Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015184.1 Kokia drynarioides strain JFW-HI SEQ_130228, 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: 277099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 559 characters in sequence are not A, C, G, or T
Found at i:279 original size:4 final size:4
Alignment explanation
Indices: 259--321 Score: 65
Period size: 4 Copynumber: 15.2 Consensus size: 4
249 AACACATTAC
* * *
259 CTTT CTTT CCTT C-TT CTTT CTTT CCTCTC CTTC CTTT CTTT CTTT CTTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT CTTT C-TTT
309 CTTT CTTT CTTT C
1 CTTT CTTT CTTT C
322 CCGTTTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
3 3 0.06
4 40 0.77
5 8 0.15
6 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:311 original size:13 final size:13
Alignment explanation
Indices: 259--320 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
249 AACACATTAC
*
259 CTTTCTTTC-CTT
1 CTTTCTTTCTTTT
*
271 C-TTCTTTCTTTC
1 CTTTCTTTCTTTT
* * *
283 CTCTCCTTCCTTT
1 CTTTCTTTCTTTT
296 CTTTCTTTCTTTT
1 CTTTCTTTCTTTT
309 CTTTCTTTCTTT
1 CTTTCTTTCTTT
321 CCCGTTTATT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
11 7 0.18
12 3 0.08
13 29 0.74
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCTTTCTTTT
Found at i:314 original size:17 final size:17
Alignment explanation
Indices: 259--321 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
249 AACACATTAC
259 CTTTCTTTCCTTCTTCTTT
1 CTTTCTTT-CTT-TTCTTT
* * *
278 CTTTCCTCTCCTTCCTTT
1 CTTT-CTTTCTTTTCTTT
296 CTTTCTTTCTTTTCTTT
1 CTTTCTTTCTTTTCTTT
313 CTTTCTTTC
1 CTTTCTTTC
322 CCGTTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 19 0.51
18 9 0.24
19 6 0.16
20 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCTTTCTTTTCTTT
Found at i:18070 original size:3 final size:3
Alignment explanation
Indices: 18062--18086 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18052 CTATTCGTTT
18062 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
18087 AATCATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19105 original size:17 final size:17
Alignment explanation
Indices: 19097--19177 Score: 92
Period size: 17 Copynumber: 4.7 Consensus size: 17
19087 TTATTTTAAA
*
19097 TTTAAATTTAAAATTAAT
1 TTTAAATTT-AAATTTAT
* *
19115 TTTAAATTTGAATTTAA
1 TTTAAATTTAAATTTAT
*
19132 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
19149 TTTAAATTTTAAA-TTAT
1 TTTAAA-TTTAAATTTAT
*
19166 TATAAATTTAAA
1 TTTAAATTTAAA
19178 ATAAATAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 6 0.11
17 33 0.61
18 15 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:19110 original size:7 final size:6
Alignment explanation
Indices: 19091--19163 Score: 78
Period size: 6 Copynumber: 12.3 Consensus size: 6
19081 TTAGATTTAT
* * * *
19091 TTTAAA TTTAAA TTTAAA ATTAAT TTTAAA TTTGAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
19138 TTTAAA TTT-AT TTTAAA TTTTAAA TT
1 TTTAAA TTTAAA TTTAAA -TTTAAA TT
19164 ATTATAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
5 9 0.16
6 40 0.73
7 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:19112 original size:41 final size:41
Alignment explanation
Indices: 19066--19164 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
19056 GATCCCTTTT
*
19066 AAATTAATTTTAAGATTAG-ATTTATTTTAAATTTAAATTTA
1 AAATTAATTTTAA-ATTAGAATTTAATTTAAATTTAAATTTA
* *
19107 AAATTAATTTTAAATTTGAATTTAATTTAAGTTTAAATTT-
1 AAATTAATTTTAAATTAGAATTTAATTTAAATTTAAATTTA
**
19147 ATTTTAAATTTTAAATTA
1 AAATT-AATTTTAAATTA
19165 TTATAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 7 0.14
41 43 0.86
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (41 bp):
AAATTAATTTTAAATTAGAATTTAATTTAAATTTAAATTTA
Found at i:19176 original size:34 final size:34
Alignment explanation
Indices: 19095--19177 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
19085 ATTTATTTTA
*
19095 AATTTAAATTTAAAATTAATTTTAAATTTGAATTT
1 AATTTAAATTT-AAATTAATTTTAAATTTGAAATT
* * *
19130 AATTTAAGTTTAAATTTATTTTAAATTTTAAATT
1 AATTTAAATTTAAATTAATTTTAAATTTGAAATT
19164 -ATTATAAATTTAAA
1 AATT-TAAATTTAAA
19178 ATAAATAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 3 0.07
34 29 0.69
35 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
AATTTAAATTTAAATTAATTTTAAATTTGAAATT
Found at i:19991 original size:29 final size:29
Alignment explanation
Indices: 19929--20163 Score: 163
Period size: 30 Copynumber: 7.9 Consensus size: 29
19919 TTTGATCCCT
** * *
19929 AAACTTCTCCAAATTCCATTTTTGACCCCA
1 AAACTTCTAAAAATTACATTTTT-ACCCCC
19959 AAACTTCTAAAAATTACATTTTTACCCCC
1 AAACTTCTAAAAATTACATTTTTACCCCC
* ** * *
19988 AAACTTCAAAAAATCCCAATTTTGACCCCA
1 AAACTTCTAAAAATTAC-ATTTTTACCCCC
*
20018 AAACTT-TCAAAAATTACCA-TTTTACCCTC
1 AAACTTCT-AAAAATTA-CATTTTTACCCCC
* ** * * *
20047 AAACTTCCAAAAATCCCAATTTTAACCTCG
1 AAACTTCTAAAAATTAC-ATTTTTACCCCC
*
20077 AAACTTCTAAAAATTACCA-TTTTACCCTC
1 AAACTTCTAAAAATTA-CATTTTTACCCCC
* * *
20106 AAACTTCTAAAAATTCCATTTTTGACCTCG
1 AAACTTCTAAAAATTACATTTTT-ACCCCC
**
20136 AAAC-TCTCAAAAAGTTACCCTTTTACCC
1 AAACTTCT-AAAAA-TTACATTTTTACCC
20164 TTGAATGTCC
Statistics
Matches: 157, Mismatches: 37, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
28 3 0.02
29 67 0.43
30 78 0.50
31 9 0.06
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCTAAAAATTACATTTTTACCCCC
Found at i:20109 original size:118 final size:118
Alignment explanation
Indices: 19959--20223 Score: 349
Period size: 118 Copynumber: 2.2 Consensus size: 118
19949 TTTGACCCCA
19959 AAACTTCTAAAAATTA-CATTTTTACCCCCAAACTTCAAAAAATCCCAATTTTGACCCCAAAACT
1 AAACTTCTAAAAATTACCA-TTTTACCCCCAAACTTCAAAAAATCCCAATTTTGACCCCAAAACT
*
20023 TTCAAAAA-TTACCATTTTACCCTCAAACT-TCCAAAAATCCCAATTTTAACCTCG
65 CTCAAAAAGTTACCATTTTACCCTCAAA-TGTCCAAAAATCCC-ATTTTAACCTCG
* * * * * *
20077 AAACTTCTAAAAATTACCATTTTACCCTCAAACTTCTAAAAATTCCATTTTTGACCTCGAAACTC
1 AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCAATTTTGACCCCAAAACTC
* ** * *
20142 TCAAAAAGTTACCCTTTTACCCTTGAATGTCCAAAAATTCCATTTTGACCTCG
66 TCAAAAAGTTACCATTTTACCCTCAAATGTCCAAAAATCCCATTTTAACCTCG
*
20195 AAAC-TCTAAAAAATTACCCTTTTACCCCC
1 AAACTTCT-AAAAATTACCATTTTACCCCC
20224 CGAATGTCCA
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
117 3 0.02
118 97 0.75
119 29 0.22
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (118 bp):
AAACTTCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCAATTTTGACCCCAAAACTC
TCAAAAAGTTACCATTTTACCCTCAAATGTCCAAAAATCCCATTTTAACCTCG
Found at i:20148 original size:30 final size:27
Alignment explanation
Indices: 19939--20220 Score: 172
Period size: 29 Copynumber: 9.6 Consensus size: 27
19929 AAACTTCTCC
* *
19939 AAATTCCATTTTTGACCCCAAAACTTCTAA
1 AAATTCCA-TTTT-ACCTCGAAACTTC-AA
* * *
19969 AAATTACATTTTTACCCCCAAACTTCAAA
1 AAATTCCA-TTTTACCTCGAAACTTC-AA
* * *
19998 AAATCCCAATTTTGACCCCAAAACTTTCAA
1 AAATTCC-ATTTT-ACCTCGAAAC-TTCAA
20028 AAATTACCATTTTACCCTC-AAACTTCCAA
1 AAATT-CCATTTTA-CCTCGAAACTT-CAA
*
20057 AAATCCCAATTTTAACCTCGAAACTTCTAA
1 AAATTCC-ATTTT-ACCTCGAAACTTC-AA
20087 AAATTACCATTTTACCCTC-AAACTTCTAA
1 AAATT-CCATTTTA-CCTCGAAACTTC-AA
20116 AAATTCCATTTTTGACCTCGAAACTCTCAA
1 AAATTCCA-TTTT-ACCTCGAAACT-TCAA
* * ** *
20146 AAAGTTACCCTTTTACCCTTGAATGTCCAA
1 AAA-TT-CCATTTTA-CCTCGAAACTTCAA
*
20176 AAATTCCATTTTGACCTCGAAACTCTAAA
1 AAATTCCATTTT-ACCTCGAAACT-TCAA
*
20205 AAATTACCCTTTTACC
1 AAATT-CCATTTTACC
20221 CCCCGAATGT
Statistics
Matches: 208, Mismatches: 22, Indels: 45
0.76 0.08 0.16
Matches are distributed among these distances:
28 20 0.10
29 82 0.39
30 82 0.39
31 22 0.11
32 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (27 bp):
AAATTCCATTTTACCTCGAAACTTCAA
Found at i:20240 original size:59 final size:57
Alignment explanation
Indices: 19939--20221 Score: 309
Period size: 59 Copynumber: 4.8 Consensus size: 57
19929 AAACTTCTCC
* * * *
19939 AAATTCCATTTTTGACCCCAAAACTTCTAAAAATTA-CATTTTTACCCCCAAACTTCAAA
1 AAATTCCA-TTTTGACCTCGAAAC-TCTAAAAATTACCA-TTTTACCCTCAAACTTCCAA
* * * *
19998 AAATCCCAATTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCTCAAACTTCCAA
1 AAATTCC-ATTTTGACCTCGAAACTCT-AAAAATTACCATTTTACCCTCAAACTTCCAA
* * *
20057 AAATCCCAATTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCTCAAACTTCTAA
1 AAATTCC-ATTTTGACCTCGAAAC-TCTAAAAATTACCATTTTACCCTCAAACTTCCAA
* **
20116 AAATTCCATTTTTGACCTCGAAACTCTCAAAAAGTTACCCTTTTACCCTTGAA-TGTCCAA
1 AAATTCCA-TTTTGACCTCGAAACTCT-AAAAA-TTACCATTTTACCCTCAAACT-TCCAA
*
20176 AAATTCCATTTTGACCTCGAAACTCTAAAAAATTACCCTTTTACCC
1 AAATTCCATTTTGACCTCGAAACTCT-AAAAATTACCATTTTACCC
20222 CCCGAATGTC
Statistics
Matches: 200, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
58 20 0.10
59 147 0.74
60 33 0.17
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (57 bp):
AAATTCCATTTTGACCTCGAAACTCTAAAAATTACCATTTTACCCTCAAACTTCCAA
Found at i:22140 original size:30 final size:31
Alignment explanation
Indices: 22087--22145 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
22077 TATATTTGTT
* ** *
22087 TTTTATTTATTTATGTTTTTATTG-ATTTGA
1 TTTTATATATTTATAATTATATTGCATTTGA
22117 TTTTATATATTTATAATTATATTGCATTT
1 TTTTATATATTTATAATTATATTGCATTT
22146 ATGAATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (31 bp):
TTTTATATATTTATAATTATATTGCATTTGA
Found at i:23262 original size:2 final size:2
Alignment explanation
Indices: 23255--23304 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
23245 TGATTTTGGT
23255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23297 TA TA -A TA T
1 TA TA TA TA T
23305 GTGATTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26281 original size:24 final size:24
Alignment explanation
Indices: 26254--26305 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
26244 AAATTTAAAA
*
26254 AAAAAAAATTCA-CTGTGAATCTAT
1 AAAAAAAATCCATC-GTGAATCTAT
*
26278 AAAAAAACTCCATCGTGAATCTAT
1 AAAAAAAATCCATCGTGAATCTAT
26302 AAAA
1 AAAA
26306 TCAACATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (24 bp):
AAAAAAAATCCATCGTGAATCTAT
Found at i:30138 original size:13 final size:14
Alignment explanation
Indices: 30121--30168 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
30111 AACAATTAAT
30121 AAAATCAATTGATC
1 AAAATCAATTGATC
* *
30135 -AAATTAATT-AAC
1 AAAATCAATTGATC
*
30147 AAAATCAATTGATT
1 AAAATCAATTGATC
30161 AAAATCAA
1 AAAATCAA
30169 CTACAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 2 0.07
13 16 0.59
14 9 0.33
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.29
Consensus pattern (14 bp):
AAAATCAATTGATC
Found at i:30174 original size:26 final size:26
Alignment explanation
Indices: 30121--30171 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
30111 AACAATTAAT
* * *
30121 AAAATCAATTGATCAAATTAATTAAC
1 AAAATCAATTGATAAAATCAACTAAC
30147 AAAATCAATTGATTAAAATCAACTA
1 AAAATCAATTGA-TAAAATCAACTA
30172 CAATAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATCAATTGATAAAATCAACTAAC
Found at i:32010 original size:60 final size:59
Alignment explanation
Indices: 31940--32235 Score: 310
Period size: 61 Copynumber: 4.9 Consensus size: 59
31930 AAAAAAAAAA
*
31940 TTGGTCATGCAATAGCCGACA-CCCTTTTTAATCTGATAAAAAAATTTAAATTTTTGGGTG
1 TTGGTCATGCAATGGCCGACACCCCTTTTT-ATCTGAT-AAAAAATTTAAATTTTTGGGTG
*
32000 TTGGTCATGCAATGGCCGACACCCCTTTTTATCTGAATAAAAAA-TCAAATTTTTGGGTG
1 TTGGTCATGCAATGGCCGACACCCCTTTTTATCTG-ATAAAAAATTTAAATTTTTGGGTG
* * * * **
32059 TTGGTCATGCCATGGCCGACATCCCCTTTTTGTCGGATAAAAAATTCGAAATTTTTTTGTG
1 TTGGTCATGCAATGGCCGACA-CCCCTTTTTATCTGATAAAAAATT-TAAATTTTTGGGTG
** * * * * **
32120 TTGGTCATGTTATGGTCGACAATCCCTTTTTTATCTGGTAAAAAA-TTAATTTTTTTTTGTG
1 TTGGTCATGCAATGGCCGAC-A-CCCCTTTTTATCTGATAAAAAATTTAA-ATTTTTGGGTG
* * * *
32181 TTGGCCATGCAATAGCCGACACCCCTTTATTATCGGATAAAAAATTTGAATTTTT
1 TTGGTCATGCAATGGCCGACACCCCTTT-TTATCTGATAAAAAATTTAAATTTTT
32236 TGTGTTTGCC
Statistics
Matches: 200, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
59 48 0.24
60 65 0.32
61 67 0.34
62 20 0.10
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (59 bp):
TTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAATTTAAATTTTTGGGTG
Found at i:32448 original size:88 final size:88
Alignment explanation
Indices: 32327--32558 Score: 283
Period size: 88 Copynumber: 2.6 Consensus size: 88
32317 AAAAGGGTGT
* *
32327 AATTTGATTTTTTAT-TCAGATAGAAAAGGGTGTCGGCCATGCAATGGCCAACACAAAAAAATTT
1 AATTTGATTTTTTTTATCAGATA-AAAAGGGTGTCGACCATGCAATGGCCAACACAAAAAAA-TT
*
32391 TGAAATTTTTA-TCTGA-AAAAAGAA
64 TGAAATTTTTATTCCGACAAAAA-AA
* *
32415 AATTTGATTTTTTTTATCAGATAAAAAGGGTGTCGACCATGGC-ATGACAAACACAAAAAAATTT
1 AATTTGATTTTTTTTATCAGATAAAAAGGGTGTCGACCAT-GCAATGGCCAACACAAAAAAATTT
* **
32479 GAATTTTTTATTCCGACACCAAAA
65 GAAATTTTTATTCCGACAAAAAAA
* * *
32503 AATTTAATTTTTTTTATCAAATTAAAAGAGGGTGTCGACCATGCAATAGCCAACAC
1 AATTTGATTTTTTTTATCAGA-TAAAA-AGGGTGTCGACCATGCAATGGCCAACAC
32559 CTAATTTTTT
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
87 12 0.10
88 71 0.57
89 19 0.15
90 22 0.18
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (88 bp):
AATTTGATTTTTTTTATCAGATAAAAAGGGTGTCGACCATGCAATGGCCAACACAAAAAAATTTG
AAATTTTTATTCCGACAAAAAAA
Found at i:42701 original size:29 final size:31
Alignment explanation
Indices: 42644--42705 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
42634 ATACTGTTAC
*
42644 TCTTTATATTTTGATAAAATTTAATATTTAA
1 TCTTTATATTTTGATAAAATTTAAAATTTAA
42675 TCTTTATATTTT-A-AAAA-TTAAGAATTTAA
1 TCTTTATATTTTGATAAAATTTAA-AATTTAA
42704 TC
1 TC
42706 ATATCTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 12 0.41
30 1 0.03
31 12 0.41
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (31 bp):
TCTTTATATTTTGATAAAATTTAAAATTTAA
Found at i:42930 original size:15 final size:14
Alignment explanation
Indices: 42893--42933 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
42883 TTAAAAAGAT
42893 ATTTTATTGAATAA
1 ATTTTATTGAATAA
42907 ATTTT-TTGAA-AA
1 ATTTTATTGAATAA
42919 ATGTTTTATTGAATA
1 A--TTTTATTGAATA
42934 GTTTATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 5 0.22
14 9 0.39
15 5 0.22
16 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (14 bp):
ATTTTATTGAATAA
Found at i:43706 original size:31 final size:31
Alignment explanation
Indices: 43616--43712 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 31
43606 TTTAATTTTA
43616 AATAAAATATCAAACATATTTTATAACTTAAATTC
1 AATAAAATATCAAACATA-TTT-T-A-TTAAATTC
* * * *
43651 AATAAAAAAATTAATCGTATTTTATTAAATTC
1 AAT-AAAATATCAAACATATTTTATTAAATTC
*
43683 AATAAAATATCAAACATATTTTATTTAATT
1 AATAAAATATCAAACATATTTTATTAAATT
43713 TCGTTTAACA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 22 0.42
32 11 0.21
33 1 0.02
34 1 0.02
35 6 0.12
36 11 0.21
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (31 bp):
AATAAAATATCAAACATATTTTATTAAATTC
Found at i:43708 original size:36 final size:37
Alignment explanation
Indices: 43616--43710 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 37
43606 TTTAATTTTA
43616 AATAAAATATCAAACATATTTTA--TAACTTAAATTC
1 AATAAAATATCAAACATATTTTATTTAACTTAAATTC
** ** *
43651 AATAAAA-A--AATTA-ATCGTATTTTA-TTAAATTC
1 AATAAAATATCAAACATATTTTATTTAACTTAAATTC
43683 AATAAAATATCAAACATATTTTATTTAA
1 AATAAAATATCAAACATATTTTATTTAA
43711 TTTCGTTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
31 4 0.09
32 18 0.41
33 3 0.07
34 1 0.02
35 10 0.23
36 8 0.18
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (37 bp):
AATAAAATATCAAACATATTTTATTTAACTTAAATTC
Found at i:54571 original size:42 final size:39
Alignment explanation
Indices: 54487--54571 Score: 98
Period size: 42 Copynumber: 2.1 Consensus size: 39
54477 TGAAAATTTG
* * * *
54487 TTTAATAAATTTATAAACAAAATACAAATTAAATATGGT
1 TTTAACAAATTTATAAAAAAAATAAAAATTAAATATGAT
*
54526 TTTAACAAATTTATTAAAAAATAATATAAAATTAAATATTAT
1 TTTAACAAATTTA-TAAAAAA-AATA-AAAATTAAATATGAT
54568 TTTA
1 TTTA
54572 TCACACATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 12 0.32
40 6 0.16
41 4 0.11
42 16 0.42
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (39 bp):
TTTAACAAATTTATAAAAAAAATAAAAATTAAATATGAT
Found at i:56540 original size:60 final size:61
Alignment explanation
Indices: 56428--56554 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 61
56418 TTATAATGCA
*
56428 CATAAATTAAAAAAAACAATAACAAATAAAAAATAAAAATAAAATCCTATATTATTGACCT
1 CATAAATTAAAAAAAACAATAACAAATAAAAAATAAAAACAAAATCCTATATTATTGACCT
* * * * *
56489 CATAAA-TATAAAAAAACAGTAACAAAT-ATAAATCATAACAAAATCCTATATTATTGGCCT
1 CATAAATTA-AAAAAAACAATAACAAATAAAAAATAAAAACAAAATCCTATATTATTGACCT
56549 CATAAA
1 CATAAA
56555 CATTCTCAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 36 0.61
61 23 0.39
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.25
Consensus pattern (61 bp):
CATAAATTAAAAAAAACAATAACAAATAAAAAATAAAAACAAAATCCTATATTATTGACCT
Found at i:56850 original size:33 final size:33
Alignment explanation
Indices: 56805--56867 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
56795 AAATATATTG
56805 AAAATTTGCATAAGCATCTTCGAAATAATCTTC
1 AAAATTTGCATAAGCATCTTCGAAATAATCTTC
56838 AAAATCTT-CATAAGCATCTTCGAAATAATC
1 AAAAT-TTGCATAAGCATCTTCGAAATAATC
56868 ACCACCCGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (33 bp):
AAAATTTGCATAAGCATCTTCGAAATAATCTTC
Found at i:58962 original size:29 final size:28
Alignment explanation
Indices: 58871--59053 Score: 145
Period size: 29 Copynumber: 6.2 Consensus size: 28
58861 TGAAAATCAT
*
58871 ATTTTAACCCTCAAACTTTTTTAGAAATTAC
1 ATTTTAACCC-CAAAC-TTTTCA-AAATTAC
* * * *
58902 ATTTTGACCTCTAA-TCTTTCTAAAAAT-C
1 ATTTTAACCCCAAACT-TTTC-AAAATTAC
58930 ATTTTAACCCCAAACTTCTTCAAAATTAC
1 ATTTTAACCCCAAACTT-TTCAAAATTAC
**** *
58959 ATTTTAACAATTTAACTTTTTAAAATTAC
1 ATTTTAAC-CCCAAACTTTTCAAAATTAC
58988 ATTTTAACCCCAAACTTTTCCAAAATTAC
1 ATTTTAACCCCAAACTTTT-CAAAATTAC
* *
59017 ATTTTAACCCCCAAGCTTTCCTAAAATTAC
1 ATTTTAA-CCCCAAACTTTTC-AAAATTAC
59047 ATATTTA
1 AT-TTTA
59054 CCCTTTAACT
Statistics
Matches: 121, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
28 26 0.21
29 54 0.45
30 29 0.24
31 12 0.10
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTTTAACCCCAAACTTTTCAAAATTAC
Found at i:58983 original size:57 final size:57
Alignment explanation
Indices: 58871--59024 Score: 186
Period size: 58 Copynumber: 2.6 Consensus size: 57
58861 TGAAAATCAT
* * *
58871 ATTTTAACCCTCAAACTTTTTTAGAAATTACATTTTGACCTCTAATCTTTCTAAAAAT-C
1 ATTTTAACCC-CAAAC-TTTTCA-AAATTACATTTTAACATCTAATCTTTCTAAAAATAC
* * *
58930 ATTTTAACCCCAAACTTCTTCAAAATTACATTTTAACAATTTAA-CTTTTTAAAATTAC
1 ATTTTAACCCCAAACTT-TTCAAAATTACATTTTAAC-ATCTAATCTTTCTAAAAATAC
58988 ATTTTAACCCCAAACTTTTCCAAAATTACATTTTAAC
1 ATTTTAACCCCAAACTTTT-CAAAATTACATTTTAAC
59025 CCCCAAGCTT
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
57 28 0.33
58 47 0.55
59 10 0.12
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (57 bp):
ATTTTAACCCCAAACTTTTCAAAATTACATTTTAACATCTAATCTTTCTAAAAATAC
Found at i:59266 original size:25 final size:25
Alignment explanation
Indices: 59223--59282 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
59213 TTCTATCATA
*
59223 TTTTGTATTTTATCTTATGTTTAAT
1 TTTTGTATTTTATCTTATGCTTAAT
*
59248 TTTTGTATTTTCT-TATATGCTTAAT
1 TTTTGTATTTTATCT-TATGCTTAAT
* *
59273 TGTTCTATTT
1 TTTTGTATTT
59283 AATGTTGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.18, C:0.07, G:0.08, T:0.67
Consensus pattern (25 bp):
TTTTGTATTTTATCTTATGCTTAAT
Found at i:60066 original size:20 final size:20
Alignment explanation
Indices: 60041--60079 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60031 ACCTAATTTT
* *
60041 TATCTTTAATTTTACAATTG
1 TATCTTTAAATTTAAAATTG
60061 TATCTTTAAATTTAAAATT
1 TATCTTTAAATTTAAAATT
60080 TTATATGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (20 bp):
TATCTTTAAATTTAAAATTG
Found at i:61156 original size:16 final size:16
Alignment explanation
Indices: 61126--61181 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
61116 ATTATATCTA
*
61126 TTATCTTTT-TAATTT
1 TTATTTTTTCTAATTT
61141 TTATTTTTTCTAATTT
1 TTATTTTTTCTAATTT
*
61157 TT-TAATTTTC-ATATTT
1 TTAT-TTTTTCTA-ATTT
61173 TTATTTTTT
1 TTATTTTTT
61182 TCAATTCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 10 0.29
16 23 0.68
17 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTTTTCTAATTT
Found at i:61158 original size:24 final size:23
Alignment explanation
Indices: 61131--61187 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
61121 ATCTATTATC
* *
61131 TTTTTAATTTTTATTTTTTCTAAT
1 TTTTTAATTTTCATATTTT-TAAT
*
61155 TTTTTAATTTTCATATTTTTATT
1 TTTTTAATTTTCATATTTTTAAT
61178 TTTTTCAATT
1 TTTTT-AATT
61188 CTATCAAGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTAATTTTCATATTTTTAAT
Found at i:62648 original size:6 final size:6
Alignment explanation
Indices: 62639--62678 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
62629 AATAAAAGAT
*
62639 AACAAT AACAAA AAC-AA AA-AAA AACAAA AAC-AA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA A
62679 TCCTACACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 13 0.43
6 17 0.57
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (6 bp):
AACAAA
Found at i:62663 original size:10 final size:10
Alignment explanation
Indices: 62648--62678 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
62638 TAACAATAAC
62648 AAAAACAAAA
1 AAAAACAAAA
62658 AAAAACAAAA
1 AAAAACAAAA
62668 ACAAAACAAAA
1 A-AAAACAAAA
62679 TCCTACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:62664 original size:16 final size:17
Alignment explanation
Indices: 62639--62678 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
62629 AATAAAAGAT
*
62639 AACAATAACAAAAACAA
1 AACAAAAACAAAAACAA
62656 AA-AAAAACAAAAACAA
1 AACAAAAACAAAAACAA
62672 AACAAAA
1 AACAAAA
62679 TCCTACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (17 bp):
AACAAAAACAAAAACAA
Found at i:64361 original size:24 final size:24
Alignment explanation
Indices: 64329--64374 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
64319 CACTCCTTGC
* * *
64329 AAAATAATCTTGAAAATCATCATA
1 AAAAAAATCTTCAAAAGCATCATA
64353 AAAAAAATCTTCAAAAGCATCA
1 AAAAAAATCTTCAAAAGCATCA
64375 CCTCCTCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAAATCTTCAAAAGCATCATA
Found at i:75694 original size:24 final size:24
Alignment explanation
Indices: 75644--75700 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 24
75634 TTTGTTTTGG
75644 AAATCATATATATTTATTTAGTTTAAT
1 AAAT-ATATATATTTATTTA--TTAAT
75671 AAATATATATAATTTATTTA-TAAT
1 AAATATATAT-ATTTATTTATTAAT
75695 ATAATA
1 A-AATA
75701 AGGATCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 6 0.21
27 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATATATATATTTATTTATTAAT
Found at i:85312 original size:14 final size:15
Alignment explanation
Indices: 85286--85314 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
85276 ATTTTTTATG
85286 GTATTTTTCAAAATT
1 GTATTTTTCAAAATT
85301 GTATTTTT-AAAATT
1 GTATTTTTCAAAATT
85315 AATTTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
GTATTTTTCAAAATT
Found at i:85716 original size:23 final size:21
Alignment explanation
Indices: 85673--85745 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
85663 TGAAATTTAT
*
85673 TTTAAATATATAATATT-ATATA
1 TTTAAATTTAT-AT-TTCATATA
*
85695 TTTAAATTTTTATTAATCATAT-
1 TTTAAATTTATATT--TCATATA
85717 TTTAATATTTATATTTCATATA
1 TTTAA-ATTTATATTTCATATA
*
85739 TTAAAAT
1 TTTAAAT
85746 ATTAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 10 0.24
22 19 0.45
23 12 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATTTATATTTCATATA
Found at i:86070 original size:37 final size:37
Alignment explanation
Indices: 86020--86094 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
86010 AACGCTATTA
*
86020 CCCCCTTTGCTAGTG-AAACTAAATAAAATTAAAATAT
1 CCCCCTTCGCTAGTGAAAAC-AAATAAAATTAAAATAT
86057 CCCCCTTCGCTAGTGAAAACAAATAAAATTAAAATAT
1 CCCCCTTCGCTAGTGAAAACAAATAAAATTAAAATAT
86094 C
1 C
86095 AAGTTGATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (37 bp):
CCCCCTTCGCTAGTGAAAACAAATAAAATTAAAATAT
Found at i:98974 original size:26 final size:25
Alignment explanation
Indices: 98935--98983 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
98925 ATATTAGTTT
* *
98935 AATAGTTTATATATTAATTGTAAAAA
1 AATAATTTAAATATTAATT-TAAAAA
98961 AATAATTTAAATATTAATTTAAA
1 AATAATTTAAATATTAATTTAAA
98984 CATCGTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAATTTAAATATTAATTTAAAAA
Found at i:101060 original size:14 final size:17
Alignment explanation
Indices: 101029--101065 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
101019 ATATTGCATG
101029 TTTATATATATATATTT
1 TTTATATATATATATTT
101046 TTTA-ATAT-TAT-TTT
1 TTTATATATATATATTT
101060 TTTATA
1 TTTATA
101066 ATTTGTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 4 0.21
17 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATATATATATTT
Found at i:104930 original size:25 final size:24
Alignment explanation
Indices: 104902--104950 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
104892 CCAATTTGTC
104902 TTTTGGAGCATCTAAATGCAATGTT
1 TTTTGGAGCATCTAAATGC-ATGTT
104927 TTTTGGAGCATCTAAATGCATGTT
1 TTTTGGAGCATCTAAATGCATGTT
104951 AAATACAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTTGGAGCATCTAAATGCATGTT
Found at i:108537 original size:293 final size:291
Alignment explanation
Indices: 107984--108568 Score: 1143
Period size: 293 Copynumber: 2.0 Consensus size: 291
107974 GAGCCTGATT
107984 AATATATTAATTTGGCTTATAGGCCATTTTTGTCATTAGAAAGAAGAATCCTTGGAGAGCAATGA
1 AATATATTAATTTGGCTTATAGGCCATTTTTGTCATTAGAAAGAAGAATCCTTGGAGAGCAATGA
*
108049 AAATGAGAAAAATGTTTTTTGGATTCTCACACAAACTAACCCTTTTACAGATTTAAGTCAATTCA
66 AAATGAGAAAAATGTTTTTTGGATTCTCACACAAACTAACCCTTTTACAGATTTAAATCAATTCA
108114 TTATGGGACTTACAATTCGTGTTTATCTTTGCATTCTTTCCATGCTTGCAATGTGTGTTTACAGT
131 TTATGGGACTTACAATTCGTGTTTATCTTTGCATTCTTTCCATGCTTGCAATGTGTGTTTACAGT
108179 CAAAACACAGAGGGGAAAAAGGCTTCAGAATTCACTGCACAGTCAAATCTGGTTGGTAAAAAATC
196 CAAAACACAGAGGGGAAAAAGGCTTCAGAATTCACTGCACAGTCAAATCTGGTTGGTAAAAAATC
108244 ACAAGATGCTGCTGTTGGCATTCTTGTTCAC
261 ACAAGATGCTGCTGTTGGCATTCTTGTTCAC
108275 AATATATTAATTTGGCTTATAGGCCATTTTTTTGTCATTAGAAAGAAGAATCCTTGGAGAGCAAT
1 AATATATTAATTTGGCTTATAGGCCA--TTTTTGTCATTAGAAAGAAGAATCCTTGGAGAGCAAT
108340 GAAAATGAGAAAAATGTTTTTTGGATTCTCACACAAACTAACCCTTTTACAGATTTAAATCAATT
64 GAAAATGAGAAAAATGTTTTTTGGATTCTCACACAAACTAACCCTTTTACAGATTTAAATCAATT
108405 CATTATGGGACTTACAATTCGTGTTTATCTTTGCATTCTTTCCATGCTTGCAATGTGTGTTTACA
129 CATTATGGGACTTACAATTCGTGTTTATCTTTGCATTCTTTCCATGCTTGCAATGTGTGTTTACA
108470 GTCAAAACACAGAGGGGAAAAAGGCTTCAGAATTCACTGCACAGTCAAATCTGGTTGGTAAAAAA
194 GTCAAAACACAGAGGGGAAAAAGGCTTCAGAATTCACTGCACAGTCAAATCTGGTTGGTAAAAAA
108535 TCACAAGATGCTGCTGTTGGCATTCTTGTTCAC
259 TCACAAGATGCTGCTGTTGGCATTCTTGTTCAC
108568 A
1 A
108569 TGCTTAGAAC
Statistics
Matches: 291, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
291 26 0.09
293 265 0.91
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (291 bp):
AATATATTAATTTGGCTTATAGGCCATTTTTGTCATTAGAAAGAAGAATCCTTGGAGAGCAATGA
AAATGAGAAAAATGTTTTTTGGATTCTCACACAAACTAACCCTTTTACAGATTTAAATCAATTCA
TTATGGGACTTACAATTCGTGTTTATCTTTGCATTCTTTCCATGCTTGCAATGTGTGTTTACAGT
CAAAACACAGAGGGGAAAAAGGCTTCAGAATTCACTGCACAGTCAAATCTGGTTGGTAAAAAATC
ACAAGATGCTGCTGTTGGCATTCTTGTTCAC
Found at i:109377 original size:31 final size:31
Alignment explanation
Indices: 109339--109400 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
109329 ATAATCTAGG
109339 GATTTAAATAAAAACTTTCAAAAAATTTAAT
1 GATTTAAATAAAAACTTTCAAAAAATTTAAT
* *
109370 GATTTAAATAAAAATTTTCAAATAATTTAAT
1 GATTTAAATAAAAACTTTCAAAAAATTTAAT
109401 TATCATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
GATTTAAATAAAAACTTTCAAAAAATTTAAT
Found at i:110723 original size:23 final size:23
Alignment explanation
Indices: 110687--110790 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
110677 AGTGCTGGGC
*
110687 AACAGAGTGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
110710 AACAGAGAGTACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
110733 ATCAAAGAGCACACACAGTGTTAA
1 AACAGAGAGCACACACAGTGCT-A
*
110757 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
110781 AACAGAGAGC
1 AACAGAGAGC
110791 GCGCTAATGT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
23 47 0.71
24 2 0.03
25 14 0.21
26 3 0.05
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:110779 original size:48 final size:45
Alignment explanation
Indices: 110695--110790 Score: 104
Period size: 48 Copynumber: 2.0 Consensus size: 45
110685 GCAACAGAGT
*
110695 GCACACACAGTGCTAAACAGAGAGTACACAAAGTGCTAATCAAAGA
1 GCACACACAGTGCTAAACAGAGAG-ACACAAAGTGCTAAACAAAGA
* * *
110741 GCACACACAGTGTTAATAACAGAGAG-CACGAGACGTGCTAAACAGAGA
1 GCACACACAGTGCT-A-AACAGAGAGACAC-A-AAGTGCTAAACAAAGA
110789 GC
1 GC
110791 GCGCTAATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
46 16 0.38
47 2 0.05
48 24 0.57
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (45 bp):
GCACACACAGTGCTAAACAGAGAGACACAAAGTGCTAAACAAAGA
Found at i:114789 original size:6 final size:6
Alignment explanation
Indices: 114778--114806 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
114768 TGAAGAGCCT
114778 GTCCCC GTCCCC GTCCCC GTCCCC GTCCC
1 GTCCCC GTCCCC GTCCCC GTCCCC GTCCC
114807 TGTCTCTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
GTCCCC
Found at i:117775 original size:108 final size:108
Alignment explanation
Indices: 117545--117781 Score: 264
Period size: 108 Copynumber: 2.2 Consensus size: 108
117535 GATGACACAA
* * * * *
117545 AAAGTCCTCAGAAGAGAAGCCATGATGCTAACATGAGTAGTCCTCAACGTATAAACCATCATGAA
1 AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAACCATAATGAA
* * *
117610 GATACAGAAAAACCTCAAGATATAAGCTGGAATGGAGATACAC
66 GATACACAAAAACCTCAAGATATAAGCTAGAATGAAGATACAC
* * * * *
117653 AAAGTCTTCGAAAGAGAGGCCGTGATGCAAAAATGAGTAGTCCTCGACATATAAATCC-TAATGA
1 AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAA-CCATAATGA
* * * *
117717 AGATGCACAAAAAGCTCGAGATATAA-ATCAGAATGAAGATACAC
65 AGATACACAAAAACCTCAAGATATAAGCT-AGAATGAAGATACAC
*
117761 AGAA-TCCTCAAAAGATAAGCC
1 A-AAGTCCTCAAAAGAGAAGCC
117782 GCAATGAAAA
Statistics
Matches: 105, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
107 1 0.01
108 100 0.95
109 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (108 bp):
AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAACCATAATGAA
GATACACAAAAACCTCAAGATATAAGCTAGAATGAAGATACAC
Found at i:123238 original size:20 final size:20
Alignment explanation
Indices: 123203--123255 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
123193 TATAGTTCGG
123203 ATATATTAATATTTTAAAAA
1 ATATATTAATATTTTAAAAA
123223 ATAT-TTAATATATTTAAATATA
1 ATATATTAATAT-TTTAAA-A-A
123245 ATAATATTAAT
1 AT-ATATTAAT
123256 TGATTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 1 0.04
22 3 0.11
23 2 0.07
24 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATTAATATTTTAAAAA
Found at i:128129 original size:23 final size:22
Alignment explanation
Indices: 128070--128147 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
128060 GGGAGTACCG
*
128070 AAGTACTAAACAGAGAGCACAT
1 AAGTACTAAACAGAGAGCACAC
**
128092 AAGTGTTAGGCAACAGAGAGCACAC
1 AAGTACTA---AACAGAGAGCACAC
* *
128117 ACAGTACTAAACAAAGAGTACAC
1 A-AGTACTAAACAGAGAGCACAC
128140 AAAGTACT
1 -AAGTACT
128148 GAGCACATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 6 0.14
23 18 0.41
24 1 0.02
25 14 0.32
26 5 0.11
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (22 bp):
AAGTACTAAACAGAGAGCACAC
Found at i:128220 original size:23 final size:22
Alignment explanation
Indices: 128148--128222 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
128138 ACAAAGTACT
128148 GAGCACATAAAGTGCTAATAACGGA
1 GAGCACA-AAAGTGCT-A-AACGGA
* * *
128173 GAGCACGAAACGTGCTAAGCAGA
1 GAGCAC-AAAAGTGCTAAACGGA
*
128196 GAGCACACAAAGTGCTAAATGGA
1 GAGCACA-AAAGTGCTAAACGGA
128219 GAGC
1 GAGC
128223 GCACTAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.02
23 25 0.61
24 1 0.02
25 13 0.32
26 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (22 bp):
GAGCACAAAAGTGCTAAACGGA
Found at i:131593 original size:85 final size:85
Alignment explanation
Indices: 131450--131623 Score: 303
Period size: 85 Copynumber: 2.0 Consensus size: 85
131440 GACATTTCTC
*
131450 TATCAATATCACTGTTGTCACATTTCCGTTCTCATTTCTCTCATTCTCCTTTAAAAAACATCACC
1 TATCAACATCACTGTTGTCACATTTCCGTTCTCATTTCTCTCATTCTCCTTTAAAAAACATCACC
*
131515 TTCCTCTTTCCTCCACTCTT
66 TTCCTCCTTCCTCCACTCTT
* *
131535 TATCAACATCATTGTTGTCACATTTCGGTTCTCATTTCTCTCATTCTCCTTTAAAAAACATCACC
1 TATCAACATCACTGTTGTCACATTTCCGTTCTCATTTCTCTCATTCTCCTTTAAAAAACATCACC
*
131600 TTCCTCCTTCTTCCACTCTT
66 TTCCTCCTTCCTCCACTCTT
131620 TATC
1 TATC
131624 TTATCTAGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.21, C:0.32, G:0.04, T:0.43
Consensus pattern (85 bp):
TATCAACATCACTGTTGTCACATTTCCGTTCTCATTTCTCTCATTCTCCTTTAAAAAACATCACC
TTCCTCCTTCCTCCACTCTT
Found at i:133732 original size:20 final size:20
Alignment explanation
Indices: 133688--133733 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
133678 ATTTAAAGTC
*
133688 TAAGAAGAGAAAAAGAAGAG
1 TAAGAAGAGAAAAAGAAGAA
* * *
133708 GAAGAGGAGAAGAAGAAGAA
1 TAAGAAGAGAAAAAGAAGAA
133728 TAAGAA
1 TAAGAA
133734 TGAAAAGAGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (20 bp):
TAAGAAGAGAAAAAGAAGAA
Found at i:139539 original size:100 final size:101
Alignment explanation
Indices: 139381--139583 Score: 345
Period size: 100 Copynumber: 2.0 Consensus size: 101
139371 TAGATGTGAT
*
139381 ATTTTACGTTGCTTCGACTCTTCATTTTTTTTTTTTCTGGAACACATGCAGAGACATAGGTACAG
1 ATTTTACGTTGCTTCGACTCTTCA--TATTTTTTTTCTGGAACACATGCAGAGACATAGGTACAG
*
139446 GATACTTGCATTCGATATTCACACCCGTACTTGACATC
64 GATACTTGCATCCGATATTCACACCCGTACTTGACATC
* *
139484 ATTTTATGTTGCTTCGACTCTTCA-ATTTTTTTTCTGGAACACATGCAGAGACATAGGTACGGGA
1 ATTTTACGTTGCTTCGACTCTTCATATTTTTTTTCTGGAACACATGCAGAGACATAGGTACAGGA
139548 TACTTGCATCCGATATTCACACCCGTACTTGACATC
66 TACTTGCATCCGATATTCACACCCGTACTTGACATC
139584 TGAAATTTTC
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
100 73 0.76
103 23 0.24
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (101 bp):
ATTTTACGTTGCTTCGACTCTTCATATTTTTTTTCTGGAACACATGCAGAGACATAGGTACAGGA
TACTTGCATCCGATATTCACACCCGTACTTGACATC
Found at i:140558 original size:2 final size:2
Alignment explanation
Indices: 140551--140577 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
140541 ATAATATGTG
140551 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
140578 TGGTTGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140831 original size:24 final size:24
Alignment explanation
Indices: 140802--140848 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
140792 ATTTAATACA
**
140802 ATTTTATTTATAAAGCATTTTATG
1 ATTTTATAGATAAAGCATTTTATG
*
140826 ATTTTATAGATGAAGCATTTTAT
1 ATTTTATAGATAAAGCATTTTAT
140849 TTGGAGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (24 bp):
ATTTTATAGATAAAGCATTTTATG
Found at i:142659 original size:8 final size:8
Alignment explanation
Indices: 142642--142671 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
142632 ATAAATAATG
142642 AAAAAA-A
1 AAAAAAGA
142649 AAAAAAGA
1 AAAAAAGA
142657 AAAAAAGA
1 AAAAAAGA
142665 AAAAAAG
1 AAAAAAG
142672 GGAGACACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:145246 original size:3 final size:3
Alignment explanation
Indices: 145238--145263 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
145228 CATTTCACCA
145238 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
145264 ATATCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:145590 original size:2 final size:2
Alignment explanation
Indices: 145583--145611 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
145573 CAGTTGTCTT
145583 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
145612 TTCAGTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:146361 original size:3 final size:3
Alignment explanation
Indices: 146353--146377 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
146343 CATAAATCAT
146353 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
146378 CTAATTCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:149028 original size:15 final size:15
Alignment explanation
Indices: 148984--149028 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
148974 ATCAGGAGGT
148984 TGATGAAGATGACGA
1 TGATGAAGATGACGA
* **
148999 TGAGGAAGACAACGA
1 TGATGAAGATGACGA
*
149014 TGATGATGATGACGA
1 TGATGAAGATGACGA
149029 AGAATTGGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18
Consensus pattern (15 bp):
TGATGAAGATGACGA
Found at i:151828 original size:14 final size:14
Alignment explanation
Indices: 151805--151837 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
151795 CTAGCACTTA
151805 CAAAAAATTAAA-T
1 CAAAAAATTAAATT
151818 CAAATAAATTAAATT
1 CAAA-AAATTAAATT
151833 CAAAA
1 CAAAA
151838 CTAATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (14 bp):
CAAAAAATTAAATT
Found at i:163588 original size:5 final size:5
Alignment explanation
Indices: 163578--163606 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
163568 ATGCTGAAAA
163578 TTGTG TTGTG TTGTG TTGTG TTGTG TTGT
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTGT
163607 TAAGAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TTGTG
Found at i:164370 original size:14 final size:14
Alignment explanation
Indices: 164332--164362 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
164322 ATCCAAACAA
*
164332 TAATAATAAAATAG
1 TAATAATATAATAG
164346 TAATAATATAATAG
1 TAATAATATAATAG
164360 TAA
1 TAA
164363 AATGATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
TAATAATATAATAG
Found at i:174420 original size:45 final size:45
Alignment explanation
Indices: 174369--174474 Score: 131
Period size: 45 Copynumber: 2.4 Consensus size: 45
174359 TAGAAGATGA
* *
174369 TCCAAAAGTAGGAGTGTTGGAAACGCCAAAAGCAGAACTTGGCAC
1 TCCAAAAGCAGGAGTGTTGGAAACGCCAAAAGCAGAACTTGACAC
* * ** * **
174414 TCCAAAAACAGGAGTCTTGGAAGTGCCAAAAGCAGAATTTGATGC
1 TCCAAAAGCAGGAGTGTTGGAAACGCCAAAAGCAGAACTTGACAC
174459 TCCAAAAGCAGGAGTG
1 TCCAAAAGCAGGAGTG
174475 CCAGAAGTGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (45 bp):
TCCAAAAGCAGGAGTGTTGGAAACGCCAAAAGCAGAACTTGACAC
Found at i:174482 original size:45 final size:45
Alignment explanation
Indices: 174393--174491 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
174383 TGTTGGAAAC
* **
174393 GCCAAAAGCAGAACTTGGCACTCCAAAAACAGGAGTCTTGGAAGT
1 GCCAAAAGCAGAACTTGACACTCCAAAAACAGGAGTCTCAGAAGT
* ** *
174438 GCCAAAAGCAGAATTTGATGCTCCAAAAGCAGGAGTGC-CAGAAGT
1 GCCAAAAGCAGAACTTGACACTCCAAAAACAGGAGT-CTCAGAAGT
174483 GCCAAAAGC
1 GCCAAAAGC
174492 TGGTACACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.14
Consensus pattern (45 bp):
GCCAAAAGCAGAACTTGACACTCCAAAAACAGGAGTCTCAGAAGT
Found at i:174645 original size:24 final size:24
Alignment explanation
Indices: 174593--174652 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
174583 CTTCCAGTTG
*
174593 AACCGAAGGCAGGAGTGCCTGTGA
1 AACCGAAGGCAGGAGTGCCTGAGA
*
174617 AACCGAAAGCAGGAGTGCCTGCAG-
1 AACCGAAGGCAGGAGTGCCTG-AGA
*
174641 CACCGAAGGCAG
1 AACCGAAGGCAG
174653 AAGTACTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.35, T:0.08
Consensus pattern (24 bp):
AACCGAAGGCAGGAGTGCCTGAGA
Found at i:176223 original size:43 final size:43
Alignment explanation
Indices: 176159--176332 Score: 303
Period size: 43 Copynumber: 4.0 Consensus size: 43
176149 GAATTCGCAC
*
176159 CACATCCAAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
1 CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
*
176202 CACATCCGAGGCACCAGGGTGCCGATGGTGTCCGAGGCTCCCG
1 CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
* *
176245 CACATCCGAGGCACCAGGGTGCCGATGGTGTCCGATGCTCCCG
1 CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
*
176288 CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGATGCTCCCG
1 CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
176331 CA
1 CA
176333 AAAAAAAGTT
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 127 1.00
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.15
Consensus pattern (43 bp):
CACATCCGAGGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCG
Found at i:183261 original size:23 final size:23
Alignment explanation
Indices: 183136--183262 Score: 157
Period size: 23 Copynumber: 5.4 Consensus size: 23
183126 ACACTAGCGC
* *
183136 GCTCTCTGTTTAGCA-GGTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
183159 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
183184 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
183207 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
183230 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
183253 GCTCTCTGTT
1 GCTCTCTGTT
183263 GCCCAGCACT
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 73 0.78
24 1 0.01
25 16 0.17
26 3 0.03
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:183306 original size:69 final size:69
Alignment explanation
Indices: 183170--183309 Score: 189
Period size: 69 Copynumber: 2.0 Consensus size: 69
183160 CTCTCTGTTA
* * *
183170 TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTGCTCT
1 TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTGTGTACCCT
183235 CTGT
66 CTGT
183239 TTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTA
1 TTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGTACTTTGTGTA
183300 CCCTCTGT
62 CCCTCTGT
183308 TT
1 TT
183310 GTTCCGTATA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
68 2 0.03
69 33 0.52
70 11 0.17
71 13 0.20
72 5 0.08
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (69 bp):
TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTGTGTACCCT
CTGT
Found at i:189705 original size:29 final size:29
Alignment explanation
Indices: 189644--189705 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
189634 CTATTATATT
* * ** *
189644 TTTAAGATTTTTTTTGTATTTTAATTTTT
1 TTTAAGATATTTTTTATATTTTAAAATTA
*
189673 TTTAATATATTTTTTATATTTTAAAATTA
1 TTTAAGATATTTTTTATATTTTAAAATTA
189702 TTTA
1 TTTA
189706 TCAAAACATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTAAGATATTTTTTATATTTTAAAATTA
Found at i:191032 original size:29 final size:29
Alignment explanation
Indices: 191006--191062 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
190996 GAGTTTCACG
191006 TGTAT-AATTG-CATCAAATTAAAGTTCA
1 TGTATCAATTGACATCAAATTAAAGTTCA
*
191033 TGTATGCAATTGCACATCAAATCAAAGTTC
1 TGTAT-CAATTG-ACATCAAATTAAAGTTC
191063 TTGTGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
29 5 0.20
31 15 0.60
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (29 bp):
TGTATCAATTGACATCAAATTAAAGTTCA
Found at i:195970 original size:21 final size:20
Alignment explanation
Indices: 195940--195978 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
195930 AGGCATAGAT
195940 TCCAACTTCAATTCTACGTA
1 TCCAACTTCAATTCTACGTA
195960 TCCAAGCTTCAATTCTACG
1 TCCAA-CTTCAATTCTACG
195979 CATCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (20 bp):
TCCAACTTCAATTCTACGTA
Found at i:208813 original size:351 final size:337
Alignment explanation
Indices: 208033--208963 Score: 1140
Period size: 344 Copynumber: 2.7 Consensus size: 337
208023 CTTTTTTGTT
* *
208033 TGCAGGTCAAAGAAGCTGAAGCTGCAGAACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
* * *
208098 GTAAATCAAGGCACTGCGCCAAGAAGAATACACTTGCAGACGAAACTTTCTACTGGGGCAATGAA
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCA-AC--AACTTTCTACTGGGCCAATGAA
* * * *
208163 GGGTTCTGCAGGTTGTGTCAATGGTGAGAACATGACTAA-TCCTGGCCTCATTGAAGAAGAAGTT
128 AGGTTCTGCAGGTCGTGTCGATGGTGGGAACATGAC-AAGTCCTGGCCTC-TT---GAAGAAGTT
*
208227 CAGTCTGCTCTTACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATATTGT
188 CAGTCTGCTCTAACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATATTGT
*
208292 TTATCTTACTGCCAAAGGCCAAGTTATAATATTAGTACACTGAAATACATTTCTCAAAGTGAACA
253 TTATCTTACTGCCAAAGGCCAAGATATAATATTAGTACACTGAAATACATTTCTCAAAGTGAACA
*
208357 ATATCTTCCAATACTTTGAA
318 ATATCTTCCAATACTTTAAA
* * * *
208377 TGCAGGTCACAGAAGCTGAAGCTGCTGGACTGACTTCTAGCTCGGATGGGTCAGAGAAGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
* *
208442 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAACTAGACTTTCTACCGGACCAATGAA
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGC-AAC-A-ACTTTCTACTGGGCCAATGAA
* * *
208507 AGGTTCTGCAGGTGGTGTCGATGGTGGGAGCATGACAAGTCCTGGCCTCGTTGAAGAAGTTCAAT
128 AGGTTCTGCAGGTCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTC-TTGAAGAAGTTCAGT
* * *
208572 CTGCTCTAACCGAGGTAGAGTTACCAGGAAAAAGCTAATTTTGAGCGCTGTTGATGCACTGTT-T
192 CTGCTCTAACTGAGGTAGAGTTACCAGG-AAAAGCTAATTTTGAGCACTGTTGAT--A-TATTGT
* * * * * * * *
208636 ATCATACTCCTTTTCTTTTGCCGAAGGTCAA-ATGTAATGTTAGT-CGCTGAATTACATTTCTCG
253 -T--TA-T-C-TTAC---TGCCAAAGGCCAAGATATAATATTAGTACACTGAAATACATTTCTCA
* *
208699 AAGTGAGCAATTTCTTCCAATACTTTAAA
309 AAGTGAACAATATCTTCCAATACTTTAAA
208728 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
* * * * * * * *
208793 GTAAACCAAGCCATTGCTCCAAGAAGATTATGTTTG--A-AACTTTCTTCTGGGCCGATGAAAGG
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAACAACTTTCTACTGGGCCAATGAAAGG
* *
208855 TTCTGCAGGCCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCTGTAAAGAAGTTCAGTCTG
131 TTCTGCAGGTCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCT-TGAAGAAGTTCAGTCTG
** * *
208920 CTCTAACTGAGGTAGAGGAACTAGGAAAAGTTAATTTT-AGCACT
195 CTCTAACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACT
208964 CTTTGTATAT
Statistics
Matches: 510, Mismatches: 60, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
341 38 0.07
342 25 0.05
343 8 0.02
344 172 0.34
345 104 0.20
346 1 0.00
347 2 0.00
348 2 0.00
349 1 0.00
350 3 0.01
351 133 0.26
352 10 0.02
353 11 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (337 bp):
TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAACAACTTTCTACTGGGCCAATGAAAGG
TTCTGCAGGTCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCTTGAAGAAGTTCAGTCTGC
TCTAACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATATTGTTTATCTTA
CTGCCAAAGGCCAAGATATAATATTAGTACACTGAAATACATTTCTCAAAGTGAACAATATCTTC
CAATACTTTAAA
Found at i:213444 original size:39 final size:38
Alignment explanation
Indices: 213358--213436 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 38
213348 ACGGTTTTTT
* * * *
213358 TTTTTATTTGAAAAATAGATATGAAGCAATTTTACGGTA
1 TTTTTGTTTGAAAAATAGATATGAAACAATTCTAC-ATA
213397 TTTTTGTTTGAAAAATAGATATGAAACAATTCTA-ATA
1 TTTTTGTTTGAAAAATAGATATGAAACAATTCTACATA
213434 TTT
1 TTT
213437 ATCTGTTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 5 0.14
39 31 0.86
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (38 bp):
TTTTTGTTTGAAAAATAGATATGAAACAATTCTACATA
Found at i:245025 original size:33 final size:34
Alignment explanation
Indices: 244980--245043 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
244970 TTACTAAAAA
244980 TAAATAAATTTAGTCAAAATAAAAATAATAACTT
1 TAAATAAATTTAGTCAAAATAAAAATAATAACTT
*
245014 TAAAT-AATTTAGTCAAAATAAAATTAATAA
1 TAAATAAATTTAGTCAAAATAAAAATAATAA
245044 AATAACAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (34 bp):
TAAATAAATTTAGTCAAAATAAAAATAATAACTT
Found at i:245283 original size:13 final size:13
Alignment explanation
Indices: 245265--245291 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
245255 CGAAATACAC
245265 AAATAAATTGCTT
1 AAATAAATTGCTT
245278 AAATAAATTGCTT
1 AAATAAATTGCTT
245291 A
1 A
245292 TCAACTTCGC
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:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATAAATTGCTT
Found at i:247745 original size:26 final size:25
Alignment explanation
Indices: 247715--247786 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
247705 CCTGTGTTTT
*
247715 ATTTAAATACATATTAAATATTTAAA
1 ATTTAAATAAATATTAAAT-TTTAAA
* *
247741 ATTTAATTATATATT-AATTTTAAA
1 ATTTAAATAAATATTAAATTTTAAA
247765 A--TAAATAAATATT--ATTTTAAA
1 ATTTAAATAAATATTAAATTTTAAA
247786 A
1 A
247787 GAAACAGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.21
22 10 0.24
24 7 0.17
25 3 0.07
26 13 0.31
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAAATAAATATTAAATTTTAAA
Found at i:255129 original size:2 final size:2
Alignment explanation
Indices: 255124--255153 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
255114 AAAAAAAAAA
255124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
255154 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262209 original size:13 final size:13
Alignment explanation
Indices: 262191--262215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262181 TCAGGATTAA
262191 ATATTTTTTTTTT
1 ATATTTTTTTTTT
262204 ATATTTTTTTTT
1 ATATTTTTTTTT
262216 ATTTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATATTTTTTTTTT
Found at i:262212 original size:12 final size:11
Alignment explanation
Indices: 262192--262221 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
262182 CAGGATTAAA
262192 TATTTTTTTTT
1 TATTTTTTTTT
262203 TATATTTTTTTT
1 TAT-TTTTTTTT
262215 TATTTTT
1 TATTTTT
262222 AAATTGTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:263929 original size:1 final size:1
Alignment explanation
Indices: 263923--263947 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
263913 GGAGGGATAA
263923 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
263948 GCTGTAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:266456 original size:23 final size:24
Alignment explanation
Indices: 266414--266461 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
266404 TATTTGGATT
266414 AGGACTAAAATTTGAAAATT-AAA
1 AGGACTAAAATTTGAAAATTCAAA
*
266437 AGGACTAAAA-TTGATCAATTCAAA
1 AGGACTAAAATTTGA-AAATTCAAA
266461 A
1 A
266462 TGTACATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AGGACTAAAATTTGAAAATTCAAA
Found at i:270933 original size:32 final size:34
Alignment explanation
Indices: 270892--270956 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
270882 AATTATATTT
270892 ATTTCAAAAT-TCGT-C-TTTTTC-TTCTTTTTTA
1 ATTTCAAAATGT-GTCCTTTTTTCTTTCTTTTTTA
270923 ATTTCGAAAATGTGTCCTTTTTTCTTTCTTTTTT
1 ATTTC-AAAATGTGTCCTTTTTTCTTTCTTTTTT
270957 TAAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
31 5 0.17
32 7 0.24
33 2 0.07
34 6 0.21
35 9 0.31
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (34 bp):
ATTTCAAAATGTGTCCTTTTTTCTTTCTTTTTTA
Found at i:270984 original size:3 final size:3
Alignment explanation
Indices: 270976--271005 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
270966 TTTTAATGAA
270976 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
271006 GATTTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.