Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 93 of 204
Found at i:29121025 original size:91 final size:92
Alignment explanation
Indices: 29120731--29121022 Score: 289
Period size: 91 Copynumber: 3.2 Consensus size: 92
29120721 GGTGGTGGAT
*
29120731 CTGTAAATTGAAGTGTTTTAAATGCTT-TAAATTGAAGTGTTTAAGTGTTGCAAATTGAAGTGTT
1 CTGTAAATTGAAGTG-TTTAAATG-TTGTAAATTGAAGTGTTTAAATGTTGCAAATTGAAGTGTT
* *
29120795 -TAGTTGCTGGAAATTG-AGATGTTTT-ATCG
64 AAAG-TGCTGCAAATTGAAG-TGTTTTAAT-G
* * * *
29120824 CTGT-AATTG-AGTTGTATAAATGTTGTTAATTGAAATG-TTAAAGTGCTGCAAATTGAAGTGTT
1 CTGTAAATTGAAG-TGTTTAAATGTTGTAAATTGAAGTGTTTAAA-TGTTGCAAATTGAAGTG-T
* * *
29120886 TAAA-TGATGTAAATTGAAGTG-TTAAATG
63 TAAAGTGCTGCAAATTGAAGTGTTTTAATG
** ** *
29120914 CTACAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTGTTAATCG-AGATGTTA
1 CTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTGCAAATTGAAG-TGTTA
29120978 AAGTGCTGCAAATTGAAGTGTTTTAATG
65 AAGTGCTGCAAATTGAAGTGTTTTAATG
*
29121006 TTGTAAATTGAAGTGTT
1 CTGTAAATTGAAGTGTT
29121023 AAAGTGCTAC
Statistics
Matches: 162, Mismatches: 24, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
90 18 0.11
91 101 0.62
92 38 0.23
93 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (92 bp):
CTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTGCAAATTGAAGTGTTAA
AGTGCTGCAAATTGAAGTGTTTTAATG
Found at i:29121955 original size:43 final size:43
Alignment explanation
Indices: 29121890--29122112 Score: 297
Period size: 43 Copynumber: 5.2 Consensus size: 43
29121880 TTTCATGACG
* * *
29121890 TTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGATCAAGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTC
*
29121933 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAA-AGTCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-TCATGTTC
* * * * *
29121976 TTTAGTGGCTTTTGTGGTAAAAGCGCCGCTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTC
* * * *
29122019 TTTAGCGGTGTTTGTGGGAAAAGCGTCGCTAAAGGTCATATTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTC
29122062 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTC
*
29122104 TATAGCGGC
1 TTTAGCGGC
29122113 TTTTTTTTAC
Statistics
Matches: 156, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
42 30 0.19
43 126 0.81
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTC
Found at i:29122032 original size:86 final size:85
Alignment explanation
Indices: 29121890--29122112 Score: 329
Period size: 86 Copynumber: 2.6 Consensus size: 85
29121880 TTTCATGACG
*
29121890 TTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGATCAAGTTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCATTTGTGG-AAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAA
*
29121955 GCGTCGCTAAAAGTCATGTTC
65 GCGTCGCTAAAAGTCATATTC
* * * * *
29121976 TTTAGTGGCTTTTGTGGTAAAAGCGCCGCTAAAGGTCATGCTCTTTAGCGGTGTTTGTGGGAAAA
1 TTTAGCGGCATTTGTGG-AAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAA
*
29122041 GCGTCGCTAAAGGTCATATTC
65 GCGTCGCTAAAAGTCATATTC
* * *
29122062 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGATCATGTTCTATAGCGGC
1 TTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGC
29122113 TTTTTTTTAC
Statistics
Matches: 121, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
85 29 0.24
86 92 0.76
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (85 bp):
TTTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAAG
CGTCGCTAAAAGTCATATTC
Found at i:29122265 original size:20 final size:20
Alignment explanation
Indices: 29122237--29122279 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
29122227 GCCGCTAAAA
*
29122237 ACCTGTTTTGCTGTAGTGAT
1 ACCTATTTTGCTGTAGTGAT
*
29122257 ACCTATTTTGCTGTAGTGCT
1 ACCTATTTTGCTGTAGTGAT
29122277 ACC
1 ACC
29122280 AGTACGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
ACCTATTTTGCTGTAGTGAT
Found at i:29122746 original size:75 final size:75
Alignment explanation
Indices: 29122623--29122773 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
29122613 AAAGGAAAAC
** *
29122623 TAGGATTATTCGCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
1 TAGGATTATTCGCTTATTAATAGAGAAAACAAATGGAAAATTAGAAAAATGAATTATATTCTTTC
29122688 CAAAAGAATA
66 CAAAAGAATA
*
29122698 TAGGATTATTCTCTTATTAATAGAGAAAACAAATGGAAAATTAGAAAAATGAATTATATTCTTTC
1 TAGGATTATTCGCTTATTAATAGAGAAAACAAATGGAAAATTAGAAAAATGAATTATATTCTTTC
29122763 CAAAAGAATA
66 CAAAAGAATA
29122773 T
1 T
29122774 TAATTTCTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.32
Consensus pattern (75 bp):
TAGGATTATTCGCTTATTAATAGAGAAAACAAATGGAAAATTAGAAAAATGAATTATATTCTTTC
CAAAAGAATA
Found at i:29122910 original size:138 final size:138
Alignment explanation
Indices: 29122749--29123032 Score: 487
Period size: 138 Copynumber: 2.1 Consensus size: 138
29122739 TAGAAAAATG
*
29122749 AATTATATTCTTTCCAAAAGAATATTAATTTCTATATCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
* *
29122814 TATAACTGTTTATATTAATAAATTCGGTACAATATATACAATTAATATTTTGTATGAATTAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
29122879 CATATATT
131 CATATATT
* ** * *
29122887 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTGATTAC
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
29122952 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
29123017 TATATATT
131 CATATATT
29123025 AATTATAT
1 AATTATAT
29123033 CTATGTTCTC
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:29125322 original size:50 final size:50
Alignment explanation
Indices: 29125253--29125389 Score: 132
Period size: 50 Copynumber: 2.7 Consensus size: 50
29125243 CTACCAATGT
* * * ** * *
29125253 CATATCCCAAATATCGTCTTACATGGGAGTTC-CAATATCGGTGCCCATGC
1 CATATCCCAGACATGGTCTTACATGGGACCTCTC-ATATCGGTGCCAACGC
** * * *
29125303 CATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGTTTCCAACGC
1 CATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGC
* *
29125353 CATGTCCCAGACATGGTCTTACATGGGACCTGTCATA
1 CATATCCCAGACATGGTCTTACATGGGACCTCTCATA
29125390 ACCTCAATGA
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
50 68 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
CATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGC
Found at i:29129318 original size:11 final size:11
Alignment explanation
Indices: 29129302--29129329 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29129292 TTCTTGGCAG
29129302 CAAAATTCGTT
1 CAAAATTCGTT
29129313 CAAAATTCGTT
1 CAAAATTCGTT
29129324 CAAAAT
1 CAAAAT
29129330 CCCTAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (11 bp):
CAAAATTCGTT
Found at i:29136738 original size:80 final size:79
Alignment explanation
Indices: 29136601--29136825 Score: 256
Period size: 80 Copynumber: 2.8 Consensus size: 79
29136591 TTGAATGCTG
* * * * * *
29136601 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
29136665 TGTGCGAGATA-CAAA
64 TGTGCGAGATATCAAA
* *
29136680 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATT
* * *
29136745 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * * * *
29136761 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
29136826 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
79 39 0.32
80 70 0.57
81 14 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:29136805 original size:39 final size:39
Alignment explanation
Indices: 29136601--29136823 Score: 225
Period size: 40 Copynumber: 5.6 Consensus size: 39
29136591 TTGAATGCTG
* * * * * *
29136601 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** *
29136641 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
* * *
29136680 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
29136721 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
29136761 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
29136800 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29136824 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
39 39 0.25
40 105 0.68
41 11 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:29136843 original size:79 final size:80
Alignment explanation
Indices: 29136681--29136858 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
29136671 AGATACAAAT
* * * *
29136681 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
29136746 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
29136761 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
29136825 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
29136840 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29136859 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:29145059 original size:16 final size:17
Alignment explanation
Indices: 29145026--29145059 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29145016 TTGGGATATA
*
29145026 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
29145043 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
29145059 A
1 A
29145060 TAGTATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:29145791 original size:132 final size:137
Alignment explanation
Indices: 29145632--29145907 Score: 445
Period size: 132 Copynumber: 2.0 Consensus size: 137
29145622 AAAAAGGAAC
29145632 TATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAAACTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAAACTAATTAATAT
*
29145697 AACTGTTTATATTAATAAATTCAG-AAA-A-ACAT-ATTAATATTTTGTATGAATCAAATTCATA
66 AACTATTTATATTAATAAATTCAGAAAATATACATAATTAATATTTTGTATGAATCAAATTCATA
29145758 TATTAAT
131 TATTAAT
* * * *
29145765 TATATTCTTTTC-AAAGAATATTAATTTCTATGTCTTTTATATTTTGATCGAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAAACTAATTAATAT
* *
29145829 AACTATTTATATTATTAAATTCAGTAAAATATATATAATTAATATTTTGTATGAATCAAATTCAT
66 AACTATTTATATTAATAAATTCAG-AAAATATACATAATTAATATTTTGTATGAATCAAATTCAT
29145894 ATATTAAT
130 ATATTAAT
29145902 TATATT
1 TATATT
29145908 TATGTTCTCT
Statistics
Matches: 131, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
132 71 0.54
133 11 0.08
134 3 0.02
135 1 0.01
136 3 0.02
137 42 0.32
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (137 bp):
TATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAAACTAATTAATAT
AACTATTTATATTAATAAATTCAGAAAATATACATAATTAATATTTTGTATGAATCAAATTCATA
TATTAAT
Found at i:29146620 original size:17 final size:18
Alignment explanation
Indices: 29146588--29146622 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29146578 TCAAAAGTCA
29146588 GTTATTTAATTTTTAATT
1 GTTATTTAATTTTTAATT
*
29146606 GTTATTTTA-TTTTAATT
1 GTTATTTAATTTTTAATT
29146623 TTAGAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
GTTATTTAATTTTTAATT
Found at i:29152166 original size:11 final size:11
Alignment explanation
Indices: 29152152--29152242 Score: 81
Period size: 11 Copynumber: 8.9 Consensus size: 11
29152142 TTTTTTTTAA
29152152 TTTTAAAATAT
1 TTTTAAAATAT
29152163 TTTTAAAATAT
1 TTTTAAAATAT
**
29152174 TTTTTTAAT-T
1 TTTTAAAATAT
*
29152184 TTTT----TAA
1 TTTTAAAATAT
29152191 TTTTAAAATAT
1 TTTTAAAATAT
*
29152202 TTTAAAAATACT
1 TTTTAAAATA-T
29152214 TTTTAAAAT-T
1 TTTTAAAATAT
29152224 TTTT-AAA-AT
1 TTTTAAAATAT
29152233 TTTTAAAATA
1 TTTTAAAATA
29152243 AAAATGGGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
6 1 0.02
7 4 0.06
9 8 0.12
10 13 0.20
11 30 0.46
12 9 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29152166 original size:39 final size:40
Alignment explanation
Indices: 29152101--29152242 Score: 162
Period size: 40 Copynumber: 3.5 Consensus size: 40
29152091 AAATATATTT
** * *
29152101 ATTTTTTAAAATTTTAAAATATTTTTTACATGA-TTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAAT-ATTTTTTTA
29152141 ATTTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
* **
29152181 A-TTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTAAA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTTA
**
29152221 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTTTTAA-TTTTAAAATA
29152243 AAAATGGGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
39 30 0.34
40 42 0.47
41 7 0.08
42 10 0.11
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (40 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:29152203 original size:10 final size:10
Alignment explanation
Indices: 29152190--29152242 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
29152180 AATTTTTTTA
29152190 ATTTTAAAAT
1 ATTTTAAAAT
29152200 ATTTTAAAAAT
1 ATTTT-AAAAT
29152211 ACTTTTTAAAAT
1 A--TTTTAAAAT
*
29152223 TTTTTAAAAT
1 ATTTTAAAAT
29152233 -TTTTAAAAT
1 ATTTTAAAAT
29152242 A
1 A
29152243 AAAATGGGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.24
10 14 0.37
11 6 0.16
12 5 0.13
13 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:29158516 original size:31 final size:31
Alignment explanation
Indices: 29158431--29158496 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
29158421 AGATCCAATC
* * **
29158431 CAAAAAAAAAGAGCAAAATCAAAATCAAAAA
1 CAAAAAAAAAAAGAAAAAGAAAAATCAAAAA
*
29158462 CAAAAAAAAAAAGAAAAAGAAAAATCAAAAT
1 CAAAAAAAAAAAGAAAAAGAAAAATCAAAAA
29158493 CAAA
1 CAAA
29158497 GTCAAAATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.77, C:0.11, G:0.06, T:0.06
Consensus pattern (31 bp):
CAAAAAAAAAAAGAAAAAGAAAAATCAAAAA
Found at i:29158549 original size:21 final size:22
Alignment explanation
Indices: 29158506--29158550 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29158496 AGTCAAAATG
* *
29158506 AAAATGAAAAAAAGATAAGGAA
1 AAAAGGAAAAAAAGATAAAGAA
*
29158528 AAAAGGAAAAAAGGA-AAAGAA
1 AAAAGGAAAAAAAGATAAAGAA
29158549 AA
1 AA
29158551 GAAGAGGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (22 bp):
AAAAGGAAAAAAAGATAAAGAA
Found at i:29159413 original size:6 final size:7
Alignment explanation
Indices: 29159393--29159442 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
29159383 TTGAGTAAAA
29159393 AAAAGATG
1 AAAA-ATG
29159401 AAAAATG
1 AAAAATG
29159408 -AAAATG
1 AAAAATG
29159414 AAAAATG
1 AAAAATG
29159421 AAAAATG
1 AAAAATG
*
29159428 AAAAAAG
1 AAAAATG
29159435 TAAAAATG
1 -AAAAATG
29159443 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 6 0.16
7 22 0.58
8 10 0.26
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:29159423 original size:20 final size:21
Alignment explanation
Indices: 29159393--29159431 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29159383 TTGAGTAAAA
29159393 AAAAGATGAAAAATGAAAATG
1 AAAAGATGAAAAATGAAAATG
29159414 AAAA-ATGAAAAATGAAAA
1 AAAAGATGAAAAATGAAAA
29159432 AAGTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (21 bp):
AAAAGATGAAAAATGAAAATG
Found at i:29159439 original size:15 final size:14
Alignment explanation
Indices: 29159389--29159442 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
29159379 GACTTTGAGT
*
29159389 AAAAA-AAAGATGA
1 AAAAAGAAAAATGA
*
29159402 AAAATG-AAAATGA
1 AAAAAGAAAAATGA
*
29159415 AAAATGAAAAATGA
1 AAAAAGAAAAATGA
29159429 AAAAAGTAAAAATG
1 AAAAAG-AAAAATG
29159443 GAGAGGCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 16 0.46
14 12 0.34
15 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
AAAAAGAAAAATGA
Found at i:29160940 original size:128 final size:128
Alignment explanation
Indices: 29160734--29161105 Score: 534
Period size: 128 Copynumber: 2.9 Consensus size: 128
29160724 CCTTGACCAG
* *
29160734 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACG
1 CAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
* * *
29160799 GTGAATCTTATCTTCAAGTGTAAAGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAG
66 GTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAATCCTATATCCCTGGTCAA
* * * * * *
29160862 TAGTGAAATAGGTTGAAAATTACAAATCTTGTCTCCCTAAGTAGTAGCGAAACAGATCGAAGACG
1 CAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
*
29160927 GTGAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAATCCTATATCCCTGGTCAA
66 GTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAATCCTATATCCCTGGTCAA
* *
29160990 CAGTGGAATAGGTT-AGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGAT-TAAGGA
1 CAGTGGAATAGGTTGA-AAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAA-GA
* * * *
29161053 CGGCGAATCTTATCTTCAAGAGTAAGGAAACAGATTGAAGCCA-ATAATCCTAT
64 CGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACA-AATCCTAT
29161106 CTTCCTGAAA
Statistics
Matches: 216, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
127 4 0.02
128 212 0.98
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (128 bp):
CAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
GTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAATCCTATATCCCTGGTCAA
Found at i:29161168 original size:44 final size:44
Alignment explanation
Indices: 29161103--29161383 Score: 182
Period size: 44 Copynumber: 6.4 Consensus size: 44
29161093 CCAATAATCC
* * * * * *
29161103 TATCTTCCTGAAATTGTAGTAGAGCGGATTAAAGTAATGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATGGATCT
* * ** * * *
29161147 TATCTCTCTGAAGTTGCAGTAGAGTGGATCGCA-TCA-GG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATGGATCT
* * * *
29161188 TATCTCCTTGAGGTTGCAGTGGAGCAGACTG-AGTAA-GCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATG--GATCT
* * *
29161232 TATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAG--ATGGTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATGG---ATCT
* * * *
29161277 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGAT-AATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AATGGATCT
* * * * *
29161321 TATCTCCCTGAAATTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATGGATCT
*
29161365 TATCTCTCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAG
29161384 CAGAGTAGAT
Statistics
Matches: 182, Mismatches: 42, Indels: 26
0.73 0.17 0.10
Matches are distributed among these distances:
40 1 0.01
41 29 0.16
42 3 0.02
43 6 0.03
44 106 0.58
45 35 0.19
48 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATGGATCT
Found at i:29161453 original size:44 final size:45
Alignment explanation
Indices: 29161184--29161502 Score: 149
Period size: 44 Copynumber: 7.3 Consensus size: 45
29161174 ATCGCATCAG
* * * * * *
29161184 GTCTTATCTCCTTGAGGTTGCAGTGGAGCAGACTGAGTA-AGCAG
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCAA
* * * * * *
29161228 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGA-AGATGGTAA
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGA-ATAGCAA
* * * ** * *
29161273 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA-AGTCG-ATA
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCA-A
* * * * * * ***
29161317 ATCCTATCTCCCTGAAATTGTAGTGGAGCGGATTAAAGTAATAG--A
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGA-CCGAG-AATAGCAA
* * * * * *
29161362 -TCTTATCTCTCTGAAGTTGCAGCAGAGTAGATC-A-CAT--CAG
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCAA
* *
29161402 GTCTTATCTCCTTGAGGTTGCAGCGGAGCAGACCGAGAA-AGCAA
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCAA
* * * *
29161446 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAATAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCAA
*
29161491 ATCTTATCTCCC
1 GTCTTATCTCCC
29161503 AGGCGGTGTA
Statistics
Matches: 208, Mismatches: 53, Indels: 27
0.72 0.18 0.09
Matches are distributed among these distances:
40 2 0.01
41 27 0.13
42 2 0.01
43 3 0.01
44 119 0.57
45 52 0.25
47 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAGAATAGCAA
Found at i:29161461 original size:218 final size:218
Alignment explanation
Indices: 29161083--29161502 Score: 682
Period size: 218 Copynumber: 1.9 Consensus size: 218
29161073 AGTAAGGAAA
* *
29161083 CAGATTGAAGCCAATAATCCTATCTTCCTGAAATTGTAGTAGAGCGGATTAAAGTAATGGATCTT
1 CAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTAGAGCGGATTAAAGTAATAGATCTT
* * * *
29161148 ATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAGGTTGCAGTGGAGC
66 ATCTCTCTGAAGTTGCAGCAGAGTAGATCACATCAGGTCTTATCTCCTTGAGGTTGCAGCGGAGC
* * * * *
29161213 AGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGA-TCGA-AGATGGTAAATC
131 AGACCGAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT-GAGA-ATAGCAAATC
29161276 TTATCTCCCTGAGGTTGCAGTGGAG
194 TTATCTCCCTGAGGTTGCAGTGGAG
* * *
29161301 CAGATTGAAGTCGATAATCCTATCTCCCTGAAATTGTAGTGGAGCGGATTAAAGTAATAGATCTT
1 CAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTAGAGCGGATTAAAGTAATAGATCTT
29161366 ATCTCTCTGAAGTTGCAGCAGAGTAGATCACATCAGGTCTTATCTCCTTGAGGTTGCAGCGGAGC
66 ATCTCTCTGAAGTTGCAGCAGAGTAGATCACATCAGGTCTTATCTCCTTGAGGTTGCAGCGGAGC
29161431 AGACCGAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAATAGCAAATCTT
131 AGACCGAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAATAGCAAATCTT
29161496 ATCTCCC
196 ATCTCCC
29161503 AGGCGGTGTA
Statistics
Matches: 186, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
218 184 0.99
219 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (218 bp):
CAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTAGAGCGGATTAAAGTAATAGATCTT
ATCTCTCTGAAGTTGCAGCAGAGTAGATCACATCAGGTCTTATCTCCTTGAGGTTGCAGCGGAGC
AGACCGAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAATAGCAAATCTT
ATCTCCCTGAGGTTGCAGTGGAG
Found at i:29161585 original size:50 final size:50
Alignment explanation
Indices: 29161520--29161762 Score: 172
Period size: 50 Copynumber: 4.9 Consensus size: 50
29161510 GTAGTGGAAT
* * *
29161520 AGATTAAAGCCACAACGGCGAATCTTGCTTTCCCGACATTGCAGTTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGCTTTCCCGACATTGCAGTGAAAA
* * * * * * * * ** * **
29161570 AGAGTAAAGCTACAACAGTGAATCTT-ATCTCCAGGCGGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTGCTTTCCCGACATTGCAGTGAAAA
* * *
29161619 AGATTGAAGCTACAATGGCGAATCTTGC-TTCTCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGCTTTC-CCGACATTGCAGTGAAAA
** * * * *
29161669 AGATTGAAGCCGCAACGGCGAATCTTAC-TTCCCTGGCGA-TGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTGCTTTCCC-GAC-ATTGCAGTGAAAA
* * *
29161719 AGATTGAAGCTACAACGGTGAATCTTG-TTTTCTGACATTGCAGT
1 AGATTGAAGCTACAACGGCGAATCTTGCTTTCCCGACATTGCAGT
29161763 CAATTTGAAA
Statistics
Matches: 141, Mismatches: 46, Indels: 13
0.70 0.23 0.06
Matches are distributed among these distances:
48 1 0.01
49 46 0.33
50 93 0.66
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTGCTTTCCCGACATTGCAGTGAAAA
Found at i:29161692 original size:99 final size:99
Alignment explanation
Indices: 29161490--29161760 Score: 339
Period size: 99 Copynumber: 2.7 Consensus size: 99
29161480 GAGAATAGCA
* * *
29161490 AATCTTATCTCCCAGGCGGTGTAGTGGAATAGATTAAAGCCACAACGGCGAATCTTGCTTTCCCG
1 AATCTTATCTCCCAGGCGGTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTTT-CCG
* * *
29161555 ACATTGCAGTTAAAAAGAGTAAAGCTACAACAGTG
65 ACATTGCAATTAAAAAGAGTAAAGCCACAACAGCG
** *
29161590 AATCTTATCT-CCAGGCGGTGCAGTGGAGCAGATTGAAGCTACAATGGCGAATCTTGCTTCTCCG
1 AATCTTATCTCCCAGGCGGTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTT-TCCG
* * * *
29161654 ACATTGCAATTAAAAAGATTGAAGCCGCAACGGCG
65 ACATTGCAATTAAAAAGAGTAAAGCCACAACAGCG
* * * * *
29161689 AATCTTA-CTTCCCTGGCGATGCAGTGGAATAGATTGAAGCTACAACGGTGAATCTTGTTTTCTG
1 AATCTTATC-TCCCAGGCGGTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTTTCCG
29161753 ACATTGCA
65 ACATTGCA
29161761 GTCAATTTGA
Statistics
Matches: 147, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
98 1 0.01
99 93 0.63
100 53 0.36
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (99 bp):
AATCTTATCTCCCAGGCGGTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTTTCCGA
CATTGCAATTAAAAAGAGTAAAGCCACAACAGCG
Found at i:29161939 original size:128 final size:127
Alignment explanation
Indices: 29161778--29162073 Score: 439
Period size: 128 Copynumber: 2.3 Consensus size: 127
29161768 TGAAAGAAAT
*
29161778 CAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAAGTAG
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAAGCAG
* * * *
29161843 TAGTGGAGCAGATCGCATCAAGTCGTATCTCCCTAAGCACTAGTGGATCAGACAAAAAAAAAC
66 TAGTGAAGCAAATCGCATCAAGTCGTATCTCCCTAAGCACTAGTGCAGCAGAC-AAAAAAAAC
* *
29161906 CAATCCTATCTCCCTGAAGTTCCAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAAGCAT
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAAGCAG
* * * *
29161971 TAGTGAAGCAAATCGCATCAAGTCTTATCTCTCTAAGCAGTAGTGCAGCAGACAAAAGAAAC
66 TAGTGAAGCAAATCGCATCAAGTCGTATCTCCCTAAGCACTAGTGCAGCAGACAAAAAAAAC
* ** **
29162033 CAATCCTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAAC
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAAC
29162074 GATGAATCAT
Statistics
Matches: 152, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
127 44 0.29
128 108 0.71
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (127 bp):
CAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAAGCAG
TAGTGAAGCAAATCGCATCAAGTCGTATCTCCCTAAGCACTAGTGCAGCAGACAAAAAAAAC
Found at i:29165185 original size:18 final size:18
Alignment explanation
Indices: 29165162--29165216 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
29165152 GAGATGGCAA
29165162 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
*
29165180 AGATGATAAATGAAATATG
1 AGATGAGAAATG-AATATG
*
29165199 AAATGATGAAATG-ATATG
1 AGATGA-GAAATGAATATG
29165217 TGAATTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.50
19 11 0.34
20 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:29165198 original size:19 final size:19
Alignment explanation
Indices: 29165162--29165212 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29165152 GAGATGGCAA
*
29165162 AGATGAGAAATG-AATATG
1 AGATGATAAATGAAATATG
29165180 AGATGATAAATGAAATATG
1 AGATGATAAATGAAATATG
*
29165199 AAATGATGAAATGA
1 AGATGAT-AAATGA
29165213 TATGTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.38
19 12 0.41
20 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (19 bp):
AGATGATAAATGAAATATG
Found at i:29166056 original size:17 final size:17
Alignment explanation
Indices: 29166034--29166066 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29166024 CACGGTCTAT
29166034 CACATGGCCGTGTGTCA
1 CACATGGCCGTGTGTCA
*
29166051 CACATGGGCGTGTGTC
1 CACATGGCCGTGTGTC
29166067 CTAAACGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.24
Consensus pattern (17 bp):
CACATGGCCGTGTGTCA
Found at i:29171970 original size:17 final size:15
Alignment explanation
Indices: 29171939--29171982 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
29171929 TTTTTCTTGG
29171939 AATA-ATTTTTATAT
1 AATATATTTTTATAT
29171953 AATATTATTTTTAGTAT
1 AATA-TATTTTTA-TAT
29171970 AATATATTTTTAT
1 AATATATTTTTAT
29171983 TTTAAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 1 0.04
16 15 0.56
17 7 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
AATATATTTTTATAT
Found at i:29172733 original size:27 final size:29
Alignment explanation
Indices: 29172702--29172762 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
29172692 ACTAAAAATT
29172702 TATTTTAAAA-ATAAAAAAT-AAAAA-AAA
1 TATTTTAAAATA-AAAAAATAAAAAATAAA
29172729 TATTTTAAAATAAAAAAATAAAAAATAAA
1 TATTTTAAAATAAAAAAATAAAAAATAAA
29172758 TATTT
1 TATTT
29172763 ATTATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 17 0.55
28 6 0.19
29 8 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
TATTTTAAAATAAAAAAATAAAAAATAAA
Found at i:29175512 original size:11 final size:11
Alignment explanation
Indices: 29175497--29175596 Score: 83
Period size: 11 Copynumber: 9.6 Consensus size: 11
29175487 AAAAACTTAA
29175497 AAAAAGTATTTT
1 AAAAA-TATTTT
29175509 AAAAATATTTT
1 AAAAATATTTT
29175520 --AAA-A--TT
1 AAAAATATTTT
*
29175526 AAAAAAATTTT
1 AAAAATATTTT
29175537 AAAAAGTATTTT
1 AAAAA-TATTTT
29175549 AAAAATATTTT
1 AAAAATATTTT
*
29175560 --AAA-A-TTA
1 AAAAATATTTT
*
29175567 AAAAAAATTTT
1 AAAAATATTTT
29175578 AAAAAGTATTTT
1 AAAAA-TATTTT
29175590 AAAAATA
1 AAAAATA
29175597 AAAAAATAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.07
9 10 0.14
10 1 0.01
11 28 0.38
12 25 0.34
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:29175571 original size:30 final size:30
Alignment explanation
Indices: 29175544--29175602 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
29175534 TTTAAAAAGT
*
29175544 ATTTTAAAAA-TATTTTAAAATTAAAAAAA
1 ATTTTAAAAAGTATTTTAAAAATAAAAAAA
29175573 ATTTTAAAAAGTATTTTAAAAATAAAAAAA
1 ATTTTAAAAAGTATTTTAAAAATAAAAAAA
29175603 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTAAAAAGTATTTTAAAAATAAAAAAA
Found at i:29175571 original size:41 final size:41
Alignment explanation
Indices: 29175471--29175596 Score: 209
Period size: 41 Copynumber: 3.0 Consensus size: 41
29175461 ACCAAAAATT
**
29175471 TATTTTAAAAATTAAAAAAAACTTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAA-TTTTAAAAAGTATTTTAAAAA
29175514 TATTTTAAAATT-AAAAAAATTTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTTTAAAAAGTATTTTAAAAA
29175554 TATTTTAAAATTAAAAAAAATTTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTTTAAAAAGTATTTTAAAAA
29175595 TA
1 TA
29175597 AAAAAATAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
40 31 0.39
41 37 0.46
42 6 0.08
43 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTTTAAAAAGTATTTTAAAAA
Found at i:29175607 original size:7 final size:8
Alignment explanation
Indices: 29175590--29175616 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29175580 AAAGTATTTT
29175590 AAAAATAA
1 AAAAATAA
29175598 AAAAATAA
1 AAAAATAA
29175606 AAAAATAA
1 AAAAATAA
29175614 AAA
1 AAA
29175617 TATTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:29175610 original size:29 final size:29
Alignment explanation
Indices: 29175549--29175610 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
29175539 AAAGTATTTT
* **
29175549 AAAAATATTTTAAAATTAAAAAAAATTTTA
1 AAAAATATTTTAAAAATAAAAAAAA-TAAA
*
29175579 AAAAGTATTTTAAAAAT-AAAAAAATAAA
1 AAAAATATTTTAAAAATAAAAAAAATAAA
29175607 AAAA
1 AAAA
29175611 TAAAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.21
29 7 0.25
30 15 0.54
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (29 bp):
AAAAATATTTTAAAAATAAAAAAAATAAA
Found at i:29175610 original size:40 final size:40
Alignment explanation
Indices: 29175475--29175610 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
29175465 AAAATTTATT
* **
29175475 TTAAAAATTAAAAAAAACTTAAAAAAAGTATTTTAAAAATA
1 TTAAAAA-TAAAAAAAAATTTTAAAAAGTATTTTAAAAATA
* *
29175516 TTTTAAAAT-TAAAAAAATTTTAAAAAGTATTTTAAAAATA
1 -TTAAAAATAAAAAAAAATTTTAAAAAGTATTTTAAAAATA
* *
29175556 TTTTAAAATTAAAAAAAATTTTAAAAAGTATTTTAAAAATA
1 -TTAAAAATAAAAAAAAATTTTAAAAAGTATTTTAAAAATA
*
29175597 -AAAAAATAAAAAAA
1 TTAAAAATAAAAAAA
29175611 TAAAAATATT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 11 0.13
40 36 0.43
41 31 0.37
42 6 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (40 bp):
TTAAAAATAAAAAAAAATTTTAAAAAGTATTTTAAAAATA
Found at i:29177932 original size:14 final size:14
Alignment explanation
Indices: 29177913--29177951 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
29177903 AATCGTTTTC
29177913 CAAAAAAAAAAAGAA
1 CAAAAAAAAAAA-AA
29177928 CAAAAGAAAAAAAAA
1 CAAAA-AAAAAAAAA
29177943 CAAAGAAAA
1 CAAA-AAAA
29177952 GGGAAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:29180119 original size:22 final size:22
Alignment explanation
Indices: 29180077--29180121 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29180067 ACTTTACTTG
* *
29180077 AAAAAACTCATCAAAAGAGGAT
1 AAAAAACTCATAAAAAAAGGAT
29180099 AAAAAA-TCATAAATAAAAGGAT
1 AAAAAACTCATAAA-AAAAGGAT
29180121 A
1 A
29180122 TTTCACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAAACTCATAAAAAAAGGAT
Found at i:29185444 original size:19 final size:19
Alignment explanation
Indices: 29185420--29185481 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
29185410 GAGATCTCAG
29185420 AGTTTGTATCGAAATGTTT
1 AGTTTGTATCGAAATGTTT
* * *
29185439 AGTTTG---CCAATAAGTTAA
1 AGTTTGTATCGAA-ATGTT-T
29185457 AGTTTGTATCGAAATGTTT
1 AGTTTGTATCGAAATGTTT
29185476 AGTTTG
1 AGTTTG
29185482 CCAATAAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 6 0.19
19 12 0.38
20 4 0.12
21 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (19 bp):
AGTTTGTATCGAAATGTTT
Found at i:29185461 original size:37 final size:37
Alignment explanation
Indices: 29185420--29185495 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
29185410 GAGATCTCAG
29185420 AGTTTGTATCGAAATGTTTAGTTTGCCAATAAGTTAA
1 AGTTTGTATCGAAATGTTTAGTTTGCCAATAAGTTAA
29185457 AGTTTGTATCGAAATGTTTAGTTTGCCAATAAGTTAA
1 AGTTTGTATCGAAATGTTTAGTTTGCCAATAAGTTAA
29185494 AG
1 AG
29185496 CCAAGCATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (37 bp):
AGTTTGTATCGAAATGTTTAGTTTGCCAATAAGTTAA
Found at i:29195870 original size:17 final size:16
Alignment explanation
Indices: 29195848--29195891 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
29195838 TGAAATTTTT
29195848 TTTATATGTTTTATAAA
1 TTTATAT-TTTTATAAA
*
29195865 TTTATATATTTATAAA
1 TTTATATTTTTATAAA
*
29195881 ATTATATTTTT
1 TTTATATTTTT
29195892 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTATATTTTTATAAA
Found at i:29196041 original size:17 final size:16
Alignment explanation
Indices: 29196019--29196062 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
29196009 TGAAAGAAAT
*
29196019 TTTATATGTTTTATAAA
1 TTTATAT-TTTTAAAAA
*
29196036 TTTATATATTTAAAAA
1 TTTATATTTTTAAAAA
*
29196052 ATTATATTTTT
1 TTTATATTTTT
29196063 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTATATTTTTAAAAA
Found at i:29196095 original size:170 final size:171
Alignment explanation
Indices: 29195822--29196172 Score: 607
Period size: 170 Copynumber: 2.1 Consensus size: 171
29195812 AGACACCATT
* **** *
29195822 TGTTTAGGTTCATTCTTGAAATTTTTTTTATATGTTTTATAAATTTATATATTTATAAAATTATA
1 TGTTTAGGTTAATTCTTGAAAGAAATTTTATATGTTTTATAAATTTATATATTTAAAAAATTATA
29195887 TTTTTTTAATTTTTAAATAATAATAAAAAAGCTAATATCTTAT-AAGTGTTTGAAAAAATATAAA
66 TTTTTTTAATTTTTAAATAATAATAAAAAAGCTAATATCTTATAAAG-GTTTGAAAAAATATAAA
29195951 ATTAATTAAAAATTAAGTCCATAATGTATCTAGACAAACTGA
130 ATTAATTAAAAATTAAGTCCATAATGTATCTAGACAAACTGA
29195993 TGTTTAGGTTAATTCTTGAAAGAAATTTTATATGTTTTATAAATTTATATATTTAAAAAATTATA
1 TGTTTAGGTTAATTCTTGAAAGAAATTTTATATGTTTTATAAATTTATATATTTAAAAAATTATA
*
29196058 -TTTTTTAATTTTTAAATAATAATATAAAAGCTAATATCTTATAAAGGTTTGAAAAAATATAAAA
66 TTTTTTTAATTTTTAAATAATAATAAAAAAGCTAATATCTTATAAAGGTTTGAAAAAATATAAAA
*
29196122 TTATTTAAAAATTAAGTCCATAATGTATCTAGACAAACTGA
131 TTAATTAAAAATTAAGTCCATAATGTATCTAGACAAACTGA
29196163 TGTTTAGGTT
1 TGTTTAGGTT
29196173 CATCTGAACT
Statistics
Matches: 171, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
170 109 0.64
171 62 0.36
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (171 bp):
TGTTTAGGTTAATTCTTGAAAGAAATTTTATATGTTTTATAAATTTATATATTTAAAAAATTATA
TTTTTTTAATTTTTAAATAATAATAAAAAAGCTAATATCTTATAAAGGTTTGAAAAAATATAAAA
TTAATTAAAAATTAAGTCCATAATGTATCTAGACAAACTGA
Found at i:29200314 original size:28 final size:28
Alignment explanation
Indices: 29200268--29200369 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
29200258 TGACTTTCGA
* *
29200268 CACTAAGTGTGCAAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
29200296 CACTAAGTGCGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
29200324 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
29200352 CACTAAGTGTGCGAGTTT
1 CACTAAGTGTGCGAGTTT
29200370 GATTATTGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:29200383 original size:28 final size:28
Alignment explanation
Indices: 29200268--29200390 Score: 98
Period size: 28 Copynumber: 4.4 Consensus size: 28
29200258 TGACTTTCGA
* *
29200268 CACTAAGTGTGCAAATTTA--ATTGTAAAG
1 CACTAAGTGTGCGAGTTTATTATTG--AAG
*
29200296 CACTAAGTGCGCGAGTTTA--ATTGTAAAG
1 CACTAAGTGTGCGAGTTTATTATTG--AAG
*
29200324 CACTAAGTGTGCGAGTTTA--ATGGCAAAG
1 CACTAAGTGTGCGAGTTTATTATTG--AAG
29200352 CACTAAGTGTGCGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAGTTT-ATTATTGAAG
29200380 CACTAAGTGTG
1 CACTAAGTGTG
29200391 TGAACTTATT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
28 79 0.93
29 3 0.04
31 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTATTATTGAAG
Found at i:29200384 original size:56 final size:55
Alignment explanation
Indices: 29200267--29200390 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 55
29200257 TTGACTTTCG
* *
29200267 ACACTAAGTGTGCAAATTTAATTGTAAAGCACTAAGTGCGCGAGTTTAATTGTAA
1 ACACTAAGTGTGCAAATTTAATGGCAAAGCACTAAGTGCGCGAGTTTAATTGTAA
* * * * * *
29200322 AGCACTAAGTGTGCGAGTTTAATGGCAAAGCACTAAGTGTGCGAGTTTGATTATTGA
1 A-CACTAAGTGTGCAAATTTAATGGCAAAGCACTAAGTGCGCGAGTTTAATT-GTAA
29200379 ACACTAAGTGTG
1 ACACTAAGTGTG
29200391 TGAACTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
55 1 0.02
56 55 0.93
57 3 0.05
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (55 bp):
ACACTAAGTGTGCAAATTTAATGGCAAAGCACTAAGTGCGCGAGTTTAATTGTAA
Found at i:29201252 original size:93 final size:93
Alignment explanation
Indices: 29201118--29201803 Score: 1081
Period size: 93 Copynumber: 7.4 Consensus size: 93
29201108 TGGTGAATAA
* * *
29201118 ATGCTGTCCAATTTT-GT-ATATACATGCTGTCAAATTTTGTATATACATGCTGTCAAATTTTGT
1 ATGCTGCCCAATTTTGGTGA-ATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGT
29201181 GTATAAGTGCTGTCCAAATTGGTATATAT
65 GTATAAGTGCTGTCCAAATTGGTATATAT
* *
29201210 ATGCTGCCAAATTTTGGTGAATAAATGCTGTCCAATTTTGTATGTACATGCTGTCAAATTTTGTG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
* * * *
29201275 TATAAGTGTTGCCCAAATTGCTACATAT
66 TATAAGTGCTGTCCAAATTGGTATATAT
* **
29201303 ATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATTTTGTATATACATGCTGTCAAATTTCATG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
* *
29201368 TATAAGTGCTGTCCAAATTGCTACATAT
66 TATAAGTGCTGTCCAAATTGGTATATAT
* * *
29201396 ATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTATCCAATTTTGTG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
29201461 TATAAGTGCTGTCCAAATTGGTATATAT
66 TATAAGTGCTGTCCAAATTGGTATATAT
*
29201489 ATGCTGCCCAATTTTGGTGAATAAATGCTGTTCAATTTTGTATATACATGCTGTCAAATTTTGTG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
29201554 TATAAGTGCTGTCCAAATTGGTATATAT
66 TATAAGTGCTGTCCAAATTGGTATATAT
* *
29201582 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATGCATGCTGTCAAGTTTTGTG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
29201647 TATAAGTGCTGTCCAAATTGGTATATAT
66 TATAAGTGCTGTCCAAATTGGTATATAT
*
29201675 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGGTGTCAAATTTTGTG
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
* * *
29201740 TATAAGTGCTATCCATATTGGTATATAC
66 TATAAGTGCTGTCCAAATTGGTATATAT
* * *
29201768 ATGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 ATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
29201804 ACAGGGTAGG
Statistics
Matches: 550, Mismatches: 40, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
92 13 0.02
93 518 0.94
94 18 0.03
95 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (93 bp):
ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
TATAAGTGCTGTCCAAATTGGTATATAT
Found at i:29208703 original size:28 final size:30
Alignment explanation
Indices: 29208671--29208726 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
29208661 TTAGGACTTA
29208671 TCTTTT-AATT-T-CTTGCTGTCAATTTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTTT
29208699 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
29208727 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 4 0.16
30 11 0.44
31 4 0.16
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (30 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTTT
Found at i:29213041 original size:28 final size:28
Alignment explanation
Indices: 29213000--29213123 Score: 160
Period size: 28 Copynumber: 4.4 Consensus size: 28
29212990 TGACTTTCGA
*
29213000 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
29213028 CACTAAGTGCGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
29213056 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * * *
29213084 CACTAAGTGTGTGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
29213112 CACTAAGTGTGC
1 CACTAAGTGTGC
29213124 AAACTTATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 81 0.98
29 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:29213927 original size:93 final size:92
Alignment explanation
Indices: 29213817--29214907 Score: 1004
Period size: 93 Copynumber: 11.7 Consensus size: 92
29213807 TCTAAAATTG
* * * * * * *
29213817 GTATATATATGCTGTCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAA
1 GTATATACATGCTGTCCAATTTT-GTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCA
* *
29213882 ATTTTGTATATACATGCTGTCAAATTTT
65 ATTTTGTATATAAATGCTGTCCAATTTT
* * * * * * * * *
29213910 GTGTATA-AGTGCTGTCCAAATTGGTATATATA-TGTTGCCCAATTTTGGTGA-ATAAATGCTGT
1 GTATATACA-TGCTGTCCAATTTTGTGTATA-AGTGCTGTCCAAATTT-GT-ATATATATGCTGC
* *
29213972 CCAATTTTGTATATACATGCTGTCAAATTTT
62 CCAATTTTGTATATAAATGCTGTCCAATTTT
* * * * ** * * * *
29214003 GTGTATA-AGTGTTGCCCAA-ATTGCTACATATA-TGCTGCCCAATTTTGGTGA-ATAAATGCTA
1 GTATATACA-TGCTGTCCAATTTTG-TGTATA-AGTGCTGTCCAAATTT-GT-ATATATATGCTG
* * *
29214064 TCCAATTTTGTATATACATGCTGTCAAATTTCAT
61 CCCAATTTTGTATATAAATGCTGTCCAATTT--T
* * ** * * * * *
29214098 GTATA-A-GTGCTGTCCAA-ATTGCTACATATA-TGCTGCCCAATTTTGGTGA-ATAAATGTTGT
1 GTATATACATGCTGTCCAATTTTG-TGTATA-AGTGCTGTCCAAATTT-GT-ATATATATGCTGC
*
29214158 CCAATTTTGTATATACATGCTGTCCAATTTT
62 CCAATTTTGTATATAAATGCTGTCCAATTTT
* * * * * * * *
29214189 GTGTATA-AGTGCTGTCCAAATTGGTATATATA-TGCTGCCCAATTTTGGTGA-ATAAATGCTGT
1 GTATATACA-TGCTGTCCAATTTTGTGTATA-AGTGCTGTCCAAATTT-GT-ATATATATGCTGC
* *
29214251 CCAATTTTGTATATACATGCTGTCAAATTTT
62 CCAATTTTGTATATAAATGCTGTCCAATTTT
* * *
29214282 GTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGTTGCCCAA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
29214347 TTTTGGTGA-ATAAATGCTGTCCAATTTT
66 TTTT-GT-ATATAAATGCTGTCCAATTTT
* * * ** * *
29214375 GTATATACACGCTGTCAAATTTTGTGTATAAGTGTTACCCAAA-TTGCTACATATAAGCTGCCCA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTG-TATATATATGCTGCCCA
*
29214439 ATTTTGGTGA-ATAAATGCTATCCAATTTT
65 ATTTT-GT-ATATAAATGCTGTCCAATTTT
* ** *
29214468 GTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAA-TTGCTACATATATGCTGCCCA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTG-TATATATATGCTGCCCA
*
29214532 ATTTTGGTGA-ATAAATGTTGTCCAATTTT
65 ATTTT-GT-ATATAAATGCTGTCCAATTTT
*
29214561 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
29214626 TTTTGGTGA-ATAAATGCTGTCCAATTTT
66 TTTT-GT-ATATAAATGCTGTCCAATTTT
*
29214654 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
29214719 TTTTGT-TGAATAAATGCTGTCCAATTTT
66 TTTTGTAT--ATAAATGCTGTCCAATTTT
* * *
29214747 GTATATGCATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
29214812 TTTTGGTGA-ATAAATGCTGTCCAATTTT
66 TTTT-GT-ATATAAATGCTGTCCAATTTT
* * * * *
29214840 GTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATACATGCTTCTCAA
1 GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
29214905 TTT
66 TTT
29214908 CTGATGTATA
Statistics
Matches: 902, Mismatches: 73, Indels: 46
0.88 0.07 0.05
Matches are distributed among these distances:
91 6 0.01
92 44 0.05
93 837 0.93
94 10 0.01
95 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (92 bp):
GTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTTGTATATATATGCTGCCCAA
TTTTGTATATAAATGCTGTCCAATTTT
Found at i:29214366 original size:279 final size:276
Alignment explanation
Indices: 29213826--29214907 Score: 1398
Period size: 279 Copynumber: 3.8 Consensus size: 276
29213816 GGTATATATA
* * * * *
29213826 TGCTGTCCAATTTTGGTGA-ATAAATGCTGTCCAATTTT-GT-ATATACATGCTGTCAAATTTTG
1 TGCTGTCCAA-ATTGGT-ATATATATGCTGCCCAATTTTGGTGA-ATAAATGCTGTCCAATTTTG
*
29213888 TATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGTTGCCCAAT
63 TATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAAT
* * * *
29213953 TTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGTTGC
128 TTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTATATAA-TGCTGT
* *
29214018 CCAAA-TTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATTTTGTATATACA
192 CCAAATTTG-TATATATATGCTGCCCAA-TTTGGT-AATAAATGCTGTCCAATTTTGTATATACA
**
29214082 TGCTGTCAAATTTCATGTATAAG
254 TGCTGTCAAATTTTGTGTATAAG
* * *
29214105 TGCTGTCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTAT
1 TGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTAT
*
29214170 ATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
66 ATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
29214235 GGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTATATACATGCTGTCAA
131 GGTGAATAAATGCTGTCCAATTTTGTATATACA---TG-C------TG--------T-C---C-A
* * *
29214300 ATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGTTGCCCAATTTTGGTGAATAAATGCT
173 ATTTTGTATATAA-TGCTGTCCAAATTTGTATATATATGCTGCCCAA-TTTGGT-AATAAATGCT
*
29214365 GTCCAATTTTGTATATACACGCTGTCAAATTTTGTGTATAAG
235 GTCCAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAG
* ** * * * *
29214407 TGTTACCCAAATTGCTACATATAAGCTGCCCAATTTTGGTGAATAAATGCTATCCAATTTTGTAT
1 TGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTAT
** * *
29214472 ATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCCAATTTT
66 ATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
* *
29214537 GGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCCA
131 GGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTATATAA-TGCTGTCCA
*
29214602 AATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCT
195 AATTTGTATATATATGCTGCCCAA-TTTGGT-AATAAATGCTGTCCAATTTTGTATATACATGCT
*
29214667 GTCCAATTTTGTGTATAAG
258 GTCAAATTTTGTGTATAAG
*
29214686 TGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGTTGAATAAATGCTGTCCAATTTTGTAT
1 TGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTAT
*
29214751 ATGCATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
66 ATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
* *
29214816 GGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCA
131 GGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTATATAA-TGCTGTCCA
* * * *
29214881 AATTGGTATATACATGCTTCTCAATTT
195 AATTTGTATATATATGCTGCCCAATTT
29214908 CTGATGTATA
Statistics
Matches: 724, Mismatches: 52, Indels: 55
0.87 0.06 0.07
Matches are distributed among these distances:
277 1 0.00
278 24 0.03
279 434 0.60
280 2 0.00
282 2 0.00
283 2 0.00
284 1 0.00
289 2 0.00
292 2 0.00
297 1 0.00
298 2 0.00
299 2 0.00
302 247 0.34
303 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (276 bp):
TGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTAT
ATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTT
GGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTATATAATGCTGTCCAA
ATTTGTATATATATGCTGCCCAATTTGGTAATAAATGCTGTCCAATTTTGTATATACATGCTGTC
AAATTTTGTGTATAAG
Found at i:29214541 original size:395 final size:395
Alignment explanation
Indices: 29213811--29214929 Score: 1863
Period size: 395 Copynumber: 2.9 Consensus size: 395
29213801 TAATGGTCTA
*
29213811 AAATTGGTATATATATGCTGTCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
29213876 TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
66 TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
29213941 ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
131 ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
29214006 TATAAGTGTTGCCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
196 TATAAGTGTTGCCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
29214071 TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
261 TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
29214136 AATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGC
326 AATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGC
29214201 TGTCC
391 TGTCC
29214206 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
29214271 TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
66 TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
*
29214336 ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACACGCTGTCAAATTTTGTG
131 ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
* *
29214401 TATAAGTGTTACCCAAATTGCTACATATAAGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
196 TATAAGTGTTGCCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
29214466 TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
261 TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
29214531 AATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGC
326 AATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGC
29214596 TGTCC
391 TGTCC
29214601 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACA---
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
29214663 TG-C------TG--------T-C---C-AATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
66 TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
* * *
29214708 ATGCTGCCCAATTTTGTTGAATAAATGCTGTCCAATTTTGTATATGCATGCTGTCAAATTTTGTG
131 ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
* * * * *
29214773 TATAAGTGCTGTCCAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATT
196 TATAAGTGTTGCCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
** * * * * *
29214838 TTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATACATGCTTCTC
261 TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
* *
29214903 AATTTCTGATGTATAAGA-GTTGTCCAA
326 AATTT-TGGTGAATAA-ATGTTGTCCAA
29214930 ACAGGGTAGA
Statistics
Matches: 698, Mismatches: 24, Indels: 26
0.93 0.03 0.03
Matches are distributed among these distances:
372 219 0.31
373 18 0.03
374 1 0.00
376 1 0.00
377 1 0.00
385 2 0.00
391 1 0.00
392 2 0.00
395 453 0.65
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (395 bp):
AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCCAAATTGGTATATAT
ATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTTTGTG
TATAAGTGTTGCCCAAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATT
TTGTATATACATGCTGTCAAATTTCATGTATAAGTGCTGTCCAAATTGCTACATATATGCTGCCC
AATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGC
TGTCC
Found at i:29217071 original size:26 final size:26
Alignment explanation
Indices: 29217035--29217125 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
29217025 TCCTGAATAA
* *
29217035 CAGGCCTTGAGTCGGTGATCATTTAG
1 CAGGCCTTGAGCCGGTGATTATTTAG
*
29217061 CAGGCCTTGAGCCGGTGATTACTTAG
1 CAGGCCTTGAGCCGGTGATTATTTAG
* * *
29217087 TAGG-CTATGAACCAGTGATTATTTAG
1 CAGGCCT-TGAGCCGGTGATTATTTAG
*
29217113 CAGGCATTGAGCC
1 CAGGCCTTGAGCC
29217126 CTTGGTTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 2 0.04
26 50 0.94
27 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (26 bp):
CAGGCCTTGAGCCGGTGATTATTTAG
Found at i:29224053 original size:18 final size:18
Alignment explanation
Indices: 29224030--29224071 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
29224020 CGATTTTGGG
29224030 CATGCATTCCATGC-AACC
1 CATGCATTCCATGCGAA-C
*
29224048 CATGCATTTCATGCGAAC
1 CATGCATTCCATGCGAAC
29224066 CATGCA
1 CATGCA
29224072 ATGTGTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (18 bp):
CATGCATTCCATGCGAAC
Found at i:29237983 original size:20 final size:20
Alignment explanation
Indices: 29237942--29237983 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29237932 ATAATTTTAT
*
29237942 TAAATTATAAATTATATTAA
1 TAAATTATAAATTATATAAA
29237962 TAAATTATTAAATTAT-TAAA
1 TAAATTA-TAAATTATATAAA
29237982 TA
1 TA
29237984 TAAATATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTATAAATTATATAAA
Found at i:29262489 original size:78 final size:78
Alignment explanation
Indices: 29262405--29262585 Score: 247
Period size: 78 Copynumber: 2.3 Consensus size: 78
29262395 AGATGCTTTA
* *
29262405 AGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTA-TATTATGATATATGCTTGAATGT
1 AGTATTGTGATATATGCTTAAAAGTTATGAGATTATATG-ACTATTATGATATATGCTTAAATGT
29262469 TATGTCATTATACG
65 TATGTCATTATACG
* *
29262483 AGTATTGTGATATATGCTTAAAAGTTATGTGATTATATGACTATTGTGATATATGCTTAAATGTT
1 AGTATTGTGATATATGCTTAAAAGTTATGAGATTATATGACTATTATGATATATGCTTAAATGTT
* * *
29262548 ATGTGATTAAATG
66 ATGTCATTATACG
* * * *
29262561 TGTAATATGATACATGCTTAAAAGT
1 AGTATTGTGATATATGCTTAAAAGT
29262586 AAAATGATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
77 1 0.01
78 90 0.99
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (78 bp):
AGTATTGTGATATATGCTTAAAAGTTATGAGATTATATGACTATTATGATATATGCTTAAATGTT
ATGTCATTATACG
Found at i:29262572 original size:39 final size:39
Alignment explanation
Indices: 29262405--29262582 Score: 223
Period size: 39 Copynumber: 4.6 Consensus size: 39
29262395 AGATGCTTTA
* *
29262405 AGTATTGTGATATATGCTTAAATGTTATGAGATTATATG
1 AGTATTATGATATATGCTTAAATGTTATGTGATTATATG
* * *
29262444 TA-TATTATGATATATGCTTGAATGTTATGTCATTATACG
1 -AGTATTATGATATATGCTTAAATGTTATGTGATTATATG
* *
29262483 AGTATTGTGATATATGCTTAAAAGTTATGTGATTATATG
1 AGTATTATGATATATGCTTAAATGTTATGTGATTATATG
* * *
29262522 ACTATTGTGATATATGCTTAAATGTTATGTGATTAAATG
1 AGTATTATGATATATGCTTAAATGTTATGTGATTATATG
* * *
29262561 TGTAATATGATACATGCTTAAA
1 AGTATTATGATATATGCTTAAA
29262583 AGTAAAATGA
Statistics
Matches: 119, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
38 1 0.01
39 117 0.98
40 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (39 bp):
AGTATTATGATATATGCTTAAATGTTATGTGATTATATG
Found at i:29265608 original size:20 final size:21
Alignment explanation
Indices: 29265566--29265608 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
29265556 AAGCCAAAAG
* *
29265566 AATAAGAAAGAATGTATGAGA
1 AATAAGAAAGAATGAACGAGA
*
29265587 AATAA-AAAGAATGAACGTGA
1 AATAAGAAAGAATGAACGAGA
29265607 AA
1 AA
29265609 ACAATGGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.16
Consensus pattern (21 bp):
AATAAGAAAGAATGAACGAGA
Found at i:29268683 original size:16 final size:16
Alignment explanation
Indices: 29268662--29268692 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29268652 TTATTTATAT
29268662 TTATTAATATAATAAG
1 TTATTAATATAATAAG
29268678 TTATTAATATAATAA
1 TTATTAATATAATAA
29268693 ATATAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTATTAATATAATAAG
Found at i:29268698 original size:22 final size:22
Alignment explanation
Indices: 29268659--29268716 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
29268649 TAATTATTTA
* *
29268659 TATT-TATTAATATA-ATAAGT
1 TATTATATTAATAAATATAAAT
29268679 TATTA-ATATAATAAATATAAAT
1 TATTATAT-TAATAAATATAAAT
29268701 TATTATATTAATAAAT
1 TATTATATTAATAAAT
29268717 TATTTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 18 0.56
23 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATATTAATAAATATAAAT
Found at i:29268816 original size:15 final size:15
Alignment explanation
Indices: 29268796--29268852 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
29268786 ATTCAATATT
29268796 AATATTTTAATAATA
1 AATATTTTAATAATA
*
29268811 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
29268830 AATATATTAATAATA
1 AATATTTTAATAATA
*
29268845 AATGTTTT
1 AATATTTT
29268853 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:29273119 original size:44 final size:44
Alignment explanation
Indices: 29273103--29273668 Score: 624
Period size: 44 Copynumber: 12.9 Consensus size: 44
29273093 ATGATCTACG
* * *
29273103 ATCTTCAACCTATTCCACTGCTGTCTAGGGAGATATGACTTTCA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
*
29273147 ATCTTCAACCTATTCCACTGTTGTCCAGGGAGATAGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
* *
29273191 ATCTTCAACCTATTCCACTGTTGTCCAGGGAGATAGAACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
* * *
29273235 ATCTTCAACCTATTCCACTGTTCTCCAGGGAGATAAGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
* * * *
29273279 ATCTTCAACCTATCCCACTACTGTCCCGAGAGATAGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
* *
29273323 ATCTTCAACCTATTCCATTACTGTCCAGGGAGATAGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
*
29273367 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGAACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
* *
29273411 ATCTTCAACCTATTCCACTGTTGTCCAGGGAGATAAGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
***
29273455 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGAC-TGGT
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
** * * * * * *
29273498 GGCTT--ATCTACTTCC-CTACT-ACCTTGGGAAGATAAGA-TTCACC
1 ATCTTCAACCTA-TTCCACTGCTGTCC-AGGG-AGATAGGACTT-ACA
* ** * * * ** * * * *
29273541 GTCTTTGATCTGTTCCACTACTGTTTAGGGAGACA-TAATCTACG
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACT-TACA
** * *
29273585 ATCTTCAACCTATTTTACTGCTGTCTAGAGAGATAGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
*
29273629 ATCTTCAACCTATTCTACTGCTGTCCAGGGAGATAGGACT
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACT
29273669 GGTATCTTCG
Statistics
Matches: 444, Mismatches: 66, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
40 2 0.00
41 11 0.02
42 12 0.03
43 9 0.02
44 395 0.89
45 15 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACA
Found at i:29273135 original size:130 final size:131
Alignment explanation
Indices: 29272844--29273142 Score: 449
Period size: 130 Copynumber: 2.3 Consensus size: 131
29272834 ATCTGCTATT
* * * *
29272844 TTCAACCCACTCCACTGCTG-CTTAGAGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTAC
1 TTCAACCTATTCCACTGCTGTC-TAGGGAGATAGGACTAGTGGCTT-AATCTACTTCCCTACTAC
* *
29272908 CTTGGGAAGATAAGATTCACCGTCTTTGATCTGTTCCACTACTGTTTAGGGAGACATGATCTACA
64 CTTGGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACTATTTAGGGAGACATGATCTACA
29272973 ATC
129 ATC
* * * * *
29272976 TTCAACCTATTCCACTACTTTCCAAGGAGATAGGACTGGTGGCTT-ATCTACTTCCCTACTACCT
1 TTCAACCTATTCCACTGCTGTCTAGGGAGATAGGACTAGTGGCTTAATCTACTTCCCTACTACCT
*
29273040 TGGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACTATTTAGGGAGACATGATCTACGAT
66 TGGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACTATTTAGGGAGACATGATCTACAAT
29273105 C
131 C
*
29273106 TTCAACCTATTCCACTGCTGTCTAGGGAGATATGACT
1 TTCAACCTATTCCACTGCTGTCTAGGGAGATAGGACT
29273143 TTCAATCTTC
Statistics
Matches: 149, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
130 113 0.76
132 35 0.23
133 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (131 bp):
TTCAACCTATTCCACTGCTGTCTAGGGAGATAGGACTAGTGGCTTAATCTACTTCCCTACTACCT
TGGGAAGATAAGATTCACCATCTTTGATCTGTTCCACTACTATTTAGGGAGACATGATCTACAAT
C
Found at i:29280835 original size:23 final size:23
Alignment explanation
Indices: 29280806--29280871 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
29280796 ATGGTTTGGG
29280806 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
29280829 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
*
29280852 TTTGGTTCGAAATGGAAATG
1 TTTGGTACGAAATGGAAATG
29280872 GTTTAAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (23 bp):
TTTGGTACGAAATGGAAATGTAA
Found at i:29281988 original size:29 final size:31
Alignment explanation
Indices: 29281924--29281988 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
29281914 AGCAAAAATT
*
29281924 AATTGAGCTGAATTTGTAAGTATTGGAGCTA
1 AATTGAGCTGAATTTGTAACTATTGGAGCTA
29281955 AATTGAGCTG-ATTTG-AACTCATT-GAGCTA
1 AATTGAGCTGAATTTGTAACT-ATTGGAGCTA
29281984 AATTG
1 AATTG
29281989 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 14 0.44
30 8 0.25
31 10 0.31
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (31 bp):
AATTGAGCTGAATTTGTAACTATTGGAGCTA
Found at i:29289018 original size:42 final size:42
Alignment explanation
Indices: 29288971--29289050 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
29288961 ATGTGTGAAC
29288971 CGTTTGAAATTCAAACATTTAAACTCTTGTTCTTATCCAAAA
1 CGTTTGAAATTCAAACATTTAAACTCTTGTTCTTATCCAAAA
*
29289013 CGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 CGTTTGAAATTCAAACATTTAAACTCTTGTTCTTATCC
29289051 CTTTGAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (42 bp):
CGTTTGAAATTCAAACATTTAAACTCTTGTTCTTATCCAAAA
Found at i:29301786 original size:24 final size:24
Alignment explanation
Indices: 29301759--29301810 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29301749 AATTAATGTC
* *
29301759 AAATATATTATGCAAATAAATGCT
1 AAATATATTATACAAATAAATACT
*
29301783 AAATATATTATACTAATAAATACT
1 AAATATATTATACAAATAAATACT
29301807 AAAT
1 AAAT
29301811 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATATATTATACAAATAAATACT
Found at i:29307082 original size:27 final size:27
Alignment explanation
Indices: 29307052--29307229 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
29307042 ATATTGAGCC
* *
29307052 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
29307079 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
29307106 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*** ** *
29307134 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
29307161 CGCACTCTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
29307188 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
29307215 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29307230 GTACAATTTA
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 93 0.79
28 22 0.19
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29307164 original size:55 final size:54
Alignment explanation
Indices: 29307052--29307229 Score: 150
Period size: 54 Copynumber: 3.3 Consensus size: 54
29307042 ATATTGAGCC
* * *
29307052 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
* * * *
29307106 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTG-C-CGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACGTA--ATCAAAT
* * ** * *
29307161 CGCACTCTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAAC-AAAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACGTAA-TCA-AAT
29307215 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29307230 GTACAATTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
53 5 0.05
54 52 0.53
55 40 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
Found at i:29315089 original size:27 final size:27
Alignment explanation
Indices: 29315059--29315236 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
29315049 ATATTGAGCC
* *
29315059 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
29315086 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
29315113 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*** ** *
29315141 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
29315168 CGCACTCTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
29315195 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
29315222 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29315237 GTACAATTTA
Statistics
Matches: 117, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 93 0.79
28 22 0.19
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29315171 original size:55 final size:54
Alignment explanation
Indices: 29315059--29315236 Score: 150
Period size: 54 Copynumber: 3.3 Consensus size: 54
29315049 ATATTGAGCC
* * *
29315059 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
* * * *
29315113 CGCACACTTAGTGCTACATAGTTAGACTCGCACACTTAGTG-C-CGTATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACGTA--ATCAAAT
* * ** * *
29315168 CGCACTCTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAAC-AAAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACGTAA-TCA-AAT
29315222 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29315237 GTACAATTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
53 5 0.05
54 52 0.53
55 40 0.41
56 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
Found at i:29324753 original size:32 final size:32
Alignment explanation
Indices: 29324716--29324777 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
29324706 CTTAGTTAAA
29324716 TATGGAAGTATAAATATGCATGTTTTTTTTTC
1 TATGGAAGTATAAATATGCATGTTTTTTTTTC
29324748 TATGGAAGTATAAATATGCATGTTTTTTTT
1 TATGGAAGTATAAATATGCATGTTTTTTTT
29324778 CTAAGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (32 bp):
TATGGAAGTATAAATATGCATGTTTTTTTTTC
Found at i:29325652 original size:69 final size:69
Alignment explanation
Indices: 29325541--29325678 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
29325531 GAACCTTTCT
*
29325541 TCTCCAAAACAATCATACCTTTTTTACTTGTATAACCAAGTCATCTATGCCTCAACTGAGTCGAA
1 TCTCCAAAACAATCATACCTTTTTTACTTGTATAACCAAGTCATCTATGCCTCAACTGAGTCAAA
29325606 TCTA
66 TCTA
29325610 TCTCCAAAACAATCATACCTTTTTTACTTGTATAACCAAGTCATCTATGCCTCAACTGAGTCAAA
1 TCTCCAAAACAATCATACCTTTTTTACTTGTATAACCAAGTCATCTATGCCTCAACTGAGTCAAA
29325675 TCTA
66 TCTA
29325679 ACTCTTTAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (69 bp):
TCTCCAAAACAATCATACCTTTTTTACTTGTATAACCAAGTCATCTATGCCTCAACTGAGTCAAA
TCTA
Found at i:29335199 original size:37 final size:37
Alignment explanation
Indices: 29335144--29335291 Score: 142
Period size: 37 Copynumber: 4.0 Consensus size: 37
29335134 AGTACACTCT
* *
29335144 ATCGAGCCAAATCTTATTGTTATACTGAATAAAGCTCA
1 ATCGAG-CAAATCTTACTGTTATACTGAATGAAGCTCA
* * *
29335182 ATCGAGCAAAT-TATATTGTTATACTGAATG-GGCTTA
1 ATCGAGCAAATCT-TACTGTTATACTGAATGAAGCTCA
* * *
29335218 AT-GAGTAAATCTTACTGTTATACTGAATGATGTTCA
1 ATCGAGCAAATCTTACTGTTATACTGAATGAAGCTCA
* * *
29335254 ATCAAGCAAAT-TCTACTGTTACACTGAGTGAAGCTCA
1 ATCGAGCAAATCT-TACTGTTATACTGAATGAAGCTCA
29335291 A
1 A
29335292 ATGAGTAGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
35 23 0.25
36 14 0.15
37 48 0.53
38 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (37 bp):
ATCGAGCAAATCTTACTGTTATACTGAATGAAGCTCA
Found at i:29336550 original size:327 final size:327
Alignment explanation
Indices: 29335956--29336610 Score: 1220
Period size: 327 Copynumber: 2.0 Consensus size: 327
29335946 GTGTGTAGGC
29335956 ACCTATGCAATAAGGGAGTGAAATTGAGCAAGAAATAGATCACTTTGGGTTCACACAGCCTGAGA
1 ACCTATGCAATAAGGGAGTGAAATTGAGCAAGAAATAGATCACTTTGGGTTCACACAGCCTGAGA
** *
29336021 CACAGGCGTGCGACTTAGCCATGTGAAGCACATGGCCTTGCGGCTCAGTCGTGTGTCATCTGAGG
66 CACAGGCGTGCGACTTAGCCATGTGAAGCACACAGCCTTGCGACTCAGTCGTGTGTCATCTGAGG
29336086 GTCTTTTGTATACAAGTCAGTGATTTGCACAGCCTAACACACGACCTGGCACACAGGCATGTGGG
131 GTCTTTTGTATACAAGTCAGTGATTTGCACAGCCTAACACACGACCTGGCACACAGGCATGTGGG
29336151 GAACTCAGAGAGCTACACGGCCTGGCACACGGGCATGTGACACGACCGTGTGACCCTACTCAGAG
196 GAACTCAGAGAGCTACACGGCCTGGCACACGGGCATGTGACACGACCGTGTGACCCTACTCAGAG
29336216 AGTTACACAGGTGAGGACATGAGCTGGGACACAACCGTGTGTCCCTTGTTTGAAAGTTACACGGC
261 AGTTACACAGGTGAGGACATGAGCTGGGACACAACCGTGTGTCCCTTGTTTGAAAGTTACACGGC
29336281 CT
326 CT
29336283 ACCTATGCAATAAGGGAGTGAAATTGAGCAAGAAATAGATCACTTTGGGTTCACACAGCCTGAGA
1 ACCTATGCAATAAGGGAGTGAAATTGAGCAAGAAATAGATCACTTTGGGTTCACACAGCCTGAGA
*
29336348 CACAGGCGTGCGACTTAGCCATGTGAGGCACACAGCCTTGCGACTCAGTCGTGTGTCATCTGAGG
66 CACAGGCGTGCGACTTAGCCATGTGAAGCACACAGCCTTGCGACTCAGTCGTGTGTCATCTGAGG
* *
29336413 GTCTTTTGTATACAAGTCAGTGATTTGCACAGCCTAACACATGACCTGGCACACCGGCATGTGGG
131 GTCTTTTGTATACAAGTCAGTGATTTGCACAGCCTAACACACGACCTGGCACACAGGCATGTGGG
* * *
29336478 GAACTCAGAGAGCTACACGGCCTGGCATACGGGCGTGTGACATGACCGTGTGACCCTACTCAGAG
196 GAACTCAGAGAGCTACACGGCCTGGCACACGGGCATGTGACACGACCGTGTGACCCTACTCAGAG
*
29336543 AGTTACACAGGTGAGGATATGAGCTGGGACACAACCGTGTGTCCCTTGTTTGAAAGTTACACGGC
261 AGTTACACAGGTGAGGACATGAGCTGGGACACAACCGTGTGTCCCTTGTTTGAAAGTTACACGGC
29336608 CT
326 CT
29336610 A
1 A
29336611 GTCACACGGC
Statistics
Matches: 318, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
327 318 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (327 bp):
ACCTATGCAATAAGGGAGTGAAATTGAGCAAGAAATAGATCACTTTGGGTTCACACAGCCTGAGA
CACAGGCGTGCGACTTAGCCATGTGAAGCACACAGCCTTGCGACTCAGTCGTGTGTCATCTGAGG
GTCTTTTGTATACAAGTCAGTGATTTGCACAGCCTAACACACGACCTGGCACACAGGCATGTGGG
GAACTCAGAGAGCTACACGGCCTGGCACACGGGCATGTGACACGACCGTGTGACCCTACTCAGAG
AGTTACACAGGTGAGGACATGAGCTGGGACACAACCGTGTGTCCCTTGTTTGAAAGTTACACGGC
CT
Found at i:29340908 original size:50 final size:50
Alignment explanation
Indices: 29340835--29341078 Score: 190
Period size: 50 Copynumber: 4.9 Consensus size: 50
29340825 CATTGAGATT
* * *
29340835 ATGAGAGGTCCCATGTAAAACCATGTTTGGGACATAGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATAGCATTGGCACCAAG
* * *
29340885 ATGAGAGG-CATCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAG
1 ATGAGAGGTC-CCATGTAAGACCATGTTTGGGACATAGCATTGGCACCAAG
** * * * *
29340935 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATAGCATTGGCACCAAG
* ** * * * * * * *
29340985 ATAAGAACTCTCATGTAAGACCATATATAGGATATGGCATTGGCAGTACAAG
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATAGCATTGGCA--CCAAG
** * * *
29341037 A--A-ACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATAGCATTGGCA
29341079 TGTTATATTC
Statistics
Matches: 153, Mismatches: 37, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
49 31 0.20
50 118 0.77
51 1 0.01
52 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATAGCATTGGCACCAAG
Found at i:29340999 original size:100 final size:103
Alignment explanation
Indices: 29340781--29341029 Score: 265
Period size: 100 Copynumber: 2.4 Consensus size: 103
29340771 CATTTGGGTA
* * *
29340781 AAGAGA-TCTCATATAAGATCATGTCTGGGATATGGCATTGGCATCATTGAGATTATGAGAGGTC
1 AAGAGACTCTCATGTAAGACCATGTCTGGGATATGGCATTGGCACCA-T-AG--TATGAGAGGTC
* * *
29340845 CCATGTAAAACCATGTTTGGGACATAGCGTTGGCACCGAGAT
62 CCACGTAAAACCATGTTTGGGACATAGCATGGGCACCGAGAT
* * * * *
29340887 GAGAGGC-ATCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AG-ATGAGAGGTCCCCC
1 AAGAGACTCTCATGTAAGACCATGTCTGGGATATGGCATTGGCACCATAGTATGAGAGGTCCCAC
* * * *
29340949 GTAAGACCATGTTTGGGACATGGCATGGGCACCTATAT
66 GTAAAACCATGTTTGGGACATAGCATGGGCACCGAGAT
* * *
29340987 AAGA-ACTCTCATGTAAGACCATATATAGGATATGGCATTGGCA
1 AAGAGACTCTCATGTAAGACCATGTCTGGGATATGGCATTGGCA
29341030 GTACAAGAAA
Statistics
Matches: 119, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
99 1 0.01
100 78 0.66
103 2 0.02
106 38 0.32
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (103 bp):
AAGAGACTCTCATGTAAGACCATGTCTGGGATATGGCATTGGCACCATAGTATGAGAGGTCCCAC
GTAAAACCATGTTTGGGACATAGCATGGGCACCGAGAT
Found at i:29343664 original size:24 final size:24
Alignment explanation
Indices: 29343637--29343686 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
29343627 AAAGACAATT
*
29343637 AATAAATAAT-AAAATAATATTTAA
1 AATAAATAATCAAAATAA-ATTAAA
**
29343661 AATATTTAATCAAAATAAATTAAA
1 AATAAATAATCAAAATAAATTAAA
29343685 AA
1 AA
29343687 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AATAAATAATCAAAATAAATTAAA
Found at i:29344282 original size:29 final size:30
Alignment explanation
Indices: 29344229--29344287 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
29344219 GAATTAGATC
* *
29344229 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
**
29344259 AAATC-AAAGTTCATGTATCCAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
29344288 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:29356323 original size:30 final size:30
Alignment explanation
Indices: 29356266--29356323 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
29356256 TTAATACAAA
* * *
29356266 TTATATATAAATTAGTATTATATAAAAATG
1 TTATATATAAATAAATATTATAAAAAAATG
* *
29356296 TTATATATACATAAATATTTTAAAAAAA
1 TTATATATAAATAAATATTATAAAAAAA
29356324 GTACCATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
TTATATATAAATAAATATTATAAAAAAATG
Found at i:29357243 original size:21 final size:22
Alignment explanation
Indices: 29357219--29357261 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29357209 TCTTTTCTTC
29357219 TTTTGAATCATTTT-TTTTTGT
1 TTTTGAATCATTTTATTTTTGT
**
29357240 TTTTGAATTTTTTTATTTTTGT
1 TTTTGAATCATTTTATTTTTGT
29357262 ATTGATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTGAATCATTTTATTTTTGT
Found at i:29358064 original size:133 final size:134
Alignment explanation
Indices: 29357904--29358182 Score: 465
Period size: 133 Copynumber: 2.1 Consensus size: 134
29357894 ACACATTGTT
*
29357904 TGAGGATTTTTCTTTTAACTTTACTTAATAATTGAATGCTCAAATTAAGGTAAATATTTGTAAAG
1 TGAGGATTTTTCTTTTAACTTTACTTAATAATTGAATGCTCAAATTAAGGTAAACATTTGTAAAG
* *
29357969 GTC-ATTCACGTTAGAGCTAAACCTTTTAAAATAATTAAATAATAGTCAAACTTTTTGAAAATGT
66 G-CAATTCACGTAAGAGCTAAACCTTTTAAAATAATCAAATAATAGTCAAACTTTTTGAAAATGT
*
29358033 TTAAA
130 TAAAA
29358038 TGAGGATTTTTC-TTTAACTTTACTTAATAATTGAATGCTCAAATTAAGGTAAACATTTGTAAAG
1 TGAGGATTTTTCTTTTAACTTTACTTAATAATTGAATGCTCAAATTAAGGTAAACATTTGTAAAG
* *
29358102 GCAATTCACGTAAGAGCTAAACCTTTTAACATAATCAAATAATGGTCAAACTTTTTGAAAATGTT
66 GCAATTCACGTAAGAGCTAAACCTTTTAAAATAATCAAATAATAGTCAAACTTTTTGAAAATGTT
29358167 AAAA
131 AAAA
29358171 TGAAGG-TTTTTC
1 TG-AGGATTTTTC
29358183 ACACATTTCA
Statistics
Matches: 137, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
132 1 0.01
133 121 0.88
134 15 0.11
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (134 bp):
TGAGGATTTTTCTTTTAACTTTACTTAATAATTGAATGCTCAAATTAAGGTAAACATTTGTAAAG
GCAATTCACGTAAGAGCTAAACCTTTTAAAATAATCAAATAATAGTCAAACTTTTTGAAAATGTT
AAAA
Found at i:29362037 original size:70 final size:70
Alignment explanation
Indices: 29361958--29362125 Score: 198
Period size: 70 Copynumber: 2.4 Consensus size: 70
29361948 AGCTAGGAGT
* * * *
29361958 TTGAGCTCTCGTTAACTGTTTTAATGGTTGCGGTATTGAACTTG-TGAACCTTAAGATT-ACAAT
1 TTGAGCTCTCGCTAACTATTTTGATGGTTGCAGTATTGAACTTGCT-AACCTTAAG-TTCACAAT
*
29362021 TGGGAGC
64 TGAGAGC
* * * * *
29362028 TTTATCTCTCGCTAACTATTTTGGA-GGCTGCAGTATTGAACTTGCTAGCTTTAAGTTCACAATT
1 TTGAGCTCTCGCTAACTATTTT-GATGGTTGCAGTATTGAACTTGCTAACCTTAAGTTCACAATT
29362092 GAGAGC
65 GAGAGC
29362098 TTGAGCTCTCGCTAACTATTTTGATGGT
1 TTGAGCTCTCGCTAACTATTTTGATGGT
29362126 CATGGTATTA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
69 4 0.05
70 75 0.93
71 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (70 bp):
TTGAGCTCTCGCTAACTATTTTGATGGTTGCAGTATTGAACTTGCTAACCTTAAGTTCACAATTG
AGAGC
Found at i:29362175 original size:70 final size:69
Alignment explanation
Indices: 29362101--29362399 Score: 218
Period size: 70 Copynumber: 4.3 Consensus size: 69
29362091 TGAGAGCTTG
* * *
29362101 AGCTCTCGCTAACTATTTTGATGGTCATGGTATTAAACCTACGAGCCCTAAGATTATAGTT-GGA
1 AGCTCTCGCTAACTGTTTTGATGGT-ATGGTATTAAACCTACGAGCCTTAAGATTACAGTTAGG-
29362165 AGCCTT
64 AGCCTT
* ** * * *
29362171 AGCTCTCGCTGACTGTTTTGGA-GGTTACAGCATTAAACCTACAAGCCTTAAG-TTCACAATTAG
1 AGCTCTCGCTAACTGTTTT-GATGG-TATGGTATTAAACCTACGAGCCTTAAGATT-ACAGTTAG
*
29362234 GAGCCTG
63 GAGCCTT
* * * * *
29362241 AGCTATCGCTAAATGTTTTGATGGT-TGCGATTTTAAACTTATGAGCCTTAAGATTACAGTTAGG
1 AGCTCTCGCTAACTGTTTTGATGGTATG-G-TATTAAACCTACGAGCCTTAAGATTACAGTTAGG
29362305 AGCCTT
64 AGCCTT
* * * * *
29362311 AGCTTTTGCTAACTGTTTTAGA-GGT-TGCAGTACTGAACC-AGCGAGCCTTAATATTACAGTT-
1 AGCTCTCGCTAACTGTTTT-GATGGTATG--GTATTAAACCTA-CGAGCCTTAAGATTACAGTTA
* *
29362372 GGAAGCGTG
62 GG-AGCCTT
* *
29362381 AGGTCTCACTAACTGTTTT
1 AGCTCTCGCTAACTGTTTT
29362400 TGAGGTGGAT
Statistics
Matches: 179, Mismatches: 38, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
69 9 0.05
70 160 0.89
71 10 0.06
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (69 bp):
AGCTCTCGCTAACTGTTTTGATGGTATGGTATTAAACCTACGAGCCTTAAGATTACAGTTAGGAG
CCTT
Found at i:29362361 original size:140 final size:138
Alignment explanation
Indices: 29361894--29362349 Score: 484
Period size: 140 Copynumber: 3.3 Consensus size: 138
29361884 TAGCTTGAGT
* * * ** *
29361894 TCTCGCTAACTGTTTTGGAGGCTGCAATATTGAACCTACAAGTCTTAAGTTCATAGCTAGGAGTT
1 TCTCGCTAACTGTTTTGGAGGCTGCAGTATTGAACCTACAAGCCTTAAGTTCACAATTAGGAGCT
* * * * * *
29361959 TGAGCTCTCGTTAACTGTTTTAATGGTTGCGGTATTGAACTTGTGAACCTTAAGATTACAATTGG
66 TGAGCTCTCGCTAACTGTTTTGATGGTTGC-GTATTAAACTTATGAGCCTTAAGATTACAGTT-G
* *
29362024 GAGCTTTATC
129 GAGCCTTAGC
* * * * *
29362034 TCTCGCTAACTATTTTGGAGGCTGCAGTATTGAACTTGCTAGCTTTAAGTTCACAATT-GAGAGC
1 TCTCGCTAACTGTTTTGGAGGCTGCAGTATTGAACCTACAAGCCTTAAGTTCACAATTAG-GAGC
* * * * *
29362098 TTGAGCTCTCGCTAACTATTTTGATGGTCATG-GTATTAAACCTACGAGCCCTAAGATTATAGTT
65 TTGAGCTCTCGCTAACTGTTTTGATGGT--TGCGTATTAAACTTATGAGCCTTAAGATTACAGTT
29362162 GGAAGCCTTAGC
128 GG-AGCCTTAGC
* * * * * *
29362174 TCTCGCTGACTGTTTTGGAGGTTACAGCATTAAACCTACAAGCCTTAAGTTCACAATTAGGAGCC
1 TCTCGCTAACTGTTTTGGAGGCTGCAGTATTGAACCTACAAGCCTTAAGTTCACAATTAGGAGCT
* * *
29362239 TGAGCTATCGCTAAATGTTTTGATGGTTGCGATTTTAAACTTATGAGCCTTAAGATTACAGTTAG
66 TGAGCTCTCGCTAACTGTTTTGATGGTTGCG-TATTAAACTTATGAGCCTTAAGATTACAGTT-G
29362304 GAGCCTTAGC
129 GAGCCTTAGC
* * * * *
29362314 TTTTGCTAACTGTTTTAGAGGTTGCAGTACTGAACC
1 TCTCGCTAACTGTTTTGGAGGCTGCAGTATTGAACC
29362350 AGCGAGCCTT
Statistics
Matches: 257, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
138 2 0.01
139 4 0.02
140 246 0.96
141 3 0.01
142 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (138 bp):
TCTCGCTAACTGTTTTGGAGGCTGCAGTATTGAACCTACAAGCCTTAAGTTCACAATTAGGAGCT
TGAGCTCTCGCTAACTGTTTTGATGGTTGCGTATTAAACTTATGAGCCTTAAGATTACAGTTGGA
GCCTTAGC
Found at i:29365397 original size:49 final size:49
Alignment explanation
Indices: 29365340--29365439 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
29365330 TTTTGTTCAC
29365340 CAGCTTCTGGTAAGTTGCACTTGCATTTTTCAAACCAAAAGGCATCATA
1 CAGCTTCTGGTAAGTTGCACTTGCATTTTTCAAACCAAAAGGCATCATA
29365389 CAGCTTCTGGTAAGTTGCACTTGCATTTTTCAAACCAAAAGGCATCATA
1 CAGCTTCTGGTAAGTTGCACTTGCATTTTTCAAACCAAAAGGCATCATA
29365438 CA
1 CA
29365440 ACAGCAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (49 bp):
CAGCTTCTGGTAAGTTGCACTTGCATTTTTCAAACCAAAAGGCATCATA
Found at i:29369082 original size:15 final size:16
Alignment explanation
Indices: 29369057--29369087 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29369047 TTAATTCTTT
29369057 TTAATATTTATTTTAA
1 TTAATATTTATTTTAA
29369073 TTAA-ATTTATTTTAA
1 TTAATATTTATTTTAA
29369088 CCAAGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTATTTTAA
Found at i:29372003 original size:20 final size:21
Alignment explanation
Indices: 29371966--29372008 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
29371956 AGCTATTTTA
29371966 ATATTTATATTATTATATCAT
1 ATATTTATATTATTATATCAT
* *
29371987 ATATTTA-ATTTTTATATGAT
1 ATATTTATATTATTATATCAT
29372007 AT
1 AT
29372009 TTAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTTATATTATTATATCAT
Found at i:29372243 original size:19 final size:19
Alignment explanation
Indices: 29372201--29372251 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
29372191 AAAATTACAA
*
29372201 AAAAATTTAAAATAATTTT
1 AAAAATCTAAAATAATTTT
*
29372220 TAAAATCTAAAAT-ATTTAT
1 AAAAATCTAAAATAATTT-T
*
29372239 AAAAATCCAAAAT
1 AAAAATCTAAAAT
29372252 TTATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCTAAAATAATTTT
Found at i:29374944 original size:18 final size:19
Alignment explanation
Indices: 29374910--29374945 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29374900 AAAAAAATAT
*
29374910 TCAAAATAATTTTTAAAAC
1 TCAAAATAATTTATAAAAC
29374929 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
29374946 ATTTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAC
Found at i:29375586 original size:29 final size:29
Alignment explanation
Indices: 29375546--29375603 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29375536 CATTAACTAT
*
29375546 TTGAACTAATTAACAATATTATAAAAATA
1 TTGAACTAATTAACAACATTATAAAAATA
* *
29375575 TTGAACTGATTAATAACATTATAAAAATA
1 TTGAACTAATTAACAACATTATAAAAATA
29375604 AAGAAACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (29 bp):
TTGAACTAATTAACAACATTATAAAAATA
Found at i:29386329 original size:29 final size:29
Alignment explanation
Indices: 29386296--29386391 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 29
29386286 GCGCAAATGG
29386296 TCTGCTCGCACAGTCCCCCTCCTGCAGCA
1 TCTGCTCGCACAGTCCCCCTCCTGCAGCA
* * *
29386325 TCTGCT-GCTACATGCCCCCCACCCTGCTGCCCCA
1 TCTGCTCGC-ACA-GTCCCCC-TCCTGCAG---CA
* * *
29386359 TCTGCCCGCACAGTACCCCTCTTGCAGCA
1 TCTGCTCGCACAGTCCCCCTCCTGCAGCA
29386388 TCTG
1 TCTG
29386392 TTGCTGTACG
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
28 2 0.04
29 15 0.29
30 6 0.12
31 6 0.12
32 5 0.10
33 5 0.10
34 10 0.20
35 2 0.04
ACGTcount: A:0.14, C:0.48, G:0.17, T:0.22
Consensus pattern (29 bp):
TCTGCTCGCACAGTCCCCCTCCTGCAGCA
Found at i:29386585 original size:14 final size:14
Alignment explanation
Indices: 29386532--29386587 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
29386522 CCATCCATCG
*
29386532 GAAGAGAGAAAGAA
1 GAAGAAAGAAAGAA
* *
29386546 -AAGAGAGAAAGGA
1 GAAGAAAGAAAGAA
29386559 GAAGAAA-ATAAGAA
1 GAAGAAAGA-AAGAA
29386573 GAAGAAAGAAAGAA
1 GAAGAAAGAAAGAA
29386587 G
1 G
29386588 GTAATCTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 13 0.36
14 22 0.61
15 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (14 bp):
GAAGAAAGAAAGAA
Found at i:29386836 original size:60 final size:60
Alignment explanation
Indices: 29386749--29386867 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
29386739 TTGCTTTTTA
* * *
29386749 TAATTATTTTAAAATTAATTTGCTAGTAAATAAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTTG
* * * *
29386809 TAATTATTTTAAAATTAGTTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTT
29386868 AGTTTAGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.51
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:29387786 original size:18 final size:17
Alignment explanation
Indices: 29387763--29387797 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29387753 TTTTATTTGA
29387763 TTTTTATTTATTTAAAAT
1 TTTTTATTTA-TTAAAAT
29387781 TTTTTATTTATTAAAAT
1 TTTTTATTTATTAAAAT
29387798 GTTGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTATTTATTAAAAT
Found at i:29389247 original size:21 final size:20
Alignment explanation
Indices: 29389218--29389261 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
29389208 GCATGTATAT
* * *
29389218 AAAACATAAAGTATAAAAATA
1 AAAAAATAAA-TAAAAAAACA
29389239 AAAAAATAAATAAAAAAACA
1 AAAAAATAAATAAAAAAACA
29389259 AAA
1 AAA
29389262 GTAACAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAATAAATAAAAAAACA
Found at i:29391552 original size:98 final size:98
Alignment explanation
Indices: 29391382--29391571 Score: 335
Period size: 98 Copynumber: 1.9 Consensus size: 98
29391372 AGTACGGTCC
* *
29391382 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGTTCATATAGTTGGGGGTCCGCA
1 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCACA
29391447 GTGTTAGCCATGCTGTATCGCAAACTTGATCGG
66 GTGTTAGCCATGCTGTATCGCAAACTTGATCGG
*
29391480 ACTTGATGTACTTACCCTTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCACA
1 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCACA
* *
29391545 GTTTTAGCCATGCTGTATCGCGAACTT
66 GTGTTAGCCATGCTGTATCGCAAACTT
29391572 TGTTGGACGA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (98 bp):
ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCACA
GTGTTAGCCATGCTGTATCGCAAACTTGATCGG
Found at i:29392660 original size:33 final size:33
Alignment explanation
Indices: 29392555--29392665 Score: 141
Period size: 33 Copynumber: 3.4 Consensus size: 33
29392545 TTCATCCTAG
* * *
29392555 CTCGTATCCACCTCAGTACTTCGCTCCTTCCAA
1 CTCGTATCCACCTTAGTACTCCGCTCCTTCCGA
* * *
29392588 CTCATATCTACCTTAGTACTCCGCTCCTTCCGG
1 CTCGTATCCACCTTAGTACTCCGCTCCTTCCGA
* *
29392621 CTCGTATCCACTTTAGTACTCCGCTCCTTCTGA
1 CTCGTATCCACCTTAGTACTCCGCTCCTTCCGA
*
29392654 CCCGTATCCACC
1 CTCGTATCCACC
29392666 ACCATACTCC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.16, C:0.41, G:0.11, T:0.32
Consensus pattern (33 bp):
CTCGTATCCACCTTAGTACTCCGCTCCTTCCGA
Found at i:29397178 original size:18 final size:18
Alignment explanation
Indices: 29397143--29397180 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29397133 TTGTTTTGAA
*
29397143 TTTTTAAAATTTAGAAAT
1 TTTTTAAAAATTAGAAAT
29397161 TTTTTAAAAAATTA-AAAT
1 TTTTT-AAAAATTAGAAAT
29397179 TT
1 TT
29397181 AGTACAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAATTAGAAAT
Found at i:29397329 original size:21 final size:21
Alignment explanation
Indices: 29397303--29397350 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
29397293 TTAAATTTAT
*
29397303 ATATTTTATATTTTTTTAAAA
1 ATATTTTATATGTTTTTAAAA
*
29397324 ATATTTTTTATGTTTTTAAAA
1 ATATTTTATATGTTTTTAAAA
29397345 ATATTT
1 ATATTT
29397351 GAATTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATATTTTATATGTTTTTAAAA
Found at i:29400071 original size:71 final size:71
Alignment explanation
Indices: 29399947--29400095 Score: 201
Period size: 71 Copynumber: 2.1 Consensus size: 71
29399937 AACCAAAGTG
* * * * *
29399947 CTACTGATACCTTGAGGACTTCTACCAAAACAAGTCAAGTCAGTAGCCAAAGTTCAGCAT-CTCT
1 CTACCGATACCTTAAAGACTTCTAACAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTC-
*
29400011 TGCACTT
65 TACACTT
* *
29400018 CTACCGATACCTTAAAGACTTCTAACAAAATAAGTCAAGTCAGTAGCCGAAGTTCAACATCCTCT
1 CTACCGATACCTTAAAGACTTCTAACAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTCT
*
29400083 ACAGTT
66 ACACTT
29400089 CTACCGA
1 CTACCGA
29400096 CACTCTGATG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 65 0.96
72 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (71 bp):
CTACCGATACCTTAAAGACTTCTAACAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTCT
ACACTT
Found at i:29403402 original size:43 final size:43
Alignment explanation
Indices: 29403354--29403447 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
29403344 CCTGAATATG
* *
29403354 GTCTTACATGCTAACACA-TATCGATGCCACTGTCTCAGACATA
1 GTCTTACATGCTAACACACT-TCGATGCCAATGTCCCAGACATA
* ** * *
29403397 GTCTTACATGTTTTCTCACTTCGATGCCAATGTCCCAGACATG
1 GTCTTACATGCTAACACACTTCGATGCCAATGTCCCAGACATA
29403440 GTCTTACA
1 GTCTTACA
29403448 CGAAATTACA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.32
Consensus pattern (43 bp):
GTCTTACATGCTAACACACTTCGATGCCAATGTCCCAGACATA
Found at i:29403632 original size:16 final size:16
Alignment explanation
Indices: 29403607--29403642 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
29403597 CATATTTGGG
*
29403607 CATTTTTTCATCAAAT
1 CATTTATTCATCAAAT
29403623 CATTTATTCATCAAAT
1 CATTTATTCATCAAAT
29403639 CATT
1 CATT
29403643 CAATTCAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
CATTTATTCATCAAAT
Found at i:29406106 original size:20 final size:20
Alignment explanation
Indices: 29406061--29406106 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29406051 TCATCGTGGA
*
29406061 AGAAAGTTTTGAGGTTTGGT
1 AGAAAGTTTTAAGGTTTGGT
* *
29406081 ACAAAGTTTTAAGGTTTTGT
1 AGAAAGTTTTAAGGTTTGGT
29406101 AGAAAG
1 AGAAAG
29406107 GGTAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
AGAAAGTTTTAAGGTTTGGT
Found at i:29408284 original size:43 final size:43
Alignment explanation
Indices: 29408223--29408313 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
29408213 CTAAATTTTT
* * * * *
29408223 CGCTATAGAATATGACCTTTAGCGGCATTTTCCCTACAAACGC
1 CGCTAAAGAACATGACCTTTAGAGGCACTTTCCCCACAAACGC
* *
29408266 CGCTAAAGAACATGACCTTTAGAGGCGCTTTCCCCGCAAACGC
1 CGCTAAAGAACATGACCTTTAGAGGCACTTTCCCCACAAACGC
29408309 CGCTA
1 CGCTA
29408314 CCTTTAGCGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGAGGCACTTTCCCCACAAACGC
Found at i:29412462 original size:12 final size:12
Alignment explanation
Indices: 29412447--29412472 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29412437 ATTTGGGGTG
29412447 TTATTTTATTTA
1 TTATTTTATTTA
29412459 TTATTTTATTTA
1 TTATTTTATTTA
29412471 TT
1 TT
29412473 TTAATAGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTATTTA
Found at i:29416740 original size:9 final size:9
Alignment explanation
Indices: 29416726--29416843 Score: 70
Period size: 9 Copynumber: 13.6 Consensus size: 9
29416716 TATTTATGTA
29416726 TTATGTAAG
1 TTATGTAAG
29416735 TTATGTAAG
1 TTATGTAAG
*
29416744 TTATGATATG
1 TTATG-TAAG
* *
29416754 ATATAT-A-
1 TTATGTAAG
* *
29416761 TT-TATAGG
1 TTATGTAAG
*
29416769 TTATGTAAA
1 TTATGTAAG
29416778 TTATGTAAG
1 TTATGTAAG
29416787 TTATGTAAG
1 TTATGTAAG
*
29416796 TTGTG-ATA-
1 TTATGTA-AG
* * *
29416804 TGATTTATAT
1 TTATGTA-AG
29416814 TTATGT-A-
1 TTATGTAAG
29416821 TTATGTAAG
1 TTATGTAAG
29416830 TTATGTAAG
1 TTATGTAAG
29416839 TTATG
1 TTATG
29416844 ATCCAAATTT
Statistics
Matches: 84, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
6 3 0.04
7 7 0.08
8 7 0.08
9 57 0.68
10 10 0.12
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29416761 original size:43 final size:44
Alignment explanation
Indices: 29416712--29416845 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 44
29416702 TTTTTATAAG
29416712 TATATATTTATGTATTATGTAAGTTATGTAAGTTATGATATGATA
1 TATATATTTATGTATTATGTAAGTTATGTAAGTTATGATATGA-A
*
29416757 TATATTTATAGGTTATGTAAATTATGTAAGTTATGTAAGTTGTGATATG-A
1 TATA--TAT---TTATGT--ATTATGTAAGTTATGTAAGTTATGATATGAA
*
29416807 TTTATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
1 TATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
29416846 CCAAATTTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
43 25 0.32
45 10 0.13
47 3 0.04
48 3 0.04
50 10 0.13
52 28 0.35
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (44 bp):
TATATATTTATGTATTATGTAAGTTATGTAAGTTATGATATGAA
Found at i:29416781 original size:52 final size:52
Alignment explanation
Indices: 29416725--29416843 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
29416715 ATATTTATGT
*
29416725 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATAG-GTTATGTAA
1 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTAT-GTATTATGTAA
* *
29416777 ATTATGTAAGTTATGTAAGTTGTGATATGATTTATATTTATGTATTATGTAA
1 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
*
29416829 GTTATGTAAGTTATG
1 ATTATGTAAGTTATG
29416844 ATCCAAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 1 0.02
52 61 0.98
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (52 bp):
ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
Found at i:29416911 original size:35 final size:35
Alignment explanation
Indices: 29416863--29416929 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
29416853 TTTTTTTATT
*
29416863 CTTTTAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
*
29416898 CTTTAAATGTTTATGTAAGTTATGATTATCAT
1 CTTTAAATGTTTATGTAAGTTATGATAATCAT
29416930 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
Found at i:29418506 original size:2 final size:2
Alignment explanation
Indices: 29418499--29418543 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29418489 AAGCATAAGA
29418499 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
29418541 AT A
1 AT A
29418544 ACGCCGTCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29418728 original size:24 final size:24
Alignment explanation
Indices: 29418696--29418748 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
29418686 AGTATTTTAT
29418696 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
*
29418720 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
29418744 AATAT
1 AATAT
29418749 TATACAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:29419288 original size:17 final size:17
Alignment explanation
Indices: 29419268--29419308 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29419258 ACATACCTCT
*
29419268 TAAAGTCCACAAGGAAG
1 TAAAGGCCACAAGGAAG
**
29419285 TAAAGGCTGCAAGGAAG
1 TAAAGGCCACAAGGAAG
29419302 TAAAGGC
1 TAAAGGC
29419309 TGCAAGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (17 bp):
TAAAGGCCACAAGGAAG
Found at i:29419309 original size:17 final size:17
Alignment explanation
Indices: 29419277--29419314 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
29419267 TTAAAGTCCA
29419277 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
29419294 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
29419311 CAAG
1 CAAG
29419315 TCCTTGGGAC
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:0.42, C:0.13, G:0.34, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:29420565 original size:24 final size:22
Alignment explanation
Indices: 29420533--29420599 Score: 89
Period size: 24 Copynumber: 2.9 Consensus size: 22
29420523 AGAAGTTGGG
29420533 AAATTGGGAAATTGGGGAAGAAT
1 AAATTGGGAAATTGGGGAA-AAT
**
29420556 AGCTTAGGGAAATTAGGGGAAAAT
1 AAATT-GGGAAATT-GGGGAAAAT
29420580 AAATTGGGAAATTGGGGAAA
1 AAATTGGGAAATTGGGGAAA
29420600 TGAAATCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 7 0.18
23 11 0.29
24 14 0.37
25 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.34, T:0.21
Consensus pattern (22 bp):
AAATTGGGAAATTGGGGAAAAT
Found at i:29420611 original size:23 final size:23
Alignment explanation
Indices: 29420562--29420615 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
29420552 GAATAGCTTA
*
29420562 GGGAAATTAGGGGAAAATAAATT
1 GGGAAATTAGGGGAAAATAAATG
29420585 GGGAAATT-GGGG-AAATGAAATCG
1 GGGAAATTAGGGGAAAAT-AAAT-G
29420608 GGGAAATT
1 GGGAAATT
29420616 TGACTTGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 4 0.14
22 8 0.29
23 16 0.57
ACGTcount: A:0.43, C:0.02, G:0.35, T:0.20
Consensus pattern (23 bp):
GGGAAATTAGGGGAAAATAAATG
Done.