Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000947.1 Hibiscus syriacus cultivar Beakdansim tig00001894_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: 275664
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1730 original size:2 final size:2
Alignment explanation
Indices: 1723--1771 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1713 TTGTTTATGC
1723 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1762 AT AT AT AT AT
1 AT AT AT AT AT
1772 GTTTTGTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1740 original size:12 final size:12
Alignment explanation
Indices: 1723--1771 Score: 77
Period size: 11 Copynumber: 4.3 Consensus size: 12
1713 TTGTTTATGC
1723 ATATATATATAT
1 ATATATATATAT
1735 ATATATATATAT
1 ATATATATATAT
1747 -TATAT-TATAT
1 ATATATATATAT
1757 AT-TATATATAT
1 ATATATATATAT
1768 ATAT
1 ATAT
1772 GTTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.24
11 13 0.38
12 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATATATAT
Found at i:10691 original size:56 final size:56
Alignment explanation
Indices: 10602--10714 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
10592 GATAAATTTA
* *
10602 ATTTGGTAAGTCGCGTGGACATGTTAAAGATCATATCAACAAATTGCGACTTTTTG
1 ATTTGGTAAGTCGCGTGGACATGTTAAAAATCATATCAACAAATTGCAACTTTTTG
*
10658 ATTTGGTGAGTCGCGTGGACATGTTAAAAATCATATCAACAAATTGCAACTTTTTG
1 ATTTGGTAAGTCGCGTGGACATGTTAAAAATCATATCAACAAATTGCAACTTTTTG
10714 A
1 A
10715 GAGATGTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (56 bp):
ATTTGGTAAGTCGCGTGGACATGTTAAAAATCATATCAACAAATTGCAACTTTTTG
Found at i:17867 original size:45 final size:44
Alignment explanation
Indices: 17770--17871 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 44
17760 CACATTCAAT
* *
17770 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGTAATTA
1 GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAATGTAATTA
* * * *
17814 GTGCATCGATGCACCCCCTTAAA-ATGAAAACATCGAA-GATGATTG
1 GTGTATCGATGCA-CCCCTTAAAGAAG-AAACATCGAATG-TAATTA
17859 GTGTATCGATGCA
1 GTGTATCGATGCA
17872 TGGGTAGTGC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 15 0.31
45 33 0.69
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (44 bp):
GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAATGTAATTA
Found at i:17924 original size:20 final size:20
Alignment explanation
Indices: 17879--17936 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
17869 GCATGGGTAG
17879 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
17903 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
17923 TGTATCGATGCACT
1 TGCATCGATGCACT
17937 TCAAGAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:19238 original size:34 final size:32
Alignment explanation
Indices: 19171--19245 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 32
19161 AGATAACCTT
* * *
19171 ACATCTCCCTAGTTTTTCCGGGCTAAACTAGA
1 ACATTTCCCTAGTTTTTACGGGATAAACTAGA
*
19203 ACATTTCCCTAGCTTTTATACGGGATAAGCTAGA
1 ACATTTCCCTAG-TTTT-TACGGGATAAACTAGA
*
19237 ACCTTTCCC
1 ACATTTCCC
19246 CTTTATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 11 0.31
33 4 0.11
34 21 0.58
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (32 bp):
ACATTTCCCTAGTTTTTACGGGATAAACTAGA
Found at i:19554 original size:21 final size:22
Alignment explanation
Indices: 19528--19570 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
19518 CCAGAATGGG
*
19528 GGGAATCGGTA-CCCCTTCATA
1 GGGAATCGATACCCCCTTCATA
19549 GGGAATCGATACCCCCTTCATA
1 GGGAATCGATACCCCCTTCATA
19571 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTCATA
Found at i:22260 original size:34 final size:34
Alignment explanation
Indices: 22183--22286 Score: 140
Period size: 34 Copynumber: 3.1 Consensus size: 34
22173 ACCTTACAAC
* * * *
22183 TCCCTAG-TTTTTC-CGGGCTAAACTATAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
22215 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
22249 TCCCTATCTTTTACACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
22283 TCCC
1 TCCC
22287 CTTTACAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
32 7 0.11
33 5 0.08
34 51 0.81
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:22750 original size:20 final size:20
Alignment explanation
Indices: 22718--22795 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
22708 ATCTGTTCCC
*
22718 GGGGAATCGATACCCCCTGG
1 GGGGAATCTATACCCCCTGG
*
22738 GGGAAATCTATACCCCCTGG
1 GGGGAATCTATACCCCCTGG
*
22758 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTATACCCCCTGG
**
22778 GGGGAATCCGTACCCCCT
1 GGGGAATCTATACCCCCT
22796 AGGCAATCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.19, C:0.32, G:0.31, T:0.18
Consensus pattern (20 bp):
GGGGAATCTATACCCCCTGG
Found at i:25339 original size:34 final size:32
Alignment explanation
Indices: 25277--25346 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
25267 ACCTTACAAC
* *
25277 TCCCTAGTTTTTCAGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACAGGGATAAACTAGAACCTT
*
25309 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTACA-GGGATAAACTAGAACCTT
25343 TCCC
1 TCCC
25347 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 6 0.18
34 20 0.61
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACAGGGATAAACTAGAACCTT
Found at i:25655 original size:21 final size:21
Alignment explanation
Indices: 25629--25668 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25619 CCAGAATGGG
*
25629 GGGAATCGGTACCCCTTCACA
1 GGGAATCGATACCCCTTCACA
25650 GGGAATCGATACCCCTTCA
1 GGGAATCGATACCCCTTCA
25669 TAATATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCACA
Found at i:26638 original size:63 final size:65
Alignment explanation
Indices: 26571--26731 Score: 197
Period size: 63 Copynumber: 2.5 Consensus size: 65
26561 TCCCTTGACA
* *
26571 GGTGCATCGATGCACTATC-TATGCATCGATACA-TAAATCCTATTCGATGTTTGCA-TTTAAGG
1 GGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCCTATTCGATGTTTGCATTTTAAAG
26633 G
65 G
* * ** **
26634 GGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGGTATTCGATGTTTTTATTTTAAAGG
1 GGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCTATTCGATGTTTGCATTTTAAAGG
*
26698 AGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGTGCATCGATGCACTATCATGTGCATCGATACAC
26732 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 45 0.53
64 39 0.46
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (65 bp):
GGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCTATTCGATGTTTGCATTTTAAAGG
Found at i:31547 original size:130 final size:130
Alignment explanation
Indices: 31406--31653 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
31396 TATTTATATA
*
31406 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
31471 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
31536 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
31601 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
31654 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:31684 original size:130 final size:129
Alignment explanation
Indices: 31420--31684 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
31410 ATTTGGTCCT
* *
31420 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
31485 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
31550 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
31615 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
31679 -A
128 CA
31680 AAATT
1 AAATT
31685 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:32144 original size:16 final size:18
Alignment explanation
Indices: 32123--32156 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
32113 ATTTCTTATT
32123 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
32139 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
32157 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:32303 original size:21 final size:21
Alignment explanation
Indices: 32279--32321 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
32269 TATTACCTTA
32279 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
32300 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
32321 A
1 A
32322 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:32339 original size:35 final size:35
Alignment explanation
Indices: 32290--32375 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
32280 ATTGAAGTAT
** * *
32290 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
32325 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
32360 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
32376 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:38644 original size:33 final size:33
Alignment explanation
Indices: 38594--38674 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
38584 GTTGGTTTTA
* *
38594 AGGTTCGGGTCATTTTAGGTATGGATTCGTTTC
1 AGGTTCGAGTCATTTTAGGTATGGATTAGTTTC
38627 AGGATT-GAGTCATTTTAGGTATGGATTAGTTTC
1 AGG-TTCGAGTCATTTTAGGTATGGATTAGTTTC
38660 AGGTTCGAGTCATTT
1 AGGTTCGAGTCATTT
38675 GGAATTGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 2 0.05
33 40 0.91
34 2 0.05
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (33 bp):
AGGTTCGAGTCATTTTAGGTATGGATTAGTTTC
Found at i:42915 original size:18 final size:18
Alignment explanation
Indices: 42892--42928 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42882 GAAATTGATA
* *
42892 AAATAATAATAACTTAAT
1 AAATAAAAATAAATTAAT
42910 AAATAAAAATAAATTAAT
1 AAATAAAAATAAATTAAT
42928 A
1 A
42929 GGGGCCGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAAAATAAATTAAT
Found at i:47691 original size:2 final size:2
Alignment explanation
Indices: 47684--47721 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47674 ACGTTGAGGG
47684 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
47722 GGGTCGGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48495 original size:20 final size:20
Alignment explanation
Indices: 48454--48495 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
48444 ATCCAGAAAG
*
48454 CACTTGCAAACATTAGCCAA
1 CACTTGCAAACATTAGCAAA
*
48474 CACTTGCAAACATTTGCAAA
1 CACTTGCAAACATTAGCAAA
48494 CA
1 CA
48496 TTTATCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (20 bp):
CACTTGCAAACATTAGCAAA
Found at i:48496 original size:10 final size:10
Alignment explanation
Indices: 48457--48498 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
48447 CAGAAAGCAC
48457 TTGCAAACAT
1 TTGCAAACAT
* * *
48467 TAGCCAACAC
1 TTGCAAACAT
48477 TTGCAAACAT
1 TTGCAAACAT
48487 TTGCAAACAT
1 TTGCAAACAT
48497 TT
1 TT
48499 ATCCCCATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (10 bp):
TTGCAAACAT
Found at i:50015 original size:12 final size:12
Alignment explanation
Indices: 49995--50059 Score: 85
Period size: 12 Copynumber: 5.4 Consensus size: 12
49985 CTGATACGCA
*
49995 ATACACATACAT
1 ATACACATACGT
*
50007 ATACGCATACGT
1 ATACACATACGT
50019 ATACACATACGT
1 ATACACATACGT
*
50031 ATACACATACGC
1 ATACACATACGT
* *
50043 ATACGCATACAT
1 ATACACATACGT
50055 ATACA
1 ATACA
50060 TATAACAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.23
Consensus pattern (12 bp):
ATACACATACGT
Found at i:50022 original size:18 final size:18
Alignment explanation
Indices: 49988--50059 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
49978 ACTCGACCTG
* *
49988 ATACGCAATACACATACAT
1 ATACGC-ATACATATACAC
*
50007 ATACGCATACGTATACAC
1 ATACGCATACATATACAC
* * *
50025 ATACGTATACACATACGC
1 ATACGCATACATATACAC
50043 ATACGCATACATATACA
1 ATACGCATACATATACA
50060 TATAACAAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
18 37 0.86
19 6 0.14
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.22
Consensus pattern (18 bp):
ATACGCATACATATACAC
Found at i:50023 original size:24 final size:24
Alignment explanation
Indices: 49988--50059 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
49978 ACTCGACCTG
*
49988 ATACGCAATACACATACATATACGC
1 ATACGC-ATACACATACATATACAC
* *
50013 ATACGTATACACATACGTATACAC
1 ATACGCATACACATACATATACAC
*
50037 ATACGCATACGCATACATATACA
1 ATACGCATACACATACATATACA
50060 TATAACAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
24 36 0.88
25 5 0.12
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.22
Consensus pattern (24 bp):
ATACGCATACACATACATATACAC
Found at i:50826 original size:18 final size:19
Alignment explanation
Indices: 50785--50826 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
50775 ATTATCCAAC
50785 AAACTTGAAATCCATAACAAT
1 AAACTTGAAATCCAT-A-AAT
50806 AAACTTGAAATCCAT-AAT
1 AAACTTGAAATCCATAAAT
50824 AAA
1 AAA
50827 AAATCAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
21 15 0.71
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (19 bp):
AAACTTGAAATCCATAAAT
Found at i:51906 original size:20 final size:20
Alignment explanation
Indices: 51873--51910 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51863 AAAAAATTAA
*
51873 TTTATAATTGTTAATCTTTT
1 TTTATAATTATTAATCTTTT
*
51893 TTTATTATTATTAATCTT
1 TTTATAATTATTAATCTT
51911 CAATTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTATAATTATTAATCTTTT
Found at i:61341 original size:35 final size:34
Alignment explanation
Indices: 61302--61376 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 34
61292 ATTAATTATT
61302 TATTAA-AGTAATAGTTTTATAATATATTT-TAAAAA
1 TATTAATAGT-ATA-TTTTA-AATATATTTATAAAAA
* *
61337 TATTAATTAGTATATTTTAAATATCTTTATTAAAA
1 TATTAA-TAGTATATTTTAAATATATTTATAAAAA
61372 TATTA
1 TATTA
61377 TTAGATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 8 0.23
35 21 0.60
36 3 0.09
37 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TATTAATAGTATATTTTAAATATATTTATAAAAA
Found at i:61374 original size:23 final size:23
Alignment explanation
Indices: 61317--61375 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
61307 AAGTAATAGT
61317 TTTA-TAATATATTTTAAAAATA
1 TTTATTAATATATTTTAAAAATA
* * * *
61339 TTAATTAGTATATTTTAAATATC
1 TTTATTAATATATTTTAAAAATA
*
61362 TTTATTAAAATATT
1 TTTATTAATATATT
61376 ATTAGATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTATTAATATATTTTAAAAATA
Found at i:61431 original size:19 final size:19
Alignment explanation
Indices: 61363--61440 Score: 65
Period size: 19 Copynumber: 4.1 Consensus size: 19
61353 TTAAATATCT
61363 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
61382 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
61401 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
61421 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
61439 TT
1 TT
61441 TATTTCTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
18 15 0.31
19 18 0.38
20 8 0.17
22 7 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:61484 original size:26 final size:25
Alignment explanation
Indices: 61394--61588 Score: 69
Period size: 26 Copynumber: 7.4 Consensus size: 25
61384 ATTATATTAA
61394 TATT-AAATATATAAATAATAT-TAT
1 TATTAAAATA-ATAAATAATATATAT
* * * *
61418 TCATTATTAATAATTTAATAATTTATTT
1 T-ATTA-AAATAA-TAAATAATATATAT
* *
61446 CTATGAAATTAATAAATAATATATAT
1 -TATTAAAATAATAAATAATATATAT
* * *
61472 T-TT-TAATAATAATTTATTATATAT
1 TATTAAAATAATAA-ATAATATATAT
*
61496 TATTAAAATAAAAATATAATATCTTATAT
1 TATTAAAATAATAA-ATAATA---TATAT
* * * *
61525 TATTATAAT-ATAATTGAT-TATTT
1 TATTAAAATAATAAATAATATATAT
*
61548 TATTATAATATTAAAAAAATAATATTATAT
1 TATTA-AA-A-T-AATAAATAATA-TATAT
61578 TATTAGAAATA
1 TATTA-AAATA
61589 TTAATAAAAA
Statistics
Matches: 122, Mismatches: 30, Indels: 35
0.65 0.16 0.19
Matches are distributed among these distances:
23 16 0.13
24 13 0.11
25 7 0.06
26 25 0.20
27 20 0.16
28 15 0.12
29 15 0.12
30 11 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTAAAATAATAAATAATATATAT
Found at i:69763 original size:2 final size:2
Alignment explanation
Indices: 69756--69786 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69746 ATCCCGTCTC
69756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69787 ATCATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73892 original size:29 final size:29
Alignment explanation
Indices: 73855--73910 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
73845 GACAAATTAT
*
73855 TTATTTATTTAATCATTTATCTATTATAA
1 TTATTTATTTAATCATTCATCTATTATAA
*
73884 TTATTTATTTAGTCATTCATCTATTAT
1 TTATTTATTTAATCATTCATCTATTAT
73911 TTTATTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATTTATTTAATCATTCATCTATTATAA
Found at i:81059 original size:60 final size:60
Alignment explanation
Indices: 80926--81061 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
80916 AAAGTATATG
** * * *
80926 AATGGT-CCCTGACTATAGGGTATTATTTTATTAAGTCCCTCGATTATTAAAAGTTATAA
1 AATGGTCCCCTGACTATAGAATATTATTTTATTAAGTCCATCGACTATCAAAAGTTATAA
* *** * *
80985 AATAGTCTTATGACTATAGAATGTT-TCTTTATTAAGTCCATCGCCTATCAAAAGTTATAA
1 AATGGTCCCCTGACTATAGAATATTAT-TTTATTAAGTCCATCGACTATCAAAAGTTATAA
81045 AATGGTCCCCTGACTAT
1 AATGGTCCCCTGACTAT
81062 TTATGATATT
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
59 6 0.10
60 54 0.90
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (60 bp):
AATGGTCCCCTGACTATAGAATATTATTTTATTAAGTCCATCGACTATCAAAAGTTATAA
Found at i:85132 original size:46 final size:48
Alignment explanation
Indices: 85060--85161 Score: 120
Period size: 46 Copynumber: 2.2 Consensus size: 48
85050 ATTTCATCTG
*
85060 ATTTCTGA-CTTGAATTCAGTTTTGATACATGACCTGAATT-TTGTTC
1 ATTTCTGATCTTGAATTCAGTTATGATACATGACCTGAATTCTTGTTC
* * * * * *
85106 ATTTCTGATC-TGGATTCTGTTATGATATATGATCTGAATTCTTTTTT
1 ATTTCTGATCTTGAATTCAGTTATGATACATGACCTGAATTCTTGTTC
85153 ATTTCTGAT
1 ATTTCTGAT
85162 ATCTCTGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
46 33 0.70
47 14 0.30
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (48 bp):
ATTTCTGATCTTGAATTCAGTTATGATACATGACCTGAATTCTTGTTC
Found at i:85340 original size:2 final size:2
Alignment explanation
Indices: 85333--85368 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
85323 CATGTTTTAA
85333 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
85369 GTTTTAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89359 original size:15 final size:15
Alignment explanation
Indices: 89339--89375 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
89329 ATATTTAGTT
89339 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
89354 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
89369 GGGCGGG
1 GGGCGGG
89376 TGAGGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.19, G:0.70, T:0.05
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:90141 original size:34 final size:33
Alignment explanation
Indices: 90065--90171 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
90055 GTGGTAATAA
* *
90065 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
90099 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
90134 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
90168 ATTT
1 ATTT
90172 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:90153 original size:36 final size:34
Alignment explanation
Indices: 90098--90176 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
90088 TTTAAATAGT
*
90098 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
90130 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
90164 TATTATTTATTTA
1 TATTATTTTTTTA
90177 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:92154 original size:22 final size:23
Alignment explanation
Indices: 92129--92177 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
92119 CAAACAACCG
92129 AAAACGAGTCA-AAAAACAAAGA
1 AAAACGAGTCATAAAAACAAAGA
* * *
92151 AAAATGTGTCATAAAAACAAATA
1 AAAACGAGTCATAAAAACAAAGA
92174 AAAA
1 AAAA
92178 TATGTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.12
Consensus pattern (23 bp):
AAAACGAGTCATAAAAACAAAGA
Found at i:92170 original size:23 final size:23
Alignment explanation
Indices: 92136--92188 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
92126 CCGAAAACGA
*
92136 GTCA-AAAAACAAAGAAAAATGT
1 GTCATAAAAACAAAGAAAAATAT
*
92158 GTCATAAAAACAAATAAAAATAT
1 GTCATAAAAACAAAGAAAAATAT
92181 GTCATAAA
1 GTCATAAA
92189 GGTATACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (23 bp):
GTCATAAAAACAAAGAAAAATAT
Found at i:93872 original size:40 final size:40
Alignment explanation
Indices: 93817--93938 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
93807 ACCGTAGTGC
* *
93817 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
93857 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
93897 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
93937 TA
1 TA
93939 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:100784 original size:40 final size:40
Alignment explanation
Indices: 100729--100890 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
100719 ACCGTAGTGC
* *
100729 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
100769 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
100809 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
100849 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
100889 TA
1 TA
100891 TAAACCTGCA
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 120 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:104835 original size:2 final size:2
Alignment explanation
Indices: 104828--104863 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
104818 GGTAAAAAGG
104828 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
104864 CAAGAGTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113232 original size:16 final size:16
Alignment explanation
Indices: 113211--113254 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
113201 CTTATATTTT
**
113211 TTTAAAAATTTTATTA
1 TTTAAAAAAATTATTA
113227 TTTAAAAAAATTATTA
1 TTTAAAAAAATTATTA
*
113243 TTCTAAATAAAT
1 TT-TAAAAAAAT
113255 ATCTATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAAAAATTATTA
Found at i:113234 original size:17 final size:18
Alignment explanation
Indices: 113214--113256 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
113204 ATATTTTTTT
*
113214 AAAAATTTTATTATT-TA
1 AAAAATATTATTATTCTA
113231 AAAAA-ATTATTATTCTA
1 AAAAATATTATTATTCTA
113248 AATAAATAT
1 AA-AAATAT
113257 CTATCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 3 0.14
19 2 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATATTATTATTCTA
Found at i:114101 original size:195 final size:195
Alignment explanation
Indices: 113769--114163 Score: 790
Period size: 195 Copynumber: 2.0 Consensus size: 195
113759 AATTATTTTA
113769 AATTATATAATCACACTTAAATTATTAGTTATTTTTTATTAATCTGGTACAATGTAATATATATT
1 AATTATATAATCACACTTAAATTATTAGTTATTTTTTATTAATCTGGTACAATGTAATATATATT
113834 CAAATATAATTATCAACCACTTGATTGAATGCTCATATCTCTGAAATTTTTTGTGCTCGAACCTG
66 CAAATATAATTATCAACCACTTGATTGAATGCTCATATCTCTGAAATTTTTTGTGCTCGAACCTG
113899 GAACATTAAAGAATAATAACAATTCATTTACCATCGATGTTGCTTAGTTTGTGTAATTATTAATT
131 GAACATTAAAGAATAATAACAATTCATTTACCATCGATGTTGCTTAGTTTGTGTAATTATTAATT
113964 AATTATATAATCACACTTAAATTATTAGTTATTTTTTATTAATCTGGTACAATGTAATATATATT
1 AATTATATAATCACACTTAAATTATTAGTTATTTTTTATTAATCTGGTACAATGTAATATATATT
114029 CAAATATAATTATCAACCACTTGATTGAATGCTCATATCTCTGAAATTTTTTGTGCTCGAACCTG
66 CAAATATAATTATCAACCACTTGATTGAATGCTCATATCTCTGAAATTTTTTGTGCTCGAACCTG
114094 GAACATTAAAGAATAATAACAATTCATTTACCATCGATGTTGCTTAGTTTGTGTAATTATTAATT
131 GAACATTAAAGAATAATAACAATTCATTTACCATCGATGTTGCTTAGTTTGTGTAATTATTAATT
114159 AATTA
1 AATTA
114164 AATTAAAAGA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 200 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (195 bp):
AATTATATAATCACACTTAAATTATTAGTTATTTTTTATTAATCTGGTACAATGTAATATATATT
CAAATATAATTATCAACCACTTGATTGAATGCTCATATCTCTGAAATTTTTTGTGCTCGAACCTG
GAACATTAAAGAATAATAACAATTCATTTACCATCGATGTTGCTTAGTTTGTGTAATTATTAATT
Found at i:123830 original size:21 final size:21
Alignment explanation
Indices: 123788--123830 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
123778 TTTCTGGGCT
* * *
123788 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
123809 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
123830 A
1 A
123831 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:123904 original size:24 final size:22
Alignment explanation
Indices: 123860--123906 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
123850 ATGTCATGGG
*
123860 GGAACCGATACCCCCACAGGAA
1 GGAACCGATACCCCCAAAGGAA
*
123882 GGAACCGATTCCCCCCTAAAGGAA
1 GGAACCGA-TACCCCC-AAAGGAA
123906 G
1 G
123907 AAAAGAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.34, C:0.34, G:0.23, T:0.09
Consensus pattern (22 bp):
GGAACCGATACCCCCAAAGGAA
Found at i:125484 original size:23 final size:23
Alignment explanation
Indices: 125452--125517 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
125442 TATTATATGG
*
125452 CACTACGGTGCAATTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
* *
125475 CAC-TCTGGTGCAATTCTACGTGG
1 CACTTC-GGTGCAATTCTACGCGA
*
125498 CACTTCGGTGCAATTATACG
1 CACTTCGGTGCAATTCTACG
125518 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.92
24 2 0.05
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:128971 original size:21 final size:21
Alignment explanation
Indices: 128929--128971 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
128919 TTTCTGGGCT
* * *
128929 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
128950 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
128971 A
1 A
128972 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:130437 original size:21 final size:21
Alignment explanation
Indices: 130411--130522 Score: 156
Period size: 21 Copynumber: 5.4 Consensus size: 21
130401 GATTCTAACT
130411 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
130432 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
130453 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
** *
130473 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
130494 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
*
130514 ATTGCAACG
1 ATCGCAACG
130523 CGATTTTTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
20 26 0.32
21 54 0.68
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:130438 original size:41 final size:41
Alignment explanation
Indices: 130388--130527 Score: 171
Period size: 41 Copynumber: 3.4 Consensus size: 41
130378 CGCGAACATA
* *
130388 TAAATCGCAAC-ACGATTC-TAACTATCGCAACGAGTATCCG
1 TAAATCGCAACGACGATTCGTAA-AATCGCAACGCGTATCCG
*
130428 TAAAATCGCAACGA-GTATCCGTAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGACG-ATTCGTAAAATCGCAACGCGTATCCG
* *
130470 TAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGACGATTCGTAAAATCGCAACGCGTATCCG
*
130511 TAAATTGCAACG-CGATT
1 TAAATCGCAACGACGATT
130528 TTTAAAGCGC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
40 4 0.05
41 59 0.68
42 21 0.24
43 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (41 bp):
TAAATCGCAACGACGATTCGTAAAATCGCAACGCGTATCCG
Found at i:131134 original size:20 final size:20
Alignment explanation
Indices: 131086--131163 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
131076 TTCTAAACTT
*
131086 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
131106 AAAAGCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
131126 ACTATCGCAATGA-AAGAAATG
1 AAAATCGCAA-CACGA-AAATG
*
131147 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
131164 CCAAAATCGC
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:131200 original size:19 final size:18
Alignment explanation
Indices: 131178--131294 Score: 61
Period size: 20 Copynumber: 6.6 Consensus size: 18
131168 AATCGCATTA
131178 CGATTTTCAGTTCGCGTTG
1 CGATTTTCA-TTCGCGTTG
*
131197 CGA--TTC--TCTCGTTG
1 CGATTTTCATTCGCGTTG
131211 CGATTTTCATTTCGCGTTG
1 CGATTTTCA-TTCGCGTTG
*
131230 CGA--TTC--TCTCGTTG
1 CGATTTTCATTCGCGTTG
**
131244 CGATAGTCATTTCCGCGTTG
1 CGATTTTCA-TT-CGCGTTG
** *
131264 CGATAGTCATTATCTCGTTG
1 CGATTTTCA-T-TCGCGTTG
131284 CGATTTTCATT
1 CGATTTTCATT
131295 TCAACCAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.26
16 5 0.06
17 6 0.08
18 1 0.01
19 15 0.19
20 30 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (18 bp):
CGATTTTCATTCGCGTTG
Found at i:131211 original size:14 final size:14
Alignment explanation
Indices: 131192--131247 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
131182 TTTCAGTTCG
131192 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
131206 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
131225 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
131239 CGTTGCGAT
1 CGTTGCGAT
131248 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:131225 original size:33 final size:33
Alignment explanation
Indices: 131178--131296 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
131168 AATCGCATTA
*
131178 CGATTTTCAGTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
131211 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
**
131244 CGATAGTCATTTCCGCGTTGCGATAGTCATTATCTCGTTG
1 CGATTTTCATTT-CGCGTTGCGAT--TC----TCTCGTTG
131284 CGATTTTCATTTC
1 CGATTTTCATTTC
131297 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
33 42 0.57
34 11 0.15
36 2 0.03
39 1 0.01
40 18 0.24
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:131293 original size:20 final size:19
Alignment explanation
Indices: 131203--131296 Score: 81
Period size: 20 Copynumber: 5.1 Consensus size: 19
131193 GTTGCGATTC
*
131203 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATATTCATT
*
131222 TCGCGTTGCG--ATTC---
1 TCTCGTTGCGATATTCATT
*
131236 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATATTCATT
* *
131255 TCCGCGTTGCGATAGTCATT
1 T-CTCGTTGCGATATTCATT
*
131275 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATATTCATT
131295 TC
1 TC
131297 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.15
16 3 0.05
17 3 0.05
19 12 0.20
20 32 0.53
21 1 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATATTCATT
Found at i:133159 original size:94 final size:95
Alignment explanation
Indices: 132943--133176 Score: 398
Period size: 95 Copynumber: 2.5 Consensus size: 95
132933 TAGATTGCTT
* * *
132943 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
133008 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAG
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
*
133038 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
133103 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
* *
133132 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTATGTATTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC
133177 ACGTTGCGAT
Statistics
Matches: 131, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
94 63 0.48
95 68 0.52
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (95 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
Found at i:133666 original size:21 final size:21
Alignment explanation
Indices: 133642--133708 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
133632 TCATTCCTCG
133642 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
133663 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
133684 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
133705 AGAG
1 AGAG
133709 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:133666 original size:42 final size:42
Alignment explanation
Indices: 133620--133708 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
133610 CCTATCGTCG
* *
133620 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* *
133662 AAGAGGCCACTATCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
133704 AAGAG
1 AAGAG
133709 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:135076 original size:14 final size:14
Alignment explanation
Indices: 135057--135092 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
135047 ATTGTTTAAT
135057 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
135071 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
135085 TGATTTGT
1 TGATTTGT
135093 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:137919 original size:24 final size:24
Alignment explanation
Indices: 137892--137938 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
137882 CAAAATCCGA
137892 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
137916 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
137939 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:137947 original size:24 final size:24
Alignment explanation
Indices: 137896--137947 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
137886 ATCCGAGTAT
** *
137896 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
137920 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
137944 TGAC
1 TGAC
137948 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:138839 original size:21 final size:21
Alignment explanation
Indices: 138815--138860 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
138805 TATTCGCATT
138815 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
138836 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
138857 GCGA
1 GCGA
138861 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:142376 original size:24 final size:22
Alignment explanation
Indices: 142333--142382 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
142323 TTATATGTTA
*
142333 TTAATGAAATTTATTGTTTAAT
1 TTAATGAAATTTATTGTTTAAG
142355 TTAATGATGAATTTAGTT-TTTAAG
1 TTAATGA--AATTTA-TTGTTTAAG
142379 TTAA
1 TTAA
142383 AGATTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
24 15 0.62
25 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TTAATGAAATTTATTGTTTAAG
Found at i:142525 original size:31 final size:30
Alignment explanation
Indices: 142490--142584 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
142480 ACTATAGGAT
142490 GTTACTTTATCAAGTCATTTGACTATTAAAA
1 GTTACTTTAT-AAGTCATTTGACTATTAAAA
*** *
142521 GTTACAAAAT-AGTCATTTGACTA-TAGAAT
1 GTTACTTTATAAGTCATTTGACTATTA-AAA
* *
142550 GTTGCTTTGTTAAGTC-TCTTGACTATTAAAA
1 GTTACTTT-ATAAGTCAT-TTGACTATTAAAA
142581 GTTA
1 GTTA
142585 TCAAATGACC
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 2 0.04
29 19 0.40
30 2 0.04
31 23 0.48
32 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (30 bp):
GTTACTTTATAAGTCATTTGACTATTAAAA
Found at i:144097 original size:19 final size:19
Alignment explanation
Indices: 144073--144117 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
144063 CTAAAATATT
*
144073 AATATTATACTCTATCTAA
1 AATATTATACTCTATCAAA
* **
144092 AATATTGTTTTCTATCAAA
1 AATATTATACTCTATCAAA
144111 AATATTA
1 AATATTA
144118 ATATTAAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (19 bp):
AATATTATACTCTATCAAA
Found at i:144130 original size:25 final size:24
Alignment explanation
Indices: 144058--144130 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 24
144048 ACATTATTTT
144058 TCTATCTAAAATATTAATATTATAC
1 TCTATCTAAAATATTAATATTA-AC
*
144083 TCTATCTAAAATATT-GT-TT---
1 TCTATCTAAAATATTAATATTAAC
*
144102 TCTATCAAAAATATTAATATTAAAC
1 TCTATCTAAAATATTAATATT-AAC
144127 TCTA
1 TCTA
144131 CGTAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 14 0.36
20 1 0.03
21 2 0.05
23 2 0.05
24 1 0.03
25 19 0.49
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (24 bp):
TCTATCTAAAATATTAATATTAAC
Found at i:144640 original size:3 final size:3
Alignment explanation
Indices: 144632--144663 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
144622 GTAACACAAA
144632 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
144664 AAAACCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:148274 original size:19 final size:18
Alignment explanation
Indices: 148240--148277 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
148230 ATAATGATGT
148240 TTATTTTATTATTCATTA
1 TTATTTTATTATTCATTA
148258 TTATTTT-TCTATATCATTA
1 TTATTTTAT-TAT-TCATTA
148277 T
1 T
148278 CGAATTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 10 0.56
19 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTTATTATTCATTA
Found at i:150584 original size:110 final size:110
Alignment explanation
Indices: 150366--150648 Score: 485
Period size: 110 Copynumber: 2.6 Consensus size: 110
150356 TTGTCGGTTT
*
150366 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGAC--AACC
*
150431 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCCGATATATTGAAA
64 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAA
* * *
150478 GTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAAAATGACAACCGG
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAACCGG
* *
150543 TCTATAAATGATAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 TCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAA
150588 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
150649 AATAGGTAAA
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
110 106 0.66
112 55 0.34
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (110 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAACCGG
TCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAA
Found at i:150676 original size:92 final size:92
Alignment explanation
Indices: 150548--150743 Score: 322
Period size: 92 Copynumber: 2.1 Consensus size: 92
150538 ACCGGTCTAT
*
150548 AAATGATAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATAT
1 AAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATAT
150613 CGATCCATAACAATATAACAGGTAAAA
66 CGATCCATAACAATATAACAGGTAAAA
* * * *
150640 AAATGACAAAATAGGTAAAGC-ATCACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
1 AAATGACAAAACAGGTAAAGCGCT-ACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATA
*
150704 TTGATCCATAACAATATAACAGGTAAAA
65 TCGATCCATAACAATATAACAGGTAAAA
150732 AAATGACAAAAC
1 AAATGACAAAAC
150744 CGGTCTATAA
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 1 0.01
92 95 0.99
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (92 bp):
AAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATAT
CGATCCATAACAATATAACAGGTAAAA
Found at i:150832 original size:204 final size:201
Alignment explanation
Indices: 150438--150854 Score: 683
Period size: 204 Copynumber: 2.1 Consensus size: 201
150428 ACCGGTCTAT
*
150438 AAATGACAAAACAAGTAAAGCGCTACCCGATATATTGAAAGTGTTGATACTTTATAAAAATGTAT
1 AAATGACAAAACAAGTAAAGCGCTACCCGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
*
150503 CGATCCATAACAATATAACAGATAAAAAAATGACAACCGGTCTATAAATGATAAAACAGGTAAAG
66 CGATCCATAACAATATAACAGATAAAAAAATGACAACCGGTCTATAAATGACAAAACAGGTAAAG
150568 CGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACA
131 CGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACA
150633 GGTAAAA
196 GGT-AAA
* * * *
150640 AAATGACAAAATAGGTAAAGC-ATCACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
1 AAATGACAAAACAAGTAAAGCGCT-ACCCGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
* *
150704 TTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGGTA
65 TCGATCCATAACAATATAACAGATAAAAAAATGAC--AACCGGTCTATAAATGACAAAACAGGTA
* * *
150769 AAGCGCTACCGGATATATTGAAAGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATA
128 AAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATA
*
150834 ACATGTAAA
193 ACAGGTAAA
150843 AAATGACAAAAC
1 AAATGACAAAAC
150855 CAGTCTATAA
Statistics
Matches: 199, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
201 1 0.01
202 90 0.45
203 14 0.07
204 94 0.47
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (201 bp):
AAATGACAAAACAAGTAAAGCGCTACCCGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAGATAAAAAAATGACAACCGGTCTATAAATGACAAAACAGGTAAAG
CGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACA
GGTAAA
Found at i:150912 original size:111 final size:112
Alignment explanation
Indices: 150640--150917 Score: 461
Period size: 112 Copynumber: 2.5 Consensus size: 112
150630 ACAGGTAAAA
* *
150640 AAATGACAAAATAGGTAAAGC-ATCACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
1 AAATGACAAAACAGGTAAAGCGCT-ACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
* *
150704 TTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTAT
65 TCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTAT
*
150752 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
*
150817 CGATCCATAACAATATAACATGT-AAAAAATGACAAAACCAGTCTAT
66 CGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTAT
* *
150863 AAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
150918 TATAAGTATC
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 74 0.47
112 81 0.52
113 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (112 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTAT
Found at i:151099 original size:180 final size:182
Alignment explanation
Indices: 150797--151234 Score: 686
Period size: 180 Copynumber: 2.4 Consensus size: 182
150787 TGAAAGTGTT
150797 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAA-ATGACAAAACCAGTCT
1 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCAGTCT
** * * *
150861 ATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTA
66 CGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGACAGTGTAGATACTTTATTATAAGTA
* * *
150926 TCGACACTTTTAGAATTTAAAAGAGAATAAGTTATAGCG-C-TAAAAATGTC
131 TCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGTCAAAAAAATGTC
*
150976 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCT
1 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCAGTCT
* *
151041 CGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGACAGTGTAGATATTTTATTATAAGTA
66 CGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGACAGTGTAGATACTTTATTATAAGTA
* *
151106 TCGACACTTTTGGATTTTAAAAGAAAAGAAGTTATAGCGTCAAAAAAATGTC
131 TCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGTCAAAAAAATGTC
* * * * *
151158 GATATTTTATAAAAATGTATCGATCTATAACAATATAACATGTAAAAATATAACAAAATCAGCCT
1 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCAGTCT
151223 CGAAATGA-AAAA
66 CGAAATGACAAAA
151235 TCGATAGTAA
Statistics
Matches: 237, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
179 48 0.20
180 108 0.46
181 5 0.02
182 76 0.32
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCAGTCT
CGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGACAGTGTAGATACTTTATTATAAGTA
TCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGTCAAAAAAATGTC
Found at i:151699 original size:23 final size:23
Alignment explanation
Indices: 151673--151720 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
151663 AAATATGTCA
* *
151673 ATATAAGCGCTATCTATTATATT
1 ATATAAGCGCTACCTAATATATT
151696 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATATATT
151719 AT
1 AT
151721 TATACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:155458 original size:21 final size:20
Alignment explanation
Indices: 155419--155458 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
155409 ACTCAACTAA
*
155419 TTTTATAAACTTAATTTAAT
1 TTTTATAAACTTAAATTAAT
*
155439 TTTTATAAAAGTTAAATTAA
1 TTTTAT-AAACTTAAATTAA
155459 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTATAAACTTAAATTAAT
Found at i:157562 original size:21 final size:20
Alignment explanation
Indices: 157538--157579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
157528 TTAATTGATA
157538 ATTGTTGACCATTGACTATTG
1 ATTGTTGACCATTGACT-TTG
* *
157559 ATTGTTGATCGTTGACTTTG
1 ATTGTTGACCATTGACTTTG
157579 A
1 A
157580 CCATTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTGTTGACCATTGACTTTG
Found at i:158211 original size:29 final size:29
Alignment explanation
Indices: 158143--158231 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
158133 CATTGACGCG
* *
158143 TTCCTCATTCTGACACTACATGGGATTAA
1 TTCCCCATTCTGACACTGCATGGGATTAA
* * *
158172 TTTCTCATTCTGACACTGTATGGGATTAA
1 TTCCCCATTCTGACACTGCATGGGATTAA
* * * *
158201 TTCCCCGTTCTAACATTGCATGTGATTAA
1 TTCCCCATTCTGACACTGCATGGGATTAA
158230 TT
1 TT
158232 ATCCCTATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (29 bp):
TTCCCCATTCTGACACTGCATGGGATTAA
Found at i:161867 original size:3 final size:3
Alignment explanation
Indices: 161859--161885 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
161849 TCATCCCTTT
161859 CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC
161886 GGACCGTCCA
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:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:171010 original size:23 final size:23
Alignment explanation
Indices: 170954--171025 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
170944 CGATAGCTAG
* * **
170954 TTTAACGTAATAGATAATACTTA
1 TTTAAAGTAATAGGTAACGCTTA
* *
170977 TTTAAAGTAATATGTATCGCTTA
1 TTTAAAGTAATAGGTAACGCTTA
*
171000 TTTAATA-TAATAGGTAACGTTTA
1 TTTAA-AGTAATAGGTAACGCTTA
171023 TTT
1 TTT
171026 TATTTTACCG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTAAAGTAATAGGTAACGCTTA
Found at i:171195 original size:75 final size:75
Alignment explanation
Indices: 171007--171390 Score: 345
Period size: 75 Copynumber: 5.1 Consensus size: 75
170997 TTATTTAATA
* ** * *
171007 TAATAGGTAACGTTTATTTTATTTTACCGTTTACATTATTATTAACCTTTAAACAAACTGGTATA
1 TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA-TCG---A
* *
171072 TAGTGTTTA-TTTAATG
62 TA--G-CTAGTTTAACG
* * * * *
171088 TAATGGGTAGCGCCTGTTTTATATTACTGTTTACATTATTATTAACCTTTAAACAAATCGATAGC
1 TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGATAGC
171153 TAGTTTAACG
66 TAGTTTAACG
* * * *
171163 TAATATGTAGCGCCTATTTTATTTTACCGTTTACAATATTAGTAACCTTTAAACAAA-CGGTAGG
1 TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGATAGC
*
171227 TAATTTAACG
66 TAGTTTAACG
* * *
171237 TAATAGGTA--G--T-GTTTATTTTACCGTTTATATTATTAGTAACCTTTAAGCAAATC-AGTAG
1 TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGA-TAG
* *
171296 ATATTTTAACG
65 CTAGTTTAACG
* * * * * * * *
171307 TAATAGTTAGCGTCTATTTTATTTTATCTTTTACATTATTAGTAATCTTAAAACAAATTGATATA
1 TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGATA-G
*
171372 C-AGTTTAACA
65 CTAGTTTAACG
171382 TAATAGGTA
1 TAATAGGTA
171391 TGAATACTTT
Statistics
Matches: 251, Mismatches: 42, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
69 37 0.15
70 22 0.09
72 2 0.01
74 25 0.10
75 109 0.43
76 1 0.00
77 3 0.01
80 2 0.01
81 50 0.20
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (75 bp):
TAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGATAGC
TAGTTTAACG
Found at i:171278 original size:144 final size:151
Alignment explanation
Indices: 171021--171363 Score: 407
Period size: 144 Copynumber: 2.3 Consensus size: 151
171011 AGGTAACGTT
* *
171021 TATTTTATTTTACCGTTTACATTATTATTAACCTTTAAACAAACTGGTATATAGTGTTTATTTAA
1 TATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGG---ATAGTGTTAATTTAA
* * * *
171086 TGTAATGGGTAGCGCCTGTTTTATATTACTGTTTACATTATTATTAACCTTTAAACAAATC-GAT
63 CGTAATAGGTA-CG-CTGTTTTATATTACCGTTTACATTATTAGTAACCTTTAAACAAATCAG-T
*
171150 AGCTAGTTTAACGTAATA-TGTAGCGCC
125 AGATAGTTTAACGTAATAGT-TAGCGCC
*
171177 TATTTTATTTTACCGTTTACAATATTAGTAACCTTTAAACAAAC-GG-TAG-G-TAATTTAACGT
1 TATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGGATAGTGTTAATTTAACGT
* * * *
171238 AATAGGTA-G-TG-TTTATTTTACCGTTTATATTATTAGTAACCTTTAAGCAAATCAGTAGATAT
66 AATAGGTACGCTGTTTTATATTACCGTTTACATTATTAGTAACCTTTAAACAAATCAGTAGATAG
*
171300 TTTAACGTAATAGTTAGCGTC
131 TTTAACGTAATAGTTAGCGCC
* * * *
171321 TATTTTATTTTATCTTTTACATTATTAGTAATCTTAAAACAAA
1 TATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
171364 TTGATATACA
Statistics
Matches: 167, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
144 98 0.59
145 4 0.02
147 1 0.01
149 16 0.10
150 1 0.01
151 3 0.02
155 2 0.01
156 42 0.25
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (151 bp):
TATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGGATAGTGTTAATTTAACGT
AATAGGTACGCTGTTTTATATTACCGTTTACATTATTAGTAACCTTTAAACAAATCAGTAGATAG
TTTAACGTAATAGTTAGCGCC
Found at i:176690 original size:2 final size:2
Alignment explanation
Indices: 176672--176709 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
176662 ACGCCTAAAA
* *
176672 TC TC CC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
176710 CCCAAGTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:177219 original size:24 final size:23
Alignment explanation
Indices: 177191--177240 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
177181 TTTGCCTTAA
*
177191 TTTTCTTTTT-TGTTGTTTTTATAT
1 TTTTCTTTTTGT-TTG-TTATATAT
177215 TTTTCTTTTTGTTTGTTATATAT
1 TTTTCTTTTTGTTTGTTATATAT
177238 TTT
1 TTT
177241 GTGTATGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 13 0.54
25 1 0.04
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (23 bp):
TTTTCTTTTTGTTTGTTATATAT
Found at i:182593 original size:15 final size:16
Alignment explanation
Indices: 182566--182598 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
182556 GGCCAAGTCG
182566 GAGCAGACCCGAAGCA
1 GAGCAGACCCGAAGCA
182582 GAGCAG-CCCGAAGCA
1 GAGCAGACCCGAAGCA
182597 GA
1 GA
182599 ACAGTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.30, G:0.33, T:0.00
Consensus pattern (16 bp):
GAGCAGACCCGAAGCA
Found at i:195584 original size:7 final size:7
Alignment explanation
Indices: 195547--195670 Score: 58
Period size: 7 Copynumber: 17.4 Consensus size: 7
195537 TATTTTGCTT
*
195547 AAAGAAG
1 AAAGAAA
*
195554 AAATAAA
1 AAAGAAA
*
195561 AGAGAAA
1 AAAGAAA
195568 AGAAGAAA
1 A-AAGAAA
195576 AAAGAAA
1 AAAGAAA
**
195583 AAATGATG
1 AAA-GAAA
**
195591 ATGGAAA
1 AAAGAAA
195598 AAACGAAA
1 AAA-GAAA
195606 AAA-AAA
1 AAAGAAA
**
195612 TGA-AAA
1 AAAGAAA
195618 AAAGAAA
1 AAAGAAA
195625 AAAG--A
1 AAAGAAA
*
195630 AGAGAAA
1 AAAGAAA
195637 AAATGGAAA
1 AAA--GAAA
*
195646 AAATAAA
1 AAAGAAA
195653 AAGAGAAA
1 AA-AGAAA
*
195661 AATGAAA
1 AAAGAAA
195668 AAA
1 AAA
195671 AAAGAGAAAT
Statistics
Matches: 85, Mismatches: 23, Indels: 18
0.67 0.18 0.14
Matches are distributed among these distances:
5 4 0.05
6 8 0.09
7 44 0.52
8 22 0.26
9 7 0.08
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (7 bp):
AAAGAAA
Found at i:195599 original size:23 final size:19
Alignment explanation
Indices: 195594--195673 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 19
195584 AATGATGATG
*
195594 GAAAAAACGAAAAAAAAAT
1 GAAAAAAAGAAAAAAAAAT
195613 GAAAAAAAGAAAAAAGAAGA-
1 GAAAAAAAGAAAAAA-AA-AT
* *
195633 GAAAAAATGGAAAAAATAAAAA
1 GAAAAAA-AG-AAAAA-AAAAT
*
195655 GAGAAAAATGAAAAAAAAA
1 GA-AAAAAAGAAAAAAAAA
195674 GAGAAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
19 14 0.27
20 13 0.25
21 8 0.16
22 10 0.20
23 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (19 bp):
GAAAAAAAGAAAAAAAAAT
Found at i:197517 original size:51 final size:51
Alignment explanation
Indices: 196997--197500 Score: 936
Period size: 51 Copynumber: 9.9 Consensus size: 51
196987 AAATTCGTTT
196997 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
197048 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
197099 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
197150 GTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
197201 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
197252 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
197303 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * *
197354 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
197405 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
197456 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
197501 CCGTTTTATG
Statistics
Matches: 443, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 443 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:197771 original size:15 final size:16
Alignment explanation
Indices: 197744--197776 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
197734 GGCCAAGTCG
197744 GAGCAGACCCGAAGCA
1 GAGCAGACCCGAAGCA
197760 GAGCAG-CCCGAAGCA
1 GAGCAGACCCGAAGCA
197775 GA
1 GA
197777 ACAGTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.30, G:0.33, T:0.00
Consensus pattern (16 bp):
GAGCAGACCCGAAGCA
Found at i:206113 original size:21 final size:21
Alignment explanation
Indices: 206084--206136 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
206074 ATTTTGACTA
206084 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
206105 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
206126 TCGCAATGCGA
1 TCGCATTGCGA
206137 ATACGTAAAT
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:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:206151 original size:20 final size:20
Alignment explanation
Indices: 206126--206196 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
206116 TTTTCCTAAT
* *
206126 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACATAAA
*
206146 TCGCAATGCGAATACATAAA
1 TCGCAACGCGAATACATAAA
206166 TCGCAACGCGAATACATAAA
1 TCGCAACGCGAATACATAAA
206186 TCGCAACGCGA
1 TCGCAACGCGA
206197 TTATGACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAATACATAAA
Found at i:206208 original size:20 final size:20
Alignment explanation
Indices: 206185--206231 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
206175 GAATACATAA
206185 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
206205 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
206225 ATCGCAA
1 ATCGCAA
206232 TACTGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:207100 original size:24 final size:24
Alignment explanation
Indices: 207073--207126 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
207063 GTATTCGAAA
207073 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
207097 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
207121 TTTGAT
1 TTTGAT
207127 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:209612 original size:20 final size:20
Alignment explanation
Indices: 209539--209611 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
209529 GACATTCATT
*
209539 TGACTATCGCAATACGGAAA
1 TGACTATCGCAACACGGAAA
*
209559 TGACTATCGCAACAAGGAAA
1 TGACTATCGCAACACGGAAA
*
209579 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
209599 TGACTATCGCAAC
1 TGACTATCGCAAC
209612 GAGAGAATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:209735 original size:14 final size:14
Alignment explanation
Indices: 209716--209750 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
209706 CATTTTTGCA
209716 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
209730 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
209744 TTGCGAT
1 TTGCGAT
209751 AGTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:211369 original size:42 final size:42
Alignment explanation
Indices: 211290--211382 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
211280 CCTCTTCAAC
* * *
211290 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
211332 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
211374 GATGACAGG
1 GATGACAGG
211383 TGAGTCGGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:211974 original size:34 final size:34
Alignment explanation
Indices: 211933--212088 Score: 127
Period size: 34 Copynumber: 4.4 Consensus size: 34
211923 TGCGATTTTC
211933 ATTTCGCATTGCGATTTTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTTTTTCGTTGCGATAGTCA
* *
211967 AATTCGCATTGCGATAGTCATTTTCGCATTACGATAGTCA
1 ATTTCGCATTGCGAT--T--TTTTCG--TTGCGATAGTCA
* * * **
212007 TTTTCGCGTTGCGA-TTTTGCTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTTTTTC-GTTGCGATAGTCA
* * *
212040 ATTTCGCATTGCGATTCTCTCGTTGCAATAGTCA
1 ATTTCGCATTGCGATTTTTTCGTTGCGATAGTCA
* *
212074 TTTTCGCGTTGCGAT
1 ATTTCGCATTGCGAT
212089 AGTCATTTTC
Statistics
Matches: 94, Mismatches: 19, Indels: 18
0.72 0.15 0.14
Matches are distributed among these distances:
33 21 0.22
34 38 0.40
35 4 0.04
36 2 0.02
37 1 0.01
38 6 0.06
40 22 0.23
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (34 bp):
ATTTCGCATTGCGATTTTTTCGTTGCGATAGTCA
Found at i:211980 original size:20 final size:20
Alignment explanation
Indices: 211955--212111 Score: 117
Period size: 20 Copynumber: 8.5 Consensus size: 20
211945 GATTTTTTCG
**
211955 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
211975 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
211995 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
212015 TTGC----G--ATTTT-GCTG
1 TTGCGATAGTCATTTTCGC-A
**
212029 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
212048 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
212062 TTGCAATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
212082 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
212102 TTGCGATAGT
1 TTGCGATAGT
212112 AAACTATTCT
Statistics
Matches: 111, Mismatches: 12, Indels: 28
0.74 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 16 0.14
16 7 0.06
17 2 0.02
18 4 0.04
19 10 0.09
20 70 0.63
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:214045 original size:20 final size:20
Alignment explanation
Indices: 213995--214033 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
213985 TCAAAAACTT
213995 AAAATCGCAACACGAAAATA
1 AAAATCGCAACACGAAAATA
214015 AAAATCGCAACACGAAAAT
1 AAAATCGCAACACGAAAAT
214034 GACTATCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATA
Found at i:214082 original size:53 final size:53
Alignment explanation
Indices: 213997--214131 Score: 209
Period size: 53 Copynumber: 2.5 Consensus size: 53
213987 AAAAACTTAA
* * *
213997 AATCGCAACACGAAAATAAAAATCGCAACACGAAAAT-GACTATCGCAACGCAAG
1 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATAG-CAATCGCAACGCAAG
*
214051 AATCGCAACGCGAAATGAAAATCACAACACGAAAATAGCAATCGCAACGCAAG
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATAGCAATCGCAACGCAAG
214104 AATCGCAACGCGAAATGAAAATCGCAAC
1 AATCGCAACGCGAAATGAAAATCGCAAC
214132 GACAGAATCA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
53 63 0.84
54 12 0.16
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAAATAGCAATCGCAACGCAAG
Found at i:214493 original size:22 final size:22
Alignment explanation
Indices: 214480--214533 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
214470 ATTTCGCCGC
*
214480 AGATGGAGACTGATATCGTCAG
1 AGATGGAGACTGATTTCGTCAG
* *
214502 AGATGGGGACTGATTTTGTCAG
1 AGATGGAGACTGATTTCGTCAG
214524 AGATGGAGAC
1 AGATGGAGAC
214534 GGATGTCGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (22 bp):
AGATGGAGACTGATTTCGTCAG
Found at i:214781 original size:20 final size:20
Alignment explanation
Indices: 214714--214784 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
214704 GCTATGTAAA
* *
214714 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACATAT
* *
214734 TCGCGTTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
214754 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
214774 TCGCATTGCGA
1 TCGCATTGCGA
214785 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:214805 original size:21 final size:21
Alignment explanation
Indices: 214781--214826 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
214771 TATTCGCATT
214781 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
214802 GCGAATTTGTAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
214823 GCGA
1 GCGA
214827 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:218096 original size:44 final size:46
Alignment explanation
Indices: 218030--218127 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 46
218020 TTATTTTCGT
218030 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAA-GCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
218077 TTTTTGAATAAA-CATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTGAATAAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
218122 TTTTTG
1 TTTTTG
218128 TGAATAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 27 0.55
45 10 0.20
46 7 0.14
47 5 0.10
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (46 bp):
TTTTTGAATAAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:227845 original size:11 final size:11
Alignment explanation
Indices: 227829--227868 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
227819 ATGATGATGG
227829 AAAAAACGAAAA
1 AAAAAACG-AAA
227841 AAAAAACGAAA
1 AAAAAACGAAA
227852 AAAAAA-GAAGA
1 AAAAAACGAA-A
227863 AAAAAA
1 AAAAAA
227869 AAAGAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.11
11 16 0.59
12 8 0.30
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAACGAAA
Found at i:227845 original size:13 final size:13
Alignment explanation
Indices: 227829--227871 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
227819 ATGATGATGG
227829 AAAAAACG-AAAA
1 AAAAAACGAAAAA
227841 AAAAAACGAAAAA
1 AAAAAACGAAAAA
227854 AAAAGAA-GAAAAA
1 AAAA-AACGAAAAA
227867 AAAAA
1 AAAAA
227872 GAAGAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.31
13 18 0.62
14 2 0.07
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAACGAAAAA
Found at i:227846 original size:12 final size:12
Alignment explanation
Indices: 227829--227893 Score: 69
Period size: 12 Copynumber: 5.2 Consensus size: 12
227819 ATGATGATGG
227829 AAAAAACGAAAA
1 AAAAAACGAAAA
227841 AAAAAACGAAAA
1 AAAAAACGAAAA
*
227853 AAAAAGAAGAAAA
1 AAAAA-ACGAAAA
227866 AAAAAA-GAAGAGA
1 AAAAAACGAA-A-A
**
227879 AAAAATGGAAAA
1 AAAAAACGAAAA
227891 AAA
1 AAA
227894 TAAAAAGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 3 0.06
12 23 0.49
13 18 0.38
14 3 0.06
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAACGAAAA
Found at i:227872 original size:14 final size:14
Alignment explanation
Indices: 227837--227907 Score: 69
Period size: 14 Copynumber: 5.3 Consensus size: 14
227827 GGAAAAAACG
*
227837 AAAAAAAAA-ACG-
1 AAAAAAAAAGAAGA
227849 AAAAAAAAAGAAGA
1 AAAAAAAAAGAAGA
227863 AAAAAAAAAGAAGA
1 AAAAAAAAAGAAGA
* **
227877 GAAAAAATGGAA-A
1 AAAAAAAAAGAAGA
227890 AAAATAAAAAG-AGA
1 AAAA-AAAAAGAAGA
227904 AAAA
1 AAAA
227908 TGAAAAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
12 9 0.19
13 7 0.15
14 32 0.67
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAGA
Found at i:227890 original size:23 final size:24
Alignment explanation
Indices: 227863--227922 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
227853 AAAAAGAAGA
* *
227863 AAAAAAAAAGAAGAGA-AAAAATGG
1 AAAAAAAGAGAAAAGAGAAAAAT-G
*
227887 AAAAAAATA-AAAAGAGAAAAATG
1 AAAAAAAGAGAAAAGAGAAAAATG
227910 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
227923 TAAAAGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (24 bp):
AAAAAAAGAGAAAAGAGAAAAATG
Found at i:227901 original size:25 final size:23
Alignment explanation
Indices: 227830--227916 Score: 86
Period size: 25 Copynumber: 3.6 Consensus size: 23
227820 TGATGATGGA
* * *
227830 AAAAACGAAAAAAAAAACGAAAAA
1 AAAAATGAAAAAAAAAA-GAAGAG
*
227854 AAAAGAAGAAAAAAAAAAGAAGAG
1 AAAA-ATGAAAAAAAAAAGAAGAG
227878 AAAAAATGGAAAAAAATAAA-AAGAG
1 -AAAAAT-GAAAAAAA-AAAGAAGAG
227903 AAAAATGAAAAAAA
1 AAAAATGAAAAAAA
227917 GAGAAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.15
24 15 0.27
25 29 0.53
26 3 0.05
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAAATGAAAAAAAAAAGAAGAG
Found at i:227923 original size:15 final size:14
Alignment explanation
Indices: 227840--227927 Score: 58
Period size: 14 Copynumber: 6.3 Consensus size: 14
227830 AAAAACGAAA
227840 AAAAAAACGAAAAA-
1 AAAAAAA-GAAAAAT
*
227854 AAAAGAAGAAAAA-
1 AAAAAAAGAAAAAT
227867 AAAAAGAAGAGAAAA-
1 AAAAA-AAGA-AAAAT
***
227882 AATGGAA-AAAAAT
1 AAAAAAAGAAAAAT
*
227895 AAAAAGAGAAAAAT
1 AAAAAAAGAAAAAT
*
227909 GAAAAAAAGAGAAAT
1 -AAAAAAAGAAAAAT
227924 AAAA
1 AAAA
227928 GGAGGGTTCA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
12 4 0.07
13 14 0.24
14 22 0.38
15 18 0.31
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAAAAGAAAAAT
Found at i:229304 original size:51 final size:51
Alignment explanation
Indices: 229243--229801 Score: 929
Period size: 51 Copynumber: 10.9 Consensus size: 51
229233 AAATTCGTTT
229243 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
229294 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
229345 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
229396 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
229447 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
229498 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
229549 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
229600 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
229651 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** *
229702 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
229753 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
229802 CCGTTTTATT
Statistics
Matches: 483, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 450 0.93
54 2 0.00
55 31 0.06
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:229369 original size:102 final size:102
Alignment explanation
Indices: 229243--229908 Score: 949
Period size: 102 Copynumber: 6.4 Consensus size: 102
229233 AAATTCGTTT
229243 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
229308 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
229345 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
229410 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
229447 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
229512 CCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
66 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
229549 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
229614 CCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
66 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
229651 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* * ** *
229716 CCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
66 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * ** ** *
229753 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGAT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGAT
* * * *
229818 TGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-
61 TG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
229863 TTATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GT-TGAAGA---TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
229909 ATGCTCGTCA
Statistics
Matches: 518, Mismatches: 35, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
102 400 0.77
105 2 0.00
106 34 0.07
107 11 0.02
110 2 0.00
111 69 0.13
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (102 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:229909 original size:55 final size:55
Alignment explanation
Indices: 229253--229909 Score: 242
Period size: 51 Copynumber: 12.6 Consensus size: 55
229243 GTTGAAGATT
* * * * **
229253 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229304 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229355 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * **
229406 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229457 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229508 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * **
229559 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229610 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * **
229661 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * *
229712 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* *
229767 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
229823 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
229878 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCA
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCA
229910 TGCTCGTCAT
Statistics
Matches: 565, Mismatches: 29, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
51 439 0.78
54 3 0.01
55 68 0.12
56 53 0.09
57 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:233997 original size:29 final size:30
Alignment explanation
Indices: 233949--234015 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
233939 GTCTTTCTGC
*
233949 AAAGGGTGTTAGATCAAGAAATAAAGA-TG
1 AAAGGGTGTTAGATCAAGAAATAAAGAGGG
233978 AAAGGGTGTCT-GA-CAGAGAAATAAAGAGGG
1 AAAGGGTGT-TAGATCA-AGAAATAAAGAGGG
234008 AAAGGGTG
1 AAAGGGTG
234016 ATTTATTGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.06
29 22 0.65
30 10 0.29
ACGTcount: A:0.45, C:0.04, G:0.34, T:0.16
Consensus pattern (30 bp):
AAAGGGTGTTAGATCAAGAAATAAAGAGGG
Found at i:250318 original size:16 final size:17
Alignment explanation
Indices: 250287--250319 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
250277 GCTGATTCGA
*
250287 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
250304 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
250320 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:256420 original size:65 final size:65
Alignment explanation
Indices: 256324--256448 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 65
256314 ATAGCGAATT
* * * * *
256324 CTTGCACAATTTGTGATTTAATATTTGTTCTTTTTTCTTCAGCTTGTACTTGTTTTCTCTCACTC
1 CTTGCACAATTTGTCATTCAATATTTGTTCTTTTTGCTTCACCTTGTACTTGTTCTCTCTCACTC
**
256389 CTTGCACAATTTGTCATTCGGTA-TTGATTCTTTTTGCTTCACCTTGTACTTGTTCTCTCT
1 CTTGCACAATTTGTCATTCAATATTTG-TTCTTTTTGCTTCACCTTGTACTTGTTCTCTCT
256449 GATTACCCCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 3 0.06
65 49 0.94
ACGTcount: A:0.14, C:0.22, G:0.12, T:0.52
Consensus pattern (65 bp):
CTTGCACAATTTGTCATTCAATATTTGTTCTTTTTGCTTCACCTTGTACTTGTTCTCTCTCACTC
Found at i:261711 original size:20 final size:20
Alignment explanation
Indices: 261686--261726 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
261676 TCATGCATCT
261686 ACATGAAAACCCTGATTACC
1 ACATGAAAACCCTGATTACC
261706 ACATGAAAACCCTGATTACC
1 ACATGAAAACCCTGATTACC
261726 A
1 A
261727 TGCAGTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
ACATGAAAACCCTGATTACC
Done.