Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013874.1 Kokia drynarioides strain JFW-HI SEQ_128902, 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: 118578
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1445 original size:6 final size:6
Alignment explanation
Indices: 1434--1465 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1424 ACCAAACCTT
1434 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
1466 GGACATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
ATCTTG
Found at i:6236 original size:6 final size:6
Alignment explanation
Indices: 6225--6259 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6215 AAACCTTATA
* *
6225 TTGATC TTGATC TTGATC TTTATC TTGATA TTGAT
1 TTGATC TTGATC TTGATC TTGATC TTGATC TTGAT
6260 GGACATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.54
Consensus pattern (6 bp):
TTGATC
Found at i:7886 original size:19 final size:19
Alignment explanation
Indices: 7848--7886 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
7838 ATTAAGAATA
*
7848 AATTTTAAAATCATACATT
1 AATTTTAAAATAATACATT
* *
7867 AATTTTAATATAATATATT
1 AATTTTAAAATAATACATT
7886 A
1 A
7887 TACACAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTTAAAATAATACATT
Found at i:14971 original size:24 final size:24
Alignment explanation
Indices: 14943--14989 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14933 ATTCACAAGT
*
14943 AAAATAAATTATGCTAATAAATAC
1 AAAATAAATTATACTAATAAATAC
* *
14967 AAAATATATTATATTAATAAATA
1 AAAATAAATTATACTAATAAATA
14990 TTAAATCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAATAAATTATACTAATAAATAC
Found at i:31375 original size:21 final size:21
Alignment explanation
Indices: 31351--31404 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31341 CCTAAGATAG
*
31351 TTCTACCGATACAAGTGA-GAC
1 TTCTACCGATACAAGTCATG-C
*
31372 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
*
31393 TACTACCGATAC
1 TTCTACCGATAC
31405 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:31597 original size:21 final size:21
Alignment explanation
Indices: 31559--31598 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31549 TACCCTATAC
* *
31559 TTCTATAGATACATGTATGAG
1 TTCTATAGAAACAAGTATGAG
*
31580 TTCTATCGAAACAAGTATG
1 TTCTATAGAAACAAGTATG
31599 CAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
TTCTATAGAAACAAGTATGAG
Found at i:54117 original size:21 final size:21
Alignment explanation
Indices: 54093--54138 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
54083 CCGATGACAG
* * *
54093 TTCTACTAATACAAGTCAAGC
1 TTCTACAAAAACAAATCAAGC
*
54114 TTCTACAAAAACAAATCATGC
1 TTCTACAAAAACAAATCAAGC
54135 TTCT
1 TTCT
54139 TTTGGTACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (21 bp):
TTCTACAAAAACAAATCAAGC
Found at i:56236 original size:16 final size:16
Alignment explanation
Indices: 56215--56245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56205 TAATCAATAG
56215 CAATTTACCCCTTTTA
1 CAATTTACCCCTTTTA
*
56231 CAATTTACTCCTTTT
1 CAATTTACCCCTTTT
56246 TCCTTAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (16 bp):
CAATTTACCCCTTTTA
Found at i:61596 original size:43 final size:43
Alignment explanation
Indices: 61549--61667 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 43
61539 TTATCCGGCA
* * * *
61549 ATGCACTTTGTGTGCTAGTATAGTTGCTTCGGTTTATCCGATG
1 ATGCACTATGTATGCCAGTATAGTTGCTTCGATTTATCCGATG
* ** *
61592 ATGCACTATGTATGCCAATATAAATGCTTCGATTTATTCGATG
1 ATGCACTATGTATGCCAGTATAGTTGCTTCGATTTATCCGATG
* * * *
61635 ATGTACTATGTCTACCGGTATAGTTGCTTCGAT
1 ATGCACTATGTATGCCAGTATAGTTGCTTCGAT
61668 GGTGCTCTAT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (43 bp):
ATGCACTATGTATGCCAGTATAGTTGCTTCGATTTATCCGATG
Found at i:64354 original size:53 final size:53
Alignment explanation
Indices: 64273--64409 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
64263 TAAATGAAAA
* **
64273 AGGTCCGATGACTAAGTGCCATCGTGAGTATATGAAATCCTTTACGGATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACAAATTATG
* *
64326 TGGTCCGATGACTACGTGTCATCGTGAGTATATGAAATCCTTTACAAATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACAAATTATG
*
64379 AGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTAAGTGTCATCGTGAGTAT
64410 TAAATGAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (53 bp):
AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTACAAATTATG
Found at i:65114 original size:21 final size:19
Alignment explanation
Indices: 65088--65140 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
65078 GGAGTTTTTA
65088 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
*
65109 GTATCGGTAGAAATTATACTT
1 GTATCGGTAG--ATCATACTT
65130 GTATCGGTAGA
1 GTATCGGTAGA
65141 ACTAGCACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
21 24 0.83
22 2 0.07
23 2 0.07
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:78191 original size:19 final size:20
Alignment explanation
Indices: 78167--78204 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
78157 ATTCAAAAGA
*
78167 AAAAAT-AAATAAAAATGCT
1 AAAAATCAAAGAAAAATGCT
78186 AAAAATCAAAGAAAAATGC
1 AAAAATCAAAGAAAAATGC
78205 AATAATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAATCAAAGAAAAATGCT
Found at i:84950 original size:17 final size:17
Alignment explanation
Indices: 84930--84976 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
84920 AACAATGTAG
84930 ATGCAGTGACAATAAAA
1 ATGCAGTGACAATAAAA
* * *
84947 ATGCAATGACATTAATA
1 ATGCAGTGACAATAAAA
*
84964 ATGCAGGGACAAT
1 ATGCAGTGACAAT
84977 TATACTACAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:89694 original size:118 final size:117
Alignment explanation
Indices: 89523--89819 Score: 353
Period size: 118 Copynumber: 2.5 Consensus size: 117
89513 TATTTCAGAC
* * * * * * *
89523 TTTCGATGAGGCACCGGGTGCCAAATGGTTGCTTCAACTACGTCTTGATGAGTGTTAGGCATAAT
1 TTTCAATGAGGCACC-GGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTGGGCACAAT
* * * *
89588 TTTTACTT-TGATTATATCAATGAGCGCTGGGCGCAAGCTAATTACTTCGGACG
65 TTTTACTTCAG-TTATATCAATGAGCGCTGAGCGCAAACTAATTACTTCGGACA
* * *
89641 TTTCAATGAGGCACCGAGTGTCAAATGGTTACTTCGACTACGTGTCGATGAGTGATGGGAACAAT
1 TTTCAATGAGGCACCG-GTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTGGGCACAAT
**
89706 TTTTACTTCAGTTATATTGATGAGCGCTGAGCGCAAACTAATTACTTCGGACA
65 TTTTACTTCAGTTATATCAATGAGCGCTGAGCGCAAACTAATTACTTCGGACA
* * * * * *
89759 TTTCTATGAAGCACCGGATGCCAAATGGTTACTTTGATTACATGTCGATGTGTGTTGGGCA
1 TTTCAATGAGGCACCGG-TGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTGGGCA
89820 AAGCTTCTAC
Statistics
Matches: 151, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
117 2 0.01
118 148 0.98
119 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (117 bp):
TTTCAATGAGGCACCGGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTGGGCACAATT
TTTACTTCAGTTATATCAATGAGCGCTGAGCGCAAACTAATTACTTCGGACA
Found at i:89846 original size:118 final size:118
Alignment explanation
Indices: 89607--89848 Score: 290
Period size: 118 Copynumber: 2.1 Consensus size: 118
89597 GATTATATCA
* * * * *
89607 ATGAGCGCTGGGCGCAAGCTAATTACTTCGGACGTTTCAATGAGGCACCGAGTGTCAAATGGTTA
1 ATGAGCGCTGAGCGCAAACTAATTACTTCGGACATTTCAATGAAGCACCGAGTGCCAAATGGTTA
* * * * **
89672 CTTCGACTACGTGTCGATGAGTGATGGGAACAATTTTTACTTCAGTTATATTG
66 CTTCGACTACATGTCGATGAGTGATGGGAACAACTTCTACTTCAGTCATACCG
*
89725 ATGAGCGCTGAGCGCAAACTAATTACTTCGGACATTTCTATGAAGCACCG-GATGCCAAATGGTT
1 ATGAGCGCTGAGCGCAAACTAATTACTTCGGACATTTCAATGAAGCACCGAG-TGCCAAATGGTT
* * * * * *
89789 ACTTTGATTACATGTCGATGTGTGTTGGGCAA-AGCTTCTACTTCGGTCATACCG
65 ACTTCGACTACATGTCGATGAGTGATGGG-AACAACTTCTACTTCAGTCATACCG
89843 ATGAGC
1 ATGAGC
89849 ACTGGGCGTA
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
117 1 0.01
118 101 0.97
119 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (118 bp):
ATGAGCGCTGAGCGCAAACTAATTACTTCGGACATTTCAATGAAGCACCGAGTGCCAAATGGTTA
CTTCGACTACATGTCGATGAGTGATGGGAACAACTTCTACTTCAGTCATACCG
Found at i:91367 original size:23 final size:23
Alignment explanation
Indices: 91331--91388 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
91321 TGACGTGCAG
* * *
91331 TCCAGTTAGGAACTTCTAGAAGA
1 TCCAGTCAGCAACTTCCAGAAGA
*
91354 TCCAGTCAGCAACTTCCAGAAGG
1 TCCAGTCAGCAACTTCCAGAAGA
*
91377 TCTAGTCAGCAA
1 TCCAGTCAGCAA
91389 GGATGGACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
TCCAGTCAGCAACTTCCAGAAGA
Found at i:97959 original size:23 final size:23
Alignment explanation
Indices: 97929--97983 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
97919 TGACGTGGCG
*
97929 TCCAGTCAACAGCTTCTAGAAGA
1 TCCAGTCAACAGCTTCCAGAAGA
* *
97952 TCCAGTCAGCAGCTTCCAGAAGG
1 TCCAGTCAACAGCTTCCAGAAGA
*
97975 TCTAGTCAA
1 TCCAGTCAA
97984 TAAGGATGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
TCCAGTCAACAGCTTCCAGAAGA
Found at i:99673 original size:43 final size:42
Alignment explanation
Indices: 99626--99899 Score: 144
Period size: 43 Copynumber: 6.4 Consensus size: 42
99616 TTATTCGGCA
*
99626 ATGCACTTTGTGTGTCAGTATAGTTACTTCGGTTTATCCGATG
1 ATGCACTTTGTGTGTCAGTATAGTTACTTCAGTTTAT-CGATG
* * * * * **
99669 ATGCA-TTGTGTATGCCAATATAGATGCTTTGGTTTATTCGATG
1 ATGCACTT-TGTGTGTCAGTATAGTTACTTCAGTTTA-TCGATG
* * * * *
99712 ATGTACTATGTTTGTCGGTATAGTTGCTTCAGTTTATTCGATG
1 ATGCACTTTGTGTGTCAGTATAGTTACTTCAGTTTA-TCGATG
* * * *
99755 GTGCACTATGTGTG-CTAGTATATTTCCTTCAGTTTATCGAATG
1 ATGCACTTTGTGTGTC-AGTATAGTTACTTCAGTTTATCG-ATG
** * * * * * *
99798 ATGCA-TTACATGTGCCAGTATATTTCCTTCGGATTATCTGGTG
1 ATGCACTT-TGTGTGTCAGTATAGTTACTTCAGTTTATC-GATG
* * * * *
99841 ATGCA-TTAAGTGTGACAGTGTAATTACTTCAGTTTAGTCGATA
1 ATGCACTT-TGTGTGTCAGTATAGTTACTTCAGTTTA-TCGATG
*
99884 AAGCAC-TTGTGTGTCA
1 ATGCACTTTGTGTGTCA
99900 ATATGATTGC
Statistics
Matches: 180, Mismatches: 41, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
42 14 0.08
43 160 0.89
44 6 0.03
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (42 bp):
ATGCACTTTGTGTGTCAGTATAGTTACTTCAGTTTATCGATG
Found at i:108441 original size:118 final size:117
Alignment explanation
Indices: 108209--108536 Score: 381
Period size: 118 Copynumber: 2.8 Consensus size: 117
108199 TTTTATTTCG
* * * *
108209 AACATTCTGATGAGGCATCGGGTGCCAAATGGTTACTTTGACTACGTGTCGATTAA-TGTTGGGC
1 AACATTC-GATGAGGCATTGGGTGCCAAATGGTTACTTCGACTACGTGTCGA-TAAGTGCTGGGA
* * ***
108273 ACAATTTTTACTTCGGTTATACTGATGAGCGCTGGGTGCAAACAAATTACTTCA
64 ACAATTTTTACTTCGGTTATACCGATGAGCGCTAGGCAAAAACAAATTACTTCA
* * *
108327 AACGTTTCGATGAGGCATTGGGTACCAAATGGTTACTTCGAATACGTGTCGATAAGTGCTGGGAA
1 AAC-ATTCGATGAGGCATTGGGTGCCAAATGGTTACTTCGACTACGTGTCGATAAGTGCTGGGAA
* * * * *
108392 CAATTTTTTCTTCAGTTATACCGATGAGCGCTAGGCAAAAACTAGTTACTTCG
65 CAATTTTTACTTCGGTTATACCGATGAGCGCTAGGCAAAAACAAATTACTTCA
* ** * * *
108445 GACATTCCTTAAGGCATTGGGTGCCAAATGGTTACTTCGACTAAGTGTCGATGAGTGCTGGGCAA
1 AACATTCGATGAGGCATTGGGTGCCAAATGGTTACTTCGACTACGTGTCGATAAGTGCTGGG-AA
* *
108510 -AATTTCTACTTCGGTCATACCGATGAG
65 CAATTTTTACTTCGGTTATACCGATGAG
108537 AATTGGGCGT
Statistics
Matches: 177, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
117 77 0.44
118 97 0.55
119 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (117 bp):
AACATTCGATGAGGCATTGGGTGCCAAATGGTTACTTCGACTACGTGTCGATAAGTGCTGGGAAC
AATTTTTACTTCGGTTATACCGATGAGCGCTAGGCAAAAACAAATTACTTCA
Found at i:108780 original size:42 final size:42
Alignment explanation
Indices: 108733--108861 Score: 213
Period size: 42 Copynumber: 3.1 Consensus size: 42
108723 AGAGATTGGA
108733 ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
1 ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
108775 ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
1 ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
** * * *
108817 ATGAAATTGTGAAAAATTTAAAGATTCAGTTCGGGAAATGGC
1 ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
108859 ATG
1 ATG
108862 TTATTATATA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (42 bp):
ATGAAATTGTGATGAATTTAACGATTTAGTTCAGGAAATGGC
Found at i:111064 original size:22 final size:22
Alignment explanation
Indices: 111017--111064 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
111007 AATAACATAG
**
111017 TTTTAATAAATACTGGAAAATC
1 TTTTAATAAATAAAGGAAAATC
111039 TTTTAATAAATGAAAGGAAAAT-
1 TTTTAATAAAT-AAAGGAAAATC
111061 TTTT
1 TTTT
111065 GAACTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTAATAAATAAAGGAAAATC
Found at i:111915 original size:20 final size:20
Alignment explanation
Indices: 111891--111938 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
111881 TTGAACTCCT
111891 CTTCTACTGATACAACTATAG
1 CTTCTACTGATACAACTAT-G
* *
111912 -TTCTACCGATACAAGTATG
1 CTTCTACTGATACAACTATG
111931 CTTCTACT
1 CTTCTACT
111939 AGAACAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
CTTCTACTGATACAACTATG
Found at i:114285 original size:33 final size:32
Alignment explanation
Indices: 114243--114305 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
114233 ACCTTTATCT
**
114243 CTTAAATTGAAAATGGTTTTTATATAAGGGGAG
1 CTTAAATTGAAAATGACTTTTAT-TAAGGGGAG
114276 CTTAAATTGAAAATGACTTTTATTAAGGGG
1 CTTAAATTGAAAATGACTTTTATTAAGGGG
114306 CAGAAATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (32 bp):
CTTAAATTGAAAATGACTTTTATTAAGGGGAG
Found at i:114508 original size:20 final size:20
Alignment explanation
Indices: 114469--114508 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
114459 CTATCGGTAG
* *
114469 AACTCCACTTCTGCCCATAC
1 AACTCCACTTCTACCAATAC
114489 AACTCCACTTCTACCAATAC
1 AACTCCACTTCTACCAATAC
114509 CTTGAAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.42, G:0.03, T:0.25
Consensus pattern (20 bp):
AACTCCACTTCTACCAATAC
Found at i:114747 original size:20 final size:20
Alignment explanation
Indices: 114694--114749 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
114684 CTACCCTGGG
* *
114694 ACTTCTACCAATAGAATTCC
1 ACTTCTACCAATACAATTAC
* **
114714 TCTTCTACTGATACAATTAC
1 ACTTCTACCAATACAATTAC
*
114734 AGTTCTACCAATACAA
1 ACTTCTACCAATACAA
114750 GTATGCTACT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (20 bp):
ACTTCTACCAATACAATTAC
Found at i:116205 original size:18 final size:19
Alignment explanation
Indices: 116182--116223 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
116172 CCACCACCAT
116182 TGAAGAAAGTGAATCAAG-
1 TGAAGAAAGTGAATCAAGA
* *
116200 TGAAG-AGGTGAATGAAGA
1 TGAAGAAAGTGAATCAAGA
116218 TGAAGA
1 TGAAGA
116224 GATGGAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (19 bp):
TGAAGAAAGTGAATCAAGA
Found at i:116212 original size:17 final size:18
Alignment explanation
Indices: 116190--116224 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
116180 ATTGAAGAAA
116190 GTGAATCAAG-TGAAGAG
1 GTGAATCAAGATGAAGAG
*
116207 GTGAATGAAGATGAAGAG
1 GTGAATCAAGATGAAGAG
116225 ATGGAAAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.03, G:0.37, T:0.17
Consensus pattern (18 bp):
GTGAATCAAGATGAAGAG
Found at i:117498 original size:20 final size:20
Alignment explanation
Indices: 117473--117526 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
117463 CTCCAGTGAG
*
117473 ACTTCTACCAATAGAACTCC
1 ACTTCTACCAATACAACTCC
*
117493 ACTTCTACCGATACAACTCC
1 ACTTCTACCAATACAACTCC
*
117513 ACTTCTACCGATAC
1 ACTTCTACCAATAC
117527 CTTGAAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.26
Consensus pattern (20 bp):
ACTTCTACCAATACAACTCC
Done.