Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 189 of 199
Found at i:55200570 original size:27 final size:27
Alignment explanation
Indices: 55200540--55200600 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
55200530 TCGACTCATA
55200540 AGGGTATATC-AGACATTTTACCCTACG
1 AGGGTATATCTA-ACATTTTACCCTACG
* * *
55200567 AGGGTATTTCTATCATTTTACCCTTCG
1 AGGGTATATCTAACATTTTACCCTACG
*
55200594 TGGGTAT
1 AGGGTAT
55200601 TTCGGTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (27 bp):
AGGGTATATCTAACATTTTACCCTACG
Found at i:55200601 original size:27 final size:27
Alignment explanation
Indices: 55200553--55200773 Score: 166
Period size: 27 Copynumber: 8.2 Consensus size: 27
55200543 GTATATCAGA
* *
55200553 CATTTTACCCTACGAGGGTATTTCTAT
1 CATTTTACCCTTCGAGGGTATTTCTGT
* *
55200580 CATTTTACCCTTCGTGGGTATTTCGGT
1 CATTTTACCCTTCGAGGGTATTTCTGT
* *
55200607 CATTTTATCC-TCTAGGGGTATTT-TGGT
1 CATTTTACCCTTCGA-GGGTATTTCT-GT
** ***
55200634 CATTTTACCCTTTAAGGGTATTGAAGT
1 CATTTTACCCTTCGAGGGTATTTCTGT
55200661 CATTTTACCCTTCGAGGGTATTT-TGGT
1 CATTTTACCCTTCGAGGGTATTTCT-GT
* * * * *
55200688 CATTTTACCATTTGGGGGTATTTCGGC
1 CATTTTACCCTTCGAGGGTATTTCTGT
* *
55200715 CATTTTACCCTTCG-GGAGTGTTTCGGT
1 CATTTTACCCTTCGAGG-GTATTTCTGT
* *
55200742 CATTTTATCCTAT-GGGGGTATTT-TAGT
1 CATTTTACCCT-TCGAGGGTATTTCT-GT
55200769 CATTT
1 CATTT
55200774 ATCAACCTCT
Statistics
Matches: 155, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
26 4 0.03
27 146 0.94
28 5 0.03
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (27 bp):
CATTTTACCCTTCGAGGGTATTTCTGT
Found at i:55200626 original size:54 final size:54
Alignment explanation
Indices: 55200553--55200773 Score: 198
Period size: 54 Copynumber: 4.1 Consensus size: 54
55200543 GTATATCAGA
* * *
55200553 CATTTTACCC-TACGAGGGTATTTCT-ATCATTTTACCCTTCGTGGGTATTTCGGT
1 CATTTTACCCTTA-GAGGGTATTT-TGGTCATTTTACCCTTTGAGGGTATTTCGGT
* * ***
55200607 CATTTTATCCTCTAG-GGGTATTTTGGTCATTTTACCCTTTAAGGGTATTGAAGT
1 CATTTTACCCT-TAGAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGGT
* * * *
55200661 CATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCATTTGGGGGTATTTCGGC
1 CATTTTACCCTTAGAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGGT
* * * * * * **
55200715 CATTTTACCCTTCG-GGAGTGTTTCGGTCATTTTATCCTATGGGGGTATTTTAGT
1 CATTTTACCCTTAGAGG-GTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGGT
55200769 CATTT
1 CATTT
55200774 ATCAACCTCT
Statistics
Matches: 137, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
53 5 0.04
54 129 0.94
55 1 0.01
56 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (54 bp):
CATTTTACCCTTAGAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGGT
Found at i:55200744 original size:81 final size:80
Alignment explanation
Indices: 55200553--55200773 Score: 223
Period size: 81 Copynumber: 2.7 Consensus size: 80
55200543 GTATATCAGA
* * *
55200553 CATTTTACCCTACGAGGGTATTTCTA-TCATTTTACCCTTCGTGGGTATTTCGGTCATTTTATCC
1 CATTTTACCCTTCG-GGGTATTTC-AGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTATCC
* *
55200617 TCTAGGGGTATTTTGGT
64 TCTAGGGGTATTTCGGC
** **
55200634 CATTTTACCCTTTAAGGGTATTGAAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTA-CCA
1 CATTTTACCC-TTCGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTATCC-
* *
55200698 TTTGGGGGTATTTCGGC
64 TCTAGGGGTATTTCGGC
* * * * *
55200715 CATTTTACCCTTCGGGAGTGTTTCGGTCATTTTATCCTAT-GGGGGTATTTTAGTCATTT
1 CATTTTACCCTTCGGG-GTATTTCAGTCATTTTACCCT-TCGAGGGTATTTTGGTCATTT
55200774 ATCAACCTCT
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
80 7 0.06
81 106 0.92
82 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (80 bp):
CATTTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTATCCTC
TAGGGGTATTTCGGC
Found at i:55213593 original size:10 final size:10
Alignment explanation
Indices: 55213578--55213602 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55213568 AAATAAAGAG
55213578 AATTCTAGAT
1 AATTCTAGAT
55213588 AATTCTAGAT
1 AATTCTAGAT
55213598 AATTC
1 AATTC
55213603 CACTTTGATC
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:0.12, G:0.08, T:0.40
Consensus pattern (10 bp):
AATTCTAGAT
Found at i:55214489 original size:42 final size:42
Alignment explanation
Indices: 55214430--55214515 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
55214420 ATGAAAAAGA
*
55214430 GAGGATTAGGTTATTAATTTATATTTATTTTATAATCTTTGT
1 GAGGATTAGGATATTAATTTATATTTATTTTATAATCTTTGT
* *
55214472 GAGGATTGGGATATTAATTTATGTTTATTTTATAATCTTTGT
1 GAGGATTAGGATATTAATTTATATTTATTTTATAATCTTTGT
55214514 GA
1 GA
55214516 TATTCTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.52
Consensus pattern (42 bp):
GAGGATTAGGATATTAATTTATATTTATTTTATAATCTTTGT
Found at i:55216668 original size:17 final size:19
Alignment explanation
Indices: 55216631--55216670 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
55216621 TTTTATTATT
55216631 ATTTTTTAAATATTGTATA
1 ATTTTTTAAATATTGTATA
*
55216650 ATTTTTT-ATTATTGT-TA
1 ATTTTTTAAATATTGTATA
55216667 ATTT
1 ATTT
55216671 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 7 0.35
19 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTTTTAAATATTGTATA
Found at i:55218142 original size:5 final size:5
Alignment explanation
Indices: 55218132--55218156 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55218122 TTCTTCTGCA
55218132 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
55218157 CAATTTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:55219291 original size:29 final size:28
Alignment explanation
Indices: 55219257--55219331 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
55219247 AAAAATTTAT
* *
55219257 TTTTAAAATTAAAAAGCATTTTAAAAAT-A
1 TTTTAAAATTAAAAA--AATTAAAAAATAA
55219286 TTTTAAAATTAAAAAAATTAAAAAATAA
1 TTTTAAAATTAAAAAAATTAAAAAATAA
*
55219314 TATTAAAATTAAAAAAAT
1 TTTTAAAATTAAAAAAAT
55219332 AAATATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.21
28 18 0.43
29 15 0.36
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
TTTTAAAATTAAAAAAATTAAAAAATAA
Found at i:55226571 original size:3 final size:3
Alignment explanation
Indices: 55226563--55226588 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55226553 ATATGTTTCT
55226563 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
55226589 TTTTTTTTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55231041 original size:21 final size:20
Alignment explanation
Indices: 55231017--55231055 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55231007 AAATTTGAAC
*
55231017 AAAATTAACATTTATTGTTA
1 AAAAATAACATTTATTGTTA
* *
55231037 AAAAATATCTTTTATTGTT
1 AAAAATAACATTTATTGTT
55231056 TTTTTACTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
AAAAATAACATTTATTGTTA
Found at i:55235332 original size:154 final size:152
Alignment explanation
Indices: 55234946--55235604 Score: 949
Period size: 154 Copynumber: 4.3 Consensus size: 152
55234936 TTTAGTGTGT
* * *
55234946 TTTTTATTGAAAGTAAT-AAAATCCGGG-AAAAAATACGAACAAAGGGCCAAAATTA-GGATTTT
1 TTTTT-TT-AAAGTAATAAAAAT-CGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
* * *
55235008 TTTAATTTATTTAAAAAATACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
63 TTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
55235073 AATAAAAAAATTAGAAAATAGTATA
128 AATAATAAAATTAGAAAATAGTATA
* * * * *
55235098 TTTTTTAAAAGTAATAAAATTCGGGGAAAAAAATATGAACAGAGGGACGAAATAAGGGTTTTTTT
1 TTTTTTTAAAGTAATAAAAATC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTT
55235163 TAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
65 TAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT-AAA
*
55235228 ATAATAAAAATTATAAAATAGTATA
129 ATAAT-AAAATTAGAAAATAGTATA
*
55235253 TTTTTTTAAAG-AATAAAAATCTGGGAAAAAAATATGAACAAAGGGCCGAAAT-AGGGTTTTTTT
1 TTTTTTTAAAGTAATAAAAATC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTT
* *
55235316 TAAGTTTATTTTAAAAACACAGAAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
65 TAA-TTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* *
55235381 ATAATAAAA-TACGGAAATAATATA
129 ATAATAAAATTA-GAAAATAGTATA
*
55235405 TTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
1 TTTTT-TT-AAAGTAATAAAAATCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
55235470 TTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
64 TT--AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
55235535 AAATAATAAAATTAGAAAATAGTAT-
127 AAATAATAAAATTAGAAAATAGTATA
*
55235560 TTTTTTT-AAGTAAT-AAAATCCGGAGAAAAAATACGAACAAAGGGC
1 TTTTTTTAAAGTAATAAAAATCGGGA-AAAAAATACGAACAAAGGGC
55235605 TAAAATACGA
Statistics
Matches: 460, Mismatches: 31, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
150 9 0.02
151 18 0.04
152 73 0.16
153 90 0.20
154 135 0.29
155 54 0.12
156 77 0.17
157 4 0.01
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (152 bp):
TTTTTTTAAAGTAATAAAAATCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTT
AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
AATAAAATTAGAAAATAGTATA
Found at i:55235566 original size:307 final size:304
Alignment explanation
Indices: 55234945--55235610 Score: 988
Period size: 307 Copynumber: 2.2 Consensus size: 304
55234935 GTTTAGTGTG
55234945 TTTTTTATTGAAAGTAATAAAATCCGGG-AAAAAATACGAACAAAGGGCCAAAATTAGGATTTTT
1 TTTTTT-TT-AAAGTAATAAAAT-CGGGAAAAAAATACGAACAAAGGGCCAAAATTAGGATTTTT
* *
55235009 TTAATTTATTTAAAAAATACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
63 TTAATTTATTTAAAAAACACACAAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* *
55235074 ATAAAAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGGGAAAAAAATATGAACA
128 ATAAAAAAATTAGAAAATAATATATTTTTTAAAAGTAATAAAATTCGGGGAAAAAAATACGAACA
*
55235139 GAGGGACGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
193 AAGGGACGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
*
55235204 ATAATGTACTAAAATAATGTAAAAATAATAAAAATTATAAAATAGTA
258 ATAATGTACTAAAATAATGTAAAAATAATAAAAATTAGAAAATAGTA
* * *
55235251 TATTTTTTTAAAG-AATAAAAATCTGGGAAAAAAATATGAACAAAGGGCCGAAA-TAGGGTTTTT
1 T-TTTTTTTAAAGTAAT-AAAATC-GGGAAAAAAATACGAACAAAGGGCCAAAATTA-GGATTTT
* * *
55235314 TTTAAGTTTATTTTAAAAACACAGAAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
62 TTTAA-TTTATTTAAAAAACACACAAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
* * *
55235379 AAATAATAAAA-TACGGAAATAATATATTTTTATTGAAAGTAATAAAATTC-GGGAAAAAAATAC
126 AAATAAAAAAATTA-GAAAATAATATA-TTTT-TTAAAAGTAATAAAATTCGGGGAAAAAAATAC
*
55235442 GAACAAAGGGCCGAAATAAGGGTTTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACAT
188 GAACAAAGGGACGAAATAAGGGTTTTTTTT--AATTTATTTAAAAAACACAGTAAATTAATACAT
55235507 TTCAAACATAATGTACTAAAATAATGT-AAAATAAT-AAAATTAGAAAATAGTA
251 TTCAAACATAATGTACTAAAATAATGTAAAAATAATAAAAATTAGAAAATAGTA
* *
55235559 TTTTTTTT-AAGTAATAAAATCCGGAGAAAAAATACGAACAAAGGGCTAAAAT
1 TTTTTTTTAAAGTAATAAAATCGGGA-AAAAAATACGAACAAAGGGCCAAAAT
55235611 ACGAACATAT
Statistics
Matches: 326, Mismatches: 20, Indels: 27
0.87 0.05 0.07
Matches are distributed among these distances:
304 4 0.01
305 17 0.05
306 70 0.21
307 89 0.27
308 61 0.19
309 25 0.08
310 60 0.18
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (304 bp):
TTTTTTTTAAAGTAATAAAATCGGGAAAAAAATACGAACAAAGGGCCAAAATTAGGATTTTTTTA
ATTTATTTAAAAAACACACAAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
AAAAAATTAGAAAATAATATATTTTTTAAAAGTAATAAAATTCGGGGAAAAAAATACGAACAAAG
GGACGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATA
ATGTACTAAAATAATGTAAAAATAATAAAAATTAGAAAATAGTA
Found at i:55235928 original size:47 final size:47
Alignment explanation
Indices: 55235837--55235928 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 47
55235827 AACATTTTAC
** *
55235837 ATTAAATCAAACTCAAACTTTAAATATTAAAAGGTAAATTTAACCAG
1 ATTAAATCAAACTCAAACTTTAAATATTAAAAACTAAATCTAACCAG
* * *
55235884 ATTAAATCAAACTCGAATTTTAGATA-TAAAAACTCAAATCTAACC
1 ATTAAATCAAACTCAAACTTTAAATATTAAAAACT-AAATCTAACC
55235929 CATATTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 6 0.16
47 32 0.84
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.29
Consensus pattern (47 bp):
ATTAAATCAAACTCAAACTTTAAATATTAAAAACTAAATCTAACCAG
Found at i:55246942 original size:39 final size:38
Alignment explanation
Indices: 55246875--55246961 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 38
55246865 AAGACATCAT
*
55246875 ATAATTTAGCATTTTTATATATTTTAAAG-ATTTTAAAA
1 ATAATTTA-CATTTTTATATATTTTAAAGAATTTGAAAA
55246913 ATAATTTA-ATTTTTAATATATTTTATAAAGAAATTTGAAAA
1 ATAATTTACATTTTT-ATATA-TTT-TAAAG-AATTTGAAAA
*
55246954 ATATTTTA
1 ATAATTTA
55246962 TAAAACTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 6 0.14
37 5 0.12
38 11 0.26
39 5 0.12
41 15 0.36
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (38 bp):
ATAATTTACATTTTTATATATTTTAAAGAATTTGAAAA
Found at i:55251627 original size:16 final size:18
Alignment explanation
Indices: 55251589--55251628 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
55251579 AATATGTGAA
55251589 TAATATTATTTAAAATTG
1 TAATATTATTTAAAATTG
55251607 T--TATT-TTTAAAATT-
1 TAATATTATTTAAAATTG
55251621 TAATATTA
1 TAATATTA
55251629 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 7
0.73 0.00 0.27
Matches are distributed among these distances:
14 1 0.05
15 9 0.47
16 8 0.42
18 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TAATATTATTTAAAATTG
Found at i:55251637 original size:18 final size:19
Alignment explanation
Indices: 55251614--55251649 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55251604 TTGTTATTTT
55251614 TAAAATTT-AATATTAAAA
1 TAAAATTTAAATATTAAAA
55251632 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
55251650 TAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTAAATATTAAAA
Found at i:55253275 original size:126 final size:126
Alignment explanation
Indices: 55253006--55253422 Score: 615
Period size: 126 Copynumber: 3.3 Consensus size: 126
55252996 TCAGGCCAAA
* * ** *
55253006 CAGGAGCTACTATAGCAAAAGCGCGTCCATATGGGAGCTTCTTTCAGTACTTTTGCTGAAAAAGC
1 CAGGAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
** *
55253071 ATCCTGCTTAAAGCG-TTTTGACACTATTTGCTCCCAAACGTCTACTCAAAATTATTGTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATT-TTTT
*
55253132 -AGGAGCTACTGTAGCAAAAACGCGTTCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
** *
55253196 ATAATGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTATACTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
** * **
55253257 CAGGAGCTACTGTAGCAAAAGTGCTTCCACGTGGGAGCTTCTTTCAGTACTTTTATTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* *
55253322 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTTGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
*
55253383 CAAGAGCTACTGTAGCAAAAGA-GCGTCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAA-ACGCGTCCACGTGGGAGCTT
55253423 TTTTAAATTA
Statistics
Matches: 262, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
125 75 0.29
126 187 0.71
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:55261887 original size:7 final size:7
Alignment explanation
Indices: 55261875--55261900 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55261865 AAGCTCAATT
55261875 AAATATA
1 AAATATA
55261882 AAATATA
1 AAATATA
55261889 AAATATA
1 AAATATA
55261896 AAATA
1 AAATA
55261901 GGTAATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:55262045 original size:20 final size:21
Alignment explanation
Indices: 55262020--55262062 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55262010 CATTTCGAGC
55262020 AATTTCTCCTT-TTTTTTTTT
1 AATTTCTCCTTGTTTTTTTTT
**
55262040 AATTTCTTTTTGTTTTTTTTT
1 AATTTCTCCTTGTTTTTTTTT
55262061 AA
1 AA
55262063 ATGTAGAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (21 bp):
AATTTCTCCTTGTTTTTTTTT
Found at i:55264086 original size:26 final size:25
Alignment explanation
Indices: 55264034--55264088 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
55264024 AATTTTAAAA
* * *
55264034 TATTTTTAAAATACTTTTTTATTTT
1 TATTTTTAAAATAATTTTTGATGTT
*
55264059 TATTTTTAAAATAAATTTTTGGTGTT
1 TATTTTTAAAAT-AATTTTTGATGTT
55264085 TATT
1 TATT
55264089 AAAAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (25 bp):
TATTTTTAAAATAATTTTTGATGTT
Found at i:55267632 original size:454 final size:454
Alignment explanation
Indices: 55266125--55267697 Score: 2214
Period size: 454 Copynumber: 3.5 Consensus size: 454
55266115 TTTTTCCTTC
* * * * ** * *
55266125 TTTTTTCTTCTCGTT-TTGCAGTGTTCAACTTTACTAATGGGCAACATAATGTTGTC-GAAGTGA
1 TTTTTTCTTCT-TTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTG-CAGAAGTGA
* * * * * *** * *
55266188 CCGAAGCTGGTTACGATG-CTTGCAACGCTGCAAAT-CCTGTATCTACGGGGAGCACCGGACCGG
64 CGGAAGATGCTTACGATGAC-TGCAACACTGCAAATGCC-ATATCTACTTTGACCACCGGTCCGG
* * * * * ** * ** * * *
55266251 CGAGGATTACGCTTAACAGGACAGGGGAGTACTACTTTATTTGTGGTATCCCTGGTCACTGTTCT
127 CAAGGATTACCCTTAACAAGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCC
* * * * * * * * * *
55266316 GCCGGCCAGAAGCTAAACGTGGAAGTACGAAATGGTAACACCACCGGCGGTGTTACTCCGTCGAC
192 GCCGGCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCC
* * * * *
55266381 GCCTGTAACTCCAACCACCACCACTTATACGGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTA
257 GCCTGTAACTCCAAGCACCACCACTTTTACGGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCA
* * *
55266446 ATAATGATGATTTTTATGAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGT
322 ATAATGATGATTTTTATGAGGATTGGGCTGATCATAAACACTTCGTTGTTGGGGATGTTTTAGGT
* * * * * * *
55266511 CAG-TTTCTTAA-GTCAACA-TTTGA-ATCGAA--AT--T-TG---ATGCTTTTTTTATCCAACT
387 CAGCTTT-TAAATTTAAAAATTTTGATAT-TAATTATGATATGTAAATGC-TTTTTGATCTAACT
55266564 GTTTGA
449 GTTTGA
* *
55266570 TTTTTTTCTT-TTCTTTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGA
1 -TTTTTTCTTCTT-TTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAAGTGA
55266634 CGGAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCA
64 CGGAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCA
* *
55266699 AGGATTACCCTTAACAAGACCGGTGACCATTACTTCATTTGCAGTGTCCCCGGTCATTGTTCCGC
129 AGGATTACCCTTAACAAGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCCGC
55266764 CGGCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCCGC
194 CGGCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCCGC
*
55266829 CTGTAACTCCAAGCACCACCACTTTTACAGTGGGTGACTCTACTGGTTGGCGTGTCCCTACC---
259 CTGTAACTCCAAGCACCACCACTTTTACGGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCAAT
55266891 AATGATGATTTTTATGAGGATTGGGCTGATCATAAACACTTCGTTGTTGGGGATGTTTTAGGTCA
324 AATGATGATTTTTATGAGGATTGGGCTGATCATAAACACTTCGTTGTTGGGGATGTTTTAGGTCA
*
55266956 GCTTTTAAATTTAAAAATTTTGATATTAATTATGATATGTAAATGTTTTTTGATCTAACTGTTTG
389 GCTTTTAAATTTAAAAATTTTGATATTAATTATGATATGTAAATGCTTTTTGATCTAACTGTTTG
55267021 A
454 A
55267022 TTTTTTCTTCTTTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAAGTGACG
1 TTTTTTCTTCTTTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAAGTGACG
55267087 GAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCAAG
66 GAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCAAG
* * *
55267152 GATTACCCTTAACAAGACCGGTGACCATTACTTCATTTGCAGTGTCCCCGGTCATTGTTCAGCCG
131 GATTACCCTTAACAAGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCCGCCG
55267217 GCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCCGCCT
196 GCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCCGCCT
*
55267282 GTAACTCCAAGCACCACCACTTTTACGGTGGGTGACTCTACCGGTTGGCGTGTCCCTACCAATAA
261 GTAACTCCAAGCACCACCACTTTTACGGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCAATAA
*
55267347 TGATGATTTTTATGAGGATTGGGCTGATCATAAAGACTTCGTTGTTGGGGATGTTTTAGGTCAGC
326 TGATGATTTTTATGAGGATTGGGCTGATCATAAACACTTCGTTGTTGGGGATGTTTTAGGTCAGC
*
55267412 TTTTAAATTTAAAAATTTTGATATTAATTATGATATGTAAATGCTGTTTGATCTAACTGTTTGA
391 TTTTAAATTTAAAAATTTTGATATTAATTATGATATGTAAATGCTTTTTGATCTAACTGTTTGA
* *
55267476 TTTTTTCTTCTTTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACT
1 TTTTTTCTTCTTTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAAGTGACG
* * * *
55267541 GAAGATGGTTACGACGACTGCAACGCTGCAAATGCCATATCTACTTTGACCACCGGCCCGGCAAG
66 GAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCAAG
* *
55267606 GATTACCCTCAACAGGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCCGCCG
131 GATTACCCTTAACAAGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCCGCCG
* * *
55267671 GCCAAAAACTCAAGGTCGAAGTCCGAA
196 GCCAAAAGCTCAAGGTTGAAGTTCGAA
55267698 ATGGCAACCG
Statistics
Matches: 1023, Mismatches: 83, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
443 66 0.06
444 7 0.01
445 11 0.01
446 260 0.25
447 5 0.00
449 1 0.00
450 2 0.00
451 312 0.30
452 20 0.02
453 3 0.00
454 336 0.33
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (454 bp):
TTTTTTCTTCTTTTCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAAGTGACG
GAAGATGCTTACGATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCGGCAAG
GATTACCCTTAACAAGACCGGTGACCACTACTTCATTTGCAGTATCCCCGGTCATTGTTCCGCCG
GCCAAAAGCTCAAGGTTGAAGTTCGAACTGGTAACACCACCGGTGGCGTTGCTCCGTCGCCGCCT
GTAACTCCAAGCACCACCACTTTTACGGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCAATAA
TGATGATTTTTATGAGGATTGGGCTGATCATAAACACTTCGTTGTTGGGGATGTTTTAGGTCAGC
TTTTAAATTTAAAAATTTTGATATTAATTATGATATGTAAATGCTTTTTGATCTAACTGTTTGA
Found at i:55269316 original size:19 final size:20
Alignment explanation
Indices: 55269294--55269357 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
55269284 AATAAACACC
55269294 AAAAAA-AAATTTAAAAATA
1 AAAAAAGAAATTTAAAAATA
* *
55269313 AAAAAAGTATTTTAAAAATA
1 AAAAAAGAAATTTAAAAATA
* *
55269333 AAAAAAGTATTTTAAAAATA
1 AAAAAAGAAATTTAAAAATA
55269353 AAAAA
1 AAAAA
55269358 TAAAATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 6 0.14
20 36 0.86
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAAGAAATTTAAAAATA
Found at i:55269326 original size:20 final size:20
Alignment explanation
Indices: 55269303--55269357 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
55269293 CAAAAAAAAA
55269303 TTTAAAAATAAAAAAAGTAT
1 TTTAAAAATAAAAAAAGTAT
55269323 TTTAAAAATAAAAAAAGTAT
1 TTTAAAAATAAAAAAAGTAT
55269343 TTTAAAAATAAAAAA
1 TTTAAAAATAAAAAA
55269358 TAAAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
TTTAAAAATAAAAAAAGTAT
Found at i:55271821 original size:18 final size:17
Alignment explanation
Indices: 55271780--55271821 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
55271770 TATTCAATAA
55271780 TTTTAAATATTAATTTT
1 TTTTAAATATTAATTTT
55271797 TTATTAAA-ATTAATATATT
1 TT-TTAAATATTAAT-T-TT
55271816 TTTTAA
1 TTTTAA
55271822 TATAACCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 10 0.45
19 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATATTAATTTT
Found at i:55273327 original size:36 final size:37
Alignment explanation
Indices: 55273280--55273465 Score: 194
Period size: 39 Copynumber: 4.9 Consensus size: 37
55273270 CACCGCCACG
* * *
55273280 CCGAGCCCCACCCCGCATGGAACTTCAAG-TCCTCGT
1 CCGAGCGCCACCCCGCCTGGAACTTCAAGCTCCTCCT
* *
55273316 CCGAGCGCCACCCCTCGTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCCACCCCGCCTGGAACTTCAAG--CTCCTCCT
* *
55273355 CCGAGAGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCCACCCCGCCTGGAACTTCAAG--CTCCTCCT
*
55273394 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCCACCCCGCCTGGAACTTCAAG--CTCCTCCT
* ** * *
55273433 CCGAGCGCCGCTACGCCTGGAACTCCGAGCTCC
1 CCGAGCGCCACCCCGCCTGGAACTTCAAGCTCC
55273466 AGCTCGCGTG
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
36 26 0.20
37 4 0.03
39 102 0.77
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.18
Consensus pattern (37 bp):
CCGAGCGCCACCCCGCCTGGAACTTCAAGCTCCTCCT
Found at i:55273456 original size:39 final size:39
Alignment explanation
Indices: 55273280--55273440 Score: 229
Period size: 39 Copynumber: 4.2 Consensus size: 39
55273270 CACCGCCACG
* * * *
55273280 CCGAGCCCCACCCCGCATGGAACTTCAAG---TCCTCGT
1 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
* * *
55273316 CCGAGCGCCACCCCTCGTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
*
55273355 CCGAGAGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
55273394 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
1 CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
55273433 CCGAGCGC
1 CCGAGCGC
55273441 CGCTACGCCT
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
36 26 0.23
39 87 0.77
ACGTcount: A:0.17, C:0.45, G:0.19, T:0.19
Consensus pattern (39 bp):
CCGAGCGCTACCCCGCCTGGAACTTCAAGTCCTCCTCCT
Found at i:55273477 original size:24 final size:24
Alignment explanation
Indices: 55273431--55273480 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
55273421 AGTCCTCCTC
55273431 CTCCGAGCGCCGCTACGCCTGGAA
1 CTCCGAGCGCCGCTACGCCTGGAA
* *
55273455 CTCCGAGCTCCAGCT-CGCGTGGAA
1 CTCCGAGCGCC-GCTACGCCTGGAA
55273479 CT
1 CT
55273481 TCAAGTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (24 bp):
CTCCGAGCGCCGCTACGCCTGGAA
Found at i:55275479 original size:22 final size:23
Alignment explanation
Indices: 55275436--55275480 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
55275426 AAGTCGGATT
* **
55275436 AAAAATTATTAAAATTTTTTTAA
1 AAAAAATATTAAAATTAGTTTAA
55275459 AAAAAATA-TAAAATTAGTTTAA
1 AAAAAATATTAAAATTAGTTTAA
55275481 CTGATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAAATATTAAAATTAGTTTAA
Found at i:55278497 original size:21 final size:21
Alignment explanation
Indices: 55278473--55278525 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
55278463 CGCTGTTTCT
* *
55278473 AATCTCACTGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
55278494 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
55278515 AATCTCACCGC
1 AATCTCACCGC
55278526 CACCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:55280505 original size:2 final size:2
Alignment explanation
Indices: 55280498--55280539 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
55280488 AAAATAGACC
55280498 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
55280540 TAAAATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55282358 original size:26 final size:25
Alignment explanation
Indices: 55282311--55282367 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
55282301 AATTAAAGCA
*
55282311 AATTAACATTATTCAAAATAATAACT
1 AATTAACATAATTCAAAATAAT-ACT
* *
55282337 AATTAACATAATT-AAATTTAATATT
1 AATTAACATAATTCAAA-ATAATACT
55282362 AATTAA
1 AATTAA
55282368 GTAATGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTAACATAATTCAAAATAATACT
Found at i:55282844 original size:29 final size:29
Alignment explanation
Indices: 55282810--55282866 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
55282800 TTTGATTCTT
*
55282810 CTTAATAATATAAAGGCTAAATTGATCCA
1 CTTAATAATAGAAAGGCTAAATTGATCCA
* *
55282839 CTTAATAATGGAATGGCTAAATTGATCC
1 CTTAATAATAGAAAGGCTAAATTGATCC
55282867 CATCCCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (29 bp):
CTTAATAATAGAAAGGCTAAATTGATCCA
Found at i:55284898 original size:22 final size:21
Alignment explanation
Indices: 55284838--55284899 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
55284828 TTAAAAATGA
* *
55284838 TAAAAATT-TAATATAATTATT
1 TAAAAATTATAA-ATTATTATG
**
55284859 TAAAAATTATATTTTTATTATCG
1 TAAAAATTATA-AATTATTAT-G
55284882 TAAAAATTATAAATTATT
1 TAAAAATTATAAATTATT
55284900 TTTTTGGGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.25
22 13 0.41
23 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAAAATTATAAATTATTATG
Found at i:55285626 original size:5 final size:5
Alignment explanation
Indices: 55285616--55285641 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55285606 ATTAAAATTT
55285616 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
55285642 TTGCAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:55288488 original size:17 final size:16
Alignment explanation
Indices: 55288459--55288500 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
55288449 TATAAATTTC
55288459 ATATA-TTTTA-TTTT
1 ATATATTTTTATTTTT
55288473 ATGATATTTTTAATTTTT
1 AT-ATATTTTT-ATTTTT
55288491 ATATATTTTT
1 ATATATTTTT
55288501 TTACAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 4 0.17
17 9 0.38
18 6 0.25
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
ATATATTTTTATTTTT
Found at i:55289990 original size:42 final size:42
Alignment explanation
Indices: 55289943--55290024 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
55289933 TATCCAGCCA
* *
55289943 TGCCACCATTATATAATTACAAGCAATTAGCCCGAAATACTT
1 TGCCACCATTATATAATTACAAACAATTAGCCCCAAATACTT
* * *
55289985 TGCCACCCTTATGTAATTACAAACAATTATCCCCAAATAC
1 TGCCACCATTATATAATTACAAACAATTAGCCCCAAATAC
55290025 AATTACTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.28
Consensus pattern (42 bp):
TGCCACCATTATATAATTACAAACAATTAGCCCCAAATACTT
Found at i:55290986 original size:3 final size:3
Alignment explanation
Indices: 55290973--55291011 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
55290963 AACATGAACG
* * *
55290973 ATA AAA ATA ATA ATA ATA ATA CTA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55291012 TGGGTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:55292609 original size:10 final size:10
Alignment explanation
Indices: 55292596--55292622 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55292586 TTTTTTTAAA
55292596 ATATATATAC
1 ATATATATAC
55292606 ATATATATAC
1 ATATATATAC
55292616 ATATATA
1 ATATATA
55292623 AATGTGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:55293298 original size:40 final size:40
Alignment explanation
Indices: 55293243--55293369 Score: 213
Period size: 40 Copynumber: 3.2 Consensus size: 40
55293233 AAATTAAATC
55293243 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
55293283 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
** *
55293323 TCTAAGATTGCATATCATATCTAGGATTGC--ATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
55293361 TCTAAGATT
1 TCTAAGATT
55293370 GCATATCCTC
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
38 17 0.20
40 67 0.80
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (40 bp):
TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
Found at i:55293343 original size:59 final size:60
Alignment explanation
Indices: 55293243--55293375 Score: 209
Period size: 59 Copynumber: 2.2 Consensus size: 60
55293233 AAATTAAATC
*
55293243 TCTAAGATT--ATATATCATATCTAAGATTGCATATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTGCA-ATATCATATCTAAGATTACATATCATA
* *
55293302 TCTAAGATTGCATATATCATATCTAAGATTGC-ATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTGCAATATCATATCTAAGATTACATATCATA
55293361 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
55293376 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
59 48 0.70
61 21 0.30
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (60 bp):
TCTAAGATTGCATATATCATATCTAAGATTGCAATATCATATCTAAGATTACATATCATA
Found at i:55293370 original size:19 final size:19
Alignment explanation
Indices: 55293243--55293376 Score: 187
Period size: 19 Copynumber: 6.8 Consensus size: 19
55293233 AAATTAAATC
**
55293243 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
55293262 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
55293283 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
55293302 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
55293323 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55293342 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55293361 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55293377 CTCAAAAATT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
19 67 0.65
21 36 0.35
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55298827 original size:25 final size:25
Alignment explanation
Indices: 55298772--55298828 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
55298762 TTTACATTTT
*
55298772 TATATTACATATACAAATAATTATA
1 TATATTACATATAAAAATAATTATA
*
55298797 TTTATTGAC-TATAAAAATAAATTA-A
1 TATATT-ACATATAAAAAT-AATTATA
55298822 TATATTA
1 TATATTA
55298829 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 7 0.26
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATTACATATAAAAATAATTATA
Found at i:55299058 original size:11 final size:11
Alignment explanation
Indices: 55299042--55299066 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55299032 TTTTTTACCG
55299042 AAATAATATAA
1 AAATAATATAA
55299053 AAATAATATAA
1 AAATAATATAA
55299064 AAA
1 AAA
55299067 AAGGAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATATAA
Found at i:55306292 original size:2 final size:2
Alignment explanation
Indices: 55306285--55306325 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
55306275 NNNNNNNAGT
55306285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55306326 GGTACAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55307699 original size:2 final size:2
Alignment explanation
Indices: 55307692--55307725 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55307682 TTATAAGCGC
55307692 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
55307726 TTACCGCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55310714 original size:15 final size:16
Alignment explanation
Indices: 55310693--55310742 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
55310683 TTAATTTATT
55310693 TAATAAAATTATAAAA
1 TAATAAAATTATAAAA
55310709 -AATAAAAATT-TAAAA
1 TAAT-AAAATTATAAAA
* *
55310724 TTATATAATTATAATAA
1 TAATAAAATTATAA-AA
55310741 TA
1 TA
55310743 TTTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 13 0.48
16 11 0.41
17 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAAAATTATAAAA
Found at i:55316618 original size:6 final size:6
Alignment explanation
Indices: 55316607--55316638 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
55316597 GGTACTGAGA
55316607 CACATG CACATG CACATG CACATG CACATG CA
1 CACATG CACATG CACATG CACATG CACATG CA
55316639 AAGGGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16
Consensus pattern (6 bp):
CACATG
Found at i:55330499 original size:18 final size:18
Alignment explanation
Indices: 55330478--55330533 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
55330468 TTTAAATTTG
*
55330478 ATTATTATTTAAAATAT-T
1 ATTATT-TTTAAAAAATAT
55330496 ATTATTTTTTATAAAAATAT
1 ATTA-TTTTTA-AAAAATAT
55330516 ATATATTTTTAAAAAATA
1 AT-TATTTTTAAAAAATA
55330534 GACTTACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 8 0.24
19 14 0.42
20 9 0.27
21 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATTTTTAAAAAATAT
Found at i:55330514 original size:21 final size:19
Alignment explanation
Indices: 55330488--55330533 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
55330478 ATTATTATTT
55330488 AAAATAT-TATTATTTTTTATA
1 AAAATATATA-TA-TTTTTA-A
55330509 AAAATATATATATTTTTAA
1 AAAATATATATATTTTTAA
55330528 AAAATA
1 AAAATA
55330534 GACTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 9 0.38
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATATATATATTTTTAA
Found at i:55330530 original size:19 final size:21
Alignment explanation
Indices: 55330488--55330533 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
55330478 ATTATTATTT
55330488 AAAATATTATTATTTTTTATA
1 AAAATATTATTATTTTTTATA
55330509 AAAATA-TA-TATATTTTTA-A
1 AAAATATTATTAT-TTTTTATA
55330528 AAAATA
1 AAAATA
55330534 GACTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATATTATTATTTTTTATA
Found at i:55347807 original size:12 final size:14
Alignment explanation
Indices: 55347790--55347822 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
55347780 TTTATCGTAT
55347790 ATAAAAATA-AAA-
1 ATAAAAATAGAAAC
55347802 ATAAAAATAGAAAC
1 ATAAAAATAGAAAC
55347816 ATAAAAA
1 ATAAAAA
55347823 AACTCTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (14 bp):
ATAAAAATAGAAAC
Found at i:55352456 original size:91 final size:91
Alignment explanation
Indices: 55352345--55352528 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
55352335 TGACAAGTTC
55352345 GTTAAACTGTGGAAGTGATTCGATCGCTTAGCTTGTGGCTGTTGTGGTTGCTCGATATGTCCGTT
1 GTTAAACTGTGGAAGTGATTCGATCGCTTAGCTTGTGGCTGTTGTGGTTGCTCGATATGTCCGTT
55352410 TTATGTGGTTTGTCTCGGCTCCCTGT
66 TTATGTGGTTTGTCTCGGCTCCCTGT
55352436 GTTAAACTGTGGAAGTGATTCGATCGCTTAGCTTGTGGCTGTTGTGGTTGCTCGATATGTCCGTT
1 GTTAAACTGTGGAAGTGATTCGATCGCTTAGCTTGTGGCTGTTGTGGTTGCTCGATATGTCCGTT
55352501 TTATGTGGTTTGTCTCGGCTCCCTGT
66 TTATGTGGTTTGTCTCGGCTCCCTGT
55352527 GT
1 GT
55352529 AACCCTAGTA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.12, C:0.17, G:0.30, T:0.41
Consensus pattern (91 bp):
GTTAAACTGTGGAAGTGATTCGATCGCTTAGCTTGTGGCTGTTGTGGTTGCTCGATATGTCCGTT
TTATGTGGTTTGTCTCGGCTCCCTGT
Found at i:55358439 original size:9 final size:9
Alignment explanation
Indices: 55358425--55358452 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55358415 TTTTGTTACA
55358425 ACAATTAAT
1 ACAATTAAT
55358434 ACAATTAAT
1 ACAATTAAT
55358443 ACAATTAAT
1 ACAATTAAT
55358452 A
1 A
55358453 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:55358474 original size:68 final size:68
Alignment explanation
Indices: 55358395--55358595 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 68
55358385 TCAAGTTTGT
*
55358395 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
55358460 AAA
66 AAA
55358463 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
55358519 AAA
66 AAA
55358522 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
55358585 AAT
66 AAA
55358588 TTTACTAA
1 TTTACTAA
55358596 CAATTAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:55358605 original size:16 final size:16
Alignment explanation
Indices: 55358584--55358625 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
55358574 AATAATTTGA
*
55358584 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
55358600 TAATTTTAATATCAAT
1 TAATTTTAATAACAAT
*
55358616 TAGTTTTAAT
1 TAATTTTAAT
55358626 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:55358609 original size:22 final size:21
Alignment explanation
Indices: 55358584--55358651 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 21
55358574 AATAATTTGA
55358584 TAATTTTACTAACAATTAATTT
1 TAATTTTA-TAACAATTAATTT
*
55358606 TAA---TAT--CAATTAGTTT
1 TAATTTTATAACAATTAATTT
* *
55358622 TAATTTTATTAAAAAATAATTT
1 TAATTTTA-TAACAATTAATTT
55358644 TAATTTTA
1 TAATTTTA
55358652 ATTTTAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 12 0.33
18 1 0.03
19 4 0.11
20 1 0.03
22 18 0.50
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (21 bp):
TAATTTTATAACAATTAATTT
Found at i:55358616 original size:59 final size:63
Alignment explanation
Indices: 55358426--55358617 Score: 204
Period size: 59 Copynumber: 3.1 Consensus size: 63
55358416 TTTGTTACAA
* *
55358426 CAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATC-A--AATGTTAGAT-T
1 CAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAATTAATTTTATATAT
**
55358485 TTATTACA-ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATT
1 CAATTA-ATACAATTAATACAATTAATAATTTGATAAATTTACTAATC-AA--TTA-ATTTTA-T
* *
55358549 ACAA
60 ATAT
*
55358553 CAATTAATACAATT-A-ACAATTAATAATTTGATAATTTTACTAA-CAATTAATTTTA-ATAT
1 CAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAATTAATTTTATATAT
55358612 CAATTA
1 CAATTA
55358618 GTTTTAATTT
Statistics
Matches: 111, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
59 51 0.46
60 1 0.01
61 7 0.06
62 3 0.03
64 2 0.02
65 2 0.02
66 32 0.29
67 3 0.03
68 10 0.09
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.41
Consensus pattern (63 bp):
CAATTAATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAATTAATTTTATATAT
Found at i:55359119 original size:30 final size:30
Alignment explanation
Indices: 55359083--55359141 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
55359073 GAGTTTGGAC
55359083 GTGCGGTGCGTTTACTTGCTGTTAGTGTAT
1 GTGCGGTGCGTTTACTTGCTGTTAGTGTAT
55359113 GTGCGGTGCGTTTACTTGCTGTTAGTGTA
1 GTGCGGTGCGTTTACTTGCTGTTAGTGTA
55359142 AAAATAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.14, G:0.34, T:0.42
Consensus pattern (30 bp):
GTGCGGTGCGTTTACTTGCTGTTAGTGTAT
Found at i:55360946 original size:14 final size:14
Alignment explanation
Indices: 55360927--55360956 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55360917 AAGATACTGC
55360927 TTCCAGTAAAGGAG
1 TTCCAGTAAAGGAG
*
55360941 TTCCAGTAATGGAG
1 TTCCAGTAAAGGAG
55360955 TT
1 TT
55360957 AACCAAGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (14 bp):
TTCCAGTAAAGGAG
Found at i:55364365 original size:26 final size:25
Alignment explanation
Indices: 55364331--55364386 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
55364321 TAGATAAAAT
*
55364331 AAAATGTTAAAAACTA-AAATATATAA
1 AAAAAGTTAAAAACTATAAA-AT-TAA
* *
55364357 AAAAAGTTATAAATTATAAAATTAA
1 AAAAAGTTAAAAACTATAAAATTAA
55364382 AAAAA
1 AAAAA
55364387 ATATATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.31
26 15 0.58
27 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAGTTAAAAACTATAAAATTAA
Found at i:55365352 original size:4 final size:4
Alignment explanation
Indices: 55365343--55365367 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55365333 TTGATTTAAG
55365343 TCCA TCCA TCCA TCCA TCCA TCCA T
1 TCCA TCCA TCCA TCCA TCCA TCCA T
55365368 AAACAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCA
Found at i:55371510 original size:4 final size:4
Alignment explanation
Indices: 55371501--55371542 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
55371491 ACGTATATAG
* * *
55371501 ATAC ATAC ATAG ATAC ATAC ATAC ATAC ATAT ATGC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
55371543 TCATTCATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:55371512 original size:12 final size:12
Alignment explanation
Indices: 55371497--55371531 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
55371487 AAATACGTAT
55371497 ATAGATACATAC
1 ATAGATACATAC
55371509 ATAGATACATAC
1 ATAGATACATAC
*
55371521 ATACATACATA
1 ATAGATACATA
55371532 TATGCATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (12 bp):
ATAGATACATAC
Found at i:55371551 original size:20 final size:20
Alignment explanation
Indices: 55371501--55371553 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
55371491 ACGTATATAG
* *
55371501 ATACATACATAGATACATAC
1 ATACATACATATATGCATAC
55371521 ATACATACATATATGCATAC
1 ATACATACATATATGCATAC
* *
55371541 ATTCATTCATATA
1 ATACATACATATA
55371554 AACCAGCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (20 bp):
ATACATACATATATGCATAC
Found at i:55372200 original size:3 final size:3
Alignment explanation
Indices: 55372194--55372238 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
55372184 ACAACAGGTC
55372194 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
55372239 ATAGAAGAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:55372543 original size:20 final size:21
Alignment explanation
Indices: 55372506--55372545 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55372496 GTCCCTTTAT
*
55372506 TTATTCTAAAATTTACAATTA
1 TTATACTAAAATTTACAATTA
55372527 TTATACTAAAA-TTACAATT
1 TTATACTAAAATTTACAATT
55372546 TAATCCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATACTAAAATTTACAATTA
Found at i:55380191 original size:16 final size:18
Alignment explanation
Indices: 55380166--55380206 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55380156 GCTTAATTTC
55380166 TTTT-AAAAATT-T-AAT
1 TTTTAAAAAATTATAAAT
55380181 TTTTAAAAAATTATAAAT
1 TTTTAAAAAATTATAAAT
*
55380199 TTGTAAAA
1 TTTTAAAA
55380207 CGTTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 1 0.05
18 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTTAAAAAATTATAAAT
Found at i:55380231 original size:18 final size:18
Alignment explanation
Indices: 55380178--55380234 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
55380168 TTAAAAATTT
*
55380178 AATTTTTAAAAA-ATTATA
1 AATTTATAAAAATATTA-A
* *
55380196 AATTTGTAAAACGTTATTAA
1 AATTTATAAAA--ATATTAA
55380216 AATTTATAAAAATATTAA
1 AATTTATAAAAATATTAA
55380234 A
1 A
55380235 TAAAGTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 17 0.53
20 11 0.34
21 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
AATTTATAAAAATATTAA
Found at i:55393133 original size:42 final size:42
Alignment explanation
Indices: 55393068--55393226 Score: 273
Period size: 42 Copynumber: 3.8 Consensus size: 42
55393058 CCAAAGTGCT
*
55393068 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATGAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
* *
55393110 TTTTGTTTTCTCCAAAACATGTTAAGTTGAATTAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
*
55393152 TTTTGTTTTCTCCGAAACGTGTTAATTTGAATTAAATTAGCA
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
*
55393194 TTTTGTTTTCTCCGCAACGTGTTAAGTTGAATT
1 TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATT
55393227 CAAAGAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 109 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTTGTTTTCTCCGAAACGTGTTAAGTTGAATTAAATTAGCA
Found at i:55398379 original size:2 final size:2
Alignment explanation
Indices: 55398372--55398401 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55398362 AAGGTGTAGG
55398372 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
55398402 GACAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55398453 original size:2 final size:2
Alignment explanation
Indices: 55398446--55398471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55398436 AAGGTGTAGG
55398446 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
55398472 TCTTATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55401834 original size:22 final size:22
Alignment explanation
Indices: 55401790--55401834 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55401780 TTGTCTTAAC
* *
55401790 AAAACATTGTTCTTCTTGTCTA
1 AAAACATTGTTCTGCTTGGCTA
*
55401812 AAAACATTGTTCTGGTTGGCTA
1 AAAACATTGTTCTGCTTGGCTA
55401834 A
1 A
55401835 GATTGTATAC
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:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (22 bp):
AAAACATTGTTCTGCTTGGCTA
Found at i:55402349 original size:26 final size:26
Alignment explanation
Indices: 55402286--55402349 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
55402276 AGTTCTTCAT
55402286 TACTTTTGAAAAATATTTTTAAAAAG
1 TACTTTTGAAAAATATTTTTAAAAAG
* * * *
55402312 TGC-TGTGAAAAAATATTTTTGAGAAG
1 TACTTTTG-AAAAATATTTTTAAAAAG
55402338 TACTTTTGAAAA
1 TACTTTTGAAAA
55402350 GTTTGGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.10
26 24 0.80
27 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (26 bp):
TACTTTTGAAAAATATTTTTAAAAAG
Found at i:55404150 original size:15 final size:15
Alignment explanation
Indices: 55404130--55404160 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55404120 ACTAGAAGCC
55404130 TCGGTTTAAGATTGT
1 TCGGTTTAAGATTGT
55404145 TCGGTTTAAGATTGT
1 TCGGTTTAAGATTGT
55404160 T
1 T
55404161 TGAGTATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (15 bp):
TCGGTTTAAGATTGT
Found at i:55404331 original size:20 final size:19
Alignment explanation
Indices: 55404297--55404361 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
55404287 TGTTCAGAGA
55404297 TTTTAATTCAATTTATAAT
1 TTTTAATTCAATTTATAAT
** * *
55404316 TTTTTTTTGCAGTTTATAAA
1 TTTTAATT-CAATTTATAAT
55404336 TTTTAATTCAATTTATAAT
1 TTTTAATTCAATTTATAAT
55404355 TTTTAAT
1 TTTTAAT
55404362 ATGTGCTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTAATTCAATTTATAAT
Found at i:55404372 original size:39 final size:39
Alignment explanation
Indices: 55404296--55404372 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
55404286 TTGTTCAGAG
* * *
55404296 ATTTTAATTCAATTTATAATTTTTTTTTGCAGTTTATAA
1 ATTTTAATTCAATTTATAATTTTTATATGCAGCTTATAA
*
55404335 ATTTTAATTCAATTTATAATTTTTAATATG-TGCTTATA
1 ATTTTAATTCAATTTATAATTTTT-ATATGCAGCTTATA
55404373 TAGAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 30 0.91
40 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (39 bp):
ATTTTAATTCAATTTATAATTTTTATATGCAGCTTATAA
Found at i:55405508 original size:26 final size:24
Alignment explanation
Indices: 55405478--55405536 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 24
55405468 AAATGCATAT
*
55405478 ATATATATATTATAAAAAACATGCA
1 ATATATATA-TAAAAAAAACATGCA
*
55405503 AGTATACTAGATAAAAAAAACATGCA
1 A-TATA-TATATAAAAAAAACATGCA
55405529 ATATATAT
1 ATATATAT
55405537 GTATTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 5 0.17
26 19 0.66
27 3 0.10
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (24 bp):
ATATATATATAAAAAAAACATGCA
Found at i:55407149 original size:44 final size:44
Alignment explanation
Indices: 55407096--55407630 Score: 574
Period size: 44 Copynumber: 12.1 Consensus size: 44
55407086 AAGACTTATA
* * *
55407096 TCTTCGATCTACTTCACACTAATACATGAAGACAAGA-CTTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC-TGCTT
* *
55407140 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCGGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
55407184 TCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * ***
55407228 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAT
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCT-T
* *
55407274 T-TTTGATCTACTTCACGCCAATACATGAGGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
55407317 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * ***
55407361 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAT
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCT-T
**
55407407 T-TTTTATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
55407450 TCTTCGATCCACTTCACGTCAATCCATGAAGGCAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *** *
55407494 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
55407539 T-TTCTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTC-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
55407583 TCTTCGATCCACTTCACGCCAATCCATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
55407627 TCTT
1 TCTT
55407631 TGCAACCTGC
Statistics
Matches: 401, Mismatches: 80, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
43 4 0.01
44 300 0.75
45 93 0.23
46 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:55407288 original size:89 final size:88
Alignment explanation
Indices: 55407101--55407625 Score: 449
Period size: 89 Copynumber: 5.9 Consensus size: 88
55407091 TTATATCTTC
* * * * ** * * *
55407101 GATCTACTTCACACTAATACATGAAGACAAGA-CTTGCTATCTTTGATCTACTTC-ACGCCAATA
1 GATCTACTTCACGCCAATACATGAAGACAAGATC-TGTTTTCTTCAATCTACTTCGCCACCAGTA
* *
55407164 CATGAAGACAAGATCGGCTTTCTTT
65 CAGGAAGACAAGATCTGCTTT-TTT
* * *
55407189 GATCTACTTCATGCCAATACATGAAGACAAGATCCGTTTTCTTCAATCTACTTCGCCACCAGTAT
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTAC
*
55407254 GGGAAGACAAGATCTGCTATTTTT
66 AGGAAGACAAGATCTGCT-TTTTT
* * *
55407278 GATCTACTTCACGCCAATACATGAGGACAAGATCTGCTTTCTTCGATCTACTTCATGCCA--A-T
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTC--GCCACCAGT
*
55407340 ACATGAAGACAAGATCTG-TTTTCTT
64 ACAGGAAGACAAGATCTGCTTTT-TT
* * * * *** * * *
55407365 CAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATTT-TT-TATCTACTTC-ACGCCA
1 -GATCTACTTC-ACGCCAATACATGAAGACAAGATCTG-T-TTTCTTCAATCTACTTCGCCACCA
* * *
55407427 ATACATGAAGACAAGATCTGCTTTCTTC
62 GTACAGGAAGACAAGATCTGCTTT-TTT
* * * * *
55407455 GATCCACTTCACGTCAATCCATGAAGGCAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTAT
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTAC
* *
55407520 GGGAAGACAAGATCTGCTATTTCT
66 AGGAAGACAAGATCTGCT-TTTTT
* * * * * * *
55407544 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCACTTC-ACGCCAATCC
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTAC
*
55407608 ATGAAGACAAGATCTGCT
66 AGGAAGACAAGATCTGCT
55407626 ATCTTTGCAA
Statistics
Matches: 348, Mismatches: 70, Indels: 38
0.76 0.15 0.08
Matches are distributed among these distances:
86 7 0.02
87 6 0.02
88 117 0.34
89 200 0.57
90 10 0.03
91 8 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (88 bp):
GATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTAC
AGGAAGACAAGATCTGCTTTTTT
Found at i:55407361 original size:133 final size:133
Alignment explanation
Indices: 55407123--55407623 Score: 851
Period size: 133 Copynumber: 3.8 Consensus size: 133
55407113 ACTAATACAT
* *
55407123 GAAGACAAGA-CTTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCGGCTTTCT
1 GAAGACAAGATC-TGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
* * * *
55407187 TTGATCTACTTCATGCCAATACATGAAGACAAGATCCGTTTTCTTCAATCTACTTCGCCACCAGT
65 TCGATCCACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGT
55407252 ATGG
130 ATGG
*
55407256 GAAGACAAGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAGGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* *
55407321 CGATCTACTTCATGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTA
66 CGATCCACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTA
55407386 TGG
131 TGG
*
55407389 GAAGACAAGATCTGCTATTTTTTATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* * *
55407454 CGATCCACTTCACGTCAATCCATGAAGGCAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTA
66 CGATCCACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTA
55407519 TGG
131 TGG
*
55407522 GAAGACAAGATCTGCTATTTCTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
*
55407587 CGATCCACTTCACGCCAATCCATGAAGACAAGATCTG
66 CGATCCACTTCACGCCAATACATGAAGACAAGATCTG
55407624 CTATCTTTGC
Statistics
Matches: 351, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
133 350 1.00
134 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (133 bp):
GAAGACAAGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
CGATCCACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGCCACCAGTA
TGG
Found at i:55411554 original size:20 final size:20
Alignment explanation
Indices: 55411514--55411554 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55411504 GGAATGCCAC
*
55411514 ACACACATATATATATATAT
1 ACACACATATATATACATAT
* *
55411534 ACACACATGTATATACGTAT
1 ACACACATATATATACATAT
55411554 A
1 A
55411555 TGTTCCCTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (20 bp):
ACACACATATATATACATAT
Found at i:55417498 original size:21 final size:19
Alignment explanation
Indices: 55417457--55417499 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
55417447 TTTAGTTAAC
**
55417457 AATCCTCATTTTTTGTCTA
1 AATCCTCATTTTTTGAATA
55417476 AATCCTTCGATTTTTTGAATA
1 AATCC-TC-ATTTTTTGAATA
55417497 AAT
1 AAT
55417500 TTTCAAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (19 bp):
AATCCTCATTTTTTGAATA
Found at i:55420772 original size:28 final size:28
Alignment explanation
Indices: 55420740--55420810 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
55420730 AATAAAAAAA
* * *
55420740 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-AATTTTTTCAT
55420768 TTACCAAAATATATATAAATTTTTTCAT
1 TTACCAAAATATATATAAATTTTTTCAT
55420796 TTACCAAAATATATA
1 TTACCAAAATATATA
55420811 AAAAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.46
Consensus pattern (28 bp):
TTACCAAAATATATATAAATTTTTTCAT
Found at i:55420912 original size:27 final size:27
Alignment explanation
Indices: 55420872--55420977 Score: 158
Period size: 27 Copynumber: 3.9 Consensus size: 27
55420862 TTCCCTGGGT
*
55420872 CAAGGGAACACTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
*
55420899 GAAGGGAACCCTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
55420926 CAAGGGTTCCCTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
55420953 CAAGGGTTCCCTGTTGGCGGCACCA
1 CAAGGGAACCCTGTTGGCGGCACCA
55420978 CTCATGTTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.15
Consensus pattern (27 bp):
CAAGGGAACCCTGTTGGCGGCACCAAA
Found at i:55422629 original size:17 final size:17
Alignment explanation
Indices: 55422609--55422642 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55422599 TTTTTTTCCT
55422609 TTTTTTA-TTCTTTTTTG
1 TTTTTTACTT-TTTTTTG
55422626 TTTTTTACTTTTTTTTG
1 TTTTTTACTTTTTTTTG
55422643 AACTATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTACTTTTTTTTG
Found at i:55422703 original size:27 final size:28
Alignment explanation
Indices: 55422646--55422711 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
55422636 TTTTTTGAAC
55422646 TATTTTGGTAAATAATAAAAATTATATA
1 TATTTTGGTAAATAATAAAAATTATATA
*
55422674 TATTTTGGTCAATAA-AAAAAGTTATA-A
1 TATTTTGGTAAATAATAAAAA-TTATATA
55422701 TATTTTGGTAA
1 TATTTTGGTAA
55422712 TTTTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (28 bp):
TATTTTGGTAAATAATAAAAATTATATA
Found at i:55423544 original size:23 final size:23
Alignment explanation
Indices: 55423511--55423557 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
55423501 CATTCCCTCT
* * *
55423511 TCTTCTTCTTTCTTTTTTTTTCC
1 TCTTCTCCTTTCCTTTTCTTTCC
55423534 TCTTCTCCTTTCCTTTTCTTTCC
1 TCTTCTCCTTTCCTTTTCTTTCC
55423557 T
1 T
55423558 TATTTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
TCTTCTCCTTTCCTTTTCTTTCC
Found at i:55423556 original size:10 final size:10
Alignment explanation
Indices: 55423516--55423641 Score: 84
Period size: 10 Copynumber: 12.7 Consensus size: 10
55423506 CCTCTTCTTC
*
55423516 TTCTTTCTTT
1 TTCTTTCCTT
*
55423526 TTTTTTCCTCT
1 TTCTTTCCT-T
55423537 TCTCCTTTCCTT
1 T-T-CTTTCCTT
55423549 TTCTTTCCTT
1 TTCTTTCCTT
55423559 ATT-TTT-C-T
1 -TTCTTTCCTT
*
55423567 TTCTTTCCTC
1 TTCTTTCCTT
**
55423577 CCCTTTCCTT
1 TTCTTTCCTT
55423587 TTCTTTCCTT
1 TTCTTTCCTT
55423597 CTT-TTTCC--
1 -TTCTTTCCTT
*
55423605 TTCTTTCCTC
1 TTCTTTCCTT
*
55423615 TCCTTTCCTT
1 TTCTTTCCTT
* *
55423625 TTCCTTCTTT
1 TTCTTTCCTT
55423635 TTCTTTC
1 TTCTTTC
55423642 TTCCTTTCTT
Statistics
Matches: 90, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
7 4 0.04
8 9 0.10
9 2 0.02
10 59 0.66
11 7 0.08
12 3 0.03
13 6 0.07
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:55423571 original size:18 final size:18
Alignment explanation
Indices: 55423548--55423658 Score: 86
Period size: 18 Copynumber: 6.1 Consensus size: 18
55423538 CTCCTTTCCT
*
55423548 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
55423566 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
55423585 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
* *
55423604 CTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
55423622 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
55423638 TTTC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
55423657 TT
1 TT
55423659 CTTCCCCTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.12
17 12 0.16
18 28 0.38
19 14 0.19
20 10 0.14
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:55423587 original size:38 final size:38
Alignment explanation
Indices: 55423540--55423649 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 38
55423530 TTCCTCTTCT
55423540 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * *
55423578 CCTTTCCTTTTCTTTCCTTCTTTTTCCTTCTTTCCTCT
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * *
55423616 CCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 CCTTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
55423650 TTTCTTCTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
37 5 0.08
38 59 0.92
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (38 bp):
CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
Found at i:55423610 original size:28 final size:28
Alignment explanation
Indices: 55423549--55423663 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 28
55423539 TCCTTTCCTT
* *
55423549 TTCTTTCCTTATT-TTTCTTTCTTTCCTCC
1 TTCTTTCCTT-TTCTTTCCTTCTTT-TTCC
*
55423578 -CCTTTCCTTTTCTTTCCTTCTTTTTCC
1 TTCTTTCCTTTTCTTTCCTTCTTTTTCC
*
55423605 TTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCT
1 TTCTTT-C-CT--TTT-C-TTTCCTTCTTTTTCC
*
55423639 TTC-TTCC-TTTCTTT-CTTCTTCTTCC
1 TTCTTTCCTTTTCTTTCCTTCTTTTTCC
55423664 CCTCTCCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
25 9 0.13
26 3 0.04
27 6 0.08
28 25 0.35
29 1 0.01
30 2 0.03
31 1 0.01
32 4 0.06
33 3 0.04
34 17 0.24
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (28 bp):
TTCTTTCCTTTTCTTTCCTTCTTTTTCC
Found at i:55423654 original size:22 final size:23
Alignment explanation
Indices: 55423509--55423661 Score: 66
Period size: 24 Copynumber: 6.5 Consensus size: 23
55423499 TTCATTCCCT
**
55423509 CTTCTTCTTCTTTCTTTTTTTTTC
1 CTTCTTCTTCTTTC-TTCCTTTTC
* *
55423533 C-TCTTCTCCTTTCCTT-TTCTTTC
1 CTTCTTCTTCTTT-CTTCCT-TTTC
* * **
55423556 CTTATTTTTCTTTCTTTCC-TCCC
1 CTTCTTCTTCTTTC-TTCCTTTTC
*
55423579 CTTTCCTT-TTCTTTCCTTCTTTTTC
1 C-TT-CTTCTTCTTT-CTTCCTTTTC
* *
55423604 CTTCTT-TCCTCTCCTTTCCTTTTC
1 CTTCTTCTTCT-TTC-TTCCTTTTC
*
55423628 CTTCTTTTTCTTTCTTCC-TTTC
1 CTTCTTCTTCTTTCTTCCTTTTC
*
55423650 TTTCTTCTTCTT
1 CTTCTTCTTCTT
55423662 CCCCTCTCCT
Statistics
Matches: 99, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
22 16 0.16
23 32 0.32
24 42 0.42
25 9 0.09
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (23 bp):
CTTCTTCTTCTTTCTTCCTTTTC
Found at i:55423672 original size:42 final size:40
Alignment explanation
Indices: 55423595--55423675 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 40
55423585 TTTTCTTTCC
* * *
55423595 TTCTTTTTCCTTCTTTCCTCTCCTTTCCTTTTCCTTCTTT
1 TTCTTTTTCCTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
* *
55423635 TTCTTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTCTTT-TTCC-TTCTTTCCTCTCCTTCCCCTCTCCTTCTT
55423676 CCCCCCACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 4 0.12
42 24 0.71
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (40 bp):
TTCTTTTTCCTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
Found at i:55423748 original size:27 final size:27
Alignment explanation
Indices: 55423710--55423777 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
55423700 ATATTTAAGG
55423710 TGGTGCCGCCAACAAGGAATCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
**
55423737 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
55423764 TGGTGCCGCCAACA
1 TGGTGCCGCCAACA
55423778 GTGTTCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAATCCTTGTT
Found at i:55423787 original size:27 final size:27
Alignment explanation
Indices: 55423710--55423788 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 27
55423700 ATATTTAAGG
*
55423710 TGGTGCCGCCAACAAGGAAT-CCTTGTT
1 TGGTGCCGCCAACAAGG-TTCCCTTGTT
*
55423737 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
55423764 TGGTGCCGCCAAC-AGTGTTCCCTTG
1 TGGTGCCGCCAACAAG-GTTCCCTTG
55423789 ACCAAGGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.06
27 45 0.94
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGTTCCCTTGTT
Found at i:55423875 original size:28 final size:28
Alignment explanation
Indices: 55423843--55423910 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
55423833 TTGGTTTTTT
55423843 TATATATTTTGGTAAATAAAAAAAAT-TA
1 TATATATTTTGGTAAAT-AAAAAAATGTA
55423871 TATATATTTTGGTAAATAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAATGTA
*
55423899 TA-ACATTTTGGT
1 TATATATTTTGGT
55423911 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAATGTA
Found at i:55424790 original size:22 final size:22
Alignment explanation
Indices: 55424765--55424827 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
55424755 TAATCGAAAT
55424765 TAAATTATAATTTTTATGATAA
1 TAAATTATAATTTTTATGATAA
* **
55424787 TAAAAATATAATTTTATCATTTTAA
1 T-AAATTATAATTTT-T-ATGATAA
*
55424812 TAATTTAT-ATTTTTAT
1 TAAATTATAATTTTTAT
55424828 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 17 0.52
24 6 0.18
25 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TAAATTATAATTTTTATGATAA
Found at i:55424829 original size:15 final size:16
Alignment explanation
Indices: 55424793--55424832 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
55424783 ATAATAAAAA
55424793 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
55424810 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
55424825 TATAATTT
1 TATAATTT
55424833 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:55425552 original size:20 final size:20
Alignment explanation
Indices: 55425502--55425553 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
55425492 ATTTTAAATT
*
55425502 AAAAATATAATAATTTAACAA
1 AAAAATA-AAAAATTTAACAA
**
55425523 AAAACA-AAAAAATTTATGAA
1 AAAA-ATAAAAAATTTAACAA
55425543 AAAAATAAAAA
1 AAAAATAAAAA
55425554 CTTTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 5 0.19
22 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATAAAAAATTTAACAA
Found at i:55427723 original size:13 final size:14
Alignment explanation
Indices: 55427697--55427725 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55427687 TTATCAATAT
55427697 TTTAAAGACTTGTA
1 TTTAAAGACTTGTA
55427711 TTTAAAG-CTTGTA
1 TTTAAAGACTTGTA
55427724 TT
1 TT
55427726 CCATGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (14 bp):
TTTAAAGACTTGTA
Found at i:55432884 original size:17 final size:17
Alignment explanation
Indices: 55432862--55432899 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55432852 AATCGGGTAT
55432862 TTAACCGAACTTAATAA
1 TTAACCGAACTTAATAA
55432879 TTAACCGAACTTAATAA
1 TTAACCGAACTTAATAA
55432896 TTAA
1 TTAA
55432900 TAATACAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (17 bp):
TTAACCGAACTTAATAA
Found at i:55433796 original size:94 final size:94
Alignment explanation
Indices: 55433558--55433839 Score: 350
Period size: 94 Copynumber: 3.0 Consensus size: 94
55433548 AATCATGTCA
** * * *
55433558 AATAAAAATATAAAAAGATTAAATCTTAGTTTTGAGTTTAGTAGAGGGACCAAAACTGTAATCTT
1 AATAAAAATAT--AAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTT
55433623 ACCATTATAATTGAAATGGCAAACAAAAGCTG
64 ACCATTATAATTGAAATGGCAAA-AAAAGCTG
* * * *
55433655 AAGTAAAAATTTAAAGATTAAATCTTAAATTTGAGTTTAACAAAGGGACCAAAACTGAAATTTTT
1 AA-TAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTA
*
55433720 CCATTATAATTGAAATGGCAAAAAGAG-TGG
65 CCATTATAATTGAAATGGCAAAAAAAGCT-G
* * * * *
55433750 CATAAAAATATAAAGATTAAATCTTAAAATTGAGTTTAATAGAGGGATCAAAAATGAAAATTTAC
1 AATAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTAC
* * *
55433815 CAGTATAATTAAAAGGGCAAAAAAA
66 CATTATAATTGAAATGGCAAAAAAA
55433840 AAAAAGTGTG
Statistics
Matches: 160, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
94 77 0.48
95 6 0.04
96 67 0.42
97 2 0.01
98 8 0.05
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (94 bp):
AATAAAAATATAAAGATTAAATCTTAAATTTGAGTTTAATAGAGGGACCAAAACTGAAATTTTAC
CATTATAATTGAAATGGCAAAAAAAGCTG
Found at i:55437675 original size:30 final size:27
Alignment explanation
Indices: 55437641--55437697 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
55437631 AAAATTATGC
55437641 AATTTTGATTCAATGTATAATTTATACATA
1 AATTTTGATT-AA-GTATAA-TTATACATA
*
55437671 AATTTTGATTTAGTATAATTATACATA
1 AATTTTGATTAAGTATAATTATACATA
55437698 CAAAACTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 6 0.23
29 1 0.04
30 10 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (27 bp):
AATTTTGATTAAGTATAATTATACATA
Found at i:55437868 original size:12 final size:12
Alignment explanation
Indices: 55437851--55437875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55437841 TAAAATGATG
55437851 TTATGTTAATAA
1 TTATGTTAATAA
55437863 TTATGTTAATAA
1 TTATGTTAATAA
55437875 T
1 T
55437876 ACAAGAATTG
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:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATGTTAATAA
Found at i:55437948 original size:29 final size:30
Alignment explanation
Indices: 55437891--55437948 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
55437881 AATTGAATCC
*
55437891 AATCAAAATTACATTTATAAAATTACATAA
1 AATCAAAATTACATATATAAAATTACATAA
* *
55437921 AATCAAAATT-TATATATAAAATTGCATA
1 AATCAAAATTACATATATAAAATTACATA
55437949 TTAGACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (30 bp):
AATCAAAATTACATATATAAAATTACATAA
Found at i:55439686 original size:18 final size:17
Alignment explanation
Indices: 55439659--55439692 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
55439649 ATATATACCT
55439659 AAAAATCTGATTAATAC
1 AAAAATCTGATTAATAC
55439676 AAAAGATCTGATTAATA
1 AAAA-ATCTGATTAATA
55439693 TCTCCGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAAATCTGATTAATAC
Found at i:55443803 original size:11 final size:11
Alignment explanation
Indices: 55443787--55443815 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55443777 GTATATACGT
55443787 ATGTGTATGTG
1 ATGTGTATGTG
55443798 ATGTGTATGTG
1 ATGTGTATGTG
55443809 A-GTGTAT
1 ATGTGTAT
55443816 ATGTATATGT
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:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (11 bp):
ATGTGTATGTG
Found at i:55443886 original size:6 final size:6
Alignment explanation
Indices: 55443875--55443916 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
55443865 GCTATCTTGA
55443875 GTATAT GTATAT GTATAT GTATAT GTATAT GCGTATAT GTAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT --GTATAT GTAT
55443917 GTTTATGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 28 0.82
8 6 0.18
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:55443917 original size:18 final size:18
Alignment explanation
Indices: 55443877--55443923 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
55443867 TATCTTGAGT
55443877 ATATGTATAT-GTATATG
1 ATATGTATATGGTATATG
55443894 TATATGTATATGCGTATATG
1 -ATATGTATATG-GTATATG
*
55443914 -TATGTTTATG
1 ATATGTATATG
55443924 TGCATACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 19 0.73
20 7 0.27
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (18 bp):
ATATGTATATGGTATATG
Found at i:55447341 original size:21 final size:21
Alignment explanation
Indices: 55447289--55447349 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
55447279 AATATTGAAT
**
55447289 AATTATTAAATGTTATAAAAA
1 AATTATTAAAAATTATAAAAA
*
55447310 ATATT-TT-AAAATTGTAAAAA
1 A-ATTATTAAAAATTATAAAAA
*
55447330 AATTATTAAAAATAATAAAA
1 AATTATTAAAAATTATAAAA
55447350 TATTAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 13 0.41
22 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AATTATTAAAAATTATAAAAA
Found at i:55447635 original size:22 final size:21
Alignment explanation
Indices: 55447597--55447669 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 21
55447587 ATGCCATCGG
**
55447597 TTCAC-AATTTTCAAATATATT
1 TTCACAAATTTTTTAATA-ATT
* *
55447618 TTTACAATTTTTTTAATAATT
1 TTCACAAATTTTTTAATAATT
55447639 TTCACAAA--TTTTAATAATT
1 TTCACAAATTTTTTAATAATT
* *
55447658 TTAATAAATTTT
1 TTCACAAATTTT
55447670 AAATAAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCACAAATTTTTTAATAATT
Found at i:55447640 original size:10 final size:9
Alignment explanation
Indices: 55447628--55447671 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
55447618 TTTACAATTT
55447628 TTTTAATAA
1 TTTTAATAA
55447637 TTTTCACA-AA
1 TTTT-A-ATAA
55447647 TTTTAATAA
1 TTTTAATAA
55447656 TTTTAATAAA
1 TTTTAAT-AA
55447666 TTTTAA
1 TTTTAA
55447672 ATAAAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 14 0.45
10 15 0.48
11 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTTAATAA
Found at i:55447652 original size:19 final size:19
Alignment explanation
Indices: 55447628--55447671 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
55447618 TTTACAATTT
*
55447628 TTTTAATAATTTTCACAAA
1 TTTTAATAATTTTAACAAA
*
55447647 TTTTAATAATTTTAATAAA
1 TTTTAATAATTTTAACAAA
55447666 TTTTAA
1 TTTTAA
55447672 ATAAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTAACAAA
Found at i:55452286 original size:14 final size:14
Alignment explanation
Indices: 55452267--55452302 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
55452257 TTTGCAATCC
55452267 GGGGCTTGGTTTAG
1 GGGGCTTGGTTTAG
*
55452281 GGGGCTCGGTTTAG
1 GGGGCTTGGTTTAG
*
55452295 GGTGCTTG
1 GGGGCTTG
55452303 AACGTTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.11, G:0.50, T:0.33
Consensus pattern (14 bp):
GGGGCTTGGTTTAG
Found at i:55457803 original size:20 final size:20
Alignment explanation
Indices: 55457778--55457839 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 20
55457768 TACTATTTAA
55457778 AAAAATAGTTTAAAAATTAT
1 AAAAATAGTTTAAAAATTAT
* *
55457798 AAAAATATTTTTAAAA--AT
1 AAAAATAGTTTAAAAATTAT
* *
55457816 AAAAAT-G-TTCAAAATTAA
1 AAAAATAGTTTAAAAATTAT
55457834 AAAAAT
1 AAAAAT
55457840 TATATAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.17
18 15 0.43
20 14 0.40
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATAGTTTAAAAATTAT
Found at i:55464962 original size:69 final size:68
Alignment explanation
Indices: 55464881--55465072 Score: 217
Period size: 69 Copynumber: 2.8 Consensus size: 68
55464871 TCATAAAATA
* * *
55464881 AGATATATCTCCAAAAAATTTATTGGAACG-GAGATCTAAATACTCGAGCGACT-TTAAATTTTT
1 AGATATATCTCCAAAAAA-TTATTGGAA-GAGATATCTAAATACTCGAG-GAATGTTAAATTCTT
* *
55464944 AAGCAT
63 AAACAC
* * * *
55464950 AGATATATCTCCAAAAAAACTGTTGGAAGAGATATCTAAATACTCGAGTAATGTTAGATTCTTAA
1 AGATATATCTCC-AAAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGTTAAATTCTTAA
55465015 ACAC
65 ACAC
* * *
55465019 AGATATATTTCCAGAAAAATTATTGGAAGAGATATCTAAATACTTGAGGGATGT
1 AGATATATCTCCA-AAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGT
55465073 GAGTTCAGAG
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
68 4 0.04
69 94 0.90
70 6 0.06
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (68 bp):
AGATATATCTCCAAAAAATTATTGGAAGAGATATCTAAATACTCGAGGAATGTTAAATTCTTAAA
CAC
Found at i:55469372 original size:12 final size:12
Alignment explanation
Indices: 55469350--55469378 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55469340 AATATGTCTT
55469350 TAAAA-TAATAA
1 TAAAATTAATAA
55469361 TAAAATTAATAA
1 TAAAATTAATAA
55469373 TAAAAT
1 TAAAAT
55469379 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:55469427 original size:22 final size:22
Alignment explanation
Indices: 55469402--55469444 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55469392 TATTCAAACA
*
55469402 ATAATATTAAAATAGTAGCAAC
1 ATAATAGTAAAATAGTAGCAAC
*
55469424 ATAATAGTAAAATGGTAGCAA
1 ATAATAGTAAAATAGTAGCAA
55469445 AATAGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (22 bp):
ATAATAGTAAAATAGTAGCAAC
Found at i:55469457 original size:22 final size:22
Alignment explanation
Indices: 55469409--55469457 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
55469399 ACAATAATAT
* *
55469409 TAAAATAGTAGCAACATAATAG
1 TAAAATAGTAGCAAAATAAGAG
*
55469431 TAAAATGGTAGCAAAATAGAGAG
1 TAAAATAGTAGCAAAATA-AGAG
55469454 -AAAA
1 TAAAA
55469458 CAACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.18
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAAGAG
Done.