Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 7 of 11
Found at i:2273914 original size:12 final size:13
Alignment explanation
Indices: 2273895--2273930 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
2273885 CAGAATAGTT
2273895 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
2273908 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
2273919 TCTTGCTGCCTC
1 TCTTGCTGCCTC
2273931 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:2277267 original size:21 final size:21
Alignment explanation
Indices: 2277241--2277287 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2277231 TTTCATGTGC
** *
2277241 TTAAAATGGGGTTTTAATTGG
1 TTAAAATCAGGTTTTAATTGA
*
2277262 TTAAAATCATGTTTTAATTGA
1 TTAAAATCAGGTTTTAATTGA
2277283 TTAAA
1 TTAAA
2277288 TTGATTTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (21 bp):
TTAAAATCAGGTTTTAATTGA
Found at i:2286379 original size:16 final size:17
Alignment explanation
Indices: 2286358--2286393 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2286348 GAAATTAATT
*
2286358 AATTAATTAAAA-TAAA
1 AATTAAATAAAACTAAA
2286374 AATTAAATAAAACTAAA
1 AATTAAATAAAACTAAA
2286391 AAT
1 AAT
2286394 CATAGCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AATTAAATAAAACTAAA
Found at i:2299111 original size:2 final size:2
Alignment explanation
Indices: 2299106--2299130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2299096 ACACTCACAA
2299106 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
2299131 GATGAGAATT
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:2299927 original size:45 final size:46
Alignment explanation
Indices: 2299876--2299973 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 46
2299866 ATTATGTAAT
* * * *
2299876 TGATTCCAAC-TATTGGGAGATTACTCTGGGTGATTACTATGCTTG
1 TGATTCCAACTTATTAGGAGATTACTCTAGGCGATGACTATGCTTG
* *
2299921 TGATTCC-ACTTGTTAGGAGATTACTTTAGGCGATGACTATGCTTG
1 TGATTCCAACTTATTAGGAGATTACTCTAGGCGATGACTATGCTTG
2299966 TGATTCCA
1 TGATTCCA
2299974 CCCGTCAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 2 0.04
45 43 0.96
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (46 bp):
TGATTCCAACTTATTAGGAGATTACTCTAGGCGATGACTATGCTTG
Found at i:2299989 original size:45 final size:45
Alignment explanation
Indices: 2299895--2300055 Score: 157
Period size: 45 Copynumber: 3.6 Consensus size: 45
2299885 CTATTGGGAG
* * ** * * *
2299895 ATTACTCTGGGTGATTACTATGCTTGTGATTCCACTTGTTAGGAG
1 ATTACTCTAGGTGATGACTATGCTTGTGATTCCACCCGTCAAGAA
* *
2299940 ATTACTTTAGGCGATGACTATGCTTGTGATTCCACCCGTCAAGAA
1 ATTACTCTAGGTGATGACTATGCTTGTGATTCCACCCGTCAAGAA
* * * * *
2299985 ATTACTCTAGGTGATCACTATGCTCGTAATGCCA-CCGCCAA-AA
1 ATTACTCTAGGTGATGACTATGCTTGTGATTCCACCCGTCAAGAA
*
2300028 GATTACTCTAGGTGATGATTATG-TTGTG
1 -ATTACTCTAGGTGATGACTATGCTTGTG
2300056 GTGCCATCTG
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 5 0.05
44 26 0.27
45 64 0.67
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (45 bp):
ATTACTCTAGGTGATGACTATGCTTGTGATTCCACCCGTCAAGAA
Found at i:2306712 original size:76 final size:66
Alignment explanation
Indices: 2306603--2306743 Score: 104
Period size: 76 Copynumber: 2.0 Consensus size: 66
2306593 CTATCCTTAA
** * * *
2306603 TTTTAGGAATTTTTTTTAAAGTAGGAAGCAATTTCCTATTTTTA-TGAATCATCCAATATTAAAA
1 TTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTATTG-ATCACCCAAAATTAAAA
2306667 TT
65 TT
* **
2306669 NNNNNNNNNNTTTTAGGAATTACTTTTAAAGTAGGAAATAATTTTTTATTTTTATTGATCACCCA
1 ----------TTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTATTGATCACCCA
2306734 AAATTAAAAT
56 AAATTAAAAT
2306744 AGGTGGTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 54 0.96
77 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.42
Consensus pattern (66 bp):
TTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTATTGATCACCCAAAATTAAAAT
T
Found at i:2315368 original size:22 final size:23
Alignment explanation
Indices: 2315340--2315386 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2315330 ATTTTTATGC
2315340 ATTATTACAAAAACTAAG-CTAA
1 ATTATTACAAAAACTAAGTCTAA
** *
2315362 ATTATTATGAAAATTAAGTCTAA
1 ATTATTACAAAAACTAAGTCTAA
2315385 AT
1 AT
2315387 AACTCTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (23 bp):
ATTATTACAAAAACTAAGTCTAA
Found at i:2327511 original size:14 final size:13
Alignment explanation
Indices: 2327494--2327561 Score: 75
Period size: 13 Copynumber: 5.0 Consensus size: 13
2327484 AGAACAAAAG
2327494 AGAAAGAAGAGGAA
1 AGAAAGAA-AGGAA
2327508 AGAAAG-AAGGAAA
1 AGAAAGAAAGG-AA
2327521 GAGAAAGCAAAGGAA
1 -AGAAAG-AAAGGAA
*
2327536 AGAAAGAAAGAAA
1 AGAAAGAAAGGAA
*
2327549 AGAGAGAAAGGAA
1 AGAAAGAAAGGAA
2327562 GGAAGGTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
12 3 0.06
13 20 0.43
14 18 0.38
15 2 0.04
16 4 0.09
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGGAA
Found at i:2327512 original size:4 final size:4
Alignment explanation
Indices: 2327494--2327558 Score: 53
Period size: 4 Copynumber: 15.5 Consensus size: 4
2327484 AGAACAAAAG
*
2327494 AGAA AGAA GAGGAA AGAA AGAA GGAA AG-- AGAA AGCAA AGGAA AGAA
1 AGAA AGAA -A-GAA AGAA AGAA AGAA AGAA AGAA AG-AA A-GAA AGAA
*
2327540 AGAA AGAAA AGAG AGAA AG
1 AGAA AG-AA AGAA AGAA AG
2327559 GAAGGAAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
2 2 0.04
4 32 0.64
5 12 0.24
6 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2327514 original size:28 final size:28
Alignment explanation
Indices: 2327483--2327553 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
2327473 ACCCACAACC
*
2327483 AAGAACAAAAGAGAAAG-AAGAGGAAAGA
1 AAGAAGAAAAGAGAAAGCAA-AGGAAAGA
*
2327511 AAGAAGGAAAGAGAAAGCAAAGGAAAGA
1 AAGAAGAAAAGAGAAAGCAAAGGAAAGA
2327539 AAGAAAGAAAAGAGA
1 AAG-AAGAAAAGAGA
2327554 GAAAGGAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (28 bp):
AAGAAGAAAAGAGAAAGCAAAGGAAAGA
Found at i:2331055 original size:66 final size:66
Alignment explanation
Indices: 2330944--2331093 Score: 221
Period size: 66 Copynumber: 2.3 Consensus size: 66
2330934 CATGTATGCC
* * * *
2330944 ATGAAATGTATG-CATTGAGAGAGTCATATACACTATGGGCGAAGCATATAGGTGATTTATAAGG
1 ATGAAATGTATGCCA-TGACAGAGTCACATACACTATGGGCGAAGCATATAAGTGATTTATAAGA
2331008 TT
65 TT
* * *
2331010 ATGAAATGTATGCCATGACATAGTCACATACACTATGGGCTAAGCATGTAAGTGATTTATAAGAT
1 ATGAAATGTATGCCATGACAGAGTCACATACACTATGGGCGAAGCATATAAGTGATTTATAAGAT
2331075 T
66 T
2331076 ATGAAATGTATGCCATGA
1 ATGAAATGTATGCCATGA
2331094 GATGTATGTG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 74 0.97
67 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (66 bp):
ATGAAATGTATGCCATGACAGAGTCACATACACTATGGGCGAAGCATATAAGTGATTTATAAGAT
T
Found at i:2338191 original size:15 final size:15
Alignment explanation
Indices: 2338173--2338215 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2338163 TAAAGTAATT
* *
2338173 TAAAATAAATTAACA
1 TAAATTAAATTAAAA
*
2338188 TAAATTAAACTAAAA
1 TAAATTAAATTAAAA
*
2338203 TAACTTAAATTAA
1 TAAATTAAATTAA
2338216 TTACTCAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATTAAATTAAAA
Found at i:2338195 original size:20 final size:20
Alignment explanation
Indices: 2338172--2338215 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2338162 TTAAAGTAAT
*
2338172 TTAAAATAAATTAACATAAA
1 TTAAAATAAAATAACATAAA
* *
2338192 TTAAACTAAAATAACTTAAA
1 TTAAAATAAAATAACATAAA
2338212 TTAA
1 TTAA
2338216 TTACTCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAATAAAATAACATAAA
Found at i:2339902 original size:21 final size:20
Alignment explanation
Indices: 2339878--2339916 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2339868 TAATTTGTAA
*
2339878 TAAAATAACTTAAAATTAAGT
1 TAAAATAACCT-AAATTAAGT
2339899 TAAAATAACCTAAATTAA
1 TAAAATAACCTAAATTAA
2339917 ACTAATCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAATAACCTAAATTAAGT
Found at i:2342265 original size:136 final size:136
Alignment explanation
Indices: 2342021--2342293 Score: 519
Period size: 136 Copynumber: 2.0 Consensus size: 136
2342011 TACAGAATAC
*
2342021 ACATCAATACATACCATTAACAAATTATGGGGAAAATGGGAGTTTTCATCCAACTCATCCCTATG
1 ACATCAATACATACCATTAACAAATTATGGGGAAAATGGGAGCTTTCATCCAACTCATCCCTATG
*
2342086 GTATTCTTACCCCAACATCGAGATTCATAAAGAGGGAAAAAGTGGTACAATGGCCAATGTAACCC
66 GTATTCTTACACCAACATCGAGATTCATAAAGAGGGAAAAAGTGGTACAATGGCCAATGTAACCC
2342151 TATGGT
131 TATGGT
*
2342157 ACATCAATACATACCATTAACAAATTATGGGGAGAATGGGAGCTTTCATCCAACTCATCCCTATG
1 ACATCAATACATACCATTAACAAATTATGGGGAAAATGGGAGCTTTCATCCAACTCATCCCTATG
2342222 GTATTCTTACACCAACATCGAGATTCATAAAGAGGGAAAAAGTGGTACAATGGCCAATGTAACCC
66 GTATTCTTACACCAACATCGAGATTCATAAAGAGGGAAAAAGTGGTACAATGGCCAATGTAACCC
2342287 TATGGT
131 TATGGT
2342293 A
1 A
2342294 TTCTTATCCC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (136 bp):
ACATCAATACATACCATTAACAAATTATGGGGAAAATGGGAGCTTTCATCCAACTCATCCCTATG
GTATTCTTACACCAACATCGAGATTCATAAAGAGGGAAAAAGTGGTACAATGGCCAATGTAACCC
TATGGT
Found at i:2346630 original size:18 final size:19
Alignment explanation
Indices: 2346591--2346634 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
2346581 TTAACATTTT
2346591 AATATTATTTTATTCATAAA
1 AATATTATTTTATT-ATAAA
2346611 AATATTATTTTATT-TAAA
1 AATATTATTTTATTATAAA
2346629 AATATT
1 AATATT
2346635 CTTTCCGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTATTTTATTATAAA
Found at i:2351417 original size:53 final size:53
Alignment explanation
Indices: 2351333--2351433 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
2351323 AATGGGAATC
*
2351333 GATAACCCTTACACAAGCCATAAAGGAATTCTTTTC-TTTTCACAAGATCAAGT
1 GATAACCCTTACACAAGCCATAAAGGAATTC-TTGCGTTTTCACAAGATCAAGT
*
2351386 GATAACCCTTACACAATCC-TCAAA-GAGATTCTTGCGTTTTCACAAGAT
1 GATAACCCTTACACAAGCCAT-AAAGGA-ATTCTTGCGTTTTCACAAGAT
2351434 GAAGCAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
52 6 0.14
53 37 0.86
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.30
Consensus pattern (53 bp):
GATAACCCTTACACAAGCCATAAAGGAATTCTTGCGTTTTCACAAGATCAAGT
Found at i:2351445 original size:53 final size:53
Alignment explanation
Indices: 2351333--2351461 Score: 133
Period size: 53 Copynumber: 2.5 Consensus size: 53
2351323 AATGGGAATC
* * *
2351333 GATAACCCTTACACAAGCCAT-AAAGGAATTCTTTTCTTTTCACAAGATCAAGT
1 GATAACCCTTACACAATCC-TCAAAGGAATTCTTTGCTTTTCACAAGATCAAGA
*
2351386 GATAACCCTTACACAATCCTCAAA-GAGATTC-TTGCGTTTTCACAAGATGAAGCA
1 GATAACCCTTACACAATCCTCAAAGGA-ATTCTTTGC-TTTTCACAAGATCAAG-A
* *
2351440 G-TAACCC-TACATAATCCACAAA
1 GATAACCCTTACACAATCCTCAAA
2351462 AGGGGTCTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
52 19 0.29
53 46 0.70
54 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (53 bp):
GATAACCCTTACACAATCCTCAAAGGAATTCTTTGCTTTTCACAAGATCAAGA
Found at i:2352620 original size:40 final size:38
Alignment explanation
Indices: 2352539--2352612 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
2352529 GTGTTGCTCT
* * * * * *
2352539 TTGATTATGTTGAATTGATATATTTCTTAATGACTTGA
1 TTGAATATGTTGAATGGAAATATATCTCAATAACTTGA
2352577 TTGAATATGTTGAATGGAAATATATCTCAATAACTT
1 TTGAATATGTTGAATGGAAATATATCTCAATAACTT
2352613 TGGATTGATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.45
Consensus pattern (38 bp):
TTGAATATGTTGAATGGAAATATATCTCAATAACTTGA
Found at i:2356819 original size:17 final size:17
Alignment explanation
Indices: 2356778--2356826 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2356768 TAAAATCTCT
*
2356778 ATAAATTAAT-A-CTTG
1 ATAAATTAATAATTTTG
2356793 ATAAATTAATAATTTTG
1 ATAAATTAATAATTTTG
*
2356810 ATTAAA-TAATATTTTTG
1 A-TAAATTAATAATTTTG
2356827 GTCTGTCCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 14 0.48
18 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAAATTAATAATTTTG
Found at i:2356974 original size:12 final size:12
Alignment explanation
Indices: 2356954--2356983 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2356944 ACATCAAAAT
*
2356954 TATACACATATA
1 TATATACATATA
2356966 TATATACATATA
1 TATATACATATA
2356978 TATATA
1 TATATA
2356984 TATACATGAC
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:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATACATATA
Found at i:2357312 original size:17 final size:17
Alignment explanation
Indices: 2357290--2357323 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2357280 GTAATTAAGT
2357290 AATATTCGTATAATTAC
1 AATATTCGTATAATTAC
2357307 AATATTCGTATAATTAC
1 AATATTCGTATAATTAC
2357324 TATAATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
AATATTCGTATAATTAC
Found at i:2376530 original size:59 final size:59
Alignment explanation
Indices: 2376433--2376548 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 59
2376423 TATCACCAAG
* * * * *
2376433 AACTGTTATAAAGTGTGAGATGGGGTTATTCTTTCCCTAAAAGGTCTTCCTTTTAAAAA
1 AACTATTATAAAGCGTGACATGGGGTCATTCTTTCCCTAAAAGGTCTTCCCTTTAAAAA
*
2376492 AACTATTATAAAGCGTGACATGGGGTCATTCTTTCCCTAAAGGGTCTTCCCTTTAAA
1 AACTATTATAAAGCGTGACATGGGGTCATTCTTTCCCTAAAAGGTCTTCCCTTTAAA
2376549 GGCTTAACAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (59 bp):
AACTATTATAAAGCGTGACATGGGGTCATTCTTTCCCTAAAAGGTCTTCCCTTTAAAAA
Found at i:2382366 original size:14 final size:14
Alignment explanation
Indices: 2382347--2382385 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2382337 ATATAAAAAG
*
2382347 TATTTTAATATTAA
1 TATTTTAAAATTAA
2382361 TATTTTAAAATTAA
1 TATTTTAAAATTAA
*
2382375 AATCTTTAAAA
1 TAT-TTTAAAA
2382386 AATATATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTTTAAAATTAA
Found at i:2383131 original size:15 final size:15
Alignment explanation
Indices: 2383101--2383129 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2383091 CAAAGCTAAT
2383101 GAATTAAAAGTAAAA
1 GAATTAAAAGTAAAA
2383116 GAATTAAAA-TAAAA
1 GAATTAAAAGTAAAA
2383130 AGTCACCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
GAATTAAAAGTAAAA
Found at i:2385201 original size:56 final size:58
Alignment explanation
Indices: 2385126--2385282 Score: 176
Period size: 58 Copynumber: 2.7 Consensus size: 58
2385116 AAATCACCCC
* * * *
2385126 CTCTCTCAATTGATTTCCCTTTCCTCTCCCTTTCTCTACAAATGATCCC-TCT-T-TCT
1 CTCTCTCAATCGATCTCCCTATCCTCTCCCTCTCTCTACAAATGA-CCCGTCTCTCTCT
* * *
2385182 CTCTCTCAATCGATCTCCCTATCTTGTCCCTCTCTCTGCAAATGACCCGTCTCTCTCT
1 CTCTCTCAATCGATCTCCCTATCCTCTCCCTCTCTCTACAAATGACCCGTCTCTCTCT
* * * * *
2385240 CTTTCTCAATCGATCTCCCTATCTTGTCCCTCTTTCTGCAAAT
1 CTCTCTCAATCGATCTCCCTATCCTCTCCCTCTCTCTACAAAT
2385283 CACTCATCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.03
56 41 0.46
57 1 0.01
58 44 0.49
ACGTcount: A:0.15, C:0.38, G:0.06, T:0.41
Consensus pattern (58 bp):
CTCTCTCAATCGATCTCCCTATCCTCTCCCTCTCTCTACAAATGACCCGTCTCTCTCT
Found at i:2385215 original size:29 final size:29
Alignment explanation
Indices: 2385182--2385272 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
2385172 CCCTCTTTCT
2385182 CTCTCTCAATCGATCTCCCTATCTTGTCCC
1 CTCTCTCAATCGATCTCCCTATCTTGT-CC
* * * *
2385212 TCTCTCTGCAAAT-GA-C-CCGTCTC-TCTCT
1 -CTCTCT-C-AATCGATCTCCCTATCTTGTCC
*
2385240 CTTTCTCAATCGATCTCCCTATCTTGTCC
1 CTCTCTCAATCGATCTCCCTATCTTGTCC
2385269 CTCT
1 CTCT
2385273 TTCTGCAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 6 0.14
28 6 0.14
29 8 0.18
30 5 0.11
31 7 0.16
32 3 0.07
33 3 0.07
ACGTcount: A:0.13, C:0.41, G:0.08, T:0.38
Consensus pattern (29 bp):
CTCTCTCAATCGATCTCCCTATCTTGTCC
Found at i:2385938 original size:6 final size:6
Alignment explanation
Indices: 2385920--2385978 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
2385910 TAATTAAACT
*
2385920 AATAAC AAT-AA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
2385967 AGTAAA AATAAA
1 AATAAA AATAAA
2385979 TTTAAAGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
5 4 0.08
6 45 0.92
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:2404207 original size:51 final size:53
Alignment explanation
Indices: 2404152--2404281 Score: 176
Period size: 51 Copynumber: 2.5 Consensus size: 53
2404142 TTGCCTTAGG
* * * *
2404152 AAATATTTTACCTTGATTTGTTGTTTATGCTTTCCTTGC-TTTGAATTA-GAA
1 AAATATTTTACCTTGATTTATTATTTATGCCTTCCTTGCAGTTGAATTAGGAA
* *
2404203 AAATATTTTACCTTGATTTATTATTTATGCCTTGCTTGCAGTTGACTTAGGAA
1 AAATATTTTACCTTGATTTATTATTTATGCCTTCCTTGCAGTTGAATTAGGAA
2404256 AAATATTTTACCTTTG-TTTATTATTT
1 AAATATTTTACC-TTGATTTATTATTT
2404282 GTTCTTTGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
51 35 0.50
52 7 0.10
53 25 0.36
54 3 0.04
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (53 bp):
AAATATTTTACCTTGATTTATTATTTATGCCTTCCTTGCAGTTGAATTAGGAA
Found at i:2405861 original size:30 final size:30
Alignment explanation
Indices: 2405825--2405891 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
2405815 AAGTAAAGAA
2405825 AGAAAATCTAGTCAAGAGTAAGATTGGTCT
1 AGAAAATCTAGTCAAGAGTAAGATTGGTCT
2405855 AGAAAATCTAGTCAAGAGTAAGATTGGTCT
1 AGAAAATCTAGTCAAGAGTAAGATTGGTCT
2405885 AGAAAAT
1 AGAAAAT
2405892 ATCATGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (30 bp):
AGAAAATCTAGTCAAGAGTAAGATTGGTCT
Found at i:2406546 original size:12 final size:12
Alignment explanation
Indices: 2406529--2406555 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2406519 CAAGAATGAC
2406529 TAAGTATATATT
1 TAAGTATATATT
2406541 TAAGTATATATT
1 TAAGTATATATT
2406553 TAA
1 TAA
2406556 ATAGTATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
TAAGTATATATT
Found at i:2412192 original size:13 final size:14
Alignment explanation
Indices: 2412162--2412194 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2412152 GGTTTAAAAC
2412162 AAAACTACCTAAGA
1 AAAACTACCTAAGA
2412176 AAAACTACCTAAGA
1 AAAACTACCTAAGA
2412190 AAAAC
1 AAAAC
2412195 AAGATCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAACTACCTAAGA
Found at i:2412893 original size:21 final size:20
Alignment explanation
Indices: 2412865--2412903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2412855 TGCTATGACT
2412865 TTTATTTTAGTTTA-TTGTGA
1 TTTATTTTA-TTTACTTGTGA
2412885 TTTAGTTTTATTTACTTGT
1 TTTA-TTTTATTTACTTGT
2412904 TAGTTTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTATTTTATTTACTTGTGA
Found at i:2428474 original size:25 final size:25
Alignment explanation
Indices: 2428446--2428520 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
2428436 CATGTGTCAA
**
2428446 AATAACTTTACGTAATCGAGTTATC
1 AATAACTTTATATAATCGAGTTATC
* *
2428471 AATAACTCTATATAATTGAGTTATC
1 AATAACTTTATATAATCGAGTTATC
* *
2428496 AATAATTTTATACAATCGAGTTATC
1 AATAACTTTATATAATCGAGTTATC
2428521 TTGCCATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (25 bp):
AATAACTTTATATAATCGAGTTATC
Found at i:2429202 original size:19 final size:17
Alignment explanation
Indices: 2429166--2429204 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2429156 TTATTTTGAG
2429166 TTATTTTTTTAATTATT
1 TTATTTTTTTAATTATT
*
2429183 TTATTTTTGTTGAGTTATT
1 TTATTTTT-TT-AATTATT
2429202 TTA
1 TTA
2429205 ATTTGGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTAATTATT
Found at i:2439246 original size:16 final size:16
Alignment explanation
Indices: 2439220--2439256 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2439210 TGAGACCGAA
*
2439220 ATTTAGATTTTGATTC
1 ATTTGGATTTTGATTC
*
2439236 TTTTGGATTTTGATTC
1 ATTTGGATTTTGATTC
2439252 ATTTG
1 ATTTG
2439257 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.59
Consensus pattern (16 bp):
ATTTGGATTTTGATTC
Found at i:2441717 original size:12 final size:12
Alignment explanation
Indices: 2441700--2441734 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2441690 AGAAAAGTTT
2441700 CTTGCTGCCTCC
1 CTTGCTGCCTCC
*
2441712 CTTGCTGCCTCT
1 CTTGCTGCCTCC
*
2441724 CTTACTGCCTC
1 CTTGCTGCCTC
2441735 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.46, G:0.14, T:0.37
Consensus pattern (12 bp):
CTTGCTGCCTCC
Found at i:2442415 original size:21 final size:22
Alignment explanation
Indices: 2442380--2442423 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2442370 CTCTTAAAGT
2442380 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
2442402 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
2442423 A
1 A
2442424 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:2448340 original size:20 final size:21
Alignment explanation
Indices: 2448305--2448346 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2448295 CTCTTAAAGT
2448305 AATTTAAATAAAATAACCTAA
1 AATTTAAATAAAATAACCTAA
* *
2448326 AATTTAACT-AAATAACTTAA
1 AATTTAAATAAAATAACCTAA
2448346 A
1 A
2448347 TTAATCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTTAAATAAAATAACCTAA
Found at i:2472572 original size:7 final size:7
Alignment explanation
Indices: 2472560--2472588 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2472550 CAAATGAACT
2472560 CAACATA
1 CAACATA
2472567 CAACATA
1 CAACATA
2472574 CAACATA
1 CAACATA
2472581 CAACATA
1 CAACATA
2472588 C
1 C
2472589 CATAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (7 bp):
CAACATA
Found at i:2472598 original size:11 final size:13
Alignment explanation
Indices: 2472562--2472598 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2472552 AATGAACTCA
2472562 ACATACAACATAC
1 ACATACAACATAC
2472575 AACATACAACATAC
1 -ACATACAACATAC
2472589 -CATA-AACATA
1 ACATACAACATA
2472599 AAAACCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.26
12 4 0.17
14 13 0.57
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (13 bp):
ACATACAACATAC
Found at i:2472696 original size:31 final size:31
Alignment explanation
Indices: 2472661--2472790 Score: 143
Period size: 31 Copynumber: 4.2 Consensus size: 31
2472651 CCCCATCAAG
* * *
2472661 CTTGGGTTGGCAATGTACATCCCTATTGTAC
1 CTTGGGTTGGCAATGTATATCCCCATTGCAC
* * *
2472692 CTTGGGCTGGTAATGTATGTCCCCATTGCAC
1 CTTGGGTTGGCAATGTATATCCCCATTGCAC
* *
2472723 TTTGGGTTGGCAATGTATATCCCCATTGCTC
1 CTTGGGTTGGCAATGTATATCCCCATTGCAC
* * * *
2472754 CTTAGGCTAGCAACGTATATCCCCATTGCAC
1 CTTGGGTTGGCAATGTATATCCCCATTGCAC
*
2472785 CGTGGG
1 CTTGGG
2472791 CATTTTATGA
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (31 bp):
CTTGGGTTGGCAATGTATATCCCCATTGCAC
Found at i:2472777 original size:62 final size:62
Alignment explanation
Indices: 2472662--2472784 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
2472652 CCCATCAAGC
* * * * * *
2472662 TTGGGTTGGCAATGTACATCCCTATTGTACCTTGGGCTGGTAATGTATGTCCCCATTGCACT
1 TTGGGTTGGCAATGTACATCCCCATTGTACCTTAGGCTAGCAACGTATATCCCCATTGCACT
*
2472724 TTGGGTTGGCAATGTATATCCCCATTGCT-CCTTAGGCTAGCAACGTATATCCCCATTGCAC
1 TTGGGTTGGCAATGTACATCCCCATTG-TACCTTAGGCTAGCAACGTATATCCCCATTGCAC
2472785 CGTGGGCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
62 52 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (62 bp):
TTGGGTTGGCAATGTACATCCCCATTGTACCTTAGGCTAGCAACGTATATCCCCATTGCACT
Found at i:2473052 original size:54 final size:54
Alignment explanation
Indices: 2472981--2473094 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
2472971 ATGCTAGCTC
* * *
2472981 AATCATCTCAAGTAGTATATGGAATATAGATTATATACATATTCTCATGGCATT
1 AATCATCTCAAGCAGTATATGGAATATACATCATATACATATTCTCATGGCATT
*
2473035 AATCATCTCATGCAGTATATGGAATATACATCATATACATATTCTCATGGCATT
1 AATCATCTCAAGCAGTATATGGAATATACATCATATACATATTCTCATGGCATT
2473089 AATCAT
1 AATCAT
2473095 GCATACTTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (54 bp):
AATCATCTCAAGCAGTATATGGAATATACATCATATACATATTCTCATGGCATT
Found at i:2473121 original size:68 final size:66
Alignment explanation
Indices: 2473049--2473232 Score: 212
Period size: 68 Copynumber: 2.7 Consensus size: 66
2473039 ATCTCATGCA
2473049 GTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATGCATACTT-AGTCATCTCA
1 GTATATGGAAT-TACATCATATACATATTCT-ATGGCATTAATCATGCATACTTGA-TCATCTCA
2473113 TATG
63 TATG
* * *
2473117 GTATATGGAATTTACATCATATACACCATCCTAT--AATATACATCATGCATACTTGATCATCTC
1 GTATATGGAA-TTACATCATATACA-TATTCTATGGCAT-TA-ATCATGCATACTTGATCATCTC
2473180 ATATG
62 ATATG
* * *
2473185 GTATATGGAATTCACATCATATACATAATCTTGTGGCATTCATCATGC
1 GTATATGGAATT-ACATCATATACATATTC-TATGGCATTAATCATGC
2473233 CAACATGCAT
Statistics
Matches: 98, Mismatches: 9, Indels: 18
0.78 0.07 0.14
Matches are distributed among these distances:
66 2 0.02
67 6 0.06
68 81 0.83
69 7 0.07
70 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (66 bp):
GTATATGGAATTACATCATATACATATTCTATGGCATTAATCATGCATACTTGATCATCTCATAT
G
Found at i:2509405 original size:21 final size:21
Alignment explanation
Indices: 2509381--2509420 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2509371 AAGCAGTTTA
2509381 GACTAATTTGTTAAATTCAAT
1 GACTAATTTGTTAAATTCAAT
2509402 GACTAATTTGTTAAATTCA
1 GACTAATTTGTTAAATTCA
2509421 GGGATGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (21 bp):
GACTAATTTGTTAAATTCAAT
Found at i:2514333 original size:58 final size:58
Alignment explanation
Indices: 2514226--2514335 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
2514216 CTTTGCATGC
* *
2514226 CATAACATTTATTAAATCATATAAAATAAATCTATTACATGCATTCTACTTTGCCTTG
1 CATAACATTTATTAAATCATATAAAATAAATCTATCACATGCATACTACTTTGCCTTG
* * *
2514284 CATAGCATTTATTAAAT-TTCATAAAATACATCTATCACATGCGA-ACTACTTT
1 CATAACATTTATTAAATCAT-ATAAAATAAATCTATCACATGC-ATACTACTTT
2514336 AGATGAACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 1 0.02
58 43 0.96
59 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (58 bp):
CATAACATTTATTAAATCATATAAAATAAATCTATCACATGCATACTACTTTGCCTTG
Found at i:2523043 original size:44 final size:44
Alignment explanation
Indices: 2522980--2523068 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
2522970 GAATAATAAA
* *
2522980 ACAAAGAAAGCTATGGTGGTTGCAACGTAGTCTAATAGTGAGAT
1 ACAAAGAAAGCTATGGTGGTTGCAACCTAGTCTAATAATGAGAT
*
2523024 ACAAAGAAAGCTATGGTGGTTGCTACCTAGTCTAATAATGAGAT
1 ACAAAGAAAGCTATGGTGGTTGCAACCTAGTCTAATAATGAGAT
2523068 A
1 A
2523069 TCTAGTTCAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (44 bp):
ACAAAGAAAGCTATGGTGGTTGCAACCTAGTCTAATAATGAGAT
Found at i:2527472 original size:95 final size:94
Alignment explanation
Indices: 2527297--2527474 Score: 284
Period size: 95 Copynumber: 1.9 Consensus size: 94
2527287 AAGGGAAAAC
* * *
2527297 GAGTGACCTAAAATTAATGGCTGAAAAAAAAGGCAAGAAATCAAAAAAGAAACCATCAGGGTTAA
1 GAGTGACCTAAAATTAATGGCTGAAAAAAAAGGCAAGAAAACAAAAAAGAAACCATCAAGGTCAA
**
2527362 AAAAAGCTGTAAAAAAAAAGGTAATTAAT
66 AAAAAGCACTAAAAAAAAAGGTAATTAAT
2527391 GAGTGACCTAAAATTAATGGCTGAAAAAAAAAGGCAAGAAAACAAAAAAGAAACCATCAAGGTCA
1 GAGTGACCTAAAATTAATGGCTG-AAAAAAAAGGCAAGAAAACAAAAAAGAAACCATCAAGGTCA
*
2527456 GAAAAAGTCACTAAAAAAA
65 AAAAAAG-CACTAAAAAAA
2527475 GAGCTTGAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
94 23 0.30
95 44 0.58
96 9 0.12
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (94 bp):
GAGTGACCTAAAATTAATGGCTGAAAAAAAAGGCAAGAAAACAAAAAAGAAACCATCAAGGTCAA
AAAAAGCACTAAAAAAAAAGGTAATTAAT
Found at i:2539114 original size:36 final size:36
Alignment explanation
Indices: 2539073--2539214 Score: 162
Period size: 36 Copynumber: 3.9 Consensus size: 36
2539063 TTTAAAAGTT
* *
2539073 AGTGTAAAGGTTATCATTTGATCTCGTTAAAAAGTC-
1 AGTGTAAAGGTTATCACTTGATCTCATTAAAAAG-CA
* **
2539109 GGTGT-AAGTGTTATTGCTTGATCTCATTAAAAAGCA
1 AGTGTAAAG-GTTATCACTTGATCTCATTAAAAAGCA
* * *
2539145 AGTGTAAGGGTTATCACTTGATCCCATTAAAAAGCT
1 AGTGTAAAGGTTATCACTTGATCTCATTAAAAAGCA
* *
2539181 AGTGTAAGGGTTATCACTTGACCTCATTAAAAAG
1 AGTGTAAAGGTTATCACTTGATCTCATTAAAAAG
2539215 AAAAAAATTT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 4 0.04
36 84 0.93
37 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (36 bp):
AGTGTAAAGGTTATCACTTGATCTCATTAAAAAGCA
Found at i:2539157 original size:72 final size:72
Alignment explanation
Indices: 2539073--2539214 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 72
2539063 TTTAAAAGTT
* * * * * ** *
2539073 AGTGTAAAGGTTATCATTTGATCTCGTTAAAAAG-TCGGTGTAAGTGTTATTGCTTGATCTCATT
1 AGTGTAAAGGTTATCACTTGATCCCATTAAAAAGCT-AGTGTAAGGGTTATCACTTGACCTCATT
2539137 AAAAAGCA
65 AAAAAGCA
*
2539145 AGTGTAAGGGTTATCACTTGATCCCATTAAAAAGCTAGTGTAAGGGTTATCACTTGACCTCATTA
1 AGTGTAAAGGTTATCACTTGATCCCATTAAAAAGCTAGTGTAAGGGTTATCACTTGACCTCATTA
2539210 AAAAG
66 AAAAG
2539215 AAAAAAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (72 bp):
AGTGTAAAGGTTATCACTTGATCCCATTAAAAAGCTAGTGTAAGGGTTATCACTTGACCTCATTA
AAAAGCA
Found at i:2541045 original size:30 final size:30
Alignment explanation
Indices: 2541011--2541085 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
2541001 ATCTCTTAAT
2541011 TGAAGATGAAGAAGATGACATGTAAAG-AGA
1 TGAAGATGAAGAAGATGACATG-AAAGAAGA
* *
2541041 TGAAGATGAAGAAGATGACATGGAGGAAGA
1 TGAAGATGAAGAAGATGACATGAAAGAAGA
*
2541071 TAAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
2541086 AGAAGCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.51, C:0.03, G:0.32, T:0.15
Consensus pattern (30 bp):
TGAAGATGAAGAAGATGACATGAAAGAAGA
Found at i:2541056 original size:15 final size:15
Alignment explanation
Indices: 2541011--2541097 Score: 72
Period size: 15 Copynumber: 5.8 Consensus size: 15
2541001 ATCTCTTAAT
2541011 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
*
2541026 TG-ACATGTAA-AGAGA
1 TGAAGATG-AAGA-AGA
2541041 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
* *
2541056 TG-ACATGGAGGAAGA
1 TGAAGAT-GAAGAAGA
*
2541071 TAAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
* *
2541086 AGAAGCTGAAGA
1 TGAAGATGAAGA
2541098 CGAAGATGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
14 8 0.14
15 40 0.71
16 8 0.14
ACGTcount: A:0.51, C:0.03, G:0.32, T:0.14
Consensus pattern (15 bp):
TGAAGATGAAGAAGA
Found at i:2543889 original size:54 final size:54
Alignment explanation
Indices: 2543822--2543924 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
2543812 ATTTTCCAAT
* * * **
2543822 GAAATTGTTGTTGG-AATTGACTTTCCAATGGAATTTTCCGTTGGAAATTTGCAAA
1 GAAATTGTCGTTGGAAATTCA-TTTCCAA-CGAAAATTCCGTTGGAAATTTGCAAA
2543877 GAAATT-TCGTTGGAAATTCATTTCCAACGAAAATTCCGTTGGAAATTT
1 GAAATTGTCGTTGGAAATTCATTTCCAACGAAAATTCCGTTGGAAATTT
2543925 CCAACCGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 18 0.43
54 13 0.31
55 11 0.26
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (54 bp):
GAAATTGTCGTTGGAAATTCATTTCCAACGAAAATTCCGTTGGAAATTTGCAAA
Found at i:2543908 original size:28 final size:29
Alignment explanation
Indices: 2543868--2543923 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2543858 TCCGTTGGAA
* *
2543868 ATTTGCAAAG-AAATTTCGTTGGAAATTC
1 ATTTCCAAAGAAAATTCCGTTGGAAATTC
*
2543896 ATTTCCAACGAAAATTCCGTTGGAAATT
1 ATTTCCAAAGAAAATTCCGTTGGAAATT
2543924 TCCAACCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (29 bp):
ATTTCCAAAGAAAATTCCGTTGGAAATTC
Found at i:2551710 original size:12 final size:12
Alignment explanation
Indices: 2551693--2551729 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2551683 ATTTTGTGTG
2551693 TGTGTATATATA
1 TGTGTATATATA
2551705 TGTGTATATATA
1 TGTGTATATATA
* *
2551717 TATATATATATA
1 TGTGTATATATA
2551729 T
1 T
2551730 ATATATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (12 bp):
TGTGTATATATA
Found at i:2551754 original size:2 final size:2
Alignment explanation
Indices: 2551697--2551737 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2551687 TGTGTGTGTG
* *
2551697 TA TA TA TA TG TG 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 TA TA TA T
2551738 GATCTTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2551760 original size:15 final size:17
Alignment explanation
Indices: 2551731--2551777 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
2551721 TATATATATA
2551731 TATATATGATCTTG-AAC
1 TATATATGA-CTTGAAAC
2551748 TATATATGA-TTGAAAC
1 TATATATGACTTGAAAC
2551764 TATAGCTATGACTT
1 TATA--TATGACTT
2551778 CATTATTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
16 7 0.27
17 9 0.35
18 5 0.19
19 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (17 bp):
TATATATGACTTGAAAC
Found at i:2553329 original size:22 final size:21
Alignment explanation
Indices: 2553300--2553359 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
2553290 ACGTGACAAG
*
2553300 GTTTTAGGAATTGCTTGACTA
1 GTTTTAGGAATTGCATGACTA
*
2553321 GTTTGTAGGCATTGCATGACTA
1 GTTT-TAGGAATTGCATGACTA
*
2553343 GTTTTTGGAAATTGCAT
1 GTTTTAGG-AATTGCAT
2553360 TGCTTTATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (21 bp):
GTTTTAGGAATTGCATGACTA
Found at i:2554116 original size:22 final size:22
Alignment explanation
Indices: 2554088--2554139 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
2554078 ATTTTATTTA
2554088 TAGGCATTAAGTGAATGGATAT
1 TAGGCATTAAGTGAATGGATAT
* ** *
2554110 TATGCATTGTGTTAATGGATAT
1 TAGGCATTAAGTGAATGGATAT
2554132 TAGGCATT
1 TAGGCATT
2554140 GCATGCCTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (22 bp):
TAGGCATTAAGTGAATGGATAT
Found at i:2554250 original size:22 final size:23
Alignment explanation
Indices: 2554200--2554251 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2554190 CGTTGGCCAA
*
2554200 TGCATGAGTGGATATTTTGGCAT
1 TGCATGAGTGGATATTTAGGCAT
**
2554223 AACATGAGTGGATA-TTAGGCAT
1 TGCATGAGTGGATATTTAGGCAT
2554245 TGCATGA
1 TGCATGA
2554252 CTTATTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (23 bp):
TGCATGAGTGGATATTTAGGCAT
Found at i:2554494 original size:211 final size:209
Alignment explanation
Indices: 2554131--2554582 Score: 543
Period size: 211 Copynumber: 2.1 Consensus size: 209
2554121 TTAATGGATA
* * *
2554131 TTAGGCATTGCATGCCTGGTTGTTATGTATTTCGTGATTGATTTTTAAGTATTGCGTGACGTTGG
1 TTAGGCATTGCATGACTAGTTGTTATGTATTTCGTGATT-ATTTTTAAGTATTGCGTGACATTGG
* * * * *
2554196 CCAATGCATGAGTGGATATTTTGGCATAACATGAGTGGATATTAGGCATTGCATGACTTATTATT
65 CCAATACATGACTGGATATTTTGGCAAAACATGAATGGATATTAGGCATTGAATGACTTATTATT
* ** * *
2554261 AAGTATTGTGAGACTGGTTTATAAGTGCTGTGTGAATTGTGCAATGCATATCTTGTTTTAAGACA
130 AAGTATTGTGAGACTGGTTTATAAGCGCTGCATGAATTATGCAATGAATATCTTGTTTTAAGACA
2554326 TTTCTTAACTACTTT
195 TTTCTTAACTACTTT
* * *
2554341 TTAGGCATTGCATGACTAGTTGTTATGTA-TTCTTTGACTT-TTTGTTATGTATTGCGTGGCATT
1 TTAGGCATTGCATGACTAGTTGTTATGTATTTC-GTGA-TTATTT-TTAAGTATTGCGTGACATT
** * * **
2554404 GGGCCAATATGTGACTGGTTATTTTGGTAAAATGTGAATGGATATTAGGCATT-AAGTGACTTAT
63 -GGCCAATACATGACTGGATATTTTGGCAAAACATGAATGGATATTAGGCATTGAA-TGACTTAT
* * * * *
2554468 TATTAGGTATTGCT-AGACTGGTTTATAGGCGTTGCATGAATTATGCAATTAATATCTTGTTTTG
126 TATTAAGTATTG-TGAGACTGGTTTATAAGCGCTGCATGAATTATGCAATGAATATCTTGTTTTA
2554532 AGACATTTCTTAACTACTTT
190 AGACATTTCTTAACTACTTT
***
2554552 TTAGGCATTATGTGACTAGTTGTTATGTATT
1 TTAGGCATTGCATGACTAGTTGTTATGTATT
2554583 GTGTGACGTT
Statistics
Matches: 205, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
209 6 0.03
210 47 0.23
211 150 0.73
212 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (209 bp):
TTAGGCATTGCATGACTAGTTGTTATGTATTTCGTGATTATTTTTAAGTATTGCGTGACATTGGC
CAATACATGACTGGATATTTTGGCAAAACATGAATGGATATTAGGCATTGAATGACTTATTATTA
AGTATTGTGAGACTGGTTTATAAGCGCTGCATGAATTATGCAATGAATATCTTGTTTTAAGACAT
TTCTTAACTACTTT
Found at i:2562107 original size:84 final size:82
Alignment explanation
Indices: 2561983--2562154 Score: 299
Period size: 84 Copynumber: 2.1 Consensus size: 82
2561973 TTAAGAACAA
*
2561983 TATGCAATTTAACTTTGGGAGAGGATTTTATTATTATTAGTATTTGTGATGGTTTAGGTTAGTTT
1 TATGCAATTTAACTTTGGGAGAGGATTTTATTATTATTAGTATTTGTGATAGTTTAGGTTAGTTT
2562048 ATTTTCATTAAATTTTTTT
66 ATTTTCATT-AA-TTTTTT
* *
2562067 TATGCAATTTAAGTTTGGGAGAGGATTTTATTATTATTAGTGTTTGTGATAGTTTAGGTTAGTTT
1 TATGCAATTTAACTTTGGGAGAGGATTTTATTATTATTAGTATTTGTGATAGTTTAGGTTAGTTT
2562132 ATTTTCATTAATTTTTT
66 ATTTTCATTAATTTTTT
2562149 TATGCA
1 TATGCA
2562155 TGTGCATTTA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
82 12 0.14
83 2 0.02
84 71 0.84
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (82 bp):
TATGCAATTTAACTTTGGGAGAGGATTTTATTATTATTAGTATTTGTGATAGTTTAGGTTAGTTT
ATTTTCATTAATTTTTT
Found at i:2567723 original size:23 final size:23
Alignment explanation
Indices: 2567697--2567746 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2567687 GTCATGCGAA
*
2567697 TCCATATTAACTAGTCACACGAT
1 TCCATATGAACTAGTCACACGAT
*
2567720 TCCATATGAACTAGTCACGCGAT
1 TCCATATGAACTAGTCACACGAT
2567743 TCCA
1 TCCA
2567747 AACACACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (23 bp):
TCCATATGAACTAGTCACACGAT
Found at i:2568109 original size:27 final size:25
Alignment explanation
Indices: 2568062--2568129 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
2568052 TGCCTTTCTC
*
2568062 TTTGTTAAATGATTCAAAAAGGAATAA
1 TTTG-TAAATGATACAAAAA-GAATAA
*
2568089 TTTGTAAATGATACAACAAAGCATAA
1 TTTGTAAATGATACAA-AAAGAATAA
* *
2568115 TTTGGAGATGATACA
1 TTTGTAAATGATACA
2568130 TAATAATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 29 0.81
27 7 0.19
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (25 bp):
TTTGTAAATGATACAAAAAGAATAA
Found at i:2570164 original size:24 final size:24
Alignment explanation
Indices: 2570093--2570165 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 24
2570083 CAAGAATAGT
* *
2570093 AACAT-GAGAAGCAGCAGGAAAAGC
1 AACATCGAGAA-CAGGAGGAAAACC
*
2570117 AACATCGAGAGCAACATGAGGAAAACC
1 AACATC--GAG-AACAGGAGGAAAACC
*
2570144 AACATCGAGAACAGGATGAAAA
1 AACATCGAGAACAGGAGGAAAA
2570166 GAAGCAGCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 16 0.40
25 3 0.08
27 19 0.47
28 2 0.05
ACGTcount: A:0.51, C:0.18, G:0.25, T:0.07
Consensus pattern (24 bp):
AACATCGAGAACAGGAGGAAAACC
Found at i:2584949 original size:14 final size:14
Alignment explanation
Indices: 2584913--2584942 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2584903 ATGATCTTAC
2584913 TTTCATCAACTTCT
1 TTTCATCAACTTCT
2584927 TTTCATCAA-TTCT
1 TTTCATCAACTTCT
2584940 TTT
1 TTT
2584943 TCTTCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCATCAACTTCT
Found at i:2595997 original size:11 final size:11
Alignment explanation
Indices: 2595983--2596019 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2595973 AAAATATTAA
2595983 TATTTTAATAT
1 TATTTTAATAT
2595994 TATTTT-AT-T
1 TATTTTAATAT
2596003 TA-TTTAATAT
1 TATTTTAATAT
2596013 TATTTTA
1 TATTTTA
2596020 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.13
9 5 0.22
10 5 0.22
11 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTAATAT
Found at i:2596008 original size:19 final size:19
Alignment explanation
Indices: 2595986--2596023 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2595976 ATATTAATAT
2595986 TTTAATATTATTTTATTTA
1 TTTAATATTATTTTATTTA
2596005 TTTAATATTATTTTATTTA
1 TTTAATATTATTTTATTTA
2596024 AAAATATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATATTATTTTATTTA
Found at i:2602617 original size:35 final size:35
Alignment explanation
Indices: 2602532--2602617 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
2602522 ATCAATTTTT
* * * *
2602532 CAAGTCTCAAGTATAACCTTTACAATGCTTTTTCA
1 CAAGTATCAAGCACAACCTTTACAATGCTCTTTCA
*
2602567 C-AGGATCAAGCACAACCTTTACAATGC-CTTTCGA
1 CAAGTATCAAGCACAACCTTTACAATGCTCTTTC-A
2602601 CAAGTATCAAGCACAAC
1 CAAGTATCAAGCACAAC
2602618 GTCACTACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 4 0.09
34 24 0.56
35 15 0.35
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (35 bp):
CAAGTATCAAGCACAACCTTTACAATGCTCTTTCA
Found at i:2603341 original size:67 final size:67
Alignment explanation
Indices: 2603199--2603342 Score: 173
Period size: 67 Copynumber: 2.1 Consensus size: 67
2603189 CCTTCTTAGT
* * *
2603199 TGTTGATCCTTCAAGATTCAATAGCTTTTCTTACATTCTATCTCAAAATAGAGCTTCATAGCATG
1 TGTTGATTCTCCAAGATTCAATAGCCTTTCTTACATTCTATCTCAAAATAGAGCTTCATAGCATG
2603264 GA
66 GA
** * * * * * *
2603266 AATCGATTCTCCAAGCTTCAAGT-GCCTTTCTTACATTCTATCTTAAGATCGCGCTTCATAGCAT
1 TGTTGATTCTCCAAGATTCAA-TAGCCTTTCTTACATTCTATCTCAAAATAGAGCTTCATAGCAT
2603330 GGA
65 GGA
2603333 TGTTGATTCT
1 TGTTGATTCT
2603343 AAAGAAAAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
67 61 0.98
68 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (67 bp):
TGTTGATTCTCCAAGATTCAATAGCCTTTCTTACATTCTATCTCAAAATAGAGCTTCATAGCATG
GA
Found at i:2615638 original size:18 final size:18
Alignment explanation
Indices: 2615585--2615638 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2615575 GCTTGTTGTC
* * *
2615585 TAGCCTATTTGGACTACT
1 TAGCCTACTTGGGCTGCT
*
2615603 TAGCCTACTTGGGTTGCT
1 TAGCCTACTTGGGCTGCT
2615621 TAGCCT-CTTCGGGCTGCT
1 TAGCCTACTT-GGGCTGCT
2615639 AACTGTTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (18 bp):
TAGCCTACTTGGGCTGCT
Found at i:2619478 original size:36 final size:35
Alignment explanation
Indices: 2619394--2619575 Score: 165
Period size: 36 Copynumber: 5.2 Consensus size: 35
2619384 TCAAGCACTA
*
2619394 GATTAAAATTGTTTAATTAAG--TTGTGCCTAATT
1 GATTAAAATTGTTTAATTAAGCATTGGGCCTAATT
* **
2619427 AATT-AAATTGTTTAATTAAGCCATTGGGCCTTGTT
1 GATTAAAATTGTTTAATTAAG-CATTGGGCCTAATT
*
2619462 GATTAAAATTGTTTAATTAAGTCATTAGGCCTAATT
1 GATTAAAATTGTTTAATTAAG-CATTGGGCCTAATT
* ** * *
2619498 GATTAAAATTGTTTGATTAAATTATTGGGCTTGATT
1 GATTAAAATTGTTTAATT-AAGCATTGGGCCTAATT
* * * * *
2619534 AATT-AAACTATTTAATTAAGTTATTGGACCTAATT
1 GATTAAAATTGTTTAATTAAG-CATTGGGCCTAATT
2619569 GATTAAA
1 GATTAAA
2619576 TTAAACAACT
Statistics
Matches: 118, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
32 16 0.14
33 3 0.03
34 2 0.02
35 36 0.31
36 59 0.50
37 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (35 bp):
GATTAAAATTGTTTAATTAAGCATTGGGCCTAATT
Found at i:2619553 original size:71 final size:71
Alignment explanation
Indices: 2619395--2619575 Score: 185
Period size: 71 Copynumber: 2.6 Consensus size: 71
2619385 CAAGCACTAG
* * * *
2619395 ATTAAAATTGTTTAATTAAG---TTGTGCCTAATTAATT-AAATTGTTTAATTAAGCCATTGGGC
1 ATTAAAACTATTTAATTAAGTCATTG-GCCTAATTGATTAAAATTGTTTAATTAAACCATTGGGC
*
2619456 CTTGTTG
65 CTTGTTA
* * * **
2619463 ATTAAAATTGTTTAATTAAGTCATTAGGCCTAATTGATTAAAATTGTTTGATTAAATTATTGGG-
1 ATTAAAACTATTTAATTAAGTCATT-GGCCTAATTGATTAAAATTGTTTAATTAAACCATTGGGC
2619527 CTTGATTA
65 CTTG-TTA
*
2619535 ATT-AAACTATTTAATTAAGTTATTGGACCTAATTGATTAAA
1 ATTAAAACTATTTAATTAAGTCATTGG-CCTAATTGATTAAA
2619576 TTAAACAACT
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
68 20 0.21
70 2 0.02
71 49 0.51
72 26 0.27
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (71 bp):
ATTAAAACTATTTAATTAAGTCATTGGCCTAATTGATTAAAATTGTTTAATTAAACCATTGGGCC
TTGTTA
Found at i:2625184 original size:30 final size:30
Alignment explanation
Indices: 2625150--2625218 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
2625140 CAAGAAGTTA
* *
2625150 ATGAAGAAATTTAAAATGATCATAGAAATC
1 ATGAAGAAATTCAAAATGATCATAGAAACC
* *
2625180 ATGAAGAGATTCAAAATTATCATAGAAACC
1 ATGAAGAAATTCAAAATGATCATAGAAACC
*
2625210 ATGATGAAA
1 ATGAAGAAA
2625219 AGGATCAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (30 bp):
ATGAAGAAATTCAAAATGATCATAGAAACC
Found at i:2626034 original size:14 final size:14
Alignment explanation
Indices: 2626015--2626057 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2626005 TTTTGATGTA
2626015 TTTCCAATGGAAAT
1 TTTCCAATGGAAAT
*
2626029 TTTCCAATAG-AAT
1 TTTCCAATGGAAAT
*
2626042 ATTTCCATTGGAAAT
1 -TTTCCAATGGAAAT
2626057 T
1 T
2626058 CGTTGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (14 bp):
TTTCCAATGGAAAT
Found at i:2626366 original size:21 final size:20
Alignment explanation
Indices: 2626336--2626376 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2626326 ATATTAAGAA
* *
2626336 TTTTTAAAAATTGTGTTAAT
1 TTTTTAAAAAATGTATTAAT
2626356 TTTTATAAAAAATGTATTAAT
1 TTTT-TAAAAAATGTATTAAT
2626377 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAAATGTATTAAT
Found at i:2627038 original size:18 final size:18
Alignment explanation
Indices: 2626987--2627029 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 18
2626977 TACAGTTAAT
*
2626987 AACTTTATTAGTTAT-T-
1 AACTTTATAAGTTATATA
2627003 -ACTTTATAAGTTATATA
1 AACTTTATAAGTTATATA
2627020 AACTTTATAA
1 AACTTTATAA
2627030 TATTTATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 13 0.57
16 1 0.04
18 9 0.39
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (18 bp):
AACTTTATAAGTTATATA
Found at i:2627748 original size:19 final size:19
Alignment explanation
Indices: 2627700--2627748 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
2627690 TTAATTTAGT
* * *
2627700 TAATATATATTAAATAATA
1 TAATATATAATGAATAAAA
*
2627719 TATTATATAATGAATAAAA
1 TAATATATAATGAATAAAA
*
2627738 TAATATTTAAT
1 TAATATATAAT
2627749 TTATTTACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATATATAATGAATAAAA
Found at i:2633376 original size:29 final size:28
Alignment explanation
Indices: 2633326--2633466 Score: 113
Period size: 28 Copynumber: 4.9 Consensus size: 28
2633316 TGGTAGCTTT
* * *
2633326 AACATGTTTGTCTTAATTTAGATAACAA
1 AACATATTTGTCTTAATGTAGACAACAA
*
2633354 AACATATTTGGTCTTAATGTAGACAAGAA
1 AACATATTT-GTCTTAATGTAGACAACAA
* * *
2633383 AATATATTTGTCTTAATTTAAGACAAGAA
1 AACATATTTGTCTTAATGT-AGACAACAA
* * * *
2633412 AA-ATATTTTTTGTCCTATTCTAGACAATAA
1 AACATA---TTTGTCTTAATGTAGACAACAA
* *
2633442 AACATATTTGTCTCAATTTAGACAA
1 AACATATTTGTCTTAATGTAGACAA
2633467 GATAAAATAT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
28 35 0.38
29 35 0.38
30 10 0.11
31 13 0.14
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (28 bp):
AACATATTTGTCTTAATGTAGACAACAA
Found at i:2633417 original size:28 final size:28
Alignment explanation
Indices: 2633326--2633476 Score: 146
Period size: 29 Copynumber: 5.2 Consensus size: 28
2633316 TGGTAGCTTT
* * *
2633326 AACATGTTTGTCTTAATTTAGATAACAA
1 AACATATTTGTCTTAATTTAGACAAGAA
*
2633354 AACATATTTGGTCTTAATGTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
*
2633383 AATATATTTGTCTTAATTTAAGACAAGAA
1 AACATATTTGTCTTAATTT-AGACAAGAA
* *
2633412 AA-ATATTTTTTGTCCT-ATTCTAGACAATAA
1 AACATA---TTTGTCTTAATT-TAGACAAGAA
*
2633442 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATATTTGTCTTAATTTAGACAAGA-A
2633471 AA-ATAT
1 AACATAT
2633477 AATGCTAGGA
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
28 38 0.37
29 41 0.40
30 13 0.13
31 11 0.11
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:2637209 original size:3 final size:3
Alignment explanation
Indices: 2637201--2637241 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2637191 AGTTTTTTAC
2637201 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2637242 CATCTTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2646066 original size:30 final size:30
Alignment explanation
Indices: 2646028--2646098 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
2646018 AAGTATGTAT
2646028 ATACATACATACATGCATATAAATATACAC
1 ATACATACATACATGCATATAAATATACAC
* * ** *
2646058 ATATATACATACATTCATATGCATATACAT
1 ATACATACATACATGCATATAAATATACAC
2646088 ATACATACATA
1 ATACATACATA
2646099 TACATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (30 bp):
ATACATACATACATGCATATAAATATACAC
Found at i:2646082 original size:22 final size:22
Alignment explanation
Indices: 2646056--2646163 Score: 74
Period size: 22 Copynumber: 5.0 Consensus size: 22
2646046 ATAAATATAC
*
2646056 ACATATATACATACATTCATAT
1 ACATATATACATACATACATAT
* * *
2646078 GCATATACATATACATACATAT
1 ACATATATACATACATACATAT
* * * *
2646100 ACATATATACGTACTTACACAC
1 ACATATATACATACATACATAT
* * * * *
2646122 ATACACACACATATATACATAT
1 ACATATATACATACATACATAT
* *
2646144 ACACATA-ACATATATACATA
1 ACATATATACATACATACATA
2646164 CAAACACATA
Statistics
Matches: 64, Mismatches: 22, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
21 13 0.20
22 51 0.80
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (22 bp):
ACATATATACATACATACATAT
Found at i:2646098 original size:16 final size:16
Alignment explanation
Indices: 2646026--2646106 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 16
2646016 TTAAGTATGT
*
2646026 ATATACATACATACATGC
1 ATATACAT--ATACATAC
* * *
2646044 ATATAAATATACACAT
1 ATATACATATACATAC
*
2646060 ATATACATACATTCATATGC
1 ATATACAT--ATACATA--C
2646080 ATATACATATACATAC
1 ATATACATATACATAC
2646096 ATATACATATA
1 ATATACATATA
2646107 TACGTACTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
16 24 0.48
18 18 0.36
20 8 0.16
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.32
Consensus pattern (16 bp):
ATATACATATACATAC
Found at i:2646156 original size:21 final size:20
Alignment explanation
Indices: 2646122--2646163 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2646112 ACTTACACAC
*
2646122 ATACACACACATATATACAT
1 ATACACAAACATATATACAT
2646142 ATACACATAACATATATACAT
1 ATACACA-AACATATATACAT
2646163 A
1 A
2646164 CAAACACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
ATACACAAACATATATACAT
Found at i:2646289 original size:4 final size:4
Alignment explanation
Indices: 2646280--2646304 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2646270 AGATACTTAT
2646280 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
2646305 CATATACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:2646339 original size:18 final size:18
Alignment explanation
Indices: 2646286--2646360 Score: 51
Period size: 20 Copynumber: 3.9 Consensus size: 18
2646276 TTATATACAT
* *
2646286 ACATACATACATACATAC
1 ACATACAAACATATATAC
* * *
2646304 ACATATACACGTGCATATAC
1 ACATACAAACAT--ATATAC
2646324 ACATACAAACATATATATAC
1 ACATACAAAC--ATATATAC
* *
2646344 ATATATAAACATATATA
1 ACATACAAACATATATA
2646361 TATGTATATT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
18 16 0.36
20 27 0.61
22 1 0.02
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.27
Consensus pattern (18 bp):
ACATACAAACATATATAC
Found at i:2646347 original size:10 final size:10
Alignment explanation
Indices: 2646318--2646362 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
2646308 ATACACGTGC
*
2646318 ATATACACAT
1 ATATACATAT
* *
2646328 ACAAACATAT
1 ATATACATAT
2646338 ATATACATAT
1 ATATACATAT
*
2646348 ATAAACATAT
1 ATATACATAT
2646358 ATATA
1 ATATA
2646363 TGTATATTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATACATAT
Found at i:2646369 original size:20 final size:20
Alignment explanation
Indices: 2646318--2646362 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2646308 ATACACGTGC
* *
2646318 ATATACACATACAAACATAT
1 ATATACATATATAAACATAT
2646338 ATATACATATATAAACATAT
1 ATATACATATATAAACATAT
2646358 ATATA
1 ATATA
2646363 TGTATATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATACATATATAAACATAT
Found at i:2646557 original size:5 final size:5
Alignment explanation
Indices: 2646549--2646582 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
2646539 TTAATTTAAA
*
2646549 TTATT TTATT TTAATT TTATG TTATT TTATT TTA
1 TTATT TTATT TT-ATT TTATT TTATT TTATT TTA
2646583 AATTACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:2646573 original size:16 final size:15
Alignment explanation
Indices: 2646549--2646582 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2646539 TTAATTTAAA
*
2646549 TTATTTTATTTTAATT
1 TTATGTTATTTT-ATT
2646565 TTATGTTATTTTATT
1 TTATGTTATTTTATT
2646580 TTA
1 TTA
2646583 AATTACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTATGTTATTTTATT
Found at i:2653317 original size:68 final size:69
Alignment explanation
Indices: 2653155--2653383 Score: 216
Period size: 68 Copynumber: 3.4 Consensus size: 69
2653145 ATGTTTGGTG
* * * * * *
2653155 TGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATAAACCATAAG-AGTTGATTAAGTA
1 TGATAAATACCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAAGATGATTAAATA
2653219 TGCA
66 TGCA
** ** * * *
2653223 TGATGTATATTATAAGATTGTATATATGATGTAAACTCCATATACCATATGAAG-TGATTAAATA
1 TGATAAATACCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAAGATGATTAAATA
2653287 TGCA
66 TGCA
* * * * * * *
2653291 TGATAAATGCCATGAGATAATGTATATAATGTATATTCCATATACTACAT-AAGATGATTGAGAA
1 TGATAAATACCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAAGATGATT-A-AA
2653355 -A-GCA
64 TATGCA
*
2653359 TGATAAATACCATGAGATTATGTAT
1 TGATAAATACCATAAGATTATGTAT
2653384 GCGATGTATT
Statistics
Matches: 131, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
67 3 0.02
68 122 0.93
69 4 0.03
70 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (69 bp):
TGATAAATACCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAAGATGATTAAATA
TGCA
Found at i:2653960 original size:20 final size:20
Alignment explanation
Indices: 2653914--2653960 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2653904 ACATTTTATT
* *
2653914 AATGTATTGATACATGTACG
1 AATGTATCGATACATGTAAG
*
2653934 AAAGTATCGATACAT-TCAAG
1 AATGTATCGATACATGT-AAG
2653954 AATGTAT
1 AATGTAT
2653961 TAATAGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATGTAAG
Found at i:2659211 original size:40 final size:41
Alignment explanation
Indices: 2659165--2659241 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
2659155 TGAAAGACAC
* *
2659165 CAATCTTGGCGAGGTTAG-AAACCCCAGTAAGGTGAACCAT
1 CAATCTTGGCAAGGTTAGAAAACCCCACTAAGGTGAACCAT
*
2659205 CAATCTTGGCAAGGTTAGAAAACCCTACTAAGGTGAA
1 CAATCTTGGCAAGGTTAGAAAACCCCACTAAGGTGAA
2659242 GAATAGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.52
41 16 0.48
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (41 bp):
CAATCTTGGCAAGGTTAGAAAACCCCACTAAGGTGAACCAT
Found at i:2671617 original size:18 final size:19
Alignment explanation
Indices: 2671594--2671634 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2671584 AATATGAATC
2671594 GAATTT-AGAAAG-GCAAAT
1 GAATTTGAGAAAGTG-AAAT
2671612 GAATTTGAGAAAGTGAAAT
1 GAATTTGAGAAAGTGAAAT
2671631 GAAT
1 GAAT
2671635 GGTGTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (19 bp):
GAATTTGAGAAAGTGAAAT
Found at i:2672036 original size:29 final size:29
Alignment explanation
Indices: 2671994--2672054 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2671984 TCCTAAGAAG
2671994 TGAGGCGAATTTACCATTACCTCATTGGT
1 TGAGGCGAATTTACCATTACCTCATTGGT
2672023 TGAGGCGAATTTACCATTACCTCATTGGT
1 TGAGGCGAATTTACCATTACCTCATTGGT
2672052 TGA
1 TGA
2672055 ACACCCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (29 bp):
TGAGGCGAATTTACCATTACCTCATTGGT
Found at i:2672970 original size:32 final size:33
Alignment explanation
Indices: 2672934--2672997 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2672924 ACCTCTCAAT
* * *
2672934 ACAATGCCTTTT-ATGGGTCAAGCACAACCTTC
1 ACAATGCCTTTTAAAGGCTAAAGCACAACCTTC
2672966 ACAATGCCTTTTAAAGGCTAAAGCACAACCTT
1 ACAATGCCTTTTAAAGGCTAAAGCACAACCTT
2672998 TTCTCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (33 bp):
ACAATGCCTTTTAAAGGCTAAAGCACAACCTTC
Found at i:2673676 original size:21 final size:21
Alignment explanation
Indices: 2673606--2673677 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
2673596 AAACTAATTT
* **
2673606 AAACAAGTTCAAAAAAAATTC
1 AAACAATTTCAAAAATCATTC
*
2673627 AAACAAGTTCAAAAATCATT-
1 AAACAATTTCAAAAATCATTC
*
2673647 AAAGCAATTTCAAAACTCATTC
1 AAA-CAATTTCAAAAATCATTC
*
2673669 AAATAATTT
1 AAACAATTT
2673678 TGAAACTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (21 bp):
AAACAATTTCAAAAATCATTC
Found at i:2673735 original size:21 final size:20
Alignment explanation
Indices: 2673709--2673798 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 20
2673699 ACTTCAGCAC
*
2673709 TTTAAAATTTTTTTAAAAAAG
1 TTTAAAA-TTATTTAAAAAAG
*
2673730 TTTAAAAAGTA-TTAAAACAAG
1 TTT-AAAATTATTTAAAA-AAG
* *
2673751 TTCAAAAACTTATTTAAAAAAC
1 TT-TAAAA-TTATTTAAAAAAG
* *
2673773 TTTAAAAATCATTTAAACAAG
1 TTT-AAAATTATTTAAAAAAG
2673794 TTTAA
1 TTTAA
2673799 GGATCACTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
20 8 0.15
21 26 0.48
22 14 0.26
23 6 0.11
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
TTTAAAATTATTTAAAAAAG
Found at i:2673804 original size:21 final size:21
Alignment explanation
Indices: 2673720--2673827 Score: 74
Period size: 21 Copynumber: 5.1 Consensus size: 21
2673710 TTAAAATTTT
* *
2673720 TTTAAAAAAGTTTAAAAAGT-A
1 TTTAAACAAGTTTAAAGA-TCA
* * * *
2673741 TTAAAACAAGTTCAAAAACTTA
1 TTTAAACAAGTTTAAAGA-TCA
* * *
2673763 TTTAAAAAACTTTAAAAATCA
1 TTTAAACAAGTTTAAAGATCA
*
2673784 TTTAAACAAGTTTAAGGATCA
1 TTTAAACAAGTTTAAAGATCA
* * *
2673805 CTCAAACAAGTTCAAAGATCA
1 TTTAAACAAGTTTAAAGATCA
2673826 TT
1 TT
2673828 GAAGCAATTT
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
21 53 0.78
22 15 0.22
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (21 bp):
TTTAAACAAGTTTAAAGATCA
Found at i:2674192 original size:23 final size:23
Alignment explanation
Indices: 2674165--2674228 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
2674155 CGGAAGATAG
*
2674165 AAACACAATAAGCACAATTTGCA
1 AAACACAACAAGCACAATTTGCA
2674188 AAACACAACAAGCACAATTTGCA
1 AAACACAACAAGCACAATTTGCA
2674211 AAACACAACAAGCACAAT
1 AAACACAACAAGCACAAT
2674229 AAGAAGCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.55, C:0.25, G:0.08, T:0.12
Consensus pattern (23 bp):
AAACACAACAAGCACAATTTGCA
Found at i:2692134 original size:32 final size:32
Alignment explanation
Indices: 2692085--2692205 Score: 109
Period size: 36 Copynumber: 3.6 Consensus size: 32
2692075 AATACTTTTT
* *
2692085 AAGGTTCAAGCATAACCTTTACAATGCCTTTC
1 AAGGATCAAGCACAACCTTTACAATGCCTTTC
* *
2692117 AAGGATCAAGCACAACCTCTCAATACAATGTCTTTT
1 AAGGATCAAGCACAACCT-T---TACAATGCCTTTC
* * *
2692153 ATGGATCAAGCACAGCCTTCACAATGCCTTTTC
1 AAGGATCAAGCACAACCTTTACAATGCC-TTTC
*
2692186 AAGGCT-AAGGCACAACCTTT
1 AAGGATCAA-GCACAACCTTT
2692206 TCTCTCTTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
32 25 0.36
33 17 0.24
35 1 0.01
36 27 0.39
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (32 bp):
AAGGATCAAGCACAACCTTTACAATGCCTTTC
Found at i:2692388 original size:70 final size:70
Alignment explanation
Indices: 2692275--2692408 Score: 250
Period size: 70 Copynumber: 1.9 Consensus size: 70
2692265 TACAATGTAC
* *
2692275 GAAGAGTATGATGAGTATAAAAATGATTACCATTTATAGGAATGAAGGAACAAGGGAATTATAGT
1 GAAGAGTATGATGAGTATAAAAATGATTACCATATATAGGAATGAAGGAACAAAGGAATTATAGT
2692340 GCTAG
66 GCTAG
2692345 GAAGAGTATGATGAGTATAAAAATGATTACCATATATAGGAATGAAGGAACAAAGGAATTATAG
1 GAAGAGTATGATGAGTATAAAAATGATTACCATATATAGGAATGAAGGAACAAAGGAATTATAG
2692409 CGCAAGAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.25
Consensus pattern (70 bp):
GAAGAGTATGATGAGTATAAAAATGATTACCATATATAGGAATGAAGGAACAAAGGAATTATAGT
GCTAG
Found at i:2692735 original size:20 final size:20
Alignment explanation
Indices: 2692656--2692735 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
2692646 TTCTAGACCA
* * * *
2692656 AATGTATCGATGCATTTTGA
1 AATGTATCCATACATTTGGG
2692676 AATGTATCCATACATTTGGG
1 AATGTATCCATACATTTGGG
2692696 AATGTATCCATACATTTGGG
1 AATGTATCCATACATTTGGG
*
2692716 AATGTATCTATACATTTGGG
1 AATGTATCCATACATTTGGG
2692736 CAAAACCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (20 bp):
AATGTATCCATACATTTGGG
Found at i:2692908 original size:21 final size:21
Alignment explanation
Indices: 2692871--2692937 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
2692861 AGACTAATTT
* *
2692871 AAACAAGTTTAAAAAATTATTC
1 AAACAAG-TTCAAAAATCATTC
2692893 AAACAAGTTCAAAAATCATT-
1 AAACAAGTTCAAAAATCATTC
* *
2692913 AAAGCAATTTCAAAACTCATTC
1 AAA-CAAGTTCAAAAATCATTC
2692935 AAA
1 AAA
2692938 TAATTTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.08
21 26 0.67
22 10 0.26
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.27
Consensus pattern (21 bp):
AAACAAGTTCAAAAATCATTC
Found at i:2692942 original size:21 final size:21
Alignment explanation
Indices: 2692871--2692950 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
2692861 AGACTAATTT
* * *
2692871 AAACAAGTTTAAAAAATTATTC
1 AAACAA-TTTCAAAACTCATTC
* *
2692893 AAACAAGTTCAAAAATCATT-
1 AAACAATTTCAAAACTCATTC
2692913 AAAGCAATTTCAAAACTCATTC
1 AAA-CAATTTCAAAACTCATTC
* *
2692935 AAATAATTTGAAAACT
1 AAACAATTTCAAAACT
2692951 TTTCACATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 3 0.06
21 37 0.76
22 9 0.18
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.29
Consensus pattern (21 bp):
AAACAATTTCAAAACTCATTC
Found at i:2693062 original size:21 final size:21
Alignment explanation
Indices: 2692999--2693092 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
2692989 AAAAAGTTTA
*
2692999 AAAAAT-ATTCGAACAAGTTC
1 AAAAATCATTCAAACAAGTTC
* * * *
2693019 AAAAACTTATTTAAATAACTTC
1 AAAAA-TCATTCAAACAAGTTC
*
2693041 AAAAATCGTTCAAACAAGTTC
1 AAAAATCATTCAAACAAGTTC
** * *
2693062 AAGGATCATTCAAAAAAGTTT
1 AAAAATCATTCAAACAAGTTC
*
2693083 AAAGATCATT
1 AAAAATCATT
2693093 GAAGCAATTT
Statistics
Matches: 57, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 5 0.09
21 37 0.65
22 15 0.26
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.29
Consensus pattern (21 bp):
AAAAATCATTCAAACAAGTTC
Found at i:2698770 original size:18 final size:18
Alignment explanation
Indices: 2698749--2698787 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2698739 TATATATGTA
*
2698749 AATTTA-TATATTGAAAAG
1 AATTTATTAT-TTCAAAAG
2698767 AATTTATTATTTCAAAAG
1 AATTTATTATTTCAAAAG
2698785 AAT
1 AAT
2698788 AATAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTTATTATTTCAAAAG
Found at i:2703344 original size:23 final size:23
Alignment explanation
Indices: 2703317--2703362 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2703307 AATTCTTCAA
2703317 AACATTACTTATGAAAGCAAAAG
1 AACATTACTTATGAAAGCAAAAG
2703340 AACATTACTTATGAAAGCAAAAG
1 AACATTACTTATGAAAGCAAAAG
2703363 GGATAACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (23 bp):
AACATTACTTATGAAAGCAAAAG
Found at i:2706963 original size:40 final size:41
Alignment explanation
Indices: 2706887--2706966 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
2706877 TTGGCTATTC
* * *
2706887 TTCACCTTAGTGGGGTTTTCTAATCTTGTCGAGATTGGTGG
1 TTCACCTTAGTGAGGTTTTCTAACCTTGTCCAGATTGGTGG
2706928 TTCACCTTAGTGAGG-TTTCTAACCTTG-CCACGATTGGTG
1 TTCACCTTAGTGAGGTTTTCTAACCTTGTCCA-GATTGGTG
2706967 CCTTTCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 2 0.06
40 19 0.54
41 14 0.40
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (41 bp):
TTCACCTTAGTGAGGTTTTCTAACCTTGTCCAGATTGGTGG
Found at i:2707056 original size:28 final size:28
Alignment explanation
Indices: 2707012--2707066 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2707002 CGACGTCACT
* *
2707012 TTATTTCTGTTTGATGTAATTTATTTGA
1 TTATTTATGTTTCATGTAATTTATTTGA
2707040 TTATTTATGTTTCATGTAATTTATTTG
1 TTATTTATGTTTCATGTAATTTATTTG
2707067 TTTGTAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.62
Consensus pattern (28 bp):
TTATTTATGTTTCATGTAATTTATTTGA
Found at i:2707063 original size:16 final size:16
Alignment explanation
Indices: 2707014--2707063 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 16
2707004 ACGTCACTTT
*
2707014 ATTTCTGTTTGATGTA
1 ATTTATGTTTGATGTA
2707030 ATTTA--TTTGAT-T-
1 ATTTATGTTTGATGTA
*
2707042 ATTTATGTTTCATGTA
1 ATTTATGTTTGATGTA
2707058 ATTTAT
1 ATTTAT
2707064 TTGTTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.18
13 1 0.04
14 11 0.39
15 1 0.04
16 10 0.36
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (16 bp):
ATTTATGTTTGATGTA
Found at i:2707954 original size:55 final size:55
Alignment explanation
Indices: 2707870--2708015 Score: 276
Period size: 55 Copynumber: 2.7 Consensus size: 55
2707860 TCATCCTATG
2707870 CAATATTAGAAAAGAATAAATTTTTATGTATAGTTTCAAACGAGCATTCTTAATA
1 CAATATTAGAAAAGAATAAATTTTTATGTATAGTTTCAAACGAGCATTCTTAATA
2707925 CAATATTAGAAAAGAATAAATTTTTATGTATAGTTTCAAACGAGCATTCTTAATA
1 CAATATTAGAAAAGAATAAATTTTTATGTATAGTTTCAAACGAGCATTCTTAATA
2707980 CAATATTAGAAAAGAATAAATTTTTATAG-ATAGTTT
1 CAATATTAGAAAAGAATAAATTTTTAT-GTATAGTTT
2708016 TGAGAAACCA
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
55 89 0.99
56 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (55 bp):
CAATATTAGAAAAGAATAAATTTTTATGTATAGTTTCAAACGAGCATTCTTAATA
Found at i:2709951 original size:15 final size:15
Alignment explanation
Indices: 2709931--2709962 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2709921 TTGCATTTGG
*
2709931 AAACTTATGTTGGAT
1 AAACTTATGCTGGAT
2709946 AAACTTATGCTGGAT
1 AAACTTATGCTGGAT
2709961 AA
1 AA
2709963 TGTTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (15 bp):
AAACTTATGCTGGAT
Found at i:2720995 original size:35 final size:35
Alignment explanation
Indices: 2720927--2720995 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2720917 ATGGAGACAC
*
2720927 AGATCACACACATGCTAAAGCAATGAACGGAGAAT
1 AGATCACACACATGCTAAAGCAATGAACAGAGAAT
* *
2720962 AGATCACACACAGTGC-AAAGCAATTAGCAGAGAA
1 AGATCACACACA-TGCTAAAGCAATGAACAGAGAA
2720996 CTAATCATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (35 bp):
AGATCACACACATGCTAAAGCAATGAACAGAGAAT
Found at i:2725355 original size:34 final size:33
Alignment explanation
Indices: 2725282--2725355 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 33
2725272 GGTTGCTTTC
* * *
2725282 AAAAATAGCCATATATGGGTTATGGTTGAGCCT
1 AAAAAAAGCCATATATGGGTTATGGTTAAACCT
*
2725315 AGAAAAAGCCACTATATGGGTTATGGTTAAACCT
1 AAAAAAAGCCA-TATATGGGTTATGGTTAAACCT
2725349 AAAAAAA
1 AAAAAAA
2725356 AATCATATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 9 0.26
34 26 0.74
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (33 bp):
AAAAAAAGCCATATATGGGTTATGGTTAAACCT
Found at i:2732024 original size:20 final size:20
Alignment explanation
Indices: 2732004--2732041 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2731994 GGTTATTAGA
2732004 AATA-TTTGAGAAGAAGAAG
1 AATATTTTGAGAAGAAGAAG
*
2732023 AATATTTTGAGTAGAAGAA
1 AATATTTTGAGAAGAAGAA
2732042 AGAGTATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (20 bp):
AATATTTTGAGAAGAAGAAG
Found at i:2734721 original size:3 final size:3
Alignment explanation
Indices: 2734713--2734742 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2734703 AGAAACCTTC
2734713 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2734743 ATTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Done.