Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 14 of 208
Found at i:4296293 original size:19 final size:18
Alignment explanation
Indices: 4296251--4296293 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4296241 GTGAATATTT
* *
4296251 TTATAATTTTTAATTATG
1 TTATAATTTTTAAATAAG
*
4296269 TAATAATTTTTTAAATAAG
1 TTATAA-TTTTTAAATAAG
4296288 TTATAA
1 TTATAA
4296294 GTTTAATCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATAATTTTTAAATAAG
Found at i:4312396 original size:30 final size:30
Alignment explanation
Indices: 4312362--4312422 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4312352 CCTTAAAAGG
*
4312362 ATTAAAAAAGATTTTAGTTGAGCCATAAAA
1 ATTAAAAAAGATTTTAGTTAAGCCATAAAA
* * *
4312392 ATTAAGAAGGATTTTAGTTAAGCCATTAAA
1 ATTAAAAAAGATTTTAGTTAAGCCATAAAA
4312422 A
1 A
4312423 CTAGGAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (30 bp):
ATTAAAAAAGATTTTAGTTAAGCCATAAAA
Found at i:4314937 original size:125 final size:125
Alignment explanation
Indices: 4314701--4315012 Score: 475
Period size: 125 Copynumber: 2.5 Consensus size: 125
4314691 AACTTTTCTT
* * *
4314701 TAGTGATATATTGCTTGAGAACCATTCA-CTTATTCGTATCATCCATGGTCGAATCATGTTTTTA
1 TAGTGATATATTGCTTGAGCACCATT-ATCTTATTCGTATCATCCATGGTTGAATCTTGTTTTTA
* * * **
4314765 ACACTAAGCTGCATTAGTTGAAATCAACCCTGAAGAACTTTTCTTTTACATGTTTCTATTC
65 ACACTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTATAATTTTACATGTTTCTATTC
* *
4314826 TAGTGATATATTGCTTGAGCACCATTTTCTTATTTGTATCATCCATGGTTGAATCTTGTTTTTAA
1 TAGTGATATATTGCTTGAGCACCATTATCTTATTCGTATCATCCATGGTTGAATCTTGTTTTTAA
*
4314891 CGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTATAATTTTACATGTTTCTATTC
66 CACTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTATAATTTTACATGTTTCTATTC
* * *
4314951 TAGTG-TATATTGCTTGAGCACCATTATCTTATTCATATCATCCATGGTTGAGTCTTATTTTT
1 TAGTGATATATTGCTTGAGCACCATTATCTTATTCGTATCATCCATGGTTGAATCTTGTTTTT
4315013 CAACCTGAAA
Statistics
Matches: 170, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
124 52 0.31
125 118 0.69
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (125 bp):
TAGTGATATATTGCTTGAGCACCATTATCTTATTCGTATCATCCATGGTTGAATCTTGTTTTTAA
CACTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTATAATTTTACATGTTTCTATTC
Found at i:4315094 original size:224 final size:227
Alignment explanation
Indices: 4314800--4315231 Score: 665
Period size: 224 Copynumber: 1.9 Consensus size: 227
4314790 AACCCTGAAG
* * *
4314800 AACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTTTCTTATTTGTAT
1 AACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTAT
* **
4314865 CATCCATGGTTGAATC-T-TGTTTTTA-ACGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAA
66 CATCCATGATCAAATCATGTGTTTTTATA-GCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAA
*
4314927 CTATAATTTTACATGTTTCTATTCTAGTG-TATATTGCTTGAGCACCATTATCTTATTCATATCA
130 CTATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCATATCA
4314991 TCCATGGTTGAGTCTTATTTTTCAACCTGAAAA
195 TCCATGGTTGAGTCTTATTTTTCAACCTGAAAA
*
4315024 AACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTGT
1 AACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTAT
* * * *
4315089 CATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATCTACCTGGAAAAAC
66 CATCCATGATCAAATCATGTGTTTTTATAGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAAC
* ** * * *
4315154 TTTTCTTTTTCATGTTTGTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCGTATCAT
131 TATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCATATCAT
4315219 CCATGGTTGAGTC
196 CCATGGTTGAGTC
4315232 ATGTTTTTAA
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
224 74 0.40
225 1 0.01
226 63 0.34
227 48 0.26
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (227 bp):
AACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTAT
CATCCATGATCAAATCATGTGTTTTTATAGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAAC
TATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCATATCAT
CCATGGTTGAGTCTTATTTTTCAACCTGAAAA
Found at i:4315112 original size:100 final size:99
Alignment explanation
Indices: 4314933--4315112 Score: 270
Period size: 100 Copynumber: 1.8 Consensus size: 99
4314923 AAAACTATAA
* *
4314933 TTTTACATGTTTCTATTCTAGTGTATATTGCTTGAGCACCATTATCTTATTCATATCATCCATGG
1 TTTTACATGTTTCTATTCTAGTGTATATTGCTTGACCACCATTATCTTATTCATATCATCCATGA
** * *
4314998 TTGAGTCTTATTTTTCAACCTGAAAAAACTTTTC
66 TCAAATCATATTTTTCAACCTGAAAAAACTTTTC
* *
4315032 TTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTGTCATCCATG
1 TTTTACATGTTTCTATTCTAGTG-TATATTGCTTGACCACCATTATCTTATTCATATCATCCATG
*
4315097 ATCAAATCATGTTTTT
65 ATCAAATCATATTTTT
4315113 TTATAGCTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 23 0.32
100 48 0.68
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.46
Consensus pattern (99 bp):
TTTTACATGTTTCTATTCTAGTGTATATTGCTTGACCACCATTATCTTATTCATATCATCCATGA
TCAAATCATATTTTTCAACCTGAAAAAACTTTTC
Found at i:4315526 original size:127 final size:127
Alignment explanation
Indices: 4315021--4315736 Score: 680
Period size: 127 Copynumber: 5.6 Consensus size: 127
4315011 TTCAACCTGA
4315021 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
* * * **
4315086 TGTCATCCATGATCAAATCATGTTTTTT-TATAGCTAAGCTGCGTTAGTTGAAATCT-ACCTGG
66 TATCATCCATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATT-GTTGAAAT-TAACCCAG
* * **
4315148 AAAAACTTTTCTTTTTCATGTTTGTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
** * * * *
4315213 TATCATCCATGGTTGAGTCATG-TTTTTA-A-AGCTAAGCTGCATTAATTGCAATCAACCC-G
66 TATCATCCATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATT-GTTGAAATTAACCCAG
*
4315272 AAAAAACTTTTCTTTTACATGATTCTATTCTAGTGATATATTGCTTGAACAGCTTGAACACCATT
1 -AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTG---A-C-----CACCATT
* ** ** * *
4315337 TTCTTTATTCGTATCATCCATAATTGAATCATG-TTTTTCTATAGCTAAGCTGCATCAGTTGAAA
56 ATC-TTATTCGTATCATCCATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCAT-TGTTGAAA
*
4315401 TTGACCCAG
119 TTAACCCAG
4315410 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCA-CATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
** *
4315474 TATCATTTATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTGTTTGAAATTGACCCAG
66 TATCATCCATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTG-TTGAAATTAACCCAG
* * *
4315537 AAAAACTTTTCTTTTTTACATG----T-TTCTAGTGATATATTGCCTGAGCACCATTCA-ATTAT
1 AAAAACTTTTC--TTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATT-ATCTTAT
* * * *
4315596 TCATATCATCCATGGT-AGGAT-A-GTATTTTTA-A-AGCTAAGCTGCATTAGTTGAAATCAATC
63 TCGTATCATCCATGGTCA-AATCATGT-TTTTTATATAGCTAAGCTGCATT-GTTGAAATTAACC
4315656 CAG
125 CAG
* * * * * * ***
4315659 TAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATATATTGCTCGAGCACTGGTATCTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGATATATTGCTTGACCACCATTATCTTATTC
* *
4315723 ATGTCATCCATGGT
65 GTATCATCCATGGT
4315737 TGAATAAGGT
Statistics
Matches: 497, Mismatches: 59, Indels: 68
0.80 0.09 0.11
Matches are distributed among these distances:
120 9 0.02
122 34 0.07
123 4 0.01
124 33 0.07
125 130 0.26
126 33 0.07
127 131 0.26
128 3 0.01
129 9 0.02
133 1 0.00
134 9 0.02
135 31 0.06
136 1 0.00
137 68 0.14
138 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (127 bp):
AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
TATCATCCATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTGTTGAAATTAACCCAG
Found at i:4315721 original size:125 final size:125
Alignment explanation
Indices: 4315363--4315736 Score: 378
Period size: 125 Copynumber: 3.0 Consensus size: 125
4315353 TCCATAATTG
* *
4315363 AATCATG-TTTTTCTATAGCTAAGCTGCATCAGTTGAAATTGACCCAGAAAAACTTTTCTTTTAC
1 AATCATGTTTTTTATATAGCTAAGCTGCATTAGTTGAAATTGACCCAGAAAAACTTTTCTTTTAC
* * * **
4315427 ATGTTTCTATTCTAGTGATATATTGCTTGACCACATTATCTTATTCGTATCATTTATGGTCA
66 ATGTTTCTATTCT-GTGATATATTGCTCGAGCAC-TTATCTTATTCATATCATCCATGGTCA
4315489 AATCATGTTTTTTATATAGCTAAGCTGCATT-GTTTGAAATTGACCCAGAAAAACTTTTCTTTTT
1 AATCATGTTTTTTATATAGCTAAGCTGCATTAG-TTGAAATTGACCCAGAAAAACTTTTC--TTT
*
4315553 TACATGTTTCTA----GTGATATATTGC-CTGAGCACCATTCA-ATTATTCATATCATCCATGGT
63 TACATGTTTCTATTCTGTGATATATTGCTC-GAGCA-C-TT-ATCTTATTCATATCATCCATGGT
4315612 -A
124 CA
* ** * * * *
4315613 GGAT-A-GTATTTTTA-A-AGCTAAGCTGCATTAGTTGAAATCAATCCAGTAAAGCTTATCTTTT
1 -AATCATGT-TTTTTATATAGCTAAGCTGCATTAGTTGAAATTGACCCAGAAAAACTTTTCTTTT
* *
4315674 ACATGTTCCTATTCCTGTGATATATTGCTCGAGCACTGGTATCTTATTCATGTCATCCATGGT
64 ACATGTTTCTATT-CTGTGATATATTGCTCGAGCACT--TATCTTATTCATATCATCCATGGT
4315737 TGAATAAGGT
Statistics
Matches: 211, Mismatches: 18, Indels: 39
0.79 0.07 0.15
Matches are distributed among these distances:
120 14 0.07
122 34 0.16
123 5 0.02
124 26 0.12
125 60 0.28
126 10 0.05
127 47 0.22
129 15 0.07
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (125 bp):
AATCATGTTTTTTATATAGCTAAGCTGCATTAGTTGAAATTGACCCAGAAAAACTTTTCTTTTAC
ATGTTTCTATTCTGTGATATATTGCTCGAGCACTTATCTTATTCATATCATCCATGGTCA
Found at i:4327938 original size:2 final size:2
Alignment explanation
Indices: 4327931--4327958 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4327921 TTGGTAAATA
4327931 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
4327959 NNNNNNNNNN
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:4328454 original size:28 final size:27
Alignment explanation
Indices: 4328410--4328468 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
4328400 ATATTTATAT
*
4328410 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTGAA-AATTTTA
* *
4328438 TATATT-TTTTATTTATTGAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTA
4328465 TATA
1 TATA
4328469 GTCATCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TATATTATTTTAATATTGAAAATTTTA
Found at i:4334069 original size:52 final size:48
Alignment explanation
Indices: 4334050--4334357 Score: 326
Period size: 46 Copynumber: 6.3 Consensus size: 48
4334040 TGACAAGTGG
* *
4334050 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
4334096 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
4334142 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AA
*
4334191 TGGAAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 ---AAAGT-G--A-T-AA--GTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
4334253 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* ** *
4334299 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
4334345 AAAGTGATAAGTG
1 AAAGTGATAAGTG
4334358 GCTACACTTA
Statistics
Matches: 233, Mismatches: 13, Indels: 32
0.84 0.05 0.12
Matches are distributed among these distances:
46 143 0.61
52 39 0.17
53 1 0.00
54 1 0.00
55 2 0.01
56 2 0.01
57 1 0.00
58 1 0.00
59 42 0.18
62 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:4334208 original size:59 final size:55
Alignment explanation
Indices: 4334135--4334301 Score: 232
Period size: 52 Copynumber: 3.0 Consensus size: 55
4334125 TTATCTGATC
*
4334135 AAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAATGGA
1 AAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AA---A
*
4334195 AAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC---
1 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAA
* *
4334247 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAA
1 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAA
4334302 GTGATAAGTA
Statistics
Matches: 99, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
52 49 0.49
59 45 0.45
60 5 0.05
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (55 bp):
AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAA
Found at i:4334460 original size:36 final size:37
Alignment explanation
Indices: 4334321--4334502 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
4334311 AATAGCTTTA
*
4334321 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4334358 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4334395 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
4334432 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
4334468 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4334503 ATCATACGTA
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
35 11 0.08
36 39 0.28
37 90 0.64
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:4337700 original size:6 final size:6
Alignment explanation
Indices: 4337689--4337730 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
4337679 AGAAAATTCT
4337689 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
4337731 GTGACAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:4345741 original size:14 final size:14
Alignment explanation
Indices: 4345705--4345734 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4345695 AAGTGAAGAA
*
4345705 AAAAATTTAATAGT
1 AAAAATTTAATAAT
4345719 AAAAATTTAATAAT
1 AAAAATTTAATAAT
4345733 AA
1 AA
4345735 GATTTTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAAATTTAATAAT
Found at i:4346866 original size:11 final size:11
Alignment explanation
Indices: 4346852--4346923 Score: 71
Period size: 11 Copynumber: 6.8 Consensus size: 11
4346842 TTTATTTTTA
4346852 TTTTAAAATAC
1 TTTTAAAATAC
4346863 TTTTAAAATAC
1 TTTTAAAATAC
4346874 TTTTTAAAAT--
1 -TTTTAAAATAC
**
4346884 TTTTTTAA-A-
1 TTTTAAAATAC
*
4346893 TTTGAAAATAC
1 TTTTAAAATAC
4346904 TTTTAAAATAC
1 TTTTAAAATAC
*
4346915 TTTTTAAAT
1 TTTTAAAAT
4346924 TTTTTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 11 0.22
10 1 0.02
11 29 0.58
12 9 0.18
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:4346902 original size:30 final size:30
Alignment explanation
Indices: 4346867--4346925 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4346857 AAATACTTTT
*
4346867 AAAATACTTTTTAAAAT-TTTTTTAAATTTG
1 AAAATAC-TTTTAAAATACTTTTTAAATTTG
4346897 AAAATACTTTTAAAATACTTTTTAAATTT
1 AAAATACTTTTAAAATACTTTTTAAATTT
4346926 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (30 bp):
AAAATACTTTTAAAATACTTTTTAAATTTG
Found at i:4346941 original size:18 final size:18
Alignment explanation
Indices: 4346915--4346954 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4346905 TTTAAAATAC
* *
4346915 TTTTTAAATTTTTTTTTA
1 TTTTAAAATTTTTTTTAA
4346933 TTTTAAAATTTTTTTTAA
1 TTTTAAAATTTTTTTTAA
4346951 TTTT
1 TTTT
4346955 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTAAAATTTTTTTTAA
Found at i:4346950 original size:41 final size:41
Alignment explanation
Indices: 4346841--4346941 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
4346831 ATAAATATAT
4346841 TTTTATTTTTATTTTAAAATACTTTTAAAATACTTTTTAAAA
1 TTTT-TTTTTATTTTAAAATACTTTTAAAATACTTTTTAAAA
** *
4346883 TTTTTTTAAATTTGAAAATACTTTTAAAATACTTTTT-AAA
1 TTTTTTTTTATTTTAAAATACTTTTAAAATACTTTTTAAAA
4346923 TTTTTTTTTATTTTAAAAT
1 TTTTTTTTTATTTTAAAAT
4346942 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 19 0.36
41 30 0.57
42 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (41 bp):
TTTTTTTTTATTTTAAAATACTTTTAAAATACTTTTTAAAA
Found at i:4346975 original size:28 final size:28
Alignment explanation
Indices: 4346875--4346976 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
4346865 TTAAAATACT
* ****
4346875 TTTTAAAATTTTTTTAAATTTGAAAATA
1 TTTTAAAATATTTTTAAATTTTTTTATA
*
4346903 CTTTTAAAATACTTTTTAAATTTTTTTTTA
1 -TTTTAAAATA-TTTTTAAATTTTTTTATA
* *
4346933 TTTTAAAATTTTTTTTAATTTTTTTA-A
1 TTTTAAAATATTTTTAAATTTTTTTATA
4346960 TTTTTAAAATGATTTTT
1 -TTTTAAAAT-ATTTTT
4346977 TGGTATTTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.02
28 23 0.38
29 23 0.38
30 13 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTAAAATATTTTTAAATTTTTTTATA
Found at i:4349644 original size:32 final size:32
Alignment explanation
Indices: 4349580--4349647 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
4349570 AGAAGTAATT
* * * *
4349580 TTTTTTGACAAGTTTAGGCACCAATTAGGTAC
1 TTTTTGGACAAGTTCAGGCACCAACTAAGTAC
* *
4349612 TTTTTGGACAAGTTCAGGTACTAACTAAGTAC
1 TTTTTGGACAAGTTCAGGCACCAACTAAGTAC
4349644 TTTT
1 TTTT
4349648 GGGGAAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
TTTTTGGACAAGTTCAGGCACCAACTAAGTAC
Found at i:4353103 original size:22 final size:22
Alignment explanation
Indices: 4353077--4353152 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
4353067 TTCTCATTTT
4353077 TCTTGTGTTTTCCATTTATGCC
1 TCTTGTGTTTTCCATTTATGCC
4353099 TCTTGTGTGTGATTTTCTCATTT-T---
1 TC---T-TGTG-TTTTC-CATTTATGCC
4353123 TCTTGTGTTTTCCATTTATGCC
1 TCTTGTGTTTTCCATTTATGCC
4353145 TCTTGTGT
1 TCTTGTGT
4353153 GTGATTATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 20
0.69 0.00 0.31
Matches are distributed among these distances:
18 5 0.11
19 6 0.14
20 4 0.09
21 1 0.02
22 10 0.23
24 2 0.05
25 1 0.02
26 4 0.09
27 6 0.14
28 5 0.11
ACGTcount: A:0.08, C:0.18, G:0.16, T:0.58
Consensus pattern (22 bp):
TCTTGTGTTTTCCATTTATGCC
Found at i:4353117 original size:46 final size:46
Alignment explanation
Indices: 4353065--4353158 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
4353055 GAACCCAAGC
4353065 TTTTCTCATTTTTCTTGTGTTTTCCATTTATGCCTCTTGTGTGTGA
1 TTTTCTCATTTTTCTTGTGTTTTCCATTTATGCCTCTTGTGTGTGA
4353111 TTTTCTCATTTTTCTTGTGTTTTCCATTTATGCCTCTTGTGTGTGA
1 TTTTCTCATTTTTCTTGTGTTTTCCATTTATGCCTCTTGTGTGTGA
4353157 TT
1 TT
4353159 ATCTTGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.09, C:0.17, G:0.15, T:0.60
Consensus pattern (46 bp):
TTTTCTCATTTTTCTTGTGTTTTCCATTTATGCCTCTTGTGTGTGA
Found at i:4353153 original size:24 final size:24
Alignment explanation
Indices: 4353080--4353154 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
4353070 TCATTTTTCT
4353080 TGTGTTTTCCATTTATGCCTCTTGTG
1 TGTGTTTTCCATTTATGCCTC-T-TG
4353106 TGTGATTTTCTCATTT-T---TC-T-
1 TGTG-TTTTC-CATTTATGCCTCTTG
4353126 TGTGTTTTCCATTTATGCCTCTTG
1 TGTGTTTTCCATTTATGCCTCTTG
4353150 TGTGT
1 TGTGT
4353155 GATTATCTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 4 0.10
21 1 0.02
22 2 0.05
23 1 0.02
24 7 0.17
26 4 0.10
27 6 0.15
28 5 0.12
ACGTcount: A:0.08, C:0.17, G:0.17, T:0.57
Consensus pattern (24 bp):
TGTGTTTTCCATTTATGCCTCTTG
Found at i:4359872 original size:3 final size:3
Alignment explanation
Indices: 4359864--4359891 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4359854 ATATATGGTA
4359864 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
4359892 CTGGTGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:4364358 original size:5 final size:5
Alignment explanation
Indices: 4364346--4364378 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4364336 TTGTTTTTGT
*
4364346 TTGGG TTGAG TTGGG TTGGG TTGGG TTGGG TTG
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTG
4364379 AGCTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.55, T:0.42
Consensus pattern (5 bp):
TTGGG
Found at i:4364680 original size:29 final size:28
Alignment explanation
Indices: 4364625--4364681 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
4364615 TAATTAATTG
*
4364625 ATGAATTTAATTTTTTTAATTAGTTATAT
1 ATGAATTTAATTTTTGTAATTA-TTATAT
4364654 ATGAACTTTAATTTTATGTAATT-TTATA
1 ATGAA-TTTAATTTT-TGTAATTATTATA
4364682 CCTCGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 10 0.40
30 9 0.36
31 6 0.24
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (28 bp):
ATGAATTTAATTTTTGTAATTATTATAT
Found at i:4365965 original size:9 final size:9
Alignment explanation
Indices: 4365940--4365973 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
4365930 CTAATTAATT
4365940 TTAAATTAA
1 TTAAATTAA
* *
4365949 TCATATTAA
1 TTAAATTAA
4365958 TTAAATTAA
1 TTAAATTAA
4365967 TTAAATT
1 TTAAATT
4365974 TAGATCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAATTAA
Found at i:4367386 original size:4 final size:4
Alignment explanation
Indices: 4367379--4367405 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4367369 ATCAACCAAT
4367379 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
4367406 TATTTGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:4371969 original size:22 final size:20
Alignment explanation
Indices: 4371944--4371997 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
4371934 GTTACAATAT
4371944 AATAGCGAAATGACAACAAAAC
1 AATAGCGAAA--ACAACAAAAC
*
4371966 AATAACGAACAACAACAAAAC
1 AATAGCGAA-AACAACAAAAC
* *
4371987 ATTAGTGAAAA
1 AATAGCGAAAA
4371998 AGAAAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 8 0.30
23 1 0.04
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.11
Consensus pattern (20 bp):
AATAGCGAAAACAACAAAAC
Found at i:4373211 original size:11 final size:11
Alignment explanation
Indices: 4373166--4373214 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
4373156 TATTTTTTAA
*
4373166 TTTTAAAATAC
1 TTTTAAAATAT
*
4373177 TTTAAAAATAT
1 TTTTAAAATAT
**
4373188 TTTTAATTTTAT
1 TTTTAA-AATAT
4373200 TTTTAAAATAT
1 TTTTAAAATAT
4373211 TTTT
1 TTTT
4373215 TTTGTGTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4373231 original size:24 final size:23
Alignment explanation
Indices: 4373177--4373232 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
4373167 TTTAAAATAC
4373177 TTTAAAAATATTTTTAATTTTATT
1 TTTAAAAATATTTTT-ATTTTATT
*
4373201 TTT-AAAATATTTTT-TTTGTGTT
1 TTTAAAAATATTTTTATTT-TATT
4373223 TATTAAAAAT
1 T-TTAAAAAT
4373233 CGGGCCGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.11
22 4 0.14
23 13 0.46
24 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTAAAAATATTTTTATTTTATT
Found at i:4392063 original size:27 final size:28
Alignment explanation
Indices: 4392033--4392098 Score: 71
Period size: 32 Copynumber: 2.2 Consensus size: 28
4392023 AGTGTAAAAA
* *
4392033 TAGCGATG-ACGATGAGATTAGATATTG
1 TAGCGATGAACGATGAGATTACATACTG
4392060 TAGCGATACTGTAACGATGAGATTACATACTG
1 TAGCG--A-TG-AACGATGAGATTACATACTG
4392092 TAGCGAT
1 TAGCGAT
4392099 ACTGTAGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
27 5 0.16
29 2 0.06
30 3 0.09
32 22 0.69
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
TAGCGATGAACGATGAGATTACATACTG
Found at i:4392077 original size:32 final size:32
Alignment explanation
Indices: 4392041--4392109 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
4392031 AATAGCGATG
* *
4392041 ACGATGAGATTAGATATTGTAGCGATACTGTA
1 ACGATGAGATTACATACTGTAGCGATACTGTA
4392073 ACGATGAGATTACATACTGTAGCGATACTGTA
1 ACGATGAGATTACATACTGTAGCGATACTGTA
*
4392105 GCGAT
1 ACGAT
4392110 ACCAAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (32 bp):
ACGATGAGATTACATACTGTAGCGATACTGTA
Found at i:4392102 original size:11 final size:11
Alignment explanation
Indices: 4392086--4392111 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4392076 ATGAGATTAC
4392086 ATACTGTAGCG
1 ATACTGTAGCG
4392097 ATACTGTAGCG
1 ATACTGTAGCG
4392108 ATAC
1 ATAC
4392112 CAAACTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (11 bp):
ATACTGTAGCG
Found at i:4403305 original size:18 final size:18
Alignment explanation
Indices: 4403282--4403324 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4403272 GAATAGGTTT
*
4403282 TTAATTATATAATTTT-AA
1 TTAATTA-AAAATTTTAAA
4403300 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
4403318 TTAATTA
1 TTAATTA
4403325 CACCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:4407962 original size:21 final size:21
Alignment explanation
Indices: 4407920--4407963 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4407910 TGTATTTGAT
**
4407920 TTTAAATTTTTATGTAGTATA
1 TTTAAATTTTTATGTAAAATA
4407941 TTTAAATTTTTAT-TAAAAATA
1 TTTAAATTTTTATGT-AAAATA
4407962 TT
1 TT
4407964 CATATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAAATTTTTATGTAAAATA
Found at i:4420672 original size:58 final size:58
Alignment explanation
Indices: 4420552--4420682 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 58
4420542 GAATTTGAAT
* * * * * * *
4420552 TTTTTTTCAAGTTAAACACTGAACTTGACAATTGTTCCCACATTGGGGTTTAAACTTT
1 TTTTATTCAAGTTAGACCCAGAACTTGACAAATGTTCCCACATTGGGGCTTAAACTTA
* * *
4420610 TTTTA-TCTAAGTTAGACCCAGAACTTGACAAATGTTCTCACATTGGGGCTTCAAGTTA
1 TTTTATTC-AAGTTAGACCCAGAACTTGACAAATGTTCCCACATTGGGGCTTAAACTTA
4420668 TTTTATTCAAGTTAG
1 TTTTATTCAAGTTAG
4420683 TCCTTGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
57 2 0.03
58 57 0.93
59 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (58 bp):
TTTTATTCAAGTTAGACCCAGAACTTGACAAATGTTCCCACATTGGGGCTTAAACTTA
Found at i:4430863 original size:83 final size:83
Alignment explanation
Indices: 4430724--4430895 Score: 326
Period size: 83 Copynumber: 2.1 Consensus size: 83
4430714 TGTGCCATTG
*
4430724 TATCTTGAAGCTCTTTGGTAACCTAAAATCGACAGATTCTCATAAGGTGAAATACAAAACCTCCC
1 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
*
4430789 TAAATTTGTCATCACTAT
66 TAAATTTGTCATCACTAC
4430807 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
1 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
4430872 TAAATTTGTCATCACTAC
66 TAAATTTGTCATCACTAC
4430890 TATCTT
1 TATCTT
4430896 CACAGTCAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (83 bp):
TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
TAAATTTGTCATCACTAC
Found at i:4433038 original size:22 final size:22
Alignment explanation
Indices: 4433013--4433079 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
4433003 ATCACTAATA
4433013 CAGGAGCACATAAGTGCTAAAT
1 CAGGAGCACATAAGTGCTAAAT
*
4433035 CAGGAGCACCA-AAATGCTAAATT
1 CAGGAGCA-CATAAGTGCTAAA-T
*
4433058 CAAGAGCAC-TGAAGTGCTAAAT
1 CAGGAGCACAT-AAGTGCTAAAT
4433080 TAATGAACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (22 bp):
CAGGAGCACATAAGTGCTAAAT
Found at i:4433075 original size:23 final size:22
Alignment explanation
Indices: 4433016--4433080 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
4433006 ACTAATACAG
*
4433016 GAGCACATAAGTGCTAAA-TCAG
1 GAGCAC-TAAGTGCTAAATTCAA
* *
4433038 GAGCACCAAAATGCTAAATTCAA
1 GAGCA-CTAAGTGCTAAATTCAA
4433061 GAGCACTGAAGTGCTAAATT
1 GAGCACT-AAGTGCTAAATT
4433081 AATGAACCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (22 bp):
GAGCACTAAGTGCTAAATTCAA
Found at i:4441594 original size:19 final size:19
Alignment explanation
Indices: 4441567--4441610 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4441557 AAAAACAAAC
*
4441567 TATTTTATTACTATT-TTGT
1 TATTATATTACTATTATT-T
*
4441586 TATTATATTGCTATTATTT
1 TATTATATTACTATTATTT
4441605 TATTAT
1 TATTAT
4441611 TGTTATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTATATTACTATTATTT
Found at i:4448781 original size:7 final size:7
Alignment explanation
Indices: 4448769--4448798 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4448759 AATCTATATC
4448769 GAGAAGG
1 GAGAAGG
4448776 GAGAAGG
1 GAGAAGG
4448783 GAGAAGG
1 GAGAAGG
4448790 G-GAAGG
1 GAGAAGG
4448796 GAG
1 GAG
4448799 GTTTTGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (7 bp):
GAGAAGG
Found at i:4448788 original size:14 final size:13
Alignment explanation
Indices: 4448769--4448798 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
4448759 AATCTATATC
4448769 GAGAAGGGAGAAGG
1 GAGAAGGG-GAAGG
4448783 GAGAAGGGGAAGG
1 GAGAAGGGGAAGG
4448796 GAG
1 GAG
4448799 GTTTTGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (13 bp):
GAGAAGGGGAAGG
Found at i:4449616 original size:3 final size:3
Alignment explanation
Indices: 4449602--4449661 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
4449592 CTATTTTCCT
*
4449602 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4449650 TTA TTA TTA TTA
1 TTA TTA TTA TTA
4449662 CTTTATGTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4456897 original size:2 final size:2
Alignment explanation
Indices: 4456890--4456933 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4456880 TACGTACCAT
4456890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4456932 TA
1 TA
4456934 ATTTATTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4460245 original size:25 final size:26
Alignment explanation
Indices: 4460203--4460252 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
4460193 ACAAATTAAA
* *
4460203 TAAACATATAAAAGATTGAAACATTT
1 TAAACATAAAAAAAATTGAAACATTT
4460229 TAAA-ATAAAAAAAATTGAAACATT
1 TAAACATAAAAAAAATTGAAACATT
4460253 GAATTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (26 bp):
TAAACATAAAAAAAATTGAAACATTT
Found at i:4460859 original size:18 final size:18
Alignment explanation
Indices: 4460819--4460853 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
4460809 ATTTAAGGTG
4460819 TAATTAATTTATAATTTA
1 TAATTAATTTATAATTTA
4460837 TAATTAA-TTA-AATTTA
1 TAATTAATTTATAATTTA
4460853 T
1 T
4460854 TTAATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTAATTTATAATTTA
Found at i:4461249 original size:13 final size:13
Alignment explanation
Indices: 4461227--4461263 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4461217 GAGCCGGCCC
4461227 ATATTAAATATAT
1 ATATTAAATATAT
*
4461240 ATATTTAATATAT
1 ATATTAAATATAT
4461253 ATA--AAATATAT
1 ATATTAAATATAT
4461264 GTTTGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 7 0.32
13 15 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:4461259 original size:24 final size:24
Alignment explanation
Indices: 4461227--4461344 Score: 77
Period size: 24 Copynumber: 5.1 Consensus size: 24
4461217 GAGCCGGCCC
*
4461227 ATATTAAATATATATATTTAATAT
1 ATATAAAATATATATATTTAATAT
* * * *
4461251 ATATAAAATATATGT-TTGATTAA
1 ATATAAAATATATATATTTAATAT
* * * *
4461274 AAATAAAAAATATAT-TTTGATTAA
1 ATATAAAATATATATATTT-AATAT
* *
4461298 AAATAAAATATATATATTTGA-AT
1 ATATAAAATATATATATTTAATAT
*
4461321 A-A-AAAA-ATATGTATTTAATAT
1 ATATAAAATATATATATTTAATAT
4461342 ATA
1 ATA
4461345 ATTCGGGCCG
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 10 0.13
21 7 0.09
22 2 0.03
23 21 0.28
24 32 0.43
25 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATATAAAATATATATATTTAATAT
Found at i:4461261 original size:22 final size:23
Alignment explanation
Indices: 4461227--4461344 Score: 77
Period size: 23 Copynumber: 5.2 Consensus size: 23
4461217 GAGCCGGCCC
4461227 ATAT-TAAATATATATATTT-AAT
1 ATATATAAA-ATATATATTTGAAT
* *
4461249 ATATATAAAATATATGTTTGATT
1 ATATATAAAATATATATTTGAAT
* * * *
4461272 AAAAATAAAAAATATATTTTGATT
1 ATATATAAAATATATA-TTTGAAT
* *
4461296 AAAAATAAAATATATATATTTGAAT
1 ATATAT-AAA-ATATATATTTGAAT
*
4461321 A-A-A-AAAATATGTATTT-AAT
1 ATATATAAAATATATATTTGAAT
4461340 ATATA
1 ATATA
4461345 ATTCGGGCCG
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.05
20 10 0.12
21 4 0.05
22 13 0.16
23 19 0.24
24 14 0.17
25 10 0.12
26 6 0.08
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATATATAAAATATATATTTGAAT
Found at i:4461300 original size:25 final size:25
Alignment explanation
Indices: 4461255--4461325 Score: 108
Period size: 24 Copynumber: 2.9 Consensus size: 25
4461245 TAATATATAT
*
4461255 AAAATATATGTTTGATTAAAAATAA
1 AAAATATATATTTGATTAAAAATAA
4461280 AAAATATAT-TTTGATTAAAAATAA
1 AAAATATATATTTGATTAAAAATAA
* *
4461304 AATATATATATTTGAATAAAAA
1 AAAATATATATTTGATTAAAAA
4461326 AATATGTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 23 0.53
25 20 0.47
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
AAAATATATATTTGATTAAAAATAA
Found at i:4461325 original size:20 final size:19
Alignment explanation
Indices: 4461302--4461340 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4461292 GATTAAAAAT
*
4461302 AAAATATATATATTTGAATA
1 AAAAAATATATATTT-AATA
*
4461322 AAAAAATATGTATTTAATA
1 AAAAAATATATATTTAATA
4461341 TATAATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAAATATATATTTAATA
Found at i:4464988 original size:7 final size:7
Alignment explanation
Indices: 4464976--4465001 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4464966 TAAGGTTTTA
4464976 TTATTAT
1 TTATTAT
4464983 TTATTAT
1 TTATTAT
4464990 TTATTAT
1 TTATTAT
4464997 TTATT
1 TTATT
4465002 CACACTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:4467679 original size:31 final size:31
Alignment explanation
Indices: 4467641--4467703 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4467631 TAGCTTGAGC
4467641 TAGCTAATGAGGGGACTATTTTGCAAAATGG
1 TAGCTAATGAGGGGACTATTTTGCAAAATGG
4467672 TAGCTAATGAGGGGACTATTTTGCAAAATGG
1 TAGCTAATGAGGGGACTATTTTGCAAAATGG
4467703 T
1 T
4467704 TGGAAGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.30
Consensus pattern (31 bp):
TAGCTAATGAGGGGACTATTTTGCAAAATGG
Found at i:4468254 original size:2 final size:2
Alignment explanation
Indices: 4468249--4468282 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4468239 AAAAATGCAA
4468249 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
4468283 GTGTAGCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4468440 original size:42 final size:42
Alignment explanation
Indices: 4468390--4468489 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
4468380 CTATACGAAT
* *
4468390 GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
4468432 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
4468474 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
4468490 TACCAAGATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
Found at i:4470246 original size:2 final size:2
Alignment explanation
Indices: 4470239--4470273 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4470229 TCATAACTTT
4470239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4470274 GAAGATGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4473745 original size:36 final size:36
Alignment explanation
Indices: 4473674--4473758 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
4473664 AAACTGTCTA
* *
4473674 AAGGTCGCCTTAGACAAAGTTTATTCTAAGCTTTTT
1 AAGGTCGCCTTAGACAAAGTTTATCCTAACCTTTTT
* **
4473710 AAGGTTGCCTTAGAC-CGGTTTATCCTAACCTTTTTT
1 AAGGTCGCCTTAGACAAAGTTTATCCTAACC-TTTTT
4473746 AAAGGTCAGCCTT
1 -AAGGTC-GCCTT
4473759 GATTAGATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 11 0.28
36 19 0.47
37 5 0.12
38 5 0.12
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (36 bp):
AAGGTCGCCTTAGACAAAGTTTATCCTAACCTTTTT
Found at i:4479388 original size:31 final size:31
Alignment explanation
Indices: 4479353--4479419 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
4479343 CCACTAGCAA
* * *
4479353 TTTTCAGTTATAGACATAACGGAGCTACCAT
1 TTTTCAGTTACAAACATAACGGAACTACCAT
* * *
4479384 TTTTC-GTTACAAACTTAACGGAATTGCCAT
1 TTTTCAGTTACAAACATAACGGAACTACCAT
4479414 TTTTCA
1 TTTTCA
4479420 TCCCCTATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (31 bp):
TTTTCAGTTACAAACATAACGGAACTACCAT
Found at i:4480324 original size:30 final size:30
Alignment explanation
Indices: 4480290--4480354 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
4480280 TGGGAGATGG
*
4480290 AAAATGACAGCTCCGTTAAGTCTGTAACAA
1 AAAATGACAGCTCCGTTAAGTCTCTAACAA
** * * *
4480320 AAAATGGTAGCTCTGTTACGTCTCTAACAG
1 AAAATGACAGCTCCGTTAAGTCTCTAACAA
4480350 AAAAT
1 AAAAT
4480355 AGTTAGTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (30 bp):
AAAATGACAGCTCCGTTAAGTCTCTAACAA
Found at i:4481439 original size:2 final size:2
Alignment explanation
Indices: 4481434--4481466 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4481424 TTAAAAAAGA
*
4481434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4481467 ATTGGGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4484319 original size:26 final size:29
Alignment explanation
Indices: 4484285--4484353 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
4484275 CCCGGCTTGA
4484285 ATAT-ATTATATTA-TAAA-AATAATTAT
1 ATATAATTATATTATTAAATAATAATTAT
*
4484311 AT-TAATTATATATATTAAATAATTATTAT
1 ATATAATTATAT-TATTAAATAATAATTAT
*
4484340 ATATATTTATATTA
1 ATATAATTATATTA
4484354 AATTACTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 1 0.03
26 9 0.25
27 2 0.06
28 4 0.11
29 12 0.33
30 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATAATTATATTATTAAATAATAATTAT
Found at i:4484354 original size:26 final size:26
Alignment explanation
Indices: 4484285--4484356 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
4484275 CCCGGCTTGA
*
4484285 ATATA-TTATATTATAAAAATAATTAT
1 ATATATTTATATTA-AATAATAATTAT
* *
4484311 ATTAATTATATATATTAAATAATTATTAT
1 A-T-A-TATTTATATTAAATAATAATTAT
4484340 ATATATTTATATTAAAT
1 ATATATTTATATTAAAT
4484357 TACTAACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 14 0.37
27 2 0.05
28 2 0.05
29 13 0.34
30 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATATTTATATTAAATAATAATTAT
Found at i:4484358 original size:20 final size:19
Alignment explanation
Indices: 4484285--4484358 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 19
4484275 CCCGGCTTGA
*
4484285 ATATATTATATTATAA--AA
1 ATATATTATATTA-AATTAT
4484303 ATA-ATTATATT-AATTAT
1 ATATATTATATTAAATTAT
*
4484320 ATATATTA-AATAATTATTAT
1 ATATATTATATTAA--ATTAT
4484340 ATATATTTATATTAAATTA
1 ATATA-TTATATTAAATTA
4484359 CTAACCTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 2 0.04
17 14 0.31
18 8 0.18
20 14 0.31
21 3 0.07
22 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTATATTAAATTAT
Found at i:4488131 original size:9 final size:11
Alignment explanation
Indices: 4488109--4488133 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4488099 AAAAATAAAA
4488109 ATATTTATTAT
1 ATATTTATTAT
4488120 ATATTTATTAT
1 ATATTTATTAT
4488131 ATA
1 ATA
4488134 AATACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATTAT
Found at i:4497008 original size:21 final size:23
Alignment explanation
Indices: 4496968--4497009 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4496958 AACCTAGAGA
*
4496968 TTAAAAATCTTGGACTTGCATGG
1 TTAAAAATATTGGACTTGCATGG
4496991 TTAAAAA-ATTGG-CTTGCAT
1 TTAAAAATATTGGACTTGCAT
4497010 TCAATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (23 bp):
TTAAAAATATTGGACTTGCATGG
Found at i:4500707 original size:11 final size:10
Alignment explanation
Indices: 4500685--4500717 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
4500675 ATAATCTGGA
4500685 AAGAG-AAGG
1 AAGAGAAAGG
4500694 AAGAGAAGAGG
1 AAGAGAA-AGG
4500705 AAGAGAAAGG
1 AAGAGAAAGG
4500715 AAG
1 AAG
4500718 GATTACCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AAGAGAAAGG
Found at i:4504958 original size:2 final size:2
Alignment explanation
Indices: 4504951--4504996 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4504941 TGTTAGTGTA
4504951 AT AT AT 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 AT AT AT
4504993 AT AT
1 AT AT
4504997 GAAGCTTGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4512874 original size:13 final size:13
Alignment explanation
Indices: 4512856--4512881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4512846 TCATTTGTCG
4512856 TTTTCTATTTGTT
1 TTTTCTATTTGTT
4512869 TTTTCTATTTGTT
1 TTTTCTATTTGTT
4512882 GTTCTGTTGG
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:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTCTATTTGTT
Found at i:4513535 original size:82 final size:84
Alignment explanation
Indices: 4513409--4513571 Score: 258
Period size: 82 Copynumber: 2.0 Consensus size: 84
4513399 GGATGAGATT
* * * *
4513409 TGTGGTTTTAGTCTGCTCCACTACAACTTCAGGGAGCTAAGACTTGATGTGATCTGCTCCACTAC
1 TGTGGTTCTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCAACTAC
4513474 TGCTTAGGGAGATAAGGTC
66 TGCTTAGGGAGATAAGGTC
**
4513493 TGTGGTTCT-GTCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGATGCGATCTGCTCAACTAC
1 TGTGGTTCTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCAACTAC
4513556 TGCTTAGGGAGATAAG
66 TGCTTAGGGAGATAAG
4513572 ATCAGTAATC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
82 48 0.66
83 17 0.23
84 8 0.11
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (84 bp):
TGTGGTTCTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCAACTAC
TGCTTAGGGAGATAAGGTC
Found at i:4513558 original size:40 final size:40
Alignment explanation
Indices: 4513420--4513572 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
4513410 GTGGTTTTAG
** * *
4513420 TCTGCTCCACTACAACTTCAGGGAGCTAAGACTTGATGTGA
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGATGCGA
* * *
4513461 TCTGCTCCACTACTGCTTAGGGAGATAAGGTCTGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAA-GACT-TGATGC-GA
4513503 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
4513543 TCTGCTCAACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
4513573 TCAGTAATCT
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
39 1 0.01
40 42 0.43
41 22 0.23
42 31 0.32
43 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:4513732 original size:45 final size:45
Alignment explanation
Indices: 4513667--4514501 Score: 256
Period size: 44 Copynumber: 19.0 Consensus size: 45
4513657 AAAATCCGCC
* *
4513667 ATCTTCGATCTGCTTCGCTGTCAATGCAGGAATGCAAGATCTGCT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* *
4513712 ATCTTC-AGTCTGC-TCTGCTGTCAGTATAGGAAGGCAAGA-CTAG-T
1 ATCTTCGA-TCTGCTTC-GCTGTCAATACAGGAAGGCAAGATCT-GCT
* * *
4513756 TTCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * *
4513801 ATCTT-TAGCCTGCTCCGCTGTTAGTACAGGAAGGCAAGA-CTGGT
1 ATCTTCGA-TCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * *
4513845 TTCTTCGATCTGCTTCGCCGTCAGTATAGGAAGACAATATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * *
4513890 GTCTTC-AACTAGC-TCTGCT-AC-A-ACCGAGAGAGGCAAGGTTTG-T
1 ATCTTCGATCT-GCTTC-GCTGTCAATACAG-GA-AGGCAAGATCTGCT
* * * *
4513933 GTCTTCGATCTGCTTCGCTATCAATGCAGGAAGGCAAAATCTG-T
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * *
4513977 CATCTTC-AACTAGCTCCACTG-CAA-ACGAGGGAGGTAAGGT-T--T
1 -ATCTTCGATCT-GCTTCGCTGTCAATAC-AGGAAGGCAAGATCTGCT
* * * *
4514019 GTGTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * * *
4514064 GTCTTCAACCAG-TTCTGCT-AC-A-ACCGAGAGAGGCAAGGTTTG-T
1 ATCTTCGATCTGCTTC-GCTGTCAATACAG-GA-AGGCAAGATCTGCT
* * * * *
4514107 GTCTTCGATCTGCTTCGCTGTCAATCCAGGAAGGAAAAATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * * * *
4514152 ATCTTCAACCAGCTCCACT-ACAA-ACGAGGGAGGCAAGGTTTG-T
1 ATCTTCGATCTGCTTCGCTGTCAATAC-AGGAAGGCAAGATCTGCT
* * * * * *
4514195 GTCTTTGATCTGCTTCACTATCAATGCAGGAAGGCAAGATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * * * *
4514240 GTATTCAACCAGCTCTC-CT-AC-A-ACCGAGAGAGGCAAGGTTTG-T
1 ATCTTCGATCTGCT-TCGCTGTCAATACAG-GA-AGGCAAGATCTGCT
* * * *
4514283 GTCTTTGGTCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * * * *
4514328 GTCTTCAACCAGCTCCGCT-AC-A-ACCGAGAGAGGCAAGGTTTG-T
1 ATCTTCGATCTGCTTCGCTGTCAATACAG-GA-AGGCAAGATCTGCT
* * *
4514371 GTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTT
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
* * * * * * * * *
4514416 GTCTTCAACCAGCTCCGCT-AC-A-ACCGAGATAGGCAAGGTTTG-T
1 ATCTTCGATCTGCTTCGCTGTCAATACAG-GA-AGGCAAGATCTGCT
* *
4514459 GTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTG
1 ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTG
4514502 TTGTCTTTAA
Statistics
Matches: 572, Mismatches: 159, Indels: 119
0.67 0.19 0.14
Matches are distributed among these distances:
41 11 0.02
42 31 0.05
43 103 0.18
44 235 0.41
45 177 0.31
46 15 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (45 bp):
ATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCT
Found at i:4513787 original size:44 final size:45
Alignment explanation
Indices: 4513667--4513886 Score: 200
Period size: 45 Copynumber: 4.9 Consensus size: 45
4513657 AAAATCCGCC
* * *
4513667 ATCTTCGATCTGCTTCGCTGTCAATGCAGGAATGCAAGATCT-GCT
1 ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTAG-T
*
4513712 ATCTTC-AGTCTGC-TCTGCTGTCAGTATAGGAAGGCAAGA-CTAGT
1 ATCTTCGA-TCTGCTTC-GCTGTCAGTACAGGAAGGCAAGATCTAGT
* * * *
4513756 TTCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACT
1 ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTAGT
* * * * *
4513801 ATCTT-TAGCCTGCTCCGCTGTTAGTACAGGAAGGCAAGA-CTGGT
1 ATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTAGT
* * * * *
4513845 TTCTTCGATCTGCTTCGCCGTCAGTATAGGAAGACAATATCT
1 ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT
4513887 GTTGTCTTCA
Statistics
Matches: 139, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
44 68 0.49
45 71 0.51
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (45 bp):
ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTAGT
Found at i:4513821 original size:89 final size:89
Alignment explanation
Indices: 4513668--4513886 Score: 312
Period size: 89 Copynumber: 2.5 Consensus size: 89
4513658 AAATCCGCCA
* * * * * *
4513668 TCTTCGATCTGCTTCGCTGTCAATGCAGGAATGCAAGATCTGCTATCTTCAGTCTGCTCTGCTGT
1 TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACTATCTTCAGCCTGCTCCGCTGT
*
4513733 CAGTATAGGAAGGCAAGACTAGTT
66 CAGTACAGGAAGGCAAGACTAGTT
*
4513757 TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACTATCTTTAGCCTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACTATCTTCAGCCTGCTCCGCTGT
* *
4513822 TAGTACAGGAAGGCAAGACTGGTT
66 CAGTACAGGAAGGCAAGACTAGTT
* * * *
4513846 TCTTCGATCTGCTTCGCCGTCAGTATAGGAAGACAATATCT
1 TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCT
4513887 GTTGTCTTCA
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 116 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACTATCTTCAGCCTGCTCCGCTGT
CAGTACAGGAAGGCAAGACTAGTT
Found at i:4513983 original size:88 final size:88
Alignment explanation
Indices: 4513668--4514673 Score: 1215
Period size: 88 Copynumber: 11.5 Consensus size: 88
4513658 AAATCCGCCA
* * * ** * * *
4513668 TCTTCGATCTGCTTCGCTGTCAATGCAGGAATGCAAGATCTGCTATCTTCAGTCTGCTCTGCTGT
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-A
** ** * *
4513733 CAGTATAG-GA-AGGCAAGACTAGTT
65 CA--ACCGAGAGAGGCAAGGTTTGTG
* * ** * * * *
4513757 TCTTCGATCTGCTTCGCCGTCAATACAGGAAGGCAAGATCTACTATCTTTAGCCTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGC---
** * ** * *
4513822 TAGTACAG-GA-AGGCAAGACTGGTT
63 TACAACCGAGAGAGGCAAGGTTTGTG
* * ** * * * *
4513846 TCTTCGATCTGCTTCGCCGTCAGTATAGGAAGACAATATCTGTTGTCTTCAACTAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
4513911 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * ** * * *
4513934 TCTTCGATCTGCTTCGCTATCAATGCAGGAAGGCAAAATCTGTCATCTTCAACTAGCTCCACTGC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
* * *
4513999 AAACGAGGGAGGTAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* *
4514022 --TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGTTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
4514085 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * * * *
4514108 TCTTCGATCTGCTTCGCTGTCAATCCAGGAAGGAAAAATCTGTTATCTTCAACCAGCTCCACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
* *
4514173 AAACGAGGGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * * *
4514196 TCTTTGATCTGCTTCACTATCAATGCAGGAAGGCAAGATCTGTTGTATTCAACCAGCTCTC-CTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTC-CGCTA
4514260 CAACCGAGAGAGGCAAGGTTTGTG
65 CAACCGAGAGAGGCAAGGTTTGTG
* * *
4514284 TCTTTGGTCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
4514349 AACCGAGAGAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* *
4514372 TCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
*
4514437 AACCGAGATAGGCAAGGTTTGTG
66 AACCGAGAGAGGCAAGGTTTGTG
* * * *
4514460 TCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTTAACCAGCTCCACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
*
4514525 AACCGAGAGAGGCATGG-TT-TG
66 AACCGAGAGAGGCAAGGTTTGTG
* *
4514546 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGTTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
4514611 AACCGAGAGAGGCAAGG-TT-TG
66 AACCGAGAGAGGCAAGGTTTGTG
4514632 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
4514674 GTAACTTCAT
Statistics
Matches: 811, Mismatches: 97, Indels: 21
0.87 0.10 0.02
Matches are distributed among these distances:
86 202 0.25
87 5 0.01
88 479 0.59
89 124 0.15
92 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTAC
AACCGAGAGAGGCAAGGTTTGTG
Found at i:4514274 original size:44 final size:45
Alignment explanation
Indices: 4514050--4514626 Score: 275
Period size: 44 Copynumber: 13.2 Consensus size: 45
4514040 CAATGCAGGA
*
4514050 AGGCAAGATCTGTTGTCTTCAACCAGTTCT-GCTACAACCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * * * * *
4514094 AGGCAAGGTTTG-TGTCTTCGATCTGCT-TCGCTGTCAATCC-AG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCT-ACAA-CCGAGAG
* * * * * *
4514137 AAGGAAAAATCTGTTATCTTCAACCAGCTC-CACTACAAACGAGGG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * ** * * * *
4514182 AGGCAAGGTTTG-TGTCTTTGATCTGCT-TCACTATCAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTA-CAACCG-AGAG
*
4514225 AAGGCAAGATCTGTTGTATTCAACCAGCTCTC-CTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * **** * * *
4514270 AGGCAAGGTTTG-TGTCTTTGGTCTGCT-TCGCTGTCAATAC-AG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCT-ACAA-CCGAGAG
4514313 AAGGCAAGATCTGTTGTCTTCAACCAGCTC-CGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * * * * *
4514358 AGGCAAGGTTTG-TGTCTTCGACCTGCT-TCGCTGTCAATAC-AG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCT-ACAA-CCGAGAG
*
4514401 AAGGCAAGATCTGTTGTCTTCAACCAGCTC-CGCTACAACCGAGAT
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * * * * *
4514446 AGGCAAGGTTTG-TGTCTTCGACCTGCT-TCGCTGTCAATAC-AG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCT-ACAA-CCGAGAG
* *
4514489 AAGGCAAGATCTGTTGTCTTTAACCAGCTC-CACTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
* * * * * * *
4514534 AGGCATG--GT-TTGTCTTCGATCTGCT-TCGCTGTCAA-TGCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCT-ACAACCG-AGAG
*
4514575 AAGGCAAGATCTGTTGTCTTCAACCAGTTCT-GCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
4514620 AGGCAAG
1 AGGCAAG
4514627 GTTTGTCTTC
Statistics
Matches: 383, Mismatches: 100, Indels: 100
0.66 0.17 0.17
Matches are distributed among these distances:
41 17 0.04
42 15 0.04
43 83 0.22
44 165 0.43
45 100 0.26
46 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (45 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCTCGCTACAACCGAGAG
Found at i:4515963 original size:28 final size:28
Alignment explanation
Indices: 4515930--4515991 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
4515920 TTCCTTTTCC
4515930 TTTTTTGCTTTTCTT-TTTTAACTTTGAT
1 TTTTTTG-TTTTCTTGTTTTAACTTTGAT
* * *
4515958 TTTTTTGTTTTTTTGTTTTGATTTTGAT
1 TTTTTTGTTTTCTTGTTTTAACTTTGAT
4515986 TTTTTT
1 TTTTTT
4515992 CTCTATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.08, C:0.05, G:0.10, T:0.77
Consensus pattern (28 bp):
TTTTTTGTTTTCTTGTTTTAACTTTGAT
Found at i:4523226 original size:37 final size:37
Alignment explanation
Indices: 4523184--4523369 Score: 282
Period size: 37 Copynumber: 5.0 Consensus size: 37
4523174 GGTAGTTTTA
*
4523184 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
4523221 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* * * *
4523258 GTTACGCTTATCTGATCAAGAAACAAAGTTATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
4523295 GTTACACTTATTTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
4523332 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
4523369 G
1 G
4523370 TAGATTCAGC
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:4523441 original size:45 final size:46
Alignment explanation
Indices: 4523332--4523455 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
4523322 GTGATAAGTG
*
4523332 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGATTCA
1 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGACTCA
* *
4523378 GCTACACTTATCTGATCAAGTG-GCAAAGTGATTAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGAG-AAAGTGATAAGTGGTAGACTCA
*
4523423 GCTACACTTATCTGATCAAG-GA-CAAGTGATAAG
1 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAG
4523456 AGGTCATATG
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 9 0.13
44 1 0.01
45 22 0.31
46 39 0.55
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGACTCA
Found at i:4524871 original size:13 final size:14
Alignment explanation
Indices: 4524845--4524881 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
4524835 TCTCTGCTTC
4524845 ATTTGTTGTTTTCT
1 ATTTGTTGTTTTCT
4524859 ATTTGTT-TTTTCT
1 ATTTGTTGTTTTCT
4524872 ATTTGTTGTT
1 ATTTGTTGTT
4524882 CTGTTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.08, C:0.05, G:0.14, T:0.73
Consensus pattern (14 bp):
ATTTGTTGTTTTCT
Found at i:4525449 original size:106 final size:106
Alignment explanation
Indices: 4525264--4525476 Score: 320
Period size: 106 Copynumber: 2.0 Consensus size: 106
4525254 AAAATGAGCA
* * * ** *
4525264 TTCTTATTTTTGGGAATTTGAGACATCGTGCCCTAAGTTACGGGGCATGATTTTCTTCCTGATTA
1 TTCTTATTTTTGGGAATTCGAGACATCATGCCCTAACTTACAAGACATGATTTTCTTCCTGATTA
4525329 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
66 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
*
4525370 TTCTTATTTTTGGGAATTCGAGGCATCATGCCCTAACTTACAAGACATGATTTTCTTCCAT-ATT
1 TTCTTATTTTTGGGAATTCGAGACATCATGCCCTAACTTACAAGACATGATTTTCTTCC-TGATT
* * *
4525434 AACTCGAAATACGAAGGCATTTTTCATAAATTTTGATTTAAT
65 AACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
4525476 T
1 T
4525477 AGCGATATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 95 0.99
107 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (106 bp):
TTCTTATTTTTGGGAATTCGAGACATCATGCCCTAACTTACAAGACATGATTTTCTTCCTGATTA
ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
Found at i:4528310 original size:24 final size:23
Alignment explanation
Indices: 4528282--4528327 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
4528272 TAATAATCCT
*
4528282 TAAAATAAAT-CCACACAAATTTAA
1 TAAAAAAAATGCCA-AC-AATTTAA
4528306 TAAAAAAAATGCCAACAATTTA
1 TAAAAAAAATGCCAACAATTTA
4528328 TTTTGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 11 0.55
25 3 0.15
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAAAAAATGCCAACAATTTAA
Found at i:4529775 original size:26 final size:26
Alignment explanation
Indices: 4529721--4529775 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
4529711 CCATGTCAAC
*
4529721 AAAAAAAGTAAAATTATAAAAATATT
1 AAAAAAAGTAAAATTACAAAAATATT
*
4529747 AAAAAAA-TAAAAATT-CAAAATTATAT
1 AAAAAAAGT-AAAATTACAAAAATAT-T
4529773 AAA
1 AAA
4529776 TAATTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAAAAGTAAAATTACAAAAATATT
Found at i:4534667 original size:10 final size:9
Alignment explanation
Indices: 4534625--4534876 Score: 86
Period size: 10 Copynumber: 25.9 Consensus size: 9
4534615 AATAATTTGT
*
4534625 ATTTTTTTA
1 ATTTTTATA
4534634 ATTTTTAT-
1 ATTTTTATA
4534642 ATTATTTATA
1 ATT-TTTATA
4534652 AGTTTTTATGA
1 A-TTTTTAT-A
4534663 ATTTTTATA
1 ATTTTTATA
* *
4534672 AGCTTTTAAA
1 A-TTTTTATA
4534682 CATGTTATTAT-
1 -AT-TT-TTATA
4534693 ATGTTTTATTA
1 AT-TTTTA-TA
*
4534704 ATTTTATAAA
1 ATTTT-TATA
****
4534714 AAAACTATA
1 ATTTTTATA
*
4534723 ATTTATTAAA
1 ATTT-TTATA
*
4534733 ATTTATTAGA
1 ATTT-TTATA
*
4534743 ATATATTATA
1 AT-TTTTATA
4534753 TATTTTTATAA
1 -ATTTTTAT-A
4534764 CATTTTTA-A
1 -ATTTTTATA
*
4534773 GTTTTTATA
1 ATTTTTATA
4534782 TATTTTTATA
1 -ATTTTTATA
4534792 ATTTTCTATA
1 ATTTT-TATA
*
4534802 AGTTTTATA
1 ATTTTTATA
*
4534811 AGTTTATATAA
1 A-TTTTTAT-A
*
4534822 AATTTTA-A
1 ATTTTTATA
4534830 GATTTTT-T-
1 -ATTTTTATA
4534838 ATTTTTA-A
1 ATTTTTATA
4534846 ATATTTCTAATA
1 AT-TTT-T-ATA
4534858 ATTTTTTTATA
1 A--TTTTTATA
4534869 ATTTTTAT
1 ATTTTTAT
4534877 GTGAAAAATA
Statistics
Matches: 184, Mismatches: 29, Indels: 60
0.67 0.11 0.22
Matches are distributed among these distances:
7 6 0.03
8 12 0.07
9 48 0.26
10 79 0.43
11 29 0.16
12 6 0.03
13 3 0.02
14 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4534779 original size:19 final size:18
Alignment explanation
Indices: 4534755--4534836 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 18
4534745 ATATTATATA
4534755 TTTTTATAACATTTTTAAG
1 TTTTTATAA-ATTTTTAAG
* *
4534774 TTTTTATATATTTTTATAA
1 TTTTTATAAATTTTTA-AG
*
4534793 TTTTCTATAAGTTTTATAAG
1 TTTT-TATAAATTTT-TAAG
* *
4534813 TTTATATAAAATTTTAAG
1 TTTTTATAAATTTTTAAG
4534831 ATTTTT
1 -TTTTT
4534837 TATTTTTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 11 0.22
19 25 0.50
20 12 0.24
21 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTTATAAATTTTTAAG
Found at i:4534807 original size:29 final size:28
Alignment explanation
Indices: 4534748--4534844 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 28
4534738 TTAGAATATA
*
4534748 TTATATATTTTTATAACATTTTTAAGTTT
1 TTATATATTTTTATAA-ATTTTTAAGATT
*
4534777 TTATATATTTTTATAATTTTCTATAAG-TT
1 TTATATATTTTTATAAATTT-T-TAAGATT
* *
4534806 TTATA-AGTTTATATAAAATTTTAAGATT
1 TTATATA-TTTTTATAAATTTTTAAGATT
4534834 TT-T-TATTTTTA
1 TTATATATTTTTA
4534845 AATATTTCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
26 5 0.09
27 6 0.10
28 9 0.16
29 34 0.59
30 4 0.07
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (28 bp):
TTATATATTTTTATAAATTTTTAAGATT
Found at i:4535310 original size:10 final size:9
Alignment explanation
Indices: 4535281--4535325 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
4535271 TTTTCAATAA
4535281 TTTATAATT
1 TTTATAATT
*
4535290 TTTTTAATT
1 TTTATAATT
4535299 TTTATAAGTT
1 TTTATAA-TT
4535309 TTTATGAATT
1 TTTAT-AATT
4535319 TTTATAA
1 TTTATAA
4535326 GCCTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 16 0.50
10 14 0.44
11 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:4535318 original size:20 final size:19
Alignment explanation
Indices: 4535281--4535326 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4535271 TTTTCAATAA
*
4535281 TTTATAA-TTTTTTTAATT
1 TTTATAAGTTTTTTGAATT
4535299 TTTATAAGTTTTTATGAATT
1 TTTATAAGTTTTT-TGAATT
4535319 TTTATAAG
1 TTTATAAG
4535327 CCTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 13 0.52
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTATAAGTTTTTTGAATT
Found at i:4535332 original size:20 final size:20
Alignment explanation
Indices: 4535295--4535332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4535285 TAATTTTTTT
**
4535295 AATTTTTATAAGTTTTTATG
1 AATTTTTATAAGCCTTTATG
4535315 AATTTTTATAAGCCTTTA
1 AATTTTTATAAGCCTTTA
4535333 AATATGTTTT
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:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (20 bp):
AATTTTTATAAGCCTTTATG
Found at i:4535395 original size:26 final size:26
Alignment explanation
Indices: 4535339--4535395 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
4535329 TTTAAATATG
* *
4535339 TTTTATTATTTTTTTAAAAAATTATC
1 TTTTATTATTATTTTAAAAAATCATC
* *
4535365 ATTTATTATATATTTTATAAAATCAT-
1 TTTTATTAT-TATTTTAAAAAATCATC
4535391 TTTTA
1 TTTTA
4535396 AGTATTTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATTATTATTTTAAAAAATCATC
Found at i:4542062 original size:24 final size:24
Alignment explanation
Indices: 4542035--4542112 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
4542025 ATTTCAAGAT
*
4542035 TTGAAATCTTGATTTTCTTCATTC
1 TTGAAATCTTGATTTTCTTGATTC
* * **
4542059 TTGAAATCATGAATTTCAAGA-T-
1 TTGAAATCTTGATTTTCTTGATTC
4542081 TTGAAATCTTGATTTTCTTGATTC
1 TTGAAATCTTGATTTTCTTGATTC
4542105 TTGAAATC
1 TTGAAATC
4542113 ATCCATAACA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 17 0.40
23 2 0.05
24 24 0.56
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (24 bp):
TTGAAATCTTGATTTTCTTGATTC
Found at i:4542077 original size:46 final size:46
Alignment explanation
Indices: 4542023--4542114 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
4542013 CTTGGACCAA
4542023 GAATTTCAAGATTTGAAATCTTGATTTTCTTCATTCTTGAAATCAT
1 GAATTTCAAGATTTGAAATCTTGATTTTCTTCATTCTTGAAATCAT
*
4542069 GAATTTCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCAT
1 GAATTTCAAGATTTGAAATCTTGATTTTCTTCATTCTTGAAATCAT
4542115 CCATAACAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (46 bp):
GAATTTCAAGATTTGAAATCTTGATTTTCTTCATTCTTGAAATCAT
Found at i:4542087 original size:22 final size:22
Alignment explanation
Indices: 4542023--4542097 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
4542013 CTTGGACCAA
4542023 GAATTTCAAGATTTGAAATCTT
1 GAATTTCAAGATTTGAAATCTT
* *** *
4542045 GATTTTCTTCATTCTTGAAATCAT
1 GAATTTCAAGA-T-TTGAAATCTT
4542069 GAATTTCAAGATTTGAAATCTT
1 GAATTTCAAGATTTGAAATCTT
*
4542091 GATTTTC
1 GAATTTC
4542098 TTGATTCTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 22 0.55
23 2 0.05
24 16 0.40
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (22 bp):
GAATTTCAAGATTTGAAATCTT
Found at i:4542979 original size:31 final size:31
Alignment explanation
Indices: 4542944--4543002 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4542934 TTATAACATA
* *
4542944 TTTCATATTCTGTTTTCAATTCACTATCGTT
1 TTTCACATTCTATTTTCAATTCACTATCGTT
4542975 TTTCACATTCTATTTTCAATTCACTATC
1 TTTCACATTCTATTTTCAATTCACTATC
4543003 TCATATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTCACATTCTATTTTCAATTCACTATCGTT
Found at i:4543124 original size:22 final size:22
Alignment explanation
Indices: 4543096--4543157 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
4543086 CTAATGAACA
4543096 GAGAGCACTAAAGTGCTATACG
1 GAGAGCACTAAAGTGCTATACG
4543118 GAGAGCACTAAAGTGCTATACG
1 GAGAGCACTAAAGTGCTATACG
* *
4543140 GAGAGCACTGACGTGCTA
1 GAGAGCACTAAAGTGCTA
4543158 AATATCAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (22 bp):
GAGAGCACTAAAGTGCTATACG
Found at i:4543170 original size:25 final size:25
Alignment explanation
Indices: 4543140--4543193 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
4543130 GTGCTATACG
**
4543140 GAGAGCACTGACGTGCTAA-ATATCA
1 GAGAGCACCAACGTGCTAATA-ATCA
4543165 GAGAGCACCAACGTGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
4543190 GAGA
1 GAGA
4543194 ACGCGCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
GAGAGCACCAACGTGCTAATAATCA
Found at i:4547883 original size:41 final size:41
Alignment explanation
Indices: 4547833--4547912 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
4547823 CCGAAATGTA
* * *
4547833 TCACTGGCATTAAGCCTGCTAGACGTAAAGTTTGTATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
4547874 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
4547913 CATTCGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:4548184 original size:12 final size:12
Alignment explanation
Indices: 4548167--4548220 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
4548157 CTTAAAAACT
4548167 TATATATATACA
1 TATATATATACA
*
4548179 TATATATATTCGA
1 TATATATATAC-A
4548192 GTAT-TATGCATACA
1 -TATATAT--ATACA
4548206 TATATATATACA
1 TATATATATACA
4548218 TAT
1 TAT
4548221 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 18 0.51
13 7 0.20
14 7 0.20
15 3 0.09
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:4548288 original size:2 final size:2
Alignment explanation
Indices: 4548281--4548312 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4548271 CTATCGTATG
4548281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4548313 ACTTTCTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4550811 original size:31 final size:31
Alignment explanation
Indices: 4550776--4550834 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4550766 TTATAACATA
* *
4550776 TTTCATATTCTGTTTTCAATTCACTATCGTT
1 TTTCACATTCTATTTTCAATTCACTATCGTT
4550807 TTTCACATTCTATTTTCAATTCACTATC
1 TTTCACATTCTATTTTCAATTCACTATC
4550835 TCATATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTCACATTCTATTTTCAATTCACTATCGTT
Found at i:4551002 original size:25 final size:24
Alignment explanation
Indices: 4550926--4551052 Score: 129
Period size: 25 Copynumber: 5.3 Consensus size: 24
4550916 CACTAATGAA
* *
4550926 CAGAGAGCACTAAAGTGCT-ATA-
1 CAGAGAGCACCAACGTGCTAATAT
*
4550948 CAGAGAGCA-CAGATGTGCTAA-A-
1 CAGAGAGCACCA-ACGTGCTAATAT
**
4550970 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACCAACGTGCT-AATAT
4550995 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
*
4551020 CAGAAAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
4551045 CAGAGAGC
1 CAGAGAGC
4551053 GCGCTAAAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 31 0.35
23 3 0.03
24 4 0.04
25 50 0.56
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTAATAT
Found at i:4553484 original size:24 final size:24
Alignment explanation
Indices: 4553452--4553501 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4553442 TTGAATAAAC
4553452 TTAAATGAAAAGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
*
4553476 TTAAATGAAAGGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
4553500 TT
1 TT
4553502 TTTTTAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (24 bp):
TTAAATGAAAAGTCAAGAGTTATG
Found at i:4557341 original size:43 final size:42
Alignment explanation
Indices: 4557186--4557349 Score: 167
Period size: 43 Copynumber: 3.9 Consensus size: 42
4557176 GACTCGTACA
* *
4557186 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ATCG
*
4557229 ATGCC-ACTGTCCCAGGCAG-GGTCTTACA--TAAATCA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAA-CACAAT-CG
* * *
4557270 ATACCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
* *
4557313 ATGCCCACGTCCCAGACGTGGTCTTACACGAAAACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACAC
4557350 GTATCAAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
40 2 0.02
41 27 0.27
42 7 0.07
43 62 0.62
44 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:4561530 original size:24 final size:24
Alignment explanation
Indices: 4561498--4561545 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4561488 TTGAATAAAC
4561498 TTAAATGAAAAGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
*
4561522 TTAAATGAAAGGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
4561546 GTTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (24 bp):
TTAAATGAAAAGTCAAGAGTTATG
Found at i:4563492 original size:17 final size:17
Alignment explanation
Indices: 4563449--4563485 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4563439 TTTGGGGAAT
* *
4563449 AAAAAGAAAAAAATTAA
1 AAAAACAAAAAAAGTAA
4563466 AAAAACAAAAAAAGTAA
1 AAAAACAAAAAAAGTAA
4563483 AAA
1 AAA
4563486 CAAAAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAACAAAAAAAGTAA
Found at i:4563758 original size:20 final size:21
Alignment explanation
Indices: 4563733--4563790 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
4563723 TTTTTTGTAT
*
4563733 TATATATTTTAAAATGAAAGTA
1 TATATATTTTAAAATGAAA-AA
* *
4563755 TATATATATTTAAAAAGGAAAA
1 TATATAT-TTTAAAATGAAAAA
4563777 TATAT-TTTTAAAAT
1 TATATATTTTAAAAT
4563791 TTTCTGGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
22 13 0.42
23 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
TATATATTTTAAAATGAAAAA
Found at i:4563760 original size:24 final size:24
Alignment explanation
Indices: 4563729--4563781 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4563719 AACTTTTTTT
* *
4563729 GTAT-TATATATTTTAAAATGAAA
1 GTATATATATATTTAAAAAGGAAA
4563752 GTATATATATATTTAAAAAGGAAA
1 GTATATATATATTTAAAAAGGAAA
*
4563776 ATATAT
1 GTATAT
4563782 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (24 bp):
GTATATATATATTTAAAAAGGAAA
Found at i:4563991 original size:29 final size:29
Alignment explanation
Indices: 4563959--4564014 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
4563949 ACATTTTTAT
4563959 ATTTTT-CTGATTTTTTGAGATTT-TTCAGC
1 ATTTTTGCT-ATTTTTTGA-ATTTATTCAGC
4563988 ATTTTTGCTATTTTTTGAATTTATTCA
1 ATTTTTGCTATTTTTTGAATTTATTCA
4564015 AAAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 19 0.76
30 2 0.08
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.61
Consensus pattern (29 bp):
ATTTTTGCTATTTTTTGAATTTATTCAGC
Found at i:4569242 original size:21 final size:22
Alignment explanation
Indices: 4569217--4569261 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
4569207 TTTATCATTT
4569217 TTACTAACT-TAA-TTTATTAAA
1 TTACTAA-TATAACTTTATTAAA
4569238 TTACTAATATAACCTTTATTAAA
1 TTACTAATATAA-CTTTATTAAA
4569261 T
1 T
4569262 ACATTAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.05
21 10 0.48
23 10 0.48
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (22 bp):
TTACTAATATAACTTTATTAAA
Found at i:4572389 original size:28 final size:28
Alignment explanation
Indices: 4572349--4572406 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
4572339 TAAATTAAAT
4572349 AATTAATCCTATAAATCAACTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
* * *
4572377 AATTAATTCTATAAATTAATTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
4572405 AA
1 AA
4572407 AAACACTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTAATCCTATAAATCAACTCAATTCA
Found at i:4576398 original size:32 final size:32
Alignment explanation
Indices: 4576361--4576421 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
4576351 AAGACAAAAG
4576361 AGTAAGCTAAAACCTTATTACTGAACCAACAA
1 AGTAAGCTAAAACCTTATTACTGAACCAACAA
4576393 AGTAAGCTAAAACCTTATTACTGAACCAA
1 AGTAAGCTAAAACCTTATTACTGAACCAA
4576422 TAAACTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (32 bp):
AGTAAGCTAAAACCTTATTACTGAACCAACAA
Found at i:4576888 original size:41 final size:41
Alignment explanation
Indices: 4576843--4576922 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
4576833 TGGCTCAATT
*
4576843 TGGTCGGTTGAGTCGGTTTTAATCGCTAACTATAATAGATG
1 TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGATG
*
4576884 TGGTCGGTTGATTCGGTTTTAATCACTAACTATAATAGA
1 TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGA
4576923 AAATATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (41 bp):
TGGTCGGTTGAGTCGGTTTTAATCACTAACTATAATAGATG
Found at i:4578516 original size:19 final size:19
Alignment explanation
Indices: 4578454--4578518 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
4578444 TTTGATGGTT
4578454 TTTAAATTTTAAAAA-TAA
1 TTTAAATTTTAAAAATTAA
** *
4578472 TTTTATAATTTTTTTTAAATT-T
1 -TTTA-AA--TTTTAAAAATTAA
4578494 TTTAAATTTTAAAAATTAA
1 TTTAAATTTTAAAAATTAA
4578513 TTTAAA
1 TTTAAA
4578519 ACTAGAAGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 4 0.11
21 4 0.11
22 7 0.20
23 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAATTTTAAAAATTAA
Found at i:4579186 original size:16 final size:15
Alignment explanation
Indices: 4579155--4579188 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4579145 CCTCTTTTTT
*
4579155 TTTTTAATTACTCAA
1 TTTTTAATTACCCAA
4579170 TTTTTAATTACCCCAA
1 TTTTTAATTA-CCCAA
4579186 TTT
1 TTT
4579189 AAAGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTAATTACCCAA
Found at i:4585112 original size:3 final size:3
Alignment explanation
Indices: 4585104--4585182 Score: 97
Period size: 3 Copynumber: 25.3 Consensus size: 3
4585094 TAACCGAATA
*
4585104 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AA- ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
4585149 AGAT AAAT AAAT AAT AAT AAT AAC AAT AAT AAT A
1 A-AT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
4585183 CAAATATAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.01
3 56 0.82
4 10 0.15
5 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4587089 original size:25 final size:26
Alignment explanation
Indices: 4587052--4587102 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
4587042 GTTGTAAATC
*
4587052 AGAAAAATATCTTTAGA-AATTTTCT
1 AGAAAAATATCTTCAGAGAATTTTCT
* *
4587077 AGAATAATCTCTTCAGAGAATTTTCT
1 AGAAAAATATCTTCAGAGAATTTTCT
4587103 CTACAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (26 bp):
AGAAAAATATCTTCAGAGAATTTTCT
Found at i:4588919 original size:2 final size:2
Alignment explanation
Indices: 4588914--4588938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4588904 TTTTTAATTT
4588914 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 T
4588939 TCTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4588967 original size:20 final size:20
Alignment explanation
Indices: 4588942--4588984 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
4588932 TATATATTCT
4588942 ATTTATTTTG-ATCGTCTATC
1 ATTTATTTTGAATCGTCT-TC
4588962 ATTTATTTTGAATCGTCTTC
1 ATTTATTTTGAATCGTCTTC
4588982 ATT
1 ATT
4588985 AATCATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (20 bp):
ATTTATTTTGAATCGTCTTC
Found at i:4589105 original size:15 final size:17
Alignment explanation
Indices: 4589072--4589106 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4589062 TATTTGGTGT
4589072 GTTGTGTGATTATTGTC
1 GTTGTGTGATTATTGTC
4589089 GTTGTGT-ATTATT-TC
1 GTTGTGTGATTATTGTC
4589104 GTT
1 GTT
4589107 TACCCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 6 0.33
17 7 0.39
ACGTcount: A:0.11, C:0.06, G:0.26, T:0.57
Consensus pattern (17 bp):
GTTGTGTGATTATTGTC
Found at i:4594372 original size:10 final size:11
Alignment explanation
Indices: 4594346--4594371 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4594336 TTAAAAATAA
4594346 AAAAATATTTT
1 AAAAATATTTT
4594357 AAAAATATTTT
1 AAAAATATTTT
4594368 AAAA
1 AAAA
4594372 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Done.