Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1161483 original size:19 final size:19
Alignment explanation
Indices: 1161461--1161555 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
1161451 GGTCGGGTCT
1161461 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
1161480 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
1161498 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
1161518 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
1161539 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
1161556 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.55
20 17 0.26
21 9 0.14
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:1161486 original size:10 final size:9
Alignment explanation
Indices: 1161462--1161554 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
1161452 GTCGGGTCTG
1161462 ACCGGTCAA
1 ACCGGTCAA
*
1161471 ACCGGTTCAG
1 ACCGG-TCAA
1161481 ACCGGTCAA
1 ACCGGTCAA
*
1161490 ACCGGTTCGA
1 ACCGG-TCAA
*
1161500 ACCGGTTGAA
1 ACCGG-TCAA
1161510 ACCGGTCAA
1 ACCGGTCAA
1161519 ACCGGTCAGA
1 ACCGGTCA-A
*
1161529 ACCGGTTGAAA
1 ACCGG-T-CAA
*
1161540 ACCGGTTAA
1 ACCGGTCAA
1161549 ACCGGT
1 ACCGGT
1161555 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1161513 original size:29 final size:28
Alignment explanation
Indices: 1161469--1161555 Score: 61
Period size: 29 Copynumber: 3.0 Consensus size: 28
1161459 CTGACCGGTC
*
1161469 AAACCGGTTCAGACCGGTCAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCAAACCGGTT-G
* *
1161499 -AACCGGTTGAAACCGGTCAAACCGG-TC
1 AAACCGG-TCAAACCGGTCAAACCGGTTG
* *
1161526 AGAACCGGTTGAAAACCGGTTAAACCGGTT
1 A-AACCGG-T-CAAACCGGTCAAACCGGTT
1161556 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 31 0.65
30 15 0.31
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (28 bp):
AAACCGGTCAAACCGGTCAAACCGGTTG
Found at i:1168717 original size:7 final size:7
Alignment explanation
Indices: 1168705--1168735 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1168695 GTCAAAGAAA
1168705 GTCAACG
1 GTCAACG
1168712 GTCAACG
1 GTCAACG
1168719 GTCAACG
1 GTCAACG
1168726 GTCAACG
1 GTCAACG
1168733 GTC
1 GTC
1168736 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1168742 original size:5 final size:5
Alignment explanation
Indices: 1168732--1168811 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
1168722 AACGGTCAAC
* * *
1168732 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG AGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
1168781 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
1168812 TGACCGGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:1168753 original size:22 final size:22
Alignment explanation
Indices: 1168725--1168811 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
1168715 AACGGTCAAC
1168725 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1168747 GGTCAACGGTCGGGTCGAGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1168769 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1168791 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1168812 TGACCGGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1168835 original size:19 final size:19
Alignment explanation
Indices: 1168813--1168907 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
1168803 GGTCGGGTCT
1168813 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
1168832 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
1168850 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
1168870 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
1168891 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
1168908 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.55
20 17 0.26
21 9 0.14
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:1168838 original size:10 final size:9
Alignment explanation
Indices: 1168814--1168906 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
1168804 GTCGGGTCTG
1168814 ACCGGTCAA
1 ACCGGTCAA
*
1168823 ACCGGTTCAG
1 ACCGG-TCAA
1168833 ACCGGTCAA
1 ACCGGTCAA
*
1168842 ACCGGTTCGA
1 ACCGG-TCAA
*
1168852 ACCGGTTGAA
1 ACCGG-TCAA
1168862 ACCGGTCAA
1 ACCGGTCAA
1168871 ACCGGTCAGA
1 ACCGGTCA-A
*
1168881 ACCGGTTGAAA
1 ACCGG-T-CAA
*
1168892 ACCGGTTAA
1 ACCGGTCAA
1168901 ACCGGT
1 ACCGGT
1168907 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1168865 original size:29 final size:28
Alignment explanation
Indices: 1168821--1168907 Score: 61
Period size: 29 Copynumber: 3.0 Consensus size: 28
1168811 CTGACCGGTC
*
1168821 AAACCGGTTCAGACCGGTCAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCAAACCGGTT-G
* *
1168851 -AACCGGTTGAAACCGGTCAAACCGG-TC
1 AAACCGG-TCAAACCGGTCAAACCGGTTG
* *
1168878 AGAACCGGTTGAAAACCGGTTAAACCGGTT
1 A-AACCGG-T-CAAACCGGTCAAACCGGTT
1168908 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 31 0.65
30 15 0.31
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (28 bp):
AAACCGGTCAAACCGGTCAAACCGGTTG
Found at i:1176125 original size:19 final size:19
Alignment explanation
Indices: 1176103--1176196 Score: 93
Period size: 19 Copynumber: 4.8 Consensus size: 19
1176093 GGTCGGGTCT
1176103 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
1176122 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
1176140 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
1176160 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
1176181 AACCGGTTAAACCGGT
1 GACCGGTCAAACCGGT
1176197 GTCCAGCAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.56
20 16 0.25
21 9 0.14
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:1176128 original size:10 final size:9
Alignment explanation
Indices: 1176104--1176196 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
1176094 GTCGGGTCTG
1176104 ACCGGTCAA
1 ACCGGTCAA
*
1176113 ACCGGTTCAG
1 ACCGG-TCAA
1176123 ACCGGTCAA
1 ACCGGTCAA
*
1176132 ACCGGTTCGA
1 ACCGG-TCAA
*
1176142 ACCGGTTGAA
1 ACCGG-TCAA
1176152 ACCGGTCAA
1 ACCGGTCAA
1176161 ACCGGTCAGA
1 ACCGGTCA-A
*
1176171 ACCGGTTGAAA
1 ACCGG-T-CAA
*
1176182 ACCGGTTAA
1 ACCGGTCAA
1176191 ACCGGT
1 ACCGGT
1176197 GTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1176172 original size:29 final size:28
Alignment explanation
Indices: 1176105--1176196 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
1176095 TCGGGTCTGA
1176105 CCGGTCAAACCGGTTCAG-ACCGGTCAAA
1 CCGGTCAAACCGGTT-AGAACCGGTCAAA
*
1176133 CCGGTTCGAACCGGTT-GAAACCGGTCAAA
1 CCGG-TCAAACCGGTTAG-AACCGGTCAAA
* *
1176162 CCGGTCAGAACCGGTTGAAAACCGGTTAAA
1 CCGGTCA-AACCGGTT-AGAACCGGTCAAA
1176192 CCGGT
1 CCGGT
1176197 GTCCAGCAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 6 0.11
29 32 0.59
30 15 0.28
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (28 bp):
CCGGTCAAACCGGTTAGAACCGGTCAAA
Found at i:1182489 original size:38 final size:39
Alignment explanation
Indices: 1182445--1182519 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
1182435 AATAAATTTT
* *
1182445 CTTTCAATTATACAATTTGAAATTTTATATAT-TATAGA
1 CTTTCAATTATAAAATTTGAAATTATATATATATATAGA
* * *
1182483 CTTTCAATTTTAAAATTTTAGATTATATATATATATA
1 CTTTCAATTATAAAATTTGAAATTATATATATATATA
1182520 TATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (39 bp):
CTTTCAATTATAAAATTTGAAATTATATATATATATAGA
Found at i:1182513 original size:2 final size:2
Alignment explanation
Indices: 1182506--1182555 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1182496 AATTTTAGAT
*
1182506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1182548 TA AA TA TA
1 TA TA TA TA
1182556 ATTTAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1190571 original size:16 final size:16
Alignment explanation
Indices: 1190547--1190582 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1190537 TTAAATATAC
* *
1190547 ATTCTAATAATATTTT
1 ATTCCAATAAAATTTT
1190563 ATTCCAATAAAATTTT
1 ATTCCAATAAAATTTT
1190579 ATTC
1 ATTC
1190583 TTTTAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTCCAATAAAATTTT
Found at i:1193077 original size:23 final size:23
Alignment explanation
Indices: 1193050--1193137 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
1193040 TTTGTGTTGT
*
1193050 TCGTTTATGTTCATTTATTGTGT
1 TCGTTTATGTTCATTTATTGTGC
*
1193073 TCGTTTATGTTCATTTATTATGC
1 TCGTTTATGTTCATTTATTGTGC
1193096 TCGTTTATGTTCATTCGT-TTGTGC
1 TCGTTTATGTTCATT--TATTGTGC
* *
1193120 TCGTTTACGTTCGTTTAT
1 TCGTTTATGTTCATTTAT
1193138 CGTTTAAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.02
23 37 0.65
24 18 0.32
25 1 0.02
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (23 bp):
TCGTTTATGTTCATTTATTGTGC
Found at i:1194531 original size:14 final size:14
Alignment explanation
Indices: 1194512--1194557 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
1194502 GCCCTCTGTT
1194512 CGAACATAAATGAA
1 CGAACATAAATGAA
1194526 CGAACATAAATGAA
1 CGAACATAAATGAA
*
1194540 CAAACATATAATCGAA
1 CGAACATA-AAT-GAA
1194556 CG
1 CG
1194558 TTCACGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1197928 original size:29 final size:30
Alignment explanation
Indices: 1197870--1197943 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
1197860 TCTAAATTAC
* * *
1197870 AATAGAATGTATTTTTAAAAGTTAAGATAAG
1 AATAAAATATATTTTT-AAAGTTAAAATAAG
1197901 AATAAAATATATTTTT-AAGTTAAAATAAG
1 AATAAAATATATTTTTAAAGTTAAAATAAG
1197930 -ATCAAAATATATTT
1 AAT-AAAATATATTT
1197944 ATTTTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.59
31 14 0.36
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (30 bp):
AATAAAATATATTTTTAAAGTTAAAATAAG
Found at i:1200139 original size:16 final size:15
Alignment explanation
Indices: 1200112--1200141 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1200102 AATAACAGAT
1200112 ATAATAATGTATATA
1 ATAATAATGTATATA
1200127 ATAATAGATGTATAT
1 ATAATA-ATGTATAT
1200142 TTTGTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATAATAATGTATATA
Found at i:1200229 original size:2 final size:2
Alignment explanation
Indices: 1200210--1200268 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
1200200 ATAATAACAG
* *
1200210 AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1200252 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1200269 AGAATTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1200995 original size:35 final size:35
Alignment explanation
Indices: 1200946--1201028 Score: 130
Period size: 35 Copynumber: 2.4 Consensus size: 35
1200936 TAAGGACAGG
* *
1200946 TATAACAATATATATACAAGAATGGTAATGACATA
1 TATAACAATGTATATACAAGAATGGTAATGACAAA
*
1200981 TATAGCAATGTATATACAAGAATGGTAATGACAAA
1 TATAACAATGTATATACAAGAATGGTAATGACAAA
*
1201016 TACAACAATGTAT
1 TATAACAATGTAT
1201029 TATGTATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (35 bp):
TATAACAATGTATATACAAGAATGGTAATGACAAA
Found at i:1216852 original size:23 final size:23
Alignment explanation
Indices: 1216834--1216892 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1216824 CTCGTATAAA
1216834 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1216857 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1216880 TGCACCGTAGTGC
1 TGCACCGAAGTGC
1216893 TATATAAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1232842 original size:46 final size:46
Alignment explanation
Indices: 1232775--1232866 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
1232765 GCATATTTAT
*
1232775 CATGATTGCGGCAATAGTGAATGTTATTACAGG-GATTATAGGTATC
1 CATGATTGCGGCAATAGTGAATGTAATTAC-GGTGATTATAGGTATC
1232821 CATGATTGCGGCAATAGTGAATGTAATTACGGTGATTATAGGTATC
1 CATGATTGCGGCAATAGTGAATGTAATTACGGTGATTATAGGTATC
1232867 GTGATTGTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (46 bp):
CATGATTGCGGCAATAGTGAATGTAATTACGGTGATTATAGGTATC
Found at i:1233614 original size:34 final size:34
Alignment explanation
Indices: 1233566--1233634 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1233556 ATAGTCATTG
** * *
1233566 AGTATATTCTTAAATAAAGGAATTGAAAGAAATT
1 AGTATATTAATAAATAAAGGAACTGAAACAAATT
*
1233600 AGTATATTAATAAATAGAGGAACTGAAACAAATT
1 AGTATATTAATAAATAAAGGAACTGAAACAAATT
1233634 A
1 A
1233635 TCTATCCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.29
Consensus pattern (34 bp):
AGTATATTAATAAATAAAGGAACTGAAACAAATT
Found at i:1240505 original size:22 final size:22
Alignment explanation
Indices: 1240480--1240529 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1240470 AATAAAATAA
* *
1240480 AAACAATAACCAAATTATAATT
1 AAACAATAACCAAAATATAATC
** *
1240502 AAACTGTGACCAAAATATAATC
1 AAACAATAACCAAAATATAATC
1240524 AAACAA
1 AAACAA
1240530 AAACAACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.16, G:0.04, T:0.22
Consensus pattern (22 bp):
AAACAATAACCAAAATATAATC
Found at i:1241748 original size:12 final size:12
Alignment explanation
Indices: 1241731--1241755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1241721 ATGGTGTTCA
1241731 TCTGGAAGTTGT
1 TCTGGAAGTTGT
1241743 TCTGGAAGTTGT
1 TCTGGAAGTTGT
1241755 T
1 T
1241756 GGAACCATCG
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:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (12 bp):
TCTGGAAGTTGT
Found at i:1242215 original size:43 final size:43
Alignment explanation
Indices: 1242133--1242217 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
1242123 ACGCTGATTC
* * *
1242133 AACTCCTTCTATGAAGAACCAAGCGAAATATTTTCACTGATCT
1 AACTCCTTCCATGAAGAACAAAGCGAAAGATTTTCACTGATCT
* * *
1242176 AACTCCTTCCATGAAGAATAAAGTGAAAGGTTGTT-ACTGATC
1 AACTCCTTCCATGAAGAACAAAGCGAAAGATT-TTCACTGATC
1242218 CAATTTCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (43 bp):
AACTCCTTCCATGAAGAACAAAGCGAAAGATTTTCACTGATCT
Found at i:1242553 original size:162 final size:162
Alignment explanation
Indices: 1242251--1242584 Score: 420
Period size: 162 Copynumber: 2.1 Consensus size: 162
1242241 GTAACATGAC
* * *
1242251 AAATGTTGATCCAACTTCTTCTGTGAAGAATCAAACAAAATGTTGATGTTGATCTATCTCTTTTT
1 AAATGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGATGTTGATCTATCTCCTTCT
* * * *
1242316 GTGATAAAATCAAGCAACATGGTTGAACAAGTTCTTCTCATTAAGAACTTATTCTTCCTCCTTGG
66 GAGATAAAATCAAGCAACAAGGTTGAACAAATACTTCTCATTAAGAACTTATTCTTCCTCCTTGG
* * * *
1242381 ACACGTTCTTCTTATTATGAACTCTCCATTGG
131 AAAAGTTCTTCTCATTATGAACTCTCCATTGA
* * *
1242413 AAATGTTGATCCATCTCCTTCTGTGATGGAATCAAACAAAATGTTTATGTTGATCTATCTCCTTC
1 AAATGTTGATCCAACTCCTTCTGTGA-AGAATCAAACAAAATGTTGATGTTGATCTATCTCCTTC
* * * * * * * * *
1242478 TGAGATAGAGTCGAGCAA-AAGGTTGAATAAATACTTTTCATTATGAACTTCTTTTTTCT-CTTC
65 TGAGATAAAATCAAGCAACAAGGTTGAACAAATACTTCTCATTAAGAACTTATTCTTCCTCCTT-
*
1242541 GGAAAAGTTCTTCTCGTTATGAACTCTCCATTGA
129 GGAAAAGTTCTTCTCATTATGAACTCTCCATTGA
1242575 AAATGTTGAT
1 AAATGTTGAT
1242585 ACTGATCTAT
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
161 3 0.02
162 95 0.65
163 48 0.33
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (162 bp):
AAATGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGATGTTGATCTATCTCCTTCT
GAGATAAAATCAAGCAACAAGGTTGAACAAATACTTCTCATTAAGAACTTATTCTTCCTCCTTGG
AAAAGTTCTTCTCATTATGAACTCTCCATTGA
Found at i:1242674 original size:124 final size:124
Alignment explanation
Indices: 1242450--1244136 Score: 1050
Period size: 124 Copynumber: 13.1 Consensus size: 124
1242440 GGAATCAAAC
* * * * * * *
1242450 AAAATGTTTATGTTGATCTATCTCCTTCTGAGATAGAGTCGAGCAAAAGGTTGAATAAATACTTT
1 AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
* ** * ** *
1242515 TCATTATGAACTTCTTTTTTCTCTTCGGAAAAGTTCTTCTCGTTATGAACTCTCCATTG
66 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * *
1242574 AAAATGTTGATACTGATCTATCTCTTTCTGTGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTT
1 AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
* *
1242639 TCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTTCATTG
66 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * * * **
1242698 GAAATGTTGACGATGATCTATCTCCTTTTGCT-ATAGAGTTGAGCAAAAATTTGAACAAGTTCTT
1 AAAATGTTGATGCTGATCTATCTCCTTCTG-TGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
* * ** **
1242762 CTCATTATGAACTTCATCTCCCTTATCGGACAAGTTCTTCTCATTATGAACTCTTTATT-
65 CTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * **
1242821 AGCAATGTTGATGCTGATATATCTCCTTCTACGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
1 A-AAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
*
1242886 CTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTTATTATGAACTCTCCATT-
65 CTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * *
1242945 AGAAATCTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGTAAAAGGTTGAACAAGTTGTT
1 A-AAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
* * * * *
1243010 CTCATTATGAACTTTTTCTCCCTTATCGGACGAGTTCTTCTCATTATGAACTTTCAATTG
65 CTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * ** ** ** *
1243070 GAAATATTGATGCTGATCTATCTTATTCTGCAATAGAGTATAGCAAAAGGTTGAATAAGTTCTTC
1 AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
1243135 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
66 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * *
1243194 AAAATGTTGATCCCTCGAGTGAGAGGTCGCTGAT-TCAACTTC-AT-ATACGACGAATCGAGC-T
1 AAAATGTTGA----T-G-CT--GA--T--CT-ATCTC--CTTCTGTGATA-GA-G--TCGAGCAA
* * *
1243255 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCCTCATCGGATGATTTCATCTCATTAT
47 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
1243320 GAACTATCCATTG
112 GAACTCTCCATTG
* * * * * * ** * * *
1243333 GAAATGTTGATCCCTCGAGTGAGGGGTTGCTGATTTAACTCTATATGCGATGAATTGAGC-TAAG
1 AAAATGTTGA----T-G-CTGA-----T-CT-ATCT-CCT-TCTGTGATA-GAGTCGAGCAAAAG
* * * *
1243397 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTGTTATTATGAA
50 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
*
1243462 CTCTCCACTG
115 CTCTCCATTG
* * * * * ** * * * *
1243472 GAATTGTTGATCACTCGAGTGAGGTGTCATTGATTCAACTCTATATATGATGAATTGAGC-TAAG
1 AAAATGTTGAT-GCT-GA-T---CTATC--TCCTT---CTGT-GATA-GA-G--TCGAGCAAAAG
* * * * * *
1243536 GTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGAGTTTTTCTTATTATGAA
50 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
*
1243601 CTCTCTATTTG
115 CTCTCCA-TTG
* *** ** * * *
1243612 -AAATGTTGAT-C---CCTA---GAGTGAGGGA-A-A-TCGAGC-TAAGGTTGAACAAGTTCTTT
1 AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
* *
1243665 TCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
66 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
** * * * ** * * * *
1243724 GTATTGTTGATCCCTCGAGTAAGGTATCGTTGATTCAACTTTATATATGATGAATTGAGC-TAAG
1 AAAATGTTGAT-GCT-GA-T---CTATC--TCCTT---CTGT-GATA-GA-G--TCGAGCAAAAG
* * * * *
1243788 GTTAAACAAGTTATTC-CTATTATGAATTTCTTCTCCCTTATCGGATGAGTTTTTCTCATTATGA
50 GTTGAACAAGTTCTTCTC-ATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGA
*
1243852 ACTATCCATTTG
114 ACTCTCCA-TTG
* * * * * *
1243864 AAATATTGATCCATCGAGTGAGGGGTCGCTGAT-TCAACTCCATATGCGATA-AATCGAGC-TAA
1 AAA-A-TG-----T----TGA----T-GCTGATCT-ATCTCCTTCTGTGATAGAGTCGAGCAAAA
* * *
1243926 GGTTGAACAAGTTATTCTCATTATGAAATTTTTCTCCCTCATCGGATGAGTTCTTCTCATTATGA
49 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGA
*
1243991 ACTCTCCACTG
114 ACTCTCCATTG
* * * * *
1244002 GAAATGTTGATGTTGATCTATCTCTTTCTGCGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTC
1 AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
* * * * * * * *
1244067 TTATTATAAACTTATTCTCCCTTATCGGACGAGTTCTTCACATTATGAACTCTTCACTG
66 TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
*
1244126 GAAATGTTGAT
1 AAAATGTTGAT
1244137 CCCTCAAGTG
Statistics
Matches: 1255, Mismatches: 215, Indels: 186
0.76 0.13 0.11
Matches are distributed among these distances:
112 2 0.00
113 80 0.06
115 1 0.00
117 1 0.00
119 1 0.00
120 1 0.00
122 17 0.01
123 10 0.01
124 626 0.50
125 1 0.00
127 3 0.00
128 4 0.00
129 2 0.00
130 1 0.00
131 2 0.00
132 5 0.00
133 4 0.00
134 3 0.00
135 7 0.01
136 12 0.01
137 8 0.01
138 9 0.01
139 413 0.33
140 14 0.01
141 2 0.00
142 6 0.00
144 3 0.00
145 1 0.00
147 1 0.00
148 2 0.00
149 1 0.00
150 2 0.00
151 3 0.00
153 1 0.00
154 2 0.00
155 4 0.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (124 bp):
AAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTC
TCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
Found at i:1243287 original size:139 final size:138
Alignment explanation
Indices: 1243116--1243635 Score: 727
Period size: 139 Copynumber: 3.7 Consensus size: 138
1243106 AGTATAGCAA
* *
1243116 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
* *
1243181 GAACTCTCCATTGAAAATGTTGATCCCTCGAGTGAGAGGTCGCTGATTCAACT-TCATATACGAC
66 GAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAG-GGTCGCTGATTCAACTCT-ATATACGAT
*
1243245 GAATCGAGCT
129 GAATTGAGCT
* * * *
1243255 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCCTCATCGGATGATTTCATCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
* * * *
1243320 GAACTATCCATTGGAAATGTTGATCCCTCGAGTGAGGGGTTGCTGATTTAACTCTATATGCGATG
66 GAACTCTCCATTGGAAATGTTGATCCCTCGAGTGA-GGGTCGCTGATTCAACTCTATATACGATG
1243385 AATTGAGCT
130 AATTGAGCT
* * *
1243394 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTGTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
* * * ** *
1243459 GAACTCTCCACTGGAATTGTTGATCACTCGAGTGAGGTGTCATTGATTCAACTCTATATATGATG
66 GAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAGG-GTCGCTGATTCAACTCTATATACGATG
1243524 AATTGAGCT
130 AATTGAGCT
* * * * *
1243533 AAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGAGTTTTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
* * *
1243598 GAACTCTCTATTTGAAATGTTGATCCCTAGAGTGAGGG
66 GAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAGGG
1243636 AAATCGAGCT
Statistics
Matches: 338, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
138 3 0.01
139 333 0.99
140 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (138 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTAT
GAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAGGGTCGCTGATTCAACTCTATATACGATGA
ATTGAGCT
Found at i:1243732 original size:113 final size:113
Alignment explanation
Indices: 1243528--1243743 Score: 306
Period size: 113 Copynumber: 1.9 Consensus size: 113
1243518 ATGATGAATT
* * * *
1243528 GAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGAGTTTTTCTT
1 GAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCTC
* * *
1243593 ATTATGAACTCTCTATTTGAAATGTTGATCCCTAGAGTGAGGGAAATC
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTAGAGTGAGGGAAATC
* * * *
1243641 GAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCTTCTC
1 GAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCTC
* * *
1243706 ATTATGAACTCTCCACTGGTATTGTTGATCCCTCGAGT
66 ATTATGAACTCTCCACTGGAAATGTTGATCCCTAGAGT
1243744 AAGGTATCGT
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 89 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (113 bp):
GAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATGTTGATCCCTAGAGTGAGGGAAATC
Found at i:1243734 original size:391 final size:394
Alignment explanation
Indices: 1243246--1244325 Score: 1299
Period size: 391 Copynumber: 2.7 Consensus size: 394
1243236 ATATACGACG
* * * * *
1243246 AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCCTCATCGGATGATTTCA
1 AATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCT
* * * * *
1243311 TCTCATTATGAACTATCCATTGGAAATGTTGATCCCTCGAGTGAGGGGTTGCTGATTTAACTCTA
66 TCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCTA
* *
1243376 TATGCGATGAATTGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCAG
131 TATACGATGAATTGAGCTAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTCTCCCTCATCAG
* * * **
1243441 ATGAGTTCTTGTTATTATGAACTCTCCACTGGAATTGTTGATCACTCGAGTGAGGTGTCATTGAT
196 ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATC-CTCGAGTGAGGTGTCGCTGAT
* * *
1243506 TCAACTCTATATATGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTC
260 TCAACTCCATATGTGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTC
* * * * * * * * *
1243571 CCTTATCAGATGAGTTTTTCTTATTATGAACTCTCTATTTGAAATGTTGA-T-CCCTA-GAGTGA
325 CCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATTGACCTATCAGTCA
*
1243633 GGGA-
390 GCGAT
1243637 AATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCT
1 AATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCT
* * * * * *
1243702 TCTCATTATGAACTCTCCACTGGTATTGTTGATCCCTCGAGTAAGGTATCGTTGATTCAACTTTA
66 TCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCTA
* * * * * *
1243767 TATATGATGAATTGAGCTAAGGTTAAACAAGTTATTCCTATTATGAATTTCTTCTCCCTTATCGG
131 TATACGATGAATTGAGCTAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTCTCCCTCATCAG
* * * * * *
1243832 ATGAGTTTTTCTCATTATGAACTATCCATTTGAAATATTGATCCATCGAGTGAGGGGTCGCTGAT
196 ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCC-TCGAGTGAGGTGTCGCTGAT
* * * * *
1243897 TCAACTCCATATGCGATAAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAAATTTTTCTC
260 TCAACTCCATATGTGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTC
* * *
1243962 CCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATGTTGATCTATCTCT
325 CCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA--TTGACCTA--TCA
* *
1244027 TTCTGCGAT
386 GTCAGCGAT
* * * * *
1244036 AGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTT-ATTAT-AAACTTATTCTCCCTTATCGGACGA
1 A-A-TCGAGC-TAAGGTTGAACAAGTTCTT-TTCATTATGAAA-TTCTTCTCCCTCATCGGATGA
* * * *
1244099 GTTCTTCACATTATGAACTCTTCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCAA
61 GTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAA
* * * * *
1244164 CTCTATATACGATGAATCGAGCTAAGGTTGAAAAAGTTTTTCTTATTATGATCATCTTCTCCCTC
126 CTCTATATACGATGAATTGAGCTAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTCTCCCTC
* ** * *
1244229 ATCAAATGAGTTCTTCTCATTATGAACTCTTTACTGGAAATGTTAATCCCTCGAGTAAGGTGTCG
191 ATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT-CCTCGAGTGAGGTGTCG
*
1244294 CTGATTCAACTCCATATGTGATGGATTTGAGC
255 CTGATTCAACTCCATATGTGAT-GAATTGAGC
1244326 GAAATGAAAT
Statistics
Matches: 574, Mismatches: 99, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
390 1 0.00
391 323 0.56
394 1 0.00
395 3 0.01
398 4 0.01
399 1 0.00
400 1 0.00
401 8 0.01
402 222 0.39
403 10 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (394 bp):
AATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCT
TCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCTA
TATACGATGAATTGAGCTAAGGTTGAACAAGTTATTCTTATTATGAACTTCTTCTCCCTCATCAG
ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCTCGAGTGAGGTGTCGCTGATT
CAACTCCATATGTGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTCC
CTCATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATTGACCTATCAGTCAG
CGAT
Found at i:1243837 original size:252 final size:252
Alignment explanation
Indices: 1243389--1243887 Score: 804
Period size: 252 Copynumber: 2.0 Consensus size: 252
1243379 GCGATGAATT
* * *
1243389 GAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTGTT
1 GAGCTAAGGTTGAACAAGTTCTTCTTATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCTC
* *
1243454 ATTATGAACTCTCCACTGGAATTGTTGATCACTCGAGTGAGGTGTCATTGATTCAACTCTATATA
66 ATTATGAACTCTCCACTGGAATTGTTGATCACTCGAGTAAGGTATCATTGATTCAACTCTATATA
1243519 TGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGA
131 TGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGA
* * * * *
1243584 GTTTTTCTTATTATGAACTCTCTATTTGAAATGTTGATCCCTAGAGTGAGGGAAATC
196 GTTTTTCTCATTATGAACTATCCATTTGAAATATTGATCCATAGAGTGAGGGAAATC
*
1243641 GAGCTAAGGTTGAACAAGTTCTT-TTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCTTCT
1 GAGCTAAGGTTGAACAAGTTCTTCTT-ATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCT
* * * *
1243705 CATTATGAACTCTCCACTGGTATTGTTGATCCCTCGAGTAAGGTATCGTTGATTCAACTTTATAT
65 CATTATGAACTCTCCACTGGAATTGTTGATCACTCGAGTAAGGTATCATTGATTCAACTCTATAT
* *
1243770 ATGATGAATTGAGCTAAGGTTAAACAAGTTATTC-CTATTATGAATTTCTTCTCCCTTATCGGAT
130 ATGATGAATTGAGCTAAGGTTAAACAAGTTATTCTC-ATTATGAACTTCTTCTCCCTTATCAGAT
*
1243834 GAGTTTTTCTCATTATGAACTATCCATTTGAAATATTGATCCATCGAGTGAGGG
194 GAGTTTTTCTCATTATGAACTATCCATTTGAAATATTGATCCATAGAGTGAGGG
1243888 GTCGCTGATT
Statistics
Matches: 227, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
251 3 0.01
252 224 0.99
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (252 bp):
GAGCTAAGGTTGAACAAGTTCTTCTTATTATGAAATTCTTCTCCCTCATCAGATGAGTTCTTCTC
ATTATGAACTCTCCACTGGAATTGTTGATCACTCGAGTAAGGTATCATTGATTCAACTCTATATA
TGATGAATTGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATCAGATGA
GTTTTTCTCATTATGAACTATCCATTTGAAATATTGATCCATAGAGTGAGGGAAATC
Found at i:1243897 original size:139 final size:139
Alignment explanation
Indices: 1243636--1244310 Score: 627
Period size: 139 Copynumber: 5.0 Consensus size: 139
1243626 AGAGTGAGGG
* * *
1243636 AAATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTC
1 AAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTTC
* * * * * **
1243701 TTCTCATTATGAACTCTCCACTGGTATTGTTGATCCCTCGAGTAAGGTATCGTTGATTCAACTTT
66 TTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGGGATCGCTGATTCAACTCC
*
1243766 ATATATGAT
131 ATATACGAT
* * * *
1243775 GAATTGAGCTAAGGTTAAACAAGTTATTC-CTATTATGAATTTCTTCTCCCTTATCGGATGAGTT
1 AAATCGAGCTAAGGTTGAACAAGTTATTCTC-ATTATGAATTTCTTCTCCCTCATCGGATGAGTT
* * * * * * *
1243839 TTTCTCATTATGAACTATCCATTTGAAATATTGATCCATCGAGTGAGGGGTCGCTGATTCAACTC
65 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGGGATCGCTGATTCAACTC
*
1243904 CATATGCGAT
130 CATATACGAT
1243914 AAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAAATTT-TTCTCCCTCATCGGATGAGTT
1 AAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATG-AATTTCTTCTCCCTCATCGGATGAGTT
* * ** * *
1243978 CTTCTCATTATGAACTCTCCACTGGAAATGTTGAT--GTTGA-T---CTATCTCT--TT---CTG
65 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGGGATCGCTGATTCAACTC
*
1244032 C-GATA-G--
130 CATATACGAT
* * * * * * * * * *
1244038 -AGTCAAGCAAAAGGTTGAACAAGTTCTTCTTATTATAAACTTATTCTCCCTTATCGGACGAGTT
1 AAATCGAGC-TAAGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTT
* * * * * *
1244102 CTTCACATTATGAACTCTTCACTGGAAATGTTGATCCCTCAAGTGAGGTG-TCACTGATTCAACT
65 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGG-GATCGCTGATTCAACT
*
1244166 CTATATACGAT
129 CCATATACGAT
* * * * * **
1244177 GAATCGAGCTAAGGTTGAAAAAGTTTTTCTTATTATG-ATCATCTTCTCCCTCATCAAATGAGTT
1 AAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAAT-TTCTTCTCCCTCATCGGATGAGTT
** * *
1244241 CTTCTCATTATGAACTCTTTACTGGAAATGTTAATCCCTCGAGTAAGGTG-TCGCTGATTCAACT
65 CTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGG-GATCGCTGATTCAACT
1244305 CCATAT
129 CCATAT
1244311 GTGATGGATT
Statistics
Matches: 432, Mismatches: 81, Indels: 46
0.77 0.14 0.08
Matches are distributed among these distances:
123 10 0.02
124 76 0.18
126 3 0.01
127 3 0.01
128 3 0.01
130 4 0.01
131 2 0.00
132 2 0.00
133 4 0.01
135 2 0.00
136 4 0.01
137 4 0.01
138 2 0.00
139 301 0.70
140 12 0.03
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (139 bp):
AAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTTC
TTCTCATTATGAACTCTCCACTGGAAATGTTGATCCATCGAGTAAGGGATCGCTGATTCAACTCC
ATATACGAT
Found at i:1244396 original size:38 final size:38
Alignment explanation
Indices: 1244347--1244549 Score: 141
Period size: 38 Copynumber: 5.3 Consensus size: 38
1244337 TGTTTTAAGA
1244347 AAAACTATCTCAAGTGAGATAAAATTTTGTTTCAAGTG
1 AAAACTATCTCAAGTGAGATAAAATTTTGTTTCAAGTG
* * * * * * *
1244385 AAAACTGTCTCAGGCGAGAT-GAAGTTTGTTTTAAG-A
1 AAAACTATCTCAAGTGAGATAAAATTTTGTTTCAAGTG
* *
1244421 AAAACTATCTCACTTCGAGTGAGAT-AAATTTCTATTTCGAGTG
1 AAAACTATCTCA-----AGTGAGATAAAATTT-TGTTTCAAGTG
* * * *
1244464 -AAACTATCTCAAGAGAGA-AAAAGTTTGTTTTAAG-A
1 AAAACTATCTCAAGTGAGATAAAATTTTGTTTCAAGTG
* * * *
1244499 AAAACAATATCAAGTGAGATAAAATTTTTGCTTCGAGTG
1 AAAACTATCTCAAGTGAGATAAAA-TTTTGTTTCAAGTG
1244538 -AAACTATCTCAA
1 AAAACTATCTCAA
1244550 ACTAGATGAA
Statistics
Matches: 121, Mismatches: 32, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
36 32 0.26
37 27 0.22
38 35 0.29
41 10 0.08
42 17 0.14
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (38 bp):
AAAACTATCTCAAGTGAGATAAAATTTTGTTTCAAGTG
Found at i:1244548 original size:74 final size:74
Alignment explanation
Indices: 1244335--1244549 Score: 245
Period size: 74 Copynumber: 2.9 Consensus size: 74
1244325 CGAAATGAAA
* * * * *
1244335 TTTGTTTTAAGAAAAACTATCTCAAGTGAGATAAAA-TTTTGTTTCAAGTGAAAACTGTCTCAGG
1 TTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTTTGTTTCGAGTG-AAACTATCTCAAG
* **
1244399 CGAGATGAAG
65 AGAGAAAAAG
* * * *
1244409 TTTGTTTTAAGAAAAACTATCTCACTTCGAGTGAGAT-AAATTTCTATTTCGAGTGAAACTATCT
1 TTTGTTTTAAGAAAAAC-A-AT-A--TCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACTATCT
1244473 CAAGAGAGAAAAAG
61 CAAGAGAGAAAAAG
*
1244487 TTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTTTGCTTCGAGTGAAACTATCTCAA
1 TTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAA
1244550 ACTAGATGAA
Statistics
Matches: 117, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
73 10 0.09
74 44 0.38
75 1 0.01
76 2 0.02
77 1 0.01
78 38 0.32
79 21 0.18
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (74 bp):
TTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGA
GAGAAAAAG
Found at i:1250263 original size:22 final size:22
Alignment explanation
Indices: 1250238--1250291 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
1250228 ACATCAGTAC
1250238 CTTCTAGAAGGTCCAGTCAGCG
1 CTTCTAGAAGGTCCAGTCAGCG
1250260 CTTCTAGAAGGTCCAGTCAGCG
1 CTTCTAGAAGGTCCAGTCAGCG
1250282 CTTCTAGAAG
1 CTTCTAGAAG
1250292 AACGAATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
CTTCTAGAAGGTCCAGTCAGCG
Found at i:1253716 original size:4 final size:4
Alignment explanation
Indices: 1253707--1253942 Score: 377
Period size: 4 Copynumber: 59.5 Consensus size: 4
1253697 CTTGCAGAGG
1253707 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1253755 ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
1253801 ATGT ATGT ATGT ACGT ACGT ACGT ACGT ACGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1253849 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
1253897 ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1253943 TAATTGCCAT
Statistics
Matches: 220, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.01
4 218 0.99
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:1255625 original size:27 final size:27
Alignment explanation
Indices: 1255587--1255639 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1255577 GGTATTGCTG
1255587 TCCTTTAATGGCATTGGTTTTGGAAGC
1 TCCTTTAATGGCATTGGTTTTGGAAGC
1255614 TCCTTTAATGGCATTGGTTTTGGAAG
1 TCCTTTAATGGCATTGGTTTTGGAAG
1255640 GTTTCTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (27 bp):
TCCTTTAATGGCATTGGTTTTGGAAGC
Found at i:1261063 original size:23 final size:23
Alignment explanation
Indices: 1261037--1261081 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1261027 TTAGGCCTGC
* *
1261037 AAAATGTAATAATATTAATAATT
1 AAAAAGTAATAATAATAATAATT
1261060 AAAAAGTAATAATAATAATAAT
1 AAAAAGTAATAATAATAATAAT
1261082 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAAGTAATAATAATAATAATT
Found at i:1261486 original size:66 final size:66
Alignment explanation
Indices: 1261363--1261693 Score: 477
Period size: 66 Copynumber: 5.0 Consensus size: 66
1261353 AGATTAATTT
* ** * * *
1261363 TGTTTTAAGAGAATTTGTCTCAAGCGAGACAAAACTTT-TTTCGACGGAAACAATCTCAAATGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAA-TTTGTTTCAAGGGAAACAATCTCAAATGTT
1261427 TA
65 TA
* * *
1261429 TGATTCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1261494 A
66 A
* * *
1261495 TGTTTCAATAGGAACTGTCTCAAGCGAGATAAAATTTGTTTCAA-GGAAACAATCTAAAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1261559 A
66 A
* *
1261560 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1261625 A
66 A
* * * *
1261626 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1261691 A
66 A
1261692 TG
1 TG
1261694 AATTTTGTTT
Statistics
Matches: 240, Mismatches: 23, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
65 65 0.27
66 175 0.73
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
A
Found at i:1261557 original size:131 final size:131
Alignment explanation
Indices: 1261363--1261694 Score: 486
Period size: 131 Copynumber: 2.5 Consensus size: 131
1261353 AGATTAATTT
* ** *
1261363 TGTTTTAAGAGAATTTGTCTCAAGCGAGACAAAACTTT-TTTCGACGGAAACAATCTCAAATGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTC-AAGGAAACAATCTCAAATGTT
* *
1261427 TATGATTCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAATGT
64 TATGATTCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGT
1261492 TTA
129 TTA
* * * *
1261495 TGTTTCAATAGGAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGGAAACAATCTAAAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAACAATCTCAAATGTTTA
* * *
1261560 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
66 TGATTCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
1261625 A
131 A
* * *
1261626 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAA-GGAAACAATCTCAAATGTTT
1261691 ATGA
65 ATGA
1261695 ATTTTGTTTC
Statistics
Matches: 177, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
131 125 0.71
132 52 0.29
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (131 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAACAATCTCAAATGTTTA
TGATTCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
A
Found at i:1261718 original size:37 final size:37
Alignment explanation
Indices: 1261660--1261730 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1261650 CAAGACAAAA
*
1261660 TTTGTTTCAAGGGAAATAATCTCAAAGGTTTATGAAT
1 TTTGTTTCAAGGGAAACAATCTCAAAGGTTTATGAAT
*
1261697 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATG
1 TTTGTTTCAAGGGAAACAATCTCAAAGGTTTATG
1261731 TTTCAAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGGTTTATGAAT
Found at i:1261738 original size:103 final size:103
Alignment explanation
Indices: 1261594--1261796 Score: 352
Period size: 103 Copynumber: 2.0 Consensus size: 103
1261584 CGAGATAAAA
1261594 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAA
* * *
1261659 ATTTGTTTCAAGGGAAATAATCTCAAAGGTTTATGAAT
66 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGAAT
* * *
1261697 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTTAAGCGAGACAAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAA
1261762 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATG
66 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATG
1261797 TTTCAAGAGA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (103 bp):
TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAA
ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGAAT
Found at i:1261779 original size:66 final size:66
Alignment explanation
Indices: 1261697--1261862 Score: 287
Period size: 66 Copynumber: 2.5 Consensus size: 66
1261687 GTTTATGAAT
* *
1261697 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTTAAGCGAGACAAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
1261762 A
66 A
*
1261763 TTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
1261828 A
66 A
* *
1261829 TTTGTTTCAAGGGAAACAATCACAAAGGTTTATG
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATG
1261863 AATTTTGTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 94 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (66 bp):
TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
A
Found at i:1261953 original size:169 final size:169
Alignment explanation
Indices: 1261529--1261885 Score: 635
Period size: 169 Copynumber: 2.1 Consensus size: 169
1261519 CGAGATAAAA
* * *
1261529 TTTGTTTCAAG-GAAACAATCTAAAATGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGATAAA
1 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
*
1261593 ATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAA
66 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAA
* *
1261658 AATTTGTTTCAAGGGAAATAATCTCAAAGGTTTATGAAT
131 AATTTGTTTCAAGGGAAACAATCACAAAGGTTTATGAAT
*
1261697 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTTAAGCGAGACAAA
1 TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
*
1261762 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAA
66 ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAA
1261827 AATTTGTTTCAAGGGAAACAATCACAAAGGTTTATGAAT
131 AATTTGTTTCAAGGGAAACAATCACAAAGGTTTATGAAT
1261866 TTTGTTTCAAGTGAAACAAT
1 TTTGTTTCAAGTGAAACAAT
1261886 TTCCCAATTT
Statistics
Matches: 180, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
168 11 0.06
169 169 0.94
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (169 bp):
TTTGTTTCAAGTGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAA
ATTTGTTTCAAGAGAAACAATCTCAAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGCAAGACAA
AATTTGTTTCAAGGGAAACAATCACAAAGGTTTATGAAT
Found at i:1262198 original size:37 final size:37
Alignment explanation
Indices: 1262157--1262227 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1262147 AGGAAGACTA
*
1262157 TCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAATTG
1 TCTCAAGTGAGACAAAATTTGTTCTTAAGAAAAATTG
1262194 TCTCAAGTGAGACAAAATTTGTTCTTAAGAAAAA
1 TCTCAAGTGAGACAAAATTTGTTCTTAAGAAAAA
1262228 ATCTCAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (37 bp):
TCTCAAGTGAGACAAAATTTGTTCTTAAGAAAAATTG
Found at i:1269600 original size:3 final size:3
Alignment explanation
Indices: 1269585--1269653 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
1269575 CTGCAAAATG
*
1269585 TAA TAA TAT TAA TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
1269630 TAA -AA GAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1269654 TTAAAACCCA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.07
3 54 0.90
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1279668 original size:25 final size:24
Alignment explanation
Indices: 1279640--1279700 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
1279630 AATATTATAT
*
1279640 ATATAATTAATATAA-AATATATAAA
1 ATATAA-T-ATATAATAATATAAAAA
*
1279665 ATATTATATATAATTAATATAAAAA
1 ATATAATATATAA-TAATATAAAAA
*
1279690 ATATAAAATAT
1 ATATAATATAT
1279701 TATATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 6 0.20
24 1 0.03
25 23 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAATATATAATAATATAAAAA
Found at i:1279671 original size:34 final size:34
Alignment explanation
Indices: 1279628--1279710 Score: 134
Period size: 32 Copynumber: 2.5 Consensus size: 34
1279618 CCCGAACCTG
*
1279628 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1279662 AAAATA-T-TATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
1279694 AAAATATTATATTTATA
1 AAAATATTATATATATA
1279711 TATATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 30 0.67
33 2 0.04
34 13 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:1280950 original size:19 final size:19
Alignment explanation
Indices: 1280926--1280969 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1280916 AAATCGTTAA
1280926 CCATGCCAATAACGACTAT
1 CCATGCCAATAACGACTAT
***
1280945 CCATGCTTCTAACGACTAT
1 CCATGCCAATAACGACTAT
1280964 CCATGC
1 CCATGC
1280970 TTTGAAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (19 bp):
CCATGCCAATAACGACTAT
Found at i:1280970 original size:19 final size:19
Alignment explanation
Indices: 1280935--1280971 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1280925 ACCATGCCAA
1280935 TAACGACTATCCATGCTTC
1 TAACGACTATCCATGCTTC
1280954 TAACGACTATCCATGCTT
1 TAACGACTATCCATGCTT
1280972 TGAAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (19 bp):
TAACGACTATCCATGCTTC
Found at i:1282570 original size:25 final size:25
Alignment explanation
Indices: 1282523--1282583 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
1282513 ATTGTTATAC
1282523 AATATTTTTT-ATGATTAATATTAAT
1 AATATTTTTTAATGATTAATATT-AT
*
1282548 TATATTTTTTAAT-ATATAA-ATTAT
1 AATATTTTTTAATGAT-TAATATTAT
1282572 AATATTATTTTA
1 AATATT-TTTTA
1282584 TAAAATTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 7 0.23
25 19 0.61
26 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AATATTTTTTAATGATTAATATTAT
Found at i:1282926 original size:11 final size:11
Alignment explanation
Indices: 1282910--1282942 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1282900 ATCTTAGAAG
1282910 TTTGATTTTTT
1 TTTGATTTTTT
1282921 TTTGA-TTTTT
1 TTTGATTTTTT
1282931 TTTGTATTTTTT
1 TTTG-ATTTTTT
1282943 ACCAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 6 0.30
12 5 0.25
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (11 bp):
TTTGATTTTTT
Found at i:1283220 original size:15 final size:15
Alignment explanation
Indices: 1283200--1283230 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1283190 TTTATAATAT
*
1283200 ATACAATATAAAAAA
1 ATACAAAATAAAAAA
1283215 ATACAAAATAAAAAA
1 ATACAAAATAAAAAA
1283230 A
1 A
1283231 CTAGATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
ATACAAAATAAAAAA
Found at i:1284687 original size:3 final size:3
Alignment explanation
Indices: 1284679--1284723 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1284669 TTGGGTTTGT
1284679 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1284724 CATGGGTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1287774 original size:20 final size:20
Alignment explanation
Indices: 1287749--1287795 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1287739 CAATGTGTTT
* *
1287749 TAAAGTTTCAAAACTCTGTC
1 TAAAGTTTCAAAACTATGCC
**
1287769 TAAAGTTTTGAAACTATGCC
1 TAAAGTTTCAAAACTATGCC
1287789 TAAAGTT
1 TAAAGTT
1287796 GTAAACTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TAAAGTTTCAAAACTATGCC
Found at i:1291095 original size:20 final size:20
Alignment explanation
Indices: 1291070--1291107 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1291060 TGTTAATTTA
1291070 AATATTAAATTTTATAAAAT
1 AATATTAAATTTTATAAAAT
*
1291090 AATATTATATTTTATAAA
1 AATATTAAATTTTATAAA
1291108 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATTAAATTTTATAAAAT
Found at i:1291143 original size:17 final size:16
Alignment explanation
Indices: 1291105--1291154 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1291095 TATATTTTAT
*
1291105 AAAT-ATTAAAAAATA
1 AAATAATTATAAAATA
*
1291120 TAAATAATTCTATAAATA
1 -AAATAATTATA-AAATA
1291138 AAATAATTATAAAATA
1 AAATAATTATAAAATA
1291154 A
1 A
1291155 CAGTATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.34
17 14 0.48
18 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAATTATAAAATA
Found at i:1291514 original size:31 final size:30
Alignment explanation
Indices: 1291437--1291519 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
1291427 TTTAAGGGTT
* *
1291437 AAATTGATATTTTATCTAAAGTTTAGAGAC
1 AAATTAATATTCTATCTAAAGTTTAGAGAC
* * *
1291467 AAAATAATATTGTATCTAAAGTTTAAGAGTC
1 AAATTAATATTCTATCTAAAGTTT-AGAGAC
*
1291498 GAATTAATATTCTATCTAAAGT
1 AAATTAATATTCTATCTAAAGT
1291520 CCAAGCATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (30 bp):
AAATTAATATTCTATCTAAAGTTTAGAGAC
Found at i:1295043 original size:32 final size:33
Alignment explanation
Indices: 1294951--1295048 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 33
1294941 TTTGTTTCAA
1294951 TTATCGAACTT-GAAGTTTTTAAGTA-TTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1294982 TTATCGAACTTGGAAGTTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-TTTTTAAGTATTTGAAT
* * *
1295016 TTATCAAACTTGGAAG-TATTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1295048 T
1 T
1295049 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
31 11 0.18
32 19 0.31
33 10 0.16
34 21 0.34
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1295322 original size:21 final size:21
Alignment explanation
Indices: 1295296--1295343 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1295286 TGGAGCGTGG
1295296 GGGAATCAGTACCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
* **
1295317 GGGAATCGGTTTCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
1295338 GGGAAT
1 GGGAAT
1295344 TGGTTCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (21 bp):
GGGAATCAGTACCCTCTCATA
Found at i:1295348 original size:21 final size:21
Alignment explanation
Indices: 1295308--1295348 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1295298 GAATCAGTAC
1295308 CCTCTCATAGGGAATCGGTTT
1 CCTCTCATAGGGAATCGGTTT
*
1295329 CCTCTCATAGGGAATTGGTT
1 CCTCTCATAGGGAATCGGTT
1295349 CCCTAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (21 bp):
CCTCTCATAGGGAATCGGTTT
Found at i:1295547 original size:16 final size:16
Alignment explanation
Indices: 1295526--1295573 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
1295516 ATATTAAAAT
*
1295526 CGGTTTTTTTATAACC
1 CGGTTTTTTTAAAACC
* *
1295542 CGGTTTTTTAAAAAAC
1 CGGTTTTTTTAAAACC
1295558 CGGTTTTTTTAAAACC
1 CGGTTTTTTTAAAACC
1295574 GAACTGGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (16 bp):
CGGTTTTTTTAAAACC
Found at i:1295571 original size:15 final size:15
Alignment explanation
Indices: 1295519--1295574 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
1295509 ATCTGGAATA
*
1295519 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1295534 TTATAACCCGGTTTTT
1 TTA-AAACCGGTTTTT
*
1295550 TAAAAAACCGGTTTTT
1 T-TAAAACCGGTTTTT
1295566 TTAAAACCG
1 TTAAAACCG
1295575 AACTGGTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 10 0.29
16 23 0.68
17 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1295684 original size:15 final size:17
Alignment explanation
Indices: 1295658--1295689 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1295648 TTCTATGAGA
1295658 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1295674 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1295690 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1302654 original size:36 final size:36
Alignment explanation
Indices: 1302614--1302686 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
1302604 AATTAAATCT
*
1302614 TTTTAT-ATTTTAAATTTTGTAAAAAAATTATATAAA
1 TTTTATGAATTTAAATTTTGTAAAAAAA-TATATAAA
*
1302650 TTTTATGAATTTAAATTTTTTAAAAAAATATATAAA
1 TTTTATGAATTTAAATTTTGTAAAAAAATATATAAA
1302686 T
1 T
1302687 ATTTTTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 15 0.44
37 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTTATGAATTTAAATTTTGTAAAAAAATATATAAA
Found at i:1304814 original size:21 final size:19
Alignment explanation
Indices: 1304790--1304829 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1304780 ATATGAAATA
1304790 AATATAAAAAAGTATATTTAT
1 AATATAAAAAA--ATATTTAT
*
1304811 AATATTAAAAAATATTTAT
1 AATATAAAAAAATATTTAT
1304830 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AATATAAAAAAATATTTAT
Found at i:1304900 original size:19 final size:17
Alignment explanation
Indices: 1304845--1304912 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
1304835 TTTAAAATTC
*
1304845 AATTAATTATTTA-TTTA
1 AATTAA-TATTAATTTTA
*
1304862 AATTAATATTATTTTTA
1 AATTAATATTAATTTTA
1304879 AATTATATATTTAATTTTA
1 AATTA-ATA-TTAATTTTA
*
1304898 AA-TAAT-TTAAATTTA
1 AATTAATATTAATTTTA
1304913 GGGTAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.18
16 4 0.09
17 17 0.39
18 5 0.11
19 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTAATATTAATTTTA
Found at i:1306747 original size:32 final size:32
Alignment explanation
Indices: 1306706--1306770 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
1306696 TAAAAGCTCT
1306706 TAAAATGGTATCTATGTAAA-CATATTATTATA
1 TAAAATGGTATCTATGTAAATC-TATTATTATA
*
1306738 TAAAATGGTATCTATTTAAATCTATTATTATA
1 TAAAATGGTATCTATGTAAATCTATTATTATA
1306770 T
1 T
1306771 TAATGTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (32 bp):
TAAAATGGTATCTATGTAAATCTATTATTATA
Found at i:1306757 original size:16 final size:16
Alignment explanation
Indices: 1306705--1306757 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1306695 CTAAAAGCTC
1306705 TTAAAATGGTATCTAT
1 TTAAAATGGTATCTAT
* **
1306721 GTAAACATATTAT-TAT
1 TTAAA-ATGGTATCTAT
*
1306737 ATAAAATGGTATCTAT
1 TTAAAATGGTATCTAT
1306753 TTAAA
1 TTAAA
1306758 TCTATTATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
TTAAAATGGTATCTAT
Found at i:1308377 original size:65 final size:64
Alignment explanation
Indices: 1308264--1308406 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
1308254 GCACCAATCC
* * *
1308264 ATGCATCGATGCACACACCATGCATCGATGCACTGGGGATTTTATGAAAACATCAAATGTATTTG
1 ATGCATCGATGCACACACCATGCATCGATGCACTCGGGATTTTATG-AAACATCAAATGCACTTG
* * * **
1308329 ATGCATCGATGCATCA-GCCATGCATCGATGCACTCTGGCTATTT-TGAAACATTGAATGCACTT
1 ATGCATCGATGCA-CACACCATGCATCGATGCACTCGGGAT-TTTATGAAACATCAAATGCACTT
1308392 G
64 G
1308393 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1308407 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 27 0.40
65 35 0.51
66 5 0.07
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCGGGATTTTATGAAACATCAAATGCACTTG
Found at i:1308406 original size:17 final size:19
Alignment explanation
Indices: 1308384--1308426 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1308374 GAAACATTGA
*
1308384 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
1308401 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
1308420 ATGCACT
1 ATGCACT
1308427 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:1309090 original size:64 final size:66
Alignment explanation
Indices: 1308938--1309097 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 66
1308928 AATTAAATTG
* * *
1308938 AACATCGAATGCATTTCATGCATTGATGCA-CATACCATGCATCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACATCGATGCACTGAGGATTTTATGA
1309002 A
66 A
* ** *
1309003 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATACATCGATGCACTTTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACATCGATGCACTGAGGAT-TTTATG
1309066 -A
65 AA
*
1309067 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1309098 TAAGGGTCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 31 0.36
65 49 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATACATCGATGCACTGAGGATTTTATGA
A
Found at i:1310571 original size:27 final size:27
Alignment explanation
Indices: 1310533--1310588 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1310523 ACCAAAAGAG
1310533 AAGGACCATATCATTTGCTATGAATGC
1 AAGGACCATATCATTTGCTATGAATGC
1310560 AAGGACCATATCATTTGCTATGAATGC
1 AAGGACCATATCATTTGCTATGAATGC
1310587 AA
1 AA
1310589 AAAGTCGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
AAGGACCATATCATTTGCTATGAATGC
Found at i:1314755 original size:21 final size:22
Alignment explanation
Indices: 1314709--1314788 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
1314699 ACACATAACA
*
1314709 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCACCCTTGAAT
* * *
1314731 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1314752 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
1314775 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1314789 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.35
22 12 0.25
23 19 0.40
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1314778 original size:23 final size:21
Alignment explanation
Indices: 1314709--1314788 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
1314699 ACACATAACA
1314709 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCA-CCTTGAAT
* * *
1314731 GTGCATCGATTCACCATGAAG
1 GTGCATCGATGCACCTTGAAT
*
1314752 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCA--CCTTGAAT
1314775 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1314789 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.38
22 12 0.25
23 18 0.38
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACCTTGAAT
Found at i:1317634 original size:20 final size:20
Alignment explanation
Indices: 1317576--1317634 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1317566 ATCCTATTCC
* *
1317576 CTGGTAATGTTACATTCCCA
1 CTGGTAATCTTACATTCCGA
*
1317596 CTGGTAATCTTAAATTCCGA
1 CTGGTAATCTTACATTCCGA
1317616 CTGGTAATCTTACATTCCG
1 CTGGTAATCTTACATTCCG
1317635 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCGA
Found at i:1319918 original size:14 final size:13
Alignment explanation
Indices: 1319899--1319932 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1319889 TTTAAAAAAT
1319899 AAAATATTATTAAA
1 AAAATATT-TTAAA
*
1319913 AAAATATTTTAGA
1 AAAATATTTTAAA
1319926 AAAATAT
1 AAAATAT
1319933 AAATGTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AAAATATTTTAAA
Found at i:1321520 original size:23 final size:23
Alignment explanation
Indices: 1321466--1321576 Score: 122
Period size: 23 Copynumber: 4.9 Consensus size: 23
1321456 CAGTTCGTAA
*
1321466 TTTGCACCGAAGTGTCACATA--
1 TTTGCACCGAAGTGCCACATAGG
* *
1321487 ATTGTC-CCGAAG-GACAACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
*
1321510 TTTGCACCGAAGTGCCACACAGG
1 TTTGCACCGAAGTGCCACATAGG
*
1321533 TTTGCACCGAAGTGCCATATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
1321556 TTTGCACCGAAATGCCACATA
1 TTTGCACCGAAGTGCCACATA
1321577 TTTGTCTCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
22 2 0.03
23 56 0.76
24 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:1321723 original size:14 final size:15
Alignment explanation
Indices: 1321704--1321737 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1321694 TGTCTCTTAT
1321704 TCACATAG-TTCTTC
1 TCACATAGATTCTTC
*
1321718 TCACATAGATTCTTT
1 TCACATAGATTCTTC
1321733 TCACA
1 TCACA
1321738 AAACTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (15 bp):
TCACATAGATTCTTC
Found at i:1322438 original size:55 final size:55
Alignment explanation
Indices: 1322378--1322524 Score: 215
Period size: 55 Copynumber: 2.7 Consensus size: 55
1322368 TCGAAATTAC
*
1322378 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGA-ACTCGATGTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAAT-GATACTCAATGTTTT
* * * * *
1322433 GAGGGTATCGATAAACTCCTCAGTGTACCGATACACATATGATATTCAATTTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGATACTCAATGTTTT
*
1322488 AAGGGTATCGATACATTCCTCAGTGTACCGATACACA
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACA
1322525 CTCATTCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 2 0.02
55 80 0.98
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (55 bp):
AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGATACTCAATGTTTT
Found at i:1326971 original size:21 final size:21
Alignment explanation
Indices: 1326905--1326994 Score: 94
Period size: 21 Copynumber: 4.2 Consensus size: 21
1326895 GAAGTGCCAG
* *
1326905 ATAATTGTCCCGAATGACCAC
1 ATAATTGTCCCAAAGGACCAC
*
1326926 ATAGGTT-TACACCAAAGTG-CCAC
1 ATA-ATTGT-C-CCAAAG-GACCAC
*
1326949 ATAATTGTCCCGAAGGACCAC
1 ATAATTGTCCCAAAGGACCAC
1326970 ATAATTGTCCCAAAGGACCAC
1 ATAATTGTCCCAAAGGACCAC
1326991 ATAA
1 ATAA
1326995 AACCCTCGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 37 0.65
22 6 0.11
23 12 0.21
24 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.21
Consensus pattern (21 bp):
ATAATTGTCCCAAAGGACCAC
Found at i:1327119 original size:14 final size:15
Alignment explanation
Indices: 1327100--1327133 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1327090 TGTCTCTTAT
1327100 TCACATAG-TTCTTC
1 TCACATAGATTCTTC
*
1327114 TCACATAGATTCTTT
1 TCACATAGATTCTTC
1327129 TCACA
1 TCACA
1327134 ACACTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (15 bp):
TCACATAGATTCTTC
Found at i:1327833 original size:55 final size:55
Alignment explanation
Indices: 1327773--1327919 Score: 213
Period size: 55 Copynumber: 2.7 Consensus size: 55
1327763 TTGAAATTAC
*
1327773 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCACTCAATGTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACACTCAATGTTTT
* * * * * * *
1327828 GAGGGTATCAATACACTCCTCAGTGTACCGATACACATATGATATTCGATTTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACACTCAATGTTTT
*
1327883 AAAGGTATCGATACACTCCTCAGTGTACCGATACACA
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACA
1327920 CTCCTTCAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACACTCAATGTTTT
Found at i:1331545 original size:49 final size:49
Alignment explanation
Indices: 1331480--1331580 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 49
1331470 ATCAGAATCG
*
1331480 AAAACAAGAACAAAAGGAATCA-AACAAGAAACCAAGAGCAAAAAAAAAA
1 AAAACAAGAACAAAAGGAA-CACAACAAGAAACCAAAAGCAAAAAAAAAA
* * *
1331529 AAAACAAGAA-ACAAAGGAACACAACAAGAACCCAAAAGCAAGATAAAAA
1 AAAACAAGAACA-AAAGGAACACAACAAGAAACCAAAAGCAAAAAAAAAA
1331578 AAA
1 AAA
1331581 TCTAAGATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
48 3 0.07
49 43 0.93
ACGTcount: A:0.70, C:0.16, G:0.12, T:0.02
Consensus pattern (49 bp):
AAAACAAGAACAAAAGGAACACAACAAGAAACCAAAAGCAAAAAAAAAA
Found at i:1334065 original size:16 final size:17
Alignment explanation
Indices: 1334044--1334079 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1334034 ATATCATCCG
*
1334044 ATCCG-AAATTTTGGAT
1 ATCCGAAAATTTTGAAT
1334060 ATCCGAAAATTTTGAAT
1 ATCCGAAAATTTTGAAT
1334077 ATC
1 ATC
1334080 TATAGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (17 bp):
ATCCGAAAATTTTGAAT
Found at i:1338219 original size:4 final size:4
Alignment explanation
Indices: 1338210--1338268 Score: 66
Period size: 4 Copynumber: 14.0 Consensus size: 4
1338200 ATCCTAAATA
*
1338210 TAAT TAAT TAAT TAAT TAAT TAAT CCTAAAT ATAAT TTAT TAAT T-AT
1 TAAT TAAT TAAT TAAT TAAT TAAT --T-AAT -TAAT TAAT TAAT TAAT
1338257 TAAT TAAT TAAT
1 TAAT TAAT TAAT
1338269 CCTAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.06
4 37 0.77
5 3 0.06
6 2 0.04
7 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:1338226 original size:32 final size:33
Alignment explanation
Indices: 1338190--1338279 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 33
1338180 AATGCATATA
1338190 TAATTAAATT-ATCCTAAATATAATTAATTAAT
1 TAATTAAATTAATCCTAAATATAATTAATTAAT
*
1338222 TAATT-AATTAATCCTAAATATAATTTATTAAT
1 TAATTAAATTAATCCTAAATATAATTAATTAAT
1338254 T-ATTAATTAATTAATCCT-AATATAAT
1 TAATT-A--AATTAATCCTAAATATAAT
1338280 ACTTTTCGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
31 7 0.13
32 27 0.52
34 8 0.15
35 10 0.19
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (33 bp):
TAATTAAATTAATCCTAAATATAATTAATTAAT
Found at i:1340064 original size:11 final size:12
Alignment explanation
Indices: 1340040--1340065 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1340030 CAGTTTTAAC
1340040 AATTGTTAAAAA
1 AATTGTTAAAAA
1340052 AATTGTTAAAAA
1 AATTGTTAAAAA
1340064 AA
1 AA
1340066 AGTTGTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATTGTTAAAAA
Found at i:1341116 original size:30 final size:31
Alignment explanation
Indices: 1341066--1341126 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
1341056 CTATCATCTG
* *
1341066 AAAACCCAAAATTTCAATCCC-T-AATCTCT
1 AAAACCCAAAAATCCAATCCCTTAAATCTCT
1341095 AAAACCCAAAACATCCAATCCCTTAAATCTCT
1 AAAACCCAAAA-ATCCAATCCCTTAAATCTCT
1341127 TTGATCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 8 0.30
31 1 0.04
32 7 0.26
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.25
Consensus pattern (31 bp):
AAAACCCAAAAATCCAATCCCTTAAATCTCT
Found at i:1342085 original size:35 final size:35
Alignment explanation
Indices: 1342033--1342241 Score: 186
Period size: 34 Copynumber: 6.1 Consensus size: 35
1342023 TCCGACGGAC
*
1342033 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAAT-A
* * *
1342069 ATATAATCTATATTTTTTAAAACGTTTTTGAAAAT-
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAATA
*
1342104 GTAT-ATATATAGTTTTTAAAACATTTTGAAAATA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATA
* *
1342138 A-AT-ATA-GT--TTTTTAAAACATTTTGAAAACA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATA
* * * *
1342168 TATATATTATATAG-TTTGAAATCATTGTGAAAACT-
1 -ATATAATATATAGTTTTTAAAACATTTTGAAAA-TA
* * *
1342203 -TATAGTATATAGTTTTAAAAACATTTTGAAAATT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATA
1342237 ATATA
1 ATATA
1342242 GTTTTGAAAA
Statistics
Matches: 140, Mismatches: 21, Indels: 25
0.75 0.11 0.13
Matches are distributed among these distances:
30 21 0.15
31 1 0.01
32 3 0.02
33 29 0.21
34 33 0.24
35 23 0.16
36 20 0.14
37 10 0.07
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (35 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATA
Found at i:1342111 original size:30 final size:29
Alignment explanation
Indices: 1342039--1342304 Score: 138
Period size: 34 Copynumber: 8.2 Consensus size: 29
1342029 GGACATATAT
*
1342039 TATATAGTTTTTAAAACATTTTGAAAATAAATA
1 TATATATTTTTTAAAACATTTTG---A-AAATA
*
1342072 TAATCTATATTTTTTAAAACGTTTTTGAAAATGTA
1 T-A--TATATTTTTTAAAAC-ATTTTGAAAA--TA
1342107 TATATATAGTTTTTAAAACATTTTGAAAATA
1 TATATAT--TTTTTAAAACATTTTGAAAATA
*
1342138 AATATAGTTTTTTAAAACATTTTGAAAACATA
1 TATATA-TTTTTTAAAACATTTTG-AAA-ATA
* * *
1342170 TATATTATATAGTTTGAAATCATTGTGAAAACTTA
1 TATA-TAT-T--TTTTAAAACATTTTGAAAA--TA
*
1342205 TAGTATATAGTTTTAAAAACATTTTGAAAAT-
1 TA-TATAT--TTTTTAAAACATTTTGAAAATA
* * *
1342236 TATATAGTTTTGAAAACATTTTTCAAAAATA
1 TATATATTTTTTAAAACA-TTTT-GAAAATA
* * *
1342267 TATAATATATAATTTAAAATATTTTGTGAAATA
1 TAT-ATAT-T-TTTTAAAACATTTTG-AAAATA
1342300 TATAT
1 TATAT
1342305 TATATAAGTT
Statistics
Matches: 186, Mismatches: 21, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
28 10 0.05
29 4 0.02
30 25 0.13
31 15 0.08
32 19 0.10
33 30 0.16
34 39 0.21
35 22 0.12
36 17 0.09
37 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (29 bp):
TATATATTTTTTAAAACATTTTGAAAATA
Found at i:1342263 original size:29 final size:28
Alignment explanation
Indices: 1342208--1342270 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1342198 AAACTTATAG
* *
1342208 TATATAGTTTTAAAAACATTTTGAAAAT
1 TATATAGTTTTAAAAACATTTTCAAAAA
*
1342236 TATATAGTTTTGAAAACATTTTTCAAAAA
1 TATATAGTTTTAAAAACA-TTTTCAAAAA
1342265 TATATA
1 TATATA
1342271 ATATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (28 bp):
TATATAGTTTTAAAAACATTTTCAAAAA
Found at i:1342297 original size:98 final size:97
Alignment explanation
Indices: 1342037--1342316 Score: 302
Period size: 98 Copynumber: 2.8 Consensus size: 97
1342027 ACGGACATAT
* * ** **
1342037 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATCTATATTTTTTAAAACGTTTT-TGAA
1 ATTATATAGTTTTTAAAACATTTTGAAAACATATATAA--TATATAATTTAAAATATTTTGTGAA
*
1342101 AATGTATATATATAGTTTTTAAAACATTTTGAAA
64 AATGTATATATATAGTTTTAAAAACATTTTGAAA
* * * *
1342135 ATAAATATAGTTTTTTAAAACATTTTGAAAACATATATATTATATAGTTTGAAATCA--TTGTGA
1 AT-TATATAG-TTTTTAAAACATTTTGAAAACATATATAATATATAATTTAAAAT-ATTTTGTGA
1342198 AAACT-TATAGTATATAGTTTTAAAAACATTTTGAAA
63 AAA-TGTATA-TATATAGTTTTAAAAACATTTTGAAA
* *
1342234 ATTATATAGTTTTGAAAACATTTTTCAAAA-ATATATAATATATAATTTAAAATATTTTGTG-AA
1 ATTATATAGTTTTTAAAACA-TTTTGAAAACATATATAATATATAATTTAAAATATTTTGTGAAA
*
1342297 ATATATATTATATAAGTTTT
65 ATGTATA-TATAT-AGTTTT
1342317 TGGAAAATAT
Statistics
Matches: 154, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
96 2 0.01
97 44 0.29
98 48 0.31
99 34 0.22
100 26 0.17
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (97 bp):
ATTATATAGTTTTTAAAACATTTTGAAAACATATATAATATATAATTTAAAATATTTTGTGAAAA
TGTATATATATAGTTTTAAAAACATTTTGAAA
Found at i:1342334 original size:5 final size:5
Alignment explanation
Indices: 1342324--1342381 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
1342314 TTTTGGAAAA
* * *
1342324 TATTT TATTT TATCT TATTAT TATAT TATTATT TATTT CTTTTT TATTT
1 TATTT TATTT TATTT TATT-T TATTT TA-T-TT TATTT -TATTT TATTT
1342373 TATTT TATT
1 TATTT TATT
1342382 AATTCATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 30 0.70
6 10 0.23
7 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:1342380 original size:25 final size:25
Alignment explanation
Indices: 1342324--1342403 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
1342314 TTTTGGAAAA
* * *
1342324 TATTTTATTT-TATC-TTATTATTA
1 TATTTTATTTATTTCTTTTTTATTT
1342347 TATTATTATTTATTTCTTTTTTATTT
1 TATT-TTATTTATTTCTTTTTTATTT
*
1342373 TATTTTA-TTAATTCATTTTTTATTT
1 TATTTTATTTATTTC-TTTTTTATTT
*
1342398 CATTTT
1 TATTTT
1342404 TCTTTCCAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
23 4 0.08
24 12 0.25
25 21 0.44
26 11 0.23
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTTTATTTATTTCTTTTTTATTT
Found at i:1349393 original size:244 final size:244
Alignment explanation
Indices: 1348985--1349704 Score: 888
Period size: 244 Copynumber: 2.9 Consensus size: 244
1348975 AGCTCAAGAC
* * * *
1348985 AAGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCAT
1 AAGAAGGGTTGTCTACCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCAT
1349050 TTGCAGCATAGCTTAAGTCGAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
64 TTGCAGCATAGCTTAAGTCGAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
1349115 TCGAGGGCATATCATTTATAGCATAACTCAAGGCTAGAAGGGT-TCTGTCACCAAAAGTCCTTCG
129 TCGAGGGCATATCATTTA-AGCATAACTCAAGGCTAGAAGGGTATCTGTCACCAAAAG-CCTTCG
*
1349179 AGTTCGACTACGTTCAGCTCCAAGGCAT-T-ATTTGCAGCACAACTTAAGTCT
192 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
* * * * *
1349230 -AG-AGGGTTGTCTGCTAACAAAAGACCTTTGAGTTTGACTACGCTCAG-TCAAACGACACATCA
1 AAGAAGGGTTGTCTACCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC-AA-GGCACATCA
* * *
1349292 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGATTTTGATTACACTCAG
63 TTTGCAGCATAGCTTAAGTCGAGAAGGG-TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAG
*
1349357 CTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTATCTGTCACC-AAA-CCTAC
127 CTTCGAGGGCATATCATTTA-AGCATAACTCAAGGCTAGAAGGGTATCTGTCACCAAAAGCCTTC
*
1349420 GAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
191 GAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
* * * * *
1349474 AAGAAGGGTTGTCTACCAACAAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
1 AAGAAGGGTTGTCTACCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCAT
* * * * * * ** * *
1349538 TTACAGCATAACTCAAGGCTAGAAGAGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTC
64 TTGCAGCATAGCTTAAGTCGAGAAG-GGTATCTG---CCAAAGACCCCCGAGTTCGATTACACTC
* * *
1349603 AGC-TC-AAGGCATATCATTGT-AGCATAACTCAGGGCTAGAAGGGTTATCTATCACCAAAAGAC
125 AGCTTCGAGGGCATATCATT-TAAGCATAACTCAAGGCTAGAAGGG-TATCTGTCACCAAAAG-C
*
1349665 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
187 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTT
1349705 ACAAACATAG
Statistics
Matches: 411, Mismatches: 44, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
241 1 0.00
242 35 0.09
243 73 0.18
244 120 0.29
245 73 0.18
246 40 0.10
247 6 0.01
248 25 0.06
249 38 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (244 bp):
AAGAAGGGTTGTCTACCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
GAGGGCATATCATTTAAGCATAACTCAAGGCTAGAAGGGTATCTGTCACCAAAAGCCTTCGAGTT
CGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
Found at i:1349398 original size:81 final size:80
Alignment explanation
Indices: 1349004--1349704 Score: 540
Period size: 81 Copynumber: 8.6 Consensus size: 80
1348994 TATTTGCCAA
* * * * * * *
1349004 CCAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTTGCAGCATAACTCAAGGC
*
1349069 GAGAAGGG-TATCTG
66 TAGAAGGGTTATCTG
* * * * **
1349083 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGG
1 CCAAAGACCTCCGAGTTCGACTACGCTCAGC-TCGAAGGCATATCATTTGCAGCATAACTCAAGG
* * *
1349148 CTAGAAGGGTTCTGTCA
65 CTAGAAGGGTTATCT-G
* * * * * * *
1349165 CCAAAAGTCCTTCGAGTTCGACTACGTTCAGCTCCAAGGCAT-T-ATTTGCAGCACAACTTAAGT
1 CC-AAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTTGCAGCATAACTCAAGG
*
1349228 CTAG-AGGGTTGTCTG
65 CTAGAAGGGTTATCTG
** * * * * * * *
1349243 CTAACAAAAGACCTTTGAGTTTGACTACGCTCAG-TCAAACGACACATCATTTGTAGCATAGCTT
1 C---C-AAAGACCTCCGAGTTCGACTACGCTCAGCTCGAA-GGCATATCATTTGCAGCATAACTC
* * *
1349307 AAGTCGAGAAGGGCTATCTG
61 AAGGCTAGAAGGGTTATCTG
* * * * * * *
1349327 CCAAAGACCCCCGATTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTCCGAGTTCGACTACGCTCAGC-TCGAAGGCATATCATTTGCAGCATAACTCAAGG
1349392 CTAGAAGGG-TATCTG
65 CTAGAAGGGTTATCTG
* * * * * *
1349407 TCACCAA-ACCTACGAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAG
1 -C-CAAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTTGCAGCATAACTCAAG
* * *
1349471 TCTAAGAAGGGTTGTCTAC
64 GCT-AGAAGGGTTATCT-G
* * * *
1349490 CAACAAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAA
1 C--CAAAGACCTCCGAGTTCGACTACGCTCAGC-TCGAAGGCATATCATTTGCAGCATAACTCAA
*
1349554 GGCTAGAAGAGTTATCTG
63 GGCTAGAAGGGTTATCTG
* * *
1349572 TCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCATATCA-TTGTAGCATAACTCAG
1 ---CCAAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTTGCAGCATAACTCAA
*
1349635 GGCTAGAAGGGTTATCTATCA
63 GGCTAGAAGGGTTATC--T-G
* * *
1349656 CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 CC-AAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTT
1349705 ACAAACATAG
Statistics
Matches: 490, Mismatches: 101, Indels: 57
0.76 0.16 0.09
Matches are distributed among these distances:
78 1 0.00
79 34 0.07
80 113 0.23
81 120 0.24
82 63 0.13
83 96 0.20
84 62 0.13
85 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (80 bp):
CCAAAGACCTCCGAGTTCGACTACGCTCAGCTCGAAGGCATATCATTTGCAGCATAACTCAAGGC
TAGAAGGGTTATCTG
Found at i:1349536 original size:164 final size:164
Alignment explanation
Indices: 1349328--1349707 Score: 507
Period size: 164 Copynumber: 2.3 Consensus size: 164
1349318 GGCTATCTGC
* *
1349328 CAAAGACCCCCGATTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGC
1 CAAAGA-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGC
1349393 TAGAAG-GGTATCTGTCACC-AA-ACCTACGAATTCGACTACGCTCAGCTCCAAGGCATATCATT
65 TAGAAGAGGTATCTGTCACCAAAGACCTACGAATTCGACTACGCTCAGCT-CAAGGCATATCA-T
* * *
1349455 TGCAGCACAACTTAAGTCTAAGAAGGGTTGTCTACCAA
128 TGCAGCACAACTCAAGGCT-AGAAGGGTTATCTACCAA
1349493 CAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCT
1 CAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCT
* * * *
1349558 AGAAGAGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCATATCATTGT
66 AGAAGAGGTATCTGTCACCAAAGACCTACGAATTCGACTACGCTCAGCTCAAGGCATATCATTGC
* * * *
1349623 AGCATAACTCAGGGCTAGAAGGGTTATCTATCAC
131 AGCACAACTCAAGGCTAGAAGGGTTATCTACCAA
* * * * * *
1349657 CAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACA
1 C-AAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACA
1349708 AACATAGCCC
Statistics
Matches: 191, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
164 78 0.41
165 57 0.30
166 32 0.17
167 24 0.13
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (164 bp):
CAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCT
AGAAGAGGTATCTGTCACCAAAGACCTACGAATTCGACTACGCTCAGCTCAAGGCATATCATTGC
AGCACAACTCAAGGCTAGAAGGGTTATCTACCAA
Found at i:1349910 original size:80 final size:83
Alignment explanation
Indices: 1349786--1349995 Score: 291
Period size: 84 Copynumber: 2.5 Consensus size: 83
1349776 ACAAAACCCC
* * * *
1349786 CGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAA-G-TA
1 CGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGTTA
*
1349849 TCTGTCACC-AAAGACCTT
65 TCTATCACCAAAAGACCTT
** *
1349867 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTCAGGGCTAGAAGGGTTA
1 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAA-GGTTA
1349932 TCTATCACCAAAAGACCTT
65 TCTATCACCAAAAGACCTT
* *
1349951 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATA
1 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATA
1349996 GCCCAAAGCA
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
80 34 0.30
81 18 0.16
82 1 0.01
83 10 0.09
84 50 0.44
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (83 bp):
CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGTTAT
CTATCACCAAAAGACCTT
Found at i:1350012 original size:84 final size:83
Alignment explanation
Indices: 1349786--1350022 Score: 228
Period size: 84 Copynumber: 2.9 Consensus size: 83
1349776 ACAAAACCCC
* * * * * * * * * *
1349786 CGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAA--G-T
1 CGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAACATAACCCAAAGCAAAAAGGGCT
*
1349848 ATCTGTCACCAAAGACCTT
65 ATCTATCACCAAAGACCTT
* ** * * ** * * *
1349867 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTCAGGGCTAGAAGGGTTA
1 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACCCAAAGCAAAAAGGGCTA
1349932 TCTATCACCAAAAGACCTT
66 TCTATCACC-AAAGACCTT
*
1349951 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCCCAAAGCAAAAAGGGCTA
1 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACCCAAAGCAAAAAGGGCTA
*
1350016 TATATCA
66 TCTATCA
1350023 ATAAAATTAT
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
80 34 0.26
81 18 0.14
82 1 0.01
83 10 0.08
84 69 0.52
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (83 bp):
CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACCCAAAGCAAAAAGGGCTA
TCTATCACCAAAGACCTT
Found at i:1350611 original size:36 final size:37
Alignment explanation
Indices: 1350563--1350903 Score: 191
Period size: 34 Copynumber: 10.1 Consensus size: 37
1350553 ATATATACAC
* *
1350563 ATATATATTATATAG-TTTGAAAACATTTTTTAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
1350599 ATATATAATATATAGTTTTGAAAACATGTTTGAAAACGT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA--T
* * *
1350638 TTATATATTATATAGTTTTTAAAACA-TTTTG-AAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* * * *
1350673 AAATA-AATATATATTTTTTAAAACGTTTTTG-AAA-
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* *
1350707 ATGTAT-AT-TATAGTTTTTAAAACA-TTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
1350741 A-A-AT-ATAGT-T--TTTTAAAAACA-TTTTG--AA-
1 ATATATAATA-TATAGTTTTGAAAACATTTTTGAAAAT
* * *
1350769 A-ACAT-ATATATAGTTTTGAAATCA-TTGTGAAAACT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA-T
*
1350804 -TATATAGTATATAGTTTT-AAAA-ATTTTTG---A-
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
1350834 A-A-AT--TATATAGTTTTGAAAACATTTTTCAAAA-
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* *
1350866 ATATAT-ATATA-A-TTTT-AAAATATTTTTGTGAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTG-AAAAT
1350900 ATAT
1 ATAT
1350904 TATATAGGTT
Statistics
Matches: 245, Mismatches: 29, Indels: 64
0.72 0.09 0.19
Matches are distributed among these distances:
27 11 0.04
28 7 0.03
29 16 0.07
30 1 0.00
31 28 0.11
32 22 0.09
33 28 0.11
34 32 0.13
35 26 0.11
36 25 0.10
37 21 0.09
38 4 0.02
39 24 0.10
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:1350652 original size:39 final size:36
Alignment explanation
Indices: 1350563--1350843 Score: 192
Period size: 34 Copynumber: 8.2 Consensus size: 36
1350553 ATATATACAC
*
1350563 ATATATATTATATAG-TTTGAAAACATTTTTTAAAAT
1 ATATATATTATATAGTTTTGAAAACA-TTTTGAAAAT
*
1350599 ATATATAATATATAGTTTTGAAAACATGTTTGAAAACGT
1 ATATATATTATATAGTTTTGAAAACAT-TTTGAAAA--T
* *
1350638 TTATATATTATATAGTTTTTAAAACATTTTG-AAAT
1 ATATATATTATATAGTTTTGAAAACATTTTGAAAAT
* * * * *
1350673 AAATA-AATATATATTTTTTAAAACGTTTTTG-AAA-
1 ATATATATTATATAGTTTTGAAAAC-ATTTTGAAAAT
* *
1350707 ATGTATA-T-TATAGTTTTTAAAACATTTTGAAAAT
1 ATATATATTATATAGTTTTGAAAACATTTTGAAAAT
*
1350741 A-A-ATA-TAGT-T--TTTTAAAAACATTTTG--AA-
1 ATATATATTA-TATAGTTTTGAAAACATTTTGAAAAT
* * *
1350769 A-ACATA-TATATAGTTTTGAAATCATTGTGAAAACT
1 ATATATATTATATAGTTTTGAAAACATTTTGAAAA-T
*
1350804 -TATATAGTATATAGTTTT-AAAA-ATTTTTGAAAAT
1 ATATATATTATATAGTTTTGAAAACA-TTTTGAAAAT
1350838 -TATATA
1 ATATATA
1350844 GTTTTGAAAA
Statistics
Matches: 202, Mismatches: 22, Indels: 44
0.75 0.08 0.16
Matches are distributed among these distances:
28 3 0.01
29 8 0.04
31 28 0.14
32 9 0.04
33 20 0.10
34 31 0.15
35 28 0.14
36 26 0.13
37 20 0.10
38 4 0.02
39 25 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATATATTATATAGTTTTGAAAACATTTTGAAAAT
Found at i:1350729 original size:33 final size:31
Alignment explanation
Indices: 1350648--1350907 Score: 178
Period size: 31 Copynumber: 8.1 Consensus size: 31
1350638 TTATATATTA
*
1350648 TATAGTTTTTAAAACATTTTGAAATAAATAAAT
1 TATAGTTTTTAAAACATTTTG-AA-AAATATAT
* * *
1350681 ATATATTTTTTAAAACGTTTTTGAAAATGTATAT
1 -TATAGTTTTTAAAAC-ATTTTGAAAA-ATATAT
*
1350715 TATAGTTTTTAAAACATTTTG-AAAATA-AA
1 TATAGTTTTTAAAACATTTTGAAAAATATAT
1350744 TATAGTTTTTTAAAAACATTTTGAAAACATATA-
1 TATAG-TTTTT-AAAACATTTTGAAAA-ATATAT
* * *
1350777 TATAGTTTTGAAATCATTGTGAAAACTTATATAGT
1 TATAGTTTTTAAAACATTTTGAAAA---ATATA-T
1350812 ATATAG-TTTTAAAA-ATTTTTG-AAAAT-TA-
1 -TATAGTTTTTAAAACA-TTTTGAAAAATATAT
* *
1350840 TATAGTTTTGAAAACATTTTTCAAAAATATAT
1 TATAGTTTTTAAAACA-TTTTGAAAAATATAT
* * **
1350872 ATATA-ATTTTAAAATATTTTTGTGAAATATAT
1 -TATAGTTTTTAAAACA-TTTTGAAAAATATAT
1350904 TATA
1 TATA
1350908 TAGGTTTTTG
Statistics
Matches: 184, Mismatches: 23, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.03
28 7 0.04
29 12 0.07
30 14 0.08
31 35 0.19
32 33 0.18
33 33 0.18
34 25 0.14
35 15 0.08
36 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (31 bp):
TATAGTTTTTAAAACATTTTGAAAAATATAT
Found at i:1350753 original size:96 final size:93
Alignment explanation
Indices: 1350647--1350885 Score: 236
Period size: 97 Copynumber: 2.5 Consensus size: 93
1350637 TTTATATATT
* * *
1350647 ATATAGTTTTTAAAACATTTTGAAATAAATAAATATATATTTTTTAAAACGTTTTTGAAAA-TGT
1 ATATAGTTTTTAAAACATTTTGAAA-AAAT-AATATATA-TTTTTAAAAC-ATTGTGAAAACTAT
1350711 ATA-T-TATAGTTTTTAAAACA-TTTTGAAAATAA
62 ATAGTATATAG-TTTTAAAA-ATTTTTGAAAAT-A
* * *
1350743 ATATAGTTTTTTAAAAACATTTTGAAAACAT-ATATATAGTTTTGAAATCATTGTGAAAACTTAT
1 ATATAG-TTTTT-AAAACATTTTGAAAAAATAATATATA-TTTTTAAAACATTGTGAAAAC-TAT
*
1350807 ATAGTATATAGTTTTAAAAATTTTTGAAAATT
62 ATAGTATATAGTTTTAAAAATTTTTGAAAATA
* ** *
1350839 ATATAGTTTTGAAAACATTTTTCAAAAATATATATATAATTTTAAAA
1 ATATAGTTTTTAAAACATTTTGAAAAAATA-ATATATATTTTTAAAA
1350886 TATTTTTGTG
Statistics
Matches: 119, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
94 23 0.19
95 25 0.21
96 25 0.21
97 27 0.23
98 19 0.16
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (93 bp):
ATATAGTTTTTAAAACATTTTGAAAAAATAATATATATTTTTAAAACATTGTGAAAACTATATAG
TATATAGTTTTAAAAATTTTTGAAAATA
Found at i:1350775 original size:29 final size:29
Alignment explanation
Indices: 1350647--1350859 Score: 135
Period size: 33 Copynumber: 6.7 Consensus size: 29
1350637 TTTATATATT
1350647 ATATAGTTTTTAAAACATTTTGAAATAAATAAA
1 ATATAGTTTTTAAAACATTTTG--A-AAAT-AA
* *
1350680 TATATATTTTTTAAAACGTTTTTGAAAATGTATA
1 -ATATAGTTTTTAAAAC-ATTTTGAAAA--TA-A
*
1350714 TTATAGTTTTTAAAACATTTTGAAAATAA
1 ATATAGTTTTTAAAACATTTTGAAAATAA
*
1350743 ATATAGTTTTTTAAAAACATTTTGAAAACATAT
1 ATATAG-TTTTT-AAAACATTTTG-AAA-ATAA
* * *
1350776 ATATAGTTTTGAAATCATTGTGAAAACTTATA
1 ATATAGTTTTTAAAACATTTTGAAAA--TA-A
*
1350808 TAGTATA-TAGTTTTAAAA-ATTTTTGAAAAT-T
1 -A-TATAGT--TTTTAAAACA-TTTTGAAAATAA
*
1350839 ATATAGTTTTGAAAACATTTT
1 ATATAGTTTTTAAAACATTTT
1350860 TCAAAAATAT
Statistics
Matches: 145, Mismatches: 16, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
28 11 0.08
29 12 0.08
30 12 0.08
31 22 0.15
32 19 0.13
33 28 0.19
34 22 0.15
35 19 0.13
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (29 bp):
ATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:1350845 original size:27 final size:29
Alignment explanation
Indices: 1350811--1350872 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1350801 ACTTATATAG
* *
1350811 TATATAGTTTT-AAAA-ATTTTTGAAAAT
1 TATATAGTTTTGAAAACATTTTTCAAAAA
1350838 TATATAGTTTTGAAAACATTTTTCAAAAA
1 TATATAGTTTTGAAAACATTTTTCAAAAA
1350867 TATATA
1 TATATA
1350873 TATAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 11 0.35
28 4 0.13
29 16 0.52
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (29 bp):
TATATAGTTTTGAAAACATTTTTCAAAAA
Found at i:1350964 original size:1 final size:1
Alignment explanation
Indices: 1350958--1350997 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
1350948 TTTATTATTA
* * *
1350958 TTTTTTTTTTATTTTTTTATTTATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1350998 CCAGGTCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:1350975 original size:12 final size:12
Alignment explanation
Indices: 1350958--1350997 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1350948 TTTATTATTA
1350958 TTTTTTTTTTAT
1 TTTTTTTTTTAT
*
1350970 TTTTTTATTTAT
1 TTTTTTTTTTAT
1350982 TTTTTTTTTT-T
1 TTTTTTTTTTAT
1350993 TTTTT
1 TTTTT
1350998 CCAGGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:1350977 original size:29 final size:30
Alignment explanation
Indices: 1350929--1350996 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
1350919 AAAATTTTTA
*
1350929 TTTTTCTTTATTCTTATTATTTATTATTAT
1 TTTTTTTTTATTCTTATTATTTATTATTAT
* * *
1350959 TTTTTTTTTATT-TTTTTATTTATTTTTTT
1 TTTTTTTTTATTCTTATTATTTATTATTAT
1350988 TTTTTTTTT
1 TTTTTTTTT
1350997 TCCAGGTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTATTCTTATTATTTATTATTAT
Found at i:1352379 original size:16 final size:17
Alignment explanation
Indices: 1352305--1352381 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 17
1352295 TATTACTATA
1352305 TATTTTTATTTGT--TTT
1 TATTTTTATTT-TCATTT
1352321 TATTTTTATTTTTAGCATTAT
1 TATTTTTA-TTTT--CATT-T
* *
1352342 TATTATTATTCATTCATCT
1 TATTTTTATT--TTCATTT
1352361 TATTTTTATTTT-ATTT
1 TATTTTTATTTTCATTT
1352377 TATTT
1 TATTT
1352382 CATCGGTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
16 17 0.35
17 5 0.10
19 10 0.20
20 7 0.14
21 8 0.16
22 2 0.04
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (17 bp):
TATTTTTATTTTCATTT
Found at i:1355180 original size:14 final size:14
Alignment explanation
Indices: 1355157--1355186 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1355147 AAGTTAAGAG
1355157 TTAATAAATTATAA
1 TTAATAAATTATAA
*
1355171 TTAATTAATTATAA
1 TTAATAAATTATAA
1355185 TT
1 TT
1355187 TTTAGAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATAAATTATAA
Found at i:1356244 original size:58 final size:58
Alignment explanation
Indices: 1356083--1356232 Score: 275
Period size: 58 Copynumber: 2.6 Consensus size: 58
1356073 GGCATTGCTG
*
1356083 TGTTGAGTTCCC-CAACTATTAAAAGTTATAAAATAATCCATTGATTGTAGGGAAGATT
1 TGTTGAG-TCCCACAACCATTAAAAGTTATAAAATAATCCATTGATTGTAGGGAAGATT
1356141 TGTTGAGTCCCACAACCATTAAAAGTTATAAAATAATCCATTGATTGTAGGGAAGATT
1 TGTTGAGTCCCACAACCATTAAAAGTTATAAAATAATCCATTGATTGTAGGGAAGATT
1356199 TGTTGAGTCCCACAACCATTAAAAGTTATAAAAT
1 TGTTGAGTCCCACAACCATTAAAAGTTATAAAAT
1356233 GATCACCTGA
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
57 4 0.04
58 86 0.96
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (58 bp):
TGTTGAGTCCCACAACCATTAAAAGTTATAAAATAATCCATTGATTGTAGGGAAGATT
Found at i:1357370 original size:35 final size:34
Alignment explanation
Indices: 1357322--1357400 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 34
1357312 AATTTATATT
1357322 AAAATATTCTAAAAAGTTTATTT-ATTTTATTATGA
1 AAAATATTCT-AAAAGTTTATTTAATTTTATT-TGA
* *
1357357 AAAATATTTTAAAATTTTATTTAAATTTTATTTGA
1 AAAATATTCTAAAAGTTTATTT-AATTTTATTTGA
1357392 AATAATATT
1 AA-AATATT
1357401 AATTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 11 0.28
35 14 0.36
36 14 0.36
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
AAAATATTCTAAAAGTTTATTTAATTTTATTTGA
Found at i:1357399 original size:36 final size:35
Alignment explanation
Indices: 1357322--1357400 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 35
1357312 AATTTATATT
1357322 AAAATATTCTAAAAAGTTTATTTATTTTATTATGA
1 AAAATATTCTAAAAAGTTTATTTATTTTATTATGA
* *
1357357 AAAATATT-TTAAAATTTTATTTAAATTTTATT-TGA
1 AAAATATTCTAAAAAGTTTATTT--ATTTTATTATGA
1357392 AATAATATT
1 AA-AATATT
1357401 AATTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 12 0.31
35 13 0.33
36 14 0.36
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (35 bp):
AAAATATTCTAAAAAGTTTATTTATTTTATTATGA
Found at i:1357400 original size:23 final size:24
Alignment explanation
Indices: 1357374--1357422 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1357364 TTTAAAATTT
1357374 TATTTAAAT-TTTATTTGAAATAA
1 TATTTAAATATTTATTTGAAATAA
*
1357397 TA-TTAATTATTTATTTGAAATAA
1 TATTTAAATATTTATTTGAAATAA
1357420 TAT
1 TAT
1357423 CATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TATTTAAATATTTATTTGAAATAA
Found at i:1358928 original size:23 final size:22
Alignment explanation
Indices: 1358902--1358965 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 22
1358892 CAGCTCATAT
1358902 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
*
1358925 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACC-TAGTGCCACGTAG
1358948 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
1358966 TATAATAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:1359159 original size:103 final size:103
Alignment explanation
Indices: 1358981--1359301 Score: 561
Period size: 103 Copynumber: 3.1 Consensus size: 103
1358971 TAATGTCCAT
* *
1358981 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGACCAAGTATGCGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
*
1359046 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1359084 AAGGACCACATATCATTCCTTAAGAATCATATACATATATCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
* *
1359149 GACCTAACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1359187 AAGGACCACATATCATTCCTTAAAAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
*
1359252 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1359290 AAGGACCACATA
1 AAGGACCACATA
1359302 GACCCTCTAC
Statistics
Matches: 206, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1365168 original size:23 final size:22
Alignment explanation
Indices: 1365142--1365205 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
1365132 CAACTCATAT
*
1365142 AATTGCACCTAAGTGCCACGTAG
1 AATTGTACCT-AGTGCCACGTAG
* *
1365165 AATTGTACCGGAGTGCCGCGTAG
1 AATTGTACC-TAGTGCCACGTAG
1365188 AATTGTACCGTAGTGCCA
1 AATTGTACC-TAGTGCCA
1365206 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
AATTGTACCTAGTGCCACGTAG
Done.