Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009385.1 Kokia drynarioides strain JFW-HI SEQ_124092, 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: 50807
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:598 original size:29 final size:29
Alignment explanation
Indices: 566--643 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 29
556 ACCACGATCT
566 TTTCATAAATTACATTTTTAAGCCT-G-AAC
1 TTTCA-AAATTACATTTTTAA-CCTCGAAAC
*
595 TTTCCAAAATT-CTATTTTTGACCTCGAAAC
1 TTT-CAAAATTAC-ATTTTTAACCTCGAAAC
625 TTTCAAAAATTACCATTTT
1 TTTC-AAAATTA-CATTTT
644 ACCCCCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
28 4 0.10
29 17 0.41
30 14 0.34
31 5 0.12
32 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTCAAAATTACATTTTTAACCTCGAAAC
Found at i:628 original size:30 final size:29
Alignment explanation
Indices: 512--635 Score: 76
Period size: 30 Copynumber: 4.2 Consensus size: 29
502 AAATTGTTCA
* *
512 AAAATTATATTTTGACCCTCAAACTTCTCC
1 AAAATTCTATTTTGACCCTCGAACTT-TCC
* * * * *
542 AAAATTCCATTTGGA-CCACGATCTTTTC
1 AAAATTCTATTTTGACCCTCGAACTTTCC
* *
570 ATAAATTAC-ATTTTTAAGCCT-GAACTTTCC
1 A-AAATT-CTA-TTTTGACCCTCGAACTTTCC
*
600 AAAATTCTATTTTTGA-CCTCGAAACTTTCA
1 AAAATTCTA-TTTTGACCCTCG-AACTTTCC
630 AAAATT
1 AAAATT
636 ACCATTTTAC
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
28 7 0.10
29 26 0.36
30 38 0.52
31 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAATTCTATTTTGACCCTCGAACTTTCC
Found at i:672 original size:59 final size:59
Alignment explanation
Indices: 608--947 Score: 436
Period size: 59 Copynumber: 5.7 Consensus size: 59
598 CCAAAATTCT
* * * * * **
608 ATTTTTGA-CCTCGAAACTTTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTTT
1 ATTTTTGATCC-CGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
*
667 GTTTTTGATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
1 ATTTTTGATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
* * *
726 GTTTTTTATCCCGAACCTTCCAAAATTTACCATTTTACCCTCAAATGTCTAAAAACTCC
1 ATTTTTGATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
785 ATTTTTGAT-CCGAAACCTTCCAAAATTTACCATTTTTACCCTCGAATGTCTAAAAACTCC
1 ATTTTTGATCCCG-AACCTTCCAAAATTTACCA-TTTTACCCTCGAATGTCTAAAAACTCC
* * * **
845 ATTTTTTATCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATTTCC
1 ATTTTTGATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
* * *
904 ATTTTT-AACCTCGAGCCTTCCATAAA-TTACCATTTCACCCTCGA
1 ATTTTTGATCC-CGAACCTTCCA-AAATTTACCATTTTACCCTCGA
948 GCATCCAAAA
Statistics
Matches: 254, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
58 6 0.02
59 188 0.74
60 57 0.22
61 3 0.01
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
ATTTTTGATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCC
Found at i:883 original size:119 final size:117
Alignment explanation
Indices: 619--947 Score: 462
Period size: 119 Copynumber: 2.8 Consensus size: 117
609 TTTTTGACCT
* * * ***
619 CGAAACTTTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTTTGTTTTTGATCCCGAACC
1 CGAACCTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAACTCCATTTTTGAT-CCGAACC
*
684 TTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCCGTTTTTTATCC
65 TTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCC
*
737 CGAACCTTCCAAAATTTACCATTTTACCCTCAAATGTCTAAAAACTCCATTTTTGATCCGAAACC
1 CGAACCTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAACTCCATTTTTGATCCG-AACC
802 TTCCAAAATTTACCATTTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCC
65 TTCCAAAATTTACCA-TTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCC
* * ** * * *
856 CGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATTTCCATTTTTAACCTCGAGCC
1 CGAACCTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAACTCCATTTTTGATC-CGAACC
*
921 TTCCATAAA-TTACCATTTCACCCTCGA
65 TTCCA-AAATTTACCATTTTACCCTCGA
948 GCATCCAAAA
Statistics
Matches: 190, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
117 3 0.02
118 80 0.42
119 102 0.54
120 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (117 bp):
CGAACCTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAACTCCATTTTTGATCCGAACCT
TCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCC
Found at i:925 original size:178 final size:177
Alignment explanation
Indices: 608--945 Score: 466
Period size: 178 Copynumber: 1.9 Consensus size: 177
598 CCAAAATTCT
* ***
608 ATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTTTGTTTTT
1 ATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTCCATTTTT
* * * *
673 GATCCCGAACCTTCCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCCGTTTTTTATCCC
66 GATCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCGATTTTTAACCC
*
738 GAACCTTCCA-AAATTTACCATTTTACCCTCAAATGTCTAAAAACTCC
131 GAACCTTCCATAAA-TTACCATTTCACCCTCAAATGTCTAAAAACTCC
* * * *
785 ATTTTTGATC-CGAAACCTTCCAAAATTTACCATTTTTACCCTCGAATGTCTAAAAACTCCATTT
1 ATTTTTGACCTCGAAA-CTTCCAAAAATTACCA-TTTTACCCCCAAATGTCTAAAAACTCCATTT
* **
849 TTTATCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATTTCC-ATTTTTAAC
64 TTGATCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCGATTTTTAAC
*
913 CTCGAGCCTTCCATAAATTACCATTTCACCCTC
129 C-CGAACCTTCCATAAATTACCATTTCACCCTC
946 GAGCATCCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
176 5 0.04
177 31 0.22
178 101 0.72
179 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (177 bp):
ATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAACTCCATTTTT
GATCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCGATTTTTAACCC
GAACCTTCCATAAATTACCATTTCACCCTCAAATGTCTAAAAACTCC
Found at i:948 original size:30 final size:28
Alignment explanation
Indices: 861--970 Score: 114
Period size: 28 Copynumber: 3.8 Consensus size: 28
851 TATCCCGAAC
861 CTTCCAAAAATTACCATTTTACCCTCGA-
1 CTTCC-AAAATTACCATTTTACCCTCGAG
* * *
889 ATGTCCAAAATTTCCATTTTTAACCTCGAG
1 CT-TCCAAAATTACCA-TTTTACCCTCGAG
*
919 CCTTCCATAAATTACCATTTCACCCTCGAG
1 -CTTCCA-AAATTACCATTTTACCCTCGAG
* *
949 CATCCAAAATTACCGTTTTACC
1 CTTCCAAAATTACCATTTTACC
971 TTCGTATCCA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
28 24 0.36
29 19 0.28
30 15 0.22
31 9 0.13
ACGTcount: A:0.30, C:0.31, G:0.06, T:0.33
Consensus pattern (28 bp):
CTTCCAAAATTACCATTTTACCCTCGAG
Found at i:1952 original size:16 final size:16
Alignment explanation
Indices: 1907--1952 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1897 ATAGAATTAC
1907 TAGATTAT-AATTTTA
1 TAGATTATGAATTTTA
*
1922 TAG-GTACTGAATTTTA
1 TAGATTA-TGAATTTTA
*
1938 TAGATTATGACTTTT
1 TAGATTATGAATTTT
1953 TCACCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 2 0.08
15 4 0.16
16 17 0.68
17 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (16 bp):
TAGATTATGAATTTTA
Found at i:8317 original size:6 final size:6
Alignment explanation
Indices: 8306--8336 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
8296 CTAACCACAG
8306 TGCAAA TGCAAA TGCAAA TGCAAA TGCAAA T
1 TGCAAA TGCAAA TGCAAA TGCAAA TGCAAA T
8337 AATCCTATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
TGCAAA
Found at i:13140 original size:2 final size:2
Alignment explanation
Indices: 13133--13160 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13123 GTTTCTTATT
13133 TA 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 TA
13161 ATTTAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13848 original size:31 final size:32
Alignment explanation
Indices: 13799--13876 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
13789 AAAAACAACT
* * *
13799 TAAATAAAAACTTTTTGAATAGTTTAATGA-CA
1 TAAAT-AAAATTTTTTGAATAATTAAATGAGCA
13831 TAAATAAAATTTTTTGAATAATTAAATGAGCA
1 TAAATAAAATTTTTTGAATAATTAAATGAGCA
*
13863 -AAATATAATTTTTT
1 TAAATAAAATTTTTT
13877 TTAATTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 34 0.83
32 7 0.17
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (32 bp):
TAAATAAAATTTTTTGAATAATTAAATGAGCA
Found at i:20795 original size:12 final size:12
Alignment explanation
Indices: 20773--20850 Score: 86
Period size: 12 Copynumber: 6.6 Consensus size: 12
20763 ATAACATCCA
*
20773 AACAAAAAAAAT
1 AACAACAAAAAT
* *
20785 AACAACCAAAAC
1 AACAACAAAAAT
20797 AACAACAAAAAT
1 AACAACAAAAAT
* * *
20809 AATAGC-AAAAC
1 AACAACAAAAAT
20820 AACAACAAAAAT
1 AACAACAAAAAT
*
20832 AGCAACAAAAAT
1 AACAACAAAAAT
20844 AACAACA
1 AACAACA
20851 TAAACAACAC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 8 0.15
12 44 0.85
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:20817 original size:23 final size:24
Alignment explanation
Indices: 20773--20859 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
20763 ATAACATCCA
*
20773 AACAAAAAAAATAACAACCAAAAC
1 AACAACAAAAATAACAACCAAAAC
* *
20797 AACAACAAAAATAA-TAGCAAAAC
1 AACAACAAAAATAACAACCAAAAC
* * *
20820 AACAACAAAAATAGCAACAAAAAT
1 AACAACAAAAATAACAACCAAAAC
* *
20844 AACAACATAAACAACA
1 AACAACAAAAATAACA
20860 CTGAAACAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 20 0.39
24 31 0.61
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAACCAAAAC
Found at i:20822 original size:20 final size:20
Alignment explanation
Indices: 20791--20836 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 20
20781 AAATAACAAC
20791 CAAAACAACAACAAAAATAATAG
1 CAAAACAACAAC--AAA-AATAG
20814 CAAAACAACAACAAAAATAG
1 CAAAACAACAACAAAAATAG
20834 CAA
1 CAA
20837 CAAAAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
23 12 0.52
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (20 bp):
CAAAACAACAACAAAAATAG
Found at i:20825 original size:35 final size:35
Alignment explanation
Indices: 20781--20859 Score: 54
Period size: 35 Copynumber: 2.2 Consensus size: 35
20771 CAAACAAAAA
* * *
20781 AAATAACAACCAAAACAACAACAAAAATAATAGC-A
1 AAATAACAA-CAAAACAACAACAAAAACAACAACAA
* * *
20816 AAACAACAACAAAA-ATAGCAACAAAAATAACAACAT
1 AAATAACAACAAAACA-A-CAACAAAAACAACAACAA
*
20852 AAACAACA
1 AAATAACA
20860 CTGAAACAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 1 0.03
34 6 0.16
35 22 0.59
36 8 0.22
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.08
Consensus pattern (35 bp):
AAATAACAACAAAACAACAACAAAAACAACAACAA
Found at i:20859 original size:12 final size:12
Alignment explanation
Indices: 20773--20859 Score: 77
Period size: 12 Copynumber: 7.3 Consensus size: 12
20763 ATAACATCCA
* *
20773 AACAAAAAAAAT
1 AACAACAAAAAC
*
20785 AACAACCAAAAC
1 AACAACAAAAAC
*
20797 AACAACAAAAAT
1 AACAACAAAAAC
* *
20809 AATAGC-AAAAC
1 AACAACAAAAAC
*
20820 AACAACAAAAAT
1 AACAACAAAAAC
* *
20832 AGCAACAAAAAT
1 AACAACAAAAAC
*
20844 AACAACATAAAC
1 AACAACAAAAAC
20856 AACA
1 AACA
20860 CTGAAACAGT
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
11 8 0.14
12 51 0.86
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:20876 original size:21 final size:22
Alignment explanation
Indices: 20852--20901 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
20842 ATAACAACAT
*
20852 AAACAACACTGAAACAG-TTAA
1 AAACAACACTGAAACAGCATAA
*
20873 AAACAGCACTGAAACAGCATAA
1 AAACAACACTGAAACAGCATAA
20895 AAACAAC
1 AAACAAC
20902 CAAAATAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.58, C:0.22, G:0.10, T:0.10
Consensus pattern (22 bp):
AAACAACACTGAAACAGCATAA
Found at i:20924 original size:21 final size:21
Alignment explanation
Indices: 20893--20964 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
20883 GAAACAGCAT
20893 AAAAACAACCAAAATAGTGAAA
1 AAAAACAACCAAAATAGT-AAA
*
20915 AAAAGC-ACCAAAATAGTAAA
1 AAAAACAACCAAAATAGTAAA
*
20935 AAAAACAACCAAAACAGTAAA
1 AAAAACAACCAAAATAGTAAA
20956 AAAAACAAC
1 AAAAACAAC
20965 ACCAAAACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.17
21 33 0.72
22 5 0.11
ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAACAACCAAAATAGTAAA
Found at i:21377 original size:41 final size:41
Alignment explanation
Indices: 21293--21380 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
21283 GAAAATGGAG
****
21293 AAATG-AAATAATTTGAAAATGAATATGATTTTTTTTTTCA
1 AAATGAAAATAATTTGAAAATGAATATGATTTTTCGAATCA
21333 AAATGAAAATAATTTGAAAATGAATTTATGA-TTTTCGAAT-A
1 AAATGAAAATAATTTGAAAATGAA--TATGATTTTTCGAATCA
21374 AAATGAA
1 AAATGAA
21381 GTTCAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.12
41 26 0.63
42 5 0.12
43 5 0.12
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (41 bp):
AAATGAAAATAATTTGAAAATGAATATGATTTTTCGAATCA
Found at i:25703 original size:50 final size:51
Alignment explanation
Indices: 25515--25787 Score: 327
Period size: 51 Copynumber: 5.4 Consensus size: 51
25505 TTTCATTTCA
* * ** * *
25515 TACTCATGATGACA-TATAATCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
** * * * *
25568 TACTCACGATGACACAAAGTCATCGAACCCTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* *
25619 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* **
25670 TACTCACG-TGACATTTAGTCATCGGACCTTTAATCTGTAAAGG-TTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
25719 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
25770 TCCTCACGATGACACTTA
1 TACTCACGATGACACTTA
25788 CCATACTGGA
Statistics
Matches: 192, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
49 14 0.07
50 64 0.33
51 82 0.43
52 9 0.05
53 23 0.12
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:32478 original size:25 final size:25
Alignment explanation
Indices: 32425--32471 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
32415 AGTGGATCCA
32425 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
32450 AATTAAA-TCTAAACA-ATAATTT
1 AATTAAATTCTAAAAAGATAATTT
32472 CTTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:38883 original size:118 final size:117
Alignment explanation
Indices: 38666--38947 Score: 395
Period size: 118 Copynumber: 2.4 Consensus size: 117
38656 GGACGTTCCA
* * *
38666 ATGAGTGTTGGCACAACCTTTACTTCGATTATACCGATGAGCGTAGGGTGCAAACTAATTACTTT
1 ATGAGTGTAGGCACAACCTTTACTTCGATTATACCGATGAGCGTTGGGTGCAAACTAATTACTTC
* *
38731 GGACGTTTCGATGAGACACCGAGTGCCAAATGGTTACTTCAACTACGTGTTG
66 GGACGTTTCGATAAGACACCGAGTGCCAAATGGTTACTTCAACTACGTGTCG
*
38783 ATGAGTGCTAGGCACAACCTTTACTTCGATTATACCAATGAGCGTTGGGTGCAAACTAATTACTT
1 ATGAGTG-TAGGCACAACCTTTACTTCGATTATACCGATGAGCGTTGGGTGCAAACTAATTACTT
* * * *
38848 CGGATGTTTCGATAAGGCACTGGGTGCCAAATGGTTACTTCAACTACGTGTCG
65 CGGACGTTTCGATAAGACACCGAGTGCCAAATGGTTACTTCAACTACGTGTCG
** * * *
38901 ATGAGTGTTTA-GCACAATTTTTACTTCAATCATATCGATGAGCGTTG
1 ATGAGTG--TAGGCACAACCTTTACTTCGATTATACCGATGAGCGTTG
38948 AGCACAATCT
Statistics
Matches: 146, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
117 7 0.05
118 137 0.94
119 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (117 bp):
ATGAGTGTAGGCACAACCTTTACTTCGATTATACCGATGAGCGTTGGGTGCAAACTAATTACTTC
GGACGTTTCGATAAGACACCGAGTGCCAAATGGTTACTTCAACTACGTGTCG
Found at i:42463 original size:17 final size:17
Alignment explanation
Indices: 42438--42470 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42428 ATCATTTTAG
42438 CATTTATTTAA-TTTTT
1 CATTTATTTAACTTTTT
42454 CATTTCATTTAACTTTT
1 CATTT-ATTTAACTTTT
42471 GAACTTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (17 bp):
CATTTATTTAACTTTTT
Found at i:42629 original size:18 final size:18
Alignment explanation
Indices: 42594--42657 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
42584 ATTTTTTAAT
*
42594 ATTTAAAAATTCATAAAAA
1 ATTTTAAAATT-ATAAAAA
42613 ATTTTAAAATTATAAAAA
1 ATTTTAAAATTATAAAAA
* ** *
42631 ATATTAATGTTATTAAAA
1 ATTTTAAAATTATAAAAA
*
42649 ATTATAAAA
1 ATTTTAAAA
42658 GTTCTAATTC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 26 0.72
19 10 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTTTAAAATTATAAAAA
Found at i:45791 original size:43 final size:43
Alignment explanation
Indices: 45716--45803 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 43
45706 TTAAATTCAA
*
45716 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAGATTATATT
1 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAAATTAT-TT
*
45760 TTTAATTGTTTTATTTTTTA-TTTGAAGCAAATAAAATTATTT
1 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAAATTATTT
45802 TT
1 TT
45804 GTATTTAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 4 0.10
43 18 0.43
44 20 0.48
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (43 bp):
TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAAATTATTT
Found at i:48630 original size:39 final size:38
Alignment explanation
Indices: 48586--48676 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 38
48576 TGGGACAAGT
*
48586 CTCTTCCAAAAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTT-CAAAAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
48625 CTCTTCAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCAAAAGGTAT-CATCCAATATGAAAGGATTGTGA
48664 CTCTTCAAAAGGT
1 CTCTTCAAAAGGT
48677 GTCCATTGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
38 8 0.18
39 28 0.64
40 8 0.18
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (38 bp):
CTCTTCAAAAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:48677 original size:39 final size:40
Alignment explanation
Indices: 48603--48682 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
48593 AAAAGGTATG
*
48603 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
48643 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
48682 T
1 T
48683 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Done.