Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 46 of 131
Found at i:9556711 original size:73 final size:73
Alignment explanation
Indices: 9556592--9556787 Score: 268
Period size: 73 Copynumber: 2.7 Consensus size: 73
9556582 ATCTTCGATT
9556592 GATTCTTTAATTTTGACTCACGCTATTGTCCCAGTCGATTCTTTATTTCTCGACTTACGGTGTTG
1 GATTCTTTAATTTTGACTCACGCTATTGTCCCAGTCGATTCTTTATTTCTCGACTTACGGTGTTG
9556657 TCCCAGTC
66 TCCCAGTC
** * * * *
9556665 GATTCTTTAATTTTGACTCGTGGTGTTG-CCTTAGTCGATTCTTTATTTTTCGACTTACGGTGTT
1 GATTCTTTAATTTTGACTCACGCTATTGTCC-CAGTCGATTCTTTATTTCTCGACTTACGGTGTT
*
9556729 GTCTCAGTC
65 GTCCCAGTC
* * * * *
9556738 GATTCATTAATTTTGACTCACGGTATTGTCCCAATCAATTATTTATTTCT
1 GATTCTTTAATTTTGACTCACGCTATTGTCCCAGTCGATTCTTTATTTCT
9556788 TGATTTACAA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
72 2 0.02
73 101 0.96
74 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (73 bp):
GATTCTTTAATTTTGACTCACGCTATTGTCCCAGTCGATTCTTTATTTCTCGACTTACGGTGTTG
TCCCAGTC
Found at i:9556815 original size:110 final size:110
Alignment explanation
Indices: 9556699--9556897 Score: 290
Period size: 110 Copynumber: 1.8 Consensus size: 110
9556689 GTTGCCTTAG
* * * * **
9556699 TCGATTCTTTATTTTTCGACTTACGGTGTTGTCTCAGTCGATTCATTAATTTTGACTCACGGTAT
1 TCGATTCTTTATTTTTCAACTTACGATGTTATCTCAATCGATTCATTAATTTTGACTCACAATAT
*
9556764 TGTCCCAATCAATTATTTATTTCTTGATTTACAATATTATCCTGA
66 TGTCCCAATCAATTATATATTTCTTGATTTACAATATTATCCTGA
* ** *
9556809 TCGATTCTTTATTTTTCAACTTACGATGTTATCTCAATCGATTCTTTAATTTTGACTTGCAATGT
1 TCGATTCTTTATTTTTCAACTTACGATGTTATCTCAATCGATTCATTAATTTTGACTCACAATAT
*
9556874 TGTCCCAATCAATTCTATATTTCT
66 TGTCCCAATCAATTATATATTTCT
9556898 CAACTTGTAG
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (110 bp):
TCGATTCTTTATTTTTCAACTTACGATGTTATCTCAATCGATTCATTAATTTTGACTCACAATAT
TGTCCCAATCAATTATATATTTCTTGATTTACAATATTATCCTGA
Found at i:9556953 original size:183 final size:182
Alignment explanation
Indices: 9556626--9556975 Score: 405
Period size: 183 Copynumber: 1.9 Consensus size: 182
9556616 ATTGTCCCAG
* * * * ***
9556626 TCGATTCTTTATTTCTCGACTTACGGTGTTGTCCCAGTCGATTCTTTAATTTTGACTCGTGGTGT
1 TCGATTCTTTATTTCTCAACTTACGATGTTATCCCAATCGATTCTTTAATTTTGACTCGCAATGT
* * * * * * * * * *
9556691 TGCCTTAGTCGATTCTTTATTTTTCGACTTACGGTGTTGTCTCAGTCGATTCATTAATTTTGACT
66 TGCCTCAATCAATTCTATATTTCTCAACTTACAGTGTTATCTCAATCGATTCATTAATCTTGACT
** *
9556756 CACGGTATTGTCCCAATCAATTATTTATTTCTTGATTTACAATATTATCCTGA
131 CACAATATTGTCCCAATCAATTATTTAATT-TTGATTTACAATATTATCCTGA
* * *
9556809 TCGATTCTTTATTTTTCAACTTACGATGTTATCTCAATCGATTCTTTAATTTTGACTTGCAATGT
1 TCGATTCTTTATTTCTCAACTTACGATGTTATCCCAATCGATTCTTTAATTTTGACTCGCAATGT
** * *
9556874 TGTCC-CAATCAATTCTATATTTCTCAACTTGTAGTGTTATCTCAATTGATTCTTTAATCTTGAC
66 TG-CCTCAATCAATTCTATATTTCTCAACTTACAGTGTTATCTCAATCGATTCATTAATCTTGAC
* * *
9556938 TTACAATATTGTCCCAGTCAATTCTTTAATTTTGATTT
130 TCACAATATTGTCCCAATCAATTATTTAATTTTGATTT
9556976 GCGGTGTTGT
Statistics
Matches: 136, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
182 7 0.05
183 127 0.93
184 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.47
Consensus pattern (182 bp):
TCGATTCTTTATTTCTCAACTTACGATGTTATCCCAATCGATTCTTTAATTTTGACTCGCAATGT
TGCCTCAATCAATTCTATATTTCTCAACTTACAGTGTTATCTCAATCGATTCATTAATCTTGACT
CACAATATTGTCCCAATCAATTATTTAATTTTGATTTACAATATTATCCTGA
Found at i:9557144 original size:74 final size:73
Alignment explanation
Indices: 9556628--9557154 Score: 283
Period size: 73 Copynumber: 7.2 Consensus size: 73
9556618 TGTCCCAGTC
* * * * * * * * *
9556628 GATTCTTTATTTCTCGACTTACGGTGTTGTCCCAGTCGATTCTTTAATTTT-GACTCGTGGTGTT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTT-ATTTTCGACTTGCGGTGTT
* *
9556692 GCCTTAGTC
65 GTCTTAGTT
* * * * * * * * ** *
9556701 GATTCTTTATTTTTCGACTTACGGTGTTGTCTCAGTCGATTCATTAATTTT-GACTCACGGTATT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTC-TTTATTTTCGACTTGCGGTGTT
** * *
9556765 GTCCCAATC
65 GTCTTAGTT
* * * * * ** * * * *
9556774 AATTATTTATTTCTTGATTTACAATATTATCCTGATCGATTCTTTATTTTTCAACTTACGATGTT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTTA-TTTTCGACTTGCGGTGTT
* * * *
9556839 ATCTCAATC
65 GTCTTAGTT
* * * * * * * **
9556848 GATTCTTTA-ATTTTGACTTGCAATGTTGTCCCAATCAATTCTATATTTCTCAACTTGTAGTGTT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTTATTT-TCGACTTGCGGTGTT
* * *
9556912 ATCTCAATT
65 GTCTTAGTT
* * * * * *
9556921 GATTCTTTA-ATCTTGACTTACAATATTGTCCCAGTCAATTCTTTAATTTT-GATTTGCGGTGTT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTT-ATTTTCGACTTGCGGTGTT
*
9556984 GTCTTGGTT
65 GTCTTAGTT
* * * * * * *
9556993 GATTCTTTACTTTTTAACTTGCAGT-TTCATCCCGATCAATTCTTTATCTTCTGACTTACGGTAT
1 GATTCTTTATTTTTTGACTTACAGTATT-ATCCCAATCAATTCTTTATTTTC-GACTTGCGGTGT
*
9557057 TGTCTCAGTT
64 TGTCTTAGTT
* * *
9557067 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTTTTTACTTTTCGACTTGTGATGTT
1 GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTTA-TTTTCGACTTGCGGTGTT
* *
9557132 GTTTTAGCT
65 GTCTTAGTT
9557141 GATTCTTTATTTTT
1 GATTCTTTATTTTT
9557155 CGATTCGTGG
Statistics
Matches: 356, Mismatches: 87, Indels: 21
0.77 0.19 0.05
Matches are distributed among these distances:
72 35 0.10
73 202 0.57
74 113 0.32
75 6 0.02
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (73 bp):
GATTCTTTATTTTTTGACTTACAGTATTATCCCAATCAATTCTTTATTTTCGACTTGCGGTGTTG
TCTTAGTT
Found at i:9557220 original size:6 final size:6
Alignment explanation
Indices: 9557205--9557245 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
9557195 ACTTGTGGTT
* *
9557205 CAAAAA -AAAAA CAAAAA CAAAAA C-AAAA GAAAAA GAAAAA C
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C
9557246 TTTTGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:9557245 original size:17 final size:17
Alignment explanation
Indices: 9557205--9557245 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9557195 ACTTGTGGTT
*
9557205 CAAAAAAAAAACAAAAA
1 CAAAAACAAAACAAAAA
*
9557222 CAAAAACAAAAGAAAAA
1 CAAAAACAAAACAAAAA
*
9557239 GAAAAAC
1 CAAAAAC
9557246 TTTTGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (17 bp):
CAAAAACAAAACAAAAA
Found at i:9558706 original size:19 final size:19
Alignment explanation
Indices: 9558665--9558709 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9558655 CAAGTAAATT
* *
9558665 TTTTTATTTTTTTATTCAT
1 TTTTTATTTTTATATTCAG
9558684 TTTTTATTTTTATATAT-AG
1 TTTTTATTTTTATAT-TCAG
9558703 TTTTTAT
1 TTTTTAT
9558710 ATTATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTATATTCAG
Found at i:9559030 original size:12 final size:12
Alignment explanation
Indices: 9558997--9559030 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9558987 TATTAAAAAA
*
9558997 AATTAATAAATT
1 AATTAATAATTT
9559009 AATTAATAATTT
1 AATTAATAATTT
*
9559021 TATTAATAAT
1 AATTAATAAT
9559031 AAAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTAATAATTT
Found at i:9559247 original size:29 final size:28
Alignment explanation
Indices: 9559182--9559373 Score: 153
Period size: 29 Copynumber: 6.8 Consensus size: 28
9559172 ACTTCAAACC
* *
9559182 CTTCAAACCTTAAAAC-AAACCCCAAAT
1 CTTCAAACCCTAAAACAAAACCCTAAAT
* *
9559209 CCTTTAAACCCTAAAACAAAATCCTAAAT
1 -CTTCAAACCCTAAAACAAAACCCTAAAT
*
9559238 CTTTCAAACCCTAAAACAAAACCTTAAAAT
1 C-TTCAAACCCTAAAACAAAACCCT-AAAT
* *
9559268 C-TCAAACCCTGAAATCGAAACCCTAAAT
1 CTTCAAACCCT-AAAACAAAACCCTAAAT
* *
9559296 CCTCAAACCCTAAAATCGAAAA-CCTAAAAC
1 CTTCAAACCCTAAAA-C-AAAACCCT-AAAT
* **
9559326 CTT-AAACCATAAAATCAAAACCCTAAGC
1 CTTCAAACCCTAAAA-CAAAACCCTAAAT
*
9559354 CTT-AAA-CCTAAAACCAAACC
1 CTTCAAACCCTAAAACAAAACC
9559374 ATTGGAGCCA
Statistics
Matches: 137, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
26 6 0.04
27 6 0.04
28 45 0.33
29 67 0.49
30 13 0.09
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (28 bp):
CTTCAAACCCTAAAACAAAACCCTAAAT
Found at i:9559282 original size:15 final size:14
Alignment explanation
Indices: 9559231--9559309 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 14
9559221 AAAACAAAAT
9559231 CCTAAATCTTTCAAAC
1 CCTAAATC--TCAAAC
* *
9559247 CCTAAAAC-AAAAC
1 CCTAAATCTCAAAC
*
9559260 CTTAAAATCTCAAAC
1 CCT-AAATCTCAAAC
*
9559275 CCTGAAATC-GAAAC
1 CCT-AAATCTCAAAC
9559289 CCTAAATCCTCAAAC
1 CCTAAAT-CTCAAAC
9559304 CCTAAA
1 CCTAAA
9559310 ATCGAAAACC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
13 10 0.20
14 12 0.24
15 21 0.42
16 7 0.14
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.20
Consensus pattern (14 bp):
CCTAAATCTCAAAC
Found at i:9559290 original size:14 final size:13
Alignment explanation
Indices: 9559243--9559323 Score: 54
Period size: 15 Copynumber: 5.8 Consensus size: 13
9559233 TAAATCTTTC
* *
9559243 AAACCCTAAAACA
1 AAACCCTAAATCG
* *
9559256 AAACCTTAAAATCTC
1 AAACCCT-AAATC-G
9559271 AAACCCTGAAATCG
1 AAACCCT-AAATCG
*
9559285 AAACCCTAAATCCTC
1 AAACCCTAAAT-C-G
9559300 AAACCCTAAAATCG
1 AAACCCT-AAATCG
*
9559314 AAAACCTAAA
1 AAACCCTAAA
9559324 ACCTTAAACC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
13 13 0.24
14 18 0.33
15 19 0.35
16 4 0.07
ACGTcount: A:0.51, C:0.30, G:0.04, T:0.16
Consensus pattern (13 bp):
AAACCCTAAATCG
Found at i:9559324 original size:14 final size:13
Alignment explanation
Indices: 9559241--9559347 Score: 54
Period size: 14 Copynumber: 7.6 Consensus size: 13
9559231 CCTAAATCTT
*
9559241 TCAAACCCTAAAA
1 TCAAAACCTAAAA
9559254 -CAAAACCTTAAAA
1 TCAAAACC-TAAAA
* *
9559267 TCTCAAACCCTGAAA
1 --TCAAAACCTAAAA
* *
9559282 TCGAAACCCTAAATCC
1 TC-AAAACCTAAA--A
*
9559298 TCAAACCCTAAAA
1 TCAAAACCTAAAA
9559311 TCGAAAACCTAAAA
1 TC-AAAACCTAAAA
* *
9559325 CCTTAAACCATAAAA
1 TC-AAAACC-TAAAA
9559340 TCAAAACC
1 TCAAAACC
9559348 CTAAGCCTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
12 6 0.08
13 9 0.12
14 30 0.41
15 20 0.27
16 8 0.11
ACGTcount: A:0.50, C:0.30, G:0.03, T:0.17
Consensus pattern (13 bp):
TCAAAACCTAAAA
Found at i:9559333 original size:58 final size:57
Alignment explanation
Indices: 9559184--9559351 Score: 171
Period size: 58 Copynumber: 2.9 Consensus size: 57
9559174 TTCAAACCCT
* ** * * * *
9559184 TCAAACCTTAAAAC-AAACCCCAAATCCTTTAAACCCTAAAACAAAATCCTAAATCTT
1 TCAAACCCTAAAACAAAACCTTAAAACC-TTAAACCCTAAATCAAAACCCTAAATCTC
* * *
9559241 TCAAACCCTAAAACAAAACCTTAAAATCTCAAACCCTGAAATCGAAACCCTAAATC-C
1 TCAAACCCTAAAACAAAACCTTAAAACCTTAAACCCT-AAATCAAAACCCTAAATCTC
*
9559298 TCAAACCCTAAAATCGAAAACC-TAAAACCTTAAACCATAAAATCAAAACCCTAA
1 TCAAACCCTAAAA-C-AAAACCTTAAAACCTTAAACCCT-AAATCAAAACCCTAA
9559352 GCCTTAAACC
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
57 34 0.37
58 52 0.57
59 6 0.07
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (57 bp):
TCAAACCCTAAAACAAAACCTTAAAACCTTAAACCCTAAATCAAAACCCTAAATCTC
Found at i:9559366 original size:21 final size:21
Alignment explanation
Indices: 9559315--9559375 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
9559305 CTAAAATCGA
*
9559315 AAACCTAAAACCTTAAACCAT
1 AAACCTAAAACCCTAAACCAT
* * *
9559336 AAA-ATCAAAACCCTAAGCCTT
1 AAACCT-AAAACCCTAAACCAT
9559357 AAACCTAAAA-CC-AAACCAT
1 AAACCTAAAACCCTAAACCAT
9559376 TGGAGCCATA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 22 0.71
22 1 0.03
ACGTcount: A:0.52, C:0.30, G:0.02, T:0.16
Consensus pattern (21 bp):
AAACCTAAAACCCTAAACCAT
Found at i:9559421 original size:15 final size:14
Alignment explanation
Indices: 9559385--9559429 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
9559375 TTGGAGCCAT
* *
9559385 AACCCTTAAATTGA
1 AACCCTAAAATTCA
*
9559399 AGCCCTAAAATCTCA
1 AACCCTAAAAT-TCA
9559414 AACCCTAAAATTCA
1 AACCCTAAAATTCA
9559428 AA
1 AA
9559430 AATCTAAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (14 bp):
AACCCTAAAATTCA
Found at i:9559559 original size:15 final size:15
Alignment explanation
Indices: 9559541--9559583 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
9559531 ATCTTAAAAT
*
9559541 CTAAAATCCCAAACC
1 CTAAAATCCAAAACC
9559556 CTAAAATCCAAAACC
1 CTAAAATCCAAAACC
*
9559571 TTAAAATCCAAAA
1 CTAAAATCCAAAA
9559584 TTCTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.16
Consensus pattern (15 bp):
CTAAAATCCAAAACC
Found at i:9559591 original size:15 final size:14
Alignment explanation
Indices: 9559536--9559583 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
9559526 CAAAAATCTT
*
9559536 AAAATCTAAAATCCC
1 AAAACCTAAAAT-CC
*
9559551 AAACCCTAAAATCC
1 AAAACCTAAAATCC
9559565 AAAACCTTAAAATCC
1 AAAACC-TAAAATCC
9559580 AAAA
1 AAAA
9559584 TTCTAAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAACCTAAAATCC
Found at i:9561793 original size:24 final size:24
Alignment explanation
Indices: 9561725--9561793 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
9561715 AGACAGATAA
* *
9561725 ATCTGTTCAAAATAGATAATTTTT
1 ATCTGTTCAAAATAGATAGTTTCT
* * * *
9561749 AACTGTTAAAAATGGACAGTTTCT
1 ATCTGTTCAAAATAGATAGTTTCT
*
9561773 ATCTGTTCAACATAGATAGTT
1 ATCTGTTCAAAATAGATAGTT
9561794 ATATCTATAA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (24 bp):
ATCTGTTCAAAATAGATAGTTTCT
Found at i:9565168 original size:2 final size:2
Alignment explanation
Indices: 9565125--9565152 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9565115 ATATATAACC
9565125 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
9565153 CAAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9576644 original size:51 final size:51
Alignment explanation
Indices: 9576568--9576689 Score: 235
Period size: 51 Copynumber: 2.4 Consensus size: 51
9576558 ACCATATGTT
9576568 TGATACCACTTGTTGGGATGGGCCTATTTCTTCTTCCCATGAACCTCGTTC
1 TGATACCACTTGTTGGGATGGGCCTATTTCTTCTTCCCATGAACCTCGTTC
9576619 TGATACCACTTGTTGGGATGGGCCTATTTCTTCTTCCCATGAACCTCGTTC
1 TGATACCACTTGTTGGGATGGGCCTATTTCTTCTTCCCATGAACCTCGTTC
9576670 TGATACCACTTGTTAGGGAT
1 TGATACCACTTGTT-GGGAT
9576690 CACCAAAGCT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
51 65 0.93
52 5 0.07
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.37
Consensus pattern (51 bp):
TGATACCACTTGTTGGGATGGGCCTATTTCTTCTTCCCATGAACCTCGTTC
Found at i:9581544 original size:11 final size:11
Alignment explanation
Indices: 9581528--9581569 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
9581518 AATCCCATAA
9581528 GAGATTTGTTT
1 GAGATTTGTTT
*
9581539 GAGATTTGTTA
1 GAGATTTGTTT
*
9581550 GAGATTTATTT
1 GAGATTTGTTT
9581561 GAGATTTGT
1 GAGATTTGT
9581570 CAGATATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:9581555 original size:22 final size:22
Alignment explanation
Indices: 9581527--9581569 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9581517 AAATCCCATA
*
9581527 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTATTTGAGATTTGTT
9581549 AGAGATTTATTTGAGATTTGT
1 AGAGATTTATTTGAGATTTGT
9581570 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTGAGATTTGTT
Found at i:9581680 original size:52 final size:51
Alignment explanation
Indices: 9581594--9581750 Score: 224
Period size: 52 Copynumber: 3.0 Consensus size: 51
9581584 TGGACAAGAA
* *
9581594 GACTTGCAAAAGAAGAATTCTAAGAGAAAGGAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAA-GAGATTCTTAATAGGCAAGTTT
9581646 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAA-GAAAGAGATTCTTAATAGGCAAGTTT
* * * * *
9581698 AACTTACAAAAGAAGAATTCTAAGAAAAAAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAA-AAGAAAGAGATTCTTAATAGGCAAGTTT
9581750 G
1 G
9581751 TATAGTTATA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 89 0.94
53 6 0.06
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (51 bp):
GACTTGCAAAAGAAGAATTCTAAAAGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:9584023 original size:21 final size:21
Alignment explanation
Indices: 9583980--9584023 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9583970 AATATAACTT
*
9583980 AATAAAAAAATAAAATGATAA
1 AATAAAAAAATAAAATGAAAA
* * *
9584001 AATAAAAGAATCAAGTGAAAA
1 AATAAAAAAATAAAATGAAAA
9584022 AA
1 AA
9584024 CAAATGTAAC
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:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AATAAAAAAATAAAATGAAAA
Found at i:9584509 original size:15 final size:14
Alignment explanation
Indices: 9584486--9584523 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
9584476 TCAATTTGAA
9584486 AAAAAAAATTGATT
1 AAAAAAAATTGATT
*
9584500 GAAAAGAAATTGATT
1 -AAAAAAAATTGATT
9584515 AAAAAAAAT
1 AAAAAAAAT
9584524 GAAACAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (14 bp):
AAAAAAAATTGATT
Found at i:9591533 original size:55 final size:55
Alignment explanation
Indices: 9591466--9591581 Score: 223
Period size: 55 Copynumber: 2.1 Consensus size: 55
9591456 CTCGGACCTT
*
9591466 AGACATTAGCTTATAAAGTGCTCGAAAAAGGTTATTATTGGTCCACCATCAGAAA
1 AGACACTAGCTTATAAAGTGCTCGAAAAAGGTTATTATTGGTCCACCATCAGAAA
9591521 AGACACTAGCTTATAAAGTGCTCGAAAAAGGTTATTATTGGTCCACCATCAGAAA
1 AGACACTAGCTTATAAAGTGCTCGAAAAAGGTTATTATTGGTCCACCATCAGAAA
9591576 AGACAC
1 AGACAC
9591582 AATCGACCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (55 bp):
AGACACTAGCTTATAAAGTGCTCGAAAAAGGTTATTATTGGTCCACCATCAGAAA
Found at i:9596626 original size:18 final size:18
Alignment explanation
Indices: 9596582--9596628 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
9596572 ACATATTAGA
9596582 CAAATAAA-TAATTAAAT
1 CAAATAAATTAATTAAAT
*
9596599 CAAATCAATTAATTAAAT
1 CAAATAAATTAATTAAAT
* *
9596617 TACATAAATTAA
1 CAAATAAATTAA
9596629 AATAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (18 bp):
CAAATAAATTAATTAAAT
Found at i:9596638 original size:13 final size:13
Alignment explanation
Indices: 9596587--9596646 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
9596577 TTAGACAAAT
*
9596587 AAATAATTAAA-TC
1 AAATAA-TAAATTA
*
9596600 AAATCAATTAATTA
1 AAAT-AATAAATTA
*
9596614 AATTACATAAATTA
1 AAATA-ATAAATTA
*
9596628 AAATAATAAATAA
1 AAATAATAAATTA
9596641 AAATAA
1 AAATAA
9596647 GGAAACAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 21 0.55
14 17 0.45
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAATAAATTA
Found at i:9597027 original size:19 final size:19
Alignment explanation
Indices: 9597003--9597046 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
9596993 TGTAAAACTC
9597003 AATTTTAAAAAAATTCCAA
1 AATTTTAAAAAAATTCCAA
*
9597022 AATTTTAAAAAATTTCCAA
1 AATTTTAAAAAAATTCCAA
9597041 AATTTT
1 AATTTT
9597047 TTGAGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTTAAAAAAATTCCAA
Found at i:9597047 original size:20 final size:20
Alignment explanation
Indices: 9597005--9597066 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 20
9596995 TAAAACTCAA
*
9597005 TTTTAAAAAAATTCCAAAA-
1 TTTTAAAAAATTTCCAAAAT
9597024 TTTTAAAAAATTTCCAAAAT
1 TTTTAAAAAATTTCCAAAAT
** *
9597044 TTTTTGAGAATTTCC-AAAT
1 TTTTAAAAAATTTCCAAAAT
9597063 TTTT
1 TTTT
9597067 TTAACTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 26 0.68
20 12 0.32
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTTAAAAAATTTCCAAAAT
Found at i:9597548 original size:3 final size:3
Alignment explanation
Indices: 9597531--9597580 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
9597521 AACCCAAATG
9597531 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9597576 AAT AA
1 AAT AA
9597581 CCTTAAACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9599776 original size:21 final size:21
Alignment explanation
Indices: 9599752--9599792 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9599742 TTACTATTCA
*
9599752 AATATTAAAATATTTTAAATT
1 AATATTAAAATATGTTAAATT
**
9599773 AATATTTTAATATGTTAAAT
1 AATATTAAAATATGTTAAAT
9599793 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTAAAATATGTTAAATT
Found at i:9599804 original size:21 final size:21
Alignment explanation
Indices: 9599760--9599799 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9599750 CAAATATTAA
*
9599760 AATATTTTAAATTAATATTTT
1 AATATGTTAAATTAATATTTT
9599781 AATATGTTAAA-T-ATATTTT
1 AATATGTTAAATTAATATTTT
9599800 TTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AATATGTTAAATTAATATTTT
Found at i:9600684 original size:3 final size:3
Alignment explanation
Indices: 9600676--9600722 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
9600666 CATTTAACTT
9600676 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
9600722 T
1 T
9600723 AATATCATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9601541 original size:2 final size:2
Alignment explanation
Indices: 9601530--9601563 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9601520 GGTGATAAGC
9601530 TA TA -A 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 TA T
9601564 TGTAGTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9604261 original size:41 final size:41
Alignment explanation
Indices: 9604216--9604298 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
9604206 TTGGGATTCC
*
9604216 TCTGTATTCTACCAATTATAGATTTACAAAATCTATCATAT
1 TCTGTATTCTACCAATTATAGATTTACAAAAGCTATCATAT
* *
9604257 TCTGTATTCTACCAATTCTAGATTTACAAAAGCTATTATAT
1 TCTGTATTCTACCAATTATAGATTTACAAAAGCTATCATAT
9604298 T
1 T
9604299 TCACTTTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (41 bp):
TCTGTATTCTACCAATTATAGATTTACAAAAGCTATCATAT
Found at i:9611753 original size:2 final size:2
Alignment explanation
Indices: 9611746--9611776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9611736 GGGTATGCGC
9611746 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
9611777 AGAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:9616101 original size:14 final size:13
Alignment explanation
Indices: 9616059--9616097 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9616049 CAAAGATATC
*
9616059 TTTTTTATTTAAT
1 TTTTTTATTTAAA
**
9616072 TTTTTTATTTTGA
1 TTTTTTATTTAAA
9616085 TTTTTTATTTAAA
1 TTTTTTATTTAAA
9616098 ATTTATGAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTATTTAAA
Found at i:9619096 original size:17 final size:15
Alignment explanation
Indices: 9619074--9619107 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
9619064 AATTTGGCTT
9619074 TTATTTTGTATTTTATA
1 TTATTTT-TATTTT-TA
9619091 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
9619106 TT
1 TT
9619108 TTATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:9619107 original size:22 final size:22
Alignment explanation
Indices: 9619072--9619145 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 22
9619062 CCAATTTGGC
9619072 TTTTATTTTGTATTTTATATTAT
1 TTTTATTTT-TATTTTATATTAT
9619095 TTTTATTTTTATTTTATATT-T
1 TTTTATTTTTATTTTATATTAT
** * *
9619116 TTTCCTTTGTATTTTAT-GTAT
1 TTTTATTTTTATTTTATATTAT
9619137 TTATTATTT
1 TT-TTATTT
9619146 ATTTATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.02
21 18 0.42
22 15 0.35
23 9 0.21
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTATTTTATATTAT
Found at i:9619147 original size:4 final size:4
Alignment explanation
Indices: 9619128--9619306 Score: 68
Period size: 4 Copynumber: 44.2 Consensus size: 4
9619118 TCCTTTGTAT
* * * *
9619128 TTTA TGTA TTTA -TTA TTTA TTTA TTTA -TTA TTACTA TGTA TTAA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA
* * * * * * * *
9619176 TGTA TATC TTTA TTTT TTTG TTAATA TTTA TATA TGTA TTTTA TTTA TCTA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA -TTTA TTTA TTTA
* *
9619227 GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA -TTA -TTA TTATA
1 TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TTTA TTTA TT-TA
* *
9619272 TTTT TTTA TTTA TCTTA -TTA -TTA TTT- TTTA ATTA T
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA T
9619307 CTGTTAATTT
Statistics
Matches: 132, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
3 24 0.18
4 82 0.62
5 17 0.13
6 9 0.07
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:9619264 original size:25 final size:25
Alignment explanation
Indices: 9619236--9619304 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
9619226 AGTTATATAT
9619236 TTATTATTATATTATAATTTATTTA-
1 TTATTATTATATT-TAATTTATTTAC
*
9619261 TTATTATTATATTT-TTTTATTTATC
1 TTATTATTATATTTAATTTATTTA-C
*
9619286 TTATTATTATTTTTTAATT
1 TTATTATTA-TATTTAATT
9619305 ATCTGTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.22
24 1 0.03
25 22 0.59
26 4 0.11
27 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTATTATATTTAATTTATTTAC
Found at i:9619292 original size:22 final size:22
Alignment explanation
Indices: 9619239--9619320 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
9619229 TATATATTTA
* *
9619239 TTATTATATTATAATTTATTTATTA
1 TTATTATATT-T-TTTTATTTA-TC
9619264 TTATTATATTTTTTTATTTATC
1 TTATTATATTTTTTTATTTATC
*
9619286 TTATTAT-TATTTTTTAATTATC
1 TTATTATAT-TTTTTTATTTATC
*
9619308 -TGTTA-ATTTTTTT
1 TTATTATATTTTTTT
9619321 TTAATTTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
20 6 0.12
21 6 0.12
22 20 0.39
23 8 0.16
24 1 0.02
25 10 0.20
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (22 bp):
TTATTATATTTTTTTATTTATC
Found at i:9619321 original size:22 final size:22
Alignment explanation
Indices: 9619272--9619326 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
9619262 TATTATTATA
* *
9619272 TTTTTTTATTTATCTTATTATT
1 TTTTTTTAATTATCTTATAATT
*
9619294 ATTTTTTAATTATCTGT-TAATT
1 TTTTTTTAATTATCT-TATAATT
9619316 TTTTTTTAATT
1 TTTTTTTAATT
9619327 TTATTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTTTAATTATCTTATAATT
Found at i:9619369 original size:24 final size:24
Alignment explanation
Indices: 9619325--9619376 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
9619315 TTTTTTTTAA
9619325 TTTTATTCATTTATCTAATTT-TT
1 TTTTATTCATTTATCTAATTTCTT
* * *
9619348 TTTTATTTCGTTTTTCTGATTTCTT
1 TTTTA-TTCATTTATCTAATTTCTT
9619373 TTTT
1 TTTT
9619377 GGGCTGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTATTCATTTATCTAATTTCTT
Found at i:9620254 original size:5 final size:5
Alignment explanation
Indices: 9620226--9620326 Score: 57
Period size: 5 Copynumber: 19.6 Consensus size: 5
9620216 TTAGATTAGG
* * * *
9620226 TTTAT TTAAT GTTCT TTTATT TTTAT TTTATT TTTATT TTTGT TTTACT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTA-T TTTA-T TTTAT TTTA-T
* *
9620275 TTT-C TTTAT TTT-T TTTAT TTCTCACT TTTAT TTTGT TTTA- -TTAT
1 TTTAT TTTAT TTTAT TTTAT TT-T-A-T TTTAT TTTAT TTTAT TTTAT
9620319 TTTAT TTT
1 TTTAT TTT
9620327 CTTTAAATAA
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
3 3 0.04
4 7 0.09
5 38 0.51
6 21 0.28
7 2 0.03
8 3 0.04
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:9620260 original size:17 final size:17
Alignment explanation
Indices: 9620240--9620326 Score: 67
Period size: 17 Copynumber: 5.2 Consensus size: 17
9620230 TTTAATGTTC
9620240 TTTTATTTTTATTTTAT
1 TTTTATTTTTATTTTAT
*
9620257 TTTTATTTTTGTTTTA-
1 TTTTATTTTTATTTTAT
* *
9620273 CTTT-TCTTTA-TTT-T
1 TTTTATTTTTATTTTAT
*
9620287 TTTTATTTCTCACTTTTAT
1 TTTTATTT-TTA-TTTTAT
9620306 TTTGT-TTTATTATTTTAT
1 TTT-TATTT-TTATTTTAT
9620324 TTT
1 TTT
9620327 CTTTAAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.11
15 6 0.11
16 5 0.09
17 15 0.28
18 12 0.22
19 9 0.17
20 1 0.02
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:9620407 original size:58 final size:57
Alignment explanation
Indices: 9620343--9620900 Score: 635
Period size: 59 Copynumber: 9.7 Consensus size: 57
9620333 ATAAAATCCA
* *
9620343 AAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
* *
9620401 -AAAAAA-A-GTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAGTTTC
* * *
9620457 CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTC
1 AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
** * *
9620515 AAAAAAAGGTTTTTGAGGAAAAGTTTAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAGTTTC
* * * * *
9620574 CAAAAAATATTTTTGGAAAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTT
1 AAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
** * *
9620632 AAAAAAAGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAGTTTC
* * * * *
9620691 CAAAAATTATTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAA-TTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
** * *
9620748 AAAAAAGGA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA-AAATTTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
* * * *
9620804 AAAAAAAGGT-TTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAGTTTC
1 AAAAAAA--TATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
* *
9620862 AAAAGAATATTTTTGAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTT
9620901 TCCTGCACAA
Statistics
Matches: 430, Mismatches: 53, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
55 37 0.09
56 58 0.13
57 82 0.19
58 120 0.28
59 132 0.31
60 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (57 bp):
AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTC
Found at i:9620568 original size:117 final size:116
Alignment explanation
Indices: 9620344--9620900 Score: 763
Period size: 117 Copynumber: 4.8 Consensus size: 116
9620334 TAAAATCCAA
*
9620344 AAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAA-
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
9620408 G--TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
65 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
* *
9620458 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTCAAAAAAAG
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
*
9620523 GTTTTTGAGGAAAAGTTTAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
65 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
* * * *
9620575 AAAAAATATTTTTGGAAAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTTAAAAAAAG
1 AAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
*
9620640 GTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
65 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
* * * *
9620692 AAAAATTATTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAAT-AAATTTC-AAAAAAG
1 AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
* * * * *
9620755 GATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAA-AAAATTTTCA
65 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
* * * * * *
9620805 AAAAAAGGT-TTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAGTTTCAAAAGAA
1 AAAAAA--TATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAA
**
9620869 TATTTTTGA-GAAAAGTTGAAAGTATCAATTTT
64 GGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
9620901 TCCTGCACAA
Statistics
Matches: 401, Mismatches: 32, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
113 42 0.10
114 95 0.24
115 56 0.14
116 7 0.02
117 200 0.50
118 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (116 bp):
AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGG
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
Found at i:9620956 original size:10 final size:10
Alignment explanation
Indices: 9620928--9620969 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
9620918 CATTCTTTTC
9620928 TTTTTTTTATT
1 TTTTTTTTA-T
9620939 TTTATTTTTAT
1 TTT-TTTTTAT
9620950 TTTTTTTTAT
1 TTTTTTTTAT
*
9620960 TTTTGTTTAT
1 TTTTTTTTAT
9620970 GTTAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 16 0.55
11 7 0.24
12 6 0.21
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:9620972 original size:6 final size:6
Alignment explanation
Indices: 9620931--9620963 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
9620921 TCTTTTCTTT
9620931 TTTTTA TTTTTA TTTTTA -TTTT- TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
9620964 GTTTATGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTA
Found at i:9629492 original size:17 final size:17
Alignment explanation
Indices: 9629467--9629517 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
9629457 ATACTATGCT
9629467 TAAAAAAAATGAAAAAAA
1 TAAAAAAAAT-AAAAAAA
*
9629485 T-GAAAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
9629501 TAAAAAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
9629518 AAGTTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 8 0.27
17 21 0.70
18 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:9629508 original size:8 final size:8
Alignment explanation
Indices: 9629469--9629517 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
9629459 ACTATGCTTA
9629469 AAAAAAAT
1 AAAAAAAT
9629477 GAAAAAAAT
1 -AAAAAAAT
*
9629486 GAAAAAAT
1 AAAAAAAT
9629494 AAAAAAAT
1 AAAAAAAT
9629502 AAAAAAAAT
1 -AAAAAAAT
9629511 AAAAAAA
1 AAAAAAA
9629518 AAGTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 21 0.57
9 16 0.43
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:9629519 original size:10 final size:9
Alignment explanation
Indices: 9629467--9629518 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
9629457 ATACTATGCT
9629467 TAAAAAAAA
1 TAAAAAAAA
*
9629476 TGAAAAAAA
1 TAAAAAAAA
*
9629485 T-GAAAAAA
1 TAAAAAAAA
9629493 T-AAAAAAA
1 TAAAAAAAA
9629501 TAAAAAAAA
1 TAAAAAAAA
9629510 TAAAAAAAA
1 TAAAAAAAA
9629519 AGTTAATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
8 14 0.36
9 25 0.64
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:9630577 original size:41 final size:43
Alignment explanation
Indices: 9630532--9630789 Score: 287
Period size: 43 Copynumber: 6.1 Consensus size: 43
9630522 ATGATTGTCA
*
9630532 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
*
9630573 AGGAGCAATTTA-C-TTC-CAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATCTTTCTC-AAAGTCGTGGAGCCTCTGTTTAG
*
9630614 AGGAGCAATTTA-CTTTC-CAAAGTCATGGAGCCTCTGTTTAG
1 AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
* * ** *
9630655 AGGAGCTATTTATGTTTCTCAAAGTCGTTAAGCCTCTGATTAG
1 AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
* * * * **
9630698 AGGAGCCATTTATATTTCTCAAAGTTGTTGAGCCTCTACTTAG
1 AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
* * * **
9630741 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTACTTAG
1 AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
9630784 AGGAGC
1 AGGAGC
9630790 TTTGGTAAAA
Statistics
Matches: 196, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
40 3 0.02
41 81 0.41
42 8 0.04
43 104 0.53
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (43 bp):
AGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTGTTTAG
Found at i:9630992 original size:17 final size:17
Alignment explanation
Indices: 9630970--9631018 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
9630960 AATTTGGCTT
9630970 TTATTTTGTATTTTA-TA
1 TTATTTT-TATTTTATTA
*
9630987 TTATTTTTATTTTTATTT
1 TTATTTTTA-TTTTATTA
9631005 TTATTTTATATTTT
1 TTATTTT-TATTTT
9631019 TTCCTTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 12 0.43
18 12 0.43
19 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
TTATTTTTATTTTATTA
Found at i:9630997 original size:23 final size:22
Alignment explanation
Indices: 9630968--9631047 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 22
9630958 CCAATTTGGC
9630968 TTTTATTTTGTATTTTATATTAT
1 TTTTATTTTGTATTTTAT-TTAT
9630991 TTTTATTTT-TATTTTTATTTTAT
1 TTTTATTTTGTA-TTTTA-TTTAT
* *
9631014 ATTTTTTCCTTTGTATTTTATGTAT
1 -TTTTAT--TTTGTATTTTATTTAT
9631039 TTATTATTT
1 TT-TTATTT
9631048 ATTTATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
22 2 0.04
23 20 0.43
24 8 0.17
25 7 0.15
26 8 0.17
27 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTATTTTGTATTTTATTTAT
Found at i:9630998 original size:6 final size:6
Alignment explanation
Indices: 9630968--9631019 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
9630958 CCAATTTGGC
*
9630968 TTTTAT TTTGTA- TTTTA- TATTAT TTTTAT TTTTAT TTTTAT TTTATAT
1 TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT
9631016 TTTT
1 TTTT
9631020 TCCTTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 6 0.15
6 27 0.66
7 8 0.20
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:9631140 original size:21 final size:20
Alignment explanation
Indices: 9631116--9631210 Score: 65
Period size: 20 Copynumber: 4.7 Consensus size: 20
9631106 TTTATATATG
9631116 TATTTTATTTATCTAGTTATA
1 TATTTTATTTATCTA-TTATA
9631137 TA-TTTA-TTAT-TA-TATTA
1 TATTTTATTTATCTATTA-TA
*
9631154 TAATTTATTTAT-TATTATTA
1 TATTTTATTTATCTATTA-TA
*
9631174 TATTTTTTATTTATCTTATTATT
1 TA--TTTTATTTATC-TATTATA
* *
9631197 TTTTTTAATTATCT
1 TATTTTATTTATCT
9631211 GTTAATTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.03
17 4 0.06
18 6 0.10
19 10 0.16
20 12 0.19
21 12 0.19
22 9 0.15
23 2 0.03
24 5 0.08
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (20 bp):
TATTTTATTTATCTATTATA
Found at i:9631182 original size:22 final size:22
Alignment explanation
Indices: 9631140--9631208 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
9631130 AGTTATATAT
9631140 TTATTATTATATTATAATTTATTTA
1 TTATTATTATATT-T--TTTATTTA
9631165 TTATTATTATATTTTTTATTTA
1 TTATTATTATATTTTTTATTTA
* * *
9631187 -TCTTATTATTTTTTTTAATTA
1 TTATTATTATATTTTTTATTTA
9631208 T
1 T
9631209 CTGTTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 18 0.45
22 8 0.20
24 1 0.03
25 13 0.32
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTATTATATTTTTTATTTA
Found at i:9631192 original size:5 final size:4
Alignment explanation
Indices: 9631030--9631197 Score: 66
Period size: 4 Copynumber: 41.8 Consensus size: 4
9631020 TCCTTTGTAT
* * * *
9631030 TTTA TGTA TTTA -TTA TTTA TTTA TTTA -TTA TTACTA TGTA TTAA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA
* * * * * *
9631078 TGTA TATC TTTA TTT- TTT- TTTG TTAATA TTTA TATA TGTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA -TTTA TTTA
* * *
9631127 TCTA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA -TTA -TTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TTTA TTTA TT-TA
9631176 TTT- TTTA TTTA TCTTA -TTA TTT
1 TTTA TTTA TTTA T-TTA TTTA TTT
9631198 TTTTTAATTA
Statistics
Matches: 126, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
3 27 0.21
4 73 0.58
5 17 0.13
6 9 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:9631197 original size:12 final size:11
Alignment explanation
Indices: 9631031--9631187 Score: 67
Period size: 11 Copynumber: 14.1 Consensus size: 11
9631021 CCTTTGTATT
*
9631031 TTATGTATTTA
1 TTATTTATTTA
9631042 TTATTTATTTA
1 TTATTTATTTA
9631053 TT-TATTATTACTA
1 TTAT-TTATT--TA
* *
9631066 TGTATTAATATA
1 T-TATTTATTTA
* *
9631078 TGTATATCTTTA
1 T-TATTTATTTA
* *
9631090 TT-TTTTTTTG
1 TTATTTATTTA
*
9631100 TTA-ATATTTA
1 TTATTTATTTA
*
9631110 TATATGTA-TT-
1 T-TATTTATTTA
*
9631120 TTATTTATCTA
1 TTATTTATTTA
*
9631131 GTTATATATTTA
1 -TTATTTATTTA
9631143 TTA-TTATATTA
1 TTATTTAT-TTA
*
9631154 TAATTTATTTA
1 TTATTTATTTA
9631165 TTA-TTATTATA
1 TTATTTATT-TA
*
9631176 TTTTTTATTTA
1 TTATTTATTTA
9631187 T
1 T
9631188 CTTATTATTT
Statistics
Matches: 109, Mismatches: 22, Indels: 30
0.68 0.14 0.19
Matches are distributed among these distances:
9 5 0.05
10 23 0.21
11 42 0.39
12 31 0.28
13 3 0.03
14 4 0.04
15 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:9631198 original size:19 final size:20
Alignment explanation
Indices: 9631118--9631200 Score: 50
Period size: 19 Copynumber: 4.2 Consensus size: 20
9631108 TATATATGTA
9631118 TTTTATTTATC-TAGTTATAT
1 TTTTATTTATCTTAGTTAT-T
* *
9631138 ATTTA-TTAT-TATA-TTATA
1 TTTTATTTATCT-TAGTTATT
* * *
9631156 ATTTATTTATTATTATTATATT
1 TTTTATTTA-TCTTAGT-TATT
9631178 TTTTATTTATCTTA-TTATT
1 TTTTATTTATCTTAGTTATT
9631197 TTTT
1 TTTT
9631201 TTAATTATCT
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
18 5 0.10
19 19 0.37
20 10 0.20
21 6 0.12
22 11 0.22
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTATTTATCTTAGTTATT
Found at i:9631218 original size:21 final size:21
Alignment explanation
Indices: 9631176--9631224 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
9631166 TATTATTATA
* *
9631176 TTTTTTATTTATCTTATTATT
1 TTTTTTAATTATCTTATAATT
9631197 TTTTTTAATTATCTGT-TAATT
1 TTTTTTAATTATCT-TATAATT
9631218 TTTTTTA
1 TTTTTTA
9631225 TAATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTTAATTATCTTATAATT
Found at i:9631219 original size:20 final size:21
Alignment explanation
Indices: 9631145--9631222 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 21
9631135 TATATTTATT
* *
9631145 ATTATATTA-TAATTTATTT-
1 ATTATCTTATTAATTTTTTTA
9631164 ATTA--TTATT-ATATTTTTTA
1 ATTATCTTATTAAT-TTTTTTA
* *
9631183 TTTATCTTATTATTTTTTTTA
1 ATTATCTTATTAATTTTTTTA
*
9631204 ATTATC-TGTTAATTTTTTT
1 ATTATCTTATTAATTTTTTT
9631223 TATAATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
17 5 0.11
18 6 0.13
19 7 0.15
20 11 0.23
21 17 0.36
22 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (21 bp):
ATTATCTTATTAATTTTTTTA
Found at i:9631258 original size:23 final size:24
Alignment explanation
Indices: 9631228--9631278 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
9631218 TTTTTTATAA
9631228 TTTTA-TTTGTTTATCTAATTTTT
1 TTTTATTTTGTTTATCTAATTTTT
*
9631251 TTTTATTTTGTTTATCTGATTTTT
1 TTTTATTTTGTTTATCTAATTTTT
9631275 TTTT
1 TTTT
9631279 TGCTGAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTTATTTTGTTTATCTAATTTTT
Found at i:9632311 original size:58 final size:58
Alignment explanation
Indices: 9632228--9632808 Score: 677
Period size: 58 Copynumber: 10.1 Consensus size: 58
9632218 TATTATTTTA
* * * * *
9632228 TTTTCTT-TAAATAAAATCTAAAAAAAATATTTTTG-GAAAAAAATTGAAAGTATCAAT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAAT
*
9632285 TTTTCTTAAAAATAAAATTTCAAAAAAA-GTTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* *
9632342 TTTTCTTGAAAATCAAAGTTTTC-AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAAT-AAA-ATTTCAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAAT
* * *
9632401 TTTCCTTAAAAATAAAATTTCAAAAAAA-GTTTTTGAGGAAAAGTTAAAAGTATCAAT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* *
9632458 TTTTCTTGAAAATCAAAGTTTTC-AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAAT-AAA-ATTTCAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAAT
* * **
9632517 TTTTCTTAAAAATAGATTTTCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * *
9632575 TTTCCTTAAAAATAAATTTTCAAAAAAA-GTTTTTGAGGAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * * * * *
9632631 TTTCCTTGAAAATCAAAGTTTCCAAAAAATATTTTTGAGAAAAACTTGAAAGTATCAAT
1 TTTTCTTAAAAAT-AAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
**
9632690 TTTTCTTAAAAAT-AAATTTC-AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * * * *
9632746 TTTT-TTCGAAATTAAAGTTTCAAAAGAATATTTTTG-GAAAAAAGTTGAAAGTATCAAT
1 TTTTCTT-AAAAATAAAATTTCAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAAT
9632804 TTTTC
1 TTTTC
9632809 CTGCACAAGA
Statistics
Matches: 457, Mismatches: 45, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
55 2 0.00
56 52 0.11
57 142 0.31
58 167 0.37
59 94 0.21
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:9632805 original size:27 final size:27
Alignment explanation
Indices: 9632727--9632808 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 27
9632717 GTTTTTGAGG
9632727 AAAAGTTGAAAGTATCAATTTTTTTCGAA
1 AAAAGTTGAAAGTATCAA--TTTTTCGAA
* * *
9632756 ATTAAAGTTTCAAAAGAAT--ATTTTTGGAA
1 A--AAAG-TT-GAAAGTATCAATTTTTCGAA
9632785 AAAAGTTGAAAGTATCAATTTTTC
1 AAAAGTTGAAAGTATCAATTTTTC
9632809 CTGCACAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 6 0.15
26 2 0.05
27 10 0.24
29 10 0.24
31 5 0.12
32 2 0.05
33 6 0.15
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (27 bp):
AAAAGTTGAAAGTATCAATTTTTCGAA
Found at i:9641816 original size:327 final size:324
Alignment explanation
Indices: 9641167--9641817 Score: 896
Period size: 327 Copynumber: 2.0 Consensus size: 324
9641157 TTTGAATATC
* * * *
9641167 TAATTGATTAAAATGAATTTAAGAGCCAAATCAATATCAATAATAGTATTTTAAGTTAAAAAGTA
1 TAATTGACTAAAATGAATTTAAGAACCAAATCAATATCAATAATAGTA-TGTAAATTAAAAAGTA
* * * *
9641232 ATTTATACTTGATAATTAGAATAATTAAACATATTATGTATTGTTTGGGAGAAATGGCAAAATAA
65 ATTTATACTTGACAATTAAAATAATTAAACATATTATGTATTGTTTGGGAGAAATAGAAAAATAA
*
9641297 AGATTTTGAAATTAATGTAACAATAGTAATGAAATTCATTTTATTTGATATATTCTAAAATTAAT
130 AGATTTTGAAATTAATGTAACAATAGTAATGAAATTCATTTTATTTGATATATTCCAAAATTAAT
* *
9641362 TTTAACTAATTTAATCATCTATTAATCATTTTAAAATTAATATATTTACAAATCAAACGTGTATA
195 TTTAACTAATTTAATCATCTATTAATCATTTTAAAATTAATATATTTACAAATCAAAAGTATATA
* * * * *
9641427 TATAGCTTAAAAAGTGAAGTAAATAAATATGTTATAGATTTCAAAATTGGAAAGTGAATTTTTTA
260 CATAGCTTAAAAAATGAAGTAAATAAATAGGTCATAGATTTCAAAATTGAAAAGTGAATTTTTTA
* *
9641492 TAATTGACTAAAATGAATTTAAGAACCAAATCAATATCAGTAATAGTA-GTAAATT-AAGAGTAA
1 TAATTGACTAAAATGAATTTAAGAACCAAATCAATATCAATAATAGTATGTAAATTAAAAAGTAA
** *
9641555 TTTATGTTTGACAATTAAAATAATTAAACCTATTATGTATTTAACTTGTTTGGGA-AAATAGAAA
66 TTTATACTTGACAATTAAAATAATTAAA-C-A-TAT-TATGT-A-TTGTTTGGGAGAAATAGAAA
* * *
9641619 AATAAAGATTTTGAAATTAGTGTAATAATGGTAATGAAATTCATTTTATTTGATATATTCCAAAA
125 AATAAAGATTTTGAAATTAATGTAACAATAGTAATGAAATTCATTTTATTTGATATATTCCAAAA
* * * * * * *
9641684 TTAATTTTGATTGATTTGATCATCTATTAATCATTTT-AAATTAATATATTTACATATTAAAATT
190 TTAATTTTAACTAATTTAATCATCTATTAATCATTTTAAAATTAATATATTTACAAATCAAAAGT
* **
9641748 ATATACATAGCTTAAAAAATGAAGTAAATACATAGGTCATAGATTTCAATTTTGAAAAGTGAAAT
255 ATATACATAGCTTAAAAAATGAAGTAAATAAATAGGTCATAGATTTCAAAATTGAAAAGTG-AAT
9641813 TTTTT
319 TTTTT
9641818 TACACAAATA
Statistics
Matches: 285, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
322 31 0.11
323 6 0.02
324 1 0.00
325 48 0.17
326 79 0.28
327 110 0.39
328 10 0.04
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (324 bp):
TAATTGACTAAAATGAATTTAAGAACCAAATCAATATCAATAATAGTATGTAAATTAAAAAGTAA
TTTATACTTGACAATTAAAATAATTAAACATATTATGTATTGTTTGGGAGAAATAGAAAAATAAA
GATTTTGAAATTAATGTAACAATAGTAATGAAATTCATTTTATTTGATATATTCCAAAATTAATT
TTAACTAATTTAATCATCTATTAATCATTTTAAAATTAATATATTTACAAATCAAAAGTATATAC
ATAGCTTAAAAAATGAAGTAAATAAATAGGTCATAGATTTCAAAATTGAAAAGTGAATTTTTTA
Found at i:9643255 original size:58 final size:58
Alignment explanation
Indices: 9643164--9643278 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
9643154 ATTTGAAAAT
* * * *
9643164 AATTTTAATTATACAGTATTGAAGTATTAATTTTAATCAAAAGATAAAATAATAATTA
1 AATTTAAATTATACAATATTAAAGCATTAATTTTAATCAAAAGATAAAATAATAATTA
* *
9643222 AATTTAAATTATATAATATTAAAGCATTGATTTTAATCAAAAGATAAAATAATAATT
1 AATTTAAATTATACAATATTAAAGCATTAATTTTAATCAAAAGATAAAATAATAATT
9643279 TTATAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.39
Consensus pattern (58 bp):
AATTTAAATTATACAATATTAAAGCATTAATTTTAATCAAAAGATAAAATAATAATTA
Found at i:9644171 original size:22 final size:21
Alignment explanation
Indices: 9644146--9644187 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
9644136 TTTTATCGAA
*
9644146 ATTTATTATTATTGTTATTATT
1 ATTTATTAATATT-TTATTATT
9644168 ATTTATTAATATTTTATTAT
1 ATTTATTAATATTTTATTAT
9644188 CTTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTATTAATATTTTATTATT
Found at i:9644175 original size:10 final size:10
Alignment explanation
Indices: 9644146--9644210 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
9644136 TTTTATCGAA
9644146 ATTTATTATT
1 ATTTATTATT
9644156 ATTGTTATTATT
1 A-T-TTATTATT
*
9644168 ATTTATTAAT
1 ATTTATTATT
9644178 ATTTTATTA-T
1 A-TTTATTATT
* *
9644188 CTTTAATA-T
1 ATTTATTATT
*
9644197 ATTTATAATT
1 ATTTATTATT
9644207 ATTT
1 ATTT
9644211 TAATATATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 12 0.27
10 15 0.33
11 9 0.20
12 9 0.20
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTATTATT
Found at i:9644184 original size:18 final size:18
Alignment explanation
Indices: 9644163--9644218 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
9644153 ATTATTGTTA
9644163 TTATTATTTATTAATAT-T
1 TTATTATTT-TTAATATAT
*
9644181 TTATTATCTTTAATATAT
1 TTATTATTTTTAATATAT
*
9644199 TTATAATTATTTTAATATAT
1 TTATTA-T-TTTTAATATAT
9644219 AAATAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.22
18 14 0.44
19 1 0.03
20 10 0.31
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATTTTTAATATAT
Found at i:9644224 original size:20 final size:21
Alignment explanation
Indices: 9644183--9644225 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
9644173 TTAATATTTT
**
9644183 ATTATCTTTAATATATTTATA
1 ATTATCTTTAATATATAAATA
9644204 ATTAT-TTTAATATATAAATA
1 ATTATCTTTAATATATAAATA
9644224 AT
1 AT
9644226 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATCTTTAATATATAAATA
Found at i:9644225 original size:11 final size:11
Alignment explanation
Indices: 9644211--9644261 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
9644201 ATAATTATTT
9644211 TAATATATAAA
1 TAATATATAAA
*
9644222 TAATAAATAAA
1 TAATATATAAA
9644233 -AATATTATAAA
1 TAATA-TATAAA
*
9644244 -AATATTTAAA
1 TAATATATAAA
9644254 TAA-ATATA
1 TAATATATA
9644262 TGGTATTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 13 0.38
11 21 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATATATAAA
Found at i:9644674 original size:129 final size:128
Alignment explanation
Indices: 9644527--9644927 Score: 450
Period size: 129 Copynumber: 3.1 Consensus size: 128
9644517 TTTAATAAGA
* *
9644527 GTATTTTAGTAATTTAATATGCAATTAATTTTATGTTATGTTAAAATTTAATATGTAATTTAATA
1 GTATTTTAGTAATTTAATATGTAATTAATTTTATATTATGTTAAAATTTAATATGTAATTTAATA
* * *
9644592 AAGATATTACAGTAAATTTCAAACAAAATGTCACAAATCAAATTTTTATGAAA-TAATGGCAAGT
66 AGGATATTACAGTAAATTTCAAATAAAATGTCACAAATCAAATTTTTAT-AAAGCAATGGCAA-T
* * * *
9644656 GTATTTTAGTAATCTAATATGTAATTAATTTTATATTAAGTTATAATTTCATATGTAATTTAATA
1 GTATTTTAGTAATTTAATATGTAATTAATTTTATATTATGTTAAAATTTAATATGTAATTTAATA
* * * * ** * *
9644721 AGGATTTTACAGTAATTTTAAAATAAAATATCACATGTCTAATTTTTATAAAGCAATGGTAAT
66 AGGATATTACAGTAAATTTCAAATAAAATGTCACAAATCAAATTTTTATAAAGCAATGGCAAT
* * * * *
9644784 GACATTTGAGTAATTTAATATGTAATTAATTTTACATTATATTAAAATTTAATACGTAATTTAAT
1 G-TATTTTAGTAATTTAATATGTAATTAATTTTATATTATGTTAAAATTTAATATGTAATTTAAT
* * ** *
9644849 AAGGATATTATAAT-AATTTCAAAATAAAATGTCACATGT-AAATTTTTTATAAAAGCACTGAG-
65 AAGGATATTACAGTAAATTTC-AAATAAAATGTCACAAATCAAA-TTTTTAT-AAAGCAATG-GC
9644911 AAT
126 AAT
* *
9644914 ATATTTTTGTAATT
1 GTATTTTAGTAATT
9644928 ATAACAAAAT
Statistics
Matches: 228, Mismatches: 38, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
128 11 0.05
129 205 0.90
130 11 0.05
131 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (128 bp):
GTATTTTAGTAATTTAATATGTAATTAATTTTATATTATGTTAAAATTTAATATGTAATTTAATA
AGGATATTACAGTAAATTTCAAATAAAATGTCACAAATCAAATTTTTATAAAGCAATGGCAAT
Found at i:9645041 original size:61 final size:62
Alignment explanation
Indices: 9644914--9645060 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 62
9644904 CACTGAGAAT
* *
9644914 ATATTTTTGTAATTATAACA-AAATAGTATTATAATAATTTTAACTAATTATAATAAAATGA
1 ATATTTTTGTAATTATAATAGAAATAGTATTATAATAATTTTAACTAATCATAATAAAATGA
* * * *
9644975 ATATTTTTGTAATTATGATAGAAAT-GTATTATAGTATTTTTAACTAATCAT-TTAAAGAT-A
1 ATATTTTTGTAATTATAATAGAAATAGTATTATAATAATTTTAACTAATCATAATAAA-ATGA
*
9645035 GGTATTTTTTGTAATTATAATAGAAA
1 -ATA-TTTTTGTAATTATAATAGAAA
9645061 GACATGAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
60 5 0.07
61 45 0.61
62 24 0.32
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (62 bp):
ATATTTTTGTAATTATAATAGAAATAGTATTATAATAATTTTAACTAATCATAATAAAATGA
Found at i:9648077 original size:17 final size:18
Alignment explanation
Indices: 9648052--9648089 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9648042 TTTCATAAAT
*
9648052 TTAAATTTATTTTTTA-A
1 TTAAATTTAATTTTTATA
*
9648069 TTAACTTTAATTTTTATA
1 TTAAATTTAATTTTTATA
9648087 TTA
1 TTA
9648090 TCTTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAAATTTAATTTTTATA
Found at i:9648243 original size:15 final size:16
Alignment explanation
Indices: 9648218--9648248 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9648208 AGAATTATAA
9648218 AATTCTTTTTTTTCAT
1 AATTCTTTTTTTTCAT
9648234 AATT-TTTTTTTTCAT
1 AATTCTTTTTTTTCAT
9648249 TTCATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTCTTTTTTTTCAT
Found at i:9649545 original size:2 final size:2
Alignment explanation
Indices: 9649540--9649571 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9649530 ACACACACAC
*
9649540 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9649572 GGAATCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9651461 original size:26 final size:27
Alignment explanation
Indices: 9651411--9651464 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
9651401 AATTTTAGAA
9651411 TTAATTTTTAAATTTTAATAAAAATTAT
1 TTAATTTTT-AATTTTAATAAAAATTAT
9651439 TTAATTTTT-ATTTTAA-AATAAATTAT
1 TTAATTTTTAATTTTAATAA-AAATTAT
9651465 AATTATCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
28 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAATTTTTAATTTTAATAAAAATTAT
Found at i:9652591 original size:25 final size:22
Alignment explanation
Indices: 9652536--9652591 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
9652526 TTATAATAAT
*
9652536 TTTAATTAATTATAAAAAATATA
1 TTTAA-TAATTATAAAAAAGATA
*
9652559 TTTTATAATTATGATAAAAAGATA
1 TTTAATAATTAT-A-AAAAAGATA
9652583 TTGTAATAA
1 TT-TAATAA
9652592 ATTTAGACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.26
23 5 0.19
24 10 0.37
25 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTAATAATTATAAAAAAGATA
Found at i:9653124 original size:24 final size:23
Alignment explanation
Indices: 9653059--9653140 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 23
9653049 TTATTAAATA
*
9653059 ATTA-AAAAATATTTTGATAATT
1 ATTATAAAAATATTTTTATAATT
* * *
9653081 -TTTTAAAAAT-TAATTAATAATT
1 ATTATAAAAATAT-TTTTATAATT
9653103 AATTATAAAAATATTTTTATAATT
1 -ATTATAAAAATATTTTTATAATT
9653127 ATGCTATAAAAATA
1 AT--TATAAAAATA
9653141 AAAAATATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
21 3 0.06
22 14 0.30
23 2 0.04
24 17 0.36
25 11 0.23
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTATAAAAATATTTTTATAATT
Found at i:9653135 original size:121 final size:127
Alignment explanation
Indices: 9652840--9653136 Score: 333
Period size: 126 Copynumber: 2.4 Consensus size: 127
9652830 AAGTTATTAT
* * * * *
9652840 ATATAATAAATACTTTAAAAAAAGAATTATTTTTATAATTATGGTACAAAGATATAATAATCAAT
1 ATATAATAAATA-ATT-ATAAAAG-A-TATTTTTATAATTATGATATAAAGACATAATAATCAAT
* * *
9652905 TGCATCATTTGTTGATTTCTTTTCAAATAATGAAAAGAGTATTTTGATAATTTTTTAGAGAATAT
62 TGCATCATATGTTGATTTCTTTTCAAATAATGAAAAGAATATTTTGATAATTTTTTAGAAAATAT
9652970 A
127 A
* * * *
9652971 TTATAATAAATAATTATAAAAGAT-TTTTTATAATTATAATATAATGACATAATAATTAATTTG-
1 ATATAATAAATAATTATAAAAGATATTTTTATAATTATGATATAAAGACATAATAATCAA-TTGC
* *
9653034 ATCATATGTT-ATTT-TTTATTAAATAATTAAAA-AATATTTTGATAATTTTTTA-AAAAT-TA
65 ATCATATGTTGATTTCTTT-TCAAATAATGAAAAGAATATTTTGATAATTTTTTAGAAAATATA
* *
9653093 AT-TAATAATTAATTATAAAA-ATATTTTTATAATTATGCTATAAA
1 ATATAATAAATAATTATAAAAGATATTTTTATAATTATGATATAAA
9653137 AATAAAAAAT
Statistics
Matches: 144, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
120 2 0.01
121 35 0.24
122 3 0.02
123 4 0.03
124 22 0.15
125 16 0.11
126 38 0.26
127 4 0.03
128 1 0.01
129 6 0.04
130 2 0.01
131 11 0.08
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (127 bp):
ATATAATAAATAATTATAAAAGATATTTTTATAATTATGATATAAAGACATAATAATCAATTGCA
TCATATGTTGATTTCTTTTCAAATAATGAAAAGAATATTTTGATAATTTTTTAGAAAATATA
Found at i:9659662 original size:25 final size:25
Alignment explanation
Indices: 9659629--9659676 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
9659619 AGTGGAATAG
*
9659629 AATTATTGAAGTAAAAACAGATTTAA
1 AATTATTGAA-AAAAAACAGATTTAA
*
9659655 AATT-TTGAAAAAAAAGAGATTT
1 AATTATTGAAAAAAAACAGATTT
9659677 TTTTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 5 0.25
26 4 0.20
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (25 bp):
AATTATTGAAAAAAAACAGATTTAA
Found at i:9670197 original size:62 final size:62
Alignment explanation
Indices: 9670073--9670513 Score: 229
Period size: 63 Copynumber: 7.1 Consensus size: 62
9670063 CATTTTTTGT
* * * * * ***
9670073 AATAATCATATCATTTTTTAAAAAG-AACTATTTAAGGTATTTTTGAAT-AAAAAATGTTTTA
1 AATAATCTTTTCATTTTTTTAAAAGAAATTATTTAAGGTATTTTT-AGTCAAAAAATACCTTA
* *
9670134 AATAATCTTTTCATTTTTTTAAAGGAAATTATTTAAGGTATTTTTGGTCAAAAAATACCTTA
1 AATAATCTTTTCATTTTTTTAAAAGAAATTATTTAAGGTATTTTTAGTCAAAAAATACCTTA
* * **** * ** * *
9670196 AATAATGCCCTTTAACAAATATATCA-ATATTATTTAAGGTATTTTTTA-TTAAAAAATACCTTA
1 AATAAT--CTTTTCATTTTTTTAAAAGAAATTATTTAAGGTA-TTTTTAGTCAAAAAATACCTTA
* ** * * * * * * **
9670259 AATAATATCATAAATTTTTTAAAAAAGAATTATTTAAAGCATTTTTTGTCAAAAAATATTTTA
1 AATAATCTTTTCATTTTTTTAAAAGA-AATTATTTAAGGTATTTTTAGTCAAAAAATACCTTA
* * * * * * *
9670322 AATAATCTCTTGATATTTTTTAACAGAGATTATTTAA-GTAATTTCTA-TCTAAAAATACCTTT
1 AATAATCTTTTCAT-TTTTTTAAAAGAAATTATTTAAGGT-ATTTTTAGTCAAAAAATACCTTA
* ** * * * * *
9670384 AATAATCCCTTT-A-TTTTTTAAAAGGGACTATTTAA-GTCATTTCTAGACCAAAAATATCTTA
1 AATAAT-CTTTTCATTTTTTTAAAAGAAATTATTTAAGGT-ATTTTTAGTCAAAAAATACCTTA
** * * *
9670445 AATAATCCTCAT-AGTTTTTTTAAAAGACATTATTTAAGGCT-TTTTTAGTCCAAAACTACCTTA
1 AATAAT-CTTTTCA-TTTTTTTAAAAGAAATTATTTAAGG-TATTTTTAGTCAAAAAATACCTTA
9670508 AATAAT
1 AATAAT
9670514 GTCATTTAAA
Statistics
Matches: 289, Mismatches: 75, Indels: 30
0.73 0.19 0.08
Matches are distributed among these distances:
60 28 0.10
61 50 0.17
62 59 0.20
63 127 0.44
64 24 0.08
65 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (62 bp):
AATAATCTTTTCATTTTTTTAAAAGAAATTATTTAAGGTATTTTTAGTCAAAAAATACCTTA
Found at i:9670249 original size:125 final size:126
Alignment explanation
Indices: 9670101--9670327 Score: 294
Period size: 125 Copynumber: 1.8 Consensus size: 126
9670091 TAAAAAGAAC
*** * ** * * **
9670101 TATTTAAGGTATTTTTGAATAAAAAATGTTTTAAATAATCTTTTCATTTTTTTAAAGGA-AATTA
1 TATTTAAGGTATTTTTGAATAAAAAATACCTTAAATAATATCATAAATTTTTTAAAAAAGAATTA
* *
9670165 TTTAAGGTATTTTTGGTCAAAAAATACCTTAAATAATGCCCTTTAACAAATATATCAATAT
66 TTTAAAGCATTTTTGGTCAAAAAATACCTTAAATAATGCCCTTTAACAAATATATCAATAT
* *
9670226 TATTTAAGGTATTTTTTATTAAAAAATACCTTAAATAATATCATAAATTTTTTAAAAAAGAATTA
1 TATTTAAGGTATTTTTGAATAAAAAATACCTTAAATAATATCATAAATTTTTTAAAAAAGAATTA
* **
9670291 TTTAAAGCATTTTTTGTCAAAAAATATTTTAAATAAT
66 TTTAAAGCATTTTTGGTCAAAAAATACCTTAAATAAT
9670328 CTCTTGATAT
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
125 47 0.56
126 37 0.44
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (126 bp):
TATTTAAGGTATTTTTGAATAAAAAATACCTTAAATAATATCATAAATTTTTTAAAAAAGAATTA
TTTAAAGCATTTTTGGTCAAAAAATACCTTAAATAATGCCCTTTAACAAATATATCAATAT
Found at i:9670452 original size:61 final size:61
Alignment explanation
Indices: 9670310--9670482 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 61
9670300 TTTTTTGTCA
* * * * * *
9670310 AAAAATATTTTAAATAATCTCTTGATATTTTTTAACAGAGATTATTTAAGTAATTTCTATCT
1 AAAAATATCTTAAATAATCCCTT-ATATTTTTTAAAAGAGACTATTTAAGTAATTTCTAACC
* * * *
9670372 AAAAATACCTTTAATAATCCCTT-TATTTTTTAAAAGGGACTATTTAAGTCATTTCTAGACC
1 AAAAATATCTTAAATAATCCCTTATATTTTTTAAAAGAGACTATTTAAGTAATTTCTA-ACC
* * *
9670433 AAAAATATCTTAAATAAT-CCTCATAGTTTTTTTAAAAGACATTATTTAAG
1 AAAAATATCTTAAATAATCCCTTATA--TTTTTTAAAAGAGACTATTTAAG
9670483 GCTTTTTTAG
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
60 33 0.36
61 19 0.21
62 19 0.21
63 20 0.22
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (61 bp):
AAAAATATCTTAAATAATCCCTTATATTTTTTAAAAGAGACTATTTAAGTAATTTCTAACC
Found at i:9671608 original size:20 final size:20
Alignment explanation
Indices: 9671595--9671640 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
9671585 TTTGACTGAT
9671595 TTTGACTATATTTGACAAAG
1 TTTGACTATATTTGACAAAG
*
9671615 TTTGACTTTATTTGATC-AAG
1 TTTGACTATATTTGA-CAAAG
9671635 TTTGAC
1 TTTGAC
9671641 CAAATTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTGACTATATTTGACAAAG
Found at i:9674733 original size:13 final size:13
Alignment explanation
Indices: 9674702--9674727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9674692 ATCTAGAATT
9674702 TGTTTATATAATG
1 TGTTTATATAATG
9674715 TGTTTATATAATG
1 TGTTTATATAATG
9674728 ATTTTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TGTTTATATAATG
Found at i:9675711 original size:30 final size:30
Alignment explanation
Indices: 9675600--9675707 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
9675590 TTGATTTATA
* *
9675600 TTAAAGATTTATTTAGATATAAATT-AAAG
1 TTAAATATTTATTTGGATATAAATTAAAAG
* *
9675629 TTTAAATATTTATTTGAATACAAATTAAAAG
1 -TTAAATATTTATTTGGATATAAATTAAAAG
* * * *
9675660 TCAAAAATTAATTTAGG-TGTAAATTAAAAG
1 TTAAATATTTATTT-GGATATAAATTAAAAG
*
9675690 TTAAATTTTTATTTGGAT
1 TTAAATATTTATTTGGAT
9675708 GTAATAAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
29 2 0.03
30 54 0.89
31 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (30 bp):
TTAAATATTTATTTGGATATAAATTAAAAG
Found at i:9684003 original size:21 final size:21
Alignment explanation
Indices: 9683979--9684049 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
9683969 TTTTTAAATG
9683979 TAAAAAAATATTAATAATATA
1 TAAAAAAATATTAATAATATA
9684000 T-AAAAAAT-TTAAGGGTAATATA
1 TAAAAAAATATTAA---TAATATA
* *
9684022 TAAAAATAAAATTAAAAAT-TA
1 TAAAAA-AATATTAATAATATA
9684043 TAAAAAA
1 TAAAAAA
9684050 TGTTATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
19 4 0.10
20 8 0.19
21 9 0.21
22 11 0.26
23 4 0.10
24 2 0.05
25 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAAAAATATTAATAATATA
Found at i:9684446 original size:9 final size:9
Alignment explanation
Indices: 9684432--9684470 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
9684422 AATTTTTTCT
9684432 TAAAATATA
1 TAAAATATA
9684441 TAAAATATA
1 TAAAATATA
9684450 TTAATAATATA
1 -TAA-AATATA
*
9684461 TAAAAAATA
1 TAAAATATA
9684470 T
1 T
9684471 TTAGGTGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 15 0.56
10 6 0.22
11 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATA
Found at i:9684458 original size:20 final size:19
Alignment explanation
Indices: 9684431--9684471 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
9684421 TAATTTTTTC
*
9684431 TTAAAATATATAAAATATA
1 TTAAAATATATAAAAAATA
9684450 TTAATAATATATAAAAAATA
1 TTAA-AATATATAAAAAATA
9684470 TT
1 TT
9684472 TAGGTGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATATATAAAAAATA
Found at i:9684695 original size:17 final size:16
Alignment explanation
Indices: 9684664--9684697 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9684654 TTAAGGCAAA
9684664 AATTATTATTATAAAT
1 AATTATTATTATAAAT
*
9684680 AATTATTTTATATAAAT
1 AATTATTAT-TATAAAT
9684697 A
1 A
9684698 TTTGAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTATTATAAAT
Found at i:9686671 original size:106 final size:106
Alignment explanation
Indices: 9686544--9686755 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
9686534 ATTCCTTTTA
*
9686544 AGTCATATCTTGTAGGTAATTAGTAATCACATACGATATATTTAATAAAATAAAAAAATCCAAAC
1 AGTCATATCTTGTAGGTAATTAGCAATCACATACGATATATTTAATAAAATAAAAAAATCCAAAC
9686609 CAAGAATGGTTTCATAATCAAAATTTCAAATGCATTGATTG
66 CAAGAATGGTTTCATAATCAAAATTTCAAATGCATTGATTG
*
9686650 AGTCATATCTTGTAGGTAATTAGCAATCACATACGATATATTTAATAAAATAAAGAAATCCAAAC
1 AGTCATATCTTGTAGGTAATTAGCAATCACATACGATATATTTAATAAAATAAAAAAATCCAAAC
9686715 CAAGAATGGTTTCATAATCAAAATTTCAAATGCATTGATTG
66 CAAGAATGGTTTCATAATCAAAATTTCAAATGCATTGATTG
9686756 TTTTAATCAA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (106 bp):
AGTCATATCTTGTAGGTAATTAGCAATCACATACGATATATTTAATAAAATAAAAAAATCCAAAC
CAAGAATGGTTTCATAATCAAAATTTCAAATGCATTGATTG
Found at i:9695322 original size:21 final size:21
Alignment explanation
Indices: 9695298--9695357 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
9695288 CCCAGCCCAA
*
9695298 TTTTCCATTTTATATTTC-TT
1 TTTTCCATTTTATATTTCGGT
** *
9695318 TTTTTAATTTTAT-TGTTAGGT
1 TTTTCCATTTTATAT-TTCGGT
9695339 TTTTCCATTTTATTATTTC
1 TTTTCCATTTTA-TATTTC
9695358 ATGATATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 11 0.38
22 3 0.10
23 1 0.03
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTCCATTTTATATTTCGGT
Found at i:9696544 original size:18 final size:19
Alignment explanation
Indices: 9696517--9696564 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
9696507 TTTCTTGTTC
*
9696517 ATTTACTTATTTAT-TTTG
1 ATTTATTTATTTATGTTTG
9696535 ATTTATTTA-TTATGTTTG
1 ATTTATTTATTTATGTTTG
9696553 ATTTATTTATTT
1 ATTTATTTATTT
9696565 TTGAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 21 0.78
19 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (19 bp):
ATTTATTTATTTATGTTTG
Found at i:9696636 original size:13 final size:13
Alignment explanation
Indices: 9696618--9696643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9696608 AAAAATAGAG
9696618 AAAATTATAAAAA
1 AAAATTATAAAAA
9696631 AAAATTATAAAAA
1 AAAATTATAAAAA
9696644 TATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATTATAAAAA
Found at i:9696686 original size:21 final size:21
Alignment explanation
Indices: 9696661--9696700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9696651 CAAAACTTTA
* *
9696661 ATAAATTTTGAATGATAAATT
1 ATAAATATTCAATGATAAATT
9696682 ATAAATATTCAATGATAAA
1 ATAAATATTCAATGATAAA
9696701 ATTCTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
ATAAATATTCAATGATAAATT
Found at i:9703957 original size:25 final size:25
Alignment explanation
Indices: 9703928--9703981 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
9703918 ATTCATATAA
9703928 AAAAAGCAAAAAAAAAGGAAAAAAAG
1 AAAAA-CAAAAAAAAAGGAAAAAAAG
* * * *
9703954 AAAAACGAAGAAAAATGAAAAATAG
1 AAAAACAAAAAAAAAGGAAAAAAAG
9703979 AAA
1 AAA
9703982 TGAAAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (25 bp):
AAAAACAAAAAAAAAGGAAAAAAAG
Found at i:9704977 original size:38 final size:39
Alignment explanation
Indices: 9704930--9705006 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
9704920 TACTCAAAGG
9704930 AGCCTTATTTTTTAAAGTT-TGTGCCTCTATTTAT-AGGA
1 AGCCTTATTTTTT-AAGTTGTGTGCCTCTATTTATGAGGA
*
9704968 AGCCTTATTTTTTAAGTTGTGTGCCTTTATTTATGAGGA
1 AGCCTTATTTTTTAAGTTGTGTGCCTCTATTTATGAGGA
9705007 GCTTTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 5 0.14
38 27 0.75
39 4 0.11
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (39 bp):
AGCCTTATTTTTTAAGTTGTGTGCCTCTATTTATGAGGA
Found at i:9707259 original size:53 final size:53
Alignment explanation
Indices: 9707199--9707300 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
9707189 CAAAAGTAGG
* *
9707199 TTCTAAATTTAA-CCCAAACGGCAAAAAATTTAGAAATGAAACTTTTAAAATAA
1 TTCTAAA-TTAAGCCCAAACGGCAAAAAATTTAGAAATAAAACTTGTAAAATAA
** **
9707252 TTCTAAATTAAGCCCAAATTGTGAAAAATTTAGAAATAAAACTTGTAAA
1 TTCTAAATTAAGCCCAAACGGCAAAAAATTTAGAAATAAAACTTGTAAA
9707301 GTAAAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 4 0.10
53 38 0.90
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (53 bp):
TTCTAAATTAAGCCCAAACGGCAAAAAATTTAGAAATAAAACTTGTAAAATAA
Found at i:9709867 original size:18 final size:18
Alignment explanation
Indices: 9709840--9709966 Score: 100
Period size: 18 Copynumber: 7.1 Consensus size: 18
9709830 CCTTTGTTCT
9709840 TGATACATTTGAGGTGGA
1 TGATACATTTGAGGTGGA
*
9709858 TGATATATTTGA---GGA
1 TGATACATTTGAGGTGGA
* *
9709873 TGATGCATTTGTGGTGGA
1 TGATACATTTGAGGTGGA
* * * *
9709891 GGGTACATTTGTGGT-AA
1 TGATACATTTGAGGTGGA
9709908 CTGATACATTTGAGGTGGA
1 -TGATACATTTGAGGTGGA
* *
9709927 GGATATATTTGAAGAGGTGGA
1 TGATACATTT---GAGGTGGA
*
9709948 GGATACATTTGAGGTGGA
1 TGATACATTTGAGGTGGA
9709966 T
1 T
9709967 AATAACCATA
Statistics
Matches: 85, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 54 0.64
19 1 0.01
21 17 0.20
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.34
Consensus pattern (18 bp):
TGATACATTTGAGGTGGA
Found at i:9709925 original size:36 final size:33
Alignment explanation
Indices: 9709840--9709938 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 33
9709830 CCTTTGTTCT
*
9709840 TGATACATTTGAGGTGGATGATATATTTGAGGA
1 TGATACATTTGAGGTGGAGGATATATTTGAGGA
* * * * *
9709873 TGATGCATTTGTGGTGGAGGGTACATTTGTGGTAA
1 TGATACATTTGAGGTGGAGGATATATTTGAGG--A
9709908 CTGATACATTTGAGGTGGAGGATATATTTGA
1 -TGATACATTTGAGGTGGAGGATATATTTGA
9709939 AGAGGTGGAG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
33 26 0.50
35 1 0.02
36 25 0.48
ACGTcount: A:0.26, C:0.05, G:0.32, T:0.36
Consensus pattern (33 bp):
TGATACATTTGAGGTGGAGGATATATTTGAGGA
Found at i:9709943 original size:21 final size:21
Alignment explanation
Indices: 9709919--9709959 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9709909 TGATACATTT
*
9709919 GAGGTGGAGGATATATTTGAA
1 GAGGTGGAGGATACATTTGAA
9709940 GAGGTGGAGGATACATTTGA
1 GAGGTGGAGGATACATTTGA
9709960 GGTGGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.39, T:0.27
Consensus pattern (21 bp):
GAGGTGGAGGATACATTTGAA
Found at i:9714068 original size:20 final size:19
Alignment explanation
Indices: 9714029--9714069 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9714019 AAACAACAAA
* *
9714029 AAAATTAAAATTCATGTAT
1 AAAATTAAAATTAATATAT
9714048 AAAATTATAAATTAATATAT
1 AAAATTA-AAATTAATATAT
9714068 AA
1 AA
9714070 CACAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTAAAATTAATATAT
Found at i:9714343 original size:40 final size:39
Alignment explanation
Indices: 9714299--9714441 Score: 117
Period size: 50 Copynumber: 3.4 Consensus size: 39
9714289 CCACCCCTAT
* *
9714299 CAATCCCTCTCCACCTTCCCCCCCAACATCCCACCACACC
1 CAATCCCTCCCCACCTT-CCCCCCAACACCCCACCACACC
* * *
9714339 CAATCCCTCCCCATCTTCCTCCCAACGCCCCACCACACCCAATCCTCAC
1 CAATCCCTCCCCACCTTCCCCCCAACACCCCA-C-CA--C-A----C-C
*
9714388 CTAATCCCTCCCCACCTTCCCCCCAACGCCCCACCACACC
1 C-AATCCCTCCCCACCTTCCCCCCAACACCCCACCACACC
9714428 CAAT-CCTCCCCACC
1 CAATCCCTCCCCACC
9714442 CCATCCAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
38 10 0.12
39 15 0.18
40 18 0.21
41 3 0.04
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 3 0.04
49 3 0.04
50 29 0.34
ACGTcount: A:0.22, C:0.62, G:0.01, T:0.15
Consensus pattern (39 bp):
CAATCCCTCCCCACCTTCCCCCCAACACCCCACCACACC
Found at i:9714374 original size:39 final size:40
Alignment explanation
Indices: 9714299--9714441 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
9714289 CCACCCCTAT
* *
9714299 CAATCCCTCTCCACCTTCCCCCCCAACATCCCACCACACC
1 CAATCCCTCCCCACCTTCCCCCCCAACACCCCACCACACC
* * *
9714339 CAATCCCTCCCCATCTTCCTCCCAACGCCCCACCACACCCAATCCTCACC
1 CAATCCCTCCCCA----CCTTCC--C-CCCCA--ACACCCCA-CCACACC
* *
9714389 TAATCCCTCCCCACCTT-CCCCCCAACGCCCCACCACACC
1 CAATCCCTCCCCACCTTCCCCCCCAACACCCCACCACACC
9714428 CAAT-CCTCCCCACC
1 CAATCCCTCCCCACC
9714442 CCATCCAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
38 10 0.12
39 9 0.11
40 18 0.22
42 5 0.06
43 1 0.01
44 5 0.06
45 1 0.01
46 4 0.05
47 5 0.06
49 6 0.07
50 18 0.22
ACGTcount: A:0.22, C:0.62, G:0.01, T:0.15
Consensus pattern (40 bp):
CAATCCCTCCCCACCTTCCCCCCCAACACCCCACCACACC
Found at i:9714399 original size:50 final size:50
Alignment explanation
Indices: 9714335--9714439 Score: 176
Period size: 50 Copynumber: 2.1 Consensus size: 50
9714325 CATCCCACCA
* *
9714335 CACCCAATCCCTCCCCATCTTCCTCCCAACGCCCCACCACACCCAATCCT
1 CACCCAATCCCTCCCCACCTTCCCCCCAACGCCCCACCACACCCAATCCT
*
9714385 CACCTAATCCCTCCCCACCTTCCCCCCAACGCCCCACCACACCCAATCCT
1 CACCCAATCCCTCCCCACCTTCCCCCCAACGCCCCACCACACCCAATCCT
9714435 C-CCCA
1 CACCCA
9714440 CCCCATCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 3 0.06
50 48 0.94
ACGTcount: A:0.22, C:0.62, G:0.02, T:0.14
Consensus pattern (50 bp):
CACCCAATCCCTCCCCACCTTCCCCCCAACGCCCCACCACACCCAATCCT
Found at i:9714438 original size:19 final size:19
Alignment explanation
Indices: 9714416--9714455 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9714406 CCCCCCAACG
*
9714416 CCCCACCACACCCAATCCT
1 CCCCACCACACCCAATACT
* *
9714435 CCCCACCCCATCCAATACT
1 CCCCACCACACCCAATACT
9714454 CC
1 CC
9714456 ACGTGCCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.62, G:0.00, T:0.12
Consensus pattern (19 bp):
CCCCACCACACCCAATACT
Found at i:9718533 original size:43 final size:43
Alignment explanation
Indices: 9718472--9718561 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
9718462 ATTAAAAGCA
9718472 TAAGAGGTAAAAAAAATCTTCAAACAAAACTTCAATAATAATT
1 TAAGAGGTAAAAAAAATCTTCAAACAAAACTTCAATAATAATT
9718515 TAAGAGGTAAAAAAAATCTTCAAACAAAACTTCAATAATAATT
1 TAAGAGGTAAAAAAAATCTTCAAACAAAACTTCAATAATAATT
9718558 TAAG
1 TAAG
9718562 TTATTAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.26
Consensus pattern (43 bp):
TAAGAGGTAAAAAAAATCTTCAAACAAAACTTCAATAATAATT
Found at i:9718650 original size:30 final size:30
Alignment explanation
Indices: 9718616--9718672 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
9718606 TTTGAATCAG
*
9718616 TTAAACATTTAAATATTTATTTGTACTCAT
1 TTAAACATTTAAATATATATTTGTACTCAT
* *
9718646 TTAAACCTTTAAATATATATTTTTACT
1 TTAAACATTTAAATATATATTTGTACT
9718673 TCAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (30 bp):
TTAAACATTTAAATATATATTTGTACTCAT
Found at i:9719308 original size:127 final size:126
Alignment explanation
Indices: 9719072--9719305 Score: 292
Period size: 127 Copynumber: 1.9 Consensus size: 126
9719062 AAATTATTAT
* * * * * * * *
9719072 AAAATTGATGTGTGATTTTTTTTTTCAAAATTATTATAATATTTTTATTAAATTATATATTAAAA
1 AAAATTGATATGTGATATTTTATTTAAAAATTACTATAATACTATTATTAAATTACATATTAAAA
9719137 TTGTAACATAATTGAAAATTAATCACAAATTAAATTATTAAAATATTATTATTATTTTTTA
66 TTGTAACATAATTGAAAATTAATCACAAATTAAATTATTAAAATATTATTATTATTTTTTA
* *
9719198 AAAATTTGATATGTGATATTTTATTTAAAAATTACTATAATCCTATTATTAAATTACATA-TGAA
1 AAAA-TTGATATGTGATATTTTATTTAAAAATTACTATAATACTATTATTAAATTACATATTAAA
* * * * * *
9719262 GTTTTAATATAATAT-AAAATTAATTATATATTAAATTATTAAAA
65 ATTGTAACATAAT-TGAAAATTAATCACAAATTAAATTATTAAAA
9719306 ATACTTTTAT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
126 43 0.48
127 47 0.52
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (126 bp):
AAAATTGATATGTGATATTTTATTTAAAAATTACTATAATACTATTATTAAATTACATATTAAAA
TTGTAACATAATTGAAAATTAATCACAAATTAAATTATTAAAATATTATTATTATTTTTTA
Found at i:9719559 original size:59 final size:59
Alignment explanation
Indices: 9719496--9719739 Score: 178
Period size: 59 Copynumber: 4.1 Consensus size: 59
9719486 CAAATTTACC
*
9719496 ATAATGACATTTTACTATAATTATAAAAATATTTTTTCTCATAATTAGTTAAAATTATT
1 ATAATGACATTTTATTATAATTATAAAAATATTTTTTCTCATAATTAGTTAAAATTATT
* * * * ** *
9719555 ATAAT-ACCATTTTGTTATAATTAGAGAAATA--TTTCCTACAGTAATTAACTAAAATTATA
1 ATAATGA-CATTTTATTATAATTATAAAAATATTTTTTCT-CA-TAATTAGTTAAAATTATT
* * * *
9719614 ATAATGTA-TTTTTATTATAATTATAAAAATATTTTTTATTATAATT-GATCAAAATTATT
1 ATAATG-ACATTTTATTATAATTATAAAAATATTTTTTCTCATAATTAG-TTAAAATTATT
* * * * * * *
9719673 ATAAT-ATC-TTCGTATCATACTTATGAAAATGTCTTTATTATCATAATTAAATTAAAATTATT
1 ATAATGA-CATT-TTATTATAATTATAAAAATAT-TTT-TTCTCATAATT-AGTTAAAATTATT
9719735 ATAAT
1 ATAAT
9719740 ATTATTATAT
Statistics
Matches: 143, Mismatches: 27, Indels: 27
0.73 0.14 0.14
Matches are distributed among these distances:
57 6 0.04
58 5 0.03
59 98 0.69
60 4 0.03
61 15 0.10
62 15 0.10
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (59 bp):
ATAATGACATTTTATTATAATTATAAAAATATTTTTTCTCATAATTAGTTAAAATTATT
Found at i:9719654 original size:24 final size:25
Alignment explanation
Indices: 9719607--9719672 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
9719597 AATTAACTAA
* *
9719607 AATTATAATAATGTATTTTTATTAT
1 AATTATAAAAATATATTTTTATTAT
9719632 AATTATAAAAATAT-TTTTTATTAT
1 AATTATAAAAATATATTTTTATTAT
*
9719656 AATTGATCAAAAT-TATT
1 AATT-ATAAAAATATATT
9719673 ATAATATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 15 0.42
25 21 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (25 bp):
AATTATAAAAATATATTTTTATTAT
Found at i:9739709 original size:8 final size:8
Alignment explanation
Indices: 9739698--9739722 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9739688 AAGTATTAAG
9739698 ATTAGACC
1 ATTAGACC
9739706 ATTAGACC
1 ATTAGACC
9739714 ATTAGACC
1 ATTAGACC
9739722 A
1 A
9739723 ATTAAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (8 bp):
ATTAGACC
Found at i:9743827 original size:273 final size:274
Alignment explanation
Indices: 9743339--9743886 Score: 773
Period size: 273 Copynumber: 2.0 Consensus size: 274
9743329 CTAAATTAAA
*
9743339 TATCACTATTTCAGCTGCCTTGTCATTCATAACATTTTCATTGTTACGTGTAAGAGAAAGAATAT
1 TATCACTATTTCAACTGCCTTGTCATTCATAACATTTTCATTGTTACGTGTAAGAGAAAGAATAT
* * * *
9743404 GAACCTTACCACATAATGGTGGAATTTTACTAGCTTCTTGTTTTTATAAAGGTACAACATTAATT
66 GAACCTTACCACATAATGGTAGAATTTCACTAGCTTCTTATTTTTACAAAGGTACAACATTAATT
* * *
9743469 ATTGTAATGACGAAATAGAACTTATAAAAAGTAAACTTTATATTCATTTAATTGAGTGCAACAAA
131 ATTGTAATGACAAAATAGAACTTATAAAAAGTAAACTTCATATTCATTTAACTGAGTGCAACAAA
* * * * *
9743534 GAAAATTGATGTATGTATCAAGGTTTGAATAAT-CTTCAAGAATGATTTTGTTGTGCAATGAAGC
196 GAAAATTGATATATGTATCAAAGTTTGAATAATCCTT-AAGAATCATTTTGTTATGCAATAAAGC
9743598 TCATCTAATTTTGAG
260 TCATCTAATTTTGAG
* * **
9743613 TATCACTATTTCAACTGCCTTGTCATTTATAACATTTTCATAT-TTATGTGTGCGAGAAAGAATA
1 TATCACTATTTCAACTGCCTTGTCATTCATAACATTTTCAT-TGTTACGTGTAAGAGAAAGAATA
* * * * *
9743677 T-ACACTTTAGCACATGATGGTAGAATTTCATTAGCTTCTTATTTTTACAAA-GTACAATATTAA
65 TGA-ACCTTACCACATAATGGTAGAATTTCACTAGCTTCTTATTTTTACAAAGGTACAACATTAA
* **
9743740 TTATTGTAATGACAAAATATAA-TATATAAAAAGTAAACTTCATATTCATTTAACTGAGTGTGAC
129 TTATTGTAATGACAAAATAGAACT-TATAAAAAGTAAACTTCATATTCATTTAACTGAGTGCAAC
* * *
9743804 AAGGAAAATTGATATATGTATCAAAGTTTGAATGATCCTTGAGAATCATTTTGTTATGCAATAAA
193 AAAGAAAATTGATATATGTATCAAAGTTTGAATAATCCTTAAGAATCATTTTGTTATGCAATAAA
9743869 GCTCATCTAATTTTGAG
258 GCTCATCTAATTTTGAG
9743886 T
1 T
9743887 GGTTTGTTTT
Statistics
Matches: 242, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
272 1 0.00
273 139 0.57
274 101 0.42
275 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (274 bp):
TATCACTATTTCAACTGCCTTGTCATTCATAACATTTTCATTGTTACGTGTAAGAGAAAGAATAT
GAACCTTACCACATAATGGTAGAATTTCACTAGCTTCTTATTTTTACAAAGGTACAACATTAATT
ATTGTAATGACAAAATAGAACTTATAAAAAGTAAACTTCATATTCATTTAACTGAGTGCAACAAA
GAAAATTGATATATGTATCAAAGTTTGAATAATCCTTAAGAATCATTTTGTTATGCAATAAAGCT
CATCTAATTTTGAG
Found at i:9750772 original size:20 final size:20
Alignment explanation
Indices: 9750747--9750793 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
9750737 TTTGCAAAGA
9750747 TTTTTATTTGA-AAAAGATTT
1 TTTTTATTT-ACAAAAGATTT
9750767 TTTTTATTTACTGAAAAGATTT
1 TTTTTATTTAC--AAAAGATTT
9750789 TTTTT
1 TTTTT
9750794 TGTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
22 14 0.58
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTTATTTACAAAAGATTT
Found at i:9751003 original size:16 final size:16
Alignment explanation
Indices: 9750938--9751004 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
9750928 CAAATTTCTC
9750938 AAAAATAAAACTAAAA-
1 AAAAATAAAA-TAAAAT
*
9750954 AAATAAT-AAA-AAACT
1 AAA-AATAAAATAAAAT
* *
9750969 AAAAATAAAATGAATT
1 AAAAATAAAATAAAAT
*
9750985 AAAAATAAGATAAAAT
1 AAAAATAAAATAAAAT
9751001 AAAA
1 AAAA
9751005 TCTGAGACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 26 0.63
17 3 0.07
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Done.