Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005971.1 Hibiscus syriacus cultivar Beakdansim tig00014039_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: 75568
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7247 original size:2 final size:2
Alignment explanation
Indices: 7240--7281 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7230 TAAAGTTATC
7240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7282 TATTCATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7492 original size:7 final size:7
Alignment explanation
Indices: 7482--7531 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
7472 TTCATTTTCC
7482 TTTTTTA
1 TTTTTTA
7489 TTTTTTA
1 TTTTTTA
7496 TTTTTTA
1 TTTTTTA
*
7503 -CTTTTA
1 TTTTTTA
7509 CTTCTTTTA
1 -TT-TTTTA
7518 TTTTCTTA
1 TTTT-TTA
7526 TTTTTT
1 TTTTTT
7532 CTCATTCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.14
7 18 0.49
8 9 0.24
9 5 0.14
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:12525 original size:24 final size:22
Alignment explanation
Indices: 12483--12559 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
12473 GAATGCAATT
12483 AGTGCATCGATGCA---TAAGG
1 AGTGCATCGATGCATTGTAAGG
12502 AGTGCATCGATGCATATGTTAAGG
1 AGTGCATCGATGCAT-TG-TAAGG
*
12526 -GATGCATCGATACATTGT-A-G
1 AG-TGCATCGATGCATTGTAAGG
*
12546 AATGCATCGATGCA
1 AGTGCATCGATGCA
12560 CTTCAAGGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 14 0.29
20 12 0.25
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (22 bp):
AGTGCATCGATGCATTGTAAGG
Found at i:18957 original size:18 final size:18
Alignment explanation
Indices: 18934--18968 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18924 TATTCAAACT
*
18934 ATCCCTATTTGCCTATAC
1 ATCCCTATTTACCTATAC
18952 ATCCCTATTTACCTATA
1 ATCCCTATTTACCTATA
18969 TCCGGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (18 bp):
ATCCCTATTTACCTATAC
Found at i:22672 original size:13 final size:12
Alignment explanation
Indices: 22654--22700 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
22644 TCCTAAGTCG
22654 AAAAAAAATAAA
1 AAAAAAAATAAA
22666 TAAAAAAAATAAA
1 -AAAAAAAATAAA
22679 AACAAAAAA-ACAA
1 AA-AAAAAATA-AA
22692 AAAACAAAA
1 AAAA-AAAA
22701 AGAGAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.16
13 26 0.84
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:22673 original size:14 final size:13
Alignment explanation
Indices: 22654--22701 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
22644 TCCTAAGTCG
*
22654 AAAAAAAATAAAT
1 AAAAAAAATAAAA
22667 AAAAAAAATAAAA
1 AAAAAAAATAAAA
*
22680 ACAAAAAAACAAAA
1 A-AAAAAAATAAAA
22694 AACAAAAA
1 AA-AAAAA
22702 GAGAAAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 14 0.45
14 17 0.55
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:22674 original size:15 final size:14
Alignment explanation
Indices: 22654--22701 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
22644 TCCTAAGTCG
* *
22654 AAAAAAAATAAATA
1 AAAAAAAAAAAACA
22668 AAAAAAATAAAAACA
1 AAAAAAA-AAAAACA
22683 AAAAAACAAAAAACA
1 AAAAAA-AAAAAACA
22698 AAAA
1 AAAA
22702 GAGAAAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 7 0.23
15 22 0.73
16 1 0.03
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:22770 original size:20 final size:21
Alignment explanation
Indices: 22741--22805 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
22731 AAGACGTCCT
22741 AAATTGAAAAAAGAAAAAGAA
1 AAATTGAAAAAAGAAAAAGAA
* *
22762 AAATT-AAAAGAGGAAAAGAA
1 AAATTGAAAAAAGAAAAAGAA
** *
22782 AAAAAGAAAAAAG-AGAAGAA
1 AAATTGAAAAAAGAAAAAGAA
22802 AAAT
1 AAAT
22806 AAGGTGGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (21 bp):
AAATTGAAAAAAGAAAAAGAA
Found at i:22800 original size:28 final size:28
Alignment explanation
Indices: 22746--22800 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
22736 GTCCTAAATT
**
22746 GAAAAAAGAAAAAGAAAAATTAAAAGAG
1 GAAAAAAGAAAAAGAAAAAAGAAAAGAG
*
22774 GAAAAGAA-AAAAAGAAAAAAGAGAAGA
1 GAAAA-AAGAAAAAGAAAAAAGAAAAGA
22801 AAAATAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (28 bp):
GAAAAAAGAAAAAGAAAAAAGAAAAGAG
Found at i:24095 original size:109 final size:109
Alignment explanation
Indices: 23949--24145 Score: 333
Period size: 109 Copynumber: 1.8 Consensus size: 109
23939 ATTTCAGAGC
* * *
23949 CAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGATAACACAAGCTCAACTTCAC-AGCGAA
1 CAATTTCAACTTCACAACGAAGGATATTGAACCCAAGACAACACAAGCTCAACTTCACGA-CGAA
24013 GGGGCGGCTGATTGTCAACAAATAGCCTTTCAATTTTTATTCAGT
65 GGGGCGGCTGATTGTCAACAAATAGCCTTTCAATTTTTATTCAGT
* *
24058 CAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGAACCCAAGACAACACAAGCTCAACTTCACGACGAAG
24123 GGGCGGCTGATTGTCAACAAATA
66 GGGCGGCTGATTGTCAACAAATA
24146 ATTTCCCAGT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 81 0.99
110 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (109 bp):
CAATTTCAACTTCACAACGAAGGATATTGAACCCAAGACAACACAAGCTCAACTTCACGACGAAG
GGGCGGCTGATTGTCAACAAATAGCCTTTCAATTTTTATTCAGT
Found at i:34801 original size:2 final size:2
Alignment explanation
Indices: 34794--34860 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
34784 TAAAGTTATC
34794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
34836 AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34861 ACTATTATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42646 original size:2 final size:2
Alignment explanation
Indices: 42641--42673 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42631 TATTTTGAAT
42641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42674 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43883 original size:16 final size:18
Alignment explanation
Indices: 43862--43899 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
43852 AACGTCTTTT
43862 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
*
43878 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
43896 AAAA
1 AAAA
43900 GTTGGTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:46134 original size:3 final size:3
Alignment explanation
Indices: 46128--46188 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
46118 AAATTATTAT
* *
46128 TAA TAA TAA TAC TAA TAA TAT TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
46173 -ATA TAA TAA T-A TAA TA
1 TA-A TAA TAA TAA TAA TA
46189 TTTTTAAGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:46143 original size:12 final size:11
Alignment explanation
Indices: 46128--46188 Score: 72
Period size: 12 Copynumber: 5.5 Consensus size: 11
46118 AAATTATTAT
46128 TAATAATAATA
1 TAATAATAATA
*
46139 CTAATAATATTAA
1 -TAATAATAAT-A
46152 TAATAATAAATA
1 TAATAAT-AATA
46164 TAATAATAA-A
1 TAATAATAATA
46174 T-ATAATAATA
1 TAATAATAATA
46184 TAATA
1 TAATA
46189 TTTTTAAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
9 7 0.16
10 4 0.09
11 5 0.12
12 24 0.56
13 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAATAATA
Found at i:47512 original size:136 final size:136
Alignment explanation
Indices: 46359--47499 Score: 1834
Period size: 136 Copynumber: 8.4 Consensus size: 136
46349 ACAATTTTTT
* * * * * * *
46359 TCATTATGAACTTCTTCTCTCT-TGTTGAATGAGTTCTTCTCATTATGAATTCTTCACTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* * * * *
46423 GTTAATCCCTCAAGCGAGGTGTTACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCAAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
46488 CTCTTC
131 CTCTTC
* * *
46494 TCATTATGAACTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTAGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
** * *
46559 GTCAATTTCTTAAGCGAGGCGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
46624 CTCTTC
131 CTCTTC
* * *
46630 TCATTATGAACTTCTTCTTCCTCTATCGGATGAGTTTTTCTCATTATAAACTCTCCATTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* * *
46695 GTCAATTCCTCAAGCGAGGCGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
46760 CTCTTC
131 CTCTTC
*
46766 TCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* * * *
46831 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCAAGTGGTAGGTTGAACAAA
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
46896 CTCTTC
131 CTCTTC
* * *
46902 TCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTTTTCTCATTATGAACTCTCCATTGAAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* * * *
46967 GTCAATCCCTCAAGCGAGGTGTCACTGATTCAAAATGCCGTGAATTGAGTGATAGGTTGAACAAA
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
47032 CTCTTC
131 CTCTTC
47038 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
47103 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
*
47168 CTATTC
131 CTCTTC
* *
47174 TCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* * *
47239 GTCAATTCCTCAAGCGAGGCGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
47304 CTCTTC
131 CTCTTC
*
47310 TCATTATGAACTTCTTCTCTCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
* *
47375 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATTGAGTGATAGGTCGAACAAG
66 GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
47440 CTCTTC
131 CTCTTC
* * *
47446 TCATTATGAACTTCTTCTCCTTCTGTCGGATGGGTTCTTCTCATTATGAACTCT
1 TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCT
47500 GTACTGGAAA
Statistics
Matches: 938, Mismatches: 67, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
135 20 0.02
136 918 0.98
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
TCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
GTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAACAAG
CTCTTC
Found at i:47891 original size:76 final size:76
Alignment explanation
Indices: 47792--47934 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
47782 GAGATAAATT
* *
47792 TTGTTTCGAAGGAAAATTATCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTCAAGTGA
1 TTGTTTCGAAGGAAAATTATCTCAAGCAAGAAGAAGTAAGTTTTAAGAAAAACCATCTCAAGGGA
47857 GATTCAAGTTC
66 GATTCAAGTTC
* * * ** *
47868 TTGTTTC-AAGGGAAAGTTGTCTCAAGCAAGAAGAATTTGGTTTTAAGAAAAACCATCTTAAGGG
1 TTGTTTCGAA-GGAAAATTATCTCAAGCAAGAAGAAGTAAGTTTTAAGAAAAACCATCTCAAGGG
47932 AGA
65 AGA
47935 CAAAACTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 2 0.03
76 56 0.97
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (76 bp):
TTGTTTCGAAGGAAAATTATCTCAAGCAAGAAGAAGTAAGTTTTAAGAAAAACCATCTCAAGGGA
GATTCAAGTTC
Found at i:47968 original size:37 final size:39
Alignment explanation
Indices: 47907--48021 Score: 117
Period size: 45 Copynumber: 2.8 Consensus size: 39
47897 GAAGAATTTG
* * * *
47907 GTTTTAAGAAAAACCATCTTAAGGGAGACAAAA-CTT-T
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATCTTGT
*
47944 GTTTCAAGAGAAACTATCTCAAGGGAGACGTTCTTAAAATTTTGT
1 GTTTCAAGAGAAACTATCTCAAGGGAGA----C--AAAATCTTGT
47989 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
48022 AAATTTCAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
37 24 0.37
39 4 0.06
41 2 0.03
43 4 0.06
44 2 0.03
45 29 0.45
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (39 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATCTTGT
Found at i:48040 original size:65 final size:65
Alignment explanation
Indices: 47962--48167 Score: 358
Period size: 65 Copynumber: 3.2 Consensus size: 65
47952 AGAAACTATC
*
47962 TCAAGGGAGACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAATT
1 TCAAGGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAATT
*
48027 TCAAGGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAAAT
1 TCAAGGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAATT
* ***
48092 TCAACGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTT
1 TCAAGGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAATT
48157 TCAAGGGAAAC
1 TCAAGGGAAAC
48168 TGTCTCAAGG
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 133 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (65 bp):
TCAAGGGAAACGTTCTTAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAAAATT
Found at i:48167 original size:35 final size:35
Alignment explanation
Indices: 48120--48228 Score: 173
Period size: 35 Copynumber: 3.1 Consensus size: 35
48110 AAATTTTGTG
* *
48120 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
48155 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
48190 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTT
1 -TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
48226 TTT
1 TTT
48229 GTTTCGAGGC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 36 0.52
36 33 0.48
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (35 bp):
TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:48247 original size:39 final size:39
Alignment explanation
Indices: 48108--48432 Score: 245
Period size: 39 Copynumber: 8.4 Consensus size: 39
48098 GAAACGTTCT
* * *
48108 TAAAAT-TTTGTGTTTCAAGAGAAACTATCTCAAGGGAGA
1 TAAAATATTT-TGTTTCGAGGGAAACTATCTCAAGCGAGA
* * * *
48147 -CAAA-A-TTT-TTTCAAGGGAAACTGTCTCAAGGGAGA
1 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * * *
48182 -CAAA-A-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * * * * * *
48218 CAAATTTTTTTGTTTCGAGGCAAATTGTCTCAAGAGAGACA
1 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAG--A
* * *
48259 AAAAAAAATTTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
* *
48298 TAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGCGAGA
1 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * *
48337 TAAAATCTTTTGTTTCGAGGAAAAATAATCTCAAGCGAGA
1 TAAAATATTTTGTTTCGAGGGAAACT-ATCTCAAGCGAGA
* * * *
48377 TAAAATATTTTGTTTCAAGGAAAAACAATCTTGAA-CGAGA
1 TAAAATATTTTGTTTCGAGG-GAAACTATC-TCAAGCGAGA
* *
48417 TAAAATCTTCTGTTTC
1 TAAAATATTTTGTTTC
48433 AAGGAAAAAC
Statistics
Matches: 242, Mismatches: 34, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
35 33 0.14
36 27 0.11
37 4 0.02
38 3 0.01
39 85 0.35
40 53 0.22
41 37 0.15
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (39 bp):
TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
Found at i:48284 original size:80 final size:80
Alignment explanation
Indices: 48118--48341 Score: 223
Period size: 80 Copynumber: 2.9 Consensus size: 80
48108 TAAAATTTTG
* * * * * *
48118 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA---TTT-TTTCAAGGGAAACTGTCTCAAGGG
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTTTGTTTCGAGGCAAACTATCTCAAGAG
48179 AGAC-----AAAATT
66 AGACAAAAAAAAATT
* * * * *
48189 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTTTTTGTTTCGAGGCAAATTGTCTCAAGAG
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTTTGTTTCGAGGCAAACTATCTCAAGAG
48254 AGACAAAAAAAAATT
66 AGACAAAAAAAAATT
* * * * * *
48269 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTTTGTTTCGAGGCAAACTATCTCAAGAG
*
48334 AGATAAAA
66 AGACAAAA
48342 TCTTTTGTTT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
71 30 0.24
74 3 0.02
75 24 0.19
80 67 0.54
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (80 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTTTGTTTCGAGGCAAACTATCTCAAGAG
AGACAAAAAAAAATT
Found at i:48379 original size:40 final size:40
Alignment explanation
Indices: 48280--48640 Score: 403
Period size: 40 Copynumber: 9.0 Consensus size: 40
48270 GTTTCGAGGG
* * * * ** *
48280 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTTGAGG-G
1 AAACAATCTGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
* * * * *
48319 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGGAA
1 AAACAATCTGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
* * * * *
48359 AAATAATCTCAAGCGAGATAAAATATTTTGTTTCAAGGAA
1 AAACAATCTGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48399 AAACAATCTTGAA-CGAGATAAAATCTTCTGTTTCAAGGAA
1 AAACAATC-TGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48439 AAACAATCTTG-AGTGAGATAAAATCTTATGTTTCAAGGAA
1 AAACAATC-TGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48479 AAACAATCTTGAA-TGAGATAAAATCTTATGTTTCAAGGAA
1 AAACAATC-TGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48519 AAACAATCTTG-AGTGAGATAAAATCTTCTATTTCAAGGAA
1 AAACAATC-TGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48559 AAACAATCTTGAA-TGAGATAAAATCTTCTGTTTCAGGGAA
1 AAACAATC-TGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
*
48599 AAACAATATTGAA-TGAGATAAAATCTTCTGTTTCAAGTGAA
1 AAACAAT-CTGAAGTGAGATAAAATCTTCTGTTTCAAG-GAA
48640 A
1 A
48641 CAGTCTCAAG
Statistics
Matches: 296, Mismatches: 18, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
39 39 0.13
40 248 0.84
41 9 0.03
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (40 bp):
AAACAATCTGAAGTGAGATAAAATCTTCTGTTTCAAGGAA
Found at i:48486 original size:23 final size:23
Alignment explanation
Indices: 48460--48528 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
48450 AGTGAGATAA
48460 AATCTTATGTTTCAAGGAAAAAC
1 AATCTTATGTTTCAAGGAAAAAC
* *
48483 AATC-T-TG----AATGAGATAA-
1 AATCTTATGTTTCAAGGA-AAAAC
48500 AATCTTATGTTTCAAGGAAAAAC
1 AATCTTATGTTTCAAGGAAAAAC
48523 AATCTT
1 AATCTT
48529 GAGTGAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
21 2 0.06
22 4 0.12
23 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (23 bp):
AATCTTATGTTTCAAGGAAAAAC
Found at i:50087 original size:12 final size:12
Alignment explanation
Indices: 50062--50120 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
50052 TTCTCGTCCC
50062 TTTTTCTTTACT
1 TTTTTCTTTACT
* *
50074 TTTTTTTTTCCT
1 TTTTTCTTTACT
*
50086 TTTTTCTTTGCTTT
1 TTTTTCTTTAC--T
50100 TTTTTCTTTA-T
1 TTTTTCTTTACT
50111 TTTTTCTTTA
1 TTTTTCTTTA
50121 TTATCCTTGC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 11 0.28
12 19 0.47
14 10 0.25
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTACT
Found at i:50092 original size:24 final size:25
Alignment explanation
Indices: 50062--50120 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
50052 TTCTCGTCCC
*
50062 TTTTTCTTTACTTTTTTTT-TTCCT
1 TTTTTCTTTACTTTTTTTTCTTCAT
* *
50086 TTTTTCTTTGCTTTTTTTTCTTTAT
1 TTTTTCTTTACTTTTTTTTCTTCAT
50111 TTTTTCTTTA
1 TTTTTCTTTA
50121 TTATCCTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTTTCTTTACTTTTTTTTCTTCAT
Found at i:50114 original size:14 final size:14
Alignment explanation
Indices: 50062--50115 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
50052 TTCTCGTCCC
50062 TTTTTCTTTAC-TT
1 TTTTTCTTTACTTT
*
50075 TTTTT-TTT-C-CT
1 TTTTTCTTTACTTT
*
50086 TTTTTCTTTGCTTT
1 TTTTTCTTTACTTT
50100 TTTTTCTTTA-TTT
1 TTTTTCTTTACTTT
50113 TTT
1 TTT
50116 CTTTATTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 7 0.20
12 6 0.17
13 12 0.34
14 10 0.29
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTACTTT
Found at i:51368 original size:27 final size:27
Alignment explanation
Indices: 51338--51399 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
51328 ATGAAATGAA
* *
51338 ATGCAAAATGCAAAGATGTAAATGCAT
1 ATGCAAAATGCAAAGATGCAAATGCAG
51365 ATGCAAAATGCAAAGATGCAAATGCAG
1 ATGCAAAATGCAAAGATGCAAATGCAG
51392 ATGCAAAA
1 ATGCAAAA
51400 ATGTTGATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.18
Consensus pattern (27 bp):
ATGCAAAATGCAAAGATGCAAATGCAG
Found at i:51383 original size:21 final size:20
Alignment explanation
Indices: 51336--51398 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
51326 AAATGAAATG
*
51336 AAATGCAAAATGCAAAGATGT
1 AAATGC-AAATGCAAAGATGC
*
51357 AAATGCATATGCAAA-ATGC
1 AAATGCAAATGCAAAGATGC
51376 AAAGATGCAAATGC--AGATGC
1 -AA-ATGCAAATGCAAAGATGC
51396 AAA
1 AAA
51399 AATGTTGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 14 0.39
21 15 0.42
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (20 bp):
AAATGCAAATGCAAAGATGC
Found at i:51395 original size:12 final size:12
Alignment explanation
Indices: 51351--51398 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
51341 CAAAATGCAA
*
51351 AGATGTAAATGC
1 AGATGCAAATGC
*
51363 ATATGCAAAATGC
1 AGATGC-AAATGC
51376 AAAGATGCAAATGC
1 --AGATGCAAATGC
51390 AGATGCAAA
1 AGATGCAAA
51399 AATGTTGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 13 0.43
13 6 0.20
14 6 0.20
15 5 0.17
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (12 bp):
AGATGCAAATGC
Found at i:51402 original size:14 final size:13
Alignment explanation
Indices: 51338--51399 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
51328 ATGAAATGAA
51338 ATGCAAAATGCAAAG
1 ATGCAAAATGC--AG
* *
51353 ATG-TAAATGCAT
1 ATGCAAAATGCAG
51365 ATGCAAAATGCAAAG
1 ATGCAAAATGC--AG
51380 ATGC-AAATGCAG
1 ATGCAAAATGCAG
51392 ATGCAAAA
1 ATGCAAAA
51400 ATGTTGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 10 0.26
13 9 0.23
14 12 0.31
15 8 0.21
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.18
Consensus pattern (13 bp):
ATGCAAAATGCAG
Found at i:55595 original size:3 final size:3
Alignment explanation
Indices: 55589--55637 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
55579 AAATTATTAT
* *
55589 TAA TAA TAA TAC TAA TAA TAT TAA TAA TAA TAA -ATA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
55633 TAA TA
1 TAA TA
55638 TTTTTAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 35 0.90
4 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:56304 original size:18 final size:20
Alignment explanation
Indices: 56277--56316 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
56267 TCCAGTTAAT
56277 GTTTACTTTCCAAAC-AAAA
1 GTTTACTTTCCAAACTAAAA
56296 GTTTA-TTTCCAAACTAAAA
1 GTTTACTTTCCAAACTAAAA
56315 GT
1 GT
56317 AGTGTTACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (20 bp):
GTTTACTTTCCAAACTAAAA
Found at i:57696 original size:42 final size:44
Alignment explanation
Indices: 57648--57742 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
57638 TAAACAACAA
* *
57648 CAAAATATCAAAAGAGTG-T-AAACAAATT-AAAAGTCTAAACTT
1 CAAAATAACAAAAGAGTGATGAAACAAATTCAAAA-TCTAAACTC
57690 CAAAATAACAAAAGAGTGTATGAAACAAATTCAAAATCTAAACTC
1 CAAAATAACAAAAGAGTG-ATGAAACAAATTCAAAATCTAAACTC
57735 CAAAATAA
1 CAAAATAA
57743 AAATTCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
42 17 0.36
44 1 0.02
45 25 0.53
46 4 0.09
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.21
Consensus pattern (44 bp):
CAAAATAACAAAAGAGTGATGAAACAAATTCAAAATCTAAACTC
Found at i:61225 original size:28 final size:28
Alignment explanation
Indices: 61172--61227 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
61162 CGTCGTTGCG
* *
61172 TTCAAACACTGGCTCGACGACGTAATGT
1 TTCAAACACTAGCTCGACGACATAATGT
**
61200 TTCAAACACTAGCTCGACTTCATAATGT
1 TTCAAACACTAGCTCGACGACATAATGT
61228 AAATAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
TTCAAACACTAGCTCGACGACATAATGT
Found at i:65557 original size:6 final size:6
Alignment explanation
Indices: 65537--65579 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
65527 GATAGATTTA
* *
65537 ATTTTT ATATTTT ATTTTT A-TTTT ATTTTT GTATTT ATTTTT A
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
65580 ATTTAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:65559 original size:24 final size:24
Alignment explanation
Indices: 65532--65588 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
65522 AAAATGATAG
65532 ATTTAATTTTTATATTTTATTTTT-
1 ATTTAATTTTTATA-TTTATTTTTA
* *
65556 ATTTTATTTTTGTATTTATTTTTA
1 ATTTAATTTTTATATTTATTTTTA
65580 ATTTAATTT
1 ATTTAATTT
65589 GATAAATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (24 bp):
ATTTAATTTTTATATTTATTTTTA
Found at i:65560 original size:11 final size:11
Alignment explanation
Indices: 65539--65584 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
65529 TAGATTTAAT
65539 TTTTATATTTTA
1 TTTT-TATTTTA
65551 TTTTTATTTTA
1 TTTTTATTTTA
*
65562 TTTTTGTATTTA
1 TTTTTAT-TTTA
*
65574 TTTTTAATTTA
1 TTTTTATTTTA
65585 ATTTGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 17 0.57
12 13 0.43
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:66481 original size:34 final size:33
Alignment explanation
Indices: 66429--66493 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
66419 CTTTTACAAC
*
66429 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
*
66462 TCCCTAGCTTTTACACGGGCTAAGCTAGAACC
1 TCCCTAG-TTTTACACGGGCTAAACTAGAACC
66494 AAAACCCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
Found at i:66987 original size:20 final size:19
Alignment explanation
Indices: 66944--67009 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
66934 TACCGTTCAT
* * *
66944 TACTGTTTACACAGTATCGG
1 TACTATTTATACAGTA-CGA
66964 TACTATTTATACAGTACCGA
1 TACTATTTATACAGTA-CGA
* *
66984 TACTATTCATACAGTACAA
1 TACTATTTATACAGTACGA
67003 TACTATT
1 TACTATT
67010 CATAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 9 0.22
20 31 0.77
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (19 bp):
TACTATTTATACAGTACGA
Found at i:67007 original size:19 final size:20
Alignment explanation
Indices: 66964--67013 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
66954 ACAGTATCGG
* *
66964 TACTATTTATACAGTACCGA
1 TACTATTCATACAGTACCAA
66984 TACTATTCATACAGTA-CAA
1 TACTATTCATACAGTACCAA
67003 TACTATTCATA
1 TACTATTCATA
67014 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTACCAA
Found at i:69289 original size:3 final size:3
Alignment explanation
Indices: 69281--69330 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
69271 AATTTAAATT
*
69281 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TATA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA
69328 TTA
1 TTA
69331 AATAATACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:70544 original size:27 final size:28
Alignment explanation
Indices: 70514--70576 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
70504 TTACTAGTTT
70514 TTTTTATTTATAGTTTTA-ATTTCATTA
1 TTTTTATTTATAGTTTTATATTTCATTA
* * *
70541 TTTTTAATTATTGTTTTATATTTTATTA
1 TTTTTATTTATAGTTTTATATTTCATTA
*
70569 TTATTATT
1 TTTTTATT
70577 ATTATTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTTTATTTATAGTTTTATATTTCATTA
Found at i:70571 original size:3 final size:3
Alignment explanation
Indices: 70537--70593 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
70527 TTTTAATTTC
* *
70537 ATT ATT TTT AATT ATT GTT -TT A-T ATT -TT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
70580 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
70594 GTATAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.13
3 39 0.83
4 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:72840 original size:11 final size:11
Alignment explanation
Indices: 72824--72856 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
72814 TTAATTTTTA
72824 TATTTTTATTT
1 TATTTTTATTT
72835 TATTTTT-TATT
1 TATTTTTAT-TT
72846 TATTTTTATTT
1 TATTTTTATTT
72857 AATTGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:73198 original size:35 final size:35
Alignment explanation
Indices: 73035--73423 Score: 346
Period size: 35 Copynumber: 10.9 Consensus size: 35
73025 TACATATATC
** *
73035 TATATAT-TATATAGTTTGCAAAACGGTTTTGAAAA
1 TATATATATATATAGTTTTTAAAAC-ATTTTGAAAA
* *
73070 CACGTATATATATATAGTTTTTAAAAAATATTTTGAAAA
1 TA--TATATATATATAGTTTTT--AAAACATTTTGAAAA
* * *
73109 TGTACATAATATATAGTTTTTAAATA-TTTTTGAAAA
1 TATATAT-ATATATAGTTTTTAAA-ACATTTTGAAAA
*
73145 -CTATATATATATAGTTTTTAAAACATTTTAGAAAA
1 TATATATATATATAGTTTTTAAAACATTTT-GAAAA
* *
73180 TATATATATATATATTTTTTAAAATTATTTTGAAAA
1 TATATATATATATAGTTTTTAAAA-CATTTTGAAAA
* *
73216 T-TATATATATATAGTTTTGAAAACGTTTATGAAAA
1 TATATATATATATAGTTTTTAAAACATTT-TGAAAA
* *
73251 CATTATATATATATAGTTTTTAAAAATATTTTG-AAA
1 TA-TATATATATATAGTTTTT-AAAACATTTTGAAAA
*
73287 TATATATA-ATATAGTTTTTAAAACATTTTTTAAAA
1 TATATATATATATAGTTTTTAAAACA-TTTTGAAAA
* *
73322 AATATATATTATATAGTTTTTAAAACGTTTTGAAAA
1 TATATATA-TATATAGTTTTTAAAACATTTTGAAAA
* *
73358 TATGTATAATATATA-TTTTTAAAA-ACTTTTGGAAA
1 TATATAT-ATATATAGTTTTTAAAACA-TTTTGAAAA
* * *
73393 TTTATATATTACATA-TTTTTGAAAATATTTT
1 TATATATA-TATATAGTTTTT-AAAACATTTT
73424 TATATATAAT
Statistics
Matches: 294, Mismatches: 36, Indels: 47
0.78 0.10 0.12
Matches are distributed among these distances:
33 6 0.02
34 39 0.13
35 84 0.29
36 70 0.24
37 52 0.18
38 30 0.10
39 9 0.03
40 4 0.01
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
TATATATATATATAGTTTTTAAAACATTTTGAAAA
Found at i:73225 original size:71 final size:70
Alignment explanation
Indices: 73074--73423 Score: 358
Period size: 71 Copynumber: 4.9 Consensus size: 70
73064 TGAAAACACG
* * * *
73074 TATATATATATAGTTTTTAAAAAATATTTTGAAAATGTACATAATATATAGTTTTT-AAATATTT
1 TATATATATATAGTTTTTAAAACAT-TTTAGAAAATATATAT-ATATATAGTTTTTAAAATA-TT
*
73138 TTGAAAAC
63 TTGAAAAT
*
73146 TATATATATATAGTTTTTAAAACATTTTAGAAAATATATATATATATATTTTTTAAAATTATTTT
1 TATATATATATAGTTTTTAAAACATTTTAGAAAATATATATATATATAGTTTTTAAAA-TATTTT
73211 GAAAAT
65 GAAAAT
* * *
73217 TATATATATATAGTTTTGAAAAC-GTTTATGAAAACATTATATATATATAGTTTTTAAAAATATT
1 TATATATATATAGTTTTTAAAACATTTTA-GAAAATA-TATATATATATAGTTTTT-AAAATATT
73281 TTG-AAA-
63 TTGAAAAT
* **
73287 TATATATAATATAGTTTTTAAAACATTTTTTAAAAAATATATAT-TATATAGTTTTTAAAACGTT
1 TATATAT-ATATAGTTTTTAAAACA--TTTTAGAAAATATATATATATATAGTTTTTAAAATATT
73351 TTGAAAAT
63 TTGAAAAT
* * * *
73359 ATGTATAATATATA-TTTTTAAAA-ACTTTT-GGAAATTTATATATTACATA-TTTTTGAAAATA
1 -TATAT-ATATATAGTTTTTAAAACA-TTTTAGAAAATATATATA-TATATAGTTTTT-AAAATA
73420 TTTT
61 TTTT
73424 TATATATAAT
Statistics
Matches: 238, Mismatches: 24, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
69 9 0.04
70 41 0.17
71 100 0.42
72 64 0.27
73 18 0.08
74 6 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (70 bp):
TATATATATATAGTTTTTAAAACATTTTAGAAAATATATATATATATAGTTTTTAAAATATTTTG
AAAAT
Done.