Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009151.1 Hibiscus syriacus cultivar Beakdansim tig00112677_pilon, whole genome shotgun sequence
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: 218317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8466 original size:41 final size:41
Alignment explanation
Indices: 8400--8560 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
8390 CGTTTATACA
8400 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
8440 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
8480 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
8523 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
8561 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:8518 original size:82 final size:81
Alignment explanation
Indices: 8401--8559 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
8391 GTTTATACAA
* *
8401 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
8465 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
8482 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
8547 TATTGCGGCGTTT
65 TATTGCGGCGTTT
8560 GAGGAATAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 18 0.25
82 54 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:8706 original size:41 final size:42
Alignment explanation
Indices: 8589--8786 Score: 172
Period size: 42 Copynumber: 4.8 Consensus size: 42
8579 ATGTGTAATA
* *
8589 TATTGCGGCGTTTGTGGTATAAACGCCACAAATTTACCACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
* * * *
8631 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTGG-TATAAACGCCGC-TAATTTACCACTC
* *
8672 TATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
* * * * * *
8714 TATTGCGGCATTTTTTGTAAAAACGCCGCTATATGT-CAACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTA-ATTTACCACTC
** **
8756 TATTGTAGCGTTTGTACTA-AAACGCCGCTAA
1 TATTGCGGCGTTTGTGGTATAAACGCCGCTAA
8787 AGTATCAATT
Statistics
Matches: 126, Mismatches: 24, Indels: 14
0.77 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 44 0.35
42 78 0.62
43 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACTC
Found at i:11924 original size:14 final size:15
Alignment explanation
Indices: 11888--11924 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
11878 CCGTGACTAT
11888 GAGTACCCGCTAATG
1 GAGTACCCGCTAATG
11903 GAGTACCCGCTAATG
1 GAGTACCCGCTAATG
11918 G-GTACCC
1 GAGTACCC
11925 ATAAAATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (15 bp):
GAGTACCCGCTAATG
Found at i:12899 original size:21 final size:20
Alignment explanation
Indices: 12851--12927 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
12841 TCTGGAATCC
*
12851 AAGGGATTGATCCTTTTACA
1 AAGGGATCGATCCTTTTACA
*
12871 AGGGGATCGATCCTTTGGT-CA
1 AAGGGATCGATCCTTT--TACA
* * *
12892 AAGGGATCGATCCATGTACC
1 AAGGGATCGATCCTTTTACA
* *
12912 AAGAGATCAATCCTTT
1 AAGGGATCGATCCTTT
12928 GAGCCAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 15 0.34
22 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTACA
Found at i:49007 original size:21 final size:20
Alignment explanation
Indices: 48979--49017 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
48969 CATTGTAGGA
*
48979 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
48999 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
49018 GACTTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:51673 original size:20 final size:21
Alignment explanation
Indices: 51633--51673 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
51623 TAAAAATATG
*
51633 TTTTATTTTGAATACTGATAAC
1 TTTTATTTTG-ATACTCATAAC
51655 TTTTATTTTG-TACTCATAA
1 TTTTATTTTGATACTCATAA
51674 ATGATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTATTTTGATACTCATAAC
Found at i:62097 original size:81 final size:80
Alignment explanation
Indices: 61910--62109 Score: 278
Period size: 80 Copynumber: 2.5 Consensus size: 80
61900 CCCAAAGGCA
* * * * * * *
61910 TTTAACCTTTCATCTAACTTGCATGATTAACA-CTTGTCTGCCAAATGTATAGCTAGGCCATGTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTT-TCTGCCAAATGAACAGCTAGACCATGTA
61974 TCTTTTACTCATAGTC
65 TCTTTTACTCATAGTC
*
61990 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGAACAGCTAGACCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGAACAGCTAGACCATGTAT
62055 CTTTTACTCA-ACGGTC
66 CTTTTACTCATA--GTC
*
62071 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCT
62110 ATCAAATGCA
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
79 1 0.01
80 63 0.58
81 44 0.41
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (80 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGAACAGCTAGACCATGTAT
CTTTTACTCATAGTC
Found at i:62170 original size:68 final size:68
Alignment explanation
Indices: 62079--62333 Score: 438
Period size: 68 Copynumber: 3.8 Consensus size: 68
62069 TCTTTAACCG
* *
62079 TTCATCTAACTGGCATAATTGACACATTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
62144 CCT
66 CCT
* * * * *
62147 TTCATCTAATTGACATAATTGACACCTTTCTGTCAAATTCATAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
62212 CCT
66 CCT
62215 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
62280 CCT
66 CCT
*
62283 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCATAGTTAGGCC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
62334 ATTTAATCTT
Statistics
Matches: 174, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 174 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:67183 original size:81 final size:81
Alignment explanation
Indices: 66894--67173 Score: 391
Period size: 81 Copynumber: 3.5 Consensus size: 81
66884 CCCAAAGGCA
* * * * * *
66894 TTTAACCTTTCACCTAACTTGCATGACTGACAC-TTGTCTTCCAAATGTACAGCTAGGCCATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATT-TCTACCAAATGTACAGCTAGGCCATTTA
66958 TCTTTTACTCAACGGTC
65 TCTTTTACTCAACGGTC
* * * * **
66975 TTTAACCATTCATCTAACTGGCATAATTGATACCTTTCTACCAAATGCACAGCTAGGTAATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATGTACAGCTAGGCCATTTAT
67040 CTTTTACTCAACGGTC
66 CTTTTACTCAACGGTC
* *
67056 TGTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATGTATAGCTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATGTACAGCTAGGCCATTTAT
67121 CTTTTACTCAACGGTC
66 CTTTTACTCAACGGTC
* * *
67137 TTTAACCGTTCATCTAATTGACATAATTAACACATTT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTT
67174 TTGTCAAATG
Statistics
Matches: 176, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 174 0.99
82 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (81 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATGTACAGCTAGGCCATTTAT
CTTTTACTCAACGGTC
Found at i:67230 original size:68 final size:68
Alignment explanation
Indices: 67145--67531 Score: 501
Period size: 68 Copynumber: 5.7 Consensus size: 68
67135 TCTTTAACCG
* * * * * * * *
67145 TTCATCTAATTGACATAATTAACACATTTTTGTCAAATGAAAAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
67210 CCT
66 CCT
* * * *
67213 TTCATCTATCTGGCATAATTGA-ACCTTTCTGTCAAATACACAA-TTAGGCCTCAAAGATAATTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA-AAGTTAGGCCTCAAAGGTACTTA
*
67276 TCCT
65 GCCT
* *
67280 TTCATCTAATTGGCATAATTGACACCTTT-TCGTCAAATGCACAGTTAGGCCTCAAAGGTACTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCT-GTCAAATGCAAAGTTAGGCCTCAAAGGTACTTA
67344 GCCT
65 GCCT
** * * *
67348 TTCATCTAACTAACATAATTGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
67413 CCT
66 CCT
* * * *
67416 TTCATCTAACTAGCATAATGGACACCTTTTTGTCAAATGCAAAGTTAGGCCTTAAAGGTACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
67481 CCT
66 CCT
* *
67484 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAAAGTTAG
67532 TCCATTTAAT
Statistics
Matches: 276, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
67 55 0.20
68 220 0.80
69 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
CCT
Found at i:67369 original size:135 final size:136
Alignment explanation
Indices: 67145--67531 Score: 569
Period size: 136 Copynumber: 2.9 Consensus size: 136
67135 TCTTTAACCG
* * * * * *
67145 TTCATCTAATTGACATAATTAACACATTTTTGTCAAATGAAAAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAATTGGCATAATTGACACCTTTTTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
* * *
67210 CCTTTCATCTATCTGGCATAATTGA-ACCTTTCTGTCAAATACACAATTAGGCCTCAAAGATAAT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGACAAT
*
67274 TATCCT
131 TACCCT
* *
67280 TTCATCTAATTGGCATAATTGACACCTTTTCGTCAAATGCACAGTTAGGCCTCAAAGGTACTTAG
1 TTCATCTAATTGGCATAATTGACACCTTTTTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
** * * * *
67345 CCTTTCATCTAACTAACATAATTGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGACAAT
67410 TACCCT
131 TACCCT
* * * *
67416 TTCATCTAACTAGCATAATGGACACCTTTTTGTCAAATGCAAAGTTAGGCCTTAAAGGTACTTAG
1 TTCATCTAATTGGCATAATTGACACCTTTTTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
67481 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAG
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAG
67532 TCCATTTAAT
Statistics
Matches: 223, Mismatches: 28, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
135 79 0.35
136 144 0.65
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (136 bp):
TTCATCTAATTGGCATAATTGACACCTTTTTGTCAAATGCAAAGTTAGGCCTCAAAGGTACTTAG
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGACAAT
TACCCT
Found at i:81809 original size:140 final size:140
Alignment explanation
Indices: 81554--82207 Score: 841
Period size: 140 Copynumber: 4.7 Consensus size: 140
81544 CTTATCATAT
* * ** *
81554 AACCTTAGCTCAATTCATCATATATGGAGTTGAATCAGCAACACCTCACTCGAGTGATCAACATT
1 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGACACCTCACTCGAGGGATCAACATT
* * * *
81619 TCCAGTGGAGAGTTCATAGTGAGAATAACTCAACTGATAGAGGGATAAGAAGTTCATAATGAGAA
66 TCCAGTAGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAATGAGAA
81684 GAACTTGTTC
131 GAACTTGTTC
* * *
81694 AACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGTGACACCTCACTTGAGGGATCAACATT
1 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGACACCTCACTCGAGGGATCAACATT
* * *
81759 TCCAGTAGAGAGTTCAAAATGAGAAGAACTCATCTGATAGAGGGAGAAGAACTTCATAATGAGAA
66 TCCAGTAGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAATGAGAA
81824 GAACTTGTTC
131 GAACTTGTTC
* * * * * * * *
81834 AACCTTTGTTCGGA-CCATCGCATATGGAGTTGAATCAGCGACACCTTACTCTATGGATCAACAT
1 AACCTTAGCTC-GATTCATCACATATGGAGTTGAATCAGTGACACCTCACTCGAGGGATCAACAT
* * *
81898 TTCCAGTGGAGAGTTCATAATGAGAATAACTCACCTGATAGATGGAGAAGAAGTTCATAATGAGA
65 TTCCAGTAGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAATGAGA
*
81963 AGAACTTGTTT
130 AGAACTTGTTC
* * * *
81974 AGCCTTAGTTTGATTCATCACATATGGAGTTGAATCAGCT-ATACCTCACTCGAGGGATCAAC-T
1 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAG-TGACACCTCACTCGAGGGATCAACAT
* * * * *
82037 TTCTAGTTGAGAGTTCATAATGAGGATAACTCATCCGATAAAGGGA-AA-AAGTTCATAATGAGA
65 TTCCAGTAGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAATGAGA
82100 AGAACTTGTTC
130 AGAACTTGTTC
* * ** * * * *
82111 AACCTTAGCTTGATTCATCATATATGGAGTTGAATCAGTGATGCCCCACTCAAGGGATCGATATT
1 AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGACACCTCACTCGAGGGATCAACATT
* *
82176 TCCAGTATAGAGTTGATAATGAGAATAACTCA
66 TCCAGTAGAGAGTTCATAATGAGAATAACTCA
82208 CAGCTTGAAA
Statistics
Matches: 449, Mismatches: 60, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
136 1 0.00
137 77 0.17
138 31 0.07
139 42 0.09
140 296 0.66
141 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (140 bp):
AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGACACCTCACTCGAGGGATCAACATT
TCCAGTAGAGAGTTCATAATGAGAATAACTCATCTGATAGAGGGAGAAGAAGTTCATAATGAGAA
GAACTTGTTC
Found at i:82401 original size:17 final size:17
Alignment explanation
Indices: 82379--82413 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
82369 AGCCAATCAT
*
82379 ACCCAAACAAACATCCA
1 ACCCAAACAAACACCCA
*
82396 ACCCAAACCAACACCCA
1 ACCCAAACAAACACCCA
82413 A
1 A
82414 AACAGAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (17 bp):
ACCCAAACAAACACCCA
Found at i:83760 original size:33 final size:33
Alignment explanation
Indices: 83718--83808 Score: 182
Period size: 33 Copynumber: 2.8 Consensus size: 33
83708 CATTAAATTG
83718 GACCCATTGAATTGGACCGTTGACTTGATCGTT
1 GACCCATTGAATTGGACCGTTGACTTGATCGTT
83751 GACCCATTGAATTGGACCGTTGACTTGATCGTT
1 GACCCATTGAATTGGACCGTTGACTTGATCGTT
83784 GACCCATTGAATTGGACCGTTGACT
1 GACCCATTGAATTGGACCGTTGACT
83809 AGTTTGACTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (33 bp):
GACCCATTGAATTGGACCGTTGACTTGATCGTT
Found at i:85080 original size:14 final size:14
Alignment explanation
Indices: 85057--85092 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
85047 ACAATATATT
*
85057 TTGTTGTAATATAC
1 TTGTTTTAATATAC
*
85071 TTGTTTTAATATAT
1 TTGTTTTAATATAC
85085 TTGTTTTA
1 TTGTTTTA
85093 TGACTTACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (14 bp):
TTGTTTTAATATAC
Found at i:91099 original size:21 final size:21
Alignment explanation
Indices: 91074--91123 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
91064 CTAACTATCA
91074 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
*
91095 CATTGCGATTTTCCTAATTCG
1 CATTGCGATTTTCCAAATTCG
*
91116 CAATGCGA
1 CATTGCGA
91124 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCG
Found at i:91159 original size:20 final size:20
Alignment explanation
Indices: 91132--91199 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
91122 GAATACGTAA
* *
91132 ATCGCAATGCGAATCTGACT
1 ATCGCAATGAGATTCTGACT
* *
91152 ATCACAATAAGATTCTGACT
1 ATCGCAATGAGATTCTGACT
*
91172 ATCGCAACGAGATTCTGACT
1 ATCGCAATGAGATTCTGACT
91192 ATCGCAAT
1 ATCGCAAT
91200 ACTGAATTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
ATCGCAATGAGATTCTGACT
Found at i:92068 original size:24 final size:24
Alignment explanation
Indices: 92036--92089 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
92026 GTATTCGAAA
92036 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
92060 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
92084 TTTGAT
1 TTTGAT
92090 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:94544 original size:20 final size:20
Alignment explanation
Indices: 94519--94587 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
94509 CAACGCGGAA
94519 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCAGAA-ATGACT
*
94539 ATCGCAACACAGAAATGACT
1 ATCGCAACGCAGAAATGACT
*
94559 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCAGAAATGACT
94579 ATCGCAACG
1 ATCGCAACG
94588 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 42 0.93
21 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAGAAATGACT
Found at i:94609 original size:33 final size:33
Alignment explanation
Indices: 94500--94639 Score: 129
Period size: 33 Copynumber: 4.0 Consensus size: 33
94490 GACATTCATT
*
94500 TGACTATCGCAACGCG-GAAATCGCAACGCGAATA
1 TGACTATCGCAACGAGAG-AATCGCAACGCGAA-A
*
94534 TGACTATCGCAACACAGAAATGACTATCGCAACGCGGAAA
1 TGACTATCGC-A-AC-GAGA-GA--ATCGCAACGC-GAAA
*
94574 TGACTATCGCAACGAGAGAATCGCAATGCGAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAA
** * *
94607 TGAAAATCGCAACGAGAGAATCGTAATGCGAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAA
94640 ATGAAAATTG
Statistics
Matches: 91, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
33 34 0.37
34 19 0.21
35 1 0.01
36 4 0.04
37 4 0.04
38 3 0.03
39 2 0.02
40 21 0.23
41 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (33 bp):
TGACTATCGCAACGAGAGAATCGCAACGCGAAA
Found at i:94731 original size:33 final size:33
Alignment explanation
Indices: 94669--94764 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
94659 TTTAGTTTCG
*
94669 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
94703 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
94736 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
94765 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 33 0.58
34 24 0.42
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:94881 original size:14 final size:14
Alignment explanation
Indices: 94862--94898 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
94852 CATCAATTAA
94862 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
94876 ACAAATCATCTTTT
1 ACAAATCAACATTT
94890 ACAAATCAA
1 ACAAATCAA
94899 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:96242 original size:21 final size:21
Alignment explanation
Indices: 96161--96247 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
96151 AGATGTTGGG
* *
96161 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
96182 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
96203 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
96224 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
96245 AGG
1 AGG
96248 TGAGTCGGGC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:96750 original size:20 final size:20
Alignment explanation
Indices: 96727--96794 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
96717 GAAACTTAAA
*
96727 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
96747 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
96767 ATCACAATGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
96787 ATCGCAAC
1 ATCGCAAC
96795 AAGAGAATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.07
20 38 0.93
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:96869 original size:20 final size:20
Alignment explanation
Indices: 96844--97036 Score: 171
Period size: 20 Copynumber: 10.3 Consensus size: 20
96834 CTTTCGTTGT
** *
96844 GATAGTCAAATTCGCATTAC
1 GATAGTCATTTTCGCATTGC
*
96864 GATAGTCATTTTCACATTGC
1 GATAGTCATTTTCGCATTGC
96884 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* *
96904 AATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
*
96924 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
*
96944 GAT--T--TTGTT-G--TTAC
1 GATAGTCATT-TTCGCATTGC
**
96958 GATTTTCATTTT-GCATTGC
1 GATAGTCATTTTCGCATTGC
*
96977 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
*
96991 GATAGTCATTTTCGAATTGC
1 GATAGTCATTTTCGCATTGC
97011 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
97031 GATAGT
1 GATAGT
97037 AAACTATTCT
Statistics
Matches: 146, Mismatches: 13, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.09
15 2 0.01
16 7 0.05
17 7 0.05
18 7 0.05
19 6 0.04
20 104 0.71
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:97597 original size:18 final size:18
Alignment explanation
Indices: 97551--97597 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
97541 TATATTCGGG
*
97551 TCGATTAGGTGATGGCTC
1 TCGATGAGGTGATGGCTC
* *
97569 TGGGTGAGGTGATGGCTC
1 TCGATGAGGTGATGGCTC
*
97587 TCGATGTGGTG
1 TCGATGAGGTG
97598 GCTGCTCATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.43, T:0.32
Consensus pattern (18 bp):
TCGATGAGGTGATGGCTC
Found at i:98943 original size:20 final size:20
Alignment explanation
Indices: 98920--98973 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
98910 GAAACTTTAA
*
98920 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
98940 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
98960 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
98974 TGAAAATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:99385 original size:22 final size:22
Alignment explanation
Indices: 99322--99387 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
99312 CGACCGTGAA
* * *
99322 TGATTTCGCCGGAGATAGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
99344 TGATATCGTTGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
99366 TGATTTCGTCGGAGACGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
99388 GGATGTCTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:99608 original size:20 final size:20
Alignment explanation
Indices: 99585--99677 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
99575 CGATAGTCAG
* *
99585 ATTCGCGTTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
99605 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
99625 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
99645 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
99665 ATTCGTATTGCGA
1 ATTCGCATTGCGA
99678 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:99719 original size:21 final size:21
Alignment explanation
Indices: 99671--99719 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
99661 ATGTATTCGT
99671 ATTGCGAATTAGGAAAATCGC
1 ATTGCGAATTAGGAAAATCGC
** *
99692 AACGCGAATTTGGAAAATCGC
1 ATTGCGAATTAGGAAAATCGC
99713 ATTGCGA
1 ATTGCGA
99720 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (21 bp):
ATTGCGAATTAGGAAAATCGC
Found at i:99740 original size:41 final size:40
Alignment explanation
Indices: 99695--99782 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
99685 AAATCGCAAC
*
99695 GCGAATTTGGAAAATCGCA-TTGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATTTGCGATA-CCAGAGATCGCGTT
* *
99736 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATTTGCGATACCAGAGATCGCGTT
99776 GCGAATT
1 GCGAATT
99783 CTCGATCGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.12
40 23 0.56
41 13 0.32
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATTTGCGATACCAGAGATCGCGTT
Found at i:101807 original size:22 final size:23
Alignment explanation
Indices: 101782--101851 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 23
101772 TAAAATGTTA
**
101782 AATTATAAAGTAC-TAAACGTAT
1 AATTATAAAGTACTTAAAAATAT
**
101804 AATTATAACTTACTTAAAAATAT
1 AATTATAAAGTACTTAAAAATAT
** *
101827 AATTATAATTTAATT-AAAATAT
1 AATTATAAAGTACTTAAAAATAT
101849 AAT
1 AAT
101852 ATTTATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 21 0.51
23 20 0.49
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (23 bp):
AATTATAAAGTACTTAAAAATAT
Found at i:101827 original size:23 final size:22
Alignment explanation
Indices: 101801--101851 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
101791 GTACTAAACG
*
101801 TATAATTATAACTTACTTAAAAA
1 TATAATTATAACTTAATT-AAAA
*
101824 TATAATTATAATTTAATTAAAA
1 TATAATTATAACTTAATTAAAA
101846 TATAAT
1 TATAAT
101852 ATTTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAATTATAACTTAATTAAAA
Found at i:103629 original size:23 final size:23
Alignment explanation
Indices: 103555--103619 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
103545 TAAATATTGT
* * * *
103555 ATTTTAATTAAATTACATTTATA
1 ATTTTAACTAATTTATAATTATA
*
103578 TTTTTAACTAATTTATAATTATA
1 ATTTTAACTAATTTATAATTATA
*
103601 ATTTTAA-TACTTTATAATT
1 ATTTTAACTAATTTATAATT
103620 TAACATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 11 0.31
23 24 0.69
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTAACTAATTTATAATTATA
Found at i:103898 original size:20 final size:20
Alignment explanation
Indices: 103861--103901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
103851 AAATTTCATA
** *
103861 TTTTATATTTATTTTTAAAT
1 TTTTATATAAATTATTAAAT
103881 TTTTATATAAATTATTAAAT
1 TTTTATATAAATTATTAAAT
103901 T
1 T
103902 GAGTCCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATATAAATTATTAAAT
Found at i:104131 original size:20 final size:20
Alignment explanation
Indices: 104106--104144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104096 TAAATATGGA
*
104106 AAAATATCAAATTTAATTTG
1 AAAATATAAAATTTAATTTG
*
104126 AAAATATAAAATTTTATTT
1 AAAATATAAAATTTAATTT
104145 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATATAAAATTTAATTTG
Found at i:111341 original size:13 final size:13
Alignment explanation
Indices: 111323--111349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
111313 ATCATGGTGT
111323 CGAAGAAGCAATG
1 CGAAGAAGCAATG
111336 CGAAGAAGCAATG
1 CGAAGAAGCAATG
111349 C
1 C
111350 AACCACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.19, G:0.30, T:0.07
Consensus pattern (13 bp):
CGAAGAAGCAATG
Found at i:113111 original size:22 final size:22
Alignment explanation
Indices: 113082--113131 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
113072 GAAATTACAC
*
113082 TTTT-GTATCAATGCTAATGCA
1 TTTTAGTATCAATGCTAAGGCA
* *
113103 TTTTAGTATCAGTTCTAAGGCA
1 TTTTAGTATCAATGCTAAGGCA
*
113125 CTTTAGT
1 TTTTAGT
113132 TACTCGATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (22 bp):
TTTTAGTATCAATGCTAAGGCA
Found at i:120345 original size:13 final size:13
Alignment explanation
Indices: 120327--120356 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
120317 AATGACACGC
*
120327 AATGTAAGTCGTA
1 AATGTAAGTCATA
120340 AATGTAAGTCATA
1 AATGTAAGTCATA
120353 AATG
1 AATG
120357 CGTGACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:120440 original size:98 final size:98
Alignment explanation
Indices: 120275--120466 Score: 244
Period size: 98 Copynumber: 2.0 Consensus size: 98
120265 ATACAATCAC
* * * * * **
120275 GACACACGAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAATGTAAGTCGTA
1 GACACACAAATGTGTGTCATCTTATTTAATGAAGTGGGCTTCAATGACACGCAATGCAAGTAATA
* *
120340 AATGTAAGTCATAAATGCGTGACATAAATTTAT
66 AATGCAAGTCATAAATGCGCGACATAAATTTAT
*
120373 GACACACAAATGTGTGTCATCTTCATTT-ATGACAG-GGGCTTCAATGACACGCAATGCACGTAA
1 GACACACAAATGTGTGTCATCTT-ATTTAATGA-AGTGGGCTTCAATGACACGCAATGCAAGTAA
* *
120436 TAAATGCACGTCATAAATGCGCGTCATAAAT
64 TAAATGCAAGTCATAAATGCGCGACATAAAT
120467 GCGTGTCATA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
98 76 0.95
99 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (98 bp):
GACACACAAATGTGTGTCATCTTATTTAATGAAGTGGGCTTCAATGACACGCAATGCAAGTAATA
AATGCAAGTCATAAATGCGCGACATAAATTTAT
Found at i:120443 original size:13 final size:13
Alignment explanation
Indices: 120425--120489 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
120415 AATGACACGC
*
120425 AATGCACGTAATA
1 AATGCACGTCATA
120438 AATGCACGTCATA
1 AATGCACGTCATA
*
120451 AATGCGCGTCATA
1 AATGCACGTCATA
**
120464 AATGCGTGTCATA
1 AATGCACGTCATA
* *
120477 AATACGCGTCATA
1 AATGCACGTCATA
120490 GATTTATGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:125785 original size:29 final size:29
Alignment explanation
Indices: 125733--125975 Score: 215
Period size: 29 Copynumber: 8.7 Consensus size: 29
125723 ACCGACCCAA
125733 TGACATTCTGGGAATTTTTATGAAAAAGG
1 TGACATTCTGGGAATTTTTATGAAAAAGG
* * * * *
125762 TGATATTTTAGGAATTGTTGTGAAAAAGG
1 TGACATTCTGGGAATTTTTATGAAAAAGG
*
125791 TGACATTCTGGGAATTTTTGTGAAAAAGG
1 TGACATTCTGGGAATTTTTATGAAAAAGG
125820 TGACATTCTGGGAATTTTTATGAAAAAGG
1 TGACATTCTGGGAATTTTTATGAAAAAGG
* *
125849 T---ATT-T-AGAATTATTT-TGAAAAAATG
1 TGACATTCTGGGAATT-TTTATG-AAAAAGG
*
125874 TGACA-T-T-GGAATTATTT-TGAAAAA-A
1 TGACATTCTGGGAATT-TTTATGAAAAAGG
* **
125899 TGACATTTTGGGAATTATTT-TGAAAAAAA
1 TGACATTCTGGGAATT-TTTATGAAAAAGG
* *
125928 TGACATTATCGGAATTATTT-TGAAAAAGG
1 TGACATTCTGGGAATT-TTTATGAAAAAGG
*
125957 TGACATTTTGGGAATTTTT
1 TGACATTCTGGGAATTTTT
125976 GAATGTGAAC
Statistics
Matches: 185, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
24 7 0.04
25 16 0.09
26 9 0.05
27 14 0.08
28 21 0.11
29 118 0.64
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (29 bp):
TGACATTCTGGGAATTTTTATGAAAAAGG
Found at i:133386 original size:29 final size:27
Alignment explanation
Indices: 133307--133500 Score: 156
Period size: 29 Copynumber: 6.7 Consensus size: 27
133297 GACCCGACCC
*
133307 AGTGACATTCTGAGAATTTTTTATGAAAA
1 AGTGACATTCTGGGAA-TTTTT-TGAAAA
* * *
133336 AGGTGACATTCTGGAAAATTTGTGAAAA
1 A-GTGACATTCTGGGAATTTTTTGAAAA
133364 ATGTGACATTCTGGGAATTTTTGTGAAAA
1 A-GTGACATTCTGGGAATTTTT-TGAAAA
133393 AGCTGACATTCTGGGAATTATTTTGAAAA
1 AG-TGACATTCTGGGAATT-TTTTGAAAA
* * *
133422 AATGACAATT-TAGGAATTATTTTTTAAAAA
1 AGTGAC-ATTCT-GGGA--ATTTTTTGAAAA
* * *
133452 AATGACATTCTAGGAATTATTTAGAAAA
1 AGTGACATTCTGGGAATT-TTTTGAAAA
* *
133480 ATGTGAAATTTTGGGAATTTT
1 A-GTGACATTCTGGGAATTTT
133501 CGAATATGGA
Statistics
Matches: 135, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.02
28 40 0.30
29 58 0.43
30 31 0.23
31 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (27 bp):
AGTGACATTCTGGGAATTTTTTGAAAA
Found at i:133420 original size:58 final size:57
Alignment explanation
Indices: 133308--133500 Score: 194
Period size: 58 Copynumber: 3.3 Consensus size: 57
133298 ACCCGACCCA
* * *
133308 GTGACATTCTGAGAATTTTTTATGAAAAAGGTGACATTCTGGAA-AATTTGTGAAAAAT
1 GTGACATTCTGGGAA-TTTTTATGAAAAAGATGACATTCTGGAATTATTT-TGAAAAAT
* *
133366 GTGACATTCTGGGAATTTTTGTGAAAAAGCTGACATTCTGGGAATTATTTTGAAAAA-
1 GTGACATTCTGGGAATTTTTATGAAAAAGATGACATTCT-GGAATTATTTTGAAAAAT
* * * * * *
133423 ATGACAATT-TAGGAATTATTTTTTAAAAAAATGACATTCTAGGAATTATTTAGAAAAAT
1 GTGAC-ATTCTGGGAATT-TTTATGAAAAAGATGACATTCT-GGAATTATTTTGAAAAAT
* *
133482 GTGAAATTTTGGGAATTTT
1 GTGACATTCTGGGAATTTT
133501 CGAATATGGA
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
57 33 0.29
58 67 0.59
59 14 0.12
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (57 bp):
GTGACATTCTGGGAATTTTTATGAAAAAGATGACATTCTGGAATTATTTTGAAAAAT
Found at i:133452 original size:30 final size:30
Alignment explanation
Indices: 133367--133473 Score: 114
Period size: 30 Copynumber: 3.7 Consensus size: 30
133357 GTGAAAAATG
* * * **
133367 TGACATTCTGGGAATT-TTTGTGAAAAAGC
1 TGACATTCTAGGAATTATTTTTTAAAAAAA
* *
133396 TGACATTCTGGGAATTA--TTTTGAAAAAA
1 TGACATTCTAGGAATTATTTTTTAAAAAAA
133424 TGACAATT-TAGGAATTATTTTTTAAAAAAA
1 TGAC-ATTCTAGGAATTATTTTTTAAAAAAA
133454 TGACATTCTAGGAATTATTT
1 TGACATTCTAGGAATTATTT
133474 AGAAAAATGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.27
29 22 0.33
30 26 0.39
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (30 bp):
TGACATTCTAGGAATTATTTTTTAAAAAAA
Found at i:136483 original size:2 final size:2
Alignment explanation
Indices: 136476--136504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
136466 TAAGAACGTG
136476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
136505 GTTTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:141898 original size:23 final size:22
Alignment explanation
Indices: 141871--141945 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
141861 ATTCGGAATA
141871 ATTAAATAAGTTTTTAAATAAAC
1 ATTAAATAA-TTTTTAAATAAAC
* * *
141894 ATTAAAT-A-TTATAATTCAGAATA
1 ATTAAATAATTTTTAAAT-A-AA-C
141917 ATTAAATAACTTTTTAAATAAAC
1 ATTAAATAA-TTTTTAAATAAAC
141940 ATTAAA
1 ATTAAA
141946 GATTATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 6 0.15
21 1 0.03
22 3 0.08
23 20 0.50
24 3 0.08
25 1 0.03
26 6 0.15
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (22 bp):
ATTAAATAATTTTTAAATAAAC
Found at i:141907 original size:46 final size:46
Alignment explanation
Indices: 141857--141957 Score: 175
Period size: 46 Copynumber: 2.2 Consensus size: 46
141847 AATTGGTATA
* * *
141857 TATAATTCGGAATAATTAAATAAGTTTTTAAATAAACATTAAATAT
1 TATAATTCAGAATAATTAAATAACTTTTTAAATAAACATTAAAGAT
141903 TATAATTCAGAATAATTAAATAACTTTTTAAATAAACATTAAAGAT
1 TATAATTCAGAATAATTAAATAACTTTTTAAATAAACATTAAAGAT
141949 TATAATTCA
1 TATAATTCA
141958 AATTATAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (46 bp):
TATAATTCAGAATAATTAAATAACTTTTTAAATAAACATTAAAGAT
Found at i:142604 original size:24 final size:24
Alignment explanation
Indices: 142532--142634 Score: 91
Period size: 24 Copynumber: 4.3 Consensus size: 24
142522 AAACGGAGAT
* * *
142532 ATCATAAATCAAAACAAAATTTAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
142556 ATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
142580 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
142604 ATAAAAAATCATAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
142628 ATC-GAAA
1 ATCAGAAA
142635 ATCAGATAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
23 3 0.05
24 58 0.95
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:146701 original size:44 final size:44
Alignment explanation
Indices: 146642--146813 Score: 168
Period size: 44 Copynumber: 3.9 Consensus size: 44
146632 ACTTATCATG
* * *
146642 TGCACAAAGGAGAGGAGCCTGCAGAAACGGTAAGATTTTACCCT
1 TGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGATCTTACCCT
* * * * * *
146686 TACACATAGCAGAGGAGCTTG-GGAAATGGTAAGGTCTTATCCT
1 TGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGATCTTACCCT
* * * * * *
146729 TGCACACAGCAAAGGAGCTTGGAGAGACGGAAAGGA-CTTACCCT
1 TGCACATAGCAGAGGAGCCTGCAGAAACGGTAA-GATCTTACCCT
* *
146773 TGCACATAGCAGAGGAGCCTGCAGTAACGGTAAGGTCTTAC
1 TGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGATCTTAC
146814 AAGTCAAAGA
Statistics
Matches: 99, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
43 36 0.36
44 62 0.63
45 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.19
Consensus pattern (44 bp):
TGCACATAGCAGAGGAGCCTGCAGAAACGGTAAGATCTTACCCT
Found at i:146957 original size:12 final size:12
Alignment explanation
Indices: 146940--146982 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
146930 AAATCCAGAT
146940 CAGAAATTAGAA
1 CAGAAATTAGAA
146952 CAGAAATTAGAA
1 CAGAAATTAGAA
*
146964 CAG-AATTCAGAT
1 CAGAAATT-AGAA
146976 CAGAAAT
1 CAGAAAT
146983 CATAACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.14
12 21 0.75
13 3 0.11
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (12 bp):
CAGAAATTAGAA
Found at i:146989 original size:24 final size:24
Alignment explanation
Indices: 146943--147010 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
146933 TCCAGATCAG
* *
146943 AAATT-AGAACAGAAATTAGAACA
1 AAATTCAGATCAGAAATCAGAACA
* *
146966 GAATTCAGATCAGAAATCATAACA
1 AAATTCAGATCAGAAATCAGAACA
*
146990 AAATTCAAATC-GAAAATCAGA
1 AAATTCAGATCAG-AAATCAGA
147011 TAAAACTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.19
Consensus pattern (24 bp):
AAATTCAGATCAGAAATCAGAACA
Found at i:148694 original size:44 final size:44
Alignment explanation
Indices: 148646--148815 Score: 195
Period size: 44 Copynumber: 3.9 Consensus size: 44
148636 ACTTATTATG
* *
148646 TGCACAAAGCAGAGGAGCTTGTAGAAACGGTAAGGTCTTACCCT
1 TGCACAAAGCAGAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* * * * * *
148690 TGCACATAGCACAGGAGCCTGGA-AAATGGCAAGGTCTTATCCT
1 TGCACAAAGCAGAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* *
148733 TGCACACAA-CAAAGGAGCCTGCAGAAACGGTAAGGACTTACCCT
1 TGCACA-AAGCAGAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* *
148777 TGCAC--AGCAGAGGAGCCTGCGGTAACGGTAAGGTCTTAC
1 TGCACAAAGCAGAGGAGCCTGCAGAAACGGTAAGGTCTTAC
148816 AAGTCAAAGA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.01
42 28 0.27
43 35 0.33
44 41 0.39
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (44 bp):
TGCACAAAGCAGAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
Found at i:148965 original size:24 final size:24
Alignment explanation
Indices: 148907--149000 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
148897 AAATTAAAAT
* **
148907 AGAATTTAGATCAGTTATCAGAAC
1 AGAATTCAGATCAGAAATCAGAAC
* * *
148931 A-AAATCTAGATCAGAAATTAGAAT
1 AGAATTC-AGATCAGAAATCAGAAC
* *
148955 AGAATTCAGATCATAAATCATAAC
1 AGAATTCAGATCAGAAATCAGAAC
*
148979 AGAATTCAAAT-AGAAAATCAGA
1 AGAATTCAGATCAG-AAATCAGA
149001 TAAAACGTTC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
23 4 0.08
24 45 0.85
25 4 0.08
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (24 bp):
AGAATTCAGATCAGAAATCAGAAC
Found at i:149173 original size:17 final size:16
Alignment explanation
Indices: 149151--149201 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
149141 TATTAGCTGA
149151 CAGAATCATATGTTATT
1 CAGAATCATAT-TTATT
*
149168 CAGAAT-GTGATTTA-T
1 CAGAATCAT-ATTTATT
149183 CAGAATCATATCTTATT
1 CAGAATCATAT-TTATT
149200 CA
1 CA
149202 TACATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (16 bp):
CAGAATCATATTTATT
Found at i:154562 original size:112 final size:112
Alignment explanation
Indices: 154364--154588 Score: 423
Period size: 112 Copynumber: 2.0 Consensus size: 112
154354 AATAACAAAG
* *
154364 ATTTATTTACTTGATTAGATTTTTCATCATAATTTCAACAAAATGTTTTCTACTTTTTCAAACAT
1 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
*
154429 TTTATAATGGAAATTTTAATCATAGTTATGTAGGGTTGAAATTTTAT
66 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
154476 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
1 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
154541 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
66 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
154588 A
1 A
154589 CAATAATAAG
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (112 bp):
ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
Found at i:154632 original size:112 final size:111
Alignment explanation
Indices: 154388--154611 Score: 285
Period size: 112 Copynumber: 2.0 Consensus size: 111
154378 TTAGATTTTT
* * * *
154388 CATCATAATTTCAACAAAATGTTTTCTACTTTTTCAAACATTTTATAATGGAAATTTTAATCATA
1 CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
* * * * * *
154453 GTTATGTAGGGTTGAAATTTTATATTTATTTACTTAATTAGATTTTT
66 GTTATGTAGGGTTGAAATTTTATA-TCATATACATAATGAGATTATA
* *
154500 CATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
1 CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
154565 GTTATGTAGGGTTGAAATTTTATA-CA-ATA-ATAAGTGAG-TTCATA
66 GTTATGTAGGGTTGAAATTTTATATCATATACATAA-TGAGATT-ATA
154609 CAT
1 CAT
154612 TCTACATGTA
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
108 5 0.05
109 9 0.09
110 1 0.01
112 87 0.85
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (111 bp):
CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
GTTATGTAGGGTTGAAATTTTATATCATATACATAATGAGATTATA
Found at i:168145 original size:19 final size:18
Alignment explanation
Indices: 168110--168145 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
168100 TGAACAGATA
*
168110 AGCCAAGCCATTGAGTCG
1 AGCCAAGCCACTGAGTCG
168128 AGCCAAGCCGACTGAGTC
1 AGCCAAGCC-ACTGAGTC
168146 AACCTACATT
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:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (18 bp):
AGCCAAGCCACTGAGTCG
Found at i:171131 original size:87 final size:86
Alignment explanation
Indices: 170997--171281 Score: 399
Period size: 87 Copynumber: 3.2 Consensus size: 86
170987 CTTACAGACT
* * * * * *
170997 TAAGAATATCCTTGGGTAGGTATATTGACCCCAGGCATATCCTTAGGTTGGTTTCCTTTGCTGTG
1 TAAGGATACCCTTGGGTAGGCA-ATAGGCCCAAGGCATATCCTTAGGTTGG-TTCCTTTGCTGTG
*
171062 TACTTAAGGTAACCCTACGGATC
64 TGCTTAAGGTAACCCTACGGATC
171085 TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGGCTTCCTTTGCTGTGT
1 TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGG-TTCCTTTGCTGTGT
* *
171150 GGTTAAGGTAACTCTACGGATC
65 GCTTAAGGTAACCCTACGGATC
* * *
171172 TAAGGATACCCTTGAGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGTTGT
1 TAAGGATACCCTTGGGTAGG-CAATAGG-CCCAAGGCATATCCTTAGGTTGGTTC-CTTTGCTGT
171237 GTGCTTAAGGTAACCCTACGGATC
63 GTGCTTAAGGTAACCCTACGGATC
*
171261 TAAGGATATCCTTGGGTAGGC
1 TAAGGATACCCTTGGGTAGGC
171282 CCGGTAGGCC
Statistics
Matches: 177, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
87 77 0.44
88 29 0.16
89 71 0.40
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (86 bp):
TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGGTTCCTTTGCTGTGTG
CTTAAGGTAACCCTACGGATC
Found at i:171245 original size:89 final size:89
Alignment explanation
Indices: 171025--171283 Score: 402
Period size: 89 Copynumber: 2.9 Consensus size: 89
171015 GGTATATTGA
*
171025 CCCC-AGGCATATCCTTAGGTTGGTT-TCCTTTGCTGTGTACTTAAGGTAACCCTACGGATCTAA
1 CCCCAAGGCATATCCTTAGGTTGGTTCT-CTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAA
*
171088 GGATACCCTTGGGTAGG-CAATAGG
65 GGATACCCTTGGGTAGGCCCATAGG
* *
171112 -CCCAAGGCATATCCTTAGGTTGGCTTC-CTTTGCTGTGTGGTTAAGGTAACTCTACGGATCTAA
1 CCCCAAGGCATATCCTTAGGTTGG-TTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAA
*
171175 GGATACCCTTGAGTAGGCCCATAGG
65 GGATACCCTTGGGTAGGCCCATAGG
*
171200 CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGTTGTGTGCTTAAGGTAACCCTACGGATCTAAG
1 CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAAG
*
171265 GATATCCTTGGGTAGGCCC
66 GATACCCTTGGGTAGGCCC
171284 GGTAGGCCTA
Statistics
Matches: 156, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
86 3 0.02
87 68 0.44
88 11 0.07
89 74 0.47
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (89 bp):
CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAAG
GATACCCTTGGGTAGGCCCATAGG
Found at i:176013 original size:26 final size:26
Alignment explanation
Indices: 175979--176028 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
175969 ATGGTCTGAC
*
175979 GTGACAGTTTCTAGAAGGTCTAGTCA
1 GTGACAGTTTCTAGAAGATCTAGTCA
*
176005 GTGATAGTTTCTAGAAGATCTAGT
1 GTGACAGTTTCTAGAAGATCTAGT
176029 AAGAGGGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (26 bp):
GTGACAGTTTCTAGAAGATCTAGTCA
Found at i:176924 original size:18 final size:18
Alignment explanation
Indices: 176903--176938 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
176893 TGCCTTTATT
* *
176903 TATTTAATCTCTTTTTAC
1 TATTAAATCTCATTTTAC
176921 TATTAAATCTCATTTTAC
1 TATTAAATCTCATTTTAC
176939 CAAAACTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAAATCTCATTTTAC
Found at i:182881 original size:13 final size:14
Alignment explanation
Indices: 182863--182898 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
182853 AAGTCAATGG
182863 GTTGACTCAG-TGA
1 GTTGACTCAGCTGA
*
182876 GTTGACTTAGCTGA
1 GTTGACTCAGCTGA
182890 GTTGACTCA
1 GTTGACTCA
182899 ATGGATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (14 bp):
GTTGACTCAGCTGA
Found at i:185222 original size:74 final size:76
Alignment explanation
Indices: 185139--185314 Score: 239
Period size: 74 Copynumber: 2.3 Consensus size: 76
185129 CCGTTGAACA
* ** *
185139 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTA-GGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCG
185203 GTTCCTCCTAT
66 GTTCCTCCTAT
* * * * *
185214 -GGGGGAATCGGTTCCCTCCGATCATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCG
185278 GTTCCTCCTAT
66 GTTCCTCCTAT
*
185289 GGGGGGGAATCGGTTCCCTCTGAGCA
1 -GGGGGGAATCGGTTCCCTCCGAGCA
185315 ATCTGTAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 44 0.51
75 21 0.24
77 22 0.25
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (76 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCG
GTTCCTCCTAT
Found at i:187995 original size:20 final size:20
Alignment explanation
Indices: 187919--188003 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
187909 AGCAGAACCC
*
187919 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
187938 CTGTGGGGGAAATCGGTTCCCCTT
1 CAG-GGGGG-AATCGATT-CCC-T
* *
187962 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
187983 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
188003 C
1 C
188004 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
19 2 0.04
20 22 0.42
21 8 0.15
22 6 0.12
23 8 0.15
24 6 0.12
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:193879 original size:75 final size:75
Alignment explanation
Indices: 193763--193961 Score: 247
Period size: 75 Copynumber: 2.6 Consensus size: 75
193753 GACCGTTGAA
* * ** *
193763 CAGGGGGAATCGGTACCCCCTGGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGAATCGGTTCCTCCT-ATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
193828 ACAAAAATGTT
65 ACAAAAACATT
* * *
193839 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGATCATTCTGGAAATCTCGGA
1 CA-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
* * *
193903 GCCAAACCATT
65 ACAAAAACATT
*
193914 CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
193962 ATCTGTAATT
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
74 21 0.20
75 66 0.63
76 1 0.01
77 17 0.16
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (75 bp):
CAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAAACATT
Found at i:194744 original size:31 final size:32
Alignment explanation
Indices: 194676--194750 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
194666 GAGGCCTGAG
** *
194676 AGCCTACCCAAGAAAGTTATCGGGGCCACGAA
1 AGCCTACCCAAGAAAAATATCGGGGCCACAAA
* *
194708 AGCCTACCCAAGAAAAATCTTGGGGCCA-AAA
1 AGCCTACCCAAGAAAAATATCGGGGCCACAAA
194739 AGCCTACCCAAG
1 AGCCTACCCAAG
194751 GGTTAGCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.37, C:0.29, G:0.21, T:0.12
Consensus pattern (32 bp):
AGCCTACCCAAGAAAAATATCGGGGCCACAAA
Found at i:204349 original size:25 final size:26
Alignment explanation
Indices: 204319--204368 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
204309 AAAACTTTAG
204319 GTCATTTTACACTTTAGGG-ATTTCA
1 GTCATTTTACACTTTAGGGCATTTCA
204344 GTCATTTTACACTTTAGGGCATTTC
1 GTCATTTTACACTTTAGGGCATTTC
204369 TATAAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (26 bp):
GTCATTTTACACTTTAGGGCATTTCA
Found at i:205262 original size:14 final size:14
Alignment explanation
Indices: 205243--205272 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
205233 GTTTACTTTT
205243 GGTCAAAGTCAATG
1 GGTCAAAGTCAATG
205257 GGTCAAAGTCAATG
1 GGTCAAAGTCAATG
205271 GG
1 GG
205273 ATGACTCGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (14 bp):
GGTCAAAGTCAATG
Found at i:206829 original size:11 final size:11
Alignment explanation
Indices: 206815--206866 Score: 63
Period size: 10 Copynumber: 4.9 Consensus size: 11
206805 ATAATGTGAA
*
206815 ATTTAAGAAAT
1 ATTTTAGAAAT
*
206826 ATTTTATAAA-
1 ATTTTAGAAAT
206836 ATTTTAGAAAT
1 ATTTTAGAAAT
*
206847 ATTTTATAAA-
1 ATTTTAGAAAT
206857 ATTTTAGAAA
1 ATTTTAGAAA
206867 GATTAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (11 bp):
ATTTTAGAAAT
Found at i:206838 original size:21 final size:21
Alignment explanation
Indices: 206813--206866 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
206803 AAATAATGTG
*
206813 AAATTTAAGAAATATTTTATA
1 AAATTTTAGAAATATTTTATA
206834 AAATTTTAGAAATATTTTATA
1 AAATTTTAGAAATATTTTATA
206855 AAATTTTAGAAA
1 AAATTTTAGAAA
206867 GATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
AAATTTTAGAAATATTTTATA
Done.