Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 11 of 126
Found at i:2989868 original size:13 final size:15
Alignment explanation
Indices: 2989850--2989881 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2989840 ATATTTTAGA
2989850 AAAAATTTA-CTT-T
1 AAAAATTTATCTTAT
2989863 AAAAATTTATCTTAT
1 AAAAATTTATCTTAT
2989878 AAAA
1 AAAA
2989882 GTAAATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATTTATCTTAT
Found at i:2991263 original size:16 final size:16
Alignment explanation
Indices: 2991238--2991273 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2991228 GCCAAATTTT
2991238 CAGG-TCAGACCATTG
1 CAGGTTCAGACCATTG
*
2991253 CAGGTTCAGACCATTT
1 CAGGTTCAGACCATTG
2991269 CAGGT
1 CAGGT
2991274 CAGGAACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (16 bp):
CAGGTTCAGACCATTG
Found at i:2994822 original size:15 final size:18
Alignment explanation
Indices: 2994802--2994851 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
2994792 AATCTAACTG
2994802 AATCAATTTAA-CA-TT-
1 AATCAATTTAATCAGTTC
2994817 AATCAATATTAATCAGTTC
1 AATCAAT-TTAATCAGTTC
*
2994836 AATCAATTAAATCAGT
1 AATCAATTTAATCAGT
2994852 ATTTCTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 2 0.07
18 10 0.33
19 7 0.23
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (18 bp):
AATCAATTTAATCAGTTC
Found at i:2997298 original size:110 final size:110
Alignment explanation
Indices: 2997105--2997317 Score: 282
Period size: 110 Copynumber: 1.9 Consensus size: 110
2997095 CAGTCCAATG
*
2997105 AGGGTATGTTCAATCTAAGTTTTGTATAATATATGCATACTTTACCAATGCCAATTCGTTACCCG
1 AGGGTATGTTCAATCTAAGTTTTGTATAATATATGCATACATTACCAATGCCAATTCGTTACCCG
*
2997170 AACTTGGGGTGAGTATTGGATACGTGTATGAGTATATTTCTGATA
66 AACTTGGGGTAAGTATTGGATACGTGTATGAGTATATTTCTGATA
* * * ** * * * **
2997215 AGGGTATGTTCAATGTCAGTTTTGTATAATATATGTATACATTAGGAATGCTACTTTGTTACTTG
1 AGGGTATGTTCAATCTAAGTTTTGTATAATATATGCATACATTACCAATGCCAATTCGTTACCCG
* * * *
2997280 GACTTGGGGTAAGTATTGGATGCTTGTATGATTATATT
66 AACTTGGGGTAAGTATTGGATACGTGTATGAGTATATT
2997318 CGGAGAATGT
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (110 bp):
AGGGTATGTTCAATCTAAGTTTTGTATAATATATGCATACATTACCAATGCCAATTCGTTACCCG
AACTTGGGGTAAGTATTGGATACGTGTATGAGTATATTTCTGATA
Found at i:3020087 original size:21 final size:22
Alignment explanation
Indices: 3020048--3020092 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3020038 TCCTAAAAGG
*
3020048 TTAAAATGTTCTGATTAAGTTC
1 TTAAAATGTTCTGATTAAGCTC
3020070 TTAAAA-GTATCT-ATTAAGCTC
1 TTAAAATGT-TCTGATTAAGCTC
3020091 TT
1 TT
3020093 CCTTCACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (22 bp):
TTAAAATGTTCTGATTAAGCTC
Found at i:3021695 original size:21 final size:22
Alignment explanation
Indices: 3021645--3021699 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
3021635 AAAGGGACGA
3021645 AGGTGGGAGAGGGAGCAGGG-C
1 AGGTGGGAGAGGGAGCAGGGAC
*
3021666 AAGTGGG-GAGAGGAG-AGGGAC
1 AGGTGGGAGAG-GGAGCAGGGAC
3021687 AGGGTGGGA-AGGG
1 A-GGTGGGAGAGGG
3021700 GGAGGGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 7 0.25
21 14 0.50
22 7 0.25
ACGTcount: A:0.27, C:0.05, G:0.62, T:0.05
Consensus pattern (22 bp):
AGGTGGGAGAGGGAGCAGGGAC
Found at i:3023870 original size:15 final size:15
Alignment explanation
Indices: 3023852--3023892 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3023842 TTGAAAATTT
3023852 TAAATGTTGAAAAAA
1 TAAATGTTGAAAAAA
* *
3023867 TAAATATTAAAAAAA
1 TAAATGTTGAAAAAA
*
3023882 TAAATGCTGAA
1 TAAATGTTGAA
3023893 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (15 bp):
TAAATGTTGAAAAAA
Found at i:3027623 original size:15 final size:15
Alignment explanation
Indices: 3027603--3027656 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
3027593 ATACGACAAA
3027603 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
3027618 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
3027635 AATTATTTATTATTAAA
1 -A-TATTTATTATTAAT
3027652 ATATT
1 ATATT
3027657 AATATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.41
16 2 0.06
17 7 0.22
18 2 0.06
19 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:3027777 original size:22 final size:22
Alignment explanation
Indices: 3027722--3027763 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
3027712 AATAAAATTG
*
3027722 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
3027742 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
3027764 TATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:3030622 original size:16 final size:16
Alignment explanation
Indices: 3030601--3030633 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3030591 AAGTTGGGTT
3030601 TAAAA-TTCTCTAATAA
1 TAAAATTTCT-TAATAA
3030617 TAAAATTTCTTAATAA
1 TAAAATTTCTTAATAA
3030633 T
1 T
3030634 TTCAGCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTTCTTAATAA
Found at i:3032150 original size:6 final size:6
Alignment explanation
Indices: 3032139--3032170 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3032129 TATTTCGATA
3032139 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
3032171 ATAGAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:3034926 original size:16 final size:16
Alignment explanation
Indices: 3034907--3034958 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3034897 TACATGTGAA
3034907 AAATAATACAATAAAT
1 AAATAATACAATAAAT
3034923 AAATAATAC-ATGAAATT
1 AAATAATACAAT-AAA-T
* *
3034940 AAAAAATA-AAAAAAT
1 AAATAATACAATAAAT
3034955 AAAT
1 AAAT
3034959 TTTTTTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.20
16 15 0.50
17 9 0.30
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (16 bp):
AAATAATACAATAAAT
Found at i:3042329 original size:12 final size:12
Alignment explanation
Indices: 3042312--3042346 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3042302 GTCCTTCCAC
3042312 TCTTATTCTTCT
1 TCTTATTCTTCT
3042324 TCTTATTCTTCT
1 TCTTATTCTTCT
*
3042336 TCTTGTTCTTC
1 TCTTATTCTTC
3042347 GAGGTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.66
Consensus pattern (12 bp):
TCTTATTCTTCT
Found at i:3049807 original size:147 final size:147
Alignment explanation
Indices: 3049540--3049884 Score: 541
Period size: 147 Copynumber: 2.3 Consensus size: 147
3049530 ACAGTTACCT
* *
3049540 CCCCGATATTCAGTAGGTTTGGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGA
1 CCCCGATATGCAGTAGGTTCGGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGA
* * * *
3049605 TCCGTATGCTGCTGCAAAGATCAGCTGAAACCGGATAATTTGAGAAGAACTCGGAGTTAAGCTCA
66 TCCATATGCTGCTGCAAAGATCAGATGAAACCGGATAATTTGAGAAGAACCCGGAGTTAAGCTAA
3049670 GTTGGTTTATTCAACCA
131 GTTGGTTTATTCAACCA
* * *
3049687 CCCCGATATGCAGCAAGTTCGGGATTCGAATCGCAACATATGCAACCATTTTCCCTATGTCTTGA
1 CCCCGATATGCAGTAGGTTCGGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGA
*
3049752 TCCATATGCTGCTGCAAGGATCCA-ATGAAACCGGATAATTTGAGAA-AAGCCCGGAGTTAAGCT
66 TCCATATGCTGCTGCAAAGAT-CAGATGAAACCGGATAATTTGAGAAGAA-CCCGGAGTTAAGCT
3049815 AAGTTGGTTTATTCAACCA
129 AAGTTGGTTTATTCAACCA
* * *
3049834 CCCTGATATGCAGTAGGTTCGGGATTCGAATCCCAACATCTGTAACCATTT
1 CCCCGATATGCAGTAGGTTCGGGATTCGAATCCCAACATATGCAACCATTT
3049885 CTCCTGTATA
Statistics
Matches: 180, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
146 2 0.01
147 176 0.98
148 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (147 bp):
CCCCGATATGCAGTAGGTTCGGGATTCGAATCCCAACATATGCAACCATTTTCCCTATGTCTTGA
TCCATATGCTGCTGCAAAGATCAGATGAAACCGGATAATTTGAGAAGAACCCGGAGTTAAGCTAA
GTTGGTTTATTCAACCA
Found at i:3059810 original size:25 final size:26
Alignment explanation
Indices: 3059745--3059813 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
3059735 GAAAATTTTG
*
3059745 TTTTATTATTTAAAAAATATATTATA
1 TTTTATTATTTAAAATATATATTATA
* * *
3059771 TTATATTAATATAAAATAT-TTTTA-A
1 TTTTATT-ATTTAAAATATATATTATA
3059796 TTTTTATTATTTAAAATA
1 -TTTTATTATTTAAAATA
3059814 GTAAATCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 10 0.29
26 16 0.46
27 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTATTATTTAAAATATATATTATA
Found at i:3062081 original size:20 final size:21
Alignment explanation
Indices: 3062038--3062081 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3062028 ACACAATACA
*
3062038 TTAAATTAAAAAAAATAACTC
1 TTAAATTAAAAAAAATAACAC
* *
3062059 TTAATTTAAAGAAAATAA-AC
1 TTAAATTAAAAAAAATAACAC
3062079 TTA
1 TTA
3062082 GTTATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAATTAAAAAAAATAACAC
Found at i:3062842 original size:4 final size:4
Alignment explanation
Indices: 3062819--3062852 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
3062809 CTCTTTTTTT
*
3062819 ATTA ATATA ATTA GTTA ATTA ATTA ATTA ATTA A
1 ATTA AT-TA ATTA ATTA ATTA ATTA ATTA ATTA A
3062853 ACTCATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:3071094 original size:96 final size:95
Alignment explanation
Indices: 3070923--3071105 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 95
3070913 TTTGATTAAC
* * * *
3070923 TCAACATTTTGATGTTCGAGACTAAATTAAAATTTTAGTTATAGTTTGAGGGTGTTTAGTAAATT
1 TCAACATTTTGAAGTTCGAGACTAAATTAAAATTTTAGTTATAATTTGAGGGTGTTAAGCAAATT
*
3070988 AATTATTTTTTTATTGCATATTTTGGTAAG
66 AATTATTTTTTCATTGCATATTTTGGTAAG
* *
3071018 TCAACGTTTTGAAGTTTGAGACTAAATTAAGAATTTTAGTTATAATTT-AGGGGTGTCTAATGCA
1 TCAACATTTTGAAGTTCGAGACTAAATTAA-AATTTTAGTTATAATTTGA-GGGTGT-TAA-GCA
3071082 AA-TAATTA-TTTTTCATTGCATATT
62 AATTAATTATTTTTTCATTGCATATT
3071106 CACTTTTTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
95 28 0.36
96 37 0.48
97 8 0.10
98 4 0.05
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (95 bp):
TCAACATTTTGAAGTTCGAGACTAAATTAAAATTTTAGTTATAATTTGAGGGTGTTAAGCAAATT
AATTATTTTTTCATTGCATATTTTGGTAAG
Found at i:3075150 original size:7 final size:7
Alignment explanation
Indices: 3075138--3075185 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
3075128 GCGTACTTTA
3075138 TAAAAAT
1 TAAAAAT
3075145 TAAAAA-
1 TAAAAAT
*
3075151 -AAAAAA
1 TAAAAAT
3075157 TAAAAAT
1 TAAAAAT
3075164 TAACAAAT
1 TAA-AAAT
3075172 TAAAAAAT
1 T-AAAAAT
3075180 TAAAAA
1 TAAAAA
3075186 ATTTCATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.14
7 19 0.53
8 10 0.28
9 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAAAAT
Found at i:3075161 original size:8 final size:8
Alignment explanation
Indices: 3075139--3075188 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
3075129 CGTACTTTAT
3075139 AAAAATT-
1 AAAAATTA
3075146 AAAAA--A
1 AAAAATTA
3075152 AAAAA-T-
1 AAAAATTA
3075158 AAAAATTA
1 AAAAATTA
*
3075166 ACAAATTA
1 AAAAATTA
3075174 AAAAATTA
1 AAAAATTA
3075182 AAAAATT
1 AAAAATT
3075189 TCATGTTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 10 0.27
7 6 0.16
8 21 0.57
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATTA
Found at i:3076189 original size:2 final size:2
Alignment explanation
Indices: 3076184--3076211 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3076174 AAAAAAAAAG
3076184 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3076212 AAACCAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3086247 original size:22 final size:22
Alignment explanation
Indices: 3086222--3086267 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3086212 GAATAAACTC
3086222 AATAATTGGTCATCTAAAACCT
1 AATAATTGGTCATCTAAAACCT
3086244 AATAATTGGTCATCTAAAACCT
1 AATAATTGGTCATCTAAAACCT
3086266 AA
1 AA
3086268 GGCAAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (22 bp):
AATAATTGGTCATCTAAAACCT
Found at i:3089947 original size:263 final size:262
Alignment explanation
Indices: 3089473--3090099 Score: 918
Period size: 263 Copynumber: 2.4 Consensus size: 262
3089463 TTTCTATTCT
* ** * * *
3089473 ACGAGTTCGAGTTTGAGCACTAATCATTGAGCTGGAAATCGAGCATGAGAGTTTAGCTTTAAACA
1 ACGAGTTCAAGTTAAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTAAGCTTTAAA-A
* *
3089538 -TGGAACTCGATTGAGCTTCTGTTGAGTTTCAGGCTTCGAGTTTCAAGTCAAACTTGAGCTCAAG
65 GTGGAACTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGAGTTTCAAGTCAAACTTGAGCTCAAG
* * * *
3089602 CTTCTTATGGCTTGAGCTGTTGAACTGGTCGAATTTGAGTATACTAATACTTTATTTGTGTAGCT
130 CTTCTTAGGGCTTGAGCTGTTGAACTGGTCAAATTTGAGTATACTAATACTTTATCTGAGTAGCT
* * * * *
3089667 TATCAGCTTAGTCCAGCTTTTTTCTATGTTTAATGAGTATTGAGAAACTTCAATTTTGAACATTT
195 TATCAGCTTAATCCAGCTTTTTTCTATATTTAATGAGTATTGAAAAACTTCAA-TGTAAACATTT
3089732 AAAC
259 AAAC
** * *
3089736 ACGAGTTCAAGTTAAAGCACTAATAATTGAAATTGAAATCGAGCATGAGAGTTGAGCTTTAAATG
1 ACGAGTTCAAGTTAAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTAAGCTTTAAAAG
*
3089801 TGGAACTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGATTTTCAAGTCAAACTTGAGCTCAAGC
66 TGGAACTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGAGTTTCAAGTCAAACTTGAGCTCAAGC
*
3089866 TTCTTAGGGCTTGAGCTGTTGAAGTGGTCAAATTTGAGTATACTAATACTTTATCTGAGTA-CGT
131 TTCTTAGGGCTTGAGCTGTTGAACTGGTCAAATTTGAGTATACTAATACTTTATCTGAGTAGC-T
3089930 TATCAGCTTAATCCAGCTTTTTTCTATATTTAATGAGTATTGAAAAACTTCAATGTAAACATTTA
195 TATCAGCTTAATCCAGCTTTTTTCTATATTTAATGAGTATTGAAAAACTTCAATGTAAACATTTA
3089995 AAC
260 AAC
* * * ** * *
3089998 ACTGAATTCTAGCTCCAGTACTAATAATTGAGCTTGAAATTGAGCATGAGAGTTAAGCTTTAAAA
1 AC-GAGTTCAAGTTAAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTAAGCTTTAAAA
*
3090063 GTGGAACTCAATTGAGCTTCTGTTGAGTTTCAA-CTTT
65 GTGGAACTCGATTGAGCTTCTGTTGAGTTTCAAGCTTT
3090100 CAAGCTTTGA
Statistics
Matches: 327, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
262 20 0.06
263 307 0.94
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (262 bp):
ACGAGTTCAAGTTAAAGCACTAATAATTGAGCTTGAAATCGAGCATGAGAGTTAAGCTTTAAAAG
TGGAACTCGATTGAGCTTCTGTTGAGTTTCAAGCTTTGAGTTTCAAGTCAAACTTGAGCTCAAGC
TTCTTAGGGCTTGAGCTGTTGAACTGGTCAAATTTGAGTATACTAATACTTTATCTGAGTAGCTT
ATCAGCTTAATCCAGCTTTTTTCTATATTTAATGAGTATTGAAAAACTTCAATGTAAACATTTAA
AC
Found at i:3093761 original size:58 final size:59
Alignment explanation
Indices: 3093697--3093840 Score: 168
Period size: 58 Copynumber: 2.4 Consensus size: 59
3093687 ATTAGTTCCC
* *
3093697 AATGTGGGAACAATTGTTAAGTTCAGGGACTAATTTGGAC-AAAAAGAATTTAGG-CTCT
1 AATGTGGGAACAATTGTTAAGTTCAGGGACTAACTTGGACTAAAAAGAATTCAGGTC-CT
* * * *
3093755 AATGTGGGAACAGTTGCCT-AGTTCAGGTACTAACTTGGACTAAAAAGAGTTCAGGTCCT
1 AATGTGGGAACAATTG-TTAAGTTCAGGGACTAACTTGGACTAAAAAGAATTCAGGTCCT
* *
3093814 AATGTTGGGAACAATTGTCAAATTCAG
1 AATG-TGGGAACAATTGTTAAGTTCAG
3093841 TGATTTAACC
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
58 34 0.48
59 19 0.27
60 18 0.25
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (59 bp):
AATGTGGGAACAATTGTTAAGTTCAGGGACTAACTTGGACTAAAAAGAATTCAGGTCCT
Found at i:3094994 original size:11 final size:11
Alignment explanation
Indices: 3094980--3095005 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3094970 AAATAGTAGT
3094980 AAAACAACAAG
1 AAAACAACAAG
3094991 AAAACAACAAG
1 AAAACAACAAG
3095002 AAAA
1 AAAA
3095006 TAGTAGATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:3097954 original size:30 final size:31
Alignment explanation
Indices: 3097918--3097979 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
3097908 AAAAAAGAAA
* *
3097918 TACCAACTTTTAAGCGTC-TAAATTTTTTTT
1 TACCAACTTTTAAGCGACTTAAAATTTTTTT
*
3097948 TACCAACTTTTAAGGGACTTAAAATTTTTTT
1 TACCAACTTTTAAGCGACTTAAAATTTTTTT
3097979 T
1 T
3097980 CTCTAACTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
TACCAACTTTTAAGCGACTTAAAATTTTTTT
Found at i:3103154 original size:9 final size:9
Alignment explanation
Indices: 3103142--3103186 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
3103132 ATTTTAAAAA
3103142 TTTTAATTT
1 TTTTAATTT
3103151 TTTTATATTT
1 TTTTA-ATTT
*
3103161 TCTTTAGAATT
1 T-TTTA-ATTT
3103172 TTTTAATTT
1 TTTTAATTT
3103181 TTTTAA
1 TTTTAA
3103187 ATATAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 14 0.45
10 9 0.29
11 8 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTAATTT
Found at i:3103219 original size:22 final size:20
Alignment explanation
Indices: 3103169--3103224 Score: 51
Period size: 24 Copynumber: 2.6 Consensus size: 20
3103159 TTTCTTTAGA
*
3103169 ATTTTTTAATTTTTTTAAAT
1 ATTTTTTAATTTTTATAAAT
*
3103189 ATAAATTTTGGAATTTTTATAAAT
1 AT---TTTT-TAATTTTTATAAAT
3103213 ATTTTTT-ATTTT
1 ATTTTTTAATTTT
3103225 AAATATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
19 5 0.17
20 2 0.07
21 4 0.14
23 4 0.14
24 14 0.48
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
ATTTTTTAATTTTTATAAAT
Found at i:3111039 original size:18 final size:19
Alignment explanation
Indices: 3111000--3111042 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3110990 ATGGAGGTAA
3111000 TAAAATATGCATAATAAAAT
1 TAAAATAT-CATAATAAAAT
3111020 TAAAATAT-ATAA-AAATAT
1 TAAAATATCATAATAAA-AT
3111038 TAAAA
1 TAAAA
3111043 CAAAACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
20 8 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAATATCATAATAAAAT
Found at i:3116313 original size:10 final size:10
Alignment explanation
Indices: 3116300--3116328 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3116290 ACAAGCGTAT
3116300 ACAAGCATGA
1 ACAAGCATGA
3116310 ACAAGCATGA
1 ACAAGCATGA
3116320 ACAAGCATG
1 ACAAGCATG
3116329 TATGTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (10 bp):
ACAAGCATGA
Found at i:3116584 original size:136 final size:142
Alignment explanation
Indices: 3116365--3116750 Score: 449
Period size: 136 Copynumber: 2.7 Consensus size: 142
3116355 ATCGGCGATC
* * *
3116365 CTATGTTACAATTTGCATATAGCTCATCAATG---ACTATGCTAACATACATATTACATGTATAT
1 CTATGTTACAATTTGCATATAGCTCATCTATGACTACTATGCTAACATATATATTACAAGTATAT
*
3116427 ACAAAGCATGAACAAGTGCTTACACAGAAACTGGGGAGCATGTATC-A-AT-G-GTTA-CAGCTG
66 ACAAAGCATGAACAAGTGCTTACACAGAAACTGGAGAGCATGTATCTACATCGTGTTACCA-CTG
*
3116487 GATCAGTG-AC-A
130 GATCAGCGAACAA
3116498 CTATGTTACAATTTGCATATAGCTCATCTATGACTACTATGCTAACATATATATTACAAGTATAT
1 CTATGTTACAATTTGCATATAGCTCATCTATGACTACTATGCTAACATATATATTACAAGTATAT
3116563 ACAAAGCATGAACAAGTGCTTACACAGAAACTGGAGAGCATGTATCTTACATCGATTGTTACCAC
66 ACAAAGCATGAACAAGTGCTTACACAGAAACTGGAGAGCATGTATC-TACATCG--TGTTACCAC
3116628 TGGATCAGCGACACTAA
128 TGGATCAGCGA-AC-AA
* * * * *
3116645 CATTATGTTACAAATTCCATCTAGAC-CATCTAT-ACCTATTCTAAGCAAACATATCATATTACA
1 C--TATGTTACAATTTGCATATAG-CTCATCTATGA-CTA--CTATGCTAACATAT-ATATTACA
*
3116708 AGTATACAC-AAGCATGAACAAGTGCTTACACA-AAACCTGGAGA
59 AGTATATACAAAGCATGAACAAGTGCTTACACAGAAA-CTGGAGA
3116751 ACATAGCGAA
Statistics
Matches: 219, Mismatches: 11, Indels: 28
0.85 0.04 0.11
Matches are distributed among these distances:
133 31 0.14
136 73 0.33
138 1 0.00
139 2 0.01
140 1 0.00
143 14 0.06
144 2 0.01
145 2 0.01
147 2 0.01
148 1 0.00
149 28 0.13
150 4 0.02
151 42 0.19
152 16 0.07
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (142 bp):
CTATGTTACAATTTGCATATAGCTCATCTATGACTACTATGCTAACATATATATTACAAGTATAT
ACAAAGCATGAACAAGTGCTTACACAGAAACTGGAGAGCATGTATCTACATCGTGTTACCACTGG
ATCAGCGAACAA
Found at i:3117042 original size:132 final size:131
Alignment explanation
Indices: 3116807--3117069 Score: 359
Period size: 132 Copynumber: 2.0 Consensus size: 131
3116797 TACAGAAAAA
3116807 GGGAGCATGTATGCTACATCAACGGTTACAAGGATCAGCAAACCTATGTTACAATTCGCATCAAG
1 GGGAGCATGTATGCTACATCAACGGTTACAAGGATCAGCAAACCTATGTTACAATTCGCATCAAG
* *
3116872 CTCATCTATGCCCCTATTACAAACTAACATATCGATTACAAGTATATACAAGCATGAACAAGTGC
66 CTCATCTATG-CCCTATTACAAACTAACAAATCAATTACAAGTATATACAAGCATGAACAAGTGC
3116937 TG
130 TG
* * * * * * *
3116939 GGGAGCATTTATGTTACATCCATGGTTACAGCTGGATCAG-AAACACTATGTTACAATTTGTATC
1 GGGAGCATGTATGCTACATCAACGGTTACA--AGGATCAGCAAAC-CTATGTTACAATTCGCATC
* * * *
3117003 TAGCTCATCTATG-CCTATTATAAATTAACAAATTAATTACAAGTATATACAAGCATGAACAAGT
63 AAGCTCATCTATGCCCTATTACAAACTAACAAATCAATTACAAGTATATACAAGCATGAACAAGT
3117067 GCT
128 GCT
3117070 TACAGAAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
132 75 0.65
133 4 0.03
134 36 0.31
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (131 bp):
GGGAGCATGTATGCTACATCAACGGTTACAAGGATCAGCAAACCTATGTTACAATTCGCATCAAG
CTCATCTATGCCCTATTACAAACTAACAAATCAATTACAAGTATATACAAGCATGAACAAGTGCT
G
Found at i:3117188 original size:130 final size:128
Alignment explanation
Indices: 3116983--3117234 Score: 353
Period size: 130 Copynumber: 1.9 Consensus size: 128
3116973 GATCAGAAAC
* * *
3116983 ACTATGTTACAATTTGTATCTAGCTCATCTATGCCTATTATAAATTAACAAATTAATTACAAGTA
1 ACTATGCTACAATTTGCATCTAGCTCATCTATGCCTATTATAAACTAACAAATTAATTACAAGTA
* * *
3117048 TATACAAGCATGAACAAGTGCTT-ACAGAAAAACTGGGAAGTATGTATGTTACATCAACAGCGAA
66 TATACAAGCATAAACAAGTGCTTAACAG-AAAACAGGG-AGTATGCATGTTACATCAACAGCGAA
* * * *
3117112 ACTATGCTACAATTTGCATCTAAGCTCATCTATGCCTATTCTAAGCTAACATATTGATTACAAGT
1 ACTATGCTACAATTTGCATCT-AGCTCATCTATGCCTATTATAAACTAACAAATTAATTACAAGT
* *
3117177 GTATACAAGCATAAACAAGTGCTTAAACAGAAACCAGGGAGTATGCATGTTACATCAA
65 ATATACAAGCATAAACAAGTGCTT-AACAGAAAACAGGGAGTATGCATGTTACATCAA
3117235 TGGTTACGGT
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 19 0.18
130 78 0.72
131 7 0.06
132 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (128 bp):
ACTATGCTACAATTTGCATCTAGCTCATCTATGCCTATTATAAACTAACAAATTAATTACAAGTA
TATACAAGCATAAACAAGTGCTTAACAGAAAACAGGGAGTATGCATGTTACATCAACAGCGAA
Found at i:3125399 original size:11 final size:11
Alignment explanation
Indices: 3125368--3125410 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
3125358 GGCCCATTTT
3125368 TATTTTAAAAA
1 TATTTTAAAAA
*
3125379 -ATTTAAAAAA
1 TATTTTAAAAA
3125389 GTATTTTAAAAA
1 -TATTTTAAAAA
3125401 TATTTTAAAA
1 TATTTTAAAA
3125411 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:3125418 original size:31 final size:31
Alignment explanation
Indices: 3125396--3125464 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 31
3125386 AAAGTATTTT
3125396 AAAAA-TATTTTAAAATTAAAAAAAATTTAA
1 AAAAAGTATTTTAAAATTAAAAAAAATTTAA
*
3125426 AAAAAGTATTTTAAAATT-AAAAAAATTTTA
1 AAAAAGTATTTTAAAATTAAAAAAAATTTAA
3125456 AAAAAGTAT
1 AAAAAGTAT
3125465 GTAAAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAAAGTATTTTAAAATTAAAAAAAATTTAA
Found at i:3125472 original size:30 final size:30
Alignment explanation
Indices: 3125375--3125472 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 30
3125365 TTTTATTTTA
3125375 AAAAATTTAAAAAAGTATTTT-AAAAA-TATTT
1 AAAAA-TTAAAAAA--ATTTTAAAAAAGTATTT
* *
3125406 TAAAATTAAAAAAAATTTAAAAAAAGTATTT
1 AAAAATT-AAAAAAATTTTAAAAAAGTATTT
* *
3125437 TAAAATTAAAAAAATTTTAAAAAAGTATGT
1 AAAAATTAAAAAAATTTTAAAAAAGTATTT
3125467 AAAAAT
1 AAAAAT
3125473 ATTTTACAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.07
30 33 0.56
31 22 0.37
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAAATTAAAAAAATTTTAAAAAAGTATTT
Found at i:3127012 original size:22 final size:24
Alignment explanation
Indices: 3126986--3127029 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3126976 GAAAAATATT
3126986 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
3127008 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
3127030 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:3127159 original size:59 final size:59
Alignment explanation
Indices: 3127096--3127265 Score: 295
Period size: 59 Copynumber: 2.9 Consensus size: 59
3127086 TCAAGTTTGT
*
3127096 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* * *
3127155 TTTACTAATCAAGTGATAAATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
3127214 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
3127266 CATAATTTGA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 103 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:3127297 original size:16 final size:16
Alignment explanation
Indices: 3127276--3127317 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3127266 CATAATTTGA
*
3127276 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
3127292 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
3127308 TAGTTTTAAT
1 TAATTTTAAT
3127318 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3127301 original size:22 final size:23
Alignment explanation
Indices: 3127293--3127352 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
3127283 ACTAACAATT
* * *
3127293 AATTTTA-ATAACAATTAGTTTT
1 AATTTTATATAAAAAATAATTTT
*
3127315 AATTTTATTTAAAAAATAATTTT
1 AATTTTATATAAAAAATAATTTT
*
3127338 AATTTTA-ATTAAAAA
1 AATTTTATATAAAAAA
3127353 CGGGCCGGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTTTATATAAAAAATAATTTT
Found at i:3129001 original size:3 final size:3
Alignment explanation
Indices: 3128995--3129028 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3128985 ACCACGTTGC
3128995 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3129029 GATTGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3130741 original size:30 final size:31
Alignment explanation
Indices: 3130707--3130765 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
3130697 ATTCAGTAAT
* *
3130707 TGAGTTTGGTTTTAATG-TCAATTTAATATA
1 TGAGTTTGGCTTCAATGTTCAATTTAATATA
3130737 TGAGTTTGGCTTCAATGTTCAATTTAATA
1 TGAGTTTGGCTTCAATGTTCAATTTAATA
3130766 CTTGACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (31 bp):
TGAGTTTGGCTTCAATGTTCAATTTAATATA
Found at i:3136192 original size:18 final size:18
Alignment explanation
Indices: 3136169--3136207 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3136159 AATTTCTATA
*
3136169 AAAATAGGATTTCTCAAT
1 AAAATAAGATTTCTCAAT
*
3136187 AAAATAAGATTTCTCTAT
1 AAAATAAGATTTCTCAAT
3136205 AAA
1 AAA
3136208 GTACAGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAATAAGATTTCTCAAT
Found at i:3136787 original size:69 final size:69
Alignment explanation
Indices: 3136708--3136845 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
3136698 GATTGACTAA
*
3136708 GAAAAATTAAACTATAATAATAAATTAATT-GGTGTAGATGAAACTTTTTAAACTCCACAAATAA
1 GAAAAATTAAACGATAATAATAAATT-ATTCGGTGTAGATGAAACTTTTTAAACTCCACAAATAA
3136772 ATTCG
65 ATTCG
** *
3136777 GAAAAATTAAACGATAATAATAAATTATTCGGTGTAGATGAAGTTTTTTAAACTCCACAAGTAAA
1 GAAAAATTAAACGATAATAATAAATTATTCGGTGTAGATGAAACTTTTTAAACTCCACAAATAAA
3136842 TTCG
66 TTCG
3136846 ATTATTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 3 0.05
69 61 0.95
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (69 bp):
GAAAAATTAAACGATAATAATAAATTATTCGGTGTAGATGAAACTTTTTAAACTCCACAAATAAA
TTCG
Found at i:3137059 original size:9 final size:9
Alignment explanation
Indices: 3137045--3137069 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3137035 CAACAATTAA
3137045 TTAAAATTT
1 TTAAAATTT
3137054 TTAAAATTT
1 TTAAAATTT
3137063 TTAAAAT
1 TTAAAAT
3137070 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAAAATTT
Found at i:3145343 original size:15 final size:15
Alignment explanation
Indices: 3145315--3145347 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3145305 CTGAGAGGAT
3145315 AGCAGCAAAAGAAGC
1 AGCAGCAAAAGAAGC
3145330 AGCAG-AAAAGGAAGC
1 AGCAGCAAAA-GAAGC
3145345 AGC
1 AGC
3145348 TAAATCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.52, C:0.18, G:0.30, T:0.00
Consensus pattern (15 bp):
AGCAGCAAAAGAAGC
Found at i:3151900 original size:31 final size:31
Alignment explanation
Indices: 3151865--3151944 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
3151855 CCCAATGTAA
*
3151865 GAACAATTGCCTAGTTCAGG-CCACAATATGG
1 GAACAATTGCCAAGTTCAGGTCC-CAATATGG
** *
3151896 GAACAATTATCAAGTTCAGGTCCCAATGTGG
1 GAACAATTGCCAAGTTCAGGTCCCAATATGG
* *
3151927 GAATAGTTGCCAAGTTCA
1 GAACAATTGCCAAGTTCA
3151945 AACCCTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (31 bp):
GAACAATTGCCAAGTTCAGGTCCCAATATGG
Found at i:3154620 original size:15 final size:14
Alignment explanation
Indices: 3154600--3154639 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3154590 TTGATTTCAA
3154600 TTTAAACAATAAAAT
1 TTTAAA-AATAAAAT
*
3154615 TTTAAATATAAAAT
1 TTTAAAAATAAAAT
*
3154629 TTTTAAAATAA
1 TTTAAAAATAA
3154640 TAATATAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTAAAAATAAAAT
Found at i:3156588 original size:87 final size:88
Alignment explanation
Indices: 3156394--3156650 Score: 317
Period size: 87 Copynumber: 3.0 Consensus size: 88
3156384 CGATCTTACA
* * * * *
3156394 ACGATTAGTAAGGAATTGATTCACTTTGTGTTGAGGCAGTTGAAATTACTTGGCACTATTTTTTT
1 ACGATTAGTAAGGAACTGATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATCTTTTT
*
3156459 TTCTAGATTCTTTTATGTTGCAT
66 CTCTAGATTCTTTTATGTTGCAT
* * * * *
3156482 ATGATTAGTAAGGAGCTGATTTACTTTGTGTTTAAGTAGTTGCAATTAGTCT-GCACT-TCTTTT
1 ACGATTAGTAAGGAACTGATTCACTTTGTGTTTAAGTAGTTGAAATTACT-TGGCACTATCTTTT
*
3156545 TCTCTAGATTTTTTTATGTTGCAT
65 TCTCTAGATTCTTTTATGTTGCAT
* * * *
3156569 ACGATTAGTAAGGAACTGATTCACTTCGTGTTTAAGTAGTTGAAGTTAC-TCG-A-TACCTTTTT
1 ACGATTAGTAAGGAACTGATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATCTTTTT
*
3156631 TTCTAGATTCTTTTATGTTG
66 CTCTAGATTCTTTTATGTTG
3156651 AATAGGAATT
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
84 1 0.01
85 26 0.18
86 1 0.01
87 69 0.48
88 46 0.32
89 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (88 bp):
ACGATTAGTAAGGAACTGATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATCTTTTT
CTCTAGATTCTTTTATGTTGCAT
Found at i:3157787 original size:13 final size:13
Alignment explanation
Indices: 3157769--3157806 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
3157759 AGTTCTTCAT
3157769 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
3157782 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
3157795 TGCTTTTGAGAA
1 TGCTTTTGAGAA
3157807 TTTTGAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:3181878 original size:21 final size:22
Alignment explanation
Indices: 3181854--3181897 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3181844 GAAAATGTCC
3181854 AAGTT-GAAAAG-TAAAATAAAA
1 AAGTTCGAAAAGCT-AAATAAAA
*
3181875 AAGTTCGAATAGCTAAATAAAA
1 AAGTTCGAAAAGCTAAATAAAA
3181897 A
1 A
3181898 GTTTCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 14 0.70
23 1 0.05
ACGTcount: A:0.61, C:0.05, G:0.14, T:0.20
Consensus pattern (22 bp):
AAGTTCGAAAAGCTAAATAAAA
Found at i:3182296 original size:19 final size:19
Alignment explanation
Indices: 3182272--3182388 Score: 63
Period size: 19 Copynumber: 5.5 Consensus size: 19
3182262 TGTTTGTTTT
3182272 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
* * *
3182291 ATTGGGTTTGGATAGACTTTAGTTT
1 ATTGGG-TTGG-TA-A--AT-GGTA
*
3182316 ATTGGGTTGGTAAATAGTA
1 ATTGGGTTGGTAAATGGTA
* * *
3182335 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGG-TT-GGTA-A--AT-GGTA
3182360 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
3182379 ATTGGGTTGG
1 ATTGGGTTGG
3182389 GTAATTGGGT
Statistics
Matches: 72, Mismatches: 14, Indels: 24
0.65 0.13 0.22
Matches are distributed among these distances:
19 25 0.35
20 8 0.11
21 6 0.08
22 4 0.06
23 6 0.08
24 8 0.11
25 15 0.21
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.42
Consensus pattern (19 bp):
ATTGGGTTGGTAAATGGTA
Found at i:3182319 original size:25 final size:24
Alignment explanation
Indices: 3182291--3182371 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 24
3182281 GTAAATGGTA
3182291 ATTGGGTTTGGATAGACTTTAGTTT
1 ATTGGGTTTGG-TAGACTTTAGTTT
* *
3182316 ATTGGG-TTGGTA-A--ATAG-TA
1 ATTGGGTTTGGTAGACTTTAGTTT
3182335 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGGTTT-GGTAGACTTTAGTTT
3182360 ATTGGG-TTGGTA
1 ATTGGGTTTGGTA
3182372 AATGGTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 7 0.15
20 5 0.11
21 4 0.09
22 2 0.04
23 6 0.13
24 9 0.20
25 13 0.28
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.44
Consensus pattern (24 bp):
ATTGGGTTTGGTAGACTTTAGTTT
Found at i:3182319 original size:44 final size:44
Alignment explanation
Indices: 3182269--3182386 Score: 218
Period size: 44 Copynumber: 2.7 Consensus size: 44
3182259 AGCTGTTTGT
3182269 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGATAGACTTTAG
1 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGATAGACTTTAG
* *
3182313 TTTATTGGGTTGGTAAATAGTAATTGGGTTTGGGTAGACTTTAG
1 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGATAGACTTTAG
3182357 TTTATTGGGTTGGTAAATGGTAATTGGGTT
1 TTTATTGGGTTGGTAAATGGTAATTGGGTT
3182387 GGGTAATTGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.44
Consensus pattern (44 bp):
TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGATAGACTTTAG
Found at i:3182393 original size:13 final size:13
Alignment explanation
Indices: 3182375--3182399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3182365 GTTGGTAAAT
3182375 GGTAATTGGGTTG
1 GGTAATTGGGTTG
3182388 GGTAATTGGGTT
1 GGTAATTGGGTT
3182400 TATTAATTTT
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:0.44, T:0.40
Consensus pattern (13 bp):
GGTAATTGGGTTG
Found at i:3191448 original size:15 final size:15
Alignment explanation
Indices: 3191399--3191449 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3191389 TTACCTTAGG
3191399 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAT
* **
3191414 TTATG-TTT-GAAAT
1 TTACGTTTTAGTCAT
3191427 GTTACGTTTTAGTCAT
1 -TTACGTTTTAGTCAT
3191443 TTACGTT
1 TTACGTT
3191450 ATCATGTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53
Consensus pattern (15 bp):
TTACGTTTTAGTCAT
Found at i:3193296 original size:31 final size:31
Alignment explanation
Indices: 3193258--3193321 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3193248 TACCATGACT
3193258 TTGATGACCGATCTGATTTTAGTTAAATAAA
1 TTGATGACCGATCTGATTTTAGTTAAATAAA
3193289 TTGATGACCGATCTGATTTTAGTTAAATAAA
1 TTGATGACCGATCTGATTTTAGTTAAATAAA
3193320 TT
1 TT
3193322 TTTAAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (31 bp):
TTGATGACCGATCTGATTTTAGTTAAATAAA
Found at i:3209775 original size:11 final size:10
Alignment explanation
Indices: 3209755--3209791 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3209745 AAAAAAGAAT
3209755 AGAAAATAAA
1 AGAAAATAAA
3209765 AGAAAATTAAA
1 AGAAAA-TAAA
*
3209776 AGAACATAAA
1 AGAAAATAAA
3209786 AGAAAA
1 AGAAAA
3209792 GAATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (10 bp):
AGAAAATAAA
Found at i:3213498 original size:31 final size:31
Alignment explanation
Indices: 3213463--3213539 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
3213453 ACTTTTAGGG
*
3213463 TTAATATACT-ATTTGGTACCTGAGTTTGGTT
1 TTAATAT-CTAATTTGATACCTGAGTTTGGTT
* *
3213494 TTAATATTTAATTTGATACCTGAGTTTTGTT
1 TTAATATCTAATTTGATACCTGAGTTTGGTT
* *
3213525 TTAATGTTTAATTTG
1 TTAATATCTAATTTG
3213540 GCACTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (31 bp):
TTAATATCTAATTTGATACCTGAGTTTGGTT
Found at i:3216569 original size:25 final size:25
Alignment explanation
Indices: 3216525--3216582 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3216515 TTTTTTTCTC
*
3216525 GAGTTTT-GAGTTAGGATTTATATT
1 GAGTTTTAGAGTTAGGATTTATATA
* *
3216549 GAGTTTTAGATTTAGGGTTTATATA
1 GAGTTTTAGAGTTAGGATTTATATA
*
3216574 GAGCTTTAG
1 GAGTTTTAG
3216583 GTTTCAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.47
Consensus pattern (25 bp):
GAGTTTTAGAGTTAGGATTTATATA
Found at i:3217159 original size:175 final size:175
Alignment explanation
Indices: 3216844--3217556 Score: 993
Period size: 175 Copynumber: 4.1 Consensus size: 175
3216834 CGAACATCAT
* * * * *
3216844 CAACCACCAAGTGGGCAGGAAAAAAAATTCCTAACATAGTAAGAAGCAAACATTATAATATAACG
1 CAACCACCAAGTGGGCAGG-AAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACA
* * * * * *
3216909 AGCCATTGAAA-AATTAATCAATTTCACCACGTTTTCAAAAAACATGCTCTGTCAATAAAATGTC
65 AACCACT-AAATAATTAATCAATTTCACCACATCTTCATAAAACATTCTCTGTCAATAAAATGTC
3216973 GGCATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGC
129 GGCATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGC
* * *
3217020 CAATCGCCAAGTGGGTAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAA
1 CAACCACCAAGTGGGCAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAA
* * * *
3217085 ACCACTAAATAATTAATCAATTTCACCACGTCTTCATAAAACATTCTCTGTCAATAAAATATAGA
66 ACCACTAAATAATTAATCAATTTCACCACATCTTCATAAAACATTCTCTGTCAATAAAATGTCGG
* * *
3217150 CATACCAATCACTTCGCGAACAGATGTTCAAAAAGAAAACTTCGC
131 CATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGC
* *
3217195 CAACCACCAAGAGGGCAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGAT-A-ATGACAG
1 CAACCACCAAGTGGGCAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAA
* * *
3217258 ACCACTGAATAATTAATCAGTTTCACCACATCTTCATAAAACTTTCTCTGTCAATAAAATGTCGG
66 ACCACTAAATAATTAATCAATTTCACCACATCTTCATAAAACATTCTCTGTCAATAAAATGTCGG
*
3217323 CATACCAATCACTTCGA-GGACAAATGTTCAAAAAGAAAACGTCGC
131 CATACCAATCACTTC-ACGAACAAATGTTCAAAAAGAAAACGTCGC
* * *
3217368 CAACCACCAAGTGGGTAAGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATACGACAA
1 CAACCACCAAGTGGGCAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAA
* * *
3217433 ACCACTAAATAATTAATCAACTTCACCACATCTCCATAAAACATTCTCTATCAATAAAATGTCGG
66 ACCACTAAATAATTAATCAATTTCACCACATCTTCATAAAACATTCTCTGTCAATAAAATGTCGG
* ** ** * * * *
3217498 CAGACCAATTGCTTCGTGAACAAACGTTGAAAAAGAAAACATCGT
131 CATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGC
3217543 CAACCACCAAGTGG
1 CAACCACCAAGTGG
3217557 TAGCTAACCG
Statistics
Matches: 477, Mismatches: 55, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
173 156 0.33
174 5 0.01
175 300 0.63
176 16 0.03
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.22
Consensus pattern (175 bp):
CAACCACCAAGTGGGCAGGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAA
ACCACTAAATAATTAATCAATTTCACCACATCTTCATAAAACATTCTCTGTCAATAAAATGTCGG
CATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGC
Found at i:3217358 original size:348 final size:351
Alignment explanation
Indices: 3216844--3217553 Score: 1061
Period size: 348 Copynumber: 2.0 Consensus size: 351
3216834 CGAACATCAT
* * *
3216844 CAACCACCAAGTGGGCAGGAAAAAAAATTCCTAACATAGTAAGAAGCAAACATTATAATATAACG
1 CAACCACCAAGAGGGCAGGAAAAAAAATTCCTAACATAGTAAAAAGCAAACATGATAATATAACG
* * *
3216909 AGCCATTGAAAAATTAATCAATTTCACCACGTTTTCAAAAAACATGCTCTGTCAATAAAATGTCG
66 AGCCACTGAAAAATTAATCAATTTCACCACATCTTCAAAAAACATGCTCTGTCAATAAAATGTCG
* * *
3216974 GCATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGCCAATCGCCAAGTGGGTAGG
131 GCATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGCCAACCACCAAGTGGGTAAG
*
3217039 AAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCA
196 AAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATACGACAAACCACTAAATAATTAATCA
* * * * *
3217104 ATTTCACCACGTCTTCATAAAACATTCTCTGTCAATAAAATATAGACATACCAATCACTTCGCGA
261 ACTTCACCACATCTCCATAAAACATTCTCTATCAATAAAATATAGACAGACCAATCACTTCGCGA
* * *
3217169 ACAGATGTTCAAAAAGAAAACTTCGC
326 ACAAACGTTCAAAAAGAAAACATCGC
* *
3217195 CAACCACCAAGAGGGCAGG-AAACAAATTCCTAACATAGTAAAAAGCAAACATGAT-A-ATGAC-
1 CAACCACCAAGAGGGCAGGAAAAAAAATTCCTAACATAGTAAAAAGCAAACATGATAATATAACG
* * * * *
3217256 AGACCACTGAATAATTAATCAGTTTCACCACATCTTCATAAAACTTTCTCTGTCAATAAAATGTC
66 AG-CCACTGAAAAATTAATCAATTTCACCACATCTTCAAAAAACATGCTCTGTCAATAAAATGTC
*
3217321 GGCATACCAATCACTTCGA-GGACAAATGTTCAAAAAGAAAACGTCGCCAACCACCAAGTGGGTA
130 GGCATACCAATCACTTC-ACGAACAAATGTTCAAAAAGAAAACGTCGCCAACCACCAAGTGGGTA
3217385 AGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATACGACAAACCACTAAATAATTAAT
194 AGAAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATACGACAAACCACTAAATAATTAAT
* * * ** *
3217450 CAACTTCACCACATCTCCATAAAACATTCTCTATCAATAAAATGTCGGCAGACCAATTGCTTCGT
259 CAACTTCACCACATCTCCATAAAACATTCTCTATCAATAAAATATAGACAGACCAATCACTTCGC
* *
3217515 GAACAAACGTTGAAAAAGAAAACATCGT
324 GAACAAACGTTCAAAAAGAAAACATCGC
3217543 CAACCACCAAG
1 CAACCACCAAG
3217554 TGGTAGCTAA
Statistics
Matches: 323, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
347 2 0.01
348 268 0.83
349 2 0.01
350 33 0.10
351 18 0.06
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (351 bp):
CAACCACCAAGAGGGCAGGAAAAAAAATTCCTAACATAGTAAAAAGCAAACATGATAATATAACG
AGCCACTGAAAAATTAATCAATTTCACCACATCTTCAAAAAACATGCTCTGTCAATAAAATGTCG
GCATACCAATCACTTCACGAACAAATGTTCAAAAAGAAAACGTCGCCAACCACCAAGTGGGTAAG
AAACAAATTCCTAACATAGTAAAAAGCAAACATGATAATACGACAAACCACTAAATAATTAATCA
ACTTCACCACATCTCCATAAAACATTCTCTATCAATAAAATATAGACAGACCAATCACTTCGCGA
ACAAACGTTCAAAAAGAAAACATCGC
Found at i:3218312 original size:22 final size:22
Alignment explanation
Indices: 3218281--3218331 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3218271 CTCATATTTC
* *
3218281 CTCTCAATTTCTTTTCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
3218303 CTCTCGATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
3218325 CTCTCAA
1 CTCTCAA
3218332 ATCCATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.43
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:3218379 original size:22 final size:22
Alignment explanation
Indices: 3218354--3218404 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3218344 TTTCAATTTC
3218354 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
3218376 CTCTTAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
3218398 CTCTCAA
1 CTCTCAA
3218405 ATCCATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:3218395 original size:73 final size:73
Alignment explanation
Indices: 3218276--3218440 Score: 285
Period size: 73 Copynumber: 2.3 Consensus size: 73
3218266 CCTCTCTCAT
* * *
3218276 ATTTCCTCTCAATTTCTTTTCAAAATTCTCTCGATTTCCTTCCAAAATTCTCTCAAATCCATATT
1 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATT
3218341 TAATTTCA
66 TAATTTCA
*
3218349 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTTAATTTCCTTCCAAAATTCTCTCAAATCCATATT
1 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATT
*
3218414 TGATTTCA
66 TAATTTCA
3218422 ATTTCCTCTCAATTTCCTT
1 ATTTCCTCTCAATTTCCTT
3218441 TTTTAAAATG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.26, C:0.27, G:0.01, T:0.45
Consensus pattern (73 bp):
ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATT
TAATTTCA
Found at i:3219591 original size:7 final size:7
Alignment explanation
Indices: 3219579--3219604 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3219569 TAGTCGATTG
3219579 GTATTTA
1 GTATTTA
3219586 GTATTTA
1 GTATTTA
3219593 GTATTTA
1 GTATTTA
3219600 GTATT
1 GTATT
3219605 ATTATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:3220577 original size:21 final size:21
Alignment explanation
Indices: 3220535--3220583 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3220525 AGATGTCGTA
* *
3220535 CCGGAAGAACCAGAATCCCCG
1 CCGGAAGAACAACAATCCCCG
3220556 CCGGAAGAACAACAA-CCGCCG
1 CCGGAAGAACAACAATCC-CCG
*
3220577 CCAGAAG
1 CCGGAAG
3220584 CTAGAGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.37, C:0.37, G:0.24, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACAACAATCCCCG
Found at i:3220817 original size:29 final size:29
Alignment explanation
Indices: 3220784--3221501 Score: 1008
Period size: 29 Copynumber: 24.6 Consensus size: 29
3220774 ATGTTTATTT
3220784 CTAACCCTAACCAAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3220813 CTAACCCTAACCAAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3220842 CTAACCCTAACCTAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3220871 CTAACCCTAACCTAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3220900 CTAACCCTAACCTAATTCAATT-AAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3220928 CTAACCCTAACCCAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3220957 CTAACCCTAACCTAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* * *
3220986 TTAACCCTAACCCAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221015 CTAACCCTAACCAAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3221044 CTAACCCTAACCTAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3221073 CTAACCCTAACCCAATTCAATTAAAAACCCTAAC
1 CTAACCCTAACCAAATTTAATTAAAAA--C---C
* *
3221107 TCTAACCCTAACCCAATTCAATTAAAAACC
1 -CTAACCCTAACCAAATTTAATTAAAAACC
*
3221137 CTAACCCTAACCAAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3221166 CTAACCCTAACCCAATTCAATT-AAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221194 CTAACCCTAACCAAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* * * *
3221223 CTAACCTTAACCTAACTTAATTAAAAATC
1 CTAACCCTAACCAAATTTAATTAAAAACC
**
3221252 CTAACCCTAACTTAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221281 CTAACCCTAACCAAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3221310 CTAACCCTAACCCAATTCAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* *
3221339 CTAACCCTAACCAAACTTAATTAAAAACT
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221368 CTAACCCTAACCTAATTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221397 CTAACCCTAACCAAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221426 CTAACCCTAACCAAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
* * *
3221455 ATAACCCTAACCTAACTTAATTAAAAACC
1 CTAACCCTAACCAAATTTAATTAAAAACC
*
3221484 CTAACCCTAACCCAATTT
1 CTAACCCTAACCAAATTT
3221502 TATATAATTT
Statistics
Matches: 631, Mismatches: 50, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
28 52 0.08
29 548 0.87
30 1 0.00
31 1 0.00
33 1 0.00
34 1 0.00
35 27 0.04
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (29 bp):
CTAACCCTAACCAAATTTAATTAAAAACC
Found at i:3221539 original size:37 final size:37
Alignment explanation
Indices: 3221497--3221698 Score: 386
Period size: 37 Copynumber: 5.5 Consensus size: 37
3221487 ACCCTAACCC
3221497 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
3221534 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
*
3221571 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
*
3221608 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
3221645 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
3221682 AATTTTATATAATTTGA
1 AATTTTATATAATTTGA
3221699 GTTAATACAA
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 163 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.50
Consensus pattern (37 bp):
AATTTTATATAATTTGATAATTTTACTAACCATTTAT
Found at i:3224894 original size:124 final size:123
Alignment explanation
Indices: 3224674--3225017 Score: 562
Period size: 124 Copynumber: 2.8 Consensus size: 123
3224664 CCCAAACATG
* *
3224674 CTACTGTAGCAAAAACGCGCTCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGC-CACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** * * *
3224739 TTGAAGCGATTTTATACTATTTGGTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
65 TAAAAGCGATTTTATACTATTTGATCAGAAAAGTAAAAAAAAAATATTTCTTACATGAC
*
3224798 CTACTATAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCG-CCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
3224863 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTAAAAAAAAAATATTTCTTACATGAC
65 TAAAAGCGATTTTATACTATTTGATCAGAAAAGTAAAAAAAAAATATTTCTTACATGAC
*
3224922 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCGATTTCACAAATTCTTCTCAAAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCG-CCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
3224987 TAAAAGCGATTTTATACTATTTTATCAGAAA
65 TAAAAGCGATTTTATACTATTTGATCAGAAA
3225018 CATCAAGTCG
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
124 205 1.00
125 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT
AAAAGCGATTTTATACTATTTGATCAGAAAAGTAAAAAAAAAATATTTCTTACATGAC
Found at i:3238892 original size:232 final size:230
Alignment explanation
Indices: 3238495--3238922 Score: 533
Period size: 232 Copynumber: 1.9 Consensus size: 230
3238485 AAACCAGCAG
* * * ***
3238495 CACAACCAAATAAATTACTCAAAGTTCAATTCTATAGAATAATTATAAATCATTTAATGAATAGG
1 CACAACCAAACAAATTACTCAAAGTTCAATTCTATAAAATAATCATAAATCAAGGAATGAATAGG
* * * * * *
3238560 TAGGTCAATATCTTAAATTCATATTAAATTTTCAAAAATTCTTGACCTGTAAATTTTCTTTTCAT
66 AAGATCAATATCTTAAATTCATATTAAATTTTAAAAAATTCCTGACCTGAAAATTTTATTTTCAT
* * *
3238625 AAAACTAAGAGTAATTAAAGCAACTCAATCTTCTAACTTAATTCTGGATCAAGAAATTCTAAAAG
131 AAAACTAAGAGTAATTAAAGCAACTCAACCTTCTAACTTAATACTAGATCAAGAAATTCTAAAAG
3238690 CTGATAGAATCGATTCTATGATCTAAAATCAGTGA
196 CTGATAGAATCGATTCTATGATCTAAAATCAGTGA
* * *
3238725 CACAACCAAACAAATTAGTCAATGTTCAATT-TCATAAAATAATCATAAATCAAGGAAT-CA-AG
1 CACAACCAAACAAATTACTCAAAGTTCAATTCT-ATAAAATAATCATAAATCAAGGAATGAATAG
*
3238787 GAAGATCAATATCTTAAATTCATATTCAAA-TTTAAAAAACTTCCTGATCTGGAACGAATTTTAT
65 GAAGATCAATATCTTAAATTCATATT-AAATTTTAAAAAA-TTCCTGACCT-GAA--AATTTTAT
* * * * **
3238851 TTTCATAAAACTAAGAGTAGTTAAAGCTAC-CGGACCTTCTAACTTTATACTAGATCCGGAAATT
125 TTTCATAAAACTAAGAGTAATTAAAGCAACTC-AACCTTCTAACTTAATACTAGATCAAGAAATT
3238915 CTAAAAGC
189 CTAAAAGC
3238923 CGAACAGTAT
Statistics
Matches: 166, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
228 34 0.20
229 13 0.08
230 50 0.30
231 1 0.01
232 68 0.41
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (230 bp):
CACAACCAAACAAATTACTCAAAGTTCAATTCTATAAAATAATCATAAATCAAGGAATGAATAGG
AAGATCAATATCTTAAATTCATATTAAATTTTAAAAAATTCCTGACCTGAAAATTTTATTTTCAT
AAAACTAAGAGTAATTAAAGCAACTCAACCTTCTAACTTAATACTAGATCAAGAAATTCTAAAAG
CTGATAGAATCGATTCTATGATCTAAAATCAGTGA
Found at i:3239734 original size:205 final size:204
Alignment explanation
Indices: 3239362--3240018 Score: 874
Period size: 205 Copynumber: 3.2 Consensus size: 204
3239352 AGGAAATGTT
* ** **
3239362 GATGAACTTCGAAACCAAT-ACGAGGTCTAGAAGGAGAAAATGA-CTCTAAACCAATTCAAACTA
1 GATGAACTTCGAAACGAATAACGAGGTCTAGAAGGAGAAAATGAGCTAAAAATGAATTCAAACTA
***
3239425 ATCAGCAAAGAAAAACTATTATAAATCAAATTAACAAAAAGGAATGGAAATATATAAATGAATAG
66 ATCAGCAAAGAAAAACTATTATAAATCAAATT-TTTAAAA--AA-GG-AA-ATATAAATGAATAG
* * *
3239490 CGAGATCTAGAAGGAAAAATTGAACAAAATAATCAGCAAAGAAAGACTAATTCAAATCAAAGTAA
125 CGAGATCTAGAACG-AAAATTGAACAAAATAATCAGCAAAGAAAGACTAATACAAATCAAACTAA
*
3239555 AAAAACCGGAAATATC
189 AAAAACCAGAAATATC
* * *
3239571 GATGAACTTTGAAATGAATAACGAGGTCTAGAAGGAGAAAATAAGCTAAAAATGAATTCAAACTA
1 GATGAACTTCGAAACGAATAACGAGGTCTAGAAGGAGAAAATGAGCTAAAAATGAATTCAAACTA
*
3239636 ATCAGCAAAGAAAAACAATTATAAATCAAATTTTTAAAAAAGGAAATATAAATGAATAGCGAGAT
66 ATCAGCAAAGAAAAACTATTATAAATCAAATTTTTAAAAAAGGAAATATAAATGAATAGCGAGAT
* * *
3239701 CTAGAACGAGAAATTGAACAAAGTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAAC
131 CTAGAACGA-AAATTGAACAAAATAATCAGCAAAGAAAGACTAATACAAATCAAACTAAAAAAAC
* *
3239766 CAGAAACATA
195 CAGAAATATC
* * *
3239776 GATGAACTTCGAAATGAATAACGAGGTCTGGAAGGAGAAAGTGAGCTAAAAATGAATTCAAACTA
1 GATGAACTTCGAAACGAATAACGAGGTCTAGAAGGAGAAAATGAGCTAAAAATGAATTCAAACTA
* * * * * *
3239841 ATCAGCAAAGAAATACTATTATAAGT--ATTTTTTTAAAAAGGAAATATAAACGAAGAGCGAGAT
66 ATCAGCAAAGAAAAACTATTATAAATCAAATTTTTAAAAAAGGAAATATAAATGAATAGCGAGAT
*
3239904 CTAGAACGAAAGATTGAACAAATTAATCAGCAAAG-AAGCACTAATACAAATCAAACTAAAAAAA
131 CTAGAACGAAA-ATTGAACAAAATAATCAGCAAAGAAAG-ACTAATACAAATCAAACTAAAAAAA
3239968 CCAGAAATATC
194 CCAGAAATATC
* * * *
3239979 GATGAACTTTGAAACGAACAGCGAGATCTAGAAGGAGAAA
1 GATGAACTTCGAAACGAATAACGAGGTCTAGAAGGAGAAA
3240019 TGGAACTAAC
Statistics
Matches: 400, Mismatches: 43, Indels: 16
0.87 0.09 0.03
Matches are distributed among these distances:
202 4 0.01
203 131 0.33
204 1 0.00
205 168 0.42
206 2 0.00
207 2 0.00
208 2 0.00
209 16 0.04
210 27 0.07
211 47 0.12
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19
Consensus pattern (204 bp):
GATGAACTTCGAAACGAATAACGAGGTCTAGAAGGAGAAAATGAGCTAAAAATGAATTCAAACTA
ATCAGCAAAGAAAAACTATTATAAATCAAATTTTTAAAAAAGGAAATATAAATGAATAGCGAGAT
CTAGAACGAAAATTGAACAAAATAATCAGCAAAGAAAGACTAATACAAATCAAACTAAAAAAACC
AGAAATATC
Found at i:3240534 original size:16 final size:16
Alignment explanation
Indices: 3240513--3240545 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3240503 TTTGTGGATC
3240513 GGATTAAGTTATTGTT
1 GGATTAAGTTATTGTT
3240529 GGATTAAGTTATTGTT
1 GGATTAAGTTATTGTT
3240545 G
1 G
3240546 AAGTGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (16 bp):
GGATTAAGTTATTGTT
Found at i:3242028 original size:20 final size:20
Alignment explanation
Indices: 3242003--3242042 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3241993 CGTAAAATGA
*
3242003 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3242023 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3242043 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3242032 original size:34 final size:35
Alignment explanation
Indices: 3241988--3242054 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3241978 TAGTAAAATA
*
3241988 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3242022 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3242055 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3242058 original size:14 final size:15
Alignment explanation
Indices: 3241982--3242058 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3241972 GATTGGTAGT
* *
3241982 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
3241996 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3242010 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3242030 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3242045 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3242059 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3242166 original size:20 final size:20
Alignment explanation
Indices: 3242141--3242179 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3242131 GTTTTTACAT
3242141 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
3242161 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
3242180 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:3242239 original size:15 final size:15
Alignment explanation
Indices: 3242210--3242262 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
3242200 TATTGCAATG
*
3242210 ATTTATTTATAAATAA
1 ATTT-TTTATTAATAA
3242226 ATTTTTTATTAATAAA
1 ATTTTTTATTAAT-AA
3242242 AGTTTTTTATCTAATTAA
1 A-TTTTTTAT-TAA-TAA
3242260 ATT
1 ATT
3242263 CCAAATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 10 0.31
18 6 0.19
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:3244947 original size:25 final size:26
Alignment explanation
Indices: 3244919--3244979 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
3244909 GAATATGCTG
3244919 AGAAGAGAAG-ATGAAGAACAGAAGA
1 AGAAGAGAAGAATGAAGAACAGAAGA
**
3244944 AGAA-A-AAGGAATGAAGAATGGAAGA
1 AGAAGAGAA-GAATGAAGAACAGAAGA
3244969 AGAAGAAGAAG
1 AGAAG-AGAAG
3244980 GAGCCTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 21 0.72
27 2 0.07
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.33, T:0.05
Consensus pattern (26 bp):
AGAAGAGAAGAATGAAGAACAGAAGA
Found at i:3245064 original size:18 final size:17
Alignment explanation
Indices: 3245041--3245074 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3245031 TTTGCAACAC
3245041 AAGGGGAAGGGAGAAGGG
1 AAGGGGAAGGGA-AAGGG
3245059 AAGGGGAAGGGAAAGG
1 AAGGGGAAGGGAAAGG
3245075 TTAAAAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGAAAGGG
Found at i:3245474 original size:25 final size:24
Alignment explanation
Indices: 3245428--3245480 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
3245418 TTTGTTGAAT
*
3245428 ATTTGTAATTTTTATAACATTTAA
1 ATTTGTAATTTTTATAAAATTTAA
*
3245452 ATTTGTAAATTTATT-TAAAATTTAG
1 ATTTGT-AATTT-TTATAAAATTTAA
3245477 ATTT
1 ATTT
3245481 ATTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTTGTAATTTTTATAAAATTTAA
Found at i:3245482 original size:17 final size:18
Alignment explanation
Indices: 3245446--3245485 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3245436 TTTTTATAAC
*
3245446 ATTTAAATTTGTAAATTT
1 ATTTAAAATTGTAAATTT
*
3245464 ATTTAAAATT-TAGATTT
1 ATTTAAAATTGTAAATTT
3245481 ATTTA
1 ATTTA
3245486 TTATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTAAAATTGTAAATTT
Found at i:3246857 original size:17 final size:17
Alignment explanation
Indices: 3246830--3246862 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3246820 TAAAATTTTA
3246830 GATCTATATTTCGAGTAG
1 GATCTATATTT-GAGTAG
3246848 GATC-ATATTTGAGTA
1 GATCTATATTTGAGTA
3246863 AGCATAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (17 bp):
GATCTATATTTGAGTAG
Found at i:3247963 original size:5 final size:5
Alignment explanation
Indices: 3247955--3247979 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3247945 TATATACAGA
3247955 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
3247980 TCACGGGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3250943 original size:69 final size:69
Alignment explanation
Indices: 3250864--3251001 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
3250854 GGGAAAAATG
3250864 GTCAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTTGGTGATATTTTACATTAATTAA
1 GTCAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTTGGTGATATTTTACATTAATTAA
3250929 TTAA
66 TTAA
*
3250933 GTCAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTTGGTGATATTTTAGATTAATTAA
1 GTCAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTTGGTGATATTTTACATTAATTAA
3250998 TTAA
66 TTAA
3251002 ATAAATATTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (69 bp):
GTCAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTTGGTGATATTTTACATTAATTAA
TTAA
Found at i:3251044 original size:11 final size:13
Alignment explanation
Indices: 3251020--3251051 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3251010 TAGTTTATTA
3251020 ATATTTTAATATG
1 ATATTTTAATATG
3251033 AT-TTTTAA-ATG
1 ATATTTTAATATG
3251044 ATATTTTA
1 ATATTTTA
3251052 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:3252070 original size:39 final size:39
Alignment explanation
Indices: 3252027--3252141 Score: 94
Period size: 39 Copynumber: 2.9 Consensus size: 39
3252017 TAGTTTCAGG
*
3252027 ATGAAATGTTAATTTAGATCAAGATTGGGTGGAAATTGC
1 ATGAAATGTTAATTTAGATCAAGATTGGGTGGAAATTGA
** * * **
3252066 ATGAAATGAATTGTTTTATCATTTAA-ATT-ACT--AAATTGA
1 ATGAAATG--TTAATTTA-GA-TCAAGATTGGGTGGAAATTGA
*
3252105 ATGAAATATTAATTTAGATCAAGATTGGGTGGAAATT
1 ATGAAATGTTAATTTAGATCAAGATTGGGTGGAAATT
3252142 TGAGAAAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
35 3 0.06
36 4 0.07
37 7 0.13
39 26 0.48
41 7 0.13
42 4 0.07
43 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.37
Consensus pattern (39 bp):
ATGAAATGTTAATTTAGATCAAGATTGGGTGGAAATTGA
Found at i:3259599 original size:38 final size:40
Alignment explanation
Indices: 3259533--3259621 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 40
3259523 TAAAAAGTAT
* * *
3259533 TTATATTAAAAAACACTACCATACATATAATAAATGTTTTA
1 TTATATT-AAAAACACTACAATAAATATAATAAATATTTTA
3259574 TTATATTAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
*
3259612 TTTTATTAAA
1 TTATATTAAA
3259622 TATAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.64
39 1 0.02
40 8 0.18
41 7 0.16
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:3266899 original size:15 final size:16
Alignment explanation
Indices: 3266879--3266914 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3266869 AATCATTTAA
3266879 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
3266894 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
3266910 AAATT
1 AAATT
3266915 TACAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:3272200 original size:6 final size:7
Alignment explanation
Indices: 3272162--3272197 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3272152 CCTGAGTATA
3272162 ATATTTG
1 ATATTTG
3272169 ATATTTG
1 ATATTTG
3272176 ATATTTG
1 ATATTTG
*
3272183 ATATCTG
1 ATATTTG
3272190 AT-TTTG
1 ATATTTG
3272196 AT
1 AT
3272198 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.56
Consensus pattern (7 bp):
ATATTTG
Found at i:3284542 original size:257 final size:257
Alignment explanation
Indices: 3284076--3284564 Score: 809
Period size: 257 Copynumber: 1.9 Consensus size: 257
3284066 CAAGCAATAT
* * *
3284076 TCCATTTAGAATTCAAGATCATTACAACTACTATGATTCTATCGTTAACCAGACCGATTCAAAAT
1 TCCATATAAAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTCAAAAT
* *
3284141 CACTTAAATTAAGAACAAAAAAAATGGAATTCAAGCAAGCAAACGATTCGGTGCATGCTTTTTAA
66 CACTTAAACTAAGAACAAAAAAAA-GGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAA
*
3284206 ACAAACAATTCAAGTAAAATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGA
130 ACAAACAATTAAAGTAAAATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGA
3284271 CCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGACGCCACCGA
195 CCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGACGCCACCGA
* *
3284334 TCCATATAAAATTCAAGATCATTTCAACTATTATGATTCTATCATTAACCAGACCGATTCAAAAT
1 TCCATATAAAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTCAAAAT
*** *
3284399 CACTTAAACTAAGGGGGAAAATAAA-GAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAA
66 CACTTAAACTAA-GAACAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAA
* * *
3284463 ACAAACAATTAAAGTAATATTTAAACATGATAATTATGCAAGTAATTAGGGTACCTAAACAGAGG
130 ACAAACAATTAAAGTAAAATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGA
*
3284528 TCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCC
195 CCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCC
3284565 TTCGACGCCA
Statistics
Matches: 214, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
257 135 0.63
258 71 0.33
259 8 0.04
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (257 bp):
TCCATATAAAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTCAAAAT
CACTTAAACTAAGAACAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAAA
CAAACAATTAAAGTAAAATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGAC
CGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGACGCCACCGA
Found at i:3293826 original size:41 final size:42
Alignment explanation
Indices: 3293769--3293856 Score: 151
Period size: 41 Copynumber: 2.1 Consensus size: 42
3293759 ATTGACCATA
*
3293769 AAATAAATATGAATGATACTTTGAT-TATAAAAAAAAAATCG
1 AAATAAATATGAATGATACTTTGATATACAAAAAAAAAATCG
3293810 AAATAAATATGAATGATACTTTGATCATACAAAAAAAAAATCG
1 AAATAAATATGAATGATACTTTGAT-ATACAAAAAAAAAATCG
3293853 AAAT
1 AAAT
3293857 TGTAAAACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 25 0.57
43 19 0.43
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (42 bp):
AAATAAATATGAATGATACTTTGATATACAAAAAAAAAATCG
Found at i:3294556 original size:33 final size:33
Alignment explanation
Indices: 3294518--3294587 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
3294508 CCTGGAAAGC
* *
3294518 ATGGGGATGTTAAAGGATTTA-AAGTGCATGGAA
1 ATGGGGATCTTAAAGGATTTAGAA-TCCATGGAA
*
3294551 ATGGGGATCTTAGAGGATTTAGAATCCATGGAA
1 ATGGGGATCTTAAAGGATTTAGAATCCATGGAA
3294584 ATGG
1 ATGG
3294588 AAACATTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.33, T:0.27
Consensus pattern (33 bp):
ATGGGGATCTTAAAGGATTTAGAATCCATGGAA
Found at i:3296914 original size:12 final size:11
Alignment explanation
Indices: 3296898--3296931 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3296888 TTTAATGAGA
3296898 TTTTTTATTAT
1 TTTTTTATTAT
*
3296909 TATTTTATTAT
1 TTTTTTATTAT
3296920 TTTGTTTATTAT
1 TTT-TTTATTAT
3296932 ATAAGGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:3299047 original size:101 final size:101
Alignment explanation
Indices: 3298872--3299111 Score: 372
Period size: 101 Copynumber: 2.4 Consensus size: 101
3298862 TGAATTGACG
* * *
3298872 GATAAGACCATAACTGGGTTATGGCACTATGAACGTGAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
* *
3298937 ATATGTAAGATCATAGCTGGGTTATGACATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
* *
3298973 GATAAGACTATAACTGGGTTATGGCACTATGAACGTAAGGCCATGGTTAGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
* *
3299038 ATATGTAAGACCATAGCTGGGCTATGGCATTTTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
* * *
3299074 GATAATACCATAAATGGGTTATGGCACTATGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
3299112 AGGATGAATT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 126 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
Found at i:3303197 original size:15 final size:15
Alignment explanation
Indices: 3303162--3303199 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3303152 ATGGTTTGAA
3303162 TTGTTTCAGGTTAGG
1 TTGTTTCAGGTTAGG
*
3303177 TAGTTT-AGGTTAGGG
1 TTGTTTCAGGTTA-GG
3303192 TTGTTTCA
1 TTGTTTCA
3303200 TTTTCAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGTTTCAGGTTAGG
Found at i:3308748 original size:39 final size:39
Alignment explanation
Indices: 3308694--3308773 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
3308684 AAGAGCTATC
* * * *
3308694 TGAAGGTGGTGATGATTTTTGCTTAGGAGGAGGAGGTGA
1 TGAAGGTGATAATGATTGTTTCTTAGGAGGAGGAGGTGA
* *
3308733 TGAAGGTGATAATGATTGTTTCTTAGGAGGTGGCGGTGA
1 TGAAGGTGATAATGATTGTTTCTTAGGAGGAGGAGGTGA
3308772 TG
1 TG
3308774 GTGACGGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.23, C:0.04, G:0.41, T:0.33
Consensus pattern (39 bp):
TGAAGGTGATAATGATTGTTTCTTAGGAGGAGGAGGTGA
Found at i:3308846 original size:3 final size:3
Alignment explanation
Indices: 3308840--3308870 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3308830 GTTTGTTCCT
*
3308840 GAG GAG GAG GAG GAG AAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
3308871 TGAAGGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:3308884 original size:12 final size:12
Alignment explanation
Indices: 3308869--3308914 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3308859 AGGAGGAGGA
*
3308869 GGTGAAGGTGGT
1 GGTGATGGTGGT
* *
3308881 GGTGATGATGAT
1 GGTGATGGTGGT
*
3308893 GATGATGGTGGT
1 GGTGATGGTGGT
3308905 GGTGATGGTG
1 GGTGATGGTG
3308915 AAGGAGGTGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.52, T:0.30
Consensus pattern (12 bp):
GGTGATGGTGGT
Found at i:3321754 original size:201 final size:198
Alignment explanation
Indices: 3321412--3321801 Score: 726
Period size: 201 Copynumber: 2.0 Consensus size: 198
3321402 ATATATTAAG
3321412 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCACGTGTCTTGTCTCCTTAAATTTCACAAT
1 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCACGTGTCTTGTCTCCTTAAATTTCACAAT
3321477 CGCAATTATTATATGATTATATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATT
66 CGCAATTATTATATGATTATATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATT
* *
3321542 GGGTTTATTTTGGTGTTTATATATATTTTGAGGGTAAATTCGATTAAACAATAAATAAAATAATG
131 GGGTTTATTTTGGTGTTTATATATATTTTGAGGATAAATTCGATTAAAAAATAAATAAAATAATG
3321607 AAA
196 AAA
3321610 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCAACGTGTCTTGTCTCCTTAAATTTCACAA
1 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCC-ACGTGTCTTGTCTCCTTAAATTTCACAA
*
3321675 TCGTAATTATTATATGATTATATATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTA
65 TCGCAATTATTATATGA-T-TATATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTA
3321740 ATTGGGTTTATTTTGGTGTTTATATATATTTTGAGGATAAATTCGATTAAAAAATAAATAAA
128 ATTGGGTTTATTTTGGTGTTTATATATATTTTGAGGATAAATTCGATTAAAAAATAAATAAA
3321802 TAAAATAATG
Statistics
Matches: 186, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
198 36 0.19
199 44 0.24
200 1 0.01
201 105 0.56
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (198 bp):
TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCACGTGTCTTGTCTCCTTAAATTTCACAAT
CGCAATTATTATATGATTATATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATT
GGGTTTATTTTGGTGTTTATATATATTTTGAGGATAAATTCGATTAAAAAATAAATAAAATAATG
AAA
Found at i:3342184 original size:223 final size:223
Alignment explanation
Indices: 3341793--3342231 Score: 612
Period size: 223 Copynumber: 2.0 Consensus size: 223
3341783 GGAAAATTTT
*
3341793 ATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
1 ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
* * * * ** *
3341858 CTATTGAAATTCTTTATGAAATTAAGTTTACAACAGCATAGCAATGTTATATTCAAGTGGCGAGG
66 CCATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAAAG
* * * *
3341923 TTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGGTAA
131 TTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGAAA
3341988 GACTTTCATGAGTTAGTGATGTTAACTC
196 GACTTTCATGAGTTAGTGATGTTAACTC
* * * * * * *
3342016 ATTTCCTTACAGTTTAGTCTCTTTTCACGATAGCTATCAAACCTTTGTCAGAAACCA-CAAAATT
1 ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAA-T
* * *
3342080 TCCATTGAAATTC-TTAGTGGAATTAAGTTTAGAACAATATAGAAAGGTTATATTCAAGTGGAAA
65 TCCATTGAAATTCTTTA-TGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAA
* * *
3342144 AGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAATATTTTAAGGA
129 AGTTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGA
*
3342209 AAGAGTTTCATGAGTTAGTGATG
194 AAGACTTTCATGAGTTAGTGATG
3342232 CTAGCATGTT
Statistics
Matches: 188, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
222 8 0.04
223 180 0.96
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (223 bp):
ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
CCATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAAAG
TTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGAAA
GACTTTCATGAGTTAGTGATGTTAACTC
Found at i:3342840 original size:891 final size:891
Alignment explanation
Indices: 3341400--3343186 Score: 3556
Period size: 891 Copynumber: 2.0 Consensus size: 891
3341390 ACGTAGAACA
*
3341400 ATTTTTTTGACCGACTGTTCATTAGCGGTCAGCTGACAGTTACTGTTTCAACTAGGTTGATGTCT
1 ATTTTTTTGACCGACTGTTCATTAACGGTCAGCTGACAGTTACTGTTTCAACTAGGTTGATGTCT
3341465 AAAAATCCGTTACATGAAGGGTTGATTTCAAAAAAATTAGGGCATATATCCAAATTCCCCCAAAT
66 AAAAATCCGTTACATGAAGGGTTGATTTCAAAAAAATTAGGGCATATATCCAAATTCCCCCAAAT
3341530 GTTGAGGGTTTTTTGCAATTATGCCATTATTAAATTAAACAATGGAGAAGATGTTATCAAATTTT
131 GTTGAGGGTTTTTTGCAATTATGCCATTATTAAATTAAACAATGGAGAAGATGTTATCAAATTTT
3341595 TGACCCTTAGATTTAAAAGGAAAATAAGAAGAAATCTTAGCCCTTGGATCAAAATTATTATGTAT
196 TGACCCTTAGATTTAAAAGGAAAATAAGAAGAAATCTTAGCCCTTGGATCAAAATTATTATGTAT
3341660 AGATTTTTATATAATATAATATTATTTTATTAAATGAATAAATAATTAGAAATTTTATTAAAAAA
261 AGATTTTTATATAATATAATATTATTTTATTAAATGAATAAATAATTAGAAATTTTATTAAAAAA
3341725 GACGAAGAATTTTCTTTCATCTTTCATACTCTCACACACCACCACCATTCATGAAAAAGGAAAAT
326 GACGAAGAATTTTCTTTCATCTTTCATACTCTCACACACCACCACCATTCATGAAAAAGGAAAAT
3341790 TTTATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAA
391 TTTATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAA
*
3341855 ATTCTATTGAAATTCTTTATGAAATTAAGTTTACAACAGCATAGCAATGTTATATTCAAGTGGCG
456 ATTCTATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGCAATGTTATATTCAAGTGGCG
3341920 AGGTTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGG
521 AGGTTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGG
3341985 TAAGACTTTCATGAGTTAGTGATGTTAACTCATTTCCTTACAGTTTAGTCTCTTTTCACGATAGC
586 TAAGACTTTCATGAGTTAGTGATGTTAACTCATTTCCTTACAGTTTAGTCTCTTTTCACGATAGC
3342050 TATCAAACCTTTGTCAGAAACCACAAAATTTCCATTGAAATTCTTAGTGGAATTAAGTTTAGAAC
651 TATCAAACCTTTGTCAGAAACCACAAAATTTCCATTGAAATTCTTAGTGGAATTAAGTTTAGAAC
3342115 AATATAGAAAGGTTATATTCAAGTGGAAAAGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAA
716 AATATAGAAAGGTTATATTCAAGTGGAAAAGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAA
3342180 GATTTAGTGAGATACTAATATTTTAAGGAAAGAGTTTCATGAGTTAGTGATGCTAGCATGTTTAA
781 GATTTAGTGAGATACTAATATTTTAAGGAAAGAGTTTCATGAGTTAGTGATGCTAGCATGTTTAA
3342245 TTCAAGTGAAAGTGCATAAAAGTGATATTAGATTTTTTTATTGTGT
846 TTCAAGTGAAAGTGCATAAAAGTGATATTAGATTTTTTTATTGTGT
3342291 ATTTTTTTGACCGACTGTTCATTAACGGTCAGCTGACAGTTACTGTTTCAACTAGGTTGATGTCT
1 ATTTTTTTGACCGACTGTTCATTAACGGTCAGCTGACAGTTACTGTTTCAACTAGGTTGATGTCT
3342356 AAAAATCCGTTACATGAAGGGTTGATTTCAAAAAAATTAGGGCATATATCCAAATTCCCCCAAAT
66 AAAAATCCGTTACATGAAGGGTTGATTTCAAAAAAATTAGGGCATATATCCAAATTCCCCCAAAT
3342421 GTTGAGGGTTTTTTGCAATTATGCCATTATTAAATTAAACAATGGAGAAGATGTTATCAAATTTT
131 GTTGAGGGTTTTTTGCAATTATGCCATTATTAAATTAAACAATGGAGAAGATGTTATCAAATTTT
3342486 TGACCCTTAGATTTAAAAGGAAAATAAGAAGAAATCTTAGCCCTTGGATCAAAATTATTATGTAT
196 TGACCCTTAGATTTAAAAGGAAAATAAGAAGAAATCTTAGCCCTTGGATCAAAATTATTATGTAT
3342551 AGATTTTTATATAATATAATATTATTTTATTAAATGAATAAATAATTAGAAATTTTATTAAAAAA
261 AGATTTTTATATAATATAATATTATTTTATTAAATGAATAAATAATTAGAAATTTTATTAAAAAA
3342616 GACGAAGAATTTTCTTTCATCTTTCATACTCTCACACACCACCACCATTCATGAAAAAGGAAAAT
326 GACGAAGAATTTTCTTTCATCTTTCATACTCTCACACACCACCACCATTCATGAAAAAGGAAAAT
3342681 TTTATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAA
391 TTTATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAA
3342746 ATTCTATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGCAATGTTATATTCAAGTGGCG
456 ATTCTATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGCAATGTTATATTCAAGTGGCG
3342811 AGGTTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGG
521 AGGTTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGG
3342876 TAAGACTTTCATGAGTTAGTGATGTTAACTCATTTCCTTACAGTTTAGTCTCTTTTCACGATAGC
586 TAAGACTTTCATGAGTTAGTGATGTTAACTCATTTCCTTACAGTTTAGTCTCTTTTCACGATAGC
3342941 TATCAAACCTTTGTCAGAAACCACAAAATTTCCATTGAAATTCTTAGTGGAATTAAGTTTAGAAC
651 TATCAAACCTTTGTCAGAAACCACAAAATTTCCATTGAAATTCTTAGTGGAATTAAGTTTAGAAC
3343006 AATATAGAAAGGTTATATTCAAGTGGAAAAGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAA
716 AATATAGAAAGGTTATATTCAAGTGGAAAAGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAA
3343071 GATTTAGTGAGATACTAATATTTTAAGGAAAGAGTTTCATGAGTTAGTGATGCTAGCATGTTTAA
781 GATTTAGTGAGATACTAATATTTTAAGGAAAGAGTTTCATGAGTTAGTGATGCTAGCATGTTTAA
3343136 TTCAAGTGAAAGTGCATAAAAGTGATATTAGATTTTTTTATTGTGT
846 TTCAAGTGAAAGTGCATAAAAGTGATATTAGATTTTTTTATTGTGT
3343182 ATTTT
1 ATTTT
3343187 ATATGTATTT
Statistics
Matches: 894, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
891 894 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (891 bp):
ATTTTTTTGACCGACTGTTCATTAACGGTCAGCTGACAGTTACTGTTTCAACTAGGTTGATGTCT
AAAAATCCGTTACATGAAGGGTTGATTTCAAAAAAATTAGGGCATATATCCAAATTCCCCCAAAT
GTTGAGGGTTTTTTGCAATTATGCCATTATTAAATTAAACAATGGAGAAGATGTTATCAAATTTT
TGACCCTTAGATTTAAAAGGAAAATAAGAAGAAATCTTAGCCCTTGGATCAAAATTATTATGTAT
AGATTTTTATATAATATAATATTATTTTATTAAATGAATAAATAATTAGAAATTTTATTAAAAAA
GACGAAGAATTTTCTTTCATCTTTCATACTCTCACACACCACCACCATTCATGAAAAAGGAAAAT
TTTATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAA
ATTCTATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGCAATGTTATATTCAAGTGGCG
AGGTTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGG
TAAGACTTTCATGAGTTAGTGATGTTAACTCATTTCCTTACAGTTTAGTCTCTTTTCACGATAGC
TATCAAACCTTTGTCAGAAACCACAAAATTTCCATTGAAATTCTTAGTGGAATTAAGTTTAGAAC
AATATAGAAAGGTTATATTCAAGTGGAAAAGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAA
GATTTAGTGAGATACTAATATTTTAAGGAAAGAGTTTCATGAGTTAGTGATGCTAGCATGTTTAA
TTCAAGTGAAAGTGCATAAAAGTGATATTAGATTTTTTTATTGTGT
Found at i:3343075 original size:223 final size:223
Alignment explanation
Indices: 3342684--3343122 Score: 621
Period size: 223 Copynumber: 2.0 Consensus size: 223
3342674 GGAAAATTTT
*
3342684 ATTTCCTTACAATTTGGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
1 ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
* * * ** *
3342749 CTATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGCAATGTTATATTCAAGTGGCGAGG
66 CCATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAAAG
* * * *
3342814 TTGTATGTTCATGTTAAAGGAGAGAGAAAATTAAGATTTAGTGATATACTAAGGGTTTAAGGTAA
131 TTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGAAA
3342879 GACTTTCATGAGTTAGTGATGTTAACTC
196 GACTTTCATGAGTTAGTGATGTTAACTC
* * * * * * *
3342907 ATTTCCTTACAGTTTAGTCTCTTTTCACGATAGCTATCAAACCTTTGTCAGAAACCA-CAAAATT
1 ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAA-T
* * *
3342971 TCCATTGAAATTC-TTAGTGGAATTAAGTTTAGAACAATATAGAAAGGTTATATTCAAGTGGAAA
65 TCCATTGAAATTCTTTA-TGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAA
* * *
3343035 AGTTGTATGTTCATGTTAGAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAATATTTTAAGGA
129 AGTTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGA
*
3343100 AAGAGTTTCATGAGTTAGTGATG
194 AAGACTTTCATGAGTTAGTGATG
3343123 CTAGCATGTT
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
222 8 0.04
223 181 0.96
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (223 bp):
ATTTCCTTACAATTTAGTCCCTCTTCACGATAGCCATCAAACCTTAGCCAAAAACCACCAAAATT
CCATTGAAATTCTTTATGAAATTAAGTTTACAACAACATAGAAAGGTTATATTCAAGTGGAAAAG
TTGTATGTTCATGTTAAAGGAGAGAGAAAATCAAGATTTAGTGAGATACTAAGAGTTTAAGGAAA
GACTTTCATGAGTTAGTGATGTTAACTC
Found at i:3347088 original size:31 final size:31
Alignment explanation
Indices: 3347022--3347093 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
3347012 TAATTTGATC
** *
3347022 AATTTTAGTTCCTGTATTTTTTGAATTGGTC
1 AATTTTAGTTCCTGTATTTTTCAAATTGGTA
* *
3347053 AATTTTAGTTCTTGTATTTTTCAAATT-TTAA
1 AATTTTAGTTCCTGTATTTTTCAAATTGGT-A
3347084 AATTTTAGTT
1 AATTTTAGTT
3347094 TTGAACCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (31 bp):
AATTTTAGTTCCTGTATTTTTCAAATTGGTA
Found at i:3348746 original size:31 final size:31
Alignment explanation
Indices: 3348706--3348765 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3348696 CTAGCGGCTC
3348706 AAATAAAAACTTTCAAATAGTTCAGTGACTT
1 AAATAAAAACTTTCAAATAGTTCAGTGACTT
*
3348737 AAATGAAAACTTTCAAATAGTTCAGTGAC
1 AAATAAAAACTTTCAAATAGTTCAGTGAC
3348766 CATTTCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (31 bp):
AAATAAAAACTTTCAAATAGTTCAGTGACTT
Found at i:3351104 original size:6 final size:6
Alignment explanation
Indices: 3351093--3351121 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3351083 ATATTAAATA
3351093 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
3351122 ATAAAATATA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:3351137 original size:18 final size:17
Alignment explanation
Indices: 3351114--3351154 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3351104 TTTTTATTTT
3351114 TATTTTTAATAAA-ATA
1 TATTTTTAATAAATATA
*
3351130 TACTTTTTATTAAATATA
1 TA-TTTTTAATAAATATA
3351148 TATTTTT
1 TATTTTT
3351155 TAGACTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTAATAAATATA
Found at i:3351155 original size:18 final size:17
Alignment explanation
Indices: 3351116--3351156 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3351106 TTTATTTTTA
3351116 TTTTTAATAAAATATAC
1 TTTTTAATAAAATATAC
* *
3351133 TTTTTATTAAATATATAT
1 TTTTTAATAAA-ATATAC
3351151 TTTTTA
1 TTTTTA
3351157 GACTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATAAAATATAC
Found at i:3353143 original size:3 final size:3
Alignment explanation
Indices: 3353128--3353289 Score: 315
Period size: 3 Copynumber: 54.0 Consensus size: 3
3353118 CTAATATGTT
*
3353128 GAA GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3353176 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3353224 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3353272 GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA
3353290 TGTAGCATTT
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 157 1.00
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:3354110 original size:334 final size:326
Alignment explanation
Indices: 3353495--3354135 Score: 923
Period size: 334 Copynumber: 1.9 Consensus size: 326
3353485 AAATTCCTTA
*
3353495 GTTTCATAATGATAATGTCATTTGATTTCCCTTTATGCATGCCTCTATAAATCCTTATTATATAT
1 GTTTCATAATGATAATGTCATTTGATTTCCCTTTATGCATGCCTCTATAAAGCC-T-TTATATAT
*
3353560 ATATATTGTAATATGGATTTACTTATCATTATACATGTATCTTATCATATATATATAGATATATG
64 ATATATTGTAATATGGATTTACTTATCATTATACATGTATCTTATCATATATATATAGATATATA
* *
3353625 ATACAATCAAAATTTAACAGTCTTACCGATAAGTATTAAGTGTAATGGTAAGATTTATTGCACTT
129 ATACAATCAAAATTTAACAATCTTACCGATAAGTATTAAGTGTAATAGTAAGATTTATTGCACTT
* * * *
3353690 CTAAGGAGAGAACTTTTGTTCGAATTTTGAAGACAGTGTTATTGAGAGAGATAATTATGAATCCA
194 CTAAGGAGAGAACTTTTGTTCAAATTTAGAAGACAATGTTATTGAGAGAGATAATTATAAATCCA
*
3353755 AAAAGGATTAATCTCCATGAACCATAAAACTTAATTGTACAAAAAAATATTTAACTATCCTAAAC
259 AAAAGGATTAATCTCCATGAACCATAAAACTTAATTATACAAAAAAATATTTAACTATCCTAAAC
3353820 TTG
324 TTG
3353823 GTTTCATAATGATAATGTCATTTGATTTCCCTTTATGCATGCCTCTATAAAGCC-TTATA-ATAT
1 GTTTCATAATGATAATGTCATTTGATTTCCCTTTATGCATGCCTCTATAAAGCCTTTATATATAT
* * *
3353886 ATATTGTAATATAGG-TTTATTTATCATTATACATGTGTCTTATCATATATATTTATATATATAT
66 ATATTGTAATAT-GGATTTACTTATCATTATACATGTATCTTATC----ATA--TATATATAGAT
* ** *
3353950 AAATATAAAATACAATCAAAATTTAACAATCTTATCGATAAGTATTGGGTGTAATAGTAAGGTTT
124 --ATAT--AATACAATCAAAATTTAACAATCTTACCGATAAGTATTAAGTGTAATAGTAAGATTT
* * *
3354015 ATTGCACTTCTAATGAGAGAACTTTTGTTCAAATATTAG-AGATAATGTTATTGAGAGAGATAGT
185 ATTGCACTTCTAAGGAGAGAACTTTTGTTCAAAT-TTAGAAGACAATGTTATTGAGAGAGATAAT
* *
3354079 TATAAATCCAGAAAGGATTGAA-CTTCATGAACCATAAAACTTAATTATACAAAAAAA
249 TATAAATCCAAAAAGGATT-AATCTCCATGAACCATAAAACTTAATTATACAAAAAAA
3354136 AAAACATATT
Statistics
Matches: 279, Mismatches: 21, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
324 43 0.15
325 7 0.03
328 56 0.20
330 10 0.04
332 4 0.01
334 154 0.55
335 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (326 bp):
GTTTCATAATGATAATGTCATTTGATTTCCCTTTATGCATGCCTCTATAAAGCCTTTATATATAT
ATATTGTAATATGGATTTACTTATCATTATACATGTATCTTATCATATATATATAGATATATAAT
ACAATCAAAATTTAACAATCTTACCGATAAGTATTAAGTGTAATAGTAAGATTTATTGCACTTCT
AAGGAGAGAACTTTTGTTCAAATTTAGAAGACAATGTTATTGAGAGAGATAATTATAAATCCAAA
AAGGATTAATCTCCATGAACCATAAAACTTAATTATACAAAAAAATATTTAACTATCCTAAACTT
G
Found at i:3354622 original size:2 final size:2
Alignment explanation
Indices: 3354617--3354656 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3354607 GGAGGGGGGG
3354617 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3354657 AATTGAAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3359587 original size:17 final size:17
Alignment explanation
Indices: 3359562--3359605 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3359552 TCACCATGTA
*
3359562 TTCATATTATGATTAAG
1 TTCAAATTATGATTAAG
*
3359579 TTCAAATTATGTTTAAG
1 TTCAAATTATGATTAAG
3359596 TTCAATATTA
1 TTCAA-ATTA
3359606 ATACATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (17 bp):
TTCAAATTATGATTAAG
Found at i:3360025 original size:28 final size:28
Alignment explanation
Indices: 3359983--3360044 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3359973 TTTTGACCTA
**
3359983 AAAAAATTACCATTCAATTCTAACACCC
1 AAAAAATTAAAATTCAATTCTAACACCC
*
3360011 AAAAAATTAAAATTCAATTCTAACCCCC
1 AAAAAATTAAAATTCAATTCTAACACCC
3360039 AAAAAA
1 AAAAAA
3360045 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (28 bp):
AAAAAATTAAAATTCAATTCTAACACCC
Found at i:3360876 original size:24 final size:24
Alignment explanation
Indices: 3360847--3360896 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3360837 ACCACCCGTA
3360847 TCCTCGATTGTAGTTTGGAATTGT
1 TCCTCGATTGTAGTTTGGAATTGT
*
3360871 TCCTCGGTTGTAGTTTGGAATTGT
1 TCCTCGATTGTAGTTTGGAATTGT
3360895 TC
1 TC
3360897 GATTAGTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.46
Consensus pattern (24 bp):
TCCTCGATTGTAGTTTGGAATTGT
Found at i:3373101 original size:27 final size:27
Alignment explanation
Indices: 3373057--3373124 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
3373047 GGAAATCGGA
* *
3373057 TGCCACAGGCAGCACCAAAGGTGCCTG
1 TGCCAGAGGCGGCACCAAAGGTGCCTG
* *
3373084 TGGCAGAGGCGGCACCAAAGGTGCCTT
1 TGCCAGAGGCGGCACCAAAGGTGCCTG
3373111 TGCCAGAGGCGGCA
1 TGCCAGAGGCGGCA
3373125 TAGGACTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (27 bp):
TGCCAGAGGCGGCACCAAAGGTGCCTG
Found at i:3378150 original size:21 final size:21
Alignment explanation
Indices: 3378124--3378164 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3378114 ATCTGCTCAA
* *
3378124 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3378145 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3378165 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3388775 original size:13 final size:13
Alignment explanation
Indices: 3388757--3388782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3388747 TACTAATAAC
3388757 ATTATAAAAGTAG
1 ATTATAAAAGTAG
3388770 ATTATAAAAGTAG
1 ATTATAAAAGTAG
3388783 GTGACCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
ATTATAAAAGTAG
Found at i:3394233 original size:24 final size:24
Alignment explanation
Indices: 3394206--3394255 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3394196 TAAACGAGAC
3394206 TAAAAAGAGGAGGAAGACTTGTGA
1 TAAAAAGAGGAGGAAGACTTGTGA
3394230 TAAAAAGAGGAGGAAGACTTGTGA
1 TAAAAAGAGGAGGAAGACTTGTGA
3394254 TA
1 TA
3394256 CCAATGACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.32, T:0.18
Consensus pattern (24 bp):
TAAAAAGAGGAGGAAGACTTGTGA
Found at i:3400584 original size:29 final size:28
Alignment explanation
Indices: 3400538--3400595 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
3400528 CCAAAAATTT
* * *
3400538 TAAGGGGTTTAATGAAATTTTTTTAAAAA
1 TAAGGGATCTAATCAAA-TTTTTTAAAAA
3400567 TAAGGGATCTAATCAAATTTTTTAAAAA
1 TAAGGGATCTAATCAAATTTTTTAAAAA
3400595 T
1 T
3400596 TTGAAGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (28 bp):
TAAGGGATCTAATCAAATTTTTTAAAAA
Found at i:3401640 original size:8 final size:8
Alignment explanation
Indices: 3401627--3401676 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
3401617 TCCTCCTATT
3401627 TTTTAAAA
1 TTTTAAAA
3401635 TTTTAAAA
1 TTTTAAAA
*
3401643 TTTT-AAT
1 TTTTAAAA
*
3401650 TTTTAAAT
1 TTTTAAAA
3401658 TTTCTAAAA
1 TTT-TAAAA
3401667 -TTTAAAA
1 TTTTAAAA
3401674 TTT
1 TTT
3401677 CGGTCTCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 11 0.30
8 22 0.59
9 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Done.