Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 143 of 226
Found at i:47497521 original size:20 final size:20
Alignment explanation
Indices: 47497490--47497553 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
47497480 ATTACAAAAA
47497490 AAAAATTT-AAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
47497509 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
47497529 AAAAATTTCAAAAT-TTATAT
1 AAAAATTTCAAAATATT-TAT
47497549 AAAAA
1 AAAAA
47497554 AGCTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:47503398 original size:39 final size:41
Alignment explanation
Indices: 47503355--47503444 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 41
47503345 TTTCCTTATG
47503355 CTATTACA-ACA-TCATTCCATTTAACCAAAC-ATAAGAATA
1 CTATTACATACATTCATTCCATTTAACCAAACAAT-AGAATA
* *
47503394 CTATTACAGTTCCATTTCATTCCATTTAACCAAACAATTGAATA
1 CTATTACA--TACA-TTCATTCCATTTAACCAAACAATAGAATA
47503438 CTATTAC
1 CTATTAC
47503445 GCCTCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 8 0.19
42 2 0.05
44 31 0.72
45 2 0.05
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.33
Consensus pattern (41 bp):
CTATTACATACATTCATTCCATTTAACCAAACAATAGAATA
Found at i:47507846 original size:43 final size:44
Alignment explanation
Indices: 47507748--47507871 Score: 112
Period size: 43 Copynumber: 2.9 Consensus size: 44
47507738 AGCTTGTACA
* * * * *
47507748 ATGCCAACGTCCTAGAC-GTGGTCTTACATGTAATCA-TAGATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACATGAAAACACAAGATAG
*
47507791 ATACC-ACTGTCCCAGACAGGGTCTTACATGAAAACACAAG-TAG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACATGAAAACACAAGATAG
* * * *
47507834 ATGCCAACGTCCCAAACATGGTCTTACACGAGAACACA
1 ATGCCAACGTCCCAGACAGGGTCTTACATGAAAACACA
47507872 TATCGGAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.03
43 59 0.89
44 5 0.08
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGAAAACACAAGATAG
Found at i:47511401 original size:3 final size:3
Alignment explanation
Indices: 47511388--47511420 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
47511378 CCAAACAGAA
47511388 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
47511421 ATAAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:47531379 original size:41 final size:41
Alignment explanation
Indices: 47531330--47531438 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
47531320 GACTTTAAGT
*
47531330 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
47531371 CTAGCAGGCTACGTACCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
47531412 CTAGCAGGCTAAGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
47531439 TTTAAATTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 56 0.92
42 5 0.08
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:47534220 original size:40 final size:40
Alignment explanation
Indices: 47534176--47534260 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 40
47534166 ATTTAATAAA
* ** *
47534176 AATATATAATTTAATAAAATTCTTA-ATATTAGATATTCTT
1 AATATATAAATTAATAAAATAATAATATATTAGATATT-TT
*
47534216 AATAT-TAAATTACTAAAATAATAATATATTAGATATTTT
1 AATATATAAATTAATAAAATAATAATATATTAGATATTTT
47534255 -ATATAT
1 AATATAT
47534261 TTTTCTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
38 4 0.11
39 17 0.45
40 17 0.45
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (40 bp):
AATATATAAATTAATAAAATAATAATATATTAGATATTTT
Found at i:47536014 original size:4 final size:4
Alignment explanation
Indices: 47535998--47536036 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
47535988 GATGTTCATA
* *
47535998 TATG TATG CATG TATG TATG CATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
47536037 TTGGTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:47536015 original size:12 final size:12
Alignment explanation
Indices: 47535998--47536036 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
47535988 GATGTTCATA
47535998 TATGTATGCATG
1 TATGTATGCATG
47536010 TATGTATGCATG
1 TATGTATGCATG
*
47536022 TATGTATGTATG
1 TATGTATGCATG
47536034 TAT
1 TAT
47536037 TTGGTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (12 bp):
TATGTATGCATG
Found at i:47542740 original size:29 final size:26
Alignment explanation
Indices: 47542676--47542741 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
47542666 TCGATTAAAC
*
47542676 AATTT-TTAAACAATTTTTTAATTTA
1 AATTTATTAAACAATTTTTTAATTCA
47542701 AAGTATCTATTAAACAATTTTTTAAACATTCA
1 AA-T-T-TATTAAACAATTTTTT--A-ATTCA
47542733 AATTTATTA
1 AATTTATTA
47542742 GTTTAAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
25 2 0.06
26 1 0.03
27 1 0.03
28 1 0.03
29 19 0.58
30 1 0.03
31 2 0.06
32 6 0.18
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
AATTTATTAAACAATTTTTTAATTCA
Found at i:47542834 original size:12 final size:12
Alignment explanation
Indices: 47542796--47542834 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
47542786 AAAAACCAAA
47542796 TTTTAAAATTAT
1 TTTTAAAATTAT
* *
47542808 TTTTATAGTTAAT
1 TTTTAAAATT-AT
47542821 TTTTAAAATTAT
1 TTTTAAAATTAT
47542833 TT
1 TT
47542835 AATATTAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:47548072 original size:2 final size:2
Alignment explanation
Indices: 47548065--47548100 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47548055 NNNNNNTTGT
47548065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47548101 CACACGACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47549394 original size:28 final size:30
Alignment explanation
Indices: 47549333--47549400 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
47549323 GTAATATATT
47549333 TATTTAATTACTTTTTATTTAAGTAAATAGA
1 TATTT-ATTACTTTTTATTTAAGTAAATAGA
*
47549364 TATTTATTA-TTTATTA-TTAGGTAAA-AGA
1 TATTTATTACTTT-TTATTTAAGTAAATAGA
47549392 TATTTATTA
1 TATTTATTA
47549401 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 12 0.34
29 11 0.31
30 7 0.20
31 5 0.14
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.53
Consensus pattern (30 bp):
TATTTATTACTTTTTATTTAAGTAAATAGA
Found at i:47549705 original size:5 final size:5
Alignment explanation
Indices: 47549695--47549722 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
47549685 TATTTAAGTA
47549695 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
47549723 TATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:47552300 original size:17 final size:18
Alignment explanation
Indices: 47552260--47552301 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 18
47552250 TAGGGGAATG
47552260 AATTTTTA-ATTTTTTAT
1 AATTTTTATATTTTTTAT
47552277 AA--TTTATA-TTTTTAT
1 AATTTTTATATTTTTTAT
47552292 AATTTTTATA
1 AATTTTTATA
47552302 GAATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTTTTATATTTTTTAT
Found at i:47552580 original size:28 final size:28
Alignment explanation
Indices: 47552549--47552603 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
47552539 AAAAAATTAT
*
47552549 CATTTTAAAAATAAATTGGGATAATTTC
1 CATTTCAAAAATAAATTGGGATAATTTC
*
47552577 CATTTCAAAAATAAATTTGGATAATTT
1 CATTTCAAAAATAAATTGGGATAATTT
47552604 GTTTGATTTC
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:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (28 bp):
CATTTCAAAAATAAATTGGGATAATTTC
Found at i:47554245 original size:14 final size:14
Alignment explanation
Indices: 47554226--47554265 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
47554216 TTGTTTGGCA
47554226 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
47554240 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
47554254 GGAAAATGTTTT
1 GTAAAATGTTTT
47554266 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:47554274 original size:20 final size:20
Alignment explanation
Indices: 47554249--47554288 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47554239 CGTAAAATGA
*
47554249 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
47554269 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
47554289 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:47554278 original size:34 final size:35
Alignment explanation
Indices: 47554234--47554300 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
47554224 CAGTAAAATG
*
47554234 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
47554268 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
47554301 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:47554304 original size:14 final size:15
Alignment explanation
Indices: 47554228--47554304 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
47554218 GTTTGGCAGT
* *
47554228 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
47554242 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
47554256 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
47554276 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
47554291 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
47554305 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:47554359 original size:32 final size:31
Alignment explanation
Indices: 47554281--47554365 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
47554271 TCTGTAAAAT
* *
47554281 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
47554314 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
47554346 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
47554366 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:47554417 original size:14 final size:14
Alignment explanation
Indices: 47554398--47554425 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47554388 ATTTTACATA
47554398 TATTAATATATATT
1 TATTAATATATATT
47554412 TATTAATATATATT
1 TATTAATATATATT
47554426 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:47554731 original size:71 final size:72
Alignment explanation
Indices: 47554615--47554772 Score: 291
Period size: 71 Copynumber: 2.2 Consensus size: 72
47554605 ATAATAATAT
*
47554615 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGT-CTAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
47554679 CCACATA
66 CCACATA
*
47554686 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
47554751 CCACATA
66 CCACATA
47554758 TATCCAAATACATAA
1 TATCCAAATACATAA
47554773 ACCTGAGAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
71 45 0.54
72 39 0.46
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
CCACATA
Found at i:47555741 original size:35 final size:36
Alignment explanation
Indices: 47555695--47555763 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
47555685 ATTCAACCAT
47555695 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
47555730 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
47555764 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:47555761 original size:27 final size:28
Alignment explanation
Indices: 47555731--47555800 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
47555721 AATAATAAAT
*
47555731 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
47555758 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
47555786 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
47555801 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:47557313 original size:15 final size:16
Alignment explanation
Indices: 47557293--47557325 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
47557283 AGTACCACTT
47557293 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
47557308 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
47557324 AA
1 AA
47557326 GTACCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:47558904 original size:22 final size:23
Alignment explanation
Indices: 47558851--47558906 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
47558841 CCCATTTTTA
* * *
47558851 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
47558874 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
47558896 ATTAAAATTAA
1 ATTAAAATTAA
47558907 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:47558919 original size:16 final size:16
Alignment explanation
Indices: 47558882--47558921 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47558872 TTAATAAAAT
* *
47558882 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
47558898 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
47558914 TAAAATTA
1 TAAAATTA
47558922 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:47559006 original size:9 final size:9
Alignment explanation
Indices: 47558994--47559021 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
47558984 TTTATCAAAT
47558994 TATTAATTG
1 TATTAATTG
47559003 TATTAATTG
1 TATTAATTG
47559012 TATTAATTG
1 TATTAATTG
47559021 T
1 T
47559022 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:47559032 original size:68 final size:68
Alignment explanation
Indices: 47558910--47559119 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
47558900 AAATTAATTG
* *
47558910 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
47558973 TGA
66 TGA
47558976 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
47559041 TGA
66 TGA
*
47559044 TTAGTAAATTTATCAAACTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
47559109 TGA
66 TGA
47559112 TTAGTAAA
1 TTAGTAAA
47559120 ACAAACTTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
TGA
Found at i:47559076 original size:9 final size:9
Alignment explanation
Indices: 47559062--47559089 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
47559052 TTTATCAAAC
47559062 TATTAATTG
1 TATTAATTG
47559071 TATTAATTG
1 TATTAATTG
47559080 TATTAATTG
1 TATTAATTG
47559089 T
1 T
47559090 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:47559226 original size:22 final size:24
Alignment explanation
Indices: 47559186--47559229 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
47559176 AAATAAACTT
47559186 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
47559210 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
47559230 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:47562374 original size:2 final size:2
Alignment explanation
Indices: 47562367--47562397 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47562357 ATCAGTTCTT
47562367 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
47562398 TTTTTCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:47574180 original size:26 final size:26
Alignment explanation
Indices: 47574126--47574186 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
47574116 GCCTAGCGAG
* *
47574126 CTTGAGTTTAAATGGGTCAGAGGACC
1 CTTGAGTTTAAATGGGTCAGAGAAAC
*
47574152 CTTGAGTTTAAGTGGGTC-GAAGAAAC
1 CTTGAGTTTAAATGGGTCAG-AGAAAC
*
47574178 CTTAAGTTT
1 CTTGAGTTT
47574187 GATTTGGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (26 bp):
CTTGAGTTTAAATGGGTCAGAGAAAC
Found at i:47577415 original size:25 final size:24
Alignment explanation
Indices: 47577387--47577442 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
47577377 TTTTTATGTA
47577387 ATCTATATCTATATTTATAATTCAT
1 ATCTATATCTATATTTAT-ATTCAT
* * *
47577412 ATCTATGTTTATATTTATATTTAT
1 ATCTATATCTATATTTATATTCAT
47577436 A-CTATAT
1 ATCTATAT
47577443 ATTAAGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.19
24 6 0.22
25 16 0.59
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
ATCTATATCTATATTTATATTCAT
Found at i:47580009 original size:34 final size:34
Alignment explanation
Indices: 47579966--47580068 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
47579956 TCAACAAGAT
*
47579966 CTCATATTTGGAAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
47580000 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
47580034 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
47580068 C
1 C
47580069 ATGTCATATA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (34 bp):
CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
Found at i:47582113 original size:23 final size:22
Alignment explanation
Indices: 47582070--47582113 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
47582060 TTCTAAGTCG
47582070 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
47582093 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
47582114 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:47582220 original size:45 final size:45
Alignment explanation
Indices: 47582158--47582251 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
47582148 AACAGATACT
* * *
47582158 CGGTGGATTCAGAACATAGCAACCACGTTATTAATCAATAATGTC
1 CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
* * *
47582203 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
47582248 CGGT
1 CGGT
47582252 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:47582315 original size:51 final size:50
Alignment explanation
Indices: 47582248--47582443 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
47582238 CAATGATGTT
* * *
47582248 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * * *
47582299 TGATACACGTAGTAGCCTGCACATAGTACTACATACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
** * * * *
47582350 CGGTATGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
47582400 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
47582444 CACTTTCACT
Statistics
Matches: 116, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 72 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:47582432 original size:101 final size:101
Alignment explanation
Indices: 47582255--47582439 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
47582245 GTTCGGTTCA
* *
47582255 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
*
47582320 CATAGTACTACATACGTGATCGAAACTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* *
47582357 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
47582421 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
47582440 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 34 0.44
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:47587563 original size:16 final size:16
Alignment explanation
Indices: 47587542--47587590 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
47587532 TTCGCTGTAT
47587542 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
47587558 TGGAATAGAGGCGAAA
1 TGGAATAGAGGCGTAA
47587574 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
47587590 T
1 T
47587591 AGTAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.37, T:0.18
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:47587665 original size:44 final size:45
Alignment explanation
Indices: 47587572--47587666 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
47587562 ATAGAGGCGA
*
47587572 AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGG
* * *
47587617 AATGGAATAGAGGTGTAATAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTAAATCAAT-TGTTTGGTTGAATGG
47587661 AATGGA
1 AATGGA
47587667 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGG
Found at i:47587843 original size:18 final size:17
Alignment explanation
Indices: 47587822--47587856 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47587812 TTATTATTAA
*
47587822 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
47587840 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
47587857 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:47588013 original size:10 final size:12
Alignment explanation
Indices: 47587980--47588031 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
47587970 TATAATACTA
47587980 TAAAATATAATT
1 TAAAATATAATT
47587992 TAAAATATAATT
1 TAAAATATAATT
*
47588004 TAAAATAATTATT
1 TAAAAT-ATAATT
*
47588017 ATTAAATATAATT
1 -TAAAATATAATT
47588030 TA
1 TA
47588032 TAATCTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 19 0.56
13 10 0.29
14 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:47588050 original size:145 final size:144
Alignment explanation
Indices: 47587745--47588035 Score: 389
Period size: 145 Copynumber: 2.0 Consensus size: 144
47587735 GATTATTGTT
* *
47587745 ATTGTTATTAAATTTTAATAAGATTATTAATATCATTAATAAATAATTTAATCATATTTTAACAT
1 ATTGTTATT-AATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
** * *
47587810 AATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTG
65 AATTATTATTAAATATATAATAATTAAAATATATAATTTAATAAAAATCTTAATAATCAATATTA
*
47587875 TTATATGAATTTATT
130 TTATATGAATTTATA
47587890 ATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
1 ATTGTTATT-AATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
*
47587955 AATTATTATTAAATATATAAT-ACTATAAA-ATATAATTTAA-AATATAAT-TTAA-AAT-AATT
65 AATTATTATTAAATATATAATAATTA-AAATATATAATTTAATAA-A-AATCTTAATAATCAA-T
47588014 ATTATTAAATAT-AATTTATA
126 ATTATT--ATATGAATTTATA
47588034 AT
1 AT
47588036 CTACTTTATT
Statistics
Matches: 132, Mismatches: 8, Indels: 13
0.86 0.05 0.08
Matches are distributed among these distances:
142 2 0.02
143 11 0.08
144 28 0.21
145 91 0.69
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (144 bp):
ATTGTTATTAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACATA
ATTATTATTAAATATATAATAATTAAAATATATAATTTAATAAAAATCTTAATAATCAATATTAT
TATATGAATTTATA
Found at i:47590775 original size:21 final size:20
Alignment explanation
Indices: 47590751--47590789 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
47590741 GTTAAAAATA
47590751 ATTATCATTTTCATCATTTGG
1 ATTATCATTTTCAT-ATTTGG
47590772 ATTATCATTTTCATATTT
1 ATTATCATTTTCATATTT
47590790 TAATCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTATCATTTTCATATTTGG
Found at i:47592551 original size:21 final size:22
Alignment explanation
Indices: 47592522--47592573 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
47592512 CTCCATTATT
* *
47592522 TTTTCATTTTTTGTTT-GATTTG
1 TTTT-ATTTTTTATTTGGATTTC
*
47592544 TTTTATTTTTTATTTGGTTTTC
1 TTTTATTTTTTATTTGGATTTC
47592566 TTTTATTT
1 TTTTATTT
47592574 CATTGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.10, C:0.04, G:0.10, T:0.77
Consensus pattern (22 bp):
TTTTATTTTTTATTTGGATTTC
Found at i:47593311 original size:3 final size:3
Alignment explanation
Indices: 47593297--47593383 Score: 120
Period size: 3 Copynumber: 28.3 Consensus size: 3
47593287 CCTGTCATTG
* * *
47593297 TTA TTT TTA TTA TTA TTAA GCTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
47593344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47593384 GTATATTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 72 0.96
4 2 0.03
5 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:47593501 original size:12 final size:12
Alignment explanation
Indices: 47593484--47593517 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
47593474 TTATTTTATA
47593484 ATCTATATACAT
1 ATCTATATACAT
47593496 ATCTATAT--AT
1 ATCTATATACAT
47593506 ATCTATATACAT
1 ATCTATATACAT
47593518 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCTATATACAT
Found at i:47593608 original size:16 final size:17
Alignment explanation
Indices: 47593589--47593620 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47593579 TACTTACATT
47593589 TTTATATAC-TATATAA
1 TTTATATACATATATAA
47593605 TTTATATACATATATA
1 TTTATATACATATATA
47593621 CATACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATATACATATATAA
Found at i:47593631 original size:24 final size:24
Alignment explanation
Indices: 47593591--47593636 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
47593581 CTTACATTTT
*
47593591 TATATACTATATAATTTATATACA
1 TATATACTACATAATTTATATACA
*
47593615 TATATACATACAT-ATTTTTATA
1 TATATAC-TACATAATTTATATA
47593637 GTATGTGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATACTACATAATTTATATACA
Found at i:47600424 original size:51 final size:51
Alignment explanation
Indices: 47600363--47600469 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
47600353 GCTATTAAAA
47600363 TTATTCACGCTTGTCAAAATTTAATGTAACTTAAAATATGTGTCTCAAATT
1 TTATTCACGCTTGTCAAAATTTAATGTAACTTAAAATATGTGTCTCAAATT
47600414 TTATTCACGCTTGTCAAAATTTAATGTAACTTAAAATATGTGTCTCAAATT
1 TTATTCACGCTTGTCAAAATTTAATGTAACTTAAAATATGTGTCTCAAATT
47600465 TTATT
1 TTATT
47600470 TCTGCTCTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (51 bp):
TTATTCACGCTTGTCAAAATTTAATGTAACTTAAAATATGTGTCTCAAATT
Found at i:47610877 original size:18 final size:18
Alignment explanation
Indices: 47610850--47610896 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
47610840 AGATAGGGAC
47610850 AGAGAAAAGGAAAAGGAA
1 AGAGAAAAGGAAAAGGAA
* **
47610868 AGAGACAAGGCGAAGGAA
1 AGAGAAAAGGAAAAGGAA
*
47610886 AGGGAAAAGGA
1 AGAGAAAAGGA
47610897 GAGAGACAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.38, T:0.00
Consensus pattern (18 bp):
AGAGAAAAGGAAAAGGAA
Found at i:47612829 original size:76 final size:76
Alignment explanation
Indices: 47612742--47612895 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
47612732 GTTTTTTGGG
* * *
47612742 TGTGTAATTTACCTATTAGCAGGTTTAATATTTTCCTTTAATATGGATTATGTTAATTAAGGTTC
1 TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
47612807 AATGAAGAGCC
66 AATGAAGAGCC
* *
47612818 TGTGTAATTTACCTACTAGCAGATTTAGTATTTACCTTTAATATGGATTATGTTAATTTAGGTTC
1 TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
*
47612883 AATGAAGATCC
66 AATGAAGAGCC
47612894 TG
1 TG
47612896 GTTCTGAGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (76 bp):
TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
AATGAAGAGCC
Found at i:47619639 original size:18 final size:18
Alignment explanation
Indices: 47619616--47619651 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
47619606 TATTAGAATT
47619616 TTGTATCAAAAA-ATTATA
1 TTGTAT-AAAAATATTATA
47619634 TTGTATAAAAATATTATA
1 TTGTATAAAAATATTATA
47619652 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
TTGTATAAAAATATTATA
Found at i:47624458 original size:139 final size:139
Alignment explanation
Indices: 47624208--47624624 Score: 736
Period size: 139 Copynumber: 3.0 Consensus size: 139
47624198 TATTTTCAAA
*
47624208 CCATGACATCCTCTATTCTCAATATTTTGATCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
* *
47624273 CAGTTCCCACAATGACTAAGACAATTATTTAGAATAGGTAACATGAAAACGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
47624338 ATGTGTAAT
131 ATGTGTAAT
47624347 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
47624412 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
47624477 ATGTGTAAT
131 ATGTGTAAT
47624486 CCATGACAT-C-C---TCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
* * *
47624546 CAGTTCCAACAACAACTAAGACAATTATTTAGAATAGGTTACATGAAAATGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
*
47624611 ATGAGTAAT
131 ATGTGTAAT
47624620 CCATG
1 CCATG
47624625 GAAATTCATC
Statistics
Matches: 271, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
134 124 0.46
137 1 0.00
138 1 0.00
139 145 0.54
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (139 bp):
CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
ATGTGTAAT
Found at i:47631212 original size:23 final size:23
Alignment explanation
Indices: 47631167--47631244 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
47631157 AAGAATCTTT
* * * *
47631167 ACTGTTCATTATAGAGAATCTTC
1 ACTGTTTATTACAGGGAAACTTC
47631190 ACTGTTTATTACA-GGAAACCTTC
1 ACTGTTTATTACAGGGAAA-CTTC
* * **
47631213 ATTGTTCATTGTAGGGAAACTTC
1 ACTGTTTATTACAGGGAAACTTC
47631236 ACTGTTTAT
1 ACTGTTTAT
47631245 CCGTAATTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 3 0.07
23 35 0.81
24 5 0.12
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (23 bp):
ACTGTTTATTACAGGGAAACTTC
Found at i:47634142 original size:45 final size:44
Alignment explanation
Indices: 47633997--47634210 Score: 221
Period size: 44 Copynumber: 4.8 Consensus size: 44
47633987 CATGATTCAG
* * * * *
47633997 ATGAGTAAGACCATAGTTGAAAGATGCTATGGAATCAGGATAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
* * * * * * *
47634041 ACGAGTAAGACCATGGCTGAAAAATGCTATGACATCAAGATAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
*
47634085 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATGGAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGAT-AAA
* * * * *
47634130 GTGAGTAAGACCATGGCTGAAAGACATTATGACATCATGGTAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
* * *
47634174 TAGGACTAAGACCATAGTTGAAAGACGTTATGGCATC
1 -ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATC
47634211 TTTTGATAGG
Statistics
Matches: 140, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 73 0.52
45 67 0.48
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (44 bp):
ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
Found at i:47636680 original size:7 final size:7
Alignment explanation
Indices: 47636661--47636721 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
47636651 GAACCTCAAA
47636661 CCTAAAC
1 CCTAAAC
47636668 CC-AAAC
1 CCTAAAC
47636674 CCTAAAC
1 CCTAAAC
*
47636681 CTTAAAC
1 CCTAAAC
*
47636688 CATAAAAC
1 CCT-AAAC
*
47636696 CC-ACAC
1 CCTAAAC
*
47636702 CTTAAAC
1 CCTAAAC
*
47636709 CTTAAAC
1 CCTAAAC
47636716 CCTAAA
1 CCTAAA
47636722 TTTAAACTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 10 0.23
7 29 0.66
8 5 0.11
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:47636693 original size:14 final size:14
Alignment explanation
Indices: 47636652--47636721 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
47636642 CTTTACTCTG
47636652 AACCTCAAA-CCTA
1 AACCTCAAACCCTA
47636665 AACC-CAAACCCTA
1 AACCTCAAACCCTA
* *
47636678 AACCTTAAACCATAA
1 AACCTCAAACCCT-A
* *
47636693 AACC-CACACCTTA
1 AACCTCAAACCCTA
*
47636706 AACCTTAAACCCTA
1 AACCTCAAACCCTA
47636720 AA
1 AA
47636722 TTTAAACTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
12 4 0.09
13 17 0.38
14 19 0.42
15 5 0.11
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCTCAAACCCTA
Found at i:47636705 original size:21 final size:22
Alignment explanation
Indices: 47636670--47636721 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
47636660 ACCTAAACCC
47636670 AAACCCTAAACCTTAAACCATA
1 AAACCCTAAACCTTAAACCATA
* *
47636692 AAACCC-ACACCTTAAACC-TT
1 AAACCCTAAACCTTAAACCATA
47636712 AAACCCTAAA
1 AAACCCTAAA
47636722 TTTAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 13 0.50
22 6 0.23
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (22 bp):
AAACCCTAAACCTTAAACCATA
Found at i:47636707 original size:28 final size:27
Alignment explanation
Indices: 47636652--47636721 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
47636642 CTTTACTCTG
*
47636652 AACCTCAAACCT-AAACCCAAACCCTA
1 AACCTTAAACCTAAAACCCAAACCCTA
* *
47636678 AACCTTAAACCATAAAACCCACACCTTA
1 AACCTTAAACC-TAAAACCCAAACCCTA
47636706 AACCTTAAACCCTAAA
1 AACCTTAAA-CCTAAA
47636722 TTTAAACTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 1 0.03
28 25 0.66
29 2 0.05
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (27 bp):
AACCTTAAACCTAAAACCCAAACCCTA
Found at i:47636745 original size:26 final size:27
Alignment explanation
Indices: 47636705--47636756 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
47636695 CCCACACCTT
*
47636705 AAACCTTAAACCCTAAA-TTTAAACTC
1 AAACCATAAACCCTAAACTTTAAACTC
* *
47636731 AAACCATAAATCCTAAACTTTGAACT
1 AAACCATAAACCCTAAACTTTAAACT
47636757 TTGAACCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (27 bp):
AAACCATAAACCCTAAACTTTAAACTC
Found at i:47636816 original size:13 final size:13
Alignment explanation
Indices: 47636798--47636853 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
47636788 GCCTTGAACC
47636798 TGAGGTTCGAGTT
1 TGAGGTTCGAGTT
*
47636811 TGAGGTTCAGGGTT
1 TGAGGTTC-GAGTT
** *
47636825 CAAGGTTTGAGTT
1 TGAGGTTCGAGTT
47636838 T-ATGGTTCGAGTT
1 TGA-GGTTCGAGTT
47636851 TGA
1 TGA
47636854 TGTTTAAGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
12 1 0.03
13 22 0.67
14 10 0.30
ACGTcount: A:0.18, C:0.07, G:0.36, T:0.39
Consensus pattern (13 bp):
TGAGGTTCGAGTT
Found at i:47636844 original size:20 final size:20
Alignment explanation
Indices: 47636800--47636866 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
47636790 CTTGAACCTG
* * *
47636800 AGGTTCGAGTTTGAGGTTCA
1 AGGTTCAAGTTTGATGTTTA
*
47636820 GGGTTCAAGGTTTGA-GTTTA
1 AGGTTCAA-GTTTGATGTTTA
* *
47636840 TGGTTCGAGTTTGATGTTTA
1 AGGTTCAAGTTTGATGTTTA
47636860 AGGTTCA
1 AGGTTCA
47636867 CGATTTTGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.16
20 26 0.68
21 6 0.16
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.40
Consensus pattern (20 bp):
AGGTTCAAGTTTGATGTTTA
Found at i:47636900 original size:14 final size:14
Alignment explanation
Indices: 47636889--47636920 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
47636879 TAGGTTTGGA
47636889 GTTTGGGGTTTGAG
1 GTTTGGGGTTTGAG
*
47636903 GTTTGGGGTTTAAG
1 GTTTGGGGTTTGAG
47636917 GTTT
1 GTTT
47636921 AGGATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (14 bp):
GTTTGGGGTTTGAG
Found at i:47636919 original size:21 final size:21
Alignment explanation
Indices: 47636880--47636920 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47636870 TTTTGGATTT
**
47636880 AGGTTTGGAGTTTGGGGTTTG
1 AGGTTTGGAGTTTAAGGTTTG
*
47636901 AGGTTTGGGGTTTAAGGTTT
1 AGGTTTGGAGTTTAAGGTTT
47636921 AGGATTTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (21 bp):
AGGTTTGGAGTTTAAGGTTTG
Found at i:47650301 original size:18 final size:18
Alignment explanation
Indices: 47650278--47650312 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47650268 TCATTCTTTC
47650278 ACTCACAATACTTTTAAT
1 ACTCACAATACTTTTAAT
* *
47650296 ACTCACCATGCTTTTAA
1 ACTCACAATACTTTTAA
47650313 CTCTCACATT
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:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (18 bp):
ACTCACAATACTTTTAAT
Found at i:47652710 original size:11 final size:11
Alignment explanation
Indices: 47652689--47652719 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
47652679 CATTGTAGGC
47652689 AAAAGAAAAAAG
1 AAAA-AAAAAAG
47652701 AAAAAAAAAAG
1 AAAAAAAAAAG
47652712 AAAAAAAA
1 AAAAAAAA
47652720 GAAAGAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:47655371 original size:18 final size:18
Alignment explanation
Indices: 47655330--47655364 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47655320 TCATTCTTTC
47655330 ACTCACAATGCTTTTAAT
1 ACTCACAATGCTTTTAAT
*
47655348 ACTCACCATGCTTTTAA
1 ACTCACAATGCTTTTAA
47655365 CTCTCACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (18 bp):
ACTCACAATGCTTTTAAT
Found at i:47662991 original size:2 final size:2
Alignment explanation
Indices: 47662984--47663011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47662974 CTTAATATGC
47662984 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
47663012 CAACATGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47663872 original size:35 final size:35
Alignment explanation
Indices: 47663824--47663963 Score: 145
Period size: 35 Copynumber: 4.0 Consensus size: 35
47663814 TATAAAAAAA
* * ** *
47663824 TTGCTTTAAACGTGTCTATCCCAATATTTTTAAGG
1 TTGCCTTAGACGTGTCTATCCCAACCTTTTAAAGG
*
47663859 TTGGCTTAGACGTGTCTATCCCAACCTTTTAAAGG
1 TTGCCTTAGACGTGTCTATCCCAACCTTTTAAAGG
* * * *
47663894 TTGCCTTATACGGGTATATCCCAACCTTTTAAACG
1 TTGCCTTAGACGTGTCTATCCCAACCTTTTAAAGG
* * * *
47663929 TTGTCTTAGATGAGTCTATCCTAACCTTTTTAAAG
1 TTGCCTTAGACGTGTCTATCCCAACC-TTTTAAAG
47663964 TCAACTTTAA
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 79 0.92
36 7 0.08
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (35 bp):
TTGCCTTAGACGTGTCTATCCCAACCTTTTAAAGG
Found at i:47664521 original size:18 final size:18
Alignment explanation
Indices: 47664498--47664532 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
47664488 TAAAATATTA
47664498 TTTTAATATTT-TTATACG
1 TTTTAAT-TTTATTATACG
47664516 TTTTAATTTTATTATAC
1 TTTTAATTTTATTATAC
47664533 ACACTCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTAATTTTATTATACG
Found at i:47668403 original size:34 final size:34
Alignment explanation
Indices: 47668360--47668430 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
47668350 AGTCCTAAGG
47668360 TCTGATGCCAAGTCCATAGAAATAGTATTGAAAA
1 TCTGATGCCAAGTCCATAGAAATAGTATTGAAAA
47668394 TCTGATGCCAAGTCCATAGAAATAGTATTGAAAA
1 TCTGATGCCAAGTCCATAGAAATAGTATTGAAAA
47668428 TCT
1 TCT
47668431 ATTAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (34 bp):
TCTGATGCCAAGTCCATAGAAATAGTATTGAAAA
Found at i:47670389 original size:27 final size:27
Alignment explanation
Indices: 47670358--47670413 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
47670348 GACATACGGA
*
47670358 CATGTAACACGACTGTGTGACCCTACT
1 CATGTAACACGACTATGTGACCCTACT
47670385 CATGTAACACGACTATGTGACCCTACT
1 CATGTAACACGACTATGTGACCCTACT
47670412 CA
1 CA
47670414 GAGAGTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (27 bp):
CATGTAACACGACTATGTGACCCTACT
Found at i:47672647 original size:98 final size:98
Alignment explanation
Indices: 47672478--47672672 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
47672468 ATACAATAAA
*
47672478 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
47672543 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* * *
47672576 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATTACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
47672641 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
47672673 CATGATTTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:47674825 original size:45 final size:43
Alignment explanation
Indices: 47674560--47675154 Score: 287
Period size: 45 Copynumber: 13.5 Consensus size: 43
47674550 CCATCCTCAT
47674560 TGCAACTTCA-GGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGC-TT-CTTAGTCTGCTCCAC
* * * * * * *
47674605 TGCATCTTCAGGGAGATAAGACTAGATGC-GA-TCTACT-CTC
1 TGCAACTTCAGGGAGATAAGACTTGCTTCTTAGTCTGCTCCAC
** * **
47674645 TGCAACTTCAAAGAGATAAGATCTGATG-TT-TTAATCCACTCCAC
1 TGCAACTTCAGGGAGATAAGA-CT--TGCTTCTTAGTCTGCTCCAC
** * * * * *
47674689 TATAATTTCAGGGAGATAGGA-TTG-TAGGCTTTAATCTGTTCCTAC
1 TGCAACTTCAGGGAGATAAGACTTGCT--TC-TTAGTCTGCTCC-AC
* * * *
47674734 TGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGCCTGC-CTCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CTTCTT-AGTCTGCTC-CAC
*
47674779 TGCAACTTCA-GGAGGATACGACTTGCTTTGCTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGC-TT-CTTAGTCTGCTCCAC
* * * * * *
47674824 TGTAACTTCAGGGAGATAAGACTAGATGC-GA-TCTGCT-CTC
1 TGCAACTTCAGGGAGATAAGACTTGCTTCTTAGTCTGCTCCAC
* * * * ** * *
47674864 TGCAACTTCAGAGAGATAAGATCTGAGGTT-TTAATCCACTCTAA
1 TGCAACTTCAGGGAGATAAGA-CT-TGCTTCTTAGTCTGCTCCAC
* *
47674908 TGCAACTTCAGGGAGATAGGATTATCGGCTT-TTA-TCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACT-T--GCTTCTTAGTCTGCTCCAC
* * *
47674952 TGCAACTTCA-GG-GATAAGATTTGCCATCTTCAGCCTGC-CTCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CTTCTT-AGTCTGCTC-CAC
* *
47674995 TGCAACTTCA-GGAGGATACGACTTGCTTTGCTTAGTCTGGTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGC-TT-CTTAGTCTGCTCCAC
* *
47675040 TGCAACTTCAGGGAGATAAGACTAGATGCGATCTTTAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACT---TGC-TTC-TTAGTCTGCTCCAC
* *
47675088 TGCAACTTCA-GGAGGATAAGACTTGCTAACTTAGTCTGCTCCAT
1 TGCAACTTCAGGGA-GATAAGACTTGCT-TCTTAGTCTGCTCCAC
*
47675132 TGTAACTTCAGGGAGATAAGACT
1 TGCAACTTCAGGGAGATAAGACT
47675155 AGTTGTGATT
Statistics
Matches: 418, Mismatches: 85, Indels: 95
0.70 0.14 0.16
Matches are distributed among these distances:
39 1 0.00
40 46 0.11
41 18 0.04
42 19 0.05
43 34 0.08
44 98 0.23
45 137 0.33
46 26 0.06
47 4 0.01
48 35 0.08
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
TGCAACTTCAGGGAGATAAGACTTGCTTCTTAGTCTGCTCCAC
Found at i:47675055 original size:216 final size:219
Alignment explanation
Indices: 47674554--47675073 Score: 857
Period size: 219 Copynumber: 2.4 Consensus size: 219
47674544 GATTTGCCAT
* * *
47674554 CCTCATTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCATCTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
*
47674619 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGATGTTTTAATCCAC
66 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
* * * * * *
47674684 TCCACTATAATTTCAGGGAGATAGGATTGTAGGCTTTAATCTGTTCCTACTGCAACTTTAGGGAG
131 TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGGGAG
47674749 ATAAGATTTGCCATCTTCAGCCTG
196 ATAAGATTTGCCATCTTCAGCCTG
*
47674773 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGTAACTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
47674838 GATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCAC
66 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
* * * *
47674903 TCTAATGCAACTTCAGGGAGATAGGATTATCGGCTTTTATCTGCTCC-ACTGCAACTTCA-GG-G
131 TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGGGAG
47674965 ATAAGATTTGCCATCTTCAGCCTG
196 ATAAGATTTGCCATCTTCAGCCTG
*
47674989 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGGTCCACTGCAACTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
47675054 GATAAGACTAGATGCGATCT
66 GATAAGACTAGATGCGATCT
47675074 TTAGTCTGCC
Statistics
Matches: 282, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
216 108 0.38
217 2 0.01
218 11 0.04
219 161 0.57
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (219 bp):
CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTCAGCCTG
Found at i:47675097 original size:48 final size:46
Alignment explanation
Indices: 47674809--47675157 Score: 172
Period size: 44 Copynumber: 7.9 Consensus size: 46
47674799 ACTTGCTTTG
*
47674809 CTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCG--
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-TGCGAA
* * * *
47674854 ---A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCT-GAG-G-T
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAGTGCGAA
* * ** * * * * *
47674893 TTTAATCCACTCTAATGCAACTTCAGGGAGATAGGATTA-T-CG-G
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTGCGAA
* * *
47674936 CTTTTA-TCTGCTCCACTGCAACTTCA-GG-GATAAGA-T-TTGCCAT
1 C--TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTGCGAA
* * ***
47674979 CTTCAGCCTGC-CTCACTGCAACTTCA-GGAGGATACGACT--TGCTTTG
1 CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTAGTGC-GAA
* *
47675025 CTTAGTCTGGTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGAT
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-TGCGAA
* *
47675072 CTTTAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACT--TGCTAA
1 C-TTAGTCTGCTCCACTGCAACTTCAGGGA-GATAAGACTAGTGCGAA
* *
47675117 CTTAGTCTGCTCCATTGTAACTTCAGGGAGATAAGACTAGT
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGT
47675158 TGTGATTTGT
Statistics
Matches: 233, Mismatches: 40, Indels: 61
0.70 0.12 0.18
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 22 0.09
41 12 0.05
42 11 0.05
43 28 0.12
44 65 0.28
45 46 0.20
46 9 0.04
47 4 0.02
48 34 0.15
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (46 bp):
CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTGCGAA
Found at i:47675101 original size:93 final size:92
Alignment explanation
Indices: 47674973--47675156 Score: 269
Period size: 93 Copynumber: 2.0 Consensus size: 92
47674963 GGATAAGATT
* * ** *
47674973 TGCCATCTTCAGCCTGCCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGGTCC
1 TGCCATCTTCAGCCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGC-TAACTTAGTCTGCTCC
47675038 ACTGCAACTTCAGGGAGATAAGACTAGA
65 ACTGCAACTTCAGGGAGATAAGACTAGA
* * *
47675066 TGCGATCTTTAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTAACTTAGTCTGCTCCA
1 TGCCATCTTCAGCCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTAACTTAGTCTGCTCCA
* *
47675131 TTGTAACTTCAGGGAGATAAGACTAG
66 CTGCAACTTCAGGGAGATAAGACTAG
47675157 TTGTGATTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 38 0.47
93 43 0.53
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (92 bp):
TGCCATCTTCAGCCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTAACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGA
Found at i:47686749 original size:98 final size:98
Alignment explanation
Indices: 47686579--47686773 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
47686569 ATACAATAAA
*
47686579 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* * *
47686644 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCATTAGAATCCCAAACTAGGAATATCTCCTTT
* * *
47686677 ACTTTAAAAGAACATCCACTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
47686742 CCATTAGAATCTCAAACTAGGAATATCTCCTT
66 CCATTAGAATCCCAAACTAGGAATATCTCCTT
47686774 CATGATTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCATTAGAATCCCAAACTAGGAATATCTCCTTT
Found at i:47695484 original size:2 final size:2
Alignment explanation
Indices: 47695477--47695502 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47695467 TATTAGATCA
47695477 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
47695503 GTATCTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47710136 original size:59 final size:61
Alignment explanation
Indices: 47710066--47710367 Score: 232
Period size: 59 Copynumber: 5.0 Consensus size: 61
47710056 AATATTGATT
47710066 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAATTATGTTAA
1 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAATTATGTTAA
* * * * * ** * ** *
47710127 ATT-A-TATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAA-TATTGATT--
1 ATTAAGAATTTTATTA-AATTATATATTTTAATTAAAATATTTTTA-ATAATAATTA-TG-TTAA
*
47710186 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATGTTAA
1 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAATTATGTTAA
* * * * * ** * ** *
47710247 ATT-A-TATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAA-TATTGATT--
1 ATTAAGAATTTTATTA-AATTATATATTTTAATTAAAATATTTTTA-ATAATAATTA-TG-TTAA
*
47710306 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATGTTAA
1 ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAATTATGTTAA
47710367 A
1 A
47710368 ATATGATTAA
Statistics
Matches: 174, Mismatches: 47, Indels: 40
0.67 0.18 0.15
Matches are distributed among these distances:
58 4 0.02
59 65 0.37
60 36 0.21
61 65 0.37
62 4 0.02
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.51
Consensus pattern (61 bp):
ATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAATTATGTTAA
Found at i:47710187 original size:120 final size:120
Alignment explanation
Indices: 47710050--47710367 Score: 627
Period size: 120 Copynumber: 2.6 Consensus size: 120
47710040 TGAATTTTGT
*
47710050 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
47710115 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
47710170 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
47710235 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
47710290 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
47710355 TAATTATGTTAAA
66 TAATTATGTTAAA
47710368 ATATGATTAA
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 197 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (120 bp):
TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
Found at i:47710197 original size:61 final size:61
Alignment explanation
Indices: 47710132--47710319 Score: 196
Period size: 57 Copynumber: 3.1 Consensus size: 61
47710122 GTTAAATTAT
47710132 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
* * * * *
47710193 ATTTTAT--TA-AAT-TA-TAT-ATTTTAATTAAAATGTT-TTTAATAATAATT-ATGT-TAAAT
1 ATTTTATAGTATCATATATTATGATTTT-AGT-AAAT-TTATATAAGAAT-ATTGAT-TATTAA-
*
47710249 TA
60 GA
47710251 TATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 -ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
47710313 ATTTTAT
1 ATTTTAT
47710320 TAAATTATAT
Statistics
Matches: 99, Mismatches: 12, Indels: 32
0.69 0.08 0.22
Matches are distributed among these distances:
55 5 0.05
56 5 0.05
57 18 0.18
58 9 0.09
59 9 0.09
61 16 0.16
62 9 0.09
63 18 0.18
64 5 0.05
65 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
Found at i:47710465 original size:157 final size:157
Alignment explanation
Indices: 47710303--47710610 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
47710293 AAGAATATTG
* *
47710303 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATGTTAAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
* *
47710368 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
47710433 ATAATTTACCAAAACAAATTTCTGGTA
131 ATAATTTACCAAAACAAATTTCTGGTA
*
47710460 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
47710525 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
47710590 ATCATTTACCAAAACAAATTT
131 ATAATTTACCAAAACAAATTT
47710611 ATGCTAAGGG
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTCTGGTA
Found at i:47710498 original size:18 final size:17
Alignment explanation
Indices: 47710470--47710504 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47710460 ATTATTAAGA
*
47710470 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
47710487 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
47710505 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:47710761 original size:16 final size:16
Alignment explanation
Indices: 47710740--47710791 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
47710730 GATTTGCTAT
47710740 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
47710756 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
**
47710772 TACATTTCTAATCCAA
1 TACACCTCTAATCCAA
47710788 TACA
1 TACA
47710792 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:47711186 original size:19 final size:19
Alignment explanation
Indices: 47711133--47711193 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 19
47711123 TGTATGCTAA
47711133 TTTTTATAATTACTTATAAACTT
1 TTTTTATAATT--TT-TAAA-TT
*
47711156 TTATTT-TTATTTTTAAATT
1 TT-TTTATAATTTTTAAATT
47711175 TTTTTATAATTTTTAAATT
1 TTTTTATAATTTTTAAATT
47711194 ATTCATTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 4 0.12
21 2 0.06
23 6 0.18
24 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTTTAAATT
Found at i:47714924 original size:14 final size:14
Alignment explanation
Indices: 47714907--47714934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47714897 CTCATTGCTT
47714907 TGAGTTCATTACAA
1 TGAGTTCATTACAA
47714921 TGAGTTCATTACAA
1 TGAGTTCATTACAA
47714935 GATTTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TGAGTTCATTACAA
Found at i:47714988 original size:43 final size:43
Alignment explanation
Indices: 47714928--47715018 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
47714918 CAATGAGTTC
* * *
47714928 ATTA-CAAGATTTTCTTGATTAAGTAAATGTATTATATCT-TTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATAT-TATTT
*
47714970 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTATTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATTATTT
47715013 ATTACC
1 ATTACC
47715019 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATTATTT
Found at i:47716443 original size:43 final size:43
Alignment explanation
Indices: 47716383--47716473 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
47716373 CTTTGAGTTC
* * *
47716383 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
47716425 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
47716468 ATTACC
1 ATTACC
47716474 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:47716932 original size:43 final size:43
Alignment explanation
Indices: 47716877--47717050 Score: 237
Period size: 43 Copynumber: 4.1 Consensus size: 43
47716867 GTTTGTTCTA
* *
47716877 TAGCGACGTTTGTGACAAAAGCGCCGCTAAAAGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* *
47716920 TAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGTCA---TCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* * * *
47716960 TTGCGGCGTTTATGATAAAAGCACCGCTAAAAGTCATTGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* *
47717003 TAGCGGCGTTTGTGATAAAAGCGCCACTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
47717046 TAGCG
1 TAGCG
47717051 ACCTTTTTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
40 35 0.31
43 78 0.69
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
Found at i:47716980 original size:83 final size:83
Alignment explanation
Indices: 47716883--47717039 Score: 260
Period size: 83 Copynumber: 1.9 Consensus size: 83
47716873 TCTATAGCGA
* * * *
47716883 CGTTTGTGACAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGTCGCT
1 CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
47716948 AAAGGTCATCTTTTGCGG
66 AAAGGTCATCTTTTGCGG
* *
47716966 CGTTTATGATAAAAGCACCGCTAAAAGTCATTGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
1 CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
47717031 AAAGGTCAT
66 AAAGGTCAT
47717040 GGTCTTTAGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (83 bp):
CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
AAAGGTCATCTTTTGCGG
Found at i:47719337 original size:161 final size:162
Alignment explanation
Indices: 47718983--47719375 Score: 549
Period size: 161 Copynumber: 2.4 Consensus size: 162
47718973 CAATCCCCCA
*
47718983 ATACCTCAAATTATTGCAGTTT-TCAACTTTTACTTCCCTTAAACTTTGGAGGCTTATGTTTGAC
1 ATACCTCAAATTATTGCAGTTTCT-AACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGAC
* * *
47719047 ACTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACTTATCTGCAGAGTTTGCAACCT
65 ACTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCT
* *
47719112 CCTAAGGCTATTAGCAATAGACATTGGGAAGAG
130 CCCAAGGCTATTAGAAATAGACATTGGGAAGAG
* * *
47719145 ATACATCAAATTATTGCCGTTTCTGACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
1 ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
** * * * * * *
47719210 CTTTTGAGCCTTGGATT-GTTCTT-TCAATTGGGAGCAGTCTCATATCTTCAAAGCTTGCAATCT
66 CTTCCGAACCTTGGATTATTTCTTCT-AATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCT
* *
47719273 CCCAAGGCTATTAGAAATAGCCATTGGGAAGGG
130 CCCAAGGCTATTAGAAATAGACATTGGGAAGAG
* * *
47719306 ATACCTCAAATTATTGTAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGTTTATGTCTGACA
1 ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
47719371 CTTCC
66 CTTCC
47719376 AATTGGGAGC
Statistics
Matches: 202, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
160 1 0.00
161 127 0.63
162 73 0.36
163 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (162 bp):
ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
CTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCTC
CCAAGGCTATTAGAAATAGACATTGGGAAGAG
Found at i:47726873 original size:31 final size:30
Alignment explanation
Indices: 47726809--47726904 Score: 156
Period size: 30 Copynumber: 3.2 Consensus size: 30
47726799 ACACATTATT
* *
47726809 ATATATGCATTACATTAGTAAACAAAAATA
1 ATATATGCAATACATTAGTAAACAAAAAGA
47726839 ATATATGCAATACATTAGTAAACAAAAAAGA
1 ATATATGCAATACATTAGTAAAC-AAAAAGA
*
47726870 ATATATGCACTACATTAGTAAACAAAAAGA
1 ATATATGCAATACATTAGTAAACAAAAAGA
47726900 ATATA
1 ATATA
47726905 CCTATCGACT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 34 0.55
31 28 0.45
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (30 bp):
ATATATGCAATACATTAGTAAACAAAAAGA
Found at i:47733988 original size:14 final size:14
Alignment explanation
Indices: 47733969--47733999 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47733959 GGAATTATTT
*
47733969 TAATCTAAATTTAC
1 TAATCTAAATTAAC
47733983 TAATCTAAATTAAC
1 TAATCTAAATTAAC
47733997 TAA
1 TAA
47734000 GAATTGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:47743158 original size:3 final size:3
Alignment explanation
Indices: 47743150--47743223 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
47743140 TTGGATTGGT
47743150 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47743198 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
47743224 TTTAATGATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47765137 original size:4 final size:4
Alignment explanation
Indices: 47765128--47765174 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
47765118 TTATAAAAAA
*
47765128 ATTT ATTT ATTTT ATTT ATTT AATTT ATTT ATCTT TTTT ATTT -TTT A
1 ATTT ATTT A-TTT ATTT ATTT -ATTT ATTT AT-TT ATTT ATTT ATTT A
47765175 AATTTGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 23 0.62
5 11 0.30
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:47765143 original size:9 final size:9
Alignment explanation
Indices: 47765129--47765170 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
47765119 TATAAAAAAA
47765129 TTTATTTAT
1 TTTATTTAT
47765138 TTTATTTAT
1 TTTATTTAT
*
47765147 TTAATTTA-
1 TTTATTTAT
47765155 TTTATCTT-T
1 TTTAT-TTAT
47765164 TTTATTT
1 TTTATTT
47765171 TTTAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:47765144 original size:13 final size:13
Alignment explanation
Indices: 47765128--47765174 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
47765118 TTATAAAAAA
47765128 ATTTATTTATTTT
1 ATTTATTTATTTT
*
47765141 ATTTATTTAATTT
1 ATTTATTTATTTT
47765154 ATTTATCTT-TTTT
1 ATTTAT-TTATTTT
47765167 ATTT-TTTA
1 ATTTATTTA
47765175 AATTTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 2 0.07
12 1 0.03
13 25 0.83
14 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:47765179 original size:22 final size:23
Alignment explanation
Indices: 47765126--47765170 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
47765116 TTTTATAAAA
47765126 AAATTTATTTATTTTATTTATTT
1 AAATTTATTTATTTTATTTATTT
47765149 -AATTTATTTATCTTT-TTTATTT
1 AAATTTATTTAT-TTTATTTATTT
47765171 TTTAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
AAATTTATTTATTTTATTTATTT
Found at i:47772417 original size:19 final size:19
Alignment explanation
Indices: 47772372--47772420 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
47772362 TGTTGTCCGA
*
47772372 AAAT-GATTTTTAAAAAAT
1 AAATAGATTTTAAAAAAAT
*
47772390 AAATTGATTTTAAAAAAAT
1 AAATAGATTTTAAAAAAAT
**
47772409 TGATAGATTTTA
1 AAATAGATTTTA
47772421 TTGTTTGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATAGATTTTAAAAAAAT
Found at i:47791990 original size:3 final size:3
Alignment explanation
Indices: 47791982--47792042 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
47791972 TTTTCAAAGC
47791982 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47792030 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
47792043 GATACTTTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47792119 original size:22 final size:22
Alignment explanation
Indices: 47792097--47792172 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 22
47792087 TGTTTCCAAA
47792097 TTTATTATTTTAAAAATTTAAAT
1 TTTATT-TTTTAAAAATTTAAAT
* *
47792120 TTAACTTTCTTTATATAATTTTAAAT
1 TTTA-TTT-TTTA-A-AAATTTAAAT
*
47792146 TTTATTTTTTAAAAATATAAAT
1 TTTATTTTTTAAAAATTTAAAT
47792168 TTTAT
1 TTTAT
47792173 AATTTTATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
22 13 0.30
23 5 0.11
24 10 0.23
25 4 0.09
26 12 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTTTTTAAAAATTTAAAT
Found at i:47792178 original size:23 final size:22
Alignment explanation
Indices: 47792141--47792186 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
47792131 TATATAATTT
*
47792141 TAAATTTTATTTTTTAAAAATA
1 TAAATTTTATATTTTAAAAATA
*
47792163 TAAATTTTATAATTTTATAAATA
1 TAAATTTTAT-ATTTTAAAAATA
47792186 T
1 T
47792187 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAATTTTATATTTTAAAAATA
Found at i:47792189 original size:48 final size:49
Alignment explanation
Indices: 47792097--47792197 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 49
47792087 TGTTTCCAAA
* * * *
47792097 TTTATTATTTTAAAAATTTAAATTTAACTTTCTTTATATAATTTTAAAT
1 TTTATTATTTTAAAAATATAAATTTAAATTTCTATAAATAATTTTAAAT
*
47792146 TTTATT-TTTTAAAAATATAAATTTTATAATTT-TATAAAT-ATTTTGAAT
1 TTTATTATTTTAAAAATATAAA-TTTA-AATTTCTATAAATAATTTTAAAT
47792194 TTTA
1 TTTA
47792198 AAAATTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 26 0.58
49 15 0.33
50 4 0.09
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (49 bp):
TTTATTATTTTAAAAATATAAATTTAAATTTCTATAAATAATTTTAAAT
Found at i:47792196 original size:18 final size:17
Alignment explanation
Indices: 47792161--47792215 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
47792151 TTTTTAAAAA
47792161 TATAAATTTTAT-AATTT
1 TATAAATTTT-TGAATTT
47792178 TATAAATATTTTGAATTT
1 TATAAAT-TTTTGAATTT
*
47792196 TAAAAATTGTTTTGAATTT
1 TATAAA-T-TTTTGAATTT
47792215 T
1 T
47792216 TTTTTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.24
18 13 0.39
19 12 0.36
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATAAATTTTTGAATTT
Found at i:47792208 original size:19 final size:18
Alignment explanation
Indices: 47792173--47792215 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
47792163 TAAATTTTAT
*
47792173 AATTTTATAAATATTTTG
1 AATTTTAAAAATATTTTG
*
47792191 AATTTTAAAAATTGTTTTG
1 AATTTTAAAAA-TATTTTG
47792210 AATTTT
1 AATTTT
47792216 TTTTTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Found at i:47797197 original size:13 final size:13
Alignment explanation
Indices: 47797161--47797190 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47797151 TCTCCACTAG
*
47797161 AATTATACTATTT
1 AATTATATTATTT
47797174 AATTATATTATTT
1 AATTATATTATTT
47797187 AATT
1 AATT
47797191 TTTTTATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:47799413 original size:15 final size:16
Alignment explanation
Indices: 47799383--47799417 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
47799373 TTCTATAGGG
*
47799383 ATTTTACTTTTATTTT
1 ATTTTACTTGTATTTT
47799399 ATTTTAC-TGTATTTT
1 ATTTTACTTGTATTTT
47799414 ATTT
1 ATTT
47799418 AAATAAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTTTACTTGTATTTT
Found at i:47805579 original size:44 final size:42
Alignment explanation
Indices: 47805364--47805672 Score: 139
Period size: 44 Copynumber: 7.2 Consensus size: 42
47805354 TCTTTAGGAG
* * * *
47805364 GATAAGATCTGCTTACTCAGTCTGCTTCGCTGCAACCTC-GGGCA
1 GATAAGATCTG-TTTCTTA-TCTGCTCCACTGCAACCTCAGGG-A
* * * ** *
47805408 GATAAGATTTATTT-TAATCCACTCCACTGCAACTTCAGGGA
1 GATAAGATCTGTTTCTTATCTGCTCCACTGCAACCTCAGGGA
* * * * * *
47805449 GATAGGACTACTGGCTTC-AATCTGCTCCACTACTA-CTTAGGGA
1 GATAAGA-T-CT-GTTTCTTATCTGCTCCACTGCAACCTCAGGGA
* ** *
47805492 GATAAGATCT-TCCATCTTCGATCTGCTCCACT--ATTGCTTAGGGA
1 GATAAGATCTGT--TTCTT--ATCTGCTCCACTGCA-ACCTCAGGGA
*
47805536 GATAAGATCTGTTTCTTATGTCTGCTCCGCTGCAACCTCAGGGA
1 GATAAGATCTGTTTCTTA--TCTGCTCCACTGCAACCTCAGGGA
* * * * * * * *
47805580 GATAAGACCTGATGC-GATCTACTCTACTGCAACTTCAGAGA
1 GATAAGATCTGTTTCTTATCTGCTCCACTGCAACCTCAGGGA
* * *
47805621 GATAAGATCTGTTATTTTAATCCGCTCCACTGTAACCTCAGGGA
1 GATAAGATCTGTT-TCTT-ATCTGCTCCACTGCAACCTCAGGGA
47805665 GATAAGAT
1 GATAAGAT
47805673 TAGTGGCTTC
Statistics
Matches: 195, Mismatches: 50, Indels: 40
0.68 0.18 0.14
Matches are distributed among these distances:
41 56 0.29
42 7 0.04
43 30 0.15
44 100 0.51
45 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (42 bp):
GATAAGATCTGTTTCTTATCTGCTCCACTGCAACCTCAGGGA
Found at i:47805777 original size:216 final size:216
Alignment explanation
Indices: 47805416--47805854 Score: 639
Period size: 216 Copynumber: 2.0 Consensus size: 216
47805406 CAGATAAGAT
* * *
47805416 TTATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGACTACTGGCTTCAATCTGCTCCACTA
1 TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAAGACTACTGGCTTCAATCTACTCCACTA
* * * ** * *
47805481 CTACTTAGGGAGATAAGATCTTCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCT
66 CAACTCAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCC
* * *
47805546 GTTTCTTATGTCTGCTCCGCTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCA
131 CTTTCTTAGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGCA
47805611 ACTTCAGAGAGATAAGATCTG
196 ACTTCAGAGAGATAAGATCTG
* * * *
47805632 TTATTTTAATCCGCTCCACTGTAACCTCAGGGAGATAAGATTAGTGGCTTCAATCTACTCCACTG
1 TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAAGACTACTGGCTTCAATCTACTCCAC--
* *
47805697 TA-AACTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCGACTACTGCTTAGGGAGATAAGA-
64 TACAACTCAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
* *
47805760 CCCTTTCTTCGGTCTGCTCTGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTG
129 CCCTTTCTTAGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTG
*
47805825 TAACTTCAGAGAGATAAGATCTG
194 CAACTTCAGAGAGATAAGATCTG
*
47805848 TAATTTT
1 TTATTTT
47805855 TTTTCAACCT
Statistics
Matches: 198, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
216 143 0.72
217 53 0.27
218 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (216 bp):
TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAAGACTACTGGCTTCAATCTACTCCACTA
CAACTCAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCC
CTTTCTTAGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGCA
ACTTCAGAGAGATAAGATCTG
Found at i:47806066 original size:44 final size:44
Alignment explanation
Indices: 47805945--47806068 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 44
47805935 TTTGTAATTT
* *
47805945 TTCAATCTATTCCACTACTGACCAGGGAGATAGAATCAACAATC
1 TTCAATCTATTCCACTACTGACCAGGGAGATAGGACCAACAATC
* *
47805989 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACCTACAATC
1 TTCAATCTATTCCACTACTGACCAGGGAGATAGGACCAACAATC
*
47806033 TTCAATCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TTCAATCTATTCCACTACTGACCAGGGAGATAGGAC
47806069 TAGTATCTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (44 bp):
TTCAATCTATTCCACTACTGACCAGGGAGATAGGACCAACAATC
Found at i:47808446 original size:22 final size:20
Alignment explanation
Indices: 47808414--47808490 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 20
47808404 TCTTTTTGTT
47808414 ATTTTTATTTTTTTGATTATG
1 ATTTTT-TTTTTTTGATTATG
* *
47808435 ATTGATTTTTTTTTTAATTTTG
1 ATT--TTTTTTTTTTGATTATG
*
47808457 ACTTTTTTTTTATTTTTGATTCTG
1 A---TTTTTTT-TTTTTGATTATG
47808481 ATTTTTTTTT
1 ATTTTTTTTT
47808491 GTGAATTGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 13 0.28
23 8 0.17
24 11 0.24
25 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (20 bp):
ATTTTTTTTTTTTGATTATG
Found at i:47808457 original size:18 final size:18
Alignment explanation
Indices: 47808436--47808477 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
47808426 TTGATTATGA
47808436 TTGATTTTTTTTTTAATT
1 TTGATTTTTTTTTTAATT
* *
47808454 TTGACTTTTTTTTTATTT
1 TTGATTTTTTTTTTAATT
47808472 TTGATT
1 TTGATT
47808478 CTGATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (18 bp):
TTGATTTTTTTTTTAATT
Found at i:47808467 original size:24 final size:23
Alignment explanation
Indices: 47808440--47808490 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
47808430 TTATGATTGA
*
47808440 TTTTT-TTTTTAATTTTGACTTTT
1 TTTTTATTTTTAATTCTGA-TTTT
*
47808463 TTTTTATTTTTGATTCTGATTTT
1 TTTTTATTTTTAATTCTGATTTT
47808486 TTTTT
1 TTTTT
47808491 GTGAATTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTTTATTTTTAATTCTGATTTT
Found at i:47809583 original size:25 final size:25
Alignment explanation
Indices: 47809533--47809598 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
47809523 AAGAAAATCC
*
47809533 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
*
47809558 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
47809583 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
47809599 TGTATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 3 0.08
25 23 0.64
26 5 0.14
27 5 0.14
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:47816883 original size:44 final size:44
Alignment explanation
Indices: 47816833--47816949 Score: 110
Period size: 44 Copynumber: 2.7 Consensus size: 44
47816823 TTTTAATCCA
* * *
47816833 CTCCACTGCAACTTTAAGGAGATAGGA-CTACTATCTTCAATCTG
1 CTCCACTACAAC-TTAAGGAGATAAGATCTACCATCTTCAATCTG
** * * *
47816877 CTCCACTACTGCTTAGGGAGATAAGATCTGCCATCTTCGATCTG
1 CTCCACTACAACTTAAGGAGATAAGATCTACCATCTTCAATCTG
*** *
47816921 CTCCACTATTGCTTAGGGAGATAAGATCT
1 CTCCACTACAACTTAAGGAGATAAGATCT
47816950 GTTTCTTCGT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 12 0.19
44 51 0.81
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACAACTTAAGGAGATAAGATCTACCATCTTCAATCTG
Found at i:47816950 original size:44 final size:43
Alignment explanation
Indices: 47816865--47816967 Score: 152
Period size: 44 Copynumber: 2.4 Consensus size: 43
47816855 TAGGACTACT
*
47816865 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-C
* *
47816909 ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGC
* *
47816952 TTCTTCGTTCTGCTCC
1 ATCTTCGATCTGCTCC
47816968 GCTGCAACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 14 0.26
44 40 0.74
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (43 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGC
Found at i:47817106 original size:44 final size:44
Alignment explanation
Indices: 47817000--47817117 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
47816990 ACCTGATGCG
* * * *
47817000 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTTATTTTA
1 ATCTACTCTACTGCAACCTCAGAGAGATAAGATCTGTGACTTCA
* * * *
47817044 ATCCACTCCACTGCAACCTCAGAGAGATAGGAT-TAGTGGCTTCA
1 ATCTACTCTACTGCAACCTCAGAGAGATAAGATCT-GTGACTTCA
* * *
47817088 ATCTACTCTACTGTAACCTAAGGGAGATAA
1 ATCTACTCTACTGCAACCTCAGAGAGATAA
47817118 AATCCACCAT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (44 bp):
ATCTACTCTACTGCAACCTCAGAGAGATAAGATCTGTGACTTCA
Done.