Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001142.1 Hibiscus syriacus cultivar Beakdansim tig00002278_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: 47444
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3061 original size:23 final size:23
Alignment explanation
Indices: 3035--3097 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
3025 AAATTTATAT
* *
3035 GGCACTACGATGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
3058 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
3081 GGCACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
3098 TATACGAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3649 original size:21 final size:21
Alignment explanation
Indices: 3625--3668 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3615 AGCTGAAGTT
*
3625 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
*
3646 ACTGTAGTAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
3667 AC
1 AC
3669 AATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:5067 original size:2 final size:2
Alignment explanation
Indices: 4989--5052 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
4979 ATAAAACATA
* *
4989 AT AT AT AC AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5031 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5053 TCTTCCTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5474 original size:18 final size:18
Alignment explanation
Indices: 5447--5494 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
5437 ACCATACTAT
*
5447 GGTACTGATACCCCTTCC
1 GGTACCGATACCCCTTCC
5465 GGTACCGATACCCCTTCC
1 GGTACCGATACCCCTTCC
*
5483 GGTATCGATACC
1 GGTACCGATACC
5495 AGTTTTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (18 bp):
GGTACCGATACCCCTTCC
Found at i:5491 original size:94 final size:94
Alignment explanation
Indices: 5310--5491 Score: 213
Period size: 94 Copynumber: 1.9 Consensus size: 94
5300 CCAAGCTCAA
* * **
5310 TAGTATCGATACCACTACCATAGTACCGATACTTCTATACTATAGTACTGATACCCCTTTTGGTA
1 TAGTATCGATACCACTACCATAGTACCGATACTACCATACTATAGTACTGATACCCCTTCCGGTA
* ** *
5375 TCAATACCAATTTTAGTTTCGATGTTGCG
66 CCAATACCAATTCCAGTATCGATGTTGCG
* * *
5404 TAGTATCGATACC-CTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCTTCCGGT
1 TAGTATCGATACCAC-TACCATAGTACCGATACTACCATACTATAGTACTGATACCCCTTCCGGT
* ** *
5468 ACCGATACCCCTTCCGGTATCGAT
65 ACCAATACCAATTCCAGTATCGAT
5492 ACCAGTTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
93 1 0.01
94 71 0.99
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (94 bp):
TAGTATCGATACCACTACCATAGTACCGATACTACCATACTATAGTACTGATACCCCTTCCGGTA
CCAATACCAATTCCAGTATCGATGTTGCG
Found at i:8495 original size:20 final size:20
Alignment explanation
Indices: 8421--8826 Score: 468
Period size: 20 Copynumber: 20.4 Consensus size: 20
8411 GATTTTCCAT
* ** *
8421 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
8441 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
8461 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
8481 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
8501 AATCGCAACGC-TATGGGTA
1 AATCGCAACGCGTATCCGTA
*
8520 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
8540 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
8560 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
8580 AA-CGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
8599 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
8619 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
8639 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
8659 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
8679 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
*
8698 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
8718 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
8738 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
8758 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
8778 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
8798 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
8818 AATCACAAC
1 AATCGCAAC
8827 ACTGAAATTT
Statistics
Matches: 333, Mismatches: 40, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.00
19 52 0.16
20 277 0.83
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:8545 original size:79 final size:80
Alignment explanation
Indices: 8440--8826 Score: 491
Period size: 79 Copynumber: 4.9 Consensus size: 80
8430 GCGAATATGA
* * *
8440 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
1 AAATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAAT
* **
8504 CGCAACGCT-ATGGGT
65 CGCAACGATAATCCGT
* * *
8519 AAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAA-C
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAATC
*
8583 GCAACG-TGTATCCGT
66 GCAACGAT-AATCCGT
* *
8598 AAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTAAATC
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAATC
8663 GCAACGATAATCCGT
66 GCAACGATAATCCGT
* * *
8678 AAATCGCAACGCGTATCCGT-AATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGTATCCGTAAAT
8741 CGCAACGATAATCCGT
65 CGCAACGATAATCCGT
* * * * * *
8757 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGTATCCGTAAAT
*
8821 CACAAC
65 CGCAAC
8827 ACTGAAATTT
Statistics
Matches: 281, Mismatches: 20, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
77 1 0.00
78 8 0.03
79 188 0.67
80 83 0.30
81 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (80 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAATC
GCAACGATAATCCGT
Found at i:8551 original size:99 final size:99
Alignment explanation
Indices: 8440--8807 Score: 478
Period size: 99 Copynumber: 3.7 Consensus size: 99
8430 GCGAATATGA
*
8440 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
1 AAATCGCAACGCGTAAC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
**
8504 CGCAACGCTATGGGTAAATCGCAATGCGTATCCGT
65 CGCAACGCTATCCGTAAATCGCAATGCGTATCCGT
* *
8539 ATATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAA-CGCAACGTGTATCCGTAAATC
1 AAATCGCAACGCGTAACCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATC
8603 GCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
66 GCAACGC-TATCCGTAAATCGCAATGCGTATCCGT
* * *
8638 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACGCGTATCCGT-AAT
1 AAATCGCAACGCGTAACCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGTGTATCCGTAAAT
* * * * *
8701 CGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
65 CGCAACGCT-ATCCGTAAATCGCAATGCGTATCCGT
* * * * *
8737 AAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGTAAA
1 AAATCGCAACGCGTAA-CCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGTAAA
8800 TCGCAACG
64 TCGCAACG
8808 AGAATCTGTA
Statistics
Matches: 240, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
98 32 0.13
99 181 0.75
100 27 0.11
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (99 bp):
AAATCGCAACGCGTAACCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATC
GCAACGCTATCCGTAAATCGCAATGCGTATCCGT
Found at i:11742 original size:19 final size:19
Alignment explanation
Indices: 11720--12041 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
11710 CGGAAAATAC
*
11720 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11739 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
11752 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
11772 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
11786 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11805 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
11823 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
11837 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11856 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11875 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
11889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11908 AATCGCAATGCGAAAT-TA
1 AATCGCAATGCGAAATGAA
*
11926 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
11945 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11964 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11983 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
11997 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12016 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
12034 AATCGCAA
1 AATCGCAA
12042 CGAGATAATC
Statistics
Matches: 262, Mismatches: 12, Indels: 59
0.79 0.04 0.18
Matches are distributed among these distances:
13 9 0.03
14 40 0.15
15 3 0.01
16 14 0.05
17 10 0.04
18 38 0.15
19 139 0.53
20 9 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:12011 original size:108 final size:103
Alignment explanation
Indices: 11751--12063 Score: 536
Period size: 108 Copynumber: 3.0 Consensus size: 103
11741 TCCCAACATG
11751 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
*
11816 GAAATGAAATCGCAACGAGAGAATCGCAATGCGAAATGA
65 GAAATGAAATCGCAACGAGAAAATCGCAATGCGAAATGA
11855 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
*
11920 AAATTAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGA
66 AAATGAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGA
*
11963 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
*
12028 AAATGAAATCGCAACGAGATAATCGCAATGCGAAAT
66 AAATGAAATCGCAACGAGAAAATCGCAATGCGAAAT
12064 TATAAACGCA
Statistics
Matches: 199, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
103 82 0.41
104 14 0.07
105 3 0.02
106 3 0.02
107 2 0.01
108 95 0.48
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (103 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
AAATGAAATCGCAACGAGAAAATCGCAATGCGAAATGA
Found at i:12079 original size:51 final size:52
Alignment explanation
Indices: 11751--12063 Score: 515
Period size: 52 Copynumber: 6.0 Consensus size: 52
11741 TCCCAACATG
11751 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
11804 AAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
11855 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* *
11907 AAATCGCAATGCGAAAT-TAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAAATGA
*
11963 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
12015 AAATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
12064 TATAAACGCA
Statistics
Matches: 246, Mismatches: 7, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
51 87 0.35
52 94 0.38
53 16 0.07
55 4 0.02
56 38 0.15
57 7 0.03
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:12179 original size:19 final size:19
Alignment explanation
Indices: 12070--12171 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
12060 AAATTATAAA
12070 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12089 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
12109 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
12125 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12142 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12161 CGCATTGCGAT
1 CGCATTGCGAT
12172 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:12296 original size:14 final size:14
Alignment explanation
Indices: 12277--12313 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12267 CATCAATTAC
12277 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12291 ACAAATCATCTTTT
1 ACAAATCAACTTTT
12305 ACAAATCAA
1 ACAAATCAA
12314 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12342 original size:38 final size:38
Alignment explanation
Indices: 12294--12366 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
12284 AACTTTTACA
*
12294 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
12332 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
12367 ACAATCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:14218 original size:19 final size:19
Alignment explanation
Indices: 14178--14312 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
14168 TAGTTTACTT
* *
14178 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
14198 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
14217 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
14236 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
14250 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
14269 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
14283 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
14302 TCGCAATGCGA
1 TCGCAACGCGA
14313 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:14253 original size:14 final size:14
Alignment explanation
Indices: 14234--14290 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
14224 GCGAAATGAA
*
14234 AATCGCAACGACAG
1 AATCGCAACGAAAG
14248 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
14265 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
14281 AATCGCAACG
1 AATCGCAACG
14291 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:14257 original size:33 final size:33
Alignment explanation
Indices: 14215--14307 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
14205 GCGAAACCAA
*
14215 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
14248 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
14281 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
14308 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:14304 original size:52 final size:54
Alignment explanation
Indices: 14178--14312 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
14168 TAGTTTACTT
*
14178 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
14236 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
14283 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
14313 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:14330 original size:19 final size:19
Alignment explanation
Indices: 14308--14436 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
14298 AAAATCGCAA
14308 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
14327 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
14341 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
14360 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
14374 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
14393 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
14412 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
14432 TGCGA
1 TGCGA
14437 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:14350 original size:33 final size:33
Alignment explanation
Indices: 14308--14399 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
14298 AAAATCGCAA
14308 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
14341 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
14374 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
14400 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:14639 original size:93 final size:93
Alignment explanation
Indices: 14480--14854 Score: 699
Period size: 93 Copynumber: 4.1 Consensus size: 93
14470 TTGAATGGAT
14480 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14545 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14573 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14638 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14666 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TATTT--CAGTGTTAAAGAAT--AC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14725 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14753 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
14818 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14846 AAATTTACT
1 AAATTTACT
14855 AAGCAATCTA
Statistics
Matches: 275, Mismatches: 1, Indels: 12
0.95 0.00 0.04
Matches are distributed among these distances:
87 64 0.23
88 4 0.01
89 19 0.07
91 19 0.07
92 4 0.01
93 165 0.60
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:14788 original size:180 final size:184
Alignment explanation
Indices: 14480--14854 Score: 695
Period size: 180 Copynumber: 2.0 Consensus size: 184
14470 TTGAATGGAT
14480 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACAGTGTTAAAGAATA-AC
14545 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
64 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
14610 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
129 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
14666 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TATTT-CAGTGTTAAAGAAT-ACAG
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACAGTGTTAAAGAATAACAG
14727 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
14792 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
14846 AAATTTACT
1 AAATTTACT
14855 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
180 131 0.70
182 14 0.07
184 5 0.03
185 4 0.02
186 34 0.18
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACAGTGTTAAAGAATAACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:16576 original size:14 final size:14
Alignment explanation
Indices: 16557--16645 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
16547 TTGAAATGAA
16557 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16571 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
16588 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
16604 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
16623 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16637 -ATCGCAACG
1 AATCGCAACG
16646 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
13 9 0.14
14 18 0.29
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:16594 original size:33 final size:33
Alignment explanation
Indices: 16549--16662 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
16539 TCTTTTGGTT
16549 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
16582 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16615 GAAATGAAAATCGCAACGAGAG-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16647 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
16663 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:16595 original size:19 final size:18
Alignment explanation
Indices: 16556--16667 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
16546 GTTGAAATGA
16556 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
16571 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
16588 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
16604 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
16621 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
16637 --ATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
16653 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
16668 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 4, Indels: 28
0.71 0.04 0.26
Matches are distributed among these distances:
13 7 0.09
14 16 0.21
15 4 0.05
16 12 0.16
17 11 0.14
19 27 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:16698 original size:14 final size:14
Alignment explanation
Indices: 16679--16733 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
16669 TTTGGTTTCG
16679 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
16693 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
16712 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
16726 CGTTGCGA
1 CGTTGCGA
16734 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:16896 original size:33 final size:33
Alignment explanation
Indices: 16854--16924 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
16844 AATACTAACT
*
16854 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
16887 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
16920 TGAAA
1 TGAAA
16925 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:17157 original size:22 final size:22
Alignment explanation
Indices: 17105--17159 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
17095 ATGTTGTGAG
**
17105 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
17127 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
17149 GGATTTCTTCG
1 GGATTTCTTCG
17160 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:17330 original size:20 final size:20
Alignment explanation
Indices: 17305--17498 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
17295 CTTTAAATAT
17305 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17325 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
17347 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17366 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
17386 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
17406 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17426 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17446 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
17466 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
17486 CGCGTTGCGATTT
1 CGCGTTGCGATTT
17499 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:17492 original size:60 final size:60
Alignment explanation
Indices: 17305--17498 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
17295 CTTTAAATAT
**
17305 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
17366 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
17426 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
17486 CGCGTTGCGATTT
1 CGCGTTGCGATTT
17499 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:17515 original size:21 final size:20
Alignment explanation
Indices: 17491--17567 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
17481 ATATTCGCGT
17491 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
17512 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
17532 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
17554 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
17568 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:17578 original size:20 final size:20
Alignment explanation
Indices: 17553--17604 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
17543 AAGAATCGCG
*
17553 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
17573 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
17593 TTGCGATTCTGG
1 TTGCGATTCTGG
17605 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:21194 original size:14 final size:15
Alignment explanation
Indices: 21165--21194 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21155 AATACCTTTT
21165 AAAATAATTTTAAAA
1 AAAATAATTTTAAAA
21180 AAAATAATTTTAAAA
1 AAAATAATTTTAAAA
21195 GATAAAAAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATTTTAAAA
Found at i:22814 original size:15 final size:14
Alignment explanation
Indices: 22769--22814 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
22759 TCTTCTCCCC
22769 TTTTTTTTCTTCGA
1 TTTTTTTTCTTCGA
22783 TTTTTTTTGCTTC--
1 TTTTTTTT-CTTCGA
22796 -TTTTTTTCTTCTGA
1 TTTTTTTTCTTC-GA
22810 TTTTT
1 TTTTT
22815 CGGGTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
11 4 0.15
12 7 0.26
14 8 0.30
15 8 0.30
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCTTCGA
Found at i:22826 original size:26 final size:26
Alignment explanation
Indices: 22770--22827 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
22760 CTTCTCCCCT
***
22770 TTTTTTTCTTCGATTTTTTTTGCTTC
1 TTTTTTTCTTCGATTTTTCGGGCTTC
*
22796 TTTTTTTCTTCTGATTTTTCGGGTTTC
1 TTTTTTTCTTC-GATTTTTCGGGCTTC
22823 TTTTT
1 TTTTT
22828 CCCTTGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.03, C:0.14, G:0.10, T:0.72
Consensus pattern (26 bp):
TTTTTTTCTTCGATTTTTCGGGCTTC
Found at i:23979 original size:134 final size:134
Alignment explanation
Indices: 23761--24304 Score: 732
Period size: 134 Copynumber: 4.1 Consensus size: 134
23751 TGTTATTCAT
* * * *
23761 GGAATATTGAATCAGAATCGATTTGCTTCACTACTCTTCGGGAAGATCAAATCTGGAAGAAGAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * ** *
23826 AATATGCTCCACTAATCTTTAGGGGAGATCAGACTCGTTAAAACTTTGATCCACTTCACTGCTCT
66 AATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCT
23891 TTAG
131 TTAG
* *
23895 GGAATATTGAATCAGAATCGATTTGCTTCACTACTCTTCAAGAAGACCAAATCTGAAAGAAGAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * * * * *
23960 AATCTGTTCCATTACTCTTTAGGGGAGA-CTAGACTCGATAAAATTTTGATTCACTTTATTGCTC
66 AATCTGCTCCACTACTCTTTAGGGGAGATC-AGACTCGAGAAAATTTTGATCCACTTCACTGCTC
*
24024 TTCAG
130 TTTAG
* * * * * *
24029 CGAAGATTAAATCATAATCGATTTCCTTCACTGCTCTTCAGGAAGGCCAAATCTGAAAGAAGAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * *
24094 AATCTTCTCCACTACTCTTTATGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTGCT-T
66 AATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCT
24158 TTCAG
131 TT-AG
* * *
24163 GGAAGATTGAATTAGAATCGATTTGCTTCACTGCTCTTCTGGAAGACCAAATCTGAAAGAAGAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * * **
24228 AATCTGCTCCACTACTCTTTAGGGGAGATCAAACTTGAGAAAATTGTGATCCACTTCACTATTCT
66 AATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCT
*
24293 TCAG
131 TTAG
24297 GGAAGATT
1 GGAAGATT
24305 TAATTGAACT
Statistics
Matches: 358, Mismatches: 48, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
133 3 0.01
134 352 0.98
135 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
GGAAGATTGAATCAGAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
AATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCT
TTAG
Found at i:24974 original size:45 final size:45
Alignment explanation
Indices: 24909--25258 Score: 306
Period size: 45 Copynumber: 7.8 Consensus size: 45
24899 GAAATATACT
*
24909 ACTAAAATG-TTGACTCTTCTTCGTGAGAAAGTCAAGAAGGACAAC
1 ACTAAAA-GATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAC
* *
24954 ACTAAAAGATCGACTTTTCTTCGCGAGAAAGT-AAGAAGGAACAAC
1 ACTAAAAGATTGACTCTTCTTCGCGAGAAAGTCAAGAAGG-ACAAC
* * * * *
24999 ACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGGAA-AACAAT
1 ACTAAAAGATTGACTCTTCTTCGCGAGAAAGTCAA-GAAGGACAAC
* * * *
25044 ACCAAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAAT
1 ACTAAAAGATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAC
* * * *
25089 ACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGGATGACAAC
1 ACTAAAAGATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAC
* * *
25134 ACCAAAAGATTGA-T-TTCTATTCGCGAGAAAGTCAAGAATGACAAT
1 ACTAAAAGATTGACTCTTC--TTCGCGAGAAAGTCAAGAAGGACAAC
* * * ** *
25179 ACTGAGATATTGACT-TCTCTTCATGAGAAAGTCAAG-A--ATAAC
1 ACTAAAAGATTGACTCT-TCTTCGCGAGAAAGTCAAGAAGGACAAC
* * * *
25221 ACTAAAAGATTTA-TCCATCTTCACGAGGAAGTCAAGAA
1 ACTAAAAGATTGACT-CTTCTTCGCGAGAAAGTCAAGAA
25259 TAATAAAGAT
Statistics
Matches: 253, Mismatches: 40, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.00
42 29 0.11
43 3 0.01
44 13 0.05
45 198 0.78
46 4 0.02
47 5 0.02
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (45 bp):
ACTAAAAGATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAC
Found at i:25027 original size:90 final size:89
Alignment explanation
Indices: 24908--25216 Score: 372
Period size: 90 Copynumber: 3.4 Consensus size: 89
24898 GGAAATATAC
* * ** * *
24908 TACTAAAATGTTGACTCTTCTTCGTGAGAAAGTCAAGAAGGACAACACTAAAAGATCGACTTTTC
1 TACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAACACCAAAAGATTGACTTTTC
24973 TTCGCGAGAAAGT-AAGAAGGAACAA
65 TTCGCGAGAAAGTCAAGAA-GAACAA
* * * **
24998 CACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGGAAAACAATACCAAAAGATTGACTCATC
1 TACTAAAATATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAACACCAAAAGATTGACTTTTC
25063 TTCGCGAGAAAGTCAAGAAGAACAA
65 TTCGCGAGAAAGTCAAGAAGAACAA
* * *
25088 TACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGGATGACAACACCAAAAGATTGA-TTTCT
1 TACTAAAATATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAACACCAAAAGATTGACTTT-T
*
25152 ATTCGCGAGAAAGTCAAGAATG-ACAA
64 CTTCGCGAGAAAGTCAAGAA-GAACAA
* * * *
25178 TACTGAGATATTGACTTCTCTTCATGAGAAAGTCAAGAA
1 TACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGAA
25217 TAACACTAAA
Statistics
Matches: 188, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
89 3 0.02
90 176 0.94
91 9 0.05
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (89 bp):
TACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGAAGACAACACCAAAAGATTGACTTTTCT
TCGCGAGAAAGTCAAGAAGAACAA
Found at i:25116 original size:135 final size:133
Alignment explanation
Indices: 24918--25258 Score: 368
Period size: 135 Copynumber: 2.5 Consensus size: 133
24908 TACTAAAATG
* * ** *
24918 TTGACTCTTCTTCGTGAGAAAGTCAAGAAGGACAACACTAAAAGATCGACTTTTCTTCGCGAGAA
1 TTGACTC-TCTTCGTGAGAAAGTCAAGAAGAACAA-ACTAAAAGATTGACTCATCTTCACGAGAA
* * *
24983 AGT-AAGAAGGAACAACACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGGAA-AACAATAC
64 AGTCAAGAAGG-ACAACACCAAAAGATTGACTCCTATTCACGAGAAAGTCAA-GAATAACAATAC
25046 CAAAAGA
127 CAAAAGA
*
25053 TTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAATACTAAAAGATTGACTCATCTTCACGAGAA
1 TTGACTC-TCTTCGTGAGAAAGTCAAGAAGAACAA-ACTAAAAGATTGACTCATCTTCACGAGAA
* * * * * * **
25118 AGTCAAGGATGACAACACCAAAAGATTGATTTCTATTCGCGAGAAAGTCAAGAATGACAATACTG
64 AGTCAAGAAGGACAACACCAAAAGATTGACTCCTATTCACGAGAAAGTCAAGAATAACAATACCA
* *
25183 AGATA
129 AAAGA
* * * *
25188 TTGACTTCTCTTCATGAGAAAGTCAAGAATAAC--ACTAAAAGATTTA-TCCATCTTCACGAGGA
1 TTGAC-TCTCTTCGTGAGAAAGTCAAGAAGAACAAACTAAAAGATTGACT-CATCTTCACGAGAA
25250 AGTCAAGAA
64 AGTCAAGAA
25259 TAATAAAGAT
Statistics
Matches: 175, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
131 1 0.01
132 33 0.19
134 3 0.02
135 131 0.75
136 7 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (133 bp):
TTGACTCTCTTCGTGAGAAAGTCAAGAAGAACAAACTAAAAGATTGACTCATCTTCACGAGAAAG
TCAAGAAGGACAACACCAAAAGATTGACTCCTATTCACGAGAAAGTCAAGAATAACAATACCAAA
AGA
Found at i:25280 original size:38 final size:38
Alignment explanation
Indices: 25187--26037 Score: 922
Period size: 38 Copynumber: 22.0 Consensus size: 38
25177 ATACTGAGAT
* *
25187 ATTGACTTCTCTTCATGAGAAAGTCAAGAATAACACTAAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-AC--AAAG
* * *
25229 ATTTA-TCCATCTTCACGAGGAAGTCAAGAATAATAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
25267 ATCGAATTCTCTTCATGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
** * *
25309 ATTGAC-TCTTCTTTGCGAGGGAGTCAAGAATAATAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACAAAG
* *
25347 ATTGACTTCTCTTAACGAGGAAGTCAAGAGTAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
25385 ATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
25423 ATCGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
** * *
25465 ATTGACACCTCTTCGCGAGGGAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
25503 ATTGACTTCTCTTTACGAGGAAGTCAAGAGTAATAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
25541 ATTGACTTCTTTTCACGAGGAAGTTAAGAATAAAAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
25579 ATTGATTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * * * *
25621 ATTGACTCCTATTCGCAAGGGAA-TCAGGAATAACAAAG
1 ATTGACTTCTCTTCACGA-GGAAGTCAAGAATAACAAAG
* * *
25659 ATTGACTTCTATTCACGAGGAAGTCAATAGTAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
25697 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * *
25735 ATCGAATTATCTTCACGAGGAAGTCAAGAGTAGCAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
25773 ATTGA-TCTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACT-TCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
25811 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
25849 ATTGACTTCTCTTCACAAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
25887 ATTGACTCCTCTTCAAGA-GAGAGTCAAGAATAAAAAAG
1 ATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAG
* * *
25925 GTTGACTTCTTTTCACGAGGAAGTCAAGAATAACAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * *
25963 ATCGACTTCTCTTCATGAAGAAGTCAAGAAGGAA-AAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAA-TAACAAAG
* * * * *
26001 ATTAACTTATCTTCAAGAGGAAGTTAATAATAACAAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
26038 TATCAACTGA
Statistics
Matches: 679, Mismatches: 106, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
37 8 0.01
38 541 0.80
39 9 0.01
40 1 0.00
41 5 0.01
42 111 0.16
43 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:25509 original size:156 final size:156
Alignment explanation
Indices: 25187--26037 Score: 1033
Period size: 156 Copynumber: 5.5 Consensus size: 156
25177 ATACTGAGAT
* * * * *
25187 ATTGACTTCTCTTCATGAGAAAGTCAAGAATAACACTAAAAGATTTA-TCCATCTTCACGAGGAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAGT-A-AC--AAAGATTGACTTC-TCTTCACGAGGAA
* *
25251 GTCAAGAATAATAAAGATCGAATTCTCTTCATGAGGAAGTCAAGAATAACATTGAAAGATTGACT
61 GTCAAGAATAACAAAGATCGAATTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACT
* * *
25316 CTTCTTTGCGAGGGAGTCAAGAATAATAAAG
126 CCTCTTCGCGAGGGAGTCAAGAATAACAAAG
* *
25347 ATTGACTTCTCTTAACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGAAAGTCAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * *
25412 GAATAACAAAGATCGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAAAGATTGACACCTCT
66 GAATAACAAAGATCGAATTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCT
25477 TCGCGAGGGAGTCAAGAATAACAAAG
131 TCGCGAGGGAGTCAAGAATAACAAAG
* * * *
25503 ATTGACTTCTCTTTACGAGGAAGTCAAGAGTAATAAAGATTGACTTCTTTTCACGAGGAAGTTAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * * *
25568 GAATAAAAAAGATTGATTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTAT
66 GAATAACAAAGATCGAATTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCT
* * *
25633 TCGCAAGGGAATCAGGAATAACAAAG
131 TCGCGAGGGAGTCAAGAATAACAAAG
* *
25659 ATTGACTTCTATTCACGAGGAAGTCAATAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * *
25724 GAATAACAAAGATCGAATTATCTTCACGAGGAAGTCAAGAGTAGC----AAAGATTGA-TCTCTC
66 GAATAACAAAGATCGAATTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTC-CTC
* *
25784 TTCACGAGGAAGTCAAGAATAACAAAG
130 TTCGCGAGGGAGTCAAGAATAACAAAG
* * * * *
25811 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAATATTGACTTCTCTTCACAAGAAAGTCAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * * * * * *
25876 GAATAACAAAGATTGACTCCTCTTCAAGA-GAGAGTCAAGAATAA-A---AAAGGTTGACTTCTT
66 GAATAACAAAGATCGAATTCTCTTCACGAGGA-AGTCAAGAATAACATTGAAAGATTGACTCCTC
* * *
25936 TTCACGAGGAAGTCAAGAATAACAAAT
130 TTCGCGAGGGAGTCAAGAATAACAAAG
* * * * * * * *
25963 ATCGACTTCTCTTCATGAAGAAGTCAAGAAGGAA-AAAGATTAACTTATCTTCAAGAGGAAGTTA
1 ATTGACTTCTCTTCACGAGGAAGTCAAG-AGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
*
26027 ATAATAACAAA
65 AGAATAACAAA
26038 TATCAACTGA
Statistics
Matches: 609, Mismatches: 76, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
151 4 0.01
152 219 0.36
153 4 0.01
156 350 0.57
157 2 0.00
158 2 0.00
159 1 0.00
160 27 0.04
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (156 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
GAATAACAAAGATCGAATTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCT
TCGCGAGGGAGTCAAGAATAACAAAG
Found at i:27888 original size:9 final size:9
Alignment explanation
Indices: 27874--27952 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
27864 ATTTATTTTC
27874 TTTCTCTTT
1 TTTCTCTTT
27883 TTTCTCTTT
1 TTTCTCTTT
** *
27892 CCTCTTTTT
1 TTTCTCTTT
*
27901 CTTTTTC-TT
1 -TTTCTCTTT
27910 TTTCTCTTT
1 TTTCTCTTT
* *
27919 TCTCTTTTT
1 TTTCTCTTT
*
27928 TATTTTCTATCT
1 T-TTCTCT-T-T
27940 TTTCTCTTT
1 TTTCTCTTT
27949 TTTC
1 TTTC
27953 CTTCTTCTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
8 5 0.10
9 32 0.63
10 6 0.12
11 6 0.12
12 2 0.04
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTCTTT
Found at i:27906 original size:7 final size:7
Alignment explanation
Indices: 27869--27964 Score: 70
Period size: 7 Copynumber: 13.4 Consensus size: 7
27859 ACTTAATTTA
27869 TTTTC-T
1 TTTTCTT
*
27875 TTCTCTT
1 TTTTCTT
*
27882 TTTTCTC
1 TTTTCTT
*
27889 TTTCCTCT
1 TTTTCT-T
27897 TTTTC-T
1 TTTTCTT
27903 TTTTCTT
1 TTTTCTT
27910 TTTCTCTT
1 TTT-TCTT
*
27918 TTCTCTT
1 TTTTCTT
*
27925 TTTTATT
1 TTTTCTT
27932 TTCTATCTT
1 TT-T-TCTT
*
27941 TTCTCTT
1 TTTTCTT
*
27948 TTTTCCT
1 TTTTCTT
*
27955 TCTTCTT
1 TTTTCTT
27962 TTT
1 TTT
27965 CTATATTTTC
Statistics
Matches: 68, Mismatches: 16, Indels: 11
0.72 0.17 0.12
Matches are distributed among these distances:
6 10 0.15
7 42 0.62
8 11 0.16
9 5 0.07
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTT
Found at i:27933 original size:27 final size:28
Alignment explanation
Indices: 27869--27977 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 28
27859 ACTTAATTTA
* * *
27869 TTTTCTTTCTCTTTTTTCTCTTTCCTCT
1 TTTTCTTTTTCATTTTTCTCTTTTCTCT
27897 TTTTCTTTTTC-TTTTTCTCTTTTCTCT
1 TTTTCTTTTTCATTTTTCTCTTTTCTCT
*
27924 TTTT-TATTTTCTATCTTTTCTCTTTTTTCCT
1 TTTTCT-TTTTC-AT-TTTTCTCTTTTCT-CT
*
27955 TCTTCTTTTTCTATATTTTCTCT
1 TTTTCTTTTTC-AT-TTTTCTCT
27978 CTCTCTCTCT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.01
27 24 0.34
28 10 0.14
29 1 0.01
30 12 0.17
31 21 0.30
32 1 0.01
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTCTTTTTCATTTTTCTCTTTTCTCT
Found at i:27965 original size:31 final size:30
Alignment explanation
Indices: 27882--27977 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 30
27872 TCTTTCTCTT
*
27882 TTTTCTCTTTCCTCTTTTTCT-TTTTC--T-
1 TTTTCTCTTTTCTC-TTTTCTATTTTCTATA
* *
27909 TTTTCTCTTTTCTCTTTTTTATTTTCTATC
1 TTTTCTCTTTTCTCTTTTCTATTTTCTATA
*
27939 TTTTCTCTTTTTTCCTTCTTCT-TTTTCTATA
1 TTTTCTCTTTTCT-CTT-TTCTATTTTCTATA
27970 TTTTCTCT
1 TTTTCTCT
27978 CTCTCTCTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.09
27 18 0.31
29 1 0.02
30 12 0.21
31 19 0.33
32 3 0.05
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTCTCTTTTCTCTTTTCTATTTTCTATA
Found at i:31040 original size:6 final size:6
Alignment explanation
Indices: 31029--31058 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31019 ACAAAACCAT
*
31029 AATGCA AATGCA AATACA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA
31059 GAAGGTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:34255 original size:14 final size:14
Alignment explanation
Indices: 34232--34273 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
34222 GTTCTTCTCC
34232 ATTTTCTTTTCTTCG
1 ATTTT-TTTTCTTCG
*
34247 GTTTTTTTTCTTCG
1 ATTTTTTTTCTTCG
34261 ATTTTTTTTCTTC
1 ATTTTTTTTCTTC
34274 TTTTTCCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (14 bp):
ATTTTTTTTCTTCG
Found at i:34938 original size:3 final size:3
Alignment explanation
Indices: 34930--34989 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
34920 AAATAAACAT
34930 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34978 TAA TAA TAA TAA
1 TAA TAA TAA TAA
34990 CAACAACGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35702 original size:22 final size:22
Alignment explanation
Indices: 35676--35727 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
35666 AGATTAATTC
35676 TTTGTTATTTTTTTCTTGTCAA
1 TTTGTTATTTTTTTCTTGTCAA
*
35698 TTTGTT-GTTTTTTCTTGTCAA
1 TTTGTTATTTTTTTCTTGTCAA
*
35719 TTTTTTATT
1 TTTGTTATT
35728 CATTAATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTGTTATTTTTTTCTTGTCAA
Found at i:43075 original size:42 final size:43
Alignment explanation
Indices: 42990--43267 Score: 317
Period size: 43 Copynumber: 6.7 Consensus size: 43
42980 TGGTATTTAG
* * *
42990 ACAAACGCCGCTATTAACTGTGTATTTAGCGGCGTTTGGCTTT
1 ACAAACGCCGCTATTGACTTTGTATTTAGCGGCGTTTGTCTTT
* *
43033 ATAAACGCCGCTATTGACTTTGTA-TTAGCGGCATTTGTCTTT
1 ACAAACGCCGCTATTGACTTTGTATTTAGCGGCGTTTGTCTTT
* *
43075 ACAAACGCCGCTATTGA-TTGTGCATTTAGCGGCGTTT-TTTTT
1 ACAAACGCCGCTATTGACTT-TGTATTTAGCGGCGTTTGTCTTT
*
43117 ACAAACGCCGCTATTGA-TTGTATATTTAGCGGCGTTTGTCTTT
1 ACAAACGCCGCTATTGACTT-TGTATTTAGCGGCGTTTGTCTTT
* * *
43160 ATAAACGCCGCTATTGACTGTATATTTAGCGGC----G--TTT
1 ACAAACGCCGCTATTGACTTTGTATTTAGCGGCGTTTGTCTTT
* *
43197 ACAAACGCCGCTATTGA-TTGTGAATTTAGCGGCGTTTTTCTTT
1 ACAAACGCCGCTATTGACTT-TGTATTTAGCGGCGTTTGTCTTT
* *
43240 ACAAACGCCTCTATTGACTATGTATTTA
1 ACAAACGCCGCTATTGACTTTGTATTTA
43268 ATGTCATTTG
Statistics
Matches: 201, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
36 1 0.00
37 30 0.15
39 1 0.00
41 2 0.01
42 74 0.37
43 91 0.45
44 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (43 bp):
ACAAACGCCGCTATTGACTTTGTATTTAGCGGCGTTTGTCTTT
Found at i:43146 original size:85 final size:83
Alignment explanation
Indices: 42990--43267 Score: 352
Period size: 85 Copynumber: 3.3 Consensus size: 83
42980 TGGTATTTAG
* *
42990 ACAAACGCCGCTATTAACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGACTT-T
1 ACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTT---TTTACAAACGCCGCTATTGA-TTGT
* *
43054 GTA-TTAGCGGCATTTGTCTTT
62 ATATTTAGCGGCGTTTGTCTTT
* *
43075 ACAAACGCCGCTATTGATTGTGCATTTAGCGGCGTTTTTTTTACAAACGCCGCTATTGATTGTAT
1 ACAAACGCCGCTATTGACTGTGTATTTAGCGGCG--TTTTTTACAAACGCCGCTATTGATTGTAT
43140 ATTTAGCGGCGTTTGTCTTT
64 ATTTAGCGGCGTTTGTCTTT
* *
43160 ATAAACGCCGCTATTGACTGTATATTTAGCGGCG---TTTACAAACGCCGCTATTGATTGTGA-A
1 ACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTTTTACAAACGCCGCTATTGATTGT-ATA
*
43221 TTTAGCGGCGTTTTTCTTT
65 TTTAGCGGCGTTTGTCTTT
* *
43240 ACAAACGCCTCTATTGACTATGTATTTA
1 ACAAACGCCGCTATTGACTGTGTATTTA
43268 ATGTCATTTG
Statistics
Matches: 173, Mismatches: 15, Indels: 15
0.85 0.07 0.07
Matches are distributed among these distances:
80 67 0.39
81 1 0.01
83 2 0.01
84 22 0.13
85 78 0.45
87 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (83 bp):
ACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTTTTACAAACGCCGCTATTGATTGTATAT
TTAGCGGCGTTTGTCTTT
Found at i:46770 original size:13 final size:13
Alignment explanation
Indices: 46752--46776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46742 CCTGTAGAGT
46752 AGGGCATAGTAGA
1 AGGGCATAGTAGA
46765 AGGGCATAGTAG
1 AGGGCATAGTAG
46777 GGCTCGCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.40, T:0.16
Consensus pattern (13 bp):
AGGGCATAGTAGA
Found at i:47204 original size:37 final size:35
Alignment explanation
Indices: 47000--47409 Score: 263
Period size: 36 Copynumber: 11.8 Consensus size: 35
46990 TTTTGACAAA
* *
47000 ATATAATATATAATTTCAGAAAACGATTTTGAAAA-TGT
1 ATAT-ATATATAGTTTTA-AAAAC-ATTTTGAAAACT-T
* * * *
47038 ATAT-TATATGGTTTTTGAAAATATTTTGAATA--T
1 ATATATATATAG-TTTTAAAAACATTTTGAAAACTT
* *
47071 ATATAATATATAG-TTT-GAAATATTTTGAAAACATT
1 ATAT-ATATATAGTTTTAAAAACATTTTGAAAAC-TT
* *
47106 ATATAGATTATA-TTTTCAAAACATTTTGAAAACTT
1 ATATATA-TATAGTTTTAAAAACATTTTGAAAACTT
* *
47141 ATATAATATATAGTTTTTAAAACATTTGGAAAACTT
1 ATAT-ATATATAGTTTTAAAAACATTTTGAAAACTT
* *
47177 ATATAGTATATAGTTTTTTAAAACATTTTTGAAAAAATT
1 ATATA-TATATAG-TTTTAAAAACA-TTTTG-AAAACTT
* *
47216 ATATA-ATATAGTTTTAAAAACATTTTTTTGAAAAATC
1 ATATATATATAGTTTTAAAAACA---TTTTGAAAACTT
* *
47253 ATATAACATATAGTTTTAAAAAACATTTTGGAAAAATT
1 ATAT-ATATATAGTTTT-AAAAACATTTT-GAAAACTT
47291 ATA-ATATATAGTTTTAAAAACAATTTTGAAAAC-T
1 ATATATATATAGTTTTAAAAAC-ATTTTGAAAACTT
* **
47325 -TATA-ATAT--TTTT-GAAGTATTTTGAAAAC-T
1 ATATATATATAGTTTTAAAAACATTTTGAAAACTT
* *
47354 ATATAATATATTGTTTT-AAAAC-TTTT-TAAA--T
1 ATAT-ATATATAGTTTTAAAAACATTTTGAAAACTT
47385 ATA-ATATATAGTTTTAAAAA-ATTTT
1 ATATATATATAGTTTTAAAAACATTTT
47410 TGAAGTATAT
Statistics
Matches: 312, Mismatches: 30, Indels: 68
0.76 0.07 0.17
Matches are distributed among these distances:
29 23 0.07
30 13 0.04
31 9 0.03
32 20 0.06
33 18 0.06
34 10 0.03
35 49 0.16
36 83 0.27
37 34 0.11
38 25 0.08
39 21 0.07
40 7 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (35 bp):
ATATATATATAGTTTTAAAAACATTTTGAAAACTT
Found at i:47226 original size:73 final size:71
Alignment explanation
Indices: 46972--47328 Score: 279
Period size: 73 Copynumber: 5.0 Consensus size: 71
46962 GTATACAATA
* * ** * *
46972 ATATAGTTTGTGAAAATGTTTTGACAAAA-TATA-ATATATAATTTCAGAAAACGATTTTGAAAA
1 ATATAGTTTTTAAAAACATTTTGA-AAAATTATATATATATAGTTTTA-AAAAC-ATTTTGAAAA
*
47035 -TGTATAT-T
63 CT-TATATAG
* * * * * *
47043 ATATGGTTTTTGAAAATATTTTG-AATA-TATATAATATATAG-TTT-GAAATATTTTGAAAACA
1 ATATAGTTTTTAAAAACATTTTGAAAAATTATAT-ATATATAGTTTTAAAAACATTTTGAAAAC-
47104 TTATATAG
64 TTATATAG
* * * *
47112 AT-TA-TATTTTCAAAACATTTTGAAAACTTATATAATATATAGTTTTTAAAACATTTGGAAAAC
1 ATATAGT-TTTTAAAAACATTTTGAAAAATTATAT-ATATATAGTTTTAAAAACATTTTGAAAAC
47175 TTATATAG
64 TTATATAG
*
47183 TATATAGTTTTTTAAAACATTTTTGAAAAAATTATATA-ATATAGTTTTAAAAACATTTTTTTGA
1 -ATATAGTTTTTAAAAACA-TTTTG-AAAAATTATATATATATAGTTTTAAAAACA---TTTTGA
* * *
47247 AAAATCATATAAC
60 AAACTTATAT-AG
*
47260 ATATAGTTTTAAAAAACATTTTGGAAAAATTATA-ATATATAGTTTTAAAAACAATTTTGAAAAC
1 ATATAGTTTTTAAAAACATTTT-GAAAAATTATATATATATAGTTTTAAAAAC-ATTTTGAAAAC
47324 TTATA
64 TTATA
47329 ATATTTTTGA
Statistics
Matches: 236, Mismatches: 28, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
67 11 0.05
68 23 0.10
69 12 0.05
70 16 0.07
71 38 0.16
72 15 0.06
73 41 0.17
74 8 0.03
75 40 0.17
76 31 0.13
77 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (71 bp):
ATATAGTTTTTAAAAACATTTTGAAAAATTATATATATATAGTTTTAAAAACATTTTGAAAACTT
ATATAG
Found at i:47292 original size:75 final size:75
Alignment explanation
Indices: 47123--47322 Score: 232
Period size: 75 Copynumber: 2.7 Consensus size: 75
47113 TTATATTTTC
* * * * **
47123 AAAACATTTT-GAAAACTTATATAATATATAGTTTTTAAAACA--TTTGGAAAACTTATATAGTA
1 AAAACATTTTGGAAAAATTATAT-ATATATAGTTTTAAAAACATTTTTGGAAAAATCATATAACA
**
47185 TATAGTTTTTT
65 TATAGTTTTAA
* *
47196 AAAACATTTTTGAAAAAATTATATA-ATATAGTTTTAAAAACATTTTTTTGAAAAATCATATAAC
1 AAAACA-TTTTGGAAAAATTATATATATATAGTTTTAAAAACA-TTTTTGGAAAAATCATATAAC
47260 ATATAGTTTTAA
64 ATATAGTTTTAA
*
47272 AAAACATTTTGGAAAAATTATA-ATATATAGTTTTAAAAACAATTTT-GAAAA
1 AAAACATTTTGGAAAAATTATATATATATAGTTTTAAAAACATTTTTGGAAAA
47323 CTTATAATAT
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
73 27 0.25
74 10 0.09
75 42 0.39
76 30 0.28
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (75 bp):
AAAACATTTTGGAAAAATTATATATATATAGTTTTAAAAACATTTTTGGAAAAATCATATAACAT
ATAGTTTTAA
Found at i:47409 original size:29 final size:29
Alignment explanation
Indices: 47354--47409 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
47344 TTTGAAAACT
* **
47354 ATATAATATATTGTTTTAAAACTTTTTAA
1 ATATAATATATAGTTTTAAAAAATTTTAA
47383 ATATAATATATAGTTTTAAAAAATTTT
1 ATATAATATATAGTTTTAAAAAATTTT
47410 TGAAGTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (29 bp):
ATATAATATATAGTTTTAAAAAATTTTAA
Done.