Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 56
Found at i:4900164 original size:22 final size:21
Alignment explanation
Indices: 4900134--4900191 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
4900124 TTGGATTATG
4900134 GTGGTGAAGAAGAAGAAACAAT
1 GTGG-GAAGAAGAAGAAACAAT
*
4900156 GT-GG-AGAAGAAGAAACAGT
1 GTGGGAAGAAGAAGAAACAAT
*
4900175 GTGGATAAGAAGAAGAA
1 GTGG-GAAGAAGAAGAA
4900192 GAAGAGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 1 0.03
22 12 0.39
ACGTcount: A:0.50, C:0.03, G:0.34, T:0.12
Consensus pattern (21 bp):
GTGGGAAGAAGAAGAAACAAT
Found at i:4900165 original size:19 final size:19
Alignment explanation
Indices: 4900141--4900188 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
4900131 ATGGTGGTGA
4900141 AGAAGAAGAAACAATGTGG
1 AGAAGAAGAAACAATGTGG
*
4900160 AGAAGAAGAAACAGTGTGG
1 AGAAGAAGAAACAATGTGG
*
4900179 ATAAGAAGAA
1 AGAAGAAGAA
4900189 GAAGAAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.31, T:0.10
Consensus pattern (19 bp):
AGAAGAAGAAACAATGTGG
Found at i:4900472 original size:17 final size:17
Alignment explanation
Indices: 4900440--4900473 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4900430 TAATTACTAT
4900440 TTTATAAATATAAAATA
1 TTTATAAATATAAAATA
4900457 TTTA-AAATATATAAATA
1 TTTATAAATATA-AAATA
4900474 AGAAATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAATATAAAATA
Found at i:4900528 original size:18 final size:18
Alignment explanation
Indices: 4900505--4900560 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
4900495 TAATTACTTA
* *
4900505 ATAATTATTTTTATGATT
1 ATAATTAATTTTATAATT
4900523 ATAATTAATTTTATAATT
1 ATAATTAATTTTATAATT
* *
4900541 AGAA-T-ATTATATAATT
1 ATAATTAATTTTATAATT
4900557 ATAA
1 ATAA
4900561 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 13 0.39
17 1 0.03
18 19 0.58
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
ATAATTAATTTTATAATT
Found at i:4902059 original size:26 final size:25
Alignment explanation
Indices: 4902025--4902074 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4902015 ATATTCAATA
*
4902025 AAATGTATAAAATACATTACTATATAC
1 AAATGTAT-AAA-ACATTAATATATAC
4902052 AAAT-TATAAAACATTAATATATA
1 AAATGTATAAAACATTAATATATA
4902075 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 3 0.14
26 3 0.14
27 4 0.18
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATGTATAAAACATTAATATATAC
Found at i:4902075 original size:2 final size:2
Alignment explanation
Indices: 4902068--4902133 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
4902058 TAAAACATTA
* * * *
4902068 AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AA AT AT -T CAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
**
4902110 AT GC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
4902134 CGACTTTGAT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4904076 original size:89 final size:90
Alignment explanation
Indices: 4903860--4904078 Score: 395
Period size: 89 Copynumber: 2.4 Consensus size: 90
4903850 GATTTTAAAA
*
4903860 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACTGAAGG
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTT-AAATCTTATTTGAAAACATCCTGCACTGAAGG
*
4903925 TCTTATGGATGGCCCGAATGACTTAC
65 TCTTATGGATGGCCCGAAGGACTTAC
*
4903951 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTTATTTGAAAACATCCTGCACTGAAGGT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTTATTTGAAAACATCCTGCACTGAAGGT
4904016 CTTATGGATGG-CCGAAGGACTTAC
66 CTTATGGATGGCCCGAAGGACTTAC
4904040 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTT
4904079 TTGTTTCGAG
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
89 50 0.40
90 43 0.35
91 31 0.25
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (90 bp):
AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTTATTTGAAAACATCCTGCACTGAAGGT
CTTATGGATGGCCCGAAGGACTTAC
Found at i:4904116 original size:39 final size:39
Alignment explanation
Indices: 4904072--4904834 Score: 1022
Period size: 39 Copynumber: 19.6 Consensus size: 39
4904062 TTAGTTTCTT
* * * * * *
4904072 AAATCTTTTGTTTCGAGAGAAACTAACTAAAGTGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
4904111 AAATCTTTTGTTTCGAGGGAAACCATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
4904150 AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
4904189 AAATCTTCTGTTTCGATGGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
4904228 AAATATTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
** *
4904267 AAATCTTCTGTTTTAAGGGAAACTACCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
4904306 AAATCTTCTGTTTCAAGAGAAACTACCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
4904345 AAATCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
4904384 AAATCTTCTATTTCAAGGGAAACTACCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * * *
4904423 AAATCTTATATTTCAAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
4904462 AAATCTTCTGTTTCAAGGGAAACTACCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* ** *
4904501 AAATCTTATGTTTTAAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * **
4904540 AAATTTTCGGTTTCGACAGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* **
4904579 AAATTTTCTGTTTCGATAGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * **
4904618 AAATCTTCTATTGCGATTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
4904657 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCAAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
4904696 AAATCTTCTGTTTCGAGGGAAATTATCTAAAGCAAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
4904735 CAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
4904774 CAATCTTTTGTTTTGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
4904813 AAATCTTTTGTTTCAAGGGAAA
1 AAATCTTCTGTTTCGAGGGAAA
4904835 ATTGTCTTAA
Statistics
Matches: 657, Mismatches: 67, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 657 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (39 bp):
AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
Found at i:4904916 original size:37 final size:37
Alignment explanation
Indices: 4904743--4905072 Score: 93
Period size: 36 Copynumber: 9.4 Consensus size: 37
4904733 TACAATCTTA
* *
4904743 TGTTTCGAGGGAAA-CTATCTCAAGCGAGATAC-AATCTTT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAG--ACGAA--TTT
** * **
4904782 TGTTTTGAGGGAAA-CTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGA-CGAA--TTT
** * *
4904821 TGTTTCAAGGGAAAATTGTCTTAAGCGAGACGAAATT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
* * ** * *
4904858 GGTTTTAAGAAAAACC-ATCTCAAGTGAGA-GACATTT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGA-ATTT
*
4904894 TGTTTCAAGGGAAACCTGTCTC-A---A-A--AA-CT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
* * * *
4904923 TGTTTCAAGAGAAA-CTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
* * *
4904959 CGTTTCAAGGGAAA-C-GT-TC--TC-A-A--ATTTCT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATT-T
* * * * *
4904988 GTGTTTCAAGAGAAA-CTATCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
* *
4905025 TGTTTCAAGAGAAA-CTGTCTCAAGAGAGAC-AA-TT
1 TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
4905059 TGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
4905073 TGTTTTCAAA
Statistics
Matches: 224, Mismatches: 44, Indels: 51
0.70 0.14 0.16
Matches are distributed among these distances:
28 9 0.04
29 16 0.07
30 15 0.07
31 3 0.01
32 4 0.02
33 2 0.01
34 17 0.08
35 9 0.04
36 69 0.31
37 18 0.08
38 2 0.01
39 48 0.21
40 12 0.05
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACCTGTCTCAAGCGAGACGAATTT
Found at i:4904964 original size:36 final size:36
Alignment explanation
Indices: 4904917--4905128 Score: 156
Period size: 36 Copynumber: 6.3 Consensus size: 36
4904907 ACCTGTCTCA
*
4904917 AAAACTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
* * **
4904953 AAAATTCGTTTCAAGGGAAAC-GTTCTCAA---ATTTC
1 AAAATTTGTTTCAAGAGAAACTG-TCTCAAGGGA-GAC
* *
4904987 ----TGTGTTTCAAGAGAAACTATCTCAAGGGAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
4905019 AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
* *
4905055 --AATTTGTTTCAAGGGAAA-TGTTTTCAA---AG--
1 AAAATTTGTTTCAAGAGAAACTG-TCTCAAGGGAGAC
*
4905084 ---TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
1 AAAATT-TGTTTCAAGAGAAACTGTCTCAAGGGAGAC
4905118 AAAATTTGTTT
1 AAAATTTGTTT
4905129 TAATAAAAAT
Statistics
Matches: 135, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
28 2 0.01
29 18 0.13
30 22 0.16
31 2 0.01
32 3 0.02
33 4 0.03
34 23 0.17
35 1 0.01
36 58 0.43
37 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
Found at i:4905010 original size:66 final size:64
Alignment explanation
Indices: 4904859--4905047 Score: 227
Period size: 66 Copynumber: 2.9 Consensus size: 64
4904849 GACGAAATTG
* * * * * * *
4904859 GTTTTAAGAAAAACCATCTCAAGTGAGAGACATTTTGTTTCAAGGGAAACCTGTCTCAAAAACTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA-CTGTCTCAAAAACTT
* * **
4904924 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAAC-GTTCTCAAATTTCT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTG-TCTCAAA-AACT
4904988 GT
64 -T
*
4904990 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAA
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
4905048 GAGAGACAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 8 0.08
65 42 0.40
66 54 0.51
67 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (64 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAACTT
Found at i:4905240 original size:39 final size:39
Alignment explanation
Indices: 4905197--4905330 Score: 116
Period size: 39 Copynumber: 3.5 Consensus size: 39
4905187 GCGAGACAAA
*
4905197 TCTTGTTTTAAGAAAAACAACATGTAGTGAAATGAAATG
1 TCTTGTTTTAAGAAAAACAACATGTAGTCAAATGAAATG
* * * **
4905236 TCTTGTTTT--GAATAA-AACATGT-CTCAAGTGAGACAAA
1 TCTTGTTTTAAGAAAAACAACATGTAGTCAAATGA-A-ATG
*
4905273 TCTTGTTTTAAGAAAAACAATAT-TGAGTCAAATGAAATG
1 TCTTGTTTTAAGAAAAACAACATGT-AGTCAAATGAAATG
* * *
4905312 TCTTCTTTCAAGTAAAACA
1 TCTTGTTTTAAGAAAAACA
4905331 GTCTCAAGTG
Statistics
Matches: 73, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
35 6 0.08
36 8 0.11
37 15 0.21
39 32 0.44
40 5 0.07
41 7 0.10
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (39 bp):
TCTTGTTTTAAGAAAAACAACATGTAGTCAAATGAAATG
Found at i:4905252 original size:76 final size:76
Alignment explanation
Indices: 4905105--4905364 Score: 246
Period size: 76 Copynumber: 3.4 Consensus size: 76
4905095 AGAGAAACTG
* * * * *
4905105 TCTCAAGGGAGACAAAAT-TTGTTTTAATAAAAATAATCTTG-AGTGAAAT-AAATCTTCTTATT
1 TCTCAAGCGAGAC-AAATCTTGTTTTAAGAAAAACAA-CATGTAGTGAAATGAAAT-GTCTTATT
*
4905167 TCGAGTAAAAAATA
63 TCGAATAAAAAATA
* *
4905181 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAATGAAATGTCTTGTTTTG
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAATGAAATGTCTTATTTCG
* *
4905246 AATAAAACATG
66 AATAAAAAATA
* * * *
4905257 TCTCAAGTGAGACAAATCTTGTTTTAAGAAAAACAATAT-TGAGTCAAATGAAATGTCTTCTTTC
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGT-AGTGAAATGAAATGTCTTATTTC
* *
4905321 -AAGTAAAACA-G
65 GAA-TAAAAAATA
* * *
4905332 TCTCAAGTGAGACAAAGT-ATATTTTAAGAAAAA
1 TCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAA
4905365 TAATCTACAG
Statistics
Matches: 161, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
75 40 0.25
76 117 0.73
77 4 0.02
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (76 bp):
TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAATGAAATGTCTTATTTCG
AATAAAAAATA
Found at i:4905290 original size:37 final size:37
Alignment explanation
Indices: 4905173--4905291 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 37
4905163 TATTTCGAGT
* *
4905173 AAAAA-ATATCTCAAGCGAGACAAATCTTGTTTTAAG
1 AAAAACATGTCTCAAGTGAGACAAATCTTGTTTTAAG
* * * **
4905209 AAAAACAACATGTAGTGAAATGA-A-ATGTCTTGTTTTGAA-
1 --AAA-AACATGT-CTCAAGTGAGACAAATCTTGTTTT-AAG
*
4905248 TAAAACATGTCTCAAGTGAGACAAATCTTGTTTTAAG
1 AAAAACATGTCTCAAGTGAGACAAATCTTGTTTTAAG
4905285 AAAAACA
1 AAAAACA
4905292 ATATTGAGTC
Statistics
Matches: 60, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
35 6 0.10
36 10 0.17
37 18 0.30
38 3 0.05
39 12 0.20
40 6 0.10
41 5 0.08
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (37 bp):
AAAAACATGTCTCAAGTGAGACAAATCTTGTTTTAAG
Found at i:4907608 original size:6 final size:6
Alignment explanation
Indices: 4907592--4907658 Score: 55
Period size: 6 Copynumber: 10.5 Consensus size: 6
4907582 AAATGCTTAA
* *
4907592 AAATG- AAATGC AAATGC AAAGATGC AAATGC AGATGC AAAATGAA AAGATGC
1 AAATGC AAATGC AAATGC -AA-ATGC AAATGC AAATGC -AAATG-C AA-ATGC
*
4907644 AAATGC AGATGC AAA
1 AAATGC AAATGC AAA
4907659 AATGTTGATC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
5 5 0.10
6 26 0.52
7 12 0.24
8 7 0.14
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:4907622 original size:20 final size:20
Alignment explanation
Indices: 4907597--4907658 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
4907587 CTTAAAAATG
4907597 AAATGCAAATGCAAAGATGC
1 AAATGCAAATGCAAAGATGC
* *
4907617 AAATGCAGATGCAAA-ATGAA
1 AAATGCAAATGCAAAGATG-C
4907637 AAGATGCAAATGC--AGATGC
1 AA-ATGCAAATGCAAAGATGC
4907656 AAA
1 AAA
4907659 AATGTTGATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 19 0.54
21 9 0.26
ACGTcount: A:0.52, C:0.13, G:0.21, T:0.15
Consensus pattern (20 bp):
AAATGCAAATGCAAAGATGC
Found at i:4907639 original size:27 final size:27
Alignment explanation
Indices: 4907599--4907659 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
4907589 TAAAAATGAA
*
4907599 ATGC-AAATGCAAAGATGCAAATGCAG
1 ATGCAAAATGAAAAGATGCAAATGCAG
4907625 ATGCAAAATGAAAAGATGCAAATGCAG
1 ATGCAAAATGAAAAGATGCAAATGCAG
4907652 ATGCAAAA
1 ATGCAAAA
4907660 ATGTTGATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (27 bp):
ATGCAAAATGAAAAGATGCAAATGCAG
Found at i:4909931 original size:26 final size:27
Alignment explanation
Indices: 4909882--4909944 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
4909872 ATATGCAATA
4909882 AAATGTATAAAATACATTACTATATAC
1 AAATGTATAAAATACATTACTATATAC
* *
4909909 AAAT-TATAAAATATA-TA-TATATAT
1 AAATGTATAAAATACATTACTATATAC
*
4909933 ATATGTATAAAA
1 AAATGTATAAAA
4909945 AAAAACACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.28
25 9 0.28
26 10 0.31
27 4 0.12
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (27 bp):
AAATGTATAAAATACATTACTATATAC
Found at i:4911957 original size:60 final size:61
Alignment explanation
Indices: 4911804--4911957 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 61
4911794 TTCCTATTTA
* * * *
4911804 AAGGGACCAAAATAGCAAAAA-AGAGACTTAAA-GGACTAAAATAACAAAAATAGAAATTG
1 AAGGGACTAAAATAGGAAAAATAGAAACTTAAAGGGACTAAAACAACAAAAATAGAAATTG
* * ** *
4911863 AAAGTACTAAAATAGAGAAAAAT-GAAACTT-AAGGGACTAAAACAGTAAGAATAGAAATCT-
1 AAGGGACTAAAATAG-GAAAAATAGAAACTTAAAGGGACTAAAACAACAAAAATAGAAAT-TG
4911923 AAGGGACTAAAAT-GGAAAAATAGAAACTTAAAGGG
1 AAGGGACTAAAATAGGAAAAATAGAAACTTAAAGGG
4911958 CTATAATAGT
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
58 7 0.09
59 22 0.28
60 48 0.62
61 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.19, T:0.16
Consensus pattern (61 bp):
AAGGGACTAAAATAGGAAAAATAGAAACTTAAAGGGACTAAAACAACAAAAATAGAAATTG
Found at i:4911972 original size:30 final size:30
Alignment explanation
Indices: 4911801--4911972 Score: 124
Period size: 30 Copynumber: 5.8 Consensus size: 30
4911791 ATATTCCTAT
* *
4911801 TTAAAGGGACCAAAATAGCAAAAA-AGAGAC
1 TTAAAGGG-CTAAAATAGCAAAAATAGAAAC
* *
4911831 TTAAAGGACTAAAATAACAAAAATAGAAA-
1 TTAAAGGGCTAAAATAGCAAAAATAGAAAC
** *
4911860 TTGAAAGTACTAAAATAGAGAAAAAT-GAAAC
1 TT-AAAGGGCTAAAATAG-CAAAAATAGAAAC
* * *
4911891 TT-AAGGGACTAAAACAGTAAGAATAGAAA-
1 TTAAAGGG-CTAAAATAGCAAAAATAGAAAC
*
4911920 TCT-AAGGGACTAAAAT-GGAAAAATAGAAAC
1 T-TAAAGGG-CTAAAATAGCAAAAATAGAAAC
* *
4911950 TTAAAGGGCTATAATAGTAAAAA
1 TTAAAGGGCTAAAATAGCAAAAA
4911973 CCAAAAGTTA
Statistics
Matches: 115, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
29 42 0.37
30 65 0.57
31 8 0.07
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.17
Consensus pattern (30 bp):
TTAAAGGGCTAAAATAGCAAAAATAGAAAC
Found at i:4913508 original size:3 final size:3
Alignment explanation
Indices: 4913500--4913558 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
4913490 AAAAATGTAT
* **
4913500 TAA TAA TAA TTAA TAA TAA TGA CGA TAA -AA TAA TAA T-A TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4913544 TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA
4913559 GTTAATAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.85
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4913548 original size:17 final size:17
Alignment explanation
Indices: 4913502--4913554 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
4913492 AAATGTATTA
4913502 ATAATAATTAATAATAAT
1 ATAATAA-TAATAATAAT
**
4913520 GACGATAA-AATAATAAT
1 -ATAATAATAATAATAAT
*
4913537 ATAATAATAATATTAAT
1 ATAATAATAATAATAAT
4913554 A
1 A
4913555 ATAAGTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
19 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:4913563 original size:11 final size:10
Alignment explanation
Indices: 4913498--4913566 Score: 63
Period size: 10 Copynumber: 6.8 Consensus size: 10
4913488 CAAAAAATGT
4913498 ATTAATAATA
1 ATTAATAATA
4913508 ATTAATAATA
1 ATTAATAATA
*
4913518 ATGACGATAA-A
1 ATTA--ATAATA
4913529 A-TAATAATA
1 ATTAATAATA
*
4913538 TAATAATAAT-
1 -ATTAATAATA
4913548 ATTAATAATA
1 ATTAATAATA
4913558 AGTTAATAA
1 A-TTAATAA
4913567 CATGAGAACC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.08
9 9 0.18
10 16 0.33
11 16 0.33
12 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (10 bp):
ATTAATAATA
Found at i:4913564 original size:17 final size:16
Alignment explanation
Indices: 4913500--4913566 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 16
4913490 AAAAATGTAT
4913500 TAATAATAATTAATAA
1 TAATAATAATTAATAA
*
4913516 TAATGACGATAAAATAATAA
1 TAAT-A--AT-AATTAATAA
*
4913536 T-ATAATAA-TAATAT
1 TAATAATAATTAATAA
4913550 TAATAATAAGTTAATAA
1 TAATAATAA-TTAATAA
4913567 CATGAGAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
14 6 0.15
15 9 0.22
16 6 0.15
17 6 0.15
18 1 0.02
19 4 0.10
20 9 0.22
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (16 bp):
TAATAATAATTAATAA
Found at i:4917855 original size:31 final size:31
Alignment explanation
Indices: 4917817--4917881 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
4917807 GGGAATGGTT
*
4917817 CCTAACATTATCGATTCGTTCGATTTTAGTC
1 CCTAACATTATCGATTAGTTCGATTTTAGTC
4917848 CCTAACATTATCGATTAGTTCGATTTTAGTC
1 CCTAACATTATCGATTAGTTCGATTTTAGTC
4917879 CCT
1 CCT
4917882 CAACCGTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (31 bp):
CCTAACATTATCGATTAGTTCGATTTTAGTC
Found at i:4918198 original size:25 final size:25
Alignment explanation
Indices: 4918122--4918200 Score: 113
Period size: 25 Copynumber: 3.2 Consensus size: 25
4918112 GGGTGCCAAA
*
4918122 TAAGGAAGACGTTCTATCATAGTAT
1 TAAGGAAGACGTTTTATCATAGTAT
**
4918147 CGAGGAAGACGTTTTATCATAGTAT
1 TAAGGAAGACGTTTTATCATAGTAT
* *
4918172 TAAGGAAGATGTTTTATCATAGCAT
1 TAAGGAAGACGTTTTATCATAGTAT
4918197 TAAG
1 TAAG
4918201 AATTAGCATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (25 bp):
TAAGGAAGACGTTTTATCATAGTAT
Found at i:4920609 original size:17 final size:18
Alignment explanation
Indices: 4920589--4920623 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4920579 TCACTTTATA
*
4920589 TTATAAAT-CTTAATTTT
1 TTATAAATACTAAATTTT
4920606 TTATAAATACTAAATTTT
1 TTATAAATACTAAATTTT
4920624 AAAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAAATACTAAATTTT
Found at i:4924118 original size:23 final size:23
Alignment explanation
Indices: 4924090--4924137 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
4924080 TGATTCCATT
4924090 ATAGTATTCTTCTTAATCTCATG
1 ATAGTATTCTTCTTAATCTCATG
4924113 ATAGTATTCTTCTTAATCTCATG
1 ATAGTATTCTTCTTAATCTCATG
4924136 AT
1 AT
4924138 TCTTTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (23 bp):
ATAGTATTCTTCTTAATCTCATG
Found at i:4925231 original size:18 final size:18
Alignment explanation
Indices: 4925204--4925261 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
4925194 TAGAAGTCAT
4925204 CTTCAAGACTATAGTACC
1 CTTCAAGACTATAGTACC
*
4925222 CTTTAAGACTATAGTACC
1 CTTCAAGACTATAGTACC
4925240 CTTCAAGACTATAGTACC
1 CTTCAAGACTATAGTACC
4925258 CTTC
1 CTTC
4925262 CCCTTGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (18 bp):
CTTCAAGACTATAGTACC
Found at i:4932565 original size:20 final size:20
Alignment explanation
Indices: 4932540--4932580 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4932530 GTATTTTCCT
*
4932540 TTAGCAGAATTTGCCTACAA
1 TTAGCAAAATTTGCCTACAA
4932560 TTAGCAAAATTTGCCTACAA
1 TTAGCAAAATTTGCCTACAA
4932580 T
1 T
4932581 AATATCTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
TTAGCAAAATTTGCCTACAA
Found at i:4950703 original size:21 final size:21
Alignment explanation
Indices: 4950679--4950720 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4950669 ATAAATAGTA
4950679 TTTTAT-TAAATCAAATTTTAT
1 TTTTATATAAAT-AAATTTTAT
* *
4950700 TTTTGTATAAATGAATTTTAT
1 TTTTATATAAATAAATTTTAT
4950721 ATTACAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTATATAAATAAATTTTAT
Found at i:4951857 original size:8 final size:8
Alignment explanation
Indices: 4951842--4951898 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
4951832 TGAAATGAGC
4951842 AAAT-ATT
1 AAATAATT
4951849 AAATAATT
1 AAATAATT
*
4951857 AAAT-ATG
1 AAATAATT
4951864 AAATAATT
1 AAATAATT
*
4951872 AAATATTT
1 AAATAATT
4951880 CAGAATAATT
1 -A-AATAATT
4951890 AAAT-ATT
1 AAATAATT
4951897 AA
1 AA
4951899 TTTAATTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 15 0.36
8 19 0.45
9 2 0.05
10 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (8 bp):
AAATAATT
Found at i:4951860 original size:15 final size:15
Alignment explanation
Indices: 4951842--4951898 Score: 78
Period size: 15 Copynumber: 3.6 Consensus size: 15
4951832 TGAAATGAGC
4951842 AAATATTAAATAATT
1 AAATATTAAATAATT
*
4951857 AAATATGAAATAATT
1 AAATATTAAATAATT
4951872 AAATATTTCAGAATAATT
1 AAATA-TT-A-AATAATT
4951890 AAATATTAA
1 AAATATTAA
4951899 TTTAATTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 20 0.54
16 2 0.05
17 3 0.08
18 12 0.32
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (15 bp):
AAATATTAAATAATT
Found at i:4963760 original size:20 final size:21
Alignment explanation
Indices: 4963735--4963786 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
4963725 TGATTAAGGT
4963735 AGTATCGATACACTAG-GTTG
1 AGTATCGATACACTAGTGTTG
* *
4963755 AGTATCGATACTCTGGTGTTG
1 AGTATCGATACACTAGTGTTG
4963776 AGGTATCGATA
1 A-GTATCGATA
4963787 TTGGACTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.50
21 5 0.18
22 9 0.32
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (21 bp):
AGTATCGATACACTAGTGTTG
Found at i:4970338 original size:30 final size:30
Alignment explanation
Indices: 4970304--4970375 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
4970294 CCCGAATGAC
* *
4970304 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
4970334 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
* *
4970364 CTGTCCATAGGT
1 CTATCCAGAGGT
4970376 ACCGAACAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:4975558 original size:30 final size:30
Alignment explanation
Indices: 4975524--4975596 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
4975514 CCCGAATGAC
4975524 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
*
4975554 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
* *
4975584 CTGTCCATAGGTC
1 CTATCCAGAGGTC
4975597 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAA
Found at i:4975620 original size:31 final size:31
Alignment explanation
Indices: 4975582--4975646 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
4975572 GATCCTCGGT
*
4975582 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
4975613 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
4975644 AAC
1 AAC
4975647 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:4980505 original size:20 final size:20
Alignment explanation
Indices: 4980477--4980516 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4980467 TGAAATAAAA
* *
4980477 TAAAATTTTATTTTGGTCAC
1 TAAAATTTTAATTTAGTCAC
*
4980497 TAAATTTTTAATTTAGTCAC
1 TAAAATTTTAATTTAGTCAC
4980517 CGGAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TAAAATTTTAATTTAGTCAC
Found at i:4987834 original size:22 final size:22
Alignment explanation
Indices: 4987806--4987881 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
4987796 CAATACACAT
* *
4987806 AAGTGCCTTAGAACAGGTACTA
1 AAGTGCCTTAGAACTGATACTA
* *
4987828 AAGTGCCTTAGTACTGATACGA
1 AAGTGCCTTAGAACTGATACTA
* * *
4987850 AAGTGCATTCGCACTGATACTA
1 AAGTGCCTTAGAACTGATACTA
4987872 AAGTGCCTTA
1 AAGTGCCTTA
4987882 TCATTGCTGG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (22 bp):
AAGTGCCTTAGAACTGATACTA
Found at i:4992217 original size:17 final size:17
Alignment explanation
Indices: 4992192--4992233 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4992182 AAGCTCGATT
* *
4992192 TTGAGCTCGATTCAAGC
1 TTGAACTCGATTAAAGC
4992209 TTGAACTCGATTAAAGC
1 TTGAACTCGATTAAAGC
*
4992226 TCGAACTC
1 TTGAACTC
4992234 AAACTCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (17 bp):
TTGAACTCGATTAAAGC
Found at i:4992535 original size:21 final size:21
Alignment explanation
Indices: 4992510--4992593 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
4992500 CATGGCATAA
4992510 CTTAAACCCTAACACATAAAC
1 CTTAAACCCTAACACATAAAC
*
4992531 CTTAAACCTTAACACATAAAC
1 CTTAAACCCTAACACATAAAC
* * *
4992552 CATAAACTCTAA-ACTTTAAAC
1 CTTAAACCCTAACAC-ATAAAC
* *
4992573 CTTAAAACCTATCACATAAAC
1 CTTAAACCCTAACACATAAAC
4992594 TCTAAATTCT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
CTTAAACCCTAACACATAAAC
Found at i:4992591 original size:35 final size:35
Alignment explanation
Indices: 4992526--4992626 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
4992516 CCCTAACACA
* * * *
4992526 TAAACCTTAAACCTTAACACATA-AACCATAAACTC
1 TAAACTTTAAACCTTAAAACCTATCA-CATAAACTC
4992561 TAAACTTTAAACCTTAAAACCTATCACATAAACTC
1 TAAACTTTAAACCTTAAAACCTATCACATAAACTC
*
4992596 TAAA-TTCTAAACCCT-AAACCTTATCACATAA
1 TAAACTT-TAAACCTTAAAACC-TATCACATAA
4992627 TTAGTTATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 7 0.12
35 50 0.86
36 1 0.02
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (35 bp):
TAAACTTTAAACCTTAAAACCTATCACATAAACTC
Found at i:4992605 original size:42 final size:43
Alignment explanation
Indices: 4992526--4992618 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
4992516 CCCTAACACA
**
4992526 TAAACCTT-AAACCTTAACACATAAACCATAAACTCTAAACTT
1 TAAACCTTAAAACCTTAACACATAAACCATAAACTCTAAACCC
* *
4992568 TAAACCTTAAAACC-TATCACATAAACTC-TAAATTCTAAACCC
1 TAAACCTTAAAACCTTAACACATAAAC-CATAAACTCTAAACCC
4992610 TAAACCTTA
1 TAAACCTTA
4992619 TCACATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (43 bp):
TAAACCTTAAAACCTTAACACATAAACCATAAACTCTAAACCC
Found at i:4992898 original size:14 final size:14
Alignment explanation
Indices: 4992881--4992921 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4992871 TTTATTCATC
4992881 AATAATGTATTTTT
1 AATAATGTATTTTT
4992895 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
4992906 AATAATGTAATTTT
1 AATAATGTATTTTT
4992920 AA
1 AA
4992922 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:4996333 original size:28 final size:29
Alignment explanation
Indices: 4996270--4996376 Score: 110
Period size: 28 Copynumber: 3.7 Consensus size: 29
4996260 ATATATTTAA
* *
4996270 ATATTTTATTATTAAT-TTAATATGAAAATAT
1 ATATTTTATTCTT-ATCTTAA-ATTAAAA-AT
* * *
4996301 ATATTTTATTCTTATCTTCACTTAAAACT
1 ATATTTTATTCTTATCTTAAATTAAAAAT
*
4996330 -TATTTTATTCTTATTTTAAATTAAAAAT
1 ATATTTTATTCTTATCTTAAATTAAAAAT
*
4996358 ATATTTTATTCTTAACTTA
1 ATATTTTATTCTTATCTTA
4996377 GCTTTAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
28 24 0.38
29 17 0.27
30 7 0.11
31 15 0.24
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
ATATTTTATTCTTATCTTAAATTAAAAAT
Found at i:4996385 original size:29 final size:28
Alignment explanation
Indices: 4996299--4996429 Score: 88
Period size: 29 Copynumber: 4.6 Consensus size: 28
4996289 ATATGAAAAT
4996299 ATATATTTTATTCTTATCTTCAC-TTAAA
1 ATATATTTTATTCTTATCTT-ACTTTAAA
* * *
4996327 ACT-TATTTTATTCTTATTTTAAATTAAAA
1 A-TATATTTTATTCTTATCTT-ACTTTAAA
*
4996356 ATATATTTTATTCTTAACTTAGCTTTAAA
1 ATATATTTTATTCTTATCTTA-CTTTAAA
* * ** * *
4996385 AAAAAGATT-TTCAAATATCTTACCTTAAA
1 ATATATTTTATTC--TTATCTTACTTTAAA
*
4996414 AAATATTTTATTCTTA
1 ATATATTTTATTCTTA
4996430 ATAAATTTCA
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
28 25 0.32
29 43 0.56
30 9 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATATTTTATTCTTATCTTACTTTAAA
Found at i:4996492 original size:12 final size:13
Alignment explanation
Indices: 4996465--4996489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4996455 TTTTTTTAAA
4996465 AAAAAGTTTTTTT
1 AAAAAGTTTTTTT
4996478 AAAAAGTTTTTT
1 AAAAAGTTTTTT
4996490 AAATATCTTA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AAAAAGTTTTTTT
Found at i:4996803 original size:34 final size:30
Alignment explanation
Indices: 4996696--4996797 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
4996686 TATGATAAAG
* *
4996696 ATAAAATATATATTATTATA-TTAAAATAAAA
1 ATAAAATATAT-TTAATA-AGTTAAAACAAAA
* *
4996727 ATAAAATATATTTAATAAGTTAAGACATAA
1 ATAAAATATATTTAATAAGTTAAAACAAAA
4996757 ATAAAATATATTTAATAAGTTAAAACAAAA
1 ATAAAATATATTTAATAAGTTAAAACAAAA
*
4996787 ATAAAAGATAT
1 ATAAAATATAT
4996798 ATATTTTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 51 0.81
31 11 0.17
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (30 bp):
ATAAAATATATTTAATAAGTTAAAACAAAA
Found at i:4999597 original size:18 final size:18
Alignment explanation
Indices: 4999574--4999617 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
4999564 GAGATAGTTT
4999574 ACAATTCTCATTTTCTCC
1 ACAATTCTCATTTTCTCC
4999592 ACAATTCTCATTTTCTCC
1 ACAATTCTCATTTTCTCC
4999610 ACAATTCT
1 ACAATTCT
4999618 AGGAGATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (18 bp):
ACAATTCTCATTTTCTCC
Found at i:5003288 original size:511 final size:510
Alignment explanation
Indices: 5002318--5003309 Score: 1657
Period size: 511 Copynumber: 1.9 Consensus size: 510
5002308 GTATTTTATA
5002318 TATTTAAATTGTTGAGAAAAATTATAAATTATCACGTTTTAAATACTAACTCATTTATTTTTTTA
1 TATTTAAATTGTTGAGAAAAATTATAAATTATCACGTTTTAAATACTAACTCATTTATTTTTTTA
* * *
5002383 GCTGTTACTATATTGAGATAAAATGGATTTTTTTAACACATTAGCTCAAGTTGCAATTTTAAAGA
66 GCTGTTACTATATCGAGATAAAATGGATTTTTTGAACACATTAGCTAAAGTTGCAATTTTAAAGA
** *
5002448 CAAACTATGCCAAACAAAATGAATTTATCCTTTATAGTTTTGTTGATAAGGTAGATATATTTATA
131 CAAACTATGCCAAACAAAATGAATTTATCCTTTATAGTTTTGCAGATAAGGAAGATATATTTATA
* *
5002513 AATATATTATAAATTATTTCTTAATATATATGTTTTTTTGTAGCTGAATGGTGAATTAATTATGG
196 AATATATTATAAATTATATATTAATATATATGTTTTTTTGTAGCTGAATGGTGAATTAATTATGG
*
5002578 AGAGTATACACCTCAACTTCAACGCATCACTGTCAAAATTTTGAGTCAAATAATTTAATCTTCAA
261 AGAGTATACACCTCAACTTCAACGCATCACTGTCAAAATTTTGAGTCAAAGAATTTAATCTTCAA
* * *
5002643 ATTGTGAGTGCAATTGGAGTACATTTAGTTTGATCCATACAAAGAAGAGAAATAGATTCAAACAT
326 ATTGTAAGCGCAATTGGAGTACATTTAGTTTGATCCATACAAAGAAAAGAAATAGATTCAAACAT
* * *
5002708 AAAAAGCTTCAAAAATTGGTTTATGTCCATTATAATATGAGATTGAAGGTGAGACACATGCGAAG
391 AAAAAGCTTAAAAAAATGGTTTATGTCCATTATAATATGAGATTGAAGATGAGACACATGCGAAG
5002773 AAAAAGTGCACAAGAGTTAGAAATGAGTTTTAATCCTATCAATCTTGAAAATATC
456 AAAAAGTGCACAAGAGTTAGAAATGAGTTTTAATCCTATCAATCTTGAAAATATC
* * *
5002828 TATTTACATTGTTGAGAAAACTTATAAATTATCATGTTTTAAATACTAACTCATTTA-TTTTTTA
1 TATTTAAATTGTTGAGAAAAATTATAAATTATCACGTTTTAAATACTAACTCATTTATTTTTTTA
*
5002892 GTTGTTACTATATCGAGATAAAATGGATTTTTTGGAACACATTAGCTAAAGCTT-CAATTTTAAA
66 GCTGTTACTATATCGAGATAAAATGGATTTTTT-GAACACATTAGCTAAAG-TTGCAATTTTAAA
* * *
5002956 GACTAACTCTGCTAAACAAAATGAATTTATCCTTTATAGTTTTTGCAGATAAGGAAGATATATTT
129 GACAAACTATGCCAAACAAAATGAATTTATCCTTTATAG-TTTTGCAGATAAGGAAGATATATTT
* *
5003021 ATAAATATTTTATAAATTATATATTAATATATATGTTTTTTTGTAGCTGAATGGTGGATTAATTA
193 ATAAATATATTATAAATTATATATTAATATATATGTTTTTTTGTAGCTGAATGGTGAATTAATTA
* * * *
5003086 TGGA-ATGTATGCACCTCAACTTCAACGCATCATTGTCAAAGTTTTGAGTCAAAGAATTTCATCT
258 TGGAGA-GTATACACCTCAACTTCAACGCATCACTGTCAAAATTTTGAGTCAAAGAATTTAATCT
5003150 TCAAATTGTAAGCGCAATTGGAGTACATTTAGTTTGATCCATACAAAGAAAAGAAATAGATTCAA
322 TCAAATTGTAAGCGCAATTGGAGTACATTTAGTTTGATCCATACAAAGAAAAGAAATAGATTCAA
*
5003215 GCATAAAAAGCTTAAAAAAATGGTTTATGTCCATTATAATATGAGATTGAAGATGAGACACATGC
387 ACATAAAAAGCTTAAAAAAATGGTTTATGTCCATTATAATATGAGATTGAAGATGAGACACATGC
*
5003280 GTAGAAAAAGTGCACAAGAGTTAGAAATGA
452 GAAGAAAAAGTGCACAAGAGTTAGAAATGA
5003310 TCTAATAAAT
Statistics
Matches: 448, Mismatches: 30, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
509 38 0.08
510 116 0.26
511 294 0.66
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (510 bp):
TATTTAAATTGTTGAGAAAAATTATAAATTATCACGTTTTAAATACTAACTCATTTATTTTTTTA
GCTGTTACTATATCGAGATAAAATGGATTTTTTGAACACATTAGCTAAAGTTGCAATTTTAAAGA
CAAACTATGCCAAACAAAATGAATTTATCCTTTATAGTTTTGCAGATAAGGAAGATATATTTATA
AATATATTATAAATTATATATTAATATATATGTTTTTTTGTAGCTGAATGGTGAATTAATTATGG
AGAGTATACACCTCAACTTCAACGCATCACTGTCAAAATTTTGAGTCAAAGAATTTAATCTTCAA
ATTGTAAGCGCAATTGGAGTACATTTAGTTTGATCCATACAAAGAAAAGAAATAGATTCAAACAT
AAAAAGCTTAAAAAAATGGTTTATGTCCATTATAATATGAGATTGAAGATGAGACACATGCGAAG
AAAAAGTGCACAAGAGTTAGAAATGAGTTTTAATCCTATCAATCTTGAAAATATC
Found at i:5004053 original size:31 final size:31
Alignment explanation
Indices: 5003991--5004080 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 31
5003981 TTATTTCGTC
* * *
5003991 ACTAAATATTTTTTTATAACTTTTTACTGTG
1 ACTAAATAATTTGTTACAACTTTTTACTGTG
*
5004022 ACTAAATAATTTGTTACAA-TTTGTTATTGTG
1 ACTAAATAATTTGTTACAACTTT-TTACTGTG
* * * *
5004053 AAATAATATTATTTGTCACAAATTTTTA
1 -ACTAA-ATAATTTGTTACAACTTTTTA
5004081 TAATGAGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
30 3 0.06
31 23 0.48
32 4 0.08
33 15 0.31
34 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (31 bp):
ACTAAATAATTTGTTACAACTTTTTACTGTG
Found at i:5004067 original size:33 final size:31
Alignment explanation
Indices: 5004030--5004115 Score: 75
Period size: 33 Copynumber: 2.6 Consensus size: 31
5004020 TGACTAAATA
* *
5004030 ATTTGTTACAATTTGTTATTGTGAAATAATATT
1 ATTTGTTACAATTTGTTATTGAGAAAT--TAAT
*
5004063 ATTTGTCACAAATTT-TTATAATGAGAAATTAAT
1 ATTTGTTAC-AATTTGTTAT--TGAGAAATTAAT
* *
5004096 ATTTGTTATAAATTGTTATT
1 ATTTGTTACAATTTGTTATT
5004116 TTTATTAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
31 1 0.02
32 4 0.09
33 26 0.60
34 5 0.12
35 7 0.16
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.50
Consensus pattern (31 bp):
ATTTGTTACAATTTGTTATTGAGAAATTAAT
Found at i:5004372 original size:199 final size:197
Alignment explanation
Indices: 5004018--5004426 Score: 606
Period size: 199 Copynumber: 2.1 Consensus size: 197
5004008 AACTTTTTAC
*
5004018 TGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAATAATATTATTTGTCACAAATTTTTATA
1 TGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAAATTTTTATA
* *
5004083 ATGAGAAATTAATATTTGTTATAAATTGTTATTTTTATTAAATAAATTTATCATAATATTTTACT
66 ATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTATCATAATATTTTACT
*
5004148 TTGACAAAATATTATGACGAAATAAATTTTGACATAACTTTTTACGTTAATTAAATTTAATGTGT
131 TTGACAAAATATTATGACGAAATAAA-TTTGACATAACTTTTTACGTTAACTAAATTTAATGTGT
5004213 TAT
195 TAT
* *
5004216 TGTGACTAAATCATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTT-TCACAATTTTTTA
1 TGTGACTAAAT-AATTTGTTACAATTTGTTATTGTGAAAGAATATTA-TTTGTCACAAATTTTTA
* * *
5004280 TATTGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCA-AATTTTTTT
64 TAATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTATCATAA-TATTTT
* * * * ** *
5004344 ATTTTGACAAAATATTTTGACTAAATAAATTTGACATAATTTTTTATTTTAACTAAATTTAATTT
128 ACTTTGACAAAATATTATGACGAAATAAATTTGACATAACTTTTTACGTTAACTAAATTTAATGT
5004409 GTTAT
193 GTTAT
* *
5004414 TTTGTCTAAATAA
1 TGTGACTAAATAA
5004427 ATGATCATAA
Statistics
Matches: 189, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
197 1 0.01
198 58 0.31
199 127 0.67
200 3 0.02
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (197 bp):
TGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAAATTTTTATA
ATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTATCATAATATTTTACT
TTGACAAAATATTATGACGAAATAAATTTGACATAACTTTTTACGTTAACTAAATTTAATGTGTT
AT
Found at i:5004494 original size:22 final size:22
Alignment explanation
Indices: 5004469--5004511 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5004459 ATTTTATTTA
*
5004469 AATTTGTTATTATAACTAAAAT
1 AATTTGTTATGATAACTAAAAT
*
5004491 AATTTGTTATGATAATTAAAA
1 AATTTGTTATGATAACTAAAA
5004512 ATATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTTGTTATGATAACTAAAAT
Found at i:5007735 original size:10 final size:10
Alignment explanation
Indices: 5007728--5007772 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
5007718 GAACGTTCAG
5007728 TTATGTTCGT
1 TTATGTTCGT
5007738 TTATGTTCGTT
1 TTATGTTCG-T
5007749 CGGTTATGTTCGT
1 ---TTATGTTCGT
5007762 TTATGTTCGT
1 TTATGTTCGT
5007772 T
1 T
5007773 CGGTTATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
13 1 0.03
14 9 0.29
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:5007738 original size:24 final size:24
Alignment explanation
Indices: 5007711--5007782 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
5007701 CGTTCATTTA
*
5007711 CGTTCGTGAACGTTCAGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* ** *
5007735 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* ** *
5007759 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
5007783 TGTTTATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (24 bp):
CGTTCATGAACGTTCAGTTATGTT
Found at i:5007749 original size:14 final size:14
Alignment explanation
Indices: 5007732--5007806 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
5007722 GTTCAGTTAT
5007732 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
5007746 GTTCGGTTA---T-
1 GTTCGTTTATGTTC
5007756 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
5007770 GTTCGGTTATG-T-
1 GTTCGTTTATGTTC
5007782 -TT-GTTTATGTTC
1 GTTCGTTTATGTTC
* *
5007794 ATTCATTTATGTT
1 GTTCGTTTATGTT
5007807 TAACCCAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
10 14 0.29
11 4 0.08
13 4 0.08
14 26 0.54
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:5007807 original size:24 final size:24
Alignment explanation
Indices: 5007721--5007806 Score: 127
Period size: 24 Copynumber: 3.6 Consensus size: 24
5007711 CGTTCGTGAA
5007721 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
5007745 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
5007769 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
5007793 CATTCATTTATGTT
1 CGTTCAGTTATGTT
5007807 TAACCCAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:5008893 original size:10 final size:10
Alignment explanation
Indices: 5008878--5008951 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
5008868 GGTCTCTAAT
5008878 GTTTATGTTC
1 GTTTATGTTC
5008888 GTTTATGTTC
1 GTTTATGTTC
*
5008898 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
5008910 GTTCGTGTTC
1 GTTTATGTTC
5008920 GTTTATGTTC
1 GTTTATGTTC
*
5008930 G----TGTTT
1 GTTTATGTTC
5008936 GTTTATGTTC
1 GTTTATGTTC
5008946 GTTTAT
1 GTTTAT
5008952 TTATTAAATG
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 32 0.67
11 7 0.15
12 4 0.08
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:5008902 original size:16 final size:16
Alignment explanation
Indices: 5008883--5008947 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
5008873 CTAATGTTTA
5008883 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
5008899 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
5008915 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
5008931 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5008947 T
1 T
5008948 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:5009220 original size:3 final size:3
Alignment explanation
Indices: 5009212--5009252 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5009202 AGTTAGTCCC
*
5009212 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5009253 TAATGCATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5013366 original size:85 final size:85
Alignment explanation
Indices: 5013213--5013383 Score: 213
Period size: 85 Copynumber: 2.0 Consensus size: 85
5013203 ACAATCACGC
* * * * * *
5013213 CACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAATTTATACA
1 CACACGAATGTGTATCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAATTCATAAA
*
5013278 TGCGTGTCATAAATTTATGA
66 TGCGCGTCATAAATTTATGA
* *
5013298 CACACGAATGTGTATCGTCTTCATTT-ATGACGGGGGCTTCAATGACGCGCAATG-AGCA-TCAT
1 CACACGAATGTGTATCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGTA--ATTCAT
5013360 AAATGCGCGTCATAAATTTATGA
63 AAATGCGCGTCATAAATTTATGA
5013383 C
1 C
5013384 GCACAGTTGC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.01
85 69 0.93
86 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (85 bp):
CACACGAATGTGTATCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAATTCATAAA
TGCGCGTCATAAATTTATGA
Found at i:5015264 original size:9 final size:9
Alignment explanation
Indices: 5015240--5015316 Score: 68
Period size: 9 Copynumber: 8.3 Consensus size: 9
5015230 AATATACATA
5015240 TTTT-TTAT
1 TTTTATTAT
*
5015248 GTTT-TTAT
1 TTTTATTAT
5015256 TTTTATTAT
1 TTTTATTAT
5015265 TTTTATTAT
1 TTTTATTAT
*
5015274 TTTTACTATT
1 TTTTATTA-T
*
5015284 TTTTATTTT
1 TTTTATTAT
5015293 TGGTTTATTAT
1 T--TTTATTAT
*
5015304 TATTATTTAT
1 TTTTA-TTAT
5015314 TTT
1 TTT
5015317 ACTTATTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
8 10 0.18
9 25 0.45
10 13 0.23
11 8 0.14
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.77
Consensus pattern (9 bp):
TTTTATTAT
Found at i:5015273 original size:45 final size:42
Alignment explanation
Indices: 5015220--5015314 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
5015210 AAATTAGCCC
*
5015220 TTTTATTATTAATATACATATTTTTTATGTTTTTATTT-TTATTAT
1 TTTTATTATT--TATAC-TATTTTTTAT-TTTTGATTTATTATTAT
* *
5015265 TTTTATTATTTTTACTATTTTTTATTTTTGGTTTATTATTAT
1 TTTTATTATTTATACTATTTTTTATTTTTGATTTATTATTAT
5015307 TATTTATT
1 T-TTTATT
5015315 TTACTTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 7 0.16
42 18 0.40
43 10 0.22
45 10 0.22
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (42 bp):
TTTTATTATTTATACTATTTTTTATTTTTGATTTATTATTAT
Found at i:5015275 original size:33 final size:34
Alignment explanation
Indices: 5015238--5015311 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
5015228 TTAATATACA
*
5015238 TATTTTT-TATGTTTTTATTTTT-ATTATTTTTAT
1 TATTTTTATAT-TTTTTATTTTTGATTATTATTAT
*
5015271 TATTTTTACTATTTTTTATTTTTGGTTTATTATTAT
1 TATTTTTA-TATTTTTTATTTTT-GATTATTATTAT
5015307 TATTT
1 TATTT
5015312 ATTTTACTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 7 0.20
34 11 0.31
35 3 0.09
36 14 0.40
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.76
Consensus pattern (34 bp):
TATTTTTATATTTTTTATTTTTGATTATTATTAT
Found at i:5015317 original size:18 final size:19
Alignment explanation
Indices: 5015251--5015329 Score: 67
Period size: 18 Copynumber: 4.2 Consensus size: 19
5015241 TTTTTATGTT
*
5015251 TTTATTTTTATTATTTTTA
1 TTTATTTTTATTATTATTA
* *
5015270 -TTATTTTTACTATTTTTTA
1 TTTATTTTTATTA-TTATTA
5015289 TTT-TTGGTTTATTATTATTA
1 TTTATT--TTTATTATTATTA
5015309 TTTA-TTTTACTTATTA-TA
1 TTTATTTTTA-TTATTATTA
5015327 TTT
1 TTT
5015330 TTCTAATGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
18 20 0.39
19 14 0.27
20 11 0.22
21 6 0.12
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTATTATTA
Found at i:5015423 original size:13 final size:13
Alignment explanation
Indices: 5015407--5015507 Score: 54
Period size: 12 Copynumber: 8.1 Consensus size: 13
5015397 TTTTTACCTA
* *
5015407 ATATTTTATATGT
1 ATATTATATATAT
5015420 ATATTATATATAT
1 ATATTATATATAT
5015433 ATA-TATAT-TAT
1 ATATTATATATAT
* * *
5015444 TTGTT-TTTCACT-T
1 ATATTATAT-A-TAT
* *
5015457 ATTTTAT-TAAAT
1 ATATTATATATAT
*
5015469 ATTATAATATATAT
1 A-TATTATATATAT
5015483 ATA-TATATATAT
1 ATATTATATATAT
5015495 ATA-TATATATAT
1 ATATTATATATAT
5015507 A
1 A
5015508 CACACACACA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
11 6 0.09
12 30 0.44
13 25 0.37
14 7 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
ATATTATATATAT
Found at i:5015427 original size:71 final size:70
Alignment explanation
Indices: 5015300--5015436 Score: 172
Period size: 71 Copynumber: 1.9 Consensus size: 70
5015290 TTTTGGTTTA
*
5015300 TTATTATTATTTATTTTACTTATTATATTTTTCTAATGTTTTATTTATACGTTTATAGATATATA
1 TTATTATTATTTATTTTACTTATTATATTTTTCTAATATTTTATTTATAC--TTATAGATATATA
5015365 TTGTACT
64 TTGTACT
* *
5015372 TTATT-TTATTTATTTTA-TTTTTATATTTTTACCTAATATTTTATATGTATA-TTATATATATA
1 TTATTATTATTTATTTTACTTATTATATTTTT--CTAATATTTTAT-T-TATACTTATAGATATA
5015434 TAT
62 TAT
5015437 ATATTATTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
70 12 0.21
71 25 0.43
72 16 0.28
73 1 0.02
74 4 0.07
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (70 bp):
TTATTATTATTTATTTTACTTATTATATTTTTCTAATATTTTATTTATACTTATAGATATATATT
GTACT
Found at i:5015526 original size:2 final size:2
Alignment explanation
Indices: 5015467--5015507 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5015457 ATTTTATTAA
5015467 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5015507 A
1 A
5015508 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5015750 original size:4 final size:4
Alignment explanation
Indices: 5015741--5015775 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5015731 TTCATTATTT
5015741 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5015776 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:5015813 original size:36 final size:35
Alignment explanation
Indices: 5015773--5015846 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
5015763 TCTTTCTTTC
* *
5015773 TTTTTTTTTT-TTT-TTTT-GTTTTTTTTATTTATT
1 TTTTTTTTTTATTTATTTTAATTTTTATTA-TTATT
*
5015806 TTTTTTTTTTATTTATTTTAATTTTTATTATTGTT
1 TTTTTTTTTTATTTATTTTAATTTTTATTATTATT
5015841 TTTTTT
1 TTTTTT
5015847 ATTTGGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 10 0.29
34 3 0.09
35 14 0.40
36 8 0.23
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (35 bp):
TTTTTTTTTTATTTATTTTAATTTTTATTATTATT
Found at i:5015815 original size:27 final size:27
Alignment explanation
Indices: 5015777--5015870 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
5015767 TCTTTCTTTT
5015777 TTTTTTTTTTTTTGTTTTTTTTATTTA
1 TTTTTTTTTTTTTGTTTTTTTTATTTA
* *
5015804 TTTTTTTTTTTTATTTATTTTAATTTTTATTA
1 TTTTTTTTTTTT-TGT-TTTT--TTTAT-TTA
* *
5015836 TTGTTTTTTTTATTTGGTTTTTTTATATA
1 TT-TTTTTTTT-TTTGTTTTTTTTATTTA
*
5015865 TATTTT
1 TTTTTT
5015871 GTATTTATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
27 12 0.23
28 6 0.11
29 7 0.13
30 4 0.08
31 4 0.08
32 9 0.17
33 9 0.17
34 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (27 bp):
TTTTTTTTTTTTTGTTTTTTTTATTTA
Found at i:5015824 original size:12 final size:12
Alignment explanation
Indices: 5015710--5015881 Score: 64
Period size: 12 Copynumber: 14.8 Consensus size: 12
5015700 TATATATATA
5015710 TATTTA-TTTTT
1 TATTTATTTTTT
*
5015721 T-TTCATTTTTT
1 TATTTATTTTTT
5015732 TCA-TTA-TTTTT
1 T-ATTTATTTTTT
* * *
5015743 TCTTTCTTTCTT
1 TATTTATTTTTT
* * *
5015755 TCTTTCTTTCTT
1 TATTTATTTTTT
* *
5015767 TCTTT-CTTTTT
1 TATTTATTTTTT
5015778 T-TTT-TTTTTT
1 TATTTATTTTTT
*
5015788 T-TGT-TTTTTT
1 TATTTATTTTTT
5015798 TATTTATTTTTT
1 TATTTATTTTTT
5015810 T-TTT-TTATTTAT
1 TATTTATT-TTT-T
*
5015822 T-TTAATTTTTAT
1 TATTTATTTTT-T
5015834 TATTGT-TTTTTT
1 TATT-TATTTTTT
*
5015846 TATTTGGTTTTTT
1 TATTT-ATTTTTT
* *
5015859 TATATATATTTTG
1 TATTTAT-TTTTT
5015872 TATTTATTTT
1 TATTTATTTT
5015882 CTTTTATTTC
Statistics
Matches: 130, Mismatches: 16, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
10 23 0.18
11 29 0.22
12 49 0.38
13 29 0.22
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.80
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:5015831 original size:1 final size:1
Alignment explanation
Indices: 5015773--5015815 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
5015763 TCTTTCTTTC
* * *
5015773 TTTTTTTTTTTTTTTTTGTTTTTTTTATTTATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5015816 ATTTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.05, C:0.00, G:0.02, T:0.93
Consensus pattern (1 bp):
T
Found at i:5018060 original size:21 final size:21
Alignment explanation
Indices: 5018034--5018081 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5018024 GTTTCCATAT
* *
5018034 TCGCAACGTAAACTTCGACTA
1 TCGCAAAGCAAACTTCGACTA
* *
5018055 TCGCAAAGCGAACTTGGACTA
1 TCGCAAAGCAAACTTCGACTA
5018076 TCGCAA
1 TCGCAA
5018082 TGTGATTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAAAGCAAACTTCGACTA
Found at i:5018134 original size:21 final size:21
Alignment explanation
Indices: 5018094--5018140 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5018084 TGATTTACAT
5018094 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
* * **
5018115 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCATTGCGATAGTCCAA
5018136 ATTCG
1 ATTCG
5018141 GCGCGGACGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (21 bp):
ATTCGCATTGCGATAGTCCAA
Found at i:5018178 original size:6 final size:6
Alignment explanation
Indices: 5018167--5018191 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5018157 GACACGTATT
5018167 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
5018192 GACGGACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5018842 original size:21 final size:21
Alignment explanation
Indices: 5018818--5018956 Score: 115
Period size: 21 Copynumber: 6.6 Consensus size: 21
5018808 TTTGGAATAA
5018818 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
5018839 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
5018858 AAATCGCAACACGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
5018881 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* * *
5018900 AAATCGCAACACGAATTTCGATT
1 --ATCGCAACGCGAACTTCGACT
*
5018923 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
5018944 ATCGCAATGCGAA
1 ATCGCAACGCGAA
5018957 TATGTAAATC
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 19 0.20
21 57 0.59
23 20 0.21
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:5018855 original size:42 final size:42
Alignment explanation
Indices: 5018793--5018941 Score: 226
Period size: 42 Copynumber: 3.5 Consensus size: 42
5018783 TGCGATTTTG
* * *
5018793 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
5018835 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
* *
5018877 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAATTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
*
5018919 GATTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
5018942 CTATCGCAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
42 89 0.91
44 9 0.09
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
Found at i:5020147 original size:42 final size:42
Alignment explanation
Indices: 5020100--5020183 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
5020090 TTTTTGATGT
* * *
5020100 TGAATATATT-GGTGAATATATGTTTCTCTATAGCTAGAGCAA
1 TGAATATATTAGCT-AACATATGTTTCTCTATAGCCAGAGCAA
*
5020142 TGAATATATTAGCTAACATATGTTTCTCTATTGCCAGAGCAA
1 TGAATATATTAGCTAACATATGTTTCTCTATAGCCAGAGCAA
5020184 GGAAATTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (42 bp):
TGAATATATTAGCTAACATATGTTTCTCTATAGCCAGAGCAA
Found at i:5022636 original size:3 final size:3
Alignment explanation
Indices: 5022622--5022660 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
5022612 AATATTTATT
*
5022622 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5022661 AAACAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5023021 original size:75 final size:74
Alignment explanation
Indices: 5022897--5023087 Score: 256
Period size: 75 Copynumber: 2.6 Consensus size: 74
5022887 TAAAATCTCA
* * ** * *
5022897 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGATTTAAAATCAAAAAGCTCCC
1 TTTGAAAACATCATGCACTGGAGGTCTTACAGATGACCCTGAGGATTTAAAATCAAAAAGCTCAC
*
5022962 GAAGGCTTTT
66 AAAGGC-TTT
* *
5022972 TTTGACAACATCATGCACTGGAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCAC
1 TTTGAAAACATCATGCACTGGAGGTCTTACAGATGACCCTGAGGATTTAAAATCAAAAAGCTCAC
5023037 AAAGGCTTT
66 AAAGGCTTT
* * * *
5023046 TTTGAAAACATCATGCAATTGAGGTATTACAGATAACCCTGA
1 TTTGAAAACATCATGCACTGGAGGTCTTACAGATGACCCTGA
5023088 AGGTTTTGAA
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 40 0.39
75 62 0.61
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (74 bp):
TTTGAAAACATCATGCACTGGAGGTCTTACAGATGACCCTGAGGATTTAAAATCAAAAAGCTCAC
AAAGGCTTT
Found at i:5023150 original size:45 final size:45
Alignment explanation
Indices: 5023045--5023261 Score: 339
Period size: 45 Copynumber: 4.8 Consensus size: 45
5023035 ACAAAGGCTT
* *
5023045 TTTTGAAAACATCATGCAATTG-AGGTA-TTACAGATAACCCTGAAGG
1 TTTTGAAAACATCATGC-ACTGAAGG-ACTTACAGATGACCC-GAAGG
*
5023091 TTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
5023136 TTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
5023181 TTTTGAAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
5023226 TTTTGAAAACATCATGCACTGAAGAACTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATG
5023262 TGGGAAATAA
Statistics
Matches: 162, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
45 131 0.81
46 31 0.19
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
Found at i:5025276 original size:75 final size:75
Alignment explanation
Indices: 5025117--5025278 Score: 227
Period size: 75 Copynumber: 2.2 Consensus size: 75
5025107 AATATGGTTC
* * * * *
5025117 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATACCTCAATATTCTAGATTCTGATT
1 TTCAGCATGTCCCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCTAGATTATGATT
5025182 GAAAGGGGCT
66 GAAAGGGGCT
* **
5025192 TTCAGCATGTCCCAGCATTGGCTAATACAAACATTCAAAATGTATCAATATTCCT-GATTATGAT
1 TTCAGCATGTCCCAACATTGGCTAATACAAACATTCAAAATACATCAATATT-CTAGATTATGAT
*
5025256 TGAAATGGGCT
65 TGAAAGGGGCT
5025267 TTCAGCATGTCC
1 TTCAGCATGTCC
5025279 TATCATTTAC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 75 0.97
76 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (75 bp):
TTCAGCATGTCCCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCTAGATTATGATT
GAAAGGGGCT
Found at i:5028067 original size:32 final size:32
Alignment explanation
Indices: 5028026--5028087 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
5028016 GAAGAAATGA
* *
5028026 TTGTTATGCTTATCTGGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
5028058 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
5028088 TGTTTCCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:5034407 original size:2 final size:2
Alignment explanation
Indices: 5034395--5034426 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5034385 TATTATTTAT
*
5034395 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5034427 CTAACGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5035797 original size:19 final size:19
Alignment explanation
Indices: 5035773--5035810 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5035763 GATTTGGATG
*
5035773 TAAATAATAAAATGATAAA
1 TAAATAATAAAATAATAAA
5035792 TAAATAATAAAATAATAAA
1 TAAATAATAAAATAATAAA
5035811 AGCAAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
TAAATAATAAAATAATAAA
Found at i:5036612 original size:14 final size:13
Alignment explanation
Indices: 5036593--5036622 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5036583 ATAATGCTCG
5036593 ATGATTGATGAAGT
1 ATGATTGAT-AAGT
5036607 ATGATTGATAAGT
1 ATGATTGATAAGT
5036620 ATG
1 ATG
5036623 TAAAGTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (13 bp):
ATGATTGATAAGT
Found at i:5037414 original size:18 final size:18
Alignment explanation
Indices: 5037377--5037430 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
5037367 GAGAAAACGA
5037377 GAATAATAAAGTAATG-AT
1 GAATAATAAA-TAATGAAT
*
5037395 GAATAATAAAAAATGAAT
1 GAATAATAAATAATGAAT
*
5037413 GATAGAATAAATAATGAA
1 GA-ATAATAAATAATGAA
5037431 ATTATTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.13
18 14 0.45
19 13 0.42
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (18 bp):
GAATAATAAATAATGAAT
Found at i:5038053 original size:43 final size:43
Alignment explanation
Indices: 5038005--5038091 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
5037995 CTAGGCATGG
5038005 ATTGGAATATGCCTAGTATTTTTGTATGATAAGAAATTAAAGA
1 ATTGGAATATGCCTAGTATTTTTGTATGATAAGAAATTAAAGA
*
5038048 ATTGGAATATGCTTAGTATTTTTGTATGATAAGAAATTAAAGA
1 ATTGGAATATGCCTAGTATTTTTGTATGATAAGAAATTAAAGA
5038091 A
1 A
5038092 GAAAGTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38
Consensus pattern (43 bp):
ATTGGAATATGCCTAGTATTTTTGTATGATAAGAAATTAAAGA
Found at i:5041111 original size:3 final size:3
Alignment explanation
Indices: 5041097--5041168 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
5041087 TGTAATATTA
* * *
5041097 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT TAT TAT AAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5041143 AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5041169 CATTAAAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:5041663 original size:113 final size:112
Alignment explanation
Indices: 5041446--5041994 Score: 686
Period size: 113 Copynumber: 4.8 Consensus size: 112
5041436 AAATGAGTTA
* * * * *
5041446 TTCTCATTATGAACTCCTTCTTTCTTTTTCAGATGACGAGTTCTTCTGATTATGAACTTTATCTG
1 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTATCTG
* * * * * *
5041511 GCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAATTC
63 GAAAAGCTGATCCATCAA-TGATGGATTTAAACATAAGGTTGAACAAATTC
* * *
5041562 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAACTTTCTCTGGAA
1 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAA
* * *
5041627 AAGCTGATCCATCAAGTTATGGATTTGAGCATAAGGTTGAACAAATTC
66 AAGCTGATCCATCAA-TGATGGATTTAAACATAAGGTTGAACAAATTC
** *
5041675 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
1 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAA
* * *
5041740 AAGTTGATCCATTGAATGATGGATTTAAATATAAGGTTGAACAAATTC
66 AAGCTGATCCA-TCAATGATGGATTTAAACATAAGGTTGAACAAATTC
* *
5041788 TTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAA
* * *
5041853 AAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTTAACAAATTC
66 AAGCTGATCCATCAA-TGATGGATTTAAACATAAGGTTGAACAAATTC
* * ** **
5041901 TTCTCATTATGAATTTCTTCTT-CTCCCTTCAGATGAGTTCTTCTCATTATTAACTCGAAATGGA
1 TTCTCATTATGAATTTCTTCTTCCT-TCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGA
* *
5041965 AAAGTTGATCCATTGAATGATGGATTTAAA
65 AAAGCTGATCCA-TCAATGATGGATTTAAA
5041995 TCTTTGCTAA
Statistics
Matches: 378, Mismatches: 51, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
112 5 0.01
113 336 0.89
114 6 0.02
116 31 0.08
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (112 bp):
TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAA
AAGCTGATCCATCAATGATGGATTTAAACATAAGGTTGAACAAATTC
Found at i:5041768 original size:226 final size:225
Alignment explanation
Indices: 5041446--5041994 Score: 830
Period size: 226 Copynumber: 2.4 Consensus size: 225
5041436 AAATGAGTTA
* * * * ** *
5041446 TTCTCATTATGAACTCCTTCTTTCTTTTTCAGATGACGAGTTCTTCTGATTATGAACTTTATCTG
1 TTCTCATTATGAATTTCTTC-TTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCGAACTG
* * * * *
5041511 GCAATGTTAATCCA-TCAATTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
62 GAAAAGTTGATCCATTGAA-TGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
* *
5041575 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAACTTTCTCTGGAAAAGCTGATCCATC
126 CTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
*
5041640 AAGTTATGGATTTGAGCATAAGGTTGAACAAATTC
191 AAGTGATGGATTTGAGCATAAGGTTGAACAAATTC
5041675 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
1 TTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
* * *
5041740 AAGTTGATCCATTGAATGATGGATTTAAATATAAGGTTGAACAAATTCTTCTCATTATGAATTTC
65 AAGTTGATCCATTGAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
5041805 TTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
130 TTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
*
5041870 GATGGATTTGAGCATAAGGTTTAACAAATTC
195 GATGGATTTGAGCATAAGGTTGAACAAATTC
* * *
5041901 TTCTCATTATGAATTTCTTCTTCTCCCTTCAGATGAGTTCTTCTCATTATTAACTCGAAATGGAA
1 TTCTCATTATGAATTTCTTCTTCT-TCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
5041966 AAGTTGATCCATTGAATGATGGATTTAAA
65 AAGTTGATCCATTGAATGATGGATTTAAA
5041995 TCTTTGCTAA
Statistics
Matches: 295, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
225 2 0.01
226 260 0.88
227 3 0.01
228 2 0.01
229 28 0.09
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (225 bp):
TTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAA
AGTTGATCCATTGAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
TATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTG
ATGGATTTGAGCATAAGGTTGAACAAATTC
Found at i:5042956 original size:83 final size:83
Alignment explanation
Indices: 5042806--5043024 Score: 366
Period size: 83 Copynumber: 2.6 Consensus size: 83
5042796 TTGGTTTTGG
*
5042806 GGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA
1 GGTTC-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCA
5042871 TCTTTCAAATTCAATAACT
65 TCTTTCAAATTCAATAACT
* *
5042890 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATGAGCACATCCAT
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCAT
* * *
5042955 CTTTCAATTTCAATGATT
66 CTTTCAAATTCAATAACT
*
5042973 GGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
5043025 AATTCAATGA
Statistics
Matches: 126, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
83 122 0.97
84 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (83 bp):
GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCAT
CTTTCAAATTCAATAACT
Found at i:5043064 original size:64 final size:64
Alignment explanation
Indices: 5042963--5043088 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
5042953 ATCTTTCAAT
*
5042963 TTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAAA
1 TTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAAA
*
5043027 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 TTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
5043089 TGAGTACATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (64 bp):
TTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAAA
Found at i:5043144 original size:147 final size:147
Alignment explanation
Indices: 5042877--5043171 Score: 491
Period size: 147 Copynumber: 2.0 Consensus size: 147
5042867 TTCATCTTTC
*
5042877 AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTA
1 AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* * * *
5042942 TGAGCACATCCATCTTTCAATTTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
66 TGAGCACATCCATCTTTCAAATTCAATAACTGGTTCTACCAAACCAGATCAGATAACTCAAAGAA
5043007 CACTTCCAGAAGATGCT
131 CACTTCCAGAAGATGCT
* *
5043024 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* * *
5043089 TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
66 TGAGCACATCCATCTTTCAAATTCAATAACTGGTTCTACCAAACCAGATCAGATAACTCAAAGAA
*
5043154 CACTTCCATAAGATGCT
131 CACTTCCAGAAGATGCT
5043171 A
1 A
5043172 TTAGCACATT
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 137 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (147 bp):
AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGCACATCCATCTTTCAAATTCAATAACTGGTTCTACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCT
Found at i:5043167 original size:83 final size:83
Alignment explanation
Indices: 5043024--5043596 Score: 894
Period size: 83 Copynumber: 6.9 Consensus size: 83
5043014 AGAAGATGCT
5043024 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
5043089 TGAGTACATTCATCTTTC
66 TGAGCACATTCATCTTCC
* * *
5043107 AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
5043172 TTAGCACATTCCTCTTCC
66 TGAGCACATTCATCTTCC
* * * * *
5043190 AATTTCAATGAGTGGTTCTGCCAAACCTGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
5043255 TGAGCATATTCATCTTCC
66 TGAGCACATTCATCTTCC
5043273 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
5043338 TGAGTACATTCATCTTTC
66 TGAGCACATTCATCTTCC
* * *
5043356 AAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
5043421 TTAGCACATTCCTCTTCC
66 TGAGCACATTCATCTTCC
* * * *
5043439 AATTTCAATGATTGGTTCTGCCAAACCTGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
5043504 TGAACATATTCATCTTCC
66 TGAGCACATTCATCTTCC
*
5043522 AAATTCAATGATTGGTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
5043587 TGAGTACATT
66 TGAGCACATT
5043597 GCATTTGTTC
Statistics
Matches: 439, Mismatches: 51, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 439 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGCACATTCATCTTCC
Found at i:5043462 original size:249 final size:249
Alignment explanation
Indices: 5043024--5043596 Score: 1119
Period size: 249 Copynumber: 2.3 Consensus size: 249
5043014 AGAAGATGCT
5043024 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
5043089 TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
66 TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
5043154 CACTTCCATAAGATGCTATTAGCACATTCCTCTTCCAATTTCAATGAGTGGTTCTGCCAAACCTG
131 CACTTCCATAAGATGCTATTAGCACATTCCTCTTCCAATTTCAATGAGTGGTTCTGCCAAACCTG
*
5043219 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCC
196 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATCTTCC
5043273 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
5043338 TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
66 TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
*
5043403 CACTTCCATAAGATGCTATTAGCACATTCCTCTTCCAATTTCAATGATTGGTTCTGCCAAACCTG
131 CACTTCCATAAGATGCTATTAGCACATTCCTCTTCCAATTTCAATGAGTGGTTCTGCCAAACCTG
5043468 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATCTTCC
196 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATCTTCC
*
5043522 AAATTCAATGATTGGTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
5043587 TGAGTACATT
66 TGAGTACATT
5043597 GCATTTGTTC
Statistics
Matches: 321, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 321 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (249 bp):
AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGTACATTCATCTTTCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCATAAGATGCTATTAGCACATTCCTCTTCCAATTTCAATGAGTGGTTCTGCCAAACCTG
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATCTTCC
Found at i:5044747 original size:1 final size:1
Alignment explanation
Indices: 5044743--5044835 Score: 60
Period size: 1 Copynumber: 93.0 Consensus size: 1
5044733 TTGACCCCCC
* * * * * * * ** * *
5044743 TTTTTCTTTTTTTCTTTTTTTCTTTTTTTTCTTTTTTCTTTTTTCTCTTTTCCTTCTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
5044808 TTTTCTTTTTTCTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
5044836 CAAGCATAAT
Statistics
Matches: 66, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:5044760 original size:7 final size:7
Alignment explanation
Indices: 5044743--5044832 Score: 108
Period size: 7 Copynumber: 11.7 Consensus size: 7
5044733 TTGACCCCCC
5044743 TTTTTCTT
1 TTTTTC-T
5044751 TTTTTCTT
1 TTTTTC-T
5044759 TTTTTCTTT
1 TTTTTC--T
5044768 TTTTTCT
1 TTTTTCT
5044775 TTTTTCTT
1 TTTTTC-T
5044783 TTTTCTCT
1 TTTT-TCT
5044791 TTTCCTTCT
1 TTT--TTCT
5044800 TTTTTCT
1 TTTTTCT
5044807 TTTTTCT
1 TTTTTCT
5044814 TTTTTCT
1 TTTTTCT
5044821 TTTTTCT
1 TTTTTCT
5044828 TTTTT
1 TTTTT
5044833 TTTCAAGCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 11
0.88 0.00 0.12
Matches are distributed among these distances:
7 37 0.48
8 23 0.30
9 16 0.21
10 1 0.01
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:5044771 original size:25 final size:24
Alignment explanation
Indices: 5044743--5044833 Score: 125
Period size: 25 Copynumber: 3.8 Consensus size: 24
5044733 TTGACCCCCC
5044743 TTTTTCTTTTTTTCTTTTTTTCTTT
1 TTTTTC-TTTTTTCTTTTTTTCTTT
5044768 TTTTTCTTTTTTCTTTTTTCTCTTT
1 TTTTTCTTTTTTCTTTTTT-TCTTT
**
5044793 TCCTTCTTTTTTC-TTTTTTC--T
1 TTTTTCTTTTTTCTTTTTTTCTTT
5044814 TTTTTCTTTTTTCTTTTTTT
1 TTTTTCTTTTTTCTTTTTTT
5044834 TTCAAGCATA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
21 12 0.20
22 6 0.10
23 2 0.03
24 18 0.30
25 22 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTCTTTTTTCTTTTTTTCTTT
Found at i:5044780 original size:32 final size:31
Alignment explanation
Indices: 5044743--5044834 Score: 141
Period size: 32 Copynumber: 2.9 Consensus size: 31
5044733 TTGACCCCCC
5044743 TTTTTCTTTTTTTCTTTTTTTCTTTTTTTTCT
1 TTTTTC-TTTTTTCTTTTTTTCTTTTTTTTCT
* *
5044775 TTTTTCTTTTTTCTCTTTTCCTTCTTTTTTCT
1 TTTTTCTTTTTTCTTTTTTTCTT-TTTTTTCT
5044807 TTTTTCTTTTTTC-TTTTTTCTTTTTTTT
1 TTTTTCTTTTTTCTTTTTTTCTTTTTTTT
5044835 TCAAGCATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.11
31 22 0.40
32 27 0.49
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (31 bp):
TTTTTCTTTTTTCTTTTTTTCTTTTTTTTCT
Found at i:5044834 original size:25 final size:25
Alignment explanation
Indices: 5044743--5044836 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 25
5044733 TTGACCCCCC
5044743 TTTTTCTTTTTT-TC-TTTTTTTCT
1 TTTTTCTTTTTTCTCTTTTTTTTCT
* *
5044766 TTTTT-TTCTTTTTTCTTTTTTCTCT
1 TTTTTCTT-TTTTCTCTTTTTTTTCT
5044791 TTTCCTTC-TTTTT-TC--TTTTTTCT
1 TTT--TTCTTTTTTCTCTTTTTTTTCT
5044814 TTTTTCTTTTTTCT-TTTTTTTTC
1 TTTTTCTTTTTTCTCTTTTTTTTC
5044837 AAGCATAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
21 3 0.05
22 7 0.12
23 20 0.34
24 9 0.15
25 13 0.22
26 4 0.07
27 3 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTCTTTTTTCTCTTTTTTTTCT
Found at i:5054948 original size:9 final size:9
Alignment explanation
Indices: 5054934--5054958 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5054924 TAAACATGCT
5054934 TTTAAATAA
1 TTTAAATAA
5054943 TTTAAATAA
1 TTTAAATAA
5054952 TTTAAAT
1 TTTAAAT
5054959 TTACATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAATAA
Found at i:5055330 original size:28 final size:27
Alignment explanation
Indices: 5055291--5055344 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
5055281 TTGCAAATAA
* *
5055291 AATGAAACATATAAATATTATGAAAAT
1 AATGAAAAATATAAAAATTATGAAAAT
*
5055318 AATGAATAAATATAAAAATTTTGAAAA
1 AATGAA-AAATATAAAAATTATGAAAA
5055345 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (27 bp):
AATGAAAAATATAAAAATTATGAAAAT
Found at i:5055352 original size:28 final size:28
Alignment explanation
Indices: 5055299--5055352 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5055289 AAAATGAAAC
* * *
5055299 ATATAAATATTATGAAAATAATGAATAA
1 ATATAAAAATTATGAAAAGAAAGAATAA
*
5055327 ATATAAAAATTTTGAAAAGAAAGAAT
1 ATATAAAAATTATGAAAAGAAAGAAT
5055353 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (28 bp):
ATATAAAAATTATGAAAAGAAAGAATAA
Found at i:5057420 original size:3 final size:3
Alignment explanation
Indices: 5057402--5057473 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
5057392 TGTAATATTA
* * * * * *
5057402 AAT AAT ATAT ATT AAT AAT AAT AAT TAT TAT TAT TAT AAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5057448 AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5057474 CATTAAAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:5065717 original size:17 final size:18
Alignment explanation
Indices: 5065695--5065729 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5065685 AAATGTATTT
5065695 TTCATTTTAA-TAAAACA
1 TTCATTTTAATTAAAACA
5065712 TTCATTTTAATTAAAACA
1 TTCATTTTAATTAAAACA
5065730 ATAAACTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTCATTTTAATTAAAACA
Found at i:5066819 original size:28 final size:28
Alignment explanation
Indices: 5066787--5066851 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
5066777 ACAAAGAAGA
5066787 AAAATAAA-TAAAACATG-GGGACTAAATT
1 AAAATAAATTAAAAC-TGAGGGAC-AAATT
*
5066815 AAAATAAATTAAAACTGTATGGACAAATT
1 AAAATAAATTAAAACTG-AGGGACAAATT
5066844 AAAATAAA
1 AAAATAAA
5066852 AAATAGATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 10 0.30
29 19 0.58
30 4 0.12
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (28 bp):
AAAATAAATTAAAACTGAGGGACAAATT
Found at i:5068266 original size:23 final size:22
Alignment explanation
Indices: 5068240--5068286 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
5068230 TGGTTCCTGT
5068240 TGGGCTCCGAGTTTGGGTCTTGA
1 TGGGCTCCGAGTTTGGGT-TTGA
* *
5068263 TGGGCTTCGGGTTTGGGTTTGA
1 TGGGCTCCGAGTTTGGGTTTGA
5068285 TG
1 TG
5068287 TAACTTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.06, C:0.13, G:0.43, T:0.38
Consensus pattern (22 bp):
TGGGCTCCGAGTTTGGGTTTGA
Found at i:5070041 original size:19 final size:19
Alignment explanation
Indices: 5070019--5070074 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
5070009 ATTATAATTT
5070019 TAAAATAATAACAATAAAA-
1 TAAAATAATAA-AATAAAAG
5070038 T-AAATAATAATAAATAAAAGG
1 TAAAATAAT-A-AAATAAAA-G
*
5070059 GAAAATAATAAAATAA
1 TAAAATAATAAAATAA
5070075 TAAATAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
20 7 0.23
21 1 0.03
22 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (19 bp):
TAAAATAATAAAATAAAAG
Found at i:5070149 original size:18 final size:18
Alignment explanation
Indices: 5070126--5070168 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5070116 TTGTTTTTTA
*
5070126 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
5070144 AAATAAAGGAAAATAATT
1 AAATAAAAGAAAAGAATT
5070162 AAATAAA
1 AAATAAA
5070169 CAAATTACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:5070917 original size:25 final size:24
Alignment explanation
Indices: 5070870--5070917 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5070860 AAATCGTAAT
*
5070870 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACATATATAAAC
5070894 TAAAATACCTAAAACA-ATGATAAA
1 TAAAATA-CTAAAACATAT-ATAAA
5070918 ATATAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACATATATAAAC
Found at i:5072873 original size:11 final size:11
Alignment explanation
Indices: 5072847--5072895 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
5072837 AAAGTTCGCT
5072847 GAAAATAAAAC
1 GAAAATAAAAC
5072858 G-AAATAAAAC
1 GAAAATAAAAC
5072868 GAAAATAAAAAC
1 GAAAAT-AAAAC
* *
5072880 AAAAATATAAC
1 GAAAATAAAAC
5072891 -AAAAT
1 GAAAAT
5072896 GGGTTACCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 15 0.44
11 9 0.26
12 10 0.29
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (11 bp):
GAAAATAAAAC
Found at i:5076117 original size:75 final size:74
Alignment explanation
Indices: 5075960--5076097 Score: 197
Period size: 75 Copynumber: 1.9 Consensus size: 74
5075950 AAACATCTTA
* *
5075960 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAACTAAAACAAAAATAATATTTAAAA
1 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAACTAAAACAAAAATAAAATATAAAA
*
5076025 TAATATTCT
66 TAAAATTCT
* * *
5076034 AAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 -AATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAACTAAAACAAAAATAAAATATAA
5076098 TGTTTAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 5 0.09
75 52 0.91
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (74 bp):
AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAACTAAAACAAAAATAAAATATAAAA
TAAAATTCT
Found at i:5079421 original size:39 final size:38
Alignment explanation
Indices: 5079359--5079438 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
5079349 TCATTTCTAA
* *
5079359 TTTCAAAATTATTTTAACCTAACATTCTAAATCTATTTTT
1 TTTCAAAATTATTTCAACCTAACATT-TAAAT-TATTTAT
* *
5079399 TTTC-AAATTATTTCATCTTAACATTTAAATTATTTAT
1 TTTCAAAATTATTTCAACCTAACATTTAAATTATTTAT
5079436 TTT
1 TTT
5079439 AATATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 9 0.25
38 5 0.14
39 18 0.50
40 4 0.11
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (38 bp):
TTTCAAAATTATTTCAACCTAACATTTAAATTATTTAT
Found at i:5079455 original size:21 final size:22
Alignment explanation
Indices: 5079403--5079461 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
5079393 ATTTTTTTTC
* *
5079403 AAATTATTTCATCTTAACATTT
1 AAATTATTTTATTTTAACATTT
*
5079425 AAATTA-TTTATTTTAATA-TT
1 AAATTATTTTATTTTAACATTT
5079445 AAATTATTTTAATTTTA
1 AAATTATTTT-ATTTTA
5079462 GTTTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 12 0.38
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATTTTATTTTAACATTT
Found at i:5079459 original size:26 final size:27
Alignment explanation
Indices: 5079430--5079508 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
5079420 CATTTAAATT
*
5079430 ATTTATTTTAATATTAAATTAT-TTTA
1 ATTTATTTTAATTTTAAATTATATTTA
*
5079456 ATTTTAGTTTTAATTTTATAATTTTATTTA
1 A-TTTA-TTTTAATTTTA-AATTATATTTA
* *
5079486 ATTT-TTATATTTTTAAATTATAT
1 ATTTATTTTAATTTTAAATTATAT
5079509 AATTTGAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.18
27 13 0.30
28 10 0.23
29 8 0.18
30 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (27 bp):
ATTTATTTTAATTTTAAATTATATTTA
Found at i:5079497 original size:18 final size:18
Alignment explanation
Indices: 5079450--5079498 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
5079440 ATATTAAATT
5079450 ATTTTA-ATTTTAGTTTTA
1 ATTTTATATTTTAG-TTTA
5079468 ATTTTATAATTTTA-TTTA
1 ATTTTAT-ATTTTAGTTTA
5079486 ATTTTTATATTTT
1 A-TTTTATATTTT
5079499 TAAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 16 0.57
19 6 0.21
20 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTATATTTTAGTTTA
Found at i:5079568 original size:15 final size:15
Alignment explanation
Indices: 5079548--5079578 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5079538 TTATGTATTA
5079548 TAAATTTTTAAGTTT
1 TAAATTTTTAAGTTT
*
5079563 TAAATTTTTATGTTT
1 TAAATTTTTAAGTTT
5079578 T
1 T
5079579 TTATATGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TAAATTTTTAAGTTT
Done.