Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005533.1 Hibiscus syriacus cultivar Beakdansim tig00012800_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: 77590
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6964 original size:7 final size:7
Alignment explanation
Indices: 6952--7064 Score: 51
Period size: 7 Copynumber: 16.3 Consensus size: 7
6942 GTTAGAGAAA
6952 AAATAAT
1 AAATAAT
*
6959 AAATAAA
1 AAATAAT
*
6966 AAAAAGATT
1 AAATA-A-T
6975 AACATAA-
1 AA-ATAAT
6982 -AATAAT
1 AAATAAT
*
6988 AAATAAA
1 AAATAAT
*
6995 AAATGA-
1 AAATAAT
7001 AAATAAT
1 AAATAAT
7008 AGAATAAT
1 A-AATAAT
*
7016 AAAT-TT
1 AAATAAT
*
7022 AAAGGAAAT
1 AAA--TAAT
**
7031 AAGGAA-
1 AAATAAT
7037 AAATAAT
1 AAATAAT
7044 AAAT-A-
1 AAATAAT
7049 AAATAAT
1 AAATAAT
7056 AAATAAT
1 AAATAAT
7063 AA
1 AA
7065 TAAAAAAAGA
Statistics
Matches: 79, Mismatches: 14, Indels: 26
0.66 0.12 0.22
Matches are distributed among these distances:
5 8 0.10
6 16 0.20
7 39 0.49
8 8 0.10
9 6 0.08
10 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (7 bp):
AAATAAT
Found at i:7006 original size:25 final size:24
Alignment explanation
Indices: 6951--7106 Score: 80
Period size: 28 Copynumber: 6.4 Consensus size: 24
6941 TGTTAGAGAA
*
6951 AAAATAATA-AATAAA-AAAAAGATT
1 AAAATAAAATAATAAATAAAAA-A-T
*
6975 AACATAAAATAATAAATAAAAAAT
1 AAAATAAAATAATAAATAAAAAAT
6999 GAAAATAATAGAATAATAAATTTAAAGGAAAT
1 -AAAAT-A-A-AATAATAAA--TAAA--AAAT
*
7031 AAGGA-AAAATAATAAATAAAATAAT
1 AA-AATAAAATAATAAATAAAA-AAT
*
7056 -AAAT--AATAATAAA-AAAAGAT
1 AAAATAAAATAATAAATAAAAAAT
*
7076 AAAAT-ATAT-ATAAATAAAAAAT
1 AAAATAAAATAATAAATAAAAAAT
7098 GAAAA-AAAA
1 -AAAATAAAA
7107 CAAATGAGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 37
0.70 0.06 0.25
Matches are distributed among these distances:
20 2 0.02
21 13 0.12
22 17 0.16
23 7 0.07
24 10 0.10
25 14 0.13
26 10 0.10
27 1 0.01
28 18 0.17
29 1 0.01
30 5 0.05
31 2 0.02
32 5 0.05
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (24 bp):
AAAATAAAATAATAAATAAAAAAT
Found at i:7052 original size:22 final size:21
Alignment explanation
Indices: 7027--7072 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
7017 AATTTAAAGG
7027 AAATAAGGAAA-AATAATAAATA
1 AAATAA-GAAATAATAATAAA-A
*
7049 AAATAATAAATAATAATAAAA
1 AAATAAGAAATAATAATAAAA
7070 AAA
1 AAA
7073 GATAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (21 bp):
AAATAAGAAATAATAATAAAA
Found at i:7104 original size:8 final size:7
Alignment explanation
Indices: 7035--7104 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
7025 GGAAATAAGG
7035 AAAAATA
1 AAAAATA
*
7042 ATAAATA
1 AAAAATA
7049 AAATAATA
1 AAA-AATA
*
7057 AATAATA
1 AAAAATA
*
7064 ATAAA-A
1 AAAAATA
*
7070 AAAGATA
1 AAAAATA
*
7077 AAATATA
1 AAAAATA
*
7084 TATAAATA
1 -AAAAATA
7092 AAAAATGA
1 AAAAAT-A
7100 AAAAA
1 AAAAA
7105 AACAAATGAG
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
6 4 0.08
7 27 0.56
8 17 0.35
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (7 bp):
AAAAATA
Found at i:8483 original size:34 final size:34
Alignment explanation
Indices: 8432--8509 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
8422 TGATTATATA
* **
8432 ATATA-TATATTTCAAAAAAATATTTTTTAAACT
1 ATATATTATATTTCAAAAAAAGATTTTCAAAACT
* *
8465 ATATATTATATTTTAAAAAAAGGTTTTCAAAACT
1 ATATATTATATTTCAAAAAAAGATTTTCAAAACT
8499 ATATATTATAT
1 ATATATTATAT
8510 AGTTTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATATTATATTTCAAAAAAAGATTTTCAAAACT
Found at i:8504 original size:36 final size:36
Alignment explanation
Indices: 8426--8676 Score: 124
Period size: 38 Copynumber: 6.7 Consensus size: 36
8416 TAATATTGAT
* * *
8426 TATATAATATATATA-TTTCAAAAAAATATTTTTTAAAC
1 TATAT-AT-TATATAGTTTTAAAAAAAGA-TTTTAAAAC
*
8464 TATATA-T-TATA-TTTTAAAAAAAGGTTTTCAAAAC
1 TATATATTATATAGTTTTAAAAAAAGATTTT-AAAAC
*
8498 TATATATTATATAGTTTTTAAAAAAGATTTTAAAATTAAAAC
1 TATATATTATATAGTTTTAAAAAAAGA--TT----TTAAAAC
* *
8540 TATATATTATATAGTTTT-CAAAATG-TTTTAAAACC
1 TATATATTATATAGTTTTAAAAAAAGATTTTAAAA-C
* *
8575 TATATATTATATATAAGTTTTCAAAAACG-TTTTAAAAAAC
1 TATATA-T-TATAT-AGTTTTAAAAAAAGATTTT--AAAAC
* * *****
8615 TATATAATATATATTTTTGAAAACCTTTTTTTGAAAAC
1 TATATATTATATAGTTTT-AAAAAAAGATTTT-AAAAC
8653 TATATATTATAT--TTTTCAAAAAAA
1 TATATATTATATAGTTTT-AAAAAAA
8677 AATTCAAAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 40
0.73 0.10 0.17
Matches are distributed among these distances:
33 4 0.02
34 30 0.18
35 9 0.05
36 13 0.08
37 22 0.13
38 37 0.22
39 15 0.09
40 7 0.04
41 9 0.05
42 23 0.13
43 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATTATATAGTTTTAAAAAAAGATTTTAAAAC
Found at i:8586 original size:40 final size:41
Alignment explanation
Indices: 8541--8626 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 41
8531 AATTAAAACT
* *
8541 ATATATTATATAGTTTTC-AAAATGTTTT-AAAACCTATATA
1 ATATATTATA-AGTTTTCAAAAACGTTTTAAAAAACTATATA
*
8581 TTATA-TATAAGTTTTCAAAAACGTTTTAAAAAACTATATA
1 ATATATTATAAGTTTTCAAAAACGTTTTAAAAAACTATATA
8621 ATATAT
1 ATATAT
8627 ATTTTTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
38 7 0.18
39 13 0.33
40 19 0.49
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (41 bp):
ATATATTATAAGTTTTCAAAAACGTTTTAAAAAACTATATA
Found at i:8586 original size:42 final size:40
Alignment explanation
Indices: 8498--8629 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 40
8488 TTTTCAAAAC
* * *
8498 TATATATTATATAGTTTTTAAAAAAGATTTTAAAATTA-AAA
1 TATATATTATATAG-TTTTCAAAAAG-TTTTAAAACTATATA
*
8539 CTATATATTATATAGTTTTCAAAATGTTTTAAAACCTATATA
1 -TATATATTATATAGTTTTCAAAAAGTTTTAAAA-CTATATA
8581 T-TATA-TATA-AGTTTTCAAAAACGTTTTAAAAAACTATATAA
1 TATATATTATATAGTTTTCAAAAA-GTTTT--AAAACTATAT-A
8622 TATATATT
1 TATATATT
8630 TTTGAAAACC
Statistics
Matches: 77, Mismatches: 5, Indels: 15
0.79 0.05 0.15
Matches are distributed among these distances:
38 11 0.14
39 9 0.12
40 18 0.23
41 18 0.23
42 20 0.26
43 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (40 bp):
TATATATTATATAGTTTTCAAAAAGTTTTAAAACTATATA
Found at i:8608 original size:79 final size:76
Alignment explanation
Indices: 8460--8611 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
8450 AATATTTTTT
*
8460 AAACTATATATTATATTTTAAAAAAAGGTTTTCAAAACTATATATTATATAGTTTTTAAAAAAGA
1 AAACTATATATTATATTTTAAAAAAAGGTTTTCAAAACTATATATTATATAGTTTTCAAAAAAGA
8525 TTTTAAAATTA
66 TTTTAAAATTA
** *
8536 AAACTATATATTATATAGTTT-TCAAAATGTTTT-AAAACCTATATATTATATATAAGTTTTCAA
1 AAACTATATATTATAT--TTTAAAAAAAGGTTTTCAAAA-CTATATA-T-TATAT-AGTTTTCAA
*
8599 AAACG-TTTTAAAA
60 AAAAGATTTTAAAA
8612 AACTATATAA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
76 20 0.31
77 16 0.25
78 4 0.06
79 13 0.20
80 12 0.18
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (76 bp):
AAACTATATATTATATTTTAAAAAAAGGTTTTCAAAACTATATATTATATAGTTTTCAAAAAAGA
TTTTAAAATTA
Found at i:9453 original size:83 final size:83
Alignment explanation
Indices: 9266--9714 Score: 436
Period size: 83 Copynumber: 5.5 Consensus size: 83
9256 ATTTTATTAA
* * * * * * * * *
9266 CAGATAGCCCTTCTTGCTTTGAGCTATGTTGTAAATTTGATTTACCTCT-GAGCTGAGTGTAATC
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGCGTAGTC
*
9330 GAACTCGAAGATCTTTGTTGA
63 GAACTCGAAGATCTTTGTTGG
* * * * *
9351 CAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
9416 CTCGAAGATCTTTGGTGG
66 CTCGAAGATCTTTGTTGG
* * * * * *
9434 CAGATAACCATTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAGAGATGAGCATAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
9499 CTCGAAGGTCTTGCGTTGG
66 CTCGAAGATCTT-TGTTGG
* * *
9518 CAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
9583 CTCGAAGGTAT-TTTGTTGG
66 CTCGAA-G-ATCTTTGTTGG
* * * *
9602 CAG--A-------TAGCCTTGAGTTATCCTACAAATGATGTACCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
9658 CTCAAAGGTTTTTTGTTGG
66 CTCGAA-GATCTTTGTTGG
9677 CAGATAAG-CCTTCTAGCCTTGAGTTATGCTGCAAATGA
1 CAGAT-AGCCCTTCTAGCCTTGAGTTATGCTGCAAATGA
9715 ACACAATATC
Statistics
Matches: 306, Mismatches: 44, Indels: 29
0.81 0.12 0.08
Matches are distributed among these distances:
74 1 0.00
75 64 0.21
78 1 0.00
82 2 0.01
83 105 0.34
84 96 0.31
85 36 0.12
86 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (83 bp):
CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGATCTTTGTTGG
Found at i:9659 original size:75 final size:76
Alignment explanation
Indices: 9533--9688 Score: 242
Period size: 75 Copynumber: 2.1 Consensus size: 76
9523 AGCCCTTCTT
** * * *
9533 GCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTG
1 GCCTTGAGTTATCCTACAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTTG
9598 TTGGCAGAT-A
66 TTGGCAGATAA
* *
9608 GCCTTGAGTTATCCTACAAATGATGTACCTTGGAGCTGAGCGTAGTTGAACTCAAAGGTTTTTTG
1 GCCTTGAGTTATCCTACAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTTG
9673 TTGGCAGATAA
66 TTGGCAGATAA
9684 GCCTT
1 GCCTT
9689 CTAGCCTTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 67 0.92
76 6 0.08
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (76 bp):
GCCTTGAGTTATCCTACAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTATTTTG
TTGGCAGATAA
Found at i:9710 original size:159 final size:160
Alignment explanation
Indices: 9328--9714 Score: 460
Period size: 159 Copynumber: 2.4 Consensus size: 160
9318 CTGAGTGTAA
* * * * * *
9328 TCGAACTCGAAGATCTT-TGTTGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGT
1 TCGAACTCAAAGGTCTTGCGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGT
9392 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGGCAGATAACCATTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGGCAG---A--A-T-TAGCCTTGAG
* *
9457 TTATACTGCAAATGATGTGCCTTAGAGATGAGCATAG
124 TTATACTACAAATGATGTACCTTAGAGATGAGCATAG
*
9494 TCGAACTCGAAGGTCTTGCGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGT
1 TCGAACTCAAAGGTCTTGCGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGT
* *
9559 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTAT-TTTGTTGGCAG-A-TAGCCTTGAGTTATC
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAA-G-ATCTTTGGTGGCAGAATTAGCCTTGAGTTATA
* * *
9621 CTACAAATGATGTACCTTGGAGCTGAGCGTAG
129 CTACAAATGATGTACCTTAGAGATGAGCATAG
* * ** * * *
9653 TTGAACTCAAAGGTTTTTTGTTGGCAGATAAG-CCTTCTAGCCTTGAGTTATGCTGCAAATGA
1 TCGAACTCAAAGGTCTTGCGTTGGCAAAT-AGCCCTTCTTGCCTTGAGTTATGTTGCAAATGA
9715 ACACAATATC
Statistics
Matches: 197, Mismatches: 20, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
159 92 0.47
160 2 0.01
162 1 0.01
166 16 0.08
167 73 0.37
168 11 0.06
169 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (160 bp):
TCGAACTCAAAGGTCTTGCGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGGCAGAATTAGCCTTGAGTTATACT
ACAAATGATGTACCTTAGAGATGAGCATAG
Found at i:9898 original size:124 final size:124
Alignment explanation
Indices: 9724--10434 Score: 1030
Period size: 124 Copynumber: 5.9 Consensus size: 124
9714 AACACAATAT
* * *
9724 CCTTCGTCGTGAAGTTGAAATCATGGAGGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * *
9789 TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGCAGGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
*
9848 CCTTCGTCGTGAAGATT-AAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGAT
1 CCTTCGTCGTGAAG-TTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGAT
* * * *
9912 ATCCTTCATCATGAAGTTGAAATCCAATTTAAAGATGAATGTTACTGGTGAGCACGATTC
65 ATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
9972 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * *
10037 ---TTCGTCGTGAAGTTTAAATCCAATCTAAAGATGAATGTTACTAGTGAGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* *
10093 CATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
*
10158 TCCTTCGTCGTAAAGTTGAAAT-C---C---A-AT--A-----CTGGTGAGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* *
10202 CCTTCGTCGTG-AGTTGAAACCGTGGATGGTCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * *
10266 TCTTTCGTAGTGAATTTGAAATCCAATCTAAAGATGAAAGTTGCTGGTGAGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* * *
10325 CCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTATGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
*
10390 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
10435 TCAAGTCCAA
Statistics
Matches: 527, Mismatches: 39, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
108 69 0.13
109 26 0.05
112 1 0.00
114 1 0.00
115 1 0.00
116 4 0.01
117 1 0.00
118 1 0.00
120 1 0.00
121 114 0.22
123 29 0.06
124 277 0.53
125 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (124 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
Found at i:10273 original size:108 final size:109
Alignment explanation
Indices: 10075--10292 Score: 357
Period size: 108 Copynumber: 2.0 Consensus size: 109
10065 AGATGAATGT
*
10075 TACTAGTGAGCACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTGTGAAGT
1 TACTAGTGAGCACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCATTGTGAAGT
*
10140 TGAGCCTTGAATTGGATATCCTTCGTCGTAAAGTTGAAATCCAA
66 TGAGCCTTGAATTGGATATCCTTCGTAGTAAAGTTGAAATCCAA
* * *
10184 TACTGGTGAGCACGATTCCCTTCGTCGTG-AGTTGAAACCGTGGATGGTCCCTTCATTGTGAAGT
1 TACTAGTGAGCACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCATTGTGAAGT
* * *
10248 TGAGCCTTGAATTGGATATCTTTCGTAGTGAATTTGAAATCCAA
66 TGAGCCTTGAATTGGATATCCTTCGTAGTAAAGTTGAAATCCAA
10292 T
1 T
10293 CTAAAGATGA
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 74 0.73
109 27 0.27
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (109 bp):
TACTAGTGAGCACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCATTGTGAAGT
TGAGCCTTGAATTGGATATCCTTCGTAGTAAAGTTGAAATCCAA
Found at i:10362 original size:232 final size:230
Alignment explanation
Indices: 9954--10416 Score: 759
Period size: 232 Copynumber: 2.0 Consensus size: 230
9944 AGATGAATGT
*
9954 TACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGT
1 TACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGT
* *
10019 TGAGCCTTGAATTGGATATTCGTCGTGAAGTTTAAATCCAATCTAAAGATGAATGTTACTAGTGA
66 TGAGCCTTGAATTGGATATTCGTAGTGAAGTTTAAATCCAATCTAAAGATGAAAGTTACTAGTGA
* *
10084 GCACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTGTGAAGTTGAGCCTTG
131 GCACGATTCCATTCATCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGCCTTG
*
10149 AATTGGATATCCTTCGTCGTAAAGTTGAAATCCAA
196 AATTGGATATCCTTCATCGTAAAGTTGAAATCCAA
*
10184 TACTGGTGAGCACGATTCCCTTCGTCGTG-AGTTGAAACCGTGGATGGTCCCTTCATTGTGAAGT
1 TACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGT
* *
10248 TGAGCCTTGAATTGGATATCTTTCGTAGTGAA-TTTGAAATCCAATCTAAAGATGAAAGTTGCTG
66 TGAGCCTTGAATTGGATA---TTCGTAGTGAAGTTT-AAATCCAATCTAAAGATGAAAGTTACTA
* * *
10312 GTGAGCACGATTCCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTATGAAGTTGAGC
127 GTGAGCACGATTCCATTCATCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGC
*
10377 CTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAA
192 CTTGAATTGGATATCCTTCATCGTAAAGTTGAAATCCAA
10416 T
1 T
10417 CTAAAGATGA
Statistics
Matches: 216, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
229 51 0.24
230 29 0.13
231 3 0.01
232 133 0.62
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (230 bp):
TACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGT
TGAGCCTTGAATTGGATATTCGTAGTGAAGTTTAAATCCAATCTAAAGATGAAAGTTACTAGTGA
GCACGATTCCATTCATCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGCCTTG
AATTGGATATCCTTCATCGTAAAGTTGAAATCCAA
Found at i:11870 original size:96 final size:95
Alignment explanation
Indices: 11656--11912 Score: 275
Period size: 96 Copynumber: 2.7 Consensus size: 95
11646 GGCTAGCTGG
** * * * * *
11656 ATCCATAAAGCCGGGGCGTTTAACTAATTTCTCTAGAGGGACAGCTCAA--TATCATTGCATAGA
1 ATCCATAAAGCCGGACCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTG--T--A
*
11719 TATTAAAATCTCCCTTAACAGGCTAGCTGAATATT
61 TATTAAAATCACCCTTAACAGGCTAGCTGAATATT
* ** *
11754 TTCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGACCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * * *
11819 TAATCACCTTTATCAGGCTTAGCTGAATCTT
66 AAATCACCCTTAACAGGC-TAGCTGAATATT
* * *
11850 ATCCATAAAGCCGGACCATTTAATCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATAT
1 ATCCATAAAGCCGGACCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
11913 ATGTAATATT
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
95 20 0.15
96 67 0.49
97 1 0.01
98 43 0.31
99 5 0.04
100 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGACCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
AAATCACCCTTAACAGGCTAGCTGAATATT
Found at i:14535 original size:7 final size:7
Alignment explanation
Indices: 14523--14572 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
14513 GATTAACTTA
14523 AAATAAT
1 AAATAAT
14530 AAATAAT
1 AAATAAT
14537 AAATGAAT
1 AAAT-AAT
*
14545 AAAAAAT
1 AAATAAT
14552 GAAAATAAT
1 --AAATAAT
14561 AGAATAAT
1 A-AATAAT
14569 AAAT
1 AAAT
14573 TTAAAGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 18 0.49
8 13 0.35
9 6 0.16
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:14619 original size:18 final size:18
Alignment explanation
Indices: 14589--14632 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
14579 GAAATAAGGA
*
14589 AAAATAATAAATA-AATAT
1 AAAATAAAAAATATAA-AT
14607 AAAATAAAAAATATAAAT
1 AAAATAAAAAATATAAAT
14625 AAAA-AAAA
1 AAAATAAAA
14633 TTAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAAATATAAAT
Found at i:14630 original size:13 final size:14
Alignment explanation
Indices: 14594--14645 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
14584 AAGGAAAAAT
14594 AATAAATAAATATAA
1 AATAAA-AAATATAA
14609 AATAAAAAATAT-A
1 AATAAAAAATATAA
*
14622 AATAAAAAAAATTAA
1 AATAAAAAATA-TAA
*
14637 AAGAAAAAA
1 AATAAAAAA
14646 CAAATGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 11 0.33
14 7 0.21
15 15 0.45
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (14 bp):
AATAAAAAATATAA
Found at i:14637 original size:60 final size:60
Alignment explanation
Indices: 14530--14642 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
14520 TTAAAATAAT
* * * * *
14530 AAATAATAAATGAATAAAAAATGAAAATAATAGAATAATAAATTTAAAGGAAATAAGGAA
1 AAATAATAAATAAATAAAAAATGAAAATAATAAAATAAAAAAATTAAAAGAAATAAGGAA
*
14590 AAATAATAAATAAATATAAAAT-AAAA-AATATAAATAAAAAAAATTAAAAGAAA
1 AAATAATAAATAAATAAAAAATGAAAATAATA-AAAT-AAAAAAATTAAAAGAAA
14643 AAACAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.09
59 7 0.16
60 34 0.76
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (60 bp):
AAATAATAAATAAATAAAAAATGAAAATAATAAAATAAAAAAATTAAAAGAAATAAGGAA
Found at i:15903 original size:5 final size:5
Alignment explanation
Indices: 15893--15922 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
15883 TAAAACAAGA
15893 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
15923 GAATAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:15947 original size:3 final size:3
Alignment explanation
Indices: 15939--15979 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
15929 AATGAAAAGA
* *
15939 AAT AAT AAT AAT AAT AAT TA- AAT ACT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15980 TAGACTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:15979 original size:17 final size:17
Alignment explanation
Indices: 15940--15979 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
15930 ATGAAAAGAA
15940 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
*
15957 -TAAATACTAATAATAAT
1 AT-AATAATAATAATAAT
15974 ATAATA
1 ATAATA
15980 TAGACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:16028 original size:33 final size:33
Alignment explanation
Indices: 15991--16067 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
15981 AGACTATATA
*
15991 ATATA-TATATTTCAAAAAAATATTTTGTAAACT
1 ATATATTATATTT-AAAAAAATATTTTGAAAACT
* *
16024 ATATATTATATTTTAAAAAATGTTTTGAAAACT
1 ATATATTATATTTAAAAAAATATTTTGAAAACT
16057 ATATATTATAT
1 ATATATTATAT
16068 AGTTTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 33 0.82
34 7 0.17
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (33 bp):
ATATATTATATTTAAAAAAATATTTTGAAAACT
Found at i:16100 original size:32 final size:32
Alignment explanation
Indices: 16057--16227 Score: 143
Period size: 33 Copynumber: 5.0 Consensus size: 32
16047 TTTGAAAACT
*
16057 ATATATTATATAGTTTTCAAAAATGATTTTAAA
1 ATATATTATATAATTTTC-AAAATGATTTTAAA
*
16090 A-ATATTATATAAGTTTTCAAAATCATTTTTTAAAA
1 ATATATTATATAA-TTTTCAAAATGA--TTTT-AAA
*
16125 CTATATATTATATAAATTTTCAAAATGTTTTTAAA
1 --ATATATTATAT-AATTTTCAAAATGATTTTAAA
* *
16160 A-ACTA-TACATTATATTTTCAAAATGATTTCAAAA
1 ATA-TATTATA-TA-ATTTTCAAAATGATTT-TAAA
16194 CTATATATTATATAATTTTCAAAATG-TTTTAAA
1 --ATATATTATATAATTTTCAAAATGATTTTAAA
16227 A
1 A
16228 CCTATATATT
Statistics
Matches: 113, Mismatches: 9, Indels: 34
0.72 0.06 0.22
Matches are distributed among these distances:
31 1 0.01
32 21 0.19
33 28 0.25
34 10 0.09
35 18 0.16
36 9 0.08
37 5 0.04
38 19 0.17
39 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
ATATATTATATAATTTTCAAAATGATTTTAAA
Found at i:16110 original size:33 final size:33
Alignment explanation
Indices: 16040--16265 Score: 151
Period size: 35 Copynumber: 6.4 Consensus size: 33
16030 TATATTTTAA
16040 AAAATGTTTTGAAAACTATATATTATAT-AGTTTTC
1 AAAATGTTTT--AAAC-ATATATTATATAAGTTTTC
16075 AAAAATGATTTTAAA-A-ATATTATATAAGTTTTC
1 -AAAATG-TTTTAAACATATATTATATAAGTTTTC
* *
16108 AAAATCATTTTTTAAAACTATATATTATATAAATTTTC
1 -AAA--ATGTTTT-AAAC-ATATATTATATAAGTTTTC
* *
16146 AAAATGTTTTTAAAAACTATA-CAT-TATA-TTTTC
1 AAAATG-TTTTAAACA-TATATTATATA-AGTTTTC
*
16179 AAAATGATTTCAAAACTATATATTATATAA-TTTTC
1 AAAATG-TTT-TAAAC-ATATATTATATAAGTTTTC
16214 AAAATGTTTTAAAACCTATATATTATATATAAGTTTTC
1 AAAATGTTTT-AAA-C-ATATA-T-TATATAAGTTTTC
*
16252 AAAAACGTTTTAAA
1 -AAAATGTTTTAAA
16266 AAACTATATA
Statistics
Matches: 158, Mismatches: 11, Indels: 40
0.76 0.05 0.19
Matches are distributed among these distances:
32 9 0.06
33 28 0.18
34 21 0.13
35 39 0.25
36 13 0.08
37 15 0.09
38 24 0.15
39 9 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (33 bp):
AAAATGTTTTAAACATATATTATATAAGTTTTC
Found at i:16136 original size:38 final size:36
Alignment explanation
Indices: 15983--16335 Score: 240
Period size: 38 Copynumber: 9.9 Consensus size: 36
15973 TATAATATAG
* **
15983 ACTATATAATATATATATTTCAAAAAAATATTTTGT-AA
1 ACTATATATTATATAT-TTTCAAAATCAT-TTTT-TAAA
* *
16021 ACTATATA-T-TATATTTT-AAAA-AATGTTTTGAAA
1 ACTATATATTATATATTTTCAAAATCAT-TTTTTAAA
*
16054 ACTATATATTATATAGTTTTCAAAA--ATGATTTTAAA
1 ACTATATATTATATA-TTTTCAAAATCAT-TTTTTAAA
*
16090 AATAT-TA-TATA-AGTTTTCAAAATCATTTTTTAAA
1 ACTATATATTATATA-TTTTCAAAATCATTTTTTAAA
* *
16124 ACTATATATTATATAAATTTTCAAAAT-GTTTTTAAAA
1 ACTATATATTATAT--ATTTTCAAAATCATTTTTTAAA
* * *
16161 ACTATACA-T-TATATTTTCAAAATGA--TTTCAAA
1 ACTATATATTATATATTTTCAAAATCATTTTTTAAA
*
16193 ACTATATATTATATAATTTTC-AAA--ATGTTTTAAA
1 ACTATATATTATAT-ATTTTCAAAATCATTTTTTAAA
* * **
16227 ACCTATATATTATATATAAGTTTTCAAAAACGTTTTAAAAA
1 A-CTATATA-T-TATAT-A-TTTTCAAAATCATTTTTTAAA
* *
16268 ACTATATAATATATATTTTCGAAAACCATTTTTTGAAA
1 ACTATATATTATATATTTTC-AAAATCATTTTTT-AAA
*
16306 ACTATATATTATAT-TTTTCAAAAACATTTT
1 ACTATATATTATATATTTTCAAAATCATTTT
16336 AAAAAATTAT
Statistics
Matches: 263, Mismatches: 25, Indels: 56
0.76 0.07 0.16
Matches are distributed among these distances:
32 14 0.05
33 40 0.15
34 33 0.13
35 29 0.11
36 43 0.16
37 42 0.16
38 44 0.17
39 4 0.02
40 7 0.03
41 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
ACTATATATTATATATTTTCAAAATCATTTTTTAAA
Found at i:18006 original size:38 final size:36
Alignment explanation
Indices: 17900--18044 Score: 134
Period size: 38 Copynumber: 3.9 Consensus size: 36
17890 AATAATATAG
* *
17900 TATAATTTTTTAAAATGTTTTTGAAAA-ATATAATA
1 TATAGTTTTTTAAAATGTTTTTGAAAATATATATTA
** *
17935 TATAGTTTTCAAAAAATGGTTTTCGAAAATATATATTA
1 TATAGTTTT-TTAAAAT-GTTTTTGAAAATATATATTA
17973 TATAGTTTTTTAAAATGTTTTTGAAAACTTATATATAATA
1 TATAGTTTTTTAAAATGTTTTTGAAAA--TATATAT--TA
* **
18013 TATAG-GTTTTAAAA-CATTTTGAAAATTATATA
1 TATAGTTTTTTAAAATGTTTTTGAAAA-TATATA
18045 ATAACAAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
35 8 0.09
36 15 0.16
37 22 0.24
38 32 0.35
39 8 0.09
40 7 0.08
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
TATAGTTTTTTAAAATGTTTTTGAAAATATATATTA
Found at i:27022 original size:31 final size:29
Alignment explanation
Indices: 26987--27075 Score: 72
Period size: 31 Copynumber: 2.9 Consensus size: 29
26977 AATGTGTTAT
26987 TTAATACATTATCTTTTCTCAAATTATAACA
1 TTAATACATTATCTTTTC-CAAATTATAA-A
* * * *
27018 TTAATGTCA-TATTCTTTTCCCAATATATTAT
1 TTAAT-ACATTA-TCTTTTCCAAAT-TATAAA
*
27049 TTATTACATTATCTTTTCCCAAATTAT
1 TTAATACATTATCTTTT-CCAAATTAT
27076 GTAGTACAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
30 11 0.24
31 22 0.48
32 13 0.28
ACGTcount: A:0.33, C:0.17, G:0.01, T:0.49
Consensus pattern (29 bp):
TTAATACATTATCTTTTCCAAATTATAAA
Found at i:27057 original size:62 final size:62
Alignment explanation
Indices: 26958--27075 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
26948 TAATAGCAAC
* * * *
26958 AATGTCATCTTCTTTCGCCAATGTGTTATTTAATACATTATCTTTTCTCAAATTATAACATT
1 AATGTCATATTCTTTCGCCAATATATTATTTAATACATTATCTTTTCCCAAATTATAACATT
*
27020 AATGTCATATTCTTTTC-CCAATATATTATTTATTACATTATCTTTTCCCAAATTAT
1 AATGTCATATTC-TTTCGCCAATATATTATTTAATACATTATCTTTTCCCAAATTAT
27076 GTAGTACAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
62 46 0.92
63 4 0.08
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (62 bp):
AATGTCATATTCTTTCGCCAATATATTATTTAATACATTATCTTTTCCCAAATTATAACATT
Found at i:29582 original size:29 final size:29
Alignment explanation
Indices: 29534--29591 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29524 ACCCGGGACG
29534 AAATAAAAGAAATGAGCCCCTATTTATGT
1 AAATAAAAGAAATGAGCCCCTATTTATGT
*
29563 AAATAAAATAAAT-AGACCCCTATTTATGT
1 AAATAAAAGAAATGAG-CCCCTATTTATGT
29592 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (29 bp):
AAATAAAAGAAATGAGCCCCTATTTATGT
Found at i:33171 original size:123 final size:122
Alignment explanation
Indices: 32946--33389 Score: 656
Period size: 123 Copynumber: 3.7 Consensus size: 122
32936 ATCTCTTAAA
* *
32946 GTTGAACAAATTCTTCTCATTATGAACTTCTTC-T-TT-TTCAAATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
** * *
33008 CACT-TCTAG-AAA--TG-T--TGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAG
66 CTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGC-AAAG
* * * *
33059 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGTTAAGTTCTTCTCATTGTGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
33124 CTTTCTCTGGAAAATTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAAAG
66 CTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAAAG
* *
33181 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TCTTCTTCAGATGAGTTCTTCTCATTATGA
33246 ACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAAAG
65 ACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAAAG
* *
33304 GTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGA
33369 ACTTTCTCTGGAAAAGTTGAT
65 ACTTTCTCTGGAAAAGTTGAT
33390 CCATTGAGTG
Statistics
Matches: 298, Mismatches: 21, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
113 32 0.11
114 1 0.00
115 1 0.00
116 24 0.08
117 4 0.01
118 3 0.01
120 2 0.01
121 1 0.00
122 37 0.12
123 193 0.65
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (122 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAAAG
Found at i:34551 original size:21 final size:21
Alignment explanation
Indices: 34522--34562 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34512 GTTTATGTGA
*
34522 AAAATAAATTGAATTTCAAAC
1 AAAAGAAATTGAATTTCAAAC
34543 AAAAGAAATTGAATTTCAAA
1 AAAAGAAATTGAATTTCAAA
34563 AAGATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAGAAATTGAATTTCAAAC
Found at i:34963 original size:6 final size:6
Alignment explanation
Indices: 34952--34989 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
34942 CATTCAATTT
34952 TTTTCA TTTTCA TTTTCA TTTT-- TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
34990 TTCTTCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
6 26 0.87
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCA
Found at i:34969 original size:22 final size:22
Alignment explanation
Indices: 34927--34989 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
34917 ATATATATAT
*
34927 ATTTTTATCATTTTTCA--TTCA
1 ATTTTTTTCA-TTTTCATTTTCA
34948 ATTTTTTTCATTTTCATTTTCA
1 ATTTTTTTCATTTTCATTTTCA
*
34970 TTTTTTTTCATTTTCATTTT
1 ATTTTTTTCATTTTCATTTT
34990 TTCTTCAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 6 0.16
21 9 0.24
22 23 0.61
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTTTTCATTTTCATTTTCA
Found at i:34977 original size:16 final size:16
Alignment explanation
Indices: 34958--34996 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
34948 ATTTTTTTCA
34958 TTTTCATTTTCATTTT
1 TTTTCATTTTCATTTT
34974 TTTTCATTTTCATTTT
1 TTTTCATTTTCATTTT
34990 TTCTTCA
1 TT-TTCA
34997 AGCATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTCATTTTCATTTT
Found at i:38533 original size:9 final size:9
Alignment explanation
Indices: 38521--38552 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
38511 GAAAAATAAT
38521 GAATGTAAA
1 GAATGTAAA
38530 GAATGTAAA
1 GAATGTAAA
38539 GAATGTAAA
1 GAATGTAAA
*
38548 TAATG
1 GAATG
38553 ATTGCCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (9 bp):
GAATGTAAA
Found at i:45424 original size:24 final size:25
Alignment explanation
Indices: 45397--45449 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
45387 ATACTTGAAG
45397 AATAAAATA-AAACATTAAT-AAAAT
1 AATAAAATATAAACATT-ATGAAAAT
* *
45421 AAT-ATATATAAATATTATGAAAAT
1 AATAAAATATAAACATTATGAAAAT
45445 AATAA
1 AATAA
45450 GTATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 6 0.25
24 17 0.71
25 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
AATAAAATATAAACATTATGAAAAT
Found at i:45469 original size:28 final size:27
Alignment explanation
Indices: 45418--45471 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
45408 ACATTAATAA
*
45418 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
45445 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
45472 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:46385 original size:2 final size:2
Alignment explanation
Indices: 46378--46405 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46368 AATTAAACAA
46378 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
46406 GACTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49087 original size:4 final size:4
Alignment explanation
Indices: 49064--49115 Score: 68
Period size: 4 Copynumber: 12.0 Consensus size: 4
49054 GTAATCTCTA
49064 TCTT TCTTT TCTTT TCCTT TCTT TACTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TC-TT TC-TT T-CTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
49112 TCTT
1 TCTT
49116 CTTACAATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 29 0.64
5 15 0.33
6 1 0.02
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:55571 original size:59 final size:58
Alignment explanation
Indices: 55502--55620 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 58
55492 AACAATAGTC
*
55502 ACTAAAACACTAGTACAAAAACAAACATATTAAACTAAAAAAATACAAAGAAAAATGAA
1 ACTAAAACACTAGTACAAAAACAAACATATTAAACT-AAAAAATACAAAGAAAAATAAA
* * *
55561 ACTAAAACACTCGTACAAAAACAAACATGTTATACTAAAAAATACAAAGAAAAATAAA
1 ACTAAAACACTAGTACAAAAACAAACATATTAAACTAAAAAATACAAAGAAAAATAAA
55619 AC
1 AC
55621 ATTCCTTGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 23 0.41
59 33 0.59
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.16
Consensus pattern (58 bp):
ACTAAAACACTAGTACAAAAACAAACATATTAAACTAAAAAATACAAAGAAAAATAAA
Found at i:57316 original size:57 final size:57
Alignment explanation
Indices: 57147--57318 Score: 272
Period size: 57 Copynumber: 3.0 Consensus size: 57
57137 CATAACCATA
* * * * *
57147 CAACCCCATCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
57204 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
57261 CAACCCCGTCACGAACAGTAAGGCTCTCACCGCAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
57318 C
1 C
57319 TTCCTCCAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 106 1.00
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.13
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:61934 original size:57 final size:58
Alignment explanation
Indices: 61765--61936 Score: 215
Period size: 57 Copynumber: 3.0 Consensus size: 58
61755 AATAACCATA
* * * * * *
61765 CAACCCCGTCACGAACATTAAGGCCCTGAGCACAAAGCCA-AGGAACCTACAAGTAAT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
* * * *
61822 CAACCCCGTCACGAATAGTAAGGCTCTCAGCACAAAGCT-GAGAAACTTGCAAGTATT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
* *
61879 CAGCCCCGTCACGAACACTAAGGCTCTCAGCGCAAAG-TAGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
61936 C
1 C
61937 TTCCTCTAAC
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
56 1 0.01
57 97 0.99
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.16
Consensus pattern (58 bp):
CAACCCCGTCACGAACACTAAGGCTCTCAGCACAAAGCTAGAGGAACCTGCAAGTATT
Found at i:62013 original size:24 final size:24
Alignment explanation
Indices: 61985--62033 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61975 ATAAATGGAT
*
61985 ATGTCAAAAATCAAAACATAATTC
1 ATGTCAAAAATCAAAACAGAATTC
** *
62009 ATGTCAAGTATCATAACAGAATTC
1 ATGTCAAAAATCAAAACAGAATTC
62033 A
1 A
62034 AATAAGAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (24 bp):
ATGTCAAAAATCAAAACAGAATTC
Found at i:66454 original size:57 final size:57
Alignment explanation
Indices: 66385--66553 Score: 248
Period size: 57 Copynumber: 3.0 Consensus size: 57
66375 CATAACCATA
* * * *
66385 CAACCCCGTCACGAACAGTAAGGCCCTTAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
* * *
66442 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCTGAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
* * *
66499 CAACCCCGTCACGAATAGTAAGGCTCTCAGTGCAAAGTCGAGGAACCTGCAAGTA
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTA
66554 TTCTTCCTCC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 100 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTAAT
Found at i:66665 original size:24 final size:25
Alignment explanation
Indices: 66607--66667 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 25
66597 AAACAGATAT
*
66607 ATCAA-AAATCAAAACATAATTCAA
1 ATCAAGAAATCAAAACAGAATTCAA
* * *
66631 GTCAAG-TATCATAACAGAATTCAA
1 ATCAAGAAATCAAAACAGAATTCAA
66655 AT-AAGAAATCAAA
1 ATCAAGAAATCAAA
66668 TAAAATATTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.21
Consensus pattern (25 bp):
ATCAAGAAATCAAAACAGAATTCAA
Done.