTAAAAAAGTTTTGAAATTTTATTATT
54379268 TTT
1 TTT
54379271 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTAAAAAAGTTTTGAAATTTTATTATT
Found at i:54380375 original size:7 final size:7
Alignment explanation
Indices: 54380363--54380402 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
54380353 TAGTCGATTG
54380363 GTATTTA
1 GTATTTA
54380370 GTATTTA
1 GTATTTA
54380377 GTATTTA
1 GTATTTA
54380384 GTATTTA
1 GTATTTA
54380391 GTATTTA
1 GTATTTA
54380398 GTATT
1 GTATT
54380403 ATGTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:54381379 original size:21 final size:21
Alignment explanation
Indices: 54381353--54381392 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54381343 CTACCGGAGG
*
54381353 AACCAGAATCCCTGCCGAAGC
1 AACCAGAACCCCTGCCGAAGC
54381374 AACCAGAACCCCTGCCGAA
1 AACCAGAACCCCTGCCGAA
54381393 AGCTAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.40, G:0.17, T:0.07
Consensus pattern (21 bp):
AACCAGAACCCCTGCCGAAGC
Found at i:54385009 original size:125 final size:125
Alignment explanation
Indices: 54384787--54385075 Score: 470
Period size: 125 Copynumber: 2.3 Consensus size: 125
54384777 CCAAACATGC
*** *
54384787 GCTACTGTAGCAAAAGTGTGTCCACGTGGGAGCGATTTCAGTACTTTTGCTGACAAAGCATCCTG
1 GCTACTGTAGCAAAAGCACGTCCACGTGGGAGCGATTTCAATACTTTTGCTGACAAAGCATCCTG
* *
54384852 CTTAAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCGAAATTACTTTTTCAGGA
66 CTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTACTTTTTCAGGA
* * *
54384912 GCTACTGTAGCAAAAGCACGTCCACGTGGGAGTGATTTCAATACTTTTGCTGACAATGCATCTTG
1 GCTACTGTAGCAAAAGCACGTCCACGTGGGAGCGATTTCAATACTTTTGCTGACAAAGCATCCTG
*
54384977 CTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 CTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTACTTTTTCAGGA
* *
54385037 GCTACTATAGCAAAAGCACGTCCACGTGAGAGCGATTTC
1 GCTACTGTAGCAAAAGCACGTCCACGTGGGAGCGATTTC
54385076 CTTAAAAAAA
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 151 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (125 bp):
GCTACTGTAGCAAAAGCACGTCCACGTGGGAGCGATTTCAATACTTTTGCTGACAAAGCATCCTG
CTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTACTTTTTCAGGA
Found at i:54396676 original size:15 final size:16
Alignment explanation
Indices: 54396658--54396688 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54396648 TTTTTTTACT
54396658 ATTATTTTTA-TTTTA
1 ATTATTTTTACTTTTA
54396673 ATTATTTTTACTTTTA
1 ATTATTTTTACTTTTA
54396689 TCAAAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTATTTTTACTTTTA
Found at i:54398201 original size:50 final size:51
Alignment explanation
Indices: 54398121--54398303 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 51
54398111 AAAGTGATGG
* *
54398121 TCACGTGTGTAGTACGATGTGCAGGCTACTACGTGTACCAGAAT-G-ATAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATAGCATAGA
* * * * * *
54398171 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGCATAGA
* ** * * * *
54398222 TCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTGAT-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-CATAGA
54398273 TCACATGTGTAG-AGCTATGTGCAGGCTACTA
1 TCACATGTGTAGTA-CTATGTGCAGGCTACTA
54398304 TGTGAACCAG
Statistics
Matches: 110, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
49 3 0.03
50 36 0.33
51 70 0.64
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGCATAGA
Found at i:54398551 original size:16 final size:16
Alignment explanation
Indices: 54398530--54398561 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54398520 TGATTGAAAG
*
54398530 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
54398546 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
54398562 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:54399708 original size:43 final size:43
Alignment explanation
Indices: 54399458--54399699 Score: 272
Period size: 43 Copynumber: 5.6 Consensus size: 43
54399448 TTTGGGAAAG
* * *
54399458 CGCCGCTAAAGACCATGACCTTTAGCGGCGCCTTTACC-ACAAA
1 CGCCGCTAAAGACCACGACCTTTAGCGGCG-CTTTTCCTAAAAA
* * * *
54399501 CGCCGCTAAAGACCACGACCTTTAGCGGCACTTGTCCCACAAA
1 CGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCTAAAAA
* * * *
54399544 CGCCGCTAAAGACAACGAGCTTTTGCGGCGCTTTTCCCAAAAA
1 CGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCTAAAAA
* * *
54399587 CGCCACTAAAGACCACGACCTTTAGCGGCGCTTCTCCTATAAA
1 CGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCTAAAAA
* * * * *
54399630 CACCGCTAAAGAGCACGACTTTTAGCGCCGCTTTTTCTAAAAA
1 CGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCTAAAAA
*
54399673 CGCCGCTAAAGA-TACTGACCTTTAGCG
1 CGCCGCTAAAGACCAC-GACCTTTAGCG
54399700 ACGTTTTTTT
Statistics
Matches: 169, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 7 0.04
43 162 0.96
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (43 bp):
CGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCTAAAAA
Found at i:54399715 original size:129 final size:129
Alignment explanation
Indices: 54399458--54399724 Score: 306
Period size: 129 Copynumber: 2.1 Consensus size: 129
54399448 TTTGGGAAAG
* * *
54399458 CGCCGCTAAAGACCATGACCTTTAGCGGCGCCTTTACCACAAACGCCGCTAAAGACCACGACCTT
1 CGCCACTAAAGACCACGACCTTTAGCGGCGCCTTTACCACAAACACCGCTAAAGACCACGACCTT
* * * * * *
54399523 TAGCGGCACTTGTCCCACAAACGCCGCTAAAGACAACGAGCTTTTGCGGCGCTTTTCCCAAAAA
66 TAGCGCCACTTGTCCCAAAAACGCCGCTAAAGACAACGACCTTTAGCGACGCTTTTCCAAAAAA
* * *
54399587 CGCCACTAAAGACCACGACCTTTAGCGGCG-CTTCT-CCTATAAACACCGCTAAAGAGCACGACT
1 CGCCACTAAAGACCACGACCTTTAGCGGCGCCTT-TACC-ACAAACACCGCTAAAGACCACGACC
* * * * * * **
54399650 TTTAGCGCCGCTTTTTCTAAAAACGCCGCTAAAGA-TACTGACCTTTAGCGACGTTTTTTTAAAA
64 TTTAGCGCCACTTGTCCCAAAAACGCCGCTAAAGACAAC-GACCTTTAGCGACGCTTTTCCAAAA
54399714 AA
128 AA
54399716 CGCCACTAA
1 CGCCACTAA
54399725 TTTTGGCAGA
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
128 7 0.06
129 108 0.94
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (129 bp):
CGCCACTAAAGACCACGACCTTTAGCGGCGCCTTTACCACAAACACCGCTAAAGACCACGACCTT
TAGCGCCACTTGTCCCAAAAACGCCGCTAAAGACAACGACCTTTAGCGACGCTTTTCCAAAAAA
Found at i:54399929 original size:19 final size:19
Alignment explanation
Indices: 54399905--54399942 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54399895 TACAAAAATG
*
54399905 TTAAAAGTTAAAATGATAA
1 TTAAAAGTCAAAATGATAA
54399924 TTAAAAGTCAAAATGATAA
1 TTAAAAGTCAAAATGATAA
54399943 AAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (19 bp):
TTAAAAGTCAAAATGATAA
Found at i:54405577 original size:9 final size:9
Alignment explanation
Indices: 54405560--54406113 Score: 138
Period size: 9 Copynumber: 64.7 Consensus size: 9
54405550 TCTATAAATG
54405560 AGTTATGTA
1 AGTTATGTA
*
54405569 AGTTGTGT-
1 AGTTATGTA
54405577 A-TTATGTA
1 AGTTATGTA
*
54405585 AGTTATTTA
1 AGTTATGTA
**
54405594 AGAAATGT-
1 AGTTATGTA
54405602 A-TTATGTA
1 AGTTATGTA
*
54405610 AGTTATTTA
1 AGTTATGTA
*
54405619 AGTTGTGTA
1 AGTTATGTA
*
54405628 AGTTGTGT-
1 AGTTATGTA
54405636 A-TTATGTA
1 AGTTATGTA
54405644 AGTTATGTA
1 AGTTATGTA
**
54405653 AGAAATGT-
1 AGTTATGTA
54405661 A-TTATGTA
1 AGTTATGTA
*
54405669 AGTTGTGT-
1 AGTTATGTA
* *
54405677 A-TAATGTT
1 AGTTATGTA
**
54405685 AGTTATCAA
1 AGTTATGTA
54405694 AGTTATGT-
1 AGTTATGTA
54405702 A-TTATGTA
1 AGTTATGTA
*
54405710 AGTTATTTA
1 AGTTATGTA
54405719 AG----GTA
1 AGTTATGTA
*
54405724 AGTTGTGT-
1 AGTTATGTA
54405732 A-TTATGTA
1 AGTTATGTA
54405740 AGTTAT-TA
1 AGTTATGTA
*
54405748 TGTTATTATGTA
1 AG---TTATGTA
* *
54405760 ACTTATGCA
1 AGTTATGTA
*
54405769 AGTTTATATACA
1 AG-TTATGT--A
*
54405781 AGTTTATATATA
1 AG--T-TATGTA
54405793 AGTTATGTA
1 AGTTATGTA
* *
54405802 AGTTGTG-C
1 AGTTATGTA
54405810 A-TTATGTA
1 AGTTATGTA
* *
54405818 AGTTGTG-C
1 AGTTATGTA
54405826 A-TTATGTA
1 AGTTATGTA
54405834 AGTTATGTA
1 AGTTATGTA
***
54405843 AAAAATGT-
1 AGTTATGTA
54405851 A-TTATGTA
1 AGTTATGTA
*
54405859 AGTTGTGT-
1 AGTTATGTA
* *
54405867 A-TAATGTT
1 AGTTATGTA
**
54405875 AGTTATCAA
1 AGTTATGTA
54405884 AGTTATGT-
1 AGTTATGTA
54405892 A-TTATGTA
1 AGTTATGTA
*
54405900 AGTTATTTA
1 AGTTATGTA
54405909 AG----GTA
1 AGTTATGTA
*
54405914 AGTTGTGT-
1 AGTTATGTA
54405922 A-TTATGTA
1 AGTTATGTA
54405930 AGTTAT-TA
1 AGTTATGTA
*
54405938 TGTTATTATGTA
1 AG---TTATGTA
* * *
54405950 ACTTGTGCA
1 AGTTATGTA
*
54405959 AGTTTATATACA
1 AG-TTATGT--A
*
54405971 AGTTAATATATA
1 AG-T--TATGTA
54405983 AGTTATGTA
1 AGTTATGTA
* *
54405992 ATTTGTGT-
1 AGTTATGTA
54406000 A-TTATGTA
1 AGTTATGTA
54406008 AGTTATGTA
1 AGTTATGTA
***
54406017 AAAAATGT-
1 AGTTATGTA
54406025 A-TTATGTA
1 AGTTATGTA
*
54406033 AGTTGTGT-
1 AGTTATGTA
* *
54406041 A-TAATGTT
1 AGTTATGTA
**
54406049 AGTTATCAA
1 AGTTATGTA
54406058 AGTTATGT-
1 AGTTATGTA
*
54406066 A-TTATTTA
1 AGTTATGTA
*
54406074 AGTTATTTA
1 AGTTATGTA
54406083 AGTTATGTA
1 AGTTATGTA
*
54406092 AGTTGTGT-
1 AGTTATGTA
54406100 A-TTATGTA
1 AGTTATGTA
54406108 AGTTAT
1 AGTTAT
54406114 TATTTTTAAA
Statistics
Matches: 391, Mismatches: 92, Indels: 124
0.64 0.15 0.20
Matches are distributed among these distances:
5 8 0.02
7 83 0.21
8 42 0.11
9 211 0.54
10 8 0.02
11 9 0.02
12 18 0.05
13 2 0.01
14 10 0.03
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:54405588 original size:25 final size:25
Alignment explanation
Indices: 54405560--54405772 Score: 138
Period size: 25 Copynumber: 8.5 Consensus size: 25
54405550 TCTATAAATG
54405560 AGTTATGTAAGTTGTGTATTATGTA
1 AGTTATGTAAGTTGTGTATTATGTA
* ***
54405585 AGTTATTTAAGAAATGTATTATGTA
1 AGTTATGTAAGTTGTGTATTATGTA
* *
54405610 AGTTATTTAAGTTGTGTAAGTTGTGT-
1 AGTTATGTAAGTTGTGT-A-TTATGTA
* **
54405636 A-TTATGTAAGTTATGTAAGAAATGT-
1 AGTTATGTAAGTTGTGT-A-TTATGTA
* *
54405661 A-TTATGTAAGTTGTGTATAATGTT
1 AGTTATGTAAGTTGTGTATTATGTA
** *
54405685 AGTTATCAAAGTTATGTATTATGTA
1 AGTTATGTAAGTTGTGTATTATGTA
54405710 AGTTATTTAAGGTAAGTTGTGTATTATGTA
1 AGTTA--T---GTAAGTTGTGTATTATGTA
54405740 AGTTAT-T-A--TGT-TATTATGTA
1 AGTTATGTAAGTTGTGTATTATGTA
* *
54405760 ACTTATGCAAGTT
1 AGTTATGTAAGTT
54405773 TATATACAAG
Statistics
Matches: 150, Mismatches: 25, Indels: 27
0.74 0.12 0.13
Matches are distributed among these distances:
20 14 0.09
21 3 0.02
22 1 0.01
23 6 0.04
24 4 0.03
25 92 0.61
26 2 0.01
27 6 0.04
28 1 0.01
30 21 0.14
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (25 bp):
AGTTATGTAAGTTGTGTATTATGTA
Found at i:54405607 original size:41 final size:41
Alignment explanation
Indices: 54405562--54406100 Score: 219
Period size: 41 Copynumber: 12.8 Consensus size: 41
54405552 TATAAATGAG
* * *
54405562 TTATGTAAGTTGTGTATTATGTAAGTTATTTAAGAAATGTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * * *
54405603 TTATGTAAGTTATTTAAGTTGTGTAAGTTGTGT-A-TTATGTAA
1 TTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTAATGT-A
** *
54405645 GTTATGTAAGAAATGTATTATGTAAGTTGTGT-A-TAATGTTA
1 -TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATG-TA
** *
54405686 GTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTA
1 -TTATGTAAGTTATGTATTATGTAAGTTATGTAA-GTAA----TGTA
* *
54405733 TTATGTAAGTTATTATGTTATTATGTAACTTATGCAAGT--T-TA
1 TTATGTAAG---TTATG-TATTATGTAAGTTATGTAAGTAATGTA
** * ** *
54405775 -TATACAAG-T-T-TA-TATATAAGTTATGTAAGTTGTGCA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * **
54405811 TTATGTAAGTTGTGCATTATGTAAGTTATGTAAAAAATGTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * * ** *
54405852 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * *
54405893 TTATGTAAGTTAT-T-TAAGGTAAGTTGTGTATTATGTAA-GTTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTA--A-GTAATG-TA
* * * * *
54405935 TTATGTTA-TTATGTAACTTGTGCAAGTTTATATACAAGTTAATATATAA
1 TTATGTAAGTTATGT-A-TTATGTAAG-TTATGT--AAG-T-A-ATGT-A
* * **
54405984 GTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTA
1 -TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * * ** *
54406026 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
* * *
54406067 TTATTTAAGTTATTTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGT-A-TTATGTAAGTTATGTA
54406101 TTATGTAAGT
Statistics
Matches: 369, Mismatches: 85, Indels: 86
0.68 0.16 0.16
Matches are distributed among these distances:
33 15 0.04
34 2 0.01
35 1 0.00
36 2 0.01
37 7 0.02
38 1 0.00
39 12 0.03
40 2 0.01
41 183 0.50
42 23 0.06
43 39 0.11
44 4 0.01
45 6 0.02
46 15 0.04
47 3 0.01
48 10 0.03
49 15 0.04
50 24 0.07
51 5 0.01
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (41 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTAATGTA
Found at i:54405657 original size:59 final size:59
Alignment explanation
Indices: 54405560--54406113 Score: 220
Period size: 59 Copynumber: 9.5 Consensus size: 59
54405550 TCTATAAATG
*
54405560 AGTTATGTAAGTTGTGTATTATGTAAGTTATTTAAGAAATGTATTATGTAAGTTATTTA
1 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTATTTA
* *
54405619 AGTTGTGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTGTGTATA
1 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTAT-T-TA
* * * *
54405680 ATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTA
1 A-GTTA--TGT--AAGTTGTGTATTATGTAAGTTATGTAA-G-AA---ATGTATTATGTAAGTTA
54405745 -TTA
56 TTTA
* * * * *
54405748 TGTTAT-T-A--TGT-AACTTATGCAAGTT-TATATA-CAA-GT-TTA--T-A--TA--TA
1 AGTTATGTAAGTTGTGTA-TTATGTAAGTTATGTA-AGAAATGTATTATGTAAGTTATTTA
* * * ** *** *
54405793 AGTTATGTAAGTTGTGCATTATGTAAGTTGTG-CA-TTATGTAAGTTATGTAAAAAATGT-
1 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGT-A-TTATGTAAGTTATTTA
* * ** **
54405851 A-TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTA
1 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTATTTA
* * * **
54405909 AG----GTAAGTTGTGTATTATGTAAGTTAT-TATG---T-TATTATGTAACTTGTGCA
1 AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTATTTA
* * * * **** *
54405959 AGTTTATATACA--AGT-TAATATATAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAA
1 AG-TTATGTA-AGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTAT-T---TA
* * ** ** *
54406021 ATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATTTAAGTTATTTA
1 A-G--TTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTATTTA
54406083 AGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 AGTTATGTAAGTTGTGTATTATGTAAGTTAT
54406114 TATTTTTAAA
Statistics
Matches: 373, Mismatches: 67, Indels: 110
0.68 0.12 0.20
Matches are distributed among these distances:
45 7 0.02
46 3 0.01
47 1 0.00
48 3 0.01
49 16 0.04
50 18 0.05
51 4 0.01
52 5 0.01
53 13 0.03
54 7 0.02
55 26 0.07
56 2 0.01
57 38 0.10
58 21 0.06
59 100 0.27
60 1 0.00
61 5 0.01
62 7 0.02
63 2 0.01
64 9 0.02
65 4 0.01
66 56 0.15
67 5 0.01
68 4 0.01
69 1 0.00
71 15 0.04
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (59 bp):
AGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTATTTA
Found at i:54405712 original size:16 final size:16
Alignment explanation
Indices: 54405693--54405935 Score: 70
Period size: 16 Copynumber: 14.4 Consensus size: 16
54405683 TTAGTTATCA
54405693 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
54405709 AAGTTAT-T-TAAGGT
1 AAGTTATGTATTATGT
*
54405723 AAGTTGTGTATTATGT
1 AAGTTATGTATTATGT
54405739 AAGTTATTATGTTATTATGT
1 AAG---TTATG-TATTATGT
* * *
54405759 AACTTATGCAAGTTTATAT
1 AAGTTATG-TA--TTATGT
*
54405778 ACAAGTTTATATATAAGTTATGT
1 --AAG--T-TATGT-A-TTATGT
* *
54405801 AAGTTGTGCATTATGT
1 AAGTTATGTATTATGT
* *
54405817 AAGTTGTGCATTATGT
1 AAGTTATGTATTATGT
**
54405833 AAGTTATGTAAAAAATGT
1 AAGTTATGT--ATTATGT
*
54405851 -A-TTATGTAAGTTGTGT
1 AAGTTATGT-A-TTATGT
* **
54405867 -A-TAATGTTAGTTATCA
1 AAGTTATG-TA-TTATGT
54405883 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
54405899 AAGTTAT-T-TAAGGT
1 AAGTTATGTATTATGT
*
54405913 AAGTTGTGTATTATGT
1 AAGTTATGTATTATGT
54405929 AAGTTAT
1 AAGTTAT
54405936 TATGTTATTA
Statistics
Matches: 167, Mismatches: 38, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
14 20 0.12
15 6 0.04
16 83 0.50
17 12 0.07
18 11 0.07
19 10 0.06
20 10 0.06
21 5 0.03
23 6 0.04
24 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:54405782 original size:12 final size:12
Alignment explanation
Indices: 54405767--54405796 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54405757 GTAACTTATG
54405767 CAAGTTTATATA
1 CAAGTTTATATA
54405779 CAAGTTTATATA
1 CAAGTTTATATA
*
54405791 TAAGTT
1 CAAGTT
54405797 ATGTAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (12 bp):
CAAGTTTATATA
Found at i:54405880 original size:25 final size:25
Alignment explanation
Indices: 54405827--54405910 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
54405817 AAGTTGTGCA
*
54405827 TTATGTAAGTTATGTAAAAAATG-TA-
1 TTATGTAAGTTATGT--ATAATGTTAG
*
54405852 TTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTATGTATAATGTTAG
** * *
54405877 TTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATAATGTTAG
*
54405902 TTATTTAAG
1 TTATGTAAG
54405911 GTAAGTTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 41 0.85
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (25 bp):
TTATGTAAGTTATGTATAATGTTAG
Found at i:54405924 original size:190 final size:179
Alignment explanation
Indices: 54405624--54406116 Score: 771
Period size: 190 Copynumber: 2.7 Consensus size: 179
54405614 ATTTAAGTTG
*
54405624 TGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTGTGTATAATGTTAGTT
1 TGTAAGTTGTG-ATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGTT
54405689 ATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATTATGTTAT
65 ATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATTATGTTAT
*
54405754 TATGTAACTTATGCAAGTTTATATACAAGTTTATATATAAGTTATGTAAGTTGTGCATT
130 TATGTAACTTATGCAAGTTTATATACAAGTTAATATATAAGTTATGT-A-------A-T
54405813 ATGTAAGTTGTGCATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGT
1 -TGTAAGTTGTG-ATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGT
54405878 TATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATTATGTTA
64 TATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATTATGTTA
*
54405943 TTATGTAACTTGTGCAAGTTTATATACAAGTTAATATATAAGTTATGTAAT
129 TTATGTAACTTATGCAAGTTTATATACAAGTTAATATATAAGTTATGTAAT
54405994 T-T--G-TGT-ATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGTTA
1 TGTAAGTTGTGATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGTTA
*
54406054 TCAAAGTTATGTATTATTTAAGTTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTATTAT
66 TCAAAGTTATGTATTATGTAAGTTATTTAAG----GTAAGTTGTGTATTATGTAAGTTATTAT
54406117 TTTTAAAATT
Statistics
Matches: 294, Mismatches: 5, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
174 84 0.29
176 3 0.01
177 1 0.00
178 28 0.10
179 1 0.00
180 1 0.00
181 1 0.00
182 1 0.00
189 1 0.00
190 173 0.59
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.46
Consensus pattern (179 bp):
TGTAAGTTGTGATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAATGTTAGTTA
TCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATTATGTTATT
ATGTAACTTATGCAAGTTTATATACAAGTTAATATATAAGTTATGTAAT
Found at i:54406010 original size:25 final size:25
Alignment explanation
Indices: 54405981--54406113 Score: 96
Period size: 25 Copynumber: 5.3 Consensus size: 25
54405971 AGTTAATATA
54405981 TAAGTTATGTAATTTGTGTATTATG
1 TAAGTTATGTAATTTGTGTATTATG
****
54406006 TAAGTTATGTAAAAAATGTATTATG
1 TAAGTTATGTAATTTGTGTATTATG
* * *
54406031 TAAGTTGTGT-ATAATGT-TAGTTATC
1 TAAGTTATGTAAT-TTGTGTA-TTATG
* *
54406056 AAAGTTATGT-ATTAT-T-TAAGTTATT
1 TAAGTTATGTAATT-TGTGT-A-TTATG
*
54406081 TAAGTTATGTAAGTTGTGTATTATG
1 TAAGTTATGTAATTTGTGTATTATG
54406106 TAAGTTAT
1 TAAGTTAT
54406114 TATTTTTAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
24 5 0.06
25 75 0.88
26 4 0.05
27 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTAATTTGTGTATTATG
Found at i:54406035 original size:50 final size:50
Alignment explanation
Indices: 54405981--54406113 Score: 121
Period size: 50 Copynumber: 2.7 Consensus size: 50
54405971 AGTTAATATA
54405981 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGT-A-TTATG
1 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGT--AAAATGTAAGTTATG
* * ** ** * *
54406031 TAAGTTGTGT-ATAATGT-TAGTTATCAAAGTTATGTATTATTTAAGTTATT
1 TAAGTTATGTAAT-TTGTGTA-TTATGTAAGTTATGTAAAATGTAAGTTATG
*
54406081 TAAGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 TAAGTTATGTAATTTGTGTATTATGTAAGTTAT
54406114 TATTTTTAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
48 4 0.06
49 5 0.08
50 52 0.81
51 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (50 bp):
TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAATGTAAGTTATG
Found at i:54406087 original size:34 final size:34
Alignment explanation
Indices: 54406049--54406114 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
54406039 GTATAATGTT
*
54406049 AGTTATCAAAGTTATGTATTATTTAAGTTATTTA
1 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
** *
54406083 AGTTATGTAAGTTGTGTATTATGTAAGTTATT
1 AGTTATCAAAGTTATGTATTATGTAAGTTATT
54406115 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.50
Consensus pattern (34 bp):
AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
Found at i:54406127 original size:12 final size:12
Alignment explanation
Indices: 54406112--54406140 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54406102 TATGTAAGTT
54406112 ATTATTTTTAAA
1 ATTATTTTTAAA
54406124 ATTATTTTTAAA
1 ATTATTTTTAAA
54406136 ATTAT
1 ATTAT
54406141 AAAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTTTTAAA
Found at i:54406246 original size:18 final size:18
Alignment explanation
Indices: 54406223--54406311 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
54406213 ATATATAAAT
54406223 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
54406241 TTTAAGTCATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
*
54406263 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
54406280 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
54406298 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
54406312 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 14 0.23
18 29 0.48
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:54406273 original size:17 final size:17
Alignment explanation
Indices: 54406251--54406311 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
54406241 TTTAAGTCAT
* *
54406251 GTAAGTTATAAATTTTA
1 GTAAGTAATATATTTTA
*
54406268 GTAAGTAATATATTTAA
1 GTAAGTAATATATTTTA
54406285 GTAATGTAATATATTTTA
1 GTAA-GTAATATATTTTA
54406303 GTAAGTAAT
1 GTAAGTAAT
54406312 GTAAGTAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (17 bp):
GTAAGTAATATATTTTA
Found at i:54406282 original size:39 final size:37
Alignment explanation
Indices: 54406215--54406425 Score: 171
Period size: 39 Copynumber: 5.6 Consensus size: 37
54406205 TTAAATATAT
*
54406215 ATATAAATTTTAAGTAATGTAATATATTTAAGTCATGTA
1 ATATAAATTTT-AGTAA-GTAATATATTTAAGTAATGTA
54406254 AGTTATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
1 A--TATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
* ** *
54406293 ATAT--ATTTTAGTAAGTAATGTAAGTAATGTAATAT-
1 ATATAAATTTTAGTAAGTAATATATTTAA-GTAATGTA
* * * *
54406328 ATACTTAAATTTTTGTAAGTCATGTATTTAAGTAATATA
1 ATA--TAAATTTTAGTAAGTAATATATTTAAGTAATGTA
* * * *
54406367 TTTAAGTAAATTTTAGTAAGTAATGTGTTTAAGTAATATA
1 -AT-A-TAAATTTTAGTAAGTAATATATTTAAGTAATGTA
*
54406407 CTAT--ATTTTAGTAAGTAAT
1 ATATAAATTTTAGTAAGTAAT
54406426 GTAAGTAATG
Statistics
Matches: 147, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
35 38 0.26
36 6 0.04
37 5 0.03
38 8 0.05
39 42 0.29
40 37 0.25
41 11 0.07
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (37 bp):
ATATAAATTTTAGTAAGTAATATATTTAAGTAATGTA
Found at i:54406368 original size:13 final size:13
Alignment explanation
Indices: 54406352--54406406 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
54406342 GTAAGTCATG
54406352 TATTTAAGTAATA
1 TATTTAAGTAATA
54406365 TATTTAAGTAA-A
1 TATTTAAGTAATA
* *
54406377 TTTTAGTAAGTAATG
1 TATT--TAAGTAATA
*
54406392 TGTTTAAGTAATA
1 TATTTAAGTAATA
54406405 TA
1 TA
54406407 CTATATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.12
13 20 0.59
14 7 0.21
15 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:54406386 original size:40 final size:38
Alignment explanation
Indices: 54406208--54406443 Score: 184
Period size: 35 Copynumber: 6.2 Consensus size: 38
54406198 AAAAATTTTA
*
54406208 AATATA-TATATAAATTTTAAGTAATGTAATATATTTAAGT
1 AATATATTA-ATAAATTTT-AGTAA-GTAATGTATTTAAGT
* * *
54406248 CATGTAAGTT-ATAAATTTTAGTAAGTAATATATTTAAGT
1 AATAT-A-TTAATAAATTTTAGTAAGTAATGTATTTAAGT
* * **
54406287 -A-AT-GTAATATATTTTAGTAAGTAATGTAAGTAATGT
1 AATATATTAATAAATTTTAGTAAGTAATGTATTTAA-GT
* * *
54406323 AATATA-TACTTAAATTTTTGTAAGTCATGTATTTAAGT
1 AATATATTA-ATAAATTTTAGTAAGTAATGTATTTAAGT
*
54406361 AATATATTTAAGTAAATTTTAGTAAGTAATGTGTTTAAGT
1 AATATA-TTAA-TAAATTTTAGTAAGTAATGTATTTAAGT
* **
54406401 AATATACT-AT--ATTTTAGTAAGTAATGTAAGTAATGT
1 AATATATTAATAAATTTTAGTAAGTAATGTATTTAA-GT
54406437 AATATAT
1 AATATAT
54406444 ACTTAAAAAT
Statistics
Matches: 160, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
34 1 0.01
35 43 0.27
36 10 0.06
37 3 0.02
38 14 0.09
39 37 0.23
40 41 0.26
41 10 0.06
43 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (38 bp):
AATATATTAATAAATTTTAGTAAGTAATGTATTTAAGT
Found at i:54406474 original size:114 final size:114
Alignment explanation
Indices: 54406259--54406483 Score: 308
Period size: 114 Copynumber: 2.0 Consensus size: 114
54406249 ATGTAAGTTA
*
54406259 TAAATTTTAGTAAGTAATATATTTAAGTAATGTAATATATTTTAGTAAGTAATGTAAGTAATGTA
1 TAAATTTTAGTAAGTAATATATTTAAGTAATATAATATATTTTAGTAAGTAATGTAAGTAATGTA
** * * * * *
54406324 ATATATACTTAAATTTTTGTAAGTCATGTATTTAAGTAATATATTTAAG
66 ATATATACTTAAAAATATATAAGTAATGTATGTAAGTAATAAATTTAAG
* * *
54406373 TAAATTTTAGTAAGTAATGTGTTTAAGTAATATACTATATTTTAGTAAGTAATGTAAGTAATGTA
1 TAAATTTTAGTAAGTAATATATTTAAGTAATATAATATATTTTAGTAAGTAATGTAAGTAATGTA
** *
54406438 ATATATACTTAAAAATATATATTTAAT-TAATGTAAGTTATAAATTT
66 ATATATACTTAAAAATATATAAGTAATGT-ATGTAAGTAATAAATTT
54406484 TAAAAATATA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
113 1 0.01
114 95 0.99
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (114 bp):
TAAATTTTAGTAAGTAATATATTTAAGTAATATAATATATTTTAGTAAGTAATGTAAGTAATGTA
ATATATACTTAAAAATATATAAGTAATGTATGTAAGTAATAAATTTAAG
Found at i:54412397 original size:15 final size:14
Alignment explanation
Indices: 54412377--54412432 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
54412367 CCGACCCCTG
*
54412377 AATCCCTAAACCTT
1 AATCCCTAAACCAT
*
54412391 AAATCCCTAATCCAT
1 -AATCCCTAAACCAT
*
54412406 AATCCTTAAATCCAT
1 AATCCCTAAA-CCAT
*
54412421 ATTCCCTAAACC
1 AATCCCTAAACC
54412433 TTAAAATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.29
15 24 0.71
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.29
Consensus pattern (14 bp):
AATCCCTAAACCAT
Found at i:54412403 original size:22 final size:22
Alignment explanation
Indices: 54412372--54412437 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
54412362 CTAACCCGAC
54412372 CCCTGAATCCCTAAACCTTAAAT
1 CCCT-AATCCCTAAACCTTAAAT
* *
54412395 CCCTAATCCATAATCCTTAAAT
1 CCCTAATCCCTAAACCTTAAAT
* *
54412417 CCATATTCCCTAAACCTTAAA
1 CCCTAATCCCTAAACCTTAAA
54412438 ATATGAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCTAATCCCTAAACCTTAAAT
Found at i:54412696 original size:15 final size:14
Alignment explanation
Indices: 54412674--54412707 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
54412664 TCTCAACCCT
54412674 TAAACCATAATCCC
1 TAAACCATAATCCC
*
54412688 TAAATCCATAATCTC
1 TAAA-CCATAATCCC
54412703 TAAAC
1 TAAAC
54412708 TTTTAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:54412878 original size:41 final size:41
Alignment explanation
Indices: 54412821--54413062 Score: 322
Period size: 41 Copynumber: 5.9 Consensus size: 41
54412811 TTCTATTATT
* * * *
54412821 ATTAGTGGCGTTTTTTCAAAAACGCCGCTAAAGGTCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
54412862 ATTAGTGGCGCTTTTTCAAAAAAGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
*
54412903 ATTAGCGGCGCTTTCTCAAAAACGCTGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
*
54412944 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAATGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *** *
54412985 ATTAGCGGCGCTTTCTCAAAAATGCTGCTAAAGTATCAAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
54413026 ATTAGCGGTGCTTTTTCAAAAACGCCGCTAAATGCCC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCC
54413063 CCAAAACTAA
Statistics
Matches: 177, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 177 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:54437504 original size:22 final size:22
Alignment explanation
Indices: 54437476--54437519 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54437466 CTAATTTCAG
54437476 TAGAACTAAGAACTTAGGTAGT
1 TAGAACTAAGAACTTAGGTAGT
54437498 TAGAACTAAGAACTTAGGTAGT
1 TAGAACTAAGAACTTAGGTAGT
54437520 GACGCCCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
TAGAACTAAGAACTTAGGTAGT
Found at i:54444464 original size:18 final size:18
Alignment explanation
Indices: 54444441--54444487 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
54444431 TTTTTATGTG
*
54444441 TGTTTATTTTTGTTTTTA
1 TGTTTATTTTTGTGTTTA
*
54444459 TGTTTATTTGTGTGTTTA
1 TGTTTATTTTTGTGTTTA
54444477 T-TTTAGTTTTT
1 TGTTTA-TTTTT
54444488 ATACATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.11, C:0.00, G:0.15, T:0.74
Consensus pattern (18 bp):
TGTTTATTTTTGTGTTTA
Found at i:54444569 original size:42 final size:43
Alignment explanation
Indices: 54444508--54444591 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
54444498 CAAAAAAATT
54444508 CAAAAATCCCAAAAATATTTTTCATT-TTTATTTTTAAATTTTC
1 CAAAAATCCCAAAAATATTTTTC-TTCTTTATTTTTAAATTTTC
* * * *
54444551 CAAAAAT-GCAAATATATTTTTCTTCTTTGTTTTTAATTTTT
1 CAAAAATCCCAAAAATATTTTTCTTCTTTATTTTTAAATTTT
54444592 GTTATTGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.06
42 27 0.75
43 7 0.19
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (43 bp):
CAAAAATCCCAAAAATATTTTTCTTCTTTATTTTTAAATTTTC
Found at i:54446038 original size:6 final size:6
Alignment explanation
Indices: 54446027--54446052 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54446017 ATATTTTAGC
54446027 TTAGTT TTAGTT TTAGTT TTAGTT TT
1 TTAGTT TTAGTT TTAGTT TTAGTT TT
54446053 CTTTAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTAGTT
Found at i:54447875 original size:23 final size:22
Alignment explanation
Indices: 54447832--54447875 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
54447822 TTCTAAATCG
54447832 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
54447855 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
54447876 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:54447992 original size:45 final size:45
Alignment explanation
Indices: 54447923--54448013 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
54447913 AAATACTCGA
* * *
54447923 TGGATTCAGCATATAGCAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
*
54447968 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
54448013 T
1 T
54448014 TCATATGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
Found at i:54448081 original size:51 final size:49
Alignment explanation
Indices: 54448021--54448203 Score: 181
Period size: 51 Copynumber: 3.6 Consensus size: 49
54448011 GGTTCATATG
* *
54448021 GTAGCCTGCACACAGTACTACACATGTTACCTTTACCATCCGATACACGTA
1 GTAGCCTGCACATAGTACTACACATGTGACC--TACCATCCGATACACGTA
* ** * *
54448072 GTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCC-AGTACGCAG-A
1 GTAGCCTGCACATAGTACTACACATGTGA-C-CTACCATCCGA-TACAC-GTA
* * * *
54448123 GTAGCCTGCACATAGTACTACACATGCGACCTATCATTTCGGTACACGTA
1 GTAGCCTGCACATAGTACTACACATGTGACCTACCA-TCCGATACACGTA
*
54448173 GTAGCCTGCACATAGTACTACACACGTGACC
1 GTAGCCTGCACATAGTACTACACATGTGACC
54448204 ATCACTTTCA
Statistics
Matches: 107, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
49 3 0.03
50 38 0.36
51 64 0.60
52 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (49 bp):
GTAGCCTGCACATAGTACTACACATGTGACCTACCATCCGATACACGTA
Found at i:54449696 original size:174 final size:178
Alignment explanation
Indices: 54449399--54449761 Score: 583
Period size: 174 Copynumber: 2.0 Consensus size: 178
54449389 TTTAGTTTAA
54449399 TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTTGCATGTTTCCTGCTTTAGA
1 TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTT--ATGTTT-CTGCTTTAGA
* *
54449464 TTTCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTT
63 TTTATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTC
* *
54449529 ATATTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
128 ACACTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
*
54449580 TGTATTTTAGTTTATTTTA-TGTCAAATATGTTAAAGTTTGTTCCTT-T-TTT-T-CTTTAGATT
1 TGTATTTTAGTTTATTTTACT-TCAAATATGTTAAAGCTTGTTCCTTATGTTTCTGCTTTAGATT
*
54449640 TATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTGCATAAAAATCTCAACTTTCAC
65 TATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTCAC
*
54449705 ACTTTTCTTAAGCTTTACTTTCATGGCTTCTTTGTTTCCTATTGTTATG
130 ACTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
*
54449754 TTTATTTT
1 TGTATTTT
54449762 CTTAACTTTG
Statistics
Matches: 173, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
174 124 0.72
175 1 0.01
177 3 0.02
178 1 0.01
180 1 0.01
181 43 0.25
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (178 bp):
TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTTATGTTTCTGCTTTAGATTT
ATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTCACA
CTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
Found at i:54453299 original size:19 final size:20
Alignment explanation
Indices: 54453272--54453311 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
54453262 ATCATGGAAA
54453272 TGCAAATTTCAT-AAAACGG
1 TGCAAATTTCATGAAAACGG
* *
54453291 TGCAGATTTTATGAAAACGG
1 TGCAAATTTCATGAAAACGG
54453311 T
1 T
54453312 CCTACTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TGCAAATTTCATGAAAACGG
Found at i:54457001 original size:21 final size:19
Alignment explanation
Indices: 54456975--54457015 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
54456965 AGTCCACCCA
*
54456975 AATTACTGAATATACATGAAT
1 AATTACTCAAT-TAC-TGAAT
54456996 AATTACTCAATTACTGAAT
1 AATTACTCAATTACTGAAT
54457015 A
1 A
54457016 TACATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (19 bp):
AATTACTCAATTACTGAAT
Found at i:54457017 original size:29 final size:29
Alignment explanation
Indices: 54456975--54457037 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
54456965 AGTCCACCCA
54456975 AATTACTGAATATACATGAATAATTACTC
1 AATTACTGAATATACATGAATAATTACTC
54457004 AATTACTGAATATACATGAATAATTACTC
1 AATTACTGAATATACATGAATAATTACTC
54457033 AATTA
1 AATTA
54457038 TTACTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTACTGAATATACATGAATAATTACTC
Found at i:54457042 original size:11 final size:11
Alignment explanation
Indices: 54457026--54457050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54457016 TACATGAATA
54457026 ATTACTCAATT
1 ATTACTCAATT
54457037 ATTACTCAATT
1 ATTACTCAATT
54457048 ATT
1 ATT
54457051 GGGCAGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTACTCAATT
Found at i:54472635 original size:25 final size:26
Alignment explanation
Indices: 54472582--54472635 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
54472572 TTCTCCTAAA
* *
54472582 TTTCAATTTTCTTTAATTATTTAATT
1 TTTCAATTTTATTGAATTATTTAATT
54472608 TTTCAA-TTTATTGAATTA-TTAATAT
1 TTTCAATTTTATTGAATTATTTAAT-T
54472633 TTT
1 TTT
54472636 ATATTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 6 0.24
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTTAATT
Found at i:54472649 original size:25 final size:25
Alignment explanation
Indices: 54472596--54472649 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
54472586 AATTTTCTTT
* *
54472596 AATTATTTAATTTTTCAATTTATTG
1 AATTATTTAATTTTTCAATTAATTA
54472621 AATTA-TTAATATTTT-ATATTAATTA
1 AATTATTTAAT-TTTTCA-ATTAATTA
54472646 AATT
1 AATT
54472650 TTTGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTTAATTTTTCAATTAATTA
Found at i:54478829 original size:35 final size:37
Alignment explanation
Indices: 54478790--54478874 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 37
54478780 TTTTTATTTG
*
54478790 CATGTTAAGCATGCT-ATTA-TTCTGATTTTGACTCA
1 CATGTTAAGCATGCTCATTATTTCTGATTCTGACTCA
* *
54478825 CATGTTAAGCATG-TCATTATTTCTGATTCTGATTCG
1 CATGTTAAGCATGCTCATTATTTCTGATTCTGACTCA
54478861 CATGTTAAGCATGC
1 CATGTTAAGCATGC
54478875 CACTATATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 1 0.02
35 17 0.39
36 26 0.59
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (37 bp):
CATGTTAAGCATGCTCATTATTTCTGATTCTGACTCA
Found at i:54481377 original size:8 final size:7
Alignment explanation
Indices: 54481355--54481405 Score: 77
Period size: 7 Copynumber: 7.1 Consensus size: 7
54481345 AAAATATTTT
54481355 AAAAT-A
1 AAAATAA
54481361 AAAATAA
1 AAAATAA
54481368 AAAATAA
1 AAAATAA
54481375 AAAATAA
1 AAAATAA
54481382 AAAATAAA
1 AAAAT-AA
54481390 AAAATAAA
1 AAAAT-AA
54481398 AAAATAA
1 AAAATAA
54481405 A
1 A
54481406 TTTATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.12
7 23 0.53
8 15 0.35
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:54489890 original size:22 final size:21
Alignment explanation
Indices: 54489834--54489890 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
54489824 ATACACAAAC
*
54489834 AATAACAACAAAATAGTAGCAA
1 AATAA-AAGAAAATAGTAGCAA
* * *
54489856 CATAATAGTAAAATGGTAGCAA
1 AATAAAAG-AAAATAGTAGCAA
54489878 AATAAGAAGAAAA
1 AATAA-AAGAAAA
54489891 CAACAAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (21 bp):
AATAAAAGAAAATAGTAGCAA
Found at i:54493055 original size:17 final size:19
Alignment explanation
Indices: 54493021--54493062 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
54493011 ATAATTTTTT
*
54493021 AAAATATATATAATACATC
1 AAAATATATATAAAACATC
*
54493040 AAAATAT-TA-AAAACATT
1 AAAATATATATAAAACATC
54493057 AAAATA
1 AAAATA
54493063 AATGTTTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATATATAAAACATC
Found at i:54497773 original size:26 final size:26
Alignment explanation
Indices: 54497744--54497795 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
54497734 ATATAATTTT
54497744 CAAATCATGTATC-TATATATCATGTA
1 CAAATCAT-TATCATATATATCATGTA
* *
54497770 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTATCATATATATCATGTA
54497796 AATACCTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTATCATATATATCATGTA
Found at i:54504217 original size:22 final size:22
Alignment explanation
Indices: 54504165--54504219 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
54504155 AATGTGCAGG
**
54504165 TCTTGAGACAATTTACCATATG
1 TCTTGAGACAATTTACCATACA
** *
54504187 TCTCAAGACAATTTATCATACA
1 TCTTGAGACAATTTACCATACA
54504209 TCTTGAGACAA
1 TCTTGAGACAA
54504220 GGCTCTCTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
TCTTGAGACAATTTACCATACA
Found at i:54504686 original size:5 final size:5
Alignment explanation
Indices: 54504660--54504722 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
54504650 TGATTTTAAA
* * *
54504660 ATAAA ATAAT ATAAAT ACTAAT ATAAT ATAAT ATAAT ATAA- ATTAT ATTAT
1 ATAAT ATAAT AT-AAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
54504711 ATTAT ATTAT AT
1 ATAAT ATAAT AT
54504723 GTGTCTAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
4 3 0.06
5 41 0.77
6 8 0.15
7 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:54509902 original size:6 final size:6
Alignment explanation
Indices: 54509889--54509924 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
54509879 CATTTTCATT
54509889 ATTT-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
54509925 ATAACTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:54514555 original size:24 final size:24
Alignment explanation
Indices: 54514528--54514584 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
54514518 AAACCTAATT
* *
54514528 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAATATATTATA
**
54514552 CTAATAAATGTTGAATATATTATA
1 CTAATAAATGTCAAATATATTATA
54514576 CTAATAAAT
1 CTAATAAAT
54514585 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATA
Found at i:54514675 original size:2 final size:2
Alignment explanation
Indices: 54514668--54514700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54514658 CAACTCTAAC
54514668 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 A
54514701 AATTTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54515875 original size:2 final size:2
Alignment explanation
Indices: 54515868--54515896 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54515858 AAACAAGCAA
54515868 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 A
54515897 ATTTATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54531583 original size:60 final size:61
Alignment explanation
Indices: 54531456--54531582 Score: 254
Period size: 61 Copynumber: 2.1 Consensus size: 61
54531446 GGGAGAGGTT
54531456 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
1 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
54531517 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
1 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
54531578 TTTTT
1 TTTTT
54531583 GGCTTAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (61 bp):
TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
Found at i:54536989 original size:41 final size:40
Alignment explanation
Indices: 54536929--54537029 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 40
54536919 AAATTAAAAT
54536929 AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
** *
54536969 AAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAA-TTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
* *
54537010 AAAAATAAAAAAAAATATTT
1 AAAAATTAAAAAAAGTATTT
54537030 ATTATTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 18 0.33
41 37 0.67
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
Found at i:54536994 original size:11 final size:11
Alignment explanation
Indices: 54536980--54537005 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54536970 AAAATTTAAA
54536980 AAAAGTATTTT
1 AAAAGTATTTT
54536991 AAAAGTATTTT
1 AAAAGTATTTT
54537002 AAAA
1 AAAA
54537006 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:54545026 original size:44 final size:44
Alignment explanation
Indices: 54544955--54545691 Score: 632
Period size: 44 Copynumber: 16.7 Consensus size: 44
54544945 GCAGGCTAAA
* * *
54544955 AAGA-AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * *
54544998 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTGGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * *
54545042 AAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * * * *
54545086 AAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * * * *
54545130 AAGATAACATATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * *
54545175 AAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * * * *
54545219 AAGAAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * * *
54545263 AAGATAACAGAT-TCTGTCTTCCTATATTGGTAGCAAAGTGGATCG
1 AAGATAGCAGATCT-TGTCTTCCTATATTGG-CGCGAAGTAGATCG
* *
54545308 AAGATA-CAGATCTTGTCTTCCCATACTGATG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTG--GCGCGAAGTAGATCG
* * * *
54545352 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * * *
54545396 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * * * *
54545441 AAGACA-TAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * * * * * *
54545485 AAGAAAGCAGATCTCGTCTTCATGTATTAGCGTGAAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * *** *
54545529 AAGGTAGCAGATCCTGTCTTCCTATATTCATAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATT-GGCGCGAAGTAGATCG
* *
54545573 AAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGCGAAGTAGATCG
* * * *** *
54545617 AAGAAAGCAGATCTTGTCTTCATGTATTGGCATTAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
* * * *
54545661 AAAATAACAGAT-TCTGTCTTCTTAAATTGGC
1 AAGATAGCAGATCT-TGTCTTCCTATATTGGC
54545692 AGTAAGGCAG
Statistics
Matches: 557, Mismatches: 117, Indels: 39
0.78 0.16 0.05
Matches are distributed among these distances:
43 52 0.09
44 358 0.64
45 146 0.26
46 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (44 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGCGCGAAGTAGATCG
Found at i:54545229 original size:133 final size:133
Alignment explanation
Indices: 54544958--54545690 Score: 1200
Period size: 133 Copynumber: 5.5 Consensus size: 133
54544948 GGCTAAAAAG
* *
54544958 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
* *
54545023 ATTGGTAG-GAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
54545087 AGA
131 AGA
* *
54545090 AAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACATATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
54545155 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
54545220 AGA
131 AGA
* *
54545223 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATTCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
* *
54545288 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
54545353 AGA
131 AGA
54545356 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
* *
54545421 ATTGGTAGCGAAGTGGATCGAAGACATAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
54545486 AGA
131 AGA
* * * * *
54545489 AAGCAGATCTCGTCTTCATGTATTAGCGTGAAGTAGATCAAAGGTAGCAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
** * *
54545554 ATTCATAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
54545618 AGA
131 AGA
* * * * * * *
54545621 AAGCAGATCTTGTCTTCATGTATTGGCATTAAGTGGATCGAAAATAACAGATTCTGTCTTCTTAA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
54545686 ATTGG
66 ATTGG
54545691 CAGTAAGGCA
Statistics
Matches: 557, Mismatches: 43, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
132 180 0.32
133 377 0.68
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (133 bp):
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
AGA
Found at i:54545770 original size:44 final size:44
Alignment explanation
Indices: 54545715--54545831 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 44
54545705 GACGTGGGCG
*
54545715 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAGGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
* * *
54545759 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
54545803 AATCTTATCTCCCTGAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
54545832 TAGACATAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
Found at i:54547766 original size:13 final size:13
Alignment explanation
Indices: 54547729--54547767 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
54547719 GTATTTTGTT
54547729 TATATAAACTTTTA
1 TATATAAA-TTTTA
*
54547743 TAATCTAAATTTTA
1 T-ATATAAATTTTA
54547757 TATATAAATTT
1 TATATAAATTT
54547768 ATGTGTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATAAATTTTA
Found at i:54547959 original size:17 final size:17
Alignment explanation
Indices: 54547939--54547973 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54547929 CCCTTATGTA
54547939 TATTTGTTTCAT-TTATT
1 TATTTGTTT-ATATTATT
54547956 TATTTGTTTATATTATT
1 TATTTGTTTATATTATT
54547973 T
1 T
54547974 CTATGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTGTTTATATTATT
Found at i:54550296 original size:41 final size:41
Alignment explanation
Indices: 54550211--54550298 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
54550201 TGAATCCATG
*
54550211 AAATGGTTGAAAAGGAAGTTATTCAAAAAGGATAACAAATGA
1 AAAT-GTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
* **
54550253 AAATGTTGAAAAGGATGTTATCCGGAAAGGATAACAAATGA
1 AAATGTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
54550294 AAATG
1 AAATG
54550299 ATGTGTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.22
Consensus pattern (41 bp):
AAATGTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
Found at i:54569139 original size:30 final size:28
Alignment explanation
Indices: 54569081--54569187 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 28
54569071 AAAAGGGTAC
* * *
54569081 AAAA-TATATACATGTACATATATAAAA
1 AAAATTATATACATATATATAGATAAAA
54569108 AAAATTATATACATATATATAGATTATAAA
1 AAAATTATATACATATATATAGA-TA-AAA
* *
54569138 AAAGATAAT-TACATATATATATATAAACA
1 AAA-ATTATATACATATATATAGATAAA-A
*
54569167 AATAATAATAATTACATATAT
1 AA-AATTAT-A-TACATATAT
54569188 TAAAATTAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.06
28 17 0.26
29 12 0.18
30 20 0.30
31 4 0.06
32 9 0.14
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTATATACATATATATAGATAAAA
Found at i:54569228 original size:26 final size:25
Alignment explanation
Indices: 54569199--54569250 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
54569189 AAAATTAATT
54569199 AATTTA-GAAAAATATATATATAAAAA
1 AATTTATGAAAAATA-ATATA-AAAAA
*
54569225 AATTTATGAAGAATAATATAAAAAA
1 AATTTATGAAAAATAATATAAAAAA
54569250 A
1 A
54569251 CATACGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (25 bp):
AATTTATGAAAAATAATATAAAAAA
Found at i:54569347 original size:17 final size:17
Alignment explanation
Indices: 54569325--54569368 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
54569315 TAGGAAATAA
54569325 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
54569342 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
54569359 -ATATGTATAT
1 AAAATGTATAT
54569369 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:54569505 original size:3 final size:3
Alignment explanation
Indices: 54569497--54569535 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
54569487 GTATATATAG
* *
54569497 TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54569536 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:54569900 original size:21 final size:21
Alignment explanation
Indices: 54569851--54569948 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
54569841 AAATTAAATC
*
54569851 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
54569871 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
54569895 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
*
54569916 TCTAAGATTG--TATATCATA
1 TCTAAGATTGCATAAATCATA
*
54569935 TCTAAGATTACATA
1 TCTAAGATTGCATA
54569949 TCCTTGAATG
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
19 18 0.26
21 32 0.46
23 11 0.16
24 8 0.12
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:54570455 original size:44 final size:44
Alignment explanation
Indices: 54570407--54570505 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 44
54570397 CAACTTTAGA
* *
54570407 GAGATAAGATCT-GTGGTTTTAATCCGCTCCACTGAAACTTC-TG
1 GAGATAAGAT-TAGTGGCTTTAATCCGCTCCACTGAAACTTCAAG
* * * * *
54570450 TGAGATAGGATTATTGGCTTTAATCTGCTCCATTGCAACTTCAAG
1 -GAGATAAGATTAGTGGCTTTAATCCGCTCCACTGAAACTTCAAG
54570495 GAGATAAGATT
1 GAGATAAGATT
54570506 CGCCATCTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.02
44 43 0.96
45 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (44 bp):
GAGATAAGATTAGTGGCTTTAATCCGCTCCACTGAAACTTCAAG
Found at i:54570984 original size:88 final size:87
Alignment explanation
Indices: 54570820--54571211 Score: 431
Period size: 88 Copynumber: 4.6 Consensus size: 87
54570810 ATAAGTCTGA
* * * * * * * * *
54570820 TGTCTTCGATTTGTTTCACTGCCAGTACAGGAAGGCAAGATCTTCTATTTTCAACCTACTCCACT
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACT
*** ** * *
54570885 GTTGCTCAGGGAGATAGGGTTGG
66 GAACCT-AGGGAGGCAAGGCTGG
* * * * *
54570908 GGTCATCGATCTGATTCACTGTCGGTCCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACT
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACT
54570973 GCAACCTAGGGAGGCAAGGCTGG
66 G-AACCTAGGGAGGCAAGGCTGG
* * *
54570996 TGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATGTTTAACCTG-TTC-C-
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACT
54571058 G---CT-GGGAGGCAAGGCTGG
66 GAACCTAGGGAGGCAAGGCTGG
*
54571076 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACTTGCT-CAGC
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCA-C
* * *
54571140 TACAACCCAGGGAGGCAAGGTTGG
65 T-GAACCTAGGGAGGCAAGGCTGG
*
54571164 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTAT
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
54571212 CTTCGATCTA
Statistics
Matches: 262, Mismatches: 32, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
80 71 0.27
81 3 0.01
82 1 0.00
85 1 0.00
86 1 0.00
87 3 0.01
88 180 0.69
89 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (87 bp):
TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACT
GAACCTAGGGAGGCAAGGCTGG
Found at i:54571259 original size:44 final size:44
Alignment explanation
Indices: 54571191--54571435 Score: 248
Period size: 44 Copynumber: 5.6 Consensus size: 44
54571181 GCTGTCGGTG
* * *
54571191 CAGGAAGGCAAGATTTGCTATCTTCGATCTACTTCACGCCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATA
* * * *
54571235 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATA
** *
54571280 TGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATA
* * * *
54571323 TAGGAAGACATGACCTGCTATCTTCGATCTACTTCACGA-CTATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATA
* *
54571367 CATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGC-CACCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACT-T-CACACCAATA
**
54571412 TGGGAAGACAAGATCTGC-ATCTTC
1 CAGGAAGACAAGATCTGCTATCTTC
54571436 CTACCAATAT
Statistics
Matches: 165, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 21 0.13
44 98 0.59
45 44 0.27
46 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATA
Found at i:54571331 original size:88 final size:87
Alignment explanation
Indices: 54571191--54571435 Score: 278
Period size: 88 Copynumber: 2.8 Consensus size: 87
54571181 GCTGTCGGTG
* * * * * *
54571191 CAGGAAGGCAAGATTTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAGATCTGCTAT
*
54571256 CTTCGATCTACTTCGCCACCAGTA
65 CTTCGATCTACTTCACCACCA-TA
** * * *
54571280 TGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGACATGACCTGCTAT
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAGATCTGCTAT
* *
54571344 CTTCGATCTACTTCACGACTATA
65 CTTCGATCTACTTCACCACCATA
* * *
54571367 CATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGCCACCAATATGGGAAGACAAGATCTGC-A
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACT-T-CCACCAATATAGGAAGACAAGATCTGCTA
54571431 TCTTC
64 TCTTC
54571436 CTACCAATAT
Statistics
Matches: 130, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
87 18 0.14
88 73 0.56
89 37 0.28
90 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (87 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCACCAATATAGGAAGACAAGATCTGCTATC
TTCGATCTACTTCACCACCATA
Found at i:54576788 original size:30 final size:30
Alignment explanation
Indices: 54576752--54576808 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54576742 CATGTACATA
*
54576752 TATAAAAA-AATTATATACATATATATAGAT
1 TATAAAAATAATAAT-TACATATATATAGAT
*
54576782 TATAAAAATGATAATTACATATATATA
1 TATAAAAATAATAATTACATATATATA
54576809 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (30 bp):
TATAAAAATAATAATTACATATATATAGAT
Found at i:54576810 original size:42 final size:42
Alignment explanation
Indices: 54576763--54576847 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
54576753 ATAAAAAAAT
* * *
54576763 TATATACATATATATAGATTATAAA-AATGATAATTACATATA
1 TATATACATATATATAGA-AACAAATAATAATAATTACATATA
* *
54576805 TATATATATATATATATAAACAAATAATAATAATTACATATA
1 TATATACATATATATAGAAACAAATAATAATAATTACATATA
54576847 T
1 T
54576848 TAAAATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (42 bp):
TATATACATATATATAGAAACAAATAATAATAATTACATATA
Found at i:54577172 original size:3 final size:3
Alignment explanation
Indices: 54577164--54577202 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
54577154 GTATATATAG
* *
54577164 TAA TAA TAA TAA TCA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54577203 GTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:54577588 original size:14 final size:12
Alignment explanation
Indices: 54577555--54577580 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54577545 GATTGCATAT
54577555 ATCATATCTAAG
1 ATCATATCTAAG
54577567 ATCATATCTAAG
1 ATCATATCTAAG
54577579 AT
1 AT
54577581 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:54580463 original size:48 final size:48
Alignment explanation
Indices: 54580393--54580566 Score: 204
Period size: 48 Copynumber: 3.6 Consensus size: 48
54580383 AGAACAAATT
* * * *
54580393 TCTCGGTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAACAGAC
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * **
54580441 TCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * **
54580489 TATTGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * * *
54580537 TATTGGTGGCTTTCACACAGTCCGTGCCAC
1 TCTCGGTGGCCTACACACAGTCCGTGCCAC
54580567 ATATGCGACC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
Found at i:54589015 original size:33 final size:32
Alignment explanation
Indices: 54588942--54589019 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
54588932 CAATGTTCAT
* * * **
54588942 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTAGGCTATGGCATACAA
*
54588974 ATGATAAGACCATAACTAGGTTATGGCACTACAA
1 ATG-TAAGACCATAACTAGGCTATGGCA-TACAA
54589008 ATGTAAGACCAT
1 ATGTAAGACCAT
54589020 GGCAGAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 30 0.79
34 5 0.13
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (32 bp):
ATGTAAGACCATAACTAGGCTATGGCATACAA
Found at i:54593044 original size:18 final size:18
Alignment explanation
Indices: 54593023--54593060 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54593013 TCTTCTTTTT
54593023 CTTTTTCATCTTCAGCAA
1 CTTTTTCATCTTCAGCAA
*
54593041 CTTTTTCTTCTTCAGCAA
1 CTTTTTCATCTTCAGCAA
54593059 CT
1 CT
54593061 ACTTCGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.47
Consensus pattern (18 bp):
CTTTTTCATCTTCAGCAA
Found at i:54601983 original size:924 final size:926
Alignment explanation
Indices: 54599319--54602361 Score: 4581
Period size: 924 Copynumber: 3.3 Consensus size: 926
54599309 TGGATTATAC
* * *
54599319 TTGCTCTAAGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTGGCATTCTAAGTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * * * * *
54599384 CCAAAATTGTTGGTTGCGTGCAGAGTTGTTGTAGGAGTTGCCATAAGAATTTTTGCGGATGTAAT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
* * * *
54599449 AATATAACATGCATTCTCTGCATGTTGTGGTCAATCTTCATAGCTATGGTTCTGACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
*
54599514 CACAACAAAAAGTAGGAACATCAACTTGTTGAGTGACTTG--TA--T--AACGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
54599573 TGCATATTTTTAATCATG-TTTGTGATAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCA
261 TGCATATTTTTAATCATGTTTTGTG--AGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCA
*
54599637 ATTCAATAACTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTC
324 ATTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTC
*
54599702 TGAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGC
389 TGAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGC
* ** *
54599767 AGATGTTTTGACAAGTTTCCTTGTATATGAATTCAACCCATTATAAAAATCTCAATTTGTGTTTC
454 TGATGCATCGACAAGTTTCC---T-TATG-A-TC-ACCCATTATAAAAATCTCAATTTGTGTTTC
* * *
54599832 TAGTTGAATGTCGTGCATGGGACAAAGTCGAAGTAAAGATTTATAATTTTCCCATGTGCTGTGAA
512 TGGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAA
* * *
54599897 GATTTTGATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGATGAGCATTCATTGTTGGC
577 GATTTTCATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGC
* * *
54599962 GGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAAAAGTAATTGATTCAGTAGGTAG
642 GGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAG
* * *
54600027 CCCAAAAAACGAAGTACTGGCTCTTCTCTCTAAGGAATAAGGAAATAATTGCATCTTCAAGGCAT
707 CCCAAAAAACCAAGTACGGGCTCTTC-CTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCAT
* * *
54600092 CATCAAGATATCATAAGGAATAAGGATATATCAATCCTACAGGGATGCTTGTCTTTTTTTCTATT
771 CATCAAGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGT-TTTTTTTCTATT
*
54600157 AGTGTCGATGCAATAACTAGATAAAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACT
835 AGTGTCGATGCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACT
*
54600222 TGAAAACAATAAAATAAAATTTGATAA
900 TGAAAACAATAAAATAAAATATGATAA
* * *
54600249 TTGCCCTAGGTAGATGAATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGACTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * * *
54600314 CCAAAATGGTTGGTTGCATGCAAAGTTGTTGTAAGAGTTACCATAAGAATTTTTGCGGATGTACT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
54600379 AATATAACAGGCA---T-T-C---TT-T-G---------ATAGCTATGGTTGTCACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
* *
54600425 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGCATAGGTGCAATGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
54600490 TGCATATTTTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
261 TGCATATTTTTAATCATGTTT-TGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
* *
54600555 TTCAATAACTCCTGGACTAGTTTTTACTTGTGCAACTATGGAGATAAGGTATTGATAATCATTCT
325 TTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCT
* * * *
54600620 GTGCAATTCTCTCGAGAATTCTCACAGCATCATTATAAGTACAAT-TCAACAGAAGTCCATTGGT
390 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCT-AACAGAGGTCCATTGGC
*
54600684 TGATGCATCGACAAGTTTCCCTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTT
454 TGATGCATCGACAAGTTT-CC--T-TATG-A-TCA-CCCATTATAAAAATCTCAATTTGTGTTTC
* * *
54600749 TGGTTAAATGTCGTGCAGGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAA
512 TGGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAA
* *
54600814 GATTTTCATCCA-GCAGCTGATGGTAAGTAGTAATATCATTTTCAAGAC-AAGCATTCATTGTTG
577 GATTTTCAT-CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAA-CATTCATTGTTG
* *
54600877 GCGAGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGATAGGT
640 GCGGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGT
54600942 AGCCCAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGC
705 AGCCCAAAAAACCAAGTACGGGCTCTT-CCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGC
* * * **
54601007 ATCATCATGATATCATAAGGATTAATGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTCG
769 ATCATCAAGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTAT
* *
54601072 AAGTGTCGATGCAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
834 TAGTGTCGATGCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
*
54601137 TTGAGAACAATAAAATAAAATATGATAA
899 TTGAAAACAATAAAATAAAATATGATAA
* * * *
54601165 TTGCCATAGGTAGATGTATTCCCATATATGAATGTCGCAGCTTTTTGTCTAGCATTCTGAGTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * *
54601230 CCAAAATAGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGTGAATGTACT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
* *
54601295 AATATAATAGGCATTCTTTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
*
54601360 CACAACAAAAAGTAGGAACATGAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
*
54601425 TGCATATTTTTAATCATGATTTTGTGAGAAGAAACTTGAGCACTTAGTGCAGTTATTGCATCCAA
261 TGCATATTTTTAATCATG-TTTTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
* * *
54601490 TTCAATAACTCCGGGAGTAGTTTTTCCTTGTGCAGCTCTGGAGATAAGGTATTGATAATCATTCT
325 TTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCT
*
54601555 GAGCAATTCTCTCAAGAATTCTCACAGCATCATCATAAGTACAATCTAACAGAGGTCCATTGGCT
390 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGCT
* * *
54601620 GATGCGTCGACAAGTTTCC-T-TG-T-ACCCGTTATAGAAATCTCAATTTGTGTTTCTGGTTGAA
455 GATGCATCGACAAGTTTCCTTATGATCACCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAA
* *
54601681 TGCCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTTTGAAGATTTTCA
520 TGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAAGATTTTCA
* * * *
54601746 TAATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAACATTCATTGTTGGCGGGTTAAA
585 TCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGCGGGTTAAA
* * * *
54601811 TTGCAAAACAAACTTTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGATAGCCTAAAAA
650 TCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAA
* *
54601876 ACCAAGTACGGGCTCTTCCGTATAAGGAATAAGGAAATAATTACATCTTCAAGGCATCATCAGGA
715 ACCAAGTACGGGCTCTTCC-TATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAAGA
* **
54601941 TATCATAAGGAATAAGGATATATCGATCCCACAGCGATGGTTGCCTTTTTTCTATTAGTGTCGAT
779 TATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTATTAGTGTCGAT
* *
54602006 GCAATAACTAGATAGGAACGAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAA
844 GCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAA
54602071 TAAAATAAAATATGATAA
909 TAAAATAAAATATGATAA
* * *
54602089 TTGCCCT-GAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATCCTAAGTTC
1 TTGCCCTAG-GTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTC
* *
54602153 CCCAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGC-AGATGTA
65 CCCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGA-ATGTA
* * *
54602217 ATAATATAACAGACATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAAT
129 ATAATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAAT
* *
54602282 CTCACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCT
194 CTCACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCT
54602347 ATTGCATATTTTTAA
259 ATTGCATATTTTTAA
54602362 CCATATGGGA
Statistics
Matches: 1931, Mismatches: 142, Indels: 86
0.89 0.07 0.04
Matches are distributed among these distances:
911 63 0.03
913 2 0.00
915 1 0.00
916 231 0.12
917 527 0.27
918 7 0.00
919 5 0.00
920 2 0.00
921 2 0.00
922 2 0.00
923 5 0.00
924 654 0.34
925 5 0.00
926 3 0.00
927 1 0.00
929 2 0.00
930 131 0.07
934 2 0.00
935 282 0.15
936 4 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (926 bp):
TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
TGCATATTTTTAATCATGTTTTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
TCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTG
AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGCTG
ATGCATCGACAAGTTTCCTTATGATCACCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAAT
GTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAAGATTTTCAT
CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGCGGGTTAAAT
CGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAAA
CCAAGTACGGGCTCTTCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAAGATA
TCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTATTAGTGTCGATGC
AATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAATA
AAATAAAATATGATAA
Found at i:54606306 original size:935 final size:934
Alignment explanation
Indices: 54604497--54607370 Score: 4978
Period size: 935 Copynumber: 3.1 Consensus size: 934
54604487 AAAAGAATAT
54604497 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
* *
54604562 TACCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTAAGTTCCC
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
* *
54604627 CAAAATGGTTGGTTGCGTGTAAAGTTGTTATAAGAGTTACCATAAGAATTGTTGCAGATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCA-ATGTAATA
54604692 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
54604757 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
*
54604822 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTACATCCAAT
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
54604887 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
390 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
* *
54604952 ACCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTA
455 AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTG
*
54605017 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCGTTATAGAAATCTCAATTTGTGTTTCTG
520 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTG
54605082 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
585 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
* *
54605147 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAACATTCATTATTGGCGG
650 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGG
* *
54605212 GTTAAATTGCAAAACAAACTTTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGATAGCC
715 GTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCC
* * * *
54605277 TAAAAAACCAAGTACGGGCTCTTCCGTATAAGAAATAAGGAAATAATTACATCTTCTAGGCATCA
780 TAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
54605342 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGT
845 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGT
54605407 GTCGATGCAATAACTAGATAGGAAC
910 GTCGATGCAATAACTAGATAGGAAC
54605432 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
54605497 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
54605562 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCATATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCA-ATGTAATA
*
54605627 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCGATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
54605692 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
*
54605757 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTACGAG-TATTGCATCCAA
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCG-GTTATTGCATCCAA
54605821 TTCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCT
389 TTCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCT
54605886 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCT
454 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCT
* *
54605951 GATGCGTCGACAAGTTTCCTTGTATATGAATTAAGCCCATTATAGAAATCTCAATTTGTGTTTCT
519 GATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCT
*
54606016 GGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATATATAATGTTCCCATGTGGTTTGAAG
584 GGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAG
*
54606081 ATTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGACG
649 ATTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCG
*
54606146 GGTTAAATTGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGC
714 GGTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGC
* *
54606211 CTAAAAACCCAAGTACGGGCTCTTCCCTATATGGAATAAGGAAATAATTGCATCTTCAAGGCATC
779 CTAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATC
*
54606276 ATCAGGTTATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAG
844 ATCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAG
54606341 TG-CGGATGCAATAACTAGATAGGAAC
909 TGTC-GATGCAATAACTAGATAGGAAC
*
54606367 GAGATAAATTGTGAGGATATTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
* * * *
54606432 TGCCCTAAGTAGATGTATTCCCATATCTAAATGTCACAGTATTTTGTCTAGCATTCTGAGCTCCA
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
* *
54606497 CAAAACGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTAACATAAGAATTGTTGCGAATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGC-AATGTAATA
* *
54606562 ATATAACAGGCATTCTCTGCAGATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
* * * *
54606627 ACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGCATAGGTGCAATGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
* * *
54606692 ACATATTTTTAATCATGTTTGTGAGAGAAGAAACTTGAGCACTTACTGCGGTTATTGCATCCAAT
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
* * * *
54606757 TCAATAACTCCTGGACTAGTTTTTGCTTGTGCAACTATGGAGATAAGGTATTGATAATCATTATG
390 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
* * * *
54606822 AGCAATTCTCTCGAGAATTCTCACAGCATCATTATAAGTGCAATTCAACAGAGGTCCATTGGCCG
455 AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTG
* *
54606887 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTTTG
520 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTG
* * *
54606952 GTTGAATGTCGTGCAGGGGACAAAGTTAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGA
585 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
* * * * * **
54607017 TTTTCATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACAAGCATTTATTGTTGGCAA
650 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGG
* *
54607082 GTTAAATCGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGGTAGCC
715 GTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCC
*
54607147 CAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
780 TAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
* ** *
54607212 TCATGATATCATAAGGAATAAGGATATATCGATCCCACAGGTCTGGTTGTGTTCTTTCTTTCTAT
845 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGG-T-TG-CCTTT-TTTCTAT
*
54607277 TAGTGTCGATGCAATAACTAGATAGAAAC
906 TAGTGTCGATGCAATAACTAGATAGGAAC
* * * * *
54607306 AAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACATGAAAATAATGAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
54607371 GAAAAATTGG
Statistics
Matches: 1844, Mismatches: 86, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
934 2 0.00
935 1740 0.94
936 3 0.00
937 2 0.00
938 4 0.00
939 92 0.05
940 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (934 bp):
GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCAATGTAATAA
TATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTCA
CAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATTG
CATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATT
CAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTGA
GCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTGA
TGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTGG
TTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGAT
TTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGGG
TTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCCT
AAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCAT
CAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGTG
TCGATGCAATAACTAGATAGGAAC
Found at i:54608607 original size:23 final size:24
Alignment explanation
Indices: 54608545--54608619 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
54608535 TAAACACGTG
* *
54608545 ATTCTGTAAGTTCCTTTGTGGCAT
1 ATTCTATAAGTTCCTTTGTGGCGT
54608569 ATTCTATAAGTTCCTTTGTGGCGT
1 ATTCTATAAGTTCCTTTGTGGCGT
*
54608593 ATT-TATAAGTGCCTTTGTGGCGT
1 ATTCTATAAGTTCCTTTGTGGCGT
54608616 ATTC
1 ATTC
54608620 GAGGTTGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 22 0.47
24 25 0.53
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.45
Consensus pattern (24 bp):
ATTCTATAAGTTCCTTTGTGGCGT
Found at i:54616088 original size:12 final size:13
Alignment explanation
Indices: 54616063--54616092 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
54616053 AGGGCTATAA
54616063 TTATTGCATTTAT
1 TTATTGCATTTAT
54616076 TTATTGC-TTTAT
1 TTATTGCATTTAT
54616088 TTATT
1 TTATT
54616093 CATGTATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:54622496 original size:213 final size:213
Alignment explanation
Indices: 54622129--54622560 Score: 864
Period size: 213 Copynumber: 2.0 Consensus size: 213
54622119 GGCTTGGTTC
54622129 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
54622194 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
66 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
54622259 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
131 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
54622324 ATAATTTACCCCATCTCA
196 ATAATTTACCCCATCTCA
54622342 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
54622407 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
66 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
54622472 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
131 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
54622537 ATAATTTACCCCATCTCA
196 ATAATTTACCCCATCTCA
54622555 GATAGT
1 GATAGT
54622561 TCATGGGTAA
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 219 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (213 bp):
GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
ATAATTTACCCCATCTCA
Found at i:54639554 original size:26 final size:26
Alignment explanation
Indices: 54639517--54639752 Score: 357
Period size: 26 Copynumber: 9.1 Consensus size: 26
54639507 GTAATAGGCC
* *
54639517 TAAATTATCGAAATACCCTCTATGGG
1 TAAATTACCGAAATACCCTCGATGGG
54639543 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
54639569 TAAATTACTGAAATACTCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
54639595 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
54639621 TAAATTACCAAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
54639647 TAAATTATCGAATTACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
54639673 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
54639699 TAAATTACCGAAATACCCTTGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
54639725 TAAATTATCGAAATAGCCC-CGAAGGG
1 TAAATTACCGAAATA-CCCTCGATGGG
54639751 TA
1 TA
54639753 GAATGACTGT
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
26 188 0.98
27 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (26 bp):
TAAATTACCGAAATACCCTCGATGGG
Found at i:54639983 original size:26 final size:26
Alignment explanation
Indices: 54639954--54640003 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54639944 GCATATAGTG
* *
54639954 TACTGGCAACTCTGCTGCGATATTAT
1 TACTGGCAACTATGCTGCAATATTAT
*
54639980 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAACTATGCTGCAATATT
54640004 GGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (26 bp):
TACTGGCAACTATGCTGCAATATTAT
Found at i:54641316 original size:15 final size:14
Alignment explanation
Indices: 54641291--54641338 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
54641281 AATTTGAGAG
*
54641291 AAGAAAAAAAGAAA
1 AAGAGAAAAAGAAA
*
54641305 TGAGAGAAAAAGAAA
1 -AAGAGAAAAAGAAA
54641320 AAGAGATAAAAGAAA
1 AAGAGA-AAAAGAAA
54641335 AAGA
1 AAGA
54641339 AATTGAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (14 bp):
AAGAGAAAAAGAAA
Found at i:54641322 original size:21 final size:21
Alignment explanation
Indices: 54641285--54641340 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
54641275 TGAATGAATT
*
54641285 TGAGAGAAGAA-AAAAAGAAA
1 TGAGAGAAAAAGAAAAAGAAA
*
54641305 TGAGAGAAAAAGAAAAAGAGA
1 TGAGAGAAAAAGAAAAAGAAA
* *
54641326 TAAAAGAAAAAGAAA
1 TGAGAGAAAAAGAAA
54641341 TTGAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.05
Consensus pattern (21 bp):
TGAGAGAAAAAGAAAAAGAAA
Found at i:54647283 original size:15 final size:14
Alignment explanation
Indices: 54647260--54647318 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 14
54647250 TGCATAATAA
54647260 AATAAAATAAAAATCT
1 AATAAAATAAAAA--T
54647276 AA-AAAATAAAAAT
1 AATAAAATAAAAAT
54647289 AATAACAATAAAAATT
1 AATAA-AATAAAAA-T
54647305 AATAAAATATAAAA
1 AATAAAATA-AAAA
54647319 CTAAATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 22 0.56
16 12 0.31
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAAAT
Found at i:54656723 original size:25 final size:25
Alignment explanation
Indices: 54656689--54656741 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
54656679 ATTGCATGGG
54656689 GTTCAAGATGATTTCAAATGAGGGA
1 GTTCAAGATGATTTCAAATGAGGGA
*
54656714 GTTCAAGATGATTTGAAATGAGGGA
1 GTTCAAGATGATTTCAAATGAGGGA
54656739 GTT
1 GTT
54656742 TCTGATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (25 bp):
GTTCAAGATGATTTCAAATGAGGGA
Found at i:54660764 original size:7 final size:7
Alignment explanation
Indices: 54660752--54660780 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54660742 TATATTACTA
54660752 TTGTTCT
1 TTGTTCT
54660759 TTGTTCT
1 TTGTTCT
54660766 TTGTTCT
1 TTGTTCT
54660773 TTGTTCT
1 TTGTTCT
54660780 T
1 T
54660781 AGTATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (7 bp):
TTGTTCT
Found at i:54670290 original size:23 final size:23
Alignment explanation
Indices: 54670242--54670295 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
54670232 AGATTTATCA
*
54670242 ATTTAAG--TTTTAAAATCAATG
1 ATTTAAGCATTTTAAAATCAAAG
54670263 ATTTAAGCATTTTAAAATCCAAAG
1 ATTTAAGCATTTTAAAAT-CAAAG
*
54670287 -TTTATGCAT
1 ATTTAAGCAT
54670296 GTCTTTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTTAAGCATTTTAAAATCAAAG
Found at i:54677412 original size:33 final size:33
Alignment explanation
Indices: 54677370--54677436 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
54677360 TCAAAACTTA
54677370 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
54677403 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
54677436 T
1 T
54677437 TAAAAGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (33 bp):
TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
Found at i:54681382 original size:40 final size:40
Alignment explanation
Indices: 54681311--54681399 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
54681301 AAATATATAA
* * *
54681311 ATTTCGATTAATTCGGTTATCAAACCAAATTAACTGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
** *
54681351 ATTTCGATTAATTCAGTTAACGGACCGAATTAACCGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
54681391 ATTTCGATT
1 ATTTCGATT
54681400 CAACTAATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (40 bp):
ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
Found at i:54688825 original size:17 final size:19
Alignment explanation
Indices: 54688792--54688830 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
54688782 ATAGATTTTG
54688792 AAACAAATAACTGTAAAAC
1 AAACAAATAACTGTAAAAC
*
54688811 AAACAAA-AA-TGTAAATC
1 AAACAAATAACTGTAAAAC
54688828 AAA
1 AAA
54688831 GGCAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (19 bp):
AAACAAATAACTGTAAAAC
Found at i:54691099 original size:26 final size:26
Alignment explanation
Indices: 54691067--54691133 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
54691057 ATAAAAAATA
* *
54691067 ACCAAAATGTTAT-TTTTTTTTCATTT
1 ACCAAAATATTATAATTTTTTT-ATTT
*
54691093 ACTAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTAT-AATTTTTTTATTT
54691120 ACCAAAATA-TATAA
1 ACCAAAATATTATAA
54691134 AAAAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.06
26 14 0.40
27 12 0.34
28 7 0.20
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:54691134 original size:26 final size:28
Alignment explanation
Indices: 54691081--54691134 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
54691071 AAATGTTATT
*
54691081 TTTTTTTCATTTACTAAAATATTATAAA
1 TTTTTTTCATTTACCAAAATATTATAAA
54691109 TTTTTTT-ATTTACCAAAATA-TATAAA
1 TTTTTTTCATTTACCAAAATATTATAAA
54691135 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTTTCATTTACCAAAATATTATAAA
Found at i:54691196 original size:27 final size:27
Alignment explanation
Indices: 54691166--54691228 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
54691156 AAAAAACTTG
* *
54691166 TGGCGGCACCAAAGGTGTCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
* *
54691193 TGGCAGCACTAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
54691220 TGGCGGCAC
1 TGGCGGCAC
54691229 AGGACTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.33, T:0.16
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Found at i:54693221 original size:27 final size:27
Alignment explanation
Indices: 54693159--54693221 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
54693149 TTTTAGTCCT
54693159 GTGCCGCCAATCTCTTTGACACCTTTG
1 GTGCCGCCAATCTCTTTGACACCTTTG
* **
54693186 GT-CAGGCCAATCTCTTTGGTACCTTTG
1 GTGC-CGCCAATCTCTTTGACACCTTTG
54693213 GTGCCGCCA
1 GTGCCGCCA
54693222 CAGTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.14, C:0.32, G:0.22, T:0.32
Consensus pattern (27 bp):
GTGCCGCCAATCTCTTTGACACCTTTG
Found at i:54693291 original size:27 final size:27
Alignment explanation
Indices: 54693237--54693300 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
54693227 TTTTTTTTGT
****
54693237 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAGGGATA
54693264 ATATTTTGGTAAATAAAAAAAGGGATA
1 ATATTTTGGTAAATAAAAAAAGGGATA
*
54693291 ACATTTTGGT
1 ATATTTTGGT
54693301 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGGGATA
Found at i:54694349 original size:22 final size:22
Alignment explanation
Indices: 54694321--54694364 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54694311 TACTCCCCCT
54694321 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
54694343 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
54694365 TCATATTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (22 bp):
CATGAGAACATCACATAATATA
Found at i:54695785 original size:23 final size:23
Alignment explanation
Indices: 54695759--54695857 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
54695749 ATAAGTGCAA
*
54695759 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54695782 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54695805 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54695828 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54695851 CACTGAT
1 CACTGAT
54695858 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54707281 original size:41 final size:41
Alignment explanation
Indices: 54707121--54707286 Score: 287
Period size: 41 Copynumber: 4.0 Consensus size: 41
54707111 TATGTATATG
* *
54707121 ATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGATATGA
1 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
54707162 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
1 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
54707203 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
1 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
*
54707244 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCCGA
1 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
54707285 AT
1 AT
54707287 ATGATGAATT
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 118 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (41 bp):
ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGA
Found at i:54707525 original size:31 final size:35
Alignment explanation
Indices: 54707489--54707576 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 35
54707479 GCATATTTAG
54707489 GCATTCGGCATAGGTGGATAT-A-TAT-T-TGTAT
1 GCATTCGGCATAGGTGGATATAAGTATATATGTAT
* *
54707520 GCATTCGGCATAGATAGATATAAGTGTATATATGTAT
1 GCATTCGGCATAGGTGGATATAA--GTATATATGTAT
54707557 GCATTCGGCATAGGTGGATA
1 GCATTCGGCATAGGTGGATA
54707577 ATAGTGAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 19 0.40
32 1 0.02
35 3 0.06
36 1 0.02
37 23 0.49
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (35 bp):
GCATTCGGCATAGGTGGATATAAGTATATATGTAT
Done.