Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003347.1 Hibiscus syriacus cultivar Beakdansim tig00007047_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: 129431
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4230 original size:23 final size:23
Alignment explanation
Indices: 4197--4264 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
4187 CATCTTTTAT
*
4197 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
4220 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCATTTCTACGC
*
4243 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
4265 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:4558 original size:18 final size:18
Alignment explanation
Indices: 4535--4598 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
4525 ATGTATTACA
4535 TGATAATGATATTGATAT
1 TGATAATGATATTGATAT
**
4553 TGATAATGATAGAGATCA-
1 TGATAATGATATTGAT-AT
* *
4571 TGATAATGATGTTGATGT
1 TGATAATGATATTGATAT
4589 TGATAATGAT
1 TGATAATGAT
4599 GGTATATGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 37 0.97
19 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.39
Consensus pattern (18 bp):
TGATAATGATATTGATAT
Found at i:4598 original size:6 final size:6
Alignment explanation
Indices: 4534--4580 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
4524 AATGTATTAC
* * *
4534 ATGATA ATGATA TTGATA TTGATA ATGATA GA-GATC ATGATA ATGAT
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGAT
4581 GTTGATGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.94
7 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (6 bp):
ATGATA
Found at i:10233 original size:13 final size:13
Alignment explanation
Indices: 10208--10275 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
10198 AATGACGCGC
*
10208 AATGAGCGTCATA
1 AATGCGCGTCATA
*
10221 AATGCGCGCCATA
1 AATGCGCGTCATA
**
10234 AATGCATGTCATA
1 AATGCGCGTCATA
* *
10247 AATGTGTGTCATA
1 AATGCGCGTCATA
*
10260 AATGTGCGTCATA
1 AATGCGCGTCATA
10273 AAT
1 AAT
10276 TTATGACGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:21043 original size:24 final size:23
Alignment explanation
Indices: 20993--21066 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
20983 GCTTCAACTT
* *
20993 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
21016 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
21040 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
21063 TTTG
1 TTTG
21067 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:23580 original size:23 final size:23
Alignment explanation
Indices: 23554--23622 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
23544 ACATCTTATA
* *
23554 CGGCACTACAGTGCATTTCTACG
1 CGGCACTTCGGTGCATTTCTACG
* *
23577 CGGCACTTCGGTGCAATTCTATG
1 CGGCACTTCGGTGCATTTCTACG
* *
23600 TGGCACTTCGGTGCATTTATACG
1 CGGCACTTCGGTGCATTTCTACG
23623 AACTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
CGGCACTTCGGTGCATTTCTACG
Found at i:24710 original size:26 final size:28
Alignment explanation
Indices: 24673--24733 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
24663 AATATATATA
* * *
24673 ATAATATGTATT-TA-TTAAAAAACTAT
1 ATAATATATATTATATTTAAAAAACAAC
*
24699 ATAATATATATTATATTTCAAAAACAAC
1 ATAATATATATTATATTTAAAAAACAAC
24727 ATAATAT
1 ATAATAT
24734 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.38
27 2 0.07
28 16 0.55
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAATATATATTATATTTAAAAAACAAC
Found at i:24721 original size:29 final size:29
Alignment explanation
Indices: 24667--24722 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
24657 ACTAATAATA
*
24667 TATATAATAATATGTATTTATTAAAAAAC
1 TATATAATAATATGTATTTATCAAAAAAC
24696 TATATAATATATAT-TATATT-TCAAAAA
1 TATATAATA-ATATGTAT-TTATCAAAAA
24723 CAACATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAATAATATGTATTTATCAAAAAAC
Found at i:24795 original size:23 final size:24
Alignment explanation
Indices: 24767--24848 Score: 123
Period size: 23 Copynumber: 3.4 Consensus size: 24
24757 CAAAAACCCG
24767 TTTTAAAAACTATATTATATAT-T
1 TTTTAAAAACTATATTATATATGT
24790 TTTTAAAAACTATA-TATTATATGT
1 TTTTAAAAACTATATTA-TATATGT
*
24814 TTTCAAAAACTATATTATATAATGT
1 TTTTAAAAACTATATTATAT-ATGT
24839 TTTTAAAAAC
1 TTTTAAAAAC
24849 CATTTTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.04
23 19 0.36
24 17 0.32
25 15 0.28
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTAAAAACTATATTATATATGT
Found at i:24861 original size:38 final size:38
Alignment explanation
Indices: 24813--24911 Score: 123
Period size: 38 Copynumber: 2.6 Consensus size: 38
24803 ATATTATATG
*
24813 TTTTCAAAAACTATATTATATA-ATGTTTTTAAAAACCA
1 TTTTCAAAAACTATATTATATATATATTTTTAAAAA-CA
* *
24851 TTTTAAAAAACTATA-TAT-TATATATTTTTAAAAATA
1 TTTTCAAAAACTATATTATATATATATTTTTAAAAACA
24887 TGTTTCCAAAAACTATATTATATAT
1 T-TTT-CAAAAACTATATTATATAT
24912 CTTCAAAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
36 4 0.08
37 18 0.35
38 24 0.46
39 3 0.06
40 3 0.06
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (38 bp):
TTTTCAAAAACTATATTATATATATATTTTTAAAAACA
Found at i:24910 original size:36 final size:35
Alignment explanation
Indices: 24808--24920 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 35
24798 ACTATATATT
24808 ATATGTTTTCAAAAACTATATTATATAATGTTTTTAAAA
1 ATATG-TTTCAAAAACTATATTATAT-A--TTTTTAAAA
* *
24847 ACCAT-TTTAAAAAACTATATATTATATATTTTTAAAA
1 A-TATGTTTCAAAAAC--TATATTATATATTTTTAAAA
* *
24884 ATATGTTTCCAAAAACTATATTATATATCTTCAAAA
1 ATATGTTT-CAAAAACTATATTATATATTTTTAAAA
24920 A
1 A
24921 CTATATATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
36 21 0.33
37 13 0.21
38 15 0.24
39 2 0.03
40 12 0.19
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (35 bp):
ATATGTTTCAAAAACTATATTATATATTTTTAAAA
Found at i:25477 original size:16 final size:15
Alignment explanation
Indices: 25444--25480 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
25434 TCTTTTCATG
25444 TATACTAATAATATTA
1 TATA-TAATAATATTA
25460 TATATAATAATATGTA
1 TATATAATAATAT-TA
25476 TATAT
1 TATAT
25481 TAAAAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (15 bp):
TATATAATAATATTA
Found at i:25495 original size:29 final size:28
Alignment explanation
Indices: 25460--25526 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
25450 AATAATATTA
25460 TATATAATA-ATATGTATATATTAAAAAAC
1 TATATAATATATAT-TATAT-TTAAAAAAC
*
25489 TATATAATATATATTATATTTCAAAAAC
1 TATATAATATATATTATATTTAAAAAAC
* *
25517 AACATAATAT
1 TATATAATAT
25527 GTTTTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 16 0.47
29 14 0.41
30 4 0.12
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (28 bp):
TATATAATATATATTATATTTAAAAAAC
Found at i:25678 original size:14 final size:14
Alignment explanation
Indices: 25659--25687 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25649 AAACTATATT
25659 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
25673 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
25687 A
1 A
25688 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:25709 original size:38 final size:37
Alignment explanation
Indices: 25543--25750 Score: 162
Period size: 38 Copynumber: 5.6 Consensus size: 37
25533 AAATATTATA
* ** *
25543 TATATTATATACGTTTT-AAAAATCCGATTTTAAAAAC
1 TATA-TATATATGTTTTCAAAAATATGTTTTTAAAAAC
* *
25580 TATATATATATATATATTCAAAATAATATGTTTTCAAAAAC
1 TATATATATATGT-T-TTC-AAA-AATATGTTTTTAAAAAC
* ***
25621 ----TATATATG-TTTCAAAAAAAACCTTTTAAAAAC
1 TATATATATATGTTTTCAAAAATATGTTTTTAAAAAC
*
25653 TATAT-TATATGTTTTCAAAAATATGTTTTCAAAAAC
1 TATATATATATGTTTTCAAAAATATGTTTTTAAAAAC
* * *
25689 TATATTATATATATTTTCAAAAA-CTGTTTTTTAAAAAT
1 TATA-TATATATGTTTTCAAAAATATG-TTTTTAAAAAC
25727 TATATATTATATGTTTTCAAAAAT
1 TATATA-TATATGTTTTCAAAAAT
25751 TATATTATAT
Statistics
Matches: 134, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
32 12 0.09
33 3 0.02
34 3 0.02
35 7 0.05
36 31 0.23
37 17 0.13
38 45 0.34
40 3 0.02
41 13 0.10
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATATATATGTTTTCAAAAATATGTTTTTAAAAAC
Found at i:25747 original size:62 final size:61
Alignment explanation
Indices: 25673--25810 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 61
25663 GTTTTCAAAA
** *
25673 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACTGTTTTTTAAAAATTATATATT
1 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAAC-CATTTTAAAAAATTATATATT
* * *
25735 ATATGTTTTCAAAAATTATATTATATATGTTTTTAAAAACCATTTTAAAAAATTATATATT
1 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACCATTTTAAAAAATTATATATT
*
25796 ATATGTTTTTAAAAA
1 ATATGTTTTCAAAAA
25811 TATGTTTCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 32 0.46
62 37 0.54
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (61 bp):
ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACCATTTTAAAAAATTATATATT
Found at i:25748 original size:24 final size:24
Alignment explanation
Indices: 25716--25773 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
25706 CAAAAACTGT
25716 TTTTTAAAAATTATA-TATTATATG
1 TTTTTAAAAATTATATTA-TATATG
*
25740 TTTTCAAAAATTATATTATATATG
1 TTTTTAAAAATTATATTATATATG
25764 TTTTTAAAAA
1 TTTTTAAAAA
25774 CCATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
TTTTTAAAAATTATATTATATATG
Found at i:25799 original size:37 final size:37
Alignment explanation
Indices: 25740--25810 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
25730 ATATTATATG
*
25740 TTTTCAAAAATTATATTATATATGTTTTTAAAAACCA
1 TTTTAAAAAATTATATTATATATGTTTTTAAAAACCA
25777 TTTTAAAAAATTATA-TATTATATGTTTTTAAAAA
1 TTTTAAAAAATTATATTA-TATATGTTTTTAAAAA
25811 TATGTTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTTAAAAAATTATATTATATATGTTTTTAAAAACCA
Found at i:25824 original size:39 final size:38
Alignment explanation
Indices: 25735--25837 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 38
25725 ATTATATATT
25735 ATATGTTTTC-AAAAATTATATTATATATGTTTTTAAAA
1 ATATG-TTTCAAAAAATTATATTATATATGTTTTTAAAA
*
25773 ACCAT-TTT-AAAAAATTATA-TATTATATGTTTTTAAAA
1 A-TATGTTTCAAAAAATTATATTA-TATATGTTTTTAAAA
* * *
25810 ATATGTTTCCAAAAACTATACTATATAT
1 ATATGTTTCAAAAAATTATATTATATAT
25838 CTTCAAAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
36 4 0.07
37 32 0.58
38 15 0.27
39 4 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
ATATGTTTCAAAAAATTATATTATATATGTTTTTAAAA
Found at i:26032 original size:2 final size:2
Alignment explanation
Indices: 26025--26049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26015 ACCATGCTTC
26025 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
26050 ATTGTCAATC
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:33728 original size:31 final size:31
Alignment explanation
Indices: 33691--33778 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
33681 TAAATTATGT
* * * *
33691 TTTTAGTACTTAAATTATTAATTTTAATATA
1 TTTTAGTAATTAAACTATCAATTTTAATACA
* * *
33722 TTTTAGTATTTAAACTATCAGTTTTAATCCA
1 TTTTAGTAATTAAACTATCAATTTTAATACA
*
33753 TTTTAGTAATTAAACTTTCAAATTTT
1 TTTTAGTAATTAAACTATC-AATTTT
33779 TTTTAAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 42 0.89
32 5 0.11
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTTAGTAATTAAACTATCAATTTTAATACA
Found at i:35897 original size:7 final size:7
Alignment explanation
Indices: 35885--35916 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
35875 TGTGATAAGA
35885 TTTAGGG
1 TTTAGGG
35892 TTTAGGG
1 TTTAGGG
35899 TTTAGGG
1 TTTAGGG
*
35906 TTTAGAG
1 TTTAGGG
35913 TTTA
1 TTTA
35917 TGTGATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:35949 original size:14 final size:14
Alignment explanation
Indices: 35880--35956 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 14
35870 AATTATGTGA
*
35880 TAAGATTTAGGGTT
1 TAAGGTTTAGGGTT
*
35894 TAGGGTTTAGGGTT
1 TAAGGTTTAGGGTT
*
35908 T-AGAGTTTATGTGATAT
1 TAAG-GTTTA-G-GGT-T
*
35925 AATAAGATTTAGGGTT
1 --TAAGGTTTAGGGTT
35941 TAAGGTTTAGGGTT
1 TAAGGTTTAGGGTT
35955 TA
1 TA
35957 TGTGATATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 1 0.02
14 33 0.67
15 1 0.02
16 3 0.06
17 3 0.06
18 1 0.02
19 5 0.10
20 2 0.04
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (14 bp):
TAAGGTTTAGGGTT
Found at i:35993 original size:21 final size:21
Alignment explanation
Indices: 35944--36061 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
35934 TAGGGTTTAA
* * *
35944 GGTTTAGGGTTTATGTGATAT
1 GGTTTAGGGTTTATATGTTAG
* * *
35965 GATGTAAGGTTTATATGTTAG
1 GGTTTAGGGTTTATATGTTAG
*
35986 GGTTTAAGGTTTATATGTTAG
1 GGTTTAGGGTTTATATGTTAG
*
36007 GGTTTAGGGTTTATATGATAG
1 GGTTTAGGGTTTATATGTTAG
*
36028 GGTTTAGGGTTTTTATGTTAAG
1 GGTTTAGGGTTTATATGTT-AG
36050 GG-TTAGGGTTTA
1 GGTTTAGGGTTTA
36062 AGTTATGCAC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 79 0.95
22 4 0.05
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTATATGTTAG
Found at i:38360 original size:15 final size:16
Alignment explanation
Indices: 38336--38368 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38326 ATTCTTATCA
*
38336 TAAAATAACT-ATTCC
1 TAAAAAAACTCATTCC
38351 TAAAAAAACTCATTCC
1 TAAAAAAACTCATTCC
38367 TA
1 TA
38369 TATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAACTCATTCC
Found at i:43752 original size:105 final size:105
Alignment explanation
Indices: 43545--43767 Score: 270
Period size: 105 Copynumber: 2.1 Consensus size: 105
43535 GATTTCCCAT
* * * * *
43545 AAGGACCACATA-TAAATTCCTTAAAAACCATATACATATAACAAGGATCAAGTAAGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAAAACCATATACATATAACAAGGACCAAATAAGTGTCGCAA
43609 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
43649 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATAT-GCTAAGGACCAAATATGTGTCGCA
1 AAGGACCACGTAGAAAATTCCTTAAAAACCATATACATATAAC-AAGGACCAAATAAGTGTCGCA
* * * * * * *
43713 AAGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
65 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
43754 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
43768 CCCTCGACTC
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 12 0.12
105 88 0.88
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAAAACCATATACATATAACAAGGACCAAATAAGTGTCGCAA
AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:45272 original size:21 final size:21
Alignment explanation
Indices: 45248--45290 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45238 TCTAGTTCGT
* *
45248 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
45269 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
45290 T
1 T
45291 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:49311 original size:13 final size:13
Alignment explanation
Indices: 49267--49312 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
49257 TGAGTCAACT
49267 CGTTGACTTTGAC
1 CGTTGACTTTGAC
* *
49280 CTGTTGACGTTGAT
1 C-GTTGACTTTGAC
49294 CGTTGACTTTGAC
1 CGTTGACTTTGAC
*
49307 AGTTGA
1 CGTTGA
49313 TTGTTGACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (13 bp):
CGTTGACTTTGAC
Found at i:49311 original size:20 final size:19
Alignment explanation
Indices: 49283--49326 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
49273 CTTTGACCTG
49283 TTGACGTTGATCGTTGACT
1 TTGACGTTGATCGTTGACT
*
49302 TTGACAGTTGATTGTTGACT
1 TTGAC-GTTGATCGTTGACT
49322 TTGAC
1 TTGAC
49327 CCAAAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (19 bp):
TTGACGTTGATCGTTGACT
Found at i:58182 original size:13 final size:14
Alignment explanation
Indices: 58157--58186 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
58147 TGAATTTTAT
58157 TTTCTTAAAAATCA
1 TTTCTTAAAAATCA
58171 TTTCTT-AAAATCA
1 TTTCTTAAAAATCA
58184 TTT
1 TTT
58187 TTACGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTCTTAAAAATCA
Found at i:59361 original size:24 final size:23
Alignment explanation
Indices: 59319--59367 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
59309 AATTACATTG
59319 AAATTATATTAAAACTATAATGTT
1 AAATTATATTAAAACTAT-ATGTT
*
59343 AAATTATAATT-AAATTATATGTT
1 AAATTAT-ATTAAAACTATATGTT
59366 AA
1 AA
59368 TATGTGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 13 0.57
25 3 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTATATTAAAACTATATGTT
Found at i:59958 original size:18 final size:18
Alignment explanation
Indices: 59935--59970 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
59925 TGAACGAAAC
59935 TAACCTATAACTTCAACA
1 TAACCTATAACTTCAACA
59953 TAACCTATAACTTCAACA
1 TAACCTATAACTTCAACA
59971 AAAAGAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (18 bp):
TAACCTATAACTTCAACA
Found at i:68831 original size:24 final size:24
Alignment explanation
Indices: 68795--68861 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
68785 CAGAGGGCTC
*
68795 GTTCGTTCATTTATGTTTGTTTAT
1 GTTCGTTCATTTATGTTTATTTAT
* *
68819 GTTCGTTCGTTTATGTTCATTTAT
1 GTTCGTTCATTTATGTTTATTTAT
*
68843 GTGCGTTCATTTATGTTTA
1 GTTCGTTCATTTATGTTTA
68862 GTCCAATCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.58
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTTATTTAT
Found at i:69150 original size:14 final size:14
Alignment explanation
Indices: 69133--69163 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
69123 GTTTACATAT
69133 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
69147 GTTCATTTGTGTTC
1 GTTCATTTATGTTC
69161 GTT
1 GTT
69164 TATCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:69540 original size:19 final size:19
Alignment explanation
Indices: 69497--69545 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
69487 CATATTGGTA
69497 AAAATAGTTAAATTTTAACT
1 AAAATA-TTAAATTTTAACT
* *
69517 TAAATCTTAAATTTTAGAC-
1 AAAATATTAAATTTTA-ACT
69536 AAAATATTAA
1 AAAATATTAA
69546 TTTAACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (19 bp):
AAAATATTAAATTTTAACT
Found at i:70433 original size:28 final size:25
Alignment explanation
Indices: 70402--70453 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
70392 ATTTCAAAAT
70402 TATAATTATGAGAAAAAAATAATTTATA
1 TATAATTAT-A-AAAAAAAT-ATTTATA
* *
70430 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
70454 TTAGTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:70854 original size:28 final size:26
Alignment explanation
Indices: 70822--70876 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
70812 TGAAAATATT
*
70822 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
70850 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
70876 T
1 T
70877 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:72133 original size:3 final size:3
Alignment explanation
Indices: 72127--72183 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
72117 TAATATTTAT
*
72127 TAA TAA TAAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
72173 T-A TAAA TAA TA
1 TAA T-AA TAA TA
72184 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:72537 original size:124 final size:123
Alignment explanation
Indices: 72318--72712 Score: 378
Period size: 124 Copynumber: 3.3 Consensus size: 123
72308 GTTGAATAAA
* * * *
72318 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCACTG--GGGATGATGTTGACC
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGAAAGGATGATGCTAACC
* * * *
72381 TATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
63 TATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
72442 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAGGTTGATGCTAATCTA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-GAAAGGATGATGCTAACCTA
* * *
72507 TCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTC
65 TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
72566 TTC-TTC---TTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAA--A--A----AA-CTGA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAGGATGATGCTAACCT-A
* * * * * * **
72617 --TCCATCAAGTGATGGATTTGA-GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
65 TCTCCTTC-TGTGATAGA-ATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
72675 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACT
72713 CGAACTGGAA
Statistics
Matches: 234, Mismatches: 26, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
108 4 0.02
109 45 0.19
110 7 0.03
113 27 0.12
114 1 0.00
118 3 0.01
119 6 0.03
120 27 0.12
121 3 0.01
122 31 0.13
123 8 0.03
124 72 0.31
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAGGATGATGCTAACCTAT
CTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
Found at i:72737 original size:113 final size:113
Alignment explanation
Indices: 72516--73247 Score: 897
Period size: 113 Copynumber: 6.5 Consensus size: 113
72506 ATCTGCTTCT
* ** *
72516 GTGATAGAA-TTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-CTTCTTCA
1 GTGAT-GAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
72576 GATGAGTTCTTCTCATTATGAACTTCT--CTGGAAAAAACTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAAC-TCTAACTGG-AAAAGCTGATCCATCAA
* * *
72625 GTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
72690 ATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAA
* * *
72738 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * **
72803 ACGAGTTCTTCTCATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAAC-TCTAACTGGAAAAGCTGATCCATCAA
* * *
72852 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--
* * * * *
72917 ACGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAA
64 A-GATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAA
* * *
72968 ATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * * * *
73033 ATGAGTTCTTCTTATTATGAACTCGAATTGGTAATGTTGATCCATTGAA
66 ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCA-TCAA
* * * *
73082 -TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * ** * *
73146 GTGAGTTCTTCTCATTATGAACTCTAACTGGTACTGCTGTTCCA-CTGA
66 ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATC-AA
* * *
73194 GTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
1 GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
73248 GGAAAAGCTG
Statistics
Matches: 555, Mismatches: 54, Indels: 24
0.88 0.09 0.04
Matches are distributed among these distances:
108 2 0.00
109 36 0.06
112 9 0.02
113 316 0.57
114 93 0.17
116 77 0.14
117 22 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (113 bp):
GTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAA
Found at i:73012 original size:343 final size:338
Alignment explanation
Indices: 72516--73247 Score: 933
Period size: 343 Copynumber: 2.2 Consensus size: 338
72506 ATCTGCTTCT
* * *
72516 GTGATAGAA-TTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTTCTTCTTCAG
1 GTGAT-GAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCTTCAG
* * * * * *
72577 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAAACTGATCCATCAAGTGATGGATTTGAGCAA
65 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAAACTAATCCATCAAATAATGAATTTAAACAA
72642 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
130 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* ** *
72707 TGAACTCGAACTGGAAAAGCTGATCCA-TCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC
195 TGAACTCGAACTGGAAAAGCTGATCCATTCAA-TGATGAATTCAAGCAAAAAGTTGAACAAATTC
* * **
72771 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTTTTTTCTGGA
259 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAAC-TCTAACTGGA
72836 AAAGCTGATCCA-TCAA
323 AAAGCTGATCCACT-AA
* * *
72852 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTT-CTTCTTC--
* ***
72917 ACGATGAGTTCTTCTCATTATGAAC-TCTACCTGG-CAATGTTAATCCATCAAATAATGAATTTA
63 A-GATGAGTTCTTCTCATTATGAACTTCT--CTGGAAAAAACTAATCCATCAAATAATGAATTTA
*
72980 AACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
125 AACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
73045 TATTATGAACTCGAATTGGTAATGTTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAA
190 CATTATGAACTCGAACTGGAAAAGCTGATCCATTCAATGATGAATTCAAGCAAAAAGTTGAACAA
* * **
73110 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGGTGAGTTCTTCTCATTATGAACTCTAACT
255 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTAACT
* ** * *
73175 GGTACTGCTGTTCCACTGA
320 GGAAAAGCTGATCCACTAA
*
73194 GTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTT-TTCT
1 GTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTTCTTCT
73248 GGAAAAGCTG
Statistics
Matches: 339, Mismatches: 44, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
335 2 0.01
336 37 0.11
339 6 0.02
340 7 0.02
342 66 0.19
343 214 0.63
344 7 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (338 bp):
GTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAAACTAATCCATCAAATAATGAATTTAAACAAA
AAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCGAACTGGAAAAGCTGATCCATTCAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTAACTGGAAAA
GCTGATCCACTAA
Found at i:73236 original size:73 final size:73
Alignment explanation
Indices: 73149--73312 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
73139 TCTTTAGGTG
* ** * * *
73149 AGTTCTTCTCATTATGAACTCTAACTGGTACTGCTGTTCCA-CTGAGTGATGAATTTAAGCAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATC-AAATGATGAATTTAAGCAAAA
73213 AGTTGAACA
65 AGTTGAACA
* ** * * *
73222 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAA
73287 GTTGAACA
66 GTTGAACA
*
73295 AATTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
73313 TTTCTTCTTC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 76 0.99
74 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAA
GTTGAACA
Found at i:74258 original size:115 final size:114
Alignment explanation
Indices: 74096--74325 Score: 372
Period size: 115 Copynumber: 2.0 Consensus size: 114
74086 GATCATACAG
* * * * *
74096 TTCATCTTTTAATTCCAATGATTGGTTATGTGGTTCCTCCTGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATCCTAAACCAGATCAGATAACTCAAAGA
74161 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCACA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCACA
*
74210 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACC-AAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGG-TTATGGGGTTCAT-CCTAAACCAGATCAGATAACTCAAA
*
74274 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
64 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCACA
74325 T
1 T
74326 GGCACTTGCT
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 23 0.21
115 82 0.77
116 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATCCTAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCACA
Found at i:75680 original size:1 final size:1
Alignment explanation
Indices: 75676--75755 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
75666 CTTGACCCCC
* * * * * * * * * * *
75676 TTTTTTCTTTTTTTTCTTCTTTTTTTTCTTCTTCTTTTTTTCTTCTTTTTTTGTTCTTTTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
75741 TTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTT
75756 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (1 bp):
T
Found at i:75697 original size:12 final size:12
Alignment explanation
Indices: 75676--75738 Score: 85
Period size: 12 Copynumber: 5.2 Consensus size: 12
75666 CTTGACCCCC
75676 TTTT-TTCTTTT
1 TTTTCTTCTTTT
75687 TTTTCTTCTTTT
1 TTTTCTTCTTTT
75699 TTTTCTTCTTCTTT
1 TTTTCTTC-T-TTT
75713 TTTTCTTC-TTT
1 TTTTCTTCTTTT
*
75724 TTTTGTTCTTTT
1 TTTTCTTCTTTT
75736 TTT
1 TTT
75739 ATTTTTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
11 14 0.30
12 21 0.45
13 1 0.02
14 11 0.23
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTCTTCTTTT
Found at i:75702 original size:14 final size:14
Alignment explanation
Indices: 75683--75759 Score: 83
Period size: 12 Copynumber: 5.9 Consensus size: 14
75673 CCCTTTTTTC
75683 TTTTTTTTCTTC--
1 TTTTTTTTCTTCTT
75695 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
*
75709 CTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
*
75723 TTTTTGTTCTT-TT
1 TTTTTTTTCTTCTT
* *
75736 TTTATTTT-TT-AT
1 TTTTTTTTCTTCTT
75748 TTTTTTTTCTTC
1 TTTTTTTTCTTC
75760 AAGCATAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
12 22 0.41
13 10 0.19
14 22 0.41
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:75754 original size:11 final size:11
Alignment explanation
Indices: 75676--75755 Score: 81
Period size: 11 Copynumber: 7.1 Consensus size: 11
75666 CTTGACCCCC
75676 TTTTTTCTTTT
1 TTTTTTCTTTT
75687 TTTTCTTCTTTT
1 TTTT-TTCTTTT
*
75699 TTTTCTTCTTCT
1 TTTT-TTCTTTT
*
75711 TTTTTTCTTCT
1 TTTTTTCTTTT
* *
75722 TTTTTTGTTCT
1 TTTTTTCTTTT
*
75733 TTTTTTATTTT
1 TTTTTTCTTTT
75744 TTATTTT-TTTT
1 TT-TTTTCTTTT
75755 T
1 T
75756 CTTCAAGCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
11 37 0.59
12 26 0.41
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:83122 original size:15 final size:15
Alignment explanation
Indices: 83099--83130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
83089 CATGAAATGT
83099 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
83114 AATGTATGTATGCAA
1 AATGAATGTATGCAA
83129 AA
1 AA
83131 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:86467 original size:19 final size:19
Alignment explanation
Indices: 86426--86467 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
86416 TATTAATAAG
*
86426 AAAATATATAAATATTATG
1 AAAATATATAAATATTATA
*
86445 AAAATA-ATAAGTATATATA
1 AAAATATATAAATAT-TATA
86464 AAAA
1 AAAA
86468 ATTTGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATATATAAATATTATA
Found at i:86474 original size:28 final size:30
Alignment explanation
Indices: 86410--86476 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
86400 TGCAAATAAA
*
86410 ATGAAATATTAATAAGAAAATATATAAATATT
1 ATGAAA-A-TAATAAGAAAATATATAAAAATT
* *
86442 ATGAAAATAATAAGTATATATA-AAAAATT
1 ATGAAAATAATAAGAAAATATATAAAAATT
86471 -TGAAAA
1 ATGAAAA
86477 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 6 0.19
30 13 0.41
31 1 0.03
32 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (30 bp):
ATGAAAATAATAAGAAAATATATAAAAATT
Found at i:86978 original size:28 final size:25
Alignment explanation
Indices: 86947--86998 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
86937 ATTTCAAAAT
86947 TATAATTATGAGAAAAAAATAATTTATA
1 TATAATTAT-A-AAAAAAAT-ATTTATA
* *
86975 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
86999 TTAGTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:87399 original size:28 final size:26
Alignment explanation
Indices: 87367--87421 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
87357 TGAAAATATT
*
87367 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
87395 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
87421 T
1 T
87422 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:88682 original size:3 final size:3
Alignment explanation
Indices: 88676--88739 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
88666 TAATATTTAT
*
88676 TAA TAA TAA -AA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88723 TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
88740 TTTAAATGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 50 0.89
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:89736 original size:23 final size:23
Alignment explanation
Indices: 89703--89746 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
89693 GAGTAGAGGG
*
89703 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGAGACAAT
*
89726 TCTACGTGGTCCTTCGAGACA
1 TCTACGCGGTCCTTCGAGACA
89747 TATATGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGAGACAAT
Found at i:89940 original size:24 final size:25
Alignment explanation
Indices: 89874--89950 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 25
89864 ACTACGGTGC
* *
89874 AATTCTACGTGACATTTCGGTG-CA
1 AATTCTACGTGGCACTTCGGTGACA
* *
89898 AATTTTTACGCGGTC-CTTCGG-GACA
1 AA-TTCTACGTGG-CACTTCGGTGACA
89923 AATTCTACGTGGCACTTCGGTGA-A
1 AATTCTACGTGGCACTTCGGTGACA
89947 AATT
1 AATT
89951 TATATGAGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
23 1 0.02
24 22 0.52
25 18 0.43
26 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (25 bp):
AATTCTACGTGGCACTTCGGTGACA
Found at i:90530 original size:12 final size:12
Alignment explanation
Indices: 90513--90558 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
90503 TTTTTAGCAT
90513 CGGTACTGTTCA
1 CGGTACTGTTCA
90525 CGGTACTGTTCA
1 CGGTACTGTTCA
* *
90537 --TTACTATTCA
1 CGGTACTGTTCA
*
90547 CGGTATTGTTCA
1 CGGTACTGTTCA
90559 TTAATGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:90546 original size:22 final size:22
Alignment explanation
Indices: 90516--90561 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
90506 TTAGCATCGG
*
90516 TACTGTTCACGGTACTGTTCAT
1 TACTATTCACGGTACTGTTCAT
*
90538 TACTATTCACGGTATTGTTCAT
1 TACTATTCACGGTACTGTTCAT
90560 TA
1 TA
90562 ATGTTCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (22 bp):
TACTATTCACGGTACTGTTCAT
Found at i:90568 original size:22 final size:22
Alignment explanation
Indices: 90519--90568 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
90509 GCATCGGTAC
*
90519 TGTTCACGGTACTGTTCATTAC
1 TGTTCACGGTACTGTTCATTAA
* *
90541 TATTCACGGTATTGTTCATTAA
1 TGTTCACGGTACTGTTCATTAA
90563 TGTTCA
1 TGTTCA
90569 TAGTACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAA
Found at i:92556 original size:23 final size:23
Alignment explanation
Indices: 92522--92590 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
92512 CACCACATCT
* *
92522 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * ** *
92545 CGTAGAATTGCACCTAAGTATCG
1 CGTAGAAATGCACCAAAGTGCCA
92568 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
92591 TATAAGATGT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:94129 original size:21 final size:22
Alignment explanation
Indices: 94096--94139 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
94086 GATGTTCAAT
*
94096 ATTTGAGAGTGCATCGATACAC
1 ATTTAAGAGTGCATCGATACAC
*
94118 ATTTAAGA-TGCATCGATGCAC
1 ATTTAAGAGTGCATCGATACAC
94139 A
1 A
94140 CAACCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (22 bp):
ATTTAAGAGTGCATCGATACAC
Found at i:94637 original size:7 final size:7
Alignment explanation
Indices: 94597--94623 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
94587 CTTCACGTAT
94597 GAAGAAA
1 GAAGAAA
94604 GAAGAAA
1 GAAGAAA
94611 GAAGAAA
1 GAAGAAA
94618 GAAGAA
1 GAAGAA
94624 GAGGAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:97325 original size:18 final size:18
Alignment explanation
Indices: 97291--97326 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
97281 GAGCCATCTT
*
97291 ACCGAGTCGATCAAGCCG
1 ACCGAGTCGAACAAGCCG
*
97309 ACCGAGTCGAACGAGCCG
1 ACCGAGTCGAACAAGCCG
97327 CGATCTAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.33, G:0.31, T:0.08
Consensus pattern (18 bp):
ACCGAGTCGAACAAGCCG
Found at i:101862 original size:7 final size:7
Alignment explanation
Indices: 101847--101876 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
101837 ATATAAAGTA
101847 TGATTTC
1 TGATTTC
*
101854 TGATATC
1 TGATTTC
101861 TGATTTC
1 TGATTTC
101868 TGATTTC
1 TGATTTC
101875 TG
1 TG
101877 TCACAATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
TGATTTC
Found at i:109188 original size:76 final size:76
Alignment explanation
Indices: 109074--109216 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 76
109064 CTGTAATCCA
* * ** * *
109074 AATTTCTTTATATTAGTTGTTCATTTTATTAAAGGTGCTCACCCTGAAATTTTATTTGGGTCCAC
1 AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
109139 CTTGAAATCTG
66 CTTGAAATCTG
* * * *
109150 AATTTCTTTATGTTAATCGTTCATTTTACGAAATGTGCTCACATTGAAATTTTATTTGTGTCAAC
1 AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
109215 CT
66 CT
109217 CGTACGAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 57 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (76 bp):
AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
CTTGAAATCTG
Found at i:110827 original size:38 final size:38
Alignment explanation
Indices: 110738--110844 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
110728 GTATGTTCAA
* * * **
110738 TTAGTTTATGTTCACAAACAAGCTCATTTATCGACTTT
1 TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
* *
110776 TTAGTTGAGGTTCATAAACAAGCTCGTTTATCAACTCG
1 TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
* * **
110814 TTCGTTTATGTTCATGAACAAATTCGTTTAT
1 TTAGTTTATGTTCATAAACAAGCTCGTTTAT
110845 AATTTTTTTA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (38 bp):
TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
Found at i:113054 original size:23 final size:23
Alignment explanation
Indices: 113036--113096 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
113026 CTCGTATAAA
113036 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
113059 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
113082 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
113097 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:113355 original size:30 final size:31
Alignment explanation
Indices: 113321--113379 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
113311 TATTGTATAG
113321 ACATATAAT-TTCCAT-ACCTTTATCACATGA
1 ACATATAATGTTCCATCA-CTTTATCACATGA
*
113351 ACATATCATGTTCCATCACTTTATCACAT
1 ACATATAATGTTCCATCACTTTATCACAT
113380 AGCTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATGA
Found at i:113456 original size:25 final size:25
Alignment explanation
Indices: 113423--113484 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
113413 CTTAATACAT
113423 ATAATATGAATTCATG-TCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
* *
113448 ATAATATGAAATGTGATCATGTATC
1 ATAATATGAATTATGATCATGTATC
*
113473 AAAATATTGAAT
1 ATAATA-TGAAT
113485 CTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:116978 original size:23 final size:23
Alignment explanation
Indices: 116944--116996 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
116934 CTCGTATAAA
*
116944 TGCACCGGAGTACCACATAGAAT
1 TGCACCGAAGTACCACATAGAAT
* *
116967 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTACCACATAGAAT
116990 TGCACCG
1 TGCACCG
116997 TAGTGGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTACCACATAGAAT
Found at i:117273 original size:31 final size:30
Alignment explanation
Indices: 117229--117288 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
117219 TGTTGTATAG
117229 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
117259 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
117289 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:122639 original size:190 final size:186
Alignment explanation
Indices: 122266--122650 Score: 515
Period size: 188 Copynumber: 2.0 Consensus size: 186
122256 ACTTTAACAT
* ** * * *
122266 ATTCAAAAGATAAACCCCTTTTACCATTCAAACTTAAATAGATATTATTTTAATTTAAAATATAC
1 ATTCAAAAGGTAAAATCATTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATATAC
* * *
122331 AAAAATATATAATTATCTTTAATATTTAAAGTTAAAAAGATAACAAATATTTTTTAAATTGACAT
66 AAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATAATTTTTAAATTGACAT
* *
122396 ATTCACAGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTGCA
131 ATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTGCA
* * *
122452 ATGGTCAAAAGGTAAAATCATTTTACTATTCAAACATAAACATATATTATTTTAATTTGAAATAT
1 AT--TCAAAAGGTAAAATCATTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATAT
* * *
122517 ACAAAAGTATTTAATTATATTTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTG
64 ACAAAAATATATAATTAT-CTTTAATATTCAAAATTAAAAAGATAACAAATA-ATTTTTAAATTG
* *
122582 AC-TCATTAAAAGAGTAATTATCCTATTAATATTCAAA-TAAA-AATTATCTTTTAATTTGCA
127 ACAT-ATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAA-TAT-ATTTAATTTGCA
122642 ATTCAAAAG
1 ATTCAAAAG
122651 AACTATGAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
186 2 0.01
188 77 0.45
189 38 0.22
190 56 0.32
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (186 bp):
ATTCAAAAGGTAAAATCATTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATATAC
AAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATAATTTTTAAATTGACAT
ATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTGCA
Found at i:123074 original size:29 final size:30
Alignment explanation
Indices: 123022--123081 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
123012 ATTTAATTTT
* *
123022 ATAAAAATAAAATTTATTTTAAATTTTAAA
1 ATAAAAATAAAATTTATTTCAAATATTAAA
123052 ATAAAATATAAAA-TTA-TTCAAATATTAAA
1 ATAAAA-ATAAAATTTATTTCAAATATTAAA
123081 A
1 A
123082 AAATTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 12 0.44
30 9 0.33
31 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAAAATAAAATTTATTTCAAATATTAAA
Found at i:123076 original size:16 final size:15
Alignment explanation
Indices: 123049--123113 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
123039 TTTAAATTTT
*
123049 AAAATAAAATATAAA
1 AAAATTAAATATAAA
**
123064 ATTATTCAAATATTAAA
1 AAAATT-AAATA-TAAA
123081 AAAATTAAATATAAA
1 AAAATTAAATATAAA
* * *
123096 AATACTAAAAATAAA
1 AAAATTAAATATAAA
123111 AAA
1 AAA
123114 TAATTTTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 21 0.54
16 10 0.26
17 8 0.21
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTAAATATAAA
Found at i:123920 original size:22 final size:22
Alignment explanation
Indices: 123865--123922 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
123855 TTTTAATATG
*
123865 TATATTCAATATTTTAGTAATTT
1 TATATTTAAT-TTTTAGTAATTT
* * *
123888 AAT-TTTTATTTTTAGTATTTT
1 TATATTTAATTTTTAGTAATTT
123909 TATATTTAATTTTT
1 TATATTTAATTTTT
123923 TGAATATCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 13 0.46
22 13 0.46
23 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
TATATTTAATTTTTAGTAATTT
Found at i:123923 original size:15 final size:15
Alignment explanation
Indices: 123889--123948 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
123879 TAGTAATTTA
* *
123889 ATTTTTATTTTTAGT
1 ATTTTTATATTTAAT
123904 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
*
123919 -TTTTTGAATATCTAAAT
1 ATTTTT--ATAT-TTAAT
*
123936 AATTTTATATTTA
1 ATTTTTATATTTA
123949 TAATTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 5 0.14
15 15 0.42
16 8 0.22
17 4 0.11
18 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Done.