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 30 of 199
Found at i:8579263 original size:15 final size:15
Alignment explanation
Indices: 8579243--8579292 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
8579233 TGATAAATTT
8579243 ATTGAATTTATATTG
1 ATTGAATTTATATTG
8579258 ATTGAATTTGTATATAT-
1 ATTGAA-TT-TATAT-TG
*
8579275 ATTGAATATATATTG
1 ATTGAATTTATATTG
8579290 ATT
1 ATT
8579293 ATTTGAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 14 0.47
16 3 0.10
17 11 0.37
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:8581954 original size:42 final size:42
Alignment explanation
Indices: 8581839--8581958 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
8581829 TGATTCAGTA
* * * * **
8581839 CACCGGCTTTAAGCTTGCTAGACTTATAGTCCAAATTTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
*
8581881 CACCGGCATTAAGCCTACTAGACGTAAAGTCTGAATTTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
8581923 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAT
8581959 GGTTTCATTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
Found at i:8581978 original size:41 final size:42
Alignment explanation
Indices: 8581872--8581984 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
8581862 TTATAGTCCA
* **
8581872 AATTTATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTG
1 AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
* ** *
8581914 AATTTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
1 AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
* **
8581956 AA-TGGTTTCATTGGCAACAAGCCTACTAG
1 AATTGATTTCACCGGCAACAAGCCTACTAG
8581985 GTGCTAAGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 20 0.32
42 43 0.68
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
Found at i:8582438 original size:21 final size:22
Alignment explanation
Indices: 8582396--8582438 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
8582386 TACCTGTACG
** *
8582396 TATATATATACATATTTTAATT
1 TATATATATACATAAATAAATT
8582418 TATA-ATATACATAAATAAATT
1 TATATATATACATAAATAAATT
8582439 CATACTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATATATACATAAATAAATT
Found at i:8582493 original size:49 final size:46
Alignment explanation
Indices: 8582417--8582509 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 46
8582407 ATATTTTAAT
8582417 TTATAATATACATAAATAAATTCATACTTAATTTCAAAACAAGATC
1 TTATAATATACATAAATAAATTCATACTTAATTTCAAAACAAGATC
* * * *
8582463 TTATATATATATATATATATAATTCTATACTTATTTTCGAAACAAGA
1 TTATA-ATATACATAAATA-AATTC-ATACTTAATTTCAAAACAAGA
8582510 ACTTGTACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 5 0.12
47 11 0.28
48 5 0.12
49 19 0.47
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (46 bp):
TTATAATATACATAAATAAATTCATACTTAATTTCAAAACAAGATC
Found at i:8587652 original size:21 final size:21
Alignment explanation
Indices: 8587612--8587671 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
8587602 CGAATATGCC
*
8587612 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTG
8587631 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
8587652 AACAGAAGCTCATAAGAGCT
1 AACAGAAGCTCATAAGAGCT
8587672 TATCCATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 11 0.29
20 2 0.05
21 25 0.66
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:8592418 original size:17 final size:19
Alignment explanation
Indices: 8592396--8592431 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
8592386 ATTATAAGTT
8592396 AAATAA-TAAAG-TAAAAA
1 AAATAAGTAAAGTTAAAAA
8592413 AAATAAGTAAAGTTAAAAA
1 AAATAAGTAAAGTTAAAAA
8592432 TAAGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AAATAAGTAAAGTTAAAAA
Found at i:8604421 original size:147 final size:147
Alignment explanation
Indices: 8604154--8604422 Score: 502
Period size: 147 Copynumber: 1.8 Consensus size: 147
8604144 GACACACGAG
8604154 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
1 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
*
8604219 ATATATATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
66 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
8604284 AAATGAAATGAAATGAA
131 AAATGAAATGAAATGAA
* *
8604301 ATGGTAAGTATGCAAATGGATTGACTCATGATCTTATTAAAATGTTGGTGTGTTAAATGATGTTT
1 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
*
8604366 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCGTTTGTATCATGAACAAGTA
66 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTA
8604423 TATTAACTTG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 118 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (147 bp):
ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
AAATGAAATGAAATGAA
Found at i:8613719 original size:31 final size:31
Alignment explanation
Indices: 8613671--8613840 Score: 127
Period size: 31 Copynumber: 5.5 Consensus size: 31
8613661 TAAGTTGCCG
* * *
8613671 AAATGATTCGTATATGGTTGA-ACATTGCTGA
1 AAATAATTTGTATATGGTT-ATACATTGTTGA
* *
8613702 AAATAATTTTTATATGGTTATTCATTGTTGA
1 AAATAATTTGTATATGGTTATACATTGTTGA
* *
8613733 AATTGAA-TTGTATAT-GTATATA-AGTTGCTG-
1 AAAT-AATTTGTATATGGT-TATACA-TTGTTGA
* * *
8613763 AAATGATTCGTATATGGTTGA-ACATTATTGA
1 AAATAATTTGTATATGGTT-ATACATTGTTGA
*
8613794 AAATAATTTTTATATGGTTATACATTGTTGA
1 AAATAATTTGTATATGGTTATACATTGTTGA
* * *
8613825 AATTAAATTGTTTATG
1 AAATAATTTGTATATG
8613841 AATATAGGAT
Statistics
Matches: 107, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
29 1 0.01
30 21 0.20
31 83 0.78
32 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (31 bp):
AAATAATTTGTATATGGTTATACATTGTTGA
Found at i:8613781 original size:92 final size:92
Alignment explanation
Indices: 8613625--8613914 Score: 361
Period size: 92 Copynumber: 3.2 Consensus size: 92
8613615 GAATTGTTTT
* * *
8613625 TGGTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGT
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
8613689 TGAACATTGCTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* *
8613716 TGGTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTCGTATATGGT
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
**
8613781 TGAACATTATTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* * * * * * * *
8613808 TGGTTATACATTGTTGAAATTAAATTGTTTATGAATATAGGATGCCGAATTTGATTTGTATATGA
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAA-ATGATTCGTATATGG
* * *
8613873 TT-ATACATTGC-CAAATTAGATTCTTATA
65 TTGA-ACATTGCTGAAAATA-ATTTTTATA
*
8613901 TGGTTATATATTGT
1 TGGTTATACATTGT
8613915 CGAATTGCTT
Statistics
Matches: 172, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
91 29 0.17
92 103 0.60
93 40 0.23
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (92 bp):
TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
TGAACATTGCTGAAAATAATTTTTATA
Found at i:8613943 original size:61 final size:63
Alignment explanation
Indices: 8613858--8613989 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 63
8613848 GATGCCGAAT
* * *
8613858 TTGATTTGTATATGATTATACATTGCCAAATTAGATTCTTATATG-GT-TATATATTG-TCGAA
1 TTGATTGGTATATGATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCT-GAA
* * * * *
8613919 TTGCTTGGTATATCGA-TATTCATTGTCGAATTTGATTCGTATATGAATATATATATTGCTGAA
1 TTGATTGGTATAT-GATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCTGAA
8613982 TTGATTGG
1 TTGATTGG
8613990 AGCATTAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
61 35 0.60
62 3 0.05
63 19 0.33
64 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (63 bp):
TTGATTGGTATATGATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCTGAA
Found at i:8618909 original size:22 final size:22
Alignment explanation
Indices: 8618881--8618942 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
8618871 TGTTGATAGT
*
8618881 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
8618903 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
8618925 ACGTACTAAGCTCTCATG
1 ACGTACTAAGCTCTCATG
8618943 GTCATTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:8620817 original size:13 final size:13
Alignment explanation
Indices: 8620799--8620824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8620789 AAATTTAAGC
8620799 CCCTAACTATTTT
1 CCCTAACTATTTT
8620812 CCCTAACTATTTT
1 CCCTAACTATTTT
8620825 TCTCCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
CCCTAACTATTTT
Found at i:8628192 original size:28 final size:28
Alignment explanation
Indices: 8628157--8628222 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
8628147 ATAAAAAATA
**
8628157 ACCAAAATATTATAATTTTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
8628185 ACCAAAATATTATAAAATTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
*
8628213 ACTAAAATAT
1 ACCAAAATAT
8628223 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (28 bp):
ACCAAAATATTATAAAATTTTTTTATTT
Found at i:8629702 original size:25 final size:27
Alignment explanation
Indices: 8629674--8629733 Score: 97
Period size: 25 Copynumber: 2.3 Consensus size: 27
8629664 TTTTTTTGGT
8629674 ATATTTTGGTAAAT-AAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
8629699 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
8629727 ATATTTT
1 ATATTTT
8629734 AGTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 14 0.44
27 6 0.19
28 12 0.38
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:8631312 original size:14 final size:14
Alignment explanation
Indices: 8631295--8631344 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
8631285 TGGATTAAAG
8631295 CTTAATTAAATTAA
1 CTTAATTAAATTAA
*
8631309 CTTAATTAACATAAA
1 CTTAATTAA-ATTAA
* *
8631324 CATAATTTAATTAA
1 CTTAATTAAATTAA
8631338 CTTAATT
1 CTTAATT
8631345 CAACATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
CTTAATTAAATTAA
Found at i:8634642 original size:28 final size:28
Alignment explanation
Indices: 8634602--8634659 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
8634592 ATCAATGGTG
*
8634602 ACAACTTTTATGGTGACTTTCTCTAGAT
1 ACAACTTTTATGGCGACTTTCTCTAGAT
*
8634630 ACAATTTTTATGGCGACTTTCTCTAGAT
1 ACAACTTTTATGGCGACTTTCTCTAGAT
8634658 AC
1 AC
8634660 CAGGTTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (28 bp):
ACAACTTTTATGGCGACTTTCTCTAGAT
Found at i:8644557 original size:2 final size:2
Alignment explanation
Indices: 8644550--8644584 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8644540 TCTACTGTTT
8644550 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
8644585 TCTCTCTTCA
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:8649190 original size:46 final size:46
Alignment explanation
Indices: 8649101--8649190 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
8649091 GAACCTTAAA
* *
8649101 TTGAAGCCTTCGTTAATTTATCATATATTCATTTTTATTCCCACCG
1 TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCACCG
* * * *
8649147 TTGAAGCTTTCGTTAATTTCTCATAAATTTATTTTTGTCCCCAC
1 TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCAC
8649191 ACCAACAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (46 bp):
TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCACCG
Found at i:8651111 original size:22 final size:22
Alignment explanation
Indices: 8651085--8651131 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
8651075 ACACAAATAA
8651085 ATATAAAGTTTCACCATGTGAT
1 ATATAAAGTTTCACCATGTGAT
8651107 ATATAAAGTTTCACCATGTGAT
1 ATATAAAGTTTCACCATGTGAT
8651129 ATA
1 ATA
8651132 GATAATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
ATATAAAGTTTCACCATGTGAT
Found at i:8652659 original size:30 final size:30
Alignment explanation
Indices: 8652615--8652671 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
8652605 CACGGGCTGG
* *
8652615 CACATGGGCATGTGTCCATCCCATGTGTAT
1 CACATGAGCATGTGTCCAGCCCATGTGTAT
* *
8652645 CACATGAGCGTGTGTCTAGCCCATGTG
1 CACATGAGCATGTGTCCAGCCCATGTG
8652672 GCTCTTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (30 bp):
CACATGAGCATGTGTCCAGCCCATGTGTAT
Found at i:8654487 original size:6 final size:6
Alignment explanation
Indices: 8654476--8654541 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
8654466 CAAGTCTAAG
* * *
8654476 AAAATA AAAATAA AACAACTA AAAATA AAAATA AACATA AACATA AAAAGA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
8654527 AAAAGA GAAATA AAA
1 AAAATA AAAATA AAA
8654542 CAAATAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
6 40 0.78
7 5 0.10
8 5 0.10
9 1 0.02
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:8655488 original size:16 final size:16
Alignment explanation
Indices: 8655467--8655498 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8655457 AAAACTCTAA
8655467 GGTCAGCTCCAAATAG
1 GGTCAGCTCCAAATAG
8655483 GGTCAGCTCCAAATAG
1 GGTCAGCTCCAAATAG
8655499 CTGGGCTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (16 bp):
GGTCAGCTCCAAATAG
Found at i:8660080 original size:6 final size:6
Alignment explanation
Indices: 8660071--8660107 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
8660061 AATTATAATG
8660071 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TATAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA
8660108 AATGGCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:8669355 original size:26 final size:26
Alignment explanation
Indices: 8669319--8669371 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
8669309 TGGAGGACCC
8669319 TATCTCGATGTTCTACTCTTAATGTT
1 TATCTCGATGTTCTACTCTTAATGTT
*
8669345 TATCTCGATGTTTTACTCTTAATGTT
1 TATCTCGATGTTCTACTCTTAATGTT
8669371 T
1 T
8669372 GTTATTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (26 bp):
TATCTCGATGTTCTACTCTTAATGTT
Found at i:8669371 original size:14 final size:14
Alignment explanation
Indices: 8669326--8669371 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
8669316 CCCTATCTCG
*
8669326 ATGTTCTACTCTTA
1 ATGTTTTACTCTTA
**
8669340 ATG-TTTA-TCTCG
1 ATGTTTTACTCTTA
8669352 ATGTTTTACTCTTA
1 ATGTTTTACTCTTA
8669366 ATGTTT
1 ATGTTT
8669372 GTTATTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 12 0.48
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (14 bp):
ATGTTTTACTCTTA
Found at i:8680084 original size:4 final size:4
Alignment explanation
Indices: 8680075--8680102 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
8680065 AAAAATATAT
8680075 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
8680103 ATCTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:8680968 original size:26 final size:25
Alignment explanation
Indices: 8680920--8680977 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
8680910 ATCGCTCCAA
*
8680920 GAAAGAGAAAATTCTTGAAAGAAATC
1 GAAAGAGAAAATTCTTG-AAGAAAAC
8680946 GAAAGAGAAATATTCTCTG-AGAAAAC
1 GAAAGAGAAA-ATTCT-TGAAGAAAAC
8680972 GAAAGA
1 GAAAGA
8680978 AGAAGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.76
27 5 0.17
28 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (25 bp):
GAAAGAGAAAATTCTTGAAGAAAAC
Found at i:8681681 original size:3 final size:3
Alignment explanation
Indices: 8681673--8681699 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8681663 GAGCAGAGCA
8681673 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
8681700 ACGGTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:8684355 original size:18 final size:18
Alignment explanation
Indices: 8684328--8684362 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8684318 CTGTAATTAG
*
8684328 TTTAAATTTTAATTTTAA
1 TTTAAATTTTAAATTTAA
*
8684346 TTTAATTTTTAAATTTA
1 TTTAAATTTTAAATTTA
8684363 GAATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTTTAAATTTAA
Found at i:8684471 original size:12 final size:12
Alignment explanation
Indices: 8684454--8684478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8684444 GGTGTTCATT
8684454 CGGTTAACCGAC
1 CGGTTAACCGAC
8684466 CGGTTAACCGAC
1 CGGTTAACCGAC
8684478 C
1 C
8684479 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:8684655 original size:9 final size:9
Alignment explanation
Indices: 8684641--8684743 Score: 143
Period size: 9 Copynumber: 11.4 Consensus size: 9
8684631 TTTGGTTAAA
8684641 AATTAACCG
1 AATTAACCG
8684650 AATTAACCG
1 AATTAACCG
*
8684659 AATTACCCG
1 AATTAACCG
8684668 AATTAACCG
1 AATTAACCG
*
8684677 AATTACCCG
1 AATTAACCG
*
8684686 AATTACCCG
1 AATTAACCG
*
8684695 AATTACCCG
1 AATTAACCG
8684704 AATTAACCG
1 AATTAACCG
*
8684713 AATTACCCG
1 AATTAACCG
*
8684722 AATTAACCA
1 AATTAACCG
*
8684731 AATTAACCA
1 AATTAACCG
8684740 AATT
1 AATT
8684744 GAATCACTAC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 87 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:8684674 original size:27 final size:27
Alignment explanation
Indices: 8684641--8684743 Score: 170
Period size: 27 Copynumber: 3.8 Consensus size: 27
8684631 TTTGGTTAAA
8684641 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
*
8684668 AATTAACCGAATTACCCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
*
8684695 AATTACCCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* *
8684722 AATTAACCAAATTAACCAAATT
1 AATTAACCGAATTAACCGAATT
8684744 GAATCACTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:8684743 original size:18 final size:18
Alignment explanation
Indices: 8684641--8684735 Score: 163
Period size: 18 Copynumber: 5.3 Consensus size: 18
8684631 TTTGGTTAAA
*
8684641 AATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
8684659 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
8684677 AATTACCCGAATTACCCG
1 AATTACCCGAATTAACCG
8684695 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
8684713 AATTACCCGAATTAACCA
1 AATTACCCGAATTAACCG
8684731 AATTA
1 AATTA
8684736 ACCAAATTGA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:8685961 original size:17 final size:17
Alignment explanation
Indices: 8685927--8685966 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
8685917 GCTTAAAAAA
*
8685927 TATTTTATTTATCCATT
1 TATTTTATTTATCAATT
* *
8685944 TATTTTATTTTTTAATT
1 TATTTTATTTATCAATT
8685961 TATTTT
1 TATTTT
8685967 TGCATTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTATTTATCAATT
Found at i:8687958 original size:17 final size:17
Alignment explanation
Indices: 8687936--8687968 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8687926 TGAATGATAC
8687936 ATTTTTTGA-ATTTTTAT
1 ATTTTTT-ATATTTTTAT
8687953 ATTTTTTATATTTTTA
1 ATTTTTTATATTTTTA
8687969 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTTTTATATTTTTAT
Found at i:8688376 original size:20 final size:18
Alignment explanation
Indices: 8688333--8688381 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
8688323 TAATATTACT
8688333 ATATTATTAATAAAATTTA
1 ATATT-TTAATAAAATTTA
*
8688352 TTATTTTAATAAATGATTTA
1 ATATTTTAATAAA--ATTTA
*
8688372 ATATTGTAAT
1 ATATTTTAAT
8688382 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATATTTTAATAAAATTTA
Found at i:8690700 original size:19 final size:19
Alignment explanation
Indices: 8690676--8690767 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
8690666 AATCTTCAGG
8690676 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8690695 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
8690714 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8690733 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8690752 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
8690768 AGATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:8690793 original size:22 final size:22
Alignment explanation
Indices: 8690676--8690790 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 22
8690666 AATCTTCAGG
8690676 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
8690695 GATATGCAATCTTAG-ATATAAT
1 GATATGCAATCTTAGAAGAT-AT
8690717 -ATAT--AATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
8690733 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
8690752 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
8690774 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
8690791 GATTTAATTT
Statistics
Matches: 82, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.02
17 7 0.09
19 44 0.54
21 7 0.09
22 10 0.12
23 12 0.15
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:8697513 original size:132 final size:132
Alignment explanation
Indices: 8696606--8697499 Score: 1551
Period size: 132 Copynumber: 6.8 Consensus size: 132
8696596 TTGACAGCGA
* * *
8696606 AGCAGATCGAAGATGGCGGATTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCCATTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
8696671 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8696736 GG
131 GG
* * *
8696738 AGCAGATCGAAGATGGTGGATTTTACCT-CATGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
8696802 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8696867 GG
131 GG
* * *
8696869 AGCAGATCGAAGATGGCAGATTTTACCTCTCTGTGGTTACACTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
8696934 TCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8696999 GG
131 GG
* *
8697001 AGCAGGTCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
8697066 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8697131 GG
131 GG
8697133 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
8697198 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8697263 GG
131 GG
8697265 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
8697330 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
8697395 GT
131 GG
*
8697397 AGCAGATCGAAGATGGCGGATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
8697461 TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
8697500 GTAAGTCCTA
Statistics
Matches: 729, Mismatches: 30, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
131 128 0.18
132 601 0.82
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:8697851 original size:19 final size:19
Alignment explanation
Indices: 8697827--8697937 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
8697817 AATCTTCAGG
8697827 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8697846 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
8697865 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8697884 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
8697903 GGTATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
8697922 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
8697938 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:8697877 original size:38 final size:38
Alignment explanation
Indices: 8697834--8697937 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
8697824 AGGGATATGC
8697834 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
**
8697872 AATCTTAGATATGATATGCAATCTTAGATATGGTATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
8697910 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
8697938 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:8697963 original size:22 final size:21
Alignment explanation
Indices: 8697827--8697963 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
8697817 AATCTTCAGG
*
8697827 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
8697846 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
8697865 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
8697884 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
8697903 GGTATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
8697922 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
8697944 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
8697964 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 77 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:8701016 original size:143 final size:143
Alignment explanation
Indices: 8700829--8701116 Score: 576
Period size: 143 Copynumber: 2.0 Consensus size: 143
8700819 CTTAAAAACA
8700829 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
1 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
8700894 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
66 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
8700959 TAAGCAAAAAGGT
131 TAAGCAAAAAGGT
8700972 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
1 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
8701037 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
66 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
8701102 TAAGCAAAAAGGT
131 TAAGCAAAAAGGT
8701115 GG
1 GG
8701117 GTAACCCAGC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 145 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (143 bp):
GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
TAAGCAAAAAGGT
Found at i:8705362 original size:14 final size:14
Alignment explanation
Indices: 8705329--8705362 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8705319 TAATCCTGAA
*
8705329 CCCAAACTTTAAAC
1 CCCAAACCTTAAAC
*
8705343 CTCAAACCTTAAAC
1 CCCAAACCTTAAAC
8705357 CCCAAA
1 CCCAAA
8705363 TGCAAAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CCCAAACCTTAAAC
Found at i:8706521 original size:20 final size:19
Alignment explanation
Indices: 8706507--8706546 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8706497 ATTATTTTGC
8706507 TTATATATTTTTTATTTTA
1 TTATATATTTTTTATTTTA
*
8706526 TTTTATATTTTTATATTTTA
1 TTATATATTTTT-TATTTTA
8706546 T
1 T
8706547 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATATATTTTTTATTTTA
Found at i:8706539 original size:8 final size:8
Alignment explanation
Indices: 8706526--8706554 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8706516 TTTTATTTTA
8706526 TTTTATAT
1 TTTTATAT
8706534 TTTTATA-
1 TTTTATAT
8706541 TTTTATAT
1 TTTTATAT
8706549 TTTTAT
1 TTTTAT
8706555 TTATCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:8706544 original size:15 final size:15
Alignment explanation
Indices: 8706524--8706554 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8706514 TTTTTTATTT
8706524 TATTTTATATTTTTA
1 TATTTTATATTTTTA
8706539 TATTTTATATTTTTA
1 TATTTTATATTTTTA
8706554 T
1 T
8706555 TTATCCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATATTTTTA
Found at i:8706661 original size:19 final size:18
Alignment explanation
Indices: 8706633--8706674 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
8706623 TTTATATATA
*
8706633 TATTTTTATATTTTCATT
1 TATTTCTATATTTTCATT
*
8706651 TCATTTCTATATTTTTATT
1 T-ATTTCTATATTTTCATT
8706670 TATTT
1 TATTT
8706675 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTCTATATTTTCATT
Found at i:8711012 original size:2 final size:2
Alignment explanation
Indices: 8710949--8711000 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
8710939 AATTATAAGA
*
8710949 AT AT AT AG A- 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
8710990 AT AT AT AT AT A
1 AT AT AT AT AT A
8711001 AGTATGTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:8711303 original size:3 final size:3
Alignment explanation
Indices: 8711295--8711339 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
8711285 AACGATACTT
* *
8711295 ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8711340 GAAAAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:8711315 original size:15 final size:15
Alignment explanation
Indices: 8711297--8711344 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
8711287 CGATACTTAT
8711297 AATAATAATAATAAA
1 AATAATAATAATAAA
**
8711312 AATAATAATAATAGT
1 AATAATAATAATAAA
8711327 AATAATAATAATAGAA
1 AATAATAATAATA-AA
8711343 AA
1 AA
8711345 AAAGATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 26 0.93
16 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:8713707 original size:14 final size:14
Alignment explanation
Indices: 8713688--8713724 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8713678 TACAATATCC
8713688 AAATAGTAACAACA
1 AAATAGTAACAACA
*
8713702 AAATAGTAGCAACA
1 AAATAGTAACAACA
*
8713716 TAATAGTAA
1 AAATAGTAA
8713725 AATAGTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:8713739 original size:11 final size:11
Alignment explanation
Indices: 8713700--8713740 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
8713690 ATAGTAACAA
8713700 CAAAATAGTAG
1 CAAAATAGTAG
* *
8713711 CAACATAATAG
1 CAAAATAGTAG
*
8713722 TAAAATAGTAG
1 CAAAATAGTAG
8713733 CAAAATAG
1 CAAAATAG
8713741 AAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:8713748 original size:22 final size:22
Alignment explanation
Indices: 8713701--8713750 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
8713691 TAGTAACAAC
* *
8713701 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAAAGT
8713723 AAAATAGTAGCAAAATAGAAAG-
1 AAAATAGTAGCAAAATA-AAAGT
8713745 AAAATA
1 AAAATA
8713751 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAAAGT
Found at i:8716860 original size:3 final size:3
Alignment explanation
Indices: 8716852--8716886 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8716842 AATCCAGAAT
8716852 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
8716887 TTAATTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:8719059 original size:16 final size:16
Alignment explanation
Indices: 8719038--8719071 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
8719028 TTAGATTCTT
8719038 TTTTTCTACTT-TTATA
1 TTTTTCTA-TTATTATA
8719054 TTTTTCTATTATTATA
1 TTTTTCTATTATTATA
8719070 TT
1 TT
8719072 AATTTAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCTATTATTATA
Found at i:8719340 original size:20 final size:20
Alignment explanation
Indices: 8719315--8719377 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
8719305 AATTTTAATA
*
8719315 AAAAATTAGAAAAAAATTAT
1 AAAAATTAGTAAAAAATTAT
* **
8719335 AAAAATTTGTAAAACTTTAT
1 AAAAATTAGTAAAAAATTAT
*
8719355 AAAAATCA-TAAAAAATTAT
1 AAAAATTAGTAAAAAATTAT
8719374 AAAA
1 AAAA
8719378 TACATAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATTAGTAAAAAATTAT
Found at i:8719347 original size:10 final size:10
Alignment explanation
Indices: 8719285--8719377 Score: 55
Period size: 10 Copynumber: 9.3 Consensus size: 10
8719275 AAAAATCAAT
*
8719285 AAAAGTTATA
1 AAAATTTATA
* *
8719295 CAAA-TTATT
1 AAAATTTATA
*
8719304 AAATTTTAATA
1 AAAATTT-ATA
* *
8719315 AAAAATTAGAA
1 AAAATTTA-TA
*
8719326 AAAAATTATA
1 AAAATTTATA
*
8719336 AAAATTTGTA
1 AAAATTTATA
*
8719346 AAACTTTATA
1 AAAATTTATA
*
8719356 AAAA-TCATA
1 AAAATTTATA
*
8719365 AAAAATTATA
1 AAAATTTATA
8719375 AAA
1 AAA
8719378 TACATAAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
9 14 0.22
10 33 0.52
11 16 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTTATA
Found at i:8719366 original size:19 final size:19
Alignment explanation
Indices: 8719351--8719388 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
8719341 TTGTAAAACT
8719351 TTATAAAA-ATCATAAAAAA
1 TTATAAAATA-CATAAAAAA
8719370 TTATAAAATACATAAAAAA
1 TTATAAAATACATAAAAAA
8719389 AATCCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TTATAAAATACATAAAAAA
Found at i:8719517 original size:10 final size:9
Alignment explanation
Indices: 8719490--8719532 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
8719480 ACATGTGGTG
8719490 AAAAATAAT
1 AAAAATAAT
8719499 AAAAA-AAT
1 AAAAATAAT
8719507 AAAAATCAAT
1 AAAAAT-AAT
8719517 AAAAAATAAT
1 -AAAAATAAT
8719527 AGAAAA
1 A-AAAA
8719533 ATTATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.27
9 6 0.20
10 10 0.33
11 6 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAATAAT
Found at i:8719645 original size:10 final size:10
Alignment explanation
Indices: 8719602--8719697 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 10
8719592 TTTCTTTACA
8719602 TTTTTATAAT
1 TTTTTATAAT
8719612 TTTCTTATAA-
1 TTT-TTATAAT
* *
8719622 -CTTTATAAA
1 TTTTTATAAT
*
8719631 ATTTTATAAT
1 TTTTTATAAT
8719641 TTTTT-TAAGAT
1 TTTTTAT-A-AT
8719652 TTTTTATAAT
1 TTTTTATAAT
*
8719662 TATTTT-TACT
1 T-TTTTATAAT
*
8719672 ATTTTTATATTT
1 -TTTTTATA-AT
*
8719684 TTTTTCTAAT
1 TTTTTATAAT
8719694 TTTT
1 TTTT
8719698 AATTTTTAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.09
9 2 0.03
10 30 0.44
11 28 0.41
12 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:8719647 original size:21 final size:22
Alignment explanation
Indices: 8719629--8719669 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8719619 TAACTTTATA
8719629 AAATTTTATAATT-TTTTTAAG
1 AAATTTTATAATTATTTTTAAG
**
8719650 ATTTTTTATAATTATTTTTA
1 AAATTTTATAATTATTTTTA
8719670 CTATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
AAATTTTATAATTATTTTTAAG
Found at i:8719667 original size:12 final size:11
Alignment explanation
Indices: 8719632--8719697 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
8719622 CTTTATAAAA
8719632 TTTTATAATTT
1 TTTTATAATTT
8719643 TTTTA-AGA-TT
1 TTTTATA-ATTT
*
8719653 TTTTATAATTA
1 TTTTATAATTT
* *
8719664 TTTT-TACTAT
1 TTTTATAATTT
*
8719674 TTTTATATTTT
1 TTTTATAATTT
*
8719685 TTTTCTAATTT
1 TTTTATAATTT
8719696 TT
1 TT
8719698 AATTTTTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
10 16 0.37
11 27 0.63
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:8719676 original size:21 final size:20
Alignment explanation
Indices: 8719632--8719704 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 20
8719622 CTTTATAAAA
**
8719632 TTTTATAATTTTTTTAAGATT
1 TTTTATAATTTTTTTACTA-T
8719653 TTTTATAATTATTTTTACTAT
1 TTTTATAATT-TTTTTACTAT
* *
8719674 TTTTAT-ATTTTTTTTCTAA
1 TTTTATAATTTTTTTACTAT
8719693 TTTT-TAATTTTT
1 TTTTATAATTTTT
8719705 AATATATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.02
19 18 0.39
20 3 0.07
21 17 0.37
22 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (20 bp):
TTTTATAATTTTTTTACTAT
Found at i:8719727 original size:26 final size:25
Alignment explanation
Indices: 8719698--8719767 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
8719688 TCTAATTTTT
8719698 AATTTTTAATATATTATTTTTTTAAA
1 AATTTTTAATATATTATTTTTTT-AA
* *
8719724 AATTTCTAATTTAATTA-TTTTTTAA
1 AATTTTTAATAT-ATTATTTTTTTAA
*
8719749 AATTTTTTATATATT-TTTT
1 AATTTTTAATATATTATTTT
8719768 CTGATTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 6 0.16
25 11 0.30
26 16 0.43
27 4 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (25 bp):
AATTTTTAATATATTATTTTTTTAA
Found at i:8719806 original size:29 final size:28
Alignment explanation
Indices: 8719753--8719851 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
8719743 TTTTAAAATT
* * **
8719753 TTTTATATATTTTTTCTGATTTTTAATA
1 TTTTATATATTTTTTATTAAATTTAATA
*
8719781 TTTTATATATTTTTTATTAAAATTTATTCA
1 TTTTATATATTTTTTATT-AAATTTAAT-A
** * * *
8719811 TTTT-TATAACTTTTATTGATTTTTATA
1 TTTTATATATTTTTTATTAAATTTAATA
8719838 TTTTATCATATTTT
1 TTTTAT-ATATTTT
8719852 AGCCACATAT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
27 5 0.09
28 22 0.41
29 22 0.41
30 5 0.09
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTTATATATTTTTTATTAAATTTAATA
Found at i:8720620 original size:31 final size:32
Alignment explanation
Indices: 8720585--8720651 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
8720575 TTACAATTTG
*
8720585 GTCAC-TGAACTATTCGAAAGTTTTCATTTAA
1 GTCACTTGAACTATTCAAAAGTTTTCATTTAA
* *
8720616 GTCACTTTAACTATTCAAAAGTTTTTATTTAA
1 GTCACTTGAACTATTCAAAAGTTTTCATTTAA
8720648 GTCA
1 GTCA
8720652 TTAGATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (32 bp):
GTCACTTGAACTATTCAAAAGTTTTCATTTAA
Found at i:8728856 original size:101 final size:102
Alignment explanation
Indices: 8728739--8728923 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
8728729 AAAGTGATGG
8728739 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGATAATGGTCGCATGTGTAGT
* *
8728802 ACTATGTGCAGGCTACTATGCGTACTGGATAGTTTCGA
65 ACTATGTGCAAGATACTATGCGTACTGGATAGTTTCGA
* *
8728840 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGTAATGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCGCATGTGTAGTA
8728905 CTATGTGCAAGATACTATG
66 CTATGTGCAAGATACTATG
8728924 TGAACCAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCGCATGTGTAGTA
CTATGTGCAAGATACTATGCGTACTGGATAGTTTCGA
Found at i:8728921 original size:51 final size:50
Alignment explanation
Indices: 8728735--8728913 Score: 209
Period size: 51 Copynumber: 3.5 Consensus size: 50
8728725 AGTGAAAGTG
* * *
8728735 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTG-ATGGT
* * * *
8728786 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CTGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCT-GATGGT
* * *
8728835 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
*
8728886 AATGGTCGCATGTGTAGTACTATGTGCA
1 -ATGGTCACATGTGTAGTACTATGTGCA
8728914 AGATACTATG
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
49 4 0.04
50 36 0.34
51 62 0.59
52 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
Found at i:8728996 original size:45 final size:45
Alignment explanation
Indices: 8728932--8729018 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
8728922 TGTGAACCAA
*
8728932 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCCACTGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
8728977 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
8729019 CGAGTATCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
Found at i:8735653 original size:21 final size:22
Alignment explanation
Indices: 8735627--8735671 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8735617 CCGAAATTAT
8735627 TAAAAAAAAAA-CAATCAAGTC
1 TAAAAAAAAAACCAATCAAGTC
8735648 TAAAAAAAAAACCAATCAAGTC
1 TAAAAAAAAAACCAATCAAGTC
8735670 TA
1 TA
8735672 TATCTTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (22 bp):
TAAAAAAAAAACCAATCAAGTC
Found at i:8740855 original size:22 final size:22
Alignment explanation
Indices: 8740808--8740855 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
8740798 ATCGTAATTC
*
8740808 GAAGTGGGTATCGTGAAACCGC
1 GAAGTGGGTATCGTGAAACCGA
* * *
8740830 GAAGTGGGTATTGTGATATCGA
1 GAAGTGGGTATCGTGAAACCGA
8740852 GAAG
1 GAAG
8740856 CCAAGACCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.23
Consensus pattern (22 bp):
GAAGTGGGTATCGTGAAACCGA
Found at i:8742461 original size:12 final size:12
Alignment explanation
Indices: 8742444--8742468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8742434 TGTGTATTTC
8742444 ATTAATTTTATA
1 ATTAATTTTATA
8742456 ATTAATTTTATA
1 ATTAATTTTATA
8742468 A
1 A
8742469 ATTATAAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAATTTTATA
Found at i:8742513 original size:16 final size:16
Alignment explanation
Indices: 8742494--8742526 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8742484 TTTTATTTTT
8742494 TTGAA-TTTTTATATAC
1 TTGAACTTTTTA-ATAC
8742510 TTGAACTTTTTAATAC
1 TTGAACTTTTTAATAC
8742526 T
1 T
8742527 ATTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (16 bp):
TTGAACTTTTTAATAC
Found at i:8745535 original size:22 final size:22
Alignment explanation
Indices: 8745482--8745526 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8745472 AAAATAAATC
* * *
8745482 AAAATTTATCAAAATTAATTAT
1 AAAATTAATTAAAATTAAATAT
8745504 AAAATTAATTAAAATTAAATAT
1 AAAATTAATTAAAATTAAATAT
8745526 A
1 A
8745527 TTAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTAATTAAAATTAAATAT
Found at i:8754094 original size:30 final size:31
Alignment explanation
Indices: 8754058--8754117 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
8754048 AGTTAATACT
* **
8754058 AAAAAATTGAGGGGTTAA-AGTGTAAATATG
1 AAAAAATTGAAGGACTAATAGTGTAAATATG
8754088 AAAAAATTGAAGGACTAATAGTGTAAATAT
1 AAAAAATTGAAGGACTAATAGTGTAAATAT
8754118 TTTAAGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAAAATTGAAGGACTAATAGTGTAAATATG
Found at i:8756292 original size:51 final size:51
Alignment explanation
Indices: 8756209--8756474 Score: 430
Period size: 51 Copynumber: 5.3 Consensus size: 51
8756199 ACTTCTGATC
8756209 AGTGACAAGTGATAAGTG-TAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
8756259 AGTGGCAAGTGATAAGTGATAGCTTCAGTTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
8756310 AGTGACAAGTGATAAGT-AGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
8756361 AGTGGCAAGTGATAAGTGATAGCTTCAGTTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
8756412 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
*
8756462 AGTGATAAGTGAT
1 AGTGACAAGTGAT
8756475 CATACGTAAG
Statistics
Matches: 202, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 52 0.26
51 149 0.74
52 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:8759688 original size:59 final size:61
Alignment explanation
Indices: 8759609--8759726 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 61
8759599 AATTACTTTA
* * *
8759609 ATATTAAATTAATATGATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATT
1 ATATTAAATTAAGATGATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATT
*
8759668 ATATTAAATTAAGA-GAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAA
1 ATATTAAATTAAGATG-ATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
8759727 GATAATAACT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 20 0.39
61 1 0.02
62 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (61 bp):
ATATTAAATTAAGATGATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATT
Found at i:8759750 original size:25 final size:24
Alignment explanation
Indices: 8759711--8759777 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
8759701 AAACATTAAA
*
8759711 TTTAAT-TTAATATTAAGATAATAAC
1 TTTAATATTAA-ATTAAGAAAAT-AC
*
8759736 TTTAATATTAAATTAATAAAATAC
1 TTTAATATTAAATTAAGAAAATAC
8759760 TATTAAGTATTAAATTAA
1 T-TTAA-TATTAAATTAA
8759778 ATTTAATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.08
25 19 0.51
26 15 0.41
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (24 bp):
TTTAATATTAAATTAAGAAAATAC
Found at i:8759752 original size:20 final size:19
Alignment explanation
Indices: 8759705--8759791 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
8759695 CAAGATAAAC
8759705 ATTAAATT--TAATTTAAT
1 ATTAAATTAATAATTTAAT
8759722 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
** *
8759742 ATTAAATTAATAAAATACT
1 ATTAAATTAATAATTTAAT
8759761 ATTAAGTATTAAATTAAATTTAAT
1 ATTAA--ATT-AA-T-AATTTAAT
8759785 ATTAAAT
1 ATTAAAT
8759792 CTATTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
17 6 0.11
18 1 0.02
19 12 0.22
20 17 0.31
21 3 0.06
22 4 0.07
23 1 0.02
24 10 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:8762327 original size:45 final size:44
Alignment explanation
Indices: 8762223--8762360 Score: 179
Period size: 45 Copynumber: 3.1 Consensus size: 44
8762213 TCCAAACACT
* * * *
8762223 CCAA-ATTTGCAGACAAGCTGTCATGTAGGTTGTGGATAAACCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGAGAAGCCA
*
8762266 CCAAAATTCGCAGACAAGCTGCCATGTAGGTTGTGGACGAAGCCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGA-GAAGCCA
* * *
8762311 CCAATATTCGCAGACAAGCTACCATGTAGGTTGTAGATGAAGGCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGA-GAAGCCA
8762356 CCAAT
1 CCAAT
8762361 TCTTTCTCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
43 4 0.05
44 30 0.36
45 50 0.60
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (44 bp):
CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGAGAAGCCA
Found at i:8766340 original size:3 final size:3
Alignment explanation
Indices: 8766332--8766357 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8766322 TAATTAAATC
8766332 ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA AC
8766358 TAATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:8770888 original size:33 final size:35
Alignment explanation
Indices: 8770851--8770948 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
8770841 ATGGTTATAT
8770851 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTACTTAA
* *
8770884 TTAAAT-TTTATAA-ATAATTAATATTTATTACTTAA
1 TTAAATATTTAAAATATAATT--TATATATTACTTAA
*
8770919 --AAATATTTAAAATTTATATTTCATATATTA
1 TTAAATATTTAAAATATA-ATTT-ATATATTA
8770949 AAATATTAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.15
35 12 0.23
36 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTACTTAA
Found at i:8770938 original size:30 final size:30
Alignment explanation
Indices: 8770899--8770955 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
8770889 TTTTATAAAT
8770899 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
8770929 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
8770956 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:8773294 original size:22 final size:22
Alignment explanation
Indices: 8773263--8773348 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
8773253 TAGGTCGAAA
* * *
8773263 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
8773285 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
**
8773307 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
*
8773329 TCACGTACTAAGCTCTCATG
1 TAACGTACTAAGCTCTCATG
8773349 TCTAGGGGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:8776361 original size:25 final size:25
Alignment explanation
Indices: 8776329--8776472 Score: 82
Period size: 25 Copynumber: 5.9 Consensus size: 25
8776319 AGCCCTCTCT
8776329 CGAGCCATATAACGGGAAGCTCATA
1 CGAGCCATATAACGGGAAGCTCATA
* * * * * *
8776354 TGAGCCATGTGACGGAAAGCTTATC
1 CGAGCCATATAACGGGAAGCTCATA
* * * ** *
8776379 CGGGCTATCTAACGAAAAGCTCAAA
1 CGAGCCATATAACGGGAAGCTCATA
* * *
8776404 AGAGCCATA-ATCGGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATA
*
8776428 CGAGCCA-ATAACGGGTAGCTTCGA-A
1 CGAGCCATATAACGGGAAGC-TC-ATA
*
8776453 -GAGCTAT-TAACGGGAAGCTC
1 CGAGCCATATAACGGGAAGCTC
8776473 CTGATAGCCA
Statistics
Matches: 85, Mismatches: 30, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
23 3 0.04
24 39 0.46
25 42 0.49
26 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTCATA
Found at i:8776572 original size:26 final size:26
Alignment explanation
Indices: 8776502--8776576 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
8776492 AAGTTCAAGC
8776502 GAGCCATAT--CGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* *
8776526 GAGCC-TTTAACCAGGAAGCTCA-AGAA
1 GAGCCATATAA-CGGGAAGCTCACA-AA
*
8776552 GAGCCATATAACGGGATGCTCACAA
1 GAGCCATATAACGGGAAGCTCACAA
8776577 GTGCTGCGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.05
24 5 0.12
25 1 0.03
26 27 0.68
27 5 0.12
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:8781964 original size:15 final size:15
Alignment explanation
Indices: 8781946--8781976 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8781936 TGACATCAGT
8781946 GATCACGTCATCGAG
1 GATCACGTCATCGAG
8781961 GATCACGTCATCGAG
1 GATCACGTCATCGAG
8781976 G
1 G
8781977 CAACACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (15 bp):
GATCACGTCATCGAG
Found at i:8794369 original size:17 final size:16
Alignment explanation
Indices: 8794349--8794380 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
8794339 TATGGAGTAA
8794349 TTTCTTTTTCTTTTTTT
1 TTTCTTTTT-TTTTTTT
8794366 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
8794381 GTTTAGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:8794380 original size:12 final size:11
Alignment explanation
Indices: 8794353--8794379 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
8794343 GAGTAATTTC
8794353 TTTTTCTTTTT
1 TTTTTCTTTTT
8794364 TTTTTCTTTTT
1 TTTTTCTTTTT
8794375 TTTTT
1 TTTTT
8794380 TGTTTAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:8795880 original size:18 final size:19
Alignment explanation
Indices: 8795838--8795880 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
8795828 TCTGCTTCAA
*
8795838 TTTAATTTTTACTAATTATT
1 TTTAATTTTTA-TAAATATT
*
8795858 ATTAATTTTT-TAAATATT
1 TTTAATTTTTATAAATATT
8795876 TTTAA
1 TTTAA
8795881 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATTTTTATAAATATT
Found at i:8796571 original size:21 final size:21
Alignment explanation
Indices: 8796546--8796616 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
8796536 GTTTTTAAGG
8796546 TTAGGGTTTTGTTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
** *** ***
8796567 TTAGGGTTAAGTTTGTAGGGT
1 TTAGGGTTTTGTTAAAATAAT
8796588 TTAGGGTTTTGTTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
*
8796609 TTAAGGTT
1 TTAGGGTT
8796617 CAAGGTTTTA
Statistics
Matches: 33, Mismatches: 17, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTGTTAAAATAAT
Found at i:8796711 original size:34 final size:34
Alignment explanation
Indices: 8796666--8796757 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
8796656 GTTCCTTTTT
8796666 AAAAATTAATTAAATTAGGGTTTAG-GGGTTTAA
1 AAAAATTAATTAAATTAGGGTTTAGTGGGTTTAA
* **
8796699 AATAAATTAATTAAATTTGGGTTTAGTGTTTTTAA
1 AA-AAATTAATTAAATTAGGGTTTAGTGGGTTTAA
*
8796734 GAAAATTAATTAAATTTA-GGTTTA
1 AAAAATTAATTAAA-TTAGGGTTTA
8796758 TTTTTAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.04
34 40 0.78
35 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.42
Consensus pattern (34 bp):
AAAAATTAATTAAATTAGGGTTTAGTGGGTTTAA
Found at i:8797105 original size:126 final size:126
Alignment explanation
Indices: 8796831--8797286 Score: 672
Period size: 126 Copynumber: 3.6 Consensus size: 126
8796821 GGATTTTGGT
* * *
8796831 TTTTTCTACAATAGTTCCT-AAAAAATAATTTTGAGAATACGGTTCTGAACAAATAGTGTC-AAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
* ** * * *
8796894 ACGCTTCAAACAGGATGCACGGTCAGC-AAATT-ACT-AGAAAAAGCTCTCACGTG-GTCGCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGA-TGA-AAAAAGCTCCCACGTGAAT-GTTC
* *
8796954 TTTTTCTATAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
8797019 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
* * *
8797080 TTTTTCTACAGTAGTTACTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
* *
8797145 ACACTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAACGTTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
* *
8797206 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGTTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
*
8797271 ACGTTTCAAGCAGGAT
66 ACGCTTCAAGCAGGAT
8797287 TTACGTGGAC
Statistics
Matches: 305, Mismatches: 22, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
123 17 0.06
124 39 0.13
125 27 0.09
126 219 0.72
127 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
Found at i:8798883 original size:18 final size:17
Alignment explanation
Indices: 8798846--8798897 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
8798836 CTAAAGGACG
* *
8798846 ACAAATAATCGATAAAT
1 ACAAATAAGCAATAAAT
8798863 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATA-AAT
*
8798881 ACACATGAGAGCAATAA
1 ACAAAT-A-AGCAATAA
8798898 TCTCACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 2 0.07
20 7 0.24
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (17 bp):
ACAAATAAGCAATAAAT
Found at i:8799608 original size:23 final size:25
Alignment explanation
Indices: 8799572--8799617 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
8799562 AAAAAATAAA
*
8799572 ATAATACATTATAA-AAT-TAAACG
1 ATAATACATGATAATAATATAAACG
*
8799595 ATAATATATGATAATAATATAAA
1 ATAATACATGATAATAATATAAA
8799618 ACTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 3 0.16
25 4 0.21
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
ATAATACATGATAATAATATAAACG
Found at i:8799639 original size:30 final size:32
Alignment explanation
Indices: 8799572--8799650 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 32
8799562 AAAAAATAAA
8799572 ATAATACATTATAAAA-TTAAACGATAATATATG
1 ATAATACA-TATAAAACTTAAAC-ATAATATATG
8799605 ATAATA-ATATAAAACTTAAA-ATAATAGTAT-
1 ATAATACATATAAAACTTAAACATAATA-TATG
*
8799635 ATAATAGA-ATAAAACT
1 ATAATACATATAAAACT
8799651 ATGTATATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
30 20 0.47
31 11 0.26
32 6 0.14
33 6 0.14
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (32 bp):
ATAATACATATAAAACTTAAACATAATATATG
Found at i:8799708 original size:3 final size:3
Alignment explanation
Indices: 8799692--8799748 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
8799682 ACTAATATAG
* * * *
8799692 TAA TAA T-A TCAA TAA TAA TAA TAT TAG TAA TAA TAA TGA TAA TGA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8799737 TAA TAA TAA TAA
1 TAA TAA TAA TAA
8799749 ATTAATTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:8799758 original size:21 final size:20
Alignment explanation
Indices: 8799702--8799771 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 20
8799692 TAATAATATC
8799702 AATAATAATAATATT-A-G-T
1 AATAATAATAA-ATTAATGAT
*
8799720 AATAATAAT-GA-TAATGAT
1 AATAATAATAAATTAATGAT
8799738 AATAATAATAAATTAATTGAT
1 AATAATAATAAATTAA-TGAT
8799759 AA-AATAAATAAAT
1 AATAAT-AATAAAT
8799772 AACAAAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
15 1 0.02
16 2 0.05
17 1 0.02
18 19 0.44
19 1 0.02
20 6 0.14
21 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
AATAATAATAAATTAATGAT
Found at i:8799823 original size:12 final size:12
Alignment explanation
Indices: 8799806--8799830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8799796 AAACTTAATT
8799806 AACAGGAAACAA
1 AACAGGAAACAA
8799818 AACAGGAAACAA
1 AACAGGAAACAA
8799830 A
1 A
8799831 CGAAATTAAA
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:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (12 bp):
AACAGGAAACAA
Found at i:8800253 original size:36 final size:37
Alignment explanation
Indices: 8800191--8800260 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
8800181 CCAAATATAA
*
8800191 TAAATATATATTTTTATTTTAAA-TTTTAAAATACTT
1 TAAAAATATATTTTTATTTTAAATTTTTAAAATACTT
**
8800227 TAAAAATAT-TTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTA-TTTTAAATTTTTAAAATA
8800261 TTTTTTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 13 0.45
37 10 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (37 bp):
TAAAAATATATTTTTATTTTAAATTTTTAAAATACTT
Found at i:8803488 original size:26 final size:27
Alignment explanation
Indices: 8803459--8803531 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
8803449 TATTCAAAAG
8803459 AAATTTTATTTTATTAAAAAATATAAA
1 AAATTTTATTTTATTAAAAAATATAAA
* * * *
8803486 AATAATTTA--CTATTAAAATATTTAAA
1 AA-ATTTTATTTTATTAAAAAATATAAA
8803512 ACAACTTTTATTTTATTAAA
1 A-AA-TTTTATTTTATTAAA
8803532 TGAAACAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
26 16 0.46
27 7 0.20
28 5 0.14
29 7 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATTTTATTTTATTAAAAAATATAAA
Found at i:8803619 original size:21 final size:21
Alignment explanation
Indices: 8803593--8803637 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
8803583 TAGTTCAGCT
*
8803593 TCCGGTGAGGGTTGTGGTTGC
1 TCCGGTGAGGGTTGTGGTTCC
8803614 TCCGGTGAGGGTTGTGGTTCC
1 TCCGGTGAGGGTTGTGGTTCC
8803635 TCC
1 TCC
8803638 TGTTGTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.20, G:0.42, T:0.33
Consensus pattern (21 bp):
TCCGGTGAGGGTTGTGGTTCC
Found at i:8805915 original size:18 final size:18
Alignment explanation
Indices: 8805892--8805927 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8805882 GGAAAAGCAA
*
8805892 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
8805910 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
8805928 GCGTACCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:8807625 original size:30 final size:30
Alignment explanation
Indices: 8807591--8807649 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
8807581 AATTAAAGAG
8807591 AGCTTTGAGAAATTGAAAGAAAAATTTGAA
1 AGCTTTGAGAAATTGAAAGAAAAATTTGAA
* * *
8807621 AGCTTTGAGAAATTTAGAGAGAAATTTGA
1 AGCTTTGAGAAATTGAAAGAAAAATTTGA
8807650 GAGTTTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (30 bp):
AGCTTTGAGAAATTGAAAGAAAAATTTGAA
Found at i:8807664 original size:30 final size:29
Alignment explanation
Indices: 8807591--8807676 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
8807581 AATTAAAGAG
*
8807591 AGCTTTGAGAAATTGA-AAGAAAAATTTGAA
1 AGCTTTGAGAAATTTAGAAG--AAATTTGAA
*
8807621 AGCTTTGAGAAATTTAGAGAGAAATTTGAG
1 AGCTTTGAGAAATTTAGA-AGAAATTTGAA
* ** *
8807651 AGTTTTGCTAAATTTTGAAGAAATTT
1 AGCTTTGAGAAATTTAGAAGAAATTT
8807677 TGTGTACAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 8 0.17
30 37 0.77
31 1 0.02
32 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
AGCTTTGAGAAATTTAGAAGAAATTTGAA
Found at i:8808302 original size:19 final size:17
Alignment explanation
Indices: 8808278--8808327 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
8808268 TTTTCTTTTT
8808278 TTCTCATTTATTTCTCAC
1 TTCTCATTTATTT-TCAC
* *
8808296 TTACTCATGTATTTTTAC
1 TT-CTCATTTATTTTCAC
*
8808314 TTTTCATTTATTTT
1 TTCTCATTTATTTT
8808328 ATTTTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 10 0.37
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (17 bp):
TTCTCATTTATTTTCAC
Found at i:8808339 original size:23 final size:23
Alignment explanation
Indices: 8808307--8808368 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
8808297 TACTCATGTA
*
8808307 TTTTTACTTTTCATTTATTTTAT
1 TTTTTTCTTTTCATTTATTTTAT
* *
8808330 TTTTTTCTTTTC-TTCTCTTTTCT
1 TTTTTTCTTTTCATT-TATTTTAT
8808353 TTCTTTT-TTTTCATTT
1 TT-TTTTCTTTTCATTT
8808369 TGAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 25 0.76
24 6 0.18
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTCTTTTCATTTATTTTAT
Found at i:8810990 original size:13 final size:13
Alignment explanation
Indices: 8810972--8810998 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8810962 AAAACAATGG
8810972 AAAAAATAGAGAA
1 AAAAAATAGAGAA
8810985 AAAAAATAGAGAA
1 AAAAAATAGAGAA
8810998 A
1 A
8810999 TGAGAAACAT
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:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAATAGAGAA
Found at i:8814106 original size:14 final size:14
Alignment explanation
Indices: 8814087--8814118 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8814077 TCAAGCAAAG
8814087 TAGTGTATTTTCCA
1 TAGTGTATTTTCCA
8814101 TAGTGTATTTTCCA
1 TAGTGTATTTTCCA
8814115 TAGT
1 TAGT
8814119 TTTTGGTAAT
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:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (14 bp):
TAGTGTATTTTCCA
Found at i:8815360 original size:20 final size:20
Alignment explanation
Indices: 8815320--8815359 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
8815310 TTCTTTAAAA
8815320 TAAAAATGAATGTCAAATTT
1 TAAAAATGAATGTCAAATTT
8815340 TAAAAAT-ATATGTC-AATTT
1 TAAAAATGA-ATGTCAAATTT
8815359 T
1 T
8815360 TGGGGGGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (20 bp):
TAAAAATGAATGTCAAATTT
Found at i:8817982 original size:21 final size:22
Alignment explanation
Indices: 8817943--8818000 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
8817933 CTCAAAAGTA
* * * *
8817943 AATAATTTTAATATCTAGATAT
1 AATATTTTTTATATCTAGAAAG
*
8817965 TATATTTTTTATAT-TAGAAAG
1 AATATTTTTTATATCTAGAAAG
8817986 AATATTGTTTTATAT
1 AATATT-TTTTATAT
8818001 AATTATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
AATATTTTTTATATCTAGAAAG
Found at i:8823397 original size:15 final size:17
Alignment explanation
Indices: 8823374--8823416 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
8823364 TAACCATAAT
8823374 TAATATATTAAT-AAATA
1 TAAT-TATTAATAAAATA
8823391 -AATTATTAAATAAAATA
1 TAATTATT-AATAAAATA
8823408 TAATTATTA
1 TAATTATTA
8823417 TAATTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 6 0.26
17 6 0.26
18 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTATTAATAAAATA
Found at i:8827950 original size:16 final size:15
Alignment explanation
Indices: 8827925--8827954 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
8827915 TCGTACTTTC
8827925 ATAGATATTAATTAT
1 ATAGATATTAATTAT
8827940 ATAGCATATTAATTA
1 ATAG-ATATTAATTA
8827955 GTTAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
ATAGATATTAATTAT
Found at i:8827964 original size:16 final size:16
Alignment explanation
Indices: 8827925--8827965 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
8827915 TCGTACTTTC
8827925 ATAG-ATATTAATTAT
1 ATAGAATATTAATTAT
*
8827940 ATAGCATATTAATTAGT
1 ATAGAATATTAATTA-T
8827957 -TAGAATATT
1 ATAGAATATT
8827966 TATAGATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (16 bp):
ATAGAATATTAATTAT
Found at i:8828318 original size:22 final size:22
Alignment explanation
Indices: 8828293--8828337 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
8828283 CTCTAATTTA
*
8828293 TTAGCACATCGGTGCTCTCTGT
1 TTAGCACATCGGAGCTCTCTGT
*
8828315 TTAGCACATTGGAGCTCTCTGT
1 TTAGCACATCGGAGCTCTCTGT
8828337 T
1 T
8828338 CTATTAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (22 bp):
TTAGCACATCGGAGCTCTCTGT
Found at i:8828938 original size:18 final size:18
Alignment explanation
Indices: 8828865--8829032 Score: 134
Period size: 17 Copynumber: 9.5 Consensus size: 18
8828855 TTAATGATGT
* * *
8828865 AAACACGAGATTTTTTTA
1 AAACACGAAAATTTTTGA
*
8828883 AAACACGAGAA-TTTTGA
1 AAACACGAAAATTTTTGA
*
8828900 AATACGA-TAATAATTTTTGA
1 AA-AC-ACGAA-AATTTTTGA
*
8828920 AAACACGAAAATTTGTG-
1 AAACACGAAAATTTTTGA
** *
8828937 AAACACGGGAATTGTTGA
1 AAACACGAAAATTTTTGA
*
8828955 AAACACGAAAATTTTAG-
1 AAACACGAAAATTTTTGA
8828972 AAACAACG-AAATTTTTGA
1 AAAC-ACGAAAATTTTTGA
* *
8828990 AAACACTAAGATTTTTG-
1 AAACACGAAAATTTTTGA
*
8829007 AAACACGAAGATTTTTG-
1 AAACACGAAAATTTTTGA
8829024 AAACACGAA
1 AAACACGAA
8829033 TTTTATTTTT
Statistics
Matches: 123, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
17 59 0.48
18 49 0.40
19 7 0.06
20 8 0.07
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (18 bp):
AAACACGAAAATTTTTGA
Found at i:8828962 original size:35 final size:34
Alignment explanation
Indices: 8828876--8829032 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 34
8828866 AACACGAGAT
* * * *
8828876 TTTTTTAAAACACGAGAATTTTGAAATACGATAATAA
1 TTTTTGAAAACACGAAAATTTTGAAACACG--GA-AA
*
8828913 TTTTTGAAAACACGAAAATTTGTGAAACACGGGAA
1 TTTTTGAAAACACGAAAATTT-TGAAACACGGAAA
*
8828948 TTGTTGAAAACACGAAAATTTTAGAAACAAC-GAAA
1 TTTTTGAAAACACGAAAATTTT-GAAAC-ACGGAAA
* *
8828983 TTTTTGAAAACACTAAGATTTTTGAAACAC-GAAGA
1 TTTTTGAAAACACGAA-AATTTTGAAACACGGAA-A
8829018 TTTTTG-AAACACGAA
1 TTTTTGAAAACACGAA
8829033 TTTTATTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
34 14 0.13
35 56 0.54
36 7 0.07
37 19 0.18
38 8 0.08
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (34 bp):
TTTTTGAAAACACGAAAATTTTGAAACACGGAAA
Found at i:8829079 original size:29 final size:29
Alignment explanation
Indices: 8829046--8829101 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
8829036 TATTTTTTTT
8829046 AAGAAACACAAAAATTTGTGAAAACACGG
1 AAGAAACACAAAAATTTGTGAAAACACGG
* *
8829075 AAGAAACACGAAGATTTGTGAAAACAC
1 AAGAAACACAAAAATTTGTGAAAACAC
8829102 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (29 bp):
AAGAAACACAAAAATTTGTGAAAACACGG
Done.