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 81 of 202
Found at i:23810053 original size:21 final size:20
Alignment explanation
Indices: 23810027--23810076 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
23810017 GCGGTGGAAA
* *
23810027 TGAGATTAATTACTGTAGCGG
1 TGAGATTAA-TACTGTAACAG
*
23810048 TGAGATTGGATACTGTAACAG
1 TGAGATT-AATACTGTAACAG
23810069 TGAGATTA
1 TGAGATTA
23810077 GAAACAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (20 bp):
TGAGATTAATACTGTAACAG
Found at i:23810634 original size:23 final size:23
Alignment explanation
Indices: 23810604--23810654 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
23810594 TAAAATAAAA
23810604 TGAAGACATTAAAAGACAACAAT
1 TGAAGACATTAAAAGACAACAAT
23810627 TGAAGACATTAAAAGACAACAAT
1 TGAAGACATTAAAAGACAACAAT
23810650 TGAAG
1 TGAAG
23810655 GAAGGCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (23 bp):
TGAAGACATTAAAAGACAACAAT
Found at i:23811060 original size:19 final size:21
Alignment explanation
Indices: 23811032--23811080 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
23811022 GGTTTTTTAC
*
23811032 TAAAATAATA-CAAAAGAA-A
1 TAAAAAAATACCAAAAGAATA
*
23811051 TAAAAAAATACCAAAATAATA
1 TAAAAAAATACCAAAAGAATA
23811072 TAAAAAAAT
1 TAAAAAAAT
23811081 TATTTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 7 0.27
21 10 0.38
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAAATACCAAAAGAATA
Found at i:23811158 original size:27 final size:27
Alignment explanation
Indices: 23811128--23811187 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
23811118 GGTAATGGAA
*
23811128 TGGCGGCA-CTGGTGGTGCCATTCTCAT
1 TGGCGGCATC-GGTGGTGCCATTCCCAT
23811155 TGGCGGCATCGGTGGTGCCATTCCCAT
1 TGGCGGCATCGGTGGTGCCATTCCCAT
23811182 TGGCGG
1 TGGCGG
23811188 TACAGGACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.10, C:0.27, G:0.37, T:0.27
Consensus pattern (27 bp):
TGGCGGCATCGGTGGTGCCATTCCCAT
Found at i:23812997 original size:39 final size:39
Alignment explanation
Indices: 23812943--23813021 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
23812933 TAGTCCTTTG
23812943 ACTCAATTACTTATTTTGTAGTCCTATATGATAAAAACT
1 ACTCAATTACTTATTTTGTAGTCCTATATGATAAAAACT
23812982 ACTCAATTACTTATTTTGTAGTCCTATATGATAAAAACT
1 ACTCAATTACTTATTTTGTAGTCCTATATGATAAAAACT
23813021 A
1 A
23813022 GGCCGCATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (39 bp):
ACTCAATTACTTATTTTGTAGTCCTATATGATAAAAACT
Found at i:23813353 original size:103 final size:105
Alignment explanation
Indices: 23813166--23813384 Score: 234
Period size: 103 Copynumber: 2.1 Consensus size: 105
23813156 TGATTATTAC
* * *
23813166 ACCTGTTTTATGCACTTAAGTTGGCATAGGTTAGGCGTTGTTGTTGATGGTATAGAATATAAGGA
1 ACCTGTTTTATGCACTTAAGTTGGCATAGGTTA-GAGTTGTTGTTGATGATATAGAATATAAAGA
* * *
23813231 TCTAAACTTTCATAGGTTTATGTGTCCAG-TT-AT-AATCT
65 TCCAAACTTTCATAGGTTTATATCTCCAGCTTAATGAATCT
* *
23813269 ACCTGTTTTATGTACTTGAGTTGGCAT-GGTTTA-AG-TGTTGTTGATGATATAGAATATAAAGA
1 ACCTGTTTTATGCACTTAAGTTGGCATAGG-TTAGAGTTGTTGTTGATGATATAGAATATAAAGA
** **
23813331 TCCAATTTTTTTTTATGTGTTTATATCTCCAGTCTTAATGAATCT
65 TCCAA-ACTTTCATA-G-GTTTATATCTCCAG-CTTAATGAATCT
23813376 ACCTGTTTT
1 ACCTGTTTT
23813385 TGTGCACTAG
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
100 29 0.30
101 6 0.06
102 3 0.03
103 40 0.42
105 2 0.02
106 2 0.02
107 14 0.15
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (105 bp):
ACCTGTTTTATGCACTTAAGTTGGCATAGGTTAGAGTTGTTGTTGATGATATAGAATATAAAGAT
CCAAACTTTCATAGGTTTATATCTCCAGCTTAATGAATCT
Found at i:23819081 original size:16 final size:16
Alignment explanation
Indices: 23819045--23819096 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
23819035 AAAAATTATG
* *
23819045 TTTTCCAT-CTTCTAG
1 TTTTCCATCCTTCCAA
23819060 TTTTCCATCCCTT-CAA
1 TTTTCCAT-CCTTCCAA
23819076 TTTTCCATCCTTCCAA
1 TTTTCCATCCTTCCAA
23819092 TTTTC
1 TTTTC
23819097 TTTTCACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 12 0.38
16 17 0.53
17 3 0.09
ACGTcount: A:0.15, C:0.33, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTTCCATCCTTCCAA
Found at i:23821007 original size:22 final size:19
Alignment explanation
Indices: 23820958--23820998 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
23820948 ATAAAAGATA
*
23820958 TAAAATGATAAATTTATTT
1 TAAAATAATAAATTTATTT
*
23820977 TTAAATAATATAATTTATTT
1 TAAAATAATA-AATTTATTT
23820997 TA
1 TA
23820999 CAAAATAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAAATAATAAATTTATTT
Found at i:23821866 original size:22 final size:23
Alignment explanation
Indices: 23821839--23821883 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
23821829 TTAAGTGTTT
23821839 AATTAGGATTTAAGG-TTTATTA
1 AATTAGGATTTAAGGTTTTATTA
* *
23821861 AATTAGGGTTTTAGGTTTTATTA
1 AATTAGGATTTAAGGTTTTATTA
23821884 TTTTCAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (23 bp):
AATTAGGATTTAAGGTTTTATTA
Found at i:23831439 original size:18 final size:19
Alignment explanation
Indices: 23831406--23831442 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
23831396 ATGTTTTAGT
23831406 TATTTATTTAAGTAAAATA
1 TATTTATTTAAGTAAAATA
*
23831425 TATTTA-TTAATTAAAATA
1 TATTTATTTAAGTAAAATA
23831443 AAATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTATTTAAGTAAAATA
Found at i:23834470 original size:47 final size:47
Alignment explanation
Indices: 23834364--23834474 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
23834354 AAAGTGGATG
* * *
23834364 TTATTGGTAGTTTATCTATAATTTTGATGGCTTGTCCACGATTTTGA
1 TTATTGATAGTTTATCTACAATTTTGATGGCTTGTCCACAATTTTGA
* * *
23834411 TTATT-AGCAGTTTATCTACGATTTTGGTGGCTTGTCCACAATTTTGA
1 TTATTGA-TAGTTTATCTACAATTTTGATGGCTTGTCCACAATTTTGA
23834458 TTATTGATAGTTTATCT
1 TTATTGATAGTTTATCT
23834475 GCATTATTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 54 0.98
48 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (47 bp):
TTATTGATAGTTTATCTACAATTTTGATGGCTTGTCCACAATTTTGA
Found at i:23834858 original size:8 final size:8
Alignment explanation
Indices: 23834845--23834875 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
23834835 AATTAAATTT
23834845 TATTTTGA
1 TATTTTGA
23834853 TATTTTGA
1 TATTTTGA
23834861 TATTTTGA
1 TATTTTGA
23834869 TATTTTG
1 TATTTTG
23834876 GGTTTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (8 bp):
TATTTTGA
Found at i:23864000 original size:36 final size:36
Alignment explanation
Indices: 23863960--23864035 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
23863950 ACAATGTTTG
*
23863960 ATAAAAATTATATATAAA-TTACAAAAAAAAATATAC
1 ATAAAAA-TATATACAAATTTACAAAAAAAAATATAC
* **
23863996 ATAAAAATATATACAAATTTATAAGTAAAAATATAC
1 ATAAAAATATATACAAATTTACAAAAAAAAATATAC
23864032 ATAA
1 ATAA
23864036 TTATATCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.26
36 26 0.74
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (36 bp):
ATAAAAATATATACAAATTTACAAAAAAAAATATAC
Found at i:23864001 original size:14 final size:14
Alignment explanation
Indices: 23863975--23864012 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23863965 AATTATATAT
23863975 AAAT-TACAAAAAA
1 AAATATACAAAAAA
*
23863988 AAATATACATAAAA
1 AAATATACAAAAAA
*
23864002 ATATATACAAA
1 AAATATACAAA
23864013 TTTATAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATATACAAAAAA
Found at i:23864003 original size:12 final size:12
Alignment explanation
Indices: 23863986--23864165 Score: 95
Period size: 12 Copynumber: 15.3 Consensus size: 12
23863976 AATTACAAAA
23863986 AAAAATATACAT
1 AAAAATATACAT
* *
23863998 AAAAATATATAC
1 AAAAATATACAT
**
23864010 AAATTTATA-AGT
1 AAAAATATACA-T
23864022 AAAAATATACAT
1 AAAAATATACAT
**
23864034 AATTATAT-CTAT
1 AAAAATATAC-AT
*
23864046 AAAAATGTACAT
1 AAAAATATACAT
***
23864058 AAAAATACGTAT
1 AAAAATATACAT
* * *
23864070 GACAATATAGA-
1 AAAAATATACAT
* *
23864081 AACAATAT-TAT
1 AAAAATATACAT
23864092 -AAAATAATACAT
1 AAAAAT-ATACAT
*
23864104 AAGAATATACAT
1 AAAAATATACAT
* * *
23864116 AGAATTATGCAT
1 AAAAATATACAT
*
23864128 AAATATATACA-
1 AAAAATATACAT
23864139 AAAAA-ATACAT
1 AAAAATATACAT
*
23864150 AAAGATATACAT
1 AAAAATATACAT
23864162 AAAA
1 AAAA
23864166 TAATATTAAC
Statistics
Matches: 121, Mismatches: 37, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
10 10 0.08
11 19 0.16
12 86 0.71
13 6 0.05
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAAATATACAT
Found at i:23866644 original size:27 final size:27
Alignment explanation
Indices: 23866614--23866691 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
23866604 AACACGTCAG
*
23866614 GAAAGAAATGCCTTTGTGGCGAAATAT
1 GAAAGAAAAGCCTTTGTGGCGAAATAT
23866641 GAAAGAAAAGCCTTTGTGGCGAAATAT
1 GAAAGAAAAGCCTTTGTGGCGAAATAT
* *
23866668 AAAAGAAAAGCCCTTGTGGC-AAAT
1 GAAAGAAAAGCCTTTGTGGCGAAAT
23866692 TTCGTATGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 4 0.08
27 44 0.92
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCGAAATAT
Found at i:23868206 original size:104 final size:105
Alignment explanation
Indices: 23867993--23868212 Score: 379
Period size: 108 Copynumber: 2.1 Consensus size: 105
23867983 AGGAGAAGAT
* *
23867993 TGTGAGATGGTCAATTGGGTTAGTGAAAATCGTGTTAATTAATTTGTGTGAGTTGTCGATTTAGG
1 TGTGTGATGGTCAATCGGGTTAGTGAAAATCGTGTTAATTAATTTGTGTGAGTTGTCG---TAGG
23868058 TACTGAACTACTTATTCGTGAAGTTACATCAATAATATTAAGG
63 TACTGAACTACTTATTCGTGAAGTTACATCAATAATATTAAGG
23868101 TGTGTGATGGTCAATCGGGTTAGTGAAAATCGTGTTAATTAATTTGTGTGAGTTGTCG-AGGTAC
1 TGTGTGATGGTCAATCGGGTTAGTGAAAATCGTGTTAATTAATTTGTGTGAGTTGTCGTAGGTAC
*
23868165 TGAACTACTTATTTGTGAAGTTACATCAATAATATTAAGG
66 TGAACTACTTATTCGTGAAGTTACATCAATAATATTAAGG
23868205 TGTGTGAT
1 TGTGTGAT
23868213 TCTAACACGA
Statistics
Matches: 109, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
104 53 0.49
108 56 0.51
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (105 bp):
TGTGTGATGGTCAATCGGGTTAGTGAAAATCGTGTTAATTAATTTGTGTGAGTTGTCGTAGGTAC
TGAACTACTTATTCGTGAAGTTACATCAATAATATTAAGG
Found at i:23870646 original size:3 final size:3
Alignment explanation
Indices: 23870638--23870691 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
23870628 CCATTCTAAG
23870638 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23870686 TAA TAA
1 TAA TAA
23870692 AAAATAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23874709 original size:18 final size:20
Alignment explanation
Indices: 23874680--23874726 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
23874670 AAACTTAAAA
* *
23874680 AAAACAATATATATAAATTG
1 AAAATAATATATATAAAATG
23874700 AAAATAATATATATAAAATG
1 AAAATAATATATATAAAATG
23874720 AAAATAA
1 AAAATAA
23874727 AAATAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
AAAATAATATATATAAAATG
Found at i:23874773 original size:26 final size:27
Alignment explanation
Indices: 23874752--23874805 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
23874742 TTAAAATTTC
* *
23874752 AAAATTTTTAAAA-AATTAAAAATTAA
1 AAAATGTTTAAAAGAATAAAAAATTAA
*
23874778 AAAATGTTTAAAAGAATAAAAAAATAA
1 AAAATGTTTAAAAGAATAAAAAATTAA
23874805 A
1 A
23874806 TTTAGTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAATGTTTAAAAGAATAAAAAATTAA
Found at i:23876642 original size:3 final size:3
Alignment explanation
Indices: 23876634--23876676 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
23876624 GCAAGAGGAC
23876634 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
23876677 AGGAGATAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:23883336 original size:42 final size:42
Alignment explanation
Indices: 23883280--23883460 Score: 220
Period size: 42 Copynumber: 4.3 Consensus size: 42
23883270 AGCTCATGAA
* * * *
23883280 AGCTAATCAGAAACCCATAAGGGTTGAACATAAGCTCATAAG
1 AGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
*
23883322 AGCTAAAC-GAAAACCCATAAGGGTTAAATAGAAGCTCAAAAG
1 AGCTAAACAG-AAACCCATAAGGGTTAAACAGAAGCTCAAAAG
* * * *
23883364 AGTTAAACGGAAAGCCATAAGTGTTAAACAGAAGCTCAAAAG
1 AGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
* * * *
23883406 AGCTAAACAGAAACTCATATGAGTTAAACAGAAGCTCAAGAG
1 AGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
*
23883448 AGCTAAATAGAAA
1 AGCTAAACAGAAA
23883461 GTAAACACGA
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 118 0.98
43 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (42 bp):
AGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
Found at i:23883349 original size:21 final size:21
Alignment explanation
Indices: 23883290--23883349 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
23883280 AGCTAATCAG
*
23883290 AAACCCATAAGGGTTGAACAT
1 AAACCCATAAGGGTTAAACAT
* * * *
23883311 AAGCTCATAAGAGCTAAACGA-
1 AAACCCATAAGGGTTAAAC-AT
23883332 AAACCCATAAGGGTTAAA
1 AAACCCATAAGGGTTAAA
23883350 TAGAAGCTCA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (21 bp):
AAACCCATAAGGGTTAAACAT
Found at i:23883368 original size:21 final size:21
Alignment explanation
Indices: 23883344--23883459 Score: 117
Period size: 21 Copynumber: 5.5 Consensus size: 21
23883334 ACCCATAAGG
*
23883344 GTTAAATAGAAGCTCAAAAGA
1 GTTAAACAGAAGCTCAAAAGA
* * *
23883365 GTTAAACGGAAAGC-CATAAGT
1 GTTAAACAG-AAGCTCAAAAGA
23883386 GTTAAACAGAAGCTCAAAAGA
1 GTTAAACAGAAGCTCAAAAGA
* * * *
23883407 GCTAAACAGAAACTCATATGA
1 GTTAAACAGAAGCTCAAAAGA
*
23883428 GTTAAACAGAAGCTCAAGAGA
1 GTTAAACAGAAGCTCAAAAGA
* *
23883449 GCTAAATAGAA
1 GTTAAACAGAA
23883460 AGTAAACACG
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 4 0.05
21 67 0.89
22 4 0.05
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (21 bp):
GTTAAACAGAAGCTCAAAAGA
Found at i:23885528 original size:10 final size:10
Alignment explanation
Indices: 23885513--23885537 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23885503 GTTGTCGTAA
23885513 ACCTGTTGGT
1 ACCTGTTGGT
23885523 ACCTGTTGGT
1 ACCTGTTGGT
23885533 ACCTG
1 ACCTG
23885538 ATGTTCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (10 bp):
ACCTGTTGGT
Found at i:23890561 original size:42 final size:41
Alignment explanation
Indices: 23890515--23890686 Score: 200
Period size: 42 Copynumber: 4.1 Consensus size: 41
23890505 GAGCTAAGTA
* * *
23890515 GAAACCTATAAGGGTTGAACAGAAGCTTATAAGAGCTAAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCA-AAGAGCTAAACG
* * *
23890557 GAAACCCATAAAGGTTAAACAGAAGCTCGAAAGAGTTAAATG
1 GAAACCCATAAGGGTTAAACAGAAGCTC-AAAGAGCTAAACG
*
23890599 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACA
1 GAAACCCATAAGGGTTAAACAGAAGCTC-AAAGAGCTAAACG
* * * * *
23890641 GAAACTCATATGAGTTAAACAGAAGCTCGAGAGAGCTAAACA
1 GAAACCCATAAGGGTTAAACAGAAGCTC-AAAGAGCTAAACG
23890683 GAAA
1 GAAA
23890687 GTAAACACGA
Statistics
Matches: 113, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 112 0.99
43 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAAAGAGCTAAACG
Found at i:23890567 original size:21 final size:21
Alignment explanation
Indices: 23890514--23890664 Score: 99
Period size: 21 Copynumber: 7.2 Consensus size: 21
23890504 AGAGCTAAGT
* * *
23890514 AGAAACCTATAAGGGTTGAAC
1 AGAAACCCATAAGAGTTAAAC
* ** *
23890535 AGAAGCTTATAAGAGCTAAAC
1 AGAAACCCATAAGAGTTAAAC
*
23890556 GGAAACCCATAA-AGGTTAAAC
1 AGAAACCCATAAGA-GTTAAAC
* * *
23890577 AGAAGCTCGA-AAGAGTTAAAT
1 AGAAAC-CCATAAGAGTTAAAC
* *
23890598 GGAAACCCATAAGGGTTAAAC
1 AGAAACCCATAAGAGTTAAAC
* * * *
23890619 AGAAGCTCAAAAGAGCTAAAC
1 AGAAACCCATAAGAGTTAAAC
* *
23890640 AGAAACTCATATGAGTTAAAC
1 AGAAACCCATAAGAGTTAAAC
23890661 AGAA
1 AGAA
23890665 GCTCGAGAGA
Statistics
Matches: 97, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.03
21 91 0.94
22 3 0.03
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.17
Consensus pattern (21 bp):
AGAAACCCATAAGAGTTAAAC
Found at i:23890636 original size:84 final size:84
Alignment explanation
Indices: 23890504--23890680 Score: 239
Period size: 84 Copynumber: 2.1 Consensus size: 84
23890494 AAAGCTCATG
* * * * * * *
23890504 AGAGCTAAGTAGAAACCTATAAGGGTTGAACAGAAGCTTATAAGAGCTAAACGGAAACCCATAA-
1 AGAGCTAAATGGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACCCATAAG
23890568 AGGTTAAACAGAAGCTCGAA
66 A-GTTAAACAGAAGCTCGAA
* * *
23890588 AGAGTTAAATGGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACTCATATG
1 AGAGCTAAATGGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACCCATAAG
*
23890653 AGTTAAACAGAAGCTCGAG
66 AGTTAAACAGAAGCTCGAA
23890672 AGAGCTAAA
1 AGAGCTAAA
23890681 CAGAAAGTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 79 0.99
85 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (84 bp):
AGAGCTAAATGGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACCCATAAG
AGTTAAACAGAAGCTCGAA
Found at i:23890680 original size:21 final size:20
Alignment explanation
Indices: 23890532--23890685 Score: 85
Period size: 21 Copynumber: 7.3 Consensus size: 20
23890522 ATAAGGGTTG
*
23890532 AACAGAAGCTTATAAGAGCTA
1 AACAGAAGCTCA-AAGAGCTA
* * * *
23890553 AACGGAAACCCATAA-AGGTTA
1 AACAGAAGCTCA-AAGA-GCTA
*
23890574 AACAGAAGCTCGAAAGAGTTA
1 AACAGAAGCTC-AAAGAGCTA
** * * * *
23890595 AATGGAAACCCATAAGGGTTA
1 AACAGAAGCTCA-AAGAGCTA
23890616 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCTC-AAAGAGCTA
* * *
23890637 AACAGAAACTCATATGAGTTA
1 AACAGAAGCTCA-AAGAGCTA
*
23890658 AACAGAAGCTCGAGAGAGCTA
1 AACAGAAGCTC-AAAGAGCTA
23890679 AACAGAA
1 AACAGAA
23890686 AGTAAACACG
Statistics
Matches: 100, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.03
21 93 0.93
22 4 0.04
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.15
Consensus pattern (20 bp):
AACAGAAGCTCAAAGAGCTA
Found at i:23899918 original size:12 final size:12
Alignment explanation
Indices: 23899890--23899961 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
23899880 CCATTTTATT
*
23899890 TTATTTTATTTA
1 TTATATTATTTA
*
23899902 -T-TATTATTTG
1 TTATATTATTTA
23899912 TTATATTATTTA
1 TTATATTATTTA
*
23899924 TTATTATTTTACTATTT
1 TTA-TA--TTA-T-TTA
23899941 TTATATTATTTA
1 TTATATTATTTA
23899953 TT-TATTATT
1 TTATATTATT
23899962 CTTATACTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.15
11 9 0.19
12 15 0.31
13 3 0.06
14 3 0.06
15 3 0.06
16 3 0.06
17 5 0.10
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (12 bp):
TTATATTATTTA
Found at i:23899920 original size:22 final size:21
Alignment explanation
Indices: 23899888--23899961 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
23899878 ACCCATTTTA
*
23899888 TTTTATTTTATTTATTATTAT
1 TTTTATATTATTTATTATTAT
23899909 TTGTTATATTATTTATTATTA-
1 TT-TTATATTATTTATTATTAT
23899930 TTTTACTATT-TTTA-TATTAT
1 TTTTA-TATTATTTATTATTAT
23899950 TTATT-TATTATT
1 TT-TTATATTATT
23899962 CTTATACTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
19 9 0.19
20 11 0.23
21 10 0.21
22 17 0.36
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTATATTATTTATTATTAT
Found at i:23899924 original size:19 final size:19
Alignment explanation
Indices: 23899889--23899961 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
23899879 CCCATTTTAT
*
23899889 TTTATTTTATT-TATTATTA
1 TTTATTATATTAT-TTATTA
*
23899908 TTTGTTATATTATTTATTA
1 TTTATTATATTATTTATTA
* *
23899927 TTATTTTACTATTTTTATATTA
1 TT-TATTA-TATTATT-TATTA
23899949 TTTATT-TATTATT
1 TTTATTATATTATT
23899962 CTTATACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 23 0.52
20 5 0.11
21 9 0.20
22 7 0.16
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (19 bp):
TTTATTATATTATTTATTA
Found at i:23899928 original size:29 final size:29
Alignment explanation
Indices: 23899883--23899960 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
23899873 AAGTCACCCA
* *
23899883 TTTTATTTTA-TT-TTATT-TATTATTAT
1 TTTTATATTATTTATTATTATATTACTAT
*
23899909 TTGTTATATTATTTATTATTATTTTACTAT
1 TT-TTATATTATTTATTATTATATTACTAT
23899939 TTTTATATTATTTATTTATTAT
1 TTTTATATTATTTA-TTATTAT
23899961 TCTTATACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.05
27 7 0.16
28 2 0.05
29 17 0.39
30 16 0.36
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (29 bp):
TTTTATATTATTTATTATTATATTACTAT
Found at i:23899966 original size:22 final size:22
Alignment explanation
Indices: 23899922--23899967 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
23899912 TTATATTATT
*
23899922 TATTATTATTTTACTATTTTTA
1 TATTATTATTTTACTATTCTTA
*
23899944 TATTATT-TATTTATTATTCTTA
1 TATTATTAT-TTTACTATTCTTA
23899966 TA
1 TA
23899968 CTTAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATTATTTTACTATTCTTA
Found at i:23899986 original size:36 final size:33
Alignment explanation
Indices: 23899912--23899987 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
23899902 TTATTATTTG
* * *
23899912 TTATATTATTTATTATTATTTTACTATTTTTATA
1 TTAT-TTATTTATTATTATTATACTAATTTTACA
*
23899946 TTATTTATTTATTATTCTTATACTTAGATTTTACA
1 TTATTTATTTATTATTATTATAC-TA-ATTTTACA
23899981 TTTATTT
1 -TTATTT
23899988 TAATTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 17 0.49
34 6 0.17
35 6 0.17
36 6 0.17
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (33 bp):
TTATTTATTTATTATTATTATACTAATTTTACA
Found at i:23900087 original size:12 final size:11
Alignment explanation
Indices: 23900071--23900112 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
23900061 TATAATTAAG
23900071 TTTATTATTAT
1 TTTATTATTAT
23900082 TATTATTATTAT
1 T-TTATTATTAT
23900094 TTTCATT-TTAT
1 TTT-ATTATTAT
23900105 TTT-TTATT
1 TTTATTATT
23900113 TTATTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 2 0.07
10 2 0.07
11 10 0.36
12 14 0.50
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:23900118 original size:12 final size:13
Alignment explanation
Indices: 23900071--23900117 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 13
23900061 TATAATTAAG
23900071 TTTATTATTATTAT
1 TTTATTATT-TTAT
23900085 TATTATTATTTTCAT
1 T-TTATTATTTT-AT
23900100 TTTATT-TTTTAT
1 TTTATTATTTTAT
23900112 TTTATT
1 TTTATT
23900118 TATCTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.26
13 4 0.13
14 8 0.26
15 11 0.35
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:23901144 original size:15 final size:15
Alignment explanation
Indices: 23901124--23901174 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 15
23901114 TTATTGAAAA
23901124 AAAAAAGATACAAAG
1 AAAAAAGATACAAAG
*
23901139 AAAAAAG--ACAAAA
1 AAAAAAGATACAAAG
*
23901152 AAAAGAAAATATCAAAG
1 AAAA-AAGATA-CAAAG
23901169 AAAAAA
1 AAAAAA
23901175 ATATTGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 7 0.24
16 3 0.10
17 8 0.28
ACGTcount: A:0.78, C:0.06, G:0.10, T:0.06
Consensus pattern (15 bp):
AAAAAAGATACAAAG
Found at i:23904630 original size:22 final size:22
Alignment explanation
Indices: 23904605--23904654 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
23904595 CCGATAGCTG
*
23904605 GTAAAAGGTATTGATACTTTTT
1 GTAAAAGGTATCGATACTTTTT
*
23904627 GT-AAAGGTATCGATATTTTTT
1 GTAAAAGGTATCGATACTTTTT
23904648 GTGAAAA
1 GT-AAAA
23904655 ATGAAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.79
22 2 0.08
23 3 0.12
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (22 bp):
GTAAAAGGTATCGATACTTTTT
Found at i:23906915 original size:54 final size:52
Alignment explanation
Indices: 23906810--23906917 Score: 121
Period size: 54 Copynumber: 2.0 Consensus size: 52
23906800 TGCCCGTGTA
* **
23906810 GGCCCACATGGCCAAAATGGCCAGCTCGTGTGGCTTACACGACCTCGCACAC
1 GGCCCACATGACCAAAATGGCCAGCTCGTGTGGCACACACGACCTCGCACAC
* *
23906862 GGCCCACACTGACCAAAATGGCCTAGACT-GTGTGTCACACAC-AGCCTGGCACAC
1 GGCCCACA-TGACCAAAATGGCC-AG-CTCGTGTGGCACACACGA-CCTCGCACAC
23906916 GG
1 GG
23906918 TCGTGTGGCG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
52 8 0.17
53 14 0.30
54 23 0.49
55 2 0.04
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (52 bp):
GGCCCACATGACCAAAATGGCCAGCTCGTGTGGCACACACGACCTCGCACAC
Found at i:23919412 original size:11 final size:10
Alignment explanation
Indices: 23919388--23919422 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
23919378 TTTTTAATAA
*
23919388 AATAAAAATT
1 AATAAAATTT
23919398 AATAAATATTT
1 AATAAA-ATTT
23919409 AATAAAATTT
1 AATAAAATTT
23919419 AATA
1 AATA
23919423 TATTTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AATAAAATTT
Found at i:23919427 original size:19 final size:20
Alignment explanation
Indices: 23919388--23919428 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
23919378 TTTTTAATAA
23919388 AATAAAAATTAATAAATATTT
1 AATAAAAATTAAT-AATATTT
*
23919409 AATAAAATTTAAT-ATATTT
1 AATAAAAATTAATAATATTT
23919428 A
1 A
23919429 TTAACAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAAAAATTAATAATATTT
Found at i:23922030 original size:36 final size:36
Alignment explanation
Indices: 23921990--23922077 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
23921980 AATGATATTC
* * *
23921990 CATTCGAAACAGACCAGATGCTCATAAGATCTAATA
1 CATTCGAAACACACCAGATGCCCATAAGAGCTAATA
*
23922026 CATTCGAAACACACCAGATGCCCATAAGAGCTAATC
1 CATTCGAAACACACCAGATGCCCATAAGAGCTAATA
* *
23922062 CATCCGAAACATACCA
1 CATTCGAAACACACCA
23922078 ATGGCTCCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.18
Consensus pattern (36 bp):
CATTCGAAACACACCAGATGCCCATAAGAGCTAATA
Found at i:23926667 original size:60 final size:60
Alignment explanation
Indices: 23926574--23926694 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
23926564 GAATCTAAGA
23926574 TAATGGAATGTGTCCATAATGTGTGCCAAAGGACCATATTTATAGCCTTCAGGTAGCCAT
1 TAATGGAATGTGTCCATAATGTGTGCCAAAGGACCATATTTATAGCCTTCAGGTAGCCAT
*
23926634 TAATGGAATGTGTCCATAATGTGTGCCAAAGGACCCTATTTATAGCCTTCAGGTAGCCAT
1 TAATGGAATGTGTCCATAATGTGTGCCAAAGGACCATATTTATAGCCTTCAGGTAGCCAT
23926694 T
1 T
23926695 GTGCTCAGCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (60 bp):
TAATGGAATGTGTCCATAATGTGTGCCAAAGGACCATATTTATAGCCTTCAGGTAGCCAT
Found at i:23928173 original size:10 final size:10
Alignment explanation
Indices: 23928158--23928200 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
23928148 TATGAACATG
23928158 ATTAATTTTA
1 ATTAATTTTA
23928168 ATTAATTTTA
1 ATTAATTTTA
*
23928178 TAGTTAATTTTT
1 -A-TTAATTTTA
23928190 ATTAATTTTA
1 ATTAATTTTA
23928200 A
1 A
23928201 CTATTTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
ATTAATTTTA
Found at i:23932430 original size:18 final size:18
Alignment explanation
Indices: 23932407--23932441 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23932397 CTTAGACATC
23932407 ATTAAA-ACATGTAATAAA
1 ATTAAACACAT-TAATAAA
23932425 ATTAAACACATTAATAA
1 ATTAAACACATTAATAA
23932442 GATGCATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAACACATTAATAAA
Found at i:23935289 original size:407 final size:407
Alignment explanation
Indices: 23934527--23935343 Score: 1526
Period size: 407 Copynumber: 2.0 Consensus size: 407
23934517 TCTGTATCGA
*
23934527 TTACCGGAAGTTGAACAATGTGACTAGGAAAGATCACTTCCCTTTGTCGTTCTTGGACCAGATGC
1 TTACCGGAAGTTGAACAATGCGACTAGGAAAGATCACTTCCCTTTGTCGTTCTTGGACCAGATGC
*
23934592 TGGATAGACTCGTAGGACGAGATTGCTACTATTTTCTCGATGGATACTCAGGGTATAATCAGATT
66 TGGATAGACTCGTAGGACGAGATTACTACTATTTTCTCGATGGATACTCAGGGTATAATCAGATT
23934657 ACAGTAGCACCGAAAGATTAACACAAAACGACATTCACCTGCCTATACGGTACGTTTGCATTTAG
131 ACAGTAGCACCGAAAGATTAACACAAAACGACATTCACCTGCCTATACGGTACGTTTGCATTTAG
** *
23934722 ATGTATGTCATTTGGTTTATGTAATGCACCTGCTACATTTCAAAGATGTATGGTGTCTATTTTTA
196 ATGTATGTCATTTGGTTTATGTAATGCACCTGAAACATTTCAAAGATGTATGATGTCTATTTTTA
23934787 CTGACATGGTTGAGAAATATTTAGAAGTTTTTATGGACGATTTTTCAGTACTCGAAGATACTTAC
261 CTGACATGGTTGAGAAATATTTAGAAGTTTTTATGGACGATTTTTCAGTACTCGAAGATACTTAC
*
23934852 GATGATTGCTTAGCCAATCTAACCAAGGTACTAAGGAGATGCGAAGAAATGATTCTCGTACTCAA
326 AATGATTGCTTAGCCAATCTAACCAAGGTACTAAGGAGATGCGAAGAAATGATTCTCGTACTCAA
23934917 CTGGGAAAAGTGTCATT
391 CTGGGAAAAGTGTCATT
*
23934934 TTACCGGAAGTTGAACAATGCGACTAGGAGAGATCACTTCCCTTTGTCGTTCTTGGACCAGATGC
1 TTACCGGAAGTTGAACAATGCGACTAGGAAAGATCACTTCCCTTTGTCGTTCTTGGACCAGATGC
23934999 TGGATAGACTCGTAGGACGAGATTACTACTATTTTCTCGATGGATACTCAGGGTATAATCAGATT
66 TGGATAGACTCGTAGGACGAGATTACTACTATTTTCTCGATGGATACTCAGGGTATAATCAGATT
* *
23935064 ACAGTAGCATCGAAAGATTAACACAAAACGACATTCACCTGCCTGTACGGTACGTTTGCATTTAG
131 ACAGTAGCACCGAAAGATTAACACAAAACGACATTCACCTGCCTATACGGTACGTTTGCATTTAG
23935129 ATGTATGTCATTTGGTTTATGTAATGCACCTGAAACATTTCAAAGATGTATGATGTCTATTTTTA
196 ATGTATGTCATTTGGTTTATGTAATGCACCTGAAACATTTCAAAGATGTATGATGTCTATTTTTA
*
23935194 CTGACATGGTTGAGAAATATTTAGAAGTTTTTATGGACGATTTTTCAGTATTCGAAGATACTTAC
261 CTGACATGGTTGAGAAATATTTAGAAGTTTTTATGGACGATTTTTCAGTACTCGAAGATACTTAC
* *
23935259 AATGATTGCTTAGCCAATCTAACTAAGGTACTATGGAGATGCGAAGAAATGATTCTCGTACTCAA
326 AATGATTGCTTAGCCAATCTAACCAAGGTACTAAGGAGATGCGAAGAAATGATTCTCGTACTCAA
23935324 CTGGGAAAAGTGTCATT
391 CTGGGAAAAGTGTCATT
23935341 TTA
1 TTA
23935344 TGGTACGAGA
Statistics
Matches: 398, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
407 398 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (407 bp):
TTACCGGAAGTTGAACAATGCGACTAGGAAAGATCACTTCCCTTTGTCGTTCTTGGACCAGATGC
TGGATAGACTCGTAGGACGAGATTACTACTATTTTCTCGATGGATACTCAGGGTATAATCAGATT
ACAGTAGCACCGAAAGATTAACACAAAACGACATTCACCTGCCTATACGGTACGTTTGCATTTAG
ATGTATGTCATTTGGTTTATGTAATGCACCTGAAACATTTCAAAGATGTATGATGTCTATTTTTA
CTGACATGGTTGAGAAATATTTAGAAGTTTTTATGGACGATTTTTCAGTACTCGAAGATACTTAC
AATGATTGCTTAGCCAATCTAACCAAGGTACTAAGGAGATGCGAAGAAATGATTCTCGTACTCAA
CTGGGAAAAGTGTCATT
Found at i:23937799 original size:15 final size:16
Alignment explanation
Indices: 23937781--23937813 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23937771 TGATAAACTT
23937781 TAATATATAA-TTATA
1 TAATATATAATTTATA
*
23937796 TAATTTATAATTTATA
1 TAATATATAATTTATA
23937812 TA
1 TA
23937814 TTAATTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATATAATTTATA
Found at i:23937809 original size:27 final size:28
Alignment explanation
Indices: 23937751--23937819 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
23937741 GAATAAATAT
23937751 ATTTAATAT-T-ATTAATAATTTGATAA
1 ATTTAATATATAATTAATAATTTGATAA
23937777 ACTTTAATATATAATTATATAATTT-AT-A
1 A-TTTAATATATAATTA-ATAATTTGATAA
23937805 ATTT-ATATATTAATT
1 ATTTAATATA-TAATT
23937820 TTTACCAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.16
27 16 0.42
28 3 0.08
29 6 0.16
30 7 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
ATTTAATATATAATTAATAATTTGATAA
Found at i:23942682 original size:23 final size:23
Alignment explanation
Indices: 23942656--23942741 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
23942646 TGCATAACAG
*
23942656 AATATGCCACAAAAGCTACACGA
1 AATATGCCACAAAGGCTACACGA
*
23942679 AATATGCCACAAAGGCTTTATA-G-
1 AATATGCCACAAAGGC--TACACGA
* *
23942702 AATATGCCACATAGGCAACACGA
1 AATATGCCACAAAGGCTACACGA
*
23942725 AATATGCCATAAAGGCT
1 AATATGCCACAAAGGCT
23942742 TTAATATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 44 0.86
24 1 0.02
25 3 0.06
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (23 bp):
AATATGCCACAAAGGCTACACGA
Found at i:23942704 original size:46 final size:46
Alignment explanation
Indices: 23942654--23942744 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
23942644 CATGCATAAC
*
23942654 AGAATATGCCACAAAAGCTACACGAAATATGCCACAAAGGCTTTAT
1 AGAATATGCCACAAAAGCAACACGAAATATGCCACAAAGGCTTTAT
* * *
23942700 AGAATATGCCACATAGGCAACACGAAATATGCCATAAAGGCTTTA
1 AGAATATGCCACAAAAGCAACACGAAATATGCCACAAAGGCTTTA
23942745 ATATTATGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (46 bp):
AGAATATGCCACAAAAGCAACACGAAATATGCCACAAAGGCTTTAT
Found at i:23952171 original size:20 final size:20
Alignment explanation
Indices: 23952146--23952189 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23952136 AATGTTTTAT
*
23952146 GTTTCA-AATATTTCTCAGAA
1 GTTTCAGAAAATTT-TCAGAA
23952166 GTTTCAGAAAATTTTCAGAA
1 GTTTCAGAAAATTTTCAGAA
23952186 GTTT
1 GTTT
23952190 TAGTCTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (20 bp):
GTTTCAGAAAATTTTCAGAA
Found at i:23958027 original size:16 final size:17
Alignment explanation
Indices: 23958006--23958037 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
23957996 AATTTTCAGA
23958006 AAATTTTCCT-AATTTC
1 AAATTTTCCTCAATTTC
23958022 AAATTTTCCTCAATTT
1 AAATTTTCCTCAATTT
23958038 AGTCCCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTTCCTCAATTTC
Found at i:23958598 original size:36 final size:36
Alignment explanation
Indices: 23958532--23958600 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
23958522 ATTATTTATC
**
23958532 AAATAAATATCTTTTACATAATGATAATAAATAAAT
1 AAATAAATATCTTTTACATAACAATAATAAATAAAT
23958568 AAATAAATATCTATTTA-ATAAACAAT-ATAAATA
1 AAATAAATATCT-TTTACAT-AACAATAATAAATA
23958601 TTACACTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (36 bp):
AAATAAATATCTTTTACATAACAATAATAAATAAAT
Found at i:23958696 original size:3 final size:3
Alignment explanation
Indices: 23958677--23958726 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
23958667 AATTTATTTC
* * *
23958677 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATA ACA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23958723 ATA A
1 ATA A
23958727 AATGTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:23958705 original size:18 final size:18
Alignment explanation
Indices: 23958677--23958723 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
23958667 AATTTATTTC
23958677 ATAAT-ATAATAACAATA
1 ATAATAATAATAACAATA
*
23958694 ATATTAATAATAACAATA
1 ATAATAATAATAACAATA
23958712 ATAATAA-AATAA
1 ATAATAATAATAA
23958724 TAAAATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAACAATA
Found at i:23959246 original size:18 final size:18
Alignment explanation
Indices: 23959223--23959260 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23959213 ACTGTAGAAA
23959223 TAAATTACTTTCTTACTG
1 TAAATTACTTTCTTACTG
23959241 TAAATTACTTTCTTACTG
1 TAAATTACTTTCTTACTG
23959259 TA
1 TA
23959261 GAAATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (18 bp):
TAAATTACTTTCTTACTG
Found at i:23962677 original size:21 final size:21
Alignment explanation
Indices: 23962632--23962678 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23962622 GAATTGAGAG
* **
23962632 TTCTACCGATACAACTCTAGG
1 TTCTACCGATACAACTCGAAC
*
23962653 TTCTACTGATACAACTCGAAC
1 TTCTACCGATACAACTCGAAC
23962674 TTCTA
1 TTCTA
23962679 TCAGTAGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAACTCGAAC
Found at i:23966664 original size:18 final size:18
Alignment explanation
Indices: 23966641--23966675 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23966631 CTTGGACATC
23966641 ATTAAA-ACATGTAATAAA
1 ATTAAACACAT-TAATAAA
23966659 ATTAAACACATTAATAA
1 ATTAAACACATTAATAA
23966676 GATGCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAACACATTAATAAA
Found at i:23967320 original size:82 final size:82
Alignment explanation
Indices: 23967183--23967413 Score: 419
Period size: 82 Copynumber: 2.8 Consensus size: 82
23967173 GTACAGCAGC
23967183 AAGCCTCCTTCCC-ATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAAAA
1 AAGCCTCC-TCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAAAA
23967247 AGGTGTCTTCGATTCCCA
65 AGGTGTCTTCGATTCCCA
23967265 AAGCCTCCTCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAAAAA
1 AAGCCTCCTCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAAAAA
23967330 GGTGTCTTCGATTCCCA
66 GGTGTCTTCGATTCCCA
* *
23967347 AAGCCTCCTCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAGCAAGGCAAAGAA
1 AAGCCTCCTCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAA-AA
23967412 AG
65 AG
23967414 TGCATTCAAT
Statistics
Matches: 145, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
81 4 0.03
82 137 0.94
83 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (82 bp):
AAGCCTCCTCCCAATGAAGATGAGAGGAGACCAACATTGTCAATGGACATCAACAAGACAAAAAA
GGTGTCTTCGATTCCCA
Found at i:23968332 original size:43 final size:43
Alignment explanation
Indices: 23968274--23968676 Score: 388
Period size: 43 Copynumber: 9.3 Consensus size: 43
23968264 TTTTTACTAA
* * *
23968274 TAAGGATTTAGGGTTTTAAAGTTAAGGGCCTCA-GGTTTTAAAGT
1 TAAGG-TTTAGGGTTTTTAAGTTAAGGG-TTTAGGGTTTTAAAGT
* *
23968318 TAAGGTTTAGGGTTTTTAGGTTAAGGG-TTAGGGTTTTAAATT
1 TAAGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
* * * *
23968360 TAAGGGTTAGTGTTTTTAAGTTAAGGGTTTAAGGTTTTTAAGT
1 TAAGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
* * * * * *
23968403 TAAGGGTCTAGGGTTTTAAAGCTAAAGG-TTAGGGTTTTTAGGT
1 TAA-GGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
* * * *
23968446 TAA-GTGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT
1 TAAGGT-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
* * * * * *
23968489 TAAGGGTTAGTGTTTTTAATTTAAGAGTTTAGGGTTTTTTAGGTT
1 TAAGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGG-TTTTAAAG-T
* * * *
23968534 TAGGGTTTAGGGTTTTTAGGTTAAGGGGTTAAGGTTTTAAAGT
1 TAAGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
*
23968577 TAATGG-TTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTAAAGT
1 TAA-GGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
* *
23968620 TAAGAG-TTAGGGTTTTTAGGTTAAGGGGTTAAGGGTTTT-AAGT
1 TAAG-GTTTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTAAAGT
23968663 TAAGGTTTAGGGTT
1 TAAGGTTTAGGGTT
23968677 AGGGTTTTTA
Statistics
Matches: 302, Mismatches: 45, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.01
42 51 0.17
43 169 0.56
44 51 0.17
45 27 0.09
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (43 bp):
TAAGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
Found at i:23968685 original size:27 final size:28
Alignment explanation
Indices: 23968645--23968704 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
23968635 TTAGGTTAAG
23968645 GGGTTAAGGGTTTTAAGTT-AAGGTTTA
1 GGGTTAAGGGTTTTAAGTTAAAGGTTTA
*
23968672 GGGTT-AGGGTTTTTAGGTTAAAGGTTTA
1 GGGTTAAGGG-TTTTAAGTTAAAGGTTTA
*
23968700 AGGTT
1 GGGTT
23968705 TTTCAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 12 0.41
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (28 bp):
GGGTTAAGGGTTTTAAGTTAAAGGTTTA
Found at i:23968697 original size:21 final size:21
Alignment explanation
Indices: 23968281--23968676 Score: 391
Period size: 21 Copynumber: 18.4 Consensus size: 21
23968271 TAATAAGGAT
*
23968281 TTAGGGTTTTAAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* * *
23968302 CCTCA-GGTTTTAAAGTTAAGGT
1 --TTAGGGTTTTTAAGTTAAGGG
*
23968324 TTAGGGTTTTTAGGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* *
23968345 TTAGGGTTTTAAATTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
23968366 TTAGTGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
23968387 TTTAAGGTTTTTAAGTTAAGGG
1 -TTAGGGTTTTTAAGTTAAGGG
* * *
23968409 TCTAGGGTTTTAAAGCTAAAGG
1 T-TAGGGTTTTTAAGTTAAGGG
* *
23968431 TTAGGGTTTTTAGGTTAAGTG
1 TTAGGGTTTTTAAGTTAAGGG
* *
23968452 TTAGAGTTTTTAATTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
23968473 TTTAGGGTTTTTAATTTAAGGG
1 -TTAGGGTTTTTAAGTTAAGGG
* * *
23968495 TTAGTGTTTTTAATTTAAGAGT
1 TTAGGGTTTTTAAGTTAAG-GG
* *
23968517 TTAGGGTTTTTTAGGTTTAGGG
1 TTAGGG-TTTTTAAGTTAAGGG
*
23968539 TTTAGGGTTTTTAGGTTAAGGGG
1 -TTAGGGTTTTTAAGTTAA-GGG
* * *
23968562 TTAAGGTTTTAAAGTTAATGG
1 TTAGGGTTTTTAAGTTAAGGG
*
23968583 TTAGGGTTTTTAGGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* *
23968604 TTTAGGGTTTTAAAGTTAAGAG
1 -TTAGGGTTTTTAAGTTAAGGG
*
23968626 TTAGGGTTTTTAGGTTAAGGGG
1 TTAGGGTTTTTAAGTTAA-GGG
*
23968648 TTAAGGG-TTTTAAGTTAAGGT
1 TT-AGGGTTTTTAAGTTAAGGG
23968669 TTAGGGTT
1 TTAGGGTT
23968677 AGGGTTTTTA
Statistics
Matches: 309, Mismatches: 52, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.02
21 141 0.46
22 137 0.44
23 25 0.08
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.44
Consensus pattern (21 bp):
TTAGGGTTTTTAAGTTAAGGG
Found at i:23968703 original size:14 final size:14
Alignment explanation
Indices: 23968646--23968704 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
23968636 TAGGTTAAGG
23968646 GGTTAAGGGTTTTAA
1 GGTTAA-GGTTTTAA
*
23968661 -GTTAAGG-TTTAG
1 GGTTAAGGTTTTAA
* *
23968673 GGTTAGGGTTTTTA
1 GGTTAAGGTTTTAA
23968687 GGTTAAAGG-TTTAA
1 GGTT-AAGGTTTTAA
23968701 GGTT
1 GGTT
23968705 TTTCAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
12 4 0.11
13 8 0.23
14 20 0.57
15 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (14 bp):
GGTTAAGGTTTTAA
Found at i:23969006 original size:21 final size:21
Alignment explanation
Indices: 23968963--23969009 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23968953 GCGGCGGTTG
* *
23968963 TGGTTCTTCCGGTGGGGATTC
1 TGGTTCTTCCAGTGGGCATTC
23968984 TGGTTCTTCCAGTAGGGCA-TC
1 TGGTTCTTCCAGT-GGGCATTC
23969005 TGGTT
1 TGGTT
23969010 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.09, C:0.19, G:0.34, T:0.38
Consensus pattern (21 bp):
TGGTTCTTCCAGTGGGCATTC
Found at i:23969283 original size:18 final size:18
Alignment explanation
Indices: 23969256--23969290 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23969246 GAAAAAAGAA
* *
23969256 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
23969274 ACATAAAAGGGCTAGGA
1 ACATAAAAGGGCTAGGA
23969291 AATGCACCTG
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:0.43, C:0.09, G:0.29, T:0.20
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:23969921 original size:7 final size:7
Alignment explanation
Indices: 23969911--23969936 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23969901 TTATATACAT
23969911 AATACTA
1 AATACTA
23969918 AATACTA
1 AATACTA
23969925 AATACTA
1 AATACTA
23969932 AATAC
1 AATAC
23969937 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:23970142 original size:20 final size:20
Alignment explanation
Indices: 23970105--23970142 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23970095 TTTATTTTTA
*
23970105 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
23970125 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
23970143 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:23971080 original size:51 final size:51
Alignment explanation
Indices: 23971025--23971122 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
23971015 AATTATTTAA
23971025 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAAAAT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAAAAT
* * * *
23971076 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
23971123 GAGGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAAAT
Found at i:23971098 original size:11 final size:11
Alignment explanation
Indices: 23971084--23971160 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
23971074 ATAAATATGG
23971084 ATTTGAGAGAA
1 ATTTGAGAGAA
*
23971095 ATTTTGA-AGGA
1 A-TTTGAGAGAA
23971106 ATTTGAGAGCAA
1 ATTTGAGAG-AA
23971118 A-TTGAGAGGAA
1 ATTTGAGA-GAA
23971129 ATTT-AGAAGAA
1 ATTTGAG-AGAA
23971140 A-TTGAGAGGAA
1 ATTTGAGA-GAA
23971151 ATTTGAGAGA
1 ATTTGAGAGA
23971161 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
10 8 0.15
11 30 0.55
12 17 0.31
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:23971109 original size:22 final size:22
Alignment explanation
Indices: 23971084--23971160 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
23971074 ATAAATATGG
23971084 ATTTGAGAGAAATTTTGA-AGG-A
1 ATTTGAGAGAAA--TTGAGAGGAA
23971106 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
23971129 ATTT-AGAAGAAATTGAGAGGAA
1 ATTTGAG-AGAAATTGAGAGGAA
23971151 ATTTGAGAGA
1 ATTTGAGAGA
23971161 GGATTAGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.08
22 34 0.68
23 12 0.24
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:23971123 original size:33 final size:33
Alignment explanation
Indices: 23971084--23971160 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
23971074 ATAAATATGG
* *
23971084 ATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAATTGAGAGCAA
*
23971118 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTTAGAAGAAATTGAGAGCAA
23971151 ATTTGAGAGA
1 ATTTGAGAGA
23971161 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAATTGAGAGCAA
Found at i:23974860 original size:21 final size:20
Alignment explanation
Indices: 23974815--23974865 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
23974805 ATTATCACTT
23974815 ATTTTTTTAAAATAATTTTAA
1 ATTTTTTTAAAAT-ATTTTAA
*
23974836 ATTTTTTTAAAGAT-TTTATAC
1 ATTTTTTTAAA-ATATTT-TAA
23974857 ATTTTTTTA
1 ATTTTTTTA
23974866 CGGTTTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTTTAAAATATTTTAA
Found at i:23975323 original size:19 final size:18
Alignment explanation
Indices: 23975298--23975344 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
23975288 TATTATAATA
*
23975298 AAAATATAAAATAATTTT
1 AAAATATAAAATAATATT
23975316 ATAAATATAAAATAATATT
1 A-AAATATAAAATAATATT
23975335 AAAATA-AAAA
1 AAAATATAAAA
23975345 ACTTGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 17 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATAAAATAATATT
Found at i:23979062 original size:81 final size:81
Alignment explanation
Indices: 23978965--23979127 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
23978955 TGAAAAATCT
*
23978965 ATGTTTATTTTGTATTGAAAAGGGGTATCGTTTTCATAGGGACTATATAAGCAAAAACTTTTGTG
1 ATGTTTATTTTGTATTGAAAAGGGGTATCGTTTTCATAGGGACTATATAAACAAAAACTTTTGTG
23979030 AAATAAAGACTTTCAC
66 AAATAAAGACTTTCAC
*
23979046 ATGTTTATTTTGTATTGAAAAGGGGTATTGTTTTCATAGGGACTATATAAACAAAAACTTTTGTG
1 ATGTTTATTTTGTATTGAAAAGGGGTATCGTTTTCATAGGGACTATATAAACAAAAACTTTTGTG
23979111 AAATAAAGACTTTCAC
66 AAATAAAGACTTTCAC
23979127 A
1 A
23979128 ATTTGGTGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (81 bp):
ATGTTTATTTTGTATTGAAAAGGGGTATCGTTTTCATAGGGACTATATAAACAAAAACTTTTGTG
AAATAAAGACTTTCAC
Found at i:23981125 original size:131 final size:131
Alignment explanation
Indices: 23980919--23981166 Score: 354
Period size: 131 Copynumber: 1.9 Consensus size: 131
23980909 TCATCAAATC
** * *
23980919 AAATCGAATGAACTTAGGTTGCGATCTTAAATCAGCCAACATTAACAATATCTGCTGCGATATTA
1 AAATCGAATGAACTTAGGTCACGATCTTAAATCAGCCAACATTAACAATATCAGCTACGATATTA
* *
23980984 AACCAACGAGCTATTTGGAGTAGCGATATTAAATT-AGCTAACTCAAATAAGATTATTATTGATA
66 AACCAACGAGCTATTTGGAGTAACAATATT-AATTCAGCTAACTCAAATAAGATTATTATTGATA
23981048 TT
130 TT
** * * * *
23981050 AAATCGAATGAACTTAGGTCACGATCTTAAATCAGTGAACCTTTACGATATCAGCTACGATCTTA
1 AAATCGAATGAACTTAGGTCACGATCTTAAATCAGCCAACATTAACAATATCAGCTACGATATTA
* *
23981115 AATCAGCGAGCTATTTGGAGTAACAATATTAATTCAGCTAACTCAAATAAGA
66 AACCAACGAGCTATTTGGAGTAACAATATTAATTCAGCTAACTCAAATAAGA
23981167 CTGTTCATAA
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 4 0.04
131 98 0.96
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (131 bp):
AAATCGAATGAACTTAGGTCACGATCTTAAATCAGCCAACATTAACAATATCAGCTACGATATTA
AACCAACGAGCTATTTGGAGTAACAATATTAATTCAGCTAACTCAAATAAGATTATTATTGATAT
T
Found at i:23991377 original size:12 final size:12
Alignment explanation
Indices: 23991345--23991385 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
23991335 TGCATAAAAT
*
23991345 AAAATAGTCCTA
1 AAAATAGTCTTA
23991357 AATAATAGTCTTA
1 AA-AATAGTCTTA
*
23991370 AAAATAGTATTA
1 AAAATAGTCTTA
23991382 AAAA
1 AAAA
23991386 AATTCCCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (12 bp):
AAAATAGTCTTA
Found at i:23991385 original size:13 final size:13
Alignment explanation
Indices: 23991345--23991386 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
23991335 TGCATAAAAT
*
23991345 AAAATAGTCCTAA
1 AAAATAGTCTTAA
*
23991358 ATAATAGTCTT-A
1 AAAATAGTCTTAA
*
23991370 AAAATAGTATTAA
1 AAAATAGTCTTAA
23991383 AAAA
1 AAAA
23991387 ATTCCCCCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATAGTCTTAA
Found at i:24004485 original size:194 final size:194
Alignment explanation
Indices: 24004126--24004518 Score: 576
Period size: 194 Copynumber: 2.0 Consensus size: 194
24004116 CACTCCCATT
* * *
24004126 AAAATTACAAACGACAAGCTGACGTGGTAATTAAAAAATAGGTATATTAACAAATTTAGCCTCCA
1 AAAAATACAAACGACAAGATGACGTGGTAATTAAAAAATAGGTATAATAACAAATTTAGCCTCCA
* * * * *
24004191 ATTTTTACATATTATATCGATTTATTCATAATTTTAAAAAATTAACCATCATAATTTACAAATGT
66 ATTTTTAAATATCATATCAATTTAGTCATAACTTTAAAAAATTAACCATCATAATTTACAAATGT
*
24004256 TCTCAATTTGATCCTAATTCTAAAAAAAATCAAAGAAATATATAAAAATACATAAATATTTTCA
131 TCTCAATTTGATCCTAATTCTAAAAAAAATCAAAGAAATATATAAAAACACATAAATATTTTCA
* * * *
24004320 AAAAATACAAACGACAAGATGATGTGGTAGTTAAAAATATATGTATAATAATAAATTTAGCC-CT
1 AAAAATACAAACGACAAGATGACGTGGTAATTAAAAA-ATAGGTATAATAACAAATTTAGCCTC-
*
24004384 CAATTTTTAAATATCATATCAATTTAGTCATAACTTT-AAAAATTAACCCTCATAATTTACAAAT
64 CAATTTTTAAATATCATATCAATTTAGTCATAACTTTAAAAAATTAACCATCATAATTTACAAAT
* * *
24004448 GTTCTCAAGTTTGATCCTAATT-TTAAAAAATTCAAAGAAATATATAAAAACACATACATATTTT
129 GTTCTCAA-TTTGATCCTAATTCTAAAAAAAATCAAAGAAATATATAAAAACACATAAATATTTT
*
24004512 TA
193 CA
24004514 AAAAA
1 AAAAA
24004519 ATATAATAAT
Statistics
Matches: 178, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
194 112 0.63
195 66 0.37
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (194 bp):
AAAAATACAAACGACAAGATGACGTGGTAATTAAAAAATAGGTATAATAACAAATTTAGCCTCCA
ATTTTTAAATATCATATCAATTTAGTCATAACTTTAAAAAATTAACCATCATAATTTACAAATGT
TCTCAATTTGATCCTAATTCTAAAAAAAATCAAAGAAATATATAAAAACACATAAATATTTTCA
Found at i:24004600 original size:27 final size:26
Alignment explanation
Indices: 24004570--24004645 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
24004560 TATTGTTCAC
24004570 AATAAATAATAATATATAAAATTTAAA
1 AATAAATAATAATA-ATAAAATTTAAA
* * *
24004597 AATATATAAAAATAAATAAATATTTTCAA
1 AATAAATAATAAT-AATAAA-A-TTTAAA
24004626 AA-AAAT-ATAATAATAAAATT
1 AATAAATAATAATAATAAAATT
24004646 AATATTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.05
25 1 0.02
26 6 0.15
27 20 0.49
28 5 0.12
29 7 0.17
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAATAATAATAATAAAATTTAAA
Found at i:24004602 original size:59 final size:54
Alignment explanation
Indices: 24004485--24004645 Score: 177
Period size: 59 Copynumber: 2.9 Consensus size: 54
24004475 AAATTCAAAG
* * * * *
24004485 AAATATATAAAAACACATACATATTTTTAAAAAAATATAATA-AT-AAGTTTAA
1 AAATATATAAAAATAAATAAATATTTTCAAAAAAATATAATATATAAAATTTAA
* *
24004537 AAATATATAAAGATAGAA-AATATTATTGTTCACAATAAATAATAATATATAAAATTTAA
1 AAATATATAAAAATA-AATAA-A-TATT-TTCA-AAAAAAT-ATAATATATAAAATTTAA
24004596 AAATATATAAAAATAAATAAATATTTTCAAAAAAATATAATA-ATAAAATT
1 AAATATATAAAAATAAATAAATATTTTCAAAAAAATATAATATATAAAATT
24004646 AATATTAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 17
0.78 0.08 0.15
Matches are distributed among these distances:
52 14 0.15
53 10 0.11
54 10 0.11
55 9 0.10
56 10 0.11
57 10 0.11
58 5 0.05
59 23 0.25
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (54 bp):
AAATATATAAAAATAAATAAATATTTTCAAAAAAATATAATATATAAAATTTAA
Found at i:24004652 original size:6 final size:6
Alignment explanation
Indices: 24004629--24004677 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
24004619 TTTTCAAAAA
* *
24004629 AATA-T AATAAT AAAATT AATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
24004676 AA
1 AA
24004678 ATCAATGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
AATATT
Found at i:24011195 original size:16 final size:16
Alignment explanation
Indices: 24011174--24011236 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 16
24011164 CGTTAATTCG
24011174 GGCTTTGTGCCTAGCA
1 GGCTTTGTGCCTAGCA
*
24011190 GGCTTTGTGCCGGTGATATTCA
1 GGCTTTGTGCC-----TA-GCA
24011212 GGCTTTGTGCCTAGCA
1 GGCTTTGTGCCTAGCA
24011228 GGCTTTGTG
1 GGCTTTGTG
24011237 TCGGTGAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
16 22 0.56
17 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.11, C:0.21, G:0.33, T:0.35
Consensus pattern (16 bp):
GGCTTTGTGCCTAGCA
Found at i:24011225 original size:38 final size:39
Alignment explanation
Indices: 24011169--24011272 Score: 147
Period size: 38 Copynumber: 2.7 Consensus size: 39
24011159 CGTAACGTTA
24011169 ATTCGGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTG-AT
1 ATTCGGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGAAT
* *
24011207 ATTCAGGCTTTGTGCCTAGCAGGCTTTGTGTCGGTGAAT
1 ATTCGGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGAAT
* * * *
24011246 ATTTGGGCTCTATGCCTAGTAGGCTTT
1 ATTCGGGCTTTGTGCCTAGCAGGCTTT
24011273 ATTCTGGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 34 0.59
39 24 0.41
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (39 bp):
ATTCGGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGAAT
Found at i:24011262 original size:39 final size:38
Alignment explanation
Indices: 24011181--24011272 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 38
24011171 TCGGGCTTTG
* *
24011181 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTTTG
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTCTA
* **
24011219 TGCCTAGCAGGCTTTGTGTCGGTGAATATTTGGGCTCTA
1 TGCCTAGCAGGCTTTGTGCCGGTG-ATATTCAGGCTCTA
*
24011258 TGCCTAGTAGGCTTT
1 TGCCTAGCAGGCTTT
24011273 ATTCTGGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 23 0.49
39 24 0.51
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (38 bp):
TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTCTA
Found at i:24016997 original size:20 final size:21
Alignment explanation
Indices: 24016959--24016998 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24016949 TAAAATGAAC
24016959 CTGATAAGCCTTGCTAAACAG
1 CTGATAAGCCTTGCTAAACAG
*
24016980 CTGATAAGTCTT-CTAAACA
1 CTGATAAGCCTTGCTAAACA
24016999 CAAGCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
CTGATAAGCCTTGCTAAACAG
Found at i:24017118 original size:15 final size:15
Alignment explanation
Indices: 24017098--24017129 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
24017088 GAGATTTTTA
24017098 AATTTAATTAAATTT
1 AATTTAATTAAATTT
24017113 AATTTAATTAAATTT
1 AATTTAATTAAATTT
24017128 AA
1 AA
24017130 GGATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTAATTAAATTT
Found at i:24017565 original size:21 final size:22
Alignment explanation
Indices: 24017537--24017592 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
24017527 AATTAATAAA
* *
24017537 ATTATAAAAATATTTAAATTTT
1 ATTATAAAAATATATAAAATTT
*
24017559 ATT-TAAAATTATATAAAATTT
1 ATTATAAAAATATATAAAATTT
24017580 ATTAT-AAAATATA
1 ATTATAAAAATATA
24017593 AATATAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTATAAAAATATATAAAATTT
Found at i:24017585 original size:12 final size:12
Alignment explanation
Indices: 24017537--24017589 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
24017527 AATTAATAAA
*
24017537 ATTATAAAA-AT
1 ATTATAAAATTT
*
24017548 ATT-TAAATTTT
1 ATTATAAAATTT
24017559 ATT-TAAAA-TT
1 ATTATAAAATTT
24017569 A-TATAAAATTT
1 ATTATAAAATTT
24017580 ATTATAAAAT
1 ATTATAAAAT
24017590 ATAAATATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 1 0.03
10 12 0.34
11 14 0.40
12 8 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTATAAAATTT
Found at i:24020876 original size:30 final size:31
Alignment explanation
Indices: 24020835--24020919 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
24020825 ATTAAATTTT
*
24020835 AAATTTTAATAAAAATATTAAAA-ATTAGAA
1 AAATATTAATAAAAATATTAAAATATTAGAA
* * *
24020865 AAATATTAATAAAAATTTGTAAAATTTTATAA
1 AAATATTAATAAAAATAT-TAAAATATTAGAA
24020897 AAATCA-TAATAAAAATA-TAAAAT
1 AAAT-ATTAATAAAAATATTAAAAT
24020920 GCATCAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
30 22 0.47
31 5 0.11
32 19 0.40
33 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (31 bp):
AAATATTAATAAAAATATTAAAATATTAGAA
Found at i:24020877 original size:21 final size:20
Alignment explanation
Indices: 24020853--24020900 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
24020843 ATAAAAATAT
24020853 TAAAAATTAGAAAAATATTAA
1 TAAAAATTAGAAAAAT-TTAA
* * *
24020874 TAAAAATTTGTAAAATTTTA
1 TAAAAATTAGAAAAATTTAA
24020894 TAAAAAT
1 TAAAAAT
24020901 CATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAAAATTAGAAAAATTTAA
Found at i:24020897 original size:10 final size:10
Alignment explanation
Indices: 24020814--24020900 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 10
24020804 TAAATTATAG
24020814 TTATAAAAA-
1 TTATAAAAAT
*
24020823 TTAT-TAAAT
1 TTATAAAAAT
*
24020832 TT-T-AAATT
1 TTATAAAAAT
24020840 TTAATAAAAAT
1 TT-ATAAAAAT
*
24020851 AT-TAAAAA-
1 TTATAAAAAT
*
24020859 TTAGAAAAAT
1 TTATAAAAAT
24020869 ATTAATAAAAAT
1 -TT-ATAAAAAT
* *
24020881 TTGTAAAATT
1 TTATAAAAAT
24020891 TTATAAAAAT
1 TTATAAAAAT
24020901 CATAATAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
8 10 0.17
9 17 0.29
10 15 0.26
11 9 0.16
12 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:24020907 original size:32 final size:30
Alignment explanation
Indices: 24020841--24020918 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 30
24020831 TTTTAAATTT
*
24020841 TAATAAAAATATTAAAAATTAGAAAAATAT
1 TAATAAAAATATTAAAAATTAGAAAAATAA
* * * *
24020871 TAATAAAAATTTGTAAAATTTTATAAAAATCA
1 TAATAAAAATAT-TAAAA-ATTAGAAAAATAA
24020903 TAATAAAAATA-TAAAA
1 TAATAAAAATATTAAAA
24020919 TGCATCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 16 0.40
31 5 0.12
32 19 0.47
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (30 bp):
TAATAAAAATATTAAAAATTAGAAAAATAA
Found at i:24033286 original size:47 final size:47
Alignment explanation
Indices: 24033229--24033318 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
24033219 CTTTATAAAA
* **
24033229 TTTTATTA-TTTTTTCTATATTTCTATATATTTTATTATTTTTTACGAT
1 TTTTATTATTTTTTTCT-CATTTAAATATATTTT-TTATTTTTTACGAT
24033277 TTTTA-TATTTTTTTCTCATTTAAATATATTTTTTATTTTTTA
1 TTTTATTATTTTTTTCTCATTTAAATATATTTTTTATTTTTTA
24033319 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 10 0.26
47 15 0.39
48 13 0.34
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (47 bp):
TTTTATTATTTTTTTCTCATTTAAATATATTTTTTATTTTTTACGAT
Found at i:24033290 original size:29 final size:28
Alignment explanation
Indices: 24033200--24033289 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
24033190 TCTTTACATT
* * *
24033200 TTTTATAATTTTCTTACGA-CTTTATAAAA
1 TTTTATTATTTT-TTACGATTTTTAT-ATA
*
24033229 TTTTATTATTTTTT-CTATATTTCTATATA
1 TTTTATTATTTTTTACGAT-TTT-TATATA
*
24033258 TTTTATTATTTTTTACGATTTTTATATT
1 TTTTATTATTTTTTACGATTTTTATATA
24033286 TTTT
1 TTTT
24033290 TCTCATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.04
28 11 0.22
29 32 0.63
30 6 0.12
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTATTATTTTTTACGATTTTTATATA
Found at i:24033373 original size:27 final size:27
Alignment explanation
Indices: 24033306--24033375 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
24033296 TTAAATATAT
24033306 TTTTTA-TTTTTTATTAAAATTTAATAA
1 TTTTTATTTTTTTA-TAAAATTTAATAA
* * * *
24033333 TTTTTATAATTTTTATAAATTTTATTGA
1 TTTTTAT-TTTTTTATAAAATTTAATAA
24033361 TTTTTATTTTTTTAT
1 TTTTTATTTTTTTAT
24033376 CATTTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 13 0.36
28 17 0.47
29 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTTTTATAAAATTTAATAA
Found at i:24037475 original size:136 final size:136
Alignment explanation
Indices: 24037245--24037688 Score: 649
Period size: 136 Copynumber: 3.3 Consensus size: 136
24037235 AGTGTAGATC
* *
24037245 GTGAGAGAGAG-T--TACTTGGGTATTTATACCTAGCCTTGGGGCATCAATGCTCCAGAGTGCTA
1 GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAGTGCTA
*
24037307 TCGGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
66 TCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
24037372 AGAAGT
131 AGAAGT
24037378 GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAGTGCTA
1 GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAGTGCTA
24037443 TCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
66 TCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
24037508 AGAAGT
131 AGAAGT
* * * *
24037514 GTGAGAGGGATTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAATGCTC
1 GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAGTGCTA
* * * * *
24037579 TTTGATGCTTAAGTTAGAAAACGAGATGGTGTAATGGGT-----AA-AGC--AAGCTAGCAGAGA
66 TCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
*
24037636 GGAAGT
131 AGAAGT
* * *
24037642 AAGAGAGAGGGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGGC
1 --GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGC
24037689 TGCCTGTTGC
Statistics
Matches: 290, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
128 18 0.06
130 45 0.16
131 2 0.01
133 11 0.04
134 1 0.00
136 213 0.73
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (136 bp):
GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAGTGCTCCAGAGTGCTA
TCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAGAGA
AGAAGT
Found at i:24041702 original size:2 final size:2
Alignment explanation
Indices: 24041695--24041729 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24041685 GTAAAACTAA
24041695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24041730 ATTGTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24052877 original size:44 final size:44
Alignment explanation
Indices: 24052827--24052981 Score: 213
Period size: 44 Copynumber: 3.5 Consensus size: 44
24052817 TCATTAGGGC
*
24052827 TTATATTCAATAGGTACTATGTATCGGTGTTGGCTATGTGCCAT
1 TTATATTCAACAGGTACTATGTATCGGTGTTGGCTATGTGCCAT
*
24052871 TTATATTCAGCAGGTACTATGTATCGGTGTTGGCTAAT-TGCCAT
1 TTATATTCAACAGGTACTATGTATCGGTGTTGGCT-ATGTGCCAT
* ** * * * *
24052915 TTGTATTCAGTAGGTACCATGTATTGATGTTGGCTATGTGTCAT
1 TTATATTCAACAGGTACTATGTATCGGTGTTGGCTATGTGCCAT
24052959 TTATATTCAACAGGTACTATGTA
1 TTATATTCAACAGGTACTATGTA
24052982 CTAGTATTGG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
43 2 0.02
44 93 0.96
45 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (44 bp):
TTATATTCAACAGGTACTATGTATCGGTGTTGGCTATGTGCCAT
Found at i:24055618 original size:22 final size:22
Alignment explanation
Indices: 24055551--24055620 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 22
24055541 ACTATGAATA
*
24055551 ACATTGGAAT-TGAATGTCACG
1 ACATTGGAATCTGAATGTCGCG
* * *
24055572 ACATTGGGA-CTGAATGTTGCA
1 ACATTGGAATCTGAATGTCGCG
*
24055593 ACATTGGAATCTGAATGTCGTG
1 ACATTGGAATCTGAATGTCGCG
24055615 ACATTG
1 ACATTG
24055621 AATACAGACG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 24 0.62
22 15 0.38
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (22 bp):
ACATTGGAATCTGAATGTCGCG
Found at i:24061977 original size:25 final size:24
Alignment explanation
Indices: 24061922--24062025 Score: 99
Period size: 25 Copynumber: 4.4 Consensus size: 24
24061912 AATTTTGGAC
24061922 TAAATTGAATAGTATGTTTTTAAA
1 TAAATTGAATAGTATGTTTTTAAA
24061946 TAAATTGAATAGTATGTTTATTAAA
1 TAAATTGAATAGTATGTTT-TTAAA
* * ** *
24061971 TAGATTG-AT-G-A-ATTTTGGAC
1 TAAATTGAATAGTATGTTTTTAAA
*
24061991 TAAATTGAATAGTATGTGTATTAAA
1 TAAATTGAATAGTATGT-TTTTAAA
*
24062016 TAGATTGAAT
1 TAAATTGAAT
24062026 TTGCTTATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
20 8 0.13
21 5 0.08
22 2 0.03
23 2 0.03
24 22 0.35
25 23 0.37
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.42
Consensus pattern (24 bp):
TAAATTGAATAGTATGTTTTTAAA
Found at i:24063657 original size:12 final size:12
Alignment explanation
Indices: 24063640--24063670 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24063630 TGGGCAAGGA
24063640 CACGAGCTCGGG
1 CACGAGCTCGGG
24063652 CACGAGCTCGGG
1 CACGAGCTCGGG
24063664 CACGAGC
1 CACGAGC
24063671 GTGTGTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.39, T:0.06
Consensus pattern (12 bp):
CACGAGCTCGGG
Found at i:24067085 original size:22 final size:22
Alignment explanation
Indices: 24067057--24067114 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
24067047 ATATGCACAA
*
24067057 AGAGCTTAGTACGTTAAACATG
1 AGAGCTTAGTACGTGAAACATG
24067079 AGAGCTTAGTACGTGAAACATG
1 AGAGCTTAGTACGTGAAACATG
24067101 AGAGCTTAGTACGT
1 AGAGCTTAGTACGT
24067115 ACTATCAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (22 bp):
AGAGCTTAGTACGTGAAACATG
Found at i:24071516 original size:21 final size:21
Alignment explanation
Indices: 24071500--24071574 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 21
24071490 AGGAAGTGAG
*
24071500 TTAGACAAAAAGAGAAGCAAC
1 TTAGACAAAAAGAGAAGTAAC
24071521 TT-GCACAAAAAGAGAAGTAAC
1 TTAG-ACAAAAAGAGAAGTAAC
* *
24071542 TTGGACAAAAAGAAACGAAGTGAC
1 TTAGACAAAAAG--A-GAAGTAAC
24071566 TTAGACAAA
1 TTAGACAAA
24071575 TCTTTTTCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 1 0.02
21 28 0.61
22 1 0.02
23 1 0.02
24 15 0.33
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (21 bp):
TTAGACAAAAAGAGAAGTAAC
Found at i:24071567 original size:24 final size:21
Alignment explanation
Indices: 24071503--24071554 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
24071493 AAGTGAGTTA
*
24071503 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGTAACTTG
*
24071524 CACAAAAAGAGAAGTAACTTG
1 GACAAAAAGAGAAGTAACTTG
24071545 GACAAAAAGA
1 GACAAAAAGA
24071555 AACGAAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.56, C:0.13, G:0.21, T:0.10
Consensus pattern (21 bp):
GACAAAAAGAGAAGTAACTTG
Found at i:24073797 original size:19 final size:19
Alignment explanation
Indices: 24073775--24073832 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
24073765 TTGCCAAAAT
24073775 TTTTTTGCTGATTCTACTA
1 TTTTTTGCTGATTCTACTA
* * * *
24073794 TTTTATCCTGA---TAATT
1 TTTTTTGCTGATTCTACTA
*
24073810 TTTTTTGCTAATTCTACTA
1 TTTTTTGCTGATTCTACTA
24073829 TTTT
1 TTTT
24073833 ATCCTGATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 6
0.64 0.21 0.14
Matches are distributed among these distances:
16 11 0.41
19 16 0.59
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTTGCTGATTCTACTA
Found at i:24073817 original size:35 final size:35
Alignment explanation
Indices: 24073774--24073851 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
24073764 TTTGCCAAAA
* *
24073774 TTTTTTTGCTGATTCTACTATTTTATCCTGATAAT
1 TTTTTTTGCTAATTCTACTATTTTATCCTGATAAC
24073809 TTTTTTTGCTAATTCTACTATTTTATCCTGATAAC
1 TTTTTTTGCTAATTCTACTATTTTATCCTGATAAC
*
24073844 TTATTTTG
1 TTTTTTTG
24073852 TTAGAACTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.58
Consensus pattern (35 bp):
TTTTTTTGCTAATTCTACTATTTTATCCTGATAAC
Found at i:24073862 original size:35 final size:35
Alignment explanation
Indices: 24073777--24073866 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
24073767 GCCAAAATTT
* * * *
24073777 TTTTGCTGATTCTACTATTTTATCCTGATAATTTT
1 TTTTGCTAATACTACTATTTTATCCTGATAACTTA
*
24073812 TTTTGCTAATTCTACTATTTTATCCTGATAACTTA
1 TTTTGCTAATACTACTATTTTATCCTGATAACTTA
*
24073847 TTTTGTTAGA-ACTACTATTT
1 TTTTGCTA-ATACTACTATTT
24073867 ATTTCTTGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
35 48 0.98
36 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.54
Consensus pattern (35 bp):
TTTTGCTAATACTACTATTTTATCCTGATAACTTA
Found at i:24095929 original size:18 final size:18
Alignment explanation
Indices: 24095889--24095930 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24095879 TGCTCACAAC
*
24095889 AATATCACCAATAACAAT
1 AATATCACCAATAAAAAT
24095907 AATATCACGCAA-AAAAAT
1 AATATCAC-CAATAAAAAT
*
24095925 GATATC
1 AATATC
24095931 GAACATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (18 bp):
AATATCACCAATAAAAAT
Found at i:24102102 original size:23 final size:25
Alignment explanation
Indices: 24102051--24102102 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
24102041 TCAAATTTTC
* * *
24102051 AAAATATTTATAAATTTTATTTTCT
1 AAAATATTTATAAATTATATATTCA
24102076 AAAAT-TTTATAAA-TATATATTCA
1 AAAATATTTATAAATTATATATTCA
24102099 AAAA
1 AAAA
24102103 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 8 0.33
25 5 0.21
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATATTTATAAATTATATATTCA
Found at i:24102121 original size:17 final size:15
Alignment explanation
Indices: 24102099--24102136 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
24102089 TATATATTCA
24102099 AAAAATTAAAAATTACT
1 AAAAATTAAAAA-TA-T
24102116 AAAAATTAAAAATAT
1 AAAAATTAAAAATAT
24102131 AAAAAT
1 AAAAAT
24102137 GATAGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 12 0.57
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAAAATAT
Found at i:24107223 original size:35 final size:34
Alignment explanation
Indices: 24107158--24107223 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 34
24107148 GTTTCTAAAA
* **
24107158 AAAAAAATCTAAAGTAAAAATTTATTAAAATAAT
1 AAAAAAATCTAAAATAAAAATTTACAAAAATAAT
* *
24107192 AAAAAAATCTAAAAATAAAACTTTCCAAAAAT
1 AAAAAAATCT-AAAATAAAAATTTACAAAAAT
24107224 GAAAGTTCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
34 10 0.38
35 16 0.62
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.26
Consensus pattern (34 bp):
AAAAAAATCTAAAATAAAAATTTACAAAAATAAT
Found at i:24110539 original size:30 final size:31
Alignment explanation
Indices: 24110474--24110544 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
24110464 TTTTGGGGAA
* * *
24110474 TAAAAGTTTGAGAGAAAGTAAATAGGGGTAG
1 TAAAATTTTGAGAAAAAGTAAATAGGAGTAG
24110505 TAAAATTTTGAGAAAAAGTAAATAGGAG-AG
1 TAAAATTTTGAGAAAAAGTAAATAGGAGTAG
24110535 TAAAATTTTG
1 TAAAATTTTG
24110545 GTGGGAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 12 0.32
31 25 0.68
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (31 bp):
TAAAATTTTGAGAAAAAGTAAATAGGAGTAG
Found at i:24110631 original size:29 final size:29
Alignment explanation
Indices: 24110589--24110668 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
24110579 GTAGGGGAGG
24110589 GGAGTAAAAGTTTTG-GGAGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGG-GAAAGTGGGAA
24110618 GGAGTAAAAGTTTTGAGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGGGAAAGTGGGAA
24110647 GGAGTAAAAGTTTTGAGGGAAA
1 GGAGTAAAAGTTTTGAGGGAAA
24110669 AATAAAAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 48 0.96
30 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.40, T:0.21
Consensus pattern (29 bp):
GGAGTAAAAGTTTTGAGGGAAAGTGGGAA
Found at i:24110734 original size:9 final size:9
Alignment explanation
Indices: 24110720--24110756 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
24110710 TATAGTTTGA
24110720 TATTCGAAT
1 TATTCGAAT
24110729 TATTCGAAT
1 TATTCGAAT
*
24110738 TATTCGAGT
1 TATTCGAAT
24110747 TATTCGAAT
1 TATTCGAAT
24110756 T
1 T
24110757 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:24121907 original size:20 final size:20
Alignment explanation
Indices: 24121872--24121920 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
24121862 ATCATGGTCT
*
24121872 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
24121891 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
24121911 TTGCTTACTT
1 TTGCTTACTT
24121921 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:24122240 original size:50 final size:50
Alignment explanation
Indices: 24122123--24122308 Score: 189
Period size: 50 Copynumber: 3.7 Consensus size: 50
24122113 GATAATAACA
* * * * *
24122123 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATGTT-TCCTGTAC--
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* *
24122172 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** *
24122222 TGCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
** *
24122272 CACCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
24122309 TCTCATCCCC
Statistics
Matches: 113, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 4 0.04
49 36 0.32
50 73 0.65
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:24126159 original size:18 final size:18
Alignment explanation
Indices: 24126136--24126173 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
24126126 TAATTGAATA
*
24126136 AAATAAA-ACCTTGTTGTT
1 AAATAAACAACTT-TTGTT
24126154 AAATAAACAACTTTTGTT
1 AAATAAACAACTTTTGTT
24126172 AA
1 AA
24126174 GTGATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (18 bp):
AAATAAACAACTTTTGTT
Found at i:24126771 original size:25 final size:25
Alignment explanation
Indices: 24126743--24126806 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
24126733 TTACTGATAC
*
24126743 TCAGCTCGTATGAGCTTACTA-TTA
1 TCAGCTCGTATGAGCTTACCATTTA
24126767 TTCAGCTCAG-ATGAGCTTACCATTTA
1 -TCAGCTC-GTATGAGCTTACCATTTA
24126793 TCA-CTCGTATGAGC
1 TCAGCTCGTATGAGC
24126807 ATACATGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 1 0.03
24 9 0.26
25 21 0.60
26 4 0.11
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTTACCATTTA
Found at i:24127653 original size:20 final size:21
Alignment explanation
Indices: 24127628--24127666 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24127618 TTGAGATGCT
24127628 TGTGGATAT-CATGATATATG
1 TGTGGATATACATGATATATG
*
24127648 TGTGGATATACATGTTATA
1 TGTGGATATACATGATATA
24127667 AGCTTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (21 bp):
TGTGGATATACATGATATATG
Done.