Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 10 of 130
Found at i:2829745 original size:21 final size:21
Alignment explanation
Indices: 2829719--2829761 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2829709 TGATATTAAA
2829719 AAATTTTAA-ATTTTAAAATTT
1 AAATTTTAACA-TTTAAAATTT
*
2829740 AAATTTTAACATTTAACATTT
1 AAATTTTAACATTTAAAATTT
2829761 A
1 A
2829762 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTTAACATTTAAAATTT
Found at i:2829761 original size:14 final size:14
Alignment explanation
Indices: 2829718--2829760 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2829708 ATGATATTAA
2829718 AAAATTTTAAATTTT
1 AAAA-TTTAAATTTT
2829733 AAAATTTAAATTTT
1 AAAATTTAAATTTT
*
2829747 AACATTTAACATTT
1 AAAATTTAA-ATTT
2829761 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
AAAATTTAAATTTT
Found at i:2829930 original size:18 final size:17
Alignment explanation
Indices: 2829902--2829938 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2829892 AAGTATTTTA
2829902 GATATTTAAATTAATTT
1 GATATTTAAATTAATTT
*
2829919 GATATGTTAAATTGATTT
1 GATAT-TTAAATTAATTT
2829937 GA
1 GA
2829939 CATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (17 bp):
GATATTTAAATTAATTT
Found at i:2830093 original size:15 final size:16
Alignment explanation
Indices: 2830058--2830095 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2830048 TATTTTAATT
*
2830058 TTTTATTATTCTCTCA
1 TTTTAATATTCTCTCA
*
2830074 TTTTAATATTCT-TTA
1 TTTTAATATTCTCTCA
2830089 TTTTAAT
1 TTTTAAT
2830096 TTTTAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTAATATTCTCTCA
Found at i:2836609 original size:12 final size:12
Alignment explanation
Indices: 2836591--2836622 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2836581 GTTTCCCAGT
2836591 GGAATGCCTGGA
1 GGAATGCCTGGA
*
2836603 GGTATGCCTGGA
1 GGAATGCCTGGA
2836615 GGAATGCC
1 GGAATGCC
2836623 CGGTGGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (12 bp):
GGAATGCCTGGA
Found at i:2836636 original size:24 final size:24
Alignment explanation
Indices: 2836561--2836637 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
2836551 CAGTAGGAAA
*
2836561 CCTGGAGGCATGCCTGGTGGGTTTC
1 CCTGGAGGAATGCCTGGT-GGTTTC
* * * * *
2836586 CC-AGTGGAATGCCTGGAGGTATG
1 CCTGGAGGAATGCCTGGTGGTTTC
*
2836609 CCTGGAGGAATGCCCGGTGGTTTC
1 CCTGGAGGAATGCCTGGTGGTTTC
2836633 CCTGG
1 CCTGG
2836638 TAGCATGCCA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
23 6 0.15
24 31 0.79
25 2 0.05
ACGTcount: A:0.13, C:0.23, G:0.39, T:0.25
Consensus pattern (24 bp):
CCTGGAGGAATGCCTGGTGGTTTC
Found at i:2837928 original size:24 final size:23
Alignment explanation
Indices: 2837873--2837926 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
2837863 TCTTCTTTTG
2837873 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
2837896 TATTATTATGTATATCT-TTATTTATT
1 TATT-TTATGTAT-TCTATTA-TTA-T
2837922 TATTT
1 TATTT
2837927 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 11 0.41
25 7 0.26
26 5 0.19
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:2838540 original size:31 final size:31
Alignment explanation
Indices: 2838469--2838541 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2838459 AATTTCCAGA
* *
2838469 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
*
2838500 TTTCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
2838531 TTCCGGCGACA
1 TTCCGGCGACA
2838542 GACCCAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:2838647 original size:19 final size:19
Alignment explanation
Indices: 2838604--2838647 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2838594 CCGGCCAATT
*
2838604 TCCGGCGAAATTCTCAGAT
1 TCCGGCGAAATTCTCAGAA
* * *
2838623 TTCGGCGAATTTTTCAGAA
1 TCCGGCGAAATTCTCAGAA
2838642 TCCGGC
1 TCCGGC
2838648 ACCGACGTTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (19 bp):
TCCGGCGAAATTCTCAGAA
Found at i:2839254 original size:160 final size:160
Alignment explanation
Indices: 2838980--2839439 Score: 750
Period size: 156 Copynumber: 2.9 Consensus size: 160
2838970 ATTTTGATCT
* * *
2838980 TGATTTT-TTTTTCTTTATTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAG
1 TGATTTTGATTTT-TTT-TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAG
2839044 TTTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAA
63 TTTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAA
*
2839109 TTGAGAATAATTTTCGATAATTAATTACTTGGC
128 TTGAGAATAATTTTCGATAATTAATTAATTGGC
*
2839142 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAATTT
1 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
* *
2839207 TTTTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTTTGCTAAAAGTATTAGAGTCAATTG
66 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
* *
2839272 AGAATAATTTTCGATAATTAGTTAATTGGT
131 AGAATAATTTTCGATAATTAATTAATTGGC
* *
2839302 TGATCTTGA----TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
1 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
*
2839363 TTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
66 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
2839428 AGAATAATTTTC
131 AGAATAATTTTC
2839440 AACAACTAAC
Statistics
Matches: 282, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
156 124 0.44
160 109 0.39
161 35 0.12
162 10 0.04
163 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (160 bp):
TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
AGAATAATTTTCGATAATTAATTAATTGGC
Found at i:2843075 original size:8 final size:8
Alignment explanation
Indices: 2843064--2843114 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
2843054 GAAAAATGAG
2843064 AAAAGAAA
1 AAAAGAAA
2843072 AAAA-AAA
1 AAAAGAAA
2843079 GAAAA-AAA
1 -AAAAGAAA
2843087 AAGAAGAAA
1 AA-AAGAAA
*
2843096 AAATGAAA
1 AAAAGAAA
*
2843104 AAATGAAA
1 AAAAGAAA
2843112 AAA
1 AAA
2843115 GAGATCCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
7 5 0.13
8 29 0.74
9 5 0.13
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (8 bp):
AAAAGAAA
Found at i:2843080 original size:11 final size:11
Alignment explanation
Indices: 2843064--2843106 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2843054 GAAAAATGAG
2843064 AAAAGAAAAAA
1 AAAAGAAAAAA
2843075 AAAAG-AAAAA
1 AAAAGAAAAAA
*
2843085 AAAAGAAGAAA
1 AAAAGAAAAAA
*
2843096 AAATGAAAAAA
1 AAAAGAAAAAA
2843107 TGAAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:2843090 original size:21 final size:21
Alignment explanation
Indices: 2843064--2843106 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2843054 GAAAAATGAG
2843064 AAAAGAAAAAAAAAAGAAAAA
1 AAAAGAAAAAAAAAAGAAAAA
* *
2843085 AAAAGAAGAAAAAATGAAAAA
1 AAAAGAAAAAAAAAAGAAAAA
2843106 A
1 A
2843107 TGAAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAGAAAAA
Found at i:2843114 original size:10 final size:10
Alignment explanation
Indices: 2843064--2843106 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
2843054 GAAAAATGAG
2843064 AAAAGAAAAAA
1 AAAAG-AAAAA
2843075 AAAAGAAAAA
1 AAAAGAAAAA
2843085 AAAAGAAGAAA
1 AAAAGAA-AAA
*
2843096 AAATGAAAAA
1 AAAAGAAAAA
2843106 A
1 A
2843107 TGAAAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:2843162 original size:1 final size:1
Alignment explanation
Indices: 2843156--2843190 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
2843146 TTTGGTACCC
* *
2843156 AAAAAAAAAAAAAAAAAAAACAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2843191 GATCCAGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2844457 original size:41 final size:41
Alignment explanation
Indices: 2844346--2844999 Score: 1024
Period size: 41 Copynumber: 15.9 Consensus size: 41
2844336 GTCTAGGAGT
2844346 ATTTACTTTGTCAAAGTTCGT--TGCCTTCTGTTTAGAGGAAGCA
1 ATTTACTTT-TCAAAG-TCGTGGTGCC-TCTGTTTAGAGG-AGCA
* *
2844389 ATTTATTTTTTTCAAAGTTCGCT--TGCCTCTATTTAGAGGAGCA
1 ATTTA--CTTTTCAAAG-TCG-TGGTGCCTCTGTTTAGAGGAGCA
2844432 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844473 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844514 ATTTACCTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
1 ATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844555 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844596 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844637 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844679 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844720 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2844761 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
2844800 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
2844841 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
2844883 ATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
2844924 ATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTTAGAGGAGCA
* * *
2844964 ATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAG
1 ATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAG
2845000 AGCTCGGCCA
Statistics
Matches: 582, Mismatches: 13, Indels: 34
0.93 0.02 0.05
Matches are distributed among these distances:
39 46 0.08
40 47 0.08
41 350 0.60
42 96 0.16
43 14 0.02
44 21 0.04
45 8 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:2845043 original size:23 final size:22
Alignment explanation
Indices: 2845008--2845081 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 22
2844998 AGAGCTCGGC
2845008 CAAAAAAAAAAAACAAAAAAAA
1 CAAAAAAAAAAAACAAAAAAAA
*
2845030 CAAAAAAAACAAAACAAAAAAAT
1 CAAAAAAAA-AAAACAAAAAAAA
*
2845053 CAAAAAAATAAAAACAAAATAAA
1 CAAAAAAA-AAAAACAAAAAAAA
2845076 -AAAAAA
1 CAAAAAA
2845082 TCAAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
22 15 0.32
23 31 0.66
24 1 0.02
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.04
Consensus pattern (22 bp):
CAAAAAAAAAAAACAAAAAAAA
Found at i:2845058 original size:30 final size:30
Alignment explanation
Indices: 2845011--2845088 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 30
2845001 GCTCGGCCAA
* * *
2845011 AAAAAAAAAACAAAAAAA-ACAAAAAAAACAA
1 AAAAAAAAATCAAAAAAATA-AAAACAAA-AT
2845042 AACAAAAAAATCAAAAAAATAAAAACAAAAT
1 AA-AAAAAAATCAAAAAAATAAAAACAAAAT
2845073 AAAAAAAAATCAAAAA
1 AAAAAAAAATCAAAAA
2845089 TAAAATGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.33
31 5 0.12
32 22 0.52
33 1 0.02
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (30 bp):
AAAAAAAAATCAAAAAAATAAAAACAAAAT
Found at i:2845087 original size:22 final size:21
Alignment explanation
Indices: 2845009--2845094 Score: 84
Period size: 23 Copynumber: 3.9 Consensus size: 21
2844999 GAGCTCGGCC
*
2845009 AAAAAAA-AAAAACAAAAAAA
1 AAAAAAATAAAAACAAAATAA
* *
2845029 ACAAAAAAAACAAAACAAAAAAA
1 A-AAAAAATA-AAAACAAAATAA
2845052 TCAAAAAAATAAAAACAAAATAA
1 --AAAAAAATAAAAACAAAATAA
*
2845075 AAAAAAATCAAAAATAAAAT
1 AAAAAAAT-AAAAACAAAAT
2845095 GTTGAGTTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 11 0.19
23 23 0.40
24 7 0.12
25 1 0.02
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAAAATAAAAACAAAATAA
Found at i:2845088 original size:1 final size:1
Alignment explanation
Indices: 2845009--2845081 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
2844999 GAGCTCGGCC
* * * * ** * * *
2845009 AAAAAAAAAAAACAAAAAAAACAAAAAAAACAAAACAAAAAAATCAAAAAAATAAAAACAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2845074 AAAAAAAA
1 AAAAAAAA
2845082 TCAAAAATAA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:2845912 original size:31 final size:29
Alignment explanation
Indices: 2845844--2845915 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
2845834 AATTTCCAGA
*
2845844 TTCCGGCGAAAATTCGGCGACTTTTTGAAT
1 TTCCGGCGACAATTCGGCGAC-TTTTGAAT
*
2845874 TTTCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATT-CGGCG-ACTTTTGAA-T
2845905 TTCCGGCGACA
1 TTCCGGCGACA
2845916 GACCCAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 18 0.50
31 16 0.44
32 2 0.06
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (29 bp):
TTCCGGCGACAATTCGGCGACTTTTGAAT
Found at i:2846005 original size:19 final size:20
Alignment explanation
Indices: 2845976--2846015 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2845966 CTTCCGGCCA
2845976 ATTTCCGGCGAAATTCCCAG
1 ATTTCCGGCGAAATTCCCAG
*
2845996 ATTT-CGGCGAAATTTCCAG
1 ATTTCCGGCGAAATTCCCAG
2846015 A
1 A
2846016 ATCGGCACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTCCGGCGAAATTCCCAG
Found at i:2846317 original size:11 final size:11
Alignment explanation
Indices: 2846303--2846332 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2846293 GTTTTTTTTT
2846303 TTTTTTTTGAA
1 TTTTTTTTGAA
2846314 TTTTTTTTGAA
1 TTTTTTTTGAA
2846325 TTTTTTTT
1 TTTTTTTT
2846333 TATTTGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:2846647 original size:162 final size:160
Alignment explanation
Indices: 2846355--2846800 Score: 730
Period size: 162 Copynumber: 2.8 Consensus size: 160
2846345 ATTTTGATCT
* *
2846355 TGATTTT--TTTTCTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGT
1 TGATTTTGATTTT-TTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGT
2846418 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
64 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
*
2846483 TGAGAATAATTTTCGATAATTAATTATTTGGC
129 TGAGAATAATTTTCGATAATTAATTAATTGGC
2846515 TGATTTTGATTTTTTTTTCTTTAATTAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTCTTTAATT-AATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
2846580 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCACATTTTCTGCTAAAAGTATTAGAGTCAAT
65 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCA-ATTTTCTGCTAAAAGTATTAGAGTCAAT
*
2846645 TGAGAATAATTTTCGATAATTAATTAATTGGT
129 TGAGAATAATTTTCGATAATTAATTAATTGGC
*
2846677 TGATCTTGA----TTTTTCTTTAA-TAAT-CGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
1 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
*
2846736 TTCTTGGCATACTCTTGAGGTGAGGG-ATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTCTT-GCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
2846800 G
130 G
2846801 GAAAAAGTTC
Statistics
Matches: 275, Mismatches: 6, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
154 30 0.11
155 49 0.18
156 22 0.08
157 1 0.00
158 11 0.04
160 7 0.03
161 60 0.22
162 95 0.35
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (160 bp):
TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
AGAATAATTTTCGATAATTAATTAATTGGC
Found at i:2851126 original size:20 final size:19
Alignment explanation
Indices: 2851101--2851201 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 19
2851091 ACAATTAATA
2851101 TAATATATTAATATAATATT
1 TAATATATTAATA-AATATT
**
2851121 TAATATATTAATAAATAAC
1 TAATATATTAATAAATATT
* *
2851140 TACTATTAATATAATATATTATT
1 TAATA-T-AT-TAATA-AATATT
* *
2851163 AAATATTTTAATAAATAATAT
1 TAATATATTAATAAAT-AT-T
2851184 T-ATATATTTAATAAATAT
1 TAATATA-TTAATAAATAT
2851202 ATAGAGAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
19 10 0.16
20 27 0.44
21 13 0.21
22 6 0.10
23 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATATTAATAAATATT
Found at i:2851126 original size:25 final size:26
Alignment explanation
Indices: 2851095--2851203 Score: 87
Period size: 25 Copynumber: 4.5 Consensus size: 26
2851085 TAATATACAA
2851095 TTAATATAATATATTAATATAATA-T
1 TTAATATAATATATTAATATAATACT
*
2851120 TTAATAT-AT-TAATAA-ATAACTACT
1 TTAATATAATATATTAATATAA-TACT
* *
2851144 ATTAATATAATATATTATTA-AATATT
1 -TTAATATAATATATTAATATAATACT
*
2851170 TTAATA-AATA-A-TATTAT-ATA-T
1 TTAATATAATATATTAATATAATACT
2851191 TTAATA-AATATAT
1 TTAATATAATATAT
2851204 AGAGAATAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
21 11 0.15
22 13 0.18
23 8 0.11
24 7 0.10
25 20 0.28
26 5 0.07
27 6 0.08
28 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATATAATATATTAATATAATACT
Found at i:2851173 original size:50 final size:51
Alignment explanation
Indices: 2851073--2851175 Score: 156
Period size: 50 Copynumber: 2.0 Consensus size: 51
2851063 TAAATAATAT
2851073 TATATTAATAAATAATATACAATTAATATAATATATTAATATAATATTTAA
1 TATATTAATAAATAATATACAATTAATATAATATATTAATATAATATTTAA
* * *
2851124 TATATTAATAAATAA-CTACTATTAATATAATATATTATTA-AATATTTTAA
1 TATATTAATAAATAATATACAATTAATATAATATATTAATATAATA-TTTAA
2851174 TA
1 TA
2851176 AATAATATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
49 4 0.08
50 29 0.60
51 15 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (51 bp):
TATATTAATAAATAATATACAATTAATATAATATATTAATATAATATTTAA
Found at i:2851190 original size:22 final size:22
Alignment explanation
Indices: 2851113--2851200 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
2851103 ATATATTAAT
*
2851113 ATAATATT-TAATATATTAATAA
1 ATAATATTAT-ATATTTTAATAA
* * *
2851135 ATAACTACTAT-TAATATAAT--
1 ATAA-TATTATATATTTTAATAA
* *
2851155 ATATTATTAAATATTTTAATAA
1 ATAATATTATATATTTTAATAA
2851177 ATAATATTATATA-TTTAATAA
1 ATAATATTATATATTTTAATAA
2851198 ATA
1 ATA
2851201 TATAGAGAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
19 4 0.08
20 10 0.20
21 11 0.22
22 21 0.42
23 3 0.06
24 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATATTATATATTTTAATAA
Found at i:2851203 original size:20 final size:20
Alignment explanation
Indices: 2851098--2851203 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 20
2851088 TATACAATTA
*
2851098 ATATAATATA-TTAATATAAT
1 ATATTATATATTTAATA-AAT
2851118 AT-TTA-ATATATTAATAAAT
1 ATATTATATAT-TTAATAAAT
* *
2851137 A-ACTA-CTA-TTAATATAAT
1 ATATTATATATTTAATA-AAT
2851155 ATATTATTAAATATTTTAATAAAT
1 ATATTA-T--ATA-TTTAATAAAT
2851179 AATATTATATATTTAATAAAT
1 -ATATTATATATTTAATAAAT
2851200 ATAT
1 ATAT
2851204 AGAGAATAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 24
0.70 0.05 0.24
Matches are distributed among these distances:
17 6 0.09
18 7 0.10
19 13 0.19
20 12 0.17
21 10 0.14
22 3 0.04
23 2 0.03
24 4 0.06
25 12 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTATATATTTAATAAAT
Found at i:2851344 original size:27 final size:27
Alignment explanation
Indices: 2851298--2851365 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
2851288 TTTTTTAAAG
*
2851298 TTAATA-ATTTT-ATTAATAAATAA-T
1 TTAATATATTTTAATAAATAAATAACT
2851322 TTAAATATATTTTAATAAATAAATAACT
1 TT-AATATATTTTAATAAATAAATAACT
*
2851350 TTGA-ATATTTTAATAA
1 TTAATATATTTTAATAA
2851366 TTATATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 2 0.05
25 4 0.11
26 17 0.45
27 12 0.32
28 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TTAATATATTTTAATAAATAAATAACT
Found at i:2853250 original size:1 final size:1
Alignment explanation
Indices: 2853244--2853273 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2853234 NNAGTCAAAT
*
2853244 AAAAAAAAAAAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2853274 CCTGGAGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2853312 original size:15 final size:15
Alignment explanation
Indices: 2853292--2853327 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2853282 GGCTCGGATC
2853292 GCGGCTCGGCTT-GGT
1 GCGGCTCGG-TTCGGT
2853307 GCGGCTCGGTTCGGT
1 GCGGCTCGGTTCGGT
2853322 GCGGCT
1 GCGGCT
2853328 GAAACTCGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.00, C:0.28, G:0.47, T:0.25
Consensus pattern (15 bp):
GCGGCTCGGTTCGGT
Found at i:2853580 original size:19 final size:19
Alignment explanation
Indices: 2853539--2853582 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2853529 AACGCCGGTG
* *
2853539 CCGGATTCTGGAAAATTCG
1 CCGGAATCTGGAAAATTCA
* *
2853558 CCGGAATCTGGGAATTTCA
1 CCGGAATCTGGAAAATTCA
2853577 CCGGAA
1 CCGGAA
2853583 ATTGGCCGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (19 bp):
CCGGAATCTGGAAAATTCA
Found at i:2853682 original size:31 final size:31
Alignment explanation
Indices: 2853644--2853713 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2853634 AAACTGGGTC
*
2853644 TGTCGCCGAAAACTTC-AAAGTTAGCCGGAAT
1 TGTCGCCGAAAAATTCAAAAG-TAGCCGGAAT
*
2853675 TGTCGCCGAAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGAAAAATTCAAAAGTAGCCGGAAT
*
2853706 TTTCGCCG
1 TGTCGCCG
2853714 GAATCTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (31 bp):
TGTCGCCGAAAAATTCAAAAGTAGCCGGAAT
Found at i:2854047 original size:12 final size:12
Alignment explanation
Indices: 2854030--2854061 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2854020 CTAGCCCTCC
2854030 AAAATAAAAATT
1 AAAATAAAAATT
2854042 AAAAT-AAAATT
1 AAAATAAAAATT
2854053 AAAA-AAAAA
1 AAAATAAAAA
2854062 AATCTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:2854307 original size:12 final size:12
Alignment explanation
Indices: 2854290--2854326 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2854280 AGAGAGAAAG
2854290 AAAAAAAAT--A
1 AAAAAAAATAAA
2854300 AAAAAAAATAAA
1 AAAAAAAATAAA
*
2854312 AATAAAAATAAA
1 AAAAAAAATAAA
2854324 AAA
1 AAA
2854327 TACGGGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:2854312 original size:6 final size:6
Alignment explanation
Indices: 2854293--2854325 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2854283 GAGAAAGAAA
2854293 AAAAAT -AAAA- AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2854326 ATACGGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:2854434 original size:21 final size:20
Alignment explanation
Indices: 2854360--2854436 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
2854350 TTGCCCATTT
* *
2854360 GGGCCAGGCCCAAATGATCT
1 GGGCCAGGCCCAATTGATCC
*
2854380 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
*
2854400 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
*
2854420 GGGCCCGGACCCAATTG
1 GGGCCAGG-CCCAATTG
2854437 GGTGTCTACA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 43 0.84
21 8 0.16
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (20 bp):
GGGCCAGGCCCAATTGATCC
Found at i:2854572 original size:21 final size:21
Alignment explanation
Indices: 2854546--2854589 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2854536 TTAAAAAATT
*
2854546 AAATATTTTTTATAAT-TTAAA
1 AAATATTTATTA-AATGTTAAA
2854567 AAATATTTATTAAATGTTAAA
1 AAATATTTATTAAATGTTAAA
2854588 AA
1 AA
2854590 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATATTTATTAAATGTTAAA
Found at i:2860715 original size:29 final size:29
Alignment explanation
Indices: 2860665--2860726 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2860655 CAGCGGGATG
*
2860665 GGTGATCAGAGGGGTAGAGGGTAAGGTAT
1 GGTGATCAGAGGGGTAGAGGGTAAGGCAT
* * * *
2860694 GGTGATCAGAGTGGTGGGGGGTAGGGCAT
1 GGTGATCAGAGGGGTAGAGGGTAAGGCAT
2860723 GGTG
1 GGTG
2860727 GTAGTGGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.05, G:0.53, T:0.21
Consensus pattern (29 bp):
GGTGATCAGAGGGGTAGAGGGTAAGGCAT
Found at i:2860829 original size:7 final size:7
Alignment explanation
Indices: 2860804--2860858 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
2860794 TTTTTTTTTC
2860804 TTTTGT-
1 TTTTGTA
* *
2860810 TTTGGTG
1 TTTTGTA
2860817 TTTTGTA
1 TTTTGTA
2860824 TTTTGTA
1 TTTTGTA
2860831 TTTTGTA
1 TTTTGTA
2860838 -TTT-T-
1 TTTTGTA
2860842 TTTTGTA
1 TTTTGTA
2860849 TTTTGTA
1 TTTTGTA
2860856 TTT
1 TTT
2860859 AATAATATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
5 4 0.10
6 9 0.21
7 29 0.69
ACGTcount: A:0.09, C:0.00, G:0.16, T:0.75
Consensus pattern (7 bp):
TTTTGTA
Found at i:2860847 original size:18 final size:18
Alignment explanation
Indices: 2860824--2860858 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2860814 GTGTTTTGTA
2860824 TTTTGTATTTTGTATTTT
1 TTTTGTATTTTGTATTTT
2860842 TTTTGTATTTTGTATTT
1 TTTTGTATTTTGTATTT
2860859 AATAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (18 bp):
TTTTGTATTTTGTATTTT
Found at i:2861294 original size:97 final size:96
Alignment explanation
Indices: 2861066--2861918 Score: 817
Period size: 96 Copynumber: 8.8 Consensus size: 96
2861056 TTTCTCACTT
* * * ** * *
2861066 GAGGCTCAACAACTTTTGAAAATTTAAAATC-TGAAAAATGCTCATCTCAATAGATGCTCAATAA
1 GAGGCTCAACAAC-TTT-AAAATCT--CATCTTGAAAAA-GCTCCTCTCAGCAGAGGCTCAACAA
* * *
2861130 CTTTAAAAATTTCATCTTGAAAAGGGCTCATTTCAGCA
61 CTTT-AAAATCTCATCTTGAAAA-AGCTCCTTTCAGCA
* * * * * * *
2861168 GAGGTTTAAAAACTTTAAAATTCTCATCTTGAAAAGGGTCCTTCTCCGCAGAGGCTCAATAACTT
1 GAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAGCTCC-TCTCAGCAGAGGCTCAACAACTT
* *
2861233 TAAAATCTCAT-TTAAAAAAGCTCATTTCAGCA
64 TAAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * * * * * * *
2861265 GAAGCTCAACTACTTTAAAAATTTTATCTTAAAAAGAGCTCCTCTCAACAGAGGCTCGACAATTT
1 GAGGCTCAACAACTTT-AAAATCTCATCTTGAAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTT
* *
2861330 TAAAATCTCAT-TTGAAAAAGATTCTTTCAGCA
64 TAAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * *
2861362 GAGGCTCAACAACTTTAAAATCTCAT-TTGGAAAAA-TTCCTCTTAGCAGAAGCTCAACAACTTT
1 GAGGCTCAACAACTTTAAAATCTCATCTT-GAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT
* *
2861425 AAAAATCTTATCTTGAAAAAGCTCCTTTTAGCA
65 -AAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
*
2861458 GAGGCTCAACAACTTTAAAATCTCATC-TGAAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTT-
1 GAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* * *
2861521 AAATTTCATCTTAAAAAAGCTCCTCTCAGCA
66 AAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * * ** * *
2861552 AAGGCTCAATAACTTTAAAAATCTCATCTTGAAAAGGGCTTATCTTAGCAGAGGCTTAACAACTT
1 GAGGCTCAACAACTTT-AAAATCTCATCTTGAAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTT
* * * *
2861617 TAAAATTTCAT-TTGAAAAAGTTCCTCTCAGTA
64 TAAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * * * *
2861649 GAGGCTCAACAACTTTAAAAATCTTATCTTAAAAAAGCTCATCTCAACAGAAGCTCAACAACTTT
1 GAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT
* * * *
2861714 AAAATCTCATCTTGGAAAAGTTCATCTCAGCA
65 AAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * * * * *
2861746 GAGGCTCAACAACTTTAAAATCTTGATCTAG-AAAAGCACATCTCAACAGAGGCTCAATAACTTT
1 GAGGCTCAACAACTTTAAAATC-TCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT
* **
2861810 AAAATTTCATCTTGAAAAAGCTCCTTTCAATA
65 AAAATCTCATCTTGAAAAAGCTCCTTTCAGCA
* * * * *
2861842 GAGGCTCAATAATTTTAAAATTTTGATC-TGAAAAAGCTCTTCTCAGCAGAGGCTCAACAACTTT
1 GAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT
*
2861906 AAAATCTTATCTT
65 AAAATCTCATCTT
2861919 CTTCAAATCG
Statistics
Matches: 631, Mismatches: 102, Indels: 42
0.81 0.13 0.05
Matches are distributed among these distances:
94 62 0.10
95 30 0.05
96 246 0.39
97 210 0.33
98 23 0.04
99 15 0.02
100 30 0.05
101 5 0.01
102 10 0.02
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (96 bp):
GAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
AAATCTCATCTTGAAAAAGCTCCTTTCAGCA
Found at i:2861514 original size:240 final size:239
Alignment explanation
Indices: 2861121--2861918 Score: 908
Period size: 240 Copynumber: 3.3 Consensus size: 239
2861111 CTCAATAGAT
* * * * * * * *
2861121 GCTCAATAACTTTAAAAATTTCATCTTGAAAAGGGCTCATTTCAGCAGAGGTTTAAAAACTTTAA
1 GCTCAACAACTTT-AAAATTTCAT-TTGAAAA-AGTTCCTCTCAGCAGAGGCTCAACAACTTTAA
* * * * * * * *
2861186 AATTCTCATCTTGAAAAGGGTCCTTCTCCGCAGAGGCTCAATAACTTTAAAATCTCATTTAAAAA
63 AAATCTTATCTTGAAAAAGCTCCTT-TCAGCAGAGGCTCAACAACTTTAAAATCTCATCTGAAAA
* * *
2861251 AGCTCAT-TTCAGCAGAAGCTCAACTACTTTAAAAATTTTATCTTAAAAAGAGCTCCTCTCAACA
127 AGCTCATCTT-AGCAGAGGCTCAACAACTTT-AAAATTTCATCTTAAAAA-AGCTCCTCTCAACA
* * *
2861315 GAGGCTCGACAATTTTAAAATCTCAT-TTGAAAAAGATTCTTTCAGCAGAG
189 GAGGCTCAATAATTTTAAAATCTCATCTTGAAAAAGCTTCTTTCAGCAGAG
* * *
2861365 GCTCAACAACTTTAAAATCTCATTTGGAAAAA-TTCCTCTTAGCAGAAGCTCAACAACTTTAAAA
1 GCTCAACAACTTTAAAATTTCATTT-GAAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
*
2861429 ATCTTATCTTGAAAAAGCTCCTTTTAGCAGAGGCTCAACAACTTTAAAATCTCATCTGAAAAAGC
65 ATCTTATCTTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTGAAAAAGC
* * *
2861494 TCCTCTTAGCAGAGGCTCAACAACTTT-AAATTTCATCTTAAAAAAGCTCCTCTCAGCAAAGGCT
130 TCATCTTAGCAGAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCCTCTCAACAGAGGCT
* * *
2861558 CAATAACTTTAAAAATCTCATCTTGAAAAGGGCTTATCTT-AGCAGAG
195 CAATAA-TTTTAAAATCTCATCTTGAAAA-AGCTTCT-TTCAGCAGAG
* *
2861605 GCTTAACAACTTTAAAATTTCATTTGAAAAAGTTCCTCTCAGTAGAGGCTCAACAACTTTAAAAA
1 GCTCAACAACTTTAAAATTTCATTTGAAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAAAAA
* * * * * * *
2861670 TCTTATCTTAAAAAAGCTCATCTCAACAGAAGCTCAACAACTTTAAAATCTCATCTTGGAAAAGT
66 TCTTATCTTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCATC-TGAAAAAGC
* * * * *
2861735 TCATCTCAGCAGAGGCTCAACAACTTTAAAATCTTGATC-TAGAAAAGCACATCTCAACAGAGGC
130 TCATCTTAGCAGAGGCTCAACAACTTTAAAAT-TTCATCTTAAAAAAGCTCCTCTCAACAGAGGC
* * * **
2861799 TCAATAACTTTAAAATTTCATCTTGAAAAAGCTCCTTTCAATAGAG
194 TCAATAATTTTAAAATCTCATCTTGAAAAAGCTTCTTTCAGCAGAG
* * * * * *
2861845 GCTCAATAATTTTAAAATTTTGATCTGAAAAAGCTCTTCTCAGCAGAGGCTCAACAACTTT-AAA
1 GCTCAACAACTTTAAAA-TTTCATTTGAAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
2861909 ATCTTATCTT
65 ATCTTATCTT
2861919 CTTCAAATCG
Statistics
Matches: 473, Mismatches: 69, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
237 22 0.05
238 29 0.06
239 15 0.03
240 207 0.44
241 136 0.29
242 33 0.07
243 19 0.04
244 12 0.03
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (239 bp):
GCTCAACAACTTTAAAATTTCATTTGAAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAAAAA
TCTTATCTTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTGAAAAAGCT
CATCTTAGCAGAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCCTCTCAACAGAGGCTC
AATAATTTTAAAATCTCATCTTGAAAAAGCTTCTTTCAGCAGAG
Found at i:2861913 original size:144 final size:147
Alignment explanation
Indices: 2861066--2861918 Score: 797
Period size: 144 Copynumber: 5.9 Consensus size: 147
2861056 TTTCTCACTT
* * * * *
2861066 GAGGCTCAACAACTTTTGAAAATTTAAAATCTGAAAAATGCTCATCTCAATAGATGCTCAATAAC
1 GAGGCTCAACAAC-TTT-AAAATTT--CATCTTAAAAAAGCTCATCTCAACAGAAGCTCAATAAC
* * * * *
2861131 TTTAAAAATTTCATCTTGAAAAGGGCTCATT-TCAGCAGAGGTTTAAAAACTTTAAAAT-TCTCA
62 TTTAAAATTTTCATCTTGAAAAGAGCTC-TTCTCAGCAGAGGCTCAACAACTTTAAAATCT-TCA
* ** *
2861194 TCTTGAAAAGGGTCCTTCTCCGCA
125 TCTTGAAAAAGCACC-TCTCAGCA
* * * *
2861218 GAGGCTCAATAACTTTAAAATCTCAT-TTAAAAAAGCTCATTTCAGCAGAAGCTCAACT-ACTTT
1 GAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCATCTCAACAGAAGCTCAA-TAACTTT
* * * * *
2861281 AAAAATTTT-ATCTTAAAAAGAGCTCCTCTCAACAGAGGCTCGACAATTTTAAAATC-TCAT-TT
65 -AAAATTTTCATCTTGAAAAGAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCTT
* *
2861343 GAAAAAG-ATTCTTTCAGCA
129 GAAAAAGCA-CCTCTCAGCA
* * * * * * *
2861362 GAGGCTCAACAACTTTAAAATCTCAT-TTGGAAAAA-TTCCTCTTAGCAGAAGCTCAACAACTTT
1 GAGGCTCAACAACTTTAAAATTTCATCTT-AAAAAAGCTCATCTCAACAGAAGCTCAATAACTTT
* *
2861425 AAAAATCTT-ATCTTGAAAA-AGCTCCTT-TTAGCAGAGGCTCAACAACTTTAAAATC-TCATC-
65 -AAAATTTTCATCTTGAAAAGAGCT-CTTCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCT
* *
2861485 TGAAAAAGCTCCTCTTAGCA
128 TGAAAAAGCACCTCTCAGCA
* *
2861505 GAGGCTCAACAACTTT-AAATTTCATCTTAAAAAAGCTCCTCTCAGCA-AAGGCTCAATAACTTT
1 GAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCATCTCAACAGAA-GCTCAATAACTTT
* * * * *
2861568 AAAAATCTCATCTTGAAAAGGGCT-TATCTTAGCAGAGGCTTAACAACTTTAAAAT-TTCAT-TT
65 AAAATTTTCATCTTGAAAAGAGCTCT-TCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCTT
** *
2861630 GAAAAAGTTCCTCTCAGTA
129 GAAAAAGCACCTCTCAGCA
*
2861649 GAGGCTCAACAACTTTAAAAATCTT-ATCTTAAAAAAGCTCATCTCAACAGAAGCTCAACAACTT
1 GAGGCTCAACAACTTT-AAAAT-TTCATCTTAAAAAAGCTCATCTCAACAGAAGCTCAATAACTT
* * * * * *
2861713 TAAAA-TCTCATCTTGGAAA-AGTTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTTGATCTA
64 TAAAATTTTCATCTTGAAAAGAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCTT
* *
2861776 G-AAAAGCACATCTCAACA
129 GAAAAAGCACCTCTCAGCA
* * * * * * *
2861794 GAGGCTCAATAACTTTAAAATTTCATCTTGAAAAAGCTCCTTTCAATAGAGGCTCAATAATTTTA
1 GAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCATCTCAACAGAAGCTCAATAACTTTA
*
2861859 AAATTTTGATC-TGAAAA-AGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATCTT-ATCTT
66 AAATTTTCATCTTGAAAAGAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCTT
2861919 CTTCAAATCG
Statistics
Matches: 588, Mismatches: 85, Indels: 65
0.80 0.12 0.09
Matches are distributed among these distances:
142 21 0.04
143 104 0.18
144 252 0.43
145 63 0.11
146 49 0.08
147 68 0.12
148 10 0.02
150 6 0.01
151 3 0.01
152 12 0.02
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (147 bp):
GAGGCTCAACAACTTTAAAATTTCATCTTAAAAAAGCTCATCTCAACAGAAGCTCAATAACTTTA
AAATTTTCATCTTGAAAAGAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATCTTCATCTTGA
AAAAGCACCTCTCAGCA
Found at i:2867626 original size:24 final size:24
Alignment explanation
Indices: 2867594--2867641 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2867584 TTCACATGCT
2867594 TCACTCTCAGAGACCGGCTTCTGA
1 TCACTCTCAGAGACCGGCTTCTGA
*
2867618 TCACTCTCAGAGATCGGCTTCTGA
1 TCACTCTCAGAGACCGGCTTCTGA
2867642 CATTCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (24 bp):
TCACTCTCAGAGACCGGCTTCTGA
Found at i:2874156 original size:17 final size:16
Alignment explanation
Indices: 2874113--2874168 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2874103 ATTTTCCTAC
*
2874113 ATTTTT-TATTAGTTT
1 ATTTTTATATTAATTT
* *
2874128 AGTATTATTATTAAATTT
1 ATTTTTA-TATT-AATTT
*
2874146 ATTTTTATATTATTTT
1 ATTTTTATATTAATTT
2874162 ATTTTTA
1 ATTTTTA
2874169 AAGTTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 8 0.25
18 9 0.28
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
ATTTTTATATTAATTT
Found at i:2875332 original size:17 final size:17
Alignment explanation
Indices: 2875310--2875343 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2875300 ATCCCCCATT
2875310 TTTTTTTGTTCTGTTTG
1 TTTTTTTGTTCTGTTTG
* *
2875327 TTTTTTTTTTCTTTTTG
1 TTTTTTTGTTCTGTTTG
2875344 GTATTTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTTTGTTCTGTTTG
Found at i:2875354 original size:7 final size:7
Alignment explanation
Indices: 2875339--2875370 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2875329 TTTTTTTTCT
2875339 TTTTGGTA
1 TTTT-GTA
2875347 TTTTGTA
1 TTTTGTA
2875354 TTTTGTA
1 TTTTGTA
2875361 TTTTGTA
1 TTTTGTA
2875368 TTT
1 TTT
2875371 AATAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (7 bp):
TTTTGTA
Found at i:2878446 original size:22 final size:20
Alignment explanation
Indices: 2878421--2878461 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2878411 ATAACTAGAT
2878421 AAATTCAACATAAAATTAAAAC
1 AAATTC-ACATAAAA-TAAAAC
*
2878443 AAATTCACATATAATAAAA
1 AAATTCACATAAAATAAAA
2878462 TTTAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATTCACATAAAATAAAAC
Found at i:2882528 original size:27 final size:24
Alignment explanation
Indices: 2882498--2882556 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 24
2882488 ATTCTAAATA
2882498 AAATTTTTAAGTAATATATTAATTAAT
1 AAATTTTTAAGTAA-ATATT-A-TAAT
* * *
2882525 AAATTTATAATTAAATATTATACT
1 AAATTTTTAAGTAAATATTATAAT
2882549 AAATTTTT
1 AAATTTTT
2882557 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
26 5 0.18
27 12 0.43
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTTTTAAGTAAATATTATAAT
Found at i:2882553 original size:24 final size:26
Alignment explanation
Indices: 2882524--2882572 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
2882514 TATTAATTAA
2882524 TAAA-TTTATAA-TTAAATATTATAC
1 TAAATTTTATAATTTAAATATTATAC
*
2882548 TAAATTTTTTTAATTTAAATATTAT
1 TAAA-TTTTATAATTTAAATATTAT
2882573 TTATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
26 6 0.29
27 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TAAATTTTATAATTTAAATATTATAC
Found at i:2886135 original size:14 final size:15
Alignment explanation
Indices: 2886116--2886156 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2886106 AAAAAAAAAA
2886116 TTTTTTTGA-ATTAT
1 TTTTTTTGATATTAT
2886130 TTTTTTT-ATATTAT
1 TTTTTTTGATATTAT
* *
2886144 TATTTTTGTTATT
1 TTTTTTTGATATT
2886157 TTGAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTTTTGATATTAT
Found at i:2886145 original size:17 final size:18
Alignment explanation
Indices: 2886125--2886181 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
2886115 ATTTTTTTGA
2886125 ATTATTTTTTTTATATT-
1 ATTATTTTTTTTATATTG
* *
2886142 ATTATTTTTGTTATTTTG
1 ATTATTTTTTTTATATTG
*
2886160 AGTTTTTTTTTTATATATTG
1 A-TTATTTTTTT-TATATTG
2886180 AT
1 AT
2886182 ACATGATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 9 0.28
20 7 0.22
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (18 bp):
ATTATTTTTTTTATATTG
Found at i:2886578 original size:16 final size:16
Alignment explanation
Indices: 2886559--2886636 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
2886549 CTAGGTTTCT
*
2886559 AAAACCCTTAAAATCC
1 AAAACCCCTAAAATCC
* *
2886575 AAAATCCCTAGAATCC
1 AAAACCCCTAAAATCC
*
2886591 -AAACCCCTAAAATCT
1 AAAACCCCTAAAATCC
*
2886606 GAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
2886622 AAAACCCCATAAAAT
1 AAAACCCC-TAAAAT
2886637 TCGAAATCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
15 12 0.23
16 34 0.65
17 6 0.12
ACGTcount: A:0.49, C:0.32, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:2886602 original size:31 final size:32
Alignment explanation
Indices: 2886559--2886646 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
2886549 CTAGGTTTCT
* * *
2886559 AAAACCCTTAAAATCCAAAATCCCTAGAATCC
1 AAAACCCCTAAAATCCGAAATCCCTAAAATCC
* *
2886591 -AAACCCCTAAAATCTGAAACCCCTAAAATCC
1 AAAACCCCTAAAATCCGAAATCCCTAAAATCC
*
2886622 AAAACCCCATAAAATTCGAAATCCC
1 AAAACCCC-TAAAATCCGAAATCCC
2886647 AAACCCTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.57
32 7 0.15
33 13 0.28
ACGTcount: A:0.47, C:0.33, G:0.03, T:0.17
Consensus pattern (32 bp):
AAAACCCCTAAAATCCGAAATCCCTAAAATCC
Found at i:2886767 original size:30 final size:29
Alignment explanation
Indices: 2886677--2886805 Score: 88
Period size: 30 Copynumber: 4.4 Consensus size: 29
2886667 CCAGACCCTT
* * *
2886677 AAATCAAAACCCCAAACC--TCAAATTTTC
1 AAATCAAAACCCTAAACCTTTCAAA-CTTA
* *
2886705 AAACCAAAACCCTAAA-ATCTTCAAACTCTA
1 AAATCAAAACCCTAAACCT-TTCAAACT-TA
2886735 AAATCAAAACCCTAAACCTTTCATAACTTA
1 AAATCAAAACCCTAAACCTTTCA-AACTTA
* * * *
2886765 AAACCAAACCCCAAAACC-CTCAAAACTT-
1 AAATCAAAACCCTAAACCTTTC-AAACTTA
*
2886793 AAATCCAAACCCT
1 AAATCAAAACCCT
2886806 TAAAATTCGA
Statistics
Matches: 79, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
28 23 0.29
29 8 0.10
30 43 0.54
31 5 0.06
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (29 bp):
AAATCAAAACCCTAAACCTTTCAAACTTA
Found at i:2886791 original size:29 final size:29
Alignment explanation
Indices: 2886674--2886804 Score: 88
Period size: 29 Copynumber: 4.5 Consensus size: 29
2886664 AATCCAGACC
* * *
2886674 CTTAAATCAAAACCCC-AAA-CCTCAAAT
1 CTTAAAACCAAACCCCAAAACCCTCAAAA
* * * * *
2886701 TTTCAAACCAAAACCCTAAAATCTTC-AAA
1 CTTAAAACC-AAACCCCAAAACCCTCAAAA
* * * * *
2886730 CTCTAAAATCAAAACCCTAAACCTTTCATAA
1 CT-TAAAACCAAACCCCAAAACC-CTCAAAA
2886761 CTTAAAACCAAACCCCAAAACCCTCAAAA
1 CTTAAAACCAAACCCCAAAACCCTCAAAA
*
2886790 CTTAAATCCAAACCC
1 CTTAAAACCAAACCC
2886805 TTAAAATTCG
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
27 5 0.06
28 6 0.08
29 34 0.44
30 28 0.36
31 4 0.05
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (29 bp):
CTTAAAACCAAACCCCAAAACCCTCAAAA
Found at i:2886797 original size:58 final size:56
Alignment explanation
Indices: 2886674--2886805 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 56
2886664 AATCCAGACC
* * * * * *
2886674 CTTAAATCAAAACCCCAAACCTCAAATTTTCAAACCAAAACCCTAAAATCTTCAAA
1 CTTAAATCAAAACCCTAAACCTCAAATCTTAAAACCAAAACCCCAAAACCCTCAAA
2886730 CTCTAAAATCAAAACCCTAAACCTTTCATAA-CTTAAAACC-AAACCCCAAAACCCTCAAAA
1 CT-T-AAATCAAAACCCTAAACC--TCA-AATCTTAAAACCAAAACCCCAAAACCCTC-AAA
*
2886790 CTTAAATCCAAACCCT
1 CTTAAATCAAAACCCT
2886806 TAAAATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
56 2 0.03
57 1 0.02
58 29 0.46
59 14 0.22
60 15 0.24
61 2 0.03
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (56 bp):
CTTAAATCAAAACCCTAAACCTCAAATCTTAAAACCAAAACCCCAAAACCCTCAAA
Found at i:2890499 original size:68 final size:68
Alignment explanation
Indices: 2890373--2890499 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 68
2890363 GTATTACATT
* * * * * * *
2890373 AATGAATAGGATGTTTATAAAATTATTTTTGTTGGTATATAAATTGATGATTATCTTCTGTATAT
1 AATGAATAAGATGTTTATAAAATTATCTCTATTGGTATATAAATGGATAATTACCTTCTGTATAT
2890438 ATG
66 ATG
* *
2890441 AATGAATAAGATGTTTATAAAATTATCTCTATTGGTATGTGAATGGATAATTACCTTCT
1 AATGAATAAGATGTTTATAAAATTATCTCTATTGGTATATAAATGGATAATTACCTTCT
2890500 TCCCTTATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 50 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.44
Consensus pattern (68 bp):
AATGAATAAGATGTTTATAAAATTATCTCTATTGGTATATAAATGGATAATTACCTTCTGTATAT
ATG
Found at i:2890512 original size:2 final size:2
Alignment explanation
Indices: 2890505--2890532 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2890495 CTTCTTCCCT
2890505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2890533 AGATAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2891555 original size:47 final size:48
Alignment explanation
Indices: 2891486--2891589 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 48
2891476 TAAAAAAATA
* *
2891486 AAAAAAAATACAAATCTATATTGATAGATATTAAGC-TCGGTATAGGT
1 AAAAAAAATACAAATCTATATTGATAGACATTAACCGTCGGTATAGGT
* * * * *
2891533 ATAAAAATTACAAGTTTATATTGATAGACATTAACCGTTGGTATAGGT
1 AAAAAAAATACAAATCTATATTGATAGACATTAACCGTCGGTATAGGT
2891581 AAAAAAAAT
1 AAAAAAAAT
2891590 TAAAACGTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 30 0.64
48 17 0.36
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (48 bp):
AAAAAAAATACAAATCTATATTGATAGACATTAACCGTCGGTATAGGT
Found at i:2891992 original size:24 final size:24
Alignment explanation
Indices: 2891965--2892023 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2891955 TTGAAATATA
*
2891965 TATTGTGACTATCATTGTAGAGTT
1 TATTGTGACTATCATTATAGAGTT
* *
2891989 TATTGTGACTATCGTTATAGGGTT
1 TATTGTGACTATCATTATAGAGTT
2892013 TATTGTG-CTAT
1 TATTGTGACTAT
2892024 ACTAATAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (24 bp):
TATTGTGACTATCATTATAGAGTT
Found at i:2892031 original size:23 final size:24
Alignment explanation
Indices: 2891965--2892031 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2891955 TTGAAATATA
* ** *
2891965 TATTGTGACTATCATTGTAGAGTT
1 TATTGTGACTATCGTAATAGGGTT
*
2891989 TATTGTGACTATCGTTATAGGGTT
1 TATTGTGACTATCGTAATAGGGTT
2892013 TATTGTG-CTATAC-TAATAG
1 TATTGTGACTAT-CGTAATAG
2892032 ATTTTTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 9 0.24
24 29 0.76
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (24 bp):
TATTGTGACTATCGTAATAGGGTT
Found at i:2894958 original size:2 final size:2
Alignment explanation
Indices: 2894951--2894978 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2894941 GGTAAGAACA
2894951 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
2894979 GGCTTGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2902132 original size:12 final size:12
Alignment explanation
Indices: 2902115--2902158 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2902105 GAATCTTAGT
2902115 GTTTTATTTAAG
1 GTTTTATTTAAG
*
2902127 GTTTTAATATTGAG
1 GTTTT-AT-TTAAG
*
2902141 GTTTTATTTAGG
1 GTTTTATTTAAG
2902153 GTTTTA
1 GTTTTA
2902159 ATTTTAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 14 0.52
13 4 0.15
14 9 0.33
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (12 bp):
GTTTTATTTAAG
Found at i:2902185 original size:28 final size:28
Alignment explanation
Indices: 2902153--2902212 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2902143 TTTATTTAGG
*
2902153 GTTTTAATTTTAGAATTTCAATTTTAAA
1 GTTTTAATTTTAGAATATCAATTTTAAA
** * *
2902181 GTTTTGGTTTTAGAGTATCAATTTTAAG
1 GTTTTAATTTTAGAATATCAATTTTAAA
2902209 GTTT
1 GTTT
2902213 CAGTTGTAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.53
Consensus pattern (28 bp):
GTTTTAATTTTAGAATATCAATTTTAAA
Found at i:2902344 original size:14 final size:15
Alignment explanation
Indices: 2902327--2902363 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2902317 ATTATTATCA
2902327 TTTATTAATTAAT-T
1 TTTATTAATTAATAT
*
2902341 TTTATTATTTAATAT
1 TTTATTAATTAATAT
2902356 TTT-TTAAT
1 TTTATTAAT
2902364 ATCTAAGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTAATTAATAT
Found at i:2902527 original size:22 final size:21
Alignment explanation
Indices: 2902480--2902527 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2902470 ATTTTAAACA
*
2902480 TTATTTTTATTATACTATTATC
1 TTATTATTATTATA-TATTATC
2902502 TTATTATTATTAT-TATTATC
1 TTATTATTATTATATATTATC
2902522 TT-TTAT
1 TTATTAT
2902528 CTTTAACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
22 12 0.48
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTATTATTATATATTATC
Found at i:2904218 original size:40 final size:40
Alignment explanation
Indices: 2904174--2904254 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
2904164 TTTGGGCTTC
* **
2904174 CTCTTCTTGTTTTT-ATTTTTTGGGCTTTCTCTGTCTATCT
1 CTCTTCTTGTTTTTAATATTTT-GGCTTTCTCTAACTATCT
* * *
2904214 CTCTTTTTTTTTTTAATATTTTGTCTTTCTCTAACTATCT
1 CTCTTCTTGTTTTTAATATTTTGGCTTTCTCTAACTATCT
2904254 C
1 C
2904255 GTTTTTCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.10, C:0.20, G:0.07, T:0.63
Consensus pattern (40 bp):
CTCTTCTTGTTTTTAATATTTTGGCTTTCTCTAACTATCT
Found at i:2904369 original size:8 final size:8
Alignment explanation
Indices: 2904358--2904402 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
2904348 ATTATTTCTT
2904358 AATTTTTA
1 AATTTTTA
*
2904366 AATTTGTA
1 AATTTTTA
2904374 AATTTTTTA
1 AA-TTTTTA
*
2904383 AATTTTAA
1 AATTTTTA
*
2904391 AATTTTAA
1 AATTTTTA
2904399 AATT
1 AATT
2904403 AATTTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
AATTTTTA
Found at i:2904377 original size:16 final size:15
Alignment explanation
Indices: 2904358--2904399 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
2904348 ATTATTTCTT
2904358 AATTTTTAAATTTGTA
1 AATTTTTAAATTT-TA
2904374 AATTTTTTAAATTTTA
1 AA-TTTTTAAATTTTA
*
2904390 AAATTTTAAA
1 AATTTTTAAA
2904400 ATTAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
AATTTTTAAATTTTA
Found at i:2904378 original size:24 final size:24
Alignment explanation
Indices: 2904351--2904399 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2904341 TATTATCATT
*
2904351 ATTTCTT-AATTTTTAAATTTGTAA
1 ATTTCTTAAATTTTAAAATTT-TAA
*
2904375 ATTTTTTAAATTTTAAAATTTTAA
1 ATTTCTTAAATTTTAAAATTTTAA
2904399 A
1 A
2904400 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTCTTAAATTTTAAAATTTTAA
Found at i:2904401 original size:16 final size:17
Alignment explanation
Indices: 2904358--2904402 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2904348 ATTATTTCTT
2904358 AATTTTTAAATTTGTAA
1 AATTTTTAAATTTGTAA
*
2904375 ATTTTTTAAATTT-TAA
1 AATTTTTAAATTTGTAA
*
2904391 AATTTTAAAATT
1 AATTTTTAAATT
2904403 AATTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTTTAAATTTGTAA
Found at i:2904411 original size:25 final size:24
Alignment explanation
Indices: 2904356--2904413 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
2904346 TCATTATTTC
* *
2904356 TTAATTTTTAAATTTGTAAATTTT
1 TTAATTTTAAAATTTGTAAATTAT
2904380 TTAAATTTTAAAATTT-TAAAATTAAT
1 TT-AATTTTAAAATTTGT-AAATT-AT
2904406 TTAATTTT
1 TTAATTTT
2904414 TTGATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 23 0.79
26 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATTTTAAAATTTGTAAATTAT
Found at i:2907803 original size:2 final size:2
Alignment explanation
Indices: 2907796--2907820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2907786 AATGGAGATG
2907796 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2907821 CTTGTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2910779 original size:24 final size:24
Alignment explanation
Indices: 2910747--2910821 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
2910737 TAAAATTTAT
* *
2910747 ATTTGATATATTATTAATATATAA
1 ATTTTATATATTATTAATAAATAA
2910771 ATTTTATATATTATTAATAAATTAA
1 ATTTTATATATTATTAATAAA-TAA
2910796 ATATATTAT-T-TTATTAATAAATAA
1 AT-T-TTATATATTATTAATAAATAA
2910820 AT
1 AT
2910822 ATTAATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 24 0.52
25 16 0.35
26 2 0.04
27 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTTTATATATTATTAATAAATAA
Found at i:2910792 original size:20 final size:21
Alignment explanation
Indices: 2910752--2910805 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2910742 TTTATATTTG
*
2910752 ATATATTATTAATATATAAATT
1 ATATA-TATTATTATATAAATT
*
2910774 TTATATATTATTA-ATAAATT
1 ATATATATTATTATATAAATT
*
2910794 AAATATATTATT
1 ATATATATTATT
2910806 TTATTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 7 0.25
22 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATATATTATTATATAAATT
Found at i:2910831 original size:24 final size:25
Alignment explanation
Indices: 2910752--2910841 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 25
2910742 TTTATATTTG
* * *
2910752 ATATATTATTAATATATAAAT-TTT
1 ATATTTTATTAATAAATAAATATTA
*
2910776 ATATATTATTAATAAATTAAATA-TA
1 ATATTTTATTAATAAA-TAAATATTA
*
2910801 TTATTTTATTAATAAATAAATATTA
1 ATATTTTATTAATAAATAAATATTA
*
2910826 AT-TTTTA-AAATAAATA
1 ATATTTTATTAATAAATA
2910842 TATAAAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
23 8 0.14
24 26 0.46
25 23 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTTTATTAATAAATAAATATTA
Found at i:2910938 original size:26 final size:29
Alignment explanation
Indices: 2910865--2910938 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
2910855 ATTTTTTAAA
2910865 ATTTTATTTATTAATAAAATGATATCATGT
1 ATTTTATTTATTAATAAAATGA-ATCATGT
* *
2910895 AATTTATTTTATCAATAAAATG-AT-AT-T
1 ATTTTA-TTTATTAATAAAATGAATCATGT
*
2910922 ATTTTATTTATTGATAA
1 ATTTTATTTATTAATAA
2910939 TATATAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 9 0.24
27 6 0.16
28 2 0.05
29 2 0.05
30 5 0.13
31 14 0.37
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTTTATTTATTAATAAAATGAATCATGT
Found at i:2912579 original size:24 final size:23
Alignment explanation
Indices: 2912546--2912602 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
2912536 TTATTAAAAT
* *
2912546 AAAATAAATAAAATTTTGAAT-TG
1 AAAATTAATAAAAGTTT-AATATG
2912569 ATAAATTAAT-AAAGTTTAATATG
1 A-AAATTAATAAAAGTTTAATATG
2912592 AAAATTAATAA
1 AAAATTAATAA
2912603 TTTGTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 11 0.38
23 11 0.38
24 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
AAAATTAATAAAAGTTTAATATG
Found at i:2912820 original size:20 final size:21
Alignment explanation
Indices: 2912785--2912828 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2912775 TTAATTCATC
*
2912785 AATTTTAATTTTTTTATTT-T
1 AATTTTAATTTATTTATTTCT
*
2912805 AATTTTTATTTATTTATTTCT
1 AATTTTAATTTATTTATTTCT
2912826 AAT
1 AAT
2912829 ACGAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
AATTTTAATTTATTTATTTCT
Found at i:2916783 original size:12 final size:11
Alignment explanation
Indices: 2916756--2916831 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 11
2916746 AATAAATGTA
2916756 TAAAATTTTAT
1 TAAAATTTTAT
2916767 TAAATATTTT-T
1 TAAA-ATTTTAT
*
2916778 TAAAATTTGA-
1 TAAAATTTTAT
* *
2916788 TAATATTTTAGA
1 TAAAATTTTA-T
2916800 TAAATATTTTTAT
1 TAAA-A-TTTTAT
*
2916813 T-AAATTTTAA
1 TAAAATTTTAT
2916823 TAAAATTTT
1 TAAAATTTT
2916832 TCGATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
10 18 0.35
11 17 0.33
12 10 0.19
13 2 0.04
14 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TAAAATTTTAT
Found at i:2916816 original size:35 final size:33
Alignment explanation
Indices: 2916755--2916831 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 33
2916745 AAATAAATGT
* *
2916755 ATAAAATTTTA-TTAAATATTTTTTAAAATTTG
1 ATAAAATTTTAGATAAATATTTTTTAAAATTTA
* *
2916787 ATAATATTTTAGATAAATATTTTTATTAAATTTTA
1 ATAAAATTTTAGATAAATA-TTTT-TTAAAATTTA
2916822 ATAAAATTTT
1 ATAAAATTTT
2916832 TCGATTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 10 0.27
33 6 0.16
34 4 0.11
35 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (33 bp):
ATAAAATTTTAGATAAATATTTTTTAAAATTTA
Found at i:2916826 original size:10 final size:11
Alignment explanation
Indices: 2916755--2916831 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
2916745 AAATAAATGT
2916755 ATAAAATTTTA
1 ATAAAATTTTA
*
2916766 TTAAATATTTT-
1 ATAAA-ATTTTA
* *
2916777 TTAAAA-TTTG
1 ATAAAATTTTA
*
2916787 ATAATATTTTA
1 ATAAAATTTTA
*
2916798 GATAAATATTTTT
1 -ATAAA-ATTTTA
*
2916811 ATTAAATTTTA
1 ATAAAATTTTA
2916822 ATAAAATTTT
1 ATAAAATTTT
2916832 TCGATTAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 26 0.50
12 13 0.25
13 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
ATAAAATTTTA
Found at i:2920821 original size:171 final size:171
Alignment explanation
Indices: 2920531--2920870 Score: 590
Period size: 171 Copynumber: 2.0 Consensus size: 171
2920521 ACAGAAATGA
*
2920531 AGACATGAAGTTTTCTCCATCATCTCCCTTCCAAGAAAAAGTGAGGGTGAGACAGCCTCTATTCC
1 AGACATGAAGTTTTCTCCATCATCTCCCGTCCAAGAAAAAGTGAGGGTGAGACAGCCTCTATTCC
*
2920596 TGTTGAGTGTTGACAATTGAGCTTTCCAAGGGCAAATGATAGAAGGTGGTGAGGCCGTCCACAGA
66 TGTTGAGTGTTGACAATTGAGCTTTCCAAGGGCAAATGATAGAAGGTGGTGAGGCCATCCACAGA
* * *
2920661 ATTTGTCGAATACAGGAAGAAAACTCTCCGGATATTTTAGT
131 ATTTGTCAAATACAGCAAGAAAACTCTCCAGATATTTTAGT
*
2920702 AGACATGAAGTTTTCTCCATCATCTCCCGTCCAAGATAAAGTGAGGGTGAGACAGCCTCTATTCC
1 AGACATGAAGTTTTCTCCATCATCTCCCGTCCAAGAAAAAGTGAGGGTGAGACAGCCTCTATTCC
* *
2920767 TGTTGAGTGTTGACAATTGAGCTTTCCAAGGGCAAATGATAGAATGTTGTGAGGCCATCCACAGA
66 TGTTGAGTGTTGACAATTGAGCTTTCCAAGGGCAAATGATAGAAGGTGGTGAGGCCATCCACAGA
* *
2920832 ATTTGTTAAATACAGCCAGAAAACTCTCCAGATATTTTA
131 ATTTGTCAAATACAGCAAGAAAACTCTCCAGATATTTTA
2920871 TATGTTATCG
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
171 159 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (171 bp):
AGACATGAAGTTTTCTCCATCATCTCCCGTCCAAGAAAAAGTGAGGGTGAGACAGCCTCTATTCC
TGTTGAGTGTTGACAATTGAGCTTTCCAAGGGCAAATGATAGAAGGTGGTGAGGCCATCCACAGA
ATTTGTCAAATACAGCAAGAAAACTCTCCAGATATTTTAGT
Found at i:2925841 original size:19 final size:19
Alignment explanation
Indices: 2925806--2925844 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2925796 CAGAGTTTTA
*
2925806 CATTCTGAACGATGAAGGT
1 CATTCTGAACGACGAAGGT
*
2925825 CATTCTGAACGGCGAAGGT
1 CATTCTGAACGACGAAGGT
2925844 C
1 C
2925845 GGGTTTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (19 bp):
CATTCTGAACGACGAAGGT
Found at i:2931886 original size:4 final size:4
Alignment explanation
Indices: 2931877--2931903 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2931867 TCTTTATCTC
2931877 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2931904 TTGAAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2934751 original size:20 final size:19
Alignment explanation
Indices: 2934726--2934768 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2934716 CCAAACTAAA
*
2934726 TATATATTGTTATTAATTTT
1 TATATATTGTTA-AAATTTT
*
2934746 TATATATTTTTAAAATTTT
1 TATATATTGTTAAAATTTT
2934765 TATA
1 TATA
2934769 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATATATTGTTAAAATTTT
Found at i:2935669 original size:2 final size:2
Alignment explanation
Indices: 2935662--2935697 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2935652 ATAAATAAAA
*
2935662 AG AG AG AG AG AG AG A- AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2935698 TCGTTGATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2935679 original size:17 final size:17
Alignment explanation
Indices: 2935659--2935693 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2935649 AGGATAAATA
2935659 AAAAGAGAGAGAGAGAG
1 AAAAGAGAGAGAGAGAG
2935676 AAAAGAGAGAGAGAGAG
1 AAAAGAGAGAGAGAGAG
2935693 A
1 A
2935694 GAGATCGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (17 bp):
AAAAGAGAGAGAGAGAG
Found at i:2945894 original size:3 final size:3
Alignment explanation
Indices: 2945886--2945911 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2945876 TACCTGACCT
2945886 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2945912 TTTTCGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2978582 original size:35 final size:36
Alignment explanation
Indices: 2978513--2978592 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
2978503 AATATTCTAC
2978513 AAAAAAATTGAATAAGATTATTTAAGACATTTTTCT-
1 AAAAAAATTGAATAAGATTATTTAAGA-ATTTTTCTG
*
2978549 AAAAAAATTG-ATCAGCATTATTTAAG-ATGTTTTCTG
1 AAAAAAATTGAATAAG-ATTATTTAAGAAT-TTTTCTG
*
2978585 ATAAAAAT
1 AAAAAAAT
2978593 GACTTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 2 0.05
35 10 0.26
36 27 0.69
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (36 bp):
AAAAAAATTGAATAAGATTATTTAAGAATTTTTCTG
Found at i:2979572 original size:22 final size:23
Alignment explanation
Indices: 2979526--2979572 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2979516 TTTCGAAAAC
*
2979526 TTTTAAAAACTTTCAAAATTTTA
1 TTTTAAAAACTTTCAAAATTATA
2979549 TTTTCAAAAA-TTTC-AAATTATA
1 TTTT-AAAAACTTTCAAAATTATA
2979571 TT
1 TT
2979573 CAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 8 0.36
24 5 0.23
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTAAAAACTTTCAAAATTATA
Found at i:2985313 original size:21 final size:20
Alignment explanation
Indices: 2985274--2985310 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2985264 TAAGATAAAA
2985274 AGATAAATTTTAAAAATAAT
1 AGATAAATTTTAAAAATAAT
*
2985294 AGAT-AATTTTATAAATA
1 AGATAAATTTTAAAAATA
2985311 TAAGCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AGATAAATTTTAAAAATAAT
Found at i:2987012 original size:29 final size:29
Alignment explanation
Indices: 2986975--2987038 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2986965 TTATTGAATA
2986975 ATAATAAATATTT-AATATAATATTTAAATT
1 ATAA-AAAT-TTTAAATATAATATTTAAATT
* *
2987005 TTAAAAATTTTAAATATATTATTTAAATT
1 ATAAAAATTTTAAATATAATATTTAAATT
2987034 ATAAA
1 ATAAA
2987039 TTTATTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 3 0.10
29 24 0.80
30 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATAAAAATTTTAAATATAATATTTAAATT
Found at i:2987038 original size:20 final size:20
Alignment explanation
Indices: 2986978--2987050 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
2986968 TTGAATAATA
2986978 ATAAATAT-TTAATATAATATT
1 ATAAATATATTAAT-TAA-ATT
2986999 -TAAAT-T-TTAA--AAATT
1 ATAAATATATTAATTAAATT
* *
2987014 TTAAATATATTATTTAAATT
1 ATAAATATATTAATTAAATT
*
2987034 ATAAATTTATTAATTAA
1 ATAAATATATTAATTAA
2987051 TTTAATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.07
16 7 0.16
17 1 0.02
18 3 0.07
19 5 0.12
20 24 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATATATTAATTAAATT
Found at i:2987046 original size:29 final size:30
Alignment explanation
Indices: 2986975--2987046 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
2986965 TTATTGAATA
*
2986975 ATAATAAA-TATTTAATATAATATTTAAATT
1 ATAA-AAATTATTAAATATAATATTTAAATT
* *
2987005 TTAAAAATT-TTAAATATATTATTTAAATT
1 ATAAAAATTATTAAATATAATATTTAAATT
*
2987034 AT-AAATTTATTAA
1 ATAAAAATTATTAA
2987047 TTAATTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.14
29 26 0.74
30 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAAAAATTATTAAATATAATATTTAAATT
Found at i:2987059 original size:15 final size:15
Alignment explanation
Indices: 2987041--2987080 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
2987031 ATTATAAATT
2987041 TATTAATTAATTTAA
1 TATTAATTAATTTAA
*
2987056 TATTTATT--TTTAA
1 TATTAATTAATTTAA
2987069 TA-TAATTAATTT
1 TATTAATTAATTT
2987081 TAAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 4 0.19
13 7 0.33
14 3 0.14
15 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATTAATTTAA
Found at i:2987074 original size:18 final size:19
Alignment explanation
Indices: 2987033--2987074 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2987023 TTATTTAAAT
2987033 TATAA-ATTTATTAATTAA
1 TATAATATTTATTAATTAA
* *
2987051 TTTAATATTTATT-TTTAA
1 TATAATATTTATTAATTAA
2987069 TATAAT
1 TATAAT
2987075 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAATATTTATTAATTAA
Found at i:2987201 original size:30 final size:30
Alignment explanation
Indices: 2987135--2987208 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
2987125 AATAAAATTT
* *
2987135 TAATGTAAATATTATATTAAAATTTTTTTA
1 TAATTTAAATATTATATTAAAATTTTATTA
* *
2987165 -AATTTAAATATTATATTTATATTTTATTA
1 TAATTTAAATATTATATTAAAATTTTATTA
*
2987194 TAATTTAAAAATTAT
1 TAATTTAAATATTAT
2987209 TTATAATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TAATTTAAATATTATATTAAAATTTTATTA
Found at i:2993833 original size:15 final size:15
Alignment explanation
Indices: 2993809--2993839 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2993799 TGTGTTTATA
*
2993809 CTTAGGTTTGAAATT
1 CTTAGCTTTGAAATT
2993824 CTTAGCTTTGAAATT
1 CTTAGCTTTGAAATT
2993839 C
1 C
2993840 AAGGACCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (15 bp):
CTTAGCTTTGAAATT
Found at i:3002638 original size:19 final size:19
Alignment explanation
Indices: 3002599--3002638 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3002589 AATTATAGTA
*
3002599 AAATATAAATATAATATCT
1 AAATATAAATATAATAACT
* *
3002618 AAATATAAATTTATTAACT
1 AAATATAAATATAATAACT
3002637 AA
1 AA
3002639 TATGATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATAAATATAATAACT
Found at i:3009052 original size:36 final size:36
Alignment explanation
Indices: 3009005--3009076 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3008995 AAAATCTATG
3009005 TTTGGTTGGTTTCCATGAAGGGGTTGCAACATGCCA
1 TTTGGTTGGTTTCCATGAAGGGGTTGCAACATGCCA
3009041 TTTGGTTGGTTTCCATGAAGGGGTTGCAACATGCCA
1 TTTGGTTGGTTTCCATGAAGGGGTTGCAACATGCCA
3009077 CAGTGATAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (36 bp):
TTTGGTTGGTTTCCATGAAGGGGTTGCAACATGCCA
Found at i:3016753 original size:13 final size:13
Alignment explanation
Indices: 3016735--3016760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3016725 TTAAATTATG
3016735 TTATATTCGTATC
1 TTATATTCGTATC
3016748 TTATATTCGTATC
1 TTATATTCGTATC
3016761 ATATTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTATATTCGTATC
Found at i:3023403 original size:31 final size:30
Alignment explanation
Indices: 3023364--3023423 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3023354 CTAGCCAGCA
*
3023364 GATGTAATAGTAGCACAACACTCAAGCTTT
1 GATGTAATAGTAGCAAAACACTCAAGCTTT
* *
3023394 GATGTTAATAGTTGCAAAACACTCGAGCTT
1 GATG-TAATAGTAGCAAAACACTCAAGCTT
3023424 CGATAGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (30 bp):
GATGTAATAGTAGCAAAACACTCAAGCTTT
Found at i:3027342 original size:24 final size:23
Alignment explanation
Indices: 3027303--3027359 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
3027293 AAATTTTTTT
*
3027303 TATT-TTATT-AAATTTATA-TA
1 TATTATTATTAAAATTTAAATTA
3027323 TAATTATTATTAAAATTTTAAATTA
1 T-ATTATTATTAAAA-TTTAAATTA
*
3027348 TATTATTTTTAA
1 TATTATTATTAA
3027360 TCATATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 5 0.17
23 3 0.10
24 15 0.50
25 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTATTATTAAAATTTAAATTA
Found at i:3028291 original size:17 final size:17
Alignment explanation
Indices: 3028271--3028304 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3028261 ATTTTAAAAT
3028271 AAATAAATTT-TATATTA
1 AAAT-AATTTGTATATTA
3028288 AAATAATTTGTATATTA
1 AAATAATTTGTATATTA
3028305 TTTGAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATAATTTGTATATTA
Found at i:3030770 original size:18 final size:17
Alignment explanation
Indices: 3030747--3030795 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
3030737 TTTTGGAATT
3030747 ATTTTAATATATTTTAAA
1 ATTTTAAT-TATTTTAAA
3030765 ATTTT-ATTA--TTAAA
1 ATTTTAATTATTTTAAA
*
3030779 ATTTTATTTTATTTTAA
1 ATTTTA-ATTATTTTAA
3030796 TTAACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 10 0.38
16 5 0.19
17 2 0.08
18 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTAATTATTTTAAA
Found at i:3030779 original size:14 final size:13
Alignment explanation
Indices: 3030756--3030789 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
3030746 TATTTTAATA
3030756 TATTTTAAAATTT
1 TATTTTAAAATTT
3030769 TATTATTAAAATTT
1 TATT-TTAAAATTT
3030783 TATTTTA
1 TATTTTA
3030790 TTTTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTAAAATTT
Found at i:3031934 original size:31 final size:31
Alignment explanation
Indices: 3031896--3031957 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3031886 TTTTATACAA
3031896 TATATGTTTTCCAATATAAGAATGTTGGTTT
1 TATATGTTTTCCAATATAAGAATGTTGGTTT
3031927 TATATGTTTTCCAATATAAGAATGTTGGTTT
1 TATATGTTTTCCAATATAAGAATGTTGGTTT
3031958 AAAAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (31 bp):
TATATGTTTTCCAATATAAGAATGTTGGTTT
Found at i:3032864 original size:2 final size:2
Alignment explanation
Indices: 3032857--3032887 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3032847 TTAATATCTG
3032857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3032888 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3036079 original size:20 final size:21
Alignment explanation
Indices: 3036056--3036106 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 21
3036046 ATTACATTTA
3036056 TATATAATTAAAATATAAT-T
1 TATATAATTAAAATATAATAT
3036076 TATAT--TTAAAA-ATAATAT
1 TATATAATTAAAATATAATAT
*
3036094 T-TTTAATTAAAAT
1 TATATAATTAAAAT
3036107 TATTAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 6 0.23
20 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATAATTAAAATATAATAT
Found at i:3036084 original size:18 final size:17
Alignment explanation
Indices: 3036058--3036105 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
3036048 TACATTTATA
3036058 TATAATTAAAATATAATT
1 TATAATTAAAA-ATAATT
*
3036076 TATATTTAAAAATAATATT
1 TATAATTAAAAAT-A-ATT
*
3036095 TTTAATTAAAA
1 TATAATTAAAA
3036106 TTATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATTAAAAATAATT
Found at i:3036557 original size:33 final size:32
Alignment explanation
Indices: 3036515--3036576 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
3036505 ATAAAAAATT
* *
3036515 AAATTTAATAATTTATGTATTTATATTATGTA
1 AAATTTAATAAATTATATATTTATATTATGTA
*
3036547 AAATATTAATAAATTATATATTTTTATTAT
1 AAAT-TTAATAAATTATATATTTATATTAT
3036577 ATTTTATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (32 bp):
AAATTTAATAAATTATATATTTATATTATGTA
Found at i:3044932 original size:24 final size:24
Alignment explanation
Indices: 3044900--3044948 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3044890 CGCTGCAGAT
3044900 CAAGCACAAGATAATGTTATGAGG
1 CAAGCACAAGATAATGTTATGAGG
3044924 CAAGCACAAGATAATGTTATGAGG
1 CAAGCACAAGATAATGTTATGAGG
3044948 C
1 C
3044949 TTTTACCAAA
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:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (24 bp):
CAAGCACAAGATAATGTTATGAGG
Found at i:3049300 original size:76 final size:76
Alignment explanation
Indices: 3049174--3049315 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 76
3049164 AGAGGGTGTA
** ** * * * *
3049174 CATCATAATTTTCCTTACTTTAAGAAAGTTTGTTAAGTGAAGTGCGAGTAAACATGGAATAAACA
1 CATCATAATTTTAATTACTTTAAGAAAGTTTGTTAAGCAAAGAGAGAGTAAAAACGGAATAAACA
3049239 TCAAAATTGTG
66 TCAAAATTGTG
* *
3049250 CATCATAATTTTAATTACTTTATGAAAGTTTGTTAAGCAAAGAGAGAGTAAAAACGGTATAAACA
1 CATCATAATTTTAATTACTTTAAGAAAGTTTGTTAAGCAAAGAGAGAGTAAAAACGGAATAAACA
3049315 T
66 T
3049316 TACAATTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (76 bp):
CATCATAATTTTAATTACTTTAAGAAAGTTTGTTAAGCAAAGAGAGAGTAAAAACGGAATAAACA
TCAAAATTGTG
Found at i:3057316 original size:2 final size:2
Alignment explanation
Indices: 3057309--3057337 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3057299 TCCACTTATG
3057309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3057338 ACACTGCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3060987 original size:2 final size:2
Alignment explanation
Indices: 3060980--3061011 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3060970 AAGTCGATAA
3060980 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
3061012 TAAAGTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3064741 original size:113 final size:113
Alignment explanation
Indices: 3064537--3064749 Score: 338
Period size: 113 Copynumber: 1.9 Consensus size: 113
3064527 TCTAGTCACG
* *
3064537 GCTCTAAGGTCCCACTTCAACCCAACACTATCACAAACTTAAAACTCAACAGGCCTAACCCTTTC
1 GCTCTAAGGTCCCACTTCAACCCAACACTATCACAAACTTAAAAATCAACAGGCCTAACCCCTTC
3064602 TCCCTACTCACTAAAAACACTTAAAACAACACAAAGTGAAACACAAGA
66 TCCCTACTCACTAAAAACACTTAAAACAACACAAAGTGAAACACAAGA
* * * *
3064650 GCTCTAAGGTCCCACTTCAACCCAACACTATCACACACTTAAAAATTAACATGCC-CACCCCTTC
1 GCTCTAAGGTCCCACTTCAACCCAACACTATCACAAACTTAAAAATCAACAGGCCTAACCCCTTC
* *
3064714 TCCTTATTCACTAAAAACACTTAAAAACAACACAAA
66 TCCCTACTCACTAAAAACACTT-AAAACAACACAAA
3064750 CAAAGTGAAC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 27 0.30
113 64 0.70
ACGTcount: A:0.41, C:0.33, G:0.06, T:0.20
Consensus pattern (113 bp):
GCTCTAAGGTCCCACTTCAACCCAACACTATCACAAACTTAAAAATCAACAGGCCTAACCCCTTC
TCCCTACTCACTAAAAACACTTAAAACAACACAAAGTGAAACACAAGA
Done.