Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014710.1 Kokia drynarioides strain JFW-HI SEQ_129749, 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: 67371
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:618 original size:29 final size:29
Alignment explanation
Indices: 524--900 Score: 342
Period size: 30 Copynumber: 12.8 Consensus size: 29
514 GAAGGTCTCA
* ***
524 AAACTATCCGAAAATTCCATTTTTGACCTTA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCC
* * * *
555 AAACTTCCAAAAATTTCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCCC
*
585 AAACTTCCAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* ***
614 AAACTTCCAAAAATTCCATTTATAACCTTG
1 AAACTTCCAAAAATTCCATTT-TTACCCCC
* * *
644 AAACTTCTAAAAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
673 AAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* ** *
702 AGAACTTACAAAAATTCCATTTTTACTTCT
1 A-AACTTCCAAAAATTCCATTTTTACCCCC
* * *
732 AAACTTCCAAAAATTCAATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
762 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * **
791 GAACTTCC-AAAATTCCATTTTTAACACTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
820 AAACTTCTAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * **
849 GAGCTTCAAAAAATTCCATATTTGACCCTG
1 AAACTTCCAAAAATTCCAT-TTTTACCCCC
*
879 AAATTTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
901 CGACGTCGAA
Statistics
Matches: 286, Mismatches: 53, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
28 14 0.05
29 118 0.41
30 149 0.52
31 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:626 original size:59 final size:59
Alignment explanation
Indices: 524--900 Score: 395
Period size: 59 Copynumber: 6.4 Consensus size: 59
514 GAAGGTCTCA
* *** * **
524 AAACTATCCGAAAATTCCATTTTTGACCTTAAAACTTCCAAAAATTTCATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
585 AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATTCCATTTATAACCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
644 AAACTTCTAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACC-CC
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCG
* ** * * *
702 AGAACTTACAAAAATTCCATTTTTACTTCTAAACTTCCAAAAATTCAATTTTTGA-CTCCG
1 A-AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCT-CG
* *
762 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCC-AAAATTCCATTTTTAACACT-A
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAAC-CTCG
* * * * * * *
820 AAACTTCTAAAAATTCCATTTTTACCCTCGAGCTTCAAAAAATTCCATATTTGACC-CTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTC-G
*
879 AAATTTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
901 CGACGTCGAA
Statistics
Matches: 266, Mismatches: 42, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
58 50 0.19
59 191 0.72
60 20 0.08
61 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:11681 original size:30 final size:30
Alignment explanation
Indices: 11647--11708 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
11637 GATACGAGCT
11647 TACGACAAAAAGGTTCGTCCCAAGAAATTC
1 TACGACAAAAAGGTTCGTCCCAAGAAATTC
11677 TACGACAAAAAGGTTCGTCCCAAGAAATTC
1 TACGACAAAAAGGTTCGTCCCAAGAAATTC
11707 TA
1 TA
11709 TGGGAAGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (30 bp):
TACGACAAAAAGGTTCGTCCCAAGAAATTC
Found at i:13404 original size:205 final size:205
Alignment explanation
Indices: 13145--13648 Score: 776
Period size: 205 Copynumber: 2.5 Consensus size: 205
13135 CCAACTCAGG
* *
13145 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGGCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
13210 ATAAAAGGTTAGCTTCCTGATGAGATACTAAAAAGTGGACCAAATTTGTCTTCCTGATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATA-
* * * *
13275 TA-AGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGATATACTGAGAAGAAGACCAA
130 GAGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
13339 ATCAAACCCAC
195 ATCAAACCCAC
* * * * * *
13350 GCTCGATGTAAGCAAATCTTCGAACCCTAGCTTCCTGATCAGACACTGAGAAGCAGGTCAAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
13415 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAG
66 ATAAAAGGTTAGCTTCCTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAG
*
13480 AGAGAAGCGAACTGAAACAAGCGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
13545 TCAAACCCAC
196 TCAAACCCAC
* * * * *
13555 ACTCAATATGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAACAGGTCGAAGTA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
13620 ATAAAACGGTTAGCTTCCTGATGAAATAC
66 ATAAAA-GGTTAGCTTCCTGATGAGATAC
13649 GGGGAAGTGA
Statistics
Matches: 268, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
204 1 0.00
205 246 0.92
206 21 0.08
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (205 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAG
AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:13674 original size:37 final size:37
Alignment explanation
Indices: 13633--13703 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
13623 AAACGGTTAG
* * *
13633 CTTCCTGATGAAATACGGGGAAGTGAATCAAAACCAT
1 CTTCCTGATGAAACACAGAGAAGTGAATCAAAACCAT
*
13670 CTTCCTGATGAAACACAGAGAAGTGGATCAAAAC
1 CTTCCTGATGAAACACAGAGAAGTGAATCAAAAC
13704 AAGTGATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (37 bp):
CTTCCTGATGAAACACAGAGAAGTGAATCAAAACCAT
Found at i:14094 original size:17 final size:16
Alignment explanation
Indices: 14068--14108 Score: 73
Period size: 17 Copynumber: 2.5 Consensus size: 16
14058 GGGCCCCTTT
14068 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
14084 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
14101 TTTAATTT
1 TTTAATTT
14109 CAAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:14146 original size:14 final size:15
Alignment explanation
Indices: 14109--14147 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
14099 AATTTAATTT
14109 CAAAATTA-AAAGTC
1 CAAAATTACAAAGTC
*
14123 CAAAAATACAAAGTC
1 CAAAATTACAAAGTC
14138 C-AAATTACAA
1 CAAAATTACAA
14148 TCTTGGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (15 bp):
CAAAATTACAAAGTC
Found at i:15896 original size:117 final size:116
Alignment explanation
Indices: 15706--16134 Score: 581
Period size: 117 Copynumber: 3.7 Consensus size: 116
15696 AAACTATTCG
* * *
15706 AAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTCAACCTCGAAACTTCTAAAAAT
1 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTC-AAACTTCT-AAAAT
* * *
15771 TCCA-TTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCGAGCTTCCA
64 TCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCGAACTTCCA
* * * * * *
15823 AAAATTCCATTTTTAACCTCGAAATTTCTAAAAATTCCATTTTTACCCTTAAATTTCCAAAATTT
1 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAA-TT
* *
15888 TCATTTTTGACCCCAAAACTTCTAAAAATTCCAATTTTACCTCCGAACTTCCA
65 CCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACC-CCGAACTTCCA
* *
15941 AAAAATCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCCAACTTCTAAAATTC
1 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAATTC
16006 CATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCA
66 CATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTA-CCCCGAACTTCCA
* * * * * *
16058 AAAATTCTATTTTTGACCTTGAAAATTCCAAAAATTCCATTTTTACCCTCGAACCTCCGAAAATT
1 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTC-AAACTTCTAAAATT
* *
16123 CTATTTTCGACC
65 CCATTTTTGACC
16135 TCGAAACTCT
Statistics
Matches: 273, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
115 4 0.01
116 10 0.04
117 173 0.63
118 86 0.32
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (116 bp):
AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAATTC
CATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCGAACTTCCA
Found at i:16007 original size:176 final size:175
Alignment explanation
Indices: 15706--16192 Score: 512
Period size: 176 Copynumber: 2.8 Consensus size: 175
15696 AAACTATTCG
** *
15706 AAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTCC-ATTTTCAACCT-CGAAACTTCTAAAA
1 AAAATT-CATTTTTGACCTCAAAACTTCCAAAAATTCCAATTTT--ACCTCCG-AACTTCCAAAA
* * *
15769 ATTCCA-TTTTGACC-CTAAAACTTCCAAAAATTCCATTTTTACCCCGAGCTTCCAAAAATTCCA
62 ATTCCATTTTTGACCTC-GAAACTTCCAAAAATTCCATTTTTACCCCCAACTTCCAAAAATTCCA
* * * ** *
15832 TTTTTAACCTCGAAATTTCTAAAAATTCCATTTTTACCCTTAAATTTCCA
126 TTTTTAACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCA
* * * *
15882 AAATTTTCATTTTTGACCCCAAAACTTCTAAAAATTCCAATTTTACCTCCGAACTTCCAAAAAAT
1 AAA-ATTCATTTTTGACCTCAAAACTTCCAAAAATTCCAATTTTACCTCCGAACTTCCAAAAATT
*
15947 CCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCCAACTT-CTAAAATTCCATTT
65 CCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCC-CCAACTTCCAAAAATTCCATTT
* *
16011 TTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCA
129 TTAACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCA
* * * *
16058 AAAATTCTATTTTTGACCTTGAAAA-TTCCAAAAATTCCATTTTTACC-CTCGAACCTCCGAAAA
1 AAAATTC-ATTTTTGACC-TCAAAACTTCCAAAAATTCCAATTTTACCTC-CGAACTTCCAAAAA
* * * *
16121 TTCTATTTTCGACCTCGAAAC-TCTC--AAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTC
63 TTCCATTTTTGACCTCGAAACTTC-CAAAAATT-CCATTTTTACCCCC-AACT-TCCAAAAATTC
*
16181 CATCTTTAACCC
124 CATTTTTAACCC
16193 TGAATTTCCC
Statistics
Matches: 263, Mismatches: 34, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
173 3 0.01
174 16 0.06
175 44 0.17
176 183 0.70
177 17 0.06
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (175 bp):
AAAATTCATTTTTGACCTCAAAACTTCCAAAAATTCCAATTTTACCTCCGAACTTCCAAAAATTC
CATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCAACTTCCAAAAATTCCATTTTT
AACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCA
Found at i:16135 original size:59 final size:59
Alignment explanation
Indices: 15706--16140 Score: 497
Period size: 59 Copynumber: 7.4 Consensus size: 59
15696 AAACTATTCG
* * * * *
15706 AAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTCAACCTCGAAACTTCTA
1 AAAATTCCATTTTTGACCTCGAAAATTCCAAAAATTCCATTTTTACCCTCG-AACTTCCA
* *
15766 AAAATTCCA-TTTTGACC-CTAAAACTTCCAAAAATTCCATTTTTACCC-CGAGCTTCCA
1 AAAATTCCATTTTTGACCTCGAAAA-TTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
* * * ** *
15823 AAAATTCCATTTTTAACCTCGAAATTTCTAAAAATTCCATTTTTACCCTTAAATTTCCA
1 AAAATTCCATTTTTGACCTCGAAAATTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
* * * * *
15882 AAATTTTCATTTTTGACC-CCAAAACTTCTAAAAATTCCAATTTTA-CCTCCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGAAAA-TTCCAAAAATTCCATTTTTACCCT-CGAACTTCCA
* * * *
15941 AAAAATCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCCAACTT-CT
1 AAAATTCCATTTTTGACCTCGAAAATTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
* * *
15999 AAAATTCCATTTTTGACC-CCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGAAAA-TTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
* * * *
16058 AAAATTCTATTTTTGACCTTGAAAATTCCAAAAATTCCATTTTTACCCTCGAACCTCCG
1 AAAATTCCATTTTTGACCTCGAAAATTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
* *
16117 AAAATTCTATTTTCGACCTCGAAA
1 AAAATTCCATTTTTGACCTCGAAA
16141 CTCTCAAATT
Statistics
Matches: 315, Mismatches: 49, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
57 19 0.06
58 87 0.28
59 189 0.60
60 20 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCTCGAAAATTCCAAAAATTCCATTTTTACCCTCGAACTTCCA
Found at i:16136 original size:29 final size:28
Alignment explanation
Indices: 15706--16139 Score: 235
Period size: 29 Copynumber: 14.8 Consensus size: 28
15696 AAACTATTCG
* *
15706 AAAATTCCATTTTTGACCTTGAAACTTCCA
1 AAAATTCTA-TTTTGACCTCG-AACTTCCA
* * *
15736 AAAATTCCATTTTCAACCTCGAAACTTCTA
1 AAAATTCTATTTT-GACCTCG-AACTTCCA
* **
15766 AAAATTCCATTTTGACCCTAAAACTTCCA
1 AAAATTCTATTTTGA-CCTCGAACTTCCA
* * * *
15795 AAAATTCCATTTTTACCCCGAGCTTCCA
1 AAAATTCTATTTTGACCTCGAACTTCCA
* * * *
15823 AAAATTCCATTTTTAACCTCGAAATTTCTA
1 AAAATTCTA-TTTTGACCTCG-AACTTCCA
* * ** *
15853 AAAATTCCATTTTTACCCTTAAATTTCC-
1 AAAATTCTATTTTGA-CCTCGAACTTCCA
* * * *
15881 AAAATTTTCATTTTTGACCCCAAAACTTCTA
1 AAAATTCT-A-TTTTGACCTC-GAACTTCCA
*
15912 AAAATTCCAATTTT-ACCTCCGAACTTCCA
1 AAAATT-CTATTTTGACCT-CGAACTTCCA
* *
15941 AAAAATCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCTA-TTTTGACCTCG-AACTTCCA
* * * *
15971 AAAATTCCATTTTTACCCTCCAACTT-CT
1 AAAATTCTATTTTGA-CCTCGAACTTCCA
* * * *
15999 AAAATTCCATTTTTGACCCCAAAACTTCTA
1 AAAATTCTA-TTTTGACCTC-GAACTTCCA
* * *
16029 AAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCTATTTTGA-CCTCGAACTTCCA
* *
16058 AAAATTCTATTTTTGACCTTGAAAATTCCA
1 AAAATTCTA-TTTTGACCTCG-AACTTCCA
* * * *
16088 AAAATTCCATTTTTACCCTCGAACCTCCG
1 AAAATTCTATTTTGA-CCTCGAACTTCCA
16117 AAAATTCTATTTTCGACCTCGAA
1 AAAATTCTATTTT-GACCTCGAA
16140 ACTCTCAAAT
Statistics
Matches: 321, Mismatches: 60, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
28 39 0.12
29 142 0.44
30 133 0.41
31 7 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTCTATTTTGACCTCGAACTTCCA
Found at i:28198 original size:6 final size:6
Alignment explanation
Indices: 28178--28251 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
28168 TATTCTAATA
** * * **
28178 TTAAAT TTATTT TTAAAT TTAAAT TTAAA- TTAAGT TTAAGT TTACTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
28225 TTAAAT TTAAAA TT-ACT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
28252 TAAAAGGTCA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
5 7 0.13
6 46 0.87
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:28209 original size:29 final size:29
Alignment explanation
Indices: 28159--28235 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
28149 ACTAGACCCC
*
28159 TTTTAAATTT--ATTCTAATATTAAATTTAT
1 TTTTAAATTTAAATT-TAA-ATTAAATTTAA
*
28188 TTTTAAATTTAAATTTAAATTAAGTTTAA
1 TTTTAAATTTAAATTTAAATTAAATTTAA
* **
28217 GTTTACTTTTAAATTTAAA
1 TTTTAAATTTAAATTTAAA
28236 ATTACTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 35 0.85
30 3 0.07
31 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTAAATTTAAATTTAAATTAAATTTAA
Found at i:28244 original size:29 final size:29
Alignment explanation
Indices: 28195--28250 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28185 TATTTTTAAA
* *
28195 TTTAAATTTAAATTAAGTTTAAGTTTACT
1 TTTAAATTTAAATTAACTTTAAATTTACT
28224 TTTAAATTTAAAATT-ACTTTAAATTTA
1 TTTAAATTT-AAATTAACTTTAAATTTA
28251 ATAAAAGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTAAATTTAAATTAACTTTAAATTTACT
Found at i:28251 original size:35 final size:35
Alignment explanation
Indices: 28178--28251 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
28168 TATTCTAATA
* * *
28178 TTAAATTTATTTTTAAATTTAAATTTAAATTAAGT
1 TTAAATTTACTTTTAAATTTAAAATTAAATTAAAT
* **
28213 TTAAGTTTACTTTTAAATTTAAAATTACTTTAAAT
1 TTAAATTTACTTTTAAATTTAAAATTAAATTAAAT
28248 TTAA
1 TTAA
28252 TAAAAGGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (35 bp):
TTAAATTTACTTTTAAATTTAAAATTAAATTAAAT
Found at i:28962 original size:3 final size:3
Alignment explanation
Indices: 28956--29009 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
28946 AATAACGTTT
28956 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29004 TAA TAA
1 TAA TAA
29010 AGTGGGATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30334 original size:59 final size:59
Alignment explanation
Indices: 30181--30711 Score: 505
Period size: 59 Copynumber: 9.1 Consensus size: 59
30171 CCCTAAACTT
* * * *** *
30181 TCCAAAAATTACATTATT-ACCCCT-AAC-TTCACAAAATTACCATTTTACCCTTAAATT
1 TCCAAAAATTCCATTTTTGA-CCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * *
30238 TCC-AAAATCCCATTTTTGA-CCTCGAACTTTCCTAAAATTATCATTTTACCCCCGAATG
1 TCCAAAAATTCCATTTTTGACCCT-GAACTTTCCCAAAATTACCATTTTACCCCCGAATG
** ** **
30296 TCCAAAAATTCCATTTTTGACCCAAAACCCTCCCAAAATTACCATTTTACCCCTAAATG
1 TCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * *
30355 TCC-AAAATTTCA-TTTTGACCCTGAACTTTCCCAAAATTATCATTTTACCCTCGAATG
1 TCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * **
30412 TCCAAAAATAT-CATTTTTGACCCCGAACATTCCCAAAATTACCATTTTA-CCCCGAACA
1 TCCAAAAAT-TCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * * * * **
30470 TCCAAAAATTCCATTTTTTAACTCTAAACTATCCTAAAATTACCATTTTACCCCCGAACA
1 TCCAAAAATTCCA-TTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * * * * **
30530 TCCAAAAATTCCATTTTT-AACCTAAAC-TTCCAAAAATTACCATTTTACCCTCAAACA
1 TCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * * *
30587 TTCAAAAATTCCATTTTT-AACCTCGAACTTTCCCAAAATTACCATTTTA-CCCCTAAAG
1 TCCAAAAATTCCATTTTTGACCCT-GAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * *
30645 ATCCAAAAATTCCATTTTTGACCTTGAAC-TTCCTAAAAATTACCATTTTACCCTCGAATG
1 -TCCAAAAATTCCATTTTTGACCCTGAACTTTCC-CAAAATTACCATTTTACCCCCGAATG
30705 TCCAAAA
1 TCCAAAA
30712 TTTATAGTTT
Statistics
Matches: 395, Mismatches: 61, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
55 3 0.01
56 11 0.03
57 96 0.24
58 77 0.19
59 175 0.44
60 33 0.08
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
Found at i:30402 original size:116 final size:116
Alignment explanation
Indices: 30181--30697 Score: 552
Period size: 116 Copynumber: 4.4 Consensus size: 116
30171 CCCTAAACTT
* * * *
30181 TCCAAAAATTACATTATT-ACCCCT-AACTTCACAAAATTACCATTTTACCCTTAAATTTCCAAA
1 TCCAAAAATTCCATTTTTGA-CCCTAAACTTCCCAAAATTACCATTTTACCCCTAAA-TTCCAAA
* * *
30244 ATCCCATTTTTGA-CCTCGAACTTTCCTAAAATTATCATTTTACCCCCGAATG
64 ATTCCATTTTTGACCCTCGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* *
30296 TCCAAAAATTCCATTTTTGACCCAAAACCCTCCCAAAATTACCATTTTACCCCTAAATGTCCAAA
1 TCCAAAAATTCCATTTTTGACCCTAAA-CTTCCCAAAATTACCATTTTACCCCTAAAT-TCCAAA
* * *
30361 ATTTCA-TTTTGACCCT-GAACTTTCCCAAAATTATCATTTTACCCTCGAATG
64 ATTCCATTTTTGACCCTCGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
** *
30412 TCCAAAAATAT-CATTTTTGACCCCGAACATTCCCAAAATTACCATTTTACCCCGAACA-TCCAA
1 TCCAAAAAT-TCCATTTTTGACCCTAAAC-TTCCCAAAATTACCATTTTACCCCTAA-ATTCC-A
* * * * * **
30475 AAATTCCATTTTTTA-ACTCTAAACTATCCTAAAATTACCATTTTACCCCCGAACA
62 AAATTCCATTTTTGACCCTC-GAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * * *
30530 TCCAAAAATTCCATTTTT-AACCTAAACTTCCAAAAATTACCATTTTACCCTCAAACATTCAAAA
1 TCCAAAAATTCCATTTTTGACCCTAAACTTCCCAAAATTACCATTTTACCC-CTAA-ATTCCAAA
* * *
30594 ATTCCATTTTT-AACCTCGAACTTTCCCAAAATTACCATTTTA-CCCCTAAAG
64 ATTCCATTTTTGACCCTCGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
* * *
30645 ATCCAAAAATTCCATTTTTGACCTTGAACTTCCTAAAAATTACCATTTTACCC
1 -TCCAAAAATTCCATTTTTGACCCTAAACTTCC-CAAAATTACCATTTTACCC
30698 TCGAATGTCC
Statistics
Matches: 343, Mismatches: 40, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
115 29 0.08
116 164 0.48
117 85 0.25
118 65 0.19
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (116 bp):
TCCAAAAATTCCATTTTTGACCCTAAACTTCCCAAAATTACCATTTTACCCCTAAATTCCAAAAT
TCCATTTTTGACCCTCGAACTTTCCCAAAATTACCATTTTACCCCCGAATG
Found at i:30452 original size:175 final size:173
Alignment explanation
Indices: 30154--30769 Score: 611
Period size: 175 Copynumber: 3.5 Consensus size: 173
30144 TAAATTTTCT
* * * * * *
30154 AAAAATTACAATTTAACCCCTAAACTTTCCAAAAATTACATTATTACCCCT-AACTTCACAAAAT
1 AAAAATTACCATTTTACCCCTAAA-TGTCCAAAAATTTCATTTTTA-CCCTGAACTTCCCAAAAT
* * * * *
30218 TACCATTTTACCCTTAAATTTCC-AAAATCCCATTTTTGACCTCGAACTTTCCTAAAATTATCAT
64 TACCATTTTACCCTCAAATGTCCAAAAAT-TCATTTTTGACCTCGAACTTTCCCAAAATTACCAT
* * *
30282 TTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCCAAAACCCTCC
128 TTTA-CCCCGAAAGTCCAAAAATTCCATTTTTGACCCTAAACCATCC
* *
30329 CAAAATTACCATTTTACCCCTAAATGTCC-AAAATTTCATTTTGACCCTGAACTTTCCCAAAATT
1 AAAAATTACCATTTTACCCCTAAATGTCCAAAAATTTCATTTTTACCCTGAAC-TTCCCAAAATT
* * * *
30393 ATCATTTTACCCTCGAATGTCCAAAAATATCATTTTTGACCCCGAACATTCCCAAAATTACCATT
65 ACCATTTTACCCTCAAATGTCCAAAAAT-TCATTTTTGACCTCGAACTTTCCCAAAATTACCATT
* * *
30458 TTACCCCGAACA-TCCAAAAATTCCATTTTTTAACTCTAAACTATCC
129 TTACCCCGAA-AGTCCAAAAATTCCA-TTTTTGACCCTAAACCATCC
* ** ** * * * *
30504 TAAAATTACCATTTTACCCCCGAACATCCAAAAATTCCATTTTTAACCTAAACTTCCAAAAATTA
1 AAAAATTACCATTTTACCCCTAAATGTCCAAAAATTTCATTTTTACCCTGAACTTCCCAAAATTA
** * *
30569 CCATTTTACCCTCAAACATTCAAAAATTCCATTTTTAACCTCGAACTTTCCCAAAATTACCATTT
66 CCATTTTACCCTCAAATGTCCAAAAATT-CATTTTTGACCTCGAACTTTCCCAAAATTACCATTT
* * * *
30634 TACCCCTAAAGATCCAAAAATTCCATTTTTGACCTTGAA-CTTCC
130 TACCCCGAAAG-TCCAAAAATTCCATTTTTGACCCTAAACCATCC
* * *
30678 TAAAAATTACCATTTTA-CCCTCGAATGTCC-AAAATTT-ATAGTTTTACCCTTGAACCT-CTAA
1 -AAAAATTACCATTTTACCCCT-AAATGTCCAAAAATTTCAT--TTTTACCC-TGAACTTCCCAA
* * *
30739 AATTACTATTTTGCCCTCGAAGTGTCCAAAA
61 AATTACCATTTTACCCTC-AAATGTCCAAAA
30770 TTACCGTTTT
Statistics
Matches: 362, Mismatches: 64, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
172 4 0.01
173 17 0.05
174 66 0.18
175 230 0.64
176 45 0.12
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (173 bp):
AAAAATTACCATTTTACCCCTAAATGTCCAAAAATTTCATTTTTACCCTGAACTTCCCAAAATTA
CCATTTTACCCTCAAATGTCCAAAAATTCATTTTTGACCTCGAACTTTCCCAAAATTACCATTTT
ACCCCGAAAGTCCAAAAATTCCATTTTTGACCCTAAACCATCC
Found at i:30682 original size:29 final size:29
Alignment explanation
Indices: 30154--30711 Score: 295
Period size: 29 Copynumber: 19.1 Consensus size: 29
30144 TAAATTTTCT
* * *
30154 AAAAATTA-CAATTTAACCCCTAAACTTTCC
1 AAAAATTACCATTTTTACCCC-GAAC-TTCC
* *
30184 AAAAATTA-CATTATTACCCCTAACTT-C
1 AAAAATTACCATTTTTACCCCGAACTTCC
** *
30211 ACAAAATTACCA-TTTTACCCTTAAATTTCC
1 A-AAAATTACCATTTTTACCC-CGAACTTCC
* *
30241 -AAAA-TCCCATTTTTGACCTCGAACTTTCC
1 AAAAATTACCATTTTT-ACCCCGAAC-TTCC
* *
30270 TAAAATTATCA-TTTTACCCCCGAA-TGTCC
1 AAAAATTACCATTTTTA-CCCCGAACT-TCC
** *
30299 AAAAATT-CCATTTTTGACCCAAAACCCTCC
1 AAAAATTACCATTTTT-ACCCCGAA-CTTCC
* * *
30329 CAAAATTACCA-TTTTACCCCTAAATGTCC
1 AAAAATTACCATTTTTACCCCGAACT-TCC
* * *
30358 -AAAATT-TCATTTTGACCCTGAACTTTCC
1 AAAAATTACCATTTTTACCCCGAAC-TTCC
* *
30386 CAAAATTATCA-TTTTACCCTCGAA-TGTCC
1 AAAAATTACCATTTTTACCC-CGAACT-TCC
*
30415 AAAAA-TATCATTTTTGACCCCGAACATTCC
1 AAAAATTACCATTTTT-ACCCCGAAC-TTCC
* *
30445 CAAAATTACCA-TTTTACCCCGAACATCC
1 AAAAATTACCATTTTTACCCCGAACTTCC
* **
30473 AAAAATT-CCATTTTTTAACTCTAAACTATCC
1 AAAAATTACCA-TTTTT-ACCCCGAACT-TCC
* *
30504 TAAAATTACCA-TTTTACCCCCGAACATCC
1 AAAAATTACCATTTTTA-CCCCGAACTTCC
* **
30533 AAAAATT-CCATTTTTAACCTAAACTTCC
1 AAAAATTACCATTTTTACCCCGAACTTCC
*
30561 AAAAATTACCA-TTTTACCCTCAAACATT-C
1 AAAAATTACCATTTTTACCC-CGAAC-TTCC
*
30590 AAAAATT-CCATTTTTAACCTCGAACTTTCC
1 AAAAATTACCATTTTT-ACCCCGAAC-TTCC
* * **
30620 CAAAATTACCA-TTTTACCCCTAAAGATCC
1 AAAAATTACCATTTTTACCCC-GAACTTCC
**
30649 AAAAATT-CCATTTTTGACCTTGAACTTCC
1 AAAAATTACCATTTTT-ACCCCGAACTTCC
30678 TAAAAATTACCA-TTTTACCCTCGAA-TGTCC
1 -AAAAATTACCATTTTTACCC-CGAACT-TCC
30708 AAAA
1 AAAA
30712 TTTATAGTTT
Statistics
Matches: 409, Mismatches: 70, Indels: 99
0.71 0.12 0.17
Matches are distributed among these distances:
27 11 0.03
28 93 0.23
29 156 0.38
30 120 0.29
31 26 0.06
32 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATTACCATTTTTACCCCGAACTTCC
Found at i:30729 original size:59 final size:58
Alignment explanation
Indices: 30181--30771 Score: 350
Period size: 59 Copynumber: 10.2 Consensus size: 58
30171 CCCTAAACTT
* * * * * ** *
30181 TCCAAAAATTACATTATTACCCCT-AACTTCACAAAATTACCATTTTACCCTTAAATT
1 TCCAAAATTTATATTTTTACCCTTGAACTTCCCAAAATTACCATTTTACCCTCGAATG
** * * * * *
30238 TCCAAAATCCCAT-TTTTGA-CCTCGAACTTTCCTAAAATTATCATTTTACCCCCGAATG
1 TCCAAAAT-TTATATTTTTACCCTTGAAC-TTCCCAAAATTACCATTTTACCCTCGAATG
* ** ** * *
30296 TCCAAAAATTCCATTTTTGACCC-AAAACCCTCCCAAAATTACCATTTTACCC-CTAAATG
1 TCCAAAATTTATATTTTT-ACCCTTGAA-CTTCCCAAAATTACCATTTTACCCTC-GAATG
* * *
30355 TCCAAAATTT-CATTTTGACCC-TGAACTTTCCCAAAATTATCATTTTACCCTCGAATG
1 TCCAAAATTTATATTTTTACCCTTGAAC-TTCCCAAAATTACCATTTTACCCTCGAATG
* * **
30412 TCCAAAA-ATATCATTTTTGACCC-CGAACATTCCCAAAATTACCATTTTACCC-CGAACA
1 TCCAAAATTTAT-ATTTTT-ACCCTTGAAC-TTCCCAAAATTACCATTTTACCCTCGAATG
* * * * * **
30470 TCCAAAAATTCCAT-TTTTTA-ACTCTAAACTATCCTAAAATTACCATTTTACCCCCGAACA
1 TCC-AAAATT-TATATTTTTACCCT-TGAACT-TCCCAAAATTACCATTTTACCCTCGAATG
* ** * * * * **
30530 TCCAAAAATTCCATTTTTAACC-TAAACTTCCAAAAATTACCATTTTACCCTCAAACA
1 TCCAAAATTTATATTTTTACCCTTGAACTTCCCAAAATTACCATTTTACCCTCGAATG
* * ** * * * *
30587 TTCAAAAATTCCATTTTTAACCTCGAACTTTCCCAAAATTACCATTTTACCC-CTAAAG
1 TCCAAAATTTATATTTTTACCCTTGAAC-TTCCCAAAATTACCATTTTACCCTCGAATG
* ** *
30645 ATCCAAAAATTCCATTTTTGA-CCTTGAACTTCCTAAAAATTACCATTTTACCCTCGAATG
1 -TCCAAAATTTATATTTTT-ACCCTTGAACTTCC-CAAAATTACCATTTTACCCTCGAATG
* * * * *
30705 TCCAAAATTTATAGTTTTACCCTTGAACCT-CTAAAATTACTATTTTGCCCTCGAAGTG
1 TCCAAAATTTATATTTTTACCCTTGAACTTCCCAAAATTACCATTTTACCCTCGAA-TG
30763 TCCAAAATT
1 TCCAAAATT
30772 ACCGTTTTGC
Statistics
Matches: 428, Mismatches: 76, Indels: 59
0.76 0.13 0.10
Matches are distributed among these distances:
56 4 0.01
57 121 0.28
58 86 0.20
59 197 0.46
60 18 0.04
61 2 0.00
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
TCCAAAATTTATATTTTTACCCTTGAACTTCCCAAAATTACCATTTTACCCTCGAATG
Found at i:30771 original size:116 final size:115
Alignment explanation
Indices: 30181--30769 Score: 461
Period size: 116 Copynumber: 5.1 Consensus size: 115
30171 CCCTAAACTT
* * * **
30181 TCCAAAAATTACATTATT-ACCCCT-AACTT-CACAAAATTACCATTTTACCCTTAAATTTCCAA
1 TCCAAAAATTCCATTTTTGA-CCCTAAACTTCCA-AAAATTACCATTTTACCC-CAAACATCCAA
** * *
30243 AATCCCATTTTTGA-CCTCGAACTTTCCTAAAATTA-TCATTTTACCCCCGAATG
63 AAT-TTATTTTTTACCCTTGAACTTTCCTAAAATTACT-ATTTTACCCCCGAATG
* * * **
30296 TCCAAAAATTCCATTTTTGACCCAAAACCCTCCCAAAATTACCATTTTACCCCTAAATGTCCAAA
1 TCCAAAAATTCCATTTTTGACCCTAAA-CTTCCAAAAATTACCATTTTACCCC-AAACATCCAAA
* * *
30361 ATTTCA-TTTTGACCC-TGAACTTTCCCAAAATTA-TCATTTTACCCTCGAATG
64 ATTT-ATTTTTTACCCTTGAACTTTCCTAAAATTACT-ATTTTACCCCCGAATG
** * *
30412 TCCAAAAATAT-CATTTTTGACCCCGAACATTCCCAAAATTACCATTTTACCCCGAACATCCAAA
1 TCCAAAAAT-TCCATTTTTGACCCTAAAC-TTCCAAAAATTACCATTTTACCCCAAACATCC-AA
* * * * * **
30476 AATTCCATTTTTTA-ACTCTAAACTATCCTAAAATTACCATTTTACCCCCGAACA
63 AATT-TATTTTTTACCCT-TGAACTTTCCTAAAATTACTATTTTACCCCCGAATG
* *
30530 TCCAAAAATTCCATTTTT-AACCTAAACTTCCAAAAATTACCATTTTACCCTCAAACATTCAAAA
1 TCCAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTACCATTTTACCC-CAAACA-TCCAAA
* * * * * * *
30594 ATTCCA-TTTTTAACCTCGAACTTTCCCAAAATTACCATTTTA-CCCCTAAAG
64 ATT-TATTTTTTACCCTTGAACTTTCCTAAAATTACTATTTTACCCCCGAATG
* * * **
30645 ATCCAAAAATTCCATTTTTGACCTTGAACTTCCTAAAAATTACCATTTTACCCTCGAATGTCCAA
1 -TCCAAAAATTCCATTTTTGACCCTAAACTTCC-AAAAATTACCATTTTACCC-CAAACATCCAA
* * * *
30710 AATTTATAGTTTTACCCTTGAAC-CT-CTAAAATTACTATTTTGCCCTCGAAGTG
63 AATTTAT-TTTTTACCCTTGAACTTTCCTAAAATTACTATTTTACCCCCGAA-TG
30763 TCCAAAA
1 TCCAAAA
30770 TTACCGTTTT
Statistics
Matches: 388, Mismatches: 60, Indels: 50
0.78 0.12 0.10
Matches are distributed among these distances:
115 31 0.08
116 179 0.46
117 95 0.24
118 83 0.21
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (115 bp):
TCCAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTACCATTTTACCCCAAACATCCAAAAT
TTATTTTTTACCCTTGAACTTTCCTAAAATTACTATTTTACCCCCGAATG
Found at i:30783 original size:29 final size:28
Alignment explanation
Indices: 30212--30779 Score: 217
Period size: 29 Copynumber: 19.5 Consensus size: 28
30202 CCTAACTTCA
** *
30212 CAAAATTACCATTTTACCCTTAAATTTC
1 CAAAATTACCATTTTACCCTCGAATGTC
* *
30240 CAAAA-TCCCATTTTTGA-CCTCGAACTTTC
1 CAAAATTACCA-TTTT-ACCCTCGAA-TGTC
* *
30269 CTAAAATTATCATTTTACCCCCGAATGTC
1 C-AAAATTACCATTTTACCCTCGAATGTC
** **
30298 CAAAAATT-CCATTTTTGACCC-AAAACCCTCC
1 C-AAAATTACCA-TTTT-ACCCTCGAA-TGT-C
*
30329 CAAAATTACCATTTTACCC-CTAAATGTC
1 CAAAATTACCATTTTACCCTC-GAATGTC
* *
30357 CAAAATT-TCATTTTGACCCT-GAACTTTCC
1 CAAAATTACCATTTT-ACCCTCGAA-TGT-C
*
30386 CAAAATTATCATTTTACCCTCGAATGTC
1 CAAAATTACCATTTTACCCTCGAATGTC
* *
30414 CAAAAATATCATTTTTGACCC-CGAACAT-TCC
1 CAAAATTACCA-TTTT-ACCCTCG-A-ATGT-C
**
30445 CAAAATTACCATTTTACCC-CGAACATC
1 CAAAATTACCATTTTACCCTCGAATGTC
* * *
30472 CAAAAATT-CCATTTTTTA-ACTCTAAACTATC
1 C-AAAATTACCA--TTTTACCCTC-GAA-TGTC
* **
30503 CTAAAATTACCATTTTACCCCCGAACATC
1 C-AAAATTACCATTTTACCCTCGAATGTC
* *
30532 CAAAAATT-CCATTTTTAACCT-AAACT-TC
1 C-AAAATTACCA-TTTTACCCTCGAA-TGTC
*
30560 CAAAAATTACCATTTTACCCTCAAACAT-TC
1 C-AAAATTACCATTTTACCCTC-GA-ATGTC
* * *
30590 AAAAATT-CCATTTTTAACCTCGAACTTTCC
1 CAAAATTACCA-TTTTACCCTCGAA-TGT-C
* *
30620 CAAAATTACCATTTTACCC-CTAAAGATC
1 CAAAATTACCATTTTACCCTCGAATG-TC
*
30648 CAAAAATT-CCATTTTTGA-CCTTGAACT-TC
1 C-AAAATTACCA-TTTT-ACCCTCGAA-TGTC
30677 CTAAAAATTACCATTTTACCCTCGAATGTC
1 C--AAAATTACCATTTTACCCTCGAATGTC
* * **
30707 CAAAATTTA-TAGTTTTACCCTTGAACCTC
1 CAAAA-TTACCA-TTTTACCCTCGAATGTC
* * *
30736 TAAAATTACTATTTTGCCCTCGAAGTGTC
1 CAAAATTACCATTTTACCCTCGAA-TGTC
*
30765 CAAAATTACCGTTTT
1 CAAAATTACCATTTT
30780 GCCCCCAAGT
Statistics
Matches: 421, Mismatches: 62, Indels: 113
0.71 0.10 0.19
Matches are distributed among these distances:
27 19 0.05
28 102 0.24
29 155 0.37
30 103 0.24
31 39 0.09
32 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCTCGAATGTC
Found at i:30798 original size:29 final size:29
Alignment explanation
Indices: 30737--30807 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
30727 TTGAACCTCT
* * *
30737 AAAATTACTATTTTGCCCTCGAAGTGTCC
1 AAAATTACCATTTTGCCCTCCAAGTATCC
*
30766 AAAATTACCGTTTTGCCC-CCAAGTATCC
1 AAAATTACCATTTTGCCCTCCAAGTATCC
30794 AAAAATTA-CATTTT
1 -AAAATTACCATTTT
30808 ATCCCGTCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCTCCAAGTATCC
Found at i:35471 original size:31 final size:31
Alignment explanation
Indices: 35436--35501 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
35426 GATTGAGGCC
35436 GGAGAAAGCACTAAAAGGCCTGCACCCAGAA
1 GGAGAAAGCACTAAAAGGCCTGCACCCAGAA
35467 GGAGAAAGCACTAAAAGGCCTGCACCCAGAA
1 GGAGAAAGCACTAAAAGGCCTGCACCCAGAA
35498 GGAG
1 GGAG
35502 GGATAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.41, C:0.24, G:0.29, T:0.06
Consensus pattern (31 bp):
GGAGAAAGCACTAAAAGGCCTGCACCCAGAA
Found at i:42672 original size:5 final size:6
Alignment explanation
Indices: 42640--42713 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
42630 CTAGACCCCT
* * * **
42640 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA -TTAAG TTTAAG TTTACT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
42686 TTTAAA TTTAAA ATT-AC TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
42714 TAAAAGGTCA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
5 11 0.20
6 43 0.80
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:42677 original size:17 final size:17
Alignment explanation
Indices: 42640--42683 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
42630 CTAGACCCCT
* *
42640 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTAAG
42657 TTTAAATTTAAATTAAG
1 TTTAAATTTAAATTAAG
*
42674 TTTAAGTTTA
1 TTTAAATTTA
42684 CTTTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTAAG
Found at i:43444 original size:3 final size:3
Alignment explanation
Indices: 43438--43466 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43428 AATATTAAAT
43438 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
43467 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:43471 original size:3 final size:3
Alignment explanation
Indices: 43465--43519 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
43455 CAACAACAAC
* * *
43465 AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAC ATT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
43510 AAT AA- AAT AA
1 AAT AAT AAT AA
43520 AAAAGGGGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 39 0.91
4 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44805 original size:30 final size:30
Alignment explanation
Indices: 44770--45226 Score: 136
Period size: 29 Copynumber: 15.5 Consensus size: 30
44760 CTCCAAATTT
44770 CCAAAA-TCTCATTTTTAACCCTAAACTTTC
1 CCAAAATTC-CATTTTTAACCCTAAACTTTC
* * *
44800 CCAAAATTACCA-TTTTACCCCTGAA-TGTC
1 CCAAAATT-CCATTTTTAACCCTAAACTTTC
** * *
44829 AAAAAATTCCATTTTTGACCTTAAACTTTC
1 CCAAAATTCCATTTTTAACCCTAAACTTTC
* ** *
44859 CCAAAATTACCA--TTTAACGCTCGA-TGTC
1 CCAAAATT-CCATTTTTAACCCTAAACTTTC
* * ** *
44887 CAAAAATTCCATTTTTGACCCCGAACGTTC
1 CCAAAATTCCATTTTTAACCCTAAACTTTC
* * *
44917 CCACAATTACCA-TTTT-ACCCTCGAA-TGTC
1 CCAAAATT-CCATTTTTAACCCT-AAACTTTC
** * ** *
44946 TAAAAATACCATTTTTAACCCCGAACATTC
1 CCAAAATTCCATTTTTAACCCTAAACTTTC
* * ** *
44976 CCACAATTACCA-TTTTACCCCCGAA-TGTC
1 CCAAAATT-CCATTTTTAACCCTAAACTTTC
* * *
45005 CAAAAATTCCATTTTTTGACTCC-GAACTTTC
1 CCAAAATTCCA-TTTTTAAC-CCTAAACTTTC
* *
45036 CCAAAATTACCA-TTTT-ACCCTCGAAC-GTC
1 CCAAAATT-CCATTTTTAACCCT-AAACTTTC
* *
45065 CAAAAATTCTATTTTTAATCCC--AACTTTC
1 CCAAAATTCCATTTTTAA-CCCTAAACTTTC
* * *
45094 CAAAAATTACCA-TTTT-ACCCTCAAC-ATC
1 CCAAAATT-CCATTTTTAACCCTAAACTTTC
* * * *
45122 CAAAAATTCTATTTTTGA-CCTCGAACTTTC
1 CCAAAATTCCATTTTTAACCCT-AAACTTTC
* **
45152 CCAAAATTACCA-TTTT-ACCCTTGAA-GGTC
1 CCAAAATT-CCATTTTTAACCC-TAAACTTTC
* * *
45181 CAAAAATTCCATTTTTGACCCCAAAC-TTC
1 CCAAAATTCCATTTTTAACCCTAAACTTTC
45210 CCAAAAATTACCATTTT
1 CC-AAAATT-CCATTTT
45227 ACTCTCGAAT
Statistics
Matches: 318, Mismatches: 69, Indels: 79
0.68 0.15 0.17
Matches are distributed among these distances:
27 8 0.03
28 47 0.15
29 112 0.35
30 110 0.35
31 37 0.12
32 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (30 bp):
CCAAAATTCCATTTTTAACCCTAAACTTTC
Found at i:44854 original size:59 final size:59
Alignment explanation
Indices: 44732--45303 Score: 612
Period size: 59 Copynumber: 9.8 Consensus size: 59
44722 ACATTATCAC
* * * *
44732 CCCCGAAC-TTCAC-AAATTACCATTTT-CCCTCCAAATTTCC-AAAA-TCTCATTTTTAA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCT-CGAATGTCCAAAAATTC-CATTTTTGA
** *
44788 CCCTAAACTTTCCCAAAATTACCATTTTACCC-CTGAATGTCAAAAAATTCCATTTTTGA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTC-GAATGTCCAAAAATTCCATTTTTGA
*** * *
44847 CCTTAAACTTTCCCAAAATTACCATTTAACGCTCG-ATGTCCAAAAATTCCATTTTTGA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
* * * * *
44905 CCCCGAACGTTCCCACAATTACCATTTTACCCTCGAATGTCTAAAAATACCATTTTTAA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
* * *
44964 CCCCGAACATTCCCACAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTTGA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCA-TTTTTGA
* * * *
45024 CTCCGAACTTTCCCAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCTATTTTTAA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
* * ** *
45083 TCCC-AACTTTCCAAAAATTACCATTTTACCCTC-AACATCCAAAAATTCTATTTTTGA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
* * *
45140 CCTCGAACTTTCCCAAAATTACCATTTTACCCTTGAAGGTCCAAAAATTCCATTTTTGA
1 CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
* * * *
45199 CCCCAAAC-TTCCCAAAAATTACCATTTTACTCTCGAATGTCCAAAAAAT--ATTATTTTA
1 CCCCGAACTTTCCC-AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATT-TTTGA
* ** * *
45257 CCCTCGAAC-CTCTAAAAATTACTATTTTGCCCTCGAAGTGTCCAAAA
1 CCC-CGAACTTTCCCAAAATTACCATTTTACCCTCGAA-TGTCCAAAA
45304 TTACCGTTTT
Statistics
Matches: 442, Mismatches: 59, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
56 6 0.01
57 32 0.07
58 155 0.35
59 194 0.44
60 55 0.12
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (59 bp):
CCCCGAACTTTCCCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA
Found at i:44872 original size:117 final size:118
Alignment explanation
Indices: 44745--45303 Score: 588
Period size: 117 Copynumber: 4.8 Consensus size: 118
44735 CGAACTTCAC
* * *
44745 AAATTACCATTTT-CCCTCCAAATTTCC-AAAA-TCTCATTTTTAACCCTAAACTTTCCCAAAAT
1 AAATTACCATTTTACCCT-CAAATGTCCAAAAATTC-CATTTTTGACCCTGAACTTTCCCAAAAT
* * **
44807 TACCATTTTACCC-CTGAATGTCAAAAAATTCCATTTTTGACCTTAAACTTTCCCA
64 TACCATTTTACCCTC-GAATGTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCA
* * * * * *
44862 AAATTACCATTTAACGCTC-GATGTCCAAAAATTCCATTTTTGACCCCGAACGTTCCCACAATTA
1 AAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTA
* * * *
44926 CCATTTTACCCTCGAATGTCTAAAAATACCATTTTTAACCCCGAACATTCCCA
66 CCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCA
* * *
44979 CAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTTGACTCC-GAACTTTCCCAAAAT
1 AAATTACCATTTTACCCTCAAATGTCCAAAAATTCCA-TTTTTGAC-CCTGAACTTTCCCAAAAT
* * * *
45043 TACCATTTTACCCTCGAACGTCCAAAAATTCTATTTTTAATCCC-AACTTTCCAA
64 TACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCA
*
45097 AAATTACCATTTTACCCTCAACA--TCCAAAAATTCTATTTTTGA-CCTCGAACTTTCCCAAAAT
1 AAATTACCATTTTACCCTCAA-ATGTCCAAAAATTCCATTTTTGACCCT-GAACTTTCCCAAAAT
* * *
45159 TACCATTTTACCCTTGAAGGTCCAAAAATTCCATTTTTGACCCCAAAC-TTCCCAA
64 TACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCCCAAACTTTCCC-A
* * * * * **
45214 AAATTACCATTTTACTCTCGAATGTCCAAAAAAT--ATTATTTTACCCTCGAAC-CTCTAAAAAT
1 AAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATT-TTTGACCCT-GAACTTTCCCAAAAT
* *
45276 TACTATTTTGCCCTCGAAGTGTCCAAAA
64 TACCATTTTACCCTCGAA-TGTCCAAAA
45304 TTACCGTTTT
Statistics
Matches: 374, Mismatches: 51, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
114 2 0.01
116 74 0.20
117 162 0.43
118 73 0.20
119 61 0.16
120 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (118 bp):
AAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTA
CCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCCCAAACTTTCCCA
Found at i:45332 original size:29 final size:30
Alignment explanation
Indices: 45092--45334 Score: 103
Period size: 29 Copynumber: 8.3 Consensus size: 30
45082 ATCCCAACTT
* * *
45092 TCCAAAAATTACCATTTTACCCT-CAA-CA
1 TCCAAAAATTACCATTTTGCCCTAGAAGTA
* * * * *
45120 TCCAAAAATT-CTATTTTTGACCTCGAACTT
1 TCCAAAAATTACCA-TTTTGCCCTAGAAGTA
* * * *
45150 TCCCAAAATTACCATTTTACCCTTGAAG-G
1 TCCAAAAATTACCATTTTGCCCTAGAAGTA
* *
45179 TCCAAAAATT-CCATTTTTGACCCCA-AACT-
1 TCCAAAAATTACCA-TTTTG-CCCTAGAAGTA
* * * *
45208 TCCCAAAAATTACCATTTTACTCTCGAA-TG
1 T-CCAAAAATTACCATTTTGCCCTAGAAGTA
* ** * * **
45238 TCCAAAAAATATTATTTTACCCTCGAA-CC
1 TCCAAAAATTACCATTTTGCCCTAGAAGTA
* * * *
45267 TCTAAAAATTACTATTTTGCCCTCGAAGTG
1 TCCAAAAATTACCATTTTGCCCTAGAAGTA
*
45297 TCC-AAAATTACCGTTTTGCCCTAG-AGTA
1 TCCAAAAATTACCATTTTGCCCTAGAAGTA
45325 TCCAAAAATT
1 TCCAAAAATT
45335 GCATTTTATG
Statistics
Matches: 163, Mismatches: 39, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
27 2 0.01
28 26 0.16
29 90 0.55
30 40 0.25
31 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTGCCCTAGAAGTA
Found at i:47175 original size:17 final size:17
Alignment explanation
Indices: 47140--47182 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
47130 AGAAAAAGTA
*
47140 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
47158 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
47175 GTTAAAGA
1 GTTAAAGA
47183 TCAAGGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:52501 original size:17 final size:17
Alignment explanation
Indices: 52475--52512 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
52465 AAGTAATTAC
*
52475 AAGAATATGAAAGGTTA
1 AAGAAAATGAAAGGTTA
52492 AAGAAAATGAAAGGTTA
1 AAGAAAATGAAAGGTTA
52509 AAGA
1 AAGA
52513 TCAAAGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (17 bp):
AAGAAAATGAAAGGTTA
Found at i:54314 original size:25 final size:25
Alignment explanation
Indices: 54286--54333 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54276 AAATTTTAGC
*
54286 GATTATACTTTTTTTAAATAAACTA
1 GATTAGACTTTTTTTAAATAAACTA
*
54311 GATTAGATTTTTTTTAAATAAAC
1 GATTAGACTTTTTTTAAATAAAC
54334 AAAGATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (25 bp):
GATTAGACTTTTTTTAAATAAACTA
Found at i:64037 original size:17 final size:17
Alignment explanation
Indices: 64015--64048 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64005 TGAGGGATTC
*
64015 CTTTTTTGGAACTAACT
1 CTTTTTTGGAACAAACT
64032 CTTTTTTGGAACAAACT
1 CTTTTTTGGAACAAACT
64049 TATCTGTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (17 bp):
CTTTTTTGGAACAAACT
Done.