Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004105.1 Hibiscus syriacus cultivar Beakdansim tig00008979_pilon, 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: 262281
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:2040 original size:22 final size:22
Alignment explanation
Indices: 2012--2062 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2002 TCAGCTGTTA
*
2012 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTAAATCATG
2034 TAACTCCTGAAATTAAATCATG
1 TAACTCCTGAAATTAAATCATG
2056 TAACTCC
1 TAACTCC
2063 CGTAACTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (22 bp):
TAACTCCTGAAATTAAATCATG
Found at i:5553 original size:16 final size:16
Alignment explanation
Indices: 5519--5553 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5509 CTATTGAGCA
*
5519 AATGAATGACAAACTC
1 AATGAATGACAAACAC
*
5535 AATGAATGACAAAGAC
1 AATGAATGACAAACAC
5551 AAT
1 AAT
5554 AGGGAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.17
Consensus pattern (16 bp):
AATGAATGACAAACAC
Found at i:8120 original size:7 final size:8
Alignment explanation
Indices: 8099--8135 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
8089 TATATTAAAT
*
8099 TTAAAAAT
1 TTAAAAAA
*
8107 TTTAAAAA
1 TTAAAAAA
8115 TTAAAAAA
1 TTAAAAAA
8123 TTAAAAAA
1 TTAAAAAA
8131 TTAAA
1 TTAAA
8136 TTTTAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
TTAAAAAA
Found at i:8141 original size:15 final size:16
Alignment explanation
Indices: 8102--8147 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
8092 ATTAAATTTA
8102 AAAATTTT-AAAAATT
1 AAAATTTTAAAAAATT
**
8117 AAAAAATTAAAAAATT
1 AAAATTTTAAAAAATT
8133 -AAATTTTAAGAAAAT
1 AAAATTTTAA-AAAAT
8148 ATTTGATATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATTTTAAAAAATT
Found at i:8747 original size:16 final size:18
Alignment explanation
Indices: 8723--8759 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
8713 TTTAATAAAC
*
8723 TTTATTTTTAAGT-TTTT
1 TTTATTTTTAAATATTTT
8740 TTTA-TTTTAAATATTTT
1 TTTATTTTTAAATATTTT
8757 TTT
1 TTT
8760 TTCAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTATTTTTAAATATTTT
Found at i:10029 original size:24 final size:25
Alignment explanation
Indices: 9997--10059 Score: 65
Period size: 29 Copynumber: 2.4 Consensus size: 25
9987 TATTTGGTAA
*
9997 TCACATTGCA-GCTAATCTGCTGGT
1 TCACTTTGCACGCTAATCTGCTGGT
*
10021 TCACTTTGCATCATCGTTAATCTGCTGGT
1 TCACTTTG---CA-CGCTAATCTGCTGGT
10050 TCACTTTGCA
1 TCACTTTGCA
10060 TCATCACGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
24 7 0.22
26 2 0.06
27 2 0.06
29 21 0.66
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (25 bp):
TCACTTTGCACGCTAATCTGCTGGT
Found at i:10042 original size:29 final size:29
Alignment explanation
Indices: 10009--10064 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
9999 ACATTGCAGC
10009 TAATCTGCTGGTTCACTTTGCATCATCGT
1 TAATCTGCTGGTTCACTTTGCATCATCGT
10038 TAATCTGCTGGTTCACTTTGCATCATC
1 TAATCTGCTGGTTCACTTTGCATCATC
10065 ACGTTGTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (29 bp):
TAATCTGCTGGTTCACTTTGCATCATCGT
Found at i:10847 original size:33 final size:33
Alignment explanation
Indices: 10804--10874 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
10794 CTTTTAAGTG
*
10804 ATAAACGAACACAAATGAACGAATATAAA-GAAC
1 ATAAACGAACAC-AATAAACGAATATAAACGAAC
* *
10837 GTAAACGAACACAATAAATGAATATAAACGAAC
1 ATAAACGAACACAATAAACGAATATAAACGAAC
10870 ATAAA
1 ATAAA
10875 TGAAAATAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.61, C:0.14, G:0.11, T:0.14
Consensus pattern (33 bp):
ATAAACGAACACAATAAACGAATATAAACGAAC
Found at i:11079 original size:14 final size:14
Alignment explanation
Indices: 11062--11095 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11052 AAATAAATGC
11062 ACATAAACGAACGA
1 ACATAAACGAACGA
*
11076 ACATAAATGAACGA
1 ACATAAACGAACGA
11090 ACATAA
1 ACATAA
11096 GCGGACAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (14 bp):
ACATAAACGAACGA
Found at i:21246 original size:12 final size:12
Alignment explanation
Indices: 21226--21256 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21216 GCTTGATTCA
21226 AGCTCGATTTTG
1 AGCTCGATTTTG
*
21238 AGCTTGATTTTG
1 AGCTCGATTTTG
21250 AGCTCGA
1 AGCTCGA
21257 ATTGCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:23016 original size:7 final size:7
Alignment explanation
Indices: 23004--23073 Score: 70
Period size: 7 Copynumber: 10.1 Consensus size: 7
22994 AATTGGATTA
23004 AGGGTTT
1 AGGGTTT
23011 AGGGTTT
1 AGGGTTT
23018 AGGGTTT
1 AGGGTTT
23025 A-GGTTT
1 AGGGTTT
23031 AGGGTTT
1 AGGGTTT
* *
23038 ATGATTT
1 AGGGTTT
** *
23045 AATGTTA
1 AGGGTTT
* *
23052 AAGATTT
1 AGGGTTT
23059 AGGGTTT
1 AGGGTTT
23066 AGGGTTT
1 AGGGTTT
23073 A
1 A
23074 TGGCTTATGG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
6 6 0.12
7 45 0.88
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:23045 original size:20 final size:20
Alignment explanation
Indices: 23006--23045 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22996 TTGGATTAAG
*
23006 GGTTTAGGGTTTAGGGTTTA
1 GGTTTAGGGTTTAGGATTTA
*
23026 GGTTTAGGGTTTATGATTTA
1 GGTTTAGGGTTTAGGATTTA
23046 ATGTTAAAGA
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:0.17, C:0.00, G:0.35, T:0.47
Consensus pattern (20 bp):
GGTTTAGGGTTTAGGATTTA
Found at i:23245 original size:28 final size:28
Alignment explanation
Indices: 23213--23309 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
23203 ATAGAATTTT
23213 TAATAT-ATTTTTAAAATTTTATAATTA
1 TAATATAATTTTTAAAATTTTATAATTA
* *
23240 TCAATAATGTATTTTTAATAAATTT-T--TTA
1 T-AAT-AT-AATTTTTAA-AATTTTATAATTA
* * *
23269 TAATATAATTTTAAAAATTCTAAAATTA
1 TAATATAATTTTTAAAATTTTATAATTA
*
23297 TAATATCATTTTT
1 TAATATAATTTTT
23310 TCAAGCTGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
25 4 0.07
26 7 0.13
27 3 0.06
28 20 0.37
29 6 0.11
31 9 0.17
32 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (28 bp):
TAATATAATTTTTAAAATTTTATAATTA
Found at i:25246 original size:2 final size:2
Alignment explanation
Indices: 25239--25274 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25229 CTTTTAAAAC
25239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25275 TTTAAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25479 original size:12 final size:12
Alignment explanation
Indices: 25452--25521 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
25442 ACAGAGATAT
* *
25452 CAGAAATCAAAA
1 CAGAATTCAGAA
*
25464 CAGAATTCAGAT
1 CAGAATTCAGAA
25476 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
25488 CATAATTCATAT
1 CAGAATTCAGAA
* *
25500 CACAAATCAGAA
1 CAGAATTCAGAA
25512 CAGAATTCAG
1 CAGAATTCAG
25522 GTCATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:25484 original size:24 final size:24
Alignment explanation
Indices: 25450--25544 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
25440 AAACAGAGAT
*
25450 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
25474 ATCAGATATCAGAACATAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
*
25498 ATCACAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
25522 GTCATG-TATCATAACAGAATTCA
1 ATCA-GAAATCAGAACAGAATTCA
25545 AGTTGGAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:25558 original size:48 final size:48
Alignment explanation
Indices: 25448--25544 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
25438 GTAAACAGAG
* *
25448 ATATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAACATAATTC
1 ATATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAACAGAATTC
* * *
25496 ATATCACAAATCAGAACAGAATTCAGGTCATG-TATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGATCA-GATATCAGAACAGAATTC
25544 A
1 A
25545 AGTTGGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAACAGAATTC
Found at i:26619 original size:9 final size:9
Alignment explanation
Indices: 26605--26630 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
26595 CCATAAGGGT
26605 ATTTTGGTC
1 ATTTTGGTC
26614 ATTTTGGTC
1 ATTTTGGTC
26623 ATTTTGGT
1 ATTTTGGT
26631 GTTTAGTTTT
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:0.12, C:0.08, G:0.23, T:0.58
Consensus pattern (9 bp):
ATTTTGGTC
Found at i:33726 original size:102 final size:107
Alignment explanation
Indices: 33504--33743 Score: 339
Period size: 102 Copynumber: 2.3 Consensus size: 107
33494 ATTACATTGT
* * * *
33504 TTCATAAACTTTTTAGTGATATTTCACTTCATTTCATAAAAAAGTGTCCTTTTCTCATACACCAT
1 TTCAGAAACTTTTCAGTGATATATCACTTCATTTCATAAAAAA--GTCATTTTCTCATACACCAT
33569 TTAATACACAATGACGAGAACTTTTCAGTGTCTAATTACTTCAC
64 TTAATACACAATGACGAGAACTTTTCAGTGTCTAATTACTTCAC
* * *
33613 TTTAGAAACTTTTCAATGATATATCACTTCATTT-A-AAAAAA-TCATTTTCTCATACATCATTT
1 TTCAGAAACTTTTCAGTGATATATCACTTCATTTCATAAAAAAGTCATTTTCTCATACACCATTT
33675 AATACACAATGAC-A-AACTTTTCAGTG-CATAATTACTTCAC
66 AATACACAATGACGAGAACTTTTCAGTGTC-TAATTACTTCAC
*
33715 TTCAGAAACTTTTCAGTGATATGTCACTT
1 TTCAGAAACTTTTCAGTGATATATCACTT
33744 TGTTTCAGTA
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
101 1 0.01
102 50 0.42
103 1 0.01
104 32 0.27
107 6 0.05
108 1 0.01
109 29 0.24
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (107 bp):
TTCAGAAACTTTTCAGTGATATATCACTTCATTTCATAAAAAAGTCATTTTCTCATACACCATTT
AATACACAATGACGAGAACTTTTCAGTGTCTAATTACTTCAC
Found at i:33897 original size:32 final size:32
Alignment explanation
Indices: 33851--33929 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
33841 GTTTCCAATT
* *
33851 ACTTCACTTCAGAAACTTTTCATTGAA-ATATC
1 ACTTCATTTCAGAAACTTTTCAAT-AATATATC
* * *
33883 ACTTTATTTTAGAAATTTTTCAATAATATATC
1 ACTTCATTTCAGAAACTTTTCAATAATATATC
33915 ACTTCATTTCAGAAA
1 ACTTCATTTCAGAAA
33930 ATAAAAAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (32 bp):
ACTTCATTTCAGAAACTTTTCAATAATATATC
Found at i:44202 original size:20 final size:20
Alignment explanation
Indices: 44179--44216 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44169 CACTCATCTA
* *
44179 TTATTTTATTTTTATTTTGG
1 TTATTTAATTATTATTTTGG
44199 TTATTTAATTATTATTTT
1 TTATTTAATTATTATTTT
44217 ATTAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTATTTAATTATTATTTTGG
Found at i:44769 original size:42 final size:44
Alignment explanation
Indices: 44622--44815 Score: 136
Period size: 42 Copynumber: 4.5 Consensus size: 44
44612 ACTCATGTTT
* * * * *
44622 TTTCAATCTCAC-TTTGACCTTTATAATTGAGGCCCATAATTT-
1 TTTCAATATCACTTTTTACCTTTAAAATTGATGCCCCTAATTTA
** * * * *
44664 TTTCAATCCCA-TTTTTA-CTCATATAATTTG-GGCCCCTAATTTT
1 TTTCAATATCACTTTTTACCT-TTA-AAATTGATGCCCCTAATTTA
*
44707 TTTCAATCTCACTTTTTACCTTTAAAATTGATGCCCCT-ATTTA
1 TTTCAATATCACTTTTTACCTTTAAAATTGATGCCCCTAATTTA
* ** * *
44750 TTT-AATATCACTTTTTACCTTTATAATTGGGGTCCTTAATTT-
1 TTTCAATATCACTTTTTACCTTTAAAATTGATGCCCCTAATTTA
*
44792 TTTCAATCAT-ACTTTTTACTTTTA
1 TTTCAAT-ATCACTTTTTACCTTTA
44816 TAGTTTAAGG
Statistics
Matches: 124, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 58 0.47
43 46 0.37
44 16 0.13
45 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (44 bp):
TTTCAATATCACTTTTTACCTTTAAAATTGATGCCCCTAATTTA
Found at i:44816 original size:43 final size:43
Alignment explanation
Indices: 44462--44817 Score: 227
Period size: 43 Copynumber: 8.3 Consensus size: 43
44452 TAATTTTAGT
*
44462 TTTTTATCC-TTATAATTGAGGTCCCTAATTTTTGT-AATC-CTAC
1 TTTTTA-CCTTTATAATTGAGGCCCCTAATTTTT-TCAATCTC-AC
* * *** * *
44505 TTTTTATCATTATAATTGAGGCTTTTAATATTTTT-AATCCCATT
1 TTTTTACCTTTATAATTGAGGCCCCTAAT-TTTTTCAATCTCA-C
* * ** *
44549 TATTTTACATTTATAATTGATGATCCTAAATTTTTT-AATCCCAC
1 T-TTTTACCTTTATAATTGAGGCCCCT-AATTTTTTCAATCTCAC
* * ** * * *
44593 ATTGTACCTTTATAATT-AAACTCAT-GTTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
* * *
44634 -TTTGACCTTTATAATTGAGGCCCATAATTTTTTCAATCCCA-
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
*
44675 TTTTTA-CTCATATAATTTG-GGCCCCTAATTTTTTTCAATCTCAC
1 TTTTTACCT-TTATAA-TTGAGGCCCCTAA-TTTTTTCAATCTCAC
* * *
44719 TTTTTACCTTTAAAATTGATGCCCCT-ATTTATTT-AATATCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTT-TTTCAATCTCAC
* * *
44761 TTTTTACCTTTATAATTGGGGTCCTTAATTTTTTCAATCAT-AC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATC-TCAC
*
44804 TTTTTACTTTTATA
1 TTTTTACCTTTATA
44818 GTTTAAGGCT
Statistics
Matches: 248, Mismatches: 45, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
40 20 0.08
41 14 0.06
42 69 0.28
43 87 0.35
44 23 0.09
45 32 0.13
46 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
Found at i:48133 original size:21 final size:19
Alignment explanation
Indices: 48097--48135 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
48087 AGGGGTTTAA
*
48097 TTTTTTAATAATATATTTG
1 TTTTTTAATAAAATATTTG
48116 TTTTTTAAATAAAAATATTT
1 TTTTTT-AAT-AAAATATTT
48136 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTTAATAAAATATTTG
Found at i:48143 original size:23 final size:23
Alignment explanation
Indices: 48092--48152 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
48082 GGGAGAGGGG
* *
48092 TTTAATTTTTTAAT-AATATATT
1 TTTAATTTTTAAATAAAAATATT
*
48114 TGT--TTTTTAAATAAAAATATT
1 TTTAATTTTTAAATAAAAATATT
48135 TTTAATTTTTTAAATAAA
1 TTTAA-TTTTTAAATAAA
48153 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 8 0.26
21 9 0.29
22 2 0.06
24 12 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTAATTTTTAAATAAAAATATT
Found at i:48155 original size:20 final size:21
Alignment explanation
Indices: 48092--48156 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
48082 GGGAGAGGGG
*
48092 TTTAATTTTTT-AATAATATA
1 TTTAATTTTTTAAATAATATT
*
48112 TTT-GTTTTTTAAATAAAAATATT
1 TTTAATTTTTTAAAT---AATATT
48135 TTTAATTTTTTAAATAA-ATT
1 TTTAATTTTTTAAATAATATT
48155 TT
1 TT
48157 CAAAATTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
19 6 0.16
20 11 0.30
21 2 0.05
23 8 0.22
24 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATTTTTTAAATAATATT
Found at i:48649 original size:16 final size:16
Alignment explanation
Indices: 48628--48659 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48618 CACATATCTT
48628 TTAGACATGTTCGATC
1 TTAGACATGTTCGATC
48644 TTAGACATGTTCGATC
1 TTAGACATGTTCGATC
48660 CCTGGATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
TTAGACATGTTCGATC
Found at i:52253 original size:21 final size:21
Alignment explanation
Indices: 52227--52271 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52217 GATTTCTGGG
* *
52227 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
52248 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
52269 CAA
1 CAA
52272 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:52948 original size:23 final size:24
Alignment explanation
Indices: 52905--52951 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
52895 ATATGGCATG
*
52905 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
52929 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
52952 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:53205 original size:31 final size:31
Alignment explanation
Indices: 53167--53308 Score: 221
Period size: 31 Copynumber: 4.6 Consensus size: 31
53157 AGGGTCGAGG
*
53167 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
53198 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
53229 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
53260 GTTTACCTATGTCCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
53291 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
53309 AAATCTATGG
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:60305 original size:16 final size:16
Alignment explanation
Indices: 60281--60314 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
60271 TATCGCCGAC
*
60281 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
60297 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
60313 CG
1 CG
60315 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:67769 original size:43 final size:44
Alignment explanation
Indices: 67659--67788 Score: 190
Period size: 43 Copynumber: 2.9 Consensus size: 44
67649 CCCTTTTTAA
* * *
67659 TGTTTACATTTTAGGATTATAAACTTAGAAAACGAATAGAGTTTTTT
1 TGTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGAG---TTT
*
67706 TTTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGAG-TT
1 TGTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGAGTTT
67749 TGTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGA
1 TGTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGA
67789 CTCCAAACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
43 41 0.53
47 37 0.47
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (44 bp):
TGTTTATATTTTAGTATTATAAACTTAGAAAATGAATAGAGTTT
Found at i:69743 original size:17 final size:18
Alignment explanation
Indices: 69711--69744 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
69701 TTGACCGGTC
*
69711 TGACCTGACTCGACCCGT
1 TGACCTGACCCGACCCGT
69729 TGACC-GACCCGACCCG
1 TGACCTGACCCGACCCG
69745 ACCCAGTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (18 bp):
TGACCTGACCCGACCCGT
Found at i:69796 original size:27 final size:29
Alignment explanation
Indices: 69750--69830 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 29
69740 ACCCGACCCA
*
69750 GTGACATTTTG-GGAATTATTTTAAAAAAT
1 GTGACA-TTTGAGGAATTATTTTAAAAAAG
*
69779 GTGACA-TTGA-GAATTATTTTGAAAAAG
1 GTGACATTTGAGGAATTATTTTAAAAAAG
*
69806 GTGACATTTTAGGAATT-TTTTAAAA
1 GTGACATTTGAGGAATTATTTTAAAA
69831 CTATTCTGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
27 24 0.53
28 10 0.22
29 11 0.24
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (29 bp):
GTGACATTTGAGGAATTATTTTAAAAAAG
Found at i:69874 original size:29 final size:29
Alignment explanation
Indices: 69841--69925 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
69831 CTATTCTGGT
* * *
69841 AATTATTTTTAAAATGATGACATTTTGGG
1 AATTATTTTTAAAAAGATGATATTTTGAG
* * * * *
69870 AATTATTTGTAAAACGGTGATATGTTGAT
1 AATTATTTTTAAAAAGATGATATTTTGAG
69899 AATTATTTTTAATAAAGATGATATTTT
1 AATTATTTTTAA-AAAGATGATATTTT
69926 TGTCATTTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AATTATTTTTAAAAAGATGATATTTTGAG
Found at i:75743 original size:37 final size:36
Alignment explanation
Indices: 75682--75803 Score: 160
Period size: 37 Copynumber: 3.4 Consensus size: 36
75672 TTATCCCATT
* *
75682 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
75717 ATTTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 A-TCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
75754 ACCA-TTTTCAAA-AAATCATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAA-CATTTACCAAACTTTGAAA
75789 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
75804 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
34 3 0.04
35 31 0.41
36 9 0.12
37 32 0.43
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:75774 original size:35 final size:34
Alignment explanation
Indices: 75682--75796 Score: 149
Period size: 35 Copynumber: 3.2 Consensus size: 34
75672 TTATCCCATT
* *
75682 ATCATTTTTCAACAAACATCTACCAAACTTTGAAA
1 ATCA-TTTTCAAAAAACATTTACCAAACTTTGAAA
*
75717 ATTTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 A-TCA-TTTTCAAA-AAACATTTACCAAACTTTGAAA
*
75754 ACCATTTTCAAAAAATCATTTACCAAACTTTGAAA
1 ATCATTTTCAAAAAA-CATTTACCAAACTTTGAAA
75789 ATCATTTT
1 ATCATTTT
75797 TTCAAAGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
34 3 0.04
35 35 0.49
36 11 0.15
37 22 0.31
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (34 bp):
ATCATTTTCAAAAAACATTTACCAAACTTTGAAA
Found at i:80365 original size:36 final size:36
Alignment explanation
Indices: 80301--80421 Score: 165
Period size: 35 Copynumber: 3.4 Consensus size: 36
80291 TTATCTCATT
* * *
80301 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAAAAATATTTACCAAACTTTGAAA
* *
80336 ATTATTTTTCAAAGAAATATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAAAAATATTTACCAAACTTTGAAA
*
80372 ACCA-TTTTCAAAAAAATATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAAAAATATTTACCAAACTTTGAAA
80407 ATCATTTTTTCAAAA
1 ATCA-TTTTTCAAAA
80422 TTGGTTGTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 42 0.56
36 24 0.32
37 9 0.12
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.36
Consensus pattern (36 bp):
ATCATTTTTCAAAAAAATATTTACCAAACTTTGAAA
Found at i:84660 original size:146 final size:146
Alignment explanation
Indices: 84418--84790 Score: 568
Period size: 146 Copynumber: 2.6 Consensus size: 146
84408 TCTGCTGTCA
* * * * * *
84418 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-CATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * * ** *
84482 CGTTCGGAATATTGATCGCAGATTCCGATCACCGGCAAGAGGCTAAAAATCGTCTGGATTTATTT
65 CGTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTT
84547 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCACCG
84564 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
* *
84629 GTTCGGAATATTGATCAAATATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
84694 CTCCGATCCGTCACCG
131 CTCCGATCCGTCACCG
* * *
84710 TTCATCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
84775 GTTCGGAATATTGATC
66 GTTCGGAATATTGATC
84791 GGAGATCCTG
Statistics
Matches: 208, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
146 205 0.99
147 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (146 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTATTTT
CTCCGATCCGTCACCG
Found at i:85185 original size:3 final size:3
Alignment explanation
Indices: 85177--85221 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
85167 TATGTAACAT
85177 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
85222 TTAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:85522 original size:54 final size:54
Alignment explanation
Indices: 85411--86315 Score: 1195
Period size: 54 Copynumber: 16.9 Consensus size: 54
85401 CTACCTACGA
* * * *
85411 GTTCGCTCCCTCTTGCT-TCAGAGAGTATGGAACTCGAACAATCTTCTGTC-AATGG
1 GTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGGAC-ATCTTCT-TCAAACGG
* * ** * ***
85466 GTTCGCTCCCTCTTTCTTTAGGGAGTA-GAAACTCAAACAATCTTCTGCCTTCGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGAC-ATCTTCTTCAAACGG
* *
85520 GTTCGCTCCCTATTTCTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* *
85574 GTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATC-TCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * * *
85627 GTTCGCTCCTTCTTTCT-TCAAGGAGTATGGAACTCAGATATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * *
85681 GTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGAACATC-TCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * * * *
85734 GTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGG--AT-ATCTTCACACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * *
85785 GTTCACTCCCTCTTTCTCTAGGAAGTATGGAACTCGGAAATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
*
85839 GTTCGCTCCCTCTTTTTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* *
85893 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGGACATCTTCTTCAAATGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
*
85947 GTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
*
86001 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGTACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * *
86055 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATTTTCTTTAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * *
86109 GTTCGCTTCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAACTG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * ** * *
86163 GTTCGCTCCCTCTTTCTTTAAGGAGTATAAAACTCGTACCTCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* * *
86217 GTTCGCTCCCTCTTTCT-TCAGGGAGTATGAAACTCGAACA--ATCTTCAAACGG
1 GTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
* *
86269 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTT
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTT
86316 TTGCTTCACT
Statistics
Matches: 752, Mismatches: 84, Indels: 29
0.87 0.10 0.03
Matches are distributed among these distances:
51 44 0.06
52 48 0.06
53 92 0.12
54 535 0.71
55 32 0.04
56 1 0.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
Found at i:86776 original size:36 final size:36
Alignment explanation
Indices: 86731--86879 Score: 131
Period size: 36 Copynumber: 4.1 Consensus size: 36
86721 ATGAAGACAC
*
86731 AAGATGGTTTGCTTCATTATTCTTTGGTGCAT-GCTT
1 AAGATGGTTTGCTTCACTATTCTTTGGTG-ATGGCTT
* * *
86767 AAGACGGTTTGCTTCACTACTCTTTAGTGATGGCTT
1 AAGATGGTTTGCTTCACTATTCTTTGGTGATGGCTT
* * * *
86803 AAGATGG-TCGCTTCACTATTATTTGGTGAAGACTT
1 AAGATGGTTTGCTTCACTATTCTTTGGTGATGGCTT
* * * ** * *
86838 CAGATTGATCTGCTTCACTCCTCTTCGGTGAAGGCTT
1 AAGA-TGGTTTGCTTCACTATTCTTTGGTGATGGCTT
86875 AAGAT
1 AAGAT
86880 TGACTTTGCT
Statistics
Matches: 89, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
35 27 0.30
36 38 0.43
37 24 0.27
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (36 bp):
AAGATGGTTTGCTTCACTATTCTTTGGTGATGGCTT
Found at i:88314 original size:125 final size:123
Alignment explanation
Indices: 87981--88360 Score: 415
Period size: 125 Copynumber: 3.0 Consensus size: 123
87971 CCTAGTGTCA
* * * * * * *
87981 CAATATTATCTTACACTGGTACGGGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCT-TGC
1 CAATATTGTCTTATACTGGTACGGGCCTTAAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTC
* * *
88045 TCTCAATGCCTTCTTGGTCTGAATCTTGTCATCTTC-ACACGATGTGGGTGCAGTCATGCCC
66 T-TC-ATGCC-TCTTGGTCTGAATCTTGTCATC-TCAACATGATGTGGGTTCAGTCGTGCCC
* * * **
88106 C-ATCAGTGTCTTATACCGGTATGGGCCTTCAAAAAAAACCCCATCACCTCAAATTGTAAGGCTC
1 CAAT-ATTGTCTTATACTGGTACGGGCCTT--AAAAATGCCCCATCACCTCAAATTGTAAGGCT-
* * * * * *
88170 CTTCTTCATGCCTTTTTGGTTTAAATCTTGTTATCTCAACATGACGTGGATTCAGTCGTGCCC
62 CTTCTTCATGCC-TCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* * *
88233 CAATATTGTCTTATACTGGTACGTGCCTTTAAAATGCCCCATCACCTCAAATTCTAAGGCTCATT
1 CAATATTGTCTTATACTGGTACGGGCCTTAAAAATGCCCCATCACCTCAAATTGTAAGGCTC-TT
*
88298 CTTCATGCCTCATTGGTCTGAATCTTGTCATCTCAACCTGATGTGGGTTCAGTCGTGCCC
65 CTTCATGCCTC-TTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
88358 CAA
1 CAA
88361 CATATCCTAA
Statistics
Matches: 210, Mismatches: 36, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
124 4 0.02
125 105 0.50
126 2 0.01
127 92 0.44
128 4 0.02
129 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (123 bp):
CAATATTGTCTTATACTGGTACGGGCCTTAAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTC
TTCATGCCTCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
Found at i:95423 original size:145 final size:145
Alignment explanation
Indices: 95174--95544 Score: 548
Period size: 145 Copynumber: 2.6 Consensus size: 145
95164 TCTGCTGTCA
* * * * * *
95174 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-CATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * * ** *
95238 CGTTCGGAATATTGATCGCAGATTCCGATCACCGGCAAGAGGCTAAAAATCGTCTGGATTT-ATT
65 CGTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGATT
95302 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCA-CG
95319 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
* *
95384 GTTCGGAATATTGATCAAATATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGATTT
95449 CTCCGATCCGTCACG
131 CTCCGATCCGTCACG
* * *
95464 TTCATCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
95529 GTTCGGAATATTGATC
66 GTTCGGAATATTGATC
95545 GGAGATCCTG
Statistics
Matches: 206, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
145 187 0.91
146 19 0.09
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (145 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAAGATTCCGATCACCGGAAAGAGGCTAAAAACCACCCGGATTTGATTT
CTCCGATCCGTCACG
Found at i:95939 original size:3 final size:3
Alignment explanation
Indices: 95931--95975 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
95921 TATGTAACAT
95931 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
95976 TTAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:96192 original size:17 final size:16
Alignment explanation
Indices: 96161--96195 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
96151 ATTATCATAA
*
96161 TTTTCATTCTTTTTTT
1 TTTTCATTCTATTTTT
96177 TTTTCTATTCTATTTTT
1 TTTTC-ATTCTATTTTT
96194 TT
1 TT
96196 CAGTCTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCATTCTATTTTT
Found at i:96715 original size:18 final size:18
Alignment explanation
Indices: 96694--96790 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 18
96684 ACATGCTTGT
96694 TTTTAGGTTGCAACCATA
1 TTTTAGGTTGCAACCATA
* * *
96712 TTTTAGGTTGGAA-CTTG
1 TTTTAGGTTGCAACCATA
*
96729 TTTTAGG-T--ACCCATA
1 TTTTAGGTTGCAACCATA
* * *
96744 TTTT-GAGTTGGAA-CTTGT
1 TTTTAG-GTTGCAACCAT-A
96762 TTTTAGGTTGCAACCATA
1 TTTTAGGTTGCAACCATA
96780 TATTTAGGTTG
1 T-TTTAGGTTG
96791 GAACTTGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 17
0.67 0.14 0.20
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
16 2 0.03
17 11 0.19
18 24 0.41
19 12 0.21
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTTAGGTTGCAACCATA
Found at i:96746 original size:32 final size:33
Alignment explanation
Indices: 96689--96991 Score: 248
Period size: 32 Copynumber: 8.9 Consensus size: 33
96679 TAGAAACATG
96689 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAA
1 CTTGTTTTTAGG-T--AACCATATTTTAGGTTGGAA
*
96725 CTTG-TTTTAGGTACCCATATTTT-GAGTTGGAA
1 CTTGTTTTTAGGTAACCATATTTTAG-GTTGGAA
96757 CTTGTTTTTAGGTTGCAACCATATATTTAGGTTGGAA
1 CTTGTTTTTAGG-T--AACCATAT-TTTAGGTTGGAA
*
96794 CTTGTTTTTAGAT-ACTCATATTTT-GAGTTGGAA
1 CTTGTTTTTAGGTAAC-CATATTTTAG-GTTGGAA
*
96827 CTTGTTTTTAGGTTGTAACCATATTTTAGGTGGGAA
1 CTTGTTTTTA-G--GTAACCATATTTTAGGTTGGAA
* * * *
96863 CTT-ATTTTAGATACCCATATTTTAAGTTGGAA
1 CTTGTTTTTAGGTAACCATATTTTAGGTTGGAA
* * *
96895 ATTATTTTTAGGTTGCAACCATATTTTAGGTTGAAA
1 CTTGTTTTTAGG-T--AACCATATTTTAGGTTGGAA
* * *
96931 CTT-ATTTTAGATACCCATA-TTT---TTGGAA
1 CTTGTTTTTAGGTAACCATATTTTAGGTTGGAA
96959 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTG
1 CTTGTTTTTAGG-T--AACCATATTTTAGGTTG
96992 CAATCATATT
Statistics
Matches: 217, Mismatches: 24, Indels: 52
0.74 0.08 0.18
Matches are distributed among these distances:
28 8 0.04
29 6 0.03
30 1 0.00
31 4 0.02
32 54 0.25
33 38 0.18
34 11 0.05
35 18 0.08
36 52 0.24
37 24 0.11
38 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (33 bp):
CTTGTTTTTAGGTAACCATATTTTAGGTTGGAA
Found at i:96767 original size:68 final size:68
Alignment explanation
Indices: 96689--97005 Score: 471
Period size: 68 Copynumber: 4.7 Consensus size: 68
96679 TAGAAACATG
* *
96689 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGGTACCCATATTTTGAGTTG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTATTTTAGATACCCATATTTTGAGTTG
96754 GAA
66 GAA
* *
96757 CTTGTTTTTAGGTTGCAACCATATATTTAGGTTGGAACTTGTTTTTAGATACTCATATTTTGAGT
1 CTTGTTTTTAGGTTGCAACCATAT-TTTAGGTTGGAACTT-ATTTTAGATACCCATATTTTGAGT
96822 TGGAA
64 TGGAA
* * *
96827 CTTGTTTTTAGGTTGTAACCATATTTTAGGTGGGAACTTATTTTAGATACCCATATTTTAAGTTG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTATTTTAGATACCCATATTTTGAGTTG
96892 GAA
66 GAA
* * *
96895 ATTATTTTTAGGTTGCAACCATATTTTAGGTTGAAACTTATTTTAGATACCCATA-TTT---TTG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTATTTTAGATACCCATATTTTGAGTTG
96956 GAA
66 GAA
* *
96959 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGCAATCATATTTTAG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAA-CTTATTTTAG
97006 GTTACAACTT
Statistics
Matches: 229, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
64 39 0.17
65 9 0.04
67 3 0.01
68 100 0.44
69 29 0.13
70 49 0.21
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (68 bp):
CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTATTTTAGATACCCATATTTTGAGTTG
GAA
Found at i:96853 original size:18 final size:18
Alignment explanation
Indices: 96832--97008 Score: 78
Period size: 18 Copynumber: 10.5 Consensus size: 18
96822 TGGAACTTGT
*
96832 TTTTAGGTTGTAACCATA
1 TTTTAGGTTGGAACCATA
* *
96850 TTTTAGGTGGGAA-CTTA
1 TTTTAGGTTGGAACCATA
* *
96867 TTTTA-GAT--ACCCATA
1 TTTTAGGTTGGAACCATA
*
96882 TTTTAAGTTGGAA--ATTA
1 TTTTAGGTTGGAACCA-TA
*
96899 TTTTTAGGTTGCAACCATA
1 -TTTTAGGTTGGAACCATA
* *
96918 TTTTAGGTT-GAAACTTA
1 TTTTAGGTTGGAACCATA
* *
96935 TTTTA-GAT--ACCCATA
1 TTTTAGGTTGGAACCATA
* *
96950 -TTT---TTGGAA-CTTGT
1 TTTTAGGTTGGAACCAT-A
*
96964 TTTTAGGTTGCAACCATA
1 TTTTAGGTTGGAACCATA
* *
96982 TTTTAGGTTGCAATCATA
1 TTTTAGGTTGGAACCATA
97000 TTTTAGGTT
1 TTTTAGGTT
97009 ACAACTTGTT
Statistics
Matches: 117, Mismatches: 26, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
12 1 0.01
13 2 0.02
14 5 0.04
15 15 0.13
16 6 0.05
17 20 0.17
18 63 0.54
19 4 0.03
20 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (18 bp):
TTTTAGGTTGGAACCATA
Found at i:96863 original size:138 final size:132
Alignment explanation
Indices: 96689--96989 Score: 458
Period size: 138 Copynumber: 2.2 Consensus size: 132
96679 TAGAAACATG
* * * *
96689 CTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGGTACCCATATTTTGAGTTG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTGGGAACTTATTTTAGATACCCATATTTTAAGTTG
* * * * *
96754 GAACTTGTTTTTAGGTTGCAACCATATATTTAGGTTGGAACTTGTTTTTAGATACTCATATTTTG
66 GAAATTATTTTTAGGTTGCAACCATAT-TTTAGGTTGAAACTT-ATTTTAGATACCCATA-TTT-
96819 AGTTGGAA
127 --TTGGAA
*
96827 CTTGTTTTTAGGTTGTAACCATATTTTAGGTGGGAACTTATTTTAGATACCCATATTTTAAGTTG
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGTGGGAACTTATTTTAGATACCCATATTTTAAGTTG
96892 GAAATTATTTTTAGGTTGCAACCATATTTTAGGTTGAAACTTATTTTAGATACCCATATTTTTGG
66 GAAATTATTTTTAGGTTGCAACCATATTTTAGGTTGAAACTTATTTTAGATACCCATATTTTTGG
96957 AA
131 AA
96959 CTTGTTTTTAGGTTGCAACCATATTTTAGGT
1 CTTGTTTTTAGGTTGCAACCATATTTTAGGT
96990 TGCAATCATA
Statistics
Matches: 152, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
132 36 0.24
135 3 0.02
136 14 0.09
137 14 0.09
138 85 0.56
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (132 bp):
CTTGTTTTTAGGTTGCAACCATATTTTAGGTGGGAACTTATTTTAGATACCCATATTTTAAGTTG
GAAATTATTTTTAGGTTGCAACCATATTTTAGGTTGAAACTTATTTTAGATACCCATATTTTTGG
AA
Found at i:99705 original size:29 final size:29
Alignment explanation
Indices: 99673--99743 Score: 98
Period size: 24 Copynumber: 2.6 Consensus size: 29
99663 CATAAATCAG
*
99673 GTCAAGTATCATATCAGATCAGAATCTAT
1 GTCAAGTATCATATCAGATCAGAATCCAT
99702 GTC-AG----ATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGATCAGAATCCAT
99726 GTCAAGTATCATATCAGA
1 GTCAAGTATCATATCAGA
99744 ATTCAAATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 21 0.58
25 2 0.06
28 2 0.06
29 11 0.31
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (29 bp):
GTCAAGTATCATATCAGATCAGAATCCAT
Found at i:102216 original size:7 final size:7
Alignment explanation
Indices: 102200--102239 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
102190 TGGTCAACGC
*
102200 CGGTCGA
1 CGGTCAA
102207 CGGTCAA
1 CGGTCAA
102214 CGGGTCAA
1 C-GGTCAA
102222 CGGTCAA
1 CGGTCAA
102229 CGGGTCAA
1 C-GGTCAA
102237 CGG
1 CGG
102240 GTCGAGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:102221 original size:8 final size:8
Alignment explanation
Indices: 102208--102242 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
102198 GCCGGTCGAC
102208 GGTCAACG
1 GGTCAACG
102216 GGTCAAC-
1 GGTCAACG
102223 GGTCAACG
1 GGTCAACG
102231 GGTCAACG
1 GGTCAACG
102239 GGTC
1 GGTC
102243 GAGTCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:102224 original size:15 final size:15
Alignment explanation
Indices: 102191--102239 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
102181 GGTCAACAAT
*
102191 GGTCAACGCCGGTCGAC
1 GGTCAACG--GGTCAAC
102208 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
102223 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
102238 GG
1 GG
102240 GTCGAGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 23 0.74
17 8 0.26
ACGTcount: A:0.22, C:0.29, G:0.37, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:102264 original size:31 final size:31
Alignment explanation
Indices: 102229--102295 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
102219 CAACGGTCAA
* * *
102229 CGGGTCAACGGGTCGAGTCAATGGGTTGGGT
1 CGGGTCAACGAGTCGAGTCAACGGGTCGGGT
*
102260 CGGGTCAACGAGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGAGTCGAGTCAACGGGTCGGGT
102291 CGGGT
1 CGGGT
102296 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGAGTCGAGTCAACGGGTCGGGT
Found at i:102276 original size:13 final size:13
Alignment explanation
Indices: 102258--102291 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
102248 AATGGGTTGG
102258 GTCGGGTCAACGA
1 GTCGGGTCAACGA
*
102271 GTCGGGTCAACGG
1 GTCGGGTCAACGA
102284 GTCGGGTC
1 GTCGGGTC
102292 GGGTTGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (13 bp):
GTCGGGTCAACGA
Found at i:108982 original size:21 final size:21
Alignment explanation
Indices: 108958--109018 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
108948 TTCAAAGAAA
108958 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
108979 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
108993 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
109014 CATTT
1 CATTT
109019 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:108992 original size:35 final size:36
Alignment explanation
Indices: 108907--109053 Score: 178
Period size: 35 Copynumber: 4.2 Consensus size: 36
108897 ATCCCATTAT
* * *
108907 CATTTTTC-AACAAACATCTACTAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
108943 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
108979 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
***
109014 CATTTTTTCAAAG-TTGA-TTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
109048 CATTTT
1 CATTTT
109054 AATAATTTCA
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 44 0.44
36 14 0.14
37 28 0.28
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:109024 original size:72 final size:68
Alignment explanation
Indices: 108910--109053 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 68
108900 CCATTATCAT
*
108910 TTTTCAACAAACATCTACTAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG-AACA-TTACCAAAC-TTGA
108975 AAACCA
63 AAACCA
* * * ***
108981 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTGATTACCAAACTTGAA
1 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGAACATTACCAAACTTGAA
109045 AACCA
64 AACCA
109050 TTTT
1 TTTT
109054 AATAATTTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
69 14 0.22
70 9 0.14
71 12 0.19
72 29 0.45
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAACATTACCAAACTTGAAAA
CCA
Found at i:119915 original size:2 final size:2
Alignment explanation
Indices: 119908--119941 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
119898 AACGATTGAA
119908 AT AT AT AT GAT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
119942 TAAAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123968 original size:31 final size:31
Alignment explanation
Indices: 123933--123997 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
123923 TCAAAAAACA
* **
123933 TAATATATAATCACTTTCGTTTTTATTTAAT
1 TAATATATAATCAATTTCGTTTCAATTTAAT
*
123964 TAATATATAGTCAATTTCGTTTCAATTTAAT
1 TAATATATAATCAATTTCGTTTCAATTTAAT
123995 TAA
1 TAA
123998 GACGTGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (31 bp):
TAATATATAATCAATTTCGTTTCAATTTAAT
Found at i:136092 original size:89 final size:89
Alignment explanation
Indices: 135941--136117 Score: 336
Period size: 89 Copynumber: 2.0 Consensus size: 89
135931 ATCCAATTCT
* *
135941 CATATGTATGGGGTGAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTTAGAGTAGCT
1 CATATGTATGGGGTAAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTGAGAGTAGCT
136006 TCCGAGAAAGACCTCCGGCAGTCC
66 TCCGAGAAAGACCTCCGGCAGTCC
136030 CATATGTATGGGGTAAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTGAGAGTAGCT
1 CATATGTATGGGGTAAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTGAGAGTAGCT
136095 TCCGAGAAAGACCTCCGGCAGTC
66 TCCGAGAAAGACCTCCGGCAGTC
136118 AGAAAATTAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.23, C:0.22, G:0.36, T:0.19
Consensus pattern (89 bp):
CATATGTATGGGGTAAGGGGGAGGTAGGGTAGTAGGCTGCCCCCAACGCCAGGTTGAGAGTAGCT
TCCGAGAAAGACCTCCGGCAGTCC
Found at i:136252 original size:14 final size:14
Alignment explanation
Indices: 136233--136271 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
136223 TAATGAGAAT
136233 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
136247 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
136261 GAATCTCTGCA
1 TAATCCCTGCA
136272 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:143102 original size:16 final size:16
Alignment explanation
Indices: 143081--143114 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
143071 CACCATAACC
143081 TTCAAAGTTCTTAAAT
1 TTCAAAGTTCTTAAAT
143097 TTCAAAGTTCTTAAAT
1 TTCAAAGTTCTTAAAT
143113 TT
1 TT
143115 TTAAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCAAAGTTCTTAAAT
Found at i:143545 original size:18 final size:20
Alignment explanation
Indices: 143513--143553 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
143503 TAAAAAAAAT
143513 ATTAAAAAATCATAAATA-A
1 ATTAAAAAATCATAAATATA
*
143532 ATTAAAAAGT-ATAAATATA
1 ATTAAAAAATCATAAATATA
143551 ATT
1 ATT
143554 TATAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTAAAAAATCATAAATATA
Found at i:147932 original size:21 final size:21
Alignment explanation
Indices: 147908--148022 Score: 80
Period size: 21 Copynumber: 5.6 Consensus size: 21
147898 AATTTGGAAA
147908 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
147929 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAACGCGAACT-TCG-ACT
* *
147949 ATCGCAACGTGAACTTAGACT
1 ATCGCAACGCGAACTTCGACT
* **
147970 ATCGCAA--CGAA-TTTGAAAA
1 ATCGCAACGCGAACTTCG-ACT
*
147989 ATCGCAACGCGAACTCCGACT
1 ATCGCAACGCGAACTTCGACT
*
148010 ATCGTAACGCGAA
1 ATCGCAACGCGAA
148023 TTTGGAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.04
19 11 0.15
20 15 0.21
21 40 0.56
22 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:147963 original size:41 final size:41
Alignment explanation
Indices: 147905--148042 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
147895 GTGAATTTGG
147905 AAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATG-
1 AAAATCGCAACGCGAACTTCGACTATCGCAA-GCGAATATGA
* * * *
147946 TAAATCGCAACGTGAACTTAGACTATCGCAA-CGAATTTGA
1 AAAATCGCAACGCGAACTTCGACTATCGCAAGCGAATATGA
* * * *
147986 AAAATCGCAACGCGAACTCCGACTATCGTAACGCGAATTTGG
1 AAAATCGCAACGCGAACTTCGACTATCGCAA-GCGAATATGA
* *
148028 AAAATTGCAATGCGA
1 AAAATCGCAACGCGA
148043 TAGTCGAAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 7 0.09
40 26 0.32
41 28 0.34
42 21 0.26
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGAACTTCGACTATCGCAAGCGAATATGA
Found at i:153081 original size:50 final size:42
Alignment explanation
Indices: 153010--153129 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
153000 CACCAATTCA
153010 TATTGAGACTTAATGGTGTTATGGTGTTATTTATTTTAGACT
1 TATTGAGACTTAATGGTGTTATGGTGTTATTTATTTTAGACT
*
153052 TATTGAGACTTAATGGTGTTATGGTGTTATTTATTTTAGTCT
1 TATTGAGACTTAATGGTGTTATGGTGTTATTTATTTTAGACT
* *
153094 TTTTGAGACTTAATTGTGTTATGGTGTTATTTATTT
1 TATTGAGACTTAATGGTGTTATGGTGTTATTTATTT
153130 ACTTGTTTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.04, G:0.21, T:0.53
Consensus pattern (42 bp):
TATTGAGACTTAATGGTGTTATGGTGTTATTTATTTTAGACT
Found at i:157252 original size:30 final size:30
Alignment explanation
Indices: 157218--157285 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
157208 TGGGATGGTT
157218 TTGAAGCTAAATGGGTTAGGGTATTTACAG
1 TTGAAGCTAAATGGGTTAGGGTATTTACAG
157248 TTGAAGCTAAATGGGTTAGGGTATTTACAG
1 TTGAAGCTAAATGGGTTAGGGTATTTACAG
157278 TTGAAGCT
1 TTGAAGCT
157286 TAAGAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (30 bp):
TTGAAGCTAAATGGGTTAGGGTATTTACAG
Found at i:162230 original size:75 final size:75
Alignment explanation
Indices: 162082--162230 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
162072 GACAACCATA
* * *
162082 AACTGAAAATTACTACTACTGGGAGAGCACCAAAATTTTGTCATATGTTCTAATCTTTTTGGAAA
1 AACTGAAAATTACTACTACTGGAAGAGCACCAAAATTTTGCCATATGTTCTAATCTTTTTGAAAA
* *
162147 TACGATTTAG
66 CACAATTTAG
* *
162157 AACTGAAAATTACTACTTCTGGAAGAGCACCAAAATTTTGCCATATGTTTTAATCTTTTTGAAAA
1 AACTGAAAATTACTACTACTGGAAGAGCACCAAAATTTTGCCATATGTTCTAATCTTTTTGAAAA
162222 CACAATTTA
66 CACAATTTA
162231 AAACATAGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (75 bp):
AACTGAAAATTACTACTACTGGAAGAGCACCAAAATTTTGCCATATGTTCTAATCTTTTTGAAAA
CACAATTTAG
Found at i:164758 original size:2 final size:2
Alignment explanation
Indices: 164753--164779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
164743 TATATGTATA
164753 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 A
164780 TCACCTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:166480 original size:19 final size:19
Alignment explanation
Indices: 166456--166506 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
166446 ACCAACAAAA
166456 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
166475 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
166494 TCGCAACGCGATC
1 TCGCAACGCGATC
166507 TCCATTATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (19 bp):
TCGCAACGCGATCGCTAAT
Found at i:166647 original size:20 final size:20
Alignment explanation
Indices: 166625--166732 Score: 155
Period size: 20 Copynumber: 5.4 Consensus size: 20
166615 AATAAGTAAA
* *
166625 TCGCAATGCGATACTGA-TT
1 TCGCAACGCGATTCTGACTT
*
166644 ATCGCAACGCGATACTGACTT
1 -TCGCAACGCGATTCTGACTT
166665 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
166685 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
166705 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTT
166725 TCGCAACG
1 TCGCAACG
166733 AGATAATACA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
20 81 0.98
21 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:167292 original size:20 final size:20
Alignment explanation
Indices: 167267--167324 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
167257 ATTCATTTGA
167267 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
167287 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
167307 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
167325 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:167384 original size:19 final size:16
Alignment explanation
Indices: 167343--167401 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 16
167333 GAAATGAAAA
167343 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
167359 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
167373 ATTTCGCATTGCGA--TTC
1 ---TCGCATTGCGATTTTC
*
167390 TCTCATTGCGAT
1 TCGCATTGCGAT
167402 AGTCAGTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
14 21 0.58
16 3 0.08
17 6 0.17
19 6 0.17
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:169021 original size:41 final size:42
Alignment explanation
Indices: 168976--169067 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
168966 CCTCTTCAAC
*
168976 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGAACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGG-ACTCTTGAGG
* * *
169017 GATGATAGGGGCCTTTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
169059 GATGACAGG
1 GATGACAGG
169068 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
41 19 0.43
42 21 0.48
43 4 0.09
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:169429 original size:20 final size:20
Alignment explanation
Indices: 169404--169456 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
169394 GAAGAATAGT
*
169404 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
* *
169424 TTACTTTTGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
169444 TGACTATCGCAAC
1 TTACTTTCGCAAC
169457 GCGGAAATGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:169457 original size:20 final size:20
Alignment explanation
Indices: 169432--169516 Score: 100
Period size: 20 Copynumber: 4.3 Consensus size: 20
169422 ACTTACTTTT
*
169432 GCAACGCGAAAATGACTATC
1 GCAACGCGGAAATGACTATC
*
169452 GCAACGCGGAAATGGCTATC
1 GCAACGCGGAAATGACTATC
*
169472 GCAACGCGGAAATGGCTATC
1 GCAACGCGGAAATGACTATC
* * **
169492 ACAATGC-GAAATGAAAATC
1 GCAACGCGGAAATGACTATC
169511 GCAACG
1 GCAACG
169517 ACAAAATCGC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.14
Consensus pattern (20 bp):
GCAACGCGGAAATGACTATC
Found at i:169564 original size:19 final size:19
Alignment explanation
Indices: 169542--169638 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
169532 GAAACACAAA
169542 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
169561 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
169577 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
169594 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
169610 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
169627 TCGCATTGCGAT
1 TCGCATTGCGAT
169639 AACCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:169583 original size:14 final size:14
Alignment explanation
Indices: 169564--169622 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
169554 TTTCATTTCG
169564 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
169578 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
169595 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
169611 CGTTGCGATTTT
1 CGTTGCGATTTT
169623 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:169589 original size:33 final size:33
Alignment explanation
Indices: 169547--169638 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
169537 ACAAATCGCA
*
169547 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
169580 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
169613 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
169639 AACCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:169665 original size:20 final size:19
Alignment explanation
Indices: 169611--169666 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
169601 GCGATTTTGT
**
169611 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAATCATTTCG
* *
169630 CATTGCGATAACCATTTCCG
1 CGTTGCGATAATCATTT-CG
*
169650 CGTTGCGATAGTCATTT
1 CGTTGCGATAATCATTT
169667 TTGTGTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAATCATTTCG
Found at i:170240 original size:18 final size:18
Alignment explanation
Indices: 170217--170264 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
170207 CGGGTCGATC
*
170217 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
*
170235 AGGTGATAGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
170253 AGGTGATGGCTC
1 AGGTGATGGCTC
170265 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:171637 original size:20 final size:20
Alignment explanation
Indices: 171583--171625 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
171573 AATAGTTTCT
*
171583 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACAC
*
171603 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACAC
171623 GAA
1 GAA
171626 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGACAATCGCAACAC
Found at i:172392 original size:20 final size:19
Alignment explanation
Indices: 172367--172418 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
172357 GAGTATGGAA
* *
172367 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
172387 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
172406 AACCGGGTTGACC
1 AACCGGTTTGACC
172419 CGACCCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:172396 original size:10 final size:10
Alignment explanation
Indices: 172367--172416 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
172357 GAGTATGGAA
172367 AACCGGTTTG
1 AACCGGTTTG
*
172377 -ACCAGTTTTG
1 AACC-GGTTTG
172387 AACCGGTTTG
1 AACCGGTTTG
*
172397 -ACCGGTCTG
1 AACCGGTTTG
*
172406 AACCGGGTTG
1 AACCGGTTTG
172416 A
1 A
172417 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:172433 original size:14 final size:14
Alignment explanation
Indices: 172414--172441 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
172404 TGAACCGGGT
172414 TGACCCGACCCGAC
1 TGACCCGACCCGAC
172428 TGACCCGACCCGAC
1 TGACCCGACCCGAC
172442 CCGACTGTTG
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:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:172437 original size:19 final size:20
Alignment explanation
Indices: 172415--172463 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
172405 GAACCGGGTT
172415 GACCCGACCCGAC-TGACCC
1 GACCCGACCCGACTTGACCC
172434 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC--TTGACCC
172456 GACCCGAC
1 GACCCGAC
172464 TGTTGACCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
22 14 0.52
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.08
Consensus pattern (20 bp):
GACCCGACCCGACTTGACCC
Found at i:172456 original size:17 final size:17
Alignment explanation
Indices: 172412--172476 Score: 94
Period size: 17 Copynumber: 3.7 Consensus size: 17
172402 TCTGAACCGG
172412 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
172429 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
172448 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
172465 GTTGACCCGACC
1 GTTGACCCGACC
172477 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 27 0.64
19 15 0.36
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:173442 original size:32 final size:32
Alignment explanation
Indices: 173359--173482 Score: 87
Period size: 31 Copynumber: 4.0 Consensus size: 32
173349 CTAATGTGAC
* * *
173359 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
173389 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* * *
173422 TCTTAGGTAGGC-CTCACGGCCCCAAAATCTA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
*
173453 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
173483 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 47 0.65
32 25 0.35
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:173442 original size:63 final size:63
Alignment explanation
Indices: 173359--173482 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
173349 CTAATGTGAC
* ** *
173359 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCCAAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
173422 TCTTAGGTAGGC-CTCACGGCCCCAAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCT-ACGGCCCCAAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
173483 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.06
63 48 0.92
64 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCTACGGCCCCAAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:174314 original size:22 final size:22
Alignment explanation
Indices: 174284--174327 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
174274 GATGGAGATA
*
174284 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
174306 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
174328 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:174617 original size:41 final size:41
Alignment explanation
Indices: 174500--174629 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 41
174490 GAAAATCGTA
* *
174500 TTGCGATTATGTATTATCTCGTTGCGAAAGTCAATATCGCG
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
* * *
174541 TTGCGA--AAGTAAGTATCGCGTTGCGAAAGTTAGTATCGCG
1 TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCGCG
* * * *
174581 TTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCA
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
174622 TTGCGATT
1 TTGCGATT
174630 TACTTATTCG
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.04
40 31 0.42
41 38 0.51
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:174628 original size:20 final size:20
Alignment explanation
Indices: 174514--174627 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
174504 GATTATGTAT
* *
174514 TATCTCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAG
*
174534 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
174554 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
** *
174574 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
174595 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
174615 TATCGCATTGCGA
1 TATCGCGTTGCGA
174628 TTTACTTATT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.78
21 13 0.16
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:174689 original size:21 final size:22
Alignment explanation
Indices: 174637--174689 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
174627 ATTTACTTAT
174637 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
174658 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
174679 TCGCATTGCGA
1 TCGCATTGCGA
174690 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:175195 original size:20 final size:20
Alignment explanation
Indices: 175170--175221 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
175160 ACAAGTAAAA
175170 AAATGACAAAACCAGTCTAT
1 AAATGACAAAACCAGTCTAT
175190 AAATGACAAAACCAGTCTAT
1 AAATGACAAAACCAGTCTAT
*
175210 AAATGAAAAAAC
1 AAATGACAAAAC
175222 ATGTAAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (20 bp):
AAATGACAAAACCAGTCTAT
Found at i:175388 original size:112 final size:112
Alignment explanation
Indices: 175190--175711 Score: 841
Period size: 112 Copynumber: 4.7 Consensus size: 112
175180 ACCAGTCTAT
* * * *
175190 AAATGACAAAACCAGTCTATAAATGAAAAAACATGTAAAACGCTACCGAATATATTGAAAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
175255 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
* *
175302 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAACGCTACTGAATATATTGAAAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
* *
175367 GATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAA
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
175414 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACC-AGATATATTGAAAGTGT
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGA-ATATATTGAAAGTGT
175478 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAA
65 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
* * *
175525 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
* * **
175590 GATACTTTATAAAAATGTATCGATCCATAACAATAAAAAAAATAAAA
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
* * * * *
175637 AAATGACAAAACCGATCTATAAATGACAAAACAGATAAAGCGCTATCGAATATGTTGATAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
175702 GATACTTTAT
66 GATACTTTAT
175712 TATAAGTATC
Statistics
Matches: 386, Mismatches: 21, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
111 104 0.27
112 282 0.73
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (112 bp):
AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAA
Found at i:175646 original size:223 final size:224
Alignment explanation
Indices: 175190--175711 Score: 850
Period size: 223 Copynumber: 2.3 Consensus size: 224
175180 ACCAGTCTAT
* * * *
175190 AAATGACAAAACCAGTCTATAAATGAAAAAACATGTAAAACGCTACCGAATATATTGAAAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
175255 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCT
*
175320 ATAAATGACAAAACAGGTAAAACGCTACTGAATATATTGAAAGTGTCGATACTTTATAAAAATAT
131 ATAAATGACAAAACAGGTAAAACGCTACCGAATATATTGAAAGTGTCGATACTTTATAAAAATAT
* * **
175385 ATCGATCCATAACAATATAACATGTAAAA
196 ATCGATCCATAACAATAAAAAAAATAAAA
175414 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACC-AGATATATTGAAAGTGT
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGA-ATATATTGAAAGTGT
175478 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACCGGTC
65 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* * * * *
175542 TATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATG
130 TATAAATGACAAAACAGGTAAAACGCTACCGAATATATTGAAAGTGTCGATACTTTATAAAAATA
175607 TATCGATCCATAACAATAAAAAAAATAAAA
195 TATCGATCCATAACAATAAAAAAAATAAAA
* * * * *
175637 AAATGACAAAACCGATCTATAAATGACAAAACAGATAAAGCGCTATCGAATATGTTGATAGTGTC
1 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
175702 GATACTTTAT
66 GATACTTTAT
175712 TATAAGTATC
Statistics
Matches: 277, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
223 174 0.63
224 103 0.37
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (224 bp):
AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTC
GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCT
ATAAATGACAAAACAGGTAAAACGCTACCGAATATATTGAAAGTGTCGATACTTTATAAAAATAT
ATCGATCCATAACAATAAAAAAAATAAAA
Found at i:175987 original size:179 final size:181
Alignment explanation
Indices: 175584--176034 Score: 672
Period size: 179 Copynumber: 2.5 Consensus size: 181
175574 ATATGTTGAT
* * * *
175584 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAAAAAATAAAAAAATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
** * * * *
175649 CGATCTATAAATGACAAAACAGATAAAGCGCTATCGAATATGTTGATAGTGTCGATACTTTATTA
66 CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGATAGTGTCGATAC-TTATTA
* * **
175714 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAA
130 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGACAATAA
* * *
175766 AGTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAATATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
*
175831 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGATAGTGTCGATAC-T-TTAT
66 CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGATAGTGTCGATACTTATTAT
*
175894 AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGTGACAATAA
131 AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGACAATAA
* * * *
175945 AGTGTCGATACTTTATAAAAATGTATTGATCCATATCAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
176010 CGATCTCGAAATGACAAAACCGGTA
66 CGATCTCGAAATGACAAAACCGGTA
176035 GTAAAAAAGT
Statistics
Matches: 243, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
179 133 0.55
180 1 0.00
182 109 0.45
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (181 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGATAGTGTCGATACTTATTAT
AAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGACAATAA
Found at i:177049 original size:29 final size:29
Alignment explanation
Indices: 177016--177110 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
177006 TGAGTTATCC
177016 GACTATTAAAAGTTATAAAATGATCATCT
1 GACTATTAAAAGTTATAAAATGATCATCT
* **** *
177045 GACTA-TAAGATGTTATTTTTTTAGTCCAT-T
1 GACTATTAA-AAGTTATAAAATGA-T-CATCT
*
177075 GACTATTAAAAGTTACAAAATGATCAATC-
1 GACTATTAAAAGTTATAAAATGATC-ATCT
177104 GACTATT
1 GACTATT
177111 CATTATATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
28 4 0.09
29 23 0.49
30 14 0.30
31 6 0.13
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (29 bp):
GACTATTAAAAGTTATAAAATGATCATCT
Found at i:178024 original size:24 final size:23
Alignment explanation
Indices: 177997--178058 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 23
177987 ATTTATCTTA
177997 AGATTTTATTTTGATTCTTTTTCT
1 AGATTTTATTTTGATT-TTTTTCT
*
178021 AGATATTTAATGTATGATTTTTTTCT
1 AGAT-TTT-AT-TTTGATTTTTTTCT
*
178047 TGATTTATATTT
1 AGATTT-TATTT
178059 AATGCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 5 0.16
25 7 0.23
26 13 0.42
27 6 0.19
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.63
Consensus pattern (23 bp):
AGATTTTATTTTGATTTTTTTCT
Found at i:178223 original size:20 final size:20
Alignment explanation
Indices: 178177--178223 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
178167 AAATATTATT
*
178177 GAAAAATGACATAATATAAT
1 GAAAAATGACATAATATAAG
*
178197 AAGAAAATGACA-AATATAACG
1 GA-AAAATGACATAATATAA-G
178218 GAAAAA
1 GAAAAA
178224 CAAGTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.64, C:0.06, G:0.13, T:0.17
Consensus pattern (20 bp):
GAAAAATGACATAATATAAG
Found at i:179301 original size:186 final size:186
Alignment explanation
Indices: 178981--179373 Score: 662
Period size: 186 Copynumber: 2.1 Consensus size: 186
178971 TAACCGAAAT
* *
178981 AAAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATA
1 AAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATA
* *
179046 ATTTAAGATTCAATAACTTTTAAACCTAAGTCAATATTAAATAATTAAAAAATTTATATAAAATT
66 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAATTTATATAAAATT
*
179111 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTCTGAATTAA
131 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAA
*
179167 AAAATATTAAATATATTATATATAACATATGGGCTCAGTCCAAACCATTTAAAACCCAATTAATA
1 AAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATA
*
179232 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
66 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAATTTATATAAAATT
* * * *
179297 TTTATTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTAT
131 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAA
* *
179353 AAAATATTTAAT-TTTTATATA
1 AAAATATTAAATATATTATATA
179374 AATTAGAAAA
Statistics
Matches: 194, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
185 8 0.04
186 186 0.96
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (186 bp):
AAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATA
ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAAAAAATTTATATAAAATT
TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAA
Found at i:180352 original size:2 final size:2
Alignment explanation
Indices: 180345--180374 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180335 CGTGAATTAG
180345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180375 CTGGATTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189247 original size:6 final size:6
Alignment explanation
Indices: 189236--189316 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
189226 ATGGTTGAAC
189236 CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG
1 CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG CAATAG
189284 CAATAG CAATAG CAATAG CAATAG CAATAG CAA
1 CAATAG CAATAG CAATAG CAATAG CAATAG CAA
189317 GAAGAGAAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (6 bp):
CAATAG
Found at i:189697 original size:20 final size:21
Alignment explanation
Indices: 189655--189696 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
189645 TATTTATTTT
189655 ATTTATATATTTCTATTAAAA
1 ATTTATATATTTCTATTAAAA
*
189676 ATTTAT-TATTGTCTCTTAAAA
1 ATTTATATATT-TCTATTAAAA
189697 TCATCTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTATATATTTCTATTAAAA
Found at i:194720 original size:24 final size:24
Alignment explanation
Indices: 194693--194738 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
194683 GTGAGCTTTC
194693 ATGAGTTTAGATTTTCTGCCTTAT
1 ATGAGTTTAGATTTTCTGCCTTAT
*
194717 ATGAGTTTAGATTTTCTTCCTT
1 ATGAGTTTAGATTTTCTGCCTT
194739 CTTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
ATGAGTTTAGATTTTCTGCCTTAT
Found at i:197254 original size:20 final size:20
Alignment explanation
Indices: 197229--197266 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
197219 AATTAGTGTA
197229 GTAATAACATG-ATTTGTACT
1 GTAATAA-ATGTATTTGTACT
197249 GTAATAAATGTATTTGTA
1 GTAATAAATGTATTTGTA
197267 TGATTCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
GTAATAAATGTATTTGTACT
Found at i:200243 original size:51 final size:51
Alignment explanation
Indices: 200143--200250 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 51
200133 GTAGCAGTAA
* * * * *
200143 AGCGCGCCCCCTGTCCCGCGCTATATGCTGATTTGGCACCACGTGGGGTAT
1 AGCGCGCACCCTGCCCCGCGCTATACGCTGAATGGGCACCACGTGGGGTAT
*
200194 AGCGCGCACCCTGCCCCGCGCTATACGCTGACATGGGTTA-CACGT-GGGTAT
1 AGCGCGCACCCTGCCCCGCGCTATACGCTGA-ATGGG-CACCACGTGGGGTAT
200245 AGCGCG
1 AGCGCG
200251 GCCCCTAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 40 0.82
52 8 0.16
53 1 0.02
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.20
Consensus pattern (51 bp):
AGCGCGCACCCTGCCCCGCGCTATACGCTGAATGGGCACCACGTGGGGTAT
Found at i:200541 original size:17 final size:18
Alignment explanation
Indices: 200504--200544 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
200494 ATATTATGTA
*
200504 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
200522 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
200539 TTTACT
1 TTTACT
200545 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:205051 original size:42 final size:42
Alignment explanation
Indices: 204992--205076 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
204982 TATCCGCAAA
204992 TTCTGGCCTGTACATTGCACCATAATCAGCTTCATACATGTG
1 TTCTGGCCTGTACATTGCACCATAATCAGCTTCATACATGTG
205034 TTCTGGCCTGTACATTGCACCATAATCAGCTTCATACATGTG
1 TTCTGGCCTGTACATTGCACCATAATCAGCTTCATACATGTG
205076 T
1 T
205077 ACATGAGGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (42 bp):
TTCTGGCCTGTACATTGCACCATAATCAGCTTCATACATGTG
Found at i:207187 original size:21 final size:25
Alignment explanation
Indices: 207152--207196 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
207142 AATTAAATTT
207152 ATAATATTGATTGAT-TGA-GTGTG
1 ATAATATTGATTGATGTGATGTGTG
207175 ATAATA-T-ATTGATGTGATGTGT
1 ATAATATTGATTGATGTGATGTGT
207197 CAACCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (25 bp):
ATAATATTGATTGATGTGATGTGTG
Found at i:207492 original size:23 final size:23
Alignment explanation
Indices: 207449--207494 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
207439 ACATATTAGG
* **
207449 TAGCGTTTATATAATGTAATAGA
1 TAGCGCTTATATAATAAAATAGA
207472 TAGCGCTTATATAATAAAATAGA
1 TAGCGCTTATATAATAAAATAGA
207495 CATTTAACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGA
Found at i:207554 original size:87 final size:87
Alignment explanation
Indices: 207408--207570 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
207398 TATATTATAT
* * * *
207408 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAATGTAATAGAT
1 CATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGATAGCGCTTATATAATGTAATAGAT
207473 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* *
207495 CATTTAACCGAAAATATTATCAAGTACAATAACAAATTAGATAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGATAGCGCTTATATAATGTAATAGAT
207560 AGCGCTTATAT
66 AGCGCTTATAT
207571 TGACATATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGATAGCGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGA
Found at i:208062 original size:199 final size:193
Alignment explanation
Indices: 207565--208076 Score: 514
Period size: 196 Copynumber: 2.6 Consensus size: 193
207555 TAGGTAGCGC
* * * * * *
207565 TTATATTGACATATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTATAAATTGACCTAT
1 TTATGTTGACCTA-TTTCTCAT-AAACCGGTATATTT-TACCGGTTACATTGTAAATTTACCTAT
*
207630 TACATTAT-GTATATCGGTTTCGATGTTTTCGGGATCGATA-TAATTTT-AAATGTATCGACACT
63 TACATTATAAT-TATCGGTTTCGATGTTTT-GGGATCGATACT--TTTTAAAATGTATCGACACT
* * * * * *
207692 TTATGCGTGCAACTCGTTTATGCTTTATTTTGGAAAAAATATCGATACATATTTAAAGAGTGTCG
124 TTATGCGTACAACTCGTTTATGCTTCATTTTGGAAAAAATATCGACACAAATTAAAAAAGTGTCG
207757 ATACA
189 ATACA
* * * * * *
207762 TAATGTAGACCTATTTGCTAATTAACTGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTT
1 TTATGTTGACCTATTT-CTCATAAACCGGTATATTTT-ACCGGTTACATTGTAAATTTACCTATT
* * **
207827 ACATAATAATTATCGATTTCGATGTTTCAAGGATCGATACTTTTTACAAATGTATCGACACTTTA
64 ACATTATAATTATCGGTTTCGATGTTT-TGGGATCGATACTTTTTA-AAATGTATCGACACTTTA
*
207892 TGCGTACACCTCG-TT-TGCCATTCATTTT-GAAAAAATGTATCGACACAAATTAAAAAAGTGTC
127 TGCGTACAACTCGTTTATG-C-TTCATTTTGGAAAAAA--TATCGACACAAATTAAAAAAGTGTC
*
207954 GATACT
188 GATACA
* *
207960 TTATGTTGACCTATTCTCTCATGAACCCGGTATATTTCTACCGGTTACATTGGAAATTTACCTAT
1 TTATGTTGACCTATT-TCTCAT-AAACCGGTATATTT-TACCGGTTACATTGTAAATTTACCTAT
* * ** *
208025 TACATTATAATTATTGGTCTCTTTGATTTTGGGATCGATACTTGTTATAAAT
63 TACATTATAATTATCGGTTTCGATG-TTTTGGGATCGATACTTTTTA-AAAT
208077 CGACACAAAA
Statistics
Matches: 257, Mismatches: 43, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
195 6 0.02
196 79 0.31
197 51 0.20
198 43 0.17
199 74 0.29
200 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (193 bp):
TTATGTTGACCTATTTCTCATAAACCGGTATATTTTACCGGTTACATTGTAAATTTACCTATTAC
ATTATAATTATCGGTTTCGATGTTTTGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCG
TACAACTCGTTTATGCTTCATTTTGGAAAAAATATCGACACAAATTAAAAAAGTGTCGATACA
Found at i:209674 original size:31 final size:31
Alignment explanation
Indices: 209639--209708 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
209629 AAATATTTTT
209639 ATTTGAAAAAGTACAAAGAAAAAAATAGGAC
1 ATTTGAAAAAGTACAAAGAAAAAAATAGGAC
209670 ATTTGAAAAAGTACAAAGAAAAAAATAGGAC
1 ATTTGAAAAAGTACAAAGAAAAAAATAGGAC
209701 ATTTGAAA
1 ATTTGAAA
209709 TTAGTTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.19
Consensus pattern (31 bp):
ATTTGAAAAAGTACAAAGAAAAAAATAGGAC
Found at i:211262 original size:198 final size:199
Alignment explanation
Indices: 210910--211492 Score: 735
Period size: 198 Copynumber: 2.9 Consensus size: 199
210900 CGTAATTTTA
* * *
210910 AAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCAGAAAACCT
1 AAAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCAGAAAACCG
* *
210975 GTAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTT
66 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTT
* ** * **
211040 TAGGATCGACACTTTTTCTAAATGTATCGACACTTT-TTTGTGAACTTGTTTGGAAAATTTATTA
131 TGGGATCGACACTTGATATAAATGTATCGACACTTTATTTGTGAACTTGTTTGG-AAATACATTA
*
211104 TGGAC
195 CGGAC
* * * * * * *
211109 ATAAAGTGTCGACACGAATGTATAAAGTATCGATACATTATGTATACCT-TTTTTTTA-ATAACC
1 A-AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCAGAAAACC
* * * * * * *
211172 GGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTT
65 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTT
* * * * *
211237 TTGGGATCAACACTTGGTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGGAAATACATT
130 TTGGGATCGACACTTGATATAAATGTATCGACACTTTATTTGTGAACTT-GTTTGGAAATACATT
*
211302 CCGGAC
194 ACGGAC
* * *
211308 AACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCAGAAAAT
1 AA-AAGTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTAGACCTATTTTCTCAGAAAAC
* * *
211372 CGGTAAATTTAAACCGGTTACATTATAAAGTGACTTATTACATTATAGTTACGAGTTTCGATGTT
64 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTT
211437 TTTGGGATCGACACTTGATATAAATGTATCGACA-TTTATTTGTGAACTTGCTTTGG
129 TTTGGGATCGACACTTGATATAAATGTATCGACACTTTATTTGTGAACTTG-TTTGG
211493 TTGGAAAATA
Statistics
Matches: 322, Mismatches: 54, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
198 96 0.30
199 66 0.20
200 70 0.22
201 90 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (199 bp):
AAAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCAGAAAACCG
GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTT
TGGGATCGACACTTGATATAAATGTATCGACACTTTATTTGTGAACTTGTTTGGAAATACATTAC
GGAC
Found at i:213295 original size:20 final size:20
Alignment explanation
Indices: 213249--213295 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
213239 ACCGGTAGCG
*
213249 CTTTATCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
213269 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
213290 -TTTACC
1 CTTTACC
213296 TATTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.51
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:213782 original size:183 final size:182
Alignment explanation
Indices: 213250--213878 Score: 848
Period size: 182 Copynumber: 3.4 Consensus size: 182
213240 CCGGTAGCGC
* * * * * * *
213250 TTTATCGGTTTTGTCATTTCGATACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATC
1 TTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
* * * * *
213315 GATACGTTT-TCATAAAGTATCGATACTTTTTAGGTGCTATAATTTCTTTTCTTTTAAATTACGA
66 GATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGA
213379 AAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATATCTT
130 AAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATATCTT
* *
213432 TTTACCGGTTTTATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTACTATGGATC
1 TTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
* *
213497 GATACATTTGTATAAAGTATTGACACTTTTTAGGCGCTATTACTTCTTCTCTTTTAAATTACGAA
66 GATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAA
* * *
213562 AGTGTCGATACTTATACTAATGTATCGACACTTTCAATATATCCGGTATCTT
131 AGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATATCTT
*
213614 TTTACCGTTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTATATTTGCTATGGAT
1 TTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTATA-TTGCTATGGAT
** *
213679 CGATACATTTGTATAAAGTATCGACACTTTTTATACGCTATAACTTCTTCTCTTTTAAATTACAA
65 CGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGA
* * * **
213744 AAGTGTCGATATTTATATTAATTTATCGATACTTTCAATATATCCGATAGCGG
130 AAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATATCTT
* * * *
213797 TTTATCGGTTTTATCATAATGATACCG-GTTTACCGGTTTTATCATATTTTTACCTGTTATATTG
1 TTTACCGGTTTTATCAT--T--T--CGAG---ACCTGTTTTGTCATATTATTACCTGTTATATTG
*
213861 CTATGTATCGATACATTT
57 CTATGGATCGATACATTT
213879 TTCATTTGTA
Statistics
Matches: 395, Mismatches: 41, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
182 212 0.54
183 131 0.33
185 1 0.00
187 1 0.00
188 1 0.00
189 2 0.01
190 20 0.05
191 27 0.07
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
TTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
GATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAA
AGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATATCTT
Done.