Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold183
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 471943
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:337681 original size:21 final size:22
Alignment explanation
Indices: 337641--337685 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
337631 CGAAATTGTT
337641 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
337663 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAGGGGGAG
337685 A
1 A
337686 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:338221 original size:20 final size:20
Alignment explanation
Indices: 338196--338312 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
338186 CAAAGCCCTG
*
338196 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATCTTC
**
338216 AAATGTATCGATACAGATTGC
1 AAATGTATCGATACATCTT-C
* ***
338237 ACA-GTATCGATACATGACC
1 AAATGTATCGATACATCTTC
* * **
338256 AAATGTATCGATACTTGTAA
1 AAATGTATCGATACATCTTC
*
338276 AGAATGTATCGATACA-CTATG
1 A-AATGTATCGATACATCT-TC
338297 AAATGTATCGATACAT
1 AAATGTATCGATACAT
338313 GCAGGCAAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.04
20 56 0.74
21 17 0.22
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACATCTTC
Found at i:352183 original size:15 final size:16
Alignment explanation
Indices: 352130--352213 Score: 75
Period size: 16 Copynumber: 5.2 Consensus size: 16
352120 CGTCCTCCAT
352130 AAAAA-AAACAAACAA
1 AAAAACAAACAAACAA
* *
352145 ACAAAACAAAAAAAGAA
1 A-AAAACAAACAAACAA
*
352162 GAGAAAACAAA-AAATAA
1 -A-AAAACAAACAAACAA
352179 AAAAACAAACAAACAA
1 AAAAACAAACAAACAA
*
352195 AAAAAAACAAC-AACAA
1 AAAAACA-AACAAACAA
352211 AAA
1 AAA
352214 GGGTCCGGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
15 9 0.16
16 24 0.41
17 16 0.28
18 9 0.16
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (16 bp):
AAAAACAAACAAACAA
Found at i:352207 original size:13 final size:12
Alignment explanation
Indices: 352130--352200 Score: 61
Period size: 13 Copynumber: 5.7 Consensus size: 12
352120 CGTCCTCCAT
352130 AAAAAAAACAAA
1 AAAAAAAACAAA
*
352142 CAAACAAAACAAA
1 -AAAAAAAACAAA
* *
352155 AAAAGAAGAGAAA
1 AAAA-AAAACAAA
* *
352168 ACAAAAAATAAA
1 AAAAAAAACAAA
*
352180 AAAACAAACAAA
1 AAAAAAAACAAA
352192 CAAAAAAAA
1 -AAAAAAAA
352201 ACAACAACAA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
12 18 0.40
13 27 0.60
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.01
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:353683 original size:28 final size:28
Alignment explanation
Indices: 353640--354024 Score: 404
Period size: 28 Copynumber: 13.5 Consensus size: 28
353630 CCTCACCCTG
*
353640 TCAAAAGCCCATAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
353668 TCAAAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
*
353696 TCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
* *
353726 TCCAAAGCCCACAAATCAGTGGC-ACCATTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC---T
*
353756 TCCAAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
*
353784 TCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
* *
353814 TCCAAAGCCCATAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
353842 TCAAAAGCCCACAAGTCAGTAGCATCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAAC-CT
* *
353871 TCCAAAGCCCACAAGTCAGTGGCAATCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
** * *
353899 TCAAAAGTGCATAAGTCAGTGGCACTCCTT
1 TCAAAAGCCCACAAGTCAGTGGCA-ACC-T
* * *
353929 TC-AAA-CCCACAAGTCAATGGTATCCTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC-T
353956 TC-AAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* *
353983 TCAAAAGCACACAAGT-TGAT-GCAACCCTT
1 TCAAAAGCCCACAAGTCAG-TGGCAA-CC-T
354012 TCAAAAGCCCACA
1 TCAAAAGCCCACA
354025 CAAGTTGGTG
Statistics
Matches: 305, Mismatches: 38, Indels: 27
0.82 0.10 0.07
Matches are distributed among these distances:
27 18 0.06
28 167 0.55
29 42 0.14
30 75 0.25
31 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (28 bp):
TCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:353790 original size:88 final size:86
Alignment explanation
Indices: 353643--353983 Score: 408
Period size: 88 Copynumber: 4.0 Consensus size: 86
353633 CACCCTGTCA
*
353643 AAAGCCCATAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
1 AAAGCCCATAAGTCAGTGGC-ACCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
353707 CAAGTCAGTGGCACCCTTTTCC
65 CAAGTCAGTGGCACCCTTTTCC
* *
353729 AAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCC
1 AAAGCCCATAAGTCAGTGGCACC--TTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCC
353794 ACAAGTCAGTGGCACCCTTTTCC
64 ACAAGTCAGTGGCACCCTTTTCC
* * * * *
353817 AAAGCCCATAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTAGCATCTTTTCCAAAGCCC
1 AAAGCCCATAAGTCAGTGGC-ACCTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCC
* * *
353881 ACAAGTCAGTGGCA--ATCTTCA
64 ACAAGTCAGTGGCACCCTTTTCC
** * * *
353902 AAAGTGCATAAGTCAGTGGCACTCCTTT-CAAA-CCCACAAGTCAATGGTATCCTTTC-AAAGCC
1 AAAGCCCATAAGTCAGTGGCA--CCTTTCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCC
*
353964 CACAAGTCAGTGGCAACCTT
63 CACAAGTCAGTGGCACCCTT
353984 CAAAAGCACA
Statistics
Matches: 222, Mismatches: 22, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
84 22 0.10
85 44 0.20
86 48 0.22
87 26 0.12
88 79 0.36
89 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.20
Consensus pattern (86 bp):
AAAGCCCATAAGTCAGTGGCACCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCAC
AAGTCAGTGGCACCCTTTTCC
Found at i:353791 original size:58 final size:57
Alignment explanation
Indices: 353643--354024 Score: 431
Period size: 58 Copynumber: 6.7 Consensus size: 57
353633 CACCCTGTCA
* *
353643 AAAGCCCATAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGC-ACCTTTTCC
* * *
353699 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCACCATTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTCAGTGGCACC-TTTTCC
353759 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCA-CCTTTTCC
* * *
353817 AAAGCCCATAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTAGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCC
* ** * *
353874 AAAGCCCACAAGTCAGTGGCAATCTTCAAAAGTGCATAAGTCAGTGGCACTCCTTT-C
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAC-CTTTTCC
* * * *
353931 AAA-CCCACAAGTCAATGGTATCCTTTC-AAAGCCCACAAGTCAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGC-ACCTTTTCC
* *
353986 AAAGCACACAAGT-TGAT-GCAACCCTTTCAAAAGCCCACA
1 AAAGCCCACAAGTCAG-TGGCAA-CC-TTCAAAAGCCCACA
354025 CAAGTTGGTG
Statistics
Matches: 280, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
54 2 0.01
55 5 0.02
56 71 0.25
57 72 0.26
58 102 0.36
59 2 0.01
60 26 0.09
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCC
Found at i:354218 original size:52 final size:49
Alignment explanation
Indices: 354041--354420 Score: 280
Period size: 49 Copynumber: 7.6 Consensus size: 49
354031 GGTGGCGTCT
* * * * *
354041 TCTTCTAAGTCCAATATCGCTGGCCTTGAACCAACATATTGGCACCTTTA
1 TCTT-TAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
** * * *
354091 TCTTTAAAACCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCA
1 TCTTT-AAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * ** * * * *
354141 TCTTGAAGACCGATGTCGTTAGCCTTGAATCAGCACATCGGCACCTCAATCA
1 TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCT---TCA
* * *
354193 TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTAGTACCTTTA
1 TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
354242 TCTTTAAATCTAATGTCGCTGGCCTTGAATCAACAGATTGGCACCTTCA
1 TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
** * * * * *
354291 T-TCTTAAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCATCTTTA
1 TCT-TTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * ** * * *
354340 ACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTAGCA--TTCT
1 TC-TT--TAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
354390 TCTTTAAATCTAATGTCGCTAGCCATGAATC
1 TCTTTAAGTCTAATGTCGCTGGCCTTGAATC
354421 GGCACATTAT
Statistics
Matches: 260, Mismatches: 61, Indels: 21
0.76 0.18 0.06
Matches are distributed among these distances:
47 20 0.08
48 1 0.00
49 119 0.46
50 50 0.19
51 1 0.00
52 69 0.27
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:354318 original size:150 final size:149
Alignment explanation
Indices: 354041--354420 Score: 410
Period size: 150 Copynumber: 2.5 Consensus size: 149
354031 GGTGGCGTCT
* * * * * *
354041 TCTTCTAAGTCCAATATCGCTGGCCTTGAACCAACATATTGGCACCTTTATCTTTAAAACCCAAT
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAG-ACCTTTATCTTT-AAATCTAAT
* * * * *
354106 ATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATCTTGAAGACCGATGTCGTTAGCCTTGAAT
63 GTCGCTGGCCTTGAATCAACAGATTGGCACCTTCATCTTGAAGACCGATATCGTTAGCCTTGAAT
*
354171 CAGCACATCGGCA-CCTCAATCA
128 CAACACATCGGCATCCTCAA-CA
*
354193 TCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTAGTACCTTTATCTTTAAATCTAATGT
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAG-ACCTTTATCTTTAAATCTAATGT
* *
354258 CGCTGGCCTTGAATCAACAGATTGGCACCTTCATTCTT-AAGTCCGATATCGTTGGCCTTGAATC
65 CGCTGGCCTTGAATCAACAGATTGGCACCTTCA-TCTTGAAGACCGATATCGTTAGCCTTGAATC
* * * *
354322 AACATATTGGCATCTTTAACA
129 AACACATCGGCATCCTCAACA
* * ** * *
354343 T-TCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTAG-CATTCT-TCTTTAAATCTAATG
1 TCT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGACCTT-TATCTTTAAATCTAATG
* *
354405 TCGCTAGCCATGAATC
64 TCGCTGGCCTTGAATC
354421 GGCACATTAT
Statistics
Matches: 195, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
148 32 0.16
149 2 0.01
150 105 0.54
151 52 0.27
152 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (149 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGACCTTTATCTTTAAATCTAATGTC
GCTGGCCTTGAATCAACAGATTGGCACCTTCATCTTGAAGACCGATATCGTTAGCCTTGAATCAA
CACATCGGCATCCTCAACA
Found at i:354366 original size:101 final size:100
Alignment explanation
Indices: 354045--354420 Score: 279
Period size: 101 Copynumber: 3.8 Consensus size: 100
354035 GCGTCTTCTT
* * * * **
354045 CTAAGTCCAATATCGCTGGCCTTGAACCAACATATTGGCACCTTTA-TCTTTAAAACCCAATATC
1 CTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATTCTTT-AAGTCCAATATC
* *
354109 GCTGGCCTTAAATCAGCATATTGGCACCTT-CA-TC
65 GCTGGCCTTGAATCAGCATATTGGCACTTTACATTC
* * * * * * * *
354143 TTGAAGACCGATGTCGTTAGCCTTGAATCAGCACATCGGCACC-TCAATCATCTTTAAGTCTAAT
1 CT-AAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTC-AT--TCTTTAAGTCCAAT
* * *
354207 GTCGCTGGCCTTGAATCAGCATATTAGTACCTTTATC-TT-
62 ATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTA-CATTC
* * * *
354246 -TAAATCTAATGTCGCTGGCCTTGAATCAACAGATTGGCACCTTCATTC-TTAAGTCCGATATCG
1 CTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATTCTTTAAGTCCAATATCG
* *
354309 TTGGCCTTGAATCAACATATTGGCATCTTTAACATTC
66 CTGGCCTTGAATCAGCATATTGGCA-CTTT-ACATTC
* ** * * * * *
354346 CTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTAGCA--TTC-TTCTTTAAATCTAATGTCG
1 CTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATTCTTTAAGTCCAATATCG
* *
354408 CTAGCCATGAATC
66 CTGGCCTTGAATC
354421 GGCACATTAT
Statistics
Matches: 212, Mismatches: 51, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
98 43 0.20
99 61 0.29
101 95 0.45
102 11 0.05
104 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (100 bp):
CTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATTCTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGGCACTTTACATTC
Found at i:355218 original size:13 final size:13
Alignment explanation
Indices: 355200--355224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355190 ACGTAAGTGT
355200 TGTATCGATACAA
1 TGTATCGATACAA
355213 TGTATCGATACA
1 TGTATCGATACA
355225 TAAGTTTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:355219 original size:32 final size:32
Alignment explanation
Indices: 355181--355256 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
355171 TTCAACGATT
*
355181 TATATCGATACGTAAGTGTT-GTATCGATACAA
1 TATATCGATACATAAGT-TTCGTATCGATACAA
*
355213 TGTATCGATACATAAGTTTCGTATCGATACAA
1 TATATCGATACATAAGTTTCGTATCGATACAA
*
355245 TATATCGCTACA
1 TATATCGATACA
355257 AAGCTACTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
TATATCGATACATAAGTTTCGTATCGATACAA
Found at i:355314 original size:13 final size:13
Alignment explanation
Indices: 355296--355320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355286 ATTACTCAAA
355296 TGTATCGATACAT
1 TGTATCGATACAT
355309 TGTATCGATACA
1 TGTATCGATACA
355321 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361644 original size:15 final size:16
Alignment explanation
Indices: 361624--361662 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
361614 TCGAGGTGGT
361624 TTCAAGT-AAGGGTAA
1 TTCAAGTAAAGGGTAA
*
361639 TTCAAGTAAAAGGTTAA
1 TTCAAGT-AAAGGGTAA
361656 TTCAAGT
1 TTCAAGT
361663 CTTTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (16 bp):
TTCAAGTAAAGGGTAA
Found at i:362019 original size:13 final size:12
Alignment explanation
Indices: 361984--362031 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
361974 AATTTTATTA
361984 AAATATAAAAAT
1 AAATATAAAAAT
* *
361996 AAAGA-ATAAAT
1 AAATATAAAAAT
*
362007 AATATTTAAAAAT
1 AA-ATATAAAAAT
362020 AAATATAAAAAT
1 AAATATAAAAAT
362032 TATAATTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
11 7 0.25
12 14 0.50
13 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:362538 original size:23 final size:23
Alignment explanation
Indices: 362508--362553 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
362498 TACATATTTT
362508 GTTACAATCCAAAATGATAATTA
1 GTTACAATCCAAAATGATAATTA
*
362531 GTTACAATGCAAAATGATAATTA
1 GTTACAATCCAAAATGATAATTA
362554 TAACTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (23 bp):
GTTACAATCCAAAATGATAATTA
Found at i:363341 original size:13 final size:13
Alignment explanation
Indices: 363323--363348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363313 CAATTTCCTT
363323 ATGTATCGATACA
1 ATGTATCGATACA
363336 ATGTATCGATACA
1 ATGTATCGATACA
363349 TTGTCCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363436 original size:13 final size:13
Alignment explanation
Indices: 363418--363443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363408 TACAATGAGT
363418 ATGTATCGATACA
1 ATGTATCGATACA
363431 ATGTATCGATACA
1 ATGTATCGATACA
363444 TCTGGGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:364000 original size:21 final size:20
Alignment explanation
Indices: 363976--364039 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
363966 TTTACTCCCC
363976 CTTAATTAAAGAATTTCTCCT
1 CTTAA-TAAAGAATTTCTCCT
* *
363997 CTTAA-AAA-AAATTCTCCCC
1 CTTAATAAAGAATTTCT-CCT
* *
364016 CTTAATCAAAGCATTTCTACT
1 CTTAAT-AAAGAATTTCTCCT
364037 CTT
1 CTT
364040 TCTCCCCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 6 0.18
19 10 0.30
21 12 0.36
22 5 0.15
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (20 bp):
CTTAATAAAGAATTTCTCCT
Found at i:364019 original size:19 final size:20
Alignment explanation
Indices: 363970--364021 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
363960 TTTCGTTTTA
*
363970 CTCCCCCTTAATTAAAGAATT
1 CTCCCCCTTAA-TAAAAAATT
*
363991 -TCTCCTCTTAA-AAAAAATT
1 CTC-CCCCTTAATAAAAAATT
364010 CTCCCCCTTAAT
1 CTCCCCCTTAAT
364022 CAAAGCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
19 14 0.56
20 4 0.16
21 7 0.28
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.35
Consensus pattern (20 bp):
CTCCCCCTTAATAAAAAATT
Found at i:367214 original size:23 final size:23
Alignment explanation
Indices: 367179--367224 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
367169 TATATATTTT
367179 GTTACAATCCAAAATGATAATTA
1 GTTACAATCCAAAATGATAATTA
* *
367202 GTTATAATGCAAAATGATAATTA
1 GTTACAATCCAAAATGATAATTA
367225 TAACTTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
GTTACAATCCAAAATGATAATTA
Found at i:367409 original size:18 final size:18
Alignment explanation
Indices: 367388--367422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
367378 ATTTTAAATA
*
367388 ATTTTTATTATTAATAAG
1 ATTTATATTATTAATAAG
*
367406 ATTTATATTATTTATAA
1 ATTTATATTATTAATAA
367423 ATAAAAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTATATTATTAATAAG
Found at i:367693 original size:19 final size:19
Alignment explanation
Indices: 367638--367690 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
367628 GAAAATGTTG
* *
367638 TATTAATCT-AATTTTAAA
1 TATTAATATAAATTTTAAT
367656 TATTAATATAAATTTTAAT
1 TATTAATATAAATTTTAAT
*
367675 TATTTATATAACATTT
1 TATTAATATAA-ATTT
367691 AATATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 8 0.27
19 18 0.60
20 4 0.13
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAATATAAATTTTAAT
Found at i:367710 original size:16 final size:15
Alignment explanation
Indices: 367691--367728 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
367681 TATAACATTT
367691 AATATATAATTTTATA
1 AATATATAATTTT-TA
*
367707 AATAAATAATTTTTA
1 AATATATAATTTTTA
367722 AAT-TATA
1 AATATATA
367729 TTATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 5 0.25
16 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATAATTTTTA
Found at i:370677 original size:2 final size:2
Alignment explanation
Indices: 370670--370708 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
370660 AATATCTTAA
370670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
370709 ATTAAGCGTA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:383617 original size:33 final size:32
Alignment explanation
Indices: 383579--383642 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
383569 AAATTTAATA
383579 TATAATATAAAGT-AAAATATTATATTTTGTACC
1 TATAAT-TAAA-TCAAAATATTATATTTTGTACC
** *
383612 TATAATTTTATCAAAATATTTTATTTTGTAC
1 TATAATTAAATCAAAATATTATATTTTGTAC
383643 TTGCGACGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 1 0.04
32 20 0.74
33 6 0.22
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (32 bp):
TATAATTAAATCAAAATATTATATTTTGTACC
Found at i:384445 original size:17 final size:16
Alignment explanation
Indices: 384425--384461 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
384415 CTATAATGTT
384425 ATTTTACTAGTAATCAC
1 ATTTT-CTAGTAATCAC
384442 A-TTTCTAGTAATCAC
1 ATTTTCTAGTAATCAC
384457 ATTTT
1 ATTTT
384462 TAAAAGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.63
16 6 0.32
17 1 0.05
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTTTCTAGTAATCAC
Found at i:384451 original size:15 final size:15
Alignment explanation
Indices: 384431--384460 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
384421 TGTTATTTTA
384431 CTAGTAATCACATTT
1 CTAGTAATCACATTT
384446 CTAGTAATCACATTT
1 CTAGTAATCACATTT
384461 TTAAAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
CTAGTAATCACATTT
Found at i:391226 original size:21 final size:22
Alignment explanation
Indices: 391197--391238 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
391187 TATTCAGACA
* *
391197 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
391219 AGTA-TACTCCAAAACAGGTG
1 AGTAGTACTCCAAAACAGGTG
391239 AAGTTTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:393209 original size:23 final size:24
Alignment explanation
Indices: 393163--393210 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
393153 TTTTTGTTTG
*
393163 TCAAAAATGGTAGCTTATTATTTA
1 TCAAAAATGGTAGCTAATTATTTA
* *
393187 TCAAAATTGGTGGCTAATT-TTTA
1 TCAAAAATGGTAGCTAATTATTTA
393210 T
1 T
393211 TACAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (24 bp):
TCAAAAATGGTAGCTAATTATTTA
Found at i:394078 original size:35 final size:35
Alignment explanation
Indices: 394031--394102 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
394021 TCAAGCTCTA
*
394031 TTGTTTTTTGTTCTGTTTTTCTGGTTCTTCCTTCT
1 TTGTTTTCTGTTCTGTTTTTCTGGTTCTTCCTTCT
394066 TTGTTTTCTGTTCTGTTTTTCTGGTTCTTCCTTCT
1 TTGTTTTCTGTTCTGTTTTTCTGGTTCTTCCTTCT
394101 TT
1 TT
394103 CAGCTGTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (35 bp):
TTGTTTTCTGTTCTGTTTTTCTGGTTCTTCCTTCT
Found at i:394926 original size:41 final size:41
Alignment explanation
Indices: 394843--394929 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
394833 TCAGATTTAA
*
394843 ATAAAAATATTTTTTTAATTAAAATTAATTTGAATTACTAT
1 ATAAAAATATTTTTTTAATTAAAATTAATTTGAAATACTAT
*
394884 ATAATAAATA-TTTTTTAATTTAAATTTAATTAT-AAATA-TAT
1 ATAA-AAATATTTTTTTAA-TTAAAATTAATT-TGAAATACTAT
394925 ATAAA
1 ATAAA
394930 TATTAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
40 1 0.02
41 19 0.46
42 20 0.49
43 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (41 bp):
ATAAAAATATTTTTTTAATTAAAATTAATTTGAAATACTAT
Found at i:395203 original size:21 final size:20
Alignment explanation
Indices: 395179--395219 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
395169 TTTTTTAATT
395179 TAAATA-TAATTATAAAATATA
1 TAAATATTAATT-T-AAATATA
395200 TAAATATTAATTTAAATATA
1 TAAATATTAATTTAAATATA
395220 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTAATTTAAATATA
Found at i:395647 original size:13 final size:13
Alignment explanation
Indices: 395631--395670 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
395621 TTTTTTAAAA
395631 TTTAATTTTCTAT
1 TTTAATTTTCTAT
395644 TTTAATTTTCTCA-
1 TTTAATTTTCT-AT
395657 TTTAATTTTC-AT
1 TTTAATTTTCTAT
395669 TT
1 TT
395671 GTTAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 2 0.08
13 21 0.84
14 1 0.04
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTAATTTTCTAT
Found at i:395724 original size:17 final size:18
Alignment explanation
Indices: 395697--395732 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
395687 TTTTATTTTT
395697 ATTTAATATAATAAATAA
1 ATTTAATATAATAAATAA
*
395715 ATTT-ATATAATATATAA
1 ATTTAATATAATAAATAA
395732 A
1 A
395733 AATTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAATATAATAAATAA
Found at i:395780 original size:19 final size:20
Alignment explanation
Indices: 395758--395805 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
395748 ATATTTCAAT
395758 AAATATATAATAT-TTATTA
1 AAATATATAATATATTATTA
*
395777 AAAT-TTTAATATATTATTA
1 AAATATATAATATATTATTA
395796 AAATATATAA
1 AAATATATAA
395806 AGATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 14 0.56
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATATAATATATTATTA
Found at i:399790 original size:29 final size:29
Alignment explanation
Indices: 399751--399819 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
399741 TTATATCGTA
399751 TTTATATTTATGTATATA-TTTAAATTA-ATT
1 TTTATA-TTATGT-TATACTTT-AATTATATT
* *
399781 TTTATATTATGTTGTACTTTAATTATTTT
1 TTTATATTATGTTATACTTTAATTATATT
399810 TTTATATTAT
1 TTTATATTAT
399820 ACTTCAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 8 0.23
29 21 0.60
30 6 0.17
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTATATTATGTTATACTTTAATTATATT
Found at i:399947 original size:19 final size:20
Alignment explanation
Indices: 399923--399964 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
399913 CTTTAATATA
399923 AATATAA-TATTTAAATTTT
1 AATATAATTATTTAAATTTT
* *
399942 AATATAATTCTTTCAATTTT
1 AATATAATTATTTAAATTTT
399962 AAT
1 AAT
399965 TCTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
AATATAATTATTTAAATTTT
Found at i:399961 original size:20 final size:19
Alignment explanation
Indices: 399910--399964 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
399900 TTTATTTGCC
* *
399910 ATTCTTTAATATAAATATA
1 ATTCTTTAATTTTAATATA
*
399929 ATAT-TTAAATTTTAATATA
1 AT-TCTTTAATTTTAATATA
399948 ATTCTTTCAATTTTAAT
1 ATTCTTT-AATTTTAAT
399965 TCTAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.62
20 10 0.34
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTCTTTAATTTTAATATA
Found at i:400121 original size:52 final size:53
Alignment explanation
Indices: 400029--400133 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 53
400019 TAATATATTT
* * *
400029 ATATTATATTCATATTATTTTTTATATTGTGTTAGATTTTATTTA-TTTATCA
1 ATATTATATTCATATTATATTTTATAATGTGTTAGATTTTATATATTTTATCA
400081 ATATTATATTCATATTATATTTTACTTAAT-T-TTACG-TTTTATATATTTTATCA
1 ATATTATATTCATATTATATTTTA--TAATGTGTTA-GATTTTATATATTTTATCA
400134 TAATAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
52 34 0.74
53 9 0.20
54 3 0.07
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (53 bp):
ATATTATATTCATATTATATTTTATAATGTGTTAGATTTTATATATTTTATCA
Found at i:400494 original size:13 final size:13
Alignment explanation
Indices: 400490--400523 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
400480 ATAATTAATT
400490 ATTATAAATATTA
1 ATTATAAATATTA
400503 ATTATAAATATTA
1 ATTATAAATATTA
*
400516 ATAATAAA
1 ATTATAAA
400524 AAATTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTATAAATATTA
Found at i:401528 original size:43 final size:42
Alignment explanation
Indices: 401447--401528 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
401437 ACTGATGATT
*
401447 AATTAATTAATTGAAATAAAAAATTTTAATAATTTATTTCCAA
1 AATTAATTAATTGAAATAAAAAAATTTAATAA-TTATTTCCAA
401490 AATTAATATATATTGAAATAAAAAAAATTTAA-AA-TATTT
1 AATTAAT-TA-ATTGAAAT-AAAAAAATTTAATAATTATTT
401529 AATCTGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
43 12 0.34
44 2 0.06
45 10 0.29
46 11 0.31
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (42 bp):
AATTAATTAATTGAAATAAAAAAATTTAATAATTATTTCCAA
Found at i:401819 original size:29 final size:29
Alignment explanation
Indices: 401734--401820 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
401724 ACCTTCCAAA
* * *
401734 AAATATATTTTTAATAGAATTTTTAAAAAT
1 AAATATATTTTTTATACAA-TTATAAAAAT
* * * *
401764 AAATAAATATTTTTAAATATTTA-AAAAAT
1 AAATATAT-TTTTTATACAATTATAAAAAT
*
401793 AAATATATTTTTTATACAACTATAAAAA
1 AAATATATTTTTTATACAATTATAAAAA
401821 GTAATTATCT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
28 10 0.23
29 18 0.41
30 9 0.20
31 7 0.16
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (29 bp):
AAATATATTTTTTATACAATTATAAAAAT
Found at i:402144 original size:16 final size:16
Alignment explanation
Indices: 402102--402144 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
402092 GTTTTATTTT
402102 TATTTTGATATTAATA
1 TATTTTGATATTAATA
* * * *
402118 TGTGTTAATATTAATG
1 TATTTTGATATTAATA
402134 TATTTTGATAT
1 TATTTTGATAT
402145 ATTATTATAG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TATTTTGATATTAATA
Found at i:403077 original size:12 final size:12
Alignment explanation
Indices: 403062--403117 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 12
403052 TCAAAAAATG
403062 AAAAAAAATTAT
1 AAAAAAAATTAT
*
403074 AAAAAAAATTTAA
1 AAAAAAAA-TTAT
403087 AATTTAAAAAATTAT
1 AA---AAAAAATTAT
403102 -AAAAAAATCTAT
1 AAAAAAAAT-TAT
403114 AAAA
1 AAAA
403118 TTAAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
11 7 0.19
12 11 0.31
13 8 0.22
14 1 0.03
15 3 0.08
16 6 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:403097 original size:38 final size:40
Alignment explanation
Indices: 403043--403117 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 40
403033 AAGAATGATT
*
403043 ATTTTAAATTCAAAAAATGA-AAAAAAAT-TATAAAAAAA
1 ATTTAAAATTCAAAAAATGATAAAAAAATCTATAAAAAAA
* *
403081 ATTTAAAATTTAAAAAATTATAAAAAAATCTATAAAA
1 ATTTAAAATTCAAAAAATGATAAAAAAATCTATAAAA
403118 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 17 0.53
39 8 0.25
40 7 0.22
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (40 bp):
ATTTAAAATTCAAAAAATGATAAAAAAATCTATAAAAAAA
Found at i:403102 original size:28 final size:28
Alignment explanation
Indices: 403064--403124 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
403054 AAAAAATGAA
403064 AAAAAATTATAAAAAAAAT-T-TAAAATTT
1 AAAAAATTAT-AAAAAAATCTATAAAA-TT
403092 AAAAAATTATAAAAAAATCTATAAAATT
1 AAAAAATTATAAAAAAATCTATAAAATT
403120 AAAAA
1 AAAAA
403125 TAAATTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 8 0.26
28 18 0.58
29 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAATTATAAAAAAATCTATAAAATT
Found at i:403172 original size:29 final size:28
Alignment explanation
Indices: 403140--403236 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 28
403130 TCTAAAAGTT
403140 TTAAAAATAAAAATAAAAAATTCAAAAAA
1 TTAAAAATAAAAAT-AAAAATTCAAAAAA
*
403169 TTAAAATTATTTAAAATATATAAAATTATAAAAAA
1 TTAAAA--A--TAAAA-ATA-AAAATT-CAAAAAA
*
403204 TTTAAAAATATAAAT-AAAATTCAAAAAA
1 -TTAAAAATAAAAATAAAAATTCAAAAAA
*
403232 ATAAA
1 TTAAA
403237 GAATCTATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.07
28 6 0.11
29 12 0.21
31 3 0.05
32 4 0.07
33 6 0.11
34 9 0.16
35 6 0.11
36 6 0.11
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
TTAAAAATAAAAATAAAAATTCAAAAAA
Found at i:403198 original size:10 final size:10
Alignment explanation
Indices: 403170--403224 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
403160 TTCAAAAAAT
*
403170 TAAAATTATT
1 TAAAATTATA
403180 TAAAA-TATA
1 TAAAATTATA
403189 TAAAATTATA
1 TAAAATTATA
*
403199 AAAAATT-TA
1 TAAAATTATA
*
403208 -AAAATATAAA
1 TAAAAT-TATA
403218 TAAAATT
1 TAAAATT
403225 CAAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 5 0.13
9 11 0.29
10 17 0.45
11 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAATTATA
Found at i:403215 original size:17 final size:17
Alignment explanation
Indices: 403189--403259 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
403179 TTAAAATATA
*
403189 TAAAATTATAAAAAATT
1 TAAAAATATAAAAAATT
403206 TAAAAATATAAATAAAATT
1 TAAAAATAT-AA-AAAATT
* * * *
403225 CAAAAAAATAAAGAATC
1 TAAAAATATAAAAAATT
*
403242 TATTAAAT-TAAAAAATT
1 TA-AAAATATAAAAAATT
403259 T
1 T
403260 TAATTTTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
17 21 0.51
18 7 0.17
19 13 0.32
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
TAAAAATATAAAAAATT
Found at i:403229 original size:18 final size:18
Alignment explanation
Indices: 403093--403230 Score: 61
Period size: 19 Copynumber: 7.3 Consensus size: 18
403083 TTAAAATTTA
403093 AAAAATTATAAAAAAATCT
1 AAAAATTATAAAAAAAT-T
403112 ATAAAATTA-AAAATAAATTCT
1 A-AAAATTATAAAA-AAA-T-T
* * *
403133 AAAAGTTTTAAAAATAAAAAT
1 AAAA--ATTATAAA-AAAATT
* *
403154 AAAAAAT-TCAAAAAATT
1 AAAAATTATAAAAAAATT
**
403171 -AAAATTAT-TTAAAATAT
1 AAAAATTATAAAAAAAT-T
*
403188 ATAAAATTATAAAAAATTT
1 A-AAAATTATAAAAAAATT
403207 AAAAA-TATAAATAAAATT
1 AAAAATTATAAA-AAAATT
403225 CAAAAA
1 -AAAAA
403231 AATAAAGAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
16 10 0.11
17 13 0.14
18 11 0.12
19 21 0.23
20 17 0.19
21 9 0.10
22 3 0.03
23 6 0.07
24 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAATTATAAAAAAATT
Found at i:403230 original size:19 final size:19
Alignment explanation
Indices: 403200--403236 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
403190 AAAATTATAA
* *
403200 AAAATTTAAAAATATAAAT
1 AAAATTCAAAAAAATAAAT
403219 AAAATTCAAAAAAATAAA
1 AAAATTCAAAAAAATAAA
403237 GAATCTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTCAAAAAAATAAAT
Found at i:403294 original size:28 final size:27
Alignment explanation
Indices: 403260--403368 Score: 81
Period size: 28 Copynumber: 4.2 Consensus size: 27
403250 TAAAAAATTT
403260 TAATTTTTAAAATTTTATAGATTTTTTA
1 TAATTTTTAAAATTTTATA-ATTTTTTA
** *
403288 TAATTTTTTGAA-TTT-T--TGTTTT-
1 TAATTTTTAAAATTTTATAATTTTTTA
*
403310 T-ATTTTTAAATTTTTATAATTTTTTA
1 TAATTTTTAAAATTTTATAATTTTTTA
**
403336 -AATTTTTTGAATTTTTTATAATTTTTTA
1 TAA-TTTTT-AAAATTTTATAATTTTTTA
403364 -AATTT
1 TAATTT
403369 AAAAATTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
21 7 0.11
22 4 0.06
23 6 0.09
25 5 0.08
26 2 0.03
27 11 0.17
28 30 0.46
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (27 bp):
TAATTTTTAAAATTTTATAATTTTTTA
Found at i:403301 original size:9 final size:9
Alignment explanation
Indices: 403257--403368 Score: 93
Period size: 9 Copynumber: 12.1 Consensus size: 9
403247 AATTAAAAAA
403257 TTTT-AATT
1 TTTTAAATT
*
403265 TTTAAAATT
1 TTTTAAATT
* *
403274 TTATAGATT
1 TTTTAAATT
403283 TTTTATAATT
1 TTTTA-AATT
*
403293 TTTTGAATT
1 TTTTAAATT
***
403302 TTTGTTTTTAT
1 TTT-TAAAT-T
403313 TTTTAAA-T
1 TTTTAAATT
403321 TTTTATAATT
1 TTTTA-AATT
403331 TTTTAAATT
1 TTTTAAATT
*
403340 TTTTGAATT
1 TTTTAAATT
403349 TTTTATAATT
1 TTTTA-AATT
403359 TTTTAAATT
1 TTTTAAATT
403368 T
1 T
403369 AAAAATTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
8 9 0.11
9 44 0.54
10 25 0.30
11 4 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (9 bp):
TTTTAAATT
Found at i:411249 original size:13 final size:13
Alignment explanation
Indices: 411229--411303 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
411219 ATATCATCTA
411229 AAATTTTAAATTTT
1 AAATTTTAAA-TTT
411243 AAA-TTTAAATTT
1 AAATTTTAAATTT
*
411255 AAATTTT--ATCT
1 AAATTTTAAATTT
* *
411266 AGATTTTCAAAATCT
1 AAATTTT--AAATTT
411281 AAA-TTTAAATTTT
1 AAATTTTAAA-TTT
411294 AAATTTTAAA
1 AAATTTTAAA
411304 ATTTGAACAG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
11 9 0.18
12 9 0.18
13 14 0.28
14 12 0.24
15 6 0.12
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (13 bp):
AAATTTTAAATTT
Found at i:411307 original size:8 final size:7
Alignment explanation
Indices: 411229--411303 Score: 66
Period size: 7 Copynumber: 10.4 Consensus size: 7
411219 ATATCATCTA
411229 AAATTTT
1 AAATTTT
411236 AAATTTT
1 AAATTTT
411243 AAA-TTT
1 AAATTTT
411249 AAA-TTT
1 AAATTTT
411255 AAATTTT
1 AAATTTT
411262 ATCTAGATTTT
1 A---A-ATTTT
* *
411273 CAAAATCT
1 -AAATTTT
411281 AAA-TTT
1 AAATTTT
411287 AAATTTT
1 AAATTTT
411294 AAATTTT
1 AAATTTT
411301 AAA
1 AAA
411304 ATTTGAACAG
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
6 17 0.29
7 30 0.52
8 3 0.05
9 1 0.02
10 1 0.02
11 5 0.09
12 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (7 bp):
AAATTTT
Found at i:412096 original size:2 final size:2
Alignment explanation
Indices: 412089--412117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
412079 ATTAGAGTTT
412089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
412118 GTATTGTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:412370 original size:19 final size:19
Alignment explanation
Indices: 412342--412380 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
412332 TCTTTAATCT
*
412342 TTGTTAATATGTATATATA
1 TTGTTAATATATATATATA
*
412361 TTGTTTATATATATATATA
1 TTGTTAATATATATATATA
412380 T
1 T
412381 ATTTACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TTGTTAATATATATATATA
Found at i:414694 original size:165 final size:164
Alignment explanation
Indices: 414360--414925 Score: 382
Period size: 165 Copynumber: 3.5 Consensus size: 164
414350 TTTAAATATC
* * * * *
414360 AAAATTATTCAAATATTATTATTTAATTAATATTAAATCAGTTTTAAAAATTTTCTTTTATTTCA
1 AAAATTCTTCAAATATTATCATTTAATTAATAGTAAATCAGTTTTAAAAATATTCATTTATTTCA
* ** * * * *
414425 TGAATTTTTCATTTTTTTTAAAATTTTTTTGTTTTCAAAATATGGAGTTTTCTACTCCGTGAATA
66 TGAATTTTTCATTTTTTTTAAAATTCTCCTATTTTCAAAATATGAAGTTTTCTACTCCATAAATA
* ** *** * *
414490 TTTTTGGGGGGATTTTTCTTGTTTTATAATTTTT
131 TTTTTGAGAAGATTTTTCTCAATTTAAAATCTTT
* *
414524 AAAATTCTTCAAATATTATCATTTAATTAATAGTAAATCATTTTTAAAAA-ATTCATTTATTTTT
1 AAAATTCTTCAAATATTATCATTTAATTAATAGTAAATCAGTTTTAAAAATATTCATTTA-TTTC
* * *
414588 AT-AATTTTTTCATTTTTCTTTGAAATTCTCCTATTTCTGAAAA-ACT-AAGTTTTCTATTCCAT
65 ATGAA-TTTTTCATTTTT-TTTAAAATTCTCCTATTT-TCAAAATA-TGAAGTTTTCTACTCCAT
414650 AAATATTTTTGAGAAGATTTTTCTCAATTTAAAATCTTT
126 AAATATTTTTGAGAAGATTTTTCTCAATTTAAAATCTTT
* * * * * * * * *
414689 AAAATTCATCTAACATTGTCA-TTAGCCTTACT-TTAAGTCAGTTTTAGAAA-ATTCAATTTATT
1 AAAATTCTTCAAATATTATCATTTA--ATTAATAGTAAATCAGTTTTAAAAATATTC-ATTTATT
*** * * * * *
414751 TCATGAA--TTTC-TTGAATTT----TTCTACTA--CT-AAGATACGAAGTTTTCTACTCCGTAA
63 TCATGAATTTTTCATTTTTTTTAAAATTCTCCTATTTTCAAAATATGAAGTTTTCTACTCCATAA
* * * *
414806 ATTTTTTCTGTTG--GATTTTTCTCAGTTTAAAATTTTT
128 ATATTTT-TG-AGAAGATTTTTCTCAATTTAAAATCTTT
* * * * * * *
414843 AAAATT-TATCAAATATTTTTATTAAATTCATATTAAATTAGTTTGTAAAAAT-TTAATTTATTT
1 AAAATTCT-TCAAATATTATCATTTAATTAATAGTAAATCAGTTT-TAAAAATATTCATTTATTT
* *
414906 TATGAATTTTGCATTTTTTT
64 CATGAATTTTTCATTTTTTT
414926 CATATAACAA
Statistics
Matches: 314, Mismatches: 67, Indels: 49
0.73 0.16 0.11
Matches are distributed among these distances:
153 6 0.02
154 84 0.27
155 11 0.04
156 4 0.01
157 11 0.04
161 3 0.01
162 2 0.01
163 13 0.04
164 66 0.21
165 97 0.31
166 17 0.05
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (164 bp):
AAAATTCTTCAAATATTATCATTTAATTAATAGTAAATCAGTTTTAAAAATATTCATTTATTTCA
TGAATTTTTCATTTTTTTTAAAATTCTCCTATTTTCAAAATATGAAGTTTTCTACTCCATAAATA
TTTTTGAGAAGATTTTTCTCAATTTAAAATCTTT
Found at i:417071 original size:148 final size:147
Alignment explanation
Indices: 416781--417204 Score: 489
Period size: 148 Copynumber: 2.9 Consensus size: 147
416771 TGTGGGTATG
* * * **
416781 TATTAGGCATAGGTTCATTTTTCCTTTTCAAGTCTTTTAGG-TTACTGAGATATTTTCATGTCGA
1 TATTAGGTATAGGTTCACTTTTCCTTTTTAAGTCTTTTAGGATTACCAAGATATTTTCATGTCGA
* * * *
416845 AGGTATACCCATAGGGGCA-TTTCGTATTTTTTTAGAACTGAGTCCTAATTTGTCACTGGGTTAC
66 AGGTATACCCATAAGGGCATTTTCGTAATTTTTTAGAACTGAGTCCTAGTTTGTCAC-GGGTCAC
*
416909 TTCTATGCCGAGGGTACA
130 TTCTATGCCAAGGGTACA
* *
416927 TATTAGGTATAGGTTCACTTTTCCTTTTTAATTCTTTTAGGATTACCAAGATATTTTCGTG-CTG
1 TATTAGGTATAGGTTCACTTTTCCTTTTTAAGTCTTTTAGGATTACCAAGATATTTTCATGTC-G
** * * *
416991 AAGGTATACCCATAAGGGTTTTTTTGTAATTTTTTAGAACTGAGTCCTAGTTTATCATCGGGTCG
65 AAGGTATACCCATAAGGGCATTTTCGTAATTTTTTAGAACTGAGTCCTAGTTTGTCA-CGGGTCA
*
417056 CTTCTATGCCAAGGGTACG
129 CTTCTATGCCAAGGGTACA
* ** * * *
417075 TATTAGGTGTAGGTTTGCCTTTCCTTTTTAAGTCCTTTA-GAGTTACCAAGATACTTTCATGTCG
1 TATTAGGTATAGGTTCACTTTTCCTTTTTAAGTCTTTTAGGA-TTACCAAGATATTTTCATGTCG
* * * * *
417139 AAGTTATATCCATAGGGGCATTTTCATAATTTTTTTAGAA-TCGAGTCTTAGTTTGTCACCGGGT
65 AAGGTATACCCATAAGGGCATTTTCGTAA-TTTTTTAGAACT-GAGTCCTAGTTTGTCA-CGGGT
417203 CA
127 CA
417205 ATTTTATGTT
Statistics
Matches: 233, Mismatches: 37, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
146 38 0.16
147 36 0.15
148 127 0.55
149 32 0.14
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (147 bp):
TATTAGGTATAGGTTCACTTTTCCTTTTTAAGTCTTTTAGGATTACCAAGATATTTTCATGTCGA
AGGTATACCCATAAGGGCATTTTCGTAATTTTTTAGAACTGAGTCCTAGTTTGTCACGGGTCACT
TCTATGCCAAGGGTACA
Found at i:417232 original size:63 final size:63
Alignment explanation
Indices: 417154--417282 Score: 172
Period size: 63 Copynumber: 2.0 Consensus size: 63
417144 ATATCCATAG
* *
417154 GGGCATTTTCATAATTTTTTTAGAATC-GAGTCTTAGTTTGTCACCGGGTCAATTT-TATGTTGA
1 GGGCATTTTCATAATTTTTCTAGAA-CAGAGTCTTAGTTTGTCACCGGATC-ATTTCTATGTTGA
* * * *
417217 GGGCATTTTCGTAATTTTTCTAGAACATAGTCTTAGTTTGTTACCGGATCTTTTCTATGTTGA
1 GGGCATTTTCATAATTTTTCTAGAACAGAGTCTTAGTTTGTCACCGGATCATTTCTATGTTGA
417280 GGG
1 GGG
417283 TACGTATTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 4 0.07
63 54 0.93
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (63 bp):
GGGCATTTTCATAATTTTTCTAGAACAGAGTCTTAGTTTGTCACCGGATCATTTCTATGTTGA
Found at i:417490 original size:34 final size:34
Alignment explanation
Indices: 417445--417511 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
417435 ATTAGGAGTA
*
417445 AGTTAGTTTTTATCTTCTTAAGTCCACTAGGATT
1 AGTTAGTTTTTATCTTCTTAACTCCACTAGGATT
*
417479 AGTTTGTTTTTATCTTCTTAACTCCACTAGGAT
1 AGTTAGTTTTTATCTTCTTAACTCCACTAGGAT
417512 CTCCAGGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.48
Consensus pattern (34 bp):
AGTTAGTTTTTATCTTCTTAACTCCACTAGGATT
Found at i:418864 original size:13 final size:13
Alignment explanation
Indices: 418846--418871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
418836 CAATTTTTTG
418846 TGTATCGATACAT
1 TGTATCGATACAT
418859 TGTATCGATACAT
1 TGTATCGATACAT
418872 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:418956 original size:20 final size:20
Alignment explanation
Indices: 418931--419004 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
418921 CATCTTTTTT
418931 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
418951 ATGTATCGATACATTTTTTTTC
1 ATGTATCGATACA--TTGCAAC
418973 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
418993 ATGTATCGATAC
1 ATGTATCGATAC
419005 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 28 0.64
22 16 0.36
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:418970 original size:41 final size:42
Alignment explanation
Indices: 418910--419004 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
418900 CTGCCAAGAA
418910 ATGTATCGATACATCTTTTTT-ATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
*
418951 ATGTATCGATACATTTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
418993 ATGTATCGATAC
1 ATGTATCGATAC
419005 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:419613 original size:48 final size:48
Alignment explanation
Indices: 419558--419653 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
419548 AAATTTTACG
419558 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
419606 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
419654 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:421513 original size:13 final size:13
Alignment explanation
Indices: 421495--421532 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
421485 ATAAACACCC
421495 TGTATCGATACAG
1 TGTATCGATACAG
*
421508 TGTATCGATACAT
1 TGTATCGATACAG
421521 TGTATCGATACA
1 TGTATCGATACA
421533 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:423632 original size:15 final size:15
Alignment explanation
Indices: 423612--423642 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
423602 ATTTCGTTTG
*
423612 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
423627 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
423642 G
1 G
423643 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:427718 original size:13 final size:13
Alignment explanation
Indices: 427700--427725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
427690 CAATTTTTTG
427700 TGTATCGATACAT
1 TGTATCGATACAT
427713 TGTATCGATACAT
1 TGTATCGATACAT
427726 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:427810 original size:20 final size:20
Alignment explanation
Indices: 427785--427858 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
427775 CATCTTTTTT
427785 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
427805 ATGTATCGATACATTTTTTTTC
1 ATGTATCGATACA--TTGCAAC
427827 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
427847 ATGTATCGATAC
1 ATGTATCGATAC
427859 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 28 0.64
22 16 0.36
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:427824 original size:41 final size:42
Alignment explanation
Indices: 427764--427858 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
427754 CTGCCAAGAA
427764 ATGTATCGATACATCTTTTTT-ATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
*
427805 ATGTATCGATACATTTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
427847 ATGTATCGATAC
1 ATGTATCGATAC
427859 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:429728 original size:2 final size:2
Alignment explanation
Indices: 429721--429755 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
429711 ATGCTCAATG
429721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
429756 ACACTTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:431874 original size:19 final size:19
Alignment explanation
Indices: 431850--431903 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
431840 TCATTATTTC
431850 AAAATCATTTATCTTTTAT
1 AAAATCATTTATCTTTTAT
*
431869 AAAATCA-TTA---TTT-C
1 AAAATCATTTATCTTTTAT
431883 AAAATCATTTATCTTTTAT
1 AAAATCATTTATCTTTTAT
431902 AA
1 AA
431904 GCCATGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
18 6 0.21
19 9 0.32
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATCATTTATCTTTTAT
Found at i:431882 original size:33 final size:33
Alignment explanation
Indices: 431840--431903 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
431830 TGAATAAGCT
431840 TCATTATTTCAAAATCATTTATCTTTTATAAAA
1 TCATTATTTCAAAATCATTTATCTTTTATAAAA
431873 TCATTATTTCAAAATCATTTATCTTTTATAA
1 TCATTATTTCAAAATCATTTATCTTTTATAA
431904 GCCATGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (33 bp):
TCATTATTTCAAAATCATTTATCTTTTATAAAA
Found at i:431888 original size:14 final size:14
Alignment explanation
Indices: 431840--431891 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
431830 TGAATAAGCT
431840 TCATTATTTCAAAA
1 TCATTATTTCAAAA
*
431854 TCATTTATCTTTTATAAAA
1 TCA-TTA---TTT-CAAAA
431873 TCATTATTTCAAAA
1 TCATTATTTCAAAA
431887 TCATT
1 TCATT
431892 TATCTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.39
15 6 0.19
18 6 0.19
19 7 0.23
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
TCATTATTTCAAAA
Found at i:433674 original size:19 final size:19
Alignment explanation
Indices: 433650--433698 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
433640 ATTGTGCATA
*
433650 TATCGATACAATGA-ACATG
1 TATCGATACAATCATA-ATG
433669 TATCGATACAAATCATAATG
1 TATCGATAC-AATCATAATG
433689 TATCGATACA
1 TATCGATACA
433699 TCTGGATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (19 bp):
TATCGATACAATCATAATG
Found at i:439830 original size:3 final size:3
Alignment explanation
Indices: 439822--439855 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
439812 TCTGAGTCAA
* *
439822 CAT CAT CAT CAT CAT CAT TAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
439856 GTTTTTGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:441441 original size:20 final size:19
Alignment explanation
Indices: 441412--441449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
441402 TTGCCAGTTT
441412 CATGTATCGATACAATTGTG
1 CATGTATCGATAC-ATTGTG
*
441432 CATGTCTCGATACATTGT
1 CATGTATCGATACATTGT
441450 ATCGATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (19 bp):
CATGTATCGATACATTGTG
Found at i:442159 original size:149 final size:147
Alignment explanation
Indices: 441985--442529 Score: 549
Period size: 149 Copynumber: 3.7 Consensus size: 147
441975 CTAAGGGACA
* * * *
441985 TAAAAAAGAAAAGCT-AACCTATGCCTAATACGTACCCTCAGTATAGAAGCGACCCGGTGACAAA
1 TAAAAAGGAAAAG-TGAACCTACGCCTAATACGTACCCTCAGCATAGAAGTGACCCGGTGACAAA
* * *
442049 TTAAGACTCAATTCTAAAATAATTACGAAAATATCC-CTATAGATATACCTTTGACATGAAAATA
65 TTAAGACTCGATTCTAAAA-AATTACAAAAATA-CCTCTATAGATATACCTTCGACATGAAAATA
*
442113 TCCCGTTAACCCTAAAAGACT
128 TCCCG-TAATCCTAAAAGACT
* ** * * * *
442134 TAAAAAGAAAAAGTGAACCTGTGCCTAATACGTACCCTTAGCATAGAAATGACTCGGTGATAAAT
1 TAAAAAGGAAAAGTGAACCTACGCCTAATACGTACCCTCAGCATAGAAGTGACCCGGTGACAAAT
* * * * *
442199 T-AGAACTCGGTTCTAAAAAAGTTACAAAAATACCTTTATA-ATTATATCTTCAACATAAAAATA
66 TAAG-ACTCGATTCTAAAAAA-TTACAAAAATACCTCTATAGA-TATACCTTCGACATGAAAATA
* *
442262 TCCTAGTAATCCTAAAAGAAT
128 TCC-CGTAATCCTAAAAGACT
* ** * * * *
442283 TGACGAGGAAAAGTGAACCTACGCCTAATACATACCCTCGGCATAGAAGTGACTCAGTGACAAAT
1 TAAAAAGGAAAAGTGAACCTACGCCTAATACGTACCCTCAGCATAGAAGTGACCCGGTGACAAAT
* * * * * * * *
442348 TAGGACTTGATTCTAATAAAATTACTAAAATACCTTTATGGGTATACCTTCGATATGAAAGTATC
66 TAAGACTCGATTCTAA-AAAATTACAAAAATACCTCTATAGATATACCTTCGACATGAAAATATC
* *
442413 TCGGTAATCCTAAAAAACT
130 -CCGTAATCCTAAAAGACT
* * * * * *
442432 TGAAAAGGAAACGTGAACGTACACCTAATACGTACCCTCAGCATATAAGTGACCCGATGACAAAT
1 TAAAAAGGAAAAGTGAACCTACGCCTAATACGTACCCTCAGCATAGAAGTGACCCGGTGACAAAT
* *
442497 TAGGACTTGATTCTAAAAAATTACAAAAATACC
66 TAAGACTCGATTCTAAAAAATTACAAAAATACC
442530 CTTAAGATGT
Statistics
Matches: 328, Mismatches: 58, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
148 24 0.07
149 297 0.91
150 7 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (147 bp):
TAAAAAGGAAAAGTGAACCTACGCCTAATACGTACCCTCAGCATAGAAGTGACCCGGTGACAAAT
TAAGACTCGATTCTAAAAAATTACAAAAATACCTCTATAGATATACCTTCGACATGAAAATATCC
CGTAATCCTAAAAGACT
Found at i:442513 original size:298 final size:297
Alignment explanation
Indices: 441992--442529 Score: 686
Period size: 298 Copynumber: 1.8 Consensus size: 297
441982 ACATAAAAAA
* * * *
441992 GAAAAGCTAACCTATGCCTAATACGTACCCTCAGTATAGAAGCGACCCGGTGACAAATTAAGACT
1 GAAAAGCTAACCTACGCCTAATACATACCCTCAGCATAGAAGCGACCCAGTGACAAATTAAGACT
* *
442057 CAATTCTAAAATAATTACGAAAATATCCCTATAGATATACCTTTGACATGAAAATATCCCGTTAA
66 CAATTCTAAAATAATTACGAAAATATCCCTATAGATATACCTTCGACATGAAAATATCCCGGTAA
* *** *
442122 CCCTAAAAGACTTAAAAAGAAAAAGTGAACCTGTGCCTAATACGTACCCTTAGCATAGAAATGAC
131 CCCTAAAAAACTTAAAAAGAAAAAGTGAACCTACACCTAATACGTACCCTCAGCATAGAAATGAC
* * * *
442187 TCGGTGATAAATTAGAACTCGGTTCTAAAAAAGTTACAAAAATACCTTTATAATTATATCTTCAA
196 CCGATGACAAATTAGAACTCGATTCTAAAAAA-TTACAAAAATACCTTTATAATTATATCTTCAA
442252 CATAAAAATATCCTAGTAATCCTAAAAGAATTGACGAG
260 CATAAAAATATCCTAGTAATCCTAAAAGAATTGACGAG
* * * *
442290 GAAAAG-TGAACCTACGCCTAATACATACCCTCGGCATAGAAGTGACTCAGTGACAAATTAGGAC
1 GAAAAGCT-AACCTACGCCTAATACATACCCTCAGCATAGAAGCGACCCAGTGACAAATTAAGAC
** * * * * * * *
442354 TTGATTCTAATAA-AATTACTAAAATA-CCTTTATGGGTATACCTTCGATATGAAAGTATCTCGG
65 TCAATTCTAA-AATAATTACGAAAATATCC-CTATAGATATACCTTCGACATGAAAATATCCCGG
* * * * * * *
442417 TAATCCTAAAAAACTTGAAAAGGAAACGTGAACGTACACCTAATACGTACCCTCAGCATATAAGT
128 TAACCCTAAAAAACTTAAAAAGAAAAAGTGAACCTACACCTAATACGTACCCTCAGCATAGAAAT
* *
442482 GACCCGATGACAAATTAGGACTTGATTCTAAAAAATTACAAAAATACC
193 GACCCGATGACAAATTAGAACTCGATTCTAAAAAATTACAAAAATACC
442530 CTTAAGATGT
Statistics
Matches: 200, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
297 16 0.08
298 182 0.91
299 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (297 bp):
GAAAAGCTAACCTACGCCTAATACATACCCTCAGCATAGAAGCGACCCAGTGACAAATTAAGACT
CAATTCTAAAATAATTACGAAAATATCCCTATAGATATACCTTCGACATGAAAATATCCCGGTAA
CCCTAAAAAACTTAAAAAGAAAAAGTGAACCTACACCTAATACGTACCCTCAGCATAGAAATGAC
CCGATGACAAATTAGAACTCGATTCTAAAAAATTACAAAAATACCTTTATAATTATATCTTCAAC
ATAAAAATATCCTAGTAATCCTAAAAGAATTGACGAG
Found at i:442835 original size:21 final size:21
Alignment explanation
Indices: 442810--442852 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
442800 AAGTTTATAT
442810 TTATTCATTTT-ATTTTGATTA
1 TTATTCATTTTCATTTT-ATTA
*
442831 TTATTTATTTTCATTTTATTA
1 TTATTCATTTTCATTTTATTA
442852 T
1 T
442853 AAAAAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTCATTTTCATTTTATTA
Found at i:443642 original size:22 final size:25
Alignment explanation
Indices: 443596--443652 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 25
443586 TCTAGTAATG
*
443596 AACATAAATCACCATAATAAAAATC
1 AACATAAATCACCATAAAAAAAATC
443621 AACATAAAT-A-CA-AAAAAAAATC
1 AACATAAATCACCATAAAAAAAATC
*
443643 AA-GTAAATCA
1 AACATAAATCA
443653 TCAAAATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 5 0.17
22 12 0.41
23 2 0.07
24 1 0.03
25 9 0.31
ACGTcount: A:0.65, C:0.16, G:0.02, T:0.18
Consensus pattern (25 bp):
AACATAAATCACCATAAAAAAAATC
Found at i:444728 original size:164 final size:166
Alignment explanation
Indices: 444556--444874 Score: 355
Period size: 164 Copynumber: 1.9 Consensus size: 166
444546 ATGTTAGATG
* * * * * *
444556 AATTTTAAAAATTTTAAATCGAGAAAAATCCCCTCAAAAATATTTATAGAATAGAAAA-GTCGGT
1 AATTTTAAAAAATATAAACCAAGAAAAATCCCCTCAAAAACATTTACAGAATAGAAAATGTC-GT
* ** *
444620 -TTTTCAAAAATAG-GGAATTTCAAAGAAAAA-A-GAAAAAATT-ATGAAA-ATAAATGAATTTT
65 ATTTT-AAAAACAGAAAAATTTCAAA-AAAAATATG-AAAAATTCATGAAATA-AAAGGAATTTT
*
444679 TCAAAACTGATTTACTATGAATTAAATGATGATGTTTGAAT
126 TCAAAACTGATTTAATATGAATTAAATGATGATGTTTGAAT
* ** * * *
444720 AATTTTAAAAAATATAAACCAAGAAAAATTCCCTTGAAAACATTTACGGAGTAGAAAATTTCGTA
1 AATTTTAAAAAATATAAACCAAGAAAAATCCCCTCAAAAACATTTACAGAATAGAAAATGTCGTA
*
444785 TTTTGAAAACAGAAAAATTTCAAAAAAAATATGAAAAATTCATGAAATAAAAGGAATTTTTCAAA
66 TTTTAAAAACAGAAAAATTTCAAAAAAAATATGAAAAATTCATGAAATAAAAGGAATTTTTCAAA
* * *
444850 ACTGGTTTAATGTGAGTTAAATGAT
131 ACTGATTTAATATGAATTAAATGAT
444875 AATATCTGAA
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
164 60 0.47
165 23 0.18
166 43 0.34
167 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (166 bp):
AATTTTAAAAAATATAAACCAAGAAAAATCCCCTCAAAAACATTTACAGAATAGAAAATGTCGTA
TTTTAAAAACAGAAAAATTTCAAAAAAAATATGAAAAATTCATGAAATAAAAGGAATTTTTCAAA
ACTGATTTAATATGAATTAAATGATGATGTTTGAAT
Found at i:446653 original size:20 final size:20
Alignment explanation
Indices: 446608--446660 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
446598 AAGCTACCTT
*
446608 TTTATTTTTAAAAATTACTCA
1 TTTA-TTTTAAAAACTACTCA
*
446629 CTTATTTTAAAAACTA-TCCA
1 TTTATTTTAAAAACTACT-CA
446649 TTTA-TTTAAAAA
1 TTTATTTTAAAAA
446661 AATTCACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.32
20 16 0.57
21 3 0.11
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTATTTTAAAAACTACTCA
Found at i:447887 original size:2 final size:2
Alignment explanation
Indices: 447874--447909 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
447864 AAAGACATAA
*
447874 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447910 TAGTAACTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:451055 original size:19 final size:18
Alignment explanation
Indices: 451014--451049 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
451004 CGACACAAAT
*
451014 TTAAAATAATTTTTTTAA
1 TTAAAATAATTATTTTAA
451032 TTAAAATAATATATTTTA
1 TTAAAATAAT-TATTTTA
451050 TATAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAAATAATTATTTTAA
Found at i:451065 original size:21 final size:22
Alignment explanation
Indices: 451048--451089 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
451038 TAATATATTT
451048 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAATTATAAAA
451069 TATATAAATATTAA-TATAAAA
1 TATATAAATATTAATTATAAAA
451090 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATAAATATTAATTATAAAA
Found at i:451405 original size:13 final size:12
Alignment explanation
Indices: 451376--451419 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
451366 AAAATTAAAA
451376 TAATTTTTATAT
1 TAATTTTTATAT
451388 TAATTTTTATAT
1 TAATTTTTATAT
* *
451400 TAA-ATTTA-AA
1 TAATTTTTATAT
451410 TAATTTTTAT
1 TAATTTTTAT
451420 CATAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 8 0.30
12 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTTTATAT
Found at i:456110 original size:29 final size:29
Alignment explanation
Indices: 456047--456317 Score: 244
Period size: 29 Copynumber: 9.5 Consensus size: 29
456037 CATTTTGGGC
* * * *
456047 TCAATGTGTAATTTTAAAAAATTTA-AGA
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
*
456075 TCAAAGTGTAATTTTGAAAAGTTTAGATG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* * *
456104 TTAAAGTGTGATTTTGAAAAGTTTAGGGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* * *
456133 TCAAAGTGTGATTTTGAAAAGCTTAAAGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* * * * *
456162 TTAATGTGCAATTATGAAAAGTTTAGGGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
*** * * **
456191 TCAAAACATGATTTTGAAAAGTTTAAAAA
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* * *
456220 TCAATGTGCAATTTTGAAAAGTTTAAAGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* *
456249 TCAAAATGTAATTTTGAAAAGTTT-TAGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
* *
456277 TCAAAGTGTAATTTCGTAAAGTTT--AGG
1 TCAAAGTGTAATTTTGAAAAGTTTAGAGG
456304 TCAAAGTGTAATTT
1 TCAAAGTGTAATTT
456318 CATAAAGTCT
Statistics
Matches: 194, Mismatches: 48, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
27 17 0.09
28 46 0.24
29 131 0.68
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
TCAAAGTGTAATTTTGAAAAGTTTAGAGG
Found at i:456318 original size:27 final size:27
Alignment explanation
Indices: 456237--456330 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
456227 GCAATTTTGA
* * *
456237 AAAGTTTAAAGGTCAAAATGTAATTTTGA
1 AAAGTTT--AGGTCAAAGTGTAATTTCGT
456266 AAAGTTTTAGGTCAAAGTGTAATTTCGT
1 AAAG-TTTAGGTCAAAGTGTAATTTCGT
*
456294 AAAGTTTAGGTCAAAGTGTAATTTCAT
1 AAAGTTTAGGTCAAAGTGTAATTTCGT
*
456321 AAAGTCTAGG
1 AAAGTTTAGG
456331 AACTTAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 31 0.53
28 21 0.36
29 4 0.07
30 3 0.05
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.35
Consensus pattern (27 bp):
AAAGTTTAGGTCAAAGTGTAATTTCGT
Found at i:456740 original size:156 final size:155
Alignment explanation
Indices: 456520--456912 Score: 406
Period size: 156 Copynumber: 2.5 Consensus size: 155
456510 CAATGTCACT
* * * * * * *
456520 TTTATGCCAAA-GAAGTGTATTTAGGATAAGTTTGTCCTTTTACTTATCTTTTTTATGTCTTTTA
1 TTTATGCCAAAGGTA-TGCATTTAGGATAGGTTAGTCATTTT-CTTATCTTTTTTGTGTCCTTTA
* *
456584 GGGTTACTAAGATACTTTCACGTCAAAAATATA-CCTGATAAGCATTTTGGTAATTTCTCTAGAA
64 GGGTTACTAAGATACTTTCACGTCAAAAATATATCCT-AAAAGCATTTTGATAATTTCTCTAGAA
* * *
456648 -TCGAGTCGTAGGTCGTCATAGGGTTGCC
128 CT-GAGTCCTAGGTCGTCACAGGGTCGCC
* *
456676 TTTATGCTAAAGGTATGCATTTAGAATAGGTTAGTCATTTTCCTTATCTTTTTTGTGTCCTTTAG
1 TTTATGCCAAAGGTATGCATTTAGGATAGGTTAGTCATTTT-CTTATCTTTTTTGTGTCCTTTAG
* * * * * * *
456741 GCTTACCT-GGATACTTTCATGTCAAAGATATATCCTAAAAGTATTTTGATAATTTTTTTAGAAC
65 GGTTA-CTAAGATACTTTCACGTCAAAAATATATCCTAAAAGCATTTTGATAATTTCTCTAGAAC
* *
456805 TGAGTCCTAGGTCGTCACCGGGTCGCT
129 TGAGTCCTAGGTCGTCACAGGGTCGCC
* * *
456832 TTTATGCCAAATGTATGCATTTAGGATAGGTTCA-TCCA-TTTATTAT-TTTTTCGTGTCCTTTA
1 TTTATGCCAAAGGTATGCATTTAGGATAGGTT-AGT-CATTTTCTTATCTTTTTTGTGTCCTTTA
* *
456894 GTGTTACCAA-ATACTTTCA
64 GGGTTACTAAGATACTTTCA
456913 TGTTGAAAGT
Statistics
Matches: 197, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
153 10 0.05
154 19 0.10
155 4 0.02
156 153 0.78
157 11 0.06
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (155 bp):
TTTATGCCAAAGGTATGCATTTAGGATAGGTTAGTCATTTTCTTATCTTTTTTGTGTCCTTTAGG
GTTACTAAGATACTTTCACGTCAAAAATATATCCTAAAAGCATTTTGATAATTTCTCTAGAACTG
AGTCCTAGGTCGTCACAGGGTCGCC
Found at i:458787 original size:78 final size:78
Alignment explanation
Indices: 458696--458863 Score: 185
Period size: 80 Copynumber: 2.1 Consensus size: 78
458686 AAAAATTTTG
* * * * *
458696 ATATTTTGAAAGTAAAAATGGGGTTCGAGTA-CTCTAAAAAATTATGGGGTTGAAGTATCACCGG
1 ATATTTTGGAAGTAAAAACGAGGTTCGAGTACCTCTAAAAAATAATGGGGTTGAAGTATCACCGA
*
458760 CGGTGAAAATTTCA
66 CGGTGAAAAATT-A
* * * *** *
458774 TTATTTTGGAAGTAAAAACGAGGTTGGAGTATCCTTTTGGAAATAATGGGGTTGAAGTATCTCCG
1 ATATTTTGGAAGTAAAAACGAGGTTCGAGTA-CCTCTAAAAAATAATGGGGTTGAAGTATCACCG
*
458839 ATGGTGAAAAATTA
65 ACGGTGAAAAATTA
458853 ATATTTTGGAA
1 ATATTTTGGAA
458864 AGAGAAATTT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
78 26 0.36
79 11 0.15
80 36 0.49
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (78 bp):
ATATTTTGGAAGTAAAAACGAGGTTCGAGTACCTCTAAAAAATAATGGGGTTGAAGTATCACCGA
CGGTGAAAAATTA
Found at i:463681 original size:69 final size:69
Alignment explanation
Indices: 463604--463742 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
463594 TGATTATTGT
463604 ATAAAAAATCTAACTATTTTCATACATCCACCGAGACCATCAAACTGGTATTCATTTCTCTTTCT
1 ATAAAAAATCTAACTATTTTCATACATCCACCGAGACCATCAAACTGGTATTCATTTCTCTTTCT
463669 TTGA
66 TTGA
*
463673 ATAAAAAATCTAACTATTTTCATACATCCACCGAGACCATCAAACTGGTATTTATTTCTCTTTCT
1 ATAAAAAATCTAACTATTTTCATACATCCACCGAGACCATCAAACTGGTATTCATTTCTCTTTCT
463738 TTGA
66 TTGA
463742 A
1 A
463743 AACAATGGTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (69 bp):
ATAAAAAATCTAACTATTTTCATACATCCACCGAGACCATCAAACTGGTATTCATTTCTCTTTCT
TTGA
Found at i:464221 original size:2 final size:2
Alignment explanation
Indices: 464214--464257 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
464204 ATAAAAACAT
*
464214 TA TA TA TA TA TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
464255 TA T
1 TA T
464258 GAATCTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:464235 original size:19 final size:19
Alignment explanation
Indices: 464213--464249 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
464203 TATAAAAACA
464213 TTATATATATATATATATT
1 TTATATATATATATATATT
464232 TTATATATATATATATAT
1 TTATATATATATATATAT
464250 ATATATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATATATATATATATT
Found at i:464686 original size:25 final size:22
Alignment explanation
Indices: 464658--464715 Score: 53
Period size: 25 Copynumber: 2.4 Consensus size: 22
464648 TTTAATATTT
*
464658 TTTATTATTAATATCACGATCGATA
1 TTTATTATT-A-ATCACGAT-AATA
464683 TTTACTGTAATTAATCACGATAATA
1 TTTA-T-T-ATTAATCACGATAATA
464708 TTTATTAT
1 TTTATTAT
464716 ATTCGCAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
22 2 0.07
23 1 0.03
24 1 0.03
25 11 0.38
26 9 0.31
27 2 0.07
28 3 0.10
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (22 bp):
TTTATTATTAATCACGATAATA
Found at i:465256 original size:21 final size:20
Alignment explanation
Indices: 465231--465307 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
465221 AAAAATTTCC
*
465231 AAATGTATCGATACATTTGT
1 AAATGTATCGATACATTTAT
* *
465251 AGAATGTATCGATACATTCAC
1 A-AATGTATCGATACATTTAT
*
465272 AAATGTATCGATACATTCTAC
1 AAATGTATCGATACATT-TAT
465293 AAATGTATCGATACA
1 AAATGTATCGATACA
465308 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACATTTAT
Found at i:465287 original size:41 final size:41
Alignment explanation
Indices: 465230--465307 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
465220 AAAAAATTTC
* *
465230 CAAATGTATCGATACATTTGTA-GAATGTATCGATACATTCA
1 CAAATGTATCGATACA-TTCTACAAATGTATCGATACATTCA
465271 CAAATGTATCGATACATTCTACAAATGTATCGATACA
1 CAAATGTATCGATACATTCTACAAATGTATCGATACA
465308 GGGTCCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (41 bp):
CAAATGTATCGATACATTCTACAAATGTATCGATACATTCA
Found at i:465367 original size:19 final size:19
Alignment explanation
Indices: 465343--465410 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
465333 AATTCAACGA
465343 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
465362 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
465377 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
465394 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
465411 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:465381 original size:32 final size:32
Alignment explanation
Indices: 465345--465407 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
465335 TTCAACGATT
*
465345 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
465377 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
465408 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:465382 original size:13 final size:13
Alignment explanation
Indices: 465364--465388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465354 ACATAAGTTT
465364 TGTATCGATACAA
1 TGTATCGATACAA
465377 TGTATCGATACA
1 TGTATCGATACA
465389 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:465468 original size:13 final size:13
Alignment explanation
Indices: 465450--465475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
465440 CATTTTTCTG
465450 TGTATCGATACAT
1 TGTATCGATACAT
465463 TGTATCGATACAT
1 TGTATCGATACAT
465476 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:465472 original size:33 final size:33
Alignment explanation
Indices: 465430--465496 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
465420 GCCAAGGAAA
***
465430 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
465463 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
465496 T
1 T
465497 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:468049 original size:51 final size:51
Alignment explanation
Indices: 467990--468162 Score: 204
Period size: 52 Copynumber: 3.4 Consensus size: 51
467980 TTATTTCTAA
* ***
467990 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * * *
468041 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
*
468093 GGGGATACTCCAACAC-CGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CTCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
468145 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
468163 TTATTTCATC
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
51 37 0.37
52 49 0.49
53 15 0.15
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:468106 original size:52 final size:52
Alignment explanation
Indices: 467815--468159 Score: 211
Period size: 51 Copynumber: 6.6 Consensus size: 52
467805 TTGAATTGCT
* * * * * * *
467815 CAATTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACAT
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
467866 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACAC
* * * * * * * * * *
467919 TAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGAGATACTC
1 CAATTT-TCCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACAC
* * * * *
467972 CAACCCCGTTATTTC-TAA--GGGGATACTCCAACCTCGACTTTATTTCC-AAAATAT
1 CAA-----TT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
** * * *
468026 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
468077 CAATTTTCCTTTAATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
468130 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
468160 TCGTTATTTC
Statistics
Matches: 224, Mismatches: 52, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
48 4 0.02
49 5 0.02
51 73 0.33
52 52 0.23
53 35 0.16
54 25 0.11
55 16 0.07
56 2 0.01
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:468178 original size:28 final size:28
Alignment explanation
Indices: 468142--468223 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
468132 ATTTTTCACA
* *
468142 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
468170 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
468198 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
468224 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:468213 original size:211 final size:211
Alignment explanation
Indices: 467826--468215 Score: 570
Period size: 211 Copynumber: 1.8 Consensus size: 211
467816 AATTCTCCAC
* * **
467826 AATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTATAATCGGGGATACTC
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* *
467891 CAACTCCGATTTTATTTCCAAAAAACACTAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACTAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * *
467956 ATCATCGGAGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCTCGACTTTATTTCCAA
131 ATCATCGGAGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCTCGACTTTATTTCCAA
468021 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* * *
468037 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* *
468102 CCAACACCGATTTTATTTCCAAAAATAC-C-AATTT-TTCACAATCGAGGATACTCCAACCTCGT
65 CCAACACCGATTTTATTTCCAAAAA-ACACTAATTTCTTCACAATCGAGGACACTCCAACCCCGT
* * *
468164 TATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACC
129 TA-ATCATCGGAGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACC
468216 CCGTTATTAT
Statistics
Matches: 158, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
210 27 0.17
211 88 0.56
212 41 0.26
213 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACTAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGAGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCTCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:469208 original size:2 final size:2
Alignment explanation
Indices: 469197--469226 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
469187 CGTCGCGACA
469197 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
469227 ACTCAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470230 original size:25 final size:26
Alignment explanation
Indices: 470198--470247 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
470188 ATAAATATCA
*
470198 ATTTTATATG-TAAC-TATATATTAT
1 ATTTTATACGATAACTTATATATTAT
470222 ATTTATATACGATAACTTATATATTA
1 ATTT-TATACGATAACTTATATATTA
470248 ATATATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 5 0.23
26 4 0.18
27 9 0.41
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTTATACGATAACTTATATATTAT
Found at i:471735 original size:79 final size:81
Alignment explanation
Indices: 471630--471780 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 81
471620 ATAGGGCTAA
* * ** *
471630 AGTATCTCCCTTTGGAGATATGGGGTTAGAGTATTTTCGAGAATGTAAAGTT-AAGATTTTTTT-
1 AGTATCTCCCTTTGGAGAGATAGGGTTAGAGTATCCTCAAGAATGTAAA-TTCAAGATTTTTTTG
471693 T-AGAAAATGGGGTCGG
65 TAAGAAAATGGGGTCGG
* *
471709 AGTATCTCCTTTTGGAGAGATAGGGTTGGAGTATCCTCAAGAATGTAAATTCAAGATTTTTTTGT
1 AGTATCTCCCTTTGGAGAGATAGGGTTAGAGTATCCTCAAGAATGTAAATTCAAGATTTTTTTGT
471774 AAGAAAA
66 AAGAAAA
471781 CGGGCTTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 2 0.03
79 53 0.85
80 1 0.02
81 6 0.10
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (81 bp):
AGTATCTCCCTTTGGAGAGATAGGGTTAGAGTATCCTCAAGAATGTAAATTCAAGATTTTTTTGT
AAGAAAATGGGGTCGG
Done.