Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006895.1 Hibiscus syriacus cultivar Beakdansim tig00017599_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: 162710
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:7806 original size:21 final size:23
Alignment explanation
Indices: 7777--7834 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
7767 ATATCAAATT
*
7777 ATATGAAAAAATTAAT-AAAA-A
1 ATATTAAAAAATTAATGAAAACA
7798 ATATTAAAAAA-T-ATGAAAACA
1 ATATTAAAAAATTAATGAAAACA
7819 AT-TTACAAAAATTAAT
1 ATATTA-AAAAATTAAT
7835 CCTAAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.06
20 8 0.26
21 18 0.58
22 1 0.03
23 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
ATATTAAAAAATTAATGAAAACA
Found at i:10925 original size:12 final size:12
Alignment explanation
Indices: 10882--10927 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
10872 CGTTGGACAC
10882 GGGTCGGGTCTT-
1 GGGTCGGGT-TTG
10894 -GGTCGGGTTTG
1 GGGTCGGGTTTG
* *
10905 GGTTTGGGTTTG
1 GGGTCGGGTTTG
10917 GGGTCGGGTTT
1 GGGTCGGGTTT
10928 TGTTATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 8 0.29
12 18 0.64
ACGTcount: A:0.00, C:0.09, G:0.52, T:0.39
Consensus pattern (12 bp):
GGGTCGGGTTTG
Found at i:11484 original size:42 final size:42
Alignment explanation
Indices: 11419--11518 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
11409 TGGATGACCC
* * *
11419 GAAGGTCTTA-TCATCTTGGTCGAAAGACTTA-TAAATGGCCT
1 GAAGGACTTACTCATCATGCTCGAAAGACTTACT-AATGGCCT
* * *
11460 GAATGACTTACTCATCATGCTCGAAAGACTTACTGATGGCTT
1 GAAGGACTTACTCATCATGCTCGAAAGACTTACTAATGGCCT
*
11502 GAAGGAATTACTCATCA
1 GAAGGACTTACTCATCA
11519 AAAAACCCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 8 0.16
42 40 0.82
43 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
GAAGGACTTACTCATCATGCTCGAAAGACTTACTAATGGCCT
Found at i:11907 original size:275 final size:275
Alignment explanation
Indices: 11382--11943 Score: 808
Period size: 275 Copynumber: 2.0 Consensus size: 275
11372 ACCGAAAATG
* *
11382 TTGAAAACATCGTGCCCGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGGTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
* * ** * * **
11447 TTATAAATGGCCTGAATGACTTACTCATCATGCTCGAAAGACTTACTGATGGCTTGAAGGAATTA
66 TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
11512 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
131 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
* *
11577 TCTTAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATC-AGACTT
196 GCTTAGCTT-CTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAG-CTT
11641 AGTTTCTAAAAACTCAT
259 AGTTTCTAAAAACTCAT
* * *
11658 TTGAGAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGTTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
* * * *
11723 TTATAGATGACCTGGAGGA-TTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAATGACTTA
66 TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
* *
11787 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATTAAGGAACCCCTAAAAAT
131 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTT-TC--CAAGGAACCCCTAAAAAT
* * * * *
11852 TAGGCTTAGCTT-TCTTGAAAATTCTTTGGAGATAATCATTAAGAAATCC-CTGAAAATCAAGCT
193 TAGGCTTAGCTTCTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAGCT
*
11915 TAGTTTTTAAAAACTCAT
258 TAGTTTCTAAAAACTCAT
11933 TTGAAAACATC
1 TTGAAAACATC
11944 AAGAAACCCT
Statistics
Matches: 254, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
275 116 0.46
276 110 0.43
278 28 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (275 bp):
TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
GCTTAGCTTCTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAGCTTAG
TTTCTAAAAACTCAT
Found at i:11908 original size:57 final size:53
Alignment explanation
Indices: 11830--11971 Score: 146
Period size: 57 Copynumber: 2.6 Consensus size: 53
11820 TTCTTAGTTG
* * *
11830 TCATTAAGGAACCCCTAAAAATTAGGCTTAGCTTTCTTGAAAATTC-TTTGGAGATAA
1 TCATTAA-GAAACCCTAAAAATTAGGCTTAGCTTT-TTAAAAACTCATTT-GA-A-AA
* * *
11887 TCATTAAGAAATCCCTGAAAATCAAGCTTAG-TTTTTAAAAACTCATTTGAAAA
1 TCATTAAGAAA-CCCTAAAAATTAGGCTTAGCTTTTTAAAAACTCATTTGAAAA
*
11940 -CATCAAGAAACCCTAAAAATTAGGCTTAGCTT
1 TCATTAAGAAACCCTAAAAATTAGGCTTAGCTT
11972 CTTTTTTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
51 16 0.22
52 11 0.15
53 2 0.03
54 1 0.01
55 10 0.14
56 9 0.12
57 23 0.32
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (53 bp):
TCATTAAGAAACCCTAAAAATTAGGCTTAGCTTTTTAAAAACTCATTTGAAAA
Found at i:13149 original size:10 final size:10
Alignment explanation
Indices: 13118--13204 Score: 77
Period size: 10 Copynumber: 8.1 Consensus size: 10
13108 TTATTTCTTC
13118 TTTCTTTCTTT
1 TTTCTTT-TTT
13129 CTTTC-TTTTT
1 -TTTCTTTTTT
13139 TTTCTTTTTT
1 TTTCTTTTTT
13149 TTTCCTTTTTTTT
1 TTT-C--TTTTTT
*
13162 TTTCTATTTT
1 TTTCTTTTTT
13172 TTTCTATTTTT
1 TTTCT-TTTTT
13183 TTTCTATTTTT
1 TTTCT-TTTTT
* *
13194 TATGTTTTTT
1 TTTCTTTTTT
13204 T
1 T
13205 CTATATCTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.06
10 27 0.41
11 21 0.32
12 5 0.08
13 9 0.14
ACGTcount: A:0.05, C:0.11, G:0.01, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:13150 original size:11 final size:11
Alignment explanation
Indices: 13115--13204 Score: 74
Period size: 11 Copynumber: 7.9 Consensus size: 11
13105 ATTTTATTTC
*
13115 TTCTTTCTTTCT
1 TTCTTT-TTTTT
13127 TTCTTTCTTTTTT
1 TTC-TT-TTTTTT
13140 TTCTTTTTTTT
1 TTCTTTTTTTT
*
13151 TCCTTTTTTTT
1 TTCTTTTTTTT
*
13162 TT-TCTATTTTT
1 TTCT-TTTTTTT
*
13173 TTCTATTTTTT
1 TTCTTTTTTTT
*
13184 TTCTATTTTTT
1 TTCTTTTTTTT
* *
13195 ATGTTTTTTT
1 TTCTTTTTTT
13205 CTATATCTCT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
10 1 0.02
11 48 0.74
12 6 0.09
13 9 0.14
14 1 0.02
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.82
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:13160 original size:23 final size:22
Alignment explanation
Indices: 13126--13204 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
13116 TCTTTCTTTC
*
13126 TTTCTTTCTTTTTTTTCTTTTTT
1 TTTCTTT-TTTTTTTTCTATTTT
13149 TTTCCTTTTTTTTTTTCTATTTT
1 TTT-CTTTTTTTTTTTCTATTTT
*
13172 TTTC-TATTTTTTTTCTATTTT
1 TTTCTTTTTTTTTTTCTATTTT
*
13193 TTATGTTTTTTT
1 TT-TCTTTTTTT
13205 CTATATCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 18 0.37
22 2 0.04
23 25 0.51
24 4 0.08
ACGTcount: A:0.05, C:0.10, G:0.01, T:0.84
Consensus pattern (22 bp):
TTTCTTTTTTTTTTTCTATTTT
Found at i:16314 original size:44 final size:44
Alignment explanation
Indices: 16211--16456 Score: 345
Period size: 44 Copynumber: 5.6 Consensus size: 44
16201 CAAGATGGCA
* *
16211 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCT-CTCTACT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
*
16254 ATGTGCAAGGGTAAGTCGTTACCGTTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
*
16298 ATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* * * **
16342 ACGTGCAAGGTTAAGTCCTTATCGTTACCACAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* *
16386 ACGTGCAAGTGTAAGT-CTTACCGTTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* *
16429 ATGTGTC-AGTGTAAATCCTTACCGTTAC
1 ATGTG-CAAGGGTAAGTCCTTACCGTTAC
16457 TACTGACTCC
Statistics
Matches: 183, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
43 71 0.39
44 112 0.61
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (44 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
Found at i:16326 original size:87 final size:88
Alignment explanation
Indices: 16211--16497 Score: 346
Period size: 87 Copynumber: 3.3 Consensus size: 88
16201 CAAGATGGCA
* * *
16211 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCT-CTCTACTATGTGCAAGGGTAAGTCGTTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
**
16275 CCGTTACCGTAGGCTCCTCTGCT
66 CCGTTACCACAGGCTCCTCTGCT
* * *
16298 ATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGCTACGTGCAAGGTTAAGTCCTTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
*
16363 TCGTTACCACAGGCTCCTCTGCT
66 CCGTTACCACAGGCTCCTCTGCT
* * * *
16386 ACGTGCAAGTGTAAGT-CTTACCGTTACCGTAGGCTCCTCTGCTATGTGTC-AGTGTAAATCCTT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTG-CAAGGGTAAGTCCTT
* * * *
16449 ACCGTTACTACTGACTCCTCTACT
65 ACCGTTACCACAGGCTCCTCTGCT
* ** *
16473 TTGTGCACAGAATAAGACCTTACCG
1 ATGTGCA-AGGGTAAGTCCTTACCG
16498 CAGGTTCCTC
Statistics
Matches: 170, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
87 98 0.58
88 65 0.38
89 7 0.04
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (88 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
CCGTTACCACAGGCTCCTCTGCT
Found at i:16409 original size:131 final size:131
Alignment explanation
Indices: 16213--16456 Score: 357
Period size: 131 Copynumber: 1.9 Consensus size: 131
16203 AGATGGCAAT
* ** *
16213 GTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCTCTCTACTATGTGCAAGGGTAAGTCGTTACCG
1 GTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCTCTACTACGTGCAAGGGTAAGTCGTTACCG
*
16278 TTACCGTAGGCTCCTCTGCTATGTG-CAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGCT
66 TTACCGTAGGCTCCTCTGCTATGTGTC-AGGGTAAATCCTTACCATTACCGTAGGCTCCTCTGCT
16342 AC
130 AC
* * * *
16344 GTGCAAGGTTAAGTCCTTATCGTTACCACAGGCTCCTCTGCTACGTGCAAGTGTAAGTC-TTACC
1 GTGCAAGGGTAAGTCCTTACCGTTACCACAGGCT-CTCTACTACGTGCAAGGGTAAGTCGTTACC
* *
16408 GTTACCGTAGGCTCCTCTGCTATGTGTCAGTGTAAATCCTTACCGTTAC
65 GTTACCGTAGGCTCCTCTGCTATGTGTCAGGGTAAATCCTTACCATTAC
16457 TACTGACTCC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 78 0.78
132 22 0.22
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (131 bp):
GTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCTCTACTACGTGCAAGGGTAAGTCGTTACCG
TTACCGTAGGCTCCTCTGCTATGTGTCAGGGTAAATCCTTACCATTACCGTAGGCTCCTCTGCTA
C
Found at i:16479 original size:131 final size:131
Alignment explanation
Indices: 16211--16497 Score: 339
Period size: 131 Copynumber: 2.2 Consensus size: 131
16201 CAAGATGGCA
* ** *
16211 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCTCTCTACTATGTGCAAGGGTAAGTCGTTAC
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCTCTACTACGTGCAAGGGTAAGTCGTTAC
* * *
16276 CGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGC
66 CGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAATCCTTACCATTACCGTAGACTCCTCTAC
16341 T
131 T
* * * * *
16342 ACGTGCAAGGTTAAGTCCTTATCGTTACCACAGGCTCCTCTGCTACGTGCAAGTGTAAGTC-TTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCT-CTCTACTACGTGCAAGGGTAAGTCGTTA
* *
16406 CCGTTACCGTAGGCTCCTCTGCTATGTGTC-AGTGTAAATCCTTACCGTTA-C-TACTGACTCCT
65 CCGTTACCGTAGGCTCCTCTGCTATGTG-CAAGGGTAAATCCTTACCATTACCGTA--GACTCCT
16468 CTACT
127 CTACT
* ** *
16473 TTGTGCACAGAATAAGACCTTACCG
1 ATGTGCA-AGGGTAAGTCCTTACCG
16498 CAGGTTCCTC
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
129 2 0.02
130 1 0.01
131 93 0.71
132 35 0.27
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (131 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCTCTACTACGTGCAAGGGTAAGTCGTTAC
CGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAATCCTTACCATTACCGTAGACTCCTCTAC
T
Found at i:20222 original size:21 final size:19
Alignment explanation
Indices: 20188--20230 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
20178 GAGAATTCAC
20188 TTTGATTTAATTCACGATTCT
1 TTTGATTTAATTCA--ATTCT
**
20209 TTTGATTTCTTTCAATTCT
1 TTTGATTTAATTCAATTCT
20228 TTT
1 TTT
20231 ATTATTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTGATTTAATTCAATTCT
Found at i:21715 original size:21 final size:21
Alignment explanation
Indices: 21691--21735 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21681 ATCAATTCCT
*
21691 TTTTTGCATTTACAT-TTTGCA
1 TTTTT-CATTCACATCTTTGCA
*
21712 TTTTTCATTCCCATCTTTGCA
1 TTTTTCATTCACATCTTTGCA
21733 TTT
1 TTT
21736 GCATGTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTTCATTCACATCTTTGCA
Found at i:23146 original size:8 final size:7
Alignment explanation
Indices: 23119--23213 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 7
23109 CAAGGAAAAG
23119 AAAGAGA
1 AAAGAGA
*
23126 AAGAGAAA
1 AA-AGAGA
23134 AAAGAGTA
1 AAAGAG-A
23142 AAAGAGGA
1 AAAGA-GA
23150 AAA-AGA
1 AAAGAGA
23156 AAAGAGA
1 AAAGAGA
*
23163 AAA-AAA
1 AAAGAGA
* *
23169 AAAAAAA
1 AAAGAGA
*
23176 AAAAAG-
1 AAAGAGA
23182 AAAGA-A
1 AAAGAGA
23188 AAAGA-A
1 AAAGAGA
23194 AAAGAAGA
1 AAAG-AGA
23202 AAA-AGA
1 AAAGAGA
23208 AGAAGA
1 A-AAGA
23214 AAATAGACAT
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
6 28 0.38
7 23 0.32
8 21 0.29
9 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (7 bp):
AAAGAGA
Found at i:23160 original size:37 final size:37
Alignment explanation
Indices: 23095--23205 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 37
23085 AAAAGAAAGC
* * * * *
23095 AAAAAAAAAGAATGCAAGGAAAAG-AAAGAGAAAGAGA
1 AAAAAAAAAAAAAGAAAGAAAAAGAAAAGAGAAA-AAA
* ** *
23132 AAAAAGAGTAAAAG-AGGAAAAAGAAAAGAGAAAAAA
1 AAAAAAAAAAAAAGAAAGAAAAAGAAAAGAGAAAAAA
*
23168 AAAAAAAAAAAAAGAAAGAAAAAGAAAA-AGAAGAAA
1 AAAAAAAAAAAAAGAAAGAAAAAGAAAAGAGAAAAAA
23204 AA
1 AA
23206 GAAGAAGAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
36 29 0.49
37 30 0.51
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.02
Consensus pattern (37 bp):
AAAAAAAAAAAAAGAAAGAAAAAGAAAAGAGAAAAAA
Found at i:23195 original size:15 final size:15
Alignment explanation
Indices: 23085--23215 Score: 83
Period size: 15 Copynumber: 8.5 Consensus size: 15
23075 AAAATACACA
23085 AAAAGAAAGCAAAAA-
1 AAAAGAAAG-AAAAAG
* * *
23100 AAAAGAATG-CAAGG
1 AAAAGAAAGAAAAAG
23114 AAAAGAAAGAGAAAGAG
1 AAAAGAAAGA-AAA-AG
*
23131 AAAA-AAGAGTAAAAG
1 AAAAGAA-AGAAAAAG
*
23146 AGGAA-AAAGAAAAGAG
1 A-AAAGAAAGAAAA-AG
* * *
23162 AAAAAAAAAAAAAAA
1 AAAAGAAAGAAAAAG
23177 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
23192 AAAA-AGAAGAAAAAG
1 AAAAGA-AAGAAAAAG
23207 AAGAAGAAA
1 AA-AAGAAA
23216 ATAGACATAT
Statistics
Matches: 90, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 46 0.51
16 25 0.28
17 8 0.09
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:23197 original size:6 final size:6
Alignment explanation
Indices: 23148--23216 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
23138 AGTAAAAGAG
* *
23148 GAAAAA GAAAAGA GAAAAA -AAAAA AAAAAA AAAGAAA GAAAAA GAAAAA
1 GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA GAAAAA
*
23197 G---AA GAAAAA GAAGAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAA
23217 TAGACATATC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
3 3 0.06
5 5 0.09
6 35 0.65
7 11 0.20
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:23206 original size:9 final size:9
Alignment explanation
Indices: 23114--23211 Score: 62
Period size: 9 Copynumber: 11.1 Consensus size: 9
23104 GAATGCAAGG
23114 AAAAGAAAGA
1 AAAAG-AAGA
*
23124 GAAAG-AGA
1 AAAAGAAGA
*
23132 AAAA-AGAGT
1 AAAAGA-AGA
*
23141 AAAAGAGGA
1 AAAAGAAGA
23150 AAAAG-A-A
1 AAAAGAAGA
*
23157 AAGAGAA-A
1 AAAAGAAGA
* *
23165 AAAAAAAAA
1 AAAAGAAGA
*
23174 AAAAAAAGA
1 AAAAGAAGA
*
23183 AAGAAAAAGA
1 AA-AAGAAGA
23193 AAAAGAAGA
1 AAAAGAAGA
23202 AAAAGAAGA
1 AAAAGAAGA
23211 A
1 A
23212 GAAAATAGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
7 5 0.07
8 13 0.18
9 39 0.55
10 14 0.20
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:23901 original size:27 final size:27
Alignment explanation
Indices: 23828--23902 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
23818 GAAGCCAACA
*
23828 TGAAACACATTACCTCCCAAATTAACC
1 TGAAACACATTACTTCCCAAATTAACC
23855 TGAAACACATTACTTCCCCAAATTAACC
1 TGAAACACATTACTT-CCCAAATTAACC
*
23883 T-AAACACATTGCATTCCCAA
1 TGAAACACATTAC-TTCCCAA
23903 GACATCCTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 29 0.66
28 15 0.34
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (27 bp):
TGAAACACATTACTTCCCAAATTAACC
Found at i:25267 original size:55 final size:54
Alignment explanation
Indices: 25187--25309 Score: 140
Period size: 55 Copynumber: 2.3 Consensus size: 54
25177 GATAATGTTT
* * * ** *
25187 TTTTAAAGAAAATAAGTCCGATTTTTGGAACTTTCTTAATTATTTTTAAATGAGC
1 TTTTAAAGAAACTAAGTACGATTTTTAGAACTTT-TTAACAATTTTCAAATGAGC
* * * *
25242 TTTTAAAGAAACTAAGTATGCTTTTTAGAAGTTTTTGACAATTTTCAAATGAGC
1 TTTTAAAGAAACTAAGTACGATTTTTAGAACTTTTTAACAATTTTCAAATGAGC
25296 -TTTAAAGAAACTAA
1 TTTTAAAGAAACTAA
25310 CTCTTATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 14 0.24
54 16 0.28
55 28 0.48
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (54 bp):
TTTTAAAGAAACTAAGTACGATTTTTAGAACTTTTTAACAATTTTCAAATGAGC
Found at i:25325 original size:53 final size:55
Alignment explanation
Indices: 25228--25333 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 55
25218 TTTCTTAATT
* * * *
25228 ATTTTTAAATGAGCTTTTAAAGAAACTAAGTATGCTTTTTAGAAGTTT-TTGACA
1 ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGACA
* *
25282 ATTTTCAAATGAGC-TTTAAAGAAACTAACTCTTATTTTCAGAAGTTTCTTGA
1 ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGA
25334 TATTTTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 28 0.62
54 17 0.38
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (55 bp):
ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGACA
Found at i:25339 original size:53 final size:55
Alignment explanation
Indices: 25218--25339 Score: 142
Period size: 53 Copynumber: 2.3 Consensus size: 55
25208 TTTTTGGAAC
* * * * * *
25218 TTTCTTAATTATTTTTAAATGAGCTTTTAAAGAAACTAAGTATGCTTTTTAGAAG
1 TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
* * *
25273 TTT-TTGACAATTTTCAAATGAGC-TTTAAAGAAACTAACTCTTATTTTCAGAAG
1 TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
25326 TTTCTTGA-TATTTT
1 TTTCTTGACTATTTT
25340 TTAAACGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 33 0.59
54 20 0.36
55 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (55 bp):
TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
Found at i:25608 original size:42 final size:42
Alignment explanation
Indices: 25561--25658 Score: 187
Period size: 42 Copynumber: 2.3 Consensus size: 42
25551 GAGCCATCAG
25561 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
1 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
*
25603 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCGAGTCATCTA
1 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
25645 TAAGTCTTTCGAGC
1 TAAGTCTTTCGAGC
25659 AAGATGATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (42 bp):
TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
Found at i:25657 original size:20 final size:20
Alignment explanation
Indices: 25594--25657 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
25584 AAATCCTTCA
25594 AGTCATCTATAAGTCTTTCG
1 AGTCATCTATAAGTCTTTCG
* * *
25614 AGCGTGATGCT-TAAATCCTTCG
1 A--GTCAT-CTATAAGTCTTTCG
25636 AGTCATCTATAAGTCTTTCG
1 AGTCATCTATAAGTCTTTCG
25656 AG
1 AG
25658 CAAGATGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
22 14 0.41
23 2 0.06
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (20 bp):
AGTCATCTATAAGTCTTTCG
Found at i:25977 original size:144 final size:141
Alignment explanation
Indices: 25666--26029 Score: 496
Period size: 144 Copynumber: 2.6 Consensus size: 141
25656 AGCAAGATGA
* *
25666 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGTTGTTTTCAGCATTTCCTTTTCTCGATT
1 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
** * *
25731 CACAACACTTCGAATCAGCAACGCCTTACCAGAGGGGACATTTCCTTTTGCTCGATTCACACACT
66 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGAACATTTCCTATTGCTCGATTCACACACT
25796 TCGAATCAGCT
131 TCGAATCAGCT
* * ** * * *
25807 TAAGTCTTTCGGGCCATCCATAAGACCTTCAGTAATGATGTTTTCAACATTTACTTTTCTCAATT
1 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
* * *
25872 CACAACACTTCGTATCAGTAATGCCCCACCAGAGAGGTTAACATTTCCTATTGCTCGATTCACAC
66 CACAACACTTCGAATCAGCAACGCCCCACCAGAG-GG--AACATTTCCTATTGCTCGATTCACAC
*
25937 ACTTTGAATCAGCT
128 ACTTCGAATCAGCT
* * * * *
25951 TAAGTCCTTCAGGCCATTCATAAGACCTTCGGGCAGGGTGTTTTCAACATTTCCTTTGCCCGATT
1 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
26016 CAC-ACACTTCGAAT
66 CACAACACTTCGAAT
26030 TGGCTTAAGT
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
141 85 0.45
142 2 0.01
143 10 0.05
144 93 0.49
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (141 bp):
TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGAACATTTCCTATTGCTCGATTCACACACT
TCGAATCAGCT
Found at i:26057 original size:84 final size:84
Alignment explanation
Indices: 25911--26124 Score: 304
Period size: 84 Copynumber: 2.5 Consensus size: 84
25901 CAGAGAGGTT
* ** *
25911 AACATTTCCTATTGCTCGATTCACACACTTTGAATCAGCTTAAGTCCTTCAGGCCATTCATAAGA
1 AACATTTCCT-TTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAGGCCATCCATAAGA
*
25976 CCTTCGGGCAGGGTGTTTTC
65 CCTTCGGGCAGGATGTTTTC
* **
25996 AACATTTCCTTTGCCCGATTCACACACTTCGAATTGGCTTAAGTAATTC-GAGCCATCCATAAGA
1 AACATTTCCTTTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAG-GCCATCCATAAGA
26060 CCTTCGGGCAGGATGTTTTC
65 CCTTCGGGCAGGATGTTTTC
* *
26080 AACATTTCCTCTGCTCGATTCACAACACTTCGAATCAGCATAAGT
1 AACATTTCCTTTGCTCGATTCAC-ACACTTCGAATCAGCTTAAGT
26125 CAGTTGGGCC
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
83 1 0.01
84 85 0.75
85 28 0.25
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (84 bp):
AACATTTCCTTTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAGGCCATCCATAAGAC
CTTCGGGCAGGATGTTTTC
Found at i:27534 original size:136 final size:136
Alignment explanation
Indices: 27238--27561 Score: 341
Period size: 136 Copynumber: 2.4 Consensus size: 136
27228 ATGGTAAACC
* * **
27238 AATCAACATTTCAAATAGAGAGTTTATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCA
1 AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGGAGAAAAAGTTCA
* *
27303 TAATGAGAAGAACTTGTTCAACCTTCGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCT
66 TAATAAGAAGAACTTGTTCAACCTTCACTCGATTAATCACATAT---GTTGAATCAGCAACACCT
27368 CGCTTGAGG
128 CGCTTGAGG
* * * *
27377 AATCAACATTTC-CAATGGAGAGTTCATAATGTGAATAACTCAT-TCGAAAAAGGGAGAAGAAGT
1 AATCAACATTTCAC-ATAGAGAGTTCATAATGAGAAGAACTCATCT-G-AAAAGGGAGAAAAAGT
* * * * ** ** *
27440 TCATAATAAGAAGAGCTTGTTCGACCTATCACTTGATTCATGGCAT-T-TTGAATCAGTGACGCC
63 TCATAATAAGAAGAACTTGTTCAACCT-TCACTCGATTAATCACATATGTTGAATCAGCAACACC
27503 TCGCTTGAGG
127 TCGCTTGAGG
* * * * *
27513 GATCAATATTTCACATAGAGAGTTCATAATCAGAAGATCTCATCCGAAA
1 AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAA
27562 GAGTGAGAGT
Statistics
Matches: 152, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
135 3 0.02
136 58 0.38
137 1 0.01
138 1 0.01
139 38 0.25
140 38 0.25
141 13 0.09
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (136 bp):
AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGGAGAAAAAGTTCA
TAATAAGAAGAACTTGTTCAACCTTCACTCGATTAATCACATATGTTGAATCAGCAACACCTCGC
TTGAGG
Found at i:31412 original size:13 final size:13
Alignment explanation
Indices: 31394--31418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31384 ATTTATTACA
31394 TTTAATAATTTAT
1 TTTAATAATTTAT
31407 TTTAATAATTTA
1 TTTAATAATTTA
31419 AAAATAAATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAATAATTTAT
Found at i:31500 original size:16 final size:18
Alignment explanation
Indices: 31468--31502 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
31458 CATTGAATTA
31468 TATAATATATATTTTTAT
1 TATAATATATATTTTTAT
31486 TATAAT-TAT-TTTTTAT
1 TATAATATATATTTTTAT
31502 T
1 T
31503 TGTATTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATAATATATATTTTTAT
Found at i:31515 original size:17 final size:16
Alignment explanation
Indices: 31479--31531 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
31469 ATAATATATA
*
31479 TTTTTATTATAATTAT-
1 TTTTTATT-TTATTATG
31495 TTTTTATTTGTATTATG
1 TTTTTATTT-TATTATG
31512 TTTTTATTTTATTATAG
1 TTTTTATTTTATTAT-G
31529 TTT
1 TTT
31532 AAATTGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 1 0.03
16 19 0.58
17 13 0.39
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTATTATG
Found at i:31938 original size:22 final size:23
Alignment explanation
Indices: 31904--31946 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31894 ATATAATAAA
31904 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
31927 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
31947 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:32024 original size:29 final size:33
Alignment explanation
Indices: 31992--32060 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 33
31982 TATCATTATT
**
31992 AAAATATTATTTCTA-TA-ATTCTA-T-AAATA
1 AAAATATTAACTCTAGTATATTCTATTAAAATA
32021 AAAATATTAACTCTAGTATATTCTATTAAAATA
1 AAAATATTAACTCTAGTATATTCTATTAAAATA
32054 AAAATAT
1 AAAATAT
32061 GATAAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.38
30 2 0.06
31 6 0.18
32 1 0.03
33 12 0.35
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (33 bp):
AAAATATTAACTCTAGTATATTCTATTAAAATA
Found at i:32331 original size:26 final size:26
Alignment explanation
Indices: 32302--32378 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
32292 ATATTATTGT
*
32302 AATAATAATATTATATTATTATTAAA
1 AATATTAATATTATATTATTATTAAA
*
32328 AATATTAATA-AATA-TATT-TTAAA
1 AATATTAATATTATATTATTATTAAA
* *
32351 TATGTTAATAATTAATATT-TTATTAAA
1 AATATTAAT-ATT-ATATTATTATTAAA
32378 A
1 A
32379 TGATTCTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 12 0.30
24 5 0.12
25 3 0.08
26 14 0.35
27 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
AATATTAATATTATATTATTATTAAA
Found at i:32349 original size:23 final size:24
Alignment explanation
Indices: 32318--32372 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
32308 AATATTATAT
32318 TATTATTAAAAATATTAATAAAT-A
1 TATT-TTAAAAATATTAATAAATAA
* * *
32342 TATTTTAAATATGTTAATAATTAA
1 TATTTTAAAAATATTAATAAATAA
32366 TATTTTA
1 TATTTTA
32373 TTAAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTTTAAAAATATTAATAAATAA
Found at i:33460 original size:14 final size:14
Alignment explanation
Indices: 33417--33460 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33407 ATATATTTTA
33417 ATTATGTTAAATAT
1 ATTATGTTAAATAT
* * * *
33431 ATTTTATAAAAAAT
1 ATTATGTTAAATAT
33445 ATTATGTTAAATAT
1 ATTATGTTAAATAT
33459 AT
1 AT
33461 AAATTATAGA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (14 bp):
ATTATGTTAAATAT
Found at i:34107 original size:26 final size:26
Alignment explanation
Indices: 34078--34191 Score: 87
Period size: 26 Copynumber: 4.4 Consensus size: 26
34068 TTAAGTTCAT
34078 AATATTTTATTTATATTAATTTAAAA
1 AATATTTTATTTATATTAATTTAAAA
*
34104 AATA-TTT-TTTATATTAACTTATTAAA
1 AATATTTTATTTATATTAA-TT-TAAAA
*
34130 TATATTTTA-TTATTAACTTAATTT--AA
1 AATATTTTATTTA-T-A-TTAATTTAAAA
* *
34156 AATATTTAATTTTATTTTAA-TTAAAA
1 AATATTTTA-TTTATATTAATTTAAAA
*
34182 TATATTTTAT
1 AATATTTTAT
34192 GTGAAAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
24 12 0.17
25 10 0.14
26 29 0.41
27 7 0.10
28 5 0.07
29 3 0.04
30 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
AATATTTTATTTATATTAATTTAAAA
Found at i:34139 original size:52 final size:52
Alignment explanation
Indices: 34079--34191 Score: 128
Period size: 52 Copynumber: 2.2 Consensus size: 52
34069 TAAGTTCATA
34079 ATATTTTATTTA-T-A-TTAATTTAAAAAATATT-TTTTATATTAACTTATTAAAT
1 ATATTTTATTTATTAACTTAATTTAAAAAAT-TTATTTTATATTAA-TTA--AAAT
* *
34131 ATATTTTA-TTATTAACTTAATTTAAAATATTTAATTTTATTTTAATTAAAAT
1 ATATTTTATTTATTAACTTAATTTAAAAAATTT-ATTTTATATTAATTAAAAT
34183 ATATTTTAT
1 ATATTTTAT
34192 GTGAAAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
51 3 0.06
52 21 0.40
53 3 0.06
54 16 0.30
55 10 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (52 bp):
ATATTTTATTTATTAACTTAATTTAAAAAATTTATTTTATATTAATTAAAAT
Found at i:34143 original size:25 final size:26
Alignment explanation
Indices: 34087--34191 Score: 96
Period size: 24 Copynumber: 4.2 Consensus size: 26
34077 TAATATTTTA
* * *
34087 TTTA-TATTAATTTAA-AAAATATTT
1 TTTATTATTAACTTAATTAAATATAT
34111 TTTA-TATTAACTT-ATTAAATATAT
1 TTTATTATTAACTTAATTAAATATAT
34135 TTTATTATTAACTTAATTTAAA-ATAT
1 TTTATTATTAACTTAA-TTAAATATAT
* **
34161 TTAATT-TTATTTTAATTAAAATATAT
1 TTTATTATTAACTTAATT-AAATATAT
34187 TTTAT
1 TTTAT
34192 GTGAAAATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
23 1 0.01
24 25 0.37
25 19 0.28
26 18 0.26
27 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTATTATTAACTTAATTAAATATAT
Found at i:34287 original size:28 final size:28
Alignment explanation
Indices: 34256--34327 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
34246 TATTAGTAAA
* *
34256 TTAAGATAA-AATATATACTTTGAAAAGT
1 TTAA-ATAAGAATAAATACTTTAAAAAGT
* *
34284 TTAAATAATAATAAAATATTTTAAAAAGT
1 TTAAATAAGAAT-AAATACTTTAAAAAGT
34313 TTAAATAAGAATAAA
1 TTAAATAAGAATAAA
34328 ATATATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 10 0.26
29 24 0.63
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (28 bp):
TTAAATAAGAATAAATACTTTAAAAAGT
Found at i:35045 original size:32 final size:31
Alignment explanation
Indices: 34972--35045 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
34962 ATTAATCCAT
* * *
34972 AGTGACCACATCTTAATTAGATTAAAACGAA
1 AGTGACCATATCTTAATTAAATAAAAACGAA
* *
35003 AGTGATCATATCTTAATTAAATAAAAATGAAA
1 AGTGACCATATCTTAATTAAATAAAAACG-AA
35035 AGTGACCATAT
1 AGTGACCATAT
35046 ATTATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (31 bp):
AGTGACCATATCTTAATTAAATAAAAACGAA
Found at i:36264 original size:22 final size:22
Alignment explanation
Indices: 36231--36284 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
36221 TATAAAAATT
* *
36231 TAAAATTCTAAATGACTTAACA
1 TAAAATTATAAATGACTTAAAA
* * *
36253 TATAATTATAAATTAGTTAAAA
1 TAAAATTATAAATGACTTAAAA
36275 TAAAATTATA
1 TAAAATTATA
36285 TTATTTTCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAAATTATAAATGACTTAAAA
Found at i:36845 original size:10 final size:10
Alignment explanation
Indices: 36832--36879 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
36822 ATATATATAG
36832 ATATAAAATA
1 ATATAAAATA
*
36842 ATATTAAAAAA
1 ATA-TAAAATA
*
36853 ACATCAAAATA
1 ATAT-AAAATA
36864 ATATAAAATA
1 ATATAAAATA
*
36874 TTATAA
1 ATATAA
36880 GTATTGTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 15 0.48
11 16 0.52
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATAAAATA
Found at i:46478 original size:417 final size:416
Alignment explanation
Indices: 45649--46490 Score: 1098
Period size: 417 Copynumber: 2.0 Consensus size: 416
45639 ATGTTTTAAT
* * * *
45649 TATAGTGACAAAGTATATTATCACAAAGATTTTCTTCCATATTTTTTTGCGCAAAAAAGTCATAT
1 TATAGTAACAAAATATATTATCACAAAGATTTTCCTCCATATTTTATTGCGCAAAAAAGTCATAT
*
45714 AATGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTGCCACAAAAAATAAA
66 AATAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTGCCACAAAAAATAAA
* * ** * *
45779 TTATATTCACGTTTTTTGTGACAAATTATATTTGTTGTTATAAATTTTAACTATAGTGATAGCAT
131 TTATATTCACGATTTTTGTGACAAATTATACTTGCAGTTATAAATTATAACTATAGTGATA-CAC
* * * *
45844 ATATTAATTGTCATAACTATTTTTCTTCACTTTTTTGTTTCAAAAGTTATATTGACAATTTTTAT
195 ATATTAATTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTCACAAGTTTTAT
* *
45909 AATTATAATTTATAGTTATTGTTATAGAAAAAATTATCAAATCAAATAATAAAATTCAGGTTTTT
260 AATTATAATTTATAGTTATTGTTATAGAAAAAATTATCAAATCAAACAATAAAATTCAAGTTTTT
* *
45974 TGTAATCAATTATTTTTTAAATTATATATTTAATCATTATAAATTTATACTATCATAACCATTTA
325 TGTAATCAATTATTTTTTAAATTATATATTTAATCATTATAAAATTATAATATCATAACCATTTA
46039 TCCCTATTTTTAGTGTCAAAAATATTA
390 TCCCTATTTTTAGTGTCAAAAATATTA
* *
46066 TATAGTAACAAAATATATTATCATAAAGATTTTCCTCTATATTTTATTGCGCCAAAAAA-TCATA
1 TATAGTAACAAAATATATTATCACAAAGATTTTCCTCCATATTTTATTGCG-CAAAAAAGTCATA
* * * *
46130 TAGTAACAATTTTTGTAACTATAAGTGTTTATAATTATTACAAAAAA-ATTTGTCACAAAAAAT-
65 TAATAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACA-TTGCCACAAAAAATA
* * *
46193 AATTGTGTTCAC-ATTTTTGTGACAAATTATACTTGCAGTTATAAATTATAATTATAGTGATA-A
129 AATTATATTCACGATTTTTGTGACAAATTATACTTGCAGTTATAAATTATAACTATAGTGATACA
* * * *
46256 CATA-T-ATTGTGATAAATATTTTTGTCCACTTTTTTTTTGTTTCAAAAATTTATATTCATC-CG
194 CATATTAATTGTCATAAATATTTTTCTCCAC---TTTTTTGTTTC-AAAAGTTATATTCA-CAAG
* * *
46318 TTTTGTAATTATAATTTATAGTTATTTTTATA-AAAAAA-TATCACATCAAACAATAAAATTCAA
254 TTTTATAATTATAATTTATAGTTATTGTTATAGAAAAAATTATCAAATCAAACAATAAAATTCAA
*
46381 GTTTTTTGTAATCAATTATTTTTGT-AGTTATATATTTTAATCATTATGTAAAATTATAATATCA
319 GTTTTTTGTAATCAATTATTTTT-TAAATTATATA-TTTAATCATTA--TAAAATTATAATATCA
* * * *
46445 TAGA-CATTTCTCCGTATTTTTTG-GTTCCAAAAATGTTA
380 TA-ACCATTTATCCCTATTTTTAGTG-T-CAAAAATATTA
46483 TATAGTAA
1 TATAGTAA
46491 AAATTTTATA
Statistics
Matches: 371, Mismatches: 40, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
411 20 0.05
412 1 0.00
413 57 0.15
414 29 0.08
415 87 0.23
416 45 0.12
417 125 0.34
418 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (416 bp):
TATAGTAACAAAATATATTATCACAAAGATTTTCCTCCATATTTTATTGCGCAAAAAAGTCATAT
AATAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTGCCACAAAAAATAAA
TTATATTCACGATTTTTGTGACAAATTATACTTGCAGTTATAAATTATAACTATAGTGATACACA
TATTAATTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTCACAAGTTTTATA
ATTATAATTTATAGTTATTGTTATAGAAAAAATTATCAAATCAAACAATAAAATTCAAGTTTTTT
GTAATCAATTATTTTTTAAATTATATATTTAATCATTATAAAATTATAATATCATAACCATTTAT
CCCTATTTTTAGTGTCAAAAATATTA
Found at i:47085 original size:15 final size:15
Alignment explanation
Indices: 47065--47095 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47055 AATAATGGTG
*
47065 TCATCATCATCTTCA
1 TCATCATCACCTTCA
47080 TCATCATCACCTTCA
1 TCATCATCACCTTCA
47095 T
1 T
47096 TAAATAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (15 bp):
TCATCATCACCTTCA
Found at i:47949 original size:2 final size:2
Alignment explanation
Indices: 47934--47967 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
47924 ATATGCATTC
*
47934 TA TA TA T- TA AA 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 TA TA TA TA T
47968 TTAGTCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51013 original size:21 final size:21
Alignment explanation
Indices: 50987--51030 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
50977 CTGGAGACCC
*
50987 AAATACTGAACGTAAAGTGAA
1 AAATACTAAACGTAAAGTGAA
51008 AAATACTAAACGTAAAGTGAA
1 AAATACTAAACGTAAAGTGAA
51029 AA
1 AA
51031 TGCAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.16, T:0.18
Consensus pattern (21 bp):
AAATACTAAACGTAAAGTGAA
Found at i:51709 original size:22 final size:22
Alignment explanation
Indices: 51668--51711 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
51658 TATAGATTTA
* *
51668 AAATTTAAAATATACAAAAAAT
1 AAATATAAAAAATACAAAAAAT
51690 AAATATAAAAAATACTAAAAAA
1 AAATATAAAAAATAC-AAAAAA
51712 GAAACTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATATAAAAAATACAAAAAAT
Found at i:52708 original size:24 final size:23
Alignment explanation
Indices: 52676--52724 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
52666 AGGAGTATGA
* *
52676 TTTTGTTTAATATTTAATTTATTG
1 TTTTATTTAATATTTAAATT-TTG
*
52700 TTTTATTTAATTTTTAAATTTTG
1 TTTTATTTAATATTTAAATTTTG
52723 TT
1 TT
52725 ACAAGTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTTATTTAATATTTAAATTTTG
Found at i:57714 original size:19 final size:20
Alignment explanation
Indices: 57669--57715 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
57659 TTAAAATATA
*
57669 TTTTTAGTTATCATAACCAAT
1 TTTTTAGTTATAATAA-CAAT
57690 TATTTTAGTTATAATAA-AAT
1 T-TTTTAGTTATAATAACAAT
57710 TTTTTA
1 TTTTTA
57716 ATAAAATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 1 0.04
22 14 0.58
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTAGTTATAATAACAAT
Found at i:58145 original size:32 final size:34
Alignment explanation
Indices: 58099--58183 Score: 84
Period size: 39 Copynumber: 2.4 Consensus size: 34
58089 TCAAAATATT
* *
58099 ATTTTGTCCCAATAACA-AA-TTGTAACAAAATG
1 ATTTAGTCACAATAACATAATTTGTAACAAAATG
*
58131 ATTTAGTCACAATAACACGTTAAGTTTTGTGACAAAATG
1 ATTTAGTCACAATAACA---TAA--TTTGTAACAAAATG
58170 ATTTAGTCACAATA
1 ATTTAGTCACAATA
58184 GTAAAAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 15 0.35
36 2 0.05
39 26 0.60
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (34 bp):
ATTTAGTCACAATAACATAATTTGTAACAAAATG
Found at i:58271 original size:33 final size:31
Alignment explanation
Indices: 58220--58353 Score: 101
Period size: 33 Copynumber: 4.1 Consensus size: 31
58210 GTCCCAATAT
58220 TTTATCAAAATGAAAAATTGTGACAAAT-TTA
1 TTTATCAAAAT-AAAAATTGTGACAAATATTA
* *
58251 TTTAATCAAAAATAACAAATTATAACAAATATTAA
1 TTT-ATC-AAAATAA-AAATTGTGACAAATATT-A
** *
58286 TTTATCATTATAAAAAATTGTGACAAATAATA
1 TTTATCAAAAT-AAAAATTGTGACAAATATTA
* * * *
58318 TTCTTTCACAATAAAAAATTGT-AAAAAAATTA
1 TT-TATCAAAAT-AAAAATTGTGACAAATATTA
58350 TTTA
1 TTTA
58354 GTCACAGTAA
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
31 4 0.05
32 17 0.21
33 50 0.61
34 7 0.09
35 4 0.05
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (31 bp):
TTTATCAAAATAAAAATTGTGACAAATATTA
Found at i:58382 original size:30 final size:32
Alignment explanation
Indices: 58323--58385 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
58313 TAATATTCTT
*
58323 TCACAATAAAAAATTGTAAAAAAATTATTTAG
1 TCACAATAAAAAATTATAAAAAAATTATTTAG
* *
58355 TCACAGTAAAAAGTTAT-AAAAAA-TATTTAG
1 TCACAATAAAAAATTATAAAAAAATTATTTAG
58385 T
1 T
58386 GATGAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 8 0.29
31 6 0.21
32 14 0.50
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (32 bp):
TCACAATAAAAAATTATAAAAAAATTATTTAG
Found at i:60096 original size:18 final size:18
Alignment explanation
Indices: 60070--60114 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
60060 GCGTAGAAGG
* *
60070 GATAAAGACCGAGACAGA
1 GATAGAGACCAAGACAGA
*
60088 GATAGAGACCAAGATAGA
1 GATAGAGACCAAGACAGA
60106 GATAGAGAC
1 GATAGAGAC
60115 TGATTCGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.29, T:0.09
Consensus pattern (18 bp):
GATAGAGACCAAGACAGA
Found at i:63146 original size:13 final size:13
Alignment explanation
Indices: 63095--63138 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
63085 GTCATAAATC
*
63095 TATGACGCGCATT
1 TATGACACGCATT
63108 TATGACACGCATT
1 TATGACACGCATT
*
63121 TATGACACACATT
1 TATGACACGCATT
63134 TATGA
1 TATGA
63139 TGCGCATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:74171 original size:66 final size:66
Alignment explanation
Indices: 74094--74225 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
74084 TCCTTCCAAC
74094 ACATTATTTAAGTCCAATTGTGTAAGGACATCTCGGATTTTCATTTCCATAATGAGAACCTAGTG
1 ACATTATTTAAGTCCAATTGTGTAAGGACATCTCGGATTTTCATTTCCATAATGAGAACCTAGTG
74159 T
66 T
74160 ACATTATTTAAGTCCAATTGTGTAAGGACATCTCGGATTTTCATTTCCATAATGAGAACCTAGTG
1 ACATTATTTAAGTCCAATTGTGTAAGGACATCTCGGATTTTCATTTCCATAATGAGAACCTAGTG
74225 T
66 T
74226 TGTGATGTAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (66 bp):
ACATTATTTAAGTCCAATTGTGTAAGGACATCTCGGATTTTCATTTCCATAATGAGAACCTAGTG
T
Found at i:75025 original size:15 final size:16
Alignment explanation
Indices: 74999--75028 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74989 ATAGGGATGC
74999 AAAATATAAACAATAT
1 AAAATATAAACAATAT
75015 AAAAT-TAAACAATA
1 AAAATATAAACAATA
75029 AAATTAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATAAACAATAT
Found at i:81482 original size:16 final size:17
Alignment explanation
Indices: 81461--81502 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
81451 TACTTGGCGG
81461 AAAAAT-AATTTGATTA
1 AAAAATGAATTTGATTA
*
81477 AAAAATGATTTTGATTTTA
1 AAAAATGAATTTGA--TTA
81496 AAAAATG
1 AAAAATG
81503 TTTTGGGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 6 0.27
19 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AAAAATGAATTTGATTA
Found at i:81489 original size:17 final size:17
Alignment explanation
Indices: 81469--81507 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
81459 GGAAAAATAA
81469 TTTGA-TTAAAAAATGAT
1 TTTGATTTAAAAAATG-T
81486 TTTGATTTTAAAAAATGT
1 TTTGA-TTTAAAAAATGT
81504 TTTG
1 TTTG
81508 GGAGTCGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
TTTGATTTAAAAAATGT
Found at i:83584 original size:3 final size:3
Alignment explanation
Indices: 83576--83611 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
83566 TAATATAAAT
83576 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
83612 AATAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:89644 original size:30 final size:29
Alignment explanation
Indices: 89579--89683 Score: 93
Period size: 30 Copynumber: 3.6 Consensus size: 29
89569 AGAAAGGGAT
* * * *
89579 ATAATCCCATACAAAAGTCAGAACATAGAA
1 ATAATCCCATGCAGATGTCAGAAC-GAGAA
* *
89609 TTAATCCCATGCAGATGTCAGAACGGGGAA
1 ATAATCCCATGCAGATGTCAGAAC-GAGAA
* ** *
89639 GTAATCTTATGCAGATGTTAGAACGAGAA
1 ATAATCCCATGCAGATGTCAGAACGAGAA
*
89668 ATATTCCCATGCAGAT
1 ATAATCCCATGCAGAT
89684 TAGAAATACA
Statistics
Matches: 59, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
29 16 0.27
30 43 0.73
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (29 bp):
ATAATCCCATGCAGATGTCAGAACGAGAA
Found at i:90276 original size:13 final size:13
Alignment explanation
Indices: 90258--90310 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
90248 GGTTTTAGAA
90258 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
90271 AAAGTCAATGGTC
1 AAAGTCAACGGTC
*
90284 AAAGTCAATGGTC
1 AAAGTCAACGGTC
**
90297 -GGGTCAACGGTC
1 AAAGTCAACGGTC
90309 AA
1 AA
90311 TGGTTAACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 9 0.26
13 25 0.74
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:90735 original size:19 final size:18
Alignment explanation
Indices: 90711--90752 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
90701 GGGAAAACAC
90711 AATAACACTAGAGAGAGAA
1 AATAACACTAGAGAGA-AA
90730 AATAACACTAGAGAGAAA
1 AATAACACTAGAGAGAAA
90748 AATAA
1 AATAA
90753 ACTGTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.62, C:0.10, G:0.17, T:0.12
Consensus pattern (18 bp):
AATAACACTAGAGAGAAA
Found at i:90744 original size:17 final size:18
Alignment explanation
Indices: 90711--90748 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
90701 GGGAAAACAC
90711 AATAACACTAGAGAGAGAA
1 AATAACACTA-AGAGAGAA
90730 AATAACACT-AGAGAGAA
1 AATAACACTAAGAGAGAA
90747 AA
1 AA
90749 ATAAACTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.61, C:0.11, G:0.18, T:0.11
Consensus pattern (18 bp):
AATAACACTAAGAGAGAA
Found at i:100316 original size:20 final size:19
Alignment explanation
Indices: 100273--100317 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
100263 CAAAATGGCC
*
100273 CAATTTCACATTCTAACAT
1 CAATTTCACACTCTAACAT
*
100292 CAATTTCAACACTCTAGCAT
1 CAATTTC-ACACTCTAACAT
*
100312 TAATTT
1 CAATTT
100318 ACAGCATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (19 bp):
CAATTTCACACTCTAACAT
Found at i:102169 original size:61 final size:60
Alignment explanation
Indices: 102071--102223 Score: 216
Period size: 61 Copynumber: 2.5 Consensus size: 60
102061 TAGTGCTATA
* * * * *
102071 ACACATAAGGTCATGCCCACCACCTACACTAAGTTTACATTCTAGTGTTGATTCGGATATG
1 ACACATAAGGTCATGCCCACCACCTGCACT-AGTTTACACTCTAGTGCTGATCCGAATATG
* *
102132 ACACATAAGGTCACGCCTACCACCTGCACTAGTTTTACACTCTAGTGCTGATCCGAATATG
1 ACACATAAGGTCATGCCCACCACCTGCACTAG-TTTACACTCTAGTGCTGATCCGAATATG
*
102193 ACACATAAGGTCATGCCCACCACATGCACTA
1 ACACATAAGGTCATGCCCACCACCTGCACTA
102224 AGTGTCCTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 2 0.02
61 79 0.98
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (60 bp):
ACACATAAGGTCATGCCCACCACCTGCACTAGTTTACACTCTAGTGCTGATCCGAATATG
Found at i:103683 original size:19 final size:20
Alignment explanation
Indices: 103659--103704 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
103649 CAAAATGGTC
*
103659 CAATTTCA-CATTCTAACAT
1 CAATTTCACCACTCTAACAT
*
103678 CAATTTAACCACTCTAACAT
1 CAATTTCACCACTCTAACAT
*
103698 TAATTTC
1 CAATTTC
103705 TAGCATATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCACCACTCTAACAT
Found at i:105000 original size:14 final size:13
Alignment explanation
Indices: 104967--105015 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
104957 TAGAATTTCT
*
104967 CTTTTCTAAATAA
1 CTTTTCCAAATAA
104980 CTTTTCCAAATAGA
1 CTTTTCCAAATA-A
*
104994 ATTTTCCAAATAA
1 CTTTTCCAAATAA
105007 CTTTTCCAA
1 CTTTTCCAA
105016 CTTTTGATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (13 bp):
CTTTTCCAAATAA
Found at i:113327 original size:37 final size:37
Alignment explanation
Indices: 113227--113327 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
113217 AACCGACAAA
* **
113227 TTCATCCATTAGGATGATAAATCAAATTATTGGTTGG
1 TTCATCCATTAGGATGATAAATCCAATTATTGACTGG
* *
113264 TTCATACATTAGGATGATAGATCCAATTATTGACTGG
1 TTCATCCATTAGGATGATAAATCCAATTATTGACTGG
* * * *
113301 TTCATCCTTTGGGATGGTAAACCCAAT
1 TTCATCCATTAGGATGATAAATCCAAT
113328 AACTGTATGG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (37 bp):
TTCATCCATTAGGATGATAAATCCAATTATTGACTGG
Found at i:120257 original size:42 final size:42
Alignment explanation
Indices: 120205--120333 Score: 213
Period size: 42 Copynumber: 3.1 Consensus size: 42
120195 TATAATCAGC
**
120205 CAGAATAGTTTTAATCACCCTTAGTAGCAATTCAATCAATAG
1 CAGAATAGTTTTAATCACCCCCAGTAGCAATTCAATCAATAG
* *
120247 CAGATTAGTTTTAATCACCCCCAATAGCAATTCAATCAATAG
1 CAGAATAGTTTTAATCACCCCCAGTAGCAATTCAATCAATAG
*
120289 AAGAATAGTTTTAATCACCCCCAGTAGCAATTCAATCAATAG
1 CAGAATAGTTTTAATCACCCCCAGTAGCAATTCAATCAATAG
120331 CAG
1 CAG
120334 TTCAGTCAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (42 bp):
CAGAATAGTTTTAATCACCCCCAGTAGCAATTCAATCAATAG
Found at i:132019 original size:25 final size:24
Alignment explanation
Indices: 131983--132045 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
131973 TTTTATTTTC
*
131983 AAATTTTTAAAAA-GATCAATTAAA
1 AAATTTTGAAAAATGATCAA-TAAA
* *
132007 AGAATTTTGAAAAATGTTTAATAAA
1 A-AATTTTGAAAAATGATCAATAAA
132032 AAATTTTGAAAAAT
1 AAATTTTGAAAAAT
132046 ATTTCCCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.41
25 16 0.47
26 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
AAATTTTGAAAAATGATCAATAAA
Found at i:136706 original size:2 final size:2
Alignment explanation
Indices: 136701--136759 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
136691 AACGTGTGTC
136701 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
136743 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
136760 GGCAACTCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:146329 original size:22 final size:22
Alignment explanation
Indices: 146295--146337 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
146285 GCATAAACAA
146295 ATAAATAATAATATACATGTAC
1 ATAAATAATAATATACATGTAC
*
146317 ATAAA-AATGAATATATATGTA
1 ATAAATAAT-AATATACATGTA
146338 TGGTAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (22 bp):
ATAAATAATAATATACATGTAC
Found at i:147966 original size:3 final size:3
Alignment explanation
Indices: 147931--147981 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
147921 AAACTTTTAT
* * * * *
147931 TAA TAA -AA TGA TAC TAA TAC TAA TAC TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
147978 TAA T
1 TAA T
147982 CCCTGGGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:148303 original size:18 final size:18
Alignment explanation
Indices: 148237--148304 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
148227 TTAAATGAGA
148237 TAGTTTAATT-AATGAAC
1 TAGTTTAATTGAATGAAC
* * *
148254 CAATTTAAATGAATGAAC
1 TAGTTTAATTGAATGAAC
*
148272 TAGTTTAATT-AATGGAC
1 TAGTTTAATTGAATGAAC
148289 TAGCTTT-ATTGAATGA
1 TAG-TTTAATTGAATGA
148305 TCCATCATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 19 0.47
18 21 0.52
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (18 bp):
TAGTTTAATTGAATGAAC
Done.