Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005479.1 Hibiscus syriacus cultivar Beakdansim tig00012565_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: 211959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:197 original size:14 final size:13
Alignment explanation
Indices: 178--222 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
168 CTGTCTGTTT
178 ATATATACATATGC
1 ATATATACATAT-C
*
192 ATATATATATAT-
1 ATATATACATATC
204 ATATATACATA-C
1 ATATATACATATC
216 ATATATA
1 ATATATA
223 TCCTCTCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATATACATATC
Found at i:2841 original size:3 final size:3
Alignment explanation
Indices: 2828--2873 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
2818 TCTCTAAGTT
* *
2828 TAA TCA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
2873 T
1 T
2874 TAGTTATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2856 original size:18 final size:18
Alignment explanation
Indices: 2828--2873 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
2818 TCTCTAAGTT
2828 TAATCATAATAATAATAAA
1 TAAT-ATAATAATAATAAA
2847 -AATAATAATAATAATAAA
1 TAAT-ATAATAATAATAAA
2865 TAATATAAT
1 TAATATAAT
2874 TAGTTATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATATAATAATAATAAA
Found at i:5410 original size:42 final size:42
Alignment explanation
Indices: 5363--5446 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
5353 AGTCGCCTCA
* *
5363 GTCATTCAAGGATTATTCTTTTTGTTCTTCAAGTAATAAGTG
1 GTCATTCAAGGATTATTCCTTTTGTTCTTCAAGTAAAAAGTG
*
5405 GTCATTCAAGGATTATTCCTTTTGTTCTTCAATTAAAAAGTG
1 GTCATTCAAGGATTATTCCTTTTGTTCTTCAAGTAAAAAGTG
5447 ATAAATTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (42 bp):
GTCATTCAAGGATTATTCCTTTTGTTCTTCAAGTAAAAAGTG
Found at i:11279 original size:22 final size:21
Alignment explanation
Indices: 11238--11279 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
11228 ATACTAAAAC
*
11238 AGATACAAATTGATAGTTTAT
1 AGATACAAATTGATAATTTAT
11259 AGATACTAAA-TGCATAATTTA
1 AGATAC-AAATTG-ATAATTTA
11280 CCCTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (21 bp):
AGATACAAATTGATAATTTAT
Found at i:15708 original size:23 final size:23
Alignment explanation
Indices: 15682--15726 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15672 AAAATTTTTA
*
15682 TATAAAATTTAAAAAAATAAAAT
1 TATAAAATTTAAAAAAAGAAAAT
* *
15705 TATATATTTTAAAAAAAGAAAA
1 TATAAAATTTAAAAAAAGAAAA
15727 CACATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TATAAAATTTAAAAAAAGAAAAT
Found at i:17997 original size:28 final size:28
Alignment explanation
Indices: 17953--18015 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
17943 AAAAGAGAAT
* *
17953 ATTGTAAATATTAAATT-GTGTAATAAAA
1 ATTGTAAACATTAAATTAG-ATAATAAAA
*
17981 ATTGTAAACATTTAATTAGATAATAAAA
1 ATTGTAAACATTAAATTAGATAATAAAA
18009 ATTGTAA
1 ATTGTAA
18016 GTCAATTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (28 bp):
ATTGTAAACATTAAATTAGATAATAAAA
Found at i:29430 original size:24 final size:24
Alignment explanation
Indices: 29379--29431 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
29369 TGATCGGAAT
*
29379 AAATAAACAAATAAATATTTAAAG
1 AAATAAACAAATAAATAATTAAAG
29403 AAATAAACAAA-AAATGGAATTAAA-
1 AAATAAACAAATAAAT--AATTAAAG
29427 AAATA
1 AAATA
29432 CCATTTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 16 0.62
25 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AAATAAACAAATAAATAATTAAAG
Found at i:37980 original size:16 final size:16
Alignment explanation
Indices: 37934--37986 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
37924 CAACCAAAAC
37934 CGAAATTAACCCGAA-
1 CGAAATTAACCCGAAT
* ** *
37949 CTAAAAGCAACTCGAAT
1 C-GAAATTAACCCGAAT
37966 CGAAATTAACCCGAAT
1 CGAAATTAACCCGAAT
37982 CGAAA
1 CGAAA
37987 GTAATCCAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.47, C:0.25, G:0.13, T:0.15
Consensus pattern (16 bp):
CGAAATTAACCCGAAT
Found at i:38777 original size:31 final size:32
Alignment explanation
Indices: 38732--38840 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 32
38722 GATCTAAAGG
* *
38732 TTGACCTAAACCGAAAATCAATCGATCTGATA
1 TTGACCTGACCCGAAAATCAATCGATCTGATA
38764 TTGA-CTGACCCG-AAATCTAA-CTGATCTGATA
1 TTGACCTGACCCGAAAATC-AATC-GATCTGATA
* * * * *
38795 TTAACCCGACCCAAAAATCAGTCGAT-TCGGTA
1 TTGACCTGACCCGAAAATCAATCGATCT-GATA
38827 TTGACCTGACCCGA
1 TTGACCTGACCCGA
38841 TATTGACATG
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
30 6 0.10
31 21 0.34
32 28 0.46
33 6 0.10
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (32 bp):
TTGACCTGACCCGAAAATCAATCGATCTGATA
Found at i:39556 original size:19 final size:21
Alignment explanation
Indices: 39519--39557 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
39509 TGAAAGAAAT
*
39519 AAAAAAAGAAGACATAATAAG
1 AAAAAAAGAAGACAAAATAAG
39540 AAAAAAA-AAG-CAAAATAA
1 AAAAAAAGAAGACAAAATAA
39558 TAATCATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (21 bp):
AAAAAAAGAAGACAAAATAAG
Found at i:40449 original size:10 final size:10
Alignment explanation
Indices: 40426--40512 Score: 84
Period size: 10 Copynumber: 8.4 Consensus size: 10
40416 CGAACGTATG
*
40426 TAAACAAACA
1 TAAACGAACA
*
40436 TAAACGAACG
1 TAAACGAACA
*
40446 TAAATGAACCCA
1 TAAACGAA--CA
*
40458 GTAAATGAACA
1 -TAAACGAACA
* *
40469 TAAATGAACG
1 TAAACGAACA
40479 TAAACGAACA
1 TAAACGAACA
*
40489 TAAATGAACA
1 TAAACGAACA
40499 TAAACGAACA
1 TAAACGAACA
40509 TAAA
1 TAAA
40513 TGGAAATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
10 54 0.83
11 2 0.03
12 1 0.02
13 8 0.12
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.15
Consensus pattern (10 bp):
TAAACGAACA
Found at i:40487 original size:20 final size:20
Alignment explanation
Indices: 40436--40514 Score: 104
Period size: 20 Copynumber: 3.8 Consensus size: 20
40426 TAAACAAACA
*
40436 TAAACGAACGTAAATGAACCCAG
1 TAAACGAACATAAATGAA--C-G
*
40459 TAAATGAACATAAATGAACG
1 TAAACGAACATAAATGAACG
*
40479 TAAACGAACATAAATGAACA
1 TAAACGAACATAAATGAACG
40499 TAAACGAACATAAATG
1 TAAACGAACATAAATG
40515 GAAATATAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.67
21 1 0.02
23 16 0.31
ACGTcount: A:0.54, C:0.15, G:0.14, T:0.16
Consensus pattern (20 bp):
TAAACGAACATAAATGAACG
Found at i:48052 original size:2 final size:2
Alignment explanation
Indices: 48047--48088 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
48037 AAAAGTGATA
48047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48089 TTAAAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51644 original size:15 final size:15
Alignment explanation
Indices: 51621--51654 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
51611 ATTTTCGTAG
* *
51621 ACCAGACCAGACCAA
1 ACCAAACCACACCAA
51636 ACCAAACCACACCAA
1 ACCAAACCACACCAA
51651 ACCA
1 ACCA
51655 GTCCTCCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.44, G:0.06, T:0.00
Consensus pattern (15 bp):
ACCAAACCACACCAA
Found at i:54687 original size:13 final size:13
Alignment explanation
Indices: 54671--54695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54661 TAAGTAATTT
54671 GGTTAATTCGATC
1 GGTTAATTCGATC
54684 GGTTAATTCGAT
1 GGTTAATTCGAT
54696 TAAAACTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
GGTTAATTCGATC
Found at i:54743 original size:8 final size:8
Alignment explanation
Indices: 54730--54781 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
54720 AAAACTAAGT
54730 AATATATA
1 AATATATA
54738 AATATATA
1 AATATATA
*
54746 TATATATA
1 AATATATA
*
54754 TATAATATA
1 AAT-ATATA
*
54763 TATATACTA
1 AATATA-TA
*
54772 AATATTTA
1 AATATATA
54780 AA
1 AA
54782 ATTTTGGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATATA
Found at i:54744 original size:2 final size:2
Alignment explanation
Indices: 54731--54768 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
54721 AAACTAAGTA
*
54731 AT AT AT AA AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54769 CTAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:54776 original size:13 final size:13
Alignment explanation
Indices: 54729--54768 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
54719 TAAAACTAAG
*
54729 TAATATATAAATA
1 TAATATATATATA
54742 TATATATATATATA
1 TA-ATATATATATA
54756 TAATATATATATA
1 TAATATATATATA
54769 CTAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATATATATATA
Found at i:62085 original size:144 final size:144
Alignment explanation
Indices: 61825--62112 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
61815 TAATGGTGAC
61825 ACTATGAGGCCGAATCACCCCGACATCGGTCTGTTTGCAAGGTGAGCTGCCACTGACAGCCCATG
1 ACTATGAGGCCGAATCACCCCGACATCGGTCTGTTTGCAAGGTGAGCTGCCACTGACAGCCCATG
61890 TAATATGACTGAAAAATGCAAGTACGAGAAGCACATCCACCAGCTGCGAAAAAATGCAAACAGAA
66 TAATATGACTGAAAAATGCAAGTACGAGAAGCACATCCACCAGCTGCGAAAAAATGCAAACAGAA
61955 CTAACCATGAAGGT
131 CTAACCATGAAGGT
61969 ACTATGAGGCCGAATCACCCCGACATCGGTCTGTTTGCAAGGTGAGCTGCCACTGACAGCCCATG
1 ACTATGAGGCCGAATCACCCCGACATCGGTCTGTTTGCAAGGTGAGCTGCCACTGACAGCCCATG
62034 TAATATGACTGAAAAATGCAAGTACGAGAAGCACATCCACCAGCTGCGAAAAAATGCAAACAGAA
66 TAATATGACTGAAAAATGCAAGTACGAGAAGCACATCCACCAGCTGCGAAAAAATGCAAACAGAA
62099 CTAACCATGAAGGT
131 CTAACCATGAAGGT
62113 TGTAGCTTTC
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.17
Consensus pattern (144 bp):
ACTATGAGGCCGAATCACCCCGACATCGGTCTGTTTGCAAGGTGAGCTGCCACTGACAGCCCATG
TAATATGACTGAAAAATGCAAGTACGAGAAGCACATCCACCAGCTGCGAAAAAATGCAAACAGAA
CTAACCATGAAGGT
Found at i:70171 original size:2 final size:2
Alignment explanation
Indices: 70166--70198 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70156 TTTTTTTTCT
70166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70199 TAATTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70355 original size:5 final size:5
Alignment explanation
Indices: 70345--70370 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
70335 TTAAAGTATC
70345 TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT T
70371 TTGTTGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:80832 original size:23 final size:23
Alignment explanation
Indices: 80806--80849 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
80796 TTAACATTAA
*
80806 ATTAAAAAAAATAAAAGTTAAAT
1 ATTAAAAAAAATAAAAATTAAAT
* *
80829 ATTAAAATAGATAAAAATTAA
1 ATTAAAAAAAATAAAAATTAA
80850 TAATTTAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (23 bp):
ATTAAAAAAAATAAAAATTAAAT
Found at i:86510 original size:20 final size:20
Alignment explanation
Indices: 86485--86561 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
86475 TTGATTCATG
86485 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGA
86505 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGA
*
86525 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGTGA
86545 GAATGTAAGATTACCAG
1 GAATGTAAGATTACCAG
86562 GAAATAGGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGA
Found at i:87699 original size:27 final size:28
Alignment explanation
Indices: 87659--87716 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
87649 GGGTCATATT
87659 TTTTTTTAAAAAGTTACGTTCAGGTCGGG
1 TTTTTTT-AAAAGTTACGTTCAGGTCGGG
* *
87688 TTTTTTT-AAAGTTATGTTCGGGTCGGG
1 TTTTTTTAAAAGTTACGTTCAGGTCGGG
87715 TT
1 TT
87717 CAGGTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 20 0.74
29 7 0.26
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.47
Consensus pattern (28 bp):
TTTTTTTAAAAGTTACGTTCAGGTCGGG
Found at i:99799 original size:18 final size:15
Alignment explanation
Indices: 99775--99821 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
99765 GATAATTCAC
99775 TTGTTTATATTCAGT
1 TTGTTTATATTCAGT
*
99790 TCAATGTTTATGTTC-GT
1 T---TGTTTATATTCAGT
99807 TTGTTTATATTCAGT
1 TTGTTTATATTCAGT
99822 CAAATCTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.38
15 3 0.12
17 3 0.12
18 10 0.38
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.57
Consensus pattern (15 bp):
TTGTTTATATTCAGT
Found at i:123810 original size:20 final size:20
Alignment explanation
Indices: 123716--124084 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
123706 GATTTTCCAT
* ** *
123716 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
123736 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
123756 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123776 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
123796 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
123816 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123836 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
123856 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
123876 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
123896 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123916 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
123936 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123956 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
123976 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123996 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
124016 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
124036 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
124056 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
124076 AATCACAAC
1 AATCGCAAC
124085 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:124796 original size:24 final size:24
Alignment explanation
Indices: 124757--124803 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
124747 AAATTTGGTC
124757 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
124781 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
124804 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:124995 original size:12 final size:12
Alignment explanation
Indices: 124978--125002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
124968 ATATAATCCT
124978 GAAGAAGAAAAA
1 GAAGAAGAAAAA
124990 GAAGAAGAAAAA
1 GAAGAAGAAAAA
125002 G
1 G
125003 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:127323 original size:19 final size:19
Alignment explanation
Indices: 127301--127625 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
127291 CGGAAAATAC
*
127301 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
127320 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
127334 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
127354 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
127368 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127387 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
127405 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
127419 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127438 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
127457 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
127471 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
127490 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
127509 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
127528 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127547 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127566 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
127580 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127599 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
127618 AATCGCAA
1 AATCGCAA
127626 CGAGATAATC
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
13 1 0.00
14 49 0.18
15 2 0.01
16 15 0.06
17 10 0.04
18 13 0.05
19 164 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:127585 original size:109 final size:104
Alignment explanation
Indices: 127329--127647 Score: 532
Period size: 109 Copynumber: 3.0 Consensus size: 104
127319 AAATCCCAAC
127329 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
* *
127394 ATGCGAAA-TGAAATCGCAACGAGAGAATCGCAATGCGAA
65 ATGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
127433 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
127498 TGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
66 TGCGAAATTAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAA
*
127542 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
* *
127607 TGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
66 TGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
127646 AT
1 AT
127648 TATAAACGCA
Statistics
Matches: 204, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
103 56 0.27
104 42 0.21
105 2 0.01
106 3 0.01
107 3 0.01
108 2 0.01
109 96 0.47
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:127663 original size:52 final size:52
Alignment explanation
Indices: 127329--127647 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
127319 AAATCCCAAC
127329 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
127382 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
127433 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
127485 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
127542 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
127594 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
127646 AT
1 AT
127648 TATAAACGCA
Statistics
Matches: 253, Mismatches: 7, Indels: 13
0.93 0.03 0.05
Matches are distributed among these distances:
51 51 0.20
52 131 0.52
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:127763 original size:19 final size:19
Alignment explanation
Indices: 127654--127755 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
127644 AAATTATAAA
127654 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
127673 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
127693 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
127709 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
127726 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
127745 CGCATTGCGAT
1 CGCATTGCGAT
127756 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:127881 original size:14 final size:14
Alignment explanation
Indices: 127862--127898 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
127852 CATCAATTAC
127862 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
127876 ACAAATCATCTTTT
1 ACAAATCAACTTTT
127890 ACAAATCAA
1 ACAAATCAA
127899 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:127910 original size:12 final size:12
Alignment explanation
Indices: 127893--127964 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
127883 ATCTTTTACA
127893 AATCAATTAAAC
1 AATCAATTAAAC
*
127905 AATCAA--AAATTG
1 AATCAATTAAA--C
**
127917 AATCAACTTTTAC
1 AATCAA-TTAAAC
127930 AAATCAATTAAAC
1 A-ATCAATTAAAC
127943 AATCAA--AAAC
1 AATCAATTAAAC
127953 AATCAATTAAAC
1 AATCAATTAAAC
127965 TATTGAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
10 13 0.28
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:127927 original size:38 final size:38
Alignment explanation
Indices: 127879--127951 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
127869 AACTTTTACA
*
127879 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
127917 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
127952 CAATCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:129807 original size:19 final size:19
Alignment explanation
Indices: 129767--129901 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
129757 TAGTTTACTT
* *
129767 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
129787 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
129806 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
129825 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
129839 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
129858 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
129872 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
129891 TCGCAATGCGA
1 TCGCAACGCGA
129902 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:129842 original size:14 final size:14
Alignment explanation
Indices: 129823--129879 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
129813 GCGAAATGAA
*
129823 AATCGCAACGACAG
1 AATCGCAACGAAAG
129837 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
129854 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
129870 AATCGCAACG
1 AATCGCAACG
129880 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:129846 original size:33 final size:33
Alignment explanation
Indices: 129804--129896 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
129794 GCGAAACCAA
*
129804 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
129837 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
129870 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
129897 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:129893 original size:52 final size:54
Alignment explanation
Indices: 129767--129901 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
129757 TAGTTTACTT
*
129767 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
129825 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
129872 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
129902 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:129919 original size:19 final size:19
Alignment explanation
Indices: 129897--130025 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
129887 AAAATCGCAA
129897 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
129916 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
129930 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
129949 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
129963 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
129982 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
130001 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
130021 TGCGA
1 TGCGA
130026 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:129939 original size:33 final size:33
Alignment explanation
Indices: 129897--129988 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
129887 AAAATCGCAA
129897 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
129930 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
129963 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
129989 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:130228 original size:93 final size:93
Alignment explanation
Indices: 130069--130448 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
130059 TTGAATGGAT
130069 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
130134 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
130162 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
130227 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
130255 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
130319 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
130347 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
130412 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
130440 AAATTTACT
1 AAATTTACT
130449 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:130382 original size:185 final size:186
Alignment explanation
Indices: 130069--130448 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
130059 TTGAATGGAT
130069 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
130134 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
130199 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130255 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
130319 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
130384 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130440 AAATTTACT
1 AAATTTACT
130449 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:132169 original size:14 final size:14
Alignment explanation
Indices: 132150--132239 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
132140 TTGAAATGAA
132150 AATCGCAACGAGAG
1 AATCGCAACGAGAG
132164 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
132181 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
132197 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
132216 AATCGCAACGAGAG
1 AATCGCAACGAGAG
132230 AATCGCAACG
1 AATCGCAACG
132240 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:132187 original size:33 final size:33
Alignment explanation
Indices: 132142--132256 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
132132 TCTTTTGGTT
132142 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
132175 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
132208 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
132241 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
132257 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:132188 original size:19 final size:18
Alignment explanation
Indices: 132149--132261 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
132139 GTTGAAATGA
132149 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
132164 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
132181 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
132197 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
132214 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
132230 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
132247 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
132262 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:132292 original size:14 final size:14
Alignment explanation
Indices: 132273--132327 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
132263 TTTGGTTTCG
132273 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
132287 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
132306 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
132320 CGTTGCGA
1 CGTTGCGA
132328 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:132490 original size:33 final size:33
Alignment explanation
Indices: 132448--132518 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
132438 AATACTAACT
*
132448 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
132481 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
132514 TGAAA
1 TGAAA
132519 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:132753 original size:22 final size:22
Alignment explanation
Indices: 132701--132755 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
132691 TGGTTGTGAG
**
132701 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
132723 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
132745 GGATTTCTTCG
1 GGATTTCTTCG
132756 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:132926 original size:20 final size:20
Alignment explanation
Indices: 132901--133094 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
132891 CTTTAAATAT
132901 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
132921 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
132943 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
132962 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
132982 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
133002 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
133022 CACGTTCCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
133042 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
133062 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
133082 CGCGTTGCGATTT
1 CGCGTTGCGATTT
133095 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:133093 original size:60 final size:60
Alignment explanation
Indices: 132901--133094 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
132891 CTTTAAATAT
**
132901 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
132962 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
133022 CACGTTCCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
133082 CGCGTTGCGATTT
1 CGCGTTGCGATTT
133095 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:133111 original size:21 final size:20
Alignment explanation
Indices: 133087--133163 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
133077 ATATTCGCGT
133087 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
133108 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
133128 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
133150 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
133164 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:133174 original size:20 final size:20
Alignment explanation
Indices: 133149--133200 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
133139 AAGAATCGCG
*
133149 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
133169 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
133189 TTGCGATTCTGG
1 TTGCGATTCTGG
133201 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:137294 original size:3 final size:3
Alignment explanation
Indices: 137286--137339 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
137276 ATTTGTTCCC
137286 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
137334 ATT ATT
1 ATT ATT
137340 CCCTTCCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:138123 original size:20 final size:20
Alignment explanation
Indices: 138083--138124 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
138073 CGGTTATACT
* *
138083 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTTAAAAAAACCG
138103 ATCCGGTTTTAAAAAAACCG
1 ATCCGGTTTTAAAAAAACCG
138123 AT
1 AT
138125 TTTTCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
ATCCGGTTTTAAAAAAACCG
Found at i:140591 original size:28 final size:28
Alignment explanation
Indices: 140560--140650 Score: 109
Period size: 26 Copynumber: 3.3 Consensus size: 28
140550 TTTTATCTAT
*
140560 TTATTTTTTTAAATATTTTATT-TTTTG-G
1 TTATTTTTTT-AATATTTT-TTATGTTGTG
140588 TTATTTTATTTAATATTTTTTATGTTGTG
1 TTATTTT-TTTAATATTTTTTATGTTGTG
*
140617 TTA--TTTTTATTATTTTTTATGTTGTG
1 TTATTTTTTTAATATTTTTTATGTTGTG
140643 TTATTTTT
1 TTATTTTT
140651 ATTATTTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 23 0.41
27 4 0.07
28 22 0.39
29 7 0.12
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.73
Consensus pattern (28 bp):
TTATTTTTTTAATATTTTTTATGTTGTG
Found at i:140652 original size:26 final size:26
Alignment explanation
Indices: 140596--140657 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
140586 GGTTATTTTA
*
140596 TTTAATATTTTTTATGTTGTGTTATT
1 TTTATTATTTTTTATGTTGTGTTATT
140622 TTTATTATTTTTTATGTTGTGTTATT
1 TTTATTATTTTTTATGTTGTGTTATT
140648 TTTATTATTT
1 TTTATTATTT
140658 AATAGAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (26 bp):
TTTATTATTTTTTATGTTGTGTTATT
Found at i:147972 original size:18 final size:19
Alignment explanation
Indices: 147935--147972 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
147925 TCTTAAACTT
* *
147935 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
147954 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
147972 T
1 T
147973 TATCGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:148113 original size:31 final size:32
Alignment explanation
Indices: 148050--148126 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
148040 CAATCTATTT
*
148050 GAGTTGCTTTCGGATCGGGTTAAAATTTGGTTC
1 GAGTTTCTTTCGGATCGGGTT-AAATTTGGTTC
*
148083 GAGTTTCTTTCGGATCGGGTT-ATTTTGGTTC
1 GAGTTTCTTTCGGATCGGGTTAAATTTGGTTC
148114 G-GTTTGCTTTCGG
1 GAGTTT-CTTTCGG
148127 TTTTGGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 4 0.10
31 17 0.41
33 20 0.49
ACGTcount: A:0.12, C:0.13, G:0.31, T:0.44
Consensus pattern (32 bp):
GAGTTTCTTTCGGATCGGGTTAAATTTGGTTC
Found at i:150422 original size:24 final size:24
Alignment explanation
Indices: 150390--150464 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 24
150380 AAACGAAAGC
* *
150390 TAAACGAACACGTTCGTGAACATA
1 TAAATGAACATGTTCGTGAACATA
* *
150414 TAAATGAACATGGTCGCGAACAT-
1 TAAATGAACATGTTCGTGAACATA
* *
150437 TAAATGAACGTGTTCGTGAGCA-A
1 TAAATGAACATGTTCGTGAACATA
150460 TAAAT
1 TAAAT
150465 AAACGAACAC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
TAAATGAACATGTTCGTGAACATA
Found at i:152891 original size:58 final size:59
Alignment explanation
Indices: 152817--152928 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
152807 AATCAATACC
* *
152817 TAAATTTTTAAACATTTAAATTTCATCCCTAAACTAT-AACTATCATTCTAAATTAGTCT
1 TAAACTTTTAAACATTTAAATTTCATCCCCAAACTATGAACT-TCATTCTAAATTAGTCT
* * *
152876 TAAACTTTT-AACATTTCATTTTCATCCCCAAACTATGATCTTCATTCTAAATT
1 TAAACTTTTAAACATTTAAATTTCATCCCCAAACTATGAACTTCATTCTAAATT
152929 GGTCCCCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 36 0.77
59 11 0.23
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.43
Consensus pattern (59 bp):
TAAACTTTTAAACATTTAAATTTCATCCCCAAACTATGAACTTCATTCTAAATTAGTCT
Found at i:153191 original size:60 final size:59
Alignment explanation
Indices: 153088--153271 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 59
153078 TTTGGATGAA
* * * * *
153088 TTTGGGGATAAAATTGGAA-GATGTAGAAGTTTAGGGACCAATTTAGAATGAAATTCATAG
1 TTTGGGGATGAAATTGGAATG-T-TAAAAGTTTAAGGACTAATTTAAAATGAAATTCATAG
*
153148 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAAT-AAGAGTCATAG
1 TTTGGGGATGAAATTGGAATGTT-AAAAGTTTAAGGACTAATTTAAAATGAA-ATTCATAG
* * * * **
153208 TTTTGGGATGAAACTGAAATATTTAAAAGTTTAAGGACTAATTTAAAATGAGGTTCATAG
1 TTTGGGGATGAAATTGGAAT-GTTAAAAGTTTAAGGACTAATTTAAAATGAAATTCATAG
153268 TTTG
1 TTTG
153272 AGGACATAGG
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.03
60 98 0.93
61 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (59 bp):
TTTGGGGATGAAATTGGAATGTTAAAAGTTTAAGGACTAATTTAAAATGAAATTCATAG
Found at i:154767 original size:16 final size:17
Alignment explanation
Indices: 154743--154775 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
154733 TTTTTATTAT
*
154743 TTAATATAAAT-ATAAA
1 TTAAAATAAATAATAAA
154759 TTAAAATAAATAATAAA
1 TTAAAATAAATAATAAA
154776 ATAATATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAAATAATAAA
Found at i:155720 original size:13 final size:13
Alignment explanation
Indices: 155682--155721 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
155672 CAAACCAATG
*
155682 CAAGTTGACTCAG
1 CAAGTTGACTCAA
* *
155695 CAAGTAGATTCAA
1 CAAGTTGACTCAA
155708 CAAGTTGACTCAA
1 CAAGTTGACTCAA
155721 C
1 C
155722 GGGCCGGTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (13 bp):
CAAGTTGACTCAA
Found at i:156857 original size:30 final size:30
Alignment explanation
Indices: 156822--156891 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 30
156812 AATATTTTTT
156822 ACCCCTCTGAA-ATTTTATAAATTTAAA-TTC
1 ACCCCTCT-AACATTTTATAAA-TTAAAGTTC
156852 A-CCC-CTAACATTTTATAAATTAAAGTTC
1 ACCCCTCTAACATTTTATAAATTAAAGTTC
*
156880 ATCCC-CTAACAT
1 ACCCCTCTAACAT
156892 AAAATTTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.19
28 16 0.43
29 13 0.35
30 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
ACCCCTCTAACATTTTATAAATTAAAGTTC
Found at i:156866 original size:28 final size:29
Alignment explanation
Indices: 156833--156891 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
156823 CCCCTCTGAA
156833 ATTTTATAAATTTAAA-TTCA-CCCCTAAC
1 ATTTTATAAA-TTAAAGTTCATCCCCTAAC
156861 ATTTTATAAATTAAAGTTCATCCCCTAAC
1 ATTTTATAAATTAAAGTTCATCCCCTAAC
156890 AT
1 AT
156892 AAAATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 5 0.17
28 14 0.48
29 10 0.34
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTTTATAAATTAAAGTTCATCCCCTAAC
Found at i:161672 original size:2 final size:2
Alignment explanation
Indices: 161667--161702 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
161657 AATTATTAGT
*
161667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
161703 ATGTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:162038 original size:15 final size:15
Alignment explanation
Indices: 162018--162058 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
162008 TCTTGGTTGC
162018 TTTTTTTCTTATTAT
1 TTTTTTTCTTATTAT
* *
162033 TTTTTTTCTTTTTCT
1 TTTTTTTCTTATTAT
*
162048 TTTTGTTCTTA
1 TTTTTTTCTTA
162059 AAGAGAGCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTCTTATTAT
Found at i:165817 original size:19 final size:19
Alignment explanation
Indices: 165793--165857 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
165783 GAACGTTGGA
165793 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
165812 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
165833 GACCGG-TTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
*
165851 GACCGGT
1 AACCGGT
165858 CACGACCCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 9 0.21
19 16 0.38
20 9 0.21
21 8 0.19
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:165818 original size:9 final size:9
Alignment explanation
Indices: 165794--165857 Score: 83
Period size: 9 Copynumber: 6.7 Consensus size: 9
165784 AACGTTGGAA
165794 ACCGGTTTTG
1 ACCGG-TTTG
*
165804 ACCGGTTTA
1 ACCGGTTTG
165813 ACCGGTTTTG
1 ACCGG-TTTG
165823 AACCGGTTTTG
1 -ACCGG-TTTG
165834 ACCGGTTTG
1 ACCGGTTTG
165843 ACCGGTTTG
1 ACCGGTTTG
165852 ACCGGT
1 ACCGGT
165858 CACGACCCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
9 27 0.54
10 13 0.26
11 10 0.20
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:165829 original size:30 final size:29
Alignment explanation
Indices: 165793--165857 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 29
165783 GAACGTTGGA
165793 AACCGGTTTTGACCGGTTTAACCGGTTTTG
1 AACCGGTTTTGACCGGTTTAACCGG-TTTG
*
165823 AACCGGTTTTGACCGGTTTGACCGGTTTG
1 AACCGGTTTTGACCGGTTTAACCGGTTTG
165852 -ACCGGT
1 AACCGGT
165858 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 6 0.18
29 4 0.12
30 24 0.71
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (29 bp):
AACCGGTTTTGACCGGTTTAACCGGTTTG
Found at i:165888 original size:13 final size:13
Alignment explanation
Indices: 165870--165906 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
165860 CGACCCGTTT
*
165870 ACCCGTTTACCCG
1 ACCCGTTGACCCG
165883 ACCCGTTGACCCG
1 ACCCGTTGACCCG
165896 ACCCGTTGACC
1 ACCCGTTGACC
165907 GTTGACCCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.46, G:0.19, T:0.19
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:165975 original size:29 final size:29
Alignment explanation
Indices: 165915--165980 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
165905 CCGTTGACCC
*** *
165915 GTGCTATTATGAGAATTAATTCGGTTTTG
1 GTGCTATTATGAGAATTAATTCGAAATGG
* *
165944 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTATGAGAATTAATTCGAAATGG
165973 GTGCTATT
1 GTGCTATT
165981 TCGGTAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (29 bp):
GTGCTATTATGAGAATTAATTCGAAATGG
Found at i:168250 original size:2 final size:2
Alignment explanation
Indices: 168243--168337 Score: 183
Period size: 2 Copynumber: 48.0 Consensus size: 2
168233 AAATAATACA
168243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
168284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168326 AT AT AT AT AT AT
1 AT AT AT AT AT AT
168338 GCGCGCGCAA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:171932 original size:17 final size:17
Alignment explanation
Indices: 171912--171952 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
171902 AAGGCACTTC
171912 AGATGCCAACTGAGCAT
1 AGATGCCAACTGAGCAT
171929 AGATGCCAACTGAGCAT
1 AGATGCCAACTGAGCAT
171946 AGATGCC
1 AGATGCC
171953 CTAAGACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (17 bp):
AGATGCCAACTGAGCAT
Found at i:173647 original size:2 final size:2
Alignment explanation
Indices: 173640--173685 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
173630 CAATAAAAAC
173640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173682 AT AT
1 AT AT
173686 TCATGTACGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183463 original size:2 final size:2
Alignment explanation
Indices: 183456--183495 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
183446 TAACTGTGTT
183456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183496 GTTGACATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:187037 original size:16 final size:16
Alignment explanation
Indices: 187016--187048 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
187006 TAATAAATAG
187016 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
187032 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
187048 A
1 A
187049 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:187139 original size:16 final size:16
Alignment explanation
Indices: 187118--187182 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
187108 TAATAAATAA
*
187118 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
187134 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
*
187150 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
187166 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
187182 A
1 A
187183 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:187944 original size:10 final size:10
Alignment explanation
Indices: 187929--187976 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
187919 ATAAATGAAT
187929 GAACATAAAC
1 GAACATAAAC
187939 GAACATAATCGAAC
1 GAACAT-A---AAC
187953 GAACATAAAC
1 GAACATAAAC
*
187963 GAACATAACC
1 GAACATAAAC
187973 GAAC
1 GAAC
187977 GAACATAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:187953 original size:14 final size:13
Alignment explanation
Indices: 187936--187991 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
187926 AATGAACATA
187936 AACGAACATAATCG
1 AACGAACATAA-CG
187950 AACGAACAT-A--
1 AACGAACATAACG
187960 AACGAACATAACCG
1 AACGAACATAA-CG
187974 AACGAACATAACTG
1 AACGAACATAAC-G
187988 AACG
1 AACG
187992 TTCACGAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 2 0.05
14 25 0.68
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:187956 original size:24 final size:24
Alignment explanation
Indices: 187916--187984 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
187906 GATTGGGTTA
*
187916 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
187940 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
187964 AACATAACCGAACGAACATAA
1 AACATAATCGAACGAACATAA
187985 CTGAACGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 3 0.07
24 39 0.93
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:191117 original size:31 final size:31
Alignment explanation
Indices: 191082--191141 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
191072 TGGCAACAAC
* *
191082 TCAATTAAAAACATTTA-AATGTTTATTTTTT
1 TCAA-TAAAAACAATTATAATATTTATTTTTT
*
191113 TCAATGAAAACAATTATAATATTTATTTT
1 TCAATAAAAACAATTATAATATTTATTTT
191142 ATTTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (31 bp):
TCAATAAAAACAATTATAATATTTATTTTTT
Found at i:195747 original size:20 final size:18
Alignment explanation
Indices: 195724--195765 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
195714 AATATACCTC
*
195724 ATAATATATATATTTATATA
1 ATAATA-ATACATTTATA-A
195744 ATAA-AATACATTTATAA
1 ATAATAATACATTTATAA
195761 ATAAT
1 ATAAT
195766 TTTTTACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 1 0.05
20 4 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATACATTTATAA
Found at i:197343 original size:20 final size:21
Alignment explanation
Indices: 197318--197358 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
197308 GTTCAATCTT
197318 CAAAAA-GTTCAAAATAAAAG
1 CAAAAAGGTTCAAAATAAAAG
*
197338 CAAAAAGGTTTAAAATAAAAG
1 CAAAAAGGTTCAAAATAAAAG
197359 AAAGAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.17
Consensus pattern (21 bp):
CAAAAAGGTTCAAAATAAAAG
Found at i:199265 original size:13 final size:13
Alignment explanation
Indices: 199247--199271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199237 ACTCTTAAAT
199247 ATCTTTATATAAC
1 ATCTTTATATAAC
199260 ATCTTTATATAA
1 ATCTTTATATAA
199272 GTGGTGCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
ATCTTTATATAAC
Done.