Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007718.1 Hibiscus syriacus cultivar Beakdansim tig00109949_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: 1062497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:199003 original size:14 final size:14
Alignment explanation
Indices: 198984--199073 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 14
198974 TTGTGTTCCG
198984 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
198998 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
* *
199014 CGCATTGTGATTTTGC
1 CG--TTGCGATTTTGT
*
199030 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
**
199046 CGCATTTTGATTTTGT
1 CG--TTGCGATTTTGT
199062 CGTTGCGATTTT
1 CGTTGCGATTTT
199074 CATTTCGCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
14 27 0.48
16 14 0.25
18 15 0.27
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:199034 original size:32 final size:32
Alignment explanation
Indices: 198990--199085 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
198980 TCCGCGTTGC
198990 GATTTTGTCGTTGCGATTTCATTTCGCATTGT
1 GATTTTGTCGTTGCGATTTCATTTCGCATTGT
* *
199022 GATTTTGCCGTTGCGATTTCATTTCGCATTTT
1 GATTTTGTCGTTGCGATTTCATTTCGCATTGT
199054 GATTTTGTCGTTGCGATTTTCATTTCGCATTG
1 GATTTTGTCGTTGCGA-TTTCATTTCGCATTG
199086 CGATAGCCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 45 0.76
33 14 0.24
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (32 bp):
GATTTTGTCGTTGCGATTTCATTTCGCATTGT
Found at i:199078 original size:20 final size:19
Alignment explanation
Indices: 199049--199132 Score: 69
Period size: 20 Copynumber: 4.3 Consensus size: 19
199039 TTCATTTCGC
*
199049 ATTTTGATTTTGTCGTTGCG
1 ATTTTCATTTTG-CGTTGCG
* *
199069 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTTGCGTTGCG
***
199088 ATAGCCATTTCTGCGTTGCG
1 ATTTTCATTT-TGCGTTGCG
**
199108 ATAGTCATTTTCGCGTTGCG
1 ATTTTCATTTT-GCGTTGCG
199128 ATTTT
1 ATTTT
199133 AAGTTTCGTG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.27
20 37 0.73
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTTCATTTTGCGTTGCG
Found at i:201019 original size:14 final size:14
Alignment explanation
Indices: 201000--201035 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
200990 ATTGTTTAAT
201000 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
201014 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
201028 TGATTTGT
1 TGATTTGT
201036 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:201175 original size:20 final size:20
Alignment explanation
Indices: 201140--201177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
201130 GCAAAACAGA
*
201140 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
201160 CTATCGCAACTAGAAAAT
1 CTATCGCAACGAGAAAAT
201178 CGCAATGCGA
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:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:201196 original size:19 final size:19
Alignment explanation
Indices: 201172--201220 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
201162 ATCGCAACTA
201172 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
201191 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
201210 GAAAATCGCAA
1 GAAAATCGCAA
201221 CGAAAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:201283 original size:20 final size:20
Alignment explanation
Indices: 201258--201349 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
201248 TCGCATTACG
*
201258 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
201278 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
201299 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
201318 ATTTTCGTGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
201338 ATTTTCGCGTTG
1 ATTTTCGAGTTG
201350 TGATTTCCCC
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 3 0.05
20 51 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:201294 original size:34 final size:36
Alignment explanation
Indices: 201246--201333 Score: 90
Period size: 40 Copynumber: 2.4 Consensus size: 36
201236 GCGATTTTCA
* * *
201246 TTTCGCATTACGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
201280 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
*
201320 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
201334 AGCCATTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 11 0.25
35 5 0.11
38 1 0.02
39 1 0.02
40 26 0.59
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.43
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:201344 original size:40 final size:41
Alignment explanation
Indices: 201258--201344 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
201248 TCGCATTACG
* * ***
201258 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
201299 A-TTTCGAATTGCGATAGCCATTTTCGTGTTGCGA-TAGCC
1 ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
201338 ATTTTCG
1 ATTTTCG
201345 CGTTGTGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.08
40 35 0.90
41 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.43
Consensus pattern (41 bp):
ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
Found at i:201592 original size:20 final size:20
Alignment explanation
Indices: 201567--201658 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
201557 TTGAAGATGA
201567 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
201587 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
201607 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
201628 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
201648 TTGCGATTTTC
1 TTGCGATTTTC
201659 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:201687 original size:20 final size:21
Alignment explanation
Indices: 201643--201690 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
201633 ATAGTCAGTA
*
201643 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
201664 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
201684 TCGCATT
1 TCGCATT
201691 TCGAATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:202505 original size:24 final size:24
Alignment explanation
Indices: 202478--202531 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
202468 GTATTCGAAA
*
202478 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
202502 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
202526 TTTGAT
1 TTTGAT
202532 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:202723 original size:12 final size:12
Alignment explanation
Indices: 202706--202730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
202696 ATATAATCCT
202706 GAAGAAGAAAAA
1 GAAGAAGAAAAA
202718 GAAGAAGAAAAA
1 GAAGAAGAAAAA
202730 G
1 G
202731 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:205039 original size:19 final size:19
Alignment explanation
Indices: 205017--205147 Score: 67
Period size: 19 Copynumber: 7.7 Consensus size: 19
205007 GAAAATTACT
*
205017 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
205036 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
205050 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
205069 ATCACAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
205083 TTTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
205102 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
205116 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
205135 ATCGCAACGCGAA
1 ATCGCAATGCGAA
205148 TTTTATTTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 6 0.08
17 6 0.08
18 3 0.04
19 36 0.46
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:205064 original size:33 final size:33
Alignment explanation
Indices: 205017--205143 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
205007 GAAAATTACT
*
205017 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
205050 ATCGCAATGCGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
205082 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
205116 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
205144 CGAATTTTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:205128 original size:66 final size:66
Alignment explanation
Indices: 205022--205151 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
205012 TTACTATCGT
*
205022 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAATTTTG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTTG
205087 C
66 C
* *
205088 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTT
205152 ATTTCGCGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTTG
C
Found at i:205175 original size:14 final size:14
Alignment explanation
Indices: 205158--205214 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
205148 TTTTATTTCG
205158 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
205172 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
205191 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
205205 CGTTGTGATT
1 CGTTGCGATT
205215 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:205189 original size:33 final size:33
Alignment explanation
Indices: 205147--205232 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
205137 CGCAACGCGA
205147 ATTTT-ATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCG
*
205179 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGTG
1 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCG
*
205212 ATTTTCATTTCGCATTGCGAT
1 ATTTTCATTTCGCGTTGCGAT
205233 AGTACGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 5 0.10
33 46 0.90
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.48
Consensus pattern (33 bp):
ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCG
Found at i:205196 original size:19 final size:19
Alignment explanation
Indices: 205172--205232 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
205162 GCGATTCTCT
205172 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
205191 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
205205 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
205224 CATTGCGAT
1 CGTTGCGAT
205233 AGTACGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 9 0.28
16 3 0.09
17 3 0.09
19 17 0.53
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:205358 original size:14 final size:14
Alignment explanation
Indices: 205339--205375 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
205329 CATCAATTAA
205339 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
205353 ACAAATCACCTTTT
1 ACAAATCAACTTTT
205367 ACAAATCAA
1 ACAAATCAA
205376 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:206789 original size:42 final size:41
Alignment explanation
Indices: 206730--206923 Score: 158
Period size: 42 Copynumber: 4.6 Consensus size: 41
206720 GTGAATCGGG
* *
206730 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
206772 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
206814 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATTACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
206856 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * *
206898 CTCTTCAACGATAGGAGTGGACTCTT
1 CTCTTGAACGGTGGGAG-GGACTCTT
206924 GAGGGATAAC
Statistics
Matches: 118, Mismatches: 26, Indels: 15
0.74 0.16 0.09
Matches are distributed among these distances:
41 9 0.08
42 100 0.85
43 9 0.08
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:206796 original size:21 final size:21
Alignment explanation
Indices: 206730--206796 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
206720 GTGAATCGGG
*
206730 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
206750 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
206772 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
206793 CTCT
1 CTCT
206797 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:206871 original size:84 final size:84
Alignment explanation
Indices: 206764--206935 Score: 335
Period size: 84 Copynumber: 2.0 Consensus size: 84
206754 TTCAACGATG
206764 ACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGG
1 ACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGG
*
206829 AGTGGACTCTTGAGGGATT
66 AGTGGACTCTTGAGGGATA
206848 ACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGG
1 ACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGG
206913 AGTGGACTCTTGAGGGATA
66 AGTGGACTCTTGAGGGATA
206932 ACAG
1 ACAG
206936 GCGAGTTGGG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (84 bp):
ACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGG
AGTGGACTCTTGAGGGATA
Found at i:206931 original size:21 final size:21
Alignment explanation
Indices: 206823--206931 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
206813 CCTCTTCAAC
206823 GATAGGAGTGGACTCTTGAGG
1 GATAGGAGTGGACTCTTGAGG
* * *
206844 GATTA-CAGTGGCCTCTTGAACG
1 GA-TAGGAGTGGACTCTTG-AGG
* * *
206866 G-TGGGAGGGGACTCTCGAGG
1 GATAGGAGTGGACTCTTGAGG
* * * * * **
206886 AAT-GATAGGGGCCTCTTCAAC
1 GATAG-GAGTGGACTCTTGAGG
206907 GATAGGAGTGGACTCTTGAGG
1 GATAGGAGTGGACTCTTGAGG
206928 GATA
1 GATA
206932 ACAGGCGAGT
Statistics
Matches: 59, Mismatches: 23, Indels: 12
0.63 0.24 0.13
Matches are distributed among these distances:
20 4 0.07
21 49 0.83
22 6 0.10
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.23
Consensus pattern (21 bp):
GATAGGAGTGGACTCTTGAGG
Found at i:207327 original size:91 final size:90
Alignment explanation
Indices: 207152--207336 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
207142 ATTTCAAACT
*
207152 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
207217 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
207245 TTCAAGCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
207309 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
207336 T
1 T
207337 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:208977 original size:19 final size:19
Alignment explanation
Indices: 208913--209077 Score: 161
Period size: 19 Copynumber: 9.1 Consensus size: 19
208903 TCTTTTGGTT
*
208913 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
208932 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
208952 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
**
208972 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
208989 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
209005 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
209024 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
209041 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
209057 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
209076 GA
1 GA
209078 TTTTGGTTTC
Statistics
Matches: 124, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
14 19 0.15
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 61 0.49
20 30 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:209021 original size:52 final size:52
Alignment explanation
Indices: 208938--209077 Score: 226
Period size: 52 Copynumber: 2.7 Consensus size: 52
208928 ACGAGATAAT
** **
208938 GAGAATCGCAACGCGGAAATGACTATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
208991 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
209043 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGA
209078 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 68 0.83
53 14 0.17
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:209095 original size:19 final size:19
Alignment explanation
Indices: 209073--209120 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
209063 AAAATCGCAA
*
209073 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
209092 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
209112 TGCGATTTT
1 TGCGATTTT
209121 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:209663 original size:20 final size:20
Alignment explanation
Indices: 209638--209690 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
209628 GCGCTATGTA
209638 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
209658 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
209678 TATCTCGTTGCGA
1 AATCGCGTTGCGA
209691 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:209843 original size:21 final size:21
Alignment explanation
Indices: 209803--209843 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
209793 ACTGTAGACC
**
209803 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
209824 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
209844 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:212418 original size:30 final size:30
Alignment explanation
Indices: 212383--212540 Score: 194
Period size: 30 Copynumber: 5.3 Consensus size: 30
212373 TAAATTTACT
*
212383 GGACTAAAATAACAAAAACAGAAACTTAAA
1 GGACTAAAATAGCAAAAACAGAAACTTAAA
* *
212413 TGACTAAAATAGCAAAAACTGAAACTTAAA
1 GGACTAAAATAGCAAAAACAGAAACTTAAA
** *
212443 GGGTTAAAATAGCAAAAACATAAA-TTAAAA
1 GGACTAAAATAGCAAAAACAGAAACTT-AAA
*
212473 GGACTAAAATAGCAAAAACTA-AAACTTAAG
1 GGACTAAAATAGCAAAAAC-AGAAACTTAAA
* * *
212503 GGATTAAAATAGTAAAAACATAAACTTAAA
1 GGACTAAAATAGCAAAAACAGAAACTTAAA
212533 GGACTAAA
1 GGACTAAA
212541 TAGTAAATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.03
30 103 0.94
31 3 0.03
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.18
Consensus pattern (30 bp):
GGACTAAAATAGCAAAAACAGAAACTTAAA
Found at i:212423 original size:60 final size:60
Alignment explanation
Indices: 212387--212540 Score: 229
Period size: 60 Copynumber: 2.6 Consensus size: 60
212377 TTTACTGGAC
* * * * *
212387 TAAAATAACAAAAACAGAAACTTAAATGACTAAAATAGCAAAAACTGAAACTTAAAGGGT
1 TAAAATAGCAAAAACATAAACTTAAAGGACTAAAATAGCAAAAACTAAAACTTAAAGGAT
*
212447 TAAAATAGCAAAAACATAAA-TTAAAAGGACTAAAATAGCAAAAACTAAAACTTAAGGGAT
1 TAAAATAGCAAAAACATAAACTT-AAAGGACTAAAATAGCAAAAACTAAAACTTAAAGGAT
*
212507 TAAAATAGTAAAAACATAAACTTAAAGGACTAAA
1 TAAAATAGCAAAAACATAAACTTAAAGGACTAAA
212541 TAGTAAATAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.02
60 81 0.95
61 2 0.02
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (60 bp):
TAAAATAGCAAAAACATAAACTTAAAGGACTAAAATAGCAAAAACTAAAACTTAAAGGAT
Found at i:212445 original size:90 final size:90
Alignment explanation
Indices: 212351--212547 Score: 240
Period size: 90 Copynumber: 2.2 Consensus size: 90
212341 TTAATAAAAT
* * ** *
212351 AAGGGATTAAATAGTAATAACATAAATTTACTGGACTAAAATAACAAAAAC-AGAAACTTAAATG
1 AAGGGATTAAATAGTAAAAACATAAATTAAAAGGACTAAAATAACAAAAACTA-AAACTTAAAGG
212415 ACTAAAATAGCAAAAAC-TGAAACTTA
65 ACTAAAATAGCAAAAACAT-AAACTTA
* * *
212441 AAGGG-TTAAAATAGCAAAAACATAAATTAAAAGGACTAAAATAGCAAAAACTAAAACTTAAGGG
1 AAGGGATT-AAATAGTAAAAACATAAATTAAAAGGACTAAAATAACAAAAACTAAAACTTAAAGG
* *
212505 ATTAAAATAGTAAAAACATAAACTTA
65 ACTAAAATAGCAAAAACATAAACTTA
*
212531 AA-GGACTAAATAGTAAA
1 AAGGGATTAAATAGTAAA
212548 TAAAGAAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
89 13 0.14
90 76 0.84
91 2 0.02
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (90 bp):
AAGGGATTAAATAGTAAAAACATAAATTAAAAGGACTAAAATAACAAAAACTAAAACTTAAAGGA
CTAAAATAGCAAAAACATAAACTTA
Found at i:212493 original size:15 final size:15
Alignment explanation
Indices: 212447--212496 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
212437 CTTAAAGGGT
212447 TAAAATAGCAAAAAC
1 TAAAATAGCAAAAAC
* *
212462 ATAAATTA--AAAGGAC
1 -TAAAATAGCAAA-AAC
212477 TAAAATAGCAAAAAC
1 TAAAATAGCAAAAAC
212492 TAAAA
1 TAAAA
212497 CTTAAGGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 9 0.33
15 9 0.33
16 9 0.33
ACGTcount: A:0.66, C:0.10, G:0.08, T:0.16
Consensus pattern (15 bp):
TAAAATAGCAAAAAC
Found at i:214126 original size:25 final size:25
Alignment explanation
Indices: 214088--214136 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
214078 TTTCTTTCAT
*
214088 TATCCCTTGGCAAAAGAAGAAAATA
1 TATCCCTTGACAAAAGAAGAAAATA
* *
214113 TATCCCTTTACAAAAGGAGAAAAT
1 TATCCCTTGACAAAAGAAGAAAAT
214137 TAATCTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (25 bp):
TATCCCTTGACAAAAGAAGAAAATA
Found at i:214348 original size:31 final size:31
Alignment explanation
Indices: 214304--214400 Score: 92
Period size: 33 Copynumber: 3.1 Consensus size: 31
214294 CGAAGCAAAG
*
214304 AAAAAAAAAGAAAAAGCAAAGAGAAAAAAAAGC
1 AAAAGAAAAGAAAAAGCAAAGA-AAAAAAAA-C
* *
214337 -AAAG-AAAGAAAAATGTAAA-AACAAAAAAC
1 AAAAGAAAAGAAAAA-GCAAAGAAAAAAAAAC
*
214366 AAAAGAAAAGAAAAAAAGCAAAGAAAAAAAGAC
1 AAAAGAAAAG--AAAAAGCAAAGAAAAAAAAAC
214399 AA
1 AA
214401 GAAGCACATG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
29 1 0.02
30 11 0.21
31 14 0.27
32 11 0.21
33 15 0.29
ACGTcount: A:0.78, C:0.06, G:0.13, T:0.02
Consensus pattern (31 bp):
AAAAGAAAAGAAAAAGCAAAGAAAAAAAAAC
Found at i:214382 original size:13 final size:13
Alignment explanation
Indices: 214353--214403 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
214343 AGAAAAATGT
*
214353 AAAAACAAAA-AA
1 AAAAAGAAAAGAA
*
214365 CAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
214378 AAAAAGCAAAGAA
1 AAAAAGAAAAGAA
*
214391 AAAAAGACAAGAA
1 AAAAAGAAAAGAA
214404 GCACATGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 8 0.25
13 24 0.75
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:214382 original size:26 final size:26
Alignment explanation
Indices: 214353--214403 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
214343 AGAAAAATGT
214353 AAAAACAAA-AAACAAAAGAAAAGAAA
1 AAAAACAAAGAAA-AAAAGAAAAGAAA
* *
214379 AAAAGCAAAGAAAAAAAGACAAGAA
1 AAAAACAAAGAAAAAAAGAAAAGAA
214404 GCACATGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (26 bp):
AAAAACAAAGAAAAAAAGAAAAGAAA
Found at i:214390 original size:44 final size:44
Alignment explanation
Indices: 214308--214393 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 44
214298 GCAAAGAAAA
* *
214308 AAAAAGAAAAAGCAAAGAGAAAAAAAAGCAAAGAAAGAAAAATGT
1 AAAAACAAAAAACAAAGAGAAAAAAAA-CAAAGAAAGAAAAATGT
214353 AAAAACAAAAAACAAA-AGAAAAGAAAA-AAAGCAAAGAAAAA
1 AAAAACAAAAAACAAAGAGAAAA-AAAACAAAG-AAAGAAAAA
214394 AAGACAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
43 4 0.11
44 15 0.41
45 18 0.49
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (44 bp):
AAAAACAAAAAACAAAGAGAAAAAAAACAAAGAAAGAAAAATGT
Found at i:214403 original size:31 final size:31
Alignment explanation
Indices: 214309--214403 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 31
214299 CAAAGAAAAA
*
214309 AAAAG-AAAAAGCAAAGAGAAAAAAAAGCAA-
1 AAAAGAAAAAAGCAAAGACAAAAAAAA-CAAG
* * *
214339 AGAAAGAAAAATGTAAAAACAAAAAACAA-AAG
1 A-AAAGAAAAAAGCAAAGACAAAAAA-AACAAG
*
214371 AAAAGAAAAAAAGCAAAGA-AAAAAAGACAAG
1 AAAAG-AAAAAAGCAAAGACAAAAAAAACAAG
214402 AA
1 AA
214404 GCACATGCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
30 2 0.04
31 21 0.41
32 26 0.51
33 2 0.04
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (31 bp):
AAAAGAAAAAAGCAAAGACAAAAAAAACAAG
Found at i:215406 original size:20 final size:20
Alignment explanation
Indices: 215381--215420 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
215371 GTGGATCTTG
*
215381 GTAGTTGACATGCGGCTCTC
1 GTAGTTGACATACGGCTCTC
215401 GTAGTTGACATACGGCTCTC
1 GTAGTTGACATACGGCTCTC
215421 AGACACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (20 bp):
GTAGTTGACATACGGCTCTC
Found at i:215895 original size:37 final size:36
Alignment explanation
Indices: 215811--215897 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
215801 TTTGAGATTG
*
215811 TTTCTTGAAACAAATTTTGTCTCCCTTGATACAATT
1 TTTCTTGAAACAAATTTTGTCTCCCTTGAGACAATT
* * * ** *
215847 TCTATTTAAACAAAGTTTTGTCTTTCTTGAGACAGTT
1 TTTCTTGAAACAAA-TTTTGTCTCCCTTGAGACAATT
215884 TTTCTTGAAACAAA
1 TTTCTTGAAACAAA
215898 ATCTTTGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
36 11 0.28
37 29 0.73
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTCTTGAAACAAATTTTGTCTCCCTTGAGACAATT
Found at i:215997 original size:21 final size:21
Alignment explanation
Indices: 215949--215998 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
215939 TAAGACAGTT
* *
215949 TCCCTTAAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTCGTC
*
215970 TCCCTTGAAATAAATTTCGTC
1 TCCCTTGAAACAAATTTCGTC
215991 TCCCTTGA
1 TCCCTTGA
215999 GATAGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTCGTC
Found at i:216006 original size:57 final size:58
Alignment explanation
Indices: 215925--216035 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
215915 CCTTTAAACG
* *
215925 AATTTTGTCTCTCTTAAGACAGTTTCCCTTAAAACAAA-TTTTGTCTCCCTTGAAATA
1 AATTTCGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCCCTTGAAATA
* * * * *
215982 AATTTCGTCTCCCTTGAGATAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGA
1 AATTTCGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCCCTTGA
216036 GAGAGTTTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 32 0.70
58 14 0.30
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (58 bp):
AATTTCGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCCCTTGAAATA
Found at i:216113 original size:34 final size:35
Alignment explanation
Indices: 215970--216189 Score: 217
Period size: 34 Copynumber: 6.4 Consensus size: 35
215960 AAATTTTGTC
* * *
215970 TCCCTTGAAATAAATTTCGTCTCCCTTGAGATAGTT
1 TCCCTTGAAACAAATTTTG-CTCTCTTGAGATAGTT
* *
216006 TCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAGAGTT
1 TCCCTTGAAACAAA-TTTTG-CTCTCTTGAGATAGTT
*
216043 TCCCTTGAAACAAA-----ATCT-TTGA-ATATGTT
1 TCCCTTGAAACAAATTTTGCTCTCTTGAGATA-GTT
*
216072 TCCCTTGAAACAAATTTTG-TCTCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGCTCTCTTGAGATAGTT
* * *
216106 TCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTG-CTCTCTTGAGATAGTT
*
216142 T-CCTTGAAA-AAGTTTTGTCTCTCTTGAGATAGTT
1 TCCCTTGAAACAAATTTTG-CTCTCTTGAGATAGTT
216176 TCCCTTGAAACAAA
1 TCCCTTGAAACAAA
216190 ATCTTTGAAT
Statistics
Matches: 157, Mismatches: 14, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
28 2 0.01
29 21 0.13
30 3 0.02
33 3 0.02
34 49 0.31
35 17 0.11
36 30 0.19
37 32 0.20
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (35 bp):
TCCCTTGAAACAAATTTTGCTCTCTTGAGATAGTT
Found at i:216131 original size:21 final size:21
Alignment explanation
Indices: 216106--216168 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
216096 TGAGACAGTT
216106 TCTCTTGAAACAAGTTTTGTC
1 TCTCTTGAAACAAGTTTTGTC
*
216127 TCTCTTGAGAC-AG---T-T-
1 TCTCTTGAAACAAGTTTTGTC
216142 TC-CTTGAAA-AAGTTTTGTC
1 TCTCTTGAAACAAGTTTTGTC
216161 TCTCTTGA
1 TCTCTTGA
216169 GATAGTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 15
0.66 0.04 0.30
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 1 0.03
17 2 0.06
18 1 0.03
19 2 0.06
20 7 0.21
21 10 0.30
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAGTTTTGTC
Found at i:216144 original size:99 final size:100
Alignment explanation
Indices: 215970--216150 Score: 294
Period size: 99 Copynumber: 1.8 Consensus size: 100
215960 AAATTTTGTC
* *
215970 TCCCTTGAAATAAATTTCGTCTCCCTTGAGATAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTG
1 TCCCTTGAAACAAATTTCGTCT-CCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTG
*
216035 AGAGAGTTTCCCTTGAAACAAAATCTTTGAATATGTT
65 AGACAGTTT-CCTTGAAACAAAATCTTTGAATATGTT
*
216072 TCCCTTGAAACAAATTTTGTCT-CTTGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGA
1 TCCCTTGAAACAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGA
216135 GACAGTTTCCTTGAAA
66 GACAGTTTCCTTGAAA
216151 AAGTTTTGTC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
98 8 0.11
99 25 0.33
100 22 0.29
102 20 0.27
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (100 bp):
TCCCTTGAAACAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGA
GACAGTTTCCTTGAAACAAAATCTTTGAATATGTT
Found at i:216635 original size:91 final size:90
Alignment explanation
Indices: 216467--216917 Score: 671
Period size: 91 Copynumber: 5.0 Consensus size: 90
216457 AGATAAACCA
* * *
216467 ATCAACATTTCCAGCGGGGAGTTCATAATGA-AAGAACTCATCCGACG-TGGAGAAGAAGTTCAT
1 ATCAACATTTCCAG-TGGGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTCAT
216530 AATGAGAAGAACTTGTTCAACCTTGC
65 AATGAGAAGAACTTGTTCAACCTTGC
* *
216556 ATCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTTATCCGAAGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTG-GGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTCAT
216621 AATGAGAAGAACTTGTTCAACCTTGC
65 AATGAGAAGAACTTGTTCAACCTTGC
* *
216647 ATAAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-AACGAGGGAGAAGAAGTTTA
1 ATCAACATTTCCAGTGG-GAGTTCATAATGAGAAGAACTCATCCGAA-GAGGGAGAAGAAGTTCA
216711 TAATGAGAAGAACTTGTTCAACCTTGC
64 TAATGAGAAGAACTTGTTCAACCTTGC
* * * * *
216738 ATCAGCAATTCCAGTTGAGAGTTCATAATGAGAAGAACTCAT-CTAATGAGGGAGAAGAAGTTCC
1 ATCAACATTTCCAG-TGGGAGTTCATAATGAGAAGAACTCATCCGAA-GAGGGAGAAGAAGTTCA
216802 TAATGAGAAGAACTTGTTCAACCTTGGC
64 TAATGAGAAGAACTTGTTCAACCTT-GC
216830 -TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGG-GAGTTCATAATGAGAAGAACTCATCCGA-AGAGGGAGAAGAAGTTCA
216893 TAATGAGAAGAACTTGTTCAACCTT
64 TAATGAGAAGAACTTGTTCAACCTT
216918 AGCTCGATTC
Statistics
Matches: 331, Mismatches: 20, Indels: 20
0.89 0.05 0.05
Matches are distributed among these distances:
88 1 0.00
89 28 0.08
90 20 0.06
91 275 0.83
92 6 0.02
93 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (90 bp):
ATCAACATTTCCAGTGGGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGC
Found at i:216911 original size:20 final size:19
Alignment explanation
Indices: 216849--216912 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
216839 CCAGTGGAGA
216849 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
216868 CATCCGATAAGGGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
216888 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
216908 GTTCA
1 GTTCA
216913 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:216984 original size:116 final size:114
Alignment explanation
Indices: 216830--217047 Score: 339
Period size: 116 Copynumber: 1.9 Consensus size: 114
216820 CAACCTTGGC
*
216830 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCATA
216895 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACCGAATAAATCGA
66 ATGAGAAGAACTTGTTCAACCTT-GCT-GATTCCATCACCGAATAAATCGA
* * *
216946 TCAATATTTCCAGTAGG-GAGTTCATAATGAGAATAACTCATCCAATGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGT-GGAGAGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCAT
* * *
217010 AATGAGAAGAATTTGTTCGACCTTGGTGATTCCATCAC
65 AATGAGAAGAACTTGTTCAACCTTGCTGATTCCATCAC
217048 ATAAGGAAGT
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
114 11 0.12
115 2 0.02
116 79 0.84
117 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (114 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCTGATTCCATCACCGAATAAATCGA
Found at i:219428 original size:3 final size:3
Alignment explanation
Indices: 219420--219456 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
219410 ATTTTTAATT
219420 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
219457 CCAAATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:219903 original size:123 final size:123
Alignment explanation
Indices: 219686--220186 Score: 442
Period size: 109 Copynumber: 4.3 Consensus size: 123
219676 GTTGAACAAA
* ** *
219686 TTCTT-CTTTTTCAGATGAGTTCTTCTCATTATGAAC-TCTTCTGGATATGTTGATGCTGATCTA
1 TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAACTTC-TCTGGAAATGTTGATGCTGATCTA
* *** **
219749 TCTCCTTCTGTGGTAGCGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
65 TCTACTTCTGTAACAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
219808 TTCTTCC-TCTTCAGAAAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTA
1 TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAAC-TTCTCTGGAAATGTTGATGCTGATCTA
* * *
219872 TCTATTTCTGTAACAGAATCTAGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
65 TCTACTTCTGTAACAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
**
219931 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTACTGGAAATGTTGAT-C----C-A
1 TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAACTTCT-CTGGAAATGTTGATGCTGATCTA
* * *
219989 TCGA---ATG--A-TGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATG---TTC
65 TCTACTTCTGTAACAGAA-TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
** * *
220040 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTATTGGAAA---T-A--CTGATCCA
1 TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAACTTCT-CTGGAAATGTTGATGCTGATCTA
* * *
220098 TCGA---ATG--A-TGAATTCGAGCAAAAGGTTG---AAGTTCTTCTCATTATGAACTTC
65 TCTACTTCTGTAACAGAA-TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
**
220149 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAACT
220187 CTACCTGGCA
Statistics
Matches: 339, Mismatches: 25, Indels: 42
0.83 0.06 0.10
Matches are distributed among these distances:
104 1 0.00
105 1 0.00
106 18 0.05
108 1 0.00
109 119 0.35
111 3 0.01
112 34 0.10
114 2 0.01
117 4 0.01
118 1 0.00
122 34 0.10
123 92 0.27
124 29 0.09
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (123 bp):
TTCTTCCTTCTTCAGAAAAGTTCTTCTCATTATGAACTTCTCTGGAAATGTTGATGCTGATCTAT
CTACTTCTGTAACAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:220204 original size:109 final size:110
Alignment explanation
Indices: 219767--220216 Score: 529
Period size: 109 Copynumber: 4.0 Consensus size: 110
219757 TGTGGTAGCG
**
219767 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAAAAGTTCT
1 TCGAGCAAAAGGTTG-A-AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
219831 TCTCATTATGAACTTTCT-CTGGAAAAGTTGATGTTGATCTATCTATTTCTGTAACAGAA-
64 TCTCATTATGAAC--TCTACTGG--AA----ATGTTGATCCATCGA---ATG--A-TGAAT
* *
219890 TCTAGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTG-A-AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
219955 TCTCATTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAAT
64 TCTCATTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAAT
220002 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATG---TTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTG-A-AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* **
220064 TCTCATTATGAACTCTATTGGAAATACTGATCCATCGAATGATGAAT
64 TCTCATTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAAT
220111 TCGAGCAAAAGGTTG-AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 TCGAGCAAAAGGTTGAAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
220175 TCATTATGAACTCTACCTGG-CATGTTGATCCATTGAGTGATG
66 TCATTATGAACTCTA-CTGGAAATGTTGATCCATCGAATGATG
220217 GATTTGAATC
Statistics
Matches: 301, Mismatches: 19, Indels: 28
0.86 0.05 0.08
Matches are distributed among these distances:
106 17 0.06
109 147 0.49
110 3 0.01
111 3 0.01
112 34 0.11
114 2 0.01
117 13 0.04
121 2 0.01
122 3 0.01
123 50 0.17
124 27 0.09
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (110 bp):
TCGAGCAAAAGGTTGAAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAAT
Found at i:220603 original size:22 final size:22
Alignment explanation
Indices: 220575--220629 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
220565 AATAAAGCAT
220575 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
220597 TCATCTTTGGAGAGTGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
220619 TCATCTTTGAA
1 TCATCTTTGAA
220630 TAATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:222084 original size:75 final size:74
Alignment explanation
Indices: 221951--222109 Score: 228
Period size: 75 Copynumber: 2.1 Consensus size: 74
221941 GATTTGGATC
* *
221951 TTCAACATGCCCCAACATTGGCTAATACAAACGTTTAAAATACATCAACATTCCTGATTCTAATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATT-TAATT
*
222016 GAAAGGGGCT
65 GAAAAGGGCT
* * * * * *
222026 TTCAGCATGCCCCAGCATTGGCTAATACATATGTTCAAAATACATCAATATTCTTGATTTGATTG
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTTAATTG
222091 AAAAGGGCT
66 AAAAGGGCT
222100 TTCAGCATGC
1 TTCAGCATGC
222110 TCTATCATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 23 0.31
75 52 0.69
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (74 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTTAATTG
AAAAGGGCT
Found at i:229599 original size:17 final size:17
Alignment explanation
Indices: 229577--229610 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
229567 GGCATTTATT
*
229577 TAAATAAAAAAATAAAA
1 TAAATAAAAAAACAAAA
229594 TAAATAAAAAAACAAAA
1 TAAATAAAAAAACAAAA
229611 GTTAGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
TAAATAAAAAAACAAAA
Found at i:230114 original size:30 final size:30
Alignment explanation
Indices: 230080--230167 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 30
230070 TAAAAACATT
230080 AATAAAAATAATATATATAAATATTATGAA
1 AATAAAAATAATATATATAAATATTATGAA
* * *
230110 AATAATAAGT-ATATATA-AAAAATTTTGAA
1 AATAA-AAATAATATATATAAATATTATGAA
* * *
230139 AAGAAAAA-ATTATAAATTAAATA-TATGAA
1 AATAAAAATAATATATA-TAAATATTATGAA
230168 TTTTTAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
28 7 0.16
29 19 0.42
30 16 0.36
31 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (30 bp):
AATAAAAATAATATATATAAATATTATGAA
Found at i:230122 original size:24 final size:24
Alignment explanation
Indices: 230059--230122 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
230049 ATTTAATACT
*
230059 TGAAAATAA-AATAAAAACATTAA
1 TGAAAATAATAATATAAACATTAA
* *
230082 TAAAAATAATATATATAAATATT-A
1 TGAAAATAATA-ATATAAACATTAA
230106 TGAAAATAATAAGTATA
1 TGAAAATAATAA-TATA
230123 TATAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.26
24 16 0.47
25 9 0.26
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (24 bp):
TGAAAATAATAATATAAACATTAA
Found at i:230802 original size:22 final size:22
Alignment explanation
Indices: 230777--230819 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
230767 ATAGATTAAT
230777 ATATATAATTTA-TAAAAATAAG
1 ATAT-TAATTTATTAAAAATAAG
*
230799 ATATTTATTTATTTAAAAATA
1 ATATTAATTTA-TTAAAAATA
230820 TCATAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTAATTTATTAAAAATAAG
Found at i:230912 original size:137 final size:136
Alignment explanation
Indices: 230628--231029 Score: 381
Period size: 137 Copynumber: 2.9 Consensus size: 136
230618 TAATTTTAAG
* *
230628 AAAATATATTAATTTTTAT-ATTT-TATAAATAAGATATTTATTTATTTTTAAAATAC-TAGAAT
1 AAAATATATTAATATATATAATTTATATAAATAAGATATTTATTTATTTTTAAAATACATA-AA-
* *
230690 AGGACATCTAGTTGCT-TTAAGACTGTCATTTTCTTAATATTAAAAATAAATAAATATTAAAACA
64 AGGACATCTAGTT-ATGTTAAGACTCTCA-TTTCTTAATATTAAAAATAAATAAATATTAAAACA
**
230754 TTTTTCTAAA
127 TTGATCTAAA
* * *
230764 AAAATAGATTAATATATATAATTTATAAAAATAAGATATTTATTTA-TTTAAAAATATCATAAAA
1 AAAATATATTAATATATATAATTTATATAAATAAGATATTTATTTATTTTTAAAATA-CATAAAA
*
230828 GGACATCCAGTTATGTTAAGACTACTC-TTTCTTAATATTGAAAAATAAATAAATATTAAAACA-
65 GGACATCTAGTTATGTTAAGACT-CTCATTTCTTAATATT-AAAAATAAATAAATATTAAAACAT
230891 TGAT-TAAA
128 TGATCTAAA
* * ** * *
230899 ATAATTTATATTAAATTAAATATATATTTTATATAAGCATGATATTTATTTATTTTTAATATACC
1 A-AA-ATATATT-AA-T--ATATATAATTTATATAAATAAGATATTTATTTATTTTTAAAATA-C
* * * * * *
230964 AGAATAGGATATCTTGTTATGTTAAAACTGC-CATTTTCTTAATATTTTAAAAATAAACAAATAT
59 ATAAAAGGACATCTAGTTATGTTAAGACT-CTCA-TTTCTTAATA--TTAAAAATAAATAAATAT
231028 TA
120 TA
231030 TTAATTTTTA
Statistics
Matches: 220, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
135 5 0.02
136 33 0.15
137 61 0.28
138 27 0.12
139 3 0.01
141 29 0.13
142 33 0.15
143 10 0.05
144 17 0.08
145 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (136 bp):
AAAATATATTAATATATATAATTTATATAAATAAGATATTTATTTATTTTTAAAATACATAAAAG
GACATCTAGTTATGTTAAGACTCTCATTTCTTAATATTAAAAATAAATAAATATTAAAACATTGA
TCTAAA
Found at i:231051 original size:27 final size:27
Alignment explanation
Indices: 231002--231088 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
230992 TGCCATTTTC
*
231002 TTAATATTTTAAAAATAAACAAATATTA
1 TTAAT-TTTTAAAAATAAACAAATAATA
* *
231030 TTAATTTTTAAAATTAATCAAATAATA
1 TTAATTTTTAAAAATAAACAAATAATA
* **
231057 TAAATTAATAAAAATAAA-ATAATAATAA
1 TTAATTTTTAAAAATAAACA-AATAAT-A
231085 TTAA
1 TTAA
231089 AATATTAAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
26 1 0.02
27 38 0.79
28 9 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTAATTTTTAAAAATAAACAAATAATA
Found at i:231061 original size:18 final size:15
Alignment explanation
Indices: 231038--231110 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 15
231028 TATTAATTTT
231038 TAAAATTAATCAAATAA
1 TAAAATTAAT-AAA-AA
231055 TATAAATTAATAAAAA
1 TA-AAATTAATAAAAA
*
231071 TAAAA-TAATAATAAT
1 TAAAATTAATAA-AAA
*
231086 TAAAA-TATTAAACATA
1 TAAAATTAATAAA-A-A
231102 TAAAATTAA
1 TAAAATTAA
231111 AATATATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.15
15 16 0.34
16 9 0.19
17 7 0.15
18 8 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATTAATAAAAA
Found at i:236100 original size:24 final size:24
Alignment explanation
Indices: 236073--236178 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 24
236063 AAACGGAGAT
236073 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACATAATTCAG
* * * *
236097 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACATAATTCAG
* * * * * *
236121 GTTAGGAATCAGAACATATTTCAT
1 ATCAGAAATCAAAACATAATTCAG
* ** *
236145 ATAAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAG
236169 ATCAGAAATC
1 ATCAGAAATC
236179 GGATAAATTA
Statistics
Matches: 59, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATTCAG
Found at i:239661 original size:212 final size:215
Alignment explanation
Indices: 239278--239704 Score: 824
Period size: 212 Copynumber: 2.0 Consensus size: 215
239268 ATGTTGCATT
239278 GTACTTACCTCATATTAATTAAAACAATTCTATATATATATATATATAAAATTTATAACATGAAA
1 GTACTTACCTCATATTAATTAAAACAATTCTATATATATATATATATAAAATTTATAACATGAAA
239343 ATATTAATTTAATTTATATATATTTAAATATTTAAAATTTTAAAATAGTTATTTTTTAGAAAATA
66 ATATTAATTTAATTTATATATATTTAAATATTTAAAATTTTAAAATAGTTATTTTTTAGAAAATA
*
239408 TTTATAACATGAAAATTTTCATTTAATTTAATATATATATATATTAAAAATTATAATTTAAATCT
131 TTTATAACAAGAAAATTTTCATTTAATTTAATATATATATATATTAAAAATTATAATTTAAATCT
239473 TTAAAATTTTTAAAAATTTA
196 TTAAAATTTTTAAAAATTTA
239493 GTACTTACCTCAT-TTAATTAAAACAATTCTATATATATATATATATAAAA-TT-TAACATGAAA
1 GTACTTACCTCATATTAATTAAAACAATTCTATATATATATATATATAAAATTTATAACATGAAA
239555 ATATTAATTTAATTTATATATATTTAAATATTTAAAATTTTAAAATAGTTATTTTTTAGAAAATA
66 ATATTAATTTAATTTATATATATTTAAATATTTAAAATTTTAAAATAGTTATTTTTTAGAAAATA
239620 TTTATAACAAGAAAATTTTCATTTAATTTAATATATATATATATTAAAAATTATAATTTAAATCT
131 TTTATAACAAGAAAATTTTCATTTAATTTAATATATATATATATTAAAAATTATAATTTAAATCT
239685 TTAAAATTTTTAAAAATTTA
196 TTAAAATTTTTAAAAATTTA
239705 ATTTGGCCTC
Statistics
Matches: 211, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
212 159 0.75
213 2 0.01
214 37 0.18
215 13 0.06
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (215 bp):
GTACTTACCTCATATTAATTAAAACAATTCTATATATATATATATATAAAATTTATAACATGAAA
ATATTAATTTAATTTATATATATTTAAATATTTAAAATTTTAAAATAGTTATTTTTTAGAAAATA
TTTATAACAAGAAAATTTTCATTTAATTTAATATATATATATATTAAAAATTATAATTTAAATCT
TTAAAATTTTTAAAAATTTA
Found at i:242018 original size:20 final size:20
Alignment explanation
Indices: 241995--242035 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
241985 AGTTTCCAAT
*
241995 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
242015 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
242035 T
1 T
242036 GTTTTTACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:246183 original size:14 final size:14
Alignment explanation
Indices: 246164--246197 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
246154 TTATTAATTG
246164 ATTTGTAAAAGTTA
1 ATTTGTAAAAGTTA
*
246178 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTA
246192 ATTTGT
1 ATTTGT
246198 TTAATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTA
Found at i:246225 original size:75 final size:77
Alignment explanation
Indices: 246111--246263 Score: 213
Period size: 80 Copynumber: 2.0 Consensus size: 77
246101 TTTTACATTG
*
246111 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTTT-TT-ATTAATTGATTTGTAAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTAAA
246173 AGTTAATTTGTA
66 AGTTAATTTGTA
* * *
246185 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTT-CTTGATTAATTGATTTGT
*
246250 AAAAGTTGATTTGT
63 AAAAGTTAATTTGT
246264 TGTTTCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 17 0.25
75 18 0.26
77 5 0.07
79 2 0.03
80 26 0.38
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (77 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTAAA
AGTTAATTTGTA
Found at i:246462 original size:20 final size:20
Alignment explanation
Indices: 246433--246497 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
246423 GCTTAATTCA
246433 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
*
246453 CGTTGTGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
246473 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
246493 CGTTG
1 CGTTG
246498 ATCGCAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:246727 original size:39 final size:39
Alignment explanation
Indices: 246673--246759 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
246663 TTAAGTTGTA
246673 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
246712 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
246751 GATTTTGAT
1 GATTTTGAT
246760 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:247093 original size:18 final size:18
Alignment explanation
Indices: 247070--247106 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
247060 CAAAATTTAT
247070 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
247088 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
247106 A
1 A
247107 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:247555 original size:20 final size:20
Alignment explanation
Indices: 247532--247627 Score: 53
Period size: 20 Copynumber: 5.1 Consensus size: 20
247522 TGTACAACAT
247532 GAAAGTTAAATTCGCAACGC
1 GAAAGTTAAATTCGCAACGC
**
247552 GAAA--T-AA---GCATTGC
1 GAAAGTTAAATTCGCAACGC
* * *
247566 GATAGTCTA-ATTCTCAACGA
1 GAAAGT-TAAATTCGCAACGC
*
247586 GAAAGTCAAATTCGCAACGC
1 GAAAGTTAAATTCGCAACGC
** *
247606 GAAAGCCAAATTTGCAACGC
1 GAAAGTTAAATTCGCAACGC
247626 GA
1 GA
247628 TTTTCGGTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
14 8 0.15
17 4 0.07
18 1 0.02
19 1 0.02
20 41 0.75
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAGTTAAATTCGCAACGC
Found at i:247687 original size:20 final size:20
Alignment explanation
Indices: 247662--247712 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
247652 CGCAACGCTT
*
247662 ATTTCGCGTTGCGAATTTGA
1 ATTTCGCGTTGCGAACTTGA
*
247682 ATTTCGCGTCGCGAACTTGA
1 ATTTCGCGTTGCGAACTTGA
* *
247702 CTTTTGCGTTG
1 ATTTCGCGTTG
247713 ATCGCAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
ATTTCGCGTTGCGAACTTGA
Found at i:252689 original size:3 final size:3
Alignment explanation
Indices: 252665--252715 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
252655 CTACAAAAGC
* * *
252665 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
252711 AAT AA
1 AAT AA
252716 CGGAATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:253170 original size:111 final size:111
Alignment explanation
Indices: 252916--253304 Score: 512
Period size: 111 Copynumber: 3.5 Consensus size: 111
252906 TTTAGGGAAG
* * * * * * **
252916 ATTGAATCAGGGTAGACTTGTTCCATTATCACTTATGAAATATCAAATCTTGAAAGAGATTTGAT
1 ATTGAATCAAGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGA-GGGAT
* * * *
252981 ATGTTCCACTTCTTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCC
65 CTGTTCCACTTCCTCTGAGGG-A-ATATCAGATCTGGGAAAGTTGATTC
* * *
253030 ATTGAATCAGGGTAGACTTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAAGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATC
* * *
253095 TGTTCCGCTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTT
66 TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
253141 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAAGGAATACCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAAGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATC
253206 TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
66 TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
253252 ATTGAATCAAAGCAGACTTGTTCCACT-T-ACTCTGAATGGAATATCAAATCTTG
1 ATTGAATCAAGGTAGACTTGTTCCACTGTCACTC--AA-GGAATATCAAATCTTG
253305 GAGAAATTGA
Statistics
Matches: 245, Mismatches: 27, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
109 4 0.02
110 1 0.00
111 150 0.61
112 16 0.07
113 21 0.09
114 53 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (111 bp):
ATTGAATCAAGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATC
TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
Found at i:253331 original size:66 final size:66
Alignment explanation
Indices: 253206--253654 Score: 776
Period size: 66 Copynumber: 6.8 Consensus size: 66
253196 GAGAGGGATC
* * * * *
253206 TGTTCCACTTCCTCTG-AGGGAATATCAGATCTGGGA-AAGTTGATTCATTGAATCAAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253269 T
66 T
* *
253270 TGTTCCACTTACTCTGAATGGAATATCAAATCTTGGAGAAATTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253335 T
66 T
*
253336 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGGTCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253401 T
66 T
*
253402 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCGATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253467 T
66 T
* *
253468 TATTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253533 T
66 T
253534 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
253599 T
66 T
*
253600 TGTTCCACTTACTCTGAAGAGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
253655 TGGGATCAAA
Statistics
Matches: 365, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
64 15 0.04
65 17 0.05
66 333 0.91
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (66 bp):
TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
T
Found at i:254878 original size:11 final size:12
Alignment explanation
Indices: 254851--254879 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
254841 TTTCTTTCTT
254851 TTTTTCCATTCA
1 TTTTTCCATTCA
254863 TTTTTCCATTCA
1 TTTTTCCATTCA
254875 TTTTT
1 TTTTT
254880 TCAGGCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTCCATTCA
Found at i:258273 original size:128 final size:129
Alignment explanation
Indices: 258045--258298 Score: 501
Period size: 128 Copynumber: 2.0 Consensus size: 129
258035 TATCTTCAGG
258045 TCAGACTTATCAGCATTCATACTATTGATATTGGAGGTCCTGAAAGAATAACGAACGAGAGGATA
1 TCAGACTTATCAGCATTCATACTATTGATATTGGAGGTCCTGAAAGAATAACGAACGAGAGGATA
258110 TATACATATACAAATACAGGAGAATCTATCCCATATCAAAATAGAATGAAATAAT-ATATAAAA
66 TATACATATACAAATACAGGAGAATCTATCCCATATCAAAATAGAATGAAATAATAATATAAAA
258173 TCAGACTTATCAGCATTCATACTATTGATATTGGAGGTCCTGAAAGAATAACGAACGAGAGGATA
1 TCAGACTTATCAGCATTCATACTATTGATATTGGAGGTCCTGAAAGAATAACGAACGAGAGGATA
258238 TATACATATACAAATACAGGAGAATCTATCCCATATCAAAATAGAATGAAATAATAATATA
66 TATACATATACAAATACAGGAGAATCTATCCCATATCAAAATAGAATGAAATAATAATATA
258299 TAAAAAAGAA
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 120 0.96
129 5 0.04
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (129 bp):
TCAGACTTATCAGCATTCATACTATTGATATTGGAGGTCCTGAAAGAATAACGAACGAGAGGATA
TATACATATACAAATACAGGAGAATCTATCCCATATCAAAATAGAATGAAATAATAATATAAAA
Found at i:258317 original size:29 final size:29
Alignment explanation
Indices: 258280--258337 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
258270 ATATCAAAAT
*
258280 AGAATGAAAT-AATAATATATAA-AAAAGAA
1 AGAAAGAAATAAATAA-ATA-AATAAAAGAA
258309 AGAAAGAAATAAATAAATAAATAAAAGAA
1 AGAAAGAAATAAATAAATAAATAAAAGAA
258338 TGGAAATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 19 0.73
30 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (29 bp):
AGAAAGAAATAAATAAATAAATAAAAGAA
Found at i:261760 original size:11 final size:11
Alignment explanation
Indices: 261746--261775 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
261736 TGCAATGTAG
261746 ATGCAATATGA
1 ATGCAATATGA
*
261757 ATGCAAGATGA
1 ATGCAATATGA
261768 ATGCAATA
1 ATGCAATA
261776 CGAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:267891 original size:3 final size:3
Alignment explanation
Indices: 267867--267917 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
267857 CTACAAAAGC
* * *
267867 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
267913 AAT AA
1 AAT AA
267918 CGGGATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:268366 original size:27 final size:27
Alignment explanation
Indices: 268335--268395 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
268325 ACAGTCGTAA
268335 CTTCCTCCTCATTATCATCAACAACAT
1 CTTCCTCCTCATTATCATCAACAACAT
268362 CTTCCTCCTCATTATCATCAACAACAT
1 CTTCCTCCTCATTATCATCAACAACAT
268389 CTTCCTC
1 CTTCCTC
268396 GGCAGCGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.34
Consensus pattern (27 bp):
CTTCCTCCTCATTATCATCAACAACAT
Found at i:268510 original size:24 final size:24
Alignment explanation
Indices: 268483--268536 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
268473 CCATCACATC
* *
268483 ATCAAAATCTGAGTATTCCCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * *
268507 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
268531 ATCAAA
1 ATCAAA
268537 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:268683 original size:12 final size:12
Alignment explanation
Indices: 268662--268695 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
268652 GGTTGTGGGT
*
268662 TTTGAGATTGTG
1 TTTGATATTGTG
268674 TTTGATATTGTG
1 TTTGATATTGTG
*
268686 TTTGGTATTG
1 TTTGATATTG
268696 GAAAAGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:269283 original size:14 final size:15
Alignment explanation
Indices: 269247--269284 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
269237 GAAATCATTG
269247 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
269262 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
269277 AAAAATTA
1 AAAAATTA
269285 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:269465 original size:19 final size:20
Alignment explanation
Indices: 269441--269612 Score: 140
Period size: 20 Copynumber: 8.6 Consensus size: 20
269431 ACTAAAACAT
*
269441 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
269460 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGC
*
269481 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
269501 GTTGCGAATTTGACAA-TCGC
1 GTTGCGAATTTGA-AATTCGC
* *
269521 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GC
*
269541 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTT-GAAATTCGC
* * *
269561 GTTGCGAAATTAGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* * *
269581 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTGAAATTCGC
*
269601 GTTACGAATTTG
1 GTTGCGAATTTG
269613 TTGGTCATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 29 0.24
20 66 0.55
21 21 0.17
22 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:269911 original size:20 final size:20
Alignment explanation
Indices: 269875--269913 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
269865 TCTTATTTTG
269875 TTTCTTTGTGATATTTTTCC
1 TTTCTTTGTGATATTTTTCC
*
269895 TTTCTGTTGTTAT-TTTTTC
1 TTTCT-TTGTGATATTTTTC
269914 TACGTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (20 bp):
TTTCTTTGTGATATTTTTCC
Found at i:270107 original size:2 final size:2
Alignment explanation
Indices: 270100--270137 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
270090 CAATTCAAAT
270100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
270138 ATTTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:272624 original size:226 final size:224
Alignment explanation
Indices: 272215--272856 Score: 953
Period size: 226 Copynumber: 2.8 Consensus size: 224
272205 ATCCGAAACT
* * *
272215 GTTATTTTAAAAAATAACAATATGAAGCATAATCGTACCAATAACAATGAATTGTTGCCACAATT
1 GTTATTTTAGAAAATAACAATATGAAGCAAAATCGTACCAATAACAATGAATTGTGGCCACAATT
* * *
272280 TAACGTATAGGACCAATTATAATAATATTAGATCATTATTCCCGCTATTATTCTACTATTATAAT
66 TAACGTATAGGACCAATTATAATAATATTAGACCATTATTCCCG-TATTTTTCTACTATTCTAAT
* * *
272345 TGCTTTTGAAAAATTAAACGAGTGGAAATTGGGCTCAGATTAGATTATTATTTTGTTTATTAAAT
130 TGATTTTGGAAAATTAAACGAGTGGAAATTGGGCTCAGATTAGATTCTTATTTTGTTTATTAAAT
*
272410 ATTTAATAAATTTAACGATGAAGCAGAATT
195 ATTTAATAAATTTAACGATGAAGCAGAATC
* * * ** *
272440 TTTATTTTAGAAAATAACAATATGAAGCAGAGTCGTACCAATATTAATGAATTGTGGCCATAATT
1 GTTATTTTAGAAAATAACAATATGAAGCAAAATCGTACCAATAACAATGAATTGTGGCCACAATT
* * *
272505 TAACGTATAGAGACCAATTATAATAATATTATACCATTATTTCCGTAATTTTTCTATTATTCTAA
66 TAACGTATAG-GACCAATTATAATAATATTAGACCATTATTCCCGT-ATTTTTCTACTATTCTAA
* *
272570 TTGATTTTGGAAGATTAAACGAGTGGAAATTGGGCTC-GAATTAGATTCTTATTTTGTTTCTTAA
129 TTGATTTTGGAAAATTAAACGAGTGGAAATTGGGCTCAG-ATTAGATTCTTATTTTGTTTATTAA
*
272634 ATATTTAATAAATTTAATGATGAAGCAGAATC
193 ATATTTAATAAATTTAACGATGAAGCAGAATC
* * * *
272666 GTTATTTTAGAAAATAACAATACGAAGCAAAATCGTACTAATAACGATGAATTGTGGACACAATT
1 GTTATTTTAGAAAATAACAATATGAAGCAAAATCGTACCAATAACAATGAATTGTGGCCACAATT
* *
272731 TAACGTATAGGACCAATTATAATAATATTAGACTATTATTCCCACTATTTTTCTACTATTCTAAT
66 TAACGTATAGGACCAATTATAATAATATTAGACCATTATTCCC-GTATTTTTCTACTATTCTAAT
* * *
272796 TGTTTTTGGAAAATTAAACGAGTGGAAATTTGGCTTAGATTAGATTCTTATTTTGTTTATT
130 TGATTTTGGAAAATTAAACGAGTGGAAATTGGGCTCAGATTAGATTCTTATTTTGTTTATT
272857 TGTGATATTT
Statistics
Matches: 371, Mismatches: 41, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
225 171 0.46
226 200 0.54
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (224 bp):
GTTATTTTAGAAAATAACAATATGAAGCAAAATCGTACCAATAACAATGAATTGTGGCCACAATT
TAACGTATAGGACCAATTATAATAATATTAGACCATTATTCCCGTATTTTTCTACTATTCTAATT
GATTTTGGAAAATTAAACGAGTGGAAATTGGGCTCAGATTAGATTCTTATTTTGTTTATTAAATA
TTTAATAAATTTAACGATGAAGCAGAATC
Found at i:278970 original size:31 final size:28
Alignment explanation
Indices: 278897--278970 Score: 69
Period size: 31 Copynumber: 2.5 Consensus size: 28
278887 GCGTTGTATT
278897 TTTATACCACTAAACTTTTAATTTTCCA
1 TTTATACCACTAAACTTTTAATTTTCCA
* * * *
278925 ATTATAGCAATAAAC-TTTGATTTTCGTTTCA
1 TTTATACCACTAAACTTTTAATTTTC----CA
278956 TTTATACCACTAAAC
1 TTTATACCACTAAAC
278971 CGTTAAATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 9 0.26
28 12 0.34
31 14 0.40
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTATACCACTAAACTTTTAATTTTCCA
Found at i:289095 original size:17 final size:17
Alignment explanation
Indices: 289062--289094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
289052 TTTTTAGCAA
289062 GTTATAAGAATCATTTT
1 GTTATAAGAATCATTTT
*
289079 GTTATTAGAAT-ATTTT
1 GTTATAAGAATCATTTT
289095 TCTATGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (17 bp):
GTTATAAGAATCATTTT
Found at i:289897 original size:17 final size:16
Alignment explanation
Indices: 289855--289897 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
289845 TATAATAACC
289855 TAAAAAAT-AATTAAA
1 TAAAAAATGAATTAAA
*
289870 TGAAAACATGAATTAAA
1 T-AAAAAATGAATTAAA
289887 TAAAAGAATGA
1 TAAAA-AATGA
289898 CCAAATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.04
16 10 0.43
17 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (16 bp):
TAAAAAATGAATTAAA
Found at i:291044 original size:20 final size:20
Alignment explanation
Indices: 290997--291033 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
290987 AAGTTAATAC
*
290997 AAATAA-AAAATGAAATAAT
1 AAATAATAAAATAAAATAAT
291016 AAATAATAAAATAAAATA
1 AAATAATAAAATAAAATA
291034 TAATATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (20 bp):
AAATAATAAAATAAAATAAT
Found at i:291126 original size:37 final size:37
Alignment explanation
Indices: 291057--291271 Score: 187
Period size: 38 Copynumber: 5.8 Consensus size: 37
291047 TATACATGGT
* *
291057 AAATATTTTT-TAAAAACTATAT-GATATA-TTTTCA
1 AAATATTTTTAAAAAAACTATATATATATATTTTTCA
*
291091 AAATGTTTTTAAAAAAACTATATATATATATTTTTCA
1 AAATATTTTTAAAAAAACTATATATATATATTTTTCA
* * **
291128 AAATATTTTCAAAAACTA-TATATTATATATATGTTTTTT
1 AAATATTTTTAAAAA-AACTATA-TATATATAT-TTTTCA
* **
291167 AAA-ATGTTTCCAAAAACTATATATTATATATATTTTCA
1 AAATATTTTTAAAAAAACTATATA-TATATAT-TTTTCA
*
291205 AAATATTTTTAAAAACTA-TATATTATATATATGTTTTCA
1 AAATATTTTTAAAAA-AACTATA-TATATATAT-TTTTCA
*
291244 AAAT-TTTAT-AAAAAACTATATAT-TATAT
1 AAATATTTTTAAAAAAACTATATATATATAT
291272 CTTATATATA
Statistics
Matches: 146, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
34 9 0.06
35 16 0.11
36 9 0.06
37 34 0.23
38 39 0.27
39 36 0.25
40 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (37 bp):
AAATATTTTTAAAAAAACTATATATATATATTTTTCA
Found at i:291182 original size:77 final size:75
Alignment explanation
Indices: 291074--291271 Score: 276
Period size: 77 Copynumber: 2.6 Consensus size: 75
291064 TTTTAAAAAC
*
291074 TATATGATATATTTTCAAAATGTTTTTAAAAAAACTATATATATATAT-TTTTCAAAATATTTTC
1 TATAT-ATATGTTTTCAAAATG--TTTAAAAAAACTATATATATATATATTTTCAAAATATTTTC
291138 AAAAACTATATAT
63 AAAAACTATATAT
* ** *
291151 TATATATATGTTTTTTAAAATGTTTCCAAAAACTATATATTATATATATTTTCAAAATATTTTTA
1 TATATATATG-TTTTCAAAATGTTTAAAAAAACTATATA-TATATATATTTTCAAAATATTTTCA
291216 AAAACTATATAT
64 AAAACTATATAT
291228 TATATATATGTTTTCAAAAT-TTTATAAAAAACTATATAT-TATAT
1 TATATATATGTTTTCAAAATGTTTA-AAAAAACTATATATATATAT
291272 CTTATATATA
Statistics
Matches: 109, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
74 5 0.05
75 19 0.17
76 32 0.29
77 53 0.49
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (75 bp):
TATATATATGTTTTCAAAATGTTTAAAAAAACTATATATATATATATTTTCAAAATATTTTCAAA
AACTATATAT
Found at i:292817 original size:44 final size:44
Alignment explanation
Indices: 292758--292842 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
292748 ACCCACCCCT
* * **
292758 TTTTTTTTAATTTAAGGTGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTTTCAACTTAAGGCACCCTTTCGGGTTTTCACCCTAAACG
*
292802 TTTTTTTCAACTTAAGGCACCCTTTTGGGTTTTCACCCTAA
1 TTTTTTTCAACTTAAGGCACCCTTTCGGGTTTTCACCCTAA
292843 GCGAAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (44 bp):
TTTTTTTCAACTTAAGGCACCCTTTCGGGTTTTCACCCTAAACG
Found at i:303101 original size:10 final size:11
Alignment explanation
Indices: 303081--303117 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
303071 ACAAAGAAAG
303081 TAAAATGAATAA
1 TAAAAT-AATAA
303093 -AAAATAATAA
1 TAAAATAATAA
303103 TAAAATAA-AA
1 TAAAATAATAA
303113 TAAAA
1 TAAAA
303118 ATGTTAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:303194 original size:17 final size:16
Alignment explanation
Indices: 303152--303194 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
303142 TATAATAACC
303152 TAAAAAAT-AATTAAA
1 TAAAAAATGAATTAAA
*
303167 TGAAAACATGAATTAAA
1 T-AAAAAATGAATTAAA
303184 TAAAAGAATGA
1 TAAAA-AATGA
303195 TCAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.04
16 10 0.43
17 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (16 bp):
TAAAAAATGAATTAAA
Found at i:304313 original size:7 final size:7
Alignment explanation
Indices: 304303--304332 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
304293 AAGAAAATTA
304303 AATAAAT
1 AATAAAT
304310 AATAAAT
1 AATAAAT
304317 AATAAAT
1 AATAAAT
304324 AATATAAT
1 AATA-AAT
304332 A
1 A
304333 TTATATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:304422 original size:38 final size:38
Alignment explanation
Indices: 304373--304655 Score: 232
Period size: 41 Copynumber: 7.1 Consensus size: 38
304363 TTTTAAAAAC
* *
304373 TATATGATATATTTTCAAAATGTTATCAAAAACTATATATA
1 TATAT-ATATATTTTCAAAATATTTTCAAAAAC--TATATA
* * *
304414 TATATATATATATATAGTCAAAACATTTTCAAAAATTATATG
1 TATATATATAT-T-T--TCAAAATATTTTCAAAAACTATATA
**
304456 T-TATATATATTTTCAAAAATATTTTTGAAAACTATATA
1 TATATATATATTTTC-AAAATATTTTCAAAAACTATATA
* * * *
304494 TTATATATATGCTTTTTAAAATGTTTTCAGAAACTATATA
1 -TATATATAT-ATTTTCAAAATATTTTCAAAAACTATATA
* *
304534 T-TATATATATATTCAAAATATTTTTAAAAACTATATA
1 TATATATATATTTTCAAAATATTTTCAAAAACTATATA
* * * *
304571 TTATATATTTGTTTTCATAACATTTTTTAAAAAACTATATA
1 -TATATATATATTTTCA-AA-ATATTTTCAAAAACTATATA
*
304612 TTATATATATGTTTTCAAAAT-TTTAT-AAAAACTATATA
1 -TATATATATATTTTCAAAATATTT-TCAAAAACTATATA
304650 TCATAT
1 T-ATAT
304656 CTTATATATA
Statistics
Matches: 200, Mismatches: 28, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
37 26 0.13
38 45 0.22
39 17 0.09
40 37 0.19
41 53 0.26
42 7 0.04
44 15 0.08
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATATATATTTTCAAAATATTTTCAAAAACTATATA
Found at i:304454 original size:40 final size:38
Alignment explanation
Indices: 304410--304655 Score: 221
Period size: 38 Copynumber: 6.3 Consensus size: 38
304400 AAAAACTATA
* * *
304410 TATATATATATATATATATAGTCAAAACATTTTCAAAAAT
1 TATATAT-TATATATATAT-TTCAAAATATTTTCAAAAAC
* **
304450 TATATGTTATATATAT-TTTCAAAAATATTTTTGAAAAC
1 TATATATTATATATATATTTC-AAAATATTTTCAAAAAC
* * * *
304488 TATATATTATATATATGCTTTTTAAAATGTTTTCAGAAAC
1 TATATATTATATATAT--ATTTCAAAATATTTTCAAAAAC
*
304528 TATATATTATATATATA-TTCAAAATATTTTTAAAAAC
1 TATATATTATATATATATTTCAAAATATTTTCAAAAAC
* * * *
304565 TATATATTATATATTTGTTTTCATAACATTTTTTAAAAAAC
1 TATATATTATATATAT-ATTTCA-AA-ATATTTTCAAAAAC
*
304606 TATATATTATATATATGTTTTCAAAAT-TTTAT-AAAAAC
1 TATATATTATATATAT-ATTTCAAAATATTT-TCAAAAAC
*
304644 TATATATCATAT
1 TATATATTATAT
304656 CTTATATATA
Statistics
Matches: 174, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
37 33 0.19
38 49 0.28
39 16 0.09
40 39 0.22
41 37 0.21
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATATTATATATATATTTCAAAATATTTTCAAAAAC
Found at i:304538 original size:78 final size:77
Alignment explanation
Indices: 304379--304655 Score: 297
Period size: 78 Copynumber: 3.5 Consensus size: 77
304369 AAACTATATG
* * * * * **
304379 ATATATTTTCAAAATGTTATCAAAAACTATATATATATATATATATATATAGTCAAAACATTTTC
1 ATATATTTTCAAAATATTTTTAAAAACTATATAT-TATATATATGT-TTTA-T-AAAATGTTTTC
* *
304444 AAAAATTATATGTTAT
62 AAAAACTATATATTAT
* *
304460 ATATATTTTCAAAAATATTTTTGAAAACTATATATTATATATATGCTTTT-TAAAATGTTTTCAG
1 ATATATTTTC-AAAATATTTTTAAAAACTATATATTATATATATG-TTTTATAAAATGTTTTCAA
304524 AAACTATATATTAT
64 AAACTATATATTAT
* * * * *
304538 ATATATATTCAAAATATTTTTAAAAACTATATATTATATATTTGTTTTCATAACATTTTTTAAAA
1 ATATATTTTCAAAATATTTTTAAAAACTATATATTATATATATGTTTT-ATAAAATGTTTTCAAA
304603 AACTATATATTAT
65 AACTATATATTAT
* *
304616 ATATATGTTTTCAAAAT-TTTATAAAAACTATATATCATAT
1 ATATA--TTTTCAAAATATTTTTAAAAACTATATATTATAT
304656 CTTATATATA
Statistics
Matches: 169, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
76 4 0.02
77 32 0.19
78 60 0.36
79 22 0.13
80 9 0.05
81 21 0.12
82 21 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (77 bp):
ATATATTTTCAAAATATTTTTAAAAACTATATATTATATATATGTTTTATAAAATGTTTTCAAAA
ACTATATATTAT
Found at i:304662 original size:41 final size:38
Alignment explanation
Indices: 304373--304655 Score: 250
Period size: 40 Copynumber: 7.1 Consensus size: 38
304363 TTTTAAAAAC
* * *
304373 TATATGATATATTTTCAAAATGTTATCAAAAACTATATAT
1 TATAT-ATATGTTTTCAAAAT-TTTTTAAAAACTATATAT
* * * * *
304413 ATATATATATATATATAGTCAAAACATTTTCAAAAATTATATGT
1 -TATATATATGT-T-T--TCAAAA-TTTTTTAAAAACTATATAT
*
304457 TATATATA--TTTTCAAAAATATTTTTGAAAACTATATAT
1 TATATATATGTTTTC-AAAAT-TTTTTAAAAACTATATAT
* * *
304495 TATATATATGCTTTTTAAAATGTTTTCAGAAACTATATAT
1 TATATATATG-TTTTCAAAAT-TTTTTAAAAACTATATAT
*
304535 TATATATA--TATTCAAAATATTTTTAAAAACTATATAT
1 TATATATATGTTTTCAAAAT-TTTTTAAAAACTATATAT
*
304572 TATATATTTGTTTTCATAACATTTTTTAAAAAACTATATAT
1 TATATATATGTTTTCA-AA-ATTTTTT-AAAAACTATATAT
*
304613 TATATATATGTTTTCAAAATTTTATAAAAACTATATAT
1 TATATATATGTTTTCAAAATTTTTTAAAAACTATATAT
*
304651 CATAT
1 TATAT
304656 CTTATATATA
Statistics
Matches: 203, Mismatches: 24, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
37 33 0.16
38 43 0.21
39 12 0.06
40 44 0.22
41 41 0.20
42 1 0.00
43 8 0.04
44 21 0.10
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATATATGTTTTCAAAATTTTTTAAAAACTATATAT
Found at i:304959 original size:20 final size:20
Alignment explanation
Indices: 304920--304959 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
304910 TTATGGGTTG
** *
304920 TAGTATCGATACTTGTTGAA
1 TAGTATCGATACCAGATGAA
304940 TAGTATCGATACCAGATGAA
1 TAGTATCGATACCAGATGAA
304960 CAAAAGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TAGTATCGATACCAGATGAA
Found at i:307751 original size:31 final size:31
Alignment explanation
Indices: 307716--307910 Score: 160
Period size: 31 Copynumber: 6.3 Consensus size: 31
307706 CCTAAGAGCT
* *
307716 TACCCAAGAAAGTTCTCAGGGGCACAGGGCC
1 TACCCAAGAAAGATCTCAGGGCCACAGGGCC
* * * *
307747 TACCCAAGAAAGATCTAAAGGCCGCAGGGAC
1 TACCCAAGAAAGATCTCAGGGCCACAGGGCC
* * *
307778 TACCCAAGAATGATCTCAGGGCCATAGAGCC
1 TACCCAAGAAAGATCTCAGGGCCACAGGGCC
* * * * *
307809 TATCCAAGAAAAATCACAGGGCCACGGGGCT
1 TACCCAAGAAAGATCTCAGGGCCACAGGGCC
* * *
307840 TACCCAAGAAAAAT-TACAGGGCCATAGGACC
1 TACCCAAGAAAGATCT-CAGGGCCACAGGGCC
* * * **
307871 TACCTAAGAATGATCTC-GTGGCCGCATAGCC
1 TACCCAAGAAAGATCTCAG-GGCCACAGGGCC
307902 TACCCAAGA
1 TACCCAAGA
307911 GTCACATTAG
Statistics
Matches: 125, Mismatches: 36, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
30 1 0.01
31 123 0.98
32 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.24, T:0.14
Consensus pattern (31 bp):
TACCCAAGAAAGATCTCAGGGCCACAGGGCC
Found at i:312635 original size:42 final size:42
Alignment explanation
Indices: 312576--312657 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
312566 CAGACAGACC
312576 AAACTGAGTGTAACCATTTGTTGAAACACTTAAATGTATTTA
1 AAACTGAGTGTAACCATTTGTTGAAACACTTAAATGTATTTA
312618 AAACTGAGTGTAACCATTTGTTGAAACACTTAAATGTATT
1 AAACTGAGTGTAACCATTTGTTGAAACACTTAAATGTATT
312658 AATGCCTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (42 bp):
AAACTGAGTGTAACCATTTGTTGAAACACTTAAATGTATTTA
Found at i:312670 original size:26 final size:26
Alignment explanation
Indices: 312641--312692 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
312631 CCATTTGTTG
312641 AAACACTTAAATGTATTAATGCCTGT
1 AAACACTTAAATGTATTAATGCCTGT
*
312667 AAACACTTAAATGTATTACTGCCTGT
1 AAACACTTAAATGTATTAATGCCTGT
312693 GATCGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (26 bp):
AAACACTTAAATGTATTAATGCCTGT
Found at i:315537 original size:59 final size:59
Alignment explanation
Indices: 315474--315861 Score: 322
Period size: 59 Copynumber: 6.6 Consensus size: 59
315464 TTACCGAATG
* *
315474 GCACTTTGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGA
* * *** * *
315533 GCACTGAGTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCAAGATAGG-
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGAT-GGA
* * * * **
315591 GCATTTTA-TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAA
1 GCA-CTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGA
* * ** * * *
315650 GCACTAAGGGTGCTGCAAGGATAAGGAAATCATATTGAGTGTATAGATTTCCATATGGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGA
* * * * *** *
315709 GCACTGAGTGTACT-AAATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATAGG-
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGAT-GGA
* * * * **
315767 GCATTTTA-TATGCTAAAAGTG-TAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAA
1 GCA-CTTAGTGTGCTAAAA-TGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGA
* * * *
315826 GCACTAAGGGTGCTACAAGGATAAGGAAATCATACT
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACT
315862 AATGGTATGG
Statistics
Matches: 252, Mismatches: 65, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
58 88 0.35
59 162 0.64
60 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (59 bp):
GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGA
Found at i:315727 original size:117 final size:117
Alignment explanation
Indices: 315486--315764 Score: 285
Period size: 117 Copynumber: 2.4 Consensus size: 117
315476 ACTTTGTGTG
* ** * * *
315486 CTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCTAAAT
1 CTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGGTGCTAAAG
* * * *
315551 GATAAGGAAATCATATTGAAAATATGGATTTCAAGATAGGGCATTTTATGTG
66 GATAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATCTGATGTA
* * * *
315603 CTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCTGCAA
1 CTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGGTGCT-AAA
*** * *
315668 GGATAAGGAAATCATATTGAGTGTATAGATTTCCATAT-GGAGCA-CTGAGTGTA
65 GGATAAGGAAATCATATTGAAAATATAGATTTCAAGATAGG-GCATCTGA-TGTA
* * *** *
315721 CT-AAATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATA
1 CTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATA
315765 GGGCATTTTA
Statistics
Matches: 131, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
117 90 0.69
118 41 0.31
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (117 bp):
CTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGGTGCTAAAG
GATAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATCTGATGTA
Found at i:315793 original size:176 final size:176
Alignment explanation
Indices: 315483--315861 Score: 670
Period size: 176 Copynumber: 2.2 Consensus size: 176
315473 GGCACTTTGT
* * *
315483 GTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCTA
1 GTGCTACAAGGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTACTA
* * *
315548 AATGATAAGGAAATCATATTGAAAATATGGATTTCAAGATAGGGCATTTTATGTGCTAAAATGGT
66 AATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATTTTATATGCTAAAATGGT
315613 AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGG
131 AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGG
* *
315659 GTGCTGCAAGGATAAGGAAATCATATTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTACTA
1 GTGCTACAAGGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTACTA
315724 AATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATTTTATATGCTAAAA-GTG
66 AATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATTTTATATGCTAAAATG-G
315788 TAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGG
130 TAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGG
315835 GTGCTACAAGGATAAGGAAATCATACT
1 GTGCTACAAGGATAAGGAAATCATACT
315862 AATGGTATGG
Statistics
Matches: 192, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
175 1 0.01
176 191 0.99
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (176 bp):
GTGCTACAAGGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTACTA
AATGACAAGGAAATCATATTGAAAATATAGATTTCAAGATAGGGCATTTTATATGCTAAAATGGT
AAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGG
Found at i:316149 original size:45 final size:45
Alignment explanation
Indices: 316096--316412 Score: 580
Period size: 45 Copynumber: 7.0 Consensus size: 45
316086 TGCAAATTAT
316096 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
316141 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
316186 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
* *
316231 AGTGTATTGATAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
*
316276 AGTATATTGGGAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
316321 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
* * *
316366 AGTATTTTGGTAAAATAAGCTTACAAGCTTATGGGATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
316411 AG
1 AG
316413 AGATTTTATA
Statistics
Matches: 263, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 263 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
Found at i:321937 original size:59 final size:59
Alignment explanation
Indices: 321874--322254 Score: 308
Period size: 59 Copynumber: 6.5 Consensus size: 59
321864 ATGGCACTTT
* * *
321874 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGATGGAGCACTAA
* * * * * * *
321933 GTGTGCT-AAATGATAAGGAAATAATATTGAGAATATGGATTTCAAGTTTGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAG-ATGGAGCA-CTAA
* * * **
321992 -TGTGCTAAACTGATAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGATGGAGCACTAA
* * ** * * *
322050 G-GCTGCTACAAGGATAAGGAAATCATACTGAGCGTATAGATTTCCATATGGAGCACTGA
1 GTG-TGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGATGGAGCACTAA
* * * * ** * *
322109 GTGTACT-AAATAACAAGGAAATCATATTGAAAATATGGATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGAT-GGAGCA-CTAA
* * * * **
322168 -TGTGCTAAAAGGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGATGGAGCACTAA
* * * *
322226 GGGTGCTACAAGGATAAGGAAAACATACT
1 GTGTGCTAAAATGATAAGGAAATCATACT
322255 AATGGTATGG
Statistics
Matches: 247, Mismatches: 63, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
58 87 0.35
59 159 0.64
60 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTATATGGATTTCCAGATGGAGCACTAA
Found at i:322187 original size:176 final size:176
Alignment explanation
Indices: 321877--322254 Score: 603
Period size: 176 Copynumber: 2.1 Consensus size: 176
321867 GCACTTTGTG
* * * *
321877 TGCTAAAATGATAAGGAAATCATACTGAGTATATAGATTTCCATATGGAGCACTGAGTGTGCTAA
1 TGCTACAAGGATAAGGAAATCATACTGAGCATATAGATTTCCATATGGAGCACTGAGTGTACTAA
* * * * * **
321942 ATGATAAGGAAATAATATTGAGAATATGGATTTCAAGTTTGGGCATTTTATGTGCTAAACTGATA
66 ATAACAAGGAAATAATATTGAAAATATGGATTTCAAGATAGGGCATTTTATGTGCTAAAAGGATA
322007 AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGC
131 AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGC
*
322053 TGCTACAAGGATAAGGAAATCATACTGAGCGTATAGATTTCCATATGGAGCACTGAGTGTACTAA
1 TGCTACAAGGATAAGGAAATCATACTGAGCATATAGATTTCCATATGGAGCACTGAGTGTACTAA
* * *
322118 ATAACAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTATGTGCTAAAAGGGTA
66 ATAACAAGGAAATAATATTGAAAATATGGATTTCAAGATAGGGCATTTTATGTGCTAAAAGGATA
*
322183 AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGG
131 AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGC
*
322229 TGCTACAAGGATAAGGAAAACATACT
1 TGCTACAAGGATAAGGAAATCATACT
322255 AATGGTATGG
Statistics
Matches: 185, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
176 185 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (176 bp):
TGCTACAAGGATAAGGAAATCATACTGAGCATATAGATTTCCATATGGAGCACTGAGTGTACTAA
ATAACAAGGAAATAATATTGAAAATATGGATTTCAAGATAGGGCATTTTATGTGCTAAAAGGATA
AGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGC
Found at i:322557 original size:45 final size:45
Alignment explanation
Indices: 322493--322815 Score: 567
Period size: 45 Copynumber: 7.2 Consensus size: 45
322483 TGCATATTAT
322493 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
322538 AGTATATTGGTAAAATAAGCTTACGAGCTTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGC-TTATGGAATAAATGGTA
322584 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
322629 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
*
322674 AGTATATTGATAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
*
322719 AGTATATTGGTAAAATAAGCTTACGAGATTATGGAATAAATGGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
* * * * *
322764 AGTATTTTGATAAAATAAGCTTACGACCTTATGGGATAAATTGTA
1 AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
322809 AG-ATATT
1 AGTATATT
322816 TTATATTAAT
Statistics
Matches: 267, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
44 4 0.01
45 218 0.82
46 45 0.17
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTA
Found at i:323189 original size:14 final size:14
Alignment explanation
Indices: 323170--323198 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
323160 TGTTCACAAT
323170 ACTGTTCACTATTC
1 ACTGTTCACTATTC
323184 ACTGTTCACTATTC
1 ACTGTTCACTATTC
323198 A
1 A
323199 TAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (14 bp):
ACTGTTCACTATTC
Found at i:328995 original size:54 final size:54
Alignment explanation
Indices: 328906--329274 Score: 416
Period size: 54 Copynumber: 6.8 Consensus size: 54
328896 GTGTATTTTT
* * * * * *
328906 GGCACTATGTGTGCAAACCAAGGAATTTATTATAAGTTAATGAACAACCATTTA
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* * * * * *
328960 GGCGCTATGTGTGCAACCCATGAAATTCATCATAAGTTGATGAAAAACCTTTTT
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* * * * * * *
329014 GGCACTATGTGTGCAAACCAAGGAATTCATTATATGTTAAGGAACAACCGTTAA
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* ** *
329068 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACTATTTT
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* *
329122 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTT
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* * *
329176 GGCACTATATGTGTGCAATCCAC-AAATTCATTATATGTTAATGAACAACCGTTTA
1 GGCAC--TATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
* * * * *
329231 GACACTATGTGTGCAACCCACAAAATTCATAATATGTTTATGAA
1 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAA
329275 TGATCGTAGT
Statistics
Matches: 268, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
53 15 0.06
54 206 0.77
55 32 0.12
56 15 0.06
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTAATGAACAACCGTTTA
Found at i:329178 original size:162 final size:162
Alignment explanation
Indices: 328906--329274 Score: 517
Period size: 162 Copynumber: 2.3 Consensus size: 162
328896 GTGTATTTTT
* * * * * *
328906 GGCACTATGTGTGCAAACCAAGGAATTTATTATAAGTTAATGAACAACCATTTAGGCGCTATGTG
1 GGCACTATGTGTGCAACCCACGAAATTCATAATAAGTTAATGAACAACCATTTAGGCACTATGTG
* *
328971 TGCAACCCATGAAATTCATCATAAGTTGATGAAAAACCTTTTTGGCAC-TATGTGTGCAAACCA-
66 TGCAACCCACGAAATTCATCATAAGTTGATGAAAAACCGTTTTGGCACATATGTGTGCAAACCAC
329034 AGGAATTCATTATATGTTAAGGAACAACCGTTAA
131 A--AATTCATTATATGTTAAGGAACAACCGTTAA
* * * *
329068 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACTATTTTGGCACTATGTG
1 GGCACTATGTGTGCAACCCACGAAATTCATAATAAGTTAATGAACAACCATTTAGGCACTATGTG
* *
329133 TGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATATGTGTGCAATCCA
66 TGCAACCCACGAAATTCATCATAAGTTGATGAAAAACCGTTTTGGCAC-ATATGTGTGCAAACCA
* *
329198 CAAATTCATTATATGTTAATGAACAACCGTTTA
130 CAAATTCATTATATGTTAAGGAACAACCGTTAA
* * * *
329231 GACACTATGTGTGCAACCCACAAAATTCATAATATGTTTATGAA
1 GGCACTATGTGTGCAACCCACGAAATTCATAATAAGTTAATGAA
329275 TGATCGTAGT
Statistics
Matches: 184, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
162 101 0.55
163 68 0.37
164 14 0.08
165 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (162 bp):
GGCACTATGTGTGCAACCCACGAAATTCATAATAAGTTAATGAACAACCATTTAGGCACTATGTG
TGCAACCCACGAAATTCATCATAAGTTGATGAAAAACCGTTTTGGCACATATGTGTGCAAACCAC
AAATTCATTATATGTTAAGGAACAACCGTTAA
Found at i:335726 original size:54 final size:54
Alignment explanation
Indices: 335633--335967 Score: 356
Period size: 54 Copynumber: 6.2 Consensus size: 54
335623 GTGTACTTTT
* *
335633 GGCACT-TGTGTGCAAACCAC-AAATTCAT--TAAGTTAATGAATAACCATTTA
1 GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCATTTA
* * * *
335683 GGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCATTTT
1 GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCATTTA
* * * * * * * *
335737 GGTACTATGTGCGCAAACCACAGAATTTATTATATGTTAATCAACAACCGTTTA
1 GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCATTTA
* * * *
335791 GGCACTATGTGTGCAACCCACGGAATTCATCCTAAGTTGATGAACAATCACTTT-
1 GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCA-TTTA
* * * * *
335845 GGCACTATGTGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTT
1 GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCATTTA
* * * *
335899 GGCAGTATATGTGTGCAAACCACGGAATTCATTATATGTTTAATGAACAATCATTTA
1 GGCA--CTATGTGTGCAAACCACGGAATTCATCATAAG-TTAATGAACAACCATTTA
335956 GGCACTATGTGT
1 GGCACTATGTGT
335968 AACCCACAAA
Statistics
Matches: 232, Mismatches: 44, Indels: 13
0.80 0.15 0.04
Matches are distributed among these distances:
50 6 0.03
51 12 0.05
52 7 0.03
53 3 0.01
54 149 0.64
55 10 0.04
56 27 0.12
57 18 0.08
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
GGCACTATGTGTGCAAACCACGGAATTCATCATAAGTTAATGAACAACCATTTA
Found at i:335791 original size:108 final size:108
Alignment explanation
Indices: 335629--335997 Score: 419
Period size: 108 Copynumber: 3.4 Consensus size: 108
335619 CTATGTGTAC
* *
335629 TTTTGGCACT-TGTGTGCAAACCACA-AATTCATTA-A-GTTAATGAATAACCATTTAGGCACTA
1 TTTTGGCACTATGTGTGCAAACCACAGAATTCATTATATGTTAATGAACAACCGTTTAGGCACTA
* *
335690 TGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCA
66 TGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAATCA
* * * *
335733 TTTTGGTACTATGTGCGCAAACCACAGAATTTATTATATGTTAATCAACAACCGTTTAGGCACTA
1 TTTTGGCACTATGTGTGCAAACCACAGAATTCATTATATGTTAATGAACAACCGTTTAGGCACTA
*
335798 TGTGTGCAACCCACGGAATTCATCCTAAGTTGATGAACAATCA
66 TGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAATCA
* * * * * *
335841 CTTTGGCACTATGTGTGCAACCCAC-GAAATTCATCATAAGTTGATGAACAACCGTTTTGGCAGT
1 TTTTGGCACTATGTGTGCAAACCACAG-AATTCATTATATGTTAATGAACAACCGTTTAGGCA--
* * * * *
335905 ATATGTGTGCAAACCACGGAATTCATTATATGTTTAATGAACAATCA
63 CTATGTGTGCAACCCACGGAATTCATCATAAG-TTGATGAACAATCA
* * * * * *
335952 TTTAGGCACTATGTGT--AACCCACAAAATTTATAATATGTTTATGAA
1 TTTTGGCACTATGTGTGCAAACCACAGAATTCATTATATGTTAATGAA
335998 TGACTAGTGG
Statistics
Matches: 224, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
104 9 0.04
105 14 0.06
106 8 0.04
107 2 0.01
108 113 0.50
109 24 0.11
110 27 0.12
111 27 0.12
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (108 bp):
TTTTGGCACTATGTGTGCAAACCACAGAATTCATTATATGTTAATGAACAACCGTTTAGGCACTA
TGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAATCA
Found at i:335855 original size:162 final size:161
Alignment explanation
Indices: 335633--335977 Score: 461
Period size: 162 Copynumber: 2.1 Consensus size: 161
335623 GTGTACTTTT
* *
335633 GGCACT-TGTGTGCAAACCACAAATTCATTAAGTTAATGAATAACCATTTAGGCACTATGTGTGC
1 GGCACTATGTGTGCAACCCACAAATTCATTAAGTTAATGAACAACCATTTAGGCACTATGTGTGC
* *
335697 AACCCATGGAATTCATCATAAGTTGATGAACAACCATTTT-G-GTACTATGTGCGCAAACCACAG
66 AACCCACGAAATTCATCATAAGTTGATGAACAACCATTTTGGAGTA-TATGTGCGCAAACCACAG
* *
335760 AATTTATTATATG-TTAATCAACAACCGTTTA
130 AATTCATTATATGTTTAATCAACAACCATTTA
* * *
335791 GGCACTATGTGTGCAACCCACGGAATTCATCCTAAGTTGATGAACAATCACTTT-GGCACTATGT
1 GGCACTATGTGTGCAACCCAC-AAATTCAT--TAAGTTAATGAACAACCA-TTTAGGCACTATGT
* *
335855 GTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTGGCAGTATATGTGTGCAAACC
62 GTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCATTTTGG-AGTATATGTGCGCAAACC
* * *
335920 ACGGAATTCATTATATGTTTAATGAACAATCATTTA
126 ACAGAATTCATTATATGTTTAATCAACAACCATTTA
335956 GGCACTATGTGT--AACCCACAAA
1 GGCACTATGTGTGCAACCCACAAA
335978 ATTTATAATA
Statistics
Matches: 163, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
158 6 0.04
159 13 0.08
160 7 0.04
162 68 0.42
163 11 0.07
164 28 0.17
165 30 0.18
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (161 bp):
GGCACTATGTGTGCAACCCACAAATTCATTAAGTTAATGAACAACCATTTAGGCACTATGTGTGC
AACCCACGAAATTCATCATAAGTTGATGAACAACCATTTTGGAGTATATGTGCGCAAACCACAGA
ATTCATTATATGTTTAATCAACAACCATTTA
Found at i:345895 original size:81 final size:80
Alignment explanation
Indices: 345782--345942 Score: 313
Period size: 81 Copynumber: 2.0 Consensus size: 80
345772 GTAACCCGAG
345782 CATGGTCTTATACCGTCCCCTATCAGTCAAGCTACACCAGTCCCAGTAGTAGATCCTAGTCCAGC
1 CATGGTCTTATACCGTCCCCTATCAGTCAAGCTACACCAGTCCCAGTAGTAGATCCTAGTCCAGC
345847 ACCAGTTTCCAGCACA
66 ACCAG-TTCCAGCACA
345863 CATGGTCTTATACCGTCCCCTATCAGTCAAGCTACACCAGTCCCAGTAGTAGATCCTAGTCCAGC
1 CATGGTCTTATACCGTCCCCTATCAGTCAAGCTACACCAGTCCCAGTAGTAGATCCTAGTCCAGC
345928 ACCAGTTCCAGCACA
66 ACCAGTTCCAGCACA
345943 ACCAACTCCT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 10 0.12
81 70 0.88
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (80 bp):
CATGGTCTTATACCGTCCCCTATCAGTCAAGCTACACCAGTCCCAGTAGTAGATCCTAGTCCAGC
ACCAGTTCCAGCACA
Done.