Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 94 of 202
Found at i:28352036 original size:20 final size:20
Alignment explanation
Indices: 28352008--28352045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28351998 TATTTTATAT
28352008 TTTGATTATTTTATTTTTGG
1 TTTGATTATTTTATTTTTGG
* *
28352028 TTTGTTTATTTTGTTTTT
1 TTTGATTATTTTATTTTT
28352046 CTATGCAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTGATTATTTTATTTTTGG
Found at i:28363209 original size:98 final size:98
Alignment explanation
Indices: 28363040--28363234 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
28363030 ATACAATAAA
*
28363040 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
28363105 CATTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CATTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
28363138 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATGCGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAA-T
*
28363203 CC-TTTAGAATCTCAAACTCGGAATATTTCCTT
65 CCATTTAGAATCCCAAACTCGGAATATTTCCTT
28363235 CATGATTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 89 0.97
99 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CATTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:28372474 original size:98 final size:98
Alignment explanation
Indices: 28372305--28372499 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
28372295 ATACAATAAA
* *
28372305 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACAATC
*
28372370 CCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* * *
28372403 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATGCGTTACGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACAATC
*
28372468 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
28372500 CATGATTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTACGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:28374375 original size:20 final size:18
Alignment explanation
Indices: 28374325--28374376 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
28374315 GTACAAGATA
28374325 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
28374342 AATATTAGGA-TAATCACTTT
1 AATATTA-AATTAAT-A-TTT
28374362 AATATTAAATTAATA
1 AATATTAAATTAATA
28374377 AAATATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:28374407 original size:68 final size:71
Alignment explanation
Indices: 28374280--28374416 Score: 208
Period size: 68 Copynumber: 2.0 Consensus size: 71
28374270 TGATTAAACT
* * *
28374280 TAATTACTTTAATATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATACTTA-GTACAAGATAAATATTAAACTAAATTTAAT
28374345 ATTAGGA
65 ATTAGGA
*
28374352 TAATCACTTTAATATTAAATTAATAAAATA-TTA-T-CAAGATAAGTATTAAACTAAATTTAATA
1 TAATCACTTTAATATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATA
28374414 TTA
66 TTA
28374417 AAAATATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 29 0.48
69 1 0.02
71 3 0.05
72 28 0.46
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (71 bp):
TAATCACTTTAATATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATA
TTAGGA
Found at i:28374433 original size:68 final size:71
Alignment explanation
Indices: 28374289--28374436 Score: 169
Period size: 68 Copynumber: 2.1 Consensus size: 71
28374279 TTAATTACTT
* * **
28374289 TAATATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAATATTAGGATA
1 TAATATTAAATTAATAAAATACTTA-GTACAAGATAAATATTAAACTAAATTTAATATTAAAATA
***
28374354 ATCACTT
65 ATCAAAA
*
28374361 TAATATTAAATTAATAAAATA-TTA-T-CAAGATAAGTATTAAACTAAATTTAATATTAAAA-AT
1 TAATATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAATA-
*
28374422 ATTAAAA
65 ATCAAAA
28374429 TAATATTA
1 TAATATTA
28374437 TTTTTGAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
67 1 0.02
68 41 0.62
69 1 0.02
71 3 0.05
72 20 0.30
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (71 bp):
TAATATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAATAA
TCAAAA
Found at i:28377131 original size:3 final size:3
Alignment explanation
Indices: 28377123--28377156 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28377113 TTTGGAGGTG
28377123 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28377157 ATAACATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28378648 original size:42 final size:42
Alignment explanation
Indices: 28378593--28378674 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
28378583 AAGGCCATGA
*
28378593 CCTTTAGCGGCGTTTGTGAATTGAGCGCCGCTAAAAGTTAAG
1 CCTTTAGCGGCGTTTGTGAATTAAGCGCCGCTAAAAGTTAAG
** *
28378635 CCTTTAGCGGCGTTTGTGGCTTAAGCGCCGCTAAAGGTTA
1 CCTTTAGCGGCGTTTGTGAATTAAGCGCCGCTAAAAGTTA
28378675 TTATCTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (42 bp):
CCTTTAGCGGCGTTTGTGAATTAAGCGCCGCTAAAAGTTAAG
Found at i:28378746 original size:43 final size:43
Alignment explanation
Indices: 28378679--28379058 Score: 212
Period size: 43 Copynumber: 8.8 Consensus size: 43
28378669 AGGTTATTAT
** *
28378679 CTTTAGCGGCGCTTAAACCTA-AAACGCCGCTAAAGAGCTTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATAGCTTGAC
* * * **
28378722 CTTTAGCGGCGCTTTCACTAAAAACGCCGCAAAAAATATT-AGC
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGCTTGA-C
* * * * * * * *
28378765 CTATGGCGGCACATT-ATTTACAAACGCCACTAGATAACTTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATAGCTTGAC
* * * *
28378808 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAA-AACTCTGATT
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGCT-TGA-C
*
28378852 TTTTAGCGGCGCTTTCACTACAAACGCCGC-AAATA-CATT-AGC
1 CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGC-TTGA-C
* * * *
28378894 CTATAGCGGCGCTTT-ATTTACAAACGCCACTATATATG-TTGAC
1 CTTTAGCGGCGCTTTCA-CTACAAACGCCGCTAAATA-GCTTGAC
** *
28378937 CTTTAGCGGCGCTTTGGGC-ACAAACGCCGCTAAA-AGACCTTGGC
1 CTTTAGCGGCGCTTT-CACTACAAACGCCGCTAAATAG--CTTGAC
* * * * *
28378981 TTTTAGCGACGCTTTTCA-TAAAAACGCCACTAAAT-GCATTAAC
1 CTTTAGCGGCGC-TTTCACTACAAACGCCGCTAAATAGC-TTGAC
* *
28379024 CTTTAGCGGCACTTTTC-CCACAAACGCCGCTAAAT
1 CTTTAGCGGCGC-TTTCACTACAAACGCCGCTAAAT
28379059 TGAGCAGCTT
Statistics
Matches: 256, Mismatches: 57, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
41 2 0.01
42 36 0.14
43 155 0.61
44 60 0.23
45 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCACTACAAACGCCGCTAAATAGCTTGAC
Found at i:28378839 original size:129 final size:128
Alignment explanation
Indices: 28378679--28379035 Score: 414
Period size: 129 Copynumber: 2.8 Consensus size: 128
28378669 AGGTTATTAT
** * *
28378679 CTTTAGCGGCGCTTAAACCTA-AAACGCCGCTAAAGAGCTTGACCTTTAGCGGCGCTTTCACTAA
1 CTTTAGCGGCGCTTTGACC-ACAAACGCCGCTAAAGAACTTGACTTTTAGCGGCGCTTTCACTAA
* *
28378743 AAACGCCGCAAAAAATATTAGCCTATGGCGGCACATTATTTACAAACGCCACTAGATAACTTGAC
65 AAACGCCGC-AAAAACATTAGCCTATAGCGGCACATTATTTACAAACGCCACTAGATAACTTGAC
*
28378808 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAA-AACTCTGATTTTTTAGCGGCGCTTTCACTA
1 CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACT-TGA-CTTTTAGCGGCGCTTTCACTA
* * * * * **
28378872 CAAACGCCGCAAATACATTAGCCTATAGCGGCGCTTTATTTACAAACGCCACTATATATGTTGAC
64 AAAACGCCGCAAAAACATTAGCCTATAGCGGCACATTATTTACAAACGCCACTAGATAACTTGAC
** * * *
28378937 CTTTAGCGGCGCTTTGGGCACAAACGCCGCTAAAAGACCTTGGCTTTTAGCGACGCTTTTCA-TA
1 CTTTAGCGGCGCTTTGACCACAAACGCCGCT-AAAGAACTTGACTTTTAGCGGCGC-TTTCACTA
* ** * *
28379001 AAAACGCCACTAAATGCATTAACCTTTAGCGGCAC
64 AAAACGCCGC-AAAAACATTAGCCTATAGCGGCAC
28379036 TTTTCCCACA
Statistics
Matches: 195, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
128 4 0.02
129 130 0.67
130 58 0.30
131 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (128 bp):
CTTTAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACTTGACTTTTAGCGGCGCTTTCACTAAA
AACGCCGCAAAAACATTAGCCTATAGCGGCACATTATTTACAAACGCCACTAGATAACTTGAC
Found at i:28382404 original size:86 final size:83
Alignment explanation
Indices: 28382301--28382457 Score: 251
Period size: 86 Copynumber: 1.9 Consensus size: 83
28382291 AAAACCAAAT
*
28382301 GCCGCTAAGTACATTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCACCAATCAAA
1 GCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCAC-ATCACCC-CCAA-CAAA
28382366 TAGCGGCGCTATGATAGAAAC
63 TAGCGGCGCTATGATAGAAAC
* * *
28382387 GCCGCTAAATACCTTAACATTAGTGGCGATTGACCAGAACACGCCACATCACCCCCAACCAATAG
1 GCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCACATCACCCCCAACAAATAG
28382452 CGGCGC
66 CGGCGC
28382458 ATACATAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
83 12 0.18
84 4 0.06
85 7 0.10
86 44 0.66
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.17
Consensus pattern (83 bp):
GCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCACATCACCCCCAACAAATAG
CGGCGCTATGATAGAAAC
Found at i:28382592 original size:124 final size:124
Alignment explanation
Indices: 28382366--28382595 Score: 356
Period size: 124 Copynumber: 1.9 Consensus size: 124
28382356 ACCAATCAAA
* * * *
28382366 TAGCGGCGCTATGATAGAAACGCCGCTAAATACCTTAACATTAGTGGCGATTGACCAGAACACGC
1 TAGCGGCGCTAGGATAGAAACACCGCTAAATACCTTAACATTAGTGGCGATTCACCAGAAAACGC
*
28382431 CACATCACCCCCAACCAATAGCGGCGCATACATAAAAACGCCAGTAAAATTCACAACAG
66 CACATCACCCCCAACCAATAGCGGCGCATACAGAAAAACGCCAGTAAAATTCACAACAG
*
28382490 TAGCGGCGCTAGGATAGAAACACCGCTAAATACCTTAACATTAGTGGCGTTTCACCA-AAAACGC
1 TAGCGGCGCTAGGATAGAAACACCGCTAAATACCTTAACATTAGTGGCGATTCACCAGAAAACGC
* *
28382554 CACTATCACCCCCAACCGATAGCGGCGC-TAAGAGAAAAACGC
66 CAC-ATCACCCCCAACCAATAGCGGCGCAT-ACAGAAAAACGC
28382596 TACTAATACC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
123 10 0.10
124 86 0.90
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (124 bp):
TAGCGGCGCTAGGATAGAAACACCGCTAAATACCTTAACATTAGTGGCGATTCACCAGAAAACGC
CACATCACCCCCAACCAATAGCGGCGCATACAGAAAAACGCCAGTAAAATTCACAACAG
Found at i:28382947 original size:39 final size:40
Alignment explanation
Indices: 28382881--28382957 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
28382871 GACGCCGTAC
*
28382881 CATTTTTTTTGCGGCGTTTTATGTGAAAACGCTGCTAATG
1 CATTTTTTTTGCGGCGTTCTATGTGAAAACGCTGCTAATG
28382921 CATTTTTTTTGCGGCGTTCTAT-TGAAAACGCTGCTAA
1 CATTTTTTTTGCGGCGTTCTATGTGAAAACGCTGCTAA
28382958 ATATCAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (40 bp):
CATTTTTTTTGCGGCGTTCTATGTGAAAACGCTGCTAATG
Found at i:28382976 original size:40 final size:40
Alignment explanation
Indices: 28382892--28382976 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
28382882 ATTTTTTTTG
* * **
28382892 CGGCGTTTTATGTGAAAACGCTGCTAATGCATTTTTTTTG
1 CGGCGTTCTATGTGAAAACGCTGCTAATGCATGTTTTTAC
*
28382932 CGGCGTTCTAT-TGAAAACGCTGCTAAATATCA-GTTTTTAC
1 CGGCGTTCTATGTGAAAACGCTGCT-AAT-GCATGTTTTTAC
28382972 CGGCG
1 CGGCG
28382977 CTTCATCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 13 0.34
40 23 0.61
41 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (40 bp):
CGGCGTTCTATGTGAAAACGCTGCTAATGCATGTTTTTAC
Found at i:28384004 original size:18 final size:18
Alignment explanation
Indices: 28383947--28384032 Score: 50
Period size: 18 Copynumber: 4.6 Consensus size: 18
28383937 AGGCCCTTTT
*
28383947 AAAATTTAAAATTAATTT-A
1 AAAAATTAAAATT--TTTAA
* *
28383966 AAAAATCATAAAAATTATAA
1 AAAAAT--TAAAATTTTTAA
28383986 AAAAATTAAAATTTTTAA
1 AAAAATTAAAATTTTTAA
** *
28384004 AATTA-TAAAAGTTTTAA
1 AAAAATTAAAATTTTTAA
*
28384021 TAAAAAATAAAA
1 -AAAAATTAAAA
28384033 ATGCCAACCC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 11 0.21
18 16 0.31
19 12 0.23
20 7 0.13
21 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAAATTAAAATTTTTAA
Found at i:28384012 original size:17 final size:17
Alignment explanation
Indices: 28383943--28384020 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
28383933 ATTAAGGCCC
28383943 TTTTAAAATT-TAAAAT
1 TTTTAAAATTATAAAAT
* *
28383959 TAATTTAAAAAATCATAAAAA
1 T--TTT--AAAATTATAAAAT
* **
28383980 TTATAAAAAAATTAAAAT
1 TTTTAAAATTA-TAAAAT
*
28383998 TTTTAAAATTATAAAAG
1 TTTTAAAATTATAAAAT
28384015 TTTTAA
1 TTTTAA
28384021 TAAAAAATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
16 1 0.02
17 16 0.35
18 16 0.35
19 2 0.04
20 5 0.11
21 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTTAAAATTATAAAAT
Found at i:28386158 original size:19 final size:19
Alignment explanation
Indices: 28386115--28386173 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
28386105 ATTACAAAAA
28386115 AAAAATTCCAAAATAATTT-T
1 AAAAATT-CAAAAT-ATTTAT
28386135 CAAAAATTCAAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
28386155 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
28386173 A
1 A
28386174 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 7 0.19
21 7 0.19
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28386175 original size:20 final size:20
Alignment explanation
Indices: 28386115--28386168 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
28386105 ATTACAAAAA
28386115 AAAAATTCCAAAATAATTT-T
1 AAAAATTCCAAAAT-ATTTAT
28386135 CAAAAATT-CAAAATATTTAT
1 -AAAAATTCCAAAATATTTAT
28386155 AAAAATTCCAAAAT
1 AAAAATTCCAAAAT
28386169 TTATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.35
20 13 0.42
21 7 0.23
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCCAAAATATTTAT
Found at i:28386192 original size:25 final size:26
Alignment explanation
Indices: 28386147--28386195 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
28386137 AAAATTCAAA
28386147 ATATTTATAAAAATTCCAAAATTTAT
1 ATATTTATAAAAATTCCAAAATTTAT
**
28386173 ATATTT-TAAAAATTTTAAAATTT
1 ATATTTATAAAAATTCCAAAATTT
28386196 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATTTATAAAAATTCCAAAATTTAT
Found at i:28386213 original size:20 final size:20
Alignment explanation
Indices: 28386115--28386212 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 20
28386105 ATTACAAAAA
* * *
28386115 AAAAATTCCAAAATAATTTTC
1 AAAAATTCTAAAAT-TTTTTT
* *
28386136 AAAAATTC-AAAATATTTAT
1 AAAAATTCTAAAATTTTTTT
*
28386155 AAAAATTCCAAAATTTATATATTTT
1 AAAAATTCTAAAA--T-T-T-TTTT
*
28386180 AAAAATTTTAAAATTTTTTT
1 AAAAATTCTAAAATTTTTTT
28386200 AAAAAATTCTAAA
1 -AAAAATTCTAAA
28386213 TAATATATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 12 0.19
20 13 0.21
21 20 0.32
22 2 0.03
23 1 0.02
24 1 0.02
25 14 0.22
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTCTAAAATTTTTTT
Found at i:28387178 original size:19 final size:19
Alignment explanation
Indices: 28387154--28387195 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
28387144 GAAAATTAAT
*
28387154 ATTTTATCTATTATATTAC
1 ATTTTATCTATTAGATTAC
*
28387173 ATTTTATCTATTAGATTCC
1 ATTTTATCTATTAGATTAC
28387192 ATTT
1 ATTT
28387196 GAAATATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTATCTATTAGATTAC
Found at i:28387848 original size:25 final size:25
Alignment explanation
Indices: 28387801--28387848 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28387791 TCAGTTTATA
* *
28387801 TTATAATAGTATATATATCTAATCT
1 TTATAATAGTATAAATATATAATCT
28387826 TTAT-ATAGTATAAATTATATAAT
1 TTATAATAGTATAAA-TATATAAT
28387849 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TTATAATAGTATAAATATATAATCT
Found at i:28387870 original size:20 final size:21
Alignment explanation
Indices: 28387842--28387883 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28387832 AGTATAAATT
28387842 ATATAATA-TATAAAAATAAA
1 ATATAATATTATAAAAATAAA
* *
28387862 ATATTATATTATAAAATTAAA
1 ATATAATATTATAAAAATAAA
28387883 A
1 A
28387884 AGTAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAATATTATAAAAATAAA
Found at i:28390812 original size:18 final size:16
Alignment explanation
Indices: 28390770--28390812 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
28390760 TGTCGTTCGT
28390770 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
28390787 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
28390806 TTTCAAA
1 TTTCAAA
28390813 ACGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:28402581 original size:59 final size:59
Alignment explanation
Indices: 28402473--28402806 Score: 368
Period size: 59 Copynumber: 5.7 Consensus size: 59
28402463 TTAACAGAGG
* * * * *
28402473 TCGCCACTAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
** * * * * * *
28402532 TCAG-CACAAAGGCTTTATTTTTAAAGATTTGCCATAAAGACATCCTTTTCATTCGGTAC
1 TC-GCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
* ** * * * *
28402591 TCACCACAAAGATTTTCCTTTCAGATATTTTCCACAAAGACAACCTTTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
* *
28402650 TCGCCACAAAGGCTTTCCTTTCAGAGGTTTGCCACAAAGGCATCC-TTTCTTTTAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
* * *
28402708 TCGCCACAAAGGCTTTCCTTTCAAATATTTGCCACAAAGGCAACC-TTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
* * * * *
28402766 TCGCCACAAGGGCTTTCATTTCAAATATTTTCCACAAAGGC
1 TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGC
28402807 TTTCCTTTCA
Statistics
Matches: 234, Mismatches: 39, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
58 103 0.44
59 130 0.56
60 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (59 bp):
TCGCCACAAAGGCTTTCCTTTCAGAGATTTGCCACAAAGGCATCCTTTTCTTTCAGTAC
Found at i:28402659 original size:31 final size:29
Alignment explanation
Indices: 28402575--28402774 Score: 87
Period size: 28 Copynumber: 6.9 Consensus size: 29
28402565 ATAAAGACAT
* * *
28402575 CCTTTTCATTCGGTACTCACCACAAAG-A
1 CCTTTTCTTTCAGTACTCGCCACAAAGCA
* **
28402603 --TTTTCCTTTCAGATATTTTCCACAAAGACAA
1 CCTTTT-CTTTCAG-TACTCGCCACAAAG-C-A
28402634 CCTTTTCTTTCAGTACTCGCCACAAAG--
1 CCTTTTCTTTCAGTACTCGCCACAAAGCA
* * * *
28402661 GCTTTCCTTTCAG-AGGTTTGCCACAAAGGCA
1 CCTTTTCTTTCAGTA--CTCGCCACAAA-GCA
*
28402692 TCC-TTTCTTTTAGTACTCGCCACAAAG--
1 -CCTTTTCTTTCAGTACTCGCCACAAAGCA
* * * * *
28402719 GCTTTCCTTTCAAATATTTGCCACAAAGGCAA
1 CCTTTTCTTTC-AGTACTCGCCACAAA-GC-A
28402751 CC-TTTCTTTCAGTACTCGCCACAA
1 CCTTTTCTTTCAGTACTCGCCACAA
28402775 GGGCTTTCAT
Statistics
Matches: 124, Mismatches: 28, Indels: 38
0.65 0.15 0.20
Matches are distributed among these distances:
26 6 0.05
27 22 0.18
28 32 0.26
29 3 0.02
30 20 0.16
31 27 0.22
32 10 0.08
33 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (29 bp):
CCTTTTCTTTCAGTACTCGCCACAAAGCA
Found at i:28402690 original size:28 final size:27
Alignment explanation
Indices: 28402652--28402832 Score: 130
Period size: 28 Copynumber: 6.3 Consensus size: 27
28402642 TTCAGTACTC
*
28402652 GCCACAAAGGCTTTCCTTTCAGAGGTTT
1 GCCACAAAGGCTTTCCTTTCAGA-ATTT
* * * * *
28402680 GCCACAAAGGCATCCTTTCTTTTAGTACTC
1 GCCACAAAGGC-T--TTCCTTTCAGAATTT
*
28402710 GCCACAAAGGCTTTCCTTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAGA-ATTT
* * *
28402738 GCCACAAAGGCAACCTTT-CTTTCAGTACTC
1 GCCACAAAGG----CTTTCCTTTCAGAATTT
* * *
28402768 GCCACAAGGGCTTTCATTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAGA-ATTT
*
28402796 TCCACAAAGGCTTTCCTTTCAGAGATTT
1 GCCACAAAGGCTTTCCTTTCAGA-ATTT
28402824 GCCACAAAG
1 GCCACAAAG
28402833 ACATCCTTTT
Statistics
Matches: 115, Mismatches: 28, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
26 4 0.03
27 12 0.10
28 56 0.49
29 2 0.02
30 23 0.20
31 14 0.12
32 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (27 bp):
GCCACAAAGGCTTTCCTTTCAGAATTT
Found at i:28402716 original size:30 final size:30
Alignment explanation
Indices: 28402622--28402774 Score: 102
Period size: 28 Copynumber: 5.2 Consensus size: 30
28402612 CAGATATTTT
* * *
28402622 CCACAAAGACAACCTTTTCTTTCAGTACTCG
1 CCACAAAGGCATCC-TTTCTTTAAGTACTCG
* ** * *
28402653 CCACAAAGGCTTTCCTTTC-AGAGGT--TTG
1 CCACAAAGGC-ATCCTTTCTTTAAGTACTCG
*
28402681 CCACAAAGGCATCCTTTCTTTTAGTACTCG
1 CCACAAAGGCATCCTTTCTTTAAGTACTCG
* * * *
28402711 CCACAAAGGC-T--TTCCTTTCAAATATTTG
1 CCACAAAGGCATCCTTTCTTT-AAGTACTCG
* *
28402739 CCACAAAGGCAACCTTTCTTTCAGTACTCG
1 CCACAAAGGCATCCTTTCTTTAAGTACTCG
28402769 CCACAA
1 CCACAA
28402775 GGGCTTTCAT
Statistics
Matches: 89, Mismatches: 25, Indels: 17
0.68 0.19 0.13
Matches are distributed among these distances:
27 13 0.15
28 29 0.33
29 1 0.01
30 25 0.28
31 19 0.21
32 2 0.02
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (30 bp):
CCACAAAGGCATCCTTTCTTTAAGTACTCG
Found at i:28403621 original size:16 final size:16
Alignment explanation
Indices: 28403600--28403632 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28403590 TCTTATTGCT
*
28403600 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
28403616 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
28403632 T
1 T
28403633 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:28403681 original size:14 final size:14
Alignment explanation
Indices: 28403662--28403688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28403652 CAAAAAAAAC
28403662 CCAATTTTATTGAG
1 CCAATTTTATTGAG
28403676 CCAATTTTATTGA
1 CCAATTTTATTGA
28403689 TAAAAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (14 bp):
CCAATTTTATTGAG
Found at i:28408646 original size:40 final size:41
Alignment explanation
Indices: 28408576--28408660 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
28408566 AGCAATTCTG
* *
28408576 ACTTATTTGAAAATCATTTTTGATGTGTTAAAATGATTTTA
1 ACTTAATTGAAAATCATTTTTGATGTGTTAAAATCATTTTA
*
28408617 ACTTAATTG-AAATCA-TTTTGACT-TGGTTAAAATCATTTTC
1 ACTTAATTGAAAATCATTTTTGA-TGT-GTTAAAATCATTTTA
28408657 ACTT
1 ACTT
28408661 GATTTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 7 0.18
40 24 0.62
41 8 0.21
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (41 bp):
ACTTAATTGAAAATCATTTTTGATGTGTTAAAATCATTTTA
Found at i:28408649 original size:20 final size:20
Alignment explanation
Indices: 28408585--28408661 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
28408575 GACTTATTTG
28408585 AAAATCATTTTTGA--TGTGTT
1 AAAATCA-TTTTGACTTG-GTT
* * **
28408605 AAAATGATTTTAACTTAATT
1 AAAATCATTTTGACTTGGTT
*
28408625 GAAATCATTTTGACTTGGTT
1 AAAATCATTTTGACTTGGTT
*
28408645 AAAATCATTTTCACTTG
1 AAAATCATTTTGACTTG
28408662 ATTTTAAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 5 0.11
20 38 0.86
21 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (20 bp):
AAAATCATTTTGACTTGGTT
Found at i:28415439 original size:20 final size:20
Alignment explanation
Indices: 28415410--28415459 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28415400 TGTTAAAGTG
*
28415410 ATTTTAACTTAATTGAAATC
1 ATTTTAACTTAATTAAAATC
* **
28415430 ATTTTGACTTGGTTAAAATC
1 ATTTTAACTTAATTAAAATC
*
28415450 ATTTTCACTT
1 ATTTTAACTT
28415460 GATTTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (20 bp):
ATTTTAACTTAATTAAAATC
Found at i:28419640 original size:20 final size:20
Alignment explanation
Indices: 28419615--28419658 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
28419605 AATTATGACA
28419615 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
28419635 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
28419655 GAAA
1 GAAA
28419659 ATTATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (20 bp):
GAAAGGTCTATCAATGTTAG
Found at i:28424459 original size:15 final size:15
Alignment explanation
Indices: 28424441--28424473 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28424431 AAATAATAAG
28424441 AAAGGAAATAAATGA
1 AAAGGAAATAAATGA
*
28424456 AAAGTAAATAAATGA
1 AAAGGAAATAAATGA
28424471 AAA
1 AAA
28424474 ATGAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAGGAAATAAATGA
Found at i:28427443 original size:24 final size:24
Alignment explanation
Indices: 28427393--28427444 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
28427383 AGGGTCGGGG
****
28427393 AAATTGTGCTCAGGAATGTTTTCA
1 AAATTGTGCTCAGGAATGTCCAAA
*
28427417 AAATTTTGCTCAGGAATGTCCAAA
1 AAATTGTGCTCAGGAATGTCCAAA
28427441 AAAT
1 AAAT
28427445 GATGATTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (24 bp):
AAATTGTGCTCAGGAATGTCCAAA
Found at i:28428066 original size:52 final size:52
Alignment explanation
Indices: 28428009--28428107 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
28427999 ACATAATATA
* *
28428009 CAAATCAGAGTAACGCAGAGAATTTGGTAATGATCATA-AAACCAGAACAAAG
1 CAAATCAGAGTAACACAGAGAATTTGATAATGATCATATAAA-CAGAACAAAG
* *
28428061 CAAATCAGAGTATCACAGAGATTTTGATAATGATCATATAAACAGAA
1 CAAATCAGAGTAACACAGAGAATTTGATAATGATCATATAAACAGAA
28428108 TAGAGAATGC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 39 0.93
53 3 0.07
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.21
Consensus pattern (52 bp):
CAAATCAGAGTAACACAGAGAATTTGATAATGATCATATAAACAGAACAAAG
Found at i:28429114 original size:42 final size:42
Alignment explanation
Indices: 28429068--28429150 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
28429058 GACCATGTAG
*
28429068 CTCAAGTCA-AAGAGTTACATGGTCTGGCACACACTCGTGTGA
1 CTCAAGTCAGAA-AGTTACACGGTCTGGCACACACTCGTGTGA
* **
28429110 CTCAAGTCAGAAAGTTACACGGTCTGTCACACGTTCGTGTG
1 CTCAAGTCAGAAAGTTACACGGTCTGGCACACACTCGTGTG
28429151 TCACACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (42 bp):
CTCAAGTCAGAAAGTTACACGGTCTGGCACACACTCGTGTGA
Found at i:28435104 original size:30 final size:31
Alignment explanation
Indices: 28435046--28435107 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
28435036 AACTTAACAG
28435046 CAGACTTGAAATAAACAAAAAAAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAAATCACC
*
28435077 CAGACTTGAAATAAAC-AAAATAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAAATCACC
28435107 C
1 C
28435108 TACACCCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.58, C:0.21, G:0.06, T:0.15
Consensus pattern (31 bp):
CAGACTTGAAATAAACAAAAAAAAAATCACC
Found at i:28439201 original size:21 final size:19
Alignment explanation
Indices: 28439170--28439208 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
28439160 TTTATAAAAG
28439170 TTAAGGCATTCAAAAGTGT
1 TTAAGGCATTCAAAAGTGT
*
28439189 TTAATGGCAATTCGAAAGTG
1 TTAA-GGC-ATTCAAAAGTG
28439209 AAAGTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (19 bp):
TTAAGGCATTCAAAAGTGT
Found at i:28440733 original size:15 final size:15
Alignment explanation
Indices: 28440713--28440769 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
28440703 TTATGGAAAG
*
28440713 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
28440728 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
28440742 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
28440758 TCAAATAT-TGGA
1 TCAAATATATGGA
28440770 AAATCAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 8 0.24
15 20 0.61
16 5 0.15
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:28440741 original size:30 final size:30
Alignment explanation
Indices: 28440705--28440791 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
28440695 ATCTGTATTT
* *
28440705 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
28440735 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* * **
28440765 TTGGAAAATCAAAGATATAAGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATCAA
28440792 GATATTGGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:28444838 original size:43 final size:44
Alignment explanation
Indices: 28444790--28444875 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
28444780 GGGTAAATCT
* * *
28444790 AACAACCGAA-GATATTTTTTCCTCTTTTTAAATTCTTTTTCTC
1 AACAACCCAAGGATATCTTCTCCTCTTTTTAAATTCTTTTTCTC
* *
28444833 AACAACCCAAGGTTATCTTCTCCTCTTTTTAAATTTTTTTTCT
1 AACAACCCAAGGATATCTTCTCCTCTTTTTAAATTCTTTTTCT
28444876 AGGATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 9 0.24
44 28 0.76
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (44 bp):
AACAACCCAAGGATATCTTCTCCTCTTTTTAAATTCTTTTTCTC
Found at i:28449661 original size:12 final size:11
Alignment explanation
Indices: 28449643--28449677 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28449633 TAACTATGTG
28449643 AATAACAAATA
1 AATAACAAATA
28449654 AATGAACAAATA
1 AAT-AACAAATA
*
28449666 AATAACTAATA
1 AATAACAAATA
28449677 A
1 A
28449678 TACTATAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (11 bp):
AATAACAAATA
Found at i:28450555 original size:55 final size:57
Alignment explanation
Indices: 28450454--28450573 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 57
28450444 CCTCCTTTGA
* *
28450454 CTTTTTATAATATTTTTTACTAGGGTAAATCTAACAACCCAAGATTATCTT-T-TTCT
1 CTTTTT-TAATATTTTTTACTAGGATAAAACTAACAACCCAAGATTATCTTCTCTTCT
* *
28450510 CTTTTTTAAT-TTTTTT-CTAGGATAAAAAACTAACATCCCAGGATTATCTTCTCTTCT
1 CTTTTTTAATATTTTTTACTAGGAT--AAAACTAACAACCCAAGATTATCTTCTCTTCT
28450567 -TTTTTTA
1 CTTTTTTA
28450574 GACAGATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
53 6 0.11
54 6 0.11
55 26 0.46
56 14 0.25
57 4 0.07
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (57 bp):
CTTTTTTAATATTTTTTACTAGGATAAAACTAACAACCCAAGATTATCTTCTCTTCT
Found at i:28456014 original size:26 final size:26
Alignment explanation
Indices: 28455922--28456086 Score: 159
Period size: 26 Copynumber: 6.2 Consensus size: 26
28455912 ATGGGGTCAA
* * * *
28455922 TAAAATGACCAAAATACCCCCAAAAGA
1 TAAAATAACCGAAATA-CCCCAAAGGG
* * *
28455949 CAAAATGACTGAAATACCCCAAAAGGG
1 TAAAATAACCGAAATACCCC-AAAGGG
* * *
28455976 TAAAATGATCGAAATACCCCAAGGGG
1 TAAAATAACCGAAATACCCCAAAGGG
28456002 TAAAATAACCGAAATACCCCAAAGGG
1 TAAAATAACCGAAATACCCCAAAGGG
* * **
28456028 TGAAATAACTGAAATACCCCCAAAGTA
1 TAAAATAACCGAAATA-CCCCAAAGGG
* *
28456055 TAAAATAACCGAAATACCTCATAGGG
1 TAAAATAACCGAAATACCCCAAAGGG
28456081 TAAAAT
1 TAAAAT
28456087 GACTGCTATA
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
26 58 0.51
27 56 0.49
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (26 bp):
TAAAATAACCGAAATACCCCAAAGGG
Found at i:28456017 original size:53 final size:54
Alignment explanation
Indices: 28455933--28456088 Score: 183
Period size: 53 Copynumber: 2.9 Consensus size: 54
28455923 AAAATGACCA
* * * * *
28455933 AAATACCCCCAAAAGACAAAATGACTGAAATACCCCAAAAGGGTAAAATGATC-G
1 AAATACCCCCAAAGGATAAAATAACCGAAATACCCC-AAAGGGTAAAATGAACTG
* * *
28455987 AAATA-CCCCAAGGGGTAAAATAACCGAAATACCCCAAAGGGTGAAAT-AACTG
1 AAATACCCCCAAAGGATAAAATAACCGAAATACCCCAAAGGGTAAAATGAACTG
* * *
28456039 AAATACCCCCAAAGTATAAAATAACCGAAATACCTCATAGGGTAAAATGA
1 AAATACCCCCAAAGGATAAAATAACCGAAATACCCCAAAGGGTAAAATGA
28456089 CTGCTATACC
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 2 0.02
52 17 0.20
53 60 0.71
54 6 0.07
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (54 bp):
AAATACCCCCAAAGGATAAAATAACCGAAATACCCCAAAGGGTAAAATGAACTG
Found at i:28456435 original size:28 final size:28
Alignment explanation
Indices: 28456403--28456463 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
28456393 ACATTACAAG
*
28456403 ACTGTTACTGTATTGGGCTAAGACCCAC
1 ACTGTTACTGTATTAGGCTAAGACCCAC
*
28456431 ACTGTTACTGTATTAGGCTAAGGCCCAC
1 ACTGTTACTGTATTAGGCTAAGACCCAC
28456459 ACTGT
1 ACTGT
28456464 ACTATCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (28 bp):
ACTGTTACTGTATTAGGCTAAGACCCAC
Found at i:28457626 original size:27 final size:27
Alignment explanation
Indices: 28457591--28457702 Score: 172
Period size: 27 Copynumber: 4.1 Consensus size: 27
28457581 ATTTATGAGT
28457591 AAATTATCGAAATACCCTCGAAGGGTA
1 AAATTATCGAAATACCCTCGAAGGGTA
28457618 AAATTATCGAAATACCCTCGAAGGGTA
1 AAATTATCGAAATACCCTCGAAGGGTA
*
28457645 AAATTATCGAAACACCCTCGAAGGGTA
1 AAATTATCGAAATACCCTCGAAGGGTA
* * *
28457672 AAATTA-CCATAATACCCCCTAAGGGTA
1 AAATTATCGA-AATACCCTCGAAGGGTA
28457699 AAAT
1 AAAT
28457703 GATCTTTATA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
26 2 0.03
27 77 0.97
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGAAGGGTA
Found at i:28458080 original size:28 final size:27
Alignment explanation
Indices: 28458040--28458099 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
28458030 ACTGAAATGA
*
28458040 TACTGTATGGGGTTAAGGCCCACACTG
1 TACTGAATGGGGTTAAGGCCCACACTG
* *
28458067 CTACTGAATTGGGTTAAGGCCCTCACTG
1 -TACTGAATGGGGTTAAGGCCCACACTG
28458095 TACTG
1 TACTG
28458100 TCACTGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (27 bp):
TACTGAATGGGGTTAAGGCCCACACTG
Found at i:28460395 original size:2 final size:2
Alignment explanation
Indices: 28460388--28460412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28460378 GGCTTTAATT
28460388 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28460413 TTCATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28462896 original size:20 final size:20
Alignment explanation
Indices: 28462871--28462916 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28462861 CTGAAATGGA
*
28462871 AACAAAAGCAGAAAAGAAAG
1 AACAAAAGAAGAAAAGAAAG
28462891 AACAAAAGAAGAAAAGAAAG
1 AACAAAAGAAGAAAAGAAAG
28462911 AA-AAAA
1 AACAAAA
28462917 AAAGGATAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (20 bp):
AACAAAAGAAGAAAAGAAAG
Found at i:28463196 original size:24 final size:24
Alignment explanation
Indices: 28463168--28463214 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28463158 CAGGGTTTTA
28463168 AATAGAAGACCAAAGGGTAAGCTG
1 AATAGAAGACCAAAGGGTAAGCTG
28463192 AATAGAAGACCAAAGGGTAAGCT
1 AATAGAAGACCAAAGGGTAAGCT
28463215 AACACCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.28, T:0.13
Consensus pattern (24 bp):
AATAGAAGACCAAAGGGTAAGCTG
Found at i:28468222 original size:18 final size:18
Alignment explanation
Indices: 28468201--28468248 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
28468191 GAAAGCAGAT
*
28468201 AAGAAAGAACAAAATAAG
1 AAGAAAGAACAAAAGAAG
*
28468219 AAG-AAGAAAAGAAAGAAG
1 AAGAAAGAACA-AAAGAAG
28468237 AAGAAA-AACAAA
1 AAGAAAGAACAAA
28468249 TGATAGGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 8 0.32
18 15 0.60
19 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (18 bp):
AAGAAAGAACAAAAGAAG
Found at i:28469618 original size:24 final size:23
Alignment explanation
Indices: 28469586--28469635 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
28469576 ATATATGGGG
* *
28469586 TTGAGAATTCTTCTCTTTTTTCAA
1 TTGACAATTCTTCTCTTATTT-AA
*
28469610 TTGACAATTCTTTTCTTATTTAA
1 TTGACAATTCTTCTCTTATTTAA
28469633 TTG
1 TTG
28469636 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (23 bp):
TTGACAATTCTTCTCTTATTTAA
Found at i:28469648 original size:18 final size:19
Alignment explanation
Indices: 28469620--28469655 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28469610 TTGACAATTC
28469620 TTTTCTTATTTAATTGTTA
1 TTTTCTTATTTAATTGTTA
*
28469639 TTTT-TTATTTATTTGTT
1 TTTTCTTATTTAATTGTT
28469656 TTTAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTCTTATTTAATTGTTA
Found at i:28470454 original size:29 final size:30
Alignment explanation
Indices: 28470392--28470460 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
28470382 ACTACCAAAA
**
28470392 TAGTTACTTTTGTTTGCCTCATGTTACATTT
1 TAGTTACTTTTGTTTG-CAAATGTTACATTT
*
28470423 TAGTTACTTTTGTTTG-AAATGTTACGTTT
1 TAGTTACTTTTGTTTGCAAATGTTACATTT
*
28470452 TAGTCACTT
1 TAGTTACTT
28470461 ACGTTATCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.54
Consensus pattern (30 bp):
TAGTTACTTTTGTTTGCAAATGTTACATTT
Found at i:28478920 original size:41 final size:41
Alignment explanation
Indices: 28478868--28478949 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
28478858 ATATTTTATT
* *
28478868 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
* *
28478909 TTATGTTTTAGTAGTTGATTAGAATAATAGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
28478950 AATTAGGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
Found at i:28486394 original size:44 final size:47
Alignment explanation
Indices: 28486330--28486454 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 47
28486320 GTGGCTGTGC
*
28486330 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATTAGGAAGT-T-T
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGTATGT
* *
28486375 -GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGTCATGT
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGT-ATGT
* * * *
28486422 AGACTTTGCAAGTTGTTGAAGATTCCCCTTGAT
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGAT
28486455 TTTTGTGAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 39 0.58
46 1 0.01
47 1 0.01
48 26 0.39
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (47 bp):
AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGTATGT
Found at i:28491168 original size:12 final size:12
Alignment explanation
Indices: 28491151--28491175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28491141 TAGATGTCTA
28491151 TTATGTTAAAGG
1 TTATGTTAAAGG
28491163 TTATGTTAAAGG
1 TTATGTTAAAGG
28491175 T
1 T
28491176 GATCTGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TTATGTTAAAGG
Found at i:28491287 original size:32 final size:30
Alignment explanation
Indices: 28491238--28491310 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 30
28491228 TCTAAAACTA
*
28491238 AAAACAGAAATAGAAGGAATTTATGCAAAT
1 AAAATAGAAATAGAAGGAATTTATGCAAAT
* *
28491268 GAAAATAGAGAATAGAAGGAATTTTTGTAAAT
1 -AAAATAGA-AATAGAAGGAATTTATGCAAAT
28491300 AAGAATAGAAA
1 AA-AATAGAAA
28491311 GAAATTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (30 bp):
AAAATAGAAATAGAAGGAATTTATGCAAAT
Found at i:28504136 original size:18 final size:17
Alignment explanation
Indices: 28504121--28504154 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28504111 TATTATTTAT
28504121 TAAATTAAACTAATTTTG
1 TAAATTAAA-TAATTTTG
*
28504139 TCAATTAAATAATTTT
1 TAAATTAAATAATTTT
28504155 ATCAACCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTAAATAATTTTG
Found at i:28504153 original size:17 final size:18
Alignment explanation
Indices: 28504123--28504159 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28504113 TTATTTATTA
*
28504123 AATTAAACTAATTTTGTC
1 AATTAAACTAATTTTATC
28504141 AATTAAA-TAATTTTATC
1 AATTAAACTAATTTTATC
28504158 AA
1 AA
28504160 CCAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAAACTAATTTTATC
Found at i:28507634 original size:33 final size:33
Alignment explanation
Indices: 28507561--28507634 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
28507551 TACTATCTGT
28507561 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
* * * *
28507594 CTAGTGTGTTGGTTGGATTAGCTCTTCTGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
28507627 TTGGTGTG
1 TTGGTGTG
28507635 CTGGAGGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.41
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
Found at i:28513761 original size:21 final size:21
Alignment explanation
Indices: 28513710--28513763 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
28513700 GTGGCTCAAG
* *
28513710 ACATGGCCGTGTGGCTACTTC
1 ACATGCCCGTGTGACTACTTC
**
28513731 ACACACCCGTGTGACTACTTC
1 ACATGCCCGTGTGACTACTTC
*
28513752 ACATGTCCGTGT
1 ACATGCCCGTGT
28513764 ACGCTGATCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.28
Consensus pattern (21 bp):
ACATGCCCGTGTGACTACTTC
Found at i:28520071 original size:18 final size:17
Alignment explanation
Indices: 28520050--28520097 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
28520040 ATTTGGTTTA
28520050 TTTTTATTTTTCTATTAT
1 TTTTTATTTTTCTATT-T
28520068 TTTTTATTTAATT-TATTT
1 TTTTTATTT--TTCTATTT
*
28520086 GTTTTATTTTTC
1 TTTTTATTTTTC
28520098 AAGTGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
18 18 0.69
19 4 0.15
20 2 0.08
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTCTATTT
Found at i:28524401 original size:15 final size:15
Alignment explanation
Indices: 28524381--28524414 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28524371 TAGGACCAAT
28524381 ACTCAAATCATGTAA
1 ACTCAAATCATGTAA
28524396 ACTCAAATCATGTAA
1 ACTCAAATCATGTAA
28524411 ACTC
1 ACTC
28524415 TAATTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (15 bp):
ACTCAAATCATGTAA
Found at i:28526985 original size:14 final size:14
Alignment explanation
Indices: 28526966--28526997 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28526956 CACAAAAGAA
28526966 ATATCTTAATACAT
1 ATATCTTAATACAT
28526980 ATATCTTAATACAT
1 ATATCTTAATACAT
28526994 ATAT
1 ATAT
28526998 TTTTCCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATCTTAATACAT
Found at i:28528748 original size:14 final size:14
Alignment explanation
Indices: 28528729--28528757 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28528719 CTTCTGCAAA
28528729 AATAAAATAATTTT
1 AATAAAATAATTTT
28528743 AATAAAATAATTTT
1 AATAAAATAATTTT
28528757 A
1 A
28528758 CACGCATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAAAATAATTTT
Found at i:28536501 original size:23 final size:24
Alignment explanation
Indices: 28536446--28536501 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
28536436 TGTAAATTCA
* *
28536446 CAACAGTCAAATTTTAAATTAGAC
1 CAACAGTAAAATTATAAATTAGAC
* * *
28536470 CAACGGTAAAATTATAAA-TGGTC
1 CAACAGTAAAATTATAAATTAGAC
28536493 CAACAGTAA
1 CAACAGTAA
28536502 CTTTTTTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (24 bp):
CAACAGTAAAATTATAAATTAGAC
Found at i:28540132 original size:2 final size:2
Alignment explanation
Indices: 28540125--28540149 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28540115 TTAGCCCAAC
28540125 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28540150 GTTAACTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28541520 original size:43 final size:43
Alignment explanation
Indices: 28541446--28541551 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
28541436 CAACGCCAAC
* ***
28541446 GTCCCAGACGTGGTCTTACATGTATTTACAAATCGATGCCACT
1 GTCCCAGACGTGGTCTTACACGTAAACACAAATCGATGCCACT
*
28541489 GTCCCAGACAG-GGTCTTACACGTAAACACAAATTGATGCCAAC-
1 GTCCCAGAC-GTGGTCTTACACGTAAACACAAATCGATGCC-ACT
* *
28541532 ATCCCAGACGTAGTCTTACA
1 GTCCCAGACGTGGTCTTACA
28541552 TGAAATCACA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 49 0.92
44 3 0.06
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACACGTAAACACAAATCGATGCCACT
Found at i:28548474 original size:30 final size:28
Alignment explanation
Indices: 28548440--28548495 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
28548430 GTGATTAAAT
28548440 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
28548470 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
28548496 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:28549593 original size:2 final size:2
Alignment explanation
Indices: 28549586--28549612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28549576 TTAGCCCAAC
28549586 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28549613 GTTAACTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28551524 original size:28 final size:29
Alignment explanation
Indices: 28551473--28551529 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
28551463 TATTTCACAT
** *
28551473 TTTAGTCCCTTAATTTACACTTTTCTTAA
1 TTTAGTCCCTTAATACACACTTTTATTAA
*
28551502 TTTAGT-CCTTAATACACATTTTTATTAA
1 TTTAGTCCCTTAATACACACTTTTATTAA
28551530 AAATTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTAGTCCCTTAATACACACTTTTATTAA
Found at i:28558417 original size:32 final size:32
Alignment explanation
Indices: 28558381--28558446 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
28558371 TCAATTATTC
28558381 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
28558413 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
28558445 AT
1 AT
28558447 CACACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (32 bp):
ATGGTTTACAAACATCAAATGATATAACAATA
Found at i:28561349 original size:23 final size:23
Alignment explanation
Indices: 28561323--28561422 Score: 110
Period size: 23 Copynumber: 4.3 Consensus size: 23
28561313 TTATGTGAAA
* ** *
28561323 CCTTTGTGTAATATTCTGTAACG
1 CCTTTGTGGAATATTCTACAATG
*
28561346 CCTTTGTGGCATATTCTACAATG
1 CCTTTGTGGAATATTCTACAATG
* *
28561369 TCTTTGTGGCATATTCTACAATG
1 CCTTTGTGGAATATTCTACAATG
* **
28561392 CCTTTGTGGAATATTTTGTAATG
1 CCTTTGTGGAATATTCTACAATG
28561415 CCTTTGTG
1 CCTTTGTG
28561423 TGGCGTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (23 bp):
CCTTTGTGGAATATTCTACAATG
Found at i:28566769 original size:33 final size:33
Alignment explanation
Indices: 28566727--28566793 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
28566717 AAGCCGATGA
28566727 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
*
28566760 AAGTCTGAAATGGGATGCTAAATGAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
28566793 A
1 A
28566794 GGTTTAGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (33 bp):
AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
Found at i:28580810 original size:25 final size:25
Alignment explanation
Indices: 28580780--28580850 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
28580770 CAGACCTATT
28580780 TCACAACTTC-TGTGAGCATTTAAAG
1 TCACAAC-TCGTGTGAGCATTTAAAG
* *
28580805 TCACAACTCGTGTGGGCATTTATAG
1 TCACAACTCGTGTGAGCATTTAAAG
*
28580830 TTACAACTCGTGTGAGCATTT
1 TCACAACTCGTGTGAGCATTT
28580851 TTCCCGCGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 2 0.05
25 39 0.95
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
TCACAACTCGTGTGAGCATTTAAAG
Found at i:28588790 original size:39 final size:39
Alignment explanation
Indices: 28588710--28588851 Score: 153
Period size: 39 Copynumber: 3.6 Consensus size: 39
28588700 TAACGATAAA
* *
28588710 TCGGCTATGTT-TAGCACTTAGTATGAAATTTGAGATAGCT
1 TCGGCTAT-TTATGGCACTTAGTGTG-AATTTGAGATAGCT
*
28588750 TCGGCTATTTATGGCACTTAGTGTGAATTTGAAATAGCT
1 TCGGCTATTTATGGCACTTAGTGTGAATTTGAGATAGCT
* * *
28588789 TCGACTATATATGGCACTTAGTGTGCGAGA-CTGAGATAGCT
1 TCGGCTATTTATGGCACTTAGTGT--GA-ATTTGAGATAGCT
* *
28588830 TCGGCTATGTAAGGCACTTAGT
1 TCGGCTATTTATGGCACTTAGT
28588852 ATGCGAGATT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
39 37 0.42
40 20 0.23
41 30 0.34
42 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (39 bp):
TCGGCTATTTATGGCACTTAGTGTGAATTTGAGATAGCT
Found at i:28588846 original size:41 final size:42
Alignment explanation
Indices: 28588740--28588860 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 42
28588730 GTATGAAATT
* *
28588740 TGAGATAGCTTCGGCTATTTATGGCACTTAGTGT--GA-ATT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* *
28588779 TGAAATAGCTTCGACTATATATGGCACTTAGTGTGCGAGA-C
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* * *
28588820 TGAGATAGCTTCGGCTATGTAAGGCACTTAGTATGCGAGAT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
28588861 TATAATAGCT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 31 0.45
41 37 0.54
42 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (42 bp):
TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
Found at i:28589574 original size:23 final size:23
Alignment explanation
Indices: 28589537--28589688 Score: 137
Period size: 23 Copynumber: 6.5 Consensus size: 23
28589527 TGACTGATTG
*
28589537 ATGCTGCCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
28589560 ATGTTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
28589583 ATGCTGTCCAATTTGATGTATTA
1 ATGCTGTCCAATTTGATGTATAA
* *
28589606 ATGCTGTCCATTTTGA-GCATATTA
1 ATGCTGTCCAATTTGATG--TATAA
* * *
28589630 ATGCTGTCCATTTTG-CGCATATTA
1 ATGCTGTCCAATTTGATG--TATAA
* * *
28589654 ATGTTGTCTAAGTTTGAGGTATAA
1 ATGCTGTCCAA-TTTGATGTATAA
*
28589678 AGGCTGTCCAA
1 ATGCTGTCCAA
28589689 AACAAGGTAG
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.01
23 57 0.51
24 48 0.43
25 4 0.04
26 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (23 bp):
ATGCTGTCCAATTTGATGTATAA
Found at i:28589633 original size:24 final size:24
Alignment explanation
Indices: 28589582--28589661 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
28589572 TTGATGTATA
*
28589582 AATGCTGTCCAATTTGATG--TATT
1 AATGCTGTCCATTTTGA-GCATATT
28589605 AATGCTGTCCATTTTGAGCATATT
1 AATGCTGTCCATTTTGAGCATATT
*
28589629 AATGCTGTCCATTTTGCGCATATT
1 AATGCTGTCCATTTTGAGCATATT
*
28589653 AATGTTGTC
1 AATGCTGTC
28589662 TAAGTTTGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.02
23 16 0.31
24 35 0.67
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.42
Consensus pattern (24 bp):
AATGCTGTCCATTTTGAGCATATT
Found at i:28592107 original size:21 final size:21
Alignment explanation
Indices: 28592081--28592130 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28592071 AGTTAAAAAT
28592081 AAAAAATCATAAAAAATTCA-A
1 AAAAAATCATAAAAAATT-ATA
* * *
28592102 AAAAAAACTTAGAAAATTATA
1 AAAAAATCATAAAAAATTATA
28592123 AAAAAATC
1 AAAAAATC
28592131 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATCATAAAAAATTATA
Found at i:28603587 original size:43 final size:43
Alignment explanation
Indices: 28603520--28603678 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
28603510 AGCTCATACA
* * * *
28603520 ATGCCTATGTCCTAAAC-GAGGTCTTATATGTAATCCAATATCG
1 ATGCCAATGTCCCAAACAGA-GTCTTACACGTAATCCAATATCG
* * **
28603563 ATGCCATTGTCCCAAACAGAGTCTTACACGAAATCTTATA-CG
1 ATGCCAATGTCCCAAACAGAGTCTTACACGTAATCCAATATCG
*
28603605 ATGCCAATGTCCCAAACATAGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAAACAGAGTCTTACACGT-AATC-CAATATCG
** *
28603649 ATGCCAACATCCCAAAC-GTGGTCTTACACG
1 ATGCCAATGTCCCAAACAG-AGTCTTACACG
28603679 ATATCATATA
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 30 0.32
43 34 0.36
44 30 0.32
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACAGAGTCTTACACGTAATCCAATATCG
Found at i:28603616 original size:42 final size:43
Alignment explanation
Indices: 28603557--28603689 Score: 153
Period size: 42 Copynumber: 3.1 Consensus size: 43
28603547 ATGTAATCCA
*
28603557 ATATCGATGCCATTGTCCCAAACAGAGTCTTACACGAAATCTT
1 ATATCGATGCCAATGTCCCAAACAGAGTCTTACACGAAATCTT
* *
28603600 ATA-CGATGCCAATGTCCCAAACATAGTCTTACACGTAAATCTC
1 ATATCGATGCCAATGTCCCAAACAGAGTCTTACACG-AAATCTT
* ** * * *
28603643 AAATCGATGCCAACATCCCAAAC-GTGGTCTTACACGATATCAT
1 ATATCGATGCCAATGTCCCAAACAG-AGTCTTACACGAAATCTT
28603686 ATAT
1 ATAT
28603690 TAGAATTCTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 30 0.40
43 18 0.24
44 27 0.36
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (43 bp):
ATATCGATGCCAATGTCCCAAACAGAGTCTTACACGAAATCTT
Found at i:28603664 original size:44 final size:42
Alignment explanation
Indices: 28603572--28603679 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 42
28603562 GATGCCATTG
* * * **
28603572 TCCCAAACAGAGTCTTACACGAAATCTTATACGATGCCAATG
1 TCCCAAACATAGTCTTACACGAAATCTCAAACGATGCCAACA
28603614 TCCCAAACATAGTCTTACACGTAAATCTCAAATCGATGCCAACA
1 TCCCAAACATAGTCTTACACG-AAATCTCAAA-CGATGCCAACA
* *
28603658 TCCCAAACGTGGTCTTACACGA
1 TCCCAAACATAGTCTTACACGA
28603680 TATCATATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
42 20 0.35
43 9 0.16
44 28 0.49
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (42 bp):
TCCCAAACATAGTCTTACACGAAATCTCAAACGATGCCAACA
Found at i:28611247 original size:23 final size:23
Alignment explanation
Indices: 28611217--28611328 Score: 100
Period size: 23 Copynumber: 4.8 Consensus size: 23
28611207 CACCAACTCC
*
28611217 GAATATGCCACAAGGGC-TCCACA
1 GAATATGCCACAAAGGCAT-CACA
* * * *
28611240 GAATATGCCGCAAAGACGTCATA
1 GAATATGCCACAAAGGCATCACA
* *
28611263 GATTATGCCACAAAGGCATCACC
1 GAATATGCCACAAAGGCATCACA
*
28611286 GAATATGCCACAAAGGCATTACA
1 GAATATGCCACAAAGGCATCACA
* **
28611309 GGATACACCACAAAAGGCAT
1 GAATATGCCAC-AAAGGCAT
28611329 TTTAGAATAC
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 62 0.87
24 9 0.13
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (23 bp):
GAATATGCCACAAAGGCATCACA
Found at i:28611338 original size:24 final size:23
Alignment explanation
Indices: 28611270--28611349 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
28611260 ATAGATTATG
* * **
28611270 CCACAAAGGCATCACCGAATATG
1 CCACAAAGGCATTACAGAATACA
*
28611293 CCACAAAGGCATTACAGGATACA
1 CCACAAAGGCATTACAGAATACA
** *
28611316 CCACAAAAGGCATTTTAGAATACG
1 CCAC-AAAGGCATTACAGAATACA
*
28611340 CTACAAAGGC
1 CCACAAAGGC
28611350 TCTGTTTGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 28 0.61
24 18 0.39
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.15
Consensus pattern (23 bp):
CCACAAAGGCATTACAGAATACA
Found at i:28612955 original size:20 final size:20
Alignment explanation
Indices: 28612905--28612957 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
28612895 GACAAGCCAA
* **
28612905 CAGTAATGCAAATAAACTGT
1 CAGTAATGCAGATAAACTAC
*
28612925 CAGTATTGCAGATAAACTAC
1 CAGTAATGCAGATAAACTAC
28612945 CAGTAATGCAGAT
1 CAGTAATGCAGAT
28612958 GAGCTGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
CAGTAATGCAGATAAACTAC
Found at i:28612987 original size:40 final size:40
Alignment explanation
Indices: 28612891--28613009 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 40
28612881 TTGCCAATAA
* *
28612891 TGTGGACAAGCCAACAGTAATGCAAATAAACTGTCAGTAT
1 TGTGGACAAGCCACCAGTAATGCAGATAAACTGTCAGTAT
** * * * * *
28612931 TGCAGATAAACTACCAGTAATGCAGATGAGCTG-CTAGTAT
1 TGTGGACAAGCCACCAGTAATGCAGATAAACTGTC-AGTAT
* * *
28612971 TGTGGACAAGCCACCAGTAATGTAGATAAAATGCCAGTA
1 TGTGGACAAGCCACCAGTAATGCAGATAAACTGTCAGTA
28613010 CTTCTTCCTT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
39 1 0.02
40 57 0.97
41 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (40 bp):
TGTGGACAAGCCACCAGTAATGCAGATAAACTGTCAGTAT
Found at i:28616142 original size:25 final size:25
Alignment explanation
Indices: 28616094--28616145 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
28616084 ATCCCGAGAT
* * *
28616094 GAAAACCTCAAATTTTAAGTGGGTG
1 GAAAACCTAAAATTCTAAGCGGGTG
*
28616119 GAAAACCTAAAATTCTACGCGGGTG
1 GAAAACCTAAAATTCTAAGCGGGTG
28616144 GA
1 GA
28616146 TACATTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (25 bp):
GAAAACCTAAAATTCTAAGCGGGTG
Found at i:28629594 original size:22 final size:22
Alignment explanation
Indices: 28629566--28629617 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
28629556 ATCACTTCTA
28629566 CTCTCATGGCTAACGTACTAAG
1 CTCTCATGGCTAACGTACTAAG
** *
28629588 CTCTCATGTTTCACGTACTAAG
1 CTCTCATGGCTAACGTACTAAG
28629610 CTCTCATG
1 CTCTCATG
28629618 TTTGAACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (22 bp):
CTCTCATGGCTAACGTACTAAG
Found at i:28629618 original size:22 final size:22
Alignment explanation
Indices: 28629578--28629620 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28629568 CTCATGGCTA
28629578 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
28629600 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
28629621 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:28630383 original size:23 final size:26
Alignment explanation
Indices: 28630357--28630404 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
28630347 AAAAACCTAT
28630357 TTTTTTCAAAA-AA-TAA-AATTTCC
1 TTTTTTCAAAAGAATTAATAATTTCC
*
28630380 TTTTTTTAAAAGAATTAATAATTTC
1 TTTTTTCAAAAGAATTAATAATTTC
28630405 ATCTCTCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 2 0.10
25 3 0.14
26 6 0.29
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTTCAAAAGAATTAATAATTTCC
Found at i:28630383 original size:24 final size:26
Alignment explanation
Indices: 28630356--28630404 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
28630346 AAAAAACCTA
28630356 TTTTTTTCAAAA-AA-TAA-AATTTCC
1 TTTTTTT-AAAAGAATTAATAATTTCC
28630380 TTTTTTTAAAAGAATTAATAATTTC
1 TTTTTTTAAAAGAATTAATAATTTC
28630405 ATCTCTCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 3 0.14
26 6 0.27
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTTTAAAAGAATTAATAATTTCC
Found at i:28631389 original size:2 final size:2
Alignment explanation
Indices: 28631382--28631416 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28631372 GAAAAGTGAC
28631382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28631417 TCAGATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28636139 original size:14 final size:14
Alignment explanation
Indices: 28636120--28636146 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28636110 TTTAGGCTCA
28636120 ATACATGAAATAAT
1 ATACATGAAATAAT
28636134 ATACATGAAATAA
1 ATACATGAAATAA
28636147 ATGCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (14 bp):
ATACATGAAATAAT
Found at i:28638467 original size:30 final size:30
Alignment explanation
Indices: 28638433--28638501 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
28638423 ATTGACAAGA
28638433 TTAATCAAGAAATTGGAGACAAAAGAGATC
1 TTAATCAAGAAATTGGAGACAAAAGAGATC
28638463 TTAATCAAGAAATTGGAGACAAAAGAGATC
1 TTAATCAAGAAATTGGAGACAAAAGAGATC
*
28638493 TTACTCAAG
1 TTAATCAAG
28638502 CTAGTTGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.22
Consensus pattern (30 bp):
TTAATCAAGAAATTGGAGACAAAAGAGATC
Found at i:28642539 original size:17 final size:17
Alignment explanation
Indices: 28642517--28642550 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28642507 CTTGAATATT
*
28642517 CTCTCTTGTTGTTGTAG
1 CTCTCTTGTTGGTGTAG
28642534 CTCTCTTGTTGGTGTAG
1 CTCTCTTGTTGGTGTAG
28642551 GACATTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.26, T:0.50
Consensus pattern (17 bp):
CTCTCTTGTTGGTGTAG
Found at i:28643907 original size:44 final size:44
Alignment explanation
Indices: 28643859--28643947 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
28643849 TTGAAATCAA
* * *
28643859 AATAGAAGTTGTGATAATTATACATTTAAAAATATTTATAATTT
1 AATAGAAGTTGTGATAATTACACAATTAAAAATAATTATAATTT
*
28643903 AATAGAAGTTGTGATAATTGCACAATTAAAAATAATTATAATTT
1 AATAGAAGTTGTGATAATTACACAATTAAAAATAATTATAATTT
28643947 A
1 A
28643948 TTTTACAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.39
Consensus pattern (44 bp):
AATAGAAGTTGTGATAATTACACAATTAAAAATAATTATAATTT
Found at i:28645739 original size:22 final size:20
Alignment explanation
Indices: 28645599--28645732 Score: 78
Period size: 20 Copynumber: 6.6 Consensus size: 20
28645589 AGTATTTTCT
* *
28645599 TTTAGGAATTTTGGTAAATC
1 TTTAGAAATTTTGATAAATC
* ** *
28645619 TTTAGATATTTCAATGAAT-
1 TTTAGAAATTTTGATAAATC
28645638 TGTTA-AATATTTTGATAAATC
1 T-TTAGAA-ATTTTGATAAATC
* *** *
28645659 TTTAAAAAAAAT-AGTAAAAC
1 TTTAGAAATTTTGA-TAAATC
*
28645679 TTTTG-AATTATTGATAAATC
1 TTTAGAAATT-TTGATAAATC
28645699 TTTAGAAATTTTGATAAATC
1 TTTAGAAATTTTGATAAATC
28645719 GTCTTAGAAATTTT
1 -T-TTAGAAATTTT
28645733 AGTAAATGAT
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
19 5 0.06
20 58 0.70
21 9 0.11
22 11 0.13
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTAGAAATTTTGATAAATC
Found at i:28647194 original size:33 final size:34
Alignment explanation
Indices: 28647146--28647355 Score: 138
Period size: 33 Copynumber: 5.7 Consensus size: 34
28647136 TTATCTGTTA
* *
28647146 TCGGTGGATTCAGCACTTAGCAATCACCAATGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
**
28647180 TCGG-GGAATCAGCACTTAGCAACCCCTTTTCACATTCAAAAAT
1 TCGGTGGAATCAGCACTTAGCAA---C----CAC---CAATGAT
* *
28647223 ACGGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
*
28647257 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGTGGAATCAGCACTTAGCAACCAC---CA-A--T--GAT
* * *
28647298 ACGGTGGGATCAACACTTAGCAACCACCAATGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
*
28647332 TCGG-GGAATTAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
28647356 CCTTGGGGGA
Statistics
Matches: 137, Mismatches: 19, Indels: 41
0.70 0.10 0.21
Matches are distributed among these distances:
33 55 0.40
34 17 0.12
36 3 0.02
37 4 0.03
38 1 0.01
39 3 0.02
40 3 0.02
41 6 0.04
42 19 0.14
43 8 0.06
44 18 0.13
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:28647274 original size:77 final size:76
Alignment explanation
Indices: 28647147--28647359 Score: 338
Period size: 75 Copynumber: 2.8 Consensus size: 76
28647137 TATCTGTTAT
* *
28647147 CGGTGGATTCAGCACTTAGCAATCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
28647212 CATTCAAAAATA
66 CATT-AAAAATA
*
28647224 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC-TTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
* *
28647288 CATTTAAGATA
66 CATTAAAAATA
* * *
28647299 CGGTGGGATCAACACTTAGCAACCACCAATGATTCGGGGAATTAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
28647360 GGGGGAATCA
Statistics
Matches: 126, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
75 60 0.48
76 10 0.08
77 56 0.44
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
CATTAAAAATA
Found at i:28647461 original size:102 final size:102
Alignment explanation
Indices: 28647259--28647458 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 102
28647249 CCAATGAATC
* * *
28647259 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
* *
28647324 CCAATGATTCGGGGAATTAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* *
28647361 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAAGT-AGCACTTAGC-ACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAA-TCAACACTTAGCAACC
28647424 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
65 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
28647459 CTTTATATTC
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 36 0.40
102 53 0.59
103 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:28650077 original size:33 final size:33
Alignment explanation
Indices: 28650022--28650095 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
28650012 TGACTTTATT
* * **
28650022 TGTGTTTATTGTCCTAGTAGACTATCTT-TGTTC
1 TGTGTTTATAGTCCCACCAGACTAT-TTCTGTTC
28650055 TGTGTTTATAGTCCCACCAGACTATTTCTGTTC
1 TGTGTTTATAGTCCCACCAGACTATTTCTGTTC
*
28650088 TATGTTTA
1 TGTGTTTA
28650096 CTGTAACACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (33 bp):
TGTGTTTATAGTCCCACCAGACTATTTCTGTTC
Found at i:28651583 original size:30 final size:30
Alignment explanation
Indices: 28651539--28651765 Score: 241
Period size: 30 Copynumber: 7.6 Consensus size: 30
28651529 GTTACCACCA
*
28651539 CTTTTCATACTTTGATAGTCGAAGCTATCC
1 CTTTTCATAATTTGATAGTCGAAGCTATCC
* * *
28651569 CTTTCCATATTTTGATAG-CTGAAGCCATCC
1 CTTTTCATAATTTGATAGTC-GAAGCTATCC
*
28651599 CTTTTCATAATTTGATAGTCGAAGCTATTC
1 CTTTTCATAATTTGATAGTCGAAGCTATCC
* *
28651629 CTTTTCATAATTCGATAG-CTGAAGCCATCC
1 CTTTTCATAATTTGATAGTC-GAAGCTATCC
28651659 CTTTTCATAATTTGATAGTCG-AG-TCATCC
1 CTTTTCATAATTTGATAGTCGAAGCT-ATCC
* * *
28651688 CTTTTCATAATTCGATGGTC-ATCA-CCATCC
1 CTTTTCATAATTTGATAGTCGA--AGCTATCC
* *
28651718 CTTTTCATAATTTGATAGCCGAAGATATCC
1 CTTTTCATAATTTGATAGTCGAAGCTATCC
* *
28651748 CTTTCCATATTTTGATAG
1 CTTTTCATAATTTGATAG
28651766 CCAAAGCCAC
Statistics
Matches: 164, Mismatches: 22, Indels: 22
0.79 0.11 0.11
Matches are distributed among these distances:
29 27 0.16
30 133 0.81
31 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (30 bp):
CTTTTCATAATTTGATAGTCGAAGCTATCC
Found at i:28651720 original size:59 final size:60
Alignment explanation
Indices: 28651539--28651785 Score: 297
Period size: 60 Copynumber: 4.1 Consensus size: 60
28651529 GTTACCACCA
* * * *
28651539 CTTTTCATACTTTGATAGTCGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCC
1 CTTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCC
*
28651599 CTTTTCATAATTTGATAGTCGAAGCTATTCCTTTTCATAATTCGATAGCTGAAGCCATCC
1 CTTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCC
* *
28651659 CTTTTCATAATTTGATAGTCG-AG-TCATCCCTTTTCATAATTCGATGGTCAT-CA-CCATCC
1 CTTTTCATAATTTGATAGTCGAAGCT-ATCCCTTTTCATAATTCGATAG-C-TGAAGCCATCC
* * * * * **
28651718 CTTTTCATAATTTGATAGCCGAAGATATCCCTTTCCATATTTTGATAGCCAAAGCCA-CTC
1 CTTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATC-C
28651778 CTTTTCAT
1 CTTTTCAT
28651786 TGATTGATAA
Statistics
Matches: 164, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
58 1 0.01
59 51 0.31
60 110 0.67
61 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.38
Consensus pattern (60 bp):
CTTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCC
Found at i:28651727 original size:89 final size:90
Alignment explanation
Indices: 28651539--28651785 Score: 281
Period size: 89 Copynumber: 2.8 Consensus size: 90
28651529 GTTACCACCA
*
28651539 CTTTTCATACTTTGATAG-TCGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTT
1 CTTTTCATAATTTGATAGCT-GAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTT
* * *
28651603 TCATAATTTGATAGTCGAAGCTATTC
65 TCATAATTCGATAGTCGAAGCCATCC
* * * * *
28651629 CTTTTCATAATTCGATAGCTGAAGCCATCCCTTTTCATAATTTGATAG-TCG-AGTCATCCCTTT
1 CTTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATATTTTGATAGCT-GAAGCCATCCCTTT
*
28651692 TCATAATTCGATGGTC-ATCA-CCATCC
65 TCATAATTCGATAGTCGA--AGCCATCC
* * **
28651718 CTTTTCATAATTTGATAGCCGAAGATATCCCTTTCCATATTTTGATAGCCAAAGCCA-CTCCTTT
1 CTTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATC-CCTTT
28651782 TCAT
65 TCAT
28651786 TGATTGATAA
Statistics
Matches: 131, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
88 1 0.01
89 73 0.56
90 56 0.43
91 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.38
Consensus pattern (90 bp):
CTTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTTT
CATAATTCGATAGTCGAAGCCATCC
Found at i:28656704 original size:51 final size:52
Alignment explanation
Indices: 28656609--28656719 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 52
28656599 ATTGAAATGG
*
28656609 TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGGTTTTCTCAAAAA
1 TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGATTTTCTCAAAAA
* * *
28656661 TGAAATTGGAGAAAT-AG-AATCATTTGGAAATGAATG-TGATTTTCTCCAAAA
1 TGAAAATGGAGAAATGAGAAAT-ATTTGAAAATG-ATGATGATTTTCTCAAAAA
28656712 TGAAAATG
1 TGAAAATG
28656720 ACCTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 3 0.06
51 32 0.62
52 17 0.33
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGATTTTCTCAAAAA
Found at i:28658658 original size:7 final size:7
Alignment explanation
Indices: 28658646--28658675 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
28658636 TGACACAAGG
28658646 AAGAAGA
1 AAGAAGA
28658653 AAGAAGA
1 AAGAAGA
*
28658660 GAGAAGA
1 AAGAAGA
28658667 AAGAAGA
1 AAGAAGA
28658674 AA
1 AA
28658676 AATTGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:28667900 original size:42 final size:42
Alignment explanation
Indices: 28667853--28667936 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
28667843 AATATTTTAT
*
28667853 TTTATCTTTTAGTAGTTTATTAGAATAAGTGAATTAATTTCC
1 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTTCC
*
28667895 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTTCC
28667937 CAATTAGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (42 bp):
TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTTCC
Found at i:28672104 original size:12 final size:12
Alignment explanation
Indices: 28672084--28672113 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28672074 GCTAGCAAAT
*
28672084 TTCTAATCCATA
1 TTCTTATCCATA
28672096 TTCTTATCCATA
1 TTCTTATCCATA
28672108 TTCTTA
1 TTCTTA
28672114 ACATTCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (12 bp):
TTCTTATCCATA
Found at i:28674110 original size:22 final size:22
Alignment explanation
Indices: 28674084--28674128 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28674074 ATTATATGTA
28674084 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
*
28674106 TTAATTTATATATAATTTAATT
1 TTAATTCATATATAATTTAATT
28674128 T
1 T
28674129 GGGTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:28679111 original size:12 final size:12
Alignment explanation
Indices: 28679091--28679120 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28679081 GCTAGCACAT
*
28679091 TTCTAATCCATA
1 TTCTTATCCATA
28679103 TTCTTATCCATA
1 TTCTTATCCATA
28679115 TTCTTA
1 TTCTTA
28679121 ACATACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (12 bp):
TTCTTATCCATA
Found at i:28680120 original size:6 final size:6
Alignment explanation
Indices: 28680086--28680110 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28680076 TTTAAATTTT
28680086 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
28680111 ATAATAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:28694893 original size:44 final size:43
Alignment explanation
Indices: 28694836--28695510 Score: 245
Period size: 44 Copynumber: 15.6 Consensus size: 43
28694826 GAAGATGACA
28694836 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC-AT
* * * *
28694880 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCAT
* * * * * *
28694923 GGATCTTATCTCTCT-AAGTTGCAG-AGAGCATA-TCGCA-TC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCCAT
* * * * *
28694963 AGTCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTAAGTAAG-C-G
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCCAT
* * * * * *
28695007 AGTCTTATC-CTCTTGAAGTTGTAGT-GAGGTAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCCAT
* *
28695052 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC-AT
* * * * * *
28695096 GATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCAT
* * * * * * *
28695139 GGATCTTATTTCTCTAAAGTTGCAG-AGAGCAGA-TCGCA-TC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCCAT
* * * *
28695180 AGTCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTAATTA-AG-C-G
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG----ATTAGAGCCAT
* * * * * *
28695224 AGTCTTATC-CTCTTGAAGTTGTAGT-GAGGTAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCCAT
28695269 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC-AT
* * * ** * * *
28695313 GATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCAT
* * * * * * *
28695356 GGATCTTATTTCTCTAAAGTTGCAG-AGAGCAGA-TCGTA-TC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCCAT
* * *
28695397 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAG-CA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCCAT
* * * *
28695441 AGTCTTATC-CTCCTGAAGTTGCAGTGAAGCAGACTAAAGATGACA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-T-TAGA-GCCAT
28695486 AATCTTATCTCCCTGAAGTTGCAGT
1 AATCTTATCTCCCTGAAGTTGCAGT
28695511 AATCCTATCT
Statistics
Matches: 478, Mismatches: 101, Indels: 103
0.70 0.15 0.15
Matches are distributed among these distances:
39 11 0.02
40 49 0.10
41 21 0.04
42 16 0.03
43 43 0.09
44 250 0.52
45 80 0.17
46 8 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCAT
Found at i:28695264 original size:217 final size:217
Alignment explanation
Indices: 28694644--28696054 Score: 1835
Period size: 217 Copynumber: 6.6 Consensus size: 217
28694634 GTTCCCTAGA
* * * ***
28694644 GAGCAGATCAAAAGCCAATGATCCTATCTCCCT-AAGGTTGCAGTGGAGCGGATTAAAACCACAG
1 GAGCAGAT-TAAAGCCGATAATCCTATCTCCCTGAA-GTTGCAGTGGAGCGGATTAAAACCTTGG
* * * *
28694708 ATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGATACAATG
64 ATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTG
* * * * * *
28694773 GAGCAAACTAAGCAAGCAAGTCTTATCCTCCTAAAGTTGCAGCGAGGTAGACTGAAGATGACAAA
129 AAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAA
28694838 TCTTATCTCCCTGAAGTTGCAGTG
194 TCTTATCTCCCTGAAGTTGCAGTG
* *
28694862 GAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGAT
1 GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
* *
28694927 CTTATCTCTCT-AAGTTGCAGAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGAA
66 CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAA
* * * * *
28694991 GCAGACTAAGTAAGCGAGTCTTATCCTCTTGAAGTTGTAGTGAGGTAGACTGAAGATGGCAAATC
131 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATC
28695056 TTATCTCCCTGAAGTTGCAGTG
196 TTATCTCCCTGAAGTTGCAGTG
* * **
28695078 GAGCATATTAAAGCCGATGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTTGGAT
1 GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
* *
28695143 CTTATTTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGCGAA
66 CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAA
* * * * * *
28695208 GCAGACTAATTAAGCGAGTCTTATCCTCTTGAAGTTGTAGTGAGGTAGACTGAAGATGGCAAATC
131 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATC
28695273 TTATCTCCCTGAAGTTGCAGTG
196 TTATCTCCCTGAAGTTGCAGTG
* * * *
28695295 GAGCAGATTAGAGCCGATGATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTTGGAT
1 GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
* *
28695360 CTTATTTCTCTAAAGTTGCAGAGAGCAGATCGTATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
66 CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT-GA
* *
28695425 A-CAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGACTAAAGATGACAAAT
130 AGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAAT
28695489 CTTATCTCCCTGAAG-T----T-
195 CTTATCTCCCTGAAGTTGCAGTG
**
28695506 --GC-------A---G-TAATCCTATCTCCCTGAAGTTGCAGTGGAATGGATTAAAACCTTGGAT
1 GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
* *
28695558 CTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
66 CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAA
* * *
28695623 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAACC
131 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATC
* *
28695688 TCATCTCACTGAAGTTGCAGTG
196 TTATCTCCCTGAAGTTGCAGTG
* * * * * * *
28695710 GAGCAGGTTAAAACTGATAATCCTATCTCCCTAAAGTTACAATAGAGCGGATTAAAACCTTGGAT
1 GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
* * *
28695775 TTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
66 CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAA
* * ** *
28695840 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAATTGCAGTTAAACAGA-TCGAAGATGACAGAT
131 GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACT-GAAGATGACAAAT
* * * *
28695904 TTTACCTCCCTGAGGTTACAGTG
195 CTTATCTCCCTGAAGTTGCAGTG
* * * *** *
28695927 GAGTAGATTGAAGCC-AGTAATCCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAATAATAGA
1 GAGCAGATTAAAGCCGA-TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGA
* * * * * *
28695991 TCTTATCTCTCTGAAGTTGCAGAGAACATATCTCATCTAGTCTCATCTCCCTGAGGTTGCAGTG
65 TCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTG
28696055 GAGAAGATTA
Statistics
Matches: 1069, Mismatches: 99, Indels: 51
0.88 0.08 0.04
Matches are distributed among these distances:
197 2 0.00
198 175 0.16
199 2 0.00
202 1 0.00
203 1 0.00
206 2 0.00
209 2 0.00
212 1 0.00
213 1 0.00
216 200 0.19
217 669 0.63
218 13 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (217 bp):
GAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGAT
CTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAA
GCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATC
TTATCTCCCTGAAGTTGCAGTG
Found at i:28695520 original size:25 final size:25
Alignment explanation
Indices: 28695486--28695535 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28695476 AAAGATGACA
*
28695486 AATCTTATCTCCCTGAAGTTGCAGT
1 AATCCTATCTCCCTGAAGTTGCAGT
28695511 AATCCTATCTCCCTGAAGTTGCAGT
1 AATCCTATCTCCCTGAAGTTGCAGT
28695536 GGAATGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (25 bp):
AATCCTATCTCCCTGAAGTTGCAGT
Found at i:28695654 original size:44 final size:44
Alignment explanation
Indices: 28695595--28695715 Score: 131
Period size: 44 Copynumber: 2.7 Consensus size: 44
28695585 GATCGCATCT
28695595 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCA
* *
28695639 AGTCTTATCCTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACTGAAGATAGCA
** *
28695684 AACCTCATCTCACTGAAGTTGCAGTGGAGCAG
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAG
28695716 GTTAAAACTG
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
43 2 0.03
44 31 0.48
45 29 0.45
46 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (44 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Done.