Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012596.1 Kokia drynarioides strain JFW-HI SEQ_127605, 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: 138653
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:5798 original size:13 final size:13
Alignment explanation
Indices: 5763--5787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5753 AAAACTCAAA
5763 ATAAAAATAAAAG
1 ATAAAAATAAAAG
5776 ATAAAAATAAAA
1 ATAAAAATAAAA
5788 TAAATAAATA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAAATAAAAG
Found at i:5798 original size:19 final size:19
Alignment explanation
Indices: 5760--5798 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5750 AAGAAAACTC
*
5760 AAAATAAAAATAAAAGATA
1 AAAATAAAAATAAAAAATA
5779 AAAAT-AAAATAAATAAATA
1 AAAATAAAAATAAA-AAATA
5798 A
1 A
5799 TTATACCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATAAAAAATA
Found at i:11493 original size:30 final size:30
Alignment explanation
Indices: 11450--11508 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
11440 ACACATGGCC
11450 TGCACACGAGCAACCCACACGGGCGTGTGG
1 TGCACACGAGCAACCCACACGGGCGTGTGG
* * ** *
11480 TGCACATGGGCAACCTGCATGGGCGTGTG
1 TGCACACGAGCAACCCACACGGGCGTGTG
11509 CCCTAAGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.36, T:0.15
Consensus pattern (30 bp):
TGCACACGAGCAACCCACACGGGCGTGTGG
Found at i:11653 original size:54 final size:54
Alignment explanation
Indices: 11535--11653 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
11525 TGCAAGGTTC
* * *
11535 ACACGAGCTGACACACGGGCTAAGACACGGGCGTGTGGCCAAAGTCAGTGAGTT
1 ACACGAGCTGACACACAGGCTAAGACACGGGCGCGTGACCAAAGTCAGTGAGTT
* * * * *
11589 ACACAAGCTGACACACATGCTGAGACACGGGCGCGTGACCCAAGTCAGTTAGTT
1 ACACGAGCTGACACACAGGCTAAGACACGGGCGCGTGACCAAAGTCAGTGAGTT
*
11643 ACACGGGCTGA
1 ACACGAGCTGA
11654 GACATGGGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.26, G:0.30, T:0.15
Consensus pattern (54 bp):
ACACGAGCTGACACACAGGCTAAGACACGGGCGCGTGACCAAAGTCAGTGAGTT
Found at i:15199 original size:183 final size:182
Alignment explanation
Indices: 14886--15431 Score: 745
Period size: 183 Copynumber: 3.0 Consensus size: 182
14876 TAGATTTTTG
* *
14886 GGTAAGCATATATTTAGCCGATTTGTTTTAAGGCTCATAAGGAATTGGGGATTTTTTATTTTTTT
1 GGTAAGCATATATTTAGCCGATTTGTTTTAGGGCTCATAAGAAATTGGGGATTTTTTATTTTTTT
* * * * * * *
14951 TATTATTATGTCGGTTGGATTAAATTGGTGTTATATTTCATCATAGCATTAGATTTTTGAGTGAA
66 TATTATTGTGTC-GCTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTGAGTGAA
* * *
15016 TTGTTGGATTTATATAATAAAAAGTTGAATTTTTTTGTGTGAATTGTATTC-T
130 TTGTAGGGTTTATATAATAAAAAGTTGAATTTTTTTGTGTGAATTGTATTCGA
* * * * *
15068 GGTAAGCATATATATAGTCGATTTGTTTTAGGGTTTATAAGAAATTAGGGATTTTCTTATTTTTT
1 GGTAAGCATATATTTAGCCGATTTGTTTTAGGGCTCATAAGAAATTGGGGATTTT-TTATTTTTT
* *
15133 TTATTATTGCGTCGCCTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTTAGTGA
65 TTATTATTGTGTCG-CTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTGAGTGA
** *** *
15198 ATTGTAGGGTTTATATAATAAAAAGTCAAAAAAATTTTGTGGGAATTGTATTCGA
129 ATTGTAGGGTTTATATAATAAAAAGT-TGAATTTTTTTGTGTGAATTGTATTCGA
*
15253 GGTAAGCATATATTTAGCCAATTTGTTTTAGGGCTCATAAGAAATTGGGGATTTTTTA-TTTTTT
1 GGTAAGCATATATTTAGCCGATTTGTTTTAGGGCTCATAAGAAATTGGGGATTTTTTATTTTTTT
*
15317 CATTATTGTGTCAGCTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTGAGTGAA
66 TATTATTGTGTC-GCTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTGAGTGAA
* * *
15382 TTGTAGGGTATATATAATAAAAAGTTGATTTTTTTTTTTTGTGAATTGTA
130 TTGTAGGGTTTATATAATAAAAAGTTGA--ATTTTTTTGTGTGAATTGTA
15432 GGTTGGTGGA
Statistics
Matches: 314, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
182 50 0.16
183 177 0.56
184 38 0.12
185 49 0.16
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (182 bp):
GGTAAGCATATATTTAGCCGATTTGTTTTAGGGCTCATAAGAAATTGGGGATTTTTTATTTTTTT
TATTATTGTGTCGCTGGACTAAATTGGTGCTACAATTCGTCATAGCATTAGATTTTTGAGTGAAT
TGTAGGGTTTATATAATAAAAAGTTGAATTTTTTTGTGTGAATTGTATTCGA
Found at i:16607 original size:157 final size:158
Alignment explanation
Indices: 16305--16762 Score: 643
Period size: 159 Copynumber: 2.9 Consensus size: 158
16295 ATATGCCATC
*
16305 TTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTGAG-AAAAAAAATCATAACCCCAAATTA
1 TTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGAAAAAAAAATCATAACCCCAAATTA
* * *
16369 GATTTAAATATTTTAGAATTGATATTAAAAAA-TGTTTACGATAAACCTGTGATCCAATTGTGTT
66 GATTTAAATATTTTGGAATTGATATTAAAAAAGTGTTTACGATATACCTGTGATCTAATTGTGTT
* *
16433 AGGCTAAATGCATGGTG-TCTGTTGTTA
131 AGGTTGAATGCATGGTGTTCTGTTGTTA
* * * * *
16460 TTTTTTTGGCTTCTAGTTCGCGTACTTGTACCAGGCTAAGAAAAAAAAATCAGAACCTCAAATTA
1 TTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGAAAAAAAAATCATAACCCCAAATTA
* * * * * *
16525 TATTTAAATATTTTGGAATTTACATTAAAAAAGTGTTTATGATATACCTGTGATCTAGTTGGGTT
66 GATTTAAATATTTTGGAATTGATATTAAAAAAGTGTTTACGATATACCTGTGATCTAATTGTGTT
16590 AGGTTGAATGCATGGTGTTCTGTTGTTA
131 AGGTTGAATGCATGGTGTTCTGTTGTTA
* * * *
16618 TTTTTTTGGCTTCTAATTCTCGTACTCGTACCAAACTAAGACCAAAAAAGTCATAACCCCAAATT
1 TTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGA-AAAAAAAATCATAACCCCAAATT
* * * * *
16683 AGATTTAAATATTTTGGAATTGATAGTGAAAAAGTGTTTGCAATATACTTGTGATCTAATTGTGT
65 AGATTTAAATATTTTGGAATTGATATTAAAAAAGTGTTTACGATATACCTGTGATCTAATTGTGT
*
16748 CAGGTTGAATGCATG
130 TAGGTTGAATGCATG
16763 ATCTTTTGTT
Statistics
Matches: 261, Mismatches: 38, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
155 36 0.14
156 50 0.19
157 42 0.16
158 46 0.18
159 87 0.33
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (158 bp):
TTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGAAAAAAAAATCATAACCCCAAATTA
GATTTAAATATTTTGGAATTGATATTAAAAAAGTGTTTACGATATACCTGTGATCTAATTGTGTT
AGGTTGAATGCATGGTGTTCTGTTGTTA
Found at i:17995 original size:15 final size:15
Alignment explanation
Indices: 17977--18010 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17967 AAACCCTCAA
*
17977 CACCTTCACCACCCT
1 CACCCTCACCACCCT
*
17992 CACCCTCACCACTCT
1 CACCCTCACCACCCT
18007 CACC
1 CACC
18011 ACCTTGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.62, G:0.00, T:0.18
Consensus pattern (15 bp):
CACCCTCACCACCCT
Found at i:18090 original size:81 final size:81
Alignment explanation
Indices: 18005--18153 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
17995 CCTCACCACT
* * * * * *
18005 CTCACCACCTTGATTG-CTAGAAACCTCAACACTCTCCCCACCTAAACTTTTAGCACACTCACCA
1 CTCACCACCTTGACTGCCAAG-AACCTCAACACACTCCCCACCTAAACCTTCACCACACTCACCA
18069 CCTTCACAACCCGAACC
65 CCTTCACAACCCGAACC
* * * *
18086 CTCACCACCTTTACTGCCAAGAACCTTAACACACTTCCCACCTAAACCTTCACCACCCTCACCAC
1 CTCACCACCTTGACTGCCAAGAACCTCAACACACTCCCCACCTAAACCTTCACCACACTCACCAC
18151 CTT
66 CTT
18154 TACTACCAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 54 0.95
82 3 0.05
ACGTcount: A:0.29, C:0.45, G:0.05, T:0.21
Consensus pattern (81 bp):
CTCACCACCTTGACTGCCAAGAACCTCAACACACTCCCCACCTAAACCTTCACCACACTCACCAC
CTTCACAACCCGAACC
Found at i:18119 original size:57 final size:57
Alignment explanation
Indices: 18058--18191 Score: 138
Period size: 57 Copynumber: 2.4 Consensus size: 57
18048 AAACTTTTAG
* *
18058 CACACTCACCACCTTCACAACC-CGA-ACCCTCACCACCTTTACTGCCAAGAACCTTAA
1 CACACTCACCACC-TCACAACCTC-ACACCCTCACCACCTTTACTACCAACAACCTTAA
*
18115 CACACTTC-CCACCT-A-AACCTTCACCACCCTCACCACCTTTACTACCAACAACCTTAC
1 CACAC-TCACCACCTCACAACC-TCA-CACCCTCACCACCTTTACTACCAACAACCTTAA
*
18172 CACCCTCA--ACCTCACAACCT
1 CACACTCACCACCTCACAACCT
18192 TTACTGCCAG
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
54 4 0.06
55 6 0.09
56 6 0.09
57 47 0.72
58 2 0.03
ACGTcount: A:0.31, C:0.49, G:0.02, T:0.19
Consensus pattern (57 bp):
CACACTCACCACCTCACAACCTCACACCCTCACCACCTTTACTACCAACAACCTTAA
Found at i:18192 original size:57 final size:57
Alignment explanation
Indices: 18083--18192 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
18073 CACAACCCGA
* * * *
18083 ACCCTCACCACCTTTACTGCCAAGAACCTTAACACACTTCCCACCTAAACCTTCACC
1 ACCCTCACCACCTTTACTACCAACAACCTTAACACACCTCCAACCTAAACCTTCACC
*
18140 ACCCTCACCACCTTTACTACCAACAACCTTACCAC-CCT-CAACCTCACAACCTT
1 ACCCTCACCACCTTTACTACCAACAACCTTAACACACCTCCAACCT-A-AACCTT
18193 TACTGCCAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 5 0.11
56 3 0.07
57 38 0.83
ACGTcount: A:0.30, C:0.47, G:0.02, T:0.21
Consensus pattern (57 bp):
ACCCTCACCACCTTTACTACCAACAACCTTAACACACCTCCAACCTAAACCTTCACC
Found at i:18195 original size:24 final size:24
Alignment explanation
Indices: 18162--18243 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
18152 TTTACTACCA
18162 ACAACC-TTACCACCCTCAACCTC
1 ACAACCTTTACCACCCTCAACCTC
** **
18185 ACAACCTTTACTGCCAGCAACCTC
1 ACAACCTTTACCACCCTCAACCTC
* * * *
18209 ACCACCTTCACCACCCTCACCCTT
1 ACAACCTTTACCACCCTCAACCTC
*
18233 ACCACCTTTAC
1 ACAACCTTTAC
18244 TTCCAACAAC
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 6 0.13
24 39 0.87
ACGTcount: A:0.27, C:0.50, G:0.02, T:0.21
Consensus pattern (24 bp):
ACAACCTTTACCACCCTCAACCTC
Found at i:18222 original size:48 final size:48
Alignment explanation
Indices: 18160--18266 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
18150 CCTTTACTAC
*
18160 CAACAACCTT-ACCACCCTCAACCTCACAACCTTTACTGCCAGCAACCT
1 CAAC-ACCTTCACCACCCTCAACCTCACAACCTTTACTGCCAACAACCT
* * * * *
18208 CACCACCTTCACCACCCTCACCCTTACCACCTTTACTTCCAACAACCT
1 CAACACCTTCACCACCCTCAACCTCACAACCTTTACTGCCAACAACCT
18256 CAACACCTTCA
1 CAACACCTTCA
18267 TAACCATCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 5 0.10
48 46 0.90
ACGTcount: A:0.29, C:0.49, G:0.02, T:0.21
Consensus pattern (48 bp):
CAACACCTTCACCACCCTCAACCTCACAACCTTTACTGCCAACAACCT
Found at i:19037 original size:30 final size:29
Alignment explanation
Indices: 19003--19171 Score: 119
Period size: 30 Copynumber: 5.8 Consensus size: 29
18993 ATAAAAAAAT
* *
19003 CCAAAACCCAAAAACTCTAAACAAAAATCC
1 CCAAAATCAAAAAAC-CTAAACAAAAATCC
*
19033 CCAAAATCAAAGAAACCTAAACAAAAATCT
1 CCAAAATCAAA-AAACCTAAACAAAAATCC
* * *
19063 CTAAAATAAAAAAACCCTAAATAAAAATCC
1 CCAAAATCAAAAAA-CCTAAACAAAAATCC
* *
19093 CCAAAAT--TAAAACCTCGAACACAAAATCC
1 CCAAAATCAAAAAACCT-AAACA-AAAATCC
* * * * *
19122 CCAAATTC-GACAACCTAAACCAAAATTC
1 CCAAAATCAAAAAACCTAAACAAAAATCC
* ** *
19150 TCAAACCCAAAAACCCTAAACA
1 CCAAAATCAAAAAACCTAAACA
19172 TTAACCAAAA
Statistics
Matches: 109, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
27 3 0.03
28 18 0.17
29 28 0.26
30 56 0.51
31 4 0.04
ACGTcount: A:0.56, C:0.29, G:0.02, T:0.14
Consensus pattern (29 bp):
CCAAAATCAAAAAACCTAAACAAAAATCC
Found at i:30542 original size:21 final size:22
Alignment explanation
Indices: 30518--30560 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30508 AAATAATTTT
*
30518 AATAATTTT-ATAGTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
30539 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
30561 TCATTTACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:35165 original size:18 final size:18
Alignment explanation
Indices: 35142--35179 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35132 GGCTACATAC
*
35142 GAGCATGGGATTGCATCT
1 GAGCATGGGACTGCATCT
*
35160 GAGCATGTGACTGCATCT
1 GAGCATGGGACTGCATCT
35178 GA
1 GA
35180 TCGTGATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (18 bp):
GAGCATGGGACTGCATCT
Found at i:45066 original size:26 final size:26
Alignment explanation
Indices: 45035--45085 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
45025 TAAAATTAAC
* *
45035 GAATGGGTTTTGTCTTTTAATGGAAG
1 GAATGGATTGTGTCTTTTAATGGAAG
*
45061 GAATGGATTGTGTTTTTTAATGGAA
1 GAATGGATTGTGTCTTTTAATGGAA
45086 ATAATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.43
Consensus pattern (26 bp):
GAATGGATTGTGTCTTTTAATGGAAG
Found at i:45469 original size:30 final size:30
Alignment explanation
Indices: 45383--45476 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
45373 TCATTTTTTG
*
45383 ACCCC-AAAATTTCCAAAAATTCAAATATA
1 ACCCCTAAAATTTCCAAAAATTCAAATTTA
* *
45412 GCCCCTAAAATTTCCAAAAGTTCAAATTTA
1 ACCCCTAAAATTTCCAAAAATTCAAATTTA
* * *
45442 ACCCCTAAAGCTTT-CAAAAATTAAAATTTG
1 ACCCCTAAA-ATTTCCAAAAATTCAAATTTA
45472 ACCCC
1 ACCCC
45477 ATTTTAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 4 0.07
30 48 0.87
31 3 0.05
ACGTcount: A:0.44, C:0.26, G:0.04, T:0.27
Consensus pattern (30 bp):
ACCCCTAAAATTTCCAAAAATTCAAATTTA
Found at i:56904 original size:50 final size:50
Alignment explanation
Indices: 56850--56947 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
56840 TTGAAACCGT
* *
56850 AATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAGTCGC
1 AATGGCAAATCTCATACACCTAAAGTTGTAAAGGGGAAGAATGAAGTCGC
* * *
56900 AATGGCAAATCTCATTCATCTAAAGTTGTAAAGGGGAAGATTGAAGTC
1 AATGGCAAATCTCATACACCTAAAGTTGTAAAGGGGAAGAATGAAGTC
56948 ACAAGGATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (50 bp):
AATGGCAAATCTCATACACCTAAAGTTGTAAAGGGGAAGAATGAAGTCGC
Found at i:57091 original size:39 final size:39
Alignment explanation
Indices: 57001--57210 Score: 192
Period size: 39 Copynumber: 5.3 Consensus size: 39
56991 TTACAACCTT
** * *
57001 CAATCTTTTACCTTAATCAGAGGGCAGATTGAAGACAATC
1 CAATCTTTTACCCCAACCAGAGGGCAGATT-AAAACAATC
*
57041 CAATCTCTTACCCCAACCATG-GGGCAGATTAAAACAATC
1 CAATCTTTTACCCCAACCA-GAGGGCAGATTAAAACAATC
* * * *
57080 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGCAATC
1 CAATCTTTTACCCCAACCAGAGGGCAGATTAAAACAATC
* * * *
57119 CAGTCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT-
1 CAATCTTTTACCCCAACCAGAGGGCAGATT-AAAACAATC
* * * *
57158 CAGATCTCTTACCCCGACCATGA-GGCGGATTGAAACAATC
1 CA-ATCTTTTACCCCAACCA-GAGGGCAGATTAAAACAATC
*
57198 TAATCTTTTACCC
1 CAATCTTTTACCC
57211 TTAAAGTTAT
Statistics
Matches: 138, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.01
39 85 0.62
40 49 0.36
41 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (39 bp):
CAATCTTTTACCCCAACCAGAGGGCAGATTAAAACAATC
Found at i:57171 original size:79 final size:78
Alignment explanation
Indices: 57001--57211 Score: 239
Period size: 79 Copynumber: 2.7 Consensus size: 78
56991 TTACAACCTT
* * *
57001 CAATCTTTTACCTTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAACCATGGGGC
1 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAG-CAATCCAATCTTTTACCCTAACCATGGGGC
57066 AGATTAAAACAATC
65 AGATTAAAACAATC
*
57080 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGCAATCCAGTCTTTTACCCTAACCA-GAGGGC
1 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCATG-GGGC
* *
57144 AGATTGAAGACCAT-
65 AGATT-AAAACAATC
* ** * * * *
57158 CAGATCTCTTACCCCGACCATGA-GGCGGATTGAAACAATCTAATCTTTTACCCT
1 CA-ATCTTTTACCCTAATCA-GAGGGCAGATTGAAGCAATCCAATCTTTTACCCT
57212 TAAAGTTATA
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
77 1 0.01
78 32 0.28
79 79 0.69
80 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (78 bp):
CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCATGGGGCA
GATTAAAACAATC
Found at i:57755 original size:11 final size:12
Alignment explanation
Indices: 57731--57760 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
57721 CAATCCAAAT
57731 TTTATTATTTTA
1 TTTATTATTTTA
57743 TTTATTA-TTTA
1 TTTATTATTTTA
57754 TTTATTA
1 TTTATTA
57761 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:58723 original size:26 final size:26
Alignment explanation
Indices: 58680--58730 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
58670 TAAAATTAAA
*
58680 GAATGAGTTTTGTCTTTTAATGGAAG
1 GAATGAGTTGTGTCTTTTAATGGAAG
* *
58706 GAATGGGTTGTGTTTTTTAATGGAA
1 GAATGAGTTGTGTCTTTTAATGGAA
58731 ATAATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.43
Consensus pattern (26 bp):
GAATGAGTTGTGTCTTTTAATGGAAG
Found at i:59065 original size:30 final size:30
Alignment explanation
Indices: 59024--59179 Score: 163
Period size: 30 Copynumber: 5.2 Consensus size: 30
59014 TAAAATCATT
* *
59024 TTTGA-CCCCAAAGTTTTCAAAAATTTAAA
1 TTTGACCCCCAAAATTTTCAAAAATTCAAA
59053 TTTGACCCCC-AAATTTTCCAAAAATTCAAA
1 TTTGACCCCCAAAATTTT-CAAAAATTCAAA
* * *
59083 TTTCACCCTCAAAATTTCCAAAAATTCAAA
1 TTTGACCCCCAAAATTTTCAAAAATTCAAA
* * * *
59113 TATGACCCCTAAAATTTCCAAAAGTTCAAA
1 TTTGACCCCCAAAATTTTCAAAAATTCAAA
* * ** *
59143 TTTAACCCCTAAAGCTTTCAAAAATTAAAA
1 TTTGACCCCCAAAATTTTCAAAAATTCAAA
59173 TTTGACC
1 TTTGACC
59180 ACGTTTTAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
29 11 0.10
30 89 0.84
31 6 0.06
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (30 bp):
TTTGACCCCCAAAATTTTCAAAAATTCAAA
Found at i:66774 original size:99 final size:98
Alignment explanation
Indices: 66602--66862 Score: 281
Period size: 99 Copynumber: 2.6 Consensus size: 98
66592 CACAGAATGA
* * * * *
66602 CAAATCTTACACCTCTAAAGTTGTAGAGGGGCAGATTAAAACAAGTAAAGAACCTCAATCTCCCT
1 CAAATCCTATACCCCTAAAGTTGTAGAGGGACAGATTAAAACAAGTAAAGAACCTTAATCTCCCT
* *
66667 AAACTTGTAATGGAATGGAGCGAAGTTACAACC
66 AAACTTGTAATGGAATGAAGCAAAGTTACAACC
* * * * *
66700 TCAAATCCTATACCCCTAGAGTTGTAGAGGGACAGATTAAAACGAGTAATGAACCTTAGTCTCCT
1 -CAAATCCTATACCCCTAAAGTTGTAGAGGGACAGATTAAAACAAGTAAAGAACCTTAATCTCCC
** * * *
66765 TGGATTTGTAGTGGAATGAAGTAAAGTTACAACC
65 TAAACTTGTAATGGAATGAAGCAAAGTTACAACC
* ** ** *
66799 CTAAATCCTATACCCTTAAAGTTGTATTGGGATGGATTAAAACTAGTAACA-AACCTTAATCTCC
1 C-AAATCCTATACCCCTAAAGTTGTAGAGGGACAGATTAAAACAAGTAA-AGAACCTTAATCTCC
66863 ATGAAGGCAG
Statistics
Matches: 134, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
98 1 0.01
99 133 0.99
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (98 bp):
CAAATCCTATACCCCTAAAGTTGTAGAGGGACAGATTAAAACAAGTAAAGAACCTTAATCTCCCT
AAACTTGTAATGGAATGAAGCAAAGTTACAACC
Found at i:68610 original size:28 final size:28
Alignment explanation
Indices: 68578--68633 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
68568 TTTACATAGA
68578 TAGAAATAAATCTTATAGATTCTTGCAC
1 TAGAAATAAATCTTATAGATTCTTGCAC
68606 TAGAAATAAATCTTATAGATTCTTGCAC
1 TAGAAATAAATCTTATAGATTCTTGCAC
68634 CCTAGTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (28 bp):
TAGAAATAAATCTTATAGATTCTTGCAC
Found at i:71239 original size:79 final size:80
Alignment explanation
Indices: 71012--71317 Score: 343
Period size: 80 Copynumber: 3.8 Consensus size: 80
71002 GTGTAAAACC
* * ** * * *
71012 GTTGGTTAATCCAACTAAAGCTGGACTCACTTTTGCGATTTATTAGCTAGGCACTAGG-TG-CTA
1 GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCGGTTTATTCGCTAGGCAC-AGGATGCCAA
*
71075 GTATTTGACAGACATTT
65 G-ATTTGACGGACATTT
* * **
71092 GTTGGTTAATCCAACTAGAGCTAGGTTCACTTTTGCGGTTTATTCGCTAGGCATTGGATGCCAAG
1 GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCGGTTTATTCGCTAGGCACAGGATGCCAAG
*
71157 ATTTGATGGACATTT
66 ATTTGACGGACATTT
* * * *
71172 GTTGGTTAATCTAACTAGA-TTGGGTTCACTTTTGCGGTTT-TTCTGTTAGGCACAGGATGTCAG
1 GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCGGTTTATTC-GCTAGGCACAGGATGCCAA
*
71235 GATTTGACGGATATTT
65 GATTTGACGGACATTT
* * * *
71251 GTTGGTTAATCCAACTAGATTTGGGCTCACTTTTGCGGTTTATCCGCTAGGCAC-TGAGTGCCAA
1 GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCGGTTTATTCGCTAGGCACAGGA-TGCCAA
71315 GAT
65 GAT
71318 CGTCGGTTTA
Statistics
Matches: 192, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.02
79 69 0.36
80 115 0.60
81 5 0.03
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAGTTGGGTTCACTTTTGCGGTTTATTCGCTAGGCACAGGATGCCAAG
ATTTGACGGACATTT
Found at i:73355 original size:12 final size:12
Alignment explanation
Indices: 73338--73362 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73328 TGTTATTATG
73338 ATGAATGCTATT
1 ATGAATGCTATT
73350 ATGAATGCTATT
1 ATGAATGCTATT
73362 A
1 A
73363 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:104563 original size:51 final size:50
Alignment explanation
Indices: 104481--104668 Score: 196
Period size: 51 Copynumber: 3.6 Consensus size: 50
104471 GCTATAAACG
*
104481 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTTTTACGGATT
1 AAAGG-TCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
104533 AAAGGTCCGATGACTAAGTGTCATCCTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * * **
104584 AAAGGTCTGATGACTCAATGCCATCATGAGTATATGAGTTCCTATACGGAAC
1 AAAGGTCCGATGACT-AATGTCATCGTGAGTAAATGA-ATCCTTTACGGATT
104636 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-ATGTCATCGTGAGTA
104669 TTAAATGAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
51 71 0.63
52 17 0.15
53 25 0.22
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (50 bp):
AAAGGTCCGATGACTAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:104649 original size:53 final size:54
Alignment explanation
Indices: 104487--104730 Score: 195
Period size: 51 Copynumber: 4.5 Consensus size: 54
104477 AACGAAAGGA
* * * **
104487 TCCGATGACTA-AGTGTCATCGTGAGTA-AATGA-ATCTTTTACGGATTAA-AGG
1 TCCGATGACTATA-TGTCATCGTGAGTATAATGAGTTCCTATACGGAACAAGAGG
* * * **
104538 TCCGATGACTA-AGTGTCATCCTGAGTA-AATGA-ATCC-ATGATGGATTAA-AGG
1 TCCGATGACTATA-TGTCATCGTGAGTATAATGAGTTCCTAT-ACGGAACAAGAGG
* * *
104589 TCTGATGACTCA-ATGCCATCATGAGTAT-ATGAGTTCCTATACGGAACAAGAGG
1 TCCGATGACT-ATATGTCATCGTGAGTATAATGAGTTCCTATACGGAACAAGAGG
104642 TCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTTCCTATACGGAACAAGAGG
1 TCCGATGACTATATGTCATCGTGAG---T--AT--AATGAGTTCCTATACGGAACAAGAGG
104703 TCCGATGACTATATGTCATCGTGAGTAT
1 TCCGATGACTATATGTCATCGTGAGTAT
104731 TAAATGAAAT
Statistics
Matches: 164, Mismatches: 14, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
50 1 0.01
51 70 0.43
52 12 0.07
53 25 0.15
56 3 0.02
58 3 0.02
61 50 0.30
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (54 bp):
TCCGATGACTATATGTCATCGTGAGTATAATGAGTTCCTATACGGAACAAGAGG
Found at i:104794 original size:59 final size:61
Alignment explanation
Indices: 104617--104795 Score: 290
Period size: 61 Copynumber: 3.0 Consensus size: 61
104607 TCATGAGTAT
104617 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
104678 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
* * * * * *
104739 ATGAGTTCCAATGC-GAACAAG-GGTCCGATCACTTTGTGTCATCGTGAGTAATAAATG
1 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATG
104796 CGAGTGAAAC
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 32 0.29
60 7 0.06
61 73 0.65
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (61 bp):
ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
Found at i:111764 original size:51 final size:50
Alignment explanation
Indices: 111682--111869 Score: 214
Period size: 51 Copynumber: 3.6 Consensus size: 50
111672 GTTATAAAAG
*
111682 AAAGGATCCGATGACTAAGTGTCATCTTGAGTAAATGAATCCTTTACGGATT
1 AAAGG-TCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
111734 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * **
111785 AAAGGTCCAATGACTCAATGTCATCATGAGTATATGAGTTCCTATACGGAAC
1 AAAGGTCCGATGACT-AATGTCATCGTGAGTAAATGA-ATCCTTTACGGATT
111837 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-ATGTCATCGTGAGTA
111870 TTAAATGAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
51 73 0.63
52 17 0.15
53 26 0.22
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (50 bp):
AAAGGTCCGATGACTAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:111861 original size:104 final size:103
Alignment explanation
Indices: 111682--111869 Score: 256
Period size: 104 Copynumber: 1.8 Consensus size: 103
111672 GTTATAAAAG
* * * **
111682 AAAGGATCCGATGACTAAGTGTCATCTTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGA
1 AAAGGATCCAATGACTAAGTGTCATCATGAGTAAATGAATCCTATACGGAACAAAGGTCCGATGA
111747 CTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
66 CTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
* *
111785 AAAGG-TCCAATGACTCAA-TGTCATCATGAGTATATGAGTTCCTATACGGAACAAGAGGTCCGA
1 AAAGGATCCAATGACT-AAGTGTCATCATGAGTAAATGA-ATCCTATACGGAACAA-AGGTCCGA
111848 TGACTATA-TGTCATCGTGAGTA
63 TGACTA-AGTGTCATCGTGAGTA
111870 TTAAATGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
102 26 0.35
103 19 0.26
104 28 0.38
105 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (103 bp):
AAAGGATCCAATGACTAAGTGTCATCATGAGTAAATGAATCCTATACGGAACAAAGGTCCGATGA
CTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
Found at i:111919 original size:61 final size:60
Alignment explanation
Indices: 111818--111996 Score: 243
Period size: 61 Copynumber: 3.0 Consensus size: 60
111808 TCATGAGTAT
* *
111818 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATAC-GAACAAGAGGTCTGATAACTATATGTCATCGTGAGTATTAAATGAA
*
111879 ATGAGTTCCTATACAGAACAAGAGGTCTGATAACTGTATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATAC-GAACAAGAGGTCTGATAACTATATGTCATCGTGAGTATTAAATGAA
* * * * * * *
111940 ATGATTTCCAATGCGAACAAG-GGTCTGATCACTTTGTGTCATCGTGAGTAATAAATG
1 ATGAGTTCCTATACGAACAAGAGGTCTGATAACTATATGTCATCGTGAGTATTAAATG
111997 CAAGTGAAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 32 0.30
60 7 0.07
61 68 0.64
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (60 bp):
ATGAGTTCCTATACGAACAAGAGGTCTGATAACTATATGTCATCGTGAGTATTAAATGAA
Found at i:117366 original size:40 final size:40
Alignment explanation
Indices: 117311--117406 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
117301 GTCTCACCCT
* *
117311 CAGATTGAAGACACACCAATATCTTACGCTGATCATGGGG
1 CAGATTGAAGACACACCAATATCTTACCCCGATCATGGGG
*
117351 CAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGG
1 CAGATTGAAGACACACCAATATCTTACCCCGATCATGGGG
*
117391 CAGATTGAAGAGACAC
1 CAGATTGAAGACACAC
117407 ATGTAATAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (40 bp):
CAGATTGAAGACACACCAATATCTTACCCCGATCATGGGG
Found at i:118666 original size:51 final size:51
Alignment explanation
Indices: 118581--118820 Score: 272
Period size: 51 Copynumber: 4.6 Consensus size: 51
118571 GCTATAAACG
* * * * *
118581 AAAGAGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* *
118633 AAAGGTCCGATGACTAAGTGTCATCATGGGTAAATGAATCCATGAC-ACATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGA-ATT
118684 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* * * *
118735 AAAGGTCCGATGACTCAGTGTTATCGTGAGTATATGAATTCCTAT-ACAGAA-C
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCC-ATGAC-GAATT
*
118787 AAAGGGGTTCGATGACTATA-TGTCATCGTGAGTA
1 AAA--GGTCCGATGACTA-AGTGTCATCGTGAGTA
118821 TTAAATGAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
51 121 0.74
52 13 0.08
53 5 0.03
54 24 0.15
55 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:119919 original size:40 final size:40
Alignment explanation
Indices: 119864--120181 Score: 449
Period size: 40 Copynumber: 8.0 Consensus size: 40
119854 GGGTGTTACA
*
119864 ACACCAATCTCTTACCCCAATCATGGGGCAGATTGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * *
119904 ACACCAATCTCTTACCCGGATCATGGGGCAGACTAAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * * *
119944 ACATCAATCTCTTACCCCGATCATGAGGCATAATGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
*
119984 ACACCAATCTCTTACCTCGATCATGGGGCAGATTGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * * *
120024 ACACTAATCTCTTATCCCGATCATAGGGTAGATTGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
*
120064 ACACCAATCTCCTACCCCGATCAT-GGGCTAGATTGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGC-AGATTGAAGAC
* *
120104 ACACTAATCTCTTACCCCGATCATGGGGTAGATTGAAGAC
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * *
120144 ACGCAAATCTCTTACCCCAATCATGGGGCAGATTGAAG
1 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
120182 CATCCGATCT
Statistics
Matches: 245, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
39 3 0.01
40 239 0.98
41 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (40 bp):
ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
Found at i:122153 original size:29 final size:30
Alignment explanation
Indices: 122099--122217 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 30
122089 AAACTTCATT
* *
122099 TTTTTAAAAATTTCTTTTTGACCC-CTAAA-
1 TTTTTAAAAATTTCATTTTAACCCTC-AAAC
*
122128 TTTTCTAAAAATTTCATTTTAACCCTCAAAG
1 TTTT-TAAAAATTTCATTTTAACCCTCAAAC
* *
122159 TTTTTGAAAATTACATTTTAACCCTCAAAC
1 TTTTTAAAAATTTCATTTTAACCCTCAAAC
* * *
122189 TTTTTGGAAAGTTGCATTTTAACCC-CAAA
1 TTTTT-AAAAATTTCATTTTAACCCTCAAA
122218 AACTTTCCAA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
29 4 0.05
30 53 0.67
31 22 0.28
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTTTAAAAATTTCATTTTAACCCTCAAAC
Found at i:131466 original size:26 final size:25
Alignment explanation
Indices: 131411--131467 Score: 62
Period size: 29 Copynumber: 2.2 Consensus size: 25
131401 TAAGATTGAC
*
131411 ATTTTTTTCTAATGTGGTACTTGTTTT
1 ATTTTTTTCTAATGTGGTAC-T-TTAT
131438 ATTTTTTGCTCTAATGTGGTAC-TTAT
1 ATTTTTT--TCTAATGTGGTACTTTAT
131464 ATTT
1 ATTT
131468 AGCAAGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
29 13 0.48
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.60
Consensus pattern (25 bp):
ATTTTTTTCTAATGTGGTACTTTAT
Found at i:132202 original size:79 final size:80
Alignment explanation
Indices: 132102--132261 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 80
132092 TTAAAAGTGT
*
132102 ACATGCAGAAGAAAATAATAATATGACCAATTTATATCCCCAATAGCAGTAGATGCAA-TTTTTT
1 ACATGCAGAAGAAAATAATAATATGAACAATTTATATCCCCAATAGCAGTAGATGCAATTTTTTT
132166 TGAAAAATTTGATAC
66 TGAAAAATTTGATAC
132181 ACATGCAGAAGAAAATAATAATATGAACAATTTATATCCCCAATAGCAGTAGATGCAATTTTTTT
1 ACATGCAGAAGAAAATAATAATATGAACAATTTATATCCCCAATAGCAGTAGATGCAATTTTTTT
132246 TGAAAAATTTGATAC
66 TGAAAAATTTGATAC
132261 A
1 A
132262 AGTGATGAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 57 0.72
80 22 0.28
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (80 bp):
ACATGCAGAAGAAAATAATAATATGAACAATTTATATCCCCAATAGCAGTAGATGCAATTTTTTT
TGAAAAATTTGATAC
Found at i:133169 original size:29 final size:29
Alignment explanation
Indices: 133122--133177 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
133112 AATTTGATTT
* *
133122 TTTAATAATACATGGATTAAATTGATCCA
1 TTTAATAATACAAGAATTAAATTGATCCA
* *
133151 TTTAATAATAGAAGAATTAATTTGATC
1 TTTAATAATACAAGAATTAAATTGATC
133178 AAATCTCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTAATAATACAAGAATTAAATTGATCCA
Found at i:134684 original size:20 final size:21
Alignment explanation
Indices: 134661--134706 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
134651 GTTGTTCCGA
134661 TAGAAGC-ATACTTGTATCAG
1 TAGAAGCTATACTTGTATCAG
* *
134681 TAGAA-CTGTAGTTGTATCAG
1 TAGAAGCTATACTTGTATCAG
134701 TAGAAG
1 TAGAAG
134707 AGGAGTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (21 bp):
TAGAAGCTATACTTGTATCAG
Found at i:134713 original size:20 final size:20
Alignment explanation
Indices: 134672--134713 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
134662 AGAAGCATAC
* *
134672 TTGTATCAGTAGAACTGTAG
1 TTGTATCAGTAGAACAGGAG
*
134692 TTGTATCAGTAGAAGAGGAG
1 TTGTATCAGTAGAACAGGAG
134712 TT
1 TT
134714 CTACCGGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (20 bp):
TTGTATCAGTAGAACAGGAG
Found at i:135100 original size:43 final size:43
Alignment explanation
Indices: 135018--135136 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 43
135008 TAACGGCGTT
*
135018 CATGTTCTTTAGCGGCGC-TTTCCCACAAACGCCGTTAAAGAC
1 CATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
* * *
135060 CATGTTCTTTAGCGGCGCTTTTCCCATAAATGCCGCTAAAGAT
1 CATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
*
135103 CATGTTCTTTAGCGGCACTTTTCCCACAAACGCC
1 CATGTTCTTTAGCGGCGCTTTTCCCACAAACGCC
135137 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 18 0.26
43 51 0.74
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (43 bp):
CATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
Found at i:135305 original size:19 final size:15
Alignment explanation
Indices: 135262--135294 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
135252 TTCACCTGTA
135262 AATTCAAATCCAACC
1 AATTCAAATCCAACC
135277 AATTCAAATCCAACC
1 AATTCAAATCCAACC
135292 AAT
1 AAT
135295 AACTTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (15 bp):
AATTCAAATCCAACC
Done.