Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 143 of 199
Found at i:43005379 original size:20 final size:20
Alignment explanation
Indices: 43005354--43005395 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
43005344 CAAATTTTAA
43005354 TTACTGCTTTCGTTAGTAAG
1 TTACTGCTTTCGTTAGTAAG
43005374 TTACTGCTTTCGTTAGTAAG
1 TTACTGCTTTCGTTAGTAAG
43005394 TT
1 TT
43005396 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (20 bp):
TTACTGCTTTCGTTAGTAAG
Found at i:43006420 original size:39 final size:40
Alignment explanation
Indices: 43006299--43006434 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 40
43006289 GTTTGGACAA
* * * * *
43006299 AAAACGTCACTAAAAATCGAGCATTAGAGGCGCCTTATGT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATGG
* * * *
43006339 AAAACACCGCTAAAGATCGAGCATTAGCGGAGCTTCCA-GG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTT-TATGG
* * *
43006379 AAAGCGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTGG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATGG
*
43006418 AAAAACGCCGCAAAAAA
1 -AAAACGCCGCTAAAAA
43006435 CCAAAGCCCA
Statistics
Matches: 75, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 17 0.23
40 57 0.76
41 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATGG
Found at i:43006554 original size:41 final size:41
Alignment explanation
Indices: 43006465--43006705 Score: 331
Period size: 41 Copynumber: 5.9 Consensus size: 41
43006455 TTTCTACCTT
* * *
43006465 TCAGATCTTTAGCGGC-ATTTGGAAAAAAAGCACCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTG--AAAAAGCGCCGCTAATGC
* *
43006507 TTAGATCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
43006548 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* ** ** *
43006589 TCAGATCTTTCGCGGCGTTTTCCATGAAGCGCCACTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
43006630 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGTTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* *
43006671 TCAGATCTTTAGCGGTGTTTTTGAAGAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
43006706 AAAAATATTT
Statistics
Matches: 175, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
41 156 0.89
42 15 0.09
43 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:43010162 original size:19 final size:20
Alignment explanation
Indices: 43010118--43010162 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
43010108 AACGTCTCTT
*
43010118 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
43010137 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
43010156 TATGCAT
1 TATGCAT
43010163 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:43012094 original size:19 final size:19
Alignment explanation
Indices: 43012057--43012096 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43012047 GCAAATGTTC
*
43012057 TTTCATTCTTTACGTTTTT
1 TTTCATTCTTTACGATTTT
43012076 TTTCATTCTTT-CAGATTTT
1 TTTCATTCTTTAC-GATTTT
43012095 TT
1 TT
43012097 CTGCCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.12, C:0.15, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTCATTCTTTACGATTTT
Found at i:43014445 original size:133 final size:133
Alignment explanation
Indices: 43014269--43014913 Score: 906
Period size: 133 Copynumber: 4.9 Consensus size: 133
43014259 AAGCAGTAGT
* * *
43014269 GGAGCAGATCGAAGATGGTGGATTTTACCTCCATGAAGTTGCAGTGGAGTACATTGAAGCCAGAA
1 GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
*
43014334 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTTAGATCTTGCCTTCCTGCATAGAC
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGCCTTCCTGCATAGAC
43014399 AGC
131 AGC
* *
43014402 GGAGCAGATCAAAGCTGGTGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGAA
1 GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
* * *
43014467 ATTCTACTTTCCTGGTCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGCCTTCTTGCATAGAC
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGCCTTCCTGCATAGAC
43014532 AGC
131 AGC
* *
43014535 GAAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
1 GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
* * * *
43014600 ATTCTACTTCCCTGGTCAGCAGTGGAATAGATTAAAAGATTTTAGATCTTGTC-TCC-CCA-AGC
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATT-AAAGATTTCAGATCTTGCCTTCCTGCATAG-
* *
43014662 AGTAGT
129 A-CAGC
* * * *
43014668 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
*
43014733 ATTCTACTTCCCTGGGCAGCAGCT-GAATAGATTAAAGATTACAGATCTTGCCTTCCTGCATAGA
66 ATTCTACTTCCCTGGGCAGCAG-TGGAATAGATTAAAGATTTCAGATCTTGCCTTCCTGCATAGA
*
43014797 TAG-
130 CAGC
* * * * * * *
43014800 TGAGCAGATCAAGGATGGCGGATTTTACTTCCCTGAGGTTACAGTGGAGTACATTGAAGCCGGTA
1 GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
* * *
43014865 ATTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTT
66 ATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTT
43014914 ATCTCCCTAG
Statistics
Matches: 467, Mismatches: 36, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
131 4 0.01
132 120 0.26
133 320 0.69
134 21 0.04
135 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (133 bp):
GGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAA
ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGCCTTCCTGCATAGAC
AGC
Found at i:43015110 original size:44 final size:44
Alignment explanation
Indices: 43015014--43015252 Score: 152
Period size: 44 Copynumber: 5.5 Consensus size: 44
43015004 AAGATGGCGA
* * * *
43015014 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGG-TTAAAGCTA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACCACA-G
* *
43015058 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* * ** *** *
43015102 ATCTTATCTCTCTGAAGTTGTAAAGG-GCGGA-TCGCATC-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* * ** *
43015143 -TCTTATCTCCCTGCAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AACCACAG
* * * * *
43015186 ATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAAAACCACAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* *
43015230 ATCTCATCTCTCTGAAGTTGCAG
1 ATCTTATCTCCCTGAAGTTGCAG
43015253 CAGAGTAGAT
Statistics
Matches: 145, Mismatches: 41, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
40 20 0.14
41 7 0.05
42 6 0.04
43 10 0.07
44 101 0.70
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
Found at i:43015902 original size:18 final size:18
Alignment explanation
Indices: 43015879--43015913 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43015869 TTTTGTTGAG
43015879 TTATCTTTTCCATTTCAT
1 TTATCTTTTCCATTTCAT
43015897 TTATCTTTTCCATTTCA
1 TTATCTTTTCCATTTCA
43015914 GCTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATCTTTTCCATTTCAT
Found at i:43018483 original size:21 final size:21
Alignment explanation
Indices: 43018443--43018483 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43018433 TAAGGTTTAT
* * *
43018443 GGGTTAGGGGTTAAGGGTTAA
1 GGGTTAGAGGTCAAGAGTTAA
43018464 GGGTTAGAGGTCAAGAGTTA
1 GGGTTAGAGGTCAAGAGTTA
43018484 GGGATTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.02, G:0.44, T:0.27
Consensus pattern (21 bp):
GGGTTAGAGGTCAAGAGTTAA
Found at i:43019959 original size:76 final size:75
Alignment explanation
Indices: 43019833--43020052 Score: 293
Period size: 75 Copynumber: 2.9 Consensus size: 75
43019823 ATAGCCGCGT
*
43019833 TTTTAT-AAAAACGCCACAAAAAAAATAATTTTACTTT-AAAAATAGCCATTTTATATAGCAAAA
1 TTTTATAAAAAACGCCAC--AAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATAGCAAAA
*
43019896 CATTTAGCGGC-G
64 CCTTTAG-GGCAG
*** * *
43019908 TTTTAGTAAAAAATTTCACAAAAAATAATTTTATTTTAAAAAATAATCATTTTATATAGCAAAAC
1 TTTTA-TAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATAGCAAAAC
*
43019973 CTTTAGGGCAT
65 CTTTAGGGCAG
* *
43019984 TTTTATAAAAAACGCCACAAAAATTAATTTTACTTTAAAAAATAGTTATTTTATATAGCAAAACC
1 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATAGCAAAACC
43020049 TTTA
66 TTTA
43020053 AAAATGCCAC
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
75 82 0.65
76 36 0.29
77 8 0.06
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (75 bp):
TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATATAGCAAAACC
TTTAGGGCAG
Found at i:43020062 original size:61 final size:62
Alignment explanation
Indices: 43019991--43020114 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 62
43019981 CATTTTTATA
* * * * * *
43019991 AAAAACGCCACAAAAATTAATTTTACTTT-AAAAAATAGTTATTTTATATAGCAAAACCTTT
1 AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAATCATTTTACATAACAAAACATTT
*
43020052 AAAAATGCCACAAAAAATAATTTTACTTTAAAAAAATAATCATTTTACATAACAAAACATTT
1 AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAATCATTTTACATAACAAAACATTT
43020114 A
1 A
43020115 GCGGCGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 27 0.49
62 28 0.51
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (62 bp):
AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAATCATTTTACATAACAAAACATTT
Found at i:43020172 original size:137 final size:134
Alignment explanation
Indices: 43019924--43020173 Score: 369
Period size: 137 Copynumber: 1.8 Consensus size: 134
43019914 TAAAAAATTT
* * * *
43019924 CACAAAAAATAATTTTATTTTAAAAAATAATCATTTTATATAGCAAAACCTTTAGGGCATTTTTA
1 CACAAAAAATAATTTTATTTAAAAAAATAATCATTTTACATAACAAAACATTTAGGGCATTTTTA
*
43019989 TAAAAAACGCCACAAAAATTAATTTTACTTTAAAAAATAGTTATTTTATATAGCAAAACCTTTAA
66 TAAAAAACGCCACAAAAATTAATTTTA--TTAAAAAATAGTCATTTTATATAGCAAAACCTTTAA
43020054 AAATGC
129 AAATGC
*
43020060 CACAAAAAATAATTTTACTTTAAAAAAATAATCATTTTACATAACAAAACATTTAGCGGCGTTTT
1 CACAAAAAATAATTTTA-TTTAAAAAAATAATCATTTTACATAACAAAACATTTAG-GGCATTTT
43020125 TATAAAAAAACGCCACAAAAA-TAATTTTA-TAAAAAATAGCGTCATTTTA
64 TAT-AAAAAACGCCACAAAAATTAATTTTATTAAAAAATA--GTCATTTTA
43020174 AAAAATCCCC
Statistics
Matches: 103, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
135 9 0.09
136 17 0.17
137 42 0.41
138 18 0.17
139 17 0.17
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (134 bp):
CACAAAAAATAATTTTATTTAAAAAAATAATCATTTTACATAACAAAACATTTAGGGCATTTTTA
TAAAAAACGCCACAAAAATTAATTTTATTAAAAAATAGTCATTTTATATAGCAAAACCTTTAAAA
ATGC
Found at i:43020223 original size:22 final size:22
Alignment explanation
Indices: 43020191--43020252 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
43020181 CCCTCCCCCT
43020191 CTCC-AAAATCCCCAACTTTCC
1 CTCCTAAAATCCCCAACTTTCC
*
43020212 CTCCTAAAATCCCTAA-TTTCC
1 CTCCTAAAATCCCCAACTTTCC
* *
43020233 C-CCTTGAAACCCCCAACTTT
1 CTCC-TAAAATCCCCAACTTT
43020253 ACAAACATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.06
21 19 0.56
22 13 0.38
ACGTcount: A:0.27, C:0.44, G:0.02, T:0.27
Consensus pattern (22 bp):
CTCCTAAAATCCCCAACTTTCC
Found at i:43020970 original size:2 final size:2
Alignment explanation
Indices: 43020963--43021008 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
43020953 TTGGTATTTA
43020963 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
43021005 AT AT
1 AT AT
43021009 GTTTTGTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43024070 original size:43 final size:43
Alignment explanation
Indices: 43024009--43024337 Score: 410
Period size: 43 Copynumber: 7.6 Consensus size: 43
43023999 TATATATATT
* * * * *
43024009 TAAAGGTTATGGTTTTTAGCGGCGTTTTTGTGAGAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
** *
43024052 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCTCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
43024095 TAAAGGTCATGGACTTTAGCAGCGTTTGTGGGAAAAGCGCCAC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
43024138 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG-AAAAGCGCCGC
* * * *
43024182 TAAATGTCTTGGTCTTTAGCGGTGTTTTTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * **
43024225 TAAAGAT-ATTAGTCTTTAGCGGCATTTGTGGGAGTAGCGCCGC
1 TAAAGGTCA-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
43024268 TAAAGAT-ATTGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
1 TAAAGGTCA-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
43024311 TAAAGGTCTTGGTCTTTAGCGGCGTTT
1 TAAAGGTCATGGTCTTTAGCGGCGTTT
43024338 TTTTCTAAAA
Statistics
Matches: 247, Mismatches: 36, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
43 209 0.85
44 38 0.15
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:43024316 original size:173 final size:173
Alignment explanation
Indices: 43024018--43024337 Score: 446
Period size: 173 Copynumber: 1.8 Consensus size: 173
43024008 TTAAAGGTTA
* * * * * *
43024018 TGGTTTTTAGCGGCGTTTTTGTGAGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGA
1 TGGTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGATCATAGTCTTTAGCGGCATTTGTGA
* * *
43024083 TAAAAGCTCCGCTAAAGGTCATGGACTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTCAT
66 GAAAAGCGCCGCTAAAGATCATGGACTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTCAT
43024148 GGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAATGTCT
131 GGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAATGTCT
*
43024191 TGGTCTTTAGCGGTGTTTTTGGGAAAAGCGCCGCTAAAGAT-ATTAGTCTTTAGCGGCATTTGTG
1 TGGTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGATCA-TAGTCTTTAGCGGCATTTGTG
* ** * * * *
43024255 GGAGTAGCGCCGCTAAAGAT-ATTGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTC
65 AGAAAAGCGCCGCTAAAGATCA-TGGACTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTC
*
43024319 TTGGTCTTTAGCGGCGTTT
129 ATGGTCTTTAGCGGCGTTT
43024338 TTTTCTAAAA
Statistics
Matches: 127, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
172 2 0.02
173 125 0.98
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (173 bp):
TGGTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGATCATAGTCTTTAGCGGCATTTGTGA
GAAAAGCGCCGCTAAAGATCATGGACTTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTCAT
GGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAATGTCT
Found at i:43024459 original size:22 final size:22
Alignment explanation
Indices: 43024431--43024473 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43024421 TAGTGGCGCT
*
43024431 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
43024453 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
43024474 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:43025226 original size:21 final size:21
Alignment explanation
Indices: 43025200--43025251 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43025190 ATTTAGAACT
43025200 TAGAAAATCATAA-AGGAAACC
1 TAGAAAATCATAATA-GAAACC
*
43025221 TAGAAAATGATAATAGAAACC
1 TAGAAAATCATAATAGAAACC
*
43025242 TGGAAAATCA
1 TAGAAAATCA
43025252 AGTTAGCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (21 bp):
TAGAAAATCATAATAGAAACC
Found at i:43026963 original size:23 final size:23
Alignment explanation
Indices: 43026937--43026981 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
43026927 TTTCTTACTG
43026937 TAGTAATTTTCAGGG-TATTACAA
1 TAGTAATTTTC-GGGATATTACAA
43026960 TAGTAATTTTCGGGATATTACA
1 TAGTAATTTTCGGGATATTACA
43026982 TTAAGGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAA
Found at i:43031158 original size:28 final size:27
Alignment explanation
Indices: 43031124--43031215 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 27
43031114 AAATATTAAT
*
43031124 ATTTTTATAATTTTTATACTTTTTAAATA
1 ATTTTAATAATTTTTA-A-TTTTTAAATA
* *
43031153 ATTTTAATGATTTTTAATTTTTAAAAATC
1 ATTTTAATAATTTTTAATTTTT--AAATA
*
43031182 ATTTTTATATATTTTTGAA-TTTTAAA-A
1 ATTTTAATA-ATTTTT-AATTTTTAAATA
43031209 ATTTTAA
1 ATTTTAA
43031216 AAAATTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 11 0.21
28 4 0.08
29 25 0.48
30 10 0.19
31 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTTAATAATTTTTAATTTTTAAATA
Found at i:43031166 original size:20 final size:19
Alignment explanation
Indices: 43031108--43031169 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
43031098 TTTTTTAAAA
*
43031108 TTTTAAA-AATATTAATAT
1 TTTTAAATAATTTTAATAT
*
43031126 TTTT--ATAATTTTTATACT
1 TTTTAAATAATTTTAATA-T
43031144 TTTTAAATAATTTTAATGAT
1 TTTTAAATAATTTTAAT-AT
43031164 TTTTAA
1 TTTTAA
43031170 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.03
17 8 0.22
18 9 0.25
20 17 0.47
21 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAAATAATTTTAATAT
Found at i:43031196 original size:30 final size:29
Alignment explanation
Indices: 43031121--43031210 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
43031111 TAAAAATATT
43031121 AATATTTTTATA-ATTTTTATACTTTTT--A
1 AATATTTTTATATATTTTTA-A-TTTTTAAA
*
43031149 AATAATTTTA-ATGATTTTTAATTTTTAAA
1 AATATTTTTATAT-ATTTTTAATTTTTAAA
43031178 AATCATTTTTATATATTTTTGAA-TTTTAAA
1 AAT-ATTTTTATATATTTTT-AATTTTTAAA
43031208 AAT
1 AAT
43031211 TTTAAAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 6 0.11
28 10 0.19
29 11 0.21
30 22 0.42
31 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
AATATTTTTATATATTTTTAATTTTTAAA
Found at i:43034618 original size:24 final size:23
Alignment explanation
Indices: 43034591--43034641 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
43034581 CTATAACAAT
*
43034591 ATGCAAAAAATTCTACCAGTAAAA
1 ATGCAAAAAA-GCTACCAGTAAAA
* * *
43034615 ATGCAGACAAGCTGCCAGTAAAA
1 ATGCAAAAAAGCTACCAGTAAAA
43034638 ATGC
1 ATGC
43034642 GATAAATTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (23 bp):
ATGCAAAAAAGCTACCAGTAAAA
Found at i:43051247 original size:192 final size:191
Alignment explanation
Indices: 43050921--43051304 Score: 696
Period size: 192 Copynumber: 2.0 Consensus size: 191
43050911 ATTTAAAGTA
*
43050921 ACACTCATGGATCCAATAAAATGAGTGAAATCTCATTATGCTCCATTTCATTTTTTCAATAGTGT
1 ACACTCATGGATACAATAAAATGAGTGAAATCTCATTATGCTCCATTTCATTTTTTCAATAGTGT
*
43050986 TTAAGACGCTGACCATTTACCTTAAAAGTTCTTCATTGTCCATTATGTAATTCAACTACTCCATA
66 TTAAGACGCTGACCATTTACCTTAAAAGTTCTTCATTGTCCATTATGCAATTCAACTACTCCATA
*
43051051 TGGATACACTCAGTGAATCATGTAAGGTCTAGTCCATCGAGACATAAGTTTTCTAAGAAAT
131 TGGATACACTCAGTGAATCATATAAGGTCTAGTCCATCGAGACATAAGTTTTCTAAGAAAT
43051112 ACACTCATGGATACAATAAAATGAGTGAAATCTCATTATGCTCCATTTCATTTTTTTCAATAGTG
1 ACACTCATGGATACAATAAAATGAGTGAAATCTCATTATGCTCCATTTCA-TTTTTTCAATAGTG
* * *
43051177 TTTAAGATGCTGACCATTTACCTTAAAAGTTCTTCGTTGTCCATTATGCAATTCCACTACTCCAT
65 TTTAAGACGCTGACCATTTACCTTAAAAGTTCTTCATTGTCCATTATGCAATTCAACTACTCCAT
*
43051242 ATGGATACACTCAGTGAATCATATAAGGTCTAGTCCATCGAGACTTAAGTTTTCTAAGAAAT
130 ATGGATACACTCAGTGAATCATATAAGGTCTAGTCCATCGAGACATAAGTTTTCTAAGAAAT
43051304 A
1 A
43051305 ATTTCATCCT
Statistics
Matches: 185, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
191 49 0.26
192 136 0.74
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (191 bp):
ACACTCATGGATACAATAAAATGAGTGAAATCTCATTATGCTCCATTTCATTTTTTCAATAGTGT
TTAAGACGCTGACCATTTACCTTAAAAGTTCTTCATTGTCCATTATGCAATTCAACTACTCCATA
TGGATACACTCAGTGAATCATATAAGGTCTAGTCCATCGAGACATAAGTTTTCTAAGAAAT
Found at i:43054720 original size:41 final size:41
Alignment explanation
Indices: 43054662--43054956 Score: 315
Period size: 41 Copynumber: 7.2 Consensus size: 41
43054652 TGAGCTTTCG
* * * * **
43054662 GGGATTTAGCGACATTTTTTAGAAAGCACTACTAATGCTCA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
43054703 TGGATTTAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTTA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
43054744 AGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
43054785 GGGATTTAGCGACGTTTTTGAGAAAGCGCCGCTAATTCTCA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
** * * * *
43054826 GGGATTTAGTAGCATTTTTAAGAAAGTGCCGCTAATGCTCG
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
43054867 GGGCTTTAGTGGCGTTTTTGATAAAGCACTGCTAATGCTC-
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
43054907 GAGGCTTTAGCGACGTTTTCT-AAAAAGCGCCGCTAATGCTCA
1 G-GGATTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTCA
43054949 GGGATTTA
1 GGGATTTA
43054957 AAATAATTTA
Statistics
Matches: 214, Mismatches: 37, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
40 1 0.00
41 211 0.99
42 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (41 bp):
GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:43054881 original size:123 final size:121
Alignment explanation
Indices: 43054662--43054956 Score: 374
Period size: 123 Copynumber: 2.4 Consensus size: 121
43054652 TGAGCTTTCG
* * ** * * *
43054662 GGGATTTAGCGACATTTTTTAGAAAGCACTACTAATGCTCATGGATTTAGCGGCATTTTTGAGAA
1 GGGATTTAGCGAC-GTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCAGCATTTTTAAGAA
* *
43054727 AGCGCCGCTAATGCTTAAGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
65 AGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTC
* *
43054784 AGGGATTTAGCGACGTTTTTGAGAAAGCGCCGCTAATTCTCAGGGATTTAGTAGCATTTTTAAGA
1 -GGGATTTAGCGACGTTTTT-AGAAAGCGCCGCTAATGCTCAGGGATTTAGCAGCATTTTTAAGA
* ** * * *
43054849 AAGTGCCGCTAATGCTCGGGGCTTTAGTGGCGTTTTTGATAAAGCACTGCTAATGCTC
64 AAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTC
* *
43054907 GAGGCTTTAGCGACGTTTTCTAAAAAGCGCCGCTAATGCTCAGGGATTTA
1 G-GGATTTAGCGACGTTTT-TAGAAAGCGCCGCTAATGCTCAGGGATTTA
43054957 AAATAATTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
122 6 0.04
123 142 0.95
124 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (121 bp):
GGGATTTAGCGACGTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCAGCATTTTTAAGAAA
GCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTC
Found at i:43055151 original size:14 final size:14
Alignment explanation
Indices: 43055132--43055315 Score: 74
Period size: 14 Copynumber: 12.9 Consensus size: 14
43055122 TATCACTATA
*
43055132 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
43055146 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
43055160 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
43055174 GTTTAGAAGTTACTAT-
1 GTTTAG-GGTT--TATG
*
43055190 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
* *
43055203 GATTATGGGTTTACG
1 GTTTA-GGGTTTATG
* **
43055218 GTTTATGGTTTAAAA
1 GTTTAGGGTTT-ATG
* **
43055233 GCTTA-GGTTTAAA
1 GTTTAGGGTTTATG
43055246 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
*
43055260 TGTTAAGGGTTTA-G
1 -GTTTAGGGTTTATG
*
43055274 AGTTTTAGGGTTTTAAG
1 -G-TTTAGGG-TTTATG
* *
43055291 ATTTA-AGTTTATG
1 GTTTAGGGTTTATG
43055304 GTTTAGGGTTTA
1 GTTTAGGGTTTA
43055316 GATTAATTTA
Statistics
Matches: 128, Mismatches: 27, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
12 3 0.02
13 16 0.12
14 58 0.45
15 44 0.34
16 4 0.03
17 3 0.02
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:43056231 original size:12 final size:12
Alignment explanation
Indices: 43056214--43056248 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
43056204 TCATGATTTA
43056214 AAATTTTAAAAT
1 AAATTTTAAAAT
43056226 AAATTTTAAAAT
1 AAATTTTAAAAT
43056238 AAATTTTAAAA
1 AAATTTTAAAA
43056249 GATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTTAAAAT
Found at i:43059727 original size:43 final size:43
Alignment explanation
Indices: 43059670--43059897 Score: 289
Period size: 43 Copynumber: 5.3 Consensus size: 43
43059660 AGATTTGTTT
* * *
43059670 TTTAGCGGCCTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
* * * *
43059713 TTTAGCAGCATTTGTGACAAAAGCGTCGCTAAAGGGCATGA-C
1 TTTAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
* * *
43059755 TTTTAGCGGCGTTTGTGACAAAAAGTGCCGCTAAAGGTCATGATC
1 -TTTAGCAGCGTTTGTGA-TAAAAGCGCCGCTAAAGGTCATGATC
* * **
43059800 TTTAGCGGCGTTTGTGATAGAAGCGCCATTAAAGGTCATGATC
1 TTTAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
*
43059843 TTTAGCAGCGTTTGTGATAAAAGCG-CGCTAAAGGCCATGATC
1 TTTAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
43059885 TTTAGCAGCGTTT
1 TTTAGCAGCGTTT
43059898 TTTCACATAA
Statistics
Matches: 160, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
42 28 0.17
43 94 0.59
44 37 0.23
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
Found at i:43059792 original size:87 final size:85
Alignment explanation
Indices: 43059669--43059893 Score: 290
Period size: 87 Copynumber: 2.6 Consensus size: 85
43059659 AAGATTTGTT
* *
43059669 TTTTAGCGGCCTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAGCATTTGTGACAAA
1 TTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCATTTGTGACAAA
* *
43059734 AGCGTCGCTAAAGGGCATGA
66 AGCGCCACTAAAGGGCATGA
* * * * *
43059754 CTTTTAGCGGCGTTTGTGACAAAAAGTGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGATA
1 -TTTTAGCGGCGTTTGTGA-TAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCATTTGTGACA
* * *
43059819 GAAGCGCCATTAAAGGTCATGA
64 AAAGCGCCACTAAAGGGCATGA
* *
43059841 TCTTTAGCAGCGTTTGTGATAAAAGCG-CGCTAAAGGCCATGATCTTTAGCAGC
1 T-TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGC
43059894 GTTTTTTCAC
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
85 24 0.20
86 24 0.20
87 72 0.60
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (85 bp):
TTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCATTTGTGACAAA
AGCGCCACTAAAGGGCATGA
Found at i:43062350 original size:5 final size:5
Alignment explanation
Indices: 43062342--43062377 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
43062332 CTGAAAAGAA
43062342 AAATT AAATT AAATT AAATT AAATT AAATT ATAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT A-AATT
43062378 TTAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:43065861 original size:13 final size:14
Alignment explanation
Indices: 43065836--43065873 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
43065826 TGGGATTTAA
43065836 AGTTTAGGG-TTTG
1 AGTTTAGGGTTTTG
43065849 AGTTT-GGGTTTTG
1 AGTTTAGGGTTTTG
43065862 AGTTTAGGGTTT
1 AGTTTAGGGTTT
43065874 ATTGTTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (14 bp):
AGTTTAGGGTTTTG
Found at i:43065880 original size:21 final size:22
Alignment explanation
Indices: 43065856--43065956 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 22
43065846 TTGAGTTTGG
43065856 GTTTTGAG-TTTAGGGTTTATT
1 GTTTTGAGATTTAGGGTTTATT
* * *
43065877 G-TTT-AGGTTTAGGGTTCAAT
1 GTTTTGAGATTTAGGGTTTATT
* * * *
43065897 GGTTTGTGTTTTAGGGTTT-TG
1 GTTTTGAGATTTAGGGTTTATT
*
43065918 GTTTT-ATGATTTAGGGTTT-TG
1 GTTTTGA-GATTTAGGGTTTATT
43065939 GTTTT-ATGATTTAGGGTT
1 GTTTTGA-GATTTAGGGTT
43065957 GAGGTATGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.03
20 15 0.23
21 39 0.59
22 10 0.15
ACGTcount: A:0.14, C:0.01, G:0.31, T:0.54
Consensus pattern (22 bp):
GTTTTGAGATTTAGGGTTTATT
Found at i:43065888 original size:6 final size:7
Alignment explanation
Indices: 43065837--43065956 Score: 50
Period size: 7 Copynumber: 17.4 Consensus size: 7
43065827 GGGATTTAAA
43065837 GTTTAGG
1 GTTTAGG
*
43065844 GTTT-GA
1 GTTTAGG
43065850 GTTT-GG
1 GTTTAGG
* *
43065856 GTTTTGA
1 GTTTAGG
43065863 GTTTAGG
1 GTTTAGG
**
43065870 GTTTATT
1 GTTTAGG
43065877 GTTTA-G
1 GTTTAGG
43065883 GTTTAGG
1 GTTTAGG
* *
43065890 GTTCAATG
1 GTT-TAGG
43065898 GTTT-GTG
1 GTTTAG-G
*
43065905 TTTTAGG
1 GTTTAGG
*
43065912 GTTTTGG
1 GTTTAGG
* *
43065919 TTTTATG
1 GTTTAGG
*
43065926 ATTTAGG
1 GTTTAGG
*
43065933 GTTTTGG
1 GTTTAGG
* *
43065940 TTTTATG
1 GTTTAGG
*
43065947 ATTTAGG
1 GTTTAGG
43065954 GTT
1 GTT
43065957 GAGGTATGAA
Statistics
Matches: 80, Mismatches: 28, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
6 15 0.19
7 59 0.74
8 6 0.08
ACGTcount: A:0.13, C:0.01, G:0.33, T:0.53
Consensus pattern (7 bp):
GTTTAGG
Found at i:43066306 original size:20 final size:20
Alignment explanation
Indices: 43066268--43066306 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43066258 GCCAAAACCC
*
43066268 TAAACTTAAACCCTAAAGCA
1 TAAACTTAAAACCTAAAGCA
*
43066288 TAAACTTAAAACCTCAAGC
1 TAAACTTAAAACCTAAAGC
43066307 TTTTAACCCT
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:0.49, C:0.26, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAACTTAAAACCTAAAGCA
Found at i:43066738 original size:21 final size:20
Alignment explanation
Indices: 43066714--43066798 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 20
43066704 ACCAGAAAAA
43066714 CTAAATCTAAAATCTCAAACC
1 CTAAATCTAAAA-CTCAAACC
* *
43066735 CTAAACACTAAACACT-AAACT
1 CTAAA-TCTAAA-ACTCAAACC
* *
43066756 TTAACTCTAGAAACTCAAACC
1 CTAAATCTA-AAACTCAAACC
* * *
43066777 CAAAACCTAAAATCCCAAACC
1 CTAAATCTAAAA-CTCAAACC
43066798 C
1 C
43066799 CAAACTCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 9 0.19
21 31 0.65
22 7 0.15
23 1 0.02
ACGTcount: A:0.48, C:0.32, G:0.01, T:0.19
Consensus pattern (20 bp):
CTAAATCTAAAACTCAAACC
Found at i:43066987 original size:20 final size:21
Alignment explanation
Indices: 43066947--43066990 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
43066937 AAGTCATTAC
*
43066947 CCCAAACATTTGAACCTTAAA
1 CCCAAACATTTAAACCTTAAA
*
43066968 CCCAAAC-TTTAAATCTTAAA
1 CCCAAACATTTAAACCTTAAA
43066988 CCC
1 CCC
43066991 TTAAACCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25
Consensus pattern (21 bp):
CCCAAACATTTAAACCTTAAA
Found at i:43066998 original size:28 final size:28
Alignment explanation
Indices: 43066961--43067016 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
43066951 AACATTTGAA
* *
43066961 CCTTAAACCC-AAACTTTAAATCTTAAAC
1 CCTTAAACCCTAAAC-ATAAACCTTAAAC
43066989 CCTTAAACCCTAAACATAAACCTTAAAC
1 CCTTAAACCCTAAACATAAACCTTAAAC
43067017 TCAAACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (28 bp):
CCTTAAACCCTAAACATAAACCTTAAAC
Found at i:43067022 original size:13 final size:13
Alignment explanation
Indices: 43066993--43067036 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
43066983 TTAAACCCTT
*
43066993 AAACCCTAAACAT-
1 AAACCTTAAAC-TC
43067006 AAACCTTAAACTC
1 AAACCTTAAACTC
*
43067019 AAACCTAAAACTC
1 AAACCTTAAACTC
43067032 AAACC
1 AAACC
43067037 CCAAACCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 27 0.96
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
AAACCTTAAACTC
Found at i:43067029 original size:20 final size:20
Alignment explanation
Indices: 43066984--43067051 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
43066974 CTTTAAATCT
* *
43066984 TAAACCCTTAAACCCTAAACA
1 TAAAACCTTAAACCC-AAACC
*
43067005 T-AAACCTTAAACTCAAACC
1 TAAAACCTTAAACCCAAACC
*
43067024 TAAAA-CTCAAACCCCAAACC
1 TAAAACCTTAAA-CCCAAACC
*
43067044 TTAAACCT
1 TAAAACCT
43067052 CAAGATTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.26
20 25 0.66
21 3 0.08
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (20 bp):
TAAAACCTTAAACCCAAACC
Found at i:43067051 original size:7 final size:7
Alignment explanation
Indices: 43066959--43067051 Score: 59
Period size: 7 Copynumber: 13.7 Consensus size: 7
43066949 CAAACATTTG
43066959 AACCTTA
1 AACCTTA
*
43066966 AACC-CA
1 AACCTTA
*
43066972 AACTTTA
1 AACCTTA
*
43066979 AATCTTA
1 AACCTTA
43066986 AACCCTTA
1 AA-CCTTA
*
43066994 AACCCTA
1 AACCTTA
*
43067001 AA-CATA
1 AACCTTA
43067007 AACCTTA
1 AACCTTA
*
43067014 AA-CTCA
1 AACCTTA
43067020 AACC-TA
1 AACCTTA
* *
43067026 AAACTCA
1 AACCTTA
**
43067033 AACCCCA
1 AACCTTA
43067040 AACCTTA
1 AACCTTA
43067047 AACCT
1 AACCT
43067052 CAAGATTCAG
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
6 18 0.28
7 40 0.62
8 6 0.09
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCTTA
Found at i:43076270 original size:20 final size:20
Alignment explanation
Indices: 43076245--43076282 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
43076235 ATCTACTCTT
43076245 GAAAAAAAAGAAATAAGAAA
1 GAAAAAAAAGAAATAAGAAA
43076265 GAAAAAAAAGAAATAAGA
1 GAAAAAAAAGAAATAAGA
43076283 GACATTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
GAAAAAAAAGAAATAAGAAA
Found at i:43078973 original size:35 final size:35
Alignment explanation
Indices: 43078927--43079000 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
43078917 TTATTTTTTG
* * *
43078927 TATTAAAGTGTATGACATATTTGGATTTCTTTGGT
1 TATTAAAGTGTATGACAGATTTAGATTTCTTTCGT
* *
43078962 TATTAAAGTGTATGGCAGGTTTAGATTTCTTTCGT
1 TATTAAAGTGTATGACAGATTTAGATTTCTTTCGT
43078997 TATT
1 TATT
43079001 GTCTGCCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (35 bp):
TATTAAAGTGTATGACAGATTTAGATTTCTTTCGT
Found at i:43082765 original size:31 final size:30
Alignment explanation
Indices: 43082709--43082766 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43082699 TGGTGACTGG
* *
43082709 TTTGTTATTTTACTAAAGTTTAGTGACTAT
1 TTTGTTATTTTAATAAAGTTGAGTGACTAT
*
43082739 TTTGTTATTTTAATCGAAGTTGAGTGAC
1 TTTGTTATTTTAAT-AAAGTTGAGTGAC
43082767 CATTAGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (30 bp):
TTTGTTATTTTAATAAAGTTGAGTGACTAT
Found at i:43083088 original size:2 final size:2
Alignment explanation
Indices: 43083077--43083115 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
43083067 GGAGCTGAAA
43083077 AT AT -T 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
43083116 CATTAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:43087899 original size:21 final size:20
Alignment explanation
Indices: 43087830--43087903 Score: 87
Period size: 19 Copynumber: 3.6 Consensus size: 20
43087820 TTGACTCAAC
43087830 TATTAAAATTTTAATAAAAA
1 TATTAAAATTTTAATAAAAA
* * *
43087850 TAATGTATATTTTTCATAAAAA
1 T-AT-TAAAATTTTAATAAAAA
43087872 T-TTAAAATTTTAATAAAAA
1 TATTAAAATTTTAATAAAAA
43087891 TACTTAAAATTTT
1 TA-TTAAAATTTT
43087904 GACAAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 15 0.34
20 2 0.05
21 12 0.27
22 15 0.34
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (20 bp):
TATTAAAATTTTAATAAAAA
Found at i:43088042 original size:32 final size:32
Alignment explanation
Indices: 43088006--43088066 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
43087996 CCATTCAAAA
*
43088006 TAAAATAATTTAATTAAATTTTAAAAGTTGGC
1 TAAAATAATTTAATTAAAATTTAAAAGTTGGC
*
43088038 TAAAATAATTTAATTAAAATTTGAAAGTT
1 TAAAATAATTTAATTAAAATTTAAAAGTT
43088067 AAAGCTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (32 bp):
TAAAATAATTTAATTAAAATTTAAAAGTTGGC
Found at i:43089540 original size:49 final size:49
Alignment explanation
Indices: 43089487--43089586 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
43089477 TGGATATAAC
43089487 TTGGAGAGTGAAGGGTTTGATTTATGTTTAATTTTGTACATAATTTTTT
1 TTGGAGAGTGAAGGGTTTGATTTATGTTTAATTTTGTACATAATTTTTT
*
43089536 TTGGAGAGTGAAGGGTTTGGTTTATGTTTAATTTTGTACATAATTTTTT
1 TTGGAGAGTGAAGGGTTTGATTTATGTTTAATTTTGTACATAATTTTTT
43089585 TT
1 TT
43089587 TAATCATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (49 bp):
TTGGAGAGTGAAGGGTTTGATTTATGTTTAATTTTGTACATAATTTTTT
Found at i:43100640 original size:44 final size:44
Alignment explanation
Indices: 43100570--43100713 Score: 139
Period size: 44 Copynumber: 3.3 Consensus size: 44
43100560 CTCACTGTAT
* * * *
43100570 CTTCAGGG-GTATCAGAATTGTCGCTTCGATTGAATCCACTACAA
1 CTTCAGGGAG-ATAAGACTTGTAGCTTCGATTGAATCCACTGCAA
** * *
43100614 CTTCAGGGAGATAAGACTTGTAGCTTCGATCCATTCCACTGTAA
1 CTTCAGGGAGATAAGACTTGTAGCTTCGATTGAATCCACTGCAA
* * * * *
43100658 CTTAAGGGAGATAAGACTTATAGCTTCAATCTG-CTCCGCTGCAA
1 CTTCAGGGAGATAAGACTTGTAGCTTCGAT-TGAATCCACTGCAA
43100702 CTTCAGGGAGAT
1 CTTCAGGGAGAT
43100714 GCAATTTATG
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
44 80 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (44 bp):
CTTCAGGGAGATAAGACTTGTAGCTTCGATTGAATCCACTGCAA
Found at i:43101039 original size:44 final size:45
Alignment explanation
Indices: 43100878--43101488 Score: 219
Period size: 44 Copynumber: 13.6 Consensus size: 45
43100868 TTTTAACCTG
* * *
43100878 CTCCATTGCAACTTCA-AGGAGATAAGATTTGGAGCCTATCTTCAATTTA
1 CTCCACTGCAACTTCAGA-GAGATAAGATTT--A--CTATCTCCAATCTA
* * * * ** * * * *
43100927 CTCCACTGTAACTTTAGGGAAATAAGATTTGTTTATTTTCAACCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATTT-ACTATCTCCAATCTA
* * ** *
43100973 CTCCACTACAACTTCA-ATGAGATAAGGTTTA-TAGT-TTTAATCTG
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTACTA-TCTCCAATCTA
* *
43101017 CTCTACTGCAACTTCGGAGAGATAAGATTTACTATCTCCAATCTA
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
* * * **
43101062 CTCCACTGCAACTTCAGA-AGATAAGATCTA-TAACTTCAATCCG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
* ** * * * * * * * *
43101105 CCCCACTAAAACTTCAGGGAGACAATATTT-GTAACCTTCAAGCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACT-ATCTCCAATCTA
* * * * * *
43101150 CTCCACTACAACTT-TGAGGAGATAAGACTT-GTAACTTCAATCTA
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTACTATCTCCAATCTA
** * * * * * * *
43101194 CTCTGCTGCAACTTTA-AGGAGATGACATTT-GTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTACTATCTCCAATCTA
* * * * * *
43101238 CTCCGCTGCGACCTCAGAGAGATAAGATTTACTATCTTCAATTTG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
* * * * * *
43101283 CTCTACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAATCTA
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
* * * * * *
43101327 CTCCGCTGTAACTTCA-AGGAGATGAGATTT-GTGTCTTCAATCTA
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTACTATCTCCAATCTA
* * * ** * *
43101371 CTCCACTGCAA-TCTCAGGGAGATAAGATTTGCTATATTTAGTCTG
1 CTCCACTGCAACT-TCAGAGAGATAAGATTTACTATCTCCAATCTA
* * * * * * *
43101416 CTCTACTGCAACTTCAGAGAGATAAGACTT-GTAACTTCAACCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
* * *
43101460 CTCCACTACAACTTTAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGAGAGATAAGATT
43101489 CGTCATAATG
Statistics
Matches: 429, Mismatches: 115, Indels: 41
0.73 0.20 0.07
Matches are distributed among these distances:
43 24 0.06
44 220 0.51
45 127 0.30
46 33 0.08
48 1 0.00
49 24 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGAGAGATAAGATTTACTATCTCCAATCTA
Found at i:43101464 original size:89 final size:88
Alignment explanation
Indices: 43100878--43101488 Score: 412
Period size: 89 Copynumber: 6.8 Consensus size: 88
43100868 TTTTAACCTG
* * * * *
43100878 CTCCATTGCAACTTCA-AGGAGATAAGATTTGGAGCCTATCTTCAATTTACTCCACTGTAACTTT
1 CTCCACTGCAACTTCAGA-GAGATAAGATTT---G--TATCTTCAATCTGCTCCACTGCAACTTC
* ** * *
43100942 AGGGAAATAAGATTTGTTTATTTTCAACCTG
60 AGGGAGATAAGATTTG--TAACTTCAATCTA
* * * * *
43100973 CTCCACTACAACTTCA-ATGAGATAAGGTTTATAGT-TTTAATCTGCTCTACTGCAACTTC-GGA
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTGTA-TCTTCAATCTGCTCCACTGCAACTTCAGG-
* * *
43101035 GAGATAAGATTTACTATCTCCAATCTA
63 GAGATAAGATTT-GTAACTTCAATCTA
* * * * * **
43101062 CTCCACTGCAACTTCAGA-AGATAAGATCTATAACTTCAATCCGCCCCACTAAAACTTCAGGGAG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * *
43101126 ACAATATTTGTAACCTTCAAGCTG
66 ATAAGATTTGTAA-CTTCAATCTA
* * * * * ** * *
43101150 CTCCACTACAACTT-TGAGGAGATAAGACTTGTAACTTCAATCTACTCTGCTGCAACTTTAAGGA
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGA
* * ** *
43101214 GATGACATTTGTGTCTTCAATCTG
65 GATAAGATTTGTAACTTCAATCTA
* * * * * *
43101238 CTCCGCTGCGACCTCAGAGAGATAAGATTTACTATCTTCAATTTGCTCTACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGAGAGATAAGATTT-GTATCTTCAATCTGCTCCACTGCAACTTCAGGGA
*
43101303 GATAAGACTTGTAACTTCAATCTA
65 GATAAGATTTGTAACTTCAATCTA
* * * * *
43101327 CTCCGCTGTAACTTCA-AGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA-TCTCAGGG
1 CTCCACTGCAACTTCAGA-GAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACT-TCAGGG
* * *
43101390 AGATAAGATTTGCTATA-TTTAGTCTG
64 AGATAAGATTTG-TA-ACTTCAATCTA
* * * * * *
43101416 CTCTACTGCAACTTCAGAGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAG
1 CTCCACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG
43101481 ATAAGATT
66 ATAAGATT
43101489 CGTCATAATG
Statistics
Matches: 402, Mismatches: 97, Indels: 40
0.75 0.18 0.07
Matches are distributed among these distances:
87 5 0.01
88 128 0.32
89 207 0.51
90 35 0.09
91 1 0.00
95 26 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (88 bp):
CTCCACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGTAACTTCAATCTA
Found at i:43101488 original size:133 final size:133
Alignment explanation
Indices: 43100917--43101488 Score: 465
Period size: 133 Copynumber: 4.3 Consensus size: 133
43100907 TGGAGCCTAT
* * * * * * * * * * *
43100917 CTTCAATTTACTCCACTGTAACTTTAGGGAAATAAGATTTGTTTATTTTCAACCTGCTCCACTAC
1 CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATTTG--TGTCTTCAATCTACTCCACTGC
* * * *
43100982 AACTTCA-ATGAGATAAGGTTTA-TAGT-TTTAATCTGCTCTACTGCAACTTCGGAGAGATAAGA
64 AACCTCAGA-GAGATAAGATTTACTA-TATTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGA
* * *
43101044 TTTACTAT
127 CTT-GTAA
* * * * * * * ** ** * **
43101052 CTCCAATCTACTCCACTGCAAC-TTCAGAAGATAAGATCTATAACTTCAATCCGCCCCACTAAAA
1 CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA
* * * * * * * * *
43101116 CTTCAGGGAGACAATATTT-GTA-ACCTTCAAGCTGCTCCACTACAACTT-TGAGGAGATAAGAC
66 CCTCAGAGAGATAAGATTTACTATA--TTCAATCTGCTCTACTGCAACTTCAGA-GAGATAAGAC
43101178 TTGTAA
128 TTGTAA
* * * * *
43101184 CTTCAATCTACTCTGCTGCAACTTTAAGGAGATGACATTTGTGTCTTCAATCTGCTCCGCTGCGA
1 CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA
* * *
43101249 CCTCAGAGAGATAAGATTTACTATCTTCAATTTGCTCTACTGCAACTTCAGGGAGATAAGACTTG
66 CCTCAGAGAGATAAGATTTACTATATTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGACTTG
43101314 TAA
131 TAA
* *
43101317 CTTCAATCTACTCCGCTGTAACTTCAAGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA
1 CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA
* * * * *
43101382 TCTCAGGGAGATAAGATTTGCTATATTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGACTTG
66 CCTCAGAGAGATAAGATTTACTATATTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGACTTG
43101447 TAA
131 TAA
* * * * * *
43101450 CTTCAACCTGCTCCACTACAACTTTAGGGAGATAAGATT
1 CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATT
43101489 CGTCATAATG
Statistics
Matches: 348, Mismatches: 79, Indels: 22
0.78 0.18 0.05
Matches are distributed among these distances:
132 57 0.16
133 257 0.74
134 15 0.04
135 19 0.05
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (133 bp):
CTTCAATCTACTCCGCTGCAACTTTAAGGAGATGAGATTTGTGTCTTCAATCTACTCCACTGCAA
CCTCAGAGAGATAAGATTTACTATATTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGACTTG
TAA
Found at i:43113493 original size:51 final size:50
Alignment explanation
Indices: 43113431--43113585 Score: 193
Period size: 51 Copynumber: 3.1 Consensus size: 50
43113421 GATCATAACA
* * *
43113431 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATATTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-ACTCTCATATCGG
* * ** * *
43113482 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGAACTCTCATATCGG
* *
43113533 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGG
43113583 TGC
1 TGC
43113586 TAGACATGGT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
50 20 0.22
51 67 0.74
52 4 0.04
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGG
Found at i:43113600 original size:37 final size:37
Alignment explanation
Indices: 43113550--43113622 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
43113540 GCCATGTCCC
43113550 AGACATGGTCTTACATGGGACCTCTCATCTCGGTGCT
1 AGACATGGTCTTACATGGGACCTCTCATCTCGGTGCT
*
43113587 AGACATGGTCTTACATGGGACCTTTCATCTCGGTGC
1 AGACATGGTCTTACATGGGACCTCTCATCTCGGTGC
43113623 CAACGCCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (37 bp):
AGACATGGTCTTACATGGGACCTCTCATCTCGGTGCT
Found at i:43113617 original size:87 final size:88
Alignment explanation
Indices: 43113499--43113664 Score: 289
Period size: 87 Copynumber: 1.9 Consensus size: 88
43113489 GCCATGTCCC
*
43113499 AGACATGGTCTTACGGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
1 AGACATGGTCTTACGAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
43113564 ATGGGACCTCTCATCTCGGTGCT
66 ATGGGACCTCTCATCTCGGTGCT
* * *
43113587 AGACATGGTCTTAC-ATGGGACCTTTCATCTCGGTGCCAACGCCATGTCCGAGACATGGTCTTAC
1 AGACATGGTCTTACGAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
43113651 ATGGGACCTCTCAT
66 ATGGGACCTCTCAT
43113665 TATCTCAAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 60 0.81
88 14 0.19
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.26
Consensus pattern (88 bp):
AGACATGGTCTTACGAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
ATGGGACCTCTCATCTCGGTGCT
Found at i:43113645 original size:50 final size:54
Alignment explanation
Indices: 43113587--43113717 Score: 171
Period size: 56 Copynumber: 2.5 Consensus size: 54
43113577 TCTCGGTGCT
*
43113587 AGACATGGTCTTACATGGGACCT-T-TCATCTC-GG-TGCCAACGCCATGTCCG
1 AGACATGGTCTTACATGGGACCTCTATCATCTCAGGATGCCAACGCCATGTCCC
* *
43113637 AGACATGGTCTTACATGGGACCTCTCATTATCTCAAGGATGCCAATGCCATGTCCC
1 AGACATGGTCTTACATGGGACCTCT-ATCATCTC-AGGATGCCAACGCCATGTCCC
* *
43113693 AGACATGATCTTACATGGGATCTCT
1 AGACATGGTCTTACATGGGACCTCT
43113718 TTACCTAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
50 23 0.33
51 1 0.01
53 6 0.09
55 2 0.03
56 38 0.54
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (54 bp):
AGACATGGTCTTACATGGGACCTCTATCATCTCAGGATGCCAACGCCATGTCCC
Found at i:43114091 original size:30 final size:30
Alignment explanation
Indices: 43114056--43114113 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
43114046 CATCGACTCT
*
43114056 AACTTTTTCAAAATTACGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
*
43114086 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
43114114 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:43116061 original size:5 final size:5
Alignment explanation
Indices: 43116035--43116077 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
43116025 AGATAAAAGA
* *
43116035 AAAAT AACAAT CAAACT AAAAT AAAAT AAAAT AAAAT ACAAT A
1 AAAAT AA-AAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
43116078 GTAAAGAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 26 0.79
6 5 0.15
7 2 0.06
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:43116129 original size:3 final size:3
Alignment explanation
Indices: 43116121--43116185 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
43116111 GGGTTTTCAA
* * * * *
43116121 AAT AAT AAT ACT AAT AAT AAT GAG AAT AAT -AT GAAT GAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
43116166 AAT AAT AAAT AAT GAAT AAT
1 AAT AAT -AAT AAT -AAT AAT
43116186 CTAAGGTTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.04
3 38 0.79
4 8 0.17
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:43124647 original size:33 final size:33
Alignment explanation
Indices: 43124605--43124671 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
43124595 AAAGGACTTT
* *
43124605 GAATTATGGAGTGAATTTTGAGAAGACAAAAGA
1 GAATTATGGAGTGAAATTTAAGAAGACAAAAGA
43124638 GAATTATGGAGTGAAATTTAAGAAGACAAAAGA
1 GAATTATGGAGTGAAATTTAAGAAGACAAAAGA
43124671 G
1 G
43124672 CTTAAGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.27, T:0.22
Consensus pattern (33 bp):
GAATTATGGAGTGAAATTTAAGAAGACAAAAGA
Found at i:43127134 original size:35 final size:35
Alignment explanation
Indices: 43127095--43127165 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
43127085 TGTTAAGTTG
*
43127095 GCAACTTGAAATCACGCCCACCTCTAAAAAGTTAT
1 GCAACTTGAAATCACGCCCACCTCTAAAAAATTAT
43127130 GCAACTTGAAATCACGCCCACCTCTAAAAAATTAT
1 GCAACTTGAAATCACGCCCACCTCTAAAAAATTAT
43127165 G
1 G
43127166 TAAATAGCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (35 bp):
GCAACTTGAAATCACGCCCACCTCTAAAAAATTAT
Found at i:43129244 original size:103 final size:103
Alignment explanation
Indices: 43129136--43129334 Score: 317
Period size: 103 Copynumber: 1.9 Consensus size: 103
43129126 ATGGGTGTAC
* * ** *
43129136 AATAATACTTTGTTATCTTTAAAATTTACTGATGCGACTTTATTTTATTAGTGTCTAAAAATTAT
1 AATAATACTTTGTTACCTTTAAAATTTAATGATGCGACACTATTTTATTAGTGCCTAAAAATTAT
*
43129201 GTTTTTTTGGATGATCCTAATATAAGTTATTCTCGTAT
66 GTTTTTTAGGATGATCCTAATATAAGTTATTCTCGTAT
* * *
43129239 AATAATACTTTGTTACCTTTAAAATTTAATGATGTGGCACTATTTTATTGGTGCCTAAAAATTAT
1 AATAATACTTTGTTACCTTTAAAATTTAATGATGCGACACTATTTTATTAGTGCCTAAAAATTAT
43129304 GTTTTTTAGGATGATCCTAATATAAGTTATT
66 GTTTTTTAGGATGATCCTAATATAAGTTATT
43129335 GTCATTTTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (103 bp):
AATAATACTTTGTTACCTTTAAAATTTAATGATGCGACACTATTTTATTAGTGCCTAAAAATTAT
GTTTTTTAGGATGATCCTAATATAAGTTATTCTCGTAT
Found at i:43141101 original size:24 final size:27
Alignment explanation
Indices: 43141062--43141114 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
43141052 AAAAAACTTT
43141062 AACCCTAACCCTTAAAAAAT-TAA-AA
1 AACCCTAACCCTTAAAAAATCTAATAA
43141087 AACCCTAACCC-TAAAAAATCTAATAA
1 AACCCTAACCCTTAAAAAATCTAATAA
43141113 AA
1 AA
43141115 GTGTGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (27 bp):
AACCCTAACCCTTAAAAAATCTAATAA
Found at i:43154112 original size:17 final size:17
Alignment explanation
Indices: 43154076--43154115 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
43154066 AATTTTACTA
*
43154076 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
43154093 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
43154110 ACAAAA
1 ACAAAA
43154116 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:43154152 original size:16 final size:16
Alignment explanation
Indices: 43154133--43154189 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
43154123 AATTTGATAC
*
43154133 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
43154149 AATTTTGATAACAATT
1 AATTTTAATAACAATT
43154165 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
43154181 AGTTTTAAT
1 AATTTTAAT
43154190 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:43154173 original size:22 final size:23
Alignment explanation
Indices: 43154163--43154224 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
43154153 TTGATAACAA
* *
43154163 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
43154185 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
43154208 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
43154225 ATGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:43154906 original size:34 final size:34
Alignment explanation
Indices: 43154863--43154931 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
43154853 GTCAATAAAA
43154863 CCCTTTGGTTGCAGAGTTGCAACCTTTTTTTTTT
1 CCCTTTGGTTGCAGAGTTGCAACCTTTTTTTTTT
43154897 CCCTTTGGTTGCAGAGTTGCAACCTTTTTTTTTT
1 CCCTTTGGTTGCAGAGTTGCAACCTTTTTTTTTT
43154931 C
1 C
43154932 TTCTTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (34 bp):
CCCTTTGGTTGCAGAGTTGCAACCTTTTTTTTTT
Found at i:43157398 original size:16 final size:16
Alignment explanation
Indices: 43157374--43157427 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
43157364 TAAATTACTG
*
43157374 ATTACAGTTCTATTCC
1 ATTATAGTTCTATTCC
43157390 ATTATAGTTCTATTCC
1 ATTATAGTTCTATTCC
**
43157406 ATT-TCAACTCTATTCC
1 ATTAT-AGTTCTATTCC
43157422 ATTATA
1 ATTATA
43157428 ACTCTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTATAGTTCTATTCC
Found at i:43157441 original size:16 final size:16
Alignment explanation
Indices: 43157382--43157435 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
43157372 TGATTACAGT
**
43157382 TCTATTCCATTATAGT
1 TCTATTCCATTATAAC
43157398 TCTATTCCATT-TCAAC
1 TCTATTCCATTAT-AAC
43157414 TCTATTCCATTATAAC
1 TCTATTCCATTATAAC
43157430 TCTATT
1 TCTATT
43157436 TTATTACAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (16 bp):
TCTATTCCATTATAAC
Found at i:43168874 original size:19 final size:20
Alignment explanation
Indices: 43168842--43168879 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
43168832 TTGAAGGTAT
43168842 TTTTAATTATTTAT-TAAAA
1 TTTTAATTATTTATGTAAAA
43168861 TTTT-ATTATCTTATGTAAA
1 TTTTAATTAT-TTATGTAAA
43168880 TATAATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTAATTATTTATGTAAAA
Found at i:43177992 original size:5 final size:6
Alignment explanation
Indices: 43177977--43178001 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43177967 CAAACTCTAG
43177977 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
43178002 CCTTTCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:43178248 original size:14 final size:17
Alignment explanation
Indices: 43178229--43178266 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
43178219 ATTTATTTCT
43178229 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
43178243 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
43178260 TAATATA
1 TAATATA
43178267 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:43178284 original size:11 final size:11
Alignment explanation
Indices: 43178246--43178284 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
43178236 ATATTTATAA
43178246 TATAATTAATT
1 TATAATTAATT
*
43178257 TAATAATATACTT
1 T-ATAAT-TAATT
43178270 TATAATTAATT
1 TATAATTAATT
43178281 TATA
1 TATA
43178285 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:43180992 original size:51 final size:51
Alignment explanation
Indices: 43180933--43181075 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 51
43180923 TACCGGTTCA
* *
43180933 CATAGTAGCCTGCACATAGTACTACAAATGTGACCATCACTAACCGATACA-
1 CATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAACCGATA-AG
* * * * * *
43180984 CGTAGTAGCCTACACATAGTACTACACACGTGATCA-AAGCTATCCGGTAAG
1 CATAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CTAACCGATAAG
43181035 CATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
43181076 TTCAATTTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 2 0.03
51 74 0.96
52 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (51 bp):
CATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAACCGATAAG
Found at i:43181090 original size:51 final size:49
Alignment explanation
Indices: 43180929--43181105 Score: 158
Period size: 51 Copynumber: 3.5 Consensus size: 49
43180919 ATGATACCGG
* * * *
43180929 TTCACATAGTAGCCTGCACATAGTACTACAAATGTGACCATCACTAACCGA
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGACCATCACT-ATC-A
* * * * *
43180980 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCA-AAGCTATCCG
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGACCATCA-CTAT-CA
* * * *
43181030 GTAAGCATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTTCAA
1 TTCA-CATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATC-A
*
43181081 TTTCACATAGTGGCCTACACATAGT
1 -TTCACATAGTAGCCTACACATAGT
43181106 CCATGCCACA
Statistics
Matches: 98, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
50 4 0.04
51 91 0.93
52 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (49 bp):
TTCACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATCA
Found at i:43184473 original size:23 final size:24
Alignment explanation
Indices: 43184424--43184474 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
43184414 TCTTCATAAA
* *
43184424 CATATATCATCCATATCATTATATC
1 CATATATCAT-CATACCATCATATC
*
43184449 CATATATCAT-ATACCATCATTTC
1 CATATATCATCATACCATCATATC
43184472 CAT
1 CAT
43184475 GCATTTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.39
Consensus pattern (24 bp):
CATATATCATCATACCATCATATC
Found at i:43184721 original size:25 final size:25
Alignment explanation
Indices: 43184693--43185013 Score: 180
Period size: 25 Copynumber: 12.8 Consensus size: 25
43184683 GTGAGTTGTA
43184693 TATCGGGAAGCTCATGCA-AGCCATT
1 TATCGGGAAGCTCATG-AGAGCCATT
* * **
43184718 TATCGGGAAGCTTAAGAGAGATATT
1 TATCGGGAAGCTCATGAGAGCCATT
* **
43184743 AATCGGGAAGCTCATGAGAGCCAAG
1 TATCGGGAAGCTCATGAGAGCCATT
** **
43184768 TATCGGGAAGCTCAAAAGAGTTATT
1 TATCGGGAAGCTCATGAGAGCCATT
* * * * **
43184793 AATTGCGAAGCTCATGAGAGCAAAG
1 TATCGGGAAGCTCATGAGAGCCATT
* * *
43184818 TATCGAGAAGCTCAAGAGAGCTATT
1 TATCGGGAAGCTCATGAGAGCCATT
* * * **
43184843 AATCGGGAAGCTCATGAAAGCAAAG
1 TATCGGGAAGCTCATGAGAGCCATT
* ** *
43184868 TATAGGGAAGCTCAAAAGAGCTATT
1 TATCGGGAAGCTCATGAGAGCCATT
* * * **
43184893 AATCAGAAAGCTCATGAGAGCCAAG
1 TATCGGGAAGCTCATGAGAGCCATT
* *
43184918 TATCGGGAAGCTCAAGAGAGCTA-T
1 TATCGGGAAGCTCATGAGAGCCATT
* ** *
43184942 TACTTGGGAAGCTCAT-ATGAGCTGTA
1 TA-TCGGGAAGCTCATGA-GAGCCATT
* * * **
43184968 TATTGGGAAGCTCTTGCGAGCCAAA
1 TATCGGGAAGCTCATGAGAGCCATT
*
43184993 TATCGGGAAGCTCAAGAGAGC
1 TATCGGGAAGCTCATGAGAGC
43185014 TGTGGTGTGT
Statistics
Matches: 214, Mismatches: 77, Indels: 10
0.71 0.26 0.03
Matches are distributed among these distances:
24 4 0.02
25 208 0.97
26 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (25 bp):
TATCGGGAAGCTCATGAGAGCCATT
Found at i:43184980 original size:50 final size:50
Alignment explanation
Indices: 43184694--43184957 Score: 350
Period size: 50 Copynumber: 5.3 Consensus size: 50
43184684 TGAGTTGTAT
** * *
43184694 ATCGGGAAGCTCATGCA-AGCCATTTATCGGGAAGCTTAAGAGAGATATTA
1 ATCGGGAAGCTCATG-AGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
* *
43184744 ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAAAGAGTTATTA
1 ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
* * * *
43184794 ATTGCGAAGCTCATGAGAGCAAAGTATCGAGAAGCTCAAGAGAGCTATTA
1 ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
* * * *
43184844 ATCGGGAAGCTCATGAAAGCAAAGTATAGGGAAGCTCAAAAGAGCTATTA
1 ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
* *
43184894 ATCAGAAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
1 ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
* *
43184944 CTTGGGAAGCTCAT
1 ATCGGGAAGCTCAT
43184958 ATGAGCTGTA
Statistics
Matches: 186, Mismatches: 27, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
49 1 0.01
50 185 0.99
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (50 bp):
ATCGGGAAGCTCATGAGAGCCAAGTATCGGGAAGCTCAAGAGAGCTATTA
Found at i:43186558 original size:3 final size:3
Alignment explanation
Indices: 43186552--43186603 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
43186542 ATCATTACAT
* * *
43186552 TTA TTA TTA TTA TTG TTA TTA TTA TTA CTA TTA TTA CTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
43186598 TTA TTA
1 TTA TTA
43186604 GTTTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43186687 original size:14 final size:14
Alignment explanation
Indices: 43186670--43186699 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43186660 GCTTTATTAT
43186670 TATATATACATACA
1 TATATATACATACA
*
43186684 TATATATACTTACA
1 TATATATACATACA
43186698 TA
1 TA
43186700 ATCTTGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATACATACA
Found at i:43190051 original size:22 final size:22
Alignment explanation
Indices: 43190023--43190076 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
43190013 AAAGCATCGT
43190023 AGTGCTAAACAGAGAACACTGA
1 AGTGCTAAACAGAGAACACTGA
** *
43190045 AGTGCTAAGTAGAGAGCACTGA
1 AGTGCTAAACAGAGAACACTGA
43190067 AGTGCTAAAC
1 AGTGCTAAAC
43190077 CTGTACAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (22 bp):
AGTGCTAAACAGAGAACACTGA
Found at i:43193349 original size:19 final size:20
Alignment explanation
Indices: 43193325--43193365 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
43193315 GAATTTAGGC
*
43193325 AAATATTGAGTA-AAAATTG
1 AAATATTCAGTATAAAATTG
*
43193344 AAATATTCAGTATGAAATTG
1 AAATATTCAGTATAAAATTG
43193364 AA
1 AA
43193366 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (20 bp):
AAATATTCAGTATAAAATTG
Found at i:43193835 original size:41 final size:39
Alignment explanation
Indices: 43193778--43193890 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 39
43193768 TTTCTTCGAG
43193778 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTTA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTC-GATTTA
* *
43193818 TTCGATGAGGCACTGGGTGTCAA--T-TTACTTCGGTTTA
1 -TCGATGAGACACTGGGTGTCAATTTATTACTTCGATTTA
* *
43193855 ACTGATGAGACACTGGGTGTCAATTTACTACTTCGA
1 TC-GATGAGACACTGGGTGTCAATTTATTACTTCGA
43193891 AGTATCCGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
36 1 0.02
37 24 0.39
38 7 0.11
39 2 0.03
40 7 0.11
41 21 0.34
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGATTTA
Found at i:43195013 original size:110 final size:110
Alignment explanation
Indices: 43194834--43195053 Score: 334
Period size: 110 Copynumber: 2.0 Consensus size: 110
43194824 TAGCATACGG
* * * *
43194834 GCGTGTGAGGCCATTTCGAAAGGGCACACGGTCTGGCACATGGGCGTGTGGTTTGGCCGTGTGAC
1 GCGTGTGAGGCCATTTCGAAAGGGCACACGATCTAGCACACGGGCGTGTGGTTCGGCCGTGTGAC
* *
43194899 CCAAGTCAGAGAGTTACACAGGTATAAACA-TCGGCTGGGACACGA
66 CCAAGCCAGAGAGTTACACAGGTATAAACACT-GGCTGAGACACGA
* * *
43194944 GCGTGTGAGGCCATTTCGAAAGGGCATACGATCTAGCACACGGGCGTGTGGTTCGGCTGTGTGAT
1 GCGTGTGAGGCCATTTCGAAAGGGCACACGATCTAGCACACGGGCGTGTGGTTCGGCCGTGTGAC
*
43195009 CCAAGCCAGAGAGTTACACAGGTATAGACACTGGCTGAGACACGA
66 CCAAGCCAGAGAGTTACACAGGTATAAACACTGGCTGAGACACGA
43195054 CCGCGTGCCC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 98 0.99
111 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.20
Consensus pattern (110 bp):
GCGTGTGAGGCCATTTCGAAAGGGCACACGATCTAGCACACGGGCGTGTGGTTCGGCCGTGTGAC
CCAAGCCAGAGAGTTACACAGGTATAAACACTGGCTGAGACACGA
Found at i:43199592 original size:17 final size:17
Alignment explanation
Indices: 43199572--43199608 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
43199562 TTTGGAAAAG
43199572 AAATTATTTT-TAATAAT
1 AAATTATTTTATAAT-AT
43199589 AAA-TATTTTATAATAT
1 AAATTATTTTATAATAT
43199605 AAAT
1 AAAT
43199609 ATGAGTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTATTTTATAATAT
Found at i:43199597 original size:16 final size:16
Alignment explanation
Indices: 43199576--43199610 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43199566 GAAAAGAAAT
43199576 TATTTT-TAATAATAAA
1 TATTTTATAAT-ATAAA
43199592 TATTTTATAATATAAA
1 TATTTTATAATATAAA
43199608 TAT
1 TAT
43199611 GAGTACTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTATAATATAAA
Found at i:43204085 original size:17 final size:17
Alignment explanation
Indices: 43204043--43204085 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
43204033 TCATATCTTC
43204043 TAAGATTGCATATCATACT
1 TAAGATTGCATATC--ACT
43204062 TAAGATTGCATATC-CT
1 TAAGATTGCATATCACT
43204078 TGAAGATT
1 T-AAGATT
43204086 ATGTTTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 6 0.26
19 14 0.61
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (17 bp):
TAAGATTGCATATCACT
Found at i:43204642 original size:44 final size:43
Alignment explanation
Indices: 43204592--43204787 Score: 141
Period size: 44 Copynumber: 4.5 Consensus size: 43
43204582 CTTTGATCTG
*
43204592 CTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAAGAT-TACAATCTTCAACCTA
* * * ***** * *
43204636 CTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCC-G
1 CTCCACTACTGCTTAGGGAGACAAGATTACAATCTTCAA-CCTA
* * * * *
43204679 CTTCCTACTA-T-C-TCGGGAAGATAAGATT-CGTCATCTTCAATCTG
1 C-TCC-ACTACTGCTTAGGG-AGACAAGATTAC--AATCTTCAACCTA
43204723 CTCCACTACTGCTTAGGGAGACAAGATTTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAAGA-TTACAATCTTCAACCTA
43204767 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
43204788 TAGGGCTGGT
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
42 8 0.07
43 21 0.18
44 77 0.66
45 10 0.09
46 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGACAAGATTACAATCTTCAACCTA
Found at i:43204755 original size:131 final size:130
Alignment explanation
Indices: 43204516--43204905 Score: 573
Period size: 131 Copynumber: 3.0 Consensus size: 130
43204506 TACTGCAACT
* * *
43204516 TTAGGGAGATAAGGCTGGTGGCTTAAATTTGCTTCACTACTACCTCGAGAAGATAAGACTCGCCG
1 TTAGGGAGAT-AGGCTGGTGGCTTAAATCTGCTTC-CTACTACCTCGGGAAGATAAGATTCGCCG
43204581 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTACT
64 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTACT
43204646 GC
129 GC
* * * *
43204648 TTAGGGAGATAGGACTGGTGGCTTAAATCCGCTTCCTACTATCTCGGGAAGATAAGATTCGTCAT
1 TTAGGGAGATAGG-CTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCGCCGT
** * *
43204713 CTTCAATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACAATCTTCAACCTACTCCACTACTG
65 CTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTACTG
43204778 C
130 C
* *
43204779 TTAGGGAGATAGGGCTGGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCGCCG
1 TTAGGGAGATA-GGCTGGTGGCTTAAATCTGCTT-CCTACTACCTCGGGAAGATAAGATTCGCCG
* * * * *
43204844 TCTTTGATATACTTCACTACTGCTTAGGAAGACAGGATCTACAATCTTCAACCTACTCCACT
64 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACT
43204906 GCAAACTCAG
Statistics
Matches: 230, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
131 119 0.52
132 111 0.48
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (130 bp):
TTAGGGAGATAGGCTGGTGGCTTAAATCTGCTTCCTACTACCTCGGGAAGATAAGATTCGCCGTC
TTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTACTGC
Found at i:43205020 original size:89 final size:89
Alignment explanation
Indices: 43204903--43205161 Score: 376
Period size: 89 Copynumber: 2.9 Consensus size: 89
43204893 AACCTACTCC
* * *
43204903 ACTGCAAACTCAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAA
1 ACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAGACAA
*
43204968 GATCTGCTATTTTTAGTCTGCTCT
66 GATCTGCTATTTTCAGTCTGCTCT
* * *
43204992 GCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTTGCTGCCAATACAGGAAGACAA
1 ACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAGACAA
* *
43205057 GATCTGTTATCTTCAGTCTGCTCT
66 GATCTGCTATTTTCAGTCTGCTCT
* * *
43205081 ACTGCAAACTCAAGGAGGCAAGGCTGGTGTCTTT-GATTTGCTTCGCTGCCAATACAGGAAGATA
1 ACTGCAAACTCAGGGAGGCAAGGCTGGTGT-TTTCGATCTGCTTCGCTGCCAATACAGGAAGACA
* *
43205145 AGATTTGCTATTGTCAG
65 AGATCTGCTATTTTCAG
43205162 CCTGTTCCGC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
89 148 0.99
90 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (89 bp):
ACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAGACAA
GATCTGCTATTTTCAGTCTGCTCT
Found at i:43205033 original size:44 final size:44
Alignment explanation
Indices: 43204984--43205122 Score: 138
Period size: 44 Copynumber: 3.1 Consensus size: 44
43204974 CTATTTTTAG
43204984 TCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGA
1 TCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGA
* * * * * * *
43205028 TCTGCTTTGCTGCCAA-TACAGGAAGACAAGATCTGTTATCTTC-A
1 TCTGCTCTGCTGCAAACT-CAGGGAGGCAAG-GCTGGTGTCTTCGA
* * *
43205072 GTCTGCTCTACTGCAAACTCAAGGAGGCAAGGCTGGTGTCTTTGA
1 -TCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGA
*
43205117 TTTGCT
1 TCTGCT
43205123 TCGCTGCCAA
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
43 1 0.01
44 38 0.53
45 32 0.44
46 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (44 bp):
TCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGA
Found at i:43205077 original size:45 final size:45
Alignment explanation
Indices: 43204939--43205078 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 45
43204929 GTGTTTTCGA
** * * *
43204939 TCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCTATTTTTAG
1 TCTGCTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG
* * * * * * *
43204984 TCTGCTCTGCTGCAAACT-CAGGGAGGCAAG-GCTGGTGTCTTC-G
1 TCTGCTTTGCTGCCAA-TACAGGAAGACAAGATCTGCTATCTTCAG
*
43205027 ATCTGCTTTGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAG
1 -TCTGCTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG
43205073 TCTGCT
1 TCTGCT
43205079 CTACTGCAAA
Statistics
Matches: 71, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
43 2 0.03
44 31 0.44
45 36 0.51
46 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (45 bp):
TCTGCTTTGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG
Found at i:43205335 original size:44 final size:44
Alignment explanation
Indices: 43205241--43205365 Score: 144
Period size: 44 Copynumber: 2.9 Consensus size: 44
43205231 AGGTATCATC
* * *
43205241 ATTTT-AATCCGCTCCACTGCAACTTCAGAGATATAGGACTAGT
1 ATTTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGT
** * * *
43205284 AGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT
1 ATTTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGT
* * *
43205328 ATTTTCAACCTGCTCCTCTGTAACTTCAGAGAGATAAG
1 ATTTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAG
43205366 GTTTGATGTG
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 3 0.04
44 64 0.96
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
ATTTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGT
Found at i:43205568 original size:181 final size:180
Alignment explanation
Indices: 43205286--43205698 Score: 480
Period size: 181 Copynumber: 2.3 Consensus size: 180
43205276 GGACTAGTAG
* * * * *
43205286 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATTTTCAACCTGCTCCTCTGTA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAACCT-CTCCGCTGCA
* * * * * *
43205350 ACTTCAGAGAGATAAGGTTTGATGTGAATTGCTCTACTGCAACTTTAGAGAGATAATATTTTATG
64 ACTTCAAAGAGATAAGATTTGATGTGAATTACTCTACTGCAACTTCAGAGAGATAAGA-TCTATG
* * * * * *
43205415 ATTTATAGCTTTGATCTTTTCCACTGCAATCTTCAGGGAAACGAGATTTGATAT
128 ATTTATAGCTTTAATCTGTTCCACTGC-AGCTTCAGGAAAACAAGATTCGATAT
43205469 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-CA-CTTCAATCCAT-TCCGCTGCA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAA-CC-TCTCCGCTGCA
*
43205531 ACTTCAAAGAGATAAGATTTG-TGATG-ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT
64 ACTTCAAAGAGATAAGATTTGATG-TGAAT-TACTCTACTGCAACTTCAGAGAGATAAGATCTAT
* *
43205594 GATTTATAGCTTTAATCTGTTCCACTGCAGCTTCAGGAAAATAAGATTCGTTAT
127 GATTTATAGCTTTAATCTGTTCCACTGCAGCTTCAGGAAAACAAGATTCGATAT
* * *
43205648 CTTCAGTTTGC-CGCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTCAA
1 CTTCAGTCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTGC-ATCTTCAA
43205699 TAAGACTTGT
Statistics
Matches: 198, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
178 1 0.01
179 56 0.28
180 34 0.17
181 59 0.30
182 9 0.05
183 37 0.19
184 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (180 bp):
CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAACCTCTCCGCTGCAAC
TTCAAAGAGATAAGATTTGATGTGAATTACTCTACTGCAACTTCAGAGAGATAAGATCTATGATT
TATAGCTTTAATCTGTTCCACTGCAGCTTCAGGAAAACAAGATTCGATAT
Found at i:43205754 original size:44 final size:44
Alignment explanation
Indices: 43205698--43205954 Score: 215
Period size: 44 Copynumber: 5.8 Consensus size: 44
43205688 GCTTTCTTCA
43205698 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAG
1 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAG
* *
43205742 ATAAGA-TATGTAACTTTAA-TCTGCTCCACTGTAACTTTAGGGAG
1 ATAAGACT-TGTAACTTTAATTC-GCTCCACTGCAACTTCAGGGAG
* * ** *
43205786 ATAGGA-TTACTGGCTTTAATTTGCTCCACTGCAACTTCAGGGAG
1 ATAAGACTT-GTAACTTTAATTCGCTCCACTGCAACTTCAGGGAG
* * * * *
43205830 ATTAGA-TTCGTCATCTTCAGTCTAC-C-CCACTACAACTTCAAGGG-G
1 ATAAGACTT-GT-AACTTTAAT-T-CGCTCCACTGCAACTTC-AGGGAG
** * * *
43205875 ATAAGACTTGCTTTC-TTCAGTCTGCTCCACTGCAACTTTAGGGAG
1 ATAAGACTTG-TAACTTTAATTC-GCTCCACTGCAACTTCAGGGAG
43205920 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAAC
1 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAAC
43205955 CTTAGAGAGA
Statistics
Matches: 167, Mismatches: 31, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 98 0.59
45 54 0.32
46 9 0.05
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAG
Found at i:43206287 original size:24 final size:24
Alignment explanation
Indices: 43206255--43206304 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
43206245 TTTCCCCCGC
43206255 TGTAATCTTCAAGGTTCAATCCAT
1 TGTAATCTTCAAGGTTCAATCCAT
43206279 TGTAATCTTCAAGGTTCAATCCAT
1 TGTAATCTTCAAGGTTCAATCCAT
43206303 TG
1 TG
43206305 CACTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (24 bp):
TGTAATCTTCAAGGTTCAATCCAT
Found at i:43206730 original size:28 final size:28
Alignment explanation
Indices: 43206690--43206757 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 28
43206680 AATATATAAT
43206690 AAATATATATTTTTTA--TTTTTATTTTTA
1 AAATA-AT-TTTTTTATTTTTTTATTTTTA
43206718 AAATAATTTTTTTATTTTTTTATTTTTA
1 AAATAATTTTTTTATTTTTTTATTTTTA
43206746 AAATAATTTTTT
1 AAATAATTTTTT
43206758 GGTGTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.18
27 2 0.05
28 29 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
AAATAATTTTTTTATTTTTTTATTTTTA
Found at i:43214411 original size:14 final size:14
Alignment explanation
Indices: 43214392--43214427 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
43214382 GAAAAGTAAG
43214392 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
* *
43214406 TCATTTTCCGGAAG
1 TCATTTTCCAGAAA
43214420 TCATTTTC
1 TCATTTTC
43214428 AGTGAAACAA
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:0.22, G:0.11, T:0.42
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:43218056 original size:73 final size:73
Alignment explanation
Indices: 43217969--43218336 Score: 513
Period size: 73 Copynumber: 5.0 Consensus size: 73
43217959 AACAATAAGC
* * *
43217969 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAATCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
*
43218034 TTGGGGGA
66 TTCGGGGA
* * * * * * *
43218042 TTTAGCGGCATTTTTGAGGAGGCACCG-AAAAAACCTAAGCCAAAACGACGCTGTTTTGTAAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
43218106 TTCGGGGA
66 TTCGGGGA
*
43218114 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACAACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
*
43218179 TTCGAGGA
66 TTCGGGGA
* * *
43218187 TTTAGCGGCGTTTTTAAGAAAGCGTCGCAAAGAACCTAAGCCAAAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
*
43218252 TTGGGGGA
66 TTCGGGGA
* * * * * *
43218260 TTTAGCTGCGTTTTTGAGGAAGCGCCGCAAAAAAATCTAAGCCAAAACAACACCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
43218325 TTTCGGGGA
65 TTTCGGGGA
43218334 TTT
1 TTT
43218337 TAGTNNNNNN
Statistics
Matches: 257, Mismatches: 36, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
72 61 0.24
73 154 0.60
74 42 0.16
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCGGGGA
Found at i:43220421 original size:29 final size:30
Alignment explanation
Indices: 43220365--43220442 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
43220355 CTATGTGGCA
* * *
43220365 TCTTTCTTGTAATTTTTAAAAAAATTAATT
1 TCTTTTTTGCAATTTTTAAAAAAATTAAAT
* *
43220395 TCTTTTTTGCAATTTTT-TAAAAGTTAAAT
1 TCTTTTTTGCAATTTTTAAAAAAATTAAAT
* * *
43220424 ACTTTTTTGAAAATTTTAA
1 TCTTTTTTGCAATTTTTAA
43220443 TTAAGTTTTC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (30 bp):
TCTTTTTTGCAATTTTTAAAAAAATTAAAT
Found at i:43223052 original size:42 final size:42
Alignment explanation
Indices: 43223005--43223190 Score: 230
Period size: 43 Copynumber: 4.4 Consensus size: 42
43222995 AGGTTATGTT
* * **
43223005 TTTAGCAGCGTTTTTGTGAGAAGCGCCGCTAAAGGT-TTATTC
1 TTTAGCGGCGTTTTTGT-AAAAGCGCCGCTAAAGGTCTTGGTC
* *
43223047 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTTTG-TAAAAGCGCCGCTAAAGGTCTTGGTC
* *
43223090 TTTAGCGGCGTTTGTAGTAAAAGCACCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTT-TTGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
43223133 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTTTTGGTC
1 TTTAGCGGCGTTT-TTGTAAAAGCGCCGCTAAAGGTCTTGGTC
43223176 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
43223191 TCCAGTGCTT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 31 0.25
43 94 0.75
44 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGTAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:43223102 original size:43 final size:43
Alignment explanation
Indices: 43223025--43223188 Score: 244
Period size: 43 Copynumber: 3.8 Consensus size: 43
43223015 TTTTTGTGAG
**
43223025 AAGCGCCGCTAAAGGT-TTATTCTTTAGCGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGATAA
*
43223067 AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-AGTAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGA-TAA
*
43223110 AAGCACCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGA-AA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GATAA
*
43223153 AAGCGCCGCTAAAGGTTTTGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
43223189 TTTCCAGTGC
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
42 16 0.14
43 94 0.85
45 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGATAA
Found at i:43223967 original size:61 final size:61
Alignment explanation
Indices: 43223868--43223992 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
43223858 CTAAGTTTTT
* *
43223868 CCACAAAGGCATTCCTTAATATTCAGTACTCACCGCAAAGGCTTTCCTGTCTAGAGCTTTG
1 CCACAAAAGCATTCCTTAACATTCAGTACTCACCGCAAAGGCTTTCCTGTCTAGAGCTTTG
* * * * *
43223929 CCACAAAAGCGTTCTTTAACATTCAGTACTCACTGCAAAGGCTTTCTTGTCTAGAGTTTTG
1 CCACAAAAGCATTCCTTAACATTCAGTACTCACCGCAAAGGCTTTCCTGTCTAGAGCTTTG
43223990 CCA
1 CCA
43223993 TAAAGACTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (61 bp):
CCACAAAAGCATTCCTTAACATTCAGTACTCACCGCAAAGGCTTTCCTGTCTAGAGCTTTG
Found at i:43227798 original size:29 final size:27
Alignment explanation
Indices: 43227766--43227827 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
43227756 TTACTTGTAG
*
43227766 TATTTAATTTCAATAATGT-TTAAATTTAT
1 TATTTAATTT-AA-AATGTAATAAA-TTAT
*
43227795 TATTATAGTTTAAAATGTAATAAATTAT
1 TATT-TAATTTAAAATGTAATAAATTAT
43227823 TATTT
1 TATTT
43227828 TAGTCCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 13 0.45
29 10 0.34
30 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTTAATTTAAAATGTAATAAATTAT
Found at i:43229957 original size:24 final size:24
Alignment explanation
Indices: 43229892--43229948 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
43229882 ATAATAGAAT
*
43229892 ACAAATGCATACTCAGATTCGGAA
1 ACAAATGCATATTCAGATTCGGAA
43229916 ACAAATGCATATTCAGATTCGGAA
1 ACAAATGCATATTCAGATTCGGAA
43229940 ACAAATGCA
1 ACAAATGCA
43229949 ATCATAGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (24 bp):
ACAAATGCATATTCAGATTCGGAA
Found at i:43234573 original size:11 final size:11
Alignment explanation
Indices: 43234559--43234605 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
43234549 TTTTTTTAAA
43234559 TTTTAAAATAT
1 TTTTAAAATAT
43234570 TTTTAAAATACTTT
1 TTTTAAAATA---T
43234584 TTTTAAAATTAT
1 TTTTAAAA-TAT
43234596 TTTTAAAATA
1 TTTTAAAATA
43234606 AATTGTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 12 0.38
12 9 0.28
14 9 0.28
15 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:43234598 original size:12 final size:12
Alignment explanation
Indices: 43234559--43234604 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
43234549 TTTTTTTAAA
43234559 TTTTAAAA-TAT
1 TTTTAAAATTAT
*
43234570 TTTTAAAATACTTT
1 TTTTAAAAT--TAT
43234584 TTTTAAAATTAT
1 TTTTAAAATTAT
43234596 TTTTAAAAT
1 TTTTAAAAT
43234605 AAATTGTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.27
12 11 0.37
14 11 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:43238026 original size:25 final size:25
Alignment explanation
Indices: 43237984--43238092 Score: 107
Period size: 25 Copynumber: 4.4 Consensus size: 25
43237974 ATCATGTAAT
43237984 CGGGAAGCTCTTTCGAGCCATATAA
1 CGGGAAGCTCTTTCGAGCCATATAA
* *
43238009 CGGGAAGTTCATTT-GAGCCATGTAA
1 CGGGAAGCTC-TTTCGAGCCATATAA
* * *
43238034 CAGGAAGCTCTTGCGAGCCA-ATTAT
1 CGGGAAGCTCTTTCGAGCCATA-TAA
* * *
43238059 CGGGAAGCTCATACAAGCCATA-AA
1 CGGGAAGCTCTTTCGAGCCATATAA
43238083 CGGGAAGCTC
1 CGGGAAGCTC
43238093 AAGAGAGCCA
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
24 13 0.19
25 51 0.75
26 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (25 bp):
CGGGAAGCTCTTTCGAGCCATATAA
Found at i:43238078 original size:50 final size:50
Alignment explanation
Indices: 43237976--43238092 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 50
43237966 CCAATGCAAT
* * ***
43237976 CATGTAATCGGGAAGCTCTTTCGAGCCATATAACGGGAAGTTCATTTGAGC
1 CATGTAA-CGGGAAGCTCTTGCGAGCCATATAACGGGAAGCTCATACAAGC
* *
43238027 CATGTAACAGGAAGCTCTTGCGAGCCA-ATTATCGGGAAGCTCATACAAGC
1 CATGTAACGGGAAGCTCTTGCGAGCCATA-TAACGGGAAGCTCATACAAGC
*
43238077 CAT-AAACGGGAAGCTC
1 CATGTAACGGGAAGCTC
43238093 AAGAGAGCCA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 12 0.21
50 37 0.66
51 7 0.12
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (50 bp):
CATGTAACGGGAAGCTCTTGCGAGCCATATAACGGGAAGCTCATACAAGC
Found at i:43239129 original size:21 final size:19
Alignment explanation
Indices: 43239103--43239142 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
43239093 TTTTGCCCGG
43239103 ACCCAAAACTAAATAAATAAA
1 ACCCAAAA-TAAA-AAATAAA
43239124 ACCCAAAATAAAAAATAAA
1 ACCCAAAATAAAAAATAAA
43239143 CAATCCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.12
Consensus pattern (19 bp):
ACCCAAAATAAAAAATAAA
Found at i:43239593 original size:13 final size:13
Alignment explanation
Indices: 43239575--43239601 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43239565 TTGATTCTAT
43239575 TTTCATTTTTTTA
1 TTTCATTTTTTTA
43239588 TTTCATTTTTTTA
1 TTTCATTTTTTTA
43239601 T
1 T
43239602 ACACAAAAAT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCATTTTTTTA
Found at i:43240651 original size:26 final size:26
Alignment explanation
Indices: 43240361--43240726 Score: 108
Period size: 26 Copynumber: 14.3 Consensus size: 26
43240351 AATTATTTAT
* *
43240361 TTATTTATTTTAAACCTT-T-TTATACA
1 TTATTTATTTTAAA--TTGTCTTCTATA
*
43240387 TTATTCATTTTAAATTGT-TT-TATTA
1 TTATTTATTTTAAATTGTCTTCTA-TA
* *
43240412 TTATTTATTTTAAGTT-T-TTCACATA
1 TTATTTATTTTAAATTGTCTTC-TATA
* * * * **
43240437 TTATGTATTTTAAACTATATTAAACTA
1 TTATTTATTTTAAATTGTCTTCTA-TA
** * *
43240464 TTATCCATTTTAAATT-TTTTATATA
1 TTATTTATTTTAAATTGTCTTCTATA
* * *
43240489 TTATTTATTTTAAACTAT-TATATATA
1 TTATTTATTTTAAATTGTCT-TCTATA
* *
43240515 TTATTTATTTTGAATTGT-TTTTATACA
1 TTATTTATTTTAAATTGTCTTCTAT--A
* * * *
43240542 TATCATTT-TCTTAAGACTGTTTTGTATA
1 T-T-ATTTATTTTAA-ATTGTCTTCTATA
* * *
43240570 TTGTTTATTTGAAATT-TCTTTTTACATA
1 TTATTTATTTTAAATTGTC-TTCT--ATA
43240598 TTATTTATTTTAAA----CTT-T-TA
1 TTATTTATTTTAAATTGTCTTCTATA
* * *
43240618 TAAATTATTTTAAATTGTCTTCTATG
1 TTATTTATTTTAAATTGTCTTCTATA
* * *
43240644 TTATTTATTTTAATTTG-CTTTGTATG
1 TTATTTATTTTAAATTGTC-TTCTATA
* *
43240670 TTATTTATTTTAATTTGTGTTGC-ATA
1 TTATTTATTTTAAATTGTCTT-CTATA
* *
43240696 TTATTTACTTTGAATTGT-TT-TATA
1 TTATTTATTTTAAATTGTCTTCTATA
43240720 TTATTTA
1 TTATTTA
43240727 CCTCAAATTA
Statistics
Matches: 264, Mismatches: 47, Indels: 60
0.71 0.13 0.16
Matches are distributed among these distances:
20 14 0.05
23 1 0.00
24 22 0.08
25 59 0.22
26 109 0.41
27 24 0.09
28 22 0.08
29 8 0.03
30 5 0.02
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTCTTCTATA
Found at i:43243324 original size:17 final size:18
Alignment explanation
Indices: 43243291--43243327 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
43243281 TGATATATTT
43243291 ATGTTATTAAATGTTATG
1 ATGTTATTAAATGTTATG
43243309 ATGTT-TTAATAT-TTATG
1 ATGTTATTAA-ATGTTATG
43243326 AT
1 AT
43243328 TGTACGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATGTTATTAAATGTTATG
Found at i:43243836 original size:9 final size:9
Alignment explanation
Indices: 43243819--43243855 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43243809 TGAGTTTTCG
43243819 AATTCGAAT
1 AATTCGAAT
*
43243828 AACTCGAAT
1 AATTCGAAT
43243837 AATTCGAAT
1 AATTCGAAT
43243846 AATTCGAAT
1 AATTCGAAT
43243855 A
1 A
43243856 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43243938 original size:30 final size:31
Alignment explanation
Indices: 43243904--43243964 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
43243894 AAACCTTTTT
* *
43243904 ACTTTTCCCTCAAAACTTTTACTCT-TTCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
43243934 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
43243965 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
Found at i:43259787 original size:15 final size:14
Alignment explanation
Indices: 43259749--43259783 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
43259739 ACTATTTTAA
43259749 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
43259763 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
43259778 GGTTTA
1 GGTTTA
43259784 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:43259796 original size:28 final size:29
Alignment explanation
Indices: 43259763--43259834 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
43259753 TAGGGAGTAT
* *
43259763 GGATTTAGGGATTATGGTTTAAGGGTT-G
1 GGATTTAGGGATTAGGGGTTAAGGGTTAG
* *
43259791 GGATTTAAGGTTTAGGGGTTAAGGGTTAG
1 GGATTTAGGGATTAGGGGTTAAGGGTTAG
* *
43259820 GGGTTTAGGGGTTAG
1 GGATTTAGGGATTAG
43259835 ACGTTAGGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (29 bp):
GGATTTAGGGATTAGGGGTTAAGGGTTAG
Found at i:43259797 original size:14 final size:14
Alignment explanation
Indices: 43259778--43259834 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
43259768 TAGGGATTAT
43259778 GGTTTAAGGGTT-G
1 GGTTTAAGGGTTAG
*
43259791 GGATTTAAGGTTTAG
1 GG-TTTAAGGGTTAG
*
43259806 GGGTTAAGGGTTAGG
1 GGTTTAAGGGTTA-G
*
43259821 GGTTTAGGGGTTAG
1 GGTTTAAGGGTTAG
43259835 ACGTTAGGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.06
14 19 0.53
15 15 0.42
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:43259804 original size:21 final size:20
Alignment explanation
Indices: 43259770--43259810 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
43259760 TATGGATTTA
*
43259770 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
43259790 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
43259811 AAGGGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:43259825 original size:22 final size:22
Alignment explanation
Indices: 43259799--43259846 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
43259789 TGGGATTTAA
*
43259799 GGTTTAGGGGTTA-AGGGTTAGG
1 GGTTTAGGGGTTAGA-CGTTAGG
43259821 GGTTTAGGGGTTAGACGTTAGG
1 GGTTTAGGGGTTAGACGTTAGG
43259843 GGTT
1 GGTT
43259847 AATAGTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.48, T:0.33
Consensus pattern (22 bp):
GGTTTAGGGGTTAGACGTTAGG
Done.