Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012455.1 Kokia drynarioides strain JFW-HI SEQ_127459, whole genome shotgun sequence
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: 421919
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 33 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1273 original size:21 final size:22
Alignment explanation
Indices: 1241--1281 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1231 GAACGATGTA
1241 GTTTTGTCTTTTAAC-TTAATG
1 GTTTTGTCTTTTAACATTAATG
1262 GTTTTGAT-TTTTAACATTAA
1 GTTTTG-TCTTTTAACATTAA
1282 AAGAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.56
Consensus pattern (22 bp):
GTTTTGTCTTTTAACATTAATG
Found at i:1931 original size:14 final size:14
Alignment explanation
Indices: 1912--1948 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1902 TATTTAATAA
*
1912 ATTTATATATTTTT
1 ATTTATATAATTTT
1926 ATTTAT-TAATTTT
1 ATTTATATAATTTT
1939 -TTTATATAAT
1 ATTTATATAAT
1949 CATTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 10 0.48
14 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTATATAATTTT
Found at i:6559 original size:21 final size:21
Alignment explanation
Indices: 6535--6590 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
6525 CTAGAGTTTG
6535 TTGTATCGGTAGAAGTAATAA
1 TTGTATCGGTAGAAGTAATAA
* * * *
6556 TTGTATCGATAGTAGTCATAC
1 TTGTATCGGTAGAAGTAATAA
*
6577 TTGTATCAGTAGAA
1 TTGTATCGGTAGAA
6591 CCTTCCCAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTAATAA
Found at i:14305 original size:29 final size:29
Alignment explanation
Indices: 14232--14297 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
14222 AGATTCATCA
14232 ACTCGACTAACTCGAAATTTTTTGACTCG
1 ACTCGACTAACTCGAAATTTTTTGACTCG
14261 ACTCGACTAACTCGAAATTTTTTGACTCG
1 ACTCGACTAACTCGAAATTTTTTGACTCG
14290 ACTCGACT
1 ACTCGACT
14298 CGATCGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (29 bp):
ACTCGACTAACTCGAAATTTTTTGACTCG
Found at i:18705 original size:15 final size:16
Alignment explanation
Indices: 18678--18708 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
18668 ATTTTATTTT
18678 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
18694 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
18709 TAGTATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:18800 original size:15 final size:16
Alignment explanation
Indices: 18755--18802 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
18745 ATTAATATTC
18755 TAAATAATAAATATTTAT
1 TAAATAATAAATA--TAT
*
18773 TACAATTATAAATATAT
1 TA-AATAATAAATATAT
18790 T-AATAATAAATAT
1 TAAATAATAAATAT
18803 TTTGTAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 11 0.41
17 4 0.15
18 2 0.07
19 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATAATAAATATAT
Found at i:19200 original size:27 final size:26
Alignment explanation
Indices: 19161--19211 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
19151 TATAAGGATT
19161 TATGACATATTTTAATCTAGTATAAAAA
1 TATGACATATTTTAAT-TA-TATAAAAA
19189 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
19212 TATGAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 10 0.43
28 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:22070 original size:21 final size:21
Alignment explanation
Indices: 22046--22097 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
22036 TGAGACAATA
*
22046 CTACTGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
22067 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
22088 CTACCGATAC
1 CTACCGATAC
22098 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:28144 original size:18 final size:18
Alignment explanation
Indices: 28114--28152 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28104 TTTCGAGTAA
28114 AATCGAATTAATTCGATT
1 AATCGAATTAATTCGATT
*
28132 AATC-AATTAAATTCGGTT
1 AATCGAATT-AATTCGATT
28150 AAT
1 AAT
28153 GGTCGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
AATCGAATTAATTCGATT
Found at i:36929 original size:21 final size:21
Alignment explanation
Indices: 36899--37009 Score: 71
Period size: 21 Copynumber: 5.3 Consensus size: 21
36889 CAAGCAAGAA
36899 CCCTGTATTACACTCCGATGC
1 CCCTGTATTACACTCCGATGC
* * *
36920 CCCT-TGATTAAACTTCGGTGC
1 CCCTGT-ATTACACTCCGATGC
* *
36941 CCCTGTATTGCACTCCAATGC
1 CCCTGTATTACACTCCGATGC
* * * * ** * *
36962 CCTTATTTTGCACTTTGGTGT
1 CCCTGTATTACACTCCGATGC
* *
36983 CCCTGTATTACACTCTGGTGC
1 CCCTGTATTACACTCCGATGC
37004 CCCTGT
1 CCCTGT
37010 GTGTTTGATC
Statistics
Matches: 66, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.17, T:0.35
Consensus pattern (21 bp):
CCCTGTATTACACTCCGATGC
Found at i:37593 original size:28 final size:28
Alignment explanation
Indices: 37558--37616 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
37548 TTTGAAAGTT
37558 AGAACAAATTGTGTAGGTTAAATAGGTA
1 AGAACAAATTGTGTAGGTTAAATAGGTA
37586 AGAACAAATTGTGTAGGTTAAATAGGTA
1 AGAACAAATTGTGTAGGTTAAATAGGTA
37614 AGA
1 AGA
37617 TAATTTCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.27
Consensus pattern (28 bp):
AGAACAAATTGTGTAGGTTAAATAGGTA
Found at i:48740 original size:145 final size:145
Alignment explanation
Indices: 48326--48725 Score: 631
Period size: 145 Copynumber: 2.8 Consensus size: 145
48316 TCATTCATTG
*
48326 TAATTCACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTCAAGTTGATTGAAT
1 TAATTCACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTTAAGTTGATTGAAT
* * * *
48391 CATAACTT-AATTGACATGAATATTGTTGCCACTACAGGAGGACATAAGTTCGAGTACGTTAGGA
66 -ATTAGTTCAATTGGCATGAATATTGTTGCCACTACAGGAGGACATAAGTTCGAGTATGTTAGGA
48455 TTTTGCTATTTTCTTA
130 TTTTGCTATTTTCTTA
*
48471 TAATTCACAAAAAAAAAATTAACATAAAAACACATTAATTTTTAAATTATTTAAGTTGATTGAAT
1 TAATTCACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTTAAGTTGATTGAAT
* * * *
48536 CTTAGCTCAATTGGTATGAATATTGTTGCCACTATAGGAGGACATAAGTTCGAGTATGTTAGGAT
66 ATTAGTTCAATTGGCATGAATATTGTTGCCACTACAGGAGGACATAAGTTCGAGTATGTTAGGAT
*
48601 TTTGCTCTTTTCTTA
131 TTTGCTATTTTCTTA
* *
48616 TAATTTACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTTAAATTGATTGAAT
1 TAATTCACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTTAAGTTGATTGAAT
* * * *
48681 TTTAGTTCAATTGGCATGAACATTATTGCCATTACAGGAGGACAT
66 ATTAGTTCAATTGGCATGAATATTGTTGCCACTACAGGAGGACAT
48726 GGGTCAAAAT
Statistics
Matches: 233, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
144 3 0.01
145 230 0.99
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (145 bp):
TAATTCACAAAAAAAATATTAACATAAAAACACATTAATTTTTAAATTATTTAAGTTGATTGAAT
ATTAGTTCAATTGGCATGAATATTGTTGCCACTACAGGAGGACATAAGTTCGAGTATGTTAGGAT
TTTGCTATTTTCTTA
Found at i:49121 original size:26 final size:27
Alignment explanation
Indices: 49092--49161 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 27
49082 TAATATGACT
*
49092 ATATAAAAAAT-TTTAATAAATAAAA-A
1 ATATAAAAAATATTAAAT-AATAAAATA
*
49118 ATATATAAAAATATTAAATACTAAAATA
1 ATATA-AAAAATATTAAATAATAAAATA
49146 ATATAATATAAATATT
1 ATATAA-A-AAATATT
49162 TGTTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 5 0.14
27 13 0.35
28 12 0.32
29 7 0.19
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATAAAAAATATTAAATAATAAAATA
Found at i:49137 original size:28 final size:28
Alignment explanation
Indices: 49091--49161 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
49081 TTAATATGAC
*
49091 TATATAAAAA-ATTTTAATAAATAAAA-AA
1 TATATAAAAATA-TTAAAT-AATAAAATAA
*
49119 TATATAAAAATATTAAATACTAAAATAA
1 TATATAAAAATATTAAATAATAAAATAA
*
49147 TATAATATAAATATT
1 TAT-ATAAAAATATT
49162 TGTTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.16
28 20 0.54
29 11 0.30
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
TATATAAAAATATTAAATAATAAAATAA
Found at i:50524 original size:28 final size:26
Alignment explanation
Indices: 50493--50560 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
50483 AATTTTAAAT
*
50493 TTTTTATATATTTAAAATTATTTTTTTA
1 TTTTTATATATTTAAAA-TA-GTTTTTA
* * *
50521 TTTTTTTAAATTTTAAATAGTTTTTA
1 TTTTTATATATTTAAAATAGTTTTTA
50547 TTTTTCATAATATT
1 TTTTT-AT-ATATT
50561 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 11 0.34
27 3 0.09
28 18 0.56
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTTTATATATTTAAAATAGTTTTTA
Found at i:50584 original size:16 final size:15
Alignment explanation
Indices: 50555--50584 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
50545 TATTTTTCAT
50555 AATATTATATTTTAA
1 AATATTATATTTTAA
50570 AATATATATATTTTA
1 AATAT-TATATTTTA
50585 TGTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTATATTTTAA
Found at i:53521 original size:44 final size:44
Alignment explanation
Indices: 53436--53532 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
53426 AAACAATAGT
53436 AAAAAC-GCATAAAAAATAACATCCAAACAACAAAAATAACAAC
1 AAAAACAGCATAAAAAATAACATCCAAACAACAAAAATAACAAC
* * * *
53479 CAAAACAGCAGTAAAAATTAACA-GCAAACAACATTAAA-AACAAC
1 AAAAACAGCA-TAAAAAATAACATCCAAACAACA-AAAATAACAAC
*
53523 AAAAATAGCA
1 AAAAACAGCA
53533 ACACAAACAG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 5 0.11
44 26 0.58
45 14 0.31
ACGTcount: A:0.65, C:0.20, G:0.05, T:0.10
Consensus pattern (44 bp):
AAAAACAGCATAAAAAATAACATCCAAACAACAAAAATAACAAC
Found at i:53534 original size:12 final size:12
Alignment explanation
Indices: 53519--53563 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
53509 ACATTAAAAA
53519 CAACAAAAATAG
1 CAACAAAAATAG
* *
53531 CAACACAAACAG
1 CAACAAAAATAG
* *
53543 TAACAAAAATAA
1 CAACAAAAATAG
53555 CAACAAAAA
1 CAACAAAAA
53564 CAATACGAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:53578 original size:23 final size:23
Alignment explanation
Indices: 53514--53601 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
53504 AAACAACATT
*
53514 AAAAAC-A-ACAAAAATAGCAAC
1 AAAAACAATACAAAAATAACAAC
* *
53535 ACAAACAGTAACAAAAATAACAAC
1 AAAAACAAT-ACAAAAATAACAAC
*
53559 AAAAACAATACGAAAATAACAAC
1 AAAAACAATACAAAAATAACAAC
* *
53582 CAAAACAATA-AAAAAAAACA
1 AAAAACAATACAAAAATAACA
53602 CGAAACAGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.09
22 8 0.15
23 22 0.40
24 20 0.36
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (23 bp):
AAAAACAATACAAAAATAACAAC
Found at i:53580 original size:56 final size:56
Alignment explanation
Indices: 53460--53568 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 56
53450 AATAACATCC
** * *
53460 AAACAACAAAAATAACAACCAAAACAGCAGTAAAAATTAACAGCAAACAACATTAA
1 AAACAACAAAAATAACAACCAAAACAGCAACAAAAATTAACAACAAACAACAATAA
* *
53516 AAACAACAAAAATAGCAA-CACAAACAGTAACAAAAA-TAACAACAAA-AACAATA
1 AAACAACAAAAATAACAACCA-AAACAGCAACAAAAATTAACAACAAACAACAATA
53569 CGAAAATAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 6 0.13
55 11 0.24
56 29 0.63
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.09
Consensus pattern (56 bp):
AAACAACAAAAATAACAACCAAAACAGCAACAAAAATTAACAACAAACAACAATAA
Found at i:53586 original size:12 final size:12
Alignment explanation
Indices: 53517--53586 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
53507 CAACATTAAA
53517 AACAACAAAAAT
1 AACAACAAAAAT
* * *
53529 AGCAACACAAAC
1 AACAACAAAAAT
**
53541 AGTAACAAAAAT
1 AACAACAAAAAT
*
53553 AACAACAAAAAC
1 AACAACAAAAAT
* *
53565 AA-TACGAAAAT
1 AACAACAAAAAT
53576 AACAACCAAAA
1 AACAA-CAAAA
53587 CAATAAAAAA
Statistics
Matches: 42, Mismatches: 14, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
11 8 0.19
12 30 0.71
13 4 0.10
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:53594 original size:20 final size:20
Alignment explanation
Indices: 53548--53673 Score: 60
Period size: 20 Copynumber: 6.1 Consensus size: 20
53538 AACAGTAACA
*
53548 AAAATAACAACAAAAACAAT
1 AAAATAACAACCAAAACAAT
53568 ACGAAAATAACAACCAAAACAAT
1 ---AAAATAACAACCAAAACAAT
* * *
53591 AAAA-AAAAACACGAAACAGT
1 AAAATAACAAC-CAAAACAAT
* * *
53611 AAAA-AAAATACAAAAACAGCAA
1 AAAATAACA-ACCAAAACA--AT
* * *
53633 AAAATAGCAAGCAAAACAGT
1 AAAATAACAACCAAAACAAT
* *
53653 AAAAAAAC-ACCAAAATAAT
1 AAAATAACAACCAAAACAAT
53672 AA
1 AA
53674 TATACTATTT
Statistics
Matches: 79, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
19 15 0.19
20 30 0.38
21 2 0.03
22 11 0.14
23 21 0.27
ACGTcount: A:0.71, C:0.16, G:0.06, T:0.08
Consensus pattern (20 bp):
AAAATAACAACCAAAACAAT
Found at i:53657 original size:23 final size:22
Alignment explanation
Indices: 53523--53659 Score: 106
Period size: 23 Copynumber: 6.2 Consensus size: 22
53513 TAAAAACAAC
*
53523 AAAAATAGCAACACAAACAGTAA
1 AAAAATAACAACA-AAACAGTAA
* *
53546 CAAAAATAACAACAAAAACAATAC
1 -AAAAATAACAAC-AAAACAGTAA
* *
53570 GAAAATAACAACCAAAACAATAA
1 AAAAATAACAA-CAAAACAGTAA
*
53593 AAAAA-AAC-ACGAAACAGTAA
1 AAAAATAACAACAAAACAGTAA
*
53613 AAAAA-ATAC-A-AAAACAG-CA
1 AAAAATA-ACAACAAAACAGTAA
*
53632 AAAAATAGCAAGCAAAACAGTAA
1 AAAAATAACAA-CAAAACAGTAA
53655 AAAAA
1 AAAAA
53660 CACCAAAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.08
20 23 0.25
21 4 0.04
22 10 0.11
23 29 0.31
24 19 0.20
25 1 0.01
ACGTcount: A:0.70, C:0.16, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAAATAACAACAAAACAGTAA
Found at i:54221 original size:13 final size:12
Alignment explanation
Indices: 54202--54233 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
54192 AAGAAAACTA
54202 TATAAAAAATTT
1 TATAAAAAATTT
54214 TAATAAAAAATTT
1 T-ATAAAAAATTT
54227 TATAAAA
1 TATAAAA
54234 TTATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAAAAAATTT
Found at i:71323 original size:30 final size:30
Alignment explanation
Indices: 71287--71348 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
71277 AGAAATTGTA
71287 GAATTTAATCCCTTAGCTCTTGATGATTTC
1 GAATTTAATCCCTTAGCTCTTGATGATTTC
71317 GAATTTAATCCCTTAGCTCTTGATGATTTC
1 GAATTTAATCCCTTAGCTCTTGATGATTTC
71347 GA
1 GA
71349 CATTCTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (30 bp):
GAATTTAATCCCTTAGCTCTTGATGATTTC
Found at i:73259 original size:21 final size:21
Alignment explanation
Indices: 73235--73278 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
73225 CTCGACAGGT
* * * *
73235 TCTTCTTCTTCTTGTTCTTTC
1 TCTTCCTCGTCTTGATCCTTC
73256 TCTTCCTCGTCTTGATCCTTC
1 TCTTCCTCGTCTTGATCCTTC
73277 TC
1 TC
73279 ATGATTACCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.34, G:0.07, T:0.57
Consensus pattern (21 bp):
TCTTCCTCGTCTTGATCCTTC
Found at i:79142 original size:15 final size:15
Alignment explanation
Indices: 79122--79162 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
79112 TTTATTGTAG
79122 TAATTCAATAACATC
1 TAATTCAATAACATC
79137 TAATTCATAAATAACATC
1 TAATTC---AATAACATC
79155 TAATTCAA
1 TAATTCAA
79163 GAACTCCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATTCAATAACATC
Found at i:86266 original size:2 final size:2
Alignment explanation
Indices: 86259--86287 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86249 AATGTGAAAA
86259 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
86288 TGAAAGGGGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:86474 original size:29 final size:30
Alignment explanation
Indices: 86433--86489 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
86423 TTTGATCACA
* *
86433 AAATTTAATTAAAGCTC-AATTTAGTCCCC
1 AAATTTAACTAAAACTCTAATTTAGTCCCC
* *
86462 AAATTTCACTAAAATTCTAATTTAGTCC
1 AAATTTAACTAAAACTCTAATTTAGTCC
86490 TTAATTCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (30 bp):
AAATTTAACTAAAACTCTAATTTAGTCCCC
Found at i:87063 original size:27 final size:27
Alignment explanation
Indices: 87032--87085 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
87022 GTTACGTTTG
* *
87032 GTTATATAAATCAGTTATATGGAAATA
1 GTTATATAAATCAGATATATGAAAATA
* *
87059 GTTATATGAATCGGATATATGAAAATA
1 GTTATATAAATCAGATATATGAAAATA
87086 AATATATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (27 bp):
GTTATATAAATCAGATATATGAAAATA
Found at i:87312 original size:39 final size:39
Alignment explanation
Indices: 87269--87343 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
87259 GTGTATATGG
*
87269 GAGATTTAATTATAATATAAGTTTATAGTAATTTTGGTT
1 GAGATTTAATTATAATATAAGTTTATAGTAAGTTTGGTT
* * *
87308 GAGATTTAATTATGATATGAGTTTATATTAAGTTTG
1 GAGATTTAATTATAATATAAGTTTATAGTAAGTTTG
87344 ATTTGATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (39 bp):
GAGATTTAATTATAATATAAGTTTATAGTAAGTTTGGTT
Found at i:87394 original size:16 final size:17
Alignment explanation
Indices: 87373--87408 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
87363 TTAAGGGAGA
*
87373 GAAATAA-TAGTTGGAT
1 GAAATAATTACTTGGAT
87389 GAAATAATTACTTGGAT
1 GAAATAATTACTTGGAT
87406 GAA
1 GAA
87409 TTATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (17 bp):
GAAATAATTACTTGGAT
Found at i:94264 original size:25 final size:25
Alignment explanation
Indices: 94203--94264 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
94193 AATGTTCATA
* * *
94203 AATATTAAACGAATATGTTCATGAAC
1 AATATT-AATGAACATGTTCACGAAC
94229 -ATA-TAATTGAACATGTTCACGAAC
1 AATATTAA-TGAACATGTTCACGAAC
94253 AATATTAATGAA
1 AATATTAATGAA
94265 TAATAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 10 0.33
26 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (25 bp):
AATATTAATGAACATGTTCACGAAC
Found at i:96323 original size:21 final size:21
Alignment explanation
Indices: 96275--96331 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
96265 TATATAAAAT
96275 AAAACCCTTAAACCCAAAACCC
1 AAAACCC-TAAACCCAAAACCC
*
96297 AAAACCCTAAACTCATAAA-CC
1 AAAACCCTAAACCCA-AAACCC
* *
96318 ATAACCTTAAACCC
1 AAAACCCTAAACCC
96332 CTGAACTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAACCCTAAACCCAAAACCC
Found at i:107211 original size:20 final size:20
Alignment explanation
Indices: 107174--107212 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
107164 ACTAAGAATC
*
107174 TGAAACAACATAACGAAAAG
1 TGAAACAACATAAAGAAAAG
107194 TGAAACAA-ATAAAAGAAAA
1 TGAAACAACAT-AAAGAAAA
107213 TAAATGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (20 bp):
TGAAACAACATAAAGAAAAG
Found at i:109730 original size:17 final size:17
Alignment explanation
Indices: 109708--109741 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
109698 GTTGCAATGT
109708 GAGTAGGAATTAACTCA
1 GAGTAGGAATTAACTCA
109725 GAGTAGGAATTAACTCA
1 GAGTAGGAATTAACTCA
109742 TTCTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
GAGTAGGAATTAACTCA
Found at i:115301 original size:18 final size:18
Alignment explanation
Indices: 115250--115301 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
115240 TAAAAAAACC
*
115250 ATTGTTTAAAAGGA-AGCT
1 ATTGTTCAAAAGGAGA-CT
**
115268 ATTGTTCAAGGGGAGACT
1 ATTGTTCAAAAGGAGACT
*
115286 ATTGTTCAAAATGAGA
1 ATTGTTCAAAAGGAGA
115302 TTGTTAGGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (18 bp):
ATTGTTCAAAAGGAGACT
Found at i:120005 original size:2 final size:2
Alignment explanation
Indices: 119998--120030 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
119988 TCGTACGTAT
119998 TA TA 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 TA TA T
120031 TTAAGTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:124444 original size:44 final size:44
Alignment explanation
Indices: 124381--124469 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
124371 AATAACTTAT
*
124381 GTGTAGCTCTCGAAACCGATGTAGGAGCGGGTTGCATAGGTGGA
1 GTGTAGCTCTCAAAACCGATGTAGGAGCGGGTTGCATAGGTGGA
124425 GTGTAGCTCTCAAAACCGATGTAGGAGCGGGTTGCATAGGTGGA
1 GTGTAGCTCTCAAAACCGATGTAGGAGCGGGTTGCATAGGTGGA
124469 G
1 G
124470 GAGGAGGTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (44 bp):
GTGTAGCTCTCAAAACCGATGTAGGAGCGGGTTGCATAGGTGGA
Found at i:127266 original size:52 final size:51
Alignment explanation
Indices: 127196--127298 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 51
127186 GATGAATTCA
127196 ATTCAAAATAAGAATTATGAATAGAAGGACAAATAAAGCTAGGTTGTAATC
1 ATTCAAAATAAGAATTATGAATAGAAGGACAAATAAAGCTAGGTTGTAATC
* *
127247 ATTCTAAATTAAGAATTATGAATAGAAGGACAAATAATGCTAGGTTGTAATC
1 ATTC-AAAATAAGAATTATGAATAGAAGGACAAATAAAGCTAGGTTGTAATC
127299 CTAGCCTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 4 0.08
52 45 0.92
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (51 bp):
ATTCAAAATAAGAATTATGAATAGAAGGACAAATAAAGCTAGGTTGTAATC
Found at i:136865 original size:12 final size:12
Alignment explanation
Indices: 136834--136882 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
136824 GAGCAATTCC
136834 TTCTTCTTATTCTT
1 TTCTTCTT-TTC-T
136848 TATCTTCTTTTCT
1 T-TCTTCTTTTCT
*
136861 TTCTTCTTCTCT
1 TTCTTCTTTTCT
*
136873 TGCTTCTTTT
1 TTCTTCTTTT
136883 TCTACTGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 4 0.13
15 7 0.23
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.69
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:136868 original size:15 final size:16
Alignment explanation
Indices: 136833--136870 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
136823 TGAGCAATTC
136833 CTTCTTCTTATTCTTT
1 CTTCTTCTTATTCTTT
*
136849 -ATCTTCTT-TTCTTT
1 CTTCTTCTTATTCTTT
136863 CTTCTTCT
1 CTTCTTCT
136871 CTTGCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTCTTCTTATTCTTT
Found at i:137709 original size:70 final size:70
Alignment explanation
Indices: 137595--137735 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
137585 GCGGGCTCAG
*
137595 TAATTTCTTGATGAAGGATTGCGCCGACATCAATTCTGCATCCCTTCAGTATAGAATGCAACAGG
1 TAATTTCTTGATGAAGGATTGCGCCGACATCAATTCTACATCCCTTCAGTATAGAATGCAACAGG
137660 AACAT
66 AACAT
*
137665 TAATTTCTTGATGAAGGATTGCGCCGACATCAATTCTACGTCCCTTCAGTATAGAATGCAACAGG
1 TAATTTCTTGATGAAGGATTGCGCCGACATCAATTCTACATCCCTTCAGTATAGAATGCAACAGG
137730 AACAT
66 AACAT
137735 T
1 T
137736 CTATTTAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (70 bp):
TAATTTCTTGATGAAGGATTGCGCCGACATCAATTCTACATCCCTTCAGTATAGAATGCAACAGG
AACAT
Found at i:145995 original size:57 final size:58
Alignment explanation
Indices: 145898--146019 Score: 142
Period size: 57 Copynumber: 2.1 Consensus size: 58
145888 ATTGCATGGT
* *
145898 GAAATGGAGAAATAGGAAACATTTGGAAATGATTAAGGTTTTAT-CTAAAATGAAAATGA
1 GAAATGGAGAAATA-GAAACATTTGGAAATGAATAAGGTTTTATAC-AAAATAAAAATGA
* ** *
145957 -AAATGGAGAAAT-GAAATCTTTTGGAAATGAATGTGGTTTTCTACAAAATAAAAATGA
1 GAAATGGAGAAATAGAAA-CATTTGGAAATGAATAAGGTTTTATACAAAATAAAAATGA
146014 GAAATG
1 GAAATG
146020 AACATTGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 4 0.07
57 32 0.59
58 18 0.33
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (58 bp):
GAAATGGAGAAATAGAAACATTTGGAAATGAATAAGGTTTTATACAAAATAAAAATGA
Found at i:150100 original size:15 final size:17
Alignment explanation
Indices: 150080--150118 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
150070 ATAATAAATT
*
150080 ATAATAATATTAGTGATA
1 ATAATAATAAT-GTGATA
150098 ATAATAATAATGTGATA
1 ATAATAATAATGTGATA
150115 ATAA
1 ATAA
150119 GATGATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (17 bp):
ATAATAATAATGTGATA
Found at i:152986 original size:20 final size:19
Alignment explanation
Indices: 152961--152999 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
152951 GATTAGCTTA
*
152961 AATTTAAGGATTATTGTTTC
1 AATTTAACGATTA-TGTTTC
*
152981 AATTTACCGATTATGTTTC
1 AATTTAACGATTATGTTTC
153000 CTTAGTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
AATTTAACGATTATGTTTC
Found at i:155157 original size:21 final size:20
Alignment explanation
Indices: 155115--155157 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
155105 AAGTGGGAAG
*
155115 AAGTAAAAGTTTTGGGTGAA
1 AAGTAAAAGTTTGGGGTGAA
155135 AAGTAAAAAGATTTGGGGT-AA
1 AAGT-AAAAG-TTTGGGGTGAA
155156 AA
1 AA
155158 TTGTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (20 bp):
AAGTAAAAGTTTGGGGTGAA
Found at i:156391 original size:17 final size:17
Alignment explanation
Indices: 156365--156404 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
156355 CTAAATTTCT
156365 AAAA-ATAAAAATATAA
1 AAAATATAAAAATATAA
*
156381 AAAATATAAAAATTTAA
1 AAAATATAAAAATATAA
*
156398 AATATAT
1 AAAATAT
156405 TTTAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATATAAAAATATAA
Found at i:160019 original size:18 final size:18
Alignment explanation
Indices: 159996--160030 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
159986 GGATGACGAT
159996 CAAAATAATCAACTTCCC
1 CAAAATAATCAACTTCCC
*
160014 CAAAATAATCAGCTTCC
1 CAAAATAATCAACTTCC
160031 TCCTGTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.31, G:0.03, T:0.23
Consensus pattern (18 bp):
CAAAATAATCAACTTCCC
Found at i:162610 original size:7 final size:8
Alignment explanation
Indices: 162593--162618 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
162583 AACCCAAGTG
162593 TTTTTATT
1 TTTTTATT
162601 TTTTTATT
1 TTTTTATT
162609 TTTTTATT
1 TTTTTATT
162617 TT
1 TT
162619 ACTTCCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:163585 original size:3 final size:3
Alignment explanation
Indices: 163579--163616 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
163569 ATTATCCCTT
*
163579 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
163617 GTTGTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:163621 original size:3 final size:3
Alignment explanation
Indices: 163615--163691 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
163605 ATTATTACTA
163615 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
163663 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
163692 CTGTTTTGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:168346 original size:45 final size:45
Alignment explanation
Indices: 168187--168348 Score: 161
Period size: 45 Copynumber: 3.6 Consensus size: 45
168177 CGAAACTAGA
* * * * *
168187 AAGACCATGGTTGAAAGATACTATGTCA-TTTAACCGGAAT-GAAT
1 AAGACCATAGTTGAAAGATACTATGGCACTAT-ATCGGAATCGAGT
* *
168231 AAGACCATAGTTGAAAGATACTATGACACTATATCGGAATTGAGT
1 AAGACCATAGTTGAAAGATACTATGGCACTATATCGGAATCGAGT
** * *
168276 AAGACCATAGTTGAAACTTACTATGGTATTATATCGGTAA-CGA-T
1 AAGACCATAGTTGAAAGATACTATGGCACTATATCGG-AATCGAGT
*
168320 CAAGACCATAGTTGAAAGATCCTATGGCA
1 -AAGACCATAGTTGAAAGATACTATGGCA
168349 TCACTTCGGC
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
44 34 0.34
45 63 0.64
46 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGATACTATGGCACTATATCGGAATCGAGT
Found at i:181809 original size:23 final size:23
Alignment explanation
Indices: 181783--182068 Score: 392
Period size: 23 Copynumber: 12.4 Consensus size: 23
181773 TTCTTATATA
*
181783 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
181806 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
181829 TGTGCTTAAGTATTAACGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
181852 TAAGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
181875 TGTGCTTAAATATTAATGTTATT
1 TATGCTTAAATATTAATGTGATT
* *
181898 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
181921 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
181944 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
181967 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
181990 TATGCTTAAACATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
182013 TGTGCTTAAATATTAGTATGATT
1 TATGCTTAAATATTAATGTGATT
*
182036 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
182059 TGTGCTTAAA
1 TATGCTTAAA
182069 GAATTAAGAT
Statistics
Matches: 227, Mismatches: 36, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 227 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:184457 original size:37 final size:38
Alignment explanation
Indices: 184416--184500 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
184406 TAAAAAGTAT
*
184416 TTATATTAAAAAA-ATC-AA-AAATATAATAAATATTTTA
1 TTATATTAAAAAACA-CAAATAAATATAATAAA-AATTTA
184453 TTATATTAAAAAACACAAATAAATATAATAAAAATTTA
1 TTATATTAAAAAACACAAATAAATATAATAAAAATTTA
184491 TTATATTAAA
1 TTATATTAAA
184501 TATAATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
37 14 0.32
38 18 0.41
39 12 0.27
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (38 bp):
TTATATTAAAAAACACAAATAAATATAATAAAAATTTA
Found at i:190489 original size:50 final size:49
Alignment explanation
Indices: 190427--190541 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 49
190417 CTATTGGAAA
190427 TATAATATTTAAATTTA-AAATTATAAATTTGGAAAATATTTATGTATTTT
1 TATAAT-TTTAAATTTATAAA-TATAAATTTGGAAAATATTTATGTATTTT
* * ** *
190477 TATATTTTTTAAATTTATTAATATATTTTTTGAAAATATTTATGTATTTT
1 TATA-ATTTTAAATTTATAAATATAAATTTGGAAAATATTTATGTATTTT
190527 TATAATTTTAAATTT
1 TATAATTTTAAATTT
190542 TTAAGAATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
49 10 0.18
50 44 0.77
51 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (49 bp):
TATAATTTTAAATTTATAAATATAAATTTGGAAAATATTTATGTATTTT
Found at i:190516 original size:21 final size:21
Alignment explanation
Indices: 190477--190527 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
190467 TATGTATTTT
*
190477 TATATTTTTTAAATTTATTAA
1 TATATTTTTTAAATATATTAA
*
190498 TATATTTTTTGAAA-ATATTTA
1 TATATTTTTT-AAATATATTAA
*
190519 TGTATTTTT
1 TATATTTTT
190528 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TATATTTTTTAAATATATTAA
Found at i:190821 original size:18 final size:17
Alignment explanation
Indices: 190800--190844 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
190790 CCACATTAAC
*
190800 AAAAAAAAATTTAAAGTT
1 AAAAAAAAA-TTAAAATT
*
190818 AAAAACATAATTAAAATT
1 AAAAA-AAAATTAAAATT
190836 AAAAAAAAA
1 AAAAAAAAA
190845 AACCTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAAAAAATTAAAATT
Found at i:192413 original size:9 final size:9
Alignment explanation
Indices: 192401--192425 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
192391 AAACCAAATA
192401 AACCATTTC
1 AACCATTTC
192410 AACCATTTC
1 AACCATTTC
192419 AACCATT
1 AACCATT
192426 ACAAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (9 bp):
AACCATTTC
Found at i:193919 original size:45 final size:45
Alignment explanation
Indices: 193855--193946 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
193845 TTGCCTAGCT
* * * *
193855 TCTTGAAGCTCCTCATCATCATCACCATTTGATAAGTAAATATCC
1 TCTTGAACCCCCTCATCATCATCACCATCTGATAAATAAATATCC
*
193900 TCTTGAACCCCCTCGTCATCATCACCATCTGATAAATAAATATCC
1 TCTTGAACCCCCTCATCATCATCACCATCTGATAAATAAATATCC
193945 TC
1 TC
193947 ACCACCTCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (45 bp):
TCTTGAACCCCCTCATCATCATCACCATCTGATAAATAAATATCC
Found at i:194128 original size:15 final size:15
Alignment explanation
Indices: 194046--194128 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
194036 TACCAGCATG
* *
194046 CTCACCACCATCTCC
1 CTCACCACCCTCACC
*
194061 CTCACCATCCTCACC
1 CTCACCACCCTCACC
* *
194076 CTCACCACCCTTACTG
1 CTCACCACCCTCAC-C
* * *
194092 C-CAGCACCTTTACC
1 CTCACCACCCTCACC
194106 CT---CACCCTCACC
1 CTCACCACCCTCACC
194118 CTCACCACCCT
1 CTCACCACCCT
194129 TACTACCAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
12 10 0.19
14 1 0.02
15 40 0.77
16 1 0.02
ACGTcount: A:0.19, C:0.58, G:0.02, T:0.20
Consensus pattern (15 bp):
CTCACCACCCTCACC
Found at i:194149 original size:42 final size:42
Alignment explanation
Indices: 194069--194151 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
194059 CCCTCACCAT
* **
194069 CCTCACCCTCACCACCCTTACTGCCAGCACCTTTACCCTCAC
1 CCTCACCCTCACCACCCTTACTACCAGCACCTAAACCCTCAC
194111 CCTCACCCTCACCACCCTTACTACCAGCATCC-AAACCCTCA
1 CCTCACCCTCACCACCCTTACTACCAGCA-CCTAAACCCTCA
194152 ACACCTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.54, G:0.04, T:0.19
Consensus pattern (42 bp):
CCTCACCCTCACCACCCTTACTACCAGCACCTAAACCCTCAC
Found at i:195830 original size:24 final size:24
Alignment explanation
Indices: 195799--195861 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
195789 CCAGACAACA
* * **
195799 TTAGCTCTCACGAGCCTAGGATGG
1 TTAGCTCTTACGAGCCCAAAATGG
195823 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAAAATGG
195847 TTAGCTCTTACGAGC
1 TTAGCTCTTACGAGC
195862 TCAGAATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAAATGG
Found at i:195873 original size:24 final size:23
Alignment explanation
Indices: 195799--195873 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
195789 CCAGACAACA
* *
195799 TTAGCTCTCACGAGCCTAGGATGG
1 TTAGCTCTTACGAGCC-AGAATGG
*
195823 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAG-CCAGAATGG
*
195847 TTAGCTCTTACGAGCTCAGAATAG
1 TTAGCTCTTACGAGC-CAGAATGG
195871 TTA
1 TTA
195874 ACCAGTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 1 0.02
24 41 0.93
25 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (23 bp):
TTAGCTCTTACGAGCCAGAATGG
Found at i:197967 original size:29 final size:29
Alignment explanation
Indices: 197934--197993 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
197924 TTCAATAATT
*
197934 AATTAAATATAGAGCATACTTCTTTTAGA
1 AATTAAATACAGAGCATACTTCTTTTAGA
197963 AATTAAATACAGAGCATACTTCTTTTAGA
1 AATTAAATACAGAGCATACTTCTTTTAGA
197992 AA
1 AA
197994 GAGAATCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (29 bp):
AATTAAATACAGAGCATACTTCTTTTAGA
Found at i:198516 original size:23 final size:23
Alignment explanation
Indices: 198490--198539 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
198480 TAGAAAGTGG
* * *
198490 AAATTTTGAAACCTAAATCCCCA
1 AAATTTTGAAACCCAAAACCCAA
198513 AAATTTTGAAACCCAAAACCCAA
1 AAATTTTGAAACCCAAAACCCAA
198536 AAAT
1 AAAT
198540 CCCCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.04, T:0.22
Consensus pattern (23 bp):
AAATTTTGAAACCCAAAACCCAA
Found at i:198540 original size:32 final size:29
Alignment explanation
Indices: 198498--198575 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 29
198488 GGAAATTTTG
*
198498 AAACCTAAATCCCCAAAATTTTGAAACCCA-
1 AAACCAAAATCCCCAAAATTTTGAAA--CAT
198528 AAACCCAAAAATCCCCAAAATTTTGAAACAT
1 AAA-CC-AAAATCCCCAAAATTTTGAAACAT
198559 AAACCAAAATCCCCAAA
1 AAACCAAAATCCCCAAA
198576 CCTAAGAACC
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
29 12 0.27
30 7 0.16
31 5 0.11
32 20 0.45
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.17
Consensus pattern (29 bp):
AAACCAAAATCCCCAAAATTTTGAAACAT
Found at i:198820 original size:19 final size:18
Alignment explanation
Indices: 198782--198826 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
198772 CCCAAATATT
*
198782 TTATTTTTTAAATTTTAA
1 TTATTTTTTAAATTTAAA
*
198800 TTATGTTTTTAACTTTAAA
1 TTAT-TTTTTAAATTTAAA
198819 TT-TTTTTT
1 TTATTTTTT
198827 GCTGACGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 5 0.21
19 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTTAAATTTAAA
Found at i:199907 original size:13 final size:14
Alignment explanation
Indices: 199891--199919 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
199881 TATTCACTTT
199891 AAATATA-ATTAAA
1 AAATATATATTAAA
199904 AAATATATATTAAA
1 AAATATATATTAAA
199918 AA
1 AA
199920 TAGATTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATATATATTAAA
Found at i:209178 original size:18 final size:19
Alignment explanation
Indices: 209155--209193 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
209145 TCATTTGTTT
209155 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTGTA
209173 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
209192 TT
1 TT
209194 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:210531 original size:17 final size:17
Alignment explanation
Indices: 210511--210546 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
210501 TCCATATATT
*
210511 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
210528 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
210545 AT
1 AT
210547 GAGTCTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:212789 original size:42 final size:42
Alignment explanation
Indices: 212683--212872 Score: 213
Period size: 42 Copynumber: 4.5 Consensus size: 42
212673 TGATGTATAA
* * *
212683 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATT-TG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATTATGAT-T
* *
212725 ACATGGAATACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 A-AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* *
212768 AAAGGAAGACTCATGTTTCGAGAAGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* * **
212810 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATACAATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* * *
212852 TAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
212873 TAGAGCATAA
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 94 0.75
43 31 0.25
44 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
Found at i:214920 original size:47 final size:47
Alignment explanation
Indices: 214851--214943 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
214841 TATTTCTTAG
214851 AACATGGAGTATGAGTCAAACCCATGCTTGAATTGAAATGGAGATAC
1 AACATGGAGTATGAGTCAAACCCATGCTTGAATTGAAATGGAGATAC
*
214898 AACATGGAGTGTGAGTCAAACCCATGCTTGAATTGAAATGGAGATA
1 AACATGGAGTATGAGTCAAACCCATGCTTGAATTGAAATGGAGATA
214944 TTGATGCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (47 bp):
AACATGGAGTATGAGTCAAACCCATGCTTGAATTGAAATGGAGATAC
Found at i:215925 original size:21 final size:22
Alignment explanation
Indices: 215901--215950 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
215891 TTTTAACTCA
215901 AGTGAAACAA-TATTAAAATCG
1 AGTGAAACAATTATTAAAATCG
* * *
215922 AGTGAAATAATTTTTTAAATCG
1 AGTGAAACAATTATTAAAATCG
215944 AGTGAAA
1 AGTGAAA
215951 TAGTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (22 bp):
AGTGAAACAATTATTAAAATCG
Found at i:215944 original size:22 final size:22
Alignment explanation
Indices: 215890--215995 Score: 78
Period size: 21 Copynumber: 5.0 Consensus size: 22
215880 ACTTCAAGTA
* * *
215890 TTTTTAACTCAAGTGAAACAA-
1 TTTTTAAATCGAGTGAAATAAT
* *
215911 TATTAAAATCGAGTGAAATAAT
1 TTTTTAAATCGAGTGAAATAAT
215933 TTTTTAAATCGAGTGAAAT-A-
1 TTTTTAAATCGAGTGAAATAAT
* * **
215953 GTTTTAAATCGATTG-AATTTT
1 TTTTTAAATCGAGTGAAATAAT
* *
215974 TTTTTAACTCAAGTGAAA-AAT
1 TTTTTAAATCGAGTGAAATAAT
215995 T
1 T
215996 GCTCCTTAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.05
20 13 0.20
21 30 0.46
22 19 0.29
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
TTTTTAAATCGAGTGAAATAAT
Found at i:215959 original size:20 final size:22
Alignment explanation
Indices: 215916--215969 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
215906 AACAATATTA
*
215916 AAATCGAGTGAAATAATTTTTT
1 AAATCGAGTGAAATAATGTTTT
215938 AAATCGAGTGAAAT-A-GTTTT
1 AAATCGAGTGAAATAATGTTTT
*
215958 AAATCGATTGAA
1 AAATCGAGTGAA
215970 TTTTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
AAATCGAGTGAAATAATGTTTT
Found at i:215977 original size:20 final size:20
Alignment explanation
Indices: 215916--215991 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
215906 AACAATATTA
215916 AAATCGAGTGAAATAATTTTTT
1 AAATCGAGTGAAAT--TTTTTT
**
215938 AAATCGAGTGAAATAGTTTT
1 AAATCGAGTGAAATTTTTTT
* *
215958 AAATCGATTGAATTTTTTTTT
1 AAATCGAGTGAA-ATTTTTTT
* *
215979 AACTCAAGTGAAA
1 AAATCGAGTGAAA
215992 AATTGCTCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 15 0.35
21 14 0.33
22 14 0.33
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (20 bp):
AAATCGAGTGAAATTTTTTT
Found at i:219390 original size:71 final size:71
Alignment explanation
Indices: 219315--219463 Score: 176
Period size: 71 Copynumber: 2.1 Consensus size: 71
219305 ACTTATCTTA
*
219315 ATAGAAGCCTCCCAG-GTATCCGTAGAAGTCCCAAGCCACAACTTCTTTGCTCTCTAGAGTTTGT
1 ATAGAAG-CTCCCAGTGTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGT
219379 TCTACCG
65 TCTACCG
*** * * * *
219386 ATAGAA-CTCTTGGTTGTATCGGTAGAAGTCCCAGGCCACAACTTCTTTACTCTTTGGAGTTTGT
1 ATAGAAGCTCCCAG-TGTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGT
*
219450 TCTACTG
65 TCTACCG
*
219457 ATTGAAG
1 ATAGAAG
219464 TCTTGGTTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
69 4 0.06
71 61 0.94
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (71 bp):
ATAGAAGCTCCCAGTGTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGTT
CTACCG
Found at i:219468 original size:71 final size:71
Alignment explanation
Indices: 219330--219473 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 71
219320 AGCCTCCCAG
*
219330 GTATCCGTAGAAGTCCCAAGCCACAACTTCTTTGCTCTCTAGAGTTTGTTCTACCGATAGAACTC
1 GTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGTTCTACCGATAGAACTC
219395 TTGGTT
66 TTGGTT
* * * * * * *
219401 GTATCGGTAGAAGTCCCAGGCCACAACTTCTTTACTCTTTGGAGTTTGTTCTACTGATTGAAGTC
1 GTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGTTCTACCGATAGAACTC
219466 TTGGTT
66 TTGGTT
219472 GT
1 GT
219474 TGATCGATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (71 bp):
GTATCCGTAGAAGTCCCAAGCCACAACTTCTTTACTCTCTAGAGTTTGTTCTACCGATAGAACTC
TTGGTT
Found at i:222941 original size:14 final size:14
Alignment explanation
Indices: 222922--222954 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
222912 TTTGTCAACC
222922 TTCTTTTTACCTTT
1 TTCTTTTTACCTTT
*
222936 TTCTTTTTTCCTTT
1 TTCTTTTTACCTTT
222950 TTCTT
1 TTCTT
222955 GGAAGTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTTTACCTTT
Found at i:234953 original size:23 final size:23
Alignment explanation
Indices: 234928--235043 Score: 133
Period size: 23 Copynumber: 5.0 Consensus size: 23
234918 GTACTGATCC
* *
234928 CACAAAGTACTAATCAGAGAGCC
1 CACAAAGTGCTAATCAGAGAGCA
* *
234951 CACGAAGTGCTATTCAGAGAGCA
1 CACAAAGTGCTAATCAGAGAGCA
* * * *
234974 CACACAGTACTAAACAAAGAGCA
1 CACAAAGTGCTAATCAGAGAGCA
* *
234997 CACACAGTGCTAATCAGAGAGTA
1 CACAAAGTGCTAATCAGAGAGCA
*
235020 CACAAAGTGCTAATTAGAGAGCA
1 CACAAAGTGCTAATCAGAGAGCA
235043 C
1 C
235044 GCTAGTGTTC
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (23 bp):
CACAAAGTGCTAATCAGAGAGCA
Found at i:236342 original size:23 final size:23
Alignment explanation
Indices: 236316--236481 Score: 130
Period size: 23 Copynumber: 7.5 Consensus size: 23
236306 AGTGCTGGGC
*
236316 AACAGAGAGCACACAAACTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
236339 AACAAAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* * *
236358 -AC--TGAGCCCACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
** * *
236378 TTCAGAGAGCCCACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
** *
236401 TTCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
236424 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
236447 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
236470 ATCAGAGAGCAC
1 AACAGAGAGCAC
236482 GCTAGTGTTC
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
16 8 0.07
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
23 104 0.87
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:237816 original size:23 final size:23
Alignment explanation
Indices: 237781--237878 Score: 142
Period size: 23 Copynumber: 4.3 Consensus size: 23
237771 ACAAAGTACT
*
237781 GAGCTCACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* * *
237804 GAGCCCACGAAGTGCTATTCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
237827 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
237850 GAGCACAAAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
237873 GAGCAC
1 GAGCAC
237879 GCTAGTGTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:239167 original size:23 final size:23
Alignment explanation
Indices: 239141--239306 Score: 130
Period size: 23 Copynumber: 7.5 Consensus size: 23
239131 AGTGCTGGGC
*
239141 AACAGAGAGCACACAAACTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
239164 AACAAAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
239183 -AC--CGAGCCCACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
239203 ATCAGAGAGCCCACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
** * *
239226 TTCAGAGAGCAGACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
239249 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
239272 AACAGAGAGCACACACAGTGTTA
1 AACAGAGAGCACACAAAGTGCTA
*
239295 ATCAGAGAGCAC
1 AACAGAGAGCAC
239307 GCTAGTGTTC
Statistics
Matches: 116, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
16 9 0.08
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
23 100 0.86
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:239269 original size:46 final size:46
Alignment explanation
Indices: 239186--239306 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 46
239176 ACAAAGTACC
* * * **
239186 GAGCCCACAAAGTGCTAATCAGAGAGCCCACGAAGTGCTATTCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
* * *
239232 GAGCAGACACAGTGCTAAACAAAGAGCACAC-ACAGTGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGA-AGTGCTAAACAGA
*
239278 GAGCACACACAGTGTTAATCAGAGAGCAC
1 GAGCACACACAGTGCTAATCAGAGAGCAC
239307 GCTAGTGTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
45 1 0.02
46 61 0.98
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
Found at i:240658 original size:23 final size:23
Alignment explanation
Indices: 240623--240720 Score: 133
Period size: 23 Copynumber: 4.3 Consensus size: 23
240613 ACAAAGTACT
*
240623 GAGCTCACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* * *
240646 GAGCCCACGAAGTGCTATTCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
240669 CAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
240692 GAGCACAAAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
240715 GAGCAC
1 GAGCAC
240721 GCTAGTGTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:242130 original size:21 final size:22
Alignment explanation
Indices: 242030--242152 Score: 97
Period size: 23 Copynumber: 5.3 Consensus size: 22
242020 ACAAAATACT
* *
242030 GAGCACATAAAGTGCTAACCAGA
1 GAGCACA-CAAGTGCTAATCAGA
*
242053 GAGCACATGAAGTGCTAATAACAGA
1 GAGCACA-CAAGTGCTAAT--CAGA
* *
242078 GAGCA-AGAGACGTGTTAAAT-AGA
1 GAGCACACA-A-GTGCT-AATCAGA
242101 GAGCACACACAGTGCTAATCAGA
1 GAGCACACA-AGTGCTAATCAGA
*
242124 GAGCACACAGAGTGCTAATCGGA
1 GAGCACACA-AGTGCTAATCAGA
242147 GAGCAC
1 GAGCAC
242153 GCTAGTGTTC
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
22 3 0.04
23 61 0.72
24 5 0.06
25 13 0.15
26 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.14
Consensus pattern (22 bp):
GAGCACACAAGTGCTAATCAGA
Found at i:243945 original size:30 final size:30
Alignment explanation
Indices: 243911--243973 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
243901 TTATTTTAGC
243911 TACATAGTCTAATTCTCAATTCTACTCTAT
1 TACATAGTCTAATTCTCAATTCTACTCTAT
243941 TACATAGTCTAATTCTCAATTCTACTCTAT
1 TACATAGTCTAATTCTCAATTCTACTCTAT
243971 TAC
1 TAC
243974 TGTTCCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (30 bp):
TACATAGTCTAATTCTCAATTCTACTCTAT
Found at i:246784 original size:23 final size:23
Alignment explanation
Indices: 246756--246809 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
246746 ATATTCAATC
* *
246756 ATAAATGTTTT-ATACTATAAAAT
1 ATAAATATTTTAATAATAT-AAAT
246779 ATAAATATTTTAATAATATAAAT
1 ATAAATATTTTAATAATATAAAT
246802 ATAAATAT
1 ATAAATAT
246810 AAATATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAAATATTTTAATAATATAAAT
Found at i:248090 original size:30 final size:30
Alignment explanation
Indices: 248038--248102 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
248028 TTAAAGGCGT
*
248038 CAAAATTTTTTTACCAACTTTTAAGGGATC
1 CAAAATTTTTTTACCAACTTTTAAGGAATC
** *
248068 CAAAATTTTTTTTTCAATTTTTAAGGAATC
1 CAAAATTTTTTTACCAACTTTTAAGGAATC
*
248098 TAAAA
1 CAAAA
248103 CTCTATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (30 bp):
CAAAATTTTTTTACCAACTTTTAAGGAATC
Found at i:248844 original size:27 final size:27
Alignment explanation
Indices: 248808--248862 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
248798 GTTTATAAAT
248808 TTTTAAAATTTATATTCTAATGTGTAA
1 TTTTAAAATTTATATTCTAATGTGTAA
* *
248835 TTTTAAAATTTATGTTTTAATGTGTAA
1 TTTTAAAATTTATATTCTAATGTGTAA
248862 T
1 T
248863 GATTGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.55
Consensus pattern (27 bp):
TTTTAAAATTTATATTCTAATGTGTAA
Found at i:250299 original size:14 final size:13
Alignment explanation
Indices: 250277--250314 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
250267 CTTAACTTAT
250277 AATTCAATAATTTA
1 AATTCAATAA-TTA
*
250291 AATTTAATAATTA
1 AATTCAATAATTA
250304 AATTC-ATAATT
1 AATTCAATAATT
250315 TTAGTACGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTCAATAATTA
Found at i:251423 original size:19 final size:19
Alignment explanation
Indices: 251392--251429 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
251382 ATCCCAAAGA
251392 CAATATAACCATAACAAAC
1 CAATATAACCATAACAAAC
251411 CAATA-AACTCATAACAAAC
1 CAATATAAC-CATAACAAAC
251430 TTCAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (19 bp):
CAATATAACCATAACAAAC
Found at i:254721 original size:43 final size:42
Alignment explanation
Indices: 254627--254744 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
254617 GTGATTGCTG
* * * *
254627 AAAGGAAGACTCATGTGTCGGATAGAGCATGAGATTATTATA
1 AAAGGAAGACTTATGTCTCGGATAAAGCATAAGATTATTATA
* * * *
254669 AATGGAAGACTTATGTCTAGGTTAAAGCATAAGATTGTTTATA
1 AAAGGAAGACTTATGTCTCGGATAAAGCATAAGATT-ATTATA
254712 AAAGGAAGACTTATGTCTCGGCA-AAAGCATAAG
1 AAAGGAAGACTTATGTCTCGG-ATAAAGCATAAG
254745 GTTAATACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (42 bp):
AAAGGAAGACTTATGTCTCGGATAAAGCATAAGATTATTATA
Found at i:261724 original size:43 final size:43
Alignment explanation
Indices: 261676--261822 Score: 181
Period size: 43 Copynumber: 3.4 Consensus size: 43
261666 TTACCAAGAA
*
261676 GGAAGA-TTCATGTCTCGGATAGAGCATGAGATTATTTATAAAT
1 GGAAGACTT-ATGTCTCGGATAGAGCATAAGATTATTTATAAAT
* *
261719 GGAAGACTTATGTCTCGG-TCAGAGCATAAGATTGTTTATAAAA
1 GGAAGACTTATGTCTCGGAT-AGAGCATAAGATTATTTATAAAT
* * * *
261762 GGAAGACTTATGTCTCGGAAAGATCATAAGGTTATTTGTAAAT
1 GGAAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAAT
*
261805 GGAAGAACTTATGACTCG
1 GGAAG-ACTTATGTCTCG
261823 ATTGGAACAT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 76 0.84
44 13 0.14
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (43 bp):
GGAAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAAT
Found at i:261834 original size:44 final size:43
Alignment explanation
Indices: 261676--261839 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 43
261666 TTACCAAGAA
* * *
261676 GGAAGA-TTCATGTCTCGGAT-AGAGCATGAGATTATTTATAAAT
1 GGAAGACTT-ATGTCTC-GATAAGAACATAAGGTTATTTATAAAT
* * * * * *
261719 GGAAGACTTATGTCTCGGTCAGAGCATAAGATTGTTTATAAAA
1 GGAAGACTTATGTCTCGATAAGAACATAAGGTTATTTATAAAT
* *
261762 GGAAGACTTATGTCTCGGA-AAGATCATAAGGTTATTTGTAAAT
1 GGAAGACTTATGTCTC-GATAAGAACATAAGGTTATTTATAAAT
* **
261805 GGAAGAACTTATGACTCGATTGGAACATAAGGTTA
1 GGAAG-ACTTATGTCTCGATAAGAACATAAGGTTA
261840 ATACAGTTTG
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.02
43 74 0.73
44 25 0.25
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (43 bp):
GGAAGACTTATGTCTCGATAAGAACATAAGGTTATTTATAAAT
Found at i:262892 original size:6 final size:6
Alignment explanation
Indices: 262881--262992 Score: 53
Period size: 6 Copynumber: 18.7 Consensus size: 6
262871 AACAGCGCAT
* * ** * **
262881 AATAAA AATAAA AATACA AATACA AATACA AATATG AATACG AATATG
1 AATACA AATACA AATACA AATACA AATACA AATACA AATACA AATACA
** * * * ** * * * *
262929 AATATG AATATA GATACG GGTACG AAGACA GATACA AATACA AACACA
1 AATACA AATACA AATACA AATACA AATACA AATACA AATACA AATACA
*
262977 AATAGA AATACA AATA
1 AATACA AATACA AATA
262993 AAAAATAAAA
Statistics
Matches: 85, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (6 bp):
AATACA
Found at i:263020 original size:10 final size:10
Alignment explanation
Indices: 262995--263058 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
262985 TACAAATAAA
262995 AAATAAAAA-
1 AAATAAAAAT
*
263004 AATATAAAACT
1 AA-ATAAAAAT
263015 AAATAAAAAT
1 AAATAAAAAT
*
263025 AACATGAAAAGT
1 AA-AT-AAAAAT
*
263037 AAA-ATAAAT
1 AAATAAAAAT
263046 AAATAAAAAT
1 AAATAAAAAT
263056 AAA
1 AAA
263059 AACACTCGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 9 0.20
10 23 0.52
11 5 0.11
12 7 0.16
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:264771 original size:24 final size:22
Alignment explanation
Indices: 264743--264789 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
264733 AGGAGCTTGA
264743 AATTAGGCATTATCATTAGGTTTT
1 AATTAGG-ATTATCATTA-GTTTT
* *
264767 AATTAGGATTTTCTTTAGTTTT
1 AATTAGGATTATCATTAGTTTT
264789 A
1 A
264790 GTTTAACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 8 0.38
24 7 0.33
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (22 bp):
AATTAGGATTATCATTAGTTTT
Found at i:267528 original size:49 final size:49
Alignment explanation
Indices: 267456--267567 Score: 208
Period size: 49 Copynumber: 2.3 Consensus size: 49
267446 GAAACAATTA
*
267456 TACCGATACAATGCAAGTCAGTAACCAAAGATAGTATGTCCTGTACTTC
1 TACCGATACAATGCAAGTCAGTAACCAAAGATAGTATGCCCTGTACTTC
267505 TACCGATACAATGCAAGTCAGTAACCAAAGATAGTATGCCCTGTACTTC
1 TACCGATACAATGCAAGTCAGTAACCAAAGATAGTATGCCCTGTACTTC
267554 TACCGATAC-ATGCA
1 TACCGATACAATGCA
267568 CGAGTTCTAC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
48 5 0.08
49 57 0.92
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (49 bp):
TACCGATACAATGCAAGTCAGTAACCAAAGATAGTATGCCCTGTACTTC
Found at i:268311 original size:25 final size:25
Alignment explanation
Indices: 268283--268372 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
268273 ATAGAGTTTA
*
268283 ACTCTTACAAGCCAGACAAAATATC
1 ACTCTTACAAGCCAGACAGAATATC
* * * *
268308 ACTCTTACGAGTCAAATAGAATATC
1 ACTCTTACAAGCCAGACAGAATATC
* *
268333 GCTCTTACAAGCTAGACAGAATATC
1 ACTCTTACAAGCCAGACAGAATATC
* *
268358 GCTCTTACGAGCCAG
1 ACTCTTACAAGCCAG
268373 TATGAATATC
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (25 bp):
ACTCTTACAAGCCAGACAGAATATC
Found at i:268379 original size:25 final size:24
Alignment explanation
Indices: 268284--268394 Score: 96
Period size: 25 Copynumber: 4.5 Consensus size: 24
268274 TAGAGTTTAA
* ** *
268284 CTCTTACAAGCCAGACAAAATATCA
1 CTCTTACGAGCCAGA-TGAATATCG
* *
268309 CTCTTACGAGTCAAATAGAATATCG
1 CTCTTACGAGCCAGAT-GAATATCG
* * *
268334 CTCTTACAAGCTAGACAGAATATCG
1 CTCTTACGAGCCAGA-TGAATATCG
268359 CTCTTACGAGCCAGTATGAATATCG
1 CTCTTACGAGCCAG-ATGAATATCG
*
268384 TTCTTACGAGC
1 CTCTTACGAGC
268395 TAGAGTTCAA
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
25 67 0.99
26 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (24 bp):
CTCTTACGAGCCAGATGAATATCG
Found at i:268396 original size:50 final size:50
Alignment explanation
Indices: 268284--268398 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
268274 TAGAGTTTAA
* *
268284 CTCTTACAAGCCAGACAAAATATCACTCTTACGAGTCAAATAGAATATCG
1 CTCTTACAAGCTAGACAAAATATCACTCTTACGAGCCAAATAGAATATCG
* * *
268334 CTCTTACAAGCTAGACAGAATATCGCTCTTACGAGCC-AGTATGAATATCG
1 CTCTTACAAGCTAGACAAAATATCACTCTTACGAGCCAAATA-GAATATCG
* *
268384 TTCTTACGAGCTAGA
1 CTCTTACAAGCTAGA
268399 GTTCAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 3 0.05
50 54 0.95
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (50 bp):
CTCTTACAAGCTAGACAAAATATCACTCTTACGAGCCAAATAGAATATCG
Found at i:272185 original size:15 final size:15
Alignment explanation
Indices: 272160--272194 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
272150 CATAGAATTT
*
272160 TAAAA-TGAAACAAG
1 TAAAAGTGAAACAAA
272174 TAAAAGTGAAACAAA
1 TAAAAGTGAAACAAA
272189 TAAAAG
1 TAAAAG
272195 AAAACGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.66, C:0.06, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAGTGAAACAAA
Found at i:282037 original size:141 final size:141
Alignment explanation
Indices: 281801--282083 Score: 485
Period size: 141 Copynumber: 2.0 Consensus size: 141
281791 AAGGTTCTAG
* * *
281801 TGGGATTTTTCTTCCCAAAATCTCGAAGCTTCTCTCTTTGCTTCTTTCAGTTTTATACTTCCTCT
1 TGGGATTTTTCTTCCCAAAATCTCGAAGCTTCTCTCTCTGCTTCTTTCAGTTGTAAACTTCCTCT
281866 ATTTTCTGTGCTCTATCTGCCAAAACAACAAATAACAGTATTTCTGAACCACTTACCATCATCTT
66 ATTTTCTGTGCTCTATCTGCCAAAACAACAAATAACAGTATTTCTGAACCACTTACCATCATCTT
*
281931 TATTTCATCGT
131 TATTTAATCGT
* **
281942 TGGGATTTTTCTTCCCAAAATCTCGAAGCTTCTCTCTCTGTTTCTTTTGGTTGTAAACTTCCTCT
1 TGGGATTTTTCTTCCCAAAATCTCGAAGCTTCTCTCTCTGCTTCTTTCAGTTGTAAACTTCCTCT
* *
282007 ATTTTCTGTGCTCTGTCTGCCAAAACAACAAATAACTGTATTTCTGAACCACTTACCATCATCTT
66 ATTTTCTGTGCTCTATCTGCCAAAACAACAAATAACAGTATTTCTGAACCACTTACCATCATCTT
282072 TATTTAATCGT
131 TATTTAATCGT
282083 T
1 T
282084 CAAACCGTCC
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 133 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (141 bp):
TGGGATTTTTCTTCCCAAAATCTCGAAGCTTCTCTCTCTGCTTCTTTCAGTTGTAAACTTCCTCT
ATTTTCTGTGCTCTATCTGCCAAAACAACAAATAACAGTATTTCTGAACCACTTACCATCATCTT
TATTTAATCGT
Found at i:287495 original size:22 final size:20
Alignment explanation
Indices: 287469--287509 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
287459 AAACCTTAAA
287469 ACTCCAATCCTCCAAAGGCTTT
1 ACTCC-ATCCT-CAAAGGCTTT
*
287491 ACTCCATCCTTAAAGGCTT
1 ACTCCATCCTCAAAGGCTT
287510 AGATCGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.27, C:0.34, G:0.10, T:0.29
Consensus pattern (20 bp):
ACTCCATCCTCAAAGGCTTT
Found at i:292181 original size:30 final size:29
Alignment explanation
Indices: 292147--292207 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
292137 TAACTTAACA
* * *
292147 AACAAATGTCTTTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAATAATAA-AAAATT
292177 AACAAATGCCTCTAAAATAATAAAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAATT
292206 AA
1 AA
292208 TAATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.26
Consensus pattern (29 bp):
AACAAATGCCTCTAAAATAATAAAAAATT
Found at i:292606 original size:17 final size:17
Alignment explanation
Indices: 292584--292617 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
292574 CTTTTTGTTC
292584 CCAAATGCTCTTCTAAG
1 CCAAATGCTCTTCTAAG
292601 CCAAATGCTCTTCTAAG
1 CCAAATGCTCTTCTAAG
292618 TATAGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CCAAATGCTCTTCTAAG
Found at i:304287 original size:20 final size:19
Alignment explanation
Indices: 304247--304286 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
304237 TAAAAATTGC
304247 ATAAAATATTAAATATTAAA
1 ATAAAATA-TAAATATTAAA
304267 ATAAAATA-AAATTATTAAA
1 ATAAAATATAAA-TATTAAA
304286 A
1 A
304287 AAATAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 8 0.42
20 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATATAAATATTAAA
Found at i:306223 original size:6 final size:6
Alignment explanation
Indices: 306216--306251 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
306206 ATGGGAGGAT
* *
306216 TGGGAT TGGGAT TGGGAG TGGGAG TGGGAG TGGGAG
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
306252 GACTGGTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.61, T:0.22
Consensus pattern (6 bp):
TGGGAG
Found at i:306229 original size:12 final size:12
Alignment explanation
Indices: 306212--306250 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
306202 AGGGATGGGA
*
306212 GGATTGGGATTG
1 GGATTGGGAGTG
306224 GGATTGGGAGTG
1 GGATTGGGAGTG
*
306236 GGAGTGGGAGTG
1 GGATTGGGAGTG
306248 GGA
1 GGA
306251 GGACTGGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.59, T:0.23
Consensus pattern (12 bp):
GGATTGGGAGTG
Found at i:314579 original size:16 final size:16
Alignment explanation
Indices: 314549--314582 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
314539 ATTTCAGCAA
314549 TTTATTCTTATTTTTC
1 TTTATTCTTATTTTTC
314565 TTTATATCTTATTTTTC
1 TTTAT-TCTTATTTTTC
314582 T
1 T
314583 CATTGTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTCTTATTTTTC
Found at i:325224 original size:44 final size:44
Alignment explanation
Indices: 325176--325307 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
325166 CTATTTTAAA
325176 TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
1 TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
* *** * * ***
325220 TAGATTAGTTTATTTAAAAT----TC----T-A-CTATTTTAAA
1 TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
325254 TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
1 TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
325298 TAGATTAGTT
1 TAGATTAGTT
325308 TATTTAAAAT
Statistics
Matches: 60, Mismatches: 18, Indels: 20
0.61 0.18 0.20
Matches are distributed among these distances:
34 22 0.37
35 1 0.02
36 1 0.02
38 1 0.02
40 1 0.02
42 1 0.02
43 1 0.02
44 32 0.53
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (44 bp):
TAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTG
Found at i:325264 original size:78 final size:78
Alignment explanation
Indices: 325162--325317 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
325152 ATTAAGAAAG
325162 TCTACTATTTTAAATAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTGTAGATTA
1 TCTACTATTTTAAATAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTGTAGATTA
325227 GTTTATTTAAAAT
66 GTTTATTTAAAAT
325240 TCTACTATTTTAAATAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTGTAGATTA
1 TCTACTATTTTAAATAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTGTAGATTA
325305 GTTTATTTAAAAT
66 GTTTATTTAAAAT
325318 ATCAAGATGG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (78 bp):
TCTACTATTTTAAATAGATTAGTTGAAACAAAATGCCGCCAAAGTGACCTCTTTTGTGTAGATTA
GTTTATTTAAAAT
Found at i:328089 original size:26 final size:26
Alignment explanation
Indices: 328053--328104 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
328043 TGTTTGATGA
328053 TTAATTTTGTTGTTGCAATTAATTCT
1 TTAATTTTGTTGTTGCAATTAATTCT
328079 TTAATTTTGTTGTTGCAATTAATTCT
1 TTAATTTTGTTGTTGCAATTAATTCT
328105 AACTTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (26 bp):
TTAATTTTGTTGTTGCAATTAATTCT
Found at i:340238 original size:26 final size:25
Alignment explanation
Indices: 340157--340250 Score: 84
Period size: 26 Copynumber: 3.7 Consensus size: 25
340147 TACAAAAATA
* *
340157 TAGCTCTTT-GAACCCAGCACAAAGTT
1 TAGCTCTTTCGAGCCCAG-ACAGA-TT
*
340183 TAGCT-TTTACGAGCCCAGACAGAGT
1 TAGCTCTTT-CGAGCCCAGACAGATT
* *
340208 TAGCTCTTTCGAGCCTAGATAGATTT
1 TAGCTCTTTCGAGCCCAGACAGA-TT
*
340234 TAGCTCATTCGAGCCCA
1 TAGCTCTTTCGAGCCCA
340251 AACATCGAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
25 21 0.38
26 28 0.50
27 7 0.12
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (25 bp):
TAGCTCTTTCGAGCCCAGACAGATT
Found at i:342777 original size:15 final size:15
Alignment explanation
Indices: 342757--342786 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
342747 TAGTTTATTC
342757 TTTAATTGAATTTTT
1 TTTAATTGAATTTTT
342772 TTTAATTGAATTTTT
1 TTTAATTGAATTTTT
342787 AACTGTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTAATTGAATTTTT
Found at i:343042 original size:21 final size:21
Alignment explanation
Indices: 343018--343061 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
343008 TTAAAAAAAT
343018 ATGAACAGATACTATCATGTC
1 ATGAACAGATACTATCATGTC
343039 ATGAACAGATACTATCATGTC
1 ATGAACAGATACTATCATGTC
343060 AT
1 AT
343062 TACAACAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
ATGAACAGATACTATCATGTC
Found at i:344717 original size:31 final size:32
Alignment explanation
Indices: 344682--344744 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
344672 ACTACCAACT
*
344682 ACACCAACTAAACTCAAG-AAACGTTAATGAA
1 ACACCAACTAAACTCAAGAAAAAGTTAATGAA
344713 ACACCAACTAAACTCAAGAAAAAGTTAATGAA
1 ACACCAACTAAACTCAAGAAAAAGTTAATGAA
344745 CTAAACCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.16
Consensus pattern (32 bp):
ACACCAACTAAACTCAAGAAAAAGTTAATGAA
Found at i:347196 original size:9 final size:9
Alignment explanation
Indices: 347182--347207 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
347172 TTGGTCCCTT
347182 CGAGGTCGA
1 CGAGGTCGA
347191 CGAGGTCGA
1 CGAGGTCGA
347200 CGAGGTCG
1 CGAGGTCG
347208 TGCACTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.46, T:0.12
Consensus pattern (9 bp):
CGAGGTCGA
Done.