Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014992.1 Kokia drynarioides strain JFW-HI SEQ_130036, 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: 321484
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 419 characters in sequence are not A, C, G, or T
Found at i:7245 original size:109 final size:108
Alignment explanation
Indices: 7123--7416 Score: 417
Period size: 110 Copynumber: 2.7 Consensus size: 108
7113 TTTGCTTATG
* *
7123 CTGAATATATGATTCGATCGAATTTATCTCTTTTTTCTCTGTTTGTTTTAGGAAGTTGGTGAGTT
1 CTGAATATATGATTCGATCGAATTT-TCCCTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGTT
*
7188 TTGATTTTTTAAGTTTAATTTTACCCTCCATTTTAGCAATTAGA
65 TTGATTTTTTAAGTTTAATTTTACCCTACATTTTAGCAATTAGA
* * **
7232 CTGAATATATGATTCGATTGAATTTGCCCCTTTTTTCTCTGCTTGTTTTAAAAAGTTGGTGAGTT
1 CTGAATATATGATTCGATCGAATTT-TCCCTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGTT
* * *
7297 TTGATTTTCTTAAGTTTAGTTTTACCCTACATTTTAGGAATTAGG
65 TTGATTTT-TTAAGTTTAATTTTACCCTACATTTTAGCAATTAGA
* * * * *
7342 TTGAATATATGATTCAATCAAAATTTTCCCTTTTTTCTTTACTTGTTTTAGGAAGTTGGTGAGTT
1 CTGAATATATGATTCGATC-GAATTTTCCCTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGTT
7407 TTGATTTTTT
65 TTGATTTTTT
7417 TTTTTTTTTA
Statistics
Matches: 163, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
109 68 0.42
110 90 0.55
111 5 0.03
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.50
Consensus pattern (108 bp):
CTGAATATATGATTCGATCGAATTTTCCCTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGTTT
TGATTTTTTAAGTTTAATTTTACCCTACATTTTAGCAATTAGA
Found at i:8790 original size:24 final size:24
Alignment explanation
Indices: 8763--8812 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8753 TTTATTTTTA
*
8763 TAATTCTCATT-TCATTTTTTATTT
1 TAATT-TCATTCTAATTTTTTATTT
*
8787 TAATTTCCTTCTAATTTTTTATTT
1 TAATTTCATTCTAATTTTTTATTT
8811 TA
1 TA
8813 TTATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (24 bp):
TAATTTCATTCTAATTTTTTATTT
Found at i:13517 original size:7 final size:7
Alignment explanation
Indices: 13505--13531 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13495 ATATGATAAA
13505 GGTTTAG
1 GGTTTAG
13512 GGTTTAG
1 GGTTTAG
13519 GGTTTAG
1 GGTTTAG
13526 GGTTTA
1 GGTTTA
13532 AGATTTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:15349 original size:30 final size:30
Alignment explanation
Indices: 15315--15375 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
15305 ATCAATACTA
15315 AAACTACCAATACTTGTAATTAAACTACCG
1 AAACTACCAATACTTGTAATTAAACTACCG
15345 AAACTACCAATACTTGTAATTAAACTACCG
1 AAACTACCAATACTTGTAATTAAACTACCG
15375 A
1 A
15376 TACAACTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (30 bp):
AAACTACCAATACTTGTAATTAAACTACCG
Found at i:18086 original size:91 final size:89
Alignment explanation
Indices: 17991--18156 Score: 210
Period size: 88 Copynumber: 1.8 Consensus size: 89
17981 GATGATTGCG
* *
17991 CCATTTAAAATGACTT-CACTAAAAATAAAATATACATTAAAAATATTATAAAACAAATAATAAA
1 CCATTTAAAATGA-TTCCACCAAAAA-AAAATA-A-ATTAAAAATATTAAAAAACAAATAATAAA
* *
18055 -AAATAGACAAAAAGAGAATTAGTGGCA
62 CAAAAAGAAAAAAAGAGAATTAGTGGCA
* * * *
18082 CCATTTAGAATGATTCCACCAAAAAGAAATAAATTTAAAATTTTAAAAAACAAATAATAAACAAA
1 CCATTTAAAATGATTCCACCAAAAAAAAATAAATTAAAAATATTAAAAAACAAATAATAAACAAA
18147 AAGAAAAAAA
66 AAGAAAAAAA
18157 AAGTACACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
88 26 0.40
89 12 0.18
90 7 0.11
91 20 0.31
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (89 bp):
CCATTTAAAATGATTCCACCAAAAAAAAATAAATTAAAAATATTAAAAAACAAATAATAAACAAA
AAGAAAAAAAGAGAATTAGTGGCA
Found at i:19831 original size:17 final size:16
Alignment explanation
Indices: 19811--19855 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
19801 AAAATAAATA
19811 TTATTTTAAAGTTATTT
1 TTATTTTAAA-TTATTT
19828 TTATTTTCTAAATTATTT
1 TTA-TTT-TAAATTATTT
19846 TTATTATTAA
1 TTATT-TTAA
19856 TGAAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTTTAAATTATTT
Found at i:19861 original size:21 final size:18
Alignment explanation
Indices: 19811--19850 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
19801 AAAATAAATA
*
19811 TTATTTTA-AAGTTATTT
1 TTATTTTATAAATTATTT
*
19828 TTATTTTCTAAATTATTT
1 TTATTTTATAAATTATTT
19846 TTATT
1 TTATT
19851 ATTAATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATTTTATAAATTATTT
Found at i:37722 original size:20 final size:18
Alignment explanation
Indices: 37676--37715 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
37666 GTTTTAAAAA
*
37676 AATTAAAATATACTTGGC
1 AATTAAAATATACTTGAC
37694 AATTAAAATATACTTGAC
1 AATTAAAATATACTTGAC
37712 AATT
1 AATT
37716 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (18 bp):
AATTAAAATATACTTGAC
Found at i:39781 original size:21 final size:22
Alignment explanation
Indices: 39757--39815 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
39747 GTTGCATAAT
39757 TTGTATCGGTAGAAATCA-TAC
1 TTGTATCGGTAGAAATCAGTAC
** *
39778 TTGTATCAATAGAACT-AGTAC
1 TTGTATCGGTAGAAATCAGTAC
**
39799 AGGTATCGGTAGAAATC
1 TTGTATCGGTAGAAATC
39816 TGCACAGTTC
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (22 bp):
TTGTATCGGTAGAAATCAGTAC
Found at i:40095 original size:21 final size:21
Alignment explanation
Indices: 40069--40112 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40059 GGTGTACGGG
* *
40069 ATTTAAGTGTTACAAAAATAA
1 ATTTAAATGTTAAAAAAATAA
*
40090 ATTTAAATTTTAAAAAAATAA
1 ATTTAAATGTTAAAAAAATAA
40111 AT
1 AT
40113 AATAAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTTAAATGTTAAAAAAATAA
Found at i:42773 original size:15 final size:14
Alignment explanation
Indices: 42730--42773 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
42720 TAATTCTAAT
42730 TTTAAACTATTTTAAA
1 TTTAAA-TATTTT-AA
*
42746 TTTAAATAATTTAA
1 TTTAAATATTTTAA
42760 TTTAATATATTTTA
1 TTTAA-ATATTTTA
42774 GCCTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 12 0.48
16 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAATATTTTAA
Found at i:44886 original size:39 final size:39
Alignment explanation
Indices: 44843--44920 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
44833 GTCCAGCTGG
*
44843 ACACGTTTTCCCTCAAAATCGACCTATTATCTAATTATT
1 ACACGCTTTCCCTCAAAATCGACCTATTATCTAATTATT
* *
44882 ACACGCTTTCCCTTAAAATCGACCTATTCTCTAATTATT
1 ACACGCTTTCCCTCAAAATCGACCTATTATCTAATTATT
44921 TTTAAAACCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.38
Consensus pattern (39 bp):
ACACGCTTTCCCTCAAAATCGACCTATTATCTAATTATT
Found at i:47302 original size:8 final size:8
Alignment explanation
Indices: 47289--47316 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
47279 TATCATGATA
47289 AATTTTAT
1 AATTTTAT
47297 AATTTTAT
1 AATTTTAT
47305 AATTTTAT
1 AATTTTAT
47313 AATT
1 AATT
47317 GCAATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:55559 original size:29 final size:29
Alignment explanation
Indices: 55527--55607 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
55517 AAAATGGTAG
*
55527 TTTTGAGAAATTTTGGGGTCAAAACG-AAA
1 TTTTGAGAAATTTAGGGGT-AAAACGTAAA
* * *
55556 TTTTTAGATATTTAGGGGTAAAATGTAAA
1 TTTTGAGAAATTTAGGGGTAAAACGTAAA
* *
55585 TTTTGA-AAAGTTCAGGGTTAAAA
1 TTTTGAGAAA-TTTAGGGGTAAAA
55608 ATGGAATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
TTTTGAGAAATTTAGGGGTAAAACGTAAA
Found at i:55615 original size:29 final size:29
Alignment explanation
Indices: 55583--55763 Score: 133
Period size: 29 Copynumber: 6.2 Consensus size: 29
55573 GTAAAATGTA
55583 AATTTTGAAAAGTTCAGGGTTAAAAATGG
1 AATTTTGAAAAGTTCAGGGTTAAAAATGG
* * * *
55612 AATTTTGGAAAGTTCAGGGCTAAAAAAGT
1 AATTTTGAAAAGTTCAGGGTTAAAAATGG
55641 AATTTTTAGAAAA-TTC-GAGGTCT--AAATGG
1 AA-TTTT-GAAAAGTTCAG-GGT-TAAAAATGG
* * *
55670 AATTTTGGAAAGTTCAAGAG-TAAAAATGT
1 AATTTTGAAAAGTTC-AGGGTTAAAAATGG
* * *
55699 AATTTTTGGAAAA-TTTAAGGTTAAAAAAGG
1 AA-TTTT-GAAAAGTTCAGGGTTAAAAATGG
* *
55729 AATTTTGGAAAGTTCGAGGG-TAAAAATGT
1 AATTTTGAAAAGTTC-AGGGTTAAAAATGG
55758 AATTTT
1 AATTTT
55764 TGGACAGTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.04
28 11 0.09
29 63 0.54
30 28 0.24
31 9 0.08
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (29 bp):
AATTTTGAAAAGTTCAGGGTTAAAAATGG
Found at i:55674 original size:87 final size:87
Alignment explanation
Indices: 55583--55747 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 87
55573 GTAAAATGTA
* * * *
55583 AATTTTGAAAAGTTC-AGGGTTAAAAATGGAA-TTTTGGAAAGTTCAGGGCTAAAAAAGTAATTT
1 AATTTTGAAAAGTTCAAGAG-TAAAAATGGAATTTTTGGAAAATTCAAGGCTAAAAAAGGAA-TT
55646 TTAGAAAATTCGAGGTCTAAATGG
64 TTAGAAAATTCGAGGTCTAAATGG
* * * *
55670 AATTTTGGAAAGTTCAAGAGTAAAAATGTAATTTTTGGAAAATTTAAGGTTAAAAAAGGAATTTT
1 AATTTTGAAAAGTTCAAGAGTAAAAATGGAATTTTTGGAAAATTCAAGGCTAAAAAAGGAATTTT
* *
55735 GGAAAGTTCGAGG
66 AGAAAATTCGAGG
55748 GTAAAAATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
87 39 0.59
88 27 0.41
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (87 bp):
AATTTTGAAAAGTTCAAGAGTAAAAATGGAATTTTTGGAAAATTCAAGGCTAAAAAAGGAATTTT
AGAAAATTCGAGGTCTAAATGG
Found at i:55752 original size:59 final size:58
Alignment explanation
Indices: 55571--55767 Score: 249
Period size: 59 Copynumber: 3.4 Consensus size: 58
55561 AGATATTTAG
* *
55571 GGGT-AAAATGTAAATTTT-GAAAAGTTCAGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGTAAAAATGTAATTTTTGGAAAA-TTCAAGGTTAAAAATGGAATTTTGGAAAGTTCA
* * *
55628 GGGCTAAAAAAGTAATTTTTAGAAAATTCGAGGTCT--AAATGGAATTTTGGAAAGTTCAA
1 GGG-TAAAAATGTAATTTTTGGAAAATTCAAGGT-TAAAAATGGAATTTTGGAAAGTTC-A
* * *
55687 GAGTAAAAATGTAATTTTTGGAAAATTTAAGGTTAAAAAAGGAATTTTGGAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAAATTCAAGGTTAAAAATGGAATTTTGGAAAGTTC-A
55746 GGGTAAAAATGTAATTTTTGGA
1 GGGTAAAAATGTAATTTTTGGA
55768 CAGTTTGAGG
Statistics
Matches: 121, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
57 4 0.03
58 48 0.40
59 63 0.52
60 6 0.05
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAAATTCAAGGTTAAAAATGGAATTTTGGAAAGTTCA
Found at i:56887 original size:3 final size:3
Alignment explanation
Indices: 56879--56922 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
56869 ACTTTTCAAC
*
56879 TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTAA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA T
56923 ATTTATTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:56938 original size:22 final size:22
Alignment explanation
Indices: 56880--56938 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
56870 CTTTTCAACT
* *
56880 TATTATTATTA-TTATTATTAA
1 TATTATTACTACTAATTATTAA
* *
56901 TATTATTATTATTAATTATT-A
1 TATTATTACTACTAATTATTAA
56922 TATTTATTACTACTAAT
1 TA-TTATTACTACTAAT
56939 AAAATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTACTACTAATTATTAA
Found at i:57587 original size:15 final size:15
Alignment explanation
Indices: 57567--57595 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57557 AGTTAATGGG
57567 TTTTGTAATTGGACA
1 TTTTGTAATTGGACA
57582 TTTTGTAATTGGAC
1 TTTTGTAATTGGAC
57596 TTTCATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
TTTTGTAATTGGACA
Found at i:57623 original size:17 final size:16
Alignment explanation
Indices: 57601--57691 Score: 85
Period size: 17 Copynumber: 5.3 Consensus size: 16
57591 TGGACTTTCA
*
57601 TTAAATTTATAATAATT
1 TTAAATTTA-AATAAAT
57618 TTAAATTTAAAAATAAAT
1 TTAAATTT--AAATAAAT
*
57636 TTAAACTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
*
57653 TTAAATTTAAAACAAAT
1 TTAAATTT-AAATAAAT
57670 TT-AATCTTAAAATAAAT
1 TTAAAT-TT-AAATAAAT
57687 TTAAA
1 TTAAA
57692 ATGGGTTTGG
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.10
17 38 0.60
18 18 0.29
19 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:57628 original size:6 final size:6
Alignment explanation
Indices: 57617--57663 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
57607 TTATAATAAT
** *
57617 TTTAAA TTTAAA AATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
57664 ACAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:57679 original size:34 final size:35
Alignment explanation
Indices: 57601--57691 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 35
57591 TGGACTTTCA
* * * *
57601 TTAAATTTATAATAATTTTAAATTTAAAAATAAAT
1 TTAAACTTAAAATAAATTTAAATTTAAAAACAAAT
*
57636 TTAAACTTAAATTAAATTTAAATTT-AAAACAAAT
1 TTAAACTTAAAATAAATTTAAATTTAAAAACAAAT
*
57670 TTAATCTTAAAATAAATTTAAA
1 TTAAACTTAAAATAAATTTAAA
57692 ATGGGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 28 0.57
35 21 0.43
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (35 bp):
TTAAACTTAAAATAAATTTAAATTTAAAAACAAAT
Found at i:57693 original size:11 final size:12
Alignment explanation
Indices: 57619--57673 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
57609 ATAATAATTT
*
57619 TAAATTTAAAAA
1 TAAATTTAAACA
*
57631 TAAATTTAAACT
1 TAAATTTAAACA
**
57643 TAAA-TTAAATT
1 TAAATTTAAACA
57654 TAAATTTAAA-A
1 TAAATTTAAACA
*
57665 CAAATTTAA
1 TAAATTTAA
57674 TCTTAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATTTAAACA
Found at i:70032 original size:19 final size:19
Alignment explanation
Indices: 70008--70045 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
69998 GAAAGTTAAT
*
70008 AACAAATTTTATTAAGGTG
1 AACAAATTTGATTAAGGTG
*
70027 AACAAATTTGATTATGGTG
1 AACAAATTTGATTAAGGTG
70046 GGTGACAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (19 bp):
AACAAATTTGATTAAGGTG
Found at i:73311 original size:29 final size:30
Alignment explanation
Indices: 73259--73320 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
73249 AGTTTATATC
73259 TTTATAATTTTTAAAGGACCAAA-TCAAATT
1 TTTATAATTTTT-AAGGACCAAATTCAAATT
* *
73289 TTTATAATTTTT-AGGAATCAAATTGAAATT
1 TTTATAATTTTTAAGG-ACCAAATTCAAATT
73319 TT
1 TT
73321 ACTTTAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 5 0.18
30 20 0.71
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTATAATTTTTAAGGACCAAATTCAAATT
Found at i:73835 original size:24 final size:24
Alignment explanation
Indices: 73807--73881 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
73797 AGAAATAATC
* * *
73807 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTATATTTATTTG
* *
73831 TTTCAATTAAATTATGTTTATTTG
1 TTTCAATTAAACTATATTTATTTG
* *
73855 TTTCAATTAAATTATGTTTATTTG
1 TTTCAATTAAACTATATTTATTTG
73879 TTT
1 TTT
73882 GAGTCAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATATTTATTTG
Found at i:73888 original size:28 final size:24
Alignment explanation
Indices: 73823--73881 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
73813 TTAAACTCTA
*
73823 TTTAATTGTTTCAATTAAATTATG
1 TTTATTTGTTTCAATTAAATTATG
73847 TTTATTTGTTTCAATTAAATTATG
1 TTTATTTGTTTCAATTAAATTATG
73871 TTTATTTGTTT
1 TTTATTTGTTT
73882 GAGTCAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.61
Consensus pattern (24 bp):
TTTATTTGTTTCAATTAAATTATG
Found at i:75825 original size:24 final size:24
Alignment explanation
Indices: 75797--75859 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
75787 ATAAATAATC
75797 TTTCAGTTAAACTCTGCTTAATTG
1 TTTCAGTTAAACTCTGCTTAATTG
* * * *
75821 TTTCAATTAAACCCTGTTTATTTG
1 TTTCAGTTAAACTCTGCTTAATTG
* * *
75845 TCTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
75860 TATTAGTCTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGCTTAATTG
Found at i:76620 original size:26 final size:25
Alignment explanation
Indices: 76582--76648 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
76572 ACGTTTATAA
76582 AATTATTATATATAAT-AGTTTTGTTT
1 AATTATT-TATATAATGA-TTTTGTTT
* *
76608 CATTATTTGATATTATGATTTTGTTT
1 AATTATTT-ATATAATGATTTTGTTT
*
76634 AATTTATTTACATAA
1 AA-TTATTTATATAA
76649 ATTGGATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.03
26 25 0.76
27 7 0.21
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATTTATATAATGATTTTGTTT
Found at i:79688 original size:2 final size:2
Alignment explanation
Indices: 79681--79705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
79671 AATTAAAGCA
79681 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
79706 TAACACGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:82435 original size:132 final size:132
Alignment explanation
Indices: 82196--82438 Score: 312
Period size: 132 Copynumber: 1.8 Consensus size: 132
82186 GTGGGTGTGG
* * * *
82196 GTCTTAGATGTTCTACCGATGGTTGAGATTCGAAATTTATTACGGATTCTCCATAGCTCGTGTGA
1 GTCTTAGATGTTCTACCGATGGTTGAGATCCGAAATTTATTACGGATTCTCCACAACTAGTGTGA
* * * *
82261 GCATCATTGTATAGCTTAACATCTCGACCCACAGCTCATGTGAGCATTACATGCTATATAGGTGC
66 GCAGCATTGTATAGCCTAACATCTCGAACCACAACTCATGTGAGCATTACATGCTATATAGGTGC
82326 TA
131 TA
** *
82328 GTCTTAGATGTTCTACCGATGGTTGAGATCCGGCATTTATTGCGGATTCTCCACAACTAGTGTGA
1 GTCTTAGATGTTCTACCGATGGTTGAGATCCGAAATTTATTACGGATTCTCCACAACTAGTGTGA
* * *
82393 GCAGCATCATGTA-A-CCTAAC-TACTCGAACTATAACTCGTGTGAGCA
66 GCAGCAT--TGTATAGCCTAACAT-CTCGAACCACAACTCATGTGAGCA
82439 GACCCATTTC
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
131 1 0.01
132 88 0.94
133 1 0.01
134 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (132 bp):
GTCTTAGATGTTCTACCGATGGTTGAGATCCGAAATTTATTACGGATTCTCCACAACTAGTGTGA
GCAGCATTGTATAGCCTAACATCTCGAACCACAACTCATGTGAGCATTACATGCTATATAGGTGC
TA
Found at i:86778 original size:24 final size:24
Alignment explanation
Indices: 86745--86795 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
86735 AGAAATAATC
* *
86745 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
86769 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
86793 TTT
1 TTT
86796 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:86804 original size:24 final size:24
Alignment explanation
Indices: 86753--86807 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
86743 TCTTTCAGTT
* *
86753 AAACTTTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * *
86777 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATC
86801 AAACTCT
1 AAACTCT
86808 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:87983 original size:48 final size:48
Alignment explanation
Indices: 87912--88008 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
87902 GCTGAGAGTA
*
87912 ACGAGGAAGTTTTAGCTGGTGCTAATTTGGCCGATGAAAGTGGTGATG
1 ACGAGGAAGTTTTAGCTGGTGCTAATTTGGCCGATGAAAGTGATGATG
*
87960 ACGAGGAAGTTTTAGTTGGTGCTAATTTGGCCGATGAAAGTGATGATG
1 ACGAGGAAGTTTTAGCTGGTGCTAATTTGGCCGATGAAAGTGATGATG
88008 A
1 A
88009 TTTCTTGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (48 bp):
ACGAGGAAGTTTTAGCTGGTGCTAATTTGGCCGATGAAAGTGATGATG
Found at i:88863 original size:24 final size:24
Alignment explanation
Indices: 88777--88851 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
88767 ACAAATAATC
* *
88777 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
88801 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
88825 TTTCAATTGAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
88849 TTT
1 TTT
88852 AAGTCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:89578 original size:21 final size:21
Alignment explanation
Indices: 89552--89634 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
89542 TGTGGAAATA
89552 CCCCTATATTGCACTTCGGTG
1 CCCCTATATTGCACTTCGGTG
* *
89573 CCCCTATTTTGCACTTTGGTG
1 CCCCTATATTGCACTTCGGTG
* *
89594 CCCCTGTATTGCAATTCGGTG
1 CCCCTATATTGCACTTCGGTG
* * *
89615 CCCTTATCTTGCACTACGGT
1 CCCCTATATTGCACTTCGGT
89635 ACCTCTGTCT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.36
Consensus pattern (21 bp):
CCCCTATATTGCACTTCGGTG
Found at i:89645 original size:21 final size:21
Alignment explanation
Indices: 89621--89692 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
89611 GGTGCCCTTA
89621 TCTTGCACTACGGTACCTCTG
1 TCTTGCACTACGGTACCTCTG
* *
89642 TCTTGCAATTA-AGTACCTCTG
1 TCTTGC-ACTACGGTACCTCTG
* * *
89663 TCTTGCACTACGATGCCTTTG
1 TCTTGCACTACGGTACCTCTG
89684 TCTTGCACT
1 TCTTGCACT
89693 TCGGGCCTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (21 bp):
TCTTGCACTACGGTACCTCTG
Found at i:89648 original size:42 final size:42
Alignment explanation
Indices: 89560--89696 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 42
89550 TACCCCTATA
* * * ** * *
89560 TTGCACTTCGGTGCCCCTATTTTGCACTTTGGTGCCCCTGTA
1 TTGCAATTCGGTGCCCTTATCTTGCACTACGGTGCCTCTGTC
*
89602 TTGCAATTCGGTGCCCTTATCTTGCACTACGGTACCTCTGTC
1 TTGCAATTCGGTGCCCTTATCTTGCACTACGGTGCCTCTGTC
** * * * *
89644 TTGCAATTAAGT-ACCTCTGTCTTGCACTACGATGCCTTTGTC
1 TTGCAATTCGGTGCCCT-TATCTTGCACTACGGTGCCTCTGTC
*
89686 TTGCACTTCGG
1 TTGCAATTCGG
89697 GCCTCAGTTT
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 3 0.04
42 73 0.96
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (42 bp):
TTGCAATTCGGTGCCCTTATCTTGCACTACGGTGCCTCTGTC
Found at i:90796 original size:27 final size:27
Alignment explanation
Indices: 90757--90811 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
90747 TAGAAATGGT
*
90757 TTGTTCTTGTGCTTCATTAAGTTATAG
1 TTGTTCTTATGCTTCATTAAGTTATAG
*
90784 TTGTTCTTATGCTTCATTGAGTTATAG
1 TTGTTCTTATGCTTCATTAAGTTATAG
90811 T
1 T
90812 GATGGTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (27 bp):
TTGTTCTTATGCTTCATTAAGTTATAG
Found at i:103939 original size:11 final size:11
Alignment explanation
Indices: 103923--103974 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
103913 CTTTTGACAC
103923 ATTATTACTTT
1 ATTATTACTTT
103934 ATTATTA-TTT
1 ATTATTACTTT
103944 ATTATCTCAGC-TT
1 ATTAT-T-A-CTTT
*
103957 ATTATTACTTC
1 ATTATTACTTT
103968 ATTATTA
1 ATTATTA
103975 GGGTGTATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.26
11 17 0.49
12 2 0.06
13 7 0.20
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTATTACTTT
Found at i:107958 original size:2 final size:2
Alignment explanation
Indices: 107951--107981 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
107941 CATTGCTTTA
107951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
107982 AAAACTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122632 original size:19 final size:21
Alignment explanation
Indices: 122593--122633 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
122583 AAGAAAACAC
*
122593 AAAATAATTCAAAGAATTTAT
1 AAAAAAATTCAAAGAATTTAT
122614 AAAAAAATTC-AAG-ATTTAT
1 AAAAAAATTCAAAGAATTTAT
122633 A
1 A
122634 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAAAAATTCAAAGAATTTAT
Found at i:142271 original size:19 final size:22
Alignment explanation
Indices: 142225--142278 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
142215 TGATATTGAC
*
142225 ATATTTAATAATATTATTTAAT
1 ATATTTAATAACATTATTTAAT
*
142247 AAATTTAAT-ACATT-TTTAAT
1 ATATTTAATAACATTATTTAAT
*
142267 -TATTTAAGAACA
1 ATATTTAATAACA
142279 CAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.22
20 9 0.33
21 4 0.15
22 8 0.30
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTTAATAACATTATTTAAT
Found at i:142681 original size:21 final size:22
Alignment explanation
Indices: 142655--142717 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
142645 AAAAAAATGC
*
142655 TATTGTTTTCTTGCTATTTT-T
1 TATTGTTTTATTGCTATTTTAT
**
142676 TATTGTTTTATTATTATTTTAT
1 TATTGTTTTATTGCTATTTTAT
* * *
142698 TGTTTTTTTTTTGCTATTTT
1 TATTGTTTTATTGCTATTTT
142718 GCTACCATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.75
Consensus pattern (22 bp):
TATTGTTTTATTGCTATTTTAT
Found at i:169420 original size:28 final size:30
Alignment explanation
Indices: 169384--169443 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
169374 TTATTTTATA
169384 AAAATAAT-ATTATAT-TA-ATTATATATGTT
1 AAAATAATAATTATATATATA-TATATAT-TT
169413 AAAA-AATAATTATATATATATATATATTT
1 AAAATAATAATTATATATATATATATATTT
169442 AA
1 AA
169444 TCATTAACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 3 0.11
29 15 0.54
30 9 0.32
31 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAATAATAATTATATATATATATATATTT
Found at i:169772 original size:21 final size:21
Alignment explanation
Indices: 169746--169786 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
169736 GACAAAAAAG
169746 TAAGACCATTTTTTGAATCGT
1 TAAGACCATTTTTTGAATCGT
169767 TAAGACCATTTTTTGAATCG
1 TAAGACCATTTTTTGAATCG
169787 GGTCGGACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (21 bp):
TAAGACCATTTTTTGAATCGT
Found at i:170402 original size:23 final size:24
Alignment explanation
Indices: 170375--170419 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
170365 GAGTTTGACT
170375 GAAAC-AATAAACAGAATTTAATC
1 GAAACAAATAAACAGAATTTAATC
* *
170398 GAAACAAATAAATAGAGTTTAA
1 GAAACAAATAAACAGAATTTAA
170420 CTGGAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (24 bp):
GAAACAAATAAACAGAATTTAATC
Found at i:171147 original size:26 final size:26
Alignment explanation
Indices: 171118--171167 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
171108 TCTACTGATA
* *
171118 CTAAAAACTCCAGATAGCTAAGAAGT
1 CTAAAAAATCCAGAGAGCTAAGAAGT
*
171144 CTAAAAAATCTAGAGAGCTAAGAA
1 CTAAAAAATCCAGAGAGCTAAGAA
171168 CTCTTACCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (26 bp):
CTAAAAAATCCAGAGAGCTAAGAAGT
Found at i:172259 original size:2 final size:2
Alignment explanation
Indices: 172252--172278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
172242 AATTGTTAGG
172252 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
172279 TATCTCAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:172641 original size:20 final size:20
Alignment explanation
Indices: 172612--172659 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
172602 TCTTGAATAA
*
172612 GTGCTCCTAATATCACTACG
1 GTGCTCCTAATAGCACTACG
* *
172632 GTGCTTCTAATAGCACTATG
1 GTGCTCCTAATAGCACTACG
*
172652 ATGCTCCT
1 GTGCTCCT
172660 GACAATACTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
GTGCTCCTAATAGCACTACG
Found at i:172682 original size:40 final size:40
Alignment explanation
Indices: 172638--172797 Score: 146
Period size: 40 Copynumber: 4.0 Consensus size: 40
172628 TACGGTGCTT
*
172638 CTAATAGCACTATGATGCTCCTGACAATACTTTCATACTC
1 CTAATAGCACTATGATGCTCCTGACAATACTTTCGTACTC
* * *
172678 CTAATAGCACTACGGTTCTCCTGACAGA-ACTTTCGTACTC
1 CTAATAGCACTATGATGCTCCTGACA-ATACTTTCGTACTC
* * * * * *
172718 ATGATAGCACTA-CAGTGCTCTTGACAGTACATTCGTACTC
1 CTAATAGCACTATGA-TGCTCCTGACAATACTTTCGTACTC
* * * *
172758 CTAATAGCACTAT-AGTGCTCTTGATAGTACTTTTGTACTC
1 CTAATAGCACTATGA-TGCTCCTGACAATACTTTCGTACTC
172798 TTGTTAGCAC
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
40 98 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (40 bp):
CTAATAGCACTATGATGCTCCTGACAATACTTTCGTACTC
Found at i:172757 original size:80 final size:80
Alignment explanation
Indices: 172653--172821 Score: 212
Period size: 80 Copynumber: 2.1 Consensus size: 80
172643 AGCACTATGA
* * * *
172653 TGCTCCTGACAATACTTTCATACTCCTAATAGCACTACGGTTCTCCTGACAGAACTTTCGTACTC
1 TGCTCTTGACAATACATTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTC
172718 ATGATAGCACTACAG
66 ATGATAGCACTACAG
* * * * * * *
172733 TGCTCTTGACAGTACATTCGTACTCCTAATAGCACTATAGTGCTCTTGATAGTACTTTTGTACTC
1 TGCTCTTGACAATACATTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTC
* * *
172798 TTGTTAGCACTACGG
66 ATGATAGCACTACAG
172813 TGCTCTTGA
1 TGCTCTTGA
172822 TAGCATATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (80 bp):
TGCTCTTGACAATACATTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTC
ATGATAGCACTACAG
Found at i:172806 original size:40 final size:40
Alignment explanation
Indices: 172665--172824 Score: 167
Period size: 40 Copynumber: 4.0 Consensus size: 40
172655 CTCCTGACAA
* * * * * * *
172665 TACTTTCATACTCCTAATAGCACTACGGTTCTCCTGACAG
1 TACTTTCGTACTCATGATAGCACTACAGTGCTCTTGATAG
* *
172705 AACTTTCGTACTCATGATAGCACTACAGTGCTCTTGACAG
1 TACTTTCGTACTCATGATAGCACTACAGTGCTCTTGATAG
* * * *
172745 TACATTCGTACTCCTAATAGCACTATAGTGCTCTTGATAG
1 TACTTTCGTACTCATGATAGCACTACAGTGCTCTTGATAG
* * * *
172785 TACTTTTGTACTCTTGTTAGCACTACGGTGCTCTTGATAG
1 TACTTTCGTACTCATGATAGCACTACAGTGCTCTTGATAG
172825 CATATTCATG
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (40 bp):
TACTTTCGTACTCATGATAGCACTACAGTGCTCTTGATAG
Found at i:172839 original size:80 final size:80
Alignment explanation
Indices: 172669--172839 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
172659 TGACAATACT
* *
172669 TTCATACTCCTAATAGCACTACGGTTCTCCTGACAGAACTTTCGTACTCATGATAGCACTACAGT
1 TTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTCATGATAGCACTACAGT
*
172734 GCTCTTGACAGTACA
66 GCTCTTGACAGCACA
* * * * * * * * *
172749 TTCGTACTCCTAATAGCACTATAGTGCTCTTGATAGTACTTTTGTACTCTTGTTAGCACTACGGT
1 TTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTCATGATAGCACTACAGT
* *
172814 GCTCTTGATAGCATA
66 GCTCTTGACAGCACA
*
172829 TTCATGCTCCT
1 TTCATACTCCT
172840 GTTTACAGTA
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (80 bp):
TTCATACTCCTAATAGCACTACAGTGCTCCTGACAGAACTTTCGTACTCATGATAGCACTACAGT
GCTCTTGACAGCACA
Found at i:172886 original size:20 final size:20
Alignment explanation
Indices: 172855--172902 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
172845 CAGTACGATG
*
172855 CCCTGGTTGTACTTATGTTC
1 CCCTGATTGTACTTATGTTC
*
172875 CCTTGATTGTACTTATGTTC
1 CCCTGATTGTACTTATGTTC
172895 CCCTGATT
1 CCCTGATT
172903 TCTCTTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (20 bp):
CCCTGATTGTACTTATGTTC
Found at i:173710 original size:19 final size:19
Alignment explanation
Indices: 173686--173734 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
173676 TAAAAGTAGC
173686 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
173705 ACAACATGAGTCCAAATAA
1 ACAACATCAACCCAAATAA
*
173724 ACAACAACAAC
1 ACAACATCAAC
173735 AATACAACAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:181872 original size:2 final size:2
Alignment explanation
Indices: 181865--181904 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
181855 GGTTACTGTT
181865 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
181905 AATGAACCCC
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:187490 original size:31 final size:31
Alignment explanation
Indices: 187450--187510 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
187440 AAATGATTAT
187450 TGAACTATTCAAAAATTTTAATTTAAGTCAA
1 TGAACTATTCAAAAATTTTAATTTAAGTCAA
* * * *
187481 TGAATTATTCGAAAGTTTTTATTTAAGTCA
1 TGAACTATTCAAAAATTTTAATTTAAGTCA
187511 CTAAATTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (31 bp):
TGAACTATTCAAAAATTTTAATTTAAGTCAA
Found at i:198256 original size:16 final size:16
Alignment explanation
Indices: 198235--198266 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
198225 GCAGGGTGTG
198235 GAGTGGTGAAGAAACA
1 GAGTGGTGAAGAAACA
198251 GAGTGGTGAAGAAACA
1 GAGTGGTGAAGAAACA
198267 TACAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.38, T:0.12
Consensus pattern (16 bp):
GAGTGGTGAAGAAACA
Found at i:201353 original size:48 final size:47
Alignment explanation
Indices: 201295--201414 Score: 150
Period size: 48 Copynumber: 2.5 Consensus size: 47
201285 CGAAGTACTT
**
201295 AACAGAGGGCACAAAAGTGCTGGGTAACAAAGGGCACACAAAGTGCTA
1 AACAGAGGGCACAAAAGTGCT-AATAACAAAGGGCACACAAAGTGCTA
* * * *
201343 ATCAGAGGGCACACGAAGTGCTAATAACAGAGGGCACACACAGTGCTA
1 AACAGAGGGCACA-AAAGTGCTAATAACAAAGGGCACACAAAGTGCTA
*
201391 AACAGAGGGCACGAAACGTGCTAA
1 AACAGAGGGCAC-AAAAGTGCTAA
201415 ACAGAGGGCG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
48 53 0.87
49 8 0.13
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.11
Consensus pattern (47 bp):
AACAGAGGGCACAAAAGTGCTAATAACAAAGGGCACACAAAGTGCTA
Found at i:201355 original size:23 final size:23
Alignment explanation
Indices: 201295--201423 Score: 136
Period size: 23 Copynumber: 5.4 Consensus size: 23
201285 CGAAGTACTT
*
201295 AACAGAGGGCACA-AAAGTGCTGGGT
1 AACAGAGGGCACACAAAGTGCT---A
*
201320 AACAAAGGGCACACAAAGTGCTA
1 AACAGAGGGCACACAAAGTGCTA
* *
201343 ATCAGAGGGCACACGAAGTGCTAA
1 AACAGAGGGCACACAAAGTGCT-A
*
201367 TAACAGAGGGCACACACAGTGCTA
1 -AACAGAGGGCACACAAAGTGCTA
*
201391 AACAGAGGGCACGA-AACGTGCTA
1 AACAGAGGGCAC-ACAAAGTGCTA
201414 AACAGAGGGC
1 AACAGAGGGC
201424 GCACTAGTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
23 48 0.53
24 3 0.03
25 31 0.34
26 8 0.09
ACGTcount: A:0.40, C:0.21, G:0.29, T:0.10
Consensus pattern (23 bp):
AACAGAGGGCACACAAAGTGCTA
Found at i:207398 original size:21 final size:21
Alignment explanation
Indices: 207372--207415 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
207362 CTGTCAATCC
207372 AAATAGCACATCTATATATCT
1 AAATAGCACATCTATATATCT
*
207393 AAATAGCACATCTATATCTCT
1 AAATAGCACATCTATATATCT
207414 AA
1 AA
207416 CTTCTAGAAG
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:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
AAATAGCACATCTATATATCT
Found at i:209161 original size:11 final size:10
Alignment explanation
Indices: 209132--209165 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
209122 TTGTTATACT
209132 TTTTAAATAA
1 TTTTAAATAA
209142 -TTTAAATAA
1 TTTTAAATAA
209151 TTTTAAAATAA
1 TTTT-AAATAA
209162 TTTT
1 TTTT
209166 TTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 3 0.14
11 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:209752 original size:19 final size:17
Alignment explanation
Indices: 209724--209766 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
209714 AATTACAAAA
209724 AAAATTAAAATAATTATT
1 AAAATTAAAATAATTA-T
*
209742 AAAATTCAAAATATTTAT
1 AAAATT-AAAATAATTAT
209760 AAAATTA
1 AAAATTA
209767 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTAAAATAATTAT
Found at i:212913 original size:23 final size:24
Alignment explanation
Indices: 212878--212922 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
212868 TTAATAGTTT
* *
212878 AAATAATAGTATAGA-TATAAACA
1 AAATAAAAATATAGATTATAAACA
*
212901 AAATAAAAATATATATTATAAA
1 AAATAAAAATATAGATTATAAA
212923 GTAGAAAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATAAAAATATAGATTATAAACA
Found at i:213367 original size:16 final size:16
Alignment explanation
Indices: 213346--213376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
213336 ATATGAATAT
*
213346 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
213362 TATTTAATATTAAAA
1 TATTTAATATTAAAA
213377 TAATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:214594 original size:64 final size:64
Alignment explanation
Indices: 214493--214618 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
214483 AAAACCAGAG
*
214493 GCAATGAATCTGGATAATAATATTAAAAAAGAAAAAAAGTGTCCATCATAAATATATATTCCAA
1 GCAATGAATCTGGATAATAATATTAAAAAAGAAAAAAAGTATCCATCATAAATATATATTCCAA
214557 GCAATGAATCTGGATAATAATATTAAAAAAGAAAAAAAGTATCCATCATAAATATATATTCC
1 GCAATGAATCTGGATAATAATATTAAAAAAGAAAAAAAGTATCCATCATAAATATATATTCC
214619 CTCATTATGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (64 bp):
GCAATGAATCTGGATAATAATATTAAAAAAGAAAAAAAGTATCCATCATAAATATATATTCCAA
Found at i:218048 original size:28 final size:28
Alignment explanation
Indices: 218017--218077 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
218007 AAAATGAGAC
* * *
218017 TTTGGATACCCGGGGGTAAAATGGTAAT
1 TTTGGACACCCGAGGGCAAAATGGTAAT
*
218045 TTTGGACACTCGAGGGCAAAATGGTAAT
1 TTTGGACACCCGAGGGCAAAATGGTAAT
218073 TTTGG
1 TTTGG
218078 GAAACTTTGG
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:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (28 bp):
TTTGGACACCCGAGGGCAAAATGGTAAT
Found at i:218133 original size:28 final size:27
Alignment explanation
Indices: 218102--218193 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 27
218092 AAAAAAATGG
218102 AATTTTAGACATTCGGGGGTAAAACGGT
1 AATTTTAGACA-TCGGGGGTAAAACGGT
* * *
218130 AATTTTTAGAAAATC-GGGATCAAAAACGGA
1 AA-TTTTAG-ACATCGGGGGT--AAAACGGT
* * *
218160 AATTTTGGACATCTGGGAGTAAAATGGT
1 AATTTTAGACATC-GGGGGTAAAACGGT
218188 AATTTT
1 AATTTT
218194 TGAATGCTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 22 0.45
29 13 0.27
30 14 0.29
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (27 bp):
AATTTTAGACATCGGGGGTAAAACGGT
Found at i:218224 original size:30 final size:29
Alignment explanation
Indices: 218180--218253 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 29
218170 ATCTGGGAGT
218180 AAAATGGTAATTTTT-GAATGCTTCGAGG-TAA
1 AAAATGG-AATTTTTGGAA-G-TTCGAGGAT-A
218211 AAAATGGAATTTTTGGAAGTTCGAGGATA
1 AAAATGGAATTTTTGGAAGTTCGAGGATA
218240 AAAATGGAATTTTT
1 AAAATGGAATTTTT
218254 TAAAATTTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
29 22 0.54
30 9 0.22
31 10 0.24
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGATA
Found at i:218264 original size:30 final size:29
Alignment explanation
Indices: 218201--218283 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
218191 TTTTGAATGC
**
218201 TTCGAGGTAAAAAATGGAA-TTTTTGGAAG
1 TTCGAGGT-AAAAATGGAATTTTTTAAAAG
*
218230 TTCGAGGATAAAAATGGAATTTTTTAAAAT
1 TTCGAGG-TAAAAATGGAATTTTTTAAAAG
* *
218260 TTCGAGGGT-TAAATGGTATTTTTT
1 TTCGA-GGTAAAAATGGAATTTTTT
218284 GGTGAAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
29 30 0.65
30 14 0.30
31 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.39
Consensus pattern (29 bp):
TTCGAGGTAAAAATGGAATTTTTTAAAAG
Found at i:218344 original size:61 final size:60
Alignment explanation
Indices: 218239--218521 Score: 317
Period size: 60 Copynumber: 4.8 Consensus size: 60
218229 GTTCGAGGAT
** * * * *
218239 AAAAATGGAATTTTTTAAAATTTCGAGGGTTAAATGGTATTTTTTGGTGAAATCAAGGTC
1 AAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTC
** * * * **
218299 AAAAATAAAATTTTGGAAAGTTCGAGAGGGTAAAATGATAATTTTTAGTGAAATCGGGGTC
1 AAAAATGGAATTTTGGAAAGTT-TAGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTC
* *
218360 AAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTTTTGGTGAAA-CTGAGGTC
1 AAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGGTAATTTTTGGTGAAATC-AAGGTC
* * *
218420 AAAAATGGAATTTTAGAAAATTTAG-GGGTAAAATGGTAA-TTTTGGTTAAATCAAGGGTC
1 AAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGGTAATTTTTGGTGAAATCAA-GGTC
*
218479 -AAAATGGAATTTTGGAAAG-TTCGAGGGTAAAAAT-GTAATTTTT
1 AAAAATGGAATTTTGGAAAGTTTAGAGGGT-AAAATGGTAATTTTT
218522 AGAAAGTTTG
Statistics
Matches: 189, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.02
58 36 0.19
59 29 0.15
60 71 0.38
61 50 0.26
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (60 bp):
AAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTC
Found at i:218373 original size:121 final size:119
Alignment explanation
Indices: 218239--218521 Score: 315
Period size: 121 Copynumber: 2.4 Consensus size: 119
218229 GTTCGAGGAT
** * * *
218239 AAAAATGGAATTTTTTAAAATTTCGAGGGTTAAATGGTATTTTTTGGTGAAA-TCAAGGTCAAAA
1 AAAAATGGAATTTTGGAAAATTTAGAGGGTAAAATGGTAATTTTTGGTGAAACT-AAGGTCAAAA
* * *
218303 ATAAAATTTTGGAAAGTTCGAGAGGGTAAAATGATAATTTTTAGTGAAATC-GGGGTC
65 ATAAAATTTTAGAAAATT-GAG-GGGTAAAATGATAA-TTTTAGTGAAATCAAGGGTC
* * *
218360 AAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTTTTGGTGAAACTGAGGTCAAAAA
1 AAAAATGGAATTTTGGAAAATTTAGAGGGTAAAATGGTAATTTTTGGTGAAACTAAGGTCAAAAA
** * * * *
218425 TGGAATTTTAGAAAATTTAGGGGTAAAATGGTAATTTTGGTTAAATCAAGGGTC
66 TAAAATTTTAGAAAATTGAGGGGTAAAATGATAATTTTAGTGAAATCAAGGGTC
* *
218479 -AAAATGGAATTTTGG-AAAGTTCGAGGGTAAAAAT-GTAATTTTT
1 AAAAATGGAATTTTGGAAAATTTAGAGGGT-AAAATGGTAATTTTT
218522 AGAAAGTTTG
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
117 18 0.13
118 31 0.22
119 18 0.13
120 2 0.01
121 68 0.49
122 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (119 bp):
AAAAATGGAATTTTGGAAAATTTAGAGGGTAAAATGGTAATTTTTGGTGAAACTAAGGTCAAAAA
TAAAATTTTAGAAAATTGAGGGGTAAAATGATAATTTTAGTGAAATCAAGGGTC
Found at i:218394 original size:29 final size:28
Alignment explanation
Indices: 218361--218530 Score: 96
Period size: 29 Copynumber: 5.8 Consensus size: 28
218351 ATCGGGGTCA
218361 AAAATGGAATTTTGGAAAGTTTAGGGGGT
1 AAAATGGAATTTTGGAAAGTTTA-GGGGT
* * ***
218390 AAAATGGTAATTTTTGGTGAAA-CTGAGGTCA
1 AAAATGG-AA-TTTT-G-GAAAGTTTAGGGGT
* *
218421 AAAATGGAATTTTAGAAAATTTAGGGGT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT
* *
218449 AAAATGGTAATTTTGGTTAAA--TCAAGGGT
1 AAAATGG-AATTTTGG--AAAGTTTAGGGGT
*
218478 CAAAATGGAATTTTGGAAAG-TTCGAGGGT
1 -AAAATGGAATTTTGGAAAGTTTAG-GGGT
* *
218507 AAAAATGTAATTTTTAGAAAGTTT
1 -AAAATGGAA-TTTTGGAAAGTTT
218531 GAGGTTGAAA
Statistics
Matches: 108, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
27 7 0.06
28 12 0.11
29 44 0.41
30 20 0.19
31 18 0.17
32 3 0.03
33 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:225850 original size:24 final size:24
Alignment explanation
Indices: 225818--225870 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
225808 AAAAATAAAT
* *
225818 TTATTATATTAAAA-AGTTATTATA
1 TTATAATATTAAAATAGTTAAT-TA
225842 TTATAATATTAAAATAGTTAATTA
1 TTATAATATTAAAATAGTTAATTA
225866 TTATA
1 TTATA
225871 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTATAATATTAAAATAGTTAATTA
Found at i:225878 original size:14 final size:14
Alignment explanation
Indices: 225859--225902 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
225849 ATTAAAATAG
*
225859 TTAATTATTATATT
1 TTAATTATAATATT
225873 TTAATTAATAAATATT
1 TTAATT-AT-AATATT
*
225889 TTAAATATAATATT
1 TTAATTATAATATT
225903 AACAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.46
15 4 0.15
16 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTATAATATT
Found at i:225973 original size:33 final size:32
Alignment explanation
Indices: 225915--225977 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
225905 CAAATATTTT
*
225915 ATTTATATGTATATAAATTACAATAATATAAC
1 ATTTATATGAATATAAATTACAATAATATAAC
*
225947 ATTTAATATGAATAATATATTA-AATAATATA
1 ATTT-ATATGAAT-ATAAATTACAATAATATA
225978 GTTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 16 0.59
34 7 0.26
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (32 bp):
ATTTATATGAATATAAATTACAATAATATAAC
Found at i:231342 original size:20 final size:21
Alignment explanation
Indices: 231317--231356 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
231307 ATTGGGTACT
231317 TATATT-TAATAAAAGTAAAA
1 TATATTATAATAAAAGTAAAA
*
231337 TATATTGATACTAAAAGTAA
1 TATATT-ATAATAAAAGTAA
231357 CAGTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
TATATTATAATAAAAGTAAAA
Found at i:232108 original size:3 final size:3
Alignment explanation
Indices: 232100--232141 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
232090 CAAGAACCCA
* * *
232100 AAG AAG AAG GAG AAG GAG AAG AGG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
232142 GTGAGTGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:239078 original size:8 final size:8
Alignment explanation
Indices: 239067--239094 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
239057 TATTTGAAAA
239067 TTTATATT
1 TTTATATT
239075 TTTATATT
1 TTTATATT
239083 TTTATATT
1 TTTATATT
239091 TTTA
1 TTTA
239095 ACTAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTATATT
Found at i:239172 original size:20 final size:20
Alignment explanation
Indices: 239147--239186 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
239137 TGATTCAAAC
239147 AAAATGAAAAATAAAATAGA
1 AAAATGAAAAATAAAATAGA
**
239167 AAAATGGTAAATAAAATAGA
1 AAAATGAAAAATAAAATAGA
239187 TTTATGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
AAAATGAAAAATAAAATAGA
Found at i:240254 original size:14 final size:14
Alignment explanation
Indices: 240235--240271 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
240225 ACGCCAATAT
*
240235 AATTATAATTTACA
1 AATTATAAATTACA
*
240249 AATTATAAATTAGA
1 AATTATAAATTACA
240263 AATTATAAA
1 AATTATAAA
240272 AAATTAATAA
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:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (14 bp):
AATTATAAATTACA
Found at i:250784 original size:23 final size:24
Alignment explanation
Indices: 250758--250805 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
250748 ATTAAGACTG
* *
250758 AAATTACCTTTTAT-ATTTATATT
1 AAATTACATTTTATAATTTAAATT
250781 AAATTACATTTTATAATTTAAATT
1 AAATTACATTTTATAATTTAAATT
250805 A
1 A
250806 TTTTATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATTACATTTTATAATTTAAATT
Found at i:250869 original size:23 final size:22
Alignment explanation
Indices: 250843--250889 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
250833 TTTGTGTTCG
250843 AATATATCAATTATATAAAATAA
1 AATATATCAATTA-ATAAAATAA
* * *
250866 AATATATTATTTAATAAATTAA
1 AATATATCAATTAATAAAATAA
250888 AA
1 AA
250890 AAATAAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATATCAATTAATAAAATAA
Found at i:251086 original size:31 final size:31
Alignment explanation
Indices: 251038--251122 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 31
251028 CTATTAAACT
* *
251038 TATACATAAATTATGATTTAATCTGTAATTG
1 TATACATGAATTTTGATTTAATCTGTAATTG
* *
251069 TATACATGAATTTTGATTT--TTTGTAATTT
1 TATACATGAATTTTGATTTAATCTGTAATTG
*
251098 TATACATGAATTTTTGGTTTAATCT
1 TATACATGAA-TTTTGATTTAATCT
251123 AATTCTTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 18 0.40
30 8 0.18
31 17 0.38
32 2 0.04
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.52
Consensus pattern (31 bp):
TATACATGAATTTTGATTTAATCTGTAATTG
Found at i:253259 original size:28 final size:30
Alignment explanation
Indices: 253227--253295 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
253217 TTATATAATT
* *
253227 TTATTTTAGAAGA-TTAAATTA-AATTTTA
1 TTATTTTAAAAGAGTTAAAATATAATTTTA
253255 TTATTTTTAAAAGAGTTAAAATATAATTTTA
1 TTA-TTTTAAAAGAGTTAAAATATAATTTTA
253286 TTATTATTAA
1 TTATT-TTAA
253296 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 3 0.09
29 9 0.26
30 9 0.26
31 14 0.40
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (30 bp):
TTATTTTAAAAGAGTTAAAATATAATTTTA
Found at i:255455 original size:83 final size:83
Alignment explanation
Indices: 255219--255795 Score: 547
Period size: 83 Copynumber: 7.0 Consensus size: 83
255209 ACCTTCATAT
* * * * *
255219 ACAAGGAAACGTTGTTGGAAATTTCTTAAAAA-GTGTTTACCAAATGAGACT-ATAAGAATATGT
1 ACAAGAAAATGTTATTGGAAAATTC-TAAAAATGTGTTTACTAAATGAGACTGA-AAGAATATGT
*** **
255282 ATTATTAGATTAAAAAATAA
64 ACCGTTAGATTAAAAAGCAA
* * * * * * * * * *
255302 ATAAGGAAATATTATTAGAAAATT-TTAAAATGTGTTTATTAAATAAGACGGGAAGGATATGTAC
1 ACAAGAAAATGTTATTGGAAAATTCTAAAAATGTGTTTACTAAATGAGACTGAAAGAATATGTAC
**
255366 CGTTAGATTAAAAAATAA
66 CGTTAGATTAAAAAGCAA
* * * *
255384 ATAAGAAAATGTAATTGGAAAATTCTAAAAATGAGTTTACTAAACGAGACTGAAAGAATATGTAC
1 ACAAGAAAATGTTATTGGAAAATTCTAAAAATGTGTTTACTAAATGAGACTGAAAGAATATGTAC
*
255449 CATTAGATTAAAAAGCAA
66 CGTTAGATTAAAAAGCAA
* * * *
255467 ACAAGGAAATGTTATTTGAAAATTCTAAAAATGTGTTTACTAAACGAGGCTGAAAGAATATGTAC
1 ACAAGAAAATGTTATTGGAAAATTCTAAAAATGTGTTTACTAAATGAGACTGAAAGAATATGTAC
255532 CGTTAGATTAAAAAGCAA
66 CGTTAGATTAAAAAGCAA
* * * *
255550 ACAAGAAAATGTTATT-GAAAATTTCTAAAAATGTGCTTATTAAATGAGACTTAAAGAACATGTA
1 ACAAGAAAATGTTATTGGAAAA-TTCTAAAAATGTGTTTACTAAATGAGACTGAAAGAATATGTA
* *
255614 CCGTTAAATTAAAAAGTAA
65 CCGTTAGATTAAAAAGCAA
* * * * * * ** *
255633 ATAAAAAAATATTATAGAAAAATTCTAAAAATGTGCTTACTAAAT-ATGGTTGAGAGAATATGTA
1 ACAAGAAAATGTTATTGGAAAATTCTAAAAATGTGTTTACTAAATGA-GACTGAAAGAATATGTA
* *
255697 -TGTTAGAGTAAAAAGCAA
65 CCGTTAGATTAAAAAGCAA
** ** * * *
255715 ACAAGAAAATGTTATT-GAAAATTTCTAAAAACATGCCTACTAAATGAAACTAAAAAGAATATAT
1 ACAAGAAAATGTTATTGGAAAA-TTCTAAAAATGTGTTTACTAAATGAGACT-GAAAGAATATGT
*
255779 ACCGTTAAATTAAAAAG
64 ACCGTTAGATTAAAAAG
255796 TAATGTGATC
Statistics
Matches: 405, Mismatches: 79, Indels: 19
0.81 0.16 0.04
Matches are distributed among these distances:
81 9 0.02
82 114 0.28
83 266 0.66
84 16 0.04
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.29
Consensus pattern (83 bp):
ACAAGAAAATGTTATTGGAAAATTCTAAAAATGTGTTTACTAAATGAGACTGAAAGAATATGTAC
CGTTAGATTAAAAAGCAA
Found at i:255578 original size:166 final size:164
Alignment explanation
Indices: 255219--255798 Score: 612
Period size: 166 Copynumber: 3.5 Consensus size: 164
255209 ACCTTCATAT
* * * * *
255219 ACAAGGAAACGTTGTTGGAAATTTCTTAAAAA-GTGTTTACCAAATGAGACTATAAGAATATGTA
1 ACAAGAAAATGTTATTGAAAATTTC-TAAAAATGTGTTTACTAAATGAGACTA-AAGAATATGTA
** * * *
255283 TTATTAGATTAAAAAATAAATAAGGAAATATTATTAGAAAATT-TTAAAATGTGTTTATTAAATA
64 CCATTAGATTAAAAAGTAAATAAGGAAATATTATTAGAAAATTCTAAAAATGTGTTTACTAAA-A
* * * * **
255347 AGACGGGAAGGATATGTACCGTTAGATTAAAAAATAA
128 AGGCTGAAAGAATATGTACCGTTAGATTAAAAAGCAA
* * * *
255384 ATAAGAAAATGTAATTGGAAAA-TTCTAAAAATGAGTTTACTAAACGAGACTGAAAGAATATGTA
1 ACAAGAAAATGTTATT-GAAAATTTCTAAAAATGTGTTTACTAAATGAGACT-AAAGAATATGTA
* * * * *
255448 CCATTAGATTAAAAAGCAAACAAGGAAATGTTATTTGAAAATTCTAAAAATGTGTTTACTAAACG
64 CCATTAGATTAAAAAGTAAATAAGGAAATATTATTAGAAAATTCTAAAAATGTGTTTACTAAA-A
255513 AGGCTGAAAGAATATGTACCGTTAGATTAAAAAGCAA
128 AGGCTGAAAGAATATGTACCGTTAGATTAAAAAGCAA
* * *
255550 ACAAGAAAATGTTATTGAAAATTTCTAAAAATGTGCTTATTAAATGAGACTTAAAGAACATGTAC
1 ACAAGAAAATGTTATTGAAAATTTCTAAAAATGTGTTTACTAAATGAGAC-TAAAGAATATGTAC
* * ** *
255615 CGTTAAATTAAAAAGTAAATAAAAAAATATTA-TAGAAAAATTCTAAAAATGTGCTTACTAAATA
65 CATTAGATTAAAAAGTAAATAAGGAAATATTATTAG-AAAATTCTAAAAATGTGTTTACTAAA-A
* * * * *
255679 TGGTTGAGAGAATATGTA-TGTTAGAGTAAAAAGCAA
128 AGGCTGAAAGAATATGTACCGTTAGATTAAAAAGCAA
** ** * *
255715 ACAAGAAAATGTTATTGAAAATTTCTAAAAACATGCCTACTAAATGAAACTAAAAAGAATATATA
1 ACAAGAAAATGTTATTGAAAATTTCTAAAAATGTGTTTACTAAATGAGACT--AAAGAATATGTA
* *
255780 CCGTTAAATTAAAAAGTAA
64 CCATTAGATTAAAAAGTAA
255799 TGTGATCCAA
Statistics
Matches: 350, Mismatches: 56, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
164 7 0.02
165 145 0.41
166 197 0.56
167 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.29
Consensus pattern (164 bp):
ACAAGAAAATGTTATTGAAAATTTCTAAAAATGTGTTTACTAAATGAGACTAAAGAATATGTACC
ATTAGATTAAAAAGTAAATAAGGAAATATTATTAGAAAATTCTAAAAATGTGTTTACTAAAAAGG
CTGAAAGAATATGTACCGTTAGATTAAAAAGCAA
Found at i:255974 original size:28 final size:28
Alignment explanation
Indices: 255919--255974 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
255909 TAGATTAATA
*
255919 CAATACATAATAAAATTGTAATTATTAT
1 CAATACATAATAAAATTATAATTATTAT
* *
255947 CAATACATTCATATAATTATAATT-TTAT
1 CAATACA-TAATAAAATTATAATTATTAT
255975 AAGAGATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (28 bp):
CAATACATAATAAAATTATAATTATTAT
Found at i:257127 original size:30 final size:29
Alignment explanation
Indices: 257052--257340 Score: 252
Period size: 30 Copynumber: 9.8 Consensus size: 29
257042 TGTTGGGTCA
*
257052 AAAATGGAA-TTTTGGAAGTTTAG-GGGT
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT
* * *
257079 AAAATAGTATTTTTTTTGAGAGTTTCGA-GGT
1 AAAAT-GGA-ATTTTTGGA-AGTTTCGAGGGT
* *
257110 CAAAGATGGAATTTTT-GAAGATTCGGGGGT
1 -AAA-ATGGAATTTTTGGAAGTTTCGAGGGT
* *
257140 AATATGGTAATTTTTGGAAGTTTCGAGGTT
1 AAAATGG-AATTTTTGGAAGTTTCGAGGGT
**
257170 AAAATCGGGTTTTTTGGAAGTTT-GAGGGT
1 AAAAT-GGAATTTTTGGAAGTTTCGAGGGT
*
257199 AAAATGGTAATTTTTGGAAGTTTCGAGGTT
1 AAAATGG-AATTTTTGGAAGTTTCGAGGGT
257229 AAAATCGGAATTTTTGGAAG-TTCGAGGGT
1 AAAAT-GGAATTTTTGGAAGTTTCGAGGGT
* *
257258 AAAATGGTAATTTTTGAAAGTTTC-ATGGT
1 AAAATGG-AATTTTTGGAAGTTTCGAGGGT
* *
257287 CAAAATCGGGATTTTTTGAAG-TTCGAGGGT
1 -AAAAT-GGAATTTTTGGAAGTTTCGAGGGT
*
257317 AAAAATGTAATTTTTGGATAGTTT
1 -AAAATGGAATTTTTGGA-AGTTT
257341 AGGGACTTTT
Statistics
Matches: 211, Mismatches: 30, Indels: 38
0.76 0.11 0.14
Matches are distributed among these distances:
27 5 0.02
28 10 0.05
29 78 0.37
30 89 0.42
31 22 0.10
32 5 0.02
33 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGT
Found at i:257184 original size:59 final size:58
Alignment explanation
Indices: 257017--257340 Score: 320
Period size: 59 Copynumber: 5.5 Consensus size: 58
257007 GGACATTTGG
* * * * *
257017 GGGTAAAA-GTGTAATTTTTGAAAGTTGTTG-GGTCAAAAAT-GGAATTTTGGAAGTT-TA
1 GGGTAAAATG-GTAATTTTTGGAAGTT-TCGAGGTC-AAAATCGGATTTTTTGAAGTTCGA
* * * * *
257074 GGGGTAAAATAGTATTTTTTTTGAGAGTTTCGAGGTCAAAGAT-GGAATTTTTGAAGATTCGG
1 -GGGTAAAATGGTA-ATTTTTGGA-AGTTTCGAGGTCAAA-ATCGGATTTTTTGAAG-TTCGA
* * * *
257136 GGGTAATATGGTAATTTTTGGAAGTTTCGAGGTTAAAATCGGGTTTTTTGGAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAATCGGATTTTTT-GAAGTTCGA
* *
257195 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAATCGGAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAATCGG-ATTTTTTGAAGTTCGA
*
257254 GGGTAAAATGGTAATTTTTGAAAGTTTC-ATGGTCAAAATCGGGATTTTTTGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGA-GGTCAAAATC-GGATTTTTTGAAGTTCGA
257313 GGGTAAAAAT-GTAATTTTTGGATAGTTT
1 GGGT-AAAATGGTAATTTTTGGA-AGTTT
257341 AGGGACTTTT
Statistics
Matches: 227, Mismatches: 25, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
58 14 0.06
59 150 0.66
60 50 0.22
61 13 0.06
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAATCGGATTTTTTGAAGTTCGA
Found at i:257258 original size:118 final size:119
Alignment explanation
Indices: 256999--257340 Score: 359
Period size: 118 Copynumber: 2.9 Consensus size: 119
256989 GATCAAAACA
* * * *
256999 GAATTTTTGGACATTTGGGGGTAAAA-GTGTAATTTTTGAAAGTTGT--TGGGTCAAAAAT--GG
1 GAATTTTTGAAGATTCGAGGGTAAAATG-GTAATTTTTGAAAGTT-TCAT-GGTC-AAAATCGGG
* * *
257059 A-ATTTTGGAAGTTT-AGGGGTAAAATAGTATTTTTTTTGAGAGTTTCGAGGTCAAAGATG
62 ATTTTTTGGAAGTTTGA-GGGTAAAAT-GTA-ATTTTTGGAGAGTTTCGAGGTCAAAGATG
* * * *
257118 GAATTTTTGAAGATTCGGGGGTAATATGGTAATTTTTGGAAGTTTCGA-GGTTAAAATCGGG-TT
1 GAATTTTTGAAGATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTC-ATGGTCAAAATCGGGATT
*
257181 TTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGA-AGTTTCGAGGTTAAA-ATCG
65 TTTTGGAAGTTTGAGGGTAAAAT-GTAATTTTTGGAGAGTTTCGAGGTCAAAGAT-G
257236 GAATTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCATGGTCAAAATCGGGATT
1 GAATTTTT-GAAGATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCATGGTCAAAATCGGGATT
* *
257300 TTTT-GAAGTTCGAGGGTAAAAATGTAATTTTTGGATAGTTT
65 TTTTGGAAGTTTGAGGGT-AAAATGTAATTTTTGGAGAGTTT
257341 AGGGACTTTT
Statistics
Matches: 193, Mismatches: 16, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
117 3 0.02
118 95 0.49
119 67 0.35
120 27 0.14
121 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (119 bp):
GAATTTTTGAAGATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCATGGTCAAAATCGGGATTT
TTTGGAAGTTTGAGGGTAAAATGTAATTTTTGGAGAGTTTCGAGGTCAAAGATG
Found at i:258459 original size:3 final size:3
Alignment explanation
Indices: 258440--258478 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
258430 TTAATACTAT
* *
258440 TTA TTA CTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
258479 ACCATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:268352 original size:26 final size:28
Alignment explanation
Indices: 268323--268383 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
268313 ATAATTTTGA
268323 TTTAATAT-GT-AATTATATACAT-AAAT
1 TTTAATATGGTCAA-TATATACATAAAAT
*
268349 TTTAATTTGGTGCAATATATACATAAAAT
1 TTTAATATGGT-CAATATATACATAAAAT
268378 TTTAAT
1 TTTAAT
268384 TGTGATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.23
27 2 0.07
28 9 0.30
29 12 0.40
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTAATATGGTCAATATATACATAAAAT
Found at i:268413 original size:32 final size:29
Alignment explanation
Indices: 268336--268422 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 29
268326 AATATGTAAT
* *
268336 TATATACAT-AAATTTTAATTTGGTGCAA
1 TATATACATAAAATTTTAATTTGATTCAA
268364 TATATACATAAAATTTTAATTGTGATTCAA
1 TATATACATAAAATTTTAATT-TGATTCAA
* *
268394 TTGTATACTTAGAAATTTTAATTTTGATT
1 -TATATACATA-AAATTTTAA-TTTGATT
268423 TAATCATACG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.18
29 11 0.22
30 6 0.12
31 8 0.16
32 14 0.28
33 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (29 bp):
TATATACATAAAATTTTAATTTGATTCAA
Found at i:271002 original size:195 final size:195
Alignment explanation
Indices: 270661--271047 Score: 720
Period size: 195 Copynumber: 2.0 Consensus size: 195
270651 CAAACTAGTG
*
270661 ATGGTTTGAAGAATACATGTTCCGATGTAAACATAGAAAAAAATGGCTTAATGGAAAAAACATCT
1 ATGGTTTGAAGAATACATGTTCCGATGTAAACATAGAAAAAAATGGCATAATGGAAAAAACATCT
*
270726 GGGTCTGATGTTGTAGAGTTGATATCTCCTGGTGAGGAAGAATCCTTTGGAGCTTCATTGGTGAA
66 GGGTCTGATGTTGTAGAGTTGATATCTCCTAGTGAGGAAGAATCCTTTGGAGCTTCATTGGTGAA
* *
270791 TGAAAGTATGGATTGTAAAGATAAAAATACATGTGCGGTTGTGAGTTAAGTTTCTCATACTAGCA
131 TGAAAGTATCGATTGTAAAGATAAAAATACATGTGCGGTTGTGAGTGAAGTTTCTCATACTAGCA
270856 ATGGTTTGAAGAATACATGTTCCGATGTAAACATAGAAAAAAATGGCATAATGGAAAAAACATCT
1 ATGGTTTGAAGAATACATGTTCCGATGTAAACATAGAAAAAAATGGCATAATGGAAAAAACATCT
270921 GGGTCTGATGTTGTAGAGTTGATATCTCCTAGTGAGGAAGAATCCTTTGGAGCTTCATTGGTGAA
66 GGGTCTGATGTTGTAGAGTTGATATCTCCTAGTGAGGAAGAATCCTTTGGAGCTTCATTGGTGAA
* *
270986 TGAATGTATCGATTGTAAAGATAAAAATACATGTGCGGTTGTGGGTGAAGTTTCTCATACTA
131 TGAAAGTATCGATTGTAAAGATAAAAATACATGTGCGGTTGTGAGTGAAGTTTCTCATACTA
271048 TTTCAGTGCA
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 186 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (195 bp):
ATGGTTTGAAGAATACATGTTCCGATGTAAACATAGAAAAAAATGGCATAATGGAAAAAACATCT
GGGTCTGATGTTGTAGAGTTGATATCTCCTAGTGAGGAAGAATCCTTTGGAGCTTCATTGGTGAA
TGAAAGTATCGATTGTAAAGATAAAAATACATGTGCGGTTGTGAGTGAAGTTTCTCATACTAGCA
Found at i:272416 original size:2 final size:2
Alignment explanation
Indices: 272404--272443 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
272394 ATACAAGGTT
* * *
272404 TC TC TC CC TC TC TA TC TC TG TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
272444 ACACACACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.47, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:279339 original size:31 final size:31
Alignment explanation
Indices: 279302--279369 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
279292 AGACGTAAAG
*
279302 TTTATTATTTA-ATGAT-ATTTTAATAATTTT
1 TTTATTATTGATAT-ATAATTTTAATAATTTT
*
279332 TTATATTATTGATATATAATTTTGATAATTTT
1 TT-TATTATTGATATATAATTTTAATAATTTT
279364 TTTATT
1 TTTATT
279370 TGAATTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 14 0.42
32 17 0.52
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (31 bp):
TTTATTATTGATATATAATTTTAATAATTTT
Found at i:280182 original size:28 final size:29
Alignment explanation
Indices: 280151--280206 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
280141 TTATTTAAGT
* *
280151 ATTTTATATAAAATTCTT-CAAAAAGAAC
1 ATTTTATATAAAAATATTACAAAAAGAAC
280179 ATTTTATATAAAAATATTACAAAAAGAA
1 ATTTTATATAAAAATATTACAAAAAGAA
280207 AAATCTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTTTATATAAAAATATTACAAAAAGAAC
Found at i:280215 original size:29 final size:28
Alignment explanation
Indices: 280155--280216 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
280145 TTAAGTATTT
* * * * *
280155 TATATAAAATTCTTCAAAAAGAACATTT
1 TATATAAAAATATTCAAAAAGAAAAATC
280183 TATATAAAAATATTACAAAAAGAAAAATC
1 TATATAAAAATATT-CAAAAAGAAAAATC
280212 TATAT
1 TATAT
280217 TAATATTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.32
Consensus pattern (28 bp):
TATATAAAAATATTCAAAAAGAAAAATC
Found at i:286417 original size:30 final size:31
Alignment explanation
Indices: 286383--286441 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
286373 TAGCTCGATT
286383 ATGTTAATATTTCATAAT-AAAATTATATTA
1 ATGTTAATATTTCATAATAAAAATTATATTA
286413 ATGTTAATATTTCATAATAAAAATTATAT
1 ATGTTAATATTTCATAATAAAAATTATAT
286442 AAAATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
ATGTTAATATTTCATAATAAAAATTATATTA
Found at i:292017 original size:174 final size:173
Alignment explanation
Indices: 291686--292339 Score: 695
Period size: 174 Copynumber: 3.7 Consensus size: 173
291676 GGTTCGCATT
* * ** * * * * *
291686 TAGGATTCACATGTGAGGTGTTTGCATCCTTTCGTGAGCTCGCA-CGGAGTGGGTTCGCACCATC
1 TAGGATTCGCACGTGAGGTGTTCACATCTTTTCATGAGCTCGCATGGGA-TGGGTTCGCACTACC
* * * * * * * * * * * *
291750 ATGCACGCAAATCCACATGTAGAAAATACGTATTAATCCTAAAA-TA-GAATATGTGTTAGCACG
65 ATACACGAAAACCCACATGTAGAAAACACATGTTAATCCTAAAACAAGGTACATGT-TGA-TATG
* * * *
291813 CATGGGGACCTACCTATGACGTCGCATCATCTAGGAATCGTATCATA
128 CAT-GGAACCTACTTATGATGTCACATCATCTAGGAATCGTATCATA
* * * * *
291860 TAAGATTCGCACGTGAGGTGTTCACATCCTTTCATGAGCTCACATGGGGTGGGTTTGCACTACCA
1 TAGGATTCGCACGTGAGGTGTTCACATCTTTTCATGAGCTCGCATGGGATGGGTTCGCACTACCA
* * * * *
291925 TACATGAAAACCTACATGTAGAAAACACGTGTTAATCCTAGAACAGGGTACATGTTGATATGCAT
66 TACACGAAAACCCACATGTAGAAAACACATGTTAATCCTAAAACAAGGTACATGTTGATATGCAT
* *
291990 GGAAACCTATTTATGATGTCACATCATCTAGGAACCGTATCATA
131 GG-AACCTACTTATGATGTCACATCATCTAGGAATCGTATCATA
* * * *
292034 TAGGATTCGCACGTGAAGTGTTCACATCTTTTCATGAGCTTGCATGGGTTGGGTTCACACTACCA
1 TAGGATTCGCACGTGAGGTGTTCACATCTTTTCATGAGCTCGCATGGGATGGGTTCGCACTACCA
*
292099 TACACGAAAACCCACATGTAGAAATCACATGTTAATCCTAAAACAAGGTACATGTTGATATGCAT
66 TACACGAAAACCCACATGTAGAAAACACATGTTAATCCTAAAACAAGGTACATGTTGATATGCAT
*
292164 GGAACCTACTTACGATGTCACATCATCTAGGAATCGTATCATA
131 GGAACCTACTTATGATGTCACATCATCTAGGAATCGTATCATA
*
292207 TAGGATTCGCATGTGAGGTGTTCACATCTTTTCATGAGCTCGCACT-GGATGGGTTCGCACTACT
1 TAGGATTCGCACGTGAGGTGTTCACATCTTTTCATGAGCTCGCA-TGGGATGGGTTCGCACTAC-
* * * * * ** * * * *
292271 ATGCATGCATGTAAATCCACAAGTAGAAAACACATGTTAATTTTAGAATAAGATACGTGTTGATA
64 ---CATACACGAAAACCCACATGTAGAAAACACATGTTAATCCTAAAACAAGGTACATGTTGATA
292336 TGCA
126 TGCA
292340 AAATTACCTA
Statistics
Matches: 404, Mismatches: 67, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
173 96 0.24
174 244 0.60
175 4 0.01
176 6 0.01
177 54 0.13
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (173 bp):
TAGGATTCGCACGTGAGGTGTTCACATCTTTTCATGAGCTCGCATGGGATGGGTTCGCACTACCA
TACACGAAAACCCACATGTAGAAAACACATGTTAATCCTAAAACAAGGTACATGTTGATATGCAT
GGAACCTACTTATGATGTCACATCATCTAGGAATCGTATCATA
Found at i:294128 original size:39 final size:39
Alignment explanation
Indices: 294049--294131 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
294039 TCGACACGTA
* ** *
294049 TAACATGTCACAACCTAATTAATCCATGTCATTCAATTT
1 TAACATGTCAAAACCTAATTAATCCACATCATCCAATTT
* ** *
294088 TAACATGTTAAAACCTAATTGGTCCACATCATCCAGTTT
1 TAACATGTCAAAACCTAATTAATCCACATCATCCAATTT
294127 TAACA
1 TAACA
294132 AAAACAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (39 bp):
TAACATGTCAAAACCTAATTAATCCACATCATCCAATTT
Found at i:298779 original size:22 final size:22
Alignment explanation
Indices: 298752--298797 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
298742 TTTTTAAAAT
298752 TTTTAAAAAT-ATGTATAATTAA
1 TTTTAAAAATAATGTAT-ATTAA
*
298774 TTTTAAAAATAATTTATATTAA
1 TTTTAAAAATAATGTATATTAA
298796 TT
1 TT
298798 ACTTCAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTAAAAATAATGTATATTAA
Found at i:307089 original size:55 final size:57
Alignment explanation
Indices: 306969--307092 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 57
306959 ATGTACTACG
* * *
306969 TAACAATCGATTTAAATATATAAACAATCGATTTAAAAGAAGAAGTATATTTCACCA
1 TAACAATCGATTTAAATATATAAACAATCGATTCAAAAGAAGAAGTATATCTCAACA
* *
307026 TAACAATCGATTTAAATATATAAATAATTGATTCAAAAGAAGCAA-TAT-TCT-AACA
1 TAACAATCGATTTAAATATATAAACAATCGATTCAAAAGAAG-AAGTATATCTCAACA
*
307081 TGACAATCGATT
1 TAACAATCGATT
307093 CAATAAATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
55 14 0.23
56 2 0.03
57 42 0.70
58 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (57 bp):
TAACAATCGATTTAAATATATAAACAATCGATTCAAAAGAAGAAGTATATCTCAACA
Found at i:307605 original size:73 final size:73
Alignment explanation
Indices: 307461--307605 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
307451 CGAAATAGTA
*
307461 TCCGCCTGCAGCAAGGGAAGAACTTCTTGAGGTGGTTCAACCAATAAAACCAGTTGTCCCATCTG
1 TCCGCCTGCAGCAAGGGAAGAACTTCATGAGGTGGTTCAACCAATAAAACCAGTTGTCCCATCTG
*
307526 CGTGTTGC
66 CATGTTGC
307534 TCCGCCTGCAGCAAGGGAAGAACTTCATGAGGTGGTTCAACCAATAAAACCAGTTGTCCC-TACT
1 TCCGCCTGCAGCAAGGGAAGAACTTCATGAGGTGGTTCAACCAATAAAACCAGTTGTCCCAT-CT
307598 GCATGTTG
65 GCATGTTG
307606 TTCCTTTGGC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 1 0.01
73 68 0.99
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (73 bp):
TCCGCCTGCAGCAAGGGAAGAACTTCATGAGGTGGTTCAACCAATAAAACCAGTTGTCCCATCTG
CATGTTGC
Found at i:309877 original size:30 final size:31
Alignment explanation
Indices: 309843--309907 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
309833 AAAGAGATTC
309843 AAAATATCATTT-TCAATTTTAAAGGG-TTAA
1 AAAATAT-ATTTATCAATTTTAAAGGGTTTAA
* **
309873 AAAATATTTTTATCAATTTTTCAGGGTTTAA
1 AAAATATATTTATCAATTTTAAAGGGTTTAA
309904 AAAA
1 AAAA
309908 ATTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 19 0.63
31 8 0.27
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (31 bp):
AAAATATATTTATCAATTTTAAAGGGTTTAA
Found at i:312509 original size:29 final size:29
Alignment explanation
Indices: 312477--312556 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
312467 AAGATTTAAA
* *
312477 TTTATTATTATAATAATATTTTATATATT
1 TTTATTATTATAATAATATTTAATAAATT
* * *
312506 TTTATAATGA-AAGTTATATTTAATAAATT
1 TTTATTATTATAA-TAATATTTAATAAATT
*
312535 TTTATTATTTAAAATAA-ATTTA
1 TTTATTA-TTATAATAATATTTA
312557 GCTCGGGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
28 2 0.05
29 32 0.80
30 4 0.10
31 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTATTATTATAATAATATTTAATAAATT
Found at i:314998 original size:16 final size:17
Alignment explanation
Indices: 314968--315012 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
314958 GGTTATGGAA
*
314968 GGGAGGGAGAGAGAGAG
1 GGGAAGGAGAGAGAGAG
314985 GGGAAGGAGA-AGAGAG
1 GGGAAGGAGAGAGAGAG
*
315001 GGAAAGGAGAGA
1 GGGAAGGAGAGA
315013 TTGAAGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (17 bp):
GGGAAGGAGAGAGAGAG
Found at i:315846 original size:22 final size:21
Alignment explanation
Indices: 315821--315861 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
315811 TTAAATGGAG
*
315821 AAGTTGACATTTTTACTTTTGT
1 AAGTTGA-ATATTTACTTTTGT
*
315843 AAGTTTAATATTTACTTTT
1 AAGTTGAATATTTACTTTT
315862 TTTTATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (21 bp):
AAGTTGAATATTTACTTTTGT
Found at i:316019 original size:20 final size:20
Alignment explanation
Indices: 315982--316019 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
315972 CCAAAAAATA
*
315982 TAATTATTTTTGTTATAATT
1 TAATTATTTTTGTAATAATT
316002 TAATATATTTTT-TAATAA
1 TAAT-TATTTTTGTAATAA
316020 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTATTTTTGTAATAATT
Found at i:318420 original size:20 final size:20
Alignment explanation
Indices: 318391--318441 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
318381 TACCCTACAC
* *
318391 CCTTATTTTAAATACCAAAA
1 CCTTAATTTAAAAACCAAAA
*
318411 CCTTAATTTAAAAACCTAAA
1 CCTTAATTTAAAAACCAAAA
318431 CC-TAA-TTAAAA
1 CCTTAATTTAAAA
318442 CAAAAACACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 19 0.68
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (20 bp):
CCTTAATTTAAAAACCAAAA
Found at i:320560 original size:17 final size:18
Alignment explanation
Indices: 320538--320586 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
320528 CCATACTCCC
*
320538 TTTAAATTTATTT-TAAA
1 TTTAAATTTATTTAAAAA
*
320555 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTTAAAAA
*
320573 ATTAAATTTATTTA
1 TTTAAATTTATTTA
320587 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTAAATTTATTTAAAAA
Found at i:320605 original size:23 final size:22
Alignment explanation
Indices: 320550--320605 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
320540 TAAATTTATT
*
320550 TTAAATTTAAATTTGTTTAAAAAA
1 TTAAATTT--ATTTATTTAAAAAA
* *
320574 TTAAATTTATTTATTTTAAAAT
1 TTAAATTTATTTATTTAAAAAA
320596 TTAAAGTTTA
1 TTAAA-TTTA
320606 AAATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.57
23 4 0.14
24 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAAATTTATTTATTTAAAAAA
Found at i:321276 original size:18 final size:19
Alignment explanation
Indices: 321242--321283 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
321232 AAAACGTTTC
*
321242 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
321261 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
321279 AATAA
1 AATAA
321284 TACTAATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:321382 original size:7 final size:7
Alignment explanation
Indices: 321357--321395 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
321347 TTGATATTAA
321357 TAATAA-
1 TAATAAT
321363 TAAT-AT
1 TAATAAT
*
321369 TATTAAT
1 TAATAAT
321376 TAATAAT
1 TAATAAT
321383 TAATAAT
1 TAATAAT
321390 TAATAA
1 TAATAA
321396 AAAAGGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 7 0.24
7 21 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Done.