Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 76 of 202
Found at i:22546294 original size:41 final size:40
Alignment explanation
Indices: 22546238--22546383 Score: 129
Period size: 41 Copynumber: 3.6 Consensus size: 40
22546228 TGATTCGATA
22546238 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * **
22546279 CACCGGCATTAAGCCTGCTAGACGTAAAGTATG-AATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
22546320 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
22546361 CACCGGCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
22546384 AATAAGTCTA
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 4 0.05
41 73 0.86
42 6 0.07
43 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:22554566 original size:30 final size:30
Alignment explanation
Indices: 22554532--22554594 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
22554522 TAGCAAAAAA
22554532 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
1 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
*
22554562 CTCAAATTTCTCCTTAATTTTCTCAAAGCT
1 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
22554592 CTC
1 CTC
22554595 TTTAATTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.03, T:0.41
Consensus pattern (30 bp):
CTCAAATTTCTCCTTAAATTTCTCAAAGCT
Found at i:22554594 original size:21 final size:21
Alignment explanation
Indices: 22554561--22554601 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22554551 TTCTCAAAGC
**
22554561 TCTCAAATTTCTCCTTAATTT
1 TCTCAAAGCTCTCCTTAATTT
*
22554582 TCTCAAAGCTCTCTTTAATT
1 TCTCAAAGCTCTCCTTAATT
22554602 GATTATTTCC
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:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (21 bp):
TCTCAAAGCTCTCCTTAATTT
Found at i:22556079 original size:30 final size:30
Alignment explanation
Indices: 22556028--22556091 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
22556018 TTAATTTCCG
*
22556028 AGTTTTGGGGAAAAAGTGTAATTATGTAAA
1 AGTTTAGGGGAAAAAGTGTAATTATGTAAA
* *
22556058 AGTTTAGGGGTAAAA-TCGTAATTTTGTAAA
1 AGTTTAGGGGAAAAAGT-GTAATTATGTAAA
22556088 AGTT
1 AGTT
22556092 AGAGTCGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AGTTTAGGGGAAAAAGTGTAATTATGTAAA
Found at i:22556531 original size:46 final size:46
Alignment explanation
Indices: 22556481--22556592 Score: 116
Period size: 50 Copynumber: 2.3 Consensus size: 46
22556471 CATTGAGATT
* * *
22556481 ATGAGAGGTCCCATGTCCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTCCATGTATGGGACATGGCATGGGCACCGAG
* * *
22556527 ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGGCACCGAT
1 ATGAGAGGT--CCC--ATGTCCATGTATGGGACATGGCATGGGCACCGAG
**
22556577 ATGAGAACTCCCATGT
1 ATGAGAGGTCCCATGT
22556593 AAGACCATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
46 11 0.21
48 6 0.12
50 35 0.67
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.21
Consensus pattern (46 bp):
ATGAGAGGTCCCATGTCCATGTATGGGACATGGCATGGGCACCGAG
Found at i:22556564 original size:50 final size:50
Alignment explanation
Indices: 22556497--22556600 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
22556487 GGTCCCATGT
* * * ** *
22556497 CCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGA
1 CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
* *
22556547 CCATGTATGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGA
1 CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
22556597 CCAT
1 CCAT
22556601 ATCTGGGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
Found at i:22556608 original size:50 final size:50
Alignment explanation
Indices: 22556504--22556613 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
22556494 TGTCCATGTT
* * ** * *
22556504 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTA
1 TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
* * *
22556554 TGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATC
1 TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
*
22556604 TGGGATATGG
1 TGGGACATGG
22556614 AATTGGCAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
TGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATA
Found at i:22562758 original size:125 final size:126
Alignment explanation
Indices: 22562174--22562819 Score: 888
Period size: 126 Copynumber: 5.1 Consensus size: 126
22562164 GGCCAAACAT
* *
22562174 GAACTACTGTAGTAAAAGAGCGTCCACATGGGAGCTTTTTTCAGT-AATTTT-TCTGACAGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCA-TCAATTTTGT-TGACAGTGCA
* * * *
22562237 TCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTTTTAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * * *
22562300 GAACTATTGTAGAAAAAGAGCATCCACGTGGGAGCCTTTTTCAGCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* * * * *
22562365 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTTTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * *
22562426 GAACTACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGATAGTGCACC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* *
22562491 CTGCTTGAAGCGTTTTTAACACTATTTGTTCAG-AATCGTCTTTTCAAAATTATTTTTTC-A
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAT-GTCTTCTCAAAATTATTTTTTCAA
* * * * *
22562551 GAAACCACTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGCAATTTTGTTGGCAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCAT
**
22562616 CCTGCTTGAAGTATTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
* * * *
22562678 GAACTACTGTAG-AAAAGAGCATCCACATGGGAGCATTTTTCATCAATTTTGTTGACAGTGCTTC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
* * * *
22562742 CTTCTTGAAGCGTTTTTGGCACTATTTGTTTAGAACTGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
22562803 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
22562820 AAAACCAAAA
Statistics
Matches: 459, Mismatches: 54, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
125 115 0.25
126 339 0.74
127 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
Found at i:22562933 original size:34 final size:34
Alignment explanation
Indices: 22562884--22562992 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 34
22562874 CAATATTATT
*
22562884 TTTAAAAAAACTAAACCCAATTTTAATTCATTT-
1 TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
*
22562917 TCTTAAAAACAA-TAAACCCAAATTTAATTTATTTA
1 T-TTAAAAA-AACTAAACCCAAATTTAATTCATTTA
*** ** *
22562952 TTTAAAACCCCTAAACCTTAATTTAATT-AATT-
1 TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
22562984 TTTAAAAAA
1 TTTAAAAAA
22562993 GAACACTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
32 7 0.11
33 4 0.06
34 48 0.77
35 3 0.05
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (34 bp):
TTTAAAAAAACTAAACCCAAATTTAATTCATTTA
Found at i:22563118 original size:15 final size:15
Alignment explanation
Indices: 22563098--22563136 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
22563088 TTATTTTAAC
* **
22563098 AAAACCCTAACCCTA
1 AAAACCCTAAACAAA
22563113 AAAACCCTAAACAAA
1 AAAACCCTAAACAAA
22563128 AAAACCCTA
1 AAAACCCTA
22563137 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAACCCTAAACAAA
Found at i:22563122 original size:42 final size:42
Alignment explanation
Indices: 22563028--22563118 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
22563018 AAAAATTCTT
* * *
22563028 AAAACCTAGAACCCTAAATTATTTTCACAAAATCCTAAACCTTA
1 AAAACCT--AACCCTAAATTATTTTAACAAAACCCTAAACCCTA
*
22563072 CAAACCTAACCCTAAATTATTTTAACAAAACCCT-AACCCTA
1 AAAACCTAACCCTAAATTATTTTAACAAAACCCTAAACCCTA
22563113 AAAACC
1 AAAACC
22563119 CTAAACAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 11 0.26
42 25 0.60
44 6 0.14
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (42 bp):
AAAACCTAACCCTAAATTATTTTAACAAAACCCTAAACCCTA
Found at i:22571448 original size:30 final size:30
Alignment explanation
Indices: 22571414--22571486 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
22571404 AAAATATCAA
22571414 ACATAAAAAAGTATCATACATTAGTTTTAC
1 ACATAAAAAAGTATCATACATTAGTTTTAC
*
22571444 ACATAAAAAAGCATCATACATTAGTTTTAC
1 ACATAAAAAAGTATCATACATTAGTTTTAC
*
22571474 ACGTAAAAAAGTA
1 ACATAAAAAAGTA
22571487 GTATAGTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (30 bp):
ACATAAAAAAGTATCATACATTAGTTTTAC
Found at i:22573059 original size:60 final size:60
Alignment explanation
Indices: 22572985--22573106 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
22572975 ATACTAAACT
* ** * * *
22572985 AAACACAACAATTTATAGTTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAGCATAATCCTAAATTACTAACAAATT-AATTATAAAAAAATTAC
*
22573045 AAACACAAAAATTTATAGCATAATCTTAAATTACTAACAAATTAATTATAAAAAAATTAC
1 AAACACAAAAATTTATAGCATAATCCTAAATTACTAACAAATTAATTATAAAAAAATTAC
22573105 AA
1 AA
22573107 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAGCATAATCCTAAATTACTAACAAATTAATTATAAAAAAATTAC
Found at i:22573121 original size:19 final size:19
Alignment explanation
Indices: 22573097--22573344 Score: 145
Period size: 19 Copynumber: 12.4 Consensus size: 19
22573087 TAATTATAAA
22573097 AAAATTACAATATTCATAC
1 AAAATTACAATATTCATAC
22573116 AAAATTACAATATTCATAC
1 AAAATTACAATATTCATAC
22573135 AAAAAATTACAATATTCATAC
1 --AAAATTACAATATTCATAC
* * *
22573156 AAAA-TACTA-ATCCAAAAC
1 AAAATTACAATATTC-ATAC
*
22573174 TATAAA-TACAAAATTAATT-ATAA
1 -A-AAATTAC--AA-T-ATTCATAC
*
22573197 AATAATTACAATATTCATTC
1 AA-AATTACAATATTCATAC
22573217 AAAATTACAATATTCATAC
1 AAAATTACAATATTCATAC
*
22573236 AAAA-TAC--TAATCAATAAC
1 AAAATTACAATATTC-AT-AC
*
22573254 TATAAA-TACAAAATTAATT-ATAA
1 -A-AAATTAC--AA-T-ATTCATAC
22573277 AATAATTACAATATTCATAC
1 AA-AATTACAATATTCATAC
* *
22573297 AAAATTATAATATTCACAC
1 AAAATTACAATATTCATAC
* *
22573316 AAAAAGTTACAATATACGTAC
1 -AAAA-TTACAATATTCATAC
22573337 AAAATTAC
1 AAAATTAC
22573345 CATTGGCGCC
Statistics
Matches: 181, Mismatches: 20, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.02
17 5 0.03
18 12 0.07
19 70 0.39
20 31 0.17
21 36 0.20
22 7 0.04
23 9 0.05
24 2 0.01
25 3 0.02
26 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAATTACAATATTCATAC
Found at i:22573139 original size:40 final size:40
Alignment explanation
Indices: 22573095--22573240 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 40
22573085 ATTAATTATA
22573095 AAAAAATTACAATATTCATACAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTCATAC
* * *
22573135 AAAAAATTACAATATTCATACAAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTC-ATAC
* * * *
22573174 TATAAA-TACAAAATTAATT-ATAAAATAATTACAATATTCATTC
1 AAAAAATTAC--AA-T-ATTCATACAA-AATTACAATATTCATAC
22573217 --AAAATTACAATATTCATACAAAAT
1 AAAAAATTACAATATTCATACAAAAT
22573241 ACTAATCAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
38 12 0.14
39 17 0.20
40 29 0.35
41 9 0.11
42 8 0.10
43 6 0.07
44 3 0.04
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (40 bp):
AAAAAATTACAATATTCATACAAAATTACAATATTCATAC
Found at i:22573236 original size:80 final size:80
Alignment explanation
Indices: 22573118--22573319 Score: 343
Period size: 80 Copynumber: 2.5 Consensus size: 80
22573108 ATTCATACAA
22573118 AATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCCAA-AACTATAAATA
1 AATTACAATATTCATAC--AAAATTACAATATTCATACAAAATACTAAT-CAATAACTATAAATA
22573182 CAAAATTAATTATAAAAT
63 CAAAATTAATTATAAAAT
*
22573200 AATTACAATATTCATTCAAAATTACAATATTCATACAAAATACTAATCAATAACTATAAATACAA
1 AATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCAATAACTATAAATACAA
22573265 AATTAATTATAAAAT
66 AATTAATTATAAAAT
* *
22573280 AATTACAATATTCATACAAAATTATAATATTCACACAAAA
1 AATTACAATATTCATACAAAATTACAATATTCATACAAAA
22573320 AGTTACAATA
Statistics
Matches: 115, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
79 3 0.03
80 96 0.83
82 16 0.14
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (80 bp):
AATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCAATAACTATAAATACAA
AATTAATTATAAAAT
Found at i:22593302 original size:6 final size:6
Alignment explanation
Indices: 22593291--22593329 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
22593281 ATCAAGGATG
* *
22593291 GGGGAA GGGGAA GGGAAA GGGGAA GGGAAA GGGGAA GGG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGG
22593330 AAGATTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:22593312 original size:12 final size:12
Alignment explanation
Indices: 22593295--22593331 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
22593285 AGGATGGGGG
22593295 AAGGGGAAGGGA
1 AAGGGGAAGGGA
22593307 AAGGGGAAGGGA
1 AAGGGGAAGGGA
22593319 AAGGGGAAGGGA
1 AAGGGGAAGGGA
22593331 A
1 A
22593332 GATTGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
AAGGGGAAGGGA
Found at i:22598876 original size:2 final size:2
Alignment explanation
Indices: 22598869--22598911 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
22598859 GACATGTGCG
*
22598869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22598911 T
1 T
22598912 TCATTAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22599135 original size:3 final size:3
Alignment explanation
Indices: 22599116--22599154 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
22599106 GCGCATGAAT
* *
22599116 ATA AGA ATA AAA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
22599155 GATACAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:22599657 original size:19 final size:19
Alignment explanation
Indices: 22599633--22599686 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
22599623 AATCATATCT
22599633 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
22599652 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
22599671 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
22599687 CTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:22599682 original size:38 final size:40
Alignment explanation
Indices: 22599610--22599686 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
22599600 AAATTAAATC
22599610 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
22599652 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
22599687 CTTAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:22600292 original size:45 final size:45
Alignment explanation
Indices: 22600235--22600702 Score: 257
Period size: 44 Copynumber: 10.7 Consensus size: 45
22600225 TTGTTTATTT
* * * *
22600235 AGTCTGCCCCACTGCAATTTTAGAGG-GATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAG-GGAGATAAGACTCGATTTCTTG
*
22600280 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
22600325 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
22600367 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCTATGATT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT--TTCTTG
* ** * * * *
22600409 AATCCACTCCACTGCAACTTCAGGGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
* * * *
22600453 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-TCATCTTC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT-TTCTTG
* * * * *
22600498 AGTCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-
1 AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTCGATTTCTTG
* * * *
22600542 AGTCTGCTCCACTGCAACTTTAGAGAGATAAGACTAGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * * *
22600584 A-TCTACT-CTCTGCAACTTTAGAGAGATAAGA-TCTG-TTAT-TTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTC-GATT-TCTTG
* * * * * * * *
22600626 AATCCGCTCCACTGCGACTTCAGGGAGAGAGGA-T-TATTAGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
* *
22600670 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
22600703 TTCGCCATCT
Statistics
Matches: 332, Mismatches: 62, Indels: 59
0.73 0.14 0.13
Matches are distributed among these distances:
39 3 0.01
40 47 0.14
41 12 0.04
42 5 0.02
43 18 0.05
44 137 0.41
45 109 0.33
46 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:22600383 original size:40 final size:43
Alignment explanation
Indices: 22600282--22600397 Score: 139
Period size: 45 Copynumber: 2.7 Consensus size: 43
22600272 ATTTCTTGAG
* * * *
22600282 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGC-T-GA
22600327 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCG-ATGC-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGCTGA
* *
22600368 TCTGCT-CTCTGCAACTTCAGAGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
22600398 TCTATGATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
40 22 0.34
41 7 0.11
44 2 0.03
45 34 0.52
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGCTGA
Found at i:22600599 original size:173 final size:173
Alignment explanation
Indices: 22600282--22600702 Score: 383
Period size: 173 Copynumber: 2.4 Consensus size: 173
22600272 ATTTCTTGAG
* ** *
22600282 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTATCTTCAGTCTGCTCCACTACAACTTCA
* * **
22600347 GGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATGATTTTAAT
66 GGGAGATAAGACCCGATACGATCTGCTCACTGCAACTTCAGAGAGATAAGATCTATGATTGCAAT
* * *
22600412 CCACTCCACTGCAACTTCAGGGAGATAGGAT-TATTGGCTTTAA
131 CCACTCCACTGCAACTTCAGAGAGATAAGATCTATT-ACTTTAA
*
22600455 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-TCATCTTCAGTCTGC-CTCACTACAACTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCT-ATCTTCAGTCTGCTC-CACTACAACTT
* ** * * *
22600518 CA-GGAGGATAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGAGAGATAAGA-CTA-GA
64 CAGGGA-GATAAGACCCG-ATAC-GA-TCTGCT-CACTGCAACTTCAGAGAGATAAGATCTATGA
* * * * * *
22600580 -TGCGATCTACT-CTCTGCAACTTTAGAGAGATAAGATCTGTTATTTTAA
124 TTGCAATCCACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAA
* * * * *** * * * *
22600628 TCCGCTCCACTGCGACTTCAGGGAGAGAGGA-TTATTAGCTTTAATCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTATCTTCAGTCTGCTCCACTACAACTTCA
*
22600692 GAGAGATAAGA
66 GGGAGATAAGA
22600703 TTCGCCATCT
Statistics
Matches: 201, Mismatches: 36, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
172 34 0.17
173 121 0.60
174 12 0.06
175 3 0.01
176 9 0.04
177 22 0.11
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (173 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTATCTTCAGTCTGCTCCACTACAACTTCA
GGGAGATAAGACCCGATACGATCTGCTCACTGCAACTTCAGAGAGATAAGATCTATGATTGCAAT
CCACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAA
Found at i:22600609 original size:217 final size:218
Alignment explanation
Indices: 22600185--22600719 Score: 681
Period size: 217 Copynumber: 2.5 Consensus size: 218
22600175 ATTTCAGAAA
* * * * * * *
22600185 GATTCTAATCCACTCCACTACAACTTTAGGGAGATGGGATTTGTTTA--TTTAGTCTGCCCCACT
1 GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGA-TT-ATTAGCTTTAATCTGCTCCACT
* * * * *
22600248 GCAATTTTAGAGG-GATAAGACTT-GAT-TTCTTGAGTCTGCTCCACTGCAACTTCAGGGAGATA
64 GCAACTTCAG-GGAGATAAGA-TTCG-TCATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATA
* * * * *
22600310 AGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGCTC
126 AGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTACTC
22600375 TCTGCAACTTCAGAGAGATAAGATCTAT
191 TCTGCAACTTCAGAGAGATAAGATCTAT
*
22600403 GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGC
1 GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTAGCTTTAATCTGCTCCACTGC
*
22600468 AACTTCAGGGAGATAAGATTCGTCATCTTCAGTCTGC-CTCACTACAACTTCA-GGAGGATAAGG
66 AACTTCAGGGAGATAAGATTCGTCATCTTCAGTCTGCTC-CACTACAACTTCAGGGA-GATAAGA
* * *
22600531 CTTGCTTACTT-AGTCTGCTCCACTGCAACTTTAGAGAGATAAGACTAGATGCGATCTACTCTCT
129 CTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTACTCTCT
* *
22600595 GCAACTTTAGAGAGATAAGATCTGT
194 GCAACTTCAGAGAGATAAGATCTAT
* * * *
22600620 TATTTTAATCCGCTCCACTGCGACTTCAGGGAGAGAGGATTATTAGCTTTAATCTGCTCCACTGC
1 GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTAGCTTTAATCTGCTCCACTGC
* *
22600685 AACTTCAGAGAGATAAGATTCGCCATCTTCAGTCT
66 AACTTCAGGGAGATAAGATTCGTCATCTTCAGTCT
22600720 TTTAAATTGC
Statistics
Matches: 279, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
216 2 0.01
217 174 0.62
218 103 0.37
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTAGCTTTAATCTGCTCCACTGC
AACTTCAGGGAGATAAGATTCGTCATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACT
CGCTTACTTGAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTACTCTCTGC
AACTTCAGAGAGATAAGATCTAT
Found at i:22601066 original size:44 final size:44
Alignment explanation
Indices: 22601018--22601137 Score: 147
Period size: 44 Copynumber: 2.7 Consensus size: 44
22601008 ATCTGTTATT
*
22601018 TTCAACCTACTCCACTGGTGCTCAGGGAGATAAGA-TTCACAATC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTT-ACAATC
* * *
22601062 TTCAACATACTCCACTACTGAC-CAAGGAGATAAGACTTACAATC
1 TTCAACCTACTCCACTGCTG-CTCAGGGAGATAAGACTTACAATC
*
22601106 TTCAACCTATTCCACTGCTG-TCTAGGGAGATA
1 TTCAACCTACTCCACTGCTGCTC-AGGGAGATA
22601138 GGGTTGCGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 60 0.94
45 3 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (44 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTTACAATC
Found at i:22601459 original size:88 final size:88
Alignment explanation
Indices: 22601310--22601786 Score: 722
Period size: 88 Copynumber: 5.4 Consensus size: 88
22601300 NNNNNNNNNN
* *
22601310 GATCTGCTTCCCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAACCC
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCC
* *
22601375 AGAGAGGCAAGGTTGGTGTCTTC
66 AGGGAGGCAAGGCTGGTGTCTTC
* * *
22601398 GATCTGCTTTGCTGTCGGTGCAGGAAGGCAATATCTGCTATTTTTAACCTACTCCGCTACAACCC
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCC
* *
22601463 AGGTAGGCAAGGCTGGTGTCTTT
66 AGGGAGGCAAGGCTGGTGTCTTC
* * * ** *
22601486 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT-ATAATTTTTAACTTGCTCCACTGTAAAC
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTGCTCCGCTACAACC
* *
22601550 CAGGGAGGCAATGCTGATGTCTTC
65 CAGGGAGGCAAGGCTGGTGTCTTC
* *
22601574 GATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACCC
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCC
22601639 AGGGAGGCAAGGCTGGTGTCTTC
66 AGGGAGGCAAGGCTGGTGTCTTC
* *
22601662 GATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCTGCTACAACCC
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCC
* *
22601727 AGGGAGGGAAGGTTGGTGTCTTC
66 AGGGAGGCAAGGCTGGTGTCTTC
*
22601750 GATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTG
1 GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
22601787 TTATCTTCAC
Statistics
Matches: 349, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 1 0.00
88 347 0.99
89 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCC
AGGGAGGCAAGGCTGGTGTCTTC
Found at i:22601647 original size:44 final size:44
Alignment explanation
Indices: 22601594--22601729 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 44
22601584 GCTGTCAGTG
22601594 CAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACC
* * * * * * * * ****
22601638 CAGGGAGGCAAG-GCTGGTGTCTTC-GATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTAT-TTCTAACCTGCTCCGCT-ACAACC
* * *
22601682 CAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCTGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACC
22601726 CAGG
1 CAGG
22601730 GAGGGAAGGT
Statistics
Matches: 60, Mismatches: 28, Indels: 8
0.62 0.29 0.08
Matches are distributed among these distances:
43 15 0.25
44 31 0.52
45 14 0.23
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACC
Found at i:22601780 original size:264 final size:264
Alignment explanation
Indices: 22601310--22601785 Score: 808
Period size: 264 Copynumber: 1.8 Consensus size: 264
22601300 NNNNNNNNNN
* *
22601310 GATCTGCTTCCCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTACAACCC
1 GATCTGCTTCCCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTACTCCGCTACAACCC
* * * *
22601375 AGAGAGGCAAGGTTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAATATCTGCTATT
66 AGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATT
* *
22601440 TTTAACCTACTCCGCTACAACCCAGGTAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGT
131 TTTAACCTACTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGT
22601505 GCAGGAAGGCAAGATCTATAATTTTTAACTTGCTCCACTGTAAACCAGGGAGGCAATGCTGATGT
196 GCAGGAAGGCAAGATCTATAATTTTTAACTTGCTCCACTGTAAACCAGGGAGGCAATGCTGATGT
22601570 CTTC
261 CTTC
* *
22601574 GATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTGCTCCGCTACAACCC
1 GATCTGCTTCCCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTACTCCGCTACAACCC
*
22601639 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATT
66 AGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATT
* * * * *
22601704 TTTAACCTGCTCTGCTACAACCCAGGGAGGGAAGGTTGGTGTCTTCGATCTGCTTCGCTGTTGGT
131 TTTAACCTACTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGT
22601769 GCAGGAAGGCAAGATCT
196 GCAGGAAGGCAAGATCT
22601786 GTTATCTTCA
Statistics
Matches: 196, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
264 196 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (264 bp):
GATCTGCTTCCCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTCTAACCTACTCCGCTACAACCC
AGAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATT
TTTAACCTACTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGT
GCAGGAAGGCAAGATCTATAATTTTTAACTTGCTCCACTGTAAACCAGGGAGGCAATGCTGATGT
CTTC
Found at i:22603135 original size:14 final size:15
Alignment explanation
Indices: 22603112--22603144 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
22603102 ATTAACGCTT
22603112 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
22603126 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
22603141 TTCC
1 TTCC
22603145 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:22608287 original size:3 final size:3
Alignment explanation
Indices: 22608279--22608316 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
22608269 GCACATGAAT
22608279 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
22608317 GATACAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22608573 original size:15 final size:15
Alignment explanation
Indices: 22608536--22608575 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
22608526 AAGAGATTTG
*
22608536 AAATCAACAATATAC
1 AAATCAATAATATAC
22608551 AAATCAATAATATAC
1 AAATCAATAATATAC
22608566 AAATCAATAA
1 AAATCAATAA
22608576 ATAAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATCAATAATATAC
Found at i:22608577 original size:23 final size:23
Alignment explanation
Indices: 22608551--22608595 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22608541 AACAATATAC
* *
22608551 AAATCAATAATATACAAATCAAT
1 AAATAAATAATACACAAATCAAT
*
22608574 AAATAAATTATACACAAATCAA
1 AAATAAATAATACACAAATCAA
22608596 CAAAATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATAAATAATACACAAATCAAT
Found at i:22608828 original size:19 final size:19
Alignment explanation
Indices: 22608804--22608852 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
22608794 TTATATCTTT
22608804 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
* *
22608823 TAAGATTACGTATCATATC
1 TAAGATTGCATATCATATC
22608842 TAAGATTGCAT
1 TAAGATTGCAT
22608853 GTCCTTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:22611362 original size:27 final size:26
Alignment explanation
Indices: 22611332--22611389 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
22611322 ATGTAACAAG
* *
22611332 CACATTTGCAAACTTAGTTCACCAAAA
1 CACATTTACAAAC-AAGTTCACCAAAA
**
22611359 CACATTTACAAACAAGTTTGCCAAAA
1 CACATTTACAAACAAGTTCACCAAAA
22611385 CACAT
1 CACAT
22611390 CTGTGAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (26 bp):
CACATTTACAAACAAGTTCACCAAAA
Found at i:22612090 original size:33 final size:33
Alignment explanation
Indices: 22612053--22612119 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
22612043 TAATTACTTA
22612053 AGTATGAACATGTAAATTAAGAAAATATCAATC
1 AGTATGAACATGTAAATTAAGAAAATATCAATC
22612086 AGTATGAACATGTAAATTAAGAAAATATCAATC
1 AGTATGAACATGTAAATTAAGAAAATATCAATC
22612119 A
1 A
22612120 AATTCAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (33 bp):
AGTATGAACATGTAAATTAAGAAAATATCAATC
Found at i:22613273 original size:31 final size:31
Alignment explanation
Indices: 22613235--22613305 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
22613225 AAACACAAGC
* *
22613235 GAACCTAGGTTC-ACACTGTTAATCTTTTGGT
1 GAACCTAGGTCCGACA-TGCTAATCTTTTGGT
*
22613266 GAACCTAGGTCCGTACATGCTAGTCTTTTGGT
1 GAACCTAGGTCCG-ACATGCTAATCTTTTGGT
22613298 GAACCTAG
1 GAACCTAG
22613306 TTTCCTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
32 21 0.60
33 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (31 bp):
GAACCTAGGTCCGACATGCTAATCTTTTGGT
Found at i:22615114 original size:24 final size:24
Alignment explanation
Indices: 22615087--22615133 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
22615077 TAACATATTT
*
22615087 AATTTTATTTAATTTAAATCGAAC
1 AATTTTATTTAATTCAAATCGAAC
*
22615111 AATTTTATTTAATTCAATTCGAA
1 AATTTTATTTAATTCAAATCGAA
22615134 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (24 bp):
AATTTTATTTAATTCAAATCGAAC
Found at i:22615361 original size:3 final size:3
Alignment explanation
Indices: 22615353--22615396 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
22615343 TAGTAAACCC
22615353 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22615397 ATTAATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:22620736 original size:2 final size:2
Alignment explanation
Indices: 22620729--22620759 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22620719 TATGTTTAGA
*
22620729 AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22620760 ACAGCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:22622170 original size:30 final size:29
Alignment explanation
Indices: 22622134--22622193 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
22622124 ATGGTTTAAC
22622134 GTGTAATTTGTATACATGAAA-TTTGATTTT
1 GTGTAATTT-TATACAT-AAAGTTTGATTTT
22622164 GTGTAATTTTATACATAAAGTTTTGATTTT
1 GTGTAATTTTATACATAAAG-TTTGATTTT
22622194 ATTTAATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 7 0.25
30 18 0.64
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (29 bp):
GTGTAATTTTATACATAAAGTTTGATTTT
Found at i:22622201 original size:30 final size:30
Alignment explanation
Indices: 22622135--22622201 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
22622125 TGGTTTAACG
*
22622135 TGTAATTTGTATACATGAAATTTGATTTTG
1 TGTAATTTGTATACATGAAATTTGATTTTA
22622165 TGTAATTT-TATACAT-AAAGTTTTGATTTTA
1 TGTAATTTGTATACATGAAA--TTTGATTTTA
*
22622195 TTTAATT
1 TGTAATT
22622202 CTTGTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 7 0.21
30 23 0.70
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTAATTTGTATACATGAAATTTGATTTTA
Found at i:22622417 original size:29 final size:30
Alignment explanation
Indices: 22622385--22622445 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
22622375 TTTCACGTGA
* *
22622385 ATAATTGCAC-TAAATTAAAGTTCATGTAT
1 ATAATTACACATAAATCAAAGTTCATGTAT
22622414 ATAATTACACATTAAATCAAAGTTCATGTAT
1 ATAATTACACA-TAAATCAAAGTTCATGTAT
22622445 A
1 A
22622446 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
31 19 0.68
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (30 bp):
ATAATTACACATAAATCAAAGTTCATGTAT
Found at i:22633703 original size:116 final size:113
Alignment explanation
Indices: 22633551--22633780 Score: 370
Period size: 116 Copynumber: 2.0 Consensus size: 113
22633541 AAATTGAATG
*
22633551 AAATAATTGTATAGACCGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
1 AAATAATTGTATAGACAGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
* *
22633616 TAGTCCTTAAAGTTTCAACTTGTTTGCTATTTTTCTCAGGTAGGTTCAT
66 TAGTCCTTAAAGTTTCAACTTG-TTGCTATTTTTCCCAAGTAGGTTCAT
* * * *
22633665 AAATAATTGTATAGACTAGGAATTGGATCAAACTAGAGATAGTTGGGGAAAAGCAAAAATTTTAG
1 AAATAATTGTATAGAC-AGG-ATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAG
22633730 ATTAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
64 ATTAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
22633780 A
1 A
22633781 TAGTACTTAC
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 16 0.15
115 27 0.25
116 64 0.60
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (113 bp):
AAATAATTGTATAGACAGGATTGGATCAAACCAGAGATAGTCGGGAAAAAACAAAAATTTTAGAT
TAGTCCTTAAAGTTTCAACTTGTTGCTATTTTTCCCAAGTAGGTTCAT
Found at i:22637642 original size:39 final size:38
Alignment explanation
Indices: 22637588--22637720 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 38
22637578 TATTATAGAT
* *
22637588 TATAATGAGATCTAGCATTTGTTGCAGATCCTCGAGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTCT-GAGTAA
* * *
22637627 TATAACAAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTC-TGAGTAA
* * * *
22637666 TATAATGAGATCTAGCATCTATTGCAGATTCTTAGGTAA
1 TATAACGAGATCTAGCATTTGTTGCAGATTCTGA-GTAA
*
22637705 TATATCGAGATCTAGC
1 TATAACGAGATCTAGC
22637721 CCATTTTGTG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 76 0.97
40 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (38 bp):
TATAACGAGATCTAGCATTTGTTGCAGATTCTGAGTAA
Found at i:22637742 original size:78 final size:78
Alignment explanation
Indices: 22637588--22637747 Score: 189
Period size: 78 Copynumber: 2.1 Consensus size: 78
22637578 TATTATAGAT
* * * *
22637588 TATAATGAGATCTAGCATTTGTTGCAGATCCTCGAGTAATATAACAAGATCTAGCCTTTGTTGCA
1 TATAATGAGATCTAGCATCTATTGCAGATCCTAGAGTAATATAACAAGATCTAGCCATTGTTGCA
*
22637653 GATTCTTGGGTAA
66 GATTCTCGGGTAA
* * *
22637666 TATAATGAGATCTAGCATCTATTGCAGATTCTTAG-GTAATATATCGAGATCTAGCCCATT-TTG
1 TATAATGAGATCTAGCATCTATTGCAGA-TCCTAGAGTAATATAACAAGATCTAG-CCATTGTTG
** *
22637729 TGGGTTCTCGGGTAA
64 CAGATTCTCGGGTAA
22637744 TATA
1 TATA
22637748 TGACATAGGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 61 0.88
79 8 0.12
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (78 bp):
TATAATGAGATCTAGCATCTATTGCAGATCCTAGAGTAATATAACAAGATCTAGCCATTGTTGCA
GATTCTCGGGTAA
Found at i:22639573 original size:19 final size:20
Alignment explanation
Indices: 22639549--22639588 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22639539 TGAGCTAGTT
*
22639549 GGAGCTGGAA-TGAGCTAAA
1 GGAGCTGAAATTGAGCTAAA
22639568 GGAGCTGAAATTGAGCTAAA
1 GGAGCTGAAATTGAGCTAAA
22639588 G
1 G
22639589 TCAGCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.10, G:0.35, T:0.17
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAA
Found at i:22646642 original size:89 final size:89
Alignment explanation
Indices: 22646491--22646669 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
22646481 GATCATATGT
* *
22646491 ATATAAATGATTAACTTACCTTATATAACAAGTACATAGGTTAAACTAATGTGTATAATCAAATT
1 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
22646556 TACCTAACATATCAAAACGCAATC
66 TACCTAACATATCAAAACGCAATC
22646580 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
1 ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
22646645 TACCTAACATATCAAAACGCAATC
66 TACCTAACATATCAAAACGCAATC
22646669 A
1 A
22646670 CAATCAAGTG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (89 bp):
ATATAAACGATTAACTTACCTTATATAACAAGTACATAGGTCAAACTAATGTGTATAATCAAATT
TACCTAACATATCAAAACGCAATC
Found at i:22647576 original size:35 final size:35
Alignment explanation
Indices: 22647530--22647599 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
22647520 AAAACATACA
*
22647530 TAGATTCACAATATAACATCTATAATGATTTAAAC
1 TAGATTCACAATATAAAATCTATAATGATTTAAAC
*
22647565 TAGATTCACAATATAAAATTTATAATGATTTAAAC
1 TAGATTCACAATATAAAATCTATAATGATTTAAAC
22647600 ATAATTACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (35 bp):
TAGATTCACAATATAAAATCTATAATGATTTAAAC
Found at i:22651472 original size:12 final size:12
Alignment explanation
Indices: 22651457--22651486 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
22651447 TTTGGGGTAA
22651457 ATGGGAGGTGGG
1 ATGGGAGGTGGG
22651469 ATGGGAGGTGGG
1 ATGGGAGGTGGG
22651481 ATGGGA
1 ATGGGA
22651487 AGAGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.63, T:0.17
Consensus pattern (12 bp):
ATGGGAGGTGGG
Found at i:22651704 original size:21 final size:21
Alignment explanation
Indices: 22651670--22651710 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22651660 GGAGGGAAGT
*
22651670 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
22651691 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
22651711 GGAGTTTAGG
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:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:22651762 original size:9 final size:9
Alignment explanation
Indices: 22651748--22651784 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
22651738 TATAGTTTGA
22651748 TATTCGAAT
1 TATTCGAAT
22651757 TATTCGAAT
1 TATTCGAAT
*
22651766 TATTCGAGT
1 TATTCGAAT
*
22651775 TATTTGAAT
1 TATTCGAAT
22651784 T
1 T
22651785 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:22651853 original size:9 final size:9
Alignment explanation
Indices: 22651836--22651866 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22651826 TCGAGTTGAT
22651836 TCGAATAAC
1 TCGAATAAC
*
22651845 TCGATTAAC
1 TCGAATAAC
22651854 TCGAATAAC
1 TCGAATAAC
22651863 TCGA
1 TCGA
22651867 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:22653465 original size:19 final size:20
Alignment explanation
Indices: 22653410--22653475 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
22653400 CCTCATCAAA
*
22653410 TTATTTTATTAATAAAATAT
1 TTATTTTATTAATATAATAT
* * *
22653430 TT-TATTATTCATGTAATAT
1 TTATTTTATTAATATAATAT
22653449 TTATTTTATTAAT-TAAT-T
1 TTATTTTATTAATATAATAT
22653467 TTAATTTTA
1 TT-ATTTTA
22653476 ATATAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.08
19 25 0.66
20 10 0.26
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTTTATTAATATAATAT
Found at i:22653782 original size:23 final size:24
Alignment explanation
Indices: 22653740--22653786 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
22653730 TATAAAATAT
22653740 TAAAAACTTTCATAAAATTATAAA
1 TAAAAACTTTCATAAAATTATAAA
22653764 TAAAAAC-TT-ATAAATATTATAAA
1 TAAAAACTTTCATAAA-ATTATAAA
22653787 AACTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 10 0.45
24 7 0.32
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAACTTTCATAAAATTATAAA
Found at i:22653785 original size:9 final size:9
Alignment explanation
Indices: 22653763--22653816 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
22653753 AAAATTATAA
22653763 ATAAAAACTT
1 ATAAAAA-TT
*
22653773 ATAAATATT
1 ATAAAAATT
*
22653782 ATAAAAACT
1 ATAAAAATT
22653791 ATAAAAATT
1 ATAAAAATT
* *
22653800 CTAATAATT
1 ATAAAAATT
22653809 ATAAAAAT
1 ATAAAAAT
22653817 AAAAATAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
9 30 0.83
10 6 0.17
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:22654548 original size:20 final size:20
Alignment explanation
Indices: 22654525--22654562 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22654515 TTCTAATAAA
*
22654525 TTATAAAAAAATTGTAAATT
1 TTATAAAAAAATTATAAATT
*
22654545 TTATAATAAAATTATAAA
1 TTATAAAAAAATTATAAA
22654563 ATATTAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TTATAAAAAAATTATAAATT
Found at i:22655183 original size:9 final size:9
Alignment explanation
Indices: 22655169--22655400 Score: 70
Period size: 9 Copynumber: 25.1 Consensus size: 9
22655159 TAAACGATTT
22655169 TTTTTATAA
1 TTTTTATAA
*
22655178 TTTTTATAC
1 TTTTTATAA
**
22655187 TTTTTA-GC
1 TTTTTATAA
*
22655195 TTTTTATGA
1 TTTTTATAA
*
22655204 TTTATTAGAA
1 TTT-TTATAA
*
22655214 TTTATAT-A
1 TTTTTATAA
22655222 TTATTTATAAA
1 TT-TTTAT-AA
*
22655233 TTTTTAGTGA
1 TTTTTA-TAA
22655243 TTTTT-TAA
1 TTTTTATAA
22655251 GTTTTTATAAA
1 -TTTTTAT-AA
* *
22655262 ATTTTAAATA
1 TTTTTATA-A
22655272 TGTTTTATAAA
1 T-TTTTAT-AA
*
22655283 TTGTATCATAA
1 TT-T-TTATAA
*
22655294 TTTAT-TAA
1 TTTTTATAA
22655302 TTTTTATAA
1 TTTTTATAA
*
22655311 TTTTTTGTAA
1 -TTTTTATAA
** *
22655321 AATTTACAA
1 TTTTTATAA
* *
22655330 GTTTTTTTTA
1 -TTTTTATAA
22655340 TTTTTATAA
1 TTTTTATAA
*
22655349 CTTTATATCAA
1 -TTTTTAT-AA
22655360 -TTTTAT--
1 TTTTTATAA
*
22655366 TTTTT-TAT
1 TTTTTATAA
22655374 TTTTTA-ACA
1 TTTTTATA-A
*
22655383 TTTTTATGA
1 TTTTTATAA
22655392 TTTTT-TAA
1 TTTTTATAA
22655400 T
1 T
22655401 GATTTCTATG
Statistics
Matches: 163, Mismatches: 35, Indels: 51
0.65 0.14 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.02
8 28 0.17
9 62 0.38
10 44 0.27
11 20 0.12
12 4 0.02
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:22655405 original size:20 final size:19
Alignment explanation
Indices: 22655372--22655411 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22655362 TTATTTTTTT
*
22655372 ATTTTTTAACATTTTTATG
1 ATTTTTTAACATTTCTATG
*
22655391 ATTTTTTAATGATTTCTATG
1 ATTTTTTAA-CATTTCTATG
22655411 A
1 A
22655412 GAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTTTTTAACATTTCTATG
Found at i:22655806 original size:3 final size:3
Alignment explanation
Indices: 22655798--22655828 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
22655788 TGCTTTTTCT
22655798 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
22655829 CTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:22661697 original size:38 final size:39
Alignment explanation
Indices: 22661635--22661708 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
22661625 CACAAAAAAA
*
22661635 TATTTTAAAAATAAAAAATAAAAAAATATATTTTTAAAG
1 TATTTTAAAAATAAAAAATAAAAAAATATATATTTAAAG
*
22661674 TATTTTAAAATTAAAAAAT-AAAAAATATATATTTA
1 TATTTTAAAAATAAAAAATAAAAAAATATATATTTA
22661709 TTATATTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (39 bp):
TATTTTAAAAATAAAAAATAAAAAAATATATATTTAAAG
Found at i:22673119 original size:23 final size:22
Alignment explanation
Indices: 22673092--22673140 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
22673082 AAATATATGA
*
22673092 AATTTGAATTC-ACTTTAAATTTT
1 AATTTG-ATTCAACTGT-AATTTT
22673115 AATTTTGATTCAACTGTAATTTT
1 AA-TTTGATTCAACTGTAATTTT
22673138 AAT
1 AAT
22673141 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 14 0.61
24 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (22 bp):
AATTTGATTCAACTGTAATTTT
Found at i:22674534 original size:2 final size:2
Alignment explanation
Indices: 22674529--22674559 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22674519 AAAATTGAAC
*
22674529 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22674560 ATAGGACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22675615 original size:6 final size:6
Alignment explanation
Indices: 22675604--22675628 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22675594 CAATATAATA
22675604 TCCATT TCCATT TCCATT TCCATT T
1 TCCATT TCCATT TCCATT TCCATT T
22675629 TCAACCTTGA
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:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCATT
Found at i:22684241 original size:18 final size:18
Alignment explanation
Indices: 22684218--22684252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22684208 ATACATATAC
*
22684218 TTTTATAATTTATAATTT
1 TTTTATAATTTAAAATTT
*
22684236 TTTTATATTTTAAAATT
1 TTTTATAATTTAAAATT
22684253 ATATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATTTAAAATTT
Found at i:22685095 original size:22 final size:22
Alignment explanation
Indices: 22685048--22685097 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
22685038 AAAAAAATGA
* *
22685048 ATTTATAAGTGAATATCTTGTC
1 ATTTATAAGAGAATATATTGTC
*
22685070 ATTTATAATGAGAATATATT-TT
1 ATTTATAA-GAGAATATATTGTC
22685092 ATTTAT
1 ATTTAT
22685098 TATTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTATAAGAGAATATATTGTC
Found at i:22700669 original size:38 final size:38
Alignment explanation
Indices: 22700601--22700716 Score: 144
Period size: 38 Copynumber: 3.1 Consensus size: 38
22700591 AACTTTTATT
* **
22700601 ACACCGGCAATAA-CCTGCTAGGCACCAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
** ** *
22700638 ACATTGGCACTAAGCCTGCTAGGCATAAAGCCCAAATT
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
*
22700676 ACACCGGCACCAAGCCTGCTAGGCATAAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
22700714 ACA
1 ACA
22700717 GTATAATTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
37 10 0.16
38 54 0.84
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (38 bp):
ACACCGGCACTAAGCCTGCTAGGCATAAAGCCTGAATA
Found at i:22707312 original size:50 final size:50
Alignment explanation
Indices: 22707201--22707447 Score: 178
Period size: 50 Copynumber: 4.8 Consensus size: 50
22707191 ATTTGGGTAA
* * *
22707201 AGAGATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCA-C--CGA-G--ATG
* *
22707257 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
* *** * * * *
22707307 AGAGGTCCCCCATAAGACCATGTATGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
* * * * * * *
22707357 AGA-ACTCCCATTTAAGACCATATATTGGATATGGTATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCG-AGATG
* * *
22707406 AAACATCCCATGTAAGACCATGTCTCGGACATGGCT-TTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGG-TATTGGCA
22707448 TGTTATTATC
Statistics
Matches: 157, Mismatches: 30, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 79 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATG
Found at i:22708903 original size:37 final size:37
Alignment explanation
Indices: 22708861--22709083 Score: 374
Period size: 37 Copynumber: 6.0 Consensus size: 37
22708851 GGTAGTTTTA
*
22708861 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
22708898 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
22708935 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
22708972 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
22709009 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
22709046 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
22709083 G
1 G
22709084 TAGCTTCAGC
Statistics
Matches: 179, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 179 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:22709155 original size:45 final size:46
Alignment explanation
Indices: 22709046--22709169 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
22709036 GTGATAAGTG
* *
22709046 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
22709092 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
22709137 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
22709170 AGATCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:22717744 original size:25 final size:25
Alignment explanation
Indices: 22717711--22717784 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
22717701 CGAGCTACAT
* * *
22717711 AACGGTAAGCTCCTTCGAGCTGAAC
1 AACGATAAGCTCATGCGAGCTGAAC
* **
22717736 AACTATAAGCTCATGCGAGCTGAGT
1 AACGATAAGCTCATGCGAGCTGAAC
**
22717761 AACGATAAGCTCATATGAGCTGAA
1 AACGATAAGCTCATGCGAGCTGAA
22717785 ATCAGTAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (25 bp):
AACGATAAGCTCATGCGAGCTGAAC
Found at i:22721868 original size:19 final size:19
Alignment explanation
Indices: 22721844--22721882 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
22721834 CCAATTGTCA
22721844 GCCAAAAATAATTAAACAT
1 GCCAAAAATAATTAAACAT
22721863 GCCAAAAATAATTAAACAT
1 GCCAAAAATAATTAAACAT
22721882 G
1 G
22721883 TCAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (19 bp):
GCCAAAAATAATTAAACAT
Found at i:22724046 original size:17 final size:17
Alignment explanation
Indices: 22724024--22724082 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
22724014 TACGAGTGGA
22724024 AAATATAATTATATAAT
1 AAATATAATTATATAAT
22724041 AAATAT-ATT-TATAA-
1 AAATATAATTATATAAT
* * *
22724055 AAATTTGATATAAATAAT
1 AAATATAAT-TATATAAT
*
22724073 AAATACAATT
1 AAATATAATT
22724083 TTATTTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 4 0.12
17 11 0.33
18 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATATAATTATATAAT
Found at i:22725144 original size:61 final size:61
Alignment explanation
Indices: 22724977--22725159 Score: 149
Period size: 61 Copynumber: 3.0 Consensus size: 61
22724967 TTATTCGTCT
* * * * * *
22724977 AATAACAAAATTAGTCCTCTAATATTTAC-ACATTCTATCAATTT-GATCCTAAATAT-AAAAA
1 AATAATAAATTTAGCCCTC-AATATTTACAAAATT-TATCACTTTAG-TCCTAACTATAAAAAA
* * * * ** * *
22725038 ATTCAACAAATTTAGCCCTCAGTGTTTACAAAATTTATCTGTTTAGTTCTAATTATAAAAAA
1 AAT-AATAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCCTAACTATAAAAAA
* *
22725100 AATAATAAATTTGGCCCTCAATATTTACAAAATCTT-TCACTTTAGTCCTAACTCTAAAAA
1 AATAATAAATTTAGCCCTCAATATTTACAAAAT-TTATCACTTTAGTCCTAACTATAAAAA
22725160 TAAAAAAAAT
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
61 69 0.71
62 28 0.29
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (61 bp):
AATAATAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCCTAACTATAAAAAA
Found at i:22725658 original size:60 final size:60
Alignment explanation
Indices: 22725524--22725659 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 60
22725514 TTAAAAATAT
* * * ** ** *
22725524 ATTTTTAAATTTTTTAGAGTTAGGACTGAATTGACTGATTTTGTAAATGTTGAGAGCTGA
1 ATTTTTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
* * * *
22725584 ATTTATTGATTTTTTTAGAATTA-GACTAAAATGACAAATTTTTTAAACATTGAGGGCTAA
1 ATTT-TTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
22725644 ATTTGTTAAATTTTTT
1 ATTT-TTAAATTTTTT
22725660 TTATATTTGG
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 45 0.75
61 15 0.25
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (60 bp):
ATTTTTAAATTTTTTAGAATTAGGACTAAAATGACAAATTTTGTAAACATTGAGAGCTAA
Found at i:22728450 original size:3 final size:3
Alignment explanation
Indices: 22728442--22728524 Score: 72
Period size: 3 Copynumber: 30.0 Consensus size: 3
22728432 TTCCATTTTC
*
22728442 TCT TCT TCT T-T TCT TCT TCT TC- TCC TCT TCT TCT T-T TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
22728486 T-T TCT TCT TC- TCA TAT TCT TCT TTT TC- TCT TGT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
22728525 ACCGCCCAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
2 14 0.21
3 52 0.79
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:22728455 original size:8 final size:8
Alignment explanation
Indices: 22728439--22728524 Score: 70
Period size: 8 Copynumber: 10.5 Consensus size: 8
22728429 TCCTTCCATT
*
22728439 TTCTCTTC
1 TTCTTTTC
22728447 TTCTTTTC
1 TTCTTTTC
22728455 TTCTTCTTC
1 TTCTT-TTC
* *
22728464 TCCTCTTC
1 TTCTTTTC
22728472 TTCTTTTC
1 TTCTTTTC
22728480 TTCTTTT-
1 TTCTTTTC
22728487 TTCTTCTTC
1 TTCTT-TTC
*
22728496 -TCATATTC
1 TTC-TTTTC
22728504 TTCTTTT-
1 TTCTTTTC
22728511 TCTCTTGTTC
1 T-TCTT-TTC
22728521 TTCT
1 TTCT
22728525 ACCGCCCAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.10
8 42 0.67
9 14 0.22
10 1 0.02
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (8 bp):
TTCTTTTC
Found at i:22728461 original size:14 final size:14
Alignment explanation
Indices: 22728437--22728524 Score: 65
Period size: 14 Copynumber: 6.1 Consensus size: 14
22728427 AGTCCTTCCA
22728437 TTTTC-TCTTCTTC
1 TTTTCTTCTTCTTC
22728450 TTTTCTTCTTCTTC
1 TTTTCTTCTTCTTC
22728464 TCCTCTTCTTCTTTTCTTC
1 T--T-TTCTTC--TTCTTC
22728483 TTTT-TTCTTCTTC
1 TTTTCTTCTTCTTC
** *
22728496 TCATATTCTTCTT-
1 TTTTCTTCTTCTTC
*
22728509 TTTCTCTTGTTCTTC
1 TTT-TCTTCTTCTTC
22728524 T
1 T
22728525 ACCGCCCAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
13 14 0.23
14 25 0.42
15 4 0.07
16 3 0.05
17 7 0.12
19 7 0.12
ACGTcount: A:0.02, C:0.28, G:0.01, T:0.68
Consensus pattern (14 bp):
TTTTCTTCTTCTTC
Found at i:22728516 original size:11 final size:11
Alignment explanation
Indices: 22728442--22728510 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
22728432 TTCCATTTTC
22728442 TCTTCTTCTTT
1 TCTTCTTCTTT
22728453 TCTTCTTCTTCT
1 TCTTCTTCTT-T
22728465 CCTCTTCTTCTTT
1 --TCTTCTTCTTT
22728478 TCTTCTT-TTT
1 TCTTCTTCTTT
**
22728488 TCTTCTTCTCA
1 TCTTCTTCTTT
*
22728499 TATTCTTCTTT
1 TCTTCTTCTTT
22728510 T
1 T
22728511 TCTCTTGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 10 0.20
11 27 0.55
12 1 0.02
13 1 0.02
14 10 0.20
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:22731687 original size:59 final size:59
Alignment explanation
Indices: 22731595--22731714 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
22731585 TTACATTGTT
* *
22731595 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTTGAAATTCATGCTTAGACATCTCA
1 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
* *
22731654 ATTCTCAGCTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACGTCTCA
1 ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
22731713 AT
1 AT
22731715 CTTCGTAGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.40
Consensus pattern (59 bp):
ATTCTCAACTATTATTGACTCTTCGTGTTCAACTTCGAAATTAATGCTTAGACATCTCA
Found at i:22732614 original size:16 final size:16
Alignment explanation
Indices: 22732593--22732625 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
22732583 AAATCTTTTT
22732593 TCTTGTAATTTCTATA
1 TCTTGTAATTTCTATA
22732609 TCTTGTAATTTCTATA
1 TCTTGTAATTTCTATA
22732625 T
1 T
22732626 TTTTGAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (16 bp):
TCTTGTAATTTCTATA
Found at i:22733486 original size:42 final size:42
Alignment explanation
Indices: 22733429--22733643 Score: 200
Period size: 42 Copynumber: 5.1 Consensus size: 42
22733419 TTTGATTATG
* * *
22733429 CACTTACGTGTCAGTATATTTTCTTCAGTATATCCGATGATA
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * *
22733471 CACTTATGTGACAGTATATTTTCTTCGATATATCCAATGATA
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * * * *
22733513 CATTTATGTGCCAGTATATTTTCTTTGGTACATCCGATAATG
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * * ** * *
22733555 CACTTACGTGCCAGCATAATTGATTCGGTTTATCCGATGATG
1 CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
* * *
22733597 CAC-TATGTGTTCCAGTATATTTCCTTCGGTTTA-CTCGATGATG
1 CACTTATGTG--CCAGTATATTTTCTTCGGTATATC-CGATGATA
22733640 CACT
1 CACT
22733644 GCGGTGCCAG
Statistics
Matches: 141, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 5 0.04
42 107 0.76
43 29 0.21
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (42 bp):
CACTTATGTGCCAGTATATTTTCTTCGGTATATCCGATGATA
Found at i:22742090 original size:19 final size:18
Alignment explanation
Indices: 22742066--22742106 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
22742056 ATTAAAAAAT
22742066 AAAAATTATTAAATTTTA
1 AAAAATTATTAAATTTTA
22742084 GAAAAATTATTAAATTTTA
1 -AAAAATTATTAAATTTTA
22742103 AAAA
1 AAAA
22742107 TATAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAAATTATTAAATTTTA
Found at i:22742113 original size:25 final size:27
Alignment explanation
Indices: 22742085--22742141 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 27
22742075 TAAATTTTAG
*
22742085 AAAAATTATTAAATTTTA-AAAAT-AT
1 AAAAATTATAAAATTTTATAAAATCAT
*
22742110 AAAAATTGTAAAATTTTATAAAATCAT
1 AAAAATTATAAAATTTTATAAAATCAT
22742137 AAAAA
1 AAAAA
22742142 AACTAGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.57
26 5 0.18
27 7 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAAATTATAAAATTTTATAAAATCAT
Found at i:22742299 original size:21 final size:22
Alignment explanation
Indices: 22742275--22742324 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
22742265 AATTTAATAA
22742275 TTTAATAAATTTTTTTAT--TT
1 TTTAATAAATTTTTTTATAATT
* *
22742295 TTTTAT-AATTTTTTTCTAATT
1 TTTAATAAATTTTTTTATAATT
22742316 TTTAATAAA
1 TTTAATAAA
22742325 GCCAAGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.42
20 5 0.21
21 7 0.29
22 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTAATAAATTTTTTTATAATT
Found at i:22742307 original size:20 final size:21
Alignment explanation
Indices: 22742275--22742324 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
22742265 AATTTAATAA
*
22742275 TTTAATAAATTTTTT-TATTT
1 TTTAATAAATTTTTTCTAATT
* *
22742295 TTTTATAATTTTTTTCTAATT
1 TTTAATAAATTTTTTCTAATT
22742316 TTTAATAAA
1 TTTAATAAA
22742325 GCCAAGGGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTAATAAATTTTTTCTAATT
Found at i:22742308 original size:49 final size:48
Alignment explanation
Indices: 22742186--22742308 Score: 110
Period size: 48 Copynumber: 2.5 Consensus size: 48
22742176 AAAAATTTAC
* *
22742186 AATTTTTTATATTTTTATGATTTTTATAAAAAAATTTCTAAAGTTTAATA
1 AATTTTTTATTTTTTTAT-ATTTTT-TAAAAAAATTTCTAAAATTTAATA
* * **
22742236 AA-TTTTAATTTTTTTCGTA-TTTTTATTAAAA-TT-TAATAATTTAATA
1 AATTTTTTATTTTTTT-ATATTTTTTAAAAAAATTTCTAA-AATTTAATA
22742282 AATTTTTTTATTTTTTTATAATTTTTT
1 AA-TTTTTTATTTTTTTAT-ATTTTTT
22742309 TCTAATTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
45 3 0.05
46 12 0.20
47 7 0.12
48 17 0.29
49 17 0.29
50 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (48 bp):
AATTTTTTATTTTTTTATATTTTTTAAAAAAATTTCTAAAATTTAATA
Found at i:22742428 original size:89 final size:89
Alignment explanation
Indices: 22742334--22742503 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 89
22742324 AGCCAAGGGA
** * * * *
22742334 TTAATTACTTTTTTTTTAAAA-GTTTGAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACCCA
1 TTAATTAC-TTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
* *
22742398 ATTGAATGTAAAAAAAAGTAGGGGC
65 AATGAATGCAAAAAAAAGTAGGGGC
*
22742423 TTAATTGCTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
1 TTAATTACTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
*
22742488 ATGAGTGCAAAAAAAA
66 ATGAATGCAAAAAAAA
22742504 TGCAAAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
88 10 0.14
89 60 0.86
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (89 bp):
TTAATTACTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
ATGAATGCAAAAAAAAGTAGGGGC
Found at i:22742525 original size:89 final size:88
Alignment explanation
Indices: 22742333--22742526 Score: 217
Period size: 89 Copynumber: 2.2 Consensus size: 88
22742323 AAGCCAAGGG
** * * * *
22742333 ATTAATTACTTTTTTTTTAAAAGTTTGAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACCCA
1 ATTAATTAC-TTTTTTGAAAAAGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
* * * ****
22742398 ATTGAATGTAAAAAAAAGTAGGGG
65 AATGAATGCAAAAAAAAGCAAAAA
* *
22742422 CTTAATTGCTTTTTTGAAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
1 ATTAATTACTTTTTTGAAAAA-GTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACA
*
22742487 AATGAGTGCAAAAAAAATGCAAAAA
65 AATGAATGCAAAAAAAA-GCAAAAA
22742512 ATTAATTACTTTTTT
1 ATTAATTACTTTTTT
22742527 TTTTTTAAGT
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
88 10 0.12
89 60 0.71
90 15 0.18
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (88 bp):
ATTAATTACTTTTTTGAAAAAGTTTGAGGGTTTTTTTGATGCATTTTAAAAATTCAAGTACACAA
ATGAATGCAAAAAAAAGCAAAAA
Found at i:22744085 original size:243 final size:241
Alignment explanation
Indices: 22743716--22744351 Score: 735
Period size: 241 Copynumber: 2.6 Consensus size: 241
22743706 TCCCCCATTT
* * * *
22743716 TCTTCATTTTTATTTCTCAATTGTTTATTTC-A-CCGTCT-GTTCGTGGGATTTGGTTTTCCATT
1 TCTTCATTTTT-TTTCTCAATTGTTAATTTCAATGCG-CTAGTTCGTGGAATTTGGTTTTTCATT
** * *
22743778 TCTGA-CAGTATTTAGGGCAAAAATAGGATCGTAGAATTCTAAATTTATATTCAATTAAATCAGC
64 TC-GAGTTGTATTTAGGGGAAAAAAAGGATCGTAGAA-TCTAAATTTATATTCAATTAAATCAGC
* * * * *
22743842 CTAACATTTTTGTTAATAATTGTTTTTAATAAAGTTTCGTAGCTAATAAATTTATTAATCTGAAT
127 CTAACATTTTTGTTAATTATTGTTTTTAAT----TTCCGTACCTAACAAATTGATTAATCTGAAT
* *
22743907 TA-TTATTTATT-TTGCGAAATTTG-A-T-A-AAAA-ATTATGTTGTTTTTTCTTTG
188 AAGTTATTTATTATT---AAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
* *
22743957 TCTTCATTTTTGTTTCTCAATTGTTAATTCCAATGCGCTAGTTCGTGGAATTAGGTTTTTCATTT
1 TCTTCATTTTT-TTTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTT
* * * *
22744022 CGAGTTGTATATAGGGGAAAAGAAAAGATCGTAGAATCTAAATTTATAGTCAATTATATCAGCCT
65 CGAGTTGTATTTAGGGGAAAA-AAAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCT
*
22744087 AACATTTTTGTTAATTATTG--TTTCATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTA
129 AACATTTTTGTTAATTATTGTTTTTAATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTA
* *
22744150 TTTATTATTTATTTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
194 TTTATTATTAAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
* * * *
22744198 TCTTCATTTTTTCTTCTCAATTATTAATTTCAATGCGCCATTTTGTGGAATTTGGTTTTTCATTT
1 TCTTCATTTTTT-TTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTT
* *
22744263 TG-GATTGTATTTAGGGGGAAAAAATAGGATCGTGGAAT-TGAAATTTATATTCAATTAAATCAG
65 CGAG-TTGTATTTA-GGGGAAAAAA-AGGATCGTAGAATCT-AAATTTATATTCAATTAAATCAG
22744326 CCTAACATTTTTGTTAATTATTGTTT
126 CCTAACATTTTTGTTAATTATTGTTT
22744352 GTTTCTAATC
Statistics
Matches: 339, Mismatches: 37, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
236 5 0.01
237 29 0.09
238 10 0.03
239 3 0.01
240 6 0.02
241 121 0.36
242 68 0.20
243 84 0.25
244 13 0.04
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (241 bp):
TCTTCATTTTTTTTCTCAATTGTTAATTTCAATGCGCTAGTTCGTGGAATTTGGTTTTTCATTTC
GAGTTGTATTTAGGGGAAAAAAAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCTAA
CATTTTTGTTAATTATTGTTTTTAATTTCCGTACCTAACAAATTGATTAATCTGAATAAGTTATT
TATTATTAAATTTGCACTGATAAAAGATTAGGTTGTTTTTTCTTTG
Found at i:22756248 original size:276 final size:276
Alignment explanation
Indices: 22755755--22756305 Score: 1021
Period size: 276 Copynumber: 2.0 Consensus size: 276
22755745 CTGCATTTTA
*
22755755 GTTGTTATCCTACTGCTGCTGGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
1 GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
*
22755820 TAATAAATCCAAGTGTTGCTAATTTCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
66 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
22755885 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
131 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
*
22755950 GTACATGAATTTTGATTTTGTGCAGTTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
196 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
22756015 ACACTAACACTGTTTG
261 ACACTAACACTGTTTG
*
22756031 GTTGTTATCCTATTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
1 GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
22756096 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
66 TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
* *
22756161 GAACTGAATTTTTTCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
131 GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
*
22756226 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACATA
196 GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
* *
22756291 GCACTGACACTGTTT
261 ACACTAACACTGTTT
22756306 TCGACATAAC
Statistics
Matches: 266, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
276 266 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (276 bp):
GTTGTTATCCTACTGCTGCTAGTAGAAATTCACATTTCCTGATTCTTTTTGTTTGGTTTAGCATG
TAATAAATCCAAGTGTTGCTAATTCCGGAGAAGCTGATGCCCATGTCCCAACCGTGAGTAATCAT
GAACTGAAATTTTCCTTTTTGTGGGATAAATATCAAAGCTACCCATGAACTTTGGTCTATATATG
GTACATGAATTTTGATTTTGTGCAATTGCATACATGAAATTTCAATTTAATTCAATTTTCACAAA
ACACTAACACTGTTTG
Found at i:22756442 original size:31 final size:31
Alignment explanation
Indices: 22756407--22756470 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
22756397 AATGTTTACG
*
22756407 ATTGAATCAATATCAAAGTTTCATATATATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
* * * *
22756438 ATTGAATTAAAATCAAATTTTCATGTGTATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
22756469 AT
1 AT
22756471 ACTATCACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTGAATCAAAATCAAAGTTTCATATATATA
Found at i:22763231 original size:4 final size:4
Alignment explanation
Indices: 22763222--22763267 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
22763212 ATATTAGAAT
*
22763222 ATAC ATAC ATAC ATAC ATAC ATAC ATAA ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
22763268 TAATGTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:22766393 original size:16 final size:16
Alignment explanation
Indices: 22766372--22766403 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22766362 ATTTTACTAT
22766372 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
22766388 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
22766404 GGTTGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATAGTGGTTCATAAAA
Found at i:22768853 original size:22 final size:24
Alignment explanation
Indices: 22768828--22768881 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
22768818 TTATAAATTC
22768828 AATTTAA-AATATATAAT-ACAAT
1 AATTTAAGAATATATAATAACAAT
* *
22768850 AATTTCAAGCATATTTAATAACAAT
1 AATTT-AAGAATATATAATAACAAT
*
22768875 AGTTTAA
1 AATTTAA
22768882 TCATCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 2 0.08
24 10 0.38
25 9 0.35
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
AATTTAAGAATATATAATAACAAT
Found at i:22770252 original size:183 final size:183
Alignment explanation
Indices: 22769937--22770302 Score: 543
Period size: 183 Copynumber: 2.0 Consensus size: 183
22769927 TATTTTCCTT
* * *
22769937 CGTTTTCGCACGCGGTTAGTGCTTGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
1 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
* * * * * * **
22770002 TCTCTTAACGACTTAAGTGGTAATGTTTTTTCTCTGCGATTTGGACATAGGGGGAGGCTTGGACT
66 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
*
22770067 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAATGGAGGGTTATCATTGG
131 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
** *
22770120 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTTTGTTTCTGTCATGAA
1 CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
* * * *
22770185 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTTTATGATTTGGGCGTAAGGAGAGGCTCAGACT
66 TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
* *
22770250 GGTGAATTCGGTGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCGTTGG
131 GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
22770303 TGGTAAGTTG
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
183 162 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (183 bp):
CGTTTTCACACGCAGTTAGTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTGCGTTTCTATCATGAA
TCTCTTAACAACTGAAGTGATAATGTTTTTTCTCTACGATTTGGACATAAGGAGAGGCTCAGACT
GGTGAATTCGATGTTCTCGTCTTAACAATAGTTAAACGGAGGGTTATCATTGG
Found at i:22783758 original size:54 final size:54
Alignment explanation
Indices: 22783695--22783807 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
22783685 AGTATCATAT
22783695 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
* *
22783749 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
22783803 ATTAT
1 ATTAT
22783808 ATATTTTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
Found at i:22783795 original size:28 final size:27
Alignment explanation
Indices: 22783710--22783795 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 27
22783700 GATTTGAGTA
*
22783710 AATTCATATAAAAATATTAATTATTAAG
1 AATTCATAT-AAAATATTGATTATTAAG
* * *
22783738 AATT-TTATTAAAT-TATGA-T-TTGAG
1 AATTCATATAAAATAT-TGATTATTAAG
22783762 TAAATTCATATAAGAATATTGATTATTAAG
1 --AATTCATATAA-AATATTGATTATTAAG
22783792 AATT
1 AATT
22783796 TTATTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 4 0.09
25 2 0.05
26 10 0.23
27 7 0.16
28 14 0.33
29 2 0.05
30 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
AATTCATATAAAATATTGATTATTAAG
Found at i:22783827 original size:16 final size:16
Alignment explanation
Indices: 22783806--22783847 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
22783796 TTATTAAATT
*
22783806 ATATATTTTAATTATA
1 ATATATTTTAATAATA
22783822 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
22783837 AT-TATGTTTAA
1 ATATAT-TTTAA
22783848 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:22783832 original size:15 final size:15
Alignment explanation
Indices: 22783797--22783838 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
22783787 TTAAGAATTT
*
22783797 TATTAAATTAT-ATA
1 TATTTAATTATAATA
22783811 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
22783825 TATTTAATAATAAT
1 TATTTAATTATAAT
22783839 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:22783959 original size:156 final size:157
Alignment explanation
Indices: 22783783--22784096 Score: 549
Period size: 156 Copynumber: 2.0 Consensus size: 157
22783773 AAGAATATTG
*
22783783 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
* * * *
22783848 ATATGATTAAATTATTTATTATTGGTATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
22783913 ATAATTTACCAAAACAAATTTCTGCTA
131 ATAATTTACCAAAACAAATTTATGCTA
22783940 ATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
*
22784004 TTATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
22784069 ATCATTTACCAAAACAAATTTATGCTA
131 ATAATTTACCAAAACAAATTTATGCTA
22784096 A
1 A
22784097 GGGTATTCTA
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
156 145 0.97
157 4 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
ATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTATGCTA
Found at i:22783977 original size:18 final size:17
Alignment explanation
Indices: 22783949--22783983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
22783939 AATTATAAGA
*
22783949 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
22783966 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
22783984 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:22783983 original size:16 final size:16
Alignment explanation
Indices: 22783949--22784006 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
22783939 AATTATAAGA
22783949 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
22783966 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
22783982 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
22783996 ATGTTTAATTA
1 AT-TTTAATTA
22784007 TGATTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:22784253 original size:17 final size:16
Alignment explanation
Indices: 22784219--22784271 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
22784209 GATTTGTTAT
22784219 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
22784235 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
22784252 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
22784268 TACA
1 TACA
22784272 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:22784529 original size:20 final size:20
Alignment explanation
Indices: 22784500--22784548 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
22784490 CAAACAATAA
*
22784500 ATATCTATACTT-TGAACATT
1 ATATCGATACTTATGAA-ATT
*
22784520 ATATCGATACTTATTAAATT
1 ATATCGATACTTATGAAATT
22784540 -TATCGATAC
1 ATATCGATAC
22784549 CAATTTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 14 0.54
21 3 0.12
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
ATATCGATACTTATGAAATT
Found at i:22784965 original size:12 final size:12
Alignment explanation
Indices: 22784948--22784994 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
22784938 ATAAATACCA
22784948 AAAAATTATTTT
1 AAAAATTATTTT
***
22784960 AAAAATTA-AAA
1 AAAAATTATTTT
22784971 AAAAATTATTTT
1 AAAAATTATTTT
*
22784983 AAAAAATATTTT
1 AAAAATTATTTT
22784995 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:22785057 original size:35 final size:37
Alignment explanation
Indices: 22784996--22785077 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 37
22784986 AAATATTTTT
* *
22784996 TATTTTTAAATTAAAATTTTACAAAGTATTTTAAAA-
1 TATTTTAAAATTAAAAATTTACAAAGTATTTTAAAAG
22785032 TATTTTAAAATTAAAAATTTA-AAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAATTTACAAAGTATTTTAAAAG
22785068 TATTTTAAAA
1 TATTTTAAAA
22785078 GTATTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 14 0.33
36 29 0.67
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TATTTTAAAATTAAAAATTTACAAAGTATTTTAAAAG
Found at i:22785065 original size:11 final size:11
Alignment explanation
Indices: 22785011--22785089 Score: 88
Period size: 11 Copynumber: 6.8 Consensus size: 11
22785001 TTAAATTAAA
22785011 ATTTTACAAAGT
1 ATTTTA-AAAGT
22785023 ATTTTAAAA-T
1 ATTTTAAAAGT
*
22785033 ATTTTAAAATT
1 ATTTTAAAAGT
*
22785044 AAAAATTTAAAAGT
1 ---ATTTTAAAAGT
22785058 ATTTTAAAAGT
1 ATTTTAAAAGT
22785069 ATTTTAAAAGT
1 ATTTTAAAAGT
22785080 ATTTTTAAAA
1 A-TTTTAAAA
22785090 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
10 10 0.17
11 26 0.44
12 14 0.24
14 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (11 bp):
ATTTTAAAAGT
Found at i:22785102 original size:47 final size:47
Alignment explanation
Indices: 22785011--22785102 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 47
22785001 TTAAATTAAA
*
22785011 ATTTTACAAAGTATTTTAAAATATTTTAAAATTAAAAATTTAAAAGT
1 ATTTTACAAAGTATTTTAAAATATTTTAAAATTAAAAATATAAAAGT
22785058 ATTTTA-AAAGTATTTTAAAAGTATTTTTAAAATTAAAAA-ATAAAA
1 ATTTTACAAAGTATTTTAAAA-TA-TTTTAAAATTAAAAATATAAAA
22785103 AATAAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
46 14 0.33
47 13 0.31
48 15 0.36
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (47 bp):
ATTTTACAAAGTATTTTAAAATATTTTAAAATTAAAAATATAAAAGT
Found at i:22789568 original size:2 final size:2
Alignment explanation
Indices: 22789561--22789593 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22789551 ATCAATTAAA
22789561 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22789594 ACTTAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22790006 original size:7 final size:7
Alignment explanation
Indices: 22789994--22790018 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22789984 AGTTGAGGGT
22789994 GGAAGAG
1 GGAAGAG
22790001 GGAAGAG
1 GGAAGAG
22790008 GGAAGAG
1 GGAAGAG
22790015 GGAA
1 GGAA
22790019 AAGAAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GGAAGAG
Found at i:22802184 original size:24 final size:23
Alignment explanation
Indices: 22802157--22802222 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 23
22802147 CCCTTCTATT
22802157 TTATTTTATTTATTATTTCTTATA
1 TTATTTTATTTATTA-TTCTTATA
22802181 TTA-TTTATTT-TTATT-TTACTA
1 TTATTTTATTTATTATTCTTA-TA
22802202 --ATTTTATTTATTATTCTTATA
1 TTATTTTATTTATTATTCTTATA
22802223 CTTAGATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 11 0.29
22 6 0.16
23 7 0.18
24 3 0.08
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTATTTATTATTCTTATA
Found at i:22802224 original size:24 final size:24
Alignment explanation
Indices: 22802159--22802233 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 24
22802149 CTTCTATTTT
*
22802159 ATTTTATTTATTATTTCTTATA-TT
1 ATTTTATTTATTA-TTCTTATACTA
22802183 A-TTTATTT-TTA-T-TT-TACTA
1 ATTTTATTTATTATTCTTATACTA
22802202 ATTTTATTTATTATTCTTATACTTA
1 ATTTTATTTATTATTCTTATAC-TA
22802227 GATTTTA
1 -ATTTTA
22802234 AATTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 8 0.19
21 3 0.07
22 4 0.10
23 9 0.21
24 4 0.10
25 2 0.05
26 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (24 bp):
ATTTTATTTATTATTCTTATACTA
Found at i:22802360 original size:24 final size:22
Alignment explanation
Indices: 22802326--22802389 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
22802316 TATCATTTAG
*
22802326 TTTATTATTATTATTTTTTCCGT
1 TTTATTTTTATTATTTTTT-CGT
* *
22802349 TTTATTTTTTATT-TATCTTTCTT
1 TTTA-TTTTTATTAT-TTTTTCGT
22802372 TTTATTTTT-TTATTTTTT
1 TTTATTTTTATTATTTTTT
22802390 AAACTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.18
22 6 0.18
23 11 0.32
24 11 0.32
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATTATTTTTTCGT
Found at i:22807202 original size:40 final size:40
Alignment explanation
Indices: 22807149--22807287 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
22807139 AACACACTAG
* *
22807149 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * *
22807189 TTTGACACACAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * *
22807227 TTAG-CACCCAATGCCTCATC-GATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA
* *
22807266 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
22807288 ACTCGAAGTC
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
36 1 0.01
37 22 0.29
38 5 0.07
39 5 0.07
40 43 0.57
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:22807744 original size:24 final size:23
Alignment explanation
Indices: 22807716--22807761 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
22807706 GGCTTTCTCT
22807716 TTCCTTTCTTTCCTTTTTCTTTTC
1 TTCCTTTCTTT-CTTTTTCTTTTC
22807740 TTCCTTTCTTTCTTTTTCTTTT
1 TTCCTTTCTTTCTTTTTCTTTT
22807762 TGTTTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCCTTTCTTTCTTTTTCTTTTC
Found at i:22807752 original size:4 final size:4
Alignment explanation
Indices: 22807713--22807787 Score: 55
Period size: 4 Copynumber: 18.2 Consensus size: 4
22807703 TGTGGCTTTC
* * *
22807713 TCTT TCCTT TCTT TCCT T-TT TCTTT TCTT CCTT TCTT TCTT T-TT CTTTT
1 TCTT T-CTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCTT -TCTT
* *
22807762 TGTT TCATT TCTA TCTT TCTT TCTT T
1 TCTT TC-TT TCTT TCTT TCTT TCTT T
22807788 TTATTTATTC
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
3 4 0.07
4 39 0.68
5 14 0.25
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.72
Consensus pattern (4 bp):
TCTT
Found at i:22808792 original size:15 final size:15
Alignment explanation
Indices: 22808772--22808800 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22808762 AATAATATTA
22808772 ATAATAATGATAATG
1 ATAATAATGATAATG
22808787 ATAATAATGATAAT
1 ATAATAATGATAAT
22808801 TTAAAGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
ATAATAATGATAATG
Found at i:22813474 original size:6 final size:7
Alignment explanation
Indices: 22813447--22813472 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22813437 ATATTTATTT
22813447 ATTTTTA
1 ATTTTTA
22813454 ATTTTTA
1 ATTTTTA
22813461 ATTTTTA
1 ATTTTTA
22813468 ATTTT
1 ATTTT
22813473 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Done.