Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 22 of 75
Found at i:6359311 original size:6 final size:6
Alignment explanation
Indices: 6359300--6359338 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6359290 GCAAATGAAT
*
6359300 CATTTC CATTTC CATTTC CATTTC CATTTT CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CAT
6359339 ATCTAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTTC
Found at i:6369129 original size:20 final size:20
Alignment explanation
Indices: 6369095--6369148 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
6369085 TATCTAAATA
*
6369095 TTTAATATTATAATTTTATATT
1 TTTAAT-TTA-AATTTAATATT
6369117 TTTAATTTAAATTTAATATT
1 TTTAATTTAAATTTAATATT
*
6369137 TTTATTTTAAAT
1 TTTAATTTAAAT
6369149 AAATCTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 21 0.70
21 3 0.10
22 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATTTAAATTTAATATT
Found at i:6372369 original size:28 final size:26
Alignment explanation
Indices: 6372332--6372419 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 26
6372322 AATATGAAAA
*
6372332 ATCAAGATTCATCCTTTCATTTCTCATC
1 ATCAAAATTCAT-CTTTCATTT-TCATC
* *
6372360 ATCAAAATTCAT-TTGGTAATTGTTCTTC
1 ATCAAAATTCATCTT--TCATT-TTCATC
6372388 ATC-AAATTCATCTCTTCATTTTCATC
1 ATCAAAATTCATCT-TTCATTTTCATC
6372414 ATCAAA
1 ATCAAA
6372420 GTCTTTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
26 10 0.20
27 14 0.29
28 23 0.47
29 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (26 bp):
ATCAAAATTCATCTTTCATTTTCATC
Found at i:6373200 original size:16 final size:16
Alignment explanation
Indices: 6373176--6373206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6373166 GTTTATTTGC
6373176 ATTTAAAATTTTTTTA
1 ATTTAAAATTTTTTTA
*
6373192 ATTTCAAATTTTTTT
1 ATTTAAAATTTTTTT
6373207 CAATATGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAAAATTTTTTTA
Found at i:6374154 original size:3 final size:3
Alignment explanation
Indices: 6374148--6374172 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6374138 GACCACCACA
6374148 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
6374173 CGACAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6394775 original size:44 final size:43
Alignment explanation
Indices: 6394644--6394779 Score: 164
Period size: 43 Copynumber: 3.1 Consensus size: 43
6394634 AGGTGTTGGC
* * * * * *
6394644 CTTTAGTGGCATTTTTGGTAAAAGCGCCGCTAAATATAAGGGT
1 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT
* * *
6394687 CTTTAGCGGCGTTTGTGGAAAAAGTGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT
* *
6394730 CTTTAGCGGCGTTTGTGGGGAAAAGCGCCGCTAGAGATCAGGGT
1 CTTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGATCAGGGT
6394774 CTTTAG
1 CTTTAG
6394780 AGGTGCTTCC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
43 50 0.64
44 28 0.36
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGGGT
Found at i:6394976 original size:31 final size:31
Alignment explanation
Indices: 6394941--6395012 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
6394931 CTTTTCAAAG
*
6394941 CGCCGCTAAAAGTATTTGCGGCGCTAAAAAA
1 CGCCGCTAAAAGTATTTGCGGCACTAAAAAA
*
6394972 CGCCGCTAAAAGTATTTGCGGCACTAAAAAG
1 CGCCGCTAAAAGTATTTGCGGCACTAAAAAA
6395003 CGCCGCTAAA
1 CGCCGCTAAA
6395013 GGCCTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (31 bp):
CGCCGCTAAAAGTATTTGCGGCACTAAAAAA
Found at i:6395025 original size:22 final size:22
Alignment explanation
Indices: 6394997--6395040 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6394987 TTGCGGCACT
6394997 AAAAAGCGCCGC-TAAAGGCCTA
1 AAAAAGCGCCGCTTAAA-GCCTA
6395019 AAAAAGCGCCGCTTAAAGCCTA
1 AAAAAGCGCCGCTTAAAGCCTA
6395041 TTTTGGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTTAAAGCCTA
Found at i:6398300 original size:9 final size:9
Alignment explanation
Indices: 6398286--6398316 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6398276 GTTAAACGAA
6398286 TCGAGTTAT
1 TCGAGTTAT
*
6398295 TCGAGTTAA
1 TCGAGTTAT
6398304 TCGAGTTAT
1 TCGAGTTAT
6398313 TCGA
1 TCGA
6398317 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:6398388 original size:9 final size:9
Alignment explanation
Indices: 6398371--6398407 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6398361 TGAGTTTTCG
6398371 AATTCGAAT
1 AATTCGAAT
*
6398380 AACTCGAAT
1 AATTCGAAT
6398389 AATTCGAAT
1 AATTCGAAT
6398398 AATTCGAAT
1 AATTCGAAT
6398407 A
1 A
6398408 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6402086 original size:5 final size:5
Alignment explanation
Indices: 6402076--6402107 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
6402066 TCTTGTAAAT
6402076 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG AT
6402108 GTAATCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (5 bp):
ATTTG
Found at i:6404959 original size:51 final size:52
Alignment explanation
Indices: 6404887--6405073 Score: 207
Period size: 53 Copynumber: 3.5 Consensus size: 52
6404877 AAATTTTTTT
* * *
6404887 TTGGGTGTTGGCACACTAATGGCCGGCACCCTTGTACCAGATTTTAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA
* *
6404939 TT-GGTGCTGGGACACTAATGGCCGACATCCTTGTACCAGAATTTAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAG-ATTTAAAAAAAA
* * * * * *
6404991 TTAGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTT-AAAAAAAA
*
6405044 TTTGGGGTG-TCGAGACACTAATGGCCGGCA
1 -TT-GGGTGCT-GGGACACTAATGGCCGGCA
6405074 ACCACTTAGT
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
51 33 0.29
52 19 0.17
53 38 0.34
54 3 0.03
55 19 0.17
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (52 bp):
TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA
Found at i:6408210 original size:51 final size:52
Alignment explanation
Indices: 6408138--6408324 Score: 207
Period size: 53 Copynumber: 3.5 Consensus size: 52
6408128 AAATTTTTTT
* * *
6408138 TTGGGTGTTGGCACACTAATGGCCGGCACCCTTGTACCAGATTTTAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA
* *
6408190 TT-GGTGCTGGGACACTAATGGCCGACATCCTTGTACCAGAATTTAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAG-ATTTAAAAAAAA
* * * * * *
6408242 TTAGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTT-AAAAAAAA
*
6408295 TTTGGGGTG-TCGAGACACTAATGGCCGGCA
1 -TT-GGGTGCT-GGGACACTAATGGCCGGCA
6408325 ACCACTTAGT
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
51 33 0.29
52 19 0.17
53 38 0.34
54 3 0.03
55 19 0.17
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (52 bp):
TTGGGTGCTGGGACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAA
Found at i:6411080 original size:22 final size:22
Alignment explanation
Indices: 6411055--6411105 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6411045 TAGTGGTCAA
6411055 CGGTGGTCGGCGA-TGGAACTTG
1 CGGTGGTCGG-GAGTGGAACTTG
* * *
6411077 CGGTGGTTGGTAGTGGAATTTG
1 CGGTGGTCGGGAGTGGAACTTG
6411099 CGGTGGT
1 CGGTGGT
6411106 GAGACAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.12, C:0.12, G:0.47, T:0.29
Consensus pattern (22 bp):
CGGTGGTCGGGAGTGGAACTTG
Found at i:6411563 original size:28 final size:29
Alignment explanation
Indices: 6411539--6411599 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
6411529 CATTTTTATT
6411539 TTTTATTAC-TTTATTT-ATTTATTTTAAC
1 TTTTA-TACTTTTATTTAATTTATTTTAAC
*
6411567 TTTTATACTTTTATTTAATTTAATTTACAC
1 TTTTATACTTTTATTTAATTTATTTTA-AC
6411597 TTT
1 TTT
6411600 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 9 0.31
30 5 0.17
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATACTTTTATTTAATTTATTTTAAC
Found at i:6411600 original size:29 final size:27
Alignment explanation
Indices: 6411539--6411613 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 27
6411529 CATTTTTATT
*
6411539 TTTTATTACTTTATTTATTTATTTTAAC
1 TTTTA-TACTTTATTTATTTAATTTAAC
6411567 TTTTATAC--T-TTTATTTAATTTAA-
1 TTTTATACTTTATTTATTTAATTTAAC
* *
6411590 -TTTACACTTTATTTATTTATTTTA
1 TTTTATACTTTATTTATTTAATTTA
6411614 CTCTATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
24 14 0.34
25 13 0.32
27 3 0.07
28 5 0.12
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATACTTTATTTATTTAATTTAAC
Found at i:6411908 original size:195 final size:196
Alignment explanation
Indices: 6411692--6412082 Score: 775
Period size: 195 Copynumber: 2.0 Consensus size: 196
6411682 TTTTCTTTTT
6411692 CTTTTTCTTTTTCTCATCATTCATTTTATTTTTTAGTAAGTTTTTATTCTTTACACTAAAAATAT
1 CTTTTTCTTTTTCTCATCATTCATTTTATTTTTTAGTAAGTTTTTATTCTTTACACTAAAAATAT
6411757 TGGCTCATAAAAGCACTTACAATATAAAAAAATAATTAATACTTTGTATTTATACTTTAATTACA
66 TGGCTCATAAAAGCACTTACAATATAAAAAAATAATTAATACTTTGTATTTATACTTTAATTACA
6411822 AGTTTTAACAATAATCACGAAATAATAAAAAATCACTTATCCTATTCGTCGTCTTCCAATCTAGC
131 AGTTTTAACAATAATCACGAAATAATAAAAAATCACTTATCCTATTCGTCGTCTTCCAATCTAGC
6411887 A
196 A
6411888 CTTTTTC-TTTTCTCATCATTCATTTTATTTTTTAGTAAGTTTTTATTCTTTACACTAAAAATAT
1 CTTTTTCTTTTTCTCATCATTCATTTTATTTTTTAGTAAGTTTTTATTCTTTACACTAAAAATAT
6411952 TGGCTCATAAAAGCACTTACAATATAAAAAAATAATTAATACTTTGTATTTATACTTTAATTACA
66 TGGCTCATAAAAGCACTTACAATATAAAAAAATAATTAATACTTTGTATTTATACTTTAATTACA
6412017 AGTTTTAACAATAATCACGAAATAATAAAAAATCACTTATCCTATTCGTCGTCTTCCAATCTAGC
131 AGTTTTAACAATAATCACGAAATAATAAAAAATCACTTATCCTATTCGTCGTCTTCCAATCTAGC
6412082 A
196 A
6412083 TTACGAGAAG
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 188 0.96
196 7 0.04
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (196 bp):
CTTTTTCTTTTTCTCATCATTCATTTTATTTTTTAGTAAGTTTTTATTCTTTACACTAAAAATAT
TGGCTCATAAAAGCACTTACAATATAAAAAAATAATTAATACTTTGTATTTATACTTTAATTACA
AGTTTTAACAATAATCACGAAATAATAAAAAATCACTTATCCTATTCGTCGTCTTCCAATCTAGC
A
Found at i:6414952 original size:54 final size:54
Alignment explanation
Indices: 6414786--6414955 Score: 135
Period size: 56 Copynumber: 3.1 Consensus size: 54
6414776 CCCTAACCAA
* * * *
6414786 AAAATTTTTT-TTGTATCTGATAAAGTGGGTGTCGGCCATCTATGTGCTAGCACCC
1 AAAATTTTTTATT-T-TCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC
* * * * * * * * * * **
6414841 AAAAATATTATATTTTTTTGTAATAATATGGTGTTGGCAATCAAAGTCCCCCAACCC
1 -AAAATTTTTTATTTTCTGGTAA-AGT-GGGTGTTGGCCATCTATGTGCCAGAACCC
*
6414898 AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGTACCC
1 AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC
6414952 AAAA
1 AAAA
6414956 AAAAAATTTT
Statistics
Matches: 82, Mismatches: 29, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
54 25 0.30
55 7 0.09
56 29 0.35
57 21 0.26
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (54 bp):
AAAATTTTTTATTTTCTGGTAAAGTGGGTGTTGGCCATCTATGTGCCAGAACCC
Found at i:6416833 original size:9 final size:9
Alignment explanation
Indices: 6416819--6416849 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6416809 GTTAAACGAA
6416819 TCGAGTTAT
1 TCGAGTTAT
*
6416828 TCGAGTTAA
1 TCGAGTTAT
6416837 TCGAGTTAT
1 TCGAGTTAT
6416846 TCGA
1 TCGA
6416850 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:6421128 original size:8 final size:9
Alignment explanation
Indices: 6421105--6421147 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
6421095 TACGTTTTTT
6421105 TATTTTTAA
1 TATTTTTAA
6421114 TAATTTTTAA
1 T-ATTTTTAA
6421124 T-TTTTTAA
1 TATTTTTAA
6421132 TAGTTTTATAA
1 TA-TTTT-TAA
6421143 TATTT
1 TATTT
6421148 GAAACCACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.27
9 1 0.03
10 16 0.53
11 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTTTAA
Found at i:6421128 original size:18 final size:19
Alignment explanation
Indices: 6421107--6421143 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6421097 CGTTTTTTTA
6421107 TTTTTAATAATTTT-TAAT
1 TTTTTAATAATTTTATAAT
*
6421125 TTTTTAATAGTTTTATAAT
1 TTTTTAATAATTTTATAAT
6421144 ATTTGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTAATAATTTTATAAT
Found at i:6424712 original size:8 final size:8
Alignment explanation
Indices: 6424699--6424733 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
6424689 TTGTTATGAT
6424699 TTTTATTA
1 TTTTATTA
6424707 TTTTATTA
1 TTTTATTA
6424715 TTTTATTA
1 TTTTATTA
6424723 TATGTTATTA
1 T-T-TTATTA
6424733 T
1 T
6424734 CTTAAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 1 0.04
10 7 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (8 bp):
TTTTATTA
Found at i:6431283 original size:2 final size:2
Alignment explanation
Indices: 6431271--6431305 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6431261 TACCAACATG
*
6431271 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6431306 TCAATTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6438195 original size:2 final size:2
Alignment explanation
Indices: 6438188--6438221 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6438178 CTGTTTCTTT
* *
6438188 TC TC TC TC CC TC TC AC 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
6438222 GGGATTGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:6451531 original size:19 final size:20
Alignment explanation
Indices: 6451507--6451550 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6451497 TTTCTACTTC
*
6451507 TTCTTCTC-GTATGTTTCTT
1 TTCTTCTCTGTACGTTTCTT
*
6451526 TTCTTCTCTTTACGTTTCTT
1 TTCTTCTCTGTACGTTTCTT
6451546 TTCTT
1 TTCTT
6451551 TTCTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.05, C:0.23, G:0.07, T:0.66
Consensus pattern (20 bp):
TTCTTCTCTGTACGTTTCTT
Found at i:6452073 original size:25 final size:25
Alignment explanation
Indices: 6452045--6452105 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
6452035 GTGTTATAAT
* *
6452045 GTTCATGTTTTGGTTTCTGTATTAG
1 GTTCATGTTTTGGTTTCAGTATTAA
6452070 GTTCATGTTTTGGTTTCAGTATTAA
1 GTTCATGTTTTGGTTTCAGTATTAA
*
6452095 GTTGATGTTTT
1 GTTCATGTTTT
6452106 CCATTTGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.15, C:0.07, G:0.23, T:0.56
Consensus pattern (25 bp):
GTTCATGTTTTGGTTTCAGTATTAA
Found at i:6452087 original size:13 final size:13
Alignment explanation
Indices: 6452046--6452087 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
6452036 TGTTATAATG
6452046 TTCATGTTTTGGT
1 TTCATGTTTTGGT
*
6452059 TTC-TGTATTAGG-
1 TTCATGT-TTTGGT
6452071 TTCATGTTTTGGT
1 TTCATGTTTTGGT
6452084 TTCA
1 TTCA
6452088 GTATTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.57
Consensus pattern (13 bp):
TTCATGTTTTGGT
Found at i:6453710 original size:29 final size:32
Alignment explanation
Indices: 6453670--6453729 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 32
6453660 TCTTTGCTTC
*
6453670 TTTCTTTAATTT-GGCCC-AATTAT-TTCCTT
1 TTTCTTTAATTTAGCCCCAAATTATATTCCTT
6453699 TTTCTTCT-ATTTAGCCCCAAATTATATTCCT
1 TTTCTT-TAATTTAGCCCCAAATTATATTCCT
6453730 GCACAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
31 6 0.23
32 5 0.19
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTCTTTAATTTAGCCCCAAATTATATTCCTT
Found at i:6463951 original size:35 final size:37
Alignment explanation
Indices: 6463912--6463988 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
6463902 TTATTAAATT
6463912 ATATTTAATAATA-ATTATGTTAA-AATATGATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
* * * *
6463947 ATATTT-ATATTATATTATTTTAATAATCTTATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
6463983 AT-TTTA
1 ATATTTA
6463989 TAACAAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 18 0.51
36 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
ATATTTAATAATATATTATGTTAATAATATGATTAAA
Found at i:6464138 original size:44 final size:44
Alignment explanation
Indices: 6464075--6464171 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
6464065 CTATTACACC
* *
6464075 TCCATTCCATTCAATCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATA-AATTACTATTACGCCTCTAT
*
6464119 TCCATTACATTCAACCAAACAATTAAATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAA-TAAATTACTATTACGCCTCTAT
*
6464164 TTCATTAC
1 TCCATTAC
6464172 GCTTCTATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.02
44 21 0.46
45 24 0.52
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (44 bp):
TCCATTACATTCAACCAAACAATAAATTACTATTACGCCTCTAT
Found at i:6464186 original size:16 final size:16
Alignment explanation
Indices: 6464149--6464187 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6464139 AATTAAATTG
6464149 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
*
6464165 -TCATTACGCTTCTATT
1 CT-ATTACGCCTCTATT
6464181 CTATTAC
1 CTATTAC
6464188 AGCGAGCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:6465341 original size:18 final size:18
Alignment explanation
Indices: 6465299--6465341 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
6465289 TTTCGAAAAA
6465299 TATTTTTTTTGTTCAAAT
1 TATTTTTTTTGTTCAAAT
* * *
6465317 AATTTTTTTTTGTTTAAGT
1 TA-TTTTTTTTGTTCAAAT
6465336 TATTTT
1 TATTTT
6465342 ATTCCACTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (18 bp):
TATTTTTTTTGTTCAAAT
Found at i:6473552 original size:16 final size:15
Alignment explanation
Indices: 6473519--6473551 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6473509 TAACTCATCA
6473519 TTTAATTTTAATATT
1 TTTAATTTTAATATT
6473534 TTTAACTTTTAAT-TT
1 TTTAA-TTTTAATATT
6473549 TTT
1 TTT
6473552 TTTCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTTAATATT
Found at i:6482505 original size:16 final size:16
Alignment explanation
Indices: 6482484--6482553 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
6482474 TTGATTTGCT
*
6482484 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
6482500 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
6482516 ATTACACATCTAATCC
1 ATTACACCTCTAATCC
*
6482532 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
6482548 AATACA
1 ATTACA
6482554 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:6483375 original size:60 final size:61
Alignment explanation
Indices: 6483258--6483387 Score: 244
Period size: 60 Copynumber: 2.1 Consensus size: 61
6483248 ATCTAGTAGA
6483258 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
*
6483319 CAAGTTCAGATACCAAAGTGAACG-AAAAAAAAGTATAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
6483379 CAAGTTCAG
1 CAAGTTCAG
6483388 GGGCTAAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
60 44 0.65
61 24 0.35
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (61 bp):
CAAGTTCAGATACCAAAGTGAACGAAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
Found at i:6485115 original size:95 final size:96
Alignment explanation
Indices: 6484952--6485144 Score: 327
Period size: 95 Copynumber: 2.0 Consensus size: 96
6484942 AATATAATGC
*
6484952 TTAGACCCAACCCACACCCTACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG
*
6485017 AAATGTTGTGATAGTGCTTGGAC-TTTTCTT
66 AAATGTTGTGATAATGCTTGGACTTTTTCTT
* *
6485047 TTAGACCCAGCCCACACCCGACCCGGTCCATCAACATCTCATAATAATATAGTCACTGATAA-GT
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGA-AAGGT
6485111 GAAATGTTGTGATAATGCTTGGACTTTTTCTT
65 GAAATGTTGTGATAATGCTTGGACTTTTTCTT
6485143 TT
1 TT
6485145 TCTTTTATAG
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 81 0.88
96 11 0.12
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (96 bp):
TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGAAAGGTG
AAATGTTGTGATAATGCTTGGACTTTTTCTT
Found at i:6487064 original size:18 final size:18
Alignment explanation
Indices: 6487037--6487072 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6487027 TTGCTATACT
* *
6487037 TTTATTTTTTTTGAGCAA
1 TTTATATTTTTCGAGCAA
6487055 TTTATATTTTTCGAGCAA
1 TTTATATTTTTCGAGCAA
6487073 GGCGAGCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTATATTTTTCGAGCAA
Found at i:6488653 original size:14 final size:15
Alignment explanation
Indices: 6488626--6488667 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
6488616 CATGCAAGCC
*
6488626 TATTAATTATAATT-
1 TATTAATTAAAATTA
*
6488640 TATTAAATAAAATTA
1 TATTAATTAAAATTA
*
6488655 TCTTAATTAAAAT
1 TATTAATTAAAAT
6488668 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAATTAAAATTA
Found at i:6489271 original size:43 final size:44
Alignment explanation
Indices: 6489208--6489294 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
6489198 GCAATCTATG
*
6489208 AATATTATGAACAATTGACCTAATAATCGATCTATCTTCCTCAT
1 AATATTATGAACAATCGACCTAATAATCGATCTATCTTCCTCAT
6489252 AATATTATG-ACAATCGACCTAATAATCGATCTATCTTCCTCAT
1 AATATTATGAACAATCGACCTAATAATCGATCTATCTTCCTCAT
6489295 TTTTAATCAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 33 0.79
44 9 0.21
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (44 bp):
AATATTATGAACAATCGACCTAATAATCGATCTATCTTCCTCAT
Found at i:6502624 original size:17 final size:15
Alignment explanation
Indices: 6502602--6502637 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
6502592 ATAATAATTT
6502602 AAAATTCAAAAATTCAA
1 AAAATTC-AAAATT-AA
6502619 AAAATTCAAAATTAA
1 AAAATTCAAAATTAA
6502634 AAAA
1 AAAA
6502638 AATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATTCAAAATTAA
Found at i:6502640 original size:17 final size:17
Alignment explanation
Indices: 6502602--6502638 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6502592 ATAATAATTT
*
6502602 AAAATTCAAAAATTCAA
1 AAAATTCAAAAATTAAA
6502619 AAAATTC-AAAATTAAA
1 AAAATTCAAAAATTAAA
6502635 AAAA
1 AAAA
6502639 ATATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATTCAAAAATTAAA
Found at i:6509020 original size:10 final size:10
Alignment explanation
Indices: 6508995--6509040 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
6508985 ACTGGAAAAA
6508995 TTTAAAAATT
1 TTTAAAAATT
6509005 CTTTAAAAATT
1 -TTTAAAAATT
*
6509016 GTTAAAAATT
1 TTTAAAAATT
* *
6509026 ATTAAGAATT
1 TTTAAAAATT
6509036 TTTAA
1 TTTAA
6509041 TTTCTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:6509562 original size:21 final size:19
Alignment explanation
Indices: 6509527--6509570 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
6509517 CAAAACAAAA
*
6509527 TTTTAAATTTTTTTACTAAT
1 TTTTAAATTTATTTA-TAAT
*
6509547 TTTTATAATTTATTTATAGT
1 TTTTA-AATTTATTTATAAT
6509567 TTTT
1 TTTT
6509571 GCAGGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAAATTTATTTATAAT
Found at i:6520980 original size:13 final size:13
Alignment explanation
Indices: 6520962--6520986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6520952 TGTCCTACTG
6520962 AGTTTTTTTGATA
1 AGTTTTTTTGATA
6520975 AGTTTTTTTGAT
1 AGTTTTTTTGAT
6520987 GAGGTAGCAT
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
AGTTTTTTTGATA
Found at i:6529449 original size:18 final size:17
Alignment explanation
Indices: 6529400--6529450 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
6529390 ATTTAAAATG
*
6529400 AAAAATTATAAAATATTT
1 AAAAAATATAAAA-ATTT
*
6529418 AAAAAAT-TATAAATTT
1 AAAAAATATAAAAATTT
*
6529434 ATAAAACTATAAAAATT
1 A-AAAAATATAAAAATT
6529451 CAAGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAATATAAAAATTT
Found at i:6529760 original size:4 final size:4
Alignment explanation
Indices: 6529753--6529782 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
6529743 AAAAAGTACA
6529753 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
6529783 TAACCTTATC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6531762 original size:125 final size:123
Alignment explanation
Indices: 6531577--6531927 Score: 540
Period size: 125 Copynumber: 2.8 Consensus size: 123
6531567 TAATTTCGAG
* *
6531577 TTGACATTTCTGATCAAATAGTATAAAATCGCTTCTAACAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
6531642 AAATCGCGCCCTCGTGGATGCACTTTAGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAA--TTTTT
* * *
6531702 TTGACATTTCTGAGAAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTA
1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
6531767 AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTCGGTCATGGAAGAAATAATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT
* * *
6531825 TTGACGTTTTTGAGCAAATAGTATAAAATCGTTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
6531890 AAAATCACGCCCTTGTGGACGCGCTTTTGCTACAGTAG
66 -AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
6531928 CATGTTTGGG
Statistics
Matches: 205, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
123 64 0.31
124 33 0.16
125 108 0.53
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (123 bp):
TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTT
Found at i:6535534 original size:28 final size:23
Alignment explanation
Indices: 6535478--6536424 Score: 639
Period size: 23 Copynumber: 42.1 Consensus size: 23
6535468 NNNNNNNNNA
6535478 AATTAGGTTAGGGTTTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
6535501 AATTAGGTTAGGGTTTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
***
6535524 AAGGGGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6535548 -A--GGGTT---TTTAATTTAA-TT
1 AATTAGGTTAGGGTT--TTTAATTT
* *
6535566 AGGTTAGG--A---TTTTTAAGTT
1 A-ATTAGGTTAGGGTTTTTAATTT
***
6535585 AAGGGGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
*** *
6535609 -AGGGGGTTAGGATTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* * ** * *
6535632 -A-GAGTTTAAAGATTTTAATTA
1 AATTAGGTTAGGGTTTTTAATTT
6535653 AATTAGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6535677 -A--GGGTTTAGGGTTTTTAAGTT
1 AATTAGG-TTAGGGTTTTTAATTT
*
6535698 AATTAGGTTAGGGTTTTTAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
***
6535721 AAAGGGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
6535745 -A--AGGTTTAGGGTTTTTTAATTT
1 AATTAGG-TTAGGG-TTTTTAATTT
6535767 AATTAGGTTAGGG-TTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
*
6535789 AATTAGGTTAGGGTTTTTAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
* *
6535812 -A--GGGTTTAGGG-TTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
* *
6535832 AATTAGGTTAGAGTTTTTAA-GT
1 AATTAGGTTAGGGTTTTTAATTT
*
6535854 --TTAGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
*
6535876 AATTAGATTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6535900 -A--GGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
* * *
6535921 AATTAGGTTAGTGTTTTAAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
*
6535944 AATTAGGTTAGGGTTTTTAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
*
6535967 AAGGGGGTTA-GTTAGGGTTTTTAATTA
1 AA-----TTAGGTTAGGGTTTTTAATTT
6535994 AATTAGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6536018 -A--GGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
* *
6536039 AATTAAGTTAGGGTTTTTAA-GT
1 AATTAGGTTAGGGTTTTTAATTT
*
6536061 --TTAGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
6536083 AATTAGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6536107 -A--GGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
*
6536128 AATTAGGTTATGGTTTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
*
6536151 AATTAGGTTAGGGTTTTTAATTA
1 AATTAGGTTAGGGTTTTTAATTT
*
6536174 AATTTGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* **
6536198 -A--GGGTTTAATGTTTTTAATTT
1 AATTAGG-TTAGGGTTTTTAATTT
* *
6536219 AATTAGGTTAGAGATTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* *
6536243 -A--GGGTTTAGGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
* *
6536264 AATTAGGTTGGGGTTTTTAATTA
1 AATTAGGTTAGGGTTTTTAATTT
6536287 AATTAGGTTAGGGTTTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
*
6536310 AATTAGGTTA-GGTTTTTAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
* *
6536332 AATTAGGTTAGGGTTTTAAAGTT
1 AATTAGGTTAGGGTTTTTAATTT
***
6536355 AAGGGGGTTAGGGTTTTTAAGTTT
1 AATTAGGTTAGGGTTTTTAA-TTT
* * *
6536379 -A--GGGTTTAAGGTTTTTAATTA
1 AATTAGG-TTAGGGTTTTTAATTT
6536400 AATTAGGTTAGGGTTTTTAATTT
1 AATTAGGTTAGGGTTTTTAATTT
6536423 AA
1 AA
6536425 GGGTATTAAT
Statistics
Matches: 740, Mismatches: 105, Indels: 158
0.74 0.10 0.16
Matches are distributed among these distances:
18 11 0.01
19 3 0.00
20 26 0.04
21 70 0.09
22 168 0.23
23 389 0.53
24 50 0.07
25 3 0.00
27 17 0.02
28 3 0.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (23 bp):
AATTAGGTTAGGGTTTTTAATTT
Found at i:6535550 original size:38 final size:38
Alignment explanation
Indices: 6535508--6535638 Score: 129
Period size: 38 Copynumber: 3.2 Consensus size: 38
6535498 TTTAATTAGG
*
6535508 TTAGGGTTTTTAATTTAAGGGGGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAGT
***
6535546 TTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAGTT
1 TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAG-T
6535585 AAGGGGGTTAGGGTTTTTAAGTTT-AGGGGGTTAGGATTTTTAAGT
1 -------TTAGGGTTTTTAA-TTTAAGGGGGTTAGGATTTTTAAGT
*
6535630 TTAGAGTTT
1 TTAGGGTTT
6535639 AAAGATTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
38 41 0.54
39 1 0.01
45 1 0.01
46 30 0.39
47 3 0.04
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (38 bp):
TTAGGGTTTTTAATTTAAGGGGGTTAGGATTTTTAAGT
Found at i:6535562 original size:14 final size:15
Alignment explanation
Indices: 6535531--6535562 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6535521 TTTAAGGGGG
6535531 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
6535546 TTAGGGTTTTTAA-T
1 TTAGGGTTTTTAAGT
6535560 TTA
1 TTA
6535563 ATTAGGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TTAGGGTTTTTAAGT
Found at i:6535619 original size:84 final size:85
Alignment explanation
Indices: 6535477--6535977 Score: 302
Period size: 91 Copynumber: 5.7 Consensus size: 85
6535467 NNNNNNNNNN
* **
6535477 AAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTTAAGGGGGTTAGGGTTTT
1 AAATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTT-AGGGGGTTAGGGTTTT
*
6535541 TAAGTTTAG-G-GTTTTTAATT
64 TAAGTTTAGAGAGATTTTAATT
* * *
6535561 TAATTAGGTTAGGATTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAGGGGGTTAGGATTTTT
1 AAATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTTAGGGGGTTAGGGTTTTT
6535626 AAGTTTAGAGTTTAAAGATTTTAATT
65 AAGTTTAGAG-----AGATTTTAATT
* * * ***
6535652 AAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTA
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTTAGGGGGTTAGGGTTTTTA
* * * *
6535717 AG-TTAAAGGGGTTAGGGTT-TTT
66 AGTTTAGAGAGATT----TTAATT
* * ** ***
6535739 AAGTTTAAGGTTTAGGGTTTTTTAATTTAATTAGGTTAGGG-TTTTAA-TTTAATTAGGTTAGGG
1 AA-ATT-AGG-TTAGGG-TTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTT-AGGGGGTTAGGG
* *
6535802 TTTTTAAG-TTAGGGTTTAGGGTTTTAATT
60 TTTTTAAGTTTAGAG---A-GATTTTAATT
* * * * *** *
6535831 AAATTAGGTTAGAGTTTTTAAGTTTA-GGTTTAGGGTTTTTAA-TTAAATTAGATTAGGGTTTTT
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTT-TAGGGGGTTAGGGTTTTT
* *
6535894 AAGTTTAGGGTTTAGGGTTTTTAATT
65 AAGTTTA--G---AGAGATTTTAATT
* * ** *
6535920 AAATTAGGTTAGTGTTTTAAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAG
1 AAATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTTAGGGGGTTAG
6535978 TTAGGGTTTT
Statistics
Matches: 331, Mismatches: 52, Indels: 61
0.75 0.12 0.14
Matches are distributed among these distances:
84 65 0.20
85 4 0.01
86 7 0.02
87 31 0.09
88 17 0.05
89 45 0.14
90 47 0.14
91 97 0.29
92 13 0.04
93 1 0.00
95 4 0.01
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (85 bp):
AAATTAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTTAGGGGGTTAGGGTTTTTA
AGTTTAGAGAGATTTTAATT
Found at i:6535663 original size:45 final size:45
Alignment explanation
Indices: 6535544--6535968 Score: 435
Period size: 45 Copynumber: 9.4 Consensus size: 45
6535534 GGGTTTTTAA
* * *
6535544 GTTTAGGGTTTTTAATTTAATTAGGTTAGGATTTTTAAGTTAAGGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA-GG
* * *** * *
6535590 GGTTAGGGTTTTTAAGTT-TAGGGGGTTAGGATTTTTAAGTTTAGA
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAGG
** *
6535635 GTTTAAAGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
6535680 GTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAAGG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTT-TAGG
* * *
6535726 GGTTAGGGTTTTTAAGTT---TAAGGTTTAGGGTTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAA-TTAAATTAGG-TTAGGG-TTTTTAAGTTT-A--GG
*
6535773 G-TTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAAG-TTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
6535815 GTTTAGGG-TTTTAATTAAATTAGGTTAGAGTTTTTAAGTTTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
6535858 GTTTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
6535903 GTTTAGGGTTTTTAATTAAATTAGGTTAGTGTTTTAAAGTTAATTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGG
6535950 G-TTAGGGTTTTTAAGTTAA
1 GTTTAGGGTTTTTAA-TTAA
6535969 GGGGGTTAGT
Statistics
Matches: 324, Mismatches: 34, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.01
43 43 0.13
44 44 0.14
45 129 0.40
46 89 0.27
47 14 0.04
48 3 0.01
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (45 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
Found at i:6535669 original size:68 final size:68
Alignment explanation
Indices: 6535590--6536423 Score: 617
Period size: 68 Copynumber: 12.3 Consensus size: 68
6535580 AAGTTAAGGG
*** * ** *
6535590 GGTTAGGGTTTTTAAGTTTAGGGGGTTAGGATTTTTAAGTTTAGAGTTTAAAGATTTTAATTAAA
1 GGTTAGGGTTTTTAAGTTTATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTAAA
6535655 TTA
66 TTA
* * * *
6535658 GGTTAGGGTTTTTAAGTTTA--GGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTT
1 GGTTAGGGTTTTTAAGTTTATTAGG-TTAGGGTTTTTAAGTTTA-GAGTTTAGGGTTTTTAA-TT
**
6535721 AAA-GG
63 AAATTA
* *
6535726 GGTTAGGGTTTTTAAGTTTA--AGGTTTAGGGTTTTTTAA-TTTAATTAGGTTAGGG-TTTTAAT
1 GGTTAGGGTTTTTAAGTTTATTAGG-TTAGGG-TTTTTAAGTTT-A-GAGTTTAGGGTTTTTAAT
*
6535787 TTAATTA
62 TAAATTA
* * * *
6535794 GGTTAGGGTTTTTAAG-TTA--GGGTTTAGGGTTTTAATTAA-ATTAG-G-TTAGAGTTTTTAAG
1 GGTTAGGGTTTTTAAGTTTATTAGG-TTAGGG-TTT--TTAAGTTTAGAGTTTAGGGTTTTTAAT
6535853 T---TTA
62 TAAATTA
* * *
6535857 GGTTTAGGGTTTTTAA-TTAAATTAGATTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTA
1 GG-TTAGGGTTTTTAAGTT-TATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTA
6535921 AATTA
64 AATTA
* * * * *
6535926 GGTTAGTGTTTTAAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGTTAGGGTTTTTAA
1 GGTTAGGGTTTTTAAGTTTATTAGGTTAGGGTTTTTAAGTTTA--GAG-T--TTAGGGTTTTTAA
6535991 TTAAATTA
61 TTAAATTA
* * *
6535999 GGTTAGGGTTTTTAAGTTTA--GGGTTTAGGGTTTTTAATTAAATTA-AG-TTAGGGTTTTTAAG
1 GGTTAGGGTTTTTAAGTTTATTAGG-TTAGGGTTTTTAAGT---TTAGAGTTTAGGGTTTTTAAT
6536060 T---TTA
62 TAAATTA
* *
6536064 GGTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTA
1 GG-TTAGGGTTTTTAAGTT-TATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTA
6536128 AATTA
64 AATTA
* * * *
6536133 GGTTATGGTTTTTAA-TTTAATTAGGTTAGGGTTTTTAA--TTAAATTTGGTTAGGGTTTTTAAG
1 GGTTAGGGTTTTTAAGTTT-ATTAGGTTAGGGTTTTTAAGTTTAGA---GTTTAGGGTTTTTAAT
6536195 T---TTA
62 TAAATTA
** * * *
6536199 GGGTTTAATGTTTTTAA-TTTAATTAGGTTAGAGATTTTAAGTTTAGGGTTTAGGGTTTTTAATT
1 -GG-TTAGGGTTTTTAAGTTT-ATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATT
6536263 AAATTA
63 AAATTA
* * * *
6536269 GGTTGGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGGTTA-GGTTTTTAAGT
1 GGTTAGGGTTTTTAAGTT-TATTAGGTTAGGGTTTTTAAGTTT-A-GAGTTTAGGGTTTTTAA-T
6536331 T-AATTA
62 TAAATTA
* * *** * *
6536337 GGTTAGGGTTTTAAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAATTAAA
1 GGTTAGGGTTTTTAAGTTTATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTAAA
6536402 TTA
66 TTA
6536405 GGTTAGGGTTTTTAA-TTTA
1 GGTTAGGGTTTTTAAGTTTA
6536424 AGGGTATTAA
Statistics
Matches: 633, Mismatches: 75, Indels: 117
0.77 0.09 0.14
Matches are distributed among these distances:
63 9 0.01
64 21 0.03
65 18 0.03
66 64 0.10
67 80 0.13
68 304 0.48
69 70 0.11
70 9 0.01
71 3 0.00
72 15 0.02
73 38 0.06
75 2 0.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (68 bp):
GGTTAGGGTTTTTAAGTTTATTAGGTTAGGGTTTTTAAGTTTAGAGTTTAGGGTTTTTAATTAAA
TTA
Found at i:6536027 original size:45 final size:44
Alignment explanation
Indices: 6535682--6536423 Score: 616
Period size: 45 Copynumber: 16.4 Consensus size: 44
6535672 AGTTTAGGGT
**
6535682 TTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAGTTAAA-GGGG
1 TTAGGGTTTTTAAG-T--TTAGGTTTAGGGTTTTTAA-TTAAATTAGG
*
6535728 TTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTT-AGGTTTAGGG-TTTTTAATTAAATTAGG
* *
6535774 TTAGGG-TTTTAATTTAATTAGG-TTAGGGTTTTTAAGTT--A--GGG
1 TTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAA-TTAAATTAGG
* * *
6535816 TTTAGGGTTTTAATTAA-ATTAGG-TTAGAGTTTTTAAGT---TTAGG
1 -TTAGGG-TTT--TTAAGTTTAGGTTTAGGGTTTTTAATTAAATTAGG
* * *
6535859 TTTAGGGTTTTTAATTAAATTA-GATTAGGGTTTTTAAGT---TTAGGG
1 -TTAGGGTTTTTAAGT---TTAGGTTTAGGGTTTTTAATTAAATTA-GG
* * *
6535904 TTTAGGGTTTTTAATTAAATTAGG-TTAGTGTTTTAAAGTT-AATTAGG
1 -TTAGGGTTTTTAAGT---TTAGGTTTAGGGTTTTTAA-TTAAATTAGG
*
6535951 TTAGGGTTTTTAAGTTAAGGGGGTTAGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAAGTTTA---GG-T--TTAGGGTTTTTAATTAAATTAGG
*
6536001 TTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTTTTAAGTTTA-GGTTTAGGGTTTTTAATTAAATTAGG
6536046 TTAGGGTTTTTAAGTTTAGGTTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAAGTTTAGGTTTAGGGTTTTTAATTAAATTAGG
6536090 TTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAAGTTTA-GGTTTAGGGTTTTTAATTAAATTAGG
* * *
6536135 TTATGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAATTAAATTTGG
1 TTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAATTAAATTAGG
** *
6536181 TTAGGGTTTTTAAGTTTAGGGTTTAATGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTTA-GGTTTAGGGTTTTTAATTAAATTAGG
* *
6536226 TTAGAGATTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAAGTTTA-GGTTTAGGGTTTTTAATTAAATTAGG
* * *
6536271 TTGGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGT---TTAGGTTTAGGGTTTTTAATTAAATTAGG
* ***
6536317 TTA-GGTTTTTAAGTTAATTAGG-TTAGGGTTTTAAAGTT-AAGGGGG
1 TTAGGGTTTTTAAG-T--TTAGGTTTAGGGTTTTTAA-TTAAATTAGG
*
6536362 TTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAAGTTTA-GGTTTAGGGTTTTTAATTAAATTAGG
6536407 TTAGGGTTTTTAA-TTTA
1 TTAGGGTTTTTAAGTTTA
6536424 AGGGTATTAA
Statistics
Matches: 597, Mismatches: 51, Indels: 98
0.80 0.07 0.13
Matches are distributed among these distances:
40 4 0.01
42 6 0.01
43 43 0.07
44 77 0.13
45 274 0.46
46 128 0.21
47 14 0.02
48 14 0.02
49 2 0.00
50 35 0.06
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTTAGGTTTAGGGTTTTTAATTAAATTAGG
Found at i:6536970 original size:18 final size:18
Alignment explanation
Indices: 6536947--6536982 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6536937 CGGAAAAGGG
*
6536947 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
6536965 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
6536983 AACGCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:6537846 original size:20 final size:20
Alignment explanation
Indices: 6537821--6537858 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6537811 TTTATTTTTA
6537821 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
6537841 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
6537859 TACCTCGNNN
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:6538627 original size:11 final size:11
Alignment explanation
Indices: 6538611--6538652 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
6538601 AAAAAAGGAG
6538611 TTAAGAGAAAC
1 TTAAGAGAAAC
*
6538622 TTAAGAGGAAC
1 TTAAGAGAAAC
*
6538633 TTAAGAGGAAC
1 TTAAGAGAAAC
6538644 TTAAGAGAA
1 TTAAGAGAA
6538653 TTTTTGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:6543695 original size:19 final size:19
Alignment explanation
Indices: 6543651--6543713 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
6543641 TTTCTTAACA
*
6543651 AAAATTAAAAATAATTTTCA
1 AAAATTAAAAATAATTTT-T
*
6543671 AAAATTCAAAATAATTTTT
1 AAAATTAAAAATAATTTTT
*
6543690 AAAATTAAAAAT-ATTTAT
1 AAAATTAAAAATAATTTTT
6543708 AAAATT
1 AAAATT
6543714 TACAAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.28
19 11 0.28
20 17 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTAAAAATAATTTTT
Found at i:6543720 original size:39 final size:42
Alignment explanation
Indices: 6543651--6543735 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 42
6543641 TTTCTTAACA
6543651 AAAATTAAAAATAATTTTCAAAAATTCAAAA-T-A-ATTTTT
1 AAAATTAAAAATAATTTTCAAAAATTCAAAATTCATATTTTT
*
6543690 AAAATTAAAAAT-ATTTAT-AAAATTTACAAAATTCATATTTTT
1 AAAATTAAAAATAATTT-TCAAAAATT-CAAAATTCATATTTTT
6543732 AAAA
1 AAAA
6543736 AAATTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
38 10 0.25
39 18 0.45
40 1 0.03
41 1 0.03
42 10 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (42 bp):
AAAATTAAAAATAATTTTCAAAAATTCAAAATTCATATTTTT
Found at i:6559062 original size:24 final size:23
Alignment explanation
Indices: 6559014--6559062 Score: 55
Period size: 24 Copynumber: 2.0 Consensus size: 23
6559004 TTTTGTAAAA
*
6559014 AAAAAAAAATTAAACTCTATAAGT
1 AAAAAAAAATTAAAC-ATATAAGT
6559038 AAAAAAAAATATAAA-ATATAGAGT
1 AAAAAAAAAT-TAAACATATA-AGT
6559062 A
1 A
6559063 GCCTTTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAAAAAAATTAAACATATAAGT
Found at i:6564065 original size:20 final size:20
Alignment explanation
Indices: 6564040--6564089 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
6564030 ACAAATTATC
*
6564040 TTGGTAAATTGTTAGATATT
1 TTGGTAAATCGTTAGATATT
*
6564060 TTGGTAGATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
6564080 TTGGTAAATC
1 TTGGTAAATC
6564090 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
TTGGTAAATCGTTAGATATT
Found at i:6565613 original size:30 final size:29
Alignment explanation
Indices: 6565549--6565604 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6565539 CCCAAATCGA
* *
6565549 TTAAAAATAATTTTTCTAATAAAAATTAC
1 TTAAAAATAAATTTTCTAACAAAAATTAC
6565578 TTAAAAATAAATTTTC-AACAAACAATT
1 TTAAAAATAAATTTTCTAACAAA-AATT
6565605 GATATAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAAATTTTCTAACAAAAATTAC
Found at i:6567350 original size:18 final size:19
Alignment explanation
Indices: 6567327--6567365 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
6567317 GAAACTCTAT
6567327 ATCCTTC-AGGGATTTT-AA
1 ATCCTTCTA-GGATTTTCAA
6567345 ATCCTTCTAGGATTTTCAA
1 ATCCTTCTAGGATTTTCAA
6567364 AT
1 AT
6567366 AAAATTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (19 bp):
ATCCTTCTAGGATTTTCAA
Found at i:6574897 original size:2 final size:2
Alignment explanation
Indices: 6574890--6574916 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6574880 TCTTATAATT
6574890 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 T
6574917 AAATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6576765 original size:12 final size:12
Alignment explanation
Indices: 6576744--6576772 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6576734 ATTTTTTTAT
6576744 AATT-AGGAAAA
1 AATTAAGGAAAA
6576755 AATTAAGGAAAA
1 AATTAAGGAAAA
6576767 AATTAA
1 AATTAA
6576773 TCTTATGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (12 bp):
AATTAAGGAAAA
Found at i:6578759 original size:17 final size:18
Alignment explanation
Indices: 6578739--6578785 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
6578729 ATTTTTCGAA
6578739 AAATAA-ATTTTTTGTTC
1 AAATAATATTTTTTGTTC
*
6578756 AAATAATTTTTTTTGTTC
1 AAATAATATTTTTTGTTC
6578774 AAAT--TATTTTTT
1 AAATAATATTTTTT
6578786 TCCTGTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
AAATAATATTTTTTGTTC
Found at i:6578802 original size:20 final size:18
Alignment explanation
Indices: 6578746--6578805 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
6578736 GAAAAATAAA
6578746 TTTTTTGTTCAAATAATT
1 TTTTTTGTTCAAATAATT
*
6578764 TTTTTTGTTCAAATTATT
1 TTTTTTGTTCAAATAATT
**
6578782 TTTTTCCTGTTGGAATAATT
1 TTTTT--TGTTCAAATAATT
6578802 TTTT
1 TTTT
6578806 GAAAAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 22 0.61
20 14 0.39
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTTTTGTTCAAATAATT
Found at i:6582994 original size:66 final size:66
Alignment explanation
Indices: 6582896--6583021 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
6582886 GCTGTAGATG
* * *
6582896 GAGTTCGTCATATTTTCTTGTTGCCTCTGCTTC-CTTCGCTACTACCTCCGCTTTAAGTTGTAGC
1 GAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTC-TCGATACTACCTCCGCTTTAAGTTGTAGC
6582960 TA
65 TA
* * *
6582962 GAGTTCATTATATTTTCTT-TGAGCCTCTGCTTCTCTCGATGCTACCTCCGTTTTAAGTTG
1 GAGTTCATCATATTTTCTTGT-AGCCTCTGCTTCTCTCGATACTACCTCCGCTTTAAGTTG
6583022 AGCAATTTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.02
66 50 0.96
67 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (66 bp):
GAGTTCATCATATTTTCTTGTAGCCTCTGCTTCTCTCGATACTACCTCCGCTTTAAGTTGTAGCT
A
Found at i:6588317 original size:44 final size:44
Alignment explanation
Indices: 6588263--6588917 Score: 307
Period size: 44 Copynumber: 14.7 Consensus size: 44
6588253 TCATCATTTT
* * * *
6588263 AATCCGCTCCACTACAACTTCAGGAAGA-GAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTA-TAGCTTC
* * * * *
6588307 AATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTATAGCTTC
6588351 AATCTGCTCCACTGCAACTTCAGGGAGATAAGCAGGAAGAGAGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGAT--------A-AG-GATTA-TAGCTTC
* * * * *
6588406 AATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTATAGCTTC
*
6588450 AATCTGCTCCACTGCAACTTCA-GGAGA-GAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTA-TAGCTTC
* * * * *
6588493 AATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTATAGCTTC
** * * *
6588537 AATCTGCTCCACTGCAA----A---AGATCTGTAATTACAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG-GATTATAGCTTC
* * * *
6588575 AATCTGTTCCACTGCAACTTCAGGGAAATAA-GATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATT--ATAGCTTC
* * * * *
6588620 AGTCTGCTCTACTGCAACTTTAGGGA-AGTAA-GACTTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGA-TAAGGA-TTATAGCTTC
*
6588664 AA-CTTGCTCCACTACAACTTCAGGGAGATAAGG-TT-T-GCTAT-
1 AATC-TGCTCCACTGCAACTTCAGGGAGATAAGGATTATAGCT-TC
* * * *
6588705 GATCTGCTCTACTGCAACTTAAGAGAGATAAGATCTGCAATTTATAGC-TC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG----G--A-TTATAGCTTC
* * * * * * * *
6588755 TAACCTGTTCCGCTGCCACTTCAGGG-GA-ATGACATTTGCTATCTTC
1 -AATCTGCTCCACTGCAACTTCAGGGAGATAAG-GA-TT-ATAGCTTC
* ** * *
6588801 AGTCTATTCCACTGCAACTTCAGGAAGATAA-AACTT-TA-CTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGA-TTATAGCTTC
* * * *
6588843 AATCCGCTCCACTGCAACTTCATGGAGATAA-GATTATTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTA-TAGCTTC
** *
6588887 AATCTATTCCACTGCAACTTCAGGAAGATAA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAA
6588918 TATTTGTCAT
Statistics
Matches: 459, Mismatches: 101, Indels: 102
0.69 0.15 0.15
Matches are distributed among these distances:
37 5 0.01
38 22 0.05
40 1 0.00
41 29 0.06
42 40 0.09
43 39 0.08
44 168 0.37
45 79 0.17
46 8 0.02
47 2 0.00
49 5 0.01
50 3 0.01
51 19 0.04
52 1 0.00
53 2 0.00
54 4 0.01
55 32 0.07
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTATAGCTTC
Found at i:6588529 original size:87 final size:87
Alignment explanation
Indices: 6588383--6588553 Score: 326
Period size: 87 Copynumber: 2.0 Consensus size: 87
6588373 GGGAGATAAG
6588383 CAGGAAGAGAGATTAGTAGCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCT
1 CAGGAAGAGAGATTAGTAGCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCT
6588448 TTAATCTGCTCCACTGCAACTT
66 TTAATCTGCTCCACTGCAACTT
6588470 CAGG-AGAGAGGATTAGTAGCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGC
1 CAGGAAGAGA-GATTAGTAGCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGC
6588534 TTTAATCTGCTCCACTGCAA
65 TTTAATCTGCTCCACTGCAA
6588554 AAGATCTGTA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
86 5 0.06
87 78 0.94
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (87 bp):
CAGGAAGAGAGATTAGTAGCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGGTTTATGGCT
TTAATCTGCTCCACTGCAACTT
Found at i:6588636 original size:45 final size:42
Alignment explanation
Indices: 6588570--6588738 Score: 128
Period size: 45 Copynumber: 3.9 Consensus size: 42
6588560 TGTAATTACA
*
6588570 ACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCT
1 ACTTC-ATCTGCTCCACTGCAACTTCAGGGAAATAAGATT-GCT
* * *
6588614 ATCTTCAGTCTGCTCTACTGCAACTTTAGGGAAGTAAGACTTG-T
1 A-CTTCA-TCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTGCT
* * * *
6588658 AACTTCAACTTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCT
1 -ACTTCATC-TGCTCCACTGCAACTTCAGGGAAATAA-GATTGCT
* * * * *
6588703 A--TGATCTGCTCTACTGCAACTTAAGAGAGATAAGAT
1 ACTTCATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
6588739 CTGCAATTTA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
40 2 0.02
41 23 0.23
42 3 0.03
43 1 0.01
44 34 0.34
45 35 0.35
46 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
ACTTCATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCT
Found at i:6590252 original size:45 final size:45
Alignment explanation
Indices: 6590201--6591650 Score: 484
Period size: 45 Copynumber: 31.6 Consensus size: 45
6590191 CTTCGATCCA
* * *
6590201 CTCCACTACAACTTCAGGGAGATAAGACTTGCTATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * * * * *
6590246 CTCCACTACAAATTCAGGAAGATAAGACTTGCTATGGTAAATTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTA---T--CTTCAATCTG
* * * * * *
6590296 AC-CTACTGCAACCTCAGAGG-TATAGGA-TT-C-ATCATTTTAATCCG
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGCTATC--TTCAATCTG
* * * * *
6590340 CTCCACTACAACTTCAGGAAGAGAGGA-TTAG-TAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG
* * * *
6590384 CTCCATTGTAACTTCAGGGAGATAAG-GTT--TATGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT--CTTCAATCTG
* *
6590428 CTCCACTGCAACTTCAGGGAGATAAGATTTATAGCCTATCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T-G-CTATCTTCAATCTG
* * * * * *
6590477 CTCTACTGCAACTTGAGGGAGATAAGA-TTGATTATTTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-CTATCTTCAATCTG
* * ** * * *
6590522 CTCTACTACAACTTCAGGGAGATAAGGTTTG--AT-AT-GATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * ** *
6590563 CTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTACAACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCT--ATCTTCAATCTG
* * *
6590614 TTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG
* * * * * *
6590659 CTCTACTGCAACTTTAGGGAGATAAGACTTGTTATGGTAGATTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTA---T--CTTCAATCTG
* * * *
6590709 AC-CTACTGCAACTTCAGAGGTG-TAGGA-TT-C-ATCTTTTTAATCTG
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGCTATC--TTCAATCTG
* ** *
6590753 CTCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAA-GACT-T-GC-TATCTTCAATCTG
* * *
6590802 CTTCACTGCAACTTCAGGGAGATAAGA-TTAGTTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG
* * * *
6590847 TTCCACTACAACTTTAGGGAGATAAGACTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * * * * *
6590892 CTCCACTACAATTTCAAGGAGATATGACTTGCTATTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * * * * *
6590937 TTCCACTGCAAATTCAGGGAGATAAGAC-TGATTTATTTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG--CTATCTTCAATCTG
* * ** * *
6590983 CTCCACTACAACTTCAGGAAGATAAGGTTTGGTA---T-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * ** *
6591024 CTCTACTGCAACTAT-AGAGAGATAAGATCTATAATTTATAGCTTCAATTTG
1 CTCCACTGCAACT-TCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG
* ** * * *
6591075 TTCCACTAAAACTTCAGGGAAATAAGA-TTCACTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG
** * *
6591120 CTCCACCACAATTTCAAGGAGATAAGACTTGCTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * * *
6591165 -TCCCACTGCAACTTCAAGGG-GATAAGA-TTAG-TAGCCTCAATTTA
1 CT-CCACTGCAACTTC-AGGGAGATAAGACTT-GCTATCTTCAATCTG
* * ** * *
6591209 CTCCACTGCAACTTCAAGGAGATAAGA-TTCGACTTTGGTAAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-G-CTATCTTCAATCTG
* * * *
6591255 ATCCGACCTATTGCAACTTCAGAGG-TATAGGATTTGTCGT-T-TT-AAT-TCG
1 CTCC-A-C---TGCAACTTCAG-GGAGATAAGACTTG-C-TATCTTCAATCT-G
* * * **
6591304 CTCCACTCCAACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG
* * * * * * *
6591355 TTCCTCTGCAACTTCAGGGAAATGAG-TTTGCTATCTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
* * * *
6591399 CTCCATTGCAACTTCAGGGAGATAAGA-TT-CGTAACTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGC-TATCTTCAATCTG
* * *
6591443 CCCCACTGCAACTTCAGTGG-GATAAGA-TTAGCTA---T-GATCTT
1 CTCCACTGCAACTTCAG-GGAGATAAGACTT-GCTATCTTCAATCTG
* * * **
6591484 CTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTAT--CTTCAATCTG
* * * * *
6591535 TTCCACTGCAACTTCAAGGAAATAAGA-TTCGCTATCCTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAATCTG
* *
6591580 CTCCACTGCAACTTCAAGGAGATAAAACTTG-T-TGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTCAATCTG
* *
6591624 -TCCCATTGCAACTTCAGGGGGATAAGA
1 CT-CCACTGCAACTTCAGGGAGATAAGA
6591651 TTTGTGGTTT
Statistics
Matches: 1053, Mismatches: 235, Indels: 235
0.69 0.15 0.15
Matches are distributed among these distances:
40 1 0.00
41 76 0.07
42 8 0.01
43 19 0.02
44 264 0.25
45 319 0.30
46 70 0.07
47 18 0.02
48 11 0.01
49 81 0.08
50 52 0.05
51 128 0.12
52 6 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTG
Found at i:6590639 original size:137 final size:138
Alignment explanation
Indices: 6590393--6590684 Score: 315
Period size: 137 Copynumber: 2.1 Consensus size: 138
6590383 GCTCCATTGT
* * * *
6590393 AACTTCAGGGAGATAAGGTTTATGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
1 AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGATTT
* * * * * * * * *
6590458 ATAGCCTATCTTCAATTTGCTCTACTGCAACTTGAGGGAGATAAGATT-GATTATTTTTAACCTG
66 ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCG-CTATCTTCAACCTG
6590522 CTCTACTAC
130 CTCTACTAC
* *
6590531 AACTTCAGGGAGATAAGG-TT-T-GATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCT
1 AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGAT-T
** * **
6590593 GTAATTTAC-AACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
65 -T-ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAACC
*
6590657 TGCTCTACTGC
128 TGCTCTACTAC
*
6590668 AACTTTAGGGAGATAAG
1 AACTTCAGGGAGATAAG
6590685 ACTTGTTATG
Statistics
Matches: 128, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
135 33 0.26
136 2 0.02
137 71 0.55
138 22 0.17
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (138 bp):
AACTTCAGGGAGATAAGGTTTATGGATATAATCTACTCCACTGCAACTTCAGAGAGATAAGATTT
ATAGACTAACTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAACCTGC
TCTACTAC
Found at i:6591117 original size:228 final size:225
Alignment explanation
Indices: 6590481--6591652 Score: 840
Period size: 228 Copynumber: 5.1 Consensus size: 225
6590471 AATTTGCTCT
* *
6590481 ACTGCAACTTGAGGGAGATAAGATTGATTATTTTTAACCTGCTCTACTACAACTTCAGGGAGATA
1 ACTGCAACTTCAGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGATA
* * *
6590546 AGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTACAACTTCAAT
66 AGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-TAATTTA-TACTTCAAT
* * *
6590611 CTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCTACTGCAACTTT-A
129 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAA-TTTCA
* * * *
6590675 GGGAGATAAGACTTGTTATGGTAGATTTAATCCG-ACC
193 AGGAGATAAGACTTGCTAT--T---TTCAATCTGTACC
* * * * * * *
6590712 TACTGCAACTTCAGAGGTG-TAGGATTCA-TCTTTTTAATCTGCTCCACTGCAACTTTAGGGAGA
1 -ACTGCAACTTCAG-GGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGA
* *
6590775 TAAGGTTT-GTAGCTTGTCTTCAATCTGCT-TCACTGCAACTTCAGGGAGATAAGA--TT-AGTT
64 TAAGGTTTGGTA---TG------ATCTGCTCT-ACTGCAACTTCAGAGAGATAAGATCTTAATTT
* * *
6590835 AT-CTTCAGTCTGTTCCACTACAACTTTAGGGAGATAAGACTT-GCTATCTTCAGTCTGCTCCAC
119 ATACTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTGCTCCAC
* * *
6590898 TACAATTTCAAGGAGATATGACTTGCTATTTTCAGTCTGTTCC
183 TACAATTTCAAGGAGATAAGACTTGCTATTTTCAATCTGTACC
* * *
6590941 ACTGCAAATTCAGGGAGATAAGACTGATTTATTTTTAACCTGCTCCACTACAACTTCAGGAAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGA-TTATTTTTAACCTGCTCCACTACAACTTCAGGGAGAT
6591006 AAGGTTTGGTATGATCTGCTCTACTGCAACTAT-AGAGAGATAAGATCTATAATTTATAGCTTCA
65 AAGGTTTGGTATGATCTGCTCTACTGCAACT-TCAGAGAGATAAGATCT-TAATTTATA-CTTCA
* * * *
6591070 ATTTGTTCCACTAAAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACCACAATTTC
127 ATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTC
* *
6591135 AAGGAGATAAGACTTGCTATCTTCAATCTGTCCC
192 AAGGAGATAAGACTTGCTATTTTCAATCTGTACC
* *** * ** * * *
6591169 ACTGCAACTTCAAGGG-GATAAGATT-AGTAGCCTCAATTTACTCCACTGCAACTTCAAGGAGAT
1 ACTGCAACTTC-AGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGAT
* * * *
6591232 AAGATTCGACTTTGGTAAATTTGATCCGAC-CTATTGCAACTTCAGAG-GTATAGGAT-TT-GTC
65 AAG----G--TTTGGT--A--TGATCTG-CTCTACTGCAACTTCAGAGAG-ATAAGATCTTAAT-
* * * * * *** *
6591293 GT-T--TT-AAT-TCGCTCCACTCCAACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATC
117 TTATACTTCAATCT-GTTCCACTACAACTTCAGGGAAATA--AGAT-T-CGCTAT--CTTCAGTC
* * * * * * * * *
6591353 TGTTCCTCTGCAACTTCAGGGAAATGAG-TTTGCTATCTTT-AGTCTGCT-CC
175 TGCTCCACTACAATTTCAAGGAGATAAGACTTGCTAT-TTTCAATCTG-TACC
* ** * * * *
6591403 ATTGCAACTTCAGGGAGATAAGATTCG--TAACTTTAATCTACCCCACTGCAACTTCAGTGG-GA
1 ACTGCAACTTCAGGGAGATAAGATT-GATTATTTTTAACCTGCTCCACTACAACTTCAG-GGAGA
* * * * *
6591465 TAAGATTAGCTATGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCA
64 TAAGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-TAATTTATA-CTTCA
* * * * *
6591530 ATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCCTCAGTCTGCTCCACTGCAACTTC
127 ATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTC
* * *
6591595 AAGGAGATAAAACTTG-T-TGCTTCAATCTGTCCC
192 AAGGAGATAAGACTTGCTAT-TTTCAATCTGTACC
* *
6591628 ATTGCAACTTCAGGGGGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
6591653 TGTGGTTTCA
Statistics
Matches: 745, Mismatches: 126, Indels: 145
0.73 0.12 0.14
Matches are distributed among these distances:
222 27 0.04
223 3 0.00
224 31 0.04
225 63 0.08
226 40 0.05
227 11 0.01
228 140 0.19
229 33 0.04
230 45 0.06
231 69 0.09
232 30 0.04
233 88 0.12
234 68 0.09
235 39 0.05
236 27 0.04
237 2 0.00
238 1 0.00
239 28 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (225 bp):
ACTGCAACTTCAGGGAGATAAGATTGATTATTTTTAACCTGCTCCACTACAACTTCAGGGAGATA
AGGTTTGGTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTAATTTATACTTCAATCT
GTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAATTTCAAGG
AGATAAGACTTGCTATTTTCAATCTGTACC
Found at i:6591437 original size:44 final size:45
Alignment explanation
Indices: 6591360--6591476 Score: 123
Period size: 44 Copynumber: 2.6 Consensus size: 45
6591350 ATCTGTTCCT
* * * * * * *
6591360 CTGCAACTTCAGGGAAATGAG-TTTGCTATCTTTAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA
*
6591404 TTGCAACTTCAGGGAGATAAGATTCG-TAACTTTAATCTACCCCA
1 CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA
*
6591448 CTGCAACTTCAGTGG-GATAAGATTAGCTA
1 CTGCAACTTCAG-GGAGATAAGATTCGCTA
6591477 TGATCTTCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
44 53 0.88
45 7 0.12
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (45 bp):
CTGCAACTTCAGGGAGATAAGATTCGCTAACTTTAATCTACCCCA
Found at i:6591648 original size:181 final size:180
Alignment explanation
Indices: 6591313--6591652 Score: 475
Period size: 181 Copynumber: 1.9 Consensus size: 180
6591303 GCTCCACTCC
* * * *
6591313 AACTTCAGGGAGATAGGATATATAATTTATAGCTTCAATCTGTTCCTCTGCAACTTCAGGGAAAT
1 AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT
* * * * * * * *
6591378 GAGTTTGCTATCTTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGATTCGTAACTTTAATCTA
66 AAGTTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAATTCGTAACTTCAATCTA
*
6591443 CCCCACTGCAACTTCAGTGGGATAAGATTAGCTATGATCTTCTCTACTGT
131 CCCCACTGCAACTTCAGGGGGATAAGATTAGCTATGATCTTCTCTACTGT
* *
6591493 AACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT
1 AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT
**
6591558 AAGATTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAACTT-GTTGCTTCAATC
66 AAG-TTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAA-TTCGTAACTTCAATC
** *
6591622 TGTCCCATTGCAACTTCAGGGGGATAAGATT
129 TACCCCACTGCAACTTCAGGGGGATAAGATT
6591653 TGTGGTTTCA
Statistics
Matches: 138, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
180 61 0.44
181 75 0.54
182 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (180 bp):
AACTTCAGAGAGATAAGATATATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAAGGAAAT
AAGTTCGCTATCCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAAATTCGTAACTTCAATCTA
CCCCACTGCAACTTCAGGGGGATAAGATTAGCTATGATCTTCTCTACTGT
Found at i:6592524 original size:20 final size:21
Alignment explanation
Indices: 6592488--6592555 Score: 86
Period size: 20 Copynumber: 3.2 Consensus size: 21
6592478 GGCCTCTCCT
6592488 TTTTCTTTTTCTTTTTCTTTTC
1 TTTTC-TTTTCTTTTTCTTTTC
6592510 TTTTCTTTT-TTTTTCTTTTC
1 TTTTCTTTTCTTTTTCTTTTC
*
6592530 TATTCTTTTCATTTTTCATTTT-
1 TTTTCTTTTC-TTTTTC-TTTTC
6592552 TTTT
1 TTTT
6592556 AAAGTGAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 19 0.46
21 4 0.10
22 14 0.34
23 4 0.10
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTCTTTTC
Found at i:6592528 original size:25 final size:26
Alignment explanation
Indices: 6592488--6592545 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
6592478 GGCCTCTCCT
*
6592488 TTTTCTTTTTCTTTTTCTTTTCTTTTC
1 TTTT-TTTTTCTTTTTCTATTCTTTTC
6592515 TTTTTTTTTC-TTTTCTATTCTTTTC
1 TTTTTTTTTCTTTTTCTATTCTTTTC
*
6592540 ATTTTT
1 TTTTTT
6592546 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 19 0.66
26 6 0.21
27 4 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTCTATTCTTTTC
Found at i:6592551 original size:6 final size:5
Alignment explanation
Indices: 6592488--6592544 Score: 69
Period size: 5 Copynumber: 10.8 Consensus size: 5
6592478 GGCCTCTCCT
* *
6592488 TTTTC TTTTTC TTTTTC TTTTC TTTTC TTTTT TTTTC TTTTC TATTC TTTTC
1 TTTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
6592540 ATTTT
1 -TTTT
6592545 TCATTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 31 0.67
6 15 0.33
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:6592553 original size:25 final size:23
Alignment explanation
Indices: 6592488--6592553 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 23
6592478 GGCCTCTCCT
*
6592488 TTTTCTTTTTC-TTTTTCTTTTC
1 TTTTCTTTTTCTTTTTTCTATTC
*
6592510 TTTTCTTTTTTTTTCTTTTCTATTC
1 TTTTC-TTTTTCTT-TTTTCTATTC
6592535 TTTTCATTTTTCATTTTTT
1 TTTTC-TTTTTC-TTTTTT
6592554 TTAAAGTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.14
23 5 0.14
24 1 0.03
25 23 0.64
26 2 0.06
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCTTTTTCTTTTTTCTATTC
Found at i:6603200 original size:80 final size:80
Alignment explanation
Indices: 6603104--6603281 Score: 356
Period size: 80 Copynumber: 2.2 Consensus size: 80
6603094 GATCCAAAGT
6603104 TTTATGTAAGTTATGATATGATATCTATTTTTTATATTCTCTAAATTTTAGAAATTGCATTTTTT
1 TTTATGTAAGTTATGATATGATATCTATTTTTTATATTCTCTAAATTTTAGAAATTGCATTTTTT
6603169 TATGTTCTTTAAATG
66 TATGTTCTTTAAATG
6603184 TTTATGTAAGTTATGATATGATATCTATTTTTTATATTCTCTAAATTTTAGAAATTGCATTTTTT
1 TTTATGTAAGTTATGATATGATATCTATTTTTTATATTCTCTAAATTTTAGAAATTGCATTTTTT
6603249 TATGTTCTTTAAATG
66 TATGTTCTTTAAATG
6603264 TTTATGTAAGTTATGATA
1 TTTATGTAAGTTATGATA
6603282 AATGTTTGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 98 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (80 bp):
TTTATGTAAGTTATGATATGATATCTATTTTTTATATTCTCTAAATTTTAGAAATTGCATTTTTT
TATGTTCTTTAAATG
Found at i:6611897 original size:23 final size:23
Alignment explanation
Indices: 6611827--6611910 Score: 106
Period size: 21 Copynumber: 3.9 Consensus size: 23
6611817 CCTGATCAGT
6611827 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
**
6611848 A-ACGACACACGAAGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
*
6611868 ATACGACACATAAAGTGCTTGAG
1 ATACGACACATAAAGTGCCTGAG
6611891 ATACGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
6611911 AATCGGCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.17
21 24 0.45
23 20 0.38
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:6611907 original size:44 final size:41
Alignment explanation
Indices: 6611827--6611910 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 41
6611817 CCTGATCAGT
*
6611827 ATACGACACATAAGTGCCTGAAACGACACACGAAGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
* *
6611868 ATACGACACATAAAGTGCTTGAGATACGACACATAAAGTGCCT
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCT
6611911 AATCGGCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.30
42 9 0.24
43 1 0.03
44 16 0.43
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:6612865 original size:17 final size:18
Alignment explanation
Indices: 6612831--6612866 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6612821 TTAGCTATTC
*
6612831 TGTTTCTATTTCTTCTTT
1 TGTTTCTATTTATTCTTT
6612849 TGTTTCT-TTTATTCTTT
1 TGTTTCTATTTATTCTTT
6612866 T
1 T
6612867 ATTTTATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (18 bp):
TGTTTCTATTTATTCTTT
Found at i:6612918 original size:19 final size:22
Alignment explanation
Indices: 6612892--6612934 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6612882 ATGCATTAGT
*
6612892 TAATAATAATAATAAT-ATATTA
1 TAATAATCAT-ATAATAATATTA
6612914 TAATAATCATATAATAATATT
1 TAATAATCATATAATAATATT
6612935 TTTTTTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATCATATAATAATATTA
Found at i:6613073 original size:5 final size:5
Alignment explanation
Indices: 6613065--6613096 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6613055 TTAATTTATT
6613065 TAATA TAATA TAATA TAATA TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAA
6613097 ATCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:6617397 original size:22 final size:22
Alignment explanation
Indices: 6617349--6617409 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
6617339 AGCATTAACA
* *
6617349 CAAAATAGTAGCAACATAATAG
1 CAAAATAGTAGCAAAACAATAG
* * *
6617371 TAAAATTGTAGCAAAACAATGG
1 CAAAATAGTAGCAAAACAATAG
6617393 CAAAA-AGTGAG-AAAACA
1 CAAAATAGT-AGCAAAACA
6617410 GTGGCGAAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.16
Consensus pattern (22 bp):
CAAAATAGTAGCAAAACAATAG
Found at i:6630070 original size:25 final size:23
Alignment explanation
Indices: 6630027--6630073 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
6630017 GGAATTTTTT
*
6630027 TTATTTTTTTAATATTAATATAG
1 TTATTTTTTTAATAATAATATAG
6630050 TTATTTTTAATTAATAATAATATA
1 TTATTTTT--TTAATAATAATATA
6630074 AAATTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTTTTTTAATAATAATATAG
Found at i:6641284 original size:16 final size:17
Alignment explanation
Indices: 6641259--6641298 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
6641249 GCCCAAATGC
6641259 CAAA-CCCAAAT-AAAA
1 CAAAGCCCAAATCAAAA
*
6641274 CAAAGCCCAAATCCAAA
1 CAAAGCCCAAATCAAAA
6641291 C-AAGCCCA
1 CAAAGCCCA
6641299 TTACAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.55, C:0.35, G:0.05, T:0.05
Consensus pattern (17 bp):
CAAAGCCCAAATCAAAA
Found at i:6642589 original size:3 final size:3
Alignment explanation
Indices: 6642577--6642623 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
6642567 TACAACTATC
6642577 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6642624 TACTCATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6642747 original size:17 final size:18
Alignment explanation
Indices: 6642718--6642754 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6642708 CCTTTTTAAT
6642718 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
6642736 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
6642753 TT
1 TT
6642755 CACACTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:6643230 original size:17 final size:18
Alignment explanation
Indices: 6643201--6643237 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6643191 CCTTTTTAAT
6643201 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
6643219 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
6643236 TT
1 TT
6643238 CACACTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:6643282 original size:483 final size:478
Alignment explanation
Indices: 6642378--6643303 Score: 1336
Period size: 483 Copynumber: 1.9 Consensus size: 478
6642368 CAATTTAATC
6642378 CATATTTTTTTTAATTTTTATATTATTTACAACTTTATACGTATATATATATACATACATACTCA
1 CATATTTTTTTTAATTTTTATATTATTTACAACTTTATACGTATATATATATACATACATACTCA
*
6642443 TATTTTTTTATATATATTTTATAATTTATGTATACATATATTTATTTGCCCCTACGATTTAGTTT
66 TATTTTTTTATATATATTTTATAATTTATGTATACATATATTTA-TTGCCCATACGATTTA-TTT
* * * * * *
6642508 ATTTTCAATTGAACCCTTTTTTAGCTATTTTATTATTAAATTAGCTATTTTAATCCTATTACAAC
129 ACTTTCAATTGAACCCTTATTTA-CTATTGTAATATTAAATTAGCTACTTTAATCATATTACAAC
* * * ** * ** * *
6642573 TATCATTATATTATTATTATTATTATTATTATTATTATTATTATTATTATTTACTCATTTATGTC
193 TATCATCATATTATTATTATCATTATTATAAACAATAACATTATCACTATTTACTCATTTATGTC
6642638 GTGTTAATTCCTAACTTTGTTATATATATATGCGCATACATACGTATTTATAATATATATACGTA
258 GTGTTAATTCCTAACTTTGTTATATATATATGCGCATACATACGTATTTATAATATATATACGTA
6642703 CATAACCTTTTTAATTTATATAGATATAAATACTTATATGATATATATACTTCACACTTACATAT
323 CATAACCTTTTTAATTTATATAGATATAAATACTTATATGATATATATACTTCACACTTACATAT
6642768 TTTTAATTTTCTTATATGTACATATTAACATTTTTATACACTTTGTAATTTACATATATATGTAC
388 TTTTAATTTTCTTATATGTACATATTAACATTTTTATACACTTTGTAATTTACATATATATGTAC
6642833 AGACATATTGTTATAGCGTACGTATG
453 AGACATATTGTTATAGCGTACGTATG
6642859 CATATTTTTTTTAATTTTTATATTATTTACAACTTTATACGTATATATATATACATACATACTCA
1 CATATTTTTTTTAATTTTTATATTATTTACAACTTTATACGTATATATATATACATACATACTCA
6642924 TATTTTTTTATATATATTTTATAATTTATGTATACATATATTTA-TGCCTACATAC-ATTT-TTT
66 TATTTTTTTATATATATTTTATAATTTATGTATACATATATTTATTGCC--CATACGATTTATTT
*** * **
6642986 AACTTTC-A-T-AAGTGTATATTTA-TATATGTACATACTTATATGTTTCATACTTT-ATCAT-T
129 -ACTTTCAATTGAACCCT-TATTTACTAT-TGTA-ATA-TTAAAT-TAGC-TACTTTAATCATAT
* * *
6643045 TACATA-TATACATACATATTTTTA-TATACATTTTTA-AACACACATACACATTGTCACTATTT
187 TACA-ACTAT-CAT-CATATTATTATTAT-CATTATTATAA-ACA-ATA-ACATTATCACTATTT
**
6643107 ACTTGTTTATAGTCGTGTTAATTCCTAACTTTGTTATATATATATGCGCATACATACGTATTTAT
245 ACTCATTTAT-GTCGTGTTAATTCCTAACTTTGTTATATATATATGCGCATACATACGTATTTAT
6643172 AATATATATACGTACATAACCTTTTTAATTTATATAGATATAAATACTTATATGATATATATACT
309 AATATATATACGTACATAACCTTTTTAATTTATATAGATATAAATACTTATATGATATATATACT
6643237 TCACACTTACATATTTTTAATTTTCTTATATGTACATATTAACATTTTTATACACTTTGTAATTT
374 TCACACTTACATATTTTTAATTTTCTTATATGTACATATTAACATTTTTATACACTTTGTAATTT
6643302 AC
439 AC
6643304 TTTTATTTAT
Statistics
Matches: 400, Mismatches: 28, Indels: 32
0.87 0.06 0.07
Matches are distributed among these distances:
475 3 0.01
476 6 0.01
477 8 0.02
478 17 0.04
479 23 0.06
480 24 0.06
481 115 0.29
482 18 0.05
483 186 0.47
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.49
Consensus pattern (478 bp):
CATATTTTTTTTAATTTTTATATTATTTACAACTTTATACGTATATATATATACATACATACTCA
TATTTTTTTATATATATTTTATAATTTATGTATACATATATTTATTGCCCATACGATTTATTTAC
TTTCAATTGAACCCTTATTTACTATTGTAATATTAAATTAGCTACTTTAATCATATTACAACTAT
CATCATATTATTATTATCATTATTATAAACAATAACATTATCACTATTTACTCATTTATGTCGTG
TTAATTCCTAACTTTGTTATATATATATGCGCATACATACGTATTTATAATATATATACGTACAT
AACCTTTTTAATTTATATAGATATAAATACTTATATGATATATATACTTCACACTTACATATTTT
TAATTTTCTTATATGTACATATTAACATTTTTATACACTTTGTAATTTACATATATATGTACAGA
CATATTGTTATAGCGTACGTATG
Found at i:6650888 original size:16 final size:17
Alignment explanation
Indices: 6650867--6650901 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6650857 AATTGAAATA
*
6650867 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
6650883 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
6650900 AA
1 AA
6650902 CCCGATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:6654367 original size:31 final size:31
Alignment explanation
Indices: 6654325--6654398 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
6654315 GTCATCTCGA
* * *
6654325 ATTGCCTGACAACAATAACTTACCA-CCCTGG
1 ATTGCCCGACAAAAATAACTTACCATCCC-AG
** *
6654356 ATTGCCCGACAAAAATGGCTTACCATGCCAG
1 ATTGCCCGACAAAAATAACTTACCATCCCAG
6654387 ATTGCCCGACAA
1 ATTGCCCGACAA
6654399 TGATGGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.20
Consensus pattern (31 bp):
ATTGCCCGACAAAAATAACTTACCATCCCAG
Found at i:6655839 original size:23 final size:23
Alignment explanation
Indices: 6655813--6655877 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
6655803 AAAAATGTTT
*
6655813 CAGAATATGTCACAAAGACATTA
1 CAGAATATGACACAAAGACATTA
* * *
6655836 CAGAAT-TCGCCACTAAGGCATTA
1 CAGAATAT-GACACAAAGACATTA
* *
6655859 CGGAATACGACACAAAGAC
1 CAGAATATGACACAAAGAC
6655878 TCTATTTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (23 bp):
CAGAATATGACACAAAGACATTA
Found at i:6672016 original size:2 final size:2
Alignment explanation
Indices: 6672005--6672038 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6671995 TCGGTTACTT
6672005 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6672039 AAGTAACCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6680252 original size:20 final size:22
Alignment explanation
Indices: 6680209--6680256 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6680199 TTTCTTTTTT
* *
6680209 AATTTTATTTAAATTTGAGGTA
1 AATTATATTTAAATTTGAGATA
6680231 AATTATATTTAAATTT-A-ATA
1 AATTATATTTAAATTTGAGATA
6680251 AATTAT
1 AATTAT
6680257 TCGTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTATATTTAAATTTGAGATA
Found at i:6681824 original size:16 final size:16
Alignment explanation
Indices: 6681803--6681833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6681793 AAGAGACATA
*
6681803 TAACCATGTCTTAATG
1 TAACCATCTCTTAATG
6681819 TAACCATCTCTTAAT
1 TAACCATCTCTTAAT
6681834 ACTCTAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (16 bp):
TAACCATCTCTTAATG
Found at i:6682525 original size:11 final size:11
Alignment explanation
Indices: 6682509--6682548 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
6682499 TTCAAAAATT
6682509 CTCTTAAGTTA
1 CTCTTAAGTTA
*
6682520 CTCTTAAGTTC
1 CTCTTAAGTTA
*
6682531 CTCTTAAGTTT
1 CTCTTAAGTTA
6682542 CTCTTAA
1 CTCTTAA
6682549 CTCTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCTTAAGTTA
Found at i:6682575 original size:12 final size:12
Alignment explanation
Indices: 6682555--6682596 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
6682545 TTAACTCTCT
6682555 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
6682567 TTTTAAAAATAT
1 TTTTTAAAATAA
6682579 TTTTTAAAAT--
1 TTTTTAAAATAA
6682589 TTTTTAAA
1 TTTTTAAA
6682597 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:6683537 original size:7 final size:7
Alignment explanation
Indices: 6683525--6683549 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6683515 AGTCGATTGA
6683525 TATTTAG
1 TATTTAG
6683532 TATTTAG
1 TATTTAG
6683539 TATTTAG
1 TATTTAG
6683546 TATT
1 TATT
6683550 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:6684697 original size:25 final size:25
Alignment explanation
Indices: 6684668--6684719 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
6684658 TATTTTAATA
6684668 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
6684693 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
6684718 TT
1 TT
6684720 TTGATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:6684818 original size:45 final size:45
Alignment explanation
Indices: 6684754--6685242 Score: 473
Period size: 45 Copynumber: 11.0 Consensus size: 45
6684744 AACCATTAAT
*
6684754 ACCCTTAAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCTTAA
1 ACCC-TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
***
6684799 ACCCTAAACTTAAAAACCCTAACC-CCCTTAACTTAAAAACCCT-A
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAA
*
6684843 A-CCTAATTAAATTAAAAA-CCTAACCTAATTTAATTAAAAACCCTAA
1 ACCCT-A--AACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*
6684889 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACTCTAA
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*
6684934 ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-A
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
* * *
6684978 A-CCT-AA-TTAAATTAA---AAACCATAA---ACTTAAAAACACTAA
1 ACCCTAAACTTAAA--AACCCTAACC-TAATTTAATTAAAAACCCTAA
* * * *
6685017 CCCCTTAACTTAAAAACCGTAACCTAA-TTAACTTAAAAGCCCT-A
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAA
* *
6685061 A-CCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAA
1 ACCCT-A--AACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
* *
6685108 ACCCTAAACTTAAAAAGCCTAACCTAATTTAATTAAAAA-CTTAA
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
* ***
6685152 ACCCTAAACTTAAAAACTCTAACC-CCCTTAACTTAAAAACCCT-A
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAA
*
6685196 A-CCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 ACCCT-A--AACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
6685243 CCTAATTTAA
Statistics
Matches: 368, Mismatches: 41, Indels: 68
0.77 0.09 0.14
Matches are distributed among these distances:
38 11 0.03
39 1 0.00
40 9 0.02
41 10 0.03
42 10 0.03
43 22 0.06
44 59 0.16
45 157 0.43
46 72 0.20
47 14 0.04
48 3 0.01
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.26
Consensus pattern (45 bp):
ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
Found at i:6684918 original size:135 final size:136
Alignment explanation
Indices: 6684754--6685264 Score: 585
Period size: 135 Copynumber: 3.8 Consensus size: 136
6684744 AACCATTAAT
*
6684754 ACCCTTAAA-TTAAAAACCCTAACCTAATTTAA-TTAAAAACCTTAAACCCT-A-AACTTAAAAA
1 ACCC-TAAACTTAAAAACCCTAACCTAATTTAACTTAAAAACCCT-AA-CCTAATAACTTAAAAA
*** *
6684815 CCCTAACCCCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTAACCTAATTTAATTAA
63 CCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTAACCTAATTTAATTAA
6684880 AAACCCTAA
128 AAACCCTAA
*
6684889 ACCCTAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACTCTAAACCCT-A-AACTTAAAAAC
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAACTTAAAAACCCT-AA-CCTAATAACTTAAAAAC
*
6684951 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACC--A--TAA---ACTTAAA
64 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTAACCTAATTTAATTAAA
*
6685009 AACACTAA
129 AACCCTAA
* * * * *
6685017 CCCCTTAACTTAAAAACCGTAACCTAA-TTAACTTAAAAGCCCTAACCTAATTAAATTAAAAACC
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAACTTAAAAACCCTAACCTAA-TAACTTAAAAACC
* * *
6685081 CTAACCTAATTTAATTAAAAACTCTAAACCCT-A--AACTTAAAAAGCCTAACCTAATTTAATTA
65 CTAACCTAATTAAATTAAAAACCCT-AA-CCTAATTAAATTAAAAA-CCTAACCTAATTTAATTA
*
6685143 AAAA-CTTAA
127 AAAACCCTAA
* ***
6685152 ACCCTAAACTTAAAAACTCTAACC-CCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACC
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAACTTAAAAACCCTAACCTAA-TAACTTAAAAACC
* *
6685216 CTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAACCCTAA
65 CTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTAA
6685265 ACCTTAAACT
Statistics
Matches: 324, Mismatches: 33, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
126 3 0.01
127 7 0.02
128 55 0.17
129 36 0.11
130 3 0.01
131 7 0.02
133 7 0.02
134 7 0.02
135 184 0.57
136 15 0.05
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.26
Consensus pattern (136 bp):
ACCCTAAACTTAAAAACCCTAACCTAATTTAACTTAAAAACCCTAACCTAATAACTTAAAAACCC
TAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTAACCTAATTTAATTAAAAA
CCCTAA
Found at i:6685047 original size:23 final size:23
Alignment explanation
Indices: 6685001--6685319 Score: 290
Period size: 23 Copynumber: 14.1 Consensus size: 23
6684991 AAAAACCATA
* **
6685001 AACTTAAAAACACTAACC-CCTT
1 AACTTAAAAACCCTAACCTAATT
*
6685023 AACTTAAAAACCGTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
*
6685046 AACTTAAAAGCCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
*
6685069 AAATTAAAAACCCTAACCTAATTT
1 AACTTAAAAACCCTAACCTAA-TT
*
6685093 AA-TTAAAAACTCTAAACCCT-A--
1 AACTTAAAAACCCT-AA-CCTAATT
*
6685114 AACTTAAAAAGCCTAACCTAATTT
1 AACTTAAAAACCCTAACCTAA-TT
*
6685138 AA-TTAAAAA-CTTAAACCCT-A--
1 AACTTAAAAACCCT-AA-CCTAATT
* ***
6685158 AACTTAAAAACTCTAACCCCCTT
1 AACTTAAAAACCCTAACCTAATT
6685181 AACTTAAAAACCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
6685204 AACTTAAAAACCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
*
6685227 AAATTAAAAACCCTAACCTAATTT
1 AACTTAAAAACCCTAACCTAA-TT
*
6685251 AA-TT-AAAACCCTAAACCT--TA
1 AACTTAAAAACCCT-AACCTAATT
*
6685271 AACTTAAAAACCCTAACCCAATTT
1 AACTTAAAAACCCTAACCTAA-TT
*
6685295 AA-TTAAAAACCCTAAACTAAATT
1 AACTTAAAAACCCTAACCT-AATT
6685318 AA
1 AA
6685320 TAATTTTACT
Statistics
Matches: 247, Mismatches: 26, Indels: 47
0.77 0.08 0.15
Matches are distributed among these distances:
20 10 0.04
21 20 0.08
22 44 0.18
23 149 0.60
24 21 0.09
25 3 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (23 bp):
AACTTAAAAACCCTAACCTAATT
Found at i:6685320 original size:23 final size:23
Alignment explanation
Indices: 6684761--6685320 Score: 273
Period size: 23 Copynumber: 25.1 Consensus size: 23
6684751 AATACCCTTA
*
6684761 AATTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAAATT
*
6684784 AATTAAAAACCTTAAACCCT-AA--
1 AATTAAAAACCCT-AA-CCTAAATT
* ***
6684806 ACTTAAAAACCCTAACC-CCCTT
1 AATTAAAAACCCTAACCTAAATT
6684828 AACTTAAAAACCCTAACCT-AATT
1 AA-TTAAAAACCCTAACCTAAATT
*
6684851 AAATTAAAAA-CCTAACCTAATTT
1 -AATTAAAAACCCTAACCTAAATT
6684874 AATTAAAAACCCTAAACCCT-AA--
1 AATTAAAAACCCT-AA-CCTAAATT
* *
6684896 ACTTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAAATT
*
6684919 AATTAAAAACTCTAAACCCT-AA--
1 AATTAAAAACCCT-AA-CCTAAATT
*
6684941 ACTTAAAAACCCTAACCT-AATT
1 AATTAAAAACCCTAACCTAAATT
6684963 AAATTAAAAACCCTAACCT-AATT
1 -AATTAAAAACCCTAACCTAAATT
* *
6684986 AAATTAAAAACCATAAACTTAAA--
1 -AATTAAAAACCCT-AACCTAAATT
* * * *
6685009 AA-CACTAACCCCTTAACTTAAA--
1 AATTA-AAAACCC-TAACCTAAATT
**** * *
6685031 AA-CCGTAA-CCTAA-TTAACTT
1 AATTAAAAACCCTAACCTAAATT
*
6685051 AA--A--AGCCCTAACCT-AATT
1 AATTAAAAACCCTAACCTAAATT
*
6685069 AAATTAAAAACCCTAACCTAATTT
1 -AATTAAAAACCCTAACCTAAATT
*
6685093 AATTAAAAACTCTAAACCCT-AA--
1 AATTAAAAACCCT-AA-CCTAAATT
* * *
6685115 ACTTAAAAAGCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAAATT
*
6685138 AATTAAAAA-CTTAAACCCT-AA--
1 AATTAAAAACCCT-AA-CCTAAATT
* * ***
6685159 ACTTAAAAACTCTAACC-CCCTT
1 AATTAAAAACCCTAACCTAAATT
6685181 AACTTAAAAACCCTAACCT-AATT
1 AA-TTAAAAACCCTAACCTAAATT
6685204 AACTTAAAAACCCTAACCT-AATT
1 AA-TTAAAAACCCTAACCTAAATT
*
6685227 AAATTAAAAACCCTAACCTAATTT
1 -AATTAAAAACCCTAACCTAAATT
*
6685251 AATT-AAAACCCTAAACCTTAA--
1 AATTAAAAACCCT-AACCTAAATT
* * *
6685272 ACTTAAAAACCCTAACCCAATTT
1 AATTAAAAACCCTAACCTAAATT
*
6685295 AATTAAAAACCCTAAACTAAATT
1 AATTAAAAACCCTAACCTAAATT
6685318 AAT
1 AAT
6685321 AATTTTACTT
Statistics
Matches: 419, Mismatches: 65, Indels: 106
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.00
18 12 0.03
19 6 0.01
20 19 0.05
21 31 0.07
22 99 0.24
23 208 0.50
24 29 0.07
25 14 0.03
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (23 bp):
AATTAAAAACCCTAACCTAAATT
Found at i:6685413 original size:27 final size:25
Alignment explanation
Indices: 6685383--6685444 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 25
6685373 TAACAATTAA
*
6685383 TAATTTTATATAATTTGATAATTTTAC
1 TAATTTTATACAATTT-ATAA-TTTAC
* *
6685410 TAATCATTAATACAATTTATCATTTAC
1 TAAT--TTTATACAATTTATAATTTAC
6685437 TAATTTTA
1 TAATTTTA
6685445 CATTCACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 3 0.10
27 13 0.45
28 3 0.10
29 10 0.34
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATTTTATACAATTTATAATTTAC
Found at i:6685527 original size:38 final size:39
Alignment explanation
Indices: 6685485--6685777 Score: 106
Period size: 38 Copynumber: 7.6 Consensus size: 39
6685475 TTTTGACTGG
6685485 TACTAACAATTAATA-ATTTTATATAATTTGATAATTTT
1 TACTAACAATTAATACATTTTATATAATTTGATAATTTT
* * * *
6685523 TACTAACCATTAATACAATTTAT-CAA-TTAATAA-TTT
1 TACTAACAATTAATACATTTTATATAATTTGATAATTTT
* * ** * * * * * * * **
6685559 TACATTCACATAATGTTAGATTTGAAAAAATGTT-TTGACTGG
1 TAC--TAACA-ATTAATACATTTTATATAAT-TTGATAATTTT
6685601 TACTAACAATTAATA-ATTTTATATAATTTGATAATTTT
1 TACTAACAATTAATACATTTTATATAATTTGATAATTTT
* * * *
6685639 TACTAACCATTAATACAATTTAT-CAA-TTAATAA-TTT
1 TACTAACAATTAATACATTTTATATAATTTGATAATTTT
* * ** * * * * * * **
6685675 TACATTCACATAATGTTAGATTTGGA-AAAATGTT-TTGACTGG
1 TAC--TAACA-ATTAATACATTT-TATATAAT-TTGATAATTTT
6685717 TACTAACAATTAATA-ATTTTATATAATTTGATAATTTT
1 TACTAACAATTAATACATTTTATATAATTTGATAATTTT
* *
6685755 TACTAACCATTAATACAATTTAT
1 TACTAACAATTAATACATTTTAT
6685778 CAATTAATAA
Statistics
Matches: 174, Mismatches: 60, Indels: 41
0.63 0.22 0.15
Matches are distributed among these distances:
36 12 0.07
37 17 0.10
38 75 0.43
39 41 0.24
40 13 0.07
41 4 0.02
42 12 0.07
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (39 bp):
TACTAACAATTAATACATTTTATATAATTTGATAATTTT
Found at i:6685561 original size:116 final size:116
Alignment explanation
Indices: 6685314--6685790 Score: 857
Period size: 116 Copynumber: 4.1 Consensus size: 116
6685304 CCCTAAACTA
* * **
6685314 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTTCCTGGTACTAACAA
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATG--TTTTGACTGGTACTAACAA
*
6685379 TTAATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
64 TTAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
* *
6685431 ATTTACTAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
6685496 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
6685547 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
6685612 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
*
6685663 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
6685728 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
6685779 AATTAATAATTT
1 AATTAATAATTT
6685791 CACAAACTTA
Statistics
Matches: 349, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
115 42 0.12
116 267 0.77
117 40 0.11
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:6689116 original size:123 final size:123
Alignment explanation
Indices: 6688797--6689171 Score: 590
Period size: 123 Copynumber: 3.0 Consensus size: 123
6688787 GCCCAAAATG
*
6688797 CTACTGTAGCAAAAGCGC-CCACACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
6688861 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTCCATGAC
* * *
6688921 CGACAGTAGCAAAAGCACGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
*
6688986 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
* * * *
6689044 CTACTGTAGCAAAAACGCGTCCATGAGGGCGCGATTTCAAAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
* ** *
6689109 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCCATGAC
6689169 CTA
1 CTA
6689172 AAAACCCTAA
Statistics
Matches: 231, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 116 0.50
124 93 0.40
125 22 0.10
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
Found at i:6690161 original size:37 final size:37
Alignment explanation
Indices: 6690117--6690208 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
6690107 CTTACATTTC
*
6690117 AATTATGT-GTTAATTTC-AAGACTTATTTAATATTTTT
1 AATTATGTAG-TAA-TTCAAAGACTTATGTAATATTTTT
* *
6690154 AATTATGTAGTGATTCAAAGACTTATGTAATGTTTTT
1 AATTATGTAGTAATTCAAAGACTTATGTAATATTTTT
*
6690191 AATTATGTAGTGATTCAA
1 AATTATGTAGTAATTCAA
6690209 TTCGGGTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 3 0.06
37 46 0.92
38 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (37 bp):
AATTATGTAGTAATTCAAAGACTTATGTAATATTTTT
Found at i:6690230 original size:18 final size:19
Alignment explanation
Indices: 6690202--6690237 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6690192 ATTATGTAGT
6690202 GATTCAATTCGGGTAATTC
1 GATTCAATTCGGGTAATTC
*
6690221 GATT-AATTCGGTTAATT
1 GATTCAATTCGGGTAATT
6690238 TTTAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (19 bp):
GATTCAATTCGGGTAATTC
Found at i:6705856 original size:27 final size:27
Alignment explanation
Indices: 6705818--6705876 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
6705808 GCGCCAAAGG
6705818 AGAATATATATAAGCGTGCATAGAGAT
1 AGAATATATATAAGCGTGCATAGAGAT
6705845 AGAATATATATAAGCGTGCATAGAGAT
1 AGAATATATATAAGCGTGCATAGAGAT
6705872 AGAAT
1 AGAAT
6705877 TTTCAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (27 bp):
AGAATATATATAAGCGTGCATAGAGAT
Found at i:6709685 original size:23 final size:22
Alignment explanation
Indices: 6709646--6709688 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
6709636 TAATTAAATG
6709646 AAAAAAAATAATGAGAAAATAT
1 AAAAAAAATAATGAGAAAATAT
6709668 AAAAACAATATAAT-AGAAAAT
1 AAAAA-AA-ATAATGAGAAAAT
6709689 CAAAATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAAAAAATAATGAGAAAATAT
Found at i:6710130 original size:22 final size:23
Alignment explanation
Indices: 6710091--6710151 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
6710081 AATATCCAAA
6710091 CAATAATAATAATAAAAT-AGTAG
1 CAATAATAATAATAAAATGA-TAG
* *
6710114 CAAT-ATAATAGTGAAATGATAG
1 CAATAATAATAATAAAATGATAG
* *
6710136 CAA-AACAATAAAAAAA
1 CAATAATAATAATAAAA
6710152 AGTACAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (23 bp):
CAATAATAATAATAAAATGATAG
Found at i:6710884 original size:36 final size:36
Alignment explanation
Indices: 6710802--6710886 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 36
6710792 CTTGTTATTT
*
6710802 TAAAATTTTAAAGTAAAATATAAAATAAATTTATTGAA
1 TAAAATTTTAAAGTAAAATATAAAATAAA--TATTCAA
*
6710840 -AAATATTTTAAATTAAAAT-TGAATAATAAA-ATTCAA
1 TAAA-ATTTTAAAGTAAAATAT-AA-AATAAATATTCAA
6710876 TAAAATTTTAA
1 TAAAATTTTAA
6710887 TTTTAGTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 12 0.29
37 7 0.17
38 16 0.39
39 6 0.15
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (36 bp):
TAAAATTTTAAAGTAAAATATAAAATAAATATTCAA
Found at i:6717764 original size:17 final size:15
Alignment explanation
Indices: 6717742--6717776 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
6717732 ACCAAATTAC
6717742 AAAAAAGAAACAGAAAA
1 AAAAAAGAAA-A-AAAA
6717759 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
6717774 AAA
1 AAA
6717777 GAGTTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:6717767 original size:11 final size:11
Alignment explanation
Indices: 6717742--6717775 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
6717732 ACCAAATTAC
6717742 AAAAAAGAAACAG
1 AAAAAA-AAA-AG
6717755 AAAAAAAAAAG
1 AAAAAAAAAAG
6717766 AAAAAAAAAA
1 AAAAAAAAAA
6717776 AGAGTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 3 0.14
13 6 0.29
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:6722839 original size:6 final size:6
Alignment explanation
Indices: 6722828--6722852 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6722818 TTGTATTACA
6722828 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
6722853 CAATTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Done.