Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001484.1 Hibiscus syriacus cultivar Beakdansim tig00002880_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: 1039362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:755664 original size:16 final size:15
Alignment explanation
Indices: 755640--755682 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
755630 GAGTAAACGA
*
755640 ATAAATATAAGAGAAT
1 ATAATTATAAGA-AAT
*
755656 ATAATTATAAGATAT
1 ATAATTATAAGAAAT
755671 A-AATTATAAGAA
1 ATAATTATAAGAA
755683 TATTGATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (15 bp):
ATAATTATAAGAAAT
Found at i:755675 original size:14 final size:15
Alignment explanation
Indices: 755638--755681 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
755628 TTGAGTAAAC
755638 GAATAAA-TATAAGA
1 GAATAAATTATAAGA
755652 GAATATAATTATAAGA
1 GAATA-AATTATAAGA
*
755668 -TATAAATTATAAGA
1 GAATAAATTATAAGA
755682 ATATTGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 15 0.56
15 5 0.19
16 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (15 bp):
GAATAAATTATAAGA
Found at i:760557 original size:23 final size:23
Alignment explanation
Indices: 760501--760559 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
760491 ATCTTATATA
* *
760501 GCACTACGGTACAATTCTAAGCG
1 GCACTTCGGTGCAATTCTAAGCG
* *
760524 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTAAGCG
760547 GCACTTCGGTGCA
1 GCACTTCGGTGCA
760560 TTTATACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTAAGCG
Found at i:760567 original size:23 final size:23
Alignment explanation
Indices: 760523--760567 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
760513 AATTCTAAGC
*
760523 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTATACGT
*
760546 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
760568 AGCTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGT
Found at i:762928 original size:2 final size:2
Alignment explanation
Indices: 762921--762951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
762911 ACGAGTGTTT
762921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
762952 TTCTAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:765887 original size:24 final size:24
Alignment explanation
Indices: 765841--765887 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
765831 TCCCGTTCAA
* *
765841 AATTTAATGTTAAGTTATGAAAAT
1 AATTAAATGTTAAGATATGAAAAT
* *
765865 AATTAAATGTTTAGATATTAAAA
1 AATTAAATGTTAAGATATGAAAA
765888 CATATCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (24 bp):
AATTAAATGTTAAGATATGAAAAT
Found at i:765918 original size:21 final size:21
Alignment explanation
Indices: 765894--765940 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
765884 AAAACATATC
*
765894 AAAATTGATAGTTTAGGTACT
1 AAAATTGATAATTTAGGTACT
765915 AAAATTGATAATTTAGGTACT
1 AAAATTGATAATTTAGGTACT
765936 AAAAT
1 AAAAT
765941 AAATCAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (21 bp):
AAAATTGATAATTTAGGTACT
Found at i:765990 original size:31 final size:31
Alignment explanation
Indices: 765920--766000 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
765910 GTACTAAAAT
*
765920 TGATAATTTAGGTACTAAAATAAATCAAAGA
1 TGATAATTTAGGTACTAAAACAAATCAAAGA
* ** *
765951 TGACAATTTAGGTACTAAAACGGATCAGAA-C
1 TGATAATTTAGGTACTAAAACAAATCA-AAGA
765982 TGATAATTTAGGTACTAAA
1 TGATAATTTAGGTACTAAA
766001 TACGTTAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (31 bp):
TGATAATTTAGGTACTAAAACAAATCAAAGA
Found at i:766173 original size:5 final size:5
Alignment explanation
Indices: 766163--766314 Score: 304
Period size: 5 Copynumber: 30.4 Consensus size: 5
766153 TACTTAGATA
766163 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
766213 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
766263 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
766313 AA
1 AA
766315 AGCCAAACCT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 147 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:767656 original size:2 final size:2
Alignment explanation
Indices: 767649--767681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
767639 ATTTTCCTAT
767649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
767682 TTTTTATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:767878 original size:2 final size:2
Alignment explanation
Indices: 767871--767909 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
767861 TACATACATT
767871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
767910 TTTATTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:771845 original size:14 final size:13
Alignment explanation
Indices: 771823--771906 Score: 71
Period size: 13 Copynumber: 6.4 Consensus size: 13
771813 CAAAAAGGGC
*
771823 AAAAAAAGAAAA-
1 AAAAAAAAAAAAG
* *
771835 AAAAGAAAAGAAG
1 AAAAAAAAAAAAG
771848 CAAAAAAAAAAAAG
1 -AAAAAAAAAAAAG
771862 AAAACAAAAAAAAG
1 AAAA-AAAAAAAAG
* * *
771876 AAAGAACAAAAAC
1 AAAAAAAAAAAAG
* *
771889 CAAAAAGAAAAAG
1 AAAAAAAAAAAAG
771902 AAAAA
1 AAAAA
771907 GGGACAAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
12 9 0.16
13 24 0.43
14 23 0.41
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:771852 original size:18 final size:17
Alignment explanation
Indices: 771831--771887 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
771821 GCAAAAAAAG
771831 AAAAAAAAGAAAAGAAGC
1 AAAAAAAAGAAAAGAA-C
771849 AAAAAAAA-AAAAGAAAAC
1 AAAAAAAAGAAAAG--AAC
771867 AAAAAAAAG-AAAGAAC
1 AAAAAAAAGAAAAGAAC
771883 AAAAA
1 AAAAA
771888 CCAAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 21 0.58
19 2 0.06
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAC
Found at i:771859 original size:22 final size:20
Alignment explanation
Indices: 771826--771906 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 20
771816 AAAGGGCAAA
771826 AAAAGAAAAAAAAGAAAAGAAGC
1 AAAA-AAAAAAAAGAAAA-AA-C
771849 AAAAAAAAAAAAG--AAAAC
1 AAAAAAAAAAAAGAAAAAAC
*
771867 AAAAAAAAGAAAGAACAAAAAC
1 AAAAAAAAAAAAG-A-AAAAAC
* *
771889 CAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAGAAAAA
771907 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
18 13 0.26
19 2 0.04
20 6 0.12
21 1 0.02
22 24 0.48
23 4 0.08
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAGAAAAAAC
Found at i:771861 original size:31 final size:31
Alignment explanation
Indices: 771823--771906 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 31
771813 CAAAAAGGGC
771823 AAAAAAAGAAAAAAAAGAAAAG-AAGCAA-AAA
1 AAAAAAAGAAAAAAAA-AAAAGAAAG-AACAAA
771854 AAAAAAAGAAAACAAAAAAAAGAAAGAACAAA
1 AAAAAAAGAAAA-AAAAAAAAGAAAGAACAAA
*
771886 AACCAAAAAGAAAAAGAAAAA
1 AA--AAAAAGAAAAAAAAAAA
771907 GGGACAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
31 19 0.40
32 12 0.26
33 6 0.13
34 10 0.21
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (31 bp):
AAAAAAAGAAAAAAAAAAAAGAAAGAACAAA
Found at i:771871 original size:35 final size:34
Alignment explanation
Indices: 771823--771907 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
771813 CAAAAAGGGC
*
771823 AAAAA-AAGAAAAAAAAGA-AAAGAAGCAAAAAAA
1 AAAAAGAAAAAAAAAAAGAGAAAGAA-CAAAAAAA
**
771856 AAAAAGAAAACAAAAAAA-AGAAAGAACAAAAACC
1 AAAAAGAAAA-AAAAAAAGAGAAAGAACAAAAAAA
*
771890 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAAAAAAAG
771908 GGACAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
33 11 0.25
34 20 0.45
35 13 0.30
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (34 bp):
AAAAAGAAAAAAAAAAAGAGAAAGAACAAAAAAA
Found at i:773624 original size:106 final size:106
Alignment explanation
Indices: 773498--774761 Score: 1998
Period size: 106 Copynumber: 12.0 Consensus size: 106
773488 ATATCGTGCC
* * *
773498 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* *
773562 CAAATTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * *
773604 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACTACTGATTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
773669 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
773710 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
773775 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
773816 ACTCAAGACAACGCAAGTTCAACTTCATGACGAATGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
773881 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
773922 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
773985 ----T------CAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
774016 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
774081 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
774122 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
774187 AATTTTGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
774228 ACTCCAGACAACGCAATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
774293 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
774334 ACTCCAGACAATGCAAGTTCAACTTCACGAGGAAGGGACCGCTGGTTGTCAACAAACAAATTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
774399 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
774440 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
774505 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
774546 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
774611 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
774652 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
774717 AATTTCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
774758 ACTC
1 ACTC
774762 GGAACAATGC
Statistics
Matches: 1072, Mismatches: 72, Indels: 28
0.91 0.06 0.02
Matches are distributed among these distances:
94 88 0.08
96 1 0.00
100 2 0.00
104 1 0.00
106 980 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:773944 original size:43 final size:43
Alignment explanation
Indices: 773896--774051 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
773886 CAGAGCCAAT
773896 TTCAACTTCAC-AGCGAAGGATATTGGACTTCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTTCAGACAACGCAAG
* * * * *
773939 TTCAACTTCACGACGAAGGGACTGTTGG-TTGTCAACAAACAACTTCTCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGGACT-T---CAGACAA---CGCAAG
* *
773990 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTTCAGACAACGCAAG
774033 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
774052 GACCGCTGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
43 37 0.42
44 5 0.06
45 6 0.07
46 6 0.07
48 6 0.07
49 5 0.06
50 4 0.04
51 20 0.22
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTTCAGACAACGCAAG
Found at i:774006 original size:51 final size:51
Alignment explanation
Indices: 773939--774088 Score: 154
Period size: 51 Copynumber: 3.1 Consensus size: 51
773929 ACAACGCAAG
*
773939 TTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCTCAAT
1 TTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCCCAAT
* * ** * * *
773990 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
1 TTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCCCAAT
* *
774033 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
1 TTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCCCAAT
774084 TTCAA
1 TTCAA
774089 AGCCAATTTC
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
43 20 0.27
44 3 0.04
45 3 0.04
46 8 0.11
48 8 0.11
49 5 0.07
50 3 0.04
51 25 0.33
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (51 bp):
TTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAACTTCCCAAT
Found at i:775564 original size:37 final size:37
Alignment explanation
Indices: 775512--775615 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
775502 ATTTTCGTCT
*
775512 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
775549 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** *
775586 TACTATTATTTAAACTCCTAAAAATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
775616 CCACAAGCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:776078 original size:2 final size:2
Alignment explanation
Indices: 776071--776099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
776061 CCTTATTATT
776071 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
776100 TAATTATATT
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:776181 original size:2 final size:2
Alignment explanation
Indices: 776174--776200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
776164 TTTCCTATTT
776174 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 T
776201 TATTTTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:776373 original size:19 final size:18
Alignment explanation
Indices: 776351--776386 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
776341 ATTTTTCATT
*
776351 TATTTATTATTATTATTAC
1 TATTTAGTATT-TTATTAC
776370 TATTTAGTATTTTATTA
1 TATTTAGTATTTTATTA
776387 TATATACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTAGTATTTTATTAC
Found at i:776420 original size:14 final size:14
Alignment explanation
Indices: 776401--776446 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
776391 TACATACATT
776401 TTTATATTTATATA
1 TTTATATTTATATA
* *
776415 TATATATATAT-TA
1 TTTATATTTATATA
776428 TTT-TATTTATACTA
1 TTTATATTTATA-TA
776442 TTTAT
1 TTTAT
776447 TTATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 6 0.24
13 4 0.16
14 14 0.56
15 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:776431 original size:28 final size:29
Alignment explanation
Indices: 776328--776433 Score: 68
Period size: 28 Copynumber: 3.8 Consensus size: 29
776318 TAGTTAATAT
* *
776328 TATATGTATAT-TTA-TTTT-TCATTTATT
1 TATATATATATATTACTTTTAT-ATTTATA
776355 TAT-TAT-TATTATTACTATTTAGTATTT-TA
1 TATATATATA-TATTACT-TTTA-TATTTATA
*
776384 T-TATATATACA-TACATTTTTATATTTATA
1 TATATATATATATTAC--TTTTATATTTATA
776413 TATATATATATATTA-TTTTAT
1 TATATATATATATTACTTTTAT
776434 TTATACTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 25
0.68 0.04 0.27
Matches are distributed among these distances:
25 2 0.03
26 3 0.05
27 6 0.10
28 16 0.26
29 16 0.26
30 16 0.26
31 3 0.05
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (29 bp):
TATATATATATATTACTTTTATATTTATA
Found at i:776432 original size:22 final size:21
Alignment explanation
Indices: 776380--776461 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
776370 TATTTAGTAT
* * * *
776380 TTTATTATATATACATACATT
1 TTTATTTTATATATATATATA
776401 TTTATATTTATATATATATATA
1 TTTAT-TTTATATATATATATA
* *
776423 TATTATTTTATTTATACTATTTA
1 T-TTATTTTATATATA-TATATA
776446 TTTATTTTCAT-TATAT
1 TTTATTTT-ATATATAT
776462 TTTTAGTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 6 0.12
22 33 0.65
23 12 0.24
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTTTATATATATATATA
Found at i:776434 original size:26 final size:25
Alignment explanation
Indices: 776377--776438 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
776367 TACTATTTAG
776377 TATTTTA-TTATATATACATACATT
1 TATTTTATTTATATATACATACATT
* * *
776401 T-TTATATTTATATATATATATATAT
1 TATTTTATTTATATATACATACAT-T
776426 TATTTTATTTATA
1 TATTTTATTTATA
776439 CTATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.13
24 15 0.48
25 2 0.06
26 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTTATTTATATATACATACATT
Found at i:776443 original size:17 final size:16
Alignment explanation
Indices: 776398--776452 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
776388 ATATACATAC
* *
776398 ATTTTTATATTTATAT
1 ATTTATATATTTATTT
*
776414 ATATATATATATTATTTT
1 ATTTATATAT-TTA-TTT
776432 ATTTATACTATTTATTT
1 ATTTATA-TATTTATTT
776449 ATTT
1 ATTT
776453 TCATTATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 8 0.25
17 10 0.31
18 11 0.34
19 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATATTTATTT
Found at i:782876 original size:16 final size:16
Alignment explanation
Indices: 782855--782887 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
782845 TAAATCCACC
782855 TCATTAGAGATGATCA
1 TCATTAGAGATGATCA
782871 TCATTAGAGATGATCA
1 TCATTAGAGATGATCA
782887 T
1 T
782888 GGCACAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (16 bp):
TCATTAGAGATGATCA
Found at i:782999 original size:23 final size:26
Alignment explanation
Indices: 782973--783044 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
782963 AGGATAAAAA
*
782973 TAAAATAGATTTATT-TC-CTTT-AT
1 TAAAAGAGATTTATTATCTCTTTAAT
782996 TAAAAGAGATTTATTATCTCTTTAAT
1 TAAAAGAGATTTATTATCTCTTTAAT
* *
783022 TAAAAGAGATTTAATAACTCTTT
1 TAAAAGAGATTTATTATCTCTTT
783045 TATTGGGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 14 0.33
24 2 0.05
25 4 0.09
26 23 0.53
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (26 bp):
TAAAAGAGATTTATTATCTCTTTAAT
Found at i:787646 original size:47 final size:47
Alignment explanation
Indices: 787569--787692 Score: 223
Period size: 47 Copynumber: 2.6 Consensus size: 47
787559 TAAAAAAATC
*
787569 TTGCTAGAGGTGCCCGAAACTGACTATAGTTGTTACATATTCAAGAA
1 TTGCTAGAGGTGCCCGAAACTGACTCTAGTTGTTACATATTCAAGAA
787616 TTGCTAGAGGTGCCCGAAA-TCGACTCTAGTTGTTACATATTCAAGAA
1 TTGCTAGAGGTGCCCGAAACT-GACTCTAGTTGTTACATATTCAAGAA
787663 TTGCTAGAGGTGCCCGAAACTGACTCTAGT
1 TTGCTAGAGGTGCCCGAAACTGACTCTAGT
787693 CGACTAAATT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
46 1 0.01
47 72 0.97
48 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (47 bp):
TTGCTAGAGGTGCCCGAAACTGACTCTAGTTGTTACATATTCAAGAA
Found at i:788371 original size:23 final size:26
Alignment explanation
Indices: 788345--788406 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
788335 AGGATAAAAA
*
788345 TAAAAGAGATTTATT-T-T-TTTTAT
1 TAAAAGAGATTTATTATCTCTTTAAT
788368 TAAAAGAGATTTATTATCTCTTTAAT
1 TAAAAGAGATTTATTATCTCTTTAAT
788394 TAAAAGAGATTTA
1 TAAAAGAGATTTA
788407 ATAGTTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 15 0.43
24 1 0.03
25 1 0.03
26 18 0.51
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (26 bp):
TAAAAGAGATTTATTATCTCTTTAAT
Found at i:788415 original size:26 final size:25
Alignment explanation
Indices: 788345--788416 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
788335 AGGATAAAAA
* *
788345 TAAAAGAGATTT-AT-TTTTTTTAT
1 TAAAAGAGATTTAATATTCTTTAAT
*
788368 TAAAAGAGATTTATTATCTCTTTAAT
1 TAAAAGAGATTTAATAT-TCTTTAAT
788394 TAAAAGAGATTTAATAGTTCTTT
1 TAAAAGAGATTTAATA-TTCTTT
788417 TATTGGGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.29
24 1 0.02
25 1 0.02
26 26 0.63
27 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TAAAAGAGATTTAATATTCTTTAAT
Found at i:788551 original size:11 final size:11
Alignment explanation
Indices: 788535--788564 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
788525 CATGATCTTC
788535 TTCTTCTTTAT
1 TTCTTCTTTAT
788546 TTCTTCTTTAT
1 TTCTTCTTTAT
788557 TT-TTCTTT
1 TTCTTCTTT
788565 TCATTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTCTTTAT
Found at i:792239 original size:57 final size:51
Alignment explanation
Indices: 792198--792296 Score: 141
Period size: 48 Copynumber: 2.0 Consensus size: 51
792188 TAACAAGAGG
*
792198 AAAATGTTAAATATTTAATATATTTTGATTAACTTAATTAATTTGAAT---
1 AAAATGTTAAATATTTAATATATTTTGATTAACTTAATTAATTTAAATAAC
* * *
792246 TATATGTTAAATATTTAATATATTTTGATTAATTTAATTAATTTAAATAAC
1 AAAATGTTAAATATTTAATATATTTTGATTAACTTAATTAATTTAAATAAC
792297 TGATATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (51 bp):
AAAATGTTAAATATTTAATATATTTTGATTAACTTAATTAATTTAAATAAC
Found at i:792285 original size:9 final size:9
Alignment explanation
Indices: 792210--792291 Score: 58
Period size: 9 Copynumber: 8.7 Consensus size: 9
792200 AATGTTAAAT
792210 ATTTAATATA
1 ATTTAAT-TA
* *
792220 TTTTGATTA
1 ATTTAATTA
*
792229 ACTTAATTA
1 ATTTAATTA
792238 ATTTGAATTA
1 ATTT-AATTA
*
792248 TATGTTAAAT-
1 -AT-TTAATTA
792258 ATTTAATATA
1 ATTTAAT-TA
* *
792268 TTTTGATTA
1 ATTTAATTA
792277 ATTTAATTA
1 ATTTAATTA
792286 ATTTAA
1 ATTTAA
792292 ATAACTGATA
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
8 4 0.07
9 29 0.53
10 15 0.27
11 5 0.09
12 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (9 bp):
ATTTAATTA
Found at i:792777 original size:10 final size:9
Alignment explanation
Indices: 792752--792776 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
792742 CAAGGTCAAG
792752 AAAAAAATA
1 AAAAAAATA
792761 AAAAAAATA
1 AAAAAAATA
792770 AAAAAAA
1 AAAAAAA
792777 AAGCTCAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:794545 original size:17 final size:17
Alignment explanation
Indices: 794500--794537 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
794490 ATCGTCATTA
*
794500 TTTATTATTATTTTTTAT
1 TTTATTCTTA-TTTTTAT
794518 TTTATTCTTATTTTT-T
1 TTTATTCTTATTTTTAT
794534 TTTA
1 TTTA
794538 CTTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTCTTATTTTTAT
Found at i:799739 original size:20 final size:21
Alignment explanation
Indices: 799701--799741 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
799691 AGACACACAG
799701 TACAAGACACTAGAGTGTATA
1 TACAAGACACTAGAGTGTATA
*
799722 TACAAGACACT-TAGTGTATA
1 TACAAGACACTAGAGTGTATA
799742 AGGTGGGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (21 bp):
TACAAGACACTAGAGTGTATA
Found at i:800880 original size:3 final size:3
Alignment explanation
Indices: 800872--800898 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
800862 AAAAAGTGAA
800872 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
800899 TTGCAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:801868 original size:20 final size:21
Alignment explanation
Indices: 801840--801879 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
801830 TTAGGGTAAA
801840 TTATGAG-TTTAATACTTAAT
1 TTATGAGTTTTAATACTTAAT
*
801860 TTATTAGTTTTAATACTTAA
1 TTATGAGTTTTAATACTTAA
801880 ACTTTTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (21 bp):
TTATGAGTTTTAATACTTAAT
Found at i:803074 original size:13 final size:13
Alignment explanation
Indices: 803056--803082 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
803046 GGCAACTTTG
803056 GTCTTTTACATTA
1 GTCTTTTACATTA
803069 GTCTTTTACATTA
1 GTCTTTTACATTA
803082 G
1 G
803083 GGCGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (13 bp):
GTCTTTTACATTA
Found at i:818635 original size:21 final size:21
Alignment explanation
Indices: 818611--818671 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
818601 AACTTTGAAA
818611 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
818632 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
818646 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
818667 AAATG
1 AAATG
818672 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:818717 original size:36 final size:36
Alignment explanation
Indices: 818603--818722 Score: 190
Period size: 35 Copynumber: 3.3 Consensus size: 36
818593 TGGTAACCAA
818603 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
818640 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
818675 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
818712 -GTTGAAAAATG
1 CTTTGAAAAATG
818723 ATAATGGGAT
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
35 35 0.44
36 17 0.22
37 27 0.34
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:823253 original size:21 final size:21
Alignment explanation
Indices: 823229--823289 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
823219 AACTTTGAAA
823229 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
823250 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
823264 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
823285 AAATG
1 AAATG
823290 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:823320 original size:37 final size:37
Alignment explanation
Indices: 823221--823339 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
823211 TGGTAACCAA
823221 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
823258 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
823293 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
823330 -GTTGAAAAAT
1 CTTTGAAAAAT
823340 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:827260 original size:19 final size:19
Alignment explanation
Indices: 827232--827290 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
827222 GAAACGTTTT
827232 TATGAATAGTATTATAC-A
1 TATGAATAGTATTATACTA
*
827250 GTATTAATAGTATTATACTA
1 -TATGAATAGTATTATACTA
*
827270 TATGAATAGTACTGATACTA
1 TATGAATAGTA-TTATACTA
827290 T
1 T
827291 GCAAATAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 26 0.74
20 9 0.26
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
TATGAATAGTATTATACTA
Found at i:828159 original size:32 final size:32
Alignment explanation
Indices: 828116--828310 Score: 338
Period size: 32 Copynumber: 6.1 Consensus size: 32
828106 AACATAAGTA
*
828116 ACTGTCCATATGTCCCGAAAGACGTAGGTAATT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAA-T
828149 A-TGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
*
828180 ATTGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
828212 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
* *
828244 ACTGTCCATATATCCCGAAAGACATAAGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
828276 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
828308 ACT
1 ACT
828311 CGACTCTTGG
Statistics
Matches: 155, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
31 2 0.01
32 152 0.98
33 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAAGACATAGGTAAT
Found at i:838225 original size:7 final size:7
Alignment explanation
Indices: 838204--838236 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
838194 TCAAATAATT
*
838204 AAATATA
1 AAATAAA
838211 AAAT-AA
1 AAATAAA
838217 AAATAAA
1 AAATAAA
838224 AAATAAA
1 AAATAAA
838231 AAATAA
1 AAATAA
838237 TTTTACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAATAAA
Found at i:845844 original size:19 final size:19
Alignment explanation
Indices: 845820--845883 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 19
845810 TCGTTGCGAT
845820 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
845839 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
845862 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
845881 TTT
1 TTT
845884 AGAAAATCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.35
21 14 0.38
23 10 0.27
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:845854 original size:21 final size:19
Alignment explanation
Indices: 845820--845894 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
845810 TCGTTGCGAT
*
845820 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
845839 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* *
845862 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* *
845881 TTTAGAAAATCGCA
1 TTTGGAATATCGCA
845895 TTGCGATAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 21 0.47
21 14 0.31
23 10 0.22
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:845921 original size:21 final size:21
Alignment explanation
Indices: 845890--845942 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
845880 ATTTAGAAAA
*
845890 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
845911 TCTCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
845932 TCGCGTTGCGA
1 TCGCGTTGCGA
845943 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:846219 original size:18 final size:21
Alignment explanation
Indices: 846196--846242 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
846186 TATTTCATTG
846196 AAAATATTTTTA-ATAC-A-T
1 AAAATATTTTTATATACGATT
*
846214 AAAATACTTTTATATACGATT
1 AAAATATTTTTATATACGATT
846235 AAAATATT
1 AAAATATT
846243 AAATTATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.46
19 4 0.17
20 1 0.04
21 8 0.33
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAATATTTTTATATACGATT
Found at i:847283 original size:18 final size:17
Alignment explanation
Indices: 847260--847367 Score: 76
Period size: 18 Copynumber: 6.2 Consensus size: 17
847250 TTATTAATCT
*
847260 ACATCTGATAATTGTAAA
1 ACATCTGATAACTG-AAA
*
847278 ACATCTTATAACTGAAA
1 ACATCTGATAACTGAAA
*
847295 ATCATCTGATAAC-GTAA
1 A-CATCTGATAACTGAAA
*
847312 ATATCTGATAACT-ATAA
1 ACATCTGATAACTGA-AA
* * *
847329 ATATCTAATAACTGTGAA
1 ACATCTGATAACTG-AAA
** *
847347 ATGTCTGATAACTGTAA
1 ACATCTGATAACTGAAA
847364 ACAT
1 ACAT
847368 TTAGAATTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
16 10 0.14
17 26 0.36
18 36 0.50
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (17 bp):
ACATCTGATAACTGAAA
Found at i:848400 original size:27 final size:29
Alignment explanation
Indices: 848370--848424 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
848360 GCTAAACTTA
848370 AATA-TAAAATTTGATA-AAAA-TAAATCC
1 AATACTAAAA-TTGATATAAAACTAAATCC
*
848397 AATACTTAAATTGATATAAAACTAAATC
1 AATACTAAAATTGATATAAAACTAAATC
848425 GTACTTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
28 8 0.33
29 6 0.25
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (29 bp):
AATACTAAAATTGATATAAAACTAAATCC
Found at i:849975 original size:29 final size:31
Alignment explanation
Indices: 849943--850025 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
849933 AATCTATAAC
849943 CTTTTAAAA-TTATATTTTTAGTCCCT-AAA
1 CTTTTAAAACTTATATTTTTAGTCCCTCAAA
*
849972 CTTTTACAAAGTT-TATATTTTAG-CCCTCAAA
1 CTTTTA-AAACTTATAT-TTTTAGTCCCTCAAA
* *
850003 CTTTCAAAACTTACA-TTTTAGTC
1 CTTTTAAAACTTATATTTTTAGTC
850026 ACTAGTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 12 0.27
30 16 0.36
31 17 0.38
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.45
Consensus pattern (31 bp):
CTTTTAAAACTTATATTTTTAGTCCCTCAAA
Found at i:858400 original size:6 final size:6
Alignment explanation
Indices: 858391--858418 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
858381 CTTGTAATTG
858391 TGTGAA TGTGAA TGTGAA TGTGAA TGTG
1 TGTGAA TGTGAA TGTGAA TGTGAA TGTG
858419 CAGAAACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (6 bp):
TGTGAA
Found at i:859712 original size:54 final size:55
Alignment explanation
Indices: 859630--859738 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 55
859620 CCTGCTCCCC
859630 ATCTCTTCTTTCCACTGATGGGATCTGACAAGGAACCCATGGAAC-ACAGCTAAA
1 ATCTCTTCTTTCCACTGATGGGATCTGACAAGGAACCCATGGAACAACAGCTAAA
859684 ATCTCTTCTTTCCACTGATGGGATCTGACAAGGAACCCATGGAACAACAGCTAAA
1 ATCTCTTCTTTCCACTGATGGGATCTGACAAGGAACCCATGGAACAACAGCTAAA
859739 CACCCATCGT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 45 0.83
55 9 0.17
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (55 bp):
ATCTCTTCTTTCCACTGATGGGATCTGACAAGGAACCCATGGAACAACAGCTAAA
Found at i:864782 original size:126 final size:124
Alignment explanation
Indices: 864468--864794 Score: 615
Period size: 126 Copynumber: 2.6 Consensus size: 124
864458 GAAATTTAAA
864468 ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
1 ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
864533 CACGTG-A-AGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGACATGATGAC
66 CACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGACATGATGAC
864590 ATAATAGGGCAATGAT-ATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
1 ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
864654 CACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGAC
66 CACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGA-GGACATG-ATGAC
864715 ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
1 ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
864780 CACGTGAATAGTGAA
66 CACGTGAATAGTGAA
864795 CCGATTATAG
Statistics
Matches: 200, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
121 54 0.27
122 17 0.09
123 38 0.19
124 7 0.04
125 21 0.10
126 63 0.31
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (124 bp):
ATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTT
CACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGACATGATGAC
Found at i:867781 original size:12 final size:12
Alignment explanation
Indices: 867764--867802 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
867754 TACATAAATA
867764 TATTTAATATAT
1 TATTTAATATAT
*
867776 TATTTAATATAA
1 TATTTAATATAT
867788 TATTTAATATTAT
1 TATTTAATA-TAT
867801 TA
1 TA
867803 GTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:869057 original size:17 final size:17
Alignment explanation
Indices: 869030--869068 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
869020 AATTTACAAT
869030 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
869046 TAATTATAAATAATATC
1 TAATTATAAATAATATC
869063 TAATTA
1 TAATTA
869069 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:870561 original size:185 final size:183
Alignment explanation
Indices: 870324--870711 Score: 584
Period size: 185 Copynumber: 2.1 Consensus size: 183
870314 ATTAAATTTT
*
870324 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACACAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACAATTTAAAACACAATTAATAA
* *
870389 TTTAAGATCTATTAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAA-TT
*
870453 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTCAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTCAATT-AA
* *
870509 AAATATTAAATATATTATATATAACATTTGGGCT-AAGCCCAAACAATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACAATTTAAAACACAATTAATA
* * ** *
870573 ATTTAAGATCCAATAATTTTTAAATCTAAATCAATATTAATTAATTAAAAATTTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATT
* *
870638 TTTATTTTATAATTATATATTATTTAAATTAATTATACACTTTTTTTGAATTAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTCAATTAA
* *
870692 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
870712 AATTAGAAAA
Statistics
Matches: 186, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
182 8 0.04
183 12 0.06
184 12 0.06
185 151 0.81
186 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACAATTTAAAACACAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTCAATTAA
Found at i:871416 original size:16 final size:16
Alignment explanation
Indices: 871395--871433 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
871385 GATTAAACGT
871395 TGATTTAAATATTAAA
1 TGATTTAAATATTAAA
* *
871411 TGATTTAAATGTTGAA
1 TGATTTAAATATTAAA
871427 TGATTTA
1 TGATTTA
871434 GGGTCTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (16 bp):
TGATTTAAATATTAAA
Found at i:871486 original size:73 final size:73
Alignment explanation
Indices: 871367--871507 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 73
871357 TTAATGTGTA
* * **
871367 GTTTGTTTATTTTAAAATGATTAAACGTTGATTTAAATATTAAATGATTTAAATGTTGAATGATT
1 GTTTGTTTATTTTAAAATGATTAAACGTTGATTCAAATATTAAATGATTCAAATACTGAATGATT
871432 TAGGGTCT
66 TAGGGTCT
* * * *
871440 GTTTGTTTATTTTAGAATGTTTAAGCGTTGATTCAAATATTGAATGATTCAAATACTGAATGATT
1 GTTTGTTTATTTTAAAATGATTAAACGTTGATTCAAATATTAAATGATTCAAATACTGAATGATT
871505 TAG
66 TAG
871508 AGGCTCTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.45
Consensus pattern (73 bp):
GTTTGTTTATTTTAAAATGATTAAACGTTGATTCAAATATTAAATGATTCAAATACTGAATGATT
TAGGGTCT
Found at i:871489 original size:16 final size:16
Alignment explanation
Indices: 871468--871504 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
871458 GTTTAAGCGT
*
871468 TGATTCAAATATTGAA
1 TGATTCAAATACTGAA
871484 TGATTCAAATACTGAA
1 TGATTCAAATACTGAA
871500 TGATT
1 TGATT
871505 TAGAGGCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (16 bp):
TGATTCAAATACTGAA
Found at i:886055 original size:17 final size:18
Alignment explanation
Indices: 886022--886063 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
886012 TAATAGTGAG
886022 TTATTATGAAATATATTT
1 TTATTATGAAATATATTT
*
886040 TTATTAT-AATTATATTT
1 TTATTATGAAATATATTT
*
886057 TTTTTAT
1 TTATTAT
886064 TATAGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTATGAAATATATTT
Found at i:886842 original size:20 final size:20
Alignment explanation
Indices: 886817--886863 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
886807 AAATTTCCAG
*
886817 TAAACTATGCA-TTTAGTATC
1 TAAACTAT-CAGTTTAGTACC
886837 TAAACTATCAGTTTTAGTACC
1 TAAACTATCAG-TTTAGTACC
886858 TAAACT
1 TAAACT
886864 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 8 0.33
21 14 0.58
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (20 bp):
TAAACTATCAGTTTAGTACC
Found at i:886872 original size:21 final size:21
Alignment explanation
Indices: 886828--886872 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
886818 AAACTATGCA
* *
886828 TTTAGTATCTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
* *
886849 TTTAGTACCTAAACTTTTAAT
1 TTTAGTACCTAAACTATCAAT
886870 TTT
1 TTT
886873 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:887454 original size:6 final size:6
Alignment explanation
Indices: 887443--887481 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
887433 AAAGCTTTCG
887443 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCC
887482 AGCTTTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCCTC
Found at i:893009 original size:16 final size:16
Alignment explanation
Indices: 892988--893019 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
892978 TTTGCTATTC
892988 CATAAAACTTCAGCAT
1 CATAAAACTTCAGCAT
893004 CATAAAACTTCAGCAT
1 CATAAAACTTCAGCAT
893020 TCTTGTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
CATAAAACTTCAGCAT
Found at i:898909 original size:26 final size:27
Alignment explanation
Indices: 898880--898933 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
898870 ATTTATGTTA
*
898880 ACAAAA-AATAGTAAAAAACTT-AAAAT
1 ACAAAATAATAATAAAAAA-TTGAAAAT
898906 ACAAAATAATAATAAAAAATTGAAAAT
1 ACAAAATAATAATAAAAAATTGAAAAT
898933 A
1 A
898934 TATAAAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (27 bp):
ACAAAATAATAATAAAAAATTGAAAAT
Found at i:900611 original size:18 final size:18
Alignment explanation
Indices: 900588--900639 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
900578 ATATAACACA
900588 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
900606 TATGTCCCAAAGGACCAC
1 TATGTCCCGAAGGACCAC
900624 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
900640 GCGTAGACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:911804 original size:214 final size:214
Alignment explanation
Indices: 911424--911825 Score: 651
Period size: 214 Copynumber: 1.9 Consensus size: 214
911414 GTGAAGCAAA
* *
911424 CCATCCATAAGACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATAATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACAATGTTTTAA
* ** * *
911489 GAAGATGGAATTTTTGAAAATGAAGGATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCATTCGG
* *
911554 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAGCCTTTAGAGCA
911619 AGATGATAAGTCCTTTGGG
196 AGATGATAAGTCCTTTGGG
* * * *
911638 CCATCCGTAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAACGATGTTTTGA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACAATGTTTTAA
* * *
911703 GAAGATGAAATTTTTTAAAACAAATAATGCGATTTTCAAAATTTCACAATTTTTAAGTCATTCGG
66 GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCATTCGG
*
911768 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTT
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAGCCTT
911826 CACCGAAGAG
Statistics
Matches: 171, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
214 171 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (214 bp):
CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACAATGTTTTAA
GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCATTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTTGGG
Found at i:911916 original size:43 final size:43
Alignment explanation
Indices: 911855--911989 Score: 199
Period size: 42 Copynumber: 3.2 Consensus size: 43
911845 AAATTCATCA
911855 GTAAGTCTTTCGAGCATGATGATGAAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGATGAAAATCCTTCGGGTCATTT
911898 GTAAGTCTTTCGAGCATGATGATG-AAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGATGAAAATCCTTCGGGTCATTT
* *
911940 GTAAGTCTTTCGAG--TGA-GATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAGCATGATGATGA-AAATCCTTCGGGTCATTT
*
911981 -TAAGCCTTT
1 GTAAGTCTTT
911990 TCGGAAGAGT
Statistics
Matches: 87, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
39 4 0.05
40 11 0.13
41 16 0.18
42 32 0.37
43 24 0.28
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (43 bp):
GTAAGTCTTTCGAGCATGATGATGAAAATCCTTCGGGTCATTT
Found at i:912422 original size:53 final size:53
Alignment explanation
Indices: 912359--912505 Score: 233
Period size: 53 Copynumber: 2.8 Consensus size: 53
912349 ATCAAACCAT
*
912359 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCAGTAGGCAG
*
912412 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCAGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCAGTAGGCAG
* *
912465 AAGATTGTTCAAGTTCCTTAATCCCTGAA-CAAGAGGGAGCG
1 AAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCG
912506 GACACATCAT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
53 65 0.75
54 12 0.14
55 10 0.11
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCAGTAGGCAG
Found at i:917914 original size:23 final size:23
Alignment explanation
Indices: 917870--917914 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
917860 TTATCTTCAT
* *
917870 ATCTCTTATTTCTTATTCATATG
1 ATCTCTTAATTCATATTCATATG
917893 ATCTCTTACATTCATATT-ATAT
1 ATCTCTTA-ATTCATATTCATAT
917915 AACTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (23 bp):
ATCTCTTAATTCATATTCATATG
Found at i:918258 original size:18 final size:18
Alignment explanation
Indices: 918235--918286 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
918225 ATATAACACA
918235 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
918253 TATGTCCCAAATGACCAC
1 TATGTCCCGAAGGACCAC
918271 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
918287 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:919117 original size:24 final size:20
Alignment explanation
Indices: 919060--919097 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
919050 TTTCCCTTGA
919060 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
919080 AGTGCATCAATGCATTCT
1 AGTGCATCGATGCATTCT
919098 TTAAACTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:919179 original size:65 final size:63
Alignment explanation
Indices: 919094--919246 Score: 182
Period size: 65 Copynumber: 2.4 Consensus size: 63
919084 CATCAATGCA
** * *
919094 TTCTTTAAACTGTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTT
1 TTCTTTAAAGAGTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGTTTC
* * * * * *
919157 TATTTTTAAAGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTC
1 T-TCTTTAAAGAG-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTC
919222 TTCTTTAAAGAGTGCATCGATGCAC
1 TTCTTTAAAGAGTGCATCGATGCAC
919247 ATTCAATGTA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 14 0.18
64 19 0.25
65 43 0.57
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (63 bp):
TTCTTTAAAGAGTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTC
Found at i:931389 original size:72 final size:73
Alignment explanation
Indices: 931303--931450 Score: 208
Period size: 72 Copynumber: 2.0 Consensus size: 73
931293 GTGACCAACT
* * *
931303 CAACTCTGTAGTTTACTCTTATGTGAAAGCTTAACAAATGGTAGTGATCCAA-TACAATCAACCC
1 CAACTCTGTAGTTTACCCTTATGTGAAAGCTCAACAAATGGTAGTGATCCAACTACAATCAACAC
931367 GTGATGAC
66 GTGATGAC
* * * * *
931375 CAACTCTGTAGTTTACCCTTATGTGAAAGCTCAATAAATGTTAGTGATTCAACTACAGTCAATAC
1 CAACTCTGTAGTTTACCCTTATGTGAAAGCTCAACAAATGGTAGTGATCCAACTACAATCAACAC
*
931440 GTGGTGAC
66 GTGATGAC
931448 CAA
1 CAA
931451 ATCTTATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 47 0.71
73 19 0.29
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (73 bp):
CAACTCTGTAGTTTACCCTTATGTGAAAGCTCAACAAATGGTAGTGATCCAACTACAATCAACAC
GTGATGAC
Found at i:938101 original size:13 final size:13
Alignment explanation
Indices: 938083--938111 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
938073 AAAAGAAATA
938083 TAATTAATATTTC
1 TAATTAATATTTC
938096 TAATTAATATTTC
1 TAATTAATATTTC
938109 TAA
1 TAA
938112 ACCTTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTAATATTTC
Found at i:943355 original size:20 final size:20
Alignment explanation
Indices: 943330--943462 Score: 81
Period size: 20 Copynumber: 6.6 Consensus size: 20
943320 AATGACCAAT
943330 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
943350 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
943370 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
943390 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
** * *
943411 AAGTTCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
943431 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
943451 AAAATCGCAACG
1 AAAATCGCAACG
943463 TTGAAAATAA
Statistics
Matches: 84, Mismatches: 24, Indels: 10
0.71 0.20 0.08
Matches are distributed among these distances:
20 70 0.83
21 14 0.17
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:943768 original size:6 final size:6
Alignment explanation
Indices: 943531--943764 Score: 414
Period size: 6 Copynumber: 39.0 Consensus size: 6
943521 AGACACGTAT
943531 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
943579 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
943627 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
943675 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
* * * * * *
943723 TACCAT TACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
943765 GACCCGACCC
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 225 1.00
ACGTcount: A:0.33, C:0.50, G:0.02, T:0.15
Consensus pattern (6 bp):
TACCAC
Found at i:949947 original size:21 final size:21
Alignment explanation
Indices: 949921--950158 Score: 158
Period size: 21 Copynumber: 11.4 Consensus size: 21
949911 ATTTTGGACT
949921 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
949942 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
* * *
949963 ATCGCAACAAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
949982 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
950003 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
950024 ATCACAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
950045 ATCGCAACGAACTTT-GAATAA
1 ATCGCAACGAA-TTTGGAATAA
* *
950066 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
950087 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
950108 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
950129 ATCGCAACG-ATCTTGAAATAA
1 ATCGCAACGAAT-TTGGAATAA
950150 ATCGCAACG
1 ATCGCAACG
950159 CGAACTTTGA
Statistics
Matches: 172, Mismatches: 26, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.01
19 49 0.28
20 2 0.01
21 84 0.49
22 2 0.01
23 34 0.20
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:949979 original size:42 final size:42
Alignment explanation
Indices: 949917--950177 Score: 350
Period size: 42 Copynumber: 6.3 Consensus size: 42
949907 TGCGATTTTG
*
949917 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
949959 GACTATCGCAACAAACTTGGACT--ATCGCAA--CGAATTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
949997 GAATAAATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
950041 GACTATCGCAACGAACTTTGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
950083 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
950125 GACTATCGCAACGATCTTGAAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
950167 GACTATCGCAA
1 GACTATCGCAA
950178 TGCGAATATG
Statistics
Matches: 189, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.05
40 23 0.12
42 148 0.78
44 9 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:950108 original size:84 final size:84
Alignment explanation
Indices: 949914--950177 Score: 394
Period size: 84 Copynumber: 3.2 Consensus size: 84
949904 CGTTGCGATT
* *
949914 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTTG
* *
949979 ACT--ATCGCAA--CGAAT
66 AATAAATCGCAACGCGAAC
* *
949994 TTGGAATAAATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTT
1 TTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTT
950059 TGAATAAATCGCAACGCGAAC
64 TGAATAAATCGCAACGCGAAC
*
950080 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGATC-TTG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTTG
950144 AAATAAATCGCAACGCGAAC
66 -AATAAATCGCAACGCGAAC
*
950164 TTTGACTATCGCAA
1 TTGGACTATCGCAA
950178 TGCGAATATG
Statistics
Matches: 167, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
80 6 0.04
82 57 0.34
83 3 0.02
84 91 0.54
86 10 0.06
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (84 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTTG
AATAAATCGCAACGCGAAC
Found at i:950182 original size:21 final size:20
Alignment explanation
Indices: 949942--950183 Score: 117
Period size: 21 Copynumber: 11.6 Consensus size: 20
949932 TTTGGAATAA
*
949942 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTTGACT
* *
949963 ATCGCAA-CAAACTTGGACT
1 ATCGCAAGCGAACTTTGACT
*
949982 ATCGCAA-CGAA-TTTGGAAT
1 ATCGCAAGCGAACTTT-GACT
*
950001 AAATCGCAA-CGAA-TTTGGAAT
1 --ATCGCAAGCGAACTTT-GACT
* *
950022 AAATCACAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTTGACT
*
950045 ATCGCAA-CGAACTTTGAAT
1 ATCGCAAGCGAACTTTGACT
*
950064 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAA-GCGAACTTTGACT
*
950087 ATCGCAA-CGAA-TTTGGAAT
1 ATCGCAAGCGAACTTT-GACT
*
950106 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTTGACT
* *
950129 ATCGCAA-CGATC-TTGAAAT
1 ATCGCAAGCGAACTTTG-ACT
950148 AAATCGCAACGCGAACTTTGACT
1 --ATCGCAA-GCGAACTTTGACT
950171 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
950184 TATGTAAATC
Statistics
Matches: 176, Mismatches: 23, Indels: 44
0.72 0.09 0.18
Matches are distributed among these distances:
18 6 0.03
19 46 0.26
21 87 0.49
23 30 0.17
24 7 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTTGACT
Found at i:957456 original size:14 final size:15
Alignment explanation
Indices: 957432--957460 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
957422 AAAAATAAAA
957432 TGTTATTAAAAATAT
1 TGTTATTAAAAATAT
957447 TGTT-TTAAAAATAT
1 TGTTATTAAAAATAT
957461 CTAAACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
TGTTATTAAAAATAT
Found at i:964939 original size:25 final size:25
Alignment explanation
Indices: 964887--964971 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
964877 TCAAAAGGTT
964887 AAAAA-GTTTGATG-AAGAAGTTTT-
1 AAAAATGTTTGATGAAAGAA-TTTTA
*
964910 GAAAATGCTTT-ATGAAAGAATTTTA
1 AAAAATG-TTTGATGAAAGAATTTTA
* *
964935 AAAAATGTTTGATGAAATAATTTTG
1 AAAAATGTTTGATGAAAGAATTTTA
*
964960 AAGAATGTTTGA
1 AAAAATGTTTGA
964972 CGAAGTTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.08
24 11 0.21
25 37 0.71
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (25 bp):
AAAAATGTTTGATGAAAGAATTTTA
Found at i:966419 original size:17 final size:17
Alignment explanation
Indices: 966397--966432 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
966387 TTTGCTCATT
966397 GTTCATAACTTCCAAAG
1 GTTCATAACTTCCAAAG
966414 GTTCATAACTTCCAAAG
1 GTTCATAACTTCCAAAG
966431 GT
1 GT
966433 AGTATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (17 bp):
GTTCATAACTTCCAAAG
Found at i:967105 original size:18 final size:18
Alignment explanation
Indices: 967079--967117 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
967069 AATCATATTG
967079 CCCAAGGGGTACAGATTC
1 CCCAAGGGGTACAGATTC
* *
967097 CCCAGGGGGTACCGATTC
1 CCCAAGGGGTACAGATTC
967115 CCC
1 CCC
967118 CTTGTCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (18 bp):
CCCAAGGGGTACAGATTC
Found at i:970349 original size:22 final size:22
Alignment explanation
Indices: 970321--970408 Score: 122
Period size: 22 Copynumber: 4.0 Consensus size: 22
970311 AATCAGATTG
*
970321 CCCAGGGGGTACATATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
* *
970343 CCCAGGGGGTACCGATTCTCCC
1 CCCAGGGGGTACAGATTCCCCC
*
970365 CCCAGGGGGAACAGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
* *
970387 CCCAGGGGGTTCCGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
970409 TTGTCTAACG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.16, C:0.42, G:0.26, T:0.16
Consensus pattern (22 bp):
CCCAGGGGGTACAGATTCCCCC
Found at i:970384 original size:44 final size:43
Alignment explanation
Indices: 970321--970408 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 43
970311 AATCAGATTG
* *
970321 CCCAGGGGGTACATATTCCCCCCCCAGGGGGTACCGATTCTCCC
1 CCCAGGGGGAACAGATTCCCCCCCCAGGGGGTACCGATTC-CCC
*
970365 CCCAGGGGGAACAGATTCCCCCCCCAGGGGGTTCCGATTCCCC
1 CCCAGGGGGAACAGATTCCCCCCCCAGGGGGTACCGATTCCCC
970408 C
1 C
970409 TTGTCTAACG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 4 0.10
44 37 0.90
ACGTcount: A:0.16, C:0.42, G:0.26, T:0.16
Consensus pattern (43 bp):
CCCAGGGGGAACAGATTCCCCCCCCAGGGGGTACCGATTCCCC
Found at i:971154 original size:26 final size:26
Alignment explanation
Indices: 971125--971176 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
971115 AGATAAGATA
971125 CCACCGTATTAATTTTAGCTTCATTC
1 CCACCGTATTAATTTTAGCTTCATTC
*
971151 CCACCGTATTAATTTTAGCTTTATTC
1 CCACCGTATTAATTTTAGCTTCATTC
971177 TTAATGTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.44
Consensus pattern (26 bp):
CCACCGTATTAATTTTAGCTTCATTC
Found at i:978399 original size:29 final size:29
Alignment explanation
Indices: 978363--978475 Score: 208
Period size: 29 Copynumber: 3.9 Consensus size: 29
978353 TATTATTTTT
*
978363 TTAATAATTAAATATATAATAAAATATTA
1 TTAATAATTAAATATATAATAATATATTA
978392 TTAATAATTAAATATATAATAATATATTA
1 TTAATAATTAAATATATAATAATATATTA
978421 TTAATAATTAAATATATAATAATATATTA
1 TTAATAATTAAATATATAATAATATATTA
*
978450 ATAATAATTAAATATATAATAATATA
1 TTAATAATTAAATATATAATAATATA
978476 ATAATAATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAATAATTAAATATATAATAATATATTA
Found at i:979254 original size:16 final size:17
Alignment explanation
Indices: 979216--979254 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
979206 TTTATAACTT
*
979216 TTAATAGTTACATAAAT
1 TTAATAGTTACATAAAC
979233 TTAATAGTTACA-AAAC
1 TTAATAGTTACATAAAC
979249 TTAATA
1 TTAATA
979255 AAACAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAATAGTTACATAAAC
Found at i:980555 original size:11 final size:10
Alignment explanation
Indices: 980530--980577 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
980520 AATTATAAAA
*
980530 AATATAAAATA
1 AATA-AAAATG
980541 AATAAAAATG
1 AATAAAAATG
*
980551 CAATAAAAAAG
1 -AATAAAAATG
980562 AATTAAAAATG
1 AA-TAAAAATG
980573 AATAA
1 AATAA
980578 TGTAAAGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (10 bp):
AATAAAAATG
Found at i:980560 original size:22 final size:21
Alignment explanation
Indices: 980530--980577 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
980520 AATTATAAAA
* *
980530 AATATAAAATAAATAAAAATG
1 AATAAAAAAGAAATAAAAATG
*
980551 CAATAAAAAAGAATTAAAAATG
1 -AATAAAAAAGAAATAAAAATG
980573 AATAA
1 AATAA
980578 TGTAAAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (21 bp):
AATAAAAAAGAAATAAAAATG
Found at i:981209 original size:10 final size:10
Alignment explanation
Indices: 981196--981224 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
981186 TAAAAGTTAA
981196 TAAATATTAT
1 TAAATATTAT
981206 TAAATATTAT
1 TAAATATTAT
981216 TAAATATTA
1 TAAATATTA
981225 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATATTAT
Found at i:984536 original size:2 final size:2
Alignment explanation
Indices: 984529--984580 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
984519 TCTCTAATTG
984529 TA TA TA TA TA TA 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 TA TA TA TA TA TA
984571 T- TA TA T- TA TA
1 TA TA TA TA TA TA
984581 AGATCTAGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:985230 original size:46 final size:47
Alignment explanation
Indices: 985124--985230 Score: 137
Period size: 47 Copynumber: 2.3 Consensus size: 47
985114 GTGTGAGCCA
*
985124 AACAA-AACGCCCATACTTTGTTGTTCCCCACGCAAACACCTTGCCC
1 AACAACAACGCCCATACTTTGTTGTTCCCCACGCAAACACCATGCCC
* * * * * *
985170 GACAGCAGCTCCCATATTTTGTTGTTCCCCACGC-CACACCATGCCC
1 AACAACAACGCCCATACTTTGTTGTTCCCCACGCAAACACCATGCCC
985216 AACAACAACGCCCAT
1 AACAACAACGCCCAT
985231 CCCCTGCCCA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
46 24 0.49
47 25 0.51
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (47 bp):
AACAACAACGCCCATACTTTGTTGTTCCCCACGCAAACACCATGCCC
Found at i:989411 original size:22 final size:22
Alignment explanation
Indices: 989385--989450 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
989375 TTGAAAACAT
989385 TTAGTGTCCACCATCTGAAAGG
1 TTAGTGTCCACCATCTGAAAGG
989407 TTAGTGTCCACCATCTGAAAGG
1 TTAGTGTCCACCATCTGAAAGG
989429 TTAGTGTCCACCATCTGAAAGG
1 TTAGTGTCCACCATCTGAAAGG
989451 GCAGACTGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TTAGTGTCCACCATCTGAAAGG
Found at i:991532 original size:31 final size:31
Alignment explanation
Indices: 991497--991555 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
991487 TTAAATTGAT
991497 AATAAAATAA-ATTTGTATAAT-TTAAAAAATA
1 AATAAAATAATATTT-TA-AATATTAAAAAATA
991528 AATAAAATAATATTTTAAATATTAAAAA
1 AATAAAATAATATTTTAAATATTAAAAA
991556 TATTAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 3 0.12
31 19 0.73
32 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (31 bp):
AATAAAATAATATTTTAAATATTAAAAAATA
Found at i:1009309 original size:18 final size:17
Alignment explanation
Indices: 1009282--1009316 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1009272 ATTTAAAAAT
1009282 ATTAAAATAATAAATTA
1 ATTAAAATAATAAATTA
*
1009299 ATTATAAATAATATATTA
1 ATTA-AAATAATAAATTA
1009317 GATTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAATAATAAATTA
Found at i:1015122 original size:35 final size:35
Alignment explanation
Indices: 1015083--1015153 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1015073 CATTCACACT
* *
1015083 TTTCTTATTTCCCTTCTTCTTCCACGCCTAATTCC
1 TTTCTTACTTCCCTTCTTCTTCCACGCATAATTCC
1015118 TTTCTTACTTCCCTTCTTCTTCCACGCATAATTCC
1 TTTCTTACTTCCCTTCTTCTTCCACGCATAATTCC
1015153 T
1 T
1015154 GTTAATAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.13, C:0.37, G:0.03, T:0.48
Consensus pattern (35 bp):
TTTCTTACTTCCCTTCTTCTTCCACGCATAATTCC
Found at i:1029144 original size:18 final size:18
Alignment explanation
Indices: 1029121--1029163 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1029111 ATTGAACGTC
1029121 GTTCTAATATAAAGAGTT
1 GTTCTAATATAAAGAGTT
1029139 GTTCTAATATAAAGAGTT
1 GTTCTAATATAAAGAGTT
1029157 GTTCTAA
1 GTTCTAA
1029164 GGAGTCGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (18 bp):
GTTCTAATATAAAGAGTT
Found at i:1036355 original size:7 final size:6
Alignment explanation
Indices: 1036309--1036515 Score: 70
Period size: 6 Copynumber: 33.0 Consensus size: 6
1036299 ATTTTGCTTG
*
1036309 AAGAATA AATGAAA AAGAAA AAGAGAA AAG-AA AAGAAA AAGGAA AA-AAA
1 AAGAA-A AA-GAAA AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA
* * * * *
1036358 ATG-AA ATGAAA TGAA-AAA ATGAAA ATGATGAA AAGAAA AGAAAAA AATGAAA
1 AAGAAA AAGAAA --AAGAAA AAGAAA AAGA--AA AAGAAA A-AGAAA AA-GAAA
* * * ** *
1036410 AA-AACG GAGAAAA ATAGAAT GGGAAA AATG-AA AA-AAA ATGAAA AA-AAA
1 AAGAA-A AAG-AAA A-AGAAA AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA
* * *
1036458 AATGACA AAGAAA AAGAAA AAGGAA AAGAAA ATGATGAAA AAGAAA AAGAGA
1 AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA A--A-GAAA AAGAAA AAGAAA
1036510 AAGAAA
1 AAGAAA
1036516 TTAAAGGGGG
Statistics
Matches: 150, Mismatches: 26, Indels: 49
0.67 0.12 0.22
Matches are distributed among these distances:
5 24 0.16
6 76 0.51
7 31 0.21
8 14 0.09
9 5 0.03
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.08
Consensus pattern (6 bp):
AAGAAA
Found at i:1036375 original size:28 final size:29
Alignment explanation
Indices: 1036333--1036458 Score: 91
Period size: 27 Copynumber: 4.3 Consensus size: 29
1036323 AAGAAAAAGA
*
1036333 GAAAAGAAAAG--AAAAAGGAAAAAAAAT
1 GAAAAGAAAAGAAAAAAATGAAAAAAAAT
* * **
1036360 GAAATGAAATG-AAAAAATG-AAAATGAT
1 GAAAAGAAAAGAAAAAAATGAAAAAAAAT
**
1036387 GAAAAGAAAAGAAAAAAATGAAAAAAACG
1 GAAAAGAAAAGAAAAAAATGAAAAAAAAT
*
1036416 GAGAAA-AATAGAATGGGAAAAATGAAAAAAAAT
1 GA-AAAGAAAAGAA----AAAAATGAAAAAAAAT
*
1036449 GAAAAAAAAA
1 GAAAAGAAAA
1036459 ATGACAAAGA
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
27 24 0.32
28 14 0.19
29 12 0.16
30 3 0.04
32 3 0.04
33 19 0.25
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (29 bp):
GAAAAGAAAAGAAAAAAATGAAAAAAAAT
Found at i:1036411 original size:10 final size:10
Alignment explanation
Indices: 1036344--1036457 Score: 62
Period size: 10 Copynumber: 11.5 Consensus size: 10
1036334 AAAAGAAAAG
*
1036344 AAAAAGGAAA
1 AAAAATGAAA
1036354 AAAAATGAAA
1 AAAAATGAAA
**
1036364 TGAAATG--A
1 AAAAATGAAA
1036372 AAAAATG-AA
1 AAAAATGAAA
**
1036381 AATGATGAAA
1 AAAAATGAAA
1036391 AGAAAA-G-AA
1 A-AAAATGAAA
1036400 AAAAATGAAA
1 AAAAATGAAA
1036410 AAAACGGA-GAAA
1 AAAA---ATGAAA
**
1036422 AATAGAATG-GG
1 AA-A-AATGAAA
1036433 AAAAATGAAA
1 AAAAATGAAA
1036443 AAAAATGAAA
1 AAAAATGAAA
1036453 AAAAA
1 AAAAA
1036458 AATGACAAAG
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
8 10 0.13
9 14 0.18
10 40 0.51
11 5 0.06
12 7 0.09
13 2 0.03
14 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:1036501 original size:33 final size:31
Alignment explanation
Indices: 1036443--1036512 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
1036433 AAAAATGAAA
* *
1036443 AAAAATGAAAAAAAAAATGACAAAGAAAAAG
1 AAAAAGGAAAAAAAAAATGAAAAAGAAAAAG
*
1036474 AAAAAGGAAAAGAAAATGATGAAAAAGAAAAAG
1 AAAAAGGAAAA-AAAA-AATGAAAAAGAAAAAG
*
1036507 AGAAAG
1 AAAAAG
1036513 AAATTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 10 0.30
32 4 0.12
33 19 0.58
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (31 bp):
AAAAAGGAAAAAAAAAATGAAAAAGAAAAAG
Found at i:1037792 original size:37 final size:36
Alignment explanation
Indices: 1037743--1037814 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
1037733 CAAAACAAGT
1037743 CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
1 CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
* *
1037779 CCATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 CCATCT-TAAGCCTTCACGAAAGAGCAGTGAAGCAA
1037815 GCTCATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAA
Found at i:1037949 original size:55 final size:53
Alignment explanation
Indices: 1037878--1038080 Score: 212
Period size: 55 Copynumber: 3.7 Consensus size: 53
1037868 TTTTTGAAGA
* * * *
1037878 TCGAGTCTTATACTCTCTGAAGGAATATGGAGCATACTCGTTTTATAAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC-C-TTTTATGAAGATTGT
* * * * * * *
1037933 TCGAGTTTTATACTCTCTGAAAGAATAGAGAGCGGGCCCATTTTCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGC-AGACC-TTTTATGAAGATTGT
*
1037988 TCGAGT-TCTATACTCCCTGAACGAATAGGGAG-AGGACCTATTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCA-GACCT-TTTA-TGAAGATTGT
1038043 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACC
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACC
1038081 CGTCATTCAA
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
53 1 0.01
54 7 0.06
55 113 0.91
56 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (53 bp):
TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACCTTTTATGAAGATTGT
Done.