Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014480.1 Kokia drynarioides strain JFW-HI SEQ_129519, 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: 41134
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:5538 original size:15 final size:16
Alignment explanation
Indices: 5518--5552 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5508 TGTTCAAAAA
5518 AAAAGAAAAAAATT-G
1 AAAAGAAAAAAATTGG
5533 AAAAGAAAAAAATTGG
1 AAAAGAAAAAAATTGG
5549 AAAA
1 AAAA
5553 AAATTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAAGAAAAAAATTGG
Found at i:5582 original size:26 final size:24
Alignment explanation
Indices: 5514--5580 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 24
5504 ATTTTGTTCA
5514 AAAAAAAAGAAAAAAATTGAAAAG
1 AAAAAAAAGAAAAAAATTGAAAAG
* * **
5538 AAAAAAATTGGAAAAAAATTTAACTG
1 AAAAAAA--AGAAAAAAATTGAAAAG
5564 TAAAAAAAAGAAAAAAA
1 -AAAAAAAAGAAAAAAA
5581 ATGTGTTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 7 0.20
25 8 0.23
26 13 0.37
27 7 0.20
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.13
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAATTGAAAAG
Found at i:6095 original size:21 final size:21
Alignment explanation
Indices: 6071--6127 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
6061 ACAAGTATAA
6071 CATCTACCGAAACTGGTTGTG
1 CATCTACCGAAACTGGTTGTG
*
6092 CATCTACCGAAATTGGTTGTG
1 CATCTACCGAAACTGGTTGTG
* *
6113 CTTCTACCGATACTG
1 CATCTACCGAAACTG
6128 AAAACTCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (21 bp):
CATCTACCGAAACTGGTTGTG
Found at i:6878 original size:41 final size:41
Alignment explanation
Indices: 6828--6919 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
6818 TCTCGAGACA
6828 TGAGTCTTCCTTATTCATAATATCATGCTTATTTTGAGTCC
1 TGAGTCTTCCTTATTCATAATATCATGCTTATTTTGAGTCC
6869 TGAGTCTTCCTTATTCATAATATCATGCTTATTTTGAGTCC
1 TGAGTCTTCCTTATTCATAATATCATGCTTATTTTGAGTCC
6910 TGAGTCTTCC
1 TGAGTCTTCC
6920 ATTTTTTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (41 bp):
TGAGTCTTCCTTATTCATAATATCATGCTTATTTTGAGTCC
Found at i:14012 original size:41 final size:41
Alignment explanation
Indices: 13923--14151 Score: 228
Period size: 41 Copynumber: 5.5 Consensus size: 41
13913 TTATGCTTTA
* * *
13923 TCGAGTCATAAGTCTTCCTT-TTGCCATATTCCCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT--CATAATCCCATTCTCATC
* *
13965 TCGAGACATTAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCCCATTCTCATC
* * * * *
14006 TTGAGACATGAGTTTTCCTTATTCATAATCTCAATCTTATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCCCATTCTCATC
14047 TCGAGACATGAGTCTTCCTTATTCATAATCCCATTCTCAT-
1 TCGAGACATGAGTCTTCCTTATTCATAATCCCATTCTCATC
* * * * * * *
14087 TCTGAGTCATGAGTCTTCCATTTTTTACAATTTCTCATGCTCAAC
1 TC-GAGACATGAGTCTTCC-TTATTCATAA--TCCCATTCTCATC
*
14132 CCGAGACATGAGTCTTCCTT
1 TCGAGACATGAGTCTTCCTT
14152 CTTATACACC
Statistics
Matches: 158, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.01
41 102 0.65
42 25 0.16
43 4 0.03
44 24 0.15
45 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.40
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCCCATTCTCATC
Found at i:15356 original size:42 final size:40
Alignment explanation
Indices: 15307--15384 Score: 129
Period size: 42 Copynumber: 1.9 Consensus size: 40
15297 AATAAGACAA
*
15307 ATTTTAAATTTAAATTTACTTTAAATTTTAAATGTCCAATGC
1 ATTTTAAATTTAAATTTA-TTTAAA-TTTAAAAGTCCAATGC
15349 ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCA
1 ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCA
15385 TTTACAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 11 0.31
41 6 0.17
42 18 0.51
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (40 bp):
ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCAATGC
Found at i:17245 original size:60 final size:61
Alignment explanation
Indices: 17163--17291 Score: 199
Period size: 60 Copynumber: 2.1 Consensus size: 61
17153 TCGATTTTCT
* *
17163 TCAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTATATTTTAACC-CTCGAACTT-
1 TCAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCTCTCGAACTTC
* *
17222 TCCAAAAATCCCATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCTCTTGAACTTC
1 T-CAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCTCTCGAACTTC
17284 TCAAAAAT
1 TCAAAAAT
17292 TATGTTTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
59 1 0.02
60 46 0.73
61 15 0.24
62 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.34
Consensus pattern (61 bp):
TCAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCTCTCGAACTTC
Found at i:17293 original size:31 final size:30
Alignment explanation
Indices: 17164--17272 Score: 182
Period size: 30 Copynumber: 3.6 Consensus size: 30
17154 CGATTTTCTT
17164 CAAAAATTACATTTTAACCCTCAAACTTTC
1 CAAAAATTACATTTTAACCCTCAAACTTTC
* *
17194 CAAAAATTATATTTTAACCCTCGAACTTTC
1 CAAAAATTACATTTTAACCCTCAAACTTTC
**
17224 CAAAAATCCCATTTTAACCCTCAAACTTTC
1 CAAAAATTACATTTTAACCCTCAAACTTTC
17254 CAAAAATTACATTTTAACC
1 CAAAAATTACATTTTAACC
17273 TCTTGAACTT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.33
Consensus pattern (30 bp):
CAAAAATTACATTTTAACCCTCAAACTTTC
Found at i:17343 original size:89 final size:90
Alignment explanation
Indices: 17164--17379 Score: 226
Period size: 89 Copynumber: 2.4 Consensus size: 90
17154 CGATTTTCTT
17164 CAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTATATTTTAACCCTCGAACTTTCCAAAA
1 CAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTATATTTTAACCCTCGAACTTTCCAAAA
*
17229 ATCCCATTTTAACCCTCAAACTTTC
66 ATCACATTTTAACCCTCAAACTTTC
** * * * *
17254 CAAAAATTACATTTTAACCTCTTGAAC-TTCTCAAAAATTATGTTTT-TCCC-CTAAGTTTCCAA
1 CAAAAATTACATTTTAACC-CTCAAACTTTC-CAAAAATTATATTTTAACCCTCGAACTTTCCAA
* * * *
17316 AAGTCACATTTTCGA-CCTCCAATTTTC
64 AAATCACATTTT-AACCCTCAAACTTTC
* ** * *
17343 CAAAAGTTTGATTTTAATCC-CAAATTTTCCAAAAATT
1 CAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATT
17380 CCAATTTTGA
Statistics
Matches: 104, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
87 10 0.10
88 4 0.04
89 45 0.43
90 26 0.25
91 19 0.18
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (90 bp):
CAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTATATTTTAACCCTCGAACTTTCCAAAA
ATCACATTTTAACCCTCAAACTTTC
Found at i:29862 original size:39 final size:39
Alignment explanation
Indices: 29814--30290 Score: 205
Period size: 39 Copynumber: 12.4 Consensus size: 39
29804 CCATCAGTTA
* *
29814 ATCTCTTACCCCGAGCCTGGGGCAAATTGTAACCATTCG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * * * * *
29853 ATCTTTTACCCTGAGCCTGGGGTAGATTGTAGCCATTTG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * * ** * * * *
29892 ATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
*
29931 ATCTCTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * ** * ** * * ** *
29970 ATCTTTTACCCTGAGCTTGGGTTAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * * * * *
30009 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * * ** * * * *
30048 ATCTTTTACCCTGAGCCTAGGGCAGATCACCATCATCCA
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
** * *
30087 ATCTTTTACCTTGAGCCTAGGGCATATTGCAACCATTCG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * * ** * * ** *
30126 A-----TACCCCGATCTTGGGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
* * *
30160 ATCTTTTACCCCAAGCTTGGGGCAGATTGCAACCATTCG
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
** * * * ** *
30199 ATCTTTTACCTTGATCATGGGGCAAA-T-CACCTTCAACCA
1 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAAC--CATTCG
* * *
30238 ATCTCTTACCCCGAACTTGGGG-AAGATTGCAACCATTCG
1 ATCTTTTACCCCGAGCCTGGGGCAA-ATTGCAACCATTCG
*
30277 ATCTCTTACCCCGA
1 ATCTTTTACCCCGA
30291 TCATAGAGCA
Statistics
Matches: 314, Mismatches: 114, Indels: 20
0.70 0.25 0.04
Matches are distributed among these distances:
34 21 0.07
37 3 0.01
38 3 0.01
39 283 0.90
40 1 0.00
41 3 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCCTGGGGCAAATTGCAACCATTCG
Found at i:29940 original size:78 final size:77
Alignment explanation
Indices: 29853--30347 Score: 489
Period size: 78 Copynumber: 6.4 Consensus size: 77
29843 TAACCATTCG
* * * * * *
29853 ATCTTTTACCCTGAGCCTGGGGTAGATTGTAGCCATTTGATCTTTTACCTCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACC-CGAGCTTGGGGCAGA
*
29918 TCACCATCAGTCA
65 TCACCATCAGCCA
* **
29931 ATCTCTTACCCCGAGCCTGGGGCAAATTGCAACCATTCGATCTTTTACCCTGAGCTTGGGTTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACCC-GAGCTTGGGGCAGA
29996 TCACCATCAGCCA
65 TCACCATCAGCCA
* * * * * *
30009 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACCC-GAGCTTGGGGCAGA
*
30074 TCACCATCATCCA
65 TCACCATCAGCCA
* ** * * *
30087 ATCTTTTACCTTGAGCCTAGGGCATATTGCAACCATTCGA-----TACCCCGATCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTA-CCCGAGCTTGGGGCAGA
30147 TCACCATCAGCCA
65 TCACCATCAGCCA
* * * * * * *
30160 ATCTTTTACCCCAAGCTTGGGGCAGATTGCAACCATTCGATCTTTTACCTTGATCATGGGGCAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACC-CGAGCTTGGGGCAGA
* *
30225 TCACCTTCAACCA
65 TCACCATCAGCCA
* * * * * * * *
30238 ATCTCTTACCCCGAACTTGGGGAAGATTGCAACCATTCGATCTCTTACCCCGATCATAGAGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTA-CCCGAGCTTGGGGCAGA
** *
30303 TCACTGTCAACCA
65 TCACCATCAGCCA
*
30316 ATCTCTTACCCCAAG-CTAGGGGCAGATTGCAA
1 ATCTCTTACCCCGAGCCT-GGGGCAGATTGCAA
30348 GGATCTAATA
Statistics
Matches: 350, Mismatches: 57, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
73 59 0.17
74 3 0.01
77 4 0.01
78 282 0.81
79 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (77 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTTTTACCCGAGCTTGGGGCAGAT
CACCATCAGCCA
Found at i:29941 original size:117 final size:116
Alignment explanation
Indices: 29774--30208 Score: 406
Period size: 117 Copynumber: 3.8 Consensus size: 116
29764 ACAGTCATCC
* * * *
29774 GATCTTTTACC-CTGAGCTTAGGACAGATTACCATCAGTTAATCTCTTACCCCGAGCCTGGGGCA
1 GATCTTTTACCTC-GAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCA
* * *
29838 AATTGTAACCATTCGATCTTTTACCCTGAGCCTGGGGTAGATTGTAGCCATTT
65 AATTGCAACCATTCGATCTTTTACCCTGAGCCTGGGGTAGATTGCA-CCATTA
29891 GATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAA
1 GATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAA
* * *
29956 ATTGCAACCATTCGATCTTTTACCCTGAGCTTGGGTTAGA-T-CACCATCA
66 ATTGCAACCATTCGATCTTTTACCCTGAGCCTGGGGTAGATTGCACCATTA
* * * * *
30005 GCCAATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATC---CGATCTTTTACCCTGAGCCTA
1 G---ATCTTTTACCTCGAGCTTGGGGCAGA-T-CA-CCATCAGTCAATCTCTTACCCCGAGCCTG
* ** * * * * * * * * *
30067 GGGCAGATCACCATCATCCAATCTTTTACCTTGAGCCTAGGGCATATTGCAACCATTC
60 GGGCAAATTGCAACCATTCGATCTTTTACCCTGAGCCTGGGGTAGATTGC-ACCATTA
* * * * * * *
30125 GA-----TACCCCGATCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCCAAGCTTGGGGCAG
1 GATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAA
30185 ATTGCAACCATTCGATCTTTTACC
66 ATTGCAACCATTCGATCTTTTACC
30209 TTGATCATGG
Statistics
Matches: 262, Mismatches: 43, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
109 5 0.02
110 2 0.01
111 1 0.00
112 58 0.22
114 5 0.02
115 1 0.00
116 1 0.00
117 172 0.66
118 3 0.01
119 3 0.01
120 11 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (116 bp):
GATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAA
ATTGCAACCATTCGATCTTTTACCCTGAGCCTGGGGTAGATTGCACCATTA
Found at i:30191 original size:229 final size:229
Alignment explanation
Indices: 29898--30325 Score: 595
Period size: 229 Copynumber: 1.9 Consensus size: 229
29888 TTTGATCTTT
* * *
29898 TACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAAATTGCAA
1 TACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCAAATTGCAA
* ** * * * *
29963 CCATTCGATCTTTTACCCTGAGCTTGGGTTAGATCACCATCAGCCAATCTCTTACCTCGAGCTTG
66 CCATTCGATCTTTTACCCTGAGCATGGGGCAAATCACCATCAACCAATCTCTTACCCCGAACTTG
* * * * * * * *
30028 GGGCAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCATCATCCAATCTTT
131 GGGAAGATTGCAACCATCCGATCTCTTACCCCGAGCATAGAGCAGATCACCATCAACCAATCTCT
30093 TACCTTGAGCCTAGGGCATATTGCAACCATTCGA
196 TACCTTGAGCCTAGGGCATATTGCAACCATTCGA
* * * *
30127 TACCCCGATCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCCAAGCTTGGGGCAGATTGCAA
1 TACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCAAATTGCAA
* * *
30192 CCATTCGATCTTTTACCTTGATCATGGGGCAAATCACCTTCAACCAATCTCTTACCCCGAACTTG
66 CCATTCGATCTTTTACCCTGAGCATGGGGCAAATCACCATCAACCAATCTCTTACCCCGAACTTG
* * **
30257 GGGAAGATTGCAACCATTCGATCTCTTACCCCGATCATAGAGCAGATCACTGTCAACCAATCTCT
131 GGGAAGATTGCAACCATCCGATCTCTTACCCCGAGCATAGAGCAGATCACCATCAACCAATCTCT
30322 TACC
196 TACC
30326 CCAAGCTAGG
Statistics
Matches: 170, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
229 170 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (229 bp):
TACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCAAATTGCAA
CCATTCGATCTTTTACCCTGAGCATGGGGCAAATCACCATCAACCAATCTCTTACCCCGAACTTG
GGGAAGATTGCAACCATCCGATCTCTTACCCCGAGCATAGAGCAGATCACCATCAACCAATCTCT
TACCTTGAGCCTAGGGCATATTGCAACCATTCGA
Found at i:30852 original size:6 final size:6
Alignment explanation
Indices: 30843--30921 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
30833 AAAATAAGAC
* * * *
30843 AAATTT AAATTT AAATTT -ACTTT AAATTTT AAATGTC CAA--T ACATTTT
1 AAATTT AAATTT AAATTT AAATTT AAA-TTT AAAT-TT AAATTT A-AATTT
30891 AAATTT AAATTT AAATTT --ATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAA
30922 AGTCCATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
4 4 0.07
5 5 0.09
6 37 0.65
7 11 0.19
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:32778 original size:30 final size:30
Alignment explanation
Indices: 32743--32966 Score: 133
Period size: 30 Copynumber: 7.5 Consensus size: 30
32733 CGATTTTCTT
32743 CAAAAATTACATTTTGACCCTTAAACTTTC
1 CAAAAATTACATTTTGACCCTTAAACTTTC
*
32773 CAAAAATCT-CATTTT-AACCTTAAAACTTTC
1 CAAAAAT-TACATTTTGACCCTT-AAACTTTC
* *
32803 AAAAAATTACATTTTGACCCCTTTAAC-TTC
1 CAAAAATTACATTTTGA-CCCTTAAACTTTC
* * *
32833 TTAAAAATTACATTTTG-CCCCTAAA-TTTT
1 -CAAAAATTACATTTTGACCCTTAAACTTTC
** * * *
32862 TGAAAATCACATTTTTGA-CCTCAAATTTTC
1 CAAAAATTACA-TTTTGACCCTTAAACTTTC
* * * *
32892 CAAAAGTT-CGATTTTAATCC-TAAATTTTC
1 CAAAAATTAC-ATTTTGACCCTTAAACTTTC
* * * *
32921 CCAAAATTCCAATTTTGACCCCTAAA-TTCC
1 CAAAAATTAC-ATTTTGACCCTTAAACTTTC
*
32951 ACAAAAATTACGTTTT
1 -CAAAAATTACATTTT
32967 CATCCCGAAT
Statistics
Matches: 151, Mismatches: 28, Indels: 30
0.72 0.13 0.14
Matches are distributed among these distances:
28 9 0.06
29 44 0.29
30 62 0.41
31 32 0.21
32 4 0.03
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCCTTAAACTTTC
Found at i:32906 original size:29 final size:29
Alignment explanation
Indices: 32874--32940 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
32864 AAAATCACAT
*
32874 TTTTGACCTCAAATTTT-CCAAAAGTT-CGA
1 TTTTGACCT-AAATTTTCCCAAAA-TTCCAA
*
32903 TTTTAATCCTAAATTTTCCCAAAATTCCAA
1 TTTTGA-CCTAAATTTTCCCAAAATTCCAA
32933 TTTTGACC
1 TTTTGACC
32941 CCTAAATTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (29 bp):
TTTTGACCTAAATTTTCCCAAAATTCCAA
Found at i:36349 original size:23 final size:21
Alignment explanation
Indices: 36316--36444 Score: 78
Period size: 23 Copynumber: 5.6 Consensus size: 21
36306 GAACACTAGC
*
36316 GTGCTCCCTGTTTAGCACGTCT
1 GTGCTCTCTGTTTAGCACGT-T
36338 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCAC-GT-T
* * *
36364 GTGCTCTTTGATTAGCACTTT
1 GTGCTCTCTGTTTAGCACGTT
* * *
36385 GTATGCTCTCTGATTAGTACTTT
1 G--TGCTCTCTGTTTAGCACGTT
*
36408 GTGTACTCTCTGTTTAGCATTGTCT
1 GTG--CTCTCTGTTTAGCA-CGT-T
36433 GTGCTCTCTGTT
1 GTGCTCTCTGTT
36445 GCCTAGCACT
Statistics
Matches: 86, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
21 4 0.05
22 1 0.01
23 56 0.65
24 2 0.02
25 20 0.23
26 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (21 bp):
GTGCTCTCTGTTTAGCACGTT
Found at i:36367 original size:25 final size:25
Alignment explanation
Indices: 36339--36466 Score: 99
Period size: 23 Copynumber: 5.4 Consensus size: 25
36329 AGCACGTCTC
36339 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* *
36364 GTGCTCT-T-TGATTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* * *
36387 ATGCTCTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* * *
36410 GTACTCTCTG-T-TTAGCATTGTCT
1 GTGCTCTCTGTTATTAGCACTGTGT
** *
36433 GTGCTCTCTGTTGCCTAGCACT-TAT
1 GTGCTCTCTGTT-ATTAGCACTGTGT
36458 GTGCTCTCT
1 GTGCTCTCT
36467 ATTAGTACTT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
23 56 0.67
24 3 0.04
25 18 0.22
26 6 0.07
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGT
Found at i:36438 original size:46 final size:47
Alignment explanation
Indices: 36323--36443 Score: 122
Period size: 46 Copynumber: 2.6 Consensus size: 47
36313 AGCGTGCTCC
* *
36323 CTGTTTAGCA-CGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCT
1 CTGTTTAGCATTGTCT-GTGCTCTCTG-TATTAGCACTGTGTGTACTCT
* * * * * *
36371 TTGATTAGCACTT-TGTATGCTCTCTG-ATTAGTACTTTGTGTACTCT
1 CTGTTTAGCA-TTGTCTGTGCTCTCTGTATTAGCACTGTGTGTACTCT
36417 CTGTTTAGCATTGTCTGTGCTCTCTGT
1 CTGTTTAGCATTGTCTGTGCTCTCTGT
36444 TGCCTAGCAC
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
45 2 0.04
46 36 0.63
48 17 0.30
49 2 0.04
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (47 bp):
CTGTTTAGCATTGTCTGTGCTCTCTGTATTAGCACTGTGTGTACTCT
Found at i:36439 original size:69 final size:68
Alignment explanation
Indices: 36342--36491 Score: 180
Period size: 69 Copynumber: 2.1 Consensus size: 68
36332 ACGTCTCGTG
* *
36342 CTCTCTGTTATTAGCACTGTGTGTG-CTCT-TTGATTAGCACTT-TGTATGCTCTCTGATTAGTA
1 CTCTCTG-T-TTAGCACTGTCTGTGCCTCTGTTGACTAGCACTTATG--TGCTCTCT-ATTAGTA
36404 CTTTGTGTA
61 CTTTG-GTA
* *
36413 CTCTCTGTTTAGCATTGTCTGTGCTCTCTGTTGCCTAGCACTTATGTGCTCTCTATTAGTACTTT
1 CTCTCTGTTTAGCACTGTCTGTGC-CTCTGTTGACTAGCACTTATGTGCTCTCTATTAGTACTTT
36478 GGTA
65 GGTA
36482 CTCTCTGTTT
1 CTCTCTGTTT
36492 GTTCTGTATA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
69 26 0.37
70 13 0.18
71 19 0.27
72 11 0.15
73 2 0.03
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (68 bp):
CTCTCTGTTTAGCACTGTCTGTGCCTCTGTTGACTAGCACTTATGTGCTCTCTATTAGTACTTTG
GTA
Found at i:39314 original size:22 final size:21
Alignment explanation
Indices: 39261--39315 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
39251 AAATTTGTTC
* **
39261 TTTGTTGTTGTTTATTGTTAT
1 TTTGTTGTTATTTATTACTAT
* *
39282 TTTGCTATTATATTATTACTAT
1 TTTGTTGTTAT-TTATTACTAT
39304 TTTGTTGTTATT
1 TTTGTTGTTATT
39316 GTTTAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.16, C:0.04, G:0.13, T:0.67
Consensus pattern (21 bp):
TTTGTTGTTATTTATTACTAT
Done.