Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_pilon, 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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 20
Found at i:1871847 original size:29 final size:30
Alignment explanation
Indices: 1871785--1871848 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
1871775 AGAGACAAAA
* *
1871785 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTTTTTCAAAAGAAACAGACTCAAAGAT
1871815 TTTTTTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTTTTTTCAAAAGAAACAGACTCAAAGAT
1871844 TTTTT
1 TTTTT
1871849 CACGAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (30 bp):
TTTTTTTTCAAAAGAAACAGACTCAAAGAT
Found at i:1871887 original size:59 final size:61
Alignment explanation
Indices: 1871820--1871967 Score: 230
Period size: 59 Copynumber: 2.5 Consensus size: 61
1871810 AAGATTTTTT
* *
1871820 TTTCAAAAGAAACGACTCAAAGATTTTTTCACGAAATTGTC-TCA-AGAGACAAAACTTTG
1 TTTCAAAAGAAACGACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
1871879 TTTCAAAAGAAACAGACTCAAAGA-TTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
1 TTTCAAAAGAAAC-GACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
* *
1871940 TTTCAAAATAAACAACTCAAAGATTTTT
1 TTTCAAAAGAAACGACTCAAAGATTTTT
1871968 ACTCAAAAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
59 30 0.37
60 21 0.26
61 30 0.37
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (61 bp):
TTTCAAAAGAAACGACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
Found at i:1872001 original size:28 final size:26
Alignment explanation
Indices: 1871940--1872008 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
1871930 CAAAACTTTA
*
1871940 TTTCAAAATAAACAACTCAAAGATTT
1 TTTCAAAAGAAACAACTCAAAGATTT
*
1871966 TTACTCAAAAGGAACAGACTCAAAGATTT
1 TT--TCAAAAGAAACA-ACTCAAAGATTT
*
1871995 GTTTCAAGAGAAAC
1 -TTTCAAAAGAAAC
1872009 TATCTCAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.06
28 19 0.54
29 12 0.34
30 2 0.06
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (26 bp):
TTTCAAAAGAAACAACTCAAAGATTT
Found at i:1872261 original size:94 final size:94
Alignment explanation
Indices: 1872141--1872349 Score: 364
Period size: 94 Copynumber: 2.2 Consensus size: 94
1872131 GTGTTTAAAT
* * *
1872141 GGGAAAATGTCTCACGCGAGACGAATCAACTTTGAAAATCCCAAGTGATATTAATTTTGTTTTAA
1 GGGAAAATGTCTCAAGTGAGACGAATCAACTTTGAAAATCCCAAGTGATATTAATTTTGTTTCAA
*
1872206 GTACAACAACTTTGAAATTTGTATTATGA
66 GTAAAACAACTTTGAAATTTGTATTATGA
*
1872235 GGGAAAATGTCTCAAGTGAGACGAATCAACTTTGAAAATCTCAAGTGATATTAATTTTGTTTCAA
1 GGGAAAATGTCTCAAGTGAGACGAATCAACTTTGAAAATCCCAAGTGATATTAATTTTGTTTCAA
*
1872300 GTAAAACAACTTTGAAATTTGTATTCTGA
66 GTAAAACAACTTTGAAATTTGTATTATGA
1872329 GGGAAAATGTCTCAAGTGAGA
1 GGGAAAATGTCTCAAGTGAGA
1872350 TGAAATTTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 109 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (94 bp):
GGGAAAATGTCTCAAGTGAGACGAATCAACTTTGAAAATCCCAAGTGATATTAATTTTGTTTCAA
GTAAAACAACTTTGAAATTTGTATTATGA
Found at i:1872412 original size:68 final size:69
Alignment explanation
Indices: 1872330--1872501 Score: 213
Period size: 72 Copynumber: 2.5 Consensus size: 69
1872320 GTATTCTGAG
*
1872330 GGAAAATGTCTCAAGTGAGATGAAATTTGTTTT-GAAATTGTCTCAAACGAGACAAAATTTGTTT
1 GGAAAATGTCTCAAGTGAGATAAAATTTGTTTTAGAAATTGTCTCAAACGAGACAAAATTTGTTT
1872394 AAAA
66 AAAA
* * *
1872398 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTTG
1 GGAAAATGTCTCAAGTGAGATAAAATTTG-TTTT--AGAAATTGTCTCAAACGAGACAAAATTTG
**
1872463 TTTATGA
63 TTTAAAA
* * *
1872470 -GAAAACGATCTCAAGTGAGATCAACTTTGTTT
1 GGAAAATG-TCTCAAGTGAGATAAAATTTGTTT
1872502 AATGTGAAAC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
68 26 0.30
69 4 0.05
71 8 0.09
72 50 0.57
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (69 bp):
GGAAAATGTCTCAAGTGAGATAAAATTTGTTTTAGAAATTGTCTCAAACGAGACAAAATTTGTTT
AAAA
Found at i:1872465 original size:72 final size:68
Alignment explanation
Indices: 1872330--1872639 Score: 212
Period size: 72 Copynumber: 4.5 Consensus size: 68
1872320 GTATTCTGAG
**
1872330 GGAAAATGTCTCAAGTGAGATGAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTA
1 GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTA
1872395 AAA
66 AAA
* *
1872398 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTTG
1 GGAAAATGTCTCAAGTGAGACAAAATTTG-TTTT---GAAATTGTCTCAAACGAGACAAAATTTG
**
1872463 TTTATGA
62 TTTAAAA
* * * * *
1872470 -GAAAACGATCTCAAGTGAGATC-AACTTTG-TTT--AA-TG--TGAAAC-AAATTCGAAATTTG
1 GGAAAATG-TCTCAAGTGAGA-CAAAATTTGTTTTGAAATTGTCTCAAACGAGA--CAAAATTTG
*
1872526 TATTTCAAA
62 --TTTAAAA
* * *
1872535 GGAAAAATGTCTCAAGCGAGACGAAATTTTTTTTCCAAGAAATTGTCTCAAACGAGACAAAATTT
1 GG-AAAATGTCTCAAGTGAGACAAAATTTGTTTT----GAAATTGTCTCAAACGAGACAAAATTT
*
1872600 GATTT--TA
61 G-TTTAAAA
* * *
1872607 -GAAAACTATCTCAAGCGAGACAAGATTTGTTTT
1 GGAAAA-TGTCTCAAGTGAGACAAAATTTGTTTT
1872640 TCAAAAGAAG
Statistics
Matches: 189, Mismatches: 28, Indels: 47
0.72 0.11 0.18
Matches are distributed among these distances:
61 2 0.01
62 4 0.02
63 8 0.04
64 2 0.01
65 7 0.04
66 17 0.09
67 8 0.04
68 26 0.14
69 4 0.02
70 7 0.04
71 29 0.15
72 51 0.27
73 3 0.02
74 6 0.03
75 8 0.04
76 5 0.03
77 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (68 bp):
GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTA
AAA
Found at i:1872484 original size:36 final size:35
Alignment explanation
Indices: 1872331--1872473 Score: 166
Period size: 36 Copynumber: 4.1 Consensus size: 35
1872321 TATTCTGAGG
* * **
1872331 GAAAATGTCTCAAGTGAGATGAAATTTGTTT-T--
1 GAAATTGTCTCAAGCGAGACAAAATTTGTTTATGA
* **
1872363 GAAATTGTCTCAAACGAGACAAAATTTGTTTAAAA
1 GAAATTGTCTCAAGCGAGACAAAATTTGTTTATGA
* *
1872398 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTAGA
1 -GAAATTGTCTCAAGCGAGACAAAATTTGTTTAT-GA
1872435 GAAATTGTCTCAAGCGAGACAAAATTTGTTTATGA
1 GAAATTGTCTCAAGCGAGACAAAATTTGTTTATGA
1872470 GAAA
1 GAAA
1872474 ACGATCTCAA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
32 26 0.28
35 6 0.06
36 60 0.65
37 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (35 bp):
GAAATTGTCTCAAGCGAGACAAAATTTGTTTATGA
Found at i:1872499 original size:36 final size:36
Alignment explanation
Indices: 1872331--1872502 Score: 133
Period size: 36 Copynumber: 4.9 Consensus size: 36
1872321 TATTCTGAGG
* **
1872331 GAAAATGTCTCAAGTGAGATGAAATTTGTTT-T---
1 GAAAACGTCTCAAGTGAGACAAAATTTGTTTATAGA
** ** *
1872363 GAAATTGTCTCAAACGAGACAAAATTTGTTTA-AAA
1 GAAAACGTCTCAAGTGAGACAAAATTTGTTTATAGA
** *
1872398 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTAGA
1 -GAAAACGTCTCAAGTGAGACAAAATTTGTTTATAGA
** *
1872435 GAAATTGTCTCAAGCGAGACAAAATTTGTTTAT-GA
1 GAAAACGTCTCAAGTGAGACAAAATTTGTTTATAGA
*
1872470 GAAAACGATCTCAAGTGAGATC-AACTTTGTTTA
1 GAAAACG-TCTCAAGTGAGA-CAAAATTTGTTTA
1872503 ATGTGAAACA
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
32 26 0.22
35 7 0.06
36 81 0.69
37 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAACGTCTCAAGTGAGACAAAATTTGTTTATAGA
Found at i:1872585 original size:36 final size:36
Alignment explanation
Indices: 1872542--1872677 Score: 118
Period size: 35 Copynumber: 3.7 Consensus size: 36
1872532 AAAGGAAAAA
1872542 TGTCTCAAGCGAGACGAA-ATTT-TTTTTCCAAGAAAT
1 TGTCTCAAGCGAGAC-AACATTTGTTTTT-CAAGAAAT
* * * *
1872578 TGTCTCAAACGAGACAAAATTTGATTTT--AGAAAAC
1 TGTCTCAAGCGAGACAACATTTGTTTTTCAAG-AAAT
* * *
1872613 TATCTCAAGCGAGACAAGATTTGTTTTTCAAAAGAAGT
1 TGTCTCAAGCGAGACAACATTTGTTTTTC--AAGAAAT
*
1872651 TGTCTCTAGCGAGACAACATTTTGTTT
1 TGTCTCAAGCGAGACAACA-TTTGTTT
1872678 CGAGAGAAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
34 2 0.03
35 29 0.36
36 18 0.22
37 4 0.05
38 18 0.22
39 9 0.11
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAACATTTGTTTTTCAAGAAAT
Found at i:1873047 original size:4 final size:4
Alignment explanation
Indices: 1872989--1873035 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
1872979 TGCATTTATG
* *
1872989 TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TGTA TGCA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1873036 GTTGATGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:1874237 original size:11 final size:11
Alignment explanation
Indices: 1874223--1874270 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
1874213 TGATTTTGTC
1874223 TTCTTTTTCTT
1 TTCTTTTTCTT
1874234 TTCTTTTTCTTT
1 TTCTTTTTC-TT
1874246 TTCTATTTTTCTT
1 TTC--TTTTTCTT
**
1874259 TGATTTTTCTT
1 TTCTTTTTCTT
1874270 T
1 T
1874271 GTACTCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 18 0.56
12 5 0.16
13 3 0.09
14 6 0.19
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:1874886 original size:20 final size:20
Alignment explanation
Indices: 1874848--1874886 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1874838 GGATAAATGC
*
1874848 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
1874868 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
1874887 AAGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:1878017 original size:28 final size:28
Alignment explanation
Indices: 1877971--1878056 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
1877961 CTAAAATAAT
*
1877971 AAAAACACAAACTAAAGGGACTAAAATGGC
1 AAAAACA-AAAC-ATAGGGACTAAAATGGC
* ** *
1878001 AAAAACAAAACATAGGGAGTAAAACAGT
1 AAAAACAAAACATAGGGACTAAAATGGC
* *
1878029 AAAAATAAAAACCTAGAGGACTAAAATG
1 AAAAA-CAAAACATAG-GGACTAAAATG
1878057 TAAACAACAT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
28 17 0.39
29 12 0.27
30 15 0.34
ACGTcount: A:0.59, C:0.13, G:0.16, T:0.12
Consensus pattern (28 bp):
AAAAACAAAACATAGGGACTAAAATGGC
Found at i:1878059 original size:29 final size:29
Alignment explanation
Indices: 1877957--1878060 Score: 79
Period size: 30 Copynumber: 3.6 Consensus size: 29
1877947 ATAAATTTGA
* * *
1877957 AGGACTAAAATAATAAAAACACAAA-CTAA
1 AGGACTAAAATAGTAAAAA-AAAAACCTAG
* * * *
1877986 AGGGACTAAAATGGCAAAAACAAAACATAG
1 A-GGACTAAAATAGTAAAAAAAAAACCTAG
* *
1878016 -GGAGTAAAACAGTAAAAATAAAAACCTAG
1 AGGACTAAAATAGTAAAAA-AAAAACCTAG
1878045 AGGACTAAAAT-GTAAA
1 AGGACTAAAATAGTAAA
1878061 CAACATAAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
28 14 0.25
29 17 0.30
30 25 0.45
ACGTcount: A:0.60, C:0.12, G:0.15, T:0.13
Consensus pattern (29 bp):
AGGACTAAAATAGTAAAAAAAAAACCTAG
Found at i:1879414 original size:3 final size:3
Alignment explanation
Indices: 1879408--1879456 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
1879398 ACATAATTAT
1879408 TAA TAA TAA TAA -ACA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1879454 TAA
1 TAA
1879457 ATTTAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1879432 original size:28 final size:28
Alignment explanation
Indices: 1879400--1879456 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1879390 TATATGTAAC
* *
1879400 ATAATTATTAATAATAATAA-ACATAATA
1 ATAATAATAAATAATAATAATA-ATAATA
1879428 ATAATAATAAATAATAATAATAATAATA
1 ATAATAATAAATAATAATAATAATAATA
1879456 A
1 A
1879457 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATAATAAATAATAATAATAATAATA
Found at i:1879440 original size:22 final size:21
Alignment explanation
Indices: 1879397--1879456 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 21
1879387 ATATATATGT
*
1879397 AACATAATTATTAATAATAATA
1 AACATAA-TAATAATAATAATA
1879419 AACATAATAATAATAATAA-A
1 AACATAATAATAATAATAATA
*
1879439 TA-ATAATAATAATAATAA
1 AACATAATAATAATAATAA
1879457 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 16 0.44
20 2 0.06
21 11 0.31
22 7 0.19
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AACATAATAATAATAATAATA
Found at i:1883092 original size:20 final size:20
Alignment explanation
Indices: 1883069--1883116 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1883059 AGAGTATTGT
1883069 TACTATTCATAAGGTATCAA
1 TACTATTCATAAGGTATCAA
*
1883089 TACT-TCTCATAAGGTATCGA
1 TACTAT-TCATAAGGTATCAA
*
1883109 TACCATTC
1 TACTATTC
1883117 TTAGATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (20 bp):
TACTATTCATAAGGTATCAA
Found at i:1884910 original size:11 final size:13
Alignment explanation
Indices: 1884850--1884925 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 13
1884840 ATATTTATGT
*
1884850 TTAAAATTAGTTA
1 TTAAAATTATTTA
* *
1884863 CTTAAATTTGAATTAA
1 -TTAAAATT--ATTTA
1884879 TT-AAATTATTTA
1 TTAAAATTATTTA
*
1884891 TTAAGATTA-TT-
1 TTAAAATTATTTA
1884902 TTAAAATTAAATTTA
1 TTAAAATT--ATTTA
1884917 TTAAAATTA
1 TTAAAATTA
1884926 AATTAAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
11 7 0.15
12 8 0.17
13 7 0.15
14 13 0.27
15 10 0.21
16 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (13 bp):
TTAAAATTATTTA
Found at i:1884920 original size:26 final size:26
Alignment explanation
Indices: 1884886--1884935 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1884876 TAATTAAATT
* **
1884886 ATTTATTAAGATTATTTTAAAATTAA
1 ATTTATTAAAATTAAATTAAAATTAA
1884912 ATTTATTAAAATTAAATTAAAATT
1 ATTTATTAAAATTAAATTAAAATT
1884936 TTCTCATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTTATTAAAATTAAATTAAAATTAA
Found at i:1915182 original size:33 final size:34
Alignment explanation
Indices: 1915145--1915211 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
1915135 CAATACACTA
* *
1915145 TAAATGGAATGCAT-ATACAATGAATTTCTTTTG
1 TAAATGGAATACATAACACAATGAATTTCTTTTG
**
1915178 TAAATTTAATACATAAACACAATGAATTTCTTTT
1 TAAATGGAATACAT-AACACAATGAATTTCTTTT
1915212 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 11 0.39
35 17 0.61
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (34 bp):
TAAATGGAATACATAACACAATGAATTTCTTTTG
Found at i:1915730 original size:14 final size:14
Alignment explanation
Indices: 1915711--1915743 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1915701 TTTAGGATAT
1915711 TATTTTTATATTT-
1 TATTTTTATATTTG
*
1915724 TATTTTTATCTTTG
1 TATTTTTATATTTG
1915738 TATTTT
1 TATTTT
1915744 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TATTTTTATATTTG
Found at i:1915780 original size:75 final size:76
Alignment explanation
Indices: 1915625--1915799 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 76
1915615 TTAAACTCAA
* * **
1915625 ATTTAGGATAATA-TTTTAAACATTATATTTTATCTTTTATTTTAGTTTAAATAGGTTATTAGTA
1 ATTTAGGATATTATTTTTATATTTTATATTTTATCTTTTATTTTAGTTTAAATAGGTTATTAGTA
1915689 TTTTAATTAAG
66 TTTTAATTAAG
*
1915700 CTTTAGGATATTATTTTTATATTTTAT-TTTTATCTTTGTATTTTAGTTTAAATAGGTT-TTAGT
1 ATTTAGGATATTATTTTTATATTTTATATTTTATCTTT-TATTTTAGTTTAAATAGGTTATTAGT
*
1915763 ATTTTAATTAGG
65 ATTTTAATTAAG
* * *
1915775 ATTTAGAATATTATATATATATTTT
1 ATTTAGGATATTATTTTTATATTTT
1915800 TAGGTATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
75 58 0.66
76 30 0.34
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (76 bp):
ATTTAGGATATTATTTTTATATTTTATATTTTATCTTTTATTTTAGTTTAAATAGGTTATTAGTA
TTTTAATTAAG
Found at i:1921094 original size:17 final size:17
Alignment explanation
Indices: 1921072--1921116 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1921062 TTTCGTTATA
1921072 TTTTTGTTTTTATTTTT
1 TTTTTGTTTTTATTTTT
*
1921089 TTTTTG-TTTGATTTTT
1 TTTTTGTTTTTATTTTT
1921105 TTTATT-TTTTTA
1 TTT-TTGTTTTTA
1921117 GTGAACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (17 bp):
TTTTTGTTTTTATTTTT
Found at i:1924811 original size:75 final size:75
Alignment explanation
Indices: 1924656--1924819 Score: 222
Period size: 75 Copynumber: 2.2 Consensus size: 75
1924646 TTAAACTCAA
* *
1924656 ATTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTAT
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGACTTTAGTAT
1924721 TTTAATTAAG
66 TTTAATTAAG
* * * * * *
1924731 TTTTAGGATATTATTTT-TATATTTTATCTTTATTTTTGTATTTTAGTTTAAATAGGCTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGACTTTAGTA
*
1924795 TTTTAATTAGG
65 TTTTAATTAAG
*
1924806 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1924820 ATATTTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 7 0.09
75 70 0.91
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGACTTTAGTAT
TTTAATTAAG
Found at i:1925539 original size:16 final size:15
Alignment explanation
Indices: 1925518--1925547 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1925508 ATCCCTTTTT
1925518 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
1925534 ATATTTATTATATT
1 ATATTTATTATATT
1925548 TTTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:1927827 original size:19 final size:19
Alignment explanation
Indices: 1927803--1927843 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1927793 CAAACGAACA
1927803 AATAGTAATAGACCTAACT
1 AATAGTAATAGACCTAACT
1927822 AATAGTAATAGACCTAACT
1 AATAGTAATAGACCTAACT
1927841 AAT
1 AAT
1927844 GGCTAACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (19 bp):
AATAGTAATAGACCTAACT
Found at i:1928314 original size:6 final size:6
Alignment explanation
Indices: 1928303--1928336 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1928293 ACTCATCAGC
1928303 CCAGTT CCAGTT CCAGTT CCAGTT CCAGTT CCAG
1 CCAGTT CCAGTT CCAGTT CCAGTT CCAGTT CCAG
1928337 AACATGGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (6 bp):
CCAGTT
Found at i:1935857 original size:26 final size:25
Alignment explanation
Indices: 1935813--1935866 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1935803 TAAACTGCAT
1935813 ATTATCTCAACAATCACTTTTGTTTTA
1 ATTATCTCAACAATCAC-TTT-TTTTA
* *
1935840 ATTA-CTCAACTATTACTTTTTTTA
1 ATTATCTCAACAATCACTTTTTTTA
1935864 ATT
1 ATT
1935867 TTATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 3 0.12
26 10 0.40
27 4 0.16
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTATCTCAACAATCACTTTTTTTA
Found at i:1942387 original size:20 final size:20
Alignment explanation
Indices: 1942362--1942404 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1942352 TCTAAAAGCA
1942362 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
** *
1942382 CATTTAGGAGTATATAGTTG
1 CATTTAGGACCATATAGATG
1942402 CAT
1 CAT
1942405 GTGGTGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1950836 original size:20 final size:20
Alignment explanation
Indices: 1950811--1950853 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1950801 TCTAAAAGCT
1950811 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
1950831 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1950851 CAT
1 CAT
1950854 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1954551 original size:54 final size:54
Alignment explanation
Indices: 1954483--1954642 Score: 140
Period size: 54 Copynumber: 3.0 Consensus size: 54
1954473 TGCAGTTAAA
* ** * * *
1954483 AATGACTGAACACCTCTGTGCTTCAGTCTAGAATCTGGCACCCCCGTGTTTTGT
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
* * * * * * *
1954537 AATGATTGAGCACCTCTGTACTTTAAACTAGGATTTGGCACCTATGTGCTTTGG
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
* * * * * * *
1954591 AATGATTGAACACCTCTGTGGTTTAATCTAAAATATGGCACCTATGTGCTTT
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTT
1954643 AAAATTGATA
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (54 bp):
AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
Found at i:1955912 original size:29 final size:30
Alignment explanation
Indices: 1955848--1955904 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1955838 ATGCTTTCGC
*
1955848 CCCTAGAATTTTGATAAGTTCAAATTCAGA
1 CCCTAAAATTTTGATAAGTTCAAATTCAGA
1955878 CCCTAAAATTTT-ATAAGTTCAAATTCA
1 CCCTAAAATTTTGATAAGTTCAAATTCA
1955905 CCTCCTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (30 bp):
CCCTAAAATTTTGATAAGTTCAAATTCAGA
Found at i:1961718 original size:20 final size:20
Alignment explanation
Indices: 1961682--1961719 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1961672 TGTTAATTTA
*
1961682 TGTATAATTTTAGAGATTAT
1 TGTATAATCTTAGAGATTAT
1961702 TGTATAAATCTTA-AGATT
1 TGTAT-AATCTTAGAGATT
1961720 TTATAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (20 bp):
TGTATAATCTTAGAGATTAT
Found at i:1968747 original size:21 final size:21
Alignment explanation
Indices: 1968722--1968825 Score: 60
Period size: 19 Copynumber: 5.2 Consensus size: 21
1968712 ATTATATAGC
1968722 ATATATATTAAGTTTAAAAAT
1 ATATATATTAAGTTTAAAAAT
* * *
1968743 GTATATA-T-AGTTTTAAAGT
1 ATATATATTAAGTTTAAAAAT
*
1968762 ATATATATTATA-TATT--ATA-
1 ATATATATTA-AGT-TTAAAAAT
* * *
1968781 ATATATATTATGTTTGAAAAC
1 ATATATATTAAGTTTAAAAAT
* *
1968802 ATATATA-TAATTTTTAAAAT
1 ATATATATTAAGTTTAAAAAT
1968822 ATAT
1 ATAT
1968826 GTATATTATA
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
18 2 0.03
19 26 0.41
20 18 0.29
21 14 0.22
22 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (21 bp):
ATATATATTAAGTTTAAAAAT
Found at i:1968765 original size:59 final size:61
Alignment explanation
Indices: 1968701--1968888 Score: 177
Period size: 59 Copynumber: 3.2 Consensus size: 61
1968691 CTATCAATGT
*
1968701 ATATATTATA-TAT-TATATAGCATATATATTAAGTTT-AAAA-ATGTATATATAGTTTTAAA
1 ATATATTATATTATATATATA-CATATATATTAAGTTTGAAAACATATATATA-AGTTTTAAA
* * *
1968760 GTATA-TATATTATATATTATA-ATATATATTATGTTTGAAAACATATATATAATTTTTAAA
1 ATATATTATATTATATA-TATACATATATATTAAGTTTGAAAACATATATATAAGTTTTAAA
* *
1968820 ATATATGTATATTATATATATAACATAT-TA-T-A-TTTGAAAGC--ATATATAA-TTTTGAA
1 ATATAT-TATATTATATATAT-ACATATATATTAAGTTTGAAAACATATATATAAGTTTTAAA
1968876 ATATATATATATT
1 ATATAT-TATATT
1968889 GAAACACATA
Statistics
Matches: 111, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
56 18 0.16
57 8 0.07
58 4 0.04
59 29 0.26
60 18 0.16
61 16 0.14
62 14 0.13
63 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (61 bp):
ATATATTATATTATATATATACATATATATTAAGTTTGAAAACATATATATAAGTTTTAAA
Found at i:1968883 original size:19 final size:18
Alignment explanation
Indices: 1968739--1968886 Score: 52
Period size: 19 Copynumber: 7.7 Consensus size: 18
1968729 TTAAGTTTAA
* *
1968739 AAATGTATATATAGTTTT
1 AAATATATATATAATTTT
*
1968757 AAAGTATATATATTATATATT
1 AAA-TATATATA-TA-ATTTT
1968778 ATAATATATAT-T-ATGTTT
1 A-AATATATATATAAT-TTT
*
1968796 GAAAACATATATATAATTTTT
1 --AAATATATATATAA-TTTT
* *
1968817 AAA-ATATATGTATATTAT
1 AAATATATATATA-ATTTT
* * *
1968835 ATATATAACATATTATATTTG
1 AAATAT-ATATA-TA-ATTTT
**
1968856 AAA-GCATATATAATTTT
1 AAATATATATATAATTTT
1968873 GAAATATATATATA
1 -AAATATATATATA
1968887 TTGAAACACA
Statistics
Matches: 95, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
17 6 0.06
18 23 0.24
19 33 0.35
20 7 0.07
21 23 0.24
22 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
AAATATATATATAATTTT
Found at i:1969006 original size:2 final size:2
Alignment explanation
Indices: 1968999--1969031 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1968989 GGGAAAAATA
1968999 AT AT AT AT AT -T AT AT AT AGT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
1969032 GTAGGTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1969015 original size:11 final size:11
Alignment explanation
Indices: 1968999--1969084 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
1968989 GGGAAAAATA
1968999 ATATATATATT
1 ATATATATATT
1969010 ATATATAGTA-T
1 ATATATA-TATT
1969021 ATATATATA-T
1 ATATATATATT
** *
1969031 AGTAGGTACATT
1 A-TATATATATT
*
1969043 ATATGT-TATT
1 ATATATATATT
*
1969053 -TGTTATATATT
1 AT-ATATATATT
1969064 ATAT-TATATT
1 ATATATATATT
1969074 AT-TAT-TATT
1 ATATATATATT
1969083 AT
1 AT
1969085 TTTATTTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
9 8 0.13
10 18 0.30
11 29 0.48
12 5 0.08
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:1970042 original size:41 final size:41
Alignment explanation
Indices: 1969985--1970065 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
1969975 TATATTTTGG
1969985 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
1 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
1970026 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGG
1 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGG
1970066 ACTTTGGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (41 bp):
CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
Found at i:1977719 original size:19 final size:18
Alignment explanation
Indices: 1977687--1977733 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 18
1977677 ATAGTATGTA
1977687 TATATATTATGTTTAAAAATG
1 TATATA-TATGTTT-AAAA-G
*
1977708 TATATATA-GTTTTAAAG
1 TATATATATGTTTAAAAG
1977725 TATATATAT
1 TATATATAT
1977734 ATATTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.38
18 3 0.12
19 4 0.17
20 2 0.08
21 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TATATATATGTTTAAAAG
Found at i:1977732 original size:21 final size:21
Alignment explanation
Indices: 1977684--1977737 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1977674 TATATAGTAT
1977684 GTATATATAT-TATGTTTAAA
1 GTATATATATATATGTTTAAA
* *
1977704 -AATGTATATATA-GTTTTAAA
1 GTATATATATATATG-TTTAAA
1977724 GTATATATATATAT
1 GTATATATATATAT
1977738 TATATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
19 8 0.31
20 8 0.31
21 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
GTATATATATATATGTTTAAA
Found at i:1977734 original size:19 final size:20
Alignment explanation
Indices: 1977684--1977735 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1977674 TATATAGTAT
1977684 GTATATATATTATGTTTAAAA
1 GTATATATA-TATGTTTAAAA
* * *
1977705 ATGTATATATA-GTTTTAAA
1 GTATATATATATGTTTAAAA
1977724 GTATATATATAT
1 GTATATATATAT
1977736 ATTATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
GTATATATATATGTTTAAAA
Found at i:1977752 original size:18 final size:18
Alignment explanation
Indices: 1977725--1977763 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1977715 AGTTTTAAAG
* *
1977725 TATATATATATATTATAT
1 TATATATATAAAATATAT
*
1977743 TATATTTATAAAATATAT
1 TATATATATAAAATATAT
1977761 TAT
1 TAT
1977764 GTTTGAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATAAAATATAT
Found at i:1977779 original size:67 final size:65
Alignment explanation
Indices: 1977654--1977780 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 65
1977644 TTTTATTCTA
* **
1977654 TTAATGTATATATTATATATTATATAGTATGTATATATATTATGTTTAAAAATGTATATATAGTT
1 TTAAAGTATATATTATATATTATATAGTATGTATATATATTATGTTTAAAAACATATATATAGTT
* *
1977719 TTAAAGTATATA-TATATATTATATTA-TATTTATAAAATATATTATGTTTGAAAACATATATA
1 TTAAAGTATATATTATATATTATA-TAGTATGTAT---ATATATTATGTTTAAAAACATATATA
1977781 CAATTGTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
64 17 0.32
65 13 0.25
67 23 0.43
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (65 bp):
TTAAAGTATATATTATATATTATATAGTATGTATATATATTATGTTTAAAAACATATATATAGTT
Found at i:1977857 original size:49 final size:48
Alignment explanation
Indices: 1977804--1977896 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
1977794 TAAATATAAT
* *
1977804 ACATATTGCATTTGAATATATATATAT-ATATATATGTTATATTTTGAAA
1 ACATATAGCATTTGAAAATATATATATAATATATA-G-TATATTTTGAAA
** *
1977853 ACATATAGTTTTTGAAAATATATGTATAATATATAGTATATTTT
1 ACATATAGCATTTGAAAATATATATATAATATATAGTATATTTT
1977897 TTAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 8 0.21
49 23 0.61
50 7 0.18
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (48 bp):
ACATATAGCATTTGAAAATATATATATAATATATAGTATATTTTGAAA
Found at i:1977912 original size:51 final size:50
Alignment explanation
Indices: 1977814--1977950 Score: 136
Period size: 49 Copynumber: 2.7 Consensus size: 50
1977804 ACATATTGCA
*
1977814 TTTGAATATATATATAT-ATATATATGT-TATATTTTGAAAACATATAGTT
1 TTTGAAAATATATATATAATATATA-GTATATATTTTGAAAACATATAGTT
* * *
1977863 TTTGAAAATATATGTATAATATATAGTATAT-TTTTTAAAATATACATAGTT
1 TTTGAAAATATATATATAATATATAGTATATATTTTGAAAACAT--ATAGTT
** *
1977914 TTAAAAAAATATATAATATTATTATATAGTATATATT
1 TT-TGAAAATATAT-ATA-TAATATATAGTATATATT
1977951 AGTATATATA
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
49 27 0.38
50 10 0.14
51 8 0.11
52 9 0.12
53 2 0.03
54 14 0.19
55 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (50 bp):
TTTGAAAATATATATATAATATATAGTATATATTTTGAAAACATATAGTT
Found at i:1977967 original size:15 final size:15
Alignment explanation
Indices: 1977923--1978054 Score: 57
Period size: 15 Copynumber: 8.9 Consensus size: 15
1977913 TTTAAAAAAA
1977923 TATATAATATTATTA-
1 TATAT-ATATTATTAG
1977938 TATAGTATA-TATTAG
1 TATA-TATATTATTAG
*
1977953 TATATATATTTTTAG
1 TATATATATTATTAG
* * * * *
1977968 GAAAAAAAATATATAG
1 TATATATATTAT-TAG
*
1977984 TATATATTTTATATA-
1 TATATATATTAT-TAG
*
1977999 TAGTATATATGTAGTAGG
1 TA-TATATAT-TATTA-G
1978017 TATATTATATT-TTA-
1 TATA-TATATTATTAG
1978031 TATAT-TATTATT-G
1 TATATATATTATTAG
1978044 T-TAT-TATTATT
1 TATATATATTATT
1978055 GTTGTTGTTG
Statistics
Matches: 90, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
12 14 0.16
13 4 0.04
14 13 0.14
15 24 0.27
16 23 0.26
17 5 0.06
18 7 0.08
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (15 bp):
TATATATATTATTAG
Found at i:1978041 original size:3 final size:3
Alignment explanation
Indices: 1978019--1978096 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
1978009 GTAGTAGGTA
* * * *
1978019 TAT TA- TAT T-T TAT ATAT TAT TAT TGT TAT TAT TAT TGT TGT TGT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1978063 TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1978097 TTCTTTTATT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 61 0.90
4 3 0.04
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1983061 original size:18 final size:18
Alignment explanation
Indices: 1983038--1983074 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1983028 GTTAGGGGCA
* *
1983038 GTTTGACTGGTCTGAACC
1 GTTTGACCGGTCCGAACC
1983056 GTTTGACCGGTCCGAACC
1 GTTTGACCGGTCCGAACC
1983074 G
1 G
1983075 GTTCGACCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (18 bp):
GTTTGACCGGTCCGAACC
Found at i:1989580 original size:35 final size:35
Alignment explanation
Indices: 1989534--1989605 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1989524 TACTATTTAT
*
1989534 ACCATCTTCCATCTCCATATCACGCCTATATCATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
*
1989569 ACCATCTTCCATCTCCATTTCACGCCTATATAATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
1989604 AC
1 AC
1989606 AATCCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.39, G:0.03, T:0.32
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACGCCTATATAATC
Found at i:1990263 original size:16 final size:15
Alignment explanation
Indices: 1990225--1990266 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1990215 ATTTACTTAC
1990225 TATTTTCA-TTTTCT
1 TATTTTCATTTTTCT
1990239 TATTCTTTCATCTTTTCT
1 TA-T-TTTCAT-TTTTCT
1990257 TATTTTCATT
1 TATTTTCATT
1990267 ACTTTATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.08
15 2 0.08
16 11 0.46
17 1 0.04
18 8 0.33
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTCATTTTTCT
Found at i:1993706 original size:35 final size:35
Alignment explanation
Indices: 1993666--1993741 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1993656 TACTATCTAT
* *
1993666 ACCATCTTCTATCTCCATATCACACCTATATCATC
1 ACCATCTTCCATCTCCATATCACACCTATATAATC
* *
1993701 ACCATCTTCCATCTCCATTTCACGCCTATATAATC
1 ACCATCTTCCATCTCCATATCACACCTATATAATC
1993736 ACCATC
1 ACCATC
1993742 CCATTATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.38, G:0.01, T:0.33
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACACCTATATAATC
Found at i:1995384 original size:19 final size:19
Alignment explanation
Indices: 1995362--1995403 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1995352 ATTTGACTGG
*
1995362 TCTGAACCGGTTTGACCAA
1 TCTGAAACGGTTTGACCAA
* *
1995381 TCTGAAATGGTTTGACCGA
1 TCTGAAACGGTTTGACCAA
1995400 TCTG
1 TCTG
1995404 GATTGGTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (19 bp):
TCTGAAACGGTTTGACCAA
Found at i:1995433 original size:12 final size:12
Alignment explanation
Indices: 1995416--1995459 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1995406 TTGGTTCGAC
1995416 CCGTTGACCCGA
1 CCGTTGACCCGA
1995428 CCGTTGACCCGA
1 CCGTTGACCCGA
* *
1995440 CCCATTGA-CCTA
1 -CCGTTGACCCGA
1995452 CCGTTGAC
1 CCGTTGAC
1995460 TTTAACCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 6 0.22
12 15 0.56
13 6 0.22
ACGTcount: A:0.18, C:0.41, G:0.20, T:0.20
Consensus pattern (12 bp):
CCGTTGACCCGA
Found at i:1995447 original size:13 final size:13
Alignment explanation
Indices: 1995412--1995449 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1995402 TGGATTGGTT
1995412 CGACCCGTTGACC
1 CGACCCGTTGACC
1995425 CGA-CCGTTGACC
1 CGACCCGTTGACC
*
1995437 CGACCCATTGACC
1 CGACCCGTTGACC
1995450 TACCGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:1995459 original size:24 final size:25
Alignment explanation
Indices: 1995412--1995459 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1995402 TGGATTGGTT
*
1995412 CGACCCGTTGACCCGACCGTTGACC
1 CGACCCATTGACCCGACCGTTGACC
*
1995437 CGACCCATTGA-CCTACCGTTGAC
1 CGACCCATTGACCCGACCGTTGAC
1995460 TTTAACCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.19
Consensus pattern (25 bp):
CGACCCATTGACCCGACCGTTGACC
Found at i:1995492 original size:17 final size:17
Alignment explanation
Indices: 1995470--1995515 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1995460 TTTAACCAAG
*
1995470 AAGTCAAATTTTTAAAA
1 AAGTCATATTTTTAAAA
**
1995487 AAGTCATATTTTTTTAA
1 AAGTCATATTTTTAAAA
1995504 AAGTCATATTTT
1 AAGTCATATTTT
1995516 ATATTTTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (17 bp):
AAGTCATATTTTTAAAA
Found at i:1997875 original size:15 final size:15
Alignment explanation
Indices: 1997852--1997882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1997842 TCCTAAAAAT
*
1997852 TCTATTTCTATTTTC
1 TCTAATTCTATTTTC
1997867 TCTAATTCTATTTTC
1 TCTAATTCTATTTTC
1997882 T
1 T
1997883 TACGACTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTAATTCTATTTTC
Found at i:2000402 original size:13 final size:14
Alignment explanation
Indices: 2000378--2000407 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2000368 TTTAGTAATT
2000378 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
2000392 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
2000405 TTA
1 TTA
2000408 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:2002763 original size:20 final size:20
Alignment explanation
Indices: 2002685--2002764 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
2002675 AGAACCCTTA
*
2002685 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
2002703 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
*
2002727 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2002747 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2002765 TGCATCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.22
20 20 0.40
21 2 0.04
22 4 0.08
23 13 0.26
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2011257 original size:3 final size:3
Alignment explanation
Indices: 2011249--2011289 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2011239 ATGATAAGAA
2011249 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2011290 GACATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2011273 original size:17 final size:17
Alignment explanation
Indices: 2011253--2011287 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2011243 TAAGAAAATA
2011253 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
2011270 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
2011287 A
1 A
2011288 ATGACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:2011273 original size:20 final size:20
Alignment explanation
Indices: 2011250--2011289 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2011240 TGATAAGAAA
2011250 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
2011270 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
2011290 GACATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:2012020 original size:20 final size:19
Alignment explanation
Indices: 2011931--2012026 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
2011921 ATTCGCGTTG
2011931 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGA-TTTT
*** *
2011951 CATTTAATGTTGCAATTTT
1 CATTTCGCGTTGCGATTTT
* *
2011970 CAATTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT--TTT
* **
2011991 AAAATCGCGTTGCGATTTT
1 CATTTCGCGTTGCGATTTT
*
2012010 CCATTTCGCGTTACGAT
1 -CATTTCGCGTTGCGAT
2012027 AGTCTACAGT
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
19 17 0.30
20 23 0.41
21 16 0.29
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42
Consensus pattern (19 bp):
CATTTCGCGTTGCGATTTT
Found at i:2012043 original size:22 final size:22
Alignment explanation
Indices: 2012018--2012081 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
2012008 TTCCATTTCG
*
2012018 CGTTACGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
2012040 CGTTGCGAT--TTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
2012059 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2012081 C
1 C
2012082 AAAATTCTTG
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 5 0.17
22 10 0.33
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2012189 original size:5 final size:5
Alignment explanation
Indices: 2012167--2012211 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
2012157 TGTATTACCA
2012167 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
2012212 GACGAGACGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:2012713 original size:6 final size:6
Alignment explanation
Indices: 2012697--2012728 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2012687 GTCCGTCTCG
2012697 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2012729 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2012868 original size:22 final size:22
Alignment explanation
Indices: 2012840--2012892 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2012830 AATTTGGAAA
2012840 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
2012862 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
2012884 ATCGCAACG
1 ATCGCAACG
2012893 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:2012909 original size:20 final size:20
Alignment explanation
Indices: 2012884--2013001 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
2012874 ACTGTAGACT
2012884 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
2012904 ATCGCACCGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
2012925 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** ** *
2012945 ATCGCGTTGCGATTTTCAAGT
1 ATCGCAACGCGAAATGGAA-A
2012966 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2012986 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
2013002 CAACGCGAAT
Statistics
Matches: 68, Mismatches: 28, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 42 0.62
21 26 0.38
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2012930 original size:41 final size:41
Alignment explanation
Indices: 2012881--2012997 Score: 180
Period size: 41 Copynumber: 2.9 Consensus size: 41
2012871 ACAACTGTAG
*
2012881 ACTATCGCAACGCGAAATGGAAAATCGCACCGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* ***
2012922 ACTATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
2012963 AGTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
2012998 AATGCAACGC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2013474 original size:17 final size:18
Alignment explanation
Indices: 2013442--2013475 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2013432 TAATACGGAT
2013442 ATTTTATTTTAAATTTAG
1 ATTTTATTTTAAATTTAG
*
2013460 ATTTT-TTTTACATTTA
1 ATTTTATTTTAAATTTA
2013476 ATACATTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTATTTTAAATTTAG
Found at i:2015081 original size:2 final size:2
Alignment explanation
Indices: 2015074--2015099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2015064 CAAGTAAAAT
2015074 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
2015100 CACAAAAAGT
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):
TA
Found at i:2015932 original size:16 final size:15
Alignment explanation
Indices: 2015874--2015932 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
2015864 TTTTAAAAAG
2015874 AAGATTAAATTGATAT
1 AAGATTAAATTGA-AT
*
2015890 AATGATTAAATT-TAT
1 AA-GATTAAATTGAAT
**
2015905 AA-ATTATTTTGAACT
1 AAGATTAAATTGAA-T
2015920 AAGATTAAATTGA
1 AAGATTAAATTGA
2015933 TAGAATGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
13 6 0.18
14 1 0.03
15 7 0.21
16 10 0.30
17 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (15 bp):
AAGATTAAATTGAAT
Found at i:2016045 original size:14 final size:15
Alignment explanation
Indices: 2015996--2016048 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 15
2015986 TTATTTTATC
*
2015996 TAATA-TTTAACTAA
1 TAATATTTTAATTAA
*
2016010 TAATATTTTATTTATAA
1 TAATATTTTA-AT-TAA
2016027 TAATATTTTAATTAA
1 TAATATTTTAATTAA
2016042 -AATATTT
1 TAATATTT
2016049 AAAAAGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.36
15 7 0.21
16 1 0.03
17 13 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATTTTAATTAA
Found at i:2016045 original size:17 final size:17
Alignment explanation
Indices: 2016008--2016045 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2015998 ATATTTAACT
* *
2016008 AATAATATTTTATTTAT
1 AATAATATTTTAATTAA
2016025 AATAATATTTTAATTAA
1 AATAATATTTTAATTAA
2016042 AATA
1 AATA
2016046 TTTAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATAATATTTTAATTAA
Found at i:2018236 original size:13 final size:13
Alignment explanation
Indices: 2018218--2018260 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
2018208 ATATCTATGG
2018218 ATGTATACATATT
1 ATGTATACATATT
2018231 ATGTATACATATT
1 ATGTATACATATT
2018244 ATGTATACATATCT
1 ATGTATACATAT-T
2018258 ATG
1 ATG
2018261 GATATAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 25 0.86
14 4 0.14
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (13 bp):
ATGTATACATATT
Found at i:2018274 original size:10 final size:10
Alignment explanation
Indices: 2018261--2018290 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2018251 CATATCTATG
2018261 GATATAACTT
1 GATATAACTT
2018271 GATATAACTT
1 GATATAACTT
2018281 GATATAACTT
1 GATATAACTT
2018291 TTTAGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (10 bp):
GATATAACTT
Found at i:2019774 original size:86 final size:86
Alignment explanation
Indices: 2019662--2019990 Score: 406
Period size: 85 Copynumber: 3.8 Consensus size: 86
2019652 ATAGCATATT
*
2019662 TTCTGTTGATAATGCACCCATATGCATTTTAACTATAGTATACTTTTCTGTTGATAATGCACCCA
1 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT-CTTTTCTGTTGATAATGCACCCA
2019727 TATGCATTTCAACTATAG-TAC
65 TATGCATTTCAACTATAGATAC
* *
2019748 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATTTTTTCTGTTGATAATACACCCAT
1 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATCTTTTCTGTTGATAATGCACCCAT
2019813 ATGCATTTCAACTATAGCATAC
66 ATGCATTTCAACTATAG-ATAC
* *
2019835 TTTTCTGTTG--AATACATCCCATA-GCATTTCAACTATAGTATACTTTT-TGTTGATAATGTA-
1 --TTCTGTTGATAATGCA-CCCATATGCATTTCAACTATAGTAT-CTTTTCTGTTGATAATGCAC
* *
2019895 CCATATACATTTCAACTATAGTATAT
62 CCATATGCATTTCAACTATAG-ATAC
* * * * * *
2019921 TTCTG-TGATAATGTACCCATATACATTTAAACTAT-GGATCCTTTCATG-CGATAATGCACCCA
1 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATCTTTTC-TGTTGATAATGCACCCA
2019983 TATGCATT
65 TATGCATT
2019991 ATTATTCATT
Statistics
Matches: 212, Mismatches: 19, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
83 6 0.03
84 22 0.10
85 66 0.31
86 63 0.30
87 37 0.17
88 10 0.05
89 8 0.04
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (86 bp):
TTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATCTTTTCTGTTGATAATGCACCCAT
ATGCATTTCAACTATAGATAC
Found at i:2019794 original size:130 final size:131
Alignment explanation
Indices: 2019621--2019990 Score: 438
Period size: 130 Copynumber: 2.9 Consensus size: 131
2019611 CCTCCATTCA
* ** * *
2019621 TGTTTATAATGCACCATTATGCACCGTCAA-TATAGCATATTTTCTGTTGATAATGCACCCATAT
1 TGTTGATAATGCACCA-TATGCA-TTTCAACTATAGTATTTTTTCTGTTGATAATGCACCCATAT
* *
2019685 GCATTTTAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAG-TAC-
64 GCATTTAAACTATAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGATACT
2019748 TTC
129 TTC
*
2019751 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATTTTTTCTGTTGATAATACACCCATATG
1 TGTTGATAATGCA-CCATATGCATTTCAACTATAGTATTTTTTCTGTTGATAATGCACCCATATG
* *
2019816 CATTTCAACTATAGCATACTTTTCTGTTG--AATACATCCCATA-GCATTTCAACTATAGTATAC
65 CATTTAAACTATAGCATACTTTTCTGTTGATAATGCA-CCCATATGCATTTCAACTATAG-ATAC
*
2019878 TTTT
128 TTTC
* * * * *
2019882 TGTTGATAATGTACCATATACATTTCAACTATAGTA-TATTTCTG-TGATAATGTACCCATATAC
1 TGTTGATAATGCACCATATGCATTTCAACTATAGTATTTTTTCTGTTGATAATGCACCCATATGC
* * *
2019945 ATTTAAACTAT-GGAT-CCTTTCATG-CGATAATGCACCCATATGCATT
66 ATTTAAACTATAGCATACTTTTC-TGTTGATAATGCACCCATATGCATT
2019991 ATTATTCATT
Statistics
Matches: 209, Mismatches: 21, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
126 6 0.03
127 11 0.05
128 56 0.27
129 17 0.08
130 102 0.49
131 17 0.08
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (131 bp):
TGTTGATAATGCACCATATGCATTTCAACTATAGTATTTTTTCTGTTGATAATGCACCCATATGC
ATTTAAACTATAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGATACTTT
C
Found at i:2020417 original size:20 final size:21
Alignment explanation
Indices: 2020389--2020427 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2020379 AAGTGATCTA
*
2020389 CTACCCTA-GTACAGATACTT
1 CTACACTAGGTACAGATACTT
*
2020409 CTACACTAGGTACCGATAC
1 CTACACTAGGTACAGATAC
2020428 CCTTCCTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (21 bp):
CTACACTAGGTACAGATACTT
Found at i:2026507 original size:45 final size:45
Alignment explanation
Indices: 2026456--2026776 Score: 493
Period size: 45 Copynumber: 7.1 Consensus size: 45
2026446 ATGCACTTTT
* * * **
2026456 AACTATAGCATACTTTTCTATTGATAATGTACTCATATGTATTT-
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
* * *
2026500 ATACTATAGTATTCTTTTCTGTTAATAA-GTCACCCATATGCATTTC
1 A-ACTATAGTATACTTTTCTGTTGATAATGT-ACCCATATACATTTC
*
2026546 AACTATAGTATACTTTTCTGTTGATAATGCACCCATATACATTTC
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
* ** *
2026591 AACTATAGCATACTTTTCTGTTGATAATACACCCATATGCATTTC
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
2026636 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
2026681 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
2026726 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
2026771 AACTAT
1 AACTAT
2026777 GGAATCCTTT
Statistics
Matches: 256, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
44 3 0.01
45 251 0.98
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (45 bp):
AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
Found at i:2026797 original size:45 final size:45
Alignment explanation
Indices: 2026428--2026813 Score: 483
Period size: 45 Copynumber: 8.6 Consensus size: 45
2026418 CCTCCATTCA
* * * *
2026428 TGTTTATAATGCA-CCATTATGCACTTTTAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCA-TATACA-TTTCAACTATAGTATACTTTTC
* * * ** *
2026474 TATTGATAATGTACTCATATGTATTT-ATACTATAGTATTCTTTTC
1 TGTTGATAATGCACCCATATACATTTCA-ACTATAGTATACTTTTC
* *
2026519 TGTTAATAA-GTCACCCATATGCATTTCAACTATAGTATACTTTTC
1 TGTTGATAATG-CACCCATATACATTTCAACTATAGTATACTTTTC
*
2026564 TGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
* *
2026609 TGTTGATAATACACCCATATGCATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
*
2026654 TGTTGATAATGTACCCATATACATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
*
2026699 TGTTGATAATGTACCCATATACATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
* * * *
2026744 TGTTGATAATGTACCCATATACATTTCAACTATGGAAT-CCTTTC
1 TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
** *
2026788 ATGCCGATAATGCACCCATATGCATT
1 -TGTTGATAATGCACCCATATACATT
2026814 ATTCTTTTCA
Statistics
Matches: 305, Mismatches: 29, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
44 7 0.02
45 279 0.91
46 17 0.06
47 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTC
Found at i:2027473 original size:20 final size:21
Alignment explanation
Indices: 2027436--2027487 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2027426 CCTTACAATG
* *
2027436 GTATCGATACTGCCTCAA-CG
1 GTATCGATACTGACTCAATCA
* *
2027456 GTTTCGATACTGATTCAATCA
1 GTATCGATACTGACTCAATCA
2027477 GTATCGATACT
1 GTATCGATACT
2027488 ATCCAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (21 bp):
GTATCGATACTGACTCAATCA
Found at i:2030096 original size:408 final size:408
Alignment explanation
Indices: 2029311--2030126 Score: 1584
Period size: 408 Copynumber: 2.0 Consensus size: 408
2029301 CAATAGCGTT
2029311 TTGAGAAGTATAGAAGAACCTCATGTCGCGCAGAATGATCTTGACGATGAAGAAGAATATTTTGA
1 TTGAGAAGTATAGAAGAACCTCATGTCGCGCAGAATGATCTTGACGATGAAGAAGAATATTTTGA
2029376 TATATCTGATACGGTCGAGTACAAAAATGATGCCACCAGAAAAGGATGCCATTTTTAAACTAGAA
66 TATATCTGATACGGTCGAGTACAAAAATGATGCCACCAGAAAAGGATGCCATTTTTAAACTAGAA
2029441 ATTTTCCAGAATCGATAAATCATTATTAAGAAATAAGAAGGTTTCGCGGAGATGGTTAGGTTCGG
131 ATTTTCCAGAATCGATAAATCATTATTAAGAAATAAGAAGGTTTCGCGGAGATGGTTAGGTTCGG
2029506 TGGAATAAGAGGAATTTAAATAAGCAAGAAAGTCGAGCGTACAAATGCATCTATTACTGATGTGG
196 TGGAATAAGAGGAATTTAAATAAGCAAGAAAGTCGAGCGTACAAATGCATCTATTACTGATGTGG
2029571 TAGTGAACTCGTGTTATGCAAAATGCGAGTTGCCTATCACGTCACGTTAGGTACATGGCTGATTA
261 TAGTGAACTCGTGTTATGCAAAATGCGAGTTGCCTATCACGTCACGTTAGGTACATGGCTGATTA
2029636 TGCCGAAAAGAATTATAATGTACGTCACTCGGTTACGTCAATTGTGAAAAAAAACGATGTGGACA
326 TGCCGAAAAGAATTATAATGTACGTCACTCGGTTACGTCAATTGTGAAAAAAAACGATGTGGACA
2029701 AGTACATGGCTTAATGTG
391 AGTACATGGCTTAATGTG
2029719 TTGAGAAGTATAGAAGAACCTCATGTCGCGCAGAATGATCTTGACGATGAAGAAGAATATTTTGA
1 TTGAGAAGTATAGAAGAACCTCATGTCGCGCAGAATGATCTTGACGATGAAGAAGAATATTTTGA
2029784 TATATCTGATACGGTCGAGTACAAAAATGATGCCACCAGAAAAGGATGCCATTTTTAAACTAGAA
66 TATATCTGATACGGTCGAGTACAAAAATGATGCCACCAGAAAAGGATGCCATTTTTAAACTAGAA
2029849 ATTTTCCAGAATCGATAAATCATTTATTAAGAAATAAGAAGGTTTCGCGGAGATGGTTAGGTTCG
131 ATTTTCCAGAATCGATAAATCA-TTATTAAGAAATAAGAAGGTTTCGCGGAGATGGTTAGGTTCG
2029914 GTGGAATAAGAGGAATTTAAATAAGCAAGAAAGTCGAGCGTAC-AATGCATCTATTACTGATGTG
195 GTGGAATAAGAGGAATTTAAATAAGCAAGAAAGTCGAGCGTACAAATGCATCTATTACTGATGTG
2029978 GTAGTGAA-TCGTGTTATGC-AAATGCGAGTTGCCTATCACGTCACGTTAGGTACATGGCTGATT
260 GTAGTGAACTCGTGTTATGCAAAATGCGAGTTGCCTATCACGTCACGTTAGGTACATGGCTGATT
*
2030041 ATGCCGAAAAGAATTATAATTTACGTCACTCGGTTACGTCAATTGTGAAAAAAAAACGATGTGGA
325 ATGCCGAAAAGAATTATAATGTACGTCACTCGGTTACGTCAATTGTG-AAAAAAAACGATGTGGA
2030106 CAAGTACATGGCTTAATGTG
389 CAAGTACATGGCTTAATGTG
2030126 T
1 T
2030127 CCACAAGTAC
Statistics
Matches: 405, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
406 90 0.22
407 49 0.12
408 181 0.45
409 85 0.21
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (408 bp):
TTGAGAAGTATAGAAGAACCTCATGTCGCGCAGAATGATCTTGACGATGAAGAAGAATATTTTGA
TATATCTGATACGGTCGAGTACAAAAATGATGCCACCAGAAAAGGATGCCATTTTTAAACTAGAA
ATTTTCCAGAATCGATAAATCATTATTAAGAAATAAGAAGGTTTCGCGGAGATGGTTAGGTTCGG
TGGAATAAGAGGAATTTAAATAAGCAAGAAAGTCGAGCGTACAAATGCATCTATTACTGATGTGG
TAGTGAACTCGTGTTATGCAAAATGCGAGTTGCCTATCACGTCACGTTAGGTACATGGCTGATTA
TGCCGAAAAGAATTATAATGTACGTCACTCGGTTACGTCAATTGTGAAAAAAAACGATGTGGACA
AGTACATGGCTTAATGTG
Found at i:2032026 original size:27 final size:27
Alignment explanation
Indices: 2031996--2032086 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
2031986 GTGTTGATAT
2031996 TACTCTCAATTGAAAGATAAGTTACAA
1 TACTCTCAATTGAAAGATAAGTTACAA
* * * * *
2032023 TACTACCTCTAATCTTATAAGTTACG-AAGATA
1 TACT--CTC-AAT-TGA-AAGATAAGTTACA-A
2032055 TTACTCTCAATTGAAAGATAAGTTACAA
1 -TACTCTCAATTGAAAGATAAGTTACAA
2032083 TACT
1 TACT
2032087 ACCTCTAATC
Statistics
Matches: 46, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
27 8 0.17
28 7 0.15
29 7 0.15
30 6 0.13
31 7 0.15
32 7 0.15
33 4 0.09
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (27 bp):
TACTCTCAATTGAAAGATAAGTTACAA
Found at i:2032064 original size:60 final size:60
Alignment explanation
Indices: 2031991--2032110 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
2031981 CGTATGTGTT
2031991 GATATTACTCTCAATTGAAAGATAAGTTACAATACTACCTCTAATCTTATAAGTTACGAA
1 GATATTACTCTCAATTGAAAGATAAGTTACAATACTACCTCTAATCTTATAAGTTACGAA
2032051 GATATTACTCTCAATTGAAAGATAAGTTACAATACTACCTCTAATCTTATAAGTTACGAA
1 GATATTACTCTCAATTGAAAGATAAGTTACAATACTACCTCTAATCTTATAAGTTACGAA
2032111 TTTTTTCATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (60 bp):
GATATTACTCTCAATTGAAAGATAAGTTACAATACTACCTCTAATCTTATAAGTTACGAA
Found at i:2032076 original size:33 final size:31
Alignment explanation
Indices: 2031991--2032081 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 31
2031981 CGTATGTGTT
2031991 GATATTACTCTCAATTGAAAGATAAGTTACA
1 GATATTACTCTCAATTGAAAGATAAGTTACA
* *
2032022 -ATACTAC-CTCTAATCT----TATAAGTTACGAA
1 GATATTACTCTC-AAT-TGAAAGATAAGTTAC--A
2032051 GATATTACTCTCAATTGAAAGATAAGTTACA
1 GATATTACTCTCAATTGAAAGATAAGTTACA
2032082 ATACTACCTC
Statistics
Matches: 46, Mismatches: 4, Indels: 20
0.66 0.06 0.29
Matches are distributed among these distances:
27 9 0.20
29 5 0.11
30 18 0.39
31 5 0.11
33 9 0.20
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (31 bp):
GATATTACTCTCAATTGAAAGATAAGTTACA
Found at i:2032102 original size:27 final size:27
Alignment explanation
Indices: 2032012--2032107 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
2032002 CAATTGAAAG
2032012 ATAAGTTACAATACTACCTCTAATCTT
1 ATAAGTTACAATACTACCTCTAATCTT
* *
2032039 ATAAGTTACGAAGATATTA-CTCTCAAT-TGAAAG
1 ATAAGTTAC--A-ATACTACCTCT-AATCT----T
2032072 ATAAGTTACAATACTACCTCTAATCTT
1 ATAAGTTACAATACTACCTCTAATCTT
2032099 ATAAGTTAC
1 ATAAGTTAC
2032108 GAATTTTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
27 18 0.33
29 6 0.11
30 16 0.29
31 6 0.11
33 9 0.16
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (27 bp):
ATAAGTTACAATACTACCTCTAATCTT
Found at i:2032845 original size:11 final size:11
Alignment explanation
Indices: 2032831--2032856 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2032821 TTTTTAATCA
2032831 TTTAATTTTCT
1 TTTAATTTTCT
2032842 TTTAATTTTCT
1 TTTAATTTTCT
2032853 TTTA
1 TTTA
2032857 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTAATTTTCT
Found at i:2033050 original size:32 final size:33
Alignment explanation
Indices: 2032999--2033065 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 33
2032989 CATCCATATT
2032999 ATTTTTCCCTTTTTTAATCTTCTTTCTCCAAAG
1 ATTTTTCCCTTTTTTAATCTTCTTTCTCCAAAG
2033032 ATTTTTCCC-TTTTTAATCTTCTTTCTCCAAAG
1 ATTTTTCCCTTTTTTAATCTTCTTTCTCCAAAG
2033064 AT
1 AT
2033066 GATAGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.74
33 9 0.26
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (33 bp):
ATTTTTCCCTTTTTTAATCTTCTTTCTCCAAAG
Found at i:2036193 original size:31 final size:31
Alignment explanation
Indices: 2036155--2036223 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
2036145 CATAAGGTTC
*
2036155 GGTCACTTTCATTTC-ATTTTAATTAAGATCT
1 GGTCACTTTCATTTCGA-TTTAATTAAAATCT
*
2036186 GGTCACTTTCATTTCGATTTAATTAAAATGT
1 GGTCACTTTCATTTCGATTTAATTAAAATCT
2036217 GGTCACT
1 GGTCACT
2036224 GAAGTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (31 bp):
GGTCACTTTCATTTCGATTTAATTAAAATCT
Found at i:2036424 original size:30 final size:31
Alignment explanation
Indices: 2036388--2036463 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
2036378 AAAAAAAACA
*
2036388 TAAGTTTTGGTCACTTACGTTATT-TTTTAT
1 TAAGTTTTGGTCACTTACGTTATTGTCTTAT
*
2036418 TAAGTTTTGGTCACTAACGTTATTGTCTTAT
1 TAAGTTTTGGTCACTTACGTTATTGTCTTAT
2036449 TAAG-TTTGGTCACTT
1 TAAGTTTTGGTCACTT
2036464 GAACGTTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 33 0.79
31 9 0.21
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATTGTCTTAT
Found at i:2042413 original size:24 final size:24
Alignment explanation
Indices: 2042337--2042445 Score: 78
Period size: 24 Copynumber: 4.4 Consensus size: 24
2042327 TCGGGTTTTG
* *
2042337 TTGTAACC-AGGCCTGTGATTTTCT
1 TTGTAACCGA-GCTTGTGATTTACT
* ** *
2042361 TTGTAACCGGGCATGTGTGCCTTATT
1 TTGTAACCGAGC-T-TGTGATTTACT
*
2042387 TTGTAACCGAGCTTGTGATTTGCT
1 TTGTAACCGAGCTTGTGATTTACT
*
2042411 TTGTAACCGGGCTTGTG-TGCCTTACT
1 TTGTAACCGAGCTTGTGAT---TTACT
2042437 TTGTAACCG
1 TTGTAACCG
2042446 GGCCTTCGGG
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 1 0.02
24 33 0.50
25 1 0.02
26 31 0.47
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (24 bp):
TTGTAACCGAGCTTGTGATTTACT
Found at i:2042413 original size:50 final size:51
Alignment explanation
Indices: 2042337--2042450 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 51
2042327 TCGGGTTTTG
* *
2042337 TTGTAACC-AGGCCTGTGATTTTCTTTGTAACCGGGCATGTGTGCCTTATT
1 TTGTAACCGAGGCCTGTGATTTGCTTTGTAACCGGGCATGTGTGCCTTACT
* *
2042387 TTGTAACCGA-GCTTGTGATTTGCTTTGTAACCGGGCTTGTGTGCCTTACT
1 TTGTAACCGAGGCCTGTGATTTGCTTTGTAACCGGGCATGTGTGCCTTACT
2042437 TTGTAACCG-GGCCT
1 TTGTAACCGAGGCCT
2042451 TCGGGCTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
50 56 0.98
51 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (51 bp):
TTGTAACCGAGGCCTGTGATTTGCTTTGTAACCGGGCATGTGTGCCTTACT
Found at i:2042461 original size:26 final size:26
Alignment explanation
Indices: 2042359--2042448 Score: 114
Period size: 26 Copynumber: 3.5 Consensus size: 26
2042349 CTGTGATTTT
*
2042359 CTTTGTAACCGGGCATGTGTGCCTTA
1 CTTTGTAACCGGGCTTGTGTGCCTTA
* * *
2042385 TTTTGTAACCGAGCTTGTGAT---TTG
1 CTTTGTAACCGGGCTTGTG-TGCCTTA
2042409 CTTTGTAACCGGGCTTGTGTGCCTTA
1 CTTTGTAACCGGGCTTGTGTGCCTTA
2042435 CTTTGTAACCGGGC
1 CTTTGTAACCGGGC
2042449 CTTCGGGCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.02
24 19 0.36
26 32 0.60
27 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (26 bp):
CTTTGTAACCGGGCTTGTGTGCCTTA
Found at i:2050612 original size:15 final size:14
Alignment explanation
Indices: 2050591--2050629 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2050581 TTGTCGTGAC
*
2050591 TAAAATATAAATAT
1 TAAAATATAAAAAT
2050605 TAAAAATATAAAAAAT
1 T-AAAATAT-AAAAAT
2050621 TAAAATATA
1 TAAAATATA
2050630 CGAAAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 14 0.64
16 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAATATAAAAAT
Found at i:2050972 original size:20 final size:20
Alignment explanation
Indices: 2050947--2050986 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2050937 TACACCAAAC
2050947 TTACCAAAAAATGTAGCTCT
1 TTACCAAAAAATGTAGCTCT
2050967 TTACCAAAAAATGTAGCTCT
1 TTACCAAAAAATGTAGCTCT
2050987 CTTTCTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
TTACCAAAAAATGTAGCTCT
Found at i:2051671 original size:49 final size:51
Alignment explanation
Indices: 2051556--2051672 Score: 125
Period size: 49 Copynumber: 2.3 Consensus size: 51
2051546 AGCTCGTCAT
* *
2051556 GTCGACGTGATGAGTTCTAATAAAATATATATTTTTATTAAAATTTATCACA
1 GTCGACGTGATAAGTT-TAATAAAATATATATTTTTATTAAAATTCATCACA
* * * * *
2051608 TTGGA-ATAAAAAGTTTAAATAAAA-ATATA-TTTTATTAAAATTCATCAC-
1 GTCGACGTGATAAGTTT-AATAAAATATATATTTTTATTAAAATTCATCACA
2051656 GTCGACGTGATAAGTTT
1 GTCGACGTGATAAGTTT
2051673 CAAGTCACTA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
48 3 0.06
49 26 0.51
50 6 0.12
51 13 0.25
52 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (51 bp):
GTCGACGTGATAAGTTTAATAAAATATATATTTTTATTAAAATTCATCACA
Found at i:2053726 original size:76 final size:72
Alignment explanation
Indices: 2053619--2053808 Score: 244
Period size: 76 Copynumber: 2.6 Consensus size: 72
2053609 ATTTTAAACA
* *
2053619 TTATATTTTATATATGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTACTTTAATTAAGTTTTA
1 TTATATTTTAT-TATGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA-TTTAATTAAGATTTA
*
2053684 GGATATTATTT
64 GAATATTA--T
* *
2053695 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTAATTAGGATTTAG
1 TTATATTTTAT-TATGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTAATTAAGATTTAG
2053760 AATATTAT
65 AATATTAT
* *
2053768 TTAGA--ATATTAT-TTTTAGGTATTTTAGTTTAAATA-GTTTTA
1 TTATATTTTATTATGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
2053809 AGTGTTTTAA
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
68 6 0.06
69 23 0.22
70 2 0.02
71 3 0.03
73 5 0.05
75 20 0.19
76 46 0.44
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (72 bp):
TTATATTTTATTATGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTAATTAAGATTTAGA
ATATTAT
Found at i:2053771 original size:12 final size:12
Alignment explanation
Indices: 2053754--2053781 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2053744 TTTAATTAGG
2053754 ATTTAGAATATT
1 ATTTAGAATATT
2053766 ATTTAGAATATT
1 ATTTAGAATATT
2053778 ATTT
1 ATTT
2053782 TTAGGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTAGAATATT
Found at i:2054496 original size:7 final size:7
Alignment explanation
Indices: 2054474--2054537 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
2054464 TCTATACTAC
2054474 TATTATT
1 TATTATT
2054481 TATTAATT
1 TATT-ATT
2054489 TATTATT
1 TATTATT
*
2054496 T-TTCTT
1 TATTATT
* *
2054502 TTTTCTTT
1 TATT-ATT
2054510 TATTATT
1 TATTATT
*
2054517 T-TTCTT
1 TATTATT
2054523 TATTTATT
1 TA-TTATT
2054531 TATTATT
1 TATTATT
2054538 ATCTATTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
6 10 0.22
7 18 0.39
8 18 0.39
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (7 bp):
TATTATT
Found at i:2054511 original size:21 final size:20
Alignment explanation
Indices: 2054487--2054555 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
2054477 TATTTATTAA
2054487 TTTATTATTTTTCTTTTTTCT
1 TTTATTATTTTTCTTTTTT-T
*
2054508 TTTATTATTTTTCTTTATTTA
1 TTTATTATTTTTCTTT-TTTT
* *
2054529 TTTATTA-TTATCTATTTTAT
1 TTTATTATTTTTCT-TTTTTT
2054549 TTTATTA
1 TTTATTA
2054556 AATCTTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.33
21 25 0.60
22 3 0.07
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTATTTTTCTTTTTTT
Found at i:2064417 original size:21 final size:23
Alignment explanation
Indices: 2064393--2064437 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
2064383 CAAACTGTGG
2064393 CAATAAGGG-AAATTGTT-TGAA
1 CAATAAGGGAAAATTGTTATGAA
2064414 CAATAAGGGAAAATTGTTATGAA
1 CAATAAGGGAAAATTGTTATGAA
2064437 C
1 C
2064438 TCTAAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (23 bp):
CAATAAGGGAAAATTGTTATGAA
Found at i:2064981 original size:3 final size:3
Alignment explanation
Indices: 2064967--2064998 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2064957 TTTTAGTTTG
2064967 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2064999 TATTTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:2065016 original size:19 final size:18
Alignment explanation
Indices: 2064990--2065025 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2064980 TATTATTATT
*
2064990 ATTATTATTTATTTAGAA
1 ATTATTATTTACTTAGAA
2065008 ATTAGTTATTTACTTAGA
1 ATTA-TTATTTACTTAGA
2065026 TATCTCGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTATTATTTACTTAGAA
Found at i:2065879 original size:17 final size:17
Alignment explanation
Indices: 2065844--2065879 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2065834 TTTTATTTAG
*
2065844 TATTTATTTATTTTAAT
1 TATTTATTTACTTTAAT
*
2065861 TATTTATTTACTTTCAT
1 TATTTATTTACTTTAAT
2065878 TA
1 TA
2065880 ATTTTAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTATTTACTTTAAT
Found at i:2071542 original size:12 final size:12
Alignment explanation
Indices: 2071514--2071563 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
2071504 GGCAATCAAT
*
2071514 TTTATTATTTTTA
1 TTTATT-TTTTTG
2071527 TTTATTTTTTTG
1 TTTATTTTTTTG
2071539 TTTATTTATTCTTG
1 TTTATTT-TT-TTG
2071553 TTTATATTTTT
1 TTTAT-TTTTT
2071564 AGGTACACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.36
13 9 0.27
14 10 0.30
15 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTTG
Found at i:2071556 original size:26 final size:25
Alignment explanation
Indices: 2071514--2071563 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2071504 GGCAATCAAT
* *
2071514 TTTATTATTTTTATTTATTTTTTTG
1 TTTATTATTCTTATTTATATTTTTG
*
2071539 TTTATTTATTCTTGTTTATATTTTT
1 TTTA-TTATTCTTATTTATATTTTT
2071564 AGGTACACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTATTATTCTTATTTATATTTTTG
Found at i:2077982 original size:27 final size:28
Alignment explanation
Indices: 2077951--2078004 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2077941 TTTAATATTG
2077951 AATTTTTTAA-AAATATAAAATAATCAT
1 AATTTTTTAATAAATATAAAATAATCAT
*
2077978 AATTTTTTAATAATTATAAAATAATCA
1 AATTTTTTAATAAATATAAAATAATCA
2078005 CTATGACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTTTTAATAAATATAAAATAATCAT
Found at i:2078729 original size:42 final size:42
Alignment explanation
Indices: 2078595--2078748 Score: 138
Period size: 41 Copynumber: 3.7 Consensus size: 42
2078585 AAAATGATAC
* *
2078595 TTTAGCGGCG-TTTTTCAACAAACGCCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTAA
* * * * * ** *
2078636 TTTAGCAGCGTTTATTGCAA-AAATGTCGGAATAGAGTTCT-T
1 TTTAGCGGCGTTT-TTTCAACAAACGCCGCAATAGAGTAGTAA
* * *
2078677 TTTAGTGGCGTTTTTTCAACAAACGCCACAATATAGTAGTAA
1 TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTAA
2078719 TTTAGCGGCG-TTTTT-ATACAAACGCCGCAA
1 TTTAGCGGCGTTTTTTCA-ACAAACGCCGCAA
2078749 CAGGATTGTT
Statistics
Matches: 87, Mismatches: 21, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
40 6 0.07
41 50 0.57
42 26 0.30
43 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTAA
Found at i:2079448 original size:22 final size:23
Alignment explanation
Indices: 2079406--2079459 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
2079396 GTGTTTTTCT
*
2079406 GCTTTCGAATAGAAAAAATAATA
1 GCTTTTGAATAGAAAAAATAATA
*
2079429 GCTTTTGAATAG-GAAAATAATA
1 GCTTTTGAATAGAAAAAATAATA
2079451 GCTTTTGAA
1 GCTTTTGAA
2079460 AACCCGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.31
Consensus pattern (23 bp):
GCTTTTGAATAGAAAAAATAATA
Found at i:2080182 original size:17 final size:16
Alignment explanation
Indices: 2080160--2080193 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2080150 TAAAGACAGT
2080160 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2080177 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2080193 A
1 A
2080194 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2090423 original size:17 final size:16
Alignment explanation
Indices: 2090401--2090434 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2090391 TAAAGACAGT
2090401 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2090418 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2090434 A
1 A
2090435 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2094301 original size:21 final size:20
Alignment explanation
Indices: 2094257--2094299 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2094247 ATCCGGAAAT
2094257 AAATCCGGTCTGGGGTTTAA
1 AAATCCGGTCTGGGGTTTAA
2094277 AAATCCGGTCTGGGGTTTAA
1 AAATCCGGTCTGGGGTTTAA
2094297 AAA
1 AAA
2094300 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (20 bp):
AAATCCGGTCTGGGGTTTAA
Found at i:2094815 original size:55 final size:55
Alignment explanation
Indices: 2094755--2094868 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
2094745 CTTGTGCATA
2094755 TTTATTTATTGTCCCTGCGTTTTGACCCATCAAATGTATATTTACATGTCATTTT
1 TTTATTTATTGTCCCTGCGTTTTGACCCATCAAATGTATATTTACATGTCATTTT
2094810 TTTATTTATTGTCCCTGCGTTTTGACCCATCAAATGTATATTTACATGTCATTTT
1 TTTATTTATTGTCCCTGCGTTTTGACCCATCAAATGTATATTTACATGTCATTTT
2094865 TTTA
1 TTTA
2094869 AGTTAGATTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.50
Consensus pattern (55 bp):
TTTATTTATTGTCCCTGCGTTTTGACCCATCAAATGTATATTTACATGTCATTTT
Found at i:2098447 original size:85 final size:86
Alignment explanation
Indices: 2098297--2098461 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 86
2098287 AACACACAAA
** *
2098297 TGCGCATCATTGAAGCCACAATCATAAATCTCATATGACACACAATTGTGTGTCATAAATCTATG
1 TGCGCATCATTGAAGCCACAATCATAAATCGAATATGACACAAAATTGTGTGTCATAAATCTATG
*
2098362 ACGCGCATTTATGACACGCAT
66 ACACGCATTTATGACACGCAT
* * ** * * *
2098383 TGCGCGTCATTGAAGCCCCCGTCATAAAT-GAATATGACA-AAAATTTGTGTTTCATAAGTTTAT
1 TGCGCATCATTGAAGCCACAATCATAAATCGAATATGACACAAAA-TTGTGTGTCATAAATCTAT
2098446 GACACGCATTTATGAC
65 GACACGCATTTATGAC
2098462 TTACATTTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
84 3 0.04
85 39 0.58
86 25 0.37
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (86 bp):
TGCGCATCATTGAAGCCACAATCATAAATCGAATATGACACAAAATTGTGTGTCATAAATCTATG
ACACGCATTTATGACACGCAT
Found at i:2098468 original size:13 final size:13
Alignment explanation
Indices: 2098452--2098481 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2098442 TTATGACACG
*
2098452 CATTTATGACTTA
1 CATTTACGACTTA
2098465 CATTTACGACTTA
1 CATTTACGACTTA
2098478 CATT
1 CATT
2098482 GCGTGTTATT
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:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:2104749 original size:15 final size:15
Alignment explanation
Indices: 2104723--2104778 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
2104713 GATGCTTTCT
2104723 TTTTCCTTCTTTGACA
1 TTTT-CTTCTTTGACA
* *
2104739 TTTTTTTCTTTGTCA
1 TTTTCTTCTTTGACA
*
2104754 TTTTCTTCTTAGACA
1 TTTTCTTCTTTGACA
*
2104769 TTGTCTTCTT
1 TTTTCTTCTT
2104779 ACCCCATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.11, C:0.20, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTCTTCTTTGACA
Found at i:2106241 original size:24 final size:25
Alignment explanation
Indices: 2106209--2106278 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
2106199 GAAATCCACG
2106209 ATTTCATATTATAAAAACTCACA-C
1 ATTTCATATTATAAAAACTCACACC
* *
2106233 ATTTCATATTA-ACAACACACACACC
1 ATTTCATATTATA-AAAACTCACACC
*
2106258 CTTT-ATATTATAAAAACTCAC
1 ATTTCATATTATAAAAACTCAC
2106279 TCACACATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 32 0.84
25 5 0.13
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTTCATATTATAAAAACTCACACC
Done.