Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 208 of 214
Found at i:61133433 original size:16 final size:17
Alignment explanation
Indices: 61133407--61133455 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
61133397 TTAAAATGAT
61133407 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
61133422 AAATTTTATAATTTATA
1 AAATTTTATAATTTATA
*
61133439 AAATTTTA-AATTAATA
1 AAATTTTATAATTTATA
61133455 A
1 A
61133456 TAAAATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 7 0.23
16 15 0.48
17 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:61135111 original size:16 final size:15
Alignment explanation
Indices: 61135090--61135133 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
61135080 TGAATTTATC
61135090 GAAATAATTGATTTA
1 GAAATAATTGATTTA
61135105 GGAAATATATTTGATTTA
1 -GAAATA-A-TTGATTTA
*
61135123 AAAATAATTGA
1 GAAATAATTGA
61135134 AATGAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 7 0.28
17 6 0.24
18 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (15 bp):
GAAATAATTGATTTA
Found at i:61135433 original size:14 final size:15
Alignment explanation
Indices: 61135403--61135435 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
61135393 AATAATATTA
61135403 TAATAAACCTAAATT
1 TAATAAACCTAAATT
*
61135418 TAATAAA-CTAATTT
1 TAATAAACCTAAATT
61135432 TAAT
1 TAAT
61135436 GTTATCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAACCTAAATT
Found at i:61140477 original size:31 final size:31
Alignment explanation
Indices: 61140404--61140479 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
61140394 AAAATTCTTT
* * *
61140404 AACAACTCAATGACTTAAATAAAAACTTTCT
1 AACAATTCAATTACTTAAATAAAAACTTTCA
* * *
61140435 AATAGTCCAATTACTTAAATAAAAACTTTCA
1 AACAATTCAATTACTTAAATAAAAACTTTCA
61140466 AACAATTCAATTAC
1 AACAATTCAATTAC
61140480 CATTTCATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (31 bp):
AACAATTCAATTACTTAAATAAAAACTTTCA
Found at i:61144166 original size:46 final size:46
Alignment explanation
Indices: 61144099--61144234 Score: 218
Period size: 46 Copynumber: 3.0 Consensus size: 46
61144089 TGCTATAACT
* *
61144099 CAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCACAACA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
* * *
61144145 CAGTATGATTTTCTTCACTGAAACACTATACCTACTTTTCACAACT
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
*
61144191 CAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCACAA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
61144235 ATTTCCATGA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (46 bp):
CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
Found at i:61144186 original size:24 final size:24
Alignment explanation
Indices: 61144158--61144232 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
61144148 TATGATTTTC
61144158 TTCACTGAAACACTATACCTACTT
1 TTCACTGAAACACTATACCTACTT
* * **
61144182 TTCAC--AACTCAGTATGGCT--TT
1 TTCACTGAA-ACACTATACCTACTT
*
61144203 CTTCACTGAAACACCATACCTACTT
1 -TTCACTGAAACACTATACCTACTT
61144228 TTCAC
1 TTCAC
61144233 AAATTTCCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 13 0.36
24 12 0.33
25 2 0.06
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (24 bp):
TTCACTGAAACACTATACCTACTT
Found at i:61145468 original size:17 final size:17
Alignment explanation
Indices: 61145446--61145493 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
61145436 AAATTCTTTT
61145446 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
61145463 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
61145480 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
61145494 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:61167893 original size:7 final size:7
Alignment explanation
Indices: 61167881--61167912 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
61167871 TTTAAGATAG
61167881 TATTCTA
1 TATTCTA
61167888 TATTCTA
1 TATTCTA
61167895 TATTCTA
1 TATTCTA
61167902 TATTCTA
1 TATTCTA
61167909 TATT
1 TATT
61167913 AAGCCACGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTCTA
Found at i:61168246 original size:5 final size:5
Alignment explanation
Indices: 61168236--61168263 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
61168226 TCAACATGAA
61168236 CCCGG CCCGG CCCGG CCCGG CCCGG CCC
1 CCCGG CCCGG CCCGG CCCGG CCCGG CCC
61168264 AGAATAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.64, G:0.36, T:0.00
Consensus pattern (5 bp):
CCCGG
Found at i:61170465 original size:114 final size:113
Alignment explanation
Indices: 61170266--61170486 Score: 259
Period size: 114 Copynumber: 1.9 Consensus size: 113
61170256 AAACTTCGAA
** * *
61170266 ACGTTCTAATTAATTTATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAATCG
1 ACGTTCTAACCAATTCATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAATCA
* *
61170331 ATGTAAAATATATTAAAAACACTTGTAT-TAAATTTTAAACACGCCAGC
66 ATGTAAAACATATTAAAAACACTTGCATCT-AATTTTAAACACGCCAGC
* * * **
61170379 ACGTTCTAACCAATTCATCAAAATA-CTAGATATCATATCAATCATGTCTTTCTATCAACTTAA-
1 ACGTTCTAACCAATTCATCAAAATATC-A-ATATAATATCAATCAAGTCATTCTATCAACCAAAT
** *
61170442 CTAATGTGGAACATATTAAAAACATTTGCATCTAATTTTAAACAC
64 C-AATGTAAAACATATTAAAAACACTTGCATCTAATTTTAAACAC
61170487 ACGTGCACTG
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
112 1 0.01
113 24 0.27
114 64 0.71
115 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (113 bp):
ACGTTCTAACCAATTCATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAATCA
ATGTAAAACATATTAAAAACACTTGCATCTAATTTTAAACACGCCAGC
Found at i:61176543 original size:30 final size:30
Alignment explanation
Indices: 61176507--61176569 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
61176497 GCACGATAAA
*
61176507 CAACATTAGACAAATATCATAAAACCATTT
1 CAACATTAGACAAATATCATAAAACCAGTT
61176537 CAACATTAGACAAATATCATAAAACCAGTT
1 CAACATTAGACAAATATCATAAAACCAGTT
61176567 CAA
1 CAA
61176570 ACTTAATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.24
Consensus pattern (30 bp):
CAACATTAGACAAATATCATAAAACCAGTT
Found at i:61180810 original size:31 final size:31
Alignment explanation
Indices: 61180775--61180834 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
61180765 AATTTGGTTT
*
61180775 TTGAACTATTCGAATGTTTTCATTTAAGTAA
1 TTGAACTATTCAAATGTTTTCATTTAAGTAA
* *
61180806 TTGAACTATTCAAATTTTTTTATTTAAGT
1 TTGAACTATTCAAATGTTTTCATTTAAGT
61180835 CACTAGGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (31 bp):
TTGAACTATTCAAATGTTTTCATTTAAGTAA
Found at i:61183752 original size:15 final size:15
Alignment explanation
Indices: 61183732--61183760 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61183722 ATAAATCCAG
61183732 AAAAAAAACTTTAAA
1 AAAAAAAACTTTAAA
61183747 AAAAAAAACTTTAA
1 AAAAAAAACTTTAA
61183761 CCTTCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAAAACTTTAAA
Found at i:61190071 original size:12 final size:12
Alignment explanation
Indices: 61190054--61190085 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
61190044 CAGTGTCTTC
61190054 TAATTACACAAT
1 TAATTACACAAT
61190066 TAATTACACAAT
1 TAATTACACAAT
*
61190078 TAAGTACA
1 TAATTACA
61190086 TATGGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (12 bp):
TAATTACACAAT
Found at i:61193116 original size:31 final size:31
Alignment explanation
Indices: 61193058--61193117 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
61193048 CTTTACTTTG
*
61193058 GTCAAGTTTAGTCATTGCAATTTTCAAATAT
1 GTCAAGTTTAGTCATTGCAATTCTCAAATAT
* *
61193089 GTCAATTTTAGTCATTAG-ACTTCTCAAAT
1 GTCAAGTTTAGTCATT-GCAATTCTCAAAT
61193118 TTTGAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
GTCAAGTTTAGTCATTGCAATTCTCAAATAT
Found at i:61198132 original size:60 final size:61
Alignment explanation
Indices: 61198020--61198181 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 61
61198010 TTTTTTAGGA
* * ** * *
61198020 CTAACTTAGACAACAAAAAAA-TTCAAGTCCTAATGTTG-GAACGTTTGCCAAGTTCAGGGC
1 CTAACTTAAACAACAAAAAAAGTTCAAGTCCTAAT-ATGAGAACAATTGCCAAGTTCAAGAC
** * * *
61198080 CTAACTTGGAC-TCAAAAAAAGTTCAAGCCCTAATATGAGAACAATTGTCAAGTTCAAGAC
1 CTAACTTAAACAACAAAAAAAGTTCAAGTCCTAATATGAGAACAATTGCCAAGTTCAAGAC
* * *
61198140 CTAATTTAAACAAAAAAAAAAGTTCAAGTCCTAATGTGAGAA
1 CTAACTTAAACAACAAAAAAAGTTCAAGTCCTAATATGAGAA
61198182 AAGTTACCAA
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 10 0.12
60 47 0.57
61 26 0.31
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (61 bp):
CTAACTTAAACAACAAAAAAAGTTCAAGTCCTAATATGAGAACAATTGCCAAGTTCAAGAC
Found at i:61201997 original size:5 final size:5
Alignment explanation
Indices: 61201987--61202012 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61201977 AAATGTATAA
61201987 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
61202013 CTCATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:61205950 original size:13 final size:14
Alignment explanation
Indices: 61205885--61205953 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 14
61205875 TTATTGCTTT
61205885 ATATAAATATAATAA
1 ATATAAAT-TAATAA
*
61205900 ATAT-AAGTAATAA
1 ATATAAATTAATAA
* **
61205913 TGTCATTAAAAGAATAA
1 -AT-A-TAAATTAATAA
61205930 ATATAAATTAATAA
1 ATATAAATTAATAA
61205944 A-ATAAATTAA
1 ATATAAATTAA
61205954 AAGCAAAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 15 0.35
14 13 0.30
15 6 0.14
16 2 0.05
17 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (14 bp):
ATATAAATTAATAA
Found at i:61208555 original size:15 final size:16
Alignment explanation
Indices: 61208528--61208557 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61208518 TTTGATTTTA
61208528 TCGATTAAATTTTAAC
1 TCGATTAAATTTTAAC
61208544 TCGATT-AATTTTAA
1 TCGATTAAATTTTAA
61208558 AGGAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (16 bp):
TCGATTAAATTTTAAC
Found at i:61221464 original size:21 final size:21
Alignment explanation
Indices: 61221438--61221489 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
61221428 TTTTTTTTAA
61221438 TTTTAAAATA-TTTTAAAATAT
1 TTTTAAAATACTTTTAAAA-AT
*
61221459 TTTTAAAATACTTTTTAAAAT
1 TTTTAAAATACTTTTAAAAAT
61221480 TTTTAAAATA
1 TTTTAAAATA
61221490 AATTTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAATACTTTTAAAAAT
Found at i:61221475 original size:12 final size:11
Alignment explanation
Indices: 61221438--61221489 Score: 74
Period size: 10 Copynumber: 4.9 Consensus size: 11
61221428 TTTTTTTTAA
61221438 TTTTAAAATA-
1 TTTTAAAATAT
61221448 TTTTAAAATAT
1 TTTTAAAATAT
61221459 TTTTAAAATACT
1 TTTTAAAATA-T
61221471 TTTT-AAA-AT
1 TTTTAAAATAT
61221480 TTTTAAAATA
1 TTTTAAAATA
61221490 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.13
10 14 0.37
11 14 0.37
12 5 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:61221495 original size:21 final size:22
Alignment explanation
Indices: 61221438--61221495 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
61221428 TTTTTTTTAA
61221438 TTTTAAAAT-ATTTTAAAATAT
1 TTTTAAAATAATTTTAAAATAT
* *
61221459 TTTTAAAATACTTTTTAAA-AT
1 TTTTAAAATAATTTTAAAATAT
61221480 TTTTAAAATAAATTTT
1 TTTTAAAAT-AATTTT
61221496 TGGTATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAATAATTTTAAAATAT
Found at i:61221503 original size:22 final size:22
Alignment explanation
Indices: 61221438--61221514 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
61221428 TTTTTTTTAA
*
61221438 TTTTAAAAT--ATTTTAAAATAT
1 TTTTAAAATAAATTTT-TAATAT
* *
61221459 TTTTAAAAT-ACTTTTTAAAAT
1 TTTTAAAATAAATTTTTAATAT
**
61221480 TTTTAAAATAAATTTTTGGTAT
1 TTTTAAAATAAATTTTTAATAT
61221502 TTATTAAAA-AAAT
1 TT-TTAAAATAAAT
61221515 AGGCCGGGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 22 0.48
22 18 0.39
23 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTTAAAATAAATTTTTAATAT
Found at i:61223325 original size:16 final size:16
Alignment explanation
Indices: 61223306--61223346 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
61223296 AATTTGATAC
61223306 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
61223322 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
61223338 AGTTTTAAT
1 AATTTTAAT
61223347 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:61223348 original size:22 final size:23
Alignment explanation
Indices: 61223320--61223381 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
61223310 TTAATAACAA
* * *
61223320 TTAATTTTGATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
61223342 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
61223365 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
61223382 ACTGGCCGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:61236113 original size:28 final size:27
Alignment explanation
Indices: 61236071--61236128 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
61236061 TTGAACTTGC
61236071 ATTTTTAAAACTAAAAAAAAAAACTTAA
1 ATTTTTAAAACTAAAAAAAAAAAC-TAA
*
61236099 ATTTCTTAAAA-TAAAAATAAAAACTAA
1 ATTT-TTAAAACTAAAAAAAAAAACTAA
61236126 ATT
1 ATT
61236129 CTAAATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 16 0.57
29 6 0.21
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTTTAAAACTAAAAAAAAAAACTAA
Found at i:61240243 original size:27 final size:27
Alignment explanation
Indices: 61240178--61240243 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
61240168 CATTAAAGCT
*
61240178 AAACTCAAGTGCTTAATTTGAAAAAAA
1 AAACTCAAGTACTTAATTTGAAAAAAA
*
61240205 AAACAT-AGGTACTTAATTTGAAAAAAA
1 AAAC-TCAAGTACTTAATTTGAAAAAAA
*
61240232 AAACTCATGTAC
1 AAACTCAAGTAC
61240244 CAAATTGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.26
Consensus pattern (27 bp):
AAACTCAAGTACTTAATTTGAAAAAAA
Found at i:61240249 original size:27 final size:27
Alignment explanation
Indices: 61240192--61240249 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
61240182 TCAAGTGCTT
**
61240192 AATTTGAAAAAAAAAACATAGGTACTT
1 AATTTGAAAAAAAAAACATAGGTACCA
*
61240219 AATTTGAAAAAAAAAAC-TCATGTACCA
1 AATTTGAAAAAAAAAACAT-AGGTACCA
61240246 AATT
1 AATT
61240250 GATCATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (27 bp):
AATTTGAAAAAAAAAACATAGGTACCA
Found at i:61240256 original size:85 final size:84
Alignment explanation
Indices: 61240115--61240280 Score: 314
Period size: 85 Copynumber: 2.0 Consensus size: 84
61240105 GTGTTCAAGT
*
61240115 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAACTCATGTTCCAAATTGATCATTAAAGCTAA
1 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTAA
61240180 ACTCAAGTGCTTAATTTGA
66 ACTCAAGTGCTTAATTTGA
61240199 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
1 AAAAAAAAACATAGGTACTTAATTTG-AAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
61240264 AACTCAAGTGCTTAATT
65 AACTCAAGTGCTTAATT
61240281 GGGACAAATG
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 26 0.32
85 54 0.68
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (84 bp):
AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTAA
ACTCAAGTGCTTAATTTGA
Found at i:61240374 original size:31 final size:32
Alignment explanation
Indices: 61240332--61240392 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
61240322 AGGTATAAAT
*
61240332 TTGAATATTGAAACC-AAATTCAAGTACTAGA
1 TTGAATATTGAAACCAAAACTCAAGTACTAGA
* *
61240363 TTGAATTTTGAAGCCAAAACTCAAGTACTA
1 TTGAATATTGAAACCAAAACTCAAGTACTA
61240393 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (32 bp):
TTGAATATTGAAACCAAAACTCAAGTACTAGA
Found at i:61248298 original size:12 final size:12
Alignment explanation
Indices: 61248281--61248307 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61248271 GGATAAGGAT
61248281 GTTTTAATTATA
1 GTTTTAATTATA
61248293 GTTTTAATTATA
1 GTTTTAATTATA
61248305 GTT
1 GTT
61248308 GTACTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (12 bp):
GTTTTAATTATA
Found at i:61252008 original size:114 final size:114
Alignment explanation
Indices: 61251817--61252063 Score: 424
Period size: 114 Copynumber: 2.2 Consensus size: 114
61251807 TCAAAGAAAA
* *
61251817 ACAAC-AACAACAAGAAGAAAACTATTGGTGGTGAACATATTATTGAAGGGTTAAGTGATAACAA
1 ACAACGAACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAA
61251881 GGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGT
66 GGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGT
* * * *
61251930 GCAATGAACAAGAAGAAGAGAACTGTTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAA
1 ACAACGAACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAA
61251995 GGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGT
66 GGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGT
*
61252044 ACAACGAAGAAGAAGAAGAA
1 ACAACGAACAAGAAGAAGAA
61252064 GAAGAAGAAG
Statistics
Matches: 123, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 3 0.02
114 120 0.98
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (114 bp):
ACAACGAACAAGAAGAAGAAAACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAA
GGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGT
Found at i:61252057 original size:3 final size:3
Alignment explanation
Indices: 61252049--61252078 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
61252039 AGGGTACAAC
61252049 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
61252079 AACTATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:61252169 original size:129 final size:129
Alignment explanation
Indices: 61251939--61252195 Score: 426
Period size: 129 Copynumber: 2.0 Consensus size: 129
61251929 TGCAATGAAC
* * *
61251939 AAGAAGAAGAGAACTGTTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAAT
1 AAGAAGAAGAAAACTATTGGTAGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAAT
*
61252004 GGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAGAAG
66 GGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAGAAG
* * *
61252068 AAGAAGAAGAAAACTATTGGTAGTGAACA-TTGTATTGAAGGGTTAAGTGATAGCAGGGTTGAAA
1 AAGAAGAAGAAAACTATTGGTAGTGAACAGAT-TATTGAAGGGTTAAGTGATAACAAGGTTGAAA
*
61252132 TGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAACGAAGAAGAAGAAGAAGAA
65 TGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAGAA
61252196 AACTATTGGT
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
128 1 0.01
129 118 0.99
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (129 bp):
AAGAAGAAGAAAACTATTGGTAGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAAT
GGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAGAAG
Found at i:61252194 original size:117 final size:117
Alignment explanation
Indices: 61252061--61252416 Score: 541
Period size: 117 Copynumber: 3.0 Consensus size: 117
61252051 AGAAGAAGAA
* ** *
61252061 GAAGAAGAAGAAGAAGAAAACTATTGGTAGTGAACATTGTATTGAAGGGTTAAGTGATAGCAGGG
1 GAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGG
*
61252126 TTGAAATGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAAC
66 TTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAAC
61252178 GAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGG
1 GAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGG
* *
61252243 TTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT
66 TTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAAC
* * * * * *
61252295 GAACAAGAAGAAGAAGAAAACTATTGGTGGTGAGCAGAGTATTGAAGTGTTTAGTAATAGCAAGG
1 GAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGG
61252360 TTGAAATGGAAGATCCCCTTAAAGCCAATCCTAAACGTGGTCGGCCAAAGGGTTCAA
66 TTGAAATGGAAGATCCCCTT-AAG-----CCTAAACGTGGTCGGCCAAAGGGTTCAA
61252417 AGAATAAACA
Statistics
Matches: 219, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
117 189 0.86
118 3 0.01
123 27 0.12
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (117 bp):
GAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGG
TTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAAC
Found at i:61279034 original size:18 final size:18
Alignment explanation
Indices: 61279011--61279047 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
61279001 TAGTTGTGTT
*
61279011 TGAATCCAAACTCATATC
1 TGAATCCAAACCCATATC
61279029 TGAATCCAAACCCATATC
1 TGAATCCAAACCCATATC
61279047 T
1 T
61279048 CACCGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (18 bp):
TGAATCCAAACCCATATC
Found at i:61279106 original size:21 final size:21
Alignment explanation
Indices: 61279059--61279109 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
61279049 ACCGATGTTT
* * *
61279059 CTAATCTCATTACTACAGTAT
1 CTAATCTCATCACTACAATAA
* *
61279080 CCAATCTCATCGCTACAATAA
1 CTAATCTCATCACTACAATAA
61279101 CTAATCTCA
1 CTAATCTCA
61279110 CCGCCACCAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (21 bp):
CTAATCTCATCACTACAATAA
Found at i:61279289 original size:22 final size:22
Alignment explanation
Indices: 61279261--61279304 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
61279251 TGGTCCCTTT
61279261 GTAATACCCCGAAAATTCCTAC
1 GTAATACCCCGAAAATTCCTAC
61279283 GTAATACCCCGAAAATTCCTAC
1 GTAATACCCCGAAAATTCCTAC
61279305 AATAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (22 bp):
GTAATACCCCGAAAATTCCTAC
Found at i:61281771 original size:51 final size:51
Alignment explanation
Indices: 61281712--61281808 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
61281702 TTATATATTT
* *
61281712 TGTGTAAATATTGC-ATGATAAATTTGTTGAAT-TAGAACCAATTTGATAGCA
1 TGTGTAAATATTGCGA-GATAAATTTGTTAAATCAAG-ACCAATTTGATAGCA
* *
61281763 TGTGTAAATGTTGCGAGCTAAATTTGTTAAATCAAGACCAATTTGA
1 TGTGTAAATATTGCGAGATAAATTTGTTAAATCAAGACCAATTTGA
61281809 CAGAAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
51 37 0.93
52 3 0.08
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (51 bp):
TGTGTAAATATTGCGAGATAAATTTGTTAAATCAAGACCAATTTGATAGCA
Found at i:61283202 original size:29 final size:30
Alignment explanation
Indices: 61283163--61283234 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
61283153 ACTTTCGAAT
* *
61283163 ATTT-AAAATTTAGTTCTTAT-ATTTTTAT
1 ATTTAAAAATTTAGTCCTTATAATTTTTAG
* * *
61283191 TTTTAAAAATTTAATCCTTTTAATTTTTAG
1 ATTTAAAAATTTAGTCCTTATAATTTTTAG
61283221 ATTTAAAAATTTAG
1 ATTTAAAAATTTAG
61283235 ATCTAATTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 3 0.09
29 13 0.37
30 19 0.54
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (30 bp):
ATTTAAAAATTTAGTCCTTATAATTTTTAG
Found at i:61293634 original size:25 final size:27
Alignment explanation
Indices: 61293563--61293634 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 27
61293553 TAAATAAAAA
61293563 AATAAAATAGTATATTAATAT-ATATAAGT
1 AATAAAAT--TATA-TAATATAATATAAGT
61293592 AATAAAATTATA-AA-ATAATATAA-T
1 AATAAAATTATATAATATAATATAAGT
61293616 AAT-AAATTATATAATATAA
1 AATAAAATTATATAATATAA
61293635 ATAGTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
23 8 0.20
24 8 0.20
25 12 0.30
27 4 0.10
29 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AATAAAATTATATAATATAATATAAGT
Found at i:61294064 original size:20 final size:19
Alignment explanation
Indices: 61294039--61294079 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
61294029 AACATAATGA
* *
61294039 TATATAATATATATTTTTAT
1 TATATAAT-TACATATTTAT
61294059 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
61294078 TA
1 TA
61294080 GTTGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:61294114 original size:15 final size:15
Alignment explanation
Indices: 61294086--61294119 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
61294076 ATTAGTTGAT
61294086 TTTATAAATAAAAAA
1 TTTATAAATAAAAAA
*
61294101 TTTATTAATTAAAAAA
1 TTTA-TAAATAAAAAA
61294117 TTT
1 TTT
61294120 TGAAACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTATAAATAAAAAA
Found at i:61297848 original size:83 final size:83
Alignment explanation
Indices: 61297706--61297866 Score: 286
Period size: 83 Copynumber: 1.9 Consensus size: 83
61297696 GTAACAATAA
**
61297706 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAATTGTTGAGACCTATTTAACACAGTTTCCTCA
1 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
61297771 AAATAGTAGCACTTTGTT
66 AAATAGTAGCACTTTGTT
* *
61297789 GTTGAAAACGACAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACATAGTTTCCTCA
1 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
61297854 AAATAGTAGCACT
66 AAATAGTAGCACT
61297867 ATGTGTAACA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (83 bp):
GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
AAATAGTAGCACTTTGTT
Found at i:61302763 original size:23 final size:23
Alignment explanation
Indices: 61302736--61302898 Score: 184
Period size: 23 Copynumber: 7.1 Consensus size: 23
61302726 AACTGCCACG
61302736 CTGATATGTAGCCGAAGCTACCA
1 CTGATATGTAGCCGAAGCTACCA
* ** *
61302759 GTGATACATAGCCGTAGCTACCA
1 CTGATATGTAGCCGAAGCTACCA
* * *
61302782 CTGAAATGTAGCCAAATCTACCA
1 CTGATATGTAGCCGAAGCTACCA
* *
61302805 CTGATACGTAGCC-ATAGCTAGCA
1 CTGATATGTAGCCGA-AGCTACCA
* *
61302828 CTGAAATGTAGCCGGAGCTACCA
1 CTGATATGTAGCCGAAGCTACCA
*
61302851 CTGATATGTAGCCGTAGCTACCA
1 CTGATATGTAGCCGAAGCTACCA
* *
61302874 CTGAAATATAGCCGAAGCTACCA
1 CTGATATGTAGCCGAAGCTACCA
61302897 CT
1 CT
61302899 AATCAATAAC
Statistics
Matches: 114, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
22 1 0.01
23 113 0.99
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CTGATATGTAGCCGAAGCTACCA
Found at i:61302794 original size:46 final size:46
Alignment explanation
Indices: 61302736--61302898 Score: 236
Period size: 46 Copynumber: 3.5 Consensus size: 46
61302726 AACTGCCACG
* * *
61302736 CTGATATGTAGCCGAAGCTACCAGTGATACATAGCCGTAGCTACCA
1 CTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCA
* * * *
61302782 CTGAAATGTAGCCAAATCTACCACTGATACGTAGCCATAGCTAGCA
1 CTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCA
* *
61302828 CTGAAATGTAGCCGGAGCTACCACTGATATGTAGCCGTAGCTACCA
1 CTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCA
*
61302874 CTGAAATATAGCCGAAGCTACCACT
1 CTGAAATGTAGCCGAAGCTACCACT
61302899 AATCAATAAC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 102 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (46 bp):
CTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCA
Found at i:61303152 original size:18 final size:17
Alignment explanation
Indices: 61303126--61303164 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
61303116 ATTTTCCTTC
61303126 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
61303143 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
61303161 CACA
1 CACA
61303165 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:61307267 original size:30 final size:31
Alignment explanation
Indices: 61307233--61307291 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
61307223 GTAAATACTC
* * *
61307233 AAAATATGATGGGCTAA-AGTGTAAATATGA
1 AAAATATGAAGGACCAATAGTGTAAATATGA
*
61307263 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATATGAAGGACCAATAGTGTAAATAT
61307292 TTTAAGGGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
AAAATATGAAGGACCAATAGTGTAAATATGA
Found at i:61310434 original size:24 final size:24
Alignment explanation
Indices: 61310407--61310454 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61310397 CATTTATATG
61310407 TTTAAAAATAATAAAA-ATATTTTA
1 TTTAAAAAT-ATAAAATATATTTTA
*
61310431 TTTAAATATATAAAATTATATTTT
1 TTTAAAAATATAAAA-TATATTTT
61310455 TGTTATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAAAAATATAAAATATATTTTA
Found at i:61310562 original size:14 final size:14
Alignment explanation
Indices: 61310543--61310573 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
61310533 GAAACTTGAA
61310543 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
61310557 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
61310571 AAG
1 AAG
61310574 TCTCGCTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AAGAAAGATTCTGG
Found at i:61314448 original size:25 final size:25
Alignment explanation
Indices: 61314420--61314468 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
61314410 AGAGAAAAGT
*
61314420 TTAAAGAACATAAAATAAAAAAAAA
1 TTAAAGAACATAAAACAAAAAAAAA
** *
61314445 TTAAATTACTTAAAACAAAAAAAA
1 TTAAAGAACATAAAACAAAAAAAA
61314469 TATGGGAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (25 bp):
TTAAAGAACATAAAACAAAAAAAAA
Found at i:61316903 original size:27 final size:25
Alignment explanation
Indices: 61316872--61316924 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
61316862 AGTTTATTTT
*
61316872 TTATATA-AAAATAAATTTAAAAATA
1 TTATATATAAAATAAA-CTAAAAATA
*
61316897 TTATATATAAAATACACTAAAAATA
1 TTATATATAAAATAAACTAAAAATA
61316922 TTA
1 TTA
61316925 AAATAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
TTATATATAAAATAAACTAAAAATA
Found at i:61317859 original size:21 final size:22
Alignment explanation
Indices: 61317835--61317882 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
61317825 ATTTTGTTTT
*
61317835 ATTTTAGTC-ATTTAATTA-TTA
1 ATTTT-GTCGATTTAATCATTTA
*
61317856 ATTTTTTCGATTTAATCATTTA
1 ATTTTGTCGATTTAATCATTTA
61317878 ATTTT
1 ATTTT
61317883 TGAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTTTGTCGATTTAATCATTTA
Found at i:61318478 original size:10 final size:10
Alignment explanation
Indices: 61318463--61318488 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
61318453 GACCCACATC
61318463 ATAAAAAATT
1 ATAAAAAATT
61318473 ATAAAAAATT
1 ATAAAAAATT
61318483 ATAAAA
1 ATAAAA
61318489 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:61319646 original size:20 final size:20
Alignment explanation
Indices: 61319621--61319661 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
61319611 GGTGGTACGT
*
61319621 ACATATT-TACAATTTGATCC
1 ACATATTGTA-AATATGATCC
61319641 ACATATTGTAAATATGATCC
1 ACATATTGTAAATATGATCC
61319661 A
1 A
61319662 TGTCGCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
ACATATTGTAAATATGATCC
Found at i:61320546 original size:32 final size:32
Alignment explanation
Indices: 61320499--61320575 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
61320489 GTGTAAATTG
*
61320499 ATACATG-AACTTTGATT-CGGTGCAATTATAT
1 ATACATGAAACTTTGATTGCGGTGCAA-AATAT
* * *
61320530 ATACATGAAACTTTGATTGTGGTTCAAAATGT
1 ATACATGAAACTTTGATTGCGGTGCAAAATAT
61320562 ATACATGAAACTTT
1 ATACATGAAACTTT
61320576 CATTTTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 27 0.68
33 6 0.15
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
ATACATGAAACTTTGATTGCGGTGCAAAATAT
Found at i:61328925 original size:17 final size:17
Alignment explanation
Indices: 61328903--61328936 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61328893 TATTAATATC
*
61328903 ATTTTAATAATTTGAAA
1 ATTTTAATAATTAGAAA
*
61328920 ATTTTATTAATTAGAAA
1 ATTTTAATAATTAGAAA
61328937 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTTAATAATTAGAAA
Found at i:61331275 original size:21 final size:19
Alignment explanation
Indices: 61331233--61331277 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
61331223 ATAATTTTGG
* *
61331233 TAAATTTTACCCTTAATCT
1 TAAATTTTACCCTGAATAT
61331252 TAAATTTTAAACCCTGAATAT
1 TAAATTTT--ACCCTGAATAT
61331273 TAAAT
1 TAAAT
61331278 CCTGAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAATTTTACCCTGAATAT
Found at i:61331281 original size:14 final size:14
Alignment explanation
Indices: 61331258--61331297 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61331248 ATCTTAAATT
61331258 TTAAACCCTGAATA
1 TTAAACCCTGAATA
* *
61331272 TTAAATCCTGAATC
1 TTAAACCCTGAATA
*
61331286 TTAAACCTTGAA
1 TTAAACCCTGAA
61331298 CAAGAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (14 bp):
TTAAACCCTGAATA
Found at i:61347813 original size:15 final size:16
Alignment explanation
Indices: 61347783--61347815 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61347773 TTGATATATA
61347783 ATATTTGAAAATTTTT
1 ATATTTGAAAATTTTT
*
61347799 ATATTT-AATATTTTT
1 ATATTTGAAAATTTTT
61347814 AT
1 AT
61347816 TAAAGTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATTTGAAAATTTTT
Found at i:61353106 original size:33 final size:33
Alignment explanation
Indices: 61353039--61353107 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
61353029 GAAACACCAT
*
61353039 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATATTAAAC
*
61353072 CACCACCCATAAATACTGAACCACATGA-TAAAC
1 CACCACCCACAAATACTGAACCACAT-ATTAAAC
61353105 CAC
1 CAC
61353108 ATATTGAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.36, G:0.06, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATATTAAAC
Found at i:61362252 original size:20 final size:19
Alignment explanation
Indices: 61362200--61362256 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
61362190 ATTACACATT
61362200 AAAA-ATATATAA-A-AAA
1 AAAATATATATAATATAAA
*
61362216 TAAATATATATAATATAGAA
1 AAAATATATATAATATA-AA
61362236 AAAATATATA-AATTATAAA
1 AAAATATATATAA-TATAAA
61362255 AA
1 AA
61362257 TTTATGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 1 0.03
19 7 0.21
20 15 0.44
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATATATAATATAAA
Found at i:61363915 original size:18 final size:18
Alignment explanation
Indices: 61363887--61363924 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
61363877 TTATTGTATT
*
61363887 TTCATTTTGTTATTTTTAG
1 TTCATTTTGTT-TTTTAAG
61363906 TTCA-TTTGTTTTTTAAG
1 TTCATTTTGTTTTTTAAG
61363923 TT
1 TT
61363925 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (18 bp):
TTCATTTTGTTTTTTAAG
Found at i:61373305 original size:76 final size:76
Alignment explanation
Indices: 61373215--61373363 Score: 298
Period size: 76 Copynumber: 2.0 Consensus size: 76
61373205 TTGGGCGCTA
61373215 AAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGGTTT
1 AAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGGTTT
61373280 CCTTCCTGGCT
66 CCTTCCTGGCT
61373291 AAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGGTTT
1 AAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGGTTT
61373356 CCTTCCTG
66 CCTTCCTG
61373364 TTTTTATATA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (76 bp):
AAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGGTTT
CCTTCCTGGCT
Found at i:61385547 original size:20 final size:20
Alignment explanation
Indices: 61385503--61385540 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61385493 AATACAATTT
61385503 ATATTTTAATAATAAATAAA
1 ATATTTTAATAATAAATAAA
61385523 ATATTTT-ATAATTAAATA
1 ATATTTTAATAA-TAAATA
61385541 GATTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTTAATAATAAATAAA
Found at i:61397640 original size:20 final size:20
Alignment explanation
Indices: 61397615--61397657 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
61397605 TAATTATAGT
61397615 AATTATATATGTTA-AATAAA
1 AATTATATAT-TTATAATAAA
*
61397635 AATTATATATTTATATTAAA
1 AATTATATATTTATAATAAA
61397655 AAT
1 AAT
61397658 CACTAACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTATATATTTATAATAAA
Found at i:61397812 original size:39 final size:41
Alignment explanation
Indices: 61397753--61397841 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 41
61397743 AAAAATTATA
* * * *
61397753 TTTAATACAATAAAATATTTATTATA-TT-TGTTTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
*
61397792 TTTAATATAATTAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
61397833 TTTAATATA
1 TTTAATATA
61397842 TTTCTAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 23 0.53
40 2 0.05
41 18 0.42
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (41 bp):
TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
Found at i:61398954 original size:15 final size:16
Alignment explanation
Indices: 61398930--61398972 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
61398920 TCCAACAGTA
* *
61398930 GGTTTTGGGTTTTTAG
1 GGTTTAGGGTTTTAAG
61398946 GG-TTAGGG-TTTAAG
1 GGTTTAGGGTTTTAAG
61398960 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
61398973 GAAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.30
15 11 0.48
16 5 0.22
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.49
Consensus pattern (16 bp):
GGTTTAGGGTTTTAAG
Found at i:61399399 original size:125 final size:125
Alignment explanation
Indices: 61399089--61399531 Score: 688
Period size: 125 Copynumber: 3.5 Consensus size: 125
61399079 GATAAAATCA
* * *
61399089 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGTCACGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
61399154 AGGTCCTGGAAAAATAATTTCAAGTTGACGTTTCTAAGAAAATAGTATAAAAAAAGGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAAACGCTTC
* * * * *
61399215 AAGCAAGATGCTTTATTAGAAGAATTTATGAAATCCCGCCCTCGTGAACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
61399280 AGGTCCTGGAAAAATAATTTTGAGTTCACGTTTCTGAGTAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* * *
61399340 AAGCAGGATGCTTTATCAGAAGAATTTTTGAAATCGCGCCTTCGTGGACGCGCTTTTGCTACAAT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
61399405 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* * *
61399465 AAGCAGGATACTTTATCAGAAGAATTTCTGAAATTGCGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
61399530 AG
66 AG
61399532 CATGTTTGGG
Statistics
Matches: 288, Mismatches: 29, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
125 187 0.65
126 101 0.35
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:61402236 original size:16 final size:16
Alignment explanation
Indices: 61402215--61402248 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
61402205 GACTTAAAAG
61402215 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
61402231 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
61402247 TT
1 TT
61402249 GAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:61403751 original size:27 final size:26
Alignment explanation
Indices: 61403712--61403807 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
61403702 AATTTAAAAG
* *
61403712 TTAAAACATTATATTAAAACAATATAA
1 TTAAAAAAGTATATTAAAACAATAT-A
* *
61403739 TTATAATAGTATATTAAAACAATATA
1 TTAAAAAAGTATATTAAAACAATATA
* * *
61403765 TTAAAAAAGTATATTTATAATAGTATA
1 TTAAAAAAGTATA-TTAAAACAATATA
61403792 TTAAAACAA-TATATTA
1 TTAAAA-AAGTATATTA
61403808 TAAATTTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 15 0.25
27 42 0.71
28 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (26 bp):
TTAAAAAAGTATATTAAAACAATATA
Found at i:61403757 original size:40 final size:40
Alignment explanation
Indices: 61403712--61403807 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 40
61403702 AATTTAAAAG
*
61403712 TTAAAACATTATATTAAAACAA-TATAATTATAATAGTATA
1 TTAAAACAATATATTAAAA-AAGTATAATTATAATAGTATA
*
61403752 TTAAAACAATATATTAAAAAAGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAAAAGTATAATTATAATAGTATA
61403792 TTAAAACAATATATTA
1 TTAAAACAATATATTA
61403808 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 2 0.04
40 51 0.96
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (40 bp):
TTAAAACAATATATTAAAAAAGTATAATTATAATAGTATA
Found at i:61403844 original size:13 final size:13
Alignment explanation
Indices: 61403712--61403845 Score: 96
Period size: 13 Copynumber: 10.2 Consensus size: 13
61403702 AATTTAAAAG
*
61403712 TTAAAACATTATA
1 TTAAAACAGTATA
*
61403725 TTAAAACAATATAA
1 TTAAAACAGTAT-A
* *
61403739 TTATAATAGTATA
1 TTAAAACAGTATA
*
61403752 TTAAAACAATATA
1 TTAAAACAGTATA
*
61403765 TTAAAAAAGTATA
1 TTAAAACAGTATA
* *
61403778 TTTATAATAGTATA
1 -TTAAAACAGTATA
*
61403792 TTAAAACAATATA
1 TTAAAACAGTATA
*
61403805 TTATAA-A-T-T-
1 TTAAAACAGTATA
*
61403814 TTATAACAGTATATTA
1 TTAAAACAG--TA-TA
61403830 TTAAAACAGTATA
1 TTAAAACAGTATA
61403843 TTA
1 TTA
61403846 CATTAAAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.06
10 2 0.02
11 1 0.01
12 1 0.01
13 54 0.56
14 23 0.24
15 1 0.01
16 8 0.08
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:61403979 original size:15 final size:15
Alignment explanation
Indices: 61403959--61403992 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
61403949 AAACTAAAAT
*
61403959 TTAATGTGTTAGAAA
1 TTAATGTGTTACAAA
61403974 TTAATGTGTTACAAA
1 TTAATGTGTTACAAA
61403989 TTAA
1 TTAA
61403993 ATGTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (15 bp):
TTAATGTGTTACAAA
Found at i:61404067 original size:27 final size:26
Alignment explanation
Indices: 61404028--61404123 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 26
61404018 AATTTAAAAG
* *
61404028 TTAAAAAATTATATTAAAAAAATATAA
1 TTAAAACAGTATATTAAAAAAATAT-A
* *
61404055 TTATAACAGTATATTAAAACAATATA
1 TTAAAACAGTATATTAAAAAAATATA
* * * * *
61404081 TTAAAAAAATATATTTATAATAGTATA
1 TTAAAACAGTATA-TTAAAAAAATATA
61404108 TTAAAACAGTATATTA
1 TTAAAACAGTATATTA
61404124 TAAATTTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 14 0.25
27 42 0.75
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (26 bp):
TTAAAACAGTATATTAAAAAAATATA
Found at i:61404073 original size:40 final size:39
Alignment explanation
Indices: 61404028--61404123 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 39
61404018 AATTTAAAAG
61404028 TTAAAAAATTATATTAAAAAAATATAATTATAACAGTATA
1 TTAAAAAA-TATATTAAAAAAATATAATTATAACAGTATA
* *
61404068 TTAAAACAATATATTAAAAAAATATATTTATAATAGTATA
1 TTAAAA-AATATATTAAAAAAATATAATTATAACAGTATA
*
61404108 TTAAAACAGTATATTA
1 TTAAAA-AATATATTA
61404124 TAAATTTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (39 bp):
TTAAAAAATATATTAAAAAAATATAATTATAACAGTATA
Found at i:61404092 original size:11 final size:13
Alignment explanation
Indices: 61404028--61404123 Score: 86
Period size: 13 Copynumber: 7.2 Consensus size: 13
61404018 AATTTAAAAG
61404028 TTAAAA-AATTATA
1 TTAAAACAA-TATA
*
61404041 TTAAAAAAATATAA
1 TTAAAACAATAT-A
* *
61404055 TTATAACAGTATA
1 TTAAAACAATATA
61404068 TTAAAACAATATA
1 TTAAAACAATATA
*
61404081 TTAAAAAAATATA
1 TTAAAACAATATA
* * *
61404094 TTTATAATAGTATA
1 -TTAAAACAATATA
*
61404108 TTAAAACAGTATA
1 TTAAAACAATATA
61404121 TTA
1 TTA
61404124 TAAATTTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
13 47 0.68
14 22 0.32
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (13 bp):
TTAAAACAATATA
Found at i:61404293 original size:15 final size:15
Alignment explanation
Indices: 61404273--61404306 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
61404263 AAACTAAAAT
*
61404273 TTAATGTGTTAGAAA
1 TTAATGTGTTACAAA
61404288 TTAATGTGTTACAAA
1 TTAATGTGTTACAAA
61404303 TTAA
1 TTAA
61404307 ATGTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (15 bp):
TTAATGTGTTACAAA
Found at i:61404360 original size:13 final size:13
Alignment explanation
Indices: 61404342--61404433 Score: 132
Period size: 13 Copynumber: 7.0 Consensus size: 13
61404332 AATTTAAAAG
*
61404342 TTAAAACATTATA
1 TTAAAACAATATA
61404355 TTAAAACAATATAA
1 TTAAAACAATAT-A
*
61404369 TTATAACAATATA
1 TTAAAACAATATA
*
61404382 TTATAACAATATA
1 TTAAAACAATATA
61404395 TTAAAACAATATA
1 TTAAAACAATATA
61404408 TTAAAA-AAGTATA
1 TTAAAACAA-TATA
61404421 TTAAAACAATATA
1 TTAAAACAATATA
61404434 ACCGAACTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
12 2 0.03
13 57 0.78
14 14 0.19
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.34
Consensus pattern (13 bp):
TTAAAACAATATA
Found at i:61404376 original size:314 final size:315
Alignment explanation
Indices: 61403658--61404433 Score: 1396
Period size: 316 Copynumber: 2.5 Consensus size: 315
61403648 ACATCAACAT
*
61403658 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATATTAAAATTTAAAAGTTAAAACATTA
1 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAACATTA
* *
61403723 TATTAAAACAATATAATTATAATAGTATATTAAAACAATATATTAAAAAAGTATATTTATAATAG
66 TATTAAAACAATATAATTATAACAGTATATTAAAACAATATATTAAAAAAATATATTTATAATAG
*
61403788 TATATTAAAACAATATATTATAAATTTTATAACAGTATATTATTAAAACAGTATATTACATTAAA
131 TATATTAAAACAATATATTATAAATTTTATAACAATATATTATTAAAACAGTATATTACATTAAA
61403853 AATTATTGTTTTAATCAAAAAATTAACAATATTAATTATTTAGTTAATAACATTAAAAAATATAA
196 AATTATTGTTTTAATCAAAAAATTAACAATATTAATTATTTAGTT-ATAACATTAAAAAATATAA
61403918 GCACCATTTTATGTTAAAAAATAAAGTATAGAAACTAAAATTTAATGTGTTAGAAA
260 GCACCATTTTATGTTAAAAAATAAAGTATAGAAACTAAAATTTAATGTGTTAGAAA
*
61403974 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAAAATTA
1 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAACATTA
*
61404039 TATTAAAAAAATATAATTATAACAGTATATTAAAACAATATATTAAAAAAATATATTTATAATAG
66 TATTAAAACAATATAATTATAACAGTATATTAAAACAATATATTAAAAAAATATATTTATAATAG
* *
61404104 TATATTAAAACAGTATATTATAAATTTTTTAACAATATATTATTAAAACAGTATATTACATTAAA
131 TATATTAAAACAATATATTATAAATTTTATAACAATATATTATTAAAACAGTATATTACATTAAA
61404169 AATTATTGTTTTAATCAAAAAATTAACAATATTAATTATTTAG-T-TAACATTACAAAAATATAA
196 AATTATTGTTTTAATCAAAAAATTAACAATATTAATTATTTAGTTATAACATTA-AAAAATATAA
61404232 GCACCATTTTATGTTAAAAAATAAAGTATAGAAACTAAAATTTAATGTGTTAGAAA
260 GCACCATTTTATGTTAAAAAATAAAGTATAGAAACTAAAATTTAATGTGTTAGAAA
61404288 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAACATTA
1 TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAACATTA
* * * * *
61404353 TATTAAAACAATATAATTATAACAATATATTATAACAATATATTAAAACAATATA-TTAAAAAAG
66 TATTAAAACAATATAATTATAACAGTATATTAAAACAATATATTAAAAAAATATATTTATAATAG
61404417 TATATTAAAACAATATA
131 TATATTAAAACAATATA
61404434 ACCGAACTCA
Statistics
Matches: 443, Mismatches: 16, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
313 31 0.07
314 181 0.41
315 1 0.00
316 230 0.52
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (315 bp):
TTAATGTGTTACAAATTAAATGTATATTTATAACAGTATACTAAAATTTAAAAGTTAAAACATTA
TATTAAAACAATATAATTATAACAGTATATTAAAACAATATATTAAAAAAATATATTTATAATAG
TATATTAAAACAATATATTATAAATTTTATAACAATATATTATTAAAACAGTATATTACATTAAA
AATTATTGTTTTAATCAAAAAATTAACAATATTAATTATTTAGTTATAACATTAAAAAATATAAG
CACCATTTTATGTTAAAAAATAAAGTATAGAAACTAAAATTTAATGTGTTAGAAA
Found at i:61404643 original size:5 final size:5
Alignment explanation
Indices: 61404635--61404660 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61404625 GAGATGGAAT
61404635 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
61404661 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:61404660 original size:26 final size:26
Alignment explanation
Indices: 61404609--61404660 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
61404599 TGAAGTTTTC
* * *
61404609 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
61404635 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
61404661 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:61405587 original size:9 final size:9
Alignment explanation
Indices: 61405571--61405607 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
61405561 TATAGTTTGA
61405571 TATTCGAAT
1 TATTCGAAT
*
61405580 TGTTCGAAT
1 TATTCGAAT
*
61405589 TATTCGAGT
1 TATTCGAAT
61405598 TATTCGAAT
1 TATTCGAAT
61405607 T
1 T
61405608 CGAAAACTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61407967 original size:51 final size:51
Alignment explanation
Indices: 61407906--61408003 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
61407896 AAAAAATTAA
61407906 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTAAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTAAGAGCAAATTGAAATT
* * * *
61407957 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTAAGAGCAAATTGA
61408004 GAGCAAATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTAAGAGCAAATTGAAATT
Found at i:61407979 original size:11 final size:10
Alignment explanation
Indices: 61407967--61408031 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 10
61407957 AAATATGGAT
61407967 TTGAGAGAAA
1 TTGAGAGAAA
61407977 TTTG-GAAGGAAA
1 -TTGAG-A-GAAA
61407989 TTGAGAGCAAA
1 TTGAGAG-AAA
61408000 TTGAGAGCAAA
1 TTGAGAG-AAA
61408011 TTGAGAGCAAA
1 TTGAGAG-AAA
61408022 TTGAGA-AAA
1 TTGAGAGAAA
61408031 T
1 T
61408032 AATTGAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.08
10 2 0.04
11 39 0.78
12 5 0.10
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:61407992 original size:22 final size:23
Alignment explanation
Indices: 61407967--61408027 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
61407957 AAATATGGAT
*
61407967 TTGAGAG-AAATTTG-GAAGGAAA
1 TTGAGAGCAAATTTGAG-AGCAAA
61407989 TTGAGAGCAAA-TTGAGAGCAAA
1 TTGAGAGCAAATTTGAGAGCAAA
61408011 TTGAGAGCAAA-TTGAGA
1 TTGAGAGCAAATTTGAGA
61408028 AAATAATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.30, T:0.21
Consensus pattern (23 bp):
TTGAGAGCAAATTTGAGAGCAAA
Found at i:61414710 original size:72 final size:72
Alignment explanation
Indices: 61414593--61414733 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
61414583 CTCTCTGTTG
* * **
61414593 TTCCTGGTTCTCCCATAACTGGAACCACAAGATTTTTTAGTTAGAATGGAATTTCAACTCAAAAT
1 TTCCTGATTCTCCCATAACTAGAACCACAAGATTTTTTAGTTAGAATGGAATACCAACTCAAAAT
61414658 TTTTCCA
66 TTTTCCA
*
61414665 TTCCTGATTCTTCCATAACTAGAACCACAAGATTTTTTAGTTAGAATGGAATACCAACTCAAAAT
1 TTCCTGATTCTCCCATAACTAGAACCACAAGATTTTTTAGTTAGAATGGAATACCAACTCAAAAT
61414730 TTTT
66 TTTT
61414734 TGAGATTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (72 bp):
TTCCTGATTCTCCCATAACTAGAACCACAAGATTTTTTAGTTAGAATGGAATACCAACTCAAAAT
TTTTCCA
Found at i:61426067 original size:19 final size:19
Alignment explanation
Indices: 61426030--61426067 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61426020 TTTAAGTATC
*
61426030 TATTTCAATTTTAATAGTA
1 TATTTCAATTTTAAAAGTA
61426049 TATTT-AATTTGTAAAAGTA
1 TATTTCAATTT-TAAAAGTA
61426068 GTGATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TATTTCAATTTTAAAAGTA
Found at i:61427019 original size:24 final size:24
Alignment explanation
Indices: 61426992--61427043 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61426982 TTAGTAAGTC
*
61426992 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
61427016 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
61427040 AAAT
1 AAAT
61427044 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:61428990 original size:24 final size:24
Alignment explanation
Indices: 61428963--61429014 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61428953 TTAGTAAGAC
*
61428963 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
61428987 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
61429011 AAAT
1 AAAT
61429015 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:61439474 original size:16 final size:16
Alignment explanation
Indices: 61439453--61439491 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
61439443 ATAATCTTAG
61439453 TTTTTTTAGATATGAT
1 TTTTTTTAGATATGAT
* *
61439469 TTTTTTTAGCTATTAT
1 TTTTTTTAGATATGAT
*
61439485 CTTTTTT
1 TTTTTTT
61439492 CTTAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTTTTTAGATATGAT
Found at i:61441005 original size:4 final size:4
Alignment explanation
Indices: 61440996--61441035 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
61440986 ATTCAAGGTG
61440996 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
61441036 TTAGTATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:61441315 original size:4 final size:4
Alignment explanation
Indices: 61441308--61441337 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
61441298 TATGATATAG
61441308 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
61441338 GAAATAACAG
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:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:61444604 original size:15 final size:16
Alignment explanation
Indices: 61444579--61444608 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61444569 ATGCTCGATA
61444579 ACTTTATTTTTATTTC
1 ACTTTATTTTTATTTC
61444595 ACTTTA-TTTTATTT
1 ACTTTATTTTTATTT
61444609 TATTTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (16 bp):
ACTTTATTTTTATTTC
Found at i:61448901 original size:13 final size:13
Alignment explanation
Indices: 61448883--61448907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61448873 GACCGCGACA
61448883 ATTTTAATTTTTT
1 ATTTTAATTTTTT
61448896 ATTTTAATTTTT
1 ATTTTAATTTTT
61448908 ACTTTCTTAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:61449507 original size:96 final size:92
Alignment explanation
Indices: 61449338--61449520 Score: 228
Period size: 96 Copynumber: 1.9 Consensus size: 92
61449328 GGCCACCACC
*
61449338 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATTCTGACAGGAAAAAAAGTAAAAAAATT
1 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATTCTGACACGAAAAAAAGT---AAAA-T
61449403 TTTGTTTTACTGTACTGGGTGCTGGCTTGTT
62 TTTGTTTTACTGTACTGGGTGCTGGCTTGTT
61449434 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATACCTGATACTGACACGAAAAAAAGT-A
1 AAATTTTTTTTTACTTTTTTCGTATACTGATACCTG--A--T--T-CTGACACGAAAAAAAGTAA
*
61449498 AA-TTT-TTTTATTGTACTGGGTGC
59 AATTTTGTTTTACTGTACTGGGTGC
61449521 CGGCCATTGA
Statistics
Matches: 78, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
96 53 0.68
97 3 0.04
98 1 0.01
99 3 0.04
100 1 0.01
102 1 0.01
103 16 0.21
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (92 bp):
AAATTTTTTTTTACTTTTTTCGTATACTGATACCTGATTCTGACACGAAAAAAAGTAAAATTTTG
TTTTACTGTACTGGGTGCTGGCTTGTT
Found at i:61459419 original size:19 final size:21
Alignment explanation
Indices: 61459381--61459419 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
61459371 CTTTTTTTAA
*
61459381 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
61459402 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
61459420 AACAGTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:61459620 original size:23 final size:22
Alignment explanation
Indices: 61459577--61459634 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
61459567 AAAGGGTATC
* *
61459577 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
61459598 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
61459621 TACATATCATATCT
1 TACAAATCATATCT
61459635 AAAATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:61459645 original size:19 final size:19
Alignment explanation
Indices: 61459613--61459668 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
61459603 AATCATATCT
*
61459613 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
61459632 TCTAAAATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
61459653 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
61459669 TTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:61459650 original size:21 final size:21
Alignment explanation
Indices: 61459624--61459667 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
61459614 CTAAGATTAC
61459624 ATATCATATCTAAAATTGCAT
1 ATATCATATCTAAAATTGCAT
*
61459645 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAAATTGCAT
61459666 AT
1 AT
61459668 CTTCGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAAATTGCAT
Found at i:61468239 original size:4 final size:4
Alignment explanation
Indices: 61468230--61468260 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
61468220 TTTCATACTT
61468230 GATA GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GATA GAT
61468261 GCTATTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:61470167 original size:11 final size:11
Alignment explanation
Indices: 61470151--61470179 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
61470141 AAACAAAGTC
61470151 ACATAAGAACA
1 ACATAAGAACA
61470162 ACATAAGAACA
1 ACATAAGAACA
61470173 ACATAAG
1 ACATAAG
61470180 CTGCAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.10
Consensus pattern (11 bp):
ACATAAGAACA
Found at i:61473181 original size:21 final size:21
Alignment explanation
Indices: 61473157--61473219 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
61473147 GAATTGAGTA
61473157 ATTTTTAATATTAATTTTT-AT
1 ATTTTT-ATATTAATTTTTAAT
*
61473178 ATTTTT-TATATATTTTTCTAAT
1 ATTTTTATAT-TAATTTT-TAAT
61473200 ATTCTATTATATTAATTTTT
1 ATT-T-TTATATTAATTTTT
61473220 TTCGTAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 7 0.21
22 5 0.15
23 2 0.06
24 8 0.24
25 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTATATTAATTTTTAAT
Found at i:61475104 original size:46 final size:45
Alignment explanation
Indices: 61475026--61475164 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 45
61475016 ACATTGCTAT
* *
61475026 AACTCAGTATGGTTTTCTTCCCGGAAATACCATACCTACAGTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC-GTTCAC
* *
61475072 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC-GTTCAC
*
61475118 AACTCAGTATGGTTTTCTTCACTAAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACG-TTCAC
61475164 A
1 A
61475165 CTTTGCCATG
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTCAC
Found at i:61478562 original size:4 final size:4
Alignment explanation
Indices: 61478555--61478608 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
61478545 TGTTTATCAC
* * * * *
61478555 GTAT GTAT GTAT GAAT GTAT GTAT GTGT ATAT ATAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
61478603 GTAT GT
1 GTAT GT
61478609 GCAGGGATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:61478618 original size:28 final size:28
Alignment explanation
Indices: 61478560--61478618 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
61478550 ATCACGTATG
* * *
61478560 TATGTATGAATGTATGTATGTGTATATA
1 TATGTATGAATGTATGTATGTGCAGAGA
* *
61478588 TATGTATGCATGTATGTATGTGCAGGGA
1 TATGTATGAATGTATGTATGTGCAGAGA
61478616 TAT
1 TAT
61478619 ATTGACATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.25, T:0.42
Consensus pattern (28 bp):
TATGTATGAATGTATGTATGTGCAGAGA
Found at i:61488804 original size:31 final size:32
Alignment explanation
Indices: 61488754--61488814 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
61488744 TTTTTAAATT
*
61488754 TAGAAAATATTAGTTTACTTTTTGATCTAATG
1 TAGAAAATATTAATTTACTTTTTGATCTAATG
*
61488786 TAGAAAA-ATTAATTTACTTTTTGGTCTAA
1 TAGAAAATATTAATTTACTTTTTGATCTAA
61488815 CATAGGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (32 bp):
TAGAAAATATTAATTTACTTTTTGATCTAATG
Found at i:61491996 original size:23 final size:23
Alignment explanation
Indices: 61491961--61492005 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61491951 TCTTATTTAA
**
61491961 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
61491984 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
61492006 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:61495896 original size:92 final size:91
Alignment explanation
Indices: 61495739--61495947 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
61495729 TTGATTTTAG
* * *
61495739 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
61495804 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
61495831 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
61495895 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
61495923 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
61495948 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:61495910 original size:24 final size:25
Alignment explanation
Indices: 61495875--61495922 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
61495865 TTATGAAATT
61495875 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
61495899 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
61495923 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:61496092 original size:120 final size:120
Alignment explanation
Indices: 61495963--61496255 Score: 441
Period size: 120 Copynumber: 2.4 Consensus size: 120
61495953 AATTATTTTA
* * *
61495963 AATTTTATTAAATCATATATTTTAATTAAAATATATGAT-ATATTAATCAT-TTCAAATTT-TCA
1 AATTTTATTAAATTATATATTTTAATTATAATATAT-ATAATAATAATCATGTT--AATTTAT-A
*
61496025 -TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
61496083 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATCATGTTAATTTATATTTT
61496148 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
61496203 AATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATCATGTT
61496256 TAAATATGAT
Statistics
Matches: 162, Mismatches: 7, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
119 7 0.04
120 153 0.94
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATATAATAATAATCATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:61496123 original size:15 final size:15
Alignment explanation
Indices: 61496088--61496139 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
61496078 TTAAGAATTT
*
61496088 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61496102 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
61496116 TATTTAATAATAAT-
1 TATTTAATTATAATA
61496130 TATGTTAATT
1 TAT-TTAATT
61496140 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61496242 original size:15 final size:15
Alignment explanation
Indices: 61496208--61496249 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61496198 TTAAGAATTT
*
61496208 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61496222 -ATTTAATTATAATA
1 TATTTAATTATAATA
*
61496236 TATTTAATAATAAT
1 TATTTAATTATAAT
61496250 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61496370 original size:157 final size:157
Alignment explanation
Indices: 61496192--61496508 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
61496182 ATAAGAATAT
*
61496192 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
* *
61496257 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
61496322 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
61496349 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
61496414 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
61496479 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
61496506 TAA
1 TAA
61496509 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:61496389 original size:18 final size:17
Alignment explanation
Indices: 61496361--61496395 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61496351 ATTATTAAGA
*
61496361 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61496378 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61496396 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61496652 original size:16 final size:16
Alignment explanation
Indices: 61496631--61496666 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
61496621 GATTTACTAT
61496631 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
61496647 TACACCTCTTATCCAA
1 TACACCTCTAATCCAA
61496663 TACA
1 TACA
61496667 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:61499152 original size:25 final size:25
Alignment explanation
Indices: 61499124--61499200 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
61499114 ACCTTAGCGC
61499124 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* * * *
61499149 GCTCTTTGATTATTAGTACGTTAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
61499174 GCTCTCCG---ATTAGCACATCTGT
1 GCTCTCTGATTATTAGCACATCAGT
61499196 GCTCT
1 GCTCT
61499201 TTGTATAGCA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
22 15 0.36
25 27 0.64
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:61499233 original size:47 final size:49
Alignment explanation
Indices: 61499124--61499233 Score: 108
Period size: 47 Copynumber: 2.3 Consensus size: 49
61499114 ACCTTAGCGC
*
61499124 GCTCTCTGATT-ATTAGCACATCAGTGCTCTTTGATTATTAGTACGTTAGT
1 GCTCTCT-ATTCATTAGCACATCAGTGCTCTTTGA-TATTAGCACGTTAGT
* * *
61499174 GCTCTC----CGATTAGCACATCTGTGCTCTTTG-TA-TAGCACTTTGGT
1 GCTCTCTATTC-ATTAGCACATCAGTGCTCTTTGATATTAGCACGTTAGT
61499218 GCTCTCTATTCATTAG
1 GCTCTCTATTCATTAG
61499234 TGCATAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
44 15 0.30
45 2 0.04
47 26 0.52
48 1 0.02
50 6 0.12
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (49 bp):
GCTCTCTATTCATTAGCACATCAGTGCTCTTTGATATTAGCACGTTAGT
Found at i:61506396 original size:6 final size:6
Alignment explanation
Indices: 61506385--61506432 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
61506375 ACAATTTTAA
61506385 ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC
1 ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC ACTCAC
61506433 TATACACTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
ACTCAC
Found at i:61510450 original size:23 final size:22
Alignment explanation
Indices: 61510383--61510456 Score: 100
Period size: 21 Copynumber: 3.5 Consensus size: 22
61510373 CCTGATCAGT
* *
61510383 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
61510404 A-ACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
61510424 ATACGACACACGAGGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
61510446 TATACGACACA
1 -ATACGACACA
61510457 TAAAGTGCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.19
21 28 0.60
23 10 0.21
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Done.