Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004816.1 Kokia drynarioides strain JFW-HI SEQ_118449, 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: 48056
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:98 original size:24 final size:21
Alignment explanation
Indices: 71--134 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
61 CATTTGGCTT
71 TAATATATATATATTTCATTAATA
1 TAATA-ATATATATTT-ATTAA-A
*
95 TAATAAGATAATATTTATTAAA
1 TAATAATAT-ATATTTATTAAA
*
117 TAATAATTTATA-TTATTA
1 TAATAATATATATTTATTA
135 TATTTTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.17
21 3 0.08
22 8 0.22
23 8 0.22
24 11 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATAATATATATTTATTAAA
Found at i:2064 original size:111 final size:112
Alignment explanation
Indices: 1780--2097 Score: 451
Period size: 113 Copynumber: 2.8 Consensus size: 112
1770 ACATAAATAC
* * *
1780 TTTT-AAATTGAGGTAATATTCTTTTGTGTGGAAACTTCAAAGAATTGTGCCCTAACGTGTTGGA
1 TTTTAAAATCGAGGTAATATTCTTTTGTGTGGAAACTTCGAAGAATTGTGCCCTAACGTGTTGGG
* *
1844 TGTGATTTTTGTAGAATTTACACAATCGATTATCCTCCCTCAATTTTT
66 TGTGATTTTTGTAGAATTTGCACAATCGATTATCCTCCCTCAA-TTTA
** *
1892 TTTTAAAATCGAGACAATATTCTTTTGTGTGGAAACTTCGAAGAATTGTGCCCTAATGTGTTGGG
1 TTTTAAAATCGAGGTAATATTCTTTTGTGTGGAAACTTCGAAGAATTGTGCCCTAACGTGTTGGG
* * *
1957 TGTGATTTTTGTAGAATTTGTACAATCGATTATCCTCTCTTAA-TTA
66 TGTGATTTTTGTAGAATTTGCACAATCGATTATCCTCCCTCAATTTA
* * * *
2003 TTTTAAAATCGAGGTAATATCCTTTTGTGTGAAAACTTCGAAGAATTGTGCCTTAACGTGTTCGG
1 TTTTAAAATCGAGGTAATATTCTTTTGTGTGGAAACTTCGAAGAATTGTGCCCTAACGTGTTGGG
*
2068 TGTGATTTTTTTGTAGAATTTGCATAATCG
66 TGTGA--TTTTTGTAGAATTTGCACAATCG
2098 TATATGTTCC
Statistics
Matches: 183, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
111 65 0.36
112 4 0.02
113 114 0.62
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (112 bp):
TTTTAAAATCGAGGTAATATTCTTTTGTGTGGAAACTTCGAAGAATTGTGCCCTAACGTGTTGGG
TGTGATTTTTGTAGAATTTGCACAATCGATTATCCTCCCTCAATTTA
Found at i:6203 original size:29 final size:28
Alignment explanation
Indices: 6171--6235 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
6161 AATTTGTGAG
*
6171 AATTAAAAAAATTTAAAA-TTCGTATATAA
1 AATTAAAAAAA-TCAAAATTTC-TATATAA
**
6200 AATTACACGAAATCAAAATTTCTATATAA
1 AATTA-AAAAAATCAAAATTTCTATATAA
6229 AATTAAA
1 AATTAAA
6236 TATTAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 7 0.23
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (28 bp):
AATTAAAAAAATCAAAATTTCTATATAA
Found at i:7180 original size:8 final size:8
Alignment explanation
Indices: 7155--7194 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
7145 TAAAATTGTT
7155 AATTA-AA
1 AATTATAA
7162 AATTATAAA
1 AATTAT-AA
7171 AATTATAA
1 AATTATAA
7179 AATTATAA
1 AATTATAA
7187 AATTATAA
1 AATTATAA
7195 GATTTACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 5 0.16
8 18 0.58
9 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTATAA
Found at i:7526 original size:20 final size:20
Alignment explanation
Indices: 7501--7557 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
7491 CTAATAATTT
7501 TTTTGTTTTTATTTTTTTCA
1 TTTTGTTTTTATTTTTTTCA
**
7521 TTTTGTTTGAATTTTTTTCA
1 TTTTGTTTTTATTTTTTTCA
*
7541 TTTTCTTTTTAATTTTT
1 TTTTGTTTTT-ATTTTT
7558 AATTAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTGTTTTTATTTTTTTCA
Found at i:8730 original size:41 final size:42
Alignment explanation
Indices: 8685--8767 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 42
8675 TGGAGTTCAC
*
8685 CATCAG-TTCCATTACTTCTAGCTTGCCACACGCAAACACAT
1 CATCAGCTTCCATTACTTCTAGCTTGCCACACACAAACACAT
8726 CATCAGCCTTCCATTACTTCTAGCTTGCCACACACAAACACA
1 CATCAG-CTTCCATTACTTCTAGCTTGCCACACACAAACACA
8768 CTATTTTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 6 0.15
43 33 0.85
ACGTcount: A:0.30, C:0.36, G:0.08, T:0.25
Consensus pattern (42 bp):
CATCAGCTTCCATTACTTCTAGCTTGCCACACACAAACACAT
Found at i:9197 original size:28 final size:28
Alignment explanation
Indices: 9129--9199 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
9119 CTTTACATCC
*
9129 GCCACAAAAGCATCCTTTAACAGAGATA
1 GCCACAAAAGCTTCCTTTAACAGAGATA
* ** * *
9157 ACCATGAATGCTTCCTTTAACAGAGTTA
1 GCCACAAAAGCTTCCTTTAACAGAGATA
*
9185 GCCACAAAGGCTTCC
1 GCCACAAAAGCTTCC
9200 CTTTTAGTAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (28 bp):
GCCACAAAAGCTTCCTTTAACAGAGATA
Found at i:9255 original size:31 final size:30
Alignment explanation
Indices: 9172--9256 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
9162 GAATGCTTCC
*
9172 TTTAACAGAGTTAGCCACAAAGGCTTCCCT
1 TTTAACAGAGTTATCCACAAAGGCTTCCCT
** * * *
9202 TTTAGTATAGATATCCATAAAGGCTTCCCTT
1 TTTAACAGAGTTATCCACAAAGGCTTCCC-T
*
9233 TTTAACAGAGTTTTCCACAAAGGC
1 TTTAACAGAGTTATCCACAAAGGC
9257 CTTCTTACAA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 23 0.55
31 19 0.45
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTAACAGAGTTATCCACAAAGGCTTCCCT
Found at i:10837 original size:51 final size:52
Alignment explanation
Indices: 10753--10853 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
10743 TGTTCTTTAC
10753 ATCTTCTTCCATATGATACCATAACCCTTTTGGCTAGGTCTTACACGATAAG
1 ATCTTCTTCCATATGATACCATAACCCTTTTGGCTAGGTCTTACACGATAAG
* *
10805 ATCTTC-TCCATATGATGCCATAA-CCTTCTTGGCTAGGTCTTATACGATA
1 ATCTTCTTCCATATGATACCATAACCCTT-TTGGCTAGGTCTTACACGATA
10854 TCGTATTCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 4 0.09
51 36 0.78
52 6 0.13
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
ATCTTCTTCCATATGATACCATAACCCTTTTGGCTAGGTCTTACACGATAAG
Found at i:13223 original size:23 final size:23
Alignment explanation
Indices: 13193--13238 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
13183 TTGCTTTTTT
13193 TTATGTTTCACAATCACAAACTA
1 TTATGTTTCACAATCACAAACTA
13216 TTATGTTTCACAATCACAAACTA
1 TTATGTTTCACAATCACAAACTA
13239 ATTACTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (23 bp):
TTATGTTTCACAATCACAAACTA
Found at i:14178 original size:39 final size:39
Alignment explanation
Indices: 14130--14252 Score: 122
Period size: 39 Copynumber: 3.1 Consensus size: 39
14120 TTTATAACCT
*
14130 AATATTCAAAGTCCTATTGGAAACCCAACTTTGTATCAA
1 AATATTCAAAGTCCTATTGGAAACCCAACTTTGTAACAA
* * * * ** *
14169 AATACTCAAATTCCTAATGAAAAAACATAACATTT-TAACCA
1 AATATTCAAAGTCCTATTG--GAAACCCAAC-TTTGTAACAA
* *
14210 AATATTCAAAGTCCTATTGGAAGCCCAACTTTGTAACTA
1 AATATTCAAAGTCCTATTGGAAACCCAACTTTGTAACAA
14249 AATA
1 AATA
14253 ATTTGTAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
38 3 0.05
39 31 0.48
41 27 0.42
42 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (39 bp):
AATATTCAAAGTCCTATTGGAAACCCAACTTTGTAACAA
Found at i:14224 original size:80 final size:78
Alignment explanation
Indices: 14093--14244 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 78
14083 CTATAACTAT
* * * *
14093 TACTCAAATTCCTAGTGAAAGCATAATTTTATAACCTAATATTCAAAGTCCTATTGGAAACCCAA
1 TACTCAAATTCCTAATGAAAACATAAATTTATAACCAAATATTCAAAGTCCTATTGGAAACCCAA
14158 CTTTGTATCAAAA
66 CTTTGTATCAAAA
*
14171 TACTCAAATTCCTAATGAAAAAACATAACATTT-TAACCAAATATTCAAAGTCCTATTGGAAGCC
1 TACTCAAATTCCTAATG--AAAACATAA-ATTTATAACCAAATATTCAAAGTCCTATTGGAAACC
14235 CAACTTTGTA
63 CAACTTTGTA
14245 ACTAAATAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
78 16 0.24
80 47 0.71
81 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (78 bp):
TACTCAAATTCCTAATGAAAACATAAATTTATAACCAAATATTCAAAGTCCTATTGGAAACCCAA
CTTTGTATCAAAA
Found at i:15937 original size:43 final size:43
Alignment explanation
Indices: 15850--15948 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
15840 ATGCCGCTAT
* * *
15850 AGAATATGGTCTTTAGCGGTGCTTTTCCAACAAACGCCACTAA
1 AGAACATGGTCTTTAGCAGCGCTTTTCCAACAAACGCCACTAA
* * **
15893 AGAACGTGGTCTTTAGCAGCGCTTTTCCAACAAACGTCGTTAA
1 AGAACATGGTCTTTAGCAGCGCTTTTCCAACAAACGCCACTAA
*
15936 AGAATATGGTCTT
1 AGAACATGGTCTT
15949 AAATTTAACT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCAGCGCTTTTCCAACAAACGCCACTAA
Found at i:18639 original size:18 final size:18
Alignment explanation
Indices: 18608--18642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18598 ATATAATATG
**
18608 CGATCACATGATCAGATA
1 CGATCACAAAATCAGATA
18626 CGATCACAAAATCAGAT
1 CGATCACAAAATCAGAT
18643 GCAGTCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (18 bp):
CGATCACAAAATCAGATA
Found at i:21483 original size:136 final size:136
Alignment explanation
Indices: 21239--21509 Score: 384
Period size: 136 Copynumber: 2.0 Consensus size: 136
21229 GCTACCATGG
* * * * *
21239 AAGCTTGAGTTTCGGAGAAAGGTGATCTGACGAGCAAAGGAGCAAGACTTTTGACGAGAAGGGCC
1 AAGCTTGAGTTTCAGAGAAAGGTGATCTGACGAGCAAAGAAGAAAGACTTCTAACGAGAAGGGCC
* * * *
21304 TATTTACGGCATAGGAGGAACTGTCATGGAATAGTTCTAGTAAACTAGGAATAGGATGCTTTGAC
66 TATCTACCGCATAGGAGGAACTGTCATGGAATAGTTCTAGTAAACCAGGAATAGGATGCTTCGAC
21369 TTTTTA
131 TTTTTA
* * *
21375 AAGCTTGAGTTTCAGAGGAAGGTGATCTGACGAGCAAAGAAGAAAGACTTCTAATGAGAAGTGCC
1 AAGCTTGAGTTTCAGAGAAAGGTGATCTGACGAGCAAAGAAGAAAGACTTCTAACGAGAAGGGCC
* *
21440 TATCTACAACGCA-A-GAGGAGCTGTCATGGAATAGTTCTAGTAAACCAGGAATTGGATGCTTCG
66 TATCTAC--CGCATAGGAGGAACTGTCATGGAATAGTTCTAGTAAACCAGGAATAGGATGCTTCG
21503 ACTTTTT
129 ACTTTTT
21510 TTTTTGATAC
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
136 115 0.97
137 1 0.01
138 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (136 bp):
AAGCTTGAGTTTCAGAGAAAGGTGATCTGACGAGCAAAGAAGAAAGACTTCTAACGAGAAGGGCC
TATCTACCGCATAGGAGGAACTGTCATGGAATAGTTCTAGTAAACCAGGAATAGGATGCTTCGAC
TTTTTA
Found at i:26687 original size:52 final size:52
Alignment explanation
Indices: 26604--26779 Score: 226
Period size: 52 Copynumber: 3.4 Consensus size: 52
26594 TCTTGTTCTG
* * *
26604 TCACTATGACACATAGTTATCGGACCTCATAATCCTTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATAC
* * * * *
26656 TCATGATGACACATAGTCATCGGACCTCATAACCCGTAAAGGATTCATTTTC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATAC
* * *
26708 TCACGATGACACGTAGTCATCAGACCTTATAATCCATAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATAC
* * *
26760 TTACAATGACACATTGTCAT
1 TCACGATGACACATAGTCAT
26780 TAGACCTTAG
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATAC
Found at i:29978 original size:34 final size:34
Alignment explanation
Indices: 29940--30014 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
29930 CTATTAGTTT
*
29940 TAATTAAATAATTAAATATTTGGGTTGTTTTAAA
1 TAATTAAATAATTAAATATTTGAGTTGTTTTAAA
*
29974 TAATTAAATAATTAAATATTTGAGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGAGTTGTTTTAAA
30008 TAATTAA
1 TAATTAA
30015 TTATTTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (34 bp):
TAATTAAATAATTAAATATTTGAGTTGTTTTAAA
Found at i:31071 original size:24 final size:25
Alignment explanation
Indices: 31025--31076 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
31015 TAAAAGAAGC
* *
31025 AGAACCAGAAGCAGATGCGGAT-GT
1 AGAACCAGAAGCAGAAGCAGATGGT
* *
31049 AGAAGCAGAAGTAGAAGCAGATGGT
1 AGAACCAGAAGCAGAAGCAGATGGT
31074 AGA
1 AGA
31077 GTCCTTGCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.12
Consensus pattern (25 bp):
AGAACCAGAAGCAGAAGCAGATGGT
Found at i:37276 original size:14 final size:14
Alignment explanation
Indices: 37241--37276 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
37231 CATTTTTACA
*
37241 TTTACTTTTACTTT
1 TTTACTTTTACTTG
37255 TTTACTTTTACTTG
1 TTTACTTTTACTTG
*
37269 TTTCCTTT
1 TTTACTTT
37277 AAATCTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.17, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTACTTTTACTTG
Found at i:39719 original size:52 final size:52
Alignment explanation
Indices: 39633--39968 Score: 451
Period size: 52 Copynumber: 6.5 Consensus size: 52
39623 AATGAAAAAG
* * * * *
39633 GGTCTGATGACTAAGTGTCATCATGAGTATATGAATCTTTTATGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
** *
39685 GGTTTGATGAATAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* *
39737 GATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT-TGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* *
39788 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * **
39840 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTGCGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* ** *
39892 GGTCCGATGACTAAGTGTCATCGTGAGTACATGAATTCCTTTACGGAACAAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTATGA
*
39945 GGTCCGATTACTATA-TGTCATCGT
1 GGTCCGATGACTA-AGTGTCATCGT
39969 AAGTGTTAAA
Statistics
Matches: 252, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
51 48 0.19
52 170 0.67
53 33 0.13
54 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
Found at i:39822 original size:103 final size:104
Alignment explanation
Indices: 39638--39938 Score: 469
Period size: 103 Copynumber: 2.9 Consensus size: 104
39628 AAAAGGGTCT
* * ** *
39638 GATGACTAAGTGTCATCATGAGTATATGAATCTTTTATGGATTATGAGGTTTGATGAATAAGTGT
1 GATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTATGAGGTCCGATGACTAAGTGT
*
39703 CATCGTGAGTAAATGAATCCTTTACGGATTATGAGATCC
66 CATCGTGAGTAAATGAATCCTTTACGGATTATAAGATCC
* *
39742 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT-TGAGGTCCGATGACTAAGTGT
1 GATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTATGAGGTCCGATGACTAAGTGT
* *
39806 CATCGTGAGTAAATGAATCCTTTACAGATTATAAGGTCC
66 CATCGTGAGTAAATGAATCCTTTACGGATTATAAGATCC
**
39845 GATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTGCGAGGTCCGATGACTAAGTGT
1 GATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTATGAGGTCCGATGACTAAGTGT
*
39910 CATCGTGAGTACATGAATTCCTTTACGGA
66 CATCGTGAGTAAATGAA-TCCTTTACGGA
39939 ACAAGAGGTC
Statistics
Matches: 180, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
103 95 0.53
104 75 0.42
105 10 0.06
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (104 bp):
GATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTATGAGGTCCGATGACTAAGTGT
CATCGTGAGTAAATGAATCCTTTACGGATTATAAGATCC
Found at i:39871 original size:155 final size:156
Alignment explanation
Indices: 39633--39934 Score: 453
Period size: 155 Copynumber: 1.9 Consensus size: 156
39623 AATGAAAAAG
* * * ** * **
39633 GGTCTGATGACTAAGTGTCATCATGAGTATATGAATCTTTTATGGATTATGAGGTTTGATGAATA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACAGATTATAAGGTCCGATGAATA
* *
39698 AGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGATCCGATGACTAAGTGTCATCGTGA
66 AGTGTCATCATGAGTAAATGAATCCTTTACGGATTACGAGATCCGATGACTAAGTGTCATCGTGA
39763 GTAAATGAA-TCCTTTAAGGATTTGA
131 GTAAATGAATTCCTTTAAGGATTTGA
* *
39788 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATAAGGTCCGATGACTA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACAGATTATAAGGTCCGATGAATA
* * *
39853 AGTGTCATCATGAGTAAATGAATCCTTTATGGATTGCGAGGTCCGATGACTAAGTGTCATCGTGA
66 AGTGTCATCATGAGTAAATGAATCCTTTACGGATTACGAGATCCGATGACTAAGTGTCATCGTGA
*
39918 GTACATGAATTCCTTTA
131 GTAAATGAATTCCTTTA
39935 CGGAACAAGA
Statistics
Matches: 130, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
155 123 0.95
156 7 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (156 bp):
GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACAGATTATAAGGTCCGATGAATA
AGTGTCATCATGAGTAAATGAATCCTTTACGGATTACGAGATCCGATGACTAAGTGTCATCGTGA
GTAAATGAATTCCTTTAAGGATTTGA
Found at i:40512 original size:21 final size:21
Alignment explanation
Indices: 40486--40532 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
40476 TCTGCATACT
40486 TGTTTCGGTAGAACTCATGTA
1 TGTTTCGGTAGAACTCATGTA
40507 TGTTTCGGTAGAACTCATGTA
1 TGTTTCGGTAGAACTCATGTA
40528 TGTTT
1 TGTTT
40533 TGATAGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (21 bp):
TGTTTCGGTAGAACTCATGTA
Found at i:40539 original size:21 final size:21
Alignment explanation
Indices: 40486--40540 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
40476 TCTGCATACT
*
40486 TGTTTCGGTAGAACTCATGTA
1 TGTTTCGATAGAACTCATGTA
*
40507 TGTTTCGGTAGAACTCATGTA
1 TGTTTCGATAGAACTCATGTA
*
40528 TGTTTTGATAGAA
1 TGTTTCGATAGAA
40541 GTACAGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (21 bp):
TGTTTCGATAGAACTCATGTA
Found at i:40931 original size:14 final size:15
Alignment explanation
Indices: 40905--40934 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
40895 TATAATATAA
40905 TGATAAGATGAACAG
1 TGATAAGATGAACAG
40920 TGATAA-ATGAACAG
1 TGATAAGATGAACAG
40934 T
1 T
40935 AAAACACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (15 bp):
TGATAAGATGAACAG
Found at i:46619 original size:17 final size:18
Alignment explanation
Indices: 46597--46630 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46587 TTGCTTATAA
46597 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
46614 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
46631 AAATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Done.