Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013639.1 Kokia drynarioides strain JFW-HI SEQ_128667, 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: 62291
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:982 original size:17 final size:18
Alignment explanation
Indices: 946--981 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
936 TGATGGAAGG
946 ACCTATTTGGAATAAAAA
1 ACCTATTTGGAATAAAAA
964 ACCTATTTGGAATAAAAA
1 ACCTATTTGGAATAAAAA
982 CAAAAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
ACCTATTTGGAATAAAAA
Found at i:2067 original size:11 final size:11
Alignment explanation
Indices: 2053--2108 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
2043 CTAAACACAT
2053 TTTAAATTTAA
1 TTTAAATTTAA
2064 TTTAAATTTAAA
1 TTTAAATTT-AA
*
2076 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
2087 TTTAAAATT-A
1 TTTAAATTTAA
2097 TTATAAATTTAA
1 TT-TAAATTTAA
2109 ATAAATAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 3 0.08
11 25 0.68
12 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:2071 original size:6 final size:6
Alignment explanation
Indices: 2053--2110 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
2043 CTAAACACAT
* *
2053 TTTAAA TTT-AA TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA ATT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2097 TTATAAA TTTAAA T
1 TT-TAAA TTTAAA T
2111 AAATAAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.05
5 10 0.23
6 28 0.65
7 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2075 original size:17 final size:17
Alignment explanation
Indices: 2053--2110 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
2043 CTAAACACAT
2053 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
*
2070 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
*
2087 TTTAAAATT-ATTATAAA
1 TTTAAATTTAATT-TAAA
2104 TTTAAAT
1 TTTAAAT
2111 AAATAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
16 2 0.06
17 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:2923 original size:12 final size:12
Alignment explanation
Indices: 2906--3014 Score: 50
Period size: 12 Copynumber: 9.1 Consensus size: 12
2896 AACTATTCAA
*
2906 ATTAATAATGAT
1 ATTAATAATAAT
*
2918 ATTAATGATAAT
1 ATTAATAATAAT
*
2930 ATTAATATTGAAT
1 ATTAATAAT-AAT
* *
2943 AATGGTAATAAATGAC
1 -AT--TAAT-AATAAT
*
2959 ATTAAT-A-AAC
1 ATTAATAATAAT
2969 ATTAATAA-AA-
1 ATTAATAATAAT
* *
2979 A-TATTACTAAT
1 ATTAATAATAAT
2990 ATTAATAATTAAT
1 ATTAATAA-TAAT
3003 ATTAAT-ATAAT
1 ATTAATAATAAT
3014 A
1 A
3015 AAAAAGGAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
9 4 0.05
10 11 0.15
11 10 0.13
12 22 0.29
13 17 0.23
14 2 0.03
15 2 0.03
16 5 0.07
17 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:4127 original size:30 final size:30
Alignment explanation
Indices: 4093--4180 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
4083 GGAGGTTCCT
4093 AAACTTTCCAAAAATTACATTTTCA-CCGTA
1 AAACTTTCC-AAAATTACATTTTCACCCGTA
* *
4123 AAACTTTCCAAAATTCCATTTTTCACCCTTA
1 AAACTTTCCAAAATTACA-TTTTCACCCGTA
* ** *
4154 AAATTTTTGAAAATTACATTTTTACCC
1 AAACTTTCCAAAATTACATTTTCACCC
4181 TCGAACTTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 8 0.16
30 23 0.47
31 18 0.37
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AAACTTTCCAAAATTACATTTTCACCCGTA
Found at i:4202 original size:29 final size:29
Alignment explanation
Indices: 4163--4588 Score: 289
Period size: 29 Copynumber: 14.7 Consensus size: 29
4153 AAAATTTTTG
* *
4163 AAAATTACATTTTTACCCTCGAACTTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* **
4192 ACAATTCCATTTTTGACCCT-GATTTTTCCA
1 AAAATTCCATTTTT-ACCCTCGA-ACTTCCA
** *
4222 AAAATTACCATTTTGT--CGACGAACTTACA
1 AAAATT-CCATTTT-TACCCTCGAACTTCCA
*
4251 AAAATTCCATTTTTGACCC-CGATCTTTCCA
1 AAAATTCCATTTTT-ACCCTCGAAC-TTCCA
* *
4281 AAAATTATCA-TTTTACCCTCGGACTTCCA
1 AAAATT-CCATTTTTACCCTCGAACTTCCA
4310 AAAATTCCATTTTTGA-CCTCGAACTTCCA
1 AAAATTCCATTTTT-ACCCTCGAACTTCCA
* *
4339 AAAATTACCA-TTTTACACTCAAACTTCCA
1 AAAATT-CCATTTTTACCCTCGAACTTCCA
4368 AAAATTCCATTTTTGA-CCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCA
* * * *
4398 AAAAATACA-ATTTACCCTCGAACTTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* **
4426 AAAATTCCATTTTTGA-CTTAAAAAAACTTCCA
1 AAAATTCCATTTTT-ACCCT---CGAACTTCCA
*
4458 AAAATTACCA-TTTTACCCT-AAACTTCCA
1 AAAATT-CCATTTTTACCCTCGAACTTCCA
* *
4486 AATATTCCA-TTTTACCCTCGAA-TGTCTA
1 AAAATTCCATTTTTACCCTCGAACT-TCCA
*
4514 AAAATTCCATTTTTGACCCT-AAACTTCC-
1 AAAATTCCATTTTT-ACCCTCGAACTTCCA
* *
4542 CAAATTACCATTTTT-CCCTC-AAGTGTCC-
1 AAAATT-CCATTTTTACCCTCGAACT-TCCA
4570 AAAATTACCA-TTTTACCCT
1 AAAATT-CCATTTTTACCCT
4589 TCAGGAATTC
Statistics
Matches: 318, Mismatches: 44, Indels: 71
0.73 0.10 0.16
Matches are distributed among these distances:
27 25 0.08
28 76 0.24
29 123 0.39
30 61 0.19
31 10 0.03
32 20 0.06
33 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTCCA
Found at i:4299 original size:88 final size:87
Alignment explanation
Indices: 4163--4439 Score: 239
Period size: 88 Copynumber: 3.2 Consensus size: 87
4153 AAAATTTTTG
* * *
4163 AAAATTACATTTTTACCCTCGAACTTTCAACAATTCCATTTTTGACCCT-GATTTTTCCAAAAAT
1 AAAATTCCATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTCGA--CTTCCAAAAAT
* *
4227 TACCA-TTTTGTCGACGAACTTACA
64 T-CCATTTTTGACCACGAACTTACA
* *
4251 AAAATTCCATTTTTGACCC-CGATCTTTCCAAAAATTATCA-TTTT-ACCCTCGGACTTCCAAAA
1 AAAATTCCATTTTT-ACCCTCGAACTTT-CAAAAATT-CCATTTTTGACCCTC-GACTTCCAAAA
* *
4313 ATTCCATTTTTGACCTCGAACTTCCA
62 ATTCCATTTTTGACCACGAACTTACA
* * *
4339 AAAATTACCA-TTTTACACTCAAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAA
1 AAAATT-CCATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTCG--ACTTCCAAAAA
* * * * *
4402 ATACA-ATTT-ACCCTCGAACTTTCA
63 TTCCATTTTTGA-CCACGAACTTACA
4426 AAAATTCCATTTTT
1 AAAATTCCATTTTT
4440 GACTTAAAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
86 7 0.04
87 47 0.30
88 81 0.52
89 18 0.11
90 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (87 bp):
AAAATTCCATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTCGACTTCCAAAAATTC
CATTTTTGACCACGAACTTACA
Found at i:4354 original size:58 final size:58
Alignment explanation
Indices: 4163--4588 Score: 383
Period size: 59 Copynumber: 7.3 Consensus size: 58
4153 AAAATTTTTG
* * **
4163 AAAATTA-CATTTTTACCCTCGAACTTTCAACAATTCCATTTTTGACC-CTGATTTTTCCA
1 AAAATTACCA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTC-GA-ACTTCCA
** ** * * *
4222 AAAATTACCATTTTGTCGACGAACTTACAAAAATTCCATTTTTGACCCCGATCTTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAC-TTCCA
* *
4281 AAAATTATCATTTTACCCTCGGACTTCCAAAAATTCCATTTTTGACCTCGAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAACTTCCA
* *
4339 AAAATTACCATTTTACACTCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG-AACTTCCA
* * * * **
4398 AAAAATA-CAATTTACCCTCGAACTTTCAAAAATTCCATTTTTGACTTAAAAAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT---CGAACTTCCA
* * *
4458 AAAATTACCATTTTACCCT-AAACTTCCAAATATTCCA-TTTT-ACCCTCGAA-TGTCTA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCTCGAACT-TCCA
* * * *
4514 AAAATT-CCATTTTTGACCCT-AAACTTCC-CAAATTACCATTTTT-CCCTC-AAGTGTCC-
1 AAAATTACCA-TTTT-ACCCTCGAACTTCCAAAAATT-CCATTTTTGACCTCGAACT-TCCA
4570 AAAATTACCATTTTACCCT
1 AAAATTACCATTTTACCCT
4589 TCAGGAATTC
Statistics
Matches: 310, Mismatches: 41, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
55 9 0.03
56 31 0.10
57 27 0.09
58 92 0.30
59 109 0.35
60 32 0.10
61 10 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAACTTCCA
Found at i:4483 original size:88 final size:86
Alignment explanation
Indices: 4217--4588 Score: 285
Period size: 88 Copynumber: 4.3 Consensus size: 86
4207 ACCCTGATTT
** ** * **** *
4217 TTCCAAAAATTACCATTTTGTCGACGAACTTACAAAAATTCCATTTTTGAC-CCCGATCTTTCCA
1 TTCCAAAAATT-CCATTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACAAAAAAAC-TTCCA
* **
4281 AAAATTATCATTTTACCCTCGGAC
64 AAAATTACCATTTTACCCT-AAAC
* ***
4305 TTCCAAAAATTCCATTTTTGA-CCTCGAACTTCCAAAAATTACCA-TTTT-ACACTCAAACTTCC
1 TTCCAAAAATTCCA-TTTT-ACCCTCGAACTTTCAAAAATT-CCATTTTTGACAAAAAAACTTCC
*
4367 AAAAATT-CCATTTTTGACCTCGAAAC
63 AAAAATTACCA-TTTT-ACC-CTAAAC
* * *
4393 TTCCAAAAAATACAATTTACCCTCGAACTTTCAAAAATTCCATTTTTGACTTAAAAAAACTTCCA
1 TTCCAAAAATTCCATTTTACCCTCGAACTTTCAAAAATTCCATTTTTGAC--AAAAAAACTTCCA
4458 AAAATTACCATTTTACCCTAAAC
64 AAAATTACCATTTTACCCTAAAC
* * *** *
4481 TTCCAAATATTCCATTTTACCCTCGAA-TGTCTAAAAATTCCATTTTTGAC-CCTAAACTTCC-C
1 TTCCAAAAATTCCATTTTACCCTCGAACTTTC-AAAAATTCCATTTTTGACAAAAAAACTTCCAA
* * *
4543 AAATTACCATTTTTCCCTCAAG
65 AAATTACCATTTTACCCTAAAC
4565 TGTCC-AAAATTACCATTTTACCCT
1 T-TCCAAAAATT-CCATTTTACCCT
4589 TCAGGAATTC
Statistics
Matches: 236, Mismatches: 32, Indels: 35
0.78 0.11 0.12
Matches are distributed among these distances:
84 25 0.11
85 23 0.10
86 6 0.03
87 48 0.20
88 104 0.44
89 7 0.03
90 20 0.08
91 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (86 bp):
TTCCAAAAATTCCATTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACAAAAAAACTTCCAAA
AATTACCATTTTACCCTAAAC
Found at i:4553 original size:57 final size:56
Alignment explanation
Indices: 4456--4588 Score: 168
Period size: 57 Copynumber: 2.4 Consensus size: 56
4446 AAAAAACTTC
*
4456 CAAAAATTACCA-TTTTACCCTAAACTTCCAAATATTCCATTTTACCCTCGAA-TGT
1 CAAAAATTACCATTTTTACCCTAAACTTCCAAATATACCATTTTACCCTC-AAGTGT
*
4511 CTAAAAATT-CCATTTTTGACCCTAAACTTCCCAAAT-TACCATTTTTCCCTCAAGTGT
1 C-AAAAATTACCATTTTT-ACCCTAAACTT-CCAAATATACCATTTTACCCTCAAGTGT
*
4568 CCAAAATTACCA-TTTTACCCT
1 CAAAAATTACCATTTTTACCCT
4589 TCAGGAATTC
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
55 9 0.13
56 23 0.33
57 31 0.45
58 6 0.09
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (56 bp):
CAAAAATTACCATTTTTACCCTAAACTTCCAAATATACCATTTTACCCTCAAGTGT
Found at i:15806 original size:18 final size:18
Alignment explanation
Indices: 15779--15813 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15769 CATCTAATAC
* *
15779 TGTTCTTTGTAATTATTT
1 TGTTCCTTGTAAATATTT
15797 TGTTCCTTGTAAATATT
1 TGTTCCTTGTAAATATT
15814 CGGCATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:16365 original size:49 final size:48
Alignment explanation
Indices: 16251--16928 Score: 326
Period size: 49 Copynumber: 13.8 Consensus size: 48
16241 CGCGAAACAC
* * * *
16251 AAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAATACCACGAAG-AT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAGCAT
** ** * * *
16298 ATGGTGGGAAAGGGTTAAGTCTCAACGGCGAACCTTGTACCTCAAAAGCAT
1 A--AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTC-AAAGCAT
* * * * *
16349 GAAGGGAAAGATTTAAGCCGCAATGGTGAATCTAGTACCACAAAG-AT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAGCAT
* * * ** * *
16396 ACCAAGGGAAAGGTTTAAGTCGCAATGATGAGCCTAGTACCTCAGAGACAT
1 A--AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAG-CAT
* * * *
16447 AAAGGGAAAGATTTAAGCCGCAATGGTGAATCC-AGTACCGCGAAG-AT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAAAGCAT
* * * * *
16494 ACCAAGGGAAAGATTTAAGTCGCAATGACGAACCTAGTACCTTAGAGACAT
1 A--AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAG-CAT
* * * *
16545 AAAGGGAAAGATTTGAGCCACAACGGTGAATCC-AGTACCAT-GAAGACAT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACC-TCAAAG-CAT
* * * * * * * *
16594 GAAGGAAAATATTTAAGCCGCAACGTCAAATCC-AGTACCGCCAAGACAC
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAAAG-CAT
*
16643 AAAGGGAAA-AGTTTAAGTCGCAACGGCGAACCTAGTACCTCAGAAGCAT
1 AAAGGGAAAGA-TTTAAGCCGCAACGGCGAACCTAGTACCTCA-AAGCAT
* * * *
16692 GAAGGGAAAGATTTAAGCCGCAACGG-GTAATCC-AGTACCACGAAAACACAA
1 AAAGGGAAAGATTTAAGCCGCAACGGCG-AA-CCTAGTACCTC--AAA-GCAT
* * * * * *
16743 AAAGGGAAAGATTTAAGCTGCAATGGCGAATCAAGTACCACGAAG-AT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAGCAT
* *** * * *
16790 ATGAAGAGAAATG-TTTAAATTGCAATGGCGAACCTAATACCTCAGATA-CACA
1 A--AAGGGAAA-GATTTAAGCCGCAACGGCGAACCTAGTACCTCA-A-AGCA-T
* ** * * *
16842 AAAGGGAAAGGTTTAAGTTGCAATGACAAACCTTA-TACCTCAGAAGCAT
1 AAAGGGAAAGATTTAAGCCGCAACGGCGAACC-TAGTACCTCA-AAGCAT
* **
16891 GAAA-GGAAA-ATTTAACCCGCAACGGCGAATTTAGTACC
1 -AAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACC
16929 ATGCAAATCA
Statistics
Matches: 484, Mismatches: 107, Indels: 79
0.72 0.16 0.12
Matches are distributed among these distances:
47 10 0.02
48 27 0.06
49 339 0.70
50 58 0.12
51 48 0.10
52 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (48 bp):
AAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAAAGCAT
Found at i:16382 original size:98 final size:98
Alignment explanation
Indices: 16251--16858 Score: 460
Period size: 98 Copynumber: 6.2 Consensus size: 98
16241 CGCGAAACAC
* * * **** *
16251 AAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAATACCACGAAGATATGGTGGGAAAGGGTTAA
1 AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
* * * * *
16316 GTCTCAACGGCGAACCTTGTACCTCA-AAAGCAT
66 GTCGCAATGACGAACCTAGTACCTCAGAGA-CAT
* * * *
16349 GAAGGGAAAGATTTAAGCCGCAATGGTGAATCTAGTACCACAAAGATACCAAGGGAAAGGTTTAA
1 AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
* *
16414 GTCGCAATGATGAGCCTAGTACCTCAGAGACAT
66 GTCGCAATGACGAACCTAGTACCTCAGAGACAT
* * *
16447 AAAGGGAAAGATTTAAGCCGCAATGGTGAATCCAGTACCGCGAAGATACCAAGGGAAAGATTTAA
1 AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
*
16512 GTCGCAATGACGAACCTAGTACCTTAGAGACAT
66 GTCGCAATGACGAACCTAGTACCTCAGAGACAT
* * * * ** * **
16545 AAAGGGAAAGATTTGAGCCACAACGGTGAATCCAGTACCATGAAGACATGAAGGAAAATATTTAA
1 AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
* * * * * *
16610 GCCGCAACGTCAAATCC-AGTACCGCCA-AGACAC
66 GTCGCAATGACGAA-CCTAGTACC-TCAGAGACAT
* * * * *
16643 AAAGGGAAA-AGTTTAAGTCGCAACGGCGAA-CCTAGTACCTCAGAAGCAT--GAAGGGAAAGAT
1 AAAGGGAAAGA-TTTAAGCCGCAACGGTGAATCC-AGTACCAC-GAAG-ATACCAAGGGAAAGGT
* * * * * * *
16704 TTAAGCCGCAACG-GGTAATCC-AGTACCACGAAAACACAA
62 TTAAGTCGCAATGACG-AA-CCTAGTACCTC--AGAGACAT
* * * * ** * *
16743 AAAGGGAAAGATTTAAGCTGCAATGGCGAATCAAGTACCACGAAGATATGAAGAGAAATGTTTAA
1 AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
* * * * * *
16808 ATTGCAATGGCGAACCTAATACCTCAGATACACA
66 GTCGCAATGACGAACCTAGTACCTCAGAGACA-T
*
16842 AAAGGGAAAGGTTTAAG
1 AAAGGGAAAGATTTAAG
16859 TTGCAATGAC
Statistics
Matches: 418, Mismatches: 74, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
97 4 0.01
98 315 0.75
99 33 0.08
100 63 0.15
101 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
AAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATACCAAGGGAAAGGTTTAA
GTCGCAATGACGAACCTAGTACCTCAGAGACAT
Found at i:16501 original size:147 final size:144
Alignment explanation
Indices: 16350--16858 Score: 441
Period size: 147 Copynumber: 3.4 Consensus size: 144
16340 CAAAAGCATG
* * * * * *
16350 AAGGGAAAGATTTAAGCCGCAATGGTGAATCTAGTACCACAAAGATACCAAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGATA-AAAGGGAAAGATTTAAG
* * * *
16415 TCGCAATGATGAGCCTAGTACCTCAGAGACATAAAGGGAAAGATTTAAGCCGCAATGGTGAATCC
65 CCGCAACGGTGATCC-AGTACCTCA-AGACATAAAGGGAAAGATTTAAGCCGCAATGGTGAATCC
*
16480 AGTACCGCGAAGATACC
128 AGTACCGCGAAGATACA
* * * * *
16497 AAGGGAAAGATTTAAGTCGCAATGACGAACCTAGTACCTTAGAGACATAAAGGGAAAGATTTGAG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGATA-AAAGGGAAAGATTTAAG
* * * * * * *
16562 CCACAACGGTGAATCCAGTACCATGAAGACATGAAGGAAAATATTTAAGCCGCAA-CGTCAAATC
65 CCGCAACGGTG-ATCCAGTACC-TCAAGACATAAAGGGAAAGATTTAAGCCGCAATGGT-GAATC
* *
16626 CAGTACCGCCAAGACACA
127 CAGTACCGCGAAGATACA
* *
16644 AAGGGAAA-AGTTTAAGTCGCAACGGCGAACCTAGTACCTCAGAAGCAT-GAAGGGAAAGATTTA
1 AAGGGAAAGA-TTTAAGTCGCAATGGCGAACCTAGTACCTCA-AAG-ATAAAAGGGAAAGATTTA
* * * * * *
16707 AGCCGCAACGGGTAATCCAGTACCACGAAAACACAAAAAGGGAAAGATTTAAGCTGCAATGGCGA
63 AGCCGCAAC-GGTGATCCAGTACCTC---AAGACATAAAGGGAAAGATTTAAGCCGCAATGGTGA
* * **
16772 ATCAAGTACCACGAAGATATG
124 ATCCAGTACCGCGAAGATACA
* * * * * * *
16793 AAGAGAAATG-TTTAAATTGCAATGGCGAACCTAATACCTCAGATACACAAAAGGGAAAGGTTTA
1 AAGGGAAA-GATTTAAGTCGCAATGGCGAACCTAGTACCTCA-A-AGATAAAAGGGAAAGATTTA
16857 AG
63 AG
16859 TTGCAATGAC
Statistics
Matches: 286, Mismatches: 61, Indels: 27
0.76 0.16 0.07
Matches are distributed among these distances:
146 3 0.01
147 178 0.62
148 10 0.03
149 78 0.27
150 17 0.06
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.17
Consensus pattern (144 bp):
AAGGGAAAGATTTAAGTCGCAATGGCGAACCTAGTACCTCAAAGATAAAAGGGAAAGATTTAAGC
CGCAACGGTGATCCAGTACCTCAAGACATAAAGGGAAAGATTTAAGCCGCAATGGTGAATCCAGT
ACCGCGAAGATACA
Found at i:17327 original size:17 final size:17
Alignment explanation
Indices: 17304--17415 Score: 129
Period size: 17 Copynumber: 6.4 Consensus size: 17
17294 CTAAACCCAT
17304 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
17322 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
17338 TTTAAATTT-TTTTAAAAAAA
1 TTTAAATTTATTTT----AAA
* *
17358 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
17375 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
17392 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
17409 TTTAAAT
1 TTTAAAT
17416 AAATAAATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.06
17 61 0.75
20 12 0.15
21 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:17372 original size:11 final size:11
Alignment explanation
Indices: 17304--17413 Score: 59
Period size: 11 Copynumber: 10.0 Consensus size: 11
17294 CTAAACCCAT
*
17304 TTTAAATTTAT
1 TTTAAATTTAA
*
17315 TTTAAGATTAAA
1 TTTAA-ATTTAA
*
17327 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
17338 TTTAAATTT-T
1 TTTAAATTTAA
**
17348 TTTAAA-AAAA
1 TTTAAATTTAA
17358 TTTAAATTTAA
1 TTTAAATTTAA
*
17369 TTTAAGTTTAAA
1 TTTAAATTT-AA
*
17381 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
17392 TTTAAAATT-A
1 TTTAAATTTAA
17402 TTATAAATTTAA
1 TT-TAAATTTAA
17414 ATAAATAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
10 17 0.23
11 37 0.50
12 20 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:17443 original size:15 final size:15
Alignment explanation
Indices: 17420--17452 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17410 TTAAATAAAT
17420 AAATATCCAATTACA
1 AAATATCCAATTACA
*
17435 AAATGTCCAATTACA
1 AAATATCCAATTACA
17450 AAA
1 AAA
17453 CCCATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATATCCAATTACA
Found at i:18288 original size:6 final size:6
Alignment explanation
Indices: 18267--18344 Score: 90
Period size: 6 Copynumber: 13.0 Consensus size: 6
18257 GACATTAATA
**
18267 AATATT AATAAA AATATT -A-A-T AATATT AATAATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AAT-ATT AATATT AATATT
18313 AATAATT AATATT AATATT AATAATT AATATT
1 AAT-ATT AATATT AATATT AAT-ATT AATATT
18345 CAGCCGGCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 2 0.03
6 39 0.63
7 18 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATATT
Found at i:18302 original size:38 final size:37
Alignment explanation
Indices: 18260--18343 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 37
18250 AATAAATGAC
18260 ATTAATA-AATATTAATAA-AAATATTAATAATATTAATA
1 ATTAATATAATATTAATAATAAATA-T--TAATATTAATA
*
18298 ATTAATATTAATATTAATAATTAATATTAATATTAATA
1 ATTAATA-TAATATTAATAATAAATATTAATATTAATA
18336 ATTAATAT
1 ATTAATAT
18344 TCAGCCGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
37 1 0.02
38 25 0.60
40 12 0.29
41 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
ATTAATATAATATTAATAATAAATATTAATATTAATA
Found at i:18305 original size:13 final size:12
Alignment explanation
Indices: 18267--18344 Score: 90
Period size: 13 Copynumber: 6.5 Consensus size: 12
18257 GACATTAATA
**
18267 AATATTAATAAA
1 AATATTAATATT
18279 AATATT-A-A-T
1 AATATTAATATT
18288 AATATTAATAATT
1 AATATTAAT-ATT
18301 AATATTAATATT
1 AATATTAATATT
18313 AATAATTAATATT
1 AAT-ATTAATATT
18326 AATATTAATAATT
1 AATATTAAT-ATT
18339 AATATT
1 AATATT
18345 CAGCCGGCCT
Statistics
Matches: 59, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 1 0.02
12 19 0.32
13 31 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATTAATATT
Found at i:18311 original size:19 final size:19
Alignment explanation
Indices: 18287--18344 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
18277 AAAATATTAA
18287 TAATATTAATAATTAATAT
1 TAATATTAATAATTAATAT
18306 TAATATTAATAATTAATAT
1 TAATATTAATAATTAATAT
18325 TAATATTAATAATTAATAT
1 TAATATTAATAATTAATAT
18344 T
1 T
18345 CAGCCGGCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATATTAATAATTAATAT
Found at i:18942 original size:29 final size:28
Alignment explanation
Indices: 18909--19296 Score: 146
Period size: 30 Copynumber: 13.1 Consensus size: 28
18899 CCCTGAAGGT
18909 CCCTAAACTTACCAAAAATTACATTTTAA
1 CCCTAAACTT-CCAAAAATTACATTTTAA
* *
18938 CCCTAAAATTTCC-AAAATTACATTTTCA
1 CCCT-AAACTTCCAAAAATTACATTTTAA
* * *
18966 CCTTAAACTTTTCAAAAATTACAATTTTAC
1 CCCTAAAC-TTCCAAAAATTAC-ATTTTAA
* * *
18996 CCCTCAACTTCCAAAAATTTCATTTTTTA
1 CCCTAAACTTCCAAAAATTACA-TTTTAA
* **
19025 -CTTCAATTTTTCCAAAAATTACCATTTT-A
1 CCCT-AA-ACTTCCAAAAATTA-CATTTTAA
* *
19054 CCCTCGAACTTCCAAAAAAATT-CTATTTTTGA
1 CCCT-AAACTTCC--AAAAATTAC-A-TTTTAA
* * *
19086 -CCTCGATCTTTCC-AAAATTACCATTTTAC
1 CCCT-AAAC-TTCCAAAAATTA-CATTTTAA
* * *
19115 CCCTGAACTTCTAAAAATTTCATTTTTAA
1 CCCTAAACTTCCAAAAATTACA-TTTTAA
* ** * *
19144 CCTCGAAACTTTAAAAAAAATACCATTTTAC
1 CC-CTAAAC-TTCCAAAAATTA-CATTTTAA
* *
19175 CCCCAAACTTCCAAAAATT-CTAATTTTGA
1 CCCTAAACTTCCAAAAATTAC--ATTTTAA
* *
19204 -CCTGAAAAATACCAAAAATTACCATTTT-A
1 CCCT--AAACTTCCAAAAATTA-CATTTTAA
** * *
19233 CCCTCGTACTTCCAAAAATTCCATTTTTGA
1 CCCT-AAACTTCCAAAAATTACA-TTTTAA
* *
19263 CCTTAAAACTTCCAAAAATTACTATTTTAC
1 CCCT-AAACTTCCAAAAATTAC-ATTTTAA
19293 CCCT
1 CCCT
19297 GATTTTCCTA
Statistics
Matches: 267, Mismatches: 59, Indels: 65
0.68 0.15 0.17
Matches are distributed among these distances:
27 4 0.01
28 32 0.12
29 91 0.34
30 95 0.36
31 37 0.14
32 8 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTAA
Found at i:19072 original size:30 final size:28
Alignment explanation
Indices: 18914--19354 Score: 159
Period size: 29 Copynumber: 14.9 Consensus size: 28
18904 AAGGTCCCTA
* **
18914 AACTTACCAAAAATTACATTTTAACCCTAA
1 AACTT-CCAAAAATTCCATTTT-ACCCTCG
* * **
18944 AATTTCC-AAAATTACATTTT-CACCTTA
1 AACTTCCAAAAATTCCATTTTAC-CCTCG
* *
18971 AACTTTTCAAAAATTACAATTTTACCCCTC-
1 AAC-TTCCAAAAATT-CCATTTTA-CCCTCG
* *
19001 AACTTCCAAAAATTTCATTTTTTA-CTTC-
1 AACTTCCAAAAATTCCA--TTTTACCCTCG
*
19029 AATTTTTCCAAAAATTACCATTTTACCCTCG
1 AA--CTTCCAAAAATT-CCATTTTACCCTCG
*
19060 AACTTCCAAAAAAATTCTATTTTTGA-CCTCG
1 AACTTCC--AAAAATTCCA-TTTT-ACCCTCG
*
19091 ATCTTTCC-AAAATTACCATTTTACCC-CTG
1 AAC-TTCCAAAAATT-CCATTTTACCCTC-G
* * *
19120 AACTTCTAAAAATTTCATTTTTAACCTCG
1 AACTTCCAAAAATTCCA-TTTTACCCTCG
** * * *
19149 AAACTTTAAAAAAAATACCATTTTACCCCCA
1 -AAC-TT-CCAAAAATTCCATTTTACCCTCG
*
19180 AACTTCCAAAAATTCTAATTTTGA-CCT-G
1 AACTTCCAAAAATTC-CATTTT-ACCCTCG
* *
19208 AAAAATACCAAAAATTACCATTTTACCCTCG
1 --AACTTCCAAAAATT-CCATTTTACCCTCG
* * **
19239 TACTTCCAAAAATTCCATTTTTGACCTTAA
1 AACTTCCAAAAATTCCA-TTTT-ACCCTCG
*
19269 AACTTCCAAAAATTACTATTTTACCC-CTG
1 AACTTCCAAAAATT-CCATTTTACCCTC-G
** *
19298 ATTTTCCTAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCA-TTTT-ACCCTCG
**
19327 ATTTTTCCAAAAAATTTCCATTTTACCC
1 A-ACTTCC-AAAAA-TTCCATTTTACCC
19355 ACGGATGTCT
Statistics
Matches: 312, Mismatches: 54, Indels: 89
0.69 0.12 0.20
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 41 0.13
29 103 0.33
30 93 0.30
31 49 0.16
32 19 0.06
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTACCCTCG
Found at i:19107 original size:60 final size:59
Alignment explanation
Indices: 18914--19409 Score: 390
Period size: 59 Copynumber: 8.4 Consensus size: 59
18904 AAGGTCCCTA
* ** * * **
18914 AACTTACCAAAAATTA-CATTTTAACCCTAAAATTTCC-AAAATTAC-A-TTTTCACCTTA
1 AACTTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATT-CTATTTTTGACCTCG
* * * *
18971 AACTTTTCAAAAATTACAATTTTACCCCTC-AACTTCCAAAAATT-TCATTTTTTACTTC-
1 AACTTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATTCT-ATTTTTGACCTCG
*
19029 AATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAATTCTATTTTTGACCTCG
1 AA-CTTTCCAAAAATTACCATTTTACCCTCGAACTTCC--AAAAATTCTATTTTTGACCTCG
* * *
19091 ATCTTTCC-AAAATTACCATTTTACCC-CTGAACTTCTAAAAATT-TCATTTTTAACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATTCT-ATTTTTGACCTCG
** * * * *
19149 AAACTTTAAAAAAAATACCATTTTACCCCCAAACTTCCAAAAATTCTAATTTTGACCT-G
1 -AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACCTCG
** * * * **
19208 AAAAATACCAAAAATTACCATTTTACCCTCGTACTTCCAAAAATTCCATTTTTGACCTTAA
1 -AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACC-TCG
* ** * *
19269 AAC-TTCCAAAAATTACTATTTTACCC-CTGATTTTCCTAAAATTCCATTTTTGACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATTCTATTTTTGACCTCG
** * * * * *
19327 ATTTTTCCAAAAAATTTCCATTTTACCCACGGA-TGTCTAAAAATTCTATTTTTGACATCG
1 AACTTTCC-AAAAATTACCATTTTACCCTCGAACT-TCCAAAAATTCTATTTTTGACCTCG
*
19387 AACTTTCCCAAAATTACCATTTT
1 AACTTTCCAAAAATTACCATTTT
19410 GCCCCTGAGT
Statistics
Matches: 354, Mismatches: 60, Indels: 48
0.77 0.13 0.10
Matches are distributed among these distances:
57 22 0.06
58 45 0.13
59 148 0.42
60 112 0.32
61 25 0.07
62 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACCTCG
Found at i:19131 original size:119 final size:118
Alignment explanation
Indices: 18978--19414 Score: 408
Period size: 119 Copynumber: 3.7 Consensus size: 118
18968 TTAAACTTTT
* * * **
18978 CAAAAATTACAATTTTACCCCTCAACTTCCAAAAATTTCATTTTTTACTTC-AATTTTTCCAAAA
1 CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACTTCGAAACTTTCCAAAA
*
19042 ATTACCATTTTACCCTCGAACTTCCAAAAAAATTCTATTTTTGACCTCGATCTTTC
66 ATTACCATTTTACCC-CGAACTTCC--AAAAATTCTATTTTTGACCTCGATATTTC
* * * **
19098 C-AAAATTACCATTTTACCCCTGAACTTCTAAAAATTTCATTTTTAACCTCGAAACTTTAAAAAA
1 CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACTTCGAAACTTTCCAAAA
* * * * * *
19162 AATACCATTTTACCCCCAAACTTCCAAAAATTCTAATTTTGACCT-GAAAAATAC
66 ATTACCATTTTA-CCCCGAACTTCCAAAAATTCTATTTTTGACCTCG-ATATTTC
* * *
19216 CAAAAATTACCATTTTA-CCCTCGTACTTCCAAAAATTCCATTTTTGACCTT-AAAAC-TTCCAA
1 CAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATTTCATTTTTGA-CTTCGAAACTTTCCAA
* ** * * *
19278 AAATTACTATTTTACCCCTGATTTTCCTAAAATTCCATTTTTGACCTCGATTTTTC
64 AAATTACCATTTTACCCC-GAACTTCCAAAAATTCTATTTTTGACCTCGATATTTC
* * * *
19334 CAAAAAATTTCCATTTTACCCAC-GGA-TGTCTAAAAA-TTCTATTTTTGACATCG-AACTTTCC
1 C-AAAAATTACCATTTTACCC-CTGAACT-TCCAAAAATTTC-ATTTTTGACTTCGAAACTTTCC
* *
19395 CAAAATTACCATTTTGCCCC
62 AAAAATTACCATTTTACCCC
19415 TGAGTGTCCA
Statistics
Matches: 257, Mismatches: 45, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
117 5 0.02
118 77 0.30
119 138 0.54
120 33 0.13
121 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACTTCGAAACTTTCCAAAA
ATTACCATTTTACCCCGAACTTCCAAAAATTCTATTTTTGACCTCGATATTTC
Found at i:19415 original size:119 final size:116
Alignment explanation
Indices: 18914--19437 Score: 377
Period size: 119 Copynumber: 4.4 Consensus size: 116
18904 AAGGTCCCTA
* * * * * * *
18914 AACTTACCAAAAATTA-CATTTTAACCCTAAAATTTCCAAAATTACA-TTTTCACCT-TAAACTT
1 AACTTTCCAAAAATTACCATTTTACCCCT-GAATTTCCAAAATTCCATTTTTGACCTCGATA-TT
* * * * * *
18976 TTCAAAAATTACAATTTTACCCCTCAACTTCCAAAAATT-TCATTTTTTACTTC-
64 TCCAAAAATTACCATTTTACCCC-GAACTTCTAAAAATTCT-ATTTTTGACATCG
* * *
19029 AATTTTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAAAATTCTATTTTTGACCTCGAT
1 AA-CTTTCCAAAAATTACCATTTTACCCCT-GAATTTCC---AAAATTCCATTTTTGACCTCGAT
* * *
19093 CTTTCC-AAAATTACCATTTTACCCCTGAACTTCTAAAAATT-TCATTTTTAACCTCG
61 ATTTCCAAAAATTACCATTTTACCCC-GAACTTCTAAAAATTCT-ATTTTTGACATCG
** * ** * * * * *
19149 AAACTTTAAAAAAAATACCATTTTACCCCCAAACTTCCAAAAATTCTAATTTTGACCT-GAAAAA
1 -AACTTTCCAAAAATTACCATTTTACCCCTGAATTTCC-AAAATTCCATTTTTGACCTCG-ATAT
* * * * * **
19213 TACCAAAAATTACCATTTTACCCTCGTACTTCCAAAAATTCCATTTTTGACCTTAA
63 TTCCAAAAATTACCATTTTACCC-CGAACTTCTAAAAATTCTATTTTTGA-CATCG
* * *
19269 AAC-TTCCAAAAATTACTATTTTACCCCTGATTTTCCTAAAATTCCATTTTTGACCTCGATTTTT
1 AACTTTCCAAAAATTACCATTTTACCCCTGAATTTCC-AAAATTCCATTTTTGACCTCGATATTT
* *
19333 CCAAAAAATTTCCATTTTACCCACGGA-TGTCTAAAAATTCTATTTTTGACATCG
65 CC-AAAAATTACCATTTTACCC-CGAACT-TCTAAAAATTCTATTTTTGACATCG
* * * *
19387 AACTTTCCCAAAATTACCATTTTGCCCCTGAGTGTCCAAAATTACCATTTT
1 AACTTTCCAAAAATTACCATTTTACCCCTGAATTTCCAAAATT-CCATTTT
19438 ACCCCTGGGT
Statistics
Matches: 326, Mismatches: 63, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
115 2 0.01
116 22 0.07
117 8 0.02
118 81 0.25
119 167 0.51
120 40 0.12
121 6 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (116 bp):
AACTTTCCAAAAATTACCATTTTACCCCTGAATTTCCAAAATTCCATTTTTGACCTCGATATTTC
CAAAAATTACCATTTTACCCCGAACTTCTAAAAATTCTATTTTTGACATCG
Found at i:19454 original size:28 final size:28
Alignment explanation
Indices: 19394--19455 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
19384 TCGAACTTTC
* *
19394 CCAAAATTACCATTTTGCCCCTGAGTGT
1 CCAAAATTACCATTTTACCCCTGAGTAT
*
19422 CCAAAATTACCATTTTACCCCTGGGTAT
1 CCAAAATTACCATTTTACCCCTGAGTAT
*
19450 TCAAAA
1 CCAAAA
19456 ATCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCTGAGTAT
Found at i:27254 original size:17 final size:18
Alignment explanation
Indices: 27232--27274 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 18
27222 TGGATGTAGC
27232 TTTTTAAATAATTATAA-
1 TTTTTAAATAATTATAAT
*
27249 TTTTT-AA-AATTTTAAT
1 TTTTTAAATAATTATAAT
27265 TTTTTAAATA
1 TTTTTAAATA
27275 TTTCCAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 7 0.32
18 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTAAATAATTATAAT
Found at i:27277 original size:17 final size:16
Alignment explanation
Indices: 27232--27277 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
27222 TGGATGTAGC
*
27232 TTTTTAAATAATTATAA
1 TTTTTAAAT-ATTTTAA
27249 TTTTTAAA-ATTTTAA
1 TTTTTAAATATTTTAA
27264 TTTTTTAAATATTT
1 -TTTTTAAATATTT
27278 CCAATGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 12 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAAATATTTTAA
Found at i:28441 original size:22 final size:21
Alignment explanation
Indices: 28395--28442 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
28385 AGTGAAAAAT
* *
28395 AAAATTTATTAAATACTTTAC
1 AAAATTTATTAAAGAATTTAC
*
28416 AAAATTATATTAAAAGAATTTAA
1 AAAATT-TATT-AAAGAATTTAC
28439 AAAA
1 AAAA
28443 GATAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTTATTAAAGAATTTAC
Found at i:28999 original size:24 final size:24
Alignment explanation
Indices: 28930--29001 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 24
28920 TTTGGATTCA
**
28930 AATAATAATACTTAAATTTAAAAG
1 AATAATAATAAATAAATTTAAAAG
*
28954 AATAATATTTATCAAAAAAATTTAAAAG
1 AATAATA---AT-AAATAAATTTAAAAG
*
28982 AATAATAATAAATGAATTTA
1 AATAATAATAAATAAATTTA
29002 GTAGTAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
24 16 0.41
25 2 0.05
27 2 0.05
28 19 0.49
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAATAATAAATAAATTTAAAAG
Found at i:35706 original size:17 final size:17
Alignment explanation
Indices: 35665--35720 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
35655 TAATATTTTG
**
35665 AAAAATATATAAAAAAAT
1 AAAAATATA-AAATTAAT
*
35683 AATAATATAAAATTAAT
1 AAAAATATAAAATTAAT
35700 AAAAATATAAATATTAA-
1 AAAAATATAAA-ATTAAT
35717 AAAA
1 AAAA
35721 TGAAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATATAAAATTAAT
Found at i:35709 original size:8 final size:8
Alignment explanation
Indices: 35666--35760 Score: 61
Period size: 8 Copynumber: 11.6 Consensus size: 8
35656 AATATTTTGA
35666 AAAATATAT
1 AAAA-ATAT
*
35675 AAAAAAAT
1 AAAAATAT
*
35683 AATAATAT
1 AAAAATAT
*
35691 AAAATTAAT
1 AAAAAT-AT
35700 AAAAATAT
1 AAAAATAT
*
35708 AAATAT-T
1 AAAAATAT
35715 AAAAA-AT
1 AAAAATAT
35722 GAAAAAT-T
1 -AAAAATAT
* *
35730 ATAATTATT
1 AAAAATA-T
*
35739 TAAAATAT
1 AAAAATAT
35747 AAAAATAT
1 AAAAATAT
35755 ATAAAA
1 A-AAAA
35761 ACAATTAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
7 10 0.15
8 35 0.54
9 20 0.31
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (8 bp):
AAAAATAT
Found at i:35712 original size:41 final size:41
Alignment explanation
Indices: 35667--35771 Score: 108
Period size: 41 Copynumber: 2.5 Consensus size: 41
35657 ATATTTTGAA
*
35667 AAATATATAAAAAAAT-AATAATATAAAATTAATAAAAATAT
1 AAATATATAAAAAAATGAAAAAT-TAAAATTAATAAAAATAT
* * *
35708 AAATAT-T-AAAAAATGAAAAATTATAATTATTTAAAATATAA
1 AAATATATAAAAAAATGAAAAATTAAAATTA-ATAAAA-ATAT
*
35749 AAATATATAAAAACAATTAAAAA
1 AAATATATAAAAA-AATGAAAAA
35772 GCACGTCTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
39 14 0.26
40 11 0.21
41 15 0.28
42 1 0.02
43 4 0.08
44 8 0.15
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.30
Consensus pattern (41 bp):
AAATATATAAAAAAATGAAAAATTAAAATTAATAAAAATAT
Found at i:35717 original size:24 final size:23
Alignment explanation
Indices: 35666--35755 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 23
35656 AATATTTTGA
*
35666 AAAATATATAAAAAAAT-AATAATAT
1 AAAATA-ATAAAAATATAAAT-AT-T
35691 AAAATTAATAAAAATATAAATATT
1 AAAA-TAATAAAAATATAAATATT
*
35715 AAAA-AATGAAAAATTATAATTATTT
1 AAAATAAT-AAAAA-TATAAATA-TT
35740 AAAAT-ATAAAAATATA
1 AAAATAATAAAAATATA
35756 TAAAAACAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.05
23 9 0.16
24 17 0.30
25 23 0.40
26 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (23 bp):
AAAATAATAAAAATATAAATATT
Found at i:35736 original size:39 final size:39
Alignment explanation
Indices: 35671--35749 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
35661 TTTGAAAAAT
*
35671 ATATAAAAAAATAATAATATAAAATTAATAAAAATATAA
1 ATATAAAAAAATAAAAATATAAAATTAATAAAAATATAA
* * * *
35710 ATATTAAAAAATGAAAAAT-TATAATTATTTAAAATATAA
1 ATATAAAAAAAT-AAAAATATAAAATTAATAAAAATATAA
35749 A
1 A
35750 AATATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (39 bp):
ATATAAAAAAATAAAAATATAAAATTAATAAAAATATAA
Found at i:38359 original size:12 final size:11
Alignment explanation
Indices: 38280--38366 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
38270 TTTTGCTATA
*
38280 ATTTCATTATT
1 ATTTTATTATT
* *
38291 ATGTTGTTATT
1 ATTTTATTATT
*
38302 ATTTTATTGTT
1 ATTTTATTATT
* *
38313 ATTGTT-TGAAT
1 ATT-TTATTATT
*
38324 ATTGTATAAATATT
1 ATT-T-T-ATTATT
38338 ATTTTATTATT
1 ATTTTATTATT
*
38349 AATTTTGTTATT
1 -ATTTTATTATT
38361 ATTTTA
1 ATTTTA
38367 GAGACATTTG
Statistics
Matches: 56, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
11 36 0.64
12 14 0.25
13 1 0.02
14 5 0.09
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:40459 original size:113 final size:117
Alignment explanation
Indices: 40293--40539 Score: 315
Period size: 113 Copynumber: 2.1 Consensus size: 117
40283 ATTTTTATAA
* * *
40293 TTCACTCGATTTAATATCACGACTTTCGATATTCTAACAGTTCATTTGATTTAATATCGCAATTG
1 TTCACTCGATTTAATATCACAACTATCGATATTCTAACAGTTCATTTGATTTAATATCGCAACTG
* * * *
40358 TCATTTTTACGATTCGCTCGGTTTAAGATTGTGACCTTT-GATATT-TGACAG
66 TCATTTTTACGATTCGCTCGATTTAAGATCGTGA-CTTTCAATATTCTAACAG
* * * * *
40409 TTCACTTGATTTAATATCGCAACTATC-A-ATT-TTACAGTTCGTTTGATTTAATATCGCGACTG
1 TTCACTCGATTTAATATCACAACTATCGATATTCTAACAGTTCATTTGATTTAATATCGCAACTG
* * *
40471 TCATTTTTATGGTTCGCTTGATTTAAGATCGTGACTTTCAATATTCTAACAG
66 TCATTTTTACGATTCGCTCGATTTAAGATCGTGACTTTCAATATTCTAACAG
40523 TTCACTCGATTTAATAT
1 TTCACTCGATTTAATAT
40540 TGTGGCTGTC
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
112 4 0.04
113 61 0.54
114 24 0.21
115 1 0.01
116 23 0.20
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (117 bp):
TTCACTCGATTTAATATCACAACTATCGATATTCTAACAGTTCATTTGATTTAATATCGCAACTG
TCATTTTTACGATTCGCTCGATTTAAGATCGTGACTTTCAATATTCTAACAG
Found at i:40537 original size:77 final size:77
Alignment explanation
Indices: 40453--40597 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 77
40443 CAGTTCGTTT
* * * *
40453 GATTTAATATCGCGACTGTCATTTTTATGGTTCGCTTGATTTAAGATCGTGACTTTCAATATTCT
1 GATTTAATATCGCGACTGTCATTTTTACGGTTCGCTCGATTTAAAATCGAGACTTTCAATATTCT
40518 AACAGTTCACTC
66 AACAGTTCACTC
* * * * **
40530 GATTTAATATTGTGGCTGTCATTTTTACGGTTCGCTCGATTTAAAATTGAGACTTTTGATATTCT
1 GATTTAATATCGCGACTGTCATTTTTACGGTTCGCTCGATTTAAAATCGAGACTTTCAATATTCT
40595 AAC
66 AAC
40598 TAGGGGTGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (77 bp):
GATTTAATATCGCGACTGTCATTTTTACGGTTCGCTCGATTTAAAATCGAGACTTTCAATATTCT
AACAGTTCACTC
Found at i:40570 original size:37 final size:37
Alignment explanation
Indices: 40263--40573 Score: 165
Period size: 37 Copynumber: 8.2 Consensus size: 37
40253 ATATTCGCAT
* * * * * *
40263 GATTTGATATCGTGATTGTTATTTTTATAATTCACTC
1 GATTTAATATCGTGACTGTCATTTTTACAGTTCGCTC
** * * ** *
40300 GATTTAATATCACGACTTTCGATATTCTAACAGTTCATTT
1 GATTTAATATCGTGACTGTC-AT-TT-TTACAGTTCGCTC
** *
40340 GATTTAATATCGCAATTGTCATTTTTAC-GATTCGCTC
1 GATTTAATATCGTGACTGTCATTTTTACAG-TTCGCTC
* * * * * * * *
40377 GGTTTAAGATTGTGACCTTTGATATTTGACAGTTCACTT
1 GATTTAATATCGTGA-CTGTCAT-TTTTACAGTTCGCTC
** * * * *
40416 GATTTAATATCGCAACTATCAATTTTACAGTTCGTTT
1 GATTTAATATCGTGACTGTCATTTTTACAGTTCGCTC
* ** *
40453 GATTTAATATCGCGACTGTCATTTTTATGGTTCGCTT
1 GATTTAATATCGTGACTGTCATTTTTACAGTTCGCTC
* * * *
40490 GATTTAAGATCGTGACTTTCAATATTCTAACAGTTCACTC
1 GATTTAATATCGTGACTGTC-AT-TT-TTACAGTTCGCTC
* * *
40530 GATTTAATATTGTGGCTGTCATTTTTACGGTTCGCTC
1 GATTTAATATCGTGACTGTCATTTTTACAGTTCGCTC
40567 GATTTAA
1 GATTTAA
40574 AATTGAGACT
Statistics
Matches: 202, Mismatches: 62, Indels: 20
0.71 0.22 0.07
Matches are distributed among these distances:
36 1 0.00
37 108 0.53
38 16 0.08
39 28 0.14
40 49 0.24
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (37 bp):
GATTTAATATCGTGACTGTCATTTTTACAGTTCGCTC
Found at i:41333 original size:77 final size:76
Alignment explanation
Indices: 41138--41334 Score: 189
Period size: 77 Copynumber: 2.6 Consensus size: 76
41128 CTCACTCCTA
* * * * * * * * *
41138 ATTCTAACAGTTCACTTGATTTAATATTACGGTTGTCATTCTTATGGTTCACTTATTTAATATTA
1 ATTCTAACAATTCGCTCGATTTAATATAACGGCTGTCATTTTTACGGTTCACTTATTTAAGATCA
41203 CGACCTTCAAT
66 CGACCTTCAAT
* * * * ** * **
41214 ATTCTAA-TAGTCTGTTCGATTTATTATCGCGACTGTTTTTTTTACGGTTCACTTTATTTAAGAT
1 ATTCTAACAATTC-GCTCGATTTAATATAACGGCTGTCATTTTTACGGTTCAC-TTATTTAAGAT
*
41278 CACGACTTTCAAT
64 CACGACCTTCAAT
*
41291 ATTCTAACAATTCGCTCAATTTAATATAACGGCTGTCATTTTTA
1 ATTCTAACAATTCGCTCGATTTAATATAACGGCTGTCATTTTTA
41335 AAGCTAGCTA
Statistics
Matches: 90, Mismatches: 28, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
75 2 0.02
76 34 0.38
77 51 0.57
78 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (76 bp):
ATTCTAACAATTCGCTCGATTTAATATAACGGCTGTCATTTTTACGGTTCACTTATTTAAGATCA
CGACCTTCAAT
Found at i:41745 original size:32 final size:32
Alignment explanation
Indices: 41704--41769 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
41694 TCTTCTCTAA
41704 TTCTTGAAATTCCCTCTCCTTCCTCACTTTTG
1 TTCTTGAAATTCCCTCTCCTTCCTCACTTTTG
*
41736 TTCTTGAAATTCCCTCTTCTTCCTCACTTTTG
1 TTCTTGAAATTCCCTCTCCTTCCTCACTTTTG
41768 TT
1 TT
41770 GATACTGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (32 bp):
TTCTTGAAATTCCCTCTCCTTCCTCACTTTTG
Found at i:42490 original size:28 final size:27
Alignment explanation
Indices: 42455--42508 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
42445 ATAACGCTTA
*
42455 ATAATAATATT-GTTATTAATAATAACC
1 ATAATAATATTAG-TAATAATAATAACC
42482 ATAATTAATATTAGTAATAATAATAAC
1 ATAA-TAATATTAGTAATAATAATAAC
42509 TGTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 19 0.79
29 1 0.04
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (27 bp):
ATAATAATATTAGTAATAATAATAACC
Found at i:43588 original size:30 final size:29
Alignment explanation
Indices: 43533--43934 Score: 365
Period size: 29 Copynumber: 13.8 Consensus size: 29
43523 GTAGGTCCCT
**
43533 AAACATTCCAAAAATTCTGTTTTT-ACCGCC
1 AAAC-TTCCAAAAATTCCATTTTTAACC-CC
* *
43563 GAACTTCCAAAAA-TCTCATTTTTTACCCC
1 AAACTTCCAAAAATTC-CATTTTTAACCCC
*
43592 GAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCC
* * * **
43621 AAAACTTCTAAAAATCCCA-TTTTGACCTT
1 -AAACTTCCAAAAATTCCATTTTTAACCCC
*
43650 AAACTTTCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCC
*
43679 AAAACTTTCAAAAATTCCATTTTTAACCCC
1 -AAACTTCCAAAAATTCCATTTTTAACCCC
*
43709 AAAACTTCCAAAAATTCCATTTTTAACCTCA
1 -AAACTTCCAAAAATTCCATTTTTAACC-CC
* *
43740 AAACTTCC-AAAATCCCA-TTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCC
* * * * *
43767 GAATTTTCAAAAATCCCATTTTT-GCACCC
1 AAACTTCCAAAAATTCCATTTTTAAC-CCC
*
43796 AAACTTCCAAAAATTCCATTTTTAACCTCT
1 AAACTTCCAAAAATTCCATTTTTAACC-CC
43826 AAACTTCCAAAAATTCCATTTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCC-C
* * * *
43855 GAACTTCTAAAAATGCCATTTTT-ACCCTA
1 AAACTTCCAAAAATTCCATTTTTAACCC-C
* * *
43884 AAACTTTCAAAAATTCTATTTTT-CCCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCC-C
43913 AAACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
43935 CAATCTCGAA
Statistics
Matches: 313, Mismatches: 45, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.02
28 40 0.13
29 154 0.49
30 112 0.36
31 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTAACCCC
Found at i:43699 original size:88 final size:87
Alignment explanation
Indices: 43533--43934 Score: 428
Period size: 88 Copynumber: 4.6 Consensus size: 87
43523 GTAGGTCCCT
** * **
43533 AAACATTCCAAAAATTCTGTTTTT-ACCGCCGAACTTCCAAAAA-TCTCATTTTTTACCCCGAAC
1 AAAC-TTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTC-CA-TTTTTACCCCGAAC
*
43596 TTCCAAAAATTCCATTTTTAACCCCA
63 TTTCAAAAATTCCATTTTT-ACCCCA
* * * * *
43622 AAACTTCTAAAAATCCCA-TTTTGACCT-TAAACTTTCAAAAATTCCATTTTTAACCCCAAAACT
1 AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTCCATTTTT-ACCCC-GAACT
43685 TTCAAAAATTCCATTTTTAACCCCA
64 TTCAAAAATTCCATTTTT-ACCCCA
* * *
43710 AAACTTCCAAAAATTCCATTTTTAACCTCAAAACTTCC-AAAATCCCA-TTTTACCCCCGAATTT
1 AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTT
* *
43773 TCAAAAATCCCATTTTTGCACCC-
65 TCAAAAATTCCATTTTTAC-CCCA
43796 AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTCCATTTTTACCCTCGAAC-T
1 AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTCCATTTTTACCC-CGAACTT
* *
43860 TCTAAAAATGCCATTTTTACCCTA
65 TC-AAAAATTCCATTTTTACCCCA
* * **
43884 AAACTTTCAAAAATTCTATTTTTCCCCTC-AAACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAAT-TCCATTTT
43935 CAATCTCGAA
Statistics
Matches: 269, Mismatches: 30, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
86 48 0.18
87 78 0.29
88 116 0.43
89 20 0.07
90 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (87 bp):
AAACTTCCAAAAATTCCATTTTTAACCTCTAAACTTCCAAAAATTCCATTTTTACCCCGAACTTT
CAAAAATTCCATTTTTACCCCA
Found at i:43933 original size:29 final size:27
Alignment explanation
Indices: 43564--43934 Score: 202
Period size: 30 Copynumber: 12.7 Consensus size: 27
43554 TTTACCGCCG
* * *
43564 AACTTCCAAAAATCTCATTTTTTACCCCG
1 AACTTCCAAAATTC-CA-TTTTTCCCCCA
*
43593 AACTTCCAAAAATTCCATTTTTAACCCCAA
1 AACTTCC-AAAATTCCATTTTT--CCCCCA
* * ** **
43623 AACTTCTAAAAATCCCATTTTGACCTTA
1 AACTTC-CAAAATTCCATTTTTCCCCCA
* *
43651 AACTTTCAAAAATTCCATTTTTAACCCCAA
1 AAC-TTCCAAAATTCCATTTTT--CCCCCA
* *
43681 AACTTTCAAAAATTCCATTTTTAACCCCAA
1 AAC-TTCCAAAATTCCATTTTT--CCCCCA
* *
43711 AACTTCCAAAAATTCCATTTTTAACCTCAA
1 AACTTCC-AAAATTCCATTTTT--CCCCCA
* *
43741 AACTTCCAAAATCCCATTTTACCCCCGA
1 AACTTCCAAAATTCCATTTTTCCCCC-A
** * * *
43769 ATTTTCAAAAATCCCATTTTTGCACCCA
1 AACTTCCAAAATTCCATTTTT-CCCCCA
* *
43797 AACTTCCAAAAATTCCATTTTTAACCTCTA
1 AACTTCC-AAAATTCCATTTTT--CCCCCA
* *
43827 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCC-AAAATTCCATTTTT-CCCCCA
* * **
43856 AACTTCTAAAAATGCCATTTTTACCCTAA
1 AACTTC-CAAAATTCCATTTTT-CCCCCA
* *
43885 AACTTTCAAAAATTCTATTTTTCCCCTCA
1 AAC-TTCCAAAATTCCATTTTTCCCC-CA
43914 AACTTCCAAAATCTCCATTTT
1 AACTTCCAAAAT-TCCATTTT
43935 CAATCTCGAA
Statistics
Matches: 278, Mismatches: 48, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
27 3 0.01
28 58 0.21
29 98 0.35
30 119 0.43
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTTCCAAAATTCCATTTTTCCCCCA
Found at i:56237 original size:207 final size:204
Alignment explanation
Indices: 55967--56355 Score: 494
Period size: 207 Copynumber: 1.9 Consensus size: 204
55957 CTCACGTTCG
* * ** * *
55967 ATCTTCGAACTCTAGCTTCTGGATGCGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCT
* * * * * * * *
56032 TCCTGATGAGATACT-GAGAAGTGAACCA-AATTCGTCTTCCTGATGAGATACATAGAAGCGGAT
66 TCCCGATGAAATA-TGGAGAAGTGAACCAGAA-CCATCTTCCTGATGAAACACAGAGAAGCAGAT
** *
56095 TGAAACAAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAAACTACAC
129 CAAAACAAG-GAT--GGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAAAACTACAC
56160 TCAAAGCAAACAAA
191 TCAAAGCAAACAAA
* * *
56174 ATCTTCGAACCCCAGCTTCCCGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAACGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCT
* *
56239 TCCCGATGAAATATGGGGAAGTGAACCAGAACCATCTTCCTGATGAAACACAGAGAAGTAGATCA
66 TCCCGATGAAATATGGAGAAGTGAACCAGAACCATCTTCCTGATGAAACACAGAGAAGCAGATCA
* * *
56304 AAACAAGTATGGTCATCTTCTTGATGAGATACTAAGAAGAAGGCCAAGTCAA
131 AAACAAGGATGGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAA
56356 TGAAACCAAA
Statistics
Matches: 155, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
204 39 0.25
206 3 0.02
207 111 0.72
208 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (204 bp):
ATCTTCGAACCCCAGCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCT
TCCCGATGAAATATGGAGAAGTGAACCAGAACCATCTTCCTGATGAAACACAGAGAAGCAGATCA
AAACAAGGATGGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAAAACTACACTCAAA
GCAAACAAA
Found at i:57355 original size:46 final size:40
Alignment explanation
Indices: 57283--57379 Score: 97
Period size: 43 Copynumber: 2.2 Consensus size: 40
57273 TTAATAACGC
*
57283 TTAATAATAATATTGTTATTAATAATAACCATAATTAATATTAA
1 TTAATAATAATACTGTTATTAATAAT-A--AT-ATTAATATTAA
*
57327 -TAATAATAACTACTGTTTTTAAATTAATAATATTAATATTAA
1 TTAATAATAA-TACTGTTATT-AA-TAATAATATTAATATTAA
57369 TTAATATATAA
1 TTAATA-ATAA
57380 ATAAAGAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
42 11 0.24
43 16 0.35
44 12 0.26
45 3 0.07
46 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (40 bp):
TTAATAATAATACTGTTATTAATAATAATATTAATATTAA
Found at i:58425 original size:29 final size:29
Alignment explanation
Indices: 58380--58687 Score: 230
Period size: 29 Copynumber: 10.7 Consensus size: 29
58370 TCCCTAAACT
* *
58380 TTCCAAAAAT-TCTTTTTTACCCTCGAAC
1 TTCCAAAAATCCCATTTTTACCCTCGAAC
*
58408 TTCCAAAAATCCCATTTTTGACCC-CAAAC
1 TTCCAAAAATCCCATTTTT-ACCCTCGAAC
*
58437 TTCCAAAAATCCCATTTTTAACCC-CAAAAC
1 TTCCAAAAATCCCATTTTT-ACCCTC-GAAC
* *
58467 TTCAAAAAATCCCATTTTT--CC-CAAAC
1 TTCCAAAAATCCCATTTTTACCCTCGAAC
* * *
58493 TTCCAAAAATTCCATTTTTAACCTCAAAAC
1 TTCCAAAAATCCCATTTTTACCCTC-GAAC
*
58523 TTTCAAAAATCCCATTTTTGA-CCTCGAAC
1 TTCCAAAAATCCCATTTTT-ACCCTCGAAC
* *
58552 TTCCAAAAATGCCATTTTGA-CCTCGAAAC
1 TTCCAAAAATCCCATTTTTACCCTCG-AAC
* * * *
58581 TTTCAAAAATTCCATTTTTGCCCTTGAAC
1 TTCCAAAAATCCCATTTTTACCCTCGAAC
*
58610 TTCC-AAAATCTCCATTTTTTA-TCTCGAAAC
1 TTCCAAAAATC-CCA-TTTTTACCCTCG-AAC
*
58640 -TCTCAAAATTACCC--TTTTACCCTCGAA-
1 TTC-CAAAAAT-CCCATTTTTACCCTCGAAC
* *
58667 TGTCTAAAAATTCCATTTTTA
1 T-TCCAAAAATCCCATTTTTA
58688 AATCTCAAAT
Statistics
Matches: 231, Mismatches: 28, Indels: 41
0.77 0.09 0.14
Matches are distributed among these distances:
26 21 0.09
27 5 0.02
28 35 0.15
29 98 0.42
30 64 0.28
31 7 0.03
32 1 0.00
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTTACCCTCGAAC
Found at i:58469 original size:30 final size:29
Alignment explanation
Indices: 58375--58628 Score: 236
Period size: 29 Copynumber: 8.8 Consensus size: 29
58365 AAAGGTCCCT
* *
58375 AAACTTTCCAAAAAT-TC-TTTTTTACCCTC
1 AAAC-TTCCAAAAATCCCATTTTTGACCC-C
*
58404 GAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACTTCCAAAAATCCCATTTTTGACCCC
*
58433 AAACTTCCAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTTGACCCC
*
58462 AAAACTTCAAAAAATCCCATTTTT---CCC
1 -AAACTTCCAAAAATCCCATTTTTGACCCC
* * *
58489 AAACTTCCAAAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTTGACC-CC
* *
58519 AAACTTTCAAAAATCCCATTTTTGACCTC
1 AAACTTCCAAAAATCCCATTTTTGACCCC
* * *
58548 GAACTTCCAAAAATGCCA-TTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTTGACC-CC
* * *
58577 AAACTTTCAAAAATTCCATTTTTG-CCCTT
1 AAACTTCCAAAAATCCCATTTTTGACCC-C
*
58606 GAACTTCC-AAAATCTCCATTTTT
1 AAACTTCCAAAAATC-CCATTTTT
58629 TATCTCGAAA
Statistics
Matches: 188, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
26 21 0.11
27 3 0.02
28 24 0.13
29 79 0.42
30 61 0.32
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:58648 original size:58 final size:59
Alignment explanation
Indices: 58380--58688 Score: 291
Period size: 58 Copynumber: 5.4 Consensus size: 59
58370 TCCCTAAACT
* * * * * *
58380 TTCCAAAAATT-CTTTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCAAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTGACCTCGAAC
* * * * *
58437 TTCCAAAAATCCCATTTTTAACCCCAAAAC-TTCAAAAAATCCCATTTTT--CC-CAAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTC-AAAAATTCCATTTTTGACCTCGAAC
* *
58493 TTCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAATCCCATTTTTGACCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTGACCTCGAAC
* * * *
58552 TTCCAAAAATGCCA-TTTTGACCTCGAAACTTTCAAAAATTCCATTTTTGCCCTTGAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTGACCTCGAAC
* * * *
58610 TTCC-AAAATCTCCATTTTTTATCTCGAAACTCTC-AAAATTACC-CTTTT-ACCCTCGAA-
1 TTCCAAAAAT-TCCATTTTTAACCTCGAAACTTTCAAAAATT-CCATTTTTGA-CCTCGAAC
*
58667 TGTCTAAAAATTCCATTTTTAA
1 T-TCCAAAAATTCCATTTTTAA
58689 ATCTCAAATT
Statistics
Matches: 215, Mismatches: 24, Indels: 25
0.81 0.09 0.09
Matches are distributed among these distances:
56 48 0.22
57 21 0.10
58 88 0.41
59 58 0.27
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTGACCTCGAAC
Found at i:59994 original size:23 final size:23
Alignment explanation
Indices: 59964--60009 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
59954 AGATAAATTC
*
59964 AAAGTTTGATGAGTTCAAAGTTT
1 AAAGTTTGATAAGTTCAAAGTTT
59987 AAAGTTTGATAAGTTCAAAGTTT
1 AAAGTTTGATAAGTTCAAAGTTT
60010 GACATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (23 bp):
AAAGTTTGATAAGTTCAAAGTTT
Found at i:60000 original size:16 final size:16
Alignment explanation
Indices: 59981--60011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59971 GATGAGTTCA
*
59981 AAGTTTAAAGTTTGAT
1 AAGTTCAAAGTTTGAT
59997 AAGTTCAAAGTTTGA
1 AAGTTCAAAGTTTGA
60012 CATACCAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (16 bp):
AAGTTCAAAGTTTGAT
Done.