Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold96
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: 1013983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:286462 original size:33 final size:32
Alignment explanation
Indices: 286351--286569 Score: 187
Period size: 33 Copynumber: 6.8 Consensus size: 32
286341 TTGTGGACTT
* ** *
286351 AAAAGAGTGCCAC-GAAGTTATGGACTTAAAAGG
1 AAAAGA-TGCCACTG-AGTCATGGACTTGGAAGA
* * ** *
286384 AAAAGGTGCCACAGAGTTGTGGACTTAG-AG-
1 AAAAGATGCCACTGAGTCATGGACTTGGAAGA
286414 AAAAGATGCCACTGAGTCATGGACTTGGAAGA
1 AAAAGATGCCACTGAGTCATGGACTTGGAAGA
* **
286446 AAAAGGATGGCACTGAGTTGTGGACTTGG-A-A
1 AAAA-GATGCCACTGAGTCATGGACTTGGAAGA
* * *
286477 AAGAGATGCCACTAAGTCATGGACTTTGGGAGAA
1 AAAAGATGCCACTGAGTCATGGAC-TTGGAAG-A
* *
286511 AAAAGATGCCACTAAATCATGGACTTGGAAGA
1 AAAAGATGCCACTGAGTCATGGACTTGGAAGA
*
286543 AAAAGGATGCCACTGAGTCGTGGACTT
1 AAAA-GATGCCACTGAGTCATGGACTT
286570 TGGGAAGGAT
Statistics
Matches: 155, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
30 39 0.25
31 12 0.08
32 29 0.19
33 52 0.34
34 23 0.15
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (32 bp):
AAAAGATGCCACTGAGTCATGGACTTGGAAGA
Found at i:286486 original size:63 final size:64
Alignment explanation
Indices: 286325--286569 Score: 229
Period size: 63 Copynumber: 3.9 Consensus size: 64
286315 ACTTAAAATG
* * * ** *
286325 AAAAGG-TACCACAGAGTTGTGGACTT--A-AAAGAG-TGCCAC-GAAGTTATGGACTTAAAAGG
1 AAAAGGATGCCACTGAGTTGTGGACTTGGAGAAAGAGATGCCACTG-AGTCATGGACTTGGAAGA
* *
286384 AAAAGG-TGCCACAGAGTTGTGGACTTAGAGAAA-AGATGCCACTGAGTCATGGACTTGGAAGA
1 AAAAGGATGCCACTGAGTTGTGGACTTGGAGAAAGAGATGCCACTGAGTCATGGACTTGGAAGA
* * *
286446 AAAAGGATGGCACTGAGTTGTGGACTTGGA-AAAGAGATGCCACTAAGTCATGGACTTTGGGAGA
1 AAAAGGATGCCACTGAGTTGTGGACTTGGAGAAAGAGATGCCACTGAGTCATGGAC-TTGGAAGA
* * * ** * *
286510 AAAAAGATGCCACTAAATCATGGACTTGGAAGAAAAAGGATGCCACTGAGTCGTGGACTT
1 AAAAGGATGCCACTGAGTTGTGGACTTGG-AGAAAGA-GATGCCACTGAGTCATGGACTT
286570 TGGGAAGGAT
Statistics
Matches: 156, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
59 25 0.16
61 3 0.02
62 32 0.21
63 41 0.26
64 30 0.19
65 1 0.01
66 6 0.04
67 18 0.12
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.20
Consensus pattern (64 bp):
AAAAGGATGCCACTGAGTTGTGGACTTGGAGAAAGAGATGCCACTGAGTCATGGACTTGGAAGA
Found at i:286531 original size:97 final size:95
Alignment explanation
Indices: 286414--286607 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 95
286404 GGACTTAGAG
* * * *
286414 AAAAGATGCCACTGAGTCATGGACTTGGAAGAAAAAGGATGGCACTGAGTTGTGGAC-TTGGAAA
1 AAAAGATGCCACTAAATCATGGACTTGGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGG-AA
286478 AGAGATGCCACT-AAGTCATGGACTTTGGGAGAA
65 AG-GATGCCA-TAAAGTCATGGACTTTGGGA-AA
*
286511 AAAAGATGCCACTAAATCATGGACTTGGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGGGAA
1 AAAAGATGCCACTAAATCATGGACTTGGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGGAAA
* *
286576 GGATGCCATAAAGTCATGGGCTTTTGGAAA
66 GGATGCCATAAAGTCATGGACTTTGGGAAA
286606 AA
1 AA
286608 GATTTGAAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
95 5 0.06
96 23 0.26
97 56 0.64
98 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (95 bp):
AAAAGATGCCACTAAATCATGGACTTGGAAGAAAAAGGATGCCACTGAGTCGTGGACTTTGGAAA
GGATGCCATAAAGTCATGGACTTTGGGAAA
Found at i:286590 original size:29 final size:29
Alignment explanation
Indices: 286481--286604 Score: 81
Period size: 33 Copynumber: 4.0 Consensus size: 29
286471 TTGGAAAAGA
*
286481 GATGCCACTAAGTCATGGACTTTGGGAGAAAAAA
1 GATGCCACTAAGTCATGGACTTT-GG-G---AAG
*
286515 GATGCCACTAAATCATGGAC-TTGGAAGAAAAAG
1 GATGCCACTAAGTCATGGACTTTGG--G---AAG
* *
286548 GATGCCACTGAGTCGTGGACTTTGGGAAG
1 GATGCCACTAAGTCATGGACTTTGGGAAG
* *
286577 GATGCCA-TAAAGTCATGGGCTTTTGGAA
1 GATGCCACT-AAGTCATGGACTTTGGGAA
286605 AAAGATTTGA
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.01
29 25 0.32
32 3 0.04
33 26 0.33
34 23 0.29
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (29 bp):
GATGCCACTAAGTCATGGACTTTGGGAAG
Found at i:287805 original size:7 final size:7
Alignment explanation
Indices: 287795--287849 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
287785 TGCTTTTGCA
287795 TTTTTTG
1 TTTTTTG
287802 TTTTTTG
1 TTTTTTG
*
287809 TTTCTTG
1 TTTTTTG
287816 TTTTTT-
1 TTTTTTG
*
287822 TTTGTTG
1 TTTTTTG
287829 -TTTTTG
1 TTTTTTG
287835 TTTTTGTTG
1 -TTTT-TTG
287844 TTTTTT
1 TTTTTT
287850 TTACTTCTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 10 0.25
7 20 0.50
8 7 0.17
9 3 0.08
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (7 bp):
TTTTTTG
Found at i:287820 original size:15 final size:14
Alignment explanation
Indices: 287795--287851 Score: 73
Period size: 13 Copynumber: 4.1 Consensus size: 14
287785 TGCTTTTGCA
287795 TTTT-TTGTTTTTT
1 TTTTGTTGTTTTTT
* *
287808 GTTTCTTG-TTTTT
1 TTTTGTTGTTTTTT
287821 TTTTGTTGTTTTTGT
1 TTTTGTTGTTTTT-T
287836 TTTTGTTGTTTTTT
1 TTTTGTTGTTTTTT
287850 TT
1 TT
287852 ACTTCTTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
13 14 0.37
14 10 0.26
15 14 0.37
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (14 bp):
TTTTGTTGTTTTTT
Found at i:295988 original size:20 final size:20
Alignment explanation
Indices: 295948--296001 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
295938 TTTTACAATT
* *
295948 TGTATAGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
* *
295969 TTTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
295989 TGTATCGATACAT
1 TGTATCGATACAT
296002 GTCCGAAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:296190 original size:52 final size:51
Alignment explanation
Indices: 296058--296194 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 51
296048 CTGGAAAAGA
*
296058 AAATGTATCGATACATTTTTTATTGTATCG--ACA-TCTTGGGTTTTGACCC
1 AAATGTATCGATACA-TTTTTATTGTATCGATACATTCTAGGGTTTTGACCC
* * * *
296107 AAATATATCGATACATTTTTCATTGTCTCGATACATTCTAGGTTTTTTACCC
1 AAATGTATCGATACATTTTT-ATTGTATCGATACATTCTAGGGTTTTGACCC
* *
296159 AAATGTATCGATACATTCTTTAATATATCGATACAT
1 AAATGTATCGATACATT-TTTATTGTATCGATACAT
296195 ACAAGCAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 5 0.07
49 22 0.30
51 3 0.04
52 41 0.55
53 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (51 bp):
AAATGTATCGATACATTTTTATTGTATCGATACATTCTAGGGTTTTGACCC
Found at i:299680 original size:42 final size:42
Alignment explanation
Indices: 299618--299700 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
299608 ATTGTTCACT
* * * *
299618 TAATTACCTTTATTTAGAGTTGAAGATAACTATTTGGACATA
1 TAATTACCTTTACTTAGAGTTAAAAATAACTATTTGAACATA
* * *
299660 TAATTACCTTTGCTTGGAGTTAAAAATAGCTATTTGAACAT
1 TAATTACCTTTACTTAGAGTTAAAAATAACTATTTGAACAT
299701 TACAAATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (42 bp):
TAATTACCTTTACTTAGAGTTAAAAATAACTATTTGAACATA
Found at i:301108 original size:25 final size:23
Alignment explanation
Indices: 301073--301123 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
301063 TAAATATTAT
*
301073 ATATTAATTTTAT-ATTTTATAAA
1 ATATTAATTTTATCA-TTTAAAAA
301096 ATATGTAATTTTTATCATTTAAAAA
1 ATAT-TAA-TTTTATCATTTAAAAA
301121 ATA
1 ATA
301124 CATATATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 3 0.12
25 16 0.67
26 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTAATTTTATCATTTAAAAA
Found at i:302159 original size:14 final size:15
Alignment explanation
Indices: 302127--302165 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
302117 GTCATTTTTT
302127 TAATATTTCATTTTAA
1 TAATATTT-ATTTTAA
*
302143 TAATATTTA-TTTGA
1 TAATATTTATTTTAA
302157 TAATATTTA
1 TAATATTTA
302166 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 1 0.05
16 8 0.36
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
TAATATTTATTTTAA
Found at i:304396 original size:149 final size:147
Alignment explanation
Indices: 304112--304413 Score: 349
Period size: 149 Copynumber: 2.0 Consensus size: 147
304102 AGTCATTATA
* * * * * *
304112 ACTTATCCTTTTTAAGTCCTTTAGGGGTACCAGGATACTTTCATGTCAAAGGTATCTTCTTGGGG
1 ACTTTTCCTTTTTAAGTCCTTTAAGGGTACCAAGATACTTTCATGTCAAAGCTATCTCCTAGGGG
* * * * * * *
304177 TATTTTTGTAATTTTTCTAAATCGAGTCTTAATTTGTCACTAGCTTGCTTCTATGCCAAATGTAT
66 CATTTTTATAATTTTTCTAAAACGAGTCCTAATTTGTCACGAGCTTGCTTCTATGCCAAAGGTAC
* *
304242 GTATTAGGTGTAGGTTT
131 ATATTAGGCGTAGGTTT
* * *
304259 GCTTTTCCTTTTTAAGTCCTTTAAGGTTACCAAGATA-TTTACATGTCGAAGCTATAC-CCATAG
1 ACTTTTCCTTTTTAAGTCCTTTAAGGGTACCAAGATACTTT-CATGTCAAAGCTAT-CTCC-TAG
* * *
304322 GGGCATTTTTATAATTTTTCTAAAACTGAGTCCTAATTTGTCATCGAG-TTGCTTTTATGCCGAG
63 GGGCATTTTTATAATTTTTCTAAAAC-GAGTCCTAATTTGTCA-CGAGCTTGCTTCTATGCCAAA
304386 GGTACATATTAGGCGTAGGTTT
126 GGTACATATTAGGCGTAGGTTT
304408 ACTTTT
1 ACTTTT
304414 TTTTTTATGT
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
146 3 0.02
147 45 0.35
148 26 0.20
149 51 0.40
150 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.42
Consensus pattern (147 bp):
ACTTTTCCTTTTTAAGTCCTTTAAGGGTACCAAGATACTTTCATGTCAAAGCTATCTCCTAGGGG
CATTTTTATAATTTTTCTAAAACGAGTCCTAATTTGTCACGAGCTTGCTTCTATGCCAAAGGTAC
ATATTAGGCGTAGGTTT
Found at i:308986 original size:112 final size:113
Alignment explanation
Indices: 308780--308988 Score: 260
Period size: 112 Copynumber: 1.9 Consensus size: 113
308770 AAGAACATCG
* *
308780 AATTTGTCTGATTTTTAAAAAAATTCATATTTTATACATTCTAATCCATTCGTGCCTAGAAAAAT
1 AATTTGTCCGATTTTTAAAAAAATTCATATTTTATACAATCTAATCCATTCGTGCCTAGAAAAAT
* * * ** *
308845 AGGGCACTTATCTTATGAGTTTTGGAATTTTTGAGCCCAAAAATATTA
66 AGGGCACTTACCCTATCAGTCCTGAAATTTTTGAGCCCAAAAATATTA
* * * * * *
308893 AATTTGTCCGA-TTTTCAAAAAATTCATATTTTTTACAATCTGATCCATTTGTGCTTAGGAAAAT
1 AATTTGTCCGATTTTTAAAAAAATTCATATTTTATACAATCTAATCCATTCGTGCCTAGAAAAAT
*
308957 GGGGCA-TGTACCCTATCAGTCCTGAAATTTTT
66 AGGGCACT-TACCCTATCAGTCCTGAAATTTTT
308989 AGGCCAACCT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
111 1 0.01
112 69 0.86
113 10 0.12
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (113 bp):
AATTTGTCCGATTTTTAAAAAAATTCATATTTTATACAATCTAATCCATTCGTGCCTAGAAAAAT
AGGGCACTTACCCTATCAGTCCTGAAATTTTTGAGCCCAAAAATATTA
Found at i:309636 original size:89 final size:89
Alignment explanation
Indices: 309518--309735 Score: 285
Period size: 89 Copynumber: 2.5 Consensus size: 89
309508 TAGTTTTATC
*
309518 TTTCACACACATCTGCACC-TTAGATGACATTGGCATTTGCATCATCTCATATGCATCTGCAATT
1 TTTCACGCACATCTGCACCATTAGATGACATTGGCATTTGCATCATCTCATATGCATCTGCAATT
** * * **
309582 TTATTAATTTTTGCATTTGCATTG
66 TTATTAATGCTTACATTTACATCA
* * * * * *
309606 TTTCACGCATATTTGCACCATTAAATGACATTGGTATTTGCATCATCTTATATGCATCTGCCATT
1 TTTCACGCACATCTGCACCATTAGATGACATTGGCATTTGCATCATCTCATATGCATCTGCAATT
309671 TTATTAATGCTTACATTTACATCA
66 TTATTAATGCTTACATTTACATCA
* * *
309695 TTTCATGTACATCTGCACCATTAGATGACATTCGCATTTGC
1 TTTCACGCACATCTGCACCATTAGATGACATTGGCATTTGC
309736 CTCGTTTAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
88 16 0.15
89 93 0.85
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (89 bp):
TTTCACGCACATCTGCACCATTAGATGACATTGGCATTTGCATCATCTCATATGCATCTGCAATT
TTATTAATGCTTACATTTACATCA
Found at i:310522 original size:92 final size:92
Alignment explanation
Indices: 310278--310696 Score: 518
Period size: 92 Copynumber: 4.6 Consensus size: 92
310268 AAACATATAT
** ** * **
310278 TTCCCAATCATATCCCTTTCATCCAATTACTAGATGGTATTGACACATCACAAAGCCTAATTTTG
1 TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCC
* *
310343 TTGGGGCAAGGATATCCCGGCCACTCA
66 TTAGGGCAAGGATATCCCGACCACTCA
* * *
310370 TTCCCAATCGTATCCC-TTCATCCAACCACTAGATGGTATTAATGCATTACAAAGCCTGATTTCC
1 TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCC
* *
310434 TTAGGGCAAAGATATCCCAACCACTCA
66 TTAGGGCAAGGATATCCCGACCACTCA
* ** * *
310461 TTCCCAATCATATCCCCTTCATTAAACCACTAGATGTTATTGATGCATCACAAAGCTTGATTTCC
1 TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCC
**
310526 TTAGGGCAAGGATATCTTGACCACAT-A
66 TTAGGGCAAGGATATCCCGACCAC-TCA
* * *
310553 TTCCCAATCATATCCCTTTCAGCGAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCT
1 TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCC
* * * *
310618 TTGGGGCAAGGATATCCCGTCCATTTA
66 TTAGGGCAAGGATATCCCGACCACTCA
* * ** *
310645 TTCTCAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACA
1 TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACA
310697 TGACCACTAA
Statistics
Matches: 281, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
91 78 0.28
92 202 0.72
93 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (92 bp):
TTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCC
TTAGGGCAAGGATATCCCGACCACTCA
Found at i:311193 original size:40 final size:40
Alignment explanation
Indices: 311143--311313 Score: 139
Period size: 40 Copynumber: 4.3 Consensus size: 40
311133 CCTTCTATTC
*
311143 GTTGACTTTATCGGTTTCACCTTGGTTAACCTTTTTACTT
1 GTTGACTTTATCGATTTCACCTTGGTTAACCTTTTTACTT
* * ** * * *
311183 GTTGGCTTTATCAATTTTGCCTTAGCTAACC-TTTTAATT
1 GTTGACTTTATCGATTTCACCTTGGTTAACCTTTTTACTT
* * * * * * *
311222 GGTTAACTTTATCGGTTTTATCTTGGTCAACCCTTTGACTT
1 -GTTGACTTTATCGATTTCACCTTGGTTAACCTTTTTACTT
* * * *
311263 ATTGGCTTTATCGATTTCACCTTGGTTAACC-TTATAATT
1 GTTGACTTTATCGATTTCACCTTGGTTAACCTTTTTACTT
311302 GGTTGACTTTAT
1 -GTTGACTTTAT
311314 GGGTTTTACC
Statistics
Matches: 97, Mismatches: 31, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
39 12 0.12
40 79 0.81
41 6 0.06
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (40 bp):
GTTGACTTTATCGATTTCACCTTGGTTAACCTTTTTACTT
Found at i:311293 original size:80 final size:80
Alignment explanation
Indices: 311147--311323 Score: 228
Period size: 80 Copynumber: 2.2 Consensus size: 80
311137 CTATTCGTTG
* * * * * **
311147 ACTTTATCGGTTTCACCTTGGTTAACCTTTTTACTTGTTGGCTTTATCAATTTTGCCTTAGCTAA
1 ACTTTATCGGTTTTACCTTGGTCAACCCTTTGACTTATTGGCTTTATCAATTTCACCTTAGCTAA
*
311212 CCTTTTAATTGGTTA
66 CCTTATAATTGGTTA
* * * *
311227 ACTTTATCGGTTTTATCTTGGTCAACCCTTTGACTTATTGGCTTTATCGATTTCACCTTGGTTAA
1 ACTTTATCGGTTTTACCTTGGTCAACCCTTTGACTTATTGGCTTTATCAATTTCACCTTAGCTAA
*
311292 CCTTATAATTGGTTG
66 CCTTATAATTGGTTA
*
311307 ACTTTATGGGTTTTACC
1 ACTTTATCGGTTTTACC
311324 CTAGCTAACT
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (80 bp):
ACTTTATCGGTTTTACCTTGGTCAACCCTTTGACTTATTGGCTTTATCAATTTCACCTTAGCTAA
CCTTATAATTGGTTA
Found at i:311340 original size:120 final size:120
Alignment explanation
Indices: 311148--311440 Score: 297
Period size: 120 Copynumber: 2.4 Consensus size: 120
311138 TATTCGTTGA
* * * ** * *
311148 CTTTATCGGTTTCACCTTGGTTAACCTTTTTACTT-GTTGGCTTTATCAATTTTGCCTTAGCTAA
1 CTTTATCGATTTCACCTTGGTTAACC-TTTTAATTGGTTGACTTTATCGGTTTTACCCTAGCTAA
* * * * * * *
311212 CCTTTTAATTGGTTAACTTTATCGGTTTTATCTTGGTCAACCCTTT-GACTTATTGG
65 CCTTTTAATTAGTTAACTTTATCAGTTTTATCCTAGTCAA-ACTTTCGACTCATTAG
* *
311268 CTTTATCGATTTCACCTTGGTTAACCTTATAATTGGTTGACTTTATGGGTTTTACCCTAGCTAA-
1 CTTTATCGATTTCACCTTGGTTAACCTTTTAATTGGTTGACTTTATCGGTTTTACCCTAGCTAAC
* * *
311332 CTTCTTAATTAGTTGACTTTATCAGTTTTGTCCTAGTCAAACTTTCTACTCATTAG
66 CTT-TTAATTAGTTAACTTTATCAGTTTTATCCTAGTCAAACTTTCGACTCATTAG
* * * ** *
311388 CTTTAT-TAGTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATTGGTTTT
1 CTTTATCGA-TTTCACCTTGGTTAACCTTTTAATTGGTTGACTTTATCGGTTTT
311441 CTTTATGGTC
Statistics
Matches: 143, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
119 14 0.10
120 129 0.90
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (120 bp):
CTTTATCGATTTCACCTTGGTTAACCTTTTAATTGGTTGACTTTATCGGTTTTACCCTAGCTAAC
CTTTTAATTAGTTAACTTTATCAGTTTTATCCTAGTCAAACTTTCGACTCATTAG
Found at i:311427 original size:80 final size:79
Alignment explanation
Indices: 311316--311775 Score: 380
Period size: 81 Copynumber: 5.7 Consensus size: 79
311306 GACTTTATGG
* * * * *
311316 GTTTTACCCTAGCTAA-CTTCTTAATTAGTTGACTTTATCAGTTTTGTCCTAGTCAAACTTTCTA
1 GTTTCACCCTAGCCAACCTT-TTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCTTTCTA
* *
311380 CTCATTAGCTTTATT
65 CTCGTTGGCTTTATT
** ** *
311395 AGTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATTGGTTTT-CTTTATGGTCAACCATTC
1 -GTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTA--GTCAACCTTTC
311459 TACTCGTTGGCTTTATT
63 TACTCGTTGGCTTTATT
** * * *
311476 GATTTCGA-CCTAATCAACCTTTTAATTGGTTGTCTTTATCAGTTTCGCCCTGGTCAACCCTTT-
1 G-TTTC-ACCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAA-CCTTTC
*
311539 TA-TCCTATTGGCTTTATCT
63 TACT-C-GTTGGCTTTAT-T
* * *
311558 GTTTCGCCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTGTTACCCTAGTCAACCATTT-TA
1 GTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACC-TTTCT-
*
311622 AC-CTGTTAGCTTTATT
64 ACTC-GTTGGCTTTATT
* * ** * * *
311638 GATTTC-CCCTTAGCCTACCTTTT-ACTCATTGACTTTATTAGTTTTGCCCTGGTCAACCCTTCT
1 G-TTTCACCC-TAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCTTTCT
* *
311701 ACTTGTTGGCTTTATAA
64 ACTCGTTGGCTTTAT-T
* * * * * *
311718 GTTTCACCCTAGCCAACCTTTTAATTAGTTGATTTTATCAATTTCGCCTTGGTCAACC
1 GTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACC
311776 CTTTTAATTT
Statistics
Matches: 305, Mismatches: 54, Indels: 42
0.76 0.13 0.10
Matches are distributed among these distances:
79 33 0.11
80 112 0.37
81 154 0.50
82 6 0.02
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (79 bp):
GTTTCACCCTAGCCAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCTTTCTAC
TCGTTGGCTTTATT
Found at i:311434 original size:40 final size:40
Alignment explanation
Indices: 311290--311802 Score: 216
Period size: 40 Copynumber: 12.8 Consensus size: 40
311280 CACCTTGGTT
* ** *
311290 AACCTTATAATTGGTTGACTTTATGGGTTTTACCCTAG-C
1 AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* * ***
311329 TAA-CTTCTTAATTAGTTGACTTTATCAGTTTTGTCCTAGTC
1 -AACCTT-TTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* * ** *
311370 AAACTTTCT-ACTCATT-AGCTTTATTAGTTTCACCCTAGCC
1 AACCTTT-TAATTGGTTGA-CTTTATTAGTTTCACCCTAGTC
* * **
311410 AACCTTTTAATTGGTTGACTTTATTGGTTT-TCTTTATGGTC
1 AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTA--GTC
* * * * *
311451 AACCATTCT-ACTCGTTGGCTTTATT-GATTTCGA-CCTAATC
1 AACC-TTTTAATTGGTTGACTTTATTAG-TTTC-ACCCTAGTC
* * * *
311491 AACCTTTTAATTGGTTGTCTTTATCAGTTTCGCCCTGGTC
1 AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* * * *
311531 AACCCTTTT-ATCCT-ATTGGCTTTATCT-GTTTCGCCCTAGCC
1 AA-CCTTTTAAT--TGGTTGACTTTAT-TAGTTTCACCCTAGTC
*
311572 AACCTTTTAATTGGTTGACTTTATCAGTGTT-ACCCTAGTC
1 AACCTTTTAATTGGTTGACTTTATTAGT-TTCACCCTAGTC
* *
311612 AACCATTTTAACCT-GTT-AGCTTTATT-GATTTC-CCCTTAGCC
1 AACC-TTTTAA-TTGGTTGA-CTTTATTAG-TTTCACCC-TAGTC
* * ** ** *
311653 TACCTTTT-ACTCATTGACTTTATTAGTTTTGCCCTGGTC
1 AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* * * * *
311692 AACCCTTCTACTT-GTTGGCTTTATAAGTTTCACCCTAGCC
1 AA-CCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* * * * * * *
311732 AACCTTTTAATTAGTTGATTTTATCAATTTCGCCTTGGTC
1 AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
* *
311772 AACCCTTTTAATTTGTTGACTTTATTGGTTT
1 AA-CCTTTTAATTGGTTGACTTTATTAGTTT
311803 TGCCTTGGTC
Statistics
Matches: 352, Mismatches: 83, Indels: 75
0.69 0.16 0.15
Matches are distributed among these distances:
38 2 0.01
39 37 0.11
40 197 0.56
41 109 0.31
42 7 0.02
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (40 bp):
AACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTC
Found at i:311784 original size:41 final size:41
Alignment explanation
Indices: 311489--311833 Score: 142
Period size: 41 Copynumber: 8.6 Consensus size: 41
311479 TTCGACCTAA
* * * *
311489 TCAA-CCTTTTAATTGGTTGTCTTTATCAGTTTCGCCCTGG
1 TCAACCCTTTTAATTAGTTGACTTTATCAATTTCGCCTTGG
* ** * *
311529 TCAACCCTTTT-ATCCTA-TTGGCTTTATCTGTTTCGCCCTAG
1 TCAACCCTTTTAAT--TAGTTGACTTTATCAATTTCGCCTTGG
* * * *
311570 CCAA-CCTTTTAATTGGTTGACTTTATCAGTGTTAC-CC-TAG
1 TCAACCCTTTTAATTAGTTGACTTTATCAAT-TT-CGCCTTGG
* * ** * *
311610 TCAACCATTTTAACCT-GTT-AGCTTTATTGATTTCCCCTTAG
1 TCAACCCTTTTAA-TTAGTTGA-CTTTATCAATTTCGCCTTGG
* * * * * * * *
311651 CCTA-CCTTTTACTCA-TTGACTTTATTAGTTTTGCCCTGG
1 TCAACCCTTTTAATTAGTTGACTTTATCAATTTCGCCTTGG
* * * * * *
311690 TCAACCCTTCTACTT-GTTGGCTTTAT-AAGTTTCACCCTAG
1 TCAACCCTTTTAATTAGTTGACTTTATCAA-TTTCGCCTTGG
* *
311730 CCAA-CCTTTTAATTAGTTGATTTTATCAATTTCGCCTTGG
1 TCAACCCTTTTAATTAGTTGACTTTATCAATTTCGCCTTGG
* *** *
311770 TCAACCCTTTTAATTTGTTGACTTTATTGGTTTTGCCTTGG
1 TCAACCCTTTTAATTAGTTGACTTTATCAATTTCGCCTTGG
* *
311811 TCAACCATTCTAACTT-GTTGACT
1 TCAACCCTTTTAA-TTAGTTGACT
311834 CATCGATTCA
Statistics
Matches: 232, Mismatches: 52, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
39 29 0.12
40 90 0.39
41 108 0.47
42 5 0.02
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (41 bp):
TCAACCCTTTTAATTAGTTGACTTTATCAATTTCGCCTTGG
Found at i:311904 original size:42 final size:42
Alignment explanation
Indices: 311858--312246 Score: 251
Period size: 42 Copynumber: 9.2 Consensus size: 42
311848 CAGTCAACTT
* *
311858 TTTTATCCTTTGTTTACCTGTCGACTTAGTCTTAGTAAATCC
1 TTTTATCCTTTGTTTACTTGTCGACTTAGTCTGAGTAAATCC
* * * * *
311900 TTTTATCCTTTGTTGACTTATCG-GTTCAATCTCG-GTCAA-CC
1 TTTTATCCTTTGTTTACTTGTCGACTT-AGTCT-GAGTAAATCC
* * *
311941 TTTTTATCCTTTGTTTACTTATCGGCCTAGTCTCGAGTAAATCC
1 -TTTTATCCTTTGTTTACTTGTCGACTTAGTCT-GAGTAAATCC
* * * * *
311985 TTTTATCCTTTGTTGACTTGTC-AATTCAATCTTAGTCAA-CC
1 TTTTATCCTTTGTTTACTTGTCGACTT-AGTCTGAGTAAATCC
* *
312026 TTTTTATCCTTTGTTTACTTGTCAACTTAGTCCTGAATAAATCC
1 -TTTTATCCTTTGTTTACTTGTCGACTTAGT-CTGAGTAAATCC
* * * * *
312070 TTTTATCTTTTGTTGACTTGTC-AGTTCAATCTCGA-TCAA-CC
1 TTTTATCCTTTGTTTACTTGTCGACTT-AGTCT-GAGTAAATCC
* * * * * *
312111 TTTTTATCCTTTATTTACCTATTGGCTTAGTCTCGAGTAAATTC
1 -TTTTATCCTTTGTTTACTTGTCGACTTAGTCT-GAGTAAATCC
* * * * *
312155 TTTTATCCTTTGTTGACTTGT-TAGTTCAATCCT-AGTCAA-CC
1 TTTTATCCTTTGTTTACTTGTCGACTT-AGT-CTGAGTAAATCC
* *
312196 TTTTTATCCTTTATTTACTTGTCGACTTAGTCCTGGGTAAATCC
1 -TTTTATCCTTTGTTTACTTGTCGACTTAGT-CTGAGTAAATCC
312240 TTTTATC
1 TTTTATC
312247 ATTTATTGAT
Statistics
Matches: 265, Mismatches: 59, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
41 9 0.03
42 147 0.55
43 100 0.38
44 9 0.03
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (42 bp):
TTTTATCCTTTGTTTACTTGTCGACTTAGTCTGAGTAAATCC
Found at i:312000 original size:85 final size:85
Alignment explanation
Indices: 311825--312317 Score: 548
Period size: 85 Copynumber: 5.8 Consensus size: 85
311815 CCATTCTAAC
** * * *
311825 TTGTTGACTCATCGATTCAATCTCAGTCAACTTTTTTATCCTTTGTTTACCTGTCGACTTAGTCT
1 TTGTTGACTTGTCAATTCAATCTCAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCT
*
311890 -TAGTAAATCCTTTTATCCT
66 CGAGTAAATCCTTTTATCCT
* ** * * * *
311909 TTGTTGACTTATCGGTTCAATCTCGGTCAACCTTTTTATCCTTTGTTTACTTATCGGCCTAGTCT
1 TTGTTGACTTGTCAATTCAATCTCAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCT
311974 CGAGTAAATCCTTTTATCCT
66 CGAGTAAATCCTTTTATCCT
* *
311994 TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCAACTTAGTC-
1 TTGTTGACTTGTCAATTCAATCTCAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCT
* *
312058 CTGAATAAATCCTTTTATCTT
66 C-GAGTAAATCCTTTTATCCT
* * * * * *
312079 TTGTTGACTTGTCAGTTCAATCTC-GATCAACCTTTTTATCCTTTATTTACCTATTGGCTTAGTC
1 TTGTTGACTTGTCAATTCAATCTCAG-TCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTC
*
312143 TCGAGTAAATTCTTTTATCCT
65 TCGAGTAAATCCTTTTATCCT
* * *
312164 TTGTTGACTTGTTAGTTCAATC-CTAGTCAACCTTTTTATCCTTTATTTACTTGTCGACTTAGTC
1 TTGTTGACTTGTCAATTCAATCTC-AGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTC
* *
312228 -CTGGGTAAATCCTTTTATCAT
65 TC-GAGTAAATCCTTTTATCCT
* * ** * * * **
312249 TTATTGATTTGTTGATTCAATCCCATTCAA-CTTTTGTATCCTTTGTTTACCTGTTAACTTAGTC
1 TTGTTGACTTGTCAATTCAATCTCAGTCAACCTTTT-TATCCTTTGTTTACTTGTCGACTTAGT-
312313 CTCGA
64 CTCGA
312318 AAACCACTTT
Statistics
Matches: 349, Mismatches: 49, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
84 66 0.19
85 277 0.79
86 5 0.01
87 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (85 bp):
TTGTTGACTTGTCAATTCAATCTCAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCT
CGAGTAAATCCTTTTATCCT
Found at i:312119 original size:170 final size:170
Alignment explanation
Indices: 311825--312300 Score: 645
Period size: 170 Copynumber: 2.8 Consensus size: 170
311815 CCATTCTAAC
** * * * *
311825 TTGTTGACTCATCGATTCAATCTCAGTCAACTTTTTTATCCTTTGTTTACCTGTCGACTTAGT-C
1 TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
* * * * *
311889 TTAGTAAATCCTTTTATCCTTTGTTGACTTATCGGTTCAATCTCGGTCAACCTTTTTATCCTTTG
66 TGAGTAAATCCTTTTATCATTTGTTGACTTGTCAGTTCAATCTCGATCAACCTTTTTATCCTTTG
*
311954 TTTACTTATCGGCCTAGTCTCGAGTAAATCCTTTTATCCT
131 TTTACCTATCGGCCTAGTCTCGAGTAAATCCTTTTATCCT
*
311994 TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCAACTTAGTCC
1 TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
* * *
312059 TGAATAAATCCTTTTATCTTTTGTTGACTTGTCAGTTCAATCTCGATCAACCTTTTTATCCTTTA
66 TGAGTAAATCCTTTTATCATTTGTTGACTTGTCAGTTCAATCTCGATCAACCTTTTTATCCTTTG
* * *
312124 TTTACCTATTGGCTTAGTCTCGAGTAAATTCTTTTATCCT
131 TTTACCTATCGGCCTAGTCTCGAGTAAATCCTTTTATCCT
* * * *
312164 TTGTTGACTTGTTAGTTCAATCCTAGTCAACCTTTTTATCCTTTATTTACTTGTCGACTTAGTCC
1 TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
* * * * *
312229 TGGGTAAATCCTTTTATCATTTATTGATTTGT-TGATTCAATC-CCATTCAA-CTTTTGTATCCT
66 TGAGTAAATCCTTTTATCATTTGTTGACTTGTCAG-TTCAATCTCGA-TCAACCTTTT-TATCCT
312291 TTGTTTACCT
128 TTGTTTACCT
312301 GTTAACTTAG
Statistics
Matches: 272, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
169 64 0.24
170 208 0.76
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (170 bp):
TTGTTGACTTGTCAATTCAATCTTAGTCAACCTTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
TGAGTAAATCCTTTTATCATTTGTTGACTTGTCAGTTCAATCTCGATCAACCTTTTTATCCTTTG
TTTACCTATCGGCCTAGTCTCGAGTAAATCCTTTTATCCT
Found at i:313087 original size:20 final size:20
Alignment explanation
Indices: 313062--313116 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
313052 AAAACCCTTA
313062 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
313082 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
313102 AATGTATCGATACAT
1 AAAGTATCGATACAT
313117 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:313206 original size:13 final size:13
Alignment explanation
Indices: 313188--313213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
313178 ACACCAAAGT
313188 ATGTATCGATACA
1 ATGTATCGATACA
313201 ATGTATCGATACA
1 ATGTATCGATACA
313214 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:313211 original size:33 final size:33
Alignment explanation
Indices: 313169--313233 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
313159 TAGCCAAACT
* *
313169 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
313202 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
313234 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:319408 original size:20 final size:20
Alignment explanation
Indices: 319383--319436 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
319373 GGAAATTCAA
319383 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
319403 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
319423 TGTATCGATACATT
1 TGTATCGATACATT
319437 GTATCGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTT
Found at i:319440 original size:13 final size:13
Alignment explanation
Indices: 319422--319460 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
319412 ACATTTTTCT
319422 TTGTATCGATACA
1 TTGTATCGATACA
319435 TTGTATCGATACA
1 TTGTATCGATACA
*
319448 CTGTATCGATACA
1 TTGTATCGATACA
319461 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:321907 original size:20 final size:20
Alignment explanation
Indices: 321882--321936 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
321872 AAAACCCTTA
321882 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
321902 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
321922 AATGTATCGATACAT
1 AAAGTATCGATACAT
321937 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:322026 original size:13 final size:13
Alignment explanation
Indices: 322008--322033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321998 ACACCAAAGT
322008 ATGTATCGATACA
1 ATGTATCGATACA
322021 ATGTATCGATACA
1 ATGTATCGATACA
322034 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:323496 original size:51 final size:51
Alignment explanation
Indices: 323407--323544 Score: 206
Period size: 51 Copynumber: 2.7 Consensus size: 51
323397 TCTGGAAAGA
323407 AAATGTATTGATACATTTTT-ATTGTATCGATACATTCTGAGTTTTGATCC
1 AAATGTATTGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
* *
323457 AAATGTGTTGATACATTTTTCATTGTATCGATACATTCTGGGTTTTGATCC
1 AAATGTATTGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
* ** * *
323508 AAATATATCAATATATTATTCATTGTATCGATACATT
1 AAATGTATTGATACATTTTTCATTGTATCGATACATT
323545 ATTCATTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 19 0.24
51 60 0.76
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (51 bp):
AAATGTATTGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
Found at i:323545 original size:20 final size:20
Alignment explanation
Indices: 323522--323564 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
323512 ATATCAATAT
323522 ATTATTCATTGTATCGATAC
1 ATTATTCATTGTATCGATAC
*
323542 ATTATTCATTGTATTGATAC
1 ATTATTCATTGTATCGATAC
323562 ATT
1 ATT
323565 CTGGGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTATTCATTGTATCGATAC
Found at i:327228 original size:166 final size:166
Alignment explanation
Indices: 327002--327623 Score: 541
Period size: 166 Copynumber: 3.7 Consensus size: 166
326992 CTTGCTACTC
* *
327002 CATAAATGTTTTCGAGG-GGATTTTTC-ACGATTTAAAATTTTTAAAATTCATCAAATATCATCA
1 CATAAATGTTTT-TAGGAGAATTTTTCTA-GATTTAAAATTTTTAAAATTCATCAAATATCATCA
** *
327065 TTTAATTCATAGTAAAGAAATTTTGAAAAATTCATTTTTTTTCTTAAGTTTTTCATTTTTTCCTT
64 TTTAATTCATAGTAAATCAGTTTTGAAAAATTCATTTTTTTTCTTAAGTTTTTCATTTTTTCCTT
* *
327130 GAAA-TCTCATTATTTCCGAAAAATGAAGTTTTCTACTT
129 AAAATTCTC-TTATTTCCGAAAAATGAAGTTTTCTATTT
* * * ** *
327168 CACAAATGTTTTTAGGAGAATTTTTCTCGGTTTAAAATTTTTAAAATAAATCAGATATCATCATT
1 CATAAATGTTTTTAGGAGAATTTTTCTAGATTTAAAATTTTTAAAATTCATCAAATATCATCATT
* * * * * * * *
327233 TAATTTATATTAAATCAGTTTTAAAAAATTTATTTATTTTCATGAA-TTTTTCTTTTTTTTCTTA
66 TAATTCATAGTAAATCAGTTTTGAAAAATTCATTTTTTTTC-TTAAGTTTTTCATTTTTTCCTTA
* * * * *
327297 AAATTTTCTTGTTCCCAAAAAATCAAGTTTTCTATTT
130 AAATTCTCTTATTTCCGAAAAATGAAGTTTTCTATTT
** * * * * * * *
327334 CATAAATGTTTTCGGGGGGATTTTTCTAGATTTAACATTTTTAACATTCACCAAATATCATTAAT
1 CATAAATGTTTTTAGGAGAATTTTTCTAGATTTAAAATTTTTAAAATTCATCAAATATCATCATT
* ** * * * * *
327399 TAATTCATAGCAAATCAGTTTTGAAATTTTCATTCATTTGT-ATGAGTTTTTTTATTTTTTTCCT
66 TAATTCATAGTAAATCAGTTTTGAAAAATTCATT-TTTTTTCTTAAG-TTTTTCA-TTTTTTCCT
*
327463 TAAAATTCTCCTA-TTCTCGAAAAATCG-AGTTTTCTATTT
128 TAAAATTCTCTTATTTC-CGAAAAAT-GAAGTTTTCTATTT
* * **
327502 CATAAATGTTTTTTA-GAGAATTTTTCTAGGTTTAAAATTTTT--AATTCATCTAATATTGTCAT
1 CATAAATG-TTTTTAGGAGAATTTTTCTAGATTTAAAATTTTTAAAATTCATCAAATATCATCAT
* * * * * * *
327564 TAAATATGCAT--TAAATTAGTTTTGCAAAATTGATTTTATTTT-ATGAGTTTTACATTTTTT
65 TTAAT-T-CATAGTAAATCAGTTTTGAAAAATTCATTTT-TTTTCTTAAGTTTTTCATTTTTT
327624 TCATAAGATA
Statistics
Matches: 355, Mismatches: 87, Indels: 30
0.75 0.18 0.06
Matches are distributed among these distances:
164 6 0.02
165 10 0.03
166 247 0.70
167 17 0.05
168 71 0.20
169 4 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (166 bp):
CATAAATGTTTTTAGGAGAATTTTTCTAGATTTAAAATTTTTAAAATTCATCAAATATCATCATT
TAATTCATAGTAAATCAGTTTTGAAAAATTCATTTTTTTTCTTAAGTTTTTCATTTTTTCCTTAA
AATTCTCTTATTTCCGAAAAATGAAGTTTTCTATTT
Found at i:327624 original size:332 final size:331
Alignment explanation
Indices: 327002--327625 Score: 753
Period size: 332 Copynumber: 1.9 Consensus size: 331
326992 CTTGCTACTC
* *
327002 CATAAATGTTTTCGAGGGGATTTTTCACGATTTAAAATTTTTAAAATTCATCAAATATCATCATT
1 CATAAATGTTTTCGAGGGGATTTTTCACGATTTAAAATTTTTAAAATTCACCAAATATCATCAAT
* * * * *
327067 TAATTCATAGTAAAGAAATTTTGAAAAATTCATTTTTTTTCTTAAGTTTTTCATTTTTTCCTTGA
66 TAATTCATAGCAAAGAAATTTTGAAAAATTCATTATTTGTCATAAGTTTTTCATTTTTTCCTTAA
* *
327132 AATCTCATTATTTCCGAAAAATGAAGTTTTCTACTTCACAAATGTTTTTAGGAGAATTTTTCTCG
131 AATCTCACTATTTCCGAAAAATGAAGTTTTCTACTTCACAAATGTTTTTAGGAGAATTTTTCTAG
* * *
327197 GTTTAAAATTTTTAAAATAAATCAGATATCATCATTTAATTTATATTAAATCAGTTTTAAAAAAT
196 GTTTAAAATTTTT-AAATAAATCAGATATCATCATTAAATATACATTAAATCAGTTTTAAAAAAT
* * *
327262 TTATTTATTTTCATGAATTTTTCTTTTTTTTCTTAAAATTTTCTTGTTCCCAAAAAATCAAGTTT
260 TGATTTATTTTCATGAATTTTACATTTTTTTCTTAAAATTTTCTTGTTCCCAAAAAATCAAGTTT
327327 TCTATTT
325 TCTATTT
* * * *
327334 CATAAATGTTTTCGGGGGGATTTTTCTA-GATTTAACATTTTTAACATTCACCAAATATCATTAA
1 CATAAATGTTTTCGAGGGGATTTTTC-ACGATTTAAAATTTTTAAAATTCACCAAATATCATCAA
** * ** * *
327398 TTAATTCATAGCAAATCAGTTTTGAAATTTTCATTCATTTGT-ATGAGTTTTTTTATTTTTTTCC
65 TTAATTCATAGCAAAGAAATTTTGAAAAATTCATT-ATTTGTCATAAG-TTTTTCA-TTTTTTCC
* *
327462 TTAAAATTCTC-CTA-TTCTCGAAAAATCG-AGTTTTCTATTTCATAAATGTTTTTTA-GAGAAT
127 TTAAAA-TCTCACTATTTC-CGAAAAAT-GAAGTTTTCTACTTCACAAATG-TTTTTAGGAGAAT
** ** * *
327523 TTTTCTAGGTTTAAAATTTTT-AATTCATCTA-ATATTGTCATTAAATATGCATTAAATTAGTTT
188 TTTTCTAGGTTTAAAATTTTTAAATAAATC-AGATATCATCATTAAATATACATTAAATCAGTTT
** *
327586 TGCAAAATTGATTTTATTTT-ATGAGTTTTACATTTTTTTC
252 TAAAAAATTGA-TTTATTTTCATGAATTTTACATTTTTTTC
327626 ATAAGATAAT
Statistics
Matches: 245, Mismatches: 37, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
332 144 0.59
333 23 0.09
334 67 0.27
335 11 0.04
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (331 bp):
CATAAATGTTTTCGAGGGGATTTTTCACGATTTAAAATTTTTAAAATTCACCAAATATCATCAAT
TAATTCATAGCAAAGAAATTTTGAAAAATTCATTATTTGTCATAAGTTTTTCATTTTTTCCTTAA
AATCTCACTATTTCCGAAAAATGAAGTTTTCTACTTCACAAATGTTTTTAGGAGAATTTTTCTAG
GTTTAAAATTTTTAAATAAATCAGATATCATCATTAAATATACATTAAATCAGTTTTAAAAAATT
GATTTATTTTCATGAATTTTACATTTTTTTCTTAAAATTTTCTTGTTCCCAAAAAATCAAGTTTT
CTATTT
Found at i:337264 original size:9 final size:9
Alignment explanation
Indices: 337235--337265 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
337225 TAAGTCAATT
337235 TCTTCATCA
1 TCTTCATCA
*
337244 TCATCATCA
1 TCTTCATCA
337253 TCTTCATCA
1 TCTTCATCA
337262 TCTT
1 TCTT
337266 TAACGGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (9 bp):
TCTTCATCA
Found at i:338872 original size:20 final size:20
Alignment explanation
Indices: 338847--338899 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
338837 GTTGGGCACA
*
338847 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-CC
338867 ATGTATCGATACAATGTCCC
1 ATGTATCGATACAATGTCCC
338887 ATGTATCGATACA
1 ATGTATCGATACA
338900 TTCACTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:338972 original size:19 final size:19
Alignment explanation
Indices: 338927--338978 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
338917 CTGCCAGTTT
338927 CATGTATCGATACAATTTGG
1 CATGTATCGATACAA-TTGG
*
338947 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTG-G
338966 CATGTATCGATAC
1 CATGTATCGATAC
338979 GCATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATTGG
Found at i:339120 original size:20 final size:21
Alignment explanation
Indices: 339095--339135 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
339085 ACTTTAAAGT
339095 AATTTAA-CTTGAAAACATTC
1 AATTTAAGCTTGAAAACATTC
*
339115 AATTTAAGGTTTGAAAACATT
1 AATTTAA-GCTTGAAAACATT
339136 TATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
AATTTAAGCTTGAAAACATTC
Found at i:340218 original size:13 final size:14
Alignment explanation
Indices: 340200--340229 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
340190 TGTTATTAAA
340200 AAATTTTAAATT-T
1 AAATTTTAAATTCT
340213 AAATTTTAAATTCT
1 AAATTTTAAATTCT
340227 AAA
1 AAA
340230 ACAACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTTAAATTCT
Found at i:344399 original size:38 final size:39
Alignment explanation
Indices: 344324--344402 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
344314 TAAAATTGAT
* * * *
344324 TATTTGAATTTATTATTCGTACGTAAAATATGAATTTAAA
1 TATTTAAATTTATTATTCATAC-AAAAATATAAATTTAAA
344364 TATTTAAATTTATTATTCATA-AAAAATATAAATTTAAA
1 TATTTAAATTTATTATTCATACAAAAATATAAATTTAAA
344402 T
1 T
344403 TCGTATCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 16 0.46
40 19 0.54
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (39 bp):
TATTTAAATTTATTATTCATACAAAAATATAAATTTAAA
Found at i:345007 original size:24 final size:25
Alignment explanation
Indices: 344968--345016 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
344958 ATTATAAAAT
*
344968 CTTAATCTCTAAACCCCAAT-TTGA
1 CTTAATCTCTAAACCCAAATCTTGA
* *
344992 CTTAATCTTTAGACCCAAATCTTGA
1 CTTAATCTCTAAACCCAAATCTTGA
345017 TTGAAACCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (25 bp):
CTTAATCTCTAAACCCAAATCTTGA
Found at i:346117 original size:24 final size:24
Alignment explanation
Indices: 346084--346137 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
346074 TTAGGCACTG
*
346084 GTAACACAGCCGGTTCAAACCATA
1 GTAACCCAGCCGGTTCAAACCATA
346108 GTAACCCAGCCGGTTCAAACCATA
1 GTAACCCAGCCGGTTCAAACCATA
346132 GTAACC
1 GTAACC
346138 AGGCTCGCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (24 bp):
GTAACCCAGCCGGTTCAAACCATA
Found at i:350641 original size:24 final size:25
Alignment explanation
Indices: 350595--350683 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 25
350585 GTCCTTTAAT
350595 TAAAAAATTTTAAATATTAAATAAA
1 TAAAAAATTTTAAATATTAAATAAA
* * *
350620 TAAATAATTTT-ATTATTAAATATGTA
1 TAAAAAATTTTAAATATTAAATA--AA
* * *
350646 TTAAAAATATTAAATATTTAATAAA
1 TAAAAAATTTTAAATATTAAATAAA
*
350671 -AAAATATATTTAA
1 TAAAAAAT-TTTAA
350684 TCACATAATA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
24 15 0.31
25 15 0.31
26 9 0.19
27 9 0.19
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (25 bp):
TAAAAAATTTTAAATATTAAATAAA
Found at i:350656 original size:20 final size:20
Alignment explanation
Indices: 350633--350672 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
350623 ATAATTTTAT
*
350633 TATTAAATATGTATTAAAAA
1 TATTAAATATGTAATAAAAA
*
350653 TATTAAATATTTAATAAAAA
1 TATTAAATATGTAATAAAAA
350673 AATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TATTAAATATGTAATAAAAA
Found at i:352047 original size:6 final size:6
Alignment explanation
Indices: 352030--352062 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
352020 TATAAAAAAA
352030 TTAAATT TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TT
352063 GATTTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:352151 original size:22 final size:21
Alignment explanation
Indices: 352118--352161 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
352108 ATTAAAAAAA
352118 ATTATTTTTAT-ATTAAAATTT
1 ATTATTTTTATAATT-AAATTT
352139 ATTATATTTTATAATTAAATTT
1 ATTAT-TTTTATAATTAAATTT
352161 A
1 A
352162 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 13 0.62
23 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTTTTATAATTAAATTT
Found at i:356939 original size:11 final size:11
Alignment explanation
Indices: 356909--356947 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
356899 ATACTTGAGT
356909 TTTTTCTTTCTC
1 TTTTTCTTT-TC
*
356921 TCTTTCTTTTC
1 TTTTTCTTTTC
*
356932 TTTTTCTTTTG
1 TTTTTCTTTTC
356943 TTTTT
1 TTTTT
356948 GCTTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:360643 original size:33 final size:33
Alignment explanation
Indices: 360601--360665 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
360591 TGTTACAAGC
*
360601 AATGTATCGATACAAT-TCATCATGTATCGATAT
1 AATGTATCGATACAATAT-ACCATGTATCGATAT
360634 AATGTATCGATACAATATACCATGTATCGATA
1 AATGTATCGATACAATATACCATGTATCGATA
360666 CAAACAGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACAATATACCATGTATCGATAT
Found at i:360722 original size:20 final size:20
Alignment explanation
Indices: 360697--360756 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
360687 CTGCCAGTTT
360697 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
*
360717 CATGTATCGATACAATGAT-
1 CATGTATCGATACAATTATC
360736 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
360757 GATACAAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:360741 original size:19 final size:19
Alignment explanation
Indices: 360696--360752 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
360686 ACTGCCAGTT
*
360696 TCATGTATCGATACAATTA
1 TCATGTATCGATACAATGA
360715 TCCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
360735 TCATGTATCGATACAATG
1 TCATGTATCGATACAATG
360753 TATCGATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:360755 original size:13 final size:13
Alignment explanation
Indices: 360737--360763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
360727 TACAATGATC
360737 ATGTATCGATACA
1 ATGTATCGATACA
360750 ATGTATCGATACA
1 ATGTATCGATACA
360763 A
1 A
360764 AGCATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:360759 original size:32 final size:33
Alignment explanation
Indices: 360718--360782 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
360708 ACAATTATCC
* * *
360718 ATGTATCGATACAATG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGCATAATATATCGATACA
360750 ATGTATCGATACAAAGCATAATATATCGATACA
1 ATGTATCGATACAAAGCATAATATATCGATACA
360783 TTTAGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATATATCGATACA
Found at i:363160 original size:13 final size:13
Alignment explanation
Indices: 363141--363179 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
363131 ACTATTTATG
363141 ATGTATCGATACA
1 ATGTATCGATACA
*
363154 CTGTATCGATACA
1 ATGTATCGATACA
363167 ATGTATCGATACA
1 ATGTATCGATACA
363180 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363266 original size:21 final size:22
Alignment explanation
Indices: 363240--363291 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
363230 TGACCTATGG
*
363240 ACAGTGATGTATCGATGCATGA
1 ACAGTGATGTATCGATACATGA
363262 A-AGTGATGTATCGATACATGA
1 ACAGTGATGTATCGATACATGA
363283 ACAGTGATG
1 ACAGTGATG
363292 AACAGTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (22 bp):
ACAGTGATGTATCGATACATGA
Found at i:363389 original size:53 final size:53
Alignment explanation
Indices: 363323--363459 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
363313 CTACTACCAA
363323 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
* * *
363376 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
363429 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
363460 TATACAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
Found at i:363492 original size:20 final size:19
Alignment explanation
Indices: 363447--363499 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
363437 TACATATTTG
363447 TGTGTATCGATACTATACAA
1 TGTGTATCGATA-TATACAA
*
363467 TCTGTATCGATATATTTA-AA
1 TGTGTATCGATATA--TACAA
363487 TGTGTATCGATAT
1 TGTGTATCGATAT
363500 TTTTCAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTGTATCGATATATACAA
Found at i:363563 original size:21 final size:21
Alignment explanation
Indices: 363539--363579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
363529 GTCAACTTTG
363539 TGTATTAATACTAATA-GTATA
1 TGTATTAATAC-AATACGTATA
*
363560 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
363580 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:364232 original size:16 final size:17
Alignment explanation
Indices: 364182--364250 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 17
364172 ATTTAAACTT
*
364182 AAAAT-ATATAAAAATC
1 AAAATAATATAAAATTC
* * * *
364198 AAAATGATCT-GAATCC
1 AAAATAATATAAAATTC
*
364214 AAAATAAT-TCAAATTC
1 AAAATAATATAAAATTC
364230 AAAATAATATAAAATT-
1 AAAATAATATAAAATTC
364246 AAAAT
1 AAAAT
364251 CATTAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 1 0.02
16 32 0.76
17 9 0.21
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATAATATAAAATTC
Found at i:364544 original size:18 final size:17
Alignment explanation
Indices: 364500--364537 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
364490 AGATTTTCGT
364500 TTTAA-TAAAAAGATTA
1 TTTAAGTAAAAAGATTA
364516 TTTAAGTAAAAA-ATTA
1 TTTAAGTAAAAAGATTA
364532 TGTTAA
1 T-TTAA
364538 CTTAAAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
TTTAAGTAAAAAGATTA
Found at i:364748 original size:2 final size:2
Alignment explanation
Indices: 364741--364776 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
364731 CTTGTGACCC
364741 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
364777 TCATCTCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:368625 original size:29 final size:30
Alignment explanation
Indices: 368583--368656 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
368573 TTCTGGTTCC
* * *
368583 AAAA-TTTTGTTACTTTCTTTTTTG-TTAA
1 AAAACTTTTGATACTTTCTTTGTTGATGAA
368611 AAAACTTTTGATACTTTCTTTGTTGATGAA
1 AAAACTTTTGATACTTTCTTTGTTGATGAA
368641 AAAACTTTTGATACTT
1 AAAACTTTTGATACTT
368657 CTTATAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.10
29 18 0.44
30 19 0.46
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (30 bp):
AAAACTTTTGATACTTTCTTTGTTGATGAA
Found at i:378219 original size:13 final size:13
Alignment explanation
Indices: 378201--378226 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
378191 CACATCCAGA
378201 TGTATCGATACAT
1 TGTATCGATACAT
378214 TGTATCGATACAT
1 TGTATCGATACAT
378227 GATCATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:378238 original size:19 final size:19
Alignment explanation
Indices: 378210--378264 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
378200 ATGTATCGAT
378210 ACATTGTATCGATACAT-G
1 ACATTGTATCGATACATGG
*
378228 ATCATTATATCGATACATGG
1 A-CATTGTATCGATACATGG
378248 ACAATTGTATCGATACA
1 AC-ATTGTATCGATACA
378265 CGAAACTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 15 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:378313 original size:13 final size:13
Alignment explanation
Indices: 378295--378343 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
378285 TTACCACTGT
378295 TTGTATCGATACA
1 TTGTATCGATACA
378308 TTGTATCGATACA
1 TTGTATCGATACA
378321 -TG-AT-G--A-A
1 TTGTATCGATACA
378328 TTGTATCGATACA
1 TTGTATCGATACA
378341 TTG
1 TTG
378344 CTTGTAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 3 0.10
9 2 0.07
10 2 0.07
11 2 0.07
12 3 0.10
13 17 0.57
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:382308 original size:18 final size:18
Alignment explanation
Indices: 382269--382309 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
382259 GAACTTTAGT
**
382269 TGTTGAAGAATCAATTGT
1 TGTTGAAGAATCAATTCA
382287 TGTTGAAGAATCAATTCA
1 TGTTGAAGAATCAATTCA
382305 TGTTG
1 TGTTG
382310 TTTTTGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (18 bp):
TGTTGAAGAATCAATTCA
Found at i:382311 original size:21 final size:18
Alignment explanation
Indices: 382267--382302 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
382257 AAGAACTTTA
382267 GTTGTTGAAGAATCAATT
1 GTTGTTGAAGAATCAATT
382285 GTTGTTGAAGAATCAATT
1 GTTGTTGAAGAATCAATT
382303 CATGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
GTTGTTGAAGAATCAATT
Found at i:385694 original size:21 final size:21
Alignment explanation
Indices: 385661--385701 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
385651 CTAAGTAAAA
385661 ATACATATTGTATCAATACAT
1 ATACATATTGTATCAATACAT
*
385682 ATAC-TATTGGTATTAATACA
1 ATACATATT-GTATCAATACA
385702 CAAAGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (21 bp):
ATACATATTGTATCAATACAT
Found at i:385863 original size:53 final size:53
Alignment explanation
Indices: 385782--385916 Score: 243
Period size: 53 Copynumber: 2.5 Consensus size: 53
385772 GATTGCATAG
385782 ATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGT
1 ATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGT
*
385836 ATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTTGT
1 ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGT
*
385889 ATCGATACACAAAATATGTATCGATACA
1 ATCGATACACACAATATGTATCGATACA
385917 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.85
54 12 0.15
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (53 bp):
ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGT
Found at i:385982 original size:21 final size:22
Alignment explanation
Indices: 385948--385999 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
385938 TTTCACTGTT
*
385948 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGCATCGATA
385970 CATCACT-TTCATGCATCGATA
1 CATCACTGTTCATGCATCGATA
385991 CATCACTGT
1 CATCACTGT
386000 CCATAGGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (22 bp):
CATCACTGTTCATGCATCGATA
Found at i:386092 original size:13 final size:13
Alignment explanation
Indices: 386074--386112 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
386064 TCACTATTCA
386074 TGTATCGATACAT
1 TGTATCGATACAT
*
386087 TGTATCGATACAG
1 TGTATCGATACAT
386100 TGTATCGATACAT
1 TGTATCGATACAT
386113 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:386644 original size:34 final size:35
Alignment explanation
Indices: 386581--386647 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
386571 CTAAGTGATT
386581 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
386617 GAGAGGTTTCTATCTTAGTC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
386648 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:388507 original size:13 final size:13
Alignment explanation
Indices: 388489--388515 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
388479 ATATTATGCT
388489 TTGTATCGATACA
1 TTGTATCGATACA
388502 TTGTATCGATACA
1 TTGTATCGATACA
388515 T
1 T
388516 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:388524 original size:19 final size:18
Alignment explanation
Indices: 388499--388556 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
388489 TTGTATCGAT
388499 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
388517 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
388537 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
388556 A
1 A
388557 AACTGGCAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:388530 original size:32 final size:33
Alignment explanation
Indices: 388470--388534 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
388460 CACACCTAGA
* * *
388470 TGTATCGATATATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
388503 TGTATCGATACATGAT-CATTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
388535 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGATGCATTGTATCGATACAT
Found at i:388545 original size:20 final size:20
Alignment explanation
Indices: 388500--388555 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
388490 TGTATCGATA
388500 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
388519 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
388538 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
388556 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:391524 original size:34 final size:35
Alignment explanation
Indices: 391461--391527 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
391451 CTAAGTGATT
391461 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
391497 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
391528 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:395129 original size:52 final size:52
Alignment explanation
Indices: 394932--395115 Score: 332
Period size: 52 Copynumber: 3.5 Consensus size: 52
394922 TCCCGAAATA
394932 GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
1 GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
394984 GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
1 GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
** *
395036 GGAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTG
1 GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
*
395088 GGCAAATTTGCCTGCATGTATCGATACA
1 GGAAAATTTGCCTGCATGTATCGATACA
395116 AAGATCAGTG
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 128 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (52 bp):
GGAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTG
Found at i:395225 original size:33 final size:33
Alignment explanation
Indices: 395188--395254 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
395178 AGTAGCTTGA
395188 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
395221 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
395254 A
1 A
395255 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:395228 original size:13 final size:13
Alignment explanation
Indices: 395210--395234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
395200 CAAAAAAATA
395210 TGTATCGATACAT
1 TGTATCGATACAT
395223 TGTATCGATACA
1 TGTATCGATACA
395235 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:396003 original size:13 final size:14
Alignment explanation
Indices: 395974--396006 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
395964 TAATTAAACA
395974 TTTTATGATATTGT
1 TTTTATGATATTGT
395988 TTTTATGATATT-T
1 TTTTATGATATTGT
396001 TTTTAT
1 TTTTAT
396007 TTTAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (14 bp):
TTTTATGATATTGT
Found at i:398689 original size:17 final size:17
Alignment explanation
Indices: 398669--398702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
398659 TTACATTTCA
398669 TAATTTAAATTTATTTT
1 TAATTTAAATTTATTTT
**
398686 TAATTTATTTTTATTTT
1 TAATTTAAATTTATTTT
398703 AATATGATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATTTAAATTTATTTT
Found at i:402373 original size:170 final size:170
Alignment explanation
Indices: 402183--402524 Score: 612
Period size: 170 Copynumber: 2.0 Consensus size: 170
402173 CGAGATTTTT
*
402183 TTACAAAATTTTAAGAAGTTGATCGTCATCATGTAATTTACATTGATATGCATTTTGAAAAATAA
1 TTACAAAAATTTAAGAAGTTGATCGTCATCATGTAATTTACATTGATATGCATTTTGAAAAATAA
* * *
402248 AAAATATTCAATGAAAAATACGTATTGATATTTTCACCATAAGATTTTAAATTGTCAATTTTGTT
66 AAAATATTCAATAAAAAATACGTATTGATATTTTCACCATAAGATGTCAAATTGTCAATTTTGTT
*
402313 AATTAATTTGAAAATTTTTATAGTATTGTTAGTATTATGC
131 AATTAATTTGAAAATTTTCATAGTATTGTTAGTATTATGC
*
402353 TTACAAAAATTTAGGAAGTTGATCGTCATCATGTAATTTACATTGATATGCATTTTGAAAAATAA
1 TTACAAAAATTTAAGAAGTTGATCGTCATCATGTAATTTACATTGATATGCATTTTGAAAAATAA
* *
402418 AAAATATTCAATAAAAAATACGTATTGGTATTTTCACCGTAAGATGTCAAATTGTCAATTTTGTT
66 AAAATATTCAATAAAAAATACGTATTGATATTTTCACCATAAGATGTCAAATTGTCAATTTTGTT
402483 AATTAATTTGAAAATTTTCATAGTATTGTTAGTATTATGC
131 AATTAATTTGAAAATTTTCATAGTATTGTTAGTATTATGC
402523 TT
1 TT
402525 GTAAAATGTT
Statistics
Matches: 164, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
170 164 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (170 bp):
TTACAAAAATTTAAGAAGTTGATCGTCATCATGTAATTTACATTGATATGCATTTTGAAAAATAA
AAAATATTCAATAAAAAATACGTATTGATATTTTCACCATAAGATGTCAAATTGTCAATTTTGTT
AATTAATTTGAAAATTTTCATAGTATTGTTAGTATTATGC
Found at i:402911 original size:24 final size:24
Alignment explanation
Indices: 402872--402936 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 24
402862 TTTAAACTTT
402872 TTAAAATTTATTAAA-TAATTTCA
1 TTAAAATTTATTAAATTAATTTCA
*
402895 TTAAATTTATATTAAATTAATTT--
1 TTAAAATT-TATTAAATTAATTTCA
402918 TTAAAA---ATTAAATTAATTT
1 TTAAAATTTATTAAATTAATTT
402937 ATGAGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 13 0.34
23 12 0.32
24 7 0.18
25 6 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAAATTTATTAAATTAATTTCA
Found at i:407629 original size:52 final size:52
Alignment explanation
Indices: 407559--407679 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
407549 GAAAATTTAT
*
407559 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
407611 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
407663 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
407680 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:407692 original size:52 final size:51
Alignment explanation
Indices: 407559--407699 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
407549 GAAAATTTAT
407559 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
407611 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
407663 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
407700 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:407706 original size:13 final size:13
Alignment explanation
Indices: 407688--407712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407678 CAAAGATCAG
407688 TGTATCGATACAA
1 TGTATCGATACAA
407701 TGTATCGATACA
1 TGTATCGATACA
407713 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:407795 original size:13 final size:13
Alignment explanation
Indices: 407777--407801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407767 CAAAAAAATA
407777 TGTATCGATACAT
1 TGTATCGATACAT
407790 TGTATCGATACA
1 TGTATCGATACA
407802 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:407797 original size:33 final size:33
Alignment explanation
Indices: 407755--407821 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
407745 AGTAGCTTAA
407755 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
407788 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
407821 A
1 A
407822 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:408906 original size:49 final size:49
Alignment explanation
Indices: 408697--410081 Score: 1818
Period size: 49 Copynumber: 28.7 Consensus size: 49
408687 AAAAGGATGT
408697 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
408749 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
408792 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
408840 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
408889 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
408938 CAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAATGGTGCAA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGC
* *
408986 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
409035 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
409084 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
409133 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409176 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
409225 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409268 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409317 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
409369 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
409412 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409460 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
409509 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
409558 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
409607 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACCT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
409658 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409707 CAATGTGCTGATTCAAGGCCAGCTTA-ATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGGTGC
* * *
409756 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
409805 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
409856 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
409899 CAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
409948 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
409997 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
410046 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
410082 GAAGGGTTGC
Statistics
Matches: 1168, Mismatches: 118, Indels: 97
0.84 0.09 0.07
Matches are distributed among these distances:
43 190 0.16
45 2 0.00
47 2 0.00
48 145 0.12
49 673 0.58
50 3 0.00
51 78 0.07
52 75 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:409706 original size:198 final size:198
Alignment explanation
Indices: 409260--410081 Score: 1315
Period size: 198 Copynumber: 4.2 Consensus size: 198
409250 TATTGGACTT
* * *
409260 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTTGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
409325 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCA
409390 GCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
128 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
*
409449 TGGTGG-
193 -GATGGA
* * *
409455 ---GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
409517 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
*
409582 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACCTAAGAT
131 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
409647 GGA
196 GGA
409650 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
409715 TGATTCAAGGCCAGCTTA-ATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGC
66 TGAGTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGC
409779 GATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGA
130 GATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGA
409844 TGGA
195 TGGA
*
409848 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
409907 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
409972 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA-A-
131 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
410035 -GA
196 GGA
*
410037 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
410082 GAAGGGTTGC
Statistics
Matches: 597, Mismatches: 16, Indels: 32
0.93 0.02 0.05
Matches are distributed among these distances:
189 43 0.07
190 42 0.07
191 4 0.01
192 227 0.38
193 1 0.00
194 5 0.01
195 43 0.07
198 230 0.39
199 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (198 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
GGA
Found at i:409984 original size:241 final size:239
Alignment explanation
Indices: 408688--410081 Score: 1870
Period size: 241 Copynumber: 5.8 Consensus size: 239
408678 AGATGATGAA
* *
408688 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
408753 ATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
62 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
408812 AGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
127 AGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
* * * *
408876 AAGATGAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
192 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * * * * *
408930 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAATGGTGCAA-GTGCCAATGTG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGGTGCCAATATG
* * * *
408993 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGC
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGC
* * *
409058 TATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG
130 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG
* * *
409123 ATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
195 ATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
409168 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
409233 TGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
*
409292 ACATTGGACTTAAAGTTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
*
409357 TGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
196 T-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * ** *
409404 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT-GGGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* * *
409468 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
* * * * *
409533 ACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
* * *
409598 TGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACCTAAGAT
196 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-CT----T
* * * *
409647 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 ---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
* *
409712 TGCTGATTCAAGGCCAGCT-TAATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
63 TGCTGATTCAAGGCCAGCTAT-ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
409776 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-
127 AGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
409840 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
192 AAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
409891 AAAGGTGCCAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
409956 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
* * * * *
410021 ACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
410082 GAAGGGTTGC
Statistics
Matches: 1023, Mismatches: 96, Indels: 66
0.86 0.08 0.06
Matches are distributed among these distances:
233 93 0.09
234 1 0.00
235 37 0.04
236 86 0.08
237 35 0.03
238 77 0.08
239 44 0.04
240 8 0.01
241 294 0.29
242 6 0.01
243 48 0.05
244 81 0.08
246 49 0.05
247 126 0.12
248 2 0.00
249 36 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (239 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
TGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:410125 original size:33 final size:33
Alignment explanation
Indices: 410081--410153 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
410071 TATTGGGCTT
410081 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
410114 AGAAGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
410147 A-AAGGGT
1 AGAAGGGT
410154 GAAAGATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:410265 original size:34 final size:34
Alignment explanation
Indices: 410155--410931 Score: 799
Period size: 33 Copynumber: 23.1 Consensus size: 34
410145 AGAAAGGGTG
* * * *
410155 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
410188 CAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAA-GG-AA
410224 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
*
410258 AAAGAGTGCCACGAAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
*
410292 AAAGAGTGCCACAGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
410326 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* * *
410359 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
410393 AAAGAATGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* * *
410426 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
* * *
410459 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
410492 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-GGAA
* * *
410529 AAAGGGTGCCACAGAGTTGTGGGCTTTAAA-AAGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGA-A
*
410563 AAAGAGTGCCACGGAATTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* *
410596 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
410629 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-GGAA
*
410666 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-GGAA
* *
410701 GAAG-GTGCCATGGAGTTGTGGGCTTT-------
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
410727 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAA
*
410764 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-GGAA
*
410799 AAAG-GTACCACGGAGTTGTGGGCTTT----G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
410826 -AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAA
* *
410862 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
* * *
410896 CAAG-GTGCCACAGAGTTGTGGGCTTTAAAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
410929 AAA
1 AAA
410932 TACCACTAAG
Statistics
Matches: 644, Mismatches: 55, Indels: 90
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.01
27 40 0.06
29 1 0.00
32 1 0.00
33 217 0.34
34 208 0.32
35 36 0.06
36 12 0.02
37 123 0.19
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
Found at i:410605 original size:137 final size:134
Alignment explanation
Indices: 410155--410924 Score: 814
Period size: 137 Copynumber: 5.7 Consensus size: 134
410145 AGAAAGGGTG
* *
410155 AAAGA-TGCCAC-GAAGTTGTGGACTTAAAAAGAACAA-AGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAA-TTGTGGGCTT-AAAGGAA-AAGAGTGCCACGGAGTTGTGGGCTTT-AA
* *
410217 AGGGAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGG
62 A-GG--AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGG
* *
410281 C-TTAGAAGGAA
124 CTTTAAAAAG-A
* *
410292 AAAGAGTGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAA
1 AAAGAGTGCCACGGAATTGTGGGCTTA-AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTTA-AA
* * *
410356 GGAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAA-GAAAAAGAATGCCACGGAGTTGTGGGC-TT
63 GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
410419 AGAAGGA
128 AAAAAGA
* * * * *
410426 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCATGTAATTGTGGGCTTTAAAGG
1 AAAGAGTGCCACGGAATTGTGGGC-TTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
* *
410491 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGGTGCCACAGAGTTGTGGGCTTT
65 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
410556 AAAAAGA
128 AAAAAGA
* *
410563 AAAGAGTGCCACGGAATTGTGGGCTTAGAAGGAAAAGAGTGCCACGTAATTGTGGGCTTTAAAGG
1 AAAGAGTGCCACGGAATTGTGGGCTTA-AAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
410628 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
65 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
410693 AAACAGA
128 AAAAAGA
* * * *
410700 AGAAG-GTGCCATGGAGTTGTGGGCTT-----TAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAA
1 A-AAGAGTGCCACGGAATTGTGGGCTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAA
*
410759 GAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAAAAAG-GTACCACGGAGTTGTGGGC
63 G-G-AAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGC
410822 TTT-----G-
125 TTTAAAAAGA
* * * *
410826 -AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTAA
1 AAAGAGTGCCACGGAATTGTGGGC-TT--AAAG-G-AAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
410890 AAGGAACAAG-GTGCCACAGAGTTGTGGGCTTTAAA
61 AAGGAA-AAGAGTGCCACGGAGTTGTGGGCTTTAAA
410925 GAAAAAATAC
Statistics
Matches: 559, Mismatches: 42, Indels: 70
0.83 0.06 0.10
Matches are distributed among these distances:
124 3 0.01
125 17 0.03
126 2 0.00
127 1 0.00
131 50 0.09
132 25 0.04
133 67 0.12
134 36 0.06
135 112 0.20
136 32 0.06
137 163 0.29
138 27 0.05
139 24 0.04
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (134 bp):
AAAGAGTGCCACGGAATTGTGGGCTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGA
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AAGA
Found at i:410753 original size:98 final size:95
Alignment explanation
Indices: 410529--410926 Score: 505
Period size: 98 Copynumber: 4.1 Consensus size: 95
410519 GAAAAGGGAA
* * * *
410529 AAAGGGTGCCACAGAGTTGTGGGCTTT-AAAA-AG-AAAAGAGTGCCACGGAATTGTGGGCTTAG
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTA-
* * *
410591 AAGGAAAAGAGTGCCACGTAATTGTGGGCTTT
65 AAAGAAAAG-GTGCCACGGAGTTGTGGGCTTT
* *
410623 AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 ------AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGG
*
410688 GCTTTAAACAGAAGAAGGTGCCATGGAGTTGTGGGCTTT
60 GC-TTAAA-AGAA-AAGGTGCCACGGAGTTGTGGGCTTT
410727 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGC-TTA
*
410792 AACAGAAAAAGGTACCACGGAGTTGTGGGCTTT
65 AA-AG-AAAAGGTGCCACGGAGTTGTGGGCTTT
* *
410825 GAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTAA
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
410890 AAGGAACAAGGTGCCACAGAGTTGTGGGCTTT
66 AA-GAA-AAGGTGCCACGGAGTTGTGGGCTTT
410922 AAAGA
1 AAAGA
410927 AAAAATACCA
Statistics
Matches: 272, Mismatches: 17, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
96 3 0.01
97 33 0.12
98 150 0.55
99 2 0.01
100 25 0.09
101 4 0.01
102 1 0.00
103 26 0.10
104 25 0.09
105 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (95 bp):
AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
AAGAAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:410847 original size:61 final size:63
Alignment explanation
Indices: 410765--410883 Score: 188
Period size: 61 Copynumber: 1.9 Consensus size: 63
410755 AAAAGAGAAA
*
410765 AAGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAAG-GTACCACGGAGTTGTGGGCTTTG
1 AAGAGTGCCACGGAGTCGTGGGCTTTAAAACAGAAAAAGAGTACCACGGAGTTGTGGGCTTTG
* *
410826 AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGG
1 AAGAGTGCCACGGAGTCGTGGGCTTT-AAAACAGAAAAAGAGTACCACGGAGTTGTGG
410884 ACTTAAAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 25 0.48
63 11 0.21
64 16 0.31
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.20
Consensus pattern (63 bp):
AAGAGTGCCACGGAGTCGTGGGCTTTAAAACAGAAAAAGAGTACCACGGAGTTGTGGGCTTTG
Found at i:410966 original size:131 final size:135
Alignment explanation
Indices: 410727--410988 Score: 322
Period size: 131 Copynumber: 2.0 Consensus size: 135
410717 TGTGGGCTTT
* *
410727 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
* * * * * * * *
410792 AACAGAAAAAGGTACCACGGAGTTGTGGGCTTTGAAGAGTGCCACGGAGTCGTGGGCTTTGAAAA
66 AACAGAAAAAGATACCACGAAGTCGTGGACTTTGAAAAATGCCACGGAGTCGTGGACTTTAAAAA
410857 GAGAA
131 GAGAA
* *
410862 AAAGAGTGCCACGGAGTTGTGGAC-TT-AAAAG-GAACAAG-GTGCCACAGAGTTGTGGGCTTT-
1 AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
* *
410922 AA-AGAAAAA-ATACCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTAA
66 AACAGAAAAAGATACCACGAAGTCGTGGACTTT--GA-AAAATGCCACGGAGTCGTGGACTTTAA
410985 AAAG
128 AAAG
410989 GTATTTGAAG
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
128 17 0.15
129 7 0.06
130 4 0.04
131 47 0.43
132 6 0.05
133 5 0.05
134 2 0.02
135 22 0.20
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (135 bp):
AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
AACAGAAAAAGATACCACGAAGTCGTGGACTTTGAAAAATGCCACGGAGTCGTGGACTTTAAAAA
GAGAA
Found at i:412348 original size:39 final size:39
Alignment explanation
Indices: 412276--412350 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
412266 GCCTTTGCAC
* **
412276 TTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTGTG
1 TTTTTTTTTGTTTTGTTTTTTTTTTATCATTTTTTTGTG
412315 TTTTTTTTTG-TTTGTTTTTTTTTTCATCATTTTTTT
1 TTTTTTTTTGTTTTGTTTTTTTTTT-ATCATTTTTTT
412351 TTAAGGGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.87
Consensus pattern (39 bp):
TTTTTTTTTGTTTTGTTTTTTTTTTATCATTTTTTTGTG
Found at i:412352 original size:1 final size:1
Alignment explanation
Indices: 412276--412338 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
412266 GCCTTTGCAC
* * * * * *
412276 TTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTGTGTTTTTTTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
412339 CATCATTTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:419275 original size:52 final size:52
Alignment explanation
Indices: 419205--419325 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
419195 GAAAATTTAT
*
419205 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
419257 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
419309 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
419326 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:419338 original size:52 final size:51
Alignment explanation
Indices: 419205--419345 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
419195 GAAAATTTAT
419205 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
419257 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
419309 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
419346 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:419352 original size:13 final size:13
Alignment explanation
Indices: 419334--419358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
419324 CAAAGATCAG
419334 TGTATCGATACAA
1 TGTATCGATACAA
419347 TGTATCGATACA
1 TGTATCGATACA
419359 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:419441 original size:13 final size:13
Alignment explanation
Indices: 419423--419447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
419413 CAAAAAAATA
419423 TGTATCGATACAT
1 TGTATCGATACAT
419436 TGTATCGATACA
1 TGTATCGATACA
419448 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:419443 original size:33 final size:33
Alignment explanation
Indices: 419401--419467 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
419391 AGTAGCTTAA
419401 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
419434 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
419467 A
1 A
419468 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:420552 original size:49 final size:49
Alignment explanation
Indices: 420343--421727 Score: 1818
Period size: 49 Copynumber: 28.7 Consensus size: 49
420333 AAAAGGATGT
420343 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
420395 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
420438 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
420486 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420535 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
420584 CAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAATGGTGCAA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGC
* *
420632 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
420681 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420730 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420779 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
420822 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420871 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
420914 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
420963 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
421015 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
421058 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
421106 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
421155 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
421204 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
421253 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACCT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
421304 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
421353 CAATGTGCTGATTCAAGGCCAGCTTA-ATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGGTGC
* * *
421402 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
421451 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
421502 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
421545 CAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
421594 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
421643 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
421692 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
421728 GAAGGGTTGC
Statistics
Matches: 1168, Mismatches: 118, Indels: 97
0.84 0.09 0.07
Matches are distributed among these distances:
43 190 0.16
45 2 0.00
47 2 0.00
48 145 0.12
49 673 0.58
50 3 0.00
51 78 0.07
52 75 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:421352 original size:198 final size:198
Alignment explanation
Indices: 420906--421727 Score: 1315
Period size: 198 Copynumber: 4.2 Consensus size: 198
420896 TATTGGACTT
* * *
420906 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTTGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
420971 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCA
421036 GCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
128 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
*
421095 TGGTGG-
193 -GATGGA
* * *
421101 ---GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
421163 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
*
421228 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACCTAAGAT
131 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
421293 GGA
196 GGA
421296 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
421361 TGATTCAAGGCCAGCTTA-ATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGC
66 TGAGTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGC
421425 GATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGA
130 GATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGA
421490 TGGA
195 TGGA
*
421494 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
421553 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
421618 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA-A-
131 ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
421681 -GA
196 GGA
*
421683 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
421728 GAAGGGTTGC
Statistics
Matches: 597, Mismatches: 16, Indels: 32
0.93 0.02 0.05
Matches are distributed among these distances:
189 43 0.07
190 42 0.07
191 4 0.01
192 227 0.38
193 1 0.00
194 5 0.01
195 43 0.07
198 230 0.39
199 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (198 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCG
ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGAT
GGA
Found at i:421630 original size:241 final size:239
Alignment explanation
Indices: 420334--421727 Score: 1870
Period size: 241 Copynumber: 5.8 Consensus size: 239
420324 AGATGATGAA
* *
420334 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
420399 ATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
62 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
420458 AGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
127 AGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
* * * *
420522 AAGATGAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
192 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * * * * *
420576 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAATGGTGCAA-GTGCCAATGTG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGGTGCCAATATG
* * * *
420639 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGC
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGC
* * *
420704 TATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG
130 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG
* * *
420769 ATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
195 ATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
420814 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
420879 TGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
*
420938 ACATTGGACTTAAAGTTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
*
421003 TGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
196 T-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * ** *
421050 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT-GGGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* * *
421114 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
* * * * *
421179 ACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
* * *
421244 TGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACCTAAGAT
196 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-CT----T
* * * *
421293 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 ---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
* *
421358 TGCTGATTCAAGGCCAGCT-TAATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
63 TGCTGATTCAAGGCCAGCTAT-ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
421422 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-
127 AGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
421486 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
192 AAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
421537 AAAGGTGCCAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
421602 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
* * * * *
421667 ACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
131 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
421728 GAAGGGTTGC
Statistics
Matches: 1023, Mismatches: 96, Indels: 66
0.86 0.08 0.06
Matches are distributed among these distances:
233 93 0.09
234 1 0.00
235 37 0.04
236 86 0.08
237 35 0.03
238 77 0.08
239 44 0.04
240 8 0.01
241 294 0.29
242 6 0.01
243 48 0.05
244 81 0.08
246 49 0.05
247 126 0.12
248 2 0.00
249 36 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (239 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
TGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:421771 original size:33 final size:33
Alignment explanation
Indices: 421727--421799 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
421717 TATTGGGCTT
421727 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
421760 AGAAGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
421793 A-AAGGGT
1 AGAAGGGT
421800 GAAAGATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:421911 original size:34 final size:34
Alignment explanation
Indices: 421801--422577 Score: 799
Period size: 33 Copynumber: 23.1 Consensus size: 34
421791 AGAAAGGGTG
* * * *
421801 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
421834 CAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAA-GG-AA
421870 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
*
421904 AAAGAGTGCCACGAAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
*
421938 AAAGAGTGCCACAGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
421972 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* * *
422005 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
422039 AAAGAATGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* * *
422072 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
* * *
422105 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
422138 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-GGAA
* * *
422175 AAAGGGTGCCACAGAGTTGTGGGCTTTAAA-AAGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGA-A
*
422209 AAAGAGTGCCACGGAATTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAA
* *
422242 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
422275 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-GGAA
*
422312 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-GGAA
* *
422347 GAAG-GTGCCATGGAGTTGTGGGCTTT-------
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
422373 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAA
*
422410 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-GGAA
*
422445 AAAG-GTACCACGGAGTTGTGGGCTTT----G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
*
422472 -AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAA
* *
422508 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
* * *
422542 CAAG-GTGCCACAGAGTTGTGGGCTTTAAAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
422575 AAA
1 AAA
422578 TACCACTAAG
Statistics
Matches: 644, Mismatches: 55, Indels: 90
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.01
27 40 0.06
29 1 0.00
32 1 0.00
33 217 0.34
34 208 0.32
35 36 0.06
36 12 0.02
37 123 0.19
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
Found at i:422251 original size:137 final size:134
Alignment explanation
Indices: 421801--422570 Score: 814
Period size: 137 Copynumber: 5.7 Consensus size: 134
421791 AGAAAGGGTG
* *
421801 AAAGA-TGCCAC-GAAGTTGTGGACTTAAAAAGAACAA-AGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAA-TTGTGGGCTT-AAAGGAA-AAGAGTGCCACGGAGTTGTGGGCTTT-AA
* *
421863 AGGGAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGG
62 A-GG--AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGG
* *
421927 C-TTAGAAGGAA
124 CTTTAAAAAG-A
* *
421938 AAAGAGTGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAA
1 AAAGAGTGCCACGGAATTGTGGGCTTA-AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTTA-AA
* * *
422002 GGAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAA-GAAAAAGAATGCCACGGAGTTGTGGGC-TT
63 GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
422065 AGAAGGA
128 AAAAAGA
* * * * *
422072 AAAGAGTGCCATGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCATGTAATTGTGGGCTTTAAAGG
1 AAAGAGTGCCACGGAATTGTGGGC-TTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
* *
422137 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGGTGCCACAGAGTTGTGGGCTTT
65 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
422202 AAAAAGA
128 AAAAAGA
* *
422209 AAAGAGTGCCACGGAATTGTGGGCTTAGAAGGAAAAGAGTGCCACGTAATTGTGGGCTTTAAAGG
1 AAAGAGTGCCACGGAATTGTGGGCTTA-AAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
422274 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
65 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
422339 AAACAGA
128 AAAAAGA
* * * *
422346 AGAAG-GTGCCATGGAGTTGTGGGCTT-----TAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAA
1 A-AAGAGTGCCACGGAATTGTGGGCTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAA
*
422405 GAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAAAAAG-GTACCACGGAGTTGTGGGC
63 G-G-AAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGC
422468 TTT-----G-
125 TTTAAAAAGA
* * * *
422472 -AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTAA
1 AAAGAGTGCCACGGAATTGTGGGC-TT--AAAG-G-AAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
422536 AAGGAACAAG-GTGCCACAGAGTTGTGGGCTTTAAA
61 AAGGAA-AAGAGTGCCACGGAGTTGTGGGCTTTAAA
422571 GAAAAAATAC
Statistics
Matches: 559, Mismatches: 42, Indels: 70
0.83 0.06 0.10
Matches are distributed among these distances:
124 3 0.01
125 17 0.03
126 2 0.00
127 1 0.00
131 50 0.09
132 25 0.04
133 67 0.12
134 36 0.06
135 112 0.20
136 32 0.06
137 163 0.29
138 27 0.05
139 24 0.04
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (134 bp):
AAAGAGTGCCACGGAATTGTGGGCTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGA
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AAGA
Found at i:422399 original size:98 final size:95
Alignment explanation
Indices: 422175--422572 Score: 505
Period size: 98 Copynumber: 4.1 Consensus size: 95
422165 GAAAAGGGAA
* * * *
422175 AAAGGGTGCCACAGAGTTGTGGGCTTT-AAAA-AG-AAAAGAGTGCCACGGAATTGTGGGCTTAG
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTA-
* * *
422237 AAGGAAAAGAGTGCCACGTAATTGTGGGCTTT
65 AAAGAAAAG-GTGCCACGGAGTTGTGGGCTTT
* *
422269 AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 ------AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGG
*
422334 GCTTTAAACAGAAGAAGGTGCCATGGAGTTGTGGGCTTT
60 GC-TTAAA-AGAA-AAGGTGCCACGGAGTTGTGGGCTTT
422373 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGC-TTA
*
422438 AACAGAAAAAGGTACCACGGAGTTGTGGGCTTT
65 AA-AG-AAAAGGTGCCACGGAGTTGTGGGCTTT
* *
422471 GAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTAA
1 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
422536 AAGGAACAAGGTGCCACAGAGTTGTGGGCTTT
66 AA-GAA-AAGGTGCCACGGAGTTGTGGGCTTT
422568 AAAGA
1 AAAGA
422573 AAAAATACCA
Statistics
Matches: 272, Mismatches: 17, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
96 3 0.01
97 33 0.12
98 150 0.55
99 2 0.01
100 25 0.09
101 4 0.01
102 1 0.00
103 26 0.10
104 25 0.09
105 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (95 bp):
AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
AAGAAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:422493 original size:61 final size:63
Alignment explanation
Indices: 422411--422529 Score: 188
Period size: 61 Copynumber: 1.9 Consensus size: 63
422401 AAAAGAGAAA
*
422411 AAGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAAG-GTACCACGGAGTTGTGGGCTTTG
1 AAGAGTGCCACGGAGTCGTGGGCTTTAAAACAGAAAAAGAGTACCACGGAGTTGTGGGCTTTG
* *
422472 AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGG
1 AAGAGTGCCACGGAGTCGTGGGCTTT-AAAACAGAAAAAGAGTACCACGGAGTTGTGG
422530 ACTTAAAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 25 0.48
63 11 0.21
64 16 0.31
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.20
Consensus pattern (63 bp):
AAGAGTGCCACGGAGTCGTGGGCTTTAAAACAGAAAAAGAGTACCACGGAGTTGTGGGCTTTG
Found at i:422612 original size:131 final size:135
Alignment explanation
Indices: 422373--422634 Score: 322
Period size: 131 Copynumber: 2.0 Consensus size: 135
422363 TGTGGGCTTT
* *
422373 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
* * * * * * * *
422438 AACAGAAAAAGGTACCACGGAGTTGTGGGCTTTGAAGAGTGCCACGGAGTCGTGGGCTTTGAAAA
66 AACAGAAAAAGATACCACGAAGTCGTGGACTTTGAAAAATGCCACGGAGTCGTGGACTTTAAAAA
422503 GAGAA
131 GAGAA
* *
422508 AAAGAGTGCCACGGAGTTGTGGAC-TT-AAAAG-GAACAAG-GTGCCACAGAGTTGTGGGCTTT-
1 AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
* *
422568 AA-AGAAAAA-ATACCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTAA
66 AACAGAAAAAGATACCACGAAGTCGTGGACTTT--GA-AAAATGCCACGGAGTCGTGGACTTTAA
422631 AAAG
128 AAAG
422635 GTATTTGAAG
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
128 17 0.15
129 7 0.06
130 4 0.04
131 47 0.43
132 6 0.05
133 5 0.05
134 2 0.02
135 22 0.20
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (135 bp):
AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
AACAGAAAAAGATACCACGAAGTCGTGGACTTTGAAAAATGCCACGGAGTCGTGGACTTTAAAAA
GAGAA
Found at i:423942 original size:14 final size:13
Alignment explanation
Indices: 423925--423987 Score: 92
Period size: 14 Copynumber: 4.8 Consensus size: 13
423915 CCTTTGCACT
423925 TTTTTTTTGTTTTG
1 TTTTTTTT-TTTTG
423939 TTTTTTTTTTTT-
1 TTTTTTTTTTTTG
*
423951 TTTTTTTTTTGTG
1 TTTTTTTTTTTTG
423964 TTTTTTTTTGTTTG
1 TTTTTTTTT-TTTG
423978 TTTTTTTTTT
1 TTTTTTTTTT
423988 CATCATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
12 11 0.24
13 14 0.31
14 20 0.44
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:423952 original size:25 final size:26
Alignment explanation
Indices: 423924--423987 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
423914 GCCTTTGCAC
* *
423924 TTTTTTTTTGTTTTGTTTTTTTTTTTT
1 TTTTTTTTTGTGTT-TTTTTTTGTTTT
423951 TTTTTTTTTTGTGTTTTTTTTTGTTTGT
1 TTTTT-TTTTGTGTTTTTTTTTGTTT-T
423979 TTTTTTTTT
1 TTTTTTTTT
423988 CATCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 19 0.58
28 14 0.42
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (26 bp):
TTTTTTTTTGTGTTTTTTTTTGTTTT
Found at i:423997 original size:40 final size:40
Alignment explanation
Indices: 423924--424000 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
423914 GCCTTTGCAC
* **
423924 TTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTTGTG
1 TTTTTTTTTGTTTTGTTTTTTTTTTATCATTTTTTTTGTG
423964 TTTTTTTTTG-TTTGTTTTTTTTTTCATCATTTTTTTT
1 TTTTTTTTTGTTTTGTTTTTTTTTT-ATCATTTTTTTT
424001 TAAGGGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.87
Consensus pattern (40 bp):
TTTTTTTTTGTTTTGTTTTTTTTTTATCATTTTTTTTGTG
Found at i:424001 original size:1 final size:1
Alignment explanation
Indices: 423924--423987 Score: 74
Period size: 1 Copynumber: 64.0 Consensus size: 1
423914 GCCTTTGCAC
* * * * * *
423924 TTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTTGTGTTTTTTTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
423988 CATCATTTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:426425 original size:155 final size:153
Alignment explanation
Indices: 426204--426751 Score: 446
Period size: 154 Copynumber: 3.5 Consensus size: 153
426194 CTAGTTTTAG
* * ** * * **
426204 GTAGTCATCGGGATGCTTTAATTTCA-AAG-GTATGCATTTAGGATAGTTTAATCGGTTTATGAT
1 GTAGTCATCGAGATGCTTTTATGCCAGAAGTGTA--CATTTAGGATAGGTTCATCCTTTTATGAT
* * * *
426267 CTTTTCGTGTCTTTTAGAGTTATCGAGATACTTTCACATTAAAGGTATATCGTAGGGGTATTTTG
64 CTTTTCGTGTCCTTTAG-GTTATCGAGATACTTTCACATCAAAGGTATATCCTAGGGGCATTTTG
* * *
426332 ATAATTTTTCTAAAATTGAGTCTTAG
128 GTAATTTTTATAAAATTGAGTCTTAA
* * *
426358 GTAGTCATTGAGTTGTTTTTATGCCAGAAGTGTACATTTAGGATAGGTTCATCCTTTTACTGATC
1 GTAGTCATCGAGATGCTTTTATGCCAGAAGTGTACATTTAGGATAGGTTCATCCTTTTA-TGATC
* * * * * *
426423 TTTTCGTATCTTTTAGGGTTATCGGGATACTTTCA-AGTCGAAA-GTTTATCTTAGAGGCATTTT
65 TTTTCGTGTCCTTTA-GGTTATCGAGATACTTTCACA-TC-AAAGGTATATCCTAGGGGCATTTT
* *
426486 GGTAATTTCTATGAAATTGAGTCTTAAA
127 GGTAATTTTTATAAAATTGAGTCTT-AA
* * *
426514 G-AGTTATCGAGATGCTTTTATACCA-AAG-GTATGCAATTAGGATAGGTTCATCCTTTTATGAT
1 GTAGTCATCGAGATGCTTTTATGCCAGAAGTGTA--CATTTAGGATAGGTTCATCCTTTTATGAT
* * * * * * * *
426576 ATTTTTGTGTCCTTTAGGATTA-CTAAGATATTTTCACATCAAAGGTACACCCTAAGAGCATTTT
64 CTTTTCGTGTCCTTTAGG-TTATC-GAGATACTTTCACATCAAAGGTATATCCTAGGGGCATTTT
* * ** ** *
426640 GGTAATTTTTTTAGAACGGAGTCCGAT
127 GGTAATTTTTATAAAATTGAGTCTTAA
* * * * * * * *
426667 GTAGTCACCGGGATGCTTTTACGCCAGAGGTGTGCATTTAGGATAGGTTTATCCATTTCTGATCT
1 GTAGTCATCGAGATGCTTTTATGCCAGAAGTGTACATTTAGGATAGGTTCATCCTTTTATGATCT
*
426732 TTTTGTGTCCTTTATGGTTA
66 TTTCGTGTCCTTTA-GGTTA
426752 CCAAAATACT
Statistics
Matches: 313, Mismatches: 64, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
153 11 0.04
154 166 0.53
155 125 0.40
156 11 0.04
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (153 bp):
GTAGTCATCGAGATGCTTTTATGCCAGAAGTGTACATTTAGGATAGGTTCATCCTTTTATGATCT
TTTCGTGTCCTTTAGGTTATCGAGATACTTTCACATCAAAGGTATATCCTAGGGGCATTTTGGTA
ATTTTTATAAAATTGAGTCTTAA
Found at i:429682 original size:23 final size:22
Alignment explanation
Indices: 429656--429707 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
429646 TTTTTTTAAA
429656 AAAATAATGAATGAAAAATCTTG
1 AAAATAAT-AATGAAAAATCTTG
* ** *
429679 AAAATACTAATGATCAATGTTG
1 AAAATAATAATGAAAAATCTTG
429701 AAAATAA
1 AAAATAA
429708 GCCTTGTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.27
Consensus pattern (22 bp):
AAAATAATAATGAAAAATCTTG
Done.