Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012366.1 Kokia drynarioides strain JFW-HI SEQ_127370, 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: 26777
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:763 original size:162 final size:162
Alignment explanation
Indices: 496--814 Score: 489
Period size: 162 Copynumber: 2.0 Consensus size: 162
486 CCCCTCAACC
* * * ** *
496 TTTTAAAAGCACCAGGAGCAGCCACGTGTCCTTATTTTGGTTTATTTGTGCAAATGGTCCCCTTT
1 TTTTAAAAGCACCAGGAGCAGCCACGTGTCATGATTTTGGCTTATTTACGCAAACGGTCCCCTTT
** *
561 GTTTCTAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTGCCTC-AAA
66 ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTGCC-CAAAA
*
625 AATTTTCCA-TGATTTTCAAAATAGTCCTCTAAT
130 AATTTT-CATTGATTTTCAAAAGAGTCCTCTAAT
* *
658 TTTTAAAAGCACTAGGAGCTGCCACGTGTCATGATTTTGGCTTATTTACGCAAACGGTCCCCTTT
1 TTTTAAAAGCACCAGGAGCAGCCACGTGTCATGATTTTGGCTTATTTACGCAAACGGTCCCCTTT
723 ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTGCCCAAAAA
66 ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTGCCCAAAAA
*
788 ATTTTCATTGGTTTTCAAAAGAGTCCT
131 ATTTTCATTGATTTTCAAAAGAGTCCT
815 TTGACTTCTA
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
161 3 0.02
162 139 0.98
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (162 bp):
TTTTAAAAGCACCAGGAGCAGCCACGTGTCATGATTTTGGCTTATTTACGCAAACGGTCCCCTTT
ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTGCCCAAAAA
ATTTTCATTGATTTTCAAAAGAGTCCTCTAAT
Found at i:922 original size:29 final size:29
Alignment explanation
Indices: 880--1148 Score: 151
Period size: 30 Copynumber: 9.1 Consensus size: 29
870 CCCCGGAGGT
880 CCCT-AAACTATCCAAAAATTACCATTTTA
1 CCCTCAAACT-TCCAAAAATTACCATTTTA
* *
909 CCCTCAAACTTCCAAAAAGT-CTTATTTTTAA
1 CCCTCAAACTTCCAAAAATTAC-CA-TTTT-A
*
940 CCC-CGAACCTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
969 CCCCCGAACTTCCAAAAGTT-CCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A
* *
999 CCC-CGAACCTTCCTAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * * ** *
1028 CCCCCCGAACTTCCAAAAGTCCCCTTTTTGA
1 -CCCTCAAACTTCCAAAAATTACCATTTT-A
* * *
1059 -CCTCGAACCTTCCTAAAATTACAATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
1088 CCCCCCGAACTTCC-AAAA-TCCCATTTTTA
1 -CCCTCAAACTTCCAAAAATTACCA-TTTTA
* *
1117 CCCT-AAACTTTCCAAAAACTACCTTTTTA
1 CCCTCAAAC-TTCCAAAAATTACCATTTTA
1146 CCC
1 CCC
1149 CCGAATGTTT
Statistics
Matches: 182, Mismatches: 37, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.02
28 14 0.08
29 61 0.34
30 77 0.42
31 26 0.14
32 1 0.01
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACCATTTTA
Found at i:1017 original size:59 final size:59
Alignment explanation
Indices: 890--1153 Score: 343
Period size: 60 Copynumber: 4.5 Consensus size: 59
880 CCCTAAACTA
* * ** *
890 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAGTCTTATTTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAGTCCCATTTTTGACCCCGAACCT
*
950 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTTCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* * *
1009 TCCTAAAATTACCATTTTACCCCCCGAACTTCCAAAAGTCCCCTTTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* * ** *
1069 TCCTAAAATTACAATTTTACCCCCCGAACTTCCAAAA-TCCCATTTTT-ACCCTAAACTT
1 TCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* *
1127 TCCAAAAACTACCTTTTTACCCCCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA
1154 TGTTTGAAAT
Statistics
Matches: 183, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
57 8 0.04
58 22 0.12
59 50 0.27
60 103 0.56
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.30
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
Found at i:1112 original size:119 final size:119
Alignment explanation
Indices: 890--1150 Score: 339
Period size: 119 Copynumber: 2.2 Consensus size: 119
880 CCCTAAACTA
* **
890 TCCAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAAGTCTTATTTTTAACCCCGAACCTTCCA
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
* * *
954 AAAATTACCATTTTACCCCCGAACTTCCAAAAGTTCCATTTTTGACCCCGAACCT
66 AAAATTACAATTTTACCCCCGAACTTCCAAAAGTCCCATTTTT-ACCCCAAACCT
* * * * * *
1009 TCCTAAAATTACCATTTTACCCCCCGAACTTCC-AAAAGTCCCCTTTTTGACCTCGAACCTTCCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
* *
1073 AAAATTACAATTTTACCCCCCGAACTTCCAAAA-TCCCATTTTTACCCTAAACTT
66 AAAATTACAATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTACCCCAAACCT
* *
1127 TCCAAAAACTACCTTTTTACCCCC
1 TCCAAAAATTACCATTTTACCCCC
1151 GAATGTTTGA
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
118 29 0.24
119 66 0.54
120 28 0.23
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.31
Consensus pattern (119 bp):
TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
AAAATTACAATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTACCCCAAACCT
Found at i:11602 original size:29 final size:29
Alignment explanation
Indices: 11560--11828 Score: 151
Period size: 30 Copynumber: 9.1 Consensus size: 29
11550 CCCCGGAGGT
11560 CCCT-AAACTATCCAAAAATTACCATTTTA
1 CCCTCAAACT-TCCAAAAATTACCATTTTA
* *
11589 CCCTCAAACTTCCAAAAAGT-CTTATTTTTAA
1 CCCTCAAACTTCCAAAAATTAC-CA-TTTT-A
*
11620 CCC-CGAACCTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
11649 CCCCCGAACTTCCAAAAGTT-CCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A
* *
11679 CCC-CGAACCTTCCTAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * * ** *
11708 CCCCCCGAACTTCCAAAAGTCCCCTTTTTGA
1 -CCCTCAAACTTCCAAAAATTACCATTTT-A
* * *
11739 -CCTCGAACCTTCCTAAAATTACAATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
11768 CCCCCCGAACTTCC-AAAA-TCCCATTTTTA
1 -CCCTCAAACTTCCAAAAATTACCA-TTTTA
* *
11797 CCCT-AAACTTTCCAAAAACTACCTTTTTA
1 CCCTCAAAC-TTCCAAAAATTACCATTTTA
11826 CCC
1 CCC
11829 CCGAATGTTT
Statistics
Matches: 182, Mismatches: 37, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.02
28 14 0.08
29 61 0.34
30 77 0.42
31 26 0.14
32 1 0.01
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACCATTTTA
Found at i:11697 original size:59 final size:59
Alignment explanation
Indices: 11570--11833 Score: 343
Period size: 60 Copynumber: 4.5 Consensus size: 59
11560 CCCTAAACTA
* * ** *
11570 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAGTCTTATTTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAGTCCCATTTTTGACCCCGAACCT
*
11630 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTTCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* * *
11689 TCCTAAAATTACCATTTTACCCCCCGAACTTCCAAAAGTCCCCTTTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* * ** *
11749 TCCTAAAATTACAATTTTACCCCCCGAACTTCCAAAA-TCCCATTTTT-ACCCTAAACTT
1 TCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
* *
11807 TCCAAAAACTACCTTTTTACCCCCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA
11834 TGTTTGAAAT
Statistics
Matches: 183, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
57 8 0.04
58 22 0.12
59 50 0.27
60 103 0.56
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.30
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
Found at i:11792 original size:119 final size:119
Alignment explanation
Indices: 11570--11830 Score: 339
Period size: 119 Copynumber: 2.2 Consensus size: 119
11560 CCCTAAACTA
* **
11570 TCCAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAAGTCTTATTTTTAACCCCGAACCTTCCA
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
* * *
11634 AAAATTACCATTTTACCCCCGAACTTCCAAAAGTTCCATTTTTGACCCCGAACCT
66 AAAATTACAATTTTACCCCCGAACTTCCAAAAGTCCCATTTTT-ACCCCAAACCT
* * * * * *
11689 TCCTAAAATTACCATTTTACCCCCCGAACTTCC-AAAAGTCCCCTTTTTGACCTCGAACCTTCCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
* *
11753 AAAATTACAATTTTACCCCCCGAACTTCCAAAA-TCCCATTTTTACCCTAAACTT
66 AAAATTACAATTTTA-CCCCCGAACTTCCAAAAGTCCCATTTTTACCCCAAACCT
* *
11807 TCCAAAAACTACCTTTTTACCCCC
1 TCCAAAAATTACCATTTTACCCCC
11831 GAATGTTTGA
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
118 29 0.24
119 66 0.54
120 28 0.23
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.31
Consensus pattern (119 bp):
TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAAGTCCCATTTTTAACCCCGAACCTTCCA
AAAATTACAATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTACCCCAAACCT
Found at i:23640 original size:204 final size:201
Alignment explanation
Indices: 22929--23646 Score: 972
Period size: 201 Copynumber: 3.6 Consensus size: 201
22919 TCAAGCCTAC
** *
22929 GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCACG-CTGAAG
1 GCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTC-GAAG
*
22993 CAATAAAAGGTTAGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
65 CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
* * * * *
23058 ACAAAGAAGCGAGTTGAAATAAACGACGCAGTCATCTTCTTGATAAGACACTAAGGAGAAGACCC
130 ACAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGACCC
23123 AAACGAG
195 AAACGAG
* * *
23130 GCTCAAAGTGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGCCGAAGC
1 GCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
* *
23195 AATAAAAGGATAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATA
66 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* *
23260 TAGAGAAGCGAGTTGAAACAAACGACGCGGTCATCTTCTTGATGAGACACTGAGAAGAAGACCCA
131 CAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGACCCA
23325 AACGAG
196 AACGAG
* *
23331 GCTCAAAGTGAGCAAAATCTTTGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGC
1 GCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
* * * * * *
23396 AATAAAAAGGTTAGCTTCCTGACGAGGTACTGAGAAGTGAATCGAATTCGTCCTCCGGATGAGAT
66 AAT-AAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
* * * * * * * * *
23461 ACGGAGGAGTGAATTGAAACAAACAGCAATGTAATCATCTTCCTGATGAGGCACTGAGAAGAAGA
130 ACAGAGAAGCGAGTTGAAACAAAC-G--ACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGA
23526 CCCAAACGAG
192 CCCAAACGAG
** * * * *
23536 GCTCAAAACGAGC-ACATCTTCGAGCCCCAACTTCCTGATGAGACGCTGAGAAGCAGGTCGAAGC
1 GCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
* * * * *
23600 CATAAAGTGGTTAGCTCCCTGATAAGATACCGAGAAGTGAACCAAAT
66 AATAAA-AGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAAT
23647 CCTGATGAAA
Statistics
Matches: 457, Mismatches: 54, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
201 249 0.54
202 73 0.16
203 4 0.01
204 79 0.17
205 52 0.11
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (201 bp):
GCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCTTGATGAGACACTGAGAAGAAGACCCA
AACGAG
Found at i:24081 original size:17 final size:17
Alignment explanation
Indices: 24059--24146 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
24049 CATACTCCCT
24059 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
24076 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
*
24093 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
24111 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
24128 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
24145 TT
1 TT
24147 TAAAATTTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
17 44 0.76
18 14 0.24
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:24099 original size:6 final size:6
Alignment explanation
Indices: 24090--24157 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
24080 ATTTGTTTAA
* * *
24090 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
24136 -ATTTT CAAATTT AAAATTT AAA
1 AAATTT -AAATTT -AAATTT AAA
24158 ATAAACAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 12 0.24
6 27 0.55
7 10 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:24109 original size:11 final size:11
Alignment explanation
Indices: 24093--24148 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
24083 TGTTTAAAAA
24093 TTTAAATTTAT
1 TTTAAATTTAT
*
24104 TTTAAATTTAAA
1 TTTAAATTT-AT
*
24116 TTT-AATTTAAG
1 TTTAAATTT-AT
*
24127 TTTAAAATTAT
1 TTTAAATTTAT
24138 TTTCAAATTTA
1 TTT-AAATTTA
24149 AAATTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:24135 original size:35 final size:35
Alignment explanation
Indices: 24058--24156 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
24048 CCATACTCCC
* *
24058 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAAA
*
24093 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
*
24127 TTTAAAATTATTTTCAAATTTAAAATTTAA
1 TTTAAATTTATTTT-AAATTT-AAATTTAA
24157 AATAAACAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 15 0.26
35 31 0.54
36 11 0.19
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
Found at i:24898 original size:7 final size:7
Alignment explanation
Indices: 24876--24919 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
24866 TCGATATCAA
24876 TAATAA-
1 TAATAAT
24882 TAAT-AT
1 TAATAAT
24888 TAATAAT
1 TAATAAT
24895 TAATAAT
1 TAATAAT
*
24902 TATTAAT
1 TAATAAT
*
24909 TATTAAT
1 TAATAAT
24916 TAAT
1 TAAT
24920 TAAAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 1 0.03
6 8 0.24
7 25 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TAATAAT
Found at i:26033 original size:162 final size:162
Alignment explanation
Indices: 25761--26083 Score: 470
Period size: 162 Copynumber: 2.0 Consensus size: 162
25751 CCCTTCGACC
* * * * *
25761 TTTTAAAAGCACCAAGAGCCGCCACGTGTCCTGATTTTGGCTTATTTGTGCTAATGGTCCCTTTT
1 TTTTAAAAGCACCAAGAGCCACCACGTGTCATGATTTTGGCTTATTTATGCAAATGGTCCCCTTT
** * * * *
25826 GTTTCTAATTTGTTTTAATTTAATCCTTAAATCAGGTTTGCTTTAATTACAAAATGGCCTCAAAA
66 ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATGACCCCAAAA
*
25891 ATTTTCCA-TGATTTTCAAAATAGTCCTCTGAT
131 ATTTT-CATTGATTTTCAAAAGAGTCCTCTGAT
*
25923 TTTTAAAAGCACC-AGTAGCTACCACGTGTCATGATTTTGGCTTATTTATGCAAATGGTCCCCTT
1 TTTTAAAAGCACCAAG-AGCCACCACGTGTCATGATTTTGGCTTATTTATGCAAATGGTCCCCTT
* *
25987 TACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATTACCCCAGA
65 TACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATGACCCCAAA
*
26052 AATTTTCATTGGTTTTCAAAAGAGTCCTCTGA
130 AATTTTCATTGATTTTCAAAAGAGTCCTCTGA
26084 CTTCCGAACG
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
161 4 0.03
162 139 0.97
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (162 bp):
TTTTAAAAGCACCAAGAGCCACCACGTGTCATGATTTTGGCTTATTTATGCAAATGGTCCCCTTT
ACTTCCAATTTGTTTTAATTTAATCCTTAAATCAGGTTCGCTTTAATTACAAAATGACCCCAAAA
ATTTTCATTGATTTTCAAAAGAGTCCTCTGAT
Found at i:26401 original size:30 final size:29
Alignment explanation
Indices: 26169--26402 Score: 172
Period size: 30 Copynumber: 7.8 Consensus size: 29
26159 AAATTTACCA
*
26169 TTTTACCCTCGAA-CTTCCAAAAGTCCCAT
1 TTTTACCCT-GAACCTTCCAAAAATCCCAT
* *
26198 TTTTGACCCTGAACCTTCCTAAAATTACCA-
1 TTTT-ACCCTGAACCTTCC-AAAAATCCCAT
* * *
26228 TTTTACCCCTCAAACTTCAAAAAATCCCAT
1 TTTTA-CCCTGAACCTTCCAAAAATCCCAT
* * *
26258 TTTTGACCCCGAACCTTTCAAAAATTACCA-
1 TTTT-ACCCTGAACCTTCCAAAAA-TCCCAT
* *
26288 TTTTACCCCCT-AAACTTCCAAAAGTCCCAT
1 TTTTA--CCCTGAACCTTCCAAAAATCCCAT
* * *
26318 TTTTAACCCCGAACCTTCCTAAAATTACCA-
1 TTTT-ACCCTGAACCTTCC-AAAAATCCCAT
** *
26348 TTTTACCCCCCAAACTTCCAAAAATCCCAT
1 TTTTA-CCCTGAACCTTCCAAAAATCCCAT
26378 TTTTGACCCTGAACCTTCCAAAAAT
1 TTTT-ACCCTGAACCTTCCAAAAAT
26403 TACCCTTTTA
Statistics
Matches: 160, Mismatches: 29, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
29 33 0.21
30 101 0.63
31 26 0.16
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.30
Consensus pattern (29 bp):
TTTTACCCTGAACCTTCCAAAAATCCCAT
Found at i:26417 original size:60 final size:60
Alignment explanation
Indices: 26155--26417 Score: 384
Period size: 60 Copynumber: 4.4 Consensus size: 60
26145 CCCTAAACTA
* * * * *
26155 TCCAAAATTTACCATTTTA-CCCTCGAACTTCCAAAAGTCCCATTTTTGACCCTGAACCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
26214 TCCTAAAATTACCATTTTACCCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
26274 TTCAAAAATTACCATTTTACCCCCTAAACTTCCAAAAGTCCCATTTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
26334 TCCTAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGAACCT
1 TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*
26394 TCCAAAAATTACCCTTTTACCCCC
1 TCCAAAAATTACCATTTTACCCCC
26418 GAATGTTTGA
Statistics
Matches: 182, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
59 17 0.09
60 165 0.91
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (60 bp):
TCCAAAAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:26443 original size:120 final size:120
Alignment explanation
Indices: 26155--26420 Score: 435
Period size: 120 Copynumber: 2.2 Consensus size: 120
26145 CCCTAAACTA
* * * *
26155 TCCAAAATTTACCATTTTACCCTCG-AACTTCCAAAAGTCCCATTTTTGACCCTGAACCTTCCTA
1 TCCAAAAATTACCATTTTACCCCCGAAACTTCCAAAAGTCCCATTTTTAACCCCGAACCTTCCTA
*
26219 AAATTACCATTTTACCCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAACCT
66 AAATTACCATTTTACCCCCCAAACTTCAAAAAATCCCATTTTTGACCCCGAACCT
* *
26274 TTCAAAAATTACCATTTTACCCCCTAAACTTCCAAAAGTCCCATTTTTAACCCCGAACCTTCCTA
1 TCCAAAAATTACCATTTTACCCCCGAAACTTCCAAAAGTCCCATTTTTAACCCCGAACCTTCCTA
* *
26339 AAATTACCATTTTACCCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGAACCT
66 AAATTACCATTTTACCCCCCAAACTTCAAAAAATCCCATTTTTGACCCCGAACCT
*
26394 TCCAAAAATTACCCTTTTACCCCCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA
26421 TGTTTGAAAT
Statistics
Matches: 134, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 21 0.16
120 113 0.84
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (120 bp):
TCCAAAAATTACCATTTTACCCCCGAAACTTCCAAAAGTCCCATTTTTAACCCCGAACCTTCCTA
AAATTACCATTTTACCCCCCAAACTTCAAAAAATCCCATTTTTGACCCCGAACCT
Done.