Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013147.1 Kokia drynarioides strain JFW-HI SEQ_128166, 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: 160002
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:8883 original size:20 final size:20
Alignment explanation
Indices: 8804--8910 Score: 74
Period size: 20 Copynumber: 5.2 Consensus size: 20
8794 GGCCTGGAGC
8804 TATTTTGACTTGTTTGAGAAA-
1 TATTTTGACTTGTTT-A-AAAT
* **
8825 CATTTTGAAGT-TTTAAAAT
1 TATTTTGACTTGTTTAAAAT
* ** *
8844 GATTTTGACTTGGCTCAAAT
1 TATTTTGACTTGTTTAAAAT
*
8864 TATTTTGACATGTTTAAAAT
1 TATTTTGACTTGTTTAAAAT
* *
8884 CATTTTAACTTGATTTTAAAAT
1 TATTTTGACTTG--TTTAAAAT
8906 TATTT
1 TATTT
8911 CAAACTTTTC
Statistics
Matches: 64, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
18 3 0.05
19 9 0.14
20 32 0.50
21 8 0.12
22 12 0.19
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (20 bp):
TATTTTGACTTGTTTAAAAT
Found at i:18659 original size:14 final size:14
Alignment explanation
Indices: 18638--18675 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
18628 CTTTTTTGCA
18638 TTTCCTTTTATCT-
1 TTTCCTTTTATCTG
*
18651 TTTCACTTTTATTTG
1 TTTC-CTTTTATCTG
18666 TTTCCTTTTA
1 TTTCCTTTTA
18676 AATTCTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATCTG
Found at i:19019 original size:20 final size:20
Alignment explanation
Indices: 18991--19033 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18981 GTTTGTTGTT
18991 TTTACTCTTACTCTCT-CAAG
1 TTTACTCTT-CTCTCTACAAG
* *
19011 TTTATTCTTTTCTCTACAAG
1 TTTACTCTTCTCTCTACAAG
19031 TTT
1 TTT
19034 CTTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.19, C:0.23, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTACTCTTCTCTCTACAAG
Found at i:21662 original size:22 final size:24
Alignment explanation
Indices: 21627--21671 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
21617 CACCTATAAA
21627 AAAAATGAGAAAAAGAAAGAAAAG
1 AAAAATGAGAAAAAGAAAGAAAAG
*
21651 AAAAA-GAG-AAAAGAATGAAAA
1 AAAAATGAGAAAAAGAAAGAAAA
21672 AAGAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
AAAAATGAGAAAAAGAAAGAAAAG
Found at i:21663 original size:18 final size:16
Alignment explanation
Indices: 21636--21677 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
21626 AAAAAATGAG
21636 AAAAAG-AAAGAAAAGA
1 AAAAAGAAAAG-AAAGA
*
21652 AAAAGAGAAAAGAATGA
1 AAAA-AGAAAAGAAAGA
21669 AAAAAGAAA
1 AAAAAGAAA
21678 TAATTTGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAGA
Found at i:29594 original size:30 final size:29
Alignment explanation
Indices: 29538--29602 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
29528 TTAGTTTAGC
29538 CAAAAAAAAAAGAAAGTAATAGAGAAAAAT
1 CAAAAAAAAAAGAAAG-AATAGAGAAAAAT
* *
29568 CAAAAAGAAAAGAAA-AAT-GAGTAGAAA-
1 CAAAAAAAAAAGAAAGAATAGAG-AAAAAT
29595 CAAAAAAA
1 CAAAAAAA
29603 TCATAAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 10 0.32
28 7 0.23
30 14 0.45
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.08
Consensus pattern (29 bp):
CAAAAAAAAAAGAAAGAATAGAGAAAAAT
Found at i:32189 original size:15 final size:15
Alignment explanation
Indices: 32169--32198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32159 CTTAATTTAG
32169 TTTTAATTTAACTTA
1 TTTTAATTTAACTTA
*
32184 TTTTAATTTAGCTTA
1 TTTTAATTTAACTTA
32199 GAATACTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTTAATTTAACTTA
Found at i:43554 original size:16 final size:15
Alignment explanation
Indices: 43519--43574 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
43509 GATGGTAAGA
43519 AATTTTTATTT-TTT
1 AATTTTTATTTATTT
*
43533 ATTTTTATATTTATTT
1 AATTTT-TATTTATTT
43549 AATTTTTAATTTATTTT
1 AATTTTT-ATTTA-TTT
43566 AAATTTTTA
1 -AATTTTTA
43575 ATATTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 5 0.14
15 6 0.17
16 13 0.37
17 4 0.11
18 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTATTT
Found at i:43570 original size:18 final size:17
Alignment explanation
Indices: 43523--43576 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
43513 GTAAGAAATT
*
43523 TTTATTTTTTATTTTTATA
1 TTTA-TTTTAATTTTTA-A
43542 TTTA-TTTAATTTTTAA
1 TTTATTTTAATTTTTAA
43558 TTTATTTTAAATTTTTAA
1 TTTATTTT-AATTTTTAA
43576 T
1 T
43577 ATTTTCTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.16
17 13 0.41
18 10 0.31
19 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTAATTTTTAA
Found at i:46991 original size:12 final size:12
Alignment explanation
Indices: 46974--46999 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46964 TGTTATTATG
46974 ATGAATGCTATT
1 ATGAATGCTATT
46986 ATGAATGCTATT
1 ATGAATGCTATT
46998 AT
1 AT
47000 TTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:47560 original size:96 final size:97
Alignment explanation
Indices: 47383--47614 Score: 403
Period size: 96 Copynumber: 2.4 Consensus size: 97
47373 TTATAGTTAA
*
47383 TTAGTCGGTTGAATTGGCATAGAGATATGTTTAAGAGATTCTTTAGCTTTTGATATAGTATGTAT
1 TTAGTCGGTTGAATTGGCATAGAGATATGTTTAAGAGATTCTTTAGCTTTTCATATAGTATGTAT
*
47448 GTGCAATAACAAATTTGCTTATTAGAATTGAT
66 GTGCAATAACAAATTTGCTTATTAGAATTCAT
*
47480 TTAGTCGGTTGAATTGGCAAAGAGATATGTTTAAGAGATTCTTTAGC-TTTCATATAGTATGTAT
1 TTAGTCGGTTGAATTGGCATAGAGATATGTTTAAGAGATTCTTTAGCTTTTCATATAGTATGTAT
*
47544 GTGCAATAACACATTTGCTTATTAGAATTCAT
66 GTGCAATAACAAATTTGCTTATTAGAATTCAT
* *
47576 TTAGTCGGTTGAATTGGCATAGGGATATGTTCAAGAGAT
1 TTAGTCGGTTGAATTGGCATAGAGATATGTTTAAGAGAT
47615 GAATGAATTT
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 82 0.64
97 46 0.36
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (97 bp):
TTAGTCGGTTGAATTGGCATAGAGATATGTTTAAGAGATTCTTTAGCTTTTCATATAGTATGTAT
GTGCAATAACAAATTTGCTTATTAGAATTCAT
Found at i:47818 original size:15 final size:15
Alignment explanation
Indices: 47798--47827 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47788 TTAATTTAAT
47798 TTTAATTTAACTTAG
1 TTTAATTTAACTTAG
*
47813 TTTAATTTAGCTTAG
1 TTTAATTTAACTTAG
47828 AATACTTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (15 bp):
TTTAATTTAACTTAG
Found at i:50794 original size:68 final size:68
Alignment explanation
Indices: 50657--50810 Score: 182
Period size: 68 Copynumber: 2.3 Consensus size: 68
50647 ATAGTTGTGA
* * * ** **
50657 GCCCAACTCTAGTTAGATTAACCAACAATGTTGCGCCCAGTGCTAGTCGGATAAATTGACGAATG
1 GCCCAACTCTAGTTAGATTAACCAACAATATAGCGCCCAATGCTAGTCGGATAAACCGACGAAAA
50722 TGT
66 TGT
* * * * * *
50725 GCCCAGCTCTAGTTGGATTAACCAATAATATAGTGCCCAATGCTAGTTGGATAAACCGATGAAAA
1 GCCCAACTCTAGTTAGATTAACCAACAATATAGCGCCCAATGCTAGTCGGATAAACCGACGAAAA
50790 TGT
66 TGT
*
50793 GCCCAACACTAGTTAGAT
1 GCCCAACTCTAGTTAGAT
50811 AAACTAACGA
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (68 bp):
GCCCAACTCTAGTTAGATTAACCAACAATATAGCGCCCAATGCTAGTCGGATAAACCGACGAAAA
TGT
Found at i:50795 original size:34 final size:34
Alignment explanation
Indices: 50723--50814 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 34
50713 TGACGAATGT
* * * *
50723 GTGCCCAGCTCTAGTTGGATTAACCAATAATATA
1 GTGCCCAACACTAGTTGGATAAACCAATAAAATA
** *
50757 GTGCCCAATGCTAGTTGGATAAACCGATGAAAAT-
1 GTGCCCAACACTAGTTGGATAAACCAAT-AAAATA
*
50791 GTGCCCAACACTAGTTAGATAAAC
1 GTGCCCAACACTAGTTGGATAAAC
50815 TAACGAAAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 44 0.92
35 4 0.08
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (34 bp):
GTGCCCAACACTAGTTGGATAAACCAATAAAATA
Found at i:54461 original size:2 final size:2
Alignment explanation
Indices: 54454--54479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54444 AATATGCTAT
54454 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54480 AGTGTGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55011 original size:22 final size:22
Alignment explanation
Indices: 54986--55028 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
54976 AAAATATTTC
*
54986 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
55008 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
55029 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:65934 original size:25 final size:25
Alignment explanation
Indices: 65906--65962 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
65896 GATTAAATTA
65906 AATAATAAAATATAAAATTATTT-TT
1 AATAATAAAATATAAAA-TATTTATT
** *
65931 AATAATTTATTATAAAATATTTCATT
1 AATAATAAAATATAAAATATTT-ATT
65957 AATAAT
1 AATAAT
65963 TTAGGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 14 0.52
26 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAATAAAATATAAAATATTTATT
Found at i:65962 original size:26 final size:25
Alignment explanation
Indices: 65916--65965 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
65906 AATAATAAAA
65916 TATAAAATTATTTTTAATAATTTAT
1 TATAAAATTATTTTTAATAATTTAT
65941 TATAAAA-TATTTCATTAATAATTTA
1 TATAAAATTATTT--TTAATAATTTA
65966 GGTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 7 0.30
26 11 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAAAATTATTTTTAATAATTTAT
Found at i:65989 original size:18 final size:18
Alignment explanation
Indices: 65949--65996 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
65939 ATTATAAAAT
* * *
65949 ATTTCATTAATAATTTAG
1 ATTTAATTAATTATTTAA
*
65967 GTTTAATTAATTATTTAA
1 ATTTAATTAATTATTTAA
*
65985 ATTTAGTTAATT
1 ATTTAATTAATT
65997 TTATACTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTAATTAATTATTTAA
Found at i:74265 original size:15 final size:15
Alignment explanation
Indices: 74245--74273 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
74235 CAGATGGACT
74245 AATACCTCGAATATC
1 AATACCTCGAATATC
74260 AATACCTCGAATAT
1 AATACCTCGAATAT
74274 TGGCTATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (15 bp):
AATACCTCGAATATC
Found at i:84904 original size:19 final size:19
Alignment explanation
Indices: 84882--84919 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
84872 TTTGATAAAA
*
84882 AGAATATATATAT-ATGTAT
1 AGAATA-ATAAATGATGTAT
84901 AGAATAATAAATGATGTAT
1 AGAATAATAAATGATGTAT
84920 TGGTTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (19 bp):
AGAATAATAAATGATGTAT
Found at i:91133 original size:43 final size:43
Alignment explanation
Indices: 91067--91264 Score: 220
Period size: 43 Copynumber: 4.6 Consensus size: 43
91057 AATGGCTTGG
*
91067 TTAGCGGCGCTTTTCCCATAAACGCCGCTATTA-AACATGGTCT
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTA-TAGAACATGGTCT
* * * *
91110 TTAGCGGTGTTTTTCCCACAAACGCCGCTATAGAACATGTTAT
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCT
* * *
91153 TCAGTGGCGCTTTTCCCACAAATGCCGCTATAGAACATGGTCT
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCT
* * ** * *
91196 TTAGCGGCGTTTTTCCCACAAATGTTGCTATAAAACATGTTCT
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCT
* *
91239 TTAGCGGCATCTTTT-CCATAAACGCC
1 TTAGCGGC-GCTTTTCCCACAAACGCC
91265 ACTAACATTA
Statistics
Matches: 128, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
42 2 0.02
43 122 0.95
44 4 0.03
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCT
Found at i:91217 original size:86 final size:86
Alignment explanation
Indices: 91072--91236 Score: 251
Period size: 86 Copynumber: 1.9 Consensus size: 86
91062 CTTGGTTAGC
* *
91072 GGCGCTTTTCCCATAAACGCCGCTATTAAACATGGTCTTTAGCGGTGTTTTTCCCACAAACGCCG
1 GGCGCTTTTCCCACAAACGCCGCTATTAAACATGGTCTTTAGCGGCGTTTTTCCCACAAACGCCG
*
91137 CTATAGAACATGTTATTCAGT
66 CTATAAAACATGTTATTCAGT
* * **
91158 GGCGCTTTTCCCACAAATGCCGCTA-TAGAACATGGTCTTTAGCGGCGTTTTTCCCACAAATGTT
1 GGCGCTTTTCCCACAAACGCCGCTATTA-AACATGGTCTTTAGCGGCGTTTTTCCCACAAACGCC
91222 GCTATAAAACATGTT
65 GCTATAAAACATGTT
91237 CTTTAGCGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
85 2 0.03
86 69 0.97
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (86 bp):
GGCGCTTTTCCCACAAACGCCGCTATTAAACATGGTCTTTAGCGGCGTTTTTCCCACAAACGCCG
CTATAAAACATGTTATTCAGT
Found at i:91927 original size:15 final size:15
Alignment explanation
Indices: 91904--91951 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
91894 ATTATTTTTA
91904 ATTAAATTTGTTTGG
1 ATTAAATTTGTTTGG
* *
91919 ATTATATTT-TTCT-A
1 ATTAAATTTGTT-TGG
91933 ATTAAATTTGTTTGG
1 ATTAAATTTGTTTGG
91948 ATTA
1 ATTA
91952 TATTCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (15 bp):
ATTAAATTTGTTTGG
Found at i:91934 original size:29 final size:28
Alignment explanation
Indices: 91898--91955 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 28
91888 TAAACTATTA
91898 TTTTTAATTAAATTTGTTTGGATTATAT
1 TTTTTAATTAAATTTGTTTGGATTATAT
91926 TTTTCTAATTAAATTTGTTTGGATTATAT
1 TTTT-TAATTAAATTTGTTTGGATTATAT
91955 T
1 T
91956 CATTTTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTTTAATTAAATTTGTTTGGATTATAT
Found at i:94453 original size:40 final size:39
Alignment explanation
Indices: 94399--94484 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 39
94389 AAATTAGCAG
94399 CGTTTATGGGAAAACGCCACTATTCCTTAACCTTTAGCGA
1 CGTTT-TGGGAAAACGCCACTATTCCTTAACCTTTAGCGA
* * *
94439 CGTTTTGGGAAAAACGCCGCTATTGCTTAACCTTTAGCGG
1 CGTTTTGGG-AAAACGCCACTATTCCTTAACCTTTAGCGA
94479 CGTTTT
1 CGTTTT
94485 TCCCATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (39 bp):
CGTTTTGGGAAAACGCCACTATTCCTTAACCTTTAGCGA
Found at i:94525 original size:41 final size:40
Alignment explanation
Indices: 94458--94576 Score: 123
Period size: 42 Copynumber: 2.9 Consensus size: 40
94448 AAAAACGCCG
* * **
94458 CTATTGC-TTAACCTTTAGCGGCGTTTTTCCCATAAATGCCA
1 CTATTGCTTTAA-CTTTTGCGGTG-TTTTCCCATAAACACCA
* *
94499 CTATTGCTTTAACTTTTTCGGTGTTTTCCCATAAACATCA
1 CTATTGCTTTAACTTTTGCGGTGTTTTCCCATAAACACCA
* *
94539 CAAATGCTCTTAACGTTTTGCGGTGTTTTCCCATAAAC
1 CTATTGCT-TTAAC-TTTTGCGGTGTTTTCCCATAAAC
94577 GATGCTACTG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
40 20 0.30
41 20 0.30
42 26 0.39
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.39
Consensus pattern (40 bp):
CTATTGCTTTAACTTTTGCGGTGTTTTCCCATAAACACCA
Found at i:94667 original size:40 final size:40
Alignment explanation
Indices: 94613--94721 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
94603 GAATTTTTCC
* ** *
94613 AAAAACGCCGCTATTGCTTTACCTTTTATGGTGTTTATAGG
1 AAAAACGCCACTATTGCTTTACCTTTTACAGTGATTAT-GG
* *
94654 -AAAATGCCACTATTGCTTTACCTTTTGCAGTGATTATGG
1 AAAAACGCCACTATTGCTTTACCTTTTACAGTGATTATGG
* *
94693 AAAAACGCCATTATTGCCTTACCTTTTAC
1 AAAAACGCCACTATTGCTTTACCTTTTAC
94722 GACATTTTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 55 0.96
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (40 bp):
AAAAACGCCACTATTGCTTTACCTTTTACAGTGATTATGG
Found at i:119522 original size:28 final size:28
Alignment explanation
Indices: 119482--119538 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
119472 TCAGTTATGC
119482 ACACTAAATTAGTCATTACTGTCATTGT
1 ACACTAAATTAGTCATTACTGTCATTGT
119510 ACACTAAATTAGTCATTACTGTCATTGT
1 ACACTAAATTAGTCATTACTGTCATTGT
119538 A
1 A
119539 TTAAAGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
ACACTAAATTAGTCATTACTGTCATTGT
Found at i:121723 original size:25 final size:26
Alignment explanation
Indices: 121690--121744 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
121680 CGTTTCCTTA
121690 AAATGAAAATGAAAAT-ACTAAAACCT
1 AAATGAAAA-GAAAATAACTAAAACCT
*
121716 AAAT-AAAAGAAAATAACTAAAAGCT
1 AAATGAAAAGAAAATAACTAAAACCT
121741 AAAT
1 AAAT
121745 TACAAGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.22
25 17 0.63
26 4 0.15
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.18
Consensus pattern (26 bp):
AAATGAAAAGAAAATAACTAAAACCT
Found at i:141088 original size:15 final size:15
Alignment explanation
Indices: 141068--141098 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
141058 CTCATCTCTT
141068 ACCATCACCTCTACC
1 ACCATCACCTCTACC
141083 ACCATCACCTCTACC
1 ACCATCACCTCTACC
141098 A
1 A
141099 AGGCCTCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.00, T:0.19
Consensus pattern (15 bp):
ACCATCACCTCTACC
Found at i:142867 original size:15 final size:15
Alignment explanation
Indices: 142847--142876 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
142837 AATTTCATGC
*
142847 TTCAATCAGCATGTT
1 TTCAATCACCATGTT
142862 TTCAATCACCATGTT
1 TTCAATCACCATGTT
142877 ATCACTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:146851 original size:83 final size:84
Alignment explanation
Indices: 146688--146856 Score: 193
Period size: 83 Copynumber: 2.0 Consensus size: 84
146678 GGTAAAGTTG
* * *
146688 TCAAGTCGAGGATCTACCCTACAGCTCTAGAAAAATGTAACTAAAAAATGAAAACAAAGAAAGTC
1 TCAAGTCGAGAATCTACCCTAAAGCTCTAGAAAAATGTAACT-AAAAACGAAAACAAAGAAAGTC
*
146753 AAATTAGTTAACAAGAAGAA
65 AAATCAGTTAACAAGAAGAA
* * *
146773 TCAAGTCGCGAATCTA-CCTAAAGCTCTAGACAAATGTAATCT-GAAACGAAAA-AAGAGAAAGA
1 TCAAGTCGAGAATCTACCCTAAAGCTCTAGAAAAATGTAA-CTAAAAACGAAAACAA-AGAAAG-
* *
146835 T-AGATCAGTTGACAAGAAGAA
63 TCAAATCAGTTAACAAGAAGAA
146856 T
1 T
146857 AATAAAACGA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
82 2 0.03
83 32 0.44
84 22 0.31
85 16 0.22
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (84 bp):
TCAAGTCGAGAATCTACCCTAAAGCTCTAGAAAAATGTAACTAAAAACGAAAACAAAGAAAGTCA
AATCAGTTAACAAGAAGAA
Found at i:150422 original size:12 final size:12
Alignment explanation
Indices: 150405--150447 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
150395 TTTCCCCCTT
150405 TTTCTCTTCTTC
1 TTTCTCTTCTTC
150417 TTTCTC-T-TTC
1 TTTCTCTTCTTC
150427 TTTCTCTTCTTC
1 TTTCTCTTCTTC
150439 TTTCTCTTC
1 TTTCTCTTC
150448 CTTAATACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.31
11 2 0.07
12 18 0.62
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTCTTCTTC
Found at i:150430 original size:22 final size:22
Alignment explanation
Indices: 150405--150446 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
150395 TTTCCCCCTT
150405 TTTCTCTTCTTCTTTCTCTTTC
1 TTTCTCTTCTTCTTTCTCTTTC
150427 TTTCTCTTCTTCTTTCTCTT
1 TTTCTCTTCTTCTTTCTCTT
150447 CCTTAATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTCTTCTTCTTTCTCTTTC
Done.