Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 14 of 91
Found at i:2515740 original size:18 final size:18
Alignment explanation
Indices: 2515719--2515766 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2515709 ATTTACAGAT
2515719 GATACATTTATGGTGGGG
1 GATACATTTATGGTGGGG
*
2515737 GATACATTTGTGGTGGGG
1 GATACATTTATGGTGGGG
2515755 GATACATTTATG
1 GATACATTTATG
2515767 ATAAATGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.06, G:0.35, T:0.35
Consensus pattern (18 bp):
GATACATTTATGGTGGGG
Found at i:2515794 original size:18 final size:18
Alignment explanation
Indices: 2515736--2515805 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
2515726 TTATGGTGGG
* **
2515736 GGATACATTTGTGGTGGG
1 GGATACATTTGAGGTGAA
* *
2515754 GGATACATTT-ATGATAAA
1 GGATACATTTGA-GGTGAA
*
2515772 TGATACATTTGAGGTGAA
1 GGATACATTTGAGGTGAA
2515790 GGATACATTTGAGGTG
1 GGATACATTTGAGGTG
2515806 GATAATAACC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 40 0.98
19 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.33
Consensus pattern (18 bp):
GGATACATTTGAGGTGAA
Found at i:2519345 original size:20 final size:21
Alignment explanation
Indices: 2519320--2519360 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2519310 AAAAAAATTG
* *
2519320 ACAACAATATAAA-TATTAAA
1 ACAACAAAAAAAATTATTAAA
2519340 ACAACAAAAAAAATTATTAAA
1 ACAACAAAAAAAATTATTAAA
2519361 TTTCATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (21 bp):
ACAACAAAAAAAATTATTAAA
Found at i:2520149 original size:150 final size:150
Alignment explanation
Indices: 2519752--2520207 Score: 835
Period size: 149 Copynumber: 3.1 Consensus size: 150
2519742 TTCAATAATT
* * *
2519752 ATATAATAAATATAATCTTCAATAATTACACAGAAATAACAATAATTAATCTAATATCAAAAGAA
1 ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAAGAA
2519817 TTGACAATAATATAAATATCAAAACAACAAAAAAAATATTAAAATTCAGATACAAAATTATAAAT
66 TTGACAATAATATAAATATCAAAACAACAAAAAAAATATTAAAATTCAGATACAAAATTATAAAT
2519882 TAATATGTAACATAATCAAA
131 TAATATGTAACATAATCAAA
2519902 ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAAGAA
1 ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAAGAA
*
2519967 TTGACAATAATATAAATATCAAAACAAC-AAAAAAATATTAAAATTCAAATACAAAATTATAAAT
66 TTGACAATAATATAAATATCAAAACAACAAAAAAAATATTAAAATTCAGATACAAAATTATAAAT
2520031 TAATATGTAACATAATCAAA
131 TAATATGTAACATAATCAAA
*
2520051 ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAACAA
1 ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAAGAA
2520116 TTGACAATAATATAAATATCAAAACAACAAAAAAAA-ATTAAAATTCAGATACAAAATTATAAAT
66 TTGACAATAATATAAATATCAAAACAACAAAAAAAATATTAAAATTCAGATACAAAATTATAAAT
*
2520180 TAATATATAACATAATCAAA
131 TAATATGTAACATAATCAAA
*
2520200 TTATAATA
1 ATATAATA
2520208 TTTAATTTTA
Statistics
Matches: 297, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
149 200 0.67
150 97 0.33
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (150 bp):
ATATAATAAACACAATCTTCAATAATTACACAAAAATAACAATAATTAATCTAATATCAAAAGAA
TTGACAATAATATAAATATCAAAACAACAAAAAAAATATTAAAATTCAGATACAAAATTATAAAT
TAATATGTAACATAATCAAA
Found at i:2520436 original size:20 final size:20
Alignment explanation
Indices: 2520411--2520456 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2520401 CCTCCTAACA
2520411 CCCCACCACACCCAATCCCT
1 CCCCACCACACCCAATCCCT
* * *
2520431 CCCCACCCCATCCAATCTCT
1 CCCCACCACACCCAATCCCT
2520451 CCCCAC
1 CCCCAC
2520457 GTGCCTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.65, G:0.00, T:0.13
Consensus pattern (20 bp):
CCCCACCACACCCAATCCCT
Found at i:2527864 original size:18 final size:18
Alignment explanation
Indices: 2527821--2527865 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2527811 AAAATTCCAT
*
2527821 ATTATTTAAAAATAAAAA
1 ATTATTTTAAAATAAAAA
* *
2527839 ATTATTTTAAATTAAAAC
1 ATTATTTTAAAATAAAAA
2527857 ATTATTTTA
1 ATTATTTTA
2527866 CTAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATTTTAAAATAAAAA
Found at i:2527903 original size:18 final size:19
Alignment explanation
Indices: 2527880--2527927 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
2527870 TAAATTATAT
2527880 TAAAAATATTAT-TTTCTA
1 TAAAAATATTATGTTTCTA
* *
2527898 TAAAAAAAATATGTTTCTA
1 TAAAAATATTATGTTTCTA
2527917 TAAAAATATTA
1 TAAAAATATTA
2527928 ATAGGAGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAATATTATGTTTCTA
Found at i:2545850 original size:22 final size:22
Alignment explanation
Indices: 2545825--2545871 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2545815 TGAAAATATT
2545825 AATTTTATAAAAAATTATTTA-A
1 AATTTTAT-AAAAATTATTTATA
**
2545847 AATTTTATTTAAATTATTTATA
1 AATTTTATAAAAATTATTTATA
2545869 AAT
1 AAT
2545872 AAATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTATAAAAATTATTTATA
Found at i:2545900 original size:26 final size:25
Alignment explanation
Indices: 2545872--2545923 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
2545862 ATTTATAAAT
*
2545872 AAATATAATAAAAAATAATAAATTTTA
1 AAAT-TAATAAAAAAAAAT-AATTTTA
2545899 AAATTAATAAAAAAAAATAATTTTA
1 AAATTAATAAAAAAAAATAATTTTA
2545924 CTGTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTAATAAAAAAAAATAATTTTA
Found at i:2549797 original size:59 final size:58
Alignment explanation
Indices: 2549557--2549922 Score: 350
Period size: 58 Copynumber: 6.1 Consensus size: 58
2549547 TTGTGCAGGA
* * *
2549557 AAAATTGATACTTTCAACTTTTCC-CTAAGAAATATTTTTTTGGAAATTTGAATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AA-AAAAATTTTTTT-GAAATTT-TATTTTTAAAG
* * * *
2549618 AAAATTGATACTTTCAACCTTTT-CT--AAAAAATATTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAA-CTTTTCCTCAAAAAAAT-TTTTTTGAAA-TTTTATTTTTAAAG
* **
2549676 AAAATTGATACTTTCAACTTTTCCTC--AAAAATATTTTTGAAAATTTTGA-TTTTCGAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTG-AAATTTT-ATTTTTAAAG
2549733 AAAAATTGATACTTTCAACTTTTCCTCAAAAAAAGTTTTTTTGAAATTTTATTTTTAAAG
1 -AAAATTGATACTTTCAACTTTTCCTCAAAAAAA-TTTTTTTGAAATTTTATTTTTAAAG
** *
2549793 AAAATTGATACTTTCAACTTTTCCAAAAAAAAAACCTTTTTTTTTTTGAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCC-TCAAAAAAA------TTTTTTTGAAATTTTATTTTTAAAG
* **
2549858 AAAATTGATACTTTCAACTTTTTCTCAAAAATCCTTTTTTTTGAAATTTTATTTTTAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--AATTTTTTTGAAATTTTATTTTTAAA-G
2549919 AAAA
1 AAAA
2549923 AGAAAATAAA
Statistics
Matches: 259, Mismatches: 24, Indels: 44
0.79 0.07 0.13
Matches are distributed among these distances:
57 17 0.07
58 73 0.28
59 34 0.13
60 48 0.19
61 30 0.12
62 5 0.02
64 5 0.02
65 47 0.18
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAATTTTATTTTTAAAG
Found at i:2549962 original size:5 final size:5
Alignment explanation
Indices: 2549920--2550008 Score: 67
Period size: 5 Copynumber: 17.8 Consensus size: 5
2549910 TTTTAAAGGA
* * * *
2549920 AAAAG AAAAT AAAAA AAAAT AAAAGT GAAA- AGAA- AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
** *
2549969 AAAGG AAAGT AAAA- AAAAT AAATAT AAAAT AAATAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAA-AT AAAA
2550009 AGAATATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
4 9 0.13
5 45 0.66
6 14 0.21
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:2549967 original size:29 final size:29
Alignment explanation
Indices: 2549920--2550001 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
2549910 TTTTAAAGGA
*
2549920 AAAAGAAAATAAAAAAAAATAAAAGTGAAA-
1 AAAA-AAAATAAAATAAAATAAAAG-GAAAG
*
2549950 AGAAAAAATAAAATAAAAT-AAAGGAAAG
1 AAAAAAAATAAAATAAAATAAAAGGAAAG
2549978 TAAAAAAAATAAATATAAAATAAA
1 -AAAAAAAATAAA-ATAAAATAAA
2550002 TATAAAAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 25 0.56
30 10 0.22
31 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (29 bp):
AAAAAAAATAAAATAAAATAAAAGGAAAG
Found at i:2550014 original size:11 final size:11
Alignment explanation
Indices: 2549954--2550023 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
2549944 GTGAAAAGAA
2549954 AAAATAAA-AT
1 AAAATAAATAT
**
2549964 AAAATAAA-GG
1 AAAATAAATAT
*
2549974 AAAGTAAA-A-
1 AAAATAAATAT
2549983 AAAATAAATAT
1 AAAATAAATAT
2549994 AAAATAAATAT
1 AAAATAAATAT
2550005 AAAA-AGAATAT
1 AAAATA-AATAT
*
2550016 TAAATAAA
1 AAAATAAA
2550024 CCTAATCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
9 7 0.14
10 17 0.34
11 25 0.50
12 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:2550039 original size:4 final size:4
Alignment explanation
Indices: 2550032--2550089 Score: 59
Period size: 4 Copynumber: 14.8 Consensus size: 4
2550022 AACCTAATCT
*
2550032 AATA AATA AA-A AATA AACA AATA AATA AATA AATTCA AA-A AATA AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AA-T-A AATA AATA AATA
*
2550079 AATA AAAA AAT
1 AATA AATA AAT
2550090 GTAACATGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
3 9 0.20
4 32 0.71
5 1 0.02
6 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:2550085 original size:6 final size:7
Alignment explanation
Indices: 2550035--2550087 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
2550025 CTAATCTAAT
2550035 AAATAAA
1 AAATAAA
2550042 AAATAAA
1 AAATAAA
2550049 CAAATAAA
1 -AAATAAA
2550057 TAAAT--A
1 -AAATAAA
*
2550063 AATTCAAA
1 AAAT-AAA
2550071 AAATAAA
1 AAATAAA
2550078 AAATAAA
1 AAATAAA
2550085 AAA
1 AAA
2550088 ATGTAACATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 3 0.08
6 1 0.03
7 20 0.51
8 15 0.38
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:2559739 original size:61 final size:59
Alignment explanation
Indices: 2559639--2560041 Score: 386
Period size: 61 Copynumber: 6.7 Consensus size: 59
2559629 TTGTGCAGGA
* *
2559639 AAAATTGATATTTTTAACTTTT-CTCCAAGAAATAA-TTTTTTGGAAATTTGGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAA-AAA-AATTTTTTTGGAAATTT-GATTTTCAAGG
* * * *
2559700 AAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTTTGAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAA--TTTTTTTGGAAATTTGATTTTCAAGG
* *
2559761 AAAATTGATACTTTTAACTTTTCCTC--AAAAATATTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGGAAA-TTTGATTTTCAAGG
* * * ** * *
2559819 AAAATTGATACTTTCAATTTTTTCTCAAAAAACCTTTTTTTTTTAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAA--ATTTTTTTGGAAATTTGATTTTCAAGG
* * * * *
2559880 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTTTTTGAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAAAA----TTTTTTTGGAAATTTGATTTTCAAGG
* * * *
2559944 AAAATTGATACTTTCAACTTTTCCTC--AAAAATATTCTTGAAAATTTTGATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGGAAA-TTTGATTTTCAAGG
* **
2560002 AAAATTGATACTTTCAAATTTTCCTCAAAAATCTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTT
2560042 TTTTAAAATT
Statistics
Matches: 284, Mismatches: 41, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
57 18 0.06
58 69 0.24
59 7 0.02
60 15 0.05
61 96 0.34
62 30 0.11
64 49 0.17
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGGAAATTTGATTTTCAAGG
Found at i:2559815 original size:119 final size:118
Alignment explanation
Indices: 2559637--2560039 Score: 435
Period size: 119 Copynumber: 3.3 Consensus size: 118
2559627 TCTTGTGCAG
* * *
2559637 GAAAAATTGATATTTTTAACTTTT-CTCCAAGAAATAATTTTTTGGAAATTTGGATTTTCAAGGA
1 GAAAAATTGATACTTTCAACTTTTCCTACAA-AAAT-A-TTTTTGGAAATTT-GATTTTCAAGGA
2559701 AAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTTTGAAATTTTATTTTTAA
62 AAATTGATACTTTCAACTTTTCCTC-AAAAAACCTTTTTTTTGAAATTTTATTTTTAA
*
2559759 GAAAAATTGATACTTTTAACTTTTCCT-CAAAAATATTTTTGGAAACTTTGATTTTCAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTACAAAAATATTTTTGGAAA-TTTGATTTTCAAGGAAAA
* * *
2559823 TTGATACTTTCAATTTTTTCTCAAAAAACCTTTTTTTTTTAAATTTTATTTTTAA
65 TTGATACTTTCAACTTTTCCTCAAAAAACC-TTTTTTTTGAAATTTTATTTTTAA
* * * * * *
2559878 GGAAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTTTTTGAAATTTTATTTTTAAG
1 GAAAAATTGATACTTTCAACTTTTCCT--ACAAAAA----TATTTTTGGAAATTTGATTTTCAAG
* * * *
2559943 AAAAATTGATACTTTCAACTTTTCCTC-AAAAA---TATTCTTGAAAATTTTGATTTTCAA
60 GAAAATTGATACTTTCAACTTTTCCTCAAAAAACCTTTTTTTTG-AAATTTT-ATTTTTAA
* *
2560000 -AGAAAATTGATACTTTCAAATTTTCCT-CAAAAATCTTTTT
1 GA-AAAATTGATACTTTCAACTTTTCCTACAAAAATATTTTT
2560040 TTTTTTAAAA
Statistics
Matches: 246, Mismatches: 22, Indels: 33
0.82 0.07 0.11
Matches are distributed among these distances:
115 6 0.02
118 8 0.03
119 98 0.40
120 9 0.04
121 11 0.04
122 62 0.25
123 2 0.01
124 5 0.02
125 35 0.14
126 10 0.04
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (118 bp):
GAAAAATTGATACTTTCAACTTTTCCTACAAAAATATTTTTGGAAATTTGATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAAACCTTTTTTTTGAAATTTTATTTTTAA
Found at i:2559948 original size:64 final size:63
Alignment explanation
Indices: 2559794--2560068 Score: 282
Period size: 64 Copynumber: 4.4 Consensus size: 63
2559784 CTCAAAAATA
* * * * * *
2559794 TTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAATTTTTTCT-CAAAAAACCTTTT
1 TTTTTTGAAA-TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTT
2559857 TTTTTT-AAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTT
1 TTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCT-AAAAAAAACCTTTT
* *
2559920 TTTTTTGAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCT--CAAAAA-----T
1 TTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTT
* * * * * * * *
2559976 ATTCTTGAAAATTTTGATTTTCAAAGAAAATTGATACTTTCAAATTTTCCT-CAAAAATCTTTTT
1 TTTTTTG-AAATTTT-ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTT
*
2560040 TTTTTTAAAATTTTATTTTTAGAGGAAAA
1 TTTTTTGAAATTTTATTTTTA-AGGAAAA
2560069 AGAAAATAAA
Statistics
Matches: 179, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
56 6 0.03
57 7 0.04
58 31 0.17
59 4 0.02
61 40 0.22
62 9 0.05
63 36 0.20
64 46 0.26
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (63 bp):
TTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTT
Found at i:2559971 original size:183 final size:181
Alignment explanation
Indices: 2559690--2560068 Score: 616
Period size: 183 Copynumber: 2.1 Consensus size: 181
2559680 GGAAATTTGG
* *
2559690 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTTTGAAATTTTATTT
1 ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTTTTTTGAAATTTTATTT
* * * *
2559755 TTAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTGGAAACTTTGATTTTCAAGGA
66 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTGAAAACTTTGATTTTCAAAGA
* *
2559820 AAATTGATACTTTCAATTTTTTCTCAAAAAACCTTTTTTTTTT-AAATTTT
131 AAATTGATACTTTCAAATTTTCCTCAAAAAACCTTTTTTTTTTAAAATTTT
2559870 ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTTTTTGAAATTTTA
1 ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCT-AAAAAAAACC--TTTTTTTTGAAATTTTA
*
2559935 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTGAAAATTTTGATTTTCAA
63 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTGAAAACTTTGATTTTCAA
* *
2560000 AGAAAATTGATACTTTCAAATTTTCCTCAAAAATCTTTTTTTTTTTAAAATTTT
128 AGAAAATTGATACTTTCAAATTTTCCTCAAAAAACCTTTTTTTTTTAAAATTTT
2560054 ATTTTTAGAGGAAAA
1 ATTTTTA-AGGAAAA
2560069 AGAAAATAAA
Statistics
Matches: 183, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
180 34 0.19
181 9 0.05
183 119 0.65
184 14 0.08
185 7 0.04
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (181 bp):
ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTTTTTTGAAATTTTATTT
TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTGAAAACTTTGATTTTCAAAGA
AAATTGATACTTTCAAATTTTCCTCAAAAAACCTTTTTTTTTTAAAATTTT
Found at i:2560108 original size:5 final size:5
Alignment explanation
Indices: 2560066--2560158 Score: 57
Period size: 5 Copynumber: 18.6 Consensus size: 5
2560056 TTTTAGAGGA
* * * *
2560066 AAAAG AAAAT AAAAC AAAAT AAAAGT GAAA- AGAA- AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
** * * *
2560115 AAAGG AAAGT AAAA- AAAAT AAATAT AAAAAT AATAT TAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT AAAAT AAAAT AAA
2560159 CCTAATCTAA
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
4 9 0.13
5 48 0.71
6 8 0.12
7 3 0.04
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:2560130 original size:29 final size:29
Alignment explanation
Indices: 2560065--2560143 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
2560055 TTTTTAGAGG
* *
2560065 AAAAAGAAAATAAAACAAAATAAAAGTGA
1 AAAAAAAAAATAAAATAAAATAAAAGTGA
*
2560094 AAAGAAAAAATAAAATAAAAT-AAAG-GA
1 AAAAAAAAAATAAAATAAAATAAAAGTGA
2560121 AAGTAAAAAAAATAAATATAAAA
1 AA--AAAAAAAATAAA-ATAAAA
2560144 ATAATATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 29 0.67
30 6 0.14
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (29 bp):
AAAAAAAAAATAAAATAAAATAAAAGTGA
Found at i:2560137 original size:4 final size:4
Alignment explanation
Indices: 2560130--2560213 Score: 66
Period size: 4 Copynumber: 20.0 Consensus size: 4
2560120 AAAGTAAAAA
*
2560130 AAAT AAAT ATAA- AAAT AATATT AAAT AAACCT AATCT AA-T AAAT AAA-
1 AAAT AAAT A-AAT AAAT AA-A-T AAAT AAA--T AA-AT AAAT AAAT AAAT
*
2560177 AAAT AAAA AAATT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT
2560214 TCAAAAAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
3 8 0.12
4 43 0.64
5 10 0.15
6 6 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2560187 original size:8 final size:8
Alignment explanation
Indices: 2560170--2560228 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
2560160 CTAATCTAAT
2560170 AAAT-AAA
1 AAATAAAA
2560177 AAATAAAA
1 AAATAAAA
*
2560185 AAATTAAAT
1 AAA-TAAAA
*
2560194 AAATAAAT
1 AAATAAAA
*
2560202 AAATAAAT
1 AAATAAAA
**
2560210 AAATTCAA
1 AAATAAAA
2560218 AAA-AAAA
1 AAATAAAA
2560225 AAAT
1 AAAT
2560229 CTAGAGGGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
7 9 0.21
8 27 0.63
9 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:2561033 original size:5 final size:5
Alignment explanation
Indices: 2561013--2561183 Score: 52
Period size: 5 Copynumber: 34.4 Consensus size: 5
2561003 CAAGTCAGAT
* **
2561013 AAATC AAAT- AAA-A AAATA AAATA AAATA AAAT- AAA-A AAATCA AACGA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA
* * * * * *
2561060 AAAT- AAATC AGAT- AAATC AAATA AATTA ACAGATA AATTA AAATT AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA A-A-ATA AAATA AAATA AAATA
* * * * * * * * * *
2561110 ACAGA TAATT ACAT- AAATA TTAATA GAA-A AAAGA AAAGA AAAGA AAATA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA
2561159 ATAATA AAATA ATAATA ATAATA AA
1 A-AATA AAATA A-AATA A-AATA AA
2561184 GATATATACC
Statistics
Matches: 126, Mismatches: 26, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
4 25 0.20
5 73 0.58
6 25 0.20
7 3 0.02
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:2561039 original size:18 final size:19
Alignment explanation
Indices: 2561013--2561110 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 19
2561003 CAAGTCAGAT
*
2561013 AAATCAAATAAAA-AAATA
1 AAATAAAATAAAATAAATA
2561031 AAATAAAATAAAATAAA-A
1 AAATAAAATAAAATAAATA
** *
2561049 AAATCAAACGAAAATAAATC
1 AAAT-AAAATAAAATAAATA
* *
2561069 AGAT-AAATCAAATAAATTA
1 AAATAAAATAAAATAAA-TA
*
2561088 ACAGATAAATTAAAATTAAATA
1 A-A-ATAAAATAAAA-TAAATA
2561110 A
1 A
2561111 CAGATAATTA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
18 26 0.43
19 16 0.27
20 3 0.05
21 2 0.03
22 9 0.15
23 4 0.07
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.20
Consensus pattern (19 bp):
AAATAAAATAAAATAAATA
Found at i:2561044 original size:23 final size:24
Alignment explanation
Indices: 2561013--2561066 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2561003 CAAGTCAGAT
* *
2561013 AAATCAAATAAAAAAAT-AAAATA
1 AAATAAAATAAAAAAATCAAAAGA
*
2561036 AAATAAAATAAAAAAATCAAACGA
1 AAATAAAATAAAAAAATCAAAAGA
2561060 AAATAAA
1 AAATAAA
2561067 TCAGATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.15
Consensus pattern (24 bp):
AAATAAAATAAAAAAATCAAAAGA
Found at i:2561094 original size:21 final size:22
Alignment explanation
Indices: 2561068--2561117 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2561058 GAAAATAAAT
*
2561068 CAGATAAA-TCAAA-TAAATTAA
1 CAGATAAATTAAAATTAAA-TAA
2561089 CAGATAAATTAAAATTAAATAA
1 CAGATAAATTAAAATTAAATAA
2561111 CAGATAA
1 CAGATAA
2561118 TTACATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.31
22 14 0.54
23 4 0.15
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (22 bp):
CAGATAAATTAAAATTAAATAA
Found at i:2561167 original size:11 final size:11
Alignment explanation
Indices: 2561153--2561182 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2561143 AAAAGAAAAG
2561153 AAAATAATAAT
1 AAAATAATAAT
2561164 AAAATAATAAT
1 AAAATAATAAT
2561175 AATAATAA
1 AA-AATAA
2561183 AGATATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2561321 original size:6 final size:6
Alignment explanation
Indices: 2561269--2561343 Score: 57
Period size: 7 Copynumber: 12.2 Consensus size: 6
2561259 TATATAAAAT
* *
2561269 AATAAT AATAAA AAT-AA AAT-AA AATAAGA ATGTAAA AATACAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAA-A A-ATAAA AATA-AA AATAAA
*
2561318 AAT-AA ATTAAAA AATAAAA AATAAA A
1 AATAAA AAT-AAA AAT-AAA AATAAA A
2561344 TGAAGTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
5 14 0.24
6 20 0.34
7 21 0.36
8 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:2561336 original size:31 final size:29
Alignment explanation
Indices: 2561262--2561343 Score: 83
Period size: 32 Copynumber: 2.7 Consensus size: 29
2561252 ATATACATAT
*
2561262 ATAAAATAATAATAATAAAAATAAAATAAA
1 ATAAAA-AATAAAAATAAAAATAAAATAAA
**
2561292 ATAAGAATGTAAAAATACAAAATAAAAATAAA
1 ATAA-AAAATAAAAATA-AAAAT-AAAATAAA
*
2561324 TTAAAAAATAAAAAATAAAA
1 ATAAAAAAT-AAAAATAAAA
2561344 TGAAGTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 11 0.26
31 13 0.31
32 18 0.43
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (29 bp):
ATAAAAAATAAAAATAAAAATAAAATAAA
Found at i:2561344 original size:24 final size:24
Alignment explanation
Indices: 2561262--2561363 Score: 82
Period size: 25 Copynumber: 4.0 Consensus size: 24
2561252 ATATACATAT
*
2561262 ATAAAATAATAA-TAATAAAAATAAA
1 ATAAAATAA-AATTAA-AAAAAAAAA
* *
2561287 ATAAAATAAGAATGTAAAAATACAAA
1 ATAAAATAA-AAT-TAAAAAAAAAAA
2561313 ATAAAA-ATAAATTAAAAAATAAAAA
1 ATAAAATA-AAATTAAAAAA-AAAAA
* *
2561338 ATAAAATGAAGTTAAAAGAAAAAAA
1 ATAAAATAAAATTAAAA-AAAAAAA
2561363 A
1 A
2561364 GAAAGAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
24 6 0.09
25 39 0.61
26 16 0.25
27 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.20
Consensus pattern (24 bp):
ATAAAATAAAATTAAAAAAAAAAA
Found at i:2561601 original size:2 final size:2
Alignment explanation
Indices: 2561594--2561632 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2561584 CTATTTATCT
2561594 TA TA 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 TA TA T
2561633 GAATGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2567112 original size:10 final size:9
Alignment explanation
Indices: 2567097--2567121 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2567087 AACTCCTATC
2567097 TTTTTTTTA
1 TTTTTTTTA
2567106 TTTTTTTTA
1 TTTTTTTTA
2567115 TTTTTTT
1 TTTTTTT
2567122 ATTGTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:2569708 original size:20 final size:20
Alignment explanation
Indices: 2569685--2569724 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2569675 TTTATATTTT
2569685 CTTTAGAAAATTTCTTTTAA
1 CTTTAGAAAATTTCTTTTAA
* **
2569705 CTTTTGATGATTTCTTTTAA
1 CTTTAGAAAATTTCTTTTAA
2569725 GTTAAGGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (20 bp):
CTTTAGAAAATTTCTTTTAA
Found at i:2570496 original size:3 final size:3
Alignment explanation
Indices: 2570488--2570542 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
2570478 CTTGACGATT
2570488 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2570535 TCAA TAA T
1 T-AA TAA T
2570543 TTCAAGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2575197 original size:3 final size:3
Alignment explanation
Indices: 2575189--2575237 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2575179 AACTATAATG
2575189 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2575237 T
1 T
2575238 CATATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2575288 original size:20 final size:19
Alignment explanation
Indices: 2575244--2575311 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
2575234 TAATCATATA
2575244 AATATAT-AA-TATCATGC
1 AATATATAAATTATCATGC
*
2575261 AAATATATTAATTATCATGC
1 -AATATATAAATTATCATGC
**
2575281 AATGATATAAATTGCCATGC
1 AAT-ATATAAATTATCATGC
2575301 AATAATATAAA
1 AAT-ATATAAA
2575312 ATACTTGGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.16
19 5 0.12
20 31 0.72
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (19 bp):
AATATATAAATTATCATGC
Found at i:2575468 original size:24 final size:24
Alignment explanation
Indices: 2575439--2575500 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2575429 GATATCATTC
*
2575439 AAATATAATATTA-ATCATGCAAT
1 AAATATAATATCATATCATGCAAT
*
2575462 AACATATAATATCATATCATGTAAT
1 AA-ATATAATATCATATCATGCAAT
*
2575487 AAATATAAAATCAT
1 AAATATAATATCAT
2575501 GCAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 21 0.62
25 11 0.32
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:2575649 original size:22 final size:22
Alignment explanation
Indices: 2575605--2575646 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2575595 CATGCAATTA
2575605 AATATATAATCATACAAATAAC
1 AATATATAATCATACAAATAAC
*
2575627 AATATA-AATCATGCAAATAA
1 AATATATAATCATACAAATAA
2575647 ACATACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (22 bp):
AATATATAATCATACAAATAAC
Found at i:2575653 original size:33 final size:33
Alignment explanation
Indices: 2575610--2575712 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
2575600 AATTAAATAT
*
2575610 ATAATCATACAAATAACAATATAAATCATGCAA
1 ATAAACATACAAATAACAATATAAATCATGCAA
* * *
2575643 ATAAACATAC-AATTA-AATATATAATAATACAA
1 ATAAACATACAAATAACAATATA-AATCATGCAA
*
2575675 ATAATA-ATATAAATCATACAA-ATAAA-CATGCAA
1 ATAA-ACATACAAAT-A-ACAATATAAATCATGCAA
*
2575708 TTAAA
1 ATAAA
2575713 TATATAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
31 6 0.11
32 20 0.36
33 21 0.38
34 2 0.04
35 4 0.07
36 2 0.04
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (33 bp):
ATAAACATACAAATAACAATATAAATCATGCAA
Found at i:2575656 original size:53 final size:53
Alignment explanation
Indices: 2575580--2575724 Score: 245
Period size: 53 Copynumber: 2.7 Consensus size: 53
2575570 ATAAATTAAT
* *
2575580 AATCATGCAAATAGACATGCAATTAAATATATAATCATACAAATAACAATATA
1 AATCATGCAAATAAACATGCAATTAAATATATAATAATACAAATAACAATATA
* *
2575633 AATCATGCAAATAAACATACAATTAAATATATAATAATACAAATAATAATATA
1 AATCATGCAAATAAACATGCAATTAAATATATAATAATACAAATAACAATATA
*
2575686 AATCATACAAATAAACATGCAATTAAATATATAATAATA
1 AATCATGCAAATAAACATGCAATTAAATATATAATAATA
2575725 ATAATCATGC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 86 1.00
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (53 bp):
AATCATGCAAATAAACATGCAATTAAATATATAATAATACAAATAACAATATA
Found at i:2575748 original size:29 final size:32
Alignment explanation
Indices: 2575695--2575780 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 32
2575685 AAATCATACA
* * *
2575695 AATAAACATGCAATTAAATATAT-AAT-AA-T
1 AATAATCATGCAATCAAATAAATAAATAAATT
*
2575724 AATAATCATGCAATCACATAAATAAATAAATT
1 AATAATCATGCAATCAAATAAATAAATAAATT
* *
2575756 GATAATCATGCATAT-AAATTAATAA
1 AATAATCATGCA-ATCAAATAAATAA
2575781 TCAAGCAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 19 0.41
30 3 0.07
31 2 0.04
32 20 0.43
33 2 0.04
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (32 bp):
AATAATCATGCAATCAAATAAATAAATAAATT
Found at i:2575857 original size:20 final size:20
Alignment explanation
Indices: 2575758--2575920 Score: 109
Period size: 20 Copynumber: 8.7 Consensus size: 20
2575748 AATAAATTGA
* *
2575758 TAATCATGCATATA-AATTAA
1 TAATCATGCAAATATAA-TAT
* * * *
2575778 TAATCAAGCAAACATATTAA
1 TAATCATGCAAATATAATAT
* * *
2575798 TAGTCATGCAAATATATTAA
1 TAATCATGCAAATATAATAT
2575818 TAA--ATTGCACAA-AT-ATAT
1 TAATCA-TGCA-AATATAATAT
*
2575836 TAATCATGCAAATAAAATAT
1 TAATCATGCAAATATAATAT
2575856 T-A--A-GC-AA-ATAA-AT
1 TAATCATGCAAATATAATAT
2575869 T-ATCATGCAAATATAATAT
1 TAATCATGCAAATATAATAT
2575888 TAATCATGCAAATATAATAT
1 TAATCATGCAAATATAATAT
*
2575908 TAGTCATGCAAAT
1 TAATCATGCAAAT
2575921 TCATGCAAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
13 4 0.03
14 3 0.03
15 3 0.03
16 4 0.03
17 3 0.03
18 12 0.10
19 15 0.13
20 71 0.61
21 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (20 bp):
TAATCATGCAAATATAATAT
Found at i:2575864 original size:16 final size:16
Alignment explanation
Indices: 2575843--2575890 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
2575833 TATTAATCAT
2575843 GCAAATAAAATATTAA
1 GCAAATAAAATATTAA
* * *
2575859 GCAAATAAATTATCAT
1 GCAAATAAAATATTAA
*
2575875 GCAAATATAATATTAA
1 GCAAATAAAATATTAA
2575891 TCATGCAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (16 bp):
GCAAATAAAATATTAA
Found at i:2575875 original size:32 final size:33
Alignment explanation
Indices: 2575827--2575890 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2575817 ATAAATTGCA
*
2575827 CAAATATATTAATCATGCAAATAAAATATTAAG
1 CAAATAAATTAATCATGCAAATAAAATATTAAG
*
2575860 CAAATAAATT-ATCATGCAAATATAATATTAA
1 CAAATAAATTAATCATGCAAATAAAATATTAA
2575891 TCATGCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (33 bp):
CAAATAAATTAATCATGCAAATAAAATATTAAG
Found at i:2577025 original size:67 final size:66
Alignment explanation
Indices: 2576940--2577116 Score: 230
Period size: 67 Copynumber: 2.6 Consensus size: 66
2576930 CAATGATCAA
* *
2576940 AATTAATAGATAAATATTATTTTTAAAAATGAAGAAACTAAAAAAATAAAGACAGCAAAAAATAC
1 AATTAATAGATAAATATTATTTTT-AAAATGAAGAAACTAAAAAAATAAAGAAAGCAAAAAAGAC
*
2577005 AT
65 AC
* * * * *
2577007 AATTAATTA-ATAACTATTATTTTTAAAATCAAAGAAAATGAAAAAGTAAAGAAAGCAAAAAAGA
1 AATTAA-TAGATAAATATTATTTTTAAAAT-GAAGAAACTAAAAAAATAAAGAAAGCAAAAAAGA
2577071 CAC
64 CAC
*
2577074 AATTAATAGATAAATATTATTTTTAAATTGAAGAAAACTAAAA
1 AATTAATAGATAAATATTATTTTTAAAATGAAG-AAACTAAAA
2577117 GATCAATAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
66 10 0.11
67 81 0.87
68 2 0.02
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (66 bp):
AATTAATAGATAAATATTATTTTTAAAATGAAGAAACTAAAAAAATAAAGAAAGCAAAAAAGACA
C
Found at i:2577135 original size:67 final size:66
Alignment explanation
Indices: 2576940--2577136 Score: 199
Period size: 67 Copynumber: 2.9 Consensus size: 66
2576930 CAATGATCAA
* *
2576940 AATTAATAGATAAATATTATTTTTAAAAATGAAG-AAACTAAAAA-AATAAAGACAGCAAAAAAT
1 AATTAATAGATAAATATTATTTTTAAAATTGAAGAAAACTAAAAATAATAAAG-C--CAAAAAAG
*
2577003 ACAT
63 ACAC
* ** *
2577007 AATTAATTA-ATAACTATTATTTTTAAAATCAAAGAAAA-TGAAAAAGTAAAGAAAG-CAAAAAA
1 AATTAA-TAGATAAATATTATTTTTAAAATTGAAGAAAACT-AAAAA-T-AATAAAGCCAAAAAA
2577069 GACAC
62 GACAC
2577074 AATTAATAGATAAATATTATTTTT-AAATTGAAGAAAACTAAAAGATCAATAAAGCCTAAAAAA
1 AATTAATAGATAAATATTATTTTTAAAATTGAAGAAAACTAAAA-AT-AATAAAGCC-AAAAAA
2577137 TCAATTATTA
Statistics
Matches: 107, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
66 24 0.22
67 61 0.57
68 16 0.15
71 6 0.06
ACGTcount: A:0.59, C:0.07, G:0.08, T:0.26
Consensus pattern (66 bp):
AATTAATAGATAAATATTATTTTTAAAATTGAAGAAAACTAAAAATAATAAAGCCAAAAAAGACA
C
Found at i:2577601 original size:12 final size:13
Alignment explanation
Indices: 2577584--2577615 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2577574 AAATGTTTAG
2577584 ATTATTTTT-ATT
1 ATTATTTTTCATT
2577596 ATTATTTTTCATT
1 ATTATTTTTCATT
2577609 -TTATTTT
1 ATTATTTT
2577616 GAGTAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTATTTTTCATT
Found at i:2588730 original size:3 final size:3
Alignment explanation
Indices: 2588724--2588756 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2588714 CAACAACAAC
2588724 AAT AAT AAT AAT AAT AAT AAT AA- AAT CAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
2588757 TTTCAAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2591210 original size:20 final size:22
Alignment explanation
Indices: 2591187--2591242 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
2591177 TTTCATCTTT
2591187 AAAACATTGTCTTTTCA-A-CA
1 AAAACATTGTCTTTTCATATCA
* * *
2591207 AAAAC-TATGTTTTTTTATATGA
1 AAAACAT-TGTCTTTTCATATCA
2591229 AAAACATTGTCTTT
1 AAAACATTGTCTTT
2591243 GTTAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 1 0.04
20 13 0.46
21 1 0.04
22 12 0.43
23 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
AAAACATTGTCTTTTCATATCA
Found at i:2593194 original size:66 final size:67
Alignment explanation
Indices: 2593099--2593289 Score: 232
Period size: 66 Copynumber: 2.9 Consensus size: 67
2593089 AACTAATAAT
*
2593099 CACAATTAATAGATAAATATTATTTTTAAAATTGAA-AAAATCG-AAGAAATAAAGAAAGCCAAA
1 CACAATTAATAGATAAATATTATTTTTAAAATTGAAGAAAAT-GAAAG-AATAAAGAAAGCAAAA
*
2593162 AATA
64 AAGA
* * *
2593166 CACAATTAATTA-ATTAA-ATTATTTTTAAAATAGAAGAAAATGAAAGAGTAAAGAAAGCAAAAA
1 CACAATTAA-TAGATAAATATTATTTTTAAAATTGAAGAAAATGAAAGAATAAAGAAAGCAAAAA
2593229 AGA
65 AGA
* * *
2593232 CATAATTAATAGATAAATATTATTTTT-AAATTGAAGAAAACTAAAAG-ATCAAGAAAGC
1 CACAATTAATAGATAAATATTATTTTTAAAATTGAAGAAAA-TGAAAGAATAAAGAAAGC
2593290 CCAACAAATC
Statistics
Matches: 107, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
65 2 0.02
66 68 0.64
67 35 0.33
68 2 0.02
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.26
Consensus pattern (67 bp):
CACAATTAATAGATAAATATTATTTTTAAAATTGAAGAAAATGAAAGAATAAAGAAAGCAAAAAA
GA
Found at i:2593345 original size:15 final size:15
Alignment explanation
Indices: 2593325--2593362 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2593315 TTATTAAAAT
2593325 TTATTATATATTAT-A
1 TTATTA-ATATTATGA
*
2593340 TTATTAATTTTATGA
1 TTATTAATATTATGA
2593355 TTATTAAT
1 TTATTAAT
2593363 GAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTAATATTATGA
Found at i:2595921 original size:3 final size:3
Alignment explanation
Indices: 2595907--2596055 Score: 178
Period size: 3 Copynumber: 49.3 Consensus size: 3
2595897 GCCAATAAGG
*
2595907 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2595955 TTA TTA -TA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA -TA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
2595998 GTA CATA GTCTA TTA GTA TTA TTA TTA TCA TAA TTA TTA TCA TTA TTA
1 TTA -TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2596046 TTA TTA TTA T
1 TTA TTA TTA T
2596056 CTTTTTTTAT
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
2 5 0.04
3 114 0.90
4 6 0.05
5 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2600069 original size:49 final size:50
Alignment explanation
Indices: 2599966--2600069 Score: 145
Period size: 50 Copynumber: 2.1 Consensus size: 50
2599956 AAAATAAAAC
* *
2599966 AAAAACAAAAAAAAATTGATAGGACAAAATGCCAATGTGCCCCACCTAAA
1 AAAAACAAAAAAAAATTGATAGGACAAAATGCCAAAGTGCCCCACATAAA
* * * * *
2600016 AAAAAGAAAAAAAAATTGATGGGACAAAATGTCAAAGTGCCTCACATGAA
1 AAAAACAAAAAAAAATTGATAGGACAAAATGCCAAAGTGCCCCACATAAA
2600066 AAAA
1 AAAA
2600070 TGATCATTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.14
Consensus pattern (50 bp):
AAAAACAAAAAAAAATTGATAGGACAAAATGCCAAAGTGCCCCACATAAA
Found at i:2601424 original size:68 final size:68
Alignment explanation
Indices: 2601277--2601425 Score: 192
Period size: 68 Copynumber: 2.2 Consensus size: 68
2601267 TTGTGAATTT
* * * * *
2601277 TTCTTACGAATCATGTATCTTTGCGAATCTAGAACCTTTGCAAAACTTGAAATTTTACGAATCTT
1 TTCTTACGAATCTTGCATCTTTACGAATCCAGAACCTTTGCAAAACTTGAAATCTTACGAATCTT
* *
2601342 TCT
66 CCA
* **
2601345 TTTTTGTGAATCTTGCATCTTTACGAATCCAGAACCTTTGCAAAACTTGAAATCTTACGAAT-TT
1 TTCTTACGAATCTTGCATCTTTACGAATCCAGAACCTTTGCAAAACTTGAAATCTTACGAATCTT
2601409 ACCA
66 -CCA
2601413 TTCTTACGAATCT
1 TTCTTACGAATCT
2601426 AAAAACCTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 2 0.03
68 65 0.97
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (68 bp):
TTCTTACGAATCTTGCATCTTTACGAATCCAGAACCTTTGCAAAACTTGAAATCTTACGAATCTT
CCA
Found at i:2601700 original size:64 final size:63
Alignment explanation
Indices: 2601574--2601763 Score: 195
Period size: 64 Copynumber: 3.0 Consensus size: 63
2601564 TCTATTAGCC
* * * *
2601574 ATTTTTTACCTCGACTCGGTCTTGGTCGTCTT-ATCTTTAGACTCGTGATTTTATCCCCATCATT
1 ATTTTTTA-CTCAACTCGGTCTTGGTCG-CTTCAT-TTTTGACTCGTGATTTCATCCCAATCATT
2601638 T
63 T
*
2601639 ATTTTTTATCTCAACTCGGTCTTGGTCGCTTCATTTTTGACTCGTGGTTTCATCCCAATCATTT
1 ATTTTTTA-CTCAACTCGGTCTTGGTCGCTTCATTTTTGACTCGTGATTTCATCCCAATCATTT
* * * * * * * *
2601703 -TTTTTCGACATTAACTCGATCCTAGTCGCTTCATTTTTAACTTGTGATTTCATCCCGATCA
1 ATTTTT-TAC-TCAACTCGGTCTTGGTCGCTTCATTTTTGACTCGTGATTTCATCCCAATCA
2601764 CTTGATCTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
63 6 0.06
64 73 0.68
65 28 0.26
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.45
Consensus pattern (63 bp):
ATTTTTTACTCAACTCGGTCTTGGTCGCTTCATTTTTGACTCGTGATTTCATCCCAATCATTT
Found at i:2601820 original size:120 final size:120
Alignment explanation
Indices: 2601696--2602239 Score: 495
Period size: 120 Copynumber: 4.5 Consensus size: 120
2601686 TTTCATCCCA
* * *
2601696 ATCATTTTTTTTCGACATTAACTCGATCCTAGTCGCTTCATTTTTAACTTGTGATTTCATCCCGA
1 ATCATTTATTTTCGACATCAACTCGATCCTAGTCGCTTCATTTTTAACTCGTGATTTCATCCCGA
* * * * * ** *
2601761 TCACTTGATCTTGGCTTAGTCTACATTATTTATTATGACTCATAGTTTCATCTTG
66 TCACTTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCATAGTTTTGTCTCG
* ** * * **
2601816 ATCATTTGTTTTCGACATTGACTCGAT-CTTGATCGCTTCATTTTTGACTCGTGATTTTGTCCCG
1 ATCATTTATTTTCGACATCAACTCGATCCTAG-TCGCTTCATTTTTAACTCGTGATTTCATCCCG
* * * * * *
2601880 ATCACTTAATCTTGACTCAATCCATATCATTTCTTATGACTCATAGTTTTGTCCCA
65 ATCACTTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCATAGTTTTGTCTCG
* * ** * * * * **
2601936 ATCATTTATTTTCGACCTGAACTC-AGTTTTGGTCGTTTCATTTTTTACTCGTGGTTTCATCATG
1 ATCATTTATTTTCGACATCAACTCGA-TCCTAGTCGCTTCATTTTTAACTCGTGATTTCATCCCG
* * * * * *
2602000 GTCACCTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCGTGGATTTGTTCTTG
65 ATCACTTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCATAGTTTTG-TCTCG
* * * * * * * ** *
2602057 -TCATTTATTTTC-AAACTCGACTTGGTCCTGGTCGCTTCATTTTTGACTCGTGATTTCGTTTCA
1 ATCATTTATTTTCGACA-TCAACTCGATCCTAGTCGCTTCATTTTTAACTCGTGATTTCATCCCG
* * * * *
2602120 ATCACTTGATCTTGGCTTAATCTAGGTAATTTCTTATGACTCATGGTTTTGTC-CC
65 ATCACTTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCATAGTTTTGTCTCG
*
2602175 AGTCATTTATTTTCGACCTCAACTCGATCCTAGTCGCTTCATTTCTTAACTCGTGATTTCATCCC
1 A-TCATTTATTTTCGACATCAACTCGATCCTAGTCGCTTCATTT-TTAACTCGTGATTTCATCCC
2602240 AGTCATTTTT
Statistics
Matches: 334, Mismatches: 80, Indels: 19
0.77 0.18 0.04
Matches are distributed among these distances:
119 7 0.02
120 306 0.92
121 21 0.06
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (120 bp):
ATCATTTATTTTCGACATCAACTCGATCCTAGTCGCTTCATTTTTAACTCGTGATTTCATCCCGA
TCACTTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCATAGTTTTGTCTCG
Found at i:2602218 original size:240 final size:240
Alignment explanation
Indices: 2601676--2602237 Score: 644
Period size: 240 Copynumber: 2.3 Consensus size: 240
2601666 GCTTCATTTT
* ** * * *
2601676 TGACTCGTGGTTTCATCCCAATCATTTTTTTTCGACATTAACTCGATCCTAGTCGCTTCATTTTT
1 TGACTCATGGTTTTGTCCCAATCATTTATTTTCGACCTCAACTCGATCCTAGTCGCTTCATTTTT
* * * * * *
2601741 AACTTGTGATTTCATCCCGATCACTTGATCTTGGCTTAGTCTACATTATTTATTATGACTCATAG
66 AACTCGTGATTTCATCACGATCACCTGATCTTGGCTCAATCTACATCATTTATTATGACTCATAG
* * * *
2601806 TTTCATCTTGATCATTTGTTTTCGACATTGACTCGATCTTGATCGCTTCATTTTTGACTCGTGAT
131 TTTCATCTTGATCATTTATTTTCAACATCGACTCGATCCTGATCGCTTCATTTTTGACTCGTGAT
* * * *
2601871 TTTGTCCCGATCACTTAATCTTGACTCAATCCATATCATTTCTTA
196 TTCGTCCCAATCACTTAATCTTGACTCAATCCAGATAATTTCTTA
* * ** * *
2601916 TGACTCATAGTTTTGTCCCAATCATTTATTTTCGACCTGAACTC-AGTTTTGGTCGTTTCATTTT
1 TGACTCATGGTTTTGTCCCAATCATTTATTTTCGACCTCAACTCGA-TCCTAGTCGCTTCATTTT
* * * * * * * *
2601980 TTACTCGTGGTTTCATCATGGTCACCTGATCTTGGCTCAATCTAGATCATTTCTTATGACTCGTG
65 TAACTCGTGATTTCATCACGATCACCTGATCTTGGCTCAATCTACATCATTTATTATGACTCATA
** * * *
2602045 GATTTGTTCTTG-TCATTTATTTTCAA-ACTCGACTTGGTCCTGGTCGCTTCATTTTTGACTCGT
130 G-TTTCATCTTGATCATTTATTTTCAACA-TCGACTCGATCCTGATCGCTTCATTTTTGACTCGT
** * * * * *
2602108 GATTTCGTTTCAATCACTTGATCTTGGCTTAATCTAGGTAATTTCTTA
193 GATTTCGTCCCAATCACTTAATCTTGACTCAATCCAGATAATTTCTTA
*
2602156 TGACTCATGGTTTTGTCCCAGTCATTTATTTTCGACCTCAACTCGATCCTAGTCGCTTCATTTCT
1 TGACTCATGGTTTTGTCCCAATCATTTATTTTCGACCTCAACTCGATCCTAGTCGCTTCATTT-T
2602221 TAACTCGTGATTTCATC
65 TAACTCGTGATTTCATC
2602238 CCAGTCATTT
Statistics
Matches: 263, Mismatches: 54, Indels: 9
0.81 0.17 0.03
Matches are distributed among these distances:
239 2 0.01
240 236 0.90
241 25 0.10
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (240 bp):
TGACTCATGGTTTTGTCCCAATCATTTATTTTCGACCTCAACTCGATCCTAGTCGCTTCATTTTT
AACTCGTGATTTCATCACGATCACCTGATCTTGGCTCAATCTACATCATTTATTATGACTCATAG
TTTCATCTTGATCATTTATTTTCAACATCGACTCGATCCTGATCGCTTCATTTTTGACTCGTGAT
TTCGTCCCAATCACTTAATCTTGACTCAATCCAGATAATTTCTTA
Found at i:2602414 original size:17 final size:18
Alignment explanation
Indices: 2602386--2602433 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
2602376 GGGTTATTTT
2602386 TAATATATTATTATAGTA
1 TAATATATTATTATAGTA
2602404 TAATATA-TATTATAGTA
1 TAATATATTATTATAGTA
*
2602421 TTAT-TATTATTAT
1 TAATATATTATTAT
2602434 TATTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 2 0.07
17 19 0.68
18 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TAATATATTATTATAGTA
Found at i:2602427 original size:3 final size:3
Alignment explanation
Indices: 2602419--2602527 Score: 114
Period size: 3 Copynumber: 36.0 Consensus size: 3
2602409 TATATTATAG
* * *
2602419 TAT TAT TAT TAT TAT TAT TAT TA- TAT T-G TACA TAGT CTAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T -TAT TAT TAT
* * * *
2602465 TTT TAT CAG AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2602513 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
2602528 CATCATTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
2 3 0.03
3 81 0.91
4 3 0.03
5 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2611499 original size:2 final size:2
Alignment explanation
Indices: 2611492--2611524 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2611482 TTAAGGGATC
*
2611492 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2611525 GAGAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2612112 original size:19 final size:19
Alignment explanation
Indices: 2612088--2612125 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2612078 ATTGAACTAG
2612088 AATATGGTAGTAAAGAGTA
1 AATATGGTAGTAAAGAGTA
2612107 AATATGGTAGTAAAGAGTA
1 AATATGGTAGTAAAGAGTA
2612126 TATAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (19 bp):
AATATGGTAGTAAAGAGTA
Found at i:2615907 original size:10 final size:10
Alignment explanation
Indices: 2615892--2615925 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2615882 TGTGTATCTT
2615892 ATAATGAGTG
1 ATAATGAGTG
*
2615902 ATAATGGGTG
1 ATAATGAGTG
2615912 ATAATGAGTG
1 ATAATGAGTG
2615922 ATAA
1 ATAA
2615926 AATAATGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
ATAATGAGTG
Found at i:2619426 original size:13 final size:13
Alignment explanation
Indices: 2619410--2619444 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2619400 TTTATGATTG
2619410 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
*
2619423 TTTTCTTTTTTTT
1 TTTTCTTTTTTCT
*
2619436 TTTTATTTT
1 TTTTCTTTT
2619445 GGTGTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:2624723 original size:15 final size:14
Alignment explanation
Indices: 2624689--2624723 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2624679 CATATCATAC
2624689 AAATTT-AAAATCT
1 AAATTTCAAAATCT
2624702 AAATTTCAAAATCT
1 AAATTTCAAAATCT
2624716 ATAATTTC
1 A-AATTTC
2624724 TTTTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 8 0.40
15 6 0.30
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTTCAAAATCT
Found at i:2636634 original size:41 final size:41
Alignment explanation
Indices: 2636582--2636662 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
2636572 TGACCAAACT
*
2636582 AAAACTCCTATAGAACAACAATTATTTATTAATATTCCAAA
1 AAAACTCCTATAGAACAACAATTATATATTAATATTCCAAA
2636623 AAAACTCCTATAGAACAACAATTATATATTAATATTCCAA
1 AAAACTCCTATAGAACAACAATTATATATTAATATTCCAA
2636663 CACTTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.31
Consensus pattern (41 bp):
AAAACTCCTATAGAACAACAATTATATATTAATATTCCAAA
Found at i:2637493 original size:14 final size:14
Alignment explanation
Indices: 2637452--2637494 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2637442 ATACATTGAG
*
2637452 AAATAATTTATATAT
1 AAAT-ATTTATATTT
*
2637467 AAATATATATATTT
1 AAATATTTATATTT
*
2637481 ATATATTTATATTT
1 AAATATTTATATTT
2637495 CTCTGTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATATTTATATTT
Found at i:2637750 original size:17 final size:16
Alignment explanation
Indices: 2637728--2637763 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2637718 TCAAAACGTA
2637728 TTTCCAAAATTATTGTC
1 TTTCCAAAATTATT-TC
*
2637745 TTTCCAAACTTATTTC
1 TTTCCAAAATTATTTC
2637761 TTT
1 TTT
2637764 ACTTCTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTCCAAAATTATTTC
Found at i:2637893 original size:16 final size:16
Alignment explanation
Indices: 2637867--2637950 Score: 69
Period size: 16 Copynumber: 4.9 Consensus size: 16
2637857 TGGTTAACAG
2637867 AAAATAATTTATTTATT
1 AAAA-AATTTATTTATT
* *
2637884 AACAAATTTATTTTTT
1 AAAAAATTTATTTATT
2637900 AAAAAATTATCATTTTATTT
1 AAAAAATT-T-A-TTTA-TT
* * *
2637920 AAAAAAATAATTTTTT
1 AAAAAATTTATTTATT
*
2637936 AAAAAAATTATTTAT
1 AAAAAATTTATTTAT
2637951 GAGTTAAACC
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
16 33 0.61
17 7 0.13
18 2 0.04
19 3 0.06
20 9 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAAATTTATTTATT
Found at i:2637922 original size:20 final size:19
Alignment explanation
Indices: 2637894--2637946 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2637884 AACAAATTTA
*
2637894 TTTTTTAAAAAATTATCAT
1 TTTTTTAAAAAATTATAAT
2637913 TTTATTTAAAAAA--ATAAT
1 TTT-TTTAAAAAATTATAAT
*
2637931 TTTTTAAAAAAATTAT
1 TTTTTTAAAAAATTAT
2637947 TTATGAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 8 0.28
18 7 0.24
19 5 0.17
20 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTTAAAAAATTATAAT
Found at i:2638520 original size:19 final size:21
Alignment explanation
Indices: 2638498--2638536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2638488 CATGTCTTAA
2638498 TATTTT-TACTTTAA-AATAT
1 TATTTTATACTTTAATAATAT
*
2638517 TATTTTATATTTTAATAATA
1 TATTTTATACTTTAATAATA
2638537 AATATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATACTTTAATAATAT
Found at i:2640576 original size:23 final size:23
Alignment explanation
Indices: 2640550--2640595 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2640540 AAATGGATGG
*
2640550 GAAAAGATGAAAAAAAT-GAAAAA
1 GAAAAAAT-AAAAAAATGGAAAAA
*
2640573 GAAAAAATAAAAGAATGGAAAAA
1 GAAAAAATAAAAAAATGGAAAAA
2640596 AGATGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (23 bp):
GAAAAAATAAAAAAATGGAAAAA
Found at i:2640596 original size:25 final size:26
Alignment explanation
Indices: 2640568--2640620 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
2640558 GAAAAAAATG
2640568 AAAAAGA-AAAAATAAAAGAA-TGGA
1 AAAAAGATAAAAATAAAAGAAGTGGA
* *
2640592 AAAAAGATGAAAATGAAAGAAGTGGA
1 AAAAAGATAAAAATAAAAGAAGTGGA
2640618 AAA
1 AAA
2640621 TTCAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 11 0.44
26 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (26 bp):
AAAAAGATAAAAATAAAAGAAGTGGA
Found at i:2641903 original size:21 final size:22
Alignment explanation
Indices: 2641854--2641911 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
2641844 AAAACTTTTG
* *
2641854 ATGAGAATTTTTGAGTTCTCAA
1 ATGAGAATATTTGAATTCTCAA
* *
2641876 ATAAGAATATTTGAATT-TTAA
1 ATGAGAATATTTGAATTCTCAA
2641897 ATGAGAATATTTGAA
1 ATGAGAATATTTGAA
2641912 ATGTAAAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (22 bp):
ATGAGAATATTTGAATTCTCAA
Found at i:2641918 original size:21 final size:21
Alignment explanation
Indices: 2641874--2641918 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2641864 TTGAGTTCTC
* *
2641874 AAATAAGAATATTTGAATTTT
1 AAATAAGAATATTTGAAATGT
*
2641895 AAATGAGAATATTTGAAATGT
1 AAATAAGAATATTTGAAATGT
2641916 AAA
1 AAA
2641919 ACCCAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (21 bp):
AAATAAGAATATTTGAAATGT
Found at i:2641977 original size:21 final size:21
Alignment explanation
Indices: 2641931--2641990 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
2641921 CCAAAATTTG
*
2641931 TCAAATGTGAATCTTTGA-AC
1 TCAAATGAGAATCTTTGAGAC
**
2641951 TCAAATGAGAATCTTTGAGTT
1 TCAAATGAGAATCTTTGAGAC
* *
2641972 TCAAATAAGAATTTTTGAG
1 TCAAATGAGAATCTTTGAG
2641991 GTGTGAAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (21 bp):
TCAAATGAGAATCTTTGAGAC
Found at i:2642002 original size:79 final size:79
Alignment explanation
Indices: 2641871--2642210 Score: 421
Period size: 79 Copynumber: 4.3 Consensus size: 79
2641861 TTTTTGAGTT
* * * * * * *
2641871 CTCAAATAAGAATATTTGAATTTTAAATGAGAATATTTGAAATGTAAAACCCAAAATTTGTCAAA
1 CTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATCAAA
2641936 TGTGAATCTTTGAA
66 TGTGAATCTTTGAA
* * * * * **
2641950 CTCAAATGAGAATCTTTGAGTTTCAAATAAGAATTTTTGAGGTGTGAAACCCAAAATTTGTTGAA
1 CTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATCAAA
2642015 TGTGAATCTTTGAA
66 TGTGAATCTTTGAA
* * **
2642029 CTCAAATGAGAATCTTTGAGTTTCAAATGAGAATCTTTGAAGTGTGAAACCAAAAATTTATTGAA
1 CTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATCAAA
*
2642094 TGTGAATCTTCGAA
66 TGTGAATCTTTGAA
*
2642108 CTCAAATGA-AGATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCTAAAATTTATCA
1 CTCAAATGAGA-ATCTTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCC-AAAATTTATCA
** *
2642172 AATGTGAGCCTTTGGA
64 AATGTGAATCTTTGAA
** *
2642188 CTTGAATGAGAAACTTTGAATTT
1 CTCAAATGAGAATCTTTGAATTT
2642211 TTGGATTTGA
Statistics
Matches: 229, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
78 1 0.00
79 188 0.82
80 39 0.17
81 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (79 bp):
CTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAAGTGTGAAACCCAAAATTTATCAAA
TGTGAATCTTTGAA
Found at i:2642056 original size:21 final size:20
Alignment explanation
Indices: 2642013--2642069 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
2642003 AAATTTGTTG
*
2642013 AATGTGAATCTTTGAACTCA
1 AATGAGAATCTTTGAACTCA
**
2642033 AATGAGAATCTTTGAGTTTCA
1 AATGAGAATCTTTGA-ACTCA
2642054 AATGAGAATCTTTGAA
1 AATGAGAATCTTTGAA
2642070 GTGTGAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (20 bp):
AATGAGAATCTTTGAACTCA
Found at i:2642122 original size:20 final size:21
Alignment explanation
Indices: 2642099--2642137 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2642089 TTGAATGTGA
2642099 ATCTTCGAA-CTCAAATGAAG
1 ATCTTCGAATCTCAAATGAAG
* *
2642119 ATCTTTGAATTTCAAATGA
1 ATCTTCGAATCTCAAATGA
2642138 GAATCTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
ATCTTCGAATCTCAAATGAAG
Found at i:2642723 original size:122 final size:122
Alignment explanation
Indices: 2642460--2642813 Score: 530
Period size: 122 Copynumber: 2.9 Consensus size: 122
2642450 CTATGACTCA
* * * *
2642460 TCTGTTTAGAGGAGCAATTTATTTTTTAAAGTTGTGATGCCTCTATTTAGAGGAACATTTTATTT
1 TCTGTTTAAATGAGC-ATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAACATTTTATTT
2642525 TCTTAAAATTGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGTT
65 TCTTAAAATTGTGGTGCCTCTATTTAGAGGA-CAATTTATTTTTCAAAGTTGTGGTGTT
*
2642584 TCTGTTTAAATGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAAAGGAACATTTTATTTT
1 TCTGTTTAAATGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAACATTTTATTTT
*
2642649 CTTAAAATTGTTGTGCCTCTATTTAGAGGACAATTTATTTTTCAAAGTTGTGGTGTT
66 CTTAAAATTGTGGTGCCTCTATTTAGAGGACAATTTATTTTTCAAAGTTGTGGTGTT
* * * * *
2642706 TCTGTTTAAATGAGCATTTATTTTTCAAAGTTGTGGTGTCTTTGTTTAGAGGAGCAATTTATTTT
1 TCTGTTTAAATGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAACATTTTATTTT
* * * *
2642771 -TTCAAAGTTGTGGTGCCTTTGTTTAGAGAAACAATTTATTTTT
66 CTT-AAAATTGTGGTGCCTCTATTTAGAG-GACAATTTATTTTT
2642814 AAAAAGTCGT
Statistics
Matches: 211, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
121 2 0.01
122 107 0.51
123 89 0.42
124 13 0.06
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.47
Consensus pattern (122 bp):
TCTGTTTAAATGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAACATTTTATTTT
CTTAAAATTGTGGTGCCTCTATTTAGAGGACAATTTATTTTTCAAAGTTGTGGTGTT
Found at i:2642820 original size:42 final size:41
Alignment explanation
Indices: 2642460--2642813 Score: 399
Period size: 42 Copynumber: 8.6 Consensus size: 41
2642450 CTATGACTCA
* *
2642460 TCTGTTTAGAGGAGCAATTTATTTTTTAAAGTTGTGATGCC
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
* * * * *
2642501 TCTATTTAGAGGAACATTTTATTTTCTTAAAATTGTGGTGCC
1 TCTGTTTAGAGGAGCAATTTATTTT-TCAAAGTTGTGGTGCC
* **
2642543 TCTATTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGTT
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
* *
2642584 TCTGTTTAAATGAGC-ATTTATTTTTCAAAGTTGTGGTGCC
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
* * * * * * *
2642624 TCTATTTAAAGGAACATTTTATTTTCTTAAAATTGTTGTGCC
1 TCTGTTTAGAGGAGCAATTTATTTT-TCAAAGTTGTGGTGCC
* **
2642666 TCTATTTAGAGGA-CAATTTATTTTTCAAAGTTGTGGTGTT
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
* * *
2642706 TCTGTTTAAATGAGC-ATTTATTTTTCAAAGTTGTGGTGTC
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
*
2642746 TTTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTGTGGTGCC
1 TCTGTTTAGAGGAGCAATTTA-TTTTTCAAAGTTGTGGTGCC
* * *
2642788 TTTGTTTAGAGAAACAATTTATTTTT
1 TCTGTTTAGAGGAGCAATTTATTTTT
2642814 AAAAAGTCGT
Statistics
Matches: 267, Mismatches: 40, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
40 92 0.34
41 75 0.28
42 100 0.37
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.47
Consensus pattern (41 bp):
TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCC
Found at i:2642831 original size:42 final size:42
Alignment explanation
Indices: 2642745--2642841 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
2642735 GTTGTGGTGT
* * ** * **
2642745 CTTTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTGTGGTGC
1 CTTTGTTTAGAGAAACAATTTATTTTTAAAAAGTCGTGAAGC
*
2642787 CTTTGTTTAGAGAAACAATTTATTTTTAAAAAGTCGTTAAGC
1 CTTTGTTTAGAGAAACAATTTATTTTTAAAAAGTCGTGAAGC
*
2642829 CTTTTATTTAGAG
1 C-TTTGTTTAGAG
2642842 GAGTTTTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 35 0.78
43 10 0.22
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (42 bp):
CTTTGTTTAGAGAAACAATTTATTTTTAAAAAGTCGTGAAGC
Found at i:2643365 original size:20 final size:21
Alignment explanation
Indices: 2643325--2643364 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2643315 AAGCAATTTA
2643325 AAAATTTTAGGATTTTTTTTC
1 AAAATTTTAGGATTTTTTTTC
2643346 AAAATTTT-GGCATTTTTTT
1 AAAATTTTAGG-ATTTTTTT
2643365 CTAGAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
AAAATTTTAGGATTTTTTTTC
Found at i:2644075 original size:8 final size:9
Alignment explanation
Indices: 2644062--2644107 Score: 55
Period size: 8 Copynumber: 5.6 Consensus size: 9
2644052 TTTTAAACAA
2644062 AAAAAAT-T
1 AAAAAATAT
2644070 AAAAAATAT
1 AAAAAATAT
2644079 -AAAAATAT
1 AAAAAATAT
*
2644087 -AAAAACAT
1 AAAAAATAT
2644095 -AAAAATAT
1 AAAAAATAT
2644103 AAAAA
1 AAAAA
2644108 TTTTGAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 29 0.85
9 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:2644108 original size:8 final size:8
Alignment explanation
Indices: 2644071--2644108 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
2644061 AAAAAAATTA
2644071 AAAAATAT
1 AAAAATAT
2644079 AAAAATAT
1 AAAAATAT
*
2644087 AAAAACAT
1 AAAAATAT
2644095 AAAAATAT
1 AAAAATAT
2644103 AAAAAT
1 AAAAAT
2644109 TTTGAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:2645195 original size:20 final size:20
Alignment explanation
Indices: 2645142--2645195 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
2645132 AATTTTCACG
2645142 TTTTCAAC--AAATATTATA
1 TTTTCAACAAAAATATTATA
* *
2645160 TTTTTATCTTAAAAATATTATA
1 TTTTCAAC--AAAAATATTATA
2645182 TTTTCAACAAAAAT
1 TTTTCAACAAAAAT
2645196 TACATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 6 0.21
20 6 0.21
22 16 0.57
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTCAACAAAAATATTATA
Found at i:2645262 original size:72 final size:72
Alignment explanation
Indices: 2645179--2645348 Score: 234
Period size: 72 Copynumber: 2.4 Consensus size: 72
2645169 TAAAAATATT
* * * *
2645179 ATATTTTCAACAAAAATTACATTTTTTATTTTCAATACG-TGATTTTTGTTGAATTTTGAAAAAT
1 ATATTTTCAACAAAAATTACATTTTTTATTTTAAAAACGTTG-TTTTTGTTGAATTATAAAAAAT
2645243 ATTTTTTC
65 ATTTTTTC
* * * *
2645251 ATGTTTTCAACAAAGATTACGTTTTCTATTTTAAAAACGTTGTTTTTGTTGAATTATAAAAAATA
1 ATATTTTCAACAAAAATTACATTTTTTATTTTAAAAACGTTGTTTTTGTTGAATTATAAAAAATA
2645316 TTTTTTC
66 TTTTTTC
* *
2645323 ATATTTTCAACAAAAAATGCATTTTT
1 ATATTTTCAACAAAAATTACATTTTT
2645349 AAAACATTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 81 0.98
73 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.49
Consensus pattern (72 bp):
ATATTTTCAACAAAAATTACATTTTTTATTTTAAAAACGTTGTTTTTGTTGAATTATAAAAAATA
TTTTTTC
Found at i:2646487 original size:14 final size:14
Alignment explanation
Indices: 2646464--2646498 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2646454 CATTTACTAT
2646464 AAACCAAATTA-AA
1 AAACCAAATTACAA
2646477 AAACTCAAATTACAA
1 AAAC-CAAATTACAA
2646492 AAACCAA
1 AAACCAA
2646499 GATTGCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 10 0.50
15 6 0.30
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACCAAATTACAA
Found at i:2649451 original size:29 final size:30
Alignment explanation
Indices: 2649397--2649479 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 30
2649387 TGTGTAGATA
* *
2649397 CAAATTAAAG-TTAAGAGCTTATTTTGATT
1 CAAATTAAAGATAAAGAGCTTATTTTGAAT
* *
2649426 CAAATTAAAGATAAAGGGTTTA-TTTGAAT
1 CAAATTAAAGATAAAGAGCTTATTTTGAAT
*
2649455 -ATAATTAAAGTATAAA-AACTTATTT
1 CA-AATTAAAG-ATAAAGAGCTTATTT
2649480 AAATAAATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 1 0.02
29 27 0.63
30 15 0.35
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.39
Consensus pattern (30 bp):
CAAATTAAAGATAAAGAGCTTATTTTGAAT
Found at i:2650958 original size:21 final size:20
Alignment explanation
Indices: 2650916--2650958 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2650906 AATGTTTGAT
*
2650916 TTGGGATCATTAAAGATTAA
1 TTGGGATCATTAAAGATCAA
* *
2650936 TTGGGAATCGTTAGAGATCAA
1 TTGGG-ATCATTAAAGATCAA
2650957 TT
1 TT
2650959 TAAGATCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGGGATCATTAAAGATCAA
Found at i:2650970 original size:21 final size:21
Alignment explanation
Indices: 2650946--2650985 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2650936 TTGGGAATCG
2650946 TTAGAGATCAATTTAAGATCA
1 TTAGAGATCAATTTAAGATCA
*
2650967 TTAGAGGTCAATTTAAGAT
1 TTAGAGATCAATTTAAGAT
2650986 TGAGATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (21 bp):
TTAGAGATCAATTTAAGATCA
Found at i:2654734 original size:16 final size:16
Alignment explanation
Indices: 2654713--2654744 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2654703 CAAAGTTCAA
2654713 GAAGACAATGTTTAAG
1 GAAGACAATGTTTAAG
2654729 GAAGACAATGTTTAAG
1 GAAGACAATGTTTAAG
2654745 AAATATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
GAAGACAATGTTTAAG
Found at i:2658516 original size:2 final size:2
Alignment explanation
Indices: 2658504--2658566 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
2658494 ATTATACAAA
* * * *
2658504 AT AT AT TT AT AT AT AT CT A- AT AT AT CT A- AT CT A- 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
2658543 AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2658567 ACAACATACA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2658996 original size:18 final size:18
Alignment explanation
Indices: 2658964--2658998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2658954 TAAGATATTA
**
2658964 AAAATTCAAGCAATTTTG
1 AAAATTCAAAAAATTTTG
2658982 AAAATTCAAAAAATTTT
1 AAAATTCAAAAAATTTT
2658999 CATCTTAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (18 bp):
AAAATTCAAAAAATTTTG
Found at i:2667268 original size:24 final size:24
Alignment explanation
Indices: 2667241--2667308 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
2667231 CAACTTCAGA
2667241 TTCCAATCTAGTTTCAAATCCAAT
1 TTCCAATCTAGTTTCAAATCCAAT
* * *
2667265 TTCCATTCTAGTTTCAACTCCAGT
1 TTCCAATCTAGTTTCAAATCCAAT
*
2667289 TT-CAAGTCTAGTTTAAAATC
1 TTCCAA-TCTAGTTTCAAATC
2667309 TAGTCAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (24 bp):
TTCCAATCTAGTTTCAAATCCAAT
Found at i:2667272 original size:48 final size:48
Alignment explanation
Indices: 2667208--2667308 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
2667198 ATTCAATTTT
* *
2667208 AAATCCACATTTCATTCCAATTTCAACTTCAGATTCCAA-TCTAGTTTC
1 AAATCCACATTTCATTCCAATTTCAACTCCAG-TTCCAAGTCTAGTTTA
* * *
2667256 AAATCCA-ATTTCCATTCTAGTTTCAACTCCAGTTTCAAGTCTAGTTTA
1 AAATCCACATTT-CATTCCAATTTCAACTCCAGTTCCAAGTCTAGTTTA
2667304 AAATC
1 AAATC
2667309 TAGTCAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 9 0.20
48 37 0.80
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (48 bp):
AAATCCACATTTCATTCCAATTTCAACTCCAGTTCCAAGTCTAGTTTA
Found at i:2667279 original size:12 final size:12
Alignment explanation
Indices: 2667245--2667312 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
2667235 TTCAGATTCC
2667245 AATCTAGTTTCA
1 AATCTAGTTTCA
* * *
2667257 AATCCAATTTCC
1 AATCTAGTTTCA
*
2667269 ATTCTAGTTTCA
1 AATCTAGTTTCA
* *
2667281 ACTCCAGTTTCA
1 AATCTAGTTTCA
* *
2667293 AGTCTAGTTTAA
1 AATCTAGTTTCA
2667305 AATCTAGT
1 AATCTAGT
2667313 CAATATTGTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (12 bp):
AATCTAGTTTCA
Found at i:2672127 original size:16 final size:17
Alignment explanation
Indices: 2672101--2672136 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2672091 ACTAAAATTA
2672101 ATAATTAATAATTAAAT
1 ATAATTAATAATTAAAT
2672118 ATAA-TAATAATTAAAT
1 ATAATTAATAATTAAAT
2672134 ATA
1 ATA
2672137 TGAAACAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATTAATAATTAAAT
Found at i:2673236 original size:15 final size:15
Alignment explanation
Indices: 2673195--2673243 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2673185 AATAAACCTT
2673195 ATAA-AATAATAAAAA
1 ATAACAATAAT-AAAA
*
2673210 ATAACTAGATAATAATA
1 ATAAC-A-ATAATAAAA
2673227 ATAACAATAATAAAA
1 ATAACAATAATAAAA
2673242 AT
1 AT
2673244 GAAAATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
17 9 0.31
18 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (15 bp):
ATAACAATAATAAAA
Found at i:2673729 original size:16 final size:16
Alignment explanation
Indices: 2673710--2673740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2673700 TCCTAAAATC
*
2673710 TTAAAACTTTAAACCT
1 TTAAAACCTTAAACCT
2673726 TTAAAACCTTAAACC
1 TTAAAACCTTAAACC
2673741 CCAAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAACCTTAAACCT
Found at i:2673958 original size:8 final size:8
Alignment explanation
Indices: 2673947--2674105 Score: 66
Period size: 8 Copynumber: 20.5 Consensus size: 8
2673937 TTAAATCTCC
2673947 AAAACCCT
1 AAAACCCT
*
2673955 AAAATCCT
1 AAAACCCT
*
2673963 AAAAACCT
1 AAAACCCT
*
2673971 GAAAA-CTT
1 -AAAACCCT
* **
2673979 TAAACTTT
1 AAAACCCT
2673987 AAAACTCC-
1 AAAAC-CCT
2673995 AAAACCCT
1 AAAACCCT
*
2674003 AAAA-CTT
1 AAAACCCT
2674010 AAAA-CCT
1 AAAACCCT
*
2674017 GAAACCCT
1 AAAACCCT
*
2674025 AAAACCAT
1 AAAACCCT
*
2674033 -AAACTCT
1 AAAACCCT
*
2674040 AAAACCTT
1 AAAACCCT
*
2674048 AAAA-TCT
1 AAAACCCT
2674055 CAAAA-CC-
1 -AAAACCCT
*
2674062 AAAATCCT
1 AAAACCCT
*
2674070 AAAACCTT
1 AAAACCCT
*
2674078 GAAA-CCT
1 AAAACCCT
*
2674085 TAAACCCTT
1 AAAACCC-T
*
2674094 AAAATCCT
1 AAAACCCT
2674102 AAAA
1 AAAA
2674106 ATCCATCAAG
Statistics
Matches: 113, Mismatches: 27, Indels: 22
0.70 0.17 0.14
Matches are distributed among these distances:
6 4 0.04
7 29 0.26
8 70 0.62
9 10 0.09
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (8 bp):
AAAACCCT
Found at i:2674015 original size:15 final size:15
Alignment explanation
Indices: 2673903--2674061 Score: 72
Period size: 16 Copynumber: 10.3 Consensus size: 15
2673893 TCAAAATCCT
**
2673903 AAACCCTAAATTTTA
1 AAACCCTAAAACTTA
*
2673918 AAACTCTAAAA-TTA
1 AAACCCTAAAACTTA
* * * *
2673932 AAAGCTTAAATCTCCA
1 AAACCCTAAAACT-TA
*
2673948 AAACCCTAAAATCCTA
1 AAACCCTAAAA-CTTA
* *
2673964 AAAACCTGAAAACTTT
1 AAACCCT-AAAACTTA
** *
2673980 AAACTTTAAAACTCCA
1 AAACCCTAAAACT-TA
2673996 AAACCCTAAAACTTA
1 AAACCCTAAAACTTA
* *
2674011 AAA-CCTGAAACCCTA
1 AAACCCT-AAAACTTA
*
2674026 AAACCAT-AAACTCTA
1 AAACCCTAAAACT-TA
* *
2674041 AAACCTTAAAATCTCA
1 AAACCCTAAAA-CTTA
2674057 AAACC
1 AAACC
2674062 AAAATCCTAA
Statistics
Matches: 104, Mismatches: 30, Indels: 19
0.68 0.20 0.12
Matches are distributed among these distances:
14 16 0.15
15 37 0.36
16 44 0.42
17 7 0.07
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (15 bp):
AAACCCTAAAACTTA
Found at i:2674029 original size:30 final size:30
Alignment explanation
Indices: 2673960--2674097 Score: 79
Period size: 30 Copynumber: 4.5 Consensus size: 30
2673950 ACCCTAAAAT
* * * *
2673960 CCTAAAAACCTGAAAACTTTAAACTTTAAAAC
1 CCTAAAACCCT-AAAACTTAAAAC-CTGAAAC
2673992 TCC-AAAACCCTAAAACTTAAAACCTGAAAC
1 -CCTAAAACCCTAAAACTTAAAACCTGAAAC
* * *
2674022 CCTAAAACCAT-AAACTCTAAAACCTTAAAA
1 CCTAAAACCCTAAAACT-TAAAACCTGAAAC
* *
2674052 TCTCAAAA-CC-AAAATCCTAAAACCTTGAAA-
1 CCT-AAAACCCTAAAA-CTTAAAACC-TGAAAC
*
2674082 CCTTAAACCCTTAAAA
1 CCTAAAACCC-TAAAA
2674098 TCCTAAAAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
29 10 0.12
30 40 0.48
31 20 0.24
32 11 0.13
33 2 0.02
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.21
Consensus pattern (30 bp):
CCTAAAACCCTAAAACTTAAAACCTGAAAC
Found at i:2674555 original size:16 final size:17
Alignment explanation
Indices: 2674536--2674569 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2674526 TTTGGGTTTA
2674536 TCTTTTT-TTATCTGAT
1 TCTTTTTATTATCTGAT
2674552 TCTTTTTATTATCTGAT
1 TCTTTTTATTATCTGAT
2674569 T
1 T
2674570 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.68
Consensus pattern (17 bp):
TCTTTTTATTATCTGAT
Found at i:2674558 original size:17 final size:17
Alignment explanation
Indices: 2674533--2674579 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2674523 ATTTTTGGGT
2674533 TTATCTTTTTTTATCTGA
1 TTAT-TTTTTTTATCTGA
* *
2674551 TTCTTTTTATTATCTGA
1 TTATTTTTTTTATCTGA
2674568 TTATTATTTTTT
1 TTATT-TTTTTT
2674580 TTTCCTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (17 bp):
TTATTTTTTTTATCTGA
Found at i:2675526 original size:5 final size:5
Alignment explanation
Indices: 2675509--2675581 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
2675499 TTAATATTCT
* * * *
2675509 TTTTA TCTTTA TTTTA TTTTA TTTTTG TTTTA CTTT- TCTTA ATTTA TTTTTA
1 TTTTA T-TTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
2675561 TTTT- TATTTA TTTT- TTTTA TT
1 TTTTA T-TTTA TTTTA TTTTA TT
2675582 ATTCTATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
4 7 0.13
5 32 0.60
6 14 0.26
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:2675565 original size:20 final size:19
Alignment explanation
Indices: 2675516--2675586 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
2675506 TCTTTTTATC
* *
2675516 TTTATTTTATTTTATTTTTGT
1 TTTATTTT-TCTTAATTTT-T
*
2675537 TTTACTTTTCTTAATTTATT
1 TTTATTTTTCTTAATTT-TT
* *
2675557 TTTATTTTTATTTATTTTT
1 TTTATTTTTCTTAATTTTT
*
2675576 TTTATTATTCT
1 TTTATTTTTCT
2675587 ATTTTCTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 11 0.27
20 22 0.54
21 8 0.20
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (19 bp):
TTTATTTTTCTTAATTTTT
Found at i:2675576 original size:12 final size:12
Alignment explanation
Indices: 2675508--2675591 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 12
2675498 TTTAATATTC
*
2675508 TTTTTATCTTTA
1 TTTTTATTTTTA
2675520 -TTTTA-TTTTA
1 TTTTTATTTTTA
*
2675530 TTTTT-GTTTTA
1 TTTTTATTTTTA
* *
2675541 CTTTTCTTAATTTA
1 TTTTTATT--TTTA
2675555 TTTTTATTTTTA
1 TTTTTATTTTTA
*
2675567 TTTATTTTTTTTA
1 TTT-TTATTTTTA
2675580 TTATTCTATTTT
1 TT-TT-TATTTT
2675592 CTTTAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 4 0.07
11 18 0.32
12 8 0.14
13 11 0.19
14 16 0.28
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:2675579 original size:25 final size:26
Alignment explanation
Indices: 2675508--2675591 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 26
2675498 TTTAATATTC
2675508 TTTTTATCTTTATTTTATTTTATTTTT-
1 TTTTTA-CTTTATTTT-TTTTATTTTTA
* **
2675535 GTTTTACTTT-TCTTAATTTATTTTTA
1 TTTTTACTTTAT-TTTTTTTATTTTTA
2675561 TTTTTA-TTTATTTTTTTTATTATTCTA
1 TTTTTACTTTATTTTTTTTATT-TT-TA
2675588 TTTT
1 TTTT
2675592 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
25 21 0.46
26 14 0.30
27 11 0.24
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTTACTTTATTTTTTTTATTTTTA
Found at i:2675589 original size:17 final size:16
Alignment explanation
Indices: 2675503--2675596 Score: 68
Period size: 16 Copynumber: 5.7 Consensus size: 16
2675493 GTTTATTTAA
* *
2675503 TATTCTTTTTA-TCTT
1 TATTTTTTTTATTATT
2675518 TATTTTATTTTATT-TT
1 TATTTT-TTTTATTATT
* *
2675534 TGTTTTACTTTTCTTAATT
1 TATTTT--TTTTATT-ATT
2675553 TATTTTTATTT-TTATT
1 TATTTTT-TTTATTATT
2675569 TATTTTTTTTATTATT
1 TATTTTTTTTATTATT
*
2675585 CTATTTTCTTTA
1 -TATTTTTTTTA
2675597 AATAAAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
15 8 0.12
16 27 0.42
17 20 0.31
18 3 0.05
19 7 0.11
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (16 bp):
TATTTTTTTTATTATT
Found at i:2675693 original size:50 final size:52
Alignment explanation
Indices: 2675633--2675731 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
2675623 ATATTTTTAG
*
2675633 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTCAAAAAGGGA
1 GGAAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTTCAAAAAGGGA
*
2675683 GGAAAAGTTGAAAGTATCAATTTCCCTTAAAGATCAAAATTTTCAAAAA
1 GGAAAAGTTGAAAGTATCAATTTCCCTTAAAAAT-AAAATTTTCAAAAA
2675732 AATATTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 32 0.73
52 3 0.07
53 9 0.20
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.28
Consensus pattern (52 bp):
GGAAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTTCAAAAAGGGA
Found at i:2675876 original size:59 final size:58
Alignment explanation
Indices: 2675681--2676011 Score: 407
Period size: 59 Copynumber: 5.5 Consensus size: 58
2675671 TTCAAAAAGG
* *
2675681 GAGGAAAAGTTGAAAGTATCAATTTCCCTTAAAGATCAAAATTTTCAAAAAAATATTTTT
1 GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTCAAAAAAATATTTTT
* *
2675741 AAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAAAAAAATAAATTTTCAAAAAAATATTTTT
1 GAGGAAAAGTTGAAAGTATCAATTTTCCTT-----AAAAATAAATTTTCAAAAAAATATTTTT
* * *
2675804 GGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAGGATTTTT
1 GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA-TATTTTT
* *
2675863 GAGGAAAAGTTGAAAGTATCAATTTTCCTAAAAAAAATCAAAATTTCCAAAAAAATATTTTT
1 GAGGAAAAGTTGAAAGTATCAATTTTCCT--TAAAAAT--AAATTTTCAAAAAAATATTTTT
*
2675925 -AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATAAA-TTTCCAAAAAATATTTTT
1 GAGG-AAAAGTTGAAAGTATCAATTTTCCTT--AAAAATAAATTTTCAAAAAAATATTTTT
2675984 G-GAGAAAAGTTGAAAGTATCAATTTTCC
1 GAG-GAAAAGTTGAAAGTATCAATTTTCC
2676012 CTACACAAGA
Statistics
Matches: 239, Mismatches: 17, Indels: 31
0.83 0.06 0.11
Matches are distributed among these distances:
58 20 0.08
59 75 0.31
60 31 0.13
61 8 0.03
62 37 0.15
63 63 0.26
65 5 0.02
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (58 bp):
GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATATTTTT
Found at i:2675933 original size:121 final size:119
Alignment explanation
Indices: 2675685--2676011 Score: 453
Period size: 121 Copynumber: 2.7 Consensus size: 119
2675675 AAAAGGGAGG
* *
2675685 AAAAGTTGAAAGTATCAATTTCCCTTAAAGATCAAAATTTTCAAAAAAATATTTTTAAGGAAAAG
1 AAAAGTTGAAAGTATCAATTTTCCTTAAA-AT--AAATTTTCAAAAAAATATTTTTGAGGAAAAG
* * * *
2675750 TTGAAAGTATCAATTTTCTTTAAAAAAAAAATAAATTTTCAAAAAAATATTTTTGGGG
63 TTGAAAGTATCAATTTTC-CTAAAAAAAAAATAAATTTCCAAAAAAATATTTTTAGGA
*
2675808 AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAGGATTTTTGAGGAAAAGT
1 AAAAGTTGAAAGTATCAATTTTCCTTA-AAATAAATTTTCAAAAAAA-TATTTTTGAGGAAAAGT
*
2675873 TGAAAGTATCAATTTTCCTAAAAAAAATCA-AAATTTCCAAAAAAATATTTTTAGGA
64 TGAAAGTATCAATTTTCCTAAAAAAAA-AATAAATTTCCAAAAAAATATTTTTAGGA
*
2675929 AAAAGTTGAAAGTATCAATTTTCCTTAAAA-AAATAAATTTCCAAAAAATATTTTTG-GAGAAAA
1 AAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAT---TTTCAAAAAAATATTTTTGAG-GAAAA
2675992 GTTGAAAGTATCAATTTTCC
62 GTTGAAAGTATCAATTTTCC
2676012 CTACACAAGA
Statistics
Matches: 187, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
119 4 0.02
120 4 0.02
121 106 0.57
122 43 0.23
123 28 0.15
124 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (119 bp):
AAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTG
AAAGTATCAATTTTCCTAAAAAAAAAATAAATTTCCAAAAAAATATTTTTAGGA
Found at i:2679929 original size:27 final size:27
Alignment explanation
Indices: 2679861--2679929 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
2679851 AACAATAGAT
*
2679861 AAAAAATGAGGAAAAAAAGATGATGAAAA
1 AAAAAATGA-GAAAAAAAGA-GAAGAAAA
*
2679890 AAAAAA-GAAAAAAAAAGA-AAGAAAGA
1 AAAAAATGAGAAAAAAAGAGAAGAAA-A
2679916 AAAAAATGAGAAAA
1 AAAAAATGAGAAAA
2679930 TGAAAAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 5 0.14
26 7 0.20
27 15 0.43
28 2 0.06
29 6 0.17
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAAATGAGAAAAAAAGAGAAGAAAA
Found at i:2681240 original size:41 final size:41
Alignment explanation
Indices: 2681177--2681552 Score: 605
Period size: 41 Copynumber: 9.1 Consensus size: 41
2681167 ATGATTGTCA
2681177 AGGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
2681218 AGGAGCAATTTACTTTTAAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2681259 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2681300 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGCTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2681341 AGGAGCAATTTA-TTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
2681382 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2681423 AGGAGCAATTTAATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTT-ACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2681465 AGGAGCAATTTATTTTTCAAAG-CTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTC-GTGGTGCCTCTGTTTAG
* * *
2681506 AGGAGCAATTTACTTTTCAAAGTCGTTGAGCCTCCGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2681547 AGGAGC
1 AGGAGC
2681553 TTTGGTAAAA
Statistics
Matches: 314, Mismatches: 15, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
40 6 0.02
41 260 0.83
42 48 0.15
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2681565 original size:1 final size:1
Alignment explanation
Indices: 2681559--2681650 Score: 94
Period size: 1 Copynumber: 92.0 Consensus size: 1
2681549 GAGCTTTGGT
* * * * * *
2681559 AAAAAAAACAAAAAAAAACAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
2681624 TAAAAAAAATACAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2681651 GACAATGTTG
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:2681602 original size:34 final size:34
Alignment explanation
Indices: 2681559--2681650 Score: 134
Period size: 34 Copynumber: 2.7 Consensus size: 34
2681549 GAGCTTTGGT
2681559 AAAAAAAACAAAAAAAAACAAAAAAAAAA-AAAA
1 AAAAAAAACAAAAAAAAACAAAAAAAAAACAAAA
*
2681592 CAAAAAAAACAAAAAAAAACAAAAAAAAAACATAA
1 -AAAAAAAACAAAAAAAAACAAAAAAAAAACAAAA
* *
2681627 AAAAAATACAAAAAATAA-AAAAAA
1 AAAAAAAACAAAAAAAAACAAAAAA
2681651 GACAATGTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
33 6 0.11
34 45 0.83
35 3 0.06
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (34 bp):
AAAAAAAACAAAAAAAAACAAAAAAAAAACAAAA
Found at i:2682522 original size:20 final size:19
Alignment explanation
Indices: 2682495--2682545 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2682485 CCGACGAACT
*
2682495 TCCGGTGAAATTTTCCAGAT
1 TCCGGTGAAATTTT-CAGAA
*
2682515 TTCGGTGACAATTTTCAGAA
1 TCCGGTGA-AATTTTCAGAA
2682535 TCCGGTGAAAT
1 TCCGGTGAAAT
2682546 CCCCACCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 6 0.22
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (19 bp):
TCCGGTGAAATTTTCAGAA
Found at i:2682956 original size:21 final size:20
Alignment explanation
Indices: 2682932--2682991 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
2682922 TGTTTTTATC
2682932 TTTATTTTATTTTATTTTTGT
1 TTTATTTTATTTTATTTTT-T
*
2682953 TTTACTTTT-CTTTATTTATTT
1 TTTA-TTTTATTTTATTT-TTT
*
2682974 TTT-TTATTATTCTATTTT
1 TTTATT-TTATTTTATTTT
2682992 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 21 0.66
22 6 0.19
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTATTTTATTTTATTTTTT
Found at i:2682973 original size:30 final size:31
Alignment explanation
Indices: 2682910--2682996 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
2682900 TTAGATTAGG
* * *
2682910 TTTATTTAATATTGTTTTTATCTTTATTTTAT
1 TTTATTTATTATTCTATTT-TCTTTATTTTAT
* *
2682942 TTTATTT-TTGTTTTACTTTTCTTTA-TTTAT
1 TTTATTTATTATTCTA-TTTTCTTTATTTTAT
*
2682972 TTTTTTTATTATTCTATTTTCTTTA
1 TTTATTTATTATTCTATTTTCTTTA
2682997 AATAAAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 20 0.43
31 16 0.35
32 10 0.22
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (31 bp):
TTTATTTATTATTCTATTTTCTTTATTTTAT
Done.