Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 89 of 185
Found at i:28236120 original size:22 final size:22
Alignment explanation
Indices: 28236077--28236120 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28236067 AACAAAATAT
* **
28236077 AAAAAATAGAAATTATTTTGTA
1 AAAAAATAGAAAATATAGTGTA
*
28236099 AAAAAATATAAAATATAGTGTA
1 AAAAAATAGAAAATATAGTGTA
28236121 GTCTTTAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (22 bp):
AAAAAATAGAAAATATAGTGTA
Found at i:28241579 original size:22 final size:22
Alignment explanation
Indices: 28241547--28241592 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
28241537 TTTTATTGAC
*
28241547 TTAGTGGAATTCAATAGCTCTA
1 TTAGTGCAATTCAATAGCTCTA
*
28241569 TTAGTGCAATTCAATGGCTCTA
1 TTAGTGCAATTCAATAGCTCTA
28241591 TT
1 TT
28241593 TTAGGTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (22 bp):
TTAGTGCAATTCAATAGCTCTA
Found at i:28242091 original size:138 final size:137
Alignment explanation
Indices: 28241785--28242092 Score: 323
Period size: 138 Copynumber: 2.2 Consensus size: 137
28241775 ATTTTAACTG
* * * * * *
28241785 GGAACGTAGGTTCGCTAGCTATTTTTGAGGTTGCGATCTTAAACCAACAAACCTTTATGACATCA
1 GGAACGTAGGTCCACTAGCT-TTTTAGAGGTTACAATCTTAAACCAACAAACATTTATGACATCA
* * * * * *
28241850 GCTGGGAGTGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCGATAAGCCTTTAGAGT
65 GCTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCGACAATCATAAACCGACAAGCCTTTAGAGT
*
28241915 ATCAGTTA
130 ATCAGCTA
* * * * **
28241923 GGAACATAAGTCCCCTAGTTGTTTTAGAGGTTACAATCTTAAATCGGA-AAACATTTATGACATC
1 GGAACGTAGGTCCACTAGCT-TTTTAGAGGTTACAATCTTAAA-CCAACAAACATTTATGACATC
* * * * * *
28241987 AGTTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCGGCAATCATAAACC-AGCGAGCCTTTAGA
64 AGCTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCGACAATCATAAACCGA-CAAGCCTTTAGA
28242051 GTATCAGCTA
128 GTATCAGCTA
*
28242061 GGAACGTAGGTCCACTAGCTTTGTTGGAGGTT
1 GGAACGTAGGTCCACTAGCTTT-TTAGAGGTT
28242093 GCGATCATAA
Statistics
Matches: 137, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
137 3 0.02
138 132 0.96
139 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (137 bp):
GGAACGTAGGTCCACTAGCTTTTTAGAGGTTACAATCTTAAACCAACAAACATTTATGACATCAG
CTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCGACAATCATAAACCGACAAGCCTTTAGAGTA
TCAGCTA
Found at i:28242100 original size:207 final size:207
Alignment explanation
Indices: 28241862--28242263 Score: 477
Period size: 207 Copynumber: 1.9 Consensus size: 207
28241852 TGGGAGTGTT
* *
28241862 GGTCCACTAGCTATATTAGAGGCTACGATCATAAACCGA-TAAGCCTTTAGAGTATCAGTTAGGA
1 GGTCCACTAGCTATATTAGAGGCTACGATCATAAA-CGAGCAAGCCTTTAGAGTATCAGCTAGGA
* * * *
28241926 ACATAAGTCCCCTAGTTGTTTTAGAGGTTACAATCTTAAATCGGA-AAACATTTATGACATCAGT
65 ACATAAGTCACCTAGCTATTTTAGAGGTTACAATCTTAAAT-GGATAAACATTTATGACATCAGC
28241990 TAGGAGCGTAGGTCCACTAGCTT-TGTTGGAGGCGGCAATCATAAACCAGCGAGCCTTTAGAGTA
129 TAGGAGCGTAGGTCCACTAG-TTGTGTTGGAGGCGGCAATCATAAACCAGCGAGCCTTTAGAGTA
28242054 TCAGCTAGGAACGTA
193 TCAGCTAGGAACGTA
* * * * * * * * *
28242069 GGTCCACTAGCTTTGTTGGAGGTTGCGATCATAAACTAGCGAGCCTTTAGAGTATTAGCTAGTAA
1 GGTCCACTAGCTATATTAGAGGCTACGATCATAAACGAGCAAGCCTTTAGAGTATCAGCTAGGAA
* * * * * * * * *
28242134 CGTAGGTTAGCTAGCTATTTTAGAGGTTACGATCTTAAATTGATGAACCTTTATGACATCAGCTG
66 CATAAGTCACCTAGCTATTTTAGAGGTTACAATCTTAAATGGATAAACATTTATGACATCAGCTA
** * * * **
28242199 GGAGCGTAGGTCTGCTAGTTGTGTTGGAGGCTGCGATCATAAACTATTGAGCCTTTAGAGTATCA
131 GGAGCGTAGGTCCACTAGTTGTGTTGGAGGCGGCAATCATAAACCAGCGAGCCTTTAGAGTATCA
28242264 TTTGGGAAGG
Statistics
Matches: 161, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
206 6 0.04
207 155 0.96
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (207 bp):
GGTCCACTAGCTATATTAGAGGCTACGATCATAAACGAGCAAGCCTTTAGAGTATCAGCTAGGAA
CATAAGTCACCTAGCTATTTTAGAGGTTACAATCTTAAATGGATAAACATTTATGACATCAGCTA
GGAGCGTAGGTCCACTAGTTGTGTTGGAGGCGGCAATCATAAACCAGCGAGCCTTTAGAGTATCA
GCTAGGAACGTA
Found at i:28242270 original size:69 final size:69
Alignment explanation
Indices: 28241984--28242263 Score: 273
Period size: 69 Copynumber: 4.1 Consensus size: 69
28241974 CATTTATGAC
* * * *
28241984 ATCAGTTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCGGCAATCATAAACCAGCGAGCCTTTA
1 ATCAGCTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACTAGCGAGCCTTTA
28242049 GAGT
66 GAGT
* *
28242053 ATCAGCTAGGAACGTAGGTCCACTAGCTTTGTTGGAGGTTGCGATCATAAACTAGCGAGCCTTTA
1 ATCAGCTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACTAGCGAGCCTTTA
28242118 GAGT
66 GAGT
* * * * * * * * * * *
28242122 ATTAGCTAGTAACGTAGGT-TAGCTAGCTATT-TTAGAGGTTACGATCTTAAA-TTGATGAACCT
1 ATCAGCTAGGAGCGTAGGTCCA-CTAGCT-TTGTTGGAGGCTGCGATCATAAACTAG-CGAGCCT
*
28242184 TTATGA-C
63 TTA-GAGT
* ** **
28242191 ATCAGCTGGGAGCGTAGGTCTGCTAG-TTGTGTTGGAGGCTGCGATCATAAACTATTGAGCCTTT
1 ATCAGCTAGGAGCGTAGGTCCACTAGCTT-TGTTGGAGGCTGCGATCATAAACTAGCGAGCCTTT
28242255 AGAGT
65 AGAGT
28242260 ATCA
1 ATCA
28242264 TTTGGGAAGG
Statistics
Matches: 173, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
67 1 0.01
68 7 0.04
69 159 0.92
70 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (69 bp):
ATCAGCTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACTAGCGAGCCTTTA
GAGT
Found at i:28242277 original size:138 final size:137
Alignment explanation
Indices: 28242031--28242437 Score: 403
Period size: 138 Copynumber: 2.9 Consensus size: 137
28242021 GCGGCAATCA
* * * * * *
28242031 TAAACCAGCGAGCCTTTA-GAGTATCAGCTAGGAACGTAGGTCCACTAGCTT-TGTTGGAGGTTG
1 TAAACCTGCGAACCTTTATGA-CATCAGCTGGGAACGTAGGTCCGCTAG-TTGTGTTGGAGGCTG
* * * **
28242094 CGATCATAAACTAGCGAGCCTTTAGAGTATTAGCTAGTAACGTAGGTTAGCTAGCTATTTTAGAG
64 CGATCATAAACTA-CGAGCCTTTAGAGTATCAGCTGGGAACGTAGGTCCGCTAGCTATTTTAGAG
* *
28242159 GTTACGATCT
128 GTTACAACCT
* * * *
28242169 TAAA-TTGATGAACCTTTATGACATCAGCTGGGAGCGTAGGTCTGCTAGTTGTGTTGGAGGCTGC
1 TAAACCTG-CGAACCTTTATGACATCAGCTGGGAACGTAGGTCCGCTAGTTGTGTTGGAGGCTGC
* ** * * *
28242233 GATCATAAACTATTGAGCCTTTAGAGTATCATTTGGGAAGGTAGGTCCGTTAGCTGA-TTTGGAG
65 GATCATAAACTA-CGAGCCTTTAGAGTATCAGCTGGGAACGTAGGTCCGCTAGCT-ATTTTAGAG
*
28242297 GTGACAACCT
128 GTTACAACCT
* * * *
28242307 TAAACCTGCGAACCTTTATGACACCAGCTGGAAACATAGGTCCGCTAGCTGTGTTGGAGGCTGC-
1 TAAACCTGCGAACCTTTATGACATCAGCTGGGAACGTAGGTCCGCTAGTTGTGTTGGAGGCTGCG
* * * *
28242371 AGTCATAAATCGACAAGCCTTTAGAGTGA-CAGCTGGGAATGTAAGTCCGCTAGCTATTTTAGAG
66 A-TCATAAA-CTACGAGCCTTTAGAGT-ATCAGCTGGGAACGTAGGTCCGCTAGCTATTTTAGAG
28242435 GTT
128 GTT
28242438 GAGATATTAA
Statistics
Matches: 217, Mismatches: 43, Indels: 18
0.78 0.15 0.06
Matches are distributed among these distances:
137 5 0.02
138 204 0.94
139 8 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (137 bp):
TAAACCTGCGAACCTTTATGACATCAGCTGGGAACGTAGGTCCGCTAGTTGTGTTGGAGGCTGCG
ATCATAAACTACGAGCCTTTAGAGTATCAGCTGGGAACGTAGGTCCGCTAGCTATTTTAGAGGTT
ACAACCT
Found at i:28242356 original size:207 final size:207
Alignment explanation
Indices: 28241905--28242356 Score: 448
Period size: 207 Copynumber: 2.2 Consensus size: 207
28241895 AACCGATAAG
* * * * * * * *
28241905 CCTTTAGAGTATCAGTTAGGAACATAAGTCCCCTAGTTGTTTTAGAGGTTACAATCTTAAATCGG
1 CCTTTAGAGCACCAGCTAGAAACATAGGTCCGCTAGCTATTTTAGAGGTTACAATCTTAAATCGG
*
28241970 AAAACATTTATGACATCAGTTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCGGCAATCATAAA
66 AAAACATTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCGGCAATCATAAA
* * *
28242035 CCAGCGAGCCTTTAGAGTATCAGCTAGGAACGTAGGTCCACTAGCTTTGTTGGAGGTTGCGATCA
131 CCAGCGAGCCTTTAGAGTATCAGCTAGGAACGTAGGTCCACTAGCTATGTTGGAGGTTGCAACCA
*
28242100 TAAACTAGCGAG
196 TAAACTAGCGAA
* ** * * ** * *
28242112 CCTTTAGAGTATTAGCTAGTAACGTAGGTTAGCTAGCTATTTTAGAGGTTACGATCTTAAAT-TG
1 CCTTTAGAGCACCAGCTAGAAACATAGGTCCGCTAGCTATTTTAGAGGTTACAATCTTAAATCGG
* * * ** * *
28242176 ATGAACCTTTATGACATCAGCTGGGAGCGTAGGTCTGCTAG-TTGTGTTGGAGGCTGCGATCATA
66 A-AAACATTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTT-TGTTGGAGGCGGCAATCATA
* ** ** * * **
28242240 AACTATTGAGCCTTTAGAGTATCATTTGGGAAGGTAGGTCCGTTAGCTGAT-TTGGAGG-TGACA
129 AACCAGCGAGCCTTTAGAGTATCAGCTAGGAACGTAGGTCCACTAGCT-ATGTTGGAGGTTG-CA
*
28242303 ACCTTAAACCT-GCGAA
192 ACCATAAA-CTAGCGAA
*
28242319 CCTTTATGA-CACCAGCTGGAAACATAGGTCCGCTAGCT
1 CCTTTA-GAGCACCAGCTAGAAACATAGGTCCGCTAGCT
28242357 GTGTTGGAGG
Statistics
Matches: 197, Mismatches: 42, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
206 6 0.03
207 186 0.94
208 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (207 bp):
CCTTTAGAGCACCAGCTAGAAACATAGGTCCGCTAGCTATTTTAGAGGTTACAATCTTAAATCGG
AAAACATTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCGGCAATCATAAA
CCAGCGAGCCTTTAGAGTATCAGCTAGGAACGTAGGTCCACTAGCTATGTTGGAGGTTGCAACCA
TAAACTAGCGAA
Found at i:28244755 original size:10 final size:10
Alignment explanation
Indices: 28244742--28244777 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28244732 AAAGCTAAAT
28244742 TGAGCTCAAA
1 TGAGCTCAAA
* *
28244752 TGAGCTGAAT
1 TGAGCTCAAA
28244762 TGAGCTCAAA
1 TGAGCTCAAA
28244772 TGAGCT
1 TGAGCT
28244778 GATTGGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:28244787 original size:20 final size:20
Alignment explanation
Indices: 28244734--28244779 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
28244724 GCTGAAAGAA
*
28244734 AGCTAAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
28244754 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
28244774 AGCTGA
1 AGCTGA
28244780 TTGGAGCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:28246930 original size:18 final size:18
Alignment explanation
Indices: 28246909--28246943 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28246899 TTTTTCTTTT
28246909 TCAATTT-TTTTCTCAATC
1 TCAATTTATTTT-TCAATC
28246927 TCAATTTATTTTTCAAT
1 TCAATTTATTTTTCAAT
28246944 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTATTTTTCAATC
Found at i:28246994 original size:18 final size:18
Alignment explanation
Indices: 28246973--28247016 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28246963 TTTTCTCTCA
*
28246973 CTTTTTCGATTTCTTTTT
1 CTTTTTCAATTTCTTTTT
*
28246991 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATTTCTTTTT
*
28247009 CTCTTTCA
1 CTTTTTCA
28247017 CATGCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.05, T:0.66
Consensus pattern (18 bp):
CTTTTTCAATTTCTTTTT
Found at i:28249394 original size:20 final size:20
Alignment explanation
Indices: 28249366--28249411 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28249356 GCTGAAAGAA
* * * *
28249366 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTAAGCTCAAACG
28249386 AGCTGAATTAAGCTCAAACG
1 AGCTGAATTAAGCTCAAACG
28249406 AGCTGA
1 AGCTGA
28249412 TTGGAGTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (20 bp):
AGCTGAATTAAGCTCAAACG
Found at i:28251382 original size:8 final size:8
Alignment explanation
Indices: 28251369--28251402 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
28251359 AAAGAAAAGT
28251369 GAAAGTGA
1 GAAAGTGA
28251377 GAAAGTGA
1 GAAAGTGA
28251385 GAAAGTGA
1 GAAAGTGA
*
28251393 GAAAGAGA
1 GAAAGTGA
28251401 GA
1 GA
28251403 TGTGTGTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (8 bp):
GAAAGTGA
Found at i:28265918 original size:42 final size:41
Alignment explanation
Indices: 28265844--28266080 Score: 210
Period size: 42 Copynumber: 5.6 Consensus size: 41
28265834 ACCGGAAAAC
** *
28265844 ATTGAATAAAAAGGGGTTGCTAAGTGCTGATTCCCCGAATT
1 ATTGAATTTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
* * *
28265885 ATTGACTTTAAAGGTGGTCGCTAAGTGCCGATTCCACCGTATCT
1 ATTGAATTTAAAGG-GGTTGCTAAGTGCTGATTCC-CCGTAT-T
*
28265929 -TT-AATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATT
1 ATTGAATT-T-AAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
* * *
28265970 ACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 ATTGAATTTAAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATT
* * * * * *
28266013 CTTGACTATGAAAGGGGTTGCTATGTGCTGATTCTCCGTATC
1 ATTGAAT-TTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
* *
28266055 ACTAAATTT-AAGGTGGTTGCTAAGTG
1 ATTGAATTTAAAGG-GGTTGCTAAGTG
28266081 TTGAATCCAC
Statistics
Matches: 158, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
40 4 0.03
41 29 0.18
42 58 0.37
43 56 0.35
44 11 0.07
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
ATTGAATTTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
Found at i:28265996 original size:85 final size:84
Alignment explanation
Indices: 28265853--28266080 Score: 312
Period size: 85 Copynumber: 2.7 Consensus size: 84
28265843 CATTGAATAA
* * * * *
28265853 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGACTTTAAAGGTGGTCGCTAAGTGCCGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGCCGATT
* * *
28265918 CCACCGTATCTTTAATTGTG
65 CCACCGTATCCTTAACTATG
*
28265938 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGCCGATT
*
28266003 CCACCGTATCCTTGACTATG
65 CCACCGTATCCTTAACTATG
* * * *
28266023 AAAGGGGTTGCTATGTGCTGATTCTCCGTATCACTAAATTTAAGGTGGTTGCTAAGTG
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTG
28266081 TTGAATCCAC
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 19 0.15
85 109 0.85
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCCGATTC
CACCGTATCCTTAACTATG
Found at i:28273315 original size:24 final size:24
Alignment explanation
Indices: 28273286--28273333 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28273276 GTACAGTTTA
*
28273286 TCTATAGTAGTCTC-AGTATATACT
1 TCTATAGCAGTCTCAAG-ATATACT
*
28273310 TCTATAGCAGTTTCAAGATATACT
1 TCTATAGCAGTCTCAAGATATACT
28273334 ATCAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (24 bp):
TCTATAGCAGTCTCAAGATATACT
Found at i:28274698 original size:18 final size:17
Alignment explanation
Indices: 28274675--28274708 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28274665 CATATTGTCG
28274675 GCCTGTATGGGCCCACAT
1 GCCTGTAT-GGCCCACAT
*
28274693 GCCTGTGTGGCCCACA
1 GCCTGTATGGCCCACA
28274709 CGGCCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.35, G:0.29, T:0.21
Consensus pattern (17 bp):
GCCTGTATGGCCCACAT
Found at i:28275973 original size:51 final size:49
Alignment explanation
Indices: 28275849--28276031 Score: 206
Period size: 51 Copynumber: 3.6 Consensus size: 49
28275839 AAAGTGATAG
* *
28275849 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGGATG-ATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GGATGTAT-GA
* * * * * *
28275899 TCGCATGTGTAGTACTATCTGCAGGCTATTATGCGTACCGGATAGTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GTAT-GA
* * *
28275950 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGC
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GT-ATGA
28276001 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
28276032 TGTGAACCAA
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 71 0.65
52 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGTATGA
Found at i:28275976 original size:101 final size:102
Alignment explanation
Indices: 28275849--28276033 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
28275839 AAAGTGATAG
* *
28275849 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGGATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GGATGATAATGCTCACATGTGTAGT
*
28275912 ACTATCTGCAGGCTATTATGCGTACCGGATAGTTTCGA
65 ACTATCTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* *
28275950 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGCTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGCTCACATGTGTAGTA
*
28276015 CTATGTGCAGGCTACTATG
66 CTATCTGCAGGCTACTATG
28276034 TGAACCAAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 6 0.08
101 39 0.51
102 31 0.41
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGCTCACATGTGTAGTA
CTATCTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:28276035 original size:26 final size:26
Alignment explanation
Indices: 28275955--28276035 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
28275945 TTCGATCACG
28275955 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * * *
28275981 CGTGTA-T-CGGATG-GTAATGCTCAC-A
1 TGTGTAGTAC-TATGTG-CAGGCT-ACTA
28276006 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
28276032 TGTG
1 TGTG
28276036 AACCAAACAT
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:28282375 original size:35 final size:35
Alignment explanation
Indices: 28282276--28282383 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
28282266 ATAACCAACC
* * * *
28282276 AGTGCAAGGCACAATTATTATCAGTTTATCCGACC
1 AGTGCAGGGCACAATTATTGTCGGTTTATCCGACT
* * ** *
28282311 AGTGCTGGGTGTA-AAGCATTGTCGATTTATCCGACT
1 AGTGC-AGG-GCACAATTATTGTCGGTTTATCCGACT
28282347 AGTGCAGGGCACAATTATTGTCGGTTTATCCGACT
1 AGTGCAGGGCACAATTATTGTCGGTTTATCCGACT
28282382 AG
1 AG
28282384 CACTGGGCGC
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
34 2 0.04
35 29 0.52
36 23 0.41
37 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (35 bp):
AGTGCAGGGCACAATTATTGTCGGTTTATCCGACT
Found at i:28282411 original size:71 final size:71
Alignment explanation
Indices: 28282275--28282462 Score: 182
Period size: 71 Copynumber: 2.6 Consensus size: 71
28282265 TATAACCAAC
* * * * * * * * **
28282275 CAGTGCAAGGCACAATTATTATCAGTTTATCCGACCAGTGCTGGGTGTAAAGCATTGTCGATTTA
1 CAGTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGCAAAACAACGTCGATTTA
28282340 TCCGA-
66 TCCGAT
*
28282345 CTAGTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCACTGGGCGCAAAACAACGTC-AGTT
1 C-AGTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGCAAAACAACGTCGA-TT
28282409 TATCCGAT
64 TATCCGAT
* * ** * * *
28282417 CACTGCTGGGCACAACAATTGTCGATTTATTCAACTAGCGCTGGGC
1 CAGTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGC
28282463 ATAAAAATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
70 2 0.02
71 93 0.97
72 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (71 bp):
CAGTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGCAAAACAACGTCGATTTA
TCCGAT
Found at i:28287058 original size:15 final size:16
Alignment explanation
Indices: 28287029--28287058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28287019 GATAGTTTTG
28287029 TAAAATGTAGAATTAA
1 TAAAATGTAGAATTAA
28287045 TAAAATGT-GAATTA
1 TAAAATGTAGAATTA
28287059 TTCTTATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (16 bp):
TAAAATGTAGAATTAA
Found at i:28292170 original size:164 final size:164
Alignment explanation
Indices: 28291899--28292231 Score: 576
Period size: 164 Copynumber: 2.0 Consensus size: 164
28291889 ATATCAAACC
* * *
28291899 AAGAATTAAGCACACATAATTGATAACAAGATCTAAGCATTTATTGGGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTAGGTAAAATAAAAATCAAAC
* *
28291964 GACAAAATTCATTATAGGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
66 GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
28292029 AAACATCCAATATACAGTATAATCGAAAGAAATA
131 AAACATCCAATATACAGTATAATCGAAAGAAATA
* *
28292063 AAGAATTAAGCACACATAATCGAGACCAAGATCTAAGTATTTATTAGGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTAGGTAAAATAAAAATCAAAC
* * *
28292128 GACAGAGTTCATCATAAGGTTCATCTCCTTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
66 GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
28292193 AAACATCCAATATACAGTATAATCGAAAGAAATA
131 AAACATCCAATATACAGTATAATCGAAAGAAATA
28292227 AAGAA
1 AAGAA
28292232 ACTCATCATA
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
164 159 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (164 bp):
AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTAGGTAAAATAAAAATCAAAC
GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
AAACATCCAATATACAGTATAATCGAAAGAAATA
Found at i:28309512 original size:42 final size:42
Alignment explanation
Indices: 28309441--28309525 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
28309431 AAATTGTTGG
*
28309441 ATATATATATGTATGCATTCGACATATGTGAATT-ATAAGTAT
1 ATATATATATGTATGCATTCGACACATGTG-ATTGATAAGTAT
* * ** *
28309483 ATATATATGTGTGTGCATTCGGTACATGTGGTTGATAAGTAT
1 ATATATATATGTATGCATTCGACACATGTGATTGATAAGTAT
28309525 A
1 A
28309526 ATTATTTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (42 bp):
ATATATATATGTATGCATTCGACACATGTGATTGATAAGTAT
Found at i:28311810 original size:14 final size:13
Alignment explanation
Indices: 28311781--28311806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28311771 AATAATATAT
28311781 TAACAATTCAAAA
1 TAACAATTCAAAA
28311794 TAACAATTCAAAA
1 TAACAATTCAAAA
28311807 ATAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
TAACAATTCAAAA
Found at i:28321518 original size:16 final size:17
Alignment explanation
Indices: 28321485--28321519 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28321475 TAATAACATG
28321485 TCACATATCATCATCTCA
1 TCACATATCA-CATCTCA
28321503 TCACATATCA-ATCTCA
1 TCACATATCACATCTCA
28321519 T
1 T
28321520 ACAATGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (17 bp):
TCACATATCACATCTCA
Found at i:28334264 original size:27 final size:27
Alignment explanation
Indices: 28334220--28334287 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
28334210 TAAAAGAAGG
**
28334220 CCTTTGTGGCGCAA-TATGAAATGAACA
1 CCTTTGTGGCG-AATTATGAAAAAAACA
**
28334247 CCTTTGTGGCGAATTATGAAAAAAATG
1 CCTTTGTGGCGAATTATGAAAAAAACA
28334274 CCTTTGTGGCGAAT
1 CCTTTGTGGCGAAT
28334288 CAAGAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (27 bp):
CCTTTGTGGCGAATTATGAAAAAAACA
Found at i:28334294 original size:27 final size:27
Alignment explanation
Indices: 28334247--28334299 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28334237 GAAATGAACA
* *
28334247 CCTTTGTGGCGAATTATGAAAAAAATG
1 CCTTTGTGGCGAATCAAGAAAAAAATG
*
28334274 CCTTTGTGGCGAATCAAGAAAGAAAT
1 CCTTTGTGGCGAATCAAGAAAAAAAT
28334300 TTCATTGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (27 bp):
CCTTTGTGGCGAATCAAGAAAAAAATG
Found at i:28334307 original size:27 final size:27
Alignment explanation
Indices: 28334250--28334311 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
28334240 ATGAACACCT
* * *
28334250 TTGTGGCGAATTATGAAAAAAATGCCT
1 TTGTGGCGAATCAAGAAAAAAATGCCA
* **
28334277 TTGTGGCGAATCAAGAAAGAAATTTCA
1 TTGTGGCGAATCAAGAAAAAAATGCCA
28334304 TTGTGGCG
1 TTGTGGCG
28334312 GATTATGAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (27 bp):
TTGTGGCGAATCAAGAAAAAAATGCCA
Found at i:28335193 original size:36 final size:35
Alignment explanation
Indices: 28335132--28335240 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 35
28335122 TGAATGCATT
* *
28335132 TATATATATAATTATTCAAATACATGTGCCAAAAGCA
1 TATAT-TATACTTA-TCAAATACATGTGCCAAATGCA
* *
28335169 TATATTTATACTTATCAATTACATGTGCCGAATGCA
1 TATA-TTATACTTATCAAATACATGTGCCAAATGCA
* * *
28335205 CATA-TATACTTAT-AAACCACATATGCCAAATGCA
1 TATATTATACTTATCAAA-TACATGTGCCAAATGCA
28335239 TA
1 TA
28335241 CATATATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
33 2 0.03
34 24 0.40
36 22 0.37
37 11 0.18
38 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (35 bp):
TATATTATACTTATCAAATACATGTGCCAAATGCA
Found at i:28335237 original size:34 final size:35
Alignment explanation
Indices: 28335175--28335248 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
28335165 AGCATATATT
* ** * *
28335175 TATACTTATCAATTACATGTGCCGAATGC-ACATA
1 TATACTTATAAACCACATATGCCAAATGCAACATA
28335209 TATACTTATAAACCACATATGCCAAATGCATACATA
1 TATACTTATAAACCACATATGCCAAATGCA-ACATA
28335245 TATA
1 TATA
28335249 TATCCAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 24 0.73
36 9 0.27
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (35 bp):
TATACTTATAAACCACATATGCCAAATGCAACATA
Found at i:28335465 original size:41 final size:41
Alignment explanation
Indices: 28335420--28335524 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
28335410 TAAAATAGAT
* **
28335420 TCACCGGCACTTAGCCTGTTAGGCTTA-AAGCCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAA-CCTAATTCAGA
28335461 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTAATTCAGA
* *
28335502 TCACCAGCACTTAGCCTACTAGG
1 TCACCGGCACTTAGCCTGCTAGG
28335525 TTTTAAAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 56 0.97
42 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTAATTCAGA
Found at i:28336346 original size:153 final size:156
Alignment explanation
Indices: 28336171--28336471 Score: 366
Period size: 153 Copynumber: 1.9 Consensus size: 156
28336161 TATATTATAC
* * *
28336171 ATATATATATGTAACATCCATACTTTTAA-TAAAATCCAAGAATTTATACTCA-TATATACATAC
1 ATATATAAATATAACATACATACTTTTAACT-AAATCCAAGAATTTAT--TCAGTATATACATAC
* * * * *
28336234 CTATTCGAACCTCTTGTA-A-ACATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATT
63 ATATTCG-ACCT-TTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATA
28336294 CATGTATATACACATA-TATCCGAACTTTAT
126 CATGTATATACACATATTATCCGAACTTTAT
* *
28336324 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATCCAAGAATTTATTCA-GTATATACATACAT
* * *
28336389 ATTCGAGCTTTATATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATG
65 ATTCGACCTTTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATACATG
*
28336454 TATATACATATATTATCC
130 TATATACACATATTATCC
28336472 ACTATTAGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
151 7 0.06
152 4 0.03
153 70 0.56
154 3 0.02
155 14 0.11
156 22 0.18
157 5 0.04
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.38
Consensus pattern (156 bp):
ATATATAAATATAACATACATACTTTTAACTAAATCCAAGAATTTATTCAGTATATACATACATA
TTCGACCTTTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATACATGT
ATATACACATATTATCCGAACTTTAT
Found at i:28336389 original size:78 final size:78
Alignment explanation
Indices: 28336272--28336471 Score: 339
Period size: 78 Copynumber: 2.6 Consensus size: 78
28336262 ACATTCAACA
*
28336272 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
28336336 AACATACATACTT
66 AACATACATACTT
* * *
28336349 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAGCTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
28336414 AACATACATACTT
66 AACATACATACTT
*
28336427 TTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
28336472 ACTATTAGTT
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
77 14 0.12
78 96 0.84
79 4 0.04
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:28342208 original size:78 final size:78
Alignment explanation
Indices: 28342091--28342368 Score: 495
Period size: 78 Copynumber: 3.6 Consensus size: 78
28342081 ACATTCAACA
*
28342091 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
28342155 AACATACATACTT
66 AACATACATACTT
*
28342168 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
28342233 AACATACATACTT
66 AACATACATACTT
*
28342246 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
28342311 AACATACATACTT
66 AACATACATACTT
* *
28342324 TTAACTAAATTCAAGAACTTATACATTTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
28342369 ACTATTAGTT
Statistics
Matches: 194, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
77 14 0.07
78 175 0.90
79 5 0.03
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:28343533 original size:37 final size:37
Alignment explanation
Indices: 28343491--28343565 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
28343481 CAATAAAATT
28343491 AATTTATGAAACTTTCACACATGTAAATTAACACATA
1 AATTTATGAAACTTTCACACATGTAAATTAACACATA
28343528 AATTTATGAAACTTTCACACATGTAAATTAACACATA
1 AATTTATGAAACTTTCACACATGTAAATTAACACATA
28343565 A
1 A
28343566 TAAATACAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (37 bp):
AATTTATGAAACTTTCACACATGTAAATTAACACATA
Found at i:28344734 original size:7 final size:7
Alignment explanation
Indices: 28344722--28344746 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28344712 TTCAAGTATT
28344722 ATTTTCA
1 ATTTTCA
28344729 ATTTTCA
1 ATTTTCA
28344736 ATTTTCA
1 ATTTTCA
28344743 ATTT
1 ATTT
28344747 GTATGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTCA
Found at i:28356989 original size:12 final size:12
Alignment explanation
Indices: 28356972--28357014 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
28356962 AAAAACAAAA
28356972 TATATATATGTG
1 TATATATATGTG
28356984 TATATATAT-T-
1 TATATATATGTG
28356994 TATATATATGTG
1 TATATATATGTG
28357006 TATATATAT
1 TATATATAT
28357015 TTAAGCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.31
11 2 0.07
12 18 0.62
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (12 bp):
TATATATATGTG
Found at i:28357000 original size:22 final size:22
Alignment explanation
Indices: 28356972--28357017 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28356962 AAAAACAAAA
28356972 TATATATATGTGTATATATATT
1 TATATATATGTGTATATATATT
28356994 TATATATATGTGTATATATATT
1 TATATATATGTGTATATATATT
28357016 TA
1 TA
28357018 AGCAAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (22 bp):
TATATATATGTGTATATATATT
Found at i:28357083 original size:41 final size:41
Alignment explanation
Indices: 28357038--28357118 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
28357028 AAAAAAAGGT
*
28357038 ATACAGATGTATAT-AGATATGTATATAAAT-TATAAAATATA
1 ATACAAATGTATATAAG-TATGTATATAAATAT-TAAAATATA
*
28357079 ATACAAATGTATATAAGTATGTATATATATATTAAAATAT
1 ATACAAATGTATATAAGTATGTATATAAATATTAAAATAT
28357119 GTATATGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (41 bp):
ATACAAATGTATATAAGTATGTATATAAATATTAAAATATA
Found at i:28362220 original size:23 final size:24
Alignment explanation
Indices: 28362190--28362241 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28362180 ACTCGAACCC
* *
28362190 TAAAATT-AATCAAGGGCTGATAT
1 TAAAATTAAATCAAAGGATGATAT
28362213 TAAAATTAAATCAAAGGATGATAT
1 TAAAATTAAATCAAAGGATGATAT
*
28362237 AAAAA
1 TAAAA
28362242 CATTTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (24 bp):
TAAAATTAAATCAAAGGATGATAT
Found at i:28362700 original size:14 final size:14
Alignment explanation
Indices: 28362681--28362710 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28362671 GATGTGTTTA
*
28362681 AAACTAAATTTACT
1 AAACTAAATTAACT
28362695 AAACTAAATTAACT
1 AAACTAAATTAACT
28362709 AA
1 AA
28362711 GAACTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
AAACTAAATTAACT
Found at i:28363594 original size:30 final size:32
Alignment explanation
Indices: 28363533--28363596 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
28363523 CACGAGTTGG
* *
28363533 CACATGGGCGTGTGTGTCCAACCCGTGTGGCT
1 CACATGGGCGTGTATGTCCAACCCGTATGGCT
* *
28363565 CACAT-GG-GTGTATGTCCAGCCTGTATGGCT
1 CACATGGGCGTGTATGTCCAACCCGTATGGCT
28363595 CA
1 CA
28363597 TGAAATCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 21 0.75
31 2 0.07
32 5 0.18
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.27
Consensus pattern (32 bp):
CACATGGGCGTGTATGTCCAACCCGTATGGCT
Found at i:28366543 original size:21 final size:21
Alignment explanation
Indices: 28366519--28366562 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28366509 AATATTAATA
*
28366519 CTCATTCATCAATCTTAAATT
1 CTCAATCATCAATCTTAAATT
* * *
28366540 CTCAATCCTCAATTTTCAATT
1 CTCAATCATCAATCTTAAATT
28366561 CT
1 CT
28366563 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCAATCATCAATCTTAAATT
Found at i:28366546 original size:14 final size:14
Alignment explanation
Indices: 28366522--28366587 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
28366512 ATTAATACTC
*
28366522 ATTCATCAATCTTAA
1 ATTC-TCAATCTTCA
*
28366537 ATTCTCAATCCTCA
1 ATTCTCAATCTTCA
*
28366551 ATTTTCAATTCTT-A
1 ATTCTCAA-TCTTCA
* * *
28366565 ATTTTTAATTTTCA
1 ATTCTCAATCTTCA
28366579 ATTCTCAAT
1 ATTCTCAAT
28366588 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 3 0.07
14 31 0.76
15 7 0.17
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTCTCAATCTTCA
Found at i:28368631 original size:6 final size:6
Alignment explanation
Indices: 28368620--28368648 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28368610 AGGTTTCCAA
28368620 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
28368649 ATCCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:28369049 original size:23 final size:23
Alignment explanation
Indices: 28369023--28369066 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28369013 GTAATTGTAA
28369023 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
28369046 ATACATTTGTAATTAATATAT
1 ATACATGTGTAATAAATATAT
28369067 ATACATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:28369069 original size:21 final size:22
Alignment explanation
Indices: 28369023--28369072 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
28369013 GTAATTGTAA
28369023 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATA-GT
* *
28369046 ATACATTTGTAATTAATATA-T
1 ATACATGTGTAATAAATATAGT
28369067 ATACAT
1 ATACAT
28369073 ACTTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (22 bp):
ATACATGTGTAATAAATATAGT
Found at i:28369158 original size:18 final size:18
Alignment explanation
Indices: 28369125--28369163 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
28369115 TTAATTAAGC
28369125 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
28369144 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
28369161 AAA
1 AAA
28369164 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:28369965 original size:18 final size:18
Alignment explanation
Indices: 28369932--28369970 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
28369922 TTAATTAAGC
28369932 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
28369951 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
28369968 AAA
1 AAA
28369971 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:28371182 original size:22 final size:20
Alignment explanation
Indices: 28371157--28371216 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
28371147 GCTCTGCCGA
28371157 TCAGGCACTTATGTGTCATATT
1 TCAGGCACTTATGTGTC--ATT
**
28371179 TCAGGCACCTCGTGTGTCATT
1 TCAGGCA-CTTATGTGTCATT
28371200 TCAGGCACTTATGTGTC
1 TCAGGCACTTATGTGTC
28371217 GTATACTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.24
21 10 0.30
22 7 0.21
23 8 0.24
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (20 bp):
TCAGGCACTTATGTGTCATT
Found at i:28374076 original size:34 final size:35
Alignment explanation
Indices: 28374032--28374098 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28374022 CAGTAAAATA
*
28374032 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
28374066 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
28374099 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:28379327 original size:17 final size:17
Alignment explanation
Indices: 28379291--28379328 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28379281 ATTATTTTAA
*
28379291 TAATTTAATATTAAATT
1 TAATTTAATATTAAACT
28379308 TAATTTAATACTT-AACT
1 TAATTTAATA-TTAAACT
28379325 TAAT
1 TAAT
28379329 AGTGTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTTAATATTAAACT
Found at i:28391567 original size:36 final size:36
Alignment explanation
Indices: 28391527--28391595 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
28391517 GAATTCTTTC
28391527 TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
1 TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
* * * *
28391563 TTCTTGATTTTCCAGCTTCTGTCCAGCAACCAA
1 TTCTTAATTTTCCAACTCCTATCCAGCAACCAA
28391596 GCACTTAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.28, C:0.32, G:0.07, T:0.33
Consensus pattern (36 bp):
TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
Found at i:28394171 original size:11 final size:11
Alignment explanation
Indices: 28394157--28394232 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
28394147 GATAATCACT
28394157 TTAATATTAAA
1 TTAATATTAAA
28394168 TTAATA--AAA
1 TTAATATTAAA
*
28394177 -TACTATTAAGA
1 TTAATATTAA-A
*
28394188 TAAATATTAAA
1 TTAATATTAAA
28394199 TTAA-ATTTAATA
1 TTAATA-TTAA-A
28394211 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
28394224 ATAATATTA
1 TTAATATTA
28394233 TTTTTAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 20 0.39
12 12 0.24
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:28394210 original size:17 final size:17
Alignment explanation
Indices: 28394125--28394218 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 17
28394115 GTAGATAAAC
*
28394125 ATTACATTAAATTTAAT
1 ATTAAATTAAATTTAAT
28394142 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAA--A-TTTAAT
**
28394162 ATTAAATT-AATAAAAT
1 ATTAAATTAAATTTAAT
* *
28394178 ACT--ATTAAGA-TAAAT
1 ATTAAATTAA-ATTTAAT
28394193 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
28394210 ATTAAATTA
1 ATTAAATTA
28394219 TTAAAATAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 3 0.05
15 7 0.12
16 8 0.13
17 26 0.43
18 1 0.02
19 3 0.05
20 12 0.20
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:28395069 original size:172 final size:172
Alignment explanation
Indices: 28394783--28395134 Score: 695
Period size: 172 Copynumber: 2.0 Consensus size: 172
28394773 CGAATAAATC
28394783 GACTCAGTTAAATTATTCCCAAAGTCGTAGAATTTTCTTCTGATTCAAATGCAGTCCGATCGAGT
1 GACTCAGTTAAATTATTCCCAAAGTCGTAGAATTTTCTTCTGATTCAAATGCAGTCCGATCGAGT
28394848 TTTTGTTGAGCTAGTTGAGGGACCAATCGGACATATACAATTAGGCTCTAGTGATTGCAATTATG
66 TTTTGTTGAGCTAGTTGAGGGACCAATCGGACATATACAATTAGGCTCTAGTGATTGCAATTATG
28394913 TCAAGAAGCATCATTCCAATAATTCGCAATTACTTAATCATA
131 TCAAGAAGCATCATTCCAATAATTCGCAATTACTTAATCATA
28394955 GACTCAGTTAAATTATTCCCAAAGTCGTAGAATTTTCTTCTGATTCAAATGCAGTCCGATCGAGT
1 GACTCAGTTAAATTATTCCCAAAGTCGTAGAATTTTCTTCTGATTCAAATGCAGTCCGATCGAGT
28395020 TTTTGTTGAGCTAGTTGAGGGACCAATCGGACATATACAATTAGGCTCTAGTGATTGCAATTATG
66 TTTTGTTGAGCTAGTTGAGGGACCAATCGGACATATACAATTAGGCTCTAGTGATTGCAATTATG
28395085 TCAAGAAGCATCATTCCAATAATTCGCAATTACTTAATCATA
131 TCAAGAAGCATCATTCCAATAATTCGCAATTACTTAATCATA
*
28395127 GAGTCAGT
1 GACTCAGT
28395135 CCATAATAAG
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 179 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (172 bp):
GACTCAGTTAAATTATTCCCAAAGTCGTAGAATTTTCTTCTGATTCAAATGCAGTCCGATCGAGT
TTTTGTTGAGCTAGTTGAGGGACCAATCGGACATATACAATTAGGCTCTAGTGATTGCAATTATG
TCAAGAAGCATCATTCCAATAATTCGCAATTACTTAATCATA
Found at i:28399414 original size:9 final size:10
Alignment explanation
Indices: 28399389--28399418 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
28399379 AGAAATATTT
28399389 TTAAAAAATA
1 TTAAAAAATA
28399399 TTAAAAAATA
1 TTAAAAAATA
28399409 TTAAAAAATA
1 TTAAAAAATA
28399419 AAGAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:28399427 original size:38 final size:38
Alignment explanation
Indices: 28399355--28399428 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
28399345 TTAAATCAAT
* *
28399355 AAAATATAAAAAAATATTAAATAGAGAAATATTTTTAA
1 AAAATATAAAAAAATATTAAATAAAGAAAAATTTTTAA
* *
28399393 AAAATATTAAAAAATATTAAA-AAATAAAGAATTTTT
1 AAAATATAAAAAAATATTAAATAAAGAAA-AATTTTT
28399429 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.16
38 26 0.84
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (38 bp):
AAAATATAAAAAAATATTAAATAAAGAAAAATTTTTAA
Found at i:28404905 original size:124 final size:124
Alignment explanation
Indices: 28404722--28404990 Score: 421
Period size: 124 Copynumber: 2.2 Consensus size: 124
28404712 CGACGCTAGC
* *
28404722 GCTTACCTTTTGCGGCGTTTTCAGCAAAAATGCCACTAAAAAATTAAATTCCTGTACTGAAACGG
1 GCTTACCTTTTGCGGCGTTTTCACCAAAAATGCCACTAAAAAATTAAATTCCTGCACTGAAACGG
* * * * * *
28404787 TGCCATTTTGAAAAATTTTAACACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATT
66 CGCCATGTTGAAAAATGTTAACACATAGTTGCGACGTTTATAGTCCAAACGCCACTATT
* * *
28404846 TCTTACCTTTTGTGGCGTTTTCACCAAAAATGCCACTAAAAAATTAAATTCTTGCACTGAAACGG
1 GCTTACCTTTTGCGGCGTTTTCACCAAAAATGCCACTAAAAAATTAAATTCCTGCACTGAAACGG
* *
28404911 CGCCATGTTGAAAAATGTTAATACATATTTGCGACGTTTATAGTCCAAACGCCACTATT
66 CGCCATGTTGAAAAATGTTAACACATAGTTGCGACGTTTATAGTCCAAACGCCACTATT
28404970 GCTTACCTTTTGCGGCGTTTT
1 GCTTACCTTTTGCGGCGTTTT
28404991 TCTCATAAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 130 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (124 bp):
GCTTACCTTTTGCGGCGTTTTCACCAAAAATGCCACTAAAAAATTAAATTCCTGCACTGAAACGG
CGCCATGTTGAAAAATGTTAACACATAGTTGCGACGTTTATAGTCCAAACGCCACTATT
Found at i:28405103 original size:6 final size:6
Alignment explanation
Indices: 28405092--28405117 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28405082 AAGATTTTAA
28405092 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
28405118 AAATGGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:28405908 original size:14 final size:14
Alignment explanation
Indices: 28405889--28406016 Score: 55
Period size: 14 Copynumber: 8.8 Consensus size: 14
28405879 CCTGAGCCCT
28405889 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
28405903 TAAACCCATAACCTTAAAA
1 TAAACCC-TAAAC-T---A
* *
28405922 TTACACCCTAAACTG
1 -TAAACCCTAAACTA
* *
28405937 TAAACACTAAACTC
1 TAAACCCTAAACTA
* *
28405951 TTAACACTAAA-TGA
1 TAAACCCTAAACT-A
*
28405965 TAAACACTAAAC-A
1 TAAACCCTAAACTA
*
28405978 TTAAACCCTAAACCA
1 -TAAACCCTAAACTA
* **
28405993 TAAA-CCTATACCC
1 TAAACCCTAAACTA
28406006 TAAACCCTAAA
1 TAAACCCTAAA
28406017 AATATATATT
Statistics
Matches: 89, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
13 13 0.15
14 58 0.65
15 5 0.06
16 1 0.01
18 1 0.01
19 5 0.06
20 6 0.07
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:28406022 original size:20 final size:20
Alignment explanation
Indices: 28405982--28406022 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28405972 TAAACATTAA
**
28405982 ACCCTAAACCATAAACCTAT
1 ACCCTAAACCATAAAAATAT
*
28406002 ACCCTAAACCCTAAAAATAT
1 ACCCTAAACCATAAAAATAT
28406022 A
1 A
28406023 TATTACAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.20
Consensus pattern (20 bp):
ACCCTAAACCATAAAAATAT
Found at i:28406074 original size:7 final size:7
Alignment explanation
Indices: 28406064--28406130 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
28406054 ATCTTAAATA
28406064 CTAAACT
1 CTAAACT
28406071 CTAAACT
1 CTAAACT
28406078 CTAAA-T
1 CTAAACT
* *
28406084 CCCAAACC
1 -CTAAACT
*
28406092 CCAAACT
1 CTAAACT
28406099 CTAAAC-
1 CTAAACT
28406105 CATAAAC-
1 C-TAAACT
28406112 CATAAACT
1 C-TAAACT
*
28406120 CAAAACT
1 CTAAACT
28406127 CTAA
1 CTAA
28406131 TTCAAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
6 2 0.04
7 47 0.94
8 1 0.02
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACT
Found at i:28406082 original size:21 final size:21
Alignment explanation
Indices: 28406058--28406103 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28406048 AAAAGAATCT
* * *
28406058 TAAATACTAAACTCTAAACTC
1 TAAATACCAAACCCCAAACTC
*
28406079 TAAATCCCAAACCCCAAACTC
1 TAAATACCAAACCCCAAACTC
28406100 TAAA
1 TAAA
28406104 CCATAAACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAATACCAAACCCCAAACTC
Found at i:28406118 original size:28 final size:28
Alignment explanation
Indices: 28406066--28406130 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
28406056 CTTAAATACT
*
28406066 AAACTCTAAACTCTAAATCCCAAACCCC
1 AAACTCTAAACTCTAAATCCCAAACCCA
* *
28406094 AAACTCTAAAC-CATAAA-CCATAAACTCA
1 AAACTCTAAACTC-TAAATCC-CAAACCCA
28406122 AAACTCTAA
1 AAACTCTAA
28406131 TTCAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.18
Consensus pattern (28 bp):
AAACTCTAAACTCTAAATCCCAAACCCA
Found at i:28406352 original size:40 final size:40
Alignment explanation
Indices: 28406308--28406398 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
28406298 CGGTGTTTTC
*
28406308 CAAAAAGCGCCACTAATGCTTGGA-CTATAGCAGCGTTT-A
1 CAAAAAGCGCCACTAATGC-TCGATCTATAGCAGCGTTTGA
* * *
28406347 TCAAAAAGCGTCGCTAATGCTCGATCTATTGCAGCGTTTGA
1 -CAAAAAGCGCCACTAATGCTCGATCTATAGCAGCGTTTGA
*
28406388 CATAAAGCGCC
1 CAAAAAGCGCC
28406399 GCGAATGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.07
40 39 0.91
41 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAAAAGCGCCACTAATGCTCGATCTATAGCAGCGTTTGA
Found at i:28406530 original size:40 final size:41
Alignment explanation
Indices: 28406467--28406556 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
28406457 GCGTTTTCCA
*
28406467 AAATGCACCGCTAATGGTTGATCTATAGCGGCATTTTTTAG-
1 AAAT-CACCGCTAATGGTTGATCTATAGCGGCACTTTTTAGT
* *
28406508 AAATCACCGCTAAT-GTTCGATCTATTGCGGCGCTTTTTAGT
1 AAATCACCGCTAATGGTT-GATCTATAGCGGCACTTTTTAGT
28406549 AAA-CACCG
1 AAATCACCG
28406557 AGAATGCTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 3 0.07
40 34 0.77
41 7 0.16
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (41 bp):
AAATCACCGCTAATGGTTGATCTATAGCGGCACTTTTTAGT
Found at i:28406576 original size:40 final size:40
Alignment explanation
Indices: 28406486--28406578 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
28406476 GCTAATGGTT
* ** ** *
28406486 GATCTATAGCGGCATTTTTTAGAAATCACCGCTAATGTTC
1 GATCTATTGCGGCGCTTTTTAGAAATCACCGAGAATGCTC
28406526 GATCTATTGCGGCGCTTTTTAGTAAA-CACCGAGAATGCTC
1 GATCTATTGCGGCGCTTTTTAG-AAATCACCGAGAATGCTC
* *
28406566 GGTCTTTTGCGGC
1 GATCTATTGCGGC
28406579 ATTTGTGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (40 bp):
GATCTATTGCGGCGCTTTTTAGAAATCACCGAGAATGCTC
Found at i:28406713 original size:40 final size:40
Alignment explanation
Indices: 28406663--28406787 Score: 133
Period size: 40 Copynumber: 3.1 Consensus size: 40
28406653 CGTTTTGCAG
* * * *
28406663 AAAGCGCCGCTAATGCTTGATCTATAGCGACGTTTCTGAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTCTGAA
* * * * * *
28406703 AAAGCACCGCTAATTCTCGAGCTATTGTGGCATTTTTTAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTCTGAA
* * *
28406743 AAAGCACTGCTAATGCTCGATCTTTTGCGGCGTTTGTGAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTCTGAA
28406783 AAAGC
1 AAAGC
28406788 GTCGTTGATG
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (40 bp):
AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTCTGAA
Found at i:28406769 original size:195 final size:195
Alignment explanation
Indices: 28406433--28406810 Score: 494
Period size: 195 Copynumber: 1.9 Consensus size: 195
28406423 AGTAAACAAT
* * *
28406433 GTTGTTTTGTTCAACTTTTTTGTGGCGTTTTCCAAAATGCACCGCTAATGGTTGATCTATAGCGG
1 GTTGTTTTGTTCAACTTTTTTATGGCGTTTTCCAAAATGCACCGCTAATGCTTGATCTATAGCGA
* * * * * * *
28406498 CATTTTTTAGAAATCACCGCTAATGTTCGATCTATTGCGGCGCTTTTTAGTAAACACCGAGAATG
66 CATTTCTGAAAAAGCACCGCTAATGTTCGAGCTATTGCGGCACTTTTTAGAAAACACCGAGAATG
*
28406563 CTCGGTCTTTTGCGGCATTTGTGAAAAAGCATCGCTGATGCCAATAAAGCTCACTGAAAAACAGC
131 CTCGATCTTTTGCGGCATTTGTGAAAAAGCATCGCTGATGCCAATAAAGCTCACTGAAAAACAGC
* *
28406628 GTTGTTTT-TCTCAACTTTTTTATGGCGTTTTGCAGAAA-GCGCCGCTAATGCTTGATCTATAGC
1 GTTGTTTTGT-TCAACTTTTTTATGGCGTTTTCCA-AAATGCACCGCTAATGCTTGATCTATAGC
* * * * **
28406691 GACGTTTCTGAAAAAGCACCGCTAAT-TCTCGAGCTATTGTGGCATTTTTTA-AAAAGCACTGCT
64 GACATTTCTGAAAAAGCACCGCTAATGT-TCGAGCTATTGCGGCACTTTTTAGAAAA-CACCGAG
* * *
28406754 AATGCTCGATCTTTTGCGGCGTTTGTGAAAAAGCGTCGTTGATGCCAATAAAGCTCA
127 AATGCTCGATCTTTTGCGGCATTTGTGAAAAAGCATCGCTGATGCCAATAAAGCTCA
28406811 ACGACATTGT
Statistics
Matches: 157, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
194 5 0.03
195 149 0.95
196 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (195 bp):
GTTGTTTTGTTCAACTTTTTTATGGCGTTTTCCAAAATGCACCGCTAATGCTTGATCTATAGCGA
CATTTCTGAAAAAGCACCGCTAATGTTCGAGCTATTGCGGCACTTTTTAGAAAACACCGAGAATG
CTCGATCTTTTGCGGCATTTGTGAAAAAGCATCGCTGATGCCAATAAAGCTCACTGAAAAACAGC
Found at i:28406937 original size:38 final size:39
Alignment explanation
Indices: 28406847--28406960 Score: 97
Period size: 39 Copynumber: 2.9 Consensus size: 39
28406837 GTTTTGCGGG
* * * * * *
28406847 AAGCACCACTATTGCTTGATCTATAGTGGCATTTTTCAGT-
1 AAGCGCCACTAATGCTCGATCTATGGCGGCGTTTTT-A-TC
* *
28406887 AAGCGCCACTAATTCTCG-TCTATGGCGGTGTTTTTATC
1 AAGCGCCACTAATGCTCGATCTATGGCGGCGTTTTTATC
* * *
28406925 AAGCGCCGCTAATGCTCGATCTTTTGCGGCGTTTTT
1 AAGCGCCACTAATGCTCGATCTATGGCGGCGTTTTT
28406961 TGTTCAAACG
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
37 1 0.02
38 17 0.29
39 27 0.46
40 14 0.24
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (39 bp):
AAGCGCCACTAATGCTCGATCTATGGCGGCGTTTTTATC
Found at i:28417823 original size:27 final size:26
Alignment explanation
Indices: 28417737--28417823 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
28417727 AAAACACATA
* *
28417737 AATAAAATACAAAAGTATACAAATCAC
1 AATAATATACAAAAGAAT-CAAATCAC
28417764 AATAATA-A-AAAA-AAT-AATATCAC
1 AATAATATACAAAAGAATCAA-ATCAC
*
28417787 AATTATATATACAAAAGCATGCAAATCAC
1 AA-TA-ATATACAAAAGAAT-CAAATCAC
28417816 AATAATAT
1 AATAATAT
28417824 CACTTGAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 2 0.04
23 7 0.14
24 4 0.08
25 7 0.14
26 2 0.04
27 14 0.29
28 4 0.08
29 7 0.14
30 2 0.04
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (26 bp):
AATAATATACAAAAGAATCAAATCAC
Found at i:28418908 original size:19 final size:18
Alignment explanation
Indices: 28418876--28418914 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28418866 TTAAACATGC
* *
28418876 TAAAAAATAGAAAATATT
1 TAAAAAATAAAAAAAATT
28418894 TAAAAGAATAAAAAAAATT
1 TAAAA-AATAAAAAAAATT
28418913 TA
1 TA
28418915 TTCAACAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAAAAAATT
Found at i:28425979 original size:235 final size:235
Alignment explanation
Indices: 28425568--28426042 Score: 797
Period size: 235 Copynumber: 2.0 Consensus size: 235
28425558 TTACAAGGCA
* *
28425568 TGGCCTCAAGGGAGCCCCCTATACACATGAATGACACCCACACTTCTACCTCCACCTAGCGTTGT
1 TGGCCTCAAGGGAGCCCCCTATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGT
*
28425633 CTAGCTTGGCCCTCCACTTGATTCTTGAGTGAAAACCTTACCCTGCAAGTAAACAAACAATTTGT
66 CTAGCTTGGCCCTCCACTTGATTCTCGAGTGAAAACCTTACCCTGCAAGTAAACAAACAATTTGT
* ** *
28425698 AAGTTCAAATGAACTTAGTGAGATTCTATGTAATGACCGTATAACAAGATTCAAAACTTCAAGAA
131 AAGTTCAAATGAACTTAGTGAGATTCTATATAATGACAATATAACAAGATTCAAAACTTCAAAAA
**
28425763 ATGAAGTTTTAAATAGAGATTTCAACTCCCTGGTCATCCT
196 ACAAAGTTTTAAATAGAGATTTCAACTCCCTGGTCATCCT
*
28425803 TGGCCTCAAGGGAGCCCCCTATACACATGAACGACACCCACACCTCTACCTCCACCTAGTGTTGT
1 TGGCCTCAAGGGAGCCCCCTATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGT
* * *
28425868 CTAGCTTGGCCCTCTACTTGATTCTCGAGTGAAAACCTTATCCTGCAAGTAAGCAAACAATTTGT
66 CTAGCTTGGCCCTCCACTTGATTCTCGAGTGAAAACCTTACCCTGCAAGTAAACAAACAATTTGT
* *
28425933 AAGTTCAAATGAACTTAGTGAGATTCTGTATAATGACAATATAACAAGATTCAAAACTTTAAAAA
131 AAGTTCAAATGAACTTAGTGAGATTCTATATAATGACAATATAACAAGATTCAAAACTTCAAAAA
* *
28425998 ACAAAGTTTTAAGTAGATATTTCAACTCCCTGGTCATCCT
196 ACAAAGTTTTAAATAGAGATTTCAACTCCCTGGTCATCCT
28426038 TGGCC
1 TGGCC
28426043 ATTCGTAGAT
Statistics
Matches: 223, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 223 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (235 bp):
TGGCCTCAAGGGAGCCCCCTATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGT
CTAGCTTGGCCCTCCACTTGATTCTCGAGTGAAAACCTTACCCTGCAAGTAAACAAACAATTTGT
AAGTTCAAATGAACTTAGTGAGATTCTATATAATGACAATATAACAAGATTCAAAACTTCAAAAA
ACAAAGTTTTAAATAGAGATTTCAACTCCCTGGTCATCCT
Found at i:28428031 original size:50 final size:50
Alignment explanation
Indices: 28427959--28428083 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
28427949 TATCCTAGAT
** ** * * *
28427959 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACGGGGGACATCTCATATCGGTGCCAACGCCATGTCCCAAAC
* * *
28428009 ATGGTTTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACGGGGGACATCTCATATCGGTGCCAACGCCATGTCCCAAAC
* *
28428059 ATGGTCTTATGTGGGACATCTCATA
1 ATGGTCTTACGGGGGACATCTCATA
28428084 ACCTCAATAA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACGGGGGACATCTCATATCGGTGCCAACGCCATGTCCCAAAC
Found at i:28433387 original size:21 final size:21
Alignment explanation
Indices: 28433346--28433387 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28433336 TGAGTCAAAA
**
28433346 ATTTTCAAAAATGTTTTAATT
1 ATTTTCAAAAATGTTAGAATT
28433367 ATTTTCAAACAA-GTTAGAATT
1 ATTTTCAAA-AATGTTAGAATT
28433388 GCTCTAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTTTCAAAAATGTTAGAATT
Found at i:28437788 original size:22 final size:22
Alignment explanation
Indices: 28437763--28437822 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
28437753 ATTTCTTTTT
28437763 TTAGTTTTTTTTATTCAGTTCA
1 TTAGTTTTTTTTATTCAGTTCA
* *
28437785 TTAGTTATTATTATTATTCTGTTTA
1 TTAGTT-TT-TT-TTATTCAGTTCA
*
28437810 TTA-TTTCTTTTAT
1 TTAGTTTTTTTTAT
28437823 ACATACCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.12
22 8 0.25
23 3 0.09
24 4 0.12
25 13 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (22 bp):
TTAGTTTTTTTTATTCAGTTCA
Found at i:28442427 original size:17 final size:19
Alignment explanation
Indices: 28442389--28442428 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
28442379 GTAGTTATCA
28442389 CAATT-TTTATTAAATTAT
1 CAATTATTTATTAAATTAT
28442407 -AATTATTT-TTAAA-TAT
1 CAATTATTTATTAAATTAT
28442423 CAATTA
1 CAATTA
28442429 GTAATAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.15
17 14 0.70
18 3 0.15
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
CAATTATTTATTAAATTAT
Found at i:28451550 original size:17 final size:18
Alignment explanation
Indices: 28451519--28451552 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28451509 GTGATGTATC
*
28451519 TTATGAAATTCACTTATG
1 TTATGAAATTAACTTATG
28451537 TTAT-AAATTAACTTAT
1 TTATGAAATTAACTTAT
28451553 ATGTGATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (18 bp):
TTATGAAATTAACTTATG
Found at i:28455935 original size:13 final size:14
Alignment explanation
Indices: 28455919--28455949 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
28455909 TAAATAAAAC
28455919 TTAATTAAAATT-A
1 TTAATTAAAATTAA
28455932 TTAATTAAAATTAA
1 TTAATTAAAATTAA
28455946 TTAA
1 TTAA
28455950 AAGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATTAAAATTAA
Found at i:28458122 original size:41 final size:42
Alignment explanation
Indices: 28458065--28458163 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
28458055 GATCTCAGTA
* * *
28458065 TCGCACATTTAGTGCCCGTTCTTC-ACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
28458106 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
*
28458148 TCACACACTTAGTGCC
1 TCGCACACTTAGTGCC
28458164 ATTCATATAG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 22 0.42
42 31 0.58
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
Found at i:28459886 original size:43 final size:43
Alignment explanation
Indices: 28459838--28460067 Score: 232
Period size: 43 Copynumber: 5.4 Consensus size: 43
28459828 ATTTCCTTAG
* * *
28459838 GTTTATCTAATGATGCACTATTTGTGCCAATATGATTGCTTCA
1 GTTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCA
* * * * **
28459881 ATTTATTTGATGATGCACTATGCGTGCCAGTATGAAAT-CTTTG
1 GTTTATCTGATGATGCACTATGTGTGCCAGTATG-ATTGCTTCA
* *
28459924 GTTTATCCGATGATGCACTATGTGTGCTAGTATGATTGCTTCA
1 GTTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCA
* * * **
28459967 GTTAATCTGATGATCCACTATGTGTGTCAGTATGATTGCTTTG
1 GTTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCA
* * * *
28460010 GTTTATTTGATGATGCACTATGTGT-ACAGTAT-ATTTCCTTCG
1 GTTTATCTGATGATGCACTATGTGTGCCAGTATGA-TTGCTTCA
*
28460052 GTTTATTTGATGATGC
1 GTTTATCTGATGATGC
28460068 TTTGCGTTGC
Statistics
Matches: 154, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 30 0.19
43 121 0.79
44 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (43 bp):
GTTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCA
Found at i:28459937 original size:86 final size:86
Alignment explanation
Indices: 28459837--28460034 Score: 263
Period size: 86 Copynumber: 2.3 Consensus size: 86
28459827 TATTTCCTTA
* * * * *
28459837 GGTTTATCTAATGATGCACTATTTGTGCCAATATGATTGCTTCAATTTATTTGATGATGCACTAT
1 GGTTTATCTGATGATGCACTATGTGTGCCAATATGATTGCTTCAATTAATCTGATGATCCACTAT
28459902 GCGTGCCAGTATGAAAT-CTTT
66 GCGTGCCAGTATG-AATGCTTT
* * * *
28459923 GGTTTATCCGATGATGCACTATGTGTGCTAGTATGATTGCTTCAGTTAATCTGATGATCCACTAT
1 GGTTTATCTGATGATGCACTATGTGTGCCAATATGATTGCTTCAATTAATCTGATGATCCACTAT
* * *
28459988 GTGTGTCAGTATGATTGCTTT
66 GCGTGCCAGTATGAATGCTTT
*
28460009 GGTTTATTTGATGATGCACTATGTGT
1 GGTTTATCTGATGATGCACTATGTGT
28460035 ACAGTATATT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 2 0.02
86 95 0.98
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (86 bp):
GGTTTATCTGATGATGCACTATGTGTGCCAATATGATTGCTTCAATTAATCTGATGATCCACTAT
GCGTGCCAGTATGAATGCTTT
Found at i:28462032 original size:27 final size:27
Alignment explanation
Indices: 28461992--28462066 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
28461982 TCTACAAGAC
**
28461992 GTTAAACATGAGATAGCCTGACAGGAA
1 GTTAAACACAAGATAGCCTGACAGGAA
* **
28462019 GTTAAACACAAGATAGTCC-AATGGGAA
1 GTTAAACACAAGATAG-CCTGACAGGAA
* *
28462046 GTTAAACACAGGATAGTCTGA
1 GTTAAACACAAGATAGCCTGA
28462067 AGGGACGTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.03
27 35 0.92
28 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (27 bp):
GTTAAACACAAGATAGCCTGACAGGAA
Found at i:28462071 original size:27 final size:27
Alignment explanation
Indices: 28462015--28462092 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
28462005 TAGCCTGACA
*
28462015 GGAAGTTAAACACAAGATAGTCCAATG
1 GGAAGTTAAACACAGGATAGTCCAATG
*
28462042 GGAAGTTAAACACAGGATAGTCTGAA-G
1 GGAAGTTAAACACAGGATAGTC-CAATG
* * *
28462069 GGACGTTAGACACTGGATAGTCCA
1 GGAAGTTAAACACAGGATAGTCCA
28462093 CTGAGACACT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 41 0.93
28 2 0.05
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (27 bp):
GGAAGTTAAACACAGGATAGTCCAATG
Found at i:28469374 original size:43 final size:43
Alignment explanation
Indices: 28469313--28469404 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
28469303 TTTAAGTACA
28469313 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
1 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
28469356 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
1 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
28469399 TCATCG
1 TCATCG
28469405 AACGAACTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (43 bp):
TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
Found at i:28469433 original size:43 final size:43
Alignment explanation
Indices: 28469313--28469423 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
28469303 TTTAAGTACA
* * *
28469313 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
1 TCATCGCGATACTCGAAGCAAATATACTGACACACGAGATGCG
* * *
28469356 TCATCGGGATAGTCGAAGCAATTATACTGACACACGAGATGCG
1 TCATCGCGATACTCGAAGCAAATATACTGACACACGAGATGCG
28469399 TCATCGAACGA-ACT-GAAGCAAATAT
1 TCATCG--CGATACTCGAAGCAAATAT
28469424 TCTAGCACAC
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
43 59 0.94
44 2 0.03
45 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (43 bp):
TCATCGCGATACTCGAAGCAAATATACTGACACACGAGATGCG
Found at i:28469513 original size:42 final size:42
Alignment explanation
Indices: 28469467--28469547 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
28469457 ATCATGTTGG
*
28469467 CACATAAGTACATCATT-GGATGTAACAAAGCAAATATACTAT
1 CACATAAGTACATC-TTCGGATATAACAAAGCAAATATACTAT
* * *
28469509 CACATAAGTGCATCTTCGGATATACCAAAGCAATTATAC
1 CACATAAGTACATCTTCGGATATAACAAAGCAAATATAC
28469548 AGGCACGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (42 bp):
CACATAAGTACATCTTCGGATATAACAAAGCAAATATACTAT
Found at i:28483110 original size:40 final size:40
Alignment explanation
Indices: 28483055--28483188 Score: 135
Period size: 40 Copynumber: 3.4 Consensus size: 40
28483045 GCATTAATGG
* * * *
28483055 CGCTTTTT-AACAAATGCCGCAATAGATCAAGAATTTGTGA
1 CGCTTTTTGAA-AAATGCCGCTATAGATCAAGAAATAGCGA
* *
28483095 CGCTTTTTGAAAAATGCCGCTATAGATAAAGAAATAGCGG
1 CGCTTTTTGAAAAATGCCGCTATAGATCAAGAAATAGCGA
* * * * * *
28483135 CGCTTTTTGAGAAATGCCACTATAGATCAAGCATTAACGG
1 CGCTTTTTGAAAAATGCCGCTATAGATCAAGAAATAGCGA
*
28483175 CGCTTTTTGGAAAA
1 CGCTTTTTGAAAAA
28483189 CGTCCAAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 77 0.97
41 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (40 bp):
CGCTTTTTGAAAAATGCCGCTATAGATCAAGAAATAGCGA
Found at i:28483455 original size:197 final size:193
Alignment explanation
Indices: 28482908--28483500 Score: 601
Period size: 195 Copynumber: 3.0 Consensus size: 193
28482898 TTTGTGGTGC
* * * *
28482908 TTTTTAACAAACGTCACTAAAGATCAAGCAATAGCGGCG-TTTAGT-GTAAAACGCCGCTATATA
1 TTTTTAA-AAACGCCGCTAAAGATCAAGCAATAGCGGCGCTTTA-TAG-AAAGCG-CGCTATAGA
* * * *
28482971 TCAAGCATTAATGGTGATTTTTGGAAAACGCCGCAATAAAGTTTAGCAAAATGA--CA---TCGT
62 TCAAGCATT-ATGGCGATTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAATGACTCATTTTCTT
* * ** * *
28483031 TTTGAGCTTTAGTGGCATTAATGGCGCTTTTTAACAAATGCCGCAATAGATCAAGAATTTGTGAC
126 TTTGAGCTTTAGTGGCATTAGTGGCGCTTTTTAACAAACGCCGCAATAGATTGAGAATTAGTGGC
28483096 GCT
191 GCT
* * * * * * *
28483099 TTTTGAAAAATGCCGCTATAGATAAAGAAATAGCGGCGCTTTTTGAGAAATGC-CACTATAGATC
1 TTTTTAAAAACGCCGCTAAAGATCAAGCAATAGCGGCGCTTTAT-AGAAA-GCGCGCTATAGATC
* * * * **
28483163 AAGCATTAACGGCGCTTTTTGGAAAACGTC-CAAAAAAGTTGAGCAACATGACATTGTTTTCTTT
64 AAGCATT-ATGGCGATTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAATGAC-TCATTTTCTTT
* * * * *
28483227 TTGAGTTTTAGTGGCATTAGTGGCCCTTTTTAACAAACGCCACAAAAGATTGAGAATTAGCGGCG
127 TTGAGCTTTAGTGGCATTAGTGGCGCTTTTTAACAAACGCCGCAATAGATTGAGAATTAGTGGCG
28483292 CT
192 CT
* *
28483294 TTTTTAAAAACGCCGTTAAAGATCAAGCAATAGCGGTGCTTTATAGAAAGCGCTGCTATAGATCA
1 TTTTTAAAAACGCCGCTAAAGATCAAGCAATAGCGGCGCTTTATAGAAAGCGC-GCTATAGATCA
* * * *
28483359 AGCATTAGTGGGCGGTTGTTGGAAAATGCCGCAAAAAAGTTGAGCAAAACGACGTCATTTTCTTT
65 AGCATTA-T-GGCGATTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAATGAC-TCATTTTCTTT
* * ** * *
28483424 TTTAGCTTTAGTGGCATTAGCGGCGCTTTTTAACAAACATCGCAATAGAATGAGAATTAGTGGTG
127 TTGAGCTTTAGTGGCATTAGTGGCGCTTTTTAACAAACGCCGCAATAGATTGAGAATTAGTGGCG
28483489 CT
192 CT
28483491 TTTTGTAAAA
1 TTTT-TAAAA
28483501 TGCCACAAAA
Statistics
Matches: 324, Mismatches: 62, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
189 18 0.06
190 61 0.19
191 12 0.04
192 2 0.01
193 2 0.01
194 7 0.02
195 112 0.35
196 16 0.05
197 89 0.27
198 5 0.02
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (193 bp):
TTTTTAAAAACGCCGCTAAAGATCAAGCAATAGCGGCGCTTTATAGAAAGCGCGCTATAGATCAA
GCATTATGGCGATTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAATGACTCATTTTCTTTTTGA
GCTTTAGTGGCATTAGTGGCGCTTTTTAACAAACGCCGCAATAGATTGAGAATTAGTGGCGCT
Found at i:28483563 original size:14 final size:14
Alignment explanation
Indices: 28483544--28483598 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
28483534 TGAGCTTTAT
28483544 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
28483558 TTTAGGGTTT-TAAGG
1 TTTAGGGTTTAT-A-G
28483573 TTTTAGGGTTTAGTA-
1 -TTTAGGGTTTA-TAG
*
28483588 TTTAAGGTTTA
1 TTTAGGGTTTA
28483599 ATGTCTATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 1 0.03
14 21 0.60
15 1 0.03
16 10 0.29
17 1 0.03
18 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:28483662 original size:14 final size:14
Alignment explanation
Indices: 28483645--28483704 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
28483635 TATTTTCATA
28483645 TTAGAGTTTTGAGT
1 TTAGAGTTTTGAGT
*
28483659 TTAGCGTTTATG-GT
1 TTAGAGTTT-TGAGT
* *
28483673 TTAGAGTTTGGGGT
1 TTAGAGTTTTGAGT
*
28483687 TTA-AGGTTTAGAGT
1 TTAGA-GTTTTGAGT
28483701 TTAG
1 TTAG
28483705 TATTTAAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (14 bp):
TTAGAGTTTTGAGT
Found at i:28483712 original size:21 final size:21
Alignment explanation
Indices: 28483650--28483704 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
28483640 TCATATTAGA
* *
28483650 GTTTTGAGTTTAGCGTTTATG
1 GTTTAGAGTTTAGCGTTTAAG
* *
28483671 GTTTAGAGTTTGGGGTTTAAG
1 GTTTAGAGTTTAGCGTTTAAG
28483692 GTTTAGAGTTTAG
1 GTTTAGAGTTTAG
28483705 TATTTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (21 bp):
GTTTAGAGTTTAGCGTTTAAG
Found at i:28483803 original size:7 final size:7
Alignment explanation
Indices: 28483777--28483995 Score: 64
Period size: 7 Copynumber: 31.0 Consensus size: 7
28483767 GTAGGTCTAT
28483777 GGTTTAG
1 GGTTTAG
*
28483784 GGTTTAA
1 GGTTTAG
**
28483791 TATTTAG
1 GGTTTAG
*
28483798 GGTTTAT
1 GGTTTAG
*
28483805 GATTTAG
1 GGTTTAG
* *
28483812 TGTTAAG
1 GGTTTAG
* *
28483819 AGATTAG
1 GGTTTAG
* *
28483826 TGTTTAC
1 GGTTTAG
*
28483833 GGATTAG
1 GGTTTAG
*
28483840 GGTGTA-
1 GGTTTAG
28483846 GGTTTAG
1 GGTTTAG
28483853 GGTTTAG
1 GGTTTAG
*
28483860 GGTTTAAA
1 GGTTT-AG
*
28483868 GG-TAAGG
1 GGTTTA-G
*
28483875 GGCTTAG
1 GGTTTAG
*
28483882 AGTTTAG
1 GGTTTAG
* *
28483889 GGTGTAA
1 GGTTTAG
** *
28483896 ATTTTAT
1 GGTTTAG
28483903 GGTTTAG
1 GGTTTAG
28483910 GGTTTAG
1 GGTTTAG
* *
28483917 ATGTTAAG
1 -GGTTTAG
*
28483925 GGCTTAG
1 GGTTTAG
*
28483932 AGTTTAG
1 GGTTTAG
* *
28483939 GGTGTAA
1 GGTTTAG
* *
28483946 AGTTTAT
1 GGTTTAG
*
28483953 AGTTTAG
1 GGTTTAG
*
28483960 GGTTTATA
1 GGTTTA-G
* *
28483968 CGCTTAG
1 GGTTTAG
*
28483975 GGTTTAT
1 GGTTTAG
28483982 GGTTTAG
1 GGTTTAG
*
28483989 TGTTTAG
1 GGTTTAG
28483996 TGTCCGATTT
Statistics
Matches: 142, Mismatches: 64, Indels: 12
0.65 0.29 0.06
Matches are distributed among these distances:
6 6 0.04
7 122 0.86
8 14 0.10
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:28483913 original size:50 final size:50
Alignment explanation
Indices: 28483836--28483965 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
28483826 TGTTTACGGA
* *
28483836 TTAGGGTGT-AGGTTTAGGGTTTAGGGTTTA-AAGGTAAGGGGCTTAGAGT
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAA-GGGCTTAGAGT
* * *
28483885 TTAGGGTGTAAATTTTATGGTTTAGGGTTTAGATGTTAAGGGCTTAGAGT
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAAGGGCTTAGAGT
*
28483935 TTAGGGTGTAAAGTTTATAGTTTAGGGTTTA
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTA
28483966 TACGCTTAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
49 9 0.12
50 58 0.81
51 5 0.07
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.40
Consensus pattern (50 bp):
TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAAGGGCTTAGAGT
Found at i:28483976 original size:15 final size:14
Alignment explanation
Indices: 28483947--28483981 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28483937 AGGGTGTAAA
*
28483947 GTTTATAGTTTAGG
1 GTTTATAGCTTAGG
28483961 GTTTATACGCTTAGG
1 GTTTATA-GCTTAGG
28483976 GTTTAT
1 GTTTAT
28483982 GGTTTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTTATAGCTTAGG
Found at i:28484962 original size:124 final size:125
Alignment explanation
Indices: 28484816--28485042 Score: 314
Period size: 125 Copynumber: 1.8 Consensus size: 125
28484806 AAACGGCGGC
* * * * * *
28484816 TTTCGGTACATGAATTTAA-TTTTTTAGTGGC-GTTTTTGCTGGAAACGTCGCAAAATGTAAGCA
1 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTG-TGAAAACGTCGCAAAAGGCAAGAA
* *
28484879 ATAGCAGCGTTTTGACCAAAAACGTCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
65 ATAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
* *
28484940 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCATTTTTTGTTAAAACGTCGCAAAAGGCAAGAAA
1 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTGTGAAAACGTCGCAAAAGGCAAGAAA
* * *
28485005 TAGCGGCGTTTGGACCTAAAACGCCGCAACTATGTATT
66 TAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATT
28485043 TACTTTCTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
124 17 0.19
125 65 0.74
126 6 0.07
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (125 bp):
TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTGTGAAAACGTCGCAAAAGGCAAGAAA
TAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
Found at i:28485155 original size:42 final size:41
Alignment explanation
Indices: 28485089--28485176 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
28485079 CCGTCCCCTC
*
28485089 TCCCCTTAGCCCTTATACCCATCTCACA-ATCCAACTAAAAAA
1 TCCCTTTAGCCCTTATACCCATCTCACATAT--AACTAAAAAA
* * * *
28485131 TCCCTTTAGCCCTTATTCCGATCTCGCATATACCTAAAAAA
1 TCCCTTTAGCCCTTATACCCATCTCACATATAACTAAAAAA
28485172 TCCCT
1 TCCCT
28485177 AATTTCTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 14 0.35
42 24 0.60
43 2 0.05
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (41 bp):
TCCCTTTAGCCCTTATACCCATCTCACATATAACTAAAAAA
Found at i:28487010 original size:65 final size:66
Alignment explanation
Indices: 28486892--28487033 Score: 216
Period size: 65 Copynumber: 2.2 Consensus size: 66
28486882 TGGTTAAATA
* * *
28486892 GAATAAATTATCAAATTTTTAATTAATTGAATAAATTATGTTTGATTATTTTATTCGGTTTAATT
1 GAATAAATTATCAAATTTTCAATTAATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAATG
28486957 T
66 T
* *
28486958 GAATAAATTATC-GATTTTCGATTGAATTGAATAAA-TATGTTTGATTAGTTTATTCGGTTTAAT
1 GAATAAATTATCAAATTTTCAATT-AATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAAT
28487021 GT
65 GT
28487023 GAATAAATTAT
1 GAATAAATTAT
28487034 GTTTGATTAG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 47 0.67
66 23 0.33
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.48
Consensus pattern (66 bp):
GAATAAATTATCAAATTTTCAATTAATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAATG
T
Found at i:28487040 original size:38 final size:38
Alignment explanation
Indices: 28486974--28487071 Score: 146
Period size: 38 Copynumber: 2.6 Consensus size: 38
28486964 ATTATCGATT
*
28486974 TTCGATTGAAT-TGAATAAA-TATGTTTGATTAGTTTA
1 TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
*
28487010 TTCGGTTTAATGTGAATAAATTATGTTTGATTAGTTTA
1 TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
* *
28487048 TTTGATTTTATGTGAATAAATTAT
1 TTCGATTTAATGTGAATAAATTAT
28487072 CAATTTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 9 0.16
37 8 0.15
38 38 0.69
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (38 bp):
TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
Found at i:28487080 original size:29 final size:28
Alignment explanation
Indices: 28487048--28487106 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
28487038 GATTAGTTTA
*
28487048 TTTGATTTTATGTGAATAAATTATCAATT
1 TTTGATTTAAT-TGAATAAATTATCAATT
*
28487077 TTTGATTTAATTGAATAAATTATCGATT
1 TTTGATTTAATTGAATAAATTATCAATT
28487105 TT
1 TT
28487107 ATATTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (28 bp):
TTTGATTTAATTGAATAAATTATCAATT
Found at i:28487505 original size:8 final size:9
Alignment explanation
Indices: 28487465--28487645 Score: 94
Period size: 9 Copynumber: 20.9 Consensus size: 9
28487455 AAATTAATAT
*
28487465 ATAATTTAC
1 ATAACTTAC
*
28487474 ATAACTCAC
1 ATAACTTAC
28487483 ATAACTTAC
1 ATAACTTAC
28487492 ATAACTTA-
1 ATAACTTAC
28487500 ATAACTTAC
1 ATAACTTAC
28487509 ATAA-TT-C
1 ATAACTTAC
* *
28487516 ATAA-ATAT
1 ATAACTTAC
* *
28487524 ATATCATATC
1 ATAACTTA-C
*
28487534 ATAACTCAC
1 ATAACTTAC
*
28487543 ATCACTTAC
1 ATAACTTAC
*
28487552 ATAACTAAC
1 ATAACTTAC
28487561 ATAA--TAC
1 ATAACTTAC
* *
28487568 ATAA-ATAT
1 ATAACTTAC
* *
28487576 ATATCATATC
1 ATAACTTA-C
*
28487586 AAAACTTAC
1 ATAACTTAC
28487595 ATAACTTAC
1 ATAACTTAC
28487604 ATAA--TAC
1 ATAACTTAC
* *
28487611 ATAA-ATAT
1 ATAACTTAC
* * *
28487619 TTATCATATC
1 ATAACTTA-C
28487629 ATAACTTAC
1 ATAACTTAC
28487638 ATAACTTA
1 ATAACTTA
28487646 ATTATACTTG
Statistics
Matches: 133, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
7 19 0.14
8 22 0.17
9 77 0.58
10 15 0.11
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28487564 original size:52 final size:51
Alignment explanation
Indices: 28487482--28487645 Score: 211
Period size: 52 Copynumber: 3.4 Consensus size: 51
28487472 ACATAACTCA
*
28487482 CATAACTTACATAACTTA-ATAACTTACATAATTCATAAATATATATCATAT
1 CATAACTTACATAACTTACATAAC-TACATAATACATAAATATATATCATAT
* *
28487533 CATAACTCACATCACTTACATAACTAACATAATACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAACT-ACATAATACATAAATATATATCATAT
*
28487585 CAAAACTTACATAACTTACATAA-TACAT-A-A-AT--AT-T-TATCATAT
1 CATAACTTACATAACTTACATAACTACATAATACATAAATATATATCATAT
28487628 CATAACTTACATAACTTA
1 CATAACTTACATAACTTA
28487646 ATTATACTTG
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
43 25 0.24
44 1 0.01
45 2 0.02
47 2 0.02
48 1 0.01
49 1 0.01
50 4 0.04
51 18 0.17
52 50 0.48
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (51 bp):
CATAACTTACATAACTTACATAACTACATAATACATAAATATATATCATAT
Found at i:28487644 original size:43 final size:43
Alignment explanation
Indices: 28487491--28487645 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
28487481 ACATAACTTA
*
28487491 CATAACTTA-ATAACTTACATAATTCATAAATATATATCATATCATAACT
1 CATAACTTACATAACTTACATAATACAT-AA-ATAT-T--TATCAT-A-T
* * *
28487540 CACATCACTTACATAACTAACATAATACATAAATATATATCATAT
1 --CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
*
28487585 CAAAACTTACATAACTTACATAATACATAAATATTTATCATAT
1 CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
28487628 CATAACTTACATAACTTA
1 CATAACTTACATAACTTA
28487646 ATTATACTTG
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
43 56 0.60
45 1 0.01
46 1 0.01
47 6 0.06
50 4 0.04
51 10 0.11
52 16 0.17
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (43 bp):
CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
Found at i:28493482 original size:43 final size:43
Alignment explanation
Indices: 28493435--28493526 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
28493425 GAATGGTACT
* *
28493435 TTTAGCAACGTTTGTGAAAAAAGCATCGCTAAAGGTCATGTTC
1 TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
** * **
28493478 TTTAGCGGCATTTGTGAAAAAGGTGCCGCTAAAGGTCATGTTC
1 TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
28493521 TTTAGC
1 TTTAGC
28493527 GGTGTTTATG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
Found at i:28493554 original size:45 final size:43
Alignment explanation
Indices: 28493445--28493555 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 43
28493435 TTTAGCAACG
**
28493445 TTTGTGAAAAAAGCATCGCTAAAGGTCATGTTCTTTAGCGGCA
1 TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCA
* * **
28493488 TTTGTGAAAAAGGTGCCGCTAAAGGTCATGTTCTTTAGCGGTGT
1 TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG-CA
*
28493532 TTATGTGAAAAAAACGCCGCTAAA
1 TT-TGTGAAAAAAGCGCCGCTAAA
28493556 ATTAGCGACA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 37 0.65
44 2 0.04
45 18 0.32
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCA
Found at i:28500874 original size:13 final size:13
Alignment explanation
Indices: 28500856--28500881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28500846 CTTTTGGAGA
28500856 TAAAATGAAAGAT
1 TAAAATGAAAGAT
28500869 TAAAATGAAAGAT
1 TAAAATGAAAGAT
28500882 GTTTGATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TAAAATGAAAGAT
Found at i:28504261 original size:18 final size:17
Alignment explanation
Indices: 28504233--28504276 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
28504223 ACCAATGTCT
*
28504233 ATATTTCACATATATAC
1 ATATTTCACATATAAAC
28504250 ATATTATCACATATAAAC
1 ATATT-TCACATATAAAC
28504268 ATATATTCA
1 ATAT-TTCA
28504277 ATTCAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 18 0.75
19 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTTCACATATAAAC
Found at i:28508257 original size:20 final size:20
Alignment explanation
Indices: 28508232--28508313 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
28508222 GCTTGTACAG
*
28508232 GTTTGCATTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTCT
28508252 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTCT
* *
28508272 GTTTGCACTTCGGTGCCACT
1 GTTTGCACTTTGGTGCCTCT
* *
28508292 GTTACGCATCTTTGATGCCTCT
1 GTT-TGCA-CTTTGGTGCCTCT
28508314 AGTGTGGTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
20 40 0.75
21 3 0.06
22 10 0.19
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (20 bp):
GTTTGCACTTTGGTGCCTCT
Found at i:28513789 original size:21 final size:21
Alignment explanation
Indices: 28513765--28513805 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28513755 ATCATATAAA
28513765 TTATAACTCATAATTATTTTT
1 TTATAACTCATAATTATTTTT
* **
28513786 TTATAATTTTTAATTATTTT
1 TTATAACTCATAATTATTTT
28513806 CCAAATTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAACTCATAATTATTTTT
Found at i:28516199 original size:22 final size:22
Alignment explanation
Indices: 28516165--28516207 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28516155 CTAACTTTGT
* *
28516165 ATGTTTCGATACATTCAAGGGC
1 ATGTATCGATACATCCAAGGGC
*
28516187 ATGTATCGTTACATCCAAGGG
1 ATGTATCGATACATCCAAGGG
28516208 TTGTATTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
ATGTATCGATACATCCAAGGGC
Found at i:28519040 original size:35 final size:35
Alignment explanation
Indices: 28518994--28519063 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
28518984 AATGAATTCG
28518994 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
1 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
28519029 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
1 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
28519064 GAGATGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (35 bp):
ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
Found at i:28529477 original size:17 final size:17
Alignment explanation
Indices: 28529435--28529477 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
28529425 AAATTTTTTT
28529435 ATAAAGTTTTATATTTAA
1 ATAAA-TTTTATATTTAA
28529453 ATATAATTTTGAT-TTTAA
1 ATA-AATTTT-ATATTTAA
28529471 ATAAATT
1 ATAAATT
28529478 ATCTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATAAATTTTATATTTAA
Found at i:28534098 original size:20 final size:20
Alignment explanation
Indices: 28534073--28534112 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28534063 TTGTACTCTT
28534073 TTGAAATTC-AATATTTAATC
1 TTGAAATTCAAAT-TTTAATC
28534093 TTGAAATTCAAATTTTAATC
1 TTGAAATTCAAATTTTAATC
28534113 CAAGATGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
TTGAAATTCAAATTTTAATC
Found at i:28534438 original size:5 final size:5
Alignment explanation
Indices: 28534428--28534452 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28534418 CTCTTTTTAA
28534428 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
28534453 TCACAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:28537522 original size:26 final size:26
Alignment explanation
Indices: 28537493--28537542 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
28537483 AATAATATTA
28537493 TTAACAT-TTTTTTATAAATTATTTAT
1 TTAACATATTTTTTA-AAATTATTTAT
*
28537519 TTAATATATTTTTTAAAATTATTT
1 TTAACATATTTTTTAAAATTATTT
28537543 TGTTTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTAACATATTTTTTAAAATTATTTAT
Found at i:28537541 original size:13 final size:13
Alignment explanation
Indices: 28537500--28537543 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
28537490 TTATTAACAT
28537500 TTTTTTATAAATTA
1 TTTTTTA-AAATTA
*
28537514 TTTATTTAATA-TA
1 TTT-TTTAAAATTA
28537527 TTTTTTAAAATTA
1 TTTTTTAAAATTA
28537540 TTTT
1 TTTT
28537544 GTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.23
13 11 0.42
14 5 0.19
15 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTTAAAATTA
Found at i:28542784 original size:5 final size:6
Alignment explanation
Indices: 28542768--28542792 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28542758 GTAGAAATGC
28542768 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
28542793 GGGGGGTTTA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Done.