Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008072.1 Hibiscus syriacus cultivar Beakdansim tig00110570_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: 1263316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 5
Found at i:1482 original size:19 final size:20
Alignment explanation
Indices: 1395--1483 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 20
1385 CGCGATTGTA
1395 AAAAATGTGTTGCGATAGT-
1 AAAAATGTGTTGCGATAGTG
* *
1414 TAAAATGTGTTGCGAGAGTTTG
1 AAAAATGTGTTGCGATAG--TG
*
1436 AAAAATGTGTTATTGCAATAGTG
1 AAAAATGTG---TTGCGATAGTG
1459 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTG
1478 AAAAAT
1 AAAAAT
1484 CCAAAATAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 31 0.54
21 1 0.02
22 11 0.19
23 7 0.12
25 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTG
Found at i:15695 original size:20 final size:20
Alignment explanation
Indices: 15670--15779 Score: 84
Period size: 20 Copynumber: 5.4 Consensus size: 20
15660 TCGAAGTTCG
15670 CGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAATT
** *
15690 CGTTGCGA--CAGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
15709 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
** *
15731 CGTTGCGA--CAGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
15750 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
15772 CGTTGCGA
1 CGTTGCGA
15780 CAGGCGAAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
18 10 0.15
19 4 0.06
20 24 0.35
21 16 0.24
22 4 0.06
23 10 0.15
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:15706 original size:41 final size:41
Alignment explanation
Indices: 15661--15821 Score: 304
Period size: 41 Copynumber: 3.9 Consensus size: 41
15651 ACGCGATAGT
15661 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
15702 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
15743 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
*
15784 CGAAGTTCGCGTTGCGATTCATTCCAAATTTGTTGCGA
1 CGAAGTTCGCGTTGCGATTCATTCC-AATTCGTTGCGA
15822 TAGTCCAAAT
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 107 0.91
42 11 0.09
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:16649 original size:21 final size:21
Alignment explanation
Indices: 16622--16981 Score: 134
Period size: 21 Copynumber: 17.4 Consensus size: 21
16612 TATTTGGACT
16622 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * * **
16643 CTCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAATTTGGAATGA
16664 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
16685 ATCGCAACGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16707 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
16726 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
16747 ATCGCAACGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16769 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
16788 ATCGCAACGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16810 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
16829 ATCGCAACGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
* * **
16851 -TCGCAATGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16872 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
16891 ATCGCAATGCGAACTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16913 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* **
16932 ATCGCAATGCGAATTTCGCCTG-
1 ATCGCAA--CGAATTTGGAATGA
16954 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAATTTGGAATGA
16973 ATCGCAACG
1 ATCGCAACG
16982 CGAACTTCGA
Statistics
Matches: 257, Mismatches: 49, Indels: 67
0.69 0.13 0.18
Matches are distributed among these distances:
18 30 0.12
19 32 0.12
20 42 0.16
21 91 0.35
22 16 0.06
23 46 0.18
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATGA
Found at i:16733 original size:41 final size:41
Alignment explanation
Indices: 16623--16999 Score: 253
Period size: 41 Copynumber: 9.1 Consensus size: 41
16613 ATTTGGACTA
* * *
16623 TCGCAACGAATTTGGAATGACTCGCAACGCGAACTTCGCCTA
1 TCGCAACGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
*
16665 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAACGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
* * **
16707 TCGCAACGAA-TTGGAATGAATCGCAA-CGAATTTGGAATG
1 TCGCAACGAACTTGGAATGAATCGCAAGCGAACTTCGCCTG
* ** * **
16746 AATCGCAACGCGAACTTCGCCTG--TCGCAA-CGAA-TTGGAATG
1 --TCGCAA--CGAACTTGGAATGAATCGCAAGCGAACTTCGCCTG
* ** * **
16787 AATCGCAACGCGAACTTCGCCTG--TCGCAA-CGAA-TTGGAATG
1 --TCGCAA--CGAACTTGGAATGAATCGCAAGCGAACTTCGCCTG
* **
16828 AATCGCAACGCGAACTTCGCCTG--TCGCAATGCGAACTTCGCCTG
1 --TCGCAA--CGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
16872 TCGCAACGAA-TTGGAATGAATCGCAATGCGAACTTCGCCTG
1 TCGCAACGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
*
16913 TCGCAACGAA-TTGGAATGAATCGCAATGCGAATTTCGCCTG
1 TCGCAACGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
* *
16954 TCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAACTTGGAATGAATCGCAA-GCGAACTTCGCCTG
16995 TCGCA
1 TCGCA
17000 TTGCGAATCT
Statistics
Matches: 305, Mismatches: 20, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
39 14 0.05
40 4 0.01
41 203 0.67
42 66 0.22
43 8 0.03
44 10 0.03
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (41 bp):
TCGCAACGAACTTGGAATGAATCGCAAGCGAACTTCGCCTG
Found at i:16742 original size:62 final size:62
Alignment explanation
Indices: 16664--16796 Score: 266
Period size: 62 Copynumber: 2.1 Consensus size: 62
16654 AACTTCGCCT
16664 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
1 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
16726 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
1 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
16788 ATCGCAACG
1 ATCGCAACG
16797 CGAACTTCGC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (62 bp):
ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
Found at i:16831 original size:103 final size:103
Alignment explanation
Indices: 16622--16947 Score: 523
Period size: 103 Copynumber: 3.1 Consensus size: 103
16612 TATTTGGACT
*
16622 ATCGCAA-CGAATTTGGAATGACTCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGAA
1 ATCGCAAGCGAATTTGGAATGA-TCGCAACGCGAACTTCGCCTGTCGCAACGAA-TTGGAATGAA
16686 TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
64 TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
16726 ATCGCAA-CGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAAT
1 ATCGCAAGCGAATTTGGAATG-ATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAAT
16790 CGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
65 CGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
* * ** *
16829 ATCGCAACGCGAACTTCGCCTG-TCGCAATGCGAACTTCGCCTGTCGCAACGAATTGGAATGAAT
1 ATCGCAA-GCGAATTTGGAATGATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAAT
*
16893 CGCAATGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
65 CGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
16932 ATCGCAATGCGAATTT
1 ATCGCAA-GCGAATTT
16948 CGCCTGTCGC
Statistics
Matches: 210, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
103 150 0.71
104 50 0.24
105 10 0.05
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (103 bp):
ATCGCAAGCGAATTTGGAATGATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
GCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGA
Found at i:16855 original size:62 final size:62
Alignment explanation
Indices: 16789--16920 Score: 246
Period size: 62 Copynumber: 2.1 Consensus size: 62
16779 TTGGAATGAA
16789 TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
* *
16851 TCGCAATGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTG
1 TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
16913 TCGCAACG
1 TCGCAACG
16921 AATTGGAATG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (62 bp):
TCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
Found at i:16958 original size:62 final size:60
Alignment explanation
Indices: 16644--16963 Score: 178
Period size: 62 Copynumber: 5.2 Consensus size: 60
16634 TTGGAATGAC
* *
16644 TCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAA-GCGAACTTCGCCTGTCGCAACGAACTTGGAATGAATCGCAA-GCGAA-TTCGCCTG
* ** *
16707 TCGCAA-CGAA-TTGGAATGAATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAAGCGAACTTCGCCTG--TCGCAACGAACTTGGAATGAATCGCAA-GCGAA-TTCGCCTG
* ** * ** * **
16769 TCGCAA-CGAA-TTGGAATGAATCGCAACGCGAACTTCGCCTG--TCGCAA-CGAATTGGAATG
1 TCGCAAGCGAACTTCGCCTG--TCGCAA--CGAACTTGGAATGAATCGCAAGCGAATTCGCCTG
* ** * **
16828 AATCGCAACGCGAACTTCGCCTGTCGCAATGCGAACTTCGCCTG--TCGCAA-CGAATTGGAATG
1 --TCGCAA-GCGAACTTCGCCTGTCGCAA--CGAACTTGGAATGAATCGCAAGCGAATTCGCCTG
16890 AATCGCAATGCGAACTTCGCCTGTCGCAACGAA-TTGGAATGAATCGCAATGCGAATTTCGCCTG
1 --TCGCAA-GCGAACTTCGCCTGTCGCAACGAACTTGGAATGAATCGCAA-GCGAA-TTCGCCTG
16954 TCGCAA-CGAA
1 TCGCAAGCGAA
16964 TTGGAATGAA
Statistics
Matches: 221, Mismatches: 22, Indels: 31
0.81 0.08 0.11
Matches are distributed among these distances:
59 10 0.05
60 16 0.07
61 16 0.07
62 146 0.66
63 14 0.06
64 19 0.09
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (60 bp):
TCGCAAGCGAACTTCGCCTGTCGCAACGAACTTGGAATGAATCGCAAGCGAATTCGCCTG
Found at i:28675 original size:49 final size:48
Alignment explanation
Indices: 28603--28697 Score: 172
Period size: 49 Copynumber: 2.0 Consensus size: 48
28593 CCACTAGACT
*
28603 GCAAAATGGTTGAAATAGACAAACGTTAAACCTAACTTAACATGGGACA
1 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTT-ACATGGGACA
28652 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGA
1 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGA
28698 TACTATCACG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 8 0.18
49 37 0.82
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (48 bp):
GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGACA
Found at i:31142 original size:20 final size:20
Alignment explanation
Indices: 31114--31250 Score: 101
Period size: 20 Copynumber: 7.2 Consensus size: 20
31104 ATTAGCAACA
* *
31114 TAATAAAAACTGATTCTATC
1 TAATTAAAACTGATCCTATC
* *
31134 TAATTAAAAATGATCCTATA
1 TAATTAAAACTGATCCTATC
* * *
31154 GAATAAAAAACTGATTCTATC
1 TAAT-TAAAACTGATCCTATC
*
31175 TAATTAAAAATGATCCTATC
1 TAATTAAAACTGATCCTATC
*
31195 TAA-T--AACT-A----ATA
1 TAATTAAAACTGATCCTATC
* * *
31207 GAATAAAAACTGATTCTATC
1 TAATTAAAACTGATCCTATC
31227 TAATTAAAACTGATCCTATC
1 TAATTAAAACTGATCCTATC
31247 TAAT
1 TAAT
31251 ATTTAATTTA
Statistics
Matches: 87, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
12 4 0.05
15 4 0.05
16 2 0.02
17 3 0.03
19 1 0.01
20 58 0.67
21 15 0.17
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.34
Consensus pattern (20 bp):
TAATTAAAACTGATCCTATC
Found at i:31200 original size:41 final size:41
Alignment explanation
Indices: 31113--31200 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
31103 AATTAGCAAC
31113 ATAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
31153 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
31194 CTAATAA
1 ATAATAA
31201 CTAATAGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (41 bp):
ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
Found at i:31230 original size:52 final size:53
Alignment explanation
Indices: 31151--31251 Score: 186
Period size: 52 Copynumber: 1.9 Consensus size: 53
31141 AAATGATCCT
31151 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
*
31204 ATAGAAT-AAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
31252 TTTAATTTAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 40 0.85
53 7 0.15
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (53 bp):
ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
Found at i:35837 original size:20 final size:20
Alignment explanation
Indices: 35814--35888 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
35804 TAATAAAGAC
35814 TGATTCTATCTAATTAAAAA
1 TGATTCTATCTAATTAAAAA
* ** *
35834 TGATCCTATAGAATAAAAAA
1 TGATTCTATCTAATTAAAAA
35854 CTGATTCTATCTAATTAAAAA
1 -TGATTCTATCTAATTAAAAA
*
35875 TGATTTTATCTAAT
1 TGATTCTATCTAAT
35889 AACTAATAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (20 bp):
TGATTCTATCTAATTAAAAA
Found at i:35890 original size:41 final size:41
Alignment explanation
Indices: 35803--35941 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 41
35793 AATTAGCAAC
*
35803 ATAAT-AAAGACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
* *
35843 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATTTTATCTAAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGA---T-CCT-AT
*
35889 AACTAATAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTAT
1 -A-TAAT---A-AAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
35936 CTAATA
1 ATAATA
35942 TTTAATTTAG
Statistics
Matches: 80, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
40 4 0.05
41 28 0.35
42 1 0.01
44 1 0.01
45 6 0.08
46 2 0.03
47 3 0.04
48 5 0.06
49 1 0.01
51 1 0.01
52 28 0.35
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (41 bp):
ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
Found at i:35920 original size:52 final size:53
Alignment explanation
Indices: 35841--35941 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
35831 AAATGATCCT
**
35841 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATTTTATCTAATAACTA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
*
35894 ATAGAAT-AAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
35942 TTTAATTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (53 bp):
ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
Found at i:35927 original size:20 final size:20
Alignment explanation
Indices: 35902--35940 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35892 TAATAGAATA
*
35902 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
35922 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
35941 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:41099 original size:21 final size:21
Alignment explanation
Indices: 41060--41100 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41050 TATTATTCCA
*
41060 CTCGACTCGTTGTTCATTAAG
1 CTCGACTCGTTCTTCATTAAG
41081 CTCGACTCGTTACTT-ATTAA
1 CTCGACTCGTT-CTTCATTAA
41101 TCTCACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (21 bp):
CTCGACTCGTTCTTCATTAAG
Found at i:44730 original size:23 final size:22
Alignment explanation
Indices: 44707--44749 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44697 CTAAACAAGC
44707 CCAAAAATCGTATCTGCTAAAG
1 CCAAAAATCGTATCTGCTAAAG
* * *
44729 CCTAGAATCGTATCTTCTAAA
1 CCAAAAATCGTATCTGCTAAA
44750 CTCGCGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (22 bp):
CCAAAAATCGTATCTGCTAAAG
Found at i:49480 original size:33 final size:32
Alignment explanation
Indices: 49425--49500 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
49415 TTTCGGATCA
*
49425 AGTTAAATTCAATTTGGGTTGCTTTTCGATTCG
1 AGTTAAATTCAATTTGGATTGCTTTT-GATTCG
* * *
49458 AGTTAAATTTAGTTTTGATTGCTTTTGATTCG
1 AGTTAAATTCAATTTGGATTGCTTTTGATTCG
* *
49490 GGTTAATTTCA
1 AGTTAAATTCA
49501 GTCCGATTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 14 0.39
33 22 0.61
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (32 bp):
AGTTAAATTCAATTTGGATTGCTTTTGATTCG
Found at i:62677 original size:31 final size:31
Alignment explanation
Indices: 62630--62699 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
62620 GTTAACCTTT
* *
62630 AGTGACCACATCTTAATTAAATAAAAACAAA
1 AGTGATCAAATCTTAATTAAATAAAAACAAA
* * *
62661 TGTGATCAAATCTTAATTGAATAAAAATAAA
1 AGTGATCAAATCTTAATTAAATAAAAACAAA
62692 AGTGATCA
1 AGTGATCA
62700 TATATTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.27
Consensus pattern (31 bp):
AGTGATCAAATCTTAATTAAATAAAAACAAA
Found at i:63093 original size:30 final size:30
Alignment explanation
Indices: 63012--63099 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 30
63002 CTTATATACC
* *
63012 TATTTTGATAAAAAAAT-ATTTTAGCTACG
1 TATTTTGATCAAAAAATAATTTTAGGTACG
63041 TATTTTGA-CTAAAAAGATAATTTTAGGTA-G
1 TATTTTGATC-AAAAA-ATAATTTTAGGTACG
63071 TTATTTTGATCAAAAAATAA-TTTAGGTAC
1 -TATTTTGATCAAAAAATAATTTTAGGTAC
63100 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
29 21 0.41
30 7 0.14
31 22 0.43
32 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (30 bp):
TATTTTGATCAAAAAATAATTTTAGGTACG
Found at i:63217 original size:4 final size:4
Alignment explanation
Indices: 63208--63269 Score: 117
Period size: 4 Copynumber: 15.8 Consensus size: 4
63198 TATTCGATAA
63208 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
63256 TCAT TCAT TC-T TCA
1 TCAT TCAT TCAT TCA
63270 CCTACTCCAC
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 3 0.05
4 54 0.95
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (4 bp):
TCAT
Found at i:66341 original size:3 final size:3
Alignment explanation
Indices: 66333--66357 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
66323 TTAGTTATTC
66333 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
66358 TGTTCTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:69567 original size:19 final size:19
Alignment explanation
Indices: 69543--69591 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
69533 AAAAATGTTT
**
69543 TATGAACAATATTATATTG
1 TATGAACAATACGATATTG
* *
69562 TATGAATAGTACGATATTG
1 TATGAACAATACGATATTG
69581 TATGAACAATA
1 TATGAACAATA
69592 ATGCACAGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (19 bp):
TATGAACAATACGATATTG
Found at i:69666 original size:19 final size:20
Alignment explanation
Indices: 69642--69682 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
69632 ATGTAAAATT
69642 TGTATCGAT-ACTGCTACAG
1 TGTATCGATAACTGCTACAG
69661 TGTATCGATACACTGCTACAG
1 TGTATCGATA-ACTGCTACAG
69682 T
1 T
69683 AATTTTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
TGTATCGATAACTGCTACAG
Found at i:70217 original size:22 final size:22
Alignment explanation
Indices: 70192--70249 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
70182 GCTCGTATAA
*
70192 ATGTCCCGAAGGACCAGTCCAT
1 ATGTCCCGAAGAACCAGTCCAT
* *
70214 ATGTTCCGAAGAACCAGTCTAT
1 ATGTCCCGAAGAACCAGTCCAT
* *
70236 ATGTTCTGAAGAAC
1 ATGTCCCGAAGAAC
70250 ATAGGTAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (22 bp):
ATGTCCCGAAGAACCAGTCCAT
Found at i:70269 original size:31 final size:31
Alignment explanation
Indices: 70228--70319 Score: 139
Period size: 31 Copynumber: 3.0 Consensus size: 31
70218 TCCGAAGAAC
* * *
70228 CAGTCTATATGTTCTGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
70259 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
70290 CAGTCCATATGTCCCGAAGAACATAAGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
70320 CCCTCGACTC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:70972 original size:43 final size:43
Alignment explanation
Indices: 70925--71024 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
70915 ACACTGCCTA
*
70925 TGTATCGGTACATAAATTACATTCGATGTTTTCCATTTCAA-AG
1 TGTATCGGTACATAAATTACATTCAATGTTTTCCATTT-AATAG
* * * *
70968 TGTATCGATACACT-CATTGCATTCAATGTTTTTCATTTAATAG
1 TGTATCGGTACA-TAAATTACATTCAATGTTTTCCATTTAATAG
71011 TGTATCGGTACATA
1 TGTATCGGTACATA
71025 TTAAATATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 3 0.06
43 44 0.92
44 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (43 bp):
TGTATCGGTACATAAATTACATTCAATGTTTTCCATTTAATAG
Found at i:82356 original size:15 final size:15
Alignment explanation
Indices: 82336--82365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82326 AAAATTAATT
*
82336 TAATTTTAGAATAAA
1 TAATTTTAAAATAAA
82351 TAATTTTAAAATAAA
1 TAATTTTAAAATAAA
82366 AATATGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATTTTAAAATAAA
Found at i:88515 original size:14 final size:14
Alignment explanation
Indices: 88496--88523 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
88486 GAAATTGCAG
88496 AAAAACAAGAAGCA
1 AAAAACAAGAAGCA
88510 AAAAACAAGAAGCA
1 AAAAACAAGAAGCA
88524 GGAACATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAACAAGAAGCA
Found at i:91781 original size:43 final size:42
Alignment explanation
Indices: 91707--91894 Score: 158
Period size: 43 Copynumber: 4.5 Consensus size: 42
91697 CTTAAGTGCT
* * *
91707 TCAATTAT-AAGTTAAAAGGTGAGATT--AAAAATTAGGGGCC
1 TCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTA-GGACC
* *
91747 TCAATTTTAAA-AGTAAATAAAG-G-GATTGAAAAAATTATAGACC
1 TCAATTATAAAGA-T-AA-AAAGTGAGATTGAAAAAATTA-GGACC
91790 TCAATTATAAAGATAAAAAGTGAGATTGAATAAAATTAGGACC
1 TCAATTATAAAGATAAAAAGTGAGATTGAA-AAAATTAGGACC
* * *
91833 TCAATTACAAAGATAAAAAGTAAGATCT-AAAAAATTAAGAACC
1 TCAATTATAAAGATAAAAAGTGAGAT-TGAAAAAATT-AGGACC
*
91876 T-AATTATGAAGATGAAAAA
1 TCAATTATAAAGAT-AAAAA
91895 TGGAGATCCT
Statistics
Matches: 122, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
40 7 0.06
41 11 0.09
42 22 0.18
43 73 0.60
44 9 0.07
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAGGACC
Found at i:92933 original size:46 final size:46
Alignment explanation
Indices: 92874--92963 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
92864 ATATATTATT
*
92874 TAGTTTTGAAAATA-AGTTATA-TCATATATTATATAGTTTTGAAAAA
1 TAGTTTTGAAAATAGA-ATATAGTC-TATATTATATAGTTTTGAAAAA
*
92920 TAGTTTTGGAAATAGAATATAGTCTATATTATATAGTTTTGAAA
1 TAGTTTTGAAAATAGAATATAGTCTATATTATATAGTTTTGAAA
92964 TAGTATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 37 0.93
47 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (46 bp):
TAGTTTTGAAAATAGAATATAGTCTATATTATATAGTTTTGAAAAA
Found at i:92972 original size:25 final size:26
Alignment explanation
Indices: 92938--93007 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 26
92928 GAAATAGAAT
* ***
92938 ATAGTCTATATTATATAGTT-TTGAA
1 ATAGTATATATTATATAGTTAAAAAA
92963 ATAGTATATATAATATATAGTTAAAAAA
1 ATAGTATATAT--TATATAGTTAAAAAA
*
92991 ATACTATATATTATATA
1 ATAGTATATATTATATA
93008 TAGTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
25 10 0.27
26 6 0.16
27 9 0.24
28 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (26 bp):
ATAGTATATATTATATAGTTAAAAAA
Found at i:93017 original size:30 final size:28
Alignment explanation
Indices: 92961--93021 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
92951 TATAGTTTTG
*
92961 AAATAGTATATATAATATATAGTTAAAA
1 AAATACTATATATAATATATAGTTAAAA
* **
92989 AAATACTATATATTATATATAGTTTTAA
1 AAATACTATATATAATATATAGTTAAAA
93017 AAATA
1 AAATA
93022 ACATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
AAATACTATATATAATATATAGTTAAAA
Found at i:94441 original size:9 final size:8
Alignment explanation
Indices: 94406--94454 Score: 50
Period size: 7 Copynumber: 6.4 Consensus size: 8
94396 TCAAATTAAA
94406 AAAATATT
1 AAAATATT
*
94414 TAAAT-TT
1 AAAATATT
94421 AAAATA-T
1 AAAATATT
94428 AAAATAATT
1 AAAAT-ATT
*
94437 AAAATGTT
1 AAAATATT
94445 AAAA-ATT
1 AAAATATT
94452 AAA
1 AAA
94455 TATAAAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
7 17 0.50
8 11 0.32
9 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:94441 original size:23 final size:23
Alignment explanation
Indices: 94406--94456 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
94396 TCAAATTAAA
*
94406 AAAAT-ATTTAAAT-TTAAAATAT
1 AAAATAATTAAAATGTTAAAA-AT
94428 AAAATAATTAAAATGTTAAAAAT
1 AAAATAATTAAAATGTTAAAAAT
*
94451 TAAATA
1 AAAATA
94457 TAAAAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 14 0.56
24 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAATAATTAAAATGTTAAAAAT
Found at i:99068 original size:94 final size:94
Alignment explanation
Indices: 98907--99099 Score: 386
Period size: 94 Copynumber: 2.1 Consensus size: 94
98897 TTCCCCATGT
98907 ATTACATGACTATCTTATATGTTTTGAAATATGTTTCACCAAAATTATTAATTTACTGGCTTATG
1 ATTACATGACTATCTTATATGTTTTGAAATATGTTTCACCAAAATTATTAATTTACTGGCTTATG
98972 AACCATGGCTACATGGTATGTGTTCTCTA
66 AACCATGGCTACATGGTATGTGTTCTCTA
99001 ATTACATGACTATCTTATATGTTTTGAAATATGTTTCACCAAAATTATTAATTTACTGGCTTATG
1 ATTACATGACTATCTTATATGTTTTGAAATATGTTTCACCAAAATTATTAATTTACTGGCTTATG
99066 AACCATGGCTACATGGTATGTGTTCTCTA
66 AACCATGGCTACATGGTATGTGTTCTCTA
99095 ATTAC
1 ATTAC
99100 GGTTTCACTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 99 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (94 bp):
ATTACATGACTATCTTATATGTTTTGAAATATGTTTCACCAAAATTATTAATTTACTGGCTTATG
AACCATGGCTACATGGTATGTGTTCTCTA
Found at i:99549 original size:31 final size:32
Alignment explanation
Indices: 99511--99585 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
99501 TAAGGCGACC
*
99511 CTTGGGTAGGCTC-TAAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCTTAAGGCCCCGAGATCCTT
*
99542 CTTGGGTAGGC-CTTACGGCCCCGAGATCCTT
1 CTTGGGTAGGCTCTTAAGGCCCCGAGATCCTT
99573 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
99586 CGTGGCCCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.13, C:0.28, G:0.31, T:0.28
Consensus pattern (32 bp):
CTTGGGTAGGCTCTTAAGGCCCCGAGATCCTT
Found at i:99593 original size:31 final size:31
Alignment explanation
Indices: 99511--99597 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
99501 TAAGGCGACC
* * *
99511 CTTGGGTAGGCTCTAAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCATGGCCCCGAGATCCTT
* *
99542 CTTGGGTAGGC-CTTACGGCCCCGAGATCCTT
1 CTTGGGTAGGCTC-CATGGCCCCGAGATCCTT
*
99573 CTTGGGTAGGCTCCGTGGCCCCGAG
1 CTTGGGTAGGCTCCATGGCCCCGAG
99598 TAACTTGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.13, C:0.30, G:0.32, T:0.25
Consensus pattern (31 bp):
CTTGGGTAGGCTCCATGGCCCCGAGATCCTT
Found at i:114504 original size:19 final size:19
Alignment explanation
Indices: 114482--114525 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
114472 CAAATTACCT
114482 TAATTACCTAAA-ATTTAAC
1 TAATT-CCTAAACATTTAAC
*
114501 TAATTCTTAAACATTTAAC
1 TAATTCCTAAACATTTAAC
114520 TAATTC
1 TAATTC
114526 TTTGACCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTCCTAAACATTTAAC
Found at i:114526 original size:19 final size:18
Alignment explanation
Indices: 114490--114527 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
114480 CTTAATTACC
114490 TAAAATTTAACTAATTCT
1 TAAAATTTAACTAATTCT
114508 TAAACATTTAACTAATTCT
1 TAAA-ATTTAACTAATTCT
114527 T
1 T
114528 TGACCAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTAACTAATTCT
Found at i:114549 original size:65 final size:65
Alignment explanation
Indices: 114440--114562 Score: 228
Period size: 65 Copynumber: 1.9 Consensus size: 65
114430 CAGACCAAAA
114440 TCTTAAACATTTAACAAATTCTTTGACCAGATCAAATTACCTTAATTACCTAAAATTTAACTAAT
1 TCTTAAACATTTAACAAATTCTTTGACCAGATCAAATTACCTTAATTACCTAAAATTTAACTAAT
* *
114505 TCTTAAACATTTAACTAATTCTTTGACCAGATCAAATTATCTTAATTACCTAAAATTT
1 TCTTAAACATTTAACAAATTCTTTGACCAGATCAAATTACCTTAATTACCTAAAATTT
114563 TAGGGTACTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (65 bp):
TCTTAAACATTTAACAAATTCTTTGACCAGATCAAATTACCTTAATTACCTAAAATTTAACTAAT
Found at i:115507 original size:17 final size:17
Alignment explanation
Indices: 115487--115520 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
115477 TTTATTAAAT
115487 TAAAAATAATATTTTAA
1 TAAAAATAATATTTTAA
* *
115504 TAAATATATTATTTTAA
1 TAAAAATAATATTTTAA
115521 GTTGGGTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATAATATTTTAA
Found at i:115574 original size:23 final size:23
Alignment explanation
Indices: 115547--115592 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
115537 ATTTTATCTC
115547 AAAAAATTGGTTCGAATTTGAAT
1 AAAAAATTGGTTCGAATTTGAAT
115570 AAAAAATTGGTTCGAATTTGAAT
1 AAAAAATTGGTTCGAATTTGAAT
115593 CGGACATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (23 bp):
AAAAAATTGGTTCGAATTTGAAT
Found at i:122451 original size:11 final size:11
Alignment explanation
Indices: 122425--122458 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
122415 TAGTAAAATG
*
122425 AAATATTATAAT
1 AAATATT-TTAT
122437 AAATATTTTAT
1 AAATATTTTAT
122448 AAATATTTTAT
1 AAATATTTTAT
122459 TTATGAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAT
Found at i:123111 original size:2 final size:2
Alignment explanation
Indices: 123025--123099 Score: 109
Period size: 2 Copynumber: 38.0 Consensus size: 2
123015 ATGCTTTCTC
* *
123025 AT AT AT AT AT AT AT GT CAT GT A- AT -T 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
123066 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
123100 TAAAGAATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
1 2 0.03
2 63 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128441 original size:58 final size:58
Alignment explanation
Indices: 128371--128484 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
128361 GATCCAGACT
* *
128371 GAAGGTACCCTACAAGCATACATATACATATATGCTATCTTTTTAGCATATGTATTCC
1 GAAGGTACCCTACAAGCATACATATACATATATGCTAACTGTTTAGCATATGTATTCC
*
128429 GAAGGTACCCTACATGCATACATATACATATATGCTAACTGTTTAGCATATGTATT
1 GAAGGTACCCTACAAGCATACATATACATATATGCTAACTGTTTAGCATATGTATT
128485 TAAGCATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (58 bp):
GAAGGTACCCTACAAGCATACATATACATATATGCTAACTGTTTAGCATATGTATTCC
Found at i:130318 original size:16 final size:18
Alignment explanation
Indices: 130286--130319 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
130276 TATTAATGTA
130286 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
130304 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
130320 AATAAGAAAT
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:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:130992 original size:130 final size:130
Alignment explanation
Indices: 130788--131035 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
130778 AATTTTCTTC
*
130788 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
** *
130853 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
130918 TAATTAGGTGGTGACATGTGTCACCAATGACATGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
130983 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
131036 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:131486 original size:35 final size:35
Alignment explanation
Indices: 131436--131511 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
131426 AATTGAATTT
* *
131436 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
131471 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
131506 AATTGA
1 AATTGA
131512 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:138294 original size:50 final size:50
Alignment explanation
Indices: 138175--138284 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 50
138165 AGATATACAG
* * ** *
138175 GTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGATGCAGGGGCCGCGCTATACCCACGTGGCACCAAATAACC
*
138225 GTATAGCGCGATGCAAGGGG-CGCGCTATACCCCACGTGGCACCAAATAATC
1 GTATAGCGCGATGC-AGGGGCCGCGCTATA-CCCACGTGGCACCAAATAACC
138276 GTATAGCGC
1 GTATAGCGC
138285 AGTACAGGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 22 0.42
51 30 0.58
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (50 bp):
GTATAGCGCGATGCAGGGGCCGCGCTATACCCACGTGGCACCAAATAACC
Found at i:144550 original size:23 final size:23
Alignment explanation
Indices: 144532--144591 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
144522 CTCGTATAAA
144532 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
144555 TGCACCGAAGTGCCCCATAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
144578 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
144592 ATATAATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:145309 original size:66 final size:65
Alignment explanation
Indices: 145202--145351 Score: 219
Period size: 66 Copynumber: 2.3 Consensus size: 65
145192 TTTTTCCCAT
* * *
145202 GGGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGTT
1 GGGGGTATCGG-T-CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
145267 GA
64 GA
* *
145269 GGGGGTATCGGTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTG
1 GGGGGTATCGGTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
145334 A
65 A
*
145335 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTCCCCC
145352 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 7 0.09
66 59 0.78
67 10 0.13
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.30
Consensus pattern (65 bp):
GGGGGTATCGGTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGA
Found at i:151429 original size:23 final size:23
Alignment explanation
Indices: 151411--151470 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
151401 CTCGTATAAA
151411 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
151434 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
151457 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
151471 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:152186 original size:66 final size:65
Alignment explanation
Indices: 152079--152228 Score: 219
Period size: 66 Copynumber: 2.3 Consensus size: 65
152069 TTTTTCCCAT
* * *
152079 GGGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGTT
1 GGGGGTATCGG-T-CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
152144 GA
64 GA
* *
152146 GGGGGTATCGGTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTG
1 GGGGGTATCGGTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
152211 A
65 A
*
152212 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTCCCCC
152229 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 7 0.09
66 59 0.78
67 10 0.13
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.30
Consensus pattern (65 bp):
GGGGGTATCGGTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGA
Found at i:162132 original size:33 final size:33
Alignment explanation
Indices: 162061--162132 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
162051 TCTATTGTTT
*
162061 AGTTTGAGGCACCAATACGGTATTACATTATAT
1 AGTTTGAGGCACCAATACGGTATTACATTATAG
* *
162094 CGTTTGAGGCACCAATACGGTATTACATTGTAG
1 AGTTTGAGGCACCAATACGGTATTACATTATAG
162127 AGTTTG
1 AGTTTG
162133 CGTTGTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (33 bp):
AGTTTGAGGCACCAATACGGTATTACATTATAG
Found at i:177515 original size:34 final size:34
Alignment explanation
Indices: 177472--177540 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
177462 AGCCATAGGA
177472 CAAGTTGTATTTCAACATCTGATCATCACCTTTT
1 CAAGTTGTATTTCAACATCTGATCATCACCTTTT
*
177506 CAAGTTGTATTTCAACATCTGATCATCACTTTTT
1 CAAGTTGTATTTCAACATCTGATCATCACCTTTT
177540 C
1 C
177541 GAGTGCATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (34 bp):
CAAGTTGTATTTCAACATCTGATCATCACCTTTT
Found at i:179744 original size:34 final size:33
Alignment explanation
Indices: 179668--179774 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
179658 GTGGTAAGAA
* *
179668 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
179702 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
179737 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
179771 ATTT
1 ATTT
179775 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:179756 original size:36 final size:34
Alignment explanation
Indices: 179701--179779 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
179691 TTTAAATAGT
*
179701 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
179733 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
179767 TATTATTTATTTA
1 TATTATTTTTTTA
179780 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:183079 original size:12 final size:13
Alignment explanation
Indices: 183046--183083 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
183036 AAATACATAA
183046 ATATATTTAATAT
1 ATATATTTAATAT
*
183059 ATTTATTTAATAT
1 ATATATTTAATAT
183072 A-ATATTTAATAT
1 ATATATTTAATAT
183084 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:186553 original size:29 final size:29
Alignment explanation
Indices: 186510--186592 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
186500 CTCACCTAAC
186510 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
186540 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
186569 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
186593 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:191323 original size:29 final size:29
Alignment explanation
Indices: 191280--191362 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
191270 CTCACCTAAC
191280 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
191310 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
191339 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
191363 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:195015 original size:6 final size:6
Alignment explanation
Indices: 195004--195164 Score: 313
Period size: 6 Copynumber: 26.8 Consensus size: 6
194994 CGTTTCAAGT
195004 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
195052 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
195100 TATATG TATATG TATATG TATATG TATATA TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
195148 TATATG TATATG TATAT
1 TATATG TATATG TATAT
195165 ACGAGCCAGG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 153 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:197017 original size:6 final size:6
Alignment explanation
Indices: 197000--197043 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
196990 AGTACATTGC
* *
197000 TCCGGT TTCGGT TCCGGT TCCGGT TCCGGT TCCGGC TCCGGT TC
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TC
197044 TGACTCTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.34, G:0.32, T:0.34
Consensus pattern (6 bp):
TCCGGT
Found at i:199191 original size:147 final size:147
Alignment explanation
Indices: 198924--199206 Score: 426
Period size: 147 Copynumber: 1.9 Consensus size: 147
198914 CTGTCCGGGG
* * *
198924 TGCATGTTTTTCGCAAATCTTTGCCTGAATCCTGAGGATTCTCATCAAGTTTCTGGTCCTGGAGT
1 TGCATGTTTCTCGCAAATCTTTGCCTGAATCCTGAGGATTCTCATCAAGTTTCTGATCCTGGAGC
* * * *
198989 GGTGGGGTATTCTCCAACCCACCATTTTCAGGCCGAGTTGAACTGTTAAAAGGCTTTTCAATCGC
66 GATGGGGTATTCTCCAACCCACCATTTTCAGGCAGAGTTGAAATGCTAAAAGGCTTTTCAATCGC
199054 TTGCTCCACCATTTCCA
131 TTGCTCCACCATTTCCA
* * *
199071 TGCATGTTTCTCGCAAAAT-TTTTCCTGAATCTTGAGGTTTCTCATCAAGTTTCTGATCCCT-GA
1 TGCATGTTTCTCGC-AAATCTTTGCCTGAATCCTGAGGATTCTCATCAAGTTTCTGAT-CCTGGA
* *
199134 GCGATGGGGTATTCTCCAATCCACCATTTTCAGGCAGAGTTGAAATGCTAAAAGGCTTTTCCATC
64 GCGATGGGGTATTCTCCAACCCACCATTTTCAGGCAGAGTTGAAATGCTAAAAGGCTTTTCAATC
199199 GCTTGCTC
129 GCTTGCTC
199207 GGACATTGAA
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
147 115 0.94
148 7 0.06
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (147 bp):
TGCATGTTTCTCGCAAATCTTTGCCTGAATCCTGAGGATTCTCATCAAGTTTCTGATCCTGGAGC
GATGGGGTATTCTCCAACCCACCATTTTCAGGCAGAGTTGAAATGCTAAAAGGCTTTTCAATCGC
TTGCTCCACCATTTCCA
Found at i:206255 original size:20 final size:20
Alignment explanation
Indices: 206217--206255 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
206207 CTTGACGGGG
*
206217 CTTTTGTTTTGTCTTCAATA
1 CTTTTGTTTTGTCTACAATA
206237 CTTTTGTTTCTG-CTACAAT
1 CTTTTGTTT-TGTCTACAAT
206256 TGGTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.56
Consensus pattern (20 bp):
CTTTTGTTTTGTCTACAATA
Found at i:220615 original size:15 final size:16
Alignment explanation
Indices: 220595--220628 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
220585 ACACATATAC
220595 ATTTATCA-TGAACAT
1 ATTTATCAGTGAACAT
*
220610 ATTTATCAGTGATCAT
1 ATTTATCAGTGAACAT
220626 ATT
1 ATT
220629 ATTATCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTTATCAGTGAACAT
Found at i:220934 original size:22 final size:22
Alignment explanation
Indices: 220909--220969 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
220899 GGCATATGAA
220909 ATTTGTCCCGAAAGACCTATGT
1 ATTTGTCCCGAAAGACCTATGT
* *
220931 ATTTATCCCGAAATACCTATGT
1 ATTTGTCCCGAAAGACCTATGT
220953 ATTTGTCCCGAAAGACC
1 ATTTGTCCCGAAAGACC
220970 GCGTAAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAAGACCTATGT
Found at i:222227 original size:4 final size:4
Alignment explanation
Indices: 222208--222246 Score: 60
Period size: 4 Copynumber: 9.2 Consensus size: 4
222198 GTTCACGGTG
222208 AAGA GAAGA GAAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA -AAGA -AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
222247 GAAGAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.74
5 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:225850 original size:31 final size:31
Alignment explanation
Indices: 225784--225857 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
225774 TTTTTGAAAT
* *
225784 TTTAGGTACTAAAATGGACAAAAACTTCTTG
1 TTTAGGTACTAAAATGGACAAAAACTTATAG
* *
225815 -TTAGGTACTAGAATGGACCAAAACTTATAG
1 TTTAGGTACTAAAATGGACAAAAACTTATAG
225845 TTTAGGTACTAAA
1 TTTAGGTACTAAA
225858 CACATTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (31 bp):
TTTAGGTACTAAAATGGACAAAAACTTATAG
Found at i:226543 original size:31 final size:30
Alignment explanation
Indices: 226480--226543 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
226470 CATCCGAATT
* *
226480 ATATTTACAATTATACCCCTACAAATCCAA
1 ATATTTACAATTATACCCCGACAAATCAAA
* * *
226510 ATATTTTCCATTATACCCCGCCAAAATCAAA
1 ATATTTACAATTATACCCCGAC-AAATCAAA
226541 ATA
1 ATA
226544 CAACTACATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.30
Consensus pattern (30 bp):
ATATTTACAATTATACCCCGACAAATCAAA
Found at i:227768 original size:36 final size:36
Alignment explanation
Indices: 227707--228188 Score: 369
Period size: 36 Copynumber: 13.8 Consensus size: 36
227697 GAGTTTGATC
* * **
227707 CTGAACCTCAAGCTAAGCCAGAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
227743 TTGAACCTCAGGCTGAGCCTCAACATGAATCGGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
227779 CTGAACCTCAGGCTGAGCCTCAATATGAATCAGCTG
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
227815 CTGAACCTCGGGCTGAGCCTCAACATGAATTAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
*
227851 CTGAACCTCGGGCTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* ** * *
227887 TTGAACCTCATGAATCAG-CT--AC-TGAACCTCAG--G
1 CTGAACCTCA-GGCTGAGCCTCAACATGAA--TCAGCTA
* * * * * *
227920 CTGAGCCTCA-ACATGAATCATCTAC-TGAACCTCAG--G
1 CTGAACCTCAGGC-TG-AGCCTCAACATGAA--TCAGCTA
*
227956 CTGAGCCTCA-----A-------CATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
227980 CTGAAACTCATGCTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * ** * *
228016 CTGAACCTCAGGATAAGATTCGACATGAATTAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * *
228052 CTGAACCTCAGACTGTGCCTCAACATGAATTAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * *
228088 CTGAACCTCAGACTGTGCCTCAACATGAATTAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * * *
228124 CTGAACCTCAGACTGTGCCTCAACATGAATTAGCAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
*
228160 CTGAACCTCAGGCTGAGCCTCGACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAA
228189 CTGGCTTCTG
Statistics
Matches: 374, Mismatches: 49, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.01
23 1 0.00
24 12 0.03
29 1 0.00
30 1 0.00
31 1 0.00
32 1 0.00
33 13 0.03
34 3 0.01
35 4 0.01
36 329 0.88
37 4 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (36 bp):
CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
Found at i:227895 original size:24 final size:23
Alignment explanation
Indices: 227863--227917 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
227853 GAACCTCGGG
*
227863 CTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTC-ACATGAATCAGCTA
*
227887 TTGAACCT--CATGAATCAGCTA
1 CTGAACCTCACATGAATCAGCTA
227908 CTGAACCTCA
1 CTGAACCTCA
227918 GGCTGAGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 20 0.77
24 6 0.23
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (23 bp):
CTGAACCTCACATGAATCAGCTA
Found at i:227896 original size:108 final size:108
Alignment explanation
Indices: 227707--228188 Score: 492
Period size: 108 Copynumber: 4.6 Consensus size: 108
227697 GAGTTTGATC
* * ** * *
227707 CTGAACCTCAAGCTAAGCCAGAACATGAATCAGCTATTGAACCTCAGGCTGAGCCTCAACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* * *
227772 TCGGCTACTGAACCTCAGGCTGAGCCTCAATATGAATCAGCTG
66 TCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
227815 CTGAACCTCGGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCGGGCTGAGCCTCAACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* ** *
227880 TCAGCTATTGAACCTCATGAATCAG-CT--AC-TGAA-C--CT-
66 TCAGCTACTGAACCTCA-GGCTGAGCCTCAACATGAATCAGCTA
** * * * * *
227916 C--AGGCTGAGCCT----C-AA-CATGAATCATCTACTGAACCTCAGGCTGAGCCTCAACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* *
227973 TCAGCTACTGAAACTCATGCTGAGCCTCAACATGAATCAGCTA
66 TCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * ** * * *
228016 CTGAACCTCAGGATAAGATTCGACATGAATTAGCTACTGAACCTCAGACTGTGCCTCAACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* * * *
228081 TTAGCTACTGAACCTCAGACTGTGCCTCAACATGAATTAGCTA
66 TCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * * *
228124 CTGAACCTCAGACTGTGCCTCAACATGAATTAGCAACTGAACCTCAGGCTGAGCCTCGACATGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
228189 CTGGCTTCTG
Statistics
Matches: 299, Mismatches: 58, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
92 3 0.01
93 56 0.19
94 1 0.00
95 3 0.01
96 4 0.01
97 1 0.00
99 8 0.03
100 1 0.00
101 1 0.00
102 8 0.03
104 1 0.00
105 4 0.01
106 1 0.00
108 203 0.68
109 4 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (108 bp):
CTGAACCTCAGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
TCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
Found at i:227900 original size:21 final size:21
Alignment explanation
Indices: 227874--227917 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
227864 TGAGCCTCAA
*
227874 CATGAATCAGCTATTGAACCT
1 CATGAATCAGCTACTGAACCT
227895 CATGAATCAGCTACTGAACCT
1 CATGAATCAGCTACTGAACCT
227916 CA
1 CA
227918 GGCTGAGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (21 bp):
CATGAATCAGCTACTGAACCT
Found at i:227926 original size:57 final size:57
Alignment explanation
Indices: 227838--227953 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
227828 TGAGCCTCAA
* * *
227838 CATGAATTAGCTACTGAACCTCGGGCTGAGCCTCAACATGAATCAGCTATTGAACCT
1 CATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCT
*
227895 CATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCATCTACTGAACCT
1 CATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCT
227952 CA
1 CA
227954 GGCTGAGCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (57 bp):
CATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCT
Found at i:227962 original size:93 final size:93
Alignment explanation
Indices: 227803--227991 Score: 315
Period size: 93 Copynumber: 2.0 Consensus size: 93
227793 GAGCCTCAAT
* * * *
227803 ATGAATCAGCTGCTGAACCTCGGGCTGAGCCTCAACATGAATTAGCTACTGAACCTCGGGCTGAG
1 ATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGCTGAG
* *
227868 CCTCAACATGAATCAGCTATTGAACCTC
66 CCTCAACATGAATCAGCTACTGAAACTC
*
227896 ATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCATCTACTGAACCTCAGGCTGAG
1 ATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGCTGAG
227961 CCTCAACATGAATCAGCTACTGAAACTC
66 CCTCAACATGAATCAGCTACTGAAACTC
227989 ATG
1 ATG
227992 CTGAGCCTCA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
ATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGCTGAG
CCTCAACATGAATCAGCTACTGAAACTC
Found at i:228052 original size:201 final size:201
Alignment explanation
Indices: 227707--228097 Score: 584
Period size: 201 Copynumber: 1.9 Consensus size: 201
227697 GAGTTTGATC
* *
227707 CTGAACCTCAAGCTAAGCCAGAACATGAATCAGCTATTGAACCTCAGGCTGAGCCTCAACATGAA
1 CTGAACCTCAAGCTAAGCCACAACATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* * * * * * * *
227772 TCGGCTACTGAACCTCAGGCTGAGCCTCAATATGAATCAGCTGCTGAACCTCGGGCTGAGCCTCA
66 TCAGCTACTGAAACTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGATAAGACTCA
* * *
227837 ACATGAATTAGCTACTGAACCTCGGGCTGAGCCTCAACATGAATCAGCTATTGAACCTCATGAAT
131 ACATGAATTAGCTACTGAACCTCAGACTGAGCCTCAACATGAATCAGCTACTGAACCTCATGAAT
227902 CAGCTA
196 CAGCTA
* * * *
227908 CTGAACCTCAGGCTGAGCCTCAACATGAATCATCTACTGAACCTCAGGCTGAGCCTCAACATGAA
1 CTGAACCTCAAGCTAAGCCACAACATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
* * *
227973 TCAGCTACTGAAACTCATGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGATAAGATTCG
66 TCAGCTACTGAAACTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGATAAGACTCA
* *
228038 ACATGAATTAGCTACTGAACCTCAGACTGTGCCTCAACATGAATTAGCTACTGAACCTCA
131 ACATGAATTAGCTACTGAACCTCAGACTGAGCCTCAACATGAATCAGCTACTGAACCTCA
228098 GACTGTGCCT
Statistics
Matches: 168, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
201 168 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (201 bp):
CTGAACCTCAAGCTAAGCCACAACATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAACATGAA
TCAGCTACTGAAACTCAGGCTGAGCCTCAACATGAATCAGCTACTGAACCTCAGGATAAGACTCA
ACATGAATTAGCTACTGAACCTCAGACTGAGCCTCAACATGAATCAGCTACTGAACCTCATGAAT
CAGCTA
Found at i:228200 original size:36 final size:36
Alignment explanation
Indices: 227895--228188 Score: 408
Period size: 36 Copynumber: 8.2 Consensus size: 36
227885 TATTGAACCT
*
227895 CATGAATCAGCTACTGAACCTCAGGCTGAGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* *
227931 CATGAATCATCTACTGAACCTCAGGCTGAGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* * *
227967 CATGAATCAGCTACTGAAACTCATGCTGAGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* * * ** *
228003 CATGAATCAGCTACTGAACCTCAGGATAAGATTCGA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* *
228039 CATGAATTAGCTACTGAACCTCAGACTGTGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* *
228075 CATGAATTAGCTACTGAACCTCAGACTGTGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* *
228111 CATGAATTAGCTACTGAACCTCAGACTGTGCCTCAA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
* *
228147 CATGAATTAGCAACTGAACCTCAGGCTGAGCCTCGA
1 CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
228183 CATGAA
1 CATGAA
228189 CTGGCTTCTG
Statistics
Matches: 235, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 235 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (36 bp):
CATGAATTAGCTACTGAACCTCAGGCTGAGCCTCAA
Found at i:231468 original size:202 final size:208
Alignment explanation
Indices: 231116--231526 Score: 780
Period size: 202 Copynumber: 2.0 Consensus size: 208
231106 AACAAAAGTT
231116 TGAAGAATTCCAATCTCTAGAAAGAGTTTACAAGGAATACTACAGTATGAAGACAAGAATGGAAG
1 TGAAGAATTCCAATCTCTAGAAAGAGTTTACAAGGAATACTACAGTATGAAGACAAGAATGGAAG
231181 CGGACATTAAAGATCTTTTGTTGAAAATGGAAGCCACAAGACGAAATCTCGGCATGTGATTTGGC
66 CGGACATTAAAGATCTTTTGTTGAAAATGGAAGCCACAAGACGAAATCTCGGCATGTGATTTGGC
231246 TTTCAGTTGGAGCTTGCTATTGAATTGTGTTCTATAATGTGTATACTTTACGATTCGAGTTTCTG
131 TTTCAGTTGGAGCTTGCTATTGAATTGTGTTCTATAATGTGTATACTTTACGATTCGAGTTTCTG
231311 TAGTTTTCCCTGG
196 TAGTTTTCCCTGG
231324 TGAAGAATTCCAATCTCTAGAAAGAGTTTACAAGG-A-A-TACAGTATGAAGACAAGAATGGAAG
1 TGAAGAATTCCAATCTCTAGAAAGAGTTTACAAGGAATACTACAGTATGAAGACAAGAATGGAAG
231386 CGGACATT-AAGATC-TTT-TTGAAAATGGAAGCCACAAGACGAAATCTCGGCATGTGATTTGGC
66 CGGACATTAAAGATCTTTTGTTGAAAATGGAAGCCACAAGACGAAATCTCGGCATGTGATTTGGC
231448 TTTCAGTTGGAGCTTGCTATTGAATTGTGTTCTATAATGTGTATACTTTACGATTCGAGTTTCTG
131 TTTCAGTTGGAGCTTGCTATTGAATTGTGTTCTATAATGTGTATACTTTACGATTCGAGTTTCTG
231513 TAGTTTTCCCTGG
196 TAGTTTTCCCTGG
231526 T
1 T
231527 ATTCTCTTGG
Statistics
Matches: 203, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
202 124 0.61
203 3 0.01
204 6 0.03
205 33 0.16
206 1 0.00
207 1 0.00
208 35 0.17
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (208 bp):
TGAAGAATTCCAATCTCTAGAAAGAGTTTACAAGGAATACTACAGTATGAAGACAAGAATGGAAG
CGGACATTAAAGATCTTTTGTTGAAAATGGAAGCCACAAGACGAAATCTCGGCATGTGATTTGGC
TTTCAGTTGGAGCTTGCTATTGAATTGTGTTCTATAATGTGTATACTTTACGATTCGAGTTTCTG
TAGTTTTCCCTGG
Found at i:247824 original size:21 final size:21
Alignment explanation
Indices: 247792--247853 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
247782 AACCATCATA
* *
247792 AACTGTCACGTCAGTACCTTG
1 AACTGACACGTCAGTACCGTG
* *
247813 AGCTGACACGTCAGTACAGTG
1 AACTGACACGTCAGTACCGTG
*
247834 AACTGTCACGTCAGTACCGT
1 AACTGACACGTCAGTACCGT
247854 AACGGTCAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (21 bp):
AACTGACACGTCAGTACCGTG
Found at i:248652 original size:3 final size:3
Alignment explanation
Indices: 248644--248677 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
248634 TATTTTTTAT
248644 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
248678 ACAGGTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:263418 original size:141 final size:135
Alignment explanation
Indices: 263227--263499 Score: 359
Period size: 141 Copynumber: 2.0 Consensus size: 135
263217 ACGAAGGAGA
263227 GTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAG
1 GTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAG
* ** *
263292 ATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTAGACGACCAGACTTCCTCAT
66 ATGACCAGAACTCTTCATCACGTATGAACCATGTCA--T-CCCTT----GACCAGACTTCCTCAT
263357 CACGTAGGAGCC
124 CACGTAGGAGCC
* * * * *
263369 GTGTCAACCTTA-GATAATCAGCTGTCCTCATTACGTAGGAACCTAGTTATCACCCTTCTTAAAG
1 GTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAG
* * * *
263433 ATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCTTGACCAGATTTCCTCATCACGTAG
66 ATGACCAGAACTCTTCATCACGTATGAACCATGTCATCCCTTGACCAGACTTCCTCATCACGTAG
263498 GA
131 GA
263500 ATCGTGTCTC
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
134 24 0.20
138 5 0.04
139 1 0.01
141 77 0.65
142 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (135 bp):
GTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAG
ATGACCAGAACTCTTCATCACGTATGAACCATGTCATCCCTTGACCAGACTTCCTCATCACGTAG
GAGCC
Found at i:263725 original size:3 final size:3
Alignment explanation
Indices: 263719--263745 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
263709 TTTTTTTTTT
263719 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
263746 ATATACATGT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:273287 original size:23 final size:23
Alignment explanation
Indices: 273253--273338 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
273243 ACATATTATA
*
273253 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
273276 TGGCACTTCGGTGC-ATCTCTACG
1 TGGCACTTCGGTGCAAT-TCTACG
*
273299 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
*
273323 TGACACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
273339 ATTTATATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
22 3 0.06
23 31 0.60
24 15 0.29
25 3 0.06
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:273931 original size:20 final size:21
Alignment explanation
Indices: 273891--273932 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
273881 TACGAAAGTA
*
273891 CTGTAGCAGGGGAATCGATTC
1 CTGTAGCAGGGGAACCGATTC
*
273912 CTGTAGCA-GGGTACCGATTC
1 CTGTAGCAGGGGAACCGATTC
273932 C
1 C
273933 CTATTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (21 bp):
CTGTAGCAGGGGAACCGATTC
Found at i:275172 original size:6 final size:6
Alignment explanation
Indices: 275163--275196 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
275153 TCTGTTCTTC
275163 CCACAG CCACAG CCACAG CCACAG CCACAG CCAC
1 CCACAG CCACAG CCACAG CCACAG CCACAG CCAC
275197 TCTTCCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.53, G:0.15, T:0.00
Consensus pattern (6 bp):
CCACAG
Found at i:275498 original size:6 final size:7
Alignment explanation
Indices: 275482--275506 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
275472 ATATGGAAAA
275482 TTTTGAT
1 TTTTGAT
275489 TTTTGAT
1 TTTTGAT
275496 TTTTGAT
1 TTTTGAT
275503 TTTT
1 TTTT
275507 TTTCCAGAGG
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:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGAT
Found at i:284515 original size:18 final size:16
Alignment explanation
Indices: 284468--284508 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
284458 TTAAGAAAAA
*
284468 ATATAAAAATTAATTT
1 ATATAAAAATTAAATT
284484 ATATAAAAATTAAATT
1 ATATAAAAATTAAATT
284500 ATATAAAAA
1 ATATAAAAA
284509 ATATAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAAAATTAAATT
Found at i:288116 original size:43 final size:42
Alignment explanation
Indices: 288069--288215 Score: 129
Period size: 43 Copynumber: 3.5 Consensus size: 42
288059 TATGGGCATG
*
288069 ATTATAAA-GTAAAAAAGTGAGATTGAAAATTTTTGATGCCTCA
1 ATTATAAATGT-AAAAAGTGAGATTGAAAATTTTAGAT-CCTCA
* * * *** *
288112 ATTATAAATGTACAACGTGAGATTAAAAATTAGGGA-CATCA
1 ATTATAAATGTAAAAAGTGAGATTGAAAATTTTAGATCCTCA
* **
288153 ATTATAAATGTAAAAAATTG-GATTGAAAAAATTAGATACCTCA
1 ATTATAAATGT-AAAAAGTGAGATTGAAAATTTTAGAT-CCTCA
*
288196 ATTATAAAAGTAAAAAGTGA
1 ATTATAAATGTAAAAAGTGA
288216 ACTTTTATAA
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
41 25 0.31
42 12 0.15
43 41 0.51
44 2 0.03
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (42 bp):
ATTATAAATGTAAAAAGTGAGATTGAAAATTTTAGATCCTCA
Found at i:288539 original size:22 final size:23
Alignment explanation
Indices: 288509--288552 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
288499 TCTAAAAAAT
288509 ATATCTAA-TAAAATGTTAAATTC
1 ATATCTAATTAAAAT-TTAAATTC
*
288532 ATAT-TAATTTAAATTTAAATT
1 ATATCTAATTAAAATTTAAATT
288553 AAATTAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATCTAATTAAAATTTAAATTC
Found at i:294880 original size:30 final size:30
Alignment explanation
Indices: 294845--294916 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
294835 AAATATATCT
*
294845 CTAATAACAAATATTGAAAAAATT-GGACCC
1 CTAATAACAAATATTAAAAAAATTAGG-CCC
* *
294875 CTAATAATAAATATTAAAAAAATTAGGTCC
1 CTAATAACAAATATTAAAAAAATTAGGCCC
*
294905 TTAATAACAAAT
1 CTAATAACAAAT
294917 GTCAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (30 bp):
CTAATAACAAATATTAAAAAAATTAGGCCC
Found at i:295442 original size:19 final size:19
Alignment explanation
Indices: 295418--295454 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
295408 GGTGACATAT
*
295418 TTTTTAATAATATTTTTAG
1 TTTTTAAGAATATTTTTAG
295437 TTTTTAAGAATATTTTTA
1 TTTTTAAGAATATTTTTA
295455 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTAAGAATATTTTTAG
Found at i:295460 original size:19 final size:19
Alignment explanation
Indices: 295419--295462 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
295409 GTGACATATT
* **
295419 TTTTAATAATATTTTTAGT
1 TTTTAAGAATATTTTTAAA
295438 TTTTAAGAATATTTTTAAA
1 TTTTAAGAATATTTTTAAA
295457 TTTTAA
1 TTTTAA
295463 AATTATAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAAGAATATTTTTAAA
Found at i:305356 original size:23 final size:23
Alignment explanation
Indices: 305330--305407 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
305320 CACCACAGCT
305330 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
305353 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
305376 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
305399 TATAATAAT
1 CAT-ATAAT
305408 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:305585 original size:103 final size:103
Alignment explanation
Indices: 305414--305631 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
305404 TAATGTCCAT
*
305414 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
305479 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
305517 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-GTCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACT-AAGGATCAAGTATGTGTCTCACC
*
305581 AGACTTCACACATGTTCCAAATAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
305620 AAGGACCACATA
1 AAGGACCACATA
305632 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 110 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:308513 original size:247 final size:248
Alignment explanation
Indices: 308060--309066 Score: 1110
Period size: 247 Copynumber: 4.1 Consensus size: 248
308050 TTTGTTGATT
* * * * *
308060 GTGCTCAATAACTTAGATCAAACATTCCTTTCACTAGGGTTTGGGAATTAAGAGGAAGAGGGGGA
1 GTGCTCAATAACTTAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGA-GGGGA
* ** * * * * *
308125 AGGGACACTTGTTTTCCCTA-CGAGGTGCTTTTTTGAATTTTGAGGGACATTTAGAGCTATTTGA
65 GGGGACACTTGCCTTCCCTATCGAGGTGCTTTGTTAAATTTTAAGGGATATTGAGAGCTATTTGA
* * * * * *
308189 AC-TTTCATTTGTTGGTTACACCCAATACCTTATATCACAATGTG-TTTCAGGAATGATTGGGTG
130 ACTTTTC-TTTATTGGTTACACCCAATACCTTAGATCACACTCTGCTTTCAGAAAGGATTGGGTG
* ** * *
308252 TGACTACTAAAAGAAAGTCCAAATAGTAACACAATTTGCTTTCAGGAAGGATTGA
194 TGACTACCAAAAGAAAGTCCAAATAACATCACAATTTGCTTTCAGAAAGGATTGA
* *
308307 GTGCTCAATAACTTAGATCAAACTTTTCTTTCGTTAGGGTTTGAGAATGAAGAGGAAGAGGGGAG
1 GTGCTCAATAACTTAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAG
* * *
308372 GGGACACTTGCCTTTCCTATAG-GGTGCTTTGTTAAATTTTAAGGGATACTGAGAGCTATTTGAA
66 GGGACACTTGCCTTCCCTATCGAGGTGCTTTGTTAAATTTTAAGGGATATTGAGAGCTATTTGAA
* * * * *
308436 CTTTTCTTTACTGGTTACACCCAATATCTTAGATCACACTCTGCTTTCAGAAAAGATTGAGTGAG
131 CTTTTCTTTATTGGTTACACCCAATACCTTAGATCACACTCTGCTTTCAGAAAGGATTGGGTGTG
** ** * * *
308501 ACTACCAAAAGAAAGTTAAAATAGGATCACACTTTGCTTTCAGGAAA-AATTGG
196 ACTACCAAAAGAAAGTCCAAATAACATCACAATTTGCTTTCA-GAAAGGATTGA
* * **
308554 GTGCTCAATAACTTAGATTAAACTTTGCTTTCGTTAGGGTTTG-GAATGAAGAGGAAGAAAGG-G
1 GTGCTCAATAACTTAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAG
* * * * * *
308617 GGAATACCTGCCATTCCCTATTG-GGTGCATTATTAAATTTTAAGGGATATTGAGAGCTATTTGA
66 GGGACACTTGCC-TTCCCTATCGAGGTGCTTTGTTAAATTTTAAGGGATATTGAGAGCTATTTGA
* * * * * *
308681 ACTTTCCTTTGTTGGTTACACTCAATACCTTAGATTATACTCTGCTTTCAGGAAGGATTGGGTGT
130 ACTTTTCTTTATTGGTTACACCCAATACCTTAGATCACACTCTGCTTTCAGAAAGGATTGGGTGT
* * * *** * * *
308746 GACTA-CTAAAGAAAAGTTCAAATAACATCACACTCAACTTTTAAAAAGGATTGG
195 GACTACCAAAAG-AAAGTCCAAATAACATCACAATTTGCTTTCAGAAAGGATTGA
* * *
308800 GTGCTCAATAACATAGATCAAACTTTGCTTTTGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAT
1 GTGCTCAATAACTTAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAG
* * * *
308865 GTGACACTT-CTCTTCCCT-TCGTGGTGCTTTGTTAAATTTTAA-GGAGCATTGAGAGTTATTTG
66 GGGACACTTGC-CTTCCCTATCGAGGTGCTTTGTTAAATTTTAAGGGA-TATTGAGAGCTATTTG
* *
308927 AACCTTTCTTTGA-TGGTTACACCCAATACCTTAGATCACACTCTCCTTTCA-AGAAGGATTGGG
129 AACTTTTCTTT-ATTGGTTACACCCAATACCTTAGATCACACTCTGCTTTCAGA-AAGGATTGGG
* *
308990 TGTGACTACCAAAGGAAAGTTCC-AATAACATCAC-ATTATGCTTTTAGAAAGGATTGA
192 TGTGACTACCAAAAGAAAG-TCCAAATAACATCACAATT-TGCTTTCAGAAAGGATTGA
309047 GTGCTCAATAACTTAGATCA
1 GTGCTCAATAACTTAGATCA
309067 CACTATCCTT
Statistics
Matches: 640, Mismatches: 103, Indels: 34
0.82 0.13 0.04
Matches are distributed among these distances:
245 18 0.03
246 285 0.45
247 322 0.50
248 15 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (248 bp):
GTGCTCAATAACTTAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAG
GGGACACTTGCCTTCCCTATCGAGGTGCTTTGTTAAATTTTAAGGGATATTGAGAGCTATTTGAA
CTTTTCTTTATTGGTTACACCCAATACCTTAGATCACACTCTGCTTTCAGAAAGGATTGGGTGTG
ACTACCAAAAGAAAGTCCAAATAACATCACAATTTGCTTTCAGAAAGGATTGA
Found at i:309053 original size:493 final size:492
Alignment explanation
Indices: 308060--309079 Score: 1249
Period size: 493 Copynumber: 2.1 Consensus size: 492
308050 TTTGTTGATT
*
308060 GTGCTCAATAACTTAGATCAAACATTCCTTTCACTAGGGTTTGGGAATTAAGAGGAAGAGGGGGA
1 GTGCTCAATAACTTAGATCAAACATTCCTTTCACTAGGGTTTGGGAATGAAGAGGAAGAGGGGGA
** * * * * *
308125 AGGGACACTTGTTTTCCCTACGAGGTGCTTTTTTGAATTTTGAGGGACATTTAGAGCTATTTGAA
66 A-GGACACTTGCATTCCCTACGAGGTGCATTATTAAATTTTAAGGGACATTGAGAGCTATTTGAA
* * *
308190 CTTTCATTTGTTGGTTACACCCAATACCTTATATCACAATGTGTTTCAGGAATGATTGGGTGTGA
130 CTTTCATTTGTTGGTTACACCCAATACCTTAGATCACAATCTGTTTCAGGAAGGATTGGGTGTGA
** *** ** *
308255 CTACTAAAAGAAAGTCCAAATAGTAACACAATTTGCTTTCAGGAAGGATTGAGTGCTCAATAACT
195 CTACTAAAAGAAAGTCCAAATAACAACACAATCAACTTTCAAAAAGGATTGAGTGCTCAATAACA
* *
308320 TAGATCAAACTTTTCTTTCGTTAGGGTTTGAGAATGAAGAGGAAGAGGGGAGGGGACACTTGCCT
260 TAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAGGGGACACTTGCCT
* *
308385 TTCCTATAGGGTGCTTTGTTAAATTTTAAGGGATACTGAGAGCTATTTGAACTTTTCTTTACTGG
325 TCCCTATAGGGTGCTTTGTTAAATTTTAAGGGATA-TGAGAGCTATTTGAACCTTTCTTTACTGG
* *
308450 TTACACCCAATATCTTAGATCACACTCTGCTTTCAGAAAAGATTGAGTGAGACTACCAAAAGAAA
389 TTACACCCAATACCTTAGATCACACTCTCCTTTCAGAAAAGATTGAGTGAGACTACCAAAAGAAA
** *
308515 GTTAAAATAGGATCACACTTTGCTTTCAGGAAAAATTGG
454 GTTAAAATAACATCACACTTTGCTTTCAGGAAAAATTGA
* * * **
308554 GTGCTCAATAACTTAGATTAAACTTTGCTTTCGTTAGGGTTT-GGAATGAAGAGGAAGAAAGGGG
1 GTGCTCAATAACTTAGATCAAACATTCCTTTCACTAGGGTTTGGGAATGAAGAGGAAG--AGGGG
* * *
308618 GAA-TAC-C-TGCCATTCCCTATTG-GGTGCATTATTAAATTTTAAGGGATATTGAGAGCTATTT
64 GAAGGACACTTG-CATTCCCTA-CGAGGTGCATTATTAAATTTTAAGGGACATTGAGAGCTATTT
* * * * *
308679 GAACTTTCCTTTGTTGGTTACACTCAATACCTTAGATTATACTCTGCTTTCAGGAAGGATTGGGT
127 GAACTTTCATTTGTTGGTTACACCCAATACCTTAGATCACAATCTG-TTTCAGGAAGGATTGGGT
* * * * *
308744 GTGACTACT-AAAGAAAAGTTCAAATAACATCACACTCAACTTTTAAAAAGGATTGGGTGCTCAA
191 GTGACTACTAAAAG-AAAGTCCAAATAACAACACAATCAACTTTCAAAAAGGATTGAGTGCTCAA
* * *
308808 TAACATAGATCAAACTTTGCTTTTGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGATGTGACACT
255 TAACATAGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAGGGGACACT
* *
308873 T-CTCTTCCCT-TCGTGGTGCTTTGTTAAATTTTAAGGAGCAT-TGAGAGTTATTTGAACCTTTC
320 TGC-CTTCCCTATAG-GGTGCTTTGTTAAATTTTAAGG-G-ATATGAGAGCTATTTGAACCTTTC
* * *
308935 TTTGA-TGGTTACACCCAATACCTTAGATCACACTCTCCTTTCA-AGAAGGATTGGGTGTGACTA
381 TTT-ACTGGTTACACCCAATACCTTAGATCACACTCTCCTTTCAGA-AAAGATTGAGTGAGACTA
* ** * *
308998 CCAAAGGAAAGTTCCAATAACATCACA-TTATGCTTTTA-GAAAGGATTGA
444 CCAAAAGAAAGTTAAAATAACATCACACTT-TGCTTTCAGGAAA-AATTGA
*
309047 GTGCTCAATAACTTAGATCACAC-TATCCTTTCA
1 GTGCTCAATAACTTAGATCAAACAT-TCCTTTCA
309080 GGAATGATCG
Statistics
Matches: 448, Mismatches: 63, Indels: 31
0.83 0.12 0.06
Matches are distributed among these distances:
491 2 0.00
492 95 0.21
493 302 0.67
494 39 0.09
495 10 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (492 bp):
GTGCTCAATAACTTAGATCAAACATTCCTTTCACTAGGGTTTGGGAATGAAGAGGAAGAGGGGGA
AGGACACTTGCATTCCCTACGAGGTGCATTATTAAATTTTAAGGGACATTGAGAGCTATTTGAAC
TTTCATTTGTTGGTTACACCCAATACCTTAGATCACAATCTGTTTCAGGAAGGATTGGGTGTGAC
TACTAAAAGAAAGTCCAAATAACAACACAATCAACTTTCAAAAAGGATTGAGTGCTCAATAACAT
AGATCAAACTTTGCTTTCGCTAGGGTTTGAGAATGAAGAGGAAGAGGGGAGGGGACACTTGCCTT
CCCTATAGGGTGCTTTGTTAAATTTTAAGGGATATGAGAGCTATTTGAACCTTTCTTTACTGGTT
ACACCCAATACCTTAGATCACACTCTCCTTTCAGAAAAGATTGAGTGAGACTACCAAAAGAAAGT
TAAAATAACATCACACTTTGCTTTCAGGAAAAATTGA
Found at i:309145 original size:102 final size:101
Alignment explanation
Indices: 308950--309138 Score: 227
Period size: 102 Copynumber: 1.9 Consensus size: 101
308940 TGGTTACACC
* * * *
308950 CAATACCTTAGATCACACTCTCCTTTCAAGAAGGATTGGGTGTGACTACCAAAGGAAAGTTCCAA
1 CAATAACTTAGATCACACTATCCTTTCAAGAAGGATCGGGTGTGACTACAAAAGGAAAG-TCCAA
* * * *
309015 TAACATCACATTATGCTTTTAGAAAGGATTGAGTGCT
65 AAACATCACACTATACTTTCAGAAAGGATTGAGTGCT
* * *
309052 CAATAACTTAGATCACACTATCCTTTCAGGAATGATCGGGTGTGACTACAAAAGGAAAG-CTAAA
1 CAATAACTTAGATCACACTATCCTTTCAAGAAGGATCGGGTGTGACTACAAAAGGAAAGTCCAAA
* *
309116 AATGGATCACACTCTACTTTCAG
66 AA--CATCACACTATACTTTCAG
309139 GGAGGATGGG
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
100 5 0.07
102 67 0.93
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (101 bp):
CAATAACTTAGATCACACTATCCTTTCAAGAAGGATCGGGTGTGACTACAAAAGGAAAGTCCAAA
AACATCACACTATACTTTCAGAAAGGATTGAGTGCT
Found at i:310025 original size:244 final size:241
Alignment explanation
Indices: 309575--311573 Score: 1423
Period size: 244 Copynumber: 8.3 Consensus size: 241
309565 CTTTAAAGAA
** * * * * * *
309575 AGATCACACTCTACTTTCAGGGAGGCTTGGATGTGACTACCAAAGGAAAGTTTAAATTGCATCAC
1 AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCAC
* * * * * * * * *
309640 ACTTTTCTTT-TAGAAGGATTAGGTGCTCAATAAATTAGATCAAACTTTGTTTTTGCCAAGGTTT
66 ACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATC-AACTTTGCTTTCGCTAGGGTTT
* ** *
309704 GGGAATGAAGA-GAAAGAGGGGGCGGGGACATGTGCCTTCCCTAC-AGGGTGCTTTATTGAATTT
130 GGGAATGAAGAGGAAA-A-GGGGAGGGGACACATGCC-T---TACGA-GGTGCTTTGTTGAATTT
* *
309767 TAAGGGACATTGAGAGATATTTGAATTTTCCTTTGCTGGTTACATCCAATAACTT
188 TAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACA-CCAATACCTT
* * * * * *
309822 AGATCACACTCTGTTTTCAAGAAGGATTTGATGTGATTACCAAAGGAAACTACAAATAGCATCAT
1 AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCAC
* * * * ** * *
309887 GCTCTACTTTCAAGAAGGATTGAGTGATTTATAACTTAGATCAAGCTATTGCTTTTGTTAGGGTT
66 ACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATCAA-CT-TTGCTTTCGCTAGGGTT
* * *
309952 TGGGAATCAAGAGGAAAAGGGAGAGGGGACACATG-CTTACGAAGTGCTTTATTGAATTTTAAGG
129 TGGGAATGAAGAGGAAAAGGG-GAGGGGACACATGCCTTACGAGGTGCTTTGTTGAATTTTAAGG
* * * * *
310016 GACATTGAGAGCA-ATTCGAACTTTCTTTTGCTGGCTACACCCAGTACTTT
193 GACATTGAGAG-ATATTTGAACTTTCCTTTGCTGGTTACA-CCAATACCTT
* * ** * * *
310066 AGATCACAGTTTACTTTCA-GATAGGATTGGGTATGACTACCAAAGGAAAGTTCAAATAACATCA
1 AGATCACACTCTGTTTTCAGGA-AGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
* * * * * *
310130 CACTTTGATTTCATGAAGGATTGGGTGCTCAATAACTTAGAACAAACCTTACTTTCGCTAGGGTT
65 CACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATC-AACTTTGCTTTCGCTAGGGTT
* * *
310195 TGGGAATAAAGA-GAAAGAGGGG-GTAGGGACACTTGACTTCCCTAC-AGGTTGCTTTGTTGAA-
129 TGGGAATGAAGAGGAAA-AGGGGAG--GGGACAC---A-TGCCTTACGAGG-TGCTTTGTTGAAT
* * * * **
310256 TTTAAGGGACATTAAAAGCTATTTGAACTTTCTTTTGCTGGTTACACCTAATATTTT
186 TTTAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACACC-AATACCTT
* * *
310313 AGTTCACATTCTGCTTTT-AGGAAGGAATGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
1 AGATCACACTCTG-TTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
* * * *
310377 CACTATGCTTTC-AGAAAGGATTGGGTGCTC---AACTTAGATCGAACTTTACTTTCGCTACGAT
65 CACTCTGCTTTCAAG-AAGGATTGGGTGCTCAATAACTTAGATC-AACTTTGCTTTCGCTAGGGT
** * * * * * *
310438 TTATGAATGAAGAAGAAAAGGGGTAGGGGACAATTACCTTCCTTATGGGGTGCTTTGTTGAATAT
128 TTGGGAATGAAGAGGAAAAGGGG-AGGGGAC----ACATGCCTTACGAGGTGCTTTGTTGAATTT
* * * * * * *
310503 TAAGAGACATTGAGAGTTGTTTGAACTTTCCTTTACTTGTTATATCGAATACCTT
188 TAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACA-CCAATACCTT
* * ** * * ** **
310558 AAATCACACTTTACTTTCACGAATGATTGATTGTGGCTACCAAAGGAAAGTTCAAAT---A--AC
1 AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCAC
* * * * * *
310618 ACTCTGCTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATTTTTCTTTTGCTA-GATAT
66 ACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATC-AACTTTGCTTTCGCTAGGGTTT
* *
310682 GAGAATGAAGAGGAAAAGGTGGGAAGGGG---CA-G-C--A-G-GGTGCTTTGTTGAATTTTATG
130 GGGAATGAAGAGGAAAA-G-GGG-AGGGGACACATGCCTTACGAGGTGCTTTGTTGAATTTTAAG
* * * * * *
310738 AGACA-CGAGAGTTATTTGAATTTTCCTTTACTAGTTACACCCAATACCTT
192 GGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACA-CCAATACCTT
* * *
310788 AGATCACACTCT-ATTTCTAGGAAGGATTTGGTGTGAATACCAAAGGAAAGTTCAAATAGCATCA
1 AGATCACACTCTGTTTTC-AGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
* * * *
310852 CACACTACTTTCATGAAGGATTGGGTGCTCAATAACTTAGATCATATTTTGCTTTCGCTAGGGTT
65 CACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATCA-ACTTTGCTTTCGCTAGGGTT
* * * * *
310917 T-GGAATGAAGAGGAAAAGGGGAAGGGACACCTGCCTTTCCTACGGCTGTTTTGTTGAA---T--
129 TGGGAATGAAGAGGAAAAGGGGAGGGGACACATGCC-TTACGA-GG-TGCTTTGTTGAATTTTAA
* * *
310976 -----ATTGAGAGCTATTTGAACTTTTCTTGGCTGGTTACACCTAATACCTT
191 GGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACACC-AATACCTT
* * * *
311023 AGATCACACTTTGCTTTT-AGGAAAGATTGGGCGTGATTA-CAAAGGAAAGTTTAAATAGCAT--
1 AGATCACACTCTG-TTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
* * * * * * **
311084 CACTCTGTTTTTAAGGAGGACTAGGTG----ATAACTTAGATTAAAC-TT--TTTCTTTAGGGTT
65 CACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGA-TCAACTTTGCTTTCGCTAGGGTT
* * *
311142 TGGGAATGAAGAGGAAAAGGGGTGGGGACA-ACTGCCTTCCCTACGAGGTGTTTTGTTGACTTTT
129 TGGGAATGAAGAGGAAAAGGGGAGGGGACACA-TGCC-T---TACGAGGTGCTTTGTTGAATTTT
* * * * *
311206 AAGGGACAATGAGAGCTATTTAAACTTTCTTTTGCTGGTTACACCAAACACCTT
189 AAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACACC-AATACCTT
* ** *
311260 AGATCACACTCTATTTTCAGGAAGGATTGGGTGTGACTT-CCAAATAAAAGTTCAAAATAGCATT
1 AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGA-TTACCAAAGGAAAGTTC-AAATAGCATC
* * * * *
311324 ACACTATGCTTTCATGAAAGATTAGGTGCTCAATAACTT-GATCAAACTTTGCTTTCGCTATGGT
64 ACACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATC-AACTTTGCTTTCGCTAGGGT
* * * * * * *
311388 TTGGAAATGAAGAGGAAGAGGGGAGAGGGGATACCTGCCTTCCCTACGGGGAGCTTTATTGAATT
128 TTGGGAATGAAGAGGAA-AAGGG-GAGGGGACACATGCC-T---TACGAGGTGCTTTGTTGAATT
* * * ** * *
311453 ATAAGGAACACTGAGA-ACTATTTGAACTTTTTTTTTTCTGGTTACACCCACTACCTT
187 TTAAGGGACATTGAGAGA-TATTTGAAC-TTTCCTTTGCTGGTTACA-CCAATACCTT
* * * * *
311510 AGATCACACTATGCTTTGAGGAAGGATTGGGTGTGACTACTAAAGGAAAGTTCAAATAGCATCA
1 AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCA
311574 GGAAGGATTG
Statistics
Matches: 1394, Mismatches: 257, Indels: 200
0.75 0.14 0.11
Matches are distributed among these distances:
225 12 0.01
226 32 0.02
227 13 0.01
228 13 0.01
229 9 0.01
230 81 0.06
231 24 0.02
232 24 0.02
233 5 0.00
234 26 0.02
235 134 0.10
236 8 0.01
237 72 0.05
238 12 0.01
239 9 0.01
240 27 0.02
241 23 0.02
242 24 0.02
243 65 0.05
244 238 0.17
245 101 0.07
246 6 0.00
247 210 0.15
248 56 0.04
249 99 0.07
250 69 0.05
251 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (241 bp):
AGATCACACTCTGTTTTCAGGAAGGATTGGGTGTGATTACCAAAGGAAAGTTCAAATAGCATCAC
ACTCTGCTTTCAAGAAGGATTGGGTGCTCAATAACTTAGATCAACTTTGCTTTCGCTAGGGTTTG
GGAATGAAGAGGAAAAGGGGAGGGGACACATGCCTTACGAGGTGCTTTGTTGAATTTTAAGGGAC
ATTGAGAGATATTTGAACTTTCCTTTGCTGGTTACACCAATACCTT
Found at i:310796 original size:230 final size:231
Alignment explanation
Indices: 310485--310942 Score: 586
Period size: 230 Copynumber: 2.0 Consensus size: 231
310475 CTTCCTTATG
* * * * * *
310485 GGGTGCTTTGTTGAATATTAAGAGACATTGAGAGTTGTTTGAACTTTCCTTTACTTGTTATATCG
1 GGGTGCTTTGTTGAATATTAAGAGACATCGAGAGTTATTTGAACTTTCCTTTACTAGTTACACCC
* * * **
310550 AATACCTTAAATCACACTTTACTTTC-ACGAATGA-TTGATTGTGGCTACCAAAGGAAAGTTCAA
66 AATACCTTAAATCACACTCTA-TTTCTACGAAGGATTTG-GTGTGAATACCAAAGGAAAGTTCAA
* * * *
310613 AT-A-ACACTCTGCTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATTTTTCTTTTGCT
129 ATAACACACACTACTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATTTTGCTTTCGCT
310676 A-GATATGAGAATGAAGAGGAAAAGGTGGGAAGGGGCAGCA
194 AGGATATG-GAATGAAGAGGAAAA-G-GGGAAGGGGCAGCA
* * *
310716 GGGTGCTTTGTTGAATTTTATGAGACA-CGAGAGTTATTTGAATTTTCCTTTACTAGTTACACCC
1 GGGTGCTTTGTTGAATATTAAGAGACATCGAGAGTTATTTGAACTTTCCTTTACTAGTTACACCC
* *
310780 AATACCTTAGATCACACTCTATTTCTAGGAAGGATTTGGTGTGAATACCAAAGGAAAGTTCAAAT
66 AATACCTTAAATCACACTCTATTTCTACGAAGGATTTGGTGTGAATACCAAAGGAAAGTTCAAAT
* *
310845 AGCATCACACACTACTTTCATGAAGGATTGGGTGCTCAATAACTTAGATCATATTTTGCTTTCGC
131 A--A-CACACACTACTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATTTTGCTTTCGC
* *
310910 TAGGGTTTGGAATGAAGAGGAAAAGGGGAAGGG
193 TAGGATATGGAATGAAGAGGAAAAGGGGAAGGG
310943 ACACCTGCCT
Statistics
Matches: 195, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
229 4 0.02
230 79 0.41
231 28 0.14
233 9 0.05
234 1 0.01
235 70 0.36
236 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (231 bp):
GGGTGCTTTGTTGAATATTAAGAGACATCGAGAGTTATTTGAACTTTCCTTTACTAGTTACACCC
AATACCTTAAATCACACTCTATTTCTACGAAGGATTTGGTGTGAATACCAAAGGAAAGTTCAAAT
AACACACACTACTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATTTTGCTTTCGCTAG
GATATGGAATGAAGAGGAAAAGGGGAAGGGGCAGCA
Found at i:311499 original size:722 final size:720
Alignment explanation
Indices: 309607--311573 Score: 1847
Period size: 722 Copynumber: 2.7 Consensus size: 720
309597 AGGCTTGGAT
* * * * * * * *
309607 GTGACTACCAAAGGAAAGTTTAAATTGCATCACACTTTTCTTTTAG-AAGGATTAGGTGCTCAAT
1 GTGATTACCAAAGGAAAGTTCAAATAGCATCACACTATGCTTTAAGAAAGGACTAGGTGATC---
* * * * * * **
309671 AAATTAGATCAAACTTTGTTTTTGCCAAGGTTTGGGAATGAAGAGAAAGAGGGGGCGGGGACATG
63 AACTTAGATCAAACTTT-ATTTCGCTACGGTTTGGGAATGAAGAGAAA-A-GGGGTGGGGACAAC
* *
309736 TGCCTTCCCTAC-AGGGTGCTTTATTGAATTTTAAGGGACATTGAGAGATATTTGAATTTTCCTT
125 TGCCTTCCCTACGA-GGTGCTTTGTTGAATTTTAAGGGACATTGAGAGATATTTGAACTTTCCTT
* *
309800 TGCTGGTTACATCCAATAA-CTTAGATCACACTCTGTTTTCAAGAAGGATTTGATGTGA-TTACC
189 TGCTGGTTACA-CCAA-AACCTTAGATCACACTCTATTTTCAAGAAGGATTGGATGTGACTT-CC
* * * * **
309863 AAAGGAAACTACAAATAGCAT-CATGCTCTACTTTCAAGAAGGATTGAGTGATTTATAACTTAGA
251 AAAGGAAAGTTCAAATAGCATACA--CTCTGCTTTCAAGAAGGATTG-GTGCTCAATAACTTAGA
* * * * * *
309927 TCAAGCTATTGCTTTTGTTAGGGTTTGGGAATCAAGAGGAAAAGGGAGAGGGGACACATGCT-TA
313 TCAAACT-TTGCTTTTGCTA-GGTTTGGAAATGAAGAGGAAAGGGGAGAGGGGA-ACCTGCTCTA
** * * * * * *
309991 CGAAGTGCTTTATTGAATTTTAAGGGACATTGAGAGCAATTCGAAC-TTTCTTTTGCTGGCTACA
375 CGGGGTGCTTTATTGAA-TTTAAGGAACACTGAGAGCTATTTGAACTTTTCTTTTACTGGTTACA
* * * * *
310055 CCCAGTACTTTAGATCACAGTTTACTTTCA-GATAGGATTGGGTATGACTACCAAAGGAAAGTTC
439 CCCAATACCTTAGATCACACTATA-TTTCAGGA-AGGATTGGGTGTGACTACCAAAGGAAAGTTC
* **
310119 AAATAACATCACACTTTGATTTCATGAAGGATTGGGTGCTCAATAACTTAGAACAAACCTTACTT
502 AAATAGCATCACACACTGATTTCATGAAGGATTGGGTGCTCAATAACTTAGAACAAACCTTACTT
* * *
310184 TCGCTAGGGTTTGGGAATAAAGAGAAAGAGGGGGTAGGGACACTTGACTTCCCTACAGGTTGCTT
567 TCGCTAGGGTTTGGGAATAAAGAGAAAGAGGGGGAAGGGACACCTGACTTCCCTACAGGCTGCTT
* **
310249 TGTTGAATTTAAGGGACATTAAAAGCTATTTGAACTTTCTTTTGCTGGTTACACCTAATATTTTA
632 TGTTGAA-TT-----A-ATTAAAAGCTATTTGAACTTTCTTTGGCTGGTTACACCTAATACCTTA
* * *
310314 GTTCACATTCTGCTTTTAGGAAGGAATGGGT
690 GATCACATTCTGCTTTTAGGAAAGAATGGGC
* * * *
310345 GTGATTACCAAAGGAAAGTTCAAATAGCATCACACTATGCTTTCAGAAAGGATTGGGTGCTCAAC
1 GTGATTACCAAAGGAAAGTTCAAATAGCATCACACTATGCTTTAAGAAAGGACTAGGTGATCAAC
* * ** * *
310410 TTAGATCGAACTTTACTTTCGCTACGATTTATGAATGAAGAAGAAAAGGGGTAGGGGACAATTAC
66 TTAGATCAAACTTTA-TTTCGCTACGGTTTGGGAATGAAG-AGAAAAGGGGT-GGGGACAACTGC
* * * * * * * *
310475 CTTCCTTATGGGGTGCTTTGTTGAATATTAAGAGACATTGAGAGTTGTTTGAACTTTCCTTTACT
128 CTTCCCTACGAGGTGCTTTGTTGAATTTTAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCT
* * * * * * * * * * *
310540 TGTTATATCGAATACCTTAAATCACACTTTACTTTCACGAATGATT-GATTGTGGCTACCAAAGG
193 GGTTACA-CCAAAACCTTAGATCACACTCTATTTTCAAGAAGGATTGGA-TGTGACTTCCAAAGG
* *
310604 AAAGTTCAAAT---A-ACACTCTGCTTTCAGGAAGGATTGGGTGCTCAATAACTTAGATCAAATT
256 AAAGTTCAAATAGCATACACTCTGCTTTCAAGAAGGATT-GGTGCTCAATAACTTAGATCAAACT
* * * *
310665 TTTCTTTTGCTAGATAT-GAGAATGAAGAGGAAAAGGTGG-GAAGGGG---CAG--C-A--GGGT
320 TTGCTTTTGCTAGGTTTGGA-AATGAAGAGG-AAAGG-GGAG-AGGGGAACCTGCTCTACGGGGT
* * * * * *
310720 GCTTTGTTGAATTTTATGAGACAC-GAGAGTTATTTGAA-TTTTCCTTTACTAGTTACACCCAAT
381 GCTTTATTGAATTTAAGGA-ACACTGAGAGCTATTTGAACTTTTCTTTTACTGGTTACACCCAAT
* * *
310783 ACCTTAGATCACACTCTATTTCTAGGAAGGATTTGGTGTGAATACCAAAGGAAAGTTCAAATAGC
445 ACCTTAGATCACACTATATTTC-AGGAAGGATTGGGTGTGACTACCAAAGGAAAGTTCAAATAGC
* * ** *
310848 ATCACACACT-ACTTTCATGAAGGATTGGGTGCTCAATAACTTAGATCATATTTTGCTTTCGCTA
509 ATCACACACTGA-TTTCATGAAGGATTGGGTGCTCAATAACTTAGAACAAACCTTACTTTCGCTA
* * * *
310912 GGGTTT-GGAATGAAGAGGAAA-A-GGGGAAGGGACACCTGCCTTTCCTAC-GGCTGTTTTGTTG
573 GGGTTTGGGAATAAAGA-GAAAGAGGGGGAAGGGACACCTGACTTCCCTACAGGCTGCTTTGTTG
* *
310973 AA-T-ATTGAGAGCTATTTGAACTTT-TCTTGGCTGGTTACACCTAATACCTTAGATCACACTT-
637 AATTAATTAAAAGCTATTTGAACTTTCT-TTGGCTGGTTACACCTAATACCTTAGATCACA-TTC
*
311034 TGCTTTTAGGAAAGATTGGGC
700 TGCTTTTAGGAAAGAATGGGC
* * * * *
311055 GTGATTA-CAAAGGAAAGTTTAAATAGCATCACTCTGT-TTTTAAG-GAGGACTAGGTGAT-AAC
1 GTGATTACCAAAGGAAAGTTCAAATAGCATCACACTATGCTTTAAGAAAGGACTAGGTGATCAAC
* ** *
311116 TTAGATTAAAC-TT-TTTCTTTAGGGTTTGGGAATGAAGAGGAAAAGGGGTGGGGACAACTGCCT
66 TTAGATCAAACTTTATTTCGCTACGGTTTGGGAATGAAGA-GAAAAGGGGTGGGGACAACTGCCT
* * * * * *
311179 TCCCTACGAGGTGTTTTGTTGACTTTTAAGGGACAATGAGAGCTATTTAAACTTTCTTTTGCTGG
130 TCCCTACGAGGTGCTTTGTTGAATTTTAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGG
* * **
311244 TTACACCAAACACCTTAGATCACACTCTATTTTCAGGAAGGATTGGGTGTGACTTCCAAATAAAA
195 TTACACCAAA-ACCTTAGATCACACTCTATTTTCAAGAAGGATTGGATGTGACTTCCAAAGGAAA
* * *
311309 GTTCAAAATAGCATTACACTATGCTTTCATGAAAGATTAGGTGCTCAATAACTT-GATCAAACTT
259 GTTC-AAATAGCA-TACACTCTGCTTTCAAGAAGGATT-GGTGCTCAATAACTTAGATCAAACTT
*
311373 TGCTTTCGCTATGGTTTGGAAATGAAGAGGAAGAGGGGAGAGGGGATACCTGCCTTCCCTACGGG
321 TGCTTTTGCTA-GGTTTGGAAATGAAGAGGAA-AGGGGAGAGGGGA-ACCTG-C-T--CTACGGG
* * * *
311438 GAGCTTTATTGAATTATAAGGAACACTGAGAACTATTTGAACTTTTTTTTTTCTGGTTACACCCA
379 GTGCTTTATTGAATT-TAAGGAACACTGAGAGCTATTTGAACTTTTCTTTTACTGGTTACACCCA
* * * *
311503 CTACCTTAGATCACACTATGCTTTGAGGAAGGATTGGGTGTGACTACTAAAGGAAAGTTCAAATA
443 ATACCTTAGATCACACTAT-ATTTCAGGAAGGATTGGGTGTGACTACCAAAGGAAAGTTCAAATA
311568 GCATCA
507 GCATCA
311574 GGAAGGATTG
Statistics
Matches: 998, Mismatches: 178, Indels: 122
0.77 0.14 0.09
Matches are distributed among these distances:
701 3 0.00
702 114 0.11
703 33 0.03
705 2 0.00
706 13 0.01
707 37 0.04
708 57 0.06
709 30 0.03
710 72 0.07
711 4 0.00
717 2 0.00
718 1 0.00
719 13 0.01
720 41 0.04
721 31 0.03
722 229 0.23
723 20 0.02
725 1 0.00
727 1 0.00
728 1 0.00
729 12 0.01
730 15 0.02
731 44 0.04
732 1 0.00
733 3 0.00
735 7 0.01
736 151 0.15
737 6 0.01
738 40 0.04
739 14 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (720 bp):
GTGATTACCAAAGGAAAGTTCAAATAGCATCACACTATGCTTTAAGAAAGGACTAGGTGATCAAC
TTAGATCAAACTTTATTTCGCTACGGTTTGGGAATGAAGAGAAAAGGGGTGGGGACAACTGCCTT
CCCTACGAGGTGCTTTGTTGAATTTTAAGGGACATTGAGAGATATTTGAACTTTCCTTTGCTGGT
TACACCAAAACCTTAGATCACACTCTATTTTCAAGAAGGATTGGATGTGACTTCCAAAGGAAAGT
TCAAATAGCATACACTCTGCTTTCAAGAAGGATTGGTGCTCAATAACTTAGATCAAACTTTGCTT
TTGCTAGGTTTGGAAATGAAGAGGAAAGGGGAGAGGGGAACCTGCTCTACGGGGTGCTTTATTGA
ATTTAAGGAACACTGAGAGCTATTTGAACTTTTCTTTTACTGGTTACACCCAATACCTTAGATCA
CACTATATTTCAGGAAGGATTGGGTGTGACTACCAAAGGAAAGTTCAAATAGCATCACACACTGA
TTTCATGAAGGATTGGGTGCTCAATAACTTAGAACAAACCTTACTTTCGCTAGGGTTTGGGAATA
AAGAGAAAGAGGGGGAAGGGACACCTGACTTCCCTACAGGCTGCTTTGTTGAATTAATTAAAAGC
TATTTGAACTTTCTTTGGCTGGTTACACCTAATACCTTAGATCACATTCTGCTTTTAGGAAAGAA
TGGGC
Found at i:312923 original size:26 final size:26
Alignment explanation
Indices: 312893--312945 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
312883 CACTAGATAT
312893 TTGGTTATTGTGACTTCTAAAAATTA
1 TTGGTTATTGTGACTTCTAAAAATTA
312919 TTGGTTATTGTGACTTCTAAAAATTA
1 TTGGTTATTGTGACTTCTAAAAATTA
312945 T
1 T
312946 GCTTATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (26 bp):
TTGGTTATTGTGACTTCTAAAAATTA
Found at i:332495 original size:133 final size:133
Alignment explanation
Indices: 332257--332522 Score: 460
Period size: 133 Copynumber: 2.0 Consensus size: 133
332247 TTTTGAAGCT
* *
332257 CTGAAGAAAATGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAATGTTGATCAACAAGTTT
1 CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAATGTTAATCAACAAGTTT
*
332322 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGGTAGTTTAAAAGGAAGGAAGAAGACAATGGT
66 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
332387 GAA
131 GAA
* * * *
332390 CTGAAGAAGACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGTTAATCAATAGGTTT
1 CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAATGTTAATCAACAAGTTT
*
332455 CTACCTTTAACTTGAGCCCAATAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
66 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
332520 GAA
131 GAA
332523 GGAAAAGAGG
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 125 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.24
Consensus pattern (133 bp):
CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAATGTTAATCAACAAGTTT
CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
GAA
Found at i:333882 original size:19 final size:20
Alignment explanation
Indices: 333837--333885 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
333827 ACCCCCTTTC
**
333837 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTAAATG
333857 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
333876 AAGATACATG
1 AAAATACATG
333886 CTCTTGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:337037 original size:11 final size:11
Alignment explanation
Indices: 337021--337063 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
337011 TCCAAATTGC
337021 TTCTTTTCGTT
1 TTCTTTTCGTT
337032 TTCTTTTCGTT
1 TTCTTTTCGTT
*
337043 TTC--TTCTTT
1 TTCTTTTCGTT
337052 TTCTTTTC-TT
1 TTCTTTTCGTT
337062 TT
1 TT
337064 GCACTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (11 bp):
TTCTTTTCGTT
Found at i:337058 original size:5 final size:5
Alignment explanation
Indices: 337021--337063 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
337011 TCCAAATTGC
*
337021 TTCTT TTCGTT TTCTT TTCGTT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TTC-TT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
337064 GCACTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:337098 original size:6 final size:6
Alignment explanation
Indices: 337087--337124 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
337077 GTTGTAGGAG
*
337087 TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
337125 GTTGCTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:337115 original size:19 final size:18
Alignment explanation
Indices: 337087--337124 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
337077 GTTGTAGGAG
*
337087 TCTTTTTCTTTTTGTTTT
1 TCTTTTTCTTTTTCTTTT
337105 TCTTCTTTCTTTTTCTTTT
1 TCTT-TTTCTTTTTCTTTT
337124 T
1 T
337125 GTTGCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (18 bp):
TCTTTTTCTTTTTCTTTT
Found at i:337352 original size:16 final size:16
Alignment explanation
Indices: 337331--337364 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
337321 ATGAAAGAAG
337331 AAAGGAAA-TGATAAGA
1 AAAGGAAATTGAT-AGA
337347 AAAGGAAATTGATAGA
1 AAAGGAAATTGATAGA
337363 AA
1 AA
337365 TGTTATCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (16 bp):
AAAGGAAATTGATAGA
Found at i:337963 original size:19 final size:20
Alignment explanation
Indices: 337916--337966 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
337906 GAAACCCCTT
**
337916 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
337936 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
337955 TGAAGATACATG
1 TGAAAATACATG
337967 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:341410 original size:18 final size:18
Alignment explanation
Indices: 341387--341421 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
341377 ACTGAATATT
* *
341387 TGTCCCGAATGACCACTA
1 TGTCCCAAAGGACCACTA
341405 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
341422 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:343348 original size:27 final size:23
Alignment explanation
Indices: 343287--343334 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
343277 ACACAAGAGG
343287 ATCAATCCTAAATCTTCTTGAAC
1 ATCAATCCTAAATCTTCTTGAAC
343310 ATCAATCCTAAATCTTCTTGAAC
1 ATCAATCCTAAATCTTCTTGAAC
343333 AT
1 AT
343335 ACTTCACTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (23 bp):
ATCAATCCTAAATCTTCTTGAAC
Found at i:349951 original size:47 final size:47
Alignment explanation
Indices: 349877--349968 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
349867 ATCAAAATCA
*
349877 ATATGTCATACCAATCCATGAAGAAAATAGCAGAACCCACATGTTCG
1 ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCG
* * *
349924 ATATGTCATACGAGTCCATGAATAAAATAACAGAACCCACATGTT
1 ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTT
349969 TGACAAGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (47 bp):
ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCG
Found at i:350949 original size:6 final size:6
Alignment explanation
Indices: 350940--350967 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
350930 CATCGAAGCA
350940 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
350968 CTGGAGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:351910 original size:29 final size:29
Alignment explanation
Indices: 351868--351933 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
351858 ATATCCTCTA
351868 GATAATTATAATTGTTAAATTGATTATAT
1 GATAATTATAATTGTTAAATTGATTATAT
351897 GATAATTATAATTGTTAAATTGATTATAT
1 GATAATTATAATTGTTAAATTGATTATAT
*
351926 GACAATTA
1 GATAATTA
351934 AGTTTATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
GATAATTATAATTGTTAAATTGATTATAT
Found at i:353699 original size:13 final size:13
Alignment explanation
Indices: 353681--353713 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
353671 TATGTGACAA
353681 ATTTTTATAATAT
1 ATTTTTATAATAT
353694 ATTTTTATAATAT
1 ATTTTTATAATAT
353707 ATTTTTA
1 ATTTTTA
353714 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATAATAT
Found at i:358109 original size:12 final size:12
Alignment explanation
Indices: 358092--358117 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
358082 GAATTTCACA
358092 CAAAGTTTAGCT
1 CAAAGTTTAGCT
358104 CAAAGTTTAGCT
1 CAAAGTTTAGCT
358116 CA
1 CA
358118 GTAACTGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
CAAAGTTTAGCT
Found at i:360604 original size:2 final size:2
Alignment explanation
Indices: 360597--360632 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
360587 AATATGTTCA
360597 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
360633 GATGAATTAA
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
Done.