Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013999.1 Corchorus olitorius cultivar O-4 contig14032, 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: 163947
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3705 original size:14 final size:14
Alignment explanation
Indices: 3686--3714 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3676 ATAGATGAAT
3686 GGTAGTGGAAAGTG
1 GGTAGTGGAAAGTG
3700 GGTAGTGGAAAGTG
1 GGTAGTGGAAAGTG
3714 G
1 G
3715 TCCTTCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.52, T:0.21
Consensus pattern (14 bp):
GGTAGTGGAAAGTG
Found at i:14110 original size:18 final size:18
Alignment explanation
Indices: 14087--14124 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
14077 GAATTAGGAC
14087 AATTATACATGGGGACAT
1 AATTATACATGGGGACAT
14105 AATTATACATGGGGACAT
1 AATTATACATGGGGACAT
14123 AA
1 AA
14125 AGAGTATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (18 bp):
AATTATACATGGGGACAT
Found at i:16545 original size:23 final size:23
Alignment explanation
Indices: 16502--16547 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16492 AATTATATAT
* * *
16502 ATATATATATGGTGATGATAATA
1 ATATATATATAGTAATAATAATA
16525 ATATATATATAGTAATAATAATA
1 ATATATATATAGTAATAATAATA
16548 GTAAAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (23 bp):
ATATATATATAGTAATAATAATA
Found at i:16629 original size:2 final size:2
Alignment explanation
Indices: 16624--16651 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16614 TGTGTGTGTG
16624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16652 CATGGCTAAT
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):
TA
Found at i:16929 original size:12 final size:12
Alignment explanation
Indices: 16914--16939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16904 CTATATATAT
16914 ATATTTGGAATA
1 ATATTTGGAATA
16926 ATATTTGGAATA
1 ATATTTGGAATA
16938 AT
1 AT
16940 TTTTTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
ATATTTGGAATA
Found at i:17871 original size:22 final size:22
Alignment explanation
Indices: 17846--17945 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
17836 TATCTGTATC
17846 AAATTTTGATAAT-TGCACTACG
1 AAATTTTGATAATAT-CACTACG
** *
17868 AAATTTCAATAATATCACTATG
1 AAATTTTGATAATATCACTACG
* * * * *
17890 AAAATTTAATAATCTCTCTACA
1 AAATTTTGATAATATCACTACG
** *
17912 AAATTTTGATAACCTCACAACG
1 AAATTTTGATAATATCACTACG
17934 AAATTTTGATAA
1 AAATTTTGATAA
17946 CTTCCCAATG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 61 0.98
23 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAATATCACTACG
Found at i:17946 original size:22 final size:22
Alignment explanation
Indices: 17912--17962 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
17902 TCTCTCTACA
17912 AAATTTTGATAACCTCACAACG
1 AAATTTTGATAACCTCACAACG
* * *
17934 AAATTTTGATAACTTCCCAATG
1 AAATTTTGATAACCTCACAACG
17956 AAATTTT
1 AAATTTT
17963 AATTTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCACAACG
Found at i:17998 original size:22 final size:22
Alignment explanation
Indices: 17973--18029 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
17963 AATTTTTCCA
*
17973 CTATAAAATTTTGTTAACCTC-C
1 CTATAAAATTTTG-TAACCACAC
* *
17995 CTATGAAATCTTAGTAACCACAC
1 CTATAAAAT-TTTGTAACCACAC
18018 C-ATAAAATTTTG
1 CTATAAAATTTTG
18030 AAAATTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 5 0.18
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (22 bp):
CTATAAAATTTTGTAACCACAC
Found at i:18064 original size:22 final size:22
Alignment explanation
Indices: 18039--18189 Score: 146
Period size: 22 Copynumber: 7.0 Consensus size: 22
18029 GAAAATTTAT
* *
18039 TTATAAAATTTTGGTAACCACA
1 TTATGAAATTTTGATAACCACA
* *
18061 TTATGAAATTGTGATGACCACA
1 TTATGAAATTTTGATAACCACA
* *
18083 GTATGGAATTTTGAT-A--ACA
1 TTATGAAATTTTGATAACCACA
18102 TTATGAAATTTTGATAACCACA
1 TTATGAAATTTTGATAACCACA
* * *
18124 TTATGAATTTTTGATAACCTCC
1 TTATGAAATTTTGATAACCACA
* * * * * *
18146 CTGTGAATTTTTTATAACCTCG
1 TTATGAAATTTTGATAACCACA
18168 TTATGAAATTTTGATAACCACA
1 TTATGAAATTTTGATAACCACA
18190 CATAGACAAC
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
19 16 0.15
20 1 0.01
21 1 0.01
22 86 0.83
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACA
Found at i:18110 original size:41 final size:41
Alignment explanation
Indices: 18058--18141 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
18048 TTTGGTAACC
*
18058 ACATTATGAAATTGTGATGACCACAGTATGGAA-TTTTGATA
1 ACATTATGAAATTGTGATAACCACAGTAT-GAATTTTTGATA
* *
18099 ACATTATGAAATTTTGATAACCACATTATGAATTTTTGATA
1 ACATTATGAAATTGTGATAACCACAGTATGAATTTTTGATA
18140 AC
1 AC
18142 CTCCCTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (41 bp):
ACATTATGAAATTGTGATAACCACAGTATGAATTTTTGATA
Found at i:18163 original size:63 final size:64
Alignment explanation
Indices: 18039--18189 Score: 162
Period size: 63 Copynumber: 2.3 Consensus size: 64
18029 GAAAATTTAT
* * * *
18039 TTATAAAATTTTGGTAACCACATTATGAAATTGTGATGACCACAGTATGGAATTTTGATAA-CA
1 TTATGAAATTTTGATAACCACATTATGAAATTGTGATAACCACACTATGGAATTTTGATAACCA
* * * * * *
18102 TTATGAAATTTTGATAACCACATTATGAATTTTTGATAACCTCCCTGT-GAATTTTTTATAACCT
1 TTATGAAATTTTGATAACCACATTATGAAATTGTGATAACCACACTATGGAA-TTTTGATAA-C-
*
18166 CG
63 CA
18168 TTATGAAATTTTGATAACCACA
1 TTATGAAATTTTGATAACCACA
18190 CATAGACAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 3 0.04
63 47 0.64
66 23 0.32
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (64 bp):
TTATGAAATTTTGATAACCACATTATGAAATTGTGATAACCACACTATGGAATTTTGATAACCA
Found at i:19240 original size:120 final size:119
Alignment explanation
Indices: 19038--19263 Score: 337
Period size: 120 Copynumber: 1.9 Consensus size: 119
19028 AAAGGGTTTA
* * * * **
19038 TATATAATACACCATCAGTGGAGTTTAATAGACTGCACAAGCGGGTTTTGAAGGGTGACATGTGT
1 TATACAATACACCATCAGTAGAGTTTAATAGACTACACAAGCGGATCCTGAAGGGTGACATGTGT
*
19103 CCCCTAGGAACTAGATTGAAATATTTAAAATTTAATTAATTTAGAAAGGCAAAT
66 CCCCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTTAGAAAGGCAAAT
*
19157 TATACAATACACCGTCAGTAGAGTTTAGCA-AGACTACACAAGCGGATCCTGAAGGGTGACATGT
1 TATACAATACACCATCAGTAGAGTTTA--ATAGACTACACAAGCGGATCCTGAAGGGTGACATGT
* *
19221 GTCCTCTGGGAACTAGATTGAAATATTTAAAACTTAATTAATT
64 GTCCCCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATT
19264 CAAAAAATGG
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
119 24 0.25
120 70 0.74
121 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (119 bp):
TATACAATACACCATCAGTAGAGTTTAATAGACTACACAAGCGGATCCTGAAGGGTGACATGTGT
CCCCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTTAGAAAGGCAAAT
Found at i:19413 original size:83 final size:83
Alignment explanation
Indices: 19267--19428 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 83
19257 ATTAATTCAA
* * * ** * *
19267 AAAATGGACATGTGTTAACTCCACAACCCACTTGTGTAGTCCAAAATTTACACCGCTGGTGTATC
1 AAAATGGACATATGTCAACTCCAAAACCCACTTACGGAGTCCAAAATTTACACCGCTGATGTATC
19332 AAATAATTACCCATTTAG
66 AAATAATTACCCATTTAG
*
19350 AAAATGGACATATGTCAACTCCAAAACCCGCTTACGGAGTCCAAAATTTACACCG-TAGATGTAT
1 AAAATGGACATATGTCAACTCCAAAACCCACTTACGGAGTCCAAAATTTACACCGCT-GATGTAT
19414 CAAATAATTACCCAT
65 CAAATAATTACCCAT
19429 ATAAATATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
82 1 0.01
83 69 0.99
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AAAATGGACATATGTCAACTCCAAAACCCACTTACGGAGTCCAAAATTTACACCGCTGATGTATC
AAATAATTACCCATTTAG
Found at i:19935 original size:19 final size:19
Alignment explanation
Indices: 19911--19947 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
19901 TATATCTGTA
19911 ACTGTTTCACCACTGTTTG
1 ACTGTTTCACCACTGTTTG
19930 ACTGTTTCACCACTGTTT
1 ACTGTTTCACCACTGTTT
19948 TGGATCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (19 bp):
ACTGTTTCACCACTGTTTG
Found at i:20023 original size:21 final size:20
Alignment explanation
Indices: 19998--20055 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
19988 GTTGCTCTAA
19998 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT-CC
* * **
20019 TAATCTAATTTGTACAGTGG
1 TAATCTCATCTGTACAGTCC
20039 T-ATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
20056 TGCAAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 14 0.45
20 1 0.03
21 16 0.52
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTCC
Found at i:21151 original size:33 final size:33
Alignment explanation
Indices: 21105--21169 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
21095 GTTCTTTTTC
21105 AAGAGCCACCGCTCAGATCTACAACTCAAGTAT
1 AAGAGCCACCGCTCAGATCTACAACTCAAGTAT
*
21138 AAGAGCCATCGCTCAGATCTACAACTCAAGTA
1 AAGAGCCACCGCTCAGATCTACAACTCAAGTA
21170 CAAATGCCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.18
Consensus pattern (33 bp):
AAGAGCCACCGCTCAGATCTACAACTCAAGTAT
Found at i:22284 original size:123 final size:122
Alignment explanation
Indices: 22066--22554 Score: 589
Period size: 123 Copynumber: 4.0 Consensus size: 122
22056 TCGAATGGCA
* * * *
22066 GAAATGATGAAGCCCTCAAGGGG-CCAACGCCAATAGGCGAGCGATCAGGCAAGGCCGAGCTCGA
1 GAAACGATGAAGCCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGGCCGAGCTCGA
* * *
22130 CCTAGTATGGCTCCCGACTGGCAACCGATCGGCAAGAACCATCCCTGACCGAGTATGG
66 CCTAGTATGGC-CCCGACCGGCAAGCGATCGGCAAGAACCATCCCTGACCAAGTATGG
* ** * *
22188 GAAATGATGAAGCCGTCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCGAGCCCGAGCTCGA
1 GAAACGATGAAGCCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGGCCGAGCTCGA
* *
22253 CCTAGTATGGCCCCTGACCGGCAGGCGATCGGCAAGAACCATCCCTGACCGAGTATGG
66 CCTAGTATGGCCCC-GACCGGCAAGCGATCGGCAAGAACCATCCCTGACCAAGTATGG
* * * * *
22311 GAAACGATGATGCCCCCAAGGGACCCAACGCAAACAAGCGAGGGATCAGGCAAGGCCAAGCTCGA
1 GAAACGATGAAGCCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGGCCGAGCTCGA
* * *
22376 CCTAGTATGG---CGATCGCCAAGCGATCGGCATGAACCAT-CC--ACCAAGTATGG
66 CCTAGTATGGCCCCGACCGGCAAGCGATCGGCAAGAACCATCCCTGACCAAGTATGG
* * *
22427 GAAACGATGATGCCCCCATGGGGCCCAACGCCAA-AAGGCGAGCGATCAGGCAAAGCCGAGCTCG
1 GAAACGATGAAGCCCCCAAGGGGCCCAACGCCAACAA-GCGAGCGATCAGGCAAGGCCGAGCTCG
* * * ** **
22491 ACCTAGTATGGCCCCCGACTGGCAGGCGATCGACACAGAGTCATCCCAAACCAAGTATGG
65 ACCTAGTATGG-CCCCGACCGGCAAGCGATCGGCA-AGAACCATCCCTGACCAAGTATGG
22551 GAAA
1 GAAA
22555 AATGATGATA
Statistics
Matches: 319, Mismatches: 37, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
115 2 0.01
116 76 0.24
118 2 0.01
119 23 0.07
120 16 0.05
121 5 0.02
122 27 0.08
123 153 0.48
124 15 0.05
ACGTcount: A:0.29, C:0.30, G:0.29, T:0.12
Consensus pattern (122 bp):
GAAACGATGAAGCCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGGCCGAGCTCGA
CCTAGTATGGCCCCGACCGGCAAGCGATCGGCAAGAACCATCCCTGACCAAGTATGG
Found at i:22517 original size:239 final size:242
Alignment explanation
Indices: 22066--22554 Score: 614
Period size: 239 Copynumber: 2.0 Consensus size: 242
22056 TCGAATGGCA
* * * * * * *
22066 GAAATGATGAAGCCCTCAAGGGGCCAACGCCAATAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
1 GAAACGATGAAGCCCCCAAGGGCCCAACGCAAACAAGCGAGCGATCAGGCAAGGCCAAGCTCGAC
* * *
22131 CTAGTATGGCTCCCGACTGGCAACCGATCGGCAAGAACCATCCCTGACCGAGTATGGGAAATGAT
66 CTAGTATGG---CCGACTGCCAACCGATCGGCAAGAACCATCCC-GACCAAGTATGGGAAACGAT
** *
22196 GAAGCCGTCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCGAGCCCGAGCTCGACCTAGTAT
127 GAAGCCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGCCCGAGCTCGACCTAGTAT
* * ** *
22261 GGCCCCTGACCGGCAGGCGATCGGCA-AGAACCATCCCTGACCGAGTATGG
192 GGCCCCCGACCGGCAGGCGATCGACACAGAACCATCCCAAACCAAGTATGG
* *
22311 GAAACGATGATGCCCCCAAGGGACCCAACGCAAACAAGCGAGGGATCAGGCAAGGCCAAGCTCGA
1 GAAACGATGAAGCCCCCAAGGG-CCCAACGCAAACAAGCGAGCGATCAGGCAAGGCCAAGCTCGA
* *
22376 CCTAGTATGG-CGA-TCGCCAAGCGATCGGCATGAACCAT-CC-ACCAAGTATGGGAAACGATGA
65 CCTAGTATGGCCGACT-GCCAACCGATCGGCAAGAACCATCCCGACCAAGTATGGGAAACGATGA
* *
22437 TGCCCCCATGGGGCCCAACGCCAA-AAGGCGAGCGATCAGGCAAAG-CCGAGCTCGACCTAGTAT
129 AGCCCCCAAGGGGCCCAACGCCAACAA-GCGAGCGATCAGGC-AAGCCCGAGCTCGACCTAGTAT
* **
22500 GGCCCCCGACTGGCAGGCGATCGACACAGAGTCATCCCAAACCAAGTATGG
192 GGCCCCCGACCGGCAGGCGATCGACACAGAACCATCCCAAACCAAGTATGG
22551 GAAA
1 GAAA
22555 AATGATGATA
Statistics
Matches: 212, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
238 2 0.01
239 94 0.44
240 25 0.12
241 3 0.01
242 23 0.11
245 19 0.09
246 46 0.22
ACGTcount: A:0.29, C:0.30, G:0.29, T:0.12
Consensus pattern (242 bp):
GAAACGATGAAGCCCCCAAGGGCCCAACGCAAACAAGCGAGCGATCAGGCAAGGCCAAGCTCGAC
CTAGTATGGCCGACTGCCAACCGATCGGCAAGAACCATCCCGACCAAGTATGGGAAACGATGAAG
CCCCCAAGGGGCCCAACGCCAACAAGCGAGCGATCAGGCAAGCCCGAGCTCGACCTAGTATGGCC
CCCGACCGGCAGGCGATCGACACAGAACCATCCCAAACCAAGTATGG
Found at i:23045 original size:21 final size:21
Alignment explanation
Indices: 22978--23298 Score: 122
Period size: 21 Copynumber: 15.5 Consensus size: 21
22968 AGGAGAGGAT
* * *
22978 AATGCTCTCCAAACAAAGAAT
1 AATGCTCCCCAAAGAAAGAAG
** * * *
22999 AATAATCCTCAAGGAGAGAAG
1 AATGCTCCCCAAAGAAAGAAG
* *
23020 TATGCTCCCCAAAGAAAGAAA
1 AATGCTCCCCAAAGAAAGAAG
* *
23041 AATGCTCTCCAAAGAGAA-AAT
1 AATGCTCCCCAAAGA-AAGAAG
* * *
23062 AACGC-CTCCAAAGAGAGAA-
1 AATGCTCCCCAAAGAAAGAAG
* * * *
23081 ATACGCTCCCCAAATAGAGGAG
1 A-ATGCTCCCCAAAGAAAGAAG
* * * *
23103 AATGATCCCCAAGGAGAGTAG
1 AATGCTCCCCAAAGAAAGAAG
*
23124 AATACTCCCC-AAG-AAGAAG
1 AATGCTCCCCAAAGAAAGAAG
* *
23143 AATGCTCTCCAAAGAAAGTTA-
1 AATGCTCCCCAAAGAAAG-AAG
*
23164 AATGCTCCCCAAAGAGAAG-AT
1 AATGCTCCCCAAAGA-AAGAAG
* * * *
23185 AACG-TTCCCAAGGAAAGGAG
1 AATGCTCCCCAAAGAAAGAAG
* * * *
23205 AACGCTCTCC-AAGAGAGGAG
1 AATGCTCCCCAAAGAAAGAAG
* * *
23225 AATGCTTCCCAAGGAGAGAAG
1 AATGCTCCCCAAAGAAAGAAG
* * *
23246 AATGGTCCCCAAACAAA-AAA
1 AATGCTCCCCAAAGAAAGAAG
* * *
23266 AATTGCTCTCCAAAGAGAGAAT
1 AA-TGCTCCCCAAAGAAAGAAG
*
23288 AACGCTCCCCA
1 AATGCTCCCCA
23299 CAGAGAGGAG
Statistics
Matches: 222, Mismatches: 63, Indels: 30
0.70 0.20 0.10
Matches are distributed among these distances:
19 17 0.08
20 53 0.24
21 141 0.64
22 11 0.05
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (21 bp):
AATGCTCCCCAAAGAAAGAAG
Found at i:23208 original size:20 final size:20
Alignment explanation
Indices: 23185--23239 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
23175 AAGAGAAGAT
23185 AACGTTCCCAAGGAAAGGAG
1 AACGTTCCCAAGGAAAGGAG
* *
23205 AACGCTCTCCAA-GAGAGGAG
1 AACGTTC-CCAAGGAAAGGAG
*
23225 AATGCTTCCCAAGGA
1 AACG-TTCCCAAGGA
23240 GAGAAGAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.36, C:0.24, G:0.27, T:0.13
Consensus pattern (20 bp):
AACGTTCCCAAGGAAAGGAG
Found at i:23455 original size:25 final size:25
Alignment explanation
Indices: 23426--23497 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
23416 CGGGAAATGG
*
23426 AGAACGCTCGCCGAACGCGAAGCAT
1 AGAACGCTCGCCGAACGCGAAACAT
* * *
23451 AGAACCCTTGCCGAACGCGAAACGT
1 AGAACGCTCGCCGAACGCGAAACAT
* *
23476 AGAATGCTCGCCGAGCGCGAAA
1 AGAACGCTCGCCGAACGCGAAA
23498 GGGAGAATGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.32, C:0.31, G:0.28, T:0.10
Consensus pattern (25 bp):
AGAACGCTCGCCGAACGCGAAACAT
Found at i:23504 original size:25 final size:25
Alignment explanation
Indices: 23419--23509 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
23409 TCGAGGTCGG
* *
23419 GAAATGGAGAACGCTCGCCGAACGC
1 GAAACGGAGAATGCTCGCCGAACGC
* ** ** *
23444 GAAGCATAGAACCCTTGCCGAACGC
1 GAAACGGAGAATGCTCGCCGAACGC
* *
23469 GAAACGTAGAATGCTCGCCGAGCGC
1 GAAACGGAGAATGCTCGCCGAACGC
*
23494 GAAAGGGAGAATGCTC
1 GAAACGGAGAATGCTC
23510 CTCGAGAACA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.32, C:0.26, G:0.31, T:0.11
Consensus pattern (25 bp):
GAAACGGAGAATGCTCGCCGAACGC
Found at i:23555 original size:123 final size:123
Alignment explanation
Indices: 23328--23558 Score: 284
Period size: 123 Copynumber: 1.9 Consensus size: 123
23318 CAAGGATAGG
* * *
23328 AGAACACTTGCCGAACGCGAAGCGTAGAACGCCCGCCGAACATGAAATGGAGAATGCTCCTCGAG
1 AGAACACTTGCCGAACGCGAAACGTAGAACGCCCGCCGAACACGAAAGGGAGAATGCTCCTCGAG
** * * * * **
23393 TGCAAATGAAGAATGCTCGAGGTCGGGAAATGGAGAACGCTCGCCGAACGCGAAGCAT
66 AACAAACGAAGAATGCCCAAGATCGGGAAACAGAGAACGCTCGCCGAACGCGAAGCAT
* * * * *
23451 AGAACCCTTGCCGAACGCGAAACGTAGAATGCTCGCCGAGCGCGAAAGGGAGAATGCTCCTCGAG
1 AGAACACTTGCCGAACGCGAAACGTAGAACGCCCGCCGAACACGAAAGGGAGAATGCTCCTCGAG
* *
23516 AACAAGCGAAGAATGCCCAAGAT-GGCGAAACAGATAACGCTCG
66 AACAAACGAAGAATGCCCAAGATCGG-GAAACAGAGAACGCTCG
23559 TAGAACACGA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
122 2 0.02
123 87 0.98
ACGTcount: A:0.33, C:0.25, G:0.29, T:0.12
Consensus pattern (123 bp):
AGAACACTTGCCGAACGCGAAACGTAGAACGCCCGCCGAACACGAAAGGGAGAATGCTCCTCGAG
AACAAACGAAGAATGCCCAAGATCGGGAAACAGAGAACGCTCGCCGAACGCGAAGCAT
Found at i:23637 original size:61 final size:61
Alignment explanation
Indices: 23525--23707 Score: 240
Period size: 61 Copynumber: 3.0 Consensus size: 61
23515 GAACAAGCGA
* ** * * *
23525 AGAATGCCCAAGATGGCGAAACAGATAACGCTCGTAGAACACGAAGCGTAGGACGTTCGCC
1 AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAGCGTAGGAAGCTCGCC
* ** * *
23586 CGAATGCTTGAGATGGCGAAACAGATAACGCTCGCCGAACGCGATGTGTAGGAAGCTCGCC
1 AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAGCGTAGGAAGCTCGCC
* * *
23647 AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAACATAGGACGCTCGCC
1 AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAGCGTAGGAAGCTCGCC
23708 GAGCGCGAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 103 1.00
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.13
Consensus pattern (61 bp):
AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAGCGTAGGAAGCTCGCC
Found at i:23690 original size:25 final size:25
Alignment explanation
Indices: 23662--23717 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
23652 GCCCGAGATG
*
23662 GCGAAACAGATAACGCTCGCCGAAC
1 GCGAAACAGAGAACGCTCGCCGAAC
* * *
23687 GCGAAACATAGGACGCTCGCCGAGC
1 GCGAAACAGAGAACGCTCGCCGAAC
23712 GCGAAA
1 GCGAAA
23718 TGGAGAATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.29, T:0.07
Consensus pattern (25 bp):
GCGAAACAGAGAACGCTCGCCGAAC
Found at i:23729 original size:25 final size:25
Alignment explanation
Indices: 23701--23827 Score: 64
Period size: 25 Copynumber: 5.2 Consensus size: 25
23691 AACATAGGAC
23701 GCTCGCCGAGCGCGAAATGGAGAAT
1 GCTCGCCGAGCGCGAAATGGAGAAT
* *
23726 GCTC-CTCGAGAGC-AAATGAAGAAT
1 GCTCGC-CGAGCGCGAAATGGAGAAT
* * * * *
23750 GCCCG-AGATG-GCGAAACGGATAAC
1 GCTCGCCGA-GCGCGAAATGGAGAAT
* * ** * * *
23774 GCTCACCGAACGCGAAGCGTAGGAC
1 GCTCGCCGAGCGCGAAATGGAGAAT
* *
23799 GCTCGTCGAGCGCGAAATGGACAAT
1 GCTCGCCGAGCGCGAAATGGAGAAT
23824 GCTC
1 GCTC
23828 CTCGAGAGCA
Statistics
Matches: 71, Mismatches: 25, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
23 4 0.06
24 25 0.35
25 42 0.59
ACGTcount: A:0.30, C:0.26, G:0.31, T:0.13
Consensus pattern (25 bp):
GCTCGCCGAGCGCGAAATGGAGAAT
Found at i:23765 original size:48 final size:48
Alignment explanation
Indices: 23712--23863 Score: 139
Period size: 48 Copynumber: 3.1 Consensus size: 48
23702 CTCGCCGAGC
* *
23712 GCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCGAGATG
1 GCGAAATGGACAATGCTCCTCGAGAGCAAGTGAAGAATGCCCGAGATG
* * * * * * * * *
23760 GCGAAACGGATAACGCTCAC-CGA-ACGCGAAGCGTAGGACGCTCGTCGA-G
1 GCGAAATGGACAATGCTC-CTCGAGA-GC-AAGTGAAGAATGCCCG-AGATG
23809 CGCGAAATGGACAATGCTCCTCGAGAGCAAGTGAAGAATGCCCGAGATG
1 -GCGAAATGGACAATGCTCCTCGAGAGCAAGTGAAGAATGCCCGAGATG
23858 GCGAAA
1 GCGAAA
23864 CGGATAAGTC
Statistics
Matches: 77, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
47 1 0.01
48 28 0.36
49 25 0.32
50 22 0.29
51 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.32, T:0.12
Consensus pattern (48 bp):
GCGAAATGGACAATGCTCCTCGAGAGCAAGTGAAGAATGCCCGAGATG
Found at i:23816 original size:98 final size:98
Alignment explanation
Indices: 23647--23900 Score: 411
Period size: 98 Copynumber: 2.6 Consensus size: 98
23637 GAAGCTCGCC
* * * *
23647 AGAATGCCCGAGATGGCGAAACAGATAACGCTCGCCGAACGCGAAACATAGGACGCTCGCCGAGC
1 AGAATGCCCGAGATGGCGAAACGGATAACGCTCACCGAACGCGAAGCGTAGGACGCTCGCCGAGC
*
23712 GCGAAATGGAGAATGCTCCTCGAGAGCAAATGA
66 GCGAAATGGACAATGCTCCTCGAGAGCAAATGA
*
23745 AGAATGCCCGAGATGGCGAAACGGATAACGCTCACCGAACGCGAAGCGTAGGACGCTCGTCGAGC
1 AGAATGCCCGAGATGGCGAAACGGATAACGCTCACCGAACGCGAAGCGTAGGACGCTCGCCGAGC
*
23810 GCGAAATGGACAATGCTCCTCGAGAGCAAGTGA
66 GCGAAATGGACAATGCTCCTCGAGAGCAAATGA
* *
23843 AGAATGCCCGAGATGGCGAAACGGATAA-GTCTCACCAAATGCGAAGCGTAGGACGCTC
1 AGAATGCCCGAGATGGCGAAACGGATAACG-CTCACCGAACGCGAAGCGTAGGACGCTC
23901 TCCAGAATGC
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
97 1 0.01
98 145 0.99
ACGTcount: A:0.32, C:0.25, G:0.30, T:0.12
Consensus pattern (98 bp):
AGAATGCCCGAGATGGCGAAACGGATAACGCTCACCGAACGCGAAGCGTAGGACGCTCGCCGAGC
GCGAAATGGACAATGCTCCTCGAGAGCAAATGA
Found at i:25132 original size:3 final size:3
Alignment explanation
Indices: 25124--25150 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25114 TGGAAGGACG
25124 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
25151 AAAAGGTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:26344 original size:51 final size:51
Alignment explanation
Indices: 26284--26385 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
26274 TGCCACAGGC
*
26284 TACCTCAAAGAACCTAGAGACCACTAGGCCTTCCGGCCTAATCATCTTCAA
1 TACCTCAAAGAACCTAGAGACCACTAGGCCATCCGGCCTAATCATCTTCAA
26335 TACCTCAAAGAACCTAGAGACCACTAGGCCATCCGGCCTAATCATCTTCAA
1 TACCTCAAAGAACCTAGAGACCACTAGGCCATCCGGCCTAATCATCTTCAA
26386 GGCCCATAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (51 bp):
TACCTCAAAGAACCTAGAGACCACTAGGCCATCCGGCCTAATCATCTTCAA
Found at i:28750 original size:6 final size:6
Alignment explanation
Indices: 28741--28789 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
28731 GATTTTGATA
28741 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
28789 A
1 A
28790 CTAAATATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:35642 original size:25 final size:25
Alignment explanation
Indices: 35614--35666 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
35604 TCATTCTAAT
35614 GTCTAGGTACATGTTCAATTCTTAC
1 GTCTAGGTACATGTTCAATTCTTAC
35639 GTCTAGGTACATGTTCAATTCTTAC
1 GTCTAGGTACATGTTCAATTCTTAC
35664 GTC
1 GTC
35667 ATCAAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (25 bp):
GTCTAGGTACATGTTCAATTCTTAC
Found at i:42111 original size:21 final size:21
Alignment explanation
Indices: 42085--42125 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42075 GAAATATAAT
*
42085 AATAAAA-AAACGATAAAAGTA
1 AATAAAAGAAAAGA-AAAAGTA
42106 AATAAAAGAAAAGAAAAAGT
1 AATAAAAGAAAAGAAAAAGT
42126 TAAAGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (21 bp):
AATAAAAGAAAAGAAAAAGTA
Found at i:56716 original size:2 final size:2
Alignment explanation
Indices: 56709--56744 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56699 TCACTTCAAG
56709 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
56745 TAAAACCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56893 original size:22 final size:21
Alignment explanation
Indices: 56868--56910 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
56858 TAGTTGACAC
56868 ATTTATTT-TTTTTCTATTTTTG
1 ATTT-TTTCTTTTTCT-TTTTTG
56890 ATTTTTTCTTTTTCTTTTTTG
1 ATTTTTTCTTTTTCTTTTTTG
56911 GGTCAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (21 bp):
ATTTTTTCTTTTTCTTTTTTG
Found at i:57070 original size:13 final size:13
Alignment explanation
Indices: 57052--57078 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57042 GTGAATTGAC
57052 TTATATATATATA
1 TTATATATATATA
57065 TTATATATATATA
1 TTATATATATATA
57078 T
1 T
57079 AACAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:57233 original size:44 final size:43
Alignment explanation
Indices: 57152--57240 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 43
57142 GTAAGGAGAC
* * * *
57152 AAAAAATTTGACATGACATGAAATCATTTACTTAGGGAGATAA
1 AAAAAAATTGACATGACATGAAATCATTGACTAAGGGAGACAA
*
57195 AAAAAAATTGACATGACATGAAATC-TCATGGCTAAGGGAGACAA
1 AAAAAAATTGACATGACATGAAATCAT--TGACTAAGGGAGACAA
57239 AA
1 AA
57241 TGACATGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.03
43 24 0.62
44 14 0.36
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAAAATTGACATGACATGAAATCATTGACTAAGGGAGACAA
Found at i:58135 original size:2 final size:2
Alignment explanation
Indices: 58128--58156 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58118 ATTGTTTGTT
58128 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 T
58157 GTTTTAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59372 original size:46 final size:46
Alignment explanation
Indices: 59297--59384 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
59287 CTATATTGCA
59297 TGAATCGTGTAAATCATCATCTTCATGATTATAATTCTGTATTGTG
1 TGAATCGTGTAAATCATCATCTTCATGATTATAATTCTGTATTGTG
* * * * *
59343 TGAATCGTGTAACTCGTCATTTTCGTGATTATAATTTTGTAT
1 TGAATCGTGTAAATCATCATCTTCATGATTATAATTCTGTAT
59385 GATTAGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.45
Consensus pattern (46 bp):
TGAATCGTGTAAATCATCATCTTCATGATTATAATTCTGTATTGTG
Found at i:59872 original size:18 final size:18
Alignment explanation
Indices: 59849--59938 Score: 114
Period size: 18 Copynumber: 5.0 Consensus size: 18
59839 GTGTTAAGGA
59849 TCATTCAAAGTCAG-TCTC
1 TCATTCAAAGTCAGTTC-C
59867 TCATTCAAAGTCAGTT-C
1 TCATTCAAAGTCAGTTCC
59884 TCCATTCAAAG-CTAGTTCC
1 T-CATTCAAAGTC-AGTTCC
59903 TCATTCAAAGTCAGTTCC
1 TCATTCAAAGTCAGTTCC
* *
59921 CCATTCAAAGTTAGTTCC
1 TCATTCAAAGTCAGTTCC
59939 CTAGGATTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.05
18 58 0.89
19 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (18 bp):
TCATTCAAAGTCAGTTCC
Found at i:59906 original size:36 final size:35
Alignment explanation
Indices: 59850--59938 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 35
59840 TGTTAAGGAT
*
59850 CATTCAAAGTCAG-TCTCTCATTCAAAGTCAGTTCTC
1 CATTCAAAGT-AGTTC-CTCATTCAAAGTCAGTTCCC
59886 CATTCAAAGCTAGTTCCTCATTCAAAGTCAGTTCCC
1 CATTCAAAG-TAGTTCCTCATTCAAAGTCAGTTCCC
59922 CATTCAAAGTTAGTTCC
1 CATTCAAAG-TAGTTCC
59939 CTAGGATTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 46 0.94
37 3 0.06
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (35 bp):
CATTCAAAGTAGTTCCTCATTCAAAGTCAGTTCCC
Found at i:68509 original size:50 final size:50
Alignment explanation
Indices: 68434--68534 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
68424 CTTATATGAA
*
68434 AAACAAACTTGAGCGTCGGTCCAAGCCTTGTGTTTTTGTAGGATACTAAG
1 AAACAAACTTGACCGTCGGTCCAAGCCTTGTGTTTTTGTAGGATACTAAG
68484 AAACAAACTTGACCGTCGGTCCAAGCCTTGTGTTTTTGTAGGATACTAAG
1 AAACAAACTTGACCGTCGGTCCAAGCCTTGTGTTTTTGTAGGATACTAAG
68534 A
1 A
68535 TAATCAAAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (50 bp):
AAACAAACTTGACCGTCGGTCCAAGCCTTGTGTTTTTGTAGGATACTAAG
Found at i:68984 original size:84 final size:84
Alignment explanation
Indices: 68843--69007 Score: 249
Period size: 84 Copynumber: 2.0 Consensus size: 84
68833 ACTAATGCTT
* * *
68843 CCTCTTCAGTGCCATTAATTCCACAGGAAAATCATTATGATTCTCTAGCCACTCATGGTTCTTTA
1 CCTCTTCAATGCCACTAATTCCACAGGAAAATCATTATGAATCTCTAGCCACTCATGGTTCTTTA
*
68908 GTGCCACTAGCTCCACAGA
66 GTGCCACTAACTCCACAGA
* * * * *
68927 CCTCTTCAATGCTACTAATTCCATAGGAAAATTATTCTGAATCTCTGGCCACTCATGGTTCTTTA
1 CCTCTTCAATGCCACTAATTCCACAGGAAAATCATTATGAATCTCTAGCCACTCATGGTTCTTTA
68992 GTGCCACTAACTCCAC
66 GTGCCACTAACTCCAC
69008 TAAATAGTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (84 bp):
CCTCTTCAATGCCACTAATTCCACAGGAAAATCATTATGAATCTCTAGCCACTCATGGTTCTTTA
GTGCCACTAACTCCACAGA
Found at i:70680 original size:18 final size:18
Alignment explanation
Indices: 70657--70746 Score: 105
Period size: 18 Copynumber: 5.0 Consensus size: 18
70647 GTGTTAAGGA
70657 TCATTCAAAGTCAG-TCTC
1 TCATTCAAAGTCAGTTC-C
*
70675 TCATTCAAAGTTAGTT-C
1 TCATTCAAAGTCAGTTCC
70692 TCCATTCAAAG-CTAGTTCC
1 T-CATTCAAAGTC-AGTTCC
70711 TCATTCAAAGTCAGTTCC
1 TCATTCAAAGTCAGTTCC
* *
70729 CCTTTCAAAGTCAGTTCC
1 TCATTCAAAGTCAGTTCC
70747 CTAGGATTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
17 2 0.03
18 57 0.90
19 4 0.06
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (18 bp):
TCATTCAAAGTCAGTTCC
Found at i:70714 original size:36 final size:36
Alignment explanation
Indices: 70658--70746 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
70648 TGTTAAGGAT
* *
70658 CATTCAAAGTCAG-TCTCTCATTCAAAGTTAGTTCTC
1 CATTCAAAGTCAGTTC-CTCATTCAAAGTCAGTTCCC
70694 CATTCAAAG-CTAGTTCCTCATTCAAAGTCAGTTCCC
1 CATTCAAAGTC-AGTTCCTCATTCAAAGTCAGTTCCC
*
70730 CTTTCAAAGTCAGTTCC
1 CATTCAAAGTCAGTTCC
70747 CTAGGATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 1 0.02
36 43 0.91
37 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (36 bp):
CATTCAAAGTCAGTTCCTCATTCAAAGTCAGTTCCC
Found at i:71423 original size:43 final size:43
Alignment explanation
Indices: 71350--71433 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
71340 AGAAGTTATT
* *
71350 GTTTGGGACAAGGATTTAGAGAGAAATGAAACAAATAATTTGGG
1 GTTTGGGACAAGAATATAGAGAGAAATGAAACAAAT-ATTTGGG
*
71394 GTTTGGGACAAGAATATA-AGAGAAATGAAACAGATATTTG
1 GTTTGGGACAAGAATATAGAGAGAAATGAAACAAATATTTG
71434 ATATGGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 5 0.14
43 16 0.43
44 16 0.43
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (43 bp):
GTTTGGGACAAGAATATAGAGAGAAATGAAACAAATATTTGGG
Found at i:74828 original size:17 final size:17
Alignment explanation
Indices: 74806--74841 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
74796 AGCATATACT
74806 TCAAAGACCAATTTAAA
1 TCAAAGACCAATTTAAA
74823 TCAAAGACCAATTTAAA
1 TCAAAGACCAATTTAAA
74840 TC
1 TC
74842 TAATTCACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (17 bp):
TCAAAGACCAATTTAAA
Found at i:78444 original size:14 final size:14
Alignment explanation
Indices: 78421--78450 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
78411 TTTCTCCTGA
78421 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
78435 AAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG
78449 AA
1 AA
78451 GACATTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:79234 original size:87 final size:87
Alignment explanation
Indices: 79067--79240 Score: 255
Period size: 87 Copynumber: 2.0 Consensus size: 87
79057 AATTCGGTTT
* * *
79067 AATTCGTTCATCTTGAAAAAAAATTTGAGTTCAAGTTTTATAAATAAAAAAAATAATAAGAAAAA
1 AATTCGTTCATCTTGAAAAAAAATTTGAGTTCAAATCTTATAAATAAAAAAAAAAATAAGAAAAA
79132 CATTATTTTGATGGAACTTTGC
66 CATTATTTTGATGGAACTTTGC
*
79154 AATTCGTT-ATCTTG-AATAAAATTTAGAGTTCAAATCTTATAAATGAAAAAAAAAAAATAAG-A
1 AATTCGTTCATCTTGAAAAAAAATTT-GAGTTCAAATCTTATAAAT--AAAAAAAAAAATAAGAA
*
79216 AAATATTATTTTGATGGAACTTTGC
63 AAACATTATTTTGATGGAACTTTGC
79241 TCCATAGTGA
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
85 9 0.11
86 23 0.29
87 33 0.42
88 14 0.18
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.34
Consensus pattern (87 bp):
AATTCGTTCATCTTGAAAAAAAATTTGAGTTCAAATCTTATAAATAAAAAAAAAAATAAGAAAAA
CATTATTTTGATGGAACTTTGC
Found at i:79422 original size:45 final size:49
Alignment explanation
Indices: 79341--79437 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 49
79331 TGTTACATTC
79341 GCAAAAGGCAAAGAGAGGGTATCCGGCACCGACGGCGAGAG-TCCATAGAAA
1 GCAAAAGGCAAAGAGAGGGTATCCGG---CGACGGCGAGAGTTCCATAGAAA
*
79392 GCAAAAGGCAAAGAGAGGGTATCC-G-G-CGGCGAGAGTTGCATAGAAA
1 GCAAAAGGCAAAGAGAGGGTATCCGGCGACGGCGAGAGTTCCATAGAAA
79438 TAAAGATGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
45 9 0.20
46 10 0.23
50 1 0.02
51 24 0.55
ACGTcount: A:0.37, C:0.19, G:0.35, T:0.09
Consensus pattern (49 bp):
GCAAAAGGCAAAGAGAGGGTATCCGGCGACGGCGAGAGTTCCATAGAAA
Found at i:89294 original size:11 final size:12
Alignment explanation
Indices: 89260--89295 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
89250 GATTTTTGAG
*
89260 TTTTGAATTTTT
1 TTTTGCATTTTT
*
89272 TTTTGGATTTTT
1 TTTTGCATTTTT
89284 TTTTGCATTTTT
1 TTTTGCATTTTT
89296 GAAAATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.03, G:0.11, T:0.75
Consensus pattern (12 bp):
TTTTGCATTTTT
Found at i:94423 original size:120 final size:120
Alignment explanation
Indices: 94210--94428 Score: 343
Period size: 120 Copynumber: 1.8 Consensus size: 120
94200 TCTAAGTTTT
*
94210 TAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAACAAAA
1 TAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATGAAACAAAA
94275 AATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTAAATATA
66 AATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTAAATATA
* * * * *
94330 TAATTAAAATT-GTAAAATGGTAAAAATTAATTAGTTATAAGGATATTATATTTAAATGAAA-TA
1 TAATT-AAATTAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTT-AATGAAACAA
*
94393 AAAATAGATTTTTTAGTTGAGTAAAACTATAAAAGT
64 AAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
94429 TTAAACAATG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
120 79 0.88
121 11 0.12
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (120 bp):
TAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATGAAACAAAA
AATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTAAATATA
Found at i:94829 original size:22 final size:22
Alignment explanation
Indices: 94715--94866 Score: 89
Period size: 22 Copynumber: 6.9 Consensus size: 22
94705 TGAATATTTT
* *
94715 TATGAAATTTTGATAA-TTACTC
1 TATGAAATTTTGATAACCTA-AC
* *
94737 TATTAAATTTTGATAACC-ACGC
1 TATGAAATTTTGATAACCTA-AC
* *
94759 TATGAAAAATTTTGATAA-TTACC
1 TATG--AAATTTTGATAACCTAAC
* * **
94782 TATGAAATTGTGATAA-ATTCC
1 TATGAAATTTTGATAACCTAAC
*
94803 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTAAC
* **
94826 TATGAAATTTTAATAAACCTTTC
1 TATGAAATTTTGAT-AACCTAAC
94849 TATGAAATTTTG-TAACCT
1 TATGAAATTTTGATAACCT
94867 TCCCTATGAG
Statistics
Matches: 104, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
21 19 0.18
22 48 0.46
23 24 0.23
24 13 0.12
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTAAC
Found at i:94895 original size:22 final size:22
Alignment explanation
Indices: 94780--94883 Score: 70
Period size: 22 Copynumber: 4.7 Consensus size: 22
94770 TTGATAATTA
* *
94780 CCTATGAAATTGTGATAA-ATTC
1 CCTATGAAATTTTG-TAACCTTC
* * *
94802 CATATGAAACTTTGATAACC-TA
1 CCTATGAAATTTTG-TAACCTTC
* *
94824 ACTATGAAATTTTAATAAACCTT-
1 CCTATGAAATTTT-GT-AACCTTC
*
94847 TCTATGAAATTTTGTAACCTTC
1 CCTATGAAATTTTGTAACCTTC
*
94869 CCTATGAGATTTTGT
1 CCTATGAAATTTTGT
94884 TAATCTCCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
21 6 0.09
22 41 0.64
23 16 0.25
24 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
CCTATGAAATTTTGTAACCTTC
Found at i:95702 original size:2 final size:2
Alignment explanation
Indices: 95687--95728 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
95677 GCCAATAATA
95687 AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T 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
95726 AT A
1 AT A
95729 ACATTAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102297 original size:40 final size:39
Alignment explanation
Indices: 102138--102564 Score: 380
Period size: 40 Copynumber: 11.2 Consensus size: 39
102128 CCTGAATCAG
* * *
102138 GATCCTGAATAGGATTTTGACATTAACTGACAAAACAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
* * *
102177 GATCCTTAATAGGATTTCGAAATCAACTGATAAAGCAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
* * *
102216 GATCCTGAATAGGATTGTG--ATTAACTGGTAAAGAAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
*
102253 GATCCTGAGTAGGATTTTGAAATTAATCTGATAAAGCAAT
1 GATCCTGAATAGGATTTTGAAATTAA-CTGATAAAGCAAT
* * *
102293 GATCCTGAATAGGATTGTGACATTTACTGATAAAGCAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
* *
102332 GATCCTGAACAGCA-TTTG------A--GA-AAA-CAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
** * * *
102360 GATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCTAT
1 GATCCTGAATAGGATTTTGAAATTAA-CTGATAAAGCAAT
* * *
102400 GATCCTGAATAGGATTCTAAAATTCACTTGATAAAGCAAT
1 GATCCTGAATAGGATTTTGAAATTAAC-TGATAAAGCAAT
** * *
102440 GATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTTTGAAATTAA-CTGATAAAGCAAT
** * * *
102480 GATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGAAAA
1 GATCCTGAATAGGATTTTGAAATTAA-CTGATAAAGCAAT
* * * *
102520 GATCCTGAATAGGATTGTG--ATTGACTGGTAAAGAAAT
1 GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
102557 GATCCTGA
1 GATCCTGA
102565 GCAGGATTAA
Statistics
Matches: 323, Mismatches: 48, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.05
29 6 0.02
30 2 0.01
32 1 0.00
35 1 0.00
37 50 0.15
38 9 0.03
39 82 0.25
40 156 0.48
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (39 bp):
GATCCTGAATAGGATTTTGAAATTAACTGATAAAGCAAT
Found at i:103087 original size:141 final size:142
Alignment explanation
Indices: 102613--103154 Score: 881
Period size: 142 Copynumber: 3.9 Consensus size: 142
102603 ACATGGAATG
* * **
102613 CCCGGAGGATATGTCAGAATTAATACCTAGAGGTTTCTGAAATTGTGCCCGGAGGTC-T-----T
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* *
102672 GCAAACTCAACCTTGAGCAAGG----TTTTGAAATTTAGACGCAGCTTTGATTAAAACTTGATGA
66 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
102733 AATGAAATGATA
131 AATGAAATGATA
* * *
102745 CCCAGAGGATTTATCAGAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
102810 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
66 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
102875 AATGAAATGATA
131 AATGAAATGATA
102887 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
*
102952 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTGAAACTTGATGA
66 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
103017 AATGAAATGATA
131 AATGAAATGATA
103029 -CCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* *
103093 GCAAACTCAACCTTGAGCAAGGTTTTTTTTTTGAAATTTAAACACAACTCTGATTAAAACTT
66 GCAAACTCAACCTTGAGCAAGG--TTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTT
103155 ACCAAAATGG
Statistics
Matches: 384, Mismatches: 14, Indels: 13
0.93 0.03 0.03
Matches are distributed among these distances:
132 52 0.14
133 1 0.00
138 23 0.06
141 86 0.22
142 187 0.49
143 35 0.09
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (142 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
AATGAAATGATA
Found at i:103111 original size:283 final size:275
Alignment explanation
Indices: 102613--103154 Score: 863
Period size: 283 Copynumber: 1.9 Consensus size: 275
102603 ACATGGAATG
* *
102613 CCCGGAGGATATGTCAGAATTAATACCTAGAGGTTTCTGAAATTGTGCCCGGAGGTCTTGCAAAC
1 CCCGGAGGATATATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGGAGGTCTTGCAAAC
* *
102678 TCAACCTTGAGCAAGGTTTTGAAATTTAGACGCAGCTTTGATTAAAACTTGATGAAATGAAATGA
66 TCAACCTTGAGCAAGGTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGAAATGAAATGA
*
102743 TACCCAGAGGATTTATCAGAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAA
131 TACCCAGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAA
* *
102808 ATGCAAACTCAACCTTGAGCAAGG-TTTTTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGA
196 ATGCAAACTCAACCTTGAGCAAGGTTTTTTTTTGAAATTTAAACACAACTCTGATTAAAACTTGA
102872 TGAAATGAAATGATA
261 TGAAATGAAATGATA
* *
102887 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATATATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGGAGGTC-T-----T
*
102952 GCAAACTCAACCTTGAGCAAGGTTTTTTTTGAAATTTAAACACAGCTTTGATTGAAACTTGATGA
60 GCAAACTCAACCTTGAGCAAGG----TTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGA
* *
103017 AATGAAATGATA-CCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGA
121 AATGAAATGATACCCAGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGA
103081 GGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTTTTTTTTGAAATTTAAACACAACTCTGA
186 GGTCTTACAAATGCAAACTCAACCTTGAGCAAGG-TTTTTTTTTGAAATTTAAACACAACTCTGA
103146 TTAAAACTT
250 TTAAAACTT
103155 ACCAAAATGG
Statistics
Matches: 244, Mismatches: 12, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
274 53 0.22
275 1 0.00
280 23 0.09
283 83 0.34
284 48 0.20
285 36 0.15
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (275 bp):
CCCGGAGGATATATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGGAGGTCTTGCAAAC
TCAACCTTGAGCAAGGTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGATGAAATGAAATGA
TACCCAGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAA
ATGCAAACTCAACCTTGAGCAAGGTTTTTTTTTGAAATTTAAACACAACTCTGATTAAAACTTGA
TGAAATGAAATGATA
Found at i:104430 original size:1 final size:1
Alignment explanation
Indices: 104426--104481 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
104416 TCTTTTTTCG
* * * * * *
104426 TTTTTTTTATTTTTTTTCTGTTTTTTTTTGTTTTTTTTGTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
104482 GCATATTTCT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:104431 original size:10 final size:9
Alignment explanation
Indices: 104418--104482 Score: 69
Period size: 9 Copynumber: 6.9 Consensus size: 9
104408 TTTTCACTTC
*
104418 TTTTTTCGT
1 TTTTTTTGT
*
104427 TTTTTTTATT
1 TTTTTTT-GT
104437 TTTTTTCTGTT
1 TTTTTT-TG-T
104448 TTTTTTTGT
1 TTTTTTTGT
104457 TTTTTTTGT
1 TTTTTTTGT
104466 TTTTTTT-T
1 TTTTTTTGT
104474 TGTTTTTTG
1 T-TTTTTTG
104483 CATATTTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
8 2 0.04
9 29 0.60
10 9 0.19
11 8 0.17
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:104441 original size:20 final size:19
Alignment explanation
Indices: 104418--104481 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
104408 TTTTCACTTC
*
104418 TTTTTTCGTTTTTTTTATT
1 TTTTTTCGTTTTTTTTTTT
104437 TTTTTTCTGTTTTTTTTTGTT
1 TTTTTTC-GTTTTTTTTT-TT
104458 TTTTTT-GTTTTTTTTTTGT
1 TTTTTTCGTTTTTTTTTT-T
104477 TTTTT
1 TTTTT
104482 GCATATTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
18 1 0.02
19 23 0.56
20 9 0.22
21 8 0.20
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (19 bp):
TTTTTTCGTTTTTTTTTTT
Found at i:104459 original size:30 final size:30
Alignment explanation
Indices: 104418--104481 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
104408 TTTTCACTTC
104418 TTTTTTCGTTTTTTTTATTTTTTTTCTGTT
1 TTTTTTCGTTTTTTTTATTTTTTTTCTGTT
* * *
104448 TTTTTTTGTTTTTTTTGTTTTTTTTTTGTT
1 TTTTTTCGTTTTTTTTATTTTTTTTCTGTT
104478 TTTT
1 TTTT
104482 GCATATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (30 bp):
TTTTTTCGTTTTTTTTATTTTTTTTCTGTT
Found at i:114517 original size:13 final size:13
Alignment explanation
Indices: 114499--114525 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
114489 AAACGGAAAA
114499 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
114512 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
114525 T
1 T
114526 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:117887 original size:31 final size:31
Alignment explanation
Indices: 117824--117907 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
117814 AATTTTATTA
* *
117824 ATTTCCCAAAATCTTCTTTTGG-GTATCTTT
1 ATTTTCCAAAATCTTCTTTTGGAGTATCCTT
*
117854 ATTTTCCAAAATCTTATTTTGGAGT-TACCTT
1 ATTTTCCAAAATCTTCTTTTGGAGTAT-CCTT
*
117885 ATTTTCCACAATCTTCTTTTGGA
1 ATTTTCCAAAATCTTCTTTTGGA
117908 TTAGCTGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTTCCAAAATCTTCTTTTGGAGTATCCTT
Found at i:118027 original size:13 final size:14
Alignment explanation
Indices: 118004--118032 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
117994 GAGAGCATGA
118004 TTTGAAAAACATTT
1 TTTGAAAAACATTT
118018 TTTG-AAAACATTT
1 TTTGAAAAACATTT
118031 TT
1 TT
118033 ATTACCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTGAAAAACATTT
Found at i:130787 original size:28 final size:27
Alignment explanation
Indices: 130734--130852 Score: 157
Period size: 27 Copynumber: 4.4 Consensus size: 27
130724 GTATTTGAAG
* *
130734 TGACCAAAATACCCCTGGATGTGCAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
* *
130761 TAACCAAAATGCCCCCTGGACGCGCAAA
1 TGACCAAAATG-CCCCTGGACGTGCAAA
* *
130789 TGACCAAAATGCCCTTGGACATGCAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
* *
130816 TGACCAAAATGCCCCTGGACATGTAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
130843 TGACCAAAAT
1 TGACCAAAAT
130853 AAGAAGTAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 57 0.70
28 24 0.30
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGGACGTGCAAA
Found at i:130822 original size:55 final size:54
Alignment explanation
Indices: 130734--130853 Score: 159
Period size: 55 Copynumber: 2.2 Consensus size: 54
130724 GTATTTGAAG
** *
130734 TGACCAAAATACCCCTGGATGTGCAAATAACCAAAATGCCCCCTGGACGCGCAAA
1 TGACCAAAATACCCCTGGACATGCAAATAACCAAAATG-CCCCTGGACACGCAAA
* * * * *
130789 TGACCAAAATGCCCTTGGACATGCAAATGACCAAAATGCCCCTGGACATGTAAA
1 TGACCAAAATACCCCTGGACATGCAAATAACCAAAATGCCCCTGGACACGCAAA
130843 TGACCAAAATA
1 TGACCAAAATA
130854 AGAAGTAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
54 23 0.41
55 33 0.59
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (54 bp):
TGACCAAAATACCCCTGGACATGCAAATAACCAAAATGCCCCTGGACACGCAAA
Found at i:131705 original size:27 final size:26
Alignment explanation
Indices: 131651--131711 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
131641 CTAATTTTCC
131651 ATTATTTTAATAATGAAATAATTAAAAT
1 ATTA-TTTAATAATGAAAT-ATTAAAAT
131679 ATTATTTAATAATGACAAT-TTAGAAAT
1 ATTATTTAATAATGA-AATATTA-AAAT
131706 A-TATTT
1 ATTATTT
131712 GAAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGAAATATTAAAAT
Found at i:131786 original size:2 final size:2
Alignment explanation
Indices: 131779--131836 Score: 57
Period size: 2 Copynumber: 28.5 Consensus size: 2
131769 TTTGTACTTT
* *
131779 TA TA TA TA GTA TA TA TA TA TA TA TA TA TCA -A T- TT TA TA CTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA -TA
131820 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
131837 CAATTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 2 0.04
2 42 0.88
3 4 0.08
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:132050 original size:38 final size:39
Alignment explanation
Indices: 132000--132076 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
131990 AAACTTACAT
132000 ACACACAGAGATATATTTTATATTTAAT-AGAAAATTAC
1 ACACACAGAGATATATTTTATATTTAATCAGAAAATTAC
*
132038 ACACACATAGATATATTTTATATTTAATCAGAAAATTAC
1 ACACACAGAGATATATTTTATATTTAATCAGAAAATTAC
132077 CTATATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.73
39 10 0.27
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (39 bp):
ACACACAGAGATATATTTTATATTTAATCAGAAAATTAC
Found at i:143589 original size:29 final size:30
Alignment explanation
Indices: 143530--143598 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
143520 CAAACAATCT
*
143530 ATCAATCAACTAACAAATAATTGCAATTC-A
1 ATCAATCAA-TAACAAATAATGGCAATTCAA
*
143560 ATCAATCAATAGCAACAT-ATGGCAATTCAA
1 ATCAATCAATAACAA-ATAATGGCAATTCAA
143590 ATCAA-CAAT
1 ATCAATCAAT
143599 TGAAAGATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (30 bp):
ATCAATCAATAACAAATAATGGCAATTCAA
Found at i:161028 original size:50 final size:50
Alignment explanation
Indices: 160967--161095 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
160957 ATCAACTTTT
* *
160967 TCGAATTGTCTTCCAA-TCTAATATTAAAAGGGCCATCTCCCGC-TCATCCC
1 TCGAACTGTCTTCCAATTC-AATATTAAAAGGACCATCTCCCGCTTC-TCCC
** * * * *
161017 TCGAACTGTCTTCCAATTCGGTCTTAAAAGGACCGTCTTCCGCTTCTCCT
1 TCGAACTGTCTTCCAATTCAATATTAAAAGGACCATCTCCCGCTTCTCCC
*
161067 TCGAACTGTCTTCCAATTCAATCTTAAAA
1 TCGAACTGTCTTCCAATTCAATATTAAAA
161096 AGACTGTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 63 0.94
51 4 0.06
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (50 bp):
TCGAACTGTCTTCCAATTCAATATTAAAAGGACCATCTCCCGCTTCTCCC
Found at i:161121 original size:27 final size:27
Alignment explanation
Indices: 161071--161127 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
161061 TCTCCTTCGA
*
161071 ACTGTCTTCCAATTCAATCTTAAAAAG
1 ACTGTCTTCCAATTCAATCCTAAAAAG
* * *
161098 ACTGTCTTCCAATTTACTCCTAAAAGG
1 ACTGTCTTCCAATTCAATCCTAAAAAG
161125 ACT
1 ACT
161128 ATCTCCCGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (27 bp):
ACTGTCTTCCAATTCAATCCTAAAAAG
Found at i:161157 original size:50 final size:49
Alignment explanation
Indices: 161103--161241 Score: 185
Period size: 46 Copynumber: 2.9 Consensus size: 49
161093 AAAAGACTGT
* *
161103 CTTCCAATTTACTCCTAAAAGGACTATCTCCCGCTTATCCTTTAAATTGC
1 CTTCCAATTTA-TCCTAAAAGGACCATCTTCCGCTTATCCTTTAAATTGC
* * *
161153 CTTCCAA--T-TCCTAAAAGGACCGTCTTCCGCTTATCCTTTGAATTGT
1 CTTCCAATTTATCCTAAAAGGACCATCTTCCGCTTATCCTTTAAATTGC
*
161199 CTTCCAATTCATTCCTAAAAGGACCATCTTCCGCTTATCCTTT
1 CTTCCAATTTA-TCCTAAAAGGACCATCTTCCGCTTATCCTTT
161242 GAACTGTCTC
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
46 40 0.51
48 1 0.01
50 37 0.47
ACGTcount: A:0.24, C:0.30, G:0.09, T:0.37
Consensus pattern (49 bp):
CTTCCAATTTATCCTAAAAGGACCATCTTCCGCTTATCCTTTAAATTGC
Found at i:161242 original size:50 final size:49
Alignment explanation
Indices: 161100--161250 Score: 200
Period size: 50 Copynumber: 3.1 Consensus size: 49
161090 TTAAAAAGAC
* * * *
161100 TGTCTTCCAATTTACTCCTAAAAGGACTATCTCCCGCTTATCCTTTAAAT
1 TGTCTTCCAA-TTATTCCTAAAAGGACCATCTTCCGCTTATCCTTTGAAT
* *
161150 TGCCTTCC-A--ATTCCTAAAAGGACCGTCTTCCGCTTATCCTTTGAAT
1 TGTCTTCCAATTATTCCTAAAAGGACCATCTTCCGCTTATCCTTTGAAT
*
161196 TGTCTTCCAATTCATTCCTAAAAGGACCATCTTCCGCTTATCCTTTGAAC
1 TGTCTTCCAATT-ATTCCTAAAAGGACCATCTTCCGCTTATCCTTTGAAT
161246 TGTCT
1 TGTCT
161251 CTGATGCAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
46 39 0.44
47 1 0.01
49 1 0.01
50 47 0.53
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (49 bp):
TGTCTTCCAATTATTCCTAAAAGGACCATCTTCCGCTTATCCTTTGAAT
Done.