Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold171
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: 1364075
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 108074 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:369156 original size:134 final size:134
Alignment explanation
Indices: 368763--369157 Score: 424
Period size: 134 Copynumber: 2.9 Consensus size: 134
368753 TATTGATGGA
* * ** *
368763 TAAAATTACCGAAATACGTTCGATGGGTAAAATTACTGAAATACCCTCGATGGGTAAAATTATCG
1 TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGG-AAAATTATCG
* ** *
368828 AAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACTAATATACCCTTG
65 AAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACCGATATACCCTTA
368893 ATAGC
130 ATAGC
* * * ** * *
368898 TAAAATTATCGAAATGCCATCGATAGGTAAAATTACCAAAATA-CCTTCAAAGGGAAAATTA-CT
1 TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTT-GATGGGAAAATTATC-
* * *
368961 GAAATACCCTCGATGGG-AAAATTTATCGAAATACCCTCGATAGG-AAAATTTATCGAAATACCC
64 GAAATACCCTCGATGGGTAAAA-TTACCGAAATACCCTCGATAGGTAAAA-TTACCGATATACCC
* *
369024 TTAATGGG
127 TTAATAGC
* * * *
369032 TGATATTA-CTAAAATACCCTTGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCG
1 TAAAATTATC-AAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCG
* * * *
369096 AAATACCCTCGATGGGTGAAATTACCGAAATACCC-CTAAAGGGTAAAATTACCGTTATACCC
65 AAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATA-GGTAAAATTACCGATATACCC
369158 CTAAAATATG
Statistics
Matches: 213, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
133 13 0.06
134 148 0.69
135 52 0.24
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (134 bp):
TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCGA
AATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACCGATATACCCTTAA
TAGC
Found at i:369171 original size:27 final size:27
Alignment explanation
Indices: 369112--369171 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
369102 CCTCGATGGG
* *
369112 TGAAATTACCGAAATACCCCTAAAGGG
1 TGAAATTACCGAAATACCCCTAAAAGA
* ** *
369139 TAAAATTACCGTTATACCCCTAAAATA
1 TGAAATTACCGAAATACCCCTAAAAGA
369166 TGAAAT
1 TGAAAT
369172 AATTGTTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (27 bp):
TGAAATTACCGAAATACCCCTAAAAGA
Found at i:369336 original size:29 final size:26
Alignment explanation
Indices: 369304--369359 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 26
369294 ACTGTTTCTA
369304 GTGGCTCTGCCACACTCATACTGATACTG
1 GTGGCTCTGCCACA-T-ATACTG-TACTG
*
369333 GTGGCTTTGCCACATATACTGTACTG
1 GTGGCTCTGCCACATATACTGTACTG
369359 G
1 G
369360 CAGCTCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 1 0.04
29 13 0.50
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
GTGGCTCTGCCACATATACTGTACTG
Found at i:369713 original size:15 final size:15
Alignment explanation
Indices: 369693--369723 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
369683 CTGTGCAGGT
369693 AATCCCCAACCTTAG
1 AATCCCCAACCTTAG
369708 AATCCCCAACCTTAG
1 AATCCCCAACCTTAG
369723 A
1 A
369724 TGATTTGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.39, G:0.06, T:0.19
Consensus pattern (15 bp):
AATCCCCAACCTTAG
Found at i:369944 original size:19 final size:19
Alignment explanation
Indices: 369903--369947 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
369893 TTCAAGTAAG
*
369903 TTTTCAAAACAAACACTGT
1 TTTTCAAAACAAACACTGA
*
369922 TTTTCATAACAAACACCT-A
1 TTTTCAAAACAAACA-CTGA
369941 TTTTCAA
1 TTTTCAA
369948 CTTCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (19 bp):
TTTTCAAAACAAACACTGA
Found at i:374110 original size:22 final size:22
Alignment explanation
Indices: 374082--374124 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
374072 GCTTAATTGA
374082 ATTATACAGTCACAAAGAAAGG
1 ATTATACAGTCACAAAGAAAGG
* *
374104 ATTATACAGTCATAGAGAAAG
1 ATTATACAGTCACAAAGAAAG
374125 AGTTACTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (22 bp):
ATTATACAGTCACAAAGAAAGG
Found at i:388042 original size:411 final size:411
Alignment explanation
Indices: 387274--388087 Score: 1351
Period size: 411 Copynumber: 2.0 Consensus size: 411
387264 TGAATTACAT
*
387274 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTTGACAAGTTTCGAATCTATCTTGTAG
1 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATCTATCTTGTAG
* * *
387339 GTACCAAAGTGACTGTTTATATGGACCAGTCGACAGTTAAGTATTTACTTACCAAGAAAGACGCT
66 GTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGCT
* * * * *
387404 AAGCCGGGACTGATGTGATGGGTATTTCTACTTAAAGAGTTGGATCTAGAAATTCAAGATCAAAA
131 AAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAAA
* *
387469 GGGAGTGGAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAATGGAACTCTCCTC
196 GGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCTC
* *
387534 TTATACCAATTCAAGAGATGTTTCCAAATGAACACATACTGAAGATAAATCATGTTGATAATACC
261 TTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATACC
* * *
387599 CCTTGGTTTGCTGATATTGCTTACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGATGTATCA
326 CCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATCA
387664 TCAAAAGAAAAAGAGAGACAC
391 TCAAAAGAAAAAGAGAGACAC
* *
387685 GGTAATAGAAAAAGAGTTACTTGCTATTGTGTTTGCTTTAGACAAGTTTCG-ATCTTATCTTGTA
1 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATC-TATCTTGTA
* *
387749 GGTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTGCCAAGAAAGACTC
65 GGTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGC
**
387814 TAAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATTGAA
130 TAAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAA
* * *
387879 AGGGAGTGCAAAACCAAGTAGCAGACCACTTGTTCAGATTGGAGCCATAAGAAGGGAACTCTCCT
195 AGGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCT
* * * *
387944 TTTATACCAATTCTAGAGACGTTTCCAGATGAACACATACTGAAGGTAAATCATGTCGATAATAC
260 CTTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATAC
388009 CCCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATC
325 CCCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATC
388074 ATCAAAAGAAAAAG
390 ATCAAAAGAAAAAG
388088 TTTCTTTACG
Statistics
Matches: 373, Mismatches: 29, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
410 3 0.01
411 370 0.99
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (411 bp):
GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATCTATCTTGTAG
GTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGCT
AAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAAA
GGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCTC
TTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATACC
CCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATCA
TCAAAAGAAAAAGAGAGACAC
Found at i:390620 original size:19 final size:19
Alignment explanation
Indices: 390598--390635 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
390588 TCCCTCATCC
390598 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
390617 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
390636 ACTCTTTTAG
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:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:397990 original size:47 final size:48
Alignment explanation
Indices: 397930--398122 Score: 219
Period size: 48 Copynumber: 4.0 Consensus size: 48
397920 TACTATGCGT
* *
397930 ACCGATAAGCTGTTATGACACAAGGGTGGCA-GGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * *
397977 ACCGATATTCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * * * * * * *
398025 ACCAATAA-CTTGTTAAGATACAAACGTGGAACAGACTATGTGTAGGCC
1 ACCGATAATC-TGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * *
398073 ACCGAGAATCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
398121 AC
1 AC
398123 TGAGAAATCT
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
47 29 0.24
48 89 0.75
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (48 bp):
ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
Found at i:399508 original size:24 final size:24
Alignment explanation
Indices: 399473--399523 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
399463 AAAGCAATGC
399473 GCCGGCTCCCGC-TCGAAGGACTGT
1 GCCGGCTCCCGCGT-GAAGGACTGT
*
399497 GCCGGCTTCCGCGTGAAGGACTGT
1 GCCGGCTCCCGCGTGAAGGACTGT
399521 GCC
1 GCC
399524 TGCGGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.12, C:0.35, G:0.35, T:0.18
Consensus pattern (24 bp):
GCCGGCTCCCGCGTGAAGGACTGT
Found at i:405523 original size:48 final size:47
Alignment explanation
Indices: 405442--405631 Score: 215
Period size: 48 Copynumber: 4.0 Consensus size: 47
405432 TGTACTGATA
** *
405442 ATCTGTTAGGACACAAGGGTGG-ATCGGATTGTGTGCAGGCCACCGAT
1 ATCTGTTTTGACACAAGGGTGGCA-CGGACTGTGTGCAGGCCACCGAT
405489 ATTCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
1 A-TCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
* ** * *
405537 AACTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCCAGA-
1 ATC-TGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCA-CC-GAT
* *
405586 ATCTGTTATT-ACACAAAGGTGGTACGGACTGTGTGCAGGCCACCGA
1 ATCTGTT-TTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGA
405632 GAAATCTATT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
46 2 0.02
47 4 0.03
48 109 0.89
49 5 0.04
50 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (47 bp):
ATCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
Found at i:405607 original size:96 final size:96
Alignment explanation
Indices: 405445--405631 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
405435 ACTGATAATC
* * * * * * *
405445 TGTTAGGACACAAGGGTGGATCGGATTGTGTGCAGGCCACCGATATTCTGTTTTGACACAAGGGT
1 TGTTAAGACACAAGGGTGGATCGGACTATGTGCAGGCCACCCAGAATCTGTTTTGACACAAAGGT
405510 GGCACGGACTGTGTGCAGGCCACCGATAACT
66 GGCACGGACTGTGTGCAGGCCACCGATAACT
*
405541 TGTTAAGATACAAGGGTGGCA-CGGACTATGTGCAGGCCACCCAGAATCTGTTATT-ACACAAAG
1 TGTTAAGACACAAGGGTGG-ATCGGACTATGTGCAGGCCACCCAGAATCTGTT-TTGACACAAAG
*
405604 GTGGTACGGACTGTGTGCAGGCCACCGA
64 GTGGCACGGACTGTGTGCAGGCCACCGA
405632 GAAATCTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 77 0.96
97 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.22
Consensus pattern (96 bp):
TGTTAAGACACAAGGGTGGATCGGACTATGTGCAGGCCACCCAGAATCTGTTTTGACACAAAGGT
GGCACGGACTGTGTGCAGGCCACCGATAACT
Found at i:411484 original size:19 final size:19
Alignment explanation
Indices: 411462--411499 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
411452 TCACTCATCC
411462 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
411481 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
411500 ACTATTTTAT
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:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:419425 original size:21 final size:22
Alignment explanation
Indices: 419401--419443 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
419391 ACTCATCCCT
*
419401 CATTCTTCA-TCCTTTCATTCA
1 CATTCTACATTCCTTTCATTCA
*
419422 CATTCTACATTCCTTTCTTTCA
1 CATTCTACATTCCTTTCATTCA
419444 TTCCATTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.49
Consensus pattern (22 bp):
CATTCTACATTCCTTTCATTCA
Found at i:440814 original size:14 final size:15
Alignment explanation
Indices: 440785--440816 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
440775 AAAAACATCA
440785 TAATTTTATCTATTT
1 TAATTTTATCTATTT
440800 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
440814 TAA
1 TAA
440817 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:447959 original size:40 final size:40
Alignment explanation
Indices: 447915--447993 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
447905 TTAGCTCTGG
447915 CACTTCTGCTAACTCCTATGGCACCATTATTTCCTGGTCC
1 CACTTCTGCTAACTCCTATGGCACCATTATTTCCTGGTCC
447955 CACTTCTGCTAACTCCTATGGCACCATTATTTCCTGGTC
1 CACTTCTGCTAACTCCTATGGCACCATTATTTCCTGGTC
447994 GTCTACCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35
Consensus pattern (40 bp):
CACTTCTGCTAACTCCTATGGCACCATTATTTCCTGGTCC
Found at i:462911 original size:40 final size:40
Alignment explanation
Indices: 462856--462936 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
462846 GCTAGTTGAG
462856 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
1 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
*
462896 TTAGAGCACAAAGCATTTTGGATAAACAAGAAATAAAACA
1 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
462936 T
1 T
462937 GGACTAGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.20
Consensus pattern (40 bp):
TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
Found at i:481026 original size:23 final size:23
Alignment explanation
Indices: 480996--481043 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
480986 TGCTTTTTTG
*
480996 AGTGGAGCAAAACTCCTTGTTTA
1 AGTGGAGCAAAACTCCCTGTTTA
*
481019 AGTGGAGCAAAAGTCCCTGTTTA
1 AGTGGAGCAAAACTCCCTGTTTA
481042 AG
1 AG
481044 AGTAAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (23 bp):
AGTGGAGCAAAACTCCCTGTTTA
Found at i:481751 original size:14 final size:14
Alignment explanation
Indices: 481732--481771 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
481722 TTGTTTGCCA
481732 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
481746 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
481760 GGAAAATGTTTT
1 GTAAAATGTTTT
481772 ACTTTTCTGT
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:481784 original size:34 final size:35
Alignment explanation
Indices: 481740--481806 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
481730 CAGTAAAATG
* *
481740 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
*
481774 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
481807 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:481792 original size:20 final size:20
Alignment explanation
Indices: 481755--481794 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
481745 CGTAAAATGA
**
481755 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATAATTTACT
*
481775 TTTCTGTAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
481795 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:483493 original size:107 final size:107
Alignment explanation
Indices: 483307--483521 Score: 414
Period size: 107 Copynumber: 2.0 Consensus size: 107
483297 ACAAATTGGG
483307 GTTTGAACTAATCAAAAACAGAGCAGCTTTAAATTAAAGACAACCACAATATGGAAAGCATCAAA
1 GTTTGAACTAATCAAAAACAGAGCAGCTTTAAATTAAAGACAACCACAATATGGAAAGCATCAAA
483372 TTTTTTAAAGGAGATGGAAACAAAAATTGAAGGCACCACAAT
66 TTTTTTAAAGGAGATGGAAACAAAAATTGAAGGCACCACAAT
483414 GTTTGAACTAATCAAAAACAGAGCAGCTTTAAATTAAAGACAACCACAAATATGGAAAG-ATCAA
1 GTTTGAACTAATCAAAAACAGAGCAGCTTTAAATTAAAGACAACCAC-AATATGGAAAGCATCAA
483478 ATTTTTTAAAGGAGATGGAAACAAAAATTGAAGGCACCACAAT
65 ATTTTTTAAAGGAGATGGAAACAAAAATTGAAGGCACCACAAT
483521 G
1 G
483522 GCTTTCAAGG
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 96 0.90
108 11 0.10
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (107 bp):
GTTTGAACTAATCAAAAACAGAGCAGCTTTAAATTAAAGACAACCACAATATGGAAAGCATCAAA
TTTTTTAAAGGAGATGGAAACAAAAATTGAAGGCACCACAAT
Found at i:484393 original size:14 final size:14
Alignment explanation
Indices: 484374--484401 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
484364 TGGAAAAGGT
484374 GGAAAATATTTTCC
1 GGAAAATATTTTCC
484388 GGAAAATATTTTCC
1 GGAAAATATTTTCC
484402 ACCAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAAAATATTTTCC
Found at i:485120 original size:20 final size:21
Alignment explanation
Indices: 485081--485126 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
485071 CGGAATGTAG
485081 TCAACCTAACATGAATTAAAT
1 TCAACCTAACATGAATTAAAT
485102 TCAACCTAA-ATTG-ATTAAAT
1 TCAACCTAACA-TGAATTAAAT
485122 T-AACC
1 TCAACC
485127 ATTCCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (21 bp):
TCAACCTAACATGAATTAAAT
Found at i:489637 original size:30 final size:30
Alignment explanation
Indices: 489581--489639 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
489571 CTTTTTGAAT
* *
489581 ATATTTACAAAAAGAGGCATCTAATTTTTA
1 ATATTTACAAAAAGAGGCACCAAATTTTTA
489611 ATATTTACAAAAAGA-GCAACCAAATTTTT
1 ATATTTACAAAAAGAGGC-ACCAAATTTTT
489640 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (30 bp):
ATATTTACAAAAAGAGGCACCAAATTTTTA
Found at i:491640 original size:519 final size:519
Alignment explanation
Indices: 490661--491699 Score: 2078
Period size: 519 Copynumber: 2.0 Consensus size: 519
490651 GTGAACACAT
490661 GTTTCTGCAAAAACTTCATTACAACCATAGCATCGTTTGTCGGATATGCCTCTACCTCAACCCAC
1 GTTTCTGCAAAAACTTCATTACAACCATAGCATCGTTTGTCGGATATGCCTCTACCTCAACCCAC
490726 TTAGACACATAGTATACTACTCCTAATATGTACTTTTGACGAAAAGATAGAGGGAAATGATCGAG
66 TTAGACACATAGTATACTACTCCTAATATGTACTTTTGACGAAAAGATAGAGGGAAATGATCGAG
490791 AAAGTCAATACCCCAAACATCGAATAATTCTACCTCAAAGATGTTTGTTCGAGGCATCTCATTTC
131 AAAGTCAATACCCCAAACATCGAATAATTCTACCTCAAAGATGTTTGTTCGAGGCATCTCATTTC
490856 TATTGGTGACATTTTTGACCCTTTGAAATCGATCACAACTCTTTTCATAAGCATATGCATATTTG
196 TATTGGTGACATTTTTGACCCTTTGAAATCGATCACAACTCTTTTCATAAGCATATGCATATTTG
490921 AATAGTGTTGGCCAAAAGAATCTGGCTTGCAATACCTTGGCTGTAATACGTGTACCTCTAAAGTG
261 AATAGTGTTGGCCAAAAGAATCTGGCTTGCAATACCTTGGCTGTAATACGTGTACCTCTAAAGTG
490986 TCCCCTACTCGGAGCTGGGTGACAATGGTATAAAATCTTATGTACTTCATCTTCTGCCACGCGTC
326 TCCCCTACTCGGAGCTGGGTGACAATGGTATAAAATCTTATGTACTTCATCTTCTGCCACGCGTC
491051 TTCTAATCATTTGATCTGCACACTTTTTAAACAAATACGGTTCTTCCCAGAAATAGTACTTCACA
391 TTCTAATCATTTGATCTGCACACTTTTTAAACAAATACGGTTCTTCCCAGAAATAGTACTTCACA
491116 TTGTGAAGAAAATTTTTCTTTTGATGATACGTCTTATACATCGGCATCAAACCACAAGCTAAAA
456 TTGTGAAGAAAATTTTTCTTTTGATGATACGTCTTATACATCGGCATCAAACCACAAGCTAAAA
491180 GTTTCTGCAAAAACTTCATTACAACCATAGCATCGTTTGTCGGATATGCCTCTACCTCAACCCAC
1 GTTTCTGCAAAAACTTCATTACAACCATAGCATCGTTTGTCGGATATGCCTCTACCTCAACCCAC
491245 TTAGACACATAGTATACTACTCCTAATATGTACTTTTGACGAAAAGATAGAGGGAAATGATCGAG
66 TTAGACACATAGTATACTACTCCTAATATGTACTTTTGACGAAAAGATAGAGGGAAATGATCGAG
491310 AAAGTCAATACCCCAAACATCGAATAATTCTACCTCAAAGATGTTTGTTCGAGGCATCTCATTTC
131 AAAGTCAATACCCCAAACATCGAATAATTCTACCTCAAAGATGTTTGTTCGAGGCATCTCATTTC
491375 TATTGGTGACATTTTTGACCCTTTGAAATCGATCACAACTCTTTTCATAAGCATATGCATATTTG
196 TATTGGTGACATTTTTGACCCTTTGAAATCGATCACAACTCTTTTCATAAGCATATGCATATTTG
491440 AATAGTGTTGGCCAAAAGAATCTGGCTTGCAATACCTTGGCTGTAATACGTGTACCTCTAAAGTG
261 AATAGTGTTGGCCAAAAGAATCTGGCTTGCAATACCTTGGCTGTAATACGTGTACCTCTAAAGTG
491505 TCCCCTACTCGGAGCTGGGTGACAATGGTATAAAATCTTATGTACTTCATCTTCTGCCACGCGTC
326 TCCCCTACTCGGAGCTGGGTGACAATGGTATAAAATCTTATGTACTTCATCTTCTGCCACGCGTC
491570 TTCTAATCATTTGATCTGCACACTTTTTAAACAAATACGGTTCTTCCCAGAAATAGTACTTCACA
391 TTCTAATCATTTGATCTGCACACTTTTTAAACAAATACGGTTCTTCCCAGAAATAGTACTTCACA
491635 TTGTGAAGAAAATTTTTCTTTTGATGATACGTCTTATACATCGGCATCAAACCACAAGCTAAAA
456 TTGTGAAGAAAATTTTTCTTTTGATGATACGTCTTATACATCGGCATCAAACCACAAGCTAAAA
491699 G
1 G
491700 GTTAGCAATA
Statistics
Matches: 520, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
519 520 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (519 bp):
GTTTCTGCAAAAACTTCATTACAACCATAGCATCGTTTGTCGGATATGCCTCTACCTCAACCCAC
TTAGACACATAGTATACTACTCCTAATATGTACTTTTGACGAAAAGATAGAGGGAAATGATCGAG
AAAGTCAATACCCCAAACATCGAATAATTCTACCTCAAAGATGTTTGTTCGAGGCATCTCATTTC
TATTGGTGACATTTTTGACCCTTTGAAATCGATCACAACTCTTTTCATAAGCATATGCATATTTG
AATAGTGTTGGCCAAAAGAATCTGGCTTGCAATACCTTGGCTGTAATACGTGTACCTCTAAAGTG
TCCCCTACTCGGAGCTGGGTGACAATGGTATAAAATCTTATGTACTTCATCTTCTGCCACGCGTC
TTCTAATCATTTGATCTGCACACTTTTTAAACAAATACGGTTCTTCCCAGAAATAGTACTTCACA
TTGTGAAGAAAATTTTTCTTTTGATGATACGTCTTATACATCGGCATCAAACCACAAGCTAAAA
Found at i:496602 original size:21 final size:20
Alignment explanation
Indices: 496573--496618 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
496563 CAAAATGCAA
496573 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
496594 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
496614 T-AACC
1 TCAACC
496619 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:501470 original size:14 final size:14
Alignment explanation
Indices: 501447--501479 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
501437 TCTCCTCTCC
501447 CTTTTT-CCTTCTT
1 CTTTTTCCCTTCTT
501460 CTTTTTCCCTTCTT
1 CTTTTTCCCTTCTT
501474 -TTTTTC
1 CTTTTTC
501480 TCTCCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTTTCCCTTCTT
Found at i:501637 original size:7 final size:7
Alignment explanation
Indices: 501625--501852 Score: 359
Period size: 7 Copynumber: 32.7 Consensus size: 7
501615 TTTCATTCTT
501625 TATTTCC
1 TATTTCC
501632 TATTTCC
1 TATTTCC
501639 TATTTCC
1 TATTTCC
501646 TATTTCC
1 TATTTCC
501653 TATTTCC
1 TATTTCC
501660 TATTTCC
1 TATTTCC
501667 TATTTCC
1 TATTTCC
501674 TATTTCC
1 TATTTCC
501681 TATTTCC
1 TATTTCC
501688 TATTTCC
1 TATTTCC
501695 TATTTCC
1 TATTTCC
501702 TATTTCC
1 TATTTCC
501709 TATTTCC
1 TATTTCC
501716 TATTTCC
1 TATTTCC
501723 TATTTCC
1 TATTTCC
501730 TATTTCC
1 TATTTCC
501737 TATTT-C
1 TATTTCC
501743 TATTTCC
1 TATTTCC
501750 TATTTCC
1 TATTTCC
501757 TATTTCC
1 TATTTCC
501764 TATTTCC
1 TATTTCC
501771 TATTTCC
1 TATTTCC
*
501778 TATTTCT
1 TATTTCC
*
501785 TATTTCG
1 TATTTCC
*
501792 TATTTCT
1 TATTTCC
*
501799 TATTTCG
1 TATTTCC
*
501806 TATTTCG
1 TATTTCC
*
501813 TATTTCT
1 TATTTCC
* *
501820 TGTTTCT
1 TATTTCC
501827 TATTTCC
1 TATTTCC
*
501834 TATTTCT
1 TATTTCC
*
501841 TATTTCT
1 TATTTCC
501848 TATTT
1 TATTT
501853 TCATTAGTTA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
6 6 0.03
7 205 0.97
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.61
Consensus pattern (7 bp):
TATTTCC
Found at i:503626 original size:6 final size:5
Alignment explanation
Indices: 503597--503648 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
503587 ATTGAGTCAA
*
503597 TTTAT TTTAT TTTAT TTTATT TTTACT TTTAT TTT-T TAT-T TTTAT GTTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT -TTTAT
503648 T
1 T
503649 GTAATTTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 6 0.15
5 20 0.49
6 15 0.37
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:505564 original size:14 final size:14
Alignment explanation
Indices: 505545--505572 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
505535 CTAATTTATT
505545 AATGAATTATTAAA
1 AATGAATTATTAAA
505559 AATGAATTATTAAA
1 AATGAATTATTAAA
505573 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:508000 original size:27 final size:26
Alignment explanation
Indices: 507969--508045 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 26
507959 TTAAAAAATG
507969 GAAATATCCCCATAGGGTAAAATAACC
1 GAAATA-CCCCATAGGGTAAAATAACC
*
507996 GAAATACTCCCATAGGGTAAAATAATC
1 GAAATAC-CCCATAGGGTAAAATAACC
508023 GAAATACCTCCATAGGGTAAAAT
1 GAAATACC-CCATAGGGTAAAAT
508046 GACTGTTATA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (26 bp):
GAAATACCCCATAGGGTAAAATAACC
Found at i:510881 original size:40 final size:40
Alignment explanation
Indices: 510837--510917 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
510827 GTAGCTTACA
510837 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
510877 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
1 TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
510917 T
1 T
510918 GTGTCATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (40 bp):
TACCTTTCCAGCATCCTTTAGATTGACAAAACCTTCAGGT
Found at i:511504 original size:9 final size:9
Alignment explanation
Indices: 511490--511514 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
511480 GTGATTCTCG
511490 AAGTTCATC
1 AAGTTCATC
511499 AAGTTCATC
1 AAGTTCATC
511508 AAGTTCA
1 AAGTTCA
511515 ATCTTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (9 bp):
AAGTTCATC
Found at i:514026 original size:49 final size:49
Alignment explanation
Indices: 513973--514120 Score: 278
Period size: 49 Copynumber: 3.0 Consensus size: 49
513963 ACAACTCTTG
513973 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
*
514022 TTCTAAACATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
*
514071 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCCAGGTTTCTAA
1 TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
514120 T
1 T
514121 CCTATTAGAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 96 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (49 bp):
TTCTAATCATCTTATGATTTATCCAAATTACTTGCCTCTAGGTTTCTAA
Found at i:515584 original size:27 final size:27
Alignment explanation
Indices: 515315--515583 Score: 502
Period size: 27 Copynumber: 10.0 Consensus size: 27
515305 TTCAAATAAC
515315 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515342 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515369 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515396 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515423 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515450 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515477 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
515504 CAAAATACCCCCATAGGGTAAAATGAA
1 CAAAATACCCCCATAGGGTAAAATGAA
*
515531 CAAAATACCCCCATAGGGTAAAATGAC
1 CAAAATACCCCCATAGGGTAAAATGAA
* * *
515558 CGAAATACCTCCATAAGGTAAAATGA
1 CAAAATACCCCCATAGGGTAAAATGA
515584 CTGTTATACC
Statistics
Matches: 238, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 238 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (27 bp):
CAAAATACCCCCATAGGGTAAAATGAA
Found at i:530095 original size:30 final size:30
Alignment explanation
Indices: 530059--530116 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
530049 CTGGGCAATT
*
530059 CCACACGGGCTAGG-CACACGCCCGTGTGAG
1 CCACACGGGCT-GGCCACACGCCCATGTGAG
*
530089 CCACACGGGCTGGCCACATGCCCATGTG
1 CCACACGGGCTGGCCACACGCCCATGTG
530117 CCAACCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGGCCACACGCCCATGTGAG
Found at i:533228 original size:20 final size:20
Alignment explanation
Indices: 533203--533242 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
533193 TATCACCACT
533203 CATAGACTCGTAGAGTCAAA
1 CATAGACTCGTAGAGTCAAA
533223 CATAGACTCGTAGAGTCAAA
1 CATAGACTCGTAGAGTCAAA
533243 TATATAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
CATAGACTCGTAGAGTCAAA
Found at i:538096 original size:652 final size:652
Alignment explanation
Indices: 536853--538816 Score: 3448
Period size: 652 Copynumber: 3.0 Consensus size: 652
536843 ATTACAGTAT
* * * * * *
536853 CAATATTCAATGCAGTAACAGATATACATTTTCGAATCCTACCCAGCCAGCATCTACACTCCAA-
1 CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
* * *
536917 TTCTGTCCAACCCTACACTCCATGTGAGAATATAATCAATCCACCTATCCCTACACTCCAGAAAG
66 TTC-GTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCCAGAAAG
* *
536982 TACCGAATGCGGCACTAAATAGTAGTTTGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTT
130 TACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTT
*
537047 CAGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAGATATGACA
195 CAGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACA
* *
537112 TGCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGTGACATCATCAG
260 TGCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAA
* * * ***
537177 ACTTAATCATATCAGTCATACAGTCATTTTAGTCAATTAGGGGTCGAGGTAAACTTGTTGTCCCT
325 ACTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGGGTCTAGGTAAACTTACCGTCCCT
* * * *
537242 ACAGTAGGTTCAAAGTCGACTTGGCCGACCCGTCCAACCTTATCAGTGAAATAGTGAAAATGGGC
390 ACAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGC
*
537307 CTACGAGCCCAAAAAGTTCACCCATGT-GCGTCCACACGCCCGTGTGGCCCACATGGCCCAAACT
455 CTACGAGCCCAAAAAGTTCACCCATGTAG-GCCCACACGCCCGTGTGGCCCACATGGCCCAAACT
* *
537371 GACCCTGGCCTCGTGATCCATTTTAGTGTAACCCATGCTAGATAATTATTCATATGTGTTTGCCC
519 GACCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCC
537436 TTTTTACTTATAATCCTTCCAAGCTGTCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAA
584 TTTTTACTTATAATCCTTCCAAGCTGTCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAA
537501 GATA
649 GATA
537505 CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
1 CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
*
537570 TTCGTCCAACCCTACACTCTATGTGGGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
66 TTCGTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
* *
537635 ACCGAATGCGGCAGTAAACAGTAGTTCGCAGCAGAGCTGCCAATAACTTAGGCTTGAGGCCTTTC
131 ACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
537700 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
196 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
*
537765 GCTGTAACATAATATCATGCATGTAAAGAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
261 GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
*
537830 CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGGGTCTAGGTAATCTTACCGTCCCTA
326 CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGGGTCTAGGTAAACTTACCGTCCCTA
537895 CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
391 CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
* * *
537960 TACGAGCCCAAAAGGTTCACTCATGTAGGCCCATACGCCCGTGTGGCCCACATGGCCCAAACTGA
456 TACGAGCCCAAAAAGTTCACCCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
538025 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
521 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
*
538090 TTTACTTATAATCCTTCCAAGCTATCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAAGA
586 TTTACTTATAATCCTTCCAAGCTGTCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAAGA
538155 TA
651 TA
538157 CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
1 CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
*
538222 TTCGTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCTAGAAAGT
66 TTCGTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
*
538287 ACTGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
131 ACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
538352 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
196 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
*
538417 GCTGTAACATAATATCATGCATGTAATTAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
261 GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
*
538482 CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGAGTCTAGGTAAACTTACCGTCCCTA
326 CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGGGTCTAGGTAAACTTACCGTCCCTA
*
538547 CAGTAGGTTCAAAGTCGACTTGGCTGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
391 CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
*
538612 TACGAGCCCAAAAAGTTCACCCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCTCAAACTGA
456 TACGAGCCCAAAAAGTTCACCCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
*
538677 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTTTCCC-
521 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTG-TTTGCCCT
* * *
538741 TTTTACTTATAATCCTTCCAAGCTGTCTACTTGCGTCACTGTTACTAAATTAATTGTATATTAAG
585 TTTTACTTATAATCCTTCCAAGCTGTCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAAG
*
538806 CTA
650 ATA
*
538809 CAAAATTC
1 CAATATTC
538817 TGAATTAAGG
Statistics
Matches: 1252, Mismatches: 57, Indels: 6
0.95 0.04 0.00
Matches are distributed among these distances:
652 1242 0.99
653 10 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (652 bp):
CAATATTCAACGCCGTAACAGATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
TTCGTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
ACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGGGTCTAGGTAAACTTACCGTCCCTA
CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
TACGAGCCCAAAAAGTTCACCCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
TTTACTTATAATCCTTCCAAGCTGTCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAAGA
TA
Found at i:546873 original size:20 final size:20
Alignment explanation
Indices: 546848--546920 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
546838 TGATGAACCT
546848 TTCCATTTACTTACTTAT-CA
1 TTCCATTTACTTACTT-TCCA
*
546868 TTCCATTTGCTTACTTTCCA
1 TTCCATTTACTTACTTTCCA
*
546888 TTTCATTTACTTACTTTCCA
1 TTCCATTTACTTACTTTCCA
*
546908 TTCTATTTACTTA
1 TTCCATTTACTTA
546921 GCATAAGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.21, C:0.25, G:0.01, T:0.53
Consensus pattern (20 bp):
TTCCATTTACTTACTTTCCA
Found at i:548374 original size:30 final size:30
Alignment explanation
Indices: 548333--548398 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
548323 GTATGTCCGA
*
548333 CCGTATACCTCTCAAAATGGCCCCACACGC
1 CCGTGTACCTCTCAAAATGGCCCCACACGC
** * *
548363 CCGTGTACCTCTTGAAATGGCCTCACATGC
1 CCGTGTACCTCTCAAAATGGCCCCACACGC
548393 CCGTGT
1 CCGTGT
548399 GCCAGGCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (30 bp):
CCGTGTACCTCTCAAAATGGCCCCACACGC
Found at i:560670 original size:3 final size:3
Alignment explanation
Indices: 560662--560686 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
560652 TGAGGTTTTT
560662 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
560687 GATAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:564617 original size:84 final size:85
Alignment explanation
Indices: 564513--564681 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 85
564503 TGATAATAAA
564513 ATAAAAATGCGAAAACTGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTGAT
1 ATAAAAATGCGAAAACTGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTGAT
564578 CAAGTGACAAAGTGATAAGT
66 CAAGTGACAAAGTGATAAGT
564598 ATAAAAATGC-AAAACTGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTGAT
1 ATAAAAATGCGAAAACTGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTGAT
564662 CAAGTGACAAAGTGATAAGT
66 CAAGTGACAAAGTGATAAGT
564682 GGTAGCCTAG
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 74 0.88
85 10 0.12
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (85 bp):
ATAAAAATGCGAAAACTGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTGAT
CAAGTGACAAAGTGATAAGT
Found at i:565634 original size:27 final size:27
Alignment explanation
Indices: 565595--565815 Score: 284
Period size: 27 Copynumber: 8.2 Consensus size: 27
565585 AGAGGTCGAT
*
565595 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
565622 AAATAACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
565649 AAATGACCGAATTAGCCCCACAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
565676 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
565703 AAATGACTG-AATACCCCTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
565729 AAATGACC-AAATTACCCCCATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
* ** * *
565756 AAATGATCGAGTTACCCCCACAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
565783 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
565810 AAATGA
1 AAATGA
565816 TTGTTATACC
Statistics
Matches: 166, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.13
27 143 0.86
28 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:565791 original size:107 final size:108
Alignment explanation
Indices: 565605--565829 Score: 328
Period size: 107 Copynumber: 2.1 Consensus size: 108
565595 AAATGACCAA
* *
565605 AATACCCCCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTAGCCCCAC
1 AATACCCCTATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTACCCCCAC
* *
565670 AGGGTAAAATGACCGAATTACCCCCACAGGGTAAAATGACTG-
66 AGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
* * * *
565712 AATACCCCTATAGGTTAAAATGACC-AAATTACCCCCATAGGGTAAAATGATCGAGTTACCCCCA
1 AATACCCCTATAGGGTAAAATAACCGAAA-TACCCCCATAGGGTAAAATGACCGAATTACCCCCA
* *
565776 CAGAGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATTGT
65 CAGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
*
565820 TATACCCCTA
1 AATACCCCTA
565830 GGAGATGAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
106 3 0.03
107 93 0.89
108 9 0.09
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (108 bp):
AATACCCCTATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTACCCCCAC
AGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
Found at i:565841 original size:54 final size:54
Alignment explanation
Indices: 565606--565843 Score: 202
Period size: 54 Copynumber: 4.4 Consensus size: 54
565596 AATGACCAAA
* * *
565606 ATACCCCCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATT
1 ATACCCCCAGA-GATAAAATGACCGAAATACCCCCATAGGGTAAAATGACCG-ATT
* * * * *
565662 A-GCCCCACAG-GGTAAAATGACCGAATTACCCCCACAGGGTAAAATGACTGA--
1 ATACCCC-CAGAGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGATT
* * * * *
565713 ATACCCCTATAGGTTAAAATGACC-AAATTACCCCCATAGGGTAAAATGATCGAGT
1 ATACCCCCAGA-GATAAAATGACCGAAA-TACCCCCATAGGGTAAAATGACCGATT
* **
565768 -TACCCCCACAGAGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATTG-TT
1 ATACCCCCAGAGA-TAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGATT
* *
565821 ATACCCCTAGGAGATGAAATGAC
1 ATACCCCCA-GAGATAAAATGAC
565844 TGTTATGGCC
Statistics
Matches: 149, Mismatches: 22, Indels: 24
0.76 0.11 0.12
Matches are distributed among these distances:
51 2 0.01
52 6 0.04
53 36 0.24
54 92 0.62
55 10 0.07
56 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (54 bp):
ATACCCCCAGAGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGATT
Found at i:581856 original size:50 final size:49
Alignment explanation
Indices: 581740--581875 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 49
581730 GATAATAACA
* * *
581740 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC
1 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCATCTAC
* * *
581789 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGA-GTTCTCATCT-C
1 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTT-TCATCTAC
* *
581837 GGTGCCAACGCCATGTCCCAAACATGATCTTACATGGGA
1 --TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGA
581876 CCTCATCCTC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.05
49 37 0.50
50 33 0.45
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCATCTAC
Found at i:588119 original size:3 final size:3
Alignment explanation
Indices: 588106--588142 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
588096 AAGCACTAAG
* *
588106 TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
588143 AGAGCTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:589291 original size:9 final size:9
Alignment explanation
Indices: 589277--589347 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
589267 AATGAATTTG
589277 AAATTATTA
1 AAATTATTA
589286 AAATTATTTTA
1 AAATTA--TTA
*
589297 AAATAATTTA
1 AAATTA-TTA
589307 AAATTATTA
1 AAATTATTA
* *
589316 AAATGATTTTG
1 AAAT--TATTA
* *
589327 AAATCAGTA
1 AAATTATTA
589336 AAATTATTA
1 AAATTATTA
589345 AAA
1 AAA
589348 ATATAAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
9 24 0.50
10 9 0.19
11 15 0.31
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (9 bp):
AAATTATTA
Found at i:589311 original size:30 final size:30
Alignment explanation
Indices: 589266--589347 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
589256 CCATGTCAGC
* *
589266 AAATGAATTTGAAATTATTAAAATTATTTTA
1 AAAT-AATTTAAAATTATTAAAATGATTTTA
*
589297 AAATAATTTAAAATTATTAAAATGATTTTG
1 AAATAATTTAAAATTATTAAAATGATTTTA
* *
589327 AAATCA-GTAAAATTATTAAAA
1 AAATAATTTAAAATTATTAAAA
589348 ATATAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.30
30 28 0.61
31 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (30 bp):
AAATAATTTAAAATTATTAAAATGATTTTA
Found at i:593283 original size:18 final size:18
Alignment explanation
Indices: 593239--593303 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
593229 GTTTTTTCCG
593239 AATATATATA-TTTAA-A
1 AATATATATATTTTAATA
593255 AA-ATATATATTTTAATA
1 AATATATATATTTTAATA
*
593272 AATATATGTATTTTAATA
1 AATATATATATTTTAATA
*
593290 ATTATATATATTTT
1 AATATATATATTTT
593304 GATAGGAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
15 7 0.16
16 7 0.16
17 3 0.07
18 26 0.60
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATATATATTTTAATA
Found at i:593500 original size:15 final size:16
Alignment explanation
Indices: 593448--593503 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
593438 TTTTATGTAT
593448 TTTATATAATTTCTATA
1 TTTATATAATTTCTA-A
* **
593465 GTTTGTATAATTTCTTC
1 -TTTATATAATTTCTAA
593482 TTTATA-AATTTCTAA
1 TTTATATAATTTCTAA
593497 TTTATAT
1 TTTATAT
593504 TTGTTGAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
18 13 0.42
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (16 bp):
TTTATATAATTTCTAA
Found at i:593602 original size:16 final size:17
Alignment explanation
Indices: 593581--593618 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
593571 TTCTTAATAT
593581 TTTTTTCTATT-TTCTA
1 TTTTTTCTATTATTCTA
*
593597 TTTTTTCTATTATTTTA
1 TTTTTTCTATTATTCTA
593614 TTTTT
1 TTTTT
593619 AGATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTATTATTCTA
Found at i:594600 original size:18 final size:18
Alignment explanation
Indices: 594579--594615 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
594569 TTTGCGCAAG
594579 AACAGTAGCTTTTTAGCT
1 AACAGTAGCTTTTTAGCT
594597 AACAGTAGCTTTTTAGCT
1 AACAGTAGCTTTTTAGCT
594615 A
1 A
594616 CTAACTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
AACAGTAGCTTTTTAGCT
Found at i:598834 original size:39 final size:38
Alignment explanation
Indices: 598748--598847 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 38
598738 GAAATCCTTG
* *
598748 TTATAATTATTTTAATTATAATTTACGATAGAATATTA
1 TTATAATTATTGTAATTATAATTTACGATAGAACATTA
* * *
598786 TTATAATTATTGTAATTGTAATTTTTCGGTCA-AACATTA
1 TTATAATTATTGTAATTATAA-TTTACGAT-AGAACATTA
* *
598825 TTATAATTATGGGAATTATAATT
1 TTATAATTATTGTAATTATAATT
598848 ATTGTATTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
38 21 0.40
39 30 0.58
40 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTACGATAGAACATTA
Found at i:602087 original size:25 final size:25
Alignment explanation
Indices: 602059--602114 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
602049 AATGTATGTA
*
602059 TGTACAGTGCATTGCTGTAAACTGT
1 TGTACAGTGCATTGCTGTAAACTAT
602084 TGTACAGTGCATTGCTGTAAACTAT
1 TGTACAGTGCATTGCTGTAAACTAT
602109 TGTACA
1 TGTACA
602115 TACATGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (25 bp):
TGTACAGTGCATTGCTGTAAACTAT
Found at i:604811 original size:30 final size:30
Alignment explanation
Indices: 604775--604836 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
604765 TGAGTGAATA
604775 TAGTTACTAATTACATAAACAAAATTTAAC
1 TAGTTACTAATTACATAAACAAAATTTAAC
604805 TAGTTACTAATTACATAAACAAAATTTAAC
1 TAGTTACTAATTACATAAACAAAATTTAAC
604835 TA
1 TA
604837 AGTATGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (30 bp):
TAGTTACTAATTACATAAACAAAATTTAAC
Found at i:606375 original size:14 final size:14
Alignment explanation
Indices: 606356--606382 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
606346 ATTCATCTAT
606356 AAGGGAAGAATATA
1 AAGGGAAGAATATA
606370 AAGGGAAGAATAT
1 AAGGGAAGAATAT
606383 TCTCAATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (14 bp):
AAGGGAAGAATATA
Found at i:608198 original size:22 final size:22
Alignment explanation
Indices: 608166--608209 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
608156 AAAACAATTA
*
608166 AAAACCTGATTATTAATGAAGC
1 AAAACCCGATTATTAATGAAGC
608188 AAAACCCGATTATTAATGAAGC
1 AAAACCCGATTATTAATGAAGC
608210 CAAGTGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (22 bp):
AAAACCCGATTATTAATGAAGC
Found at i:608381 original size:19 final size:19
Alignment explanation
Indices: 608344--608381 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
608334 GTCCAAAACC
608344 AAATAAATTTAGCGAACTTT
1 AAATAAATTTA-CGAACTTT
608364 AAATAAATTATA-GAACTT
1 AAATAAATT-TACGAACTT
608382 AAGTACGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (19 bp):
AAATAAATTTACGAACTTT
Found at i:610835 original size:14 final size:14
Alignment explanation
Indices: 610816--610844 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
610806 AAAACCTTGA
610816 TTCCTCCTCAAATG
1 TTCCTCCTCAAATG
610830 TTCCTCCTCAAATG
1 TTCCTCCTCAAATG
610844 T
1 T
610845 CAAATTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (14 bp):
TTCCTCCTCAAATG
Found at i:614127 original size:6 final size:6
Alignment explanation
Indices: 614116--614142 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
614106 TCCGTCCTTG
614116 ATTACC ATTACC ATTACC ATTACC ATT
1 ATTACC ATTACC ATTACC ATTACC ATT
614143 TCTGTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTACC
Found at i:615516 original size:50 final size:50
Alignment explanation
Indices: 615457--615579 Score: 147
Period size: 50 Copynumber: 2.5 Consensus size: 50
615447 CTCCATTTAC
* * * *
615457 GGACAAGCCACCAATGATTTGTAGATAAACTGCCTCTGATAACACTTTGT
1 GGACAAGCCACCAATGATATGCAGATAAACTACCACTGATAACACTTTGT
* * ** *
615507 GGACAAGCCACCACTAATATGCAGATGTACTACCACTTATAACACTTTGT
1 GGACAAGCCACCAATGATATGCAGATAAACTACCACTGATAACACTTTGT
* *
615557 AGACTAGCCACCAATGATATGCA
1 GGACAAGCCACCAATGATATGCA
615580 AATATACTGC
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (50 bp):
GGACAAGCCACCAATGATATGCAGATAAACTACCACTGATAACACTTTGT
Found at i:621602 original size:23 final size:23
Alignment explanation
Indices: 621558--621602 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
621548 GAGTTTTCAA
* *
621558 AGTCTATAGTTTTTAGAATCTAC
1 AGTCTATAGTCTTTACAATCTAC
*
621581 AGTCTATAGTCTTTACAGTCTA
1 AGTCTATAGTCTTTACAATCTA
621603 TAGTTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (23 bp):
AGTCTATAGTCTTTACAATCTAC
Found at i:628877 original size:20 final size:20
Alignment explanation
Indices: 628840--628877 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
628830 AATTTTTGAG
*
628840 GTATCGATACCTTGGTAAGA
1 GTATCGATACCTTAGTAAGA
*
628860 GTATCGATACTTTAGTAA
1 GTATCGATACCTTAGTAA
628878 TTTCTCTTTA
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:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (20 bp):
GTATCGATACCTTAGTAAGA
Found at i:633889 original size:73 final size:73
Alignment explanation
Indices: 633770--633916 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 73
633760 TAGCCTTCTC
*
633770 AATCTAGCCTCTACGCCGGGTTTGGAAAGCTACAAAACCTCAAATAACACCATTGATAAACAAGA
1 AATCTAGCCTCTACGCCGAGTTTGGAAAGCTACAAAACCTCAAATAACACCATTGATAAACAAGA
633835 AGAACATT
66 AGAACATT
* * *
633843 AATCTAGCCTCTACGCCGAGTTTGGGAAGTTACAAAACCTCAAATAACACCATTGATAAATAAGA
1 AATCTAGCCTCTACGCCGAGTTTGGAAAGCTACAAAACCTCAAATAACACCATTGATAAACAAGA
633908 AGAACATT
66 AGAACATT
633916 A
1 A
633917 TGAAAATGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (73 bp):
AATCTAGCCTCTACGCCGAGTTTGGAAAGCTACAAAACCTCAAATAACACCATTGATAAACAAGA
AGAACATT
Found at i:634564 original size:146 final size:144
Alignment explanation
Indices: 634302--634586 Score: 394
Period size: 146 Copynumber: 2.0 Consensus size: 144
634292 ATTGCTACCC
* * * * *
634302 AAATTTTATGGTTTCTTTAACCGATAAAAAATTTTACACTCTTTGACCCTTCCATTCCATACCTC
1 AAATTTTATGGCTTCTTTAACCAATAAAAAATTTTACAATCTTTGACCCTTCAATTCCATACCTA
* * * * *
634367 TAATTACAAAATGCTTCATGGTTTTGAAGTAGTAACTCTAGTTTATCGACTCCACTTTTAAGCTA
66 TAATTACAAAATGCTTCATAGATCTGAAGTACTAACTCTAGTTTATCGACTCCACTTCTAAGCTA
634432 TGTATTCTGCAATA
131 TGTATTCTGCAATA
* *
634446 AAATTTTATGGCTTCTTTGA-CAATAAAAAAATATTTTACAATTTTTGACCCTTCAAATT-CATA
1 AAATTTTATGGCTTCTTTAACCAAT--AAAAA-ATTTTACAATCTTTGACCCTTC-AATTCCATA
*
634509 CCTATAATTACAAAATGCTTCCTAGATCTGAAGTACTAACTCTAGTTTATCGACTCCACTTCTAA
62 CCTATAATTACAAAATGCTTCATAGATCTGAAGTACTAACTCTAGTTTATCGACTCCACTTCTAA
*
634574 GTTATGTATTCTG
127 GCTATGTATTCTG
634587 TAGTCAATAC
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
143 3 0.02
144 18 0.15
145 5 0.04
146 94 0.76
147 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (144 bp):
AAATTTTATGGCTTCTTTAACCAATAAAAAATTTTACAATCTTTGACCCTTCAATTCCATACCTA
TAATTACAAAATGCTTCATAGATCTGAAGTACTAACTCTAGTTTATCGACTCCACTTCTAAGCTA
TGTATTCTGCAATA
Found at i:636974 original size:15 final size:15
Alignment explanation
Indices: 636950--636980 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
636940 ACATCTCCTA
*
636950 AATCAGATGAATTAC
1 AATCAAATGAATTAC
636965 AATCAAATGAATTAC
1 AATCAAATGAATTAC
636980 A
1 A
636981 TACAACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (15 bp):
AATCAAATGAATTAC
Found at i:638988 original size:24 final size:24
Alignment explanation
Indices: 638959--639004 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
638949 TCAAATAGAT
638959 ATAACTC-GACTAACTTTTCAAATG
1 ATAACTCAG-CTAACTTTTCAAATG
638983 ATAACTCAGCTAACTTTTCAAA
1 ATAACTCAGCTAACTTTTCAAA
639005 CGACTAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.33
Consensus pattern (24 bp):
ATAACTCAGCTAACTTTTCAAATG
Found at i:642257 original size:17 final size:17
Alignment explanation
Indices: 642237--642270 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
642227 TTTCTCTATA
642237 ATTTGCCATTACATTTT
1 ATTTGCCATTACATTTT
642254 ATTTGCCATTACATTTT
1 ATTTGCCATTACATTTT
642271 TCTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTGCCATTACATTTT
Found at i:649941 original size:25 final size:25
Alignment explanation
Indices: 649866--649961 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
649856 ACAAACTGTG
**
649866 AATTGGTATGCTCACTTGAGTTGTA
1 AATTGGTATGCTCACACGAGTTGTA
* * * * * *
649891 GATCGATATGCTCTCATGAGCTGTA
1 AATTGGTATGCTCACACGAGTTGTA
* *
649916 AATTTGTATTCTCACACGAGTTGTA
1 AATTGGTATGCTCACACGAGTTGTA
649941 AATTGGTATGCTCACACGAGT
1 AATTGGTATGCTCACACGAGT
649962 GTGGGCCAGA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (25 bp):
AATTGGTATGCTCACACGAGTTGTA
Found at i:655551 original size:13 final size:13
Alignment explanation
Indices: 655533--655557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
655523 ACTTGCATTG
655533 TACCGTTTCAAGA
1 TACCGTTTCAAGA
655546 TACCGTTTCAAG
1 TACCGTTTCAAG
655558 GAAAATGTAT
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:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (13 bp):
TACCGTTTCAAGA
Found at i:666072 original size:41 final size:41
Alignment explanation
Indices: 666012--666147 Score: 245
Period size: 41 Copynumber: 3.3 Consensus size: 41
666002 NNNNNNNNNN
* *
666012 CTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCA
1 CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCA
*
666053 CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCAGCA
1 CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCA
666094 CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCA
1 CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCA
666135 CTTAGCCTGCTAG
1 CTTAGCCTGCTAG
666148 ACGTGTAGTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
CTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCA
Found at i:667341 original size:13 final size:13
Alignment explanation
Indices: 667323--667347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
667313 ACCAACGATA
667323 AAATTTTCACACG
1 AAATTTTCACACG
667336 AAATTTTCACAC
1 AAATTTTCACAC
667348 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:678707 original size:39 final size:39
Alignment explanation
Indices: 678631--678926 Score: 409
Period size: 39 Copynumber: 7.6 Consensus size: 39
678621 CATATTCACT
* * * * *
678631 TTTAATCATATATCATATTACACAT-TAATCACCTAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
678669 TTCAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
678708 TTTAAACATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
678747 TTCAAGCATATCTCACAATA-TACATATAATCACATAACA
1 TTTAAGCATATATCACAATACT-CATATAATCACATAACA
**
678786 TTTAAGCATATATCACCGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
678825 TTTATGCATATATCACAGTACTCGTATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
678864 TTCAAGCATATATCATAATA-TACATATAATCACATAACA
1 TTTAAGCATATATCACAATACT-CATATAATCACATAACA
678903 TTTAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
678927 AAACATCTTA
Statistics
Matches: 228, Mismatches: 25, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
38 22 0.10
39 204 0.89
40 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:678801 original size:117 final size:117
Alignment explanation
Indices: 678637--678926 Score: 456
Period size: 117 Copynumber: 2.5 Consensus size: 117
678627 CACTTTTAAT
* * * * *
678637 CATATATCATATTACACAT-TAATCACCTAACATTCAAGCATATATCACAATACTCATATAATCA
1 CATATATCACAATATACATATAATCACATAACATTTAAGCATATATCACAATACTCATATAATCA
678701 CATAACATTTAAACATATATCACAATACTCATATAATCACATAACATTCAAG
66 CATAACATTTAAACATATATCACAATACTCATATAATCACATAACATTCAAG
* **
678753 CATATCTCACAATATACATATAATCACATAACATTTAAGCATATATCACCGTACTCATATAATCA
1 CATATATCACAATATACATATAATCACATAACATTTAAGCATATATCACAATACTCATATAATCA
** * *
678818 CATAACATTTATGCATATATCACAGTACTCGTATAATCACATAACATTCAAG
66 CATAACATTTAAACATATATCACAATACTCATATAATCACATAACATTCAAG
*
678870 CATATATCATAATATACATATAATCACATAACATTTAAGCATATATCACAATACTCA
1 CATATATCACAATATACATATAATCACATAACATTTAAGCATATATCACAATACTCA
678927 AAACATCTTA
Statistics
Matches: 157, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
116 15 0.10
117 142 0.90
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (117 bp):
CATATATCACAATATACATATAATCACATAACATTTAAGCATATATCACAATACTCATATAATCA
CATAACATTTAAACATATATCACAATACTCATATAATCACATAACATTCAAG
Found at i:679754 original size:30 final size:30
Alignment explanation
Indices: 679720--679779 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
679710 TTAGAGTAAG
679720 GGCTTAGGCTACAACTAAATTCTCAAATAA
1 GGCTTAGGCTACAACTAAATTCTCAAATAA
679750 GGCTTAGGCTACAACTAAATTCTCAAATAA
1 GGCTTAGGCTACAACTAAATTCTCAAATAA
679780 CGCATTGAAT
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:0.20, G:0.13, T:0.27
Consensus pattern (30 bp):
GGCTTAGGCTACAACTAAATTCTCAAATAA
Found at i:684154 original size:18 final size:18
Alignment explanation
Indices: 684131--684170 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
684121 ATTACTGGGT
684131 CAAAATTCAATATAACAC
1 CAAAATTCAATATAACAC
684149 CAAAATTCAATATAACAC
1 CAAAATTCAATATAACAC
684167 CAAA
1 CAAA
684171 GTGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAAATTCAATATAACAC
Found at i:685887 original size:57 final size:57
Alignment explanation
Indices: 685815--685958 Score: 177
Period size: 57 Copynumber: 2.5 Consensus size: 57
685805 AAAAATGATG
*
685815 CAAGAAAAGACGAGTGAATAGGAAATATTCCATAACGAAAACAGTAAATATTCCCT-T
1 CAAGAAAAGACGAGTGAATAGGAAATATTCC-TAACAAAAACAGTAAATATTCCCTGT
* * * *
685872 CAAGAAAATACGAGTGAAGAGGAAATATTTCCTGACAAAAACAGTAAATATTCTCTGT
1 CAAGAAAAGACGAGTGAATAGGAAATA-TTCCTAACAAAAACAGTAAATATTCCCTGT
* *
685930 -AAGAAAAGATGCA-TGAATAGTAAATATTC
1 CAAGAAAAGACG-AGTGAATAGGAAATATTC
685959 TCTGTAATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 3 0.04
57 66 0.88
58 6 0.08
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (57 bp):
CAAGAAAAGACGAGTGAATAGGAAATATTCCTAACAAAAACAGTAAATATTCCCTGT
Found at i:686189 original size:18 final size:18
Alignment explanation
Indices: 686152--686200 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
686142 TCAAAACTCA
686152 TTTCTCCAAAGTTTTAAAG
1 TTTCTCCAAA-TTTTAAAG
*
686171 TTTCTCCAAATTTTTAAG
1 TTTCTCCAAATTTTAAAG
*
686189 TTT-TCAAAATTT
1 TTTCTCCAAATTT
686201 AAGTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.29
18 10 0.36
19 10 0.36
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTCTCCAAATTTTAAAG
Found at i:686213 original size:14 final size:15
Alignment explanation
Indices: 686183--686214 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
686173 TCTCCAAATT
686183 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
686198 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
686212 TTT
1 TTT
686215 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:690452 original size:21 final size:21
Alignment explanation
Indices: 690426--690469 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
690416 TTTTATAGAA
*
690426 AAACCAAAAATAAGAAATTTC
1 AAACCAAAAATAAGAAATCTC
690447 AAACCAAAAATAAGAAATCTC
1 AAACCAAAAATAAGAAATCTC
690468 AA
1 AA
690470 CTTATTAAAA
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:0.64, C:0.16, G:0.05, T:0.16
Consensus pattern (21 bp):
AAACCAAAAATAAGAAATCTC
Found at i:690566 original size:21 final size:23
Alignment explanation
Indices: 690524--690566 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
690514 TAATTAATTA
*
690524 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
690547 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
690567 AAAAAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:693528 original size:57 final size:57
Alignment explanation
Indices: 693456--693565 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 57
693446 AAAAATGATG
693456 CAAGAAAAATCGAGTGAACAGGAAATA-TTCCATAACGAAAACAGTAAATATTCCCTT
1 CAAGAAAAATCGAGTGAACAGGAAATATTTCC-TAACGAAAACAGTAAATATTCCCTT
* *
693513 CAAG-AAAATACGAGTGAACAGGAAATATTTCCTGACGGAAACAGTAAATATTC
1 CAAGAAAAAT-CGAGTGAACAGGAAATATTTCCTAACGAAAACAGTAAATATTC
693566 TCTGTAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
56 5 0.10
57 40 0.82
58 4 0.08
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (57 bp):
CAAGAAAAATCGAGTGAACAGGAAATATTTCCTAACGAAAACAGTAAATATTCCCTT
Found at i:693830 original size:18 final size:18
Alignment explanation
Indices: 693792--693841 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
693782 ATCAAAACTC
693792 GTTTCTCCAAAGTTTTAAA
1 GTTTCTCCAAA-TTTTAAA
*
693811 GTTTCTCCAAATTTTTAA
1 GTTTCTCCAAATTTTAAA
*
693829 GTTT-TCAAAATTT
1 GTTTCTCCAAATTT
693842 AAGTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.28
18 10 0.34
19 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (18 bp):
GTTTCTCCAAATTTTAAA
Found at i:693854 original size:14 final size:15
Alignment explanation
Indices: 693824--693855 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
693814 TCTCCAAATT
693824 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
693839 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
693853 TTT
1 TTT
693856 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:720983 original size:35 final size:35
Alignment explanation
Indices: 720910--721002 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 35
720900 TTAGACTAGT
* * *
720910 TCTTATGAGCATTGGTGTATTTTGGAGGGATTAGC
1 TCTTACGAGCATTGGTGTGTTTTGGAGGGATGAGC
* *
720945 TCTTACGAGCATTGGTATGTTTTGGATGGACTGA-C
1 TCTTACGAGCATTGGTGTGTTTTGGAGGGA-TGAGC
*
720980 TCTTACAAGCATCTGGTGTGTTT
1 TCTTACGAGCAT-TGGTGTGTTT
721003 GGGTGGTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 38 0.78
36 11 0.22
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (35 bp):
TCTTACGAGCATTGGTGTGTTTTGGAGGGATGAGC
Found at i:721771 original size:19 final size:18
Alignment explanation
Indices: 721725--721772 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
721715 GATAGAAATT
*
721725 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
721744 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
721762 TTGTATTAAAA
1 TTGTA-TAAAA
721773 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:722408 original size:14 final size:14
Alignment explanation
Indices: 722385--722414 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
722375 CATCCCTCAT
*
722385 TCACATCTCTTCTC
1 TCACAACTCTTCTC
722399 TCACAACTCTTCTC
1 TCACAACTCTTCTC
722413 TC
1 TC
722415 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:726953 original size:16 final size:17
Alignment explanation
Indices: 726932--726972 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
726922 TTAGTTTCGA
726932 AACTTTGTAATT-ATAT
1 AACTTTGTAATTGATAT
*
726948 AACTTT-TAATTGATTT
1 AACTTTGTAATTGATAT
*
726964 AAATTTGTA
1 AACTTTGTA
726973 TAAGTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
AACTTTGTAATTGATAT
Found at i:739307 original size:14 final size:14
Alignment explanation
Indices: 739290--739356 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
739280 TTTGAAAAAT
739290 AATTGAGGATTGAA
1 AATTGAGGATTGAA
*
739304 AATTTGA-AATTGAA
1 AA-TTGAGGATTGAA
*
739318 AATTGAAGATTG-A
1 AATTGAGGATTGAA
*
739331 AACTGAGGATTGAA
1 AATTGAGGATTGAA
*
739345 GATTGAGGATTG
1 AATTGAGGATTG
739357 TGAATTTAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 15 0.34
14 25 0.57
15 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.27, T:0.30
Consensus pattern (14 bp):
AATTGAGGATTGAA
Found at i:739332 original size:20 final size:20
Alignment explanation
Indices: 739307--739350 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
739297 GATTGAAAAT
*
739307 TTGAAATTGAAAATTGAAGA
1 TTGAAACTGAAAATTGAAGA
**
739327 TTGAAACTGAGGATTGAAGA
1 TTGAAACTGAAAATTGAAGA
739347 TTGA
1 TTGA
739351 GGATTGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGAAACTGAAAATTGAAGA
Found at i:739348 original size:7 final size:7
Alignment explanation
Indices: 739291--739356 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
739281 TTGAAAAATA
*
739291 ATTGAGG
1 ATTGAAG
*
739298 ATTGAAA
1 ATTGAAG
739305 ATTTGAA-
1 A-TTGAAG
*
739312 ATTGAAA
1 ATTGAAG
739319 ATTGAAG
1 ATTGAAG
739326 ATTGAA-
1 ATTGAAG
* *
739332 ACTGAGG
1 ATTGAAG
739339 ATTGAAG
1 ATTGAAG
*
739346 ATTGAGG
1 ATTGAAG
739353 ATTG
1 ATTG
739357 TGAATTTAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 9 0.19
7 34 0.71
8 5 0.10
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.30
Consensus pattern (7 bp):
ATTGAAG
Found at i:770842 original size:29 final size:29
Alignment explanation
Indices: 770798--771023 Score: 220
Period size: 29 Copynumber: 7.8 Consensus size: 29
770788 GCATGCTAAA
*
770798 TGATGGTCGTAACCATCCCTTTTCATATT
1 TGATGGTCGTCACCATCCCTTTTCATATT
*
770827 TAATGGTCGTCACCATCCCTTTTCATATT
1 TGATGGTCGTCACCATCCCTTTTCATATT
* *
770856 CGATGGTCGTCACCATCCCTTTTCATTAAT
1 TGATGGTCGTCACCATCCCTTTTCA-TATT
* *
770886 TGATAGTCGTCACCATCCCTTTTCATAGT
1 TGATGGTCGTCACCATCCCTTTTCATATT
* **
770915 TGATGGTCGTCACCATCTCTTTTCATAGC
1 TGATGGTCGTCACCATCCCTTTTCATATT
* * * ** * *
770944 CGCTTGTCGAAACTATCCCTTTTCATAGT
1 TGATGGTCGTCACCATCCCTTTTCATATT
* *** **
770973 CGATGGTCAAAATTATCCCTTTTCATATT
1 TGATGGTCGTCACCATCCCTTTTCATATT
**
771002 CAATGGTCGTCACCAT-CCTTTT
1 TGATGGTCGTCACCATCCCTTTT
771024 ATAACGTTGA
Statistics
Matches: 166, Mismatches: 30, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
28 6 0.04
29 134 0.81
30 26 0.16
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (29 bp):
TGATGGTCGTCACCATCCCTTTTCATATT
Found at i:770920 original size:59 final size:58
Alignment explanation
Indices: 770798--770940 Score: 216
Period size: 59 Copynumber: 2.4 Consensus size: 58
770788 GCATGCTAAA
* * *
770798 TGATGGTCGTAACCATCCCTTTTCA-TATTTAATGGTCGTCACCATCCCTTTTCATAT
1 TGATGGTCGTCACCATCCCTTTTCATTAATTAATAGTCGTCACCATCCCTTTTCATAT
*
770855 TCGATGGTCGTCACCATCCCTTTTCATTAATTGATAGTCGTCACCATCCCTTTTCATAGT
1 T-GATGGTCGTCACCATCCCTTTTCATTAATTAATAGTCGTCACCATCCCTTTTCATA-T
*
770915 TGATGGTCGTCACCATCTCTTTTCAT
1 TGATGGTCGTCACCATCCCTTTTCAT
770941 AGCCGCTTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
57 1 0.01
58 23 0.29
59 52 0.67
60 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (58 bp):
TGATGGTCGTCACCATCCCTTTTCATTAATTAATAGTCGTCACCATCCCTTTTCATAT
Found at i:770962 original size:88 final size:88
Alignment explanation
Indices: 770798--771023 Score: 251
Period size: 88 Copynumber: 2.6 Consensus size: 88
770788 GCATGCTAAA
* * **
770798 TGATGGTCGTAACCATCCCTTTTCATATTTAATGGTCGTCACCATCCCTTTTCATATTCGATGGT
1 TGATAGTCGTAACCATCCCTTTTCATAGTTAATGGTCGTCACCATCCCTTTTCATAGCCGATGGT
**
770863 CGTCACCATCCCTTTTCATTAAT
66 CGAAACCATCCCTTTTCATTAAT
* * * * *
770886 TGATAGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCTCTTTTCATAGCCGCTTGT
1 TGATAGTCGTAACCATCCCTTTTCATAGTTAATGGTCGTCACCATCCCTTTTCATAGCCGATGGT
* *
770951 CGAAACTATCCCTTTTCA-TAGT
66 CGAAACCATCCCTTTTCATTAAT
* * ** **
770973 CGATGGTCAAAATTATCCCTTTTCATA-TTCAATGGTCGTCACCAT-CCTTTT
1 TGATAGTCGTAACCATCCCTTTTCATAGTT-AATGGTCGTCACCATCCCTTTT
771024 ATAACGTTGA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
86 7 0.06
87 37 0.32
88 71 0.62
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (88 bp):
TGATAGTCGTAACCATCCCTTTTCATAGTTAATGGTCGTCACCATCCCTTTTCATAGCCGATGGT
CGAAACCATCCCTTTTCATTAAT
Found at i:777937 original size:18 final size:18
Alignment explanation
Indices: 777914--777950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
777904 TTCCAAACAC
*
777914 CCCAAACCTCTCATATTT
1 CCCAAACCTCTCAAATTT
*
777932 CCCAAATCTCTCAAATTT
1 CCCAAACCTCTCAAATTT
777950 C
1 C
777951 AAATCCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
CCCAAACCTCTCAAATTT
Found at i:779944 original size:18 final size:18
Alignment explanation
Indices: 779917--779963 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
779907 TTTATTTTCC
779917 TTGT-TTTTATGATTGTT
1 TTGTGTTTTATGATTGTT
*
779934 TTGTGTTTTATTATTGTT
1 TTGTGTTTTATGATTGTT
*
779952 TTATGTGTTTAT
1 TTGTGT-TTTAT
779964 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (18 bp):
TTGTGTTTTATGATTGTT
Found at i:782265 original size:21 final size:21
Alignment explanation
Indices: 782226--782265 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
782216 AATCAAACTT
*
782226 ACCAAACATAATATGATTTAA
1 ACCAAACATAATATCATTTAA
* *
782247 ACCAAGCATAATTTCATTT
1 ACCAAACATAATATCATTT
782266 TATCATGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (21 bp):
ACCAAACATAATATCATTTAA
Found at i:783961 original size:14 final size:15
Alignment explanation
Indices: 783932--783961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
783922 GTGAAAAAAA
783932 TATTTTTCTTCTCCT
1 TATTTTTCTTCTCCT
783947 TATTTTTCTTC-CCT
1 TATTTTTCTTCTCCT
783961 T
1 T
783962 GGCTGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTCTTCTCCT
Found at i:787825 original size:23 final size:23
Alignment explanation
Indices: 787792--787844 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
787782 TGATGTGACT
*
787792 TTTAATGTTTATATTTTTGTT-AA
1 TTTAATGTTTAT-TTTTAGTTAAA
*
787815 TTTAATTTTTATTTTTAGTTAAA
1 TTTAATGTTTATTTTTAGTTAAA
787838 TTTAATG
1 TTTAATG
787845 ATTAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (23 bp):
TTTAATGTTTATTTTTAGTTAAA
Found at i:788038 original size:18 final size:18
Alignment explanation
Indices: 787991--788044 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
787981 TGTCACATTG
787991 ATAAATAATTTAAAAA-AT
1 ATAAA-AATTTAAAAATAT
788009 AT-AAAATATTAAAAATAT
1 ATAAAAAT-TTAAAAATAT
788027 ATAAAAATTTAATAAATA
1 ATAAAAATTTAA-AAATA
788045 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 10 0.31
19 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATTTAAAAATAT
Found at i:788523 original size:34 final size:35
Alignment explanation
Indices: 788479--788547 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
788469 AGGTAGTAAG
*
788479 AAAATTTTCTCACAA-TTTAATACATGCATGGTTA
1 AAAATCTTCTCACAATTTTAATACATGCATGGTTA
*
788513 AAAATCTTCTCACAATTTTCATACATGCATGGTTA
1 AAAATCTTCTCACAATTTTAATACATGCATGGTTA
788548 TCTAATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (35 bp):
AAAATCTTCTCACAATTTTAATACATGCATGGTTA
Found at i:795043 original size:12 final size:12
Alignment explanation
Indices: 795026--795050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
795016 GGTGTTCATT
795026 CGGTTAACCGAC
1 CGGTTAACCGAC
795038 CGGTTAACCGAC
1 CGGTTAACCGAC
795050 C
1 C
795051 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:795226 original size:9 final size:9
Alignment explanation
Indices: 795210--795286 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
795200 TTTGGTTAAA
795210 AATTACCCG
1 AATTACCCG
*
795219 AGTTACCCG
1 AATTACCCG
795228 AATTACCCG
1 AATTACCCG
795237 AATTACCCG
1 AATTACCCG
*
795246 AATTAACCG
1 AATTACCCG
795255 AATTA-CCG
1 AATTACCCG
*
795263 AAAAATACCCG
1 --AATTACCCG
795274 AATTACCCG
1 AATTACCCG
795283 AATT
1 AATT
795287 TTTTTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.05
9 50 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:795443 original size:13 final size:13
Alignment explanation
Indices: 795425--795454 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
795415 TTTTAGTTTT
795425 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
795438 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
795451 ATTG
1 ATTG
795455 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:796523 original size:33 final size:33
Alignment explanation
Indices: 796481--796548 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
796471 AAGGTTACTT
*
796481 GGGGTTGGATCAAATGACGAAGACACTGGTATA
1 GGGGTTGGATCAAATGACGAAGACACTGATATA
* *
796514 GGGGTTGGATCTAATGATGAAGACACTGATATA
1 GGGGTTGGATCAAATGACGAAGACACTGATATA
796547 GG
1 GG
796549 ACATGTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.34, T:0.24
Consensus pattern (33 bp):
GGGGTTGGATCAAATGACGAAGACACTGATATA
Found at i:798614 original size:2 final size:2
Alignment explanation
Indices: 798607--798633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
798597 TAAACCCTAG
798607 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
798634 GTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:801274 original size:3 final size:3
Alignment explanation
Indices: 801257--801295 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
801247 GGCTTCACAT
801257 TTA TT- TTA CTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
801296 GGAAATGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:802643 original size:17 final size:17
Alignment explanation
Indices: 802621--802684 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
802611 AATCTTAGAG
802621 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
802638 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
802657 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
802674 TTTTAATTGTA
1 TTCTAATTGTA
802685 GCCCTTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:802660 original size:36 final size:36
Alignment explanation
Indices: 802613--802683 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
802603 GATTATGTAA
*
802613 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
*
802649 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
802684 AGCCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:802662 original size:19 final size:19
Alignment explanation
Indices: 802612--802668 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
802602 TGATTATGTA
802612 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
802631 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
802648 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
802667 AT
1 AT
802669 ACAACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:802949 original size:49 final size:48
Alignment explanation
Indices: 802877--802973 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
802867 TGAGGGAATT
* *
802877 CTGTTGAATCCTTTGTCATTGCGAGATTAAGCTAACTTAGGTGTTTTTA
1 CTGTTGAATCCGTTATCATTGCGAG-TTAAGCTAACTTAGGTGTTTTTA
* *
802926 CTGTTGAATCCGTTATCATTGCGAGTTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCGTTATCATTGCGAGTTAAGCTAACTTAGGTGTTTTTA
802974 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 21 0.48
49 23 0.52
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCGTTATCATTGCGAGTTAAGCTAACTTAGGTGTTTTTA
Found at i:807737 original size:17 final size:17
Alignment explanation
Indices: 807715--807778 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
807705 AATCTTAGAG
807715 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
807732 TTCTAATTGTGT-CTTAGAT
1 TTCTAATTGTATAC--AG-C
*
807751 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
807768 TTTTAATTGTA
1 TTCTAATTGTA
807779 GCCCTTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:807755 original size:36 final size:36
Alignment explanation
Indices: 807707--807777 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
807697 GATTATGTAA
*
807707 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* *
807743 TCTTAGATTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
807778 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:824365 original size:19 final size:20
Alignment explanation
Indices: 824323--824365 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
824313 TCATGCTTTC
*
824323 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
824343 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
824361 TATTC
1 TATTC
824366 CACTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:824597 original size:51 final size:50
Alignment explanation
Indices: 824542--824728 Score: 200
Period size: 51 Copynumber: 3.7 Consensus size: 50
824532 CCGATTCACA
* *
824542 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTCCATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TTCCATCCGGTACATG
* ** * * ***
824593 TAGTAGCCTGCACATAGTACTACACACGTGATCAAAGCTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATTCCATCCGGTACATG
* *
824644 TAGTA-CCTTGCACATAGTACTACACATGCGACCCA-T-CATTCCGGTACATG
1 TAGTAGCC-TGCACATAGTACTACACACGTGA-CCATTCCA-TCCGGTACATG
824694 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
824729 CACTTTCACT
Statistics
Matches: 109, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
49 4 0.04
50 35 0.32
51 68 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTCCATCCGGTACATG
Found at i:824716 original size:101 final size:101
Alignment explanation
Indices: 824540--824724 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 101
824530 ACCCGATTCA
*
824540 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTCCATCCGATACATGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TTCCATCCGATACATGTAGTAGCCTGCA
824605 CATAGTACTACACACGTGATCAAAGCTATCTGGTACG
65 CATAGTACTACACACGTGATCAAAGCTATCTGGTACG
*
824642 CATAGTA-CCTTGCACATAGTACTACACATGCGACCCA-T-CATTCCGGTACATGTAGTAGCCTG
1 CATAGTAGCC-TGCACATAGTACTACACATGCGA-CCATTCCA-TCCGATACATGTAGTAGCCTG
824704 CACATAGTACTACACACGTGA
63 CACATAGTACTACACACGTGA
824725 CCATCACTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
100 2 0.03
101 44 0.56
102 29 0.37
103 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATTCCATCCGATACATGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCAAAGCTATCTGGTACG
Found at i:836140 original size:21 final size:20
Alignment explanation
Indices: 836112--836151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
836102 AATGATTTGT
* *
836112 ACATTTCTTGCGGTATATCC
1 ACATTTCTGGCAGTATATCC
836132 ACATATTCTGGCAGTATATC
1 ACAT-TTCTGGCAGTATATC
836152 TGCAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
ACATTTCTGGCAGTATATCC
Found at i:842218 original size:7 final size:7
Alignment explanation
Indices: 842206--842235 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
842196 TTTTAACTAA
842206 CTTTGAC
1 CTTTGAC
842213 CTTTGAC
1 CTTTGAC
842220 CTTTGAC
1 CTTTGAC
*
842227 TTTTGAC
1 CTTTGAC
842234 CT
1 CT
842236 AATTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (7 bp):
CTTTGAC
Done.