Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 97 of 320
Found at i:31161285 original size:24 final size:24
Alignment explanation
Indices: 31161258--31161426 Score: 234
Period size: 24 Copynumber: 7.0 Consensus size: 24
31161248 GGAGGAAGTG
31161258 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
31161282 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
31161306 AAAAAGGGCTTATGCCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
*
31161329 CTAAAAGGGCTTACGCCCCAGTTAT
1 C-AAAAGGGCTTATGCCCCAGTTAT
*
31161354 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
31161378 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
31161402 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
31161427 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
24 122 0.92
25 11 0.08
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:31167614 original size:39 final size:39
Alignment explanation
Indices: 31167571--31167684 Score: 174
Period size: 39 Copynumber: 2.9 Consensus size: 39
31167561 CTGGACATAT
* * *
31167571 TTCCAGCACGTAGCCTGCAGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
*
31167610 TTCCAGCACATAGCCTGTGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
* *
31167649 TTCCAGCACATAGCATGCGGACCCTAAGTCCGGATA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
31167685 AACATCACTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
Found at i:31169778 original size:27 final size:27
Alignment explanation
Indices: 31169740--31169801 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
31169730 TTGAGCACAT
* *
31169740 AAAGTAGAACTCAGCAAAGAAAAAAGA
1 AAAGCAGAACTCAACAAAGAAAAAAGA
31169767 AAAGCAGAACTCAACAAAGAAAAAAGA
1 AAAGCAGAACTCAACAAAGAAAAAAGA
31169794 AAAGCAGA
1 AAAGCAGA
31169802 TACTTGTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.65, C:0.13, G:0.18, T:0.05
Consensus pattern (27 bp):
AAAGCAGAACTCAACAAAGAAAAAAGA
Found at i:31172246 original size:18 final size:18
Alignment explanation
Indices: 31172219--31172254 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31172209 AGTTAAAGAA
31172219 TTAAGGAAGCTACCTGGG
1 TTAAGGAAGCTACCTGGG
*
31172237 TTAAGTAAGCTACCTGGG
1 TTAAGGAAGCTACCTGGG
31172255 AATCGGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25
Consensus pattern (18 bp):
TTAAGGAAGCTACCTGGG
Found at i:31174755 original size:23 final size:22
Alignment explanation
Indices: 31174719--31174876 Score: 108
Period size: 23 Copynumber: 7.0 Consensus size: 22
31174709 AGACTCACTA
*
31174719 CAGCTTGAAAGAGCTTACTGTTT
1 CAGCTT-ATAGAGCTTACTGTTT
* *
31174742 CAGCTTATTGGAGCTTACCGATTT
1 CAGCTTA-TAGAGCTTACTG-TTT
* *
31174766 -AGCTTGAAAGAGCTTATTG-TT
1 CAGCTT-ATAGAGCTTACTGTTT
* * *
31174787 GAGCTCAACAGAGCTTA-TCGTTT
1 CAGCT-TATAGAGCTTACT-GTTT
*
31174810 CAGCTTGTATGAGCTTACTG-TT
1 CAGCTTATA-GAGCTTACTGTTT
*
31174832 CAGCTTGATAGAGCTTACCGTTT
1 CAGCTT-ATAGAGCTTACTGTTT
*
31174855 CAGCTCACTAGAGCTTACTGTT
1 CAGCTTA-TAGAGCTTACTGTT
31174877 CATCAGCTCA
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
21 3 0.03
22 34 0.32
23 64 0.60
24 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (22 bp):
CAGCTTATAGAGCTTACTGTTT
Found at i:31174816 original size:45 final size:45
Alignment explanation
Indices: 31174719--31174878 Score: 171
Period size: 45 Copynumber: 3.5 Consensus size: 45
31174709 AGACTCACTA
* *
31174719 CAGCTTGAAAGAGCTTACTGTTTCAGCTTATTGGAGCTTACCGATTT
1 CAGCTTGAAAGAGCTTACTG-TTCAGCTTAATAGAGCTTACCG-TTT
* * * * *
31174766 -AGCTTGAAAGAGCTTATTGTTGAGCTCAACAGAGCTTATCGTTT
1 CAGCTTGAAAGAGCTTACTGTTCAGCTTAATAGAGCTTACCGTTT
* * *
31174810 CAGCTTGTATGAGCTTACTGTTCAGCTTGATAGAGCTTACCGTTT
1 CAGCTTGAAAGAGCTTACTGTTCAGCTTAATAGAGCTTACCGTTT
* *
31174855 CAGC-TCACTAGAGCTTACTGTTCA
1 CAGCTTGA-AAGAGCTTACTGTTCA
31174879 TCAGCTCAGG
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
44 4 0.04
45 70 0.76
46 18 0.20
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (45 bp):
CAGCTTGAAAGAGCTTACTGTTCAGCTTAATAGAGCTTACCGTTT
Found at i:31174836 original size:22 final size:22
Alignment explanation
Indices: 31174808--31174878 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
31174798 AGCTTATCGT
31174808 TTCAGCTTGTATGAGCTTACTG
1 TTCAGCTTGTATGAGCTTACTG
*
31174830 TTCAGCTTG-ATAGAGCTTACCG
1 TTCAGCTTGTAT-GAGCTTACTG
**
31174852 TTTCAGCTCACTA-GAGCTTACTG
1 -TTCAGCT-TGTATGAGCTTACTG
31174875 TTCA
1 TTCA
31174879 TCAGCTCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.05
22 22 0.54
23 16 0.39
25 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (22 bp):
TTCAGCTTGTATGAGCTTACTG
Found at i:31174860 original size:68 final size:68
Alignment explanation
Indices: 31174728--31174876 Score: 171
Period size: 68 Copynumber: 2.2 Consensus size: 68
31174718 ACAGCTTGAA
* ** *
31174728 AGAGCTTACTGTTTCAGCTTATTGGAGCTTACCGATTTAGCTTGAAAGAGCTTATTGTTGAGCTC
1 AGAGCTTACTGTTTCAGCTTATTGGAGCTTACCGATTCAGCTTGAAAGAGCTTACCGTTCAGCTC
31174793 AAC-
66 -ACT
* * *
31174796 AGAGCTTA-TCGTTTCAGCTTGTAT-GAGCTTACTG-TTCAGCTTGATAGAGCTTACCGTTTCAG
1 AGAGCTTACT-GTTTCAGCTTAT-TGGAGCTTACCGATTCAGCTTGAAAGAGCTTACCG-TTCAG
31174858 CTCACT
63 CTCACT
31174864 AGAGCTTACTGTT
1 AGAGCTTACTGTT
31174877 CATCAGCTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
67 21 0.30
68 46 0.67
69 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (68 bp):
AGAGCTTACTGTTTCAGCTTATTGGAGCTTACCGATTCAGCTTGAAAGAGCTTACCGTTCAGCTC
ACT
Found at i:31176057 original size:67 final size:67
Alignment explanation
Indices: 31175986--31176131 Score: 229
Period size: 67 Copynumber: 2.2 Consensus size: 67
31175976 ACGGGCCGCC
* ** *
31175986 ACACGGGCGTGTCTTGAGACTATGTCGATAAGTCAGTATGTATGCCCTATTTTGCCATGGCCTAG
1 ACACGGGCGTGTCTTGAGACCATGTAAATAAGTCAGTATGTATGCCCTATTTTGCCACGGCCTAG
31176051 AT
66 AT
* *
31176053 ACACGGCCGTGTCTTGAGACCATGTAAATAAGTCAGTATGTATGTCCTATTTTGCCACGGCCTAG
1 ACACGGGCGTGTCTTGAGACCATGTAAATAAGTCAGTATGTATGCCCTATTTTGCCACGGCCTAG
31176118 AT
66 AT
*
31176120 ACATGGGCGTGT
1 ACACGGGCGTGT
31176132 GACACATAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (67 bp):
ACACGGGCGTGTCTTGAGACCATGTAAATAAGTCAGTATGTATGCCCTATTTTGCCACGGCCTAG
AT
Found at i:31183895 original size:23 final size:23
Alignment explanation
Indices: 31183869--31184026 Score: 121
Period size: 23 Copynumber: 7.0 Consensus size: 23
31183859 GGACTCACTA
*
31183869 CAGCTCGAAAGAGCTTACTATTT
1 CAGCTCGAAAGAGCTTACTGTTT
* ** *
31183892 CAGCT-TATTGGAGCTTATTGATTT
1 CAGCTCGA-AAGAGCTTACTG-TTT
*
31183916 -AGCTCGAAAGATCTTACTGTTT
1 CAGCTCGAAAGAGCTTACTGTTT
*
31183938 -AGATC-AATAGAGCTTACTGTTT
1 CAGCTCGAA-AGAGCTTACTGTTT
* *
31183960 CAGCTCGTATGAGCTTACTG-TT
1 CAGCTCGAAAGAGCTTACTGTTT
* * *
31183982 CAACTCGATAGAGCTTACCGTTT
1 CAGCTCGAAAGAGCTTACTGTTT
*
31184005 CAGCT-TAATAGAGCTTACTGTT
1 CAGCTCGAA-AGAGCTTACTGTT
31184027 CATCAGCTTA
Statistics
Matches: 103, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.02
22 39 0.38
23 57 0.55
24 5 0.05
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (23 bp):
CAGCTCGAAAGAGCTTACTGTTT
Found at i:31183963 original size:68 final size:66
Alignment explanation
Indices: 31183878--31184036 Score: 167
Period size: 68 Copynumber: 2.3 Consensus size: 66
31183868 ACAGCTCGAA
* * * * * *
31183878 AGAGCTTACTATTTCAGCTTATTGGAGCTTATTGATTTAGCTCGAAAGATCTTACTGTTT-AGAT
1 AGAGCTTACTGTTTCAGCTTA-T-GAGCTTACTG-TTCAACTCGAAAGAGCTTACCGTTTCAGAT
31183942 CAAT
63 CAAT
* * *
31183946 AGAGCTTACTGTTTCAGCTCGTATGAGCTTACTGTTCAACTCGATAGAGCTTACCGTTTCAGCTT
1 AGAGCTTACTGTTTCAGCT--TATGAGCTTACTGTTCAACTCGAAAGAGCTTACCGTTTCAGATC
31184011 AAT
64 AAT
31184014 AGAGCTTACTGTTCATCAGCTTA
1 AGAGCTTACTGTT--TCAGCTTA
31184037 GGATGAGGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
67 20 0.26
68 48 0.62
69 1 0.01
70 8 0.10
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (66 bp):
AGAGCTTACTGTTTCAGCTTATGAGCTTACTGTTCAACTCGAAAGAGCTTACCGTTTCAGATCAA
T
Found at i:31183966 original size:45 final size:45
Alignment explanation
Indices: 31183869--31184026 Score: 142
Period size: 45 Copynumber: 3.5 Consensus size: 45
31183859 GGACTCACTA
* * * * * *
31183869 CAGCTCGAAAGAGCTTACTATTTCAGCTTATTGGAGCTTATTGATTT
1 CAGCTCGAAAGAGCTTACTGTTT-AGATCAATAGAGCTTACTG-TTT
*
31183916 -AGCTCGAAAGATCTTACTGTTTAGATCAATAGAGCTTACTGTTT
1 CAGCTCGAAAGAGCTTACTGTTTAGATCAATAGAGCTTACTGTTT
* * * * *
31183960 CAGCTCGTATGAGCTTACTGTTCA-ACTCGATAGAGCTTACCGTTT
1 CAGCTCGAAAGAGCTTACTGTTTAGA-TCAATAGAGCTTACTGTTT
*
31184005 CAGCT-TAATAGAGCTTACTGTT
1 CAGCTCGAA-AGAGCTTACTGTT
31184027 CATCAGCTTA
Statistics
Matches: 92, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
44 5 0.05
45 67 0.73
46 20 0.22
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (45 bp):
CAGCTCGAAAGAGCTTACTGTTTAGATCAATAGAGCTTACTGTTT
Found at i:31189967 original size:18 final size:19
Alignment explanation
Indices: 31189944--31189979 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31189934 AATATTACAC
31189944 AATTCAA-TTTCACATTAA
1 AATTCAATTTTCACATTAA
31189962 AATTCAATTTTCACATTA
1 AATTCAATTTTCACATTA
31189980 TATTTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTCAATTTTCACATTAA
Found at i:31190405 original size:13 final size:13
Alignment explanation
Indices: 31190387--31190418 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
31190377 GTGACTCTTC
31190387 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
31190400 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
31190413 TTCTTT
1 TTCTTT
31190419 ATAATTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:31194074 original size:51 final size:51
Alignment explanation
Indices: 31194019--31194118 Score: 112
Period size: 51 Copynumber: 2.0 Consensus size: 51
31194009 CTACCACATA
* * *
31194019 ACATGTAA-CACATCCATAATGAACTCAGACCTCTCAACGAGCTCGAATGTT
1 ACATG-AATCACATCCAGAATGAACTCAGACCACTCAACGAGCTCCAATGTT
** * * *
31194070 ACATGAATCGTATCCAGCATGAACTCGGACCACTCTACGAGCTCCAATG
1 ACATGAATCACATCCAGAATGAACTCAGACCACTCAACGAGCTCCAATG
31194119 CTCGCATCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 2 0.05
51 38 0.95
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (51 bp):
ACATGAATCACATCCAGAATGAACTCAGACCACTCAACGAGCTCCAATGTT
Found at i:31202100 original size:14 final size:14
Alignment explanation
Indices: 31202081--31202109 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31202071 ACTTCTCGAT
31202081 CATAGTTTTCCAAG
1 CATAGTTTTCCAAG
31202095 CATAGTTTTCCAAG
1 CATAGTTTTCCAAG
31202109 C
1 C
31202110 CTTAAACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (14 bp):
CATAGTTTTCCAAG
Found at i:31211575 original size:30 final size:30
Alignment explanation
Indices: 31211517--31211575 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
31211507 ATTTTCGGGC
* * **
31211517 CTAGGGTTAAATTGGTCATTTTGTCAAAGT
1 CTAGGGGTAAAATGGTCATTTTACCAAAGT
*
31211547 CTAGGGGTAAAATGTTCATTTTACCAAAG
1 CTAGGGGTAAAATGGTCATTTTACCAAAG
31211576 ATATGAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (30 bp):
CTAGGGGTAAAATGGTCATTTTACCAAAGT
Found at i:31215021 original size:95 final size:95
Alignment explanation
Indices: 31214864--31215053 Score: 353
Period size: 95 Copynumber: 2.0 Consensus size: 95
31214854 GAAGTCTATC
*
31214864 ACAAAACTCTAAAGCATATCTTCCCGAATCTGAATGACTCACTCAGATTGTCCGTCGGTCTGAGG
1 ACAAAACTCTAAAGCATATCTTCCCGAATCTGAATGACTCACTCAGATTGTCCGTCGATCTGAGG
31214929 GTGATACGCAGTACTAAAATTAAGTCAGGT
66 GTGATACGCAGTACTAAAATTAAGTCAGGT
31214959 ACAAAACTCTAAAGCATATCTTCCCGAATCTGAATGACTCACTCAGATTGTCCGTCGATCTGAGG
1 ACAAAACTCTAAAGCATATCTTCCCGAATCTGAATGACTCACTCAGATTGTCCGTCGATCTGAGG
* *
31215024 GTTATACGTAGTACTAAAATTAAGTCAGGT
66 GTGATACGCAGTACTAAAATTAAGTCAGGT
31215054 GTCTAAGGCC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (95 bp):
ACAAAACTCTAAAGCATATCTTCCCGAATCTGAATGACTCACTCAGATTGTCCGTCGATCTGAGG
GTGATACGCAGTACTAAAATTAAGTCAGGT
Found at i:31216540 original size:55 final size:55
Alignment explanation
Indices: 31216479--31216592 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
31216469 AGTACAGTAC
* *
31216479 GAAAGTGATTATCATGTTCATTTTTAGTTTTGGAGTAAATTAGGA-TGTCATCAAT
1 GAAAGTGATTATCATGTTCAATTTCAGTTTTGGAGTAAATTAGGAGT-TCATCAAT
31216534 GAAAGTGATTATCATGTTCAATTTCAGTTTTGGAGTAAATTAGGAGTTCATCAAT
1 GAAAGTGATTATCATGTTCAATTTCAGTTTTGGAGTAAATTAGGAGTTCATCAAT
31216589 GAAA
1 GAAA
31216593 ACCACTACAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 55 0.98
56 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (55 bp):
GAAAGTGATTATCATGTTCAATTTCAGTTTTGGAGTAAATTAGGAGTTCATCAAT
Found at i:31222234 original size:21 final size:22
Alignment explanation
Indices: 31222196--31222237 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31222186 TTTTATATGT
31222196 TAAATATAATTTTAATTTTAAA
1 TAAATATAATTTTAATTTTAAA
* *
31222218 TAAAT-TATTTTTTATTTTAA
1 TAAATATAATTTTAATTTTAA
31222238 GGCTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAAATATAATTTTAATTTTAAA
Found at i:31222666 original size:15 final size:15
Alignment explanation
Indices: 31222646--31222677 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31222636 AGTAGTTAAA
31222646 TATTTTTTAAAATAT
1 TATTTTTTAAAATAT
*
31222661 TATTTTTTAAATTAT
1 TATTTTTTAAAATAT
31222676 TA
1 TA
31222678 ATGATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTTAAAATAT
Found at i:31228212 original size:20 final size:20
Alignment explanation
Indices: 31228187--31228226 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31228177 TTGTACTCTT
*
31228187 TTGAAATTCAATATTTAATC
1 TTGAAATTCAAAATTTAATC
31228207 TTGAAATTCAAAATTTAATC
1 TTGAAATTCAAAATTTAATC
31228227 CTAGATGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (20 bp):
TTGAAATTCAAAATTTAATC
Found at i:31228537 original size:14 final size:13
Alignment explanation
Indices: 31228518--31228548 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
31228508 AAGTAATTTA
31228518 TTTTTAAATTACT
1 TTTTTAAATTACT
31228531 CTTTTTAAATTACT
1 -TTTTTAAATTACT
31228545 TTTT
1 TTTT
31228549 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTAAATTACT
Found at i:31234479 original size:47 final size:48
Alignment explanation
Indices: 31234425--31234552 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 48
31234415 GATATGTGTG
* *
31234425 TGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCACATT-ATG-AA-A
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTGAGGCAAGA
31234472 TGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CATTGAGGCAAGA
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGGCAAGA
* *
31234519 -GCCAGTGTAAGACATGTCTGGGACATCCATCGGC
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
31234553 TACGAGATGT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
44 4 0.05
45 2 0.03
46 33 0.45
47 34 0.47
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGGCAAGA
Found at i:31234538 original size:46 final size:44
Alignment explanation
Indices: 31234429--31234552 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 44
31234419 TGTGTGTGCT
* * *
31234429 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGG---CATTAGGAAATGCC
31234476 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGGCAAGA-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATT-AGG-AA-ATGCC
*
31234522 AGTGTAAGACATGTCTGGGACATCCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
31234553 TACGAGATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
44 4 0.06
45 2 0.03
46 34 0.49
47 30 0.43
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATTAGGAAATGCC
Found at i:31234607 original size:44 final size:44
Alignment explanation
Indices: 31234521--31234633 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 44
31234511 AGGCAAGAGC
* * *
31234521 CAGTGTAAGA-CATGTCTGGGACAT-CCATCGGCTACGAGATGTG
1 CAGT-TAAGACCATGTCTAGGACATGGCATCAGCTACGAGATGTG
31234564 TCAGTATAAGACCATGTCTAGGACATGGCATCAGC-ACG-GATGTG
1 -CAGT-TAAGACCATGTCTAGGACATGGCATCAGCTACGAGATGTG
31234608 C----AAGACCATGTCTAGGACATGGCATC
1 CAGTTAAGACCATGTCTAGGACATGGCATC
31234634 GACTTGATGG
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
38 25 0.40
43 1 0.02
44 15 0.24
45 16 0.25
46 6 0.10
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (44 bp):
CAGTTAAGACCATGTCTAGGACATGGCATCAGCTACGAGATGTG
Found at i:31240789 original size:45 final size:45
Alignment explanation
Indices: 31240738--31240826 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
31240728 GAGGTTAGAC
31240738 CAGACTTGACTTTTGAGGAGGTGCCGGTTCAGATTTTGGATCGTA
1 CAGACTTGACTTTTGAGGAGGTGCCGGTTCAGATTTTGGATCGTA
*
31240783 CAGACTTGACTTTTGAGGAGGTGCCGGTTCAGGTTTTGGATCGT
1 CAGACTTGACTTTTGAGGAGGTGCCGGTTCAGATTTTGGATCGT
31240827 GATATTAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.34
Consensus pattern (45 bp):
CAGACTTGACTTTTGAGGAGGTGCCGGTTCAGATTTTGGATCGTA
Found at i:31241520 original size:21 final size:22
Alignment explanation
Indices: 31241469--31241522 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
31241459 TGCAGAGCTC
*
31241469 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGACCAAGGG
** **
31241491 ACAAACCCGTGT-GACCCTGGG
1 ACACGCCCGTGTGGACCAAGGG
31241512 ACACGCCCGTG
1 ACACGCCCGTG
31241523 CTAGAGGCCG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.20, C:0.35, G:0.31, T:0.13
Consensus pattern (22 bp):
ACACGCCCGTGTGGACCAAGGG
Found at i:31243980 original size:93 final size:93
Alignment explanation
Indices: 31243873--31244043 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
31243863 GCCCCTAAGT
*** *
31243873 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATCCACATCCATAAGTGAACTCGGACTCAACTCAA
31243938 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
31243966 GAACTCGGACTCAACTCAACGAGTTCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATCCACATCCATAAGTGAACTCGGACTCAACTCAA
*
31244031 TGAGTTCGGATGC
66 CGAGTTCGGATGC
31244044 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATCCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:31244059 original size:46 final size:46
Alignment explanation
Indices: 31243868--31244046 Score: 195
Period size: 46 Copynumber: 3.9 Consensus size: 46
31243858 AACCCGCCCC
* * *
31243868 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACATCCA
** *
31243914 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACATCCA
* * *
31243960 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA--CATCCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-T-CACATCCA
*
31244007 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCA
31244047 ACCATCCTAG
Statistics
Matches: 108, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
45 4 0.04
46 67 0.62
47 33 0.31
48 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACATCCA
Found at i:31249481 original size:93 final size:93
Alignment explanation
Indices: 31249374--31249544 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
31249364 GCCCCTAAGT
* *
31249374 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
31249439 CGAGTTTGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
31249467 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31249532 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31249545 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:31249541 original size:46 final size:46
Alignment explanation
Indices: 31249369--31249541 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
31249359 AACCCGCCCC
* * *
31249369 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
31249415 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
31249463 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
31249508 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31249542 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:31255647 original size:13 final size:13
Alignment explanation
Indices: 31255608--31255671 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 13
31255598 GATTTTTCCA
*
31255608 AAATATTATCACT
1 AAATATAATCACT
31255621 -AA-ATAATC-CT
1 AAATATAATCACT
31255631 AAATATAATCACT
1 AAATATAATCACT
*
31255644 -AA-ATAAT-TCT
1 AAATATAATCACT
*
31255654 AAATATTATCACT
1 AAATATAATCACT
31255667 AAATA
1 AAATA
31255672 ATTCAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 4 0.10
11 14 0.34
12 14 0.34
13 9 0.22
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATAATCACT
Found at i:31255674 original size:23 final size:23
Alignment explanation
Indices: 31255608--31255680 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
31255598 GATTTTTCCA
*
31255608 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATTCT
*
31255631 AAATATAATCACTAAATAATTCT
1 AAATATTATCACTAAATAATTCT
*
31255654 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCT
31255677 AAAT
1 AAAT
31255681 TTAAAAATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCT
Found at i:31262313 original size:42 final size:41
Alignment explanation
Indices: 31262246--31262352 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 41
31262236 ATATGTAGGG
*
31262246 CCATATCTGGATATGGCATCTATATGAGACTTCGTGTAAGA
1 CCATATCTGGATATGGCATCGATATGAGACTTCGTGTAAGA
* *
31262287 CCATATCTATGATATGGCATCGATATGAGACTTCGTGTAGGA
1 CCATATCT-GGATATGGCATCGATATGAGACTTCGTGTAAGA
* *
31262329 CCATAACTGGGATATTGACATCGA
1 CCATATCT-GGATA-TGGCATCGA
31262353 CACGAGATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 8 0.14
42 41 0.72
43 8 0.14
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (41 bp):
CCATATCTGGATATGGCATCGATATGAGACTTCGTGTAAGA
Found at i:31269857 original size:42 final size:42
Alignment explanation
Indices: 31269804--31269953 Score: 176
Period size: 42 Copynumber: 3.5 Consensus size: 42
31269794 TAAGACTATG
* * * *
31269804 TGTAAGGCCATATATGGGATATGGCATCTATATGAGACTTCA
1 TGTAAGACCATATCTGGGATATGACATCAATATGAGACTTCA
*
31269846 TGTAAGACCATATCTGGGATATGACATCAATATGAGACTTCG
1 TGTAAGACCATATCTGGGATATGACATCAATATGAGACTTCA
* * * * * *
31269888 TGTAAGACCATAGCTGGGCTATTGACATCGAGACGAGA-TCCCA
1 TGTAAGACCATATCTGGGATA-TGACATCAATATGAGACT-TCA
31269931 TGTAAGACCATATCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
31269954 GCATTGGTAT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
42 59 0.64
43 33 0.36
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGACATCAATATGAGACTTCA
Found at i:31270397 original size:17 final size:17
Alignment explanation
Indices: 31270375--31270410 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31270365 GTACCAATAA
31270375 ATTCGACATTTTGAGTT
1 ATTCGACATTTTGAGTT
31270392 ATTCGACATTTTGAGTT
1 ATTCGACATTTTGAGTT
31270409 AT
1 AT
31270411 GGCATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (17 bp):
ATTCGACATTTTGAGTT
Found at i:31270973 original size:42 final size:42
Alignment explanation
Indices: 31270909--31270996 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
31270899 AGAGACACGG
* *
31270909 GCGTGTGTCTCAGCAGTGTGGATGACATGACCTCAGGCACAA
1 GCGTATGTCTCAGCAGTGTGGATGACAAGACCTCAGGCACAA
*
31270951 GCGTATGTCTCAGCCGTGTGGATGACAAGACCTCAGGCACAA
1 GCGTATGTCTCAGCAGTGTGGATGACAAGACCTCAGGCACAA
31270993 GCGT
1 GCGT
31270997 GTGCCCTGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (42 bp):
GCGTATGTCTCAGCAGTGTGGATGACAAGACCTCAGGCACAA
Found at i:31273238 original size:43 final size:42
Alignment explanation
Indices: 31273156--31273239 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
31273146 CATTTATGAA
* *
31273156 TTATTTTTTGGTATAATTTTATATATTTAATTTTAATTTATT
1 TTATTTTTTGATATAATTTTATATATTTAATCTTAATTTATT
*
31273198 TTATTTTTT-ATA-AATTATTATATATTATCATCTTATATTTAT
1 TTATTTTTTGATATAATT-TTATATATT-TAATCTTA-ATTTAT
31273240 ATACGCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 4 0.11
41 11 0.31
42 15 0.42
43 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (42 bp):
TTATTTTTTGATATAATTTTATATATTTAATCTTAATTTATT
Found at i:31274214 original size:14 final size:14
Alignment explanation
Indices: 31274195--31274226 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31274185 TGGAAAAATA
*
31274195 AATAAATCTATAAT
1 AATAAATCTATAAC
31274209 AATAAATCTATAAC
1 AATAAATCTATAAC
31274223 AATA
1 AATA
31274227 CTTAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATCTATAAC
Found at i:31275948 original size:22 final size:22
Alignment explanation
Indices: 31275910--31275956 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
31275900 GATTTACTAA
31275910 TTTAATTATAAATAATT-TTAAT
1 TTTAATTATAAATAATTATT-AT
*
31275932 TTTAATTAT-ATTAAATTATTAT
1 TTTAATTATAAAT-AATTATTAT
31275954 TTT
1 TTT
31275957 CACATGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 2 0.09
22 18 0.82
23 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAATTATAAATAATTATTAT
Found at i:31276475 original size:13 final size:13
Alignment explanation
Indices: 31276457--31276483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31276447 AAGGGTTGAT
31276457 TTAGGTTAGATCA
1 TTAGGTTAGATCA
31276470 TTAGGTTAGATCA
1 TTAGGTTAGATCA
31276483 T
1 T
31276484 ACCAACTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TTAGGTTAGATCA
Found at i:31285288 original size:35 final size:34
Alignment explanation
Indices: 31285247--31285351 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 34
31285237 CTTCAATGAT
*
31285247 ATGCAATCTTAAATATGATACAATCTTAGATATC
1 ATGCAATCTTAGATATGATACAATCTTAGATATC
* *
31285281 ATTGCAATCTTAGATATGATTGCAATCTTAGATATG
1 A-TGCAATCTTAGATATGA-TACAATCTTAGATATC
*
31285317 ATACAATCTTAGATATGATATACAATCTTAGATAT
1 ATGCAATCTTAGATATG--ATACAATCTTAGATAT
31285352 AATCATTTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 1 0.02
35 31 0.50
36 29 0.47
37 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (34 bp):
ATGCAATCTTAGATATGATACAATCTTAGATATC
Found at i:31285290 original size:18 final size:18
Alignment explanation
Indices: 31285250--31285351 Score: 145
Period size: 18 Copynumber: 5.7 Consensus size: 18
31285240 CAATGATATG
*
31285250 CAATCTTAAATATGA-TA
1 CAATCTTAGATATGATTA
* *
31285267 CAATCTTAGATATCATTG
1 CAATCTTAGATATGATTA
*
31285285 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
31285303 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
31285320 CAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
31285339 CAATCTTAGATAT
1 CAATCTTAGATAT
31285352 AATCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
17 29 0.38
18 33 0.43
19 15 0.19
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (18 bp):
CAATCTTAGATATGATTA
Found at i:31285306 original size:53 final size:55
Alignment explanation
Indices: 31285242--31285351 Score: 179
Period size: 53 Copynumber: 2.0 Consensus size: 55
31285232 ATAATCTTCA
*
31285242 ATGATATGCAATCTTAAATATGATACAATCTTAGATATCAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAAATATGATACAATCTTAGATATCATATACAATCTTAGAT
* *
31285296 ATGAT-TGCAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGAT
1 ATGATATGCAATCTTAAATATGATACAATCTTAGATATCATATACAATCTTAGAT
31285350 AT
1 AT
31285352 AATCATTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 33 0.63
54 19 0.37
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (55 bp):
ATGATATGCAATCTTAAATATGATACAATCTTAGATATCATATACAATCTTAGAT
Found at i:31285446 original size:17 final size:17
Alignment explanation
Indices: 31285426--31285479 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
31285416 CTAATATATT
31285426 TTATATATTTTATATAA
1 TTATATATTTTATATAA
31285443 TTAT-TATTCTTATA-AA
1 TTATATATT-TTATATAA
31285459 -TATAT-TTTT-T-T-A
1 TTATATATTTTATATAA
31285471 TTATATATT
1 TTATATATT
31285480 ATATTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
12 1 0.03
13 6 0.19
14 4 0.12
15 5 0.16
16 7 0.22
17 9 0.28
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATATTTTATATAA
Found at i:31290916 original size:21 final size:22
Alignment explanation
Indices: 31290886--31290934 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
31290876 CTTCTATTTC
31290886 AAAAAAAGAAAAAAATAAA-AG
1 AAAAAAAGAAAAAAATAAAGAG
*
31290907 AAAAAGAGAAAAAAATAAAGAG
1 AAAAAAAGAAAAAAATAAAGAG
31290929 AAAAAA
1 AAAAAA
31290935 TAAAAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAAAAAAATAAAGAG
Found at i:31290918 original size:13 final size:13
Alignment explanation
Indices: 31290889--31290932 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
31290879 CTATTTCAAA
* *
31290889 AAAAGAAAAAAAT
1 AAAAGAAAAAGAG
31290902 AAAAGAAAAAGAG
1 AAAAGAAAAAGAG
*
31290915 AAAAAAATAAAGAG
1 AAAAGAA-AAAGAG
31290929 AAAA
1 AAAA
31290933 AATAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:31290933 original size:13 final size:14
Alignment explanation
Indices: 31290909--31290938 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31290899 AATAAAAGAA
31290909 AAAGAGAAAAAAAT
1 AAAGAGAAAAAAAT
31290923 AAAGAG-AAAAAAT
1 AAAGAGAAAAAAAT
31290936 AAA
1 AAA
31290939 AATATGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (14 bp):
AAAGAGAAAAAAAT
Found at i:31290939 original size:21 final size:20
Alignment explanation
Indices: 31290887--31290940 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
31290877 TTCTATTTCA
31290887 AAAAAAGAAAAAAATAAAAG
1 AAAAAAGAAAAAAATAAAAG
31290907 AAAAAGAGAAAAAAATAAAGAG
1 AAAAA-AGAAAAAAATAAA-AG
*
31290929 AAAAAATAAAAA
1 AAAAAAGAAAAA
31290941 TATGGAGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 5 0.16
21 19 0.61
22 7 0.23
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (20 bp):
AAAAAAGAAAAAAATAAAAG
Found at i:31291961 original size:44 final size:44
Alignment explanation
Indices: 31291820--31291999 Score: 177
Period size: 44 Copynumber: 4.1 Consensus size: 44
31291810 CAAAGAAACA
** * *
31291820 AGATTTGGCATCTTTATGTTTATAGGGAACATATTGAAGATAGT
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATTGAAGATAGC
* * * * * * * **
31291864 AGATCTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTC
1 AGATTTGGCATCCCTATGTTTATAGGGAA-CAGATTGAAGATAGC
*
31291909 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTATGTTTATAGGGAACAGA-TTGAAGATAGC
*
31291952 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATTGAAGATAGC
31291996 AGAT
1 AGAT
31292000 CTAACCTTCA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
42 2 0.02
43 13 0.12
44 78 0.72
45 14 0.13
46 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (44 bp):
AGATTTGGCATCCCTATGTTTATAGGGAACAGATTGAAGATAGC
Found at i:31292346 original size:122 final size:121
Alignment explanation
Indices: 31291991--31292349 Score: 592
Period size: 121 Copynumber: 3.0 Consensus size: 121
31291981 CAGATCGAAG
*
31291991 ATAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
*
31292056 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACAC
* * *
31292112 ATAGCAGATCTAAACTTCAGATGTTTATTCTGAAGTAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
*
31292177 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTTAGACAC
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACAC
* **
31292233 ATGGCAGATCTAACCTTCAGATGTTTATACTGAAGCCAGATCCAAGATGATTTGACATTCTTGTG
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAG-CAGATCCAAGATGATTTGGTATTCTTGTG
* * * *
31292298 TTTACAAGAAACAATTCGAAGACATAGTAGATTTGACTCTCAGATGTTCTCA
65 TTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
31292350 AACAGACTCT
Statistics
Matches: 220, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
121 147 0.67
122 73 0.33
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (121 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACAC
Found at i:31293010 original size:35 final size:37
Alignment explanation
Indices: 31292964--31293088 Score: 195
Period size: 35 Copynumber: 3.5 Consensus size: 37
31292954 ATAATCTTCA
* *
31292964 ATGATATGCAATCTTAGATATGA-TACAATCTTAGAT
1 ATGATATACAATCTTAGATATGATTGCAATCTTAGAT
*
31293000 ATGAT-TGCAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATACAATCTTAGATATGATTGCAATCTTAGAT
31293036 ATG--ATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATACAATCTTAGATATGATTGCAATCTTAGAT
31293071 ATGATATACAATCTTAGA
1 ATGATATACAATCTTAGA
31293089 AGATATGATT
Statistics
Matches: 83, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
35 50 0.60
36 20 0.24
37 13 0.16
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (37 bp):
ATGATATACAATCTTAGATATGATTGCAATCTTAGAT
Found at i:31293012 original size:18 final size:18
Alignment explanation
Indices: 31292964--31293088 Score: 191
Period size: 18 Copynumber: 6.9 Consensus size: 18
31292954 ATAATCTTCA
31292964 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
31292983 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31293000 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31293018 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
31293036 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31293053 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
31293071 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
31293089 AGATATGATT
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
17 32 0.33
18 51 0.52
19 15 0.15
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:31293032 original size:53 final size:54
Alignment explanation
Indices: 31292964--31293088 Score: 234
Period size: 53 Copynumber: 2.3 Consensus size: 54
31292954 ATAATCTTCA
31292964 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
31293018 ATGAT-TGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
*
31293071 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
31293089 AGATATGATT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
53 53 0.77
54 16 0.23
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (54 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
Found at i:31293607 original size:16 final size:16
Alignment explanation
Indices: 31293569--31293619 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
31293559 TTCTAAACTA
31293569 ATATATTTTATATAAT
1 ATATATTTTATATAAT
31293585 -TATTATTCTTATA-AAT
1 ATA-TATT-TTATATAAT
*
31293601 ATATATTTT-TATTAT
1 ATATATTTTATATAAT
31293616 ATAT
1 ATAT
31293620 TATATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
16 11 0.37
17 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTTTATATAAT
Found at i:31293621 original size:32 final size:35
Alignment explanation
Indices: 31293546--31293622 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 35
31293536 ATTTGATATT
* * *
31293546 TTATACATTATTTTTCTAAACTAATATATTTTATA
1 TTATATATTATTCTTATAAACTAATATATTTTATA
*
31293581 TAAT-TATTATTCTTATAAA-T-ATATATTTT-TA
1 TTATATATTATTCTTATAAACTAATATATTTTATA
31293612 TTATATATTAT
1 TTATATATTAT
31293623 ATTTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 5 0.14
32 15 0.42
33 1 0.03
34 12 0.33
35 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATATATTATTCTTATAAACTAATATATTTTATA
Found at i:31293652 original size:26 final size:25
Alignment explanation
Indices: 31293605--31293653 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
31293595 ATAAATATAT
* * *
31293605 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATAACATTTTAA
31293630 ATTTATTATTAAATATAACATTTT
1 ATTT-TTATTAAATATAACATTTT
31293654 TTTATATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATAACATTTTAA
Found at i:31312754 original size:11 final size:12
Alignment explanation
Indices: 31312731--31312794 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
31312721 TGAATTAATA
31312731 ATATAATTATTT
1 ATATAATTATTT
31312743 ATATAA-TATTT
1 ATATAATTATTT
* **
31312754 ATATAGTTACAT
1 ATATAATTATTT
* *
31312766 ATATAAATAATT
1 ATATAATTATTT
31312778 ATAT--TTATTT
1 ATATAATTATTT
31312788 AATATAA
1 -ATATAA
31312795 AAATAAATTG
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
10 4 0.10
11 14 0.36
12 21 0.54
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
ATATAATTATTT
Found at i:31312757 original size:23 final size:22
Alignment explanation
Indices: 31312726--31312794 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
31312716 TTTTATGAAT
31312726 TAATAA-TATA-ATTATTTATA
1 TAATAATTATATATTATTTATA
* **
31312746 TAATATTTATATAGTTACATATA
1 TAATAATTATATA-TTATTTATA
31312769 TAAATAATTATAT-TTATTTAATA
1 T-AATAATTATATATTATTT-ATA
31312792 TAA
1 TAA
31312795 AAATAAATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.13
21 4 0.11
22 7 0.18
23 12 0.32
24 10 0.26
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
TAATAATTATATATTATTTATA
Found at i:31312792 original size:25 final size:28
Alignment explanation
Indices: 31312764--31312818 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
31312754 ATATAGTTAC
*
31312764 ATATATAAAT-AATT-A-TATTTATTTA
1 ATATAAAAATAAATTGAGTATTTATTTA
31312789 ATATAAAAATAAATTGATGTATTTATTTA
1 ATATAAAAATAAATTGA-GTATTTATTTA
31312818 A
1 A
31312819 ATACATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 4 0.16
27 1 0.04
29 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATAAAAATAAATTGAGTATTTATTTA
Found at i:31317903 original size:15 final size:15
Alignment explanation
Indices: 31317883--31317914 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31317873 GAAGTTGTCA
31317883 TACTCAATATGTAGC
1 TACTCAATATGTAGC
31317898 TACTCAATATGTAGC
1 TACTCAATATGTAGC
31317913 TA
1 TA
31317915 TCTCTGTCTT
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:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (15 bp):
TACTCAATATGTAGC
Found at i:31319176 original size:43 final size:44
Alignment explanation
Indices: 31319115--31319197 Score: 159
Period size: 43 Copynumber: 1.9 Consensus size: 44
31319105 TTTCTAGGAA
31319115 TATGACTTTCGATTAAGAATTAATTTT-CTTAAACATGAGTTCC
1 TATGACTTTCGATTAAGAATTAATTTTACTTAAACATGAGTTCC
31319158 TATGACTTTCGATTAAGAATTAATTTTACTTAAACATGAG
1 TATGACTTTCGATTAAGAATTAATTTTACTTAAACATGAG
31319198 AATATGATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 27 0.69
44 12 0.31
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (44 bp):
TATGACTTTCGATTAAGAATTAATTTTACTTAAACATGAGTTCC
Found at i:31330907 original size:26 final size:26
Alignment explanation
Indices: 31330870--31330925 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
31330860 TGATACAAAT
31330870 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
31330896 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
31330922 TGAT
1 TGAT
31330926 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:31334394 original size:27 final size:27
Alignment explanation
Indices: 31334363--31334540 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
31334353 TAAATTGTAC
31334363 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31334390 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
** * *
31334416 ATGCACTAAGTGTGCGAACTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31334444 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31334472 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31334499 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31334526 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31334541 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 106 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31334477 original size:82 final size:81
Alignment explanation
Indices: 31334364--31334514 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
31334354 AAATTGTACA
* *
31334364 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31334428 TGCGAACTGACCATGCG
65 TGCGAACTGACCATGCG
** *
31334445 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
31334510 TGCGA
65 TGCGA
31334515 GTTGATTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 47 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAACTGACCATGCG
Found at i:31336039 original size:30 final size:30
Alignment explanation
Indices: 31336005--31336064 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31335995 CTTTAATACG
*
31336005 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* * *
31336035 AACTTTTGCATAATTTCACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
31336065 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:31339013 original size:29 final size:30
Alignment explanation
Indices: 31338967--31339024 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31338957 CGAATTGATC
* *
31338967 ATTTTATGATTGTATGTGATAATT-GATGTG
1 ATTTAATGAATGTATGTGA-AATTAGATGTG
31338997 ATTTAATGAATGT-TGTGAAATTAGATGT
1 ATTTAATGAATGTATGTGAAATTAGATGT
31339025 ATATTCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (30 bp):
ATTTAATGAATGTATGTGAAATTAGATGTG
Found at i:31341915 original size:49 final size:49
Alignment explanation
Indices: 31341843--31342029 Score: 257
Period size: 49 Copynumber: 3.8 Consensus size: 49
31341833 TGAGGTCACG
31341843 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
** ** * *
31341892 TGTGTAGTACTAAGTGCAGGCTACTACGTGTTTCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
* * *
31341942 TGTGTAGTACTAAGTGTAGGCTACTATGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
31341991 TGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
31342030 GCTTTGGCTA
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 78 0.66
50 40 0.34
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:31342006 original size:99 final size:99
Alignment explanation
Indices: 31341835--31342013 Score: 331
Period size: 99 Copynumber: 1.8 Consensus size: 99
31341825 ATCTATTGTG
31341835 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
31341900 ACTAAGTGCAGGCTACTACGTGTTTCAGATGGTT
66 ACTAAGTGCAGGCTACTACGTGTTTCAGATGGTT
* * *
31341934 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
31341999 ACTAAGTGCAGGCTA
66 ACTAAGTGCAGGCTA
31342014 TTATGCGTAC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (99 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTTTCAGATGGTT
Found at i:31344331 original size:45 final size:45
Alignment explanation
Indices: 31344265--31344393 Score: 195
Period size: 45 Copynumber: 2.9 Consensus size: 45
31344255 GGGTGTTACA
* * *
31344265 ATGGTAGTTTGTCTGCAAATATTGATGACTTTGTCCACAACCTAC
1 ATGGTAGCTTGTCTGCGAATATTGATGGCTTTGTCCACAACCTAC
* * *
31344310 ATGGTAGCTTGTTTGCGAATATTGGTGGCTTTGTCCACAACCTCC
1 ATGGTAGCTTGTCTGCGAATATTGATGGCTTTGTCCACAACCTAC
*
31344355 ATGGTAGCTTGTCTGCGAATATTGTTGGCTTTGTCCACA
1 ATGGTAGCTTGTCTGCGAATATTGATGGCTTTGTCCACA
31344394 TTAGAGTGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (45 bp):
ATGGTAGCTTGTCTGCGAATATTGATGGCTTTGTCCACAACCTAC
Found at i:31347709 original size:19 final size:19
Alignment explanation
Indices: 31347685--31347721 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31347675 ATCTTATGCA
31347685 TTTAAATCATACATAAGCG
1 TTTAAATCATACATAAGCG
31347704 TTTAAATCATACATAAGC
1 TTTAAATCATACATAAGC
31347722 TTAATATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTAAATCATACATAAGCG
Found at i:31350251 original size:109 final size:109
Alignment explanation
Indices: 31350057--31350425 Score: 479
Period size: 109 Copynumber: 3.4 Consensus size: 109
31350047 CACAATGCTC
* * * * * * ** *
31350057 CTCATACAAGCTATAGAGAATTCGAAATAGATGCATGATCTCAAGCCATCATTACGGTCTATATC
1 CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCTC-AGCCATCGCTACGGTCTGTATC
** *
31350122 ACCGATACATAGTACTTGCTAAATAATCACCGGCTCACGATTCTG
65 ACCGGCACATAGTACCTGCTAAATAATCACCGGCTCACGATTCTG
* * *
31350167 CTCACACAAGCTGTAGAGAATCCATAACAAATGCAGGATCTCAGCCATTGCTACGGTCTGTATCA
1 CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCTCAGCCATCGCTACGGTCTGTATCA
* **
31350232 CTGGCACATAGTACCTGCTAAATAATCATTGGCTCACGATGT-TG
66 CCGGCACATAGTACCTGCTAAATAATCACCGGCTCACGAT-TCTG
*** *
31350276 CTCACACAAGCTGTAGAGAATCTGCAATAGATGCAGGATCTCAGCCATCGCTACGGTCTGTATCA
1 CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCTCAGCCATCGCTACGGTCTGTATCA
* * **
31350341 CCGGCACGTAGTACCTGCTAAATAATCACCGGATCACGACGCTG
66 CCGGCACATAGTACCTGCTAAATAATCACCGGCTCACGATTCTG
31350385 CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCT
1 CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCT
31350426 ATTAAAGCCT
Statistics
Matches: 222, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
109 187 0.84
110 35 0.16
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (109 bp):
CTCACACAAGCTGTAGAGAATCCAAAACAGATGCAGGATCTCAGCCATCGCTACGGTCTGTATCA
CCGGCACATAGTACCTGCTAAATAATCACCGGCTCACGATTCTG
Found at i:31353473 original size:20 final size:20
Alignment explanation
Indices: 31353417--31353479 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
31353407 CCGAAACGTT
**
31353417 AACAGAGGCACCGTAGTGCAA
1 AACAGAGGCACCAAAGTGC-A
*
31353438 ATACAGCA-GCATCAAAGTGCA
1 A-ACAG-AGGCACCAAAGTGCA
31353459 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
31353479 A
1 A
31353480 TCTCGTACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 17 0.49
21 3 0.09
22 13 0.37
23 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.10
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:31357126 original size:46 final size:49
Alignment explanation
Indices: 31356983--31357342 Score: 263
Period size: 46 Copynumber: 7.6 Consensus size: 49
31356973 ATTGTATGCC
* * * *
31356983 AGTGTAAGA-CATGTCTGGGACAT-GTATCAGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGA-GATGTAGAGCT
* * * * *
31357029 AGTGTAAGACCATGTCTGAGACATGGCATCGGCATTGAGACG-AGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGTAGAGCT
31357077 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGTA-AGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGTAGAGCT
** *
31357123 AGTGTAAGA-CATGTCTGGGACAT-GCATC-GGTTACGAGATGT-G-TC-
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-CGAGATGTAGAGCT
* * * ** * *
31357167 AGTGTAAGACCATGTCTAGGACATGGCATCGGTACGTATAGAGGT-G-TC-
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG--CCTCGAGATGTAGAGCT
* ** * *
31357215 AGTGTAAGACCATGTCTGGGATATGGCATTGGCAC-AGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTCGAGATGT-AGAGCT
* * * * *
31357265 AGTGTAAGACCATGTCTGGTACATGGCATCAGCCTCGA-TTTTGATAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGT-AGAGCT
31357314 AGTGTAAGACCATGTCTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
31357343 TAACTTGATG
Statistics
Matches: 256, Mismatches: 41, Indels: 31
0.78 0.12 0.09
Matches are distributed among these distances:
44 9 0.04
45 16 0.06
46 73 0.29
47 28 0.11
48 60 0.23
49 39 0.15
50 31 0.12
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGTAGAGCT
Found at i:31357497 original size:30 final size:30
Alignment explanation
Indices: 31357461--31357520 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
31357451 GGTGAGAGTT
31357461 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
1 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
31357491 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
1 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
31357521 CATGTTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (30 bp):
ACAGTTTGAGTTAAACAAGAAAAGTATAGC
Found at i:31357540 original size:31 final size:30
Alignment explanation
Indices: 31357461--31357533 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
31357451 GGTGAGAGTT
*
31357461 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
1 ACAGTTTGAGTGAAACAAGAAAAGTATAGC
*
31357491 ACAGTTTGAGTTAAACAAGAAAAGTATAGC
1 ACAGTTTGAGTGAAACAAGAAAAGTATAGC
31357521 -CATGTTGTGAGTG
1 ACA-GTT-TGAGTG
31357534 GTACAAGTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 2 0.05
30 33 0.82
31 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
ACAGTTTGAGTGAAACAAGAAAAGTATAGC
Found at i:31358632 original size:20 final size:21
Alignment explanation
Indices: 31358593--31358632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31358583 GTTATAATGA
*
31358593 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCATGTTGCCCTT
*
31358614 CCACACGGGTATG-TGCCCT
1 CCACACGGGCATGTTGCCCT
31358633 ATCTCAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (21 bp):
CCACACGGGCATGTTGCCCTT
Found at i:31364710 original size:47 final size:47
Alignment explanation
Indices: 31364619--31365082 Score: 784
Period size: 47 Copynumber: 9.7 Consensus size: 47
31364609 TTAGGATTCT
31364619 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
31364668 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
31364715 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31364762 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31364809 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31364858 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31364905 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31364954 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
31365001 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
31365048 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
31365083 TCCCGAAGGG
Statistics
Matches: 399, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
47 286 0.72
49 113 0.28
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31364723 original size:96 final size:96
Alignment explanation
Indices: 31364619--31365082 Score: 810
Period size: 96 Copynumber: 4.9 Consensus size: 96
31364609 TTAGGATTCT
*
31364619 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31364684 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
*
31364715 ATGTGATGAACGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31364778 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31364809 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31364874 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31364905 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31364970 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * * * *
31365001 ATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31365064 AGTGTATAAATGTGATAAG
66 AGTGTATATATGTGATAAG
31365083 TCCCGAAGGG
Statistics
Matches: 355, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
94 146 0.41
96 209 0.59
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31364766 original size:143 final size:143
Alignment explanation
Indices: 31364619--31365082 Score: 801
Period size: 143 Copynumber: 3.3 Consensus size: 143
31364609 TTAGGATTCT
*
31364619 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31364684 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
31364749 GGCCTAATGGCCG
131 GGCCTAATGGCCG
31364762 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31364825 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
66 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
31364890 AAGGCCTAATGGCCG
129 AAGGCCTAATGGCCG
31364905 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
31364970 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * *
31365035 GGCCGAGTGGCCA
131 GGCCTAATGGCCG
* *
31365048 ACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
31365083 TCCCGAAGGG
Statistics
Matches: 308, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
141 56 0.18
142 1 0.00
143 204 0.66
145 47 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCG
Found at i:31365251 original size:37 final size:37
Alignment explanation
Indices: 31365201--31365316 Score: 187
Period size: 37 Copynumber: 3.1 Consensus size: 37
31365191 CCGAGCTCTA
31365201 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
*
31365238 AAGACCCGATGACTACGTGTGGGGATTTTGTCCAGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
31365275 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
31365312 AAGAC
1 AAGAC
31365317 TTCGTAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:31367251 original size:40 final size:39
Alignment explanation
Indices: 31367206--31367310 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 39
31367196 AAGTGACCAT
* *
31367206 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-CCCGAAGGCATTGGTGCGAGATACTAA
* * *
31367246 TTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGACTAAGCCCGAAGGCATTGGTGCGAGATACTAA
**
31367285 ATCCGGGTTAAGTCCCGAAGAGCATT
1 ATCCGGACTAAG-CCCGAAG-GCATT
31367311 CATGCTAGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
39 34 0.61
40 17 0.30
41 5 0.09
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (39 bp):
ATCCGGACTAAGCCCGAAGGCATTGGTGCGAGATACTAA
Found at i:31367268 original size:39 final size:40
Alignment explanation
Indices: 31367167--31367310 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
31367157 TCGAATGATG
* *
31367167 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31367206 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
31367247 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31367286 TCCGGGTTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAG-GCATT
31367311 CATGCTAGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
39 34 0.38
40 37 0.42
41 17 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31367329 original size:40 final size:40
Alignment explanation
Indices: 31367285--31367601 Score: 445
Period size: 40 Copynumber: 7.9 Consensus size: 40
31367275 GAGTTACTAA
*
31367285 ATCCGGGTTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
31367325 ATCCGAGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
31367365 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
31367405 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
31367445 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
** * *
31367485 ATCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * *
31367525 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
31367565 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
31367602 CGTGTATTCG
Statistics
Matches: 250, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 250 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:31367423 original size:120 final size:120
Alignment explanation
Indices: 31367247--31367601 Score: 489
Period size: 120 Copynumber: 3.0 Consensus size: 120
31367237 AGATACTAAT
* * * * *
31367247 TCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATATCCGGGCTAAGTCCCGAAGAGCAT
*
31367310 TCATGCTAGTGATGTATCCGAGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
65 TCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
* * *
31367366 TCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
31367431 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
66 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
** * **
31367486 TCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
* * * * * * * *
31367551 CGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
66 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGA
31367602 CGTGTATTCG
Statistics
Matches: 209, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
119 10 0.05
120 186 0.89
121 13 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
Found at i:31371196 original size:47 final size:47
Alignment explanation
Indices: 31371105--31371568 Score: 784
Period size: 47 Copynumber: 9.7 Consensus size: 47
31371095 TTAGGATTCT
31371105 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
31371154 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
31371201 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31371248 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31371295 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31371344 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31371391 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31371440 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
31371487 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
31371534 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
31371569 TCCCGAAGGG
Statistics
Matches: 399, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
47 286 0.72
49 113 0.28
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31371209 original size:96 final size:96
Alignment explanation
Indices: 31371105--31371568 Score: 810
Period size: 96 Copynumber: 4.9 Consensus size: 96
31371095 TTAGGATTCT
*
31371105 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31371170 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
*
31371201 ATGTGATGAACGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31371264 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31371295 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31371360 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31371391 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31371456 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * * * *
31371487 ATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31371550 AGTGTATAAATGTGATAAG
66 AGTGTATATATGTGATAAG
31371569 TCCCGAAGGG
Statistics
Matches: 355, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
94 146 0.41
96 209 0.59
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31371252 original size:143 final size:143
Alignment explanation
Indices: 31371105--31371568 Score: 801
Period size: 143 Copynumber: 3.3 Consensus size: 143
31371095 TTAGGATTCT
*
31371105 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31371170 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
31371235 GGCCTAATGGCCG
131 GGCCTAATGGCCG
31371248 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31371311 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
66 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
31371376 AAGGCCTAATGGCCG
129 AAGGCCTAATGGCCG
31371391 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
31371456 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * *
31371521 GGCCGAGTGGCCA
131 GGCCTAATGGCCG
* *
31371534 ACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
31371569 TCCCGAAGGG
Statistics
Matches: 308, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
141 56 0.18
142 1 0.00
143 204 0.66
145 47 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCG
Found at i:31371757 original size:37 final size:37
Alignment explanation
Indices: 31371687--31371800 Score: 178
Period size: 36 Copynumber: 3.1 Consensus size: 37
31371677 CCGAGCTCTA
31371687 AAGACCCGATGACTACGTGT-GGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
31371723 AAGACCCGATGACTACGTGTGGGGATTTTGTCC-GGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
31371759 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
31371796 AAGAC
1 AAGAC
31371801 TTCGTAATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
36 52 0.72
37 20 0.28
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:31373746 original size:39 final size:40
Alignment explanation
Indices: 31373651--31373792 Score: 143
Period size: 39 Copynumber: 3.6 Consensus size: 40
31373641 TCGAATGATG
* *
31373651 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-ATGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGAT-ACTAAT
*
31373689 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
31373730 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31373769 T-CGGGTTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAG-GCATT
31373793 CATGCTAGTG
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
38 8 0.09
39 50 0.57
40 26 0.30
41 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31373819 original size:40 final size:40
Alignment explanation
Indices: 31373770--31374083 Score: 439
Period size: 40 Copynumber: 7.8 Consensus size: 40
31373760 GTTACTAAAT
*
31373770 CGGGTTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* *
31373810 CGAGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* *
31373850 CGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
*
31373890 CGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
*
31373930 CGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
** * *
31373970 CGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* ** * * * *
31374010 CGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * *
31374050 CGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
31374084 CGTGTATTCG
Statistics
Matches: 247, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 247 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
Found at i:31373914 original size:120 final size:120
Alignment explanation
Indices: 31373730--31374083 Score: 480
Period size: 120 Copynumber: 3.0 Consensus size: 120
31373720 AGATACTAAT
* * * * *
31373730 TCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAAT-CGGGTTAAGTCCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATATCCGGGCTAAGTCCCGAAGAGCAT
*
31373792 TCATGCTAGTGATGTATCCGAGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
65 TCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
* * *
31373848 TCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
31373913 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
66 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
** * **
31373968 TCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
* * * * * * * *
31374033 CGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
66 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGA
31374084 CGTGTATTCG
Statistics
Matches: 208, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
118 10 0.05
119 10 0.05
120 188 0.90
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTA
Found at i:31377683 original size:47 final size:47
Alignment explanation
Indices: 31377592--31378055 Score: 784
Period size: 47 Copynumber: 9.7 Consensus size: 47
31377582 TTAGGATTCT
31377592 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
31377641 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
31377688 ATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31377735 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31377782 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31377831 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
31377878 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
31377927 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
31377974 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
31378021 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
31378056 TCCCGAAGGG
Statistics
Matches: 399, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
47 286 0.72
49 113 0.28
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31377696 original size:96 final size:96
Alignment explanation
Indices: 31377592--31378055 Score: 810
Period size: 96 Copynumber: 4.9 Consensus size: 96
31377582 TTAGGATTCT
*
31377592 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31377657 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
*
31377688 ATGTGATGAACGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31377751 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31377782 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31377847 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
31377878 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31377943 AGTGTATATATGTGATAAGGCCTAATGGCCG
66 AGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * * * *
31377974 ATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31378037 AGTGTATAAATGTGATAAG
66 AGTGTATATATGTGATAAG
31378056 TCCCGAAGGG
Statistics
Matches: 355, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
94 146 0.41
96 209 0.59
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:31377739 original size:143 final size:143
Alignment explanation
Indices: 31377592--31378055 Score: 801
Period size: 143 Copynumber: 3.3 Consensus size: 143
31377582 TTAGGATTCT
*
31377592 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31377657 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
31377722 GGCCTAATGGCCG
131 GGCCTAATGGCCG
31377735 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31377798 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
66 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
31377863 AAGGCCTAATGGCCG
129 AAGGCCTAATGGCCG
31377878 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
31377943 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
66 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * *
31378008 GGCCGAGTGGCCA
131 GGCCTAATGGCCG
* *
31378021 ACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
31378056 TCCCGAAGGG
Statistics
Matches: 308, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
141 56 0.18
142 1 0.00
143 204 0.66
145 47 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCG
Found at i:31378224 original size:37 final size:37
Alignment explanation
Indices: 31378174--31378289 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
31378164 CCGAGCTCTA
31378174 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
31378211 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
31378248 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
31378285 AAGAC
1 AAGAC
31378290 TTCGTAATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:31385029 original size:27 final size:27
Alignment explanation
Indices: 31384989--31385147 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
31384979 TGGAAGCGTC
*
31384989 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
31385016 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
31385042 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
31385070 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
31385097 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
31385124 CTGGTGACTCCGTCACAA-TATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
31385148 GCAGCCTCGC
Statistics
Matches: 117, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.09
27 102 0.87
28 4 0.03
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:31385068 original size:54 final size:54
Alignment explanation
Indices: 31384986--31385147 Score: 256
Period size: 54 Copynumber: 3.0 Consensus size: 54
31384976 TGGTGGAAGC
31384986 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
31385040 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* * * * *
31385094 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACTCCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATATATCT
31385147 G
1 G
31385148 GCAGCCTCGC
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
53 13 0.13
54 89 0.87
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:31385141 original size:81 final size:80
Alignment explanation
Indices: 31384989--31385147 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 80
31384979 TGGAAGCGTC
* *
31384989 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAC
31385054 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * *
31385070 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGTGGCTCTGCCACATATATCTGT-CCTGGTGACT
* *
31385133 CCGTCACAATATCTG
64 ACGCCACAATATCTG
31385148 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
80 16 0.23
81 53 0.77
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAC
GCCACAATATCTGAT
Found at i:31403933 original size:23 final size:23
Alignment explanation
Indices: 31403901--31404032 Score: 76
Period size: 23 Copynumber: 5.7 Consensus size: 23
31403891 CTCAAGGGTG
*
31403901 TTATAAAATATGCCACACAAGTA
1 TTATAGAATATGCCACACAAGTA
* * *
31403924 TTATAGAATACGCCACACGAGCA
1 TTATAGAATATGCCACACAAGTA
* *
31403947 TCATAGAATATGACACA-AAGCCT-
1 TTATAGAATATGCCACACAAG--TA
* *
31403970 TTACAGAACATGCCACA-AAG-A
1 TTATAGAATATGCCACACAAGTA
* *
31403991 CTTTACAGAATATGCCGCACAAGCT-
1 --TTATAGAATATGCCACACAAG-TA
* *
31404016 TTATTGAATACGCCACA
1 TTATAGAATATGCCACA
31404033 AAGGCTTTAC
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
22 2 0.02
23 77 0.94
24 3 0.04
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (23 bp):
TTATAGAATATGCCACACAAGTA
Found at i:31404001 original size:46 final size:46
Alignment explanation
Indices: 31403951--31404046 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
31403941 CGAGCATCAT
*
31403951 AGAATATGACACA-AAGCCTTTACAGAACATGCCACAAAGACTTTAC
1 AGAATATGACACACAAG-CTTTACAGAACACGCCACAAAGACTTTAC
* * ** * *
31403997 AGAATATGCCGCACAAGCTTTATTGAATACGCCACAAAGGCTTTAC
1 AGAATATGACACACAAGCTTTACAGAACACGCCACAAAGACTTTAC
31404043 AGAA
1 AGAA
31404047 CATTACATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 39 0.93
47 3 0.07
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.21
Consensus pattern (46 bp):
AGAATATGACACACAAGCTTTACAGAACACGCCACAAAGACTTTAC
Found at i:31404039 original size:23 final size:23
Alignment explanation
Indices: 31403951--31404046 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
31403941 CGAGCATCAT
* * *
31403951 AGAATATGACACAAAGCCTTTAC
1 AGAATACGCCACAAAGGCTTTAC
* * *
31403974 AGAACATGCCACAAAGACTTTAC
1 AGAATACGCCACAAAGGCTTTAC
* * *
31403997 AGAATATGCCGCACAA-GCTTTAT
1 AGAATACGCCACA-AAGGCTTTAC
*
31404020 TGAATACGCCACAAAGGCTTTAC
1 AGAATACGCCACAAAGGCTTTAC
31404043 AGAA
1 AGAA
31404047 CATTACATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 2 0.03
23 55 0.93
24 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.21
Consensus pattern (23 bp):
AGAATACGCCACAAAGGCTTTAC
Found at i:31406801 original size:46 final size:47
Alignment explanation
Indices: 31406613--31406829 Score: 202
Period size: 46 Copynumber: 4.7 Consensus size: 47
31406603 GGGTCATTTG
* * *
31406613 TGTA-AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTA
1 TGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GA
* *
31406659 TG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGA
1 TGTAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGA
* * *
31406707 TG-AGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGGGA
1 TGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGA
* *
31406753 TGTA-AGCCAGTATAAGACATGTCTAGGACATGCATCAGCTACGAGA
1 TGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGA
* *
31406799 TGT---GTCAGTGTAAGACCATGTTTGGGACATG
1 TGTAGAGCCAGTGTAAGA-CATGTCTGGGACATG
31406830 GAATCGACAC
Statistics
Matches: 143, Mismatches: 18, Indels: 21
0.79 0.10 0.12
Matches are distributed among these distances:
44 10 0.07
45 16 0.11
46 62 0.43
47 31 0.22
48 23 0.16
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
TGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGA
Found at i:31408322 original size:68 final size:68
Alignment explanation
Indices: 31408172--31408329 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 68
31408162 CTAGCCAATT
* * *
31408172 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACA
**
31408237 TTTA
65 CATA
* * *
31408241 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTA
31408303 CTACATA
63 C-ACATA
*
31408310 GTATCTCGTAGCTTTCTTGT
1 -TATCTCGTAGCTCTCTTGT
31408330 ACACATGATG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
68 36 0.49
69 8 0.11
70 5 0.07
71 25 0.34
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:31419268 original size:19 final size:19
Alignment explanation
Indices: 31419246--31419284 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31419236 ACATGATAGG
31419246 TTATTTCCCATTTTGTGTT
1 TTATTTCCCATTTTGTGTT
31419265 TTATTTCCCATTTTGTGTT
1 TTATTTCCCATTTTGTGTT
31419284 T
1 T
31419285 ATGGGTTCCC
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:0.10, C:0.15, G:0.10, T:0.64
Consensus pattern (19 bp):
TTATTTCCCATTTTGTGTT
Found at i:31425993 original size:29 final size:29
Alignment explanation
Indices: 31425921--31425979 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31425911 CCAAGAAAAG
31425921 TACTTTAAGAAAAATCATCAATTAAACAA
1 TACTTTAAGAAAAATCATCAATTAAACAA
31425950 TACTTTAAGAAAAATCATCAATTAAACAA
1 TACTTTAAGAAAAATCATCAATTAAACAA
31425979 T
1 T
31425980 CTTAGAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (29 bp):
TACTTTAAGAAAAATCATCAATTAAACAA
Found at i:31431651 original size:47 final size:46
Alignment explanation
Indices: 31431570--31431778 Score: 194
Period size: 47 Copynumber: 4.5 Consensus size: 46
31431560 GCTGATGCTG
* * *
31431570 TGTCCCAGACATGGTCTTACTCTGGCTCAT-ATCTCAAGTCGAAGCCA
1 TGTCCCAGACATGGTCTTACACTGGCT-ATCATCTCAAGCCGATG-CA
* * * *
31431617 TGTCCCAAACATGGTCTTACACTGACTATCATCTCGTAGCCGACGCA
1 TGTCCCAGACATGGTCTTACACTGGCTATCATCTC-AAGCCGATGCA
* * *
31431664 TGTCCCAGACAT-GTCTTACACTGGCT-TACGTCTCGAGGCGATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTAT-CATCTCAAGCCGATGCA
* * * *
31431709 TGTCCCAGATAT-GTCTTACACTTGC-ACTCGTATCAATGCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTA-TCATCTCAA-GCCGATG-CA
31431756 TGTCCCAGACATGGTCTTACACT
1 TGTCCCAGACATGGTCTTACACT
31431779 AGCTCACACA
Statistics
Matches: 136, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
45 38 0.28
46 27 0.20
47 55 0.40
48 16 0.12
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
TGTCCCAGACATGGTCTTACACTGGCTATCATCTCAAGCCGATGCA
Found at i:31433111 original size:45 final size:45
Alignment explanation
Indices: 31433048--31433170 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 45
31433038 CGATGCCGAT
* * * * * * *
31433048 GTCCCAAACATGGCCTTACATGTAACCACATATATCGATGCTAAC
1 GTCCCAGACATGGCCTTACACGAAAACACATATACCAATGCCAAC
* *
31433093 GTCCCAGACGTGGTCTTACACGAAAACACATATACCAATGCCAAC
1 GTCCCAGACATGGCCTTACACGAAAACACATATACCAATGCCAAC
* ** *
31433138 ATCCCAGACACAGTCTTACACGAAAACACATAT
1 GTCCCAGACATGGCCTTACACGAAAACACATAT
31433171 CGGAATCCTA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (45 bp):
GTCCCAGACATGGCCTTACACGAAAACACATATACCAATGCCAAC
Found at i:31434832 original size:55 final size:53
Alignment explanation
Indices: 31434690--31434879 Score: 173
Period size: 55 Copynumber: 3.5 Consensus size: 53
31434680 TTACCATTTT
* *
31434690 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTGC
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGC
* * * * ** * *
31434743 CATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAATGC
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATGC
* * * * * * * *
31434798 CATGTCTTGACATGGTCTTAAATGATTTCCTTGCCTTGTAAAACTTACCAAAGT
1 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGC
* *
31434852 CATGTCTTGGCATGGTCTTACTTGGTAT
1 CATGTCTTGACATGGTCTTACATGGTAT
31434880 TCTTAAACCC
Statistics
Matches: 106, Mismatches: 29, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 34 0.32
54 32 0.30
55 40 0.38
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (53 bp):
CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGC
Found at i:31444582 original size:25 final size:25
Alignment explanation
Indices: 31444550--31444599 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31444540 TTATAGTATG
31444550 TTTAATTCTAATAAATGAACTTGGT
1 TTTAATTCTAATAAATGAACTTGGT
31444575 TTTAATTCTAATAAATGAACTTGGT
1 TTTAATTCTAATAAATGAACTTGGT
31444600 AAGTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
TTTAATTCTAATAAATGAACTTGGT
Found at i:31447738 original size:12 final size:12
Alignment explanation
Indices: 31447718--31447747 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31447708 GCTACACGAG
*
31447718 CGTGCGCTCGAT
1 CGTGTGCTCGAT
31447730 CGTGTGCTCGAT
1 CGTGTGCTCGAT
31447742 CGTGTG
1 CGTGTG
31447748 GTAATCCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.27, G:0.37, T:0.30
Consensus pattern (12 bp):
CGTGTGCTCGAT
Found at i:31450853 original size:28 final size:28
Alignment explanation
Indices: 31450821--31450900 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
31450811 CATACATGCT
*
31450821 TATGGCCCACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAGGCCCAATCACATCT-A
*
31450849 TATGGCCCATTAGGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATCTA
*
31450878 TATGGCCCACTAGGTCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
31450901 TTTTTCAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.48
29 23 0.50
30 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATCTA
Found at i:31450881 original size:29 final size:28
Alignment explanation
Indices: 31450821--31450900 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
31450811 CATACATGCT
*
31450821 TATGGCCCACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
*
31450849 TATGGCCCATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
*
31450878 TATGGCCCACTAGGTCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
31450901 TTTTTCAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:31451103 original size:16 final size:15
Alignment explanation
Indices: 31451082--31451129 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
31451072 CCAAACTTTT
31451082 AGCTTTTCAGCATTTC
1 AGCTTTTC-GCATTTC
31451098 AGCTTTTCGACATTTC
1 AGCTTTTCG-CATTTC
*
31451114 AACTTTTCGGCATTTC
1 AGCTTTTC-GCATTTC
31451130 GGGATTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (15 bp):
AGCTTTTCGCATTTC
Found at i:31453430 original size:49 final size:49
Alignment explanation
Indices: 31453358--31453589 Score: 239
Period size: 49 Copynumber: 4.7 Consensus size: 49
31453348 CTGATACTCA
* * *
31453358 TAGTATCCTGCACTTAGTACTACACATACGACCAATTATCTGGTATACG
1 TAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCTGGTACACG
* * ** ** *
31453407 TAGTAGCGTGCAGTTAGTACTACACACGGGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACACGACC-AATTATCTGGTACACG
* ** * * * *
31453457 TAGTAGCCTCCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACACGA-CCAA-TTATCTGGTACACG
* * *
31453508 TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCTAGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCTGGTACACG
* *
31453557 TAGTAGCCTGCACTTAGTATTACACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACACGACC
31453590 TCACAATAGA
Statistics
Matches: 146, Mismatches: 34, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
49 66 0.45
50 44 0.30
51 36 0.25
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCTGGTACACG
Found at i:31453866 original size:27 final size:27
Alignment explanation
Indices: 31453836--31453889 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31453826 TCATACAACC
* *
31453836 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
31453863 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
31453890 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:31457534 original size:18 final size:18
Alignment explanation
Indices: 31457511--31457547 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31457501 GTAAGTATAA
31457511 TTATGATGATTTAAATGT
1 TTATGATGATTTAAATGT
31457529 TTATGATGATTTAAATGT
1 TTATGATGATTTAAATGT
31457547 T
1 T
31457548 CAATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (18 bp):
TTATGATGATTTAAATGT
Found at i:31470636 original size:19 final size:19
Alignment explanation
Indices: 31470573--31470649 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 19
31470563 ATACCAACTA
* *
31470573 AAAAATATCGATA-CTTTT
1 AAAAATATCAATACCATTT
* *
31470591 ATAAAACTATCAATCCTCATGT
1 A-AAAA-TATCAATAC-CATTT
31470613 AAAAATATCAATACCATTT
1 AAAAATATCAATACCATTT
31470632 AAAAATATCAATACCATT
1 AAAAATATCAATACCATT
31470650 AGGCTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.53
20 14 0.29
21 4 0.08
22 4 0.08
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATATCAATACCATTT
Found at i:31474357 original size:29 final size:29
Alignment explanation
Indices: 31474318--31474409 Score: 175
Period size: 29 Copynumber: 3.2 Consensus size: 29
31474308 GCATGTATGA
31474318 GAATGTGATTTGGGCCTAATGGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATAT
*
31474347 GAATGTGATTTGGGCCTAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAT
31474376 GAATGTGATTTGGGCCTAATGGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATAT
31474405 GAATG
1 GAATG
31474410 ATATTGGGCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCATAT
Done.