Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 134 of 186
Found at i:44144741 original size:37 final size:37
Alignment explanation
Indices: 44144677--44144752 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
44144667 TTACAAGACA
44144677 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
44144714 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
44144751 AA
1 AA
44144753 CATCGATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 30 0.86
38 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:44148554 original size:19 final size:19
Alignment explanation
Indices: 44148504--44148556 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
44148494 ATATTTTTTT
*
44148504 ATTTTAT-TAATTGCAATA
1 ATTTTATATAATTTCAATA
* * *
44148522 ATTTTTTATTATTTTAATA
1 ATTTTATATAATTTCAATA
44148541 ATTTTATATAATTTCA
1 ATTTTATATAATTTCA
44148557 TTTAACATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTATATAATTTCAATA
Found at i:44153772 original size:40 final size:40
Alignment explanation
Indices: 44153694--44153917 Score: 310
Period size: 40 Copynumber: 5.5 Consensus size: 40
44153684 ACCCAAGTAT
* *
44153694 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
44153733 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
44153773 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
44153813 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
44153856 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
44153896 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
44153918 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:44153890 original size:83 final size:80
Alignment explanation
Indices: 44153694--44153917 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 80
44153684 ACCCAAGTAT
* * * *
44153694 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
44153758 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
44153773 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
44153837 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
44153856 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
44153918 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:44156093 original size:19 final size:20
Alignment explanation
Indices: 44156069--44156116 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
44156059 AAATAATAGT
44156069 TTGATTAAGATAA-TTAAAC
1 TTGATTAAGATAAGTTAAAC
*
44156088 TTGATTAAGTTAAGTTAAAC
1 TTGATTAAGATAAGTTAAAC
44156108 TTGATTAAG
1 TTGATTAAG
44156117 CCTAATTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGATTAAGATAAGTTAAAC
Found at i:44160669 original size:11 final size:11
Alignment explanation
Indices: 44160653--44160678 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44160643 CATAACATAC
44160653 AAAACAATTTG
1 AAAACAATTTG
44160664 AAAACAATTTG
1 AAAACAATTTG
44160675 AAAA
1 AAAA
44160679 TTATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAACAATTTG
Found at i:44161159 original size:27 final size:27
Alignment explanation
Indices: 44161129--44161188 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
44161119 GGTAATTCAA
* * *
44161129 AATAAATATTATACAAAATTTTTAAAC
1 AATAAATATAAAACAAAATTTTAAAAC
* *
44161156 AATATAATATAAAAGAGAATTTTAAAAC
1 AATA-AATATAAAACAAAATTTTAAAAC
44161184 AATAA
1 AATAA
44161189 TTTTAGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (27 bp):
AATAAATATAAAACAAAATTTTAAAAC
Found at i:44163157 original size:44 final size:44
Alignment explanation
Indices: 44163094--44163202 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
44163084 GGAGAACAGT
* * ***
44163094 TTGCTTCCTTACTACCTCAGAAAGATAAGACTACAATTTTTGGC
1 TTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATTTTCAAC
* *
44163138 TTGCTCCCTTGCTACCTCAGGAAGATAAGGCTACAATTTTCAAC
1 TTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATTTTCAAC
* *
44163182 CTGCTCTCTTGCTACCTCAGA
1 TTGCTCCCTTGCTACCTCAGA
44163203 GAGAAAAGGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.32
Consensus pattern (44 bp):
TTGCTCCCTTGCTACCTCAGAAAGATAAGACTACAATTTTCAAC
Found at i:44163467 original size:178 final size:178
Alignment explanation
Indices: 44163144--44163481 Score: 514
Period size: 178 Copynumber: 1.9 Consensus size: 178
44163134 TGGCTTGCTC
* * * *
44163144 CCTTGCTACCTCAGGAAGATAAGGCTACAATTTTCAACCTGCTCTCTTGCTACCTCAGAGAGAAA
1 CCTTGCTACCTCAAGAAGATAAGACTACAATCTCCAACCTGCTCTCTTGCTACCTCAGAGAGAAA
* * * *
44163209 AGGCTGGTGGCTAAAATCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTTGATCTG
66 AGGCTGGCGGCTAAAATCTGCTCCCCTACTACCTCGAGAAGATAAGATTCGCCATCTTCGATATG
*
44163274 CTCCACTACTATCTCAGGGAAATAAGATCTTCAATCTTCAGTCTACTT
131 CTCCACTACTATCTCAAGGAAATAAGATCTTCAATCTTCAGTCTACTT
* * *
44163322 CCTTGCTACCTCAAGAAGATAAGACTACAATCTCCAACCTGCTCTCTTGCTACTTTAGAGAGATA
1 CCTTGCTACCTCAAGAAGATAAGACTACAATCTCCAACCTGCTCTCTTGCTACCTCAGAGAGAAA
* *
44163387 AGGCTGGCGGCTAAAATCTGCTCCCCTGCTACCTCGAGAAGATAAGATTCGCTATCTTCGATATG
66 AGGCTGGCGGCTAAAATCTGCTCCCCTACTACCTCGAGAAGATAAGATTCGCCATCTTCGATATG
* ** *
44163452 CTCTACTGTTATCTCAAGGAGATAAGATCT
131 CTCCACTACTATCTCAAGGAAATAAGATCT
44163482 GTGAATTCAC
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
178 142 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (178 bp):
CCTTGCTACCTCAAGAAGATAAGACTACAATCTCCAACCTGCTCTCTTGCTACCTCAGAGAGAAA
AGGCTGGCGGCTAAAATCTGCTCCCCTACTACCTCGAGAAGATAAGATTCGCCATCTTCGATATG
CTCCACTACTATCTCAAGGAAATAAGATCTTCAATCTTCAGTCTACTT
Found at i:44164671 original size:13 final size:13
Alignment explanation
Indices: 44164653--44164678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44164643 GCCTCTCCTC
44164653 TTTATTTTTTATT
1 TTTATTTTTTATT
44164666 TTTATTTTTTATT
1 TTTATTTTTTATT
44164679 AGGTCTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:44168868 original size:27 final size:29
Alignment explanation
Indices: 44168801--44168868 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
44168791 AGGAATGAAC
44168801 TATATACAT-AATAGATTTGAAAAGAAATA
1 TATATACATAAATAGATTT-AAAAGAAATA
* * *
44168830 GATATACCTAAATAGATTT-AAA-ATATA
1 TATATACATAAATAGATTTAAAAGAAATA
44168857 TATATACATAAA
1 TATATACATAAA
44168869 AAACAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 14 0.42
28 3 0.09
29 7 0.21
30 9 0.27
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.32
Consensus pattern (29 bp):
TATATACATAAATAGATTTAAAAGAAATA
Found at i:44173256 original size:24 final size:24
Alignment explanation
Indices: 44173228--44173275 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44173218 AGCGACTTGA
44173228 TAGTGTGATGCTACCTCCGATGAT
1 TAGTGTGATGCTACCTCCGATGAT
44173252 TAGTGTGATGCTACCTCCGATGAT
1 TAGTGTGATGCTACCTCCGATGAT
44173276 GTCCAACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TAGTGTGATGCTACCTCCGATGAT
Found at i:44174589 original size:46 final size:49
Alignment explanation
Indices: 44174446--44174667 Score: 205
Period size: 46 Copynumber: 4.7 Consensus size: 49
44174436 TCCATCAACT
* **
44174446 CGATGCCATGTCCTAGACATGGTCTTACACTGACTAT-CGAAATCGAGGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATAC-ATCTCGAGGC
* * * * *
44174495 CAATGCCATATCCTAGTCATGGTCTTACACT---AACACATCTCGTA-GC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATACATCTCG-AGGC
*
44174541 CGATG-CATGTCCTAGACAT-GTCTTACACTGGCT-TACATCTTGAGGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATACATCTCGAGGC
* * * * * *
44174587 CGATG-CATGTCCTAGACA-CGTCTTACACTAGCTCT-CATCTCAATGT
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATACATCTCGAGGC
*
44174633 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCT
44174668 CACAAATAAC
Statistics
Matches: 142, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
44 10 0.07
45 13 0.09
46 63 0.44
47 15 0.11
48 13 0.09
49 28 0.20
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATACATCTCGAGGC
Found at i:44176515 original size:27 final size:27
Alignment explanation
Indices: 44176452--44176516 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
44176442 CTTCATAATC
*
44176452 TCCCATGTTTATTGTCCAAGAGGACTA
1 TCCCATGTTTAGTGTCCAAGAGGACTA
* *
44176479 -CCCAGAGTTTAGTGTCCTAA-TGGACTA
1 TCCCA-TGTTTAGTGTCC-AAGAGGACTA
44176506 TCCCATGTTTA
1 TCCCATGTTTA
44176517 ATGTGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 4 0.13
27 21 0.68
28 6 0.19
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (27 bp):
TCCCATGTTTAGTGTCCAAGAGGACTA
Found at i:44176869 original size:45 final size:45
Alignment explanation
Indices: 44176801--44176922 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 45
44176791 AAAGGATGTT
* * * * * *
44176801 ATAACGTCTTTTAGCTATAGTCTTCTTCAT-TTATATCATGATGCC
1 ATAACATCTTTCAGCTATGGTCTTATTCATCTT-TAGCATGATACC
* ** *
44176846 ATAACATCTTTCAGTTATGGTCTTATTGGTCTTTAGCGTGATACC
1 ATAACATCTTTCAGCTATGGTCTTATTCATCTTTAGCATGATACC
*
44176891 ATAACATCTTCCAGCTATGGTCTTATTCATCT
1 ATAACATCTTTCAGCTATGGTCTTATTCATCT
44176923 CTAGGCATAT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
45 60 0.97
46 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (45 bp):
ATAACATCTTTCAGCTATGGTCTTATTCATCTTTAGCATGATACC
Found at i:44178882 original size:181 final size:181
Alignment explanation
Indices: 44178573--44178921 Score: 644
Period size: 181 Copynumber: 1.9 Consensus size: 181
44178563 AATGCAACAA
* *
44178573 AAGATGAGGGAAAGGTAAGAGTTGTAGATGAGTACCTATTACGATTTGTACTCTCATAATTTGAG
1 AAGAGGAGGGAAAGGTAAGAGTTGTAGATGAGTAACTATTACGATTTGTACTCTCATAATTTGAG
* *
44178638 TTCAATATATATAAGTTGTTACAAGCTAGCTTATTTGAGGTATGCATTCTATTTTTCTCATGATT
66 TTCAATAGATATAAGTTGTTACAAGATAGCTTATTTGAGGTATGCATTCTATTTTTCTCATGATT
44178703 CGGTTTGCATATGATGATATGGAATGTCGAGAATTGAAACCGGGCTATCTC
131 CGGTTTGCATATGATGATATGGAATGTCGAGAATTGAAACCGGGCTATCTC
44178754 AAGAGGAGGGAAAGGTAAGAGTTGTAGATGAGTAACTATTACGATTTGTACTCTCATAATTTGAG
1 AAGAGGAGGGAAAGGTAAGAGTTGTAGATGAGTAACTATTACGATTTGTACTCTCATAATTTGAG
*
44178819 TTCAATAGATATAAGTTGTTACAAGATAGCTTATTTGAGGTATGGATTCTATTTTTCTCATGATT
66 TTCAATAGATATAAGTTGTTACAAGATAGCTTATTTGAGGTATGCATTCTATTTTTCTCATGATT
*
44178884 CGGTTTGTATATGATGATATGGAATGTCGAGAATTGAA
131 CGGTTTGCATATGATGATATGGAATGTCGAGAATTGAA
44178922 TTGAGATGAC
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 162 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (181 bp):
AAGAGGAGGGAAAGGTAAGAGTTGTAGATGAGTAACTATTACGATTTGTACTCTCATAATTTGAG
TTCAATAGATATAAGTTGTTACAAGATAGCTTATTTGAGGTATGCATTCTATTTTTCTCATGATT
CGGTTTGCATATGATGATATGGAATGTCGAGAATTGAAACCGGGCTATCTC
Found at i:44185644 original size:26 final size:26
Alignment explanation
Indices: 44185604--44185660 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
44185594 AAGCATCAAA
* *
44185604 TATAATCCTTAGCATATCTAAACACC
1 TATAATCCTTAGCATAGCCAAACACC
*
44185630 TATAATCCTTGGCATAGCCAAACACC
1 TATAATCCTTAGCATAGCCAAACACC
44185656 TATAA
1 TATAA
44185661 ACACATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (26 bp):
TATAATCCTTAGCATAGCCAAACACC
Found at i:44185703 original size:11 final size:11
Alignment explanation
Indices: 44185687--44185712 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44185677 ATATACATAC
44185687 TCATCCTAGAT
1 TCATCCTAGAT
44185698 TCATCCTAGAT
1 TCATCCTAGAT
44185709 TCAT
1 TCAT
44185713 ATAGCACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (11 bp):
TCATCCTAGAT
Found at i:44191508 original size:14 final size:14
Alignment explanation
Indices: 44191489--44191515 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44191479 AAAAAGAATA
44191489 AGGAAGAAGAGAAG
1 AGGAAGAAGAGAAG
44191503 AGGAAGAAGAGAA
1 AGGAAGAAGAGAA
44191516 ACTAATGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGGAAGAAGAGAAG
Found at i:44192956 original size:27 final size:27
Alignment explanation
Indices: 44192943--44193271 Score: 511
Period size: 27 Copynumber: 12.2 Consensus size: 27
44192933 AAAGTACTCC
44192943 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
44192970 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
44192997 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
44193024 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
44193051 C-AGTTTACAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
44193078 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
44193105 C-AGTTTACAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
44193132 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
44193159 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
44193186 TGATTTACAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
44193213 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
44193240 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
44193267 TGATT
1 CGATT
44193272 GTGAAATTAC
Statistics
Matches: 275, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
26 3 0.01
27 269 0.98
28 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:44193306 original size:27 final size:27
Alignment explanation
Indices: 44193276--44193471 Score: 248
Period size: 27 Copynumber: 7.3 Consensus size: 27
44193266 TTGATTGTGA
*
44193276 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
44193303 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
44193330 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
44193357 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
44193384 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
44193411 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* ** * *
44193438 AATTACCGAGATACCTTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
44193465 AATTACC
1 AATTACC
44193472 ATTTTGCCCC
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 145 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:44193708 original size:27 final size:26
Alignment explanation
Indices: 44193670--44193752 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
44193660 CGGAGGAAGC
*
44193670 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
44193697 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
44193723 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
44193750 GTT
1 GTT
44193753 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:44193872 original size:22 final size:22
Alignment explanation
Indices: 44193840--44193898 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
44193830 CCCGTTATTA
*
44193840 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
44193862 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
44193884 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
44193899 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:44194085 original size:27 final size:27
Alignment explanation
Indices: 44194063--44194136 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
44194053 TAGGTGGGTT
*
44194063 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
44194090 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
44194117 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
44194137 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:44194263 original size:6 final size:6
Alignment explanation
Indices: 44194254--44194439 Score: 163
Period size: 6 Copynumber: 30.8 Consensus size: 6
44194244 TTGCATTCAC
* * *
44194254 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
44194303 -TTACTA ATACTA ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG
44194351 ATTCTG ATTCTG -TTACTG ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG
1 ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG
*
44194399 ATTCTG ATTCTG ATTCTG -TTATTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
44194440 CATTTTGGTT
Statistics
Matches: 149, Mismatches: 14, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
5 13 0.09
6 124 0.83
7 9 0.06
8 3 0.02
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:44194321 original size:30 final size:30
Alignment explanation
Indices: 44194254--44194416 Score: 236
Period size: 30 Copynumber: 5.4 Consensus size: 30
44194244 TTGCATTCAC
* *
44194254 ATTCTGATTCTGATTCTGTCACGTAATTCTG
1 ATTCTGATTCTGATTCTGTTAC-TAATACTG
* *
44194285 ATTCTGATTCTGATTTTGTTACTAATACTA
1 ATTCTGATTCTGATTCTGTTACTAATACTG
*
44194315 ATTCTGATTCTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
44194345 ATTCTGATTCTGATTCTGTTACTGATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
44194375 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
44194405 ATTCTGATTCTG
1 ATTCTGATTCTG
44194417 TTATTGATTC
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
30 102 0.84
31 20 0.16
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:44200002 original size:294 final size:294
Alignment explanation
Indices: 44199441--44200028 Score: 838
Period size: 294 Copynumber: 2.0 Consensus size: 294
44199431 CTCCTGTAGA
* * *
44199441 ATCAATCGCCTCAACTCTTTATTGTTAGGCACACAAATCCGATCCCTGAAACACAAAACCTTGTA
1 ATCAATCACCTCAACTCTTTATTGTTAGGCACACAAATCCGAGCCCTGAAACACAAAACCTTATA
* *
44199506 ACTACTTAAACTAAAATCCGAAGTTTCACTTAAATCAATCTGTTGCAGACGTTAAACTAGAGACT
66 ACTACTTAAACTAAAATCCGAAGTTTCACTTAAATCAATCTATTGCAGACGTTAAACTAGAGACA
*
44199571 TATCACTCAACTGTTTAGATCGAATCTAATTGACCCAAGTTGGTTTAACCTGTAATTTAGCTAGC
131 TATCACTCAACTGTTTAGATCGAATCTAATTGACCCAAGTTGGTTTAACCTGCAATTTAGCTAGC
*
44199636 AAACTCCCATCCTCGAAAAAACTCAGACGAGCGAACATCACCCTCAGATCAATCATCGCTCTACA
196 AAACTCCCATCCTCGAAAAAACTCAGACGAGCGAACATCACCCTCAGATCAATCATCACTCTACA
* *
44199701 TCTAAGAGCATCTACCACCATATTAGCCTTATCG
261 GCTAAGAGCATCTACCACCACATTAGCCTTATCG
* * *
44199735 ATCAATCACCTCAACTCTTTGTTGTTAGGCACACAAATCTGAGCCCTGAAACACAAAGCCTTAT-
1 ATCAATCACCTCAACTCTTTATTGTTAGGCACACAAATCCGAGCCCTGAAACACAAAACCTTATA
* ** ** * * *
44199799 AGTTGTTCAAACTAAAATTTGAAGTTTCACTTGAATCAATCTATTGTAGATGTTAAACTAGAGAC
66 ACTACTT-AAACTAAAATCCGAAGTTTCACTTAAATCAATCTATTGCAGACGTTAAACTAGAGAC
* * * *
44199864 ATATCACTCAACTGTTTAGCTTGAATCTGATTGACCCATGTTGGTTTAACCTGCAATTTAGCTAG
130 ATATCACTCAACTGTTTAGATCGAATCTAATTGACCCAAGTTGGTTTAACCTGCAATTTAGCTAG
* ** * ** *
44199929 CAGACTCCCATCCTC-AAACAAACTCAGACGAGCGAACATTGCCCTCATATCGGTCATTACTCTA
195 CAAACTCCCATCCTCGAAA-AAACTCAGACGAGCGAACATCACCCTCAGATCAATCATCACTCTA
* * *
44199993 CGGCTAAGAGCATTTACCACTACATTAGCCTTATCG
259 CAGCTAAGAGCATCTACCACCACATTAGCCTTATCG
44200029 GAATGGTATT
Statistics
Matches: 258, Mismatches: 34, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
293 7 0.03
294 251 0.97
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (294 bp):
ATCAATCACCTCAACTCTTTATTGTTAGGCACACAAATCCGAGCCCTGAAACACAAAACCTTATA
ACTACTTAAACTAAAATCCGAAGTTTCACTTAAATCAATCTATTGCAGACGTTAAACTAGAGACA
TATCACTCAACTGTTTAGATCGAATCTAATTGACCCAAGTTGGTTTAACCTGCAATTTAGCTAGC
AAACTCCCATCCTCGAAAAAACTCAGACGAGCGAACATCACCCTCAGATCAATCATCACTCTACA
GCTAAGAGCATCTACCACCACATTAGCCTTATCG
Found at i:44208194 original size:32 final size:32
Alignment explanation
Indices: 44208148--44208210 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
44208138 ACGATAAAAG
*
44208148 TATATAAAAAATCATTATAAAGTGAAGCTTTA
1 TATAAAAAAAATCATTATAAAGTGAAGCTTTA
44208180 TATAAAAAAAATCATTATAAAGTGAAGCTTT
1 TATAAAAAAAATCATTATAAAGTGAAGCTTT
44208211 CACATTAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (32 bp):
TATAAAAAAAATCATTATAAAGTGAAGCTTTA
Found at i:44220449 original size:91 final size:89
Alignment explanation
Indices: 44220352--44220539 Score: 213
Period size: 90 Copynumber: 2.1 Consensus size: 89
44220342 GAATTTTTTC
* * * *
44220352 AAAAAAATAAAATAAAATTAAGCCCCTAC-TTTTTTTT-ATTC-ATTTAGGTATTTGAAATTTCA
1 AAAAAAA-AAAAAAAAATTAAGCCCC-ACTTTTTTTTTCACTCAATTT-CGTACTTGAAATTTCA
*
44220414 AAATGCAT-CAAAAGACCCTCAAATCTT
63 AAATGCATAAAAAAGACCCTCAAA-CTT
* ** * *
44220441 TAAAAAAAAAAAGCAATTAAGCCCCACTTTTTTTTTGCACTCAATTTCGTACTTGAACTTTTAAA
1 AAAAAAAAAAAAAAAATTAAGCCCCACTTTTTTTTT-CACTCAATTTCGTACTTGAAATTTCAAA
44220506 ATGCATAAAAAAGACCCTCAAACTT
65 ATGCATAAAAAAGACCCTCAAACTT
44220531 AAAAAAAAA
1 AAAAAAAAA
44220540 GTAATTAAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
87 2 0.02
88 23 0.28
89 6 0.07
90 34 0.41
91 18 0.22
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (89 bp):
AAAAAAAAAAAAAAAATTAAGCCCCACTTTTTTTTTCACTCAATTTCGTACTTGAAATTTCAAAA
TGCATAAAAAAGACCCTCAAACTT
Found at i:44220668 original size:39 final size:38
Alignment explanation
Indices: 44220609--44220717 Score: 116
Period size: 39 Copynumber: 2.9 Consensus size: 38
44220599 AATTTTATTT
*
44220609 AAAAAAT-T-AAAATATTAAAAAATTATTAAAATTAG-A
1 AAAAAATATAAAAATAGTAAAAAATTA-TAAAATTAGTA
* * *
44220645 AAAAAATATAAAAATTGTAAAAAAATATAAAATATTGTA
1 AAAAAATATAAAAATAGTAAAAAATTATAAAAT-TAGTA
***
44220684 AAATTTTATAAAAATAGTAAAAAATTATAAAATT
1 AAAAAATATAAAAATAGTAAAAAATTATAAAATT
44220718 TTATAAAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
36 7 0.12
37 7 0.12
38 17 0.28
39 29 0.48
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (38 bp):
AAAAAATATAAAAATAGTAAAAAATTATAAAATTAGTA
Found at i:44220699 original size:21 final size:19
Alignment explanation
Indices: 44220617--44220715 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 19
44220607 TTAAAAAATT
*
44220617 AAAATATTAAAAAATTATTA
1 AAAATAGTAAAAAATTA-TA
* *
44220637 AAATTAG-AAAAAAATATA
1 AAAATAGTAAAAAATTATA
* *
44220655 AAAATTGTAAAAAAATATA
1 AAAATAGTAAAAAATTATA
* **
44220674 AAATATTGTAAAATTTTATA
1 AAA-ATAGTAAAAAATTATA
44220694 AAAATAGTAAAAAATTATA
1 AAAATAGTAAAAAATTATA
44220713 AAA
1 AAA
44220716 TTTTATAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
18 7 0.11
19 38 0.58
20 21 0.32
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATAGTAAAAAATTATA
Found at i:44220716 original size:29 final size:29
Alignment explanation
Indices: 44220589--44220741 Score: 120
Period size: 29 Copynumber: 5.3 Consensus size: 29
44220579 ACAAAAAAAT
* *
44220589 AAAAACTAT-AAATTTTATTTAAAAA-ATTA
1 AAAAATTATAAAATTTTA--TAAAAATAGTA
* * * *
44220618 AAATATTAAAAAATTAT-TAAAATTAG-A
1 AAAAATTATAAAATTTTATAAAAATAGTA
* * *
44220645 AAAAAATATAAAAATTGTAAAAAAATA-TA
1 AAAAATTAT-AAAATTTTATAAAAATAGTA
* *
44220674 AAATATTGTAAAATTTTATAAAAATAGTA
1 AAAAATTATAAAATTTTATAAAAATAGTA
*
44220703 AAAAATTATAAAATTTTAT-AAAATCGTA
1 AAAAATTATAAAATTTTATAAAAATAGTA
44220731 AGAAAATTATA
1 A-AAAATTATA
44220742 CAAAATATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
27 12 0.12
28 32 0.33
29 47 0.48
30 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATTATAAAATTTTATAAAAATAGTA
Found at i:44220721 original size:10 final size:10
Alignment explanation
Indices: 44220616--44220726 Score: 72
Period size: 10 Copynumber: 11.6 Consensus size: 10
44220606 TTTAAAAAAT
44220616 TAAAATATTA
1 TAAAATATTA
44220626 -AAAA-ATTA
1 TAAAATATTA
*
44220634 TTAAA-ATTA
1 TAAAATATTA
* * *
44220643 GAAAAAAATA
1 TAAAATATTA
*
44220653 TAAAA-ATTG
1 TAAAATATTA
* *
44220662 TAAAAAAATA
1 TAAAATATTA
*
44220672 TAAAATATTG
1 TAAAATATTA
*
44220682 TAAAATTTTA
1 TAAAATATTA
44220692 TAAAA-A-TA
1 TAAAATATTA
*
44220700 GTAAAAAATTA
1 -TAAAATATTA
*
44220711 TAAAATTTTA
1 TAAAATATTA
44220721 TAAAAT
1 TAAAAT
44220727 CGTAAGAAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
8 6 0.08
9 26 0.33
10 44 0.56
11 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (10 bp):
TAAAATATTA
Found at i:44220737 original size:39 final size:39
Alignment explanation
Indices: 44220651--44220730 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
44220641 TAGAAAAAAA
* * **
44220651 TATAAAAATTGTAAAAAAATATAAAATATTGTAAAATTT
1 TATAAAAATAGTAAAAAAATATAAAATATTATAAAATCG
* *
44220690 TATAAAAATAGTAAAAAATTATAAAATTTTATAAAATCG
1 TATAAAAATAGTAAAAAAATATAAAATATTATAAAATCG
44220729 TA
1 TA
44220731 AGAAAATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (39 bp):
TATAAAAATAGTAAAAAAATATAAAATATTATAAAATCG
Found at i:44220750 original size:28 final size:27
Alignment explanation
Indices: 44220690--44220752 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
44220680 TGTAAAATTT
44220690 TATA-AAAATAGTAAAAAATTATAAAA
1 TATATAAAATAGTAAAAAATTATAAAA
* *
44220716 TTTTATAAAATCGTAAGAAAATTATACAAA
1 -TATATAAAATAGTAA-AAAATTATA-AAA
44220746 -ATATAAA
1 TATATAAA
44220753 GAAATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 15 0.50
29 9 0.30
30 3 0.10
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (27 bp):
TATATAAAATAGTAAAAAATTATAAAA
Found at i:44220955 original size:19 final size:19
Alignment explanation
Indices: 44220933--44221039 Score: 73
Period size: 18 Copynumber: 5.7 Consensus size: 19
44220923 TTTTTATGAC
44220933 TTTTATAAAATTTTACAAT
1 TTTTATAAAATTTTACAAT
***
44220952 TTTT-TATTTTTTTACAAT
1 TTTTATAAAATTTTACAAT
* *
44220970 TTTTATAGAAA--ATATAAT
1 TTTTATA-AAATTTTACAAT
*
44220988 TTTTA-ATAAATTTTAAAAT
1 TTTTATA-AAATTTTACAAT
44221007 TTTTATTAAAATTTAATA-AAT
1 TTTTA-TAAAATTT--TACAAT
44221028 TTTT-TAAAATTT
1 TTTTATAAAATTT
44221040 ATTTTTATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
17 4 0.06
18 25 0.36
19 24 0.35
20 6 0.09
21 8 0.12
22 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (19 bp):
TTTTATAAAATTTTACAAT
Found at i:44221001 original size:10 final size:10
Alignment explanation
Indices: 44220983--44221030 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
44220973 TATAGAAAAT
*
44220983 ATAATTTTTA
1 ATAAATTTTA
44220993 ATAAATTTTA
1 ATAAATTTTA
*
44221003 A-AATTTTTA
1 ATAAATTTTA
* *
44221012 TTAAAATTTA
1 ATAAATTTTA
44221022 ATAAATTTT
1 ATAAATTTT
44221031 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:44221040 original size:19 final size:19
Alignment explanation
Indices: 44220980--44221040 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
44220970 TTTTATAGAA
*
44220980 AATATAATTTTTAATAAATTTT
1 AATA-AATTTTT--TAAAATTT
*
44221002 AA-AATTTTTATTAAAATTT
1 AATAAATTTT-TTAAAATTT
44221021 AATAAATTTTTTAAAATTT
1 AATAAATTTTTTAAAATTT
44221040 A
1 A
44221041 TTTTTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 19 0.56
20 11 0.32
21 2 0.06
22 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATAAATTTTTTAAAATTT
Found at i:44226900 original size:3 final size:3
Alignment explanation
Indices: 44226892--44226929 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
44226882 TTAAATGAAT
*
44226892 TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
44226930 TGCATGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:44230485 original size:42 final size:42
Alignment explanation
Indices: 44230426--44230546 Score: 152
Period size: 43 Copynumber: 2.9 Consensus size: 42
44230416 TAGGGTTAGT
* * *
44230426 TGAGATTACGTGTAAGACCATATTTGAGATATGACATCGATA
1 TGAGATTACATGTAAGACCATATCTGGGATATGACATCGATA
* * * *
44230468 TGAGATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATTACATGTAAGACCATATCTGGGATA-TGACATCGATA
**
44230511 TGAGATCCCATGTAAGACCATATCTGGGATATGACA
1 TGAGATTACATGTAAGACCATATCTGGGATATGACA
44230547 ATGGTATGGT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 29 0.44
43 37 0.56
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (42 bp):
TGAGATTACATGTAAGACCATATCTGGGATATGACATCGATA
Found at i:44245882 original size:48 final size:48
Alignment explanation
Indices: 44245806--44245905 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
44245796 CTCACACACT
* * *
44245806 AAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTATCTCCCACCCG
1 AAGTACTAATATCATGGCCCAAAGCCAAATCAATGAATCTCCCACCCG
*
44245854 AAGTACTAATATCATGGCCCAAAGCCAAATCAATGAATCTCGCACCCG
1 AAGTACTAATATCATGGCCCAAAGCCAAATCAATGAATCTCCCACCCG
44245902 AAGT
1 AAGT
44245906 GTAACACCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (48 bp):
AAGTACTAATATCATGGCCCAAAGCCAAATCAATGAATCTCCCACCCG
Found at i:44246295 original size:5 final size:5
Alignment explanation
Indices: 44246287--44246312 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44246277 TATTTATTTC
44246287 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
44246313 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:44247292 original size:21 final size:20
Alignment explanation
Indices: 44247268--44247306 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
44247258 CTTGTATAAC
44247268 TATCATCAAACATTCAAAATT
1 TATCATCAAACA-TCAAAATT
*
44247289 TATCATTAAACATCAAAA
1 TATCATCAAACATCAAAA
44247307 CACATGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (20 bp):
TATCATCAAACATCAAAATT
Found at i:44261566 original size:47 final size:47
Alignment explanation
Indices: 44261497--44261810 Score: 196
Period size: 47 Copynumber: 6.7 Consensus size: 47
44261487 GGTATAATGC
*
44261497 CGATGCCATGTCCCAGCCATGGTCTTACACTAG-CTTATCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGACTTAT-CATCAAGT
* *
44261544 CGATGCCATGTCCCAGACATGGTCTTACACT-GAC-TATTGAAATCGAGAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGACTTA-T--CATCAAG-T
* * * ** *
44261593 CGACGCCATGTCCCAGACACGGTCTTACACTGACACCTCTAT-A-CGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACT-AGA-CT-TATCATCAAGT
* * * *
44261641 CGATGCCATGTCCCAAACATGGTCTTACATTGAGAC--ATC-TCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACT-AGACTTATCATC-AAGT
* *
44261687 CGATG-CATGTCCAAGACAT-GTCTTACACTAG-CTTA-CATCTCGAAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGACTTATCA--TC-AAGT
44261733 CGAATG-CATGTCCCAGACAT-GTCTTACACTAG-CTCTCATC-TCAA-T
1 CG-ATGCCATGTCCCAGACATGGTCTTACACTAGACT-T-ATCATCAAGT
*
44261778 GCTGATGCCATGTCTCAGACAT-GTCTTACACTA
1 -C-GATGCCATGTCCCAGACATGGTCTTACACTA
44261811 ACACACAAAA
Statistics
Matches: 220, Mismatches: 23, Indels: 48
0.76 0.08 0.16
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 12 0.05
45 13 0.06
46 24 0.11
47 90 0.41
48 36 0.16
49 34 0.15
50 2 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGACTTATCATCAAGT
Found at i:44261610 original size:49 final size:47
Alignment explanation
Indices: 44261501--44261626 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 47
44261491 TAATGCCGAT
* ** *
44261501 GCCATGTCCCAGCCATGGTCTTACACT-AGCTTATCCATCAAGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTTATAAATCAAGTCGAC
*
44261548 GCCATGTCCCAGACATGGTCTTACACTGAC-TATTGAAATCGAGATCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGACTTA-T-AAATCAAG-TCGAC
*
44261597 GCCATGTCCCAGACACGGTCTTACACTGAC
1 GCCATGTCCCAGACATGGTCTTACACTGAC
44261627 ACCTCTATAC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
46 2 0.03
47 28 0.41
48 6 0.09
49 33 0.48
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTTATAAATCAAGTCGAC
Found at i:44261665 original size:48 final size:47
Alignment explanation
Indices: 44261494--44261715 Score: 135
Period size: 49 Copynumber: 4.7 Consensus size: 47
44261484 TAGGGTATAA
** * *
44261494 TGCCGATGCCATGTCCCAGCCATGGTCTTACACT-AGCTTA-TCCATCAAG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGA-C--ACTCTAT-ACG
* *
44261543 T--CGATGCCATGTCCCAGACATGGTCTTACACTGACTA-T-TGAAATCG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGAC-ACTCT-ATA-CG
* * * * *
44261589 AGATCGACGCCATGTCCCAGACACGGTCTTACACTGACACCTCTATACG
1 TG-CCGATGCCATGTCCCAAACATGGTCTTACACTGACA-CTCTATACG
* *
44261638 TGCCGATGCCATGTCCCAAACATGGTCTTACATTGAGACATC--T-CG
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGACAC-TCTATACG
44261683 TAGCCGATG-CATGT-CCAAGACAT-GTCTTACACT
1 T-GCCGATGCCATGTCCCAA-ACATGGTCTTACACT
44261716 AGCTTACATC
Statistics
Matches: 145, Mismatches: 16, Indels: 29
0.76 0.08 0.15
Matches are distributed among these distances:
44 13 0.09
45 13 0.09
46 13 0.09
47 32 0.22
48 34 0.23
49 36 0.25
50 3 0.02
51 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCTATACG
Found at i:44264968 original size:48 final size:46
Alignment explanation
Indices: 44264897--44265115 Score: 150
Period size: 47 Copynumber: 4.7 Consensus size: 46
44264887 TTTTATCGAC
* * *
44264897 GCCATGTCTCAGACATGGTCTTACACTGACACCTCTATACGT-GCCGAT
1 GCCATGTCCCAAACATGGTCTTACACTGACACATC--T-CGTAGCCGAT
* *
44264945 GCCATGTCCCAAACATGGTCTTACATTGAGACATCTCGTAGCCGAT
1 GCCATGTCCCAAACATGGTCTTACACTGACACATCTCGTAGCCGAT
*
44264991 G-CATGT-CCAAGACAT-GTCTTACACT-AGCTTACATCTCGAAGCCGAAT
1 GCCATGTCCCAA-ACATGGTCTTACACTGA-C--ACATCTCGTAGCCG-AT
* * * * *
44265038 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTC-AATGCTGAT
1 GCCATGTCCCAAACATGGTCTTACACT-G-ACACATCTCGTA-GCCGAT
* * *
44265084 GCCATGTCTCAGACAT-GTCTTACACTAACACA
1 GCCATGTCCCAAACATGGTCTTACACTGACACA
44265116 CAAAAAACCC
Statistics
Matches: 143, Mismatches: 16, Indels: 27
0.77 0.09 0.15
Matches are distributed among these distances:
43 1 0.01
44 13 0.09
45 15 0.10
46 26 0.18
47 54 0.38
48 33 0.23
49 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (46 bp):
GCCATGTCCCAAACATGGTCTTACACTGACACATCTCGTAGCCGAT
Found at i:44265051 original size:47 final size:47
Alignment explanation
Indices: 44264975--44265110 Score: 188
Period size: 47 Copynumber: 2.9 Consensus size: 47
44264965 TTACATTGAG
* *
44264975 ACATCTCGTAGCCGATGCATGTCCAAGACATGTCTTACACTAGCT-T
1 ACATCTCGAAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
44265021 ACATCTCGAAGCCGAATGCATGTCCCAGACATGTCTTACACTAGCTCT
1 ACATCTCGAAGCCG-ATGCATGTCCCAGACATGTCTTACACTAGCTCT
* *
44265069 -CATCTC-AATGCTGATGCCATGTCTCAGACATGTCTTACACTA
1 ACATCTCGAA-GCCGATG-CATGTCCCAGACATGTCTTACACTA
44265111 ACACACAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
46 18 0.22
47 63 0.77
48 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (47 bp):
ACATCTCGAAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
Found at i:44280857 original size:49 final size:48
Alignment explanation
Indices: 44280785--44280959 Score: 251
Period size: 49 Copynumber: 3.5 Consensus size: 48
44280775 CTGGTGCGCA
44280785 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCTGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-CTGTACACG
* * * * * *
44280834 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGATACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCTG-TACACG
44280885 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCT-GTACACG
44280934 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
44280960 CGTGACCTCA
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
49 64 0.58
50 9 0.08
51 37 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGTACACG
Found at i:44280939 original size:100 final size:100
Alignment explanation
Indices: 44280781--44280964 Score: 352
Period size: 100 Copynumber: 1.8 Consensus size: 100
44280771 CTATCTGGTG
44280781 CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCTGTACACGTAGTAGCCTGCA
1 CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCTGTACACGTAGTAGCCTGCA
44280846 CTTAGTACTACACACGTGATCGAAGTTATCAGATA
66 CTTAGTACTACACACGTGATCGAAGTTATCAGATA
44280881 CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-CTGGTACACGTAGTAGCCTGC
1 CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCT-GTACACGTAGTAGCCTGC
44280945 ACTTAGTACTACACACGTGA
65 ACTTAGTACTACACACGTGA
44280965 CCTCACAATA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 2 0.02
100 81 0.98
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (100 bp):
CGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCTGTACACGTAGTAGCCTGCA
CTTAGTACTACACACGTGATCGAAGTTATCAGATA
Found at i:44287136 original size:43 final size:43
Alignment explanation
Indices: 44287022--44287136 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
44287012 TACAATGCCA
* * *
44287022 ATGTCCCAAACGTGGTCTTACATGT-AATCAAATATCGATGCT
1 ATGTCCCAAACATGGTCTTACACGTAAATCAAATATCGATGCG
* * *
44287064 ACTGTCCCAGATAGGGTCTTACACG-AAATCAAATA-CGATGTCG
1 A-TGTCCCAAACATGGTCTTACACGTAAATCAAATATCGATG-CG
44287107 ATGTCCCAAACATGGTCTTACACGTAAATC
1 ATGTCCCAAACATGGTCTTACACGTAAATC
44287137 TCAAATTGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 26 0.43
43 34 0.57
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGTCCCAAACATGGTCTTACACGTAAATCAAATATCGATGCG
Found at i:44288493 original size:22 final size:22
Alignment explanation
Indices: 44288467--44288511 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
44288457 ATTATGTGTA
44288467 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
44288489 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
44288511 T
1 T
44288512 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:44288931 original size:24 final size:25
Alignment explanation
Indices: 44288887--44288938 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
44288877 ACCCTTCTCA
*
44288887 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCTCTCTCATTGTTC
44288912 TCTCTTCA-TTCTCT-TCCATTGTTC
1 TCTCTTCACTTCTCTCT-CATTGTTC
44288936 TCT
1 TCT
44288939 ATTTTCTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 16 0.64
25 8 0.32
ACGTcount: A:0.08, C:0.35, G:0.02, T:0.56
Consensus pattern (25 bp):
TCTCTTCACTTCTCTCTCATTGTTC
Found at i:44303020 original size:25 final size:25
Alignment explanation
Indices: 44302992--44303041 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
44302982 CGAAATAGGG
44302992 TTACGGAGCATTACCATAAAATTGT
1 TTACGGAGCATTACCATAAAATTGT
44303017 TTACGGAGCATTACCATAAAATTGT
1 TTACGGAGCATTACCATAAAATTGT
44303042 AACTTAAATC
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:0.16, G:0.16, T:0.32
Consensus pattern (25 bp):
TTACGGAGCATTACCATAAAATTGT
Found at i:44310674 original size:12 final size:12
Alignment explanation
Indices: 44310657--44310698 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
44310647 GGACACGCGG
44310657 CCGTGTCCCA-GC
1 CCGTGT-CCATGC
44310669 CCGTGTCCATGC
1 CCGTGTCCATGC
44310681 CCGTGTCCATGC
1 CCGTGTCCATGC
44310693 CCGTGT
1 CCGTGT
44310699 AACTCTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 3 0.10
12 26 0.90
ACGTcount: A:0.07, C:0.43, G:0.26, T:0.24
Consensus pattern (12 bp):
CCGTGTCCATGC
Found at i:44311755 original size:40 final size:40
Alignment explanation
Indices: 44311700--44311837 Score: 213
Period size: 40 Copynumber: 3.5 Consensus size: 40
44311690 TAAACATGGA
*
44311700 CACGTATGTGCAATCAGTGGTACCAAAGTACAAATAGGGG
1 CACGTATGTGCAATCAGGGGTACCAAAGTACAAATAGGGG
*
44311740 CACGTATGTGCAATCAGGGGTACCGAAGTACAAATAGGGG
1 CACGTATGTGCAATCAGGGGTACCAAAGTACAAATAGGGG
* * * *
44311780 CACATATATGCAATCAGGGGTACCAAGGTACAGATAGGGG
1 CACGTATGTGCAATCAGGGGTACCAAAGTACAAATAGGGG
*
44311820 CACGTGTGTGCAATCAGG
1 CACGTATGTGCAATCAGG
44311838 TATAAGTACC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (40 bp):
CACGTATGTGCAATCAGGGGTACCAAAGTACAAATAGGGG
Found at i:44311778 original size:20 final size:20
Alignment explanation
Indices: 44311718--44311779 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
44311708 TGCAATCAGT
*
44311718 GGTACCAAAGTACAAATAGG
1 GGTACCGAAGTACAAATAGG
* * *
44311738 GGCA-CGTATGTGC-AATCAGG
1 GGTACCG-AAGTACAAAT-AGG
44311758 GGTACCGAAGTACAAATAGG
1 GGTACCGAAGTACAAATAGG
44311778 GG
1 GG
44311780 CACATATATG
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.71
21 5 0.16
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.16
Consensus pattern (20 bp):
GGTACCGAAGTACAAATAGG
Found at i:44314012 original size:16 final size:17
Alignment explanation
Indices: 44313991--44314023 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44313981 AAACACAGTG
44313991 GTAAAAT-AATATAGAA
1 GTAAAATCAATATAGAA
*
44314007 GTAAAATCCATATAGAA
1 GTAAAATCAATATAGAA
44314024 CTACACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (17 bp):
GTAAAATCAATATAGAA
Found at i:44314076 original size:45 final size:47
Alignment explanation
Indices: 44314023--44314133 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 47
44314013 TCCATATAGA
* * *
44314023 ACTACACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCTTCTATTTATATTGTTAGAACAAGGTGTTTCAACCTT
* **
44314068 ATTACACTTAATCTATTTGATATTGGTTAGAACAAGGTGTTTCAACCTT
1 ACTACACTTCTTCTATTT-ATATT-GTTAGAACAAGGTGTTTCAACCTT
*
44314117 ACTACACTCCTTCTATT
1 ACTACACTTCTTCTATT
44314134 AGAATATAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 14 0.27
47 4 0.08
49 34 0.65
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (47 bp):
ACTACACTTCTTCTATTTATATTGTTAGAACAAGGTGTTTCAACCTT
Found at i:44315894 original size:39 final size:40
Alignment explanation
Indices: 44315849--44315959 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
44315839 CGGGGTTTAG
* * *
44315849 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
44315888 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
44315928 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
44315960 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:44315919 original size:40 final size:40
Alignment explanation
Indices: 44315872--44316016 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
44315862 CTCGCACAAG
* * * * *
44315872 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
44315912 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * *
44315952 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTATCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
44315993 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
44316017 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.65
41 26 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:44326421 original size:17 final size:17
Alignment explanation
Indices: 44326381--44326427 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
44326371 CAGAAGCTCG
44326381 ATAAAATAATTATAATA
1 ATAAAATAATTATAATA
44326398 A-AGAAATAA-TATTAATA
1 ATA-AAATAATTA-TAATA
*
44326415 ATAAAATTATTAT
1 ATAAAATAATTAT
44326428 TTAAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATAAAATAATTATAATA
Found at i:44328836 original size:14 final size:13
Alignment explanation
Indices: 44328809--44328834 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44328799 TAAAAGTATT
44328809 TAATTTTTTAAAA
1 TAATTTTTTAAAA
44328822 TAATTTTTTAAAA
1 TAATTTTTTAAAA
44328835 ATTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTTTTTAAAA
Found at i:44331731 original size:21 final size:21
Alignment explanation
Indices: 44331705--44331745 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44331695 GCTTTTCTGC
44331705 TGCTGGGTTGATCTTCATTTT
1 TGCTGGGTTGATCTTCATTTT
44331726 TGCTGGGTTGATCTTCATTT
1 TGCTGGGTTGATCTTCATTT
44331746 GTTTGCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (21 bp):
TGCTGGGTTGATCTTCATTTT
Found at i:44336289 original size:28 final size:28
Alignment explanation
Indices: 44336257--44336314 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
44336247 TATCTTCCAT
44336257 TAAAATTCATTCTTACAAACCAATCAAG
1 TAAAATTCATTCTTACAAACCAATCAAG
44336285 TAAAATTCATTCTTACAAACCAATCAAG
1 TAAAATTCATTCTTACAAACCAATCAAG
44336313 TA
1 TA
44336315 TGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAATTCATTCTTACAAACCAATCAAG
Found at i:44337416 original size:14 final size:14
Alignment explanation
Indices: 44337399--44337441 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
44337389 ATAAAGTAAT
44337399 TAAAATAAAA-GAAA
1 TAAAA-AAAATGAAA
44337413 TAAAAAAAATGAAA
1 TAAAAAAAATGAAA
*
44337427 TAAAGAAAAAGGAAA
1 TAAA-AAAAATGAAA
44337442 GAAAGAAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 13 0.50
15 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
TAAAAAAAATGAAA
Found at i:44337435 original size:15 final size:14
Alignment explanation
Indices: 44337405--44337448 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
44337395 TAATTAAAAT
44337405 AAAAGAAATAAA-A
1 AAAAGAAATAAAGA
44337418 AAAATGAAATAAAGA
1 AAAA-GAAATAAAGA
*
44337433 AAAAGGAAAGAAAGA
1 AAAA-GAAATAAAGA
44337448 A
1 A
44337449 GGCCACGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 4 0.15
14 8 0.30
15 15 0.56
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAAGAAATAAAGA
Found at i:44342629 original size:16 final size:16
Alignment explanation
Indices: 44342608--44342642 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
44342598 ATGAATCGGT
*
44342608 AAAAGTTGAAATGCCG
1 AAAAGTCGAAATGCCG
44342624 AAAAGTCGAAATGCCG
1 AAAAGTCGAAATGCCG
44342640 AAA
1 AAA
44342643 TTTGGGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (16 bp):
AAAAGTCGAAATGCCG
Found at i:44342890 original size:29 final size:28
Alignment explanation
Indices: 44342857--44342971 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
44342847 GCATGAGTGT
*
44342857 AATATGATTTGGGCCTAATGGGCCATATG
1 AATATGAATTGGGCC-AATGGGCCATATG
* *
44342886 AATATGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCC-AATGGGCCATATG
* *
44342915 AATATGAACTGGGCCAGATGGGTCATATG
1 AATATGAATTGGGCCA-ATGGGCCATATG
* *
44342944 AATGTG-ATTGGGACCAGTGGGCCATATG
1 AATATGAATTGGG-CCAATGGGCCATATG
44342972 CATGTATGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.22
29 57 0.78
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (28 bp):
AATATGAATTGGGCCAATGGGCCATATG
Found at i:44345814 original size:19 final size:19
Alignment explanation
Indices: 44345786--44345831 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
44345776 TAGTTGGAAA
* *
44345786 TTTCGAGGACGAAATTTCT
1 TTTCGGGGACAAAATTTCT
44345805 TTTCGGGGACAAAATTTCT
1 TTTCGGGGACAAAATTTCT
44345824 TTTCGGGG
1 TTTCGGGG
44345832 GGTAGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (19 bp):
TTTCGGGGACAAAATTTCT
Found at i:44347192 original size:8 final size:8
Alignment explanation
Indices: 44347176--44347210 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
44347166 GCCAAAAGCT
44347176 GAAATGCC
1 GAAATGCC
*
44347184 GAAAAGCC
1 GAAATGCC
44347192 GAAATGCC
1 GAAATGCC
44347200 GAAATGCC
1 GAAATGCC
44347208 GAA
1 GAA
44347211 GAGCTGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.09
Consensus pattern (8 bp):
GAAATGCC
Found at i:44347219 original size:16 final size:16
Alignment explanation
Indices: 44347169--44347210 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
44347159 ATGAATCGCC
*
44347169 AAAAGCTGAAATGCCG
1 AAAAGCCGAAATGCCG
44347185 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
*
44347201 AAATGCCGAA
1 AAAAGCCGAA
44347211 GAGCTGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:44347467 original size:29 final size:29
Alignment explanation
Indices: 44347434--44347548 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
44347424 GTATGAGTAT
44347434 AATATGAATTGGGCCTAATGGGCCATATG
1 AATATGAATTGGGCCTAATGGGCCATATG
* *
44347463 AATATGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCCTAATGGGCCATATG
* * *
44347492 AATTTGAACTAGGCC-AGATGGGCCATATG
1 AATATGAATTGGGCCTA-ATGGGCCATATG
* *
44347521 AATGTG-ATTGGGCCCAATGGGCCATATG
1 AATATGAATTGGGCCTAATGGGCCATATG
44347549 CATGTTTGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
28 19 0.26
29 55 0.74
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (29 bp):
AATATGAATTGGGCCTAATGGGCCATATG
Found at i:44351163 original size:45 final size:45
Alignment explanation
Indices: 44351112--44351203 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
44351102 GCAAGTGATC
**
44351112 ACAATGTAGAAGTTGTCCTTCTGCAAAGAATCAGAAAGGAACCCT
1 ACAATGTAGAAGTTGTCCTTAGGCAAAGAATCAGAAAGGAACCCT
*
44351157 ACAATGTAGAAGTTGTCCTTAGGCAAAGAATCAGGAAGGAACCCT
1 ACAATGTAGAAGTTGTCCTTAGGCAAAGAATCAGAAAGGAACCCT
44351202 AC
1 AC
44351204 GCATCTCTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (45 bp):
ACAATGTAGAAGTTGTCCTTAGGCAAAGAATCAGAAAGGAACCCT
Found at i:44352849 original size:14 final size:14
Alignment explanation
Indices: 44352830--44352856 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44352820 AATTCTCATA
44352830 TTTAATTTATTTAT
1 TTTAATTTATTTAT
44352844 TTTAATTTATTTA
1 TTTAATTTATTTA
44352857 ACTTTGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTTATTTAT
Found at i:44357116 original size:25 final size:24
Alignment explanation
Indices: 44357087--44357142 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
44357077 ATGAATAGAA
*
44357087 TTTTTAATAAAATTATTAATTTACT
1 TTTTTAATAAAATAATTAATTTA-T
* * *
44357112 TTTTTTATGAAATAATTTATTTAT
1 TTTTTAATAAAATAATTAATTTAT
44357136 TTTTTAA
1 TTTTTAA
44357143 AATAAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTTAATAAAATAATTAATTTAT
Found at i:44357128 original size:21 final size:21
Alignment explanation
Indices: 44357103--44357147 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
44357093 ATAAAATTAT
*
44357103 TAATTTACTTT-TTTTATGAAA
1 TAATTTA-TTTATTTTATAAAA
*
44357124 TAATTTATTTATTTTTTAAAA
1 TAATTTATTTATTTTATAAAA
44357145 TAA
1 TAA
44357148 ACAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTTATTTATTTTATAAAA
Found at i:44358311 original size:20 final size:21
Alignment explanation
Indices: 44358277--44358319 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
44358267 AATTTACAAT
44358277 TTATAAAAAAACTCAAAAAAA
1 TTATAAAAAAACTCAAAAAAA
* *
44358298 TTAT-AAAAAGCTCATAAAAA
1 TTATAAAAAAACTCAAAAAAA
44358318 TT
1 TT
44358320 CAAAACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TTATAAAAAAACTCAAAAAAA
Found at i:44358887 original size:15 final size:16
Alignment explanation
Indices: 44358844--44358889 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
44358834 TGTTTTCCAT
44358844 CCATT-TAATTTTCTA
1 CCATTCTAATTTTCTA
* *
44358859 CCCTTACAAATTTTC-A
1 CCATT-CTAATTTTCTA
44358875 CCATTCTAATTTTCT
1 CCATTCTAATTTTCT
44358890 TTCTATCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 12 0.50
16 5 0.21
17 7 0.29
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (16 bp):
CCATTCTAATTTTCTA
Found at i:44360191 original size:20 final size:18
Alignment explanation
Indices: 44360148--44360180 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44360138 TTAATAAAAA
44360148 ATTT-AACTATATTAATT
1 ATTTGAACTATATTAATT
44360165 ATTTGAACTA-ATTAAT
1 ATTTGAACTATATTAAT
44360181 AATATTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (18 bp):
ATTTGAACTATATTAATT
Found at i:44366195 original size:126 final size:125
Alignment explanation
Indices: 44365958--44366473 Score: 599
Period size: 125 Copynumber: 4.1 Consensus size: 125
44365948 AGCACCCTTG
* * * * *
44365958 ACTATTGTAGAAAAAGTGTGTCGACATGAGAG-TTTTTTCATCAATTTTGCTGATAGTGCATCCT
1 ACTACTGTAGAAAAAGAGAGTCGACATGGGAGCTTTTTTCAT-AATTTTGCTGACAGTGCATCCT
* * * * *
44366022 GCTTGAAGCGTTTTTGACTCTATTTGTTCAGAACCATCTTTTTAAAATTATTTTTTCAGGA
65 GCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGA
* *
44366083 ACTACTGTAGAAAAAGAGAGTCGATATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCAT
1 ACTACTGTAGAAAAAGAGAGTCGACATGGGAGCTTTTTTCAT-AATTTTGCTGACAGTGCATCCT
* *
44366148 GCCTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTA-TTTTTCAAGA
65 GCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGA
* * * * ** *
44366208 ACTACTATAGAAAAATAGCGTCCACATGGGAGCTTTTTTTGGTAATTTTGTTGACAGTGCATCCT
1 ACTACTGTAGAAAAAGAGAGTCGACATGGGAGC-TTTTTTCATAATTTTGCTGACAGTGCATCCT
* ** * ** *
44366273 ACTTGAAGCGCTTTTGACACTATTTGTTCATAAATGTCTTTTCAAAATTATTTTTT-AGGA
65 GCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGA
* * * * * * * *
44366333 ATTACTGTAGAAAAAGA-ACGTCTACGTGTGAGCTTTTTTCAGTATTTTTACTGATAATGCATCC
1 ACTACTGTAGAAAAAGAGA-GTCGACATGGGAGCTTTTTTCA-TAATTTTGCTGACAGTGCATCC
* * *
44366397 TGCTTGAAGCATTTTTTACACTATTTGTTTAGAACCGTATTCTCAAAATTATTTTTTCAGGA
64 TGCTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGA
*
44366459 ACCACTGTAGAAAAA
1 ACTACTGTAGAAAAA
44366474 AAATCCTTAT
Statistics
Matches: 327, Mismatches: 58, Indels: 11
0.83 0.15 0.03
Matches are distributed among these distances:
124 6 0.02
125 218 0.67
126 103 0.31
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (125 bp):
ACTACTGTAGAAAAAGAGAGTCGACATGGGAGCTTTTTTCATAATTTTGCTGACAGTGCATCCTG
CTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGA
Found at i:44366423 original size:250 final size:252
Alignment explanation
Indices: 44366000--44366473 Score: 659
Period size: 250 Copynumber: 1.9 Consensus size: 252
44365990 TTTTTTCATC
* * * * * *
44366000 AATTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACTCTATTTGTTCAGAACCATCTTTTT
1 AATTTTGCTGACAGTGCATCCTACTTGAAGCGCTTTTGACACTATTTGTTCAGAAACATCTTTTC
*
44366065 AAAATTATTTTTTCAGGAACTACTGTAGAAAAAGAGAGTCGATATGGGAGCTTTTTTCATCAATT
66 AAAATTATTTTTTCAGGAACTACTGTAGAAAAAGAGAGTCGACATGGGAGCTTTTTTCATCAATT
* * *
44366130 TTGCTGACAGTGCATCATGCCTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAA
131 TTACTGACAATGCATCATGCCTGAAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAA
*
44366195 TTA-TTTTTCAAGAACTACTATAGAAAAATAGCGTCCACATGGGAGCTTTTTTTGGT
196 TTATTTTTTCAAGAACCACTATAGAAAAATAGCGTCCACATGGGAGCTTTTTTTGGT
* * **
44366251 AATTTTGTTGACAGTGCATCCTACTTGAAGCGCTTTTGACACTATTTGTTCATAAATGTCTTTTC
1 AATTTTGCTGACAGTGCATCCTACTTGAAGCGCTTTTGACACTATTTGTTCAGAAACATCTTTTC
* * * * *
44366316 AAAATTATTTTTT-AGGAATTACTGTAGAAAAAGA-ACGTCTACGTGTGAGCTTTTTTCAGT-AT
66 AAAATTATTTTTTCAGGAACTACTGTAGAAAAAGAGA-GTCGACATGGGAGCTTTTTTCA-TCAA
* * * * *
44366378 TTTTACTGATAATGCATCCTGCTTGAAGCATTTTTTACACTATTTGTTTAGAACCGTATTCTCAA
129 TTTTACTGACAATGCATCATGCCTGAAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAA
* *
44366443 AATTATTTTTTCAGGAACCACTGTAGAAAAA
194 AATTATTTTTTCAAGAACCACTATAGAAAAA
44366474 AAATCCTTAT
Statistics
Matches: 193, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
249 1 0.01
250 101 0.52
251 91 0.47
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (252 bp):
AATTTTGCTGACAGTGCATCCTACTTGAAGCGCTTTTGACACTATTTGTTCAGAAACATCTTTTC
AAAATTATTTTTTCAGGAACTACTGTAGAAAAAGAGAGTCGACATGGGAGCTTTTTTCATCAATT
TTACTGACAATGCATCATGCCTGAAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAA
TTATTTTTTCAAGAACCACTATAGAAAAATAGCGTCCACATGGGAGCTTTTTTTGGT
Found at i:44366571 original size:34 final size:33
Alignment explanation
Indices: 44366529--44366640 Score: 127
Period size: 34 Copynumber: 3.4 Consensus size: 33
44366519 CACAATATTC
44366529 TTTTTTAAAAAAACTAAACCCTAATTTAATTAA
1 TTTTTTAAAAAAACTAAACCCTAATTTAATTAA
* * * *
44366562 TTTTCTTAAAAACACTAAACCCCAGTTTAATTTA
1 TTTT-TTAAAAAAACTAAACCCTAATTTAATTAA
* ***
44366596 TTTATTTTAAATCCCTAAACCCTAATTTAATTAA
1 TTT-TTTAAAAAAACTAAACCCTAATTTAATTAA
44366630 -TTTTTAAAAAA
1 TTTTTTAAAAAA
44366641 GAACACTAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
32 6 0.09
33 6 0.09
34 51 0.80
35 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.41
Consensus pattern (33 bp):
TTTTTTAAAAAAACTAAACCCTAATTTAATTAA
Found at i:44368970 original size:40 final size:40
Alignment explanation
Indices: 44368861--44369002 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 40
44368851 GACTTCAAGT
* *
44368861 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGG-TTTATC
* * * *
44368902 CGATGAGGCACTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGTTTATC
* ***
44368939 CGATGAGACATTGGGTGTCAAATTATTACTTCACATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGTTTATC
* * *
44368979 CGATGAGGCATTGGGTGCCAAATT
1 CGATGAGACACTGGGTGTCAAATT
44369003 GGTGTGTTTG
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 17 0.21
38 12 0.15
39 2 0.02
40 36 0.44
41 15 0.18
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGTTTATC
Found at i:44372721 original size:11 final size:11
Alignment explanation
Indices: 44372689--44372721 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
44372679 CCAATAGAAG
44372689 TTATAGAAAAA
1 TTATAGAAAAA
*
44372700 ATATAG-AAAA
1 TTATAGAAAAA
44372710 TTATAGAAAAA
1 TTATAGAAAAA
44372721 T
1 T
44372722 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (11 bp):
TTATAGAAAAA
Found at i:44372756 original size:18 final size:19
Alignment explanation
Indices: 44372696--44372815 Score: 95
Period size: 20 Copynumber: 6.2 Consensus size: 19
44372686 AAGTTATAGA
*
44372696 AAAAATA-TAGAAAATTAT
1 AAAAATAGTAAAAAATTAT
* * *
44372714 AGAAAAATATTTAAAATTTATT
1 --AAAAATAGTAAAAAATTA-T
44372736 AAAAATAG-AAAAAATTAT
1 AAAAATAGTAAAAAATTAT
* *
44372754 AAAAATCA--CAAAAGTTAT
1 AAAAAT-AGTAAAAAATTAT
44372772 AAAAATAGTAAAAAATTTAT
1 AAAAATAGTAAAAAA-TTAT
*
44372792 AAAAAATTGTAAAAAATTAT
1 -AAAAATAGTAAAAAATTAT
44372812 AAAA
1 AAAA
44372816 TATATAGTGA
Statistics
Matches: 82, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.01
18 21 0.26
19 16 0.20
20 22 0.27
21 21 0.26
22 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATAGTAAAAAATTAT
Found at i:44372794 original size:11 final size:10
Alignment explanation
Indices: 44372689--44372815 Score: 77
Period size: 10 Copynumber: 12.8 Consensus size: 10
44372679 CCAATAGAAG
44372689 TTATAGAAAAA
1 TTATA-AAAAA
* *
44372700 ATATAGAAAA
1 TTATAAAAAA
44372710 TTATAGAAAAA
1 TTATA-AAAAA
* *
44372721 -TATTTAAAAT
1 TTA-TAAAAAA
*
44372731 TTATTAAAAA
1 TTATAAAAAA
*
44372741 -TAGAAAAAA
1 TTATAAAAAA
44372750 TTAT-AAAAA
1 TTATAAAAAA
* * *
44372759 TCA-CAAAAG
1 TTATAAAAAA
44372768 TTAT-AAAAA
1 TTATAAAAAA
44372777 -TAGTAAAAAA
1 TTA-TAAAAAA
44372787 TTTATAAAAAA
1 -TTATAAAAAA
*
44372798 TTGTAAAAAA
1 TTATAAAAAA
44372808 TTATAAAA
1 TTATAAAA
44372816 TATATAGTGA
Statistics
Matches: 90, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
8 2 0.02
9 25 0.28
10 43 0.48
11 18 0.20
12 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.29
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:44373868 original size:10 final size:10
Alignment explanation
Indices: 44373855--44373918 Score: 51
Period size: 11 Copynumber: 6.4 Consensus size: 10
44373845 ATTTATAAAA
44373855 TTTTATATTT
1 TTTTATATTT
* *
44373865 TTTTCTATAT
1 TTTTATATTT
* *
44373875 TTCTATA-TA
1 TTTTATATTT
44373884 TTTTATAATTT
1 TTTTAT-ATTT
44373895 TTTTATGATTT
1 TTTTAT-ATTT
*
44373906 TTATA-ATTT
1 TTTTATATTT
44373915 TTTT
1 TTTT
44373919 CAAATTTTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
9 12 0.29
10 14 0.34
11 15 0.37
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTATATTT
Found at i:44373888 original size:29 final size:28
Alignment explanation
Indices: 44373853--44373915 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
44373843 ATATTTATAA
*
44373853 AATTTTATATTTTTTTCTAT-ATTTCTAT
1 AATTTTATAATTTTTT-TATGATTTCTAT
*
44373881 ATATTTTATAATTTTTTTATGATTTTTAT
1 A-ATTTTATAATTTTTTTATGATTTCTAT
44373910 AATTTT
1 AATTTT
44373916 TTTCAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
AATTTTATAATTTTTTTATGATTTCTAT
Found at i:44373916 original size:29 final size:28
Alignment explanation
Indices: 44373846--44374014 Score: 80
Period size: 29 Copynumber: 5.8 Consensus size: 28
44373836 ATACTTAATA
* *
44373846 TTTATAAAATTTTATATTTTTTTCTATATT
1 TTTAT-AATTTTTATAATTTTTT-TATATT
*
44373876 TCTAT-ATATTTTATAATTTTTTTATGATT
1 TTTATAAT-TTTTATAATTTTTTTAT-ATT
* * * *
44373905 TTTATAATTTTTTTCAAATTTTTAATAAAT
1 TTTATAATTTTTAT-AATTTTTTTAT-ATT
** *
44373935 TTTA-AATTTTTTATTAA-AATTTAATAATT
1 TTTATAA-TTTTTA-TAATTTTTTTAT-ATT
*
44373964 TTTATAATTTTTGATAACTTTTATTA-ATT
1 TTTATAATTTTT-ATAA-TTTTTTTATATT
*
44373993 TTTAT--TTTATTATTATTTTTTT
1 TTTATAATTT-TTATAATTTTTTT
44374015 CCATATGTCA
Statistics
Matches: 109, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
26 6 0.06
27 6 0.06
28 6 0.06
29 56 0.51
30 31 0.28
31 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTATAATTTTTATAATTTTTTTATATT
Found at i:44373980 original size:19 final size:18
Alignment explanation
Indices: 44373884--44373997 Score: 77
Period size: 20 Copynumber: 5.8 Consensus size: 18
44373874 TTTCTATATA
*
44373884 TTTTATAATTTTTTTATGAT
1 TTTTATAA--TTTTTATAAT
*
44373904 TTTTATAATTTTTTTCAAAT
1 TTTTATAATTTTTAT--AAT
*
44373924 TTTTAATAAATTTTA-AATT
1 TTTT-ATAATTTTTATAA-T
* *
44373943 TTTTATTAAAATTTAATAAT
1 TTTTA-T-AATTTTTATAAT
*
44373963 TTTTATAATTTTTGATAAC
1 TTTTATAATTTTT-ATAAT
44373982 TTTTATTAATTTTTAT
1 TTTTA-TAATTTTTAT
44373998 TTTATTATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
18 14 0.18
19 18 0.23
20 35 0.45
21 10 0.13
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTATAAT
Found at i:44373998 original size:10 final size:9
Alignment explanation
Indices: 44373884--44373997 Score: 77
Period size: 9 Copynumber: 11.7 Consensus size: 9
44373874 TTTCTATATA
44373884 TTTTATAATTT
1 TTTTATAA--T
*
44373895 TTTTATGAT
1 TTTTATAAT
44373904 TTTTATAAT
1 TTTTATAAT
*
44373913 TTTTTTCAAAT
1 TTTTAT--AAT
*
44373924 TTTTAATAAA
1 TTTT-ATAAT
44373934 TTTTA-AATT
1 TTTTATAA-T
*
44373943 TTTTATTAAAA
1 TTTTA-T-AAT
*
44373954 TTTAATAAT
1 TTTTATAAT
44373963 TTTTATAAT
1 TTTTATAAT
*
44373972 TTTTGATAAC
1 TTTT-ATAAT
44373982 TTTTATTAAT
1 TTTTA-TAAT
44373992 TTTTAT
1 TTTTAT
44373998 TTTATTATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
8 2 0.02
9 36 0.44
10 23 0.28
11 18 0.22
12 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:44374479 original size:22 final size:22
Alignment explanation
Indices: 44374448--44374489 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44374438 AATTCAAACA
*
44374448 AAATGTTGATTGTGCCACCATG
1 AAATGCTGATTGTGCCACCATG
*
44374470 AAATGCTGATTGTGCTACCA
1 AAATGCTGATTGTGCCACCA
44374490 CATGTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (22 bp):
AAATGCTGATTGTGCCACCATG
Found at i:44377755 original size:18 final size:19
Alignment explanation
Indices: 44377721--44377756 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44377711 GTACATCCCC
44377721 ACAAACAACATGAATACAA
1 ACAAACAACATGAATACAA
*
44377740 ACAAATAACA-GAATACA
1 ACAAACAACATGAATACA
44377757 GTTATTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.19, G:0.06, T:0.11
Consensus pattern (19 bp):
ACAAACAACATGAATACAA
Found at i:44381517 original size:14 final size:14
Alignment explanation
Indices: 44381498--44381549 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
44381488 GATTGTAGGG
44381498 TATGAATATGCGAA
1 TATGAATATGCGAA
* **
44381512 TATGAATGATTGTAGGG
1 TATGAAT-A-TG-CGAA
44381529 TATGAATATGCGAA
1 TATGAATATGCGAA
44381543 TATGAAT
1 TATGAAT
44381550 GATTAACATG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 15 0.52
15 3 0.10
16 3 0.10
17 8 0.28
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (14 bp):
TATGAATATGCGAA
Found at i:44381521 original size:31 final size:31
Alignment explanation
Indices: 44381486--44381553 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
44381476 GTAAACGTGG
44381486 ATGATTGTAGGGTATGAATATGCGAATATGA
1 ATGATTGTAGGGTATGAATATGCGAATATGA
44381517 ATGATTGTAGGGTATGAATATGCGAATATGA
1 ATGATTGTAGGGTATGAATATGCGAATATGA
44381548 ATGATT
1 ATGATT
44381554 AACATGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (31 bp):
ATGATTGTAGGGTATGAATATGCGAATATGA
Found at i:44381534 original size:17 final size:17
Alignment explanation
Indices: 44381486--44381535 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
44381476 GTAAACGTGG
44381486 ATGATTGTAGGGTATGA
1 ATGATTGTAGGGTATGA
* **
44381503 AT-A-TG-CGAATATGA
1 ATGATTGTAGGGTATGA
44381517 ATGATTGTAGGGTATGA
1 ATGATTGTAGGGTATGA
44381534 AT
1 AT
44381536 ATGCGAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 3 0.12
17 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (17 bp):
ATGATTGTAGGGTATGA
Found at i:44385046 original size:13 final size:13
Alignment explanation
Indices: 44385030--44385061 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
44385020 TTCAACCTAA
44385030 GTGCCTAACCAAT
1 GTGCCTAACCAAT
44385043 GTGCCTAACCAAT
1 GTGCCTAACCAAT
44385056 GTGCCT
1 GTGCCT
44385062 TCATTGGCAC
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:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (13 bp):
GTGCCTAACCAAT
Found at i:44388175 original size:9 final size:10
Alignment explanation
Indices: 44388134--44388176 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
44388124 ATGGGACAAG
44388134 AAATCATTAA
1 AAATCATTAA
* *
44388144 AAATTAGTAA
1 AAATCATTAA
44388154 AAATCATTAA
1 AAATCATTAA
44388164 AAA-CATTAA
1 AAATCATTAA
44388173 AAAT
1 AAAT
44388177 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (10 bp):
AAATCATTAA
Found at i:44388208 original size:16 final size:17
Alignment explanation
Indices: 44388168--44388199 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44388158 CATTAAAAAC
44388168 ATTA-AAAATTTGTAAA
1 ATTATAAAATTTGTAAA
44388184 ATTATAAAA-TTGTAAA
1 ATTATAAAATTTGTAAA
44388200 CTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTATAAAATTTGTAAA
Found at i:44388209 original size:17 final size:17
Alignment explanation
Indices: 44388169--44388217 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
44388159 ATTAAAAACA
44388169 TTAAAAATTTGTAAAATT
1 TTAAAAA-TTGTAAAATT
* *
44388187 AT-AAAATTGTAAACTT
1 TTAAAAATTGTAAAATT
*
44388203 TTAAAAAATGTAAAA
1 TTAAAAATTGTAAAA
44388218 AAGATTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.40
17 14 0.56
18 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (17 bp):
TTAAAAATTGTAAAATT
Found at i:44388524 original size:25 final size:24
Alignment explanation
Indices: 44388496--44388544 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44388486 TAATAATTTG
* *
44388496 ATATAATTATTTAAAAATTATAAAA
1 ATATAATTAATT-AAAATAATAAAA
*
44388521 ATATAGTTAATTAAAATAATAAAA
1 ATATAATTAATTAAAATAATAAAA
44388545 TTACATTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATATAATTAATTAAAATAATAAAA
Found at i:44388851 original size:9 final size:9
Alignment explanation
Indices: 44388839--44388872 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
44388829 CCATTTTACC
44388839 ATTTTTAAT
1 ATTTTTAAT
44388848 ATTTTTAAT
1 ATTTTTAAT
* *
44388857 AGTTTTAAC
1 ATTTTTAAT
44388866 ATTTTTA
1 ATTTTTA
44388873 GTTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:44388981 original size:35 final size:35
Alignment explanation
Indices: 44388941--44389010 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
44388931 CTTTTTCATA
44388941 TTTAAAATA-ATTTTAACAAATTTTTT-TTTCTAAAT
1 TTTAAAATACATTTTAAC-AATTTTTTATTT-TAAAT
* *
44388976 TTTAAAATACTTTTTTACAATTTTTTATTTTAAAT
1 TTTAAAATACATTTTAACAATTTTTTATTTTAAAT
44389011 AAGTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTAAAATACATTTTAACAATTTTTTATTTTAAAT
Found at i:44390015 original size:35 final size:35
Alignment explanation
Indices: 44389964--44390033 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
44389954 AAAAATTGGT
*
44389964 GTAGTCAAAGAGATTAGTGTTACCAACATACCACG
1 GTAGTCAAAGAAATTAGTGTTACCAACATACCACG
44389999 GTAGTCAAAGAAATTAGTGTTACCAACATACCACG
1 GTAGTCAAAGAAATTAGTGTTACCAACATACCACG
44390034 TCAGCCGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (35 bp):
GTAGTCAAAGAAATTAGTGTTACCAACATACCACG
Found at i:44397911 original size:16 final size:19
Alignment explanation
Indices: 44397880--44397921 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
44397870 TTTTTTGATT
*
44397880 TATTTTTATAAATAT-AGA
1 TATTTTTATAAATATAAAA
44397898 TATTTTT-T-AATATAAAA
1 TATTTTTATAAATATAAAA
44397915 TATTTTT
1 TATTTTT
44397922 GTTTACCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTTTATAAATATAAAA
Found at i:44398062 original size:17 final size:17
Alignment explanation
Indices: 44398040--44398073 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44398030 CTAAACAATT
44398040 GTACTAATTTAGTATTC
1 GTACTAATTTAGTATTC
44398057 GTACTAATTTAGTATTC
1 GTACTAATTTAGTATTC
44398074 TTGATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
GTACTAATTTAGTATTC
Found at i:44398869 original size:6 final size:6
Alignment explanation
Indices: 44398846--44398883 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
44398836 TTTTTATGTA
*
44398846 ATAATT GTAATT -TAAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT AT-AATT ATAATT ATAATT ATAATT AT
44398884 CACAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 1 0.03
6 27 0.93
7 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:44402345 original size:14 final size:14
Alignment explanation
Indices: 44402326--44402352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44402316 TTATCAGCTC
44402326 TTATTATTTTATTA
1 TTATTATTTTATTA
44402340 TTATTATTTTATT
1 TTATTATTTTATT
44402353 TCAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:44407245 original size:27 final size:27
Alignment explanation
Indices: 44407227--44407296 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
44407217 AATGCATGCT
44407227 TTTAATATGTCTTAGTTAATACATATC
1 TTTAATATGTCTTAGTTAATACATATC
* * **
44407254 TTTAATTTGTCTTAGCTTATTACATAAA
1 TTTAATATGTCTTAG-TTAATACATATC
*
44407282 TTTAATATGTTTTAG
1 TTTAATATGTCTTAG
44407297 CTTCAGTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (27 bp):
TTTAATATGTCTTAGTTAATACATATC
Found at i:44410654 original size:15 final size:16
Alignment explanation
Indices: 44410629--44410660 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
44410619 TGAAAATAAA
44410629 ATGAGAAAAGAAAAAT
1 ATGAGAAAAGAAAAAT
44410645 ATGA-AAAAGAAAAAT
1 ATGAGAAAAGAAAAAT
44410660 A
1 A
44410661 ATTTGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
ATGAGAAAAGAAAAAT
Found at i:44417491 original size:22 final size:23
Alignment explanation
Indices: 44417452--44417494 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
44417442 GAAATCCTAC
*
44417452 CCATCCATCCTCTACACTCCACT
1 CCATCCAGCCTCTACACTCCACT
44417475 CCATCCAGCC-CTACACTCCA
1 CCATCCAGCCTCTACACTCCA
44417495 TGTGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.53, G:0.02, T:0.21
Consensus pattern (23 bp):
CCATCCAGCCTCTACACTCCACT
Found at i:44417740 original size:27 final size:27
Alignment explanation
Indices: 44417702--44417754 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
44417692 AGTTATACAT
44417702 CTCATAAGGGCATAATAGTCATTTTAC
1 CTCATAAGGGCATAATAGTCATTTTAC
* * *
44417729 CTCATAGGGGCATATTAGTTATTTTA
1 CTCATAAGGGCATAATAGTCATTTTA
44417755 TTAATTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (27 bp):
CTCATAAGGGCATAATAGTCATTTTAC
Found at i:44426812 original size:15 final size:15
Alignment explanation
Indices: 44426723--44426817 Score: 67
Period size: 15 Copynumber: 6.5 Consensus size: 15
44426713 TTTCTTCTCA
44426723 TCTTTCTCTTCATCT
1 TCTTTCTCTTCATCT
* * *
44426738 TC-TTCTCCCTCAACC
1 TCTTTCT-CTTCATCT
*
44426753 TCTTTCTCTTTATGCT
1 TCTTTCTCTTCAT-CT
* *
44426769 TCTTT-TATT--TTT
1 TCTTTCTCTTCATCT
44426781 TCTTGT-TCTTC-TCT
1 TCTT-TCTCTTCATCT
44426795 TCTTTCTCTTCATCT
1 TCTTTCTCTTCATCT
44426810 TCTTTCTC
1 TCTTTCTC
44426818 CCACAACAGA
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
12 5 0.08
13 6 0.10
14 15 0.24
15 26 0.42
16 10 0.16
ACGTcount: A:0.06, C:0.32, G:0.02, T:0.60
Consensus pattern (15 bp):
TCTTTCTCTTCATCT
Found at i:44428243 original size:30 final size:30
Alignment explanation
Indices: 44428207--44428268 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
44428197 AAAAGTTTAT
44428207 AATAGAATATGTTTTATATTAAGAATAGAA
1 AATAGAATATGTTTTATATTAAGAATAGAA
44428237 AATAGAATATGTTTTATATTAAGAATAGAA
1 AATAGAATATGTTTTATATTAAGAATAGAA
44428267 AA
1 AA
44428269 GCCCAACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (30 bp):
AATAGAATATGTTTTATATTAAGAATAGAA
Found at i:44428712 original size:18 final size:17
Alignment explanation
Indices: 44428682--44428715 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44428672 TTCTTTTATA
*
44428682 TAAAATACTTAAATTTC
1 TAAAATACATAAATTTC
44428699 TAAATATACATAAATTT
1 TAAA-ATACATAAATTT
44428716 TATTATCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATACATAAATTTC
Found at i:44430356 original size:18 final size:18
Alignment explanation
Indices: 44430335--44430385 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
44430325 CATGATGGCT
44430335 TAAATAATATATAAAACA
1 TAAATAATATATAAAACA
*
44430353 TAAAAGAATA-ATAAAACA
1 T-AAATAATATATAAAACA
* *
44430371 CATAATAAGATATAA
1 TA-AATAATATATAA
44430386 TGTATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
19 11 0.42
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (18 bp):
TAAATAATATATAAAACA
Found at i:44433102 original size:176 final size:176
Alignment explanation
Indices: 44432774--44433571 Score: 918
Period size: 176 Copynumber: 4.5 Consensus size: 176
44432764 AATAAGACCG
* * * *
44432774 GCGGCTCAAATCTGCTCCATCACCGATACATGGAGATAAGATCTGC-CATC-CTCAA-CTTACTC
1 GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGAT-T-CACCTCTTTCAATC-TACTC
* * * * *
44432836 CACAACTACTTCGGGAAAT-AGATCTTCAATGTTCAGTCTGCTTCTTTT-CTACCTCAAGAAA-A
63 CGCTACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTT-TTTTGCTACCTC-AGAAAGA
** *
44432898 TAAGACTTCAATCGCCAA-TCTGCTCTCTTGCTACCTCAGAGAGATAAAGCTA
126 TAAGAC-TCAATCTTCAACT-TGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
* * *
44432950 GCGGCTAAAATCTTCTCCATTACCGATACATGGAGATAAGATTCACCTCTTCCAATCTGCTCCGC
1 GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCTCTTTCAATCTACTCCGC
* * *
44433015 TACTACTTAAGGAGATAAAATCTTCAATCTTCAGTCTGCTTTTTTGCTACCTCAGAGAGATAAGA
66 TACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTTTTGCTACCTCAGAAAGATAAGA
* *
44433080 CTCAATCTTCAACTTGCTCTCTTGCTACCTTAGAGAGATAAGGCTT
131 CTCAATCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
* * * ** * **
44433126 GAGGCTTAAATCTGCTCCATTACTGATACATGGAGATAAGATTTGCCTCTTTCGATCTGTTCCGC
1 GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCTCTTTCAATCTACTCCGC
* * * * * *
44433191 TACTGCTTAGGGAGATAAGATATTCAATCTTCAATCTACTTTATTGCTACTTCAGAAAGATAAGA
66 TACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTTTTGCTACCTCAGAAAGATAAGA
* * * *
44433256 CTCAATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATATGGCTT
131 CTCAATCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
* * *
44433302 GGGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCTCTTTCGATCTACTCCGC
1 GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCTCTTTCAATCTACTCCGC
* * *
44433367 TACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCTACTTCAGAAAGATAGGA
66 TACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTTTTGCTACCTCAGAAAGATAAGA
* * * *
44433432 CTCAATCTTCAACATGCTATCTTGCTACCTCAAAGAGATGAGGCTA
131 CTCAATCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
* * * * * *
44433478 GTGG-TAAAATCTGCTCCATT-GC-ATACATGGAGATAAAATTCACCAT-TTTCGATCTGCTCCA
1 GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACC-TCTTTCAATCTACTCCG
* *
44433539 CT-GTAACTTTAGGGAGATAAGATATTCAATCTT
65 CTACT-AC-TTAGGGAGATAAGATCTTCAATCTT
44433572 TACCAATATC
Statistics
Matches: 543, Mismatches: 69, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
172 1 0.00
173 38 0.07
174 27 0.05
175 19 0.03
176 420 0.77
177 38 0.07
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (176 bp):
GCGGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCTCTTTCAATCTACTCCGC
TACTACTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTTTTGCTACCTCAGAAAGATAAGA
CTCAATCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
Found at i:44433264 original size:43 final size:43
Alignment explanation
Indices: 44433214--44433295 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
44433204 GATAAGATAT
* * *
44433214 TCAATCTTCAATCTACTTTATTGCTACTTCAGAAAGATAAGAC
1 TCAATCTTCAACCTACTCTATTGCTACCTCAGAAAGATAAGAC
* *
44433257 TCAATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATA
1 TCAATCTTCAACCTACTCTATTGCTACCTCAGAAAGATA
44433296 TGGCTTGGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.33
Consensus pattern (43 bp):
TCAATCTTCAACCTACTCTATTGCTACCTCAGAAAGATAAGAC
Found at i:44434811 original size:48 final size:49
Alignment explanation
Indices: 44434718--44434944 Score: 354
Period size: 49 Copynumber: 4.7 Consensus size: 49
44434708 TTTATTATTG
* *
44434718 AGTCTCAAAGCACCCTTTGCGGGTTTTCACTTTGGCCTTTTTTTTTGAA
1 AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTTTTTTTGAA
* *
44434767 AGTCTCAAAGCGTCCTTTGCGGTTTTTCACTTTGGTCTTTTTTTTTGAA
1 AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTTTTTTTGAA
*
44434816 AGTCTTAAAGCGCCCTTTGCGGGTTTTCACTTTGG---TTTTTTTTGAA
1 AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTTTTTTTGAA
* *
44434862 AGTCTCAAAGCGCTCTTTGCAGGTTTTCACTTTGGTCTTTTTTTTT-AA
1 AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTTTTTTTGAA
*
44434910 AGTCTCAAAGCGCCCTTTGCGGGTTTTTACTTTGG
1 AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGG
44434945 CTTCCTTCCC
Statistics
Matches: 162, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
46 43 0.27
48 34 0.21
49 85 0.52
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (49 bp):
AGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTTTTTTTGAA
Done.