Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 73 of 93
Found at i:28206655 original size:69 final size:69
Alignment explanation
Indices: 28206567--28206703 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
28206557 CACGCTAACC
* *
28206567 ATGGCTTATCACGGGTTTTTGTACATAGCGTGTAAAAAGCTAACCATAGCTTGTCACA-AGTTTT
1 ATGGCTTATCACGGATTTTTGTACATAGCATGTAAAAAGCTAACCATAGCTTGTCACATA-TTTT
28206631 TGTAT
65 TGTAT
* * * * * *
28206636 ATGGCTTATCACGTATTTTTGTGCATGGCATGTAACAAGCTAACCGTGGCTTGTCACATATTTTT
1 ATGGCTTATCACGGATTTTTGTACATAGCATGTAAAAAGCTAACCATAGCTTGTCACATATTTTT
28206701 GTA
66 GTA
28206704 CATAGAGTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
69 58 0.98
70 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (69 bp):
ATGGCTTATCACGGATTTTTGTACATAGCATGTAAAAAGCTAACCATAGCTTGTCACATATTTTT
GTAT
Found at i:28206698 original size:45 final size:45
Alignment explanation
Indices: 28206636--28206896 Score: 294
Period size: 45 Copynumber: 5.8 Consensus size: 45
28206626 GTTTTTGTAT
* * *
28206636 ATGGCTTATCACGTATTTTTGTGCATGGCATGTAACAAGCTAACC
1 ATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACC
* * *
28206681 GTGGCTTGTCACATATTTTTGTACATAG-AGTGTAACACGCTAACC
1 ATGGCTTGTCACATATTTTTGTACATGGCA-TGTAACAAGCTAACC
** *
28206726 ATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACC
1 ATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACC
* * *
28206771 ATAGCTTGTCACA-AGTTTTTGTACATGGCGTGTAACAAGCTAATC
1 ATGGCTTGTCACATA-TTTTTGTACATGGCATGTAACAAGCTAACC
* *** * *
28206816 ATGGATTGTCACATATTTTTG-ACATATTATGTAACACGTTAACC
1 ATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACC
** *
28206860 ATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACA
1 ATGGCTTGTCACATATTTTTGTACATGGCATGTAACA
28206897 TCATAGCGTG
Statistics
Matches: 180, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.19
45 144 0.80
46 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (45 bp):
ATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACC
Found at i:28206819 original size:21 final size:21
Alignment explanation
Indices: 28206749--28206819 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
28206739 GGTTTTTGTA
*
28206749 CATGGCGTGTAACAAGCTAAC
1 CATGGCGTGTAACAAGCTAAT
* * * * **
28206770 CATAGCTTGTCACAAGTTTTTGT
1 CATGGCGTGTAACAAG--CTAAT
28206793 ACATGGCGTGTAACAAGCTAAT
1 -CATGGCGTGTAACAAGCTAAT
28206815 CATGG
1 CATGG
28206820 ATTGTCACAT
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 18 0.53
22 2 0.06
23 1 0.03
24 13 0.38
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
CATGGCGTGTAACAAGCTAAT
Found at i:28206892 original size:134 final size:135
Alignment explanation
Indices: 28206651--28206896 Score: 406
Period size: 134 Copynumber: 1.8 Consensus size: 135
28206641 TTATCACGTA
* * *
28206651 TTTTTGTGCATGGCATGTAACAAGCTAACCGTGGCTTGTCACATATTTTTGTACATAGAGTGTAA
1 TTTTTGTACATGGCATGTAACAAGCTAACCATGGATTGTCACATATTTTTGTACATAGAGTGTAA
28206716 CACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTC
66 CACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTC
28206781 ACAAG
131 ACAAG
* * *
28206786 TTTTTGTACATGGCGTGTAACAAGCTAATCATGGATTGTCACATATTTTTG-ACATATTA-TGTA
1 TTTTTGTACATGGCATGTAACAAGCTAACCATGGATTGTCACATATTTTTGTACATA-GAGTGTA
*
28206849 ACACGTTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACA
65 ACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACA
28206897 TCATAGCGTG
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
134 56 0.54
135 47 0.46
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (135 bp):
TTTTTGTACATGGCATGTAACAAGCTAACCATGGATTGTCACATATTTTTGTACATAGAGTGTAA
CACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTC
ACAAG
Found at i:28208890 original size:104 final size:102
Alignment explanation
Indices: 28208771--28208974 Score: 381
Period size: 104 Copynumber: 2.0 Consensus size: 102
28208761 AAATCTAGAG
*
28208771 TTCTTTGTTTTTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTG
1 TTCTTTGTTTGTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTG
28208836 CTAGAAAGGAAAAAAAAACTATAGGATTTTGGATTNGT
66 CTAGAAAGGAAAAAAAAACTATAGGATTTTGGATT-GT
28208874 TTCTTATGTTTGTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTT
1 TTCTT-TGTTTGTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTT
28208939 GCTAGAAAGGAAAAAAAAACTATAGGATTTTGGATT
65 GCTAGAAAGGAAAAAAAAACTATAGGATTTTGGATT
28208975 CCTCAAATCA
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 5 0.05
104 94 0.95
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (102 bp):
TTCTTTGTTTGTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTG
CTAGAAAGGAAAAAAAAACTATAGGATTTTGGATTGT
Found at i:28208994 original size:104 final size:104
Alignment explanation
Indices: 28208776--28209008 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 104
28208766 TAGAGTTCTT
28208776 TGTTTTTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTGCTAGA
1 TGTTTTTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTGCTAGA
** *** *
28208841 AAGGAAAAAAAAACTATAGGATTTTGGATTNGTTTCTTA
66 AAGGAAAAAAAAACTATAGGATTTTGGATTCCTAAATCA
*
28208880 TGTTTGTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTGCTAGA
1 TGTTTTTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTGCTAGA
28208945 AAGGAAAAAAAAACTATAGGATTTTGGATTCCTCAAATCA
66 AAGGAAAAAAAAACTATAGGATTTTGGATTCCT-AAATCA
*
28208985 TTTTTTTTTTTTGTTTTTGTTTTT
1 TGTTTTTTTTTT-TTTTT-TTTTT
28209009 CTCCCTCCCA
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
104 95 0.81
105 12 0.10
106 5 0.04
107 5 0.04
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (104 bp):
TGTTTTTTTTTTTTTTTTTTTTGTTTTTTGGAAACAAGTAAGAAAAGGTTGTTATAGTTGCTAGA
AAGGAAAAAAAAACTATAGGATTTTGGATTCCTAAATCA
Found at i:28211608 original size:26 final size:27
Alignment explanation
Indices: 28211552--28211611 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
28211542 GGCCGGCCAT
* *
28211552 AAGG-AAAGAACAAGAGAGAAAATAGA
1 AAGGAAAAGAACAAAAGAGAAAATACA
* *
28211578 GAGGAAAAGAAGAAAAGAGAAAA-ACA
1 AAGGAAAAGAACAAAAGAGAAAATACA
28211604 AAGGAAAA
1 AAGGAAAA
28211612 CTAGAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.68, C:0.03, G:0.27, T:0.02
Consensus pattern (27 bp):
AAGGAAAAGAACAAAAGAGAAAATACA
Found at i:28212432 original size:10 final size:10
Alignment explanation
Indices: 28212417--28212441 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28212407 TAAACTTATT
28212417 ATTATTGTAA
1 ATTATTGTAA
28212427 ATTATTGTAA
1 ATTATTGTAA
28212437 ATTAT
1 ATTAT
28212442 CTAGAGTTTA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
ATTATTGTAA
Found at i:28215887 original size:21 final size:21
Alignment explanation
Indices: 28215863--28215904 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28215853 TATTCAAGTT
*
28215863 CACATGATGTTACAAGCCATG
1 CACATAATGTTACAAGCCATG
*
28215884 CACATAATGTTACACGCCATG
1 CACATAATGTTACAAGCCATG
28215905 TTGAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
CACATAATGTTACAAGCCATG
Found at i:28216091 original size:29 final size:29
Alignment explanation
Indices: 28216049--28216127 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
28216039 AAAAAATTTT
28216049 TTGAAAAAATATTGTTGTTACATACCATG
1 TTGAAAAAATATTGTTGTTACATACCATG
*
28216078 TTGAAAAAATATTGTTGTTACATGCCATG
1 TTGAAAAAATATTGTTGTTACATACCATG
* *
28216107 TTCAAAAAA-GTT-TTGTTACAT
1 TTGAAAAAATATTGTTGTTACAT
28216128 TTTAATGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 9 0.19
28 2 0.04
29 36 0.77
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TTGAAAAAATATTGTTGTTACATACCATG
Found at i:28223201 original size:43 final size:43
Alignment explanation
Indices: 28223153--28223258 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
28223143 TTGACTTGAC
* * **
28223153 TATGTGCGAGTAGAGAGTGTGCATAAGCCAAG-GATGACCCGGT
1 TATGTGCGAGTAGGGAGTGCGCATAA-CCAAGTGATGACCCAAT
* **
28223196 TATGTGAGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAAT
1 TATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCAAT
*
28223239 CATGTGCGAGTAGGGAGTGC
1 TATGTGCGAGTAGGGAGTGC
28223259 ACATGAGCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.06
43 50 0.94
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (43 bp):
TATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCAAT
Found at i:28223302 original size:23 final size:23
Alignment explanation
Indices: 28223272--28223331 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
28223262 TGAGCTGGTG
* ** *
28223272 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATAATGTGC
28223295 ATGATGATGATGGGATAATGTGC
1 ATGATGATGATGGGATAATGTGC
*
28223318 ATGATAATGATGGG
1 ATGATGATGATGGG
28223332 TATATGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATAATGTGC
Found at i:28226169 original size:21 final size:21
Alignment explanation
Indices: 28226140--28226182 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28226130 AAAAAAGATA
*
28226140 ATAGGCACTTAGTCAACTAAG
1 ATAGACACTTAGTCAACTAAG
*
28226161 ATAGACACTTAGTCAATTAAG
1 ATAGACACTTAGTCAACTAAG
28226182 A
1 A
28226183 GTGTTCTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (21 bp):
ATAGACACTTAGTCAACTAAG
Found at i:28240102 original size:46 final size:46
Alignment explanation
Indices: 28240012--28240104 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
28240002 AAACTCTCAC
* *
28240012 ATGTCATTTTCTATATGAAAAGAACAAAAACATGCTGAATTAAATA
1 ATGTCATTTTCTAAATGAAAAGAACAAAAACATGATGAATTAAATA
* ** *
28240058 ATGTCATTTTCTAAATGACAAGAATTAAAACTTGATGGAA-TAAATA
1 ATGTCATTTTCTAAATGAAAAGAACAAAAACATGAT-GAATTAAATA
28240104 A
1 A
28240105 GTTAAATAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 37 0.93
47 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (46 bp):
ATGTCATTTTCTAAATGAAAAGAACAAAAACATGATGAATTAAATA
Found at i:28244231 original size:23 final size:23
Alignment explanation
Indices: 28244201--28244260 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
28244191 TGAGCTGGTG
* ** *
28244201 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATAATGTGC
28244224 ATGATGATGATGGGATAATGTGC
1 ATGATGATGATGGGATAATGTGC
*
28244247 ATGATAATGATGGG
1 ATGATGATGATGGG
28244261 TATATGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATAATGTGC
Found at i:28262587 original size:201 final size:201
Alignment explanation
Indices: 28262214--28262619 Score: 658
Period size: 201 Copynumber: 2.0 Consensus size: 201
28262204 GGGTATAGTA
* * **
28262214 ACTAACTTAACCTTGAAAAGTTTAGGTTTTGGGTTTTGGTTGATCCCGGTAAAAACTATTTTGAA
1 ACTAACTTAAACTTGAAAAGTTTAGGTGTTGGGTTTTGGTTGATCCCGGTAAAAACTATTGGGAA
*
28262279 AGGTTTTGGGCTAAGCTTGGTAAAAGCAATTATAAAGCTTGGTGAAAGCTTGTGAATTTCACCTT
66 AGGTTTTGGGCTAAGCTTGGTAAAAGCAATTATAAAGCTTAGTGAAAGCTTGTGAATTTCACCTT
28262344 TTATAATAGATTGATTTGGAAAAACTTTAGTTGAATAATTAAGGTAGTGAATGTAGGTCTTGGA-
131 TTATAATAGATTGATTTGGAAAAACTTTAGTTGAATAATTAAGGTAGTGAATGTAGGTCTT-GAC
28262408 CCAAACC
195 CCAAACC
* *
28262415 ACTNAACTTAAACTTGAAAAG-TTAGGTGTTGGGTTTTTGTTGATCCTGGTAAAAACTATTGGGA
1 ACT-AACTTAAACTTGAAAAGTTTAGGTGTTGGGTTTTGGTTGATCCCGGTAAAAACTATTGGGA
* *
28262479 AAGGTTTT-GGCTGAG-TCTGGTAAAAGCCATTATAAAGCTTAGTGAAAGCTTGTGAATTTTCAC
65 AAGGTTTTGGGCTAAGCT-TGGTAAAAGCAATTATAAAGCTTAGTGAAAGCTTGTGAA-TTTCAC
*
28262542 CTTTTATAATAGATTGATTTGGAAAAACTTTAGTTGAATAATTAAGGTAGTGGATGTAGGTCTTG
128 CTTTTATAATAGATTGATTTGGAAAAACTTTAGTTGAATAATTAAGGTAGTGAATGTAGGTCTTG
28262607 ACCCAAACC
193 ACCCAAACC
28262616 ACTA
1 ACTA
28262620 TAAATTCCTA
Statistics
Matches: 191, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
199 1 0.01
200 46 0.24
201 128 0.67
202 16 0.08
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (201 bp):
ACTAACTTAAACTTGAAAAGTTTAGGTGTTGGGTTTTGGTTGATCCCGGTAAAAACTATTGGGAA
AGGTTTTGGGCTAAGCTTGGTAAAAGCAATTATAAAGCTTAGTGAAAGCTTGTGAATTTCACCTT
TTATAATAGATTGATTTGGAAAAACTTTAGTTGAATAATTAAGGTAGTGAATGTAGGTCTTGACC
CAAACC
Found at i:28264131 original size:12 final size:12
Alignment explanation
Indices: 28264116--28264140 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28264106 ACATGTGATA
28264116 TCATACATACAT
1 TCATACATACAT
28264128 TCATACATACAT
1 TCATACATACAT
28264140 T
1 T
28264141 TTCAAAAGGC
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATACATACAT
Found at i:28282979 original size:2 final size:2
Alignment explanation
Indices: 28282967--28283014 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
28282957 CAACAGAACT
*
28282967 TA TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28283008 TA TA TA T
1 TA TA TA T
28283015 TGTAATTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28283405 original size:3 final size:3
Alignment explanation
Indices: 28283397--28283422 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28283387 TTTCAATTGC
28283397 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28283423 GTAGTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28286552 original size:29 final size:30
Alignment explanation
Indices: 28286508--28286576 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
28286498 TTGAATATGT
28286508 CATGTAACAACAATA-TTTTTTCAACATGA
1 CATGTAACAACAATATTTTTTTCAACATGA
* * * *
28286537 CGTGTAACAATAATATTTTTTTTAACATGG
1 CATGTAACAACAATATTTTTTTCAACATGA
28286567 CATGTAACAA
1 CATGTAACAA
28286577 ACTTTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
CATGTAACAACAATATTTTTTTCAACATGA
Found at i:28286591 original size:26 final size:25
Alignment explanation
Indices: 28286554--28286625 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
28286544 CAATAATATT
28286554 TTTTTTAACATGGCATGTAACAAAC
1 TTTTTTAACATGGCATGTAACAAAC
* **
28286579 TTTTTTAACCATGGCGTGTAAC-ATG
1 TTTTTTAA-CATGGCATGTAACAAAC
*
28286604 TTTTTTTACATGGCATGTAACA
1 TTTTTTAACATGGCATGTAACA
28286626 GTGGTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 12 0.30
25 16 0.40
26 12 0.30
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTTTTAACATGGCATGTAACAAAC
Found at i:28286615 original size:24 final size:24
Alignment explanation
Indices: 28286553--28286625 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
28286543 ACAATAATAT
28286553 TTTTTTTAACATGGCATGTAACAAAC
1 TTTTTTT-ACATGGCATGTAAC-AAC
* * **
28286579 TTTTTTAACCATGGCGTGTAACATG
1 TTTTTTTA-CATGGCATGTAACAAC
28286604 TTTTTTTACATGGCATGTAACA
1 TTTTTTTACATGGCATGTAACA
28286626 GTGGTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 13 0.32
25 9 0.22
26 18 0.45
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (24 bp):
TTTTTTTACATGGCATGTAACAAC
Found at i:28286709 original size:45 final size:45
Alignment explanation
Indices: 28286651--28286845 Score: 264
Period size: 45 Copynumber: 4.3 Consensus size: 45
28286641 CAACATGGTA
* * *
28286651 TGTAAAAACCTAACCATGGCTTGTCACGGGTTTTTGTACATGGCG
1 TGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCG
* * *
28286696 TGTAACAAGCTAACCATAGCTTGTCACAGGTTTTTGTACATGACT
1 TGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCG
* ** * *
28286741 TGTAAAAAGCTAACCATGGCTTGTCACATATTTTTGTATATAGCG
1 TGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCG
* * *
28286786 TGTAACACGCTAACTATGGCTTGTCACAGGTTTTTGTAAATGGCG
1 TGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCG
28286831 TGTAACAAGCTAACC
1 TGTAACAAGCTAACC
28286846 GTAACTTTTA
Statistics
Matches: 127, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 127 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (45 bp):
TGTAACAAGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCG
Found at i:28294942 original size:15 final size:15
Alignment explanation
Indices: 28294922--28294954 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28294912 CTATTCAATC
28294922 TAACCTAACTTAACT
1 TAACCTAACTTAACT
*
28294937 TAACCTAACTTATCT
1 TAACCTAACTTAACT
28294952 TAA
1 TAA
28294955 TTGGACTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (15 bp):
TAACCTAACTTAACT
Found at i:28295022 original size:15 final size:15
Alignment explanation
Indices: 28295002--28295043 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
28294992 TAAAACAACC
28295002 TTAAAATCAAAAACT
1 TTAAAATCAAAAACT
* *
28295017 TTAAAATCCAAAGCT
1 TTAAAATCAAAAACT
28295032 TTAAAATCAAAA
1 TTAAAATCAAAA
28295044 TATCTGATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.26
Consensus pattern (15 bp):
TTAAAATCAAAAACT
Found at i:28297786 original size:19 final size:19
Alignment explanation
Indices: 28297762--28297798 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28297752 GGGGACTTTA
28297762 AAATTCTCAATTTCATCTT
1 AAATTCTCAATTTCATCTT
* *
28297781 AAATTCTCTATTTGATCT
1 AAATTCTCAATTTCATCT
28297799 AGTTCGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATTCTCAATTTCATCTT
Found at i:28298160 original size:8 final size:8
Alignment explanation
Indices: 28298147--28298211 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
28298137 AATAAAATTA
28298147 TTATTATT
1 TTATTATT
28298155 TTATTATT
1 TTATTATT
*
28298163 TT-TTTTT
1 TTATTATT
* *
28298170 TTTTTTTT
1 TTATTATT
* *
28298178 TTTTTTTT
1 TTATTATT
*
28298186 TTTTTATT
1 TTATTATT
28298194 TTAATT-TT
1 TT-ATTATT
28298202 TTATTATT
1 TTATTATT
28298210 TT
1 TT
28298212 TAAACATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
7 9 0.18
8 40 0.78
9 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTATTATT
Found at i:28298201 original size:16 final size:15
Alignment explanation
Indices: 28298153--28298212 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
28298143 ATTATTATTA
28298153 TTTTATTATTTTTTTT
1 TTTTATTA-TTTTTTT
* *
28298169 TTTTTTTTTTTTTTT
1 TTTTATTATTTTTTT
* *
28298184 TTTTTTTATTTTAATT
1 TTTTATTATTTT-TTT
28298200 TTTTATTATTTTT
1 TTTTATTATTTTT
28298213 AAACATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 18 0.49
16 19 0.51
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTATTATTTTTTT
Found at i:28298212 original size:1 final size:1
Alignment explanation
Indices: 28298161--28298195 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
28298151 TATTTTATTA
*
28298161 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28298196 AATTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:28298212 original size:11 final size:11
Alignment explanation
Indices: 28298144--28298212 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
28298134 TCAAATAAAA
*
28298144 TTATTATTATT
1 TTATTATTTTT
28298155 TTATTATTTTTT
1 TTATTA-TTTTT
* *
28298167 TTTTTTTTTTT
1 TTATTATTTTT
* *
28298178 TTTTTTTTTTT
1 TTATTATTTTT
*
28298189 TTATTTTAATTTT
1 TTA--TTATTTTT
28298202 TTATTATTTTT
1 TTATTATTTTT
28298213 AAACATTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 31 0.65
12 8 0.17
13 9 0.19
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTATTATTTTT
Found at i:28301789 original size:19 final size:19
Alignment explanation
Indices: 28301765--28301802 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28301755 ACTTCTAAAC
28301765 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
28301784 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
28301803 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:28307113 original size:21 final size:21
Alignment explanation
Indices: 28307089--28307130 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28307079 TAGTCAAGTT
28307089 CACATGATGTTACAAGCCATG
1 CACATGATGTTACAAGCCATG
*
28307110 CACATGATGTTACACGCCATG
1 CACATGATGTTACAAGCCATG
28307131 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (21 bp):
CACATGATGTTACAAGCCATG
Found at i:28307154 original size:26 final size:25
Alignment explanation
Indices: 28307117--28307220 Score: 88
Period size: 26 Copynumber: 4.0 Consensus size: 25
28307107 ATGCACATGA
*
28307117 TGTTACACGCCATGTTAAAAATATAT
1 TGTTACATGCCATGTTAAAAA-ATAT
* *
28307143 TGTTACATGCCATG-TACAAACACA-
1 TGTTACATGCCATGTTA-AAAAATAT
*
28307167 TGTTATATGCCATGGTTAAAAAA-AGT
1 TGTTACATGCCAT-GTTAAAAAATA-T
*
28307193 TGTTATATGCCATGTTGAAAAAAATAT
1 TGTTACATGCCATGTT--AAAAAATAT
28307220 T
1 T
28307221 ATTGTTGCAC
Statistics
Matches: 65, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
24 13 0.20
25 12 0.18
26 31 0.48
27 8 0.12
28 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (25 bp):
TGTTACATGCCATGTTAAAAAATAT
Found at i:28322803 original size:22 final size:22
Alignment explanation
Indices: 28322778--28322822 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28322768 TGTGATTTTT
* * *
28322778 TTAAGACATTTATTTATTTATA
1 TTAAGACATATATATATATATA
28322800 TTAAGACATATATATATATATA
1 TTAAGACATATATATATATATA
28322822 T
1 T
28322823 ATATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTAAGACATATATATATATATA
Found at i:28322814 original size:2 final size:2
Alignment explanation
Indices: 28322807--28322833 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28322797 ATATTAAGAC
28322807 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28322834 AGTAATGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28324192 original size:25 final size:25
Alignment explanation
Indices: 28324155--28324210 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
28324145 CATAAGAACT
*
28324155 AAATTGAATAAAAATATAAAGTACA
1 AAATTGAACAAAAATATAAAGTACA
* * * *
28324180 AAATTTAACAAAATTGTACAGTACA
1 AAATTGAACAAAAATATAAAGTACA
28324205 AGAATT
1 A-AATT
28324211 AAATTGAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (25 bp):
AAATTGAACAAAAATATAAAGTACA
Found at i:28326212 original size:12 final size:13
Alignment explanation
Indices: 28326188--28326219 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28326178 AACAAAATAG
28326188 AACAAAAACGAAC
1 AACAAAAACGAAC
28326201 AACAAAAA-GAAC
1 AACAAAAACGAAC
28326213 AA-AAAAA
1 AACAAAAA
28326220 AAATGGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.26
12 6 0.32
13 8 0.42
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAACGAAC
Found at i:28338480 original size:139 final size:133
Alignment explanation
Indices: 28338241--28338499 Score: 410
Period size: 139 Copynumber: 1.9 Consensus size: 133
28338231 ATAAATATTG
* *
28338241 TTTTACAAGAAATTAGAATATTTTATTGAATATTTTTATTTTATTCAAATAGTTGCAATATCATT
1 TTTTACAAGAAAATAGAATATGTTATTGAATATTTTTATTTTATTCAAATAGTTGCAATATCATT
28338306 TTTAATAAATGTTTTAAACACTCAAATTTATTTTAAATCATGAAATATGTGTTTTNNNNNNTTTA
66 TTTAATAAATGTTTTAAACACTCAAATTTATTTTAAATCATGAAATATGTGTTTT------TTTA
28338371 TAAAATTTA
125 TAAAATTTA
**
28338380 TTTTACAAGAAAATAGTTTATGTTATTGAATATTTTTATTTTATTCAAATAGTTGCAATATCATT
1 TTTTACAAGAAAATAGAATATGTTATTGAATATTTTTATTTTATTCAAATAGTTGCAATATCATT
* *
28338445 TTTAATAAATGTTTTAAACACTCAAATTTATTTTAAATTATGAAATGTGTGTTTT
66 TTTAATAAATGTTTTAAACACTCAAATTTATTTTAAATCATGAAATATGTGTTTT
28338500 CCACTCATCT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 114 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.48
Consensus pattern (133 bp):
TTTTACAAGAAAATAGAATATGTTATTGAATATTTTTATTTTATTCAAATAGTTGCAATATCATT
TTTAATAAATGTTTTAAACACTCAAATTTATTTTAAATCATGAAATATGTGTTTTTTTATAAAAT
TTA
Found at i:28342238 original size:16 final size:16
Alignment explanation
Indices: 28342217--28342344 Score: 51
Period size: 16 Copynumber: 8.3 Consensus size: 16
28342207 TTATTTATAA
28342217 ATTTTAAAATATTAAT
1 ATTTTAAAATATTAAT
28342233 ATTTT---ATA-T-AT
1 ATTTTAAAATATTAAT
*
28342244 AATTTAAACATTATTAAT
1 ATTTTAAA-A-TATTAAT
* *
28342262 A--TTAATATGATTAAAA
1 ATTTTAAAAT-ATT-AAT
* * *
28342278 ATATTATAATATAAAT
1 ATTTTAAAATATTAAT
28342294 ATTTTAAAATATTAAT
1 ATTTTAAAATATTAAT
* **
28342310 GTTTT-ATTTATTAA-
1 ATTTTAAAATATTAAT
*
28342324 ATTATTAATATATTAA-
1 ATT-TTAAAATATTAAT
28342340 ATTTT
1 ATTTT
28342345 TAATGAGTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 27
0.67 0.12 0.21
Matches are distributed among these distances:
11 6 0.07
12 1 0.01
13 3 0.04
14 3 0.04
15 16 0.19
16 44 0.52
17 3 0.04
18 8 0.10
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAAAATATTAAT
Found at i:28342287 original size:26 final size:25
Alignment explanation
Indices: 28342253--28342307 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
28342243 TAATTTAAAC
*
28342253 ATTATTAATATTAATATGATTAAAAAT
1 ATTATTAATATAAATAT--TTAAAAAT
*
28342280 ATTA-TAATATAAATATTTTAAAAT
1 ATTATTAATATAAATATTTAAAAAT
28342304 ATTA
1 ATTA
28342308 ATGTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
26 11 0.42
27 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTATTAATATAAATATTTAAAAAT
Found at i:28342347 original size:16 final size:17
Alignment explanation
Indices: 28342263--28342348 Score: 58
Period size: 16 Copynumber: 5.3 Consensus size: 17
28342253 ATTATTAATA
* *
28342263 TTAATATGATTAAAAATA
1 TTAATAT-ATTAAATATT
28342281 TT-ATA-ATATAAATATT
1 TTAATATAT-TAAATATT
* *
28342297 TTAAAATATT-AATGTT
1 TTAATATATTAAATATT
* *
28342313 TT-ATTTATTAAAT-TA
1 TTAATATATTAAATATT
28342328 TTAATATATTAAAT-TT
1 TTAATATATTAAATATT
28342344 TTAAT
1 TTAAT
28342349 GAGTATATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
15 10 0.19
16 34 0.63
17 6 0.11
18 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAATATATTAAATATT
Found at i:28342439 original size:25 final size:26
Alignment explanation
Indices: 28342394--28342489 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 26
28342384 TTAATCATAA
*
28342394 TAAT-ATTAAATTATAAATAAAATAT
1 TAATAATTAAACTATAAATAAAATAT
*
28342419 TAATAATTAAACTAT-ACTAAAATAT
1 TAATAATTAAACTATAAATAAAATAT
* * * *
28342444 TAATATTTAAATTATTAATTATTAATAT
1 TAATAATTAAACTA-TAAATA-AAATAT
* *
28342472 T-TTAATTAAATTATAAAT
1 TAATAATTAAACTATAAAT
28342490 TATTAATATT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
25 25 0.43
26 14 0.24
27 13 0.22
28 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATAATTAAACTATAAATAAAATAT
Found at i:28342509 original size:22 final size:22
Alignment explanation
Indices: 28342374--28342513 Score: 79
Period size: 22 Copynumber: 6.1 Consensus size: 22
28342364 ATAAAAGAAT
* **
28342374 TATTAATATTTTAATCATAATAA
1 TATTAATATTTAAAAAATAA-AA
*
28342397 TATTAA-A-TT-ATAAATAAAA
1 TATTAATATTTAAAAAATAAAA
* *
28342416 TATTAATAATTAAACTATACTAAAA
1 TATTAATATTTAAA--A-AATAAAA
** * *
28342441 TATTAATATTTAAATTATTAAT
1 TATTAATATTTAAAAAATAAAA
*
28342463 TATTAATATTTTAATTAAATTATAAAT
1 TATTAATA-TTTAA--AAA--ATAAAA
28342490 TATTAATATTTAAAAAATAAAA
1 TATTAATATTTAAAAAATAAAA
28342512 TA
1 TA
28342514 AAAATAAATA
Statistics
Matches: 91, Mismatches: 15, Indels: 23
0.71 0.12 0.18
Matches are distributed among these distances:
19 8 0.09
20 6 0.07
21 4 0.04
22 20 0.22
23 11 0.12
24 4 0.04
25 20 0.22
26 5 0.05
27 13 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAATATTTAAAAAATAAAA
Found at i:28348818 original size:24 final size:23
Alignment explanation
Indices: 28348766--28348819 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
28348756 CACGAGTGTG
*
28348766 AGAGATGATAAAAAATGGAATAA
1 AGAGATTATAAAAAATGGAATAA
* *
28348789 AGAGATTATAAAAATTGGAATAG
1 AGAGATTATAAAAAATGGAATAA
28348812 AGAAGATT
1 AG-AGATT
28348820 TGGATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (23 bp):
AGAGATTATAAAAAATGGAATAA
Found at i:28350617 original size:18 final size:17
Alignment explanation
Indices: 28350594--28350644 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
28350584 CGACACGATT
*
28350594 AATAACATGTTTAACAC
1 AATAACACGTTTAACAC
*
28350611 GAATAACACGTTCAACAC
1 -AATAACACGTTTAACAC
28350629 AATTAACACGTTTAAC
1 AA-TAACACGTTTAAC
28350645 GTGATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (17 bp):
AATAACACGTTTAACAC
Found at i:28352924 original size:42 final size:42
Alignment explanation
Indices: 28352875--28352959 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
28352865 AACAATTAAA
* *
28352875 GATAGATTCTATGCATATGCCCTTGCTTTCTAAATTAACGGG
1 GATAGATTCTATGCATATGCCCTTGCTCTCTAAATTAAAGGG
28352917 GATAGATTCTATGCATATGCCCTTGCTCTCTAAATTAAAGGG
1 GATAGATTCTATGCATATGCCCTTGCTCTCTAAATTAAAGGG
28352959 G
1 G
28352960 TTGTTGGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (42 bp):
GATAGATTCTATGCATATGCCCTTGCTCTCTAAATTAAAGGG
Found at i:28353154 original size:64 final size:64
Alignment explanation
Indices: 28353076--28353203 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
28353066 CTTTCGAATG
* *
28353076 GCGGCCGTATTGAATTTTTACTACTAAAAGGACTAGTGATGAAATAGATTTATTCTGGTCTACA
1 GCGGCCGTAATGAATTATTACTACTAAAAGGACTAGTGATGAAATAGATTTATTCTGGTCTACA
* *
28353140 GCGGCCGTAATGAATTATTACTAGTAAAAGGACTAGTGATGAAATAGATTTATTTTGGTCTACA
1 GCGGCCGTAATGAATTATTACTACTAAAAGGACTAGTGATGAAATAGATTTATTCTGGTCTACA
28353204 TTTGGTTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (64 bp):
GCGGCCGTAATGAATTATTACTACTAAAAGGACTAGTGATGAAATAGATTTATTCTGGTCTACA
Found at i:28354059 original size:24 final size:24
Alignment explanation
Indices: 28354026--28354080 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
28354016 GCAACTTATT
*
28354026 TTCCAATTGAAATCATCATTGCTAA
1 TTCC-ATTGAAATCATCATTACTAA
28354051 TTCCATTGAAATCATCATTACTAA
1 TTCCATTGAAATCATCATTACTAA
28354075 TTCCAT
1 TTCCAT
28354081 GTAAGTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (24 bp):
TTCCATTGAAATCATCATTACTAA
Found at i:28357836 original size:2 final size:2
Alignment explanation
Indices: 28357829--28357874 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
28357819 NNNNNNNNNN
28357829 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G
28357872 AG A
1 AG A
28357875 AACAAACTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:28365865 original size:12 final size:12
Alignment explanation
Indices: 28365850--28365874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28365840 TTTTTGTAAG
28365850 TATTTGGAAAAC
1 TATTTGGAAAAC
28365862 TATTTGGAAAAC
1 TATTTGGAAAAC
28365874 T
1 T
28365875 GTTCCATGTG
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TATTTGGAAAAC
Found at i:28366693 original size:17 final size:16
Alignment explanation
Indices: 28366652--28366695 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
28366642 AATTGCTCTC
28366652 CTTCTTTCATTAAAAT
1 CTTCTTTCATTAAAAT
*
28366668 CTTTTTTTCATTAAAATT
1 C-TTCTTTCATTAAAA-T
28366686 CTTCTTTCAT
1 CTTCTTTCAT
28366696 CAAACACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.25, C:0.18, G:0.00, T:0.57
Consensus pattern (16 bp):
CTTCTTTCATTAAAAT
Found at i:28368651 original size:44 final size:44
Alignment explanation
Indices: 28368598--28368729 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 44
28368588 CATAATTGTT
*
28368598 CTTTGGCCTAGGCACATGCCTCTAGGCAAACATACATATTCACA
1 CTTTAGCCTAGGCACATGCCTCTAGGCAAACATACATATTCACA
* * * * ***
28368642 CNTTAGCCTAGGCATC-T-CATCTAAGCACACA-ATCATAATT-GTT
1 CTTTAGCCTAGGCA-CATGCCTCTAGGCAAACATA-CAT-ATTCACA
*
28368685 CTTTGGCCTAGGCACATGCCTCTAGGCAAACATACATATTCACA
1 CTTTAGCCTAGGCACATGCCTCTAGGCAAACATACATATTCACA
28368729 C
1 C
28368730 ACACACACAC
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
42 2 0.03
43 30 0.46
44 31 0.48
45 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (44 bp):
CTTTAGCCTAGGCACATGCCTCTAGGCAAACATACATATTCACA
Found at i:28368670 original size:87 final size:87
Alignment explanation
Indices: 28368556--28368729 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
28368546 GGATAACTAA
28368556 TTAGCCTAGGCATCCTCATCTAAGCACACAATCATAATTGTTCTTTGGCCTAGGCACATGCCTCT
1 TTAGCCTAGGCATCCTCATCTAAGCACACAATCATAATTGTTCTTTGGCCTAGGCACATGCCTCT
28368621 AGGCAAACATACATATTCACAC
66 AGGCAAACATACATATTCACAC
28368643 NTTAGCCTAGGCAT-CTCATCTAAGCACACAATCATAATTGTTCTTTGGCCTAGGCACATGCCTC
1 -TTAGCCTAGGCATCCTCATCTAAGCACACAATCATAATTGTTCTTTGGCCTAGGCACATGCCTC
28368707 TAGGCAAACATACATATTCACAC
65 TAGGCAAACATACATATTCACAC
28368730 ACACACACAC
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 73 0.85
88 13 0.15
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (87 bp):
TTAGCCTAGGCATCCTCATCTAAGCACACAATCATAATTGTTCTTTGGCCTAGGCACATGCCTCT
AGGCAAACATACATATTCACAC
Found at i:28368698 original size:43 final size:43
Alignment explanation
Indices: 28368559--28368698 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 43
28368549 TAACTAATTA
28368559 GCCTAGGCATCCTCATCTAAGCACACAATCATAATTGTTCTTTG
1 GCCTAGGCAT-CTCATCTAAGCACACAATCATAATTGTTCTTTG
* * * *** * *
28368603 GCCTAGGCA-CATGCCTCTAGGCAAAC-ATACAT-ATTCACACNTTA
1 GCCTAGGCATC-T-CATCTAAGCACACAAT-CATAATT-GTTCTTTG
28368647 GCCTAGGCATCTCATCTAAGCACACAATCATAATTGTTCTTTG
1 GCCTAGGCATCTCATCTAAGCACACAATCATAATTGTTCTTTG
28368690 GCCTAGGCA
1 GCCTAGGCA
28368699 CATGCCTCTA
Statistics
Matches: 73, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
42 1 0.01
43 31 0.42
44 40 0.55
45 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (43 bp):
GCCTAGGCATCTCATCTAAGCACACAATCATAATTGTTCTTTG
Found at i:28368732 original size:2 final size:2
Alignment explanation
Indices: 28368725--28368768 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28368715 CATACATATT
28368725 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28368767 CA
1 CA
28368769 TATACATACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28369045 original size:18 final size:19
Alignment explanation
Indices: 28369022--28369058 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28369012 ATTATTTATT
28369022 TCCTAGC-TTTCAAAAATA
1 TCCTAGCTTTTCAAAAATA
28369040 TCCTAGCTTTTCAAAAATA
1 TCCTAGCTTTTCAAAAATA
28369059 CCCAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (19 bp):
TCCTAGCTTTTCAAAAATA
Found at i:28369443 original size:20 final size:21
Alignment explanation
Indices: 28369418--28369456 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28369408 TTCCTCTTTG
28369418 ATGTATCCATACAT-TGCCAA
1 ATGTATCCATACATATGCCAA
*
28369438 ATGTATCGATACATATGCC
1 ATGTATCCATACATATGCC
28369457 CTAATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
ATGTATCCATACATATGCCAA
Found at i:28382459 original size:15 final size:16
Alignment explanation
Indices: 28382432--28382461 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28382422 ATCGAGCTTC
28382432 CATGAACATCAATAAA
1 CATGAACATCAATAAA
28382448 CATGAA-ATCAATAA
1 CATGAACATCAATAA
28382462 CAATTAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (16 bp):
CATGAACATCAATAAA
Found at i:28384032 original size:11 final size:11
Alignment explanation
Indices: 28384016--28384044 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28384006 TAAATATTTA
28384016 TAATTAATTAT
1 TAATTAATTAT
28384027 TAATTAATTAT
1 TAATTAATTAT
28384038 T-ATTAAT
1 TAATTAAT
28384045 CAAAATGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTAATTAT
Found at i:28385146 original size:23 final size:23
Alignment explanation
Indices: 28385116--28385260 Score: 182
Period size: 23 Copynumber: 6.3 Consensus size: 23
28385106 GTTTAAAGTT
* *
28385116 TGTGACACGCCATGGTGGGAATG
1 TGTGACACGGCATGGTGAGAATG
* *
28385139 TGTGACACGACATGGTGAGAATA
1 TGTGACACGGCATGGTGAGAATG
* *
28385162 TGTGACATGGCATGGTGGGAATG
1 TGTGACACGGCATGGTGAGAATG
* *
28385185 TGTGACACGGCATGGTAAGAATT
1 TGTGACACGGCATGGTGAGAATG
**
28385208 TGTGACATAGCATGGTGAGAATG
1 TGTGACACGGCATGGTGAGAATG
* *
28385231 TGTGACACGGCATAGTGAGAATA
1 TGTGACACGGCATGGTGAGAATG
28385254 TGTGACA
1 TGTGACA
28385261 TGGTTGTGAC
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 103 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (23 bp):
TGTGACACGGCATGGTGAGAATG
Found at i:28385261 original size:46 final size:46
Alignment explanation
Indices: 28385126--28385261 Score: 218
Period size: 46 Copynumber: 3.0 Consensus size: 46
28385116 TGTGACACGC
* *
28385126 CATGGTGGGAATGTGTGACACGACATGGTGAGAATATGTGACATGG
1 CATGGTGGGAATGTGTGACACGGCATGGTGAGAATATGTGACATAG
* *
28385172 CATGGTGGGAATGTGTGACACGGCATGGTAAGAATTTGTGACATAG
1 CATGGTGGGAATGTGTGACACGGCATGGTGAGAATATGTGACATAG
* *
28385218 CATGGTGAGAATGTGTGACACGGCATAGTGAGAATATGTGACAT
1 CATGGTGGGAATGTGTGACACGGCATGGTGAGAATATGTGACAT
28385262 GGTTGTGACA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.29, C:0.11, G:0.35, T:0.25
Consensus pattern (46 bp):
CATGGTGGGAATGTGTGACACGGCATGGTGAGAATATGTGACATAG
Found at i:28385302 original size:73 final size:77
Alignment explanation
Indices: 28385210--28385412 Score: 225
Period size: 73 Copynumber: 2.6 Consensus size: 77
28385200 TAAGAATTTG
* * * *
28385210 TGACATAGCATGGTGAGAATGTGTGACACGGCATAGTGAGAATATGTGACATGGTTGTGACACGG
1 TGACATAGCATGGTGAGAATGTGTGACACGGCATGGTGAGAATGTGTGACATGGCTGTGACACGA
28385275 C-AG-G-G-TTA
66 CAAGTGAGTTTA
* *** * * *
28385283 TGACATGGCATGGTGAGAATCCATAACACGACATGGTGAGAATGTTTGACATGGCTGTGACACGA
1 TGACATAGCATGGTGAGAATGTGTGACACGGCATGGTGAGAATGTGTGACATGGCTGTGACACGA
*
28385348 CAAGATTTAGAGTTTG
66 CAAG---T-GAGTTTA
*
28385364 TGACATAGCATGGTGGGAATGTGTGACACGGCATGGTGAGAATGTGTGA
1 TGACATAGCATGGTGAGAATGTGTGACACGGCATGGTGAGAATGTGTGA
28385413 GAAGGCATGG
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
73 55 0.54
74 2 0.02
79 1 0.01
80 1 0.01
81 43 0.42
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (77 bp):
TGACATAGCATGGTGAGAATGTGTGACACGGCATGGTGAGAATGTGTGACATGGCTGTGACACGA
CAAGTGAGTTTA
Found at i:28385391 original size:23 final size:23
Alignment explanation
Indices: 28385362--28385458 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
28385352 ATTTAGAGTT
* *
28385362 TGTGACATAGCATGGTGGGAATG
1 TGTGACACAGCATGGTGAGAATG
*
28385385 TGTGACACGGCATGGTGAGAATG
1 TGTGACACAGCATGGTGAGAATG
* * *
28385408 TGTGAGA-AGGCATGGTGAAAATA
1 TGTGACACA-GCATGGTGAGAATG
** ** *
28385431 TGTGGGATGGCATGGTGAGAATA
1 TGTGACACAGCATGGTGAGAATG
28385454 TGTGA
1 TGTGA
28385459 TATGATTGTG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.29, C:0.07, G:0.39, T:0.25
Consensus pattern (23 bp):
TGTGACACAGCATGGTGAGAATG
Found at i:28385421 original size:46 final size:46
Alignment explanation
Indices: 28385371--28385458 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
28385361 TTGTGACATA
** * *
28385371 GCATGGTGGGAATGTGTGACACGGCATGGTGAGAATGTGTGAGAAG
1 GCATGGTGAAAATATGTGACACGGCATGGTGAGAATATGTGAGAAG
** *
28385417 GCATGGTGAAAATATGTGGGATGGCATGGTGAGAATATGTGA
1 GCATGGTGAAAATATGTGACACGGCATGGTGAGAATATGTGA
28385459 TATGATTGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.41, T:0.24
Consensus pattern (46 bp):
GCATGGTGAAAATATGTGACACGGCATGGTGAGAATATGTGAGAAG
Found at i:28385662 original size:25 final size:25
Alignment explanation
Indices: 28385603--28385686 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 25
28385593 TTAGAGTTTA
* *
28385603 TGACATGCCATGGTAAGAAT-T-TG
1 TGACACGCCATGGTGAGAATATATG
* *
28385626 TGAGACGGCATGGTGAGAATATATG
1 TGACACGCCATGGTGAGAATATATG
*
28385651 TGACATGCCATGGATG-G-A-ATATG
1 TGACACGCCATGG-TGAGAATATATG
28385674 TGACACGCCATGG
1 TGACACGCCATGG
28385687 CTTGAATATG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
23 33 0.66
24 2 0.04
25 13 0.26
26 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (25 bp):
TGACACGCCATGGTGAGAATATATG
Found at i:28385676 original size:23 final size:23
Alignment explanation
Indices: 28385646--28385699 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
28385636 TGGTGAGAAT
*
28385646 ATATGTGACATGCCATGGATGGA
1 ATATGTGACACGCCATGGATGGA
* *
28385669 ATATGTGACACGCCATGGCTTGA
1 ATATGTGACACGCCATGGATGGA
28385692 ATATGTGA
1 ATATGTGA
28385700 TACGACATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (23 bp):
ATATGTGACACGCCATGGATGGA
Found at i:28386626 original size:31 final size:31
Alignment explanation
Indices: 28386581--28386684 Score: 154
Period size: 31 Copynumber: 3.4 Consensus size: 31
28386571 ATGGGTTGGT
*
28386581 GTGTTACAACATTTTACTTGGTATGCATAAC
1 GTGTAACAACATTTTACTTGGTATGCATAAC
* * *
28386612 GTGTAACAATATTTTACTTGGTCTGCATACC
1 GTGTAACAACATTTTACTTGGTATGCATAAC
* *
28386643 ATGTAACAACATTTTACTTGGTATGCATAGC
1 GTGTAACAACATTTTACTTGGTATGCATAAC
28386674 GTGTAACAACA
1 GTGTAACAACA
28386685 AATATTTCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (31 bp):
GTGTAACAACATTTTACTTGGTATGCATAAC
Found at i:28387206 original size:3 final size:3
Alignment explanation
Indices: 28387200--28387234 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
28387190 TTTTCAAATA
28387200 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
28387235 ATAAATCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28388922 original size:90 final size:90
Alignment explanation
Indices: 28388764--28388942 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
28388754 AGACATAAGG
* * *
28388764 GTCAACATTAGGGTGAACGATTTTTTTTTATTATTTTAGGTTCGAATTCGGTGGTTTTGTTTAGG
1 GTCAACATTAGGGTGAAAGATTTTTTTTTATTATTTTAGGTTCGAATTCGGTGGTTTTATTTAAG
*
28388829 CCTTCCGATCATTGCTTCAGAAAGA
66 CCTTCCAATCATTGCTTCAGAAAGA
* *
28388854 GTCAGCATTAGGGTGAAAGATTTTTTTTTATTATTTTAGGTTCGGATTCGGTGGTTTTATTTAAG
1 GTCAACATTAGGGTGAAAGATTTTTTTTTATTATTTTAGGTTCGAATTCGGTGGTTTTATTTAAG
28388919 CCTTCCAATCATTGCTTCAGAAAG
66 CCTTCCAATCATTGCTTCAGAAAG
28388943 GGATTGGAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (90 bp):
GTCAACATTAGGGTGAAAGATTTTTTTTTATTATTTTAGGTTCGAATTCGGTGGTTTTATTTAAG
CCTTCCAATCATTGCTTCAGAAAGA
Found at i:28389659 original size:21 final size:21
Alignment explanation
Indices: 28389625--28389691 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
28389615 AAAAAATGTG
*
28389625 AAAAATGATGTAAATAAAAATA
1 AAAAAT-ATATAAATAAAAATA
*
28389647 AAAAATATATAAATAACAATA
1 AAAAATATATAAATAAAAATA
*
28389668 ATAATAATA-ATAACATAGAAATA
1 A-AA-AATATATAA-ATAAAAATA
28389691 A
1 A
28389692 TAGTGAGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 14 0.37
22 12 0.32
23 12 0.32
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAAATATATAAATAAAAATA
Found at i:28389940 original size:21 final size:21
Alignment explanation
Indices: 28389922--28389963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28389912 AAAAAAATGA
28389922 AACAATGAA-AATAATAAATAT
1 AACAAT-AATAATAATAAATAT
*
28389943 AGCAATAATAATAATAAATAT
1 AACAATAATAATAATAAATAT
28389964 GAAAGGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
AACAATAATAATAATAAATAT
Found at i:28403013 original size:2 final size:2
Alignment explanation
Indices: 28403008--28403050 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28402998 ANGACATTAC
28403008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28403050 A
1 A
28403051 AGAATAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28404221 original size:23 final size:23
Alignment explanation
Indices: 28404186--28404229 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28404176 TCAACTTTTG
*
28404186 CCTTAAGAGTTTGTAAAAGAATT
1 CCTTAAAAGTTTGTAAAAGAATT
*
28404209 CCTTAAAATTTTGTAAAAGAA
1 CCTTAAAAGTTTGTAAAAGAA
28404230 ACTGGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (23 bp):
CCTTAAAAGTTTGTAAAAGAATT
Found at i:28404678 original size:23 final size:24
Alignment explanation
Indices: 28404648--28404700 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
28404638 AACTTTCATT
28404648 GGAAATTTCAAACAAAAAT-TGTA
1 GGAAATTTCAAACAAAAATCTGTA
* * *
28404671 GGAAATTTCTATCAAAATTCTGTA
1 GGAAATTTCAAACAAAAATCTGTA
28404695 GGAAAT
1 GGAAAT
28404701 GCTCTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (24 bp):
GGAAATTTCAAACAAAAATCTGTA
Found at i:28405118 original size:25 final size:25
Alignment explanation
Indices: 28405084--28405133 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28405074 ATTTAGAATG
*
28405084 TTGTGCAAATATGCAAAAGCAAATA
1 TTGTACAAATATGCAAAAGCAAATA
* *
28405109 TTGTACAAATATGCGAAAGTAAATA
1 TTGTACAAATATGCAAAAGCAAATA
28405134 CAATTGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (25 bp):
TTGTACAAATATGCAAAAGCAAATA
Found at i:28411821 original size:21 final size:21
Alignment explanation
Indices: 28411797--28411870 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
28411787 GTTTTTAGGT
**
28411797 ATTGCGTGACTGACTTTGGAT
1 ATTGCGTGACTGACTTTGGGC
28411818 ATTGCGTGACTGACTTTGGGC
1 ATTGCGTGACTGACTTTGGGC
28411839 ATTGCGTGACTGACTTTGGGC
1 ATTGCGTGACTGACTTTGGGC
28411860 ATTGCGTGACT
1 ATTGCGTGACT
28411871 AATTTTTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (21 bp):
ATTGCGTGACTGACTTTGGGC
Found at i:28411936 original size:95 final size:96
Alignment explanation
Indices: 28411836--28412040 Score: 304
Period size: 95 Copynumber: 2.1 Consensus size: 96
28411826 ACTGACTTTG
* * * * *
28411836 GGCATTGCGTGACTGACTTTGGGCATTGCGTGACTAATTTTTGATAAGGCATTGCGTGACTAGTT
1 GGCATTGAGTGACTAACTTTAGGCATTGCATGACTAATATTTGATAAGGCATTGCGTGACTAGTT
** *
28411901 TCTGATAAGGTTTTGCGTGACTAGTTGAT-A
66 TCTGATAAGGCATTGCGTGACTAGTTAATAA
* *
28411931 GGCATTGAGTGACTAACTTTAGGTATTGCATGACTACTATTTGATAAGGCATTGCGTGACTAGTT
1 GGCATTGAGTGACTAACTTTAGGCATTGCATGACTAATATTTGATAAGGCATTGCGTGACTAGTT
28411996 TCTGATAAGGCATTGCGTGACTAGTTAATAA
66 TCTGATAAGGCATTGCGTGACTAGTTAATAA
*
28412027 GGCATTGTGTGACT
1 GGCATTGAGTGACT
28412041 TAGGCATTGC
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 84 0.86
96 14 0.14
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.36
Consensus pattern (96 bp):
GGCATTGAGTGACTAACTTTAGGCATTGCATGACTAATATTTGATAAGGCATTGCGTGACTAGTT
TCTGATAAGGCATTGCGTGACTAGTTAATAA
Found at i:28411965 original size:69 final size:72
Alignment explanation
Indices: 28411886--28412018 Score: 175
Period size: 69 Copynumber: 1.9 Consensus size: 72
28411876 TTGATAAGGC
* * **
28411886 ATTGCGTGACTAGT-TTCTGATAAGGTTTTGCGTGACTAG-T-TGAT-AGGCATTGAGTGACTAA
1 ATTGCATGACTACTATT-TGATAAGGCATTGCGTGACTAGTTCTGATAAGGCATTGAGTGACTAA
28411947 CTTTAGGT
65 CTTTAGGT
*
28411955 ATTGCATGACTACTATTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTA
1 ATTGCATGACTACTATTTGATAAGGCATTGCGTGACTAG-TTCTGATAAGGCATTGAGTGACTA
28412019 GTTAATAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
69 32 0.59
70 2 0.04
71 1 0.02
72 4 0.07
73 15 0.28
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.36
Consensus pattern (72 bp):
ATTGCATGACTACTATTTGATAAGGCATTGCGTGACTAGTTCTGATAAGGCATTGAGTGACTAAC
TTTAGGT
Found at i:28412019 original size:26 final size:26
Alignment explanation
Indices: 28411857--28412021 Score: 161
Period size: 26 Copynumber: 6.7 Consensus size: 26
28411847 ACTGACTTTG
* *
28411857 GGCATTGCGTGACTAATTTTTGATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
28411883 GGCATTGCGTGACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
**
28411909 GGTTTTGCGTGACTAG--T-TGAT-A
1 GGCATTGCGTGACTAGTTTCTGATAA
* * *
28411931 GGCATTGAGTGACTA---ACT--TTA
1 GGCATTGCGTGACTAGTTTCTGATAA
* * *
28411952 GGTATTGCATGACTACTATT-TGATAA
1 GGCATTGCGTGACTAGT-TTCTGATAA
28411978 GGCATTGCGTGACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTCTGATAA
28412004 GGCATTGCGTGACTAGTT
1 GGCATTGCGTGACTAGTT
28412022 AATAAGGCAT
Statistics
Matches: 114, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
20 1 0.01
21 13 0.11
22 14 0.12
23 4 0.04
24 2 0.02
25 2 0.02
26 78 0.68
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.36
Consensus pattern (26 bp):
GGCATTGCGTGACTAGTTTCTGATAA
Found at i:28412085 original size:22 final size:22
Alignment explanation
Indices: 28412052--28412130 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
28412042 AGGCATTGCT
*
28412052 TAAAAA-TCAGTCACGCAATGTC
1 TAAAAACT-AGTCACGTAATGTC
*
28412074 TAAAAACTAGTCACGTAATGCC
1 TAAAAACTAGTCACGTAATGTC
* *
28412096 T-AAAACCAATCACGTAATGTC
1 TAAAAACTAGTCACGTAATGTC
28412117 TAAAAACTAGTCAC
1 TAAAAACTAGTCAC
28412131 ACAGTAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 18 0.38
22 29 0.60
23 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGTC
Found at i:28412906 original size:184 final size:181
Alignment explanation
Indices: 28412551--28412915 Score: 694
Period size: 184 Copynumber: 2.0 Consensus size: 181
28412541 GCCTGCAAAG
28412551 AGCAAAATCGTTGCTTATCGCCCTTAAGAACCCAAAATCCACCATCCAAAAAAATAAAACAAAAT
1 AGCAAAATCGTTGCTTATCGCCCTTAAGAACCCAAAATCCACCATCCAAAAAAATAAAACAAAAT
*
28412616 AAGAAAGAGCTTGATGTCATCTCTACGAATTGGATGACGAGATAGATATATTTGAGCAAAGAGAG
66 AAGAAAAAGCTTGATGTCATCTCTACGAATTGGATGACGAGATAGATATATTTGAGCAAAGAGAG
28412681 AAATAGAGATTTAATTTTGAAATTTTTATCTAGATGGTGGGAGAGAGAAAA
131 AAATAGAGATTTAATTTTGAAATTTTTATCTAGATGGTGGGAGAGAGAAAA
28412732 NAGCAAAATCGTTGCTTATCGCCCTTAAGAACCCAAAATCCACCATCCAAAAAAATAAAACAAAA
1 -AGCAAAATCGTTGCTTATCGCCCTTAAGAACCCAAAATCCACCATCCAAAAAAATAAAACAAAA
28412797 TAAGAAAAAGCTTGATGTCATCTCTCTACGAATTGGATGACGAGATAGATATATTTGAGCAAAGA
65 TAAGAAAAAGCTTGATGTCA--TCTCTACGAATTGGATGACGAGATAGATATATTTGAGCAAAGA
28412862 GAGAAATAGAGATTTAATTTTGAAATTTTTATCTAGATGGTGGGAGAGAGAAAA
128 GAGAAATAGAGATTTAATTTTGAAATTTTTATCTAGATGGTGGGAGAGAGAAAA
28412916 CTGAAACCAT
Statistics
Matches: 180, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 83 0.46
184 97 0.54
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (181 bp):
AGCAAAATCGTTGCTTATCGCCCTTAAGAACCCAAAATCCACCATCCAAAAAAATAAAACAAAAT
AAGAAAAAGCTTGATGTCATCTCTACGAATTGGATGACGAGATAGATATATTTGAGCAAAGAGAG
AAATAGAGATTTAATTTTGAAATTTTTATCTAGATGGTGGGAGAGAGAAAA
Found at i:28413497 original size:14 final size:15
Alignment explanation
Indices: 28413478--28413510 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28413468 TTCAGAAAGG
*
28413478 TTTTCATC-TCTCAA
1 TTTTCATCTTCCCAA
28413492 TTTTCATCTTCCCAA
1 TTTTCATCTTCCCAA
28413507 TTTT
1 TTTT
28413511 TTTCAATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTCATCTTCCCAA
Found at i:28424084 original size:19 final size:19
Alignment explanation
Indices: 28424060--28424096 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28424050 CGTTTAACTT
*
28424060 ATTGGAGTATGATTTGAGC
1 ATTGGAGTATAATTTGAGC
28424079 ATTGGAGTATAATTTGAG
1 ATTGGAGTATAATTTGAG
28424097 GGTTTGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (19 bp):
ATTGGAGTATAATTTGAGC
Found at i:28424303 original size:28 final size:29
Alignment explanation
Indices: 28424262--28424321 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
28424252 GTCTATGGGC
* *
28424262 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
28424290 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
28424320 AA
1 AA
28424322 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:28425490 original size:13 final size:13
Alignment explanation
Indices: 28425472--28425496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28425462 AGAGAAATTG
28425472 TGATTTTATAAAA
1 TGATTTTATAAAA
28425485 TGATTTTATAAA
1 TGATTTTATAAA
28425497 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:28433593 original size:44 final size:44
Alignment explanation
Indices: 28433529--28433951 Score: 337
Period size: 44 Copynumber: 9.7 Consensus size: 44
28433519 TAATATTGGT
* * * **
28433529 TTATTCATTTTTAAAATTATGTAGCTTCCTTTTAGATGAAGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
*
28433573 TTATTTATTTTTAAAGTTATGTAGCCTCATT-CAAGATG-AGAAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTAC-AGATGAAG-AGC
* * * *
28433617 TTATTTATTTTTAAAGTTATGTAGCCTCATTCCAAATGAGGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
* * *
28433661 TTATTTA-TTTTAAAGTTACGTAGCCTCATTACAGATGATGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
* * ** * *
28433704 TTATTCATTTAT-AATTTACATAGCCTCATTACAGATGAAAAGT
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
*
28433747 TTATTCATTTTTAAAGTTATGTAGCCTCATTCCA-A-GTAAGGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATG-AA-GAGC
* * * ** *
28433791 TTATTCA-TTTCAAAGTTACGTAACCTCATT-CTAGACAAAAAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTAC-AGATGAAGAGC
* * * * * *
28433834 ATATTCATTTTTCAAGTTACGTAACCTCATTCCAAATGAAGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
* * * ** ** *
28433878 TAATTCA-TTTCAAAGTTACGTAATCTCATTTTAGATGAGGAGC
1 TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
*
28433921 -TATTTC-TTCTTTAAAGTTATGTAACCTCATT
1 TTA-TTCATT-TTTAAAGTTATGTAGCCTCATT
28433952 CTAAATGAGG
Statistics
Matches: 313, Mismatches: 50, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
42 3 0.01
43 143 0.46
44 164 0.52
45 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (44 bp):
TTATTCATTTTTAAAGTTATGTAGCCTCATTACAGATGAAGAGC
Found at i:28433758 original size:130 final size:131
Alignment explanation
Indices: 28433562--28433895 Score: 381
Period size: 130 Copynumber: 2.6 Consensus size: 131
28433552 GCTTCCTTTT
* * ** * *
28433562 AGATGAAGAGCTTATTTATTTTTAAAGTTATGTAGCCTCATTCAAGATGAGAAGCTTATTTATTT
1 AGATGAAGAGCTTATTCATTTATAAAGTTACATAGCCTCATTCAAGATGAAAAGCTTATTCATTT
* * * *
28433627 TTAAAGTTATGTAGCCTCATTCCAAATGAGGAGCTTATTTATTTTAAAGTTACGTAGCCTCATTA
66 TTAAAGTTATGTAGCCTCATTCCAAATAAGGAGCTTATTCATTTCAAAGTTACGTAACCTCATTA
28433692 C
131 C
* * *
28433693 AGATGATGAGCTTATTCATTTAT-AATTTACATAGCCTCATT-ACAGATGAAAAGTTTATTCATT
1 AGATGAAGAGCTTATTCATTTATAAAGTTACATAGCCTCATTCA-AGATGAAAAGCTTATTCATT
*
28433756 TTTAAAGTTATGTAGCCTCATTCCAAGTAAGGAGCTTATTCATTTCAAAGTTACGTAACCTCATT
65 TTTAAAGTTATGTAGCCTCATTCCAAATAAGGAGCTTATTCATTTCAAAGTTACGTAACCTCATT
28433821 -C
130 AC
** * * * * * * * *
28433822 TAGACAAAAAGCATATTCATTTTTCAAGTTACGTAACCTCATTCCAA-ATGAAGAGCTAATTCA-
1 -AGATGAAGAGCTTATTCATTTATAAAGTTACATAGCCTCATT-CAAGATGAAAAGCTTATTCAT
*
28433885 TTTCAAAGTTA
64 TTTTAAAGTTA
28433896 CGTAATCTCA
Statistics
Matches: 171, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
129 2 0.01
130 119 0.70
131 48 0.28
132 1 0.01
133 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (131 bp):
AGATGAAGAGCTTATTCATTTATAAAGTTACATAGCCTCATTCAAGATGAAAAGCTTATTCATTT
TTAAAGTTATGTAGCCTCATTCCAAATAAGGAGCTTATTCATTTCAAAGTTACGTAACCTCATTA
C
Found at i:28433759 original size:87 final size:85
Alignment explanation
Indices: 28433562--28433966 Score: 327
Period size: 87 Copynumber: 4.7 Consensus size: 85
28433552 GCTTCCTTTT
* * * * *
28433562 AGATGAAGAGCTTATTTATTTTTAAAGTTATGTAGCCTCATTCAAGATGAGAAGCTTATTTATTT
1 AGATGAAAAGCTTATTCATTTTTAAAGTTACGTAGCCTCATTCCAGATGAG-AGCTTATTCATTT
* *
28433627 TTAAAGTTATGTAGCCTCATTCC
65 AT-AAGTTACGTAGCCTCATT-C
* ** * *
28433650 AAATGAGGAGCTTATTTA-TTTTAAAGTTACGTAGCCTCATTACAGATGATGAGCTTATTCATTT
1 AGATGAAAAGCTTATTCATTTTTAAAGTTACGTAGCCTCATTCCAGATGA-GAGCTTATTCATTT
* *
28433714 ATAATTTACATAGCCTCATTAC
65 ATAAGTTACGTAGCCTCATT-C
* * *
28433736 AGATGAAAAGTTTATTCATTTTTAAAGTTATGTAGCCTCATTCCA-AGTAAGGAGCTTATTCATT
1 AGATGAAAAGCTTATTCATTTTTAAAGTTACGTAGCCTCATTCCAGA-TGA-GAGCTTATTCATT
*
28433800 TCA-AAGTTACGTAACCTCATTC
64 T-ATAAGTTACGTAGCCTCATTC
** * * * * *
28433822 TAGACAAAAAGCATATTCATTTTTCAAGTTACGTAACCTCATTCCAAATGAAGAGCTAATTCATT
1 -AGATGAAAAGCTTATTCATTTTTAAAGTTACGTAGCCTCATTCCAGATG-AGAGCTTATTCATT
** *
28433887 TCA-AAGTTACGTAATCTCATTTT
64 T-ATAAGTTACGTAGCCTCA-TTC
** * * * *
28433910 AGATGAGGAGC-TATTTC-TTCTTTAAAGTTATGTAACCTCATTCTAAATGAGGAGCTT
1 AGATGAAAAGCTTA-TTCATT-TTTAAAGTTACGTAGCCTCATTCCAGATGA-GAGCTT
28433967 TTTCTTTGGA
Statistics
Matches: 264, Mismatches: 42, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
86 36 0.14
87 206 0.78
88 22 0.08
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (85 bp):
AGATGAAAAGCTTATTCATTTTTAAAGTTACGTAGCCTCATTCCAGATGAGAGCTTATTCATTTA
TAAGTTACGTAGCCTCATTC
Found at i:28433936 original size:174 final size:173
Alignment explanation
Indices: 28433558--28433966 Score: 430
Period size: 174 Copynumber: 2.3 Consensus size: 173
28433548 TGTAGCTTCC
* *
28433558 TTTTAGATGAAGAGCTTATTTATTTTTAAAGTTATGTAGCCTCATT-CAAGATGAGAAGCTTATT
1 TTTTAGATGAAGAGC-TATTTCTTTTTAAAGTTATGTAGCCTCATTCCAAG-TGAGGAGCTTATT
* * * * ** ** * * *
28433622 TATTTTTAAAGTTATGTAGCCTCATTCCAAATGAGGAGCTTATTTATTTTAAAGTTACGTAGCCT
64 CATTTTCAAAGTTACGTAACCTCATTCCAAACAAAAAGCATATTCATTTTAAAGTTACGTAACCT
* * * * *
28433687 CATTACAGATGATGAGCTTATTCATTTATAATTTACATAGCCTCA
129 CATTACAAATGAAGAGCTAATTCATTTATAAGTTACATAACCTCA
** * * *
28433732 TTACAGATGAAAAG-TTTATTCATTTTTAAAGTTATGTAGCCTCATTCCAAGTAAGGAGCTTATT
1 TTTTAGATGAAGAGCTAT-TTC-TTTTTAAAGTTATGTAGCCTCATTCCAAGTGAGGAGCTTATT
* * *
28433796 CA-TTTCAAAGTTACGTAACCTCATTCTAGACAAAAAGCATATTCATTTTTCAAGTTACGTAACC
64 CATTTTCAAAGTTACGTAACCTCATTCCAAACAAAAAGCATATTCA-TTTTAAAGTTACGTAACC
* * *
28433860 TCATTCCAAATGAAGAGCTAATTCATTTCA-AAGTTACGTAATCTCA
128 TCATTACAAATGAAGAGCTAATTCATTT-ATAAGTTACATAACCTCA
* * * *
28433906 TTTTAGATGAGGAGCTATTTCTTCTTTAAAGTTATGTAACCTCATTCTAAATGAGGAGCTT
1 TTTTAGATGAAGAGCTATTTCTT-TTTAAAGTTATGTAGCCTCATTCCAAGTGAGGAGCTT
28433967 TTTCTTTGGA
Statistics
Matches: 190, Mismatches: 38, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
172 2 0.01
173 36 0.19
174 145 0.76
175 7 0.04
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (173 bp):
TTTTAGATGAAGAGCTATTTCTTTTTAAAGTTATGTAGCCTCATTCCAAGTGAGGAGCTTATTCA
TTTTCAAAGTTACGTAACCTCATTCCAAACAAAAAGCATATTCATTTTAAAGTTACGTAACCTCA
TTACAAATGAAGAGCTAATTCATTTATAAGTTACATAACCTCA
Found at i:28434362 original size:32 final size:31
Alignment explanation
Indices: 28434305--28434364 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
28434295 ATAATTGGCA
*
28434305 AAATAGAGAAAAAAAATTAGTGAGAGAACAC
1 AAATAGAGAAAAAAAATTAGGGAGAGAACAC
*
28434336 AAATTGAGAAAAAATGAA-TAGGGAGAGAA
1 AAATAGAGAAAAAA--AATTAGGGAGAGAA
28434365 AAGAATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.52
32 10 0.40
33 2 0.08
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.13
Consensus pattern (31 bp):
AAATAGAGAAAAAAAATTAGGGAGAGAACAC
Found at i:28438055 original size:28 final size:29
Alignment explanation
Indices: 28437997--28438060 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
28437987 GCAAATTTTT
* * *
28437997 AAAAATTACACTTTTGCCCCTATAAAGTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
* *
28438026 AAAAATTACATTTTTACCTC-AAAAACTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
28438054 AAAAATT
1 AAAAATT
28438061 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCTAAAAACTG
Found at i:28446892 original size:21 final size:21
Alignment explanation
Indices: 28446850--28446892 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28446840 CTTGTACCGG
*
28446850 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
28446871 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
28446892 T
1 T
28446893 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:28451517 original size:18 final size:19
Alignment explanation
Indices: 28451486--28451521 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28451476 ACTTTTGTAT
28451486 AAAAAAAAACAATTTTTAG
1 AAAAAAAAACAATTTTTAG
*
28451505 AAAATAAAA-AATTTTTA
1 AAAAAAAAACAATTTTTA
28451522 ATTAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAAAAAACAATTTTTAG
Found at i:28462466 original size:22 final size:22
Alignment explanation
Indices: 28462438--28462488 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
28462428 CAGAAGATTT
28462438 TAATTTTGATAAAAAAATATTA
1 TAATTTTGATAAAAAAATATTA
28462460 TAATTTTGATAAAAAAATATTA
1 TAATTTTGATAAAAAAATATTA
*
28462482 GAATTTT
1 TAATTTT
28462489 TTTTGGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
TAATTTTGATAAAAAAATATTA
Found at i:28465320 original size:20 final size:21
Alignment explanation
Indices: 28465292--28465330 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28465282 CTCTTATTTG
28465292 TTCCTTGCT-TC-TATATCTA
1 TTCCTTGCTGTCATATATCTA
28465311 TTCCTATGCTGTCATATATC
1 TTCCT-TGCTGTCATATATC
28465331 ATGTTGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 2 0.12
22 6 0.35
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.49
Consensus pattern (21 bp):
TTCCTTGCTGTCATATATCTA
Found at i:28471850 original size:3 final size:3
Alignment explanation
Indices: 28471842--28471870 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28471832 TTATGCTTAA
28471842 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28471871 AGGTAAAGGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28479818 original size:61 final size:60
Alignment explanation
Indices: 28479723--28479843 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
28479713 TAAAAAATCG
28479723 AAACATATGCAAATAGGGCTACTGTTCATTATGCACCTTTCTTCACCAATTAAAATTATT
1 AAACATATGCAAATAGGGCTACTGTTCATTATGCACCTTTCTTCACCAATTAAAATTATT
* * *
28479783 NAAACATATGCAAATTA-GGTTATTGTTCATTATGCACCTTTCTTCACCAATTTAAATTATT
1 -AAACATATGCAAA-TAGGGCTACTGTTCATTATGCACCTTTCTTCACCAATTAAAATTATT
28479844 TTGATCCTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 54 0.96
62 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (60 bp):
AAACATATGCAAATAGGGCTACTGTTCATTATGCACCTTTCTTCACCAATTAAAATTATT
Found at i:28488341 original size:96 final size:96
Alignment explanation
Indices: 28488169--28488352 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
28488159 ACACTATTGA
* ** **
28488169 CTACACTATTATCATACCCAGTAAAGCATGCAAGTACGTAAATTCCCAAAGGACGAAAATCAAGA
1 CTACACTATTATCATACCCAGTAAAGCATGCAAGAACGTAAAAACCCAAACAACGAAAATCAAGA
*
28488234 ATGAAGCAAAGAATGAAAACCAATAACCTAG
66 ATCAAGCAAAGAATGAAAACCAATAACCTAG
* * *
28488265 CTACACTATTATGATACCCAGTAAAGCATGCAGGAATGTAAAAACCCAAACAACGAAAAT-AGAG
1 CTACACTATTATCATACCCAGTAAAGCATGCAAGAACGTAAAAACCCAAACAACGAAAATCA-AG
* *
28488329 AATCAAGTAAAGAATGAACACCAA
65 AATCAAGCAAAGAATGAAAACCAA
28488353 CAATCCAGCA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 75 0.99
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (96 bp):
CTACACTATTATCATACCCAGTAAAGCATGCAAGAACGTAAAAACCCAAACAACGAAAATCAAGA
ATCAAGCAAAGAATGAAAACCAATAACCTAG
Found at i:28489908 original size:71 final size:71
Alignment explanation
Indices: 28489787--28489946 Score: 205
Period size: 71 Copynumber: 2.3 Consensus size: 71
28489777 ATGACATGGT
* * *
28489787 TTAAACATAGTATGTAACTTAATTTCTATCTTTGTGTTTCACTAGAACATAAACTCTCGGAGTTA
1 TTAAACATGGCATGTAACTTAATTTCTATCTTTGTATTTCACTAGAACATAAACTCTCGGAGTTA
*
28489852 AATACT
66 AATACC
* * * * * * *
28489858 TTAAATATGGCGTGTAACTTGATTTCTATTTTTGTATTTTATTA-AGACATAAACTCTTGGAGTT
1 TTAAACATGGCATGTAACTTAATTTCTATCTTTGTATTTCACTAGA-ACATAAACTCTCGGAGTT
28489922 AAATACC
65 AAATACC
28489929 TTAAACATGGCATGTAAC
1 TTAAACATGGCATGTAAC
28489947 AATTTTATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
70 1 0.01
71 74 0.99
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (71 bp):
TTAAACATGGCATGTAACTTAATTTCTATCTTTGTATTTCACTAGAACATAAACTCTCGGAGTTA
AATACC
Found at i:28490135 original size:21 final size:22
Alignment explanation
Indices: 28490100--28490141 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28490090 ATGATGTGTA
*
28490100 ATAACTTTTTTTTTCAACATGT
1 ATAACTTTTTCTTTCAACATGT
28490122 ATAAC-TTTTCTTTCAACATG
1 ATAACTTTTTCTTTCAACATG
28490142 GCTTGCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (22 bp):
ATAACTTTTTCTTTCAACATGT
Found at i:28490259 original size:27 final size:27
Alignment explanation
Indices: 28490207--28490259 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28490197 AAACACTTTA
*
28490207 AACATGACATTTAAGAACATTTTTTTG
1 AACATGACATTTAAGAACATTATTTTG
* *
28490234 AACATGAC-TTGTAATAATATTATTTT
1 AACATGACATT-TAAGAACATTATTTT
28490260 TTAAACATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (27 bp):
AACATGACATTTAAGAACATTATTTTG
Found at i:28490268 original size:29 final size:27
Alignment explanation
Indices: 28490203--28490276 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 27
28490193 AGTTAAACAC
28490203 TTTAAACATGACATT-TAAGAACATTTT
1 TTTAAACATGAC-TTGTAAGAACATTTT
* * *
28490230 TTTGAACATGACTTGTAATAATATTATTT
1 TTTAAACATGACTTGTAAGAACA-T-TTT
*
28490259 TTTAAACATGACGTGTAA
1 TTTAAACATGACTTGTAA
28490277 CTTGGTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 17 0.44
28 1 0.03
29 19 0.49
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTAAACATGACTTGTAAGAACATTTT
Found at i:28490310 original size:127 final size:121
Alignment explanation
Indices: 28490007--28490334 Score: 300
Period size: 120 Copynumber: 2.7 Consensus size: 121
28489997 GTAACAATGA
* * * * * * * * *
28490007 TATTTTTTAAATATAACATATAACTTGATATCTATCTTTGTATTTCATTAAAATATAAACTCTTA
1 TATTTTTTAAACATGACATGTAACTTGGTTTCAATCTTTGTATTTCAATAAAACATAAACTCTTG
* * ** * ** *
28490072 GAGTTAAATACCTTAAACATGATGTGTAATAACTTTTTTTTTCAACATGTATAACT
66 GAGTTAAACACTTTAAACATGACATGTAAGAACTTTTTTTAACAACATGTATAAAT
* * * * * * * * *
28490128 T-TTCTTTCAACATGGCTTGCAACTTGGTCTT-ATTCTTTATATTTCACTAAGACATAAACTCTT
1 TATTTTTTAAACATGACATGTAACTTGGT-TTCAATCTTTGTATTTCAATAAAACATAAACTCTT
* *
28490191 GGAGTTAAACACTTTAAACATGACATTTAAGAACATTTTTTTGAACATGACTTGTAATAATAT
65 GGAGTTAAACACTTTAAACATGACATGTAAGAAC-TTTTTTT-AACA--ACATGT-ATAA-AT
*
28490254 TATTTTTTAAACATGACGTGTAACTTGGTTTCAATCTTTGTATTTCAATAAAACATAAACTCTTG
1 TATTTTTTAAACATGACATGTAACTTGGTTTCAATCTTTGTATTTCAATAAAACATAAACTCTTG
* *
28490319 AAGTTAAACATTTTAA
66 GAGTTAAACACTTTAA
28490335 GTATGGCGTG
Statistics
Matches: 160, Mismatches: 38, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
120 71 0.44
121 9 0.06
122 2 0.01
124 5 0.03
125 4 0.03
126 4 0.03
127 65 0.41
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (121 bp):
TATTTTTTAAACATGACATGTAACTTGGTTTCAATCTTTGTATTTCAATAAAACATAAACTCTTG
GAGTTAAACACTTTAAACATGACATGTAAGAACTTTTTTTAACAACATGTATAAAT
Found at i:28491359 original size:2 final size:2
Alignment explanation
Indices: 28491352--28491387 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
28491342 CTTTGCATGA
28491352 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28491388 TAGGCATCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:28492728 original size:14 final size:15
Alignment explanation
Indices: 28492702--28492753 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 15
28492692 AATTACAAAT
28492702 TTAA-ATTTATAAAA
1 TTAATATTTATAAAA
28492716 TTAATATTT-T-AAA
1 TTAATATTTATAAAA
* *
28492729 TTAAAATTTAAAAATA
1 TTAATATTTATAAA-A
28492745 TTAATATTT
1 TTAATATTT
28492754 TTATATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.35
14 5 0.16
15 6 0.19
16 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATATTTATAAAA
Found at i:28492737 original size:28 final size:29
Alignment explanation
Indices: 28492698--28492754 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
28492688 TAAAAATTAC
* *
28492698 AAATTTAAATTTATAAA-ATTAATATTTT
1 AAATTAAAATTTAAAAATATTAATATTTT
28492726 AAATTAAAATTTAAAAATATTAATATTTT
1 AAATTAAAATTTAAAAATATTAATATTTT
28492755 TATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATTAAAATTTAAAAATATTAATATTTT
Found at i:28492775 original size:16 final size:16
Alignment explanation
Indices: 28492756--28492786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28492746 TAATATTTTT
*
28492756 ATATTTTAATTATAAC
1 ATATTTAAATTATAAC
28492772 ATATTTAAATTATAA
1 ATATTTAAATTATAA
28492787 ATAAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTTAAATTATAAC
Found at i:28492978 original size:51 final size:51
Alignment explanation
Indices: 28492917--28493019 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
28492907 ATTATATATT
*
28492917 ATAAAATATTTTGAATTTAAAAATT-AATTA-AAAGTATTAATATTTT-AATC
1 ATAAAATA-TTT-AAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
* * *
28492967 ATAATAATATTTAAATTATAAATTAAATTACCAATTATTAATATTTTCAATC
1 ATAA-AATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
28493019 A
1 A
28493020 ATTATAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 10 0.22
50 12 0.27
51 18 0.40
52 5 0.11
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (51 bp):
ATAAAATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
Found at i:28492987 original size:17 final size:17
Alignment explanation
Indices: 28492954--28492987 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28492944 TTAAAAGTAT
*
28492954 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
28492971 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
28492988 ATTAAATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:28493186 original size:23 final size:23
Alignment explanation
Indices: 28493129--28493202 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
28493119 TAAATTACAA
* * *
28493129 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
28493151 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
28493174 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
28493198 A-AAAT
1 ATAAAT
28493203 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:28493199 original size:22 final size:21
Alignment explanation
Indices: 28493127--28493203 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
28493117 ATTAAATTAC
*
28493127 AAATAAAATATTAATACTTAA
1 AAATAAAATATTAATATTTAA
* *
28493148 ATAATCAACTATTAATATTTAA
1 A-AATAAAATATTAATATTTAA
28493170 AAATATAAATTATTAATATTTAA
1 AAATA-AAA-TATTAATATTTAA
28493193 AAGATAAAATA
1 AA-ATAAAATA
28493204 AAATAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:28493316 original size:27 final size:27
Alignment explanation
Indices: 28493286--28493360 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
28493276 CTATCAATTT
* *
28493286 TTAATATTT-TAAATAAATTATACATTA
1 TTAATATTTAAAAATAAATAAT-CATTA
*
28493313 TTAATGTTTAAAAATAAATAATCATTA
1 TTAATATTTAAAAATAAATAATCATTA
* *
28493340 -TAACATTTAAATTATAAATAA
1 TTAATATTTAAA-AATAAATAA
28493361 AATATTAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 9 0.22
27 21 0.52
28 10 0.25
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (27 bp):
TTAATATTTAAAAATAAATAATCATTA
Found at i:28493996 original size:27 final size:27
Alignment explanation
Indices: 28493952--28494043 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
28493942 TTATCTATTT
28493952 TAATTT-T-ATTT-TTTAAAATATTAA
1 TAATTTATAATTTATTTAAAATATTAA
*
28493976 TAATTTATAATTTATTTAAAATATTGA
1 TAATTTATAATTTATTTAAAATATTAA
28494003 TAATTTATAATTTATTTAAAATATTAA
1 TAATTTATAATTTATTTAAAATATTAA
* *
28494030 TAATTGATGATTTA
1 TAATTTATAATTTA
28494044 AATATTAACA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
24 6 0.10
25 1 0.02
26 4 0.07
27 50 0.82
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
TAATTTATAATTTATTTAAAATATTAA
Found at i:28494310 original size:23 final size:20
Alignment explanation
Indices: 28494257--28494316 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 20
28494247 TTGATAATTT
*
28494257 AAATATTAATATTTTATTTA
1 AAATATTAATATTTTATGTA
28494277 AAAT-TTAAATATTATTATGAGTA
1 AAATATT-AATATT-TTAT--GTA
28494300 AAATATTAATAATTTTA
1 AAATATTAAT-ATTTTA
28494317 ATTAAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 10 0.30
21 4 0.12
23 12 0.36
24 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
AAATATTAATATTTTATGTA
Found at i:28494439 original size:7 final size:7
Alignment explanation
Indices: 28494429--28494478 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
28494419 TAAAATATCA
28494429 ATAATTT
1 ATAATTT
28494436 ATAATTT
1 ATAATTT
28494443 ATAATTT
1 ATAATTT
28494450 AT--TTT
1 ATAATTT
*
28494455 AAAATATTT
1 -ATA-ATTT
*
28494464 ATAATTG
1 ATAATTT
28494471 ATAATTT
1 ATAATTT
28494478 A
1 A
28494479 AATATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.09
6 1 0.03
7 26 0.74
8 2 0.06
9 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (7 bp):
ATAATTT
Found at i:28494440 original size:35 final size:34
Alignment explanation
Indices: 28494401--28494478 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
28494391 TTATCTATTA
*
28494401 ATAATTTAT-TTTATTTTTTAAAATATCAATAATTT
1 ATAATTTATATTTA--TTTTAAAATATCAATAATTG
**
28494436 ATAATTTATAATTTATTTTAAAATATTTATAATTG
1 ATAATTTAT-ATTTATTTTAAAATATCAATAATTG
28494471 ATAATTTA
1 ATAATTTA
28494479 AATATTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 34 0.89
37 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
ATAATTTATATTTATTTTAAAATATCAATAATTG
Found at i:28494488 original size:28 final size:28
Alignment explanation
Indices: 28494421--28494491 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
28494411 TTATTTTTTA
* *
28494421 AAATATCAATAATTTATAATTTATAATTT
1 AAATATTAAT-ATTTATAATTGATAATTT
*
28494450 --ATTTTAAAATATTTATAATTGATAATTT
1 AAATATT--AATATTTATAATTGATAATTT
28494478 AAATATTAATATTT
1 AAATATTAATATTT
28494492 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
27 3 0.09
28 24 0.71
29 3 0.09
30 4 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
AAATATTAATATTTATAATTGATAATTT
Found at i:28494499 original size:214 final size:210
Alignment explanation
Indices: 28493970--28494499 Score: 650
Period size: 213 Copynumber: 2.5 Consensus size: 210
28493960 TTTTTTAAAA
* *
28493970 TATTAATAATTTATAATTTA--TTTAAAATATT--GATAATTTATAATTTA-TTTAAAATATTAA
1 TATTAATAATTTAT--TTTATTTTTTAAATATTAATATAATTTATAATTTATTTTAAAATATTAA
* *
28494030 TAATTGATGATTTAAATATTAACATTTTATTTATAATTTAAATATTATTATGATTAAAATATTAA
64 TAATTGATAATTTAAATATT-A-A---TATTT-TAATTTAAATATTATTATGAGTAAAATATTAA
* * *
28494095 TAATTTTAATTAATTTTTAAATTTAAAATATTAATTTTTTGTAATTTATAATTGAAACTTAAAAT
123 TAATTTTAATTAATTTTTAAATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAAT
* *
28494160 ATTTATTATAGTGTATAATTATC
188 ATTTATTATAATATATAATTATC
** * *
28494183 TATTTTTATTTTATTTTATTTTTTAAATATTAATA-ACA--TATAATCTATTTTAAAATATTAAT
1 TATTAATAATTTATTTTATTTTTTAAATATTAATATA-ATTTATAATTTATTTTAAAATATTAAT
28494245 AATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAATATTATTATGAGTAAAATATTAAT
65 AATTGATAATTTAAATATTAATA---T-TTT--AATTTAAATATTATTATGAGTAAAATATTAAT
28494310 AATTTTAATTAAATTTTT-AATTTAAAATATT-ATTTTTTATAATATATAATTGAAACTAAAAAT
124 AATTTTAATT-AATTTTTAAATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAAT
*
28494373 ATTTATTATAATATATGATTATC
188 ATTTATTATAATATATAATTATC
28494396 TATTAATAATTTATTTTATTTTTTAAAATATCAATAATTTATAATTTATAATTTATTTTAAAATA
1 TATTAATAATTTATTTTATTTTTT-AAATAT---TAA--TATAATTTATAATTTATTTTAAAATA
*
28494461 TTTATAATTGATAATTTAAATATTAATATTTT-ATTTAAA
60 TTAATAATTGATAATTTAAATATTAATATTTTAATTTAAA
28494500 ATTTAATCAT
Statistics
Matches: 276, Mismatches: 19, Indels: 43
0.82 0.06 0.13
Matches are distributed among these distances:
209 2 0.01
211 4 0.01
212 3 0.01
213 102 0.37
214 100 0.36
215 9 0.03
217 6 0.02
218 1 0.00
219 3 0.01
220 1 0.00
221 45 0.16
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (210 bp):
TATTAATAATTTATTTTATTTTTTAAATATTAATATAATTTATAATTTATTTTAAAATATTAATA
ATTGATAATTTAAATATTAATATTTTAATTTAAATATTATTATGAGTAAAATATTAATAATTTTA
ATTAATTTTTAAATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAATATTTATTA
TAATATATAATTATC
Found at i:28494525 original size:221 final size:216
Alignment explanation
Indices: 28493970--28494548 Score: 770
Period size: 214 Copynumber: 2.7 Consensus size: 216
28493960 TTTTTTAAAA
* *
28493970 TATTAATAATTTATAATTTA--TTTAAAATATT--GATAATTTATAATTTA-TTTAAAATATTAA
1 TATTAATAATTTAT--TTTATTTTTTAAATATTAATATAATTTATAATTTATTTTAAAATATTAA
* * *
28494030 TAATTGATGATTTAAATATTAACATTTTATTTATAATTTAAATATTATTATGATTAAAATATTAA
64 TAATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAATATTATTATGATTAAAATATTAA
* * *
28494095 TAATTTTAATT-AATTTTTAAATTTAAAATATTAATTTTTTGTAATTTATAATTGAAACTTAAAA
129 TAATTTTAATTAAATTTTT-AATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAA
* *
28494159 TATTTATTATAGTGTATAATTATC
193 TATTTATTATAATATATAATTATC
** * *
28494183 TATTTTTATTTTATTTTATTTTTTAAATATTAATA-ACA--TATAATCTATTTTAAAATATTAAT
1 TATTAATAATTTATTTTATTTTTTAAATATTAATATA-ATTTATAATTTATTTTAAAATATTAAT
*
28494245 AATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAATATTATTATGAGTAAAATATTAAT
65 AATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAATATTATTATGATTAAAATATTAAT
28494310 AATTTTAATTAAATTTTTAATTTAAAATATT-ATTTTTTATAATATATAATTGAAACTAAAAATA
130 AATTTTAATTAAATTTTTAATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAATA
*
28494374 TTTATTATAATATATGATTATC
195 TTTATTATAATATATAATTATC
28494396 TATTAATAATTTATTTTATTTTTTAAAATATCAATAATTTATAATTTATAATTTATTTTAAAATA
1 TATTAATAATTTATTTTATTTTTT-AAATAT---TAA--TATAATTTATAATTTATTTTAAAATA
* ** **
28494461 TTTATAATTGATAATTTAAATATTAATATTTTATTTAAAATTT-AATCATTAACATTTTTAAAAT
60 TTAATAATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAAT-ATTATTATGATTAAAAT
*
28494525 ATTAAT-ATTTT-ATTAATTTTTTAA
124 ATTAATAATTTTAATTAAATTTTTAA
28494549 ATATTATTAT
Statistics
Matches: 322, Mismatches: 27, Indels: 28
0.85 0.07 0.07
Matches are distributed among these distances:
211 4 0.01
213 99 0.31
214 105 0.33
215 9 0.03
217 3 0.01
219 15 0.05
220 9 0.03
221 78 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (216 bp):
TATTAATAATTTATTTTATTTTTTAAATATTAATATAATTTATAATTTATTTTAAAATATTAATA
ATTGATAATTTAAATATTAATATTTTATTTAAAATTTAAATATTATTATGATTAAAATATTAATA
ATTTTAATTAAATTTTTAATTTAAAATATTAATTTTTTATAATATATAATTGAAACTAAAAATAT
TTATTATAATATATAATTATC
Found at i:28494614 original size:45 final size:43
Alignment explanation
Indices: 28494478--28494619 Score: 137
Period size: 43 Copynumber: 3.2 Consensus size: 43
28494468 TTGATAATTT
** **
28494478 AAATATTAATATTTTATTTAAAATTT--AATCATTAACATTTTTA
1 AAATATTAATATTTTA-TTAATTTTTAAAAT-ATTATTATTTTTA
* **
28494521 AAATATTAATATTTTATTAATTTTTTAAATATTATTATGATTA
1 AAATATTAATATTTTATTAATTTTTAAAATATTATTATTTTTA
28494564 AAATATTAATAATTTTAATTAATTTTTAAAATATTAGTT-TTTTTA
1 AAATATTAAT-ATTTT-ATTAATTTTTAAAATATTA-TTATTTTTA
*
28494609 TAATATATAAT
1 AAATAT-TAAT
28494620 TAAAGTCTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
42 7 0.08
43 35 0.42
44 8 0.10
45 27 0.33
46 6 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (43 bp):
AAATATTAATATTTTATTAATTTTTAAAATATTATTATTTTTA
Done.