Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 58 of 144
Found at i:17837460 original size:28 final size:27
Alignment explanation
Indices: 17837416--17837474 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
17837406 ATATATTTTT
*
17837416 TCTTTTTTTTCTTCTTTCTT-TTCTTTC
1 TCTTTTTCTTCTTCTTT-TTCTTCTTTC
17837443 TCTTTTTCTTCTCTCTTTTTCTTCTTTC
1 TCTTTTTCTTCT-TCTTTTTCTTCTTTC
17837471 TCTT
1 TCTT
17837475 CGGGCCGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TCTTTTTCTTCTTCTTTTTCTTCTTTC
Found at i:17837467 original size:24 final size:23
Alignment explanation
Indices: 17837412--17837469 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
17837402 TGTGATATAT
*
17837412 TTTTTCTT-TTTTTTCTTCTTTC
1 TTTTTCTTCTTTTTTCTTCTCTC
17837434 -TTTTCTTTCTCTTTTTCTTCTCTC
1 TTTTTC-TTCT-TTTTTCTTCTCTC
17837458 TTTTTCTTCTTT
1 TTTTTCTTCTTT
17837470 CTCTTCGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
23 3 0.10
24 16 0.52
25 5 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTCTTTTTTCTTCTCTC
Found at i:17837474 original size:9 final size:9
Alignment explanation
Indices: 17837425--17837475 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
17837415 TTCTTTTTTT
17837425 TCTTCTTTC
1 TCTTCTTTC
*
17837434 TTTTCTTTC
1 TCTTCTTTC
17837443 TCTT-TTTC
1 TCTTCTTTC
*
17837451 TTCTCTCTTTT
1 -TCT-TCTTTC
17837462 TCTTCTTTC
1 TCTTCTTTC
17837471 TCTTC
1 TCTTC
17837476 GGGCCGAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.11
9 24 0.69
10 4 0.11
11 3 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TCTTCTTTC
Found at i:17838117 original size:30 final size:30
Alignment explanation
Indices: 17837988--17838123 Score: 104
Period size: 30 Copynumber: 4.6 Consensus size: 30
17837978 AGAAAACATG
*
17837988 GGGCCAAAATGTAATTTCTAG-AAAGTTTAA
1 GGGCCAAAATGTAAATT-TAGAAAAGTTTAA
*
17838018 -GGCC-AAATGT-AATTTA-AAAAATATTAA
1 GGGCCAAAATGTAAATTTAGAAAAGT-TTAA
* * * * * * *
17838045 GGGTCAAGATGCAAATTCAAAAAAAGGTTAG
1 GGGCCAAAATGTAAATT-TAGAAAAGTTTAA
* *
17838076 GGGTCACAATGTAAATTTAGAAAAGTTTAA
1 GGGCCAAAATGTAAATTTAGAAAAGTTTAA
17838106 GGGCCAAAATGT-AATTTA
1 GGGCCAAAATGTAAATTTA
17838124 TATTTTTTGT
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
26 6 0.07
27 7 0.09
28 9 0.11
29 14 0.17
30 23 0.28
31 18 0.22
32 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (30 bp):
GGGCCAAAATGTAAATTTAGAAAAGTTTAA
Found at i:17838334 original size:5 final size:5
Alignment explanation
Indices: 17838324--17838385 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
17838314 AATCATAATT
** * *
17838324 TAAAA TAAAA TAAAAA TAAAA -ATTCA TATATA TAAAA TAAAA TAAGA
1 TAAAA TAAAA T-AAAA TAAAA TA-AAA TA-AAA TAAAA TAAAA TAAAA
17838371 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
17838386 CATGAACTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 1 0.02
5 36 0.77
6 10 0.21
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:17838880 original size:79 final size:75
Alignment explanation
Indices: 17838516--17839139 Score: 618
Period size: 79 Copynumber: 8.1 Consensus size: 75
17838506 ATTATTGTTT
* * ** *
17838516 TTTTTGAAAAATAGAAATTGAAAATGCCTCAGC--ATGATTCAAGGCTCAACTCACCTCTCGCAT
1 TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAT
*
17838579 TATGAGTTAA
66 TATGAGTTGA
* * * * *
17838589 TTTTTGAAAAACATAAATTGAGAAAATACCTTAGCGTGT--CCCGATGCTCAACTCACCTCTCGT
1 TTTTTGAAAAATAGAAATT--GAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
*
17838652 AATATGAGTTGA
64 ATTATGAGTTGA
* * * * *
17838664 TTTTTTTTTG-AAAATAACGGAAATTGAAAATACCTCGGCGTGCGGCCCGAAGCTCAACTCACAT
1 ----TTTTTGAAAAAT-A--GAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCT
17838728 CTCGCATTATGAGTTGA
59 CTCGCATTATGAGTTGA
** * * * * *
17838745 TTTTAAAAAAAATAGAAATTGAAAATACCTCGGTGTGTGGCCTGGGGCTCAACTCACCTCTCGCA
1 TTTT-TGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
*
17838810 TTATGATTTGA
65 TTATGAGTTGA
* *
17838821 TTTTTGAAAAATAGAAATTTAAAAGAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTC
1 TTTTTGAAAAATAGAAA-TT--GA-AAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTC
17838886 GCATTATGAGTTGA
62 GCATTATGAGTTGA
*
17838900 TTTTTTTTTTGAAAAAAAGAAATTGAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT
1 -----TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCT
* *
17838963 CGCAATATGATTTGA
61 CGCATTATGAGTTGA
* *
17838978 TTTTTGAAAAATAGAAATTTAAAAGAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTC
1 TTTTTGAAAAATAGAAA-TT--GA-AAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTC
*
17839043 GCAATATGAGTTGA
62 GCATTATGAGTTGA
*
17839057 TTTTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT
1 -----TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCT
*
17839120 CGCAATATGAGTTGA
61 CGCATTATGAGTTGA
17839135 TTTTT
1 TTTTT
17839140 AAGAGACAAA
Statistics
Matches: 466, Mismatches: 50, Indels: 70
0.80 0.09 0.12
Matches are distributed among these distances:
73 38 0.08
74 2 0.00
75 52 0.11
76 62 0.13
77 17 0.04
78 82 0.18
79 114 0.24
80 24 0.05
81 39 0.08
83 4 0.01
84 32 0.07
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (75 bp):
TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAT
TATGAGTTGA
Found at i:17839153 original size:157 final size:153
Alignment explanation
Indices: 17838557--17839158 Score: 687
Period size: 157 Copynumber: 3.8 Consensus size: 153
17838547 GCATGATTCA
* * *
17838557 AGGCTCAACTCACCTCTCGCATTATGAGTT-AATTTTTGAAAAACATAAATTGAGAAAATACCTT
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATT--GAAAATACCTC
* * *
17838621 AGCGTGTCCCGATGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTG-AAAATAACGGA
64 AGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAATAA---A
* * * *
17838685 AATTG---A-AAATACCTCGGCGTGCGGCCCG
122 AATTGAAAAGAAATACCTCAGCGTGTGACCTG
* * *** *
17838713 AAGCTCAACTCACATCTCGCATTATGAGTTGATTTTAAAAAAAATAGAAATTGAAAATACCTCGG
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTC--
* * * * * * * * *
17838778 TGTGTGGCCTGGGGCTCAACTCACCTCTCGCATTATGATTTGATTTTTGAAAAATAGAAATTTAA
64 AGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAAAAATTGAA
17838843 AAGAAATACCTCAGCGTGTGACCTG
129 AAGAAATACCTCAGCGTGTGACCTG
*
17838868 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTTGAAAAAAAGAAATTGAAAATACC
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGA----TTTTTTGAAAAACAGAAATTGAAAATACC
* * *
17838933 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGATTTGATTTTTGAAAAATAGAAATTT
62 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAAAAATTG
17838998 AAAAGAAATACCTCAGCGTGTGACCTG
127 AAAAGAAATACCTCAGCGTGTGACCTG
*
17839025 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTGAAAATACC
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGA----TTTTTTGAAAAACAGAAATTGAAAATACC
* *
17839090 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAGAGACAAAAATT
62 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA-AAATAAAAATT
17839154 GAAAA
126 GAAAA
17839159 ATATAATTCT
Statistics
Matches: 390, Mismatches: 43, Indels: 25
0.85 0.09 0.05
Matches are distributed among these distances:
151 5 0.01
153 6 0.02
154 7 0.02
155 58 0.15
156 30 0.08
157 257 0.66
159 27 0.07
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (153 bp):
AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAAAAATTGAAAA
GAAATACCTCAGCGTGTGACCTG
Found at i:17840041 original size:16 final size:16
Alignment explanation
Indices: 17840022--17840076 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
17840012 GATTTTTCTT
*
17840022 TTTCTTTTTCTTTTTG
1 TTTCTTTTTATTTTTG
17840038 TTTCTTTTTATTTTT-
1 TTTCTTTTTATTTTTG
* *
17840053 TTTGTTTTTGTTTTTTG
1 TTTCTTTTT-ATTTTTG
17840070 TTT-TTTT
1 TTTCTTTT
17840077 AGGCATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.24
16 23 0.68
17 3 0.09
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (16 bp):
TTTCTTTTTATTTTTG
Found at i:17840073 original size:6 final size:6
Alignment explanation
Indices: 17840014--17840074 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
17840004 TTCATCTTGA
* * * *
17840014 TTTTTC TTTTTC TTTTTC TTTTTG TTTCTT- TTTATTT TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT-TTG TTT-TTG TTTTTG TTTTTG
17840063 TTTTTTG TTTTT
1 -TTTTTG TTTTT
17840075 TTAGGCATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
6 38 0.78
7 11 0.22
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:17845323 original size:13 final size:13
Alignment explanation
Indices: 17845282--17845335 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
17845272 AATTTTAAAC
17845282 CACTTTTCAAAAG
1 CACTTTTCAAAAG
* * **
17845295 CATTTTTCCACTG
1 CACTTTTCAAAAG
17845308 CACTTTTCAAAAG
1 CACTTTTCAAAAG
17845321 CACTTTTCAAAAG
1 CACTTTTCAAAAG
17845334 CA
1 CA
17845336 ATGAAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (13 bp):
CACTTTTCAAAAG
Found at i:17849555 original size:3 final size:3
Alignment explanation
Indices: 17849547--17849607 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
17849537 ATTTTCTACC
17849547 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
17849595 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
17849608 CTTTCAATTC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17849728 original size:12 final size:12
Alignment explanation
Indices: 17849711--17849744 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
17849701 ATATTTTATA
17849711 ATCTATATACAT
1 ATCTATATACAT
17849723 ATCTATAT--AT
1 ATCTATATACAT
17849733 ATCTATATACAT
1 ATCTATATACAT
17849745 TTTTTTAATT
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:17850503 original size:108 final size:106
Alignment explanation
Indices: 17850370--17850569 Score: 292
Period size: 108 Copynumber: 1.9 Consensus size: 106
17850360 ATAATAAAGG
* * * *
17850370 CAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAGTGTGTTGGGTTTCGATTTTTCTCGT
1 CAATATTTTACGTTTGGAAACTCGAGAAAACGTCCCCTAATGTGCTGGGTTTCGA--TTTCTCGT
* *
17850435 TCGACTAAATAGCCAAATATCCTTTTAAAATTTCAAAGTAAGA
64 TCGACCAAATAGCCAAATATCCTCTTAAAATTTCAAAGTAAGA
* * * *
17850478 CAATATTTTGCGTTTGGAAACTCGAGGAAATGTCCCCTAATGTGCTGGGTTTCGATTTCTCGTTT
1 CAATATTTTACGTTTGGAAACTCGAGAAAACGTCCCCTAATGTGCTGGGTTTCGATTTCTCGTTC
17850543 GACCAAATAGCCAAATATCCTCTTAAA
66 GACCAAATAGCCAAATATCCTCTTAAA
17850570 TCTCAATCCA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 34 0.41
108 48 0.59
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (106 bp):
CAATATTTTACGTTTGGAAACTCGAGAAAACGTCCCCTAATGTGCTGGGTTTCGATTTCTCGTTC
GACCAAATAGCCAAATATCCTCTTAAAATTTCAAAGTAAGA
Found at i:17858714 original size:20 final size:21
Alignment explanation
Indices: 17858675--17858716 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17858665 GTTAACTAAG
*
17858675 ATAAATAAAATAGAATAATAA
1 ATAAATAAAATAGAACAATAA
*
17858696 ATAAA-AAATTAGAACAATAA
1 ATAAATAAAATAGAACAATAA
17858716 A
1 A
17858717 GAAGCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (21 bp):
ATAAATAAAATAGAACAATAA
Found at i:17866270 original size:104 final size:105
Alignment explanation
Indices: 17866109--17866307 Score: 265
Period size: 104 Copynumber: 1.9 Consensus size: 105
17866099 ATCTAAAGCT
* *
17866109 TTGAACATCGATCAACATTCAAATGATTGTAACCTATGTTATACAAACTCTTAGTTTTCCCTAAA
1 TTGAACATCGATCAACATTCAAATGATTGTAACCTATATTACACAAACTCTTAGTTTTCCCTAAA
*
17866174 ATATTTATCACCAGGACCCTG-ATTTTCGTTTTTTGAATC
66 ACATTTATCACCAGGACCCTGAATTTTCGTTTTTTGAATC
* ** * ** *
17866213 TTGACCATCGATCAATGTTCAAATGTTTGTAACCTATATTACACACTCTCTTTGTTTTCCCTAAA
1 TTGAACATCGATCAACATTCAAATGATTGTAACCTATATTACACAAACTCTTAGTTTTCCCTAAA
* * * *
17866278 ACATTTGTCTCTAGGATCCTGAATTTTCGT
66 ACATTTATCACCAGGACCCTGAATTTTCGT
17866308 ATCTAGGGCA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
104 72 0.90
105 8 0.10
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (105 bp):
TTGAACATCGATCAACATTCAAATGATTGTAACCTATATTACACAAACTCTTAGTTTTCCCTAAA
ACATTTATCACCAGGACCCTGAATTTTCGTTTTTTGAATC
Found at i:17867020 original size:9 final size:9
Alignment explanation
Indices: 17867002--17867056 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
17866992 GGAAACAAAC
*
17867002 AGAAAAAAA
1 AGAAAGAAA
*
17867011 AGAAGGAAA
1 AGAAAGAAA
17867020 A-AAATGAAA
1 AGAAA-GAAA
*
17867029 AGAAAAAAA
1 AGAAAGAAA
*
17867038 AGAACG-AA
1 AGAAAGAAA
17867046 AGAAAGAAA
1 AGAAAGAAA
17867055 AG
1 AG
17867057 GTAATTTACC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
8 9 0.25
9 24 0.67
10 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (9 bp):
AGAAAGAAA
Found at i:17867033 original size:14 final size:13
Alignment explanation
Indices: 17867002--17867046 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
17866992 GGAAACAAAC
17867002 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
* *
17867015 GGAAAAAAATGAAA
1 AGAAAAAAAAG-AA
17867029 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
*
17867042 CGAAA
1 AGAAA
17867047 GAAAGAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:17867040 original size:27 final size:26
Alignment explanation
Indices: 17867002--17867056 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
17866992 GGAAACAAAC
*
17867002 AGAAAAAAAAGAAGGAAAAAAATGAAA
1 AGAAAAAAAAGAACGAAAAAAA-GAAA
*
17867029 AGAAAAAAAAGAACGAAAGAAAGAAA
1 AGAAAAAAAAGAACGAAAAAAAGAAA
17867055 AG
1 AG
17867057 GTAATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (26 bp):
AGAAAAAAAAGAACGAAAAAAAGAAA
Found at i:17869049 original size:24 final size:24
Alignment explanation
Indices: 17869019--17869086 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
17869009 AAACAGTATT
*
17869019 AAAAATTTAACTATATACATGATA
1 AAAAATTTAACTATATACATGAAA
*
17869043 AAAAATTAAACTATATACATGAAA
1 AAAAATTTAACTATATACATGAAA
17869067 AAAAATTTAACTATATACAT
1 AAAAATTTAACTATATACAT
17869087 TAACTATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (24 bp):
AAAAATTTAACTATATACATGAAA
Found at i:17869091 original size:13 final size:13
Alignment explanation
Indices: 17869073--17869099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17869063 GAAAAAAAAT
17869073 TTAACTATATACA
1 TTAACTATATACA
17869086 TTAACTATATACA
1 TTAACTATATACA
17869099 T
1 T
17869100 GAACAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAACTATATACA
Found at i:17871083 original size:42 final size:43
Alignment explanation
Indices: 17871037--17871134 Score: 128
Period size: 45 Copynumber: 2.3 Consensus size: 43
17871027 ATAAACTCAC
* *
17871037 CAGCAGAGGG-CAG-AACAAAGCAGAGGGCAGAGAGCAGTGTAG
1 CAGCAGAGGGACAGCAA-AAAGCAAAGAGCAGAGAGCAGTGTAG
*
17871079 CAGCAGAGGGAACCAGCAAAGAGCAAAGAGCAGAGAGCAGTGTAG
1 CAGCAGAGGG-A-CAGCAAAAAGCAAAGAGCAGAGAGCAGTGTAG
17871124 CAGCAGAGGGA
1 CAGCAGAGGGA
17871135 ACCAGCGTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
42 10 0.20
44 1 0.02
45 36 0.73
46 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.39, T:0.04
Consensus pattern (43 bp):
CAGCAGAGGGACAGCAAAAAGCAAAGAGCAGAGAGCAGTGTAG
Found at i:17871619 original size:18 final size:17
Alignment explanation
Indices: 17871596--17871635 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
17871586 ATTGAATTAA
*
17871596 TTTATAATTTTAATATTT
1 TTTATAATTTTAA-ATTG
17871614 TTTATAATTTTAAATTG
1 TTTATAATTTTAAATTG
17871631 TTTAT
1 TTTAT
17871636 TTAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTATAATTTTAAATTG
Found at i:17874567 original size:27 final size:27
Alignment explanation
Indices: 17874517--17874580 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
17874507 TAGTGATTGT
* *
17874517 GGCACTTTGGTGCAAATCAGTGATAGA
1 GGCACTTCGGTGCAAATCAATGATAGA
* * *
17874544 GGCACTTCGGTGCAACTTAATGATAGT
1 GGCACTTCGGTGCAAATCAATGATAGA
*
17874571 GGCTCTTCGG
1 GGCACTTCGG
17874581 AGCATTTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GGCACTTCGGTGCAAATCAATGATAGA
Found at i:17875230 original size:3 final size:3
Alignment explanation
Indices: 17875222--17875259 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17875212 ATATATTTTT
17875222 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
17875260 TCCATTTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:17878237 original size:11 final size:11
Alignment explanation
Indices: 17878223--17878365 Score: 55
Period size: 11 Copynumber: 13.9 Consensus size: 11
17878213 AACATATTTA
17878223 TTTTTAAAATT
1 TTTTTAAAATT
17878234 TTTTT--AA--
1 TTTTTAAAATT
17878241 -TTTTAAAATAT
1 TTTTTAAAAT-T
*
17878252 TTTTAAAATACTT
1 TTTTTAAA-A-TT
**
17878265 TTTTTTTAATT
1 TTTTTAAAATT
17878276 TTTTT-AAA--
1 TTTTTAAAATT
*
17878284 -TTTTAAAATA
1 TTTTTAAAATT
*
17878294 TTTTTAAAATA
1 TTTTTAAAATT
*
17878305 CTTTTAAAATACT
1 TTTTTAAAAT--T
*
17878318 TTTTTTAAA-T
1 TTTTTAAAATT
17878328 TTTTT--AA--
1 TTTTTAAAATT
*
17878335 -TTTTAAAATA
1 TTTTTAAAATT
*
17878345 TTTTTAAAATA
1 TTTTTAAAATT
17878356 TTTTTAAAAT
1 TTTTTAAAAT
17878366 ACTTTTTTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 38
0.69 0.06 0.25
Matches are distributed among these distances:
6 8 0.08
7 4 0.04
8 9 0.09
9 2 0.02
10 8 0.08
11 51 0.49
12 7 0.07
13 14 0.13
14 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:17878244 original size:17 final size:17
Alignment explanation
Indices: 17878219--17878351 Score: 62
Period size: 17 Copynumber: 8.3 Consensus size: 17
17878209 AATAAACATA
* *
17878219 TTTATTTTTAAAATTTT
1 TTTAATTTTAAAATATT
17878236 TTTAATTTTAAAATA--
1 TTTAATTTTAAAATATT
17878251 --T--TTTTAAAATACTT
1 TTTAATTTTAAAATA-TT
*
17878265 TTT--TTTT--AATTTT
1 TTTAATTTTAAAATATT
17878278 TTTAAATTTTAAAATATT
1 TTT-AATTTTAAAATATT
*
17878296 TTTAAAATACTTTTAAAATA-C
1 TTT---A-A-TTTTAAAATATT
17878317 TTT--TTTT-AAAT-TT
1 TTTAATTTTAAAATATT
17878330 TTTAATTTTAAAATATT
1 TTTAATTTTAAAATATT
17878347 TTTAA
1 TTTAA
17878352 AATATTTTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 38
0.67 0.04 0.28
Matches are distributed among these distances:
11 10 0.11
13 13 0.14
14 7 0.08
15 4 0.04
16 13 0.14
17 20 0.22
18 8 0.09
20 2 0.02
21 4 0.04
22 10 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATTTTAAAATATT
Found at i:17878277 original size:51 final size:51
Alignment explanation
Indices: 17878222--17878387 Score: 219
Period size: 51 Copynumber: 3.2 Consensus size: 51
17878212 AAACATATTT
** *
17878222 ATTTTTAAAATTTT-TTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 ATTTTTAAAATTTTAAATATTTTTAAAATATTTTTAAAATAC-TTTTTTTTA
* * *
17878273 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTAAAATACTTTTTTTAA
1 A-TTTTTAAAATTTT-AAATATTTTTAAAATATTTTTAAAATACTTTTTTTTA
*
17878326 ATTTTT-TAATTTTAAAATATTTTTAAAATATTTTTAAAATACTTTTTTTTA
1 ATTTTTAAAATTTT-AAATATTTTTAAAATATTTTTAAAATACTTTTTTTTA
17878377 ATTTTTAAAAT
1 ATTTTTAAAAT
17878388 AAATTTTTAA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
51 49 0.49
52 20 0.20
53 9 0.09
54 23 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (51 bp):
ATTTTTAAAATTTTAAATATTTTTAAAATATTTTTAAAATACTTTTTTTTA
Found at i:17878366 original size:11 final size:11
Alignment explanation
Indices: 17878241--17878372 Score: 95
Period size: 11 Copynumber: 12.4 Consensus size: 11
17878231 ATTTTTTTAA
17878241 TTTTAAAATAT
1 TTTTAAAATAT
17878252 TTTTAAAATACTTT
1 TTTTAAAATA---T
**
17878266 TTTTTTAAT-T
1 TTTTAAAATAT
*
17878276 TTTT-TAA-A-
1 TTTTAAAATAT
17878284 TTTTAAAATAT
1 TTTTAAAATAT
*
17878295 TTTTAAAATAC
1 TTTTAAAATAT
17878306 TTTTAAAATACTT
1 TTTTAAAATA--T
*
17878319 TTTTTAAAT-T
1 TTTTAAAATAT
17878329 TTTT---A-A-
1 TTTTAAAATAT
17878335 TTTTAAAATAT
1 TTTTAAAATAT
17878346 TTTTAAAATAT
1 TTTTAAAATAT
17878357 TTTTAAAATACT
1 TTTTAAAATA-T
17878369 TTTT
1 TTTT
17878373 TTTAATTTTT
Statistics
Matches: 99, Mismatches: 6, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 4 0.04
9 6 0.06
10 12 0.12
11 51 0.52
12 5 0.05
13 8 0.08
14 8 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:17878380 original size:22 final size:21
Alignment explanation
Indices: 17878327--17878388 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
17878317 TTTTTTTAAA
17878327 TTTTTTAA-TTTTAAAATATT
1 TTTTTTAATTTTTAAAATATT
***
17878347 TTTAAAATATTTTTAAAATACTT
1 TTTTTTA-ATTTTTAAAATA-TT
17878370 TTTTTTAATTTTTAAAATA
1 TTTTTTAATTTTTAAAATA
17878389 AATTTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 22 0.67
23 6 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTTAATTTTTAAAATATT
Found at i:17878402 original size:22 final size:22
Alignment explanation
Indices: 17878323--17878413 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
17878313 ATACTTTTTT
*
17878323 TAAATTTTT--TAATTTTAAAA
1 TAAATTTTTAATATTTTTAAAA
17878343 T--ATTTTTAAAATATTTTTAAAA
1 TAAATTTTT--AATATTTTTAAAA
* **
17878365 T-ACTTTTTTTTAATTTTTAAAA
1 TAAATTTTTAAT-ATTTTTAAAA
17878387 TAAATTTTTAATATTTATTAAAA
1 TAAATTTTTAATATTT-TTAAAA
17878410 -AAAT
1 TAAAT
17878414 GGGCCGGGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.11
20 1 0.02
21 1 0.02
22 30 0.54
23 18 0.32
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAATTTTTAATATTTTTAAAA
Found at i:17880099 original size:20 final size:21
Alignment explanation
Indices: 17880074--17880112 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17880064 ATCATTTAAT
17880074 TTTAAAAAGTTA-TTAAATTA
1 TTTAAAAAGTTATTTAAATTA
*
17880094 TTTAAAAATTTATTTAAAT
1 TTTAAAAAGTTATTTAAAT
17880113 CACTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTAAAAAGTTATTTAAATTA
Found at i:17891163 original size:30 final size:31
Alignment explanation
Indices: 17891123--17891259 Score: 106
Period size: 31 Copynumber: 4.5 Consensus size: 31
17891113 GATAGCTAAC
*
17891123 TAAATTTTTAAAAATTTTGAG-GGTTTTAAT
1 TAAAATTTTAAAAATTTTGAGAGGTTTTAAT
* *
17891153 GAGAATTTTAAATAATTTTG-GCA-GTTTTAAT
1 TAAAATTTTAAA-AATTTTGAG-AGGTTTTAAT
*
17891184 TAAAACTTTCAAAAATTTT-AGAGG-TTTAAT
1 TAAAA-TTTTAAAAATTTTGAGAGGTTTTAAT
* * *
17891214 TAAAATTTATAAAAAAATTTGAGAAG-TCTAAT
1 TAAAATTT-T-AAAAATTTTGAGAGGTTTTAAT
* *
17891246 TGAAATTTAAAAAA
1 TAAAATTTTAAAAA
17891260 AAAATTAAAG
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
29 3 0.03
30 27 0.31
31 34 0.40
32 22 0.26
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.41
Consensus pattern (31 bp):
TAAAATTTTAAAAATTTTGAGAGGTTTTAAT
Found at i:17891260 original size:30 final size:32
Alignment explanation
Indices: 17891194--17891262 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
17891184 TAAAACTTTC
* * *
17891194 AAAAATTTTAGAGGTTTAATTAAAATTTATAA
1 AAAAATTTGAGAAGTCTAATTAAAATTTATAA
* *
17891226 AAAAATTTGAGAAGTCTAATTGAAATTTAAAA
1 AAAAATTTGAGAAGTCTAATTAAAATTTATAA
17891258 AAAAA
1 AAAAA
17891263 ATTAAAGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.33
Consensus pattern (32 bp):
AAAAATTTGAGAAGTCTAATTAAAATTTATAA
Found at i:17893176 original size:21 final size:23
Alignment explanation
Indices: 17893144--17893199 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
17893134 ATATATATAC
17893144 TTAATATATATTT-A-ATATATT
1 TTAATATATATTTAACATATATT
17893165 TTAAT-TATTATTTAACATATATT
1 TTAATATA-TATTTAACATATATT
*
17893188 TTAA-AAATATTT
1 TTAATATATATTT
17893200 TTTATTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 10 0.33
22 6 0.20
23 12 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATATATTTAACATATATT
Found at i:17893187 original size:11 final size:11
Alignment explanation
Indices: 17893136--17893188 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
17893126 TAATTTTGAT
*
17893136 ATATATACTTA
1 ATATATATTTA
17893147 ATATATATTTA
1 ATATATATTTA
17893158 ATATAT-TTTA
1 ATATATATTTA
17893168 AT-TATTATTTA
1 ATATA-TATTTA
*
17893179 ACATATATTT
1 ATATATATTT
17893189 TAAAAATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 2 0.05
10 7 0.19
11 26 0.70
12 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATATTTA
Found at i:17893190 original size:12 final size:11
Alignment explanation
Indices: 17893146--17893200 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
17893136 ATATATACTT
17893146 AATATATATTT-
1 AATATAT-TTTA
17893157 AATATATTTTA
1 AATATATTTTA
*
17893168 ATTAT-TATTTA
1 AATATAT-TTTA
17893179 ACATATATTTTA
1 A-ATATATTTTA
*
17893191 AAAATATTTT
1 AATATATTTT
17893201 TTATTAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 4 0.11
11 24 0.65
12 8 0.22
13 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
AATATATTTTA
Found at i:17893401 original size:21 final size:21
Alignment explanation
Indices: 17893352--17893402 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17893342 TATGCTATTT
* * *
17893352 CTAATCTTATTGCTACAGTAT
1 CTAATCTCATCGCTACAGTAA
* *
17893373 CCAGTCTCATCGCTACAGTAA
1 CTAATCTCATCGCTACAGTAA
17893394 CTAATCTCA
1 CTAATCTCA
17893403 ACGCCACCGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (21 bp):
CTAATCTCATCGCTACAGTAA
Found at i:17893621 original size:30 final size:31
Alignment explanation
Indices: 17893563--17893630 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
17893553 TCTTTGGTAA
* * *
17893563 GTTTAATTAAAACTTTTAAAAATTTTG-AAG
1 GTTTAATGAAAACTTTAAAAAATATTGAAAG
17893593 GTTTAATGAAAA-TTTAAAAAATAATTGAAAG
1 GTTTAATGAAAACTTTAAAAAAT-ATTGAAAG
*
17893624 GTCTAAT
1 GTTTAAT
17893631 TGAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.28
30 14 0.44
31 9 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (31 bp):
GTTTAATGAAAACTTTAAAAAATATTGAAAG
Found at i:17895911 original size:16 final size:15
Alignment explanation
Indices: 17895890--17895937 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
17895880 GATGTGAATA
17895890 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
17895906 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
17895921 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
17895937 A
1 A
17895938 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:17895913 original size:24 final size:24
Alignment explanation
Indices: 17895886--17895941 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17895876 TAATGATGTG
*
17895886 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
17895910 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
17895934 AATAATAA
1 AATAATAA
17895942 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:17895920 original size:8 final size:8
Alignment explanation
Indices: 17895886--17895937 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
17895876 TAATGATGTG
*
17895886 AATAATAA
1 AATATTAA
17895894 AATATATAA
1 AATAT-TAA
17895903 AATA-TAA
1 AATATTAA
17895910 AATATTAA
1 AATATTAA
*
17895918 AATATCAA
1 AATATTAA
*
17895926 AATATTAG
1 AATATTAA
17895934 AATA
1 AATA
17895938 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:17896106 original size:20 final size:20
Alignment explanation
Indices: 17896054--17896110 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
17896044 ATACTACATC
*
17896054 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
17896075 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
17896094 AATATGTACATAATATA
1 AATATGTACATAATATA
17896111 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:17896152 original size:22 final size:24
Alignment explanation
Indices: 17896089--17896153 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
17896079 CGTGATAATA
*
17896089 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
17896114 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
17896137 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
17896154 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:17896210 original size:25 final size:25
Alignment explanation
Indices: 17896180--17896236 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
17896170 AAATATATAT
* *
17896180 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAAAATAATATAAAAG
* * *
17896205 ATATATACATAAAATAGTATAAAAT
1 ATATATAAATAAAATAATATAAAAG
17896230 ATATATA
1 ATATATA
17896237 TACGTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAAAATAATATAAAAG
Found at i:17896235 original size:27 final size:27
Alignment explanation
Indices: 17896169--17896248 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
17896159 CATGTAAAAA
* *
17896169 AAAATATATATATATAT-AAATAATAT
1 AAAATATATATATACATAAAATAGTAT
* *
17896195 AATATTAAAGATATATACATAAAATAGTAT
1 AA-A--ATATATATATACATAAAATAGTAT
* *
17896225 AAAATATATATATACGTAATATAG
1 AAAATATATATATACATAAAATAG
17896249 AATTTAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.05
27 18 0.43
29 12 0.29
30 10 0.24
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (27 bp):
AAAATATATATATACATAAAATAGTAT
Found at i:17896744 original size:26 final size:26
Alignment explanation
Indices: 17896694--17896743 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
17896684 TTCTCTCCCA
*
17896694 AAAACTCTCCAAAAAAAATTCCCCCT
1 AAAACTCTCCAAAAAAAATCCCCCCT
17896720 AAAACTCTCC-AAAAAAATCCCCCC
1 AAAACTCTCCAAAAAAAATCCCCCC
17896744 CATATACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (26 bp):
AAAACTCTCCAAAAAAAATCCCCCCT
Found at i:17896975 original size:30 final size:30
Alignment explanation
Indices: 17896825--17896999 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
17896815 TAGGTACAAG
* *
17896825 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
17896855 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
17896885 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
17896915 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
17896945 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
17896975 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
17897000 TGAGAAAAGT
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 2 0.02
30 128 0.98
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:17897766 original size:14 final size:14
Alignment explanation
Indices: 17897747--17897796 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
17897737 GAGTTGATTT
* *
17897747 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
17897761 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
17897776 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
17897790 TT-AAAAA
1 TTGAAAAA
17897797 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:17897976 original size:76 final size:74
Alignment explanation
Indices: 17897776--17898091 Score: 365
Period size: 72 Copynumber: 4.3 Consensus size: 74
17897766 AAAACAGAAA
* * ** *
17897776 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
*
17897841 GAGTT-AATTT
64 GAGTTGATTTT
* * * *
17897851 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
17897916 GTTGATTTTT
66 GTTGA-TTTT
*
17897926 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
**
17897991 AGTTGA--AA
65 AGTTGATTTT
* * * *
17897999 TT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATG
1 TTGAAAA-ACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
*
17898063 AGCTGA--TT
65 AGTTGATTTT
*
17898071 TTGAAAAAGTAGAAATTAAAA
1 TTGAAAAA-CAGAAATTAAAA
17898092 GGTTCAACCC
Statistics
Matches: 207, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
72 58 0.28
73 55 0.27
74 1 0.00
75 41 0.20
76 52 0.25
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (74 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:17898184 original size:73 final size:73
Alignment explanation
Indices: 17898095--17898355 Score: 337
Period size: 84 Copynumber: 3.5 Consensus size: 73
17898085 ATTAAAAGGT
* *
17898095 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
*
17898160 CCCGAGGC
66 CCTGAGGC
* *
17898168 TCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAATTGAAAATA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTG----AC---AA---A-CAGAAATTGAAATTA
17898233 CCTCAGCGTGTCCTGAGGC
55 CCTCAGCGTGTCCTGAGGC
*
17898252 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCA--GTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
*
17898315 CTTGAGGC
66 CCTGAGGC
*
17898323 TCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTT
17898356 TTTGAAACAT
Statistics
Matches: 167, Mismatches: 10, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
71 43 0.26
73 49 0.29
74 1 0.01
77 4 0.02
80 4 0.02
83 1 0.01
84 65 0.39
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
CCTGAGGC
Found at i:17898197 original size:127 final size:127
Alignment explanation
Indices: 17897969--17898206 Score: 356
Period size: 127 Copynumber: 1.9 Consensus size: 127
17897959 GTCCTGAGGC
*
17897969 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
1 TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
17898034 CCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGAAAAAGTAGAAATTAAAAGGT
66 CCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGAAAAAGTAGAAATTAAAAGGT
** * * *
17898095 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAATTACCTCAGCGTG
1 TCAACCCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAAATTGAAAATACCTCAGCGTG
* *
17898159 TCCCGAGGCTCAACTCACCT-TTCGCAATATGAGTTGATTTTTGAAAAA
64 CCCCGAGGCTCAACTCACCTCTT-GCAATATGAGCTGATTTTTGAAAAA
17898207 CATAAATTGA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
126 29 0.29
127 58 0.58
128 13 0.13
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (127 bp):
TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
CCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGAAAAAGTAGAAATTAAAAGGT
Found at i:17898339 original size:71 final size:72
Alignment explanation
Indices: 17898221--17898355 Score: 227
Period size: 71 Copynumber: 1.9 Consensus size: 72
17898211 AATTGAGCAG
17898221 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCA-CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
17898286 ACAAACAA
65 ACAAACAA
* * *
17898294 AAATTGAAATTACCTCA-GTGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
17898356 TTTGAAACAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 43 0.73
73 16 0.27
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (72 bp):
AAATTGAAAATACCTCACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
CAAACAA
Found at i:17898553 original size:232 final size:232
Alignment explanation
Indices: 17898131--17898772 Score: 708
Period size: 232 Copynumber: 2.7 Consensus size: 232
17898121 GATTCTTGAC
*
17898131 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGT-CCGAGGCTCAACTCACCTTTCGCAATATGAGTTGA
*
17898196 TTTTTGAAAAACATAAATTGAGCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
65 -ATTTG-AAAAC--------A-CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
* *
17898261 CTCTCGCAATATGAGTTGA-TTTTTGACAAACAAAAATTGAAATTACCTCAGTGTCTTGAGGCTC
119 CTCTCGCAATATGAGTTGATTTTTTG--AAACAAAAATTGAAAATACCTCAGTGACTTGAGGCTC
* * * * *
17898325 AACTCACTTCTCGCAATATGAGTTGA-TTTTT-TTTGAAACATAAATTAAA
182 AACTCACCTCTCACAATATGAGTTGACTTTTTAATTAAAACAGAAATTAAA
17898374 AAA-ACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTTTCGCAATATGAGTT
1 AAACA-G-AAATTGAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTTTCGCAATATGAGTT
* * * * * * *
17898438 GAAATT-AAAACACAAAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCATCTCTCGCAA
63 GAATTTGAAAACACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
** * *
17898502 TATGAGTTGATTTTTTG-ATGATAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCT
128 TATGAGTTGATTTTTTGAAACAAAAATTGAAAATACCTC-A-GTGACTTGAGGCTCAACTCACCT
*
17898566 CTCACAATATGAGTTGACTTTTTGAATTAAAACAGAAATTGAA
191 CTCACAATATGAGTTGACTTTTT-AATTAAAACAGAAATTAAA
* * * *
17898609 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAACAGAAATTGAAAATACCTCAGC--GTG-TCCGAGGCTCAACTCACCTTTCGCAATATGAGTT
* * *
17898674 -AATTTTTGACAA-ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
63 GAA--TTTGAAAACACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
* *
17898737 AATATGAGTCGA-TTTTTGAAAAACAGAAATTGAAAA
126 AATATGAGTTGATTTTTTG--AAACAAAAATTGAAAA
17898773 CCAGAAATTG
Statistics
Matches: 341, Mismatches: 39, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
230 17 0.05
231 1 0.00
232 92 0.27
233 12 0.04
234 18 0.05
235 19 0.06
236 40 0.12
237 58 0.17
238 3 0.01
239 12 0.04
241 5 0.01
242 1 0.00
243 8 0.02
244 55 0.16
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (232 bp):
AAACAGAAATTGAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGAA
TTTGAAAACACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTGAAACAAAAATTGAAAATACCTCAGTGACTTGAGGCTCAACTCACCTCTCAC
AATATGAGTTGACTTTTTAATTAAAACAGAAATTAAA
Found at i:17898554 original size:71 final size:72
Alignment explanation
Indices: 17898380--17898590 Score: 253
Period size: 71 Copynumber: 2.9 Consensus size: 72
17898370 TAAAAAAACG
* * * * * *
17898380 AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGAAATTA
1 AAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGAATTTT
**
17898445 AAACACA
66 TGACACA
* * *
17898452 AAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCATCTCTCGCAATATGAGTTGATTTTT
1 AAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGAATTTT
**
17898517 TGA-TGA
66 TGACACA
* * * * *
17898523 TAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGACTTTT
1 AAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGAATTTT
17898588 TGA
66 TGA
17898591 ATTAAAACAG
Statistics
Matches: 119, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
71 62 0.52
72 57 0.48
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (72 bp):
AAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGAATTTT
TGACACA
Found at i:17898615 original size:14 final size:14
Alignment explanation
Indices: 17898596--17898622 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17898586 TTTGAATTAA
17898596 AACAGAAATTGAAG
1 AACAGAAATTGAAG
17898610 AACAGAAATTGAA
1 AACAGAAATTGAA
17898623 AAGACCTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.15
Consensus pattern (14 bp):
AACAGAAATTGAAG
Found at i:17898657 original size:93 final size:87
Alignment explanation
Indices: 17898524--17898697 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 87
17898514 TTTTGATGAT
* * * *
17898524 AAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1 AAATTGAAAAGACCTCAATGTGACTCGAGGCTCAACTCACCTCTCACAATATGAGTT-AATTTTT
17898589 GAATTAAAACAGAAATTGAAGAACAG
65 G-A--AAAACAGAAATTGAAGAACAG
*
17898615 AAATTGAAAAGACCTCAGCATGTGAGC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTT
1 AAATTGAAAAGACCTCA--ATGTGA-CTCGAGGCTCAACTCACCTCTCACAATATGAGTTAATTT
*
17898679 TTGACAAACAGAAATTGAA
63 TTGAAAAACAGAAATTGAA
17898698 ATTACCTCAG
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
89 14 0.19
91 17 0.23
92 7 0.09
93 35 0.47
94 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (87 bp):
AAATTGAAAAGACCTCAATGTGACTCGAGGCTCAACTCACCTCTCACAATATGAGTTAATTTTTG
AAAAACAGAAATTGAAGAACAG
Found at i:17898735 original size:73 final size:73
Alignment explanation
Indices: 17898610--17898986 Score: 287
Period size: 73 Copynumber: 4.9 Consensus size: 73
17898600 GAAATTGAAG
** ** *
17898610 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTA
1 AACAGAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
17898675 ATTTTTGACA
64 ATTTTTGACA
*
17898685 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
17898750 TTTTGAAA
66 TTTTGACA
** *** *
17898758 AACAGAAATTGAAA--ACCAGAAATTGAAAATACCTCAGCTTGTGAGC-CAAGGCTCAACTCACC
1 AACAGAAATTGAAATTACCTCAGCGTG----T--C-C--C--GAG-GCTCAA--CTC-----ACC
* * * **
17898820 TCTTGCAATATGAGCTAATTTTTGATG
47 TCTCGCAATATGAGTTGATTTTTGACA
* * ** *
17898847 AACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
17898912 TTTTGACA
66 TTTTGACA
* ** *
17898920 AACAAAAATTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
17898983 TTTT
66 TTTT
17898987 TTTGAAACAT
Statistics
Matches: 241, Mismatches: 39, Indels: 48
0.73 0.12 0.15
Matches are distributed among these distances:
71 47 0.20
73 103 0.43
75 23 0.10
77 1 0.00
78 4 0.02
79 2 0.01
80 6 0.02
82 5 0.02
83 2 0.01
84 4 0.02
85 1 0.00
87 1 0.00
89 36 0.15
91 6 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (73 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGACA
Found at i:17898771 original size:14 final size:14
Alignment explanation
Indices: 17898752--17898786 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
17898742 GAGTCGATTT
17898752 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
17898766 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
17898780 TTGAAAA
1 TTGAAAA
17898787 TACCTCAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:17898803 original size:162 final size:159
Alignment explanation
Indices: 17898479--17898933 Score: 581
Period size: 162 Copynumber: 2.8 Consensus size: 159
17898469 AACGGGTCTT
* * * ** **
17898479 GAGGTTCAACTCATCTCTCGCAATATGAGTTGATTTTTTG-ATGATAAATTGAAAATACCTCAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTGAAACATAAATTGAAAATACCTCAGC
* * * *
17898543 GTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGACTTTTTGAATTAAAACAGAAATTGA
65 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A--AAAACAGAAATTGA
17898608 AGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC
126 A-AACAGAAATTGAAAAGACCTCAGCATGTGAGCC
* *
17898643 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTG--AAACATAAATTGAAAATACCTCAG
* *
17898708 CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGAAAA
64 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
* *
17898773 CCAGAAATTGAAAATACCTCAGCTTGTGAGCC
129 -CAGAAATTGAAAAGACCTCAGCATGTGAGCC
* * * *
17898805 AAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATT-AAAACCACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGA--AACATAAATTGAAAA-TACCTCA
* *
17898869 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAA
63 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
17898934 TTACCTCAGC
Statistics
Matches: 257, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
160 1 0.00
161 5 0.02
162 156 0.61
163 7 0.03
164 30 0.12
165 6 0.02
166 52 0.20
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (159 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAACATAAATTGAAAATACCTCAGCG
TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAACA
GAAATTGAAAAGACCTCAGCATGTGAGCC
Found at i:17898841 original size:89 final size:87
Alignment explanation
Indices: 17898679--17898863 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 87
17898669 GAGTTAATTT
* * *
17898679 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGA-AAACCAGAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATG
*
17898743 AGTCGATTTTTGAAAAACAGAAA
65 AGTCAATTTTTGAAAAACAGAAA
* *
17898766 TTGAAAACCAGAAATTGAAAATACCTCAGCTTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAACCAGAAATTGAAAATACCTCAGC--GTGACCCAAGGCTCAACTCACCTCTCGCAATAT
** *
17898831 GAG-CTAATTTTTGATGAACATAAA
64 GAGTC-AATTTTTGAAAAACAGAAA
17898855 TT-AAAACCA
1 TTGAAAACCA
17898864 CCTCAGCGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 3 0.04
87 25 0.29
88 8 0.09
89 49 0.58
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (87 bp):
TTGAAAACCAGAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGA
GTCAATTTTTGAAAAACAGAAA
Found at i:17898934 original size:235 final size:232
Alignment explanation
Indices: 17898615--17899563 Score: 698
Period size: 232 Copynumber: 4.3 Consensus size: 232
17898605 TGAAGAACAG
* ** *
17898615 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTT
1 AAATTGAAAACACCTCAGC--GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
17898680 TGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
64 TGACAAACAAAAATTGAAATTACCTCAGC--GTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
** *
17898745 TCGA-TTTTTGAAAAACAGAAATTGAAAACCA-G-AAATTGAAAATACCTCAGCTTGTGAGCC-A
127 TCGATTTTTTGAAAAACAGAAATT-AAAAAAATGAAAAATGAAAATACCTCAGC--GTG-GCCTA
* * ** *
17898806 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGA-ACAT
188 AGGCTCAACTCACCTCTCGCAATATGAGCTGAA--ATT-AAAACACAA
* *
17898852 AAATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-CACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
** * *
17898916 GACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
65 GACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCG
*** * * *
17898981 ATTTTTTTTGAAACATAAATTAAAAAAATGAAAAATGAAAATACCTCAGCGTGTCCTGAGGCTCA
130 ATTTTTTGAAAAACAGAAATTAAAAAAATGAAAAATGAAAATACCTCAGCGTGGCCTAAGGCTCA
*
17899046 ACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
195 ACTCACCTCTCGCAATATGAGCTGAAATTAAAACACAA
* * *
17899084 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTG
1 AAATTGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * * * *
17899148 ----A-AAAAGTAGAAATTA----A-------AAGGTTCAACCCACCTCTCGCAATATGAGTTGA
66 ACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGA
* * * * *
17899197 -TTCTTGACAAACAGAAA-T-------TG--AAAT-----TACCTCATCGTGTCCTGAGGCTCAA
131 TTTTTTGAAAAACAGAAATTAAAAAAATGAAAAATGAAAATACCTCAGCGTGGCCTAAGGCTCAA
** * *
17899246 CTCACCTCTCGCAATATGAATTGAAA--AAAATACCA
196 CTCACCTCTCGCAATATGAGCTGAAATTAAAACACAA
* * * *
17899281 CAGTGTG--TA-A--T---C-T-----GAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAAT-TGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*** ** * *
17899332 TTTAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
65 GACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCG
*** * * * *
17899397 ATTTTTTTTGAAACATAAATTAAAAAAATGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
130 ATTTTTTGAAAAACAGAAATTAAAAAAATGAAAAATGAAAATACCTCAGCGTGGCCTAAGGCTCA
** * * * *
17899462 ACTCATTTCTCGCAATATAAGTTGAATTTTAAAA-ACAG
195 ACTCACCTCTCGCAATATGAGCTGAA-ATTAAAACACAA
** ** * **
17899500 AAATTGAAATTACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
17899564 TNNNNNNNNN
Statistics
Matches: 574, Mismatches: 79, Indels: 123
0.74 0.10 0.16
Matches are distributed among these distances:
184 30 0.05
185 4 0.01
189 2 0.00
190 13 0.02
193 1 0.00
194 1 0.00
195 1 0.00
196 1 0.00
197 9 0.02
198 2 0.00
199 49 0.09
201 29 0.05
202 12 0.02
203 1 0.00
204 4 0.01
206 2 0.00
210 2 0.00
212 3 0.01
213 1 0.00
214 12 0.02
215 29 0.05
217 45 0.08
218 2 0.00
219 4 0.01
220 4 0.01
221 1 0.00
222 1 0.00
223 1 0.00
226 13 0.02
227 2 0.00
231 7 0.01
232 91 0.16
233 74 0.13
234 18 0.03
235 86 0.15
236 4 0.01
237 13 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (232 bp):
AAATTGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
ACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGA
TTTTTTGAAAAACAGAAATTAAAAAAATGAAAAATGAAAATACCTCAGCGTGGCCTAAGGCTCAA
CTCACCTCTCGCAATATGAGCTGAAATTAAAACACAA
Found at i:17899165 original size:160 final size:157
Alignment explanation
Indices: 17898863--17899152 Score: 415
Period size: 160 Copynumber: 1.8 Consensus size: 157
17898853 AATTAAAACC
** *
17898863 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAA
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
* ** * *
17898928 TTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAA
66 TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGA---TTTTTGAA
*
17898993 ACATAAATTAAAAAAATGAAAAATGAAAAT
128 AAATAAATTAAAAAAATGAAAAATGAAAAT
17899023 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAA
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAA-ACAAAA
*
17899086 ATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGAA
65 ATTGAAAATACCTCAGCGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAA
17899150 AAA
128 AAA
17899153 GTAGAAATTA
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
157 9 0.08
158 3 0.03
159 26 0.22
160 48 0.41
161 31 0.26
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (157 bp):
ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAAAAA
TAAATTAAAAAAATGAAAAATGAAAAT
Found at i:17899537 original size:72 final size:72
Alignment explanation
Indices: 17899428--17899563 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
17899418 AAAAAAATGA
*
17899428 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTA
1 AAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTA
17899493 AAAACAG
66 AAAACAG
* * *
17899500 AAATTGAAATTACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTT
17899564 TNNNNNNNNN
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (72 bp):
AAATTGAAAATACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTA
AAAACAG
Found at i:17910270 original size:16 final size:15
Alignment explanation
Indices: 17910249--17910296 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
17910239 GATGTGAATA
17910249 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
17910265 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
17910280 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
17910296 A
1 A
17910297 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:17910272 original size:24 final size:24
Alignment explanation
Indices: 17910245--17910300 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17910235 TAATGATGTG
*
17910245 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
17910269 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
17910293 AATAATAA
1 AATAATAA
17910301 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:17910279 original size:8 final size:8
Alignment explanation
Indices: 17910245--17910296 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
17910235 TAATGATGTG
*
17910245 AATAATAA
1 AATATTAA
17910253 AATATATAA
1 AATAT-TAA
17910262 AATA-TAA
1 AATATTAA
17910269 AATATTAA
1 AATATTAA
*
17910277 AATATCAA
1 AATATTAA
*
17910285 AATATTAG
1 AATATTAA
17910293 AATA
1 AATA
17910297 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:17910511 original size:22 final size:24
Alignment explanation
Indices: 17910448--17910512 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
17910438 CGTGATAATA
*
17910448 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
17910473 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
17910496 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
17910513 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:17910569 original size:25 final size:25
Alignment explanation
Indices: 17910533--17910662 Score: 100
Period size: 23 Copynumber: 5.6 Consensus size: 25
17910523 AAAAAAATAT
*
17910533 ATATATAAATAATATAATATTAAAG
1 ATATATACATAATATAATATTAAAG
* *
17910558 ATATATACATAAAATAGTA-TAAA-
1 ATATATACATAATATAATATTAAAG
* *
17910581 ATATATACGTAATATAGA-ATTTAA-
1 ATATATACATAATATA-ATATTAAAG
* *
17910605 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
*
17910627 A-ATATATATAATATAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
17910650 AAATATA-ATAATA
1 ATATATACATAATA
17910663 ACAAAAAAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 39 0.46
24 14 0.16
25 16 0.19
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:17911299 original size:30 final size:30
Alignment explanation
Indices: 17911149--17911323 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
17911139 TAGGTACAAG
* *
17911149 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
17911179 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
17911209 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
17911239 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
17911269 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
17911299 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
17911324 TGAGAAAAGT
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 2 0.02
30 128 0.98
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:17921871 original size:22 final size:22
Alignment explanation
Indices: 17921826--17921865 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17921816 TCTAAATTAC
17921826 TATTTAATAATTTATAAATATT
1 TATTTAATAATTTATAAATATT
17921848 TATTTAA-AATTTA-AAATA
1 TATTTAATAATTTATAAATA
17921866 GGTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTAATAATTTATAAATATT
Found at i:17922155 original size:10 final size:9
Alignment explanation
Indices: 17922129--17922173 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
17922119 TTGAATATGG
17922129 TATAAAAAT
1 TATAAAAAT
17922138 T-T-AAAAT
1 TATAAAAAT
17922145 TATTAAAAAT
1 TA-TAAAAAT
17922155 TATAAAACAT
1 TATAAAA-AT
17922165 TATAAAAAT
1 TATAAAAAT
17922174 ATTTAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.19
8 1 0.03
9 9 0.28
10 16 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
TATAAAAAT
Found at i:17922172 original size:20 final size:18
Alignment explanation
Indices: 17922132--17922182 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
17922122 AATATGGTAT
*
17922132 AAAAATTT-AAAATTATT
1 AAAAATTTAAAAATTATA
17922149 AAAAATTATAAAACATTATA
1 AAAAATT-TAAAA-ATTATA
17922169 AAAATATTTAAAAA
1 AAAA-ATTTAAAAA
17922183 GAGAAACGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 7 0.24
18 1 0.03
19 4 0.14
20 14 0.48
21 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTTAAAAATTATA
Found at i:17923345 original size:10 final size:10
Alignment explanation
Indices: 17923330--17923354 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17923320 TGATGTTAAA
17923330 TAATTATATT
1 TAATTATATT
17923340 TAATTATATT
1 TAATTATATT
17923350 TAATT
1 TAATT
17923355 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TAATTATATT
Found at i:17927888 original size:19 final size:20
Alignment explanation
Indices: 17927847--17927888 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
17927837 AGAAAAAAGA
* *
17927847 AAAGCTTGTGTAATAATAGT
1 AAAGCTTATGTAAAAATAGT
*
17927867 AAAGCTTATG-AAAAATATT
1 AAAGCTTATGTAAAAATAGT
17927886 AAA
1 AAA
17927889 ATAAAGCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAGCTTATGTAAAAATAGT
Found at i:17930670 original size:109 final size:112
Alignment explanation
Indices: 17930551--17930779 Score: 349
Period size: 109 Copynumber: 2.1 Consensus size: 112
17930541 TCTAGCCCCT
*
17930551 CCCAAAACTTAAAAAAATTCAATTTAACCTTTTTTAGACTTTGGTCAAATGAA-TTTTTTTTAA-
1 CCCAAAACTTAAAAAAATTCAATTTAACCTTTTTTAGACTTCGGTCAAAT-AATTTTTTTTTAAT
* * * *
17930614 TT-G-TCTCTAAAAAGTAGTAATTTAATTTAAGCATTTTAACTTTGGC
65 TTGGCCCTCAAAAAAGTACTAATTTAATTTAAGCATTTTAACTTTGAC
17930660 CCCAAAACTTAAAAAAATTCAATTTAACCTTTTTTAGACTTCGGTCAAATAATTTTTTTTTAATT
1 CCCAAAACTTAAAAAAATTCAATTTAACCTTTTTTAGACTTCGGTCAAATAATTTTTTTTTAATT
*
17930725 TGGCCCCTCAAAAAAGTACTAATTTAATTTAAGCATTTTAATTTTGAC
66 TGG-CCCTCAAAAAAGTACTAATTTAATTTAAGCATTTTAACTTTGAC
*
17930773 CCAAAAA
1 CCCAAAA
17930780 TTTTATATTT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
108 2 0.02
109 59 0.55
110 2 0.02
111 1 0.01
113 44 0.41
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (112 bp):
CCCAAAACTTAAAAAAATTCAATTTAACCTTTTTTAGACTTCGGTCAAATAATTTTTTTTTAATT
TGGCCCTCAAAAAAGTACTAATTTAATTTAAGCATTTTAACTTTGAC
Found at i:17946958 original size:18 final size:19
Alignment explanation
Indices: 17946925--17946960 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17946915 TTATATATAT
*
17946925 ATATTAATAGATAGATTAC
1 ATATTAATAAATAGATTAC
17946944 ATATT-ATAAATAGATTA
1 ATATTAATAAATAGATTA
17946961 TAGGTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATTAATAAATAGATTAC
Found at i:17948558 original size:12 final size:12
Alignment explanation
Indices: 17948541--17948565 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17948531 TGTTTTTCGG
17948541 ATTTTAAAATTT
1 ATTTTAAAATTT
17948553 ATTTTAAAATTT
1 ATTTTAAAATTT
17948565 A
1 A
17948566 AGTCCAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTAAAATTT
Found at i:17949816 original size:159 final size:153
Alignment explanation
Indices: 17949495--17949856 Score: 422
Period size: 159 Copynumber: 2.3 Consensus size: 153
17949485 AAGGTTATGG
** *
17949495 ACAACAAATATGTGCTGAGGCTTTGCTGAATGCATGTATCATGAAATGATGGATATGTGCTCACG
1 ACAACAAATATGTGCTGAGGCTGAGCTGAATGCATGTATCATGAACTGATGGATATGTGCTCACG
* * * * *
17949560 GAAATCAAATCCGCAATCAACCATGGTCAGACTGGAAGTGGGAGTAGGATCGACATCATTAATGG
66 GAAATCAAATCCGCAATCAACCATGGTCAGACTGGAAGTGGAAGAAGGATCGACAACATCAATCG
17949625 TTGCATAAAGATGAAAAAATTTC
131 TTGCATAAAGATGAAAAAATTTC
* *
17949648 ACAACAAATATGTGCTGAGGCTGAGCTGAATGCATGTCTCATGAACTGATGGATATGTGCCGTTG
1 ACAACAAATATGTGCTGAGGCTGAGCTGAATGCATGTATCATGAACTGATGGATATGTG-C--TC
** * * *
17949713 AGTGCGGAAATCAAATCCGTGATCAACCATGGTCGGA-TGGAAGATGGAAGAAGGCTTGACAACA
63 A---CGGAAATCAAATCCGCAATCAACCATGGTCAGACTGGAAG-TGGAAGAAGGATCGACAACA
* *
17949777 TCAA-CGTCTGCATAAAGATGATAAACTTTC
124 TCAATCGT-TGCATAAAGATGAAAAAATTTC
** * * * * *
17949807 ATTATAAATATGTGTTGAGGCTGAGTTGAATACATGTATCAAGAACTGAT
1 ACAACAAATATGTGCTGAGGCTGAGCTGAATGCATGTATCATGAACTGAT
17949857 CGAATTTCAT
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
153 55 0.31
154 1 0.01
156 2 0.01
158 8 0.05
159 110 0.62
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (153 bp):
ACAACAAATATGTGCTGAGGCTGAGCTGAATGCATGTATCATGAACTGATGGATATGTGCTCACG
GAAATCAAATCCGCAATCAACCATGGTCAGACTGGAAGTGGAAGAAGGATCGACAACATCAATCG
TTGCATAAAGATGAAAAAATTTC
Found at i:17961243 original size:18 final size:18
Alignment explanation
Indices: 17961220--17961312 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
17961210 CCCAACTACT
*
17961220 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
17961238 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
17961256 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
17961274 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
17961292 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
17961310 GTA
1 GTA
17961313 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:17961272 original size:36 final size:36
Alignment explanation
Indices: 17961220--17961312 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
17961210 CCCAACTACT
*
17961220 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
17961256 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
17961292 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
17961313 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:17968651 original size:90 final size:90
Alignment explanation
Indices: 17968498--17968679 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 90
17968488 TAAGTTACAA
* *
17968498 CTGTCAAAAGGAGAAATAGACTCTAAATGAACTCATTTCTCATTGTGTGCAAGAGGAAAAAAGGT
1 CTGTCAAAAGGAGAAATAGACTCTAAATGAACTCATATCTCATTGTGTGCAAAAGGAAAAAAGGT
17968563 TGAAGCATGATTAAGTCTGAAAGTG
66 TGAAGCATGATTAAGTCTGAAAGTG
* * *
17968588 CTGTCAAAAGGAGAAATAGACTTTAAATGAGCTCATATCTCATTGTGTGCAAAAGGGAAAAAGGT
1 CTGTCAAAAGGAGAAATAGACTCTAAATGAACTCATATCTCATTGTGTGCAAAAGGAAAAAAGGT
*
17968653 TGAAGCATGATTAAGTTTGAAAGTG
66 TGAAGCATGATTAAGTCTGAAAGTG
17968678 CT
1 CT
17968680 CATTTGGTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (90 bp):
CTGTCAAAAGGAGAAATAGACTCTAAATGAACTCATATCTCATTGTGTGCAAAAGGAAAAAAGGT
TGAAGCATGATTAAGTCTGAAAGTG
Found at i:17969865 original size:16 final size:16
Alignment explanation
Indices: 17969841--17969882 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
17969831 TTTTCTTGTG
17969841 TTTTA-TTTTAT-TTT
1 TTTTATTTTTATGTTT
17969855 ATTTTATTTTTATGTTT
1 -TTTTATTTTTATGTTT
*
17969872 GTTTATTTTTA
1 TTTTATTTTTA
17969883 CAACCCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTATGTTT
Found at i:17971293 original size:21 final size:21
Alignment explanation
Indices: 17971267--17971308 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17971257 AGAATATATA
*
17971267 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
17971288 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
17971309 GATTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:17971970 original size:41 final size:41
Alignment explanation
Indices: 17971920--17972011 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
17971910 GGCTATGTGC
*
17971920 CTAGTAGGCTTAATGCCGGTGAAATAATTCAGACCT-TACGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGA-CTATACGT
* * * *
17971961 CTAGCAGGCTTAATGCCGGTGATATATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTATACGT
17972002 CTAGCAGGCT
1 CTAGCAGGCT
17972012 AAGAGCTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
40 2 0.04
41 43 0.96
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTATACGT
Found at i:17978860 original size:41 final size:41
Alignment explanation
Indices: 17978803--17978889 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
17978793 NNNNNNNNNN
17978803 AGGCTTAATGCCGGTGAAATAATTCAGACCT-TACGTCTAGC
1 AGGCTTAATGCCGGTGAAATAATTCAGA-CTATACGTCTAGC
* * * * *
17978844 AGGCTTAATGTCGGTGATATATTTCGGACTATAGGTCTAGC
1 AGGCTTAATGCCGGTGAAATAATTCAGACTATACGTCTAGC
17978885 AGGCT
1 AGGCT
17978890 AAGAGCTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 2 0.05
41 38 0.95
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (41 bp):
AGGCTTAATGCCGGTGAAATAATTCAGACTATACGTCTAGC
Found at i:17979986 original size:12 final size:12
Alignment explanation
Indices: 17979971--17979995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17979961 TTTATACATT
17979971 TCATTATTATTA
1 TCATTATTATTA
17979983 TCATTATTATTA
1 TCATTATTATTA
17979995 T
1 T
17979996 GATGATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTATTATTA
Found at i:17986650 original size:28 final size:29
Alignment explanation
Indices: 17986607--17986693 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 29
17986597 GTGTCGATGA
*
17986607 TTACAGTTTCTAGGTACTATGTACCGGTG
1 TTACAATTTCTAGGTACTATGTACCGGTG
* *
17986636 TTACAATTT-TAGGTACTCTGTACCGGAG
1 TTACAATTTCTAGGTACTATGTACCGGTG
* * * *
17986664 ATATATATTTCTAGGTGCTATGTATCGGTG
1 TTACA-ATTTCTAGGTACTATGTACCGGTG
17986694 GTGGATACCA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 20 0.43
29 12 0.26
30 15 0.32
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (29 bp):
TTACAATTTCTAGGTACTATGTACCGGTG
Found at i:17989757 original size:11 final size:12
Alignment explanation
Indices: 17989735--17989763 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
17989725 ACTTTCGCAT
17989735 TTAATGTTGTTC
1 TTAATGTTGTTC
17989747 TTAAT-TTGTTC
1 TTAATGTTGTTC
17989758 TTAATG
1 TTAATG
17989764 ATTTGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (12 bp):
TTAATGTTGTTC
Found at i:17990448 original size:17 final size:17
Alignment explanation
Indices: 17990391--17990449 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
17990381 TTCGACCACT
*
17990391 ATTCCGATTTATAAAAC
1 ATTCCGATTTAAAAAAC
* *
17990408 ATTGC-AATTAAAAAA-
1 ATTCCGATTTAAAAAAC
**
17990423 ATTTGGATTTAAAAAAC
1 ATTCCGATTTAAAAAAC
17990440 ATTCCGATTT
1 ATTCCGATTT
17990450 TAGAATGACA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
17 12 0.38
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (17 bp):
ATTCCGATTTAAAAAAC
Found at i:17991705 original size:193 final size:191
Alignment explanation
Indices: 17991438--17991813 Score: 490
Period size: 193 Copynumber: 2.0 Consensus size: 191
17991428 AAAGGTCCCA
* * *
17991438 AACTTGGTCTATTATGTTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTTCA
1 AACTTAGTCTATTATATTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCA
* * * * *
17991503 ACTCCAAAGTT-GTCTAAAGAAGCTTTGCAGGATATGA-AAACACAAGTGCATTTCCATTCAAGT
66 ACCCCAAAGTTAAT-TAAA-AAGCATTGCAGGATA-CACAAACACAAATGCATTTCCATTCAAGT
** * *
17991566 AAATTGTTGTGTTGTAATCACAAAG-TTCAAATGAAAACCAATGACTCGAACCCATAAAAAATTC
128 -AATAATTGTGTTGTAATCACAAAGCTACAAATGAAAACCAATGACTCAAACCCATAAAAAATTC
* *
17991630 AACTTAGTCTATTGTATTCATTAACATCA-ACATAAAAACATCAATTACTTCCTAATAACAATTC
1 AACTTAGTCTATTATATTCATTAACATCATA-A-AAAAACATCAATTACATCCTAATAACAATTC
**
17991694 CAACCCCAAAGTTCAATTAAAAAGCATTGCAGGATACACAAATGCAAATGCATTTCCATTCAAGT
64 CAACCCCAAAGTT-AATTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGT
* * *
17991759 AATAATTGTGTTTTAATCACAAAGCTACAAATGAAAATCAATGACTTAAACCCAT
128 AATAATTGTGTTGTAATCACAAAGCTACAAATGAAAACCAATGACTCAAACCCAT
17991814 TATAGATTAC
Statistics
Matches: 159, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
191 1 0.01
192 49 0.31
193 104 0.65
194 4 0.03
195 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (191 bp):
AACTTAGTCTATTATATTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCA
ACCCCAAAGTTAATTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGTAAT
AATTGTGTTGTAATCACAAAGCTACAAATGAAAACCAATGACTCAAACCCATAAAAAATTC
Found at i:17995373 original size:13 final size:13
Alignment explanation
Indices: 17995357--17995396 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
17995347 TTTAAACTAA
17995357 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
17995370 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
17995383 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
17995396 A
1 A
17995397 ATGAAGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:17995724 original size:28 final size:28
Alignment explanation
Indices: 17995683--17995739 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
17995673 ATATGTTTAC
17995683 TTAAAGTATCTGTAC-TTCACTTAAAGTA
1 TTAAAGTATCTGTACATT-ACTTAAAGTA
* *
17995711 TTAAAGTATTTGTACATTGCTTAAAGTA
1 TTAAAGTATCTGTACATTACTTAAAGTA
17995739 T
1 T
17995740 GGACACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (28 bp):
TTAAAGTATCTGTACATTACTTAAAGTA
Found at i:17996760 original size:13 final size:13
Alignment explanation
Indices: 17996742--17996768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17996732 TCGAGTCTTA
17996742 AATGTGAACCATG
1 AATGTGAACCATG
17996755 AATGTGAACCATG
1 AATGTGAACCATG
17996768 A
1 A
17996769 CACAAGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (13 bp):
AATGTGAACCATG
Found at i:18003035 original size:12 final size:12
Alignment explanation
Indices: 18003018--18003042 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18003008 GGTGTTCAGT
18003018 CGGTTAACCGAC
1 CGGTTAACCGAC
18003030 CGGTTAACCGAC
1 CGGTTAACCGAC
18003042 C
1 C
18003043 CGAAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:18003218 original size:9 final size:9
Alignment explanation
Indices: 18003202--18003291 Score: 117
Period size: 9 Copynumber: 9.6 Consensus size: 9
18003192 GTTGGTTAAA
18003202 AATTACCCG
1 AATTACCCG
*
18003211 ACTTACCCG
1 AATTACCCG
18003220 AATTACCCG
1 AATTACCCG
*
18003229 ACTTACCCG
1 AATTACCCG
18003238 AATTACCCG
1 AATTACCCG
18003247 AATTACCCG
1 AATTACCCG
18003256 AAAATTACCCG
1 --AATTACCCG
*
18003267 AAAATTACCCA
1 --AATTACCCG
18003278 AATTACCCG
1 AATTACCCG
18003287 AATTA
1 AATTA
18003292 AATCACTACA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
9 54 0.74
11 19 0.26
ACGTcount: A:0.37, C:0.32, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:18003394 original size:17 final size:17
Alignment explanation
Indices: 18003338--18003395 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
18003328 GAATCACTAT
18003338 ATAATTAAAAATATTAC
1 ATAATTAAAAATATTAC
*** *
18003355 ATAAGTCTTTGAATCACTAC
1 ATAA-T-TAAAAAT-ATTAC
18003375 ATAATTAAAAATATTAC
1 ATAATTAAAAATATTAC
18003392 ATAA
1 ATAA
18003396 GTCTTGAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 12 0.40
18 5 0.17
19 5 0.17
20 8 0.27
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATTAAAAATATTAC
Found at i:18003396 original size:37 final size:37
Alignment explanation
Indices: 18003292--18003404 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
18003282 ACCCGAATTA
* * *
18003292 AATCACTACATAATTAAAAACATTACATAAATATTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
18003329 AATCACTATATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
18003366 AATCACTACATAATTAAAAATATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
18003402 AAT
1 AAT
18003405 TAACACATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
36 6 0.08
37 65 0.92
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:18003472 original size:24 final size:24
Alignment explanation
Indices: 18003445--18003503 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
18003435 ATTCTCCATT
*
18003445 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
18003469 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
18003493 TATCTCCATTT
1 TATATCCATTT
18003504 GCATTAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:18006457 original size:8 final size:8
Alignment explanation
Indices: 18006444--18006468 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18006434 AAATGTTCGC
18006444 ATTTAATT
1 ATTTAATT
18006452 ATTTAATT
1 ATTTAATT
18006460 ATTTAATT
1 ATTTAATT
18006468 A
1 A
18006469 ACAATATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:18006604 original size:27 final size:27
Alignment explanation
Indices: 18006574--18006653 Score: 160
Period size: 27 Copynumber: 3.0 Consensus size: 27
18006564 AAAGATGAAA
18006574 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
18006601 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
18006628 GAAAAAATTAAGACAATAGTATACAA
1 GAAAAAATTAAGACAATAGTATACAA
18006654 CGACATAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.21
Consensus pattern (27 bp):
GAAAAAATTAAGACAATAGTATACAAT
Found at i:18020118 original size:13 final size:13
Alignment explanation
Indices: 18020097--18020149 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
18020087 GACACTTCTA
18020097 TAATATTATTAAT
1 TAATATTATTAAT
*
18020110 TAATGTTATTAAT
1 TAATATTATTAAT
*
18020123 TAAT-TTAAATAAT
1 TAATATT-ATTAAT
*
18020136 TAATATTGTTAAT
1 TAATATTATTAAT
18020149 T
1 T
18020150 TTTTTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (13 bp):
TAATATTATTAAT
Found at i:18020196 original size:13 final size:13
Alignment explanation
Indices: 18020178--18020299 Score: 128
Period size: 13 Copynumber: 9.7 Consensus size: 13
18020168 ATTTTTAAGG
18020178 TAATATACTGTTT
1 TAATATACTGTTT
*
18020191 TAATATACTGTTA
1 TAATATACTGTTT
*
18020204 TAA-A-A-T-TTA
1 TAATATACTGTTT
18020213 TAATATACTGTTT
1 TAATATACTGTTT
*
18020226 TAATATACTATTAT
1 TAATATACTGTT-T
* *
18020240 AAATATATTGTTT
1 TAATATACTGTTT
*
18020253 TAATATATTGTTT
1 TAATATACTGTTT
*
18020266 TAATATATTGTTT
1 TAATATACTGTTT
*
18020279 TAATATACTGTTA
1 TAATATACTGTTT
18020292 TAA-ATACT
1 TAATATACT
18020300 ACACCTTAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 11
0.83 0.08 0.10
Matches are distributed among these distances:
9 6 0.06
10 2 0.02
11 2 0.02
12 7 0.07
13 68 0.72
14 10 0.11
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:18020386 original size:13 final size:13
Alignment explanation
Indices: 18020368--18020401 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18020358 TTTTTTAATG
*
18020368 TAATATACTGTTT
1 TAATATACTGTTA
18020381 TAATATACTGTTA
1 TAATATACTGTTA
18020394 TAA-ATACT
1 TAATATACT
18020402 ACACCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (13 bp):
TAATATACTGTTA
Found at i:18020421 original size:52 final size:52
Alignment explanation
Indices: 18020289--18020449 Score: 272
Period size: 52 Copynumber: 3.1 Consensus size: 52
18020279 TAATATACTG
* *
18020289 TTATAAATACTACACCTTAATTTTTAATGTAATATATTGTTTTAATATATTG
1 TTATAAATACTACACCTTAATTTTTAATGTAATATACTGTTTTAATATACTG
*
18020341 -TA-AAATACTACACCTTATTTTTTAATGTAATATACTGTTTTAATATACTG
1 TTATAAATACTACACCTTAATTTTTAATGTAATATACTGTTTTAATATACTG
*
18020391 TTATAAATACTACACCTTAATTTTTAATGTAATTTACTGTTTTAATATACTG
1 TTATAAATACTACACCTTAATTTTTAATGTAATATACTGTTTTAATATACTG
18020443 TTATAAA
1 TTATAAA
18020450 ATTTGTAACT
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
50 45 0.44
51 4 0.04
52 53 0.52
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (52 bp):
TTATAAATACTACACCTTAATTTTTAATGTAATATACTGTTTTAATATACTG
Found at i:18020884 original size:8 final size:8
Alignment explanation
Indices: 18020828--18020857 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
18020818 TTAATACATG
18020828 TATATAAA
1 TATATAAA
18020836 TATATAAA
1 TATATAAA
18020844 TATATAAA
1 TATATAAA
18020852 TATATA
1 TATATA
18020858 TAAGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:18023692 original size:21 final size:22
Alignment explanation
Indices: 18023668--18023713 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
18023658 GAAATTTATT
*
18023668 TTTTTTATTTTTAT-TTTAAAA
1 TTTTTAATTTTTATATTTAAAA
*
18023689 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTATATTTAAAA
18023711 TTT
1 TTT
18023714 CAAAATTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTAATTTTTATATTTAAAA
Found at i:18038730 original size:17 final size:18
Alignment explanation
Indices: 18038710--18038743 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18038700 CATATTGTCA
18038710 TTATTAC-TTTATTTTTT
1 TTATTACTTTTATTTTTT
*
18038727 TTATTTCTTTTATTTTT
1 TTATTACTTTTATTTTT
18038744 AGTACTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTACTTTTATTTTTT
Found at i:18039056 original size:20 final size:20
Alignment explanation
Indices: 18039013--18039057 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18039003 TATTGATATT
*
18039013 ATTATAAAATTGATATTATT
1 ATTATAAAATTGATATTATC
* *
18039033 ATTATAAAATTGGTATTCTC
1 ATTATAAAATTGATATTATC
18039053 ATTAT
1 ATTAT
18039058 TATCGTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTATAAAATTGATATTATC
Found at i:18039060 original size:23 final size:20
Alignment explanation
Indices: 18039009--18039049 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
18038999 CCATTATTGA
18039009 TATTATTATAAAATTGATAT
1 TATTATTATAAAATTGATAT
*
18039029 TATTATTATAAAATTGGTAT
1 TATTATTATAAAATTGATAT
18039049 T
1 T
18039050 CTCATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TATTATTATAAAATTGATAT
Found at i:18049080 original size:31 final size:31
Alignment explanation
Indices: 18049043--18049104 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
18049033 TTACAAAATG
*
18049043 GTTATTAAACTATTTAAAAGTTTTTATTTAA
1 GTTATTAAACTATTCAAAAGTTTTTATTTAA
**
18049074 GTTATTAAACTATTCGGAAGTTTTTATTTAA
1 GTTATTAAACTATTCAAAAGTTTTTATTTAA
18049105 AATTTTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (31 bp):
GTTATTAAACTATTCAAAAGTTTTTATTTAA
Found at i:18049161 original size:17 final size:18
Alignment explanation
Indices: 18049122--18049164 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18049112 GATGCATTAC
18049122 AAATACAATTATATTGAT
1 AAATACAATTATATTGAT
**
18049140 AAATACAATTAT-TTTTT
1 AAATACAATTATATTGAT
18049157 AAATACAA
1 AAATACAA
18049165 CTGTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATACAATTATATTGAT
Found at i:18057718 original size:25 final size:25
Alignment explanation
Indices: 18057667--18057723 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
18057657 TTAATGTAGA
* **
18057667 ATTTTTTTTCATTTCTTTTTATTTT
1 ATTTTTTTTCATTTCTTTTAACGTT
18057692 ATTTTATTTT-ATTTCTTTTAACGTT
1 ATTTT-TTTTCATTTCTTTTAACGTT
*
18057717 ATCTTTT
1 ATTTTTT
18057724 AAAAATTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 21 0.78
26 4 0.15
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (25 bp):
ATTTTTTTTCATTTCTTTTAACGTT
Found at i:18060999 original size:16 final size:16
Alignment explanation
Indices: 18060978--18061010 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18060968 TAAATATATA
*
18060978 TTAAGTTTTTTATGTT
1 TTAAGTTTTCTATGTT
18060994 TTAAGTTTTCTATGTT
1 TTAAGTTTTCTATGTT
18061010 T
1 T
18061011 AAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (16 bp):
TTAAGTTTTCTATGTT
Found at i:18061197 original size:19 final size:19
Alignment explanation
Indices: 18061143--18061209 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 19
18061133 ATTTATTTAT
*
18061143 TTTTATGTTTAAGTTTTCAA
1 TTTTAT-TTTTAGTTTTCAA
18061163 TTTTATTTTTATGTTTTCAA
1 TTTTATTTTTA-GTTTTCAA
18061183 TTTTATTTTTAGTTTTCAA
1 TTTTATTTTTAGTTTTCAA
*
18061202 TTTCATTT
1 TTTTATTT
18061210 CCCCGACAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 19 0.43
20 25 0.57
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTATTTTTAGTTTTCAA
Found at i:18061451 original size:9 final size:9
Alignment explanation
Indices: 18061437--18061471 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18061427 TTTTGTTACA
18061437 ACAATTAAT
1 ACAATTAAT
18061446 ACAATT-A-
1 ACAATTAAT
18061453 ACAATTAAT
1 ACAATTAAT
18061462 ACAATTAAT
1 ACAATTAAT
18061471 A
1 A
18061472 ATTTGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.25
8 2 0.08
9 16 0.67
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (9 bp):
ACAATTAAT
Found at i:18061457 original size:16 final size:16
Alignment explanation
Indices: 18061436--18061474 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
18061426 ATTTTGTTAC
18061436 AACAATTAATACAATT
1 AACAATTAATACAATT
18061452 AACAATTAATACAATT
1 AACAATTAATACAATT
*
18061468 AATAATT
1 AACAATT
18061475 TGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:18061565 original size:16 final size:16
Alignment explanation
Indices: 18061544--18061585 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
18061534 AATAATTTGA
*
18061544 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
18061560 TAATTTTAATAATAAT
1 TAATTTTAATAACAAT
*
18061576 TAGTTTTAAT
1 TAATTTTAAT
18061586 TTTATCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:18066520 original size:3 final size:3
Alignment explanation
Indices: 18066452--18066505 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
18066442 ATCATATCAC
18066452 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18066500 TAA TAA
1 TAA TAA
18066506 GGACAATGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18066598 original size:12 final size:12
Alignment explanation
Indices: 18066581--18066608 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18066571 AGAAGGTTGA
18066581 AAAATAATAAAT
1 AAAATAATAAAT
18066593 AAAATAATAAAT
1 AAAATAATAAAT
18066605 AAAA
1 AAAA
18066609 CAACTTATAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:18067762 original size:23 final size:23
Alignment explanation
Indices: 18067736--18067780 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
18067726 GTTTTTGGAT
*
18067736 TTTGATATCTTTTATTTTTATTA
1 TTTGATATCGTTTATTTTTATTA
* * *
18067759 TTTGGTTTGGTTTATTTTTATT
1 TTTGATATCGTTTATTTTTATT
18067781 CGAGCTAGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (23 bp):
TTTGATATCGTTTATTTTTATTA
Done.