Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold484
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: 288598
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.28
Warning! 45481 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:200 original size:42 final size:42
Alignment explanation
Indices: 151--347 Score: 154
Period size: 41 Copynumber: 4.7 Consensus size: 42
141 CTTCAACAAC
151 AACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGA
1 AACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGA
* ** * * * *
193 CACGCCGCTAAAAGTCTTAACTTTAGCGTCGCTTAT-ATAAA
1 AACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGA
** * * *
234 AACGCCGCTAAAAGACCAAATATTAGCGGCGC-T-TCAAAGA
1 AACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGA
* * * *
274 AATTGCCGCTAAATA-CCTTAACTTTAGCGGCGGTTGATCA-A-A
1 AA-CGCCGCTAAA-ACCCCTAACATTAGCGGCGCTT-ATCATAGA
* *
316 AACGCCACTAAAACCCCTGACCATTAGCGGCG
1 AACGCCGCTAAAACCCCT-AACATTAGCGGCG
348 AAAGCCTAAA
Statistics
Matches: 119, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.01
40 7 0.06
41 61 0.51
42 46 0.39
43 1 0.01
44 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (42 bp):
AACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGA
Found at i:317 original size:82 final size:83
Alignment explanation
Indices: 137--347 Score: 198
Period size: 83 Copynumber: 2.5 Consensus size: 83
127 TGTTTTTTGT
* * * * *
137 GGCGCTTCA-ACAACAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCATAGACACGCCGC
1 GGCGCTT-ATACAAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTATCAAAGAAACGCCGC
*
201 TAAAAGTCTTAACTTTAGC
65 TAAAAGCCTTAACTTTAGC
* * * * *
220 GTCGCTTATATAAAAACGCCGCTAAAAGACCAAATATTAGCGGCGC-T-TCAAAGAAATTGCCGC
1 GGCGCTTATACAAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTATCAAAGAAA-CGCCGC
283 TAAATA-CCTTAACTTTAGC
65 TAAA-AGCCTTAACTTTAGC
* * * * *
302 GGCGGTTGAT-CAAAAACGCCACTAAAACCCCTGACCATTAGCGGCG
1 GGCGCTT-ATACAAAAACGCCGCTAAAACACC-AAACATTAGCGGCG
348 AAAGCCTAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
81 7 0.07
82 45 0.44
83 51 0.50
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (83 bp):
GGCGCTTATACAAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTATCAAAGAAACGCCGCT
AAAAGCCTTAACTTTAGC
Found at i:774 original size:14 final size:13
Alignment explanation
Indices: 755--785 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
745 TGTTTCTATC
755 AAATATAAATATA
1 AAATATAAATATA
768 TAAATATAAATATA
1 -AAATATAAATATA
782 AAAT
1 AAAT
786 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:3645 original size:89 final size:88
Alignment explanation
Indices: 3529--3718 Score: 348
Period size: 89 Copynumber: 2.2 Consensus size: 88
3519 TTTATGTGTC
3529 TATATATTATTTATCTTAAAAAAAATCTAAAGTTATGACCAAAAAGTTTATTATAAAAAATAATT
1 TATATATTATTTATCTTAAAAAAAATCTAAAGTTATGACCAAAAAGTTTATTATAAAAAATAATT
3594 TACATGTTATACAAGTGCTATAA
66 TACATGTTATACAAGTGCTATAA
3617 TATATATT-TTTAAATCTTAAAAAAAATCTAAAGTTATGACCAAAAAGTTTATTATAAAAAATAA
1 TATATATTATTT--ATCTTAAAAAAAATCTAAAGTTATGACCAAAAAGTTTATTATAAAAAATAA
3681 TTTACATGTTATACAAGTGCTATAA
64 TTTACATGTTATACAAGTGCTATAA
3706 TATAT-TTATTTAT
1 TATATATTATTTAT
3719 AAAAAGCTAT
Statistics
Matches: 99, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
87 5 0.05
88 10 0.10
89 84 0.85
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.39
Consensus pattern (88 bp):
TATATATTATTTATCTTAAAAAAAATCTAAAGTTATGACCAAAAAGTTTATTATAAAAAATAATT
TACATGTTATACAAGTGCTATAA
Found at i:6152 original size:31 final size:31
Alignment explanation
Indices: 6114--6193 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
6104 CATGGTTGAT
* *
6114 TTAGCAGCAAAAATCAATAGAATGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
*
6145 TTAGCAGCAAAACCCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
*
6176 TTAGCTGCAAAAACCAAT
1 TTAGCAGCAAAAACCAAT
6194 TAAAATCCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.20
Consensus pattern (31 bp):
TTAGCAGCAAAAACCAATAGAAGGTACCATC
Found at i:7749 original size:21 final size:21
Alignment explanation
Indices: 7723--7763 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7713 ATGCATTGTT
* *
7723 TAAACCTTAAACCATTAACAC
1 TAAACCGTAAACCATAAACAC
7744 TAAACCGTAAACCATAAACA
1 TAAACCGTAAACCATAAACA
7764 TCAAGCCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAACCGTAAACCATAAACAC
Found at i:7845 original size:7 final size:7
Alignment explanation
Indices: 7835--7902 Score: 75
Period size: 7 Copynumber: 9.9 Consensus size: 7
7825 CATTAAAACG
7835 TAAACCC
1 TAAACCC
7842 TAAACCC
1 TAAACCC
*
7849 TAAACCT
1 TAAACCC
*
7856 TAAACCT
1 TAAACCC
7863 TAAACCC
1 TAAACCC
*
7870 CAAACCC
1 TAAACCC
*
7877 TAAGCCC
1 TAAACCC
7884 TAAA-CC
1 TAAACCC
* *
7890 TACACCA
1 TAAACCC
7897 TAAACC
1 TAAACC
7903 TTGAACTCAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
6 5 0.10
7 46 0.90
ACGTcount: A:0.43, C:0.40, G:0.01, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:8199 original size:41 final size:41
Alignment explanation
Indices: 8118--8333 Score: 202
Period size: 41 Copynumber: 5.2 Consensus size: 41
8108 TGCTAAAGCC
* * * *
8118 CCGCTAAAAGCCCCTGAGCATTAGCGACACTT-TCTAAAAAACG
1 CCGCT-AAAG-CCCAGAGCATTAGCGGCGCTTCT-TCAAAAACG
* * * * *
8161 TCGATAAAGGCCAGAGCATTAGCGTCGCTTCTTCAAAAAAG
1 CCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
* * * * *
8202 CCGCTAAAGCCTAGATCATTAGCGACAG-TTTTTCAAAAATG
1 CCGCTAAAGCCCAGAGCATTAGCGGC-GCTTCTTCAAAAACG
*
8243 CCGCTAAAGCCCAGATCATTAGCGGCGCTTCTTCAAAAACG
1 CCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
* ** * *
8284 CCGCTAAATCCCCCAGCATTAGCGGCGCTTTTTGAAAAACG
1 CCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
8325 CCGCTAAAG
1 CCGCTAAAG
8334 TCCCCAAAGC
Statistics
Matches: 143, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
40 1 0.01
41 133 0.93
42 6 0.04
43 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (41 bp):
CCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
Found at i:8304 original size:82 final size:82
Alignment explanation
Indices: 8134--8333 Score: 231
Period size: 82 Copynumber: 2.4 Consensus size: 82
8124 AAAGCCCCTG
* * * * * *
8134 AGCATTAGCGACACTTTCTAAAAAACGTCGATAAAGGCCAGAGCATTAGCGTCGCTTCTTCAAAA
1 AGCATTAGCGACAGTTTTTAAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAA
* *
8199 AAGCCGCTAAAGCCTAG
66 AAGCCGCTAAAGCCCAC
* * * *
8216 ATCATTAGCGACAGTTTTTCAAAAATGCCGCTAAAGCCCAGATCATTAGCGGCGCTTCTTCAAAA
1 AGCATTAGCGACAGTTTTTAAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAA
* * *
8281 ACGCCGCTAAATCCCCC
66 AAGCCGCTAAAGCCCAC
* *
8298 AGCATTAGCGGC-GCTTTTTGAAAAACGCCGCTAAAG
1 AGCATTAGCGACAG-TTTTTAAAAAACGCCGCTAAAG
8334 TCCCCAAAGC
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 1 0.01
82 97 0.99
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (82 bp):
AGCATTAGCGACAGTTTTTAAAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTTCAAAA
AAGCCGCTAAAGCCCAC
Found at i:8459 original size:39 final size:40
Alignment explanation
Indices: 8396--8495 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
8386 TTATAAACGG
* * *
8396 CGCTAATGCTCTATTTTTAGCAGCG-TTTCTCAAAAAGTGC
1 CGCTAATGCTTTATCTTTAGCAGCGTTTTC-CAAAAAGCGC
* *
8436 CGCTAATGCTTTA-CTTTAGCAGCGTTTTCCTAAATGCGC
1 CGCTAATGCTTTATCTTTAGCAGCGTTTTCCAAAAAGCGC
* *
8475 CGCTAATGCTTGATTTTTAGC
1 CGCTAATGCTTTATCTTTAGC
8496 GGCATTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
39 29 0.57
40 22 0.43
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (40 bp):
CGCTAATGCTTTATCTTTAGCAGCGTTTTCCAAAAAGCGC
Found at i:22749 original size:62 final size:62
Alignment explanation
Indices: 22553--22750 Score: 200
Period size: 63 Copynumber: 3.2 Consensus size: 62
22543 CGGGTCATAC
* *
22553 GCCCGTGTGCCCTGGCCGTATGGTTTTTTTGCATAAACAGTGAGTTACATGGCCTAGACACAT
1 GCCCGTGT-CCCTGGCCGTATGGTCTTTTTCCATAAACAGTGAGTTACATGGCCTAGACACAT
** ** * * * * * * * *
22616 GCCAATGTCCCTTCCCGTGT-GACTTTTATACTACAAACAGTGAGTTATACGGCCTGGACACAC
1 GCCCGTGTCCCTGGCCGTATGGTCTTTT-T-CCATAAACAGTGAGTTACATGGCCTAGACACAT
* * * *
22679 ACCTGTGTCCCTGGCCGTATGGTCTTGTTCCATAAACAGTGAGTTACATGGCCCAGACACAT
1 GCCCGTGTCCCTGGCCGTATGGTCTTTTTCCATAAACAGTGAGTTACATGGCCTAGACACAT
22741 GCCCGTGTCC
1 GCCCGTGTCC
22751 GTTGCCCGTG
Statistics
Matches: 101, Mismatches: 31, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
61 5 0.05
62 44 0.44
63 47 0.47
64 5 0.05
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (62 bp):
GCCCGTGTCCCTGGCCGTATGGTCTTTTTCCATAAACAGTGAGTTACATGGCCTAGACACAT
Found at i:25483 original size:18 final size:18
Alignment explanation
Indices: 25460--25519 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
25450 GGTAATGGGT
25460 ACTTGTTCTTAATTGTCA
1 ACTTGTTCTTAATTGTCA
**
25478 ACTTGTTC-TAACAAGT--
1 ACTTGTTCTTAA-TTGTCA
*
25494 ACTTGTTCTTGATTGTCA
1 ACTTGTTCTTAATTGTCA
25512 ACTTGTTC
1 ACTTGTTC
25520 AACTGTCCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.30
17 5 0.15
18 18 0.55
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (18 bp):
ACTTGTTCTTAATTGTCA
Found at i:31285 original size:3 final size:3
Alignment explanation
Indices: 31279--31331 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
31269 TAATGTTACC
* * * *
31279 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATC AAT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31327 ATT AT
1 ATT AT
31332 ATTTCCATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:31302 original size:15 final size:15
Alignment explanation
Indices: 31282--31331 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
31272 TGTTACCATT
31282 ATTATTATTATTATC
1 ATTATTATTATTATC
31297 ATTATTATTATTATC
1 ATTATTATTATTATC
*
31312 AATATTATTATTATC
1 ATTATTATTATTATC
31327 ATTAT
1 ATTAT
31332 ATTTCCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTATC
Found at i:31871 original size:110 final size:110
Alignment explanation
Indices: 31678--31880 Score: 302
Period size: 110 Copynumber: 1.8 Consensus size: 110
31668 TTATTTATTC
* * * *
31678 TAGCTAAATATCCTTTTAAAAATTCTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAA
1 TAGCTAAACAGCCTTTCAAAAATTCTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAA
31743 CATGCCCTAAGGTACTGGGTGTCGATTTTTTCTCGTTCAACCAAA
66 CATGCCCTAAGGTACTGGGTGTCGATTTTTTCTCGTTCAACCAAA
*
31788 TAGCTAAACAGCCTTTCAAAAATT-TCAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCAAG-G
1 TAGCTAAACAGCCTTTCAAAAATTCT-AAAATAAGGCAATGTTTTGCGTTT-GGAAATTCAAGAA
* * *
31851 AACGTGCCCTAAGGTGCTGGGTTTCGATTT
64 AACATGCCCTAAGGTACTGGGTGTCGATTT
31881 CTCGTTTAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
109 1 0.01
110 72 0.87
111 10 0.12
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (110 bp):
TAGCTAAACAGCCTTTCAAAAATTCTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAA
CATGCCCTAAGGTACTGGGTGTCGATTTTTTCTCGTTCAACCAAA
Found at i:35275 original size:28 final size:27
Alignment explanation
Indices: 35220--35276 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
35210 AAGAAAAATC
* * **
35220 AAAATCAAAGTCAAAATGAAAATGAAA
1 AAAATCAAAATCAAAATAAAAAACAAA
35247 AAAATCAAAAATCAAAATAAAAAACAAA
1 AAAATC-AAAATCAAAATAAAAAACAAA
35275 AA
1 AA
35277 GAAGAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (27 bp):
AAAATCAAAATCAAAATAAAAAACAAA
Found at i:36155 original size:20 final size:20
Alignment explanation
Indices: 36130--36196 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
36120 TGAGTCGGAA
*
36130 AAAAATGAAAAATG-AGATCG
1 AAAAATGAAAAATGAAAAT-G
36150 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
*
36170 AAAAATG-AAAATGAAAAATA
1 AAAAATGAAAAATG-AAAATG
36190 AAAAATG
1 AAAAATG
36197 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.14
20 34 0.79
21 3 0.07
ACGTcount: A:0.69, C:0.01, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:36167 original size:6 final size:6
Alignment explanation
Indices: 36151--36186 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
36141 ATGAGATCGA
36151 AAAATG AAAAATG AAAATG AAAAATG AAAATG AAAA
1 AAAATG -AAAATG AAAATG -AAAATG AAAATG AAAA
36187 ATAAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:36167 original size:13 final size:13
Alignment explanation
Indices: 36151--36192 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
36141 ATGAGATCGA
36151 AAAATGAAAAATG
1 AAAATGAAAAATG
36164 AAAATGAAAAATG
1 AAAATGAAAAATG
36177 AAAATGAAAAAT-
1 AAAATGAAAAATG
36189 AAAA
1 AAAA
36193 AATGGAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 4 0.14
13 25 0.86
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:36192 original size:6 final size:7
Alignment explanation
Indices: 36130--36196 Score: 79
Period size: 7 Copynumber: 10.0 Consensus size: 7
36120 TGAGTCGGAA
36130 AAAAATG
1 AAAAATG
36137 AAAAATG
1 AAAAATG
*
36144 --AGATCG
1 AAAAAT-G
36150 AAAAATG
1 AAAAATG
36157 AAAAATG
1 AAAAATG
36164 -AAAATG
1 AAAAATG
36170 AAAAATG
1 AAAAATG
36177 -AAAATG
1 AAAAATG
*
36183 AAAAATA
1 AAAAATG
36190 AAAAATG
1 AAAAATG
36197 GAGAGGCTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
5 3 0.06
6 13 0.25
7 32 0.63
8 3 0.06
ACGTcount: A:0.69, C:0.01, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:37853 original size:46 final size:44
Alignment explanation
Indices: 37470--39090 Score: 642
Period size: 44 Copynumber: 37.4 Consensus size: 44
37460 CTTACTAAGA
* * * *
37470 TTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCTGAAG
1 TTACAGTGGAGCAGATCGAAGAATCA-GATCTTATCTCCCTGAGG
* * * * * *
37513 TTACAGTGGAGCGGAT-TAA-AATAAAGGATCTCATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAAT-CA-GATCTTATCTCCCTGAGG
** * * * *
37557 TTACAGCAGAGTAGATC---GCATCAGGTCTTATCTCACTGAGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* * *
37598 TTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGT
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* * * * **
37644 TTACAGTGGAGCAAATTGAAGCCA-GAGATCTTATCTCCCTGATA
1 TTACAGTGGAGCAGATCGAAG-AATCAGATCTTATCTCCCTGAGG
* * * **
37688 TTACAGCGGAGCAGATTGAAG-AT-AGTAATCATATCTCCCTGATA
1 TTACAGTGGAGCAGATCGAAGAATCAG--ATCTTATCTCCCTGAGG
* * * * * * *
37732 TTATAGTGGAGCGGAT-TAA-AATAAAGGATCTCATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAAT-CA-GATCTTATCTCCCTGAGG
** * * * *
37776 TTACAGCAGAGTAGATC--A-CATCAGGTCTTATCTCACTGAGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* *
37817 TTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* *
37863 TTACAGTGGAGCAGATTGAAGCCAA--AGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCGAAG--AATCAGATCTTATCTCCCTGAGG
* * * * *
37907 TTACAGCGGAGCAAATTGAAG-AT-AGTAATCCTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCGAAGAATCAG--ATCTTATCTCCCTGAGG
* * * *
37951 TTACAATGGAGCGGAT-TAA-AATCAAGGATCTTATCTCCCTGAAG
1 TTACAGTGGAGCAGATCGAAGAATC-A-GATCTTATCTCCCTGAGG
** * * * *
37995 TTACAGCAGAGTAGATC---GCATCAGGTCTTATCTCCCTGGGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* *
38036 TTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* * * *
38082 TTACAGTGGAGCAGATTGAAGCCA-GAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCGAAG-AATCAGATCTTATCTCCCTGAGG
* * *
38126 TTACAGTGGAGCAGATTGAAG-AT-AGAAATCCTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCGAAGAATCAG--ATCTTATCTCCCTGAGG
* * * *
38170 TTACAGTGGAGCGGAT-TAA-AATCAAGGATCTTATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAATC-A-GATCTTATCTCCCTGAGG
** * * * *
38214 TTACAGCAGAGTAGATC--A-CATCAGGTCTTATCTCCTTGAGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* * * *
38255 TTGCAGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCT-AAG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* * ** * * *
38298 -TAGTAGTAGAGCAGAT-GAA-TTTCAGA-CTTACCCCCCTGAGA
1 TTA-CAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* * *
38339 TTACAGCGGAGCAGATCCAAG-A-CACTATCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCGAAGAATCA-GATCTTATCTCCCTGAGG
* *
38382 TTACAGTGGAGCAGATTGAAGCCAA--AGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCGAAG--AATCAGATCTTATCTCCCTGAGG
* * * * * * *
38426 TTACAGCGGAGTAGATTGAAG-CT-AGTAATCCTATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAATCAG--ATCTTATCTCCCTGAGG
* * * * * * *
38470 TTACAGTAGAGCGGAT-TAA-AATAAAGGATCTCATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAAT-CA-GATCTTATCTCCCTGAGG
* * * *
38514 TTACAGTAGAGCAGATC---GCATCAGGTCTTATC-CCCTAAGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* *
38554 TTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* * * *
38600 TTACAGTGGAGCAGAT-GAAAGAAATTA-ATCATATCTTCCTGAAG
1 TTACAGTGGAGCAGATCG-AAG-AATCAGATCTTATCTCCCTGAGG
* ** * * *
38644 TTGCAGTGGAGTGGAT-TAA-AATCACAGATCTTATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAAT--CAGATCTTATCTCCCTGAGG
* * * * *
38688 TTACACTAGAGTAGATC---GCATCAGGTCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
* * * *
38729 TTACAGTGGAGCAGA-CGAAAGAAATTA-ATCCTATCTTCCTGAAG
1 TTACAGTGGAGCAGATCG-AAG-AATCAGATCTTATCTCCCTGAGG
* * * * * * *
38773 TTGCAGTGGAGCGGAT-TAA-AACCACAGATCTTATTTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* * * * *
38817 TTGCAGTAGAGCAGATC--A-CATCTAG-TCTTATCTTCCTGAAG
1 TTACAGTGGAGCAGATCGAAGAATC-AGATCTTATCTCCCTGAGG
* * * * *
38858 TTGCAGTGGAGCAGA-CGAAAGAAACAAATCCTATCTCCCTGAAG
1 TTACAGTGGAGCAGATCG-AAGAATCAGATCTTATCTCCCTGAGG
* * * * * * * *
38902 TTATAGTAGAACGGAT-TAA-AACCACAGATCTTATCTCTCTGAAG
1 TTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCCTGAGG
* * * * *
38946 TTGCAGTAGAGCAGTTC--A-CATCCAG-TCTTATCTCCCTGAAG
1 TTACAGTGGAGCAGATCGAAGAAT-CAGATCTTATCTCCCTGAGG
* * * * *
38987 TTGCAGTGGAGCAGA-CTG-AGTAAGCAGGTCTTATCCCCCTGAAG
1 TTACAGTGGAGCAGATC-GAAG-AATCAGATCTTATCTCCCTGAGG
* * *
39031 TTGCAG-GG-GCCAGA-CTGAAG-ATGGCAAACCTTATCTCCCTGAGG
1 TTACAGTGGAG-CAGATC-GAAGAAT--CAGATCTTATCTCCCTGAGG
*
39075 TTGCAGTGGAGCAGAT
1 TTACAGTGGAGCAGAT
39091 TAAAGCCGAT
Statistics
Matches: 1201, Mismatches: 260, Indels: 231
0.71 0.15 0.14
Matches are distributed among these distances:
40 31 0.03
41 226 0.19
42 37 0.03
43 117 0.10
44 617 0.51
45 28 0.02
46 139 0.12
47 4 0.00
48 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCCTGAGG
Found at i:37883 original size:219 final size:219
Alignment explanation
Indices: 37467--38441 Score: 1384
Period size: 219 Copynumber: 4.5 Consensus size: 219
37457 GATCTTACTA
* * *
37467 AGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT
1 AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATT
*
37530 AAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCACTG
65 AAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCACTG
* *
37595 AGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGTTTACAGTGGAGCAAAT
130 AGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT
37660 TGAAGCCAGAGATCTTATCTCCCTG
195 TGAAGCCAGAGATCTTATCTCCCTG
* * * *
37685 ATATTACAGCGGAGCAGATTGAAGATAGTAATCATATCTCCCTGATATTATAGTGGAGCGGATTA
1 AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
37750 AAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCACTGA
66 AAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCACTGA
37815 GGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
131 GGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
*
37880 GAAGCCAAAGATCTTATCTCCCTG
196 GAAGCCAGAGATCTTATCTCCCTG
* *
37904 AGATTACAGCGGAGCAAATTGAAGATAGTAATCCTATCTCCCTGAGATTACAATGGAGCGGATTA
1 AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
* * * * * *
37969 AAATCAAGGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGG
66 AAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCACTGA
38034 GGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
131 GGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
38099 GAAGCCAGAGATCTTATCTCCCTG
196 GAAGCCAGAGATCTTATCTCCCTG
* *
38123 AGATTACAGTGGAGCAGATTGAAGATAGAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
1 AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
* *
38188 AAATCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTC-CTTG
66 AAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCAC-TG
* * * * * *
38252 AGGTTGCAGTGGAGCAGACCGAAGAA--ACAGATCTTATCTCCCT-AAG-TAGTAGTAGAGCAGA
130 AGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA-CAGTGGAGCAGA
** * *
38313 -TGAATTTC--AGA-CTTACCCCCCTG
194 TTGAA-GCCAGAGATCTTATCTCCCTG
** * * * * *
38336 AGATTACAGCGGAGCAGATCCAAGACACT-ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTG
1 AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-
*** * * *
38400 AAGCCAAA-GATCTTATCTCCCTG-AGATTACAGCGGAGTAGAT
65 AAAATAAAGGATCTCATCTCTCTGAAG-TTACAGCAGAGTAGAT
38442 TGAAGCTAGT
Statistics
Matches: 695, Mismatches: 55, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
211 2 0.00
212 60 0.09
213 37 0.05
214 3 0.00
215 6 0.01
216 13 0.02
217 16 0.02
218 26 0.04
219 531 0.76
220 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (219 bp):
AGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
AAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCACTGA
GGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
GAAGCCAGAGATCTTATCTCCCTG
Found at i:38413 original size:300 final size:300
Alignment explanation
Indices: 38062--38911 Score: 963
Period size: 300 Copynumber: 2.8 Consensus size: 300
38052 CGAAGAATTT
38062 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGAT
1 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-AGATCTTATCTCCCTGAGAT
*
38127 TACAGTGGAGCAGATTGAAGATAGAAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAA
65 TACAGTGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAA
* *
38191 TCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATCTCCTTGAGGT
129 TCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCC-TGAGGT
*
38256 TGCAGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCT-AAG-TAGTAGTAGAGCAGAT-GAAT
193 TGCAGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCTGAAGTTA-TAGTAGAGCAGATAGAAA
* *
38318 TTCAGA-CTTACCCCCCTG-AGATTACAGCGGAGCAGATCCAAGA-CA
257 TT-A-ATCATACCCCCCTGAAG-TTACAGCGGAGCAGAT-CAAAATCA
*
38363 C-TATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAGATCTTATCTCCCTGAGAT
1 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCC-AAGATCTTATCTCCCTGAGAT
* * * * *
38427 TACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCTCTGAAGTTACAGTAGAGCGGATTAAAAT
65 TACAGTGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT
* * * * * *
38492 AAAGGATCTCATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCCCCTAAGGTTA
130 CAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCCTGAGGTTG
* * * * *
38557 CAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAGA
195 CAGTGGAGCAGACCGAAGAA--ACAGATCTTATCTCCCTGAAGTTATAGTAGAGCAGAT---AGA
* ** * * ** *
38622 AATTAATCATATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATCA
255 AATTAATCATACCCCCCTGAAGTTACAGCGGAGCAGATCAAAATCA
* * * * * * * * * *
38668 CAGATCTTATCTCTCTGAAGTTACACTAGAGTAGATCGCA-TC-AGGTCTTATCTCCCTGAGGTT
1 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAGATCTTATCTCCCTGAGATT
* * * * * *
38731 ACAGTGGAGCAGA-CGAAAGAAATTAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAAC
66 ACAGTGGAGCAGATTG-AAGATAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT
* * *
38795 CACA-GATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATCACATCTA-GTCTTATCTTCCTGAAG
130 CA-AGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATC-AGGTCTTATC-TCCTGAGG
* *
38858 TTGCAGTGGAGCAGA-CGAAAGAAACAAATCCTATCTCCCTGAAGTTATAGTAGA
192 TTGCAGTGGAGCAGACCG-AAGAAACAGATCTTATCTCCCTGAAGTTATAGTAGA
38912 ACGGATTAAA
Statistics
Matches: 461, Mismatches: 69, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
299 25 0.05
300 167 0.36
301 20 0.04
302 39 0.08
303 119 0.26
304 29 0.06
305 25 0.05
306 37 0.08
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (300 bp):
CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAGATCTTATCTCCCTGAGATT
ACAGTGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATC
AAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCCTGAGGTTGC
AGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCTGAAGTTATAGTAGAGCAGATAGAAATTAA
TCATACCCCCCTGAAGTTACAGCGGAGCAGATCAAAATCA
Found at i:38729 original size:129 final size:128
Alignment explanation
Indices: 38579--39002 Score: 614
Period size: 129 Copynumber: 3.3 Consensus size: 128
38569 CCGAAGAATT
* * *
38579 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAGAAATTAATCATATCTTCCTGAAG
1 TCAG-TCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAG
* * * * * *
38644 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACACTAGAGTAGATCGCA
65 TTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
*
38708 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAG
1 TCA-GTCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAG
*
38773 TTGCAGTGGAGCGGATTAAAACCACAGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATCACA
65 TTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
* * ** *
38837 TCTAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACAAATCCTATCTCCCTGAAG
1 TC-AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAG
** * * *
38902 TTATAGTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGTTCACA
65 TTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
*
38966 TCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
1 T-CAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGAC
39003 TGAGTAAGCA
Statistics
Matches: 270, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
129 267 0.99
130 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (128 bp):
TCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAGT
TGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA
Found at i:38815 original size:44 final size:44
Alignment explanation
Indices: 38062--39218 Score: 255
Period size: 44 Copynumber: 26.8 Consensus size: 44
38052 CGAAGAATTT
* * * * *
38062 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * * *
38106 GAGATCTTATCTCCCTG-AGATTACAGTGGAGCAGATTGAAGA-TA
1 CAGATCTTATCTCCCTGAAG-TTGCAGTAGAGCAGATT-AAAACCA
* * * * * * *
38150 GAAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATCA
1 CAGATCTTATCTCCCTGAAG-TTGCAGTAGAGCAGATTAAAACCA
* * * * *
38194 -AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA-T--CA-CA
1 CA-GATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * * **
38234 TCAGGTCTTATCTCCTTGAGGTTGCAGTGGAGCAGACCGAAGAA--A
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTAA-AACCA
* * * ***
38279 CAGATCTTATCTCCCT-AAGTAGTAGTAGAGCAGA-T-GAATTT
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * ** * *
38320 CAGA-CTTACCCCCCTG-AGATTACAGCGGAGCAGATCCAAGA-CA
1 CAGATCTTATCTCCCTGAAG-TTGCAGTAGAGCAGAT-TAAAACCA
* * * * * *
38363 C-TATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * ** * * * *
38406 AAGATCTTATCTCCCTG-AGATTACAGCGGAGTAGATTGAAGCTA
1 CAGATCTTATCTCCCTGAAG-TTGCAGTAGAGCAGATTAAAACCA
* * * * * *
38450 GTA-ATCCTATCTCTCTGAAGTTACAGTAGAGCGGATTAAAA-TA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * *
38493 AAGGATCTCATCTCTCTGAAGTTACAGTAGAGCAGA-T----CGCA
1 CA-GATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC-CA
* * * * ** ***
38534 TCAGGTCTTATC-CCCT-AAGGTTACAGTGGAGTAGACCGAAGAATTT
1 -CAGATCTTATCTCCCTGAA-GTTGCAGTAGAGCAGA-TTAA-AACCA
* * * * *
38580 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAGA-AA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA-ACCA
* * * * ** *
38624 TTA-ATCATATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATCA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * *
38668 CAGATCTTATCTCTCTGAAGTTACACTAGAGTAGA-T----CGCA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC-CA
* * * * ** *
38708 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACGAAAGA-AA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA-ACCA
* * * * *
38753 TTA-ATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * * *
38797 CAGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGA-TCACATC-
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * ** *
38839 TAG-TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA-ACCA
* * ** * *
38882 CAAATCCTATCTCCCTGAAGTTATAGTAGAACGGATTAAAACCA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * *
38926 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG-TTCACATC-
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
* * * *
38968 CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAA--G
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTA-AAACCA
* * * * * ***
39011 CAGGTCTTATCCCCCTGAAGTTGCAG--GGGCCAGACTGAAGATGG
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAG-CAGA-TTAAAACCA
* * * * *
39055 CAAACCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCCGA
1 CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACC-A
* * * **
39100 TA-ATCCTATCTCCCTGAAGTTGCAG-AGGAGCGGATT-AAAGTA
1 CAGATCTTATCTCCCTGAAGTTGCAGTA-GAGCAGATTAAAACCA
* * * * **
39142 GTAGATCGTATCTCTCTGAAGTTGTAGTAGAGTGGA-T----CGCA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC-CA
* *
39183 TCAGGTCTTATCTCCCTGAAGTTGCAGCAGAGCAGA
1 -CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
39219 CTAAGTAAGC
Statistics
Matches: 819, Mismatches: 218, Indels: 155
0.69 0.18 0.13
Matches are distributed among these distances:
39 4 0.00
40 32 0.04
41 160 0.20
42 15 0.02
43 86 0.11
44 468 0.57
45 31 0.04
46 22 0.03
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA
Found at i:39064 original size:129 final size:128
Alignment explanation
Indices: 38584--39090 Score: 399
Period size: 129 Copynumber: 3.9 Consensus size: 128
38574 GAATTTCAGA
* * * ** * ** *
38584 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAGAAATTAATCATATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACG-AAGAAACAAATCCTATCCCCCTGAAGTTACA
* *** * * * * * * * *
38649 GTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACACTAGAGTAGATCGCAT-CAGG
65 GTAGAACAGATGAAAACCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCA-G
* * ** ** *
38713 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACG-AAGAAACAAATCCTATCCCCCTGAAGTTACA
* * * * * * * *
38778 GTGGAGCGGATTAAAACCACAGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATCACATCTAG
65 GTAGAACAGATGAAAACCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
* * *
38842 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACAAATCCTATCTCCCTGAAGTTATA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACG-AAGAAACAAATCCTATCCCCCTGAAGTTACA
* * * * *
38907 GTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGTTCACATCCAG
65 GTAGAACAGATGAAAACCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
* ** * *
38971 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGTAAGCAGGTCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-GAAG-AAACAAATCCTATCCCCCTGAAGTTAC
* ** * *** * * *
39035 AG-GGGCCAGACTGAAGATGGCAAACCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT
64 AGTAGAACAGA-TGAAAACCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
39091 TAAAGCCGAT
Statistics
Matches: 328, Mismatches: 46, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
128 6 0.02
129 320 0.98
130 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAGAAACAAATCCTATCCCCCTGAAGTTACAG
TAGAACAGATGAAAACCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
Found at i:39080 original size:258 final size:257
Alignment explanation
Indices: 38584--39090 Score: 572
Period size: 258 Copynumber: 2.0 Consensus size: 257
38574 GAATTTCAGA
* * ** * *
38584 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAGAAATTAATCATATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAACAAATCATATCTCCCTGAAGTTACA
* ** * * *
38649 GTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACACTAGAGTAGATCGCATCAGGT
66 GTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACACTAGAGCAGATCACATCAGGT
* ** **
38714 CTTATCTCCCTGAGGTTACAGTGGAGCAGACGAAAGAAATTAATCCTATCTTCCTGAAGTTGCAG
131 CTTATCTCCCTGAAGTTACAGTGGAGCAGACG-AAGAAAGCAATCCTATCCCCCTGAAGTTGCAG
* * * * * *
38779 TGGAGCGGATTAAAACCACAGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATCACATCTAG
195 TGGAGCAGATGAAAACCACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCTAG
* * * *
38842 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACAAATCCTATCTCCCTGAAGTTATA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAACAAATCATATCTCCCTGAAGTTACA
* * *
38907 GTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGTTCACATCCA-G
66 GTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACACTAGAGCAGATCACAT-CAGG
* * * *
38971 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGTAAGCAGGTCTTATCCCCCTGAAGTTGC
130 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAC-GAAGAAAGCA-ATCCTATCCCCCTGAAGTTGC
* *** * *
39035 AG-GG-GCCAGACTGAAGATGGCAAACCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT
193 AGTGGAG-CAGA-TGAAAACCACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
39091 TAAAGCCGAT
Statistics
Matches: 204, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
256 1 0.00
257 10 0.05
258 190 0.93
259 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (257 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAAGAAACAAATCATATCTCCCTGAAGTTACA
GTAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACACTAGAGCAGATCACATCAGGT
CTTATCTCCCTGAAGTTACAGTGGAGCAGACGAAGAAAGCAATCCTATCCCCCTGAAGTTGCAGT
GGAGCAGATGAAAACCACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCTAG
Found at i:39108 original size:217 final size:217
Alignment explanation
Indices: 38843--39284 Score: 563
Period size: 217 Copynumber: 2.0 Consensus size: 217
38833 CACATCTAGT
* *
38843 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACAAATCCTATCTCCCTGAAGTTATAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAG-AACAAATCCTATCTCCCTGAAGTTACAG
* *
38908 TA-GAACGGATTAAAACCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGTTCACATCCA-
65 -AGGAACGGATT-AAACCAGCAGATCGTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT-CAG
** * *
38970 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGC
127 GTCTTATCTCCCTGAAGTTGCAGCAGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTAAAGTTGC
39035 AG-GGGCCAGA-CTGAAGATGGCAAAC
192 AGTGGGCCAGATC-GAAGATGGCAAAC
* ** * *
39060 CTTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAG-CCGATAATCCTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAC-A-AATCCTATCTCCCTGAAGTTACA
* ** * * ** *
39124 GAGGAGCGGATTAAAGTAGTAGATCGTATCTCTCTGAAGTTGTAGTAGAGTGGATCGCATCAGGT
64 GAGGAACGGATTAAACCAGCAGATCGTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAGGT
39189 CTTATCTCCCTGAAGTTGCAGCAGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAG
129 CTTATCTCCCTGAAGTTGCAGCAGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAG
** *
39254 TGGGGTAGATCGAAGATGGCAAAT
194 TGGGCCAGATCGAAGATGGCAAAC
39278 CTTATCT
1 CTTATCT
39285 TCCCAATACA
Statistics
Matches: 194, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
215 1 0.01
216 8 0.04
217 159 0.82
218 25 0.13
219 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (217 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAACAAATCCTATCTCCCTGAAGTTACAGA
GGAACGGATTAAACCAGCAGATCGTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAGGTCT
TATCTCCCTGAAGTTGCAGCAGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
GGCCAGATCGAAGATGGCAAAC
Found at i:39265 original size:85 final size:85
Alignment explanation
Indices: 39106--39265 Score: 180
Period size: 85 Copynumber: 1.9 Consensus size: 85
39096 CCGATAATCC
* * * * * * *
39106 TATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAGTAGTAGATCGTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTGCAGAGGAGCAGACTAAAGTAGCAGATCGTATCCCCCTAAAGTTGCAGTA
*
39171 GAGTGGATCGCATCAGGTCT
66 GAGTAGATCGCATCAGGTCT
* *
39191 TATCTCCCTGAAGTTGCAGCA-GAGCAGACT-AAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAG-AGGAGCAGACTAAAGT-AGCAGATCGTATCCCCCTAAAGTTGCAG
* *
39254 TGGGGTAGATCG
64 TAGAGTAGATCG
39266 AAGATGGCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
84 4 0.07
85 56 0.92
86 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGAGGAGCAGACTAAAGTAGCAGATCGTATCCCCCTAAAGTTGCAGTA
GAGTAGATCGCATCAGGTCT
Found at i:40992 original size:3 final size:3
Alignment explanation
Indices: 40986--41038 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
40976 TAATGTTACC
* * * *
40986 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATC AAT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41034 ATT AT
1 ATT AT
41039 ATTTCCATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:41009 original size:15 final size:15
Alignment explanation
Indices: 40989--41038 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
40979 TGTTACCATT
40989 ATTATTATTATTATC
1 ATTATTATTATTATC
41004 ATTATTATTATTATC
1 ATTATTATTATTATC
*
41019 AATATTATTATTATC
1 ATTATTATTATTATC
41034 ATTAT
1 ATTAT
41039 ATTTCCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTATC
Found at i:51402 original size:89 final size:89
Alignment explanation
Indices: 51299--51474 Score: 232
Period size: 89 Copynumber: 2.0 Consensus size: 89
51289 TGTAAAAATT
* * *
51299 CTTCAAACGATTTC-AAAAATTAATTAAGCACT-TTTTTTCTTTTTTGCACTTAATTGGGTACTT
1 CTTCAAACGATTTCAAAAAAATAATTAAAC-CTCTTTTTT-TTTTTTGCACTGAATTGGGTACTT
51362 GAACT-TTCAAAATGAATCAAAAAGGC
64 GAACTGTT-AAAATGAATCAAAAAGGC
** *
51388 CTTCAAACTTTTTCAAAAAAATAATTAAACCTCTTTTTTTTTTTTGCACTGGATTGGGTACTTGA
1 CTTCAAACGATTTCAAAAAAATAATTAAACCTCTTTTTTTTTTTTGCACTGAATTGGGTACTTGA
**
51453 ACTGTTAAAATGCCTCAAAAAG
66 ACTGTTAAAATGAATCAAAAAG
51475 ATCCTTTGAC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
89 55 0.72
90 21 0.28
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (89 bp):
CTTCAAACGATTTCAAAAAAATAATTAAACCTCTTTTTTTTTTTTGCACTGAATTGGGTACTTGA
ACTGTTAAAATGAATCAAAAAGGC
Found at i:51516 original size:26 final size:26
Alignment explanation
Indices: 51487--51542 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
51477 CCTTTGACCG
*
51487 TTAACTTTAGCAGTTGATC-ATTAAAC
1 TTAACTTTAACAGTTGA-CAATTAAAC
*
51513 TTAACTTTAACAGTTGACAATTAAAG
1 TTAACTTTAACAGTTGACAATTAAAC
51539 TTAA
1 TTAA
51543 TTGTCCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
TTAACTTTAACAGTTGACAATTAAAC
Found at i:51644 original size:10 final size:9
Alignment explanation
Indices: 51610--51703 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 9
51600 GGCAAAGAAA
*
51610 TATAAAAAA
1 TATAAAAAT
51619 TA-AAAAAT
1 TATAAAAAT
* *
51627 CAATAAAAGT
1 -TATAAAAAT
51637 TATAAAAAT
1 TATAAAAAT
**
51646 TATTAAATTT
1 TA-TAAAAAT
51656 TAATAAAAA-
1 T-ATAAAAAT
51665 TATTAAAAAT
1 TA-TAAAAAT
51675 TATAAAAATAT
1 TAT-AAAA-AT
51686 ATATAAAAAT
1 -TATAAAAAT
*
51696 TGTAAAAA
1 TATAAAAA
51704 ACCATAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 6 0.09
9 27 0.41
10 23 0.35
11 7 0.11
12 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (9 bp):
TATAAAAAT
Found at i:51645 original size:19 final size:18
Alignment explanation
Indices: 51607--51685 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 18
51597 TGTGGCAAAG
*
51607 AAATA-TAAAAAATA-AA
1 AAATATTAAAAATTATAA
* *
51623 AAATCAATAAAAGTTATAA
1 AAAT-ATTAAAAATTATAA
**
51642 AAATTATTAAATTTTAATAA
1 AAA-TATTAAAAATT-ATAA
51662 AAATATTAAAAATTATAA
1 AAATATTAAAAATTATAA
51680 AAATAT
1 AAATAT
51686 ATATAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.08
17 1 0.02
18 17 0.33
19 21 0.41
20 8 0.16
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (18 bp):
AAATATTAAAAATTATAA
Found at i:51674 original size:21 final size:20
Alignment explanation
Indices: 51620--51704 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
51610 TATAAAAAAT
* *
51620 AAAAAATCAATAAAAGTTAT-
1 AAAAAAT-ATTAAAAATTATA
* *
51640 AAAAATTATT--AAATTTTA
1 AAAAAATATTAAAAATTATA
51658 ATAAAAATATTAAAAATTATA
1 A-AAAAATATTAAAAATTATA
* *
51679 AAAATATATATAAAAATTGTA
1 AAAAAATAT-TAAAAATTATA
51700 AAAAA
1 AAAAA
51705 CCATAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.10
18 1 0.02
19 10 0.20
20 13 0.25
21 22 0.43
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAAATATTAAAAATTATA
Found at i:51693 original size:20 final size:20
Alignment explanation
Indices: 51609--51703 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 20
51599 TGGCAAAGAA
*
51609 ATATAAAA-AATAAAAA-AT
1 ATATAAAATTATAAAAATAT
51627 CA-ATAAAAGTTATAAAAAT-T
1 -ATATAAAA-TTATAAAAATAT
*
51647 AT-TAAATTTTAATAAAAATAT
1 ATATAAA-ATT-ATAAAAATAT
51668 -TA-AAAATTATAAAAATAT
1 ATATAAAATTATAAAAATAT
*
51686 ATATAAAAATTGTAAAAA
1 ATAT-AAAATTATAAAAA
51704 ACCATAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
18 16 0.26
19 12 0.20
20 20 0.33
21 13 0.21
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (20 bp):
ATATAAAATTATAAAAATAT
Found at i:51694 original size:30 final size:29
Alignment explanation
Indices: 51618--51703 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
51608 AATATAAAAA
* *
51618 ATAAAAA-ATCAATAAAAGTTATAAAAATT
1 ATAAAAATAT-AATAAAAATTGTAAAAATT
* * *
51647 ATTAAATTTTAATAAAAATAT-TAAAAATT
1 ATAAAAATATAATAAAAAT-TGTAAAAATT
51676 ATAAAAATATATATAAAAATTGTAAAAA
1 ATAAAAATATA-ATAAAAATTGTAAAAA
51704 ACCATAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 30 0.65
30 16 0.35
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAAAAATATAATAAAAATTGTAAAAATT
Found at i:51711 original size:49 final size:49
Alignment explanation
Indices: 51658--51762 Score: 117
Period size: 49 Copynumber: 2.1 Consensus size: 49
51648 TTAAATTTTA
* * *
51658 ATAAAAATATTAAAA-ATTATAAAAATAT-ATATAAAA-ATTGTAAAAAACC
1 ATAAAAAT-GTAAAATATTATAAAAAAATCATA-AAAATATTATAAAAAA-C
* *
51707 ATAAAAATGTAAAATCTTATAAAAAAATCATAAAAATATTATAAAATAC
1 ATAAAAATGTAAAATATTATAAAAAAATCATAAAAATATTATAAAAAAC
51756 ATAAAAA
1 ATAAAAA
51763 AAAGTCTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
48 5 0.10
49 31 0.65
50 12 0.25
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (49 bp):
ATAAAAATGTAAAATATTATAAAAAAATCATAAAAATATTATAAAAAAC
Found at i:53097 original size:14 final size:14
Alignment explanation
Indices: 53056--53097 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
53046 TATCATTAAA
53056 TTTTATATAAATTT
1 TTTTATATAAATTT
*
53070 TCTTAT-TAATATTT
1 TTTTATATAA-ATTT
53084 TTTTATATAAATTT
1 TTTTATATAAATTT
53098 ATGAAATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATATAAATTT
Found at i:57724 original size:29 final size:30
Alignment explanation
Indices: 57662--57726 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
57652 GAATAGATTG
* *
57662 AAAGATTGAAGATTTGAATTTTGGCTGGAT
1 AAAGATTAAAGATTTGAATATTGGCTGGAT
57692 AAAGATTAAAGATTTGAA-ATTGGCTGGAT
1 AAAGATTAAAGATTTGAATATTGGCTGGAT
57721 AAAGAT
1 AAAGAT
57727 CAAATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAGATTAAAGATTTGAATATTGGCTGGAT
Found at i:58894 original size:22 final size:22
Alignment explanation
Indices: 58859--58900 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
58849 TTTCTTGGGT
58859 TTTTGGGGTCTTTTGGTTAATA
1 TTTTGGGGTCTTTTGGTTAATA
58881 TTTTGAGGGT-TTTTGGTTAA
1 TTTTG-GGGTCTTTTGGTTAA
58901 AGTTAGCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.14, C:0.02, G:0.29, T:0.55
Consensus pattern (22 bp):
TTTTGGGGTCTTTTGGTTAATA
Found at i:59661 original size:18 final size:18
Alignment explanation
Indices: 59624--59669 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
59614 ATGTATACGC
*
59624 ATACATATATTTTAGTAT
1 ATACATATATTCTAGTAT
59642 ATACATATATTCTA-TAAT
1 ATACATATATTCTAGT-AT
*
59660 ATATATATAT
1 ATACATATAT
59670 ACACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (18 bp):
ATACATATATTCTAGTAT
Found at i:59662 original size:20 final size:18
Alignment explanation
Indices: 59624--59670 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
59614 ATGTATACGC
*
59624 ATACATATATTTTAGTAT
1 ATACATATATTTTAATAT
59642 ATACATATATTCTATAATAT
1 ATACATATATT-T-TAATAT
*
59662 ATATATATA
1 ATACATATA
59671 CACATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 13 0.52
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (18 bp):
ATACATATATTTTAATAT
Found at i:59730 original size:30 final size:30
Alignment explanation
Indices: 59696--59755 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
59686 TATAAAAAAA
59696 AACTA-CCTATATATATACATATATTTTTAT
1 AACTATCC-ATATATATACATATATTTTTAT
*
59726 AACTATGCATATATATACATATATTTTTAT
1 AACTATCCATATATATACATATATTTTTAT
59756 TTTCATAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (30 bp):
AACTATCCATATATATACATATATTTTTAT
Found at i:63393 original size:25 final size:25
Alignment explanation
Indices: 63315--63433 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
63305 GAAGAGTTAT
* *
63315 TATCAGGAAGCTC-CGAATAGCCATA
1 TATCAGGAAGCTCACAAAGAGCC-TA
* * ** *
63340 TAACAGGAAGTTCA-AGCGAACC-A
1 TATCAGGAAGCTCACAAAGAGCCTA
63363 TATCAGGAAGCTCACAAAGAGCCTA
1 TATCAGGAAGCTCACAAAGAGCCTA
* *
63388 TATCAGGACGCTCACAAAGAGCCTT
1 TATCAGGAAGCTCACAAAGAGCCTA
* *
63413 TATCAGGACGCTCATAAAGAG
1 TATCAGGAAGCTCACAAAGAG
63434 TTGCGGTATG
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
23 13 0.17
24 5 0.07
25 58 0.76
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (25 bp):
TATCAGGAAGCTCACAAAGAGCCTA
Found at i:67311 original size:14 final size:16
Alignment explanation
Indices: 67292--67335 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
67282 GGCAACCCAT
67292 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
67306 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
*
67322 ATTCAGTTTAATTT
1 ATTTA-TTTAATTT
67336 ATGTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:69810 original size:115 final size:111
Alignment explanation
Indices: 69580--69947 Score: 463
Period size: 114 Copynumber: 3.3 Consensus size: 111
69570 TAATCATTCC
* * *
69580 CGGCGTTTTTGAGAAAGCGCCGCAAAAAACCT-AGCGCAACGACGCCGTTTCCCCAGCATTCGGT
1 CGGCGTTTTTG-GAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTCCCGAGCTTTCGG-
* *
69644 GATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATGCTCAAGGCTTTAG
64 GATTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
* * * *
69692 CGGCGTTTCTAGGAAAGCGCCGCAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCAG
1 CGGCGTTT-TTGGAAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTCCCGAGCTTTC-G
* *
69757 GGATTTAGCGGCGCTTTTACAGAAAGCGCCGCTAATGCTGAAGTCTTTAG
63 GGATTTAGCGGCG-TTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
* * *
69807 CGGCGTTTTTGTTAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTG-GCTTTCGGG
1 CGGCGTTTTTG-GAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTCCCGAGCTTTC-GG
*** *
69871 GATTTTAGCGGCGTTTTTGTTAAAGCGCCGCTAATGTTC-AGTCTTTAG
64 GA-TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
69919 CGGCGTTTTTTGGAAAGCGCCGCAAAAAA
1 CGGCG-TTTTTGGAAAGCGCCGCAAAAAA
69948 AANNNNNNNN
Statistics
Matches: 222, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
112 54 0.24
113 41 0.18
114 70 0.32
115 57 0.26
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (111 bp):
CGGCGTTTTTGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTCCCGAGCTTTCGGGA
TTTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
Found at i:82271 original size:43 final size:43
Alignment explanation
Indices: 82203--82302 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
82193 NNNNNNNNNN
* * *
82203 AAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTTACTAA
1 AAACGCCGCTAAAGACCCAGATCTATAGCGGCGCTTATACTAA
82246 AAACGCCGCTAAAGACCCCAG-TCTATAGCGGCGCTTATACTAA
1 AAACGCCGCTAAAGA-CCCAGATCTATAGCGGCGCTTATACTAA
82289 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
82303 GTATTAGTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
43 49 0.92
44 4 0.08
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCAGATCTATAGCGGCGCTTATACTAA
Found at i:82319 original size:43 final size:43
Alignment explanation
Indices: 82229--82368 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 43
82219 CCTGATCTAT
* * **
82229 AGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCCCAGTCTAT-
1 AGCGGCGCTTATACTAAAAACGCCGCTAAAGATCTTAGTCT-TC
* *
82272 AGCGGCGCTTATACTAAAAACGCCGCTAAAGGTATTAGTCTTC
1 AGCGGCGCTTATACTAAAAACGCCGCTAAAGATCTTAGTCTTC
* * * * *
82315 AGCGGCGCTTCTACT-AAAGCGCCACTAAAGCTCTTACTCTTC
1 AGCGGCGCTTATACTAAAAACGCCGCTAAAGATCTTAGTCTTC
*
82357 AGCGGCGTTTAT
1 AGCGGCGCTTAT
82369 GATAGAAGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 33 0.40
43 49 0.60
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (43 bp):
AGCGGCGCTTATACTAAAAACGCCGCTAAAGATCTTAGTCTTC
Found at i:82497 original size:22 final size:22
Alignment explanation
Indices: 82469--82511 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
82459 CTGCGGCGCT
*
82469 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
82491 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
82512 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:94290 original size:2 final size:2
Alignment explanation
Indices: 94283--94311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
94273 CATCATCATC
94283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94312 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94316 original size:2 final size:2
Alignment explanation
Indices: 94311--94339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
94301 ATATATATAT
94311 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
94340 AAAGGCCCTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:101434 original size:2 final size:2
Alignment explanation
Indices: 101427--101454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
101417 AATTTCAATC
101427 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
101455 TGTGGAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103724 original size:20 final size:22
Alignment explanation
Indices: 103696--103735 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
103686 TTTAATTGAA
103696 AATTC-AAAAATAAA-ATAATT
1 AATTCAAAAAATAAATATAATT
*
103716 AATTGAAAAAATAAATATAA
1 AATTCAAAAAATAAATATAA
103736 AAACATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (22 bp):
AATTCAAAAAATAAATATAATT
Found at i:112354 original size:44 final size:44
Alignment explanation
Indices: 112294--112974 Score: 453
Period size: 44 Copynumber: 15.8 Consensus size: 44
112284 TAGTGGTCGG
* * *
112294 GATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * ***
112338 GATTTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
112379 G-TATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* **
112423 G-TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGATTGAAGATAACA
1 GATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATT-AAAATCTCA
* ** **
112467 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
112511 AATCCTATCACCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * **
112555 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATT-GTATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * **
112596 G-TCTTATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
** * ***
112639 GATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-TCGCATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * * * *
112680 G-TATTATCTCCCTGGATTTGCAGTGGAGCAGACTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* * * **
112724 G-TCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA
1 GATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAATCTCA
* * *
112768 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGGCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TCA
* *
112813 -AT-TCTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAATCTCA
1 GATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * ***
112856 GATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGTATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * *
112897 G-TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGGAA--GCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* * *
112940 AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGATT
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
112975 GAAGCACTAG
Statistics
Matches: 488, Mismatches: 113, Indels: 72
0.73 0.17 0.11
Matches are distributed among these distances:
40 76 0.16
41 35 0.07
42 26 0.05
43 35 0.07
44 248 0.51
45 64 0.13
46 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
Found at i:112440 original size:84 final size:87
Alignment explanation
Indices: 112299--112504 Score: 208
Period size: 84 Copynumber: 2.4 Consensus size: 87
112289 GTCGGGATCC
* * * * * *
112299 TATCTCCCTGAAGTTGCAGTGGAACGGATTAAAATCTCAGATTTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCTAAGATCTTATCTCTCTGAAGTTGCAGAG
* *
112364 A-GCAGATCG-CAT-CTAGTAT
66 AGGCAGATCGACATACAAATAT
112383 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAG-TCTTATC-CTCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAGCTAAGATCTTATCTCT-CTGAAGTTGCA
* * * *
112445 GTGAGGCAGATTGAAGATAACAAATCT
63 GAGAGGCAGATCG-ACAT-ACAAATAT
*
112472 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA
112505 GCCGAAAATC
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
83 2 0.02
84 49 0.49
85 9 0.09
86 3 0.03
87 3 0.03
89 35 0.35
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (87 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCTAAGATCTTATCTCTCTGAAGTTGCAGAG
AGGCAGATCGACATACAAATAT
Found at i:112704 original size:84 final size:84
Alignment explanation
Indices: 112516--112693 Score: 275
Period size: 84 Copynumber: 2.1 Consensus size: 84
112506 CCGAAAATCC
* * * **
112516 TATCACCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
* * *
112581 AGCAGATTGTATCTAGTCT
66 AGCAGATCGCATCTAGTAT
*
112600 TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTTTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
112665 AGCAGATCGCATCTAGTAT
66 AGCAGATCGCATCTAGTAT
112684 TATCTCCCTG
1 TATCTCCCTG
112694 GATTTGCAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (84 bp):
TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTAT
Found at i:112729 original size:84 final size:84
Alignment explanation
Indices: 112516--112746 Score: 232
Period size: 84 Copynumber: 2.8 Consensus size: 84
112506 CCGAAAATCC
* * * * * * * *
112516 TATCACCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTGGCAGTGCAGCAGACTAAAAGCTAAGATCTTATCTTTCTGAAGTTGCAGAG
* * *
112581 AGCAGATTGTATCTAGTCT
66 AGCAGATCGCATCTAGTAT
** * * *
112600 TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTTTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTGGCAGTGCAGCAGACTAAAAGCTAAGATCTTATCTTTCTGAAGTTGCAGAG
112665 AGCAGATCGCATCTAGTAT
66 AGCAGATCGCATCTAGTAT
* * * * * *
112684 TATCTCCCTGGATTTGCAGTGGAGCAGACTAAGTAAGC-AAG-TCTTATCCTCCTGAAGTTGCAG
1 TATCTCCCTGAAGTGGCAGTGCAGCAGACTAA--AAGCTAAGATCTTATCTTTCTGAAGTTGCAG
112747 TGGGGCAGAC
Statistics
Matches: 125, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 120 0.96
85 2 0.02
86 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (84 bp):
TATCTCCCTGAAGTGGCAGTGCAGCAGACTAAAAGCTAAGATCTTATCTTTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTAT
Found at i:112841 original size:301 final size:301
Alignment explanation
Indices: 112299--112921 Score: 1039
Period size: 301 Copynumber: 2.1 Consensus size: 301
112289 GTCGGGATCC
* *
112299 TATCTCCCTGAAGTTGCAGTGGAACGGATTAAAATCTCAGATTTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGCAACGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
112364 AGCAGATCGCATCTAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCAGATCGCATCTAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
*
112429 TCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGG
131 TCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGG
*
112494 AGCAGATTAAAGCCGAAAATCCTATCACCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATC
196 AGCAGATTAAAGCCGAAAATCCTATCACCCTAAAGTTGCAGTGGAGCGGATTAAAATCTCAGATC
* *
112559 TTATCTCTCTGAAGTTGCAGAGAGCAGATTGTATCTAGTCT
261 TTATCTCTCTGAAGTTACAGAGAGCAGATCGTATCTAGTCT
* *** *
112600 TATCTCCCTGAAGTGGCAGTGCAGTTGATTAAAATCTCAGATCTTATCTTTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGCAACGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
* *
112665 AGCAGATCGCATCTAGTATTATCTCCCTGGATTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCAGATCGCATCTAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
* **
112730 TCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGG
131 TCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGG
* ** * * *
112795 AGCAGATTAAAGTCGGCAATTCTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAATCTCAGATC
196 AGCAGATTAAAGCCGAAAATCCTATCACCCTAAAGTTGCAGTGGAGCGGATTAAAATCTCAGATC
112860 TTATCTCTCTGAAGTTACAGAGAGCAGATCGTATCTAGTCT
261 TTATCTCTCTGAAGTTACAGAGAGCAGATCGTATCTAGTCT
*
112901 TATCTACCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTG
112922 GAGCAGACTA
Statistics
Matches: 298, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
301 298 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (301 bp):
TATCTCCCTGAAGTTGCAGTGCAACGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
TCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGG
AGCAGATTAAAGCCGAAAATCCTATCACCCTAAAGTTGCAGTGGAGCGGATTAAAATCTCAGATC
TTATCTCTCTGAAGTTACAGAGAGCAGATCGTATCTAGTCT
Found at i:115023 original size:98 final size:97
Alignment explanation
Indices: 114876--115129 Score: 445
Period size: 98 Copynumber: 2.6 Consensus size: 97
114866 CACGTTGTGT
* *
114876 CCTAACGTATTGGATGTGACGTTCTTAAATCTTGGATGAGTGGATGTTCTTTTAAAGTAAAGGAA
1 CCTAACGTATTGGGTGTGA--TTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAGGAA
114941 ATATTCCGAGTTTGGGATTTTAGTGGAATCGTGC
64 ATATTCCGAGTTTGGGATTTTAGTGGAATCGTGC
*
114975 CCTAACGTATTGGGTGTGATTCCTTAAATCTTTGATAAGTGGATGTTCTTTTAAAGTAAAGGAAA
1 CCTAACGTATTGGGTGTGATT-CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAGGAAA
115040 TATTCCGAGTTTGGGATTTTAGTGGAATCGTGC
65 TATTCCGAGTTTGGGATTTTAGTGGAATCGTGC
115073 CCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGT
1 CCTAACGTATTGGGTGTGA-TTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGT
115130 TTTATTGCAC
Statistics
Matches: 149, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
97 2 0.01
98 127 0.85
99 20 0.13
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (97 bp):
CCTAACGTATTGGGTGTGATTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAGGAAAT
ATTCCGAGTTTGGGATTTTAGTGGAATCGTGC
Found at i:115642 original size:43 final size:43
Alignment explanation
Indices: 115595--115827 Score: 213
Period size: 43 Copynumber: 5.4 Consensus size: 43
115585 TCGATACTGC
* * *
115595 TGTCCCAGACACGGTCTTATATGAAATCATATAATAATGCCAA
1 TGTCCCAGACATGGTCTTATACGTAATCATATAATAATGCCAA
* * *
115638 TGTCCCAAACATGGTCTTATACGTAATCACA-ATACAATGCCAA
1 TGTCCCAGACATGGTCTTATACGTAATCATATA-ATAATGCCAA
* * * * * * * *
115681 TGTCCTAGACATTGTCTTACATGTTATCACAT-ATCGATGCCAC
1 TGTCCCAGACATGGTCTTATACGTAATCATATAAT-AATGCCAA
* ** * *
115724 TGTCCCAGACAGGGTCTTATACAAAATCATATAATGATGCAAA
1 TGTCCCAGACATGGTCTTATACGTAATCATATAATAATGCCAA
*
115767 TGT-CCAGACATGGTCTTATACGTAATCATAGT-ACAATGCCAA
1 TGTCCCAGACATGGTCTTATACGTAATCATA-TAATAATGCCAA
* *
115809 TGTTCTAGACATGGTCTTA
1 TGTCCCAGACATGGTCTTA
115828 CATGTTATCA
Statistics
Matches: 151, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
42 36 0.24
43 113 0.75
44 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (43 bp):
TGTCCCAGACATGGTCTTATACGTAATCATATAATAATGCCAA
Found at i:115757 original size:129 final size:128
Alignment explanation
Indices: 115527--115844 Score: 483
Period size: 129 Copynumber: 2.5 Consensus size: 128
115517 TGGTTTCGAC
* * *
115527 ATACGTAATCACAGTACAATGTCAATGTCCCAGACATGGTTTTACATGTTATCACATATCGATAC
1 ATACGTAATCACAGTACAATGCCAATGTCCTAGACATGGTCTTACATGTTATCACATATCGATAC
** ** *
115592 TGCTGTCCCAGACACGGTCTTATATGAAATCATATAATAATGCCAATGTCCCAAACATGGTCTT
66 CACTGTCCCAGACACGGTCTTATACAAAATCATATAATAATGCAAATGT-CCAAACATGGTCTT
* * *
115656 ATACGTAATCACAATACAATGCCAATGTCCTAGACATTGTCTTACATGTTATCACATATCGATGC
1 ATACGTAATCACAGTACAATGCCAATGTCCTAGACATGGTCTTACATGTTATCACATATCGATAC
* * *
115721 CACTGTCCCAGACAGGGTCTTATACAAAATCATATAATGATGCAAATGTCCAGACATGGTCTT
66 CACTGTCCCAGACACGGTCTTATACAAAATCATATAATAATGCAAATGTCCAAACATGGTCTT
* *
115784 ATACGTAATCATAGTACAATGCCAATGTTCTAGACATGGTCTTACATGTTATCACATATCG
1 ATACGTAATCACAGTACAATGCCAATGTCCTAGACATGGTCTTACATGTTATCACATATCG
115845 GTAACCCTAA
Statistics
Matches: 171, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 70 0.41
129 101 0.59
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (128 bp):
ATACGTAATCACAGTACAATGCCAATGTCCTAGACATGGTCTTACATGTTATCACATATCGATAC
CACTGTCCCAGACACGGTCTTATACAAAATCATATAATAATGCAAATGTCCAAACATGGTCTT
Found at i:118680 original size:21 final size:21
Alignment explanation
Indices: 118654--118697 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
118644 CAAAGTGGGC
**
118654 GGTCAACACGCTTGTGTGAGA
1 GGTCAACACGCCCGTGTGAGA
*
118675 GGTCAACATGCCCGTGTGAGA
1 GGTCAACACGCCCGTGTGAGA
118696 GG
1 GG
118698 AGGCACACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.20
Consensus pattern (21 bp):
GGTCAACACGCCCGTGTGAGA
Found at i:118735 original size:21 final size:21
Alignment explanation
Indices: 118684--118736 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
118674 AGGTCAACAT
118684 GCCCGTGTGAGAGGAGGCACAC
1 GCCCGTGTG-GAGGAGGCACAC
* * * *
118706 ACCCATGTGGATGAGGCATAC
1 GCCCGTGTGGAGGAGGCACAC
118727 GCCCGTGTGG
1 GCCCGTGTGG
118737 GCCAGGGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (21 bp):
GCCCGTGTGGAGGAGGCACAC
Found at i:120864 original size:20 final size:20
Alignment explanation
Indices: 120819--120875 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
120809 TTAAAAATTT
*
120819 ATATTTTTTA-AA-TATTAA
1 ATATTTTTTATAATTTTTAA
120837 ATATTTTTTTATAATTTTTAA
1 ATA-TTTTTTATAATTTTTAA
* *
120858 ATATTTTTAATGATTTTT
1 ATATTTTTTATAATTTTT
120876 TGACTGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 15 0.45
21 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATTTTTTATAATTTTTAA
Found at i:121089 original size:28 final size:28
Alignment explanation
Indices: 121057--121110 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
121047 ATAACAGTGC
121057 AAAGTTTAAGTA-CAAAATGAGCAAAAAA
1 AAAGTTTAAGTACCAAAATGAG-AAAAAA
*
121085 AAAGTTTAAGTACCAAAGTGAGAAAA
1 AAAGTTTAAGTACCAAAATGAGAAAA
121111 TTAGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (28 bp):
AAAGTTTAAGTACCAAAATGAGAAAAAA
Found at i:121582 original size:21 final size:19
Alignment explanation
Indices: 121544--121585 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
121534 TATTATTATG
*
121544 TTAAAAATATTTTAATTTT
1 TTAAAAATATTGTAATTTT
121563 TTAAAAATATTAAGTAATTTT
1 TTAAAAATATT--GTAATTTT
121584 TT
1 TT
121586 TATGTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAAAAATATTGTAATTTT
Found at i:122152 original size:13 final size:13
Alignment explanation
Indices: 122134--122158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
122124 TAACATATTT
122134 ATTAATTAAAAAC
1 ATTAATTAAAAAC
122147 ATTAATTAAAAA
1 ATTAATTAAAAA
122159 TAATAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:129407 original size:1 final size:1
Alignment explanation
Indices: 129403--129430 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
129393 ATAAAAAATT
129403 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
129431 CCCAGTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:129468 original size:1 final size:1
Alignment explanation
Indices: 129464--129501 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
129454 AAAGGCCCCC
129464 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
129502 GCATACCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:130759 original size:11 final size:11
Alignment explanation
Indices: 130739--130775 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
130729 GGTCCGGCCC
*
130739 ATATTAAATAT
1 ATATTTAATAT
130750 ATATTTAATAT
1 ATATTTAATAT
130761 ATA--TAATAT
1 ATATTTAATAT
130770 ATATTT
1 ATATTT
130776 GATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:130797 original size:25 final size:25
Alignment explanation
Indices: 130765--130825 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
130755 TAATATATAT
130765 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
130790 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
*
130815 TATATATATTT
1 AATATATATTT
130826 AATATGGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AATATATATTTGATTAAAAATAAAA
Found at i:131076 original size:31 final size:32
Alignment explanation
Indices: 131038--131110 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
131028 NNNNNNNNNN
131038 ATTTTTAAAAAAATTTTAAAATAATTTTTTT-
1 ATTTTTAAAAAAATTTTAAAATAATTTTTTTA
* * *
131069 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAAAAATTTTAAAATAATTTTTTTA
131101 ATTTTCTAAA
1 ATTTT-TAAA
131111 TTTTTTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 28 0.76
32 5 0.14
33 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
ATTTTTAAAAAAATTTTAAAATAATTTTTTTA
Found at i:131082 original size:11 final size:11
Alignment explanation
Indices: 131038--131097 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
131028 NNNNNNNNNN
*
131038 ATTTTTAAAAA
1 ATTTTTAAAAT
*
131049 AATTTTAAAAT
1 ATTTTTAAAAT
*
131060 AATTTTT---TT
1 -ATTTTTAAAAT
131069 ATTTTTAAAAT
1 ATTTTTAAAAT
131080 ATTTTTAAAAT
1 ATTTTTAAAAT
131091 ACTTTTT
1 A-TTTTT
131098 TTAATTTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.15
9 1 0.03
11 22 0.56
12 10 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:131729 original size:18 final size:20
Alignment explanation
Indices: 131691--131754 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 20
131681 TATTAAATAT
131691 ATATATATTTAATATATAAA
1 ATATATATTTAATATATAAA
* *
131711 ATATATATTTGATTAAAAATAAAAA
1 ATATATA--T--TT-AATATATAAA
131736 ATATATATTTAATATATAA
1 ATATATATTTAATATATAA
131755 TTCGGGCCGG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
20 14 0.40
21 2 0.06
22 1 0.03
23 1 0.03
24 2 0.06
25 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATATATTTAATATATAAA
Found at i:131742 original size:25 final size:24
Alignment explanation
Indices: 131685--131746 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
131675 AACCCATATT
* * * *
131685 AAATATATATATATTTAATATATA
1 AAATATATATTTATTAAAAATAAA
131709 AAATATATATTTGATTAAAAATAAA
1 AAATATATATTT-ATTAAAAATAAA
131734 AAATATATATTTA
1 AAATATATATTTA
131747 ATATATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AAATATATATTTATTAAAAATAAA
Found at i:140773 original size:29 final size:30
Alignment explanation
Indices: 140726--140804 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
140716 AAAGTAAAAA
** * *
140726 TTAATAAAAGTTATGAAAATTA-TTAGATT
1 TTAATAAAAAATATAAAAAGTATTTAGATT
*
140755 TTAATAAAAAATATAAAAAGTATTTATATT
1 TTAATAAAAAATATAAAAAGTATTTAGATT
*
140785 TTATTTAAAAAATTATAAAA
1 TTA-ATAAAAAA-TATAAAA
140805 TACATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.44
30 9 0.22
31 7 0.17
32 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (30 bp):
TTAATAAAAAATATAAAAAGTATTTAGATT
Found at i:141009 original size:10 final size:10
Alignment explanation
Indices: 140990--141113 Score: 59
Period size: 10 Copynumber: 12.9 Consensus size: 10
140980 TTTTAGTACG
140990 ATAA-TTTTT
1 ATAATTTTTT
140999 ATAATTTTTT
1 ATAATTTTTT
*
141009 ACGAA--TTTT
1 A-TAATTTTTT
141018 AT-ATTTCTTT
1 ATAATTT-TTT
*
141028 GT-A-TTTTT
1 ATAATTTTTT
141036 ATAATTTTTT
1 ATAATTTTTT
* *
141046 ATGA--CTTT
1 ATAATTTTTT
**
141054 ATAAAATTTT
1 ATAATTTTTT
141064 ATAATTTTTT
1 ATAATTTTTT
***
141074 GCGA-TTTTT
1 ATAATTTTTT
*
141083 ATAATTTTTA
1 ATAATTTTTT
141093 ATAAATTTTTTT
1 AT-AA-TTTTTT
141105 ATAATTTTT
1 ATAATTTTT
141114 ATTTAAATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 23
0.67 0.14 0.18
Matches are distributed among these distances:
7 1 0.01
8 10 0.12
9 19 0.22
10 42 0.49
11 6 0.07
12 7 0.08
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:141071 original size:37 final size:36
Alignment explanation
Indices: 140990--141072 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
140980 TTTTAGTACG
*
140990 ATAATTTTTATAATTTTTTACGAATTTTATATTTCT
1 ATAATTTTTATAATTTTTTACGAATTTTAAATTTCT
* * * *
141026 TTGTATTTTTATAATTTTTTATGACTTTATAAAATTT-T
1 AT-AATTTTTATAATTTTTTACGAATTT-T-AAATTTCT
141064 ATAATTTTT
1 ATAATTTTT
141073 TGCGATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
36 1 0.03
37 28 0.76
38 3 0.08
39 5 0.14
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (36 bp):
ATAATTTTTATAATTTTTTACGAATTTTAAATTTCT
Found at i:141091 original size:28 final size:28
Alignment explanation
Indices: 141030--141103 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
141020 ATTTCTTTGT
*
141030 ATTTTTATAATTTTTTATGACTTTATAA
1 ATTTTTATAATTTTTTACGACTTTATAA
* * *
141058 AATTTTATAATTTTTTGCGA-TTTTTATA
1 ATTTTTATAATTTTTTACGACTTTATA-A
141086 ATTTTTAATAAATTTTTT
1 ATTTTT-AT-AATTTTTT
141104 TATAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 5 0.13
28 23 0.61
29 2 0.05
30 8 0.21
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (28 bp):
ATTTTTATAATTTTTTACGACTTTATAA
Found at i:141099 original size:11 final size:9
Alignment explanation
Indices: 140990--141115 Score: 62
Period size: 9 Copynumber: 13.2 Consensus size: 9
140980 TTTTAGTACG
140990 ATAATTTTT
1 ATAATTTTT
140999 ATAATTTTT
1 ATAATTTTT
*
141008 -TACGAATTTT
1 ATA--ATTTTT
*
141018 ATATTTCTTT
1 ATAATT-TTT
*
141028 GT-ATTTTT
1 ATAATTTTT
141036 ATAATTTTTT
1 ATAA-TTTTT
* *
141046 ATGA-CTTT
1 ATAATTTTT
*
141054 ATAAAATTTT
1 AT-AATTTTT
141064 ATAATTTTT
1 ATAATTTTT
*
141073 -TGCGATTTTT
1 AT--AATTTTT
141083 ATAATTTTT
1 ATAATTTTT
141092 AATAAATTTTTTT
1 -AT-AA--TTTTT
141105 ATAATTTTT
1 ATAATTTTT
141114 AT
1 AT
141116 TTAAATTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
8 12 0.13
9 33 0.37
10 30 0.34
11 7 0.08
12 2 0.02
13 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:141106 original size:22 final size:23
Alignment explanation
Indices: 141078--141123 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
141068 TTTTTTGCGA
141078 TTTTTATAATTTTTA-ATAAATT
1 TTTTTATAATTTTTATATAAATT
*
141100 TTTTTATAATTTTTATTTAAATT
1 TTTTTATAATTTTTATATAAATT
141123 T
1 T
141124 AATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTATAATTTTTATATAAATT
Found at i:188049 original size:12 final size:12
Alignment explanation
Indices: 188032--188056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
188022 CTATATCATC
188032 AAAAAAATTAAA
1 AAAAAAATTAAA
188044 AAAAAAATTAAA
1 AAAAAAATTAAA
188056 A
1 A
188057 TGTCAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:190619 original size:75 final size:76
Alignment explanation
Indices: 190534--190685 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 76
190524 TTTTATAAAT
190534 AAGTATATTATAGCACTTTGTCATTTTATAACACGTAAATTATTTTTATAATATACTTTTTGGTC
1 AAGTATATTATAGCACTTTGTCATTTTATAACACGTAAATTATTTTTATAATATACTTTTTGGTC
190599 -TAAATTTAGA
66 ATAAATTTAGA
190609 AAGTATATTATAGCACTTTGTCATTTTATAACACGTAAATTATTTTTATAATATACTTTTTGGTC
1 AAGTATATTATAGCACTTTGTCATTTTATAACACGTAAATTATTTTTATAATATACTTTTTGGTC
190674 ATAAATTTAGA
66 ATAAATTTAGA
190685 A
1 A
190686 TTTTTTAGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 65 0.86
76 11 0.14
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (76 bp):
AAGTATATTATAGCACTTTGTCATTTTATAACACGTAAATTATTTTTATAATATACTTTTTGGTC
ATAAATTTAGA
Found at i:193704 original size:45 final size:45
Alignment explanation
Indices: 193655--193745 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
193645 GCCACCGGGA
* * **
193655 TGTGGGTGCACTGCAAAATATCGCAGATAAAATCTGTCACTAGGC
1 TGTGGGTGCACAGCAAAATATCACAGATAAAATCTACCACTAGGC
*
193700 TGTGGGTGTACAGCAAAATATCACAGATAAAATCTACCACTAGGC
1 TGTGGGTGCACAGCAAAATATCACAGATAAAATCTACCACTAGGC
193745 T
1 T
193746 ATAGATGTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
TGTGGGTGCACAGCAAAATATCACAGATAAAATCTACCACTAGGC
Found at i:193755 original size:45 final size:45
Alignment explanation
Indices: 193667--193756 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
193657 TGGGTGCACT
* ** * * *
193667 GCAAAATATCGCAGATAAAATCTGTCACTAGGCTGTGGGTGTACA
1 GCAAAATATCACAGATAAAATCTACCACTAGGCTATAGATGTACA
193712 GCAAAATATCACAGATAAAATCTACCACTAGGCTATAGATGTACA
1 GCAAAATATCACAGATAAAATCTACCACTAGGCTATAGATGTACA
193757 ATATATTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (45 bp):
GCAAAATATCACAGATAAAATCTACCACTAGGCTATAGATGTACA
Found at i:193991 original size:34 final size:34
Alignment explanation
Indices: 193948--194028 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
193938 ATGATACAAT
* * **
193948 TTAATTATGCTTTTAACAGGACAGTACAGTAGCAA
1 TTAA-TATGCTTATAACAGGACAATACAACAGCAA
**
193983 TTAATATGCTTATAACAGTTCAATACAACAGCAA
1 TTAATATGCTTATAACAGGACAATACAACAGCAA
*
194017 ATAATATGCTTA
1 TTAATATGCTTA
194029 AAATAGATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (34 bp):
TTAATATGCTTATAACAGGACAATACAACAGCAA
Found at i:198386 original size:20 final size:21
Alignment explanation
Indices: 198351--198389 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
198341 ATGGTATATA
198351 TAATTAACTAGTTAATCAATT
1 TAATTAACTAGTTAATCAATT
*
198372 TAATTAA-TTGTTAATCAA
1 TAATTAACTAGTTAATCAA
198390 ATGGATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (21 bp):
TAATTAACTAGTTAATCAATT
Found at i:201866 original size:51 final size:52
Alignment explanation
Indices: 201785--201882 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 52
201775 CCAAAAATAG
* * *
201785 CAGAGGATTTTCCTCAACCGAAAATATTCTGAAAATA-TTTTTTGCAACATT
1 CAGAAGATTTTCCACAACCAAAAATATTCTGAAAATACTTTTTTGCAACATT
*
201836 CAGAAGATTTTCCACAACTAAAAATATTCTGAAAATACTTTTTTGCA
1 CAGAAGATTTTCCACAACCAAAAATATTCTGAAAATACTTTTTTGCA
201883 TTATCAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 33 0.79
52 9 0.21
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (52 bp):
CAGAAGATTTTCCACAACCAAAAATATTCTGAAAATACTTTTTTGCAACATT
Found at i:205884 original size:26 final size:25
Alignment explanation
Indices: 205855--205912 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
205845 CCGCTCATAA
* *
205855 TCCTCTACCTAACTTAAACTCAAGGG
1 TCCTCTACC-AACTCAAACTCAAAGG
*
205881 TCCTCCAACCAACTCAAACTCAAAGG
1 TCCT-CTACCAACTCAAACTCAAAGG
*
205907 ACCTCT
1 TCCTCT
205913 GACCCATCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.04
26 21 0.81
27 4 0.15
ACGTcount: A:0.33, C:0.36, G:0.09, T:0.22
Consensus pattern (25 bp):
TCCTCTACCAACTCAAACTCAAAGG
Found at i:209856 original size:17 final size:16
Alignment explanation
Indices: 209831--209886 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
209821 TTACTTAAAT
*
209831 ATTATAAAAAATAATTA
1 ATTACAAAAAATAA-TA
*
209848 ATTACAAAAAAAAATA
1 ATTACAAAAAATAATA
*
209864 A--A-AAAACATAATA
1 ATTACAAAAAATAATA
209877 ATTACAAAAA
1 ATTACAAAAA
209887 TAAGTATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.32
14 1 0.03
15 1 0.03
16 7 0.23
17 12 0.39
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
ATTACAAAAAATAATA
Found at i:210381 original size:282 final size:283
Alignment explanation
Indices: 209877--210441 Score: 1123
Period size: 282 Copynumber: 2.0 Consensus size: 283
209867 AAACATAATA
209877 ATTACAAAAATAAGTATTTACTGCAGTGTTTTGACAATTCTACCTAGATCTGTTCATAGGTTAGG
1 ATTACAAAAATAAGTATTTACTGCAGTGTTTTGACAATTCTACCTAGATCTGTTCATAGGTTAGG
209942 CCACCCGTCCCGGCCCGAAGGCTCGCCTGAAATGTGAGAGAGTTTGGGTAAAAATATAAGCTCAA
66 CCACCCGTCCCGGCCCGAAGGCTCGCCTGAAATGTGAGAGAGTTTGGGTAAAAATATAAGCTCAA
210007 AAATGGGCTTAGACAAAAAAATAAGGCCCATTTAATAAACGGGTCAGACCTCGGGTTAGACATTT
131 AAATGGGCTTAGACAAAAAAATAAGGCCCATTTAATAAACGGGTCAGACCTCGGGTTAGACATTT
210072 TTGGACTGGGCCCGACTCGAATTCACTAAAGGACAAAAAAATATGTTTTTTTTTGTTTTTTTAAT
196 TTGGACTGGGCCCGACTCGAATTCACTAAAGGACAAAAAAATATGTTTTTTTTTGTTTTTTTAAT
210137 AGTGTTTTCTTA-TGTTTTCTCC
261 AGTGTTTTCTTATTGTTTTCTCC
210159 ATTACAAAAATAAGTATTTACTGCAGTGTTTTGACAATTCTACCTAGATCTGTTCATAGGTTAGG
1 ATTACAAAAATAAGTATTTACTGCAGTGTTTTGACAATTCTACCTAGATCTGTTCATAGGTTAGG
210224 CCACCCGTCCCGGCCCGAAGGCTCGCCTGAAATGTGAGAGAGTTTGGGTAAAAATATAAGCTCAA
66 CCACCCGTCCCGGCCCGAAGGCTCGCCTGAAATGTGAGAGAGTTTGGGTAAAAATATAAGCTCAA
210289 AAATGGGCTTAGACAAAAAAATAAGGCCCATTTAATAAACGGGTCAGACCTCGGGTTAGACATTT
131 AAATGGGCTTAGACAAAAAAATAAGGCCCATTTAATAAACGGGTCAGACCTCGGGTTAGACATTT
210354 TTGGACTGGGCCCGACTCGAATTCACTAAAGGACAAAAAAATATGTTTTTTTTTGTTTTTTTAAT
196 TTGGACTGGGCCCGACTCGAATTCACTAAAGGACAAAAAAATATGTTTTTTTTTGTTTTTTTAAT
210419 AGTGTTTTCTTATTGTTTTCTCC
261 AGTGTTTTCTTATTGTTTTCTCC
210442 CTATTTTGCT
Statistics
Matches: 282, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
282 272 0.96
283 10 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (283 bp):
ATTACAAAAATAAGTATTTACTGCAGTGTTTTGACAATTCTACCTAGATCTGTTCATAGGTTAGG
CCACCCGTCCCGGCCCGAAGGCTCGCCTGAAATGTGAGAGAGTTTGGGTAAAAATATAAGCTCAA
AAATGGGCTTAGACAAAAAAATAAGGCCCATTTAATAAACGGGTCAGACCTCGGGTTAGACATTT
TTGGACTGGGCCCGACTCGAATTCACTAAAGGACAAAAAAATATGTTTTTTTTTGTTTTTTTAAT
AGTGTTTTCTTATTGTTTTCTCC
Found at i:210477 original size:14 final size:14
Alignment explanation
Indices: 210458--210488 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
210448 TGCTACCATT
210458 TTACTATTATGTTG
1 TTACTATTATGTTG
*
210472 TTACTATTTTGTTG
1 TTACTATTATGTTG
210486 TTA
1 TTA
210489 TTGTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:210555 original size:30 final size:30
Alignment explanation
Indices: 210519--210581 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
210509 ACTTATTTTA
210519 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
210549 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
210579 TTG
1 TTG
210582 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:223899 original size:21 final size:21
Alignment explanation
Indices: 223858--223900 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
223848 TGACCTCTGC
*
223858 TGGTGTCATTTGACTTATTTG
1 TGGTGTCATTTGACTCATTTG
* *
223879 TGGTTTCATTTGACTCGTTTG
1 TGGTGTCATTTGACTCATTTG
223900 T
1 T
223901 TGATTTACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (21 bp):
TGGTGTCATTTGACTCATTTG
Found at i:238890 original size:6 final size:6
Alignment explanation
Indices: 238872--238945 Score: 112
Period size: 6 Copynumber: 12.3 Consensus size: 6
238862 TAAAGTCCTT
* *
238872 TACAGA TATAGA TACAGA TACAGA TACAGA TACAGA TACATA TACAGA
1 TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA
* *
238920 TACAGA TACAGA TATAAA TACAGA TA
1 TACAGA TACAGA TACAGA TACAGA TA
238946 GCAAATAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (6 bp):
TACAGA
Found at i:244870 original size:16 final size:17
Alignment explanation
Indices: 244849--244887 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
244839 GAAAAATTAT
* *
244849 ATTTTCTATGA-TTCTA
1 ATTTTCTATCACTTCAA
244865 ATTTTCTATCACTTCAA
1 ATTTTCTATCACTTCAA
244882 ATTTTC
1 ATTTTC
244888 ATTTTTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTCTATCACTTCAA
Found at i:245161 original size:19 final size:21
Alignment explanation
Indices: 245134--245186 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
245124 TTCATGTTTC
245134 AAGATTTAGGGTTCAA-ATTT
1 AAGATTTAGGGTTCAAGATTT
* * *
245154 GA-ATTTAGAGTTTAAGATTT
1 AAGATTTAGGGTTCAAGATTT
245174 AAGATTTAGGGTT
1 AAGATTTAGGGTT
245187 TGAGTTTAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
21 9 0.35
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (21 bp):
AAGATTTAGGGTTCAAGATTT
Found at i:245222 original size:21 final size:20
Alignment explanation
Indices: 245184--245223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
245174 AAGATTTAGG
*
245184 GTTTGAGTTTAGGATTCGGT
1 GTTTGAGTTCAGGATTCGGT
*
245204 GTTTGAAGTTCAGGGTTCGG
1 GTTTG-AGTTCAGGATTCGG
245224 GATAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.07, G:0.38, T:0.40
Consensus pattern (20 bp):
GTTTGAGTTCAGGATTCGGT
Found at i:246100 original size:18 final size:18
Alignment explanation
Indices: 246074--246166 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 18
246064 GTTTATATTT
*
246074 TTTTTGAATTTTTATATA
1 TTTTGGAATTTTTATATA
** *
246092 TTTTGGAATAATTATGTA
1 TTTTGGAATTTTTATATA
* * *
246110 TATTGGATTTTTTCA-ATT
1 TTTTGGAATTTTT-ATATA
**
246128 TGTTTATAATTCTTTTATATA
1 T-TTTGGAA-T-TTTTATATA
246149 TTTT-GAATTTTTATATA
1 TTTTGGAATTTTTATATA
246166 T
1 T
246167 CTTTTTATAT
Statistics
Matches: 54, Mismatches: 16, Indels: 11
0.67 0.20 0.14
Matches are distributed among these distances:
17 10 0.19
18 26 0.48
19 6 0.11
20 5 0.09
21 7 0.13
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (18 bp):
TTTTGGAATTTTTATATA
Found at i:247179 original size:16 final size:16
Alignment explanation
Indices: 247141--247179 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
247131 TGGCAGTAGC
* *
247141 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
247157 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
247173 AAAGAAA
1 AAAGAAA
247180 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:252661 original size:16 final size:16
Alignment explanation
Indices: 252623--252661 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
252613 TGGCAGTAGC
* *
252623 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
252639 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
252655 AAAGAAA
1 AAAGAAA
252662 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:256695 original size:22 final size:21
Alignment explanation
Indices: 256651--256701 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
256641 ATAAGGTTAG
256651 TTTTTAAAAAACTCAAATTTAT
1 TTTTTAAAAAACTCAAA-TTAT
*
256673 TTCTTTAAAAATACTCACA-TAT
1 TT-TTTAAAAA-ACTCAAATTAT
256695 TTTTTAA
1 TTTTTAA
256702 GGGCTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 8 0.31
24 6 0.23
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTTAAAAAACTCAAATTAT
Found at i:259833 original size:13 final size:14
Alignment explanation
Indices: 259817--259850 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
259807 AATAAATACA
259817 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
259830 TATTTTTTAATTTT
1 TATTTTTTAATTTT
259844 TAATTTT
1 T-ATTTT
259851 AAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:259888 original size:20 final size:20
Alignment explanation
Indices: 259865--259902 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
259855 TATTAAATAT
*
259865 ATATTTTTTTTATTTTTAAA
1 ATATTTTTTTTATGTTTAAA
259885 ATATTTTTTTTATGTTTA
1 ATATTTTTTTTATGTTTA
259903 TTAAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
ATATTTTTTTTATGTTTAAA
Found at i:259906 original size:23 final size:23
Alignment explanation
Indices: 259855--259908 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
259845 AATTTTAAAA
259855 TATTAAATATATATTTTTTTTATT
1 TATTAAA-ATATATTTTTTTTATT
*
259879 T-TTAAAATAT-TTTTTTTATGTT
1 TATTAAAATATATTTTTTT-TATT
259901 TATTAAAA
1 TATTAAAA
259909 ATCGGGCCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 8 0.30
23 11 0.41
24 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTAAAATATATTTTTTTTATT
Found at i:264701 original size:14 final size:14
Alignment explanation
Indices: 264666--264704 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
264656 TGTAATTTTG
*
264666 AAATTTAATTTTTCT
1 AAATTTAA-TTTTAT
*
264681 AATTTTAATTTTAT
1 AAATTTAATTTTAT
264695 AAATTTAATT
1 AAATTTAATT
264705 CCTCTACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATTTAATTTTAT
Found at i:264710 original size:29 final size:29
Alignment explanation
Indices: 264653--264710 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
264643 TCTATGTACT
**
264653 ATTTGTAATTTTGAAATTTAATTTTTCTA
1 ATTTGTAATTTTGAAATTTAATTCCTCTA
*
264682 ATTT-TAATTTTATAAATTTAATTCCTCTA
1 ATTTGTAATTTT-GAAATTTAATTCCTCTA
264711 CTTCTCAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTTGTAATTTTGAAATTTAATTCCTCTA
Found at i:268171 original size:18 final size:18
Alignment explanation
Indices: 268148--268193 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
268138 GCATTATTTT
* *
268148 TAAAAAATATTTTTGGAA
1 TAAAAAATATTTTCGAAA
*
268166 TAAAAAATACTTTCGAAA
1 TAAAAAATATTTTCGAAA
268184 T-AAAAATATT
1 TAAAAAATATT
268194 ACTAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (18 bp):
TAAAAAATATTTTCGAAA
Found at i:269078 original size:22 final size:22
Alignment explanation
Indices: 269050--269094 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
269040 AATGGATGTC
*
269050 TATCATGATCAAGATATAGTTG
1 TATCATGATAAAGATATAGTTG
269072 TATCATGATAAAGATATAGTTG
1 TATCATGATAAAGATATAGTTG
269094 T
1 T
269095 GATGTACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (22 bp):
TATCATGATAAAGATATAGTTG
Found at i:270968 original size:9 final size:9
Alignment explanation
Indices: 270954--270979 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
270944 GAAAGGGAAG
270954 AACAAGAAC
1 AACAAGAAC
270963 AACAAGAAC
1 AACAAGAAC
270972 AACAAGAA
1 AACAAGAA
270980 GAAGATGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (9 bp):
AACAAGAAC
Found at i:274900 original size:19 final size:19
Alignment explanation
Indices: 274866--274927 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
274856 TGAATATTAG
*
274866 ATTTTATAAA-TATTTTGA
1 ATTTTAAAAATTATTTTGA
*
274884 ATTTTAAAAATTATTTTAA
1 ATTTTAAAAATTATTTTGA
*
274903 ATTTTTGAAAAGTTATTTTG-
1 A-TTTT-AAAAATTATTTTGA
274923 ATTTT
1 ATTTT
274928 TTTATAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.24
19 12 0.32
20 5 0.14
21 11 0.30
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTAAAAATTATTTTGA
Found at i:274918 original size:21 final size:19
Alignment explanation
Indices: 274866--274921 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
274856 TGAATATTAG
* *
274866 ATTTTATAAA-TATTTTGA
1 ATTTTAAAAATTATTTTAA
274884 ATTTTAAAAATTATTTTAA
1 ATTTTAAAAATTATTTTAA
*
274903 ATTTTTGAAAAGTTATTTT
1 A-TTTT-AAAAATTATTTT
274922 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.28
19 8 0.25
20 4 0.12
21 11 0.34
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTTAAAAATTATTTTAA
Found at i:274929 original size:21 final size:19
Alignment explanation
Indices: 274867--274928 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
274857 GAATATTAGA
* *
274867 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAT
*
274885 TTTTAAAAATTATTTTAAAT
1 TTTTAAAAATTATTTT-GAT
*
274905 TTTTGAAAAGTTATTTTGAT
1 TTTT-AAAAATTATTTTGAT
274925 TTTT
1 TTTT
274929 TTATAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 8 0.22
19 6 0.17
20 11 0.31
21 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAT
Found at i:276179 original size:12 final size:12
Alignment explanation
Indices: 276140--276172 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
276130 AGTAAGTAAA
276140 TAAATAAAATAT
1 TAAATAAAATAT
*
276152 TAAATGAAATAT
1 TAAATAAAATAT
276164 TAAATAAAA
1 TAAATAAAA
276173 CAGTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:278544 original size:9 final size:9
Alignment explanation
Indices: 278530--278566 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
278520 TATAGTTTGA
278530 TATTCGAAT
1 TATTCGAAT
278539 TATTCGAAT
1 TATTCGAAT
*
278548 TATTCGAGT
1 TATTCGAAT
278557 TATTCGAAT
1 TATTCGAAT
278566 T
1 T
278567 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:278826 original size:45 final size:44
Alignment explanation
Indices: 278758--278871 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
278748 TCTTTTTAAC
* * **
278758 CCACTGTAACTTCAGGAATATAAGATTTACT-ACTTTCAATCTGCT
1 CCACTGCAACTTCAGGAAGATAAG-GCTACTGAC-TTCAATCTGCT
* *
278803 CCACTGCAACTTCA-GAGAGATAAGGCTAGTGGCTTCAATCTGCT
1 CCACTGCAACTTCAGGA-AGATAAGGCTACTGACTTCAATCTGCT
* *
278847 CCACTGCAACTTCAAGAAGACAAGG
1 CCACTGCAACTTCAGGAAGATAAGG
278872 TCCGCCATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
44 37 0.63
45 22 0.37
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
CCACTGCAACTTCAGGAAGATAAGGCTACTGACTTCAATCTGCT
Found at i:278982 original size:46 final size:46
Alignment explanation
Indices: 278911--279136 Score: 231
Period size: 46 Copynumber: 4.8 Consensus size: 46
278901 CCACTACAAT
* * *
278911 GCCAGAGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAGC
1 GCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAATGCAAC
* * ** *
278957 GCCAGGGAAATAAGACTCGCAGCCTTCAGCTTTAATCTGTTGCAAT
1 GCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAATGCAAC
* * * *
279003 GCCAGAGAAATAAGACTT-GCTGCCTTCAACTTTAGTCT-GTGCAAC
1 GCCAGGGAAATAAGA-TTCGCTGCCTTCAGCTTTAATCTAATGCAAC
* * *
279048 GCTAGGGAAATAAGATTTGCTGCCTTGAGCTTTAATCTGTTCCAATGCAAC
1 GCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--AATGCAAC
* *
279099 GCCGGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCT
1 GCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
279137 GTTTCACTAC
Statistics
Matches: 147, Mismatches: 25, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.01
45 34 0.23
46 70 0.48
47 1 0.01
48 2 0.01
51 38 0.26
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (46 bp):
GCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAATGCAAC
Found at i:279094 original size:91 final size:92
Alignment explanation
Indices: 278907--279136 Score: 266
Period size: 91 Copynumber: 2.5 Consensus size: 92
278897 TGTTCCACTA
* *
278907 CAATGCCAGAGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAGCGCCAGGGAAATAAGA
1 CAATGCCAGAGAAATAAGATTCGCTGCCTTCAACTTTAATCTACTGCAACGCCAGGGAAATAAGA
*
278972 CTCGCAGCCTTCAGCTTTAATCTGTTG
66 CTCGCAGCCTTCAGCTTTAATCTGTTC
* * *
278999 CAATGCCAGAGAAATAAGACTT-GCTGCCTTCAACTTTAGTCT-GTGCAACGCTAGGGAAATAAG
1 CAATGCCAGAGAAATAAGA-TTCGCTGCCTTCAACTTTAATCTACTGCAACGCCAGGGAAATAAG
* * * *
279062 ATTTGCTGCCTTGAGCTTTAATCTGTTC
65 ACTCGCAGCCTTCAGCTTTAATCTGTTC
* * * *
279090 CAATGCAACGCCGGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCT
1 CAAT-----GCCAGAGAAATAAGATTCGCTGCCTTCAACTTTAATCT
279137 GTTTCACTAC
Statistics
Matches: 116, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
91 45 0.39
92 37 0.32
93 2 0.02
95 2 0.02
96 30 0.26
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (92 bp):
CAATGCCAGAGAAATAAGATTCGCTGCCTTCAACTTTAATCTACTGCAACGCCAGGGAAATAAGA
CTCGCAGCCTTCAGCTTTAATCTGTTC
Done.