Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 190 of 295
Found at i:65290817 original size:15 final size:14
Alignment explanation
Indices: 65290794--65290838 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
65290784 GGATTCAAAG
65290794 ATGGGTTTATGGAT
1 ATGGGTTTATGGAT
* *
65290808 ATGAGGTTTATGTAG
1 ATG-GGTTTATGGAT
65290823 ATGGGTTTATGGAT
1 ATGGGTTTATGGAT
65290837 AT
1 AT
65290839 AAAGTTTTTG
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:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (14 bp):
ATGGGTTTATGGAT
Found at i:65290845 original size:29 final size:29
Alignment explanation
Indices: 65290792--65290851 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65290782 AAGGATTCAA
* *
65290792 AGATGGGTTTATGGATATGAGGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
65290821 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
65290850 AG
1 AG
65290852 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:65294382 original size:17 final size:16
Alignment explanation
Indices: 65294323--65294382 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
65294313 GAGACAGCCA
* *
65294323 CCATACATGCATTTAAG
1 CCATTCATGCATTT-AT
65294340 CCATTCATGCATTCTAT
1 CCATTCATGCATT-TAT
*
65294357 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTT-AT
65294374 CCATTCATG
1 CCATTCATG
65294383 GACTAGCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 27 0.77
18 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
CCATTCATGCATTTAT
Found at i:65294832 original size:20 final size:20
Alignment explanation
Indices: 65294786--65294832 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
65294776 AGCTCGTTTC
*
65294786 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
65294806 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
65294826 CAGCTCA
1 CAGCTCA
65294833 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:65296244 original size:11 final size:10
Alignment explanation
Indices: 65296228--65296257 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
65296218 TTCGTAACGT
65296228 AAAAAAAAGTC
1 AAAAAAAA-TC
65296239 AAAAAAAATC
1 AAAAAAAATC
65296249 AAAAAAAAT
1 AAAAAAAAT
65296258 TGAGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:65298286 original size:30 final size:30
Alignment explanation
Indices: 65298252--65298348 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65298242 AGCTCACTCC
65298252 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
65298282 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
65298312 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
65298342 TAGCTCA
1 TAGCTCA
65298349 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:65301081 original size:37 final size:37
Alignment explanation
Indices: 65301030--65301100 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
65301020 CATTCTTGTA
65301030 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
65301067 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
65301101 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:65301100 original size:6 final size:6
Alignment explanation
Indices: 65301040--65301089 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
65301030 AAGAGAAAAC
*
65301040 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
65301089 A
1 A
65301090 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:65301182 original size:11 final size:12
Alignment explanation
Indices: 65301150--65301180 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65301140 TTGAGAGAAC
65301150 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65301162 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65301174 TTGAAAA
1 TTGAAAA
65301181 GCAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:65301192 original size:6 final size:6
Alignment explanation
Indices: 65301183--65301257 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
65301173 TTTGAAAAGC
* * *
65301183 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA-G AAATTTG AGAGTG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA-ATG AAAATG
* * * *
65301231 AAAAAG AAGATG AAAAAG AAATTG AAA
1 AAAATG AAAATG AAAATG AAAATG AAA
65301258 CAAAAGAATC
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 4 0.07
6 48 0.87
7 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:65301196 original size:18 final size:17
Alignment explanation
Indices: 65301175--65301220 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
65301165 AAAAAGCCTT
65301175 TGAAAAGCAAAATGAAAA
1 TGAAAAG-AAAATGAAAA
65301193 TGAAAATGAAAATGAAAA
1 TGAAAA-GAAAATGAAAA
65301211 TGAAAAGAAA
1 TGAAAAGAAA
65301221 TTTGAGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (17 bp):
TGAAAAGAAAATGAAAA
Found at i:65303366 original size:30 final size:30
Alignment explanation
Indices: 65303332--65303428 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65303322 AGCTCACTCC
65303332 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
65303362 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
65303392 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
65303422 TAGCTCA
1 TAGCTCA
65303429 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:65308867 original size:15 final size:15
Alignment explanation
Indices: 65308841--65308896 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
65308831 CAAGGAAACC
65308841 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
65308856 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
65308871 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
65308886 GAATAAAGAAA
1 GAATAAAGAAA
65308897 CCCAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:65311902 original size:46 final size:45
Alignment explanation
Indices: 65311835--65312011 Score: 212
Period size: 46 Copynumber: 3.9 Consensus size: 45
65311825 TGTAACCCGC
*
65311835 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTT-GCAT
* *
65311881 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG--TTGCAT
* *** * **
65311927 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGATGTTGCAT
*
65311973 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
65312012 CTCAACCATC
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
45 31 0.28
46 48 0.44
47 29 0.27
48 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTGCAT
Found at i:65312001 original size:92 final size:93
Alignment explanation
Indices: 65311843--65312012 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 93
65311833 GCCCATAAGT
***
65311843 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
65311908 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
65311936 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
65312000 CGAGTTCGGATGC
66 CGAGCTCGGATGC
65312013 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 43 0.60
93 29 0.40
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:65315693 original size:10 final size:10
Alignment explanation
Indices: 65315658--65315702 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
65315648 ATTTTCAGCA
65315658 ATTTTTATTG
1 ATTTTTATTG
* *
65315668 ATTCTTAGCGTG
1 ATTTTTA--TTG
65315680 ATTTTTATTG
1 ATTTTTATTG
65315690 ATTTTTATTG
1 ATTTTTATTG
65315700 ATT
1 ATT
65315703 CAGGCCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 21 0.72
12 8 0.28
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.62
Consensus pattern (10 bp):
ATTTTTATTG
Found at i:65323150 original size:18 final size:19
Alignment explanation
Indices: 65323106--65323150 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
65323096 ATTAACACAC
*
65323106 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65323125 -ATTCATAAAAATATAA-T
1 AATTAATAAAAATATAACT
65323142 AATTAATAA
1 AATTAATAA
65323151 TTACACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65325024 original size:19 final size:19
Alignment explanation
Indices: 65325000--65325039 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65324990 AGCTCCCATG
65325000 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65325019 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65325038 TA
1 TA
65325040 TTAGCTCACG
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:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65328358 original size:10 final size:10
Alignment explanation
Indices: 65328344--65328379 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
65328334 CAAGCTCGGT
*
65328344 TGAGCTGAAA
1 TGAGCTCAAA
*
65328354 CGAGCTCAAA
1 TGAGCTCAAA
65328364 TGAGCTCAAA
1 TGAGCTCAAA
65328374 TGAGCT
1 TGAGCT
65328380 GAGTTGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:65329914 original size:18 final size:19
Alignment explanation
Indices: 65329891--65329929 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
65329881 ATTATCTCAA
*
65329891 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
65329909 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
65329928 TT
1 TT
65329930 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:65329968 original size:18 final size:18
Alignment explanation
Indices: 65329947--65329996 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
65329937 AAACTCTTTT
65329947 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* * *
65329965 TCATTTTCTGTTTCACTC
1 TCATTCTCTTTTTCAATC
* *
65329983 TCAATCTCCTTTTC
1 TCATTCTCTTTTTC
65329997 TTTTTCTTTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.02, T:0.54
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:65330063 original size:42 final size:42
Alignment explanation
Indices: 65330000--65330096 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
65329990 CCTTTTCTTT
* * * *
65330000 TTCTTTCA-TTTCTTTGTTTCTTTTCTTGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
65330041 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
65330083 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
65330097 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:65332212 original size:19 final size:19
Alignment explanation
Indices: 65332167--65332212 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65332157 ATTAACACAC
*
65332167 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65332186 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
65332204 AATTAATAA
1 AATTAATAA
65332213 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65332688 original size:19 final size:19
Alignment explanation
Indices: 65332664--65332703 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65332654 AGCTCCCATG
65332664 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65332683 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65332702 TA
1 TA
65332704 TCAGTTCACG
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:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65333967 original size:14 final size:14
Alignment explanation
Indices: 65333945--65333992 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
65333935 ACCTAAATCG
* *
65333945 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65333959 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
65333973 ATCC-TTTCGTTCCT
1 A-CCATTTTGTTCCT
65333987 ACCATT
1 ACCATT
65333993 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65337452 original size:30 final size:30
Alignment explanation
Indices: 65337418--65337500 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
65337408 TAAACTAAAA
65337418 TGAGCTAAGCTTTAGCTCGTGAGCAAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCAAAAGT
* * * * * **
65337448 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCAAAAGT
*
65337478 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
65337501 TTGAAAGTGA
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
29 2 0.05
30 33 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCAAAAGT
Found at i:65343055 original size:10 final size:10
Alignment explanation
Indices: 65343040--65343066 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65343030 TACTCCTTCA
65343040 AGCTCAAATC
1 AGCTCAAATC
65343050 AGCTCAAATC
1 AGCTCAAATC
65343060 AGCTCAA
1 AGCTCAA
65343067 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65343679 original size:30 final size:30
Alignment explanation
Indices: 65343645--65343741 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65343635 AGCTCACTCC
65343645 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
65343675 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
65343705 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
65343735 TAGCTCA
1 TAGCTCA
65343742 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:65345834 original size:56 final size:55
Alignment explanation
Indices: 65345718--65345835 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
65345708 TGCATGCTTT
* * * *
65345718 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
65345772 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
65345828 CATTAAAT
1 CATTAAAT
65345836 CAGTAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:65346484 original size:20 final size:20
Alignment explanation
Indices: 65346459--65346513 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
65346449 ACGAGTTAAA
* *
65346459 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
65346479 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
65346499 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
65346514 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:65347632 original size:19 final size:18
Alignment explanation
Indices: 65347598--65347633 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65347588 AAAAAATTCA
*
65347598 AAAAAAAAATTCAAAAAG
1 AAAAAAAAATTAAAAAAG
65347616 AAAAAAAAATCTAAAAAA
1 AAAAAAAAAT-TAAAAAA
65347634 AAGTGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAAAAAATTAAAAAAG
Found at i:65347635 original size:13 final size:12
Alignment explanation
Indices: 65347573--65347620 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
65347563 TTATACAAGT
65347573 AAAAAAAAATCGA
1 AAAAAAAAATC-A
*
65347586 AAAAAAAATTCA
1 AAAAAAAAATCA
65347598 AAAAAAAAATTCA
1 AAAAAAAAA-TCA
65347611 AAAAGAAAAA
1 AAAA-AAAAA
65347621 AAAATCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 9 0.29
13 17 0.55
14 5 0.16
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:65348562 original size:9 final size:10
Alignment explanation
Indices: 65348555--65348611 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
65348545 AAGAGAAAAC
65348555 AAAGAAAAGA
1 AAAGAAAAGA
65348565 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
65348577 AAAGAAGA-A
1 AAAGAAAAGA
65348586 AAAGAAAATGA
1 AAAGAAAA-GA
65348597 AATA-AAAAGA
1 AA-AGAAAAGA
65348607 AAAGA
1 AAAGA
65348612 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65348578 original size:21 final size:20
Alignment explanation
Indices: 65348544--65348611 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
65348534 ACATTCTTGT
65348544 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
65348565 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
65348586 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
65348607 AAAGA
1 AAAGA
65348612 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:65348579 original size:6 final size:5
Alignment explanation
Indices: 65348555--65348611 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65348545 AAGAGAAAAC
*
65348555 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
65348602 AAAGA AAAGA
1 AAAGA AAAGA
65348612 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:65348586 original size:15 final size:14
Alignment explanation
Indices: 65348555--65348611 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65348545 AAGAGAAAAC
65348555 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
65348571 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
65348586 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
65348602 AAAGAAAAGA
1 AAAGAAAAGA
65348612 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:65348691 original size:11 final size:12
Alignment explanation
Indices: 65348659--65348689 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65348649 TTGAGAGAAC
65348659 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65348671 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65348683 TTGAAAA
1 TTGAAAA
65348690 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:65348766 original size:30 final size:30
Alignment explanation
Indices: 65348692--65348773 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
65348682 TTTGAAAAGC
* ** *
65348692 AAAAAGAAAATGAAAA-AAAAATGAGATTG
1 AAAAAGAAGATGAAAAGAAATTTGAGAGTG
*
65348721 AAAAAG-AGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAG-ATGAAAAGAAATTTGAGAGTG
65348751 AAAAAGAAGATGAAAAAGAAATT
1 AAAAAGAAGATG-AAAAGAAATT
65348774 GAAACAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 12 0.28
30 18 0.42
31 12 0.28
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (30 bp):
AAAAAGAAGATGAAAAGAAATTTGAGAGTG
Found at i:65350901 original size:30 final size:30
Alignment explanation
Indices: 65350867--65350963 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65350857 AGCTCACTCC
65350867 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
65350897 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
65350927 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
65350957 TAGCTCA
1 TAGCTCA
65350964 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:65352590 original size:14 final size:14
Alignment explanation
Indices: 65352548--65352592 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
65352538 TTAAAGAAGC
65352548 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
65352562 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
65352575 AACTCATTTAATTA
1 AACTCATTAAATTA
65352589 AACT
1 AACT
65352593 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:65354474 original size:13 final size:14
Alignment explanation
Indices: 65354456--65354491 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
65354446 CATAAATCAC
65354456 TTTTTTTTCG-AAT
1 TTTTTTTTCGAAAT
*
65354469 TTTTTTTTGGAAAT
1 TTTTTTTTCGAAAT
65354483 TTTTTTTTC
1 TTTTTTTTC
65354492 AAACTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCGAAAT
Found at i:65355262 original size:30 final size:30
Alignment explanation
Indices: 65355177--65355273 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
65355167 TAAACTAAAA
* *
65355177 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * * *
65355207 TAAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
65355237 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
65355266 ATGAGCTA
1 -TGAGCTA
65355274 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:65357223 original size:26 final size:26
Alignment explanation
Indices: 65357194--65357243 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
65357184 AAATCGTAGC
65357194 TTCGAAAAAAAAAGT-TAAAAAAAAGT
1 TTCGAAAAAAAAA-TCTAAAAAAAAGT
65357220 TTCGAAAAAAAAATCTAAAAAAAA
1 TTCGAAAAAAAAATCTAAAAAAAA
65357244 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (26 bp):
TTCGAAAAAAAAATCTAAAAAAAAGT
Found at i:65357249 original size:20 final size:20
Alignment explanation
Indices: 65357224--65357266 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
65357214 AAAAGTTTCG
65357224 AAAAAAAAA-TCTAAAAAAAA
1 AAAAAAAAATTC-AAAAAAAA
65357244 AAAAAAAAATTGCAAAAAAAA
1 AAAAAAAAATT-CAAAAAAAA
65357265 AA
1 AA
65357267 TTGCATACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 11 0.52
22 1 0.05
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAAAAAATTCAAAAAAAA
Found at i:65357260 original size:14 final size:14
Alignment explanation
Indices: 65357243--65357271 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
65357233 TCTAAAAAAA
65357243 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
65357257 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
65357271 A
1 A
65357272 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:65359551 original size:24 final size:25
Alignment explanation
Indices: 65359524--65359577 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
65359514 ATGAGTGATA
*
65359524 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
65359548 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
65359572 AAAAAA
1 AAAAAA
65359578 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:65365284 original size:12 final size:12
Alignment explanation
Indices: 65365267--65365307 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
65365257 CATAAATCAC
65365267 TTTTTTTCGATT
1 TTTTTTTCGATT
* *
65365279 TTTTTTTCAAAT
1 TTTTTTTCGATT
65365291 TTTTTTT-GATT
1 TTTTTTTCGATT
65365302 TTTTTT
1 TTTTTT
65365308 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTTTTCGATT
Found at i:65369387 original size:18 final size:18
Alignment explanation
Indices: 65369366--65369413 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
65369356 TAAAGCACAA
65369366 TTAATT-ATTTAAGCTAAC
1 TTAATTAATTTAA-CTAAC
65369384 TTAATTAATTTAACTAAC
1 TTAATTAATTTAACTAAC
*
65369402 TTATTTAATTTA
1 TTAATTAATTTA
65369414 TTCCAGCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTAATTTAACTAAC
Found at i:65371319 original size:11 final size:10
Alignment explanation
Indices: 65371294--65371354 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
65371284 ACCAATAAAA
65371294 TAAA-TGAGC
1 TAAATTGAGC
*
65371303 TGAATTGTAGC
1 TAAATTG-AGC
65371314 TAAATTGAGC
1 TAAATTGAGC
**
65371324 TCGATTGAGC
1 TAAATTGAGC
65371334 TGAAA-TGAGC
1 T-AAATTGAGC
*
65371344 TCAATTGAGC
1 TAAATTGAGC
65371354 T
1 T
65371355 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:65371355 original size:20 final size:20
Alignment explanation
Indices: 65371295--65371355 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
65371285 CCAATAAAAT
*
65371295 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
65371315 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
65371336 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
65371356 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:65374130 original size:27 final size:28
Alignment explanation
Indices: 65374075--65374137 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
65374065 ACTAATCCAG
* * * *
65374075 CTAACACACATTAAAAATCATGTAGTAA
1 CTAAGACACATTAAAAATAATGCACTAA
*
65374103 CTATGACACATT-AAAATAATGCACTAA
1 CTAAGACACATTAAAAATAATGCACTAA
65374130 CTAAGACA
1 CTAAGACA
65374138 AATTCAATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (28 bp):
CTAAGACACATTAAAAATAATGCACTAA
Found at i:65378753 original size:24 final size:25
Alignment explanation
Indices: 65378700--65378753 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
65378690 AACAAATTCT
* *
65378700 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
65378725 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
65378748 TTTTTT
1 TTTTTT
65378754 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:65384512 original size:10 final size:9
Alignment explanation
Indices: 65384486--65384519 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
65384476 ATTACTCATC
65384486 TTAGTTAAT
1 TTAGTTAAT
*
65384495 TGAGTTAATT
1 TTAGTTAA-T
65384505 TTAGTTAAT
1 TTAGTTAAT
65384514 TTAGTT
1 TTAGTT
65384520 CACCTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (9 bp):
TTAGTTAAT
Found at i:65384527 original size:19 final size:19
Alignment explanation
Indices: 65384485--65384532 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
65384475 AATTACTCAT
*
65384485 CTTAGTTAATTGAGTTAAT
1 CTTAGTTAATTGAGTTAAC
* * *
65384504 TTTAGTTAATTTAGTTCAC
1 CTTAGTTAATTGAGTTAAC
65384523 CTTAGTTAAT
1 CTTAGTTAAT
65384533 AACTCATCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (19 bp):
CTTAGTTAATTGAGTTAAC
Found at i:65384777 original size:17 final size:18
Alignment explanation
Indices: 65384757--65384806 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
65384747 TTTATTGAAG
65384757 TTAAGTGTTTAAT-GTGT
1 TTAAGTGTTTAATAGTGT
65384774 TTAA--GTTTAATTAGTGT
1 TTAAGTGTTTAA-TAGTGT
65384791 TTAATTGTGTTTAATA
1 TTAA--GTGTTTAATA
65384807 AGTTCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
15 6 0.22
16 1 0.04
17 12 0.44
20 2 0.07
21 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (18 bp):
TTAAGTGTTTAATAGTGT
Found at i:65385857 original size:24 final size:25
Alignment explanation
Indices: 65385830--65385881 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
65385820 GCCTAGCCTC
65385830 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
65385854 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
65385879 TTT
1 TTT
65385882 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:65386097 original size:27 final size:27
Alignment explanation
Indices: 65386063--65386166 Score: 156
Period size: 27 Copynumber: 3.9 Consensus size: 27
65386053 CAAAACAGTC
* *
65386063 ATTT-TACCCCACAAGGGTATCTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGAT
* *
65386089 AATTCTACCCTACAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGAT
*
65386116 ATTTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGAT
65386143 ATTTCTACCCTACAAGGGTATTTC
1 ATTTCTACCCTACAAGGGTATTTC
65386167 AGTGACCCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
26 3 0.04
27 67 0.96
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (27 bp):
ATTTCTACCCTACAAGGGTATTTCGAT
Found at i:65386177 original size:27 final size:27
Alignment explanation
Indices: 65386093--65386192 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
65386083 CTCGATAATT
* **
65386093 CTACCCTACAGGGGTATTTC-GATATTT
1 CTACCCTACAAGGGTATTTCAG-TATCC
* **
65386120 CTACCCTACAAGGGTATTTCGGTATTT
1 CTACCCTACAAGGGTATTTCAGTATCC
65386147 CTACCCTACAAGGGTATTTCAGTGA-CC
1 CTACCCTACAAGGGTATTTCAGT-ATCC
*
65386174 CTACCCTACAGGGGTATTT
1 CTACCCTACAAGGGTATTT
65386193 TGGTAATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 64 0.97
28 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (27 bp):
CTACCCTACAAGGGTATTTCAGTATCC
Found at i:65386178 original size:54 final size:54
Alignment explanation
Indices: 65386067--65386200 Score: 155
Period size: 54 Copynumber: 2.5 Consensus size: 54
65386057 ACAGTCATTT
* * * * **
65386067 TACCCCACAAGGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGATATTTC
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGATATCCC
*
65386121 TACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC-AGTGA-CCC
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGA-T-ATCCC
* *
65386175 TACCCTACAGGGGTATTTTGGTAATT
1 TACCCTACAAGGGTATTTCGGTAATT
65386201 TTACAAACTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 66 0.97
55 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGATATCCC
Found at i:65386215 original size:27 final size:27
Alignment explanation
Indices: 65386185--65386606 Score: 431
Period size: 27 Copynumber: 15.7 Consensus size: 27
65386175 TACCCTACAG
65386185 GGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAA
* *
65386212 GGGTATTTTGGTAATTTTAC-AAGTCGA
1 GGGTATTTTGGTAATTTTACAAACT-AA
* * *
65386239 GGGTATTTTAGTAATTTCACAAA-TCAG
1 GGGTATTTTGGTAATTTTACAAACT-AA
*** *
65386266 GGGTATTTTGGTAATTTGGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAA
* *
65386293 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAA
* *
65386320 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAA
* * * *
65386347 TGGTATTTTGGTAATTCTAC-AAGTCGA
1 GGGTATTTTGGTAATTTTACAAACT-AA
** * * *
65386374 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACTAA
** *
65386401 GGGTATTTT-GTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAA
*
65386427 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAA
** *
65386454 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAA
* *
65386481 GGGTATTTTGGTAATTTTAC-AAGTCGA
1 GGGTATTTTGGTAATTTTACAAACT-AA
* * * *
65386508 GGGTATTTTAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACTAA
* *
65386535 GGGTATTTTGGTAATTTCACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAA
*
65386562 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAA
65386589 GGGTATTTTGGTAATTTT
1 GGGTATTTTGGTAATTTT
65386607 GCTAATCGAG
Statistics
Matches: 327, Mismatches: 60, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
26 27 0.08
27 292 0.89
28 8 0.02
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAA
Found at i:65389304 original size:30 final size:30
Alignment explanation
Indices: 65389270--65389366 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65389260 AGCTCACTCC
65389270 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
65389300 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
65389330 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
65389360 TAGCTCA
1 TAGCTCA
65389367 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:65391729 original size:5 final size:5
Alignment explanation
Indices: 65391719--65391775 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65391709 AAGAGAAAAT
*
65391719 AAAGA AAAGA AAAGA AAA-A AAAAA AGAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A-AAG-A AAAGA AAA-GA AA-AGA
65391766 AAAGA AAAGA
1 AAAGA AAAGA
65391776 GAGGCAACAG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
4 5 0.11
5 28 0.62
6 9 0.20
7 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:65391738 original size:21 final size:20
Alignment explanation
Indices: 65391708--65391777 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
65391698 ACATTCTTGT
65391708 AAAGAGAAAATAAAGAAAAGA
1 AAAGAGAAAATAAA-AAAAGA
*
65391729 AAAGA-AAAAAAAAAAGAAGA
1 AAAGAGAAAATAAAAA-AAGA
65391749 AAA-AGAAAATGAAATAAAAAGA
1 AAAGAGAAAAT--AA-AAAAAGA
65391771 AAAGAGA
1 AAAGAGA
65391778 GGCAACAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 18 0.44
21 5 0.12
22 9 0.22
23 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAGAGAAAATAAAAAAAGA
Found at i:65391855 original size:11 final size:12
Alignment explanation
Indices: 65391823--65391853 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65391813 TTGAGAGAAC
65391823 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65391835 TTGAAAAAGCCT
1 TTGAAAAAGCCT
65391847 TTGAAAA
1 TTGAAAA
65391854 GCAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:65391901 original size:28 final size:28
Alignment explanation
Indices: 65391866--65391919 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
65391856 AAAAAAAAGA
*
65391866 AAAAGAAA-ATGAGATTGAAAAGAGAACG
1 AAAAGAAATATGAGAGTGAAAA-AGAACG
*
65391894 AAAAGAAATTTGAGAGTGAAAAAGAA
1 AAAAGAAATATGAGAGTGAAAAAGAA
65391920 GATGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAATATGAGAGTGAAAAAGAACG
Found at i:65394077 original size:30 final size:30
Alignment explanation
Indices: 65394043--65394139 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65394033 AGCTCACTCC
65394043 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
65394073 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
65394103 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
65394133 TAGCTCA
1 TAGCTCA
65394140 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:65395603 original size:20 final size:20
Alignment explanation
Indices: 65395580--65395626 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
65395570 GGGTTAAGAT
*
65395580 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
65395600 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
65395620 TGAGCTG
1 TGAGCTG
65395627 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:65396938 original size:48 final size:48
Alignment explanation
Indices: 65396886--65396991 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
65396876 ATTGTCTTTT
* *
65396886 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTTAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
65396934 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
65396982 TTTCTTTTTC
1 TTTCTTTTTC
65396992 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:65398924 original size:30 final size:30
Alignment explanation
Indices: 65398890--65398986 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
65398880 TAAACTAAAA
65398890 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65398920 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
65398950 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
65398979 ATGAGCTA
1 -TGAGCTA
65398987 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65401151 original size:12 final size:12
Alignment explanation
Indices: 65401136--65401166 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65401126 TTCTTTTTGC
65401136 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65401148 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65401160 TTTTCAA
1 TTTTCAA
65401167 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:65401243 original size:6 final size:6
Alignment explanation
Indices: 65401227--65401276 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
65401217 TTTCTTTTTA
*
65401227 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
65401276 T
1 T
65401277 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:65401259 original size:37 final size:37
Alignment explanation
Indices: 65401216--65401286 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
65401206 CTTGCCTCTC
65401216 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
65401253 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
65401287 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:65401287 original size:16 final size:16
Alignment explanation
Indices: 65401212--65401272 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
65401202 GCCTCTTGCC
*
65401212 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
65401228 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
65401244 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
65401260 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
65401273 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:65402202 original size:11 final size:10
Alignment explanation
Indices: 65402188--65402243 Score: 62
Period size: 9 Copynumber: 5.5 Consensus size: 10
65402178 TTTTAACTCG
65402188 ATTTTTTTTT
1 ATTTTTTTTT
65402198 CATTTTTTTTT
1 -ATTTTTTTTT
65402209 -TTTTTTTTT
1 ATTTTTTTTT
65402218 -TTTTTTTTT
1 ATTTTTTTTT
*
65402227 GAATTTTTTTTA
1 --ATTTTTTTTT
65402239 ATTTT
1 ATTTT
65402244 CTCTTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
9 18 0.44
10 5 0.12
11 10 0.24
12 8 0.20
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.86
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:65402205 original size:10 final size:10
Alignment explanation
Indices: 65402190--65402243 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
65402180 TTAACTCGAT
*
65402190 TTTTTTTTCA
1 TTTTTTTTAA
*
65402200 TTTTTTTT-T
1 TTTTTTTTAA
**
65402209 TTTTTTTTTT
1 TTTTTTTTAA
65402219 TTTTTTTTGAA
1 TTTTTTTT-AA
65402230 TTTTTTTTAA
1 TTTTTTTTAA
65402240 TTTT
1 TTTT
65402244 CTCTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
9 8 0.21
10 23 0.59
11 8 0.21
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.87
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:65402223 original size:30 final size:30
Alignment explanation
Indices: 65402189--65402255 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
65402179 TTTAACTCGA
* ** * *
65402189 TTTTTTTTT-CATTTTTTTTTTTTTTTTTT
1 TTTTTTTTTGAATTTTTTTTAATTTTCTCT
65402218 TTTTTTTTTGAATTTTTTTTAATTTTCTCT
1 TTTTTTTTTGAATTTTTTTTAATTTTCTCT
65402248 TTTTTTTT
1 TTTTTTTT
65402256 AAATCAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.07, C:0.04, G:0.01, T:0.87
Consensus pattern (30 bp):
TTTTTTTTTGAATTTTTTTTAATTTTCTCT
Found at i:65402237 original size:1 final size:1
Alignment explanation
Indices: 65402189--65402226 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
65402179 TTTAACTCGA
**
65402189 TTTTTTTTTCATTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
65402227 GAATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:65403977 original size:30 final size:30
Alignment explanation
Indices: 65403943--65404039 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65403933 TAAACTAAAA
*
65403943 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
65403973 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65404003 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
65404032 ATGAGCTA
1 -TGAGCTA
65404040 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:65404271 original size:13 final size:14
Alignment explanation
Indices: 65404253--65404282 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
65404243 AGTTGTAAAG
65404253 TTTTATTT-TTTAT
1 TTTTATTTATTTAT
65404266 TTTTATTTATTTAT
1 TTTTATTTATTTAT
65404280 TTT
1 TTT
65404283 ACTTAGTTTA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:65412642 original size:19 final size:18
Alignment explanation
Indices: 65412618--65412663 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
65412608 AAAAAAAGTT
**
65412618 AAAAAAAAAGTTTCGCAAA
1 AAAAAAAAAAATT-GCAAA
65412637 AAAAAAAAAAATTGCAAA
1 AAAAAAAAAAATTGCAAA
65412655 AAAAAAAAA
1 AAAAAAAAA
65412664 TTGCATACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAAATTGCAAA
Found at i:65412655 original size:16 final size:16
Alignment explanation
Indices: 65412636--65412668 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
65412626 AGTTTCGCAA
65412636 AAAAAAAAAAAATTGC
1 AAAAAAAAAAAATTGC
65412652 AAAAAAAAAAAATTGC
1 AAAAAAAAAAAATTGC
65412668 A
1 A
65412669 TACGGTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAAAAAAATTGC
Found at i:65414940 original size:17 final size:18
Alignment explanation
Indices: 65414901--65414942 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
65414891 AAGAAGAAAA
65414901 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
65414918 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
65414935 TCAAAAGA
1 ACAAAAGA
65414943 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:65420592 original size:30 final size:30
Alignment explanation
Indices: 65420521--65420603 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
65420511 CTTTTGTTTC
* * *
65420521 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATATCA
65420552 AATTTC-TTTTCGTTCTCTTTTTCAATATC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATATCA
* *
65420581 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
65420604 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 8 0.18
ACGTcount: A:0.14, C:0.20, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATATCA
Found at i:65420603 original size:18 final size:18
Alignment explanation
Indices: 65420554--65420609 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65420544 CACTCTCAAA
* *
65420554 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
65420571 TTTCAATATCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
65420589 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
65420608 TT
1 TT
65420610 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:65420610 original size:12 final size:12
Alignment explanation
Indices: 65420579--65420603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65420569 TTTTTCAATA
65420579 TCATTTTCTTTT
1 TCATTTTCTTTT
65420591 TCATTTTCTTTT
1 TCATTTTCTTTT
65420603 T
1 T
65420604 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:65420698 original size:21 final size:19
Alignment explanation
Indices: 65420672--65420735 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
65420662 CTCTTGCCTC
65420672 TCTTTTCCTTTTATTTCGTTT
1 TCTTTT-CTTTT-TTTCGTTT
* *
65420693 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTT-TTTTTCGTTT
65420714 TCTTTTCTTTTCTTT-GTTT
1 TCTTTTCTTTT-TTTCGTTT
65420733 TCT
1 TCT
65420736 CTTTACAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.22
20 9 0.25
21 13 0.36
22 6 0.17
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.75
Consensus pattern (19 bp):
TCTTTTCTTTTTTTCGTTT
Found at i:65420712 original size:15 final size:14
Alignment explanation
Indices: 65420672--65420728 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 14
65420662 CTCTTGCCTC
65420672 TCTTTTCCTTTTAT-T
1 TCTTTT-CTTTT-TCT
65420687 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65420702 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65420719 TCTTTTCTTT
1 TCTTTTCTTT
65420729 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 5 0.14
15 17 0.46
16 8 0.22
17 7 0.19
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65420738 original size:21 final size:20
Alignment explanation
Indices: 65420670--65420739 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
65420660 GCCTCTTGCC
65420670 TCTCTTTTCCTTTTATTTCGTTT
1 TCTCTTTT-CTTTT-TTT-GTTT
*
65420693 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTTTTTTTG-TTT
65420713 T-TCTTTTCTTTTCTTTGTTT
1 TCTCTTTTCTTTT-TTTGTTT
65420733 TCTCTTT
1 TCTCTTT
65420740 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 19 0.46
21 13 0.32
22 4 0.10
23 3 0.07
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.74
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTGTTT
Found at i:65423277 original size:30 final size:30
Alignment explanation
Indices: 65423243--65423339 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65423233 TAAACTAAAA
65423243 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65423273 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65423303 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65423333 TGAGCTA
1 TGAGCTA
65423340 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65424191 original size:15 final size:15
Alignment explanation
Indices: 65424171--65424218 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65424161 TCAAAGATGG
65424171 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
65424186 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
65424200 GTTTATGGATATAAA
1 GTTTATGGATATGAA
65424215 GTTT
1 GTTT
65424219 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:65424205 original size:14 final size:14
Alignment explanation
Indices: 65424165--65424208 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
65424155 AAGGATTCAA
65424165 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
65424179 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
65424194 AGATGGGTTTATGG
1 AGATGGGTTTATGG
65424208 A
1 A
65424209 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:65424234 original size:29 final size:29
Alignment explanation
Indices: 65424165--65424224 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
65424155 AAGGATTCAA
*
65424165 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
65424194 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
65424223 AG
1 AG
65424225 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:65430146 original size:23 final size:22
Alignment explanation
Indices: 65430095--65430146 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
65430085 CCTCGTCTTT
*
65430095 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
65430117 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
65430140 TTCTTTT
1 TTCTTTT
65430147 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:65430155 original size:12 final size:12
Alignment explanation
Indices: 65430104--65430158 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
65430094 TTTCTTTTGT
65430104 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
65430117 -TCATTTTC-TC
1 TTCTTTTTCAAC
65430127 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
65430140 TTCTTTTTCAAT
1 TTCTTTTTCAAC
65430152 TTCTTTT
1 TTCTTTT
65430159 CTGTTACACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:65433125 original size:13 final size:13
Alignment explanation
Indices: 65433107--65433131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65433097 TCATCTTTTT
65433107 TGATTTTTTTGAC
1 TGATTTTTTTGAC
65433120 TGATTTTTTTGA
1 TGATTTTTTTGA
65433132 GGGAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TGATTTTTTTGAC
Found at i:65444114 original size:10 final size:10
Alignment explanation
Indices: 65444098--65444155 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
65444088 CAACTCCGAC
65444098 CAGCTCAATT
1 CAGCTCAATT
* *
65444108 GAGCTCATTT
1 CAGCTCAATT
65444118 CAGCTCAA-T
1 CAGCTCAATT
65444127 CGAGCTCAATT
1 C-AGCTCAATT
*
65444138 TAGCTACAATT
1 CAGCT-CAATT
65444149 CAGCTCA
1 CAGCTCA
65444156 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:65444121 original size:20 final size:20
Alignment explanation
Indices: 65444098--65444158 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
65444088 CAACTCCGAC
65444098 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
65444118 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
65444139 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
65444159 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:65450842 original size:20 final size:20
Alignment explanation
Indices: 65450817--65450871 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
65450807 TGTGGTTCAA
*
65450817 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
65450837 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
65450857 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
65450872 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:65453562 original size:12 final size:12
Alignment explanation
Indices: 65453543--65453576 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65453533 AGAAAGAAAA
65453543 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
65453555 GTGTGAAAAAGT
1 GAGTGAAAAGGT
65453567 GAGTGAAAAG
1 GAGTGAAAAG
65453577 AAACGAGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:65455281 original size:19 final size:19
Alignment explanation
Indices: 65455236--65455281 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65455226 ATTAACACAC
*
65455236 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65455255 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
65455273 AATTAATAA
1 AATTAATAA
65455282 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65455538 original size:30 final size:32
Alignment explanation
Indices: 65455472--65455539 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 32
65455462 GAAGAAAGAA
65455472 GGAGCTCAAAGTAAGCTCGATTGAGCTGAAAC
1 GGAGCTCAAAGTAAGCTCGATTGAGCTGAAAC
* *
65455504 -GAGCTCAAA-TGAGCT-GAGTTGAGCT-AGAC
1 GGAGCTCAAAGTAAGCTCGA-TTGAGCTGAAAC
65455533 GGAGCTC
1 GGAGCTC
65455540 GAGGAGCTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 5 0.16
30 18 0.56
31 9 0.28
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (32 bp):
GGAGCTCAAAGTAAGCTCGATTGAGCTGAAAC
Found at i:65456362 original size:30 final size:29
Alignment explanation
Indices: 65456328--65456423 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
65456318 AGCTCACTCC
*
65456328 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ATTTAGCTCACGAGCTAAACCT
* * * * * *
65456358 TAGCTCAGCTTTAGCTTAGGAGTTTAATCT
1 TAGCTCA-ATTTAGCTCACGAGCTAAACCT
* *
65456388 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAA-TTTAGCTCACGAGCTAAACCT
65456418 TAGCTC
1 TAGCTC
65456424 TTTTTAGTTT
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (29 bp):
TAGCTCAATTTAGCTCACGAGCTAAACCT
Found at i:65458091 original size:13 final size:13
Alignment explanation
Indices: 65458073--65458107 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
65458063 TACAAGTTTG
65458073 AAAAAAAAAACCC
1 AAAAAAAAAACCC
**
65458086 AAAAAAAAAATTC
1 AAAAAAAAAACCC
65458099 AAAAAAAAA
1 AAAAAAAAA
65458108 GAAGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAAAAAACCC
Found at i:65459050 original size:21 final size:20
Alignment explanation
Indices: 65459016--65459081 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
65459006 ACATTCTTGT
65459016 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
65459037 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
*
65459058 AAAGAAAACAAAATAAAAAGAA
1 AAAGAAAA-ACAA-AAAAAGAA
65459080 AA
1 AA
65459082 GAGAGGCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.21
21 20 0.53
22 10 0.26
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:65459051 original size:6 final size:5
Alignment explanation
Indices: 65459027--65459083 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
65459017 AAGAGAAAAC
* * *
65459027 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
65459074 AAAGA AAAGA
1 AAAGA AAAGA
65459084 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:65459076 original size:25 final size:25
Alignment explanation
Indices: 65459031--65459079 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
65459021 GAAAACAAAG
*
65459031 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACAAAAA-CAAAAGAAGA
65459057 AAAAGAAAACAAAATA-AAAAGAA
1 AAAAGAAAACAAAA-ACAAAAGAA
65459080 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAACAAAAGAAGA
Found at i:65459215 original size:30 final size:31
Alignment explanation
Indices: 65459152--65459222 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
65459142 TTTGAAAAGC
* *
65459152 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
65459182 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
65459212 AAAAAGAAATT
1 AAAAAGAAATT
65459223 GTAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:65461787 original size:17 final size:15
Alignment explanation
Indices: 65461767--65461805 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
65461757 GCGAGTGAGA
65461767 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
65461784 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
65461799 AAGATGA
1 AA-ATGA
65461806 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:65463304 original size:20 final size:20
Alignment explanation
Indices: 65463279--65463333 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
65463269 TGTGGTTCAA
*
65463279 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
65463299 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
65463319 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
65463334 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:65466016 original size:12 final size:12
Alignment explanation
Indices: 65465997--65466030 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65465987 AGAAAGAAAA
65465997 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
65466009 GTGTGAAAAAGT
1 GAGTGAAAAGGT
65466021 GAGTGAAAAG
1 GAGTGAAAAG
65466031 AAACGAGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:65467827 original size:19 final size:19
Alignment explanation
Indices: 65467782--65467827 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65467772 ATTAACACAC
*
65467782 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65467801 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
65467819 AATTAATAA
1 AATTAATAA
65467828 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65468909 original size:30 final size:29
Alignment explanation
Indices: 65468875--65468969 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 29
65468865 AGCTCACTCC
*
65468875 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ATTTAGCTCACGAGCTAAACCT
* * * * * *
65468905 TAGCTCAGCTTTAGCTTAGGAGTTTAATCT
1 TAGCTCA-ATTTAGCTCACGAGCTAAACCT
* *
65468935 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAA-TTTAGCTCACGAGCTAAACCT
65468965 TAGCT
1 TAGCT
65468970 TTTTTTAGTT
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (29 bp):
TAGCTCAATTTAGCTCACGAGCTAAACCT
Found at i:65471574 original size:21 final size:20
Alignment explanation
Indices: 65471540--65471605 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
65471530 AGATTCTTGT
65471540 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
65471561 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
*
65471582 AAAGAAAACAAAATAAAAAGAA
1 AAAGAAAA-ACAA-AAAAAGAA
65471604 AA
1 AA
65471606 GAGAGGCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.21
21 20 0.53
22 10 0.26
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:65471575 original size:6 final size:5
Alignment explanation
Indices: 65471551--65471607 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
65471541 AAGAGAAAAC
* * *
65471551 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
65471598 AAAGA AAAGA
1 AAAGA AAAGA
65471608 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:65471600 original size:25 final size:25
Alignment explanation
Indices: 65471555--65471603 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
65471545 GAAAACAAAG
*
65471555 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACAAAAA-CAAAAGAAGA
65471581 AAAAGAAAACAAAATA-AAAAGAA
1 AAAAGAAAACAAAA-ACAAAAGAA
65471604 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAACAAAAGAAGA
Found at i:65471739 original size:30 final size:31
Alignment explanation
Indices: 65471676--65471746 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
65471666 TTTGAAAAGC
* *
65471676 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
65471706 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
65471736 AAAAAGAAATT
1 AAAAAGAAATT
65471747 GTAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:65473989 original size:30 final size:30
Alignment explanation
Indices: 65473955--65474052 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
65473945 AGCTCACTCC
65473955 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
65473985 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * *
65474015 CAACTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
65474045 TAGCTCAT
1 TAGCTCAT
65474053 TTTAGTTTAA
Statistics
Matches: 48, Mismatches: 18, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:65477035 original size:14 final size:14
Alignment explanation
Indices: 65477016--65477060 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
65477006 AACTCATCTT
*
65477016 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
65477030 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
65477043 AATTTAATTTAATG
1 AGTTTAATTTAATG
65477057 AGTT
1 AGTT
65477061 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:65478086 original size:15 final size:15
Alignment explanation
Indices: 65478040--65478086 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
65478030 AAACCTACAA
*
65478040 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
65478055 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
65478069 AAACTTCATATCCAT
1 AAACTTCATATCCAT
65478084 AAA
1 AAA
65478087 ACCAACTTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:65479765 original size:30 final size:30
Alignment explanation
Indices: 65479680--65479776 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
65479670 TAAACTAAAA
* * *
65479680 TGAGCTAAGATTTAGCTTGTGAGCTAAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
65479710 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
65479740 TGAGCTAAGTTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
65479769 ATGAGCTA
1 -TGAGCTA
65479777 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Done.