Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:15468 original size:23 final size:23
Alignment explanation
Indices: 15442--15501 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
15432 CACCACAGCT
15442 CATATAATTGCACCAAAGTGCCG
1 CATATAATTGCACCAAAGTGCCG
*
15465 CATATAATTGCACCAGAGTGCCG
1 CATATAATTGCACCAAAGTGCCG
* *
15488 CGTAGAATTGCACC
1 CATATAATTGCACC
15502 GTAGTGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCAAAGTGCCG
Found at i:15507 original size:23 final size:22
Alignment explanation
Indices: 15442--15509 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
15432 CACCACAGCT
* *
15442 CATATAATTGCACCAAAGTGCCG
1 CATAGAATTGCACC-GAGTGCCG
*
15465 CATATAATTGCACCAGAGTGCCG
1 CATAGAATTGCACC-GAGTGCCG
*
15488 CGTAGAATTGCACCGTAGTGCC
1 CATAGAATTGCACCG-AGTGCC
15510 ATATAATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (22 bp):
CATAGAATTGCACCGAGTGCCG
Found at i:15698 original size:103 final size:103
Alignment explanation
Indices: 15526--15845 Score: 568
Period size: 103 Copynumber: 3.1 Consensus size: 103
15516 TACTGTCCAT
* * * *
15526 AAGGACCACATATCATTCCTTAAGAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
15591 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
15629 AATGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
15694 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
15732 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
15797 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
15835 AAGGACCACAT
1 AAGGACCACAT
15846 GGACCCTCGA
Statistics
Matches: 206, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:16675 original size:64 final size:64
Alignment explanation
Indices: 16567--16786 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 64
16557 TAATGAAGGT
* * * * ** *
16567 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGGG
*
16631 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
* * ** **
16695 ATGCAT-GATGCACTACTTATGCATCAATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCCTTATTAATGGG
**
16757 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
16787 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 47 0.36
64 82 0.62
65 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:21539 original size:23 final size:23
Alignment explanation
Indices: 21495--21563 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
21485 CACCACAGCT
* *
21495 CATATAATTGCACCAAACTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
21518 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
21541 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
21564 TATAATACTG
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:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:21751 original size:103 final size:103
Alignment explanation
Indices: 21582--21899 Score: 591
Period size: 103 Copynumber: 3.1 Consensus size: 103
21572 TGTCCATAAG
* * *
21582 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
21647 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
21685 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
21750 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
21788 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
21853 TTCACACATGTTCTAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
21891 GACCACATA
1 GACCACATA
21900 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:22724 original size:64 final size:64
Alignment explanation
Indices: 22616--22792 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
22606 TAATGAAGGT
* * * ** * * ** *
22616 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATAGATGCACGAATTGCATTCGATGTTTCCTTATTAATGGG
* *
22680 ATGCATCGATGCA-TGCCTTATGCATAGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATAGATGCACGAATTGCATTCGATGTTTCCTTATTAATGGG
*
22744 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATAGATGCACGAATTGCATTCGATGT
22793 ATTTATTTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
63 1 0.01
64 95 0.98
65 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATAGATGCACGAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:22813 original size:64 final size:64
Alignment explanation
Indices: 22616--22836 Score: 214
Period size: 64 Copynumber: 3.5 Consensus size: 64
22606 TAATGAAGGT
* * ** * * ** ** *
22616 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
* * * * * *
22680 ATGCATCGATGCA-TGCCTTATGCATAGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
*
22744 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAAAGAG
**
22807 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
22837 ACACCTTCAA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.02
64 125 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:27701 original size:16 final size:15
Alignment explanation
Indices: 27664--27703 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
27654 TGAAACATTA
27664 AAAATATTTTTCACT
1 AAAATATTTTTCACT
**
27679 ATTATATTTTTCACT
1 AAAATATTTTTCACT
27694 ACAAATATTT
1 A-AAATATTT
27704 GCTTTTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATATTTTTCACT
Found at i:40978 original size:48 final size:48
Alignment explanation
Indices: 40785--40978 Score: 223
Period size: 48 Copynumber: 4.1 Consensus size: 48
40775 CTCATCGGAT
* *
40785 AAAGGAAAAGGAATAGAACCT---TCCAAAACTGTTAAAAATCCAGAA
1 AAAGGAAAAGGAACAGAACCTCCAACCAAAACTGTTAAAAATCCAGAA
* * * * *
40830 AAAAGCAAAGGAACGGAACCTCCAACCAAATCTGTTAAAAATCCAGAC
1 AAAGGAAAAGGAACAGAACCTCCAACCAAAACTGTTAAAAATCCAGAA
** * * * *
40878 AAAGGAGGAGGAGCAGAAACTCCAACCAAAACTGTCAAAAATCCAGAC
1 AAAGGAAAAGGAACAGAACCTCCAACCAAAACTGTTAAAAATCCAGAA
* * *
40926 AAAGGAAAAGGAGCAGAACCTCCTACCAAATCTGTTAAAAATCCAGAA
1 AAAGGAAAAGGAACAGAACCTCCAACCAAAACTGTTAAAAATCCAGAA
40974 AAAGG
1 AAAGG
40979 TAGAGGACCA
Statistics
Matches: 123, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
45 17 0.14
48 106 0.86
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (48 bp):
AAAGGAAAAGGAACAGAACCTCCAACCAAAACTGTTAAAAATCCAGAA
Found at i:40985 original size:96 final size:96
Alignment explanation
Indices: 40807--40990 Score: 271
Period size: 96 Copynumber: 1.9 Consensus size: 96
40797 ATAGAACCTT
* * *
40807 CCAAAACTGTTAAAAATCCAGAAAAAAGCAAAGGAACGGAACCTCCAACCAAATCTGTTAAAAAT
1 CCAAAACTGTCAAAAATCCAGAAAAAAGAAAAGGAACAGAACCTCCAACCAAATCTGTTAAAAAT
* *
40872 CCAGACAAAGGAGGAGGAGCAGAAACTCCAA
66 CCAGAAAAAGGAGGAGGACCAGAAACTCCAA
* * * *
40903 CCAAAACTGTCAAAAATCCAGACAAAGGAAAAGGAGCAGAACCTCCTACCAAATCTGTTAAAAAT
1 CCAAAACTGTCAAAAATCCAGAAAAAAGAAAAGGAACAGAACCTCCAACCAAATCTGTTAAAAAT
40968 CCAGAAAAAGGTA-GAGGACCAGA
66 CCAGAAAAAGG-AGGAGGACCAGA
40991 CATGAGCCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 77 0.99
97 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (96 bp):
CCAAAACTGTCAAAAATCCAGAAAAAAGAAAAGGAACAGAACCTCCAACCAAATCTGTTAAAAAT
CCAGAAAAAGGAGGAGGACCAGAAACTCCAA
Found at i:45012 original size:20 final size:20
Alignment explanation
Indices: 44987--45058 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
44977 CTTGAAGTGT
44987 ATCGATGCATTCTACAATGC
1 ATCGATGCATTCTACAATGC
*
45007 ATCGATGCATTCTTTAACATGTGC
1 ATCGATGCATTC--T-ACA-ATGC
*
45031 ATCGATGCA--CTACCCATGC
1 ATCGATGCATTCTA-CAATGC
45050 ATCGATGCA
1 ATCGATGCA
45059 CTCCTTATGC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 13 0.30
20 14 0.32
22 2 0.05
23 3 0.07
24 12 0.27
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCGATGCATTCTACAATGC
Found at i:45052 original size:19 final size:19
Alignment explanation
Indices: 45028--45074 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
45018 CTTTAACATG
45028 TGCATCGATGCACTACC-CA
1 TGCATCGATGCACT-CCTCA
*
45047 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTCA
45066 TGCATCGAT
1 TGCATCGAT
45075 ACACCAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:59053 original size:173 final size:172
Alignment explanation
Indices: 58747--59090 Score: 481
Period size: 173 Copynumber: 2.0 Consensus size: 172
58737 GTAAAATAGT
* * *
58747 GGGAGATATAAGGGTAAAAATGAAATTTTAGTATTGTTGTTTGTTAACTTTTCTAATAGAAAATT
1 GGGAGATATAAGGATAAAAATGAAATTTAAATATTGTTGTTTGTTAACTTTTCTAATAGAAAATT
* * * * * * * *
58812 TTGAATGAGAGATTTTTAAAAAATAAAAGAGATATATTTAGTGGGACAAATTGAGTATTTCTTTT
66 TTGAATGAAACAATTTTAAAAAACAAAAGAAATACATTTAGTGGGACAAATGGAGTATTTCATTT
58877 TAAATAAATGTGTATGCAACTATCCGAAATCAACAAGCAACC
131 TAAATAAATGTGTATGCAACTATCCGAAATCAACAAGCAACC
* * * *
58919 GGGATATATAAGGATAAAAAATGAAATTTAAATGTTGTTGTTTGTTAACTTTTTTAATATAAAAT
1 GGGAGATATAAGGAT-AAAAATGAAATTTAAATATTGTTGTTTGTTAACTTTTCTAATAGAAAAT
* * *
58984 TTTGAATGAAACAATTTTAAAAAACAAAATAAATACATTTAGTGTGACAAATGGATTATTTCATT
65 TTTGAATGAAACAATTTTAAAAAACAAAAGAAATACATTTAGTGGGACAAATGGAGTATTTCATT
** * *
59049 TTAAATAAATGTGTATGCATTTATCTGAAATCAGCAAGCAAC
130 TTAAATAAATGTGTATGCAACTATCCGAAATCAACAAGCAAC
59091 TACAACCAAA
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
172 13 0.09
173 136 0.91
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (172 bp):
GGGAGATATAAGGATAAAAATGAAATTTAAATATTGTTGTTTGTTAACTTTTCTAATAGAAAATT
TTGAATGAAACAATTTTAAAAAACAAAAGAAATACATTTAGTGGGACAAATGGAGTATTTCATTT
TAAATAAATGTGTATGCAACTATCCGAAATCAACAAGCAACC
Found at i:59724 original size:64 final size:63
Alignment explanation
Indices: 59656--59789 Score: 171
Period size: 64 Copynumber: 2.1 Consensus size: 63
59646 CCATGCATCG
* * *
59656 ATGCACCCCGACTATTTTAAAACATTGAATG-TGCTCTATGCATCGATGCACTCTCAGTGTACCA
1 ATGCACCCAGACTATTTTAAAACATCGAA-GAT-ATCTATGCATCGATGCACTCTCAGTGTACCA
* * * *
59720 ATGCACCCAGGCTTTTTTAAAACATCGAAGCATATTTATGCATCGATGCACTCTCAGTGTACCG
1 ATGCACCCAGACTATTTTAAAACATCGAAG-ATATCTATGCATCGATGCACTCTCAGTGTACCA
59784 ATGCAC
1 ATGCAC
59790 TAAGTCTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
63 1 0.02
64 59 0.97
65 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (63 bp):
ATGCACCCAGACTATTTTAAAACATCGAAGATATCTATGCATCGATGCACTCTCAGTGTACCA
Found at i:70490 original size:22 final size:22
Alignment explanation
Indices: 70462--70524 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
70452 GAATGACCAT
*
70462 TATGTCCCGAATGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
*
70484 TATGTCCCAAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
* *
70506 TATATCCTGAAGGACCACT
1 TATGTCCCGAAGGACCACT
70525 CCTTAAGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:70885 original size:2 final size:2
Alignment explanation
Indices: 70878--70911 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70868 ACTGTATCCA
70878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70912 GTGTGTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75160 original size:12 final size:12
Alignment explanation
Indices: 75143--75173 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
75133 CGTGATTTCG
75143 GGGTTTAGGTAA
1 GGGTTTAGGTAA
75155 GGGTTTAGGTAA
1 GGGTTTAGGTAA
75167 GGGTTTA
1 GGGTTTA
75174 CTGAGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (12 bp):
GGGTTTAGGTAA
Found at i:75963 original size:135 final size:135
Alignment explanation
Indices: 75717--75975 Score: 385
Period size: 135 Copynumber: 1.9 Consensus size: 135
75707 TAGGGTGGCT
*
75717 CATTCGCTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTTGT
1 CATTCGCTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTAAAATCCAA---T-T
* * *
75782 GTAAGTTGCGTTGTTTTGAGTCCAATATCCTTCACCGTGAAGTTGAAATTGACTCTGAATGAAAC
62 GTAAGTTGCGTTGTTTCGAGGCCAATATCCTTCACCGTGAAGTTGAAATTGACTATGAATGAAAC
75847 TAGAAAGCC
127 TAGAAAGCC
* *
75856 CATTCGCTGTGAAGTTGAGCTTTGAAATTGGATATCCTTCGTTGTGAAGTTAAAATCCAA-TGTA
1 CATTCGCTGTGAAGTTGAGCTTTG-AATTGGATATCATTCGTCGTGAAGTTAAAATCCAATTGTA
** *
75920 AGTTGCGTTGTTTCGAGGCCAATATCCTTTGCTGTGAAGTTGAAATTGACTATGAA
65 AGTTGCGTTGTTTCGAGGCCAATATCCTTCACCGTGAAGTTGAAATTGACTATGAA
75976 ACTGGAAAGT
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
135 54 0.49
139 24 0.22
140 32 0.29
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (135 bp):
CATTCGCTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTAAAATCCAATTGTAA
GTTGCGTTGTTTCGAGGCCAATATCCTTCACCGTGAAGTTGAAATTGACTATGAATGAAACTAGA
AAGCC
Found at i:76395 original size:43 final size:44
Alignment explanation
Indices: 76334--76442 Score: 150
Period size: 43 Copynumber: 2.5 Consensus size: 44
76324 ATTCCCTTCG
* *
76334 TCGTGAAGTTGAAATCGTGGATGT-GTGGGCATAATATCCTCCA
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGGCACAATATCCTCCA
* * *
76377 TCGTGGAGTTGAAATCGTGGAT-TCGTTGGTACGATATCCTCCA
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGGCACAATATCCTCCA
*
76420 TCGTGGAATTGAAATCGTGGATG
1 TCGTGGAGTTGAAATCGTGGATG
76443 GCCCCTTCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (44 bp):
TCGTGGAGTTGAAATCGTGGATGTCGTGGGCACAATATCCTCCA
Found at i:81299 original size:18 final size:18
Alignment explanation
Indices: 81276--81314 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
81266 TATCAAGTTA
81276 AAATATGATACATTT-ATT
1 AAATATGAT-CATTTCATT
*
81294 AAATATTATCATTTCATT
1 AAATATGATCATTTCATT
81312 AAA
1 AAA
81315 ACATCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATATGATCATTTCATT
Found at i:96462 original size:15 final size:13
Alignment explanation
Indices: 96442--96480 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
96432 TTTACTGGAT
96442 AAAAACCGGTTTGAA
1 AAAAACCGGTTT--A
96457 AAAAACCGG-TTA
1 AAAAACCGGTTTA
96469 AAAAACCGGTTT
1 AAAAACCGGTTT
96481 TTATCCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 2 0.09
15 9 0.39
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (13 bp):
AAAAACCGGTTTA
Found at i:98789 original size:21 final size:21
Alignment explanation
Indices: 98765--98806 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
98755 AGTTTATTTT
*
98765 TAAATTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
98786 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
98807 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:98854 original size:33 final size:33
Alignment explanation
Indices: 98795--98903 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
98785 GTAAACTTTG
98795 TTTCAA-TTATCGAACTT-GAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
*
98826 TTTGAATTTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
98859 TTTTAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
98892 TTTCAA-TTATCG
1 TTTCAATTTATCG
98904 TAAACTTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 5 0.07
32 17 0.24
33 50 0.69
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
Found at i:99117 original size:15 final size:17
Alignment explanation
Indices: 99091--99122 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
99081 TTCTATGGGA
99091 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
99107 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
99123 CGGATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:99120 original size:21 final size:21
Alignment explanation
Indices: 99096--99148 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
99086 TGGGAAAAAA
99096 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
99117 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
99138 CCGGATCGGAT
1 CCGGATCGGAT
99149 TGAAATCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (21 bp):
CCGGATCGGATAAAAACCGAT
Found at i:106892 original size:14 final size:14
Alignment explanation
Indices: 106870--106923 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
106860 TCAACCCAGA
106870 CTGAGTCAACTCAT
1 CTGAGTCAACTCAT
* *
106884 CTGAATCAACCCGAAT
1 CTGAGTCAACTC--AT
*
106900 TTGAGTCAACTCAT
1 CTGAGTCAACTCAT
106914 CTGAGTCAAC
1 CTGAGTCAAC
106924 CCGTTGACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 21 0.66
16 11 0.34
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (14 bp):
CTGAGTCAACTCAT
Found at i:106942 original size:13 final size:13
Alignment explanation
Indices: 106924--106949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106914 CTGAGTCAAC
106924 CCGTTGACTTTGA
1 CCGTTGACTTTGA
106937 CCGTTGACTTTGA
1 CCGTTGACTTTGA
106950 TCGAAAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:112164 original size:2 final size:2
Alignment explanation
Indices: 112157--112181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
112147 GTCATAGTTT
112157 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
112182 TAATCTGAGG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:114441 original size:69 final size:69
Alignment explanation
Indices: 114355--114490 Score: 272
Period size: 69 Copynumber: 2.0 Consensus size: 69
114345 AATGTTATAT
114355 CATTTACAATATTTTCGGTTCAACGGAAAATATTAGGAAAAAAATTAACATTTTAAGTTTATTAC
1 CATTTACAATATTTTCGGTTCAACGGAAAATATTAGGAAAAAAATTAACATTTTAAGTTTATTAC
114420 GTAA
66 GTAA
114424 CATTTACAATATTTTCGGTTCAACGGAAAATATTAGGAAAAAAATTAACATTTTAAGTTTATTAC
1 CATTTACAATATTTTCGGTTCAACGGAAAATATTAGGAAAAAAATTAACATTTTAAGTTTATTAC
114489 GT
66 GT
114491 TTTTGGTTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (69 bp):
CATTTACAATATTTTCGGTTCAACGGAAAATATTAGGAAAAAAATTAACATTTTAAGTTTATTAC
GTAA
Found at i:121431 original size:31 final size:31
Alignment explanation
Indices: 121396--121457 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
121386 TTTACTTCCT
121396 CGCAGAAAGCTATTGATCTTTCTAATTCCAA
1 CGCAGAAAGCTATTGATCTTTCTAATTCCAA
121427 CGCAGAAAGCTATTGATCTTTCTAATTCCAA
1 CGCAGAAAGCTATTGATCTTTCTAATTCCAA
121458 TGAACTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (31 bp):
CGCAGAAAGCTATTGATCTTTCTAATTCCAA
Found at i:128720 original size:44 final size:44
Alignment explanation
Indices: 128670--128757 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
128660 AATGCCAAAC
* * *
128670 GAAATAAATAACTAAGAATAGTGCCAGTAGATGCTAGAATCTAT
1 GAAATAAATAACCAAGAATAGTGCCAGTAGAAGCGAGAATCTAT
128714 GAAATAAATAACCAAGAATAGTGCCAGTAGAAGCGAGAATCTAT
1 GAAATAAATAACCAAGAATAGTGCCAGTAGAAGCGAGAATCTAT
128758 CTTACGTGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (44 bp):
GAAATAAATAACCAAGAATAGTGCCAGTAGAAGCGAGAATCTAT
Found at i:131237 original size:141 final size:141
Alignment explanation
Indices: 130983--131269 Score: 574
Period size: 141 Copynumber: 2.0 Consensus size: 141
130973 ATGAACTCTG
130983 TTAAAAATTAACGACTAGTGGTTTGATTAAATCAATTAAATAGTTGGGTAGTCTGATTGATTCAA
1 TTAAAAATTAACGACTAGTGGTTTGATTAAATCAATTAAATAGTTGGGTAGTCTGATTGATTCAA
131048 TTGAAAATTCGGTGGTTACATTGATTTTTTACCATAGTTTAGTGGTCTCCCGTGTAGTTTATCCT
66 TTGAAAATTCGGTGGTTACATTGATTTTTTACCATAGTTTAGTGGTCTCCCGTGTAGTTTATCCT
131113 AGTTTTTAAAT
131 AGTTTTTAAAT
131124 TTAAAAATTAACGACTAGTGGTTTGATTAAATCAATTAAATAGTTGGGTAGTCTGATTGATTCAA
1 TTAAAAATTAACGACTAGTGGTTTGATTAAATCAATTAAATAGTTGGGTAGTCTGATTGATTCAA
131189 TTGAAAATTCGGTGGTTACATTGATTTTTTACCATAGTTTAGTGGTCTCCCGTGTAGTTTATCCT
66 TTGAAAATTCGGTGGTTACATTGATTTTTTACCATAGTTTAGTGGTCTCCCGTGTAGTTTATCCT
131254 AGTTTTTAAAT
131 AGTTTTTAAAT
131265 TTAAA
1 TTAAA
131270 GTACTATAAT
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 146 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (141 bp):
TTAAAAATTAACGACTAGTGGTTTGATTAAATCAATTAAATAGTTGGGTAGTCTGATTGATTCAA
TTGAAAATTCGGTGGTTACATTGATTTTTTACCATAGTTTAGTGGTCTCCCGTGTAGTTTATCCT
AGTTTTTAAAT
Found at i:135504 original size:127 final size:127
Alignment explanation
Indices: 135278--135531 Score: 508
Period size: 127 Copynumber: 2.0 Consensus size: 127
135268 AGGATTCAAG
135278 GAAGATCAAGAACAGAGGTTGCCATTAATTATTAGTGAAGACGTATCTTCAATCACAGATGACAA
1 GAAGATCAAGAACAGAGGTTGCCATTAATTATTAGTGAAGACGTATCTTCAATCACAGATGACAA
135343 ACTCAACTTGATTGCAGCTTGTTGGTACAATATCAGGAAGTAATCACAACATCCATTTGGTT
66 ACTCAACTTGATTGCAGCTTGTTGGTACAATATCAGGAAGTAATCACAACATCCATTTGGTT
135405 GAAGATCAAGAACAGAGGTTGCCATTAATTATTAGTGAAGACGTATCTTCAATCACAGATGACAA
1 GAAGATCAAGAACAGAGGTTGCCATTAATTATTAGTGAAGACGTATCTTCAATCACAGATGACAA
135470 ACTCAACTTGATTGCAGCTTGTTGGTACAATATCAGGAAGTAATCACAACATCCATTTGGTT
66 ACTCAACTTGATTGCAGCTTGTTGGTACAATATCAGGAAGTAATCACAACATCCATTTGGTT
135532 CAAACTTCAG
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (127 bp):
GAAGATCAAGAACAGAGGTTGCCATTAATTATTAGTGAAGACGTATCTTCAATCACAGATGACAA
ACTCAACTTGATTGCAGCTTGTTGGTACAATATCAGGAAGTAATCACAACATCCATTTGGTT
Found at i:143513 original size:12 final size:12
Alignment explanation
Indices: 143496--143583 Score: 67
Period size: 12 Copynumber: 7.0 Consensus size: 12
143486 TATTTAGTCA
143496 TTTAATTATTAT
1 TTTAATTATTAT
143508 TTTAATT-TTAAT
1 TTTAATTATT-AT
*
143520 TTTATTTAATTAT
1 TTTAATT-ATTAT
143533 CTTTAAAATTATTAT
1 -TTT--AATTATTAT
143548 TATT-ATTATTAT
1 T-TTAATTATTAT
143560 TATT-ATTATTAT
1 T-TTAATTATTAT
143572 TATT-ATTATTAT
1 T-TTAATTATTAT
143584 ATTTTCATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
11 2 0.03
12 47 0.70
13 2 0.03
14 6 0.09
15 7 0.10
16 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATTATTAT
Found at i:143548 original size:3 final size:3
Alignment explanation
Indices: 143540--143583 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
143530 TATCTTTAAA
143540 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
143584 ATTTTCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:144396 original size:23 final size:23
Alignment explanation
Indices: 144359--144420 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
144349 AAAGAATCGA
144359 AAAC-TGCCA-AAAGACA-AAGAT
1 AAACATGCCATAAAGACAGAA-AT
* *
144380 AAATATGTCATAAAGACAGAAAT
1 AAACATGCCATAAAGACAGAAAT
144403 AAACATGCCATAAAGACA
1 AAACATGCCATAAAGACA
144421 TAATTATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 25 0.74
24 2 0.06
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACATGCCATAAAGACAGAAAT
Found at i:148692 original size:19 final size:20
Alignment explanation
Indices: 148663--148700 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
148653 AGAAATTTGT
148663 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
148683 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
148701 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:148743 original size:63 final size:62
Alignment explanation
Indices: 148668--148826 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
148658 TTTGTTGAAG
* * *
148668 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GAAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
* ** **
148731 GTGCATCGATGCATAAAGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAGA-AGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
*
148794 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGAAGTGCATCGATGCAT
148827 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.01
63 77 0.93
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGAAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:150169 original size:18 final size:18
Alignment explanation
Indices: 150143--150178 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
150133 AGGAATGATA
*
150143 TGTGGTCCTTCGGGACAT
1 TGTGATCCTTCGGGACAT
150161 TGTGATCCTTCGGGACAT
1 TGTGATCCTTCGGGACAT
150179 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (18 bp):
TGTGATCCTTCGGGACAT
Found at i:150203 original size:121 final size:121
Alignment explanation
Indices: 150040--150403 Score: 674
Period size: 121 Copynumber: 3.0 Consensus size: 121
150030 CGAGGGTTTA
150040 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
150105 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
150161 TGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
150226 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
150282 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
150347 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTAGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
150403 T
1 T
150404 ATTATATGGC
Statistics
Matches: 235, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 235 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:150287 original size:18 final size:18
Alignment explanation
Indices: 150264--150299 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
150254 AGGAATGATA
150264 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
150282 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
150300 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:150470 original size:23 final size:23
Alignment explanation
Indices: 150410--150462 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
150400 CATTATTATA
*
150410 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
150433 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
150456 TGGCACT
1 TGGCACT
150463 TTGGTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:154314 original size:19 final size:20
Alignment explanation
Indices: 154285--154322 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
154275 AGAAATTTGT
154285 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
154305 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
154323 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:154365 original size:63 final size:62
Alignment explanation
Indices: 154290--154448 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
154280 TTTGTTGAAG
* * * *
154290 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
154353 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
154416 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
154449 GCCTCCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 80 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:155837 original size:103 final size:103
Alignment explanation
Indices: 155658--155887 Score: 453
Period size: 103 Copynumber: 2.2 Consensus size: 103
155648 GTCGAGGGTC
155658 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
155723 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
155761 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
155826 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
155864 TATGTGGTCCTTCGGGACAT-TATG
1 TATGTGGTCCTTCGGGACATATATG
155888 GTCCTTTGGG
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 4 0.03
103 123 0.97
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:155891 original size:18 final size:19
Alignment explanation
Indices: 155863--155906 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
155853 TTAAGGAATG
*
155863 ATATGTGGTCCTTCGGGAC
1 ATATATGGTCCTTCGGGAC
*
155882 AT-TATGGTCCTTTGGGAC
1 ATATATGGTCCTTCGGGAC
155900 ATATATG
1 ATATATG
155907 TATTCTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (19 bp):
ATATATGGTCCTTCGGGAC
Found at i:155979 original size:121 final size:121
Alignment explanation
Indices: 155765--156007 Score: 450
Period size: 121 Copynumber: 2.0 Consensus size: 121
155755 GAATGATATG
155765 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
155830 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTAGGGACATTA
* *
155886 TGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
155951 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTAGGGACATTA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTAGGGACATTA
156007 T
1 T
156008 TATATGGCAC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 118 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (121 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTAGGGACATTA
Found at i:156073 original size:23 final size:23
Alignment explanation
Indices: 156012--156080 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
156002 CATTATTATA
* *
156012 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTATG
*
156035 CGGCACTACGGTGCATTTCTATG
1 TGGCACTACGGTGCATTTCTATG
* *
156058 TGGCACTTCGGTGCATTTATATG
1 TGGCACTACGGTGCATTTCTATG
156081 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTATG
Found at i:161298 original size:22 final size:22
Alignment explanation
Indices: 161202--161285 Score: 125
Period size: 22 Copynumber: 3.8 Consensus size: 22
161192 GAAATTATTT
*
161202 AAATTTATTTTAAAATATAAAT
1 AAATTTATTTTAAAATATAAAA
*
161224 TAATTTATTTTAAAATATGAAAA
1 AAATTTATTTTAAAATAT-AAAA
161247 AAA-TTATTTTAAAATATAAAA
1 AAATTTATTTTAAAATATAAAA
*
161268 AAAATTATTTTAAAATAT
1 AAATTTATTTTAAAATAT
161286 GGATTGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
21 7 0.12
22 45 0.79
23 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
AAATTTATTTTAAAATATAAAA
Found at i:163371 original size:20 final size:21
Alignment explanation
Indices: 163338--163378 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
163328 AAAACCAACA
163338 AAATCAATTCTTTTATTGTTT
1 AAATCAATTCTTTTATTGTTT
*
163359 AAAT-AATTTTTTTATTGTTT
1 AAATCAATTCTTTTATTGTTT
163379 GACTGGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
AAATCAATTCTTTTATTGTTT
Found at i:168178 original size:20 final size:21
Alignment explanation
Indices: 168137--168180 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
168127 GGTAAAAAAA
168137 TATCTAAAACATTATTATTTTT
1 TATCTAAAACATTA-TATTTTT
168159 TATCTAAAACATTA-ATTTTT
1 TATCTAAAACATTATATTTTT
168179 TA
1 TA
168181 ACATTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (21 bp):
TATCTAAAACATTATATTTTT
Found at i:168990 original size:19 final size:19
Alignment explanation
Indices: 168966--169017 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
168956 TAGTGACCTT
168966 ATTGGTCGTTAAGTGCTTC
1 ATTGGTCGTTAAGTGCTTC
168985 ATTGGTCGTTAAGTGCTTC
1 ATTGGTCGTTAAGTGCTTC
* *
169004 ATAGGTCGCTAAGT
1 ATTGGTCGTTAAGT
169018 ATTCTTTGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (19 bp):
ATTGGTCGTTAAGTGCTTC
Found at i:169523 original size:70 final size:68
Alignment explanation
Indices: 169405--169543 Score: 188
Period size: 70 Copynumber: 2.0 Consensus size: 68
169395 AATTACTGAT
* * ** *
169405 TAATTTAATTACTTCACCACCGACGTTATTTGGTTCGTGCAAAATATCAACAATAAGTTCATTAT
1 TAATATAATTAATTCACCACCGACGCCATTTGGTTCATGCAAAATATCAACAATAAGTT-A-TAT
169470 ATATA
64 ATATA
* * *
169475 TAATATAATTAATTTACCACCGAGGCCATTTGGTTTATGCAAAATATCAACAATAAGTTATATAT
1 TAATATAATTAATTCACCACCGACGCCATTTGGTTCATGCAAAATATCAACAATAAGTTATATAT
169540 ATA
66 ATA
169543 T
1 T
169544 TTTGGATTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 9 0.15
69 1 0.02
70 51 0.84
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (68 bp):
TAATATAATTAATTCACCACCGACGCCATTTGGTTCATGCAAAATATCAACAATAAGTTATATAT
ATA
Found at i:172481 original size:27 final size:26
Alignment explanation
Indices: 172443--172504 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 26
172433 AGAGATTACC
*
172443 AGTAGGG-GCTTTGAATAGGGTGACG
1 AGTAGGGAGCTTTGAACAGGGTGACG
172468 AGTAGTGGAGCTTTGAACAGGGTGACG
1 AGTAG-GGAGCTTTGAACAGGGTGACG
172495 AGTAGCGGAG
1 AGTAG-GGAG
172505 TAGTTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 5 0.15
26 2 0.06
27 26 0.79
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (26 bp):
AGTAGGGAGCTTTGAACAGGGTGACG
Found at i:181044 original size:13 final size:12
Alignment explanation
Indices: 180996--181047 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
180986 ACCTGAAAAG
*
180996 ACAAGGAAAATA
1 ACAAGTAAAATA
181008 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
**
181021 TACAAAAAAAATGA
1 -ACAAGTAAAAT-A
181035 ACAAGTAAAATA
1 ACAAGTAAAATA
181047 A
1 A
181048 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 11 0.34
13 12 0.38
14 9 0.28
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:186700 original size:26 final size:26
Alignment explanation
Indices: 186659--186713 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
186649 CCAGAAGGAG
*
186659 CACTGACTAGATCTTCTAGAAACTGC
1 CACTGACTAGACCTTCTAGAAACTGC
* *
186685 CACTGACTGGACCTTCTAGAAACTTC
1 CACTGACTAGACCTTCTAGAAACTGC
186711 CAC
1 CAC
186714 GTCAGACCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (26 bp):
CACTGACTAGACCTTCTAGAAACTGC
Found at i:208282 original size:120 final size:120
Alignment explanation
Indices: 208066--208306 Score: 385
Period size: 120 Copynumber: 2.0 Consensus size: 120
208056 TAATGACAAC
* **
208066 ACTCCTGAGATATAGAGAATGAAAATCTTGCTATGCAGAACATGCTGCCAGCATGAAAATAATTA
1 ACTCCTGAGATATAGAGAAAGAAAATAATGCTATGCAGAACATGCTGCCAGCATGAAAATAATTA
* *
208131 TGTAATATTTAAGAATTCTTGCATCAGCCAAGTTTTCTCAGATAAATATATCTAA
66 AGTAATATTTAAGAATTCTTGCATCACCCAAGTTTTCTCAGATAAATATATCTAA
* *
208186 ACTCCTGAGATATAGAGAAAGAAAATAATGCTATGCAGAACATGCTGCTAGCATGTAAATAATTA
1 ACTCCTGAGATATAGAGAAAGAAAATAATGCTATGCAGAACATGCTGCCAGCATGAAAATAATTA
* *
208251 AGT-ATGATTTAAGAATTCTTGTATCACCCAAGTTTTCTCAGTTAAATATATCTAA
66 AGTAAT-ATTTAAGAATTCTTGCATCACCCAAGTTTTCTCAGATAAATATATCTAA
208306 A
1 A
208307 TGCACCTTTC
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
119 2 0.02
120 109 0.98
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (120 bp):
ACTCCTGAGATATAGAGAAAGAAAATAATGCTATGCAGAACATGCTGCCAGCATGAAAATAATTA
AGTAATATTTAAGAATTCTTGCATCACCCAAGTTTTCTCAGATAAATATATCTAA
Found at i:210158 original size:17 final size:17
Alignment explanation
Indices: 210127--210159 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
210117 TCTTTTCTTT
210127 TAATTCTCTTTAATTTC
1 TAATTCTCTTTAATTTC
210144 TAATT-TCTTTCAATTT
1 TAATTCTCTTT-AATTT
210160 AATCTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTCTCTTTAATTTC
Found at i:211765 original size:20 final size:19
Alignment explanation
Indices: 211720--211775 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
211710 AATTTCCCAA
* *
211720 AAAGTTTTGAAACTATCTC
1 AAAGTTTCGAAACTTTCTC
*
211739 AAGAGTTTCGAAACTTTCCTT
1 AA-AGTTTCGAAACTTT-CTC
*
211760 AAAGTTTCGATACTTT
1 AAAGTTTCGAAACTTT
211776 AGCTCCAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 25 0.81
21 4 0.13
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
AAAGTTTCGAAACTTTCTC
Found at i:217767 original size:24 final size:23
Alignment explanation
Indices: 217734--217805 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
217724 TAAATAATAT
* *
217734 AAAAATTAAAATTAAAAAATCCC
1 AAAAAATAAAATTAAAAAATACC
*
217757 AAAAAAATAAAATTAAAAATTTACC
1 -AAAAAATAAAATTAAAAA-ATACC
*
217782 AAAAAATAATATTAAAAAACTACC
1 AAAAAATAAAATTAAAAAA-TACC
217806 TTGGAGCGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 38 0.93
25 3 0.07
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAAATAAAATTAAAAAATACC
Found at i:219843 original size:37 final size:39
Alignment explanation
Indices: 219794--219866 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
219784 TATGTTTTTT
219794 TTTGAAAACATTTTAAAAATATAT-ATA-ATATATAGTC
1 TTTGAAAACATTTTAAAAATATATAATATATATATAGTC
* *
219831 TTTGAAAACATTTTGAAAATGTATAATATATATATA
1 TTTGAAAACATTTTAAAAATATATAATATATATATA
219867 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 22 0.69
38 3 0.09
39 7 0.22
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (39 bp):
TTTGAAAACATTTTAAAAATATATAATATATATATAGTC
Found at i:219863 original size:2 final size:2
Alignment explanation
Indices: 219852--219891 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
219842 TTTGAAAATG
219852 TA TA -A 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 TA T
219892 TTAAAAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:219886 original size:61 final size:58
Alignment explanation
Indices: 219812--219925 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 58
219802 CATTTTAAAA
* *
219812 ATATATATAATATATAGTCTTTGAAAA-CA-TTTTGAAAATGTATAATATATATATATATAT
1 ATATATATAATATATA-TATTT-AAAAGCATTTTTGAAAACGTAT-ATA-ATATATATATAT
219872 ATATATATATATATATATATTTAAAAGCATTTTTGAAAACGTATATAATATATA
1 ATATATATA-ATATATATATTTAAAAGCATTTTTGAAAACGTATATAATATATA
219926 GTTTTGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
59 11 0.22
60 18 0.37
61 20 0.41
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (58 bp):
ATATATATAATATATATATTTAAAAGCATTTTTGAAAACGTATATAATATATATATAT
Found at i:219941 original size:38 final size:38
Alignment explanation
Indices: 219875--220039 Score: 153
Period size: 38 Copynumber: 4.3 Consensus size: 38
219865 TATATATATA
* *
219875 TATATATATATATA-TATTT-AAAAGCATTTTTGAAAACG
1 TATATA-ATATATAGT-TTTGAAAAACATTTTTGAAAACT
*
219913 TATATAATATATAGTTTTGAAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTGAAAAACATTTTTGAAAACT
*
219951 TATATGATATATAGTTTTG-AAAACA-TTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAAACATTTTTGAAAAC--T
* * * * *
219989 TATATATTACATAGTTTTAAAAAAAAATATTTT-AAAA-A
1 TATATAATATATAGTTTT-GAAAAACAT-TTTTGAAAACT
220027 TATATAATATATA
1 TATATAATATATA
220040 ATTTGTTTAA
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
36 9 0.08
37 16 0.15
38 68 0.64
40 5 0.05
41 4 0.04
42 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
TATATAATATATAGTTTTGAAAAACATTTTTGAAAACT
Found at i:219981 original size:11 final size:11
Alignment explanation
Indices: 219965--219989 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
219955 TGATATATAG
219965 TTTTGAAAACA
1 TTTTGAAAACA
219976 TTTTGAAAACA
1 TTTTGAAAACA
219987 TTT
1 TTT
219990 ATATATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:220031 original size:76 final size:74
Alignment explanation
Indices: 219874--220115 Score: 188
Period size: 77 Copynumber: 3.2 Consensus size: 74
219864 ATATATATAT
* * *
219874 ATATATATATATATATATTTAAAAGCATTTTTGAAAACGTATATAATATATAGTTTTGAAAAACA
1 ATATATATATATATATATTTAAAAGCATTTTTGAAAACGTATATAATACATAGTTTTAAAAAAAA
219939 TTTTTGAAA
66 TTTTTGAAA
* * *
219948 ATTTATATGATATATAGT-TTTGAAAA-CA-TTTTGAAAACATTTATATATTACATAGTTTTAAA
1 ATATATAT-ATATATA-TATTT-AAAAGCATTTTTGAAAAC--GTATATAATACATAGTTTT-AA
*
220010 AAAAAATATTTTAAAA
60 AAAAAAT-TTTTGAAA
* * * ** * * * *
220026 ATATATA-ATATATAATTTGTTTAAAGCATTTTTTTAAAATATATATATTATATAATTTAAAAAA
1 ATATATATATATAT-ATAT-TTAAAAGCA-TTTTTGAAAACGTATATAATACATAGTTTTAAAAA
*
220090 AACATTTTGGAAA
63 AA-ATTTTTGAAA
*
220103 TTATATAT-TATAT
1 ATATATATATATAT
220116 GTTTTTTAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
74 17 0.13
75 12 0.09
76 28 0.21
77 36 0.27
78 34 0.25
80 8 0.06
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (74 bp):
ATATATATATATATATATTTAAAAGCATTTTTGAAAACGTATATAATACATAGTTTTAAAAAAAA
TTTTTGAAA
Found at i:220096 original size:40 final size:39
Alignment explanation
Indices: 219989--220097 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 39
219979 TGAAAACATT
* * *
219989 TATATATTACATAGTTTTAAAAAAAA-A-TATTTTAAAAA
1 TATATATTATATA-ATTTAAAAAAAACATTTTTTTAAAAA
* **** *
220027 TATATAATATATAATTTGTTTAAAGCATTTTTTTAAAATA
1 TATATATTATATAATTTAAAAAAAACATTTTTTTAAAA-A
220067 TATATATTATATAATTTAAAAAAAACATTTT
1 TATATATTATATAATTTAAAAAAAACATTTT
220098 GGAAATTATA
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
37 6 0.11
38 12 0.23
39 9 0.17
40 26 0.49
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (39 bp):
TATATATTATATAATTTAAAAAAAACATTTTTTTAAAAA
Found at i:220155 original size:3 final size:3
Alignment explanation
Indices: 220147--220215 Score: 77
Period size: 3 Copynumber: 22.3 Consensus size: 3
220137 TATATTATAC
* * *
220147 TAT TAT TAT TAT TAT TATT TAT TAT TAT CATT TAT TAT TAT TGT AAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT
220194 TAT T-T TATT TAT TAT TAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT T
220216 TCTTATTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 46 0.82
4 8 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:220170 original size:13 final size:13
Alignment explanation
Indices: 220147--220222 Score: 95
Period size: 13 Copynumber: 6.1 Consensus size: 13
220137 TATATTATAC
220147 TATTA-TTATTAT
1 TATTATTTATTAT
220159 TATTATTTATTAT
1 TATTATTTATTAT
*
220172 TATCATTTATTAT
1 TATTATTTATTAT
* *
220185 TATT-GTAATTAT
1 TATTATTTATTAT
220197 T-TTATTTATTAT
1 TATTATTTATTAT
*
220209 TATTATTTCTTAT
1 TATTATTTATTAT
220222 T
1 T
220223 TAATTATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
11 2 0.04
12 19 0.35
13 33 0.61
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:220205 original size:9 final size:8
Alignment explanation
Indices: 220149--220232 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 8
220139 TATTATACTA
220149 TTATTATT
1 TTATTATT
220157 ATTATTA-T
1 -TTATTATT
220165 TTATTATT
1 TTATTATT
* *
220173 ATCATT-TA
1 -TTATTATT
220181 TTATTATT
1 TTATTATT
*
220189 GTAATTATT
1 -TTATTATT
220198 TTATTTATT
1 TTA-TTATT
220207 ATTATTA-T
1 -TTATTATT
*
220215 TTCTTATT
1 TTATTATT
*
220223 TAATTATT
1 TTATTATT
220231 TT
1 TT
220233 GTTTTTGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
7 15 0.26
8 15 0.26
9 25 0.43
10 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (8 bp):
TTATTATT
Found at i:220221 original size:7 final size:7
Alignment explanation
Indices: 220127--220231 Score: 73
Period size: 6 Copynumber: 15.7 Consensus size: 7
220117 TTTTTTAAAA
220127 TATTTAT
1 TATTTAT
*
220134 ATATATAT
1 -TATTTAT
*
220142 TATACTAT
1 TAT-TTAT
220150 TA-TTAT
1 TATTTAT
220156 TA-TTAT
1 TATTTAT
220162 TATTTAT
1 TATTTAT
220169 TA-TTAT
1 TATTTAT
*
220175 CATTTAT
1 TATTTAT
220182 TA-TTAT
1 TATTTAT
* *
220188 T-GTAAT
1 TATTTAT
220194 TA-TT-T
1 TATTTAT
220199 TATTTAT
1 TATTTAT
220206 TA-TTAT
1 TATTTAT
*
220212 TATTTCT
1 TATTTAT
220219 TATTTAAT
1 TATTT-AT
220227 TATTT
1 TATTT
220232 TGTTTTTGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 3 0.04
6 34 0.43
7 25 0.32
8 17 0.22
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (7 bp):
TATTTAT
Found at i:221487 original size:11 final size:11
Alignment explanation
Indices: 221471--221515 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
221461 ATATTTTTCT
221471 TATTTATTTAA
1 TATTTATTTAA
*
221482 TATTTATTTAT
1 TATTTATTTAA
221493 TATTTATTTAA
1 TATTTATTTAA
221504 T-TTTAATTTAA
1 TATTT-ATTTAA
221515 T
1 T
221516 TTCTTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 3 0.10
11 28 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:221498 original size:22 final size:22
Alignment explanation
Indices: 221470--221513 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
221460 AATATTTTTC
221470 TTATTTATTTAATATTT-ATTTA
1 TTATTTATTTAAT-TTTAATTTA
221492 TTATTTATTTAATTTTAATTTA
1 TTATTTATTTAATTTTAATTTA
221514 ATTTCTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTATTTAATTTTAATTTA
Found at i:222148 original size:2 final size:2
Alignment explanation
Indices: 222141--222212 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
222131 TGTAAAACTA
222141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222213 GCTAACCTGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230755 original size:2 final size:2
Alignment explanation
Indices: 230748--230780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
230738 AAGGTAAAGT
230748 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
230781 TGAATAATCA
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:237044 original size:13 final size:13
Alignment explanation
Indices: 237026--237059 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
237016 CACATGCAGA
237026 TAACGATAAAATT
1 TAACGATAAAATT
237039 TAACGATAAAATT
1 TAACGATAAAATT
237052 TAACGATA
1 TAACGATA
237060 TTTACGGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (13 bp):
TAACGATAAAATT
Found at i:238246 original size:15 final size:14
Alignment explanation
Indices: 238200--238246 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
238190 CATTACACAT
*
238200 TCACATA-TTCATA
1 TCACATAGTTCTTA
*
238213 TCACGTAGTTCTT-
1 TCACATAGTTCTTA
238226 TCACATAGTTCTTTA
1 TCACATAGTTC-TTA
238241 TCACAT
1 TCACAT
238247 TTCATATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 16 0.57
14 6 0.21
15 6 0.21
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (14 bp):
TCACATAGTTCTTA
Found at i:238802 original size:24 final size:24
Alignment explanation
Indices: 238774--238833 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
238764 CATTATACCA
238774 TGCATCGATGCATCCCTTAACATG
1 TGCATCGATGCATCCCTTAACATG
*
238798 TGCATCGATGCATCCCTTAATATG
1 TGCATCGATGCATCCCTTAACATG
238822 TGCATCGATGCA
1 TGCATCGATGCA
238834 CTACCCATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTAACATG
Found at i:238927 original size:46 final size:43
Alignment explanation
Indices: 238841--238943 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 43
238831 GCACTACCCA
* *
238841 TGCATCGATACACCAATCACATTCGATGTTTTCATTTTTAAGGGGG
1 TGCATCGATGCACCAATCACATTCGATG-TTTCATTTTTAA--GAG
* **
238887 TGCATCGATGCACTAATGGCATTCGATG-TTCATTTATTTAAGAG
1 TGCATCGATGCACCAATCACATTCGATGTTTCA-TT-TTTAAGAG
238931 TGCATCGATGCAC
1 TGCATCGATGCAC
238944 ATTGAAGATG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
44 19 0.38
45 2 0.04
46 29 0.58
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (43 bp):
TGCATCGATGCACCAATCACATTCGATGTTTCATTTTTAAGAG
Found at i:239331 original size:21 final size:21
Alignment explanation
Indices: 239305--239360 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
239295 TCTTGGTGTT
239305 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTTTCC
*
239326 TTAAGCTTATATAAGCTTTCT
1 TTAAGCTTATATAAGCTTTCC
239347 TTAAGCTTATATAA
1 TTAAGCTTATATAA
239361 CACTCAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTCC
Found at i:240080 original size:24 final size:24
Alignment explanation
Indices: 240053--240114 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
240043 TTATTATATA
240053 TATATTAACTTTAAAAAATAT-TTT
1 TATATTAA-TTTAAAAAATATATTT
**
240077 TATATTAATTTATTAAATATATTT
1 TATATTAATTTAAAAAATATATTT
240101 TATTATTAATTTAA
1 TA-TATTAATTTAA
240115 TTTGAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.30
24 13 0.39
25 10 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTAATTTAAAAAATATATTT
Found at i:240140 original size:29 final size:28
Alignment explanation
Indices: 240039--240148 Score: 65
Period size: 28 Copynumber: 4.0 Consensus size: 28
240029 TCATTTTCAT
*
240039 AATATTATTATA-TATATATTAACTTT-AA
1 AATA-TATTATATTATAAATTAA-TTTGAA
*
240067 AAAATATT-T-TTAT--ATTAATTT-ATTA
1 AATATATTATATTATAAATTAATTTGA--A
* *
240092 AATATATTTTATTATTAATTTAATTTGAA
1 AATATATTATATTA-TAAATTAATTTGAA
*
240121 AATATATTATATGT-TAAATTATTTTGAA
1 AATATATTATAT-TATAAATTAATTTGAA
240149 GCTGAGATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
23 4 0.06
24 5 0.08
25 8 0.12
26 5 0.08
27 7 0.11
28 16 0.24
29 12 0.18
30 8 0.12
31 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
AATATATTATATTATAAATTAATTTGAA
Found at i:240147 original size:28 final size:29
Alignment explanation
Indices: 240091--240148 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
240081 TTAATTTATT
* *
240091 AAATATATTTTATTATTAATTTAATTTGA
1 AAATATATTATATTATTAAATTAATTTGA
* *
240120 AAATATATTATA-TGTTAAATTATTTTGA
1 AAATATATTATATTATTAAATTAATTTGA
240148 A
1 A
240149 GCTGAGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AAATATATTATATTATTAAATTAATTTGA
Found at i:245854 original size:21 final size:19
Alignment explanation
Indices: 245827--245876 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
245817 AAAATAGTTG
245827 AGTATCGATACCCTTACCT
1 AGTATCGATACCCTTACCT
* *
245846 AAGGTATCGGTTCCCTTACCT
1 -A-GTATCGATACCCTTACCT
245867 AGTATCGATA
1 AGTATCGATA
245877 TTCAAGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 16 0.64
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
AGTATCGATACCCTTACCT
Found at i:247139 original size:7 final size:7
Alignment explanation
Indices: 247127--247151 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
247117 TTAACTAACG
247127 AAATTCT
1 AAATTCT
247134 AAATTCT
1 AAATTCT
247141 AAATTCT
1 AAATTCT
247148 AAAT
1 AAAT
247152 CTGGTACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTCT
Found at i:247227 original size:22 final size:21
Alignment explanation
Indices: 247181--247228 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
247171 ATTGGGTATT
247181 GATA-CCTAATGAACAATATC
1 GATACCCTAATGAACAATATC
*
247201 AATACCCT-ATGAACATGATATC
1 GATACCCTAATGAACA--ATATC
247223 GATACC
1 GATACC
247229 ACTAGTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
22 10 0.43
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (21 bp):
GATACCCTAATGAACAATATC
Found at i:247286 original size:50 final size:50
Alignment explanation
Indices: 247211--247313 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
247201 AATACCCTAT
247211 GAACATGATATCGATACCACTAGTCAATAACTCCCTAATCTTAACTATCC
1 GAACATGATATCGATACCACTAGTCAATAACTCCCTAATCTTAACTATCC
247261 GAACATGATATCGATACCACTAGTCAATAACTCCCTAATCTTAACTATCC
1 GAACATGATATCGATACCACTAGTCAATAACTCCCTAATCTTAACTATCC
247311 GAA
1 GAA
247314 TAACAATATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.27
Consensus pattern (50 bp):
GAACATGATATCGATACCACTAGTCAATAACTCCCTAATCTTAACTATCC
Found at i:251464 original size:60 final size:59
Alignment explanation
Indices: 251370--251517 Score: 237
Period size: 60 Copynumber: 2.5 Consensus size: 59
251360 TTGAGAAGGA
*
251370 AATGCAAGGTGGCAAAAT-AGAGATTAAAAGAATGCAGTCTATGTAGTTCAAATCTTCT
1 AATGCAAGGTGGCAAACTAAGAGATTAAAAGAATGCAGTCTATGTAGTTCAAATCTTCT
* * *
251428 AATGCAAGGTGACAAACTAGAGAGATTAAAAGAATGCAGTCTTTGTAGTTCCAATCTTCT
1 AATGCAAGGTGGCAAACTA-AGAGATTAAAAGAATGCAGTCTATGTAGTTCAAATCTTCT
251488 AATGCAAGGTGGCAAACT-AGAGATTAAAAG
1 AATGCAAGGTGGCAAACTAAGAGATTAAAAG
251518 TTTGCAAAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
58 28 0.34
60 55 0.66
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (59 bp):
AATGCAAGGTGGCAAACTAAGAGATTAAAAGAATGCAGTCTATGTAGTTCAAATCTTCT
Found at i:254421 original size:23 final size:24
Alignment explanation
Indices: 254372--254430 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
254362 TTTGTCTTCA
254372 TTCATTTATATTTTTTTATGCTGG
1 TTCATTTATATTTTTTTATGCTGG
* *
254396 TTCATTTAT-TTTTTTTATGTTTG
1 TTCATTTATATTTTTTTATGCTGG
*
254419 TTCGTTTATATT
1 TTCATTTATATT
254431 CAATCCAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (24 bp):
TTCATTTATATTTTTTTATGCTGG
Found at i:254783 original size:16 final size:18
Alignment explanation
Indices: 254742--254785 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
254732 AATTTTAACC
254742 TTAAACCC-ATTAATATT
1 TTAAACCCAATTAATATT
254759 TTAAAACCCAATT-A-ATT
1 TT-AAACCCAATTAATATT
254776 TTAAACCCAA
1 TTAAACCCAA
254786 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 7 0.28
19 3 0.12
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAACCCAATTAATATT
Found at i:255127 original size:20 final size:20
Alignment explanation
Indices: 255102--255146 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
255092 GCACAGCTAG
*
255102 TAAAATATTTATGCAACTAA
1 TAAAATATTTATCCAACTAA
255122 TAAAATATTTATCCAACTAA
1 TAAAATATTTATCCAACTAA
255142 TAAAA
1 TAAAA
255147 AAATAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAATATTTATCCAACTAA
Found at i:265857 original size:18 final size:17
Alignment explanation
Indices: 265819--265857 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
265809 TAAATGCTGA
*
265819 ATGATTCAATGGTCTGG
1 ATGATTCAAAGGTCTGG
*
265836 ATGATTCAAAGGCTCTGT
1 ATGATTCAAAGG-TCTGG
265854 ATGA
1 ATGA
265858 ATTGGCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (17 bp):
ATGATTCAAAGGTCTGG
Found at i:266144 original size:22 final size:20
Alignment explanation
Indices: 266114--266153 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
266104 CACTGAATGT
266114 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTC--CATTCAGCGC
*
266136 TGAATGGTTCCATTCAGC
1 TGAACGGTTCCATTCAGC
266154 AGTAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (20 bp):
TGAACGGTTCCATTCAGCGC
Found at i:266938 original size:83 final size:83
Alignment explanation
Indices: 266799--266967 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
266789 GAAGAGGTTG
266799 AAGCTACGTGGAAAATCAGCAATATGATGGGCATAAACTTTCAAGATAAGAAGGTGTTTGTGGAT
1 AAGCTACGTGGAAAATCAGCAATATGATGGGCATAAACTTTCAAGATAAGAAGGTGTTTGTGGAT
266864 AAAGTGGCCAAGTTGAAC
66 AAAGTGGCCAAGTTGAAC
266882 AAGCTACGTGGAAAATCAGCAATATGATGGGCATAAACTTTCAAGATAAGAAGGTGTTTGTGGAT
1 AAGCTACGTGGAAAATCAGCAATATGATGGGCATAAACTTTCAAGATAAGAAGGTGTTTGTGGAT
266947 AAAGTGGCCAAGTTGAAC
66 AAAGTGGCCAAGTTGAAC
266965 AAG
1 AAG
266968 GAGAGGATGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.24
Consensus pattern (83 bp):
AAGCTACGTGGAAAATCAGCAATATGATGGGCATAAACTTTCAAGATAAGAAGGTGTTTGTGGAT
AAAGTGGCCAAGTTGAAC
Found at i:274770 original size:19 final size:19
Alignment explanation
Indices: 274735--274771 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
274725 ATAAAAGGCT
*
274735 GAAGATATTTAGGAGGAAC
1 GAAGATATTTAGAAGGAAC
*
274754 GAAGATATTTTGAAGGAA
1 GAAGATATTTAGAAGGAA
274772 AGGTGGAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.24
Consensus pattern (19 bp):
GAAGATATTTAGAAGGAAC
Found at i:277623 original size:2 final size:2
Alignment explanation
Indices: 277616--277644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
277606 AGAAAACTTG
277616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
277645 ATTTACACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:282698 original size:19 final size:17
Alignment explanation
Indices: 282673--282724 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
282663 TTTAATAATG
*
282673 ATATTATTTTATGTTATT
1 ATATTATTTTAT-TTATC
282691 ATTATTATTTTTCATTTATC
1 A-TATTA-TTTT-ATTTATC
282711 ATATTATTTTATTT
1 ATATTATTTTATTT
282725 TAAGCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 5 0.17
19 10 0.33
20 9 0.30
21 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTATTTTATTTATC
Found at i:283941 original size:17 final size:17
Alignment explanation
Indices: 283919--283951 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
283909 TTGGGTTTCT
283919 TGGGCCTGAACCGGGTC
1 TGGGCCTGAACCGGGTC
*
283936 TGGGCCTGAATCGGGT
1 TGGGCCTGAACCGGGT
283952 TGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.24, G:0.42, T:0.21
Consensus pattern (17 bp):
TGGGCCTGAACCGGGTC
Found at i:283995 original size:3 final size:3
Alignment explanation
Indices: 283989--284048 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
283979 ATATTATTTG
* **
283989 TAA TAA TAA TAA TAA TAA TAA TAA T-A TGA TAA TAA TAA TAA TTG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
284036 TAA -AA TAA TAA TA
1 TAA TAA TAA TAA TA
284049 TATATATATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:284021 original size:23 final size:23
Alignment explanation
Indices: 283993--284048 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
283983 TATTTGTAAT
*
283993 AATAATAATAATAATAATAATAT
1 AATAATAATAATAATAATAATAA
* **
284016 GATAATAATAATAATTGTAATAA
1 AATAATAATAATAATAATAATAA
284039 AATAATAATA
1 AATAATAATA
284049 TATATATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
AATAATAATAATAATAATAATAA
Found at i:299081 original size:22 final size:22
Alignment explanation
Indices: 299056--299103 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
299046 TTTCTACTAT
*
299056 AATTTGTTTTTTTTAAAAAGAA
1 AATTTGATTTTTTTAAAAAGAA
299078 AATTTGATTTTTTTAAAAAGAA
1 AATTTGATTTTTTTAAAAAGAA
299100 AATT
1 AATT
299104 AGCTTTGACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (22 bp):
AATTTGATTTTTTTAAAAAGAA
Found at i:299940 original size:6 final size:6
Alignment explanation
Indices: 299929--299978 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
299919 AGACACGTAT
299929 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
299977 GA
1 GA
299979 GACGGCGGCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:300492 original size:22 final size:22
Alignment explanation
Indices: 300464--300508 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
300454 CCGCGTCTCG
300464 GGTCGTGGTCGTGGTAATACGT
1 GGTCGTGGTCGTGGTAATACGT
300486 GGTCGTGGTCGTGGTAATACGT
1 GGTCGTGGTCGTGGTAATACGT
300508 G
1 G
300509 TCTTCGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.42, T:0.31
Consensus pattern (22 bp):
GGTCGTGGTCGTGGTAATACGT
Found at i:300619 original size:20 final size:20
Alignment explanation
Indices: 300594--300707 Score: 79
Period size: 20 Copynumber: 5.6 Consensus size: 20
300584 ACTGTAGACT
300594 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
300614 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
300635 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** ** *
300655 ATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
300676 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
300696 ATCGCAACGCGA
1 ATCGCAACGCGA
300708 TTTTCAACTA
Statistics
Matches: 66, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 33 0.50
21 21 0.32
22 3 0.05
23 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:300641 original size:41 final size:41
Alignment explanation
Indices: 300584--300732 Score: 178
Period size: 41 Copynumber: 3.6 Consensus size: 41
300574 TTTTTAATTT
300584 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC-
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACG-CG
***
300625 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCGTTGCG
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCG
* *
300666 ATTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCG
1 ACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCG
* * *
300707 ATTTTCA-ACTATCGCAATGCGAAATG
1 ACTGT-AGACTATCGCAACGCGAAATG
300733 CAACGTGAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.01
41 95 0.98
42 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCG
Found at i:300736 original size:21 final size:21
Alignment explanation
Indices: 300591--300736 Score: 77
Period size: 21 Copynumber: 7.1 Consensus size: 21
300581 TTTACTGTAG
*
300591 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
300612 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
*
300631 GACTATCGCAACGCGAAATGGA
1 -ACTATCGCAACGCGAAATGCA
* *** ** *
300653 A-AATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
300673 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
300694 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
300714 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
300735 AC
1 AC
300737 GTGAATTTGC
Statistics
Matches: 86, Mismatches: 32, Indels: 14
0.65 0.24 0.11
Matches are distributed among these distances:
18 3 0.03
19 4 0.05
20 35 0.41
21 37 0.43
22 4 0.05
23 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:302376 original size:29 final size:29
Alignment explanation
Indices: 302204--302383 Score: 179
Period size: 29 Copynumber: 6.2 Consensus size: 29
302194 CGTTGACCGA
302204 GTGATATTTTAGTAATTATTTTTAAAATG
1 GTGATATTTTAGTAATTATTTTTAAAATG
* * *
302233 ATGATATTTTGGTAATTATTTTGAAAATG
1 GTGATATTTTAGTAATTATTTTTAAAATG
* * **
302262 GTGCTA-TTTCGTAATT-TTTTTAAAAAA
1 GTGATATTTTAGTAATTATTTTTAAAATG
*
302289 GTGATAATTTT-GTAATTTTTTTTTAAAAAT-
1 GTGAT-ATTTTAGTAA-TTATTTTT-AAAATG
* * *
302319 GTGATATTTTCGTAATTAGTTTTAAAAAG
1 GTGATATTTTAGTAATTATTTTTAAAATG
* *
302348 GTGATATTTTAGTAAATATTTATTAAAAGG
1 GTGATATTTTAGTAATTATTT-TTAAAATG
302378 GTGATA
1 GTGATA
302384 ATTGTGTCAA
Statistics
Matches: 125, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
27 12 0.10
28 18 0.14
29 64 0.51
30 27 0.22
31 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (29 bp):
GTGATATTTTAGTAATTATTTTTAAAATG
Found at i:304554 original size:6 final size:7
Alignment explanation
Indices: 304532--304561 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
304522 GTCAAAGAAA
304532 GTCAACG
1 GTCAACG
304539 GTCAACG
1 GTCAACG
304546 GTC-ACG
1 GTCAACG
304552 GTCAACG
1 GTCAACG
304559 GTC
1 GTC
304562 GGGCCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:304554 original size:13 final size:13
Alignment explanation
Indices: 304536--304561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
304526 AAGAAAGTCA
304536 ACGGTCAACGGTC
1 ACGGTCAACGGTC
304549 ACGGTCAACGGTC
1 ACGGTCAACGGTC
304562 GGGCCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:304573 original size:17 final size:17
Alignment explanation
Indices: 304551--304608 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
304541 CAACGGTCAC
* *
304551 GGTCAACGGTCGGGCCG
1 GGTCAACAGTCGGGTCG
*
304568 GGTCAACAGTCGAGTCG
1 GGTCAACAGTCGGGTCG
304585 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
304602 GGTCAAC
1 GGTCAAC
304609 CAGCAGCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:311591 original size:7 final size:7
Alignment explanation
Indices: 311579--311611 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
311569 GTCAAAGAAA
311579 GTCAACG
1 GTCAACG
311586 GTCAACG
1 GTCAACG
311593 GTC-ACG
1 GTCAACG
311599 GTCAACG
1 GTCAACG
311606 GTCAAC
1 GTCAAC
311612 TGTCGGGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:311601 original size:13 final size:13
Alignment explanation
Indices: 311583--311609 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
311573 AAGAAAGTCA
311583 ACGGTCAACGGTC
1 ACGGTCAACGGTC
311596 ACGGTCAACGGTC
1 ACGGTCAACGGTC
311609 A
1 A
311610 ACTGTCGGGT
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:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:311627 original size:17 final size:17
Alignment explanation
Indices: 311605--311645 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
311595 CACGGTCAAC
*
311605 GGTCAACTGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
311622 GGTCAACAGTTGGGTCG
1 GGTCAACAGTCGGGTCG
311639 GGTCAAC
1 GGTCAAC
311646 CCGGTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:311663 original size:19 final size:19
Alignment explanation
Indices: 311639--311709 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
311629 AGTTGGGTCG
*
311639 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
311658 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
311677 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
311697 GGTCAAACCGGTT
1 GGTCAAACCGGTT
311710 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:311677 original size:10 final size:10
Alignment explanation
Indices: 311641--311709 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
311631 TTGGGTCGGG
*
311641 TCAACCCGGT
1 TCAAACCGGT
*
311651 TCAGACCGG-
1 TCAAACCGGT
311660 TCAAACCGGT
1 TCAAACCGGT
*
311670 TCAGACCGG-
1 TCAAACCGGT
311679 TCAAACCGGT
1 TCAAACCGGT
*
311689 TCAAAACTGG-
1 TC-AAACCGGT
311699 TCAAACCGGT
1 TCAAACCGGT
311709 T
1 T
311710 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:316602 original size:18 final size:17
Alignment explanation
Indices: 316570--316603 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
316560 GTTTGAATGT
*
316570 AAAATTAAGATTAAGGA
1 AAAATTAAAATTAAGGA
316587 AAAATGTAAAATTAAGG
1 AAAAT-TAAAATTAAGG
316604 CAGCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
AAAATTAAAATTAAGGA
Found at i:317175 original size:41 final size:41
Alignment explanation
Indices: 317130--317289 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 41
317120 ATTCGCGTTG
* *
317130 CATTTCGCGTTTCGATAATTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
317171 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATACTTG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTC
* ** * ** **
317213 AAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
317253 CAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
317290 AGTCTACAGT
Statistics
Matches: 93, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 15 0.16
41 63 0.68
42 15 0.16
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:317180 original size:20 final size:20
Alignment explanation
Indices: 317155--317444 Score: 113
Period size: 20 Copynumber: 14.6 Consensus size: 20
317145 TAATTGAAAA
*
317155 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* ** *
317175 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
* * ** *
317196 TCACGTTGCGATACTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
*
317217 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
*
317237 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
* ** *
317257 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
* * *
317278 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
317300 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
* * *
317321 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
317341 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
*
317362 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAAT
*
317374 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
* * *
317394 TCCCGTTGCGATAGTT--AAA
1 TCGCGTTGCGAT-TTTCCAAT
*
317413 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
*
317433 TCGCATTGCGAT
1 TCGCGTTGCGAT
317445 AGTTGAAAAT
Statistics
Matches: 202, Mismatches: 47, Indels: 42
0.69 0.16 0.14
Matches are distributed among these distances:
12 3 0.01
14 8 0.04
18 2 0.01
19 29 0.14
20 79 0.39
21 60 0.30
22 21 0.10
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAAT
Found at i:317217 original size:62 final size:61
Alignment explanation
Indices: 317137--317289 Score: 216
Period size: 62 Copynumber: 2.5 Consensus size: 61
317127 TTGCATTTCG
* *
317137 CGTTTCGATAATTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCA
1 CGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-GTTCAAAATCA
* * * ** *
317199 CGTTGCGATACTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
1 CGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATGTTCAAAATCA
*
317260 CGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CGTTGCGATAATTGAAAATCGCGTTGCGAT
317290 AGTCTACAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 34 0.41
62 48 0.59
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (61 bp):
CGTTGCGATAATTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATGTTCAAAATCA
Done.