Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005488.1 Hibiscus syriacus cultivar Beakdansim tig00012630_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: 201507
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6886 original size:2 final size:2
Alignment explanation
Indices: 6879--6903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6869 AAACTTATTA
6879 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 A
6904 CATTTTAATT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8368 original size:13 final size:14
Alignment explanation
Indices: 8350--8382 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8340 TTTTTTTTAA
8350 TTAAAAT-ATATTT
1 TTAAAATAATATTT
8363 TTAAAATAATATTT
1 TTAAAATAATATTT
*
8377 CTAAAA
1 TTAAAA
8383 AATGAGAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAATAATATTT
Found at i:9681 original size:2 final size:2
Alignment explanation
Indices: 9674--9704 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9664 TCTAATTTAA
9674 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
9705 ATGCATCCAA
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:11036 original size:20 final size:20
Alignment explanation
Indices: 11013--11059 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
11003 ATGTGAACAA
*
11013 TATCGATACTGGATGATCAG
1 TATCGATACTGGATGATAAG
*
11033 TATCGATATTGGATGATAAG
1 TATCGATACTGGATGATAAG
11053 TATCGAT
1 TATCGAT
11060 TTCTACGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (20 bp):
TATCGATACTGGATGATAAG
Found at i:11969 original size:64 final size:65
Alignment explanation
Indices: 11863--12022 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 65
11853 TTGTTCAGTA
* * ** *
11863 TGCATCGATGCACATGTAATGCATCGATGCA-CCCATTAAAAATGGAAACATCAAATGCAATTAG
1 TGCATCGATGCATATGTAGTGCATCGATGCACCCCATTAAAAATAAAAACATCAAAGGCAATTAG
* * ** *
11927 TGCATCGATGCATAATG-AGTGCATCGATGCACCCCCTT-AAAATAAAAACATCGAAGGTGATTG
1 TGCATCGATGCAT-ATGTAGTGCATCGATGCACCCCATTAAAAATAAAAACATCAAAGGCAATTA
11990 G
65 G
* **
11991 TGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGCATCGATGCATATGTAGTGCATCGATGCAC
12023 ATGTTAAAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 71 0.89
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (65 bp):
TGCATCGATGCATATGTAGTGCATCGATGCACCCCATTAAAAATAAAAACATCAAAGGCAATTAG
Found at i:12037 original size:24 final size:20
Alignment explanation
Indices: 12010--12067 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
12000 GCATGGGTAG
12010 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
12034 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
12054 TGTATCGATGCACT
1 TGCATCGATGCACT
12068 TCAAGGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:13670 original size:23 final size:23
Alignment explanation
Indices: 13619--13683 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
13609 ACAACCTTAT
*
13619 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
* * *
13642 ACGGCACTACGGTGCAATTCTAT
1 ATGGCACTTCGGTGCAATTCTAC
*
13665 GTGGCACTTCGGTGCAATT
1 ATGGCACTTCGGTGCAATT
13684 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:24863 original size:2 final size:2
Alignment explanation
Indices: 24856--24887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24846 AATAATATGA
24856 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
24888 TTGTTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26608 original size:3 final size:3
Alignment explanation
Indices: 26600--26625 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26590 TCCACAACTC
26600 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
26626 AATTACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:27129 original size:11 final size:11
Alignment explanation
Indices: 27113--27139 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27103 AGAACAAAAT
27113 AAAAAAGGAAA
1 AAAAAAGGAAA
27124 AAAAAAGGAAA
1 AAAAAAGGAAA
27135 AAAAA
1 AAAAA
27140 CTTTTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:28493 original size:17 final size:19
Alignment explanation
Indices: 28459--28499 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28449 CTATATAGAT
28459 TATCGATACTACCCCTTG-G
1 TATCGATACTA-CCCTTGAG
28478 TATCGATACT-CCCTTGAG
1 TATCGATACTACCCTTGAG
28496 TATC
1 TATC
28500 AGTACTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 10 0.48
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (19 bp):
TATCGATACTACCCTTGAG
Found at i:30292 original size:21 final size:21
Alignment explanation
Indices: 30266--30311 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
30256 GGGGCCTCAA
*
30266 TATCGATACTGACACCCTGAG
1 TATCGATACTGACACCATGAG
*
30287 TATCGATATTGACACCATGAG
1 TATCGATACTGACACCATGAG
30308 TATC
1 TATC
30312 ATTACTGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (21 bp):
TATCGATACTGACACCATGAG
Found at i:40408 original size:30 final size:30
Alignment explanation
Indices: 40372--40433 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
40362 TAATCACTTG
* *
40372 ATGAAATTTGTTATACAATTAACGAGATTC
1 ATGAAATTTGTTAAACAATTAACGAGAGTC
40402 ATGAAATTTGTTAAACAATTAACGAGAGTC
1 ATGAAATTTGTTAAACAATTAACGAGAGTC
40432 AT
1 AT
40434 ACTTAAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (30 bp):
ATGAAATTTGTTAAACAATTAACGAGAGTC
Found at i:41703 original size:54 final size:54
Alignment explanation
Indices: 41621--41741 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
41611 CTCATAGGGT
*
41621 GTACTGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGTCAAATGG
1 GTACTGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* * *
41675 GTACTGATACTCCTATGCCAATTTTGGCTCTGAGAAAAACAGAATGCCCAATGG
1 GTACTGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* *
41729 GTACCGATGCCCC
1 GTACTGATACCCC
41742 CTTAGAGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (54 bp):
GTACTGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
Found at i:44672 original size:16 final size:16
Alignment explanation
Indices: 44651--44682 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44641 AGTAAGAGGG
*
44651 TTGCCAAAGCTAAAAT
1 TTGCCAAAGATAAAAT
44667 TTGCCAAAGATAAAAT
1 TTGCCAAAGATAAAAT
44683 CTGTTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (16 bp):
TTGCCAAAGATAAAAT
Found at i:47475 original size:21 final size:21
Alignment explanation
Indices: 47449--47521 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 21
47439 TGTGCACCAG
47449 GTATCGATAACCCTTCAATGT
1 GTATCGATAACCCTTCAATGT
* *
47470 GTATCGATACCCTCTTTGAATGT
1 GTATCGATAACC-C-TTCAATGT
* * *
47493 GTATTGAT-ACCCTTCGATGG
1 GTATCGATAACCCTTCAATGT
*
47513 GTACCGATA
1 GTATCGATA
47522 CCCCCTGTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 11 0.28
21 12 0.30
22 3 0.08
23 14 0.35
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (21 bp):
GTATCGATAACCCTTCAATGT
Found at i:47495 original size:23 final size:22
Alignment explanation
Indices: 47449--47505 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
47439 TGTGCACCAG
*
47449 GTATCGATAACC-CTTCAATGT
1 GTATCGATACCCTCTTCAATGT
*
47470 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCCTC-TTCAATGT
*
47493 GTATTGATACCCT
1 GTATCGATACCCT
47506 TCGATGGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
23 19 0.61
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (22 bp):
GTATCGATACCCTCTTCAATGT
Found at i:50108 original size:51 final size:54
Alignment explanation
Indices: 50027--50143 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 54
50017 CTCATAGGGT
* *
50027 GTACCGATACCCCTATGCCAATTTTGGCTCCGAG-AAAA-A-CATGCCAAATGG
1 GTACCGATACCCCTATGCCAATTTTAGCTCCGAGAAAAATAGAATGCCAAATGG
* *
50078 GTACCGATACCCCTATGCCAATTTTAGCTCCTAGAAAAATAGAATGCCCAATGG
1 GTACCGATACCCCTATGCCAATTTTAGCTCCGAGAAAAATAGAATGCCAAATGG
*
50132 GTACTGATACCC
1 GTACCGATACCC
50144 ACTTAGAGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 32 0.55
52 4 0.07
53 1 0.02
54 21 0.36
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (54 bp):
GTACCGATACCCCTATGCCAATTTTAGCTCCGAGAAAAATAGAATGCCAAATGG
Found at i:60503 original size:18 final size:18
Alignment explanation
Indices: 60480--60515 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
60470 AAAATTATGA
*
60480 CCATTTTGATATATTTTG
1 CCATTTTGATAGATTTTG
60498 CCATTTTGATAGATTTTG
1 CCATTTTGATAGATTTTG
60516 TAAGTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (18 bp):
CCATTTTGATAGATTTTG
Found at i:62712 original size:5 final size:5
Alignment explanation
Indices: 62698--62732 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
62688 ATATCAGAAC
62698 CCCCA CCCCCA CCCCA CCCCA CCCCA CCCCA CCCC
1 CCCCA -CCCCA CCCCA CCCCA CCCCA CCCCA CCCC
62733 TTGTGTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:65547 original size:2 final size:2
Alignment explanation
Indices: 65536--65630 Score: 124
Period size: 2 Copynumber: 47.5 Consensus size: 2
65526 TTGAAACAAG
65536 TA TA -A 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 TA
* *
65577 TA TA TA TA TA TA TA TA CTA TA TA GTT TA TA TT TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
65619 TA TA CTA TA TA T
1 TA TA -TA TA TA T
65631 GTTGAGTTAA
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.04
2 75 0.90
3 5 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66743 original size:11 final size:11
Alignment explanation
Indices: 66727--66895 Score: 63
Period size: 11 Copynumber: 15.6 Consensus size: 11
66717 ACTATTGAAC
66727 TATATATAAAT
1 TATATATAAAT
66738 TATATAGT---T
1 TATATA-TAAAT
66747 TATATATAAAT
1 TATATATAAAT
66758 TATATATAAA-
1 TATATATAAAT
* *
66768 -CTATATAATT
1 TATATATAAAT
*
66778 TATATTTATATAT
1 TATA--TATAAAT
*
66791 TATGTAT-AAT
1 TATATATAAAT
*
66801 TATAAAT-AA-
1 TATATATAAAT
**
66810 TATAT-TCTAT
1 TATATATAAAT
66820 GTATAACTATAAAT
1 -TAT-A-TATAAAT
**
66834 TATATAGTTTAT
1 TATATA-TAAAT
*
66846 TA-ATATAAAC
1 TATATATAAAT
*
66856 TATATATAAAC
1 TATATATAAAT
**
66867 TATATAGTTTA-
1 TATATA-TAAAT
*
66878 TATATATATAT
1 TATATATAAAT
66889 TATATAT
1 TATATAT
66896 GGTTTAGTGT
Statistics
Matches: 119, Mismatches: 21, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
8 2 0.02
9 19 0.16
10 16 0.13
11 57 0.48
12 10 0.08
13 12 0.10
14 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TATATATAAAT
Found at i:66761 original size:50 final size:48
Alignment explanation
Indices: 66707--66869 Score: 124
Period size: 50 Copynumber: 3.3 Consensus size: 48
66697 ACTATATAGT
66707 TTATAAATAAACTATTGAACTATATATAAATTATATAGTTTATATATAAA
1 TTATAAATAAACTATT-AA-TATATATAAATTATATAGTTTATATATAAA
* * *
66757 TTATATATAAACTATATAAT-T-TAT-ATTTATATA--TTATGTAT-AA
1 TTATAAATAAACTAT-TAATATATATAAATTATATAGTTTATATATAAA
*
66800 TTATAAATAATA-TATTCTATGTATAACTATAAATTATATAGTTTATTAATATAAA
1 TTATAAATAA-ACTA-T-TA-ATAT-A-TATAAATTATATAGTTTA-T-ATATAAA
* *
66855 CTATATATAAACTAT
1 TTATAAATAAACTAT
66870 ATAGTTTATA
Statistics
Matches: 88, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
43 13 0.15
44 11 0.12
45 1 0.01
46 9 0.10
47 3 0.03
48 1 0.01
49 4 0.05
50 24 0.27
51 1 0.01
52 3 0.03
53 1 0.01
54 5 0.06
55 12 0.14
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (48 bp):
TTATAAATAAACTATTAATATATATAAATTATATAGTTTATATATAAA
Found at i:66772 original size:20 final size:20
Alignment explanation
Indices: 66728--66782 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
66718 CTATTGAACT
**
66728 ATATATAAATTATATAGTTT
1 ATATATAAATTATATAGTAA
66748 ATATATAAATTATATA-TAA
1 ATATATAAATTATATAGTAA
*
66767 ACTATATAATTTATAT
1 A-TATATAAATTATAT
66783 TTATATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATAAATTATATAGTAA
Found at i:66793 original size:33 final size:33
Alignment explanation
Indices: 66727--66895 Score: 163
Period size: 33 Copynumber: 5.2 Consensus size: 33
66717 ACTATTGAAC
66727 TATATATAAATTATATAGTTTATATATA-A-AT
1 TATATATAAATTATATAGTTTATATATATATAT
* * *
66758 TATATATAAACTATATAATTTATATTTATATAT
1 TATATATAAATTATATAGTTTATATATATATAT
* * * *
66791 TATGTAT-AATTATA-A-ATAATATAT-TCTAT
1 TATATATAAATTATATAGTTTATATATATATAT
* *
66820 GTATAACTATAAATTATATAGTTTAT-TAATATAAAC
1 -TAT-A-TATAAATTATATAGTTTATAT-ATATATAT
*
66856 TATATATAAACTATATAGTTTATATATATATAT
1 TATATATAAATTATATAGTTTATATATATATAT
66889 TATATAT
1 TATATAT
66896 GGTTTAGTGT
Statistics
Matches: 109, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
29 4 0.04
30 9 0.08
31 26 0.24
32 10 0.09
33 46 0.42
34 4 0.04
35 8 0.07
36 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TATATATAAATTATATAGTTTATATATATATAT
Found at i:66947 original size:9 final size:9
Alignment explanation
Indices: 66935--66976 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
66925 TATGGAATTA
66935 TATATAAAC
1 TATATAAAC
66944 TATATAAAC
1 TATATAAAC
**
66953 TATATTTTA-
1 TATA-TAAAC
66962 TATATAAAC
1 TATATAAAC
66971 TATATA
1 TATATA
66977 CTATAGTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATAAAC
Found at i:66981 original size:18 final size:18
Alignment explanation
Indices: 66944--66981 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
66934 ATATATAAAC
**
66944 TATATAAACTATATTTTA
1 TATATAAACTATATACTA
66962 TATATAAACTATATACTA
1 TATATAAACTATATACTA
66980 TA
1 TA
66982 GTTGACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATAAACTATATACTA
Found at i:67084 original size:18 final size:18
Alignment explanation
Indices: 67061--67096 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
67051 TATAGTTGAT
67061 ATTTACATATGAACTATA
1 ATTTACATATGAACTATA
67079 ATTTACATATGAACTATA
1 ATTTACATATGAACTATA
67097 TATAAACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTTACATATGAACTATA
Found at i:87970 original size:27 final size:27
Alignment explanation
Indices: 87940--87994 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
87930 TGCACAAAAG
87940 TAAGCACCCAATTATTAAACCAATTGA
1 TAAGCACCCAATTATTAAACCAATTGA
87967 TAAGCACCCAATTATTAAACCAATTGA
1 TAAGCACCCAATTATTAAACCAATTGA
87994 T
1 T
87995 CAGGCAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (27 bp):
TAAGCACCCAATTATTAAACCAATTGA
Found at i:87979 original size:15 final size:15
Alignment explanation
Indices: 87940--87984 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
87930 TGCACAAAAG
87940 TAAGCACCCAATTAT
1 TAAGCACCCAATTAT
87955 TAA--A-CCAATTGA-
1 TAAGCACCCAATT-AT
87967 TAAGCACCCAATTAT
1 TAAGCACCCAATTAT
87982 TAA
1 TAA
87985 ACCAATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
14 2 0.08
15 12 0.48
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (15 bp):
TAAGCACCCAATTAT
Found at i:91384 original size:23 final size:23
Alignment explanation
Indices: 91330--91384 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
91320 AGATTATCGG
91330 TATTCTTTATTTTTTTCTATATTA
1 TATT-TTTATTTTTTTCTATATTA
* * *
91354 TATCTTTATTTTCTTT-TATTTTT
1 TATTTTTATTTT-TTTCTATATTA
91377 TATTTTTA
1 TATTTTTA
91385 ATAAGTATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (23 bp):
TATTTTTATTTTTTTCTATATTA
Found at i:92112 original size:27 final size:28
Alignment explanation
Indices: 92072--92124 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
92062 AGGTTTTGAA
92072 TATTTTTTCCCTTTCCCTTGTCAATGAC
1 TATTTTTTCCCTTTCCCTTGTCAATGAC
* *
92100 TATTTTTT-TCTTTCTCTTGTCAATG
1 TATTTTTTCCCTTTCCCTTGTCAATG
92125 GCTGTTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.13, C:0.23, G:0.08, T:0.57
Consensus pattern (28 bp):
TATTTTTTCCCTTTCCCTTGTCAATGAC
Found at i:92391 original size:3 final size:3
Alignment explanation
Indices: 92383--92420 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
92373 TAAATTTTAT
92383 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
92421 TTGAATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:97857 original size:24 final size:24
Alignment explanation
Indices: 97830--97923 Score: 81
Period size: 23 Copynumber: 4.0 Consensus size: 24
97820 CACCACAGCT
*
97830 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
97854 CGTAGAAATTATC-CCGAAAGAT--CG
1 CGTAGAAATT-GCACCG-AAG-TGCCA
97878 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
97901 CATAG-AATTGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
97924 TATAAGATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
21 1 0.02
22 6 0.11
23 23 0.41
24 21 0.38
25 4 0.07
26 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:104318 original size:24 final size:24
Alignment explanation
Indices: 104291--104376 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
104281 CACCACAGCT
*
104291 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
104315 CGTAGAAATTGTC-CCGAAG-GACCG
1 CGTAGAAATTG-CACCGAAGTG-CCA
*
104339 CGTAGAAA-TACACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
104362 CATAG-AATTGCACCG
1 CGTAGAAATTGCACCG
104377 TAGTTCCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 3 0.06
23 20 0.39
24 27 0.53
25 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:108793 original size:64 final size:65
Alignment explanation
Indices: 108721--108846 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 65
108711 GGTGCACTAA
* * * * *
108721 GTGTGCATCGATGCATAAAATGCATTTGATGTTTTTAAT-AAGCCTAATTGCATCGATGCATGGC
1 GTGTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGGC
* * *
108785 GTGTGCATCGATTCATAAAATGCAATCGATGTTTTCATTAAAACCTGAGTGCATCGATGCAT
1 GTGTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTGCATCGATGCAT
108847 AAACTGCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 34 0.64
65 19 0.36
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
GTGTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGGC
Found at i:109268 original size:15 final size:15
Alignment explanation
Indices: 109248--109277 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
109238 TGAAAAGTTG
109248 AAAATTACTTACTCC
1 AAAATTACTTACTCC
109263 AAAATTACTTACTCC
1 AAAATTACTTACTCC
109278 CCCTTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTACTTACTCC
Found at i:117520 original size:83 final size:84
Alignment explanation
Indices: 117431--117594 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 84
117421 GGTGCACTAA
* * * * *
117431 GTGTGCATCGATGCATAAAATACATTCGATGTTTTTAAT-AAGCCTAAGTGCATTGATACATGGT
1 GTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTAAGTGCATCGATACATGGA
*
117495 GTGTGCATCGATGCATGGT
66 GAGTGCATCGATGCATGGT
* * * * *
117514 GTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTGAGTGTATCGATGCATGGA
1 GTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTAAGTGCATCGATACATGGA
117579 GAGTGCATCGATGCAT
66 GAGTGCATCGATGCAT
117595 AAATTGCATT
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
83 35 0.51
84 34 0.49
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (84 bp):
GTGTGCATCGATGCATAAAATACAATCGATGTTTTCAATAAAACCTAAGTGCATCGATACATGGA
GAGTGCATCGATGCATGGT
Found at i:117526 original size:19 final size:19
Alignment explanation
Indices: 117478--117529 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
117468 ATAAGCCTAA
* *
117478 GTGCATTGATACATGGTGT
1 GTGCATCGATGCATGGTGT
117497 GTGCATCGATGCATGGTGT
1 GTGCATCGATGCATGGTGT
117516 GTGCATCGATGCAT
1 GTGCATCGATGCAT
117530 AAAATGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGTGT
Found at i:119519 original size:16 final size:16
Alignment explanation
Indices: 119495--119531 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
119485 CTTTGCTGTA
*
119495 AAGTTCAGTATCACGT
1 AAGTCCAGTATCACGT
119511 AAGTCCAGTATCACGT
1 AAGTCCAGTATCACGT
119527 AAGTC
1 AAGTC
119532 GAGAATCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (16 bp):
AAGTCCAGTATCACGT
Found at i:127335 original size:19 final size:20
Alignment explanation
Indices: 127311--127361 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
127301 AATGACCAAT
127311 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
127330 AAAATCGCAATGCGATTTAG
1 AAAATCGCAACGCGATATAC
127350 AAAATCGCAACG
1 AAAATCGCAACG
127362 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:127371 original size:20 final size:20
Alignment explanation
Indices: 127348--127401 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
127338 AATGCGATTT
*
127348 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
127368 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
127388 AGAAAATCGCAACG
1 AGAAAATCGCAACG
127402 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:127461 original size:20 final size:20
Alignment explanation
Indices: 127436--127734 Score: 211
Period size: 20 Copynumber: 14.4 Consensus size: 20
127426 TTTAGAAGAA
*
127436 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
127456 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
127476 AATCGCAATGCGATTGAGCGATTGAG
1 AATCGCAATGCGATT----GA--GAG
* * *
127502 AGAGTCGCAACGTGATTTAGAAGAA
1 A-A-TCGCAATGCGA-TT-G-AGAG
*
127527 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
127547 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
127567 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
127587 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
127607 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
* ** *** *
127627 AATCGCAACGTTAAAAAGAA
1 AATCGCAATGCGATTGAGAG
* ** *** *
127647 AATCGCAACGTTAAAAAGAA
1 AATCGCAATGCGATTGAGAG
*
127667 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
127687 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
127707 AATCGCAATGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
127727 AATCGCAA
1 AATCGCAA
127735 CGTTAAAAAG
Statistics
Matches: 233, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
20 200 0.86
21 1 0.00
22 1 0.00
23 9 0.04
24 2 0.01
25 3 0.01
26 4 0.02
27 2 0.01
28 9 0.04
29 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:127510 original size:48 final size:50
Alignment explanation
Indices: 127445--127544 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 50
127435 AAATCGCAAT
* * * *
127445 GCGATTGATAGAATCGCAATGCGATTTA-TAG-AATCGCAATGCGATTGA
1 GCGATTGAGAGAATCGCAACGCGATTTAGAAGAAATCGCAATGCGACTGA
* *
127493 GCGATTGAGAGAGTCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGA
1 GCGATTGAGAGAATCGCAACGCGATTTAGAAG-AAATCGCAATGCGACTGA
127544 G
1 G
127545 AGAATCGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
48 24 0.56
49 2 0.05
51 17 0.40
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (50 bp):
GCGATTGAGAGAATCGCAACGCGATTTAGAAGAAATCGCAATGCGACTGA
Found at i:127570 original size:91 final size:91
Alignment explanation
Indices: 127415--127581 Score: 280
Period size: 91 Copynumber: 1.8 Consensus size: 91
127405 GCTTCCAAGT
* * * * *
127415 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
127480 GCAATGCGATTGAGCGATTGAGAGAG
66 GCAATGCGATTGAGCGATTGAGAGAG
*
127506 TCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
127571 GCAATGCGATT
66 GCAATGCGATT
127582 TATAGAATCG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (91 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGCGATTGAGAGAG
Found at i:127651 original size:80 final size:79
Alignment explanation
Indices: 127587--127754 Score: 228
Period size: 80 Copynumber: 2.1 Consensus size: 79
127577 CGATTTATAG
*
127587 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCG
127652 CAACGTTAAAAAGAA
66 CAACGTTAAAAAG-A
* * * * ** ***
127667 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTTAGAAAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCG
127732 CAACGTTAAAAAGAA
66 CAACGTTAAAAAG-A
127747 AATCGCAA
1 AATCGCAA
127755 CGGTCAAAAG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (79 bp):
AATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCG
CAACGTTAAAAAGA
Found at i:127675 original size:100 final size:100
Alignment explanation
Indices: 127567--127766 Score: 328
Period size: 100 Copynumber: 2.0 Consensus size: 100
127557 CGACTGAGAG
* * *
127567 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCG
*
127632 CAACGTTAAAAAGAAAATCGCAACGTTAAAAAGAA
66 CAACGTTAAAAAGAAAATCGCAACGGTAAAAAGAA
* * *
127667 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTTAGAAAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCG
*
127732 CAACGTTAAAAAGAAAATCGCAACGGTCAAAAGAA
66 CAACGTTAAAAAGAAAATCGCAACGGTAAAAAGAA
127767 TAGTTAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (100 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCG
CAACGTTAAAAAGAAAATCGCAACGGTAAAAAGAA
Found at i:127746 original size:20 final size:20
Alignment explanation
Indices: 127723--127766 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
127713 AATGCGATTT
*
127723 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
127743 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
127763 AGAA
1 AGAA
127767 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:127855 original size:6 final size:6
Alignment explanation
Indices: 127844--127899 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
127834 GACACGTATT
127844 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
127892 ACC-CG ACC
1 ACCACG ACC
127900 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:128609 original size:6 final size:6
Alignment explanation
Indices: 128584--128627 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
128574 CCGCCGTCTC
128584 GTCG-G GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGT
128628 ACGTGTCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 14 0.37
6 24 0.63
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GTCGTG
Found at i:128736 original size:20 final size:20
Alignment explanation
Indices: 128713--129030 Score: 165
Period size: 20 Copynumber: 15.6 Consensus size: 20
128703 TTCTTTTGAC
128713 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
128733 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
128753 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
128773 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
128793 CATTGCGATTTTCTTCTAAAACG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
128816 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
128836 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
128856 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
128876 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
128896 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
128919 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
128940 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
128958 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
128980 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
129000 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
129019 CGTTGCGATTTT
1 CGTTGCGATTTT
129031 ATTGGTCATT
Statistics
Matches: 245, Mismatches: 42, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 179 0.73
21 14 0.06
22 6 0.02
23 27 0.11
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:128759 original size:40 final size:40
Alignment explanation
Indices: 128715--128905 Score: 247
Period size: 40 Copynumber: 4.7 Consensus size: 40
128705 CTTTTGACCG
* *
128715 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
128755 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
128795 TTGCGATTTTCTTCTAAAACGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
128838 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
128878 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATT
128906 TTCTTCTAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 94 0.72
41 3 0.02
42 3 0.02
43 31 0.24
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:128857 original size:83 final size:83
Alignment explanation
Indices: 128723--128885 Score: 263
Period size: 83 Copynumber: 2.0 Consensus size: 83
128713 CGTTGCGATT
* * * * * *
128723 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAAACGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
128788 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
128806 TTCTAAAACGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAAACGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
128871 AATCGCATTGCGATT
66 AATCGCATTGCGATT
128886 CTATCAATCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (83 bp):
TTCTAAAACGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:128897 original size:103 final size:103
Alignment explanation
Indices: 128713--128926 Score: 329
Period size: 103 Copynumber: 2.1 Consensus size: 103
128703 TTCTTTTGAC
* * * * * * *
128713 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
* *
128778 CGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAAACG
66 CGATTCTATCAATCGCATTGCGATTTTCTTCTAAAACG
*
128816 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
*
128881 CGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
66 CGATTCTATCAATCGCATTGCGATTTTCTTCTAAAACG
128919 CGTTGCGA
1 CGTTGCGA
128927 ACTTGGAAGC
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (103 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTCTATCAATCGCATTGCGATTTTCTTCTAAAACG
Found at i:129020 original size:19 final size:20
Alignment explanation
Indices: 128980--129030 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
128970 TTCTTTTTAA
*
128980 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
129000 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
129019 CGTTGCGATTTT
1 CGTTGCGATTTT
129031 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:129681 original size:45 final size:46
Alignment explanation
Indices: 129613--129720 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
129603 CTTCACTGGC
* * ***
129613 TTCTTCTCTGATCTC-TCCATGGGTTTGGGTCTCACCTTCGCCAGG
1 TTCTTCACGGATCTCTTCCATGGGTTTGGGTCTCACCTAAACCAGG
* *
129658 TTCTTCACGGATCTCTTCC-TGGGTTTGGGTCTCACCTAAATCGGG
1 TTCTTCACGGATCTCTTCCATGGGTTTGGGTCTCACCTAAACCAGG
129703 TTCTTCACGGATCTCTTC
1 TTCTTCACGGATCTCTTC
129721 TTCGGGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 52 0.95
46 3 0.05
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (46 bp):
TTCTTCACGGATCTCTTCCATGGGTTTGGGTCTCACCTAAACCAGG
Found at i:132537 original size:39 final size:39
Alignment explanation
Indices: 132494--132583 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 39
132484 CATTCTTAGG
132494 ATCTTCTCA-ATTTA-CTTGAAGACGCTC-TGCAATAGTAGA
1 ATCTT-TCATATTTATC-TGAAGACG-TCATGCAATAGTAGA
* *
132533 ATCTTTTATATTTATCTGAAGACGTCATGCAATCGTAGA
1 ATCTTTCATATTTATCTGAAGACGTCATGCAATAGTAGA
*
132572 GT-TTTCATATTT
1 ATCTTTCATATTT
132584 TAGATTGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
38 13 0.30
39 30 0.68
40 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (39 bp):
ATCTTTCATATTTATCTGAAGACGTCATGCAATAGTAGA
Found at i:133950 original size:15 final size:15
Alignment explanation
Indices: 133927--133956 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
133917 AGGGAAAAAT
133927 ATGAAAGCCTTGAAG
1 ATGAAAGCCTTGAAG
*
133942 ATGAGAGCCTTGAAG
1 ATGAAAGCCTTGAAG
133957 GTAAGAGGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (15 bp):
ATGAAAGCCTTGAAG
Found at i:134527 original size:69 final size:69
Alignment explanation
Indices: 134366--134504 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
134356 ATGATGAAGA
* *
134366 GGATGGAGAATCAAAAAACCCTAAAGGGCAGCAGGAGCAAGAAAAGCTACCTGAAGATCCAGTAA
1 GGATGGAGAATCAGAAAACCCTAAAGGGAAGCAGGAGCAAGAAAAGCTACCTGAAGATCCAGTAA
134431 AGCT
66 AGCT
* *
134435 GGATGGAGAATCAGAAAACCCTAAAGGGAAGCAGGAGCAAGAAAAGCTACCTGTAGATCTAGTAA
1 GGATGGAGAATCAGAAAACCCTAAAGGGAAGCAGGAGCAAGAAAAGCTACCTGAAGATCCAGTAA
134500 AGCT
66 AGCT
134504 G
1 G
134505 CAGATGTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.27, T:0.13
Consensus pattern (69 bp):
GGATGGAGAATCAGAAAACCCTAAAGGGAAGCAGGAGCAAGAAAAGCTACCTGAAGATCCAGTAA
AGCT
Found at i:135220 original size:27 final size:27
Alignment explanation
Indices: 135179--135311 Score: 158
Period size: 27 Copynumber: 4.9 Consensus size: 27
135169 GTAACGAACG
* * *
135179 GCCGCCATCCAAGGCCAAGAAGCAGCA
1 GCCGCCACCCCAGGCCAAGAAGCAGAA
135206 GCCGCCACCCCAGGCCAAGAAGCAGAA
1 GCCGCCACCCCAGGCCAAGAAGCAGAA
* * * * * * *
135233 ACAGCCTCCCAAGGCCAAGGAGGAGGA
1 GCCGCCACCCCAGGCCAAGAAGCAGAA
*
135260 GCCGCCACCCCAGGCCAAGGAGCAGAA
1 GCCGCCACCCCAGGCCAAGAAGCAGAA
*
135287 GCAGCCACCCCAGGCCAAGAAGCAG
1 GCCGCCACCCCAGGCCAAGAAGCAG
135312 CCGCCAAGTA
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.02
Consensus pattern (27 bp):
GCCGCCACCCCAGGCCAAGAAGCAGAA
Found at i:135269 original size:54 final size:54
Alignment explanation
Indices: 135182--135312 Score: 190
Period size: 54 Copynumber: 2.4 Consensus size: 54
135172 ACGAACGGCC
*
135182 GCCATCCAAGGCCAAGAAGCAGCAGCCGCCACCCCAGGCCAAGAAGCAGAAACA
1 GCCACCCAAGGCCAAGAAGCAGCAGCCGCCACCCCAGGCCAAGAAGCAGAAACA
* * * * * *
135236 GCCTCCCAAGGCCAAGGAGGAGGAGCCGCCACCCCAGGCCAAGGAGCAGAAGCA
1 GCCACCCAAGGCCAAGAAGCAGCAGCCGCCACCCCAGGCCAAGAAGCAGAAACA
*
135290 GCCACCCCAGGCCAAGAAGCAGC
1 GCCACCCAAGGCCAAGAAGCAGC
135313 CGCCAAGTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.33, C:0.37, G:0.28, T:0.02
Consensus pattern (54 bp):
GCCACCCAAGGCCAAGAAGCAGCAGCCGCCACCCCAGGCCAAGAAGCAGAAACA
Found at i:146594 original size:43 final size:43
Alignment explanation
Indices: 146539--146772 Score: 227
Period size: 43 Copynumber: 5.4 Consensus size: 43
146529 TTTCAAGAAA
146539 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGA-AGAC
* * *
146582 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGCC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * *
146625 AAATGCCGCAATAGATGTTGATATTTAGTGGCATTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * * ***** *
146668 AAACGCCGCAGTAGGTGTCGCTTTTTAGCGGCGTTTTTCCCAG
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * ** **
146711 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCGTTTTTATCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
*
146754 AAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTT
146773 AAGGTTTCGC
Statistics
Matches: 159, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
43 157 0.99
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:147240 original size:21 final size:21
Alignment explanation
Indices: 147215--147296 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
147205 ATATGTTGCT
147215 TCTCTTTGTGCTGCCGCTGTC
1 TCTCTTTGTGCTGCCGCTGTC
* *
147236 TCTCTTTGTGCTGTCGCTGCC
1 TCTCTTTGTGCTGCCGCTGTC
* * *
147257 TCTCTTTGTGCTTCCACTGTT
1 TCTCTTTGTGCTGCCGCTGTC
* * *
147278 TCTCTCTCTGCTTCCGCTG
1 TCTCTTTGTGCTGCCGCTG
147297 CTGCTCTGGC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.01, C:0.34, G:0.20, T:0.45
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGTC
Found at i:147296 original size:42 final size:41
Alignment explanation
Indices: 147215--147334 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 41
147205 ATATGTTGCT
* * * *
147215 TCTCTTTGTGCTGCCGCTGTCTCTCTTTGTGCTGT-CGCTGCC
1 TCTCTTTGTGCTTCCGCTGTTTCTCTCTCTGCT-TCCGCTG-C
*
147257 TCTCTTTGTGCTTCCACTGTTTCTCTCTCTGCTTCCGCTGC
1 TCTCTTTGTGCTTCCGCTGTTTCTCTCTCTGCTTCCGCTGC
* * *
147298 TGCTC-TGGCTGCTTCCGCTGCTGCTCTCTCTGCTTCC
1 T-CTCTTTG-TGCTTCCGCTGTTTCTCTCTCTGCTTCC
147335 CTTGCTTCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
41 5 0.08
42 61 0.92
ACGTcount: A:0.01, C:0.37, G:0.20, T:0.42
Consensus pattern (41 bp):
TCTCTTTGTGCTTCCGCTGTTTCTCTCTCTGCTTCCGCTGC
Found at i:147340 original size:21 final size:21
Alignment explanation
Indices: 147265--147334 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
147255 CCTCTCTTTG
* * *
147265 TGCTTCCACTGTTTCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
**
147286 TGCTTCCGCTGCTGCTCTGGC
1 TGCTTCCGCTGCTGCTCTCTC
147307 TGCTTCCGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
147328 TGCTTCC
1 TGCTTCC
147335 CTTGCTTCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.01, C:0.40, G:0.19, T:0.40
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCTC
Found at i:151368 original size:46 final size:46
Alignment explanation
Indices: 151301--151391 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
151291 TAGCAATTCT
*
151301 GAAATAACTACATGGTCAAACAAGACAGAGGAACGAAGGCAAGTAC
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
151347 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
151392 AGTACCTTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.49, C:0.15, G:0.24, T:0.11
Consensus pattern (46 bp):
GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
Found at i:152402 original size:41 final size:42
Alignment explanation
Indices: 152318--152424 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 42
152308 TTTCGTAAGT
* * * * *
152318 GGCG-TTTTCATACGAACGCCACTAAAGTAGAAGTCTATAGC
1 GGCGATTTTCATACAAACGCCACTAAAATAAAAATATATAGC
* *
152359 GGC-ATTTTCATACAAACGCCACTAAAATAAAAATATTTTGC
1 GGCGATTTTCATACAAACGCCACTAAAATAAAAATATATAGC
* * *
152400 GGCGTTTTTTATAAAAACGCCACTA
1 GGCGATTTTCATACAAACGCCACTA
152425 TATAATACAC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 36 0.67
42 18 0.33
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (42 bp):
GGCGATTTTCATACAAACGCCACTAAAATAAAAATATATAGC
Found at i:152714 original size:57 final size:57
Alignment explanation
Indices: 152646--152776 Score: 253
Period size: 57 Copynumber: 2.3 Consensus size: 57
152636 ATTAAAACAG
*
152646 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
152703 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
152760 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
152777 CAGTCTTCAC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
Found at i:154397 original size:3 final size:3
Alignment explanation
Indices: 154389--154464 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
154379 TTTTATTTAT
* * * * *
154389 TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TAA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
154437 TTA TTA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA
154465 AAAAAATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:155844 original size:16 final size:18
Alignment explanation
Indices: 155814--155855 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
155804 ATAATAAATA
155814 ATAATTTATTTTTTTA-C
1 ATAATTTATTTTTTTATC
155831 ATAATTTA-TTTTTTATC
1 ATAATTTATTTTTTTATC
*
155848 ATATTTTA
1 ATAATTTA
155856 ATATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
ATAATTTATTTTTTTATC
Found at i:155953 original size:22 final size:24
Alignment explanation
Indices: 155922--155965 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
155912 CCTTTTCTGA
*
155922 TATTTCTAAATA-A-ATAAATTTT
1 TATTTATAAATATATATAAATTTT
155944 TATTTATAAATATATATAAATT
1 TATTTATAAATATATATAAATT
155966 AATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTATAAATATATATAAATTTT
Found at i:155971 original size:24 final size:22
Alignment explanation
Indices: 155921--155972 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
155911 TCCTTTTCTG
* *
155921 ATATTTCTAAATAAATAAATTT
1 ATATTTATAAATAAATAAATTA
*
155943 TTATTTATAAATATATATAAATTA
1 ATATTTATAAATA-A-ATAAATTA
155967 ATATTT
1 ATATTT
155973 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 11 0.46
23 1 0.04
24 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTTATAAATAAATAAATTA
Found at i:156510 original size:26 final size:27
Alignment explanation
Indices: 156458--156515 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
156448 TAATTCTTTC
*
156458 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
156486 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
156512 TTTT
1 TTTT
156516 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:159806 original size:15 final size:15
Alignment explanation
Indices: 159786--159817 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
159776 GATCAATACC
159786 TTTTGCATACATGCA
1 TTTTGCATACATGCA
159801 TTTTGCATACATGCA
1 TTTTGCATACATGCA
159816 TT
1 TT
159818 ATTCATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:167145 original size:9 final size:9
Alignment explanation
Indices: 167131--167164 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
167121 TGCTTGAAGG
167131 AAAAAAGAA
1 AAAAAAGAA
167140 AAAAAAGAA
1 AAAAAAGAA
167149 AAAAAAGAA
1 AAAAAAGAA
167158 AAGAAAA
1 AA-AAAA
167165 AGAGGGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:167150 original size:5 final size:5
Alignment explanation
Indices: 167133--167164 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
167123 CTTGAAGGAA
167133 AAAAG AAAA- AAAAG AAAA- AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
167165 AGAGGGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:167159 original size:14 final size:15
Alignment explanation
Indices: 167132--167167 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
167122 GCTTGAAGGA
167132 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
*
167147 AAAAA-AAAGAAAAG
1 AAAAAGAAAAAAAAG
167161 AAAAAGA
1 AAAAAGA
167168 GGGGGTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:167562 original size:19 final size:18
Alignment explanation
Indices: 167520--167568 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
167510 TATTTTCTTT
167520 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
167536 AGATTCAATTTATTTTTG
1 AAATTCAATTTATTTTTG
167554 AAAATTCAATTTATT
1 -AAATTCAATTTATT
167569 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:168951 original size:114 final size:113
Alignment explanation
Indices: 168751--169087 Score: 532
Period size: 114 Copynumber: 3.0 Consensus size: 113
168741 TGTCACATTA
168751 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
168816 TTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAA-CCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
* * *
168865 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATTTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
168930 TTTGGTATGAACCCTAAAATCAATCATTGGATTTAAAAGATGAATTTGC
66 TTTGGTATGAACCC-AAAATCAATCATTGGATTTAAAAGATGAATTTGC
* *
168979 TCATAGTACAAATAA-AGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATCTG
1 TCATAGTAGAAATAAGA-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * *
169043 GTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
65 GTTTGGTATGAACC-CAAAATCAATCATTGGATTTAAAAGATGAA
169088 CAGCATGATC
Statistics
Matches: 206, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
113 4 0.02
114 201 0.98
115 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (113 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
Found at i:169971 original size:113 final size:113
Alignment explanation
Indices: 169773--170455 Score: 660
Period size: 113 Copynumber: 6.0 Consensus size: 113
169763 TAGCAAAGAT
* * * *
169773 TTAAATCCATCATTCAATGGATCAACATTTCAAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* * *
169838 AGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
169886 TTAAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTTATCTGA
1 TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* *
169951 AGAAGGAAGAAGAAATTCATAATGAGAAAAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
169999 TTGAATTCATGATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* *
170064 AGAAGGAAG-AGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * * *
170112 TTAAATTCATCATTTGATGGATCAACATTGCTAGGTAGAGTTCATGATGAGAAAAACTCGTCAT-
1 TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATC-TG
** *
170176 CTGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * **** *
170224 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGA
1 TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* *
170289 AGAA-GAAGAAG---TTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** * * ****
170333 ATAATTTTATCACAGAAGGAGATATATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAG
1 TTAAATTCATCAC---------TCGA-T-GGATCAACATTTCCAGTTCGAGTTCATAATGAGAAG
* * * * *
170398 AACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
55 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
170456 AATGACTCTA
Statistics
Matches: 479, Mismatches: 72, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
109 38 0.08
111 1 0.00
112 99 0.21
113 255 0.53
114 1 0.00
118 2 0.00
119 1 0.00
120 46 0.10
121 6 0.01
124 30 0.06
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TTAAATTCATCACTCGATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:170468 original size:124 final size:124
Alignment explanation
Indices: 170251--170543 Score: 368
Period size: 124 Copynumber: 2.4 Consensus size: 124
170241 TGGATCAGCT
*
170251 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTG---AAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
* * * * * * * *
170312 AGAGCTTGTTCAACCTTTTGCATAATTTTATCACAGAAGGAGATATATTAGCATCAA-CC
66 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACAT-AATCC
*
170371 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
* *
170436 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATAATCC
66 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATAATCC
* *
170495 ---CCAGCGGAAAGTTCATAATGAGAAAAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
170544 TTTATTCAAC
Statistics
Matches: 151, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
120 36 0.24
121 4 0.03
122 30 0.20
123 10 0.07
124 71 0.47
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATAATCC
Found at i:170713 original size:3 final size:3
Alignment explanation
Indices: 170705--170758 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
170695 ATTTATTTAT
*
170705 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
170750 TTA TTA TTA
1 TTA TTA TTA
170759 AAAAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:174354 original size:19 final size:19
Alignment explanation
Indices: 174331--174393 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
174321 TTAATAATTC
* *
174331 ATTTTCTGATTCAGAACTT
1 ATTTTCAGATTCATAACTT
*
174350 TTTTTCAGATTCATAACTT
1 ATTTTCAGATTCATAACTT
*
174369 ACTTTCAGATTCATAACTT
1 ATTTTCAGATTCATAACTT
174388 AATTTT
1 -ATTTT
174394 TAAATTCGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 33 0.89
20 4 0.11
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTTCAGATTCATAACTT
Found at i:175934 original size:19 final size:20
Alignment explanation
Indices: 175910--175956 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
175900 CCAAAATGGC
*
175910 TCAATTTC-ACATTCTAACA
1 TCAATTTCAACACTCTAACA
175929 TCAATTTCAACACTCTAACA
1 TCAATTTCAACACTCTAACA
*
175949 TTAATTTC
1 TCAATTTC
175957 CAGAAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAATTTCAACACTCTAACA
Found at i:177114 original size:21 final size:21
Alignment explanation
Indices: 177052--177115 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
177042 CCATTAGACA
** * *
177052 GGGGGAATCAATACCCCTTGA
1 GGGGGAATCTGTACCCCCTGG
*
177073 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
177094 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
177115 G
1 G
177116 CAATCTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:180217 original size:21 final size:21
Alignment explanation
Indices: 180180--180242 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
180170 CCGTTAGACA
* *
180180 GGGGGG-ATCGGTACCCCATG
1 GGGGGGAATCTGTACCCCCTG
*
180200 GGGGGGAATCTGTTCCCCCT-
1 GGGGGGAATCTGTACCCCCTG
180220 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
180241 GG
1 GG
180243 CAATCTGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.13, C:0.27, G:0.41, T:0.19
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:180249 original size:18 final size:19
Alignment explanation
Indices: 180201--180249 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
180191 TACCCCATGG
* *
180201 GGGGGAATCTGTTCCCCCT
1 GGGGCAATCTGTACCCCCT
*
180220 GGGGGGAATCTGTACCCCCT
1 -GGGGCAATCTGTACCCCCT
180240 -GGGCAATCTG
1 GGGGCAATCTG
180250 ATTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.14, C:0.29, G:0.35, T:0.22
Consensus pattern (19 bp):
GGGGCAATCTGTACCCCCT
Found at i:193330 original size:15 final size:16
Alignment explanation
Indices: 193300--193345 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
193290 GTTTACTTCA
*
193300 GAATGATT-AAACGCT
1 GAATGATTCAAATGCT
193315 GAAT-ATTCAAATGCT
1 GAATGATTCAAATGCT
*
193330 GAATGATTCATATGCT
1 GAATGATTCAAATGCT
193346 CTGTATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 3 0.11
15 14 0.52
16 10 0.37
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:193344 original size:16 final size:15
Alignment explanation
Indices: 193312--193345 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
193302 ATGATTAAAC
193312 GCTGAATATTCAAAT
1 GCTGAATATTCAAAT
*
193327 GCTGAATGATTCATAT
1 GCTGAAT-ATTCAAAT
193343 GCT
1 GCT
193346 CTGTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (15 bp):
GCTGAATATTCAAAT
Done.