Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004291.1 Kokia drynarioides strain JFW-HI SEQ_117591, 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: 168746
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8232 original size:34 final size:34
Alignment explanation
Indices: 8189--8256 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
8179 TGGAAATATG
**
8189 TATATTTTGGTTGCTGTTGACTATGTTTCAAAAT
1 TATATTTTGGTCACTGTTGACTATGTTTCAAAAT
8223 TATATTTTGGTCACTGTTGACTATGTTTCAAAAT
1 TATATTTTGGTCACTGTTGACTATGTTTCAAAAT
8257 GGATCGAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (34 bp):
TATATTTTGGTCACTGTTGACTATGTTTCAAAAT
Found at i:10837 original size:15 final size:15
Alignment explanation
Indices: 10817--10860 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
10807 GTATTGAAGC
10817 AGAAGAAGAGAAAAG
1 AGAAGAAGAGAAAAG
10832 AGAAGAAGAAGGAAAAG
1 AGAAGAAG-A-GAAAAG
*
10849 AAAAGAAG-GAAA
1 AGAAGAAGAGAAA
10861 TAGAAGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 1 0.04
17 13 0.50
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAGAAAAG
Found at i:10856 original size:14 final size:16
Alignment explanation
Indices: 10817--10866 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
10807 GTATTGAAGC
* *
10817 AGAAGAAG-AGAAAAG
1 AGAAGAAGAAGGAAAT
10832 AGAAGAAGAAGGAAA-
1 AGAAGAAGAAGGAAAT
10847 AGAA-AAGAAGGAAAT
1 AGAAGAAGAAGGAAAT
10862 AGAAG
1 AGAAG
10867 TTGCCTCGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 10 0.32
15 16 0.52
16 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (16 bp):
AGAAGAAGAAGGAAAT
Found at i:13425 original size:23 final size:24
Alignment explanation
Indices: 13392--13440 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
13382 ACAATCAATT
* *
13392 CATTTTCTATTA-ATTTGCTCTGA
1 CATTTTATATTATATTTGCACTGA
*
13415 CATTTTATATTATATTTTCACTGA
1 CATTTTATATTATATTTGCACTGA
13439 CA
1 CA
13441 GATTTAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (24 bp):
CATTTTATATTATATTTGCACTGA
Found at i:20596 original size:17 final size:17
Alignment explanation
Indices: 20576--20619 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
20566 AAATGAACTA
*
20576 ACAAGTAAAATGCAGTG
1 ACAAATAAAATGCAGTG
20593 ACAAATAAAAATGCAGTG
1 ACAAAT-AAAATGCAGTG
*
20611 ACAACTAAA
1 ACAAATAAA
20620 TGAGAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (17 bp):
ACAAATAAAATGCAGTG
Found at i:20605 original size:18 final size:18
Alignment explanation
Indices: 20582--20619 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
20572 ACTAACAAGT
20582 AAAATGCAGTGACAAATA
1 AAAATGCAGTGACAAATA
*
20600 AAAATGCAGTGACAACTA
1 AAAATGCAGTGACAAATA
20618 AA
1 AA
20620 TGAGAAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (18 bp):
AAAATGCAGTGACAAATA
Found at i:33921 original size:20 final size:20
Alignment explanation
Indices: 33898--33936 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33888 ATTTTGACAA
*
33898 GTTAAAAGAATTTTTACTTT
1 GTTAAAAGAATTTTAACTTT
*
33918 GTTAAAAGTATTTTAACTT
1 GTTAAAAGAATTTTAACTT
33937 GATTTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
GTTAAAAGAATTTTAACTTT
Found at i:38066 original size:3 final size:3
Alignment explanation
Indices: 38058--38094 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38048 CCCACAAGTT
38058 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38095 ATTTTTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42113 original size:13 final size:13
Alignment explanation
Indices: 42097--42122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42087 TCAACATGTT
42097 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
42110 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
42123 CAGGTCGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:42135 original size:12 final size:12
Alignment explanation
Indices: 42117--42151 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42107 CAATGGTCAA
42117 AGTCAACAGGTC
1 AGTCAACAGGTC
* *
42129 GGTCAACGGGTC
1 AGTCAACAGGTC
42141 AGTCAACAGGT
1 AGTCAACAGGT
42152 TTGGTCAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (12 bp):
AGTCAACAGGTC
Found at i:47833 original size:29 final size:29
Alignment explanation
Indices: 47800--47890 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
47790 TCCCTTTGCC
* * * **
47800 ATAGATAGCGATAGAGGCGTCCTTGAACA
1 ATAGATAGCAACAAAGGCGTCCTCAAACA
47829 ATAGATAGCAACAAAGGCGTCCTCAAACA
1 ATAGATAGCAACAAAGGCGTCCTCAAACA
* * ***
47858 TTAGATAGCCACAAAGATTTCCTCAAACA
1 ATAGATAGCAACAAAGGCGTCCTCAAACA
47887 ATAG
1 ATAG
47891 TTATCCAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (29 bp):
ATAGATAGCAACAAAGGCGTCCTCAAACA
Found at i:48011 original size:28 final size:28
Alignment explanation
Indices: 47980--48048 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
47970 AAAGATAGCA
47980 ACAAAGGCTCTATTTAACAGAATCAACC
1 ACAAAGGCTCTATTTAACAGAATCAACC
* * ***
48008 ACAAAGGCT-TACTTTAATAGATTTTCCC
1 ACAAAGGCTCTA-TTTAACAGAATCAACC
48036 ACAAAGGCTCTAT
1 ACAAAGGCTCTAT
48049 CACATCCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (28 bp):
ACAAAGGCTCTATTTAACAGAATCAACC
Found at i:52065 original size:21 final size:21
Alignment explanation
Indices: 52041--52081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52031 CTATTATTTC
*
52041 AAATTATATTTGA-ATTTAAAG
1 AAATTA-AATTGATATTTAAAG
52062 AAATTAAATTGATATTTAAA
1 AAATTAAATTGATATTTAAA
52082 TATTGTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTAAATTGATATTTAAAG
Found at i:52777 original size:37 final size:37
Alignment explanation
Indices: 52729--52823 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
52719 TGAGATTTGA
* *
52729 TTGCATGTTAAACATGCCCAACATGATATTATTCAAT
1 TTGCATGTTAAACATGCCCAACATAATATTATCCAAT
* *
52766 TTGCATGTTAAACATGCCCTACATAATATTATCCGAT
1 TTGCATGTTAAACATGCCCAACATAATATTATCCAAT
* * *
52803 TTTCATGTTCAACAAGCCCAA
1 TTGCATGTTAAACATGCCCAA
52824 TGTGACAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (37 bp):
TTGCATGTTAAACATGCCCAACATAATATTATCCAAT
Found at i:53813 original size:28 final size:28
Alignment explanation
Indices: 53735--53806 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
53725 GTGTTACAGT
* * * *
53735 CTCACTTCAACAGATTCAACCAACAAGA
1 CTCACTTTAACAGATTCAGCTACCAAGA
53763 CTCACTTTAACAGATTCAGCTACCAAGA
1 CTCACTTTAACAGATTCAGCTACCAAGA
53791 CTCACTTTAACAGATT
1 CTCACTTTAACAGATT
53807 ATGCTACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.25
Consensus pattern (28 bp):
CTCACTTTAACAGATTCAGCTACCAAGA
Found at i:54001 original size:54 final size:54
Alignment explanation
Indices: 53933--54236 Score: 387
Period size: 54 Copynumber: 5.6 Consensus size: 54
53923 CTTCTTCCAC
* * *
53933 ATGACGCCATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCAT
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCTTTCCCCAT
* ** *
53987 ATGATGCCATAGCCACCAAACTAGGTCACACATTATATGGTCTTCTTTCCCCAT
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCTTTCCCCAT
* * * *
54041 ATGATGCCATAGCCACCAAACTAGGTCATACATTATATGGTCTTCTTTCCTCAT
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCTTTCCCCAT
* * * ** *
54095 ATGATGACATAGCCACAAAACTACATCTTACACTATATGGTCTTCAATCCCTAT
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCTTTCCCCAT
* * *
54149 ATGATGCCATAGCCACTAGACTACGTCTTACACTATATGGTCTT-TGATCCCCAT
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCT-TTCCCCAT
* *
54203 ATGGTG-CATAGCCACCAGACTACGTCTTACACTA
1 ATGATGCCATAGCCACCAAACTACGTCTTACACTA
54237 GTCATCGATT
Statistics
Matches: 224, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
53 27 0.12
54 197 0.88
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (54 bp):
ATGATGCCATAGCCACCAAACTACGTCTTACACTATATGGTCTTCTTTCCCCAT
Found at i:68737 original size:3 final size:3
Alignment explanation
Indices: 68729--68765 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
68719 GGGCTCATAT
68729 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
68766 AACCTAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:73676 original size:17 final size:18
Alignment explanation
Indices: 73636--73691 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 18
73626 GAAATGCAAT
* *
73636 GACAATGTAGATGCCGT-
1 GACAATTTAGATGCAGTG
73653 GACAATTTAGATGCAGTG
1 GACAATTTAGATGCAGTG
* *
73671 GA-AATTAAAATGCAGT-
1 GACAATTTAGATGCAGTG
73687 GACAA
1 GACAA
73692 AAGAAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.06
17 29 0.88
18 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (18 bp):
GACAATTTAGATGCAGTG
Found at i:76937 original size:26 final size:27
Alignment explanation
Indices: 76908--76967 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
76898 ATTCTGGGCG
76908 CAATTCTTG-ACACATTCATGCAGCGA
1 CAATTCTTGTACACATTCATGCAGCGA
** *
76934 CAATT-TTGTACATGTTCATGTAGCGA
1 CAATTCTTGTACACATTCATGCAGCGA
76960 C-ATTCTTG
1 CAATTCTTG
76968 GGTGCAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (27 bp):
CAATTCTTGTACACATTCATGCAGCGA
Found at i:81100 original size:29 final size:29
Alignment explanation
Indices: 81043--81174 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
81033 TCCCTTTCCC
* * * **
81043 ATAGATAGCCACAAAGGCAACATTGAACA
1 ATAGATAGCCATAAAGGCATCCTCAAACA
* * *
81072 ATAGATAGACATAAAGGCATCCACTAACA
1 ATAGATAGCCATAAAGGCATCCTCAAACA
* *
81101 TTAGATAGCCA-AAATGACATCCTCAAACA
1 ATAGATAGCCATAAA-GGCATCCTCAAACA
*
81130 ATAGATATCCATAAAGGCATCCTCAAACA
1 ATAGATAGCCATAAAGGCATCCTCAAACA
* *
81159 ATATATAGCCACAAAG
1 ATAGATAGCCATAAAG
81175 ACGTTCGTTC
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.04
29 77 0.93
30 3 0.04
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (29 bp):
ATAGATAGCCATAAAGGCATCCTCAAACA
Found at i:83347 original size:54 final size:54
Alignment explanation
Indices: 83097--83350 Score: 341
Period size: 54 Copynumber: 4.7 Consensus size: 54
83087 CACATGACGT
* * * *
83097 CATAGCCACTAGACTAGGTCTTACACTATGTGGTATTCTTTCCCCATATGATGC
1 CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGC
* * * * *
83151 CATAGCCACCAGACTAGGTCTAACACTATGTGATCATCTTTCCCCATATGATGC
1 CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGC
* * * *
83205 CATA-TCCACCAGACTAGGTTTTACACTTTATGGCCTTCTTTCCCCATATGATTC
1 CATAGT-CACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGC
* *
83259 CATAGTCACCAGACTAGGCCTTACACTTTATGGTCTTCTTTCCCCATATGATTG-
1 CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGA-TGC
83313 CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTC
1 CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTC
83351 AATTGTCATG
Statistics
Matches: 177, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
54 175 0.99
55 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (54 bp):
CATAGTCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGC
Found at i:87638 original size:13 final size:13
Alignment explanation
Indices: 87617--87824 Score: 52
Period size: 13 Copynumber: 14.9 Consensus size: 13
87607 ATTTAGTGAT
87617 AAATAAATAAATA
1 AAATAAATAAATA
*
87630 AAATCAATAAATGA
1 AAATAAATAAAT-A
*
87644 AAGAGAAA-AACATA
1 AA-ATAAATAA-ATA
87658 AAATAAA-AAA-A
1 AAATAAATAAATA
**
87669 ATCACCAAATAAATA
1 A--AATAAATAAATA
* *
87684 AAACACATAAA-A
1 AAATAAATAAATA
* * *
87696 GCAGTAAAGAAATA
1 -AAATAAATAAATA
87710 AAATTAAATAAAGGTGGGA
1 AAA-TAAATAAA--T---A
*
87729 ATATAAATAACATAA
1 AAATAAATAA-AT-A
*
87744 AAATAAATAACAAA
1 AAATAAATAA-ATA
87758 CAAATAAATAAA-A
1 -AAATAAATAAATA
*
87771 GAAT-AATAAATAA
1 AAATAAATAAAT-A
*
87784 AACAGTAAATAAAATT
1 AA-A-TAAAT-AAATA
*
87800 AAAT-AACAAATA
1 AAATAAATAAATA
87812 AAATAAAATAAAT
1 AAAT-AAATAAAT
87825 GGATCAAATA
Statistics
Matches: 144, Mismatches: 26, Indels: 49
0.66 0.12 0.22
Matches are distributed among these distances:
11 8 0.06
12 13 0.09
13 41 0.28
14 29 0.20
15 31 0.22
16 6 0.04
17 5 0.03
18 7 0.05
19 4 0.03
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:87749 original size:11 final size:10
Alignment explanation
Indices: 87728--87824 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 10
87718 TAAAGGTGGG
*
87728 AATATAAATA
1 AATAAAAATA
87738 ACATAAAAATA
1 A-ATAAAAATA
*
87749 AATAACAAACA
1 AATAA-AAATA
*
87760 AATAAATA-A
1 AATAAAAATA
* *
87769 AAGAATAATA
1 AATAAAAATA
87779 AATAAAACAGTA
1 AATAAAA-A-TA
*
87791 AATAAAATTA
1 AATAAAAATA
87801 AATAACAAATA
1 AATAA-AAATA
87812 AA-ATAAAATA
1 AATA-AAAATA
87822 AAT
1 AAT
87825 GGATCAAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
9 6 0.09
10 28 0.41
11 26 0.38
12 9 0.13
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (10 bp):
AATAAAAATA
Found at i:87810 original size:17 final size:17
Alignment explanation
Indices: 87728--87822 Score: 67
Period size: 15 Copynumber: 5.9 Consensus size: 17
87718 TAAAGGTGGG
*
87728 AATATAAATAACATAA-A
1 AATA-AAATAAAATAACA
*
87745 AAT-AAATAACA-AACA
1 AATAAAATAAAATAACA
* *
87760 AAT-AAATAAAAGAA-T
1 AATAAAATAAAATAACA
* **
87775 AAT-AAATAAAACAGTA
1 AATAAAATAAAATAACA
*
87791 AATAAAATTAAATAACA
1 AATAAAATAAAATAACA
87808 AATAAAATAAAATAA
1 AATAAAATAAAATAA
87823 ATGGATCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
14 2 0.03
15 31 0.48
16 5 0.08
17 26 0.41
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAAATAAAATAACA
Found at i:87849 original size:11 final size:11
Alignment explanation
Indices: 87728--87852 Score: 53
Period size: 11 Copynumber: 11.0 Consensus size: 11
87718 TAAAGGTGGG
*
87728 AATATAAATAA
1 AATAAAAATAA
*
87739 CATAAAAAT-A
1 AATAAAAATAA
*
87749 AATAACAAA-CA
1 AATAA-AAATAA
87760 AATAAATAA-AA
1 AATAAA-AATAA
87771 GAATAATAAATAA
1 -AATAA-AAATAA
* *
87784 AACAGTAAATAA
1 AATA-AAAATAA
*
87796 AAT-TAAATAA
1 AATAAAAATAA
87806 CAA-ATAAAATAA
1 -AATA-AAAATAA
* *
87818 AATAAATGGATCA
1 AATAAA--AATAA
87831 AATAAAAATAA
1 AATAAAAATAA
*
87842 AATGAAAATAA
1 AATAAAAATAA
87853 TAGGGTCTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 26
0.69 0.10 0.20
Matches are distributed among these distances:
10 13 0.15
11 38 0.43
12 25 0.28
13 12 0.14
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:94962 original size:2 final size:2
Alignment explanation
Indices: 94957--94988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
94947 AGAAAAAAGA
94957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94989 GTAAAAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98161 original size:43 final size:42
Alignment explanation
Indices: 98112--98231 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 42
98102 GACATTGAGA
* * **
98112 GGAACACTGTTTCCTAAAATTGAAAGTATGTGATCGATTGTGT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGAT-GAATGAAT
*
98155 GGAACACTGTTTCCTATTATTGAAAGTATGTGAATGAATGAAT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTG-ATGAATGAAT
**
98198 GGAACACTGTTTCCTAATATTGATTGTATGTGAT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGAT
98232 TGGTTGAGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.03
43 64 0.94
44 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.37
Consensus pattern (42 bp):
GGAACACTGTTTCCTAATATTGAAAGTATGTGATGAATGAAT
Found at i:98474 original size:28 final size:28
Alignment explanation
Indices: 98427--98484 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
98417 TATCGAGAGG
* * *
98427 ATTGGCGATCTTTATCGCATTTTTTGTT
1 ATTGGCGATCTCTATCGCATTATTTATT
*
98455 ATTGGCGATCTCTATTGCATTATTTATT
1 ATTGGCGATCTCTATCGCATTATTTATT
98483 AT
1 AT
98485 ACGGTAGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.52
Consensus pattern (28 bp):
ATTGGCGATCTCTATCGCATTATTTATT
Found at i:109556 original size:34 final size:34
Alignment explanation
Indices: 109513--109580 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
109503 GGTACATTCC
109513 ATAAGTCCAAAATGAAACGAACTATACAAACTTT
1 ATAAGTCCAAAATGAAACGAACTATACAAACTTT
109547 ATAAGTCCAAAATGAAACGAACTATACAAACTTT
1 ATAAGTCCAAAATGAAACGAACTATACAAACTTT
109581 GTTAAGTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (34 bp):
ATAAGTCCAAAATGAAACGAACTATACAAACTTT
Found at i:110301 original size:19 final size:19
Alignment explanation
Indices: 110264--110349 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
110254 GTTGGCACGT
*
110264 AAAGTGCATCCT-AAAGCAC
1 AAAGTGCATCCTGACA-CAC
* *
110283 GAAGTGCATCCTGACGCAC
1 AAAGTGCATCCTGACACAC
* * *
110302 AAAGCGCATGCTGACAAAC
1 AAAGTGCATCCTGACACAC
* * *
110321 AAAGTGCATCTTCACACAT
1 AAAGTGCATCCTGACACAC
*
110340 GAAGTGCATC
1 AAAGTGCATC
110350 TTGATGTGTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
19 50 0.98
20 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (19 bp):
AAAGTGCATCCTGACACAC
Found at i:152787 original size:3 final size:3
Alignment explanation
Indices: 152753--152806 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
152743 TGCAGCTGAC
* * *
152753 GAA GAA GCAA GACA GGAA GGA GAA GGA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA G-AA GA-A -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
152801 GAA GAA
1 GAA GAA
152807 ATTGCCGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 35 0.83
4 5 0.12
5 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:153879 original size:19 final size:19
Alignment explanation
Indices: 153823--153880 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
153813 TTAGTCGCAT
*
153823 AAAGAAAAGAAAAAGAGA-A
1 AAAG-AAAGAAAAAGAAATA
*
153842 AAAGAAAG-AAAAGTTAATA
1 AAAGAAAGAAAAAG-AAATA
153861 AAAGAAAGAAAAAGAAATA
1 AAAGAAAGAAAAAGAAATA
153880 A
1 A
153881 TATATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 18 0.55
20 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAGAAAGAAAAAGAAATA
Done.