Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 138 of 196
Found at i:40944448 original size:3 final size:3
Alignment explanation
Indices: 40944435--40944491 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
40944425 TAACACCTTG
40944435 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40944481 AAT AAT AAT AA
1 AAT AAT AAT AA
40944492 AAGAGAACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40945586 original size:85 final size:85
Alignment explanation
Indices: 40945427--40945591 Score: 251
Period size: 85 Copynumber: 1.9 Consensus size: 85
40945417 ATTCAAATCC
* * * *
40945427 ATGCTGAAGAACTTTGCATGCCTTAAATACAAGGCTAATAAGACCCCAACAGCAAAAAGAGAAAG
1 ATGCTAAAGAACTTTGCATACCTTAAATACAAGGCTAATAAGACCCCAACACCAAAAAGAGAAAA
*
40945492 ACGGTATCACAAAATTGGAT
66 ACGGCATCACAAAATTGGAT
40945512 ATGCTAAAGAACTTTGCATACCTTAAATACAAGGCTAATAGAGACCCCAACACCAAAAAG-GAAA
1 ATGCTAAAGAACTTTGCATACCTTAAATACAAGGCTAATA-AGACCCCAACACCAAAAAGAGAAA
* *
40945576 AATGGCATCACGAAAT
65 AACGGCATCACAAAAT
40945592 CAGCTATGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 54 0.75
86 18 0.25
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (85 bp):
ATGCTAAAGAACTTTGCATACCTTAAATACAAGGCTAATAAGACCCCAACACCAAAAAGAGAAAA
ACGGCATCACAAAATTGGAT
Found at i:40953155 original size:20 final size:20
Alignment explanation
Indices: 40953130--40953167 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40953120 ATAATTATAT
*
40953130 TAATTATATATGTTAAATAA
1 TAATTATATATATTAAATAA
40953150 TAATTATATATATTAAAT
1 TAATTATATATATTAAAT
40953168 TACTAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAATTATATATATTAAATAA
Found at i:40953311 original size:39 final size:39
Alignment explanation
Indices: 40953268--40953376 Score: 157
Period size: 39 Copynumber: 2.8 Consensus size: 39
40953258 AAAAATTATA
*
40953268 TTTAATACAATAAAAAAATTATTATATTTA-TTTGTGTTT
1 TTTAATACAATAAAAAATTTATTATATTTATTTTG-GTTT
*
40953307 TTTAATACAATAAAACATTTATTATATTTATTTTGGTTT
1 TTTAATACAATAAAAAATTTATTATATTTATTTTGGTTT
* * *
40953346 TTTAATATAATAAAATATTTATCATATTTAT
1 TTTAATACAATAAAAAATTTATTATATTTAT
40953377 GGTAATTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 60 0.94
40 4 0.06
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTAATACAATAAAAAATTTATTATATTTATTTTGGTTT
Found at i:40953394 original size:39 final size:38
Alignment explanation
Indices: 40953268--40953391 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 38
40953258 AAAAATTATA
*
40953268 TTTAATACAATAAAAAAATTATTATATTTATTTGTGTTT
1 TTTAATACAATAAAAAATTTATTATATTTA-TTGTGTTT
* *
40953307 TTTAATACAATAAAACATTTATTATATTTATTTTGGTTT
1 TTTAATACAATAAAAAATTTATTATATTTATTGT-GTTT
* * * * *
40953346 TTTAATATAATAAAATATTTATCATATTTATGGTAATTT
1 TTTAATACAATAAAAAATTTATTATATTTATTGT-GTTT
40953385 TTTAATA
1 TTTAATA
40953392 TAAATACTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 3 0.04
39 71 0.96
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (38 bp):
TTTAATACAATAAAAAATTTATTATATTTATTGTGTTT
Found at i:40967039 original size:31 final size:31
Alignment explanation
Indices: 40966975--40967041 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
40966965 AACATCACAA
* *
40966975 TGACTTAAATAGAAACTTTTGAATAGTTGAG
1 TGACTTAAATAGAAACTTTAGAATAATTGAG
* *
40967006 TGACTTAAAT-GAAAACTTTAGCATAATTTAG
1 TGACTTAAATAG-AAACTTTAGAATAATTGAG
40967037 TGACT
1 TGACT
40967042 ATTTTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAGAAACTTTAGAATAATTGAG
Found at i:40969206 original size:22 final size:19
Alignment explanation
Indices: 40969162--40969211 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
40969152 TGCTCAATCT
40969162 CTTTT-TTTTTTTGTTTTA
1 CTTTTGTTTTTTTGTTTTA
*
40969180 ATTTTGTTTTTATTGTTTTA
1 CTTTTGTTTTT-TTGTTTTA
40969200 TCCTTTTGTTTT
1 --CTTTTGTTTT
40969212 GTAGTTCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 5 0.19
20 8 0.31
22 9 0.35
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (19 bp):
CTTTTGTTTTTTTGTTTTA
Found at i:40976611 original size:11 final size:11
Alignment explanation
Indices: 40976597--40976623 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40976587 GATTTTATCT
40976597 TTTTTTTTTTG
1 TTTTTTTTTTG
40976608 TTTTTTTTTTG
1 TTTTTTTTTTG
40976619 TTTTT
1 TTTTT
40976624 GCTTTGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:40980819 original size:37 final size:37
Alignment explanation
Indices: 40980772--40980844 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
40980762 CATGATTTAA
40980772 ACTTACGTTCTTCTTTACGAGTACAATTTACTTTACT
1 ACTTACGTTCTTCTTTACGAGTACAATTTACTTTACT
* * * * *
40980809 ACTTATGTTCTTCTTTATGTGTATAATTTAGTTTAC
1 ACTTACGTTCTTCTTTACGAGTACAATTTACTTTAC
40980845 CACTACACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (37 bp):
ACTTACGTTCTTCTTTACGAGTACAATTTACTTTACT
Found at i:40982955 original size:11 final size:11
Alignment explanation
Indices: 40982939--40982963 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40982929 GGCCGCGATT
40982939 TTATAAAAAAA
1 TTATAAAAAAA
40982950 TTATAAAAAAA
1 TTATAAAAAAA
40982961 TTA
1 TTA
40982964 AGCTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TTATAAAAAAA
Found at i:40983031 original size:21 final size:22
Alignment explanation
Indices: 40982991--40983036 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
40982981 TGGCCAGTAC
*
40982991 AAATAACAAAAACAATAGCA-A
1 AAATAACAAAAACAACAGCAGA
40983012 AAATAACAACAAA-AACAGCAGA
1 AAATAACAA-AAACAACAGCAGA
40983034 AAA
1 AAA
40983037 ATAATAGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.72, C:0.15, G:0.07, T:0.07
Consensus pattern (22 bp):
AAATAACAAAAACAACAGCAGA
Found at i:40983596 original size:28 final size:27
Alignment explanation
Indices: 40983545--40983597 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40983535 TTTGACTCTA
* *
40983545 ATTTTTTTTTTAAATTTCTCTCAATTT
1 ATTTATTTTTTAAATTTATCTCAATTT
*
40983572 ATTTATTTTTTAACTTTATCGTCAAT
1 ATTTATTTTTTAAATTTATC-TCAAT
40983598 ATGCTTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTATTTTTTAAATTTATCTCAATTT
Found at i:40983708 original size:14 final size:11
Alignment explanation
Indices: 40983672--40983704 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
40983662 CTCAACACCA
40983672 AAATTGAGAGG
1 AAATTGAGAGG
40983683 AAATTGAGAGG
1 AAATTGAGAGG
40983694 AAATTTGAGAG
1 AAA-TTGAGAG
40983705 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:40986398 original size:68 final size:68
Alignment explanation
Indices: 40986280--40986413 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 68
40986270 TATTGAAGTA
* * * ** ** * *
40986280 AATTAGTGCCAACACACATCATAACAGGTATTATATCAATGATTTTAACTCAGACAATTTTTAAA
1 AATTACTGCCAACACACAGCACAACACCTATTATATCAATGATTCAAACTCAAACAATTTCTAAA
40986345 AAT
66 AAT
*
40986348 AATTACTGCCAACACACAGCACAACACCTATTATATCAATGATTCAAACTCAAATAATTTCTAAA
1 AATTACTGCCAACACACAGCACAACACCTATTATATCAATGATTCAAACTCAAACAATTTCTAAA
40986413 A
66 A
40986414 GAAAATAACC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (68 bp):
AATTACTGCCAACACACAGCACAACACCTATTATATCAATGATTCAAACTCAAACAATTTCTAAA
AAT
Found at i:40987039 original size:22 final size:24
Alignment explanation
Indices: 40986982--40987048 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
40986972 ATGAATTATA
40986982 AAAAAATATATTTATATTAAAACGTT
1 AAAAAATATATTTATATT-AAAC-TT
** *
40987008 AAAAGTTATATTTATATT-GA-TT
1 AAAAAATATATTTATATTAAACTT
*
40987030 AAAAAATATATTGATATTA
1 AAAAAATATATTTATATTA
40987049 GCCGTTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 17 0.50
24 1 0.03
26 16 0.47
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (24 bp):
AAAAAATATATTTATATTAAACTT
Found at i:41001605 original size:13 final size:13
Alignment explanation
Indices: 41001587--41001616 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41001577 AGCCCAAACT
41001587 CAATTACCCAACC
1 CAATTACCCAACC
41001600 CAATTACCCAACC
1 CAATTACCCAACC
41001613 CAAT
1 CAAT
41001617 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:41001770 original size:9 final size:9
Alignment explanation
Indices: 41001758--41001816 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
41001748 AATAAAAAAA
41001758 AATTCGGGT
1 AATTCGGGT
41001767 AATTCGGGT
1 AATTCGGGT
* **
41001776 ATTTTTTGGT
1 A-ATTCGGGT
*
41001786 AATTCGGTT
1 AATTCGGGT
*
41001795 AATTCGGTT
1 AATTCGGGT
41001804 AATTCGGGT
1 AATTCGGGT
41001813 AATT
1 AATT
41001817 GTTAACCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 35 0.85
10 6 0.15
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (9 bp):
AATTCGGGT
Found at i:41002716 original size:2 final size:2
Alignment explanation
Indices: 41002709--41002737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41002699 ACATCATAAT
41002709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41002738 GAATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41003113 original size:16 final size:13
Alignment explanation
Indices: 41003080--41003104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41003070 TGTTTGACAG
41003080 ATTTTCTGAAAAT
1 ATTTTCTGAAAAT
41003093 ATTTTCTGAAAA
1 ATTTTCTGAAAA
41003105 AGTTATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTCTGAAAAT
Found at i:41003560 original size:13 final size:13
Alignment explanation
Indices: 41003542--41003572 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
41003532 ATTCTTTCTC
41003542 TATTTATGAAGTT
1 TATTTATGAAGTT
41003555 TATTTATGAAGTT
1 TATTTATGAAGTT
41003568 TATTT
1 TATTT
41003573 GTACAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:41011272 original size:3 final size:3
Alignment explanation
Indices: 41011264--41011296 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41011254 CTTTAATTAC
41011264 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41011297 TTCTTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41016901 original size:22 final size:21
Alignment explanation
Indices: 41016875--41016918 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41016865 ACAAAAGAAA
41016875 ATGTTT-TACAAACAAGACAAAG
1 ATGTTTCT-CAAACAAGA-AAAG
*
41016897 ATGTTTCTGAAACAAGAAAAG
1 ATGTTTCTCAAACAAGAAAAG
41016918 A
1 A
41016919 CATTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 14 0.70
23 1 0.05
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (21 bp):
ATGTTTCTCAAACAAGAAAAG
Found at i:41017930 original size:13 final size:13
Alignment explanation
Indices: 41017912--41017959 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
41017902 AACTTTGAAA
41017912 TTTAGGGTTTGGG
1 TTTAGGGTTTGGG
* * *
41017925 TTTAGGATTTAGA
1 TTTAGGGTTTGGG
*
41017938 TTTTGGGTTTGGG
1 TTTAGGGTTTGGG
*
41017951 TTTGGGGTT
1 TTTAGGGTT
41017960 ACAAGTTATA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (13 bp):
TTTAGGGTTTGGG
Found at i:41018567 original size:29 final size:29
Alignment explanation
Indices: 41018501--41018567 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
41018491 AAGTTTGATG
*
41018501 TGTATAATTACATTAAATTAAAATTTATA
1 TGTATAATTACATTAAATTAAAAATTATA
* * *
41018530 TATACAATTATATCCTAAA-TAAAAATTA-A
1 TGTATAATTACAT--TAAATTAAAAATTATA
41018559 TGTATAATT
1 TGTATAATT
41018568 TTTTAAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
29 18 0.60
30 8 0.27
31 4 0.13
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (29 bp):
TGTATAATTACATTAAATTAAAAATTATA
Found at i:41026787 original size:26 final size:26
Alignment explanation
Indices: 41026718--41026787 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
41026708 AGAACTTGAA
*
41026718 AATATATAAAATT-TATTATAAAATG
1 AATATATAAAATTAAATTATAAAATG
41026743 ACATA-A-AAAATATAAATTATTAAAA-G
1 A-ATATATAAAAT-TAAATTA-TAAAATG
*
41026769 AATATATAAAATTACATTA
1 AATATATAAAATTAAATTA
41026788 AGGCTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
24 5 0.14
25 6 0.16
26 16 0.43
27 10 0.27
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (26 bp):
AATATATAAAATTAAATTATAAAATG
Found at i:41028432 original size:20 final size:20
Alignment explanation
Indices: 41028407--41028446 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41028397 CGTAAAATGA
*
41028407 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
41028427 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
41028447 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:41028436 original size:34 final size:35
Alignment explanation
Indices: 41028392--41028458 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41028382 CAGTAAAATA
*
41028392 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
41028426 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
41028459 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:41028462 original size:14 final size:15
Alignment explanation
Indices: 41028386--41028462 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41028376 GATTGCCAGT
* *
41028386 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
41028400 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
41028414 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
41028434 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
41028449 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
41028463 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:41032642 original size:3 final size:3
Alignment explanation
Indices: 41032634--41032719 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
41032624 AAACTATCGT
*
41032634 ATA ATA AT- ATG ATAA ATA A-A ATA AT- ATA ATA ATA ATA GA-A ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * *
41032677 ATA AGA ATA ATA ATA ATA ATGA ATG ATA AT- ATA TTA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
41032720 GAAGAAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
2 11 0.16
3 50 0.75
4 6 0.09
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:41032659 original size:20 final size:21
Alignment explanation
Indices: 41032634--41032691 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
41032624 AAACTATCGT
*
41032634 ATAATAAT-ATGATAAATA-AA
1 ATAATAATAATAAT-AATAGAA
41032654 ATAAT-ATAATAATAATAGAA
1 ATAATAATAATAATAATAGAA
*
41032674 ATAATAAGAATAATAATA
1 ATAATAATAATAATAATA
41032692 ATAATGAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 6 0.18
20 16 0.48
21 11 0.33
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
ATAATAATAATAATAATAGAA
Found at i:41033750 original size:20 final size:20
Alignment explanation
Indices: 41033722--41033764 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41033712 GCTGAAAATG
*
41033722 GGTTGGGGTGTTTTGGGC-TA
1 GGTTGGGGT-ATTTGGGCTTA
*
41033742 GGTTTGGGTATTTGGGCTTA
1 GGTTGGGGTATTTGGGCTTA
41033762 GGT
1 GGT
41033765 AGGTTATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.07, C:0.05, G:0.47, T:0.42
Consensus pattern (20 bp):
GGTTGGGGTATTTGGGCTTA
Found at i:41034152 original size:44 final size:42
Alignment explanation
Indices: 41034055--41034296 Score: 211
Period size: 44 Copynumber: 5.7 Consensus size: 42
41034045 ATGATTTATG
* * * **
41034055 TCTGCTCCACTGCAAGTTTAGGGAGATAAGAC-TGGATGCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGTTTTAA
* *
41034096 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGGTTTTAA
* * **
41034140 TCTGCTCCACTGCAACTTTAGGGAGATAGGA-TTGGCTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGG-TT-TT-AA
* * * * ***
41034184 TGTGTTCCACTACAACTTCAGGGAGATAAGAC-TGGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGTTTTAA
* *
41034225 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGGTTTTAA
*
41034269 TCCGCTCCACTGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
41034297 GGATTGGCTT
Statistics
Matches: 156, Mismatches: 35, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
41 56 0.36
42 5 0.03
43 3 0.02
44 92 0.59
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (42 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGTTTTAA
Found at i:41034254 original size:129 final size:129
Alignment explanation
Indices: 41034060--41034310 Score: 439
Period size: 129 Copynumber: 1.9 Consensus size: 129
41034050 TTATGTCTGC
* * *
41034060 TCCACTGCAAGTTTAGGGAGATAAGACTGGATGCAATCTGCTCTACTGCAACTTCAGAGAGATAA
1 TCCACTACAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTGCAACTTCAGAGAGATAA
* *
41034125 GATCTATGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTGTGTGT
66 GATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCTGTGTGT
*
41034189 TCCACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 TCCACTACAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTGCAACTTCAGAGAGATAA
*
41034254 GATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTC
66 GATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTC
41034311 AATCTGTTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 115 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (129 bp):
TCCACTACAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTGCAACTTCAGAGAGATAA
GATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCTGTGTGT
Found at i:41034325 original size:44 final size:44
Alignment explanation
Indices: 41034055--41034327 Score: 163
Period size: 44 Copynumber: 6.3 Consensus size: 44
41034045 ATGATTTATG
* * * * * *
41034055 TCTGCTCCACTGCAAGTTTAGGGAGATAAGACTGG---ATGCAA
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTCAA
* * *
41034096 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG-TT-TT-AA
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGA--T-TGGCTTCTTCAA
* * * **
41034140 TCTGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTG
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTCAA
* * * * * *
41034184 TGTGTTCCACTACAACTTCAGGGAGATAAGACTGG---ATGCGA
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTCAA
* * * *
41034225 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TT-AA
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGAT-TG-GCTTCTTCAA
* * *
41034269 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCAA
1 TCTGTTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTCAA
**
41034313 TCTGTTTAACTGCAA
1 TCTGTTCCACTGCAA
41034328 TGTCGAGAAA
Statistics
Matches: 178, Mismatches: 39, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
41 58 0.33
42 8 0.04
43 7 0.04
44 103 0.58
45 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (44 bp):
TCTGTTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTCAA
Found at i:41034452 original size:100 final size:100
Alignment explanation
Indices: 41034307--41035622 Score: 1704
Period size: 100 Copynumber: 13.1 Consensus size: 100
41034297 GGATTGGCTT
* * * ** * * * **
41034307 CTTCAATCTGTTTAACTGCAATGTCGAGAAAGTAAAATTCGCCGTCGTAGCTTCAATCTGTTCTG
1 CTTCAATCT-TTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* *
41034372 CTGCACTGCCTGGG-GAGTAAGATTCGCCGTTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * * * * *
41034407 CTTTAATCTTTTAAATTGCAATGTCGAGGAAGTGAGTTTCACCGTCGTAGCTTCAATCTATTTCG
1 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* *
41034472 CTGCATCGCCT-GGAAAGTAAGATTCGCCATTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * * * * **
41034507 CTTCAATCTTTTAAATTGTAACGTCGGGGAAGTGAGATACGCCGTCGTAGCTTCAATTTGTTCTG
1 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
** *
41034572 CTATATCGCCTGGG-AAGTAAGATTCGCCGTTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * **
41034607 CTTCAATCTTTTAAATTGTAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTCTG
1 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* * *
41034672 CTGCACTGCCT-GGAGAGTAAGATTCGCCGTTGTAG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * **
41034707 CTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCTG
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
*
41034772 CTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * * *
41034808 CTTCAATTTTTTGAATTACAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCA
41034873 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
65 CTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * *
41034909 CCTCAATCTTTTAATTGCAATGTTGGGGAAGCGAGATTCACTGTTGTAGCTTCAATTTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
41034974 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * *
41035009 CTTCAATCTTTTAATTGCAATGTCGAGGAAACGAGATTCGCCATTGTAGCTTTAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* *
41035074 TGCACCGCCTGGGAAAGTAAGATCCGCCGTTATGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* ***
41035109 CTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTTGTCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* *
41035174 TGTACCGCCTGGAAAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * *
41035209 CTTCAATCTTTTAATTGCAATGTCGAGGAAGCGAGATTCATCGTTGTAGCTTCAATTTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* * * *
41035274 TGCACCGCCTAGAAAAGTAAGATCCGCTGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* **
41035309 CTTCAATATTTTAATTGCAATGTCGAAGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
* *
41035374 TGCACCGCCTGGGAAAGTAAGATCCGCCGTTATGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * *
41035409 CTTCAATCTTTTAATTACAATATCGGGGAAGCGAGATTCACCATTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
41035474 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
* * * * *
41035509 CCTCAATCTTTTAATTGCAATATCGGGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
41035574 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
*
41035609 CTTCAATATTTTAA
1 CTTCAATCTTTTAA
41035623 ATTACAAACT
Statistics
Matches: 1082, Mismatches: 127, Indels: 14
0.88 0.10 0.01
Matches are distributed among these distances:
99 7 0.01
100 953 0.88
101 122 0.11
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTGTTCCAC
TGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTGG
Found at i:41034955 original size:49 final size:49
Alignment explanation
Indices: 41034391--41035622 Score: 416
Period size: 50 Copynumber: 24.6 Consensus size: 49
41034381 CTGGGGAGTA
* * * *
41034391 AGATTCGCCGTTGTGGCTTTAATCTTTTAAATTGCAATGTCGAGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGTTGGGGAAGCG
* * * * *** * * **
41034441 AGTTTCACCGTCGTAGCTTCAATCTATTTCGCTGC-ATCGCCT-GGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAAT-G-TTGGGGAAGCG
* * * * *
41034491 AGATTCGCCATTGTGGCTTCAATCTTTTAAATTGTAACGTCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGTTGGGGAAGCG
* * * * * **
41034541 AGATACGCCGTCGTAGCTTCAAT-TTGTT--CTGCTATATCGCCT-GGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTT-TTAATTGC-A-AT-G-TTGGGGAAGCG
* * * *
41034591 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGTAATGTCGAGGAAGCA
1 AGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGTTGGGGAAGCG
* * ** * * * **
41034641 AGATTCACCGTTGTAGCTTCAATCTATTCT-GCTGCACTGCCTGGAG-AGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TT-TAATTGCAATG-TTGGGGAAGCG
* * * * *
41034691 AGATTCGCCGTTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACA
1 AGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATGTTGGGGAAGCG
* ** ** * * **
41034741 AGATTCGCCGTTGTAGCTTCAATCTGTTCT-GCTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TT-TAATTGCAATG-TTGGGGAAGCG
* * * * *
41034792 AGATTCACCGTTGTGGCTTCAATTTTTTGAATTACAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGTTGGGGAAGCG
* * * * **** ** * * **
41034842 AGATTCACCATCGTAGCTTCAATCTGTTCCGCTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
*
41034893 AGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTTGGGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* * * * * ** * * **
41034942 AGATTCACTGTTGTAGCTTCAAT-TTGTTCCACTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTT-TT-AATTGCAATG-TTGGGGAAGCG
* * *
41034993 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGAGGAAACG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* * * ** * ** * * **
41035042 AGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
* * * *
41035093 AGATCCGCCGTTATGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* * * ** * * ** * ** **
41035142 AGATTTGTCGTTGTAGCTTCAATCTGTTCCACTGTACCGCCTGGAAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
* *
41035193 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGAGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
** * * * ** * * ** **
41035242 AGATTCATCGTTGTAGCTTCAAT-TTGTTCCACTGCACCGCCTAGAAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTT-TT-AATTGCAATG-TTGGGGAAGCG
* * * * **
41035293 AGATCCGCTGTTGTGGCTTCAATATTTTAATTGCAATGTCGAAGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* * ** * ** * * **
41035342 AGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
* * * * *
41035393 AGATCCGCCGTTATGGCTTCAATCTTTTAATTACAATATCGGGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* * * ** * ** * * **
41035442 AGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
* * * *
41035493 AGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATATCGGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
* ** * ** * * **
41035542 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATG-TTGGGGAAGCG
*
41035593 AGATTCGCCGTTGTGGCTTCAATATTTTAA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAA
41035623 ATTACAAACT
Statistics
Matches: 818, Mismatches: 317, Indels: 94
0.67 0.26 0.08
Matches are distributed among these distances:
47 2 0.00
48 5 0.01
49 201 0.25
50 341 0.42
51 261 0.32
52 6 0.01
53 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
AGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGGAAGCG
Found at i:41040519 original size:14 final size:14
Alignment explanation
Indices: 41040502--41040529 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41040492 AAAGAAACCG
41040502 TATAAATATATATA
1 TATAAATATATATA
41040516 TATAAATATATATA
1 TATAAATATATATA
41040530 CATATATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATATATATA
Found at i:41040668 original size:3 final size:3
Alignment explanation
Indices: 41040660--41040739 Score: 64
Period size: 3 Copynumber: 27.7 Consensus size: 3
41040650 AAACTATCGT
*
41040660 ATA ATA AT- ATG ATAA ATA A-A ATA AT- ATA ATA ATA GA-A ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
41040703 ATA ATA ATA ATA ATGA ATG ATA AT- ATA TTA A-A ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
41040740 GAAGAAAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
2 11 0.17
3 46 0.73
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41040684 original size:17 final size:17
Alignment explanation
Indices: 41040662--41040711 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
41040652 ACTATCGTAT
*
41040662 AATAATATGATAAATA-A
1 AATAATATAAT-AATAGA
41040679 AATAATATAATAATAGA
1 AATAATATAATAATAGA
41040696 AATAATAATAATAATA
1 AATAAT-ATAATAATA
41040712 ATAATGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 4 0.13
17 17 0.57
18 9 0.30
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
AATAATATAATAATAGA
Found at i:41041392 original size:21 final size:21
Alignment explanation
Indices: 41041367--41041407 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
41041357 CCACAAACCC
41041367 CTGGAAACGAAGGGAAACCGA
1 CTGGAAACGAAGGGAAACCGA
41041388 CTGGAAACGAAGGGAAACCG
1 CTGGAAACGAAGGGAAACCG
41041408 TTCGGTTCCT
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:0.41, C:0.20, G:0.34, T:0.05
Consensus pattern (21 bp):
CTGGAAACGAAGGGAAACCGA
Found at i:41041960 original size:204 final size:204
Alignment explanation
Indices: 41041610--41042017 Score: 762
Period size: 204 Copynumber: 2.0 Consensus size: 204
41041600 CCCCTTACAA
*
41041610 TTTGTTTTGAATGGCCTTTTATAGCCATTTTTTCAATGTTTTTATATTATTTCTTGTCCTTTCTT
1 TTTGTTTTGAATGGCCTTTTATAGCCATTTTTACAATGTTTTTATATTATTTCTTGTCCTTTCTT
41041675 GCAGGCCACTTGAAGGCGGTGGAGTAGGTGGGCAGAGACGTGACGTGCGGCGGCCAACAGAGCAA
66 GCAGGCCACTTGAAGGCGGTGGAGTAGGTGGGCAGAGACGTGACGTGCGGCGGCCAACAGAGCAA
*
41041740 CAGTGGCAGGGCAAGTGGGCGACCCTAGGTGTGGCGCACCTAGGGTTAAGGTTACTGTTTTTTTG
131 CAGTGGCAGGGCAAGTGGGCGACCCTAGGTGCGGCGCACCTAGGGTTAAGGTTACTGTTTTTTTG
*
41041805 TTGAAAATG
196 CTGAAAATG
41041814 TTTGTTTTGAATGGCCTTTTATAGCCATTTTTACAATGTTTTTATATTATTTCTTGTCCTTTCTT
1 TTTGTTTTGAATGGCCTTTTATAGCCATTTTTACAATGTTTTTATATTATTTCTTGTCCTTTCTT
**
41041879 GCAGGCCACTTGAAGGCGGTGGAGTAGGTGGGCAGAGACGTGACGTGCGGCGGCCGGCAGAGCAA
66 GCAGGCCACTTGAAGGCGGTGGAGTAGGTGGGCAGAGACGTGACGTGCGGCGGCCAACAGAGCAA
*
41041944 CGGTGGCAGGGCAAGTGGGCGACCCTAGGTGCGGCGCACCTAGGGTTAAGGTTACTGTTTTTTTG
131 CAGTGGCAGGGCAAGTGGGCGACCCTAGGTGCGGCGCACCTAGGGTTAAGGTTACTGTTTTTTTG
41042009 CTGAAAATG
196 CTGAAAATG
41042018 GGTTGGGTGT
Statistics
Matches: 198, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
204 198 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (204 bp):
TTTGTTTTGAATGGCCTTTTATAGCCATTTTTACAATGTTTTTATATTATTTCTTGTCCTTTCTT
GCAGGCCACTTGAAGGCGGTGGAGTAGGTGGGCAGAGACGTGACGTGCGGCGGCCAACAGAGCAA
CAGTGGCAGGGCAAGTGGGCGACCCTAGGTGCGGCGCACCTAGGGTTAAGGTTACTGTTTTTTTG
CTGAAAATG
Found at i:41046197 original size:19 final size:17
Alignment explanation
Indices: 41046164--41046196 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41046154 ATATATGTTA
41046164 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
41046181 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
41046197 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:41052273 original size:31 final size:32
Alignment explanation
Indices: 41052235--41052296 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
41052225 GGCCCATTTT
41052235 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTAAAAAATTAAAAAAAG
* *
41052266 TATTTTAAAAATATTTTAAAATTTAAAAAAA
1 TATTTTAAAAATATTTAAAAAATTAAAAAAA
41052297 TTAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (32 bp):
TATTTTAAAAATATTTAAAAAATTAAAAAAAG
Found at i:41052275 original size:11 final size:11
Alignment explanation
Indices: 41052235--41052367 Score: 92
Period size: 11 Copynumber: 12.9 Consensus size: 11
41052225 GGCCCATTTT
41052235 TATTTT-AAAA
1 TATTTTAAAAA
41052245 -ATTTTAAAAA
1 TATTTTAAAAA
**
41052255 -ATTAAAAAAA
1 TATTTTAAAAA
41052265 GTATTTTAAAAA
1 -TATTTTAAAAA
41052277 TATTTT--AAA
1 TATTTTAAAAA
41052286 -A-TTTAAAAA
1 TATTTTAAAAA
* **
41052295 AATTAAAAAAA
1 TATTTTAAAAA
41052306 GTATTTTAAAAA
1 -TATTTTAAAAA
41052318 TATTTT--AAA
1 TATTTTAAAAA
41052327 -A-TTTAAAAA
1 TATTTTAAAAA
**
41052336 -ATTAAAAAAA
1 TATTTTAAAAA
41052346 GTATTTTAAAAA
1 -TATTTTAAAAA
41052358 TATTTTAAAA
1 TATTTTAAAA
41052368 TTAAAAAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 18 0.19
10 19 0.20
11 28 0.29
12 24 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:41052303 original size:40 final size:41
Alignment explanation
Indices: 41052235--41052377 Score: 254
Period size: 41 Copynumber: 3.5 Consensus size: 41
41052225 GGCCCATTTT
*
41052235 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
41052277 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
41052318 TATTTTAAAATTT-AAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
41052358 TATTTTAAAA-TTAAAAAAAT
1 TATTTTAAAATTTAAAAAAAT
41052378 AAATATATTT
Statistics
Matches: 99, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
39 2 0.02
40 44 0.44
41 47 0.47
42 6 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:41052318 original size:31 final size:32
Alignment explanation
Indices: 41052283--41052376 Score: 84
Period size: 40 Copynumber: 2.7 Consensus size: 32
41052273 AAAATATTTT
41052283 AAAATTTAAAAAAATTAAAAAAAGTATTTTAA
1 AAAATTTAAAAAAATTAAAAAAAGTATTTTAA
41052315 AAATATTTTAAAATTTAAAAAATTAAAAAAAGTATTTTAA
1 AAA-A-TTT---A---AAAAAATTAAAAAAAGTATTTTAA
*
41052355 AAATATTT--TAAAATTAAAAAAA
1 AAA-ATTTAAAAAAATTAAAAAAA
41052377 TAAATATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
31 13 0.25
32 3 0.06
33 1 0.02
34 3 0.06
37 1 0.02
39 3 0.06
40 29 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (32 bp):
AAAATTTAAAAAAATTAAAAAAAGTATTTTAA
Found at i:41053670 original size:38 final size:37
Alignment explanation
Indices: 41053617--41053720 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 37
41053607 CATTTAATTA
*
41053617 ATTTTTAAAATTTAAAAAAATTAA-AAACT-ATAAAAACT
1 ATTTTTAAAAATTAAAAAAATTAATAAA-TAAT-AAAA-T
*
41053655 ATTTTTAAAAATT--AAAAATTATATTAATAATAAAAT
1 ATTTTTAAAAATTAAAAAAATTA-ATAAATAATAAAAT
*
41053691 ATTTTTAAAAATAAAAAAAATTAATTAAAT
1 ATTTTTAAAAATTAAAAAAATTAA-TAAAT
41053721 GTTGATGTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
36 21 0.38
37 7 0.12
38 28 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (37 bp):
ATTTTTAAAAATTAAAAAAATTAATAAATAATAAAAT
Found at i:41053698 original size:17 final size:17
Alignment explanation
Indices: 41053649--41053706 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
41053639 AAAAACTATA
41053649 AAAACTATTTTTAAAAATT
1 AAAA-TATTTTTAAAAA-T
*
41053668 AAAA-ATTATATTAATAAT
1 AAAATATT-T-TTAAAAAT
41053686 AAAATATTTTTAAAAAT
1 AAAATATTTTTAAAAAT
41053703 AAAA
1 AAAA
41053707 AAAATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 14 0.41
18 7 0.21
19 13 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATTTTTAAAAAT
Found at i:41053709 original size:20 final size:20
Alignment explanation
Indices: 41053637--41053709 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
41053627 TTTAAAAAAA
*
41053637 TTAAAAACTATAAAAACTATTT
1 TTAAAAA-TA-AAAAAATATTT
* * *
41053659 TTAAAAATTAAAAATTA-TA
1 TTAAAAATAAAAAAATATTT
*
41053678 TT---AATAATAAAATATTT
1 TTAAAAATAAAAAAATATTT
41053695 TTAAAAATAAAAAAA
1 TTAAAAATAAAAAAA
41053710 ATTAATTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
16 9 0.23
17 3 0.08
19 3 0.08
20 16 0.41
21 1 0.03
22 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAATAAAAAAATATTT
Found at i:41056617 original size:21 final size:19
Alignment explanation
Indices: 41056593--41056631 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
41056583 GCGACGAAGA
41056593 ATATTTATAGAAAAAAAAAGC
1 ATATTTA-A-AAAAAAAAAGC
41056614 ATATTTAAAAAAAAAAAG
1 ATATTTAAAAAAAAAAAG
41056632 TTGTGATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (19 bp):
ATATTTAAAAAAAAAAAGC
Found at i:41060232 original size:30 final size:30
Alignment explanation
Indices: 41060196--41060254 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
41060186 CCATAATATT
* *
41060196 ATATTATTTTGTTTAATTTATTTGGTTAAG
1 ATATTATCTTGTTTAATTCATTTGGTTAAG
*
41060226 ATATTATCTTGTTTAATTCATTTGTTTAA
1 ATATTATCTTGTTTAATTCATTTGGTTAA
41060255 AATGTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.59
Consensus pattern (30 bp):
ATATTATCTTGTTTAATTCATTTGGTTAAG
Found at i:41064749 original size:42 final size:42
Alignment explanation
Indices: 41064710--41064814 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
41064700 CTGAAGAGTC
41064710 AGAGAAACCTG-GTTATAGCACAAAACCACAGCCAGAAGAGGA
1 AGAGAAACCTGAG-TATAGCACAAAACCACAGCCAGAAGAGGA
* * * *
41064752 AGGGAAGCCTGAGTATGGCACTAAACCACAGCCAGAAGAGGA
1 AGAGAAACCTGAGTATAGCACAAAACCACAGCCAGAAGAGGA
* *
41064794 AGA-AAAGCCTGATTATGGCAC
1 AGAGAAA-CCTGAGTATAGCAC
41064815 CAAGCAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.94
43 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (42 bp):
AGAGAAACCTGAGTATAGCACAAAACCACAGCCAGAAGAGGA
Found at i:41064888 original size:165 final size:165
Alignment explanation
Indices: 41064614--41064955 Score: 639
Period size: 165 Copynumber: 2.1 Consensus size: 165
41064604 TCAACCAACA
41064614 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
1 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
* *
41064679 AAGACAAGGAGAAGGCCATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
66 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACAACAGCCA
41064744 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
131 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
41064779 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
1 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
* *
41064844 AAGACAAGGAGAAGGCAATGCCTGAGGAGTCAGAGAAGCCTGGTTATAGCACAAAACAACAGCCA
66 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACAACAGCCA
*
41064909 GAAGAGGAAGGGAAGCCTGAGTATGGTACTAAACC
131 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
41064944 ACAGCCAGAAGA
1 ACAGCCAGAAGA
41064956 CAAGGAAAAG
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 172 1.00
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.13
Consensus pattern (165 bp):
ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACAACAGCCA
GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
Found at i:41075187 original size:25 final size:25
Alignment explanation
Indices: 41075141--41075207 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
41075131 GGTTACCTGG
* *
41075141 AAAGCCTTTGTGG-CATATTATCTAT
1 AAAGCCTTTGTGGTGA-ACTATCTAT
*
41075166 AAAGCCTTTGTGGTGAACTATCTGT
1 AAAGCCTTTGTGGTGAACTATCTAT
* *
41075191 AAAACCCTTGTGGTGAA
1 AAAGCCTTTGTGGTGAA
41075208 TTCTCTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (25 bp):
AAAGCCTTTGTGGTGAACTATCTAT
Found at i:41078273 original size:40 final size:39
Alignment explanation
Indices: 41078200--41078276 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
41078190 TGCCAAAAGC
*
41078200 ATATATTTATACTTATCAACCACATGTACCGAATGCACAT
1 ATATATATATACTTATCAACCACATGTA-CGAATGCACAT
41078240 ATATATATATACTTAT-AATCCACACATGT-CGAATGCA
1 ATATATATATACTTATCAA--C-CACATGTACGAATGCA
41078277 TACACATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
39 2 0.06
40 23 0.70
41 1 0.03
42 7 0.21
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (39 bp):
ATATATATATACTTATCAACCACATGTACGAATGCACAT
Found at i:41078521 original size:41 final size:41
Alignment explanation
Indices: 41078464--41078603 Score: 196
Period size: 41 Copynumber: 3.4 Consensus size: 41
41078454 GATTCATCGG
41078464 CACTTAGCCTGCTAGGCTTCTAGCCTGATTCAGTTCACTGC
1 CACTTAGCCTGCTAGGCTTCTAGCCTGATTCAGTTCACTGC
*
41078505 CACTTAGCCTGCTAGGCTTCTAGCCTGATTCAGTTCACTTC
1 CACTTAGCCTGCTAGGCTTCTAGCCTGATTCAGTTCACTGC
* *
41078546 CACTTAGCCTGCTAGGCTT-TAAGCCTGAATTGA-TTCACTGT
1 CACTTAGCCTGCTAGGCTTCT-AGCCTG-ATTCAGTTCACTGC
*
41078587 CAATATA-CCTGCTAGGC
1 CACT-TAGCCTGCTAGGC
41078604 GCTGAGCCTG
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
40 1 0.01
41 84 0.92
42 6 0.07
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (41 bp):
CACTTAGCCTGCTAGGCTTCTAGCCTGATTCAGTTCACTGC
Found at i:41086435 original size:41 final size:41
Alignment explanation
Indices: 41086381--41086502 Score: 163
Period size: 41 Copynumber: 3.0 Consensus size: 41
41086371 TTAATTTAAA
*
41086381 CAGATTCATCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
**
41086423 CAGATCACCGGCACTTAGCCTGCTAGGCTTCTAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* * * * *
41086464 CAGTTCACTGCCACTTAGCTTGCTAGGCTTTAAGCCTGA
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGA
41086503 ATTGATTCAC
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 67 0.94
42 4 0.06
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:41086512 original size:41 final size:40
Alignment explanation
Indices: 41086393--41086532 Score: 142
Period size: 41 Copynumber: 3.4 Consensus size: 40
41086383 GATTCATCGG
* * *
41086393 CACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA-TCACCGG
1 CACTTAGCCTGCTAGGCTTTAAGCCTGATT--GATTCACTGC
*
41086434 CACTTAGCCTGCTAGGCTTCT-AGCCTGATTCAGTTCACTGC
1 CACTTAGCCTGCTAGGCTT-TAAGCCTGATTGA-TTCACTGC
* *
41086475 CACTTAGCTTGCTAGGCTTTAAGCCTGAATTGATTCACTGG
1 CACTTAGCCTGCTAGGCTTTAAGCCTG-ATTGATTCACTGC
*
41086516 CAATATA-CCTGCTAGGC
1 CACT-TAGCCTGCTAGGC
41086533 GCTGAGCCTG
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 76 0.90
42 6 0.07
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (40 bp):
CACTTAGCCTGCTAGGCTTTAAGCCTGATTGATTCACTGC
Found at i:41086541 original size:82 final size:81
Alignment explanation
Indices: 41086393--41086543 Score: 191
Period size: 82 Copynumber: 1.8 Consensus size: 81
41086383 GATTCATCGG
* *
41086393 CACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTCTAGC
1 CACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACCGGCAATTAGCCTGCTAGGCTGCTAGC
41086458 CTGATTCAGTTCACTGC
65 CTGATTCAGTTCACTGC
* * *
41086475 CACTTAGCTTGCTAGGCTTTAAGCCTGAATT-GATTCACTGGCAATATA-CCTGCTAGGC-GCTG
1 CACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCACCGGCAAT-TAGCCTGCTAGGCTGCT-
41086537 AGCCTGA
62 AGCCTGA
41086544 ATACTCAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
81 4 0.07
82 51 0.85
83 5 0.08
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (81 bp):
CACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCACCGGCAATTAGCCTGCTAGGCTGCTAGCC
TGATTCAGTTCACTGC
Found at i:41099771 original size:8 final size:8
Alignment explanation
Indices: 41099758--41099822 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
41099748 CGTGGAGGCA
41099758 AAAAAAAC
1 AAAAAAAC
*
41099766 AAAAAAAT
1 AAAAAAAC
41099774 AAAAAAA-
1 AAAAAAAC
*
41099781 AAAGAATAC
1 AAA-AAAAC
* *
41099790 AAGAAAAT
1 AAAAAAAC
*
41099798 AAAAAAATA
1 AAAAAAA-C
*
41099807 AAAAAAAT
1 AAAAAAAC
41099815 AAAAAAAC
1 AAAAAAAC
41099823 CTCTACCAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 3 0.07
8 33 0.73
9 9 0.20
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.08
Consensus pattern (8 bp):
AAAAAAAC
Found at i:41099796 original size:24 final size:22
Alignment explanation
Indices: 41099757--41099820 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 22
41099747 CCGTGGAGGC
41099757 AAAAAAAACAAAAAAATAAAAA
1 AAAAAAAACAAAAAAATAAAAA
*
41099779 AAAAAGAATACAAGAAAATAAAAA
1 AAAAA-AA-ACAAAAAAATAAAAA
*
41099803 AATAAAAAAAATAAAAAA
1 AA-AAAAAACA-AAAAAA
41099821 ACCTCTACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 5 0.14
23 4 0.11
24 23 0.66
25 3 0.09
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (22 bp):
AAAAAAAACAAAAAAATAAAAA
Found at i:41101267 original size:45 final size:46
Alignment explanation
Indices: 41101202--41101407 Score: 273
Period size: 45 Copynumber: 4.6 Consensus size: 46
41101192 TGAAGTCATC
41101202 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGAAT-GAAG
1 ATAGCAGAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAG-ATCGAAG
*
41101247 GTAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
41101292 ATTGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAGGTAGATCGAAG
1 ATAGCAGAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
41101337 ATAG-AAAGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-CTGAAG
1 ATAGCAGAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
** *
41101382 ATAATAGA-TCTTGCCTTCCTGTATTG
1 ATAGCAGAGTCTTGTCTTCCTGTATTG
41101408 ATGGTGAAGC
Statistics
Matches: 145, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
44 5 0.03
45 137 0.94
46 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (46 bp):
ATAGCAGAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
Found at i:41101515 original size:50 final size:50
Alignment explanation
Indices: 41101461--41102018 Score: 263
Period size: 50 Copynumber: 11.2 Consensus size: 50
41101451 ATTGAAATTG
* *
41101461 CAACGGCGAATCTTACCTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* * * * * ** * * *
41101511 CAACGGTGAATC-T-CGTTCCCCGACATTGTAATTTAAAATATTGAAGCTG
1 CAACGGCGAATCTTAC-TTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
** * * * * * *
41101560 CAATAGTGAATTTTACTTTCCTGGC-GATACAGTGGATCAGATTGAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAG-TGCAATGGAACAGATTGAAGCTA
* ** * ** * *
41101610 CAACGG-TAATC-T-CGTTCCCTAACATTGCAATTTAAAAGATTGAAGCCGA
1 CAACGGCGAATCTTAC-TTCCCTGGCAGTGCAATGGAACAGATTGAAG-CTA
* * * ** * * * * *
41101659 -AATGGCGAATTTTACTTTCCTGGTGGTGTAGTGGAGCAAATTAAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* * * * * ** * *
41101708 CGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* * * * *
41101758 CAACGGTGAATCTTACTTTCCTAGC-GATGCAGTGGATCAGATTGAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAG-TGCAATGGAACAGATTGAAGCTA
* * * * * * * *
41101808 CAACGACAAATCTTA-TTCCCCGACATTGCAAT-TAAAAGGATTGAAGCCA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACA-GATTGAAGCTA
* * * * *
41101857 CAACGGTGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* ** * ** * * * **
41101907 CGACGGCGAATCTTACTTCCCTGATATTGCAATTTAAAATATTAAAGCCG
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* * *
41101957 CAACGACGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
* *
41102007 CGACTGCGAATC
1 CAACGGCGAATC
41102019 GTGTTCCCTG
Statistics
Matches: 343, Mismatches: 149, Indels: 32
0.65 0.28 0.06
Matches are distributed among these distances:
47 1 0.00
48 28 0.08
49 74 0.22
50 236 0.69
51 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
CAACGGCGAATCTTACTTCCCTGGCAGTGCAATGGAACAGATTGAAGCTA
Found at i:41101856 original size:99 final size:99
Alignment explanation
Indices: 41101461--41102039 Score: 574
Period size: 100 Copynumber: 5.8 Consensus size: 99
41101451 ATTGAAATTG
* * * *
41101461 CAACGGCGAATCTTACCTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTCG
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTG
* * **
41101526 TTCCCCGACATTGTAATTTAAAATATTGAAGCTG
66 TTCCCCGACATTGCAATTTAAAAGATTGAAGCCA
** * * * * * * * *
41101560 CAATAGTGAATTTTACTTTCCTGGC-GATACAGTGGATCAGATTGAAGCTACAACGG-TAATCTC
1 CAACGGCGAATCTTACTTCCCTGGCAG-TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTT
**
41101623 GTTCCCTAACATTGCAATTTAAAAGATTGAAGCCGA
65 GTTCCCCGACATTGCAATTTAAAAGATTGAAGCC-A
* * * ** * * * *
41101659 -AATGGCGAATTTTACTTTCCTGGTGGTGTAGTGGAGCAAATTAAAGCTACGACGGCGAATCTTG
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTG
*
41101723 CTTCCCCGACATTGCAATTAAAAAGATTGAAGCCA
66 -TTCCCCGACATTGCAATTTAAAAGATTGAAGCCA
* * * * * * *
41101758 CAACGGTGAATCTTACTTTCCTAGC-GATGCAGTGGATCAGATTGAAGCTACAACGACAAATCTT
1 CAACGGCGAATCTTACTTCCCTGGCAG-TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTT
*
41101822 ATTCCCCGACATTGCAA-TTAAAAGGATTGAAGCCA
65 GTTCCCCGACATTGCAATTTAAAA-GATTGAAGCCA
* * * * * *
41101857 CAACGGTGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTACGACGGCGAATCTTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTT-
* * * * * *
41101922 CTTCCCTGATATTGCAATTTAAAATATTAAAGCCG
65 GTTCCCCGACATTGCAATTTAAAAGATTGAAGCCA
* * * *
41101957 CAACGACGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACGACTGCGAATCGTG
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTG
*
41102022 TTCCCTGACATTGCAATT
66 TTCCCCGACATTGCAATT
41102040 AAGGCCGCAA
Statistics
Matches: 400, Mismatches: 69, Indels: 22
0.81 0.14 0.04
Matches are distributed among these distances:
98 85 0.21
99 151 0.38
100 158 0.40
101 6 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (99 bp):
CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTG
TTCCCCGACATTGCAATTTAAAAGATTGAAGCCA
Found at i:41101938 original size:199 final size:197
Alignment explanation
Indices: 41101461--41102041 Score: 675
Period size: 199 Copynumber: 2.9 Consensus size: 197
41101451 ATTGAAATTG
* * * * *
41101461 CAACGGCGAATCTTACCTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATC-TC
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTC
* * ** * *
41101525 GTTCCCCGACATTGTAATTTAAAATATTGAAGCTGCAATAGTGAATTTTACTTTCCTGGCGATAC
66 -TTCCCCGACATTGCAATTTAAAATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGC
** * *
41101590 AGTGGATCAGATTGAAGCTACAACGGTAATCTCGTTCCCTAACATTGCAATTTAAAAGATTGAAG
130 AGTGGATCAGATTGAAGCTACAACGCAAATCTTGTTCCCTGACATTGCAA-TTAAAAGATTGAAG
41101655 CCGA
194 CCGA
* * * ** * *
41101659 -AATGGCGAATTTTACTTTCCTGGTGGTGTAGTGGAGCAAATTAAAGCTACGACGGCGAATCTTG
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGACGGCGAATCTT-
* * * *
41101723 CTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTAGCGATGC
65 CTTCCCCGACATTGCAATTTAAAATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGC
* *
41101788 AGTGGATCAGATTGAAGCTACAACGACAAATCTTATTCCCCGACATTGCAATTAAAAGGATTGAA
130 AGTGGATCAGATTGAAGCTACAACG-CAAATCTTGTTCCCTGACATTGCAATTAAAA-GATTGAA
41101853 GCC-A
193 GCCGA
* * * *
41101857 CAACGGTGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTACGACGGCGAATCTTA
1 CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGACGGCGAATCTT-
* * * ** *
41101922 CTTCCCTGATATTGCAATTTAAAATATTAAAGCCGCAACGACGAATCTTACTTCCCTGGC-AGTG
65 CTTCCCCGACATTGCAATTTAAAATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGA-TG
* * * * *
41101986 CAGTGGAACAGATTAAAGCTACGACTGCGAATCGTGTTCCCTGACATTGCAATTAA
129 CAGTGGATCAGATTGAAGCTACAAC-GCAAATCTTGTTCCCTGACATTGCAATTAA
41102042 GGCCGCAATG
Statistics
Matches: 319, Mismatches: 57, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
197 49 0.15
198 88 0.28
199 181 0.57
200 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (197 bp):
CAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTC
TTCCCCGACATTGCAATTTAAAATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCA
GTGGATCAGATTGAAGCTACAACGCAAATCTTGTTCCCTGACATTGCAATTAAAAGATTGAAGCC
GA
Found at i:41102115 original size:44 final size:44
Alignment explanation
Indices: 41102060--41102361 Score: 194
Period size: 44 Copynumber: 7.0 Consensus size: 44
41102050 TGGCGAATCC
41102060 TATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAACCACAGATCT
* * * * * * * *
41102104 TATCTCTCTGAAGTTGCAGTAGAGTAG-TTCACATC-TAG-TTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * * *
41102145 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC-AGATCT
* * * *
41102189 TATCTCCTTGAAGTTGTAGTGGAGCAGATTAAGACCACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * * *** *
41102233 TATCTCTCTAAAGTTGTAGTAGAGCAGA-TCGCATC-CAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * ** *
41102274 TATCTCCCTGAAGTTGCAGTGGAACAGA-CAAAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CCA-CAGATCT
* *
41102318 TATCTCCCTGAAGTT-CTAGTGGAGCGGATTAAAACCACAAATCT
1 TATCTCCCTGAAGTTGC-AGTGGAGCAGATTAAAACCACAGATCT
41102362 CGTCCCCATG
Statistics
Matches: 190, Mismatches: 55, Indels: 26
0.70 0.20 0.10
Matches are distributed among these distances:
41 53 0.28
42 6 0.03
43 12 0.06
44 114 0.60
45 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
Found at i:41102377 original size:129 final size:129
Alignment explanation
Indices: 41102055--41102361 Score: 427
Period size: 129 Copynumber: 2.4 Consensus size: 129
41102045 CGCAATGGCG
* *
41102055 AATCCTATCTCCCTGAAGTTGC-AGTGGAGCGAATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 AATCCTATCTCCCTGAAGTT-CTAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTT
* * * * * ** ** *
41102119 GCAGTAGAGTAGTTCACATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
65 GCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAAAAGAAACC
* * * * *
41102184 AATCCTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAGACCACAAATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTCTAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTG
* *
41102249 TAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAAAAGAAACC
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAAAAGAAACC
41102313 AATCCTATCTCCCTGAAGTTCTAGTGGAGCGGATTAAAACCACAAATCT
1 AATCCTATCTCCCTGAAGTTCTAGTGGAGCGGATTAAAACCACAAATCT
41102362 CGTCCCCATG
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
129 154 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGTTCTAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTG
CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAAAAGAAACC
Found at i:41106769 original size:3 final size:3
Alignment explanation
Indices: 41106761--41106788 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41106751 CTGAAATACT
41106761 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41106789 ACTACTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41107513 original size:30 final size:30
Alignment explanation
Indices: 41107477--41107562 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 30
41107467 AAAATCAGTC
* *
41107477 TGGGCCTGAGCCCTATACAGTAGCAGTGTG
1 TGGGCCTGAGCCCAATACAGTAACAGTGTG
*
41107507 TGGGCCTTAGCCCAATACAGTAACA--GTG
1 TGGGCCTGAGCCCAATACAGTAACAGTGTG
* * *
41107535 TGGGCGTTAGCCCAAAACAGTAATCAGT
1 TGGGCCTGAGCCCAATACAGTAA-CAGT
41107563 ACAAATGCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 24 0.50
29 2 0.04
30 22 0.46
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (30 bp):
TGGGCCTGAGCCCAATACAGTAACAGTGTG
Found at i:41107732 original size:26 final size:26
Alignment explanation
Indices: 41107669--41107771 Score: 125
Period size: 26 Copynumber: 4.0 Consensus size: 26
41107659 ACATCAATAT
* * *
41107669 CGCAGTAAAGCTACCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
41107695 CACAACAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* * * *
41107721 CGTAGCAGAGCTGCCAGTATCAGTAT
1 CGCAGCAAAGCTGCCAGTAACAGTAA
41107747 CGCAGCAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
41107772 TTTGTGGCAA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:41108408 original size:14 final size:14
Alignment explanation
Indices: 41108382--41108432 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
41108372 GAAAACAAAA
41108382 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
41108396 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
41108410 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
41108425 G-AATAAAA
1 GAAATAAAA
41108433 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:41109174 original size:3 final size:3
Alignment explanation
Indices: 41109153--41109196 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
41109143 GTAAGTATAA
* * *
41109153 TAT TAG TAT TAA T-T TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41109197 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:41109610 original size:37 final size:39
Alignment explanation
Indices: 41109551--41109646 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
41109541 CGGATAGATT
* * * *
41109551 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
41109588 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
41109627 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
41109647 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:41110708 original size:27 final size:27
Alignment explanation
Indices: 41110687--41110857 Score: 206
Period size: 27 Copynumber: 6.3 Consensus size: 27
41110677 CTACCTTTCA
*
41110687 AGGGTGTTTCAGTAATTTTACCCATCG
1 AGGGTATTTCAGTAATTTTACCCATCG
*
41110714 AGGGTATTTCAGTAATTTTACCCATCA
1 AGGGTATTTCAGTAATTTTACCCATCG
* *
41110741 AGGGTA-TTCGAGTCATTTTACCCTTCG
1 AGGGTATTTC-AGTAATTTTACCCATCG
41110768 AGGGTATTTC-GATAATTTTACCCATCG
1 AGGGTATTTCAG-TAATTTTACCCATCG
* **
41110795 AGGGTATTTCGGTAATTTTACCC-TTT
1 AGGGTATTTCAGTAATTTTACCCATCG
*
41110821 AGAGGTATTTC-GATAATTTTACCCATTG
1 AG-GGTATTTCAG-TAATTTTACCCATCG
41110849 AGGGTATTT
1 AGGGTATTT
41110858 AGGGTTTAGG
Statistics
Matches: 127, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
26 8 0.06
27 111 0.87
28 8 0.06
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACCCATCG
Found at i:41110719 original size:54 final size:53
Alignment explanation
Indices: 41110661--41110846 Score: 194
Period size: 54 Copynumber: 3.5 Consensus size: 53
41110651 TATCGTATAG
* * * **
41110661 GGGTATTTTGGTCATTCTACCTTTCAAGGGTGTTTCAGTAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCATCAAGGGT-TTTCAGTAATTTTACCCATCGA
* * * *
41110715 GGGTATTTCAGTAATTTTACCCATCAAGGGTATTCGAGTCATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCATCAAGGGTTTTC-AGTAATTTTACCCATCGA
* * * **
41110769 GGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCC-TTTA
1 GGGTATTTCGGTAATTTTACCCATCAAGGGT-TTTCAGTAATTTTACCCATCGA
*
41110822 GAGGTATTTCGATAATTTTACCCAT
1 G-GGTATTTCGGTAATTTTACCCAT
41110847 TGAGGGTATT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
53 6 0.05
54 103 0.92
55 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (53 bp):
GGGTATTTCGGTAATTTTACCCATCAAGGGTTTTCAGTAATTTTACCCATCGA
Found at i:41110828 original size:81 final size:82
Alignment explanation
Indices: 41110661--41110857 Score: 244
Period size: 81 Copynumber: 2.4 Consensus size: 82
41110651 TATCGTATAG
* * * * *
41110661 GGGTATTTTG-GTCATTCTACCTTTCAAGGGTGTTTCAGTAATTTTACCCATCGAGGGTATTTCA
1 GGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCA
41110725 GTAATTTTACCCATCAA
66 GTAATTTTACCCATCAA
41110742 GGGTA-TTCGAGTCATTTTACCCTTCGAGGGTATTTC-GATAATTTTACCCATCGAGGGTATTTC
1 GGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTTCAG-TAATTTTACCCATCGAGGGTATTTC
* **
41110805 GGTAATTTTACCC-TTTA
65 AGTAATTTTACCCATCAA
*
41110822 GAGGTATTTCGA-TAATTTTACCCATT-GAGGGTATTT
1 G-GGTATTTCGAGTCATTTTACCC-TTCGAGGGTATTT
41110858 AGGGTTTAGG
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
80 7 0.07
81 88 0.86
82 7 0.07
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (82 bp):
GGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCA
GTAATTTTACCCATCAA
Found at i:41110852 original size:54 final size:54
Alignment explanation
Indices: 41110687--41110857 Score: 231
Period size: 54 Copynumber: 3.2 Consensus size: 54
41110677 CTACCTTTCA
* * * *
41110687 AGGGTGTTTCAGTAATTTTACCCATCGAGGGTATTTC-AGTAATTTTACCCATCA
1 AGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCCATCG
*
41110741 AGGGTA-TTCGAGTCATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCG-GTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCATCG
* *
41110795 AGGGTATTTCGGTAATTTTACCCTT-TAGAGGTATTTCGATAATTTTACCCATTG
1 AGGGTATTTCGGTAATTTTACCCTTCGAG-GGTATTTCGATAATTTTACCCATCG
41110849 AGGGTATTT
1 AGGGTATTT
41110858 AGGGTTTAGG
Statistics
Matches: 105, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
53 5 0.05
54 95 0.90
55 5 0.05
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCATCG
Found at i:41110867 original size:7 final size:7
Alignment explanation
Indices: 41110855--41110884 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41110845 ATTGAGGGTA
41110855 TTTAGGG
1 TTTAGGG
41110862 TTTAGGG
1 TTTAGGG
41110869 TTTAGGG
1 TTTAGGG
*
41110876 TTTAAGG
1 TTTAGGG
41110883 TT
1 TT
41110885 CAGTAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:41111020 original size:27 final size:27
Alignment explanation
Indices: 41110990--41111628 Score: 614
Period size: 27 Copynumber: 23.7 Consensus size: 27
41110980 TATCCTATAG
* *
41110990 GGGTA-TTCTGGTCATTTTACCCTTTGA
1 GGGTATTTC-GGTAATTTTACCCTTCGA
* * *
41111017 GGGTATTTTGATAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111044 GGGTATTTCAGTAATTTTACCCGTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111071 GGGTATTTCAGTCATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
41111098 GGGTATTTCGATAATTTTA-CCTATCGA
1 GGGTATTTCGGTAATTTTACCCT-TCGA
*
41111125 GGGTATTTCGGTAATTTTA-CCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* * * * *
41111151 TGGTATTTTGATAATTTTACTCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* * *
41111178 GGGTATTTCAGTCATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
**
41111205 GGGTATTTTAGTAATTTTA-CCTATC-A
1 GGGTATTTCGGTAATTTTACCCT-TCGA
* *
41111231 GGGGTATTTCGATCATTTTACCCTTCGA
1 -GGGTATTTCGGTAATTTTACCCTTCGA
* **
41111259 AGGTATTTTAGTAATTTTA-CCTATCGA
1 GGGTATTTCGGTAATTTTACCCT-TCGA
* * * *
41111286 GGGTATTTTGGTCATTTTACCCTTTGG
1 GGGTATTTCGGTAATTTTACCCTTCGA
** *
41111313 GGGTATTTTAGTCATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
41111340 -GGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111366 GGGTATTTCAGTAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
41111393 GGGTATTTAGGTAATTTTACCCTTC-A
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111419 GGGGTATTTTGGTAATTTTACCCTTCAA
1 -GGGTATTTCGGTAATTTTACCCTTCGA
***
41111447 GGGTATTTTAATAATTTTACCCTTC-A
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111473 GGGGTATTTCAGTAATTTTACCTTTCGA
1 -GGGTATTTCGGTAATTTTACCCTTCGA
* ** *
41111501 GGGTATTTCGATAATTTTTTCCTTCGG
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
41111528 GGGTATTTCAGTAATTTTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
** * * *
41111555 ACGTATTTCGGTCATTCTACCCATCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
** *
41111582 GGGTATTTTAGTAATTTTACCCATT-AA
1 GGGTATTTCGGTAATTTTACCC-TTCGA
41111609 GGGTATTTCGGTAATTTTAC
1 GGGTATTTCGGTAATTTTAC
41111629 GACCCAAACC
Statistics
Matches: 510, Mismatches: 87, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
26 53 0.10
27 445 0.87
28 12 0.02
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCTTCGA
Found at i:41111100 original size:81 final size:81
Alignment explanation
Indices: 41111000--41111628 Score: 677
Period size: 81 Copynumber: 7.8 Consensus size: 81
41110990 GGGTATTCTG
*
41111000 GTCATTTTACCCTTTGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
*
41111065 CGTCGAGGGTATTTCA
66 CATCGAGGGTATTTCA
* * *
41111081 GTCATTTTACCCTTCGAGGGTATTTCGATAATTTTACCTATCGAGGGTATTTCGGTAATTTTA-C
1 GTCATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
* *
41111145 CATCGATGGTATTT-T
66 CATCGAGGGTATTTCA
* * * * * *
41111160 GATAATTTTACTCATCGAGGGTA-TTTCAGTCATTTTACCCATCGAGGGTATTTTAGTAATTTTA
1 G-TCATTTTACCCTTCGAGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCAGTAATTTTA
*
41111224 CCTATC-AGGGGTATTTC-
64 CCCATCGA-GGGTATTTCA
* * ** *
41111241 GATCATTTTACCCTTCGAAGGTATTTT-AGTAATTTTACCTATCGAGGGTATTTTGGTCATTTTA
1 G-TCATTTTACCCTTCGAGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCAGTAATTTTA
* * * *
41111305 CCCTTTGGGGGTATTTTA
64 CCCATCGAGGGTATTTCA
* *
41111323 GTCATTTTACCCTTCGA-GGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
41111387 CATCGAGGGTATTT-A
66 CATCGAGGGTATTTCA
* * * * * *
41111402 GGTAATTTTACCCTTC-AGGGGTATTTTGGTAATTTTACCCTTCAAGGGTATTTTAATAATTTTA
1 -GTCATTTTACCCTTCGA-GGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTA
*
41111466 CCCTTC-AGGGGTATTTCA
64 CCCATCGA-GGGTATTTCA
* * * ** * *
41111484 GTAATTTTACCTTTCGAGGGTATTTCGATAATTTTTTCCTTCGGGGGTATTTCAGTAATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
** *
41111549 CATCGAACGTATTTCG
66 CATCGAGGGTATTTCA
* * ** *
41111565 GTCATTCTACCCATCGAGGGTATTTT-AGTAATTTTACCCATTAAGGGTATTTCGGTAATTTTAC
1 GTCATTTTACCCTTCGAGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCAGTAATTTTAC
41111629 GACCCAAACC
Statistics
Matches: 459, Mismatches: 72, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
79 6 0.01
80 130 0.28
81 316 0.69
82 7 0.02
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (81 bp):
GTCATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACC
CATCGAGGGTATTTCA
Found at i:41116247 original size:22 final size:22
Alignment explanation
Indices: 41116219--41116264 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
41116209 AAAGGCAATC
*
41116219 TACAAATTAAATCTCTTAAGAT
1 TACAAATCAAATCTCTTAAGAT
* *
41116241 TACAAATCAAATTTTTTAAGAT
1 TACAAATCAAATCTCTTAAGAT
41116263 TA
1 TA
41116265 TAGATCTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
TACAAATCAAATCTCTTAAGAT
Found at i:41126183 original size:19 final size:19
Alignment explanation
Indices: 41126140--41126177 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41126130 TTAATTTATT
*
41126140 AAATTTTAAAAATTCAAAA
1 AAATTATAAAAATTCAAAA
41126159 AAATTATAAAAATT-AAAA
1 AAATTATAAAAATTCAAAA
41126177 A
1 A
41126178 TTATTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAATTCAAAA
Found at i:41126793 original size:98 final size:98
Alignment explanation
Indices: 41126616--41126794 Score: 286
Period size: 98 Copynumber: 1.8 Consensus size: 98
41126606 GAGTAATATG
* * *
41126616 TGGAAACAATAAGTTGACATGGTATTTCATATGTGTTAATATGTTTATCACATTAAATTTTGGAA
1 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
*
41126681 ATAGTTAAACTTAATAAACTTAATATCCAATTT
66 ATAGCTAAACTTAATAAACTTAATATCCAATTT
* * *
41126714 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAGTATGTCTGTCGCATTAAATTTTGGAA
1 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
*
41126779 ATAGCTAAATTTAATA
66 ATAGCTAAACTTAATA
41126795 TTCAATTTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 73 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (98 bp):
TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
ATAGCTAAACTTAATAAACTTAATATCCAATTT
Found at i:41128183 original size:29 final size:30
Alignment explanation
Indices: 41128107--41128175 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
41128097 GTGGTCAGGG
* *
41128107 TTGCTCATACAAGCTGACA-TTTATGAATC
1 TTGCTCACACAAGCTGACATTTTATAAATC
*
41128136 TT-CTCACACAAGTTGACATTTTATAAAT-
1 TTGCTCACACAAGCTGACATTTTATAAATC
41128164 TTGCTCACACAA
1 TTGCTCACACAA
41128176 ACTAACATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.46
29 19 0.54
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (30 bp):
TTGCTCACACAAGCTGACATTTTATAAATC
Found at i:41129504 original size:43 final size:42
Alignment explanation
Indices: 41129438--41129595 Score: 217
Period size: 43 Copynumber: 3.7 Consensus size: 42
41129428 TTTTAGAAAT
*
41129438 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGTCA-GACCTTTAGCGGCGCTTTTCCCAC
* * * *
41129481 AAACGACGCTATAGGTCGAGACCTTTAGCGACGCTTTTTCCAA
1 AAACGCCGCTATAGGTC-AGACCTTTAGCGGCGCTTTTCCCAC
41129524 AAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGTC-AGACCTTTAGCGGCGCTTTTCCCAC
** *
41129567 AAACGCCGCTATAGAACAAACCTTTAGCG
1 AAACGCCGCTATAGGTCAGACCTTTAGCG
41129596 ATGCTTCTCA
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 11 0.11
43 89 0.88
44 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGGTCAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:41129613 original size:42 final size:43
Alignment explanation
Indices: 41129438--41129615 Score: 144
Period size: 43 Copynumber: 4.2 Consensus size: 43
41129428 TTTTAGAAAT
* * * * ** *
41129438 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCAAAA
* ** * * *
41129481 AAACGACGCTATAGGTCGAGACCTTTAGCGACGCTTTTTC-CAA
1 AAACGCCGCTATAGAACAAGACCTTTAGCGACGC-TTCTCAAAA
** * * ** *
41129524 AAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCAAAA
*
41129567 AAACGCCGCTATAGAACAA-ACCTTTAGCGATGCTTCTCAAAA
1 AAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCAAAA
41129609 AAACGCC
1 AAACGCC
41129616 ACTAAAAACA
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 29 0.25
43 81 0.70
44 5 0.04
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCAAAA
Found at i:41129661 original size:16 final size:14
Alignment explanation
Indices: 41129620--41129662 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
41129610 AACGCCACTA
41129620 AAAACATAATATTTT
1 AAAA-ATAATATTTT
41129635 AAAAA-AATATTTT
1 AAAAATAATATTTT
41129648 AATCAAATAATATTT
1 AA--AAATAATATTT
41129663 ATTTTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 7 0.28
16 7 0.28
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATAATATTTT
Found at i:41129917 original size:12 final size:13
Alignment explanation
Indices: 41129889--41129921 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41129879 TATTAAAGTA
41129889 AAAATAAAAATTT
1 AAAATAAAAATTT
*
41129902 AAAATCAAAA-TT
1 AAAATAAAAATTT
41129914 AAAATAAA
1 AAAATAAA
41129922 TCAATAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAAATTT
Found at i:41133163 original size:29 final size:29
Alignment explanation
Indices: 41133113--41133174 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
41133103 TTGCACCATT
41133113 TTTTTAAAAGTAGAATGATTTTTGCGGCC
1 TTTTTAAAAGTAGAATGATTTTTGCGGCC
*
41133142 TTTTT-AAAGTAGAATGATTTTTGCGGCG
1 TTTTTAAAAGTAGAATGATTTTTGCGGCC
41133170 TTTTT
1 TTTTT
41133175 TATAAAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (29 bp):
TTTTTAAAAGTAGAATGATTTTTGCGGCC
Found at i:41133323 original size:149 final size:148
Alignment explanation
Indices: 41133142--41134308 Score: 1876
Period size: 149 Copynumber: 7.9 Consensus size: 148
41133132 TTTTGCGGCC
* * * * *
41133142 TTTTT-AAAGTAGAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTTCTGACCTTTAGC
1 TTTTTAAAAGTAAAATTA-TTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGC
* **
41133206 GGTGTTTTTTCATAAAAGTACCGCAAAAAAATTCATTTTGAACAAAACTATC-CCGTTTTGCTAT
65 GGCG-TTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTA-CGCCGTTTTGCTAT
41133270 GCTATGCTAAAAGGGGGCTAT
128 GCTATGCTAAAAGGGGGCTAT
* *
41133291 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACACCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
* *
41133356 GCGTTTTTCGTAAAAGCGCCGCAAAAAAATTTCATTTTAAACAAAACTACGCCGTTTTGCTATGC
66 GCGTTTTTCATAAAAGCGCCGCAAAAAAA-TTCATTTTGAACAAAACTACGCCGTTTTGCTATGC
* *
41133421 TATGCTAAAAGGGAGTTAT
130 TATGCTAAAAGGGGGCTAT
*
41133440 TTTTT-AAAGTAAAATTATTTTGTGGCGTTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGC
1 TTTTTAAAAGTAAAATTATTTTGTGGCG-TTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGC
*
41133504 GGCGTTTTTCGTAAAAGCGCCGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATG
65 GGCGTTTTTCATAAAAGCGCCGC-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATG
41133569 CTATGCTAAAAGGGGGCTAT
129 CTATGCTAAAAGGGGGCTAT
41133589 TTTTTAAAA-TAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
41133653 GCGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
66 GCGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
41133718 ATGCTAAAAGGGGGCTAT
131 ATGCTAAAAGGGGGCTAT
* *
41133736 TTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
*
41133801 GCGTTTTTCGTAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
66 GCGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
41133866 ATGCTAAAAGGGGGCTAT
131 ATGCTAAAAGGGGGCTAT
* *
41133884 TTTTTTAAAGTAAAATTATTTTGTGGCATTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGC
1 TTTTTAAAAGTAAAATTATTTTGTGGC-GTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGC
* * * *
41133949 GGCGTTTTTCATAAAAGCGCCACAAAAAAAAATCGTTTTGAACAAAACTACGCCATTTTGCTATG
65 GGCGTTTTTCATAAAAGCGCCGC-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATG
*
41134014 CTGTGCTAAAAGGGGGCTAT
129 CTATGCTAAAAGGGGGCTAT
** *
41134034 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATTTAAACGCCGCTATTGCTTACATTTAGCG
1 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
* * * * *
41134099 GCATTTTTCGTAAAAGCGTCACAAAAAAATTTCGTTTTGAACAAAACTACGCCGTTTTGCTATGC
66 GCGTTTTTCATAAAAGCGCCGCAAAAAAA-TTCATTTTGAACAAAACTACGCCGTTTTGCTATGC
41134164 TATGCTAAAA-GGGGCTAT
130 TATGCTAAAAGGGGGCTAT
* *
41134182 TTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCG
1 TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
* *
41134247 GCGTTTTTCATAAAAGTGCCGTAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
66 GCGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
41134309 TCTAAAAATT
Statistics
Matches: 954, Mismatches: 54, Indels: 22
0.93 0.05 0.02
Matches are distributed among these distances:
147 101 0.11
148 364 0.38
149 386 0.40
150 103 0.11
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (148 bp):
TTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
GCGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
ATGCTAAAAGGGGGCTAT
Found at i:41134294 original size:594 final size:595
Alignment explanation
Indices: 41133142--41134308 Score: 1948
Period size: 594 Copynumber: 2.0 Consensus size: 595
41133132 TTTTGCGGCC
* *
41133142 TTTTTAAAGTAGAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTTCTGACCTTTAGCG
1 TTTTTAAAGTAAAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTGCTGACCTTTAGCG
* *
41133207 GTGTTTTTTCATAAAAGTACCGCAAAAAAATTCATTTTGAACAAAACTATCCCGTTTTGCTATGC
66 GCGTTTTTTCATAAAAGCACCGCAAAAAAATTCATTTTGAACAAAACTATCCCGTTTTGCTATGC
*
41133272 TATGCTAAAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACACCG
131 TATGCTAAAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACACCG
* * **
41133337 CTATTGCTTACCTTTAGCGGCGTTTTTCGTAAAAGCGCCGCAAAAAAATTTCATTTTAAACAAAA
196 CTATTGCTTACCTTTAGCGGCGTTTTTCATAAAAGCGCCACAAAAAAAAATCATTTTAAACAAAA
* *
41133402 CTACGCCGTTTTGCTATGCTATGCTAAAAGGGAGTTATTTTTTAAAGTAAAATTATTTTGTGGCG
261 CTACGCCATTTTGCTATGCTATGCTAAAAGGGAGCTATTTTTTAAAGTAAAATTATTTTGTGGCG
* * *
41133467 TTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGCGGCGTTTTTCGTAAAAGCGCCGCAAAAA
326 TTTTTTTATATAAACGCCGCTATTGCTTACATTTAGCGGCATTTTTCGTAAAAGCGCCACAAAAA
41133532 AAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTTTTTAAA
391 AAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTTTTTAAA
*
41133597 ATAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGGCGTTTTTC
456 ATAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTTTTTC
41133662 ATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAA
521 ATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAA
41133727 GGGGGCTATT
586 GGGGGCTATT
* * * *
41133737 TTTTTAAAGTAAAATTA-TTTTGTGGCGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAGTAAAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTGCTGACCTTTAGCG
* *
41133801 GCG-TTTTTCGTAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTA-CGCCGTTTTGCTATG
66 GCGTTTTTTCATAAAAGCACCGCAAAAAAATTCATTTTGAACAAAACTATC-CCGTTTTGCTATG
* * *
41133864 CTATGCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCATTTTTTTATAAAAACGC
130 CTATGCTAAAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGC-GTTTTTTATAAAAACAC
* *
41133929 CGCTATTGCTTACCTTTAGCGGCGTTTTTCATAAAAGCGCCACAAAAAAAAATCGTTTTGAACAA
194 CGCTATTGCTTACCTTTAGCGGCGTTTTTCATAAAAGCGCCACAAAAAAAAATCATTTTAAACAA
* *
41133994 AACTACGCCATTTTGCTATGCTGTGCTAAAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTG
259 AACTACGCCATTTTGCTATGCTATGCTAAAAGGGAGCTATTTTTT-AAAGTAAAATTATTTTGTG
* *
41134059 GCG-TTTTTTATTTAAACGCCGCTATTGCTTACATTTAGCGGCATTTTTCGTAAAAGCGTCACAA
323 GCGTTTTTTTATATAAACGCCGCTATTGCTTACATTTAGCGGCATTTTTCGTAAAAGCGCCACAA
* *
41134123 AAAAATTTCGTTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAA-GGGGCTATTTTTT
388 AAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTA-TTTTT
*
41134187 TAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTT
452 TAAAATAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTT
* *
41134252 TTTCATAAAAGTGCCGTAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
517 TTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
41134309 TCTAAAAATT
Statistics
Matches: 533, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
592 1 0.00
593 108 0.20
594 387 0.73
595 37 0.07
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (595 bp):
TTTTTAAAGTAAAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTGCTGACCTTTAGCG
GCGTTTTTTCATAAAAGCACCGCAAAAAAATTCATTTTGAACAAAACTATCCCGTTTTGCTATGC
TATGCTAAAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACACCG
CTATTGCTTACCTTTAGCGGCGTTTTTCATAAAAGCGCCACAAAAAAAAATCATTTTAAACAAAA
CTACGCCATTTTGCTATGCTATGCTAAAAGGGAGCTATTTTTTAAAGTAAAATTATTTTGTGGCG
TTTTTTTATATAAACGCCGCTATTGCTTACATTTAGCGGCATTTTTCGTAAAAGCGCCACAAAAA
AAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTTTTTAAA
ATAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTTTTTC
ATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAA
GGGGGCTATT
Found at i:41134334 original size:148 final size:145
Alignment explanation
Indices: 41133142--41134316 Score: 1694
Period size: 148 Copynumber: 7.9 Consensus size: 145
41133132 TTTTGCGGCC
* * * * *
41133142 TTTTTAAAGTAGAATGATTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTTCTGACCTTTAGCG
1 TTTTTAAAGTAAAATTA-TTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
* **
41133207 GTGTTTTTTCATAAAAGTACCGCAAAAAAATTCATTTTGAACAAAACTATC-CCGTTTTGCTATG
65 GCG-TTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTA-CGCCGTTTTGCTATG
41133271 CTATGCTAAAAGGGGGCTATT
128 CTA---TAAAAGGGGGCTATT
* * *
41133292 TTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACACCGCTATTGCTTACCTTTAGCGG
1 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
* *
41133357 CGTTTTTCGTAAAAGCGCCGCAAAAAAATTTCATTTTAAACAAAACTACGCCGTTTTGCTATGCT
66 CGTTTTTCATAAAAGCGCCGCAAAAAAA-TTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
* *
41133422 ATGCTAAAAGGGAGTTA-T
130 A---TAAAAGGGGGCTATT
*
41133440 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAGTAAAATTATTTTGTGGCG-TTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
*
41133505 GCGTTTTTCGTAAAAGCGCCGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGC
65 GCGTTTTTCATAAAAGCGCCGC-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGC
41133570 TATGCTAAAAGGGGGCTA-T
129 TA---TAAAAGGGGGCTATT
*
41133589 TTTTTAAAATAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
1 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
41133654 CGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
66 CGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
41133719 TGCTAAAAGGGGGCTATT
131 ---TAAAAGGGGGCTATT
*
41133737 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAGCGG
1 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
*
41133802 CGTTTTTCGTAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
66 CGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
41133867 TGCTAAAAGGGGGCTATT
131 ---TAAAAGGGGGCTATT
*
41133885 TTTTTAAAGTAAAATTATTTTGTGGCATTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
1 TTTTTAAAGTAAAATTATTTTGTGGC-GTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCG
* * * *
41133950 GCGTTTTTCATAAAAGCGCCACAAAAAAAAATCGTTTTGAACAAAACTACGCCATTTTGCTATGC
65 GCGTTTTTCATAAAAGCGCCGC-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGC
*
41134015 TGTGCTAAAAGGGGGCTATT
129 --T-ATAAAAGGGGGCTATT
* ** *
41134035 TTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATTTAAACGCCGCTATTGCTTACATTTAGCGG
1 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
* * * * *
41134100 CATTTTTCGTAAAAGCGTCACAAAAAAATTTCGTTTTGAACAAAACTACGCCGTTTTGCTATGCT
66 CGTTTTTCATAAAAGCGCCGCAAAAAAA-TTCATTTTGAACAAAACTACGCCGTTTTGCTATGCT
41134165 ATGCTAAAA-GGGGCTATT
130 A---TAAAAGGGGGCTATT
*
41134183 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCCTACCTTTAGCGG
1 TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
* * *
41134248 CGTTTTTCATAAAAGTGCCGTAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATTCTA
66 CGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
41134313 -AAAA
131 TAAAA
41134317 TTTTTTATTT
Statistics
Matches: 953, Mismatches: 58, Indels: 35
0.91 0.06 0.03
Matches are distributed among these distances:
143 4 0.00
147 96 0.10
148 378 0.40
149 374 0.39
150 100 0.10
152 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (145 bp):
TTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTAGCGG
CGTTTTTCATAAAAGCGCCGCAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
TAAAAGGGGGCTATT
Found at i:41134757 original size:15 final size:15
Alignment explanation
Indices: 41134732--41134817 Score: 56
Period size: 15 Copynumber: 5.8 Consensus size: 15
41134722 CCTTAACTCG
41134732 ACCTCTAAATCCCTAA
1 ACCT-TAAATCCCTAA
41134748 ACCTTAAATCCCT-A
1 ACCTTAAATCCCTAA
*
41134762 ACTCTT-AA-CCCTTA
1 AC-CTTAAATCCCTAA
* *
41134776 ACATCT-AACCCCTAA
1 ACCT-TAAATCCCTAA
* *
41134791 ACC-CATAACCCCTAA
1 ACCTTA-AATCCCTAA
41134806 ACCTTAAATCCC
1 ACCTTAAATCCC
41134818 GACACTTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.09
14 11 0.19
15 36 0.63
16 5 0.09
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (15 bp):
ACCTTAAATCCCTAA
Found at i:41135087 original size:15 final size:15
Alignment explanation
Indices: 41135040--41135093 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41135030 CTCACCCCTA
* *
41135040 AACCCCTAA-CTTTT
1 AACCCCTAACCCTCT
* *
41135054 AACCCCTAGCACGTCT
1 AACCCCTAAC-CCTCT
41135070 AACCCCTAACCCTCT
1 AACCCCTAACCCTCT
41135085 AACCCCTAA
1 AACCCCTAA
41135094 ACCTTAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 8 0.24
15 13 0.39
16 12 0.36
ACGTcount: A:0.30, C:0.44, G:0.04, T:0.22
Consensus pattern (15 bp):
AACCCCTAACCCTCT
Found at i:41135128 original size:14 final size:14
Alignment explanation
Indices: 41135109--41135157 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
41135099 AAATCCCAAC
41135109 CCCTAATCCATAAT
1 CCCTAATCCATAAT
41135123 CCCTAATCCATAAT
1 CCCTAATCCATAAT
* * *
41135137 CTCTAAACCCATACT
1 CCCT-AATCCATAAT
41135152 CCCTAA
1 CCCTAA
41135158 ACTGACCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.27
Consensus pattern (14 bp):
CCCTAATCCATAAT
Found at i:41135437 original size:73 final size:73
Alignment explanation
Indices: 41135311--41135460 Score: 228
Period size: 73 Copynumber: 2.1 Consensus size: 73
41135301 ATTTTTTTGG
* * * * *
41135311 CCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTCT
1 CCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCGGCGCTTACT
*
41135376 TAAAAACA
66 CAAAAACA
*
41135384 CCGCTAAATCCCCGAAAGCTCACAAAACGGCATTGTTGGGCTTAGGTTATTTTGCGGCGCTTACT
1 CCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCGGCGCTTACT
*
41135449 CAAAAACG
66 CAAAAACA
41135457 CCGC
1 CCGC
41135461 CAAAGCCGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (73 bp):
CCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCGGCGCTTACT
CAAAAACA
Found at i:41135568 original size:114 final size:114
Alignment explanation
Indices: 41135364--41135574 Score: 325
Period size: 114 Copynumber: 1.9 Consensus size: 114
41135354 ATGTTTTTTT
* *
41135364 GCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGGCATTGTTGGGCTTAG
1 GCGGCGCCTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
41135429 GTTATTTTGCGGCGCTTACTCAAAAACGCCGCCAAAGCCGTAAGCATTA
66 GTTATTTTGCGGCGCTTACTCAAAAACGCCGCCAAAGCCGTAAGCATTA
* * * * *
41135478 GCGGCGCCTTCTTAAAAACGCTGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTAT
1 GCGGCGCCTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
* *
41135543 GTTTTTTTGCGGCGCTTTC-CTAAAAACGCCGC
66 GTTATTTTGCGGCGCTTACTC-AAAAACGCCGC
41135575 TAAATCCCCA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 1 0.01
114 86 0.99
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCCTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
GTTATTTTGCGGCGCTTACTCAAAAACGCCGCCAAAGCCGTAAGCATTA
Found at i:41135569 original size:73 final size:72
Alignment explanation
Indices: 41135478--41135651 Score: 258
Period size: 73 Copynumber: 2.4 Consensus size: 72
41135468 GTAAGCATTA
* * * * *
41135478 GCGGCGCCTTCTTAAAAACGCTGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTAT
1 GCGGCG-CTTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
*
41135543 GTTTTTTT
65 GTTATTTT
41135551 GCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGC-TTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
41135616 GTTATTTT
65 GTTATTTT
*
41135624 GCGGCGCTTACTCAAAAACGCCGCTAAA
1 GCGGCGCTTCCT-AAAAACGCCGCTAAA
41135652 GACCTAAGCA
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
72 5 0.05
73 87 0.95
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (72 bp):
GCGGCGCTTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGG
TTATTTT
Found at i:41135628 original size:187 final size:187
Alignment explanation
Indices: 41135310--41135765 Score: 745
Period size: 187 Copynumber: 2.4 Consensus size: 187
41135300 TATTTTTTTG
41135310 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
* * *
41135375 TTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGGCATTGTTGGGCTTAGGTTATTTTGCG
66 TTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
* *
41135440 GCGCTTACTCAAAAACGCCGCCAAAG-CCGTAAGCATTAGCGGCGCCTTCTTAAAAAC
131 GCGCTTACTCAAAAACGCCGCCAAAGACC-TAAGCATTAGCGGCGCCTTATGAAAAAC
*
41135497 GCTGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
* *
41135562 CTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGGTTATTTTGCG
66 TTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
* * *
41135627 GCGCTTACTCAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTATGGAAAAC
131 GCGCTTACTCAAAAACGCCGCCAAAGACCTAAGCATTAGCGGCGCCTTATGAAAAAC
* * * *
41135684 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAAGTTTTTTTGCGGCACTTT-
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
41135748 TTCAAAAACGCCGCTAAA
66 TT-AAAAACGCCGCTAAA
41135766 GACCTGAACA
Statistics
Matches: 250, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
186 1 0.00
187 247 0.99
188 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (187 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
TTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
GCGCTTACTCAAAAACGCCGCCAAAGACCTAAGCATTAGCGGCGCCTTATGAAAAAC
Found at i:41135670 original size:114 final size:113
Alignment explanation
Indices: 41135551--41135877 Score: 478
Period size: 114 Copynumber: 2.9 Consensus size: 113
41135541 ATGTTTTTTT
*
41135551 GCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
**
41135616 GTTATTTTGCGGCGCTTACTCAAAAACGCCGCTAAAGACCT-AAGCATTA
66 GTT-TTTTGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTGAA-CATTA
* * *
41135665 GCGGCGCTTT-ATGGAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTA
1 GCGGCGCTTTCAT-AAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTT-
* *
41135729 AGTTTTTTTGCGGCACTTTTTCAAAAACGCCGCTAAAGACCTGAACATTA
64 AGGTTTTTTGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTGAACATTA
* * * *
41135779 GCGGCGCTTTCTTAAAAACGCTGCTAAATCCCCCAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
**
41135844 GTTTTTTGCGGCGCTTTTTGGAAAACGCCGCTAA
66 GTTTTTTGCGGCGCTTTTTCAAAAACGCCGCTAA
41135878 TGCTAATTTT
Statistics
Matches: 191, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
113 33 0.17
114 151 0.79
115 7 0.04
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (113 bp):
GCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
GTTTTTTGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTGAACATTA
Found at i:41137344 original size:27 final size:27
Alignment explanation
Indices: 41137306--41137359 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
41137296 TATTATTTTG
*
41137306 TGATTAGAGTTTTGAGTTTAGGGTTTA
1 TGATTAGAGTTTAGAGTTTAGGGTTTA
* *
41137333 TGATATAG-GTTTAGTGTTTTGGGTTTA
1 TGAT-TAGAGTTTAGAGTTTAGGGTTTA
41137360 AGGTTTAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (27 bp):
TGATTAGAGTTTAGAGTTTAGGGTTTA
Found at i:41137394 original size:21 final size:21
Alignment explanation
Indices: 41137339--41137402 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
41137329 TTTATGATAT
* *
41137339 AGGTTTAGTGTTTTGGGTTTA
1 AGGTTTAGAGTTTGGGGTTTA
41137360 AGGTTTAGGAGTTTGGGGTTTA
1 AGGTTTA-GAGTTTGGGGTTTA
*
41137382 AGGTTT-GAGGTTTGGAGTTTA
1 AGGTTTAGA-GTTTGGGGTTTA
41137403 GGCCGCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.05
21 18 0.47
22 18 0.47
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (21 bp):
AGGTTTAGAGTTTGGGGTTTA
Found at i:41139523 original size:10 final size:10
Alignment explanation
Indices: 41139508--41139533 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41139498 TCTTTGAAAA
41139508 CTATGTTAAG
1 CTATGTTAAG
41139518 CTATGTTAAG
1 CTATGTTAAG
41139528 CTATGT
1 CTATGT
41139534 AAGACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (10 bp):
CTATGTTAAG
Found at i:41140933 original size:44 final size:42
Alignment explanation
Indices: 41140878--41141046 Score: 133
Period size: 44 Copynumber: 3.9 Consensus size: 42
41140868 GCGTTTTTAT
* **
41140878 AAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGAA
1 AAAAACGCCGCTAAAA--CATGACCTATAGCGGCGTTTGTGGAA
* *
41140922 AAAATCGCCGCTAACGAACATGACCTTTAGCGGCGTTTGTGGAA
1 AAAAACGCCGCTAA--AACATGACCTATAGCGGCGTTTGTGGAA
* * * * *
41140966 AAAAACGCCACTAAAGAACATTACTTTTAGTGGCGTTTGTGG-A
1 AAAAACGCCGCT-AA-AACATGACCTATAGCGGCGTTTGTGGAA
* * * *
41141009 GAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTT
1 AAAAACGCCGCT-AA-AACATGACCTATAGCGGCGTTT
41141047 ATTTCTGTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
43 32 0.30
44 70 0.66
45 2 0.02
46 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAACATGACCTATAGCGGCGTTTGTGGAA
Found at i:41141044 original size:43 final size:44
Alignment explanation
Indices: 41140905--41141046 Score: 196
Period size: 44 Copynumber: 3.2 Consensus size: 44
41140895 TCATGTTCTA
* *
41140905 TAGCGGCGTTTGTGGAAAAAATCGCCGCTAACGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAAACGCCGCTAAAGAACATGACCTT
* * *
41140949 TAGCGGCGTTTGTGGAAAAAAACGCCACTAAAGAACATTACTTT
1 TAGCGGCGTTTGTGGAAAAAAACGCCGCTAAAGAACATGACCTT
* * *
41140993 TAGTGGCGTTTGTGG-AGAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAAACGCCGCTAAAGAACATGACCTT
*
41141036 TAACGGCGTTT
1 TAGCGGCGTTT
41141047 ATTTCTGTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 32 0.38
44 53 0.62
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
TAGCGGCGTTTGTGGAAAAAAACGCCGCTAAAGAACATGACCTT
Found at i:41146261 original size:25 final size:26
Alignment explanation
Indices: 41146232--41146285 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
41146222 ACATCTCTTA
41146232 TGAGCTTCCCGATT-A-TGGCTCTTCG
1 TGAGCTTCCCG-TTAATTGGCTCTTCG
* *
41146257 TGAGCTTTCCGTTAATTGGCTCTTTG
1 TGAGCTTCCCGTTAATTGGCTCTTCG
41146283 TGA
1 TGA
41146286 CTTTCCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 11 0.44
26 12 0.48
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (26 bp):
TGAGCTTCCCGTTAATTGGCTCTTCG
Found at i:41147897 original size:25 final size:26
Alignment explanation
Indices: 41147868--41147921 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
41147858 ACATCTCTTA
41147868 TGAGCTTCCCGATT-A-TGGCTCTTCG
1 TGAGCTTCCC-ATTAATTGGCTCTTCG
* *
41147893 TGAGCTTTCCATTAATTGGCTCTTTG
1 TGAGCTTCCCATTAATTGGCTCTTCG
41147919 TGA
1 TGA
41147922 CTTTCCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 10 0.40
26 12 0.48
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (26 bp):
TGAGCTTCCCATTAATTGGCTCTTCG
Found at i:41147906 original size:24 final size:24
Alignment explanation
Indices: 41147868--41147931 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
41147858 ACATCTCTTA
*
41147868 TGAGCTTCCCGATTATGGCTCTTCG
1 TGAGCTTTCC-ATTATGGCTCTTCG
*
41147893 TGAGCTTTCCATTAATTGGCTCTTTG
1 TGAGCTTTCCATT-A-TGGCTCTTCG
41147919 TGA-CTTTCC-TTAT
1 TGAGCTTTCCATTAT
41147932 AAGGCTCGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 5 0.14
25 16 0.46
26 12 0.34
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (24 bp):
TGAGCTTTCCATTATGGCTCTTCG
Found at i:41163490 original size:18 final size:19
Alignment explanation
Indices: 41163457--41163496 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
41163447 AACATGTTTC
* *
41163457 TTTTATTTT-ATTTTTTAT
1 TTTTATTTTAAATTTTAAT
41163475 TTTTATTTTAAATTTTAAT
1 TTTTATTTTAAATTTTAAT
41163494 TTT
1 TTT
41163497 CTCATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTAAATTTTAAT
Found at i:41167093 original size:19 final size:20
Alignment explanation
Indices: 41167051--41167103 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
41167041 ATGCCTTTTT
41167051 TGCATT-CATTTCATTCATCA
1 TGCATTACATTTCA-TCATCA
41167071 -GCATTACATTTCATCA-CA
1 TGCATTACATTTCATCATCA
*
41167089 TGCATTAAATTTCAT
1 TGCATTACATTTCAT
41167104 AAAAAGACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 21 0.70
20 7 0.23
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (20 bp):
TGCATTACATTTCATCATCA
Found at i:41171517 original size:43 final size:43
Alignment explanation
Indices: 41171431--41171707 Score: 308
Period size: 43 Copynumber: 6.5 Consensus size: 43
41171421 CACTAAAAGT
* *
41171431 CATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTATATAC
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
* * * * *
41171473 CACGACCTTTAGCGACGCTTTTTCCATAAACGCCGCTAAATAC
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
* * *
41171516 CATGATCTTTAGCGGCGCTTTTCCCACAAACACCGCTATAA-AG
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA-AAGAC
* *
41171559 CATGACCTTTAACGGCGCTTTTCCCACAAACGCTGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
** * *
41171602 CATGACCTTTAGCGGCGCTTTTGTCACAAACGCCGTTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
** * * *
41171645 CATGACCTTTAGCGGCGCTTTTTATCACAAACGCCACTATAGAA
1 CATGACCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGAC
* *
41171689 CA-AACCTTTAGCGACGCTT
1 CATGACCTTTAGCGGCGCTT
41171708 CTCGGCAAAA
Statistics
Matches: 202, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
42 20 0.10
43 157 0.78
44 25 0.12
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
Found at i:41171633 original size:129 final size:129
Alignment explanation
Indices: 41171426--41171666 Score: 351
Period size: 129 Copynumber: 1.9 Consensus size: 129
41171416 AATGCCACTA
* * *
41171426 AAAGTCATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTATATACCACGACCTTTAGCGACGC
1 AAAGTCATGACCTTTAACGGCGCTTTCCCACAAACGCCGCTAAAGACCACGACCTTTAGCGACGC
* * * *
41171491 TTTTTCCATAAACGCCGCTAAATACCATGATCTTTAGCGGCGCTTTTCCCACAAACACCGCTAT
66 TTTTTCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAT
* * *
41171555 AAAG-CATGACCTTTAACGGCGCTTTTCCCACAAACGCTGCTAAAGACCATGACCTTTAGCGGCG
1 AAAGTCATGACCTTTAACGGCGC-TTTCCCACAAACGCCGCTAAAGACCACGACCTTTAGCGACG
*
41171619 CTTTTGT-CACAAACGCCGTTAAAGAACATGACCTTTAGCGGCGCTTTT
65 CTTTT-TCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTT
41171667 TATCACAAAC
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
128 17 0.17
129 81 0.82
130 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (129 bp):
AAAGTCATGACCTTTAACGGCGCTTTCCCACAAACGCCGCTAAAGACCACGACCTTTAGCGACGC
TTTTTCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAT
Found at i:41171696 original size:129 final size:129
Alignment explanation
Indices: 41171420--41171707 Score: 343
Period size: 129 Copynumber: 2.2 Consensus size: 129
41171410 GAAATAAATG
* * *
41171420 CCACTA-AAAGTCATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTATATACCACGACCTTT
1 CCACTATAAAG-CATAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTTT
* * * * *
41171483 AGCGACGCTTTTTCCATAAACGCCGCTAAATACCATGATCTTTAGCGGCGCTTTTCCCACAAACA
65 AGCGACGCTTTTTCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCACAAACA
* * * * *
41171548 CCGCTATAAAGCATGACCTTTAACGGCGCTTTTCCCACAAACGCTGCTAAAGACCATGACCTTTA
1 CCACTATAAAGCATAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTTTA
* * *
41171613 GCGGCGCTTTTGT-CACAAACGCCGTTAAAGAACATGACCTTTAGCGGCGCTTTTTATCACAAAC
66 GCGACGCTTTT-TCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTTACCACAAAC
*
41171677 G
129 A
*
41171678 CCACTATAGAA-CA-AACCTTTAGCGACGCTT
1 CCACTATA-AAGCATAACCTTTAGCGGCGCTT
41171708 CTCGGCAAAA
Statistics
Matches: 136, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
128 22 0.16
129 91 0.67
130 21 0.15
131 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (129 bp):
CCACTATAAAGCATAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTTTA
GCGACGCTTTTTCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCACAAACA
Found at i:41177165 original size:14 final size:15
Alignment explanation
Indices: 41177145--41177173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41177135 AAACCAGAAC
41177145 CCCTAA-TCCATAAT
1 CCCTAATTCCATAAT
41177159 CCCTAATTCCATAAT
1 CCCTAATTCCATAAT
41177174 ATATAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (15 bp):
CCCTAATTCCATAAT
Found at i:41177621 original size:41 final size:40
Alignment explanation
Indices: 41177575--41177727 Score: 209
Period size: 41 Copynumber: 3.8 Consensus size: 40
41177565 AAATGTTTTT
* * *
41177575 GCGGCGCTTTTTAAAAAACGCCGTTAAAGCACTGAGCATTA
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAGC-CGGAGCATTA
*
41177616 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAG-CCGGAGCATTA
*
41177657 GCGGCGCTTCTCAAAAAACGCCGCTAAAGTCCGGAGCATTA
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAG-CCGGAGCATTA
* *
41177698 GCGGCGCTTCTC-CAAAACGCCGCTAAAGCC
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAGCC
41177728 CCGAAAGGTC
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 2 0.02
40 15 0.15
41 85 0.83
42 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAAACGCCGCTAAAGCCGGAGCATTA
Found at i:41177712 original size:82 final size:81
Alignment explanation
Indices: 41177575--41177728 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 81
41177565 AAATGTTTTT
* * * * *
41177575 GCGGCGCTTTTTAAAAAACGCCGTTAAAGCACTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGC
1 GCGGCGCTTCTCAAAAAACGCCGCTAAAGCACGGAGCATTAGCGGCGCTTCTCC-AAAACGCCGC
41177640 TAAAGCCCGGAGCATTA
65 TAAAGCCCGGAGCATTA
41177657 GCGGCGCTTCTCAAAAAACGCCGCTAAAGTC-CGGAGCATTAGCGGCGCTTCTCCAAAACGCCGC
1 GCGGCGCTTCTCAAAAAACGCCGCTAAAG-CACGGAGCATTAGCGGCGCTTCTCCAAAACGCCGC
41177721 TAAAGCCC
65 TAAAGCCC
41177729 CGAAAGGTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 18 0.27
82 47 0.71
83 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (81 bp):
GCGGCGCTTCTCAAAAAACGCCGCTAAAGCACGGAGCATTAGCGGCGCTTCTCCAAAACGCCGCT
AAAGCCCGGAGCATTA
Found at i:41182642 original size:12 final size:11
Alignment explanation
Indices: 41182611--41182640 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41182601 TCCTACTGTC
*
41182611 AACAAACATAA
1 AACAAAAATAA
41182622 AACAAAAATAA
1 AACAAAAATAA
41182633 AACAAAAA
1 AACAAAAA
41182641 ATGGGCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (11 bp):
AACAAAAATAA
Found at i:41187661 original size:20 final size:20
Alignment explanation
Indices: 41187633--41187675 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41187623 AAAAAATTTT
* *
41187633 ATATTTAAAACCATAATAAA
1 ATATATAAAACCAAAATAAA
*
41187653 ATATATAAAACTAAAATAAA
1 ATATATAAAACCAAAATAAA
41187673 ATA
1 ATA
41187676 AAAACACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
ATATATAAAACCAAAATAAA
Found at i:41189784 original size:29 final size:29
Alignment explanation
Indices: 41189745--41189800 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
41189735 GCTAATTAAG
*
41189745 ATTAAGTTTTGGTTAATTAAAGTTTAATAA
1 ATTAAGTTTTGATTAATTAAA-TTTAATAA
41189775 ATTAA-TTTTGATTAATTAAATTTAAT
1 ATTAAGTTTTGATTAATTAAATTTAAT
41189801 CAAAAGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 14 0.56
30 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (29 bp):
ATTAAGTTTTGATTAATTAAATTTAATAA
Found at i:41193321 original size:14 final size:15
Alignment explanation
Indices: 41193294--41193325 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41193284 AAATGGTTAA
41193294 TGTAAAAAGAAAAAT
1 TGTAAAAAGAAAAAT
41193309 TGTAAAAAGAAAAAT
1 TGTAAAAAGAAAAAT
41193324 TG
1 TG
41193326 AAATGAATGA
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:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (15 bp):
TGTAAAAAGAAAAAT
Done.