Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 128 of 313
Found at i:41370478 original size:13 final size:13
Alignment explanation
Indices: 41370459--41370523 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
41370449 TCTTAACATA
41370459 TTAATTTAAATTT
1 TTAATTTAAATTT
*
41370472 TTTATTTAAAATTT
1 TTAATTT-AAATTT
**
41370486 ATATAATTTAAACAT
1 -T-TAATTTAAATTT
*
41370501 TTAATTTTAATTT
1 TTAATTTAAATTT
*
41370514 TTTATTTAAA
1 TTAATTTAAA
41370524 AATTATATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
13 23 0.57
14 7 0.17
15 5 0.12
16 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
TTAATTTAAATTT
Found at i:41370513 original size:42 final size:42
Alignment explanation
Indices: 41370453--41370552 Score: 164
Period size: 42 Copynumber: 2.3 Consensus size: 42
41370443 TCAATCTCTT
* *
41370453 AACATATTAATTTAAATTTTTTATTTAAAATTTATATAATTTA
1 AACAT-TTAATTTTAATTTTTTATTTAAAAATTATATAATTTA
41370496 AACATTTAATTTTAATTTTTTATTTAAAAATTATATAATTTA
1 AACATTTAATTTTAATTTTTTATTTAAAAATTATATAATTTA
41370538 AACATTTTAATTTTA
1 AACA-TTTAATTTTA
41370553 GCCACAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 39 0.72
43 15 0.28
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (42 bp):
AACATTTAATTTTAATTTTTTATTTAAAAATTATATAATTTA
Found at i:41371430 original size:125 final size:126
Alignment explanation
Indices: 41371174--41371431 Score: 367
Period size: 125 Copynumber: 2.1 Consensus size: 126
41371164 ACCTCACACC
41371174 CCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAAAAACATCAACTCGAAATTATTTCTTCTAAGA
1 CCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAAAAACATCAACTCGAAATTATTTCTTCTAAGA
* * * *
41371239 CCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGAAT
66 CCAACTGTAGCAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGAAT
* * * *
41371300 CCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTC-CAGT
1 CCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAAAAACATCAACTCGAAATTATTTCTTCTAAG-
* * * * **
41371363 ACCTACTTTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCAT
65 ACCAACTGTAGCAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGAAT
41371425 CCTGCTT
1 CCTGCTT
41371432 TGATTTTATC
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
124 2 0.02
125 62 0.53
126 53 0.45
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (126 bp):
CCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAAAAACATCAACTCGAAATTATTTCTTCTAAGA
CCAACTGTAGCAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGAAT
Found at i:41371559 original size:9 final size:9
Alignment explanation
Indices: 41371545--41371573 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
41371535 ACTTTTTTCC
41371545 AAAAACCCT
1 AAAAACCCT
41371554 AAAAACCCT
1 AAAAACCCT
41371563 AAAAACCCT
1 AAAAACCCT
41371572 AA
1 AA
41371574 GGTGGTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAACCCT
Found at i:41378633 original size:56 final size:56
Alignment explanation
Indices: 41378547--41378656 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
41378537 CACAAAACGA
*
41378547 CGCCGTTTTACCCTTAGGGGTCAGGTGCCAAAACGACGCCGTTTTGGCCCTGACGG
1 CGCCGTTTTACCCTTAGGGGTCAAGTGCCAAAACGACGCCGTTTTGGCCCTGACGG
*
41378603 CGCCGTTTTACCCTTAGGGGTCAAGTGCCAAAACGACGCCGTTTTGGCCTTGAC
1 CGCCGTTTTACCCTTAGGGGTCAAGTGCCAAAACGACGCCGTTTTGGCCCTGAC
41378657 CCGCGCGGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (56 bp):
CGCCGTTTTACCCTTAGGGGTCAAGTGCCAAAACGACGCCGTTTTGGCCCTGACGG
Found at i:41379188 original size:3 final size:3
Alignment explanation
Indices: 41379180--41379219 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41379170 TTATTTAGCG
41379180 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
41379220 ATTATTAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:41379532 original size:24 final size:24
Alignment explanation
Indices: 41379503--41379549 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41379493 ACGCCTTTAT
*
41379503 TATATACTTACATCTATAAATATA
1 TATATACTTACATATATAAATATA
41379527 TATATACTTACATATATAAATAT
1 TATATACTTACATATATAAATAT
41379550 GCTTTCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (24 bp):
TATATACTTACATATATAAATATA
Found at i:41379655 original size:28 final size:27
Alignment explanation
Indices: 41379623--41379700 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 27
41379613 TTATATTCTT
41379623 CATATTTCATA-ATTTTTATATACATA
1 CATATTTCATATATTTTTATATACATA
* * *
41379649 CGTATATGTACATATTTTTTTATATATATA
1 C--ATAT-TTCATATATTTTTATATACATA
41379679 CATATTT-ATATATTCTTTATAT
1 CATATTTCATATATT-TTTATAT
41379701 TTTAAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.17
27 8 0.19
28 8 0.19
29 5 0.12
30 14 0.33
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (27 bp):
CATATTTCATATATTTTTATATACATA
Found at i:41379710 original size:21 final size:21
Alignment explanation
Indices: 41379686--41379725 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41379676 ATACATATTT
* *
41379686 ATATATTCTTTATATTTTAAA
1 ATATATTATATATATTTTAAA
41379707 ATATATTATATATATTTTA
1 ATATATTATATATATTTTA
41379726 TAATTCACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTATATATATTTTAAA
Found at i:41380992 original size:20 final size:20
Alignment explanation
Indices: 41380967--41381006 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41380957 AATATTTTCC
*
41380967 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41380987 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41381007 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41381012 original size:34 final size:34
Alignment explanation
Indices: 41380955--41381020 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
41380945 CAAACACCAG
*
41380955 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
41380990 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
41381021 ATATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:41386832 original size:21 final size:21
Alignment explanation
Indices: 41386806--41386847 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41386796 TTTATCTGTA
41386806 AAATTTAGAGTATGAATTTTG
1 AAATTTAGAGTATGAATTTTG
41386827 AAATTTAGAGTATGAATTTTG
1 AAATTTAGAGTATGAATTTTG
41386848 GTTAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
AAATTTAGAGTATGAATTTTG
Found at i:41402873 original size:63 final size:63
Alignment explanation
Indices: 41402774--41403025 Score: 425
Period size: 63 Copynumber: 4.0 Consensus size: 63
41402764 GCAATAATAG
*
41402774 AAAGAGACAAAGGAA-CAGTATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACCA-TATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
41402837 AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
* *
41402900 AAAGAGAGAAAGGAACCATCTGCACAGTAAGAGTTCATCAAACAAACCAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
* * * *
41402963 AAAGAGAGAAAGGAACCATCTGCACAGTAAGAGTTCATCAAATAAACGAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
41403026 TGCTGTTTGC
Statistics
Matches: 183, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
63 181 0.99
64 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (63 bp):
AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
Found at i:41405197 original size:2 final size:2
Alignment explanation
Indices: 41405190--41405217 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41405180 CATTAGGTTC
41405190 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41405218 TTATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41408826 original size:13 final size:13
Alignment explanation
Indices: 41408808--41408833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41408798 TTAAGGTTTT
41408808 CAAAATCGGATTG
1 CAAAATCGGATTG
41408821 CAAAATCGGATTG
1 CAAAATCGGATTG
41408834 ATGGTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAAATCGGATTG
Found at i:41409268 original size:18 final size:18
Alignment explanation
Indices: 41409245--41409283 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
41409235 CAAGGAGGTC
41409245 CTAAAAAGGACCATGATG
1 CTAAAAAGGACCATGATG
*
41409263 CTAAAATGGACCATGATG
1 CTAAAAAGGACCATGATG
41409281 CTA
1 CTA
41409284 TCTTTGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (18 bp):
CTAAAAAGGACCATGATG
Found at i:41418815 original size:22 final size:22
Alignment explanation
Indices: 41418790--41418841 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
41418780 CTGTTTTTTC
* *
41418790 ATTATTTTGCTATCATTTTGTT
1 ATTATATTACTATCATTTTGTT
*
41418812 ATTATATTACTATTATTTTGTT
1 ATTATATTACTATCATTTTGTT
*
41418834 GTTA-ATTA
1 ATTATATTA
41418842 TTGGATATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.62
Consensus pattern (22 bp):
ATTATATTACTATCATTTTGTT
Found at i:41419483 original size:15 final size:15
Alignment explanation
Indices: 41419463--41419500 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
41419453 CATTGCAGAA
41419463 AGAAGTAAGAAGCAT
1 AGAAGTAAGAAGCAT
41419478 AGAAGTAAGAAGCAT
1 AGAAGTAAGAAGCAT
41419493 AGAAGTAA
1 AGAAGTAA
41419501 AACAAGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.05, G:0.26, T:0.13
Consensus pattern (15 bp):
AGAAGTAAGAAGCAT
Found at i:41421619 original size:4 final size:4
Alignment explanation
Indices: 41421612--41421655 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
41421602 AATACGCATG
41421612 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
41421656 TTAACTGACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:41425223 original size:31 final size:29
Alignment explanation
Indices: 41425182--41425239 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
41425172 AAATTATATA
41425182 TATTTATATTTATAAATTTTAAATATTTTTT
1 TATTTATATTTAT-AATTTTAAAT-TTTTTT
* * *
41425213 TATTTTTATTTGTATTTTTAAATTTTT
1 TATTTATATTTATAATTTTAAATTTTT
41425240 GTCACATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 9 0.38
31 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (29 bp):
TATTTATATTTATAATTTTAAATTTTTTT
Found at i:41429948 original size:25 final size:26
Alignment explanation
Indices: 41429906--41429956 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
41429896 ATATAAGGTA
*
41429906 TACATGATAGATTAAATTTTTAATAG
1 TACATGATAAATTAAATTTTTAATAG
*
41429932 TACA-GATAAATTGAATTTTTAATAG
1 TACATGATAAATTAAATTTTTAATAG
41429957 AAAAGACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (26 bp):
TACATGATAAATTAAATTTTTAATAG
Found at i:41429968 original size:25 final size:25
Alignment explanation
Indices: 41429911--41429962 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
41429901 AGGTATACAT
* * * *
41429911 GATAGATTAAATTTTTAATAGTACA
1 GATAAATTGAATTTTTAATAGAAAA
41429936 GATAAATTGAATTTTTAATAGAAAA
1 GATAAATTGAATTTTTAATAGAAAA
41429961 GA
1 GA
41429963 CTAATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (25 bp):
GATAAATTGAATTTTTAATAGAAAA
Found at i:41443271 original size:16 final size:16
Alignment explanation
Indices: 41443250--41443282 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41443240 TACCTGCAAT
41443250 GATCCATATGCATGGG
1 GATCCATATGCATGGG
41443266 GATCCATATGCATGGG
1 GATCCATATGCATGGG
41443282 G
1 G
41443283 CAGTTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (16 bp):
GATCCATATGCATGGG
Found at i:41444199 original size:188 final size:188
Alignment explanation
Indices: 41443872--41444221 Score: 486
Period size: 188 Copynumber: 1.9 Consensus size: 188
41443862 CATCTCCTGC
* * * * *
41443872 CTTCATGTGGGATTTTTGCATAAATTAGGTTAATTGCCTCTGTATGCTGCCTGGACTTTTAGCTT
1 CTTCATGTGGGACTTATACATAAATTAGGTTAATTGCCTCTGTATGCTGCCTAGACTTCTAGCTT
* * * * * * *
41443937 TTTTCCTTACTTTGAGGTGCTTCTTGTATGCACCAGTACTTATGCTTGGGTTGCTAAATTTATAA
66 TTTTCCTTACTTTGAGATGCTTCCTGCATGCACCAGTACTTAAGCCTGAGTTACTAAATTTATAA
*
41444002 CTGAAATGTAGTTTGTGGGAGTTCCTTGAACCCAAGATAGCAACACTGGTATTTCTAT
131 CTGAAATGTAGTTTGTGGGAGTTCCTTAAACCCAAGATAGCAACACTGGTATTTCTAT
* *
41444060 CTTCATGTGGTACTTATACATAAATTAGGTTAATTGCCTCTGTATGCTG-TTCAGACTTCTAGCT
1 CTTCATGTGGGACTTATACATAAATTAGGTTAATTGCCTCTGTATGCTGCCT-AGACTTCTAGCT
* *** *
41444124 TTTTTCTTTACTTTGAGATGCTTCCTGCATGCATTGGTACTTAAGCCTGAGTTACTAAATTTCTA
65 TTTTTCCTTACTTTGAGATGCTTCCTGCATGCACCAGTACTTAAGCCTGAGTTACTAAATTTATA
* *
41444189 ACTTAAATGTAGTTTGTGGGCGTTCCTTAAACC
130 ACTGAAATGTAGTTTGTGGGAGTTCCTTAAACC
41444222 TTCTTCATTT
Statistics
Matches: 139, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
187 1 0.01
188 138 0.99
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (188 bp):
CTTCATGTGGGACTTATACATAAATTAGGTTAATTGCCTCTGTATGCTGCCTAGACTTCTAGCTT
TTTTCCTTACTTTGAGATGCTTCCTGCATGCACCAGTACTTAAGCCTGAGTTACTAAATTTATAA
CTGAAATGTAGTTTGTGGGAGTTCCTTAAACCCAAGATAGCAACACTGGTATTTCTAT
Found at i:41446421 original size:131 final size:127
Alignment explanation
Indices: 41446181--41446422 Score: 313
Period size: 131 Copynumber: 1.9 Consensus size: 127
41446171 TGGGACATGC
* * * * * * *
41446181 AATATTAAATTGGAATGAAAACTAATTTGGTATGTCAAGATTTTTTTTTTTTCGGTCATTCTCTA
1 AATATTAAATTGGAATGAAAACAAATTTGGTATGTCAAGACTCTTTTATGTTCAGTCATTCCCTA
* * *
41446246 GATCATTCACATATGCAGAAAACATTCTTAATTTGTTTGGTCCTACTATATTTTTTGTTTAT
66 GATCATTCACAAATGCAGAAAACATTCTTAAATCGTTTGGTCCTACTATATTTTTTGTTTAT
41446308 AATATTAAATTGGAATGAAAACAAATTTGGTATGTCAAGAAAAGCTCTTTTATGTTCAGTCATTC
1 AATATTAAATTGGAATGAAAACAAATTTGGTATGTCAAG---A-CTCTTTTATGTTCAGTCATTC
* * * * *
41446373 CCTATATGATTCATAAATGCAGAGAGCATTCTTAAATCGTTTGGTCCTAC
62 CCTAGATCATTCACAAATGCAGAAAACATTCTTAAATCGTTTGGTCCTAC
41446423 CATACTTCGT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
127 38 0.40
130 1 0.01
131 57 0.59
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (127 bp):
AATATTAAATTGGAATGAAAACAAATTTGGTATGTCAAGACTCTTTTATGTTCAGTCATTCCCTA
GATCATTCACAAATGCAGAAAACATTCTTAAATCGTTTGGTCCTACTATATTTTTTGTTTAT
Found at i:41458427 original size:20 final size:20
Alignment explanation
Indices: 41458404--41458444 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
41458394 TTTATAAATT
41458404 AATAAATA-ATTATAAAATAA
1 AATAAATATATT-TAAAATAA
*
41458424 AATAATTATATTTAAAATAA
1 AATAAATATATTTAAAATAA
41458444 A
1 A
41458445 TCTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAATATATTTAAAATAA
Found at i:41459467 original size:31 final size:29
Alignment explanation
Indices: 41459401--41459476 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
41459391 CATGGAGGAT
*
41459401 TTAATTGACTTTTTATTATTTTACAATAAC
1 TTAATTGA-TTTTTATTATTTTACAAGAAC
* *
41459431 TTAATTGATTTATTATTATTTTACGAGGGAC
1 TTAATTGATTT-TTATTATTTTAC-AAGAAC
41459462 TTAATTGATTCTTTA
1 TTAATTGATT-TTTA
41459477 AATAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 3 0.08
30 20 0.50
31 16 0.40
32 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (29 bp):
TTAATTGATTTTTATTATTTTACAAGAAC
Found at i:41459528 original size:41 final size:42
Alignment explanation
Indices: 41459467--41459571 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 42
41459457 GGGACTTAAT
*
41459467 TGATTCTTTAAATAA-A-AAATTATTAAATTC-TAAAAA-ATATA
1 TGATT-TTTAAA-AATATAAATTATAAAATTCATAAAAATAT-TA
41459508 TGATTTTTAAAAATATAAATTATAAAATTCATAAAAATATTA
1 TGATTTTTAAAAATATAAATTATAAAATTCATAAAAATATTA
*
41459550 TAAATTTATTAAAAATTATAAA
1 T-GATTT-TTAAAAA-TATAAA
41459572 AAAATTAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
39 2 0.04
40 7 0.13
41 18 0.33
42 9 0.16
43 6 0.11
44 7 0.13
45 6 0.11
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (42 bp):
TGATTTTTAAAAATATAAATTATAAAATTCATAAAAATATTA
Found at i:41459551 original size:20 final size:19
Alignment explanation
Indices: 41459524--41459572 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
41459514 TTAAAAATAT
41459524 AAATTATAAAATTCATAAA
1 AAATTATAAAATTCATAAA
* *
41459543 AATATTAT-AAATTTATTAA
1 AA-ATTATAAAATTCATAAA
41459562 AAATTATAAAA
1 AAATTATAAAA
41459573 AAATTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTATAAAATTCATAAA
Found at i:41460391 original size:30 final size:30
Alignment explanation
Indices: 41460326--41460391 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
41460316 AAACTTTCTA
* * *
41460326 TAATTTTTAGTAATTTTTCTAATTATTTAT
1 TAATTTCTAATAATTTTTCTAATGATTTAT
* *
41460356 AAATTTCTAATAATTTTT-TAATGATTTTTT
1 TAATTTCTAATAATTTTTCTAATGA-TTTAT
41460386 TAATTT
1 TAATTT
41460392 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
TAATTTCTAATAATTTTTCTAATGATTTAT
Found at i:41460624 original size:31 final size:31
Alignment explanation
Indices: 41460589--41460658 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
41460579 AAGGGGCTTT
*
41460589 ATTGGGTAGAAATCATGATTCAAATGGCTCA
1 ATTGGGTAGAAATCATGATTCAAATGACTCA
* *
41460620 ATTGGGTAGAAATTATGATTCAATTGACTCA
1 ATTGGGTAGAAATCATGATTCAAATGACTCA
41460651 ATTGGGTA
1 ATTGGGTA
41460659 CACTTTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (31 bp):
ATTGGGTAGAAATCATGATTCAAATGACTCA
Found at i:41461364 original size:3 final size:3
Alignment explanation
Indices: 41461356--41461384 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41461346 TGAGCTTCTT
41461356 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41461385 TACTTACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41478040 original size:12 final size:12
Alignment explanation
Indices: 41478023--41478048 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41478013 CAAAACAGGC
41478023 TTTTAGCGGCGT
1 TTTTAGCGGCGT
41478035 TTTTAGCGGCGT
1 TTTTAGCGGCGT
41478047 TT
1 TT
41478049 GGACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:41478082 original size:41 final size:39
Alignment explanation
Indices: 41478037--41478165 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 39
41478027 AGCGGCGTTT
*
41478037 TTAGCGGCG-TTTGGACAAAAAACGCCGCTAAAAATGGAGCA
1 TTAGCGGCGCTTT--ACATAAAACGCCGCTAAAAAT-GAGCA
* * *
41478078 TTAGCGGCGCTTTACGTAAAACGCCGCTAAAGATCAAGCA
1 TTAGCGGCGCTTTACATAAAACGCCGCTAAAAAT-GAGCA
* * **
41478118 TTAGTGGCGCTTTTA-TTAAAGTGCCGCTAAAAATGAGCA
1 TTAGCGGCGC-TTTACATAAAACGCCGCTAAAAATGAGCA
41478157 TTAGCGGCG
1 TTAGCGGCG
41478166 TTTTTTGGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 12 0.16
40 46 0.62
41 13 0.18
42 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
TTAGCGGCGCTTTACATAAAACGCCGCTAAAAATGAGCA
Found at i:41478103 original size:40 final size:39
Alignment explanation
Indices: 41478055--41478190 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
41478045 GTTTGGACAA
41478055 AAAACGCCGCTAAAAATGGAGCATTAGCGGCGC-TTTACGT
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTA-GT
* * * *
41478095 AAAACGCCGCTAAAGATCAAGCATTAGTGGCGCTTTTATT
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAGT
** * * *
41478135 AAAGTGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTGGA
1 AAAACGCCGCTAAAAATGAGCATTAGCGGCG-CTTTTAGT
*
41478175 AAAACGCCGTTAAAAA
1 AAAACGCCGCTAAAAA
41478191 CCTAAGCACA
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 12 0.16
40 61 0.79
41 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTAGT
Found at i:41478445 original size:26 final size:26
Alignment explanation
Indices: 41478397--41478446 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
41478387 AAAATGTATA
** * *
41478397 AATTTGAAATAATGACACGTAGAAGT
1 AATTTGAAATAAAAAAACATAGAAGT
41478423 AATTTGAAATAAAAAAACATAGAA
1 AATTTGAAATAAAAAAACATAGAA
41478447 AAATATTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAGT
Found at i:41478734 original size:14 final size:15
Alignment explanation
Indices: 41478705--41478738 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
41478695 TAAGGTTTAT
41478705 AGATTATGGAATTAG
1 AGATTATGGAATTAG
41478720 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
41478734 AGATT
1 AGATT
41478739 CTGATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:41478981 original size:7 final size:7
Alignment explanation
Indices: 41478969--41478993 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41478959 TATTAAATAA
41478969 GGTTTGG
1 GGTTTGG
41478976 GGTTTGG
1 GGTTTGG
41478983 GGTTTGG
1 GGTTTGG
41478990 GGTT
1 GGTT
41478994 AAAAGTTAGT
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:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (7 bp):
GGTTTGG
Found at i:41480975 original size:30 final size:30
Alignment explanation
Indices: 41480939--41480998 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41480929 GTTTATTATG
41480939 ATGCAGTAAATGGCATTGAAGTGTTCAAAA
1 ATGCAGTAAATGGCATTGAAGTGTTCAAAA
41480969 ATGCAGTAAATGGCATTGAAGTGTTCAAAA
1 ATGCAGTAAATGGCATTGAAGTGTTCAAAA
41480999 TGAACATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (30 bp):
ATGCAGTAAATGGCATTGAAGTGTTCAAAA
Found at i:41483602 original size:41 final size:42
Alignment explanation
Indices: 41483544--41483633 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
41483534 TAATTTTTTT
* * **
41483544 TAAAGATTATGTTTTTAGCGGCGTTT-TGCTAGTAGCGCCGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTGTGATAAAAGCGCCGC
41483585 TAAAGGTT-TGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTTATGTT-TTTAGCGGCGTTTGTGATAAAAGCGCCGC
41483627 TAAAGGT
1 TAAAGGT
41483634 CATGGTCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 4 0.09
41 20 0.47
42 19 0.44
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (42 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTGTGATAAAAGCGCCGC
Found at i:41483631 original size:42 final size:43
Alignment explanation
Indices: 41483577--41483780 Score: 207
Period size: 43 Copynumber: 4.8 Consensus size: 43
41483567 TTTTGCTAGT
* **
41483577 AGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGATAAA
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAA
* ** * *
41483619 AGCGCCGCTAAAGGTCATGGTCTACAGTGGCATTTGTGGGAAA
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAA
* * * * *
41483662 AGCTCCGTTAAAGGTCTTGGTATTTAGTGGCGTTTGTGGGGAA
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAA
** * * *
41483705 AGCATCGCTAAAGATCTTGGTC-TTAGTGGTGTTTGTGGG-AA
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAA
* *
41483746 AGCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTT
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
41483781 TTTCCGGCGC
Statistics
Matches: 131, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 19 0.15
42 41 0.31
43 71 0.54
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAA
Found at i:41483699 original size:86 final size:84
Alignment explanation
Indices: 41483577--41483780 Score: 230
Period size: 86 Copynumber: 2.4 Consensus size: 84
41483567 TTTTGCTAGT
* * * *
41483577 AGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTC
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTC
41483641 TACAGTGGCATTTGTGGGAAA
66 T-CAGTGGCATTTGTGGG-AA
* * * * * * * *
41483662 AGCTCCGTTAAAGGTCTTGGTATTTAGTGGCGTTTGTGGGGAAAGCATCGCTAAAGATCTTGGTC
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTC
* **
41483727 TTAGTGGTGTTTGTGGGAA
66 TCAGTGGCATTTGTGGGAA
* *
41483746 AGCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTT
1 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
41483781 TTTCCGGCGC
Statistics
Matches: 97, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
84 31 0.32
85 26 0.27
86 40 0.41
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (84 bp):
AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTC
TCAGTGGCATTTGTGGGAA
Found at i:41489467 original size:25 final size:25
Alignment explanation
Indices: 41489439--41489487 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41489429 ATATTTTCTA
*
41489439 CTTAAATCA-AATATAAATAATTAAT
1 CTTAAAT-AGAATAAAAATAATTAAT
*
41489464 CTTAAATAGTATAAAAATAATTAA
1 CTTAAATAGAATAAAAATAATTAA
41489488 CTAGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (25 bp):
CTTAAATAGAATAAAAATAATTAAT
Found at i:41489487 original size:19 final size:19
Alignment explanation
Indices: 41489465--41489507 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41489455 ATAATTAATC
*
41489465 TTAAATAGTATAAAAAT-AA
1 TTAAATAGAAT-AAAATGAA
*
41489484 TTAACTAGAATAAAATGAA
1 TTAAATAGAATAAAATGAA
41489503 TTAAA
1 TTAAA
41489508 AATAAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (19 bp):
TTAAATAGAATAAAATGAA
Found at i:41498609 original size:19 final size:18
Alignment explanation
Indices: 41498562--41498597 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41498552 TGTTTTCTAA
41498562 CTTAATCTATAAATTCAT
1 CTTAATCTATAAATTCAT
41498580 CTTAATCTATAAATTCAT
1 CTTAATCTATAAATTCAT
41498598 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
CTTAATCTATAAATTCAT
Found at i:41500183 original size:9 final size:9
Alignment explanation
Indices: 41500169--41500199 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41500159 TTTAGTTAAA
41500169 AATTAACCG
1 AATTAACCG
41500178 AATTAACCG
1 AATTAACCG
*
41500187 AATTACCCG
1 AATTAACCG
41500196 AATT
1 AATT
41500200 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:41503078 original size:18 final size:18
Alignment explanation
Indices: 41503055--41503090 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41503045 TAACGCCAAT
41503055 TTTAAATAGATATTAAAA
1 TTTAAATAGATATTAAAA
41503073 TTTAAATAGATATTAAAA
1 TTTAAATAGATATTAAAA
41503091 AATCTATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TTTAAATAGATATTAAAA
Found at i:41504218 original size:21 final size:21
Alignment explanation
Indices: 41504193--41504254 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
41504183 GGAACTTAAA
41504193 AAGAAAAAAAAAGAAGAACTG
1 AAGAAAAAAAAAGAAGAACTG
41504214 AAGAAAAAAAAAGAAGAACTG
1 AAGAAAAAAAAAGAAGAACTG
*
41504235 AAGAAGAAGAAGAAGAAGAA
1 AAGAA-AA-AAAAAGAAGAA
41504255 AAGTTAAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 26 0.68
22 2 0.05
23 10 0.26
ACGTcount: A:0.71, C:0.03, G:0.23, T:0.03
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAGAACTG
Found at i:41504240 original size:24 final size:23
Alignment explanation
Indices: 41504184--41504242 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
41504174 CAGTGATTCG
*
41504184 GAACTTAAAAAGAAAAAAAAAGAA
1 GAAC-TAAGAAGAAAAAAAAAGAA
41504208 GAACT--GAAGAAAAAAAAAGAA
1 GAACTAAGAAGAAAAAAAAAGAA
41504229 GAACTGAAGAAGAA
1 GAACT-AAGAAGAA
41504243 GAAGAAGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 20 0.65
23 1 0.03
24 10 0.32
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (23 bp):
GAACTAAGAAGAAAAAAAAAGAA
Found at i:41505300 original size:25 final size:26
Alignment explanation
Indices: 41505258--41505316 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
41505248 GAAGATCCGG
41505258 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * **
41505284 AGAGCC-TTTATCGGGAAGCTCATGA
1 AGAGCCATTAATCAGGAAGCTCACAA
41505309 AGAGCCAT
1 AGAGCCAT
41505317 ATAACGGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:41514744 original size:18 final size:18
Alignment explanation
Indices: 41514702--41514745 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
41514692 ATTTTTTCTA
* *
41514702 TATTTTATACTTATAATTT
1 TATTTTA-ACTAATAAATT
41514721 TA-TTTAACTAATAAATT
1 TATTTTAACTAATAAATT
41514738 TATTTTAA
1 TATTTTAA
41514746 ATAGTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 9 0.41
19 2 0.09
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTAACTAATAAATT
Found at i:41514842 original size:44 final size:44
Alignment explanation
Indices: 41514753--41514842 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
41514743 TAAATAGTTA
* * * * *
41514753 TAATAAATTATAATTATTTTTAAAAGTTTAATTATCACGACTTC
1 TAATAAATTATAATTATATTTAAAACTATAATTATCACAAATTC
** *
41514797 TAATAAATTATAATTATATTTAACTCTATAATTATCGCAAATTC
1 TAATAAATTATAATTATATTTAAAACTATAATTATCACAAATTC
41514841 TA
1 TA
41514843 TTTTACTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (44 bp):
TAATAAATTATAATTATATTTAAAACTATAATTATCACAAATTC
Found at i:41522688 original size:36 final size:35
Alignment explanation
Indices: 41522580--41522691 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 35
41522570 ACTTTCAAAA
* * * * *
41522580 AGAAGCACAAGTAAAAGTCCTGCAAGATATTCTCGG
1 AGAAGCACTAGCAGAAGTCCTGTAAGAT-TTCTAGG
* * ** *
41522616 AGAAGCATTAGCAGAAGCCCCATAAG--GTCTAGG
1 AGAAGCACTAGCAGAAGTCCTGTAAGATTTCTAGG
41522649 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG
1 AGAAGCACTAGCAGAAGTCCTGTAAGAT-TTCTAGG
41522685 AGAAGCA
1 AGAAGCA
41522692 TAAGTAGGAG
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
33 27 0.47
36 31 0.53
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (35 bp):
AGAAGCACTAGCAGAAGTCCTGTAAGATTTCTAGG
Found at i:41523416 original size:36 final size:36
Alignment explanation
Indices: 41523369--41523451 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
41523359 TGGTCATAGC
* * *
41523369 CGCAGTCGTAGCCCAAGTCGTAGTCGAACCTCTATT
1 CGCAGCCGTAGCCCAAGTCGAAGTCGAACCCCTATT
41523405 CGCAGCCGTAGCCCAAGTCGAAGTCGAACCCCTATT
1 CGCAGCCGTAGCCCAAGTCGAAGTCGAACCCCTATT
*
41523441 CGCAGCTGTAG
1 CGCAGCCGTAG
41523452 TCCAGTTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (36 bp):
CGCAGCCGTAGCCCAAGTCGAAGTCGAACCCCTATT
Found at i:41529115 original size:84 final size:84
Alignment explanation
Indices: 41528963--41529123 Score: 227
Period size: 84 Copynumber: 1.9 Consensus size: 84
41528953 GTGGATGCAA
* *
41528963 GATTCTTCCTTCTTTTAATATTTTAAAATCCAATTATTTCATGGAAATGATTTAAACAGTGTACT
1 GATTCTTCCTTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAACAGTGTACT
41529028 ATTTGTGTTATGGGTACAG
66 ATTTGTGTTATGGGTACAG
* * * *
41529047 GATTC-TCCTTTCTTTTAATATATTAAAATTCAATCATTTCATGTAAATGTTTTAAAC-GTTTTA
1 GATTCTTCC-TTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAACAG-TGTA
*
41529110 GTATTTGTGTTATG
64 CTATTTGTGTTATG
41529124 CACATGCTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 4 0.06
84 64 0.94
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (84 bp):
GATTCTTCCTTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAACAGTGTACT
ATTTGTGTTATGGGTACAG
Found at i:41532737 original size:18 final size:18
Alignment explanation
Indices: 41532714--41532762 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
41532704 GGAGGACTCA
41532714 TAGCCGGAGCCCAAGTCT
1 TAGCCGGAGCCCAAGTCT
* * *
41532732 TAGCCGAAGCCGAAGTGT
1 TAGCCGGAGCCCAAGTCT
* *
41532750 GAGCAGGAGCCCA
1 TAGCCGGAGCCCA
41532763 GTAGCAAGTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12
Consensus pattern (18 bp):
TAGCCGGAGCCCAAGTCT
Found at i:41533108 original size:33 final size:32
Alignment explanation
Indices: 41533027--41533124 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 32
41533017 AAGCACAAGT
*
41533027 GGAAGTCCTGCAAGATCTCGGAGAAGCATTAGC
1 GGAAGTCCTG-AAGATCTAGGAGAAGCATTAGC
* * *
41533060 AGAAGCCCCAGAAGATCTAGGAGAAGCATTAGC
1 GGAAG-TCCTGAAGATCTAGGAGAAGCATTAGC
41533093 GGAAGTCCTGTAAGATCTTCTAGGAGAAGCAT
1 GGAAGTCCTG-AAGA---TCTAGGAGAAGCAT
41533125 AAGTAGGAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
32 3 0.06
33 33 0.62
34 3 0.06
36 14 0.26
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (32 bp):
GGAAGTCCTGAAGATCTAGGAGAAGCATTAGC
Found at i:41534734 original size:17 final size:18
Alignment explanation
Indices: 41534712--41534747 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41534702 TATAATAAAA
41534712 ATTAAAAATTA-AAAATT
1 ATTAAAAATTATAAAATT
*
41534729 ATTAAAACTTATAAAATT
1 ATTAAAAATTATAAAATT
41534747 A
1 A
41534748 ACTTCAATGA
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:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAATTATAAAATT
Found at i:41541074 original size:26 final size:26
Alignment explanation
Indices: 41541038--41541089 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41541028 GTATCGCATG
41541038 TGGAAGATTGAAAATCACATGGTCAT
1 TGGAAGATTGAAAATCACATGGTCAT
41541064 TGGAAGATTGAAAATCACATGGTCAT
1 TGGAAGATTGAAAATCACATGGTCAT
41541090 GTCATGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (26 bp):
TGGAAGATTGAAAATCACATGGTCAT
Found at i:41550461 original size:21 final size:21
Alignment explanation
Indices: 41550429--41550469 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41550419 GAACATTTGG
41550429 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
41550450 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
41550470 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:41554969 original size:12 final size:13
Alignment explanation
Indices: 41554923--41554964 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
41554913 ATAATAAAGA
41554923 TTATTGAAAAGTATT
1 TTATT-AAAA-TATT
41554938 ATTATT-AAATATT
1 -TTATTAAAATATT
41554951 TTATTAAAATATT
1 TTATTAAAATATT
41554964 T
1 T
41554965 GTTAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 12 0.48
14 3 0.12
16 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (13 bp):
TTATTAAAATATT
Found at i:41560889 original size:25 final size:26
Alignment explanation
Indices: 41560856--41560908 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
41560846 TTAAATCAAT
* *
41560856 TTTTATAAT-TTTTATTTTTTTTGAA
1 TTTTATAATAATTTATTTGTTTTGAA
*
41560881 TTTTCTAATAATTTATTTGTTTTGAA
1 TTTTATAATAATTTATTTGTTTTGAA
41560907 TT
1 TT
41560909 GTTCAGACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (26 bp):
TTTTATAATAATTTATTTGTTTTGAA
Found at i:41561017 original size:23 final size:23
Alignment explanation
Indices: 41560987--41561033 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
41560977 TGACAGATAC
41560987 TCATATTTATATAAT-TAAAATAT
1 TCATATTT-TATAATATAAAATAT
*
41561010 TCATATTTTATACTATAAAATAT
1 TCATATTTTATAATATAAAATAT
41561033 T
1 T
41561034 TATTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
TCATATTTTATAATATAAAATAT
Found at i:41561105 original size:25 final size:26
Alignment explanation
Indices: 41561050--41561106 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
41561040 TAATATATTT
* *
41561050 ATAATTTTAATATATATTTATTATCA
1 ATAATATTAATATAAATTTATTATCA
41561076 A-AATATTAATATAAATATT-TT-TCA
1 ATAATATTAATATAAAT-TTATTATCA
41561100 ATAATAT
1 ATAATAT
41561107 ATTTAGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAATATTAATATAAATTTATTATCA
Found at i:41561146 original size:14 final size:15
Alignment explanation
Indices: 41561127--41561156 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41561117 TTACTTAAGA
41561127 TTTAAAA-TTATTAT
1 TTTAAAATTTATTAT
41561141 TTTAAAATTTATTAT
1 TTTAAAATTTATTAT
41561156 T
1 T
41561157 AAAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAAATTTATTAT
Found at i:41561158 original size:13 final size:14
Alignment explanation
Indices: 41561126--41561162 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
41561116 ATTACTTAAG
41561126 ATTTAAAA-TTATT
1 ATTTAAAATTTATT
41561139 ATTTTAAAATTTATT
1 A-TTTAAAATTTATT
41561154 A-TTAAAATT
1 ATTTAAAATT
41561163 AAATTGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTAAAATTTATT
Found at i:41564101 original size:19 final size:19
Alignment explanation
Indices: 41564064--41564101 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41564054 GGATATAAGT
*
41564064 ATAAAATTTAATATTAAAG
1 ATAAAATTTAAAATTAAAG
41564083 ATAAAA-TTAAAATTCAAAG
1 ATAAAATTTAAAATT-AAAG
41564102 GTTAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAAAATTTAAAATTAAAG
Found at i:41575658 original size:26 final size:27
Alignment explanation
Indices: 41575590--41575658 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
41575580 ATCCATATTT
*
41575590 AATTATTT-ATAATTATTCATATAATA
1 AATTATTTAATATTTATTCATATAATA
*
41575616 AATTATATTAATAATTTATT-ATTTTAA-A
1 AATTAT-TTAAT-ATTTATTCA-TATAATA
41575644 AATTATTTAATATTT
1 AATTATTTAATATTT
41575659 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 10 0.27
27 7 0.19
28 10 0.27
29 10 0.27
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTATTTAATATTTATTCATATAATA
Found at i:41580907 original size:10 final size:10
Alignment explanation
Indices: 41580901--41580925 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41580891 TTCAAATATT
41580901 AAAAAATTAG
1 AAAAAATTAG
41580911 AAAAAATTAG
1 AAAAAATTAG
41580921 AAAAA
1 AAAAA
41580926 TATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAAAATTAG
Found at i:41580907 original size:16 final size:17
Alignment explanation
Indices: 41580876--41580908 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41580866 AAATAGTATT
41580876 AAATATTATTAAAAATTC
1 AAATATTA-TAAAAATTC
41580894 AAATATTA-AAAAATT
1 AAATATTATAAAAATT
41580909 AGAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTATAAAAATTC
Found at i:41580943 original size:19 final size:19
Alignment explanation
Indices: 41580921--41581005 Score: 50
Period size: 19 Copynumber: 4.5 Consensus size: 19
41580911 AAAAAATTAG
41580921 AAAAATATATAAAAATCAT
1 AAAAATATATAAAAATCAT
* * **
41580940 AAAAAAAT-TGTAAAATTGT
1 AAAAATATAT-AAAAATCAT
* * *
41580959 AAAATTTTATAAAAATCTT
1 AAAAATATATAAAAATCAT
41580978 AAAAA-ATTATAAAATAT-AT
1 AAAAATA-TATAAAA-ATCAT
*
41580997 AGAAATATA
1 AAAAATATA
41581006 AAATTTTATA
Statistics
Matches: 47, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
18 1 0.02
19 42 0.89
20 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
AAAAATATATAAAAATCAT
Found at i:41580955 original size:38 final size:37
Alignment explanation
Indices: 41580913--41580992 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
41580903 AAAATTAGAA
*
41580913 AAAATTAG-AAAAATATATAAAAATCATAAAAAAATTGT
1 AAAATT-GTAAAAATATATAAAAATC-TAAAAAAATTAT
* * *
41580951 AAAATTGTAAAATTTTATAAAAATCTTAAAAAATTAT
1 AAAATTGTAAAAATATATAAAAATCTAAAAAAATTAT
41580988 AAAAT
1 AAAAT
41580993 ATATAGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 16 0.43
38 21 0.57
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (37 bp):
AAAATTGTAAAAATATATAAAAATCTAAAAAAATTAT
Found at i:41581286 original size:16 final size:17
Alignment explanation
Indices: 41581265--41581301 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41581255 TATGATTTTC
41581265 TTTTAA-AAATTCT-AAT
1 TTTTAATAAATT-TAAAT
41581281 TTTTAATAAATTTAAAT
1 TTTTAATAAATTTAAAT
41581298 TTTT
1 TTTT
41581302 TATATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATAAATTTAAAT
Found at i:41589128 original size:7 final size:7
Alignment explanation
Indices: 41589116--41589140 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41589106 GCAGGTTTAA
41589116 TTTTATT
1 TTTTATT
41589123 TTTTATT
1 TTTTATT
41589130 TTTTATT
1 TTTTATT
41589137 TTTT
1 TTTT
41589141 TTTAAAAACT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:41593590 original size:21 final size:21
Alignment explanation
Indices: 41593561--41593609 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
41593551 TTGAGTTCAT
*
41593561 TAATATTGG-AATTAAGTTGA
1 TAATTTTGGTAATTAAGTTGA
*
41593581 TATATTTTGGTTTATTAAGTTGA
1 TA-ATTTTGG-TAATTAAGTTGA
41593604 TAATTT
1 TAATTT
41593610 AGTTATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 6 0.25
22 4 0.17
23 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
TAATTTTGGTAATTAAGTTGA
Found at i:41593617 original size:20 final size:23
Alignment explanation
Indices: 41593571--41593617 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
41593561 TAATATTGGA
*
41593571 ATTAAGTTGATATATTTTGGTTT
1 ATTAAGTTGATATATTTTAGTTT
41593594 ATTAAGTTGATA-A-TTTAG-TT
1 ATTAAGTTGATATATTTTAGTTT
41593614 ATTA
1 ATTA
41593618 GTTTATCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 1 0.04
23 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (23 bp):
ATTAAGTTGATATATTTTAGTTT
Found at i:41594091 original size:21 final size:22
Alignment explanation
Indices: 41594049--41594095 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
41594039 TGTAACTCAA
41594049 TTCCATGTAGAAACTTATATTT
1 TTCCATGTAGAAACTTATATTT
41594071 TTCCATGTA-AAACTCTA-ATTT
1 TTCCATGTAGAAACT-TATATTT
41594092 TTCC
1 TTCC
41594096 CCTTTACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (22 bp):
TTCCATGTAGAAACTTATATTT
Found at i:41602678 original size:14 final size:13
Alignment explanation
Indices: 41602647--41602694 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
41602637 TAAACCAAAC
41602647 TTTTCAAAAGTA-T
1 TTTTCAAAA-TATT
41602660 TTTTCAAAATCATT
1 TTTTCAAAAT-ATT
*
41602674 TTTTCACAATATT
1 TTTTCAAAATATT
41602687 TTTT-AAAA
1 TTTTCAAAA
41602695 ACACTTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 17 0.55
14 10 0.32
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATATT
Found at i:41603117 original size:19 final size:19
Alignment explanation
Indices: 41603089--41603136 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
41603079 GTTATATATA
* *
41603089 AATTAAAAATAAATTTTAC
1 AATTATAAATAAATGTTAC
* *
41603108 AATTATAAATTAGTGTTAC
1 AATTATAAATAAATGTTAC
*
41603127 ACTTATAAAT
1 AATTATAAAT
41603137 CATTAAGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (19 bp):
AATTATAAATAAATGTTAC
Found at i:41603360 original size:24 final size:24
Alignment explanation
Indices: 41603333--41603378 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41603323 TACACAATTG
41603333 AATATATTAATT-AATTAATTATTA
1 AATATA-TAATTAAATTAATTATTA
*
41603357 AATATATATTTAAATTAATTAT
1 AATATATAATTAAATTAATTAT
41603379 CATTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATAATTAAATTAATTATTA
Found at i:41605647 original size:18 final size:17
Alignment explanation
Indices: 41605624--41605658 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
41605614 ATGTGTTATG
41605624 AATAACATAATATGTAAA
1 AATAACATAATAT-TAAA
41605642 AATAACATAATATTAAA
1 AATAACATAATATTAAA
41605659 CATTATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AATAACATAATATTAAA
Found at i:41615151 original size:44 final size:43
Alignment explanation
Indices: 41615119--41615503 Score: 325
Period size: 44 Copynumber: 8.9 Consensus size: 43
41615109 TAAAATTCAC
* *
41615119 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATC-T
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCAA
* * *
41615161 GA--TACGATCTACTCTACTACTGCTTAGGGAGATAGGATCTAA
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATC-AA
* * *
41615203 CATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGA-C-T
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCAA
** ** * * * * **
41615244 GGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGC
1 CAT--CTTCGATCTACTCCACTACTGCTTAGGGAGATAGGA-TCAA
*
41615290 CGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAA
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATC-AA
* * *
41615334 CATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA-C-T
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCAA
** ** * * * * **
41615375 GGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGC
1 CAT--CTTCGATCTACTCCACTACTGCTTAGGGAGATAGGA-TCAA
*
41615421 CGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAA
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATC-AA
* *
41615465 CATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGA
41615504 CTGGTGGCTT
Statistics
Matches: 272, Mismatches: 55, Indels: 30
0.76 0.15 0.08
Matches are distributed among these distances:
40 34 0.12
41 2 0.01
42 2 0.01
43 65 0.24
44 163 0.60
45 2 0.01
46 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCAA
Found at i:41615307 original size:87 final size:86
Alignment explanation
Indices: 41615119--41615568 Score: 369
Period size: 87 Copynumber: 5.2 Consensus size: 86
41615109 TAAAATTCAC
* * *
41615119 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGA-T-CT-G-ATACGATCTAC-TCTACT
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGACTGCTGGCTTA-GATCTGCTTC-ACT
41615179 ACTGCTTAGGGAGATAGGATCTAA
64 ACTGCTTAGGGAGATAGGATC-AA
* * * *
41615203 CATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTAC
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGACTGCTGGCTTAGATCTGCTTCACTAC
* * **
41615268 TGCTTAGGAAGATAAGATTCGC
66 TGCTTAGGGAGATAGGA-TCAA
* * * * *
41615290 CGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACAT--CTTCGACCTGCTCCAC
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGA-CT-GC-TGGCTTAGATCTGCTTCAC
*
41615353 TACTGCTTAGGGAGATAGGA-C-T
63 TACTGCTTAGGGAGATAGGATCAA
** ** * * * * * * * * * *
41615375 GGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTACTCCAC
1 CAT--CTTCGATCTACTCCACTACTGCTTAGGGAGATAGGACT-GCTGGCTTAGATCTGCTTCAC
41615440 TACTGCTTAGGGAGATAGGATCTAA
63 TACTGCTTAGGGAGATAGGATC-AA
* * * *
41615465 CATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTAC
1 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGACTGCTGGCTTAGATCTGCTTCACTAC
* * * *
41615530 TGCTTAAGAAGATAAGATTCAC
66 TGCTTAGGGAGATAGGA-TCAA
*
41615552 CATCTTCGATCTGCTCC
1 CATCTTCGATCTACTCC
41615569 GCTAGTACTT
Statistics
Matches: 291, Mismatches: 58, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
84 36 0.12
85 3 0.01
86 4 0.01
87 174 0.60
88 72 0.25
90 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (86 bp):
CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAGGACTGCTGGCTTAGATCTGCTTCACTAC
TGCTTAGGGAGATAGGATCAA
Found at i:41615601 original size:131 final size:131
Alignment explanation
Indices: 41615165--41615568 Score: 745
Period size: 131 Copynumber: 3.1 Consensus size: 131
41615155 AGATCTGATA
* * *
41615165 CGATCTACTCTACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTACTCCACTACTGCTT
1 CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
41615230 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
66 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
41615295 T
131 T
41615296 CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
1 CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
41615361 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
66 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
41615426 T
131 T
41615427 CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
1 CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
* * *
41615492 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAAGAAGATAAGATTCACCATCT
66 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
41615557 T
131 T
*
41615558 CGATCTGCTCC
1 CGATCTACTCC
41615569 GCTAGTACTT
Statistics
Matches: 266, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 266 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (131 bp):
CGATCTACTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTCGACCTGCTCCACTACTGCTT
AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCT
T
Found at i:41615875 original size:175 final size:175
Alignment explanation
Indices: 41615579--41616124 Score: 859
Period size: 175 Copynumber: 3.1 Consensus size: 175
41615569 GCTAGTACTT
* * * * *
41615579 AGGAAGGCAAGATTTGCTATCTTTAACCAGCT-TCACTGCAACCGATG-GAGGCAAGGCTTTGT-
1 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCT-GCTACAACCGA-GAGAGGCAAGG-TTTGTG
* * * * *
41615641 T-TTCGATCTGCTTCGCTATTAACGCAGGAAGGCAAGATTTGCTGTCTTCAACTAGCTCTGCTAC
63 TCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
* * *
41615705 AACCGAGAGAGGCAAAGTTTTGTTTTCGATCTGCTTCGTTGTTAATGC
128 AACCGAGAGAGGCAAGGTTTTGTTTTTGATCTGCTTCGCTGTTAATGC
*
41615753 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
41615818 TCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAAC
66 TCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAAC
* *
41615883 CGAGAGAGGCAAGGTTTTATTTTTGATGTGCTTCGCTGTTAATGC
131 CGAGAGAGGCAAGGTTTTGTTTTTGATCTGCTTCGCTGTTAATGC
41615928 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
*
41615993 TCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAAC
66 TCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAAC
*
41616058 CGAGAGAGGCAAGGTTTTGTTTTTTATCTGCTTCGCTGTTAATGC
131 CGAGAGAGGCAAGGTTTTGTTTTTGATCTGCTTCGCTGTTAATGC
*
41616103 AGGAAGGCAAGACCTGTT-TCTT
1 AGGAAGGCAAGATCTGTTATCTT
41616125 TGATCTGTTC
Statistics
Matches: 346, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
173 6 0.02
174 51 0.15
175 289 0.84
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (175 bp):
AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
TCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAAC
CGAGAGAGGCAAGGTTTTGTTTTTGATCTGCTTCGCTGTTAATGC
Found at i:41616138 original size:88 final size:87
Alignment explanation
Indices: 41615579--41616124 Score: 819
Period size: 87 Copynumber: 6.3 Consensus size: 87
41615569 GCTAGTACTT
* * * * * * *
41615579 AGGAAGGCAAGATTTGCTATCTTTAACCAGCT-TCACTGCAACCGATG-GAGGCAAGGCTTTGTT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCT-GCTACAACCGA-GAGAGGCAAGGTTTTGTT
* *
41615642 TTCGATCTGCTTCGCTATTAACGC
64 TTCGATCTGCTTCGCTGTTAATGC
* * * *
41615666 AGGAAGGCAAGATTTGCTGTCTTCAACTAGCTCTGCTACAACCGAGAGAGGCAAAGTTTTGTTTT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTGTTTT
*
41615731 CGATCTGCTTCGTTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
*
41615753 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTT-TGTTT
41615818 TCGATCTGCTTCGCTGTTAATGC
65 TCGATCTGCTTCGCTGTTAATGC
*
41615841 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTATTTT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTGTTTT
* *
41615906 TGATGTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* *
41615928 AGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTT-TGTTT
*
41615993 TCGATCTGCTTCACTGTTAATGC
65 TCGATCTGCTTCGCTGTTAATGC
41616016 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTGTTTT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTGTTTT
**
41616081 TTATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
*
41616103 AGGAAGGCAAGACCTGTT-TCTT
1 AGGAAGGCAAGATCTGTTGTCTT
41616125 TGATCTGTTC
Statistics
Matches: 423, Mismatches: 32, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
86 5 0.01
87 251 0.59
88 167 0.39
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTTGTTTT
CGATCTGCTTCGCTGTTAATGC
Found at i:41617370 original size:7 final size:7
Alignment explanation
Indices: 41617351--41617415 Score: 55
Period size: 7 Copynumber: 9.0 Consensus size: 7
41617341 TTAGCCTCTC
41617351 CATTTTT
1 CATTTTT
41617358 -ACTTTTT
1 CA-TTTTT
41617365 CATTTTTT
1 CA-TTTTT
41617373 CATTTTT
1 CATTTTT
41617380 CATTTTT
1 CATTTTT
41617387 -ATTTTTCT
1 CA-TTTT-T
41617395 CATTTCTT
1 CATTT-TT
*
41617403 CTTTTTT
1 CATTTTT
41617410 C-TTTTT
1 CATTTTT
41617416 TTTTGACTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
6 7 0.14
7 24 0.48
8 17 0.34
9 2 0.04
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
CATTTTT
Found at i:41617376 original size:22 final size:22
Alignment explanation
Indices: 41617351--41617417 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
41617341 TTAGCCTCTC
41617351 CATTTTT-ACTTTTTCATTTTTT
1 CATTTTTCA-TTTTTCATTTTTT
41617373 CATTTTTCATTTTT-ATTTTTCT
1 CATTTTTCATTTTTCATTTTT-T
* *
41617395 CATTTCTTCTTTTTTCTTTTTTT
1 CATTT-TTCATTTTTCATTTTTT
41617418 TTGACTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.15
22 18 0.46
23 10 0.26
24 5 0.13
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (22 bp):
CATTTTTCATTTTTCATTTTTT
Found at i:41617378 original size:15 final size:14
Alignment explanation
Indices: 41617351--41617419 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 14
41617341 TTAGCCTCTC
*
41617351 CATTTTTACTTTTT
1 CATTTTTATTTTTT
41617365 CATTTTT-TCATTTTT
1 CATTTTTAT--TTTTT
41617380 CATTTTTATTTTTCT
1 CATTTTTATTTTT-T
*
41617395 CATTTCTTCTTTTTT
1 CATTT-TTATTTTTT
41617410 C-TTTTT-TTTT
1 CATTTTTATTTT
41617420 GACTCAAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
12 4 0.08
13 2 0.04
14 14 0.29
15 20 0.42
16 8 0.17
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.75
Consensus pattern (14 bp):
CATTTTTATTTTTT
Found at i:41618274 original size:10 final size:10
Alignment explanation
Indices: 41618261--41618314 Score: 65
Period size: 10 Copynumber: 5.1 Consensus size: 10
41618251 TATTTTTGAC
41618261 TTTGATTTTT
1 TTTGATTTTT
41618271 TTTGA-TTTT
1 TTTGATTTTT
41618280 TTTGATTTTT
1 TTTGATTTTT
41618290 TTGATGATTTTTTT
1 TT--TGA--TTTTT
41618304 TTTGATTTTT
1 TTTGATTTTT
41618314 T
1 T
41618315 GACTTTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 9 0.23
10 17 0.44
12 6 0.15
14 7 0.18
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (10 bp):
TTTGATTTTT
Found at i:41618281 original size:12 final size:12
Alignment explanation
Indices: 41618276--41618314 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41618266 TTTTTTTTGA
41618276 TTTTTTTGATTT
1 TTTTTTTGATTT
**
41618288 TTTTGATGATTT
1 TTTTTTTGATTT
41618300 TTTTTTTGATTT
1 TTTTTTTGATTT
41618312 TTT
1 TTT
41618315 GACTTTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (12 bp):
TTTTTTTGATTT
Found at i:41618298 original size:31 final size:29
Alignment explanation
Indices: 41618263--41618335 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 29
41618253 TTTTTGACTT
*
41618263 TGATTTTTTTTGATTTTTTTGATTTTTTTGA
1 TGATTTTTTTTGA-TTTTTTGA-CTTTTTGA
41618294 TGATTTTTTTTTTGATTTTTTGACTTTTTGA
1 TGA--TTTTTTTTGATTTTTTGACTTTTTGA
41618325 --ATTTTTTTTGA
1 TGATTTTTTTTGA
41618336 GTCTGAACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 10 0.26
29 1 0.03
31 10 0.26
32 8 0.21
33 10 0.26
ACGTcount: A:0.14, C:0.01, G:0.12, T:0.73
Consensus pattern (29 bp):
TGATTTTTTTTGATTTTTTGACTTTTTGA
Found at i:41618302 original size:32 final size:29
Alignment explanation
Indices: 41618266--41618333 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 29
41618256 TTGACTTTGA
*
41618266 TTTTTTTTGATTTTTTTGATTTTTTTGATGATT
1 TTTTTTTTGA-TTTTTTGA-CTTTTTGA--ATT
41618299 TTTTTTTTGATTTTTTGACTTTTTGAATT
1 TTTTTTTTGATTTTTTGACTTTTTGAATT
41618328 TTTTTT
1 TTTTTT
41618334 GAGTCTGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.26
31 7 0.21
32 8 0.24
33 10 0.29
ACGTcount: A:0.12, C:0.01, G:0.10, T:0.76
Consensus pattern (29 bp):
TTTTTTTTGATTTTTTGACTTTTTGAATT
Found at i:41618322 original size:10 final size:9
Alignment explanation
Indices: 41618261--41618332 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
41618251 TATTTTTGAC
41618261 TTTGATTTTT
1 TTTGA-TTTT
41618271 TTTGATTTT
1 TTTGATTTT
41618280 TTTGATTTT
1 TTTGATTTT
**
41618289 TTTGA-TGA
1 TTTGATTTT
41618297 TTT--TTTT
1 TTTGATTTT
41618304 TTTGA-TTT
1 TTTGATTTT
*
41618312 TTTGA-CTT
1 TTTGATTTT
41618320 TTTGAATTTT
1 TTTG-ATTTT
41618330 TTT
1 TTT
41618333 TGAGTCTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 4 0.08
8 18 0.35
9 19 0.37
10 10 0.20
ACGTcount: A:0.12, C:0.01, G:0.11, T:0.75
Consensus pattern (9 bp):
TTTGATTTT
Found at i:41618333 original size:12 final size:11
Alignment explanation
Indices: 41618261--41618314 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
41618251 TATTTTTGAC
41618261 TTTGA-TTTTT
1 TTTGATTTTTT
41618271 TTTGA--TTTT
1 TTTGATTTTTT
41618280 TTTGATTTTTT
1 TTTGATTTTTT
*
41618291 TGATGATTTTTTT
1 T-TTGA-TTTTTT
41618304 TTTGATTTTTT
1 TTTGATTTTTT
41618315 GACTTTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 9 0.24
10 5 0.13
11 11 0.29
12 6 0.16
13 7 0.18
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (11 bp):
TTTGATTTTTT
Found at i:41626260 original size:24 final size:24
Alignment explanation
Indices: 41626210--41626261 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41626200 AATCAAAGTC
* *
41626210 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
41626234 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
41626258 AAAT
1 AAAT
41626262 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41630679 original size:24 final size:24
Alignment explanation
Indices: 41630663--41630715 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
41630653 TAATCAAAGT
41630663 TAAATATATTATGCTAATAAATGC
1 TAAATATATTATGCTAATAAATGC
* *
41630687 TAAATATATTATACTCATAAATGC
1 TAAATATATTATGCTAATAAATGC
41630711 TAAAT
1 TAAAT
41630716 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAATATATTATGCTAATAAATGC
Found at i:41632039 original size:17 final size:16
Alignment explanation
Indices: 41632019--41632051 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
41632009 TATTATAAGT
41632019 AATAAATTAAATAGTTA
1 AATAAATTAAA-AGTTA
41632036 AATAAATTAAAAGTTA
1 AATAAATTAAAAGTTA
41632052 CAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AATAAATTAAAAGTTA
Found at i:41632513 original size:3 final size:3
Alignment explanation
Indices: 41632505--41632533 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41632495 CCATGCCTAC
41632505 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
41632534 ACTGTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:41636921 original size:14 final size:14
Alignment explanation
Indices: 41636903--41636942 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
41636893 ACTAATAATC
41636903 ATTTATTAATATAT
1 ATTTATTAATATAT
* *
41636917 TTTTATAAATATAT
1 ATTTATTAATATAT
41636931 ATTT-TTAATATA
1 ATTTATTAATATA
41636943 AAATATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATTAATATAT
Found at i:41636932 original size:16 final size:16
Alignment explanation
Indices: 41636910--41636954 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
41636900 ATCATTTATT
41636910 AATATATTTTTATA-A
1 AATATATTTTTATATA
41636925 ATATATATTTTTAATATA
1 A-ATATATTTTT-ATATA
41636943 AA-ATATTTTTAT
1 AATATATTTTTAT
41636955 TTACCCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 18 0.67
17 4 0.15
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATATTTTTATATA
Found at i:41653932 original size:474 final size:474
Alignment explanation
Indices: 41653045--41653996 Score: 1877
Period size: 474 Copynumber: 2.0 Consensus size: 474
41653035 CAATTTGAGA
41653045 AAATTTAATAATAAAGGCGGTAAAAGGTAAATTTCATCAACATGATAAAGGTTTCAGTCTCAGCA
1 AAATTTAATAATAAAGGCGGTAAAAGGTAAATTTCATCAACATGATAAAGGTTTCAGTCTCAGCA
*
41653110 TAAATATAACATTATGATACATTGACAATTTGCTCTGTCACAATTTAAATACGATATATCTAGAG
66 TAAATATAACATTATGATACATTGACAATTTGCTCTGTCACAACTTAAATACGATATATCTAGAG
41653175 TGGTTGCAAGCATTTAATATAATAAGGAAATCAGCTCCGAATGGTCCAAACCTATTCGTGAAATA
131 TGGTTGCAAGCATTTAATATAATAAGGAAATCAGCTCCGAATGGTCCAAACCTATTCGTGAAATA
41653240 ATTTATTATTCTGAAATACTCTCAAAACAGAAATTGACGAAGAGTCATCCGCTTTCTAAAAAAGT
196 ATTTATTATTCTGAAATACTCTCAAAACAGAAATTGACGAAGAGTCATCCGCTTTCTAAAAAAGT
41653305 TGCTGGTAGCCAGTGGAGTTTCAATGATGACAGGCATTGTCATTGATCCATCACTATTTGTGATA
261 TGCTGGTAGCCAGTGGAGTTTCAATGATGACAGGCATTGTCATTGATCCATCACTATTTGTGATA
41653370 TATGAATTATAGTATGTGAAGTGATGATGTAATTAAATTTACATGTAAGCTTTAAGGTACTAAAT
326 TATGAATTATAGTATGTGAAGTGATGATGTAATTAAATTTACATGTAAGCTTTAAGGTACTAAAT
41653435 AGAATAATAATCAAAAGTATAATGTTATGTGCAATTAAATGATCTTGTATAAGAATCGAATAGTT
391 AGAATAATAATCAAAAGTATAATGTTATGTGCAATTAAATGATCTTGTATAAGAATCGAATAGTT
41653500 GATAAGTGAAATAAGTGCT
456 GATAAGTGAAATAAGTGCT
41653519 AAATTTAATAATAAAGGCGGTAAAAGGTAAATTTCATCAACATGATAAAGGTTTCAGTCTCAGCA
1 AAATTTAATAATAAAGGCGGTAAAAGGTAAATTTCATCAACATGATAAAGGTTTCAGTCTCAGCA
41653584 TAAATATAACATTATGATACATTGACAATTTGCTCTGTCACAACTTAAATACGATATATCTAGAG
66 TAAATATAACATTATGATACATTGACAATTTGCTCTGTCACAACTTAAATACGATATATCTAGAG
*
41653649 TGGTTGCAAGCATTTAATATAATAAGGAAATCAGCTCCGAATGGTCCAAACCTATTCGTGAAATC
131 TGGTTGCAAGCATTTAATATAATAAGGAAATCAGCTCCGAATGGTCCAAACCTATTCGTGAAATA
41653714 ATTTATTATTCTGAAATACTCTCAAAACAGAAATTGACGAAGAGTCATCCGCTTTCTAAAAAAGT
196 ATTTATTATTCTGAAATACTCTCAAAACAGAAATTGACGAAGAGTCATCCGCTTTCTAAAAAAGT
41653779 TGCTGGTAGCCAGTGGAGTTTCAATGATGACAGGCATTGTCATTGATCCATCACTATTTGTGATA
261 TGCTGGTAGCCAGTGGAGTTTCAATGATGACAGGCATTGTCATTGATCCATCACTATTTGTGATA
41653844 TATGAATTATAGTATGTGAAGTGATGATGTAATTAAATTTACATGTAAGCTTTAAGGTACTAAAT
326 TATGAATTATAGTATGTGAAGTGATGATGTAATTAAATTTACATGTAAGCTTTAAGGTACTAAAT
*
41653909 AGAATAATAATCAAAAGTATAATGTTATGTGGAATTAAATGATCTTGTATAAGAATCGAATAGTT
391 AGAATAATAATCAAAAGTATAATGTTATGTGCAATTAAATGATCTTGTATAAGAATCGAATAGTT
41653974 GATAAGTGAAATAAGTGCT
456 GATAAGTGAAATAAGTGCT
41653993 AAAT
1 AAAT
41653997 GTTGGTTTGA
Statistics
Matches: 475, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
474 475 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (474 bp):
AAATTTAATAATAAAGGCGGTAAAAGGTAAATTTCATCAACATGATAAAGGTTTCAGTCTCAGCA
TAAATATAACATTATGATACATTGACAATTTGCTCTGTCACAACTTAAATACGATATATCTAGAG
TGGTTGCAAGCATTTAATATAATAAGGAAATCAGCTCCGAATGGTCCAAACCTATTCGTGAAATA
ATTTATTATTCTGAAATACTCTCAAAACAGAAATTGACGAAGAGTCATCCGCTTTCTAAAAAAGT
TGCTGGTAGCCAGTGGAGTTTCAATGATGACAGGCATTGTCATTGATCCATCACTATTTGTGATA
TATGAATTATAGTATGTGAAGTGATGATGTAATTAAATTTACATGTAAGCTTTAAGGTACTAAAT
AGAATAATAATCAAAAGTATAATGTTATGTGCAATTAAATGATCTTGTATAAGAATCGAATAGTT
GATAAGTGAAATAAGTGCT
Found at i:41656042 original size:11 final size:11
Alignment explanation
Indices: 41656026--41656091 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 11
41656016 ATTCTTTTTC
41656026 TTGTTGTTATT
1 TTGTTGTTATT
*
41656037 TTGTTGTTGTT
1 TTGTTGTTATT
* **
41656048 TTGATGACATT
1 TTGTTGTTATT
* * *
41656059 TTGCTATTATA
1 TTGTTGTTATT
*
41656070 TTGTTATTATT
1 TTGTTGTTATT
41656081 TTGTTGTTATT
1 TTGTTGTTATT
41656092 GTTTTGATAT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.65
Consensus pattern (11 bp):
TTGTTGTTATT
Found at i:41661836 original size:107 final size:108
Alignment explanation
Indices: 41661415--41661857 Score: 606
Period size: 109 Copynumber: 4.1 Consensus size: 108
41661405 AAAAACATAC
* * * * * *
41661415 TTTGAAGTTTTAAGAGGATA-TTTGGCTATTTGGTCAAACG-AGAAATCAAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACGTTA
* * * *
41661478 GGGCACACTTTCTCGAATTTTCAAATGCAAAATATTACCTTTAT
66 GGGCACATTTTCTCGAACTTCCAAACGCAAAATATTACC-TTAT
* * * *
41661522 TATGAAATTTTAGAAGGATATTTTAGCTATTTGGTCGAACGAAAAAAATCGAAACCTAACACGTT
1 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACG-AAAAAATCGAAACCCAGCACGTT
* ** *
41661587 AGGGCACGTTTT-TCGAACTTCCAAACGTGAAATATTGCCTTAT
65 AGGGCACATTTTCTCGAACTTCCAAACGCAAAATATTACCTTAT
41661630 TTTGAAATTTTAAAAGGATATTTTTAGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACGT
1 TTTGAAATTTTAAAAGGATA-TTTTAGCTATTTGGTCGAACG-AAAAAATCGAAACCCAGCACGT
* * *
41661695 TAGGGCACATTTTCTCAAACTTCCAAACGTAAAATATTGCCTTAT
64 TAGGGCACATTTTCTCGAACTTCCAAACGCAAAATATTACCTTAT
* *
41661740 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACG-AAAAATCGAGACCCAGCAAGTTA
1 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACGTTA
*
41661804 GGGCACGTTTTCTCGAACTTCCAAACGCAAAATATTACCTTAT
66 GGGCACATTTTCTCGAACTTCCAAACGCAAAATATTACCTTAT
41661847 TTTGAAATTTT
1 TTTGAAATTTT
41661858 TATTTGGATA
Statistics
Matches: 300, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
107 87 0.29
108 40 0.13
109 96 0.32
110 77 0.26
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (108 bp):
TTTGAAATTTTAAAAGGATATTTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACGTTA
GGGCACATTTTCTCGAACTTCCAAACGCAAAATATTACCTTAT
Found at i:41662108 original size:15 final size:15
Alignment explanation
Indices: 41662078--41662111 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41662068 GATTAATGAT
41662078 ATAAATAACAATATA
1 ATAAATAACAATATA
41662093 ATAAA-AACAATAATA
1 ATAAATAACAAT-ATA
41662108 ATAA
1 ATAA
41662112 TCAACGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAATAACAATATA
Found at i:41662260 original size:20 final size:21
Alignment explanation
Indices: 41662235--41662285 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
41662225 AAATCGATAC
41662235 TAAAATAATAA-GCAAAT-AAA
1 TAAAATAATAATG-AAATGAAA
41662255 TAAAATAA-AATGAAATGAAA
1 TAAAATAATAATGAAATGAAA
41662275 T-AAATAATAAT
1 TAAAATAATAAT
41662286 AATGTAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (21 bp):
TAAAATAATAATGAAATGAAA
Found at i:41663572 original size:20 final size:19
Alignment explanation
Indices: 41663529--41663577 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
41663519 TTTTTGGGCC
*
41663529 ATTTGGGCTTAGGGTTAAA
1 ATTTGGGCTGAGGGTTAAA
*
41663548 ATTTGGGCTGAGGGTTTAAT
1 ATTTGGGCTGAGGG-TTAAA
*
41663568 GTTTGGGCTG
1 ATTTGGGCTG
41663578 GTTTAGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.18, C:0.06, G:0.37, T:0.39
Consensus pattern (19 bp):
ATTTGGGCTGAGGGTTAAA
Found at i:41668983 original size:20 final size:20
Alignment explanation
Indices: 41668955--41668992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41668945 AGGAAAATTC
*
41668955 AATTCTTTTTTATTATTTTA
1 AATTCTTTTTAATTATTTTA
*
41668975 AATTTTTTTTAATTATTT
1 AATTCTTTTTAATTATTT
41668993 GGTACATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
AATTCTTTTTAATTATTTTA
Found at i:41674000 original size:15 final size:16
Alignment explanation
Indices: 41673980--41674012 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41673970 ATAAGGGTAT
41673980 AATAAA-ATATTAAAA
1 AATAAATATATTAAAA
*
41673995 AATAAATATTTTAAAA
1 AATAAATATATTAAAA
41674011 AA
1 AA
41674013 AGAGACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATATATTAAAA
Found at i:41681095 original size:14 final size:14
Alignment explanation
Indices: 41681078--41681112 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41681068 TATAATATCC
41681078 AAATAATAACAATA
1 AAATAATAACAATA
*
41681092 AAATAGTAACAATA
1 AAATAATAACAATA
*
41681106 TAATAAT
1 AAATAAT
41681113 TGAGAAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:41690654 original size:19 final size:19
Alignment explanation
Indices: 41690630--41690672 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
41690620 ATATCCATGC
* *
41690630 AATTAAATTTTTTTAAAAA
1 AATTAAATATATTTAAAAA
*
41690649 AATTAAATATATTTAATAA
1 AATTAAATATATTTAAAAA
41690668 AATTA
1 AATTA
41690673 CAAAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTAAATATATTTAAAAA
Found at i:41720619 original size:29 final size:29
Alignment explanation
Indices: 41720566--41720649 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
41720556 ATATGAACGA
*
41720566 AAATAAAAGTTTAATGTGTATAATT-ACACT
1 AAATAAAAG-TTAATGTATA-AATTCACACT
*
41720596 AAATAAAAGTTAATGTATCAAATTGCACATT
1 AAATAAAAGTTAATGTAT-AAATT-CACACT
*
41720627 AAATTAAAA-TTGATGTATAAATT
1 AAA-TAAAAGTTAATGTATAAATT
41720650 TGATATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 12 0.26
30 15 0.32
31 15 0.32
32 5 0.11
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (29 bp):
AAATAAAAGTTAATGTATAAATTCACACT
Found at i:41721317 original size:65 final size:65
Alignment explanation
Indices: 41721243--41721372 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
41721233 AAAATGATAG
*
41721243 CAAAAGAGATATATATACATAATTAGTAAATATTAACAAACAATAATTTTATTTTTTAAAAATTA
1 CAAAAGAGATATATATACATAATTAGTAAAAATTAACAAACAATAATTTTATTTTTTAAAAATTA
41721308 CAAAAGAGATATATATACATAATTAGTAAAAATTAACAAACAATAATTTTATTTTTTAAAAATTA
1 CAAAAGAGATATATATACATAATTAGTAAAAATTAACAAACAATAATTTTATTTTTTAAAAATTA
41721373 AAATTATAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (65 bp):
CAAAAGAGATATATATACATAATTAGTAAAAATTAACAAACAATAATTTTATTTTTTAAAAATTA
Found at i:41721370 original size:30 final size:30
Alignment explanation
Indices: 41721269--41721373 Score: 95
Period size: 30 Copynumber: 3.3 Consensus size: 30
41721259 ACATAATTAG
*
41721269 TAAATATTAACAAACAATAATTTTATTTTT
1 TAAAAATTAACAAACAATAATTTTATTTTT
* * * **
41721299 TAAAAATT-ACAAAAGAGATATATATACATAATTAG
1 TAAAAATTAAC-AAACA-ATA-AT-T--TTATTTTT
41721334 TAAAAATTAACAAACAATAATTTTATTTTT
1 TAAAAATTAACAAACAATAATTTTATTTTT
41721364 TAAAAATTAA
1 TAAAAATTAA
41721374 AATTATAGAC
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
29 2 0.04
30 25 0.44
31 3 0.05
32 3 0.05
33 3 0.05
34 3 0.05
35 16 0.28
36 2 0.04
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (30 bp):
TAAAAATTAACAAACAATAATTTTATTTTT
Found at i:41724419 original size:37 final size:37
Alignment explanation
Indices: 41724358--41724503 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
41724348 TACGTATGAT
* *
41724358 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41724393 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41724430 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41724467 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41724504 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:41724520 original size:46 final size:46
Alignment explanation
Indices: 41724467--41724735 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
41724457 TAAGTGTAGC
* **
41724467 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
41724513 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
41724559 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
41724611 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
41724657 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
41724709 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
41724736 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:41724586 original size:52 final size:52
Alignment explanation
Indices: 41724510--41724729 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
41724500 TAGCTAAAGC
* *
41724510 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
41724563 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
41724615 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
41724661 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
41724713 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
41724730 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:41724632 original size:98 final size:98
Alignment explanation
Indices: 41724467--41724735 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
41724457 TAAGTGTAGC
* * *
41724467 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
41724532 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
41724566 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
41724631 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
41724664 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
41724729 GATCAGA
66 GATCAGA
41724736 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:41729933 original size:4 final size:4
Alignment explanation
Indices: 41729924--41729953 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
41729914 AAAGCTAGAT
41729924 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
41729954 TGAAGTAGAT
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:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:41730233 original size:85 final size:84
Alignment explanation
Indices: 41730057--41730220 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 84
41730047 TTACAAGAAG
**
41730057 ATAATTTAATTTACAATTATTTGTTAAAAATAATTATAATTTAATTTTAATGTTATTATAGGAAA
1 ATAATTTAATTTACAATTATTCATTAAAAATAATTATAATTTAATTTTAATGTTATTATA-GAAA
* ****
41730122 AAATTGTGATCATTTTAATT
65 AAATTGAGATCAAAAAAATT
* *
41730142 ATAATTTAATTTACAATTATTCATTAAAAATAATTTTAATTTAATTTTAATTTTATTAT-G-AAA
1 ATAATTTAATTTACAATTATTCATTAAAAATAATTATAATTTAATTTTAATGTTATTATAGAAAA
*
41730205 AATTGAGGT-AAAAAAA
66 AATTGAGATCAAAAAAA
41730221 GTTGTGCTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 3 0.04
82 10 0.14
83 1 0.01
85 55 0.80
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (84 bp):
ATAATTTAATTTACAATTATTCATTAAAAATAATTATAATTTAATTTTAATGTTATTATAGAAAA
AATTGAGATCAAAAAAATT
Done.