Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005298.1 Hibiscus syriacus cultivar Beakdansim tig00011994_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119684
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:5603 original size:110 final size:109
Alignment explanation
Indices: 5459--5671 Score: 277
Period size: 110 Copynumber: 1.9 Consensus size: 109
5449 CAACGCACGA
* * * *
5459 AATTCATCATAAGTTTGAACAATCGTTTTTGCACTATGTGTGCAACCGAC-GTAATTCATCATA-
1 AATTCATCATAAGTTCGAACAACCGTTTTGGCACTATGTGTGCAACCCACAG-AATTCATCATAT
* *
5522 ACTGATGAACAACCGTTTTGGCACTATGTGTGCAACCCATGATGG
65 ACTGATGAACAACCATTTAGGCACTATGTGTGCAACCCATGATGG
*
5567 AATTCATCATAAGTTGACGAACAACCGTTTTGGCACTATGTTTGCAACCCACAGAATTCATCATA
1 AATTCATCATAAGTT--CGAACAACCGTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATA
** * * *
5632 TGTTGATGAACAATCATTTAGGCACTGTGTTTGCAACCCA
64 TACTGATGAACAACCATTTAGGCACTATGTGTGCAACCCA
5672 CAGAATTCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
108 15 0.17
110 41 0.46
111 33 0.37
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (109 bp):
AATTCATCATAAGTTCGAACAACCGTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATATA
CTGATGAACAACCATTTAGGCACTATGTGTGCAACCCATGATGG
Found at i:5656 original size:54 final size:54
Alignment explanation
Indices: 5445--5681 Score: 268
Period size: 54 Copynumber: 4.4 Consensus size: 54
5435 AGCCATTATA
* * *
5445 TGTGCAACGCAC-GAAATTCATCATAAGTT--TGAACAATCGTTTTTGCACTATG
1 TGTGCAACCCACAG-AATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* *
5497 TGTGCAACCGAC-GTAATTCATCATAA-CTGATGAACAACCGTTTTGGCACTATG
1 TGTGCAACCCACAG-AATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* *
5550 TGTGCAACCCATGATGGAATTCATCATAAGTTGACGAACAACCGTTTTGGCACTATG
1 TGTGCAACCCA-CA--GAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
* * * * * *
5607 TTTGCAACCCACAGAATTCATCATATGTTGATGAACAATCATTTAGGCACTGTG
1 TGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
*
5661 TTTGCAACCCACAGAATTCAT
1 TGTGCAACCCACAGAATTCAT
5682 AATATATTTA
Statistics
Matches: 160, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
51 1 0.01
52 23 0.14
53 31 0.19
54 56 0.35
56 13 0.08
57 36 0.22
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (54 bp):
TGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATG
Found at i:5710 original size:54 final size:53
Alignment explanation
Indices: 5474--5710 Score: 201
Period size: 54 Copynumber: 4.3 Consensus size: 53
5464 ATCATAAGTT
* * * * * *
5474 TGAACAATCGTTTTTGCACTATGTGTGCAACCGAC-GTAATTCATCATA-ACTGA
1 TGAACAACCG-TTTGGCACTATGTTTGCAACCCACAG-AATTCATAATATATTGA
* * *
5527 TGAACAACCGTTTTGGCACTATGTGTGCAACCCATGATGGAATTCATCATA-AGTTGA
1 TGAACAACCG-TTTGGCACTATGTTTGCAACCCA-CA--GAATTCATAATATA-TTGA
* * *
5584 CGAACAACCGTTTTGGCACTATGTTTGCAACCCACAGAATTCATCATATGTTGA
1 TGAACAACCG-TTTGGCACTATGTTTGCAACCCACAGAATTCATAATATATTGA
* * * *
5638 TGAACAATCATTTAGGCACTGTGTTTGCAACCCACAGAATTCATAATATATTTA
1 TGAACAACCGTTT-GGCACTATGTTTGCAACCCACAGAATTCATAATATATTGA
**
5692 TGAATGACCGTATTGGCAC
1 TGAACAACCGT-TTGGCAC
5711 CACGTGTACA
Statistics
Matches: 156, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
53 34 0.22
54 71 0.46
55 2 0.01
56 13 0.08
57 36 0.23
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (53 bp):
TGAACAACCGTTTGGCACTATGTTTGCAACCCACAGAATTCATAATATATTGA
Found at i:7140 original size:31 final size:30
Alignment explanation
Indices: 7044--7142 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
7034 AAAAATGGTT
* * *
7044 AAATTTTAATTTAACCCTTAACTTTTAGATA
1 AAATATTAATTTAACCCATAA-ATTTAGATA
* * *
7075 AAATACTAGTTTAACCCAAAAATTTAGATA
1 AAATATTAATTTAACCCATAAATTTAGATA
* *
7105 AAATATTAATATAACCCATAAATTATATATA
1 AAATATTAATTTAACCCATAAATT-TAGATA
7136 AAATATT
1 AAATATT
7143 TTATCTATAG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 28 0.50
31 28 0.50
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATATTAATTTAACCCATAAATTTAGATA
Found at i:8532 original size:37 final size:37
Alignment explanation
Indices: 8483--8811 Score: 347
Period size: 37 Copynumber: 8.8 Consensus size: 37
8473 GGTTTTTGAA
8483 ATATATATATATATAGTTTTTGAAAACATTTT-AAAA-
1 ATATATA-ATATATAGTTTTTGAAAACATTTTGAAAAC
* * ** *
8519 ACATATAACATATAGTTTTTG-AAATTTTTTGAATATATATATAT
1 ATATATAATATATAGTTTTTGAAAACATTTTG-----A-A-A-AC
8563 ATATATATATATATAGTTTTTGAAAACATTTTG-AAA-
1 ATATATA-ATATATAGTTTTTGAAAACATTTTGAAAAC
* *
8599 ATATATAATATATAGTTTTTGAACACATTTTGAACAC
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
*
8636 ATATATAATATATAG-TTTTGAAATCATTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
* *
8673 TTATATAATATATAGTTTTTGAAAACATTTTGGAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
* *
8710 TTATATAATATATAG-TTTTGAAAACATTTTTGAAAAAA
1 ATATATAATATATAGTTTTTGAAAACA-TTTTG-AAAAC
8748 ATATATAATATATAG-TTTTGAAAACATTTTTG-AAA-
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
8783 ATATATAATATATAGTTTTT-AAAACATTT
1 ATATATAATATATAGTTTTTGAAAACATTT
8812 CACGAAACGA
Statistics
Matches: 255, Mismatches: 19, Indels: 40
0.81 0.06 0.13
Matches are distributed among these distances:
34 10 0.04
35 58 0.23
36 42 0.16
37 68 0.27
38 45 0.18
39 1 0.00
40 1 0.00
41 1 0.00
42 1 0.00
43 1 0.00
44 6 0.02
45 13 0.05
46 8 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:8556 original size:2 final size:2
Alignment explanation
Indices: 8551--8577 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8541 AATTTTTTGA
8551 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 A
8578 GTTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8567 original size:80 final size:80
Alignment explanation
Indices: 8482--8649 Score: 257
Period size: 80 Copynumber: 2.1 Consensus size: 80
8472 TGGTTTTTGA
**
8482 AATATATATATATATAGTTTTTGAAAACATTTTAAAAACATATAACATATAGTTTTTGAA-ATTT
1 AATATATATATATATAGTTTTTGAAAACATTTTAAAAACATATAACATATAGTTTTTGAACACAT
* *
8546 TTTGAATATATATAT
66 TTTGAACACATATAT
* * *
8561 ATATATATATATATATAGTTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTTGAACACA
1 A-ATATATATATATATAGTTTTTGAAAACATTTTAAAAACATATAACATATAGTTTTTGAACACA
8626 TTTTGAACACATATAT
65 TTTTGAACACATATAT
8642 AATATATA
1 AATATATA
8650 GTTTTGAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 63 0.79
81 16 0.20
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (80 bp):
AATATATATATATATAGTTTTTGAAAACATTTTAAAAACATATAACATATAGTTTTTGAACACAT
TTTGAACACATATAT
Found at i:11657 original size:16 final size:16
Alignment explanation
Indices: 11636--11676 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
11626 GAATAAACAC
11636 TGGACACACCGAGCAT
1 TGGACACACCGAGCAT
* *
11652 TGGACATACTGAGCAT
1 TGGACACACCGAGCAT
*
11668 TGAACACAC
1 TGGACACAC
11677 TCGTTCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (16 bp):
TGGACACACCGAGCAT
Found at i:13198 original size:36 final size:36
Alignment explanation
Indices: 13129--13199 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
13119 ATCCTGTTCG
*
13129 AACTTGTTTTTTGAACTTTCTCATGTATCTTTTTGT
1 AACTTGTTTTTTGAACTTTCTCATATATCTTTTTGT
* *
13165 AACTTGTTTTTTGAACTTTCTCATATTTGTTTTTG
1 AACTTGTTTTTTGAACTTTCTCATATATCTTTTTG
13200 CAAGGATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (36 bp):
AACTTGTTTTTTGAACTTTCTCATATATCTTTTTGT
Found at i:13890 original size:99 final size:98
Alignment explanation
Indices: 13698--13896 Score: 310
Period size: 99 Copynumber: 2.0 Consensus size: 98
13688 TTATAATATT
* * * *
13698 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCGACTTTATGGA
1 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAAACGCCCGACTTTAGGGA
*
13763 TAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 TAAGATTCAACTAGCCTGATAAAGGTGATTATA
* *
13796 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTAGTTAAGTAC-CCCGGCTTTAGG
1 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAA--ACGCCCGACTTTAGG
13860 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
64 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
13895 AT
1 AT
13897 CTTGAGCGGT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 44 0.48
99 46 0.50
100 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (98 bp):
ATATCTATACAATAAAGCTTGAGTTATCCCTCTAGAGAAATTAGTTAAACGCCCGACTTTAGGGA
TAAGATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:15819 original size:43 final size:40
Alignment explanation
Indices: 15766--16027 Score: 263
Period size: 43 Copynumber: 6.1 Consensus size: 40
15756 TGGTAACAAA
*
15766 AAACGCCGCAATAGGTGTTGATATTTGGCAGTATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTGGC-GT-TTTTTCC-AC
* * * *
15809 AAACGCCGCAATAAGTGTTAATATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTT---GGCGTTTTTTCCAC
* *
15852 AAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTGTTGAGATTT---GGCGTTTTTTCCAC
* * *
15895 AAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTT---GGCGTTTTTTCCAC
15938 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTGTTGAGATTT---GGCGTTTTTTCCAC
*
15981 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTGTTGAGATTT---GGCGTTTTTTCCAC
16024 AAAC
1 AAAC
16028 ACCGTAAAAG
Statistics
Matches: 202, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
43 191 0.95
44 6 0.03
45 2 0.01
46 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
AAACGCCGCAATAGGTGTTGAGATTTGGCGTTTTTTCCAC
Found at i:15897 original size:86 final size:86
Alignment explanation
Indices: 15766--16027 Score: 386
Period size: 86 Copynumber: 3.0 Consensus size: 86
15756 TGGTAACAAA
* * *
15766 AAACGCCGCAATAGGTGTTGATATTT---GGCAGTATTTTTCCAACAAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGC-GT-TTTTTCC-ACAAACGCCGCAATAGGTCTT
* *
15828 AATATTTAGCGGCGTTTTTCCCAC
63 GAGATTTAGCGGCGTTTTTCCCAC
* * * *
15852 AAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTTCCACAAATGCCGCAATAGGTTTTGAG
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAG
15917 ATTTAGCGGCGTTTTTCCCAC
66 ATTTAGCGGCGTTTTTCCCAC
15938 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAG
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAG
*
16003 ATTTAGCGGCGTTTTTTCCAC
66 ATTTAGCGGCGTTTTTCCCAC
16024 AAAC
1 AAAC
16028 ACCGTAAAAG
Statistics
Matches: 160, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
86 148 0.93
87 7 0.04
88 2 0.01
89 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (86 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAG
ATTTAGCGGCGTTTTTCCCAC
Found at i:16002 original size:129 final size:129
Alignment explanation
Indices: 15770--16026 Score: 397
Period size: 129 Copynumber: 2.0 Consensus size: 129
15760 AACAAAAAAC
* * * *
15770 GCCGCAATAGGTGTTGATATTTGGCAGTATTTTTCCAACAAACGCCGCAATAAGTGTTAATATTT
1 GCCGCAATAGGTGTTGAGATTTAGCAGCATTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTT
* *
15835 AGCGGCGTTTTTCCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTTCCACAAAT
66 AGCGGCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAAT
* * * * * *
15899 GCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTT
1 GCCGCAATAGGTGTTGAGATTTAGCAGCATTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTT
*
15964 AGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAA
66 AGCGGCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAA
16027 CACCGTAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 115 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (129 bp):
GCCGCAATAGGTGTTGAGATTTAGCAGCATTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTT
AGCGGCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAAT
Found at i:16061 original size:43 final size:43
Alignment explanation
Indices: 15799--16079 Score: 208
Period size: 43 Copynumber: 6.5 Consensus size: 43
15789 TTTGGCAGTA
* * * * *
15799 TTTTTCCAACAAACGCCGCAATAAG-TGTTAATATTTAGCGGCGT
1 TTTTTCC-ACAAACACCGCAA-AAGATCTTGAGATATAGCGGCGT
* ** * * * *
15843 TTTTCCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCGT
1 TTTTTCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCGT
** * * * *
15886 TTTTTCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCGT
1 TTTTTCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCGT
* * * * * *
15929 TTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGT
1 TTTTTCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCGT
* * * *
15972 TTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGT
1 TTTTTCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCGT
* *
16015 TTTTTCCACAAACACCGTAAAAGATC-TG-GTATATAGCGACGT
1 TTTTTCCACAAACACCGCAAAAGATCTTGAG-ATATAGCGGCGT
** *
16057 TTTTTATAACAAACGCCGCAAAA
1 TTTTT-CCACAAACACCGCAAAA
16080 TGTCATATCT
Statistics
Matches: 212, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.00
42 19 0.09
43 186 0.88
44 6 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TTTTTCCACAAACACCGCAAAAGATCTTGAGATATAGCGGCGT
Found at i:16061 original size:86 final size:85
Alignment explanation
Indices: 15799--16077 Score: 335
Period size: 86 Copynumber: 3.2 Consensus size: 85
15789 TTTGGCAGTA
* * * * *
15799 TTTTTCCAACAAACGCCGCAATAAGTGTTAATATTTAGCGGCGTTTTTCCCACAAATGCCGCAAT
1 TTTTTCC-ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAA-
* *
15864 AGGTTTTGAGATTTAGCGGCGT
64 AAGATTTGAGATTTAGCGGCGT
* * *
15886 TTTTTCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATA
1 TTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAAA
*
15951 GGTGTTGAGATTTAGCGGCGT
66 GAT-TTGAGATTTAGCGGCGT
* * *
15972 TTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAACACCGTAAAA
1 TTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAAA
* * *
16037 GATCTG-GTATATAGCGACGT
66 GATTTGAG-ATTTAGCGGCGT
**
16057 TTTTTATAACAAACGCCGCAA
1 TTTTT-CCACAAACGCCGCAA
16078 AATGTCATAT
Statistics
Matches: 168, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 19 0.11
86 141 0.84
87 7 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (85 bp):
TTTTTCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAAA
GATTTGAGATTTAGCGGCGT
Found at i:16061 original size:129 final size:129
Alignment explanation
Indices: 15799--16077 Score: 373
Period size: 129 Copynumber: 2.2 Consensus size: 129
15789 TTTGGCAGTA
* *
15799 TTTTTCCAACAAACGCCGCAATAAGTGTTAATATTTAGCGGCGTTTTTCCCACAAATGCCGCAAT
1 TTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAT
* ** * * * * *
15864 AGGTTTTGAGATTTAGCGGCGTTTTTTCCACAAATGCCGCAATAGGTTTTGAGATTTAGCGGCG
66 AGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAACACCGCAATAAGATCTGAGATATAGCGACG
* * * *
15928 TTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAAT
1 TTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAT
*
15993 AGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAACACCGTAA-AAGATCTG-GTATATAGCGACG
66 AGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAACACCGCAATAAGATCTGAG-ATATAGCGACG
**
16056 TTTTTTATAACAAACGCCGCAA
1 -TTTTTCCAACAAACGCCGCAA
16078 AATGTCATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
127 1 0.01
128 14 0.11
129 115 0.88
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (129 bp):
TTTTTCCAACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAAT
AGGTCTTGAGATTTAGCGGCGTTTTTTCCACAAACACCGCAATAAGATCTGAGATATAGCGACG
Found at i:16250 original size:21 final size:21
Alignment explanation
Indices: 16224--16282 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
16214 ATTTTCCAAT
*
16224 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
16245 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
16266 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
16283 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:20499 original size:41 final size:41
Alignment explanation
Indices: 20389--20780 Score: 266
Period size: 41 Copynumber: 9.6 Consensus size: 41
20379 GTTGTTTTAT
* * * * *
20389 AGTACGAGTATTTAGTGGTGTTTGTGCTTAAAACGCCACTAA
1 AGTACCAGTATTTAGCGGCGTTTGT-ATAAAAACGCCACTAA
* * * * * * *
20431 AGTA-TATTATTTTGAGGCATTTATATAAAAACGCCACTAT
1 AGTACCAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAA
* * *
20471 AGTACCAGTATTTAGCAGTGTTTGTATAAAAAACGCCGCTAA
1 AGTACCAGTATTTAGCGGCGTTTGTAT-AAAAACGCCACTAA
*
20513 AG-ACTC-GTACTATAGCGGCGTTTGTATAAAAACGCCACTAA
1 AGTAC-CAGTA-TTTAGCGGCGTTTGTATAAAAACGCCACTAA
* * * * * *
20554 A-TCACGAGTCTATAGCGGCGTTTGTTCTACAAACGCCAGTAA
1 AGT-ACCAGTATTTAGCGGCGTTTG-TATAAAAACGCCACTAA
* * *
20596 ATTA-CAGTCTTTCGCGGCGTTTGTATAAAAACGCCACTAA
1 AGTACCAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAA
* * **
20636 AGTA-AATTATTTAGCGGCGTTTGTATAAAAAACGCCGGTAA
1 AGTACCAGTATTTAGCGGCGTTTGTAT-AAAAACGCCACTAA
* * *
20677 AG-ACTC-GTATTATAGCGTCATTTGTACAAAAACGCCACTAA
1 AGTAC-CAGTATT-TAGCGGCGTTTGTATAAAAACGCCACTAA
* * * * *
20718 A-T--TAGTCTTTAGCGCCGTTTGTATAAAAACGCCGCTAT
1 AGTACCAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAA
* * *
20756 AGTACGAGTCTTTACCGGCGTTTGT
1 AGTACCAGTATTTAGCGGCGTTTGT
20781 TCTAGAAATG
Statistics
Matches: 273, Mismatches: 59, Indels: 37
0.74 0.16 0.10
Matches are distributed among these distances:
38 25 0.09
39 5 0.02
40 53 0.19
41 124 0.45
42 65 0.24
43 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
AGTACCAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAA
Found at i:20701 original size:82 final size:82
Alignment explanation
Indices: 20446--20751 Score: 293
Period size: 82 Copynumber: 3.8 Consensus size: 82
20436 ATTATTTTGA
* * * * * *
20446 GGCATTTATATAAAAACGCCACTATAGTACCAGTATTTAGCAGTGTTTGTATAAAAAACGCCGCT
1 GGCATTTGTATAAAAACGCCACTA-AATACAAGTATTTAGCGGCGTTTGTATAAAAAACGCCGGT
*
20511 AAAGACTCGTACTATAGC
65 AAAGACTCGTATTATAGC
* * * * * * *
20529 GGCGTTTGTATAAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGT-TCTACAAACGCCAG
1 GGCATTTGTATAAAAACGCCACTAAAT-ACAAGTATTTAGCGGCGTTTGTAT-AAAAAACGCCGG
* * * *
20593 TAAATTAC-AGTCTT-TCGC
64 TAAA-GACTCGTATTATAGC
* *
20611 GGCGTTTGTATAAAAACGCCACTAAAGTA-AATTATTTAGCGGCGTTTGTATAAAAAACGCCGGT
1 GGCATTTGTATAAAAACGCCACTAAA-TACAAGTATTTAGCGGCGTTTGTATAAAAAACGCCGGT
20675 AAAGACTCGTATTATAGC
65 AAAGACTCGTATTATAGC
* * * * *
20693 GTCATTTGTACAAAAACGCCACTAAAT--TAGTCTTTAGCGCCGTTTGTAT-AAAAACGCCG
1 GGCATTTGTATAAAAACGCCACTAAATACAAGTATTTAGCGGCGTTTGTATAAAAAACGCCG
20752 CTATAGTACG
Statistics
Matches: 181, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
79 10 0.06
80 20 0.11
81 34 0.19
82 60 0.33
83 55 0.30
84 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (82 bp):
GGCATTTGTATAAAAACGCCACTAAATACAAGTATTTAGCGGCGTTTGTATAAAAAACGCCGGTA
AAGACTCGTATTATAGC
Found at i:21148 original size:85 final size:85
Alignment explanation
Indices: 21012--21669 Score: 906
Period size: 85 Copynumber: 7.8 Consensus size: 85
21002 CTATTACAAT
* * ** * * *
21012 ATAGCTTAAGTCGAGAAAAGCTATATGTCAACAAAAACCTACGAGTTCGATTACATTCATCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
21077 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* ** * * *
21097 ATAACTCAAGGTAAGAAGGGATATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTTAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
21162 GGGCATATCAAATTTACAGT
66 GGGCATATCAAATTTACAGC
* * *
21182 ATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTTGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
21247 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * * *
21267 ATAGCTCAAGGAGAGAAGGGCTATATGTCAGCAAAAACCTTTGAGTTCGATTACATTCAGCTTAG
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* *
21332 GGGCATATTAAATTTACAAC
66 GGGCATATCAAATTTACAGC
* * ** *
21352 ATAGCTCAAGACGAGAAGGGCTATTTGTCAGTAAAAA-CTTCGAGTTTGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* *
21416 GAGCATATCAAATTTACAGT
66 GGGCATATCAAATTTACAGC
* * *
21436 ATAGCTCAAGGCGAGAAGGGATATCTGTCAA-TAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
21500 GGGCATATCAAATTTACAGT
66 GGGCATATCAAATTTACAGC
* * * * *
21520 ATAACTCAAGGTGAGAAGGGCTATCGGTCAACAAAATCCTTCGAGTTCGATTTCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
21585 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * *
21605 ATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTTCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
21670 CGACAATGAG
Statistics
Matches: 506, Mismatches: 65, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
83 4 0.01
84 137 0.27
85 365 0.72
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGGCATATCAAATTTACAGC
Found at i:22237 original size:2 final size:2
Alignment explanation
Indices: 22230--22259 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22220 TATGGAGATT
22230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22260 ATAATATCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22425 original size:73 final size:73
Alignment explanation
Indices: 22330--22653 Score: 290
Period size: 73 Copynumber: 4.3 Consensus size: 73
22320 AAAAATCGGT
* *
22330 TTTTG-AAATATATATAT-TATATAGCTTTTG-AATTTTTTTAAAAACATACATAATATATAGTT
1 TTTTGAAAATATATATATATATATAG-TTTTGAAATATTTTT-AAAACATATATAATATATAGTT
22392 TTTGAAAACA
64 TTTGAAAACA
* * * *
22402 ATTTGAAAATATTTATATAATATATAGTTTTTGAAA-ACATTTTGAAA-ATATATAATATATAG-
1 TTTTGAAAATATATATAT-ATATATAG-TTTTGAAATA-TTTTTAAAACATATATAATATATAGT
*
22464 TTTTGGAAACA
63 TTTTGAAAACA
* * *
22475 TTTTGAAAACATATATA-ATATATAGTTTTGAAATCATTTCTGAAAACTTATATAATATATAGTT
1 TTTTGAAAATATATATATATATATAGTTTTGAAAT-ATTT-TTAAAACATATATAATATATAGTT
22539 TTTGAAAACA
64 TTTGAAAACA
* * *
22549 TTTTGAAAAACTCAAAAACATATATAATATATAGTTTTGAAAACATTTTTTAAA-ATATATAATA
1 TTTTG-AAAA-T-----ATATATAT-ATATATAGTTTTG-AAATATTTTTAAAACATATATAATA
*
22613 TATAG-TTTTAAAAACA
57 TATAGTTTTTGAAAACA
*
22629 TTTTTGAAAACATATATA-ATATATA
1 -TTTTGAAAATATATATATATATATA
22654 ATTTAAAAAA
Statistics
Matches: 206, Mismatches: 25, Indels: 42
0.75 0.09 0.15
Matches are distributed among these distances:
70 8 0.04
71 10 0.05
72 16 0.08
73 49 0.24
74 35 0.17
75 19 0.09
76 6 0.03
80 14 0.07
81 25 0.12
82 4 0.02
83 17 0.08
84 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (73 bp):
TTTTGAAAATATATATATATATATAGTTTTGAAATATTTTTAAAACATATATAATATATAGTTTT
TGAAAACA
Found at i:22454 original size:110 final size:108
Alignment explanation
Indices: 22330--22653 Score: 330
Period size: 118 Copynumber: 2.9 Consensus size: 108
22320 AAAAATCGGT
* ***
22330 TTTTGAAATATATATATTATATAGCTTTT-GAATTTTTTTAAAAACATACATAATATATAGTTTT
1 TTTTGAAA-ATATATAATATATAG-TTTTGGAAACATTTTAAAAACATACATAATATATAG-TTT
*
22394 TGAAAACAATT-TGAAAATATTTATATAATATATAGTTTTTGAAAACA
63 TGAAAACAATTCTG-AAA-ACTTATATAATATATAGTTTTTGAAAACA
* *
22441 TTTTGAAAATATATAATATATAGTTTTGGAAACATTTTGAAAACATATATAATATATAGTTTTGA
1 TTTTGAAAATATATAATATATAGTTTTGGAAACATTTTAAAAACATACATAATATATAGTTTTGA
* *
22506 AATCATTTCTGAAAACTTATATAATATATAGTTTTTGAAAACA
66 AAACAATTCTGAAAACTTATATAATATATAGTTTTTGAAAACA
* ** *
22549 TTTTGAAAAACTCAAAAACATATATAATATATAGTTTTGAAAACATTTTTTAAA-ATATATAATA
1 TTTTG----------AAA-ATATATAATATATAGTTTTGGAAACATTTTAAAAACATACATAATA
* * * *
22613 TATAGTTTTAAAAACATTTTTGAAAACATATATAATATATA
55 TATAGTTTTGAAAACAATTCTGAAAACTTATATAATATATA
22654 ATTTAAAAAA
Statistics
Matches: 184, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
108 33 0.18
109 19 0.10
110 42 0.23
111 8 0.04
118 50 0.27
119 32 0.17
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (108 bp):
TTTTGAAAATATATAATATATAGTTTTGGAAACATTTTAAAAACATACATAATATATAGTTTTGA
AAACAATTCTGAAAACTTATATAATATATAGTTTTTGAAAACA
Found at i:22527 original size:37 final size:37
Alignment explanation
Indices: 22330--22653 Score: 324
Period size: 36 Copynumber: 8.6 Consensus size: 37
22320 AAAAATCGGT
* * * ***
22330 TTTTG-AAATATATATATTATATAGCTTTTG-AATTT
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* *
22365 TTTTAAAAACATACATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* *
22402 ATTTGAAAATATTTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACA--TATATAATATATAGTTTTTGAAAACA
*
22441 TTTTG-AAA-ATATATAATATATAG-TTTTGGAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
22475 TTTTGAAAACATATATAATATATAG-TTTTGAAATCA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
22511 TTTCTGAAAACTTATATAATATATAGTTTTTGAAAACA
1 TTT-TGAAAACATATATAATATATAGTTTTTGAAAACA
22549 TTTTGAAAAACTCAAAAACATATATAATATATAG-TTTTGAAAACA
1 TTTTG---------AAAACATATATAATATATAGTTTTTGAAAACA
** *
22594 TTTTTTAAA-ATATATAATATATAG-TTTTAAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
22629 TTTTTGAAAACATATATAATATATA
1 -TTTTGAAAACATATATAATATATA
22654 ATTTAAAAAA
Statistics
Matches: 246, Mismatches: 24, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
34 15 0.06
35 46 0.19
36 58 0.24
37 48 0.20
38 16 0.07
39 29 0.12
45 15 0.06
46 19 0.08
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
Found at i:22577 original size:83 final size:81
Alignment explanation
Indices: 22480--22638 Score: 248
Period size: 83 Copynumber: 1.9 Consensus size: 81
22470 AAACATTTTG
* *
22480 AAAACATATATAATATATAGTTTTGAAATCATTTCTGAAAACTTATATAATATATAGTTTTTGAA
1 AAAACATATATAATATATAGTTTTGAAAACATTTCTGAAAA--TATATAATATATAG-TTTTAAA
22545 AACA-TTTTGAAAAACTCA
63 AACATTTTTGAAAAACTCA
* *
22563 AAAACATATATAATATATAGTTTTGAAAACATTTTTTAAAATATATAATATATAGTTTTAAAAAC
1 AAAACATATATAATATATAGTTTTGAAAACATTTCTGAAAATATATAATATATAGTTTTAAAAAC
22628 ATTTTTGAAAA
66 ATTTTTGAAAA
22639 CATATATAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
80 10 0.14
81 23 0.32
83 38 0.54
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (81 bp):
AAAACATATATAATATATAGTTTTGAAAACATTTCTGAAAATATATAATATATAGTTTTAAAAAC
ATTTTTGAAAAACTCA
Found at i:22663 original size:37 final size:36
Alignment explanation
Indices: 22563--22677 Score: 151
Period size: 35 Copynumber: 3.1 Consensus size: 36
22553 GAAAAACTCA
*
22563 AAAACATATATAATATATAGTTTTGAAAACATTTTT
1 AAAACATATATAATATATAGTTTTAAAAACATTTTT
*
22599 TAAA-ATATATAATATATAGTTTTAAAAACATTTTT
1 AAAACATATATAATATATAGTTTTAAAAACATTTTT
* * *
22634 GAAAACATATATAATATATAATTTAAAAAAACTTTTTTT
1 -AAAACATATATAATATATAGTTT-TAAAAAC-ATTTTT
22673 AAAAC
1 AAAAC
22678 GTTTTAAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
35 30 0.43
36 6 0.09
37 17 0.25
38 11 0.16
39 5 0.07
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (36 bp):
AAAACATATATAATATATAGTTTTAAAAACATTTTT
Found at i:22745 original size:6 final size:6
Alignment explanation
Indices: 22711--22784 Score: 58
Period size: 6 Copynumber: 11.3 Consensus size: 6
22701 TATACTTTCA
* * *
22711 TTATTA TTATTA TTATTA TTATTTCT TTATTT TTATTT TTATTTTT TCTATTT
1 TTATTT TTATTT TTATTT TTA-TT-T TTATTT TTATTT TTA--TTT T-TATTT
*
22764 TTATTT ATTATCT TTATTT TT
1 TTATTT -TTATTT TTATTT TT
22785 TGTAAGGGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
6 37 0.63
7 13 0.22
8 7 0.12
9 2 0.03
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:22746 original size:20 final size:19
Alignment explanation
Indices: 22717--22784 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
22707 TTCATTATTA
*
22717 TTATTATTATTATTATTTCT
1 TTATTTTTATT-TTATTTCT
*
22737 TTATTTTTATTTTTATTTTT
1 TTATTTTTA-TTTTATTTCT
22757 TCTATTTTTA-TTTATTATCT
1 T-TATTTTTATTTTATT-TCT
22777 TTATTTTT
1 TTATTTTT
22785 TGTAAGGGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.31
20 19 0.45
21 10 0.24
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATTTTTATTTTATTTCT
Found at i:22764 original size:15 final size:14
Alignment explanation
Indices: 22740--22785 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
22730 TATTTCTTTA
22740 TTTTTATTTTTATT
1 TTTTTATTTTTATT
22754 TTTTCTATTTTTA-T
1 TTTT-TATTTTTATT
* *
22768 TTATTATCTTTATT
1 TTTTTATTTTTATT
22782 TTTT
1 TTTT
22786 GTAAGGGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 7 0.26
14 12 0.44
15 8 0.30
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:28968 original size:2 final size:2
Alignment explanation
Indices: 28961--28989 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28951 AACAATACTT
28961 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 T
28990 CACCTTATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34766 original size:17 final size:17
Alignment explanation
Indices: 34726--34768 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
34716 TTAATACATA
* *
34726 TAGTTCATTTAGTTATG
1 TAGTTCATTTAATTAAG
* *
34743 CACTTCATTTAATTAAG
1 TAGTTCATTTAATTAAG
34760 TAGTTCATT
1 TAGTTCATT
34769 AATGCATAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (17 bp):
TAGTTCATTTAATTAAG
Found at i:34818 original size:35 final size:36
Alignment explanation
Indices: 34762--34865 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 36
34752 TAATTAAGTA
* **
34762 GTTCATTAATGCATAA-T-GTTCATTCAATG-AAGTTG
1 GTTCATTAATGTA-AACTAGTTCATTC-ATGTAAACTG
34797 GTTCATTAAT-TAAACTAGTTCATTCATGTAAACTG
1 GTTCATTAATGTAAACTAGTTCATTCATGTAAACTG
* * *
34832 GTTCATTCATGTAAACTGGTTCATTAAT-TAAACT
1 GTTCATTAATGTAAACTAGTTCATTCATGTAAACT
34866 AGCTCTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 2 0.03
34 5 0.08
35 37 0.63
36 15 0.25
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (36 bp):
GTTCATTAATGTAAACTAGTTCATTCATGTAAACTG
Found at i:34830 original size:18 final size:17
Alignment explanation
Indices: 34797--34867 Score: 88
Period size: 18 Copynumber: 4.1 Consensus size: 17
34787 AATGAAGTTG
34797 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
* *
34814 GTTCATTCATGTAAACTG
1 GTTCATTAAT-TAAACTA
* *
34832 GTTCATTCATGTAAACTG
1 GTTCATTAAT-TAAACTA
34850 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
34867 G
1 G
34868 CTCTTTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.33
18 33 0.67
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:39315 original size:14 final size:14
Alignment explanation
Indices: 39291--39325 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39281 ATTTTCCATC
*
39291 TCTTC-TCTTCATT
1 TCTTCTTCTTCATA
39304 TCTTCTTCTTCATA
1 TCTTCTTCTTCATA
39318 TCTTCTTC
1 TCTTCTTC
39326 CTCCATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.09, C:0.31, G:0.00, T:0.60
Consensus pattern (14 bp):
TCTTCTTCTTCATA
Found at i:39833 original size:20 final size:21
Alignment explanation
Indices: 39795--39834 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39785 TTAGAGTTCG
39795 AATATCGATACTGGGATGAAC
1 AATATCGATACTGGGATGAAC
*
39816 AATATCGATA-TTGGATGAA
1 AATATCGATACTGGGATGAA
39835 TTAGGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
AATATCGATACTGGGATGAAC
Found at i:57991 original size:2 final size:2
Alignment explanation
Indices: 57986--58120 Score: 270
Period size: 2 Copynumber: 67.5 Consensus size: 2
57976 TATATATATA
57986 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58028 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58070 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58112 TG TG TG TG T
1 TG TG TG TG T
58121 CTATAATGTG
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 133 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:58284 original size:81 final size:81
Alignment explanation
Indices: 58179--58787 Score: 862
Period size: 81 Copynumber: 7.5 Consensus size: 81
58169 CTGTTTTAAA
*
58179 TAAAAGATTAATTGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
58244 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
58260 TACAAGATTAATAGCCTAGTTGTGCATTTGATAGAAATGTGTTAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
58325 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * **
58341 TAAAAGATTAATTACCAAGTTGTGCATTTGACAGAAATGTGTCAATTATAACAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
58406 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
58422 TAAAAGATTAATTGCCTAGCTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGCTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
58487 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
58503 TAAAATATTAATCGCCTAGTTGTGCATTTGATAGAAATGTGTCAATTATGCTAGTTAGAGGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
58568 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
58584 TAAAAGATTAATTGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATTAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
58649 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
58665 TAAAAGATTAATTGCCTAGCTATGCATTTGACAAAAATGTTTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* * *
58730 GCTAAATGCCTTTAAG
66 GTTAAATACCTTTGAG
* * * * ** *
58746 TTAAATATTAAATGTCTAATTGTGCATTTGGCA-AAA-GTGTCA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCA
58788 GAGATGAAAG
Statistics
Matches: 471, Mismatches: 57, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
79 5 0.01
80 3 0.01
81 463 0.98
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:86604 original size:21 final size:20
Alignment explanation
Indices: 86578--86630 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
86568 TTATAATGGT
** *
86578 AGTATCGATACTCATTCATTG
1 AGTATCGATACTCAGGCA-GG
86599 AGTATCGATAC-CAGGCAGG
1 AGTATCGATACTCAGGCAGG
86618 AGTATCGATACTC
1 AGTATCGATACTC
86631 CCCATAGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTCAGGCAGG
Found at i:86799 original size:19 final size:19
Alignment explanation
Indices: 86775--86824 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
86765 CTCATTCATT
86775 GAGTATCGATACCAGGCAG
1 GAGTATCGATACCAGGCAG
86794 GAGTATCGATACCAGGCAG
1 GAGTATCGATACCAGGCAG
86813 GAGTATCGATAC
1 GAGTATCGATAC
86825 TCCCCGTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (19 bp):
GAGTATCGATACCAGGCAG
Found at i:88276 original size:20 final size:20
Alignment explanation
Indices: 88245--88336 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
88235 CAAGATTGGA
*
88245 TAGTCTCTATACCAAAGGAC
1 TAGTCTCCATACCAAAGGAC
* * * *
88265 TGGTCTCCATACCGAAGAAT
1 TAGTCTCCATACCAAAGGAC
* *
88285 TATTCTTCATACCAAAGGAC
1 TAGTCTCCATACCAAAGGAC
* *
88305 TAATATCCATACCAAA-GAC
1 TAGTCTCCATACCAAAGGAC
*
88324 TAAGTATCCATAC
1 T-AGTCTCCATAC
88337 TGAAGGCTCC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
19 4 0.07
20 52 0.93
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (20 bp):
TAGTCTCCATACCAAAGGAC
Found at i:92048 original size:81 final size:81
Alignment explanation
Indices: 91949--92256 Score: 451
Period size: 81 Copynumber: 3.8 Consensus size: 81
91939 CTGTTTTAAA
* *
91949 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAAATATG-CATGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCA-GTTAGATGAAA
*
92013 GATTAAATATCTTTGAG
65 GATTAAATACCTTTGAG
* * *
92030 TAAAAGATTAATCGCCTAGTTGTGCATTTTACTGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
92095 GTTAAATACCTTTGAG
66 ATTAAATACCTTTGAG
*
92111 TAAAAGATTAATTGCCTAGCTT-TGTATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAG-TTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
92175 -AGTTAAATACCTTTGAG
65 GA-TTAAATACCTTTGAG
* * * * *
92192 TAAAAGATTAATTGTCTAGCTATGCATTTGACAGAAAGGGGTCAATTATACCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
92257 GCTAAACTGC
Statistics
Matches: 205, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
80 1 0.00
81 200 0.98
82 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
ATTAAATACCTTTGAG
Found at i:92281 original size:60 final size:59
Alignment explanation
Indices: 92207--92327 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 59
92197 GATTAATTGT
* *
92207 CTAGCTATGCATTTGACAGAAAGGGGTCAATTATACCAGTTAGATGAAAGGCTAAACTGC
1 CTAGCTATGCATTTGACAGAAAGGGGTCAATCATACAAGTTAGATGAAAGGCTAAA-TGC
* * * * * *
92267 CTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATGC
1 CTAGCTATGCATTTGACAGAAAGGGGTCAATCATACAAGTTAGATGAAAGGCTAAATGC
92326 CT
1 CT
92328 TTGGGTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 5 0.09
60 48 0.91
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (59 bp):
CTAGCTATGCATTTGACAGAAAGGGGTCAATCATACAAGTTAGATGAAAGGCTAAATGC
Found at i:94026 original size:13 final size:13
Alignment explanation
Indices: 94008--94032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93998 TAGTTATAAA
94008 ATAATATTTATTT
1 ATAATATTTATTT
94021 ATAATATTTATT
1 ATAATATTTATT
94033 ATCTCAAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATAATATTTATTT
Found at i:95319 original size:12 final size:12
Alignment explanation
Indices: 95296--95337 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
95286 ATCTATATTT
95296 ATATTA-CTTTG
1 ATATTATCTTTG
95307 ATATTATCTTTG
1 ATATTATCTTTG
95319 ATATTATCTTTG
1 ATATTATCTTTG
95331 ATATTAT
1 ATATTAT
95338 ATAATTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 6 0.20
12 24 0.80
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (12 bp):
ATATTATCTTTG
Found at i:96644 original size:51 final size:50
Alignment explanation
Indices: 96499--96748 Score: 204
Period size: 51 Copynumber: 5.0 Consensus size: 50
96489 TCATACTATG
* * *
96499 AAAATATATAGCACTTAATACATACTTACATCAATATAATGAAT--AA-AA
1 AAAAT-TATAGCACTTAACACATACTTACATCGATGTAATGAATAAAATAA
* * *** **
96547 AAAATTATAGCACTTAATACATATTTATGCCGATGTGGTGAATAAAATAA
1 AAAATTATAGCACTTAACACATACTTACATCGATGTAATGAATAAAATAA
* * *
96597 AAAATTGTAGCACTTAACACATATTTACATCGGTGTAAATGAATAAAATAA
1 AAAATTATAGCACTTAACACATACTTACATCGATGT-AATGAATAAAATAA
* * * * *
96648 AAAAGTATAACAATTAACATATACTTACATTGATGTAAGTGAATAAAATAA
1 AAAATTATAGCACTTAACACATACTTACATCGATGTAA-TGAATAAAATAA
* * * *
96699 AATATATATA-TAATGTAACACATACTTACA-CTAGTGTAAGTGAATAAAAT
1 AAAAT-TATAGCACT-TAACACATACTTACATCGA-TGTAA-TGAATAAAAT
96749 TAAAGTGTAG
Statistics
Matches: 164, Mismatches: 30, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
47 30 0.18
48 5 0.03
49 2 0.01
50 34 0.21
51 59 0.36
52 34 0.21
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (50 bp):
AAAATTATAGCACTTAACACATACTTACATCGATGTAATGAATAAAATAA
Found at i:97012 original size:49 final size:49
Alignment explanation
Indices: 96920--97013 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
96910 CAAATTTTAT
* * *
96920 TAAAAATATATATAAATTATAAATAATAAGAAATTTTATTTTATTTGTG
1 TAAAAATATATATAAATTAGAAATAATAAGAAAATTTAATTTATTTGTG
*
96969 TAAAAATATA-ATAAATTAGAAAT-ATAATTATAAATTTAATTTATT
1 TAAAAATATATATAAATTAGAAATAATAA-GA-AAATTTAATTTATT
97014 AACGGTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 4 0.10
48 13 0.33
49 22 0.56
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (49 bp):
TAAAAATATATATAAATTAGAAATAATAAGAAAATTTAATTTATTTGTG
Found at i:97550 original size:27 final size:27
Alignment explanation
Indices: 97513--97564 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
97503 TCGTTTACAT
97513 TATGTCATTGAGTCAA-TTCTTAAAACA
1 TATGTCATTGAGT-AAGTTCTTAAAACA
*
97540 TATGTCGTTGAGTAAGTTCTTAAAA
1 TATGTCATTGAGTAAGTTCTTAAAA
97565 GCAACGGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (27 bp):
TATGTCATTGAGTAAGTTCTTAAAACA
Found at i:98030 original size:19 final size:19
Alignment explanation
Indices: 98016--98052 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
98006 GATAAAATAA
98016 CATCTTATAATTAAAAAAT
1 CATCTTATAATTAAAAAAT
* *
98035 TATTTTATAATTAAAAAA
1 CATCTTATAATTAAAAAA
98053 ATATTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
CATCTTATAATTAAAAAAT
Found at i:98057 original size:19 final size:19
Alignment explanation
Indices: 98020--98066 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
98010 AAATAACATC
*
98020 TTATAATTAAAAAATTATT
1 TTATAATTAAAAAAATATT
98039 TTATAATTAAAAAAATATT
1 TTATAATTAAAAAAATATT
*
98058 TTATGATTA
1 TTATAATTA
98067 CTAATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTATAATTAAAAAAATATT
Found at i:98505 original size:2 final size:2
Alignment explanation
Indices: 98498--98523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98488 AACATAACTC
98498 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
98524 GACATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99684 original size:27 final size:27
Alignment explanation
Indices: 99645--99697 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
99635 ATTCTCCCTG
* * *
99645 CCCTTTGCATGTGCTTTCCCCATCATT
1 CCCTTCGCATGTGCTCTCCACATCATT
*
99672 CCCTTCGCCTGTGCTCTCCACATCAT
1 CCCTTCGCATGTGCTCTCCACATCAT
99698 CCCATGCTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.11, C:0.42, G:0.11, T:0.36
Consensus pattern (27 bp):
CCCTTCGCATGTGCTCTCCACATCATT
Found at i:100002 original size:20 final size:20
Alignment explanation
Indices: 99975--100015 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
99965 TTTAAGATTT
99975 AAAAAAAATAGATTATTTTTTC
1 AAAAAAAA-AG-TTATTTTTTC
99997 AAAAAAAAAGTTATTTTTT
1 AAAAAAAAAGTTATTTTTT
100016 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAAAAAAAGTTATTTTTTC
Found at i:101466 original size:6 final size:6
Alignment explanation
Indices: 101455--101487 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
101445 GAGAAACCGC
101455 AAAAAG AAAAAG -AAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
101488 AGAGGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:101472 original size:11 final size:11
Alignment explanation
Indices: 101456--101487 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
101446 AGAAACCGCA
101456 AAAAGAAAAAG
1 AAAAGAAAAAG
101467 AAAAGAAAAAG
1 AAAAGAAAAAG
101478 AAAAGAAAAA
1 AAAAGAAAAA
101488 AGAGGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:115120 original size:2 final size:2
Alignment explanation
Indices: 115113--115144 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
115103 TTCCTAATTA
115113 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
115145 TGAATTTGAT
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:115711 original size:22 final size:24
Alignment explanation
Indices: 115683--115726 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
115673 GAACAAAGAC
115683 AAATGATAAAATT-TTT-AAATGT
1 AAATGATAAAATTATTTCAAATGT
*
115705 AAATGATTAAATTATTTCAAAT
1 AAATGATAAAATTATTTCAAAT
115727 TACAACCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (24 bp):
AAATGATAAAATTATTTCAAATGT
Found at i:117378 original size:65 final size:65
Alignment explanation
Indices: 117259--117488 Score: 208
Period size: 65 Copynumber: 3.6 Consensus size: 65
117249 TTTTTCAGAG
* * *
117259 TGATGCACCGATGCAC-CAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCACTC-ATCCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
117320 CATT
62 CATT
* * * *
117324 TCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGTA
1 TGATGCATCGATGCACTCATCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
117387 TT
64 TT
* * * * *
117389 TGATGCATCGATGCAC-CATCTATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTCATCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
* *
117453 TGATGCATCAATGCACTC-T-TAGTGCACCGATGCACT
1 TGATGCATCGATGCACTCATCCA-TGCACCGATGCACT
117489 AAGGGTCCAA
Statistics
Matches: 137, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 59 0.43
65 70 0.51
66 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (65 bp):
TGATGCATCGATGCACTCATCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Done.