Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 91 of 170
Found at i:28529061 original size:18 final size:19
Alignment explanation
Indices: 28529025--28529062 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28529015 GACCCCTGTA
28529025 TCCAAAATTTTCATGTTTT
1 TCCAAAATTTTCATGTTTT
28529044 TCCAAAATTTTC-TGTTTT
1 TCCAAAATTTTCATGTTTT
28529062 T
1 T
28529063 GTTTCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (19 bp):
TCCAAAATTTTCATGTTTT
Found at i:28529456 original size:3 final size:3
Alignment explanation
Indices: 28529448--28529486 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
28529438 TATGGAAATG
*
28529448 GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
28529487 AGCTAGCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:28533547 original size:23 final size:23
Alignment explanation
Indices: 28533519--28533566 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
28533509 ATCTCTTCCC
* *
28533519 TTTATTCTATTCTTTATGTCTCT
1 TTTATTCTATTATTTATATCTCT
28533542 TTTATTCTATTATTTATATCTCT
1 TTTATTCTATTATTTATATCTCT
28533565 TT
1 TT
28533567 CTTTAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTCTATTATTTATATCTCT
Found at i:28544632 original size:25 final size:25
Alignment explanation
Indices: 28544596--28544645 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28544586 CATGTGATTT
* *
28544596 TGTATGATGCCTTCGTGGTGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
*
28544621 TGTATGACGCCTTTGTGGCGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
28544646 GATTTGGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.18, G:0.28, T:0.42
Consensus pattern (25 bp):
TGTATGACGCCTTCGTGGCGTATTC
Found at i:28546252 original size:46 final size:46
Alignment explanation
Indices: 28546075--28546268 Score: 210
Period size: 46 Copynumber: 4.2 Consensus size: 46
28546065 TACTCATCAA
* * * ** *
28546075 GGTTAAACCTACACGAATCAGATAATAGTGTCTTATAACCCGTTAG
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTGGTCACCCGTTAG
* * * *
28546121 GGTTGAGCCTACACGAATTGAATAATAGTGCCTAGTCACCCGTTAG
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTGGTCACCCGTTAG
* * * *
28546167 GTTTGAACCTACA-GAAATCGGATAATAATGCTTGCTCACCCGTTAG
1 GGTTGAACCTACACG-AATCGGATAATAGTGCCTGGTCACCCGTTAG
* ** *
28546213 GGTTGAACCTACATGAATCGGATAATAGTGCCTGGTCACCTATTAA
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTGGTCACCCGTTAG
28546259 GGTTGAACCT
1 GGTTGAACCT
28546269 TCATAACAAA
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
45 1 0.01
46 120 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (46 bp):
GGTTGAACCTACACGAATCGGATAATAGTGCCTGGTCACCCGTTAG
Found at i:28546265 original size:92 final size:92
Alignment explanation
Indices: 28546026--28546268 Score: 244
Period size: 92 Copynumber: 2.6 Consensus size: 92
28546016 TTACCCATTT
* * * * *
28546026 GGGTTAAACCTACACGAGTAAT-GAATCATAGTGCCTGGTTA-CTCATCAAGGTTAAACCTACAC
1 GGGTTGAACCTACAC--G-AATCGAATAATAGTGCCTGGTCACCT-ATTAAGGTTGAACCTACAC
*
28546089 GAATCAGATAATAGTGTCTTATAACCCGTTA
62 GAATCAGATAATAATGTCTTATAACCCGTTA
* * * **
28546120 GGGTTGAGCCTACACGAATTGAATAATAGTGCCTAGTCACCCGTT-AGGTTTGAACCTACA-GAA
1 GGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACCTATTAAGG-TTGAACCTACACG-A
* * *
28546183 ATCGGATAATAATG-CTTGCTCACCCGTTA
64 ATCAGATAATAATGTCTT-ATAACCCGTTA
* *
28546212 GGGTTGAACCTACATGAATCGGATAATAGTGCCTGGTCACCTATTAAGGTTGAACCT
1 GGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACCTATTAAGGTTGAACCT
28546269 TCATAACAAA
Statistics
Matches: 123, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
91 10 0.08
92 96 0.78
93 4 0.03
94 13 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (92 bp):
GGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACCTATTAAGGTTGAACCTACACGAAT
CAGATAATAATGTCTTATAACCCGTTA
Found at i:28550071 original size:21 final size:22
Alignment explanation
Indices: 28550047--28550097 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
28550037 CGATGTTGCA
** *
28550047 ACATAGTAAGTTG-GTGTCGCG
1 ACATAGTAAGGGGCGTGTCACG
28550068 ACATAGT-AGGGGCGTGTCACG
1 ACATAGTAAGGGGCGTGTCACG
28550089 ACATAGTAA
1 ACATAGTAA
28550098 ATAGTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (22 bp):
ACATAGTAAGGGGCGTGTCACG
Found at i:28552240 original size:21 final size:20
Alignment explanation
Indices: 28552205--28552257 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 20
28552195 TAAAACACTG
28552205 AAATAAG-AAATATAAAATAT
1 AAATAAGAAAATA-AAAATAT
28552225 AATATAAAGAAAATAAAAATAT
1 AA-AT-AAGAAAATAAAAATAT
28552247 AAATAAGAAAA
1 AAATAAGAAAA
28552258 CAAATAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.30
21 4 0.13
22 12 0.40
23 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (20 bp):
AAATAAGAAAATAAAAATAT
Found at i:28553642 original size:6 final size:6
Alignment explanation
Indices: 28553633--28553664 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28553623 ATAACAATTT
28553633 TCACCA TCACCA TCACCA TCACCA TCACCA TC
1 TCACCA TCACCA TCACCA TCACCA TCACCA TC
28553665 CTCAACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (6 bp):
TCACCA
Found at i:28570139 original size:5 final size:5
Alignment explanation
Indices: 28570131--28570163 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
28570121 AAGAAAAGAA
*
28570131 GAGAG GAGAG GAAAG GAGAG GAGAG GAGAG GAG
1 GAGAG GAGAG GAGAG GAGAG GAGAG GAGAG GAG
28570164 GAAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:28581132 original size:25 final size:25
Alignment explanation
Indices: 28581104--28581158 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
28581094 GTCACGCGGT
28581104 CGTGTCACAC-TCCCATGTGCAAAGC
1 CGTGTCACACGT-CCATGTGCAAAGC
* *
28581129 CGTGTCACACGTCCGTGTGCCAAGC
1 CGTGTCACACGTCCATGTGCAAAGC
28581154 CGTGT
1 CGTGT
28581159 AACTCACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (25 bp):
CGTGTCACACGTCCATGTGCAAAGC
Found at i:28582312 original size:35 final size:34
Alignment explanation
Indices: 28582273--28582386 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 34
28582263 GAGCCCAACT
28582273 CTAGTTGGATATACCAACAGTATTTGCGTCCAGCG
1 CTAGTTGGATATACCAACAGTATTTGCG-CCAGCG
* * * * * * * *
28582308 CTAGTCGAATAAATCGACAAATAATTAGTGAGCCTAGCT
1 CTAGTTGGATATACCAAC-AGT-ATT--TGCGCC-AGCG
*
28582347 CTAGTTGGATATACCAACAGTATTTGCACCCAGCG
1 CTAGTTGGATATACCAACAGTATTTGC-GCCAGCG
28582382 CTAGT
1 CTAGT
28582387 CCGTTAAACC
Statistics
Matches: 56, Mismatches: 17, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
35 23 0.41
36 4 0.07
37 6 0.11
38 4 0.07
39 19 0.34
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (34 bp):
CTAGTTGGATATACCAACAGTATTTGCGCCAGCG
Found at i:28582470 original size:75 final size:74
Alignment explanation
Indices: 28582227--28582485 Score: 317
Period size: 74 Copynumber: 3.5 Consensus size: 74
28582217 GAAAGTTGTG
* * *
28582227 CCCAACGCTAGTCGAATAAACCGACAAATAATTAGGGAGCCCAACTCTAGTTGGATATACCAACA
1 CCCAGCGCTAGTCGAATAAACCGACAAATAAATAGTGAGCCCAACTCTAGTTGGATATACCAACA
*
28582292 GTATTTGCG
66 GTATTTGCA
* * * * *
28582301 TCCAGCGCTAGTCGAATAAATCGACAAATAATTAGTGAGCCTAGCTCTAGTTGGATATACCAACA
1 CCCAGCGCTAGTCGAATAAACCGACAAATAAATAGTGAGCCCAACTCTAGTTGGATATACCAACA
28582366 GTATTTGCA
66 GTATTTGCA
* * *
28582375 CCCAGCGCTAGTCCG-TTAAACCGA-AGTAATAAATAGTGAGCCCAACTCTAGTTGGATTTAACA
1 CCCAGCGCTAGT-CGAATAAACCGACA--AATAAATAGTGAGCCCAACTCTAGTTGGATATACCA
* * *
28582438 A-TGAAAATTGCA
63 ACAG-TATTTGCA
*
28582450 CCCAGCACTAGTCGAATAAACCGACAAATAAATAGT
1 CCCAGCGCTAGTCGAATAAACCGACAAATAAATAGT
28582486 TATTTATTTT
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
73 1 0.01
74 98 0.62
75 59 0.37
76 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (74 bp):
CCCAGCGCTAGTCGAATAAACCGACAAATAAATAGTGAGCCCAACTCTAGTTGGATATACCAACA
GTATTTGCA
Found at i:28591693 original size:15 final size:16
Alignment explanation
Indices: 28591673--28591705 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28591663 CTTTATAACC
*
28591673 TCTTTCTTGA-CAAAT
1 TCTTTCATGATCAAAT
28591688 TCTTTCATGATCAAAT
1 TCTTTCATGATCAAAT
28591704 TC
1 TC
28591706 AGTATTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (16 bp):
TCTTTCATGATCAAAT
Found at i:28594392 original size:15 final size:15
Alignment explanation
Indices: 28594372--28594410 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
28594362 TGGATTCAAT
28594372 GGATCATTCAAACCA
1 GGATCATTCAAACCA
28594387 GGATCATTCAAACCA
1 GGATCATTCAAACCA
28594402 GGATCATTC
1 GGATCATTC
28594411 CCTACCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (15 bp):
GGATCATTCAAACCA
Found at i:28596919 original size:22 final size:20
Alignment explanation
Indices: 28596872--28596924 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
28596862 GAGAAGAAAT
*
28596872 AACAAAGAAAACGAACTAAC
1 AACAAAGAAAACAAACTAAC
*
28596892 ACACAAAGAAAAGCAAACTTACC
1 A-ACAAAGAAAA-CAAAC-TAAC
28596915 AACAAA-AAAA
1 AACAAAGAAAA
28596925 TAAGGTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 14 0.50
22 9 0.32
23 4 0.14
ACGTcount: A:0.66, C:0.21, G:0.08, T:0.06
Consensus pattern (20 bp):
AACAAAGAAAACAAACTAAC
Found at i:28602399 original size:73 final size:74
Alignment explanation
Indices: 28602322--28602459 Score: 242
Period size: 73 Copynumber: 1.9 Consensus size: 74
28602312 TCTTTTAATA
* *
28602322 TATTATATTTTTCATTTGTTAAAATTAATCCTTATAC-TTTTTTTAAACAATTTAAATTTTTTTC
1 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
28602386 TTTTTAACG
66 TTTTTAACG
*
28602395 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTGAACAATTTAAATTTTTTTC
1 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
28602460 CTTATACTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
73 35 0.57
74 26 0.43
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (74 bp):
TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
TTTTTAACG
Found at i:28614824 original size:21 final size:21
Alignment explanation
Indices: 28614783--28614825 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28614773 AATAAAGTAG
*
28614783 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
28614804 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
28614825 A
1 A
28614826 AATTCATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:28615116 original size:45 final size:44
Alignment explanation
Indices: 28615035--28615123 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 44
28615025 ACATCTATTC
*
28615035 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
28615079 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
28615124 TGCCTCTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:28625261 original size:41 final size:38
Alignment explanation
Indices: 28625216--28625320 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 38
28625206 CAAATATTAT
* * *
28625216 AATTATAATTACCATAATTATAATAATGTTTGACCGAAAAA
1 AATTATAATTACAATAATTATAATAATATTCGACCG---AA
* * *
28625257 AATTACAATTACAATAATTATAATAATATTCGATCGTA
1 AATTATAATTACAATAATTATAATAATATTCGACCGAA
28625295 AATTATAATTACAATAATTATAATAA
1 AATTATAATTACAATAATTATAATAA
28625321 GGATTTTGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 26 0.46
41 31 0.54
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGACCGAA
Found at i:28633022 original size:20 final size:20
Alignment explanation
Indices: 28632997--28633076 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
28632987 GTATGGGATC
*
28632997 GCACTTTGGTGCCTTTGTTT
1 GCACTTTGGTGCCTCTGTTT
*
28633017 GCACTTTGATGCCTCTGTTT
1 GCACTTTGGTGCCTCTGTTT
*
28633037 GCACTTCGGGTGCCTCTGTTT
1 GCACTT-TGGTGCCTCTGTTT
**
28633058 GCACTACGGTGCCTCTGTT
1 GCACTTTGGTGCCTCTGTT
28633077 AGCATTTCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 36 0.68
21 17 0.32
ACGTcount: A:0.07, C:0.26, G:0.25, T:0.41
Consensus pattern (20 bp):
GCACTTTGGTGCCTCTGTTT
Found at i:28633052 original size:21 final size:21
Alignment explanation
Indices: 28633004--28633085 Score: 96
Period size: 20 Copynumber: 4.0 Consensus size: 21
28632994 ATCGCACTTT
* *
28633004 GGTGCCTTTGTTTGCACTT-T
1 GGTGCCTCTGTTTGCACTTCG
*
28633024 GATGCCTCTGTTTGCACTTCG
1 GGTGCCTCTGTTTGCACTTCG
*
28633045 GGTGCCTCTGTTTGCACTAC-
1 GGTGCCTCTGTTTGCACTTCG
* *
28633065 GGTGCCTCTGTTAGCATTTCG
1 GGTGCCTCTGTTTGCACTTCG
28633086 ATGCTCTCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (21 bp):
GGTGCCTCTGTTTGCACTTCG
Found at i:28633057 original size:41 final size:41
Alignment explanation
Indices: 28633004--28633085 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
28632994 ATCGCACTTT
* ** *
28633004 GGTGCCTTTGTTTGCACTTTGATGCCTCTGTTTGCACTTCG
1 GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
* *
28633045 GGTGCCTCTGTTTGCACTACGGTGCCTCTGTTAGCATTTCG
1 GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
28633086 ATGCTCTCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (41 bp):
GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
Found at i:28633095 original size:41 final size:41
Alignment explanation
Indices: 28632997--28633095 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
28632987 GTATGGGATC
* * ** *
28632997 GCACTTTGG-TGCCTTTGTTTGCACTTTGATGCCTCTGTTT
1 GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
* *
28633037 GCACTTCGGGTGCCTCTGTTTGCACTACGGTGCCTCTGTTA
1 GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
*
28633078 GCATTTC-GATGCTCTCTG
1 GCACTTCGGATGC-CTCTG
28633096 ATGTGTTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 12 0.24
41 37 0.76
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.40
Consensus pattern (41 bp):
GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
Found at i:28634283 original size:42 final size:41
Alignment explanation
Indices: 28634200--28634284 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
28634190 CATGTTATCA
* * * *
28634200 CATATCGATGCCACTGTCCTAGACAGGGTCTTATATGAAAT
1 CATATCGATGCCAATGTCCCAGACAGAGTCTTACATGAAAT
*
28634241 CATATACGATGCCAATGTCCCAGACATAGTCTTACACT-AAAT
1 CATAT-CGATGCCAATGTCCCAGACAGAGTCTTACA-TGAAAT
28634283 CA
1 CA
28634285 CACCTCGGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 5 0.14
42 31 0.84
43 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAGACAGAGTCTTACATGAAAT
Found at i:28645980 original size:7 final size:6
Alignment explanation
Indices: 28645964--28645988 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28645954 GCAATTTAGT
28645964 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
28645989 ATAACTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:28649208 original size:16 final size:16
Alignment explanation
Indices: 28649187--28649217 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28649177 CTCACTCAAG
28649187 TTTCTTTCACTTTTTT
1 TTTCTTTCACTTTTTT
*
28649203 TTTCTTTCTCTTTTT
1 TTTCTTTCACTTTTT
28649218 CTCCACTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCACTTTTTT
Found at i:28657027 original size:23 final size:23
Alignment explanation
Indices: 28656999--28657050 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
28656989 TTGATAAAGA
28656999 TTTTGAAATGTGCCATTGATGAT
1 TTTTGAAATGTGCCATTGATGAT
28657022 TTTTGAAATGTGCCATTGATGAT
1 TTTTGAAATGTGCCATTGATGAT
28657045 TTTTGA
1 TTTTGA
28657051 TAAAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTTGAAATGTGCCATTGATGAT
Found at i:28657749 original size:43 final size:42
Alignment explanation
Indices: 28657698--28657824 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
28657688 AGGAACTCTG
28657698 ATATGTGTTTTCATGTAAGACCACGTCTAGGACATTGGCATCGA
1 ATATGTGTTTTCATGTAAGACCACGTCT-GGACATTGGCATC-A
* * * *
28657742 CT-TGTGTTTACGTGTAAGACC-CTGTCTGGAACAGTGGCATCA
1 ATATGTGTTTTCATGTAAGACCAC-GTCTGG-ACATTGGCATCA
*
28657784 ATATGTGATTAT-ATGTAAGACCACGTCTGGGACATTGGCAT
1 ATATGTG-TTTTCATGTAAGACCACGTCT-GGACATTGGCAT
28657825 TGTACAAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
42 5 0.07
43 57 0.84
44 6 0.09
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATATGTGTTTTCATGTAAGACCACGTCTGGACATTGGCATCA
Found at i:28660486 original size:40 final size:41
Alignment explanation
Indices: 28660440--28660516 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
28660430 TATATTCGTG
*
28660440 GCGTTTGGA-AAAAAACGCCATTATTGCTCGACTTTTAGCA
1 GCGTTTGGACAAAAAACGCCATTATTGCTCAACTTTTAGCA
*
28660480 GCGTTTGGACAAAAAACGCCATTATTGTTCAACTTTT
1 GCGTTTGGACAAAAAACGCCATTATTGCTCAACTTTT
28660517 TTGCGGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 9 0.26
41 25 0.74
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
GCGTTTGGACAAAAAACGCCATTATTGCTCAACTTTTAGCA
Found at i:28661102 original size:7 final size:7
Alignment explanation
Indices: 28661071--28661176 Score: 56
Period size: 7 Copynumber: 15.0 Consensus size: 7
28661061 ACTAATTAAT
28661071 CTAAACC
1 CTAAACC
28661078 CTAAATCC
1 CTAAA-CC
*
28661086 CTATTA-C
1 CTA-AACC
28661093 CTAAACC
1 CTAAACC
*
28661100 CTAAATC
1 CTAAACC
* *
28661107 ATAAAAC
1 CTAAACC
*
28661114 ATAAACC
1 CTAAACC
28661121 CTAAACC
1 CTAAACC
*
28661128 CT-AATC
1 CTAAACC
* *
28661134 ATAAAAC
1 CTAAACC
*
28661141 ATAAACCC
1 CTAAA-CC
28661149 CTAAACC
1 CTAAACC
*
28661156 C-CAACC
1 CTAAACC
28661162 CTTAAACC
1 C-TAAACC
*
28661170 ATAAACC
1 CTAAACC
28661177 ATAATCTGTA
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
6 10 0.13
7 52 0.68
8 14 0.18
9 1 0.01
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:28661140 original size:21 final size:20
Alignment explanation
Indices: 28661067--28661148 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
28661057 AAACACTAAT
28661067 TAATC-TAAACCCTAAATCCC
1 TAATCATAAACCCTAAA-CCC
* * * *
28661087 TATTACCTAAACCCTAAATCA
1 TAAT-CATAAACCCTAAACCC
*
28661108 TAAAACATAAACCCTAAACCC
1 T-AATCATAAACCCTAAACCC
* *
28661129 TAATCATAAAACATAAACCC
1 TAATCATAAACCCTAAACCC
28661149 CTAAACCCCA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 19 0.40
21 17 0.35
22 12 0.25
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (20 bp):
TAATCATAAACCCTAAACCC
Found at i:28661141 original size:27 final size:29
Alignment explanation
Indices: 28661092--28661156 Score: 116
Period size: 28 Copynumber: 2.3 Consensus size: 29
28661082 ATCCCTATTA
28661092 CCTAAACCCTAAATCATAAAACATAAA-C
1 CCTAAACCCTAAATCATAAAACATAAACC
28661120 CCTAAACCCT-AATCATAAAACATAAACC
1 CCTAAACCCTAAATCATAAAACATAAACC
28661148 CCTAAACCC
1 CCTAAACCC
28661157 CAACCCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (29 bp):
CCTAAACCCTAAATCATAAAACATAAACC
Found at i:28661168 original size:28 final size:28
Alignment explanation
Indices: 28661092--28661176 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
28661082 ATCCCTATTA
* *
28661092 CCTAAACCCTAAATCATAAAACATAAA-C
1 CCTAAACCC-CAACCATAAAACATAAACC
* *
28661120 CCTAAACCCTAATCATAAAACATAAACC
1 CCTAAACCCCAACCATAAAACATAAACC
* *
28661148 CCTAAACCCCAACCCTTAAACCATAAACC
1 CCTAAACCCCAA-CCATAAAACATAAACC
28661177 ATAATCTGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 16 0.32
28 21 0.42
29 13 0.26
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (28 bp):
CCTAAACCCCAACCATAAAACATAAACC
Found at i:28661193 original size:15 final size:15
Alignment explanation
Indices: 28661170--28661205 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28661160 CCCTTAAACC
28661170 ATAAA-CCATAATCT
1 ATAAACCCATAATCT
*
28661184 GTAAACCCATAATCT
1 ATAAACCCATAATCT
28661199 ATAAACC
1 ATAAACC
28661206 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAACCCATAATCT
Found at i:28661743 original size:40 final size:40
Alignment explanation
Indices: 28661698--28661956 Score: 217
Period size: 40 Copynumber: 6.6 Consensus size: 40
28661688 TTTTGCGACG
* * *
28661698 TTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
* *
28661738 TTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
* * *
28661778 TTTTTCAAAAAGCGTCGCTAATGC-C-A-CTAAAGC-TCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
*** * * ** ** * * *
28661814 -ACAT-AAAACGACGGCG-TTGTGCTTAATTTTTTTGCGGCA
1 TTTTTCAAAAAG-CGCCGCTAATGCTCGA-TCTATAGCGGCA
* * *
28661853 TTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
* *
28661893 TTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
*
28661933 TTTTTCAAAAAGCGTCGCTAATGC
1 TTTTTCAAAAAGCGCCGCTAATGC
28661957 CACTAAAGCT
Statistics
Matches: 165, Mismatches: 45, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
34 9 0.05
35 5 0.03
36 2 0.01
37 6 0.04
38 4 0.02
39 3 0.02
40 127 0.77
41 9 0.05
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCA
Found at i:28662099 original size:154 final size:155
Alignment explanation
Indices: 28661592--28662180 Score: 941
Period size: 155 Copynumber: 3.8 Consensus size: 155
28661582 GTTTTTTATG
* * * * *
28661592 AAGCGCCGCTAATGCTCGATCTATAACGGTGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCT
1 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
* * *
28661657 CAACATAAAGCGATAGCGTTGTGCTTAATTTTTTTGCGACGTTTTTCGAAAAGCGCCGCTAATGG
66 CAACATAAAACGACAGCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGG
28661722 TCGACCTATAGCGGCATTTTTCAAA
131 TCGACCTATAGCGGCATTTTTCAAA
28661747 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
1 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
* *
28661812 CAACATAAAACGACGGCGTTGTGCTTAATTTTTTTGCGGCATTTTTCGAAAAGCGCCGCTAATGG
66 CAACATAAAACGACAGCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGG
28661877 TCGACCTATAGCGGCATTTTTCAAA
131 TCGACCTATAGCGGCATTTTTCAAA
28661902 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
1 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
* * *
28661967 CAACAT-AAACGACGGCGTTGTGCTTAATTTTTTTGCAGCGTTTTTCGAAAAGCACCGCTAATGG
66 CAACATAAAACGACAGCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGG
*
28662031 TCAACCTATAGCGGCATTTTTCAAA
131 TCGACCTATAGCGGCATTTTTCAAA
* * * * * *
28662056 AAGCTCCGCTAATGTTCAATCTATAGTGGCGTTTTTCAAAAAGCG-CTGCTAATGTCACTAAAGC
1 AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTC-GCTAATGCCACTAAAGC
* * *
28662120 TCAACATAAAACGATAGCGTTGTGCTTAA-TTTTTTGCGGCGTTTTTCAAAAAGCGTCGCTA
65 TCAACATAAAACGACAGCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTA
28662181 GTGCCACTAA
Statistics
Matches: 406, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
153 1 0.00
154 170 0.42
155 235 0.58
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (155 bp):
AAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCT
CAACATAAAACGACAGCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGG
TCGACCTATAGCGGCATTTTTCAAA
Found at i:28662110 original size:40 final size:40
Alignment explanation
Indices: 28662004--28662110 Score: 142
Period size: 40 Copynumber: 2.7 Consensus size: 40
28661994 TTTTTTTGCA
* *
28662004 GCGTTTTTCGAAAAGCACCGCTAATGGTCAACCTATAGCG
1 GCGTTTTTCAAAAAGCACCGCTAATGTTCAACCTATAGCG
* * * *
28662044 GCATTTTTCAAAAAGCTCCGCTAATGTTCAATCTATAGTG
1 GCGTTTTTCAAAAAGCACCGCTAATGTTCAACCTATAGCG
* *
28662084 GCGTTTTTCAAAAAGCGCTGCTAATGT
1 GCGTTTTTCAAAAAGCACCGCTAATGT
28662111 CACTAAAGCT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCACCGCTAATGTTCAACCTATAGCG
Found at i:28669144 original size:59 final size:58
Alignment explanation
Indices: 28669077--28669190 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
28669067 TGAATGAATA
* * * *
28669077 ATCATATTCTTGTTTAAGTATAAACTTACCTATTGTGAACTGTGATTGACAGGAAAATG
1 ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGA-TGACAAGAAAATG
* *
28669136 ATCATATTCTTGTTTGAGTATAGACTCACCTACTATGAACTGTGATGACAAGAAA
1 ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGATGACAAGAAA
28669191 CTTTGATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 9 0.18
59 40 0.82
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (58 bp):
ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGATGACAAGAAAATG
Found at i:28672910 original size:26 final size:26
Alignment explanation
Indices: 28672881--28672932 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
28672871 ACCAATGAAA
*
28672881 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
28672907 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
28672933 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:28672955 original size:104 final size:103
Alignment explanation
Indices: 28672643--28673010 Score: 598
Period size: 103 Copynumber: 3.6 Consensus size: 103
28672633 TAGCCGTTAT
** *
28672643 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAA-CCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
28672707 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
28672745 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
28672810 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
28672848 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
28672912 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
28672952 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
28673011 TTTATATACA
Statistics
Matches: 252, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
102 51 0.20
103 132 0.52
104 68 0.27
105 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:28675280 original size:25 final size:25
Alignment explanation
Indices: 28675258--28675341 Score: 123
Period size: 25 Copynumber: 3.4 Consensus size: 25
28675248 GTATGCTCTC
* * *
28675258 ACGAGCTGTGAATTGGGAAGCTCAT
1 ACGAGCTGTAAATCGAGAAGCTCAT
28675283 ACGAGCTGTAAATCGAGAAGCTCAT
1 ACGAGCTGTAAATCGAGAAGCTCAT
* *
28675308 ATGAGCTGTAAATCAAGAAGCTCAT
1 ACGAGCTGTAAATCGAGAAGCTCAT
28675333 ACGAGCTGT
1 ACGAGCTGT
28675342 GGTGTGTCCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (25 bp):
ACGAGCTGTAAATCGAGAAGCTCAT
Found at i:28675286 original size:50 final size:50
Alignment explanation
Indices: 28675227--28675339 Score: 131
Period size: 50 Copynumber: 2.3 Consensus size: 50
28675217 ATTCATGTAT
* * ***
28675227 GCTCATACGAGCTCTAAATC-AGTATGCTC-TCACGAGCTGTGAATTGGGAA
1 GCTCATACGAGCTCTAAATCGAG-AAGCTCAT-ACGAGCTGTAAATCAAGAA
* *
28675277 GCTCATACGAGCTGTAAATCGAGAAGCTCATATGAGCTGTAAATCAAGAA
1 GCTCATACGAGCTCTAAATCGAGAAGCTCATACGAGCTGTAAATCAAGAA
28675327 GCTCATACGAGCT
1 GCTCATACGAGCT
28675340 GTGGTGTGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 51 0.94
51 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (50 bp):
GCTCATACGAGCTCTAAATCGAGAAGCTCATACGAGCTGTAAATCAAGAA
Found at i:28680391 original size:138 final size:138
Alignment explanation
Indices: 28680163--28680426 Score: 447
Period size: 138 Copynumber: 1.9 Consensus size: 138
28680153 TTTCCAAAAC
* * * *
28680163 AATATTAATTTCCCTGTCTTTTATATTTTGGCTGAAATTAATTAATATAATTGTTTATATTAATA
1 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTATATATTAATA
*** *
28680228 AATTCGGTAAAATATATGTAATTAATATTTTGTATGAATTAAATTCATATATTAATTATATTTTT
66 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTT
28680293 TACCAAAG
131 TACCAAAG
28680301 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTATATATTAATA
1 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTATATATTAATA
*
28680366 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTTATATATTAATTATAT
66 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATAT
28680427 CTATGTTCTC
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 117 1.00
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (138 bp):
AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTATATATTAATA
AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTT
TACCAAAG
Found at i:28683785 original size:27 final size:27
Alignment explanation
Indices: 28683755--28683834 Score: 115
Period size: 29 Copynumber: 2.9 Consensus size: 27
28683745 GGGTTATGGG
*
28683755 TTAGGGATTTAAAAAATAAATTAGGGT
1 TTAGGGATTTAAAAAATAAATTAAGGT
*
28683782 TTAGGAATTTTAAAAAAATAAATTAAGGT
1 TTAGGGA-TTT-AAAAAATAAATTAAGGT
*
28683811 TTAGGGTTTTAAAAAATAAATTAA
1 TTAGGGATTTAAAAAATAAATTAA
28683835 ATTAGGGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.43
28 6 0.13
29 21 0.45
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (27 bp):
TTAGGGATTTAAAAAATAAATTAAGGT
Found at i:28683844 original size:32 final size:30
Alignment explanation
Indices: 28683768--28683861 Score: 120
Period size: 32 Copynumber: 3.1 Consensus size: 30
28683758 GGGATTTAAA
*
28683768 AAATAAATTAGGGTTTAGGAATTTT-AAAA-
1 AAATAAATTAGGGTTTAGG-GTTTTAAAAAT
*
28683797 AAATAAATTAAGGTTTAGGGTTTTAAAAAAT
1 AAATAAATTAGGGTTTAGGGTTTT-AAAAAT
28683828 AAATTAAATTAGGGTTTAGGGTTTTTAAAAAT
1 AAA-TAAATTAGGGTTTAGGG-TTTTAAAAAT
28683860 AA
1 AA
28683862 TTTTGTATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
28 4 0.07
29 18 0.32
30 4 0.07
31 3 0.05
32 24 0.42
33 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (30 bp):
AAATAAATTAGGGTTTAGGGTTTTAAAAAT
Found at i:28684185 original size:125 final size:123
Alignment explanation
Indices: 28683955--28684250 Score: 434
Period size: 125 Copynumber: 2.4 Consensus size: 123
28683945 TTTTTTCGTC
* * * *
28683955 CAGTAATTTCT-AAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTC
1 CAGTAGTTTCTGAAAAAA-TAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
* * *
28684019 AAGCAGGATGCACTATCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACGCTCTTTTTCT
65 AAGCAGGATGCACTATCAGCAAAAGTACTGAAAAAAACTCCCAC-TGGACGCACTTTTT-T
*
28684080 ACAGTAGTTTCTG-TAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
1 -CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
*
28684144 AAGCAGGATGCACTATCAGCAAAAGTACTGAAAAAAACTCCCACTTGACGCACTTTTTT
65 AAGCAGGATGCACTATCAGCAAAAGTACTGAAAAAAACTCCCACTGGACGCACTTTTTT
* * *
28684203 TAGTAGTTTCTGAAAAAATAATTTTGAAAACACGGCTCTAAAAAAATA
1 CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATA
28684251 ATTTTGAGAA
Statistics
Matches: 155, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
122 11 0.07
123 33 0.21
124 12 0.08
125 85 0.55
126 14 0.09
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (123 bp):
CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTCA
AGCAGGATGCACTATCAGCAAAAGTACTGAAAAAAACTCCCACTGGACGCACTTTTTT
Found at i:28684274 original size:28 final size:28
Alignment explanation
Indices: 28684210--28684278 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
28684200 TTTTAGTAGT
*
28684210 TTCTGAAAAAATAATTTTGAAAACACGG
1 TTCTGAAAAAATAATTTTGAAAACACAG
* * * *
28684238 CTCTAAAAAAATAATTTTGAGAAGACAG
1 TTCTGAAAAAATAATTTTGAAAACACAG
28684266 TTCTGAAAAAATA
1 TTCTGAAAAAATA
28684279 GTGTCAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (28 bp):
TTCTGAAAAAATAATTTTGAAAACACAG
Found at i:28687882 original size:18 final size:18
Alignment explanation
Indices: 28687861--28687896 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28687851 AAAAGGAAAC
*
28687861 ATATAATGGTTAGGATAT
1 ATATAAGGGTTAGGATAT
28687879 ATATAAGGGTTAGGATAT
1 ATATAAGGGTTAGGATAT
28687897 GCACTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (18 bp):
ATATAAGGGTTAGGATAT
Found at i:28690700 original size:25 final size:25
Alignment explanation
Indices: 28690671--28690727 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
28690661 CATATGTTAG
28690671 TAATCGACATTAGCGTGGCATCTGT
1 TAATCGACATTAGCGTGGCATCTGT
28690696 TAATCGACATTAGCGTGGCATCTGT
1 TAATCGACATTAGCGTGGCATCTGT
28690721 TAA-CGAC
1 TAATCGAC
28690728 CATGTCAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (25 bp):
TAATCGACATTAGCGTGGCATCTGT
Found at i:28691836 original size:24 final size:22
Alignment explanation
Indices: 28691798--28691843 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
28691788 ATTGAAAAAC
28691798 CTAAAAAAATAAAAAGTATAAA
1 CTAAAAAAATAAAAAGTATAAA
*
28691820 CTAAAAAAATTACAAAATTATAAA
1 CTAAAAAAA-TA-AAAAGTATAAA
28691844 AAGATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 10 0.48
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
CTAAAAAAATAAAAAGTATAAA
Found at i:28691850 original size:11 final size:10
Alignment explanation
Indices: 28691833--28691878 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
28691823 AAAAAATTAC
28691833 AAAATTATAA
1 AAAATTATAA
*
28691843 AAAGATTACAA
1 AAA-ATTATAA
28691854 AAAATTAT-A
1 AAAATTATAA
*
28691863 TAAA-TATAA
1 AAAATTATAA
28691872 AAAATTA
1 AAAATTA
28691879 CTAATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
8 3 0.10
9 8 0.28
10 9 0.31
11 9 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATTATAA
Found at i:28691856 original size:29 final size:28
Alignment explanation
Indices: 28691823--28691879 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
28691813 GTATAAACTA
28691823 AAAAAATTACA-AAATTATAAAAAGATTAC
1 AAAAAATTACATAAA-TATAAAAA-ATTAC
*
28691852 AAAAAATTATATAAATATAAAAAATTAC
1 AAAAAATTACATAAATATAAAAAATTAC
28691880 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 18 0.69
30 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAAAATTACATAAATATAAAAAATTAC
Found at i:28692422 original size:20 final size:20
Alignment explanation
Indices: 28692399--28692442 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28692389 TTTTAAAAAG
28692399 TTTTAACATATT-TTTAAATT
1 TTTTAA-ATATTATTTAAATT
* *
28692419 TTTTAAATTTTATTTATATT
1 TTTTAAATATTATTTAAATT
28692439 TTTT
1 TTTT
28692443 TGTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATATTATTTAAATT
Found at i:28697636 original size:23 final size:23
Alignment explanation
Indices: 28697588--28697630 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
28697578 TAATTAAATT
*
28697588 TATATTTGATATACATTTTATAA
1 TATATTTGATATACATTATATAA
*
28697611 TATATTTTA-ATACATTATAT
1 TATATTTGATATACATTATAT
28697631 TTATATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTGATATACATTATATAA
Found at i:28701396 original size:23 final size:23
Alignment explanation
Indices: 28701370--28701415 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28701360 AAAAATCACA
28701370 CATAGT-GTGCCTTTACATATAAT
1 CATAGTCGTGCCTTTACAT-TAAT
* *
28701393 CATAGTCTTTCCTTTACATTAAT
1 CATAGTCGTGCCTTTACATTAAT
28701416 GCTCACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (23 bp):
CATAGTCGTGCCTTTACATTAAT
Found at i:28707689 original size:18 final size:18
Alignment explanation
Indices: 28707653--28707691 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28707643 GAAATATTTA
*
28707653 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTATAGTAT
28707671 TTTTGATGTATTATA-TAT
1 TTTTGATGT-TTATAGTAT
28707689 TTT
1 TTT
28707692 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTGATGTTTATAGTAT
Found at i:28707715 original size:12 final size:12
Alignment explanation
Indices: 28707692--28707725 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28707682 TATATATTTT
28707692 AAAATT-ATATA
1 AAAATTAATATA
28707703 AAAATTAATATA
1 AAAATTAATATA
28707715 AAAATTAATAT
1 AAAATTAATAT
28707726 GGGCGGGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:28709516 original size:23 final size:23
Alignment explanation
Indices: 28709469--28709520 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28709459 AACTATTTTT
*
28709469 TTATTTTAATTGCATACTTATTA
1 TTATTTTAATTGCATACTTACTA
28709492 TTATTTTCAATT-CATACGTT-CTA
1 TTATTTT-AATTGCATAC-TTACTA
28709515 TTATTT
1 TTATTT
28709521 ATTATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTTTAATTGCATACTTACTA
Found at i:28717589 original size:14 final size:14
Alignment explanation
Indices: 28717570--28717606 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28717560 AATTTTCCTC
28717570 TTCTCTCTTTT-TT
1 TTCTCTCTTTTCTT
28717583 GTTCTCTCTTTTCTT
1 -TTCTCTCTTTTCTT
28717598 TTCT-TCTTT
1 TTCTCTCTTT
28717607 CGATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (14 bp):
TTCTCTCTTTTCTT
Found at i:28718410 original size:33 final size:33
Alignment explanation
Indices: 28718364--28718438 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
28718354 AGCTCCAAAG
* * *
28718364 TGTTCCCACCATAATGCCGTTCCAAAAGTTAGT
1 TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
* * *
28718397 TGTTCCTAACATAATATCGTTCCCAAGGTTAGT
1 TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
28718430 TGTTCCTAA
1 TGTTCCTAA
28718439 GATTACTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
Found at i:28720177 original size:53 final size:53
Alignment explanation
Indices: 28720096--28720210 Score: 194
Period size: 53 Copynumber: 2.2 Consensus size: 53
28720086 AAGGGGCTCT
* *
28720096 GTTTTTCGTGAACTTGGTTCGAATATCTTTGTTGACTCTGTTTTTTTGGGTTTC
1 GTTTTT-GTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
*
28720150 GTTTTTGTGAACTTGCTTCGACTATCTTTGTTGACTCCGTTTTTTTGGGTTTC
1 GTTTTTGTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
28720203 GTTTTTGT
1 GTTTTTGT
28720211 TTCTTTTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 52 0.90
54 6 0.10
ACGTcount: A:0.10, C:0.14, G:0.22, T:0.55
Consensus pattern (53 bp):
GTTTTTGTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
Found at i:28724471 original size:13 final size:14
Alignment explanation
Indices: 28724446--28724474 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28724436 GAGTAATTTT
28724446 AAAAATTATATTAA
1 AAAAATTATATTAA
28724460 AAAAATTA-ATTAA
1 AAAAATTATATTAA
28724473 AA
1 AA
28724475 TTTATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTATATTAA
Found at i:28733136 original size:20 final size:20
Alignment explanation
Indices: 28733085--28733138 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
28733075 TGGATTGTTT
28733085 AAAAATTATAAATAAATTAGA
1 AAAAATTATAAAT-AATTAGA
* *
28733106 AGAGATATATAAAT-ATTAGA
1 AAAAAT-TATAAATAATTAGA
28733126 GAAAAATTATAAA
1 -AAAAATTATAAA
28733139 AAGATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.44
21 8 0.30
22 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAATAATTAGA
Found at i:28733559 original size:39 final size:41
Alignment explanation
Indices: 28733490--28733568 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 41
28733480 TATAATAAAT
* * *
28733490 AAATATTTTTTATTTTTATTTTTAATTTTAAAATACTTTTA
1 AAATAATTTTTATTATTATTTTTAATTTTAAAATAATTTTA
*
28733531 AAATAATTTTT-TTATT-TTTTTATTTTTAAAATAATTTT
1 AAATAATTTTTATTATTATTTTTAATTTTAAAATAATTTT
28733569 TTAATGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 20 0.59
40 4 0.12
41 10 0.29
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (41 bp):
AAATAATTTTTATTATTATTTTTAATTTTAAAATAATTTTA
Found at i:28733578 original size:26 final size:28
Alignment explanation
Indices: 28733526--28733589 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 28
28733516 TTTAAAATAC
* *
28733526 TTTTAAAATAATTTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTTATATGTTTAT
28733554 TTTTAAAATAA-TTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTTATATGTTTAT
*
28733580 TTTAAAAATA
1 TTTTAAAATA
28733590 GGCCGGACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 15 0.45
27 7 0.21
28 11 0.33
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAAAATAATTTTTTTATATGTTTAT
Found at i:28734010 original size:17 final size:18
Alignment explanation
Indices: 28733982--28734016 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
28733972 TTTATTTATT
28733982 TATTTATAATTTTTAAAA
1 TATTTATAATTTTTAAAA
28734000 TATTTAT-ATTTTTAAAA
1 TATTTATAATTTTTAAAA
28734017 CAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATAATTTTTAAAA
Found at i:28734022 original size:18 final size:18
Alignment explanation
Indices: 28733983--28734022 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
28733973 TTATTTATTT
*
28733983 ATTTATAATTTTTAAAAT
1 ATTTATAATTTTTAAAAA
28734001 ATTTAT-ATTTTTAAAACA
1 ATTTATAATTTTTAAAA-A
28734019 ATTT
1 ATTT
28734023 TTTAGAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATAATTTTTAAAAA
Found at i:28740159 original size:11 final size:12
Alignment explanation
Indices: 28740136--28740160 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28740126 AAAAGAGAAG
28740136 AAATTCAAAAAA
1 AAATTCAAAAAA
28740148 AAATTCAAAAAA
1 AAATTCAAAAAA
28740160 A
1 A
28740161 TCGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:28740178 original size:21 final size:21
Alignment explanation
Indices: 28740122--28740181 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
28740112 ATTGGATTTT
* * *
28740122 AAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAGAAAAAAAAATCA
*** *
28740143 AAAAAAAATTCAAAAAAATCG
1 AAAAAAAAGAAAAAAAAATCA
28740164 AAAAAAAAGAAAAAAAAA
1 AAAAAAAAGAAAAAAAAA
28740182 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAATCA
Found at i:28741227 original size:11 final size:10
Alignment explanation
Indices: 28741211--28741240 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
28741201 TCGTAATGTA
28741211 AAAAAAAAGTC
1 AAAAAAAA-TC
28741222 AAAAAAAATC
1 AAAAAAAATC
28741232 AAAAAAAAT
1 AAAAAAAAT
28741241 TTTGAGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:28741341 original size:11 final size:12
Alignment explanation
Indices: 28741318--28741342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28741308 AAAAGAGAAG
28741318 AAATTCAAAAAA
1 AAATTCAAAAAA
28741330 AAATTCAAAAAA
1 AAATTCAAAAAA
28741342 A
1 A
28741343 TCGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:28741360 original size:21 final size:21
Alignment explanation
Indices: 28741304--28741362 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
28741294 ATTGGATTTT
* * *
28741304 AAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAGAAAAAAAAATCA
*** *
28741325 AAAAAAAATTCAAAAAAATCG
1 AAAAAAAAGAAAAAAAAATCA
28741346 AAAAAAAAGAAAAAAAA
1 AAAAAAAAGAAAAAAAA
28741363 GAAGTGAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAATCA
Found at i:28741375 original size:15 final size:15
Alignment explanation
Indices: 28741355--28741404 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
28741345 GAAAAAAAAG
28741355 AAAAAAAAGAAGTGA
1 AAAAAAAAGAAGTGA
* *
28741370 AAAAAAATCG-AGTTA
1 AAAAAAA-AGAAGTGA
28741385 AAAAAAAAGAA--GA
1 AAAAAAAAGAAGTGA
28741398 AAAAAAA
1 AAAAAAA
28741405 GTGAAAAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 8 0.28
14 1 0.03
15 19 0.66
16 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (15 bp):
AAAAAAAAGAAGTGA
Found at i:28742389 original size:18 final size:18
Alignment explanation
Indices: 28742368--28742455 Score: 52
Period size: 18 Copynumber: 4.7 Consensus size: 18
28742358 GGAACAAGAA
28742368 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGAGAGTGAG
**
28742386 ATTGAAGAAAGA-AACGAG
1 ATTGAA-AAAGAGAGTGAG
* * **
28742404 AGTGTAAAAGAAACGAGTGTC
1 ATTG-AAAA-AGA-GAGTGAG
* * *
28742425 ATGGAAAAAGAAATTGAG
1 ATTGAAAAAGAGAGTGAG
28742443 ATTGAAAAAGAGA
1 ATTGAAAAAGAGA
28742456 AGAGTGAAAA
Statistics
Matches: 48, Mismatches: 17, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
18 29 0.60
19 11 0.23
20 4 0.08
21 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.28, T:0.16
Consensus pattern (18 bp):
ATTGAAAAAGAGAGTGAG
Found at i:28765002 original size:5 final size:5
Alignment explanation
Indices: 28764992--28765030 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
28764982 TCCTAGGATG
* *
28764992 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
28765031 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:28765434 original size:17 final size:17
Alignment explanation
Indices: 28765412--28765450 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28765402 TCCCGAATTG
*
28765412 GTTGTGGTCCTGCATAT
1 GTTGTGATCCTGCATAT
* *
28765429 GTTGTGATTCTGCATGT
1 GTTGTGATCCTGCATAT
28765446 GTTGT
1 GTTGT
28765451 AGACACACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.31, T:0.46
Consensus pattern (17 bp):
GTTGTGATCCTGCATAT
Found at i:28776513 original size:20 final size:20
Alignment explanation
Indices: 28776488--28776529 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28776478 ATTTATTGTT
28776488 GAACATTACTCACCTGTTGA
1 GAACATTACTCACCTGTTGA
28776508 GAACATTACTCACCTGTTGA
1 GAACATTACTCACCTGTTGA
28776528 GA
1 GA
28776530 GCTGTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (20 bp):
GAACATTACTCACCTGTTGA
Found at i:28785684 original size:19 final size:20
Alignment explanation
Indices: 28785652--28785689 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28785642 TCCTAGATAT
*
28785652 TTTTTAAAATTTTATAATAA
1 TTTTTAAAATTTTAGAATAA
*
28785672 TTTTTCAAA-TTTAGAATA
1 TTTTTAAAATTTTAGAATA
28785690 GGGGACCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTTAAAATTTTAGAATAA
Found at i:28797616 original size:28 final size:28
Alignment explanation
Indices: 28797585--28797652 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
28797575 AAGAAATTAC
28797585 ATTAAGTTAATTTA-GATTAATTAATTTA
1 ATTAAGTTAATTTAGGA-TAATTAATTTA
*
28797613 ATTATA-TTATTTTAGGATAATTAATTTA
1 ATTA-AGTTAATTTAGGATAATTAATTTA
28797641 ATT-AGTTTAATT
1 ATTAAG-TTAATT
28797653 AATAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.03
28 30 0.88
29 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTAAGTTAATTTAGGATAATTAATTTA
Found at i:28806262 original size:29 final size:29
Alignment explanation
Indices: 28806162--28806290 Score: 108
Period size: 29 Copynumber: 4.7 Consensus size: 29
28806152 CGTATAAGTG
* * *
28806162 AGCCTTTGT-G-GATATCTATGAAGTG-A
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* *
28806188 AGCCTTTATGGCGATCACTATTAAATGAA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* * *
28806217 AGCCTTTGTGACAATCTCTATTAAATAAA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* * *
28806246 AGCCTTTGTGGGGATCTC--TGAAA-GGA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
*
28806272 AGCCTTTGTGGGGATCTCT
1 AGCCTTTGTGGCGATCTCT
28806291 GAAAGGAAGC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
26 27 0.33
27 5 0.06
28 11 0.13
29 40 0.48
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (29 bp):
AGCCTTTGTGGCGATCTCTATTAAATGAA
Found at i:28806314 original size:26 final size:26
Alignment explanation
Indices: 28806245--28806308 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
28806235 TATTAAATAA
28806245 AAGCCTTTGTGGGGATCTCTGAAAGG
1 AAGCCTTTGTGGGGATCTCTGAAAGG
28806271 AAGCCTTTGTGGGGATCTCTGAAAGG
1 AAGCCTTTGTGGGGATCTCTGAAAGG
*
28806297 AAGCTTTTGTGG
1 AAGCCTTTGTGG
28806309 CTATCTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.30
Consensus pattern (26 bp):
AAGCCTTTGTGGGGATCTCTGAAAGG
Found at i:28811770 original size:26 final size:26
Alignment explanation
Indices: 28811703--28811806 Score: 68
Period size: 26 Copynumber: 4.0 Consensus size: 26
28811693 GGTTATATTT
*
28811703 AATGGCTATACGAAATAAATATATGA
1 AATGGTTATACGAAATAAATATATGA
** * *
28811729 AATGGTTGCACAAAAT-ACTAATATGA
1 AATGGTTATACGAAATAAAT-ATATGA
* **
28811755 GATGGTTATACGAAATAGTTATAT-A
1 AATGGTTATACGAAATAAATATATGA
* * * * *
28811780 ATTGGGTATATGAAATGATTATATGA
1 AATGGTTATACGAAATAAATATATGA
28811806 A
1 A
28811807 CCGATTAAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
25 21 0.36
26 36 0.62
27 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
AATGGTTATACGAAATAAATATATGA
Found at i:28811804 original size:13 final size:13
Alignment explanation
Indices: 28811786--28811857 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
28811776 TATAATTGGG
28811786 TATATGAAATGAT
1 TATATGAAATGAT
**
28811799 TATATGAACCGAT
1 TATATGAAATGAT
*
28811812 TAAATGGAAAT-AGT
1 TATAT-GAAATGA-T
*
28811826 TATATGAAGTGAT
1 TATATGAAATGAT
* *
28811839 TATACGAAATGTT
1 TATATGAAATGAT
28811852 TATATG
1 TATATG
28811858 GATAGATATG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
13 36 0.80
14 9 0.20
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (13 bp):
TATATGAAATGAT
Found at i:28822471 original size:14 final size:13
Alignment explanation
Indices: 28822452--28822490 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
28822442 AATTTCCAAA
28822452 TTTTCAAATTAAGG
1 TTTTCAAATTAA-G
28822466 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
28822480 CTTTCAAATTA
1 TTTTCAAATTA
28822491 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:28825060 original size:13 final size:13
Alignment explanation
Indices: 28825042--28825068 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28825032 AGATAGAATT
28825042 ATTTTAGACGAAC
1 ATTTTAGACGAAC
28825055 ATTTTAGACGAAC
1 ATTTTAGACGAAC
28825068 A
1 A
28825069 AGGAAGAAAT
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):
ATTTTAGACGAAC
Found at i:28826823 original size:21 final size:21
Alignment explanation
Indices: 28826799--28826854 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
28826789 ATGAACAATT
*
28826799 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
28826820 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
28826840 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
28826855 CAATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:28826840 original size:20 final size:23
Alignment explanation
Indices: 28826810--28826854 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
28826800 AGAAAAAGAG
28826810 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
28826831 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
28826853 AA
1 AA
28826855 CAATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:28829775 original size:67 final size:67
Alignment explanation
Indices: 28829654--28829892 Score: 236
Period size: 67 Copynumber: 3.5 Consensus size: 67
28829644 GTCCAAAAAG
* * * * * *
28829654 AAATAATACATGAACATGAGAGATTCCCTACAAGAAATGA--TGTGAACAGGAGAGATTCCCTGC
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAAAAAATAATGTGTGAACAGGAGAGATTCCCTGC
*
28829717 AAG
65 AAA
*
28829720 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGC
1 AAATAATCGTGAACAGGAAAGATTCCCTGCAA-AAAATAATGTGTGAACAGGAGAGATTCCCTGC
28829784 AACA
65 AA-A
* * * * **
28829788 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA--TGTGAACAGGAAAGATTCCCTAT
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAAAAAATAATGTGTGAACAGGAGAGATTCCCTGC
28829851 AACA
65 AA-A
* *
28829855 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAA-AAAA
28829893 GACAAGTGAA
Statistics
Matches: 147, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
64 20 0.14
65 5 0.03
66 6 0.04
67 79 0.54
68 9 0.06
69 5 0.03
70 23 0.16
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (67 bp):
AAATAATCGTGAACAGGAAAGATTCCCTGCAAAAAATAATGTGTGAACAGGAGAGATTCCCTGCA
AA
Found at i:28829777 original size:35 final size:35
Alignment explanation
Indices: 28829664--28829892 Score: 235
Period size: 35 Copynumber: 6.8 Consensus size: 35
28829654 AAATAATACA
* *
28829664 TGAACATGAGAGATTCCCT---ACAAGA-AATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-TG
* *
28829696 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
*
28829728 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
*
28829763 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
* *
28829798 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
* ** * *
28829830 TGAACAGGAAAGATTCCCTATAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
* * *
28829865 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAACAAAA
28829893 GACAAGTGAA
Statistics
Matches: 163, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
32 63 0.39
33 9 0.06
34 7 0.04
35 84 0.52
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (35 bp):
TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
Found at i:28829827 original size:102 final size:99
Alignment explanation
Indices: 28829654--28829892 Score: 334
Period size: 102 Copynumber: 2.4 Consensus size: 99
28829644 GTCCAAAAAG
* * * * * *
28829654 AAATAATACATGAACATGAGAGATTCCCTACAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAA
*
28829719 GAAATGATGTGAACAGGAAAGATTCCCTGCAACA
66 GAAATGATGTGAACAGGAAAGATTCCCTACAACA
*
28829753 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-AAAATAAT--GTGAACAGGAGAGATTCCCTG
*
28829818 CAAGAAATGATGTGAACAGGAAAGATTCCCTATAACA
63 CAAGAAATGATGTGAACAGGAAAGATTCCCTACAACA
* * *
28829855 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-AAAA
28829893 GACAAGTGAA
Statistics
Matches: 123, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
99 28 0.23
100 6 0.05
102 89 0.72
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (99 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAA
GAAATGATGTGAACAGGAAAGATTCCCTACAACA
Found at i:28830133 original size:29 final size:29
Alignment explanation
Indices: 28830101--28830173 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
28830091 TTCTCAAGAC
* *
28830101 ATTTAAGTTTTCAAAAATTTAGTTTTTAA
1 ATTTAAGTTTTCAAAAATTAAGTTTTCAA
*
28830130 ATTTCCAAATTTTC--AAATTAAGTTTTCAA
1 ATTT--AAGTTTTCAAAAATTAAGTTTTCAA
* *
28830159 ACTTAAGCTTTCAAA
1 ATTTAAGTTTTCAAA
28830174 TTACAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
27 6 0.18
29 21 0.62
31 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTAAGTTTTCAAAAATTAAGTTTTCAA
Found at i:28830157 original size:13 final size:13
Alignment explanation
Indices: 28830139--28830176 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
28830129 AATTTCCAAA
28830139 TTTTCAAATTAAG
1 TTTTCAAATTAAG
28830152 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
28830166 CTTTCAAATTA
1 TTTTCAAATTA
28830177 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:28838922 original size:68 final size:72
Alignment explanation
Indices: 28838838--28838992 Score: 228
Period size: 68 Copynumber: 2.2 Consensus size: 72
28838828 ACTTAGGTAA
*
28838838 TGTTTGGTTCAATGTAATGGCTATACCATTACAAGTTTATTATAAGTATATTCTACAGG-CC-CA
1 TGTTTGGTTCAATGTAATGGCTATACCATTACAAGTTTATTACAAGTATATTCTACAGGACCACA
28838901 C-AC-GC
66 CAACAGC
* * * *
28838906 TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTTTATTACAAGTCTCTTCTATAGGACCACA
1 TGTTTGGTTCAATGTAATGGCTATACCATTACAAGTTTATTACAAGTATATTCTACAGGACCACA
28838971 CAAACAGC
66 C-AACAGC
28838979 TGTTTGGTTCAATG
1 TGTTTGGTTCAATG
28838993 GAATACCCTA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
68 54 0.70
69 2 0.03
70 3 0.04
72 2 0.03
73 16 0.21
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (72 bp):
TGTTTGGTTCAATGTAATGGCTATACCATTACAAGTTTATTACAAGTATATTCTACAGGACCACA
CAACAGC
Found at i:28852349 original size:56 final size:50
Alignment explanation
Indices: 28852254--28852550 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
28852244 ATTTGGGTAA
* * *
28852254 AGAGATCCCATGTAAGACCATGTCTAGGACATGGTATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATG
* *
28852310 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCT-AGGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CTGAGATG
*
28852360 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * ** *
28852410 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * * * * *
28852460 AGAACTCCCATGTAAGACCATTTCTGGGATATGGCATTGGTAGT-ACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* ** * *
28852509 AAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28852551 TGTTATTATC
Statistics
Matches: 204, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
49 39 0.19
50 121 0.59
53 2 0.01
54 1 0.00
56 41 0.20
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:28852445 original size:100 final size:100
Alignment explanation
Indices: 28852254--28852550 Score: 319
Period size: 100 Copynumber: 2.9 Consensus size: 100
28852244 ATTTGGGTAA
* *
28852254 AGAGATCCCATGTAAGACCATGTCTAGGACATGGTATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAGGTCCC
* * * *
28852319 ATGTAAGACCATGTCTAGGACATGGCATTGGCACCTAGGTG
60 ATGTAAGACCATGTTTGGGACATGGCATTGGCACCAAGATG
* * **
28852360 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCCCCGTAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTAA
* *
28852425 GACCATGTTTGGGACATGGCATGGGCACCAATATG
66 GACCATGTTTGGGACATGGCATTGGCACCAAGATG
* * * * * * * **
28852460 AGA-ACTCCCATGTAAGACCATTTCTGGGATATGGCATTGGTAGT-ACAGGAAACATCCCATGTA
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTA
*
28852523 AGACCATGTTTGGGACATGGCTTTGGCA
65 AGACCATGTTTGGGACATGGCATTGGCA
28852551 TGTTATTATC
Statistics
Matches: 163, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
99 38 0.23
100 82 0.50
103 4 0.02
105 1 0.01
106 38 0.23
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (100 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTAA
GACCATGTTTGGGACATGGCATTGGCACCAAGATG
Found at i:28854535 original size:58 final size:59
Alignment explanation
Indices: 28854461--28854596 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 59
28854451 TTTAATTCAT
* *
28854461 ATAATAATTATATTAAAA-ATGTTATTAAATTA-TATATTATTTTT-CTAAATTGTATTTA
1 ATAATAATTATATTAAAATATG--ATTAAATTATTATATTATTTTTACTAAAATATATTTA
* * * * *
28854519 ATAATAATTGTGTTAAAATATGATTAAATTATTTTTTTATTTTTATTAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTATTATATTATTTTTACTAAAATATATTTA
* *
28854578 ACAATAATTTTATTAAAAT
1 ATAATAATTATATTAAAAT
28854597 TTAATAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
57 9 0.14
58 26 0.40
59 30 0.46
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (59 bp):
ATAATAATTATATTAAAATATGATTAAATTATTATATTATTTTTACTAAAATATATTTA
Found at i:28854589 original size:26 final size:25
Alignment explanation
Indices: 28854559--28854609 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
28854549 ATTTTTTTAT
*
28854559 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATA-ATAACAATAA
*
28854585 TTTTATTAAAATTTAATAACAATAA
1 TTTTATTAAAATATAATAACAATAA
28854610 CAATAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTATTAAAATATAATAACAATAA
Found at i:28854799 original size:16 final size:16
Alignment explanation
Indices: 28854774--28854815 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28854764 ATTGCAGTTT
* *
28854774 TATTCCATTACAGCTC
1 TATTCCATTACAACCC
*
28854790 TATTCAATTACAACCC
1 TATTCCATTACAACCC
28854806 TATTCCATTA
1 TATTCCATTA
28854816 TAGTGAACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.38
Consensus pattern (16 bp):
TATTCCATTACAACCC
Found at i:28856309 original size:56 final size:55
Alignment explanation
Indices: 28856162--28856315 Score: 186
Period size: 53 Copynumber: 2.8 Consensus size: 55
28856152 AAGGGGGTGT
* * ** * *
28856162 TAGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAGTGGGATTTTG
1 TAGGATATTATTATGGAAT-TTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
* ** *
28856218 TAAGATATTATTAT-GAA-TTATCCCTTAGCAATTTGATTCTTAATCAGATATTA
1 TAGGATATTATTATGGAATTTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
28856271 TAGGATATTATTATGGAATGTTATCTTTTAGCAATTTGATTCCTA
1 TAGGATATTATTATGGAAT-TTATCTTTTAGCAATTTGATTCCTA
28856316 CATAACTATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
53 41 0.51
54 3 0.04
55 2 0.02
56 35 0.43
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (55 bp):
TAGGATATTATTATGGAATTTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
Found at i:28861095 original size:3 final size:3
Alignment explanation
Indices: 28861087--28861127 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
28861077 AGATAAACCA
* * *
28861087 AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28861128 ATAAGCACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:28863751 original size:31 final size:31
Alignment explanation
Indices: 28863705--28863781 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
28863695 ATAATAAAAC
* * * **
28863705 AATCATTGAACTATTTAAGAATTTTTATTTA
1 AATCATTAAATTATTTAAAAAAATTTATTTA
*
28863736 AATTATTAAATTATTTAAAAAAATTTATTTA
1 AATCATTAAATTATTTAAAAAAATTTATTTA
* *
28863767 AGTCATTAGATTATT
1 AATCATTAAATTATT
28863782 AACTTTTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (31 bp):
AATCATTAAATTATTTAAAAAAATTTATTTA
Found at i:28866744 original size:48 final size:48
Alignment explanation
Indices: 28866673--28866846 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
28866663 ATTAGTGTGA
28866673 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
28866721 TGTGATATGTGATTTTCATGTAAGACCATATCTAGGATATGGCATCAG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
28866769 TGTGATATGTG-TTTTCGTGTAAGACCATAGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
***
28866816 TATGTGATATGTGACGAT-GTGTAAGACCATA
1 --TGTGATATGTGATTTTCGTGTAAGACCATA
28866847 GTTATACTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 30 0.27
48 56 0.50
49 24 0.22
50 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
Found at i:28869471 original size:15 final size:16
Alignment explanation
Indices: 28869446--28869475 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28869436 TGTGTGGTTA
28869446 TAATAAAATATATATG
1 TAATAAAATATATATG
28869462 TAAT-AAATATATAT
1 TAATAAAATATATAT
28869476 ACATTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATAAAATATATATG
Found at i:28869496 original size:20 final size:20
Alignment explanation
Indices: 28869460--28869500 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28869450 AAAATATATA
28869460 TGTAATAAATATATATACATT
1 TGTAATAAATATATATA-ATT
*
28869481 TGTAAT-AATATGTATAATT
1 TGTAATAAATATATATAATT
28869500 T
1 T
28869501 ACTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
TGTAATAAATATATATAATT
Found at i:28875715 original size:25 final size:24
Alignment explanation
Indices: 28875669--28875783 Score: 90
Period size: 25 Copynumber: 4.7 Consensus size: 24
28875659 TGTAGACTTG
*
28875669 TAAACGGGAAGCTC-TTTCGAGCCA
1 TAAACGGGAAGCTCATGT-GAGCCA
28875693 TAAACTGGGAAGCTCATGTGAGCCA
1 TAAAC-GGGAAGCTCATGTGAGCCA
* *
28875718 TGTAACAGGAAGCTCATGTGAGCCA
1 T-AAACGGGAAGCTCATGTGAGCCA
* * * *
28875743 TGTAACGAGAAGCT-TTAGAGAGCCA
1 T-AAACGGGAAGCTCAT-GTGAGCCA
* *
28875768 TTAATGGGAAGCTCAT
1 TAAACGGGAAGCTCAT
28875784 ACAAGCCAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.21
25 55 0.72
26 5 0.07
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (24 bp):
TAAACGGGAAGCTCATGTGAGCCA
Found at i:28875878 original size:25 final size:25
Alignment explanation
Indices: 28875850--28875912 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
28875840 TTAATCAAGT
* *
28875850 AGCTCATAAGATCCAGTTATCGGGA
1 AGCTCATAAGAGCCAATTATCGGGA
**
28875875 AGCTCCGAAGAGCCAATTATCGGGA
1 AGCTCATAAGAGCCAATTATCGGGA
* *
28875900 CGCTTATAAGAGC
1 AGCTCATAAGAGC
28875913 TTCTATGTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (25 bp):
AGCTCATAAGAGCCAATTATCGGGA
Found at i:28888027 original size:45 final size:44
Alignment explanation
Indices: 28887974--28888107 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 44
28887964 AATGATACTC
* * **
28887974 GGTGGAATCAGCACATAGCAACCACCTTCGTAATCAATAGTACCT
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACCT
*
28888019 GGTGGAATCAGCACACAATAACCACCTTTATAATCAATGATACCT
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCT
*
28888064 GGTGGAATCAACACACAACAACCACCTTTATAATCAATGGTACC
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACC
28888108 CGGTACACGT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.01
45 78 0.98
46 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (44 bp):
GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGTACCT
Found at i:28897227 original size:23 final size:23
Alignment explanation
Indices: 28897194--28897239 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28897184 GAATTAGGTC
28897194 ACACGGCCAAGTCACACACCCGT
1 ACACGGCCAAGTCACACACCCGT
*
28897217 ACACGGTCAAGTCACACACCCGT
1 ACACGGCCAAGTCACACACCCGT
28897240 GTGCTAGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.41, G:0.17, T:0.11
Consensus pattern (23 bp):
ACACGGCCAAGTCACACACCCGT
Found at i:28898379 original size:25 final size:25
Alignment explanation
Indices: 28898351--28898427 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 25
28898341 CTTATACGAA
28898351 CCATGTAATGGGAAGCTCTAGAGAG
1 CCATGTAATGGGAAGCTCTAGAGAG
* *
28898376 CCAT-TAACGGGAAGCTCATA-TGAG
1 CCATGTAATGGGAAGCTC-TAGAGAG
*
28898400 CCA-GTTATCGGGAAGCTCT-GAAGAG
1 CCATGTAAT-GGGAAGCTCTAG-AGAG
28898425 CCA
1 CCA
28898428 ATTATCGGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (25 bp):
CCATGTAATGGGAAGCTCTAGAGAG
Found at i:28898392 original size:24 final size:24
Alignment explanation
Indices: 28898351--28898437 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 24
28898341 CTTATACGAA
*
28898351 CCATGTAATGGGAAGCTCTAGAGAG
1 CCAT-TAACGGGAAGCTCTAGAGAG
*
28898376 CCATTAACGGGAAGCTCATA-TGAG
1 CCATTAACGGGAAGCTC-TAGAGAG
*
28898400 CCAGTTATCGGGAAGCTCT-GAAGAG
1 CCA-TTAACGGGAAGCTCTAG-AGAG
*
28898425 CCAATTATCGGGA
1 CC-ATTAACGGGA
28898438 TGCTTATAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
24 19 0.36
25 33 0.62
26 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.21
Consensus pattern (24 bp):
CCATTAACGGGAAGCTCTAGAGAG
Found at i:28898432 original size:25 final size:24
Alignment explanation
Indices: 28898360--28898437 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 24
28898350 ACCATGTAAT
*
28898360 GGGAAGCTCTAGAGAGCC-ATTAAC
1 GGGAAGCTCTA-AGAGCCAATTATC
* *
28898384 GGGAAGCTCATATGAGCCAGTTATC
1 GGGAAGCTC-TAAGAGCCAATTATC
28898409 GGGAAGCTCTGAAGAGCCAATTATC
1 GGGAAGCTCT-AAGAGCCAATTATC
28898434 GGGA
1 GGGA
28898438 TGCTTATAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.33
25 31 0.67
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (24 bp):
GGGAAGCTCTAAGAGCCAATTATC
Found at i:28898448 original size:25 final size:25
Alignment explanation
Indices: 28898372--28898449 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
28898362 GAAGCTCTAG
* *
28898372 AGAGCC-ATTAACGGGAAGCTCATA
1 AGAGCCAATTATCGGGAAGCTTATA
* * *
28898396 TGAGCCAGTTATCGGGAAGCTCT-GA
1 AGAGCCAATTATCGGGAAGCT-TATA
*
28898421 AGAGCCAATTATCGGGATGCTTATA
1 AGAGCCAATTATCGGGAAGCTTATA
28898446 AGAG
1 AGAG
28898450 TTGCGGTGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
24 6 0.14
25 36 0.86
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
AGAGCCAATTATCGGGAAGCTTATA
Found at i:28898528 original size:24 final size:25
Alignment explanation
Indices: 28898501--28898547 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28898491 GGATGCTCCG
*
28898501 AAGAGCTAT-TAACGAGAAGCTCAC
1 AAGAGCCATATAACGAGAAGCTCAC
*
28898525 AAGAGCCATATAACGGGAAGCTC
1 AAGAGCCATATAACGAGAAGCTC
28898548 GTGAGAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (25 bp):
AAGAGCCATATAACGAGAAGCTCAC
Found at i:28902215 original size:42 final size:41
Alignment explanation
Indices: 28902091--28902215 Score: 117
Period size: 42 Copynumber: 3.0 Consensus size: 41
28902081 ATGAGTTTCT
* * * *
28902091 GTTCAACCCTAATGGGTTTCCGTTTTGCACTTTTGAGCTTCA
1 GTTCAACCCTTATGGGTTTCTGTTTAGCACTTAT-AGCTTCA
* * * * *
28902133 GTTTAACCTTTATGGGTTT-TCGTTCAGCTCTTACGAGCTTCA
1 GTTCAACCCTTATGGGTTTCT-GTTTAGCACTTA-TAGCTTCA
*
28902175 GTTCAACCCTTACGGGTTTCTGTTTAGCACTTATATGCTTC
1 GTTCAACCCTTATGGGTTTCTGTTTAGCACTTATA-GCTTC
28902216 TATTTAGCCT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
GTTCAACCCTTATGGGTTTCTGTTTAGCACTTATAGCTTCA
Found at i:28910912 original size:21 final size:21
Alignment explanation
Indices: 28910886--28910926 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28910876 CCGTTCAACC
*
28910886 CTTATGGGTTTCTATTTAGCA
1 CTTATGGGCTTCTATTTAGCA
* *
28910907 CTTATGTGCTTCTGTTTAGC
1 CTTATGGGCTTCTATTTAGC
28910927 CTTCGAGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (21 bp):
CTTATGGGCTTCTATTTAGCA
Found at i:28910918 original size:42 final size:42
Alignment explanation
Indices: 28910828--28910907 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
28910818 CAGCTCTTTT
* * *
28910828 GAGCTTCAGTTTAACCCTTATGGGTTTCTGTTTAGCTCCTAC
1 GAGCTTCAGTTCAACCCTTATGGGTTTCTATTTAGCACCTAC
*
28910870 GAGCTTCCGTTCAACCCTTATGGGTTTCTATTTAGCAC
1 GAGCTTCAGTTCAACCCTTATGGGTTTCTATTTAGCAC
28910908 TTATGTGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (42 bp):
GAGCTTCAGTTCAACCCTTATGGGTTTCTATTTAGCACCTAC
Found at i:28917959 original size:56 final size:56
Alignment explanation
Indices: 28917873--28917987 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
28917863 ACATTACTAT
*
28917873 ATGAAAAAACATGTTTTAAAATGGTCCGGAGATATCACACTATCACAGGTTATACA
1 ATGAAAAAACATGTTTTAAAATGGTCCGGAGATATCACACTATCACAAGTTATACA
* *
28917929 ATGAAAAAACATGTTTTAAAATGGTTCGGAGATATCACACTATCACAAGTTATATA
1 ATGAAAAAACATGTTTTAAAATGGTCCGGAGATATCACACTATCACAAGTTATACA
28917985 ATG
1 ATG
28917988 GCATGTATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (56 bp):
ATGAAAAAACATGTTTTAAAATGGTCCGGAGATATCACACTATCACAAGTTATACA
Found at i:28919627 original size:24 final size:24
Alignment explanation
Indices: 28919538--28919695 Score: 90
Period size: 24 Copynumber: 6.5 Consensus size: 24
28919528 ACTTGTAAAT
* * *
28919538 GGGAAGCTCTTTCGAGCCATAAATC
1 GGGAAGCTCATACGAGCCATTAA-C
**
28919563 GGGAAGCTCATGTGAGCCATGTAAC
1 GGGAAGCTCATACGAGCCAT-TAAC
*
28919588 -GGAAGCTC-TAGAGAGCCATTAAC
1 GGGAAGCTCATA-CGAGCCATTAAC
*
28919611 GGGAAGCTCATACGAGCCAATAAC
1 GGGAAGCTCATACGAGCCATTAAC
** * * * *
28919635 AAGAAGTTCA-AGTGAGCCAATATC
1 GGGAAGCTCATA-CGAGCCATTAAC
*
28919659 GGGAAGCTCCAGA-GAGCCATTAATC
1 GGGAAGCT-CATACGAGCCATTAA-C
* *
28919684 AGGTAGCTCATA
1 GGGAAGCTCATA
28919696 AAAGCCAATT
Statistics
Matches: 104, Mismatches: 21, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
23 6 0.06
24 66 0.63
25 29 0.28
26 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
GGGAAGCTCATACGAGCCATTAAC
Found at i:28919652 original size:48 final size:48
Alignment explanation
Indices: 28919551--28919667 Score: 119
Period size: 48 Copynumber: 2.4 Consensus size: 48
28919541 AAGCTCTTTC
* ** * * *
28919551 GAGCCATAAATCGGGAAGCTCATGTGAGCCATGTAACGGAAGCTCTAGA
1 GAGCCATTAA-CGGGAAGCTCATACGAGCCATATAACAGAAGCTCAAGA
* *
28919600 GAGCCATTAACGGGAAGCTCATACGAGCCA-ATAACAAGAAGTTCAAGT
1 GAGCCATTAACGGGAAGCTCATACGAGCCATATAAC-AGAAGCTCAAGA
* *
28919648 GAGCCAATATCGGGAAGCTC
1 GAGCCATTAACGGGAAGCTC
28919668 CAGAGAGCCA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
47 4 0.07
48 44 0.77
49 9 0.16
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.17
Consensus pattern (48 bp):
GAGCCATTAACGGGAAGCTCATACGAGCCATATAACAGAAGCTCAAGA
Done.