Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 91 of 182
Found at i:29230186 original size:25 final size:23
Alignment explanation
Indices: 29230152--29230199 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
29230142 TAGTGTACTA
*
29230152 ATTTTTATTTTCATTATTTTTTGTT
1 ATTTTTATTTT-ATT-TTTCTTGTT
29230177 ATTTTTATTTTATTTTTCTTGTT
1 ATTTTTATTTTATTTTTCTTGTT
29230200 GACCGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 11 0.50
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (23 bp):
ATTTTTATTTTATTTTTCTTGTT
Found at i:29230953 original size:12 final size:12
Alignment explanation
Indices: 29230935--29230972 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
29230925 TTGAATCAGT
29230935 AGTAGATGTAGC
1 AGTAGATGTAGC
*
29230947 GGTAGATGTA--
1 AGTAGATGTAGC
29230957 AGTAGATGTAGC
1 AGTAGATGTAGC
29230969 AGTA
1 AGTA
29230973 TAATTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.26
Consensus pattern (12 bp):
AGTAGATGTAGC
Found at i:29247964 original size:21 final size:21
Alignment explanation
Indices: 29247939--29247982 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29247929 CAACCTCTCT
* *
29247939 CCGATACAAGTGACAGTTCTA
1 CCGATACAAATGACACTTCTA
*
29247960 CCGATACAAATGACTCTTCTA
1 CCGATACAAATGACACTTCTA
29247981 CC
1 CC
29247983 AAAATAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (21 bp):
CCGATACAAATGACACTTCTA
Found at i:29248095 original size:191 final size:191
Alignment explanation
Indices: 29247765--29248131 Score: 644
Period size: 191 Copynumber: 1.9 Consensus size: 191
29247755 AGTGTAAACC
* * * *
29247765 TCTACGGATACAAGTGACTCTTCTACCGAAACAAATCTTATTTTTACCGATCCTAAAAACTCCAA
1 TCTACCGATACAAATGACTCTTCTACCAAAACAAATCTTATTTTTACCGATACTAAAAACTCCAA
*
29247830 AGAGCTAAAAATCTCACCCCTGTAACTTCTACCTATACAAGTATACAAACTATCGATACTTCTAA
66 AGAGCTAAAAATCTCACCCCTGTAACTTCTACCTAGACAAGTATACAAACTATCGATACTTCTAA
*
29247895 ACACATAACTACCAATACAACCCAAGTTAGTGAGCAACCTCTCTCCGATACAAGTGACAGT
131 ACACATAACTACCAATACAACCCAAGTCAGTGAGCAACCTCTCTCCGATACAAGTGACAGT
* *
29247956 TCTACCGATACAAATGACTCTTCTACCAAAATAAATCTTATTTTTACTGATACTAAAAACTCCAA
1 TCTACCGATACAAATGACTCTTCTACCAAAACAAATCTTATTTTTACCGATACTAAAAACTCCAA
29248021 AGAGCTAAAAATCTCACCCCTGTAACTTCTACCTAGACAAGTATACAAACTATCGATACTTCTAA
66 AGAGCTAAAAATCTCACCCCTGTAACTTCTACCTAGACAAGTATACAAACTATCGATACTTCTAA
**
29248086 ACACATAACTACTGATACAACCCAAGTCAGTGAGCAACCTCTCTCC
131 ACACATAACTACCAATACAACCCAAGTCAGTGAGCAACCTCTCTCC
29248132 TACCTTGTAC
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
191 166 1.00
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.26
Consensus pattern (191 bp):
TCTACCGATACAAATGACTCTTCTACCAAAACAAATCTTATTTTTACCGATACTAAAAACTCCAA
AGAGCTAAAAATCTCACCCCTGTAACTTCTACCTAGACAAGTATACAAACTATCGATACTTCTAA
ACACATAACTACCAATACAACCCAAGTCAGTGAGCAACCTCTCTCCGATACAAGTGACAGT
Found at i:29248784 original size:53 final size:52
Alignment explanation
Indices: 29248654--29248953 Score: 284
Period size: 53 Copynumber: 5.7 Consensus size: 52
29248644 TTCGCATTTG
* * * * * *
29248654 ATAAATCACAATGAAACAGAATCATCGAACCTTTAATCCATGAT-GGATTCGT
1 ATAACTCACAATGACACA-AGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * * * * * *
29248706 GTATCTCACGATGACATAAATTCATCGGACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCACAATGACA-CAAGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * *
29248759 ATAACTCACAGTGGCACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT
1 ATAACTCACAATGACACA-AGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * * **
29248812 ATAACTCATGAA-GAAACAGAGTCATCGGACTTTTAATCTGTAATAGGATTCAT
1 ATAACTCA-CAATGACACA-AGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * * *
29248865 ATAACTCACAATGACACAAGATTCATCAGACC-ATAATCCATGATAAGATTCAT
1 ATAACTCACAATGACACAAG--TCATCGGACCTTTAATCCATAATAGGATTCAT
29248918 ATAACTCACAATGACAC-AGTCATCGGACCTTTAATC
1 ATAACTCACAATGACACAAGTCATCGGACCTTTAATC
29248954 TTTGGCACAA
Statistics
Matches: 198, Mismatches: 42, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
50 9 0.05
51 5 0.03
52 38 0.19
53 137 0.69
54 9 0.05
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (52 bp):
ATAACTCACAATGACACAAGTCATCGGACCTTTAATCCATAATAGGATTCAT
Found at i:29248856 original size:106 final size:104
Alignment explanation
Indices: 29248654--29248954 Score: 315
Period size: 106 Copynumber: 2.9 Consensus size: 104
29248644 TTCGCATTTG
* * * * * *
29248654 ATAAATCACAATGAAAC-AGAATCATCGAACCTTTAATCCATGAT-GGATTCGTGTATCTCACGA
1 ATAACTCACAATGACACAAG-ATCATCGGACCTTTAATCCATGATAGGATTCATATAACTCA-GA
* * * * *
29248717 TGACATAAATTCATCGGACCCTTAATCCGTAATAGGATTCAT
64 AGA-ACAAAGTCATCGGACCTTTAATCTGTAATAGGATTCAT
* *
29248759 ATAACTCACAGTGGCACATAG-TCATCGGACCTTTAATCCATGATAGGATTCATATAACTCATGA
1 ATAACTCACAATGACACA-AGATCATCGGACCTTTAATCCATGATAGGATTCATATAACTCA-GA
* *
29248823 AGAAACAGAGTCATCGGACTTTTAATCTGTAATAGGATTCAT
64 AG-AACAAAGTCATCGGACCTTTAATCTGTAATAGGATTCAT
* * * *
29248865 ATAACTCACAATGACACAAGATTCATCAGACC-ATAATCCATGATAAGATTCATATAACTCACAA
1 ATAACTCACAATGACACAAGA-TCATCGGACCTTTAATCCATGATAGGATTCATATAACTCAGAA
*
29248929 TG-ACACAGTCATCGGACCTTTAATCT
65 -GAACAAAGTCATCGGACCTTTAATCT
29248955 TTGGCACAAG
Statistics
Matches: 165, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
104 22 0.13
105 39 0.24
106 92 0.56
107 12 0.07
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (104 bp):
ATAACTCACAATGACACAAGATCATCGGACCTTTAATCCATGATAGGATTCATATAACTCAGAAG
AACAAAGTCATCGGACCTTTAATCTGTAATAGGATTCAT
Found at i:29255866 original size:18 final size:18
Alignment explanation
Indices: 29255845--29255879 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29255835 ACACCTTCGG
29255845 TAAGGCC-TCTACCTCCTA
1 TAAGGCCTTC-ACCTCCTA
29255863 TAAGGCCTTCACCTCCT
1 TAAGGCCTTCACCTCCT
29255880 CCTATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.20, C:0.40, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAGGCCTTCACCTCCTA
Found at i:29258801 original size:24 final size:24
Alignment explanation
Indices: 29258762--29258868 Score: 146
Period size: 24 Copynumber: 4.5 Consensus size: 24
29258752 CTGGTTGACT
*
29258762 ATTCTAGGCTCATAAGAGCTAACC
1 ATTCTAGGCTCGTAAGAGCTAACC
29258786 ATTCT-GGACTCGTAAGAGCTAACC
1 ATTCTAGG-CTCGTAAGAGCTAACC
*
29258810 ATTCTAGGCGCGTAAGAGCTAACC
1 ATTCTAGGCTCGTAAGAGCTAACC
*
29258834 ATTCTAGG-TGCGTAAGAGTTAACC
1 ATTCTAGGCT-CGTAAGAGCTAACC
*
29258858 ATCCTAGGCTC
1 ATTCTAGGCTC
29258869 TTGAAAGCTA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.03
24 69 0.93
25 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (24 bp):
ATTCTAGGCTCGTAAGAGCTAACC
Found at i:29261629 original size:50 final size:50
Alignment explanation
Indices: 29261537--29261652 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 50
29261527 TAAGGAGGAA
* *
29261537 GTATCTGGCAGTAAATCTTCAAATATTTAGTGGCATGTCCACA-TATTTCT
1 GTATCTGGCAGTAAATCTTCAAATATTTAGTAGCATGTCCACACTA-ATCT
* * *
29261587 GTATCTGGCAGTAAAT-TTGCAAATATTTGGTAG-TTTTACCACACTAATCT
1 GTATCTGGCAGTAAATCTT-CAAATATTTAGTAGCATGT-CCACACTAATCT
* *
29261637 ATTTCTGGCAGTAAAT
1 GTATCTGGCAGTAAAT
29261653 ATACAATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.07
50 50 0.89
51 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (50 bp):
GTATCTGGCAGTAAATCTTCAAATATTTAGTAGCATGTCCACACTAATCT
Found at i:29275391 original size:41 final size:40
Alignment explanation
Indices: 29275343--29275443 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
29275333 TCGACCTTGA
** *
29275343 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
29275383 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
29275421 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
29275444 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:29293423 original size:23 final size:22
Alignment explanation
Indices: 29293397--29293440 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29293387 AAAATATTTC
*
29293397 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
29293420 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
29293441 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:29295602 original size:23 final size:25
Alignment explanation
Indices: 29295576--29295621 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29295566 CCAATTAGGG
29295576 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
29295599 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
29295622 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:29299218 original size:19 final size:17
Alignment explanation
Indices: 29299194--29299232 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
29299184 CTTTTTCTTT
*
29299194 TTCTCTTGCTTCTTCTCTC
1 TTCTCTT-CTTCCTC-CTC
29299213 TTCTCTTCTTCCTCCTC
1 TTCTCTTCTTCCTCCTC
29299230 TTC
1 TTC
29299233 CTGAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (17 bp):
TTCTCTTCTTCCTCCTC
Found at i:29303723 original size:13 final size:14
Alignment explanation
Indices: 29303679--29303739 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
29303669 ACTTCAACCA
**
29303679 TTTTTTATTTTTGT
1 TTTTTTATTTTAAT
* **
29303693 TTTATTATTTGCAT
1 TTTTTTATTTTAAT
29303707 TTTTTTA-TTTAAT
1 TTTTTTATTTTAAT
*
29303720 TTTTATATTTTAAT
1 TTTTTTATTTTAAT
29303734 TTTTTT
1 TTTTTT
29303740 CCCTTTTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTATTTTAAT
Found at i:29303723 original size:28 final size:27
Alignment explanation
Indices: 29303679--29303739 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
29303669 ACTTCAACCA
* *
29303679 TTTTTTATTTTTGTTTTATTATTTGCAT
1 TTTTTTATTTATGTTTTA-TATTTGAAT
*
29303707 TTTTTTATTTAAT-TTTTATATTTTAAT
1 TTTTTTATTT-ATGTTTTATATTTGAAT
29303734 TTTTTT
1 TTTTTT
29303740 CCCTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 13 0.45
28 15 0.52
29 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTTTATTTATGTTTTATATTTGAAT
Found at i:29306617 original size:6 final size:6
Alignment explanation
Indices: 29306606--29306720 Score: 76
Period size: 6 Copynumber: 18.8 Consensus size: 6
29306596 TAGTACATTT
* *
29306606 ATTTTC ATTTTC ATTTTC ATTTT- ATTTTTC ATTCT- ATTTTCC ATTTCCC
1 ATTTTC ATTTTC ATTTTC ATTTTC A-TTTTC ATTTTC ATTTT-C ATTT-TC
* * * *
29306655 ATTTTCC ATTTTCC ATTTTT ATTTTT ATTTTT ATTTTT AGTTTT- ATTTT-
1 ATTTT-C ATTTT-C ATTTTC ATTTTC ATTTTC ATTTTC A-TTTTC ATTTTC
* *
29306704 ATTTTT ATTTTT ATTTT
1 ATTTTC ATTTTC ATTTT
29306721 ATTATGCACT
Statistics
Matches: 96, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
5 14 0.15
6 55 0.57
7 27 0.28
ACGTcount: A:0.17, C:0.12, G:0.01, T:0.70
Consensus pattern (6 bp):
ATTTTC
Found at i:29306656 original size:7 final size:7
Alignment explanation
Indices: 29306606--29306673 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
29306596 TAGTACATTT
29306606 ATTTT-C
1 ATTTTCC
29306612 ATTTT-C
1 ATTTTCC
29306618 ATTTT-C
1 ATTTTCC
29306624 ATTTT--
1 ATTTTCC
*
29306629 ATTTTTC
1 ATTTTCC
*
29306636 A--TTCT
1 ATTTTCC
29306641 ATTTTCC
1 ATTTTCC
*
29306648 ATTTCCC
1 ATTTTCC
29306655 ATTTTCC
1 ATTTTCC
29306662 ATTTTCC
1 ATTTTCC
29306669 ATTTT
1 ATTTT
29306674 TATTTTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
5 8 0.15
6 17 0.32
7 28 0.53
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (7 bp):
ATTTTCC
Found at i:29306703 original size:17 final size:17
Alignment explanation
Indices: 29306669--29306723 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
29306659 TCCATTTTCC
29306669 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTA-TTTT
*
29306687 ATTTTTAGTTTTATTTT
1 ATTTTTATTTTTATTTT
29306704 ATTTTTATTTTTATTTT
1 ATTTTTATTTTTATTTT
29306721 ATT
1 ATT
29306724 ATGCACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 23 0.66
18 12 0.34
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (17 bp):
ATTTTTATTTTTATTTT
Found at i:29306739 original size:6 final size:6
Alignment explanation
Indices: 29306669--29306720 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
29306659 TCCATTTTCC
*
29306669 ATTTTT ATTTTT ATTTTT ATTTTT AGTTTT A-TTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
29306716 ATTTT
1 ATTTT
29306721 ATTATGCACT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:29310928 original size:31 final size:32
Alignment explanation
Indices: 29310890--29310949 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
29310880 TTTTCTTTAG
* *
29310890 TCAAATTTGACCCTCAACCTCTT-AAAAAGAA
1 TCAAATTTAACCATCAACCTCTTGAAAAAGAA
*
29310921 TCAAATTTAACCATCAACCTTTTGAAAAA
1 TCAAATTTAACCATCAACCTCTTGAAAAA
29310950 AAGTCGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.28
Consensus pattern (32 bp):
TCAAATTTAACCATCAACCTCTTGAAAAAGAA
Found at i:29314245 original size:16 final size:15
Alignment explanation
Indices: 29314214--29314242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29314204 ATAATATTAT
29314214 AAAAAAATTAATTTC
1 AAAAAAATTAATTTC
29314229 AAAAAAATTAATTT
1 AAAAAAATTAATTT
29314243 TCATAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAATTAATTTC
Found at i:29321693 original size:10 final size:11
Alignment explanation
Indices: 29321678--29321710 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29321668 TTTTAAAATA
29321678 TAAAA-TATTT
1 TAAAATTATTT
*
29321688 TAAAATTAATT
1 TAAAATTATTT
29321699 TAAAATTATTT
1 TAAAATTATTT
29321710 T
1 T
29321711 TTAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:29321724 original size:19 final size:19
Alignment explanation
Indices: 29321660--29321727 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
29321650 CAAAAAAAAT
29321660 AATTATTTTTTTAAAATATAA
1 AATTA-TTTTTT-AAATATAA
*
29321681 AA-TATTTTAAAATT-AATTTAA
1 AATTATTTT----TTAAATATAA
29321702 AATTATTTTTTAAATATAA
1 AATTATTTTTTAAATATAA
29321721 AATTATT
1 AATTATT
29321728 AGAATCATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
18 2 0.05
19 17 0.44
20 2 0.05
21 10 0.26
22 6 0.15
23 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTATTTTTTAAATATAA
Found at i:29338271 original size:6 final size:6
Alignment explanation
Indices: 29338260--29338302 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
29338250 ATTGTGAATG
29338260 AGAAAA AG-AAA AGAAAAA GAGAAAA AGAGAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AG-AAAA -AGAAAA AGA-AAA AGAAAA AGAAA
29338303 TATTGCTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.15
6 13 0.39
7 13 0.39
8 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:29338284 original size:13 final size:13
Alignment explanation
Indices: 29338262--29338302 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29338252 TGTGAATGAG
29338262 AAAAAG-AAAAGA
1 AAAAAGAAAAAGA
29338274 AAAAGAGAAAAAGA
1 AAAA-AGAAAAAGA
*
29338288 GAAAAGAAAAAGA
1 AAAAAGAAAAAGA
29338301 AA
1 AA
29338303 TATTGCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 12 0.48
14 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:29338290 original size:21 final size:20
Alignment explanation
Indices: 29338262--29338300 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29338252 TGTGAATGAG
29338262 AAAAAGAAAAGAAAAAGAGA
1 AAAAAGAAAAGAAAAAGAGA
29338282 AAAAGAGAAAAGAAAAAGA
1 AAAA-AGAAAAGAAAAAGA
29338301 AATATTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAAGAGA
Found at i:29340155 original size:21 final size:22
Alignment explanation
Indices: 29340130--29340177 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
29340120 CCAAAAAGAG
*
29340130 AGAAATAGAAAAA-AATTAAAA
1 AGAAATAGAAAAATAAGTAAAA
*
29340151 AGAAA-AGAAAAATAAGTATAA
1 AGAAATAGAAAAATAAGTAAAA
29340172 AGAAAT
1 AGAAAT
29340178 GACTCATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (22 bp):
AGAAATAGAAAAATAAGTAAAA
Found at i:29347997 original size:20 final size:20
Alignment explanation
Indices: 29347972--29348073 Score: 102
Period size: 20 Copynumber: 5.1 Consensus size: 20
29347962 GTTGGTAAAA
29347972 AAAGTCAACGGTCAATGGTC
1 AAAGTCAACGGTCAATGGTC
*
29347992 AAAGTCAACGATCAATGGTC
1 AAAGTCAACGGTCAATGGTC
*
29348012 AAAGTCAACAGTCAA-GGTC
1 AAAGTCAACGGTCAATGGTC
* * *
29348031 AACAATCAGCTGGTCAA-AGTC
1 AA-AGTCAAC-GGTCAATGGTC
*
29348052 AAAGGTCAA-GCTCAATGGTC
1 AAA-GTCAACGGTCAATGGTC
29348072 AA
1 AA
29348074 TGTGTCGGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 11 0.16
20 43 0.64
21 13 0.19
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAGTCAACGGTCAATGGTC
Found at i:29348019 original size:13 final size:14
Alignment explanation
Indices: 29347975--29348073 Score: 57
Period size: 13 Copynumber: 7.4 Consensus size: 14
29347965 GGTAAAAAAA
*
29347975 GTCAACGGTCAATG
1 GTCAACAGTCAATG
*
29347989 GTCAA-AGTCAACG
1 GTCAACAGTCAATG
* ** *
29348002 ATCAATGGTCAA-A
1 GTCAACAGTCAATG
29348015 GTCAACAGTCAA-G
1 GTCAACAGTCAATG
* *
29348028 GTCAACAATCAGCTG
1 GTCAACAGTCA-ATG
*
29348043 GTCAA-AGTCAAAG
1 GTCAACAGTCAATG
29348056 GTC-A-AGCTCAATG
1 GTCAACAG-TCAATG
29348069 GTCAA
1 GTCAA
29348074 TGTGTCGGTA
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
12 3 0.05
13 41 0.63
14 15 0.23
15 6 0.09
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (14 bp):
GTCAACAGTCAATG
Found at i:29348045 original size:34 final size:33
Alignment explanation
Indices: 29347982--29348066 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
29347972 AAAGTCAACG
* * *
29347982 GTCAATGGTCAAAGTCAACGATCAATGGTCAAA
1 GTCAAAGGTCAAGGTCAACAATCAATGGTCAAA
*
29348015 GTCAACA-GTCAAGGTCAACAATCAGCTGGTCAAA
1 GTCAA-AGGTCAAGGTCAACAATCA-ATGGTCAAA
*
29348049 GTCAAAGGTCAAGCTCAA
1 GTCAAAGGTCAAGGTCAA
29348067 TGGTCAATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 21 0.48
34 23 0.52
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (33 bp):
GTCAAAGGTCAAGGTCAACAATCAATGGTCAAA
Found at i:29349756 original size:8 final size:8
Alignment explanation
Indices: 29349717--29349755 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
29349707 GCTGACGTGG
29349717 TAAAAAAA
1 TAAAAAAA
29349725 TAAAAAAA
1 TAAAAAAA
*
29349733 TAAATAAA
1 TAAAAAAA
* *
29349741 TATAAAAC
1 TAAAAAAA
29349749 TAAAAAA
1 TAAAAAA
29349756 CCCTAAATCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:29350975 original size:33 final size:34
Alignment explanation
Indices: 29350938--29351060 Score: 101
Period size: 33 Copynumber: 3.7 Consensus size: 34
29350928 TATGAAGTTA
*
29350938 TAGAAGTTGATGGGGAGGGTGATGAT-GAAGGGG
1 TAGAAGCTGATGGGGAGGGTGATGATAGAAGGGG
* * * * * *
29350971 TAGAATCTGATGGTGAAGGTGAT-CTGGAAAGGG
1 TAGAAGCTGATGGGGAGGGTGATGATAGAAGGGG
* * *
29351004 TAGAAGCT-ATTGAGGAAGGTGATG-TAGGAGGGG
1 TAGAAGCTGA-TGGGGAGGGTGATGATAGAAGGGG
**
29351037 TAGAAGCTGATTTGGAGGGTGATG
1 TAGAAGCTGATGGGGAGGGTGATG
29351061 TAAGAGGGTT
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
32 2 0.03
33 68 0.96
34 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.45, T:0.24
Consensus pattern (34 bp):
TAGAAGCTGATGGGGAGGGTGATGATAGAAGGGG
Found at i:29351061 original size:33 final size:33
Alignment explanation
Indices: 29351001--29351068 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
29350991 GATCTGGAAA
*
29351001 GGGTAGAAGCTATTGAGGAAGGTGATGTAGGAG
1 GGGTAGAAGCTATTGAGGAAGGTGATGTAAGAG
* *
29351034 GGGTAGAAGCTGATT-TGGAGGGTGATGTAAGAG
1 GGGTAGAAGCT-ATTGAGGAAGGTGATGTAAGAG
29351067 GG
1 GG
29351069 TTTACTGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.47, T:0.22
Consensus pattern (33 bp):
GGGTAGAAGCTATTGAGGAAGGTGATGTAAGAG
Found at i:29351179 original size:51 final size:51
Alignment explanation
Indices: 29351107--29351215 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 51
29351097 AAGTTGCTGT
* * * * *
29351107 TAATAAATATGCTGCTGATTTTGCATCATTAGAT-GAAGGGGATAATGTTGC
1 TAATGAATATGATGCTAATTTTGCAACATCAGATAG-AGGGGATAATGTTGC
* *
29351158 TAATGAATATGATGCTAATTTTGCAACCTCAGATAGAGTGGATAATGTTGC
1 TAATGAATATGATGCTAATTTTGCAACATCAGATAGAGGGGATAATGTTGC
*
29351209 TGATGAA
1 TAATGAA
29351216 GTTGCTGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 48 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (51 bp):
TAATGAATATGATGCTAATTTTGCAACATCAGATAGAGGGGATAATGTTGC
Found at i:29353217 original size:17 final size:17
Alignment explanation
Indices: 29353195--29353227 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29353185 AAGTGGTCTT
29353195 GTACAAATTTGAAACAG
1 GTACAAATTTGAAACAG
29353212 GTACAAATTTGAAACA
1 GTACAAATTTGAAACA
29353228 AGTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (17 bp):
GTACAAATTTGAAACAG
Found at i:29356672 original size:32 final size:31
Alignment explanation
Indices: 29356572--29356677 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 31
29356562 CGTAAAAGAG
* * *
29356572 GATTCGTAGATATGACAGACATCATACATGT
1 GATTCATAGATATGGCAGACATCATACATGA
* * * * * *
29356603 GAATTTATAGATAAGGAAGATATCACACATGTG
1 G-ATTCATAGATATGGCAGACATCATACATG-A
*
29356636 GATTCATAGATATGGCAGACATCATGCATGCA
1 GATTCATAGATATGGCAGACATCATACATG-A
*
29356668 GATTCGTAGA
1 GATTCATAGA
29356678 AGAGGATTCA
Statistics
Matches: 56, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
31 1 0.02
32 54 0.96
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (31 bp):
GATTCATAGATATGGCAGACATCATACATGA
Found at i:29366073 original size:22 final size:22
Alignment explanation
Indices: 29366020--29366067 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
29366010 TAGGGGTTGA
*
29366020 TGTCGCGACACACCAGGTCTTG
1 TGTCGCGACACACCAGGTCCTG
*
29366042 TGTCGCGACACATCAGGTCCTG
1 TGTCGCGACACACCAGGTCCTG
29366064 TGTC
1 TGTC
29366068 CTGACATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (22 bp):
TGTCGCGACACACCAGGTCCTG
Found at i:29372689 original size:20 final size:21
Alignment explanation
Indices: 29372651--29372688 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
29372641 AATATATATA
29372651 TTTTTCTTTTCTTCTTTTTCC
1 TTTTTCTTTTCTTCTTTTTCC
29372672 TTTTT-TTTTC-TCTTTTT
1 TTTTTCTTTTCTTCTTTTT
29372689 TTATATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTTTTCTTCTTTTTCC
Found at i:29373276 original size:17 final size:17
Alignment explanation
Indices: 29373246--29373303 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
29373236 TAATTTACAG
*
29373246 TGACAAATGTAAATGCAA
1 TGAC-AATGAAAATGCAA
*
29373264 TGACAATGAAAATGCAG
1 TGACAATGAAAATGCAA
* *
29373281 TGATAATTAAAATGCAA
1 TGACAATGAAAATGCAA
29373298 TGACAA
1 TGACAA
29373304 AGGGGATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.22
Consensus pattern (17 bp):
TGACAATGAAAATGCAA
Found at i:29384756 original size:16 final size:16
Alignment explanation
Indices: 29384735--29384765 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29384725 TTGTGGATCC
29384735 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
29384751 CATTTTATCTTTATT
1 CATTTTACCTTTATT
29384766 TTCACATAAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:29391437 original size:14 final size:15
Alignment explanation
Indices: 29391413--29391443 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29391403 GAGTTGTTTG
29391413 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
29391428 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
29391442 AA
1 AA
29391444 TAAAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:29393132 original size:289 final size:289
Alignment explanation
Indices: 29392613--29393337 Score: 883
Period size: 289 Copynumber: 2.5 Consensus size: 289
29392603 AACCGCGCGA
* * * * * * * *
29392613 GTCATTTATATCCGATCACTACCTCCCTTGACGAAATCCAACTAGCTTTTTCTAATTAAACATGT
1 GTCATTTAAATTCAATCATTACCTCCCTTGACGGAATCCAACTAGCTTTTTCTAATTGAACACGC
* * * * * * *
29392678 CAATTTGCTCGTGAGAATTCGAACTCGATAGACGACCGTCTCGTTTTCCTAACTATACACCAAAC
66 CAATTTGTTCATGGGAATTCGAACTCGGTAAACAACAGTCTCGTTTTCCTAACTATACACCAAAC
* * * * **
29392743 AACTCCAACCTAACTTTTTCTTGTGTAGTCGATTCTTGTACGACCTGCAAACCGACCATTGATGA
131 AACTCCAACCCAACTTTTCCTTGTGTAGTCGATTCCTGTACGACCTACAAACCGACCATTGACAA
* *
29392808 ATTTCTAACCACGTAACTTGTGTCCGTAATTTAAGATTTCGGTAGCCTTGCGATCTTGAAAGCCC
196 ATTTCTAACCACGTAACATGTGTCCGTAATTTAAGATTTCGGTAGCCTTGCGATCTAGAAAGCCC
* ***
29392873 AACTCGAATTAACGGCCACAACCACGTTG
261 AACTCGAATTAACGACCACAACCACACAG
* * *
29392902 GTCATTTAAATTCAATTATTACCTCCCTTGACGGAATCCAACTAGCTTTGTCCAATTGAACACGC
1 GTCATTTAAATTCAATCATTACCTCCCTTGACGGAATCCAACTAGCTTTTTCTAATTGAACACGC
* * * * * *
29392967 CAATTTGTTCATGGGAATTCGAACTCGGTAAACAATAGTCTTGTTTTCTTGACTGTACGCCAAAC
66 CAATTTGTTCATGGGAATTCGAACTCGGTAAACAACAGTCTCGTTTTCCTAACTATACACCAAAC
* * *
29393032 AACTCCAACCCAACTTTTCCTTGTGTAGTCGATTCCTGTACGACCTACAAGCCGACCCTTGGCAA
131 AACTCCAACCCAACTTTTCCTTGTGTAGTCGATTCCTGTACGACCTACAAACCGACCATTGACAA
* *
29393097 ATTTCTAACCACGTAACATGTGTCTGTAATTTAAGATTTTGGTAGCCTTGCGATCTAGAAAGCCC
196 ATTTCTAACCACGTAACATGTGTCCGTAATTTAAGATTTCGGTAGCCTTGCGATCTAGAAAGCCC
* *
29393162 AACTCGAATTAACGACCTCAACCGCACAG
261 AACTCGAATTAACGACCACAACCACACAG
* * * * *
29393191 GTCGTTTAAATTCAATCATTGCCTCCCTTGATGGAATCGAACTAGATTTTTCTAATTGAACACGC
1 GTCATTTAAATTCAATCATTACCTCCCTTGACGGAATCCAACTAGCTTTTTCTAATTGAACACGC
* * * * * * ** ** * * * * *
29393256 AAATTTGTTCTTGGGAATTTGAACTTGGTAGACGACCTTCTCAATTTCCCAATTGTACGCCAAAT
66 CAATTTGTTCATGGGAATTCGAACTCGGTAAACAACAGTCTCGTTTTCCTAACTATACACCAAAC
29393321 AACTCCAACCCAACTTT
131 AACTCCAACCCAACTTT
29393338 CAAAATAAAT
Statistics
Matches: 368, Mismatches: 68, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
289 368 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (289 bp):
GTCATTTAAATTCAATCATTACCTCCCTTGACGGAATCCAACTAGCTTTTTCTAATTGAACACGC
CAATTTGTTCATGGGAATTCGAACTCGGTAAACAACAGTCTCGTTTTCCTAACTATACACCAAAC
AACTCCAACCCAACTTTTCCTTGTGTAGTCGATTCCTGTACGACCTACAAACCGACCATTGACAA
ATTTCTAACCACGTAACATGTGTCCGTAATTTAAGATTTCGGTAGCCTTGCGATCTAGAAAGCCC
AACTCGAATTAACGACCACAACCACACAG
Found at i:29400953 original size:34 final size:34
Alignment explanation
Indices: 29400915--29400980 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
29400905 GTTAGTAATC
*
29400915 ATTGTCA-TCACATTCTCATTA-TCATTGCATTTTA
1 ATTGTCACT-ACATTCGCA-TAGTCATTGCATTTTA
*
29400949 ATTGTCACTGCATTCGCATAGTCATTGCATTT
1 ATTGTCACTACATTCGCATAGTCATTGCATTT
29400981 CCATTTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.07
34 25 0.89
35 1 0.04
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (34 bp):
ATTGTCACTACATTCGCATAGTCATTGCATTTTA
Found at i:29401821 original size:21 final size:21
Alignment explanation
Indices: 29401797--29401853 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29401787 TGAAGAGTGT
*
29401797 TGTGGCTGCATCTGATTTTGG
1 TGTGGCTGCATCTGACTTTGG
* * *
29401818 TGTGGCTGCATTTGGCTTTGT
1 TGTGGCTGCATCTGACTTTGG
*
29401839 TGTGGATGCATCTGA
1 TGTGGCTGCATCTGA
29401854 GTATGCTGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.14, G:0.33, T:0.42
Consensus pattern (21 bp):
TGTGGCTGCATCTGACTTTGG
Found at i:29404553 original size:64 final size:64
Alignment explanation
Indices: 29404441--29404570 Score: 226
Period size: 63 Copynumber: 2.0 Consensus size: 64
29404431 AGAAGATGTT
*
29404441 CCATTTGTTTTTTATAATAGTTGCATTGAAGCTTTGAGAAGACAAAAG-AAAACTGATAACTGC
1 CCATTTGTTTTTTATAATAGTTGCATTGAAGCTTTGAGAAGACAAAAGAAAAAATGATAACTGC
*
29404504 CCATTTGTTTTTTATAATAGTTGCATTGAAGCTTTTGAGAAGATAAAAGAAAAAATGATAACTGC
1 CCATTTGTTTTTTATAATAGTTGCATTGAAGC-TTTGAGAAGACAAAAGAAAAAATGATAACTGC
29404569 CC
1 CC
29404571 CTATTATTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 32 0.51
64 15 0.24
65 16 0.25
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (64 bp):
CCATTTGTTTTTTATAATAGTTGCATTGAAGCTTTGAGAAGACAAAAGAAAAAATGATAACTGC
Found at i:29407737 original size:17 final size:17
Alignment explanation
Indices: 29407715--29407752 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29407705 TTTAAAACAT
29407715 TTTTGAGACAATTTTTA-
1 TTTTGA-ACAATTTTTAG
*
29407732 TTTTGAATAATTTTTAG
1 TTTTGAACAATTTTTAG
29407749 TTTT
1 TTTT
29407753 TTTCTTAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTTGAACAATTTTTAG
Found at i:29416878 original size:14 final size:14
Alignment explanation
Indices: 29416853--29416891 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
29416843 CGCATTTTTA
29416853 TATTTCCTTTTA-T
1 TATTTCCTTTTACT
*
29416866 TGTTTCACTTTTACT
1 TATTTC-CTTTTACT
29416881 TATTTCCTTTT
1 TATTTCCTTTT
29416892 CCATTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 11 0.50
15 6 0.27
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.67
Consensus pattern (14 bp):
TATTTCCTTTTACT
Found at i:29419844 original size:13 final size:13
Alignment explanation
Indices: 29419823--29419860 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
29419813 TGAATGAGAA
29419823 AAAAG-AAAAGAAG
1 AAAAGAAAAAG-AG
*
29419836 AAGAGAAAAAGAG
1 AAAAGAAAAAGAG
29419849 AAAAGAAAAAGA
1 AAAAGAAAAAGA
29419861 AATATTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:29419850 original size:21 final size:20
Alignment explanation
Indices: 29419818--29419860 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
29419808 AATTGTGAAT
*
29419818 GAGAAAAAAGAAAAGAAGAA
1 GAGAAAAAAGAAAAGAAAAA
29419838 GAGAAAAAGAGAAAAGAAAAA
1 GAGAAAAA-AGAAAAGAAAAA
29419859 GA
1 GA
29419861 AATATTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
GAGAAAAAAGAAAAGAAAAA
Found at i:29422489 original size:50 final size:50
Alignment explanation
Indices: 29422433--29422537 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 50
29422423 TTGTAATTTA
* *
29422433 CTCAAAATCACTTAAATCGTTGTTTAAAATAATAACTCATGCAAAAATTC
1 CTCAAAATCACTTAAATCATTGTTTAAAATAATAACCCATGCAAAAATTC
29422483 CTCAAAATCACTTAAATCATTGTTTAAAATAATAACCCATGCAAAAATTC
1 CTCAAAATCACTTAAATCATTGTTTAAAATAATAACCCATGCAAAAATTC
29422533 C-CAAA
1 CTCAAA
29422538 TCAAAATTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.30
Consensus pattern (50 bp):
CTCAAAATCACTTAAATCATTGTTTAAAATAATAACCCATGCAAAAATTC
Found at i:29422559 original size:21 final size:20
Alignment explanation
Indices: 29422535--29422589 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
29422525 AAAAATTCCC
*
29422535 AAATCAAAATTCAAAGTCCTA
1 AAATCAAAATCCAAAGTCC-A
*
29422556 AAATCAAAAACCAAAGTCCA
1 AAATCAAAATCCAAAGTCCA
29422576 AAACTCAAAATCCA
1 AAA-TCAAAATCCA
29422590 CAATGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (20 bp):
AAATCAAAATCCAAAGTCCA
Found at i:29424271 original size:30 final size:30
Alignment explanation
Indices: 29424237--29424295 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
29424227 GGTGTTACAT
29424237 GGTTGACCAA-ATAGTCGTGTGTCACACACG
1 GGTTG-CCAACATAGTCGTGTGTCACACACG
** *
29424267 GGTTGGTAACATAGTTGTGTGTCACACAC
1 GGTTGCCAACATAGTCGTGTGTCACACAC
29424296 AGTTGTGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (30 bp):
GGTTGCCAACATAGTCGTGTGTCACACACG
Found at i:29436118 original size:26 final size:26
Alignment explanation
Indices: 29436088--29436139 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29436078 AACACATAAG
29436088 TATGAATAACTAAGATTGCAACTTCA
1 TATGAATAACTAAGATTGCAACTTCA
29436114 TATGAATAACTAAGATTGCAACTTCA
1 TATGAATAACTAAGATTGCAACTTCA
29436140 ACTTCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
TATGAATAACTAAGATTGCAACTTCA
Found at i:29437185 original size:15 final size:15
Alignment explanation
Indices: 29437140--29437186 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29437130 TGGGTGGACT
* *
29437140 TTTCTCAGCATCTTT
1 TTTCTCAACATCTTC
*
29437155 TTTCTCAACATTTTC
1 TTTCTCAACATCTTC
*
29437170 TTTCTCGACATCTTC
1 TTTCTCAACATCTTC
29437185 TT
1 TT
29437187 CTTTATCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.28, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTCTCAACATCTTC
Found at i:29442518 original size:19 final size:20
Alignment explanation
Indices: 29442481--29442520 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29442471 TAATAAATCT
*
29442481 TAAGTAAAACCTTGCATGCC
1 TAAGTAAAACCTTGAATGCC
*
29442501 TAAG-AAAACTTTGAATGCC
1 TAAGTAAAACCTTGAATGCC
29442520 T
1 T
29442521 CTCACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
TAAGTAAAACCTTGAATGCC
Found at i:29452175 original size:3 final size:3
Alignment explanation
Indices: 29452150--29452207 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
29452140 TAACATTTGG
* * *
29452150 TTC TTC TTT TTC TTCC TTC -TC TTC TTT TTC TTT TTC TT- TTC TTAC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
29452195 TTC TTC TTC TTC T
1 TTC TTC TTC TTC T
29452208 GCCCCAATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:29452197 original size:24 final size:23
Alignment explanation
Indices: 29452150--29452205 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
29452140 TAACATTTGG
29452150 TTCTTCTTTTTCTTCCTTCTCTTC
1 TTCTTCTTTTTCTT-CTTCTCTTC
*
29452174 TTTTTCTTTTTCTT-TTCTTACTTC
1 TTCTTCTTTTTCTTCTTC-T-CTTC
29452198 TTCTTCTT
1 TTCTTCTT
29452206 CTGCCCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 1 0.04
24 24 0.86
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (23 bp):
TTCTTCTTTTTCTTCTTCTCTTC
Found at i:29458290 original size:13 final size:13
Alignment explanation
Indices: 29458272--29458297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29458262 GTCTGTAATC
29458272 GCATATGGTCATG
1 GCATATGGTCATG
29458285 GCATATGGTCATG
1 GCATATGGTCATG
29458298 AGATTGCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
GCATATGGTCATG
Found at i:29466487 original size:20 final size:23
Alignment explanation
Indices: 29466456--29466497 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
29466446 TTCGATCCTT
29466456 TTGGGATATTT-ATC-CTTTTTG
1 TTGGGATATTTAATCTCTTTTTG
29466477 TTGGG-TATTTAATCTCTTTTT
1 TTGGGATATTTAATCTCTTTTT
29466498 CTTTGTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.60
Consensus pattern (23 bp):
TTGGGATATTTAATCTCTTTTTG
Found at i:29469901 original size:10 final size:10
Alignment explanation
Indices: 29469886--29469910 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29469876 TCTGGGTCTA
29469886 TGATCGCATC
1 TGATCGCATC
29469896 TGATCGCATC
1 TGATCGCATC
29469906 TGATC
1 TGATC
29469911 AGGTTACGCA
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:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (10 bp):
TGATCGCATC
Found at i:29471545 original size:24 final size:24
Alignment explanation
Indices: 29471512--29471558 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29471502 GTTAAGAGTA
**
29471512 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAAAGCAAAT-TAATAT
29471537 AAAA-TGTCAAAGCAAATTAATA
1 AAAATTGTCAAAGCAAATTAATA
29471559 AAAGATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAAAGCAAATTAATAT
Found at i:29484000 original size:15 final size:17
Alignment explanation
Indices: 29483964--29483999 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29483954 GAAATCAAAT
29483964 AAAATGCAAGGACAATA
1 AAAATGCAAGGACAATA
*
29483981 AAAATGCAATGACAA-A
1 AAAATGCAAGGACAATA
29483997 AAA
1 AAA
29484000 TAAAATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (17 bp):
AAAATGCAAGGACAATA
Found at i:29484006 original size:20 final size:18
Alignment explanation
Indices: 29483960--29484008 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
29483950 CTATGAAATC
29483960 AAATAAAATGCAAGGACA
1 AAATAAAATGCAAGGACA
* *
29483978 ATA-AAAATGCAATGACAAA
1 AAATAAAATGCAAGGAC--A
29483997 AAATAAAATGCA
1 AAATAAAATGCA
29484009 TGCAACTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 12 0.48
18 2 0.08
19 3 0.12
20 8 0.32
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.14
Consensus pattern (18 bp):
AAATAAAATGCAAGGACA
Found at i:29484434 original size:24 final size:23
Alignment explanation
Indices: 29484390--29484441 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
29484380 CATTTGCTTC
29484390 TTCTTTTTCTTCCTTCTCTTCTTT
1 TTCTTTTTCTT-CTTCTCTTCTTT
* *
29484414 TTCTTTTTCTT-TTCT-TACTTC
1 TTCTTTTTCTTCTTCTCTTCTTT
29484435 TTCTTTT
1 TTCTTTT
29484442 GCCCCAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 4 0.15
24 11 0.42
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (23 bp):
TTCTTTTTCTTCTTCTCTTCTTT
Found at i:29484440 original size:21 final size:23
Alignment explanation
Indices: 29484386--29484441 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
29484376 GTAACATTTG
*
29484386 CTTCTTCTTTTTCTTCCTTCTCTT
1 CTTCTTCTTTTTCTT-CTTCTCTA
*
29484410 CTTTTTCTTTTTCTT-TTCT-TA
1 CTTCTTCTTTTTCTTCTTCTCTA
29484431 CTTCTTCTTTT
1 CTTCTTCTTTT
29484442 GCCCCAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.38
22 4 0.14
24 14 0.48
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (23 bp):
CTTCTTCTTTTTCTTCTTCTCTA
Found at i:29490600 original size:13 final size:13
Alignment explanation
Indices: 29490582--29490607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29490572 GTCTATAATC
29490582 GCATATGGTCATG
1 GCATATGGTCATG
29490595 GCATATGGTCATG
1 GCATATGGTCATG
29490608 AGATTGCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
GCATATGGTCATG
Found at i:29528031 original size:18 final size:18
Alignment explanation
Indices: 29528005--29528078 Score: 103
Period size: 18 Copynumber: 4.1 Consensus size: 18
29527995 GCATGCACAT
* *
29528005 CATGATCAAATGTAGTCA
1 CATGCTCAAATGCAGTCA
29528023 CATGCTCAAATGCAGTCA
1 CATGCTCAAATGCAGTCA
*
29528041 CATGCTCAGATGCAGTCA
1 CATGCTCAAATGCAGTCA
* *
29528059 CATGCTCGAATGCAGCCA
1 CATGCTCAAATGCAGTCA
29528077 CA
1 CA
29528079 ACAGACTGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (18 bp):
CATGCTCAAATGCAGTCA
Found at i:29541769 original size:14 final size:14
Alignment explanation
Indices: 29541747--29541805 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
29541737 AATTTATCCT
*
29541747 TTTTCTCTTGCTGG
1 TTTTATCTTGCTGG
*
29541761 TTTTATCTTTCTGG
1 TTTTATCTTGCTGG
*
29541775 TTTTATTTTGCTGG
1 TTTTATCTTGCTGG
* *
29541789 TTTCAT-TTGTTGG
1 TTTTATCTTGCTGG
29541802 TTTT
1 TTTT
29541806 GATGAGTCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
13 9 0.24
14 29 0.76
ACGTcount: A:0.05, C:0.12, G:0.19, T:0.64
Consensus pattern (14 bp):
TTTTATCTTGCTGG
Found at i:29544316 original size:41 final size:41
Alignment explanation
Indices: 29544234--29544576 Score: 340
Period size: 41 Copynumber: 8.3 Consensus size: 41
29544224 AAAGGTAAAG
** * *
29544234 CATTAGCGGCGC-TTAACAAAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGT
29544274 CATTAGCGGCGCTTTACCCACAAG-GCCGCTAAAGGTCAGGT
1 CATTAGCGGCGCTTT-CCCACAAGCGCCGCTAAAGGTCAGGT
** * * *
29544315 CATTAGCGGCGCTTTATCACAAGTGCCGCTAAAGTTCAAGT
1 CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGT
* * *
29544356 CATTAGCGGCGCTTTCTCTA-ATGCACCGCTAAAGGT-AGGGT
1 CATTAGCGGCGCTTTC-CCACAAGCGCCGCTAAAGGTCA-GGT
* * *
29544397 AATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGTT
1 CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGT
* ** * *
29544438 AATTAGCGGCGCTTTAACTCAAGCGCCGCTAAAGGT-ATGAT
1 CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCA-GGT
* *
29544479 CATTAGCGGCGCTTTCCCTA-AAGCGCCACTAAAAGGTCCGGT
1 CATTAGCGGCGCTTTCCC-ACAAGCGCCGCT-AAAGGTCAGGT
* * *
29544521 CATTAACGGCGCTTTCCCTCAAGCTCCGCTAAAGGT-AGGAT
1 CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGG-T
29544562 CATTTAGCGGCGCTT
1 CA-TTAGCGGCGCTT
29544577 AAGTAGTGGC
Statistics
Matches: 251, Mismatches: 38, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
40 23 0.09
41 177 0.71
42 51 0.20
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (41 bp):
CATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCAGGT
Found at i:29544425 original size:123 final size:123
Alignment explanation
Indices: 29544210--29544716 Score: 450
Period size: 123 Copynumber: 4.0 Consensus size: 123
29544200 GGCGTTTGGA
* * * ** * *
29544210 AACA-AAGCGCTGCAAAAGGTAA-AGCATTAGCGGCGC-TTAACAAAAGCGCCGCTAAAGGTCGG
1 AACACAAGCGCCGCTAAAGGTAAGATCATTAGCGGCGCTTTCCCTAAAGCACCGCTAAAGGTCGG
*
29544272 GTCATTAGCGGCGCTTTACCCACAAG-GCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT
66 GTCATTAGCGGCGCTTT-CCCTCAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT
* * * * * *
29544330 ATCACAAGTGCCGCTAAAGTTCAAG-TCATTAGCGGCGCTTTCTCTAATGCACCGCTAAAGGTAG
1 AACACAAGCGCCGCTAAAGGT-AAGATCATTAGCGGCGCTTTCCCTAAAGCACCGCTAAAGGTCG
* * *
29544394 GGTAATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGTTAATTAGCGGCGCTTT
65 GGTCATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT
* * * * *
29544453 AACTCAAGCGCCGCTAAAGGTATGATCATTAGCGGCGCTTTCCCTAAAGCGCCACTAAAAGGTCC
1 AACACAAGCGCCGCTAAAGGTAAGATCATTAGCGGCGCTTTCCCTAAAGCACCGCT-AAAGGTCG
* *
29544518 GGTCATTAACGGCGCTTTCCCTCAAGCTCCGCTAAAGGT-AGGATCATTTAGCGGCGCTTAAGT
65 GGTCATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGG-TCA-TTAGCGGCGCTT---T
* ** * ** * *
29544581 AGTGGCGCTTTCACTCAAGCGCCGCTAAAAGGTCGGGTCATTAGCGGCGCTTTTTCTCAAGCGCC
1 A-----------ACACAAGCGCCGCT-AAAGGTAAGATCATTAGCGGCGCTTTCCCTAAAGCACC
* *** *
29544646 GCTAAAGTTCGGGTCATTAGCGGCGCTTATATATAAAGCGCCGCTAAAGGTCAGGTCATTAGCGG
54 GCTAAAGGTCGGGTCATTAGCGGCGCTT-TCCCTCAAGCGCCGCTAAAGGTCAGGTCATTAGCGG
29544711 CGCTTT
118 CGCTTT
29544717 TCTAATAAGC
Statistics
Matches: 314, Mismatches: 47, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
120 3 0.01
121 12 0.04
122 23 0.07
123 112 0.36
124 44 0.14
125 12 0.04
128 2 0.01
136 1 0.00
139 48 0.15
140 54 0.17
141 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (123 bp):
AACACAAGCGCCGCTAAAGGTAAGATCATTAGCGGCGCTTTCCCTAAAGCACCGCTAAAGGTCGG
GTCATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT
Found at i:29544663 original size:98 final size:97
Alignment explanation
Indices: 29544486--29544674 Score: 270
Period size: 98 Copynumber: 1.9 Consensus size: 97
29544476 GATCATTAGC
* *
29544486 GGCGCTTTCCCTAAAGCGCCACTAAAAGGTCCGGTCATTAACGGCGCTTTCCCTCAAGCTCCGCT
1 GGCGCTTTCACTAAAGCGCCACTAAAAGGTCCGGTCATTAACGGCGCTTTCCCTCAAGCGCCGCT
29544551 AAAGGTAGGATCATTTAGCGGCGCTTAAGTAGT
66 AAAGGTAGGATCA-TTAGCGGCGCTTAAGTAGT
* * * * **
29544584 GGCGCTTTCACTCAAGCGCCGCTAAAAGGTCGGGTCATTAGCGGCGCTTTTTCTCAAGCGCCGCT
1 GGCGCTTTCACTAAAGCGCCACTAAAAGGTCCGGTCATTAACGGCGCTTTCCCTCAAGCGCCGCT
* * *
29544649 AAAGTTCGGGTCATTAGCGGCGCTTA
66 AAAGGTAGGATCATTAGCGGCGCTTA
29544675 TATATAAAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 13 0.16
98 67 0.84
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (97 bp):
GGCGCTTTCACTAAAGCGCCACTAAAAGGTCCGGTCATTAACGGCGCTTTCCCTCAAGCGCCGCT
AAAGGTAGGATCATTAGCGGCGCTTAAGTAGT
Found at i:29544727 original size:42 final size:41
Alignment explanation
Indices: 29544597--29544773 Score: 189
Period size: 42 Copynumber: 4.3 Consensus size: 41
29544587 GCTTTCACTC
*
29544597 AAGCGCCGCTAAAAGGTCGGGTCATTAGCGGCGCTTTTTCT-C
1 AAGCGCCGCT-AAAGGTCGGGTCATTAGCGGCGC-TTTTCTAT
* * *
29544639 AAGCGCCGCTAAAGTTCGGGTCATTAGCGGCGCTTATATAT
1 AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCTAT
*
29544680 AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCTAAT
1 -AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCT-AT
* * * * * *
29544723 AAGCGTCGCTAAAGGT-GTG-AATTAGCGACGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCTAT
*
29544762 AAGTGCCGCTAA
1 AAGCGCCGCTAA
29544774 TTTATTTAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 12 0.10
40 18 0.16
41 23 0.20
42 60 0.52
43 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCTAT
Found at i:29547536 original size:26 final size:26
Alignment explanation
Indices: 29547507--29547637 Score: 93
Period size: 22 Copynumber: 5.3 Consensus size: 26
29547497 ACACTATCGA
*
29547507 TTAATTAAATATTTAAGTTAAAAGAT
1 TTAATTAATTATTTAAGTTAAAAGAT
* *
29547533 TTAATTATTTAATTATA-TT-AAAG--
1 TTAATTAATTATTTA-AGTTAAAAGAT
*
29547556 -TAAATAATTATATTAAGTTAAAAGAT
1 TTAATTAATTAT-TTAAGTTAAAAGAT
* *
29547582 TTAATTATTTAATTTTA-TT-AAAG--
1 TTAATTAATT-ATTTAAGTTAAAAGAT
*
29547605 -TAAATAATTATATTAAGTTAAAAGAT
1 TTAATTAATTAT-TTAAGTTAAAAGAT
29547631 TTAATTA
1 TTAATTA
29547638 TTTAATTATA
Statistics
Matches: 78, Mismatches: 13, Indels: 27
0.66 0.11 0.23
Matches are distributed among these distances:
21 2 0.03
22 19 0.24
23 7 0.09
24 8 0.10
25 8 0.10
26 16 0.21
27 16 0.21
28 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
TTAATTAATTATTTAAGTTAAAAGAT
Found at i:29547565 original size:18 final size:17
Alignment explanation
Indices: 29547542--29547715 Score: 91
Period size: 18 Copynumber: 10.6 Consensus size: 17
29547532 TTTAATTATT
29547542 TAATTATATTAAAGTAAA
1 TAATTATATT-AAGTAAA
*
29547560 TAATTATATTAAGTTAA
1 TAATTATATTAAGTAAA
* * **
29547577 -AA-GAT-TTAATTATT
1 TAATTATATTAAGTAAA
*
29547591 TAATTTTATTAAAGTAAA
1 TAATTATATT-AAGTAAA
*
29547609 TAATTATATTAAGTTAA
1 TAATTATATTAAGTAAA
* * **
29547626 -AA-GAT-TTAATTATT
1 TAATTATATTAAGTAAA
29547640 TAATTATATTAAAGTAAA
1 TAATTATATT-AAGTAAA
*
29547658 TAATTATATTAAATTAAA
1 TAATTATATT-AAGTAAA
* *
29547676 TATTTA-ATT-A-T--T
1 TAATTATATTAAGTAAA
29547688 TAATTATATTAAAGTAAA
1 TAATTATATT-AAGTAAA
*
29547706 TAAGTATATT
1 TAATTATATT
29547716 CAATTTATAA
Statistics
Matches: 114, Mismatches: 28, Indels: 28
0.67 0.16 0.16
Matches are distributed among these distances:
12 5 0.04
13 3 0.03
14 11 0.10
15 10 0.09
16 8 0.07
17 19 0.17
18 58 0.51
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
TAATTATATTAAGTAAA
Found at i:29547579 original size:49 final size:49
Alignment explanation
Indices: 29547519--29547715 Score: 351
Period size: 49 Copynumber: 4.0 Consensus size: 49
29547509 AATTAAATAT
29547519 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
29547568 TTAAGTTAAAAGATTTAATTATTTAATTTTATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
29547617 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
29547666 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
29547714 TT
1 TT
29547716 CAATTTATAA
Statistics
Matches: 143, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
48 41 0.29
49 102 0.71
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:29553279 original size:65 final size:66
Alignment explanation
Indices: 29553133--29553301 Score: 209
Period size: 65 Copynumber: 2.6 Consensus size: 66
29553123 GCAAATTGCT
*
29553133 CAACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTAAAAAAAAATATGATGAACTCCATCT
1 CAACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTAAAAAAAAATATGAAGAACTCCATCT
29553198 A
66 A
* * ** * *
29553199 AAACTTAAAGAGGAGGTTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAA-ATGAAGAACTCCA-CA
1 CAACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTAAAAAAAAATATGAAGAACTCCATC-
29553262 TA
65 TA
* * *
29553264 CAACTTAAAGTGGAGGCAGCAGCGAG-GCAAGCAGAGGC
1 CAACTTAAAGAGGAGGCTGCAACGAGAG-AAGCAGAGGC
29553302 AGCAGCGAGG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 2 0.02
65 44 0.50
66 42 0.48
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.14
Consensus pattern (66 bp):
CAACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTAAAAAAAAATATGAAGAACTCCATCT
A
Found at i:29553292 original size:11 final size:11
Alignment explanation
Indices: 29553276--29553313 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29553266 ACTTAAAGTG
29553276 GAGGCAGCAGC
1 GAGGCAGCAGC
29553287 GAGGCA--AGC
1 GAGGCAGCAGC
29553296 AGAGGCAGCAGC
1 -GAGGCAGCAGC
29553308 GAGGCA
1 GAGGCA
29553314 AGTGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.12
10 6 0.25
11 12 0.50
12 3 0.12
ACGTcount: A:0.32, C:0.24, G:0.45, T:0.00
Consensus pattern (11 bp):
GAGGCAGCAGC
Found at i:29553302 original size:21 final size:21
Alignment explanation
Indices: 29553276--29553315 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29553266 ACTTAAAGTG
29553276 GAGGCAGCAGCGAGGCAAGCA
1 GAGGCAGCAGCGAGGCAAGCA
29553297 GAGGCAGCAGCGAGGCAAG
1 GAGGCAGCAGCGAGGCAAG
29553316 TGAAGGAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.45, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGCAAGCA
Found at i:29553326 original size:21 final size:21
Alignment explanation
Indices: 29553271--29553327 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
29553261 ATACAACTTA
*
29553271 AAGTGGAGGCAGCAGCGAGGC
1 AAGTGAAGGCAGCAGCGAGGC
*
29553292 AAG-CAGAGGCAGCAGCGAGGC
1 AAGTGA-AGGCAGCAGCGAGGC
*
29553313 AAGTGAAGGAAGCAG
1 AAGTGAAGGCAGCAG
29553328 AGGCTACAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGTGAAGGCAGCAGCGAGGC
Found at i:29553691 original size:43 final size:43
Alignment explanation
Indices: 29553626--29553723 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
29553616 ATCTGTTATA
* *
29553626 TTAGCGGCGCTTTTGGATAAAGCGCCGCTAAAGAACATGGCCT
1 TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCT
* *
29553669 TTAGCGGTGCTTGTGGAAAAAGCGCCGCTGAAGAACATGGCCT
1 TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCT
*
29553712 TCAGCGGCGCTT
1 TTAGCGGCGCTT
29553724 TTTCGCATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.22
Consensus pattern (43 bp):
TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCT
Found at i:29555304 original size:36 final size:36
Alignment explanation
Indices: 29555257--29555401 Score: 200
Period size: 36 Copynumber: 4.0 Consensus size: 36
29555247 CTGTTATGAA
* * *
29555257 AGTAAACATGTGGGTATGTTATTCATGCCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATACCATGTGAC
** *
29555293 AGTAAATATGTGAATATGTTATTCACACCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATACCATGTGAC
* *
29555329 AGTAAATATGTGGGTATGTTATTCCTACCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATACCATGTGAC
* *
29555365 AGTAAAAATGTGGGTATGTTATTCATGCCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATACCATGTGAC
29555401 A
1 A
29555402 ATGAATATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATACCATGTGAC
Found at i:29555866 original size:58 final size:58
Alignment explanation
Indices: 29555760--29555875 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
29555750 GGTGATTATA
* *
29555760 TGATTATATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATG
1 TGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATACTCATGTGACTAATG
* * ** *
29555818 TGATTAAATGTGATTAATATGTGTTGTGTTAAATGCTT-ATGTACTCATGTGATTAATG
1 TGATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATACTCATGTGACTAATG
29555876 CAATTAATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 48 0.96
59 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (58 bp):
TGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATACTCATGTGACTAATG
Found at i:29559786 original size:101 final size:101
Alignment explanation
Indices: 29559611--29559816 Score: 394
Period size: 101 Copynumber: 2.0 Consensus size: 101
29559601 CCAAATAGAG
29559611 CTTAATCTCGCGATTCAGTCCGAACCTAAACCTCTTACAATGGCTCGCCTCATGAGCCACCATCT
1 CTTAATCTCGCGATTCAGTCCGAACCTAAACCTCTTACAATGGCTCGCCTCATGAGCCACCATCT
29559676 CGGGAGCGTACTGGCTCAACCGAACAAACTCAGCCT
66 CGGGAGCGTACTGGCTCAACCGAACAAACTCAGCCT
* *
29559712 CTTAATCTCGCGGTTCAGTCCGAACCTAAACCTCTTACAATGGCTCGCCTTATGAGCCACCATCT
1 CTTAATCTCGCGATTCAGTCCGAACCTAAACCTCTTACAATGGCTCGCCTCATGAGCCACCATCT
29559777 CGGGAGCGTACTGGCTCAACCGAACAAACTCAGCCT
66 CGGGAGCGTACTGGCTCAACCGAACAAACTCAGCCT
29559813 CTTA
1 CTTA
29559817 CTCTTCCACT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 103 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (101 bp):
CTTAATCTCGCGATTCAGTCCGAACCTAAACCTCTTACAATGGCTCGCCTCATGAGCCACCATCT
CGGGAGCGTACTGGCTCAACCGAACAAACTCAGCCT
Found at i:29561551 original size:7 final size:7
Alignment explanation
Indices: 29561541--29561577 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
29561531 CAAAATTAAA
29561541 AATGTCC
1 AATGTCC
29561548 AATGTCC
1 AATGTCC
29561555 AATGTCC
1 AATGTCC
29561562 AATGTCC
1 AATGTCC
29561569 -ATGTCC
1 AATGTCC
29561575 AAT
1 AAT
29561578 TACAACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (7 bp):
AATGTCC
Found at i:29563698 original size:19 final size:19
Alignment explanation
Indices: 29563674--29563712 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29563664 TTTAAAATTA
29563674 ATTTTTCAAAAATATTTTT
1 ATTTTTCAAAAATATTTTT
* *
29563693 ATTTTTCCAAATTATTTTT
1 ATTTTTCAAAAATATTTTT
29563712 A
1 A
29563713 ATCAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTCAAAAATATTTTT
Found at i:29573911 original size:22 final size:22
Alignment explanation
Indices: 29573851--29573917 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
29573841 TTCAACACAA
**
29573851 ATCACAAAATAATAT-TATTGT
1 ATCACAAAATAATATATATCAT
* *
29573872 ATGCA-ACAATCATATATATCAT
1 AT-CACAAAATAATATATATCAT
*
29573894 ATCACAAAATAATATATATGAT
1 ATCACAAAATAATATATATCAT
29573916 AT
1 AT
29573918 AAATAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
21 12 0.33
22 24 0.67
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.34
Consensus pattern (22 bp):
ATCACAAAATAATATATATCAT
Found at i:29573921 original size:18 final size:18
Alignment explanation
Indices: 29573900--29573938 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
29573890 TCATATCACA
29573900 AAATAATATATATGATAT
1 AAATAATATATATGATAT
29573918 AAATAATATATATGATAT
1 AAATAATATATATGATAT
29573936 AAA
1 AAA
29573939 AGAAAGCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATAATATATATGATAT
Found at i:29576672 original size:16 final size:16
Alignment explanation
Indices: 29576633--29576683 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
29576623 GATAGCTTAC
* *
29576633 ATATATATATCATATC
1 ATATATATATAATATA
* *
29576649 ACAAATATATAATATA
1 ATATATATATAATATA
*
29576665 ATATATATATAATAAA
1 ATATATATATAATATA
29576681 ATA
1 ATA
29576684 GAATTTTTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATATATATAATATA
Found at i:29580566 original size:50 final size:50
Alignment explanation
Indices: 29580512--29580619 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 50
29580502 CAAACTTCAT
* **
29580512 ACGTTTATACTCGTCAGCATATTTC-TGCGTTTACGCTCACTTGCTTGCAC
1 ACGTTTATACTCGTCAGCATA-TTCATGCATTTACGCTCACCAGCTTGCAC
** * *
29580562 ACGTTTAGGCTTGTCAGCTTATTCATGCATTTACGCTCACCAGCTTGCAC
1 ACGTTTATACTCGTCAGCATATTCATGCATTTACGCTCACCAGCTTGCAC
*
29580612 ACATTTAT
1 ACGTTTAT
29580620 GCTCCCCAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
49 3 0.06
50 45 0.94
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (50 bp):
ACGTTTATACTCGTCAGCATATTCATGCATTTACGCTCACCAGCTTGCAC
Found at i:29580647 original size:24 final size:24
Alignment explanation
Indices: 29580591--29580684 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
29580581 TATTCATGCA
* * **
29580591 TTTACGCTCACCAGCTTGCACACA
1 TTTACGCTCGCCAGCTTGCATATG
* *
29580615 TTTATGCTCCCCAGCTTGCATATG
1 TTTACGCTCGCCAGCTTGCATATG
* ***
29580639 TTTACGCTCGTCAGCTTATTTATGCG
1 TTTACGCTCGCCAGCTTGCATAT--G
29580665 TTTACGCTCGCCAGCTTGCA
1 TTTACGCTCGCCAGCTTGCA
29580685 CAAATAGGTA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 36 0.68
26 17 0.32
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTGCATATG
Found at i:29587665 original size:50 final size:50
Alignment explanation
Indices: 29587595--29587952 Score: 134
Period size: 50 Copynumber: 7.2 Consensus size: 50
29587585 ACACATATCA
* * * **
29587595 AACTT-CATACATTTATACTCGACAACATATTTGTGCATTTATGCTCGCC
1 AACTTGCACACATTTACACTCGACAACATATTTATGCATTTACACTCGCC
* ** * *
29587644 AACTTGCACACTTTTACACTCGTTAGCTTATTTATGCATTTACACTCGCC
1 AACTTGCACACATTTACACTCGACAACATATTTATGCATTTACACTCGCC
* ** * * * ** *
29587694 AGCTTGCACACATTTATGCTC-ATCAGCTTATTTACGTGTTGACACTCGCC
1 AACTTGCACACATTTACACTCGA-CAACATATTTATGCATTTACACTCGCC
* * ** ** * * **
29587744 -AGTCTACACATGTTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCC
1 AACT-TGCACACATTTACACTCGACAACATATTTATGCATTTACACTCGCC
* * * * * * * * *
29587794 AATTTGCACACGTTTACGCTCGTCACCTTATTTATGCGTTTACGCTCGTC
1 AACTTGCACACATTTACACTCGACAACATATTTATGCATTTACACTCGCC
* * * ** * ** *
29587844 AGCGTGCACA-AGTTTACTCTCCTCAACTTATTTATGTGTTTACACTCGCT
1 AACTTGCACACA-TTTACACTCGACAACATATTTATGCATTTACACTCGCC
* ** * * * * *
29587894 AGCTTGCACATGTTTAC-GTTGTCAGCTTATTTATGCATTTA-ACCTCGCC
1 AACTTGCACACATTTACACTCGACAACATATTTATGCATTTACA-CTCGCC
*
29587943 AACTTACACA
1 AACTTGCACA
29587953 AATAGGTATA
Statistics
Matches: 238, Mismatches: 63, Indels: 16
0.75 0.20 0.05
Matches are distributed among these distances:
48 1 0.00
49 37 0.16
50 198 0.83
51 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (50 bp):
AACTTGCACACATTTACACTCGACAACATATTTATGCATTTACACTCGCC
Found at i:29587785 original size:26 final size:26
Alignment explanation
Indices: 29587755--29587844 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
29587745 GTCTACACAT
*
29587755 GTTTATGCTCGTCAACTTATTTATGC
1 GTTTACGCTCGTCAACTTATTTATGC
* * * ** **
29587781 ATTTATGCTCGCCAA-TT-TGCACAC
1 GTTTACGCTCGTCAACTTATTTATGC
*
29587805 GTTTACGCTCGTCACCTTATTTATGC
1 GTTTACGCTCGTCAACTTATTTATGC
29587831 GTTTACGCTCGTCA
1 GTTTACGCTCGTCA
29587845 GCGTGCACAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
24 14 0.29
25 4 0.08
26 30 0.62
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (26 bp):
GTTTACGCTCGTCAACTTATTTATGC
Found at i:29587877 original size:150 final size:150
Alignment explanation
Indices: 29587606--29587952 Score: 414
Period size: 150 Copynumber: 2.3 Consensus size: 150
29587596 ACTTCATACA
* * * * * * *
29587606 TTTATACTCGACAACATATTTGTGCATTTATGCTCGCCAACTTGCACACTTTTACACTCGTTAGC
1 TTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCCAACTTGCACACGTTTACACTCGTCACC
* *
29587671 TTATTTATGCATTTACACTCGCCAGCTTGCACACATTTATGCTCATCAGCTTATTTACGTGTTGA
66 TTATTTATGCATTTACACTCGCCAGCGTGCACACATTTATGCTCATCAACTTATTTACGTGTTGA
29587736 CACTCGCCAG-TCTACACATG
131 CACTCGCCAGCT-TACACATG
* *
29587756 TTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCCAATTTGCACACGTTTACGCTCGTCACC
1 TTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCCAACTTGCACACGTTTACACTCGTCACC
* * * * *
29587821 TTATTTATGCGTTTACGCTCGTCAGCGTGCACA-AGTTTACT-CTCCTCAACTTATTTATGTGTT
66 TTATTTATGCATTTACACTCGCCAGCGTGCACACA-TTTA-TGCTCATCAACTTATTTACGTGTT
* * *
29587884 TACACTCGCTAGCTTGCACATG
129 GACACTCGCCAGCTTACACATG
* * * ** *
29587906 TTTACG-TTGTCAGCTTATTTATGCATTTAACCTCGCCAACTTACACA
1 TTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCCAACTTGCACA
29587953 AATAGGTATA
Statistics
Matches: 168, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
149 36 0.21
150 130 0.77
151 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.37
Consensus pattern (150 bp):
TTTATGCTCGTCAACTTATTTATGCATTTATGCTCGCCAACTTGCACACGTTTACACTCGTCACC
TTATTTATGCATTTACACTCGCCAGCGTGCACACATTTATGCTCATCAACTTATTTACGTGTTGA
CACTCGCCAGCTTACACATG
Found at i:29587909 original size:100 final size:100
Alignment explanation
Indices: 29587670--29587943 Score: 295
Period size: 100 Copynumber: 2.8 Consensus size: 100
29587660 CACTCGTTAG
* * * * * *
29587670 CTTATTTATGCATTTACACTCGCCAGCTTGCACACATTTATGCTCATCAGCTTATTTACGTGTTG
1 CTTATTTATGCATTTACACTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTT
* *
29587735 ACACTCGCCAGTCTACACATGTTTATGCTCGTCAA
66 ACACTCGCCAGTCTACACAAGTTTATGCTCCTCAA
** ** *
29587770 CTTATTTATGCATTTATGCTCGCCAATTTGCACACGTTTACGCTCGTCACCTTATTTATGCGTTT
1 CTTATTTATGCATTTACACTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTT
* * *
29587835 ACGCTCGTCAG-CGTGCACAAGTTTACT-CTCCTCAA
66 ACACTCGCCAGTC-TACACAAGTTTA-TGCTCCTCAA
** * * * *
29587870 CTTATTTATGTGTTTACACTCGCTAGCTTGCACATGTTTACG-TTGTCAGCTTATTTATGCATTT
1 CTTATTTATGCATTTACACTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTT
29587934 A-ACCTCGCCA
66 ACA-CTCGCCA
29587944 ACTTACACAA
Statistics
Matches: 142, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
99 27 0.19
100 114 0.80
101 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (100 bp):
CTTATTTATGCATTTACACTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTATGCGTTT
ACACTCGCCAGTCTACACAAGTTTATGCTCCTCAA
Found at i:29589334 original size:20 final size:20
Alignment explanation
Indices: 29589271--29589361 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
29589261 GCCTGGAGCT
* *
29589271 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGGTT-AAAATC
** * *
29589292 ATTTTGAAGT-ATTAAAATG
1 ATTTTGACTTGGTTAAAATC
* *
29589311 ATTTTGACTTGGTTCAAATT
1 ATTTTGACTTGGTTAAAATC
*
29589331 ATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
29589351 ATTTTAACTTG
1 ATTTTGACTTG
29589362 ATTTTAAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
19 12 0.22
20 35 0.64
21 8 0.15
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:29591879 original size:50 final size:50
Alignment explanation
Indices: 29591804--29591911 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 50
29591794 AAGTATCGAT
29591804 ACTCGGGTAAAATTATCGATACTTTTTATGTGGTACTGATAATTTTTGAG
1 ACTCGGGTAAAATTATCGATACTTTTTATGTGGTACTGATAATTTTTGAG
29591854 ACTCGGGTAAAATTATCGATACTTTTTATGTGGTACTGATAATTTTTGAG
1 ACTCGGGTAAAATTATCGATACTTTTTATGTGGTACTGATAATTTTTGAG
*
29591904 ACTTGGGT
1 ACTCGGGT
29591912 TTTTAAATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (50 bp):
ACTCGGGTAAAATTATCGATACTTTTTATGTGGTACTGATAATTTTTGAG
Found at i:29593692 original size:17 final size:17
Alignment explanation
Indices: 29593642--29593721 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
29593632 CACTAAATTC
*
29593642 TAATGACAAATGGAAATG
1 TAATGAC-AATGAAAATG
* *
29593660 CAATGACAATGCAAATG
1 TAATGACAATGAAAATG
*
29593677 TAATGACAATTAAAATG
1 TAATGACAATGAAAATG
* * **
29593694 TAATAACAACGGGAATG
1 TAATGACAATGAAAATG
*
29593711 TGATGACAATG
1 TAATGACAATG
29593722 CTTACTAACT
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
17 43 0.88
18 6 0.12
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (17 bp):
TAATGACAATGAAAATG
Found at i:29593693 original size:34 final size:34
Alignment explanation
Indices: 29593655--29593720 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
29593645 TGACAAATGG
* *
29593655 AAATGCAATGACAATGCAAATGTAATGACAATTA
1 AAATGCAATAACAACGCAAATGTAATGACAATTA
* ** *
29593689 AAATGTAATAACAACGGGAATGTGATGACAAT
1 AAATGCAATAACAACGCAAATGTAATGACAAT
29593721 GCTTACTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (34 bp):
AAATGCAATAACAACGCAAATGTAATGACAATTA
Found at i:29601732 original size:37 final size:37
Alignment explanation
Indices: 29601681--29601786 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
29601671 GTTCTTGGAT
*
29601681 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* *
29601718 CACCGGCACGAAGCCTACTAGACACATAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * *
29601755 CATCGGCACAAAGCCTTCTAGGCACAAAGCCT
1 CACCGGCACAAAGCCTACTAGGCACATAGCCT
29601787 TCTAGGCACA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.14
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
Found at i:29601779 original size:53 final size:53
Alignment explanation
Indices: 29601722--29601839 Score: 173
Period size: 53 Copynumber: 2.2 Consensus size: 53
29601712 TGAATACACC
* * *
29601722 GGCACGAAGCCTACTAGACACATAGCCTGAATACATCGGCACAAAGCCTTCTA
1 GGCACAAAGCCTACTAGACACATAGCCTGAATACACCGGCACAAAGCCTACTA
* * *
29601775 GGCACAAAGCCTTCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTA
1 GGCACAAAGCCTACTAGACACATAGCCTGAATACACCGGCACAAAGCCTACTA
*
29601828 GGCACATAGCCT
1 GGCACAAAGCCT
29601840 GAATACACCG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.16
Consensus pattern (53 bp):
GGCACAAAGCCTACTAGACACATAGCCTGAATACACCGGCACAAAGCCTACTA
Found at i:29601780 original size:16 final size:16
Alignment explanation
Indices: 29601759--29601802 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
29601749 TGAATACATC
29601759 GGCACAAAGCCTTCTA
1 GGCACAAAGCCTTCTA
29601775 GGCACAAAGCCTTCTA
1 GGCACAAAGCCTTCTA
*
29601791 GGCACATAGCCT
1 GGCACAAAGCCT
29601803 GAATACACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (16 bp):
GGCACAAAGCCTTCTA
Found at i:29601816 original size:37 final size:37
Alignment explanation
Indices: 29601775--29601955 Score: 272
Period size: 37 Copynumber: 4.9 Consensus size: 37
29601765 AAGCCTTCTA
* *
29601775 GGCACAAAGCCTTCTAGGCACATAGCCTGAATACACC
1 GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
29601812 GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
1 GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
* * *
29601849 GGCACGAAGCCTACTACGTACATAGCTTGAATACACC
1 GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
* *
29601886 GGCACGAAGCCTACTAGGCATATAGCCTGAAAACACC
1 GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
* * *
29601923 GGCACAAAACCTACTAGGCACATAACCTGAATA
1 GGCACGAAGCCTACTAGGCACATAGCCTGAATA
29601956 TTGTGTAAGC
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 129 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.15
Consensus pattern (37 bp):
GGCACGAAGCCTACTAGGCACATAGCCTGAATACACC
Found at i:29601822 original size:21 final size:21
Alignment explanation
Indices: 29601798--29601860 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
29601788 CTAGGCACAT
29601798 AGCCTGAATACACCGGCACGA
1 AGCCTGAATACACCGGCACGA
*
29601819 AGCCT-ACT--A--GGCAC-A
1 AGCCTGAATACACCGGCACGA
29601834 TAGCCTGAATACACCGGCACGA
1 -AGCCTGAATACACCGGCACGA
29601856 AGCCT
1 AGCCT
29601861 ACTACGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 1 0.03
16 10 0.30
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 15 0.45
22 1 0.03
ACGTcount: A:0.32, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
AGCCTGAATACACCGGCACGA
Found at i:29601838 original size:90 final size:90
Alignment explanation
Indices: 29601685--29601860 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 90
29601675 TTGGATCACC
29601685 GGCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTAGACACATAGCCT
1 GGCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTAGACACATAGCCT
*
29601750 GAATACATCGGCACAAAGCCTTCTA
66 GAATACACCGGCACAAAGCCTTCTA
* *
29601775 GGCACAAAGCCTTCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTAGGCACATAGCCT
1 GGCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTAGACACATAGCCT
*
29601840 GAATACACCGGCACGAAGCCT
66 GAATACACCGGCACAAAGCCT
29601861 ACTACGTACA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (90 bp):
GGCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTACTAGACACATAGCCT
GAATACACCGGCACAAAGCCTTCTA
Found at i:29602388 original size:26 final size:26
Alignment explanation
Indices: 29602352--29602405 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
29602342 ACTCAAATTT
*
29602352 TAATTAAACAAGTGTAAATATATATA
1 TAATTAAACAAGAGTAAATATATATA
29602378 TAATTAAACAAGAGTAAATATATATA
1 TAATTAAACAAGAGTAAATATATATA
29602404 TA
1 TA
29602406 TAGATAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (26 bp):
TAATTAAACAAGAGTAAATATATATA
Found at i:29607002 original size:22 final size:22
Alignment explanation
Indices: 29606907--29607003 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 22
29606897 CGAAGTACTT
*
29606907 AACAGAAGCACATA-AGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
* *
29606930 CAACAGTAGGCACACAAAGTGCT-
1 -AACAG-AAGCACACACAGTGCTG
* *
29606953 AATCAAAAGCACACACAGTGCTA
1 AA-CAGAAGCACACACAGTGCTG
29606976 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
29606998 AACAGA
1 AACAGA
29607004 GGACACGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
22 40 0.65
23 4 0.06
24 5 0.08
25 7 0.11
26 6 0.10
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:29607024 original size:23 final size:22
Alignment explanation
Indices: 29606939--29607025 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
29606929 GCAACAGTAG
* *
29606939 GCACACAA-AGTGCTAATCAAAA
1 GCACA-AACAGTGCTAAACAGAA
*
29606961 GCACACACAGTGCTAAACAGAA
1 GCACAAACAGTGCTAAACAGAA
* * *
29606983 GCACACACAGTGCTGAACAGAG
1 GCACAAACAGTGCTAAACAGAA
29607005 GACACGAAAC-GTGCTAAACAG
1 G-CAC-AAACAGTGCTAAACAG
29607026 TAGGCATGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
21 1 0.02
22 38 0.69
23 13 0.24
24 3 0.05
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.10
Consensus pattern (22 bp):
GCACAAACAGTGCTAAACAGAA
Found at i:29607129 original size:26 final size:24
Alignment explanation
Indices: 29607093--29607140 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
29607083 TCTACATGGG
29607093 CATAATCTCATATATTCATCATTTCT
1 CATAATCTCATATA-TCA-CATTTCT
*
29607119 CATAATTTCATATATCACATTT
1 CATAATCTCATATATCACATTT
29607141 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 13 0.62
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (24 bp):
CATAATCTCATATATCACATTTCT
Found at i:29612009 original size:37 final size:37
Alignment explanation
Indices: 29611942--29612268 Score: 395
Period size: 37 Copynumber: 8.9 Consensus size: 37
29611932 TGGATTACCA
* * *
29611942 GCACAAAGCTTGCTAGGCACATAGCTTGAATACACCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
** *
29611979 GCATGAAGCCTACTAGGCGCATAGCCTGAATACACCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* *
29612016 GCACAAAGCCTACTAGGCACATAACCTGAATACATCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
** * * *
29612053 GCATGAAGCCTACTAGGTACATAGCTTGAATACACCA
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
*
29612090 GCACAAAGCCTAC-AGACACATAGCCTGAATACACCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
** * * *
29612126 GCATGAAGCCTACTATGCATATAGCCTGAAAACACCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* ** *
29612163 GCACAAAGCCCACTACACACATAGCCTGAATACACTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * * * *
29612200 ACACGAAGCCTACTAGGCACATAGCTTGAAAATACCG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
29612237 GCACAAAGCCTACTAGGCACATAGCCTGAATA
1 GCACAAAGCCTACTAGGCACATAGCCTGAATA
29612269 TTGTGTAAGC
Statistics
Matches: 238, Mismatches: 51, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
36 30 0.13
37 208 0.87
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (37 bp):
GCACAAAGCCTACTAGGCACATAGCCTGAATACACCG
Found at i:29612063 original size:74 final size:74
Alignment explanation
Indices: 29611942--29612268 Score: 449
Period size: 74 Copynumber: 4.4 Consensus size: 74
29611932 TGGATTACCA
* * * *
29611942 GCACAAAGCTTGCTAGGCACATAGCTTGAATACACCGGCATGAAGCCTACTAGGCGCATAGCCTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAGCCTG
*
29612007 AATACACCG
66 AAAACACCG
* * * *
29612016 GCACAAAGCCTACTAGGCACATAACCTGAATACATCGGCATGAAGCCTACTAGGTACATAGCTTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAGCCTG
* *
29612081 AATACACCA
66 AAAACACCG
* * *
29612090 GCACAAAGCCTAC-AGACACATAGCCTGAATACACCGGCATGAAGCCTACTATGCATATAGCCTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAGCCTG
29612154 AAAACACCG
66 AAAACACCG
* ** * * * *
29612163 GCACAAAGCCCACTACACACATAGCCTGAATACACTGACACGAAGCCTACTAGGCACATAGCTTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAGCCTG
*
29612228 AAAATACCG
66 AAAACACCG
29612237 GCACAAAGCCTACTAGGCACATAGCCTGAATA
1 GCACAAAGCCTACTAGGCACATAGCCTGAATA
29612269 TTGTGTAAGC
Statistics
Matches: 222, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
73 63 0.28
74 159 0.72
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (74 bp):
GCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAGCCTG
AAAACACCG
Found at i:29612226 original size:147 final size:148
Alignment explanation
Indices: 29611938--29612268 Score: 477
Period size: 147 Copynumber: 2.2 Consensus size: 148
29611928 TTCTTGGATT
* * * *
29611938 ACCAGCACAAAGCTTGCTAGGCACATAGCTTGAATACACCGGCATGAAGCCTACTAGGCGCATAG
1 ACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAG
* * ** * *
29612003 CCTGAATACACCGGCACAAAGCCTACTAGGCACATAACCTGAATACATCGGCATGAAGCCTACTA
66 CCTGAAAACACCGGCACAAAGCCCACTACACACATAACCTGAATACATCGACACGAAGCCTACTA
* *
29612068 GGTACATAGCTTGAATAC
131 GGCACATAGCTTGAAAAC
* * *
29612086 ACCAGCACAAAGCCTAC-AGACACATAGCCTGAATACACCGGCATGAAGCCTACTATGCATATAG
1 ACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAG
*
29612150 CCTGAAAACACCGGCACAAAGCCCACTACACACATAGCCTGAATACA-CTGACACGAAGCCTACT
66 CCTGAAAACACCGGCACAAAGCCCACTACACACATAACCTGAATACATC-GACACGAAGCCTACT
*
29612214 AGGCACATAGCTTGAAAAT
130 AGGCACATAGCTTGAAAAC
*
29612233 ACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
1 ACCAGCACAAAGCCTACTAGGCACATAGCCTGAATA
29612269 TTGTGTAAGC
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
146 1 0.01
147 129 0.80
148 32 0.20
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.16
Consensus pattern (148 bp):
ACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCATGAAGCCTACTAGGCACATAG
CCTGAAAACACCGGCACAAAGCCCACTACACACATAACCTGAATACATCGACACGAAGCCTACTA
GGCACATAGCTTGAAAAC
Found at i:29618239 original size:15 final size:15
Alignment explanation
Indices: 29618219--29618279 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
29618209 AGTGACAATG
**
29618219 TTCTCAGCAGATTCT
1 TTCTCAGCATCTTCT
*
29618234 TTCTCAGGATCTTCT
1 TTCTCAGCATCTTCT
*
29618249 TTCTCAACATCTTCT
1 TTCTCAGCATCTTCT
* *
29618264 TTCTCAACACCTTCT
1 TTCTCAGCATCTTCT
29618279 T
1 T
29618280 CTAGGGCTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.18, C:0.31, G:0.07, T:0.44
Consensus pattern (15 bp):
TTCTCAGCATCTTCT
Found at i:29618281 original size:18 final size:15
Alignment explanation
Indices: 29618230--29618279 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
29618220 TCTCAGCAGA
**
29618230 TTCTTTCTCAGGATC
1 TTCTTTCTCAACATC
29618245 TTCTTTCTCAACATC
1 TTCTTTCTCAACATC
*
29618260 TTCTTTCTCAACACC
1 TTCTTTCTCAACATC
29618275 TTCTT
1 TTCTT
29618280 CTAGGGCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.04, T:0.48
Consensus pattern (15 bp):
TTCTTTCTCAACATC
Found at i:29623929 original size:18 final size:18
Alignment explanation
Indices: 29623902--29623936 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29623892 ATACATCAAA
29623902 TTGCACCGACAACTTTGT
1 TTGCACCGACAACTTTGT
* *
29623920 TTGCATCGACAATTTTG
1 TTGCACCGACAACTTTG
29623937 AGGGTCGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (18 bp):
TTGCACCGACAACTTTGT
Found at i:29636015 original size:20 final size:20
Alignment explanation
Indices: 29635942--29636024 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
29635932 AAATTTTTAT
29635942 AATTTTTAAAAATATAAATTTATG
1 AATTTTTAAAAAT-T--ATTT-TG
* *
29635966 AATTTTTATAAA-TATTCT-
1 AATTTTTAAAAATTATTTTG
*
29635984 AAATTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
*
29636004 AATTTTTGAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
29636024 A
1 A
29636025 TTCTTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 10 0.20
19 6 0.12
20 22 0.44
22 1 0.02
24 11 0.22
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:29636132 original size:18 final size:18
Alignment explanation
Indices: 29636109--29636147 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29636099 ACACCAATAT
* *
29636109 ATTATTTGAACTATTCGA
1 ATTATTCGAACTATTCAA
*
29636127 ATTATTCGAGCTATTCAA
1 ATTATTCGAACTATTCAA
29636145 ATT
1 ATT
29636148 GTAAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
ATTATTCGAACTATTCAA
Found at i:29639371 original size:54 final size:54
Alignment explanation
Indices: 29639289--29639420 Score: 230
Period size: 54 Copynumber: 2.4 Consensus size: 54
29639279 AGGCACCTGT
29639289 ATCACTCCATTTTGAACCAGTCCATGAGTTGTTCACATCATTTGAAGCATC-AG
1 ATCACTCCATTTTGAACCAGTCCATGAGTTGTTCACATCATTTGAAGCATCAAG
*
29639342 CATCACTCCATTTTGAACCAGTCCATGAGTTGTTCGCATCATTTGAAGCATCAAG
1 -ATCACTCCATTTTGAACCAGTCCATGAGTTGTTCACATCATTTGAAGCATCAAG
*
29639397 ATCACTCCATTTTGGACCAGTCCA
1 ATCACTCCATTTTGAACCAGTCCA
29639421 GGGTATCTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
54 73 0.97
55 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (54 bp):
ATCACTCCATTTTGAACCAGTCCATGAGTTGTTCACATCATTTGAAGCATCAAG
Found at i:29642546 original size:47 final size:47
Alignment explanation
Indices: 29642477--29642571 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
29642467 AAATCTAAGA
29642477 TTTAGGAGTTTAGTTCACAAAATATAAGATTACTTAAAAGTACAATT
1 TTTAGGAGTTTAGTTCACAAAATATAAGATTACTTAAAAGTACAATT
29642524 TTTAGGAGTTTAGTTCACAAAATATAAGATTACTTAAAAGTACAATT
1 TTTAGGAGTTTAGTTCACAAAATATAAGATTACTTAAAAGTACAATT
29642571 T
1 T
29642572 AATAAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (47 bp):
TTTAGGAGTTTAGTTCACAAAATATAAGATTACTTAAAAGTACAATT
Found at i:29664814 original size:13 final size:13
Alignment explanation
Indices: 29664796--29664830 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
29664786 TCAAATGATA
29664796 ATCAACAATATTC
1 ATCAACAATATTC
29664809 ATCAACAATATTC
1 ATCAACAATATTC
29664822 ATCAACAAT
1 ATCAACAAT
29664831 TAATAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAACAATATTC
Found at i:29666986 original size:24 final size:24
Alignment explanation
Indices: 29666937--29666988 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
29666927 TGTCGAGGCA
* *
29666937 TCTTCATCCTTTTCATTCTTCTTT
1 TCTTCATCCTTCTCATTCTTCGTT
*
29666961 TCTTCCTCCTTCTC-TTCTTCAGTT
1 TCTTCATCCTTCTCATTCTTC-GTT
29666985 TCTT
1 TCTT
29666989 TCTCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.60
Consensus pattern (24 bp):
TCTTCATCCTTCTCATTCTTCGTT
Done.