Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 83 of 204
Found at i:25577915 original size:40 final size:40
Alignment explanation
Indices: 25577866--25578084 Score: 242
Period size: 40 Copynumber: 5.5 Consensus size: 40
25577856 AAGAAAATGT
* ** *
25577866 CCCTAAATGCACATGCGTGCCCCTGATTGTACTTCGGTAC
1 CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
* *
25577906 CCCTGAATGCACATATG-GGCCCTTTTTGTACTTCGGTAC
1 CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
* * * * * *
25577945 CTCTGAATGTACTTATGTGCCCCTGTTTGTACTTTGATGC
1 CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
* * *
25577985 CCCTGAATGCACATACGTGCCCCTTTTTGTACTTGGGTAC
1 CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
* * *
25578025 CCCTGAATGCACATATATGCCCCTGTTTGTACTTCAGTTC
1 CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
* * *
25578065 CCTTGAAGGCACATTTGTGC
1 CCCTGAATGCACATATGTGC
25578085 TTTAAATGCA
Statistics
Matches: 146, Mismatches: 32, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
39 33 0.23
40 113 0.77
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (40 bp):
CCCTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTAC
Found at i:25577975 original size:20 final size:20
Alignment explanation
Indices: 25577952--25578058 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
25577942 TACCTCTGAA
25577952 TGTACTTATGTGCCCCTGTT
1 TGTACTTATGTGCCCCTGTT
**
25577972 TGTACTT-TGATGCCCCTGAA
1 TGTACTTATG-TGCCCCTGTT
* * * *
25577992 TGCACATACGTGCCCCTTTT
1 TGTACTTATGTGCCCCTGTT
** * **
25578012 TGTACTTGGGTACCCCTGAA
1 TGTACTTATGTGCCCCTGTT
* * *
25578032 TGCACATATATGCCCCTGTT
1 TGTACTTATGTGCCCCTGTT
25578052 TGTACTT
1 TGTACTT
25578059 CAGTTCCCTT
Statistics
Matches: 59, Mismatches: 26, Indels: 4
0.66 0.29 0.04
Matches are distributed among these distances:
19 2 0.03
20 56 0.95
21 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (20 bp):
TGTACTTATGTGCCCCTGTT
Found at i:25581696 original size:25 final size:25
Alignment explanation
Indices: 25581668--25581725 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
25581658 TCCTCCGAGT
25581668 TGAATAACGGGAAGCTCATGAGAGC
1 TGAATAACGGGAAGCTCATGAGAGC
* * *
25581693 TGAATATCGGGAAGCTTATGCGAGC
1 TGAATAACGGGAAGCTCATGAGAGC
*
25581718 TGTATAAC
1 TGAATAAC
25581726 AGACTGCTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (25 bp):
TGAATAACGGGAAGCTCATGAGAGC
Found at i:25593581 original size:9 final size:9
Alignment explanation
Indices: 25593567--25593598 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
25593557 TTTAAATTTT
*
25593567 ATAATTTAA
1 ATAATTCAA
25593576 ATAATTCAA
1 ATAATTCAA
25593585 ATAATTCAA
1 ATAATTCAA
25593594 ATAAT
1 ATAAT
25593599 AGATTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (9 bp):
ATAATTCAA
Found at i:25593726 original size:20 final size:20
Alignment explanation
Indices: 25593673--25593718 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
25593663 ACAAAACTAC
25593673 AAAATAATTCAAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
25593694 AAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
25593714 AAAAA
1 AAAAA
25593719 TTCCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:25595844 original size:4 final size:4
Alignment explanation
Indices: 25595835--25595911 Score: 91
Period size: 4 Copynumber: 17.8 Consensus size: 4
25595825 AACTTGAGCC
*
25595835 TTAT TTAT TTAT TTAT TTAT TCAT TTCAT TTCAT TTAT TTAT TTAT TTCATT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT TTAT TTAT TTAT TT-A-T
25595887 TTAT TTCAT TTCAT TTAT TTAT TTA
1 TTAT TT-AT TT-AT TTAT TTAT TTA
25595912 CAAGAAAATA
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
4 44 0.66
5 20 0.30
6 3 0.04
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:25595864 original size:5 final size:5
Alignment explanation
Indices: 25595854--25595910 Score: 70
Period size: 5 Copynumber: 12.4 Consensus size: 5
25595844 TATTTATTTA
*
25595854 TTCAT TTCAT TTCAT TT-AT TT-AT TT-AT TTCAT TTTAT TTCAT TTCAT
1 TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT
25595901 TT-AT TT-AT TT
1 TTCAT TTCAT TT
25595911 ACAAGAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
4 20 0.41
5 29 0.59
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (5 bp):
TTCAT
Found at i:25595870 original size:22 final size:20
Alignment explanation
Indices: 25595835--25595911 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 20
25595825 AACTTGAGCC
25595835 TTATTTATTTATTTATTTAT
1 TTATTTATTTATTTATTTAT
*
25595855 TCATTTCATTTCATTTATTTAT
1 TTATTT-ATTT-ATTTATTTAT
25595877 TTATTTCATTTTATTTCATTTCAT
1 TTATTT-A-TTTATTT-ATTT-AT
25595901 TTATTTATTTA
1 TTATTTATTTA
25595912 CAAGAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.10
21 4 0.08
22 25 0.50
23 8 0.16
24 8 0.16
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTTATTTATTTATTTAT
Found at i:25599727 original size:237 final size:237
Alignment explanation
Indices: 25599312--25599785 Score: 680
Period size: 237 Copynumber: 2.0 Consensus size: 237
25599302 TTGCTTACAG
* *
25599312 ACCGGGAGTAGCCATTTTTGAATGTTGTAGTATCCTGCGCAATGCTCCAGGGTTAAAACCCTCGT
1 ACCGGGAGTAGACATTTTTGAATGTTGCAGTATCCTGCGCAATGCTCCAGGGTTAAAACCCTCGT
*
25599377 AATCGTCCTTTGGTGGGAACAGTGTAGGTACGATCTCGCCTATTACGTTGACCATCTTACGACTA
66 AATCGTCCTTTGGTGGGAACAGTGTAGGTACGACCTCGCCTATTACGTTGACCATCTTACGACTA
* * * *
25599442 AATTTTTTGTCAAACGAGCCGAGTGGTGGACTTGAATTTCCAACATCGTCAGTACTACTGTGTAG
131 AAATTTTTATCAAACGAGCCGAGTGGTGGACTTGAATTTCCAACATCGTCAATACAACTGTGTAG
*
25599507 AGGCCTCTATGTCACATTTATCGGTGGTGGACAGGACCGAGT
196 AGGCCTCGATGTCACATTTATCGGTGGTGGACAGGACCGAGT
* * * * * * *
25599549 ACCGGGAGTGGACATTTTTGAATGTTGCCGTATCTTGGGCGATGCTCTAGGGTTGAAACCCTCGT
1 ACCGGGAGTAGACATTTTTGAATGTTGCAGTATCCTGCGCAATGCTCCAGGGTTAAAACCCTCGT
* *
25599614 AATCGTCCTTTGGTGGGAACAGTGTAGGTACGACCTCGCCTATTACGTTGATCGTCTTACGACTA
66 AATCGTCCTTTGGTGGGAACAGTGTAGGTACGACCTCGCCTATTACGTTGACCATCTTACGACTA
* * ** * * *
25599679 AAATTTTTATCAGATGAGTTTG-GTGGTGGGCTTGAATTTTCAACATCGTCAATACAACTGTGTG
131 AAATTTTTATCAAACGAG-CCGAGTGGTGGACTTGAATTTCCAACATCGTCAATACAACTGTGTA
* * * *
25599743 GAGGCGTCGATGTCTCCTTTATCGGTGGTTGACAGGACCGAGT
195 GAGGCCTCGATGTCACATTTATCGGTGGTGGACAGGACCGAGT
25599786 GGTGGACGAC
Statistics
Matches: 208, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
237 207 1.00
238 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (237 bp):
ACCGGGAGTAGACATTTTTGAATGTTGCAGTATCCTGCGCAATGCTCCAGGGTTAAAACCCTCGT
AATCGTCCTTTGGTGGGAACAGTGTAGGTACGACCTCGCCTATTACGTTGACCATCTTACGACTA
AAATTTTTATCAAACGAGCCGAGTGGTGGACTTGAATTTCCAACATCGTCAATACAACTGTGTAG
AGGCCTCGATGTCACATTTATCGGTGGTGGACAGGACCGAGT
Found at i:25608075 original size:24 final size:24
Alignment explanation
Indices: 25608048--25608116 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
25608038 TGAAATTATG
25608048 TGAATATGTGAATTTTGTATTGAT
1 TGAATATGTGAATTTTGTATTGAT
* *
25608072 TGAA-AAGTG--GTTTG-A-TG--
1 TGAATATGTGAATTTTGTATTGAT
25608089 TGAATATGTGAATTTTGTATTGAT
1 TGAATATGTGAATTTTGTATTGAT
25608113 TGAA
1 TGAA
25608117 AAGTGGTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 2 0.06
20 5 0.15
21 5 0.15
22 2 0.06
23 4 0.12
24 8 0.24
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (24 bp):
TGAATATGTGAATTTTGTATTGAT
Found at i:25608131 original size:21 final size:21
Alignment explanation
Indices: 25608061--25608132 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
25608051 ATATGTGAAT
25608061 TTTGTATTGATTGAAAAGTGG
1 TTTGTATTGATTGAAAAGTGG
* *
25608082 TTTG-A-TG--TGAATATGTGAAT
1 TTTGTATTGATTGAA-AAGTG--G
25608102 TTTGTATTGATTGAAAAGTGG
1 TTTGTATTGATTGAAAAGTGG
*
25608123 TTTGAATTGA
1 TTTGTATTGA
25608133 ATCGATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 2 0.05
20 5 0.13
21 14 0.36
22 2 0.05
23 4 0.10
24 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (21 bp):
TTTGTATTGATTGAAAAGTGG
Found at i:25608134 original size:41 final size:41
Alignment explanation
Indices: 25608045--25608127 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
25608035 ATTTGAAATT
25608045 ATGTGAATATGTGAATTTTGTATTGATTGAAAAGTGGTTTG
1 ATGTGAATATGTGAATTTTGTATTGATTGAAAAGTGGTTTG
25608086 ATGTGAATATGTGAATTTTGTATTGATTGAAAAGTGGTTTG
1 ATGTGAATATGTGAATTTTGTATTGATTGAAAAGTGGTTTG
25608127 A
1 A
25608128 ATTGAATCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (41 bp):
ATGTGAATATGTGAATTTTGTATTGATTGAAAAGTGGTTTG
Found at i:25608260 original size:36 final size:36
Alignment explanation
Indices: 25608213--25608286 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
25608203 TCGGGCTGAG
25608213 TCGGATATAGTTGGCATGCCATAGGATTGGAAGTGT
1 TCGGATATAGTTGGCATGCCATAGGATTGGAAGTGT
25608249 TCGGATATAGTTGGCATGCCATAGGATTGGAAGTGT
1 TCGGATATAGTTGGCATGCCATAGGATTGGAAGTGT
25608285 TC
1 TC
25608287 AGGGATACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.31
Consensus pattern (36 bp):
TCGGATATAGTTGGCATGCCATAGGATTGGAAGTGT
Found at i:25608900 original size:17 final size:18
Alignment explanation
Indices: 25608869--25608902 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25608859 ATAAATAGAA
25608869 ATGATAATGAATGAGTTG
1 ATGATAATGAATGAGTTG
*
25608887 ATGA-AATGATTGAGTT
1 ATGATAATGAATGAGTT
25608903 TGTATGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (18 bp):
ATGATAATGAATGAGTTG
Found at i:25615766 original size:13 final size:13
Alignment explanation
Indices: 25615750--25615774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25615740 GTTTTTAGAG
25615750 TATTTTTTGTTAT
1 TATTTTTTGTTAT
25615763 TATTTTTTGTTA
1 TATTTTTTGTTA
25615775 ATTCTTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TATTTTTTGTTAT
Found at i:25630525 original size:11 final size:11
Alignment explanation
Indices: 25630509--25630542 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
25630499 TCAATTATTT
25630509 TCTCAATTTCC
1 TCTCAATTTCC
*
25630520 TCTCAATTTGC
1 TCTCAATTTCC
25630531 TCTCAATTTCC
1 TCTCAATTTCC
25630542 T
1 T
25630543 TCCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:25630537 original size:22 final size:22
Alignment explanation
Indices: 25630505--25630558 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
25630495 TCTCTCAATT
25630505 ATTT-TCTCAATTTCC-TCTC-A
1 ATTTCTCTCAATTTCCTTC-CAA
25630525 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAATTTCCTTCCAA
25630548 ATTTCTCTCAA
1 ATTTCTCTCAA
25630559 ATCCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCCAA
Found at i:25631778 original size:7 final size:7
Alignment explanation
Indices: 25631766--25631790 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25631756 AGTCGATTGT
25631766 TATTTAG
1 TATTTAG
25631773 TATTTAG
1 TATTTAG
25631780 TATTTAG
1 TATTTAG
25631787 TATT
1 TATT
25631791 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:25632461 original size:18 final size:18
Alignment explanation
Indices: 25632438--25632480 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
25632428 TGCCAGATGC
* *
25632438 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
25632456 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
25632474 GTTTCCT
1 GTATCCT
25632481 TTCTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:25632776 original size:21 final size:21
Alignment explanation
Indices: 25632734--25632782 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25632724 CCAGATGCCT
* *
25632734 TACCGGAGGAACCAAAATCCC
1 TACCGGAGCAACCAAAACCCC
* *
25632755 TACCGGAGCAATCATAACCCC
1 TACCGGAGCAACCAAAACCCC
*
25632776 TGCCGGA
1 TACCGGA
25632783 AGCTGGACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.20, T:0.12
Consensus pattern (21 bp):
TACCGGAGCAACCAAAACCCC
Found at i:25633072 original size:20 final size:21
Alignment explanation
Indices: 25633028--25633076 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
25633018 CAAAAACTCT
25633028 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
25633049 AACCCTAACCCTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
25633069 AACCCTAA
1 AACCCTAA
25633077 ACTAATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:25633094 original size:116 final size:127
Alignment explanation
Indices: 25632975--25633208 Score: 364
Period size: 128 Copynumber: 1.8 Consensus size: 127
25632965 ATTTATTAAA
* *
25632975 AATTTATAAATTTATAATTTATAATTTAATTGACAAACCCTAACAAAAACTCTAACCCTAA-CCC
1 AATTTAT-AA-TTA-AATTTATAATTTAATTGACAAACCCTAACAAAAACCCAAACCCTAATCCC
25633039 TTAACTTAAAAACCCT-AACCCTTAACTTAAAACCCTAAACTAATTTACTAAAAATTTATAAATT
63 -TAACTTAAAAACCCTAAACCCTTAACTTAAAACCCTAAACTAATTTACTAAAAATTTAT-AA-T
25633103 TAT
125 TAT
25633106 AATTTATAATTAAATTTATAATTTAATTGACAAACCCTAACAAAAACCCAAACCCTAATCCCTAA
1 AATTTATAATTAAATTTATAATTTAATTGACAAACCCTAACAAAAACCCAAACCCTAATCCCTAA
*
25633171 CTTAAAACCCCTAAACCCTTAACTTAAAAACCCTAAAC
66 CTTAAAAACCCTAAACCCTTAACTT-AAAACCCTAAAC
25633209 CCTAAACATA
Statistics
Matches: 97, Mismatches: 3, Indels: 7
0.91 0.03 0.07
Matches are distributed among these distances:
128 58 0.60
129 18 0.19
130 14 0.14
131 7 0.07
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (127 bp):
AATTTATAATTAAATTTATAATTTAATTGACAAACCCTAACAAAAACCCAAACCCTAATCCCTAA
CTTAAAAACCCTAAACCCTTAACTTAAAACCCTAAACTAATTTACTAAAAATTTATAATTAT
Found at i:25633111 original size:7 final size:7
Alignment explanation
Indices: 25633091--25633130 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
25633081 ATTTACTAAA
25633091 AATTTAT
1 AATTTAT
25633098 AAATTTAT
1 -AATTTAT
25633106 AATTTAT
1 AATTTAT
25633113 AA-TTA-
1 AATTTAT
25633118 AATTTAT
1 AATTTAT
25633125 AATTTA
1 AATTTA
25633131 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 15 0.50
8 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:25633196 original size:22 final size:22
Alignment explanation
Indices: 25633155--25633251 Score: 144
Period size: 22 Copynumber: 4.5 Consensus size: 22
25633145 ACAAAAACCC
*
25633155 AAACCCTAATCCC-TAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25633176 AACCCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25633198 AAACCCTAAACCCTAAACATAA
1 AAACCCTAAACCCTTAACTTAA
25633220 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
25633241 AAACCCTAAAC
1 AAACCCTAAAC
25633252 TAATTTATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
21 30 0.45
22 37 0.55
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:25633204 original size:43 final size:43
Alignment explanation
Indices: 25633155--25633251 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
25633145 ACAAAAACCC
* * *
25633155 AAACCCTAATCCCT-AACTTAAAACCCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTAAACATAAAAACCCT-AACCCTTAACTTAA
25633198 AAACCCTAAACCCTAAACATAAAAACCCTAACCCTTAACTTAA
1 AAACCCTAAACCCTAAACATAAAAACCCTAACCCTTAACTTAA
25633241 AAACCCTAAAC
1 AAACCCTAAAC
25633252 TAATTTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 38 0.76
44 12 0.24
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (43 bp):
AAACCCTAAACCCTAAACATAAAAACCCTAACCCTTAACTTAA
Found at i:25633347 original size:21 final size:21
Alignment explanation
Indices: 25633317--25633365 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
25633307 GACAAACCCT
* *
25633317 AACCCTAACCCTTAACTTAAA
1 AACCCCAACCCTTAACATAAA
25633338 AACCCCAACCCTTAACATAAA
1 AACCCCAACCCTTAACATAAA
25633359 AACCCCA
1 AACCCCA
25633366 TAATCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (21 bp):
AACCCCAACCCTTAACATAAA
Found at i:25633473 original size:19 final size:18
Alignment explanation
Indices: 25633428--25633475 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
25633418 TAATTTGATA
25633428 AATTTACTAACAATTAAT
1 AATTTACTAACAATTAAT
* *
25633446 -A-TAATTAACAATTAAT
1 AATTTACTAACAATTAAT
25633462 AATTTTACTAACAA
1 AA-TTTACTAACAA
25633476 AATGTTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
16 13 0.57
17 2 0.09
19 8 0.35
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTACTAACAATTAAT
Found at i:25636722 original size:124 final size:124
Alignment explanation
Indices: 25636501--25636896 Score: 614
Period size: 124 Copynumber: 3.2 Consensus size: 124
25636491 GCGGTTTCAT
* * *
25636501 AAATTCTTCTGATAAAGCATCCTGCTTGAAGCATTTTTTATACTATTCGCTCAGAAATGTCAACT
1 AAATTCTTCAGATAAAGCATCCTGCTTGAAGC-GTTTTTATACTATTCGCTCAGAAACGTCAACT
* * * * *
25636566 CAAAATTATTTTTTTAGGACCTACTGTAGCAAAAGCGCGTCCACATGGGCGCAATTTAAA
65 CAAAATTATTTTTTCAGGACCAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAAG
25636626 AAATTCTTCAGATAAAGCATCCTGCTTGAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTC
1 AAATTCTTCAGATAAAGCATCCTGCTTGAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTC
* *
25636691 AAAATTATTTTTTCAGGAGCAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAG
66 AAAATTATTTTTTCAGGACCAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAAG
* ** *
25636750 AAATTCTTCTGATAAAGCATCCTGCTTGAAGCGTTTTTATACTATTTTCTCAGAAACATCAACTC
1 AAATTCTTCAGATAAAGCATCCTGCTTGAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTC
* * *
25636815 GAAATTATTTTTTCAGGACCAACTGTAGCAAAAGCGCGCCCACGTGGGCGCGATTTCAG
66 AAAATTATTTTTTCAGGACCAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAAG
25636874 AAATTCTTCTA-ATAAAGCATCCT
1 AAATTCTTC-AGATAAAGCATCCT
25636897 AAACCCTAAA
Statistics
Matches: 251, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
124 220 0.88
125 31 0.12
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (124 bp):
AAATTCTTCAGATAAAGCATCCTGCTTGAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTC
AAAATTATTTTTTCAGGACCAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAAG
Found at i:25636985 original size:21 final size:22
Alignment explanation
Indices: 25636942--25636987 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
25636932 TTTTCTCTAA
* *
25636942 AACCCTAAAAACCTTAAATCCT
1 AACCCTAAAAACCTCAAAACCT
25636964 AACCCTAAAAA-CTCAAAACCT
1 AACCCTAAAAACCTCAAAACCT
25636985 AAC
1 AAC
25636988 AATGGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (22 bp):
AACCCTAAAAACCTCAAAACCT
Found at i:25639400 original size:25 final size:25
Alignment explanation
Indices: 25639346--25639411 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
25639336 TTTTGAACTT
25639346 ATATTATTTATTTTAAATTGTTCTA
1 ATATTATTTATTTTAAATTGTTCTA
* *
25639371 TTATTATTTATTTTAAATTTTTC-A
1 ATATTATTTATTTTAAATTGTTCTA
**
25639395 CATATTATGCATTTTAA
1 -ATATTATTTATTTTAA
25639412 GCTATATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (25 bp):
ATATTATTTATTTTAAATTGTTCTA
Found at i:25639665 original size:24 final size:23
Alignment explanation
Indices: 25639628--25639675 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
25639618 TTCTTGGTTA
*
25639628 TTTATTTTAATTTGCTATGTTATT
1 TTTATTTTAATTTGC-ATATTATT
**
25639652 TTTATTTTTCTTTGCATATTATT
1 TTTATTTTAATTTGCATATTATT
25639675 T
1 T
25639676 ACTTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTATTTTAATTTGCATATTATT
Found at i:25651475 original size:948 final size:936
Alignment explanation
Indices: 25649209--25651969 Score: 4514
Period size: 948 Copynumber: 2.9 Consensus size: 936
25649199 CTATCCCACA
25649209 AGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
1 AGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
25649274 AGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAG
66 AGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAG
* * *
25649339 GGAGAAAAGAATGATAGCCCTTGGTATAAAGATATATTG-TATATGTGAAGAATCGTTAGTATCC
131 GGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCC
* *
25649403 TGACCAGGCAGCTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATG
196 TGAACAGGCAACTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATG
25649468 GGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGCT
261 GGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGCT
* *
25649533 AAGAAAATCTTAAAGGAGGTCCATTAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGGC
326 AAGAAAATCTTAGAGGAGGTCCATAAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGGC
*
25649598 TAGACAGATTATGAGGTTCGGGTACTACTGGTTCACCATAGAAGGAGATTGCATCAATTATGCCA
391 TAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCA
*
25649663 AGAAATGCCATAAATGCCAAATTTATGGTGATAAA--G--TGCACCTCCTTCGCCTCTTCATGTT
456 AGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCG-CTCTTCATGTT
*
25649724 ATGACTTCTCCGTGGCCTTTCGT-TATGTGGGGTATGGATGTTATCGGGCCAATATCACTGAAGG
520 ATGACTTCTCCATGGCCTTTC-TCTATGTGGGGTATGGATGTTATCGGGCCAATATCAC-GAAGG
*
25649788 CTTCTAATGGGAATTGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCT
583 CTTCTAATGGGAATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCT
*
25649853 TCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGAAGATCATATGTCGATA
648 TCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATA
* ** *
25649918 TGGAATGCCTGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGTAGATA
713 TGGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGCGGATG
*
25649983 TCTGCAGTCAATTTAAGAACAGACACCATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCA
778 TCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCA
* * * *
25650048 ATAGAAGCGACCAATAAAAATATTAAGAAAATTATGGGGAAAATGACTGAGACTTACAAGAACTG
843 ATGGAAGCGGCC-------A-A-T-A-AAAA-TATCGGGAAAATGACTAAGACTTACAAGAACTG
*
25650113 GCATCAGAAATAAACAGACAAGACTTACAAGGACTGGCACG
896 ACATCAGAAATAAACAGACAAGACTTACAAGGACTGGCACG
* * *
25650154 AGATGAAAATCAGATGGCTGACTCGTTGGCTTCTCTAGCCTCCATGATTAAAATGAGCAGACAAG
1 AGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
*
25650219 AGGACATGAAGCCTATCCAGATGAGCATCTTTGAAACCCCAGCTCACTGTTACAATATCGAAGAG
66 AGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAG
* * * *
25650284 GGAGAAAATGATGATAGCCCTTGGTATAAAGATATATTACGACATGTGAAGAATCATGAGTAT-C
131 GGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCC
* *
25650348 TTAACCAGGCAACTGAGAATGATAAAAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGAT
196 TGAA-CAGGCAACTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGAT
*
25650413 GGGGAGATCTTATATAAAAAGGGAAATGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGC
260 GGGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGC
* *
25650478 TAAGAAAATCTTAGAGGAAGTCCATGAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGG
325 TAAGAAAATCTTAGAGGAGGTCCATAAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGG
*
25650543 TTAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCC
390 CTAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCC
25650608 AAGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCGTCTCTTCATGT
455 AAGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCG-CTCTTCATGT
* * *
25650673 TATGACTTCGCCTTGGCCTTTCTCTATGTGGGGTATGGATGTTATTGGGCCAATATCATCGAAGG
519 TATGACTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTTATCGGGCCAATATCA-CGAAGG
*
25650738 CTTCTAATGGGCATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCT
583 CTTCTAATGGGAATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCT
*
25650803 TCGTATGCTAATGTCCCAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATA
648 TCGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATA
25650868 TGGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGCGGATG
713 TGGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGCGGATG
*
25650933 TCTGCAGTCAATTTAAGATCAGACAACATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCA
778 TCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCA
25650998 ATGGAAGCGGCCAATAAAAATATCGGGAAAATGACTAAGACTTACAATG-ACTGACATCAGAAAT
843 ATGGAAGCGGCCAATAAAAATATCGGGAAAATGACTAAGACTTACAA-GAACTGACATCAGAAAT
25651062 AAACAGACAAGACTTACAATGACTTACAAGGACTGGCACG
907 --A-A-AC-AG----ACAA-GACTTACAAGGACTGGCACG
* *
25651102 ATATGAAAATCAGATGGCTGACGCGTTGCCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
1 AGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
* *
25651167 AGGACATGAAGCCTATCCAGATGACCATCTATGAAACACCAGCTCACTGTTACAATATCGAAGAG
66 AGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAG
*
25651232 GGAGAAAAGGATGATAGCCCATGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCC
131 GGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCC
25651297 TGAACAGGCAACTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATG
196 TGAACAGGCAACTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATG
*
25651362 GGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACGCTGTGAAGGCT
261 GGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGCT
* * **
25651427 AAGAAAATATTAGAGGAGGTCCATAAGAGTATTTGCGGAATGCATGCCAGTGGGTTCACAATGGC
326 AAGAAAATCTTAGAGGAGGTCCATAAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGGC
* *
25651492 TAGATAGATTATGAGATTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCA
391 TAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCA
25651557 AGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCGCTTCTTCATGTT
456 AGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCGC-TCTTCATGTT
* * * * *
25651622 ATAACTTCTCCATAGCCTTTCTCTATGTGGGGTATGGATGTCATCGGGCCCATATCGCCGAAGGC
520 ATGACTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTTATCGGGCCAATATC-ACGAAGGC
** *
25651687 TTCTAATGGGTTTCGTTTCATCTTTCTGGTTACTGATTACTTCACTAAATGGGTAGAAGCTGCTT
584 TTCTAATGGGAATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCTT
* * *
25651752 CGTATGCTAATATCAGAAAGTCAGCAGTCAGCAAGTTCTTGAAAAATGAGATCATATGTCGATAT
649 CGTATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATAT
** ** *
25651817 GGAATGCCCGAAAGAATCATATCTGACAATACGTTGAATTTGAAC-AGCATTTCAATAGCGGAGG
714 GGAATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAG-AGCTCAATAGCGGATG
* * *
25651881 TCTGCAGTTAATTTAAGATCAGACACCATAATTCGTCACCGTACTACCTAAAAATGAATGGTGAA
778 TCTGCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCA
25651946 ATGGAAGCGGCCAATAAAAATATC
843 ATGGAAGCGGCCAATAAAAATATC
25651970 AAGAAAATTG
Statistics
Matches: 1702, Mismatches: 91, Indels: 43
0.93 0.05 0.02
Matches are distributed among these distances:
938 39 0.02
939 5 0.00
940 2 0.00
941 2 0.00
942 3 0.00
943 3 0.00
945 165 0.10
946 301 0.18
947 7 0.00
948 828 0.49
949 5 0.00
950 341 0.20
951 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (936 bp):
AGATGAAAATCAGATGGCTGACGCGTTGGCTACTCTAGCCTCCATGATTAAAATGAACAGACAAG
AGGACATGAAGCCTATCCAGATGAGCATCTATGAAACCCCAGCTCACTGTTACAATATCGAAGAG
GGAGAAAAGGATGATAGCCCTTGGTATAAAGATATATTGCGATATGTGAAGAATCGTGAGTATCC
TGAACAGGCAACTGAGAATGATAAGAGGGCTCTGAGAAGACTAGCCATTGATTATGTCTTAGATG
GGGAGATCTTATATAAAAAGGGAAAGGATCAGGTACTATTAAGATGTGTGGACACTGTGAAGGCT
AAGAAAATCTTAGAGGAGGTCCATAAGGGTATTTGCGGAACACATGCCAGTGGGTTCACAATGGC
TAGACAGATTATGAGGTTCGGGTACTACTGGTCCACCATAGAAGGAGATTGCATCAATTATGCCA
AGAAGTGCCATAAATGCCAAATTTATGGTGATAAAGTGCATGCACCTCCTTCGCTCTTCATGTTA
TGACTTCTCCATGGCCTTTCTCTATGTGGGGTATGGATGTTATCGGGCCAATATCACGAAGGCTT
CTAATGGGAATCGTTTCATCTTTCTGGTTATTGATTACTTCACTAAATGGGTAGAAGCTGCTTCG
TATGCTAATGTCACAAAGTCAGCAGTCAGCAAGTTCTTGAAAAAGGAGATCATATGTCGATATGG
AATGCCCGAAAGAATCATATCTGACAATGGGTTGAATTTGAACAAGAGCTCAATAGCGGATGTCT
GCAGTCAATTTAAGATCAGACACCATAATTCGTCACCGTACTGCCTAAAAATGAATGGTGCAATG
GAAGCGGCCAATAAAAATATCGGGAAAATGACTAAGACTTACAAGAACTGACATCAGAAATAAAC
AGACAAGACTTACAAGGACTGGCACG
Found at i:25654297 original size:132 final size:132
Alignment explanation
Indices: 25653886--25654286 Score: 523
Period size: 132 Copynumber: 3.0 Consensus size: 132
25653876 TGGATTGAAG
* * ** *
25653886 AAGATGGTGAATCTTATCTTCCCGAGGTAGTAGATAAACAGATTTAAGCCACCAGTCCTGTCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTGTCTCC
* * * *
25653951 TTGAGCAGCAGTGGAGTAGGTTGAAGATGGTAGATCCTGTCTCCCTAAGCAGCAGTGGAGCAGAT
66 CTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
*
25654016 CC
131 CA
* * * *
25654018 AAGACGGTGAATATTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCTGTCTTC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTGTCTCC
* * **
25654083 CTGAGTAGTAGTGGAGTAGGTTGAAGAATGTAGATCCTGTCTCCCTAAATAGTAGTGGAGCAGAT
66 CTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
25654148 CA
131 CA
* * * * * *
25654150 AAGATGGTGAATCTTATCTTCCTAAAGTAGTAGGGAAGCAGATTTAAACCACCAGTTCTATCTCC
1 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTGTCTCC
* * * * * *
25654215 CTGAGTAGCAGTGGAGTAGGTTCAATATTGTAGATCATGTATCTCTGAGCAGTAGTGGAGCAGAT
66 CTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
*
25654280 CG
131 CA
25654282 AAGAC
1 AAGAC
25654287 AACGAATCTT
Statistics
Matches: 229, Mismatches: 40, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
132 229 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (132 bp):
AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTGTCTCC
CTGAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGAT
CA
Found at i:25654343 original size:50 final size:50
Alignment explanation
Indices: 25654289--25654449 Score: 214
Period size: 50 Copynumber: 3.2 Consensus size: 50
25654279 TCGAAGACAA
* * *
25654289 CGAATCTTACTTCTTCGATGTTACAGTAAAACAGATTGAAGCTACAACAG
1 CGAATCTTACTTCTTCGACGTTGCAGTAAAACAGATTAAAGCTACAACAG
* * * * * *
25654339 CGAATCTTACTTCCTCGACATTGCAGTGAAGCGGGTTAAAGCTACAACAG
1 CGAATCTTACTTCTTCGACGTTGCAGTAAAACAGATTAAAGCTACAACAG
* * *
25654389 CGAATCTTACTTCTCCGACGTTGCAATAAAATAGATTAAAGCTACAACAG
1 CGAATCTTACTTCTTCGACGTTGCAGTAAAACAGATTAAAGCTACAACAG
25654439 CGAATCTTACT
1 CGAATCTTACT
25654450 ACCCTAGCAT
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (50 bp):
CGAATCTTACTTCTTCGACGTTGCAGTAAAACAGATTAAAGCTACAACAG
Found at i:25654474 original size:50 final size:49
Alignment explanation
Indices: 25654321--25654474 Score: 157
Period size: 50 Copynumber: 3.1 Consensus size: 49
25654311 ACAGTAAAAC
* * * *
25654321 AGATTGAAGCTACAACAGCGAATCTTACTTCCTCGACATTGCAGTGAAGC
1 AGATTAAAGCTACAACAGCGAATCTTACTCCCTAG-CATTGCAGTGAAGT
* * * * * * *
25654371 GGGTTAAAGCTACAACAGCGAATCTTACTTCTCCGA-CGTTGCAATAAAAT
1 AGATTAAAGCTACAACAGCGAATCTTAC-TC-CCTAGCATTGCAGTGAAGT
*
25654421 AGATTAAAGCTACAACAGCGAATCTTACTACCCTAGCATTGCAGTGGAGT
1 AGATTAAAGCTACAACAGCGAATCTTACT-CCCTAGCATTGCAGTGAAGT
25654471 AGAT
1 AGAT
25654475 CGAAGCCACT
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 4 0.05
50 74 0.91
51 1 0.01
52 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (49 bp):
AGATTAAAGCTACAACAGCGAATCTTACTCCCTAGCATTGCAGTGAAGT
Found at i:25655928 original size:25 final size:25
Alignment explanation
Indices: 25655874--25655939 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
25655864 TTTTGAACTT
* *
25655874 ATATTATTTCTTTTAAATTGTTCTA
1 ATATTATTTATTTTAAATTGTTCCA
*
25655899 TTATTATTTATTTTAAATT-TTCCA
1 ATATTATTTATTTTAAATTGTTCCA
**
25655923 CATATTATGCATTTTAA
1 -ATATTATTTATTTTAA
25655940 GCTATATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (25 bp):
ATATTATTTATTTTAAATTGTTCCA
Found at i:25656175 original size:26 final size:24
Alignment explanation
Indices: 25656146--25656203 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 24
25656136 GTCTTCTTGG
*
25656146 TTATTTA-TTTTAATTTGCTTTGCATA
1 TTATTTACTTTGAA-TTGCTTT--ATA
25656172 TTATTTACTTTGAATTGCTTTATA
1 TTATTTACTTTGAATTGCTTTATA
25656196 TTATTTAC
1 TTATTTAC
25656204 CTCAAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 11 0.37
26 14 0.47
27 5 0.17
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (24 bp):
TTATTTACTTTGAATTGCTTTATA
Found at i:25656211 original size:24 final size:24
Alignment explanation
Indices: 25656160--25656227 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
25656150 TTATTTTAAT
* **
25656160 TTGCTTTGCATATTATTTACTTTGAA
1 TTGCTTT--ATATTATTTACCTCAAA
25656186 TTGCTTTATATTATTTACCTCAAA
1 TTGCTTTATATTATTTACCTCAAA
*
25656210 TTGTTCTATATATTATTT
1 TTG--CTTTATATTATTT
25656228 CGTTTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 17 0.47
26 19 0.53
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (24 bp):
TTGCTTTATATTATTTACCTCAAA
Found at i:25664024 original size:114 final size:112
Alignment explanation
Indices: 25663662--25664086 Score: 457
Period size: 113 Copynumber: 3.8 Consensus size: 112
25663652 AAAATAAGAA
* ** * *
25663662 TTAGCTGCGTTTTCCAGAAAGCGTCGCAAAAAACCTAAGCCCAACGACGCCGTTTAGC-GAGC-T
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTT-TCTGAGCTT
* *
25663725 TTCGGGGATTTAGCGACGTTTTATAA-AAGTGCCGCTAATTTTTAGGGCT
65 TTCGGGGATTTAGCGACG-TTTATAAGAAGTGCCGCTAA-TGTTATGGCT
* * * * * * * *
25663774 TTAGCGGCGTTTTTGGGGAAGCGCCACAAAAGACCTAATCCCAATGATGCCGTTTTCTAAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
25663839 T-GGGGATTTAGCGACGCTTGTA-AAGAAGTGCCGCTAAAGTTCTGGGCT
66 TCGGGGATTTAGCGACG-TT-TATAAGAAGTGCCGCTAATGTTAT-GGCT
25663887 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
25663952 TCGGGGATTTGGCGGCGTTTATAAGGAAGTGCCGCTAATGCTTATGGCT
66 TCGGGGATTTAGCGACGTTTATAA-GAAGTGCCGCTAATG-TTATGGCT
* * * * * * * * *
25664001 ATAACAGCGTTTTTAAAAAAGCGCTGCAAAAAAAACCTAAGCCCAACGATGCCGTTTCCTGAG-A
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC--AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
25664065 TTTCGGGGATTTAGCGGCGTTT
64 TTTCGGGGATTTAGCGACGTTT
25664087 CTAGCAAAAA
Statistics
Matches: 262, Mismatches: 40, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
111 1 0.00
112 70 0.27
113 83 0.32
114 52 0.20
115 24 0.09
116 32 0.12
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
TCGGGGATTTAGCGACGTTTATAAGAAGTGCCGCTAATGTTATGGCT
Found at i:25664586 original size:14 final size:14
Alignment explanation
Indices: 25664567--25664593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25664557 GTGTCGTTCT
25664567 TTATACCAAATTTG
1 TTATACCAAATTTG
25664581 TTATACCAAATTT
1 TTATACCAAATTT
25664594 TATAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (14 bp):
TTATACCAAATTTG
Found at i:25664860 original size:21 final size:21
Alignment explanation
Indices: 25664836--25664978 Score: 116
Period size: 21 Copynumber: 7.5 Consensus size: 21
25664826 GGTTTGGGCT
*
25664836 TTATGGTTTAGAGGTTAGGGG
1 TTATGCTTTAGAGGTTAGGGG
* *
25664857 TTATACTTTAGGGGTTAGGGG
1 TTATGCTTTAGAGGTTAGGGG
*
25664878 --AT--TTAAG-GGTTAGGGG
1 TTATGCTTTAGAGGTTAGGGG
25664894 TTATGCTTTAGAGGTTA-GGG
1 TTATGCTTTAGAGGTTAGGGG
* * *
25664914 ---TGATTTAGGGGTTAGGAG
1 TTATGCTTTAGAGGTTAGGGG
25664932 TTATGCTTTAGAGGTTAGGGG
1 TTATGCTTTAGAGGTTAGGGG
*
25664953 --A---TTTAGGGGTTAGGGG
1 TTATGCTTTAGAGGTTAGGGG
25664969 TTATGCTTTA
1 TTATGCTTTA
25664979 AGGGTTAAGG
Statistics
Matches: 96, Mismatches: 12, Indels: 28
0.71 0.09 0.21
Matches are distributed among these distances:
16 23 0.24
17 16 0.17
18 5 0.05
19 3 0.03
20 7 0.07
21 42 0.44
ACGTcount: A:0.20, C:0.03, G:0.39, T:0.38
Consensus pattern (21 bp):
TTATGCTTTAGAGGTTAGGGG
Found at i:25664874 original size:7 final size:7
Alignment explanation
Indices: 25664864--25664971 Score: 63
Period size: 7 Copynumber: 14.4 Consensus size: 7
25664854 GGGTTATACT
25664864 TTAGGGG
1 TTAGGGG
25664871 TTAGGGG
1 TTAGGGG
*
25664878 ATTTAAGGG
1 --TTAGGGG
25664887 TTAGGGG
1 TTAGGGG
* **
25664894 TTATGCT
1 TTAGGGG
*
25664901 TTAGAGG
1 TTAGGGG
25664908 TTAGGGTG
1 TTAGGG-G
25664916 ATTTAGGGG
1 --TTAGGGG
*
25664925 TTAGGAG
1 TTAGGGG
* **
25664932 TTATGCT
1 TTAGGGG
*
25664939 TTAGAGG
1 TTAGGGG
25664946 TTAGGGG
1 TTAGGGG
25664953 ATTTAGGGG
1 --TTAGGGG
25664962 TTAGGGG
1 TTAGGGG
25664969 TTA
1 TTA
25664972 TGCTTTAAGG
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
7 54 0.72
8 1 0.01
9 14 0.19
10 6 0.08
ACGTcount: A:0.20, C:0.02, G:0.43, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:25664903 original size:37 final size:37
Alignment explanation
Indices: 25664842--25665003 Score: 236
Period size: 37 Copynumber: 4.3 Consensus size: 37
25664832 GGCTTTATGG
* * *
25664842 TTTAGAGGTTAGGGGTTATACTTTAGGGGTTAGGGGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGAGGTTAGGGGA
*
25664879 TTTAAGGGTTAGGGGTTATGCTTTAGAGGTTAGGGTGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGAGGTTAGGG-GA
*
25664917 TTTAGGGGTTAGGAGTTATGCTTTAGAGGTTAGGGGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGAGGTTAGGGGA
25664954 TTTAGGGGTTAGGGGTTATGCTTTA-AGGGTTAAGGAGGA
1 TTTAGGGGTTAGGGGTTATGCTTTAGA-GGTT-AGG-GGA
25664993 TTTAGGGGTTA
1 TTTAGGGGTTA
25665004 TGTGTTAGGG
Statistics
Matches: 114, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
36 1 0.01
37 61 0.54
38 38 0.33
39 14 0.12
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (37 bp):
TTTAGGGGTTAGGGGTTATGCTTTAGAGGTTAGGGGA
Found at i:25664927 original size:75 final size:76
Alignment explanation
Indices: 25664842--25665003 Score: 240
Period size: 75 Copynumber: 2.1 Consensus size: 76
25664832 GGCTTTATGG
* * *
25664842 TTTAGAGGTTAGGGGTTATACTTTAGGGGTTAGGGGATTTAAGGGTTAGGGGTTATGCTTT-AGA
1 TTTAGGGGTTAGGAGTTATACTTTAGAGGTTAGGGGATTTAAGGGTTAGGGGTTATGCTTTAAG-
25664906 GGTT-AGG-GTGA
65 GGTTAAGGAG-GA
* *
25664917 TTTAGGGGTTAGGAGTTATGCTTTAGAGGTTAGGGGATTTAGGGGTTAGGGGTTATGCTTTAAGG
1 TTTAGGGGTTAGGAGTTATACTTTAGAGGTTAGGGGATTTAAGGGTTAGGGGTTATGCTTTAAGG
25664982 GTTAAGGAGGA
66 GTTAAGGAGGA
25664993 TTTAGGGGTTA
1 TTTAGGGGTTA
25665004 TGTGTTAGGG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
75 60 0.76
76 18 0.23
77 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (76 bp):
TTTAGGGGTTAGGAGTTATACTTTAGAGGTTAGGGGATTTAAGGGTTAGGGGTTATGCTTTAAGG
GTTAAGGAGGA
Found at i:25664983 original size:21 final size:21
Alignment explanation
Indices: 25664917--25664985 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
25664907 GTTAGGGTGA
* *
25664917 TTTAGGGGTTAGGAGTTATGC
1 TTTAAGGGTTAGGGGTTATGC
25664938 TTT-AGAGGTTAGGGG--A---
1 TTTAAG-GGTTAGGGGTTATGC
*
25664954 TTTAGGGGTTAGGGGTTATGC
1 TTTAAGGGTTAGGGGTTATGC
25664975 TTTAAGGGTTA
1 TTTAAGGGTTA
25664986 AGGAGGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
16 12 0.32
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 21 0.57
ACGTcount: A:0.20, C:0.03, G:0.39, T:0.38
Consensus pattern (21 bp):
TTTAAGGGTTAGGGGTTATGC
Found at i:25665926 original size:231 final size:230
Alignment explanation
Indices: 25665646--25666334 Score: 1096
Period size: 231 Copynumber: 3.0 Consensus size: 230
25665636 AAACGGCACC
* *
25665646 GTTTCGGTTAATAATTTGTGGCGTGTTTTATGAAAACGCCAGAAAATTGACTTATATTTTAATAA
1 GTTTCAGTTAATAATTTGTGGCGTTTTTTATGAAAACGCCAGAAAATTGACTTATATTTTAATAA
* *
25665711 AACGGCACCGTCTTTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAACGTG
66 AACGGCACCGTCTCTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAATGTG
25665776 GATGCAATAGCCGCAAATTCTTATAAATAAAGTGAATATTTAGTGACGTTTCTATGAAAAATGCC
131 GATGCAATAGCCGCAAATTCTTATAAATAAAGTGAATATTTAGTGACGTTTCTATGAAAAATGCC
* *
25665841 ACAAATAATATTTTAATAATTGAACGAAACGGCGCCT
196 ACAAATAATATTTTAAAAATTGAACAAAACGG-G-CT
* * *
25665878 -TTTGAGTTAATAATTTGTGGCGTTTTTTGTGAAAACGCCAGAAAATTGACTTATATTTTAATAG
1 GTTTCAGTTAATAATTTGTGGCGTTTTTTATGAAAACGCCAGAAAATTGACTTATATTTTAATAA
*
25665942 AACGGCGCCGTCTCTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAATGTG
66 AACGGCACCGTCTCTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAATGTG
* *
25666007 GATGCAATAGTCTCAAATTCTTATAAATAAAGTGAATATTTAGT-AGCGTTTCTATGAAAAACT-
131 GATGCAATAGCCGCAAATTCTTATAAATAAAGTGAATATTTAGTGA-CGTTTCTATGAAAAA-TG
*
25666070 CCGCAAATAATATTTTAAAAATTGAACAAAACGGGCT
194 CCACAAATAATATTTTAAAAATTGAACAAAACGGGCT
* * * * *
25666107 GTTTCAGTTAATAGTTTGTGGCGTTTTTTATGGAAATGCCAGAAAATTGACTTAAATTTTTATAA
1 GTTTCAGTTAATAATTTGTGGCGTTTTTTATGAAAACGCCAGAAAATTGACTTATATTTTAATAA
*
25666172 AACGGCACCGTCTCTTTCTATACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAAATGT
66 AACGGCACCGTCTCTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGC-AAATGT
* * * *
25666237 GGATGCAATAGCCGCAGATACTTATAAATAAAGTGAATATTTAGTGGCGTTTCTATGAAAAACGC
130 GGATGCAATAGCCGCAAATTCTTATAAATAAAGTGAATATTTAGTGACGTTTCTATGAAAAATGC
*
25666302 CTCAAATAATATTTTAAAAATTGAACAAAACGG
195 CACAAATAATATTTTAAAAATTGAACAAAACGG
25666335 TGCCATTGCA
Statistics
Matches: 421, Mismatches: 30, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
229 2 0.00
230 114 0.27
231 304 0.72
232 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (230 bp):
GTTTCAGTTAATAATTTGTGGCGTTTTTTATGAAAACGCCAGAAAATTGACTTATATTTTAATAA
AACGGCACCGTCTCTTTCTGTACTTGAAATTTTAGTGGCGTTTTTATTAAAACGCCGCAAATGTG
GATGCAATAGCCGCAAATTCTTATAAATAAAGTGAATATTTAGTGACGTTTCTATGAAAAATGCC
ACAAATAATATTTTAAAAATTGAACAAAACGGGCT
Found at i:25668293 original size:5 final size:5
Alignment explanation
Indices: 25668270--25668309 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
25668260 ATAACACTTC
*
25668270 TTTTA TTTTAA TATGTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTT-A T-TTTA TTTTA TTTTA TTTTA TTTTA TTT
25668310 AATAATACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 25 0.81
6 4 0.13
7 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:25668480 original size:18 final size:17
Alignment explanation
Indices: 25668454--25668544 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 17
25668444 CATTACTTAC
25668454 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
* *
25668471 GTTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
25668489 ATTACTTACTAAAATTTAT
1 ATTACTTACTAAAA--TAT
*
25668508 AATTTACATTACTTAAATAT
1 -A-TTAC-TTACTAAAATAT
25668528 ATTACGTTACTTAAAAT
1 ATTAC-TTAC-TAAAAT
25668545 TTATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.20
18 23 0.38
19 9 0.15
20 4 0.07
21 4 0.07
22 8 0.13
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:25668494 original size:31 final size:31
Alignment explanation
Indices: 25668436--25668525 Score: 90
Period size: 35 Copynumber: 2.6 Consensus size: 31
25668426 ATTCTTAAGT
*
25668436 ATATATTACATTACTTACATTACTTACTAAA
1 ATATATTACATTACTTAAATTACTTACTAAA
*
25668467 ATATGTTACATTACTTAAATATATTACTTACTAAA
1 ATATATTACATTACTT--A-A-ATTACTTACTAAA
25668502 ATTTATAATTTACATTACTTAAAT
1 A--TAT-A-TTACATTACTTAAAT
25668526 ATATTACGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
31 15 0.31
33 1 0.02
35 16 0.33
36 1 0.02
37 4 0.08
39 11 0.23
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATATTACATTACTTAAATTACTTACTAAA
Found at i:25668497 original size:22 final size:22
Alignment explanation
Indices: 25668445--25668537 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
25668435 TATATATTAC
*
25668445 ATTACTTACATTACTTACTAAAAT
1 ATTACTTACATTACTTA--AATAT
*
25668469 A-T-GTTACATTACTTAAATAT
1 ATTACTTACATTACTTAAATAT
*
25668489 ATTACTTAC--TA---AAATTT
1 ATTACTTACATTACTTAAATAT
* *
25668506 ATAATTTACATTACTTAAATAT
1 ATTACTTACATTACTTAAATAT
25668528 ATTACGTTAC
1 ATTAC-TTAC
25668538 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 17
0.67 0.12 0.22
Matches are distributed among these distances:
17 12 0.23
19 2 0.04
20 7 0.13
21 1 0.02
22 24 0.46
23 5 0.10
24 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTACTTACATTACTTAAATAT
Found at i:25668515 original size:39 final size:41
Alignment explanation
Indices: 25668472--25668549 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 41
25668462 CTAAAATATG
25668472 TTACATTACTTAAATATATTAC-TTAC-TAAAATTTATAAT
1 TTACATTACTTAAATATATTACGTTACTTAAAATTTATAAT
25668511 TTACATTACTTAAATATATTACGTTACTTAAAATTTATA
1 TTACATTACTTAAATATATTACGTTACTTAAAATTTATA
25668550 TATATATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 22 0.59
40 4 0.11
41 11 0.30
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.46
Consensus pattern (41 bp):
TTACATTACTTAAATATATTACGTTACTTAAAATTTATAAT
Found at i:25668870 original size:34 final size:34
Alignment explanation
Indices: 25668827--25669163 Score: 136
Period size: 34 Copynumber: 9.9 Consensus size: 34
25668817 ATAATAACAT
* *
25668827 AATAACTTACATAATACACAACTTACATAATTTA
1 AATAACTTACATAATACATAACTTACATAACTTA
* **
25668861 AATAACTTACATAGTACATAACTTTGATAACTTA
1 AATAACTTACATAATACATAACTTACATAACTTA
* * *
25668895 CATAACATACACTTAAATACATAACTTACATAACGTA
1 AATAACTTACA--T-AATACATAACTTACATAACTTA
* * *
25668932 CAT-A-GTACATAACTTACATAA--TACACAACTTA
1 AATAACTTACATAA--TACATAACTTACATAACTTA
* * *
25668964 ATTAA--T--ATTATACATAACATACATAA--TA
1 AATAACTTACATAATACATAACTTACATAACTTA
* * *
25668992 CAT-A--T--ATAATACACAACTTA-ATTAATATTA
1 AATAACTTACATAATACATAACTTACA-TAA-CTTA
* *
25669022 TACATAACATACATAATACATAA-TACACATAACTTACATA
1 -A-ATAACTTACATAATACATAACT-TACATAAC-T---TA
* * *
25669062 GTACATAACTAACATAATACACAACTTACGTAACTTA
1 --A-ATAACTTACATAATACATAACTTACATAACTTA
*
25669099 AATAACTTACATAGCTTACATAA--TACATAACTTA
1 AATAACTTACATA--ATACATAACTTACATAACTTA
* *
25669133 CATAACTTATATAATTACATAACTTACATAA
1 AATAACTTACATAA-TACATAACTTACATAA
25669164 TTTACCTAAT
Statistics
Matches: 232, Mismatches: 39, Indels: 63
0.69 0.12 0.19
Matches are distributed among these distances:
26 1 0.00
27 17 0.07
28 10 0.04
30 11 0.05
32 15 0.06
33 10 0.04
34 77 0.33
35 13 0.06
36 9 0.04
37 38 0.16
38 1 0.00
40 3 0.01
41 26 0.11
42 1 0.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (34 bp):
AATAACTTACATAATACATAACTTACATAACTTA
Found at i:25668883 original size:16 final size:16
Alignment explanation
Indices: 25668828--25669164 Score: 131
Period size: 16 Copynumber: 20.9 Consensus size: 16
25668818 TAATAACATA
25668828 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* *
25668844 ACAACTTACATAATTTAA
1 ATAACTTACATAA--TAC
*
25668862 ATAACTTACATAGTAC
1 ATAACTTACATAATAC
**
25668878 ATAACTTTGATAACTTAC
1 ATAACTTACATAA--TAC
*
25668896 ATAACATACACT--T--
1 ATAACTTACA-TAATAC
25668909 A-AA--TACATAACTTAC
1 ATAACTTACATAA--TAC
* *
25668924 ATAACGTACATAGTAC
1 ATAACTTACATAATAC
25668940 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* *
25668956 ACAACTTAATTAATATTATAC
1 ATAACTT-A--CATA--ATAC
*
25668977 ATAACATACATAATAC
1 ATAACTTACATAATAC
25668993 AT-A--T--ATAATAC
1 ATAACTTACATAATAC
*
25669004 ACAACTTA-AT--TA-
1 ATAACTTACATAATAC
*
25669016 AT-ATTATACATAACATAC
1 ATAACT-TACAT-A-ATAC
25669034 ATAA--TACATAATACAC
1 ATAACTTACATAAT--AC
*
25669050 ATAACTTACATAGTAC
1 ATAACTTACATAATAC
*
25669066 ATAACTAACATAATAC
1 ATAACTTACATAATAC
* * *
25669082 ACAACTTACGTAACTTAA
1 ATAACTTACATAA--TAC
*
25669100 ATAACTTACATAGCTTAC
1 ATAACTTACATA--ATAC
25669118 ATAA--TACATAACTTAC
1 ATAACTTACATAA--TAC
*
25669134 ATAACTTATATAATTAC
1 ATAACTTACATAA-TAC
25669151 ATAACTTACATAAT
1 ATAACTTACATAAT
25669165 TTACCTAATA
Statistics
Matches: 242, Mismatches: 36, Indels: 86
0.66 0.10 0.24
Matches are distributed among these distances:
9 1 0.00
10 4 0.02
11 10 0.04
12 6 0.02
13 7 0.03
14 3 0.01
15 6 0.02
16 106 0.44
17 19 0.08
18 65 0.27
19 5 0.02
20 1 0.00
21 9 0.04
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:25668899 original size:9 final size:9
Alignment explanation
Indices: 25668828--25669168 Score: 163
Period size: 9 Copynumber: 39.0 Consensus size: 9
25668818 TAATAACATA
25668828 ATAACTTAC
1 ATAACTTAC
25668837 ATAA--TAC
1 ATAACTTAC
*
25668844 ACAACTTAC
1 ATAACTTAC
* *
25668853 ATAATTTAA
1 ATAACTTAC
25668862 ATAACTTAC
1 ATAACTTAC
*
25668871 AT-A-GTAC
1 ATAACTTAC
**
25668878 ATAACTTTG
1 ATAACTTAC
25668887 ATAACTTAC
1 ATAACTTAC
*
25668896 ATAACATAC
1 ATAACTTAC
*
25668905 ACTTAA-ATAC
1 A--TAACTTAC
25668915 ATAACTTAC
1 ATAACTTAC
*
25668924 ATAACGTAC
1 ATAACTTAC
*
25668933 AT-A-GTAC
1 ATAACTTAC
25668940 ATAACTTAC
1 ATAACTTAC
25668949 ATAA--TAC
1 ATAACTTAC
*
25668956 ACAACTTA-
1 ATAACTTAC
*
25668964 ATTAATATTATAC
1 A-T-A-ACT-TAC
*
25668977 ATAACATAC
1 ATAACTTAC
25668986 ATAA--TAC
1 ATAACTTAC
25668993 ATATA-TAATAC
1 ATA-ACT--TAC
*
25669004 ACAACTTA-
1 ATAACTTAC
*
25669012 ATTAATATTATAC
1 A-T-A-ACT-TAC
*
25669025 ATAACATAC
1 ATAACTTAC
25669034 ATAA--TAC
1 ATAACTTAC
*
25669041 ATAA-TACAC
1 ATAACT-TAC
25669050 ATAACTTAC
1 ATAACTTAC
*
25669059 AT-A-GTAC
1 ATAACTTAC
*
25669066 ATAACTAAC
1 ATAACTTAC
25669075 ATAA--TAC
1 ATAACTTAC
*
25669082 ACAACTTAC
1 ATAACTTAC
* *
25669091 GTAACTTAA
1 ATAACTTAC
25669100 ATAACTTAC
1 ATAACTTAC
*
25669109 ATAGCTTAC
1 ATAACTTAC
25669118 ATAA--TAC
1 ATAACTTAC
25669125 ATAACTTAC
1 ATAACTTAC
*
25669134 ATAACTTAT
1 ATAACTTAC
25669143 ATAA-TTAC
1 ATAACTTAC
25669151 ATAACTTAC
1 ATAACTTAC
*
25669160 ATAATTTAC
1 ATAACTTAC
25669169 CTAATACGTA
Statistics
Matches: 253, Mismatches: 43, Indels: 72
0.69 0.12 0.20
Matches are distributed among these distances:
7 53 0.21
8 19 0.08
9 147 0.58
10 11 0.04
11 15 0.06
12 6 0.02
13 2 0.01
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:25668923 original size:28 final size:28
Alignment explanation
Indices: 25668887--25668986 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
25668877 CATAACTTTG
25668887 ATAACTTACATAACATACACTTAAATAC
1 ATAACTTACATAACATACACTTAAATAC
* *
25668915 ATAACTTACATAACGTACA--T-AGTAC
1 ATAACTTACATAACATACACTTAAATAC
* * *
25668940 ATAACTTACATAATACACAACTTAATTA-
1 ATAACTTACATAACATAC-ACTTAAATAC
*
25668968 AT-ATTATACATAACATACA
1 ATAACT-TACATAACATACA
25668987 TAATACATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
25 19 0.33
26 2 0.03
27 3 0.05
28 31 0.53
29 3 0.05
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAACTTACATAACATACACTTAAATAC
Found at i:25668976 original size:21 final size:21
Alignment explanation
Indices: 25668952--25669025 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 21
25668942 AACTTACATA
25668952 ATACACAACTTAATTAATATT
1 ATACACAACTTAATTAATATT
* *
25668973 ATACATAACATACATAATACATATAT
1 ATACACAACTTA-AT--TA-ATAT-T
25668999 AATACACAACTTAATTAATATT
1 -ATACACAACTTAATTAATATT
25669021 ATACA
1 ATACA
25669026 TAACATACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 15 0.35
22 3 0.07
23 4 0.09
24 4 0.09
25 4 0.09
26 3 0.07
27 10 0.23
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
ATACACAACTTAATTAATATT
Found at i:25669016 original size:48 final size:48
Alignment explanation
Indices: 25668949--25669043 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
25668939 CATAACTTAC
25668949 ATAATACACAACTTAATTAATATTATACATAACATACATAATACATAT
1 ATAATACACAACTTAATTAATATTATACATAACATACATAATACATAT
25668997 ATAATACACAACTTAATTAATATTATACATAACATACATAATACATA
1 ATAATACACAACTTAATTAATATTATACATAACATACATAATACATA
25669044 ATACACATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (48 bp):
ATAATACACAACTTAATTAATATTATACATAACATACATAATACATAT
Found at i:25669120 original size:43 final size:42
Alignment explanation
Indices: 25669022--25669164 Score: 164
Period size: 43 Copynumber: 3.4 Consensus size: 42
25669012 ATTAATATTA
* * * * *
25669022 TACATAACATACATAATACATAA-TACACATAACTTACAT-AG
1 TACATAACTTACATAATACACAACT-TACATAACTTAAATAAT
* *
25669063 TACATAACTAACATAATACACAACTTACGTAACTTAAATAACT
1 TACATAACTTACATAATACACAACTTACATAACTTAAATAA-T
* * *
25669106 TACATAGCTTACATAATACATAACTTACATAACTTATATAAT
1 TACATAACTTACATAATACACAACTTACATAACTTAAATAAT
25669148 TACATAACTTACATAAT
1 TACATAACTTACATAAT
25669165 TTACCTAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
41 31 0.36
42 19 0.22
43 36 0.42
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (42 bp):
TACATAACTTACATAATACACAACTTACATAACTTAAATAAT
Found at i:25669133 original size:25 final size:26
Alignment explanation
Indices: 25668820--25669212 Score: 145
Period size: 25 Copynumber: 15.2 Consensus size: 26
25668810 GACTTACATA
25668820 ATAACATA-ATAACTTACATAA--TAC
1 ATAAC-TACATAACTTACATAACTTAC
* * *
25668844 ACAACTTACATAATTTAAATAACTTAC
1 ATAAC-TACATAACTTACATAACTTAC
* **
25668871 AT-AGTACATAACTTTGATAACTTAC
1 ATAACTACATAACTTACATAACTTAC
*
25668896 ATAACATACACTTAA-ATACATAACTTAC
1 ATAAC-TACA--TAACTTACATAACTTAC
*
25668924 ATAACGTACAT-A-GTACATAACTTAC
1 ATAAC-TACATAACTTACATAACTTAC
* *
25668949 ATAA-TACACAACTTA-ATTAATATTATAC
1 ATAACTACATAACTTACA-T-A-ACT-TAC
25668977 ATAACATACATAA--TACAT-A-TATA-
1 ATAAC-TACATAACTTACATAACT-TAC
* * *
25669000 ATACACAACTTAA-TTA-AT-ATTATAC
1 ATA-ACTACATAACTTACATAACT-TAC
*
25669025 ATAACATACATAA--TACATAA-TACAC
1 ATAAC-TACATAACTTACATAACT-TAC
* *
25669050 ATAACTTACAT-A-GTACATAACTAAC
1 ATAAC-TACATAACTTACATAACTTAC
* * *
25669075 ATAA-TACACAACTTACGTAACTTAA
1 ATAACTACATAACTTACATAACTTAC
*
25669100 ATAACTTACATAGCTTACATAA--TAC
1 ATAAC-TACATAACTTACATAACTTAC
*
25669125 ATAACTTACATAACTTATATAA-TTAC
1 ATAAC-TACATAACTTACATAACTTAC
* * *
25669151 ATAACTTACATAATTTACCTAATACGTAC
1 ATAAC-TACATAACTTACAT-A-ACTTAC
* * * *
25669180 ATAAATATATATCATATCATAACTTAC
1 ATAACTACATAACTTA-CATAACTTAC
25669207 ATAACT
1 ATAACT
25669213 CATTTATAGT
Statistics
Matches: 286, Mismatches: 49, Indels: 65
0.71 0.12 0.16
Matches are distributed among these distances:
23 19 0.07
24 26 0.09
25 124 0.43
26 26 0.09
27 34 0.12
28 38 0.13
29 13 0.05
30 6 0.02
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (26 bp):
ATAACTACATAACTTACATAACTTAC
Found at i:25669173 original size:26 final size:26
Alignment explanation
Indices: 25668828--25669173 Score: 152
Period size: 25 Copynumber: 13.9 Consensus size: 26
25668818 TAATAACATA
*
25668828 ATAACTTACATAA--TACACAACTTAC
1 ATAACTTACATAACTTACATAA-TTAC
* * *
25668853 ATAATTTAAATAACTTACAT-AGTAC
1 ATAACTTACATAACTTACATAATTAC
** *
25668878 ATAACTTTGATAACTTACATAACATAC
1 ATAACTTACATAACTTACATAA-TTAC
* *
25668905 ACTTAA-ATACATAACTTACATAACGTAC
1 A--TAACTTACATAACTTACATAA-TTAC
*
25668933 AT-A-GTACATAACTTACATAA-TAC
1 ATAACTTACATAACTTACATAATTAC
* *
25668956 ACAAC-T---TAA-TTA-ATATTATAC
1 ATAACTTACATAACTTACATAAT-TAC
*
25668977 ATAACATACATAA--TACAT-ATATA-
1 ATAACTTACATAACTTACATAAT-TAC
* * *
25669000 ATACAC-AACTTAA-TTA-ATATTATAC
1 ATA-ACTTACATAACTTACATAAT-TAC
* *
25669025 ATAACATACATAA--TACATAATACAC
1 ATAACTTACATAACTTACATAAT-TAC
* *
25669050 ATAACTTACAT-A-GTACATAACTAAC
1 ATAACTTACATAACTTACATAA-TTAC
* * *
25669075 ATAA--TACACAACTTACGTAACTTAA
1 ATAACTTACATAACTTACATAA-TTAC
*
25669100 ATAACTTACATAGCTTACATAA-TAC
1 ATAACTTACATAACTTACATAATTAC
*
25669125 ATAACTTACATAACTTATATAATTAC
1 ATAACTTACATAACTTACATAATTAC
* *
25669151 ATAACTTACATAATTTACCTAAT
1 ATAACTTACATAACTTACATAAT
25669174 ACGTACATAA
Statistics
Matches: 253, Mismatches: 40, Indels: 55
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.01
20 3 0.01
21 10 0.04
22 1 0.00
23 18 0.07
24 22 0.09
25 126 0.50
26 27 0.11
27 21 0.08
28 19 0.08
29 3 0.01
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (26 bp):
ATAACTTACATAACTTACATAATTAC
Found at i:25671034 original size:21 final size:21
Alignment explanation
Indices: 25671010--25671057 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
25671000 GGCGGAAACA
*
25671010 AGGGAAGCAGAGGCGGCAGTG
1 AGGGAAGCAGAGGCGGCAGCG
*
25671031 AGGGCAGCAGAGGCGGCAGCG
1 AGGGAAGCAGAGGCGGCAGCG
25671052 AGGGAA
1 AGGGAA
25671058 ACAAAGCAGA
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:0.29, C:0.17, G:0.52, T:0.02
Consensus pattern (21 bp):
AGGGAAGCAGAGGCGGCAGCG
Found at i:25671992 original size:24 final size:24
Alignment explanation
Indices: 25671965--25672013 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25671955 TAAACAACTT
25671965 TTGAATTAATGGTTTATCATATTA
1 TTGAATTAATGGTTTATCATATTA
25671989 TTGAATTAATGGTTTATCATATTA
1 TTGAATTAATGGTTTATCATATTA
25672013 T
1 T
25672014 AACATGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (24 bp):
TTGAATTAATGGTTTATCATATTA
Found at i:25675958 original size:27 final size:27
Alignment explanation
Indices: 25675928--25675983 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
25675918 TTAGTGTATC
25675928 AAGTAATTAAAGTGGAACATAAAGTCT
1 AAGTAATTAAAGTGGAACATAAAGTCT
25675955 AAGTAATTAAAGTGGAACATAAAGTCT
1 AAGTAATTAAAGTGGAACATAAAGTCT
25675982 AA
1 AA
25675984 TTTCTAATAT
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:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (27 bp):
AAGTAATTAAAGTGGAACATAAAGTCT
Found at i:25679952 original size:2 final size:2
Alignment explanation
Indices: 25679945--25679979 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25679935 CTATGTAATT
25679945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25679980 TCTTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25680650 original size:20 final size:20
Alignment explanation
Indices: 25680613--25680651 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25680603 TTAAAAGGTC
25680613 TTTTTGATGCATTTTATAAT
1 TTTTTGATGCATTTTATAAT
*
25680633 TTTTTTATG-ATTTATATAA
1 TTTTTGATGCATTT-TATAA
25680652 AAATTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTGATGCATTTTATAAT
Found at i:25680683 original size:20 final size:19
Alignment explanation
Indices: 25680651--25680689 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
25680641 GATTTATATA
25680651 AAAATTTACAATTTTTATT
1 AAAATTTACAATTTTTATT
*
25680670 AAAATTTAATAATTTTTATT
1 AAAATTT-ACAATTTTTATT
25680690 CTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATTTACAATTTTTATT
Found at i:25680991 original size:97 final size:97
Alignment explanation
Indices: 25680827--25681024 Score: 251
Period size: 97 Copynumber: 2.0 Consensus size: 97
25680817 AATTGAGCGT
* *
25680827 AAAAAAAAGAAGCAAGAGCTTAATTGTTTTTTTTTTGAAAAAGCTTGAGGGCCTTTATGATTCAT
1 AAAAAAAAGAAGCAAGAGCTTAA-TATTTCTTTTTT-AAAAAGCTTGAGGGCCTTTATGATTCAT
* *
25680892 TTTG-ACAGTTCAAGTATCTAATTGAGTACAAAAAA
64 TTTGAAC-GTTCAAGTATCCAATTAAGT-CAAAAAA
* *
25680927 AAAAAAACAGAAGCAAGGGCTTAA-ATTTCTTTTTT-AAAAGCTTGAGGGCCTTTTTGATGT-AT
1 AAAAAAA-AGAAGCAAGAGCTTAATATTTCTTTTTTAAAAAGCTTGAGGGCCTTTATGAT-TCAT
*
25680989 TTTGAACGTTCAAGTATCCAATTAAGTGAAAAAA
64 TTTGAACGTTCAAGTATCCAATTAAGTCAAAAAA
25681023 AA
1 AA
25681025 GAACTTAATT
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
96 8 0.09
97 46 0.52
98 3 0.03
99 9 0.10
100 7 0.08
101 15 0.17
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (97 bp):
AAAAAAAAGAAGCAAGAGCTTAATATTTCTTTTTTAAAAAGCTTGAGGGCCTTTATGATTCATTT
TGAACGTTCAAGTATCCAATTAAGTCAAAAAA
Found at i:25689495 original size:5 final size:5
Alignment explanation
Indices: 25689478--25689516 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
25689468 TAGGTCTAAG
25689478 GAAGA GAAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAA
1 GAAGA G-AAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAA
25689517 AAAAGAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:25696171 original size:33 final size:33
Alignment explanation
Indices: 25696133--25696225 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 33
25696123 GAAAGTGGTG
* *
25696133 AAGGTGGTGAGGGTGGTGAGGTTGTTGGCAATA
1 AAGGTGGTGAGGGTGGTGAGGTTGCTAGCAATA
*
25696166 AAGGTGGTGAGGGTGAGGGTGGTGAGGTTGCTAGCAGTA
1 AA---GGT---GGTGAGGGTGGTGAGGTTGCTAGCAATA
*
25696205 AAGGTGGTGAGGGTGTTGAGG
1 AAGGTGGTGAGGGTGGTGAGG
25696226 GTCAGGGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
33 17 0.34
36 6 0.12
39 27 0.54
ACGTcount: A:0.20, C:0.03, G:0.52, T:0.25
Consensus pattern (33 bp):
AAGGTGGTGAGGGTGGTGAGGTTGCTAGCAATA
Found at i:25696183 original size:39 final size:39
Alignment explanation
Indices: 25696138--25696219 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
25696128 TGGTGAAGGT
* *
25696138 GGTGAGGGTGGTGAGGTTGTTGGCAATAAAGGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGCTAGCAATAAAGGTGGTGAG
*
25696177 GGTGAGGGTGGTGAGGTTGCTAGCAGTAAAGGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGCTAGCAATAAAGGTGGTGAG
25696216 GGTG
1 GGTG
25696220 TTGAGGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.04, G:0.52, T:0.24
Consensus pattern (39 bp):
GGTGAGGGTGGTGAGGTTGCTAGCAATAAAGGTGGTGAG
Found at i:25696389 original size:54 final size:54
Alignment explanation
Indices: 25696281--25696389 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
25696271 GGGAGGGTGA
* * **
25696281 TGATGTTGCTGTCAATGAAGGTGATGAAAGTGATGGAGGTGGCGAGGAGAGGGT
1 TGATGTTACTGTCAATGAAGGTGATGAAAGTGATGGAGGTGGCAAAAAGAGGGT
* * * * * *
25696335 TGATGTTACTGTTAGTGAAGGTGGTGAGAGTGATGGAGGTGGTAAAAAGGGGGT
1 TGATGTTACTGTCAATGAAGGTGATGAAAGTGATGGAGGTGGCAAAAAGAGGGT
25696389 T
1 T
25696390 AGGGATGAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.04, G:0.44, T:0.27
Consensus pattern (54 bp):
TGATGTTACTGTCAATGAAGGTGATGAAAGTGATGGAGGTGGCAAAAAGAGGGT
Found at i:25696447 original size:26 final size:26
Alignment explanation
Indices: 25696418--25696472 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
25696408 GATTCAGAGG
25696418 ATGAGAGTGCTTATTTGATGAAGGTT
1 ATGAGAGTGCTTATTTGATGAAGGTT
25696444 ATGAGAGTGCTTATTTGATGAAGGTT
1 ATGAGAGTGCTTATTTGATGAAGGTT
25696470 ATG
1 ATG
25696473 TACTTACCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (26 bp):
ATGAGAGTGCTTATTTGATGAAGGTT
Found at i:25697872 original size:21 final size:21
Alignment explanation
Indices: 25697832--25697882 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
25697822 ATTTATAACA
* *
25697832 TATTCAATTCTCATCTCTTGC
1 TATTCAAATCTCATCACTTGC
25697853 TATTTCAAATCTCAT-ACTTGC
1 TA-TTCAAATCTCATCACTTGC
25697874 TATTCAAAT
1 TATTCAAAT
25697883 AGCTTTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (21 bp):
TATTCAAATCTCATCACTTGC
Found at i:25698128 original size:41 final size:38
Alignment explanation
Indices: 25698003--25698135 Score: 108
Period size: 40 Copynumber: 3.4 Consensus size: 38
25697993 CCAGTTTGGT
* **
25698003 ACCCAGTACCTCATCGGATAATTTGAAGTAATAATTTGAC
1 ACCCAGTGCCTCATC-GATAATCCGAAGTAATAA-TTGAC
** * * * *
25698043 GTCCAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGGC
1 ACCCAGTGCCTCATC-GATAATCCGAAGTAATAATTGAC
25698080 ACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGATTGAC
1 ACCCAGTGCCTCATCG-A-TAATCCGAAGTAATA-ATTGAC
*
25698121 ACCCAGTGTCTCATC
1 ACCCAGTGCCTCATC
25698136 AACTCGAAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
36 1 0.01
37 16 0.22
38 12 0.17
39 2 0.03
40 22 0.31
41 19 0.26
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (38 bp):
ACCCAGTGCCTCATCGATAATCCGAAGTAATAATTGAC
Found at i:25699052 original size:4 final size:4
Alignment explanation
Indices: 25699043--25699080 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
25699033 CTAGTTTCAC
25699043 CTTT CTTT CTTT CTTT CTTTT CTTT CTTT CCTTT CTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT -CTTT CTTT
25699081 TCTCCCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:25699066 original size:9 final size:9
Alignment explanation
Indices: 25699044--25699083 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
25699034 TAGTTTCACC
25699044 TTTCTTTC-
1 TTTCTTTCT
25699052 TTTCTTTCT
1 TTTCTTTCT
25699061 TTTCTTTCT
1 TTTCTTTCT
*
25699070 TTCCTTTCT
1 TTTCTTTCT
25699079 TTTCT
1 TTTCT
25699084 CCCTATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:25699140 original size:17 final size:15
Alignment explanation
Indices: 25699118--25699172 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 15
25699108 TTTCTTTTCT
25699118 TTATTTATTTTATTTA
1 TTATTTATTTTA-TTA
25699134 CTTATTTATTTTATTA
1 -TTATTTATTTTATTA
*
25699150 -TATTTACTTTATTA
1 TTATTTATTTTATTA
25699164 TTATATTAT
1 TTAT-TTAT
25699173 ATATATTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 13 0.38
15 3 0.09
16 6 0.18
17 12 0.35
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTTATTTTATTA
Found at i:25699146 original size:22 final size:23
Alignment explanation
Indices: 25699117--25699185 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
25699107 TTTTCTTTTC
*
25699117 TTTA-TTTATTTTATTTACTTA-
1 TTTATTTTATTATATTTACTTAT
25699138 TTTATTTTATTATATTTACTTTAT
1 TTTATTTTATTATATTTAC-TTAT
*
25699162 TATTATATTATATATATTTACTTA
1 T-TTATTTTAT-TATATTTACTTA
25699186 AATATTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.10
22 13 0.32
23 3 0.07
24 1 0.02
25 11 0.27
26 9 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATTTTATTATATTTACTTAT
Found at i:25699191 original size:26 final size:24
Alignment explanation
Indices: 25699118--25699192 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 24
25699108 TTTCTTTTCT
*
25699118 TTAT-TTATTTTATTTACTT-AT-
1 TTATATTATTATATTTACTTAATA
* *
25699139 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTAC-TTAATA
25699164 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTT-AATA
25699190 TTA
1 TTA
25699193 AGTAATACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.09
22 12 0.27
23 2 0.05
24 1 0.02
25 10 0.23
26 15 0.34
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATTATTATATTTACTTAATA
Found at i:25699204 original size:26 final size:26
Alignment explanation
Indices: 25699149--25699206 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
25699139 TTATTTTATT
* * * *
25699149 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
25699175 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
25699201 ATATTT
1 ATATTT
25699207 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:25701201 original size:159 final size:157
Alignment explanation
Indices: 25700871--25701328 Score: 555
Period size: 159 Copynumber: 2.9 Consensus size: 157
25700861 AACAAAGGAT
* * * *
25700871 CATGCATTCAACCTAACACAAC-AGGAGCACAGGTATATGGTAAACACTTTTTCATTGTCAATTC
1 CATGCATTCAGCCTAACACAACTA-GATCACAGGTATATCGTAAACACTTTTT-AATGTCAATTC
* * * *
25700935 CAAAATATTAAAATCTAATTT-GGGTTCTAATTTTTTTGGTCTTAGTCTGGTACTAGTACGAGAA
64 CAAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACGAGTA-TAGAA
* * * *
25700999 CTAGAAACCCAAAAAATAACAACATAACAC
128 CTAGAAGCCAAAAAAAGAACAACAGAACAC
* * * * **
25701029 CATGCATTAAGCCTAATACAACTAGATCATAGGTATATCGTATACACTATTTTAATGTCAATTTA
1 CATGCATTCAGCCTAACACAACTAGATCACAGGTATATCGTAAACACT-TTTTAATGTCAATTCC
* * *
25701094 AAAATATTTTAATCTAATTTGGGGTTTTGATTTTTTTGGTGTTAGTCTGGTACGAGTATACGAAC
65 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACGAGTATA-GAAC
*
25701159 TAGAAGTCAAAAAAAGAACAACAGAACAC
129 TAGAAGCCAAAAAAAGAACAACAGAACAC
* * *
25701188 CATGCATTCAGCCTAACACAACTGGATCGCAGGTATATCGTAAACATTTTTTTAATGTCAATTCC
1 CATGCATTCAGCCTAACACAACTAGATCACAGGTATATCGTAAACA-CTTTTTAATGTCAATTCC
* * * *
25701253 AAATTATTTAAATCTAATTTGGGGTTCTGA--CTTTTGTTCTCAGTCTGGTACGAGTATGAGAAC
65 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACGAGTAT-AGAAC
*
25701316 TACAAGCCAAAAA
129 TAGAAGCCAAAAA
25701329 TGGATGGCAT
Statistics
Matches: 254, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
157 38 0.15
158 68 0.27
159 147 0.58
160 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (157 bp):
CATGCATTCAGCCTAACACAACTAGATCACAGGTATATCGTAAACACTTTTTAATGTCAATTCCA
AAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCTGGTACGAGTATAGAACTA
GAAGCCAAAAAAAGAACAACAGAACAC
Found at i:25701542 original size:82 final size:82
Alignment explanation
Indices: 25701406--25701689 Score: 471
Period size: 82 Copynumber: 3.5 Consensus size: 82
25701396 TAAAGATGGT
* *
25701406 TAACATGTTTTGTTT-GTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGTTATA
1 TAACATATTTTGTTTGGTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTGTTATA
25701470 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
**
25701487 TAACATATTTTGTTTATTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTGTTATA
1 TAACATATTTTGTTTGGTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTGTTATA
25701552 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
* **
25701569 TAACATATTTTGTTTGTTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTACTATA
1 TAACATATTTTGTTTGGTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTGTTATA
* *
25701634 TGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGCA
*
25701651 TAACATATTTTGTTTGGTTTTTGAAATGATTTTTTGAAA
1 TAACATATTTTGTTTGGTTTTTGAAATGATTTATTGAAA
25701690 GATGTATACT
Statistics
Matches: 192, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
81 14 0.07
82 178 0.93
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (82 bp):
TAACATATTTTGTTTGGTTTTTGAAATGATTTATTGAAATGGTTGGTTAACATCTTACTGTTATA
GGATCATTTTGTTAGCA
Found at i:25703193 original size:112 final size:115
Alignment explanation
Indices: 25703037--25703247 Score: 338
Period size: 112 Copynumber: 1.9 Consensus size: 115
25703027 TACTCTAATA
* *
25703037 TTCACATATGGGAAAGAAATGTTTCATCAATATCCAATT-AAAAAAT-AAAAAAAATC-CCCAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
25703099 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
*
25703149 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTTAAAAAATCAAAAAAAATCACACAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
* * * *
25703214 TTTTTATGAACCTTAAAACAAATCGGCTAAATAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATAT
25703248 ACAGTGCCTA
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
112 38 0.42
113 7 0.08
114 10 0.11
115 35 0.39
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (115 bp):
TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
Found at i:25710037 original size:21 final size:19
Alignment explanation
Indices: 25710013--25710056 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
25710003 ATATAATATA
*
25710013 TTTAAATATTTTTTTGAAAAT
1 TTTAAATATTATTTT--AAAT
*
25710034 TTTAATTATTATTTTAAAT
1 TTTAAATATTATTTTAAAT
25710053 TTTA
1 TTTA
25710057 TGTTGATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAAATATTATTTTAAAT
Found at i:25711537 original size:21 final size:21
Alignment explanation
Indices: 25711503--25711542 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25711493 CCATTCATCA
* *
25711503 ACATCTCATCTCACATATCTT
1 ACATCACATATCACATATCTT
25711524 ACATCACATATCACATATC
1 ACATCACATATCACATATC
25711543 GCATATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (21 bp):
ACATCACATATCACATATCTT
Found at i:25718301 original size:22 final size:21
Alignment explanation
Indices: 25718276--25718316 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
25718266 AGGTAATGTG
*
25718276 TAAATATTAAGTACTAAATTTT
1 TAAAAATTAAG-ACTAAATTTT
*
25718298 TAAAAATTAAGATTAAATT
1 TAAAAATTAAGACTAAATT
25718317 GACACAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAAAATTAAGACTAAATTTT
Found at i:25719470 original size:18 final size:18
Alignment explanation
Indices: 25719449--25719497 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
25719439 AAATTAACCA
25719449 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
25719467 AATTAACTGAATTACCTG
1 AATTAACCGAATTACCCG
*
25719485 AATTACCCGAATT
1 AATTAACCGAATT
25719498 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:25719478 original size:9 final size:9
Alignment explanation
Indices: 25719440--25719497 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
25719430 TTTGGTTAAA
*
25719440 AATTAACCA
1 AATTAACCG
25719449 AATTAACCG
1 AATTAACCG
*
25719458 AATTACCCG
1 AATTAACCG
*
25719467 AATTAACTG
1 AATTAACCG
25719476 AATT-ACCTG
1 AATTAACC-G
*
25719485 AATTACCCG
1 AATTAACCG
25719494 AATT
1 AATT
25719498 GAATCACTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 2 0.05
9 37 0.90
10 2 0.05
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:25719479 original size:27 final size:27
Alignment explanation
Indices: 25719440--25719497 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
25719430 TTTGGTTAAA
25719440 AATTAACCAAATTAACC-GAATTACCCG
1 AATTAACCAAATT-ACCTGAATTACCCG
**
25719467 AATTAACTGAATTACCTGAATTACCCG
1 AATTAACCAAATTACCTGAATTACCCG
25719494 AATT
1 AATT
25719498 GAATCACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTACCTGAATTACCCG
Found at i:25719527 original size:17 final size:17
Alignment explanation
Indices: 25719505--25719567 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
25719495 ATTGAATCAC
25719505 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
25719522 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
25719542 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
25719559 TACATAATT
1 TACATAATT
25719568 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:25719542 original size:37 final size:37
Alignment explanation
Indices: 25719496--25719570 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
25719486 ATTACCCGAA
*
25719496 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
25719533 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
25719570 T
1 T
25719571 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:25719740 original size:37 final size:39
Alignment explanation
Indices: 25719699--25719790 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
25719689 ACTTAAGAGT
*
25719699 TAGACTTTAGTTTTATTTTTATT-GGTT-GATAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
*
25719736 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
25719775 TAGACTTTAGTTTTAG
1 TAGACTTTAGTTTTAG
25719791 GGTCAGTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 22 0.43
38 4 0.08
39 25 0.49
ACGTcount: A:0.21, C:0.03, G:0.25, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
Found at i:25719870 original size:13 final size:13
Alignment explanation
Indices: 25719805--25719881 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 13
25719795 AGTTCTTCAT
*
25719805 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
25719818 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
25719831 TACTATAGAAAAG
1 TGCTTTTGAAAAG
*
25719844 TGATTTT-AAGAAG
1 TGCTTTTGAA-AAG
25719857 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
25719870 TGCTGTTGAAAA
1 TGCTTTTGAAAA
25719882 TTTTGAGTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
12 2 0.04
13 48 0.92
14 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:25722529 original size:18 final size:18
Alignment explanation
Indices: 25722508--25722573 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
25722498 TCCATCAATT
* *
25722508 TGAACATCATCTGAGATG
1 TGAACATCATTTGAAATG
25722526 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
25722544 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
25722562 TGAACATCATTT
1 TGAACATCATTT
25722574 CTCATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:25724518 original size:17 final size:17
Alignment explanation
Indices: 25724473--25724519 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
25724463 AGAGGAACAA
*
25724473 AGAACAAGCACCAGCAG
1 AGAACCAGCACCAGCAG
25724490 AGGAACACCAGCACCAGCAG
1 A-G-A-ACCAGCACCAGCAG
25724510 AGAACCAGCA
1 AGAACCAGCA
25724520 GAGAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 2 0.08
20 14 0.54
ACGTcount: A:0.45, C:0.32, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAACCAGCACCAGCAG
Found at i:25724900 original size:12 final size:13
Alignment explanation
Indices: 25724883--25724914 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
25724873 AATAATTGGG
25724883 TTGGGTT-GGTAA
1 TTGGGTTGGGTAA
25724895 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
25724908 TTGGGTT
1 TTGGGTT
25724915 TGGTTGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:25727300 original size:18 final size:18
Alignment explanation
Indices: 25727265--25727302 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25727255 TAAACAAATA
25727265 AAAAGTAAAAAAAAAAAG
1 AAAAGTAAAAAAAAAAAG
*
25727283 AAAAG-AAAAGAAAGAAAG
1 AAAAGTAAAA-AAAAAAAG
25727301 AA
1 AA
25727303 GCCCTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAGTAAAAAAAAAAAG
Found at i:25741098 original size:107 final size:106
Alignment explanation
Indices: 25740921--25741115 Score: 284
Period size: 107 Copynumber: 1.8 Consensus size: 106
25740911 GATTTAAGAG
* * * * * * *
25740921 GATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAGCACGTTAGGGCATGTTTTCTCAAAT
1 GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAAAT
25740986 TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
66 TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
* *
25741027 GATATTTGACTATTTGGTCTAAA-GAAAAAATCGAAACCCAACATATTAGGGCACGTTTCCTCGA
1 GATATTTGACTATTTGGTC-AAACG-AAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAA
25741091 ATTTCCAAACGCAAAATATTGCCTT
64 ATTTCCAAACGCAAAATATTGCCTT
25741116 TATTATTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 19 0.24
107 59 0.76
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAAAT
TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
Found at i:25741341 original size:73 final size:73
Alignment explanation
Indices: 25741257--25741394 Score: 240
Period size: 73 Copynumber: 1.9 Consensus size: 73
25741247 TCTTGGGTTT
* *
25741257 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
25741322 TTTTGAGG
66 TTTTGAGG
* *
25741330 AAAAAAGGGATCATGCCCGGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATAGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
25741395 CTTGAATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
TTTTGAGG
Found at i:25741833 original size:47 final size:47
Alignment explanation
Indices: 25741741--25741832 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
25741731 GAAAATGAAT
*
25741741 AAAATTATAGAAATATAAAAAGATATATATGAATATATATGTATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
* *
25741788 AAAATTATA-AAATATAAAAA-ATATATGT-AAGTATGTATATATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAA-TATATATATATATA
25741833 TTCGTGTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 2 0.05
45 19 0.46
46 11 0.27
47 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (47 bp):
AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
Found at i:25742644 original size:6 final size:6
Alignment explanation
Indices: 25742633--25742660 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25742623 CGAAATAAAT
25742633 AAATAG AAATAG AAATAG AAATAG AAAT
1 AAATAG AAATAG AAATAG AAATAG AAAT
25742661 GCAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AAATAG
Found at i:25743602 original size:44 final size:45
Alignment explanation
Indices: 25743520--25743652 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 45
25743510 TTCAGTCTGT
* ** * *
25743520 TCCACTGCAATTTCAGGGAGATAAGACTCGTA-ATTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
* *
25743564 TCCACTGCAACTTCAAGGAGATAAGGTTTGTATA-TTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
* * *
25743608 -CCTACTGCAACTTTAGGGGGATAACGTTTGT-TACTTCAACCTGC
1 TCC-ACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
25743652 T
1 T
25743653 TTGCTGCGAC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 4 0.05
44 69 0.93
45 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
Found at i:25743951 original size:46 final size:44
Alignment explanation
Indices: 25743475--25743953 Score: 199
Period size: 45 Copynumber: 10.5 Consensus size: 44
25743465 TTTCATCCGT
* * * * *
25743475 TCCACTGTAACTTTAGAGAAATAAGACTTGCTATCTTCAGTCTGT
1 TCCACTGCAACTTCAG-GAGATAAGACTTGTTATCTTCAGTCTGC
* * * **
25743520 TCCACTGCAATTTCAGGGAGATAAGACTCGTAAT-TTCAACCTGC
1 TCCACTGCAACTTCA-GGAGATAAGACTTGTTATCTTCAGTCTGC
** * *
25743564 TCCACTGCAACTTCAAGGAGATAAGGTTTG-TATATTCAATCTGC
1 TCCACTGCAACTTC-AGGAGATAAGACTTGTTATCTTCAGTCTGC
* * * *
25743608 -CCTACTGCAACTTTAGGGGGATAACG-TTTGTTA-CTTCAACCTGCTTTGC
1 TCC-ACTGCAACTTCA-GGAGATAA-GACTTGTTATCTTC-A---G-TCTGC
* * * * *
25743657 TGCGAC-GTAACTTCA-GAGGTAAGATTTGTTATCTTCAGTCTAC
1 T-CCACTGCAACTTCAGGAGATAAGACTTGTTATCTTCAGTCTGC
* * ** * *
25743700 TCCATTGCAACTTCAAGGAGATAAGACTCGTTATGGT-AGATTTAATTC
1 TCCACTGCAACTTC-AGGAGATAAGACTTGTTATCTTCAG---T-CTGC
* * * * * *
25743748 GACCTACTGCAACTT-TGGAGGTATAAGAATAG-TAGCTTCAATCTGC
1 -TCC-ACTGCAACTTCAGGA-G-ATAAGACTTGTTATCTTCAGTCTGC
* * * ** *
25743794 TTCACTGTAACTTCAGGGAGATAGGA-TTGGTTATCTTCAACCTAC
1 TCCACTGCAACTTCA-GGAGATAAGACTT-GTTATCTTCAGTCTGC
* *
25743839 TCCACTACAACTTCAGGAAGATAAGATTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGG-AGATAAGACTTGTTATCTTCAGTCTGC
* *
25743884 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGA-TCTGC
1 TCCACTGCAACTTCA-GGAGATAAGACTTGTTAT-CT-TCAGTCTGC
* *
25743930 TCTACTTCAACTTCAGAGAGATAA
1 TCCACTGCAACTTCAG-GAGATAA
25743954 TATCTGTAGC
Statistics
Matches: 325, Mismatches: 71, Indels: 75
0.69 0.15 0.16
Matches are distributed among these distances:
42 2 0.01
43 17 0.05
44 85 0.26
45 120 0.37
46 37 0.11
47 17 0.05
48 9 0.03
49 17 0.05
50 20 0.06
51 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGAGATAAGACTTGTTATCTTCAGTCTGC
Found at i:25744257 original size:85 final size:85
Alignment explanation
Indices: 25744120--25744582 Score: 354
Period size: 85 Copynumber: 5.4 Consensus size: 85
25744110 CATCATTTTA
* * *
25744120 ATCTGCTTCACTGCAACTTCAG-GAAGATAGGAT-TG-GTTTCTTTAATCTGCTCCACTGCAACT
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGTG-GT-TTTAATCTGCTCCACTGCAACT
25744182 TTAGGGAGATAAGATTGGATGCG
63 TTAGGGAGATAAGATTGGATGCG
* * * * *
25744205 ATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTACAACTTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTTA
* * * *
25744270 GTGAGATAGGATTGGCTTCTTCTG
66 GGGAGATAAGATTGG---ATGC-G
* * * * * *
25744294 -TTTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGG-ATGAGATCTGCTCTACTGCAACTTC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA-ATCTGCTCCACTGCAACTTT
* ***
25744354 AGAGAGATAAGATTTGTGATTTTA
65 AGGGAGATAAGA-TTG-GA-TGCG
* * * * ** *
25744378 ATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GCTTCTTCTGTCTGCTCCACTGTAACTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TT-AATCTGCTCCACTGCAACTT
*
25744441 TAGGGAGATAAGACTGGATGCG
64 TAGGGAGATAAGATTGGATGCG
** *
25744463 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTTA
* * *
25744528 GGGAGATAGGATTGGCTTCTTCTG
66 GGGAGATAAGATTGG---ATGC-G
* *
25744552 -TCTGCTCCACTGCAACTTTAGGGAGATAAGA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGA
25744583 CTGGATGCGA
Statistics
Matches: 296, Mismatches: 58, Indels: 45
0.74 0.15 0.11
Matches are distributed among these distances:
84 2 0.01
85 182 0.61
86 14 0.05
87 8 0.03
88 88 0.30
89 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (85 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTTA
GGGAGATAAGATTGGATGCG
Found at i:25744430 original size:44 final size:43
Alignment explanation
Indices: 25744121--25744582 Score: 325
Period size: 44 Copynumber: 10.7 Consensus size: 43
25744111 ATCATTTTAA
* * * * *
25744121 TCTGCTTCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTT-G
* * * **
25744165 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGAT-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTTG
* * * **
25744207 T-TGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GCTTCTTTG
* * * *
25744250 TCCGCTCCACTACAACTTCAGTGAGATAGGATTGGCTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTT-TG
* * * **
25744294 TTTGCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTTG
* * * **
25744334 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATT-TTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-GCTTCTTTG
* *
25744379 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTT-TG
* * * * *
25744423 TCTGCTCCACTGTAACTTTAGGGAGATAAGACTGGATGC---G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTTG
** * * **
25744463 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GCTTCTTTG
* * *
25744508 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTT-TG
*
25744552 TCTGCTCCACTGCAACTTTAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
25744583 CTGGATGCGA
Statistics
Matches: 323, Mismatches: 73, Indels: 44
0.73 0.17 0.10
Matches are distributed among these distances:
40 2 0.01
41 82 0.25
42 16 0.05
43 19 0.06
44 202 0.63
45 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGCTTCTTTG
Found at i:25744610 original size:85 final size:84
Alignment explanation
Indices: 25744253--25744671 Score: 285
Period size: 85 Copynumber: 4.9 Consensus size: 84
25744243 GTTTTAATCC
* * * *
25744253 GCTCCACTACAACTTCAGTGAGATAGGATTGGCTTCTTCTGTTTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTT-TTCAGTCTGCTCCACTGCAACTTCAGGGA
* *
25744318 GATAAGACTGGATGAGATCT
65 GATAAGACTGGATGCGATAT
* * * * *
25744338 GCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTT-AATCCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAGGA-TTG-GCTTTTCAGTCTGCTCCACTGCAACTTCAGGG
* * * * *
25744402 AGATAGGATTGGCTTCTTCTG-TCT
64 AGATAAGACTGG---ATGC-GATAT
* * * * * * * ** *
25744426 GCTCCACTGTAACTTTAGGGAGATAAGACTGG--ATGC-GATCTGCTTTACTGCAACTTCAGAGA
1 GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTTTTCAG-TCTGCTCCACTGCAACTTCAGGGA
* ***
25744488 GATAAGATCTGTGGTTTTA-AT
65 GATAAGA-CTG-GATGCGATAT
* * * *
25744509 CCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGG
1 --GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTT-TTCAGTCTGCTCCACTGCAACTTCAGG
25744574 GAGATAAGACTGGATGCGATAT
63 GAGATAAGACTGGATGCGATAT
* * * * * *
25744596 GCTCTACTGCAACTTCAGAAAGATAGCATCTGTGGTTTT-AATCCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAGGAT-TG-GCTTTTCAGTCTGCTCCACTGCAACTTCAGGG
*
25744660 AGATAGGACTGG
64 AGATAAGACTGG
25744672 TGTTTTAAAT
Statistics
Matches: 258, Mismatches: 56, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
83 1 0.00
84 3 0.01
85 166 0.64
86 15 0.06
87 14 0.05
88 57 0.22
89 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTTTTCAGTCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTGGATGCGATAT
Found at i:25744651 original size:44 final size:43
Alignment explanation
Indices: 25744087--25744679 Score: 313
Period size: 44 Copynumber: 13.8 Consensus size: 43
25744077 TCTGTTCTAT
** * *
25744087 TGCAACTTCAGAGAGATAAGATCCAT-CATTTTAATCTGCTTCAC
1 TGCAACTTCAGAGAGATAAGAT-C-TGGGTTTTAATCCGCTCCAC
* * *
25744131 TGCAACTTCAG-GAAGATAGGAT-TGGTTTCTTTAATCTGCTCCAC
1 TGCAACTTCAGAG-AGATAAGATCTGG-GT-TTTAATCCGCTCCAC
* * * *** ** *
25744175 TGCAACTTTAGGGAGATAAGAT-T-GGATGCGATTTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTTTTAATCCGCTCCAC
25744216 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTG-GGTTTTAATCCGCTCCAC
* * * * ** **
25744260 TACAACTTCAGTGAGATAGGAT-TGGCTTCTTCTGTTTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTT-TT-AATCCGCTCCAC
* * * * *
25744304 TGCAACTTCAGGGAGATAAGA-CT-GG-ATGAGATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTTTTA-ATCCGCTCCAC
* *
25744345 TGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTG-GGTTTTAATCCGCTCCAC
* * * ** *
25744389 TGCAACTTCAGGGAGATAGGAT-TGGCTTCTTCTGTCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTT-TT-AATCCGCTCCAC
* * * * *** * **
25744433 TGTAACTTTAGGGAGATAAGA-CT-GGATGCGATCTGCTTTAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTTTTAATCCGCTCCAC
25744474 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTG-GGTTTTAATCCGCTCCAC
* * * * ** *
25744518 TGCAACTTTAGGGAGATAGGAT-TGGCTTCTTCTGTCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTT-TT-AATCCGCTCCAC
* * * *** *
25744562 TGCAACTTTAGGGAGATAAGA-CTGGATGCGATAT--GCTCTAC
1 TGCAACTTCAGAGAGATAAGATCTGGGTTTTA-ATCCGCTCCAC
*
25744603 TGCAACTTCAGAAAGAT-AGCATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAG-ATCTG-GGTTTTAATCCGCTCCAC
* *
25744647 TGCAACTTCAGGGAGATAGGA-CTGGTGTTTTAA
1 TGCAACTTCAGAGAGATAAGATCTGG-GTTTTAA
25744680 ATCTGCTTCC
Statistics
Matches: 416, Mismatches: 100, Indels: 67
0.71 0.17 0.11
Matches are distributed among these distances:
40 2 0.00
41 107 0.26
42 19 0.05
43 32 0.08
44 252 0.61
45 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAAGATCTGGGTTTTAATCCGCTCCAC
Found at i:25744711 original size:129 final size:129
Alignment explanation
Indices: 25744070--25744667 Score: 939
Period size: 129 Copynumber: 4.6 Consensus size: 129
25744060 AATAAAGTCT
* * ** ** * *
25744070 GATGCGATCTGTTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCTGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * * *
25744135 ACTTCAGGAAGATAGGATTGGTTTCTT-TAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCT-GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* *
25744199 GATGCGATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * *
25744264 ACTTCAGTGAGATAGGATTGGCTTCTTCTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* * *
25744328 GATGAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
*
25744393 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGTAACTTTAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
*
25744457 GATGCGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
*
25744522 ACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* *
25744586 GATGCGATATGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTGGTTTTAATCCGCTCCACTGC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAG-ATCTGTGGTTTTAATCCGCTCCACTGC
25744650 AACTTCAGGGAGATAGGA
65 AACTTCAGGGAGATAGGA
25744668 CTGGTGTTTT
Statistics
Matches: 431, Mismatches: 36, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
128 2 0.00
129 428 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
Found at i:25745094 original size:24 final size:23
Alignment explanation
Indices: 25745062--25745118 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
25745052 CAGATTGCCC
25745062 CCACTGTAATCTTCAAGGTCCAAT
1 CCACTGTAAT-TTCAAGGTCCAAT
* * *
25745086 CCACTGTAA-TTCTATGTTCAAT
1 CCACTGTAATTTCAAGGTCCAAT
25745108 CCACTGTAATT
1 CCACTGTAATT
25745119 CTTGGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
24 9 0.31
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (23 bp):
CCACTGTAATTTCAAGGTCCAAT
Found at i:25746077 original size:20 final size:21
Alignment explanation
Indices: 25746052--25746090 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
25746042 TTGGCCTCTC
25746052 TTTCTTCTT-TTTCTTTTTGT
1 TTTCTTCTTATTTCTTTTTGT
25746072 TTTCTTCTTATTTCTTTTT
1 TTTCTTCTTATTTCTTTTT
25746091 TCTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTCTTCTTATTTCTTTTTGT
Found at i:25750000 original size:107 final size:106
Alignment explanation
Indices: 25749792--25749986 Score: 302
Period size: 107 Copynumber: 1.8 Consensus size: 106
25749782 GATTTAAGAG
* * * * *
25749792 GATATTTGGCTATTTGGTCAAACAAGAAGTCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGACTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAAT
25749857 TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
66 TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
*
25749898 GATATTTGACTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAA
1 GATATTTGACTATTTGGTCAAAC-AAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAA
*
25749963 TTTCC-AAGTGCAAAATATTGTCTT
65 TTTCCAAACT-CAAAATATTGTCTT
25749987 TATTATTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 24 0.30
107 56 0.70
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAAT
TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
Found at i:25750280 original size:73 final size:73
Alignment explanation
Indices: 25750126--25750280 Score: 222
Period size: 73 Copynumber: 2.1 Consensus size: 73
25750116 CTATCTCAGG
* *
25750126 TTTGGAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAA
1 TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
*
25750191 AAATTTGA
66 AAACTTGA
**** *
25750199 GGAAAAAAGGGATCATGCCCAGTAAGTTAGGACATGATCTCTTCTTAATTCCCGAGATCGTTT-A
1 TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
25750263 AAACTTGAA
66 AAACTTG-A
25750272 TTTGAAAAG
1 TTTGAAAAG
25750281 ATTCGTGTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
72 7 0.10
73 62 0.90
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (73 bp):
TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
AAACTTGA
Found at i:25750698 original size:10 final size:10
Alignment explanation
Indices: 25750619--25750708 Score: 50
Period size: 10 Copynumber: 9.6 Consensus size: 10
25750609 AAAATGAATA
*
25750619 AAAT-TATAG
1 AAATATATAT
*
25750628 AAATATA-AA
1 AAATATATAT
25750637 AAGATATATAT
1 AA-ATATATAT
*
25750648 GAATATATAT
1 AAATATATAT
* *
25750658 --GTATATAA
1 AAATATATAT
25750666 AAAT-TATA-
1 AAATATATAT
*
25750674 AAATATA-AA
1 AAATATATAT
25750683 AAATATATAT
1 AAATATATAT
*
25750693 AAATATGTAT
1 AAATATATAT
*
25750703 ATATAT
1 AAATAT
25750709 TCGTGAGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
8 11 0.17
9 20 0.31
10 31 0.48
11 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:25753662 original size:20 final size:20
Alignment explanation
Indices: 25753637--25753676 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25753627 AATATTTTCC
*
25753637 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25753657 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
25753677 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25753678 original size:34 final size:35
Alignment explanation
Indices: 25753625--25753691 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25753615 CAAACACCAA
*
25753625 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
25753660 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25753692 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25753987 original size:2 final size:2
Alignment explanation
Indices: 25753975--25754030 Score: 94
Period size: 2 Copynumber: 27.0 Consensus size: 2
25753965 AAGTCTCGAA
25753975 AT AT GAT AT AT AT 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
25754018 AT AT AT AT CAT AT
1 AT AT AT AT -AT AT
25754031 TTTGAGACTT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25755088 original size:3 final size:3
Alignment explanation
Indices: 25755080--25755135 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
25755070 GCAAATTTGT
* *
25755080 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25755128 TTA TTA TT
1 TTA TTA TT
25755136 TCATGTTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25755280 original size:24 final size:23
Alignment explanation
Indices: 25755243--25755294 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
25755233 TCTTTTTTAT
25755243 TTATATAAATAAAATAATATGTAA
1 TTATATAAATAAAAT-ATATGTAA
*
25755267 TTATAT-AATAAAAATATATTTAA
1 TTATATAAAT-AAAATATATGTAA
25755290 -TATAT
1 TTATAT
25755295 TTCATTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.19
23 10 0.38
24 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TTATATAAATAAAATATATGTAA
Found at i:25755569 original size:48 final size:47
Alignment explanation
Indices: 25755508--25755618 Score: 138
Period size: 45 Copynumber: 2.4 Consensus size: 47
25755498 TATTATAAAA
25755508 TCAAATAATTATTTCAAACACAAAT-ATTATTTTTATATGTAAAATATT
1 TCAAATAATTATTTCAAA-A-AAATCATTATTTTTATATGTAAAATATT
* * * * *
25755556 TTAAATAACTATTT--AAAATATCATTATTTTTATATGTGAAGTATT
1 TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
25755601 TCAAATAATTATTTCAAA
1 TCAAATAATTATTTCAAA
25755619 TACACATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
44 3 0.06
45 34 0.64
46 2 0.04
47 2 0.04
48 12 0.23
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (47 bp):
TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
Found at i:25775670 original size:26 final size:27
Alignment explanation
Indices: 25775641--25775702 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
25775631 ATTATACAAT
* *
25775641 TATGAAAATATATAAACAATTA-AAAA
1 TATGAAAAAAAATAAACAATTAGAAAA
*
25775667 TATGAAAAAAAATATACAATTATGAAAA
1 TATGAAAAAAAATAAACAATTA-GAAAA
*
25775695 TATCAAAA
1 TATGAAAA
25775703 CATTTTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 19 0.63
28 11 0.37
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (27 bp):
TATGAAAAAAAATAAACAATTAGAAAA
Done.