Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 54 of 56
Found at i:12373373 original size:34 final size:34
Alignment explanation
Indices: 12373334--12373440 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
12373324 TAAGTTGAAA
* *
12373334 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
12373368 TTTAATTTTAAATTTCGAACAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
12373402 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
12373436 TTTAA
1 TTTAA
12373441 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:12374012 original size:21 final size:21
Alignment explanation
Indices: 12373961--12374054 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
12373951 TATGGTATAA
*
12373961 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
12373982 AA-CATGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
12374003 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
12374024 AACCCTGCGGAGAT-GGCATGT
1 AACCCTGCGG-GCTAGGAATGT
12374045 AACCCTGCGG
1 AACCCTGCGG
12374055 AGATGGCATA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.03
21 58 0.91
22 4 0.06
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:12374055 original size:21 final size:21
Alignment explanation
Indices: 12373999--12374063 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
12373989 CGGGCTAGGA
* *
12373999 ATGTAACCCTGCGG-GCTCGGA
1 ATGTAACCCTGCGGAGAT-GGC
12374020 ATGTAACCCTGCGGAGATGGC
1 ATGTAACCCTGCGGAGATGGC
12374041 ATGTAACCCTGCGGAGATGGC
1 ATGTAACCCTGCGGAGATGGC
12374062 AT
1 AT
12374064 ATAAACTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.20
Consensus pattern (21 bp):
ATGTAACCCTGCGGAGATGGC
Found at i:12374098 original size:21 final size:21
Alignment explanation
Indices: 12374060--12374099 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12374050 TGCGGAGATG
*
12374060 GCATATAAACTGGTGGGCTTC
1 GCATATAAACTGGAGGGCTTC
* *
12374081 GCATATGAAGTGGAGGGCT
1 GCATATAAACTGGAGGGCT
12374100 GGGCATGTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (21 bp):
GCATATAAACTGGAGGGCTTC
Found at i:12375872 original size:34 final size:31
Alignment explanation
Indices: 12375829--12375917 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
12375819 TTAATAATTC
*
12375829 TAAATAAATAATAATTATTTAAATATTATTTTAA
1 TAAAAAAATAATAATTATTTAAATA-TA--TTAA
* **
12375863 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATTTAAATATATTAA
* *
12375894 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATTTAAA
12375918 AAAATACTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.36
33 2 0.04
34 21 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
TAAAAAAATAATAATTATTTAAATATATTAA
Found at i:12375874 original size:31 final size:33
Alignment explanation
Indices: 12375832--12375906 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
12375822 ATAATTCTAA
* * *
12375832 ATAAATAATAATTATTTAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATTTAAATAAATATATTAAT
*
12375864 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATTTAAATAAATATATTAAT
*
12375895 ATAAAATATAAT
1 ATAAAAAATAAT
12375907 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 8 0.23
31 18 0.51
32 9 0.26
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
ATAAAAAATAATTATTTAAATAAATATATTAAT
Found at i:12376214 original size:51 final size:51
Alignment explanation
Indices: 12376112--12376215 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 51
12376102 CATTTAATGG
* * * * * **
12376112 AAGGCGCGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGTTGGCGA
1 AAGGAGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGTCAACTCAGCGA
*
12376163 AAGGAGCGTTCCCGGGGATGCGCCTTCCACACGTGACA-TCTAACTCAGCGA
1 AAGGAGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGTC-AACTCAGCGA
12376214 AA
1 AA
12376216 ACACGGGTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.17
Consensus pattern (51 bp):
AAGGAGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGTCAACTCAGCGA
Found at i:12380436 original size:141 final size:140
Alignment explanation
Indices: 12380179--12380436 Score: 329
Period size: 141 Copynumber: 1.8 Consensus size: 140
12380169 TAAAATTTCT
* * **
12380179 TTAATTCAGGAAATAATTTGATTTGGCTCTCACATTAAAAGGCCTGAGGATTTTCATTGACTATT
1 TTAATTCAGGAAATAATTCGATTTGGCTCTCACATTAAAAGGCCCGAGGATTTTCACGGACTATT
* * * * *
12380244 CACTTTAATAATTGGCTAAAATCAATTAGGTTATTAATATGAGCTTCCATTTTAAGTAGAATTAC
66 CACATCAATAATTGGCTAAAATCAATTAGG-TATTAATATGAACCTACATTTTAAGTAGAATTAC
12380309 ACTTTATTCCC
130 ACTTTATTCCC
* * * * * *
12380320 TTAATTTAGGGAATAATTCGATTTGGCTCTCACATTAAAATGCCCGAGGGTTTTCGCGGATTATT
1 TTAATTCAGGAAATAATTCGATTTGGCTCTCACATTAAAAGGCCCGAGGATTTTCACGGACTATT
* *
12380385 CGCATCAATAATTGGTTAAAATCAATTAGG-ATTAATATTAGAACCTACATTT
66 CACATCAATAATTGGCTAAAATCAATTAGGTATTAATA-T-GAACCTACATTT
12380437 CTAGGTTTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
139 7 0.07
140 1 0.01
141 90 0.92
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (140 bp):
TTAATTCAGGAAATAATTCGATTTGGCTCTCACATTAAAAGGCCCGAGGATTTTCACGGACTATT
CACATCAATAATTGGCTAAAATCAATTAGGTATTAATATGAACCTACATTTTAAGTAGAATTACA
CTTTATTCCC
Found at i:12382266 original size:26 final size:26
Alignment explanation
Indices: 12382237--12382308 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
12382227 TTCGTACTGT
* *
12382237 ATTCACATTCACATTTGCATTTTTAC
1 ATTCACATGCACATTTACATTTTTAC
**
12382263 ATTCGTATGCACATTTACATTTTTAC
1 ATTCACATGCACATTTACATTTTTAC
**
12382289 ATTCGTATGCACATTTACAT
1 ATTCACATGCACATTTACAT
12382309 CTATATTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (26 bp):
ATTCACATGCACATTTACATTTTTAC
Found at i:12382283 original size:32 final size:29
Alignment explanation
Indices: 12382254--12382309 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 29
12382244 TTCACATTTG
12382254 CATTTTTACATTCGTATGCACATTT--A-
1 CATTTTTACATTCGTATGCACATTTACAT
12382280 CATTTTTACATTCGTATGCACATTTACAT
1 CATTTTTACATTCGTATGCACATTTACAT
12382309 C
1 C
12382310 TATATTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 25 0.93
28 1 0.04
29 1 0.04
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (29 bp):
CATTTTTACATTCGTATGCACATTTACAT
Found at i:12388804 original size:3 final size:3
Alignment explanation
Indices: 12388783--12388861 Score: 140
Period size: 3 Copynumber: 26.3 Consensus size: 3
12388773 ATTTCTCATT
* *
12388783 TAA TAA GAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12388831 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12388862 GTTGAGTTAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12392318 original size:22 final size:23
Alignment explanation
Indices: 12392268--12392329 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
12392258 CGATTCCCTT
* *
12392268 AGGGGAAATTGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
12392291 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
12392313 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
12392330 TATGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:12396177 original size:22 final size:21
Alignment explanation
Indices: 12396135--12396174 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12396125 GAGTTTATTT
*
12396135 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
12396156 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
12396175 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:12400403 original size:22 final size:22
Alignment explanation
Indices: 12400378--12400441 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
12400368 TGTTTGAATC
*
12400378 TTCATAGGGGTATTGATACCCA
1 TTCATAGGGGTATCGATACCCA
* *
12400400 TTCATAGAGGTATCGGTACCCA
1 TTCATAGGGGTATCGATACCCA
12400422 TTCATAGGGGTATCGATACC
1 TTCATAGGGGTATCGATACC
12400442 TCTTAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCA
Found at i:12402255 original size:140 final size:140
Alignment explanation
Indices: 12401999--12402255 Score: 374
Period size: 140 Copynumber: 1.8 Consensus size: 140
12401989 CAAACGTTCT
* *
12401999 TTAATTTAAGGAATAATTCGATTTGGCTCTCGCACTAAAATGCCCGAGGGTTTTCATCGATTATT
1 TTAATTTAAGGAATAATTCAATTTAGCTCTCGCACTAAAATGCCCGAGGGTTTTCATCGATTATT
* * * * * * *
12402064 TGCTTCAATAATTTGTTACAATAAATTAGGTTATTAATTAGAGCTTTCATTTTAAGTAGAATTAC
66 CGCATCAATAATTGGTTAAAATAAATTAGGTTAATAATTAGAGCCTACATTTTAAGTAGAATTAC
12402129 ACTTTAGCCC
131 ACTTTAGCCC
* *
12402139 TTAATTT-AGGAAATAATTCAATTTAGCTCTCGCATTAAAATGCCCGAGGGTTTTCATCGGTTAT
1 TTAATTTAAGG-AATAATTCAATTTAGCTCTCGCACTAAAATGCCCGAGGGTTTTCATCGATTAT
*
12402203 TCGCATCAATAATTGGTTAAAATCAATTAGGATTAAT-ATTAGAGCCTACATTT
65 TCGCATCAATAATTGGTTAAAATAAATTAGG-TTAATAATTAGAGCCTACATTT
12402256 CTAGGTTCTT
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
139 3 0.03
140 96 0.93
141 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (140 bp):
TTAATTTAAGGAATAATTCAATTTAGCTCTCGCACTAAAATGCCCGAGGGTTTTCATCGATTATT
CGCATCAATAATTGGTTAAAATAAATTAGGTTAATAATTAGAGCCTACATTTTAAGTAGAATTAC
ACTTTAGCCC
Found at i:12403858 original size:31 final size:31
Alignment explanation
Indices: 12403822--12403880 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
12403812 AACTTAAAAG
* *
12403822 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
12403853 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
12403881 CCATACAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:12403956 original size:22 final size:22
Alignment explanation
Indices: 12403907--12403955 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12403897 ATAAATTATT
**
12403907 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
12403929 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
12403952 TAAA
1 TAAA
12403956 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12403959 original size:54 final size:54
Alignment explanation
Indices: 12403895--12404237 Score: 364
Period size: 54 Copynumber: 6.4 Consensus size: 54
12403885 ACAACCACAA
*
12403895 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
12403949 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * * ** *
12404006 TTTTAAAATAAAT-CAATACATACTAATAAAT-TATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
12404061 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
12404109 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
12404163 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATCAATCAATCAATAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
12404217 TAATAAATTATTTTAAATAAA
1 TAATAAATTATTTAAAATAAA
12404238 GTATTTTAAA
Statistics
Matches: 241, Mismatches: 31, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
48 29 0.12
49 4 0.02
50 7 0.03
51 1 0.00
52 1 0.00
53 1 0.00
54 153 0.63
55 6 0.02
56 6 0.02
57 13 0.05
58 20 0.08
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:12404000 original size:80 final size:79
Alignment explanation
Indices: 12403910--12404139 Score: 415
Period size: 80 Copynumber: 2.9 Consensus size: 79
12403900 AATTATTTAA
12403910 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATC-ATACTAATAAATTATTTAAAATAAATCAAT
12403975 CCATACAACTACAAT
65 CCATACAACTACAAT
12403990 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAAT
*
12404055 CTATACAACTACAAT
65 CCATACAACTACAAT
12404070 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAAT
*
12404135 TCATA
65 CCATA
12404140 TTTTAAAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
80 144 0.99
81 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (79 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATC
CATACAACTACAAT
Found at i:12404036 original size:22 final size:22
Alignment explanation
Indices: 12403964--12404036 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
12403954 AATTATTTAA
* *
12403964 AATAAATCAATCCATACA-ACT
1 AATAAATAAATCAATACATACT
*
12403985 ACA-ATAATAAATCAATCCATA-T
1 A-ATA-AATAAATCAATACATACT
**
12404007 TTTAAAATAAATCAATACATACT
1 AAT-AAATAAATCAATACATACT
12404030 AATAAAT
1 AATAAAT
12404037 TATTTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.05
22 32 0.84
23 4 0.11
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAATAAATCAATACATACT
Found at i:12404116 original size:22 final size:22
Alignment explanation
Indices: 12404041--12404115 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
12404031 ATAAATTATT
* *
12404041 TAAAATAAATCAATCTATACAA
1 TAAAATAAATCAATCCATATAA
**
12404063 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
12404089 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12404112 TAAA
1 TAAA
12404116 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12404126 original size:32 final size:32
Alignment explanation
Indices: 12404087--12404193 Score: 144
Period size: 32 Copynumber: 3.7 Consensus size: 32
12404077 CAATCCATAT
12404087 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12404119 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12404141 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12404173 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
12404194 TTTTAAAATC
Statistics
Matches: 65, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
22 16 0.25
23 1 0.02
24 1 0.02
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
30 1 0.02
31 1 0.02
32 37 0.57
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:12404145 original size:22 final size:22
Alignment explanation
Indices: 12404119--12404161 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12404109 TAATAAATTA
*
12404119 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
12404141 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
12404162 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:12404170 original size:22 final size:22
Alignment explanation
Indices: 12404121--12404169 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12404111 ATAAATTATT
* **
12404121 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
12404143 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12404166 TAAA
1 TAAA
12404170 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12404199 original size:22 final size:22
Alignment explanation
Indices: 12404173--12404273 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
12404163 TAATAAATTA
*
12404173 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCAATAT
*
12404195 TTTAAAATCAATCAATCAATAAT
1 TTTAAAATAAATCAATCAAT-AT
** * ** * *
12404218 AATAAATTATTTTAAATAAAGTAT
1 TTTAAAATA-AATCAATCAA-TAT
*
12404242 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCAATAT
*
12404264 TTTATAATAA
1 TTTAAAATAA
12404274 TTTATTTTAA
Statistics
Matches: 57, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
22 30 0.53
23 12 0.21
24 14 0.25
25 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCAATAT
Found at i:12404251 original size:15 final size:15
Alignment explanation
Indices: 12404218--12404395 Score: 223
Period size: 15 Copynumber: 11.5 Consensus size: 15
12404208 AATCAATAAT
12404218 AATAAATTATTTT-A
1 AATAAATTATTTTAA
*
12404232 AATAAAGTATTTTAA
1 AATAAATTATTTTAA
*
12404247 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
12404269 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
12404284 CATAAATTATTTTAT
1 AATAAATTATTTTAA
12404299 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
12404314 AATAAATTATTTTAT
1 AATAAATTATTTTAA
12404329 AATAAATTATTTTAA
1 AATAAATTATTTTAA
12404344 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
12404359 AATAAATTATTTTAT
1 AATAAATTATTTTAA
12404374 AATAAATTATTTTAA
1 AATAAATTATTTTAA
12404389 AATAAAT
1 AATAAAT
12404396 AACCTTATTA
Statistics
Matches: 142, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
14 12 0.08
15 114 0.80
17 1 0.01
18 2 0.01
19 2 0.01
20 1 0.01
22 10 0.07
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:12404252 original size:69 final size:67
Alignment explanation
Indices: 12404163--12404395 Score: 220
Period size: 75 Copynumber: 3.3 Consensus size: 67
12404153 CAATCCATAC
12404163 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATCAATCAATCAATAATAATAAATTA
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-AATAA-AATAAATTA
12404227 TTTTA
63 TTTTA
* * ** ** *
12404232 -AATAAAGTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAACATAAATTATTT
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATAATAAAATAAATTATTT
12404296 TA
66 TA
* ** * **
12404298 TAATAAATTATTTTAAAATAAATTATTTTATAATAAATTATTTTAAAATAAAT-TATTTTAAAAT
1 TAATAAATTATTTTAAAAT-AA--A---T-CAATCCA-TATTTTAAAAT-AATCAATAATAAAAT
12404362 AAATTATTTTA
57 AAATTATTTTA
12404373 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
12404396 AACCTTATTA
Statistics
Matches: 140, Mismatches: 13, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
66 13 0.09
67 20 0.14
68 15 0.11
69 30 0.21
70 1 0.01
72 1 0.01
73 1 0.01
74 6 0.04
75 50 0.36
76 3 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (67 bp):
TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATAATAAAATAAATTATTT
TA
Found at i:12406346 original size:19 final size:20
Alignment explanation
Indices: 12406300--12406347 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
12406290 CTAAAATGAA
* *
12406300 GGTATCGATACTGAGCCCTT
1 GGTATCGATACCGAGCCATT
12406320 GAGTATCGATACCGA-CCATT
1 G-GTATCGATACCGAGCCATT
12406340 GGTATCGA
1 GGTATCGA
12406348 CACCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 6 0.24
21 12 0.48
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCGAGCCATT
Found at i:12406631 original size:20 final size:22
Alignment explanation
Indices: 12406595--12406647 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12406585 ACTATGCTAG
*
12406595 TATCGATA-TTCATTGAACA-A
1 TATCGATACTACATTGAACAGA
*
12406615 TATCGATACTACA-TGAACAGG
1 TATCGATACTACATTGAACAGA
12406636 TATCGATACTAC
1 TATCGATACTAC
12406648 CATCCCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (22 bp):
TATCGATACTACATTGAACAGA
Found at i:12406641 original size:21 final size:21
Alignment explanation
Indices: 12406593--12406647 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
12406583 TTACTATGCT
*
12406593 AGTATCGATA-TTCATTGAAC
1 AGTATCGATACTACATTGAAC
*
12406613 AATATCGATACTACA-TGAAC
1 AGTATCGATACTACATTGAAC
12406633 AGGTATCGATACTAC
1 A-GTATCGATACTAC
12406648 CATCCCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (21 bp):
AGTATCGATACTACATTGAAC
Found at i:12410114 original size:60 final size:60
Alignment explanation
Indices: 12410028--12410140 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
12410018 GATCCCCAAT
* * *
12410028 TATAGGATATTATTTTATTGAATCCCTCGACTATCAAAAGTTATAAAATGATCCCTTGAC
1 TATAAGATATTATTTTATTGAATCCCTCGACTATCAAAAATTACAAAATGATCCCTTGAC
* * * *
12410088 TATAAGATATTATTTTGTTGAGTCCCTTGACTATTAAAAATTACAAAATGATC
1 TATAAGATATTATTTTATTGAATCCCTCGACTATCAAAAATTACAAAATGATC
12410141 ACCGGGTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (60 bp):
TATAAGATATTATTTTATTGAATCCCTCGACTATCAAAAATTACAAAATGATCCCTTGAC
Found at i:12410680 original size:23 final size:23
Alignment explanation
Indices: 12410628--12410680 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
12410618 TATTAAATAA
*
12410628 TAAATTAAAATAAATTTATAGAC
1 TAAATTAAAATAAATTTATAAAC
* * *
12410651 TATATTATAAT-AATTTAATAAAT
1 TAAATTAAAATAAATTT-ATAAAC
12410674 TAAATTA
1 TAAATTA
12410681 CATTTTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTAAAATAAATTTATAAAC
Found at i:12410696 original size:30 final size:32
Alignment explanation
Indices: 12410655--12410722 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
12410645 ATAGACTATA
* *
12410655 TTATAATAATTTAATAAA-TTAAATTA-CATT
1 TTATAACAATTTAATAAATTTAAATGATCATT
* *
12410685 TTATAACAATTTGATAAATTTTAATGATCATT
1 TTATAACAATTTAATAAATTTAAATGATCATT
12410717 TTATAA
1 TTATAA
12410723 TTATTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 16 0.50
31 6 0.19
32 10 0.31
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (32 bp):
TTATAACAATTTAATAAATTTAAATGATCATT
Found at i:12412277 original size:38 final size:38
Alignment explanation
Indices: 12412226--12412300 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
12412216 ACCCTAAACC
*
12412226 CGACCCGAATATCACACTTAAAAATACCCGACCCGACT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
*
12412264 CGACCCGAATATCACACTTAAAAAAACCTGACCCGAC
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGAC
12412301 CCGAACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.15
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
Found at i:12415940 original size:21 final size:22
Alignment explanation
Indices: 12415895--12415940 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12415885 AATTCTTATG
* *
12415895 GATAATTTGTATTAGATTATTA
1 GATAATTTGGATTAAATTATTA
*
12415917 GATAATTTGGA-TAAATTTTTA
1 GATAATTTGGATTAAATTATTA
12415938 GAT
1 GAT
12415941 CAAATTAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (22 bp):
GATAATTTGGATTAAATTATTA
Found at i:12418284 original size:71 final size:71
Alignment explanation
Indices: 12418156--12418290 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 71
12418146 ATCCTTTTGA
* * * **
12418156 AAAGGGATCGATCTTTTACACAATAGAAAGTATGGGATTGATCTTTTTAGTTTAGGGATCGATCT
1 AAAGGGATCGATCCTTTACACAATAGAAAGTATGGGATCGATCATTTTAGTCGAGGGATCGATCT
12418221 TATTGG
66 TATTGG
* * * *
12418227 AAAGGGATCGATCCTTTGCACAATAGAAAGTTTGGGATCGATCATTTTGGTCGAGGGATTGATC
1 AAAGGGATCGATCCTTTACACAATAGAAAGTATGGGATCGATCATTTTAGTCGAGGGATCGATC
12418291 CTCTTTCTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (71 bp):
AAAGGGATCGATCCTTTACACAATAGAAAGTATGGGATCGATCATTTTAGTCGAGGGATCGATCT
TATTGG
Found at i:12419755 original size:26 final size:26
Alignment explanation
Indices: 12419726--12419776 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
12419716 CCAGAAGACG
* *
12419726 CGCTGAGTAGATCTTCTAGAAACTGT
1 CGCTGACTAGACCTTCTAGAAACTGT
*
12419752 CGCTGACTGGACCTTCTAGAAACTG
1 CGCTGACTAGACCTTCTAGAAACTG
12419777 CCACATCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAGAAACTGT
Found at i:12429329 original size:6 final size:6
Alignment explanation
Indices: 12429314--12429346 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12429304 TGCTTAATCG
*
12429314 AAATAA AAATAG AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
12429347 ATGTAACGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:12431101 original size:19 final size:17
Alignment explanation
Indices: 12431069--12431103 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
12431059 CATCGATGCA
12431069 TACACAAGGTGCATCGG
1 TACACAAGGTGCATCGG
12431086 TACACTAAGAGTGCATCG
1 TACAC-AAG-GTGCATCG
12431104 ATGCATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (17 bp):
TACACAAGGTGCATCGG
Found at i:12431143 original size:45 final size:46
Alignment explanation
Indices: 12431094--12431201 Score: 159
Period size: 45 Copynumber: 2.4 Consensus size: 46
12431084 GGTACACTAA
*
12431094 GAGTGCATCGATGCATGAACTGCATTCGATG-TTTCA-A-AATAGCAT
1 GAGTGCATCGATGCATGAAATGCATTCGATGCTTTCATAGAA-A-CAT
*
12431139 GAGTGCATCGATGCATGAAATGCATTCGATGCTTTCATAGAAACCT
1 GAGTGCATCGATGCATGAAATGCATTCGATGCTTTCATAGAAACAT
12431185 GAGTGCATCGATGCATG
1 GAGTGCATCGATGCATG
12431202 GTATGTGGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
45 30 0.52
46 24 0.41
47 2 0.03
48 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (46 bp):
GAGTGCATCGATGCATGAAATGCATTCGATGCTTTCATAGAAACAT
Found at i:12431283 original size:20 final size:20
Alignment explanation
Indices: 12431247--12431284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12431237 CAATTTATTC
*
12431247 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
12431267 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
12431285 TCATTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:12431597 original size:13 final size:13
Alignment explanation
Indices: 12431579--12431636 Score: 66
Period size: 12 Copynumber: 4.6 Consensus size: 13
12431569 AATTTTAAGA
* *
12431579 TTTGAAAATTATT
1 TTTGAAAATCAAT
12431592 TTTG-AAATCAAT
1 TTTGAAAATCAAT
* *
12431604 TTTGAAAATTATT
1 TTTGAAAATCAAT
12431617 TTTG-AAATCAAT
1 TTTGAAAATCAAT
12431629 TTTGAAAA
1 TTTGAAAA
12431637 ATTACTCCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
12 20 0.54
13 17 0.46
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:12431611 original size:25 final size:25
Alignment explanation
Indices: 12431579--12431636 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
12431569 AATTTTAAGA
12431579 TTTGAAAATTATTTTTGAAATCAAT
1 TTTGAAAATTATTTTTGAAATCAAT
12431604 TTTGAAAATTATTTTTGAAATCAAT
1 TTTGAAAATTATTTTTGAAATCAAT
12431629 TTTGAAAA
1 TTTGAAAA
12431637 ATTACTCCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (25 bp):
TTTGAAAATTATTTTTGAAATCAAT
Found at i:12439683 original size:64 final size:62
Alignment explanation
Indices: 12439615--12439773 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
12439605 TGCACTAAGA
** *
12439615 GTGCATCGATATATAAATTGCATTCGATGTTTCA-A-AATAGCCTGAGTGCATCGATGCAT-GTC
1 GTGCATCGATGCATAAA-TGCATTCGATGTTTCATAGAA-A--CTGAGTGCATCGATGAATGGT-
*
12439677 TT
61 AT
12439679 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAGAAACTGAGTGCATCGATGAATGGTAT
1 GTGCATCGATGCAT-AAATGCATTCGATG-TTTCATAGAAACTGAGTGCATCGATGAATGGTAT
*
12439743 GTGTATCGATGCATACAATGCATTCGATGTT
1 GTGCATCGATGCATA-AATGCATTCGATGTT
12439774 CAATTTATTC
Statistics
Matches: 84, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
63 3 0.04
64 67 0.80
65 10 0.12
66 2 0.02
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCATAGAAACTGAGTGCATCGATGAATGGTAT
Found at i:12439809 original size:20 final size:20
Alignment explanation
Indices: 12439784--12439821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12439774 CAATTTATTC
12439784 ATTGGTACATCGATGCATGG
1 ATTGGTACATCGATGCATGG
* *
12439804 ATTGGTGCATCGGTGCAT
1 ATTGGTACATCGATGCAT
12439822 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:12454886 original size:43 final size:43
Alignment explanation
Indices: 12454821--12454922 Score: 141
Period size: 43 Copynumber: 2.4 Consensus size: 43
12454811 CTGTTCATAA
* * *
12454821 GTGATGAAGAGTTTTGATCGTCTAAGGGTGACACAACTTCTAC
1 GTGATGAAGAGTTCTGAACGTCTAAGGATGACACAACTTCTAC
**
12454864 GTGATGAAGAGTTCTGAACGTCTAAGGATGACACGGCTTCTAC
1 GTGATGAAGAGTTCTGAACGTCTAAGGATGACACAACTTCTAC
* *
12454907 ATGATGAAGAGATCTG
1 GTGATGAAGAGTTCTG
12454923 GTCGGTGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (43 bp):
GTGATGAAGAGTTCTGAACGTCTAAGGATGACACAACTTCTAC
Found at i:12455171 original size:131 final size:133
Alignment explanation
Indices: 12454884--12455242 Score: 413
Period size: 131 Copynumber: 2.7 Consensus size: 133
12454874 GTTCTGAACG
* * * * *** *
12454884 TCTAAGGATGACACGGCTTCTACATGATGAA-GAGATCTGGTCGGTGGATGACATTTTTCCTATG
1 TCTAAGGGTGACACGGCTCCTATATGAT-AAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACG
* * *
12454948 TGATGAGGATGGCTTAG-CCATCTTTAGGGAAGGTGATAACACGATCCCTACGCAATGAGGATGG
65 TGATGAGGATGGC-TAGACCATCTTTAGGG-A-GCGATAACACGATCCCTACGCAATGAGGACGA
12455012 CTGGTTA
127 CTGGTTA
12455019 TCTAAGGGTGACACGGCTCCTATATGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
1 TCTAAGGGTGACACGGCTCCTATATGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
* * * * * ** *
12455084 GATGAGGATGAC-AGACCATCTTTAGGGA-CGATAACATGGTTCCTATGTGATGAGGACGATTGG
66 GATGAGGATGGCTAGACCATCTTTAGGGAGCGATAACACGATCCCTACGCAATGAGGACGACTGG
12455147 TTA
131 TTA
* * * * * **
12455150 TCTAAGGGTGACACGACTCCTATGTGATGAGGAGGTCTGGTCAGTGGATGACACGGTTCTTACAC
1 TCTAAGGGTGACACGGCTCCTATATGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
12455215 GATGAGGATGGCTA-ACCATCTTTAGGGA
66 GATGAGGATGGCTAGACCATCTTTAGGGA
12455243 TTTGTTTCAA
Statistics
Matches: 194, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
131 111 0.57
132 1 0.01
133 3 0.02
134 14 0.07
135 65 0.34
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (133 bp):
TCTAAGGGTGACACGGCTCCTATATGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
GATGAGGATGGCTAGACCATCTTTAGGGAGCGATAACACGATCCCTACGCAATGAGGACGACTGG
TTA
Found at i:12455378 original size:26 final size:26
Alignment explanation
Indices: 12455349--12455398 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12455339 GACAAAATTC
* * *
12455349 TTTTCAAGGGAAACGATCTCAAAGAT
1 TTTTCAAGAGAAACAATATCAAAGAT
12455375 TTTTCAAGAGAAACAATATCAAAG
1 TTTTCAAGAGAAACAATATCAAAG
12455399 TTTGTCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (26 bp):
TTTTCAAGAGAAACAATATCAAAGAT
Found at i:12456823 original size:1 final size:1
Alignment explanation
Indices: 12456807--12456854 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
12456797 TCTTGTCCTA
* * * * *
12456807 TTTTTTCTTTTCTTTTTCTTTTTCTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12456855 CTTTGCTTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:12456823 original size:6 final size:6
Alignment explanation
Indices: 12456808--12456851 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
12456798 CTTGTCCTAT
12456808 TTTTTC -TTTTC TTTTTC TTTTTC TTTTT- TTTTT- TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
12456852 TTTCTTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTTTC
Found at i:12456838 original size:16 final size:16
Alignment explanation
Indices: 12456808--12456858 Score: 77
Period size: 15 Copynumber: 3.2 Consensus size: 16
12456798 CTTGTCCTAT
12456808 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTT-TTTTTC
*
12456825 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTC
12456841 TTTTTC-TTTTTTTTC
1 TTTTTCTTTTTTTTTC
12456856 TTT
1 TTT
12456859 GCTTTGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.34
16 11 0.34
17 10 0.31
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:12460341 original size:16 final size:15
Alignment explanation
Indices: 12460314--12460345 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
12460304 TTAAATAAAG
12460314 AAATACAATGGAAAT
1 AAATACAATGGAAAT
12460329 AAATACGAATGGAAAT
1 AAATAC-AATGGAAAT
12460345 A
1 A
12460346 TGCAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (15 bp):
AAATACAATGGAAAT
Found at i:12465930 original size:30 final size:30
Alignment explanation
Indices: 12465874--12465938 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
12465864 GGGCTATGTT
* *
12465874 TTGAAAATATGAAAAGCACAAGTTATATGA
1 TTGAAAATAGGAAAAGCACAAATTATATGA
*
12465904 GTTGAAAAT-GGAAAAGTACAAATTATATGA
1 -TTGAAAATAGGAAAAGCACAAATTATATGA
12465934 TTGAA
1 TTGAA
12465939 TGGTTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 5 0.16
30 18 0.58
31 8 0.26
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (30 bp):
TTGAAAATAGGAAAAGCACAAATTATATGA
Found at i:12472744 original size:10 final size:11
Alignment explanation
Indices: 12472723--12472747 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12472713 GTTTTTGAAA
12472723 TTTTGGCTTTT
1 TTTTGGCTTTT
12472734 TTTTGGCTTTT
1 TTTTGGCTTTT
12472745 TTT
1 TTT
12472748 ATTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:12478807 original size:29 final size:29
Alignment explanation
Indices: 12478772--12478856 Score: 109
Period size: 31 Copynumber: 2.9 Consensus size: 29
12478762 ACTTTTGAAC
* *
12478772 TAGTGACTAAAATGTAAATTTTGAAAGTT
1 TAGTGACTAAAGTGTAAATTTTAAAAGTT
* *
12478801 TAGTGACCAAAGTATAAACTTTGTAAAAGTT
1 TAGTGACTAAAGTGTAAA-TTT-TAAAAGTT
12478832 TAGTGACTAAAGTG-AAATTTTAAAA
1 TAGTGACTAAAGTGTAAATTTTAAAA
12478857 AATAATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
28 5 0.10
29 18 0.38
30 6 0.12
31 19 0.40
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (29 bp):
TAGTGACTAAAGTGTAAATTTTAAAAGTT
Found at i:12479910 original size:24 final size:24
Alignment explanation
Indices: 12479882--12479928 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12479872 GATATAATAT
*
12479882 GGTACATATT-TGTACATTTTATAA
1 GGTACAT-TTGTGTACATTCTATAA
12479906 GGTACATTTGTGTACATTCTATA
1 GGTACATTTGTGTACATTCTATA
12479929 TGGCACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (24 bp):
GGTACATTTGTGTACATTCTATAA
Found at i:12498335 original size:9 final size:9
Alignment explanation
Indices: 12498330--12498359 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
12498320 ACGTAAAAAT
12498330 AATAAACAA
1 AATAAACAA
12498339 AATAAACAA
1 AATAAACAA
12498348 AATAAACAA
1 AATAAACAA
12498357 AAT
1 AAT
12498360 GAATAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (9 bp):
AATAAACAA
Found at i:12498667 original size:37 final size:36
Alignment explanation
Indices: 12498579--12498683 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 36
12498569 TAAAAAAGTA
*
12498579 AAAAAAGTAAAAATATAATA-TATA-AAAATA-A-AT
1 AAAAACGTAAAAATATAATATTA-AGAAAATATATAT
*
12498612 AAAAAC--AAAAATAGAATATTAAGAAAATATATAT
1 AAAAACGTAAAAATATAATATTAAGAAAATATATAT
*
12498646 AAAAACGTATAAAATATAATATTAAGAAAAAATATAT
1 AAAAACGTA-AAAATATAATATTAAGAAAATATATAT
12498683 A
1 A
12498684 CATAGTAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
31 12 0.20
32 8 0.13
33 6 0.10
34 8 0.13
36 1 0.02
37 26 0.43
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (36 bp):
AAAAACGTAAAAATATAATATTAAGAAAATATATAT
Found at i:12498717 original size:2 final size:2
Alignment explanation
Indices: 12498710--12498765 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
12498700 AAATTAATAC
12498710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
12498752 A- AG AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
12498766 ATAACAATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 46 0.92
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12498778 original size:27 final size:29
Alignment explanation
Indices: 12498726--12498780 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
12498716 ATATATATAT
* *
12498726 ATATATATATATATATATAATGATATAAG
1 ATATATATATATATATACAATAATATAAG
12498755 ATATATATATA-ATA-ACAATAATATAA
1 ATATATATATATATATACAATAATATAA
12498781 TATAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (29 bp):
ATATATATATATATATACAATAATATAAG
Found at i:12498788 original size:14 final size:14
Alignment explanation
Indices: 12498716--12498789 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 14
12498706 ATACATATAT
*
12498716 ATATATATATATATA
1 ATATA-ATATAAATA
*
12498731 TATATATATATATAATG
1 -ATATA-ATATA-AATA
* *
12498748 ATATAAGATATAT-
1 ATATAATATAAATA
12498761 ATATAATA-ACAATA
1 ATATAATATA-AATA
12498775 ATATAATATAAATA
1 ATATAATATAAATA
12498789 A
1 A
12498790 AAAAAGAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 9 0.19
14 15 0.31
15 5 0.10
16 16 0.33
17 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:12498831 original size:14 final size:14
Alignment explanation
Indices: 12498809--12498839 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12498799 AATATAGTAA
12498809 ATAAATAAAAAAAT
1 ATAAATAAAAAAAT
*
12498823 ATAATTAAAAAAAT
1 ATAAATAAAAAAAT
12498837 ATA
1 ATA
12498840 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAAAAT
Found at i:12501306 original size:65 final size:67
Alignment explanation
Indices: 12501131--12501314 Score: 196
Period size: 65 Copynumber: 2.7 Consensus size: 67
12501121 GGAAACGATC
* * * * *
12501131 TCAAAGATATCTGTTGTTTCATGA-AAATGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TTTGATTTAAGGGAAA
12501195 TAAAT
63 TAAAT
** * *
12501200 TTGAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGATTT-AGAGGAAATA
1 TCAAAGATTTTGTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGATTTAAG-GGAAATA
12501264 AAT
65 AAT
* * *
12501267 TCAAAGA-TTT-TGTTTCAAGGGAAATTGTCTCAAGAGAGACGAAATTTG
1 TCAAAGATTTTGTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTG
12501315 TTTCAAGAGA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
65 33 0.34
66 5 0.05
67 31 0.32
68 22 0.23
69 6 0.06
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGATTTAAGGGAAATAA
AT
Found at i:12501332 original size:36 final size:36
Alignment explanation
Indices: 12501275--12501495 Score: 192
Period size: 36 Copynumber: 6.3 Consensus size: 36
12501265 ATTCAAAGAT
* *
12501275 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
12501311 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * * * *
12501347 CTTAGTTCCAAAAGAAACTATCTCAAGGGATATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * *
12501384 TTTGTTTCAA-ATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAAA
* *
12501413 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
12501449 TTTGTTTCAA-AGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGA-GAAACTGTCTCAAGAGAGACGAAA
*
12501485 TTTATTTCAAG
1 TTTGTTTCAAG
12501496 GGAATTGTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 27
0.75 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 91 0.61
37 31 0.21
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:12501372 original size:37 final size:36
Alignment explanation
Indices: 12501294--12501373 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
12501284 AGGGAAATTG
* * * * *
12501294 TCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTA
12501330 TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTA
1 TCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTA
12501367 TCTCAAG
1 TCTCAAG
12501374 GGATATGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
36 16 0.42
37 22 0.58
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTA
Found at i:12501374 original size:138 final size:138
Alignment explanation
Indices: 12501221--12501480 Score: 380
Period size: 138 Copynumber: 1.9 Consensus size: 138
12501211 GTGTTTCAAG
* * * *
12501221 AGAAACTATCTCAAGGGAGACAAAATTTGATTT-AGAGGAAATAAATTCAAAGATTTTGTTTCAA
1 AGAAACTATCTCAAGGGAGACAAAATTTG-TTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAA
* *
12501285 GGGAAATTGTCTCAAGAGAGACGAAATTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAACT
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAACT
12501349 TAGTTCCAAA
129 TAGTTCCAAA
* ** * * *
12501359 AGAAACTATCTCAAGGGATATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
12501424 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGAC
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGAC
12501481 GAAATTTATT
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
137 3 0.03
138 102 0.94
139 3 0.03
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (138 bp):
AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:12501521 original size:101 final size:101
Alignment explanation
Indices: 12501309--12501581 Score: 305
Period size: 101 Copynumber: 2.7 Consensus size: 101
12501299 AGAGAGACGA
* * *
12501309 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAGGAAACTATCTCAAG
* * * * *
12501374 GGATATGAAATTTGTTTCAAATAAAACATATTCAAAT
65 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
* *
12501411 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGA
* * *** *
12501476 GAGACGAAATTTATTTCAAGGGAATTGTTTTC-AAT
66 GAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * * *
12501511 GTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGATAAAATATTGTTTCAAGGGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-TTGTTTCAAAGGAAACTATCTCAA
*
12501576 GCGAGA
64 GAGAGA
12501582 TAAAATCTTC
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
100 5 0.03
101 75 0.52
102 64 0.44
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGA
GAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:12501567 original size:37 final size:37
Alignment explanation
Indices: 12501516--12501587 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
12501506 TCAATGTTTA
* * *
12501516 TGTTTCAAGAGAAACTGTCTTAAGGGAGATAAAATAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATAT
*
12501553 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAAT
12501588 CTTCTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATAT
Found at i:12503241 original size:27 final size:28
Alignment explanation
Indices: 12503190--12503246 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
12503180 GTTTAATCAC
12503190 TGTTATTTTAATTTTTCCCTTTAAAATTA
1 TGTTATTTTAATTTTT-CCTTTAAAATTA
12503219 TGTTATTTTAATTTCTT-C-TTAAAATTA
1 TGTTATTTTAATTT-TTCCTTTAAAATTA
12503246 T
1 T
12503247 TAATTGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 10 0.37
28 1 0.04
29 14 0.52
30 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (28 bp):
TGTTATTTTAATTTTTCCTTTAAAATTA
Found at i:12503779 original size:139 final size:139
Alignment explanation
Indices: 12503589--12503969 Score: 421
Period size: 137 Copynumber: 2.8 Consensus size: 139
12503579 AACTTTTAAT
* ** * * * * * *
12503589 TTAGAAGAATTTTCGATTTGGTCATCGCTTATGCTAGAGGTTCTAAATTAATTATTTGATAGTCC
1 TTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCAATTTAATTATTCGATAGTCA
* *
12503654 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCTTACATCTTAGGCCTAATTTCATATTAA
66 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTACATCTTAGGCCTAATTTCACATTAA
**
12503719 ATCCCTATT
131 ATCCCTAAA
* * *
12503728 TTATGTGAATTTTTAATTTGGTTATCGCTTTTGCTCGAGGTTCCAATTTAATTATTCGA-A-TCA
1 TTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCAATTTAATTATTCGATAGTCA
* * * * *
12503791 ATAATTGATTAAAGTTTATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACCTTTA
66 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTACATCTTAGGCCTAATTTCACATTAA
* *
12503856 GTCCTTAAA
131 ATCCCTAAA
* * * * * *
12503865 TTAGGAGAATTCTTAATTTGGTCCTCCCTTTTGCTCGAGATTCCACTTTAATTATTCGAATTGT-
1 TTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCAATTTAATTATTCG-ATAGTC
* *
12503929 AAT-ATTGATTAAAAATTAACTTA-AATTAATATTAGGGCCTA
65 AATAATTGATT-AAAATTAA-TTAGGATTAATATTAGAGCCTA
12503970 TATTTTTAGG
Statistics
Matches: 200, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
137 115 0.57
138 9 0.05
139 72 0.36
140 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (139 bp):
TTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCAATTTAATTATTCGATAGTCA
ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTACATCTTAGGCCTAATTTCACATTAA
ATCCCTAAA
Found at i:12507209 original size:18 final size:19
Alignment explanation
Indices: 12507174--12507224 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
12507164 ACACAGAGAG
*
12507174 AAAA-AAGAAAAGATATAA
1 AAAAGAAGAAAAGACATAA
12507192 AAAAGAAGAAAA-ACATAA
1 AAAAGAAGAAAAGACATAA
12507210 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
12507225 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.48
19 14 0.48
20 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAAGAAGAAAAGACATAA
Found at i:12507229 original size:13 final size:13
Alignment explanation
Indices: 12507211--12507263 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
12507201 AAAACATAAA
12507211 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
12507224 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
*
12507237 --AGAAAAAAAAG
1 AAAGAAAGAAAAG
12507248 AAAGTAAA-AAAAG
1 AAAG-AAAGAAAAG
12507261 AAA
1 AAA
12507264 AAGAAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 10 0.28
13 23 0.64
14 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:12507242 original size:20 final size:21
Alignment explanation
Indices: 12507217--12507269 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
12507207 TAAAAAAGAA
*
12507217 AGAAAAGAAAGAAAG-AAAAG
1 AGAAAAAAAAGAAAGTAAAAG
12507237 AGAAAAAAAAGAAAGTAAAA-
1 AGAAAAAAAAGAAAGTAAAAG
*
12507257 A-AAGAAAAAGAAA
1 AGAAAAAAAAGAAA
12507270 AATACTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAAGAAAGTAAAAG
Found at i:12507263 original size:33 final size:33
Alignment explanation
Indices: 12507168--12507263 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
12507158 TTGACAACAC
*
12507168 AGAGAGAAAAAAGAAAAGATATAAAAAAG-AAGAAA
1 AGAGAAAAAAAAG-AAAG-TA-AAAAAAGAAAGAAA
* *
12507203 A-ACATAAAAAAGAAAG-AAAAGAAAGAAAGAAA
1 AGAGAAAAAAAAGAAAGTAAAA-AAAGAAAGAAA
12507235 AGAGAAAAAAAAGAAAGTAAAAAAAGAAA
1 AGAGAAAAAAAAGAAAGTAAAAAAAGAAA
12507264 AAGAAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
30 3 0.06
31 5 0.09
32 7 0.13
33 24 0.45
34 13 0.25
35 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (33 bp):
AGAGAAAAAAAAGAAAGTAAAAAAAGAAAGAAA
Found at i:12507270 original size:24 final size:23
Alignment explanation
Indices: 12507191--12507270 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
12507181 AAAAGATATA
*
12507191 AAAAAGAAGAA-AAACATAAAAAAG
1 AAAAAGAA-AAGAAAGA-AAAAAAG
12507215 --AAAGAAAAGAAAGAAAGAAAAG
1 AAAAAGAAAAGAAAGAAA-AAAAG
12507237 AGAAAA-AAAAGAAAGTAAAAAAAG
1 A-AAAAGAAAAGAAAG-AAAAAAAG
12507261 AAAAAGAAAA
1 AAAAAGAAAA
12507271 ATACTTCAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
21 4 0.08
22 15 0.31
23 4 0.08
24 19 0.40
25 6 0.12
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAAGAAAGAAAAAAAG
Found at i:12508051 original size:28 final size:28
Alignment explanation
Indices: 12508011--12508113 Score: 163
Period size: 28 Copynumber: 3.7 Consensus size: 28
12508001 AGCCAACTTG
12508011 AAACACATTACCTCCCCAAATTAACCTA
1 AAACACATTACCTCCCCAAATTAACCTA
*
12508039 AAACACATTACCTCCCCAAATTAACCTG
1 AAACACATTACCTCCCCAAATTAACCTA
*
12508067 AAACACATTACCTCCCTAAATTAACCTA
1 AAACACATTACCTCCCCAAATTAACCTA
*
12508095 AAACAC-TCTACCTTCCCAA
1 AAACACAT-TACCTCCCCAA
12508114 GTTAGGCTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
27 1 0.01
28 68 0.99
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (28 bp):
AAACACATTACCTCCCCAAATTAACCTA
Found at i:12509487 original size:62 final size:58
Alignment explanation
Indices: 12509414--12509566 Score: 191
Period size: 62 Copynumber: 2.6 Consensus size: 58
12509404 GATATGATTC
*
12509414 TTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTGACATGATGTTTTCAAAAGAATTT
1 TTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTAACATGATGTTTTCAAAAGAA--T
* * * *
12509474 TTTAAAAAGAAACT-AGTTTTGATTTTTAGAGGTTTCTTAACATGATGTTTTCAAATGAAT
1 TTT--AAAGAAACTAAG-TCTGATTTTCAAAGGTTTCTTAACATGATGTTTTCAAAAGAAT
* *
12509534 TTTAAAGAAGCTAAGTCTGATTTTCAAAAGTTT
1 TTTAAAGAAACTAAGTCTGATTTTCAAAGGTTT
12509567 ATAAATAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
58 22 0.28
59 2 0.03
60 7 0.09
61 2 0.03
62 46 0.58
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.41
Consensus pattern (58 bp):
TTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTAACATGATGTTTTCAAAAGAAT
Found at i:12510486 original size:240 final size:239
Alignment explanation
Indices: 12509694--12510993 Score: 1635
Period size: 240 Copynumber: 5.4 Consensus size: 239
12509684 ATTTTCAAGG
* * *
12509694 GTTTCTTGA-TTAGTAAGTCCTTCGGGCCATCAGTAAGCCTTTCTAGCATGATGTCTAAATCCTT
1 GTTTCTT-ACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTT
* * * *
12509758 CGGGTCATCTATAAGCCTTTCAAGCAAGATCATAAGTCCTTCCGACCATCCATAAGACCTTCAGG
65 CGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCA-G
* * * * *
12509823 CATGATGTTTTCACATGATTTTTGAAAAATGAGAAAGTGATTTCCAAAGCTTCTCATTTAAATCT
129 CAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAATCT
* * * * * * *
12509888 TTTCTAAAAATTAATTTTTTTTAAAAGCAGGAAAAAGATTTTGCAAA
194 TTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACGA-TTTCCAAA
* * * * *
12509935 GTTTGTTATTTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAACATGATACCTAAATCCTTC
1 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
* * **
12510000 GGGTCATCTATAAGCATTTCGAGCAAGATGATAAATCCTTTTGGCCATCCATAAGACCTTCAGCC
66 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAG-C
* * * *
12510065 ATGATGTTTTCACATGATTTTTGAAAAATGAGAAAGCGATTTTCAAAGCTTCTCATTTAAAGCTT
130 AGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAATCTT
* **
12510130 TTCTGATAATTGA-TTTTTTGAAAAGTAAGAAAATAATTTCCAAA
195 TTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACGATTTCCAAA
* * * * *
12510174 GTTTCTTACTTAGTAAGTCCTTCGAGTCATCATTAAGTCTTTTGAGCATGATGCCTAAATCCATC
1 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
* * * * * *
12510239 GGGTCATCTGTAAGCCTTTCCAACAAGTTGATAAGTCCTTCGGGACATCCATATGACCTTCGAGC
66 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-AGC
* *
12510304 AGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTTCAAAGTTTCTTATTTAAATCTT
130 AGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAATCTT
* * *
12510369 TTATGAAAATTGATTTTTTTGAAAAGTAAGAATATGATTTCCAAA
195 TTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACGATTTCCAAA
* * *
12510414 GTTTCTTATTTAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAATCCTTC
1 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
*
12510479 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGC
66 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-AGC
* * * *
12510544 AGGATGTTTTCACATGATTTTCAAAAAAT-AAAAAGCGATTTTCAAGGATTT-TTATTTAAATCT
130 AGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTTCAAAG-TTTCTCATTTAAATCT
* * * * *
12510607 TTTTTGAAATTTGATTTTTTTTTAAAAAAGTAAGAAAACAATTACCAAA
194 TTTCTGAAAATTGA--TTTTTTT-GAAAAGTAAGAAAACGATTTCCAAA
* * * * *
12510656 TTTTCTTACTTAGTAAGTCTTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAAT--TTT
1 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
* * * * *
12510719 GGGTCATTTATAAACCTTTCGAGCAAGTTGATAAGTCTTTCAGGCCATCCATAAGACCTTCAGGC
66 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCA-GC
* * * * *
12510784 AGGAAGTTTTCACGTGATTTTC-AAAAATTGAGAAAGCGATTTCCAAAATTTATCATTTAAATCT
130 AGGATGTTTTCACATGATTTTCGAAAAA-TGAGAAAGCGATTTTCAAAGTTTCTCATTTAAATCT
* *
12510848 TTTCTAAAAATTGATTTTTTT-AAAAGTAAGAAAACGATTTCTAAA
194 TTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACGATTTCCAAA
* * * *
12510893 GTTTCTTACTTAGTAAGTCCTTCGGTCCATCAGTAAGTCTTTCCAACATGATGCCTAAATCCTTT
1 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
** * *
12510958 AAGTCATATATAAGCCTTTCGAGGAAGATGATAAGT
66 GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGT
12510994 GTTTCGGGTC
Statistics
Matches: 927, Mismatches: 118, Indels: 30
0.86 0.11 0.03
Matches are distributed among these distances:
237 74 0.08
239 268 0.29
240 282 0.30
241 227 0.24
242 76 0.08
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (239 bp):
GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTC
GGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGCA
GGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAATCTTT
TCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACGATTTCCAAA
Found at i:12510498 original size:42 final size:41
Alignment explanation
Indices: 12510434--12510538 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
12510424 TAGTAAGTCA
* * *
12510434 TTCGGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAATCC
1 TTCGGGCCATCAATAAGCCTTTCGAGCAAGATG-ATAAATCC
* * *
12510476 TTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCATCAATAAGCCTTTCGAGCAAGATGATAAATCC
*
12510517 TTCGGGCCATCCATAAGACCTT
1 TTCGGGCCATCAATAAG-CCTT
12510539 CGGGCAGGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 21 0.39
42 33 0.61
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (41 bp):
TTCGGGCCATCAATAAGCCTTTCGAGCAAGATGATAAATCC
Found at i:12510875 original size:479 final size:475
Alignment explanation
Indices: 12509694--12511034 Score: 1695
Period size: 479 Copynumber: 2.8 Consensus size: 475
12509684 ATTTTCAAGG
* * * *
12509694 GTTTCTTGA-TTAGTAAGTCCTTCGGGCCATCAGTAAGCCTTTCTAGCATGATGTCTAAATCCTT
1 GTTTCTT-ACTTAGTAAGTCCTTC-GGCCATCAATAAGTCTTTCGAGCATGATGCCTAAAT-CTT
* * * *
12509758 CGGGTCATCTATAAGCCTTTCAAGCAAGATCATAAGTCCTTCCGACCATCCATAAGACCTTCAGG
63 CGGGTCATCTATAAGCCTTTCAAGCAAGTTGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGG
* * * *
12509823 CATGATGTTTTCACATGATTTTTGAAAAATGAGAAAGTGATTTCCAAAGCTTCTCATTTAAATCT
128 CAGGATGTTTTCACATGA-TTTTCAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCT
* * * * * *
12509888 TTTCTAAAAATTAATTTTTTTTAAAAGCAGGAAAAAGATTTTGCAAAGTTTGTTATTTAATAAGT
192 TTTCTAAAAATTGA-TTTTTTTAAAAGTAAGAAAAAGA-TTTCCAAAGTTTCTTATTTAGTAAGT
* *
12509953 CCTTCGGGCCATCAGTAAGTCTTTCGAACATGATACCTAAATCCTTCGGGTCATCTATAAGCATT
255 CCTTCGGGCCATCAGTAAGTCTTTCGAACATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTT
* ** * * *
12510018 TCGAGCAAGATGATAAATCCTTTTGGCCATCCATAAGACCTTCAGCCATGATGTTTTCACATGAT
320 TCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAT
** * *
12510083 TTTTGAAAAATGAGAAAGCGATTTTCAAAGCTTCTCATTTAAAGCTTTTCTGATAATTGATTTTT
385 TTTCAAAAAATGAAAAAGCGATTTTCAAAGATTCTCATTTAAAGCTTTTCTGATAATTGATTTTT
* * *
12510148 TGAAAAGTAAGAAAATAATTTCCAAA
450 TAAAAAGTAAGAAAACAATTACCAAA
* * * *
12510174 GTTTCTTACTTAGTAAGTCCTTCGAGTCATCATTAAGTCTTTTGAGCATGATGCCTAAATCCATC
1 GTTTCTTACTTAGTAAGTCCTTCG-GCCATCAATAAGTCTTTCGAGCATGATGCCTAAAT-CTTC
* * * *
12510239 GGGTCATCTGTAAGCCTTTCCAA-CAAGTTGATAAGTCCTTCGGGACATCCATATGACCTTC-GA
64 GGGTCATCTATAAGCCTTT-CAAGCAAGTTGATAAGTCCTTCAGGCCATCCATAAGACCTTCAG-
* * *
12510302 GCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTTCAAAGTTTCTTATTTAAATC
127 GCAGGATGTTTTCACATGATTTTC-AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATC
* * * *
12510367 TTTTATGAAAATTGATTTTTTTGAAAAGTAAGAATATGATTTCCAAAGTTTCTTATTTAGTAAGT
191 TTTTCTAAAAATTGATTTTTTT-AAAAGTAAGAAAAAGATTTCCAAAGTTTCTTATTTAGTAAGT
* * *
12510432 CATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTT
255 CCTTCGGGCCATCAGTAAGTCTTTCGAACATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTT
12510497 TCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAT
320 TCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAT
* * * * *
12510562 TTTCAAAAAAT-AAAAAGCGATTTTCAAGGATTTTTATTTAAATCTTTTTTGA-AATTTGATTTT
385 TTTCAAAAAATGAAAAAGCGATTTTCAAAGATTCTCATTTAAAGCTTTTCTGATAA-TTGA---T
12510625 TTTTTAAAAAAGTAAGAAAACAATTACCAAA
446 TTTTT-AAAAAGTAAGAAAACAATTACCAAA
* * *
12510656 TTTTCTTACTTAGTAAGTCTTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAAT-TTTG
1 GTTTCTTACTTAGTAAGTCCTTC-GGCCATCAATAAGTCTTTCGAGCATGATGCCTAAATCTTCG
* * * *
12510720 GGTCATTTATAAACCTTTCGAGCAAGTTGATAAGTCTTTCAGGCCATCCATAAGACCTTCAGGCA
65 GGTCATCTATAAGCCTTTCAAGCAAGTTGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCA
* * * *
12510785 GGAAGTTTTCACGTGATTTTCAAAAATTGAGAAAGCGATTTCCAAAATTTATCATTTAAATCTTT
130 GGATGTTTTCACATGATTTTCAAAAA-TGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTT
* * *
12510850 TCTAAAAATTGATTTTTTTAAAAGTAAGAAAACGATTTCTAAAGTTTCTTACTTAGTAAGTCCTT
194 TCTAAAAATTGATTTTTTTAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTATTTAGTAAGTCCTT
* * *** *
12510915 CGGTCCATCAGTAAGTCTTTCCAACATGATGCCTAAATCCTTTAAGTCATATATAAGCCTTTCGA
259 CGGGCCATCAGTAAGTCTTTCGAACATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGA
* ** * * *** * *
12510980 GGAAGATGATAAGTGTTTCGGGTCTTCTGCAAGACATTTGGGCAGGATGTTTTCA
324 GCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
12511035 TATGGTGTTA
Statistics
Matches: 745, Mismatches: 101, Indels: 31
0.85 0.12 0.04
Matches are distributed among these distances:
477 2 0.00
478 38 0.05
479 315 0.42
480 304 0.41
481 10 0.01
482 75 0.10
483 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (475 bp):
GTTTCTTACTTAGTAAGTCCTTCGGCCATCAATAAGTCTTTCGAGCATGATGCCTAAATCTTCGG
GTCATCTATAAGCCTTTCAAGCAAGTTGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCAG
GATGTTTTCACATGATTTTCAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTC
TAAAAATTGATTTTTTTAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTATTTAGTAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAACATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGC
AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCAA
AAAATGAAAAAGCGATTTTCAAAGATTCTCATTTAAAGCTTTTCTGATAATTGATTTTTTAAAAA
GTAAGAAAACAATTACCAAA
Found at i:12511807 original size:116 final size:116
Alignment explanation
Indices: 12511602--12511850 Score: 365
Period size: 116 Copynumber: 2.1 Consensus size: 116
12511592 TCATCACTTT
* * * *
12511602 GTTCGATTCTATCACAGAAGGTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAAC
1 GTTCGATTCCATCACAGAA-GTGGTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAAC
* *
12511667 TCATCCGATAAGGGAGAAGAAGTTCATAGTGAGAAGAACTTGTTCAACCTTG
65 TCATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* *
12511719 GTTCGATTCCATCACAGAA-TGAGTGGATCAATATTTTCAGTAGAGAGTTCAAAATGAGAAGAAC
1 GTTCGATTCCATCACAGAAGTG-GTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAAC
* * *
12511783 TCATCCGATGAGGGAGTATAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
65 TCATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
*
12511835 GCTCGATTCCATCACA
1 GTTCGATTCCATCACA
12511851 TAAGGAGTTG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 2 0.02
116 99 0.83
117 18 0.15
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (116 bp):
GTTCGATTCCATCACAGAAGTGGTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAACT
CATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
Found at i:12512119 original size:203 final size:202
Alignment explanation
Indices: 12511720--12512119 Score: 527
Period size: 203 Copynumber: 2.0 Consensus size: 202
12511710 TCAACCTTGG
* *
12511720 TTCGATTCCATCACAGAATGAGTGGATCAATATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
1 TTCGATTCCATCACAGAATGAGTGGATAAACATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
* * * *
12511785 ATCCGATGAGGGAGTATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCAC
66 ATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATCAC
** * * * * *
12511850 ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCGTATATGGAGTTCGATCAGCATCAT
131 ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACATCAT
12511915 CACTTTA
196 CACTTTA
* * *
12511922 TTCGATTCCATCACAGAATGAGGTGGGTAAACA-TTTCTAGTGGAGAGTTCATAATGAGAAGAAC
1 TTCGATTCCATCACAGAATGA-GTGGATAAACATTTTC-AGTAGAGAGTTCAAAATGAGAAGAAC
*
12511986 TCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATC
64 TCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATC
* * * * * * *
12512051 GCATAAGGAGTTTG-ATCAACA-TCATCATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATA
129 ACATAAGGAGTTGGAAT-AACACTAAT-ACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACA
12512114 TCATCA
192 TCATCA
12512120 TTTTGCTCGC
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
202 30 0.18
203 140 0.82
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (202 bp):
TTCGATTCCATCACAGAATGAGTGGATAAACATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
ATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATCAC
ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACATCAT
CACTTTA
Found at i:12512579 original size:116 final size:116
Alignment explanation
Indices: 12512374--12512622 Score: 365
Period size: 116 Copynumber: 2.1 Consensus size: 116
12512364 TCATCACTTT
* * * *
12512374 GTTCGATTCTATCACAGAAGGTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAAC
1 GTTCGATTCCATCACAGAA-GTGGTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAAC
* *
12512439 TCATCCGATAAGGGAGAAGAAGTTCATAGTGAGAAGAACTTGTTCAACCTTG
65 TCATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* *
12512491 GTTCGATTCCATCACAGAA-TGAGTGGATCAATATTTTCAGTAGAGAGTTCAAAATGAGAAGAAC
1 GTTCGATTCCATCACAGAAGTG-GTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAAC
* * *
12512555 TCATCCGATGAGGGAGTATAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
65 TCATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
*
12512607 GCTCGATTCCATCACA
1 GTTCGATTCCATCACA
12512623 TAAGGAGTTG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 2 0.02
116 99 0.83
117 18 0.15
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (116 bp):
GTTCGATTCCATCACAGAAGTGGTGGATCAACATTTCCAGTAGAGAGTTCAAAATGAGAAGAACT
CATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
Found at i:12512891 original size:203 final size:202
Alignment explanation
Indices: 12512492--12512891 Score: 527
Period size: 203 Copynumber: 2.0 Consensus size: 202
12512482 TCAACCTTGG
* *
12512492 TTCGATTCCATCACAGAATGAGTGGATCAATATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
1 TTCGATTCCATCACAGAATGAGTGGATAAACATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
* * * *
12512557 ATCCGATGAGGGAGTATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCAC
66 ATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATCAC
** * * * * *
12512622 ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCGTATATGGAGTTCGATCAGCATCAT
131 ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACATCAT
12512687 CACTTTA
196 CACTTTA
* * *
12512694 TTCGATTCCATCACAGAATGAGGTGGGTAAACA-TTTCTAGTGGAGAGTTCATAATGAGAAGAAC
1 TTCGATTCCATCACAGAATGA-GTGGATAAACATTTTC-AGTAGAGAGTTCAAAATGAGAAGAAC
*
12512758 TCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATC
64 TCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATC
* * * * * * *
12512823 GCATAAGGAGTTTG-ATCAACA-TCATCATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATA
129 ACATAAGGAGTTGGAAT-AACACTAAT-ACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACA
12512886 TCATCA
192 TCATCA
12512892 TTTTGCTCGC
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
202 30 0.18
203 140 0.82
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (202 bp):
TTCGATTCCATCACAGAATGAGTGGATAAACATTTTCAGTAGAGAGTTCAAAATGAGAAGAACTC
ATCCGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCAATTCCATCAC
ATAAGGAGTTGGAATAACACTAATACTTGGCTCATCCATCAAAAAAGAAGTTAGATCAACATCAT
CACTTTA
Found at i:12512909 original size:772 final size:772
Alignment explanation
Indices: 12511427--12512970 Score: 3088
Period size: 772 Copynumber: 2.0 Consensus size: 772
12511417 TGAAAGAAAT
12511427 ATATCAACATATCCAATGAAGAGTTCATAATGAGAAGAACTGATCCAATAAGGGAGAAGTTCATA
1 ATATCAACATATCCAATGAAGAGTTCATAATGAGAAGAACTGATCCAATAAGGGAGAAGTTCATA
12511492 ATGAGAAGAACTTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATAC
66 ATGAGAAGAACTTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATAC
12511557 TTGGTTTATCCATCGTATATGGAGTTGGATTAGCATCATCACTTTGTTCGATTCTATCACAGAAG
131 TTGGTTTATCCATCGTATATGGAGTTGGATTAGCATCATCACTTTGTTCGATTCTATCACAGAAG
12511622 GTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAACTCATCCGATAAGGGAGAAGA
196 GTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAACTCATCCGATAAGGGAGAAGA
12511687 AGTTCATAGTGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGTGGATCAATA
261 AGTTCATAGTGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGTGGATCAATA
12511752 TTTTCAGTAGAGAGTTCAAAATGAGAAGAACTCATCCGATGAGGGAGTATAAGTTCATAATGAGA
326 TTTTCAGTAGAGAGTTCAAAATGAGAAGAACTCATCCGATGAGGGAGTATAAGTTCATAATGAGA
12511817 AGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAATAACACTAATACTTGGCT
391 AGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAATAACACTAATACTTGGCT
12511882 CATCCATCGTATATGGAGTTCGATCAGCATCATCACTTTATTCGATTCCATCACAGAATGAGGTG
456 CATCCATCGTATATGGAGTTCGATCAGCATCATCACTTTATTCGATTCCATCACAGAATGAGGTG
12511947 GGTAAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
521 GGTAAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
12512012 TAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATCGCATAAGGAGTTTGATCAACATCATC
586 TAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATCGCATAAGGAGTTTGATCAACATCATC
12512077 ATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATATCATCATTTTGCTCGCCCATCACATAAG
651 ATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATATCATCATTTTGCTCGCCCATCACATAAG
12512142 GAGTTGAATCGGTGTCACCTCGGCTCGTCCATCACATAAAGAGTTGGATCAACATCA
716 GAGTTGAATCGGTGTCACCTCGGCTCGTCCATCACATAAAGAGTTGGATCAACATCA
12512199 ATATCAACATATCCAATGAAGAGTTCATAATGAGAAGAACTGATCCAATAAGGGAGAAGTTCATA
1 ATATCAACATATCCAATGAAGAGTTCATAATGAGAAGAACTGATCCAATAAGGGAGAAGTTCATA
12512264 ATGAGAAGAACTTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATAC
66 ATGAGAAGAACTTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATAC
12512329 TTGGTTTATCCATCGTATATGGAGTTGGATTAGCATCATCACTTTGTTCGATTCTATCACAGAAG
131 TTGGTTTATCCATCGTATATGGAGTTGGATTAGCATCATCACTTTGTTCGATTCTATCACAGAAG
12512394 GTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAACTCATCCGATAAGGGAGAAGA
196 GTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAACTCATCCGATAAGGGAGAAGA
12512459 AGTTCATAGTGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGTGGATCAATA
261 AGTTCATAGTGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGTGGATCAATA
12512524 TTTTCAGTAGAGAGTTCAAAATGAGAAGAACTCATCCGATGAGGGAGTATAAGTTCATAATGAGA
326 TTTTCAGTAGAGAGTTCAAAATGAGAAGAACTCATCCGATGAGGGAGTATAAGTTCATAATGAGA
12512589 AGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAATAACACTAATACTTGGCT
391 AGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAATAACACTAATACTTGGCT
12512654 CATCCATCGTATATGGAGTTCGATCAGCATCATCACTTTATTCGATTCCATCACAGAATGAGGTG
456 CATCCATCGTATATGGAGTTCGATCAGCATCATCACTTTATTCGATTCCATCACAGAATGAGGTG
12512719 GGTAAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
521 GGTAAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
12512784 TAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATCGCATAAGGAGTTTGATCAACATCATC
586 TAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATCGCATAAGGAGTTTGATCAACATCATC
12512849 ATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATATCATCATTTTGCTCGCCCATCACATAAG
651 ATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATATCATCATTTTGCTCGCCCATCACATAAG
12512914 GAGTTGAATCGGTGTCACCTCGGCTCGTCCATCACATAAAGAGTTGGATCAACATCA
716 GAGTTGAATCGGTGTCACCTCGGCTCGTCCATCACATAAAGAGTTGGATCAACATCA
12512971 CCTTTTGTAA
Statistics
Matches: 772, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
772 772 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (772 bp):
ATATCAACATATCCAATGAAGAGTTCATAATGAGAAGAACTGATCCAATAAGGGAGAAGTTCATA
ATGAGAAGAACTTATTCAACCTTAGCTTGATTCCATCACATAAGGAGTTGGAACAACACCAATAC
TTGGTTTATCCATCGTATATGGAGTTGGATTAGCATCATCACTTTGTTCGATTCTATCACAGAAG
GTGGTGGATCAACATTTCCAGTGGAGAGTTCATAATTAGAAGAACTCATCCGATAAGGGAGAAGA
AGTTCATAGTGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGTGGATCAATA
TTTTCAGTAGAGAGTTCAAAATGAGAAGAACTCATCCGATGAGGGAGTATAAGTTCATAATGAGA
AGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAATAACACTAATACTTGGCT
CATCCATCGTATATGGAGTTCGATCAGCATCATCACTTTATTCGATTCCATCACAGAATGAGGTG
GGTAAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
TAATGAGAAAAACTTGTTCAACCTTAGCTCAATTTCATCGCATAAGGAGTTTGATCAACATCATC
ATTTTGCTCGTCCATCAAAAAAGAAGTTAGATCAATATCATCATTTTGCTCGCCCATCACATAAG
GAGTTGAATCGGTGTCACCTCGGCTCGTCCATCACATAAAGAGTTGGATCAACATCA
Found at i:12512972 original size:40 final size:40
Alignment explanation
Indices: 12512896--12512973 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
12512886 TCATCATTTT
* ****
12512896 GCTCGCCCATCACATAAGGAGTTGAATCGGTGTCACCTCG
1 GCTCGCCCATCACATAAAGAGTTGAATCAACATCACCTCG
* *
12512936 GCTCGTCCATCACATAAAGAGTTGGATCAACATCACCT
1 GCTCGCCCATCACATAAAGAGTTGAATCAACATCACCT
12512974 TTTGTAAACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
GCTCGCCCATCACATAAAGAGTTGAATCAACATCACCTCG
Found at i:12515336 original size:137 final size:138
Alignment explanation
Indices: 12515055--12515433 Score: 453
Period size: 137 Copynumber: 2.7 Consensus size: 138
12515045 ACCTAAACTT
* * *
12515055 TTAATTTAGGACAATT-TTAGATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAA-TTAATTATTCG
1 TTAAATTAGGAGAATTCTTA-ATTTGGTCATCGCTTTTGCTCGAGGTT-CAAATTTAATTATTCG
* * * *
12515118 ATAGTCCATAATTGATTAAAATTAATTACAATTAATATTAGAGCCTCCATCTTAGGCCTAGTTTT
64 A-AGTCAATAATTGATTAAAATTAATTACAATTAATATTAGAACCTCCATCTTAGGCCTAATTCT
* *
12515183 ATATTTAATCT
128 ACATTTAATCC
*
12515194 TTAAATTAGGTGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGGTTCAAATTTAATTATTCGAA
1 TTAAATTAGGAGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGGTTCAAATTTAATTATTCGAA
* * ** * *
12515259 -TCAATAATTGATTAAAGTTGATTAGGATTAATATTAGAACCTCCATCTTAGGCCTAATTCTCCC
66 GTCAATAATTGATTAAAATTAATTACAATTAATATTAGAACCTCCATCTTAGGCCTAATTCTACA
*
12515323 TTTAGTCC
131 TTTAATCC
* * * * * * *
12515331 TTAAATTAGGAGAATTCTTAATTTGGTCTTCACTTTTGCTCGAGATCCCACTTTAATTATTTGAA
1 TTAAATTAGGAGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGGTTCAAATTTAATTATTCGAA
*
12515396 TTGCAAT-ATTGATTAAAATTAATTTA-AATTAATATTAG
66 GT-CAATAATTGATTAAAATTAA-TTACAATTAATATTAG
12515434 GGACTACATT
Statistics
Matches: 207, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
137 116 0.56
138 30 0.14
139 58 0.28
140 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (138 bp):
TTAAATTAGGAGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGGTTCAAATTTAATTATTCGAA
GTCAATAATTGATTAAAATTAATTACAATTAATATTAGAACCTCCATCTTAGGCCTAATTCTACA
TTTAATCC
Found at i:12517449 original size:2 final size:2
Alignment explanation
Indices: 12517442--12517681 Score: 154
Period size: 2 Copynumber: 127.5 Consensus size: 2
12517432 ATAAAACGTA
12517442 AT AT AT AT -T AT A- AT AT ACT A- AT AT AT AT ACT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
12517482 A- AT AT GA- AT AT AT AT ACT AT A- AT AT AT A- AT AT ACT AT AT
1 AT AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
* *
12517521 A- AT CT A- AT AC AT A- AT AT AT AT -T AT A- AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
12517556 A- AT AT ACT AT AT A- ACT AT AT A- AT GAT AT AT ACC AT AT AA AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT -AT AT AT A-T AT AT AT AT
12517597 AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
12517638 A- AT AT AT AT -T AT AT A- AA AT A- AT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12517674 AT GAT AT A
1 AT -AT AT A
12517682 ATGAAAAGGA
Statistics
Matches: 192, Mismatches: 9, Indels: 74
0.70 0.03 0.27
Matches are distributed among these distances:
1 26 0.14
2 147 0.77
3 19 0.10
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:12517457 original size:12 final size:11
Alignment explanation
Indices: 12517440--12517681 Score: 177
Period size: 12 Copynumber: 21.6 Consensus size: 11
12517430 AAATAAAACG
12517440 TAATATATATTA
1 TAATATATA-TA
12517452 TAATATACTA-A
1 TAATATA-TATA
12517463 T-ATATATACTA
1 TAATATATA-TA
12517474 TAATATATAATA
1 TAATATAT-ATA
12517486 TGAATATATATA
1 T-AATATATATA
12517498 CT-ATA-ATATA
1 -TAATATATATA
12517508 TAATATACTATA
1 TAATATA-TATA
* *
12517520 TAATCTAATACA
1 TAATAT-ATATA
12517532 TAATATATATTA
1 TAATATATA-TA
12517544 TAATA-ATATAA
1 TAATATATAT-A
12517555 TAATATACTATA
1 TAATATA-TATA
12517567 TAACTATATA-A
1 TAA-TATATATA
* *
12517578 TGATATATACCA
1 TAATATATA-TA
12517590 T-ATA-A-ATA
1 TAATATATATA
12517598 TAATATATATA
1 TAATATATATA
12517609 T-ATATATATA
1 TAATATATATA
12517619 TATATATATAATA
1 TA-ATATAT-ATA
*
12517632 TCATATA-ATA
1 TAATATATATA
12517642 T-ATAT-TATA
1 TAATATATATA
*
12517651 TAAAATAATATA
1 TAATAT-ATATA
12517663 TAATATATAATA
1 TAATATAT-ATA
*
12517675 TGATATA
1 TAATATA
12517682 ATGAAAAGGA
Statistics
Matches: 191, Mismatches: 10, Indels: 58
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.01
9 15 0.08
10 39 0.20
11 32 0.17
12 80 0.42
13 23 0.12
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (11 bp):
TAATATATATA
Found at i:12523444 original size:4 final size:4
Alignment explanation
Indices: 12523435--12524497 Score: 1818
Period size: 4 Copynumber: 267.8 Consensus size: 4
12523425 AAATCCCATG
12523435 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523483 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * *
12523531 CACA CACA CACA CACA CACA CACA CACA CATA C--A CACA CATA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
12523577 CACA TACA CACA CATA CATA CATA CATA C--A CATA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523623 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523671 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523719 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523767 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523815 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523863 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523911 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12523959 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524007 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524055 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524103 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524151 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
12524199 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
12524247 CACA CACA CACA CACA CACA CACA CACA CATA CACA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
12524295 CATA CATA CATA C--A CATA CACA CACA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524341 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524389 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524437 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
12524485 CAT- -ATA CATA CAT
1 CATA CATA CATA CAT
12524498 GATACATAAA
Statistics
Matches: 1036, Mismatches: 15, Indels: 16
0.97 0.01 0.01
Matches are distributed among these distances:
2 8 0.01
4 1028 0.99
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:12523545 original size:10 final size:10
Alignment explanation
Indices: 12523530--12523624 Score: 118
Period size: 10 Copynumber: 9.5 Consensus size: 10
12523520 ATACATACAT
12523530 ACACACACAC
1 ACACACACAC
12523540 ACACACACAC
1 ACACACACAC
12523550 ACACACACAC
1 ACACACACAC
*
12523560 ATACACACAC
1 ACACACACAC
*
12523570 ATACACACAC
1 ACACACACAC
*
12523580 ATACACACAC
1 ACACACACAC
* * *
12523590 ATACATACAT
1 ACACACACAC
* *
12523600 ACATACACAT
1 ACACACACAC
12523610 ACACACACAC
1 ACACACACAC
12523620 ACACA
1 ACACA
12523625 TACATACATA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 77 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (10 bp):
ACACACACAC
Found at i:12524864 original size:38 final size:35
Alignment explanation
Indices: 12524820--12524946 Score: 130
Period size: 35 Copynumber: 3.5 Consensus size: 35
12524810 ACAAAATGTC
12524820 GTCTCGCTAT-AGACAACTTCTTTTGAAAAACAAATTTT
1 GTCTCGCT-TGAGACAA-TT-TTTT-AAAAACAAATTTT
* **
12524858 GTCTCGCTTGAGACAATTTTCTAAAAACAACGTTT
1 GTCTCGCTTGAGACAATTTTTTAAAAACAAATTTT
* * **
12524893 GTCTCACTTGAGACAATTTTTTCAAAACAAATTCC
1 GTCTCGCTTGAGACAATTTTTTAAAAACAAATTTT
**
12524928 GTCTCAATTGAGACAATTT
1 GTCTCGCTTGAGACAATTT
12524947 CTCTAAGAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 57 0.74
36 3 0.04
37 3 0.04
38 14 0.18
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (35 bp):
GTCTCGCTTGAGACAATTTTTTAAAAACAAATTTT
Found at i:12525156 original size:30 final size:30
Alignment explanation
Indices: 12525122--12525179 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12525112 ATAAAATACT
*
12525122 CATCTTTGAG-TCTGCTTCTCTTGAAACACC
1 CATCTATGAGATC-GCTTCTCTTGAAACACC
*
12525152 CATCTATGAGATCGTTTCTCTTGAAACA
1 CATCTATGAGATCGCTTCTCTTGAAACA
12525180 AATTTTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (30 bp):
CATCTATGAGATCGCTTCTCTTGAAACACC
Found at i:12525256 original size:34 final size:34
Alignment explanation
Indices: 12525213--12525279 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
12525203 ATTTTGAAGG
*
12525213 ATCATCTTTGAG-TCGTTTCTCTTGAAACAAAACA
1 ATCATCTTTGAGATCATTT-TCTTGAAACAAAACA
12525247 ATCATCTTTGAGATCATTTTCTTGAAACAAAAC
1 ATCATCTTTGAGATCATTTTCTTGAAACAAAAC
12525280 TTATTTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (34 bp):
ATCATCTTTGAGATCATTTTCTTGAAACAAAACA
Found at i:12525533 original size:44 final size:43
Alignment explanation
Indices: 12525419--12525539 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 43
12525409 CAAAATCCCC
*
12525419 TGGCCAAGACTCATGAACAGATGAGCAGTG--TCAACCCTAGG
1 TGGCCAAGACTCATGAACAGATGAGCAGTGTATCAACCCTAGA
** * * * * *
12525460 TAACCAAGACTTAT-CATAGTATGAGCAGTGTTATCATCCTTAGA
1 TGGCCAAGACTCATGAACAG-ATGAGCAGTG-TATCAACCCTAGA
*
12525504 TGGCCAAGACTCATGAACAGATGATCAGTGTCATCA
1 TGGCCAAGACTCATGAACAGATGAGCAGTGT-ATCA
12525540 CATGACCAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
40 3 0.05
41 21 0.35
43 1 0.02
44 32 0.53
45 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
TGGCCAAGACTCATGAACAGATGAGCAGTGTATCAACCCTAGA
Found at i:12526777 original size:11 final size:11
Alignment explanation
Indices: 12526761--12526791 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12526751 CTGGAGAGAG
*
12526761 TTTTCTCTCTC
1 TTTTCTCTCTA
12526772 TTTTCTCTCTA
1 TTTTCTCTCTA
12526783 TTTTCTCTC
1 TTTTCTCTC
12526792 GATGAGGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTCTCTCTA
Found at i:12529746 original size:118 final size:118
Alignment explanation
Indices: 12529599--12529818 Score: 323
Period size: 118 Copynumber: 1.9 Consensus size: 118
12529589 GATAAAACAA
* * * * *
12529599 CAAAAATAGAAATTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAAGGGCTAAAATAGAAAAA
1 CAAAAACAGAAATATAAAGGACTAAAATAGAAAAAATAGAAACCTAAAGGGATAAAACAGAAAAA
* * * *
12529664 ATAGAAGTTTAAAGGACTAAAATGGAAAAAATAGAAAATTAAAGGCTAAATAG
66 ATAAAAATTTAAAAGACTAAAATAGAAAAAATAGAAAATTAAAGGCTAAATAG
* * *
12529717 CAAAAACATAAATATAAAGGACTAAAATAGCAAAAATAGAAACCTAAAGGGATAAAACAGTAAAA
1 CAAAAACAGAAATATAAAGGACTAAAATAGAAAAAATAGAAACCTAAAGGGATAAAACAGAAAAA
*
12529782 ATAAAAATTTAAAAGACTAAAATAGCAAAAATAGAAA
66 ATAAAAATTTAAAAGACTAAAATAGAAAAAATAGAAA
12529819 TTTAGAGGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
118 89 1.00
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (118 bp):
CAAAAACAGAAATATAAAGGACTAAAATAGAAAAAATAGAAACCTAAAGGGATAAAACAGAAAAA
ATAAAAATTTAAAAGACTAAAATAGAAAAAATAGAAAATTAAAGGCTAAATAG
Found at i:12529820 original size:30 final size:30
Alignment explanation
Indices: 12529550--12529822 Score: 293
Period size: 30 Copynumber: 9.2 Consensus size: 30
12529540 ATCATATTCG
* * *
12529550 ATTTAAAGGACCAAAATAGCAAAAACATAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
* * *
12529580 ACTTAAAGGGA-TAAAACAACAAAAATAGAA
1 ATTTAAA-GGACTAAAATAGCAAAAATAGAA
*
12529610 ATTTAAAGGACTAAAATAGAAAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
* * *
12529640 ACTTAAAGGGCTAAAATAGAAAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
* * *
12529670 GTTTAAAGGACTAAAATGGAAAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
* * *
12529700 AATTAAAGG-CT-AAATAGCAAAAACATAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
*
12529728 ATATAAAGGACTAAAATAGCAAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
** * * *
12529758 ACCTAAAGGGA-TAAAACAGTAAAAATAAAA
1 ATTTAAA-GGACTAAAATAGCAAAAATAGAA
*
12529788 ATTTAAAAGACTAAAATAGCAAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAAATAGAA
12529818 ATTTA
1 ATTTA
12529823 GAGGGTTAAA
Statistics
Matches: 200, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
28 20 0.10
29 9 0.05
30 165 0.82
31 6 0.03
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGCAAAAATAGAA
Found at i:12531841 original size:130 final size:131
Alignment explanation
Indices: 12531531--12531888 Score: 373
Period size: 130 Copynumber: 2.7 Consensus size: 131
12531521 GTTCTGGTAG
* * * ** * *
12531531 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTTTGTGGATGAAACGGTTCCTACGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGT
* * ** * *
12531596 GATGAGGACGAAAGGCCATCTTTAGGGAGGGTGATAACACGATTTTTACGCGATGAGGATGACTG
66 GATGAGAACGAAAGACCATCTTTAGGGA--GTGATAACACGATTCCTACACGATGAGGAAGACTG
12531661 TTA
129 TTA
* * * *
12531664 TCTCGAGGTGACAC-AGCCCCTACGTGATGAGAAGGTTTGGTCGGGGGATGACACGGTTCCTACG
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACG
* * * *
12531728 TGATGAGAATGATAGACCATCTTTAGGGA-TGATAACGC-AGTTCCTACATGATGAGGAAGACTA
65 TGATGAGAACGAAAGACCATCTTTAGGGAGTGATAACACGA-TTCCTACACGATGAGGAAGACT-
12531791 GTTA
128 GTTA
* * * *
12531795 TCTAGGGGTG-CACGACTCTTACATGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTATGC
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGT
* * * * *
12531859 GATAAGGACGACAGTCTATCTTTAGGGAGT
66 GATGAGAACGAAAGACCATCTTTAGGGAGT
12531889 TGTTTCAAGA
Statistics
Matches: 185, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
129 1 0.01
130 93 0.50
131 14 0.08
132 1 0.01
133 76 0.41
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (131 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGT
GATGAGAACGAAAGACCATCTTTAGGGAGTGATAACACGATTCCTACACGATGAGGAAGACTGTT
A
Found at i:12532171 original size:65 final size:65
Alignment explanation
Indices: 12531888--12532146 Score: 333
Period size: 65 Copynumber: 4.0 Consensus size: 65
12531878 CTTTAGGGAG
* * ** ** *
12531888 TTGTTTCAAGAGAAACAGACTCACAA-ATGATGCTTCAAGAGAAGTTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACACACTCA-AAGATGATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
12531952 -
65 C
* **
12531952 TTCTTTCAAGGGAAACACACTCAAAGACTTTTATTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TTGTTTCAAGGGAAACACACTCAAAGA-TGATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
12532017 C
65 C
* * *
12532018 TTGTTTCAAGGGAATCAGACTCAAAGATGATATTTCAAGAGAAACTATCTCAAGGGAGACAAAAC
1 TTGTTTCAAGGGAAACACACTCAAAGATGATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
* * * *
12532083 TTTTTTCAAGGGAAACAAACTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGGGTGACAAAA
1 TTGTTTCAAGGGAAACACACTCAAAGATGATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
12532147 TATGTTTTGA
Statistics
Matches: 170, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
63 2 0.01
64 21 0.12
65 123 0.72
66 24 0.14
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (65 bp):
TTGTTTCAAGGGAAACACACTCAAAGATGATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
Found at i:12532273 original size:36 final size:35
Alignment explanation
Indices: 12532230--12532328 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 35
12532220 AAAGGAAAAA
**
12532230 TGTCTCAAATGAGACGAAATTTGTTTTAATAGAAA-T
1 TGTCTCAAGCGAGAC-AAATTTGTTTTAATA-AAACT
* *
12532266 TGTCTCAAGCGAGACAAATTTTTTTTTTATAAAACT
1 TGTCTCAAGCGAGACAAA-TTTGTTTTAATAAAACT
12532302 TGTCTCAAGCGAGACAAAATTATGTTT
1 TGTCTCAAGCGAGAC-AAATT-TGTTT
12532329 CGAGAAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
35 6 0.11
36 41 0.76
37 7 0.13
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTGTTTTAATAAAACT
Found at i:12533680 original size:2 final size:2
Alignment explanation
Indices: 12533673--12533699 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12533663 TCAGCTTTAT
12533673 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12533700 TCTGAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12535150 original size:3 final size:3
Alignment explanation
Indices: 12535144--12535215 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
12535134 CCTGCAAAAG
12535144 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12535192 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
12535216 TTTTTTCGAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12540321 original size:14 final size:14
Alignment explanation
Indices: 12540284--12540326 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12540274 GTTAAAAGTT
* *
12540284 GAATAAGAATGAAA
1 GAATAAAAATTAAA
*
12540298 CAATACAAAATTAAA
1 GAATA-AAAATTAAA
12540313 GAATAAAAATTAAA
1 GAATAAAAATTAAA
12540327 ATTTATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (14 bp):
GAATAAAAATTAAA
Found at i:12547087 original size:33 final size:33
Alignment explanation
Indices: 12547045--12547114 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
12547035 TGAGGTGTAG
12547045 CTGACGAAGGGTTTTAAAGGTCTCTTTCAACCA
1 CTGACGAAGGGTTTTAAAGGTCTCTTTCAACCA
* *
12547078 CTGACGAAGGGTTTTAAAGGTCTTTTTCGACCA
1 CTGACGAAGGGTTTTAAAGGTCTCTTTCAACCA
12547111 CTGA
1 CTGA
12547115 TGGATGCTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (33 bp):
CTGACGAAGGGTTTTAAAGGTCTCTTTCAACCA
Found at i:12554232 original size:17 final size:18
Alignment explanation
Indices: 12554206--12554243 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12554196 ATGTTGTTCA
12554206 TTAAAGCATGCATTGCAT
1 TTAAAGCATGCATTGCAT
* *
12554224 TTAAA-CATGTATTTCAT
1 TTAAAGCATGCATTGCAT
12554241 TTA
1 TTA
12554244 GGGAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAAAGCATGCATTGCAT
Found at i:12554342 original size:18 final size:18
Alignment explanation
Indices: 12554300--12554344 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12554290 TTCATGCATT
*
12554300 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGG
*
12554318 TAGTTCATTGAATAATGG
1 TAGTTCATTGAATAAAGG
*
12554336 TATTTCATT
1 TAGTTCATT
12554345 AATCAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGG
Found at i:12557178 original size:17 final size:18
Alignment explanation
Indices: 12557152--12557189 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12557142 ATGTTGTTCA
12557152 TTAAAGCATGCATTGCAT
1 TTAAAGCATGCATTGCAT
* *
12557170 TTAAA-CATGTATTTCAT
1 TTAAAGCATGCATTGCAT
12557187 TTA
1 TTA
12557190 GGGAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAAAGCATGCATTGCAT
Found at i:12557268 original size:18 final size:18
Alignment explanation
Indices: 12557245--12557290 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12557235 ATTCATGCAT
12557245 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
12557263 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
12557281 TTATTTCATT
1 TTAGTTCATT
12557291 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:12560117 original size:17 final size:18
Alignment explanation
Indices: 12560091--12560129 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12560081 ATGTTGTTCA
12560091 TTAAAGCATGCATTGCAT
1 TTAAAGCATGCATTGCAT
* *
12560109 TTAAA-CATGTATTTCAT
1 TTAAAGCATGCATTGCAT
12560126 TTAA
1 TTAA
12560130 TAAACTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (18 bp):
TTAAAGCATGCATTGCAT
Found at i:12560174 original size:18 final size:18
Alignment explanation
Indices: 12560151--12560196 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12560141 ATTCATGCAT
12560151 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
12560169 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
12560187 TTATTTCATT
1 TTAGTTCATT
12560197 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:12563032 original size:17 final size:17
Alignment explanation
Indices: 12563007--12563046 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
12562997 GTATGTTGTT
*
12563007 CATTAAAACATGCATTG
1 CATTTAAACATGCATTG
* *
12563024 CATTTAAACATGTATTT
1 CATTTAAACATGCATTG
12563041 CATTTA
1 CATTTA
12563047 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (17 bp):
CATTTAAACATGCATTG
Found at i:12563125 original size:18 final size:18
Alignment explanation
Indices: 12563102--12563147 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12563092 ATTCATGCAT
12563102 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
12563120 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
12563138 TTATTTCATT
1 TTAGTTCATT
12563148 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:12566078 original size:18 final size:18
Alignment explanation
Indices: 12566055--12566100 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12566045 ATTCACGCAT
12566055 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
12566073 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
12566091 TTATTTCATT
1 TTAGTTCATT
12566101 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:12567874 original size:20 final size:21
Alignment explanation
Indices: 12567849--12567896 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
12567839 AAATAATTTT
**
12567849 TATTTTTTTTAAATATAATAA
1 TATTTTTTAAAAATATAATAA
12567870 T-TTTTTTAAAAATATAATAA
1 TATTTTTTAAAAATATAATAA
12567890 TATTTTT
1 TATTTTT
12567897 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTTTAAAAATATAATAA
Found at i:12568258 original size:20 final size:21
Alignment explanation
Indices: 12568225--12568268 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
12568215 TTAATAACTC
*
12568225 TATCTTTATGACATTTTTTTT
1 TATCTTTATGACATATTTTTT
12568246 TATCTTT-TGACATATTTTTT
1 TATCTTTATGACATATTTTTT
12568266 TAT
1 TAT
12568269 TGATTGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (21 bp):
TATCTTTATGACATATTTTTT
Found at i:12568945 original size:8 final size:7
Alignment explanation
Indices: 12568918--12568943 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12568908 GGTTGTTTAC
12568918 AAAAATA
1 AAAAATA
12568925 AAAAATA
1 AAAAATA
12568932 AAAAATA
1 AAAAATA
12568939 AAAAA
1 AAAAA
12568944 ATTGCGAAGG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:12570932 original size:290 final size:293
Alignment explanation
Indices: 12570364--12570950 Score: 794
Period size: 290 Copynumber: 2.0 Consensus size: 293
12570354 TTTTCAAGGC
* * *
12570364 ATGACGTCTTCTTGAAATAGAACTGGCTTTCAATTAACTTTCTAATATATTTTGAAACTTCTCAA
1 ATGACGTCTTCTTGAAATAGAACTGACTTTCAATTAACTTTCTAACATATTTTGAAACTCCTCAA
* *
12570429 TCGGAAATTAAAAACTAATGATATGCTTAATTTAGTGAAGATAACACATGCAATAAAATTAAATA
66 TCAGAAATTAAAAACTAATGATATGCTTAATTAAGTGAAGATAACACATGCAATAAAATTAAATA
* *
12570494 TGAGTCAAATACATAAACTTTATTTAATTACAAATTTTCAATTATTTTATTGATTATTTGTAATT
131 TGAGTCAAATACAGAAACTTTATTTAATTACAAATTTTCAATTATTTTATTGATTATTTATAATT
* * **
12570559 AAGTTCAACTTTATATTTTTTATTATTTATTTTAAAAAATGTATTATCATTTTATTATTTTAATA
196 AAGTTCAACTTTATACTTTCTATTATTTATTTTAAAAAATGTAAGATCATTTTATTATTTTAATA
* *
12570624 TCACTTTTCTTTTAATTAGTGTACCTAGCATTA
261 TCACTTCTATTTTAATTAGTGTACCTAGCATTA
* * * *
12570657 ATGATGTCTTCTTGAGATAGAACTGACTTTCAGTTAGC-TTCTAACATATTTTGAAA-TGCCTCA
1 ATGACGTCTTCTTGAAATAGAACTGACTTTCAATTAACTTTCTAACATATTTTGAAACT-CCTCA
* * ** *
12570720 TTCAGACA-TAAAGAACTCAAT-ATATGCTTAATTAAGTGAAGATAACATGTG-TA-AAAATTAA
65 ATCAGAAATTAAA-AACT-AATGATATGCTTAATTAAGTGAAGATAACACATGCAATAAAATTAA
** * * *
12570781 ATATGAGTCAAATATGGAAATTTTAATTT-ATTACGAATTTTTAATTATTTTATTGATTATTTAT
128 ATATGAGTCAAATACAGAAACTTT-ATTTAATTACAAATTTTCAATTATTTTATTGATTATTTAT
* *
12570845 AATTAAGTTCAACTTTATACTTTCTATTATTTA-TTTAAGAAAATTTAAGATCTTTTTATTATTT
192 AATTAAGTTCAACTTTATACTTTCTATTATTTATTTTAA-AAAATGTAAGATCATTTTATTATTT
**
12570909 TAATATCACTTCTATTTTAATTAGTGTATTTAGCATTA
256 TAATATCACTTCTATTTTAATTAGTGTACCTAGCATTA
12570947 ATGA
1 ATGA
12570951 AAATATGCTA
Statistics
Matches: 258, Mismatches: 31, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
289 5 0.02
290 150 0.58
291 10 0.04
292 57 0.22
293 36 0.14
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (293 bp):
ATGACGTCTTCTTGAAATAGAACTGACTTTCAATTAACTTTCTAACATATTTTGAAACTCCTCAA
TCAGAAATTAAAAACTAATGATATGCTTAATTAAGTGAAGATAACACATGCAATAAAATTAAATA
TGAGTCAAATACAGAAACTTTATTTAATTACAAATTTTCAATTATTTTATTGATTATTTATAATT
AAGTTCAACTTTATACTTTCTATTATTTATTTTAAAAAATGTAAGATCATTTTATTATTTTAATA
TCACTTCTATTTTAATTAGTGTACCTAGCATTA
Found at i:12571235 original size:16 final size:16
Alignment explanation
Indices: 12571214--12571319 Score: 76
Period size: 16 Copynumber: 6.6 Consensus size: 16
12571204 TTTTAATTTA
12571214 TATATATTTATTTATT
1 TATATATTTATTTATT
12571230 TATATATTTATTTA--
1 TATATATTTATTTATT
*
12571244 AATATATCTT-TTTATT
1 TATATAT-TTATTTATT
* * *
12571260 AATATATATATTTATA
1 TATATATTTATTTATT
* * *
12571276 TATTTATATTATTAATA
1 TATATAT-TTATTTATT
12571293 TATATATGATTATTGTA-T
1 TATATAT--TTATT-TATT
12571311 TATATATTT
1 TATATATTT
12571320 CTATTTCTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
14 10 0.14
15 3 0.04
16 33 0.45
17 13 0.18
18 13 0.18
19 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (16 bp):
TATATATTTATTTATT
Found at i:12587226 original size:2 final size:2
Alignment explanation
Indices: 12587212--12587245 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
12587202 AGATGGCCAA
12587212 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
12587246 TACACATCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 28 0.93
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.