Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold121
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1096690
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30
Warning! 96926 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:1356 original size:53 final size:53
Alignment explanation
Indices: 1293--1446 Score: 258
Period size: 51 Copynumber: 2.9 Consensus size: 53
1283 CTTTTTGCAT
*
1293 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAAGAATTTTACAA
1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA
*
1346 AATCCTTGTTGTCAAG--TTTTTGTATACAAGGTAGGTTCAATAATTTTACAA
1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA
* *
1397 AATCCTTGTAGTCAAATTTTTTTGTATACAAGGTAGGTACAATAATTTTA
1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTA
1447 ACATAACAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 47 0.50
53 47 0.50
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (53 bp):
AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA
Found at i:1391 original size:51 final size:51
Alignment explanation
Indices: 1293--1446 Score: 236
Period size: 53 Copynumber: 2.9 Consensus size: 51
1283 CTTTTTGCAT
*
1293 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAAGAATTTTACAA
1 AATCCTTGTTGTCAAG--TTTTTGTATACAAGGTAGGTACAATAATTTTACAA
*
1346 AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTTCAATAATTTTACAA
1 AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTACAATAATTTTACAA
* *
1397 AATCCTTGTAGTCAAATTTTTTTGTATACAAGGTAGGTACAATAATTTTA
1 AATCCTTGTTGTC-AA-GTTTTTGTATACAAGGTAGGTACAATAATTTTA
1447 ACATAACAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 45 0.48
52 2 0.02
53 47 0.50
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (51 bp):
AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTACAATAATTTTACAA
Found at i:4878 original size:53 final size:54
Alignment explanation
Indices: 4820--4931 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
4810 AATAAGCCTT
* * * *
4820 TTTTACAAAATCCTTGTTGTCAA-GTTTTTTTGTATACGAGGTAGGTACAATAA
1 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA
4873 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA
1 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA
4927 TTTTA
1 TTTTA
4932 ATGTGGCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
53 22 0.41
54 32 0.59
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (54 bp):
TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA
Found at i:4983 original size:16 final size:16
Alignment explanation
Indices: 4959--4995 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4949 GATAGATTTT
4959 AAAAATAAAAAATGTG
1 AAAAATAAAAAATGTG
* *
4975 AAAAGTAAAAATTGTG
1 AAAAATAAAAAATGTG
4991 AAAAA
1 AAAAA
4996 AAATAATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAAATGTG
Found at i:9029 original size:2 final size:2
Alignment explanation
Indices: 9022--9158 Score: 213
Period size: 2 Copynumber: 69.0 Consensus size: 2
9012 ATAAGATACA
*
9022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
9064 TC TT TC TC TC TC TT TC TC TC TC TC TT TC TC TC GC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9106 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9147 TC TC TC TC TC TC
1 TC TC TC TC TC TC
9159 CTGTAACTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
1 1 0.01
2 121 0.99
ACGTcount: A:0.00, C:0.47, G:0.01, T:0.53
Consensus pattern (2 bp):
TC
Found at i:10086 original size:32 final size:32
Alignment explanation
Indices: 10045--10155 Score: 179
Period size: 32 Copynumber: 3.5 Consensus size: 32
10035 GTTTAGTGAT
10045 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
10077 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
* * *
10109 GTACAATGCTGTTCAGTGCCCTGTAAAGTGGC
1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
10141 GTACAGT-CTAGGTCA
1 GTACAGTGCT-GGTCA
10156 CTAGAACTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 2 0.03
32 71 0.97
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (32 bp):
GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC
Found at i:10275 original size:21 final size:21
Alignment explanation
Indices: 10235--10285 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
10225 GGGTCAGTGA
*
10235 AATGTACAGTGAGATACAGAT
1 AATGTACAGTGAGATACAGAC
*
10256 AATGTACAGT-AGATGTCAGAC
1 AATGTACAGTGAGAT-ACAGAC
10277 AATGT-CAGT
1 AATGTACAGT
10286 CAATTTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (21 bp):
AATGTACAGTGAGATACAGAC
Found at i:18365 original size:2 final size:2
Alignment explanation
Indices: 18358--18413 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
18348 TATCTCCCCT
18358 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
18400 AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC
18414 TTTAAGAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27207 original size:25 final size:25
Alignment explanation
Indices: 25487--27198 Score: 2309
Period size: 25 Copynumber: 68.5 Consensus size: 25
25477 CTCCGTGACT
* **
25487 AATGTCACAACACATGGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
25512 AATGTCACAACGTACAGTCAGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25537 ACTGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
25562 AATGTTACAACATACAGTCTACACC
1 AATGTCACAACATACAGTCTGCACC
*
25587 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25612 AATGTCACAACATACAGTCTGAACC
1 AATGTCACAACATACAGTCTGCACC
* * *
25637 AATGTTACAACATACAATCTGCAGC
1 AATGTCACAACATACAGTCTGCACC
*
25662 AATGTCACAACATTCAGTCTGCA-C
1 AATGTCACAACATACAGTCTGCACC
* *
25686 AATTTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
25711 AATTTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25736 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25761 AATGTCACAACATTCAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25786 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25811 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
25836 AATGTCACAACGTATAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
25861 AATGAT-ACAACATACAGTCTGCACT
1 AATG-TCACAACATACAGTCTGCACC
** *
25886 AATGTCACAACATTTAGTCTGCACA
1 AATGTCACAACATACAGTCTGCACC
*
25911 AATGTCACAACATACAGTCTGCACT
1 AATGTCACAACATACAGTCTGCACC
**
25936 AATGTCACAACATACAGTCTGCATT
1 AATGTCACAACATACAGTCTGCACC
** * * *
25961 AATGTTTCAACAAACAGTTTACACC
1 AATGTCACAACATACAGTCTGCACC
*
25986 AATATCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* **
26011 AATGTTACAACATTTAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26036 AATGTTACAACATACCA-TCTGCACT
1 AATGTCACAACATA-CAGTCTGCACC
*
26061 AATGTTACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26086 AATGTCACAACATACAGTCTGCATC
1 AATGTCACAACATACAGTCTGCACC
* * *
26111 AATGTCCCAAAATACAATCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26136 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* **
26161 AATGTCACAACGTATTGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26186 AATGTCACAACGTACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26211 AATGTCACAACATACCGTATGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26236 AATGTCACAACATACAGTCTGAACC
1 AATGTCACAACATACAGTCTGCACC
* *
26261 AATGTTACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26286 AATGTCACAACGTACAGTCTTCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26311 AGTGTTACAACATACAGTCTGCA-C
1 AATGTCACAACATACAGTCTGCACC
* *
26335 ATATCTCACAACATACAGTCTGCAACA
1 A-ATGTCACAACATACAGTCTGC-ACC
** * *
26362 AATGTCACAAGGTACCGTCTGCAAC
1 AATGTCACAACATACAGTCTGCACC
* * ** *
26387 AATGTTACAATATTTAGACTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26412 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
**
26437 AATGTCACAACATATTGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* * *
26462 AATGTCACAACGTAAAATCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26487 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26512 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26537 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26562 AATGTCACAACGTACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26587 AATGTTACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* * *
26612 AATGTCACAGCGTACAGACTGCACC
1 AATGTCACAACATACAGTCTGCACC
26637 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* * *
26662 AATGTCACAACACACGGTTTGCACC
1 AATGTCACAACATACAGTCTGCACC
* * * *
26687 AATATTATAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26712 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* *
26737 AATGAT-ACAACGTACAGTATGCACC
1 AATG-TCACAACATACAGTCTGCACC
*
26762 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26787 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26812 AATGTCACAACATACCGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26837 AATGTCACAACGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
* **
26862 AATGTTACAACATTTAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26887 AATGTCACAATATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26912 AATGTCAAAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
26937 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
26962 AATGTCAAAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
26987 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
27012 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
27037 AATGACACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
**
27062 AATGTCACAATGTACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
** *
27087 AATGTCACAATGTGCAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
*
27112 AATGTCACAACATTCAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
27137 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
27162 AATGTCACAACATACAGTCTGCACC
1 AATGTCACAACATACAGTCTGCACC
27187 AATGTCACAACA
1 AATGTCACAACA
27199 CATGGTCTGT
Statistics
Matches: 1487, Mismatches: 190, Indels: 20
0.88 0.11 0.01
Matches are distributed among these distances:
24 27 0.02
25 1438 0.97
26 21 0.01
27 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (25 bp):
AATGTCACAACATACAGTCTGCACC
Found at i:28073 original size:20 final size:20
Alignment explanation
Indices: 28048--28086 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28038 AAATTATGAT
28048 AATATC-ATCATCATGAAACA
1 AATATCGATCATC-TGAAACA
28068 AATATCGGATCATCTGAAA
1 AATATC-GATCATCTGAAA
28087 TGATTGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (20 bp):
AATATCGATCATCTGAAACA
Found at i:29245 original size:29 final size:29
Alignment explanation
Indices: 29193--29249 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
29183 CAGTTCCGGC
* * *
29193 GCACGTGGTTTTGAATAACCCTCAGGTGA
1 GCACATGGTTTTGAAGAACACTCAGGTGA
*
29222 GCACATGGTTTTGAAGAATACTCAGGTG
1 GCACATGGTTTTGAAGAACACTCAGGTG
29250 CATGTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (29 bp):
GCACATGGTTTTGAAGAACACTCAGGTGA
Found at i:46282 original size:2 final size:2
Alignment explanation
Indices: 46275--46322 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
46265 TGTTTACTAT
46275 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
46317 GA GA GA
1 GA GA GA
46323 AGCTCAATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46755 original size:63 final size:63
Alignment explanation
Indices: 46632--46755 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
46622 TTTCTGTCGA
* * * *
46632 CATGCGACTTATCTATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATATTCATGTTGG
1 CATGCGACTTATCTATGTCAACATGCAGCTTAATTATGTCAACATGCAAGATAATAATGTTGG
* * * *
46695 CATGCGACTTAAT-TATGTCGACATGC-GACTTATTTGTGTCAACATGCAAGTTAATAATGTT
1 CATGCGACTT-ATCTATGTCAACATGCAG-CTTAATTATGTCAACATGCAAGATAATAATGTT
46756 AACATGCAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.94
64 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (63 bp):
CATGCGACTTATCTATGTCAACATGCAGCTTAATTATGTCAACATGCAAGATAATAATGTTGG
Found at i:46847 original size:21 final size:21
Alignment explanation
Indices: 46645--46873 Score: 156
Period size: 21 Copynumber: 10.9 Consensus size: 21
46635 GCGACTTATC
*
46645 TATGTCAACATGCAGGTTAAT
1 TATGTCAACATGCAAGTTAAT
* *
46666 TATGTTAACATGCAAGAT-AT
1 TATGTCAACATGCAAGTTAAT
*** * *
46686 TCATGTTGGCATGCGACTTAAT
1 T-ATGTCAACATGCAAGTTAAT
* * * *
46708 TATGTCGACATGCGACTTATT
1 TATGTCAACATGCAAGTTAAT
*
46729 TGTGTCAACATGCAAGTTAAT
1 TATGTCAACATGCAAGTTAAT
* * *
46750 AATGTTAACATGCAAGAT-AT
1 TATGTCAACATGCAAGTTAAT
*** * *
46770 TCATGTTGGCATGCGACTTAAT
1 T-ATGTCAACATGCAAGTTAAT
* * * *
46792 TATGTCGACATGCGATTTATT
1 TATGTCAACATGCAAGTTAAT
46813 TATGTCAACATGCAAGTTAAT
1 TATGTCAACATGCAAGTTAAT
* * *
46834 TATGTTAACATGCAAGATACT
1 TATGTCAACATGCAAGTTAAT
* *
46855 TAAGTAAACATGCAAGTTA
1 TATGTCAACATGCAAGTTA
46874 TCCCGAATGT
Statistics
Matches: 164, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
20 5 0.03
21 153 0.93
22 6 0.04
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (21 bp):
TATGTCAACATGCAAGTTAAT
Found at i:46865 original size:42 final size:41
Alignment explanation
Indices: 46645--46873 Score: 188
Period size: 42 Copynumber: 5.5 Consensus size: 41
46635 GCGACTTATC
*
46645 TATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATAT
1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT
*** * * ** * **
46686 TCATGTTGGCATGCGACTTAATTATGTCGACATGCGACTTATT
1 T-ATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T
* *
46729 TGTGTCAACATGCAAGTTAATAATGTTAACATGCAAGATAT
1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT
*** * * ** * **
46770 TCATGTTGGCATGCGACTTAATTATGTCGACATGCGATTTATT
1 T-ATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T
46813 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATACT
1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T
* *
46855 TAAGTAAACATGCAAGTTA
1 TATGTCAACATGCAAGTTA
46874 TCCCGAATGT
Statistics
Matches: 136, Mismatches: 48, Indels: 7
0.71 0.25 0.04
Matches are distributed among these distances:
41 3 0.02
42 129 0.95
43 4 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (41 bp):
TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT
Found at i:46867 original size:84 final size:84
Alignment explanation
Indices: 46626--46852 Score: 409
Period size: 84 Copynumber: 2.7 Consensus size: 84
46616 AACATATTTC
* *
46626 TGTCGACATGCGACTTATCTATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATATTCATG
1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG
46691 TTGGCATGCGACTTAATTA
66 TTGGCATGCGACTTAATTA
* *
46710 TGTCGACATGCGACTTATTTGTGTCAACATGCAAGTTAATAATGTTAACATGCAAGATATTCATG
1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG
46775 TTGGCATGCGACTTAATTA
66 TTGGCATGCGACTTAATTA
*
46794 TGTCGACATGCGATTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA
1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA
46853 CTTAAGTAAA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 136 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (84 bp):
TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG
TTGGCATGCGACTTAATTA
Found at i:47226 original size:21 final size:21
Alignment explanation
Indices: 47200--47286 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
47190 AAGATTTGAA
* *
47200 CTTGCATGTTGACATAAGTCT
1 CTTGCATGTTGACATAATTAT
***
47221 CTTGCATAAGGACATAATTAT
1 CTTGCATGTTGACATAATTAT
47242 CTTGCATGTTGACATAATTAT
1 CTTGCATGTTGACATAATTAT
* *
47263 CTTGGATGTAGACATAATTCAT
1 CTTGCATGTTGACATAATT-AT
47285 CT
1 CT
47287 AACATGTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 51 0.93
22 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTGCATGTTGACATAATTAT
Found at i:47277 original size:42 final size:43
Alignment explanation
Indices: 47200--47286 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 43
47190 AAGATTTGAA
*
47200 CTTGCATGTTGACATAAGTCTCTTGCATAAGGACATAATT-AT
1 CTTGCATGTTGACATAAGTATCTTGCATAAGGACATAATTCAT
* * *
47242 CTTGCATGTTGACATAATTATCTTGGATGTA-GACATAATTCAT
1 CTTGCATGTTGACATAAGTATCTTGCAT-AAGGACATAATTCAT
47285 CT
1 CT
47287 AACATGTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 34 0.87
43 5 0.13
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (43 bp):
CTTGCATGTTGACATAAGTATCTTGCATAAGGACATAATTCAT
Found at i:49306 original size:4 final size:4
Alignment explanation
Indices: 49297--49326 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
49287 AGCAAAGATG
49297 ACTT ACTT ACTT ACTT ACTT ACTT ACTT AC
1 ACTT ACTT ACTT ACTT ACTT ACTT ACTT AC
49327 ATAACTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (4 bp):
ACTT
Found at i:49353 original size:2 final size:2
Alignment explanation
Indices: 49340--49372 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49330 ACTAAGTTTG
*
49340 CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
49373 ATTGTACATT
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:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:50313 original size:19 final size:19
Alignment explanation
Indices: 50289--50327 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
50279 TTCCTGGTAA
50289 TTTAAGATAATCTCCCTGT
1 TTTAAGATAATCTCCCTGT
50308 TTTAAGATAATCTCCCTGT
1 TTTAAGATAATCTCCCTGT
50327 T
1 T
50328 GTCCTGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44
Consensus pattern (19 bp):
TTTAAGATAATCTCCCTGT
Found at i:61383 original size:24 final size:25
Alignment explanation
Indices: 61332--61394 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
61322 TATGTGATGA
*
61332 AGGGGGCTGGGCTATATAAAGTACC
1 AGGGGGCAGGGCTATATAAAGTACC
* * *
61357 AGGGGGCAGAGCTATGTATAGTA-C
1 AGGGGGCAGGGCTATATAAAGTACC
*
61381 AGGGGCCAGGGCTA
1 AGGGGGCAGGGCTA
61395 ACTACCTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.27, C:0.16, G:0.40, T:0.17
Consensus pattern (25 bp):
AGGGGGCAGGGCTATATAAAGTACC
Found at i:64173 original size:2 final size:2
Alignment explanation
Indices: 64168--64225 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
64158 TATACGTGTG
64168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
64210 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
64226 CTTTTTTCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:65896 original size:26 final size:26
Alignment explanation
Indices: 65860--65937 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
65850 TAATTCCCCA
65860 AAACTCTATTTCAATCTCTCCTTCAT
1 AAACTCTATTTCAATCTCTCCTTCAT
* *
65886 AAACTCTATTTCAATCTAT-CTGTCAC
1 AAACTCTATTTCAATCTCTCCT-TCAT
* *
65912 AAACTCTATTCCAATCTCTCCGTCAT
1 AAACTCTATTTCAATCTCTCCTTCAT
65938 CACATTGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.05
26 41 0.93
27 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38
Consensus pattern (26 bp):
AAACTCTATTTCAATCTCTCCTTCAT
Found at i:68956 original size:33 final size:33
Alignment explanation
Indices: 68895--69043 Score: 160
Period size: 33 Copynumber: 4.5 Consensus size: 33
68885 TGAATGATGG
* * *
68895 TGTTCGACTCCACTAG-ATGTTCGTGAATGATTT
1 TGTTCTACTCCACTAGAAT-TACGAGAATGATTT
*
68928 TTTTCTACTCCACTAGAATTACGAGAATGATTT
1 TGTTCTACTCCACTAGAATTACGAGAATGATTT
* * * *
68961 TTTTCTACTCCGCTAGAAGTACGAGAATTATTT
1 TGTTCTACTCCACTAGAATTACGAGAATGATTT
* *
68994 TGTTCTA-TACTACTAGAATTACGAGATTGATTT
1 TGTTCTACT-CCACTAGAATTACGAGAATGATTT
69027 TGTTCTA-TACCACTAGA
1 TGTTCTACT-CCACTAGA
69044 TGACCGGGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
32 1 0.01
33 97 0.97
34 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTTCTACTCCACTAGAATTACGAGAATGATTT
Found at i:68977 original size:66 final size:66
Alignment explanation
Indices: 68895--69059 Score: 183
Period size: 66 Copynumber: 2.5 Consensus size: 66
68885 TGAATGATGG
* * * *
68895 TGTTCGACTCCACTAGATGTTCGTGAATGATTTTTTTCTACT-CCACTAGAATTACGAGAATGAT
1 TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTA-TACCACTAGAATTACGAGAATGAT
68959 TT
65 TT
* * * * * *
68961 TTTTCTACTCCGCTAGAAGTACGAGAATTATTTTGTTCTATACTACTAGAATTACGAGATTGATT
1 TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTATACCACTAGAATTACGAGAATGATT
69026 T
66 T
*
69027 TGTTCTA-TACCACTAGATG-ACCGGGAATGATTT
1 TGTTCTACT-CCACTAGATGTA-CGAGAATGATTT
69060 GGCTTCAGAT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
65 3 0.04
66 78 0.96
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (66 bp):
TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTATACCACTAGAATTACGAGAATGATT
T
Found at i:73116 original size:2 final size:2
Alignment explanation
Indices: 73109--73142 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
73099 ATAAACCAAC
73109 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
73143 GTGGTGGAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:73658 original size:14 final size:14
Alignment explanation
Indices: 73623--73669 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
73613 GATGAGAGTG
73623 GGGGTGAAGGGGGT
1 GGGGTGAAGGGGGT
*
73637 GGGGGTGAAGTGGGT
1 -GGGGTGAAGGGGGT
*
73652 GGTGTGAAGGGGGT
1 GGGGTGAAGGGGGT
73666 GGGG
1 GGGG
73670 GTAAGGTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.13, C:0.00, G:0.70, T:0.17
Consensus pattern (14 bp):
GGGGTGAAGGGGGT
Found at i:73675 original size:14 final size:15
Alignment explanation
Indices: 73620--73680 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
73610 AAAGATGAGA
73620 GTGGGGGTGAAGGGG
1 GTGGGGGTGAAGGGG
*
73635 GTGGGGGTGAAGTGG
1 GTGGGGGTGAAGGGG
*
73650 GT-GGTGTGAAGGGG
1 GTGGGGGTGAAGGGG
73664 GTGGGGGT-AAGGTGG
1 GTGGGGGTGAAGG-GG
73679 GT
1 GT
73681 AGACACAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.40
15 24 0.60
ACGTcount: A:0.13, C:0.00, G:0.67, T:0.20
Consensus pattern (15 bp):
GTGGGGGTGAAGGGG
Found at i:74770 original size:2 final size:2
Alignment explanation
Indices: 74763--74817 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
74753 AATGCTTAAT
74763 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
74805 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
74818 GTGAGAGACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:78682 original size:2 final size:2
Alignment explanation
Indices: 78675--78729 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
78665 TCATATAATA
78675 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
78717 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
78730 GAGACATCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:80766 original size:1 final size:1
Alignment explanation
Indices: 80762--80789 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
80752 ATACTCCACT
80762 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
80790 TTACACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:81042 original size:106 final size:106
Alignment explanation
Indices: 80847--81048 Score: 334
Period size: 106 Copynumber: 1.9 Consensus size: 106
80837 TATATTTTGA
* * *
80847 ATATTTTCCCATTCTTATGACAACAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAATTCAA
1 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA
* *
80912 CAAATTCTCCATAAGATCTGCCTTAAACTTTNTAATATTCAT
66 CAAATTCACCATAAGAGCTGCCTTAAACTTT-TAATATTCAT
*
80954 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCC-ATTAAGGAGGCTGGGAGGTAAA
1 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA
81018 CAAATTCACCATAAGAGCTGCCTTAAACTTT
66 CAAATTCACCATAAGAGCTGCCTTAAACTTT
81049 GATATATGGT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
106 48 0.54
107 41 0.46
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (106 bp):
ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA
CAAATTCACCATAAGAGCTGCCTTAAACTTTTAATATTCAT
Found at i:82778 original size:2 final size:2
Alignment explanation
Indices: 82771--82830 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
82761 AATTATTGGA
82771 TC TC TC TC -C TC TC -C TC TC -C TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
82810 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
82831 TGCATCTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:83187 original size:1 final size:1
Alignment explanation
Indices: 83181--83206 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
83171 TTCATCAACT
83181 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
83207 TTTTCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:84424 original size:58 final size:58
Alignment explanation
Indices: 84354--84514 Score: 259
Period size: 58 Copynumber: 2.8 Consensus size: 58
84344 TTGTCTTCAG
84354 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC
1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC
* **
84412 CAACAAATATGGGATTTCTTTAAGTGTTTTAGATTATGCAAGGGGGGTGGGGGTGGGC
1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC
** * *
84470 CAACAAATATGGGATTTCTTTGGGTGTGTAAGATTGTGCAAGGGG
1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGG
84515 AGGCAATAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 95 1.00
ACGTcount: A:0.27, C:0.09, G:0.35, T:0.30
Consensus pattern (58 bp):
CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC
Found at i:86266 original size:14 final size:14
Alignment explanation
Indices: 86242--86275 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
86232 TCTCCAAAAC
86242 TCTCTCGACTGTCAT
1 TCTC-CGACTGTCAT
86257 TCTCCGACTGTCAT
1 TCTCCGACTGTCAT
86271 TCTCC
1 TCTCC
86276 AAGGGGGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (14 bp):
TCTCCGACTGTCAT
Found at i:90591 original size:32 final size:32
Alignment explanation
Indices: 90550--90624 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
90540 TAATACTTGA
*
90550 TTAATACCAAAGAAAGGCAAAGATATCAATGT
1 TTAATACCAAAGAAAGGCAAAGACATCAATGT
*** **
90582 TTAATACCAAAGAGTTGTTAAGACATCAATGT
1 TTAATACCAAAGAAAGGCAAAGACATCAATGT
90614 TTAATACCAAA
1 TTAATACCAAA
90625 TGGGGATTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (32 bp):
TTAATACCAAAGAAAGGCAAAGACATCAATGT
Found at i:100730 original size:25 final size:25
Alignment explanation
Indices: 100701--100749 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
100691 TTCCCCATCA
*
100701 GCTGATCTAACATAAAGGGTATAAC
1 GCTGATCTAACACAAAGGGTATAAC
*
100726 GCTGATCTAACACATAGGGTATAA
1 GCTGATCTAACACAAAGGGTATAA
100750 AATTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTGATCTAACACAAAGGGTATAAC
Found at i:102761 original size:42 final size:42
Alignment explanation
Indices: 102682--102761 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
102672 AAAATTACAC
* * **
102682 ATAAAATGCCGCAAAACCAAACACAGTTTTACAATATTTCAT
1 ATAAAATGCCACAAAACCAAACACAGATACACAATATTTCAT
* *
102724 ATAAAATGCCACAAAACTAAACACAGATACACGATATT
1 ATAAAATGCCACAAAACCAAACACAGATACACAATATT
102762 ATTCATTAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (42 bp):
ATAAAATGCCACAAAACCAAACACAGATACACAATATTTCAT
Found at i:102948 original size:2 final size:2
Alignment explanation
Indices: 102941--102974 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
102931 ACATTTTTCA
* *
102941 TC TC TC TC TC TC TC TC TT TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
102975 CACACACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:107008 original size:2 final size:2
Alignment explanation
Indices: 107001--107036 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
106991 TCAGGACAAT
107001 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
107037 ATATGTCTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:107822 original size:2 final size:2
Alignment explanation
Indices: 107684--107806 Score: 145
Period size: 2 Copynumber: 65.5 Consensus size: 2
107674 TCTCTTTGAT
*
107684 TC TC TC TC TC TC TC TC TC TC TC TC T- TC -C TC -C TC CC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
107722 TC -C CC T- TC TC CC TC TC -C TC T- TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
107760 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
107802 TC TC T
1 TC TC T
107807 GTGATCCAAT
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
1 8 0.08
2 96 0.92
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:108617 original size:2 final size:2
Alignment explanation
Indices: 108610--108643 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
108600 GTATGGTGCC
*
108610 GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
108644 ATATTCAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:112364 original size:2 final size:2
Alignment explanation
Indices: 112357--112463 Score: 125
Period size: 2 Copynumber: 56.0 Consensus size: 2
112347 ATGTCAACAA
*
112357 TC TC TC TC TC -C TC TC TC TC TC TC -C TC AC TC TC TC TC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
112396 TC TC TC TC TC TC -C CC TC TC TC TC TC -C TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
112436 TC TT TC TC TC TT TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
112464 CTTGAATACT
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
1 5 0.06
2 84 0.94
ACGTcount: A:0.01, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:115116 original size:18 final size:18
Alignment explanation
Indices: 115093--115130 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
115083 ACCTCAATGA
115093 ATGACAATGATCACATGT
1 ATGACAATGATCACATGT
115111 ATGACAATGATCACATGT
1 ATGACAATGATCACATGT
115129 AT
1 AT
115131 ACACACGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (18 bp):
ATGACAATGATCACATGT
Found at i:115818 original size:2 final size:2
Alignment explanation
Indices: 115811--115864 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
115801 TTAACATACA
115811 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
115853 TC TC TC TC TC TC
1 TC TC TC TC TC TC
115865 AGTATAGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:146171 original size:69 final size:69
Alignment explanation
Indices: 146058--146289 Score: 428
Period size: 69 Copynumber: 3.4 Consensus size: 69
146048 NNNNNNNNNN
146058 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT
1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT
146123 TTAG
66 TTAG
*
146127 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATATGAACAGATTCTTGGTTGACAGAAT
1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT
146192 TTAG
66 TTAG
*
146196 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTTTTGGTTGACAGAAT
1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT
146261 TTAG
66 TTAG
**
146265 TATGACCCCTTACTCTTCAATGTTT
1 TACAACCCCTTACTCTTCAATGTTT
146290 TGCCTGTCAT
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 158 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (69 bp):
TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT
TTAG
Found at i:147773 original size:39 final size:36
Alignment explanation
Indices: 147730--147834 Score: 104
Period size: 43 Copynumber: 2.8 Consensus size: 36
147720 ATATTCTATT
147730 GACTGACTTACAAATATATGGAGGGACAGTTATTTCAAC
1 GACTGACTTACAAATATATGGAGGGACAGTTA-TTC--C
** **
147769 GACTGACTTAATAACAAATATATGGAAAGATGGTTATTCC
1 GACTGAC-T--T-ACAAATATATGGAGGGACAGTTATTCC
147809 -ACTGACTTACAAATATATGGAGGGAC
1 GACTGACTTACAAATATATGGAGGGAC
147835 GGATATTCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
35 15 0.27
36 1 0.02
38 1 0.02
39 13 0.24
40 2 0.04
42 4 0.07
43 19 0.35
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
GACTGACTTACAAATATATGGAGGGACAGTTATTCC
Found at i:149409 original size:25 final size:25
Alignment explanation
Indices: 149340--149466 Score: 98
Period size: 25 Copynumber: 5.2 Consensus size: 25
149330 TCCTCTAATA
* *
149340 ATCTATTTTAACAGGTACTCCACA-
1 ATCTATTTTAACAGGTACTCTAGAC
* * * *
149364 ATTTGTTTT-ACATGTATTCTAGAC
1 ATCTATTTTAACAGGTACTCTAGAC
* *
149388 ATCTATTTAAACAGGTACTCTAGAA
1 ATCTATTTTAACAGGTACTCTAGAC
* * *
149413 ACCTATTTTGACAGGTATTCTAGAC
1 ATCTATTTTAACAGGTACTCTAGAC
* * *
149438 ATAT-TTTTTACAGGTACCCTCAGAC
1 ATCTATTTTAACAGGTACTCT-AGAC
149463 ATCT
1 ATCT
149467 TTTGTTTACC
Statistics
Matches: 77, Mismatches: 23, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
23 10 0.13
24 26 0.34
25 41 0.53
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (25 bp):
ATCTATTTTAACAGGTACTCTAGAC
Found at i:153234 original size:2 final size:2
Alignment explanation
Indices: 153227--153265 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
153217 AAAAATTAAT
153227 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
153266 AGAAAAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:159653 original size:28 final size:28
Alignment explanation
Indices: 159616--159737 Score: 156
Period size: 28 Copynumber: 4.3 Consensus size: 28
159606 TGATGTCCTT
*
159616 TTCATGTAAAGTTTACACCTTATTTCCC
1 TTCATGTAAAGTTTACACCTTATTCCCC
* *
159644 TTCATTTAAAGTTTACACCTTGTTCCCC
1 TTCATGTAAAGTTTACACCTTATTCCCC
* * *
159672 TTCATTTATAGTTTACACCTTGTTCCCC
1 TTCATGTAAAGTTTACACCTTATTCCCC
159700 TTCATGTAAAGTTTACACCTTGATTTTCCCC
1 TTCATGTAAAGTTTACACCTT-A--TTCCCC
159731 -TCATGTA
1 TTCATGTA
159738 CGTTTTCCTC
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
28 71 0.85
30 7 0.08
31 6 0.07
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.43
Consensus pattern (28 bp):
TTCATGTAAAGTTTACACCTTATTCCCC
Found at i:164795 original size:21 final size:21
Alignment explanation
Indices: 164745--164795 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
164735 GTGTTTTACT
* *
164745 TTTTATCATAATTTGATGTAG
1 TTTTATCATAAATTGACGTAG
164766 -TTTAGTCATAAATTGACGT-G
1 TTTTA-TCATAAATTGACGTAG
164786 CTTTTATCAT
1 -TTTTATCAT
164796 TTTGTGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTTATCATAAATTGACGTAG
Found at i:164937 original size:4 final size:4
Alignment explanation
Indices: 164928--164983 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
164918 TACCCTTGTG
* * * * * *
164928 TGTC TGTC TGTC CGTC CGTC CGTC CGTC TGTC TGTC TGTC CGTC CGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
164976 TGTC TGTC
1 TGTC TGTC
164984 CGTCCGTAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39
Consensus pattern (4 bp):
TGTC
Found at i:164958 original size:20 final size:20
Alignment explanation
Indices: 164933--164990 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
164923 TTGTGTGTCT
*
164933 GTCTGTCCGTCCGTCCGTCC
1 GTCTGTCTGTCCGTCCGTCC
*
164953 GTCTGTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCCGTCC
164973 GTCTGTCTGTCCGTCCGT
1 GTCTGTCTGTCCGTCCGT
164991 AACAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (20 bp):
GTCTGTCTGTCCGTCCGTCC
Found at i:164988 original size:4 final size:4
Alignment explanation
Indices: 164937--164990 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
164927 GTGTCTGTCT
* * * * *
164937 GTCC GTCC GTCC GTCC GTCT GTCT GTCT GTCC GTCC GTCT GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
164985 GTCC GT
1 GTCC GT
164991 AACAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.35
Consensus pattern (4 bp):
GTCC
Found at i:164988 original size:16 final size:16
Alignment explanation
Indices: 164928--164990 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
164918 TACCCTTGTG
*
164928 TGTCTGTCTGTCCGTC
1 TGTCTGTCCGTCCGTC
* * *
164944 CGTCCGTCCGTCTGTC
1 TGTCTGTCCGTCCGTC
164960 TGTCTGTCCGTCCGTC
1 TGTCTGTCCGTCCGTC
164976 TGTCTGTCCGTCCGT
1 TGTCTGTCCGTCCGT
164991 AACAAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.00, C:0.37, G:0.25, T:0.38
Consensus pattern (16 bp):
TGTCTGTCCGTCCGTC
Found at i:165388 original size:166 final size:167
Alignment explanation
Indices: 165014--165974 Score: 1468
Period size: 166 Copynumber: 5.8 Consensus size: 167
165004 GTCGCATTTA
* *
165014 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATTCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
* **
165079 TGTGGGATATATTTTTGTACCAATCGGACGTCAACTTATTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
165144 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
165181 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTA-AGGCATGCCATA
* *
165245 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGATTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
* * * *
165310 TTT-GCCAAAATTTTAAAACAAATTTTCGTCAATGAAT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
165347 TCTCAGCAACTGTTTATCTCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTA-AGGCATGCCATA
* *
165411 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACAACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
165476 TTTAACC-AAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
165513 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
* * **
165578 CGTGGGACATATTGTTGTACCAATCGGACGTCAACTTATTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
165643 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
165680 TCTCAGCAGCTATTTATCGGAGATGCTTTAAATTTTAACACAGTATTTTTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
* *
165745 CGTGGGATATATTTTTGTACCAATCGGACGTCATCTTCCTGTTAAATGA-GTACTTTG-TT-TAT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT
* *
165807 TTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
165845 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
* * * * * * *
165910 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
165975 GCATATTCAC
Statistics
Matches: 728, Mismatches: 58, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
165 146 0.20
166 316 0.43
167 266 0.37
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:170126 original size:13 final size:13
Alignment explanation
Indices: 170108--170137 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
170098 AAAAATGTTA
*
170108 CTATCAAAAATTC
1 CTATCAAAAATCC
170121 CTATCAAAAATCC
1 CTATCAAAAATCC
170134 CTAT
1 CTAT
170138 GAACACCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (13 bp):
CTATCAAAAATCC
Found at i:172670 original size:11 final size:11
Alignment explanation
Indices: 172656--172685 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
172646 TGTATGAAAA
172656 TTGCATGATAT
1 TTGCATGATAT
172667 TTGCATGATAT
1 TTGCATGATAT
*
172678 TCGCATGA
1 TTGCATGA
172686 AACAACAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (11 bp):
TTGCATGATAT
Found at i:177521 original size:2 final size:2
Alignment explanation
Indices: 177514--177627 Score: 119
Period size: 2 Copynumber: 59.0 Consensus size: 2
177504 CTCTATTCCC
* * *
177514 CT CT CT CT AT -T CT CT CT CT CC CT CT CT CT CT CT AT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
177554 CC CT CT CT CT CT CT CT CT CT AT -T CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
177595 CT AT -T CT CT CT CT CC CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
177628 GTATTTTTGT
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
1 4 0.04
2 90 0.96
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:177542 original size:25 final size:25
Alignment explanation
Indices: 177514--177617 Score: 167
Period size: 25 Copynumber: 4.2 Consensus size: 25
177504 CTCTATTCCC
177514 CTCTCTCTATTCTCTCTCTCCCTCT
1 CTCTCTCTATTCTCTCTCTCCCTCT
*
177539 CTCTCTCTATTCTCTCCCTCTCTCTCT
1 CTCTCTCTATTCTCT--CTCTCCCTCT
177566 CTCTCTCTATTCTCTCTCT-CC-CT
1 CTCTCTCTATTCTCTCTCTCCCTCT
177589 CTCTCTCTATTCTCTCTCTCCCTCT
1 CTCTCTCTATTCTCTCTCTCCCTCT
177614 CTCT
1 CTCT
177618 TTCTCTCTCT
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
23 21 0.29
24 3 0.04
25 25 0.34
27 24 0.33
ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (25 bp):
CTCTCTCTATTCTCTCTCTCCCTCT
Found at i:182659 original size:10 final size:10
Alignment explanation
Indices: 182640--182817 Score: 80
Period size: 10 Copynumber: 17.7 Consensus size: 10
182630 AGTGCCATTT
182640 TTTACTGATA
1 TTTACTGATA
182650 GTTT-CTGATA
1 -TTTACTGATA
182660 TTTACTGATA
1 TTTACTGATA
*
182670 TTGTACTGTTA
1 TT-TACTGATA
* * *
182681 -GTGCTGAGA
1 TTTACTGATA
* *
182690 ATTGCTGATA
1 TTTACTGATA
182700 TTTACTGATAA
1 TTTACTGAT-A
**
182711 TTTTACTG-CC
1 -TTTACTGATA
*
182721 GTTACTGATA
1 TTTACTGATA
* * * *
182731 ATTGCTGTTG
1 TTTACTGATA
*
182741 GTT-CTGATA
1 TTTACTGATA
182750 TTTACTGATA
1 TTTACTGATA
*
182760 TTTACTGATGCT
1 TTTACTGAT--A
*
182772 TTTGCTG-TGA
1 TTTACTGAT-A
**
182782 GCT-CTGATA
1 TTTACTGATA
*
182791 ATTACTGATA
1 TTTACTGATA
182801 TTTACTGATA
1 TTTACTGATA
182811 TTTACTG
1 TTTACTG
182818 TTGGTACTGA
Statistics
Matches: 125, Mismatches: 31, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
9 25 0.20
10 75 0.60
11 12 0.10
12 13 0.10
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (10 bp):
TTTACTGATA
Found at i:183664 original size:2 final size:2
Alignment explanation
Indices: 183657--183687 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
183647 GCCCACCCTG
*
183657 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
183688 GCTCGCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:183882 original size:2 final size:2
Alignment explanation
Indices: 183875--183924 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
183865 ATGCTTTAAT
183875 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
183917 TC TC TC TC
1 TC TC TC TC
183925 AGATAATCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:184043 original size:2 final size:2
Alignment explanation
Indices: 184036--184078 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
184026 GATTGAAAAC
*
184036 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
184078 C
1 C
184079 ATTAATACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:184456 original size:134 final size:134
Alignment explanation
Indices: 184226--184478 Score: 400
Period size: 134 Copynumber: 1.9 Consensus size: 134
184216 GAAAAAAATA
* *
184226 TTTTGTATGTCTGGGATTAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGACTATACACACGA
1 TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGAATATACACACGA
* *
184291 CAGGGTGACCACGGCAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAG
66 CAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAGTCGCTGAAAAG
184356 ATTC
131 ATTC
* * *
184360 TTTTGTATGTCTGGGATCAAGAAAACCCTCAGAACTAACAGACG-GCGCTCAGAATATATACACG
1 TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGA-GAGCACTCAGAATATACACACG
** *
184424 ACAGAGTGACCGTGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTTGCAG
65 ACAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAG
184479 CCTCAGAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
134 107 0.99
135 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (134 bp):
TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGAATATACACACGA
CAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAGTCGCTGAAAAG
ATTC
Found at i:185140 original size:10 final size:10
Alignment explanation
Indices: 185125--185302 Score: 80
Period size: 10 Copynumber: 17.7 Consensus size: 10
185115 TCAGTACCAA
*
185125 CAGTAAATCT
1 CAGTAAATAT
185135 CAGTAAATAT
1 CAGTAAATAT
*
185145 CAGTAATTAT
1 CAGTAAATAT
**
185155 CAG-AGCTCA-
1 CAGTAAAT-AT
* *
185164 CAGCAAAAGCAT
1 CAG-TAAA-TAT
185176 CAGTAAATAT
1 CAGTAAATAT
185186 CAGTAAATAT
1 CAGTAAATAT
** *
185196 CAG-AACCAA
1 CAGTAAATAT
* *
185205 CAGCAATTAT
1 CAGTAAATAT
* *
185215 CAGT-AACAG
1 CAGTAAATAT
185224 CAGTAAAATTAT
1 CAGT-AAA-TAT
185236 CAGTAAATAT
1 CAGTAAATAT
* * *
185246 CAGCAATTCT
1 CAGTAAATAT
* **
185256 CAGCACTTA-
1 CAGTAAATAT
185265 CAGTACAATAT
1 CAGTA-AATAT
185276 CAGTAAATAT
1 CAGTAAATAT
185286 CAG-AAACTAT
1 CAGTAAA-TAT
185296 CAGTAAA
1 CAGTAAA
185303 AAATGGCACT
Statistics
Matches: 126, Mismatches: 29, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
9 24 0.19
10 76 0.60
11 18 0.14
12 8 0.06
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (10 bp):
CAGTAAATAT
Found at i:185150 original size:20 final size:20
Alignment explanation
Indices: 185088--185157 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
185078 TCCCCTGCCT
*
185088 GTAATTCTCAGTAATTATCA
1 GTAATTCTCAGTAAATATCA
* *
185108 GCAATTCTCAGTACCA-A-CA
1 GTAATTCTCAGTA-AATATCA
*
185127 GTAAATCTCAGTAAATATCA
1 GTAATTCTCAGTAAATATCA
*
185147 GTAATTATCAG
1 GTAATTCTCAG
185158 AGCTCACAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.36
20 24 0.62
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
GTAATTCTCAGTAAATATCA
Found at i:185208 original size:41 final size:40
Alignment explanation
Indices: 185094--185210 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 40
185084 GCCTGTAATT
* * * * * *
185094 CTCAGTAATTATCAGCAATTCTCAGTACCAACAG-TAAAT
1 CTCAGTAAATATCAGTAATTATCAGAACCAACAGCAAAAG
*
185133 CTCAGTAAATATCAGTAATTATCAGAGCTC-ACAGCAAAAG
1 CTCAGTAAATATCAGTAATTATCAGAAC-CAACAGCAAAAG
*
185173 CATCAGTAAATATCAGTAAATATCAGAACCAACAGCAA
1 C-TCAGTAAATATCAGTAATTATCAGAACCAACAGCAA
185211 TTATCAGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 27 0.42
40 6 0.09
41 32 0.49
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (40 bp):
CTCAGTAAATATCAGTAATTATCAGAACCAACAGCAAAAG
Found at i:188548 original size:62 final size:63
Alignment explanation
Indices: 188431--188684 Score: 203
Period size: 62 Copynumber: 4.1 Consensus size: 63
188421 ATCGCCCGAG
* * * ** * * *
188431 TTTTAATAAAACAAATGTAACATGTTCTTCCTCTGTAAGAGCTGAATCAGCAAGTCCCCTGAT
1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT
* *
188494 TTTTAAGAAAACAAATGCATCATGCACTT-CTCGGTCAGGGCTGAATCAGCAAGTCGCCAGAT
1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT
* * * * ** ** * * * * *
188556 TTTTAA-CAAACCAATGCAACATGCACTTCCCCTTTCAAAGCTTAATCAGCCATTCACCTGGT
1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT
* * * * * *
188618 TTTTAAGAAAACAAAT--TTCATGCACTTCCTCGGTAAGGACTGTATCAGTAAGTCGCCC-GAA
1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTC-CCCTGAT
188679 TTTTAA
1 TTTTAA
188685 AAAGGGTCCG
Statistics
Matches: 145, Mismatches: 43, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
61 50 0.34
62 64 0.44
63 31 0.21
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (63 bp):
TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT
Found at i:189372 original size:10 final size:9
Alignment explanation
Indices: 189346--189371 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
189336 TCCCGTAATT
189346 AAAAAAAAG
1 AAAAAAAAG
189355 AAAAAAAAG
1 AAAAAAAAG
189364 AAAAAAAA
1 AAAAAAAA
189372 ATTCATACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:193098 original size:2 final size:2
Alignment explanation
Indices: 193091--193131 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
193081 TTATTCCCCG
193091 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
193132 TACAGTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:193842 original size:3 final size:3
Alignment explanation
Indices: 193836--193909 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
193826 TATTAATGTA
193836 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
193884 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
193910 AGAATACTGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:196639 original size:21 final size:21
Alignment explanation
Indices: 196605--196684 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
196595 AATTTAATGC
* * *
196605 TATGCTATGGTATGCGATTT-
1 TATGATATGCTATGAGATTTG
196625 TAATGATATGCTATGAGATTTG
1 T-ATGATATGCTATGAGATTTG
*
196647 TATGCTATGCTATGAGATTTG
1 TATGATATGCTATGAGATTTG
* *
196668 TATGCTTTGCTATGAGA
1 TATGATATGCTATGAGA
196685 GATTGAAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (21 bp):
TATGATATGCTATGAGATTTG
Found at i:196666 original size:42 final size:42
Alignment explanation
Indices: 196605--196684 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
196595 AATTTAATGC
* *
196605 TATGCTATGGTATGCGATTT-TAATGATATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTGT-ATGATATGCTATGAGATTTG
* *
196647 TATGCTATGCTATGAGATTTGTATGCTTTGCTATGAGA
1 TATGCTATGCTATGAGATTTGTATGATATGCTATGAGA
196685 GATTGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (42 bp):
TATGCTATGCTATGAGATTTGTATGATATGCTATGAGATTTG
Found at i:196907 original size:10 final size:10
Alignment explanation
Indices: 196889--196922 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
196879 TATAATGTTG
*
196889 TATGCTATGC
1 TATGGTATGC
196899 TATGGTATGC
1 TATGGTATGC
*
196909 TATGGTATGA
1 TATGGTATGC
196919 TATG
1 TATG
196923 ACGAATGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:196908 original size:15 final size:15
Alignment explanation
Indices: 196888--196922 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
196878 ATATAATGTT
196888 GTATGCTATGCTATG
1 GTATGCTATGCTATG
*
196903 GTATGCTATGGTATG
1 GTATGCTATGCTATG
*
196918 ATATG
1 GTATG
196923 ACGAATGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (15 bp):
GTATGCTATGCTATG
Found at i:196973 original size:21 final size:21
Alignment explanation
Indices: 196935--197022 Score: 126
Period size: 21 Copynumber: 4.2 Consensus size: 21
196925 GAATGAGATT
196935 CTATGAGATTGT--ATGCTATG
1 CTATGAGATT-TCAATGCTATG
* *
196955 GTATGAGATTCCAATGCTATG
1 CTATGAGATTTCAATGCTATG
*
196976 CTATGAGATTTCTATGCTATG
1 CTATGAGATTTCAATGCTATG
196997 CTATGAGATTTCAATGCTATG
1 CTATGAGATTTCAATGCTATG
197018 CTATG
1 CTATG
197023 CTATGGTGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.15
21 51 0.85
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (21 bp):
CTATGAGATTTCAATGCTATG
Found at i:196992 original size:42 final size:41
Alignment explanation
Indices: 196935--197022 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 41
196925 GAATGAGATT
* *
196935 CTATGAGATTGTATGCTATGGTATGAGATTCCAATGCTATG
1 CTATGAGATTCTATGCTATGCTATGAGATTCCAATGCTATG
*
196976 CTATGAGATTTCTATGCTATGCTATGAGATTTCAATGCTATG
1 CTATGAGA-TTCTATGCTATGCTATGAGATTCCAATGCTATG
197018 CTATG
1 CTATG
197023 CTATGGTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 8 0.19
42 35 0.81
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (41 bp):
CTATGAGATTCTATGCTATGCTATGAGATTCCAATGCTATG
Found at i:200509 original size:21 final size:21
Alignment explanation
Indices: 200485--200578 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 21
200475 AACAAATAAA
200485 GACGAATTAGATATTTGTTCG
1 GACGAATTAGATATTTGTTCG
* **** *
200506 GACGAATTTTGA-ACAAATTAG
1 GACGAA-TTAGATATTTGTTCG
**
200527 GACGAATTAGATATTTGTTTA
1 GACGAATTAGATATTTGTTCG
* **
200548 GACGAATAACTTATTTGTTCG
1 GACGAATTAGATATTTGTTCG
*
200569 GACGTATTAG
1 GACGAATTAG
200579 CCTTTAGTTC
Statistics
Matches: 50, Mismatches: 21, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
20 4 0.08
21 42 0.84
22 4 0.08
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (21 bp):
GACGAATTAGATATTTGTTCG
Found at i:200514 original size:42 final size:42
Alignment explanation
Indices: 200451--200554 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
200441 CGGGCGAGTA
* **
200451 AGATATTTTTTCGGATAAATTTTGAACAAATAAAGACGAATT
1 AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT
* *
200493 AGATATTTGTTCGGACGAATTTTGAACAAATTAGGACGAATT
1 AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT
**
200535 AGATATTTGTTTAGACGAAT
1 AGATATTTGTTCGGACGAAT
200555 AACTTATTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (42 bp):
AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT
Found at i:200612 original size:2 final size:2
Alignment explanation
Indices: 200605--200654 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
200595 GTAAAAGAAC
200605 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
200647 GA GA GA GA
1 GA GA GA GA
200655 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:205046 original size:17 final size:17
Alignment explanation
Indices: 205024--205056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
205014 AATATGAGCA
205024 TTAATATATATTTTGCT
1 TTAATATATATTTTGCT
*
205041 TTAATATTTATTTTGC
1 TTAATATATATTTTGC
205057 CGTGGCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTAATATATATTTTGCT
Found at i:207970 original size:22 final size:23
Alignment explanation
Indices: 207918--207963 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
207908 CGTAGACGTA
* *
207918 GAAGTTACGAATGACGTAAGATT
1 GAAGTTACGAATGACGTAAAATG
207941 GAAGTTACGAAT-ACGTAAAATG
1 GAAGTTACGAATGACGTAAAATG
207963 G
1 G
207964 TATTTACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (23 bp):
GAAGTTACGAATGACGTAAAATG
Found at i:212839 original size:8 final size:8
Alignment explanation
Indices: 212826--212854 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
212816 TGGTTTCACC
212826 CTGTCCGT
1 CTGTCCGT
212834 CTGTCCGT
1 CTGTCCGT
212842 CTGTCCGT
1 CTGTCCGT
212850 CTGTC
1 CTGTC
212855 TGTAGACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.24, T:0.38
Consensus pattern (8 bp):
CTGTCCGT
Found at i:252805 original size:32 final size:33
Alignment explanation
Indices: 252730--252806 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
252720 GATTTTGGTC
252730 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG
1 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG
* *
252763 TCAATATTCAATGTTGAAAAATGACCCCC-GGG
1 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG
*
252795 TCCATTTTCAAC
1 TCAATTTTCAAC
252807 CCGGGTCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 12 0.31
33 27 0.69
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (33 bp):
TCAATTTTCAACGTTGAAAAATGACCCCCTGGG
Found at i:256832 original size:169 final size:164
Alignment explanation
Indices: 256345--256922 Score: 445
Period size: 169 Copynumber: 3.5 Consensus size: 164
256335 AATGAATCAT
* * * * * *
256345 CTGGCTGATTAGTTTCTAAGAAGTAGAT-TCTTTTAAAGATGTACTCTATATATTCCTATGTAAA
1 CTGGCTGATTAGTTTCTTAGACG-A-ATAT-TTTTAAAGGTTTACTCAATATATTCCTATGAAAA
** * * * * * * * * * *
256409 ACTTCCAACCCCCCATTGTTGCCACAAAATTCCCCCGGAGGTCATAATTTTTACAAC-TTGGAAT
63 AAGT-CGACCCCCCAATGTGGCCCCACAATACCCCCGGA-GTCATGATTTTCACGACAGT-GAAT
* **
256473 CTACACTACCCTACAATGCTTCCACACAAATTTCAGCTTTC
125 CTACACTACCTTAGGATGCTTCCACACAAA-TTCAGCTTTC
*
256514 CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCTTATGAAAAAAG
1 CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAAG
* * ** **
256579 TCGACCCTCTAATGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACGACTTTGAATCTACA
66 TCGACCCCCCAATGTGGCCCCACAATACCCCCGGA-GTCATGATTTTCACGACAGTGAATCTACA
*
256644 CTACCTGAGGATGCTTCCACACAAATGTCAGCTTTC
130 CTACCTTAGGATGCTTCCACACAAAT-TCAGCTTTC
* ** * * *
256680 CTGGTTTTTTTAGTTTCTTAGA-GGATGATTTTTAAAGTTTTACTCAATATATTCCTATGTTAAA
1 CTGG-CTGATTAGTTTCTTAGACGAAT-ATTTTTAAAGGTTTACTCAATATATTCCTATG-AAAA
*** * *
256744 CTTTAAC-ACCCCCCCATTGTGGCCCCA-AATACCCCAATGGA-TCATGATTTTCAC-ATCAGTG
63 AAGT--CGA-CCCCCCAATGTGGCCCCACAATACCCC--CGGAGTCATGATTTTCACGA-CAGTG
*
256805 AATCTACACTATCTTAGGATGCTTCCACACAAATTCCAGCTTTC
122 AATCTACACTACCTTAGGATGCTTCCACACAAATT-CAGCTTTC
* * * ** * ** * *
256849 CTGGCCGACTAGATTT-TGAGATTAAGATTTTTAAAGAATTACTCAATATATTCCTTTG-TAAAA
1 CTGGCTGATTAG-TTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAA
*
256912 TTCGACCCCCC
65 GTCGACCCCCC
256923 CCCCCCCCTA
Statistics
Matches: 332, Mismatches: 61, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
164 7 0.02
165 2 0.01
166 89 0.27
167 79 0.24
168 44 0.13
169 92 0.28
170 16 0.05
171 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (164 bp):
CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAAG
TCGACCCCCCAATGTGGCCCCACAATACCCCCGGAGTCATGATTTTCACGACAGTGAATCTACAC
TACCTTAGGATGCTTCCACACAAATTCAGCTTTC
Found at i:257018 original size:11 final size:11
Alignment explanation
Indices: 257002--257026 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
256992 GCGGGGGTCA
257002 TGATTTTTACC
1 TGATTTTTACC
257013 TGATTTTTACC
1 TGATTTTTACC
257024 TGA
1 TGA
257027 GGATGCTTCC
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:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (11 bp):
TGATTTTTACC
Found at i:281606 original size:178 final size:179
Alignment explanation
Indices: 281281--281643 Score: 435
Period size: 178 Copynumber: 2.0 Consensus size: 179
281271 GAGAAATGGA
* * ** *
281281 GTACCC-ATATGCAATATTTTGTCAAAAAATTATTAAGTTTTAAAGCTAGTATTTCTTCATTGAT
1 GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTATTTCTTCATTAAT
* * * * *
281345 AATCAGAAATCAAAATCCTAGCAATTTGCACACCTCTGATTTATGTACAATTGATCTGCAAAAAA
66 AACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAAA
*
281410 AGAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG
131 ACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG
* * *
281459 GTACCCTATATGTAATATTTTGCCAAAAAATGA-TAAGTTCAAAAGCTGGTATATTTTTCATTAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTAT-TTCTTCATTAA
* * * ** * *
281523 TTACCAG-AATTAAAATTCTAGCTCTGTACACACTTCTCATATATGTACAATTGATCTGCAAAAG
65 TAACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAA
* * * * * **
281587 AACTACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACCATAAGG
130 AACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG
*
281637 ATACCCT
1 GTACCCT
281644 CTTGGCAGCC
Statistics
Matches: 154, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
178 117 0.76
179 37 0.24
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (179 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTATTTCTTCATTAAT
AACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAAA
ACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG
Found at i:285852 original size:200 final size:200
Alignment explanation
Indices: 285509--285903 Score: 790
Period size: 200 Copynumber: 2.0 Consensus size: 200
285499 AGGTATCTGA
285509 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA
1 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA
285574 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC
66 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC
285639 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA
131 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA
285704 CCCCC
196 CCCCC
285709 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA
1 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA
285774 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC
66 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC
285839 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA
131 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA
285904 NCTCCCCCCC
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 195 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (200 bp):
CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA
CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC
AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA
CCCCC
Found at i:286557 original size:97 final size:97
Alignment explanation
Indices: 286391--286580 Score: 371
Period size: 97 Copynumber: 2.0 Consensus size: 97
286381 TGATATAAAT
*
286391 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACTATATTTTGGCTTTGAGAAGTATCTTGA
1 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA
286456 TATTTTACCTGTAAAACTAAGAAAAAAATTCA
66 TATTTTACCTGTAAAACTAAGAAAAAAATTCA
286488 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA
1 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA
286553 TATTTTACCTGTAAAACTAAGAAAAAAA
66 TATTTTACCTGTAAAACTAAGAAAAAAA
286581 ACTCAAGACC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (97 bp):
TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA
TATTTTACCTGTAAAACTAAGAAAAAAATTCA
Found at i:287656 original size:53 final size:54
Alignment explanation
Indices: 287570--287686 Score: 157
Period size: 53 Copynumber: 2.2 Consensus size: 54
287560 TGCTAATACT
* * * *
287570 TTATTTCAA-AAGTGGTTGTAATGAAATGTATACCCAACCACTATTGGAATAAA
1 TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA
* * *
287623 TTATTTCAATAAAT-GTTATAATGCAATGCATACCCAAGCACTATTGAAATAAT
1 TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA
287676 TTATTTCAATA
1 TTATTTCAATA
287687 GTGGTTGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 53 0.95
54 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (54 bp):
TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA
Found at i:327706 original size:14 final size:15
Alignment explanation
Indices: 327687--327723 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
327677 TTGCTTTTGA
327687 GTTTTTTTTTG-TTT
1 GTTTTTTTTTGTTTT
*
327701 GTTTTTGTTTGTTTT
1 GTTTTTTTTTGTTTT
327716 GTTTTTTT
1 GTTTTTTT
327724 ATAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
GTTTTTTTTTGTTTT
Found at i:331699 original size:2 final size:2
Alignment explanation
Indices: 331694--331735 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
331684 CCCCCCCCCC
331694 CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
331735 C
1 C
331736 ATTGAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:343823 original size:27 final size:27
Alignment explanation
Indices: 343793--343869 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
343783 CAAAATCACA
343793 AAAGTTTTACATAATAAAGGTCAGAGG
1 AAAGTTTTACATAATAAAGGTCAGAGG
** *
343820 AAAGAATTAC---A-AAA--TCACA--
1 AAAGTTTTACATAATAAAGGTCAGAGG
343839 AAAGTTTTACATAATAAAGGTCAGAGG
1 AAAGTTTTACATAATAAAGGTCAGAGG
343866 AAAG
1 AAAG
343870 AATGACAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 8 0.22
21 4 0.11
22 1 0.03
23 6 0.17
24 1 0.03
25 4 0.11
27 12 0.33
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (27 bp):
AAAGTTTTACATAATAAAGGTCAGAGG
Found at i:344006 original size:46 final size:46
Alignment explanation
Indices: 343779--343998 Score: 377
Period size: 46 Copynumber: 4.8 Consensus size: 46
343769 CAAGTATAAC
343779 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
343825 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
* * *
343871 ATGACAAAATCGCAAAAGTTTTAAATAATAAAGGTCAGAGGAAAGA
1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
* **
343917 ATGACAAAATTGCAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
*
343963 TTTACAAAATCACAAAAGTTTTACATAATAAAGGTC
1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTC
343999 TGGGGAAATT
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 165 1.00
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (46 bp):
ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA
Found at i:345252 original size:25 final size:25
Alignment explanation
Indices: 345220--345282 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
345210 GAGGGCTATA
345220 ATATCAATGTACCCGTCCAAACACT
1 ATATCAATGTACCCGTCCAAACACT
345245 ATATCAATGTACCCGTCCAAACACT
1 ATATCAATGTACCCGTCCAAACACT
345270 ATATCAATGTACC
1 ATATCAATGTACC
345283 TGCCCAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (25 bp):
ATATCAATGTACCCGTCCAAACACT
Found at i:345287 original size:89 final size:91
Alignment explanation
Indices: 345146--345327 Score: 280
Period size: 89 Copynumber: 2.0 Consensus size: 91
345136 AATGTACTTA
* *
345146 TCCAAACACTATATCAATGTACCCGTCCAAATACTATGTCAATGTGACTGCCCAGATA-A-TTGT
1 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGACTGCCCAGATATACTTGT
*
345209 AGAGGGCTATAATATCAATGTACCCG
66 AGAGGGCTATAATATCAATATACCCG
345235 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGT-ACCTGCCCAGATACTGTAC
1 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGA-CTGCCCAGATA---TAC
345299 TTGTAGAGGGCTATAATATCAATATACCC
62 TTGTAGAGGGCTATAATATCAATATACCC
345328 ACCCAACTAC
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
88 1 0.01
89 54 0.64
93 1 0.01
94 28 0.33
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (91 bp):
TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGACTGCCCAGATATACTTGT
AGAGGGCTATAATATCAATATACCCG
Found at i:345543 original size:194 final size:195
Alignment explanation
Indices: 345296--346854 Score: 639
Period size: 194 Copynumber: 7.8 Consensus size: 195
345286 CCAGATACTG
*
345296 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAACTACTTGTAGAGGGCTATAATATCAAT
1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
* * *
345361 TTAACTAACCAAATACTTGTATAGAGCTATAATATCAATGTACCCACCCAAATACCTGTAGAGGG
66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
* * * * *
345426 CTATGATATCATTGTAACTGTCCTAATACTTGTGGAGAGTT-ATAAT-TCAATTTAACTGTCCTA
131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGA-TTAATAATATCAATGTAACTGTCCAA
345489 A
195 A
* * * *
345490 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
** * * ** ** *
345555 GTAACTGTCCAAATACTTGTAGAGGGTTATAATAACAATGTATTCGTCCAAATACTTGTAGAGGG
66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
*
345620 TTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA
131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA
* * **** * * * * *
345685 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATATCACT
1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
* ** * * * * * * *** *
345749 TTAACTGTCCTAATACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAATACTTGTAGAGGG
66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
* * * * * * * * ** *
345814 TTAAAATATCTATGTAACTGT-CTAAATAC-TGT-GACATCATTAGATTTCGTGGTGGCTCAATT
131 CTATAATATCAATGTAACTGTCCT-AATACTTATGGAGATTAATA-ATATC--AAT-G-T-AACT
* **
345876 TTCGTGGAA
189 GTC--CAAA
* * * ** * * * * ** *
345885 TTCGTGGGTACATGTACCTCTCATCCATGAAT-TA-ACATCTTCCATTAATAAAT-T--AGGGTT
1 TAC-T-TGTAGA-G-GGCTATAAT--ATCAATATACCCA-C--CCA--AATACTTGTAGAGGGCT
** *** ** *
345945 ATAA-AGTC-A--T-A-TATTCTTTTGA-AGGTATA-AG--ATAATACACGAAAT-TACTTCC-C
55 ATAATA-TCAATGTAACTAACCAAAT-ACTTGTAGAGAGCTATAATA-AC--AATGTAC--CCAC
* * ** * * * * * * * * * *
345998 CGC-TA-ACTTGTA-A--AATTTAAGCAATCCACGAAGATTGGCCCCCACTTATTTTAATGTTTC
113 C-CAAATACCTGTAGAGGGCTATAA--TATCAATGTA-ACT-G-TCCTA-ATA-CTT-ATG----
* * * * **
346058 CACATTATTTGTGCAATGTACAATGTAACTGTCGTAA
165 GAGATTA---AT--AATAT-CAATGTAACTGTCCAAA
* * ** * *
346095 TACTTGTAGAGGGCTATAATATCAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATATCAT
1 TACTTGTAGAGGGCTATAATATCAATATACCC-ACCCAAATACTTGTAGAGGGCTATAATATCAA
** * * * ** * *
346160 TG-AGACTGTCCAAATACTTGTAGATG-GATATAATATCAATGTAACTGCCCAGATACTTGTAGA
65 TGTA-ACTAACCAAATACTTGTAGA-GAGCTATAATAACAATGTACCCACCCAAATACCTGTAGA
* * * * * * ** * *
346223 GGACTATAATTTCCATGTACCCGTCCAAATACTATATCAATGTACCCGTCCAAACACTATATCAA
128 GGGCTATAATATCAATGTAACTGTCCTAATACT-TATGGA-G-A----T--TAATA--ATATCAA
* *
346288 TGTACCTGCCCAGATA
182 TGTAACTGTCCA-A-A
* * *
346304 CTGTACTTGTAGAGGGTTATAATATCAATATACCCACCGAACTACTTGTAGAGGGCTATAATATC
1 ---TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATC
* * * *
346369 AATTTAACTAACCAAATACTTGTATATAGCTATAATATCAATGTACCCACCCAAATACCTGTAGA
63 AATGTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGA
* * * *
346434 GGGCTATGATATCATTGTAACTGTCCTAATACTTGTGGAGAGTT-ATAAT-TCAATTTAACTGTC
128 GGGCTATAATATCAATGTAACTGTCCTAATACTTATGGAGA-TTAATAATATCAATGTAACTGTC
*
346497 CTAA
192 CAAA
* * * *
346501 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
** * * ** ** *
346566 GTAACTGTCCAAATACTTGTAGAGGGTTATAATAACAATGTATTCGTCCAAATACTTGTAGAGGG
66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
*
346631 TTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA
131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA
* * **** * * * * *
346696 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATATCACT
1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
* ** * * * * * * *** *
346760 TTAACTGTCCTAATACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAATACTTGTAGAGGG
66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
* * *
346825 TTAAAATATCTATGTAACTGT-CTAAATACT
131 CTATAATATCAATGTAACTGTCCT-AATACT
346855 GTGACATCAT
Statistics
Matches: 1018, Mismatches: 249, Indels: 196
0.70 0.17 0.13
Matches are distributed among these distances:
192 7 0.01
193 14 0.01
194 488 0.48
195 113 0.11
196 1 0.00
197 2 0.00
198 9 0.01
199 18 0.02
200 14 0.01
201 13 0.01
202 24 0.02
203 8 0.01
204 15 0.01
205 18 0.02
206 19 0.02
207 24 0.02
208 13 0.01
209 15 0.01
210 23 0.02
211 111 0.11
212 49 0.05
213 7 0.01
214 6 0.01
215 2 0.00
216 3 0.00
217 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (195 bp):
TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT
GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG
CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA
Found at i:345716 original size:39 final size:39
Alignment explanation
Indices: 345296--345843 Score: 564
Period size: 39 Copynumber: 14.1 Consensus size: 39
345286 CCAGATACTG
* * * *** *
345296 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAC
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * **
345335 TACTTGTAGAGGGCTATAATATCAATTTAACTAACCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * * * ***
345374 TACTTGTATAGAGCTATAATATCAATGTACCCACCCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * * * *
345413 TACCTGTAGAGGGCTATGATATCATTGTAACTGTCCTAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * * *
345452 TACTTGTGGAGAGTTATAAT-TCAATTTAACTGTCCTAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * * ***
345490 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
*
345529 TACTTGTAGAGGGCTATAATATCAATGTAACTGTCCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* *
345568 TACTTGTAGAGGGTTATAATAACAATGT-ATTCGTCCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACT-GTCCAAA
*
345607 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCTAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * *
345646 TACTTATGGA-GATTAATAATATCAATGTAACTGTCCAAA
1 TACTTGTAGAGGGTT-ATAATATCAATGTAACTGTCCAAA
* * * *
345685 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAG
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * * * * *
345724 TACTTGTCGAGAG-AATAATATCACTTTAACTGTCCTAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
*
345762 TACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
* * *
345801 TACTTGTAGAGGGTTAAAATATCTATGTAACTGTCTAAA
1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
345840 TACT
1 TACT
345844 GTGACATCAT
Statistics
Matches: 426, Mismatches: 77, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
38 70 0.16
39 352 0.83
40 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (39 bp):
TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA
Found at i:346142 original size:40 final size:39
Alignment explanation
Indices: 346078--346854 Score: 540
Period size: 39 Copynumber: 19.5 Consensus size: 39
346068 GTGCAATGTA
* **
346078 CAATGTAACTGTCGTAATACTTGTAGAGGGCTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * *
346117 CAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATAT
1 CAATGTAACCGTC-CAAATACTTGTAGAGGGCTATAATAT
* * * *
346157 CATTG-AGACTGTCCAAATACTTGTAGATGGATATAATAT
1 CAATGTA-ACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * *
346196 CAATGTAACTGCCCAGATACTTGTAGAGGACTATAATTT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * ** * *
346235 CCATGTACCCGTCCAAATACTATATCAATGTACCCGTCCAAACACTATAT
1 CAATGTAACCGTCCAAATACT-TGT--A-G-A---GGGC-TATA--ATAT
* *
346285 CAATGT-ACCTGCCCAGATACTGTACTTGTAGAGGGTTATAATAT
1 CAATGTAACC-GTCCA-A-A---TACTTGTAGAGGGCTATAATAT
* ** *
346329 CAATAT-ACCCACCGAACTACTTGTAGAGGGCTATAATAT
1 CAATGTAACCGTCC-AAATACTTGTAGAGGGCTATAATAT
* *** * **
346368 CAATTTAACTAACCAAATACTTGTATATAGCTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* ** * *
346407 CAATGTACCCACCCAAATACCTGTAGAGGGCTATGATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * * *
346446 CATTGTAACTGTCCTAATACTTGTGGAGAGTTATAAT-T
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * * *
346484 CAATTTAACTGTCCTAATACTTGAAGAGAGTTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* **
346523 CAATGTACCCACCCAAATACTTGTAGAGGGCTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * *
346562 CAATGTAACTGTCCAAATACTTGTAGAGGGTTATAATAA
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
** *
346601 CAATGTATTCGTCCAAATACTTGTAGAGGGTTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * **
346640 CAATGTAACTGTCCTAATACTTATGGA-GATTAATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCT-ATAATAT
*
346679 CAATGTAACTGTCCAAATACTTGTAGAGGGCTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * * * *
346718 CAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * * *
346756 CACTTTAACTGTCCTAATACTTGTAGAGGGTTATAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * * *
346795 CAGTGTAACTGTCCAAATACTTGTAGAGGGTTAAAATAT
1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
* * *
346834 CTATGTAACTGTCTAAATACT
1 CAATGTAACCGTCCAAATACT
346855 GTGACATCAT
Statistics
Matches: 586, Mismatches: 126, Indels: 52
0.77 0.16 0.07
Matches are distributed among these distances:
38 68 0.12
39 426 0.73
40 41 0.07
42 1 0.00
43 4 0.01
44 14 0.02
46 2 0.00
47 3 0.01
48 2 0.00
49 2 0.00
50 13 0.02
51 2 0.00
52 2 0.00
54 2 0.00
55 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (39 bp):
CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT
Found at i:346267 original size:25 final size:25
Alignment explanation
Indices: 346237--346293 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
346227 TATAATTTCC
*
346237 ATGTACCCGTCCAAATACTATATCA
1 ATGTACCCGTCCAAACACTATATCA
346262 ATGTACCCGTCCAAACACTATATCA
1 ATGTACCCGTCCAAACACTATATCA
346287 ATGTACC
1 ATGTACC
346294 TGCCCAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (25 bp):
ATGTACCCGTCCAAACACTATATCA
Found at i:347147 original size:40 final size:40
Alignment explanation
Indices: 347101--347207 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
347091 CTGTCGTAAT
*
347101 ACTTGTAGAGGGCTATAATATCAATGTA-CCCGTCAAAAAA
1 ACTTGTAGAGGGCTATAATATCAATGTAGACCGTC-AAAAA
* * * *
347141 ACTTGTAGAGGGCTATAATATCATTG-AGACTGTCCAAAT
1 ACTTGTAGAGGGCTATAATATCAATGTAGACCGTCAAAAA
* *
347180 ACTTGTAGATGGATATAATATCAATGTA
1 ACTTGTAGAGGGCTATAATATCAATGTA
347208 ACTGCCCAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
39 27 0.47
40 30 0.53
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (40 bp):
ACTTGTAGAGGGCTATAATATCAATGTAGACCGTCAAAAA
Found at i:347197 original size:39 final size:38
Alignment explanation
Indices: 347083--347237 Score: 132
Period size: 39 Copynumber: 3.9 Consensus size: 38
347073 GTGCAATGTA
* ** *
347083 CAATGTAACTGTCGTAATACTTGTAGAGGGCTATAATAT
1 CAATGTAACTGCCCAAATACTTGTAGA-GGATATAATAT
* * ** * *
347122 CAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATAT
1 CAATGTAACTG-CCCAAATACTTGTAGA-GGATATAATAT
* *
347162 CATTG-AGACTGTCCAAATACTTGTAGATGGATATAATAT
1 CAATGTA-ACTGCCCAAATACTTGTAGA-GGATATAATAT
*
347201 CAATGTAACTGCCCAGATACTTGTAGAGGACTATAAT
1 CAATGTAACTGCCCAAATACTTGTAGAGGA-TATAAT
347238 TTCNNNNNNN
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
38 3 0.03
39 60 0.65
40 30 0.32
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (38 bp):
CAATGTAACTGCCCAAATACTTGTAGAGGATATAATAT
Found at i:354865 original size:24 final size:24
Alignment explanation
Indices: 354817--354878 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
354807 TCTGTTCATC
*
354817 CTCATCACCTCAGTCATCCTCGTT
1 CTCATCGCCTCAGTCATCCTCGTT
* * *
354841 CTCATCGCCTCATTCATCGTTGTT
1 CTCATCGCCTCAGTCATCCTCGTT
*
354865 CTAATCG-CTCAGTC
1 CTCATCGCCTCAGTC
354879 GTCTTCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.16, C:0.37, G:0.11, T:0.35
Consensus pattern (24 bp):
CTCATCGCCTCAGTCATCCTCGTT
Found at i:366379 original size:8 final size:8
Alignment explanation
Indices: 366366--366417 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
366356 AGGAATCACC
366366 CTGTCCGT
1 CTGTCCGT
366374 CTGTCCGT
1 CTGTCCGT
* *
366382 CCGTCTGT
1 CTGTCCGT
* *
366390 CCGTCAGT
1 CTGTCCGT
366398 CTGTCCGT
1 CTGTCCGT
* *
366406 CCGTCTGT
1 CTGTCCGT
366414 CTGT
1 CTGT
366418 GCAATCGTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.02, C:0.37, G:0.25, T:0.37
Consensus pattern (8 bp):
CTGTCCGT
Found at i:366385 original size:12 final size:12
Alignment explanation
Indices: 366368--366414 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
366358 GAATCACCCT
366368 GTCCGTCTGTCC
1 GTCCGTCTGTCC
366380 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
366392 GTCAGTCTGTCC
1 GTCCGTCTGTCC
366404 GTCCGTCTGTC
1 GTCCGTCTGTC
366415 TGTGCAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.38, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:366417 original size:4 final size:4
Alignment explanation
Indices: 366368--366410 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
366358 GAATCACCCT
* * * *
366368 GTCC GTCT GTCC GTCC GTCT GTCC GTCA GTCT GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
366411 TGTCTGTGCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.02, C:0.40, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:366686 original size:146 final size:145
Alignment explanation
Indices: 366422--367369 Score: 1304
Period size: 146 Copynumber: 6.5 Consensus size: 145
366412 GTCTGTGCAA
* *
366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
366552 AGAAAAATACAAAAAT
131 AGAAAAATAC-AAAAT
* *
366568 TCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
366633 TTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
366698 AGAAAAAATACAAAAT
131 AG-AAAAATACAAAAT
* * * *
366714 TCGTGTCCGGCCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTACTTCATACAACGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
366779 TTATCACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
366844 AGAAAAAATACAAAAAT
131 AG-AAAAATAC-AAAAT
* *
366861 TCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * *
366926 TTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
366991 AGAAAAAGTGCAAAAT
131 AGAAAAA-TACAAAAT
** * * * *
367007 TTTTGTCCGGCCCATATCTTT-TGTATGGAGAAACATTGGAAGTTCATAATTCACACAAATATTG
1 TCGTGTCCGGTCCATATCTTTCT-TATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG
* * * * * * *
367071 CTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTAAGGTCAAGG-GAGTTG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCA-CTG
367135 G--GAAAAATAGTGCAAAAT
129 GCAGAAAAATA---CAAAAT
* * * *
367153 TCGTGTCCGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTCTAACTTAACACAAATATT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
* * *
367216 GCTTAGGACCAAAGGGTGTGTCATGACCTTG-CCCAAGGTCATTTGGGCAAGGTCAAGGTCACTG
64 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTG
*
367280 GCAGAAAAAGTGCAAAAT
129 GCAGAAAAA-TACAAAAT
* ** *
367298 TCGTGTCTGGT-CATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT
1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
367361 -CTTATGACC
64 GCTTATGACC
367370 AACAGTTTTA
Statistics
Matches: 720, Mismatches: 67, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
143 1 0.00
144 14 0.02
145 99 0.14
146 461 0.64
147 144 0.20
148 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (145 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAATACAAAAT
Found at i:366980 original size:293 final size:293
Alignment explanation
Indices: 366422--367369 Score: 1371
Period size: 293 Copynumber: 3.2 Consensus size: 293
366412 GTCTGTGCAA
** *
366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC
1 TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
*
366552 AG-AAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTA
131 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA
366616 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA
196 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA
* *
366681 AGGTCAAGGTCACTGGCAGAAAAAATACAAAAT
261 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
* * *
366714 TCGTGTCCGGCCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTACTTCATACAACGATTGC
1 TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
366779 TTATCACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
*
366844 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTA
131 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA
* *
366909 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCA
196 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA
366974 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
261 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
** * * *
367007 TTTTGTCCGGCCCATATCTTT-TGTATGGAGAAACATTGGAAGTTCATAATTCACACAAATATTG
1 TCGTGTCCGGCCCATATCTTTCT-TATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG
* * * * * *
367071 CTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTAAGGTCAAGG-GAGTTG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCA-CTG
* * *
367135 G--GAAAAATAGTGC-AAAATTCGTGTCCGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATG
129 GCAGAAAAA-A-TACAAAAATTCGTGTCCGGTCCA-TATCTTTCGTATGGAGAAACATTGGAA-G
* * * * * *
367195 TTCTAACTTAACACAAATATTGCTTAGGACCAAAGGGTGTGTCATGACCTTG-CCCAAGGTCATT
190 TTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATT
*
367259 TGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
255 CGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
* * ** *
367298 TCGTGTCTGG-TCATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT
1 TCGTGTCCGGCCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT
367361 -CTTATGACC
64 GCTTATGACC
367370 AACAGTTTTA
Statistics
Matches: 596, Mismatches: 50, Indels: 22
0.89 0.07 0.03
Matches are distributed among these distances:
290 14 0.02
291 106 0.18
292 211 0.35
293 265 0.44
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (293 bp):
TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA
CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA
AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
Found at i:367240 original size:439 final size:435
Alignment explanation
Indices: 366422--367369 Score: 1334
Period size: 439 Copynumber: 2.2 Consensus size: 435
366412 GTCTGTGCAA
*
366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC
1 TCGTGTCCGGT-CATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * *
366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
65 TTATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
* * *
366552 AGAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTAC
130 AGAAAAATACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATAA
* *
366617 TTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCAA
195 TTCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCAA
*
366682 GGTCAAGGTCACTGGCAGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATTGAGAAA
260 GGTCAAGGTCACTGG-AGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATGGAGAAA
* * * * * *
366747 CATTGGAAGTTCTTACTTCATACAACGATTGCTTATCACCTAAGGGTGTGTCATGACCTTGACCC
324 CATTGGAAGTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTTG-CCC
366812 AAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAAT
388 AAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATAC-AAAAT
* *
366861 TCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGT-CATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
366926 TTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
65 TTATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
* ** * *
366991 AGAAAAAGTGC-AAAATTTTTGTCCGGCCCATATCTTTTGTATGGAGAAACATTGGAAGTTCATA
130 AGAAAAA-TACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATA
* * * * *
367055 ATTCACACAAATATTGCTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTA
194 ATTCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCA
* * * *
367120 AGGTCAAGG-GAGTTGG-GAAAAATAGTGCAAAATTCGTGTCCGG-TCATTATCTTTCTTATGGA
259 AGGTCAAGGTCA-CTGGAGAAAAA-A-TACAAAATTCGTGTCCGGCCCA-TATCTTTCTTATGGA
* * *
367182 GAAGCATT-GAATGTTCTAACTTAACACAAATATTGCTTAGGACCAAAGGGTGTGTCATGACCTT
320 GAAACATTGGAA-GTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTT
* * *
367246 GCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
384 GCCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAT
* ** *
367298 TCGTGTCTGGTCATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT-
1 TCGTGTCCGGTCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATTG
367361 CTTATGACC
64 CTTATGACC
367370 AACAGTTTTA
Statistics
Matches: 454, Mismatches: 47, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
436 14 0.03
437 61 0.13
438 50 0.11
439 327 0.72
440 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (435 bp):
TCGTGTCCGGTCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCT
TATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGCA
GAAAAATACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATAAT
TCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAG
GTCAAGGTCACTGGAGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATGGAGAAACA
TTGGAAGTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTTGCCCAAG
GTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAT
Found at i:375786 original size:166 final size:162
Alignment explanation
Indices: 375187--376246 Score: 1042
Period size: 166 Copynumber: 6.6 Consensus size: 162
375177 AAACTTTGCC
* * * * * **
375187 AGAATATTTTTAAAGATTTTCTGTATATATTCCTATGTAAACATTTAAACCGCCATCATGGCCCC
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAA-A-TTGATCCCCCATTGTGGCCCC
* * * * ** * * * * * * *
375252 GCCCAACCACTAGAGACTGTGATTT-TACAAACTTGCATTTACACTACCCGAGGATGCCTCTAC-
64 ACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT
** * * *
375315 ACAAGTTTAAGCTTTTCTGGCC-AATAGTCTTTAAAA
128 TTAA-TTTGAGCTTTTCTGGCCTAATAGT-TTTTAGA
* *
375351 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTACAAATTCATCCCCCATTGTGGCCTCA
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTA-AAATTGATCCCCCATTGTGGCCCCA
* * * * * * * **
375416 CCCTACCCCTGGG-CTATTATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCA
65 CCCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTTT
* *
375480 AATTTGGGCTTTCCTGGCCTAATAG-TTTT-G-
130 AATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA
* * *
375510 AGAAGATTTTTAAAGATTTTCTCTATATA----TA---AAAATTTATCTCCCATTGTGGCCCCGC
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCAC
* * * * **
375568 CCTACCCCCAAGGACCATGATTTGAACAAATTTGAATCTACATTATCTGAGGATAG-TTACACGC
66 CCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGAT-GCTTCCACTT
* * * *
375632 CAATTTGAGCTTTTTTGGCCAAATAGTTTTTAAA
129 TAATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA
** * *
375666 AGAATTTTTTTTATAGATTTTCTCTATATATTCCTGTATG-AAAA-TGTATCCCCCTATTGTAGC
1 AGAA-GATTTTTAAAGATTTTCTCTATATATTCC--TATGTAAAATTG-ATCCCCC-ATTGTGGC
* *
375729 CCCTCCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCC
61 CCCACCCTACCC-CAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCC
* *
375794 ATTTTATTTTGA-CTTTTCCTGGCCTAATAGTTTTTGAGA
125 ACTTTAATTTGAGCTTTT-CTGGCCTAATAGTTTTT-AGA
* ** *
375833 AGAAGATTTTTAAAGATTTTCTCTATATGTTCCTATGTAAAAATCCATTCCCCCCTTGTGGCCCC
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT-AAAATTGA-TCCCCCATTGTGGCCCC
* * *
375898 ACCATACCACCAGGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACT
64 ACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT
375963 TTAATTTGAGCTTTTCTGGCCTAATAGTTTTT-G-
128 TTAATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA
375996 AGAAG-------AAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCC
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCC-ATTGTGGCCCC
* *
376054 ACCCTACCCCCGGGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCA-T
64 ACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT
*
376118 ATTAATTTGAGCTTTTCTGGCCTGATAGTTTTTGAGA
128 -TTAATTTGAGCTTTTCTGGCCTAATAGTTTTT-AGA
*
376155 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCACTTGTGGCCCT
1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCCA-TTGTGGCCCC
* *
376220 TCCCTACCCCGGGGACCATGATTTGAA
64 ACCCTACCCCAGGGACCATGATTTGAA
376247 TCTACACTAC
Statistics
Matches: 750, Mismatches: 100, Indels: 91
0.80 0.11 0.10
Matches are distributed among these distances:
151 26 0.03
152 7 0.01
153 59 0.08
154 5 0.01
155 13 0.02
156 127 0.17
157 24 0.03
158 1 0.00
159 34 0.05
161 10 0.01
162 45 0.06
163 35 0.05
164 44 0.06
165 42 0.06
166 260 0.35
167 18 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (162 bp):
AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCAC
CCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTTTA
ATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA
Found at i:375842 original size:156 final size:153
Alignment explanation
Indices: 375680--376164 Score: 600
Period size: 156 Copynumber: 3.0 Consensus size: 153
375670 TTTTTTTTAT
* *
375680 AGATTTTCTCTATATATTCCTGTATGAAAATGTATCCCCCTATTGTAGCCCCTCCCTACCCACAG
1 AGATTTTCTCTATATATTCCT-TATGAAAAT-TATCCCCC-ATTGTGGCCCCACCCTACCCACAG
*
375745 GGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTATTTTGA-CTT
63 GGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTT
375809 TTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAA
128 TT-CTGGCCTAATAGTTTTT--G-AGAAG-------A
* * * *
375846 AGATTTTCTCTATATGTTCC-TATGTAAAAATCCATTCCCCCCTTGTGGCCCCACCATA-CCACC
1 AGATTTTCTCTATATATTCCTTATG--AAAAT-TA-TCCCCCATTGTGGCCCCACCCTACCCA-C
* *
375909 AGGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACTTTAATTTGAGC
61 AGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGC
375974 TTTTCTGGCCTAATAGTTTTTGAGAAGA
126 TTTTCTGGCCTAATAGTTTTTGAGAAGA
* *
376002 AGATTTTCTCTATATATTCC-TATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCCG
1 AGATTTTCTCTATATATTCCTTATG-AAAA-TT-ATCCCCC-ATTGTGGCCCCACCCTACCCACA
* * *
376066 GGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTAATTTGAGCT
62 GGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCT
*
376131 TTTCTGGCCTGATAGTTTTTGAGAAGA
127 TTTCTGGCCTAATAGTTTTTGAGAAGA
376158 AGATTTT
1 AGATTTT
376165 TAAAGATTTT
Statistics
Matches: 287, Mismatches: 23, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
155 10 0.03
156 135 0.47
157 2 0.01
163 5 0.02
164 5 0.02
165 3 0.01
166 116 0.40
167 11 0.04
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (153 bp):
AGATTTTCTCTATATATTCCTTATGAAAATTATCCCCCATTGTGGCCCCACCCTACCCACAGGGA
CCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTC
TGGCCTAATAGTTTTTGAGAAGA
Found at i:376089 original size:322 final size:315
Alignment explanation
Indices: 375363--376319 Score: 998
Period size: 322 Copynumber: 3.0 Consensus size: 315
375353 AAGATTTTTA
* * *
375363 AAGATTTTCTCTATATATTCCTATGTACAAATTCATCCCCCATTGTGGCCTCACCCTA-CCCCTG
1 AAGATTTTCTCTATATATTCCTATGTA-AAATTGATCCCCCATTGTGGCCCCACCCTACCCCCAG
* * * * * * * * *
375427 GG-CTATTATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCA-AATTTGGGC-
65 GGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCA-T-ATTATTTTGACT
375489 TTTCCTGGCCTAATAG-TTTT--G-AGAAGATTTTTAAAGATTTTCTCTATA-----TA--TAAA
128 TTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATTTCCTATGTAAA
* * * * *
375543 AATTTATCTCCCATTGTGGCCCCGCCCTACCCCCAAGGACCATGATTTGAACAAATTTGAATCTA
193 AATTCATCCCCCCTTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAA-TTGAATCTA
* * * * * *
375608 CATTATCTGAGGATAG-TTACACGCCAATTTGAGCTTTTTTGGCCAAATAGTTTTTAAAAGAATT
256 CACTACCTGAGGAT-GCTTCCAC-ACAATTTGAGCTTTTCTGGCCAAATAGTTTTT--GAGAA--
*
375672 TTTTTT
315 -----G
* *
375678 ATAGATTTTCTCTATATATTCCTGTATG-AAAA-TGTATCCCCCTATTGTAGCCCCTCCCTACCC
1 A-AGATTTTCTCTATATATTCC--TATGTAAAATTG-ATCCCCC-ATTGTGGCCCCACCCTACCC
* * *
375741 ACAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTATTTTGA
61 CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGA
375806 CTTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATGTTCCTATGT
126 CTTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATAT-TTCCTATGT
* * *
375871 AAAAATCCATTCCCCCCTTGTGGCCCCACCATACCACCAGGGACTATGATTTGAACAAACTTGAA
190 AAAAATTCA-TCCCCCCTTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAA-TTGAA
** *
375936 TCTACACTACCTGAGGATGCTTCCACTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAG
252 TCTACACTACCTGAGGATGCTTCCAC-ACAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG
*
376001 AAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCCG
1 AAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCC-ATTGTGGCCCCACCCTACCCCCA
* *
376066 GGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTAATTTGAGCT
64 GGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGA-CT
*
376131 TTT-CTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAA
128 TTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATAT-TTCCTATGTAA
* * ** *
376195 AACTTGATCCCCCACTTGTGGCCCTTCCCTACCCCGGGGACCATGA--T-------TTGAATCTA
192 AAATTCATCCCCC-CTTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAATTGAATCTA
* * * *
376251 CACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCAGGCCGAATAGTTTTTGAGAAG
256 CACTACCTGAGGATGCTTCCACACAA-TTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG
376312 AAGATTTT
1 AAGATTTT
376320 TGAAAAATAC
Statistics
Matches: 551, Mismatches: 61, Indels: 64
0.82 0.09 0.09
Matches are distributed among these distances:
310 2 0.00
311 69 0.13
315 2 0.00
316 30 0.05
317 15 0.03
318 17 0.03
319 57 0.10
320 8 0.01
321 21 0.04
322 184 0.33
323 35 0.06
329 2 0.00
330 4 0.01
331 11 0.02
332 94 0.17
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (315 bp):
AAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCAGG
GACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGACTTTT
CCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATTTCCTATGTAAAAAT
TCATCCCCCCTTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAATTGAATCTACACTA
CCTGAGGATGCTTCCACACAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG
Found at i:382367 original size:14 final size:15
Alignment explanation
Indices: 382348--382379 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
382338 TGCACATTGA
382348 TTTCTT-AATTTTTT
1 TTTCTTAAATTTTTT
382362 TTTCTTAAATTTTTT
1 TTTCTTAAATTTTTT
382377 TTT
1 TTT
382380 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTAAATTTTTT
Found at i:387277 original size:16 final size:16
Alignment explanation
Indices: 387236--387277 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
387226 GAATATGTTG
* *
387236 TCTATAAAATATGTAA
1 TCTATAAAAAAGGTAA
387252 TCTATAAAAAAGGTAA
1 TCTATAAAAAAGGTAA
387268 TCTATAAAAA
1 TCTATAAAAA
387278 TAATTCACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (16 bp):
TCTATAAAAAAGGTAA
Found at i:391727 original size:25 final size:25
Alignment explanation
Indices: 391698--391748 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
391688 TTGATGAAAT
*
391698 ATAATCAATGGTTAAATTAGACCAA
1 ATAATCAATGGTTAAATTAGAACAA
391723 ATAATCAATGGTTAAATTAGAACAA
1 ATAATCAATGGTTAAATTAGAACAA
391748 A
1 A
391749 CTAAGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (25 bp):
ATAATCAATGGTTAAATTAGAACAA
Found at i:401991 original size:15 final size:15
Alignment explanation
Indices: 401948--402003 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
401938 TGCACAATGT
*
401948 ACTAAACTAAACTGG
1 ACTAAACTAAACTGA
* *
401963 ACTGAATCT-GACTGA
1 ACT-AAACTAAACTGA
401978 ACTAAACTAAACTGA
1 ACTAAACTAAACTGA
*
401993 ACTGAACTAAA
1 ACTAAACTAAA
402004 TCACTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 4 0.12
15 25 0.76
16 4 0.12
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.21
Consensus pattern (15 bp):
ACTAAACTAAACTGA
Found at i:403276 original size:21 final size:21
Alignment explanation
Indices: 403137--403324 Score: 100
Period size: 21 Copynumber: 9.0 Consensus size: 21
403127 TATTTATGTT
* *
403137 AAAGTTTCGCGTTTATTCACA
1 AAAGTTTCGCGTTTATTCGCG
* ** * *
403158 AAACTAACGCGTTTATTTGCA
1 AAAGTTTCGCGTTTATTCGCG
** *
403179 AAAGTTTCTTGTTTATTCGCT
1 AAAGTTTCGCGTTTATTCGCG
* *
403200 AAAGTTACGCG-TTATATCACG
1 AAAGTTTCGCGTTTAT-TCGCG
* *
403221 AACGTTT-GCGTTTATTTGCG
1 AAAGTTTCGCGTTTATTCGCG
*** *
403241 AAAGAAAACCGCGTTTATTTGCG
1 AAAG--TTTCGCGTTTATTCGCG
*
403264 AAAGTTTCGCG-TTATATCGCT
1 AAAGTTTCGCGTTTAT-TCGCG
*
403285 AAAGTTTTC-CATTTATTCGCG
1 AAAG-TTTCGCGTTTATTCGCG
*
403306 AAA--TTCGCGTTTAGTCGCG
1 AAAGTTTCGCGTTTATTCGCG
403325 GAATTTTTTT
Statistics
Matches: 124, Mismatches: 34, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
18 3 0.02
19 10 0.08
20 17 0.14
21 69 0.56
22 8 0.06
23 17 0.14
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (21 bp):
AAAGTTTCGCGTTTATTCGCG
Done.