Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002900.1 Hibiscus syriacus cultivar Beakdansim tig00005991_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: 258366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1148 original size:19 final size:19
Alignment explanation
Indices: 1065--1148 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 19
1055 TTGGTGCAGA
* *
1065 GGGAATCGATACCCCCATG
1 GGGAACCGATACCCCCTTG
*
1084 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATACCCCC-TT---G
*
1108 GGGAACCGAT-CCCCTCTAG
1 GGGAACCGATACCCC-CTTG
*
1127 GGGAATCGATACCCCCTTG
1 GGGAACCGATACCCCCTTG
1146 GGG
1 GGG
1149 TTTTGGTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
19 16 0.31
20 18 0.35
21 1 0.02
22 5 0.10
23 11 0.21
24 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.18
Consensus pattern (19 bp):
GGGAACCGATACCCCCTTG
Found at i:6127 original size:23 final size:23
Alignment explanation
Indices: 6080--6128 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6070 TTGTGAAACG
** *
6080 TTTATCTTTATTTTTATGCCACA
1 TTTATCTTTATCATTATGACACA
*
6103 TTTATCTTTATCATTATGACTCA
1 TTTATCTTTATCATTATGACACA
6126 TTT
1 TTT
6129 TTCGATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTATCTTTATCATTATGACACA
Found at i:10681 original size:3 final size:3
Alignment explanation
Indices: 10664--10697 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
10654 GGGTATTTTC
10664 TAT T-T TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
10698 TACAATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:11267 original size:15 final size:14
Alignment explanation
Indices: 11231--11257 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11221 ATTAGAACCA
11231 AACACAAAAAAGAG
1 AACACAAAAAAGAG
11245 AACACAAAAAAGA
1 AACACAAAAAAGA
11258 AAGAAACAAA
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:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (14 bp):
AACACAAAAAAGAG
Found at i:18209 original size:104 final size:101
Alignment explanation
Indices: 18053--18375 Score: 299
Period size: 104 Copynumber: 3.2 Consensus size: 101
18043 CTTGAGACAA
* * * *
18053 TTTCT-TTCAAAACAAATTTTGTCTCACTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATT
1 TTTCTCTT-AAAACAAACTTT-CCTCTCTTGAGACATTTTTCCTTTGAAATACAAAATTTGAATT
*
18117 TGTTTCACATTAAACAAAGTTGATCTCATTTGAGATCG
64 TGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCG
* *
18155 CTTTCTCTTAAAACAAACTTATCCT-TGCTTGAGACATTTTTTCCTTTGATATACAAATTTTGAA
1 -TTTCTCTTAAAACAAACTT-TCCTCT-CTTGAGACA-TTTTTCCTTTGAAATACAAAATTTGAA
* * * *
18219 TTTGATTCAC-TTGAAACAAAAATTAATCTCACTTGAGATTG
62 TTTGTTTCACATT-AAAC-AAAGTTGATCTCACTTGAGATCG
* * *
18260 TTATTTTTTCAAAACAAA-TTTCGTCTCGTGTGAGACATTTTTCCTTTGAGAATAC-AAATTTG-
1 TT-TCTCTT-AAAACAAACTTTCCTCTC-T-TGAGACATTTTTCCTTTGA-AATACAAAATTTGA
*
18322 ---T-TTTCATATTAAACAAAGTTGATCTCACTTGAGATCG
61 ATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCG
*
18359 TTT-TCTCAAAAACAAAC
1 TTTCTCT-TAAAACAAAC
18376 GTTGTCTCGC
Statistics
Matches: 183, Mismatches: 22, Indels: 35
0.76 0.09 0.15
Matches are distributed among these distances:
97 10 0.05
98 1 0.01
99 22 0.12
100 8 0.04
101 3 0.02
103 28 0.15
104 47 0.26
105 45 0.25
106 19 0.10
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (101 bp):
TTTCTCTTAAAACAAACTTTCCTCTCTTGAGACATTTTTCCTTTGAAATACAAAATTTGAATTTG
TTTCACATTAAACAAAGTTGATCTCACTTGAGATCG
Found at i:18373 original size:36 final size:36
Alignment explanation
Indices: 18332--18469 Score: 154
Period size: 36 Copynumber: 3.8 Consensus size: 36
18322 TTTTCATATT
**
18332 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAACGTTG-TCTCACTTGAGA-CAATTTCTCTAA
* *
18368 AAACAAACGTTGTCTCGCTTCAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
*** **
18404 AAACAATTTTTGTCTCGTTTGAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
*
18440 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAACGTTGTCTCACTTGAGACAATTT
18470 TCCAAATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.08
36 76 0.87
37 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:18561 original size:31 final size:30
Alignment explanation
Indices: 18507--18565 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
18497 AACAAACATC
*
18507 ATCTTTGAGTAGTTTCTTTTGAAACAAAGG
1 ATCTTTGAGTAGTTTCTTATGAAACAAAGG
18537 ATCTTTGAGTCTA-TTTCTTATGAAACAAA
1 ATCTTTGAG--TAGTTTCTTATGAAACAAA
18566 ACTTTGTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 15 0.58
32 2 0.08
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (30 bp):
ATCTTTGAGTAGTTTCTTATGAAACAAAGG
Found at i:18672 original size:99 final size:100
Alignment explanation
Indices: 18537--18716 Score: 258
Period size: 99 Copynumber: 1.8 Consensus size: 100
18527 GAAACAAAGG
* *
18537 ATCTTTGAGTCTATTTCTTATGAAACAAAACTTTGTCTCTCTTGAGACAGATTT-TATTGAAA-A
1 ATCTTTGAGTATATTTCTTATGAAACAAAACTTTGTCTCTCTTGAGAAAG-TTTATATTGAAAGA
*
18600 ATCTTTGAGTCTGTTTCACCTAAAACAAAATGAAAA
65 ATCTTTGAGTATGTTTCACCTAAAACAAAATGAAAA
* * * *
18636 ATCTTTGAGTATGTTTCTT-TGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTATTTTGAAAGA
1 ATCTTTGAGTATATTTCTTATGA-AACAAAACTTTGTCTCTCTTGAGAAAGTTTATATTGAAAGA
18700 ATCTTTGAGTATGTTTC
65 ATCTTTGAGTATGTTTC
18717 TTTGGAAACA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
98 6 0.08
99 48 0.68
100 17 0.24
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (100 bp):
ATCTTTGAGTATATTTCTTATGAAACAAAACTTTGTCTCTCTTGAGAAAGTTTATATTGAAAGAA
TCTTTGAGTATGTTTCACCTAAAACAAAATGAAAA
Found at i:18801 original size:66 final size:65
Alignment explanation
Indices: 18631--18808 Score: 216
Period size: 64 Copynumber: 2.7 Consensus size: 65
18621 AAAACAAAAT
* *
18631 GAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTATTTTGA
1 GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCATTTTGA
* * * * * *
18696 -AAGAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCACTTTTGTGACAGTTCCTTTTGA
1 GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCATTTTG-
18760 A
65 A
* * **
18761 GAAAAATCTTTAAATATGTTT-TTATGAAAACAAAGGTTTGTCTCTTTT
1 GAAAAATCTTTGAGTATGTTTCTT-TGAAAACAAAATTTTGTCTCTTTT
18809 AAGACAATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
64 55 0.58
65 3 0.03
66 37 0.39
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (65 bp):
GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCATTTTGA
Found at i:18859 original size:30 final size:29
Alignment explanation
Indices: 18816--18969 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 29
18806 TTTAAGACAA
* *
18816 TTTCTCTTAAAACAAACATCTTTGAGATTG
1 TTTCCCTTGAAACAAACATCTTTGAG-TTG
18846 TTTCCC-TGTAAACAAAACCTATCTTTGAGTTTG
1 TTTCCCTTG-AAAC-AAA-C-ATCTTTGAG-TTG
* *
18879 TTTCTCTTGAAACAAA-AGTCTGTGAGTTG
1 TTTCCCTTGAAACAAACA-TCTTTGAGTTG
** * * **
18908 TTTCTTTTGAAATAAAAATCTGCGAGTTG
1 TTTCCCTTGAAACAAACATCTTTGAGTTG
** * *
18937 TTTCTTTTGAAATAAAAATCTTTGAGTTG
1 TTTCCCTTGAAACAAACATCTTTGAGTTG
18966 TTTC
1 TTTC
18970 TTTTGAAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
29 60 0.56
30 17 0.16
31 3 0.03
32 4 0.04
33 21 0.20
34 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTCCCTTGAAACAAACATCTTTGAGTTG
Found at i:18872 original size:33 final size:33
Alignment explanation
Indices: 18833--18895 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
18823 TAAAACAAAC
18833 ATCTTTGAGATTGTTTCCC-TGTAAACAAAACCT
1 ATCTTTGAGATTGTTTCCCTTG-AAACAAAACCT
* *
18866 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA
1 ATCTTTGAGATTGTTTCCCTTGAAACAAAA
18896 GTCTGTGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
ATCTTTGAGATTGTTTCCCTTGAAACAAAACCT
Found at i:18909 original size:29 final size:29
Alignment explanation
Indices: 18866--19007 Score: 164
Period size: 29 Copynumber: 5.0 Consensus size: 29
18856 AACAAAACCT
* * *
18866 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA
1 ATCTGTGAG-TTGTTTCTTTTGAAATAAAA
*
18896 GTCTGTGAGTTGTTTCTTTTGAAATAAAA
1 ATCTGTGAGTTGTTTCTTTTGAAATAAAA
*
18925 ATCTGCGAGTTGTTTCTTTTGAAATAAAA
1 ATCTGTGAGTTGTTTCTTTTGAAATAAAA
*
18954 ATCTTTGAGTTGTTTCTTTTG-AA-AAAA
1 ATCTGTGAGTTGTTTCTTTTGAAATAAAA
* * * *
18981 TTCTGAGACTT-TTTCTTTTGAACTAAA
1 ATCTGTGAGTTGTTTCTTTTGAAATAAA
19008 GTTTTGTTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.09
27 12 0.12
28 5 0.05
29 64 0.66
30 7 0.07
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
ATCTGTGAGTTGTTTCTTTTGAAATAAAA
Found at i:19073 original size:29 final size:30
Alignment explanation
Indices: 19038--19095 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19028 ATTTCGTGAA
19038 AAAATCTTTGAG-TCATTTCTTTTGAAACT
1 AAAATCTTTGAGTTCATTTCTTTTGAAACT
**
19067 AAAATCTTTGAGTTTGTTTCTTTTGAAAC
1 AAAATCTTTGAGTTCATTTCTTTTGAAAC
19096 AAAGTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (30 bp):
AAAATCTTTGAGTTCATTTCTTTTGAAACT
Found at i:19162 original size:91 final size:88
Alignment explanation
Indices: 18950--19174 Score: 264
Period size: 91 Copynumber: 2.5 Consensus size: 88
18940 CTTTTGAAAT
*
18950 AAAAATCTTTGAGT-TGTTTCTTTTGAAAAAAT-TCTGAGACTT-TTTCTTTTGAACTAAAGTTT
1 AAAAATCTTTGAGTCTG-TTCTTTTGAAAAAATCTTTGAGA-TTGTTTCTTTTGAACTAAAGTTT
*
19012 TGTTTCTCTTAAGACAATTTCGTGA
64 TGTCTCTCTTAAGACAATTTCGTGA
*
19037 AAAAATCTTTGAGTCAT-TTCTTTTGAAACTAAAATCTTTGAGTTTGTTTCTTTTGAAAC-AAAG
1 AAAAATCTTTGAGTC-TGTTCTTTTG-AA--AAAATCTTTGAGATTGTTTCTTTTG-AACTAAAG
* *
19100 TTTTGTCTCTCTTGAGACAATTTTTCTTGA
61 TTTTGTCTCTCTTAAGACAA--TTTCGTGA
19130 GAAAAATCTTTGAGTCTGTTCCTTTTG-AAAAATCTTTGAGATTGT
1 -AAAAATCTTTGAGTCTGTT-CTTTTGAAAAAATCTTTGAGATTGT
19175 GTCTCTTAAC
Statistics
Matches: 119, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
87 22 0.18
88 2 0.02
89 1 0.01
90 7 0.06
91 52 0.44
92 3 0.03
93 9 0.08
94 17 0.14
95 6 0.05
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (88 bp):
AAAAATCTTTGAGTCTGTTCTTTTGAAAAAATCTTTGAGATTGTTTCTTTTGAACTAAAGTTTTG
TCTCTCTTAAGACAATTTCGTGA
Found at i:19327 original size:29 final size:29
Alignment explanation
Indices: 19287--19366 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
19277 AAAAAAAATC
*
19287 TTTGAGTTTGTTTCTTTTGAAACATCATA
1 TTTGAGTCTGTTTCTTTTGAAACATCATA
*
19316 TTTGAGTCTGTTTCTTTTGAAACATCATC
1 TTTGAGTCTGTTTCTTTTGAAACATCATA
*
19345 TTTGAGTCGGTTTCTTTTGAAA
1 TTTGAGTCTGTTTCTTTTGAAA
19367 TCATTATCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.50
Consensus pattern (29 bp):
TTTGAGTCTGTTTCTTTTGAAACATCATA
Found at i:19441 original size:40 final size:39
Alignment explanation
Indices: 19386--19461 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
19376 TTATAGATGG
19386 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCA-CCCCCGA
*
19426 CCAGATCTCTTCATCACGTATGAGCCGTGTCACCCC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCACCCC
19462 TAGATAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (39 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCACCCCCGA
Found at i:19575 original size:40 final size:39
Alignment explanation
Indices: 19520--19595 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
19510 CTAAAGATGG
* * *
19520 CCAGAACTTTTCATCACGTATGAGTCGTGTCATCCCCCGA
1 CCAGAACTATTCATCACATATGAGCCGTGTCA-CCCCCGA
*
19560 CCAGATCTATTCATCACATATGAGCCGTGTCACCCC
1 CCAGAACTATTCATCACATATGAGCCGTGTCACCCC
19596 TAGATAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (39 bp):
CCAGAACTATTCATCACATATGAGCCGTGTCACCCCCGA
Found at i:19708 original size:134 final size:134
Alignment explanation
Indices: 19380--19734 Score: 539
Period size: 134 Copynumber: 2.6 Consensus size: 134
19370 TTATCCTTAT
*
19380 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCATCACGT
1 AGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCATCACGT
* ** *
19445 ATGAGCCGTGTCACCCCTAGATAACCAGTCATCCTCATCGTGTAGGAACCGAGTTATCACCATTC
66 ATGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCACAATTC
19510 CTAA
131 CTAA
* * *
19514 AGATGGCCAGAACTTTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTATTCATCACAT
1 AGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCATCACGT
*
19579 ATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACAATTC
66 ATGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCACAATTC
19644 CTAA
131 CTAA
* * * * * *
19648 AGATGGCCAGAACTCTTCATCACGTATAAGTCGTGTCATACCCTGACTAGATTTCCTCATCACGT
1 AGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCATCACGT
* ** *
19713 AGGAATCGTGTCACCCTTAGAT
66 ATGAGCCGTGTCACCCCTAGAT
19735 GACCCGAACT
Statistics
Matches: 199, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 199 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (134 bp):
AGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCATCACGT
ATGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCACAATTC
CTAA
Found at i:23367 original size:42 final size:44
Alignment explanation
Indices: 23289--23389 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
23279 TTGAGAACAA
* * *
23289 AAACGCCGCAATAGGTCAAGATCTATCGCGGCG-TTTTTGGAAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGGAAC
* * * **
23332 AAACGTCGCAAAATGTC-AGATCTATAGCGATGTTTTTTGTCAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGGAAC
23375 AAACGCCGCAAAAGG
1 AAACGCCGCAAAAGG
23390 GCTCATGATA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 12 0.26
43 35 0.74
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGACGTTTTTTGGAAC
Found at i:25143 original size:253 final size:252
Alignment explanation
Indices: 24695--25200 Score: 949
Period size: 253 Copynumber: 2.0 Consensus size: 252
24685 AAACTAAGAT
* *
24695 TTATCCCTTAAAAAGCTCACATGGACATCGCAAATTGAAACAAAAATATGCAGGAACAAAAATTA
1 TTATCCCTTAAAAAGCTCACATGGACATCACAAATTGAAACAAAAAAATGCAGGAACAAAAATTA
24760 ACGGAACTAGACAACTTAGTTCTTCTACTTATACAGTGGATTAATATGATTAATAAATTTATGGA
66 ACGGAACTAGACAACTTAGTTCTTCTACTTATACAGTGGATTAATATGATTAATAAATTTATGGA
* *
24825 TTTTAATTTTCTATTGTACTAATCTTTTATGCAATAGACTTGAAAATGGTGTTAACCAAATGAAA
131 TTTTAATTTTCTATTGTACTAATCTTTTATGCAAAAGACTTGAAAATGGTCTTAACCAAATGAAA
24890 ACTACCAACACAAAAGATTAAAGCATCACAAAAAAAATGCTAGAACAGACTACAATTA
196 ACTACCAACACAAAAGATTAAAGCATCAC-AAAAAAATGCTAGAACAGACTACAATTA
*
24948 TTATCCCTTAAAAAGCTCACATGGACATCACAAATTGAAACAAAAAAATTCAGGAACAAAAATTA
1 TTATCCCTTAAAAAGCTCACATGGACATCACAAATTGAAACAAAAAAATGCAGGAACAAAAATTA
25013 ACGGAACTAGACAACTTAGTTCTTCTACTTATACAGTGGATTAATATGATTAATAAATTTATGGA
66 ACGGAACTAGACAACTTAGTTCTTCTACTTATACAGTGGATTAATATGATTAATAAATTTATGGA
25078 TTTTAATTTTCTATTGTACTAATCTTTTATGCAAAAGACTTGAAAATGGTCTTAACCAAATGAAA
131 TTTTAATTTTCTATTGTACTAATCTTTTATGCAAAAGACTTGAAAATGGTCTTAACCAAATGAAA
*
25143 ACTACCAACACAAAATATTAAAGCATCACAAAAAAATGCTAGAACAGACTACAATTA
196 ACTACCAACACAAAAGATTAAAGCATCACAAAAAAATGCTAGAACAGACTACAATTA
25200 T
1 T
25201 GGATGTTACT
Statistics
Matches: 247, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
252 29 0.12
253 218 0.88
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (252 bp):
TTATCCCTTAAAAAGCTCACATGGACATCACAAATTGAAACAAAAAAATGCAGGAACAAAAATTA
ACGGAACTAGACAACTTAGTTCTTCTACTTATACAGTGGATTAATATGATTAATAAATTTATGGA
TTTTAATTTTCTATTGTACTAATCTTTTATGCAAAAGACTTGAAAATGGTCTTAACCAAATGAAA
ACTACCAACACAAAAGATTAAAGCATCACAAAAAAATGCTAGAACAGACTACAATTA
Found at i:26636 original size:21 final size:21
Alignment explanation
Indices: 26610--26650 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
26600 TGAGATCGAC
*
26610 AGTGAAGCAGATGGGTTTGGT
1 AGTGAAGCAGACGGGTTTGGT
26631 AGTGAAGCAGACGGGTTTGG
1 AGTGAAGCAGACGGGTTTGG
26651 GTAAACGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.44, T:0.24
Consensus pattern (21 bp):
AGTGAAGCAGACGGGTTTGGT
Found at i:26859 original size:41 final size:41
Alignment explanation
Indices: 26740--26932 Score: 188
Period size: 41 Copynumber: 4.7 Consensus size: 41
26730 TACAAGCCAC
** * * * * *
26740 GTTTGTATAAAAATACCACTAAAGTATAAATGTATAACGGT
1 GTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGT
* * *
26781 GTTTGTATGAAGAACGCCACTAAAATACAAGTGTATAGCGAT
1 GTTTGTAT-AAAAACGCCACTAAAATACAAGTATATAGCGGT
* * * *
26823 GTTTGTATAAAAACGTCACCAAAGTACAAGTCTATAGCGGT
1 GTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGT
* * * *
26864 ATTTGTATACAAACGCCACTAAAATACGAGTATTTAGCGGT
1 GTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGT
* * *
26905 GTTTGAATAAAAAAGCCACTAAAGTACA
1 GTTTGTATAAAAACGCCACTAAAATACA
26933 CTTTATTGTG
Statistics
Matches: 123, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
41 90 0.73
42 33 0.27
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (41 bp):
GTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGT
Found at i:26908 original size:82 final size:83
Alignment explanation
Indices: 26740--26932 Score: 230
Period size: 82 Copynumber: 2.3 Consensus size: 83
26730 TACAAGCCAC
* * *
26740 GTTTGTATAAAAATA-CCACTAAAGTATAAATGTATAACGGTGTTTGTATGAAGAACGCCACTAA
1 GTTTGTATAAAAA-AGCCACTAAAGTACAAATCTATAACGGTATTTGTATGAAGAACGCCACTAA
*
26804 AATACAAGTGTATAGCGAT
65 AATACAAGTATATAGCGAT
* * * * *
26823 GTTTGTATAAAAACGTCACCAAAGTACAAGTCTATAGCGGTATTTGTAT-ACA-AACGCCACTAA
1 GTTTGTATAAAAAAGCCACTAAAGTACAAATCTATAACGGTATTTGTATGA-AGAACGCCACTAA
* * *
26886 AATACGAGTATTTAGCGGT
65 AATACAAGTATATAGCGAT
*
26905 GTTTGAATAAAAAAGCCACTAAAGTACA
1 GTTTGTATAAAAAAGCCACTAAAGTACA
26933 CTTTATTGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
82 51 0.55
83 41 0.45
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (83 bp):
GTTTGTATAAAAAAGCCACTAAAGTACAAATCTATAACGGTATTTGTATGAAGAACGCCACTAAA
ATACAAGTATATAGCGAT
Found at i:32436 original size:3 final size:3
Alignment explanation
Indices: 32424--32452 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
32414 ATTAGCAGTC
32424 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32453 CAAACGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:33146 original size:17 final size:17
Alignment explanation
Indices: 33124--33158 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33114 TCGTTAAAAC
33124 ACCCTTCATAACCTTCA
1 ACCCTTCATAACCTTCA
33141 ACCCTTCATAACCTTCA
1 ACCCTTCATAACCTTCA
33158 A
1 A
33159 GCTACACATG
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:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
ACCCTTCATAACCTTCA
Found at i:33303 original size:20 final size:20
Alignment explanation
Indices: 33258--33303 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
33248 CCCCTTGATT
33258 ACAACCTTCCCCATAAAACA
1 ACAACCTTCCCCATAAAACA
33278 AC-ACCTCTCCCC-TCAAAA-A
1 ACAACCT-TCCCCAT-AAAACA
33297 ACAACCT
1 ACAACCT
33304 ACACATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.15
Consensus pattern (20 bp):
ACAACCTTCCCCATAAAACA
Found at i:36559 original size:20 final size:21
Alignment explanation
Indices: 36524--36563 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
36514 TCATTATAAA
36524 TATCAATACTTCTCCACAAAG
1 TATCAATACTTCTCCACAAAG
*
36545 TATCAA-ACTTTTCCACAAA
1 TATCAATACTTCTCCACAAA
36564 TACTAGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.30
Consensus pattern (21 bp):
TATCAATACTTCTCCACAAAG
Found at i:36732 original size:73 final size:73
Alignment explanation
Indices: 36654--36819 Score: 183
Period size: 73 Copynumber: 2.3 Consensus size: 73
36644 CATCAACTAG
* * * ** *
36654 TTCAATATCTAAAAGTATCAATTATCATCACATAAGTATCGATTTTTTAAATTTTGATA-TT-TT
1 TTCAATATTTAAAAGTATCAATTATCACCACATAAGTATCGATATTTTAAATTCCGA-ACTTATC
36717 TATTAACTTT
65 T-TTAACTTT
* * * * * *
36727 TTCAATTTTTAAAAGTATCAATTCTTACCATATAAGTATTGATATTTTAACTTCCGAACTTATCT
1 TTCAATATTTAAAAGTATCAATTATCACCACATAAGTATCGATATTTTAAATTCCGAACTTATCT
36792 TTAACTTT
66 TTAACTTT
36800 TTCAATATTTATAAAGTATC
1 TTCAATATTTA-AAAGTATC
36820 GATAACAATA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
72 1 0.01
73 66 0.86
74 10 0.13
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (73 bp):
TTCAATATTTAAAAGTATCAATTATCACCACATAAGTATCGATATTTTAAATTCCGAACTTATCT
TTAACTTT
Found at i:36931 original size:18 final size:18
Alignment explanation
Indices: 36908--36963 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
36898 ATATTCATAA
36908 TATTTTTAACTTTTAACT
1 TATTTTTAACTTTTAACT
*
36926 TA-TTTT--CTTCATAA--
1 TATTTTTAACTT-TTAACT
36940 TATTTTTAACTTTTAACT
1 TATTTTTAACTTTTAACT
36958 TATTTT
1 TATTTT
36964 CTTTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
16 6 0.20
17 7 0.23
18 8 0.27
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTAACTTTTAACT
Found at i:36937 original size:32 final size:32
Alignment explanation
Indices: 36901--36966 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
36891 CTTATATATA
36901 TTCATAATATTTTTAACTTTTAACTTATTTTC
1 TTCATAATATTTTTAACTTTTAACTTATTTTC
36933 TTCATAATATTTTTAACTTTTAACTTATTTTC
1 TTCATAATATTTTTAACTTTTAACTTATTTTC
36965 TT
1 TT
36967 TCAATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (32 bp):
TTCATAATATTTTTAACTTTTAACTTATTTTC
Found at i:37710 original size:264 final size:262
Alignment explanation
Indices: 37240--37963 Score: 916
Period size: 264 Copynumber: 2.7 Consensus size: 262
37230 CACAACCTAA
* * *
37240 TTTCTTTATGAACCATAATATTCTCGAGAACAACCTATTTTATTAATAAAAATATTAACATTACG
1 TTTCTTTATGAACCATAACATTCTTG-GAACAACCTATTTTATTAATAAAAATGTTAACATTAC-
* * *
37305 A-A-TGATAACCTATTTCTTAGTGAACCGGGACATTATTGGGTGCAACCGTATTTCTTATATATA
64 ATATTG-TAACATATTTCTTAGTGAACCTGGACATTATTGGGTGCAATCGTATTTCTTATATATA
* * * * *
37368 TTCATAACATTTTAAGCTTTTAACTTGTTTTCTCATTGTGGGAAAATTCAAGGTTCCATCAGCTT
128 TTCATAACATTTTAA-CTTTTAACTTATTTTCTTATTGTGGGAATATCCAAGGCTCCATCAGCTT
* * * * *
37433 AAAGTCTAATAATATTTTGGGCACAACCCATTTTATTATTAAAAACATTAAGATTCGAGATTGCA
192 AAACTCTAATAATATTTTAGACACAACCCATTTTATTATAAAAAACATTAAGATTCAAGATTGCA
37498 ACATGC
257 ACATGC
* * *
37504 TTTCTTTGTGAACCATAACATTCTTGGATACAACTTATTTTATTAATAAAAATGTTAAAATTACA
1 TTTCTTTATGAACCATAACATTCTTGGA-ACAACCTATTTTATTAATAAAAATGTTAACATTACA
*
37569 TATTGTAACATATTTCTTAGTGAACCTGGACATTATTGGGTGCAATCGTATTTATTATATATATT
65 TATTGTAACATATTTCTTAGTGAACCTGGACATTATTGGGTGCAATCGTATTTCTTATATATATT
* * *
37634 CATTACATTTTCAACTTTTAACTTATTTCCTTATTGTGGGAATATCCAAGGCTCCATTAGCTTAA
130 CATAACATTTT-AACTTTTAACTTATTTTCTTATTGTGGGAATATCCAAGGCTCCATCAGCTTAA
* ** * * *
37699 ACTCTAATAATATTTTATACGTAACCTATTTTATTATAAAAAATATTAAGATTCAAGATTGCAAT
194 ACTCTAATAATATTTTAGACACAACCCATTTTATTATAAAAAACATTAAGATTCAAGATTGCAAC
*
37764 ATGT
259 ATGC
* * *
37768 TTTCTTAATGAACCATGACATTCTTGG-GCGGAACCTATTTTATTAATAAAAATGTTAACATTAC
1 TTTCTTTATGAACCATAACATTCTTGGAAC--AACCTATTTTATTAATAAAAATGTTAACATTAC
* * * *
37832 ATATTGTAACATATTTCTTAGTGAACCAT-GATATTATTGAGCGAAATCGTATTTCTTATATATA
64 ATATTGTAACATATTTCTTAGTGAACC-TGGACATTATTGGGTGCAATCGTATTTCTTATATATA
* * * * ** * * *
37896 TTCATAATATTTTTAGTTATTAACTTATTTTCTTATCGTCAGAATGTCTAAGGCTCCATCAACTT
128 TTCATAACATTTTAACTT-TTAACTTATTTTCTTATTGTGGGAATATCCAAGGCTCCATCAGCTT
37961 AAA
192 AAA
37964 ATTGACAATC
Statistics
Matches: 399, Mismatches: 53, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
262 1 0.00
263 6 0.02
264 387 0.97
265 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (262 bp):
TTTCTTTATGAACCATAACATTCTTGGAACAACCTATTTTATTAATAAAAATGTTAACATTACAT
ATTGTAACATATTTCTTAGTGAACCTGGACATTATTGGGTGCAATCGTATTTCTTATATATATTC
ATAACATTTTAACTTTTAACTTATTTTCTTATTGTGGGAATATCCAAGGCTCCATCAGCTTAAAC
TCTAATAATATTTTAGACACAACCCATTTTATTATAAAAAACATTAAGATTCAAGATTGCAACAT
GC
Found at i:40565 original size:31 final size:31
Alignment explanation
Indices: 40527--40635 Score: 173
Period size: 31 Copynumber: 3.5 Consensus size: 31
40517 AGGGTCGAGG
*
40527 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
40558 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
40589 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
40620 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
40636 TGAAATCTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:40647 original size:62 final size:62
Alignment explanation
Indices: 40527--40651 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
40517 AGGGTCGAGG
* * * **
40527 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTTGAAACATATGGACT
*
40589 GTTTACCTATGTTCTTCGGGACATATTGACTGATTACCTAGGTTCTTTGAAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTTGAAA-CATATGGACT
40651 G
1 G
40652 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTTGAAACATATGGACT
Found at i:42627 original size:12 final size:12
Alignment explanation
Indices: 42569--42620 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
42559 AACTAGCCGA
42569 GGTGGAGATGAT
1 GGTGGAGATGAT
*
42581 GGTGGTGATGAT
1 GGTGGAGATGAT
*
42593 GGTGGAGGTAGA-
1 GGTGGAGAT-GAT
42605 GGTGGAGATGAT
1 GGTGGAGATGAT
42617 GGTG
1 GGTG
42621 ATGATGAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 30 0.88
13 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.54, T:0.25
Consensus pattern (12 bp):
GGTGGAGATGAT
Found at i:44134 original size:27 final size:27
Alignment explanation
Indices: 44104--44157 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
44094 TAAATTTGGA
44104 CTGTAGAAAACTGATGAACTTGAGGGG
1 CTGTAGAAAACTGATGAACTTGAGGGG
44131 CTGTAGAAAACTGATGAACTTGAGGGG
1 CTGTAGAAAACTGATGAACTTGAGGGG
44158 TTGTTGGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (27 bp):
CTGTAGAAAACTGATGAACTTGAGGGG
Found at i:53326 original size:20 final size:21
Alignment explanation
Indices: 53289--53329 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
53279 GATATTTTTA
**
53289 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
53310 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
53330 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:55617 original size:23 final size:24
Alignment explanation
Indices: 55586--55636 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
55576 TTGAATTGCA
*
55586 CATTT-TGCATTCTT-ATTTTTTT
1 CATTTATGCATTCTTCATATTTTT
*
55608 CATTTATGCATTTTTCATATTTTT
1 CATTTATGCATTCTTCATATTTTT
55632 -ATTTA
1 CATTTA
55637 ATTACTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.65
Consensus pattern (24 bp):
CATTTATGCATTCTTCATATTTTT
Found at i:60536 original size:83 final size:83
Alignment explanation
Indices: 60393--61325 Score: 1498
Period size: 83 Copynumber: 11.2 Consensus size: 83
60383 ACATTAAATG
60393 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
60458 AACCAATCAGTGAGTTTA
66 AACCAATCAGTGAGTTTA
* *
60476 GAACATGAATGTGCTCATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
60541 AACCAATCAGTGAGTTTA
66 AACCAATCAGTGAGTTTA
*
60559 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
60623 GAACCAATCAGTGAGTTTA
65 GAACCAATCAGTGAGTTTA
*
60642 GAACATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
60707 AACCAATCAGTGAGTTTA
66 AACCAATCAGTGAGTTTA
* *
60725 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTCTGGTTTGGCA
1 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
60789 GAACCAATCAGTGAGTTTA
65 GAACCAATCAGTGAGTTTA
*
60808 GAACATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
60873 AACCAATCAGTGAGTTTA
66 AACCAATCAGTGAGTTTA
* *
60891 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCA
1 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
* * *
60955 GAACCAATCATTGAATTTG
65 GAACCAATCAGTGAGTTTA
*
60974 GAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
* * *
61038 GAACCAATCATTGAATTTG
65 GAACCAATCAGTGAGTTTA
* * **
61057 GAAGATGAATGTGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGATAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
61122 AACCAATCATTGAATTTA
66 AACCAATCAGTGAGTTTA
* * *
61140 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTAGACAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
61205 AACCAATCATTGAATTTA
66 AACCAATCAGTGAGTTTA
*
61223 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAT-ACA
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-TGGCA
* * *
61287 TAACCAATCATTGAATTTA
65 GAACCAATCAGTGAGTTTA
*
61306 GAAGATGAATTTGCTCATAG
1 GAAGATGAATGTGCTCATAG
61326 GAGAAATAAG
Statistics
Matches: 808, Mismatches: 33, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
82 7 0.01
83 796 0.99
84 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACCAATCAGTGAGTTTA
Found at i:63851 original size:22 final size:22
Alignment explanation
Indices: 63822--63876 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
63812 ATCTACACTC
*
63822 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
63844 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
63866 TTCAAAGATGA
1 TTCAAAGATGA
63877 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:64593 original size:113 final size:113
Alignment explanation
Indices: 64279--65061 Score: 1184
Period size: 113 Copynumber: 7.0 Consensus size: 113
64269 GCAAAGTTTA
** * **
64279 AATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * **
64342 AAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * *
64391 AATCCATCATTCGATGGATTGA-CATTTCCATAG-AAGTTCATAATGAGAAGAACTCATATGAAG
1 AATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
64454 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
*
64503 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
64568 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
*
64616 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
64681 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* *
64729 AATCTATTATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
64794 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT-TG
* * * *
64842 AATTCATCACTTGATGGATCAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
64906 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * *
64955 AATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
65019 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
65062 GCATAATTCT
Statistics
Matches: 628, Mismatches: 34, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
111 2 0.00
112 194 0.31
113 426 0.68
114 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
Found at i:65567 original size:76 final size:76
Alignment explanation
Indices: 65467--65801 Score: 589
Period size: 76 Copynumber: 4.4 Consensus size: 76
65457 ACTATTTCCC
* * *
65467 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
65532 AAGCCTTCGGG
66 AAGCCTTAGGG
*
65543 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
65608 AAGCCTTCGGG
66 AAGCCTTAGGG
65619 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
65684 AAACCTTAGGG
66 AAGCCTTAGGG
* *
65695 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
65760 AAGCCTTAGGG
66 AAGCCTTAGGG
65771 TCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTT
65802 TCAACATTTC
Statistics
Matches: 247, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 247 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGG
Found at i:65939 original size:3 final size:3
Alignment explanation
Indices: 65931--65971 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
65921 TCAGTTCATT
*
65931 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65972 AATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:67386 original size:20 final size:21
Alignment explanation
Indices: 67349--67389 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
67339 GATATTTTTA
**
67349 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
67370 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
67390 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:69540 original size:18 final size:18
Alignment explanation
Indices: 69519--69555 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
69509 GATGGTGGTA
* *
69519 ATGACAATGATGATGAAG
1 ATGACAACGACGATGAAG
69537 ATGACAACGACGATGAAG
1 ATGACAACGACGATGAAG
69555 A
1 A
69556 ATCTTCAGAT
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:0.46, C:0.11, G:0.27, T:0.16
Consensus pattern (18 bp):
ATGACAACGACGATGAAG
Found at i:75255 original size:22 final size:22
Alignment explanation
Indices: 75227--75285 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
75217 CAACTGCTTA
*
75227 TTCTTCCTTCTCCTTATTTTTC
1 TTCTTCCTCCTCCTTATTTTTC
75249 TTCTTCCTCCTCCTTATTTTTC
1 TTCTTCCTCCTCCTTATTTTTC
75271 TTCTTCCTCCTCCTT
1 TTCTTCCTCCTCCTT
75286 GCAACAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCTTCCTCCTCCTTATTTTTC
Found at i:82134 original size:26 final size:26
Alignment explanation
Indices: 82085--82134 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
82075 TTTTAACATA
* *
82085 TACTGAAATAAGTTGCTCATCTTTTT
1 TACTGAAATAAGTTGCTAAACTTTTT
82111 TACTGAAATAAGCTT-CTAAACTTT
1 TACTGAAATAAG-TTGCTAAACTTT
82135 AATTTATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (26 bp):
TACTGAAATAAGTTGCTAAACTTTTT
Found at i:86680 original size:25 final size:25
Alignment explanation
Indices: 86625--86681 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
86615 TAGATCTAGT
* * * **
86625 ATTGCACTTGAAAGTGCCTCGTATT
1 ATTGCACTCGAAAATGCCTCATAGG
*
86650 AATGCACTCGAAAATGCCTCATAGG
1 ATTGCACTCGAAAATGCCTCATAGG
86675 ATTGCAC
1 ATTGCAC
86682 CATAGGTTTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (25 bp):
ATTGCACTCGAAAATGCCTCATAGG
Found at i:89086 original size:24 final size:24
Alignment explanation
Indices: 89059--89104 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
89049 TGTCTGTTGG
89059 ACTTGTTTTTGGATAATTTATCGA
1 ACTTGTTTTTGGATAATTTATCGA
89083 ACTTGTTTTTGGATAATTTATC
1 ACTTGTTTTTGGATAATTTATC
89105 AATATCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
ACTTGTTTTTGGATAATTTATCGA
Found at i:89293 original size:35 final size:34
Alignment explanation
Indices: 89235--89309 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
89225 ACACTATGAG
*
89235 TTCTAACAGCTACCAATATCTACTTTTCAAATAT
1 TTCTAACAGCTACCAATAACTACTTTTCAAATAT
* *
89269 TTCTAATCGGCTATCAATAACTACTTTTCAAATAT
1 TTCTAA-CAGCTACCAATAACTACTTTTCAAATAT
89304 TTCTAA
1 TTCTAA
89310 AAGACTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (34 bp):
TTCTAACAGCTACCAATAACTACTTTTCAAATAT
Found at i:96637 original size:30 final size:32
Alignment explanation
Indices: 96581--96645 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
96571 TCAAAAAACA
96581 TAAAATATAGTCACTTTCATTTTTTATTTAAT
1 TAAAATATAGTCACTTTCATTTTTTATTTAAT
96613 TAAAATATAGTCACTTT-A-TTTTTATTTAAT
1 TAAAATATAGTCACTTTCATTTTTTATTTAAT
96643 TAA
1 TAA
96646 GATGTGCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 15 0.45
31 1 0.03
32 17 0.52
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (32 bp):
TAAAATATAGTCACTTTCATTTTTTATTTAAT
Found at i:96868 original size:25 final size:24
Alignment explanation
Indices: 96810--96869 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
96800 ATGTTTTTAA
96810 ATTAAGTTAATAAAAAAAATATTT
1 ATTAAGTTAATAAAAAAAATATTT
*
96834 AATAAGTTAATATACAAAAAATA-TT
1 ATTAAGTTAATA-A-AAAAAATATTT
*
96859 ATTAATTTAAT
1 ATTAAGTTAAT
96870 TATTTATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.35
25 12 0.39
26 8 0.26
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTAAGTTAATAAAAAAAATATTT
Found at i:99765 original size:15 final size:15
Alignment explanation
Indices: 99747--99824 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 15
99737 AAAAAGGCCA
99747 AAATAAAAAATGAAT
1 AAATAAAAAATGAAT
*
99762 AAATAAAGGAAATAAAT
1 AAATAAA--AAATGAAT
*
99779 ATGCAT-AAAAATGAAAT
1 A--AATAAAAAATG-AAT
*
99796 GAAA-AAAAAATAAAT
1 -AAATAAAAAATGAAT
*
99811 AACTAAAAAATGAA
1 AAATAAAAAATGAA
99825 AGTAATAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
14 2 0.04
15 19 0.40
16 11 0.23
17 11 0.23
18 3 0.06
19 2 0.04
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (15 bp):
AAATAAAAAATGAAT
Found at i:99907 original size:15 final size:15
Alignment explanation
Indices: 99882--99937 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
99872 AAATAAAATA
99882 ATAAGTAAAAATATAT
1 ATAA-TAAAAATATAT
* *
99898 ATAATAAAAATGTAC
1 ATAATAAAAATATAT
*
99913 ATAAGAAAAATATAAT
1 ATAATAAAAATAT-AT
*
99929 ACAATAAAA
1 ATAATAAAA
99938 TACATGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (15 bp):
ATAATAAAAATATAT
Found at i:99941 original size:28 final size:28
Alignment explanation
Indices: 99873--99953 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 28
99863 ATAATAATCA
*
99873 AATAAAATA-ATAAGTAAAAATAT-ATAT
1 AATAAAATACATAAG-AAAAATATAATAC
99900 AATAAAAATGTACATAAGAAAAATATAATAC
1 AAT-AAAA--TACATAAGAAAAATATAATAC
*
99931 AATAAAATACATGA-AAAAATATA
1 AATAAAATACATAAGAAAAATATA
99954 GCTAAATACA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 12 0.26
28 10 0.21
30 14 0.30
31 11 0.23
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (28 bp):
AATAAAATACATAAGAAAAATATAATAC
Found at i:99961 original size:27 final size:27
Alignment explanation
Indices: 99918--99984 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
99908 TGTACATAAG
99918 AAAAATATAATACAATA-AAATACATGA
1 AAAAATATAATACAATACAAATA-ATGA
* *
99945 AAAAATATAGCTA-AATACATATAATGA
1 AAAAATATA-ATACAATACAAATAATGA
*
99972 GAAAATAATAATA
1 AAAAAT-ATAATA
99985 AAAATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAAATATAATACAATACAAATAATGA
Found at i:100143 original size:28 final size:32
Alignment explanation
Indices: 100056--100143 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
100046 AATATAATTA
*
100056 AATAATAATAATGATATATATATATATATATATAGT
1 AATAATAA-AATGA-A-A-ATATATATATATATAGC
*
100092 AATAATAAAATGAAAATATGTATATATATA-C
1 AATAATAAAATGAAAATATATATATATATAGC
*
100123 AA-AATAAGAT-AAAATA-ATATA
1 AATAATAAAATGAAAATATATATA
100144 ATTATTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.08
29 6 0.12
30 7 0.15
31 2 0.04
32 14 0.29
33 1 0.02
34 1 0.02
35 5 0.10
36 8 0.17
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (32 bp):
AATAATAAAATGAAAATATATATATATATAGC
Found at i:102071 original size:3 final size:3
Alignment explanation
Indices: 102063--102094 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
102053 AATAAAATAG
102063 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
102095 AAACAGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:102256 original size:17 final size:17
Alignment explanation
Indices: 102230--102262 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
102220 GTATATATAT
*
102230 ATATATATAAATAATAC
1 ATATAGATAAATAATAC
102247 ATATAGATAAATAATA
1 ATATAGATAAATAATA
102263 GAGAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAGATAAATAATAC
Found at i:102847 original size:37 final size:37
Alignment explanation
Indices: 102797--102908 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
102787 TTACTTATGG
* *
102797 ATCATATTTTTAGGAATTTGAATCATAGTAAAACTTT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
102834 ATCATACTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
102871 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
102908 A
1 A
102909 ACGTTATGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:104235 original size:110 final size:110
Alignment explanation
Indices: 104052--104590 Score: 889
Period size: 110 Copynumber: 4.9 Consensus size: 110
104042 TTGTGTCGCT
* * *
104052 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTAT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
104117 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* **
104162 TCGAGTCCAATATCCTTCGTTGCAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
104227 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
104272 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
104337 TCATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
104382 TCGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
104447 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * * * **
104492 TCGAGTTCAATATCCTTCACAGTGAATTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTAA
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
104557 TGACCGTCAGTCGCCCCTTCGCTGTGAAGTTGAG
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAG
104591 AAACCACCAT
Statistics
Matches: 399, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 399 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:108304 original size:25 final size:25
Alignment explanation
Indices: 108264--108318 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
108254 AAGAAGATAA
108264 AAAAATAAATATAA-GGAATAAAAAT
1 AAAAATAAATATAAGGGAA-AAAAAT
*
108289 AAAAATGAAATA-AAGGGGAAAAAAT
1 AAAAAT-AAATATAAGGGAAAAAAAT
108314 AAAAA
1 AAAAA
108319 AAAGGGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (25 bp):
AAAAATAAATATAAGGGAAAAAAAT
Found at i:108319 original size:27 final size:26
Alignment explanation
Indices: 108260--108320 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
108250 TGTAAAGAAG
108260 ATAAAAAAATAAATATAAGGAATAAA
1 ATAAAAAAATAAATATAAGGAATAAA
*
108286 A-ATAAAAATGAAATA-AAGGGGAA-AAA
1 ATAAAAAAAT-AAATATAA--GGAATAAA
108312 ATAAAAAAA
1 ATAAAAAAA
108321 AGGGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 9 0.31
26 10 0.34
27 10 0.34
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (26 bp):
ATAAAAAAATAAATATAAGGAATAAA
Found at i:108547 original size:21 final size:23
Alignment explanation
Indices: 108523--108570 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
108513 ATACGTATAG
108523 ATAAATAATAG-AGAGAAAT-AA
1 ATAAATAATAGTAGAGAAATGAA
* *
108544 AT-AATAATGGTAGGGAAATGAA
1 ATAAATAATAGTAGAGAAATGAA
108566 ATAAA
1 ATAAA
108571 ATAAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 4 0.18
23 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (23 bp):
ATAAATAATAGTAGAGAAATGAA
Found at i:108729 original size:17 final size:20
Alignment explanation
Indices: 108694--108730 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
108684 AAGTATATAT
108694 AATAATAATAGTAAGAAAAA
1 AATAATAATAGTAAGAAAAA
108714 AATAA-AATA-TAA-AAAAA
1 AATAATAATAGTAAGAAAAA
108731 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 4 0.24
20 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAATAATAGTAAGAAAAA
Found at i:109052 original size:22 final size:22
Alignment explanation
Indices: 109027--109102 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
109017 GTGTGTACCC
109027 GGATCCTATTTATATTGCTTAT
1 GGATCCTATTTATATTGCTTAT
* *
109049 GGATCTTATTTATAATGCTT-T
1 GGATCCTATTTATATTGCTTAT
*
109070 -GATGGCTATTTATATTGCTTAT
1 GGAT-CCTATTTATATTGCTTAT
109092 GGATCCTATTT
1 GGATCCTATTT
109103 TTAAGAGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.07
21 14 0.31
22 25 0.56
23 3 0.07
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (22 bp):
GGATCCTATTTATATTGCTTAT
Found at i:109139 original size:37 final size:37
Alignment explanation
Indices: 109098--109168 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
109088 TTATGGATCC
*
109098 TATTTTTAAGAGTTTGAATTATAGTAAAACTCTATCA
1 TATTTTTAAGAGTTTGAATCATAGTAAAACTCTATCA
* *
109135 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAAGAGTTTGAATCATAGTAAAACTCTA
109169 ACGTTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (37 bp):
TATTTTTAAGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:114539 original size:13 final size:13
Alignment explanation
Indices: 114521--114546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
114511 GTCTGATTCG
114521 TCACGGTCAAATT
1 TCACGGTCAAATT
114534 TCACGGTCAAATT
1 TCACGGTCAAATT
114547 ATTAAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TCACGGTCAAATT
Found at i:115365 original size:15 final size:16
Alignment explanation
Indices: 115347--115380 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
115337 TTTAAAAATA
115347 TTTTTA-TTATTATAT
1 TTTTTATTTATTATAT
*
115362 TTTTTATTTATTTTAT
1 TTTTTATTTATTATAT
115378 TTT
1 TTT
115381 GATAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTTATTATAT
Found at i:115599 original size:2 final size:2
Alignment explanation
Indices: 115594--115626 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
115584 TTTTTACTAG
115594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115627 ATCTCAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116901 original size:20 final size:20
Alignment explanation
Indices: 116872--117104 Score: 118
Period size: 20 Copynumber: 11.5 Consensus size: 20
116862 GATTTTCCAT
* *
116872 AATCGTAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
116892 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
116912 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* *
116933 AATCGCAACGCGTATTC-ATA
1 AATCGCAACGCGAATACGA-A
116953 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * *
116974 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
116994 AATTGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
117014 AATCCCAACGC--ATATCTGTA
1 AATCGCAACGCGAATA-C-GAA
* *
117034 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
117054 AATCGCAATGCGCATCCGTA
1 AATCGCAACGCGAATACGAA
117074 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
117095 AATCGCAACG
1 AATCGCAACG
117105 TGATTTTTAA
Statistics
Matches: 164, Mismatches: 35, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
18 3 0.02
19 4 0.02
20 107 0.65
21 46 0.28
22 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:116935 original size:41 final size:41
Alignment explanation
Indices: 116890--117104 Score: 215
Period size: 41 Copynumber: 5.3 Consensus size: 41
116880 CGCGAATATG
* ** *
116890 AAAATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGTATTCAT-A-AATCGCAACGACAATACGT
116931 AAAATCGCAACGCGTATTCATAAATCGCAACGACAATACGT
1 AAAATCGCAACGCGTATTCATAAATCGCAACGACAATACGT
* * * * *
116972 AAAATCGTAACGCGTATCCGTAAATTGCAACGAGAATACGT
1 AAAATCGCAACGCGTATTCATAAATCGCAACGACAATACGT
* * * *
117013 -AAATCCCAACGCATA-TCTGTAAATCGCAACGAGAATACGT
1 AAAATCGCAACGCGTATTC-ATAAATCGCAACGACAATACGT
* * * *
117053 -AAATCGCAATGCGCATCCGTAAATCGCAACGACAATACGT
1 AAAATCGCAACGCGTATTCATAAATCGCAACGACAATACGT
117093 AAAATCGCAACG
1 AAAATCGCAACG
117105 TGATTTTTAA
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 65 0.44
41 76 0.51
42 5 0.03
43 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGTATTCATAAATCGCAACGACAATACGT
Found at i:117035 original size:40 final size:41
Alignment explanation
Indices: 116913--117104 Score: 253
Period size: 40 Copynumber: 4.7 Consensus size: 41
116903 GATTCTGACT
* * * *
116913 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATTCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
116954 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
116995 ATTGCAACGAGAATACGT-AAATCCCAACGCATATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
117035 ATCGCAACGAGAATACGT-AAATCGCAATGCGCATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
117075 ATCGCAACGACAATACGTAAAATCGCAACG
1 ATCGCAACGAGAATACGTAAAATCGCAACG
117105 TGATTTTTAA
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 69 0.53
41 61 0.47
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:117689 original size:20 final size:20
Alignment explanation
Indices: 117664--117754 Score: 123
Period size: 20 Copynumber: 4.5 Consensus size: 20
117654 TTCTAAACTT
*
117664 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
117684 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
117704 ACCATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
117725 AAAATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
117744 AAAATCGCAAC
1 AAAATCGCAAC
117755 GAGATAATCG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.25
20 31 0.49
21 16 0.25
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:117743 original size:40 final size:40
Alignment explanation
Indices: 117664--117758 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
117654 TTCTAAACTT
117664 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
**
117704 ACCATCGCAACGAGAGAAATGAAAATCGCAACACG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
117744 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
117759 TAATCGCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 29 0.59
41 20 0.41
ACGTcount: A:0.52, C:0.20, G:0.18, T:0.11
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:117828 original size:33 final size:33
Alignment explanation
Indices: 117784--117867 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
117774 ACCAAAATCG
*
117784 CATTGCGATTTTCATTTTGCATTACGATTCTCT
1 CATTGCGATTTTCATTTCGCATTACGATTCTCT
* * *
117817 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCATTACGATTCTCT
**
117850 CATTGCGATAGTCATTTC
1 CATTGCGATTTTCATTTC
117868 CGCGTTGCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTACGATTCTCT
Found at i:118802 original size:94 final size:94
Alignment explanation
Indices: 118641--119020 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
118631 TAGATTGCTT
* *
118641 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118706 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
118735 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118800 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
118829 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
118894 ATCTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
118923 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTATGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118988 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
119016 AGTAA
1 AGTAA
119021 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 26 0.09
94 248 0.91
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:119124 original size:19 final size:19
Alignment explanation
Indices: 119068--119154 Score: 102
Period size: 19 Copynumber: 4.4 Consensus size: 19
119058 TAGTTTACTT
* *
119068 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
119088 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
119109 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
119128 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
119147 TCGCAACG
1 TCGCAACG
119155 ACAAAATCGC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 34 0.60
20 8 0.14
21 12 0.21
22 3 0.05
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:119183 original size:19 final size:18
Alignment explanation
Indices: 119068--119183 Score: 80
Period size: 19 Copynumber: 6.2 Consensus size: 18
119058 TAGTTTACTT
*
119068 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA--TAAAA
*
119088 TCGCAACGTGAAA-AATGACTA
1 TCGCAACGCGAAATAA--A--A
119109 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
119128 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
*
119147 TCGCAA--CG--ACAAAA
1 TCGCAACGCGAAATAAAA
*
119161 TCGCAACGCGAAACTATAA
1 TCGCAACGCGAAA-TAAAA
119180 TCGC
1 TCGC
119184 TTTGCGATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 4 0.05
18 1 0.01
19 34 0.43
20 11 0.14
21 14 0.18
23 2 0.03
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (18 bp):
TCGCAACGCGAAATAAAA
Found at i:119202 original size:19 final size:18
Alignment explanation
Indices: 119180--119276 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
119170 GAAACTATAA
119180 TCGCTTTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
119199 TCGCATTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
119215 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
119232 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
*
119248 TCG-TTGTGATTTTCATT
1 TCGCTTGCGATTTTCATT
119265 TCGCGTTGCGAT
1 TCGC-TTGCGAT
119277 AGTCATTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 11 0.18
16 14 0.23
17 14 0.23
19 22 0.36
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:119227 original size:33 final size:33
Alignment explanation
Indices: 119185--119276 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
119175 TATAATCGCT
*
119185 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
119218 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
119251 TTGTGATTTTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
119277 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:119777 original size:21 final size:21
Alignment explanation
Indices: 119753--119819 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
119743 TCATTCCTCG
119753 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
119774 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
119795 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
119816 AGAG
1 AGAG
119820 CCTGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:119777 original size:42 final size:42
Alignment explanation
Indices: 119701--119819 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
119691 GACTCGCCTG
* * * * * * *
119701 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
119743 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
119785 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
119820 CCTGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:121305 original size:19 final size:17
Alignment explanation
Indices: 121289--121339 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
121279 AAAAATGACT
121289 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
121308 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
121322 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
121339 A
1 A
121340 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:121331 original size:33 final size:33
Alignment explanation
Indices: 121289--121368 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
121279 AAAAATGACT
* *
121289 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
121322 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
121355 ATCGTAACGCGAAA
1 ATCGCAATGCGAAA
121369 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:121345 original size:19 final size:19
Alignment explanation
Indices: 121289--121347 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
121279 AAAAATGACT
121289 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
121308 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
121322 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
121341 ATCGCAA
1 ATCGCAA
121348 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:121396 original size:19 final size:19
Alignment explanation
Indices: 121374--121524 Score: 125
Period size: 19 Copynumber: 8.7 Consensus size: 19
121364 CGAAACTAAA
*
121374 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
121393 TTCGCTTTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
121408 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
121426 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
121445 TTCCGCGTTGCGATTTTCA-
1 TT-CGCATTGCGATTTTCAT
121464 --CG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
121479 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
121495 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
121512 TTCGCATTGCGAT
1 TTCGCATTGCGAT
121525 AGACATTAAG
Statistics
Matches: 105, Mismatches: 11, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
14 27 0.26
16 12 0.11
17 12 0.11
19 41 0.39
20 13 0.12
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:121467 original size:14 final size:14
Alignment explanation
Indices: 121450--121510 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
121440 GTCATTTCCG
121450 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
121464 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
* *
121478 TTTCGCATTGCGATTCTCT
1 ---CG--TTGCGATTTTCA
121497 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
121511 TTTCGCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 24 0.63
16 2 0.05
17 2 0.05
19 10 0.26
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:121476 original size:53 final size:52
Alignment explanation
Indices: 121374--121491 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 52
121364 CGAAACTAAA
* ** * *
121374 TTCGCGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCATTGCGATTTTCAT
1 TTCGCATTGCGATAGTCATTTCGCGTTGCGATTCTCACATTGCGATTTTCAT
* *
121426 TTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTCACGTTGCGATTTTCAT
1 TTCGCATTGCGATAGTCATTT-CGCGTTGCGATTCTCACATTGCGATTTTCAT
121479 TTCGCATTGCGAT
1 TTCGCATTGCGAT
121492 TCTCTCGTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 18 0.31
53 40 0.69
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (52 bp):
TTCGCATTGCGATAGTCATTTCGCGTTGCGATTCTCACATTGCGATTTTCAT
Found at i:121501 original size:33 final size:33
Alignment explanation
Indices: 121432--121524 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
121422 TCATTTCGCA
** * *
121432 TTGCGATAGTCATTTCCGCGTTGCGATTTTCACG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCACG
*
121466 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCACG
121499 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
121525 AGACATTAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 41 0.76
34 13 0.24
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCACG
Found at i:124821 original size:20 final size:20
Alignment explanation
Indices: 124796--125034 Score: 216
Period size: 20 Copynumber: 11.8 Consensus size: 20
124786 ATGTGAATAT
*
124796 GTATTCGCATTGCGATTTAC
1 GTATTCGCGTTGCGATTTAC
124816 GTATTCGCGTTGCGATTTAC
1 GTATTCGCGTTGCGATTTAC
124836 GTATTCGCGTTGCGATTTAC
1 GTATTCGCGTTGCGATTTAC
124856 GTATTCGCGTTGCGATTTAC
1 GTATTCGCGTTGCGATTTAC
* *
124876 GGATACGCGTTGCGATTTAC
1 GTATTCGCGTTGCGATTTAC
* *
124896 GGATAT-GCGTTACGATTTAC
1 GTAT-TCGCGTTGCGATTTAC
* *
124916 GGATACGCGTTGCGATTTTAC
1 GTATTCGCGTTGCGA-TTTAC
* *
124937 GTATT-GTCTTTGTGATTTAC
1 GTATTCG-CGTTGCGATTTAC
* * *
124957 GAATACGCATTGCGATTTTAC
1 GTATTCGCGTTGCGA-TTTAC
* * * *
124978 GGATACTCGTTGCGATAGT-C
1 GTATTCGCGTTGCGAT-TTAC
* *
124998 AG-AATCGCGTTGCGATTTTC
1 -GTATTCGCGTTGCGATTTAC
* *
125018 ATATTCGCGTTACGATT
1 GTATTCGCGTTGCGATT
125035 CTTGAAAATC
Statistics
Matches: 183, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.01
20 148 0.81
21 34 0.19
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTATTCGCGTTGCGATTTAC
Found at i:143614 original size:23 final size:23
Alignment explanation
Indices: 143588--143633 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
143578 TCTCATTTGA
* *
143588 TTACTGTCTGGTGGG-TCATTTTC
1 TTACTG-CTAGTGGGATCAATTTC
143611 TTACTGCTAGTGGGATCAATTTC
1 TTACTGCTAGTGGGATCAATTTC
143634 CAAGCGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.43
Consensus pattern (23 bp):
TTACTGCTAGTGGGATCAATTTC
Found at i:143627 original size:113 final size:113
Alignment explanation
Indices: 143429--143643 Score: 412
Period size: 113 Copynumber: 1.9 Consensus size: 113
143419 AAAGAAGAAT
143429 CCCCAACTCTTGGGCAGAATGATTCTCTATCACAACTCTCATTTGATTACTGTATGGTGGGTCAT
1 CCCCAACTCTTGGGCAGAATGATTCTCTATCACAACTCTCATTTGATTACTGTATGGTGGGTCAT
*
143494 TTTCTTACTGCTAGTGGGATCAATTTCCAGGCGATGAAGAGGAGGAAG
66 TTTCTTACTGCTAGTGGGATCAATTTCCAAGCGATGAAGAGGAGGAAG
*
143542 CCCCAACTCTTGGGCAGAATGATTCTCTATCACAACTCTCATTTGATTACTGTCTGGTGGGTCAT
1 CCCCAACTCTTGGGCAGAATGATTCTCTATCACAACTCTCATTTGATTACTGTATGGTGGGTCAT
143607 TTTCTTACTGCTAGTGGGATCAATTTCCAAGCGATGA
66 TTTCTTACTGCTAGTGGGATCAATTTCCAAGCGATGA
143644 GGATAACTTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 100 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (113 bp):
CCCCAACTCTTGGGCAGAATGATTCTCTATCACAACTCTCATTTGATTACTGTATGGTGGGTCAT
TTTCTTACTGCTAGTGGGATCAATTTCCAAGCGATGAAGAGGAGGAAG
Found at i:150506 original size:33 final size:33
Alignment explanation
Indices: 150459--150524 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
150449 TTGGGGTTCA
*
150459 CCACAAAGGCTAAGGCCACTGAATTCAAAAAAG
1 CCACAAAGGATAAGGCCACTGAATTCAAAAAAG
150492 CCACAAAGGATAAGGCCACTGAATTCAAAAAAG
1 CCACAAAGGATAAGGCCACTGAATTCAAAAAAG
150525 TGACATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
CCACAAAGGATAAGGCCACTGAATTCAAAAAAG
Found at i:151398 original size:21 final size:21
Alignment explanation
Indices: 151372--151421 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
151362 TAGGTCATCC
*
151372 AGGGTGCTGCCAGCCGATACT
1 AGGGTGCTGCCAGCCGACACT
*
151393 AGGGTGCTGCCAGCTGACACT
1 AGGGTGCTGCCAGCCGACACT
151414 AGGGTGCT
1 AGGGTGCT
151422 ACTTAGTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.20
Consensus pattern (21 bp):
AGGGTGCTGCCAGCCGACACT
Found at i:164140 original size:20 final size:20
Alignment explanation
Indices: 164120--164223 Score: 154
Period size: 20 Copynumber: 5.2 Consensus size: 20
164110 TCTAAATTCA
* *
164120 CAACGCGAATATGTAAATCA
1 CAACGCGAATTTGTAAATCG
164140 CAACGCGAATTTGTAAATCG
1 CAACGCGAATTTGTAAATCG
*
164160 CAACGCGAATTTATAAATCG
1 CAACGCGAATTTGTAAATCG
* *
164180 CAACGCGAATCTATAAATCG
1 CAACGCGAATTTGTAAATCG
*
164200 CAACGCGAATTTGTAATTCG
1 CAACGCGAATTTGTAAATCG
164220 CAAC
1 CAAC
164224 ACATAAGTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (20 bp):
CAACGCGAATTTGTAAATCG
Found at i:164237 original size:20 final size:20
Alignment explanation
Indices: 164214--164259 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
164204 GCGAATTTGT
*
164214 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
*
164234 AATTCGCAACACGGAAGTCA
1 AATTCGCAACACAGAAGTCA
164254 AATTCG
1 AATTCG
164260 AAAAGCACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:164241 original size:60 final size:59
Alignment explanation
Indices: 164113--164243 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
164103 CTCAGTTTCT
* * * * *
164113 AAATTCACAACGCGAATATGTAAATCACAACGCGAATTTGTAAATCGCAACGCGAATTT
1 AAATTCGCAACGCGAATATATAAATCACAACGCGAATTTGTAAATCGCAACACGAAGTC
* * * * *
164172 ATAAATCGCAACGCGAATCTATAAATCGCAACGCGAATTTGTAATTCGCAACACATAAGTC
1 A-AATTCGCAACGCGAATATATAAATCACAACGCGAATTTGTAAATCGCAACAC-GAAGTC
164233 AAATTCGCAAC
1 AAATTCGCAAC
164244 ACGGAAGTCA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 54 0.92
61 4 0.07
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (59 bp):
AAATTCGCAACGCGAATATATAAATCACAACGCGAATTTGTAAATCGCAACACGAAGTC
Found at i:164415 original size:22 final size:22
Alignment explanation
Indices: 164397--164468 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
164387 CTACGACAAC
*
164397 ATCCGTCCCTATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
164419 ATTCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
164441 ATTCATCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
164463 ATCCGT
1 ATCCGT
164469 ATATCTCCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.24, C:0.38, G:0.12, T:0.26
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:164866 original size:19 final size:20
Alignment explanation
Indices: 164828--164873 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
164818 AAAATGAAAA
* * *
164828 TCGCAACGCGATCTCGAA-T
1 TCGCAACGCAAACTCCAATT
164847 TCGCAACGCAAACTCCAATT
1 TCGCAACGCAAACTCCAATT
164867 TCGCAAC
1 TCGCAAC
164874 TCAGTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (20 bp):
TCGCAACGCAAACTCCAATT
Found at i:164910 original size:21 final size:21
Alignment explanation
Indices: 164884--164946 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
164874 TCAGTTTCCA
* *
164884 TTCCAATTTCGCATTGTAATT
1 TTCCAATTTCGCGTTGCAATT
* *
164905 TTCCAAATTCGCGTTGCGATT
1 TTCCAATTTCGCGTTGCAATT
164926 TT-C-ATTTCGCGTTGCAATT
1 TTCCAATTTCGCGTTGCAATT
164945 TT
1 TT
164947 AAGTTTCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
21 19 0.53
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (21 bp):
TTCCAATTTCGCGTTGCAATT
Found at i:167074 original size:21 final size:22
Alignment explanation
Indices: 167043--167106 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
167033 GATTCACCTG
* *
167043 TCATAGTTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCCCCTCC
*
167065 T-ATCGTTCAAGAGGCCCCT-G
1 TCATCGTTCAAGAGGCCCCTCC
*
167085 TCATCCTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
167107 CACCATTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:168557 original size:64 final size:64
Alignment explanation
Indices: 168456--168604 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
168446 AAATTTATGT
168456 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * ***
168520 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
168584 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
168605 GTTTTAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:168691 original size:20 final size:20
Alignment explanation
Indices: 168666--168787 Score: 138
Period size: 20 Copynumber: 6.1 Consensus size: 20
168656 GTACATTTTT
*
168666 GCAACGCGAAAATCAAATTC
1 GCAACGCGAAAGTCAAATTC
168686 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
***
168706 GCGTTGC-AATAGTCAAATTC
1 GCAACGCGAA-AGTCAAATTC
* *
168726 GCAATGCGAAAGTCAAATTA
1 GCAACGCGAAAGTCAAATTC
* * *
168746 GTAATGCGAAAGTCAAATTT
1 GCAACGCGAAAGTCAAATTC
*
168766 GCAACGCAAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
168786 GC
1 GC
168788 GTTGCGATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 83 0.95
21 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTC
Found at i:168735 original size:40 final size:40
Alignment explanation
Indices: 168671--168794 Score: 160
Period size: 40 Copynumber: 3.1 Consensus size: 40
168661 TTTTTGCAAC
*
168671 GCGAAAATCAAATTCGCAACGCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCGTT
* * ***
168711 GC-AATAGTCAAATTCGCAATGCGAAAGTCAAATTAGTAAT
1 GCGAA-AGTCAAATTCGCAACGCGAAAGTCAAATTCGCGTT
* *
168751 GCGAAAGTCAAATTTGCAACGCAAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCGTT
168791 GCGA
1 GCGA
168795 TTTTCGCGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
39 2 0.03
40 65 0.94
41 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (40 bp):
GCGAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCGTT
Found at i:168794 original size:60 final size:60
Alignment explanation
Indices: 168666--168787 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
168656 GTACATTTTT
* * *** *
168666 GCAACGCGAAAATCAAATTCGCAACGCGAAAGTCAAATTCGCGTTGCAATAGTCAAATTC
1 GCAATGCGAAAATCAAATTAGCAACGCGAAAGTCAAATTCGCAACGCAAAAGTCAAATTC
* * * *
168726 GCAATGCGAAAGTCAAATTAGTAATGCGAAAGTCAAATTTGCAACGCAAAAGTCAAATTC
1 GCAATGCGAAAATCAAATTAGCAACGCGAAAGTCAAATTCGCAACGCAAAAGTCAAATTC
168786 GC
1 GC
168788 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (60 bp):
GCAATGCGAAAATCAAATTAGCAACGCGAAAGTCAAATTCGCAACGCAAAAGTCAAATTC
Found at i:171528 original size:12 final size:12
Alignment explanation
Indices: 171507--171540 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
171497 GGTTGTGGGT
*
171507 TTTGAGATTGTG
1 TTTGATATTGTG
171519 TTTGATATTGTG
1 TTTGATATTGTG
*
171531 TTTGGTATTG
1 TTTGATATTG
171541 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:172418 original size:20 final size:21
Alignment explanation
Indices: 172393--172432 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
172383 TCAGTGTTGC
*
172393 GAATTTTG-AAATCGCAATGT
1 GAATTTGGAAAATCGCAATGT
172413 GAATTTGGAAAATCGCAATG
1 GAATTTGGAAAATCGCAATG
172433 CGATTTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAATGT
Found at i:195553 original size:13 final size:14
Alignment explanation
Indices: 195519--195553 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
195509 TACTAGCTGG
195519 GGCAAATCTTCAGA
1 GGCAAATCTTCAGA
195533 GTGCAAATCTTCA-A
1 G-GCAAATCTTCAGA
195547 GGCAAAT
1 GGCAAAT
195554 ACTTACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
GGCAAATCTTCAGA
Found at i:198704 original size:21 final size:21
Alignment explanation
Indices: 198676--198789 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
198666 TACATGTTCG
198676 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* * *
198697 CATTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
198716 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
* *
198739 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
198758 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
*
198781 CATTGCGAT
1 CGTTGCGAT
198790 AGTCCAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 17 0.24
21 38 0.54
23 16 0.23
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:198721 original size:42 final size:42
Alignment explanation
Indices: 198671--198793 Score: 228
Period size: 42 Copynumber: 2.9 Consensus size: 42
198661 CGATTTACAT
*
198671 GTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCGAA
1 GTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCGAA
*
198713 GTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAA
1 GTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCGAA
198755 GTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTC
1 GTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTC
198794 CAAAATCGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
GTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCGAA
Found at i:198893 original size:6 final size:6
Alignment explanation
Indices: 198882--198908 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
198872 GACACGTATT
198882 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
198909 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:199534 original size:21 final size:21
Alignment explanation
Indices: 199508--199561 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
199498 GATTTACATA
199508 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
199529 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
199550 TTCGCGTTGCGA
1 TTCGCATTGCGA
199562 ATCTGGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:206466 original size:16 final size:17
Alignment explanation
Indices: 206435--206468 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
206425 TAAATATTTG
206435 ATAAATTCTAATAAATA
1 ATAAATTCTAATAAATA
*
206452 ATAATTTCTAA-AAATA
1 ATAAATTCTAATAAATA
206468 A
1 A
206469 ACATGTTGCA
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:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAATTCTAATAAATA
Found at i:206964 original size:57 final size:57
Alignment explanation
Indices: 206876--207007 Score: 264
Period size: 57 Copynumber: 2.3 Consensus size: 57
206866 GAGAAGGTCA
206876 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
1 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
206933 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
1 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
206990 TTATGGCACGGGCATGAC
1 TTATGGCACGGGCATGAC
207008 AGGGGCCACG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 75 1.00
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (57 bp):
TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
Found at i:208705 original size:4 final size:4
Alignment explanation
Indices: 208684--208753 Score: 54
Period size: 4 Copynumber: 16.8 Consensus size: 4
208674 GTTTTAATGA
* * *
208684 ATTT ATTT AATCT CTTT ATTT ATTT ATTT ATTT ATTT -TATT ATTT AATGCT
1 ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT -AT-TT
208735 ATTT -TTT ATGTT ATTT ATT
1 ATTT ATTT AT-TT ATTT ATT
208754 GTTGTTTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 4 0.08
4 36 0.68
5 12 0.23
6 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:208848 original size:17 final size:17
Alignment explanation
Indices: 208828--208965 Score: 61
Period size: 18 Copynumber: 7.8 Consensus size: 17
208818 AAATTTAAAA
*
208828 TTTTGTTATTATTTCTT
1 TTTTATTATTATTTCTT
*
208845 TTTTTTTATTTTATTTCATT
1 TTTTATTA--TTATTTC-TT
*
208865 TTTTATTATT-TTTATTT
1 TTTTATTATTATTT-CTT
*
208882 TTTTTTTCATT-TTTCATT
1 TTTTATT-ATTATTTC-TT
* *
208900 TTTTCATTTTTATATCTT
1 TTTT-ATTATTATTTCTT
*
208918 TATTTATCTA-T-GTTCTT
1 T-TTTAT-TATTATTTCTT
*
208935 TATTATTATTATTAT-TAT
1 TTTTATTATTATT-TCT-T
*
208953 TATTATTATTATT
1 TTTTATTATTATT
208966 ATTATTATTA
Statistics
Matches: 94, Mismatches: 13, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
15 2 0.02
16 5 0.05
17 25 0.27
18 37 0.39
19 16 0.17
20 9 0.10
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTATTATTATTTCTT
Found at i:208873 original size:15 final size:15
Alignment explanation
Indices: 208827--208910 Score: 57
Period size: 15 Copynumber: 5.4 Consensus size: 15
208817 AAAATTTAAA
208827 ATTTTGTTATTATTTC
1 ATTTT-TTATTATTTC
*
208843 TTTTTTTTTATTTTATTTC
1 --ATTTTTTA--TTATTTC
208862 ATTTTTTATTATTT-
1 ATTTTTTATTATTTC
*
208876 -TTATTTT-TTTTTTC
1 ATT-TTTTATTATTTC
* *
208890 ATTTTTCATTTTTTC
1 ATTTTTTATTATTTC
208905 ATTTTT
1 ATTTTT
208911 ATATCTTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.12
14 7 0.12
15 21 0.38
17 10 0.18
18 4 0.07
19 7 0.12
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.79
Consensus pattern (15 bp):
ATTTTTTATTATTTC
Found at i:208877 original size:28 final size:27
Alignment explanation
Indices: 208839--208910 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
208829 TTTGTTATTA
208839 TTTC-TTTTTTT-TTATTTTATTTCATT
1 TTTCATTTTTTTATT-TTTTATTTCATT
* *
208865 TTTTATTATTTTTATTTTTTTTTTCATT
1 TTTCATT-TTTTTATTTTTTATTTCATT
*
208893 TTTCATTTTTTCATTTTT
1 TTTCATTTTTTTATTTTT
208911 ATATCTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 3 0.08
27 12 0.31
28 22 0.56
29 2 0.05
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTCATTTTTTTATTTTTTATTTCATT
Found at i:208878 original size:9 final size:9
Alignment explanation
Indices: 208864--208977 Score: 65
Period size: 9 Copynumber: 12.2 Consensus size: 9
208854 TTTATTTCAT
208864 TTTTTATTA
1 TTTTTATTA
208873 TTTTTATT-
1 TTTTTATTA
*
208881 TTTTTTTTCA
1 TTTTTATT-A
208891 TTTTTCATT-
1 TTTTT-ATTA
*
208900 TTTTCATT-
1 TTTTTATTA
*
208908 TTTATATCT-
1 TTTTTAT-TA
208917 TTATTTATCTA
1 TT-TTTAT-TA
208928 TGTTCTTTATTA
1 --TT-TTTATTA
*
208940 TTATTATTA
1 TTTTTATTA
*
208949 TTATTATTA
1 TTTTTATTA
*
208958 TTATTATTA
1 TTTTTATTA
*
208967 TTATTATTA
1 TTTTTATTA
208976 TT
1 TT
208978 ATATTAACAT
Statistics
Matches: 89, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
8 15 0.17
9 50 0.56
10 13 0.15
11 2 0.02
12 2 0.02
13 7 0.08
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTTTATTA
Found at i:208881 original size:6 final size:6
Alignment explanation
Indices: 208843--208979 Score: 55
Period size: 6 Copynumber: 21.0 Consensus size: 6
208833 TTATTATTTC
*
208843 TTTT-T TTTTA- TTTTAT TTCATTTT TTATTAT TTTTAT TTTT-T TTTTCAT
1 TTTTAT TTTTAT TTTTAT TT--TTAT TT-TTAT TTTTAT TTTTAT TTTT-AT
*
208892 TTTTCATT TTTTCAT TTTTAT ATCTTTAT TTATCTATGT TCTTTAT TATTAT
1 TTTT-A-T TTTT-AT TTTTAT -T-TTTAT TT-T-TA--T T-TTTAT TTTTAT
* * * * * *
208944 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
208980 ATTAACATTT
Statistics
Matches: 115, Mismatches: 3, Indels: 27
0.79 0.02 0.19
Matches are distributed among these distances:
5 14 0.12
6 53 0.46
7 23 0.20
8 19 0.17
9 2 0.02
10 3 0.03
11 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTAT
Done.